Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold9
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: 3883850
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 144036 characters in sequence are not A, C, G, or T
File 18 of 24
Found at i:2657331 original size:12 final size:13
Alignment explanation
Indices: 2657313--2657350 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
2657303 CCTAGCTTTT
2657313 TTATTTTTTTCTA
1 TTATTTTTTTCTA
*
2657326 -TATTTTCTTCTA
1 TTATTTTTTTCTA
2657338 TTTATTTTTTTCT
1 -TTATTTTTTTCT
2657351 TTCTCTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 11 0.52
14 10 0.48
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:2658424 original size:164 final size:164
Alignment explanation
Indices: 2658015--2658488 Score: 551
Period size: 166 Copynumber: 2.8 Consensus size: 164
2658005 ATTTCAAAGA
* * *
2658015 AAAAAATTTAAAAAATTCATGAAAATGAATTTATTTTTTAAAACTGAATTAATATGAAATACATA
1 AAAAAA-TTCAAAAACTCATGAAAATGAATTTATTTTTT-AAACTGAATTAATATGAAATAAATA
* * *
2658080 ATGATGTTTGATGAATGTTAGAAATTAAAAACTAAGAAAAATCCCCTCAAAAAA-TTACGGAGTA
64 ATGATGTTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATCTCCTCAAAAAATTTACGGAG-A
* *
2658144 GAAAACACCGTATTTCGAAAAAAAAGGAAATTTGAAGG
128 AAAAACACCGTATTTCGAAAAAAAA-GAAATTTGAACG
* * * ** *
2658182 AAAAAAATCCAAAACTCATGAAAATGAATTTATTTTTTAAAATGGAATTAATATGAACCAAATGA
1 AAAAAATTCAAAAACTCATGAAAATGAATTTATTTTTTAAACT-GAATTAATATGAAATAAATAA
* * * *
2658247 TGATGTCTGATGAATTTTAAAAATTGAAAACCACGAAAAATCTCCTCAAAAATATTTACGGAGCA
65 TGATGTTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATCTCCTCAAAAA-ATTTACGGAG-A
*
2658312 AAAAACACCGTATTTCG-AAAAAAA-AAATTTTAACG
128 AAAAACACCGTATTTCGAAAAAAAAGAAATTTGAACG
* * *
2658347 -AAAAATTCAAAAACTCATGAAAATTAATTAATTTTTGAGAACTGAATTAATATGAAATAAATAA
1 AAAAAATTCAAAAACTCATGAAAATGAATTTATTTTTTA-AACTGAATTAATATGAAATAAATAA
** * * * **
2658411 AAATATTTGATGAATTTTGAAAATTAAAAATTAAGAAAAATCCTTCCAAAAAAAATTTACGGAGA
65 TGATGTTTGATGAATTTTAAAAATTAAAAACTAAGAAAAAT-C-TCCTCAAAAAATTTACGGAGA
*
2658476 AGAAAACTCCGTA
128 A-AAAACACCGTA
2658489 ATTTGATAAT
Statistics
Matches: 259, Mismatches: 41, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
164 85 0.33
165 37 0.14
166 98 0.38
167 14 0.05
168 25 0.10
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28
Consensus pattern (164 bp):
AAAAAATTCAAAAACTCATGAAAATGAATTTATTTTTTAAACTGAATTAATATGAAATAAATAAT
GATGTTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATCTCCTCAAAAAATTTACGGAGAAAA
AACACCGTATTTCGAAAAAAAAGAAATTTGAACG
Found at i:2664949 original size:20 final size:20
Alignment explanation
Indices: 2664924--2664997 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
2664914 AAAAAAAGAC
2664924 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
2664944 AGAATGTATCGATACAGTCA
1 AGAATGTATCGATACATTGA
* *
2664964 TA-CATGTATTGATACATTGA
1 -AGAATGTATCGATACATTGA
*
2664984 AAAATGTATCGATA
1 AGAATGTATCGATA
2664998 TATCTAGGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:2665041 original size:91 final size:91
Alignment explanation
Indices: 2664875--2665170 Score: 416
Period size: 91 Copynumber: 3.3 Consensus size: 91
2664865 TTTTAACTAG
* * * * *
2664875 ATGTATCGATGCATTGAAAAATATATCGATACATCTGGGAAAAAAAGACAGAATGTATCGATACA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGG-TAAAAAGATAGAATGTATCAATACA
2664940 TTGAAGAATGTATCGATACAGTCATAC
65 TTGAAGAATGTATCGATACAGTCATAC
* * * * * *
2664967 ATGTATTGATACATTGAAAAATGTATCGATATATCTAGGTAAAAAGATAAAATGTATCCATACAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCAATACAT
*
2665032 TGAAGAATGTATCAATACAGTCATAC
66 TGAAGAATGTATCGATACAGTCATAC
*
2665058 ATGTATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAAA-ATAGAATGTATCAATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCAATACAT
2665122 TGAAGAATGTATCGATACA-TCCATAC
66 TGAAGAATGTATCGATACAGT-CATAC
* * *
2665148 ATGTGTCGATACACTGAAGAATG
1 ATGTATCGATACATTGAAAAATG
2665171 ATCCTCTACC
Statistics
Matches: 181, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
89 1 0.01
90 59 0.33
91 87 0.48
92 34 0.19
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (91 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCAATACAT
TGAAGAATGTATCGATACAGTCATAC
Found at i:2665091 original size:20 final size:20
Alignment explanation
Indices: 2665015--2665091 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
2665005 GTAAAAAGAT
* *
2665015 AAAATGTATCCATACAATGA
1 AAAATGTATCAATACATTGA
* * *
2665035 AGAATGTATCAATACAGTCA
1 AAAATGTATCAATACATTGA
* * *
2665055 TACATGTATCGATACATTGA
1 AAAATGTATCAATACATTGA
2665075 AAAATGTATCAATACAT
1 AAAATGTATCAATACAT
2665092 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (20 bp):
AAAATGTATCAATACATTGA
Found at i:2665535 original size:3 final size:3
Alignment explanation
Indices: 2665527--2665566 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2665517 TATCTACAAC
2665527 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2665567 GCTTTTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2667970 original size:19 final size:18
Alignment explanation
Indices: 2667931--2667975 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
2667921 TAATAGTAAA
*
2667931 ATAATTATTATTTTATAT
1 ATAATTATTATTTAATAT
2667949 ATAATTGATTATTATAAT-T
1 ATAATT-ATTATT-TAATAT
2667968 ATAATTAT
1 ATAATTAT
2667976 ATAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 13 0.54
20 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
ATAATTATTATTTAATAT
Found at i:2668840 original size:11 final size:10
Alignment explanation
Indices: 2668821--2668850 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
2668811 AAAAAACTAA
2668821 TTTTTTTTCT
1 TTTTTTTTCT
2668831 TTTTTATTTCT
1 TTTTT-TTTCT
2668842 TTTTTTTTC
1 TTTTTTTTC
2668851 AAGTCTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:2678354 original size:2 final size:2
Alignment explanation
Indices: 2678349--2678383 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2678339 TTTTTATTTG
*
2678349 TA TA TA TG 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 TA TA TA TA T
2678384 GAACCTTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2678759 original size:46 final size:46
Alignment explanation
Indices: 2678666--2678762 Score: 133
Period size: 46 Copynumber: 2.1 Consensus size: 46
2678656 AATTTTATCA
** *
2678666 TTAATTAAATTAAATTAATTAAGAGATACTTGAAGAAATTTTATTT
1 TTAATTAAATTAAATTAATTAAGAGATAAATGAAGAAACTTTATTT
*
2678712 TTAATTAAATTAAATTAATTAAGAGATAAAT-AAGATAAACTTTTTTT
1 TTAATTAAATTAAATTAATTAAGAGATAAATGAAG--AAACTTTATTT
2678759 TTAA
1 TTAA
2678763 AAAAAATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
45 3 0.07
46 29 0.64
47 13 0.29
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.43
Consensus pattern (46 bp):
TTAATTAAATTAAATTAATTAAGAGATAAATGAAGAAACTTTATTT
Found at i:2684629 original size:27 final size:25
Alignment explanation
Indices: 2684598--2684651 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
2684588 TTGCTAATGT
2684598 TTGCTTGTTGTTTTTGCTGGTATTTGC
1 TTGCTTGTTGTTTTTG--GGTATTTGC
* *
2684625 TTGCTTTTTTTTTTTGGGTATTTGC
1 TTGCTTGTTGTTTTTGGGTATTTGC
2684650 TT
1 TT
2684652 CCTATTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 11 0.44
27 14 0.56
ACGTcount: A:0.04, C:0.09, G:0.22, T:0.65
Consensus pattern (25 bp):
TTGCTTGTTGTTTTTGGGTATTTGC
Found at i:2684644 original size:25 final size:26
Alignment explanation
Indices: 2684598--2684660 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
2684588 TTGCTAATGT
* *
2684598 TTGCTTGTTGTTTTTGCTGGTATTTGC
1 TTGCTTTTTTTTTTTGC-GGTATTTGC
2684625 TTGCTTTTTTTTTTTG-GGTATTTGC
1 TTGCTTTTTTTTTTTGCGGTATTTGC
* *
2684650 TTCCTATTTTT
1 TTGCTTTTTTT
2684661 GCTAGTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 18 0.56
27 14 0.44
ACGTcount: A:0.05, C:0.11, G:0.19, T:0.65
Consensus pattern (26 bp):
TTGCTTTTTTTTTTTGCGGTATTTGC
Found at i:2684910 original size:32 final size:32
Alignment explanation
Indices: 2684872--2684981 Score: 91
Period size: 34 Copynumber: 3.3 Consensus size: 32
2684862 TCTCCTTCTT
2684872 TATTTGTTTTCTTTTTCTCTTTGTTTCGATTC
1 TATTTGTTTTCTTTTTCTCTTTGTTTCGATTC
** *
2684904 TATTTGTTTT-TTCTTT-TGCTATAATTTC-CTTC
1 TATTTGTTTTCTT-TTTCT-CT-TTGTTTCGATTC
* *
2684936 TTTATTTGTTTTCTTTTTCCCCTTTTGTTTTGATTC
1 --TATTTGTTTTCTTTTT-CTC-TTTGTTTCGATTC
2684972 TATTTGTTTT
1 TATTTGTTTT
2684982 TTCTTTTGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
31 3 0.05
32 18 0.30
33 5 0.08
34 23 0.38
35 7 0.12
36 4 0.07
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (32 bp):
TATTTGTTTTCTTTTTCTCTTTGTTTCGATTC
Found at i:2684939 original size:66 final size:68
Alignment explanation
Indices: 2684864--2684989 Score: 220
Period size: 68 Copynumber: 1.9 Consensus size: 68
2684854 TTTCCGAATC
*
2684864 TCCTTCTTTATTTGTTTTCTTTTT-CTC-TTTGTTTCGATTCTATTTGTTTTTTCTTTTGCTATA
1 TCCTTCTTTATTTGTTTTCTTTTTCCCCTTTTGTTTCGATTCTATTTGTTTTTTCTTTTGCTATA
2684927 ATT
66 ATT
*
2684930 TCCTTCTTTATTTGTTTTCTTTTTCCCCTTTTGTTTTGATTCTATTTGTTTTTTCTTTTG
1 TCCTTCTTTATTTGTTTTCTTTTTCCCCTTTTGTTTCGATTCTATTTGTTTTTTCTTTTG
2684990 TTGCAATTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
66 24 0.43
67 2 0.04
68 30 0.54
ACGTcount: A:0.07, C:0.16, G:0.08, T:0.69
Consensus pattern (68 bp):
TCCTTCTTTATTTGTTTTCTTTTTCCCCTTTTGTTTCGATTCTATTTGTTTTTTCTTTTGCTATA
ATT
Found at i:2685384 original size:16 final size:16
Alignment explanation
Indices: 2685363--2685394 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2685353 CAATAGCTAT
2685363 AGCTGCTTCCATTTCA
1 AGCTGCTTCCATTTCA
2685379 AGCTGCTTCCATTTCA
1 AGCTGCTTCCATTTCA
2685395 CTCTGACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.38
Consensus pattern (16 bp):
AGCTGCTTCCATTTCA
Found at i:2685446 original size:12 final size:12
Alignment explanation
Indices: 2685408--2685449 Score: 66
Period size: 12 Copynumber: 3.3 Consensus size: 12
2685398 TGACTTTGCC
2685408 TTGCTTTCTTCA
1 TTGCTTTCTTCA
2685420 TTGCATTTGCTTCA
1 TTGC-TTT-CTTCA
2685434 TTGCTTTCTTCA
1 TTGCTTTCTTCA
2685446 TTGC
1 TTGC
2685450 ACCTCGATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 13 0.46
13 6 0.21
14 9 0.32
ACGTcount: A:0.10, C:0.24, G:0.12, T:0.55
Consensus pattern (12 bp):
TTGCTTTCTTCA
Found at i:2685840 original size:8 final size:8
Alignment explanation
Indices: 2685827--2685855 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
2685817 TATATATTTT
2685827 TTATTTAA
1 TTATTTAA
2685835 TTATTTAA
1 TTATTTAA
2685843 TTATTTAA
1 TTATTTAA
2685851 TTATT
1 TTATT
2685856 ATTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTATTTAA
Found at i:2686987 original size:125 final size:123
Alignment explanation
Indices: 2686816--2687353 Score: 401
Period size: 125 Copynumber: 4.3 Consensus size: 123
2686806 AGGGTAAATA
* * * * ** * *
2686816 AGTCTCTAGGGTCAAAGCCGATAGGCAAACTTGAGGTGAGGCAGTCTCCAGGGTTAAAGCCGATA
1 AGTCTCTAAGGTCAAAGCCGACAGGCAGACTTGAGGTAAGAAAGTCTCCAGGGTCAAAGCCGACA
*
2686881 GGCAAACTGACGGTAAGAAAGTCTCTAAGGTTAAAGCTGACAGGCAGATTTGAGGTGAAG
66 GGCAAACTGA-GGTAAGAAAGTCTC-AAGGTCAAAGCTGACAGGCAGATTTGAGGTGAAG
*
2686941 TAGTCTC-AAGGTCAAAGCCGACAGGCAGAC-TGAGGGTAAGAAAGTCTCCAGGGTTAAAGCCGA
1 -AGTCTCTAAGGTCAAAGCCGACAGGCAGACTTGA-GGTAAGAAAGTCTCCAGGGTCAAAGCCGA
* ** * ** * * *
2687004 CAAGCAGATTTGAGGTGAGGCAGTCTCAAGGTCAAAG-TCGACAAGTAGA-CTGAGGGTTAGAA-
64 CAGGCA-AACTGAGGTAAGAAAGTCTCAAGGTCAAAGCT-GACAGGCAGATTTGA-GG-T-GAAG
* * * ** *
2687066 AGTCTCTAAGGTCAAAGTCGACAAGCAGACTTGAGGTGAGTCAGTCTCCAAGGTCAAAGCCGACA
1 AGTCTCTAAGGTCAAAGCCGACAGGCAGACTTGAGGTAAGAAAGTCTCCAGGGTCAAAGCCGACA
* * * * * *
2687131 GGCAGACTGAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACTTTGAGATGAGG
66 GGCAAACTGA-GGTAAGAAAGTCT-CAAGGTCAAAGCTGACAGGCAGA-TTTGAGGTGAAG
* * * *
2687192 CAGTCTCTAGGGTCAAAGCCAATAGGCAGAC-TGAGGGTAAGAAAGTCTCTAGGGTCAAAGCCGA
1 -AGTCTCTAAGGTCAAAGCCGACAGGCAGACTTGA-GGTAAGAAAGTCTCCAGGGTCAAAGCCGA
* * * * * ** * ** * *
2687256 TAAGCAGACTTTAGGTGAGGTAGTCTCCAAGGTCAAAG-TCGACAGACAGA-TAAAGGGTAAAA
64 CAGGCAAAC-TGAGGTAAGAAAGTCT-CAAGGTCAAAGCT-GACAGGCAGATTTGA-GGTGAAG
*
2687318 AGGTCTC-AAGGGTCAAAGCCGACAAGCAGACTTGAG
1 A-GTCTCTAA-GGTCAAAGCCGACAGGCAGACTTGAG
2687354 ATTAAAGTAT
Statistics
Matches: 321, Mismatches: 69, Indels: 44
0.74 0.16 0.10
Matches are distributed among these distances:
123 4 0.01
124 31 0.10
125 127 0.40
126 65 0.20
127 89 0.28
128 5 0.02
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (123 bp):
AGTCTCTAAGGTCAAAGCCGACAGGCAGACTTGAGGTAAGAAAGTCTCCAGGGTCAAAGCCGACA
GGCAAACTGAGGTAAGAAAGTCTCAAGGTCAAAGCTGACAGGCAGATTTGAGGTGAAG
Found at i:2687011 original size:83 final size:83
Alignment explanation
Indices: 2686473--2687353 Score: 784
Period size: 84 Copynumber: 10.5 Consensus size: 83
2686463 GAAAACTTAA
* * * * * **
2686473 AGGGTAA-AGAAGTCTCCAAGGTCAAGGCTGACAGGCAGACTTGAGATGAGGTAGTCTCCAACAT
1 AGGGTAAGA-AAGTCTCTAAGGTCAAAGCCGACAAGCAGACTTGAGGTGAGGTAGTCT-CAAGGT
*
2686537 CAAAGACGACAGGCAGACTG
64 CAAAGCCGACAGGCAGACTG
* * * * *
2686557 AGGGTAAAAAAGTCTCT-AGGTTCAAAGCCGACAGGCAAACTTGGGGTGAGGTAATCTCTAAGGT
1 AGGGTAAGAAAGTCTCTAAGG-TCAAAGCCGACAAGCAGACTTGAGGTGAGGTAGTCTC-AAGG-
* * *
2686621 TC-AAGCTGACAGGTAGATTG
63 TCAAAGCCGACAGGCAGACTG
* * * * *
2686641 AGGGTAAGAAAGTCTCTAGGGTTAAAGCTGACAAGTAGACTTAAGGTGAGGTAGTCTTC-AGCGT
1 AGGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAAGCAGACTTGAGGTGAGGTAGTC-TCAAG-GT
* *
2686705 CAAAGCCGATAGGTA-A---
64 CAAAGCCGACAGGCAGACTG
* ** * ** * * *
2686721 A-GGTAAGAAAGT-TTTCAAGGTCAAAGCCGACATTCAGACTTAAAATGAGGCAATCCCCAAGGT
1 AGGGTAAGAAAGTCTCT-AAGGTCAAAGCCGACAAGCAGACTTGAGGTGAGGTAGT-CTCAAGGT
* * * *
2686784 CAAAGTCGATAAGCAGACTTAA
64 CAAAGCCGACAGGCAGAC-T-G
* * * * * *
2686806 AGGGTAA-ATAAGTCTCTAGGGTCAAAGCCGATAGGCAAACTTGAGGTGAGGCAGTCTCCAGGGT
1 AGGGTAAGA-AAGTCTCTAAGGTCAAAGCCGACAAGCAGACTTGAGGTGAGGTAGTCT-CAAGGT
* * *
2686870 TAAAGCCGATAGGCAAACTG
64 CAAAGCCGACAGGCAGACTG
* * * * * *
2686890 ACGGTAAGAAAGTCTCTAAGGTTAAAGCTGACAGGCAGATTTGAGGTGAAGTAGTCTCAAGGTCA
1 AGGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAAGCAGACTTGAGGTGAGGTAGTCTCAAGGTCA
2686955 AAGCCGACAGGCAGACTG
66 AAGCCGACAGGCAGACTG
* * * * *
2686973 AGGGTAAGAAAGTCTCCAGGGTTAAAGCCGACAAGCAGATTTGAGGTGAGGCAGTCTCAAGGTCA
1 AGGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAAGCAGACTTGAGGTGAGGTAGTCTCAAGGTCA
* * *
2687038 AAGTCGACAAGTAGACTG
66 AAGCCGACAGGCAGACTG
* *
2687056 AGGGTTAGAAAGTCTCTAAGGTCAAAGTCGACAAGCAGACTTGAGGTGA-GTCAGTCTCCAAGGT
1 AGGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAAGCAGACTTGAGGTGAGGT-AGTCT-CAAGGT
2687120 CAAAGCCGACAGGCAGACTG
64 CAAAGCCGACAGGCAGACTG
* * * * * * *
2687140 AGGGTAAAAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACTTTGAGATGAGGCAGTCTCTAGGGT
1 AGGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAAGCAGAC-TTGAGGTGAGGTAGTCTC-AAGGT
* *
2687205 CAAAGCCAATAGGCAGACTG
64 CAAAGCCGACAGGCAGACTG
* * *
2687225 AGGGTAAGAAAGTCTCTAGGGTCAAAGCCGATAAGCAGACTTTAGGTGAGGTAGTCTCCAAGGTC
1 AGGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAAGCAGACTTGAGGTGAGGTAGTCT-CAAGGTC
* * *
2687290 AAAGTCGACAGACAGA-TAA
65 AAAGCCGACAGGCAGACT-G
2687309 AGGGTAA-AAAGGTCTC-AAGGGTCAAAGCCGACAAGCAGACTTGAG
1 AGGGTAAGAAA-GTCTCTAA-GGTCAAAGCCGACAAGCAGACTTGAG
2687354 ATTAAAGTAT
Statistics
Matches: 649, Mismatches: 117, Indels: 62
0.78 0.14 0.07
Matches are distributed among these distances:
78 2 0.00
79 54 0.08
80 5 0.01
82 1 0.00
83 157 0.24
84 286 0.44
85 84 0.13
86 58 0.09
87 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (83 bp):
AGGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAAGCAGACTTGAGGTGAGGTAGTCTCAAGGTCA
AAGCCGACAGGCAGACTG
Found at i:2687253 original size:42 final size:41
Alignment explanation
Indices: 2686482--2687349 Score: 420
Period size: 42 Copynumber: 20.8 Consensus size: 41
2686472 AAGGGTAAAG
* * * * * *
2686482 AAGTCTCCAAGGTCAAGGCTGACAGGCAGACTTGAGATGAGG
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGAC-TGAGGTAAGA
* * ** * *
2686524 TAGTCTCCAACATCAAAGACGACAGGCAGACTGAGGGTAAAA
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGACTGA-GGTAAGA
* * * *
2686566 AAGTCTCT-AGGTTCAAAGCCGACAGGCAAACTTGGGGTGAGGT
1 AAGTCTCTAAGG-TCAAAGCCGACAGGCAGAC-TGAGGT-AAGA
* * *
2686609 AA-TCTCTAAGGTTC-AAGCTGACAGGTAGATTGAGGGTAAGA
1 AAGTCTCTAAGG-TCAAAGCCGACAGGCAGACTGA-GGTAAGA
* * * * * * * *
2686650 AAGTCTCTAGGGTTAAAGCTGACAAGTAGACTTAAGGTGAGG
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGAC-TGAGGTAAGA
* * * *
2686692 TAGTCT-TCAGCGTCAAAGCCGATAGGTA-A---AGGTAAGA
1 AAGTCTCTAAG-GTCAAAGCCGACAGGCAGACTGAGGTAAGA
* ** * ** * *
2686729 AAGT-TTTCAAGGTCAAAGCCGACATTCAGACTTAAAATGAGGC
1 AAGTCTCT-AAGGTCAAAGCCGACAGGCAGAC-TGAGGT-AAGA
* * * * * *
2686772 AA-TCCCCAAGGTCAAAGTCGATAAGCAGACTTAAAGGGTAA-A
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGAC-T-GA-GGTAAGA
* * * * *
2686814 TAAGTCTCTAGGGTCAAAGCCGATAGGCAAACTTGAGGTGAGG
1 -AAGTCTCTAAGGTCAAAGCCGACAGGCAGAC-TGAGGTAAGA
* * * * * *
2686857 CAGTCTCCAGGGTTAAAGCCGATAGGCAAACTGACGGTAAGA
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGACTGA-GGTAAGA
* * *
2686899 AAGTCTCTAAGGTTAAAGCTGACAGGCAGATTTGAGGTGAAG-
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGA-CTGAGGT-AAGA
*
2686941 TAGTCTC-AAGGTCAAAGCCGACAGGCAGACTGAGGGTAAGA
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGACTGA-GGTAAGA
* * * * * * *
2686982 AAGTCTCCAGGGTTAAAGCCGACAAGCAGATTTGAGGTGAGG
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGA-CTGAGGTAAGA
* * * * *
2687024 CAGTCTC-AAGGTCAAAGTCGACAAGTAGACTGAGGGTTAGA
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGACTGA-GGTAAGA
* * * *
2687065 AAGTCTCTAAGGTCAAAGTCGACAAGCAGACTTGAGGTGAGT
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGAC-TGAGGTAAGA
* * *
2687107 CAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGTAAAA
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGACTGA-GGTAAGA
* * * * *
2687149 AAGTCTCCAAGGTCAAAGCCGATAGGCAGACTTTGAGATGAGG
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGAC--TGAGGTAAGA
* * * *
2687192 CAGTCTCTAGGGTCAAAGCCAATAGGCAGACTGAGGGTAAGA
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGACTGA-GGTAAGA
* * * * * *
2687234 AAGTCTCTAGGGTCAAAGCCGATAAGCAGACTTTAGGTGAGG
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGAC-TGAGGTAAGA
* * * * *
2687276 TAGTCTCCAAGGTCAAAGTCGACAGACAGA-TAAAGGGTAA-A
1 AAGTCTCTAAGGTCAAAGCCGACAGGCAGACT-GA-GGTAAGA
*
2687317 AAGGTCTC-AAGGGTCAAAGCCGACAAGCAGACT
1 AA-GTCTCTAA-GGTCAAAGCCGACAGGCAGACT
2687350 TGAGATTAAA
Statistics
Matches: 634, Mismatches: 148, Indels: 87
0.73 0.17 0.10
Matches are distributed among these distances:
36 1 0.00
37 23 0.04
38 3 0.00
40 10 0.02
41 85 0.13
42 416 0.66
43 68 0.11
44 28 0.04
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.19
Consensus pattern (41 bp):
AAGTCTCTAAGGTCAAAGCCGACAGGCAGACTGAGGTAAGA
Found at i:2687632 original size:36 final size:35
Alignment explanation
Indices: 2687581--2687663 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 35
2687571 AGGCCCTAAT
2687581 ACCA-ATACAGTCAAACGAG-GGAAGAAAAGAGTTTG
1 ACCAGATACAGTCAAACG-GTGG-AGAAAAGAGTTTG
* **
2687616 ACCAGATACAGTCAAACGGTGGTGGGAAGAGTTTG
1 ACCAGATACAGTCAAACGGTGGAGAAAAGAGTTTG
2687651 ACCAGATACAGTC
1 ACCAGATACAGTC
2687664 GATGATGATG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
35 28 0.65
36 15 0.35
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.17
Consensus pattern (35 bp):
ACCAGATACAGTCAAACGGTGGAGAAAAGAGTTTG
Found at i:2687786 original size:30 final size:30
Alignment explanation
Indices: 2687702--2687772 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
2687692 GTCCAAAAAT
2687702 GAAAGATTTGACCGAATATAGTCAAGTGAG
1 GAAAGATTTGACCGAATATAGTCAAGTGAG
*
2687732 GAAAGATTTGACCAAATATAGTCAAGTGAG
1 GAAAGATTTGACCGAATATAGTCAAGTGAG
2687762 GAAAGATTTGA
1 GAAAGATTTGA
2687773 TTGATTACAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.24
Consensus pattern (30 bp):
GAAAGATTTGACCGAATATAGTCAAGTGAG
Found at i:2695035 original size:23 final size:22
Alignment explanation
Indices: 2694999--2695066 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 22
2694989 CCTTCCTTGA
2694999 TTGCTA-TTTTGCTGGTGTTTGC
1 TTGCTATTTTTGCTGGT-TTTGC
*
2695021 TTGCTGTTTTTGCTGGTATTTGC
1 TTGCTATTTTTGCTGGT-TTTGC
* *
2695044 TTGTTATTTTTGCTAGTTTTGC
1 TTGCTATTTTTGCTGGTTTTGC
2695066 T
1 T
2695067 GCCGTTGCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.28
23 29 0.73
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.59
Consensus pattern (22 bp):
TTGCTATTTTTGCTGGTTTTGC
Found at i:2695245 original size:66 final size:67
Alignment explanation
Indices: 2695168--2695310 Score: 234
Period size: 68 Copynumber: 2.1 Consensus size: 67
2695158 TTGCTTTTCG
2695168 AATCTCCTTCTTTATTTGTTTTCTTTTTCCCC-TTGTTTCGATTCTATTTGTTTTTTCTTTTGCT
1 AATCTCCTTCTTTATTTGTTTTCTTTTTCCCCTTTGTTTCGATTCTATTTGTTTTTTCTTTTGCT
2695232 GC
66 GC
* * *
2695234 AATCTCTTTCTTTATTTGTTTTCTTTTTCCCCTTTTGTTTTGATTCTATTTGTTTTTTCTTTTGT
1 AATCTCCTTCTTTATTTGTTTTCTTTTTCCCC-TTTGTTTCGATTCTATTTGTTTTTTCTTTTGC
2695299 TGC
65 TGC
*
2695302 AATTTCCTT
1 AATCTCCTT
2695311 GTTCTTAGAG
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 31 0.44
68 39 0.56
ACGTcount: A:0.08, C:0.19, G:0.08, T:0.64
Consensus pattern (67 bp):
AATCTCCTTCTTTATTTGTTTTCTTTTTCCCCTTTGTTTCGATTCTATTTGTTTTTTCTTTTGCT
GC
Found at i:2695718 original size:12 final size:12
Alignment explanation
Indices: 2695703--2695744 Score: 66
Period size: 12 Copynumber: 3.3 Consensus size: 12
2695693 ACTTTGCCGT
2695703 TTGCTTTCTTCA
1 TTGCTTTCTTCA
2695715 TTGCATTTGCTTCA
1 TTGC-TTT-CTTCA
2695729 TTGCTTTCTTCA
1 TTGCTTTCTTCA
2695741 TTGC
1 TTGC
2695745 ACCTCAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 13 0.46
13 6 0.21
14 9 0.32
ACGTcount: A:0.10, C:0.24, G:0.12, T:0.55
Consensus pattern (12 bp):
TTGCTTTCTTCA
Found at i:2696808 original size:22 final size:22
Alignment explanation
Indices: 2696753--2696830 Score: 149
Period size: 22 Copynumber: 3.6 Consensus size: 22
2696743 AGTAACAACA
2696753 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
2696775 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
2696796 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
2696818 ATGAACAGTGATG
1 ATGAACAGTGATG
2696831 AATAGTGATG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.38
22 34 0.62
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:2696837 original size:10 final size:10
Alignment explanation
Indices: 2696818--2696848 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2696808 GTATCGATAC
2696818 ATGAACAGTG
1 ATGAACAGTG
*
2696828 ATGAATAGTG
1 ATGAACAGTG
2696838 ATGAACAGTG
1 ATGAACAGTG
2696848 A
1 A
2696849 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:2702922 original size:13 final size:13
Alignment explanation
Indices: 2702904--2702928 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2702894 CAAAGATCAG
2702904 TGTATCGATACAA
1 TGTATCGATACAA
2702917 TGTATCGATACA
1 TGTATCGATACA
2702929 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2703013 original size:33 final size:33
Alignment explanation
Indices: 2702971--2703037 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2702961 AATAGCTTAA
2702971 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* * ***
2703004 ATTGTATCGATGCAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2703037 A
1 A
2703038 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2714088 original size:50 final size:50
Alignment explanation
Indices: 2714029--2714124 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
2714019 ATACATCGAA
* * *
2714029 GAATGTATCGATACATTCATATATGTATCGATACATCTGGGTAAAAGACT
1 GAATGTATCGATACATTCAAAAATGTATCGATACATCTGAGTAAAAGACT
*
2714079 GAATGTATCGATACATTGAAAAATGTATCGATACATCTGAGTAAAA
1 GAATGTATCGATACATTCAAAAATGTATCGATACATCTGAGTAAAA
2714125 ATGTGACTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (50 bp):
GAATGTATCGATACATTCAAAAATGTATCGATACATCTGAGTAAAAGACT
Found at i:2714112 original size:70 final size:71
Alignment explanation
Indices: 2713960--2714114 Score: 222
Period size: 70 Copynumber: 2.2 Consensus size: 71
2713950 TTTTAACTAG
* *
2713960 ATGTATCGATACATTGAAAAATATATCGTTACATCTGGGTAAAAAGACAAAATGTATCGATACAT
1 ATGTATCGATACATTCAAAAATATATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACAT
*
2714025 CGAAGA
66 CGAAAA
* * * **
2714031 ATGTATCGATACATTCATATATGTATCGATACATCTGGGT-AAAAGACTGAATGTATCGATACAT
1 ATGTATCGATACATTCAAAAATATATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACAT
*
2714095 TGAAAA
66 CGAAAA
2714101 ATGTATCGATACAT
1 ATGTATCGATACAT
2714115 CTGAGTAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
70 40 0.53
71 35 0.47
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (71 bp):
ATGTATCGATACATTCAAAAATATATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACAT
CGAAAA
Found at i:2714127 original size:24 final size:20
Alignment explanation
Indices: 2714008--2714114 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
2713998 GTAAAAAGAC
*
2714008 AAAATGTATCGATACATCGA
1 AAAATGTATCGATACATTGA
* *
2714028 AGAATGTATCGATACATTCA
1 AAAATGTATCGATACATTGA
* *
2714048 TATATGTATCGATACATCTGGGTAAA
1 AAAATGTATCGATACAT-T--G---A
2714074 AGACTGAATGTATCGATACATTGA
1 A-A---AATGTATCGATACATTGA
2714098 AAAATGTATCGATACAT
1 AAAATGTATCGATACAT
2714115 CTGAGTAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
20 46 0.68
21 1 0.01
23 1 0.01
24 2 0.03
26 1 0.01
27 2 0.03
29 1 0.01
30 14 0.21
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (20 bp):
AAAATGTATCGATACATTGA
Found at i:2715099 original size:13 final size:13
Alignment explanation
Indices: 2715081--2715107 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2715071 ACATTATGCT
2715081 TTGTATCAATACA
1 TTGTATCAATACA
2715094 TTGTATCAATACA
1 TTGTATCAATACA
2715107 T
1 T
2715108 ATTTATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TTGTATCAATACA
Found at i:2723893 original size:52 final size:52
Alignment explanation
Indices: 2723815--2724015 Score: 314
Period size: 52 Copynumber: 3.9 Consensus size: 52
2723805 CGAAATATGA
*
2723815 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* *
2723867 AAATTTGCCTGCACGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* *
2723919 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* **
2723971 AACTTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
2724016 ATGTATCGAT
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
51 2 0.01
52 136 0.99
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:2724022 original size:13 final size:13
Alignment explanation
Indices: 2724004--2724028 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2723994 CAAAGATCAG
2724004 TGTATCGATACAA
1 TGTATCGATACAA
2724017 TGTATCGATACA
1 TGTATCGATACA
2724029 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2724106 original size:33 final size:33
Alignment explanation
Indices: 2724069--2724135 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2724059 AGTAGCTTAA
2724069 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2724102 ATTGTATCGATACAACACTCTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2724135 A
1 A
2724136 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.31
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2724109 original size:13 final size:13
Alignment explanation
Indices: 2724091--2724115 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2724081 CAAAAAAATA
2724091 TGTATCGATACAT
1 TGTATCGATACAT
2724104 TGTATCGATACA
1 TGTATCGATACA
2724116 ACACTCTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2724972 original size:30 final size:30
Alignment explanation
Indices: 2724862--2725315 Score: 366
Period size: 30 Copynumber: 15.5 Consensus size: 30
2724852 CACCGACTTG
* * *
2724862 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
2724892 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
2724919 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
2724947 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* * *
2724977 TGTGGGCTTTTGAACAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* *
2725007 TGTGGG-TTTT-TAAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
2725035 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* * *
2725065 TGTGGGCTCTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* *
2725095 TGTGGGC---TGAAAA-GAGTGCTA-TAGAGT
1 TGTGGGCTTTTGAAAAGGA-TGCCACT-GACT
* ** * * *
2725122 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT----TTGAAAAGGA-TGCCACTGACT
* * *
2725157 TGTGGACTTTGGAAAA-GATGCCACCGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
** * *
2725186 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
2725216 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* ** *
2725243 TGTGGGCTTTCGAAAAAAATGCCACCGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
2725273 TGTGGGC-TTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
2725302 TGTGGACTTTTGAA
1 TGTGGGCTTTTGAA
2725316 GGGTGATGAA
Statistics
Matches: 347, Mismatches: 55, Indels: 44
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.01
27 60 0.17
28 53 0.15
29 62 0.18
30 142 0.41
31 5 0.01
34 5 0.01
35 18 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (30 bp):
TGTGGGCTTTTGAAAAGGATGCCACTGACT
Found at i:2725028 original size:58 final size:59
Alignment explanation
Indices: 2724846--2725312 Score: 296
Period size: 57 Copynumber: 7.9 Consensus size: 59
2724836 GGCTTAGAAG
* * * *
2724846 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC--TTTGAA
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTTAAA
* *
2724905 GGTTGCCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTGAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTTAAA
** * *
2724962 AATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGG-TTTTTAAA
1 GGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTTAAA
*** **
2725021 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTCTTGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCT-TTTTAAA
* * * * * * ***
2725081 GGGTGCCACTAACTTGTGGGC---TGAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACT-GACTTGTGGGCTTTTTAAA
* * * * * * * ***
2725137 GAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAA-GATGCCACCGACTTGTGGGCTTCGGAAA
1 G-----G-TTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTT-TTTAA
2725201 A
59 A
* * * **
2725202 GGGTGCCACTGATTTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTCGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTT-TTAAA
*** * *** *
2725259 AAATGCCACCGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTT
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTT
2725313 GAAGGGTGAT
Statistics
Matches: 324, Mismatches: 61, Indels: 47
0.75 0.14 0.11
Matches are distributed among these distances:
55 22 0.07
56 9 0.03
57 80 0.25
58 68 0.21
59 59 0.18
60 45 0.14
61 1 0.00
62 15 0.05
64 15 0.05
65 10 0.03
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (59 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTTAAA
Found at i:2725032 original size:88 final size:87
Alignment explanation
Indices: 2724846--2725102 Score: 374
Period size: 88 Copynumber: 2.9 Consensus size: 87
2724836 GGCTTAGAAG
* * *** * *
2724846 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGTT
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGT
*
2724909 GCCACTGACTTGTGGGCTTTTAAA
64 GCCACTAACTTGTGGGCTTTTAAA
2724933 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTG
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA-AGGGTG
*
2724998 CCACTAACTTGTGGGTTTTTAAA
65 CCACTAACTTGTGGGCTTTTAAA
*
2725021 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTCTTGAAAAGGGTG
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG-AAAGGGTG
2725086 CCACTAACTTGTGGGCT
65 CCACTAACTTGTGGGCT
2725103 GAAAAGAGTG
Statistics
Matches: 155, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
85 32 0.21
86 5 0.03
87 13 0.08
88 103 0.66
89 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (87 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGTGC
CACTAACTTGTGGGCTTTTAAA
Found at i:2725188 original size:29 final size:29
Alignment explanation
Indices: 2725139--2725311 Score: 170
Period size: 29 Copynumber: 5.9 Consensus size: 29
2725129 TTACAAAAGA
* * *
2725139 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
* *
2725169 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
2725198 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
2725227 -AAGGTTGCCACTGACTTGTGGGCTTTCGA
1 AAAAGATGCCACTGACTTGTGGGCTTT-GG
* * *
2725256 AAAAAATGCCACCGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
2725285 AAAAAATGCCACTGACTTGTGGACTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
2725312 TGAAGGGTGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
27 21 0.17
28 2 0.02
29 51 0.42
30 47 0.39
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:2725246 original size:121 final size:116
Alignment explanation
Indices: 2725024--2725306 Score: 293
Period size: 121 Copynumber: 2.4 Consensus size: 116
2725014 TTTTAAAGGT
* * *
2725024 TGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTCTTGAAAAGGGTGCCA
1 TGCCACCGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGGCTCTGGAAAAGGGTGCCA
* * *
2725089 CTAACTTGTGGGCTGAAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGAAAAAGAG
65 CTAACTTGTGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTAC----GAAAAA-AA
* * * * * *
2725146 TGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCT-TCGGAAAAGGGTGCCA
1 TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTCT-GGAAAAGGGTGCCA
* * *** * *
2725210 CTGATTTGTGGGCTTTGAAG-GTTGCCACT-GACTTGTGGGCTTTCGAAAAAAA
65 CTAACTTGTGGGCTGAAAAGAG-TGCCA-TAGACTTGTGAGCTTACGAAAAAAA
2725262 TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
1 TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
2725307 ACTTTTGAAG
Statistics
Matches: 135, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
116 40 0.30
117 6 0.04
120 2 0.01
121 71 0.53
122 16 0.12
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (116 bp):
TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTCTGGAAAAGGGTGCCAC
TAACTTGTGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTACGAAAAAAA
Found at i:2726744 original size:1 final size:1
Alignment explanation
Indices: 2726740--2726838 Score: 54
Period size: 1 Copynumber: 99.0 Consensus size: 1
2726730 CCGGACCCCC
* * * * * ** * *
2726740 TTTTTTTTGTTTGTTTTTTTATTGTTTTTTGTTTTTTTTTTCCTTTTGTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*** ** **
2726805 TCGGTTTTTCATTTTTTCGTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2726839 GGTTTGGAGG
Statistics
Matches: 73, Mismatches: 25, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (1 bp):
T
Found at i:2726768 original size:23 final size:22
Alignment explanation
Indices: 2726740--2726803 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
2726730 CCGGACCCCC
2726740 TTTTTTTTGTTTGTTTTTTT-AT
1 TTTTTTTTGTTT-TTTTTTTCAT
* *
2726762 TGTTTTTTGTTTTTTTTTTCCT
1 TTTTTTTTGTTTTTTTTTTCAT
2726784 TTTGTTTTTGTTTTTTTTTT
1 TTT-TTTTTGTTTTTTTTTT
2726804 TTCGGTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.19
22 14 0.38
23 16 0.43
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.86
Consensus pattern (22 bp):
TTTTTTTTGTTTTTTTTTTCAT
Found at i:2726803 original size:11 final size:11
Alignment explanation
Indices: 2726740--2726803 Score: 67
Period size: 11 Copynumber: 5.7 Consensus size: 11
2726730 CCGGACCCCC
2726740 TTTTTTTTGTT
1 TTTTTTTTGTT
*
2726751 TGTTTTTTT-AT
1 T-TTTTTTTGTT
*
2726762 TGTTTTTTGTT
1 TTTTTTTTGTT
*
2726773 TTTTTTTTCCTT
1 TTTTTTTT-GTT
*
2726785 TTGTTTTTGTT
1 TTTTTTTTGTT
2726796 TTTTTTTT
1 TTTTTTTT
2726804 TTCGGTTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
10 6 0.14
11 20 0.48
12 16 0.38
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.86
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:2726811 original size:15 final size:14
Alignment explanation
Indices: 2726740--2726835 Score: 74
Period size: 15 Copynumber: 6.6 Consensus size: 14
2726730 CCGGACCCCC
2726740 TTTTTTTT-GTTTGT
1 TTTTTTTTCGTTT-T
2726754 TTTTTTATT-GTTTT
1 TTTTTT-TTCGTTTT
2726768 TTGTTTTTT--TTTT
1 TT-TTTTTTCGTTTT
*
2726781 CCTTTTGTTTTTGTTTT
1 --TTTT-TTTTCGTTTT
2726798 TTTTTTTTCGGTTTT
1 TTTTTTTTC-GTTTT
*
2726813 TCATTTTTTCGTTTT
1 T-TTTTTTTCGTTTT
2726828 TTTTTTTT
1 TTTTTTTT
2726836 TTTGGTTTGG
Statistics
Matches: 70, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
13 4 0.06
14 23 0.33
15 32 0.46
16 7 0.10
17 4 0.06
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.83
Consensus pattern (14 bp):
TTTTTTTTCGTTTT
Found at i:2726837 original size:45 final size:44
Alignment explanation
Indices: 2726740--2726844 Score: 106
Period size: 45 Copynumber: 2.3 Consensus size: 44
2726730 CCGGACCCCC
**
2726740 TTTTTTTTGTTTGTTTTTTTATTGTTTTTTGTTTTTTTTTTCCTT
1 TTTTTTTTGTTTGTTTTTTTATTGTTTTTCATTTTTTTTTT-CTT
* *
2726785 TTGTTTTTGTTT-TTTTTTT-TTCGGTTTTTCATTTTTTCGTTTTTTT
1 TTTTTTTTGTTTGTTTTTTTATT--GTTTTTCATTTTTT--TTTTCTT
2726831 TTTTTTTTGGTTTG
1 TTTTTTTT-GTTTG
2726845 GAGGACGCCG
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
43 2 0.04
44 7 0.14
45 23 0.47
46 9 0.18
47 8 0.16
ACGTcount: A:0.02, C:0.05, G:0.11, T:0.82
Consensus pattern (44 bp):
TTTTTTTTGTTTGTTTTTTTATTGTTTTTCATTTTTTTTTTCTT
Found at i:2736547 original size:10 final size:10
Alignment explanation
Indices: 2736532--2736558 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2736522 ATGTATCAAG
2736532 CAAAAACAAA
1 CAAAAACAAA
2736542 CAAAAACAAA
1 CAAAAACAAA
2736552 CAAAAAC
1 CAAAAAC
2736559 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:2740802 original size:52 final size:51
Alignment explanation
Indices: 2740663--2740811 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
2740653 CGAAATATGA
*
2740663 AAATTTGCCTGCATGTATCGATACATTGAATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
2740715 AAATTTGCCTGCACGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
2740767 AACTTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
2740812 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:2740818 original size:13 final size:13
Alignment explanation
Indices: 2740800--2740824 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2740790 CAAAGATCAG
2740800 TGTATCGATACAA
1 TGTATCGATACAA
2740813 TGTATCGATACA
1 TGTATCGATACA
2740825 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2740902 original size:33 final size:33
Alignment explanation
Indices: 2740865--2740931 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2740855 AGTAGCTTAA
2740865 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2740898 ATTGTATCGATACAACACTCTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2740931 A
1 A
2740932 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.31
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2740905 original size:13 final size:13
Alignment explanation
Indices: 2740887--2740911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2740877 CAAAAAAATA
2740887 TGTATCGATACAT
1 TGTATCGATACAT
2740900 TGTATCGATACA
1 TGTATCGATACA
2740912 ACACTCTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2741880 original size:20 final size:20
Alignment explanation
Indices: 2741855--2741908 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
2741845 CCACCACTGT
* **
2741855 TTGTATCGATACATGGCATG
1 TTGTATCGATACATGACAAA
*
2741875 TTGTATCGATACATGATAAA
1 TTGTATCGATACATGACAAA
2741895 TTGTATCGATACAT
1 TTGTATCGATACAT
2741909 TGCTTCAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGACAAA
Found at i:2745188 original size:13 final size:13
Alignment explanation
Indices: 2745170--2745195 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2745160 CAATTTTTTG
2745170 TGTATCGATACAT
1 TGTATCGATACAT
2745183 TGTATCGATACAT
1 TGTATCGATACAT
2745196 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2745945 original size:21 final size:21
Alignment explanation
Indices: 2745904--2745947 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2745894 TTCCCTTTTA
* *
2745904 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
2745925 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
2745946 TC
1 TC
2745948 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:2747770 original size:13 final size:13
Alignment explanation
Indices: 2747752--2747777 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2747742 ATAATCACCC
2747752 TGTATCGATACAA
1 TGTATCGATACAA
2747765 TGTATCGATACAA
1 TGTATCGATACAA
2747778 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2749871 original size:15 final size:15
Alignment explanation
Indices: 2749851--2749881 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2749841 ATTTCGTTTG
*
2749851 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2749866 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2749881 G
1 G
2749882 GATATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2753982 original size:13 final size:13
Alignment explanation
Indices: 2753964--2753989 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2753954 CAATTTTTTG
2753964 TGTATCGATACAT
1 TGTATCGATACAT
2753977 TGTATCGATACAT
1 TGTATCGATACAT
2753990 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2758064 original size:20 final size:19
Alignment explanation
Indices: 2758019--2758073 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
2758009 TGTATCGATA
* **
2758019 CATTGTATCGATATATGTT
1 CATTGTATCGATACATACT
2758038 CATTGTATCGATACATACT
1 CATTGTATCGATACATACT
*
2758057 CAATTGTATCAATACAT
1 C-ATTGTATCGATACAT
2758074 GAAAGTGGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:2758126 original size:20 final size:20
Alignment explanation
Indices: 2758099--2758155 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2758089 TACCCTAAGT
*
2758099 GAAATGTATCGATACATG-G
1 GAAATGTATCGATACATGAA
*
2758118 GACAATGTATCGATATATGAA
1 GA-AATGTATCGATACATGAA
*
2758139 GAATTGTATCGATACAT
1 GAAATGTATCGATACAT
2758156 TATGCCCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.30
Consensus pattern (20 bp):
GAAATGTATCGATACATGAA
Found at i:2759068 original size:17 final size:19
Alignment explanation
Indices: 2759040--2759085 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
2759030 TCAAAGTTGA
2759040 AAAAAT-AAAAT-GCATGG
1 AAAAATGAAAATGGCATGG
*
2759057 -GAAATGAAAATGGCATGG
1 AAAAATGAAAATGGCATGG
2759075 AAAAATGAAAA
1 AAAAATGAAAA
2759086 AAATAATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.17
17 5 0.21
18 6 0.25
19 9 0.38
ACGTcount: A:0.59, C:0.04, G:0.22, T:0.15
Consensus pattern (19 bp):
AAAAATGAAAATGGCATGG
Found at i:2761067 original size:150 final size:150
Alignment explanation
Indices: 2760801--2761072 Score: 338
Period size: 150 Copynumber: 1.8 Consensus size: 150
2760791 ATCAAACACT
*
2760801 TCTAAGTTGATGGTAAACCTTAGGAATATTTTAGTATTTTTCCCAAAACCTAATCCTATAAAACT
1 TCTAAGTTGATGGTAAACCTTAGGAATATTTTAGCATTTTTCCCAAAACCTAATCCTATAAAACT
* * * *
2760866 ACCAAGTCGGCTTCCATACCTAAGGTATGAATTAGGAGTGGGTTTCTTTTTTTCTTTTCCAAGTC
66 ACCAAGTCGGCTTCCATACCTAAGGTACGAATTAGGAGTAGGTTTCGTTTTTCCTTTTCCAAGTC
2760931 CTTTAGGATCACCGGCCACC
131 CTTTAGGATCACCGGCCACC
* * * *
2760951 TCTAAGTTGATGG-AAGACCTTAGGGACTTTTTTAGCATTTTTCCCCAAAACCTAGTCTTATAAA
1 TCTAAGTTGATGGTAA-ACCTTA-GGAATATTTTAGCATTTTT-CCCAAAACCTAATCCTATAAA
* * * * *
2761015 ACTATCAAGTC-GCTT-C-TACGTCGAGGTACGTATTAGG-GATAGGTTTGGTTTTTCCTTT
63 ACTACCAAGTCGGCTTCCATACCT-AAGGTACGAATTAGGAG-TAGGTTTCGTTTTTCCTTT
2761073 ATTTTCCAAT
Statistics
Matches: 103, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
149 7 0.07
150 47 0.46
151 20 0.19
152 29 0.28
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (150 bp):
TCTAAGTTGATGGTAAACCTTAGGAATATTTTAGCATTTTTCCCAAAACCTAATCCTATAAAACT
ACCAAGTCGGCTTCCATACCTAAGGTACGAATTAGGAGTAGGTTTCGTTTTTCCTTTTCCAAGTC
CTTTAGGATCACCGGCCACC
Found at i:2761457 original size:108 final size:109
Alignment explanation
Indices: 2761308--2761523 Score: 274
Period size: 108 Copynumber: 2.0 Consensus size: 109
2761298 TGGTTTTTAA
* *
2761308 AAAAATAAAAACCTTTCACATTCTTCTGATATTCTAGTAGGGTGCAAAAGACATTTTGACTTCTA
1 AAAAATAAAAACCTTTCACATTCTTCTGATATTCCAATAGGGTGCAAAAGACATTTTGACTTCTA
* * * * *
2761373 AAACCTTTTCTTTTCCTCTGGTTGTCTA-GAAGGATATGGAAAGG
66 AAACCTCTTATGTTCCTCGGGTTGT-TAGGAAGGACATGGAAAGG
* * * * * * *
2761417 AAAAA-AAAAACCTTTCGCATTCTTTTGGTATTCCAATAGGGTGCGAAAGGCATTTTTATTTCTA
1 AAAAATAAAAACCTTTCACATTCTTCTGATATTCCAATAGGGTGCAAAAGACATTTTGACTTCTA
*
2761481 AAACCTCTTATGTTCCTCGGGTTGTTAGGAGGGACATGGAAAG
66 AAACCTCTTATGTTCCTCGGGTTGTTAGGAAGGACATGGAAAG
2761524 AATGATCAAA
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
107 2 0.02
108 84 0.92
109 5 0.05
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (109 bp):
AAAAATAAAAACCTTTCACATTCTTCTGATATTCCAATAGGGTGCAAAAGACATTTTGACTTCTA
AAACCTCTTATGTTCCTCGGGTTGTTAGGAAGGACATGGAAAGG
Found at i:2766548 original size:78 final size:79
Alignment explanation
Indices: 2766393--2766572 Score: 238
Period size: 78 Copynumber: 2.3 Consensus size: 79
2766383 TTTTGGAGAT
* * *
2766393 AATAATGGGGTTGGAGTATCCCCATTTGTGAAAAATCGATGATTAGGAAATAAAATCGGGATTGG
1 AATAATGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTAGGAAATAAAATCGGGATTGG
2766458 AGTATCCCCTCGGA
66 AGTATCCCCTCGGA
* * * * *
2766472 AATAATGGGGTTGGAGTAACCCCAATTATGAGAAATCAAT-ATTTTGG-AATAAAGTCGGGGTTG
1 AATAATGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGA-TTAGGAAATAAAATCGGGATTG
2766535 GAGTATCCCCTCGGA
65 GAGTATCCCCTCGGA
** *
2766550 GGTAACGGGGTTGGAGTATCCCC
1 AATAATGGGGTTGGAGTATCCCC
2766573 GATGAAATAA
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
78 49 0.56
79 39 0.44
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (79 bp):
AATAATGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTAGGAAATAAAATCGGGATTGG
AGTATCCCCTCGGA
Found at i:2766583 original size:28 final size:28
Alignment explanation
Indices: 2766527--2766603 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
2766517 GGAATAAAGT
*** **
2766527 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
2766555 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
2766583 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
2766604 TGTGAAATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2766736 original size:51 final size:50
Alignment explanation
Indices: 2766586--2766806 Score: 253
Period size: 51 Copynumber: 4.3 Consensus size: 50
2766576 GAAATAACGA
* * * *
2766586 GGTTGGAGTATCCTCGATTGTGAAATATTGGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAA-ATTAGTG-TTTTGGAAATAAAACCGG
* * * * * *
2766638 AGTTGAAGTATCCCCGATTAAAGCAAAATTGGTGTTTTGAAAATAAAACCAG
1 GGTTGGAGTATCCCCGATT-ATG-AAAATTAGTGTTTTGGAAATAAAACCGG
* *
2766690 GGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTGGAAATAAAACCGG
* * *
2766741 GGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGA-AAATTAGTGTTTTGGAAATAAAACCGG
2766792 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
2766807 TCGGAGTTAA
Statistics
Matches: 144, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
50 2 0.01
51 82 0.57
52 49 0.34
53 8 0.06
54 3 0.02
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:2766845 original size:28 final size:28
Alignment explanation
Indices: 2766789--2766865 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
2766779 GAAATAAAAC
*** **
2766789 CGGGGTTGGAGTATCCCCTCGGAGTTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
2766817 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* * *
2766845 CGTGATTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
2766866 TGTGAAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.26
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2769299 original size:13 final size:13
Alignment explanation
Indices: 2769281--2769340 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
2769271 ACAAAGATCG
2769281 ATGTATCGATACA
1 ATGTATCGATACA
2769294 ATGTATCGATAC-
1 ATGTATCGATACA
* *
2769306 AT-T-TC-CT-TA
1 ATGTATCGATACA
2769315 ATGTATCGATACA
1 ATGTATCGATACA
2769328 ATGTATCGATACA
1 ATGTATCGATACA
2769341 TTTCCTTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
9 3 0.08
10 3 0.08
11 3 0.08
12 3 0.08
13 26 0.68
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2769324 original size:34 final size:34
Alignment explanation
Indices: 2769281--2769361 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
2769271 ACAAAGATCG
2769281 ATGTATCGATACAATGTATCGATACATTTCCTTA
1 ATGTATCGATACAATGTATCGATACATTTCCTTA
2769315 ATGTATCGATACAATGTATCGATACATTTCCTTA
1 ATGTATCGATACAATGTATCGATACATTTCCTTA
2769349 ATGTATCGATACA
1 ATGTATCGATACA
2769362 TTTCCTTGGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.37
Consensus pattern (34 bp):
ATGTATCGATACAATGTATCGATACATTTCCTTA
Found at i:2769353 original size:21 final size:21
Alignment explanation
Indices: 2769327--2769368 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2769317 GTATCGATAC
2769327 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
2769348 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
2769369 GGCAGAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:2771310 original size:55 final size:55
Alignment explanation
Indices: 2771217--2771557 Score: 393
Period size: 55 Copynumber: 6.0 Consensus size: 55
2771207 GACGCCTTTT
* *
2771217 CCTTTCGAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG
* *
2771272 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAGGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * *
2771327 CCTTTTAAAGCCCACACCAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * * *
2771382 CCTTTGAAAGCCCACACAAGTTGGTGGCATTTTCTAATCCTCAAAGAGCA-GATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
** *
2771436 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTTAAAGAGCAGGACG
1 C-----C-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
*
2771496 CCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACG
1 CCTT-TC-----AAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGACG
2771557 C
1 C
2771558 TCTCTCCTTT
Statistics
Matches: 251, Mismatches: 19, Indels: 26
0.85 0.06 0.09
Matches are distributed among these distances:
54 10 0.04
55 148 0.59
59 17 0.07
60 56 0.22
61 20 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
Found at i:2771670 original size:55 final size:55
Alignment explanation
Indices: 2771576--2772027 Score: 572
Period size: 55 Copynumber: 8.0 Consensus size: 55
2771566 TTTGCCTTTT
*
2771576 CCTTTCAAAGCCCACACAAGTCGGTGGCACCTTTT--AGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA--TTTTCCAGTCCTCAAAGAGCAGGACG
* *
2771631 CCTTTCAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * * *
2771686 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTTAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * *
2771741 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAAGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
2771796 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
1 C-----C-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * * * *
2771857 CCTTTTAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCTTAAGGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
**
2771912 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
2771966 CCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTT--AGTCCTCAAAGAGCAGGACG
1 CCTT-T-C----AAAGCCCACACAAGTTGGTGGCA-TT-TTCCAGTCCTCAAAGAGCAGGACG
2772027 C
1 C
2772028 ACTCTCCTTT
Statistics
Matches: 352, Mismatches: 29, Indels: 26
0.86 0.07 0.06
Matches are distributed among these distances:
53 4 0.01
54 22 0.06
55 226 0.64
56 2 0.01
60 24 0.07
61 72 0.20
62 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
Found at i:2771672 original size:129 final size:130
Alignment explanation
Indices: 2771438--2771683 Score: 363
Period size: 129 Copynumber: 1.9 Consensus size: 130
2771428 AGCAGATGCT
* * *
2771438 TTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTTAAAGAGCAGGACGCCTTCTC
1 TTTTCCTTTCAAAGCCCACACAAGTCGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTC
2771503 TTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTT
66 ----TAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTT
2771568 TGCC
127 TGCC
*
2771572 TTTTCCTTTCAAAGCCCACACAAGTCGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTT-T
1 TTTTCCTTTCAAAGCCCACACAAGTCGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGCCTTCT
* *
2771636 C-AAAGCCCACATAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGA
65 CTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGA
2771684 TGCCTTTTAA
Statistics
Matches: 104, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
129 40 0.38
130 4 0.04
134 35 0.34
135 25 0.24
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (130 bp):
TTTTCCTTTCAAAGCCCACACAAGTCGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTC
TAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTTGCC
Found at i:2771853 original size:171 final size:170
Alignment explanation
Indices: 2771576--2772246 Score: 773
Period size: 171 Copynumber: 4.0 Consensus size: 170
2771566 TTTGCCTTTT
* *
2771576 CCTTTCAAAGCCCACACAAGTCGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTT-T-C--
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTT
* *
2771637 --AAAGCCCACATAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCC
65 TTAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCC
* *
2771699 ACACAAGTTGGTGGCATTTTTCAGTCCTTAAAGAGCAGGATG
129 ACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATG
** * * * *
2771741 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAAGATG-CTTTTTCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGACGCCTTCTCCTT
2771805 TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCC
65 TT-AAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCC
* * *
2771869 CACACAAGTTAGTGGCATTTTCCAGTCCTTAAGGAGCAGGATG
128 CACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATG
2771912 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
* *
2771977 TAAAGCCCACACAAGTTGGTGGCACTTCTT-AGTCCTCAAAGAGCAGGACG-C------A-CTCT
66 TAAAGCCCACACAAGTTGGTGGCACTT-TTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCA
* * * *
2772033 C-C---TT--TCGCCTTTT--TGTCATCAAAGAGCAGGATG
130 CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATG
* ** *
2772066 CCTTTTAAAGCCCACACAAGCGGGTGGCACCTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
* * *
2772131 TAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTGAAAGGGCAGGATGCTTTCTTTTTGCAAA
66 TAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGC---C-TTTT--AAA
** *
2772196 GCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGGGCAGGATG
125 GCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATG
2772242 CCTTT
1 CCTTT
2772247 TCTTTTCAAA
Statistics
Matches: 431, Mismatches: 41, Indels: 57
0.81 0.08 0.11
Matches are distributed among these distances:
153 2 0.00
154 121 0.28
156 7 0.02
158 3 0.01
161 1 0.00
162 3 0.01
163 1 0.00
164 5 0.01
165 47 0.11
166 1 0.00
167 1 0.00
168 3 0.01
169 2 0.00
170 61 0.14
171 142 0.33
172 4 0.01
174 5 0.01
176 22 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (170 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
TAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCAC
ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATG
Found at i:2772203 original size:61 final size:61
Alignment explanation
Indices: 2772068--2772294 Score: 266
Period size: 61 Copynumber: 3.7 Consensus size: 61
2772058 GCAGGATGCC
** * * * * *
2772068 TTTT-AAAGCCCACACAAGCGGGTGGCAC-CTTCAGTCCTCAAAGAGTAGGACGCCTTCTCC
1 TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGGGCAGGATGCCTT-TCT
*
2772128 TTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTGAAAGGGCAGGATG-CTTTCT
1 TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGGGCAGGATGCCTTTCT
* *
2772187 TTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGGGCAGGATGCCTTT-T
1 TTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGGGCAGGATGCCTTTCT
* * *
2772248 CTTTTCAAAGCCGACACGAGTTGGTGGCACTTTTTCAGTCCTTAAAG
1 -TTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTTCAGTCCTCAAAG
2772295 AGTAGGACAC
Statistics
Matches: 145, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
59 6 0.04
60 29 0.20
61 89 0.61
62 21 0.14
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.27
Consensus pattern (61 bp):
TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGGGCAGGATGCCTTTCT
Found at i:2772228 original size:215 final size:209
Alignment explanation
Indices: 2771842--2772239 Score: 525
Period size: 215 Copynumber: 1.9 Consensus size: 209
2771832 TTTCCAGTCC
** ** * *
2771842 TCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCTTAAGGAGCA
1 TCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGCGAGTGGCACCTTCCAGTCCTCAAAGAGCA
*
2771907 GGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCT
66 GGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCT
*
2771972 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAGCAGGACGCACTCTCCTT
131 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGACGCACTCTCCTT
2772037 TCGCCTTTTTGTCA
196 TCGCCTTTTTGTCA
* * *
2772051 TCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCGGGTGGCACCTT-CAGTCCTCAAAGAGTA
1 TCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGCGAGTGGCACCTTCCAGTCCTCAAAGAGCA
* * * *
2772115 GGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTGAAAGGGCAGGAT
66 GGACGCCTT-T-C----AAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGAC
* *
2772180 G-CTT-TCTTTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC-CAGTCCTCAAAGGGCAGGA
124 GCCTTCTCCTTTT--AAAGCCCACACAAGTTGGTGGCA-CTTCTCAGTCCTCAAAGAGCAGGA
2772240 TGCCTTTTCT
Statistics
Matches: 162, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
208 21 0.13
209 43 0.27
210 1 0.01
213 6 0.04
214 27 0.17
215 60 0.37
216 4 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (209 bp):
TCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGCGAGTGGCACCTTCCAGTCCTCAAAGAGCA
GGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCT
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGACGCACTCTCCTT
TCGCCTTTTTGTCA
Found at i:2772340 original size:45 final size:42
Alignment explanation
Indices: 2772285--2772389 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 42
2772275 CACTTTTTCA
* * * *
2772285 GTCCTTAAAGAGTAGGACACACTTCCTTCCCTTCTTTTCTCTTTT
1 GTCCTCAAAGAGCAGGACACACTTCATT--CTCCTTTT-TCTTTT
* *
2772330 GTCCTCAAAGAGCAGGACGCACTTTATTCTCCTTTTTCTTTT
1 GTCCTCAAAGAGCAGGACACACTTCATTCTCCTTTTTCTTTT
2772372 GTCCTCAAAGAGCAGGAC
1 GTCCTCAAAGAGCAGGAC
2772390 GTATTTCGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
42 24 0.44
43 7 0.13
45 23 0.43
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACACACTTCATTCTCCTTTTTCTTTT
Found at i:2773191 original size:24 final size:22
Alignment explanation
Indices: 2773159--2773214 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 22
2773149 TTTCAATAAT
2773159 TTGTATCGATACAAACAGTAAGTG
1 TTGTATCGATAC-AACA-TAAGTG
2773183 TTGTATCGAT---ACATAAGTG
1 TTGTATCGATACAACATAAGTG
2773202 TTGTATCGATACA
1 TTGTATCGATACA
2773215 TTGTATCGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 16 0.55
20 3 0.10
24 10 0.34
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (22 bp):
TTGTATCGATACAACATAAGTG
Found at i:2773201 original size:19 final size:19
Alignment explanation
Indices: 2773177--2773215 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2773167 ATACAAACAG
2773177 TAAGTGTTGTATCGATACA
1 TAAGTGTTGTATCGATACA
2773196 TAAGTGTTGTATCGATACA
1 TAAGTGTTGTATCGATACA
2773215 T
1 T
2773216 TGTATCGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (19 bp):
TAAGTGTTGTATCGATACA
Found at i:2773284 original size:13 final size:13
Alignment explanation
Indices: 2773266--2773291 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2773256 CATTATTAAA
2773266 TGTATCGATACAT
1 TGTATCGATACAT
2773279 TGTATCGATACAT
1 TGTATCGATACAT
2773292 CGATCTTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2773355 original size:20 final size:20
Alignment explanation
Indices: 2773330--2773403 Score: 123
Period size: 20 Copynumber: 3.7 Consensus size: 20
2773320 TTTACCCAGA
*
2773330 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
2773350 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
2773370 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
2773390 TGTATCGATACATT
1 TGTATCGATACATT
2773404 TTATAATGTA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
20 51 0.98
21 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:2773413 original size:20 final size:19
Alignment explanation
Indices: 2773330--2773424 Score: 120
Period size: 20 Copynumber: 4.8 Consensus size: 19
2773320 TTTACCCAGA
*
2773330 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTCT-CAT
2773350 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-CTCAT
2773370 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-CTCAT
*
2773390 TGTATCGATACATT-TTAT
1 TGTATCGATACATTCTCAT
2773408 AATGTATCGATACATTC
1 --TGTATCGATACATTC
2773425 AGGCATTTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
18 3 0.04
20 65 0.94
21 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTCTCAT
Found at i:2775796 original size:51 final size:51
Alignment explanation
Indices: 2775721--2775884 Score: 163
Period size: 51 Copynumber: 3.2 Consensus size: 51
2775711 TAATCTCAGG
* * * *
2775721 GATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAA-TTTCTCTTAATCGGA
1 GATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTTTC-CATAATCGGA
* * * *
2775772 GATACTCCAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAATTGGG
1 GATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAATCGGA
* * * * *
2775823 GATACTCCAACTCTGATTTTATTTCCAAAGCACCGACTTTT-CATAATTGGG
1 GATACTCCAACTCCGATTTTATTTCCAAAACACC-AATTTTCCATAATCGGA
2775874 GATACTCCAAC
1 GATACTCCAAC
2775885 CCCATTATTT
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
51 88 0.91
52 9 0.09
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (51 bp):
GATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAATCGGA
Found at i:2775954 original size:79 final size:79
Alignment explanation
Indices: 2775860--2776117 Score: 374
Period size: 79 Copynumber: 3.3 Consensus size: 79
2775850 AAGCACCGAC
* * * *
2775860 TTTTCATAATTGGGGATACTCCAACCCCATTATTTCTGAGGGGACACTCCAACCCCAGTTTTATT
1 TTTTCATAATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATT
*
2775925 TCTAAAATATTAAT
66 TCTAAAATATCAAT
* * * *
2775939 TTCTCATAATCGGGGATACTCTAACCCCGTTATTTCCGAGGGGATACTCCAGCCCCGGTTTTATT
1 TTTTCATAATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATT
*
2776004 TCTAAAACATCAAT
66 TCTAAAATATCAAT
* *
2776018 TTTTCATAATCGGGGATGCTCCAACCCCGTTATTT-TCGAGGGGATACTCCAACCCCGGCTTTAT
1 TTTTCATAATCGGGGATACTCCAACCCCGTTATTTCT-GAGGGGATACTCCAACCCCGGTTTTAT
*
2776082 TTCTAAAATACCAAT
65 TTCTAAAATATCAAT
*
2776097 TTTTCACAATCGGGGATACTC
1 TTTTCATAATCGGGGATACTC
2776118 TAACTCCGAT
Statistics
Matches: 158, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
79 158 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (79 bp):
TTTTCATAATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATT
TCTAAAATATCAAT
Found at i:2776146 original size:51 final size:51
Alignment explanation
Indices: 2776057--2776306 Score: 223
Period size: 51 Copynumber: 4.9 Consensus size: 51
2776047 TTATTTTCGA
* * *
2776057 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATACCAATTTTTCACAATC
1 GGGGATACTCTAACCCCGACTTTATTTCTAAAACACCAATTTTTCACAATC
* * * * *
2776108 GGGGATACTCTAACTCCGATTTTAGTTCCAAAACACCAATTTCTCACAATC
1 GGGGATACTCTAACCCCGACTTTATTTCTAAAACACCAATTTTTCACAATC
* * * * * *
2776159 GGGGATACTCCAACCCCGGCCTTATTTCTAAAGCATCAATTTTTTCATAATC
1 GGGGATACTCTAACCCCGACTTTATTTCTAAAACACCAA-TTTTTCACAATC
* * * * * * * *
2776211 GAGGATGCTCTAACCCCGATTTTATTTTTTAGAACACCGATTTTCCATAATC
1 GGGGATACTCTAACCCCGACTTTA-TTTCTAAAACACCAATTTTTCACAATC
* * * * *
2776263 GGGGATACTCTAGCCCCG-TTGTTATCTCTAAAATACTAATTTTT
1 GGGGATACTCTAACCCCGACT-TTATTTCTAAAACACCAATTTTT
2776307 TTCGTCGGGA
Statistics
Matches: 155, Mismatches: 41, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
51 88 0.57
52 57 0.37
53 10 0.06
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (51 bp):
GGGGATACTCTAACCCCGACTTTATTTCTAAAACACCAATTTTTCACAATC
Found at i:2776304 original size:104 final size:102
Alignment explanation
Indices: 2776057--2776307 Score: 274
Period size: 104 Copynumber: 2.4 Consensus size: 102
2776047 TTATTTTCGA
* *
2776057 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATACCAA-TTTTTCACAATCGGGGATACTCTAA
1 GGGGATACTCCAACCCCGGCCTTATTTCTAAAATA-CAATTTTTTCACAATCGAGGATACTCTAA
*
2776121 CTCCGATTTTAGTTCCAAAACACCAATTTCTCACAATC
65 CCCCGATTTTAGTTCCAAAACACCAATTTCTCACAATC
* *
2776159 GGGGATACTCCAACCCCGGCCTTATTTCTAAAGCAT-CAATTTTTTCATAATCGAGGATGCTCTA
1 GGGGATACTCCAACCCCGGCCTTATTTCTAAA--ATACAATTTTTTCACAATCGAGGATACTCTA
* ** * * *
2776223 ACCCCGATTTTATTTTTTAGAACACCGATTT-TCCATAATC
64 ACCCCGATTTTA-GTTCCAAAACACCAATTTCT-CACAATC
* * *** *
2776263 GGGGATACTCTAGCCCCGTTGTTATCTCTAAAATACTAATTTTTT
1 GGGGATACTCCAACCCCGGCCTTATTTCTAAAATAC-AATTTTTT
2776308 TCGTCGGGAG
Statistics
Matches: 125, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
102 36 0.29
103 34 0.27
104 55 0.44
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (102 bp):
GGGGATACTCCAACCCCGGCCTTATTTCTAAAATACAATTTTTTCACAATCGAGGATACTCTAAC
CCCGATTTTAGTTCCAAAACACCAATTTCTCACAATC
Found at i:2779832 original size:52 final size:52
Alignment explanation
Indices: 2779747--2779871 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
2779737 ATATGAAAAG
* * *
2779747 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATTTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
2779799 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
2779851 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
2779872 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:2779884 original size:52 final size:51
Alignment explanation
Indices: 2779747--2779891 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
2779737 ATATGAAAAG
* *
2779747 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATTTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
2779799 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
2779851 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2779892 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:2779898 original size:13 final size:13
Alignment explanation
Indices: 2779880--2779904 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2779870 CAAAGATCAG
2779880 TGTATCGATACAA
1 TGTATCGATACAA
2779893 TGTATCGATACA
1 TGTATCGATACA
2779905 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2779982 original size:33 final size:33
Alignment explanation
Indices: 2779945--2780011 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2779935 AGTAGCTTAA
2779945 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2779978 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2780011 A
1 A
2780012 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2779985 original size:13 final size:13
Alignment explanation
Indices: 2779967--2779991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2779957 CAAAAAAATA
2779967 TGTATCGATACAT
1 TGTATCGATACAT
2779980 TGTATCGATACA
1 TGTATCGATACA
2779992 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2782165 original size:19 final size:19
Alignment explanation
Indices: 2782121--2782176 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
2782111 CTGCCAGTTT
**
2782121 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
*
2782141 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
*
2782160 CATGTATCGATATAATG
1 CATGTATCGATACAATG
2782177 TATCGATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:2787240 original size:165 final size:165
Alignment explanation
Indices: 2786975--2788507 Score: 888
Period size: 165 Copynumber: 9.1 Consensus size: 165
2786965 TCAAACATCC
* * * * * * * *
2786975 AAATTCGTCAAGTATTATCATTTATTTTATATTAAATCAGTTTTTAAAAATTAATTCATTTTCAA
1 AAATTCATCAAATATCATTATTTAATTCATATTAAATCAGTTTTCAAAAATTAATTCATTTTCAT
* * * ***
2787040 GA-TTTTTTCATTTTTCCTTGAAATTCTCCTTTTTTCGAAATAATTTGTTTTCTACTTCGTAAAT
66 GAGTTTTGT-ATTTTTTCTTGAAA-TCTCTTTTTTTCGAAATAAGGAGTTTTCTACTTCGTAAAT
* * *
2787104 TTTTTTAGGGTGATTTTTCTTAG-TTTCTAATTTTTA
129 TTTTTCAGGGGGATTTTTCTTAGATTTTTAATTTTTA
* * *
2787140 AAATTCATCAAATATCA-TATTTAATTCATCTTTAAATTA-TTTTGCAAAAATTAATCCATTTTC
1 AAATTCATCAAATATCATTATTTAATTCAT-ATTAAATCAGTTTT-CAAAAATTAATTCATTTTC
* * *
2787203 ATGAGTTTTTGTTTTTTTTCTTGAAATCTCTTTTTTTCGAAATACGGA-TTCTTCTACTACGTAA
64 ATGAG-TTTTGTATTTTTTCTTGAAATCTCTTTTTTTCGAAATAAGGAGTT-TTCTACTTCGTAA
* * * * *
2787267 ATTTTTTCAAGGGAATCTTT-TTCGTTTTTTAATTTTTA
127 ATTTTTTCAGGGGGATTTTTCTTAGATTTTTAATTTTTA
* * * * *
2787305 AAATTCATCAAATATTATTATTTAATTCATATTAAATTAGTTCTCAAAAATTTATTTATTTTCAT
1 AAATTCATCAAATATCATTATTTAATTCATATTAAATCAGTTTTCAAAAATTAATTCATTTTCAT
* * * * * * *
2787370 AAAGTTTTGAATTTTTTCTTTGAAAT-TCTCTTTTTCTAAAATACGGTA-TTTTCTACTCCGTTA
66 -GAGTTTTGTATTTTTTC-TTGAAATCTCTTTTTTTC-GAAATAAGG-AGTTTTCTACTTCGTAA
* * *
2787433 ATATTTTCAAGGAGG-TTTTTCTTA-A--TTTCATTTTTCA
127 ATTTTTTC-AGGGGGATTTTTCTTAGATTTTTAATTTTT-A
* * * * * * *
2787470 AAATTCATCAAACATAATTATTTAATTTATATTAAATCACTTTACAAAAATTCATCCATTTTTTC
1 AAATTCATCAAATATCATTATTTAATTCATATTAAATCAGTTTTCAAAAATTAATTCA--TTTTC
* * * *
2787535 ATGAGTTTTCT-TGTTTTTCCTTGAAAT-T-TTTCCGTTTCTGAAAT-ACGAGGTTTTCTACTTT
64 ATGAGTTTTGTAT-TTTTT-CTTGAAATCTCTTT--TTTTC-GAAATAAGGA-GTTTTCTACTTC
* * *
2787596 GTAAACGTAGTCTTCTACTTCATAAATATTTTTGGGGGGATCTTTC-TCGATTTTTAATGTTTA
123 GT-AA---A-T-TT-T--TTC------A------GGGGGATTTTTCTTAGATTTTTAATTTTTA
* * * * *
2787659 AAATTCATCAAATATTATTATTTAATTGATATTAAATTAGTTCTCAAAAATTTATTCATTTTCAT
1 AAATTCATCAAATATCATTATTTAATTCATATTAAATCAGTTTTCAAAAATTAATTCATTTTCAT
* * * * *
2787724 AAAGTTTTGAATTTTTTTCCTTGAAAT-TCTTTTTTTCTAAAATACAGTA-TTTTCTAAC-CCGT
66 -GAGTTTTGTA-TTTTTT-CTTGAAATCTCTTTTTTTC-GAAATA-AGGAGTTTTCT-ACTTCGT
* ** * *
2787786 TAATTTTTTCTTGGAGATTTTTCTT-GA-TTTCAATTTTTA
125 AAATTTTTTCAGGGGGATTTTTCTTAGATTTTTAATTTTTA
* * * * * *
2787825 AAATTCATCAAATATAATTATTTAATTTATATTAAATCAATTTACAAAAATTCATCCATTTTCAT
1 AAATTCATCAAATATCATTATTTAATTCATATTAAATCAGTTTTCAAAAATTAATTCATTTTCAT
* ** * * *
2787890 GA-CTTTCCATTTTTTTCTTGAAATTCTCTTGTTTTT-GAAATACGGAGTTTTTTACTTTGTAAA
66 GAGTTTTGTA-TTTTTTCTTGAAA-TCTCTT-TTTTTCGAAATAAGGAGTTTTCTACTTCGTAAA
* * *
2787953 TTTTTTCAGGGTGATTTTTCTTGGTTTTTTAA-TTTTA
128 TTTTTTCAGGGGGATTTTTCTTAGATTTTTAATTTTTA
** * * * *
2787990 AAATTCATCAAATATCACCATTTAACTCATATCATATCAGTTTT-AAGAAATTCATTCATTTTCA
1 AAATTCATCAAATATCATTATTTAATTCATATTAAATCAGTTTTCAA-AAATTAATTCATTTTCA
* * * * * * * * * * * *
2788054 TAACTTTTGGAGTTTTTCTTTGAAAGGC-CCTTTTTCCCAAAAAATCGAGTTTTCTATTTCATAA
65 TGAGTTTTGTATTTTTTC-TTGAAA-TCTCTTTTTTTCGAAATAA-GGAGTTTTCTACTTCGTAA
* *
2788118 ATTTTTTCGGGGGGATTTTTCTTAG-TTTTTTATTTTTA
127 ATTTTTTCAGGGGGATTTTTCTTAGATTTTTAATTTTTA
* * * * * * *
2788156 AAATTTATAAAATATCATCATTTAACTT-ATATTAAATTATTTTTAAAAAATTAATTCATTTTTA
1 AAATTCATCAAATATCATTATTTAA-TTCATATTAAATCAGTTTTCAAAAATTAATTCATTTTCA
* * * ** * * * * * *
2788220 TAAATTTTGGATTTTTTCTTTGAAATGC-CCCTTTTCCCAAAAAACTGAGTTTTCTATTTCATAA
65 TGAGTTTTGTATTTTTTC-TTGAAAT-CTCTTTTTTTCGAAATAA-GGAGTTTTCTACTTCGTAA
*** *
2788284 A-TTTTGGGGGGGGATTTTTCTT-GGTTTTGT-ATTTTTA
127 ATTTTTTCAGGGGGATTTTTCTTAGATTTT-TAATTTTTA
* * * * * ** *
2788321 AAATTCATAAAATATCATCATTTAACTCATATTAAATCATTTTTGAAATTTTAATTCAATTTCAT
1 AAATTCATCAAATATCATTATTTAATTCATATTAAATCAGTTTTCAAAAATTAATTCATTTTCAT
* * * ** * * *
2788386 GAGTTTTGGATTTTTTCTTTGAAATCCCTTGTTTTCGAAA-AACCAAGTTTTCTTCTTTGTATA-
66 GAGTTTTGTATTTTTTC-TTGAAATCTCTTTTTTTCGAAATAA-GGAGTTTTCTACTTCGTAAAT
* * * **
2788449 TATTTCTGGAGAGATTTTTCTT-GATTTAAAATTTTTA
129 TTTTTCAGG-GGGATTTTTCTTAGATTTTTAATTTTTA
* *
2788486 AAATTCATCTAATATTATTATT
1 AAATTCATCAAATATCATTATT
2788508 AAACTCCCAT
Statistics
Matches: 1083, Mismatches: 208, Indels: 154
0.75 0.14 0.11
Matches are distributed among these distances:
163 11 0.01
164 102 0.09
165 451 0.42
166 323 0.30
167 55 0.05
168 2 0.00
171 1 0.00
172 1 0.00
173 1 0.00
174 1 0.00
176 3 0.00
179 3 0.00
181 2 0.00
182 2 0.00
183 1 0.00
184 1 0.00
187 13 0.01
188 29 0.03
189 67 0.06
190 14 0.01
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.50
Consensus pattern (165 bp):
AAATTCATCAAATATCATTATTTAATTCATATTAAATCAGTTTTCAAAAATTAATTCATTTTCAT
GAGTTTTGTATTTTTTCTTGAAATCTCTTTTTTTCGAAATAAGGAGTTTTCTACTTCGTAAATTT
TTTCAGGGGGATTTTTCTTAGATTTTTAATTTTTA
Found at i:2788124 original size:166 final size:165
Alignment explanation
Indices: 2787949--2788409 Score: 631
Period size: 166 Copynumber: 2.8 Consensus size: 165
2787939 TTTTACTTTG
* * * * *
2787949 TAAATTTTTTCAGGGTGATTTTTCTTGGTTTTTTAATTTTAAAATTCATCAAATATCACCATTTA
1 TAAATTTTTTCGGGGGGATTTTTCTTGGTTTTTTATTTTTAAAATTCATAAAATATCATCATTTA
* * * * *
2788014 ACTCATATCATATCAGTTTTAAGAAATTCATTCATTTTCATAACTTTTGGAGTTTTTCTTTGAAA
66 ACTCATATTAAATCA-TTTTAAGAAATTAATTCATTTTCATAAATTTTGGATTTTTTCTTTGAAA
*
2788079 GGCCCTTTTTCCCAAAAAA-TCGAGTTTTCTATTTCA
130 GGCCCCTTTTCCCAAAAAACT-GAGTTTTCTATTTCA
* *
2788115 TAAATTTTTTCGGGGGGATTTTTCTTAGTTTTTTATTTTTAAAATTTATAAAATATCATCATTTA
1 TAAATTTTTTCGGGGGGATTTTTCTTGGTTTTTTATTTTTAAAATTCATAAAATATCATCATTTA
* * * *
2788180 ACTTATATTAAATTATTTTTAAAAAATTAATTCATTTTTATAAATTTTGGATTTTTTCTTTGAAA
66 ACTCATATTAAATCA-TTTTAAGAAATTAATTCATTTTCATAAATTTTGGATTTTTTCTTTGAAA
*
2788245 TGCCCCTTTTCCCAAAAAACTGAGTTTTCTATTTCA
130 GGCCCCTTTTCCCAAAAAACTGAGTTTTCTATTTCA
** *
2788281 TAAA-TTTTGGGGGGGGATTTTTCTTGGTTTTGTATTTTTAAAATTCATAAAATATCATCATTTA
1 TAAATTTTTTCGGGGGGATTTTTCTTGGTTTTTTATTTTTAAAATTCATAAAATATCATCATTTA
* * * *
2788345 ACTCATATTAAATCATTTT-TGAAATTTTAATTCAATTTCATGAGTTTTGGATTTTTTCTTTGAA
66 ACTCATATTAAATCATTTTAAGAAA--TTAATTCATTTTCATAAATTTTGGATTTTTTCTTTGAA
2788409 A
129 A
2788410 TCCCTTGTTT
Statistics
Matches: 260, Mismatches: 32, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
163 3 0.01
164 4 0.02
165 103 0.40
166 149 0.57
167 1 0.00
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (165 bp):
TAAATTTTTTCGGGGGGATTTTTCTTGGTTTTTTATTTTTAAAATTCATAAAATATCATCATTTA
ACTCATATTAAATCATTTTAAGAAATTAATTCATTTTCATAAATTTTGGATTTTTTCTTTGAAAG
GCCCCTTTTCCCAAAAAACTGAGTTTTCTATTTCA
Found at i:2790097 original size:13 final size:13
Alignment explanation
Indices: 2790078--2790142 Score: 112
Period size: 13 Copynumber: 5.0 Consensus size: 13
2790068 ACTATTTATG
2790078 ATGTATCGATACA
1 ATGTATCGATACA
*
2790091 CTGTATCGATACA
1 ATGTATCGATACA
2790104 ATGTATCGATACA
1 ATGTATCGATACA
*
2790117 CTGTATCGATACA
1 ATGTATCGATACA
2790130 ATGTATCGATACA
1 ATGTATCGATACA
2790143 TGAACAGTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2790114 original size:26 final size:26
Alignment explanation
Indices: 2790078--2790142 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
2790068 ACTATTTATG
2790078 ATGTATCGATACACTGTATCGATACA
1 ATGTATCGATACACTGTATCGATACA
2790104 ATGTATCGATACACTGTATCGATACA
1 ATGTATCGATACACTGTATCGATACA
2790130 ATGTATCGATACA
1 ATGTATCGATACA
2790143 TGAACAGTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (26 bp):
ATGTATCGATACACTGTATCGATACA
Found at i:2790161 original size:10 final size:10
Alignment explanation
Indices: 2790142--2790172 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2790132 GTATCGATAC
2790142 ATGAACAGTG
1 ATGAACAGTG
*
2790152 ATGAATAGTG
1 ATGAACAGTG
2790162 ATGAACAGTG
1 ATGAACAGTG
2790172 A
1 A
2790173 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:2790312 original size:20 final size:20
Alignment explanation
Indices: 2790249--2790319 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
2790239 GCCAATGTCC
**
2790249 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
2790269 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
2790289 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
2790309 TGTATCGATAC
1 TGTATCGATAC
2790320 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:2790385 original size:21 final size:21
Alignment explanation
Indices: 2790359--2790399 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2790349 GTCAACCTTG
2790359 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
2790380 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
2790400 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:2792292 original size:34 final size:35
Alignment explanation
Indices: 2792254--2792320 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2792244 CCTTACAACA
2792254 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
2792288 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2792321 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:2792796 original size:13 final size:13
Alignment explanation
Indices: 2792778--2792803 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2792768 CAATTTTTTG
2792778 TGTATCGATACAT
1 TGTATCGATACAT
2792791 TGTATCGATACAT
1 TGTATCGATACAT
2792804 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2792887 original size:20 final size:20
Alignment explanation
Indices: 2792842--2792935 Score: 107
Period size: 20 Copynumber: 4.6 Consensus size: 20
2792832 CTGCCAAGAA
* **
2792842 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGTAAC
*
2792863 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGTAAC
* **
2792883 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGTAAC
2792904 ATGTATCGATACATTGTAAC
1 ATGTATCGATACATTGTAAC
2792924 ATGTATCGATAC
1 ATGTATCGATAC
2792936 TTTGAATTGT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTGTAAC
Found at i:2792899 original size:41 final size:41
Alignment explanation
Indices: 2792842--2792935 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2792832 CTGCCAAGAA
2792842 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
*
2792883 ATGTATCGATACATCTTTTTCATGTATCGATACATTGTAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2792924 ATGTATCGATAC
1 ATGTATCGATAC
2792936 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2793812 original size:30 final size:31
Alignment explanation
Indices: 2793756--2793823 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
2793746 ATTCAACAAC
* *
2793756 TAATACCAAAAGTTTATGCAAGCTCTCCCCCT
1 TAATA-CAAAAGTTTATACAAACTCTCCCCCT
2793788 TAATACAAAA-TTTATACAAACTCTCCCCCT
1 TAATACAAAAGTTTATACAAACTCTCCCCCT
2793818 TAATAC
1 TAATAC
2793824 GTTGTCACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 24 0.71
31 5 0.15
32 5 0.15
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.29
Consensus pattern (31 bp):
TAATACAAAAGTTTATACAAACTCTCCCCCT
Found at i:2794655 original size:13 final size:13
Alignment explanation
Indices: 2794637--2794661 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2794627 ACTGAAGTAA
2794637 TGTATCGATACAT
1 TGTATCGATACAT
2794650 TGTATCGATACA
1 TGTATCGATACA
2794662 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2795269 original size:23 final size:24
Alignment explanation
Indices: 2795224--2795270 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
2795214 CAAAGAATTG
*
2795224 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
2795248 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
2795271 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:2797862 original size:32 final size:33
Alignment explanation
Indices: 2797823--2797887 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 33
2797813 CCTTACAACA
2797823 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCT
2797855 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2797888 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (33 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCT
Found at i:2798363 original size:13 final size:13
Alignment explanation
Indices: 2798345--2798370 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2798335 CAATTTTTTG
2798345 TGTATCGATACAT
1 TGTATCGATACAT
2798358 TGTATCGATACAT
1 TGTATCGATACAT
2798371 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2798435 original size:21 final size:21
Alignment explanation
Indices: 2798409--2798484 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
2798399 CTGCCAAGAA
2798409 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
2798430 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2798450 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2798471 ATGTATCGATACAT
1 ATGTATCGATACAT
2798485 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2798454 original size:20 final size:20
Alignment explanation
Indices: 2798429--2798502 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
2798419 ACATCTTTTT
2798429 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
2798449 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
2798470 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
2798490 CATGTATCGATAC
1 CATGTATCGATAC
2798503 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:2798466 original size:41 final size:41
Alignment explanation
Indices: 2798409--2798502 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
2798399 CTGCCAAGAA
2798409 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2798450 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2798491 ATGTATCGATAC
1 ATGTATCGATAC
2798503 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2802093 original size:34 final size:35
Alignment explanation
Indices: 2802055--2802121 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2802045 CCTTACAACA
2802055 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
2802089 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2802122 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:2802622 original size:10 final size:10
Alignment explanation
Indices: 2802603--2802633 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2802593 GTATCGATAC
2802603 ATGAACAGTG
1 ATGAACAGTG
*
2802613 ATGAATAGTG
1 ATGAACAGTG
2802623 ATGAACAGTG
1 ATGAACAGTG
2802633 A
1 A
2802634 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:2802731 original size:53 final size:53
Alignment explanation
Indices: 2802657--2802793 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
2802647 CTACTACCAA
*
2802657 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
2802710 TGTATCGATACGTATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
*
2802763 TGTATCGATATATATTTGTGTGTATCGATAC
1 TGTATCGATACATA-TTGTGTGTATCGATAC
2802794 TATGCAATCT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 62 0.79
54 16 0.21
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:2802826 original size:20 final size:20
Alignment explanation
Indices: 2802781--2802834 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2802771 TATATATTTG
*
2802781 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATGAAA
* *
2802801 TCTGTATCGATAC-ATTTAAA
1 TGTGTATCGATACTA-TGAAA
2802821 TGTGTATCGATACT
1 TGTGTATCGATACT
2802835 TTTCAGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTGTATCGATACTATGAAA
Found at i:2802899 original size:21 final size:21
Alignment explanation
Indices: 2802873--2802913 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2802863 GTCAACCTTG
2802873 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
2802894 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
2802914 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:2804769 original size:20 final size:19
Alignment explanation
Indices: 2804724--2804795 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
2804714 TACAATTGTG
* *
2804724 TATGTATTGATACAATGAA
1 TATGTATCGATACAAAGAA
*
2804743 TATGTATCGATACAAAGCA
1 TATGTATCGATACAAAGAA
** *
2804762 TGATGTATCGATACATCTGGA
1 T-ATGTATCGATACA-AAGAA
2804783 TATGTATCGATAC
1 TATGTATCGATAC
2804796 TTTCAAGGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 17 0.38
20 25 0.56
21 3 0.07
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (19 bp):
TATGTATCGATACAAAGAA
Found at i:2813705 original size:21 final size:21
Alignment explanation
Indices: 2813681--2813731 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
2813671 TTTTTACTTA
*
2813681 AAAACATTCTATTTA-AAGCTC-
1 AAAACATT-TATTCATAA-CTCT
2813702 AAAAGCATTTATTCATAACTCT
1 AAAA-CATTTATTCATAACTCT
2813724 AAAACATT
1 AAAACATT
2813732 AATTGATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAACATTTATTCATAACTCT
Found at i:2820689 original size:88 final size:87
Alignment explanation
Indices: 2820544--2821001 Score: 423
Period size: 88 Copynumber: 5.2 Consensus size: 87
2820534 AAAAAAGTAA
* *
2820544 CACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGGATGCC
1 CACTAAC-T-TGTGGGCTTTG-AAAG-GATGCCACCGACTTGTGTGGGCTTTGAAA-GGGATGCC
* *
2820609 ACTGACTTGTAGGCTTTAAAAGGGTGC
61 ACTGACTTGTGGGCTTTAAAAGGATGC
* * * *
2820636 CACTAACTTGTGAGCTTTGGAAAGG-TGCCACTGATTTGTGTGGGATTTGAAAGGGTATGCCACT
1 CACTAACTTGTGGGCTTT-GAAAGGATGCCACCGACTTGTGTGGGCTTTGAAAGGG-ATGCCACT
* * *
2820700 AACTTGTGGGCTTTGAAAGGGTGC
64 GACTTGTGGGCTTTAAAAGGATGC
** * * *
2820724 CACTAACTTGTGGGCTTTGAAAGGATGCCACAAAC-T-TGTGGTCTTTTGAAA-AGATGACACTG
1 CACTAACTTGTGGGCTTTGAAAGGATGCCACCGACTTGTGTGGGC-TTTGAAAGGGATGCCACTG
* *
2820786 ACTTGTGGGCTTTGGAAAGAGTTGC
65 ACTTGTGGGCTTT-AAAAG-GATGC
** * * *
2820811 CACCGACTTGTGTGGGCTTTGAAAGGGTGCCACCGA-GT-TATGGGCTTTGAAAGGG-TGCCACT
1 CACTAAC-T-TGTGGGCTTTGAAAGGATGCCACCGACTTGTGTGGGCTTTGAAAGGGATGCCACT
*
2820873 GACTTGTGGGCTTTTAAAGGATGC
64 GACTTGTGGGCTTTAAAAGGATGC
* * *** * *
2820897 CACTAACTTATGGGCTTTGAAAGGATACCATTAAC-T-TGTGAGCTTTGAAA-AGATGCCACTGA
1 CACTAACTTGTGGGCTTTGAAAGGATGCCACCGACTTGTGTGGGCTTTGAAAGGGATGCCACTGA
*
2820959 CTTGTGAGCTTTAAAAGGATGC
66 CTTGTGGGCTTTAAAAGGATGC
* * *
2820981 CACTGACCTGTGGGTTTTGAA
1 CACTAACTTGTGGGCTTTGAA
2821002 GAGATGAACG
Statistics
Matches: 308, Mismatches: 46, Indels: 32
0.80 0.12 0.08
Matches are distributed among these distances:
83 1 0.00
84 79 0.26
85 21 0.07
86 20 0.06
87 30 0.10
88 104 0.34
89 31 0.10
90 13 0.04
91 2 0.01
92 7 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (87 bp):
CACTAACTTGTGGGCTTTGAAAGGATGCCACCGACTTGTGTGGGCTTTGAAAGGGATGCCACTGA
CTTGTGGGCTTTAAAAGGATGC
Found at i:2820855 original size:145 final size:144
Alignment explanation
Indices: 2820586--2820964 Score: 444
Period size: 145 Copynumber: 2.6 Consensus size: 144
2820576 CACCGACTTG
* ** * * * *
2820586 TGTGGGCTTTAAAAGGGGATGCCACTGACTTGTAGGCTTT-AAAAGGGTGCCACTAACTTGTGAG
1 TGTGGGCTTTGAAA--GGATGCCACAAACTTATGGGCTTTGAAAA-GATACCACTAACTTGTGAG
* * *
2820650 CTTTGGAAAG-GTGCCACTGATTTGTGTGGGATTTGAAAGGGTATGCCACTAACTTGTGGGCTTT
63 CTTTGGAAAGAGTGCCACTGACTTGTGTGGGATTTGAAAGGG-ATGCCACCAACTTATGGGCTTT
2820714 GAAAGGGTGCCACTAACT
127 GAAAGGGTGCCACTAACT
* * * *
2820732 TGTGGGCTTTGAAAGGATGCCACAAACTTGTGGTCTTTTGAAAAGATGA-CACTGACTTGTGGGC
1 TGTGGGCTTTGAAAGGATGCCACAAACTTATGGGC-TTTGAAAAGAT-ACCACTAACTTGTGAGC
* * * *
2820796 TTTGGAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAGGG-TGCCACCGAGTTATGGGCTTTG
64 TTTGGAAAGAG-TGCCACTGACTTGTGTGGGATTTGAAAGGGATGCCACCAACTTATGGGCTTTG
*
2820860 AAAGGGTGCCACTGACT
128 AAAGGGTGCCACTAACT
* * * *
2820877 TGTGGGCTTTTAAAGGATGCCACTAACTTATGGGCTTTGAAAGGATACCATTAACTTGTGAGCTT
1 TGTGGGCTTTGAAAGGATGCCACAAACTTATGGGCTTTGAAAAGATACCACTAACTTGTGAGCTT
*
2820942 TGAAAAGA-TGCCACTGACTTGTG
66 TGGAAAGAGTGCCACTGACTTGTG
2820965 AGCTTTAAAA
Statistics
Matches: 200, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
142 14 0.07
143 1 0.00
144 48 0.24
145 92 0.46
146 18 0.09
147 27 0.14
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (144 bp):
TGTGGGCTTTGAAAGGATGCCACAAACTTATGGGCTTTGAAAAGATACCACTAACTTGTGAGCTT
TGGAAAGAGTGCCACTGACTTGTGTGGGATTTGAAAGGGATGCCACCAACTTATGGGCTTTGAAA
GGGTGCCACTAACT
Done.