Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 156 of 202
Found at i:48796529 original size:2 final size:2
Alignment explanation
Indices: 48796524--48796570 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
48796514 TTATATGTTC
48796524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48796566 AT AT A
1 AT AT A
48796571 CACGTATGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48796921 original size:13 final size:14
Alignment explanation
Indices: 48796887--48796923 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
48796877 TGCTTTTATA
48796887 TATATTCATTTCGTT
1 TATATT-ATTTCGTT
48796902 TAT-TTATTT-GTT
1 TATATTATTTCGTT
48796914 TATATTATTT
1 TATATTATTT
48796924 TTATGCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (14 bp):
TATATTATTTCGTT
Found at i:48796954 original size:15 final size:15
Alignment explanation
Indices: 48796930--48796963 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
48796920 ATTTTTATGC
48796930 TATTGATGTATTTAT
1 TATTGATGTATTTAT
*
48796945 TATTGTTGTATTTAT
1 TATTGATGTATTTAT
48796960 TATT
1 TATT
48796964 ATAGCATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (15 bp):
TATTGATGTATTTAT
Found at i:48797442 original size:98 final size:98
Alignment explanation
Indices: 48797273--48797469 Score: 360
Period size: 98 Copynumber: 2.0 Consensus size: 98
48797263 TTAAAAATAA
* *
48797273 TAAAGGAAATATTCCGAGTTTGGGATTTTTAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTTAAGGAATCGTGCCCTAACGTATTCGGTGTGATTTC
48797338 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
48797371 TAAAGGAAATATTCCGAGTTTGGGA-TTTTAGAGGAATCGTGCCCTAACGTATTCGGTGTGATTT
1 TAAAGGAAATATTCCGAGTTTGGGATTTTTA-AGGAATCGTGCCCTAACGTATTCGGTGTGATTT
48797435 CTTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
65 CTTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
48797469 T
1 T
48797470 TTTATTGCAC
Statistics
Matches: 96, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
97 5 0.05
98 91 0.95
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTTTTAAGGAATCGTGCCCTAACGTATTCGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:48799079 original size:24 final size:24
Alignment explanation
Indices: 48799052--48799097 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
48799042 AGAACAATCC
*
48799052 CAAAAGGAAATGTATGAGCAACTT
1 CAAAAGGAAATGAATGAGCAACTT
*
48799076 CAAAAGTAAATGAATGAGCAAC
1 CAAAAGGAAATGAATGAGCAAC
48799098 AAAAAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.13, G:0.20, T:0.17
Consensus pattern (24 bp):
CAAAAGGAAATGAATGAGCAACTT
Found at i:48801446 original size:6 final size:6
Alignment explanation
Indices: 48801437--48801470 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
48801427 GTTCAGATTC
48801437 AAAACA AAAACA AAAACA AAAACA AAAACA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAA
48801471 TGAAAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:48801487 original size:18 final size:19
Alignment explanation
Indices: 48801443--48801497 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 19
48801433 ATTCAAAACA
* **
48801443 AAAACAAAAA-CAAAAACA
1 AAAACAAAAAGGAAAAATG
*
48801461 AAAACAAAAATGAAAAATG
1 AAAACAAAAAGGAAAAATG
48801480 AAAA-AAAAAGGAAAAATG
1 AAAACAAAAAGGAAAAATG
48801498 GAGAGGCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 23 0.72
19 9 0.28
ACGTcount: A:0.78, C:0.07, G:0.09, T:0.05
Consensus pattern (19 bp):
AAAACAAAAAGGAAAAATG
Found at i:48804014 original size:3 final size:3
Alignment explanation
Indices: 48804006--48804280 Score: 247
Period size: 3 Copynumber: 92.3 Consensus size: 3
48803996 TATTTTCTCC
48804006 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
48804054 TTA TTA TTA TTA TTA TTA TTA CTTA GTA TTA TTA TTG GTA TTG TAA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
* * * ** ** * * *
48804100 TTA TTA TT- TTGG TT- TT- TTT TTG CAA TT- TCGC TTT TTT TTA AT-
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* **
48804142 TTA TT- TTC TCC TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
48804189 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
48804237 TTA TTA CTTA GTA TTA TTA TTG GTA TTG TAA TTA TTA TTT TTA T
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
48804281 GTACATACAA
Statistics
Matches: 224, Mismatches: 39, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
2 10 0.04
3 205 0.92
4 9 0.04
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:48804387 original size:2 final size:2
Alignment explanation
Indices: 48804380--48804406 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48804370 CTATACATTT
48804380 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
48804407 TATTCTCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48804529 original size:2 final size:2
Alignment explanation
Indices: 48804524--48804570 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
48804514 TTATATGTTC
48804524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48804566 AT AT A
1 AT AT A
48804571 CACGTATGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48804921 original size:13 final size:14
Alignment explanation
Indices: 48804887--48804923 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
48804877 TGCTTTTATA
48804887 TATATTCATTTCGTT
1 TATATT-ATTTCGTT
48804902 TAT-TTATTT-GTT
1 TATATTATTTCGTT
48804914 TATATTATTT
1 TATATTATTT
48804924 TTATGCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (14 bp):
TATATTATTTCGTT
Found at i:48804954 original size:15 final size:15
Alignment explanation
Indices: 48804930--48804963 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
48804920 ATTTTTATGC
48804930 TATTGATGTATTTAT
1 TATTGATGTATTTAT
*
48804945 TATTGTTGTATTTAT
1 TATTGATGTATTTAT
48804960 TATT
1 TATT
48804964 ATAGCATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (15 bp):
TATTGATGTATTTAT
Found at i:48805357 original size:98 final size:98
Alignment explanation
Indices: 48805238--48805434 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
48805228 TTAAAAATAA
* *
48805238 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGCGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTCGGTGCGATTTC
48805303 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* * *
48805336 TAAATGAAATATTCCGAGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTCGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTCGGTGCGATTTC
48805401 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
48805434 T
1 T
48805435 TTTATTGCAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTCGGTGCGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:48816867 original size:83 final size:84
Alignment explanation
Indices: 48816769--48816928 Score: 241
Period size: 83 Copynumber: 1.9 Consensus size: 84
48816759 GTTTACAAAC
* * * *
48816769 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAA-AAAAAACGCCACTAAAGACCATGT
1 AAAAACACCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAGAAAAAACGCCACTAAAAAACATGG
48816833 TCTTTAGCGGCGCTTAGAT
66 TCTTTAGCGGCGCTTAGAT
* * *
48816852 AAAAACACCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAGACAAAATGCCGCTAAAAAACATGG
1 AAAAACACCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAGAAAAAACGCCACTAAAAAACATGG
*
48816917 TCTTTAGTGGCG
66 TCTTTAGCGGCG
48816929 TTTATTTCTA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
83 39 0.57
84 29 0.43
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (84 bp):
AAAAACACCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAGAAAAAACGCCACTAAAAAACATGG
TCTTTAGCGGCGCTTAGAT
Found at i:48816869 original size:42 final size:41
Alignment explanation
Indices: 48816769--48816928 Score: 221
Period size: 42 Copynumber: 3.9 Consensus size: 41
48816759 GTTTACAAAC
48816769 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAA
* *
48816810 AAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTA-AA
*
48816852 AAAAACACCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAGA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAA-A
* * * * * *
48816894 CAAAATGCCGCTAAAAAACATGGTCTTTAGTGGCG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
48816929 TTTATTTCTA
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
41 39 0.37
42 66 0.63
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAA
Found at i:48816956 original size:42 final size:41
Alignment explanation
Indices: 48816900--48817075 Score: 199
Period size: 42 Copynumber: 4.2 Consensus size: 41
48816890 AAGACAAAAT
* *
48816900 GCCGCTAAAAAACATGGTCTTTAGTGGCGTTTATTTCTAAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTT-TTTCTAAGC
* * * *
48816942 GCCTCTGAAGAACATGTTCTTTAGCGGCGTTTTGTCTTAAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTC-TAAGC
* *
48816984 GCCGCTAAAGAACATTGTCTTTAGCGGCGTTTTTTTCCAAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTTCTAAGC
* ** * *
48817026 GCCGGTAAAGAACATTATCTTTAGCGGTGTTTTTTTTAAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCTAAGC
*
48817067 GTCGCTAAA
1 GCCGCTAAA
48817076 AATTTAGCGG
Statistics
Matches: 113, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
41 20 0.18
42 87 0.77
43 6 0.05
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (41 bp):
GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCTAAGC
Found at i:48816988 original size:84 final size:83
Alignment explanation
Indices: 48816900--48817077 Score: 232
Period size: 84 Copynumber: 2.1 Consensus size: 83
48816890 AAGACAAAAT
* * * *
48816900 GCCGCTAAAAAACATGGTCTTTAGTGGCGTTTATTTCTAAGCGCCTCTGAAGAACATGT-TCTTT
1 GCCGCTAAAAAACATGGTCTTTAGCGGCGTTTATTTCCAAGCGCCGCTAAAGAACAT-TATCTTT
48816964 AGCGGCGTTTTGTCTTAAGC
65 AGCGGCGTTTT-TCTTAAGC
* * * *
48816984 GCCGCTAAAGAACATTGTCTTTAGCGGCGTTTTTTTCCAAGCGCCGGTAAAGAACATTATCTTTA
1 GCCGCTAAAAAACATGGTCTTTAGCGGCGTTTATTTCCAAGCGCCGCTAAAGAACATTATCTTTA
* *
48817049 GCGGTGTTTTTTTTAAGC
66 GCGGCGTTTTTCTTAAGC
*
48817067 GTCGCTAAAAA
1 GCCGCTAAAAA
48817078 TTTAGCGGCG
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
83 17 0.21
84 64 0.79
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (83 bp):
GCCGCTAAAAAACATGGTCTTTAGCGGCGTTTATTTCCAAGCGCCGCTAAAGAACATTATCTTTA
GCGGCGTTTTTCTTAAGC
Found at i:48817318 original size:21 final size:21
Alignment explanation
Indices: 48817294--48817340 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
48817284 TTAACTATTT
* *
48817294 AAATTAGTTAATGATATTGTA
1 AAATTAGATAATGAAATTGTA
*
48817315 AAATTAGATGATGAAATTGTA
1 AAATTAGATAATGAAATTGTA
48817336 AAATT
1 AAATT
48817341 TCAAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (21 bp):
AAATTAGATAATGAAATTGTA
Found at i:48823139 original size:146 final size:147
Alignment explanation
Indices: 48822935--48823606 Score: 1078
Period size: 146 Copynumber: 4.6 Consensus size: 147
48822925 TTTTGGGAAA
*
48822935 TTTTTTATAAATTGA-TT-TTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
1 TTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
*
48822998 GCGGCGCTTC-TATAAAGCGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
66 GCGGCGCTCCTTATAAAGCGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
*
48823062 TTC-AAATTTTTTTTTAT
131 TTCTAAA-ATTTTTTTAT
*
48823079 TTTTTTATAAGTTGATTTGTTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
1 TTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
*
48823144 GCGGCGCTTCTTATAAAGCGCCGCAAAA-TTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
66 GCGGCGCTCCTTATAAAGCGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
48823208 TTCTAAAATTTTTTTAT
131 TTCTAAAATTTTTTTAT
* *
48823225 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGTCGCTATTGCTTACCTTTA
1 TTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
**
48823290 GCGGCGCTCCTTATAAAATGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
66 GCGGCGCTCCTTATAAAGCGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
48823355 TTCT-AAA-TTTTTTA-
131 TTCTAAAATTTTTTTAT
*
48823369 TTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTCTATA-AAAACGCCGCTATTGCTTGCCTT
1 TTTTTTATAAGTTGATTTATTTTTTGCGGCG-TTTT-TATAGAAAACGCCGCTATTGCTTACCTT
* *
48823433 TAGCGACGCTCCTTAAAAAGCGCCGC-AAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGC
64 TAGCGGCGCTCCTTATAAAGCGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGC
48823497 TATTCTAAAATTTTTTTATT
129 TATTCTAAAATTTTTTTA-T
*
48823517 TTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTCTATA-AAAACGCCGCTATTGCTTGCCTT
1 TTTTTTATAAGTTGATTTATTTTTTGCGGCG-TTTT-TATAGAAAACGCCGCTATTGCTTACCTT
* *
48823581 TAGCGACGCTCCTTAAAAAGCGCCGC
64 TAGCGGCGCTCCTTATAAAGCGCCGC
48823607 NNNNNNNNNN
Statistics
Matches: 502, Mismatches: 15, Indels: 18
0.94 0.03 0.03
Matches are distributed among these distances:
144 88 0.18
145 59 0.12
146 205 0.41
147 60 0.12
148 90 0.18
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (147 bp):
TTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
GCGGCGCTCCTTATAAAGCGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
TTCTAAAATTTTTTTAT
Found at i:48823460 original size:291 final size:292
Alignment explanation
Indices: 48822935--48823606 Score: 1092
Period size: 291 Copynumber: 2.3 Consensus size: 292
48822925 TTTTGGGAAA
48822935 TTTTTTATAAATTGA-TT-TTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
1 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
* *
48822998 GCGGCGCTTC-TATAAAGCGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
66 GCGGCGCTCCTTATAAAACGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
*
48823062 TTCAAATTTTTTTTTATTTTTTTATAAGTTGATTTGTTTTTTGCGGCGTTTTTATAGAAAACGCC
131 TTCAAA--TTTTTTTATTTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCC
* * *
48823127 GCTATTGCTTACCTTTAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAA
194 GCTATTGCTTACCTTTAGCGACGCTCCTTAAAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAA
48823192 CGACGCCGTTTTGCTATTCTAAAATTTTTTTA-T
259 CGACGCCGTTTTGCTATTCTAAAATTTTTTTATT
*
48823225 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGTCGCTATTGCTTACCTTTA
1 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
*
48823290 GCGGCGCTCCTTATAAAATGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
66 GCGGCGCTCCTTATAAAACGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
48823355 TTCTAAA-TTTTTTA-TTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTCTATA-AAAACGC
131 TTC-AAATTTTTTTATTTTTTTATAAGTTGATTTATTTTTTGCGGCG-TTTT-TATAGAAAACGC
* *
48823417 CGCTATTGCTTGCCTTTAGCGACGCTCCTTAAAAAGCGCCGCAAATTTTTTTCATTTTGAACAAA
193 CGCTATTGCTTACCTTTAGCGACGCTCCTTAAAAAGCGCCGCAAAATTTTTTCATTTTGAACAAA
48823482 ACGACGCCGTTTTGCTATTCTAAAATTTTTTTATT
258 ACGACGCCGTTTTGCTATTCTAAAATTTTTTTATT
* *
48823517 TTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTCTATA-AAAACGCCGCTATTGCTTGCCTT
1 TTTTTTATAAATTGATTTATTTTTTGCGGCG-TTTT-TATAGAAAACGCCGCTATTGCTTACCTT
*
48823581 TAGCGACGCTCCTTA-AAAAGCGCCGC
64 TAGCGGCGCTCCTTATAAAA-CGCCGC
48823607 NNNNNNNNNN
Statistics
Matches: 357, Mismatches: 15, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
290 45 0.13
291 113 0.32
292 93 0.26
293 99 0.28
294 7 0.02
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (292 bp):
TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
GCGGCGCTCCTTATAAAACGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
TTCAAATTTTTTTATTTTTTTATAAGTTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGC
TATTGCTTACCTTTAGCGACGCTCCTTAAAAAGCGCCGCAAAATTTTTTCATTTTGAACAAAACG
ACGCCGTTTTGCTATTCTAAAATTTTTTTATT
Found at i:48825803 original size:146 final size:146
Alignment explanation
Indices: 48825372--48825841 Score: 684
Period size: 148 Copynumber: 3.2 Consensus size: 146
48825362 TTTTGGGAAA
48825372 TTTTTTATAAATTTGA-TT-TTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTT
1 TTTTTTATAAA-TTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTT
48825435 AGCGGCGCTTC-TATAAAGCGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCT
65 AGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCT
48825499 ATTC-AAATTTTTTTTTAT
130 ATTCTAAA--TTTTTTTAT
* ****** **** *
48825517 TTTTTTATAAGTTCCCCCGTTTTTTGCGGCGTTTTTCCCCCACCAACGCCGCTATTGCTTACCTT
1 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTT-ATAGA-AAACGCCGCTATTGCTTACCTT
48825582 TAGCGGCGCTTCTTATAAAGCGCCGCAAAA-TTTTTTCATTTTGAACAAAACGACGCCGTTTTGC
64 TAGCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGC
48825646 TATTCTAAAATTTTTTTAT
129 TATTCT-AAATTTTTTTAT
*
48825665 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGTCGCTATTGCTTACCTTTA
1 TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
* **
48825730 GCGGCGCTCCTTATAAAATGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
66 GCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
48825795 TTCTAAA-TTTTTTA-
131 TTCTAAATTTTTTTAT
*
48825809 TTTTTTATAAGTTGATTTATTTTTTGCGGCGTT
1 TTTTTTATAAATTGATTTATTTTTTGCGGCGTT
48825842 AGCGACGCAT
Statistics
Matches: 290, Mismatches: 27, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
144 34 0.12
145 17 0.06
146 67 0.23
147 42 0.14
148 110 0.38
149 17 0.06
150 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (146 bp):
TTTTTTATAAATTGATTTATTTTTTGCGGCGTTTTTATAGAAAACGCCGCTATTGCTTACCTTTA
GCGGCGCTTCTTATAAAGCGCCGCAAAATTTTTTTCATTTTGAACAAAACGACGCCGTTTTGCTA
TTCTAAATTTTTTTAT
Found at i:48847002 original size:27 final size:27
Alignment explanation
Indices: 48846961--48847044 Score: 141
Period size: 27 Copynumber: 3.1 Consensus size: 27
48846951 TAGTATTGGC
*
48846961 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
48846988 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
48847015 GCCTATCTGGGGGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
48847042 GCC
1 GCC
48847045 ATACTGCAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.14, C:0.23, G:0.40, T:0.23
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:48847057 original size:27 final size:27
Alignment explanation
Indices: 48846961--48847063 Score: 136
Period size: 27 Copynumber: 3.8 Consensus size: 27
48846951 TAGTATTGGC
48846961 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCGCCAATGGTGGT
* *
48846988 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCGCCAATGGTGGT
**
48847015 GCCTATCTGGGGGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCGCCAATGGTGGT
* *
48847042 GCC-ATACTGCAAGGCGTCAATG
1 GCCTAT-CTGGAAGGCGCCAATG
48847064 CTGTGATTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
26 2 0.03
27 65 0.97
ACGTcount: A:0.17, C:0.22, G:0.38, T:0.22
Consensus pattern (27 bp):
GCCTATCTGGAAGGCGCCAATGGTGGT
Found at i:48847167 original size:18 final size:20
Alignment explanation
Indices: 48847125--48847171 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
48847115 GAAACGGAAG
48847125 AAAGAAGAAGGAAGGAAGCA
1 AAAGAAGAAGGAAGGAAGCA
* *
48847145 GAAGAA-AA-GAAGGAAGGA
1 AAAGAAGAAGGAAGGAAGCA
48847163 AAAGAAGAA
1 AAAGAAGAA
48847172 AAAAATTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGGAAGGAAGCA
Found at i:48847174 original size:22 final size:23
Alignment explanation
Indices: 48847121--48847174 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
48847111 TACAGAAACG
*
48847121 GAAGAAAGAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
48847145 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
48847166 GAAGAAAAA
1 GAAGAAAAA
48847175 AATTAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Found at i:48854037 original size:8 final size:8
Alignment explanation
Indices: 48854024--48854163 Score: 50
Period size: 8 Copynumber: 16.4 Consensus size: 8
48854014 CATACAAAAA
48854024 ATTACAAT
1 ATTACAAT
48854032 ATTACAAT
1 ATTACAAT
* * *
48854040 ATATCCCCAC
1 AT-T-ACAAT
48854050 ATTACAAT
1 ATTACAAT
*
48854058 ATTCATACAAA
1 A-T--TACAAT
48854069 ATTACAAT
1 ATTACAAT
48854077 ATTACAAT
1 ATTACAAT
48854085 ATT-C-AT
1 ATTACAAT
** * *
48854091 ACAAAAAA
1 ATTACAAT
*
48854099 ATTGCAAT
1 ATTACAAT
*
48854107 ATTCATACAAA
1 A-T--TACAAT
*
48854118 ATTATAAT
1 ATTACAAT
48854126 ATTACAAT
1 ATTACAAT
*
48854134 ATTCATACAAA
1 A-T--TACAAT
*
48854145 ATTACAAA
1 ATTACAAT
48854153 ATTACAAT
1 ATTACAAT
48854161 ATT
1 ATT
48854164 CATATAAAAA
Statistics
Matches: 95, Mismatches: 24, Indels: 26
0.66 0.17 0.18
Matches are distributed among these distances:
6 3 0.03
7 1 0.01
8 62 0.65
9 5 0.05
10 7 0.07
11 17 0.18
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.33
Consensus pattern (8 bp):
ATTACAAT
Found at i:48854086 original size:27 final size:26
Alignment explanation
Indices: 48854050--48854253 Score: 225
Period size: 27 Copynumber: 8.1 Consensus size: 26
48854040 ATATCCCCAC
48854050 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
48854077 ATTACAATATTCATAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
*
48854099 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
*
48854126 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTA-AAT
*
48854153 ATTACAATATTCATA-TAAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
* *
48854175 ATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
48854202 ATTACAATATTCATAC-AAA--AAAT
1 ATTACAATATTCATACAAAATTAAAT
*
48854225 -TTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
48854251 ATT
1 ATT
48854254 CATCCCCCCA
Statistics
Matches: 153, Mismatches: 9, Indels: 30
0.80 0.05 0.16
Matches are distributed among these distances:
22 43 0.28
23 16 0.10
24 3 0.02
25 3 0.02
26 16 0.10
27 72 0.47
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.33
Consensus pattern (26 bp):
ATTACAATATTCATACAAAATTAAAT
Found at i:48854142 original size:76 final size:76
Alignment explanation
Indices: 48854050--48854243 Score: 317
Period size: 76 Copynumber: 2.6 Consensus size: 76
48854040 ATATCCCCAC
48854050 ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATAC
1 ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATAC
*
48854115 AAAATTATAAT
66 AAAACTATAAT
* *
48854126 ATTACAATATTCATACAAAATTACAAAATTACAATATTCATATAAAAAAATTGCAATATTCATAC
1 ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATAC
48854191 AAAACTATAAT
66 AAAACTATAAT
*
48854202 ATTACAATATTCATAC-AAA--A-AAT-TTATAATATTCATACAAAA
1 ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAA
48854244 TTACAATATT
Statistics
Matches: 112, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
71 17 0.15
72 2 0.02
73 1 0.01
75 3 0.03
76 89 0.79
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (76 bp):
ATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATAC
AAAACTATAAT
Found at i:48854252 original size:49 final size:49
Alignment explanation
Indices: 48854003--48854253 Score: 223
Period size: 49 Copynumber: 5.1 Consensus size: 49
48853993 TTATAAAATA
** * *
48854003 ATTACAATATTCATACAAAAAA-TTACAATA-T--TACAATATATCCCCAC
1 ATTACAATATTCATACAAAAAATTTACAATATTCATACAA-A-ATTACAAT
48854050 ATTACAATATTCATACAAAATTACAATATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATAC-AAA--A-AAT-TTACAATATTCATACAAAATTACAAT
* *
48854099 ATTGCAATATTCATACAAAATTATAATATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATAC-AAA--A-AAT-TTACAATATTCATACAAAATTACAAT
* * * * *
48854153 ATTACAATATTCATATAAAAAAATTGCAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAAAATTTACAATATTCATACAAAATTACAAT
*
48854202 ATTACAATATTCATACAAAAAATTTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAAAATTTACAATATTCATACAAAATTACAAT
48854251 ATT
1 ATT
48854254 CATCCCCCCA
Statistics
Matches: 173, Mismatches: 17, Indels: 26
0.80 0.08 0.12
Matches are distributed among these distances:
47 16 0.09
48 3 0.02
49 109 0.63
50 7 0.04
51 3 0.02
52 1 0.01
53 14 0.08
54 16 0.09
55 1 0.01
56 3 0.02
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.33
Consensus pattern (49 bp):
ATTACAATATTCATACAAAAAATTTACAATATTCATACAAAATTACAAT
Found at i:48854378 original size:22 final size:22
Alignment explanation
Indices: 48854332--48854389 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
48854322 ACAACATTAC
*
48854332 AATATTCATA-AAAAAAAATAT
1 AATATTCATACAAAAAAAATAA
**
48854353 AATATTCATACAAAAAATTTAA
1 AATATTCATACAAAAAAAATAA
48854375 AATATTCATACAAAA
1 AATATTCATACAAAA
48854390 TTCTAATCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 10 0.30
22 23 0.70
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (22 bp):
AATATTCATACAAAAAAAATAA
Found at i:48854563 original size:3 final size:3
Alignment explanation
Indices: 48854557--48854591 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
48854547 TTTTTTTTCT
48854557 TTC TTC TTC TTC TTC -TC TTC TTC TTC -TC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
48854592 CCTTTCTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:48854575 original size:11 final size:11
Alignment explanation
Indices: 48854561--48854591 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
48854551 TTTTCTTTCT
48854561 TCTTCTTCTTC
1 TCTTCTTCTTC
48854572 TCTTCTTCTTC
1 TCTTCTTCTTC
48854583 TCTTCTTCT
1 TCTTCTTCT
48854592 CCTTTCTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (11 bp):
TCTTCTTCTTC
Found at i:48854577 original size:14 final size:13
Alignment explanation
Indices: 48854553--48854603 Score: 61
Period size: 14 Copynumber: 3.9 Consensus size: 13
48854543 CCTTTTTTTT
48854553 TTCTTTCTTCTTC
1 TTCTTTCTTCTTC
48854566 TTC-TTC-TCTTC
1 TTCTTTCTTCTTC
48854577 TTCTTCTCTTCTTC
1 TTCTT-TCTTCTTC
*
48854591 TCCTTTCTCTCTT
1 TTCTTTCT-TCTT
48854604 TTTTTTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
11 8 0.24
12 4 0.12
13 8 0.24
14 13 0.39
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
TTCTTTCTTCTTC
Found at i:48854960 original size:29 final size:28
Alignment explanation
Indices: 48854927--48854993 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
48854917 GAAAAAGTAA
48854927 CCTATTTTGGTAAATTTTTTTTCTGACAT
1 CCTATTTTGGTAAATTTTTTTTCT-ACAT
*
48854956 CCTATTTTAGT--ATTTTTTTTCTACAT
1 CCTATTTTGGTAAATTTTTTTTCTACAT
*
48854982 --TATTTGGGTAAA
1 CCTATTTTGGTAAA
48854994 AAACTCATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 7 0.21
26 5 0.15
27 11 0.33
29 10 0.30
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.55
Consensus pattern (28 bp):
CCTATTTTGGTAAATTTTTTTTCTACAT
Found at i:48855135 original size:15 final size:15
Alignment explanation
Indices: 48855115--48855147 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
48855105 GAGAGACGAC
48855115 AAAGGAGAAAAAAAG
1 AAAGGAGAAAAAAAG
*
48855130 AAAGGAGAGAAAAAG
1 AAAGGAGAAAAAAAG
48855145 AAA
1 AAA
48855148 AAAAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAGGAGAAAAAAAG
Found at i:48857603 original size:20 final size:21
Alignment explanation
Indices: 48857578--48857616 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
48857568 ATCTTACATG
*
48857578 AAATTAAA-AATATAACTCTT
1 AAATTAAAGAAAATAACTCTT
48857598 AAATTAAAGAAAATAACTC
1 AAATTAAAGAAAATAACTC
48857617 AATAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (21 bp):
AAATTAAAGAAAATAACTCTT
Found at i:48859479 original size:24 final size:24
Alignment explanation
Indices: 48859451--48859502 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
48859441 TTAGTAAGTC
* *
48859451 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
48859475 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
48859499 AAAT
1 AAAT
48859503 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:48861446 original size:24 final size:24
Alignment explanation
Indices: 48861418--48861469 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
48861408 TTAGTAAGTC
*
48861418 AAATAAACTATGCTAATAAATACT
1 AAATAAACTATACTAATAAATACT
* *
48861442 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
48861466 AAAT
1 AAAT
48861470 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:48869478 original size:21 final size:19
Alignment explanation
Indices: 48869431--48869478 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
48869421 TAACGTGTCC
48869431 ATGTTATATATTATAAAAA
1 ATGTTATATATTATAAAAA
** *
48869450 ATAATATACTTATTTTAAAAA
1 ATGTTATA--TATTATAAAAA
48869471 ATGTTATA
1 ATGTTATA
48869479 ATTTTTGCCT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 6 0.27
21 16 0.73
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (19 bp):
ATGTTATATATTATAAAAA
Found at i:48870620 original size:11 final size:11
Alignment explanation
Indices: 48870583--48870624 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
48870573 TAAGAAATAA
48870583 AAATCAGAATC
1 AAATCAGAATC
**
48870594 AAATCCCAA-C
1 AAATCAGAATC
48870604 -AATCAGAATC
1 AAATCAGAATC
48870614 AAATCAGAATC
1 AAATCAGAATC
48870625 TGAATCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 6 0.24
10 2 0.08
11 17 0.68
ACGTcount: A:0.52, C:0.24, G:0.07, T:0.17
Consensus pattern (11 bp):
AAATCAGAATC
Found at i:48870911 original size:151 final size:151
Alignment explanation
Indices: 48870637--48870939 Score: 579
Period size: 151 Copynumber: 2.0 Consensus size: 151
48870627 AATCAAAACC
*
48870637 TAACAAATGCTATGGTCTACTGTTTGAATTTGAATGAAGATTTAGAAGGCTTCAAAGTCCTGATA
1 TAACAAATGCTATGGTCTACTATTTGAATTTGAATGAAGATTTAGAAGGCTTCAAAGTCCTGATA
48870702 CATACAATGTTTAACGTTACATATGTGCTAATGTAATTCTTGTTGCTTCTTGACTTCCTTGCATG
66 CATACAATGTTTAACGTTACATATGTGCTAATGTAATTCTTGTTGCTTCTTGACTTCCTTGCATG
48870767 TCTATGACGGTTTGGTCCTCT
131 TCTATGACGGTTTGGTCCTCT
48870788 TAACAAATGCTATGGTCTACTATTTGAATTTGAATGAAGATTTAGAAGGCTTCAAAGTCCTGATA
1 TAACAAATGCTATGGTCTACTATTTGAATTTGAATGAAGATTTAGAAGGCTTCAAAGTCCTGATA
*
48870853 CATACAATGTTTAACTTTACATATGTGCTAATGTAATTCTTGTTGCTTCTTGACTTCCTTGCATG
66 CATACAATGTTTAACGTTACATATGTGCTAATGTAATTCTTGTTGCTTCTTGACTTCCTTGCATG
*
48870918 TCTATGATGGTTTGGTCCTCT
131 TCTATGACGGTTTGGTCCTCT
48870939 T
1 T
48870940 GCAGAAACGT
Statistics
Matches: 149, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 149 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (151 bp):
TAACAAATGCTATGGTCTACTATTTGAATTTGAATGAAGATTTAGAAGGCTTCAAAGTCCTGATA
CATACAATGTTTAACGTTACATATGTGCTAATGTAATTCTTGTTGCTTCTTGACTTCCTTGCATG
TCTATGACGGTTTGGTCCTCT
Found at i:48874931 original size:18 final size:18
Alignment explanation
Indices: 48874887--48874931 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
48874877 CATTCGTTTC
*
48874887 CAAAACATTATTCATTTA
1 CAAAACGTTATTCATTTA
*
48874905 CAAATCGTTATTCAATTT-
1 CAAAACGTTATTC-ATTTA
48874923 CAAAACGTT
1 CAAAACGTT
48874932 TTCTTATTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (18 bp):
CAAAACGTTATTCATTTA
Found at i:48882605 original size:25 final size:24
Alignment explanation
Indices: 48882577--48882625 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
48882567 TAATAAAATA
48882577 TAAAATTATTT-TTAATAATTAATTT
1 TAAAA-TATTTATTAAT-ATTAATTT
48882602 TAAAATATTTCATTAATATTAATT
1 TAAAATATTT-ATTAATATTAATT
48882626 AATTAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 12 0.55
26 5 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAAATATTTATTAATATTAATTT
Found at i:48888175 original size:12 final size:12
Alignment explanation
Indices: 48888158--48888189 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
48888148 ATCTTGGTAA
48888158 GGCCAATGTGGT
1 GGCCAATGTGGT
48888170 GGCCAATGTGGT
1 GGCCAATGTGGT
*
48888182 AGCCAATG
1 GGCCAATG
48888190 CTTTTAGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.22
Consensus pattern (12 bp):
GGCCAATGTGGT
Found at i:48897829 original size:759 final size:754
Alignment explanation
Indices: 48895834--48897982 Score: 2708
Period size: 759 Copynumber: 2.8 Consensus size: 754
48895824 ATTATTTGTT
* * *
48895834 ATTTTATTTTTTAAATCAAATCCCTATTATTTTTCTATTTCGGCAACCGTCAAACCACCTTCTAT
1 ATTTTATTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCT
* * * * * * *
48895899 TTAGCTACACATTTCTTTCCCTTCTTTCAATTTTGTTTGACATTTGTTTCTCTCTTTTCCACTTT
66 TTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACACTTGTTT-T-TC-TTT-C-TTTT
* * ** * *
48895964 CTTTCCTTTTTTTTCGCCTTGCCAATGCTGACTCCTTCTTTTACTATTGTGCCCATTGTAAAATC
126 C-TT-C--TTTTTT-GCCTTGCCAACGCCGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATC
* * *
48896029 TTTCTTTTGTTGCATAAGAACACTATTGTGGCTTGTTATGATTCTATTGTTCGCTTGTTTCTTTC
186 TTTCTTTTGTTGCGTAAGAACACTATTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTC
* *
48896094 TTCTCCTCATGGTGGCTTGGTTGTGTTGGTAAGTTATGTGGAAGATTAGTTCTTTATAAGGTTGG
251 TTTTCCTCGT-GTGGCTTGGTTGTGTTGGTAAGTTATGTGGAAGATTAGTTCTTTATAAGGTTGG
* * * * * *
48896159 GG-TTTGTTGTTTTAAGCAAAAAATTTCGCAGATTAATGATTTTACGATTGATACAGTATTGTGG
315 GGTTTTGTTGTTTTAAGCAAAAAA-TCCGTAGATTAATGATTTTATGATTGATATAGTGTTGTTG
* * * * ** * *
48896223 CTGGTTGTTGTGGATAAGAAAAGAGCGCGTGGTGATAGA-ACGCCCTCTGAAAAATTAAGTTTTT
379 CTGGTTGTTGTGGATAGGAGAAGAGCGCATGGTGATAGACA-ACTTTC-GGAAAATTAAGGTTTT
* * * *
48896287 GGAGTAGTTGCTGGAAGTTTGTGGTAATTGCTTATTTATGAATATAGGGACTATTTCTTTGAGAA
442 GGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTATTTCTTTGAGAA
* * * * * *
48896352 AAGA-ATGAATTTAAATGGTAATGTTCGTGTTAAATCGAAGTTGTAGTCGTTGATTTTGGTGTTA
507 AAGAGA-GAATTTAAATGGTAATGTTCGTGTTAAATCGAAGTTGTAATAGTT-AGTTTGATGCTG
* * **
48896416 TTTGTAGGATTTTTAGTGTACGACTGCTTGGTGGATTAATCCCGC-AGTCAGGTGTGTGAAAACA
570 TTTGTAGGA-TTTTAGTGTACGACTGCGTAGTGGATTAATGTCGCTA-TCAGGTGTGTGAAAACA
* * * * * *
48896480 ATCCTAAAACTCGGTAGAAACTCATTAAATTGTGAAACAGGGGTTGTTTTTCAAAATTGCCTAGT
633 ATCCTAAAACTCGATAGAAACTCATTAAATCGTGAAACAGGGCTTGTTTTTCAAAACTGCCCAAT
* * * * *
48896545 GCCACACAGCCGTGTGTCAGGCTGTGTGGTAGATTATGTGTGCCACACTGCCGTTTA
698 GCCACACAGCCGTGTGTCAGGCTGTATGGTAAATTATGTGTGCCACACAGCCATGTA
* *
48896602 GTTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCTTCAAACCAACTTCTC
1 ATTTTA-TTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTC
* *
48896667 TTTGGTTGCACGTTT-TTTCCCTTCTTTCAATTTTGTTTTA-ACTT-TTTTTCTTTCTTTCCTTA
65 TTTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACACTTGTTTTTCTTTCTTTTCTTC
* *
48896729 TTTTTTGCCTTGCCAACGCCGACTCCTTCTTTTGTTTTTTTGCCAATTGCAAAATCTTTCTTTTG
130 TTTTTTGCCTTGCCAACGCCGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTG
* * *
48896794 TTGCGTAAGAACACTGTTGAAGCTTGTTATGATTCAGTTGTTCGCTTGTTTCTTTCTTTTCCTCG
195 TTGCGTAAGAACACTATTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCG
* *
48896859 TGATGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTATTGTT
260 TG-TGGCTTGGTTGTGTTGGTAAGTTATGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTT
* *
48896924 GTTTTAAGCAAAAAAATCCGTGGATTAATGATTTTATGATTGATATAGTGTTTTTGGCTGGTTGT
324 GTTTTAAGC-AAAAAATCCGTAGATTAATGATTTTATGATTGATATAGTGTTGTT-GCTGGTTGT
* * * *
48896989 TATGGATAGGAGAAGAGCGCGA-GGTGAAAGACAATCTTTCGGAAAATTAAGGTTTCGGTGTAGT
387 TGTGGATAGGAGAAGAGCGC-ATGGTGATAGACAA-CTTTCGGAAAATTAAGGTTTTGGAGTAGT
* *
48897053 TGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTATTTCTTTGAGAAAATAGCGA
450 TGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTATTTCTTTGAGAAAAGAGAGA
* * *
48897118 GTTTAAATGGGAATGTTCGTGTTAAATCGAAGTTTTAATAGTTAGTTGTGATGCTGTTTGTAGGA
515 ATTTAAATGGTAATGTTCGTGTTAAATCGAAGTTGTAATAGTTAGTT-TGATGCTGTTTGTAGGA
* ** *
48897183 TTTTACGTGTACGACTACGTCTTGGATTAATGTCGCTATCAGGTGTGTGAAAACGATCCTAAAAC
579 TTTTA-GTGTACGACTGCGTAGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAAC
* * * **
48897248 TTGATAGAAACTCGTTATATCGTGAAACAAGGGCTT-TTTTTCAAAACTGCCCAATGCCACATGG
643 TCGATAGAAACTCATTAAATCGTGAAAC-AGGGCTTGTTTTTCAAAACTGCCCAATGCCACACAG
* * *
48897312 TCGTGTGTCAGGCTGTATGG-AAATTGTGTGTGTCACACAGCCATGTA
707 CCGTGTGTCAGGCTGTATGGTAAATTATGTGTGCCACACAGCCATGTA
* * * * *
48897359 ATTTAATTTTTTAAAATTAAATCCCTATTATTTTTCTCTTTCGGTATCCGTCAAAGCAACTTCTC
1 ATTTTATTTTTT-AAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTC
48897424 TTTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACA-TTGTTTTTCTTTCTTTTCTTC
65 TTTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACACTTGTTTTTCTTTCTTTTCTTC
* *
48897488 TTTCTTGCCGTGCCAACGCCGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTG
130 TTTTTTGCCTTGCCAACGCCGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTG
* *
48897553 TTGCGTAAGAACACTATTGAGGCTTTTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCTTCG
195 TTGCGTAAGAACACTATTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCG
* * *
48897618 TCGTGGCTTGGTTGTGTTGGCAAGTTTTGTGGAAGATTAGTTCTTTATCAGGTTGGGGATTTTGT
260 T-GTGGCTTGGTTGTGTTGGTAAGTTATGTGGAAGATTAGTTCTTTATAAGGTTGGGG-TTTTGT
* * *
48897683 TGTTTTAAGCAGAAAAATCCGTAGATTAATAATTTTATGATAGATATAGTGTTGTTGATGGTTGT
323 TGTTTTAAGCA-AAAAATCCGTAGATTAATGATTTTATGATTGATATAGTGTTGTTGCTGGTTGT
* * * **
48897748 TGTGGATAGGAGAAGAGTGCATGGTGGTAGACAACTTTC-CAACAAGTTGTGGTTTTGGAGTAGT
387 TGTGGATAGGAGAAGAGCGCATGGTGATAGACAACTTTCGGAA-AA-TTAAGGTTTTGGAGTAGT
* * * * ** * *
48897812 TGTTACAAGTTTGTGGTAACTACTTGTTTATGGATATAGGAACGGTTTATTTGACAAAAGAGAGA
450 TGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTATTTCTTTGAGAAAAGAGAGA
** * *
48897877 ATTTATGTGGTAATGTTTGTGTTAAATCGAAGTTGTAATCA--TAGGTTT-ATGCCGTTTGTAGG
515 ATTTAAATGGTAATGTTCGTGTTAAATCGAAGTTGTAAT-AGTTA-GTTTGATGCTGTTTGTAGG
* * *
48897939 ATTTTAAATGTACGACTGCGTAGTGGATTAAAGTCGCTGTCAGG
578 ATTTT-AGTGTACGACTGCGTAGTGGATTAATGTCGCTATCAGG
48897983 CCGTGTGGTA
Statistics
Matches: 1203, Mismatches: 152, Indels: 63
0.85 0.11 0.04
Matches are distributed among these distances:
755 1 0.00
756 169 0.14
757 197 0.16
758 323 0.27
759 344 0.29
760 59 0.05
761 3 0.00
762 1 0.00
763 3 0.00
764 2 0.00
765 1 0.00
766 3 0.00
767 3 0.00
768 29 0.02
769 65 0.05
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.42
Consensus pattern (754 bp):
ATTTTATTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCT
TTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACACTTGTTTTTCTTTCTTTTCTTCT
TTTTTGCCTTGCCAACGCCGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGT
TGCGTAAGAACACTATTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGT
GTGGCTTGGTTGTGTTGGTAAGTTATGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGT
TTTAAGCAAAAAATCCGTAGATTAATGATTTTATGATTGATATAGTGTTGTTGCTGGTTGTTGTG
GATAGGAGAAGAGCGCATGGTGATAGACAACTTTCGGAAAATTAAGGTTTTGGAGTAGTTGCTGC
AAGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTATTTCTTTGAGAAAAGAGAGAATTTAA
ATGGTAATGTTCGTGTTAAATCGAAGTTGTAATAGTTAGTTTGATGCTGTTTGTAGGATTTTAGT
GTACGACTGCGTAGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGA
AACTCATTAAATCGTGAAACAGGGCTTGTTTTTCAAAACTGCCCAATGCCACACAGCCGTGTGTC
AGGCTGTATGGTAAATTATGTGTGCCACACAGCCATGTA
Found at i:48898913 original size:12 final size:12
Alignment explanation
Indices: 48898891--48898924 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
48898881 TATGTTTTAC
48898891 ATTTT-TTCTTT
1 ATTTTCTTCTTT
48898902 ATTTTCTTCTTT
1 ATTTTCTTCTTT
*
48898914 CTTTTCTTCTT
1 ATTTTCTTCTT
48898925 ATACGTCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTCTTCTTT
Found at i:48899121 original size:768 final size:767
Alignment explanation
Indices: 48897976--48903007 Score: 6142
Period size: 768 Copynumber: 6.6 Consensus size: 767
48897966 TTAAAGTCGC
* * *
48897976 TGTCAGGCCGTGTGGTAGATTTTTTGTGTCACACGACCGTGTAA-ATT-TTTTTT-AAATCAAAT
1 TGTCAGGCCGTGTGGTAGATTGTGTGTGTCACACGACCGTGTAATTTTATTTTTTAAAATCAAAT
* * * *
48898038 CTCTATTATTTTTCTCTTTCGGAAACCGTCAAACCAACTTCTCTTTGGTTGCACGTGTCTTT-TC
66 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
* * * *
48898102 TTTTTGTCATTTTTGTTTTACATTTTTTAGTCTTTCTTTTTTTCTTTCTTTCCATCTTTTTCACC
131 TTCTT-TCA-ATTTGTTTTACA-TTTTT--TCTTTCTTTTCTTCTTTCTTTCCTTCTTTTTCACC
* * *
48898167 TTTCCAACGTTCG-CT-C--CTTTTGTTATTGTGCCAATTACGAAATCTTTCTTTTGTTGTGTAA
191 TTGCCAACG-TCGACTCCTTCTTTTGTTATTGTGCCAATTGCGAAATCTTTCTTTTGTTGCGTAA
* * * *
48898228 AAACACTGTTGAGGCATGTTATGATTCTGTTGTTCGCTTGTTTGTTTATTTTCCTCGTGGTGGCT
255 GAACACTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCT
* *
48898293 TGGTTGTGTTTGTAAGTTGTGTGGAAGATTATGTT-TTTATAAGGTTAGGGTTTTGTTGTTTTAA
320 TGGTTGTGTTGGTAAGTTGTGTGGAAGATTA-GTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAA
* * *
48898357 GTAGAAAAATTCGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTCATTGTTGTGGATA
384 GCAAAAAAATTCGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGATTGTTGTGGATA
* * *
48898422 TGAGAAGAGCACATGGTGATAGACAACACTCCGACAAATTAAGGTTTTGGAGTAGTTGTTGCAAG
449 GGAGAAGAGCGCGTGGTGATAGACAAC-CTCCGACAAATTAAGGTTTTGGAGTAGTTGTTGCAAG
* * **
48898487 TTTGTGTTAACGACTTGTTTATGAATATAGGGACTG-TTCATTTGAGAAAAGAATGAATTTAAGT
513 TTTGTGGTAACTACTTGTTTATGAATATAGGGACTGTTTC-TTTGAGAAAAGAGCGAATTTAAGT
* * *
48898551 GGTAATGTTCGTGTTTAATCGAAGTTGTAACCGTTGGTTTTGGTGTCGATTGTAGGATTTTAAGT
577 GGTAATGTTCGTGTTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGATTGTAGGATTTTAAGT
* ** *
48898616 GTACGACTGTGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAATGATCTTAAAACTCGATAGA
642 GTACGACTGCGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGA
* * *
48898681 AACTCATTAAATGGTGAAACAGGGGCTGTTTTTCGAAACTGCCTAGTGCCACACGGCTGTG
707 AACTCGTTAAATCGTGAAACAGGGGCTATTTTTCGAAACTGCCTAGTGCCACACGGCTGTG
* * *
48898742 TGTCAAGCCGTTTGGTAGGTTGTGTGTGTCACACGACCGTGTAATTTTATTTTTTAAAATCAAAT
1 TGTCAGGCCGTGTGGTAGATTGTGTGTGTCACACGACCGTGTAATTTTATTTTTTAAAATCAAAT
* * * *
48898807 CCCTATCATTTTTCTCTTTCAGTAACCTTCAAACCAACTTCTCTTTGGTTGCACG-TTCTTTCCC
66 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
* * * * **
48898871 TTCTTTCAATTATGTTTTACATTTTTTCTTTATTTTCTTCTTTCTTTTCTTCTTATACGTCTTGC
131 TTCTTTCAATT-TGTTTTACATTTTTTCTTTCTTTTCTTCTTTCTTTCCTTCTTTTTCACCTTGC
*
48898936 CAACGCCGACTCCTTCTTTTGTTATTGTGCCAATTGCGAAATCTTTCTTTTGTTGCGTAAGAACA
195 CAACGTCGACTCCTTCTTTTGTTATTGTGCCAATTGCGAAATCTTTCTTTTGTTGCGTAAGAACA
* * * * *
48899001 CTGTT-AGGGCTTATTATGATTTTATTGTTTGCATGTTTCTTTCTTTTCCTCGTGGTGGCTTGGT
260 CTGTTGA-GGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGT
48899065 TGTGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAA
324 TGTGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAA
*
48899130 AAAATCCGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCT-AGTTGTTGTGGATAGGAG
389 AAAATTCGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGA-TTGTTGTGGATAGGAG
* * * *
48899194 AAGAGCGCGTGGTGATAGACAACCTTTCGTCAAATTAAGGTTTTGGTGTAGTTGCTGCAAGTTTG
453 AAGAGCGCGTGGTGATAGACAACC-TCCGACAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTG
* * * *
48899259 TAGTAACAACTTGTTTATGAATATAGGGATTGTTTCTTTGAGAAAAGAGCGAATGTAAGTGGTAA
517 TGGTAACTACTTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAA
* * * *
48899324 TGTTCATGTTAAATCGAATTTGTAATCGTTGGTTTTGGTACCGTTTGTAGGATTTTAAGTGTACG
582 TGTTCGTGTTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGATTGTAGGATTTTAAGTGTACG
* * * * *
48899389 ACTGCATGGTGGATTAATCTCGCTATCAGGTGTGTTAAAACGATCCTAAAACTCGGTAGAAACTC
647 ACTGCGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAACTC
* * * * **
48899454 GTTAAATCGTGAAACATGGGCTATTTTTTGAAATTTCCTAGTGCCACAC-AATAGTG
712 GTTAAATCGTGAAACAGGGGCTATTTTTCGAAACTGCCTAGTGCCACACGGCT-GTG
* *** * * * *
48899510 TGTTAGGCCGTGTGGTAGATTGTGTGCACCACATGATCGTGTGATTTTATTTTTTAATATCAAAT
1 TGTCAGGCCGTGTGGTAGATTGTGTGTGTCACACGACCGTGTAATTTTATTTTTTAAAATCAAAT
* * * *
48899575 TCCTATTATTTTTCTATTTCGGCAACCGTCAAACCAACTTCTCTTTAGTTGCACGTTTCTTTCTC
66 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
* * * * **
48899640 TTCTTTCAAGTTTGTTTTATATTTTTTTCCTTCTTTCCTTCTTTCTTTCCTT-GTTTTCACCCCG
131 TTCTTTCAA-TTTGTTTTACA-TTTTTTCTTTCTTTTCTTCTTTCTTTCCTTCTTTTTCACCTTG
* * ** * *
48899704 CCAACGTCGACTCCTTCTTTTGTTATTGTGCAAATAGAAAAATCTTTCTTTTTTTGTGTAAGAAC
194 CCAACGTCGACTCCTTCTTTTGTTATTGTGCCAATTGCGAAATCTTTCTTTTGTTGCGTAAGAAC
* * *
48899769 ATTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCATGGTGCCTTGGT
259 ACTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGT
* * * *
48899834 TGTGTTGTTAAGTTGT-TGGAAGTTTAGTTCTTTATAAGGTTGGGGTTTTGTTGCTTTAAGCAGA
324 TGTGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAA
* * * **
48899898 AAAA-TCTGTAGATTAATGATTTTATGATTGATATAATGTTGTGGTTGGTTGTTGTGGATTTGAG
389 AAAATTC-GTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGATTGTTGTGGATAGGAG
* * *
48899962 AAGAGCGCATGGTGATAGACAACTCTCCAACAAATTAAGGTTTTGGAGTAGTTGTTGCAATTTTG
453 AAGAGCGCGTGGTGATAGACAAC-CTCCGACAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTG
* * * * * * *
48900027 TGGTAACTACAAT-TTTATGAATAAAGGGACTCTTTCTCTGAGGAAAGAGCGAATTTAAATGGAA
517 TGGTAACTAC-TTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTA
* * * * *
48900091 AAGTTCATGTTAAACCAAAGTTGTAATCGTTTG-TTT--TG--G--TG-AGGATTTTAAGTGTAC
581 ATGTTCGTGTTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGATTGTAGGATTTTAAGTGTAC
** * * *
48900148 GACTGCAAGGTGGATTAATGTCACTATTAGGTGTGTGAAAAGAATCCTAAAACTCGATAGAAACT
646 GACTGCGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAACT
* * * *
48900213 CGTTAAATC-TGAAATAGGGG-TAATGTTTT-GAAACTGCCCAGTGCCACACGGCCGAG
711 CGTTAAATCGTGAAACAGGGGCT-AT-TTTTCGAAACTGCCTAGTGCCACACGGCTGTG
* * * * *
48900269 TGTCAAGCCGTTTGGTAGATTGTGTGTGTCACACGACCATGTAACTTTATTTTTTTAAATCAAAT
1 TGTCAGGCCGTGTGGTAGATTGTGTGTGTCACACGACCGTGTAATTTTATTTTTTAAAATCAAAT
** *
48900334 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTCAGTTGCACGTTTCTTTCCG
66 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
* *
48900399 TTCTTTCAATTTTGTTTTACATTTTTTTCTTT-TTTCTCTTCTTTCGTTCCTTCTTTTTCTCCTT
131 TTCTTTCAA-TTTGTTTTACA-TTTTTTCTTTCTTT-TCTTCTTTCTTTCCTTCTTTTTCACCTT
* * ** *
48900463 GCCAATGCCGACT-C--CTTTTGTTATTGTGCCAATTGTAAAATCTTTCTCTTGTTGCGTAAGAA
193 GCCAACGTCGACTCCTTCTTTTGTTATTGTGCCAATTGCGAAATCTTTCTTTTGTTGCGTAAGAA
* * ** *
48900525 CACTATTGAGGCTTGTTATGATTCGGTTGTTAACTTGTTTCTTTCTTTTCCTGGTGGTGGCCTT-
258 CACTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGG-CTTG
* * *
48900589 GTTGCT-TTGG-AAGTTATGTGGAAGATTAGTTCTTTATAATGTTGGAGTTTTGTTGTTTTAAGC
322 GTTG-TGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGC
* ** * *
48900652 AAAAAAA-TCTGTAGATTAATGATTTTATGATAGATATAGTGTTGTGTTTGGTTGTTGTAGATAG
386 AAAAAAATTC-GTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGATTGTTGTGGATAG
* * * * * *
48900716 GAGAAGTGCACGTGGTGGTAGACAACCCTCCGAAAAATTAAAGTTTTGGAGTAGTTGTAGCAAGT
450 GAGAAGAGCGCGTGGTGATAGACAA-CCTCCGACAAATTAAGGTTTTGGAGTAGTTGTTGCAAGT
* * * *
48900781 TTGTGGTAACTACTTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGTGACTGTAAGTCG
514 TTGTGGTAACTACTTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGG
* * *
48900846 TAATGGTCGTGTTAAATTGAAGTTGTAATCGTTGGTTTTGGTGCCGTTTGTAGGATTTTAAGTGT
579 TAATGTTCGTGTTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGATTGTAGGATTTTAAGTGT
* * * *
48900911 ACAAATGCGTGGTGGATTAATGTCACTATCAGGTGTGTGAAAACAATCCGAAAACTCGATAGAAA
644 ACGACTGCGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAA
* * * * * * * *
48900976 CTCGTTAAATCGTGAAACATGTGCTATTTTACTAAACTACCTAGTGCCACAAGGCCGTT
709 CTCGTTAAATCGTGAAACAGGGGCTATTTTTCGAAACTGCCTAGTGCCACACGGCTGTG
* * * * * * *
48901035 TGTCAGGCCGTGTGGTAGATTGTGAGCGACACACAACCGTGAAATTTTAATTTCTAAAATCAAAT
1 TGTCAGGCCGTGTGGTAGATTGTGTGTGTCACACGACCGTGTAATTTTATTTTTTAAAATCAAAT
* * *
48901100 CCCTATTATTTTTCTCTTTCAGCAACCGTCAAACCAACTTCTCTTCGGTTGCATGTTTCTTTCCC
66 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
* * * *
48901165 TTCTTTCAAATTTGTTTTACA-TTTTTCCTTCTTTTCCTCTTTTTTTCCCTTTTTTTTCACCTTG
131 TTCTTTC-AATTTGTTTTACATTTTTTCTTTCTTTTCTTCTTTCTTT-CCTTCTTTTTCACCTTG
* * *
48901229 CCAACGTCGGCTCCTTCTTTTGTTTTTGAT-CCAATTGAGAAATCTTTCTTTTGTTGCGTAAGAA
194 CCAACGTCGACTCCTTCTTTTGTTATTG-TGCCAATTGCGAAATCTTTCTTTTGTTGCGTAAGAA
* * *
48901293 CACTGTTGAGGCTTGTTATGATTCTGTTGTTTGCTTGTTTTTTTCTTTTCCTCAT-GTGGCTTGG
258 CACTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGG
* * * *
48901357 TTGTGTTGGTAAGTTGTGTGCAATATTAGTTCTTTATAAGGTTGGGGTTTTGTT-TTTTAAGTAG
323 TTGTGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAA
* * * * *
48901421 AAAAATCCGTAGATTAATGATTTTATGATAGATATAGTGTAGTGGCTGATTGTTTTGGATATGAG
388 AAAAATTCGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGATTGTTGTGGATAGGAG
* * ** * *
48901486 AAGAGTGCGTAGTGATAGACAACTCTCTAACAAATTAAGGTTTTGGAGTAGTTATTGCATGTTTG
453 AAGAGCGCGTGGTGATAGACAAC-CTCCGACAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTG
* * * *
48901551 TGGTAACTACTTGTTTAGGAATATAGGGATTGCTTCTCTGAGAAAAGAGCGAATTTAAGTGGTAA
517 TGGTAACTACTTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAA
** * * * * * *
48901616 CATTCGTGTTAAATCGAAGATCTAATCGTTTGTTTTGGGGCC-ATTTTTTAGTATTTTAAGTGTA
582 TGTTCGTGTTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGA--TTGTAGGATTTTAAGTGTA
* * * *
48901680 CGACTGCGTGGTGGATTGATGTTGCTATCAGGTGTTTGAAAACAATCCTAAAACTCGATAAAAAC
645 CGACTGCGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAAC
* * * * *
48901745 TCGTTAAATCGTGAAACAGAGGCTATTTTTTGAAACTACCCAGTGGCACACGG-TCGTG
710 TCGTTAAATCGTGAAACAGGGGCTATTTTTCGAAACTGCCTAGTGCCACACGGCT-GTG
* * ** * *
48901803 TGTCAGGCTGTATGGTAGATTGTGTGTGTCACAC-AGCTTTGTGATTTTATTTTTTTAAATCAAA
1 TGTCAGGCCGTGTGGTAGATTGTGTGTGTCACACGA-CCGTGTAATTTTATTTTTTAAAATCAAA
* * * *
48901867 TCCCTATTATTTTTCTCTTTCGACAACTGTCAAACCAACTTCTCTTTGGTTGAACGTTTCTTTCA
65 TCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCC
* * *
48901932 CTTCCTTCATTTTTGTTTTACATATTTTTCTTTCTTTTCTTCTTTATTTCCTTCTTTTTCACCTT
130 CTTCTTTCA-ATTTGTTTTACAT-TTTTTCTTTCTTTTCTTCTTTCTTTCCTTCTTTTTCACCTT
* *
48901997 GCCAACGTCGGCTCCTTCTTTTGTTATTGTGCCAATTGCGAAATCTTTCTTTTGTTGTGTAAGAA
193 GCCAACGTCGACTCCTTCTTTTGTTATTGTGCCAATTGCGAAATCTTTCTTTTGTTGCGTAAGAA
* ** * *
48902062 CACTGTTGAGGCTTTTTATGATTCTGTTGTTCGCTCATGTCTTTCTTTTCCTCGTGGTGGCCTGG
258 CACTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGG
* * *
48902127 TTATGTTGGTAAGTTGTGTGGAAGATTAGTTTTTTATAAGGTTGGGGTTTTGTTGTTTTAAGGAA
323 TTGTGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAA
* * * *
48902192 AAAAATTCGTAGATTAATTATTTTATGATTGATATAGTGTTGTGGCTGGTTGTTCTCGATAGGAG
388 AAAAATTCGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGATTGTTGTGGATAGGAG
* * * *
48902257 AAGAACGCGTGGTGATAGACAATCCTTCGAGAAATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTG
453 AAGAGCGCGTGGTGATAGACAA-CCTCCGACAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTG
* * * * * *
48902322 TGGTAGCTACTTCTTTGTGAATATAAGGTA-TTTTTCTTTGAGAAAAGAGTGAATTTAAGTGGTA
517 TGGTAACTACTTGTTTATGAATAT-AGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTA
* * *
48902386 ATATTCGTGTCT-AATTGAAGTTGTAATCGTTGGTTTTGGTGTC-ATTCGTAGGATTTTAAGTGT
581 ATGTTCGTGT-TAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGATT-GTAGGATTTTAAGTGT
* * * * ** * *
48902449 ATGACTTCGTGGTGGATTAATCTCGCTATCATGTGTAAGAAAACAATCCTAAAACTCAAGAGAAA
644 ACGACTGCGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAA
* * ** * * * * * **
48902514 CTCGTTAAGTCGTGAAACAGGGGTTGGTTTCCAAAACTGCCCTA-TGCGACACAGCAGCA
709 CTCGTTAAATCGTGAAACAGGGGCTATTTTTCGAAACTG-CCTAGTGCCACACGGCTGTG
* * * * ** * * * *
48902573 TGTCTGGCCGTGTGGTAGATTTTCTGTGCCACTTGGCTGTTTAATTTTATTTTTTAAAATCATAT
1 TGTCAGGCCGTGTGGTAGATTGTGTGTGTCACACGACCGTGTAATTTTATTTTTTAAAATCAAAT
* * * *
48902638 CCCTATTATTTTTCTCATTCTGCAACAGTCAAACCAACTTCTCTTCGGTTGCACGTTTCTTTCCC
66 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
* *
48902703 TTCTTTCAAATTTGTTTT--A--TTAT-TTTC---T-TTCTTTC--T--TTCTTTTTCGCCTTG-
131 TTCTTTC-AATTTGTTTTACATTTTTTCTTTCTTTTCTTCTTTCTTTCCTTCTTTTTCACCTTGC
* * * *
48902754 CAACGCCAACACCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACA
195 CAACGTCGACTCCTTCTTTTGTTATTGTGCCAATTGCGAAATCTTTCTTTTGTTGCGTAAGAACA
* * *
48902819 CTGTTGAGGCTTGTTATGATTTTGTTGTTTGCTTGTTTCTTTCTGTTCCTCGTGGTGGCTTGGTT
260 CTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTT
* * *
48902884 GTGGTGGTAAGGTT-TGTTGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTATTTTAAGCAAA
325 GTGTTGGTAA-GTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAA
* * *
48902948 AAAAATCGTAGATTAATGATTTTAGGATTGATATAGTGTAGTGGCT-AGTTGTTGTGGATA
389 AAAATTCGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGA-TTGTTGTGGATA
48903008 AGAAAAGCAA
Statistics
Matches: 3656, Mismatches: 534, Indels: 163
0.84 0.12 0.04
Matches are distributed among these distances:
755 222 0.06
756 24 0.01
757 333 0.09
758 13 0.00
759 186 0.05
760 112 0.03
761 3 0.00
762 1 0.00
763 1 0.00
764 25 0.01
765 154 0.04
766 209 0.06
767 242 0.07
768 1228 0.34
769 353 0.10
770 337 0.09
771 207 0.06
772 6 0.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (767 bp):
TGTCAGGCCGTGTGGTAGATTGTGTGTGTCACACGACCGTGTAATTTTATTTTTTAAAATCAAAT
CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
TTCTTTCAATTTGTTTTACATTTTTTCTTTCTTTTCTTCTTTCTTTCCTTCTTTTTCACCTTGCC
AACGTCGACTCCTTCTTTTGTTATTGTGCCAATTGCGAAATCTTTCTTTTGTTGCGTAAGAACAC
TGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTG
TGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAAAA
AATTCGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGATTGTTGTGGATAGGAGAAG
AGCGCGTGGTGATAGACAACCTCCGACAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTGTGGT
AACTACTTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAATGTT
CGTGTTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGATTGTAGGATTTTAAGTGTACGACTG
CGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAACTCGTTA
AATCGTGAAACAGGGGCTATTTTTCGAAACTGCCTAGTGCCACACGGCTGTG
Found at i:48903417 original size:12 final size:12
Alignment explanation
Indices: 48903402--48903436 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
48903392 TTTGTTTTAA
*
48903402 TTTTTTTCTTTC
1 TTTTCTTCTTTC
48903414 TTTTCTTCTTTC
1 TTTTCTTCTTTC
*
48903426 TTTCCTTCTTT
1 TTTTCTTCTTT
48903437 TTCACATAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:48904815 original size:41 final size:41
Alignment explanation
Indices: 48904753--48904852 Score: 173
Period size: 41 Copynumber: 2.4 Consensus size: 41
48904743 GAAAATGCCC
* *
48904753 AGTGCCACACGGTCGTGTGTCAGGCCGTATTCTAGATTGTT
1 AGTGTCACACGGCCGTGTGTCAGGCCGTATTCTAGATTGTT
48904794 AGTGTCACACGGCCGTGTGTCAGGCCGTATTCTAGATTGTT
1 AGTGTCACACGGCCGTGTGTCAGGCCGTATTCTAGATTGTT
*
48904835 AGTGTCACACGTCCGTGT
1 AGTGTCACACGGCCGTGT
48904853 AATTTTATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.17, C:0.23, G:0.29, T:0.31
Consensus pattern (41 bp):
AGTGTCACACGGCCGTGTGTCAGGCCGTATTCTAGATTGTT
Found at i:48906907 original size:769 final size:762
Alignment explanation
Indices: 48903271--48906950 Score: 3731
Period size: 755 Copynumber: 4.8 Consensus size: 762
48903261 TGTGTGGTAC
* * *
48903271 ATTGTGTGCGTCACACGACCGTGTAATTTTATTTTTGT-AAATCAAAT-CCTATTATTTTTCTCT
1 ATTGTGTGAGCCACACGGCCGTGTAATTTTATTTTT-TAAAATCAAATCCCTATTATTTTTCTCT
* * *
48903334 TTCGGCAACCGTCAAACCAACCTCTCTTTGGTTGCACGTTTCTTT-CCTTTCTTTCAATTTTGTT
65 TTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTT-TTTCAATTTTCTT
* * *
48903398 TTAATTTTTTTCTTTCTTTTCTTCTTTCTTTCCTTCTTTTTC-ACATAGCCAACACCGACTCCTT
129 TT-A-TTTTTTCCTTCTTTTCTTCTTT-TTTCCTTCTTTTTCGAC-TTGCCAACGCCGACTCCTT
* * * *
48903462 CTTTTGTTAATGTGCCAATTGCAAAATCTTTATTTTGTTGCTTAAGAACATTGTTGAGGCTTGTT
190 CTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTT
* * *
48903527 ATGATTCTGCTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGT
255 ATGATTATGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTTT
* *
48903592 GTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTGTAAGCAATAAAGTCCGTAGATTAA
320 GTGGAAGATTAGTTCTTTATAAGGTT-GGG-TTTGTTGTTTTAAGCAA-AAAATCCGTAGATTAA
* * * * * * * * * *
48903657 TGATTTTAT-GATATATATAGTGTTGTTGTTGGTTATTTTGAATATGAGAAGAGTGTGTGGTGAT
382 TGATTTT-TGGATAGATATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGCGTGGTGAT
* * ** *
48903721 AGACAACCCTCCAAAAAATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTAATTGTTT
446 AGACAATCCTCCGAAAAATTAAGGTTTTGGAGTAGTTATTGCAAGTTTGTGGTAACTACTTGTTT
* * * * * * * * *
48903786 ATGAATATAGGGACTATTTATTTGGGAAAAGATCGAATGTAAGTGGTAATGTTCGTGTTAAAT-T
511 ATGAATATAAGGACTGTTTCTTTGAGAAAAGAGCAAATTTAAGTGGTAATATTCGTGTTAAATCG
* * * * * * *
48903850 AGAGTTGTAATCGTTGG-TTTGTGTGGCATTTATAGGATTTTAAGTGTACGACTACGTGGTGGAT
576 A-AGTTGTAATCGTTGGTTTTG-GTGCCATTTGTAAGATTTTAAGTGTACAATTGCATGGTGGAT
** * * *
48903914 TAATCTTGCTATCAGGTGTGTA-AAAACAATCCAAAAACTC-GGTAGAAACTCGTTAAATCGTGA
639 TAATCTCACTATCAGGTGCG-AGAAAACAATCCTAAAACTCAAG-AGAAACTCGTTAAATCGTGA
* * * * * * * * * *
48903977 AACATGAGCTCTTTTTTGAAACTGCCTAGTGCCGCA--CAACCCTATGTCAGGCTGTGTGGTAG
702 AACATGGGGTGTTTTTCGAAACTACCCAGTGCCACAGGCAA--C-ATGTCAGGCCGTATGGCAG
* * * ** *
48904039 AATGTGGGCGCTGCACGACCGTGTAATTTTATTTTTT-AAATCAAATCCCTATTATTTTTCTCTT
1 ATTGTGTGAGCCACACGGCCGTGTAATTTTATTTTTTAAAATCAAATCCCTATTATTTTTCTCTT
*** * * * * * *
48904103 TTTACAACTGTTAAACCAACTTCTCTTTGGTTACA-AGTTTCTTTCCCTTCTTTCGATTTTGTTT
66 TCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACA-TTTCTTTCCCTTTTTTCAATTTTCTTT
** * * * *
48904167 TA----------C----AAT-TTTTTTCCTTTTTTTTCGCCTTTCCAACACCGACTCCTTCTTTT
130 TATTTTTTCCTTCTTTTCTTCTTTTTTCCTTCTTTTTCGACTTGCCAACGCCGACTCCTTCTTTT
* * *
48904217 GTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGTGTAAGATCACTGTTGGGGCTTGTTATGAT
195 GTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGAT
* * * * * * *
48904282 TCTGTTGTTCGCTTATTTCTTTCTTTTCCTTGTGGTAGCCTGGTTGTGTTGGAAAGTTGT-TGGA
260 TATGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTTTGTGGA
* *
48904346 AGGTTAGTTCTTGATAAGGTTGGGGTTTTGTTGTTTTAA-CAAAAAAAAATCCGTAGATTAATGA
325 AGATTAGTTCTTTATAAGGTT-GGG-TTTGTTGTTTTAAGC---AAAAAATCCGTAGATTAATGA
* *
48904410 -TTTTGTGATAGAGATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGAGTGGTGATAGA
385 TTTTTG-GATAGATATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGCGTGGTGATAGA
* * ** * *
48904474 CAA-CTCTCTGACAAATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGCTAACTACTTGTTAAT
449 CAATC-CTCCGAAAAATTAAGGTTTTGGAGTAGTTATTGCAAGTTTGTGGTAACTACTTGTTTAT
* ** * * *
48904538 GAATAT-AGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAATGGTCATGTTAATTCAAA
513 GAATATAAGGACTGTTTCTTTGAGAAAAGAGCAAATTTAAGTGGTAATATTCGTGTTAAATCGAA
* * * * * * *
48904602 GTTGTAATCATTGGTTTTGGTGCTATTTGTAGGATTTTACA-TGTACGACTACGTGGTGGATTAA
578 GTTGTAATCGTTGGTTTTGGTGCCATTTGTAAGATTTTA-AGTGTACAATTGCATGGTGGATTAA
* * * * * * *
48904666 TCTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAACTCGTTGAATCATGAAACA-
642 TCTCACTATCAGGTGCGAGAAAACAATCCTAAAACTCAAGAGAAACTCGTTAAATCGTGAAACAT
* * *** *
48904730 GGGGATGTTTTTCGAAAATGCCCAGTGCCACACGGTC-GTGTGTCAGGCCGTAT-TCTAG
707 GGGG-TGTTTTTCGAAACTACCCAGTGCCACA-GG-CAACATGTCAGGCCGTATGGC-AG
*
48904788 ATTGTTAGTGTCACACGGCCGTGTGTCAGGCCGTATTCTAGATTGTTAGTGTCACACGTCCGTGT
1 ATTG-T-GTG----A--G-C------CA---C--A--C----------G-G---C-CGT--GT-A
* *
48904853 AATTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCT
26 ATTTT-ATTTTTTAAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCT
* *
48904918 CTTTGGTTGCACGTTTC-TTCCCTTCTTTCAATTTTCTTTTACATTTTTTCCTTCTTTTCTTCTT
90 CTTTGGTTGCACATTTCTTTCCCTTTTTTCAATTTTCTTTT--ATTTTTTCCTTCTTTTCTTCTT
* * * * *
48904982 TCTTTCCTTCTTTCTC-ACATTGCCAACGCCGGCTCCTTCATTTT-TTATTGTGCAAATTACAGA
153 T-TTTCCTTCTTTTTCGAC-TTGCCAACGCCGACTCCTTC-TTTTGTTATTGTGCCAATTGCAAA
* *
48905045 ATCTTTCTTTTGTTGCGTAAGAACATTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCT
215 ATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTATGTTGTTCGCTTGTTTCT
* *
48905110 TTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATGAGTTCTTTATAAGGT
280 TTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTTTGTGGAAGATTAGTTCTTTATAAGGT
* *
48905175 TGGGGTATTGTTGTTTTAAGCAGAAAAATTCGTAGGTTAATGATTTTAT-GATAGATATAGTGTT
345 T-GGGT-TTGTTGTTTTAAGCA-AAAAATCCGTAGATTAATGATTTT-TGGATAGATATAGTGTT
* * * *
48905239 GTGG-TTGATTGTTGTGGATATGAGAAGAGCGCGTAGTGATAGACAA-CTCTCCGAGAAATTAAG
406 GTGGCTAG-TTGTTGTGGATAGGAGAAGAGCGCGTGGTGATAGACAATC-CTCCGAAAAATTAAG
* * *
48905302 GTTTTGGAGTAGTTGTTGGAAGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTGTTTCTTT
469 GTTTTGGAGTAGTTATTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAAGGACTGTTTCTTT
* * * *
48905367 GAGAAAAGAGCGAATTTATGTGGTAACATTCGTGTTAAATCGAAGTTGTAATCGTTTGTTTTGGT
534 GAGAAAAGAGCAAATTTAAGTGGTAATATTCGTGTTAAATCGAAGTTGTAATCGTTGGTTTTGGT
* * * * *
48905432 GCCGTTTGTAAGATTTTAAGTGTACAATTGCGTGGTGGATTAATGTCACTATCAGGTGTGTGAAA
599 GCCATTTGTAAGATTTTAAGTGTACAATTGCATGGTGGATTAATCTCACTATCAGGTGCGAGAAA
** * * * *
48905497 ATGATCCTAAAACTCGATAGAAAGTCGTTAAATCGTGAAACATGGGGTGTTTTTCGAAACTGCCC
664 ACAATCCTAAAACTCAAGAGAAACTCGTTAAATCGTGAAACATGGGGTGTTTTTCGAAACTACCC
**** * *
48905562 AGTGCCACATGGCCTTGTGTCAGGTCGTATGGTAG
729 AGTGCCACA-GGCAACATGTCAGGCCGTATGGCAG
* * *
48905597 ATTGTGTGAGTCACACGGTCGTGTAATTTTATTTTTTTGAAATCAAATCCCTATTATTTTTTCTC
1 ATTGTGTGAGCCACACGGCCGTGTAATTTTA-TTTTTTAAAATCAAATCCCTATTA-TTTTTCTC
48905662 TTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTCTTTT-AATTTTCT
64 TTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTT-TTTTCAATTTTCT
** * * * * *
48905726 TTTACATTTT-GTT-ATTTCTTC----TT--TTCTTTTTCGCCTTGCCAAAGTCGACTCCTTCTT
128 TTTATTTTTTCCTTCTTTTCTTCTTTTTTCCTTCTTTTTCGACTTGCCAACGCCGACTCCTTCTT
* * * **
48905783 TTGTTATTGTGCCAATTGCAAAATCTATCTTCTGTTGCGTAAGAACACTATTGAATCTTGTTATG
193 TTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATG
** * *
48905848 ATTATGTTGTTCGCTAATTTCTTTCTTTTCCTCGTAGTGGCTTGGTTATGTTGGTAAGTTGTT-T
258 ATTATGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTT-TTGT
* * *
48905912 GGAAGATTAGTTCTTTATAATGTTGGG-TT-TT-TTTTCAGCAAAAAAATCCGTAGATTAATGGT
322 GGAAGATTAGTTCTTTATAAGGTTGGGTTTGTTGTTTTAAGC-AAAAAATCCGTAGATTAATGAT
* * * *
48905974 ATTATGG-TAGATATCGTGTTGTGGCTGGTGGTTGTGGATAGGAGAAGAGCGCGTGGTGATAGAC
386 -TTTTGGATAGATATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGCGTGGTGATAGAC
* ** *
48906038 AATCCTTCGAAAAATTAAGGTTTTGGAGTAACTACTGCAAGTTTGTGGTAACTACTTGTTTATGA
450 AATCCTCCGAAAAATTAAGGTTTTGGAGTAGTTATTGCAAGTTTGTGGTAACTACTTGTTTATGA
* *
48906103 ATATAAGGACTGTTTCTTTGAGAAAAGAGCAAATTTAAGTGGTAATATTCGTGTTAAATCAAAAT
515 ATATAAGGACTGTTTCTTTGAGAAAAGAGCAAATTTAAGTGGTAATATTCGTGTTAAATCGAAGT
* * * *
48906168 TGTATTCGTTGGTTTTGGTGTCATTTGTAGGATTTTAAGTGTATGAATT-CATGGTGGATTAATC
580 TGTAATCGTTGGTTTTGGTGCCATTTGTAAGATTTTAAGTGTA-CAATTGCATGGTGGATTAATC
* * * * *
48906232 TCGCTATTATGTGCGAGAAAGCAATCCTAAAACTCAAGAGAAACTCGTTAAATCTTGAAACA-GG
644 TCACTATCAGGTGCGAGAAAACAATCCTAAAACTCAAGAGAAACTCGTTAAATCGTGAAACATGG
* ** * *
48906296 GTTTGGTTTTT-GAAACTACCTTGTGCGTCACA-GCAACATGTCTGGCCGTGTGGCAG
709 G-GT-GTTTTTCGAAACTACCCAGTGC--CACAGGCAACATGTCAGGCCGTATGGCAG
* * ** * *
48906352 ATTTTGTGCGCCACTTGGCCGTTTAATTTTATTTTTTAAAATCATATCCCTATTATTTTTCTCTT
1 ATTGTGTGAGCCACACGGCCGTGTAATTTTATTTTTTAAAATCAAATCCCTATTATTTTTCTCTT
** ** *
48906417 TTAGCAACCGTCAAACCAACTTCTCTTCAGTTGCACATTTCTTTCCCTTTTTTCAATTTTGTTTT
66 TCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTTTTTCAATTTTCTTTT
* * *
48906482 ATTTTTTTTCTTTCTTTTCTTCTTTGTTTCCTTCTTTTTCGGCTTGCCAACGCCGACACCTTCTT
131 A--TTTTTTCCTTCTTTTCTTCTTT-TTTCCTTCTTTTTCGACTTGCCAACGCCGACTCCTTCTT
*
48906547 TTGTTATTGTGCCAATTGCAAAATCTTTCTTTTATTGCGTAAGAACACTGTTGAGGCTTGTTATG
193 TTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATG
* * * * * *
48906612 ATTTTGTTGTTCGTTTGTTACTTTCTGTTCCTCGTGGAGGCTTGGTTGTGGTGGTAAGTTTTGTG
258 ATTATGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTTTGTG
* *
48906677 GAAGATTAGTTCTTTATAAGGTTGGGATTTTGTTGTTTTAAGTAAAAATATCCGTAGATTAATGC
323 GAAGATTAGTTCTTTATAAGGTTGGG--TTTGTTGTTTTAAGCAAAAA-ATCCGTAGATTAATGA
* *
48906742 TTTTTGGATTGATATAGTGTAGTGGCTAGTTGTTGTGGATAGGAGAAGAGC-CTGTGGTGATAGA
385 TTTTTGGATAGATATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGC-GTGGTGATAGA
*
48906806 TAATCCTCCGAAAAATTAAGGTTTTGGAGTAGTTATTGCAAGTTTGTGGTAACTACTTGTTTATG
449 CAATCCTCCGAAAAATTAAGGTTTTGGAGTAGTTATTGCAAGTTTGTGGTAACTACTTGTTTATG
* * * * * * *
48906871 AGTATAAGGACTGTTTCATTGAGATAAGAGCAAATTTCAGTGGTAATGTTTGTGCTAAATCGAAG
514 AATATAAGGACTGTTTCTTTGAGAAAAGAGCAAATTTAAGTGGTAATATTCGTGTTAAATCGAAG
48906936 TTGTAATCGTTGGTT
579 TTGTAATCGTTGGTT
48906951 GATGGTTGTC
Statistics
Matches: 2455, Mismatches: 323, Indels: 267
0.81 0.11 0.09
Matches are distributed among these distances:
748 4 0.00
749 236 0.10
750 281 0.11
751 8 0.00
752 5 0.00
753 67 0.03
754 25 0.01
755 348 0.14
756 22 0.01
757 14 0.01
758 1 0.00
759 7 0.00
760 156 0.06
761 2 0.00
762 4 0.00
763 2 0.00
764 166 0.07
767 21 0.01
768 113 0.05
769 238 0.10
770 52 0.02
771 19 0.01
772 6 0.00
776 1 0.00
777 1 0.00
781 1 0.00
785 1 0.00
786 3 0.00
787 1 0.00
788 2 0.00
789 5 0.00
790 28 0.01
791 61 0.02
792 1 0.00
794 2 0.00
801 1 0.00
802 1 0.00
803 1 0.00
806 1 0.00
807 10 0.00
808 277 0.11
809 254 0.10
810 6 0.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (762 bp):
ATTGTGTGAGCCACACGGCCGTGTAATTTTATTTTTTAAAATCAAATCCCTATTATTTTTCTCTT
TCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTTTTTCAATTTTCTTTT
ATTTTTTCCTTCTTTTCTTCTTTTTTCCTTCTTTTTCGACTTGCCAACGCCGACTCCTTCTTTTG
TTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATT
ATGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTTTGTGGAA
GATTAGTTCTTTATAAGGTTGGGTTTGTTGTTTTAAGCAAAAAATCCGTAGATTAATGATTTTTG
GATAGATATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGCGTGGTGATAGACAATCCT
CCGAAAAATTAAGGTTTTGGAGTAGTTATTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAA
GGACTGTTTCTTTGAGAAAAGAGCAAATTTAAGTGGTAATATTCGTGTTAAATCGAAGTTGTAAT
CGTTGGTTTTGGTGCCATTTGTAAGATTTTAAGTGTACAATTGCATGGTGGATTAATCTCACTAT
CAGGTGCGAGAAAACAATCCTAAAACTCAAGAGAAACTCGTTAAATCGTGAAACATGGGGTGTTT
TTCGAAACTACCCAGTGCCACAGGCAACATGTCAGGCCGTATGGCAG
Found at i:48907190 original size:15 final size:15
Alignment explanation
Indices: 48907172--48907202 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
48907162 GTAAAAGCTG
48907172 AAAATAATTAAATAA
1 AAAATAATTAAATAA
*
48907187 AAAATAGTTAAATAA
1 AAAATAATTAAATAA
48907202 A
1 A
48907203 TCTGAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAAATAATTAAATAA
Found at i:48909016 original size:5 final size:5
Alignment explanation
Indices: 48909006--48909061 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
48908996 GTCTACTTGC
* **
48909006 AAAAT AAAAT AAAAT AAAAT AGAA- GGAAT AAAAAT AAAAT AAAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT -AAAAT AAAAT
48909057 AAAAT
1 AAAAT
48909062 GTGTAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
4 3 0.07
5 33 0.75
6 8 0.18
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:48909048 original size:11 final size:11
Alignment explanation
Indices: 48909006--48909060 Score: 67
Period size: 11 Copynumber: 4.8 Consensus size: 11
48908996 GTCTACTTGC
48909006 AAAAT-AAAAT
1 AAAATAAAAAT
*
48909016 AAAATAAAATAG
1 AAAATAAAA-AT
48909028 AAGGAATAAAAAT
1 AA--AATAAAAAT
48909041 AAAATAAAAAT
1 AAAATAAAAAT
48909052 AAAATAAAA
1 AAAATAAAA
48909061 TGTGTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
10 5 0.13
11 21 0.54
12 3 0.08
13 3 0.08
14 7 0.18
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:48913253 original size:16 final size:16
Alignment explanation
Indices: 48913232--48913263 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
48913222 GTAAAAGCTG
48913232 AAAACAATTAAATAAA
1 AAAACAATTAAATAAA
*
48913248 AAAACAGTTAAATAAA
1 AAAACAATTAAATAAA
48913264 TCTGAAGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAACAATTAAATAAA
Found at i:48915528 original size:12 final size:12
Alignment explanation
Indices: 48915513--48915547 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
48915503 TTGTTTTACA
*
48915513 TTTTTTTCTTTC
1 TTTTCTTCTTTC
48915525 TTTTCTTCTTTC
1 TTTTCTTCTTTC
*
48915537 TTTCCTTCTTT
1 TTTTCTTCTTT
48915548 AAACCTTGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:48916296 original size:12 final size:12
Alignment explanation
Indices: 48916281--48916314 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
48916271 TTGTTTTACA
*
48916281 TTTTTTTCTTTC
1 TTTTCTTCTTTC
48916293 TTTTCTTCTTTC
1 TTTTCTTCTTTC
*
48916305 TTTCCTTCTT
1 TTTTCTTCTT
48916315 ATACGCCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:48916910 original size:770 final size:766
Alignment explanation
Indices: 48914431--48916913 Score: 3578
Period size: 768 Copynumber: 3.2 Consensus size: 766
48914421 TTTTAGCATT
* * * * *
48914431 TAATCATCGGTTTTGGTGTCATTTGTAGGATTTTAAGTGTATGACTTCGCGGTAGATTAATCTCG
1 TAATCATTGGTTTTGGTGTCGTTTGTAGGATTTTAAGTGTATGACTACGTGGTGGATTAATCTCG
* ** * ** * *
48914496 CTATCAGGTGTGTGAAAATAATATTAAAA-TTTGATAGAAACTTGTTAAATCGTGAAATAGAGGC
66 CTATCAGGTGTGTGAAAACAATCCTAAAACTCT-ATAGAAACTCATTAAATCGTGAAACAGGGGC
* *
48914560 TATTTTTCGAAACTGCCTAGTGCCACACGGCCCTGGGTCAGGCCGTGTGGTAGATTGTGTGCGTC
130 TATTTTTCGAAACTGCCTAGTGCCACACGGCCGTGTGTCAGGCCGTGTGGTAGATTGTGTGCGTC
* * * * * ** *
48914625 ACACGACCATGTACTTTTATTTTTTTAAATTAAATCCTTATTATTTTTCTCTTTCGATAACTGTC
195 ACACGACCGTGTAATTTTATTTTTTTAAATCAAATCCCTGTTATTTTTCTCTTTCGGCAACCGTC
* * * * * * *
48914690 AAACAAACTTCTTTTTGGTGGTACGTTTCTTTCCTTTCCTTCAATTTTGTTTTAAATTTTTTTAT
260 AAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTT-CTTCAATTTTGTTTTACATTTTTTTCT
* *
48914755 TTCTTTTCTTCTTTCTTTCCTTCTTTTTCACCTTGCCAACGCCGAAT-C--CTTTTGTTATTGTG
324 TTCTTTTCTTCTTTCTTTCCTTC-TTTACACCTTGCCAACGCCGACTCCTTCTTTTGTTATTGTG
48914817 CCAATTGTAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTATTGTT
388 CCAATTGTAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTATTGTT
* **
48914882 TGCTTCATTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTT
453 CGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTT
* * * * * * *
48914947 TTTTATAAAGTTGGGGTTTTGTTGTTTTAAGTAGAAAATTCCATATATTAATGATTTTATGATAG
518 CTTTATAAGGTTGGGGTTTTGTTGTTTTAA-CAAAAAAATCCGTAGATTAATGATTTTATGATAG
* * *
48915012 ATATAGTGTTTTGGCTAGTTGTTGTGGATATGAGAAGAGCGCGTGGTGATAGACAACCTTCCGAC
582 ATATAGTGTTGTGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAACCTTCCGAC
* * *
48915077 AAATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTAATAGTTGATGAATATAGGGACT
647 AAATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATA-GGACT
* * * *
48915142 ATTTATTTGGGAAAAGTGCGAATGTAAGTGGTAATGTTCGTGTTAAATC-AGAGTTG
711 ATTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAATGTTCGTGTTAAATCGA-AGTTG
* * *
48915198 TAATCATTAGTTTTGGTGTCGTTTGTAAGATTTTAAGTGTACGACTACGTGGTGGATTAATCTCG
1 TAATCATTGGTTTTGGTGTCGTTTGTAGGATTTTAAGTGTATGACTACGTGGTGGATTAATCTCG
* * *
48915263 CTATCAGGTGTGTGAAAACAATCCTAAAACTCTGTAGAAACTCATTAAATCGTGAAACATGGTCT
66 CTATCAGGTGTGTGAAAACAATCCTAAAACTCTATAGAAACTCATTAAATCGTGAAACAGGGGCT
* * * * * **
48915328 GTTTTTCAAAACCGCCTAGTGCCACACGGTCGTGTGTCAGGCCGTGTTGTAGATTGTGTGCACCA
131 ATTTTTCGAAACTGCCTAGTGCCACACGGCCGTGTGTCAGGCCGTGTGGTAGATTGTGTGCGTCA
* ** * * *
48915393 CACGACCGTCTAATTTTATTTTTAAAAATCAAATACCTGTTATTTTTCTCTTTCAGCAACCGTTA
196 CACGACCGTGTAATTTTATTTTTTTAAATCAAATCCCTGTTATTTTTCTCTTTCGGCAACCGTCA
*
48915458 AACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTCTT
261 AACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTC-TTCAATTTTGTTTTACATTTTTTTCTT
* *
48915523 TCTTTTCTTCTTTCTTTCCTTCTTTAAACCTTGCCAACACCGACTCCTTCTTTTGTTATTGTGCC
325 TCTTTTCTTCTTTCTTTCCTTCTTTACACCTTGCCAACGCCGACTCCTTCTTTTGTTATTGTGCC
* * * *
48915588 AATTGCAAAATCTTTCTTTTGTTGTGTGAGAACACTGTTGAGGCTTGTTATGATTCTATTGTTCA
390 AATTGTAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTATTGTTCG
48915653 CTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGT-TGGAAGATTAGTTCT
455 CTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTCT
* *
48915717 TTATAAGGTTGGAGTTTTGTTGTTTTAAGCAAAAAAATACGTAGATTAATGATTTTATGATAGAT
520 TTATAAGGTTGGGGTTTTGTTGTTTTAA-CAAAAAAATCCGTAGATTAATGATTTTATGATAGAT
* *
48915782 ATAGTGTTGTGGCTGGTTTTTGTGGATAAGAGAAGAGCGCATGGTGATAGACAA-CTCTCCGACA
584 ATAGTGTTGTGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAACCT-TCCGACA
*
48915846 ATTTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAAGGACTA
648 AATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATAT-AGGACTA
* * *
48915911 TTTCTTTGAGAAAAGAGCGAATTTAAATGGTAATGTTCATGTTAAATCGAAGTTT
712 TTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAATGTTCGTGTTAAATCGAAGTTG
* * * * ** * *
48915966 TAATCGTTGGCTTTGGTGTTGTTTGTAGGATTTTACGTGTAAAACTACGTGCTGGATTAATGTCG
1 TAATCATTGGTTTTGGTGTCGTTTGTAGGATTTTAAGTGTATGACTACGTGGTGGATTAATCTCG
* * *
48916031 CTATCAGGTGTGTGAAAACGATCCTAAAACTCGATAGAAACTTATTAAATCGTGAAACAGGGGCT
66 CTATCAGGTGTGTGAAAACAATCCTAAAACTCTATAGAAACTCATTAAATCGTGAAACAGGGGCT
* * * * * *
48916096 ATTTTTTGAAACTGCCCAGTGCCACACGGCTGTGTGTCAGGCCGTATGGTAGATTGTGTGTGTGA
131 ATTTTTCGAAACTGCCTAGTGCCACACGGCCGTGTGTCAGGCCGTGTGGTAGATTGTGTGCGTCA
* *
48916161 CACGTCCGTGTAATTTTATTTTTTTAAATCAAATCCCTGTTATTTTTCTCTTTCGGCAACCATCA
196 CACGACCGTGTAATTTTATTTTTTTAAATCAAATCCCTGTTATTTTTCTCTTTCGGCAACCGTCA
48916226 AACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTTCCAATTTTGTTTTACATTTTTTTCTT
261 AACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTT-CAATTTTGTTTTACATTTTTTTCTT
* *
48916291 TCTTTTCTTCTTTCTTTCCTTCTTATACGCCTTGCCAACGCTGACTCCTTCTTTTGTTATTGTGC
325 TCTTTTCTTCTTTCTTTCCTTCTT-TACACCTTGCCAACGCCGACTCCTTCTTTTGTTATTGTGC
* *
48916356 CAATTGTAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTCTTATTATTCTATTGTTC
389 CAATTGTAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTATTGTTC
* * *
48916421 GCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTTGTTGTGTTGGTAAGTTGTGTGAAAGATAAGTTC
454 GCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTC
* **
48916486 TTAATAAGGTTGGGGTTTTGTTGTTTTAACAAAAAAAATCCGTAGATTAATGATTTTATGATTTA
519 TTTATAAGGTTGGGGTTTTGTTGTTTTAAC-AAAAAAATCCGTAGATTAATGATTTTATGATAGA
* * *
48916551 TATAGTGTTGTGGCTGGTTGTTGTGGATAGGAGAAGAGCGCGTGGTGGTGGACAACCTTCCGACA
583 TATAGTGTTGTGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAACCTTCCGACA
*
48916616 AATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGTGACTG
648 AATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAG-GACTA
**
48916681 TTTCTTTGAGAAAAGAGTAAATTTAAGTGGTAATGTTCGTGTTAAATCGAAGTTG
712 TTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAATGTTCGTGTTAAATCGAAGTTG
* * * *
48916736 TAATTATTGGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTATGACTACGAGGTGGATTAATGTCG
1 TAATCATTGGTTTTGGTGTCGTTTGTAGGATTTTAAGTGTATGACTACGTGGTGGATTAATCTCG
* * * *
48916801 CTATCAGGTGTGTGAAAACGATTCTAAAACCCTATAGAAACTCGTTAAATCGTGAAACAGGGGCT
66 CTATCAGGTGTGTGAAAACAATCCTAAAACTCTATAGAAACTCATTAAATCGTGAAACAGGGGCT
* * * *
48916866 ATTTTTCGAAACTACCTAGTGCCATACAGCCGTATGGT-AGGCCGTGTG
131 ATTTTTCGAAACTGCCTAGTGCCACACGGCCGTGT-GTCAGGCCGTGTG
48916914 CCAGATCGTG
Statistics
Matches: 1524, Mismatches: 177, Indels: 27
0.88 0.10 0.02
Matches are distributed among these distances:
766 20 0.01
767 297 0.19
768 542 0.36
769 272 0.18
770 389 0.26
771 4 0.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (766 bp):
TAATCATTGGTTTTGGTGTCGTTTGTAGGATTTTAAGTGTATGACTACGTGGTGGATTAATCTCG
CTATCAGGTGTGTGAAAACAATCCTAAAACTCTATAGAAACTCATTAAATCGTGAAACAGGGGCT
ATTTTTCGAAACTGCCTAGTGCCACACGGCCGTGTGTCAGGCCGTGTGGTAGATTGTGTGCGTCA
CACGACCGTGTAATTTTATTTTTTTAAATCAAATCCCTGTTATTTTTCTCTTTCGGCAACCGTCA
AACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTTCAATTTTGTTTTACATTTTTTTCTTT
CTTTTCTTCTTTCTTTCCTTCTTTACACCTTGCCAACGCCGACTCCTTCTTTTGTTATTGTGCCA
ATTGTAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTATTGTTCGC
TTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTCTT
TATAAGGTTGGGGTTTTGTTGTTTTAACAAAAAAATCCGTAGATTAATGATTTTATGATAGATAT
AGTGTTGTGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAACCTTCCGACAAAT
TAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGACTATTTC
TTTGAGAAAAGAGCGAATTTAAGTGGTAATGTTCGTGTTAAATCGAAGTTG
Found at i:48924952 original size:43 final size:41
Alignment explanation
Indices: 48924880--48925034 Score: 152
Period size: 43 Copynumber: 3.7 Consensus size: 41
48924870 TGTATTTTCA
* *
48924880 TGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTATACG
1 TGTAAGACCACGTCTGGGACATTGGCATCGA-TTGTG-ATACG
* * * **
48924923 TGTAAGACCATGTCTAGGACATTGACATCGTATT-TGATTTG
1 TGTAAGACCACGTCTGGGACATTGGCATCG-ATTGTGATACG
* *
48924964 TGTAAGACC-CTGTCTGGGACAGTGGCATCGATATGTGATTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGAT-TGTGA-TACG
*
48925007 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
48925035 TGTACGAGCC
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
40 2 0.02
41 29 0.32
42 5 0.06
43 52 0.58
44 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATTGTGATACG
Found at i:48924978 original size:41 final size:42
Alignment explanation
Indices: 48924922--48925026 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 42
48924912 TTGTGTATAC
* *
48924922 GTGTAAGACCATGTCTAGGACATTGACATCG-TATTTGATTT
1 GTGTAAGACCATGTCTAGGACAGTGACATCGATATGTGATTT
* * * *
48924963 GTGTAAGACCCTGTCTGGGACAGTGGCATCGATATGTGATTAC
1 GTGTAAGACCATGTCTAGGACAGTGACATCGATATGTGATT-T
* * *
48925006 ATGTAAGACCACGTCTGGGAC
1 GTGTAAGACCATGTCTAGGAC
48925027 GTTGGCATTG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 27 0.51
42 8 0.15
43 18 0.34
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATGTCTAGGACAGTGACATCGATATGTGATTT
Found at i:48925225 original size:16 final size:17
Alignment explanation
Indices: 48925196--48925227 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
48925186 TGAATTGATG
48925196 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
48925213 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
48925228 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:48928107 original size:16 final size:17
Alignment explanation
Indices: 48928078--48928110 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
48928068 AGCATATTTA
48928078 ATAAAAATAATTTAATC
1 ATAAAAATAATTTAATC
*
48928095 ATAAAAA-ATTTTAATC
1 ATAAAAATAATTTAATC
48928111 TTCCAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAAATAATTTAATC
Found at i:48931754 original size:21 final size:22
Alignment explanation
Indices: 48931730--48931777 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
48931720 AAACTAAGGG
48931730 GAAGTTC-ATCACTGAG-GAGAA
1 GAAGTTCTATCACT-AGTGAGAA
48931751 GAAG-TCTATCACTAGTGAGAA
1 GAAGTTCTATCACTAGTGAGAA
48931772 GAAGTT
1 GAAGTT
48931778 TATTTCCGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.17
21 19 0.79
22 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (22 bp):
GAAGTTCTATCACTAGTGAGAA
Found at i:48933509 original size:26 final size:26
Alignment explanation
Indices: 48933480--48933536 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
48933470 TAAAAAGGGA
48933480 TTTAGTTAATTGAATGGAATTATTAT
1 TTTAGTTAATTGAATGGAATTATTAT
48933506 TTTAGTTAATTGAATGGAATTATTAT
1 TTTAGTTAATTGAATGGAATTATTAT
48933532 TTTAG
1 TTTAG
48933537 ATATGGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (26 bp):
TTTAGTTAATTGAATGGAATTATTAT
Found at i:48942098 original size:26 final size:27
Alignment explanation
Indices: 48942045--48942099 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
48942035 TCAAGGAAAA
* *
48942045 TATTATAAATTGTGGATAAATATGGGC
1 TATTATAAATTGTGGATAAAAATCGGC
48942072 TATTATAAGATTG-GG-TAAAAATCGGC
1 TATTATAA-ATTGTGGATAAAAATCGGC
48942098 TA
1 TA
48942100 GCATGATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.44
27 10 0.40
28 4 0.16
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (27 bp):
TATTATAAATTGTGGATAAAAATCGGC
Found at i:48944923 original size:17 final size:17
Alignment explanation
Indices: 48944901--48944933 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
48944891 CTATTATTTT
48944901 AATTTAATCTAATATTA
1 AATTTAATCTAATATTA
48944918 AATTTAATCTAATATT
1 AATTTAATCTAATATT
48944934 TAATCATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTAATCTAATATTA
Found at i:48948516 original size:30 final size:29
Alignment explanation
Indices: 48948472--48948545 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
48948462 TTGATGAAGC
*
48948472 TTCA-AAAACCAAAAAAATGGAGA-AAGT
1 TTCAGAAAACCAAAAAAATGGAGAGAACT
* *
48948499 TTCAAGAAAACCCAAAAAATGGATAGAACT
1 TTC-AGAAAACCAAAAAAATGGAGAGAACT
48948529 TTCAGAAAACCAAAAAA
1 TTCAGAAAACCAAAAAA
48948546 GAAAAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
27 3 0.08
28 1 0.03
29 30 0.75
30 6 0.15
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (29 bp):
TTCAGAAAACCAAAAAAATGGAGAGAACT
Found at i:48949484 original size:9 final size:9
Alignment explanation
Indices: 48949470--48949500 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
48949460 GTTAAACGAA
48949470 TCGAGTTAT
1 TCGAGTTAT
*
48949479 TCGAGTTAA
1 TCGAGTTAT
48949488 TCGAGTTAT
1 TCGAGTTAT
48949497 TCGA
1 TCGA
48949501 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:48949571 original size:9 final size:9
Alignment explanation
Indices: 48949554--48949590 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
48949544 TAAGTTTTCA
48949554 AATTCGAAT
1 AATTCGAAT
*
48949563 AACTCGAAT
1 AATTCGAAT
48949572 AATTCGAAT
1 AATTCGAAT
48949581 AATTCGAAT
1 AATTCGAAT
48949590 A
1 A
48949591 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:48959824 original size:23 final size:23
Alignment explanation
Indices: 48959795--48959841 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
48959785 ATCTCTAACC
48959795 AAATATTGAAACCTCTAACATAT
1 AAATATTGAAACCTCTAACATAT
*
48959818 AAATATTGAAATCTCTAACATAT
1 AAATATTGAAACCTCTAACATAT
48959841 A
1 A
48959842 CCCAAATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (23 bp):
AAATATTGAAACCTCTAACATAT
Found at i:48966197 original size:89 final size:89
Alignment explanation
Indices: 48966034--48966278 Score: 325
Period size: 89 Copynumber: 2.7 Consensus size: 89
48966024 ATTCAATTTT
* * ** * *
48966034 TTTGTATTATTTTTGTATATGTAAATCAAATTTAGTCAGTATTATTTGTTGTTCGAATTTTATAT
1 TTTGTATT-TTCTTGTATCTGTAAATTTAATTTAGTCTGTATTATTTATTGTTCGAATTTTATAT
* * *
48966099 TTTCGTGTATTAATTTTTTAGAATG
65 TTTCATGTATTAATATTCTAGAATG
48966124 TTTGTATTTTCTTGTATCTGTAAATTTAATTTAGTCTGTATTATTTATTGTTCGAATTTTATATT
1 TTTGTATTTTCTTGTATCTGTAAATTTAATTTAGTCTGTATTATTTATTGTTCGAATTTTATATT
48966189 TTCATGTATTAATATTCTAGAATG
66 TTCATGTATTAATATTCTAGAATG
* * *
48966213 TTTGTATTTTCTTGTATCTATAAATTTAATTT-GT-TGCGTATTA-TTATTTTTTCGAATTATAT
1 TTTGTATTTTCTTGTATCTGTAAATTTAATTTAGTCT--GTATTATTTA-TTGTTCGAATTTTAT
48966275 ATTT
63 ATTT
48966279 GTTCTATTAA
Statistics
Matches: 140, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
87 1 0.01
88 5 0.04
89 126 0.90
90 8 0.06
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (89 bp):
TTTGTATTTTCTTGTATCTGTAAATTTAATTTAGTCTGTATTATTTATTGTTCGAATTTTATATT
TTCATGTATTAATATTCTAGAATG
Found at i:48966287 original size:16 final size:17
Alignment explanation
Indices: 48966241--48966294 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
48966231 TATAAATTTA
48966241 ATTTGTTGCGTATTAT-T
1 ATTTGTT-CGTATTATAT
* *
48966258 ATTTTTTCGAATTATAT
1 ATTTGTTCGTATTATAT
*
48966275 ATTTGTTC-TATTAAAT
1 ATTTGTTCGTATTATAT
48966291 ATTT
1 ATTT
48966295 TGAAGTCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (17 bp):
ATTTGTTCGTATTATAT
Found at i:48966339 original size:22 final size:20
Alignment explanation
Indices: 48966314--48966363 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
48966304 TTATCCAAAC
*
48966314 AAATAATTATTTTAGAAAAATT
1 AAATAATTATATT-GAAAAA-T
48966336 AAAT--TTATATTGAAAAAT
1 AAATAATTATATTGAAAAAT
48966354 AGAATAATTA
1 A-AATAATTA
48966364 CAAACTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
18 2 0.08
19 9 0.38
20 6 0.25
21 3 0.12
22 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (20 bp):
AAATAATTATATTGAAAAAT
Found at i:48968941 original size:19 final size:20
Alignment explanation
Indices: 48968902--48968954 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
48968892 CAACAGAACC
*
48968902 GAACAAAACAGAATGAAGCA
1 GAACAAAACAGAATCAAGCA
*
48968922 GAACATAACA-AATCAAGCA
1 GAACAAAACAGAATCAAGCA
* *
48968941 GAGCAGAACAGAAT
1 GAACAAAACAGAAT
48968955 AGAGCATAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.57, C:0.17, G:0.19, T:0.08
Consensus pattern (20 bp):
GAACAAAACAGAATCAAGCA
Found at i:48969587 original size:79 final size:78
Alignment explanation
Indices: 48969437--48969595 Score: 210
Period size: 79 Copynumber: 2.0 Consensus size: 78
48969427 TCACATGCAT
* * ***
48969437 GGTTATAAATCAGAATCAATAACAATCAGTCTAACATATTTAGATATCGTGTATTCCTCATCAAC
1 GGTTATAAATCAGAATCAATAACAATCAATCTAACATAATTAGATATCACATATTCCTCATCAAC
*
48969502 AAAGTAATGCAGAA
66 AAAGTAACGCA-AA
* * * *
48969516 GGTTATAAATCAGAATCAGTAACAATCAATCTAACATAATTAGATGTCACATATTCTTCATCAAT
1 GGTTATAAATCAGAATCAATAACAATCAATCTAACATAATTAGATATCACATATTCCTCATCAAC
*
48969581 AGAGTAACGCAAA
66 AAAGTAACGCAAA
48969594 GG
1 GG
48969596 CGTATCAACA
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
78 4 0.06
79 65 0.94
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (78 bp):
GGTTATAAATCAGAATCAATAACAATCAATCTAACATAATTAGATATCACATATTCCTCATCAAC
AAAGTAACGCAAA
Found at i:48973212 original size:6 final size:6
Alignment explanation
Indices: 48973203--48973280 Score: 83
Period size: 6 Copynumber: 13.5 Consensus size: 6
48973193 TTTTTATTTT
* *
48973203 ATTTGA ATTTC- ATTTCA ATTTCA ATTTGA ATTTC- ATTTCA ATTTCA
1 ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA
* *
48973249 ATTTGA ATTTCA A-TTCA A-TGCA ACTTTCA ATT
1 ATTTCA ATTTCA ATTTCA ATTTCA A-TTTCA ATT
48973281 AAACTTTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
5 19 0.31
6 38 0.62
7 4 0.07
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (6 bp):
ATTTCA
Found at i:48973280 original size:23 final size:23
Alignment explanation
Indices: 48973203--48973267 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
48973193 TTTTTATTTT
48973203 ATTTGAATTTCATTTCAATTTCA
1 ATTTGAATTTCATTTCAATTTCA
48973226 ATTTGAATTTCATTTCAATTTCA
1 ATTTGAATTTCATTTCAATTTCA
*
48973249 ATTTGAATTTCAATTCAAT
1 ATTTGAATTTCATTTCAAT
48973268 GCAACTTTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (23 bp):
ATTTGAATTTCATTTCAATTTCA
Found at i:48975376 original size:23 final size:23
Alignment explanation
Indices: 48975342--48975405 Score: 94
Period size: 22 Copynumber: 2.8 Consensus size: 23
48975332 CGGCCCAGCC
*
48975342 TATTTTTAATTAAAATTAAAATTA
1 TATTTTT-ATTAAAATTAAAACTA
48975366 TATTTTTATTAAAATTAAAACTA
1 TATTTTTATTAAAATTAAAACTA
*
48975389 -ATTGTTATTAAAATTAA
1 TATTTTTATTAAAATTAA
48975406 TTGTTATCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.42
23 15 0.39
24 7 0.18
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TATTTTTATTAAAATTAAAACTA
Found at i:48975400 original size:16 final size:16
Alignment explanation
Indices: 48975379--48975435 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
48975369 TTTTATTAAA
*
48975379 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
48975395 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
48975411 ATCAAAATTAATTGTT
1 ATTAAAATTAATTGTT
48975427 ATTAAAATT
1 ATTAAAATT
48975436 GTATCTAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:48975492 original size:19 final size:18
Alignment explanation
Indices: 48975468--48975638 Score: 61
Period size: 18 Copynumber: 9.3 Consensus size: 18
48975458 ATCTAACATT
48975468 TTGTTAGTAAAATTATTAA
1 TTGTTA-TAAAATTATTAA
**
48975487 TTG-T-TAATTTTATTAA
1 TTGTTATAAAATTATTAA
*
48975503 TTGTTACTAAAATTATCAAA
1 TTGTTA-TAAAATTAT-TAA
* *
48975523 TT-ATATCAAATTATTAA
1 TTGTTATAAAATTATTAA
* *** *
48975540 TTATTA-ATTGTTACTAACA
1 TTGTTATAAAATTA-TTA-A
48975559 TTTTGTTAGTAAAATTATTAA
1 --TTGTTA-TAAAATTATTAA
*
48975580 TTG-T-T-AATTGTATTAA
1 TTGTTATAAAAT-TATTAA
*
48975596 TTGTTAGTAAAATTATCAAA
1 TTGTTA-TAAAATTAT-TAA
* *
48975616 TT-ATATCAAATTATTAA
1 TTGTTATAAAATTATTAA
48975633 TTGTTA
1 TTGTTA
48975639 ATTGTATTAA
Statistics
Matches: 108, Mismatches: 26, Indels: 37
0.63 0.15 0.22
Matches are distributed among these distances:
15 3 0.03
16 23 0.21
17 13 0.12
18 24 0.22
19 22 0.20
20 11 0.10
21 6 0.06
22 2 0.02
23 4 0.04
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (18 bp):
TTGTTATAAAATTATTAA
Found at i:48975579 original size:93 final size:93
Alignment explanation
Indices: 48975460--48975643 Score: 341
Period size: 93 Copynumber: 2.0 Consensus size: 93
48975450 TTTGTAAAAT
*
48975460 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTTTATTAATTGTTACTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATT
48975525 ATATCAAATTATTAATTATTAATTGTTA
66 ATATCAAATTATTAATTATTAATTGTTA
*
48975553 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATT
*
48975618 ATATCAAATTATTAATTGTTAATTGT
66 ATATCAAATTATTAATTATTAATTGT
48975644 ATTAATTGTT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (93 bp):
CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATT
ATATCAAATTATTAATTATTAATTGTTA
Found at i:48978789 original size:16 final size:16
Alignment explanation
Indices: 48978768--48978798 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
48978758 TTTCATTTGA
48978768 TGTATGTATGTGTGTC
1 TGTATGTATGTGTGTC
48978784 TGTATGTATGTGTGT
1 TGTATGTATGTGTGT
48978799 ATGTGGAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.03, G:0.32, T:0.52
Consensus pattern (16 bp):
TGTATGTATGTGTGTC
Found at i:48983749 original size:43 final size:42
Alignment explanation
Indices: 48983702--48983829 Score: 104
Period size: 37 Copynumber: 3.1 Consensus size: 42
48983692 TGAAATAGCG
* *
48983702 AAAAAGTCATTACATAAATAAAAAGTTGACAATTTAAATTGT
1 AAAAAATCATTACATAAATAAAAAGTTGACAATTTAAATTGC
* * * * * * * *
48983744 AAAAAATTA-AAC-T-CAT-AAAA-TTAATAAATAAAATGGC
1 AAAAAATCATTACATAAATAAAAAGTTGACAATTTAAATTGC
* *
48983781 AAAAAATTCATTACATAAATACAAAGTTGACTATTTAAATTGC
1 AAAAAA-TCATTACATAAATAAAAAGTTGACAATTTAAATTGC
48983824 AAAAAA
1 AAAAAA
48983830 AAAACCCCAT
Statistics
Matches: 60, Mismatches: 20, Indels: 11
0.66 0.22 0.12
Matches are distributed among these distances:
37 17 0.28
38 6 0.10
39 4 0.07
40 2 0.03
41 4 0.07
42 10 0.17
43 17 0.28
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (42 bp):
AAAAAATCATTACATAAATAAAAAGTTGACAATTTAAATTGC
Found at i:48983792 original size:80 final size:79
Alignment explanation
Indices: 48983669--48983888 Score: 271
Period size: 80 Copynumber: 2.8 Consensus size: 79
48983659 TTTAAATTGC
* * * * * *
48983669 AAAAAACTCCTAAAATTAATAATTGAAATAGCGAAAAAGTCATTACATAAATAAAAAGTTGACAA
1 AAAAAACTCATAAAATTAATAAATAAAATGGCAAAAAATTCATTACATAAATAAAAAGTTGACAA
*
48983734 TTTAAATTGTAAAA
66 TTTAAATTGCAAAA
* * *
48983748 AATTAAACTCATAAAATTAATAAATAAAATGGCAAAAAATTCATTACATAAATACAAAGTTGACT
1 AA-AAAACTCATAAAATTAATAAATAAAATGGCAAAAAATTCATTACATAAATAAAAAGTTGACA
48983813 ATTTAAATTGCAAAA
65 ATTTAAATTGCAAAA
* * * * *
48983828 AAAAAACCCCATAAAATTAATAACTAAAATGGAAAAAAAGTT-ATTATATAAATATAAAGTT
1 AAAAAA-CTCATAAAATTAATAAATAAAATGGCAAAAAA-TTCATTACATAAATAAAAAGTT
48983889 ATTTAAATTA
Statistics
Matches: 122, Mismatches: 16, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
79 5 0.04
80 115 0.94
81 2 0.02
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.27
Consensus pattern (79 bp):
AAAAAACTCATAAAATTAATAAATAAAATGGCAAAAAATTCATTACATAAATAAAAAGTTGACAA
TTTAAATTGCAAAA
Found at i:48984163 original size:33 final size:33
Alignment explanation
Indices: 48984121--48984192 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
48984111 GGGAGGAGTA
* *
48984121 GATACGGGTC-GAGAGGAGTGGAGTACGGCGGTG
1 GATACGGGTCGGA-AGGAGCGGAGTACGGAGGTG
*
48984154 GATACGGGTCGGAAGGAGCGGAGTACTGAGGTG
1 GATACGGGTCGGAAGGAGCGGAGTACGGAGGTG
48984187 GATACG
1 GATACG
48984193 AGCCGGGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 33 0.94
34 2 0.06
ACGTcount: A:0.24, C:0.12, G:0.49, T:0.15
Consensus pattern (33 bp):
GATACGGGTCGGAAGGAGCGGAGTACGGAGGTG
Found at i:48986821 original size:25 final size:26
Alignment explanation
Indices: 48986793--48986842 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
48986783 TAACTTAGGT
*
48986793 TAAATAT-TTTTTATAATACATAAAA
1 TAAATATAATTTTATAATACATAAAA
*
48986818 TAAATATAAATTTTATAATATATAA
1 TAAATAT-AATTTTATAATACATAA
48986843 CTTTTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
27 14 0.67
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAATATAATTTTATAATACATAAAA
Found at i:48986837 original size:18 final size:18
Alignment explanation
Indices: 48986816--48986869 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 18
48986806 TAATACATAA
48986816 AATAAATATAAATTTTAT
1 AATAAATATAAATTTTAT
*
48986834 AAT--ATATAACTTTTAT
1 AATAAATATAAATTTTAT
48986850 AAATAAA-A-AAAGTTTTAT
1 -AATAAATATAAA-TTTTAT
48986868 AA
1 AA
48986870 ATTGTCCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 12 0.40
17 7 0.23
18 10 0.33
19 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
AATAAATATAAATTTTAT
Found at i:48986839 original size:14 final size:15
Alignment explanation
Indices: 48986820--48986856 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
48986810 ACATAAAATA
48986820 AATATAAA-TTTTAT
1 AATATAAACTTTTAT
48986834 AATATATAACTTTTAT
1 AATATA-AACTTTTAT
48986850 AA-ATAAA
1 AATATAAA
48986857 AAAAGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.38
15 5 0.24
16 8 0.38
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATAAACTTTTAT
Found at i:48986842 original size:16 final size:15
Alignment explanation
Indices: 48986817--48986854 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
48986807 AATACATAAA
48986817 ATAAATATAAATTTT
1 ATAAATATAAATTTT
*
48986832 ATAATATATAACTTTT
1 ATAA-ATATAAATTTT
48986848 ATAAATA
1 ATAAATA
48986855 AAAAAAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAATATAAATTTT
Found at i:48995526 original size:11 final size:11
Alignment explanation
Indices: 48995510--48995561 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
48995500 TCAATTATTT
48995510 TCTCAAATTCC
1 TCTCAAATTCC
* *
48995521 TCTCAATTTGC
1 TCTCAAATTCC
*
48995532 TCTCAATTTCC
1 TCTCAAATTCC
*
48995543 T-TCCAAATTTC
1 TCT-CAAATTCC
48995554 TCTCAAAT
1 TCTCAAAT
48995562 CCATATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 1 0.03
11 32 0.94
12 1 0.03
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.42
Consensus pattern (11 bp):
TCTCAAATTCC
Found at i:48995542 original size:22 final size:22
Alignment explanation
Indices: 48995506--48995561 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
48995496 TCTCTCAATT
48995506 ATTT-TCTCAAATTCC-TCTC-A
1 ATTTCTCTCAAATTCCTTC-CAA
*
48995526 ATTTGCTCTCAATTTCCTTCCAA
1 ATTT-CTCTCAAATTCCTTCCAA
48995549 ATTTCTCTCAAAT
1 ATTTCTCTCAAAT
48995562 CCATATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 4 0.13
22 19 0.63
23 7 0.23
ACGTcount: A:0.25, C:0.29, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTCTCTCAAATTCCTTCCAA
Found at i:48995579 original size:40 final size:40
Alignment explanation
Indices: 48995532--48995609 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
48995522 CTCAATTTGC
48995532 TCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* * * *
48995572 TCTCAATTTGCTCTCAATTTTCTCTTAAATCCCTATTT
1 TCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
48995610 TTTATTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.26, C:0.27, G:0.01, T:0.46
Consensus pattern (40 bp):
TCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:48996556 original size:21 final size:20
Alignment explanation
Indices: 48996517--48996554 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48996507 TAACGAGGTA
48996517 AATTTTATATTAGATTTTAC
1 AATTTTATATTAGATTTTAC
48996537 AATTATTATA-TAGATTTT
1 AATT-TTATATTAGATTTT
48996555 TAAAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTTTATATTAGATTTTAC
Found at i:48996735 original size:7 final size:7
Alignment explanation
Indices: 48996723--48996748 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
48996713 TAGTCGATTG
48996723 GTATTTA
1 GTATTTA
48996730 GTATTTA
1 GTATTTA
48996737 GTATTTA
1 GTATTTA
48996744 GTATT
1 GTATT
48996749 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:48997431 original size:18 final size:18
Alignment explanation
Indices: 48997395--48997437 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
48997385 TGCTAGGTGC
* * *
48997395 GTATCCTAGCTCTTTTAT
1 GTATCCTAACCCTTATAT
48997413 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
48997431 GTTTCCT
1 GTATCCT
48997438 TTTTCGAGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:48998193 original size:171 final size:169
Alignment explanation
Indices: 48997988--48998518 Score: 708
Period size: 171 Copynumber: 3.1 Consensus size: 169
48997978 AAACCCTAAC
* * *
48997988 AAAAATCCTAACCCTTAACTTAAAAACACTAACCCTTAACTTAAAAATCCTAACCCTTAACATAG
1 AAAAACCCTAACACTTAACTTAAAAACACTAACCCTTAACTTAAAAACCCTAACCCTTAACATA-
48998053 AAAACTCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACACTAACCCTTAACTTAA
65 AAAACTCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACACTAACCCTTAACTTAA
* *
48998118 AAACCCTAAAGCTTAACTTAAAAACCCTAACCCTTAA-TCT
130 AAACCCTAAACCTTAACTTAAAAACCATAACCCTTAACT-T
* ** *
48998158 AAAAACCGTAAACACTTAACTTAAAAATTCTAACCCTTAACCTAAAAACCCTAACCCTTAACATA
1 AAAAACCCT-AACACTTAACTTAAAAACACTAACCCTTAACTTAAAAACCCTAACCCTTAACATA
* * * * * *
48998223 AAAAATCCTAAACCTTTAACTTAAAAACCCTAACCCTTAACCTAAAAGCCCTAACCTTTAACTTA
65 AAAACT-CTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACACTAACCCTTAACTTA
*
48998288 AAAACCCTAAACCGTTAACTTAAAAACCGTAACCCTTAACTT
129 AAAACCCTAAACC-TTAACTTAAAAACCATAACCCTTAACTT
* * * * *
48998330 AAAAACCCTAACCCTTAACATAAAAAACCCTAAACCATTAACTTAAAAACCCTAACCCTTAACCT
1 AAAAACCCTAACACTTAAC-TTAAAAACACT-AACCCTTAACTTAAAAACCCTAACCCTTAACAT
* *
48998395 AAAAACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACATTAACCCTTAACTTA
64 AAAAACTCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACACTAACCCTTAACTTA
* * * *
48998459 AAAACCCTAACCCATAACCTAAAAACCATAACCCTTCACTT
129 AAAACCCTAAACCTTAACTTAAAAACCATAACCCTTAACTT
* *
48998500 AAGAACTCC-AACCCTTAAC
1 AAAAAC-CCTAACACTTAAC
48998519 GTAAGAGCCC
Statistics
Matches: 317, Mismatches: 37, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
170 51 0.16
171 187 0.59
172 43 0.14
173 36 0.11
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.23
Consensus pattern (169 bp):
AAAAACCCTAACACTTAACTTAAAAACACTAACCCTTAACTTAAAAACCCTAACCCTTAACATAA
AAACTCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACACTAACCCTTAACTTAAA
AACCCTAAACCTTAACTTAAAAACCATAACCCTTAACTT
Found at i:48998524 original size:21 final size:21
Alignment explanation
Indices: 48997988--48998518 Score: 679
Period size: 21 Copynumber: 24.9 Consensus size: 21
48997978 AAACCCTAAC
*
48997988 AAAAATCCTAACCCTTAACTT
1 AAAAACCCTAACCCTTAACTT
*
48998009 AAAAACACTAACCCTTAACTT
1 AAAAACCCTAACCCTTAACTT
* *
48998030 AAAAATCCTAACCCTTAACAT
1 AAAAACCCTAACCCTTAACTT
*
48998051 AGAAAACTCTAAACCCTTAACTT
1 A-AAAACCCT-AACCCTTAACTT
48998074 AAAAACCCTAACCCTTAACTT
1 AAAAACCCTAACCCTTAACTT
*
48998095 AAAAACACTAACCCTTAACTT
1 AAAAACCCTAACCCTTAACTT
**
48998116 AAAAACCCTAAAGCTTAACTT
1 AAAAACCCTAACCCTTAACTT
48998137 AAAAACCCTAACCCTTAA-TCT
1 AAAAACCCTAACCCTTAACT-T
* *
48998158 AAAAACCGTAAACACTTAACTT
1 AAAAACCCT-AACCCTTAACTT
** *
48998180 AAAAATTCTAACCCTTAACCT
1 AAAAACCCTAACCCTTAACTT
*
48998201 AAAAACCCTAACCCTTAACATA
1 AAAAACCCTAACCCTTAAC-TT
* *
48998223 AAAAATCCTAAACCTTTAACTT
1 AAAAACCCT-AACCCTTAACTT
*
48998245 AAAAACCCTAACCCTTAACCT
1 AAAAACCCTAACCCTTAACTT
* *
48998266 AAAAGCCCTAACCTTTAACTT
1 AAAAACCCTAACCCTTAACTT
*
48998287 AAAAACCCTAAACCGTTAACTT
1 AAAAACCCT-AACCCTTAACTT
*
48998309 AAAAACCGTAACCCTTAACTT
1 AAAAACCCTAACCCTTAACTT
*
48998330 AAAAACCCTAACCCTTAACATA
1 AAAAACCCTAACCCTTAAC-TT
*
48998352 AAAAACCCTAAACCATTAACTT
1 AAAAACCCT-AACCCTTAACTT
*
48998374 AAAAACCCTAACCCTTAACCT
1 AAAAACCCTAACCCTTAACTT
48998395 AAAAACCCTAACCCTTAACTT
1 AAAAACCCTAACCCTTAACTT
48998416 AAAAACCCTAACCCTTAACTT
1 AAAAACCCTAACCCTTAACTT
**
48998437 AAAAACATTAACCCTTAACTT
1 AAAAACCCTAACCCTTAACTT
* *
48998458 AAAAACCCTAACCCATAACCT
1 AAAAACCCTAACCCTTAACTT
* *
48998479 AAAAACCATAACCCTTCACTT
1 AAAAACCCTAACCCTTAACTT
*
48998500 AAGAACTCC-AACCCTTAAC
1 AAAAAC-CCTAACCCTTAAC
48998519 GTAAGAGCCC
Statistics
Matches: 440, Mismatches: 59, Indels: 22
0.84 0.11 0.04
Matches are distributed among these distances:
20 1 0.00
21 323 0.73
22 85 0.19
23 31 0.07
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.23
Consensus pattern (21 bp):
AAAAACCCTAACCCTTAACTT
Found at i:48998600 original size:22 final size:21
Alignment explanation
Indices: 48998575--48998615 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
48998565 AACGGTAGGG
*
48998575 CCTTAATATAAAAAGCCCTAAC
1 CCTTAACATAAAAA-CCCTAAC
*
48998597 CCTTAACCTAAAAACCCTA
1 CCTTAACATAAAAACCCTA
48998616 GCCGTGATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (21 bp):
CCTTAACATAAAAACCCTAAC
Found at i:48999475 original size:21 final size:21
Alignment explanation
Indices: 48999438--48999697 Score: 337
Period size: 21 Copynumber: 12.3 Consensus size: 21
48999428 NNNNNNNCTA
48999438 AACCCTTAA-TT-AAAACCCT
1 AACCCTTAACTTAAAAACCCT
*
48999457 AACCCTTAACCTAAAAACCCT
1 AACCCTTAACTTAAAAACCCT
*
48999478 AACCCTTAACTTAAAAACCTT
1 AACCCTTAACTTAAAAACCCT
* * * *
48999499 AAATCCTTAACCTAAAACCCCA
1 -AACCCTTAACTTAAAAACCCT
*
48999521 AACCCTTAACTTGAAAACCCT
1 AACCCTTAACTTAAAAACCCT
*
48999542 AACCCTTAACATAAAAAACCCT
1 AACCCTTAAC-TTAAAAACCCT
48999564 AAACCCTTAACTTAAAAACCCT
1 -AACCCTTAACTTAAAAACCCT
*
48999586 AACCCTTAACTT-AAAACTCTT
1 AACCCTTAACTTAAAAAC-CCT
*
48999607 AACCCTTAACCTAAAAACCCT
1 AACCCTTAACTTAAAAACCCT
*
48999628 AACCCTTAACTTAAAAACCTT
1 AACCCTTAACTTAAAAACCCT
* *
48999649 AAATCCTTAACTTAAAAACACT
1 -AACCCTTAACTTAAAAACCCT
48999671 AACCCTTAACTTAAAAACCCT
1 AACCCTTAACTTAAAAACCCT
48999692 AACCCT
1 AACCCT
48999698 AAACCTAGCC
Statistics
Matches: 207, Mismatches: 26, Indels: 14
0.84 0.11 0.06
Matches are distributed among these distances:
19 9 0.04
20 6 0.03
21 124 0.60
22 58 0.28
23 10 0.05
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
AACCCTTAACTTAAAAACCCT
Found at i:48999540 original size:64 final size:64
Alignment explanation
Indices: 48999435--48999697 Score: 329
Period size: 64 Copynumber: 4.1 Consensus size: 64
48999425 NNNNNNNNNN
* *
48999435 CTAAACCCTTAA-TTAAAA-CCCTAACCCTTAACCTAAAAACCCTAACCCTTAACTTAAAAACC
1 CTAAACCCTTAACTTAAAACCCCAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACC
* * * * *
48999497 TTAAATCCTTAACCTAAAACCCCAAACCCTTAACTTGAAAACCCTAACCCTTAACATAAAAAACC
1 CTAAACCCTTAACTTAAAACCCCAAACCCTTAACTTAAAAACCCTAACCCTTAAC-TTAAAAACC
* * * *
48999562 CTAAACCCTTAACTTAAAAACCCTAACCCTTAACTT-AAAACTCTTAACCCTTAACCTAAAAACC
1 CTAAACCCTTAACTTAAAACCCCAAACCCTTAACTTAAAAAC-CCTAACCCTTAACTTAAAAACC
** * *
48999626 CT-AACCCTTAACTTAAAAACCTTAAATCCTTAACTTAAAAACACTAACCCTTAACTTAAAAACC
1 CTAAACCCTTAACTT-AAAACCCCAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACC
48999690 CT-AACCCT
1 CTAAACCCT
48999698 AAACCTAGCC
Statistics
Matches: 172, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
62 10 0.06
63 17 0.10
64 89 0.52
65 56 0.33
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.24
Consensus pattern (64 bp):
CTAAACCCTTAACTTAAAACCCCAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACC
Found at i:49003244 original size:24 final size:24
Alignment explanation
Indices: 49003212--49003261 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
49003202 TCACAAAAAA
* *
49003212 AAATATTATTAATTAATTAAATTAT
1 AAATATTATAAAATAATTAAA-TAT
*
49003237 AAAT-TTATAAAATCATTAAATAT
1 AAATATTATAAAATAATTAAATAT
49003260 AA
1 AA
49003262 TTAGATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 5 0.23
24 13 0.59
25 4 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATTATAAAATAATTAAATAT
Found at i:49004219 original size:21 final size:22
Alignment explanation
Indices: 49004195--49004242 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
49004185 TTAATTTTCA
*
49004195 AAATTA-ATGAACTTTTATTAT
1 AAATTAGATCAACTTTTATTAT
*
49004216 AAATTAGATCAATTTTTATT-T
1 AAATTAGATCAACTTTTATTAT
49004237 -AATTAG
1 AAATTAG
49004243 TGAATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 7 0.29
22 11 0.46
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (22 bp):
AAATTAGATCAACTTTTATTAT
Found at i:49004271 original size:21 final size:23
Alignment explanation
Indices: 49004245--49004290 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
49004235 TTAATTAGTG
*
49004245 AATATA-TATTTTA-AAATTAAA
1 AATATATTATTTAATAAATTAAA
49004266 AATATATTATTTAATAAATTAAA
1 AATATATTATTTAATAAATTAAA
49004289 AA
1 AA
49004291 ATACATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 6 0.27
23 10 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATATTATTTAATAAATTAAA
Found at i:49005338 original size:8 final size:8
Alignment explanation
Indices: 49005325--49005349 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
49005315 TCTGCTTTCA
49005325 TATTTAAT
1 TATTTAAT
49005333 TATTTAAT
1 TATTTAAT
49005341 TATTTAAT
1 TATTTAAT
49005349 T
1 T
49005350 TTCACAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTTAAT
Found at i:49007004 original size:18 final size:17
Alignment explanation
Indices: 49006973--49007007 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
49006963 GATTTAGGGT
49006973 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
49006990 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
49007008 AAATCTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:49013260 original size:43 final size:43
Alignment explanation
Indices: 49013200--49013345 Score: 229
Period size: 43 Copynumber: 3.4 Consensus size: 43
49013190 GCTTTGACCA
* * *
49013200 CATGACCTTTAGCGGCGCTTTTCCCACAAACGTCGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTATCCGACAAACGCCGCTAAAGAC
*
49013243 CATGACCTTTAGTGGCGCTTATCCGACAAACGCCGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTATCCGACAAACGCCGCTAAAGAC
*
49013286 CATGACCTTTAGCGGCGCTTATCCGACAAATGCCGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTATCCGACAAACGCCGCTAAAGAC
* *
49013329 AATGACCTTTAGTGGCG
1 CATGACCTTTAGCGGCG
49013346 TTTTTTTTTA
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 95 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (43 bp):
CATGACCTTTAGCGGCGCTTATCCGACAAACGCCGCTAAAGAC
Found at i:49013734 original size:21 final size:21
Alignment explanation
Indices: 49013689--49013737 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
49013679 TCTACGCTAC
*
49013689 TCTGCTTCCCTCGCTGCAGCC
1 TCTGCTTCCCTCGCTGCAGCA
* * *
49013710 TCTGCTTCTCTCGCTGCCGTA
1 TCTGCTTCCCTCGCTGCAGCA
49013731 TCTGCTT
1 TCTGCTT
49013738 TAAGCTGCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.04, C:0.41, G:0.18, T:0.37
Consensus pattern (21 bp):
TCTGCTTCCCTCGCTGCAGCA
Found at i:49013790 original size:66 final size:66
Alignment explanation
Indices: 49013708--49013854 Score: 188
Period size: 66 Copynumber: 2.2 Consensus size: 66
49013698 CTCGCTGCAG
* * * * *
49013708 CCTCTGCTTCTCTCGCTGCCGTATCTGCTTTAAGCTGCAGCTGGTGTTCTTCATA-CTTTCATTG
1 CCTCAGCTTCTCTCGCTACCGCATCTGCTTTAAGCTGCAGCTAGAGTTCTTCATATCTTT-ATTG
49013772 AA
65 AA
** * * *
49013774 CCTCAGCTTCTCTCGCTATTGCATCTGCTTTAAGTTGTAGCTAGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTACCGCATCTGCTTTAAGCTGCAGCTAGAGTTCTTCATATCTTTATTGA
49013839 A
66 A
49013840 CCTCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
49013855 ATGCTACCTC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
66 66 0.94
67 4 0.06
ACGTcount: A:0.15, C:0.28, G:0.16, T:0.41
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTACCGCATCTGCTTTAAGCTGCAGCTAGAGTTCTTCATATCTTTATTGA
A
Found at i:49013871 original size:66 final size:66
Alignment explanation
Indices: 49013735--49013877 Score: 162
Period size: 66 Copynumber: 2.2 Consensus size: 66
49013725 GCCGTATCTG
* * * * * * * *
49013735 CTTTAAGCTGCAGCTGGTGTTCTTCATACTTTCATTGAACCTCAGCTTCTCTCGCTATTGCATCT
1 CTTTAAGTTGTAGCTAGAGTTCTTCATACTTTCATTGAACCTCAGCTTCTCTCGATACTACATCC
*
49013800 G
66 A
* * *
49013801 CTTTAAGTTGTAGCTAGAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGCTACCTC
1 CTTTAAGTTGTAGCTAGAGTTCTTCATA-CTTTCATTGAACCTCAGCTTCTCTCGATACTACATC
49013865 CA
65 CA
49013867 CTTTAAGTTGT
1 CTTTAAGTTGT
49013878 GTAATTTGCT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
66 60 0.94
67 4 0.06
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.41
Consensus pattern (66 bp):
CTTTAAGTTGTAGCTAGAGTTCTTCATACTTTCATTGAACCTCAGCTTCTCTCGATACTACATCC
A
Found at i:49014209 original size:38 final size:38
Alignment explanation
Indices: 49014154--49014236 Score: 157
Period size: 38 Copynumber: 2.2 Consensus size: 38
49014144 TAGTTTTTCC
49014154 TAAAAAATAAATAACATAGTTAGGAACGCAATATATAT
1 TAAAAAATAAATAACATAGTTAGGAACGCAATATATAT
*
49014192 TAAAAAATAAATCACATAGTTAGGAACGCAATATATAT
1 TAAAAAATAAATAACATAGTTAGGAACGCAATATATAT
49014230 TAAAAAA
1 TAAAAAA
49014237 ACAAATGCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.57, C:0.08, G:0.10, T:0.25
Consensus pattern (38 bp):
TAAAAAATAAATAACATAGTTAGGAACGCAATATATAT
Found at i:49017457 original size:15 final size:15
Alignment explanation
Indices: 49017422--49017464 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
49017412 CAAGTTTTGG
*
49017422 AAAAATATATAAATT
1 AAAAATATATATATT
**
49017437 TTAAATATATATATT
1 AAAAATATATATATT
*
49017452 AAAAATGTATATA
1 AAAAATATATATA
49017465 AATATTAATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAAAATATATATATT
Found at i:49017663 original size:21 final size:25
Alignment explanation
Indices: 49017625--49017673 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
49017615 TCCATACCAT
49017625 ATATATGGGGTGATATA-TTA-AAA
1 ATATATGGGGTGATATATTTAGAAA
*
49017648 ATATA-GGGGTTA-ATATTTAGAAA
1 ATATATGGGGTGATATATTTAGAAA
49017671 ATA
1 ATA
49017674 ACATTTACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 3 0.13
22 9 0.39
23 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (25 bp):
ATATATGGGGTGATATATTTAGAAA
Found at i:49017729 original size:69 final size:69
Alignment explanation
Indices: 49017640--49017803 Score: 238
Period size: 69 Copynumber: 2.4 Consensus size: 69
49017630 TGGGGTGATA
* ** * * *
49017640 TATTAAAAATATAGGGGTTAATATTTAGAAAATAACATTTACAATTATTTTTCAAATTGTAAAAT
1 TATTCAAAATATAGATGTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAAT
49017705 TTAT
66 TTAT
* * *
49017709 TATTCCAAATATAGATGTTAATCTTTAGAAAATAACATTTAGAATTATTTCTAAAATTATAAAAT
1 TATTCAAAATATAGATGTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAAT
49017774 TTAT
66 TTAT
*
49017778 TATTGAAAATATAGATGTTAATATTT
1 TATTCAAAATATAGATGTTAATATTT
49017804 TCTCACAATT
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 83 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (69 bp):
TATTCAAAATATAGATGTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAAT
TTAT
Found at i:49018417 original size:26 final size:26
Alignment explanation
Indices: 49018387--49018444 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
49018377 ATAGATTTAT
*
49018387 ATTATTTTATAAGCTATAGAGTAAGA
1 ATTATTTGATAAGCTATAGAGTAAGA
49018413 ATTATTTGATAAGCTATAGAGTAAGA
1 ATTATTTGATAAGCTATAGAGTAAGA
49018439 ATTATT
1 ATTATT
49018445 ATGCAACGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.40
Consensus pattern (26 bp):
ATTATTTGATAAGCTATAGAGTAAGA
Found at i:49018834 original size:12 final size:12
Alignment explanation
Indices: 49018817--49018841 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49018807 CAGGATAGTG
49018817 AAAATTATGAAC
1 AAAATTATGAAC
49018829 AAAATTATGAAC
1 AAAATTATGAAC
49018841 A
1 A
49018842 GTTTCAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAATTATGAAC
Found at i:49019276 original size:24 final size:24
Alignment explanation
Indices: 49019244--49019289 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
49019234 TTCTAGATTT
49019244 GGGGGATTTTTGGGGA-AAAATTG
1 GGGGGATTTTTGGGGAGAAAATTG
49019267 GGGGGAATTTTTGGGGAGAAAAT
1 GGGGG-ATTTTTGGGGAGAAAAT
49019290 AGCTTTTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.28, C:0.00, G:0.43, T:0.28
Consensus pattern (24 bp):
GGGGGATTTTTGGGGAGAAAATTG
Found at i:49019989 original size:4 final size:4
Alignment explanation
Indices: 49019980--49020006 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
49019970 TCTCACATCT
49019980 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
49020007 CTTCTATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:49020513 original size:36 final size:36
Alignment explanation
Indices: 49020468--49020543 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
49020458 AACATTACCA
*
49020468 AAATACCGAATGGGGGCTTCTAGCTTCCAACACTCC
1 AAATACCGAAAGGGGGCTTCTAGCTTCCAACACTCC
49020504 AAATACCGAAAGGGGGCTTCTAGCTTCCAACACTCC
1 AAATACCGAAAGGGGGCTTCTAGCTTCCAACACTCC
49020540 AAAT
1 AAAT
49020544 CCCGTCGTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (36 bp):
AAATACCGAAAGGGGGCTTCTAGCTTCCAACACTCC
Found at i:49020799 original size:17 final size:17
Alignment explanation
Indices: 49020777--49020811 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
49020767 ACCCTTGACA
49020777 CCCTAACCCCTAAATCC
1 CCCTAACCCCTAAATCC
*
49020794 CCCTAACCCTTAAATCC
1 CCCTAACCCCTAAATCC
49020811 C
1 C
49020812 TAACTCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.51, G:0.00, T:0.20
Consensus pattern (17 bp):
CCCTAACCCCTAAATCC
Found at i:49020814 original size:15 final size:16
Alignment explanation
Indices: 49020777--49020821 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
49020767 ACCCTTGACA
49020777 CCCTAACCCCTAAATCC
1 CCCTAACCCCTAAAT-C
*
49020794 CCCTAACCCTTAAAT-
1 CCCTAACCCCTAAATC
*
49020809 CCCTAACTCCTAA
1 CCCTAACCCCTAA
49020822 CCCCTAATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.44
17 14 0.56
ACGTcount: A:0.31, C:0.47, G:0.00, T:0.22
Consensus pattern (16 bp):
CCCTAACCCCTAAATC
Found at i:49021545 original size:19 final size:21
Alignment explanation
Indices: 49021509--49021548 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
49021499 AAATCATACT
49021509 ATTTGTTTTACGATTATATAA
1 ATTTGTTTTACGATTATATAA
*
49021530 ATTT-TTTTACTA-TATATAA
1 ATTTGTTTTACGATTATATAA
49021549 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (21 bp):
ATTTGTTTTACGATTATATAA
Done.