Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 41 of 109
Found at i:13409687 original size:108 final size:109
Alignment explanation
Indices: 13409484--13409696 Score: 277
Period size: 108 Copynumber: 2.0 Consensus size: 109
13409474 ATATTATTAT
* * * *
13409484 TATAATATTAATAACCCTTTAAAATAAGATATTTTAGTAATTTTATAATTGAGTTGGTGTAGAGT
1 TATAATATTAATAACCCTTTAAAATAAGATA-TTTAGTAATTTCACAACTGAGTTGGTGTAGAAT
* * * * *
13409549 TGGCTCGTGACACCAACTCACTCAGCCATTT-TATTTATAAAATA
65 TGACTCATGACACCAACTCAATCAACCATTTATATATATAAAATA
* * *
13409593 TATAATATTTATTACCCTTTAAAATAAGAGTA-TTAGTAATTTCACAACTGAGTTGGTGTCGAAT
1 TATAATATTAATAACCCTTTAAAATAAGA-TATTTAGTAATTTCACAACTGAGTTGGTGTAGAAT
*
13409657 TGACTCATGACACCAACTCAATCAATCATTTATATATATA
65 TGACTCATGACACCAACTCAATCAACCATTTATATATATA
13409697 GTATAGATTA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
108 53 0.60
109 34 0.38
110 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (109 bp):
TATAATATTAATAACCCTTTAAAATAAGATATTTAGTAATTTCACAACTGAGTTGGTGTAGAATT
GACTCATGACACCAACTCAATCAACCATTTATATATATAAAATA
Found at i:13410371 original size:22 final size:22
Alignment explanation
Indices: 13410346--13410406 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
13410336 TATTTCTGCA
13410346 TTTCAACACTTACAA-TTTTAAC
1 TTTCAACACTTA-AATTTTTAAC
13410368 TTTCAACACTTAAATTTTTAAC
1 TTTCAACACTTAAATTTTTAAC
* *
13410390 TTTCCACACTAAAATTT
1 TTTCAACACTTAAATTT
13410407 CAAAATTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 2 0.06
22 34 0.94
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTCAACACTTAAATTTTTAAC
Found at i:13410621 original size:37 final size:37
Alignment explanation
Indices: 13410587--13410928 Score: 330
Period size: 37 Copynumber: 9.2 Consensus size: 37
13410577 CTATCATATA
* *
13410587 TTGAAACATGAGGACAAGTCCAGCGAATTGTCATAAC
1 TTGAAACATGAGGAAAAGTCCAGCGAACTGTCATAAC
* * * * *
13410624 TTGAAGCATGACGATAAGTCCAGCGGACTGCCATAAC
1 TTGAAACATGAGGAAAAGTCCAGCGAACTGTCATAAC
* * *
13410661 TTGAAACGTGA-GAATAAGTCCAACGAAATGTCATAAC
1 TTGAAACATGAGGAA-AAGTCCAGCGAACTGTCATAAC
* * * *
13410698 TTGAAACGTGAGGAAAAGTCTAGCGGATTGTCATAAC
1 TTGAAACATGAGGAAAAGTCCAGCGAACTGTCATAAC
* * * * * *
13410735 TTGAAGCATGACGATAAGTCCAGCGGACAGCCATAAC
1 TTGAAACATGAGGAAAAGTCCAGCGAACTGTCATAAC
* * * *
13410772 TTGAAACGTGAGGACAAGTCCAACGAAATGTCATAAC
1 TTGAAACATGAGGAAAAGTCCAGCGAACTGTCATAAC
* *
13410809 TTGAAACGTGAGGAAAAGTTCAGCGGAA-TGTCATAAC
1 TTGAAACATGAGGAAAAGTCCAGC-GAACTGTCATAAC
* * * **
13410846 TTGATACGAT-AGGACAAGTTCAGCGGGCTGTCATAAC
1 TTGAAAC-ATGAGGAAAAGTCCAGCGAACTGTCATAAC
* * *
13410883 TTGAAACATGAGGAAAAGTCCAGCAAACTATTATAAC
1 TTGAAACATGAGGAAAAGTCCAGCGAACTGTCATAAC
13410920 TTGAAACAT
1 TTGAAACAT
13410929 AACGACAAGT
Statistics
Matches: 249, Mismatches: 50, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
36 5 0.02
37 237 0.95
38 7 0.03
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (37 bp):
TTGAAACATGAGGAAAAGTCCAGCGAACTGTCATAAC
Found at i:13410695 original size:74 final size:74
Alignment explanation
Indices: 13410574--13410955 Score: 369
Period size: 74 Copynumber: 5.2 Consensus size: 74
13410564 CACATTCAAT
* * * * *
13410574 GGACTATCATATA-TTGAAACATGAGGACAAGTCCAGCGAATTGTCATAACTTGAAGCATGACGA
1 GGACTGTCATA-ACTTGAAACATGAGGAAAAGTCCAGCGAAATGTCATAACTTGAAACATGAGGA
*
13410638 TAAGTCCAGC
65 CAAGTCCAGC
* * * *
13410648 GGACTGCCATAACTTGAAACGTGA-GAATAAGTCCAACGAAATGTCATAACTTGAAACGTGAGGA
1 GGACTGTCATAACTTGAAACATGAGGAA-AAGTCCAGCGAAATGTCATAACTTGAAACATGAGGA
* *
13410712 AAAGTCTAGC
65 CAAGTCCAGC
* * * * * * *
13410722 GGATTGTCATAACTTGAAGCATGACGATAAGTCCAGCGGACA-GCCATAACTTGAAACGTGAGGA
1 GGACTGTCATAACTTGAAACATGAGGAAAAGTCCAGC-GAAATGTCATAACTTGAAACATGAGGA
*
13410786 CAAGTCCAAC
65 CAAGTCCAGC
* * * * * *
13410796 GAAATGTCATAACTTGAAACGTGAGGAAAAGTTCAGCGGAATGTCATAACTTGATACGAT-AGGA
1 GGACTGTCATAACTTGAAACATGAGGAAAAGTCCAGCGAAATGTCATAACTTGAAAC-ATGAGGA
*
13410860 CAAGTTCAGC
65 CAAGTCCAGC
* * * * *
13410870 GGGCTGTCATAACTTGAAACATGAGGAAAAGTCCAGC-AAACTATTATAACTTGAAACATAACGA
1 GGACTGTCATAACTTGAAACATGAGGAAAAGTCCAGCGAAA-TGTCATAACTTGAAACATGAGGA
*
13410934 CAAGTCTAGC
65 CAAGTCCAGC
* *
13410944 AGACTATCATAA
1 GGACTGTCATAA
13410956 ATTGCATAAT
Statistics
Matches: 249, Mismatches: 51, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
73 9 0.04
74 234 0.94
75 6 0.02
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.21
Consensus pattern (74 bp):
GGACTGTCATAACTTGAAACATGAGGAAAAGTCCAGCGAAATGTCATAACTTGAAACATGAGGAC
AAGTCCAGC
Found at i:13410733 original size:111 final size:110
Alignment explanation
Indices: 13410587--13410926 Score: 445
Period size: 111 Copynumber: 3.1 Consensus size: 110
13410577 CTATCATATA
* * * *
13410587 TTGAAACATGAGGACAAGTCCAGCGAATTGTCATAACTTGAAGCATGACGATAAGTCCAGCGGAC
1 TTGAAACGTGAGGAAAAGTCTAGCGGATTGTCATAACTTGAAGCATGACGATAAGTCCAGCGGAC
13410652 TGCCATAACTTGAAACGTGAGAATAAGTCCAACGAAATGTCATAAC
66 TGCCATAACTTGAAACGTGAGAA-AAGTCCAACGAAATGTCATAAC
13410698 TTGAAACGTGAGGAAAAGTCTAGCGGATTGTCATAACTTGAAGCATGACGATAAGTCCAGCGGAC
1 TTGAAACGTGAGGAAAAGTCTAGCGGATTGTCATAACTTGAAGCATGACGATAAGTCCAGCGGAC
* *
13410763 AGCCATAACTTGAAACGTGAGGACAAGTCCAACGAAATGTCATAAC
66 TGCCATAACTTGAAACGTGA-GAAAAGTCCAACGAAATGTCATAAC
* * * *
13410809 TTGAAACGTGAGGAAAAGT-TCAGCGGAATGTCATAACTTGATA-CGAT-AGGACAAGTTCAGCG
1 TTGAAACGTGAGGAAAAGTCT-AGCGGATTGTCATAACTTGA-AGC-ATGACGATAAGTCCAGCG
* * * * * *
13410871 GGCTGTCATAACTTGAAACATGAGGAAAAGTCCAGC-AAACTATTATAAC
63 GACTGCCATAACTTGAAACGTGA-GAAAAGTCCAACGAAA-TGTCATAAC
13410920 TTGAAAC
1 TTGAAAC
13410927 ATAACGACAA
Statistics
Matches: 206, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
110 4 0.02
111 197 0.96
112 5 0.02
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (110 bp):
TTGAAACGTGAGGAAAAGTCTAGCGGATTGTCATAACTTGAAGCATGACGATAAGTCCAGCGGAC
TGCCATAACTTGAAACGTGAGAAAAGTCCAACGAAATGTCATAAC
Found at i:13413726 original size:25 final size:25
Alignment explanation
Indices: 13413692--13413740 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
13413682 ACTCTACTTC
*
13413692 TCCGAAAAGATGAGAAATTTGTATA
1 TCCGAAAAGATGAAAAATTTGTATA
13413717 TCCGAAAAGATGAAAAATTTGTAT
1 TCCGAAAAGATGAAAAATTTGTAT
13413741 GTTTTAAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (25 bp):
TCCGAAAAGATGAAAAATTTGTATA
Found at i:13427283 original size:20 final size:20
Alignment explanation
Indices: 13427230--13427375 Score: 99
Period size: 20 Copynumber: 7.4 Consensus size: 20
13427220 TAATATTTTA
*
13427230 AGTACTTTTGTAAGAAATTT
1 AGTAATTTTGTAAGAAATTT
*
13427250 -GATAATAGTT-TAAGAAATTT
1 AG-TAAT-TTTGTAAGAAATTT
*
13427270 AGTACTTTTGTAAGAAA-TT
1 AGTAATTTTGTAAGAAATTT
* *
13427289 ACGTAATGTT-TAAGAGATTGT
1 A-GTAATTTTGTAAGAAATT-T
* * *
13427310 -GTAATTGTCTAAGAGATTT
1 AGTAATTTTGTAAGAAATTT
** *
13427329 AGTAGGTTTGTAAGAAATTA
1 AGTAATTTTGTAAGAAATTT
13427349 AG-AACTTTTGTAAGAAATTT
1 AGTAA-TTTTGTAAGAAATTT
13427369 AG-AATTT
1 AGTAATTT
13427376 ATAAGAGATT
Statistics
Matches: 98, Mismatches: 18, Indels: 21
0.72 0.13 0.15
Matches are distributed among these distances:
19 23 0.23
20 71 0.72
21 4 0.04
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.40
Consensus pattern (20 bp):
AGTAATTTTGTAAGAAATTT
Found at i:13429045 original size:19 final size:20
Alignment explanation
Indices: 13429023--13429071 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
13429013 CGATAAAGTC
*
13429023 TAAGAAATTCAATAAT-TTT
1 TAAGAAATTCAATAATCTTG
* *
13429042 TAAGAGATTCAGTAATCTTG
1 TAAGAAATTCAATAATCTTG
*
13429062 TAAGGAATTC
1 TAAGAAATTC
13429072 CTAAATCTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (20 bp):
TAAGAAATTCAATAATCTTG
Found at i:13438817 original size:17 final size:18
Alignment explanation
Indices: 13438784--13438823 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
13438774 CGAATGGCTT
*
13438784 GCCCTTGTGGACCCACAC
1 GCCCATGTGGACCCACAC
13438802 GCCCATGTGG-CCCACAC
1 GCCCATGTGGACCCACAC
13438819 GCCCA
1 GCCCA
13438824 GATTGGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.12
Consensus pattern (18 bp):
GCCCATGTGGACCCACAC
Found at i:13439985 original size:28 final size:28
Alignment explanation
Indices: 13439953--13440010 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
13439943 TATGACAATA
* *
13439953 TCATTGGATGATCACTGAGTAGTTGCTT
1 TCATTGGACGAGCACTGAGTAGTTGCTT
13439981 TCATTGGACGAGCACTGAGTAGTTGCTT
1 TCATTGGACGAGCACTGAGTAGTTGCTT
13440009 TC
1 TC
13440011 GTAATGGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (28 bp):
TCATTGGACGAGCACTGAGTAGTTGCTT
Found at i:13440321 original size:6 final size:6
Alignment explanation
Indices: 13440310--13440338 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
13440300 AGGCTTTGAA
13440310 AAATGG AAATGG AAATGG AAATGG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATG
13440339 ATCTATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:13440512 original size:26 final size:26
Alignment explanation
Indices: 13440483--13440548 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 26
13440473 ACATATTTTC
13440483 TTAAAATTTTACCAGGGGTAAAATCG
1 TTAAAATTTTACCAGGGGTAAAATCG
* *
13440509 TTAAAAAATTTTACCATGGGTAAAATTG
1 TT--AAAATTTTACCAGGGGTAAAATCG
* *
13440537 TCAAAATGTTAC
1 TTAAAATTTTAC
13440549 TGGAGGTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 11 0.32
28 23 0.68
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (26 bp):
TTAAAATTTTACCAGGGGTAAAATCG
Found at i:13440542 original size:28 final size:28
Alignment explanation
Indices: 13440485--13440542 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
13440475 ATATTTTCTT
*
13440485 AAAATTTTACCAGGGGTAAAATCGTTAA
1 AAAATTTTACCAGGGGTAAAATCGTCAA
* *
13440513 AAAATTTTACCATGGGTAAAATTGTCAA
1 AAAATTTTACCAGGGGTAAAATCGTCAA
13440541 AA
1 AA
13440543 TGTTACTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (28 bp):
AAAATTTTACCAGGGGTAAAATCGTCAA
Found at i:13448915 original size:24 final size:23
Alignment explanation
Indices: 13448886--13448942 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
13448876 TTATTTATCC
* **
13448886 TATTTATTTTTAATAAAATTAATT
1 TATTTATTTTAAATAAAA-TAAAA
*
13448910 TATTTACTTTAAATAAAATAAAA
1 TATTTATTTTAAATAAAATAAAA
13448933 TATTTATTTT
1 TATTTATTTT
13448943 GTTATCTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTATTTTAAATAAAATAAAA
Found at i:13450114 original size:64 final size:64
Alignment explanation
Indices: 13449992--13450115 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 64
13449982 GTATTATTTT
* * **
13449992 CTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGTCACTAAATTATGCTTTTTTTTTTCC
1 CTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGCCACTAAACTATGCGATTTTTTTTCC
* * * *
13450056 CTTTTTTGGTCTCCCAACTATGAAAAGTTATAAAATGGCCACTCAACTATTCGATTTTTT
1 CTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGCCACTAAACTATGCGATTTTTT
13450116 CCTTTTTTTG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (64 bp):
CTTTTTTGGTCACCCAACTATGAAAAGTTACAAAATGGCCACTAAACTATGCGATTTTTTTTCC
Found at i:13450280 original size:61 final size:59
Alignment explanation
Indices: 13450167--13450319 Score: 193
Period size: 61 Copynumber: 2.5 Consensus size: 59
13450157 TACGTTAGTC
* * *
13450167 AGTTGGTGACCAAGAAAGACAAAATTAA-ATAGTTGGTTGACCATATTTTAACTTTTCAT
1 AGTTGGTGACCAAAAAAGA-AAAATAAACATAGTTGGGTGACCATATTTTAACTTTTCAT
*
13450226 AGTTGAGTGACCAAAAAAGAAAAAGTAAACATAGTTGGGTGAGCAT-TTTGTAACTTTTCAT
1 AGTTG-GTGACCAAAAAAGAAAAA-TAAACATAGTTGGGTGACCATATTT-TAACTTTTCAT
* *
13450287 AATTGGGTGACCAAAAAAGAAAAAAAAACATAG
1 AGTT-GGTGACCAAAAAAGAAAAATAAACATAG
13450320 GTGACTACTA
Statistics
Matches: 83, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
59 9 0.11
60 27 0.33
61 46 0.55
62 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.27
Consensus pattern (59 bp):
AGTTGGTGACCAAAAAAGAAAAATAAACATAGTTGGGTGACCATATTTTAACTTTTCAT
Found at i:13450400 original size:23 final size:23
Alignment explanation
Indices: 13450351--13450401 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
13450341 CCTAATTATT
**
13450351 ATTTT-ATAAATAATTTTTATGG
1 ATTTTAATAAATAATTTTTATAA
* *
13450373 TTTTTAATAAATTATTTTTATAA
1 ATTTTAATAAATAATTTTTATAA
13450396 ATTTTA
1 ATTTTA
13450402 TGGTTATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (23 bp):
ATTTTAATAAATAATTTTTATAA
Found at i:13459576 original size:20 final size:20
Alignment explanation
Indices: 13459551--13459591 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
13459541 CTCATTGGAG
13459551 GACTTAACCTAACACTTTAT
1 GACTTAACCTAACACTTTAT
13459571 GACTTAACCTAACACTTTAT
1 GACTTAACCTAACACTTTAT
13459591 G
1 G
13459592 GAACAAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (20 bp):
GACTTAACCTAACACTTTAT
Found at i:13460190 original size:18 final size:17
Alignment explanation
Indices: 13460161--13460196 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
13460151 TTACATTCTT
13460161 TCAATCTCAATTTATCA
1 TCAATCTCAATTTATCA
13460178 TCAATCATCAATTTATCA
1 TCAATC-TCAATTTATCA
13460196 T
1 T
13460197 ATAACACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (17 bp):
TCAATCTCAATTTATCA
Found at i:13464756 original size:200 final size:202
Alignment explanation
Indices: 13464398--13464813 Score: 723
Period size: 200 Copynumber: 2.1 Consensus size: 202
13464388 TTTTTTTGAG
13464398 TTGAA-TCGAGTTTTGCTCATCCCTACTTAAAGATATATATTTTTTAATTTCTTAAAATTTTTTT
1 TTGAATTCG-GTTTTGCTCATCCCTACTTAAAGATATATATTTTTTAATTTCTT-AAATTTTTTT
*
13464462 TGGGGGGGGGAATATTCAAAAAAAATTGGCGGGAAAATGAGTTTGGGGTAGACAGGGGTGGGATC
64 TGGGGGGAGGAATATTCAAAAAAAATTGGCGGGAAAATGAGTTTGGGGTAGACAGGGGTGGGATC
* *
13464527 GGAGGGGAGTAAAAGTTTTGGGGGAAAAGTAAAAAGGTTTGGGGGTTT-GGGTAAAAATGTAAAA
129 GAAGGGGAGTAAAAGTTTTGGGAGAAAAGTAAAAAGGTTTGGGGGTTTGGGGTAAAAATGTAAAA
13464591 TATTATAAT
194 TATTATAAT
*
13464600 TTGAATTCGGTTTTGCTCATCCCTACTTAAAGATGTATATTTTTTAATTTCTT-AATTTTTTTTA
1 TTGAATTCGGTTTTGCTCATCCCTACTTAAAGATATATATTTTTTAATTTCTTAAATTTTTTTT-
*
13464664 GGGGGGAGGAATATTC-AAAAAAATTGGCGGGAAAATGAGTTTGGGGTAGACGGGGGTGGGATCG
65 GGGGGGAGGAATATTCAAAAAAAATTGGCGGGAAAATGAGTTTGGGGTAGACAGGGGTGGGATCG
13464728 AAGGGGAGTAAAAGTTTTGGGAGAAAAGTAAAAAGGTTTGGGGGTTTGGGGTAAAAATGTAAAAT
130 AAGGGGAGTAAAAGTTTTGGGAGAAAAGTAAAAAGGTTTGGGGGTTTGGGGTAAAAATGTAAAAT
13464793 ATTATAAT
195 ATTATAAT
*
13464801 TTGTATTCGGTTT
1 TTGAATTCGGTTT
13464814 ATTCGAATTA
Statistics
Matches: 205, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
200 102 0.50
201 52 0.25
202 48 0.23
203 3 0.01
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (202 bp):
TTGAATTCGGTTTTGCTCATCCCTACTTAAAGATATATATTTTTTAATTTCTTAAATTTTTTTTG
GGGGGAGGAATATTCAAAAAAAATTGGCGGGAAAATGAGTTTGGGGTAGACAGGGGTGGGATCGA
AGGGGAGTAAAAGTTTTGGGAGAAAAGTAAAAAGGTTTGGGGGTTTGGGGTAAAAATGTAAAATA
TTATAAT
Found at i:13465267 original size:12 final size:12
Alignment explanation
Indices: 13465250--13465292 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
13465240 TCATATAAGC
*
13465250 TTAGAATTGGTT
1 TTAGAATTAGTT
13465262 TTAGAATTAGTCT
1 TTAGAATTAGT-T
* *
13465275 CTAGAACTAGTT
1 TTAGAATTAGTT
13465287 TTAGAA
1 TTAGAA
13465293 CTAGACTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (12 bp):
TTAGAATTAGTT
Found at i:13466534 original size:64 final size:64
Alignment explanation
Indices: 13466411--13466535 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 64
13466401 GGATGCATTG
* * *
13466411 TTTAAATGCGTGACATTTATAAGTATTAGATTTATTTATTGAGTTTTATGGATGCTTATTTTTC
1 TTTAAATGCATGACATTTATAAGTATTAGATTTATTTATTGAGTTTCACGGATGCTTATTTTTC
* * * *
13466475 TTTAAATGCATGACATTTATAAGTCTTGGATTTATTTATTGAGTTTCACGTATGTTTATTT
1 TTTAAATGCATGACATTTATAAGTATTAGATTTATTTATTGAGTTTCACGGATGCTTATTT
13466536 GACATATCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.51
Consensus pattern (64 bp):
TTTAAATGCATGACATTTATAAGTATTAGATTTATTTATTGAGTTTCACGGATGCTTATTTTTC
Found at i:13468760 original size:3 final size:3
Alignment explanation
Indices: 13468752--13468776 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13468742 CACAACTTAA
13468752 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
13468777 TTATGTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:13472367 original size:62 final size:64
Alignment explanation
Indices: 13472292--13472417 Score: 159
Period size: 63 Copynumber: 2.0 Consensus size: 64
13472282 CAATTTGTAG
** * *
13472292 TAGATATCGCAATTATTTAAGTTTATCTT-TAATCAAATTAATATTTAAATACTACTTT-TATT
1 TAGATATCGCAATTATTTAACATTATCTTCTAACCAAATTAATATATAAATACTACTTTATATT
* * *
13472354 TAGATA-CGACAATTATTTAACATTATTTTCTTACCAAATTAATATATAGATACTACTTTATATT
1 TAGATATCG-CAATTATTTAACATTATCTTCTAACCAAATTAATATATAAATACTACTTTATATT
13472418 AGTTTACCAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
61 2 0.04
62 23 0.43
63 25 0.46
64 4 0.07
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (64 bp):
TAGATATCGCAATTATTTAACATTATCTTCTAACCAAATTAATATATAAATACTACTTTATATT
Found at i:13473359 original size:21 final size:21
Alignment explanation
Indices: 13473335--13473384 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
13473325 ATATATTTAT
13473335 TATTTATATATATTT-AATATA
1 TATTTATAT-TATTTGAATATA
* *
13473356 TATTTTTATTTTTTGAATATA
1 TATTTATATTATTTGAATATA
13473377 TATTTATA
1 TATTTATA
13473385 AGATTTTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TATTTATATTATTTGAATATA
Found at i:13473818 original size:41 final size:41
Alignment explanation
Indices: 13473773--13473913 Score: 212
Period size: 41 Copynumber: 3.4 Consensus size: 41
13473763 TGAAATCTAT
* * *
13473773 GTAAATATCCATATCATGTTTGCCTTGAAGACAAAGCTTAA
1 GTAAATATCCATATCATGCTCGCCTTGAAGGCAAAGCTTAA
* *
13473814 GTAAATA-CCTGTATCATGCTCGCCTTGAAGGTAAAGCTTAA
1 GTAAATATCC-ATATCATGCTCGCCTTGAAGGCAAAGCTTAA
13473855 GTAAATATCCATATCATGCTCGCCTTGAAGGCAAAGCTTAA
1 GTAAATATCCATATCATGCTCGCCTTGAAGGCAAAGCTTAA
*
13473896 GTAAATATTCATATCATG
1 GTAAATATCCATATCATG
13473914 TAACACTCTA
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
40 2 0.02
41 86 0.96
42 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (41 bp):
GTAAATATCCATATCATGCTCGCCTTGAAGGCAAAGCTTAA
Found at i:13477995 original size:15 final size:14
Alignment explanation
Indices: 13477952--13477996 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
13477942 AAAAGGGGAC
*
13477952 AACAAAGAAAAAACA
1 AACAAA-AAAAAAGA
*
13477967 AACAAAAAACAAGA
1 AACAAAAAAAAAGA
13477981 AGACAAAAAAAAAGA
1 A-ACAAAAAAAAAGA
13477996 A
1 A
13477997 TCTTGTAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (14 bp):
AACAAAAAAAAAGA
Found at i:13480565 original size:41 final size:41
Alignment explanation
Indices: 13480508--13480786 Score: 233
Period size: 41 Copynumber: 6.8 Consensus size: 41
13480498 ATTTTTAAAA
* * *
13480508 CTTTAGCGGCGTTTTTATTTGTGCGCCGCTAATGCTTGGAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * * * *
13480549 CTTTAGTGTCGTTTTTATCTTG-GCACTGCTAATACTCCGAT
1 CTTTAGCGGCGTTTTTATC-TGAGCGCCGCTAATGCTCGGAT
* * *
13480590 CTTTAGCGGTGTTTTTATATGAGCGCCGCTAAAT-CTCTGG-C
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCT-AATGCTC-GGAT
* * * *
13480631 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAGGCTCGGAG
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * * *
13480672 CTTTAGTGGCGTTTTTATCTCAGCGCCACTAATCCTCTGG-C
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTC-GGAT
* * *
13480713 CTTTAGCGGCGTTTTTGTCTAAGCGTCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* ** * *
13480754 CTTTAGTGATGTTTTTATTTGAGCGCCACTAAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAAT
13480787 TCTACGCCGC
Statistics
Matches: 186, Mismatches: 44, Indels: 16
0.76 0.18 0.07
Matches are distributed among these distances:
40 8 0.04
41 170 0.91
42 8 0.04
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
Found at i:13480645 original size:82 final size:81
Alignment explanation
Indices: 13480508--13480786 Score: 283
Period size: 82 Copynumber: 3.4 Consensus size: 81
13480498 ATTTTTAAAA
* * * * * * * **
13480508 CTTTAGCGGCGTTTTTATTTGTGCGCCGCTAATGCT-TGGATCTTTAGTGTCGTTTTTATCTTGG
1 CTTTAGCGGCGTTTTTATTTGAGCGCCACTAATCCTCTGG-CCTTTAGCGGCGTTTTTGTCTAAG
* *
13480572 CACTGCTAATACTCCGAT
65 C-CTGCTAATGCTCGGAT
* * *
13480590 CTTTAGCGGTGTTTTTATATGAGCGCCGCTAAAT-CTCTGGCCTTTAGCGGCGTTTTTGTCTAAG
1 CTTTAGCGGCGTTTTTATTTGAGCGCCACT-AATCCTCTGGCCTTTAGCGGCGTTTTTGTCTAAG
* * *
13480654 CGCCGCTAAGGCTCGGAG
65 C-CTGCTAATGCTCGGAT
* * *
13480672 CTTTAGTGGCGTTTTTATCTCAGCGCCACTAATCCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
1 CTTTAGCGGCGTTTTTATTTGAGCGCCACTAATCCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
*
13480737 GTCGCTAATGCTCGGAT
66 CT-GCTAATGCTCGGAT
* **
13480754 CTTTAGTGATGTTTTTATTTGAGCGCCACTAAT
1 CTTTAGCGGCGTTTTTATTTGAGCGCCACTAAT
13480787 TCTACGCCGC
Statistics
Matches: 165, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
81 3 0.02
82 156 0.95
83 6 0.04
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (81 bp):
CTTTAGCGGCGTTTTTATTTGAGCGCCACTAATCCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
CTGCTAATGCTCGGAT
Found at i:13480759 original size:123 final size:123
Alignment explanation
Indices: 13480508--13480744 Score: 276
Period size: 123 Copynumber: 1.9 Consensus size: 123
13480498 ATTTTTAAAA
* ** * * * * **
13480508 CTTTAGCGGCGTTTTTATTTGTGCGCCGCTAATGCTTGGATCTTTAGTGTCGTTTTTATCTTGGC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAAGGCTCGGAGCTTTAGTGGCGTTTTTATCTCAGC
** * * *
13480573 ACTGCTAATACTCCGATCTTTAGCGGTGTTTTTATATGAGCGCCGCTAAATCTCTGGC
66 ACCACTAATACTCCGACCTTTAGCGGCGTTTTTATATAAGCGCCGCTAAATCTCTGGC
*
13480631 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAGGCTCGGAGCTTTAGTGGCGTTTTTATCTCAGC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAAGGCTCGGAGCTTTAGTGGCGTTTTTATCTCAGC
* * * * * * *
13480696 GCCACTAATCCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGCGTCGCTAA
66 ACCACTAATACTCCGACCTTTAGCGGCGTTTTTATATAAGCGCCGCTAA
13480745 TGCTCGGATC
Statistics
Matches: 92, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
123 92 1.00
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (123 bp):
CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAAGGCTCGGAGCTTTAGTGGCGTTTTTATCTCAGC
ACCACTAATACTCCGACCTTTAGCGGCGTTTTTATATAAGCGCCGCTAAATCTCTGGC
Found at i:13480779 original size:123 final size:123
Alignment explanation
Indices: 13480508--13480785 Score: 272
Period size: 123 Copynumber: 2.3 Consensus size: 123
13480498 ATTTTTAAAA
* * * * * * **
13480508 CTTTAGCGGCGTTTTTATTTGTGCGCCGCTAATGCTTGGATCTTTAGTGTCGTTTTTATCTTGGC
1 CTTTAGCGACGTTTTTATTTGAGCGCCGCTAAGGCTCGGAGCTTTAGTGGCGTTTTTATCTCAGC
** * * *
13480573 ACTGCTAATACTCCGATCTTTAGCGGTGTTTTTATATGAGCGCCGCTAAATCTCTGGC
66 ACCACTAATACTCCGACCTTTAGCGGCGTTTTTATATAAGCGCCGCTAAATCTCTGGC
* * * *
13480631 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAGGCTCGGAGCTTTAGTGGCGTTTTTATCTCAGC
1 CTTTAGCGACGTTTTTATTTGAGCGCCGCTAAGGCTCGGAGCTTTAGTGGCGTTTTTATCTCAGC
* * * * * * * *
13480696 GCCACTAATCCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGCGTCGCT-AATGCTC-GGAT
66 ACCACTAATACTCCGACCTTTAGCGGCGTTTTTATATAAGCGCCGCTAAAT-CTCTGG-C
* * *
13480754 CTTTAGTGATGTTTTTATTTGAGCGCCACTAA
1 CTTTAGCGACGTTTTTATTTGAGCGCCGCTAA
13480786 TTCTACGCCG
Statistics
Matches: 123, Mismatches: 30, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
122 5 0.04
123 118 0.96
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (123 bp):
CTTTAGCGACGTTTTTATTTGAGCGCCGCTAAGGCTCGGAGCTTTAGTGGCGTTTTTATCTCAGC
ACCACTAATACTCCGACCTTTAGCGGCGTTTTTATATAAGCGCCGCTAAATCTCTGGC
Found at i:13481474 original size:14 final size:15
Alignment explanation
Indices: 13481441--13481476 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
13481431 TTAAGGTTAA
13481441 TTTAGGGGTTAGAGG
1 TTTAGGGGTTAGAGG
*
13481456 TTTAGGGGTTTGA-G
1 TTTAGGGGTTAGAGG
13481470 TTTAGGG
1 TTTAGGG
13481477 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.17, C:0.00, G:0.44, T:0.39
Consensus pattern (15 bp):
TTTAGGGGTTAGAGG
Found at i:13482857 original size:27 final size:27
Alignment explanation
Indices: 13482827--13482878 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
13482817 AATAAACAAA
*
13482827 TAAATAAGTAAGTAATTATTTATTTGT
1 TAAATAAATAAGTAATTATTTATTTGT
**
13482854 TAAATAAATTGGTAATTATTTATTT
1 TAAATAAATAAGTAATTATTTATTT
13482879 AAATGTAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (27 bp):
TAAATAAATAAGTAATTATTTATTTGT
Found at i:13483773 original size:11 final size:11
Alignment explanation
Indices: 13483757--13483783 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
13483747 TTTGTTTAAT
13483757 TTACTTTCATA
1 TTACTTTCATA
13483768 TTACTTTCATA
1 TTACTTTCATA
13483779 TTACT
1 TTACT
13483784 GGTTGAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.56
Consensus pattern (11 bp):
TTACTTTCATA
Found at i:13492681 original size:87 final size:87
Alignment explanation
Indices: 13492528--13492726 Score: 231
Period size: 87 Copynumber: 2.3 Consensus size: 87
13492518 ACACAACTTA
* * * *
13492528 AAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTT
1 AAGCAGAGGCAGCAACGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAACTACAACTT
* *
13492593 AAAGTAGATGCGGCAACGAGAG
66 AAAGCAGATGCAGCAACGAGAG
* * *
13492615 AAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAAC-AGCAGC
1 AAGCAGAGGCAGCAACGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAACTA-CAAC
* *
13492678 TTAAAGCAGATGCAGCAGCGAGGG
64 TTAAAGCAGATGCAGCAACGAGAG
** * *
13492702 AATTAGAGGCTGCAACGAGGGAAGC
1 AAGCAGAGGCAGCAACGAGAGAAGC
13492727 AGAACAGCAT
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
86 1 0.01
87 90 0.95
88 4 0.04
ACGTcount: A:0.39, C:0.18, G:0.31, T:0.12
Consensus pattern (87 bp):
AAGCAGAGGCAGCAACGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAACTACAACTT
AAAGCAGATGCAGCAACGAGAG
Found at i:13493098 original size:43 final size:43
Alignment explanation
Indices: 13493041--13493551 Score: 605
Period size: 43 Copynumber: 11.8 Consensus size: 43
13493031 ATTAGCGGCA
** * * * * *
13493041 TTTTTTGGGTAAGCGCCACTAAAGAACACGGCCTATAGTGGCA
1 TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * *
13493084 TTTTTCGTATAAGCGCCGCTAAAGACCATGGTCTAGAGTGGCG
1 TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * *
13493127 TTTTTTGGCTAAGTGCCGCTAAAGACCATGGTCTATAGTGGCA
1 TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
13493170 TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
1 TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* *
13493213 TTTTTTGGCTAAGCGCCGCTAAATACCATGG-CTTATAGTGGCG
1 TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTC-TATAGTGGCG
* * *
13493256 TTTTTTTGTCTAAACGCCGCTAAAGACAATGGCCTATAGTGGCG
1 -TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* *
13493300 TTTTTTTGTCCAAGCGCCGCTAAAGACCATGGTCTATAGTGGCC
1 -TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * * * *
13493344 TTTTTTGTCCAATCGCCGCTAAAGAACACGATCTATAGTGGCG
1 TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* *
13493387 TTTTTTGTCCAAGCACCGCTAAAGACCATGGTCTATAGTGGCG
1 TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * * *
13493430 TTTTATGTAC-AAACACCGCTAAAAGACCATGATCTATAGTGGCG
1 TTTTTTGT-CTAAGCGCCGCT-AAAGACCATGGTCTATAGTGGCG
* * * * *
13493474 TTTTTTGTAT-AGCGCCGCGAAAGACTATGGTCTATAGCGGCA
1 TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * *
13493516 TTTTTTGTGTTAGCGCCGCTAAAGACCATAGTCTAT
1 TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTAT
13493552 TGCGGCGCTT
Statistics
Matches: 406, Mismatches: 55, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
42 29 0.07
43 270 0.67
44 106 0.26
45 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (43 bp):
TTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
Found at i:13493333 original size:174 final size:171
Alignment explanation
Indices: 13493041--13493551 Score: 632
Period size: 174 Copynumber: 3.0 Consensus size: 171
13493031 ATTAGCGGCA
* * * * * * * * *
13493041 TTTTTTGGGTAAGCGCCACTAAAGAACACGGCCTATAGTGGCATTTTTCGTATAAGCGCCGCTAA
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGCTTATAGTGGCGTTTTTTGTCTAAACGCCGCTAA
* * *
13493106 AGACCATGGTCTAGAGTGGCGTTTTTTGGCTAAGTGCCGCTAAAGACCATGGTCTATAGTGGCAT
66 AGACCATGGTCTATAGTGGCGTTTTTTGTC-AAGCGCCGCTAAAGACCATGGTCTATAGTGGCAT
13493171 TTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
130 TTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
*
13493213 TTTTTTGGCTAAGCGCCGCTAAATACCATGGCTTATAGTGGCGTTTTTTTGTCTAAACGCCGCTA
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGCTTATAGTGGCG-TTTTTTGTCTAAACGCCGCTA
* *
13493278 AAGACAATGGCCTATAGTGGCGTTTTTTTGTCCAAGCGCCGCTAAAGACCATGGTCTATAGTGGC
65 AAGACCATGGTCTATAGTGGCG-TTTTTTGT-CAAGCGCCGCTAAAGACCATGGTCTATAGTGGC
* * * * * *
13493343 CTTTTTTGTCCAATCGCCGCTAAAGAACACGATCTATAGTGGCG
128 ATTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
* * * * *
13493387 TTTTTTGTCCAAGCACCGCTAAAGACCATGG-TCTATAGTGGCGTTTTATGTAC-AAACACCGCT
1 TTTTTTGGCTAAGCGCCGCTAAAGACCATGGCT-TATAGTGGCGTTTTTTGT-CTAAACGCCGCT
* * * *
13493450 AAAAGACCATGATCTATAGTGGCGTTTTTTGT-ATAGCGCCGCGAAAGACTATGGTCTATAGCGG
64 -AAAGACCATGGTCTATAGTGGCGTTTTTTGTCA-AGCGCCGCTAAAGACCATGGTCTATAGTGG
* * *
13493514 CATTTTTTGTGTTAGCGCCGCTAAAGACCATAGTCTAT
127 CATTTTTTGTCTAAGCGCCGCTAAAGACCATGGTCTAT
13493552 TGCGGCGCTT
Statistics
Matches: 290, Mismatches: 42, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
171 1 0.00
172 92 0.32
173 62 0.21
174 134 0.46
175 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (171 bp):
TTTTTTGGCTAAGCGCCGCTAAAGACCATGGCTTATAGTGGCGTTTTTTGTCTAAACGCCGCTAA
AGACCATGGTCTATAGTGGCGTTTTTTGTCAAGCGCCGCTAAAGACCATGGTCTATAGTGGCATT
TTTTGTCTAAGCGCCGCTAAAGACCATGGTCTATAGTGGCG
Found at i:13497189 original size:6 final size:6
Alignment explanation
Indices: 13497178--13497226 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
13497168 TTACTTTAAA
* *
13497178 AAAAAG AAAAAG GAAAAG AAAAAT AAAAA- AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
13497225 AA
1 AA
13497227 TGAGAGGCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:13497205 original size:17 final size:17
Alignment explanation
Indices: 13497178--13497223 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
13497168 TTACTTTAAA
*
13497178 AAAAAGAAAAAGGAAAAG
1 AAAAAGAAAAA-AAAAAG
*
13497196 AAAAATAAAAAAAAAAG
1 AAAAAGAAAAAAAAAAG
13497213 AAAAAGAAAAA
1 AAAAAGAAAAA
13497224 GAATGAGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAG
Found at i:13497205 original size:23 final size:22
Alignment explanation
Indices: 13497175--13497223 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
13497165 ATTTTACTTT
* *
13497175 AAAAAAAAGAAAAAGGAAAAGA
1 AAAAAAAAAAAAAAGAAAAAGA
13497197 AAAATAAAAAAAAAAGAAAAAGA
1 AAAA-AAAAAAAAAAGAAAAAGA
13497220 AAAA
1 AAAA
13497224 GAATGAGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAAAAAGAAAAAGA
Found at i:13498172 original size:44 final size:44
Alignment explanation
Indices: 13498112--13498412 Score: 277
Period size: 44 Copynumber: 6.7 Consensus size: 44
13498102 CATATCAAAC
* *
13498112 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTA-CAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAA-T
* * *
13498156 CTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CCAAT
* * * * *
13498201 CTTATTTCCCTGAAGTTGTAGTGGAACAGATTGAAACTATAAATTGCAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-AA-GAT--A--CCA-AT
* * * * * * *
13498252 ATTATCTCTCTGAAGTTGCAGTAGAGCAGA-T-CATAT-CAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAAT
* *
13498293 CTTATCTCCTTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAAT
* * * *
13498337 CTTATCTCCCTAAAATTGCAGTGGAGCAGATTGAAGCTACTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAAT
*
13498381 CCTATCTCCCTGAAGTTGCAGTGGAGCAGATT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
13498413 AAAACAATGA
Statistics
Matches: 204, Mismatches: 42, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
41 26 0.13
42 2 0.01
43 3 0.01
44 105 0.51
45 29 0.14
46 4 0.02
47 5 0.02
48 1 0.00
49 1 0.00
50 2 0.01
51 26 0.13
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAAT
Found at i:13509029 original size:10 final size:10
Alignment explanation
Indices: 13509010--13509051 Score: 68
Period size: 10 Copynumber: 4.3 Consensus size: 10
13509000 CTATTTTGAC
13509010 TTTGATTTTT
1 TTTGATTTTT
*
13509020 TTTTATTTTT
1 TTTGATTTTT
13509030 TTTGA-TTTT
1 TTTGATTTTT
13509039 TTTGATTTTT
1 TTTGATTTTT
13509049 TTT
1 TTT
13509052 TGAACTCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (10 bp):
TTTGATTTTT
Found at i:13509030 original size:9 final size:9
Alignment explanation
Indices: 13509016--13509051 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
13509006 TGACTTTGAT
13509016 TTTTTTTTA
1 TTTTTTTTA
13509025 TTTTTTTTGA
1 TTTTTTTT-A
*
13509035 TTTTTTTGA
1 TTTTTTTTA
13509044 TTTTTTTT
1 TTTTTTTT
13509052 TGAACTCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.08, C:0.00, G:0.06, T:0.86
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:13509035 original size:20 final size:19
Alignment explanation
Indices: 13509010--13509051 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
13509000 CTATTTTGAC
*
13509010 TTTGATTTTTTTTTATTTTT
1 TTTGA-TTTTTTTGATTTTT
13509030 TTTGATTTTTTTGATTTTT
1 TTTGATTTTTTTGATTTTT
13509049 TTT
1 TTT
13509052 TGAACTCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (19 bp):
TTTGATTTTTTTGATTTTT
Found at i:13512869 original size:109 final size:109
Alignment explanation
Indices: 13512515--13512903 Score: 602
Period size: 110 Copynumber: 3.6 Consensus size: 109
13512505 GTTAATCAAG
* * * *
13512515 AAATCGAAACCCAGCACCTTAGGGTACG-TTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* * *
13512579 TTGAAATTTTTTGAAAGGATATTTAA-CTATTTGGTTAAACGAGAA
66 TT-AAAATTTTTAAAAGGATA-TTAAGCCATTTGGTTAAACGAGAA
*
13512624 AAATCGACACCCAGCACCTTAGAGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* * *
13512689 TTAAGATTTTTGAAAAGGATATTAAGCCATTTGGTTGAACAAGAA
66 TTAAAATTTTT-AAAAGGATATTAAGCCATTTGGTTAAACGAGAA
* * *
13512734 CAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTTCAAACGCAAAACGTTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
13512799 TTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTAAACGAGAA
66 TTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTAAACGAGAA
*
13512843 AAATCGACACCCAGCACCTTAGGGCATATTTTCTCGAATTTCCAAACGCAAAACATTGCCT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCT
13512904 CAATTAGAAA
Statistics
Matches: 255, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
109 123 0.48
110 132 0.52
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (109 bp):
AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTAAACGAGAA
Found at i:13512902 original size:219 final size:217
Alignment explanation
Indices: 13512500--13512903 Score: 643
Period size: 219 Copynumber: 1.9 Consensus size: 217
13512490 ATATTTGGCA
*
13512500 ATTTGGTTAATCAAGAAATCGAAACCCAGCACCTTAGGGTACGTTCCTCGAATTTCCAAACGCAA
1 ATTTGGTTAATCAAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* * *
13512565 AACATTGCCTTATTTTGAAATTTTTTGAAAGGATATTTAACTATTTGGTTAAACGAGAAAAATCG
66 AACATTGCCTTATTTTGAAAATTTTTAAAAGGATATTTAACCATTTGGTTAAACGAGAAAAATCG
*
13512630 ACACCCAGCACCTTAGAGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAGA
131 ACACCCAGCACCTTAGAGCATATTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAGA
13512695 TTTTTGAAAAGGATATTAAGCC
196 TTTTTGAAAAGGATATTAAGCC
* * * *
13512717 ATTTGGTTGAA-CAAGAACAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTTCAAAC
1 ATTTGGTT-AATCAAG-A-AATCGAAACCCAGCACCTTAGGGCACG-TTCCTCGAATTTCCAAAC
*
13512781 GCAAAACGTTGCCTTATTTT-AAAATTTTTAAAAGGATA-TTAAGCCATTTGGTTAAACGAGAAA
62 GCAAAACATTGCCTTATTTTGAAAATTTTTAAAAGGATATTTAA-CCATTTGGTTAAACGAGAAA
*
13512844 AATCGACACCCAGCACCTTAGGGCATATTTTCTCGAATTTCCAAACGCAAAACATTGCCT
126 AATCGACACCCAGCACCTTAGAGCATATTTTCTCGAATTTCCAAACGCAAAACATTGCCT
13512904 CAATTAGAAA
Statistics
Matches: 171, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
217 12 0.07
218 7 0.04
219 117 0.68
220 35 0.20
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (217 bp):
ATTTGGTTAATCAAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
AACATTGCCTTATTTTGAAAATTTTTAAAAGGATATTTAACCATTTGGTTAAACGAGAAAAATCG
ACACCCAGCACCTTAGAGCATATTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTAAGA
TTTTTGAAAAGGATATTAAGCC
Found at i:13513269 original size:14 final size:16
Alignment explanation
Indices: 13513217--13513290 Score: 62
Period size: 16 Copynumber: 4.4 Consensus size: 16
13513207 GAGTACATAG
*
13513217 ATATATGTAAATAAAT
1 ATATATATAAATAAAT
*
13513233 ATATATAAAAAGT-AAT
1 ATATATATAAA-TAAAT
13513249 ATATATATTAAATAAAT
1 ATATATA-TAAATAAAT
*
13513266 -TATATGATATATTGAAAT
1 ATATAT-ATA-AAT-AAAT
13513284 ATATATA
1 ATATATA
13513291 AGCACTTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
16 27 0.57
17 10 0.21
18 5 0.11
19 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (16 bp):
ATATATATAAATAAAT
Found at i:13513396 original size:21 final size:22
Alignment explanation
Indices: 13513366--13513424 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
13513356 TGGAAATATA
*
13513366 ATAATAATAATAATAATA-TTG
1 ATAATAATAATAATAATAGATG
*
13513387 ATATTAATAATAATAA-AGATG
1 ATAATAATAATAATAATAGATG
13513408 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
13513425 GGTAACATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
ATAATAATAATAATAATAGATG
Found at i:13513443 original size:3 final size:3
Alignment explanation
Indices: 13513363--13513424 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
13513353 TAATGGAAAT
* * * *
13513363 ATA ATA ATA ATA ATA ATA ATA TTG ATA TTA ATA ATA ATA A-A GATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
13513408 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
13513425 GGTAACATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 1 0.02
3 48 0.98
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:13513970 original size:30 final size:30
Alignment explanation
Indices: 13513910--13513966 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
13513900 TGTTCAGGGT
13513910 ATTTAAACCCTATTTTTCTTCCAAAAAACC
1 ATTTAAACCCTATTTTTCTTCCAAAAAACC
*
13513940 ATTTCAACCACTA-TTTTC-TCCAAAAAA
1 ATTTAAACC-CTATTTTTCTTCCAAAAAA
13513967 ACCAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 13 0.52
31 3 0.12
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (30 bp):
ATTTAAACCCTATTTTTCTTCCAAAAAACC
Found at i:13516013 original size:26 final size:26
Alignment explanation
Indices: 13515980--13516055 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
13515970 CATTTTTTTT
* *
13515980 AAAT-AAAAACCAAAAATTATTTTAA
1 AAATAAAAAACAAAAAAGTATTTTAA
*
13516005 AAATAAAAAATAAAAAAGTATTTTAA
1 AAATAAAAAACAAAAAAGTATTTTAA
* * *
13516031 AATTAAAAAAATAAAAAAATATTTT
1 AAAT-AAAAAACAAAAAAGTATTTT
13516056 TACTAAACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
25 4 0.09
26 21 0.48
27 19 0.43
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (26 bp):
AAATAAAAAACAAAAAAGTATTTTAA
Found at i:13516014 original size:27 final size:25
Alignment explanation
Indices: 13515980--13516055 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 25
13515970 CATTTTTTTT
** *
13515980 AAATAAAAACCAAAAATTATTTTAA
1 AAATAAAAAAAAAAAAATATTTTAA
*
13516005 AAATAAAAAATAAAAAAGTATTTTAA
1 AAATAAAAAA-AAAAAAATATTTTAA
*
13516031 AATTAAAAAAATAAAAAAATATTTT
1 AAAT-AAAAAA-AAAAAAATATTTT
13516056 TACTAAACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
25 9 0.20
26 16 0.36
27 19 0.43
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (25 bp):
AAATAAAAAAAAAAAAATATTTTAA
Found at i:13516068 original size:27 final size:27
Alignment explanation
Indices: 13515991--13516055 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
13515981 AATAAAAACC
* *
13515991 AAAAATTATTTTAAAA-ATAAAAAATA
1 AAAAAATATTTTAAAATAAAAAAAATA
* *
13516017 AAAAAGTATTTTAAAATTAAAAAAATA
1 AAAAAATATTTTAAAATAAAAAAAATA
13516044 AAAAAATATTTT
1 AAAAAATATTTT
13516056 TACTAAACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 15 0.44
27 19 0.56
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAAAATATTTTAAAATAAAAAAAATA
Found at i:13516803 original size:29 final size:29
Alignment explanation
Indices: 13516715--13516803 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 29
13516705 ACATAAAACT
* * *
13516715 AAACTTTTAAAAATGATCATATAAGAGCC
1 AAACTTTTCAAAATGATCAAATAAGAGTC
* * *
13516744 TAAC-TTTCATAAATATATTTAAATGAA-AGTC
1 AAACTTTTCA-AAAT-GA-TCAAAT-AAGAGTC
13516775 AAACTTTTCAAAATGATCAAATAAGAGTC
1 AAACTTTTCAAAATGATCAAATAAGAGTC
13516804 CAATATTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
28 6 0.13
29 16 0.36
30 2 0.04
31 14 0.31
32 7 0.16
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (29 bp):
AAACTTTTCAAAATGATCAAATAAGAGTC
Found at i:13530113 original size:20 final size:20
Alignment explanation
Indices: 13530090--13530164 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
13530080 GAACACGAGT
*
13530090 GTGCAATCAGGGGCACTAGA
1 GTGCATTCAGGGGCACTAGA
* *
13530110 GTGCATTCAAGGGCACGA-A
1 GTGCATTCAGGGGCACTAGA
*
13530129 TGTGC-TGTGAGGGGCACTAGA
1 -GTGCAT-TCAGGGGCACTAGA
*
13530150 GTGCATTTAGGGGCA
1 GTGCATTCAGGGGCA
13530165 TAAATGTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.37, T:0.20
Consensus pattern (20 bp):
GTGCATTCAGGGGCACTAGA
Found at i:13530164 original size:40 final size:40
Alignment explanation
Indices: 13530098--13530173 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
13530088 GTGTGCAATC
*
13530098 AGGGGCACTAGAGTGCATTCAAGGGCACGAATGTGCTGTG
1 AGGGGCACTAGAGTGCATTCAAGGGCACAAATGTGCTGTG
* * *
13530138 AGGGGCACTAGAGTGCATTTAGGGGCATAAATGTGC
1 AGGGGCACTAGAGTGCATTCAAGGGCACAAATGTGC
13530174 AATTAGAGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.26, C:0.16, G:0.37, T:0.21
Consensus pattern (40 bp):
AGGGGCACTAGAGTGCATTCAAGGGCACAAATGTGCTGTG
Found at i:13530202 original size:40 final size:40
Alignment explanation
Indices: 13530158--13530241 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
13530148 GAGTGCATTT
* * *
13530158 AGGGGCATAAATGTGCAATTAGAGACACCGAAGTGTTTAC
1 AGGGGCACAAATGTGCAAATAGAGACACCGAACTGTTTAC
** *
13530198 AGGGGCACAGTTGTGCAAATAGGGACACCGAACTGTTTAC
1 AGGGGCACAAATGTGCAAATAGAGACACCGAACTGTTTAC
13530238 AGGG
1 AGGG
13530242 ACATCCAGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.32, C:0.17, G:0.31, T:0.20
Consensus pattern (40 bp):
AGGGGCACAAATGTGCAAATAGAGACACCGAACTGTTTAC
Found at i:13532671 original size:68 final size:68
Alignment explanation
Indices: 13532575--13532710 Score: 202
Period size: 68 Copynumber: 2.0 Consensus size: 68
13532565 TCTATTTGTT
* * *
13532575 TGGGTCAACATCGATAATCGTCGTTTCCTTATGAATTTGGATTACCTCATAAAGAGAAATGTGCT
1 TGGGTCAACATCGATAATCGTCGCTTCCTTATAAATTTGGATTACCTCATAAAGAGAAATGTGAT
13532640 TGA
66 TGA
* * *
13532643 TGGGTCGATATCGATAA-CTGTCGCTTCCTTATAAATTTGGATTATCTCATAAAGAGAAATGTGA
1 TGGGTCAACATCGATAATC-GTCGCTTCCTTATAAATTTGGATTACCTCATAAAGAGAAATGTGA
13532707 TTGA
65 TTGA
13532711 CGTGAAAACA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 1 0.02
68 60 0.98
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.35
Consensus pattern (68 bp):
TGGGTCAACATCGATAATCGTCGCTTCCTTATAAATTTGGATTACCTCATAAAGAGAAATGTGAT
TGA
Found at i:13536750 original size:27 final size:27
Alignment explanation
Indices: 13536712--13536767 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
13536702 ATAATTGAAG
*
13536712 TTCAAAACTTGTGTAGTATATGTGCAA
1 TTCAAAACTTGTGCAGTATATGTGCAA
13536739 TTCAAAACTTGTGCAGTATATGTGCAA
1 TTCAAAACTTGTGCAGTATATGTGCAA
13536766 TT
1 TT
13536768 ATATTAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (27 bp):
TTCAAAACTTGTGCAGTATATGTGCAA
Found at i:13540527 original size:13 final size:12
Alignment explanation
Indices: 13540484--13540527 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
13540474 AGAAGTCTAA
*
13540484 AAATAAAAA-AC
1 AAATAAAAACAG
*
13540495 AACTAAAAACAG
1 AAATAAAAACAG
*
13540507 AAATAAAAACAT
1 AAATAAAAACAG
13540519 AAATAAAAA
1 AAATAAAAA
13540528 GAAAAAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.11
Consensus pattern (12 bp):
AAATAAAAACAG
Found at i:13541972 original size:16 final size:17
Alignment explanation
Indices: 13541953--13541992 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
13541943 AAGAAATACG
13541953 AATAATCAATAATA-GT-
1 AATAAT-AATAATACGTA
13541969 AATAATAA-AATACGTA
1 AATAATAATAATACGTA
13541985 AATAATAA
1 AATAATAA
13541993 ATAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 4 0.18
16 14 0.64
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (17 bp):
AATAATAATAATACGTA
Found at i:13542002 original size:6 final size:6
Alignment explanation
Indices: 13541984--13542036 Score: 52
Period size: 6 Copynumber: 8.0 Consensus size: 6
13541974 TAAAATACGT
*
13541984 AAATAA TAAATAA AAATAA TACTAATAA AAATAA AAATACA AACTAA AAATAA
1 AAATAA -AAATAA AAATAA -A--AATAA AAATAA AAATA-A AAATAA AAATAA
13542037 TGAGTAAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
6 22 0.55
7 12 0.30
8 1 0.03
9 5 0.12
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (6 bp):
AAATAA
Found at i:13542009 original size:19 final size:20
Alignment explanation
Indices: 13541987--13542036 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
13541977 AATACGTAAA
*
13541987 TAATAAATAAAAATA-ATAC
1 TAATAAATAAAAATACAAAC
13542006 TAATAAAAATAAAAATACAAAC
1 TAAT--AAATAAAAATACAAAC
13542028 TAA-AAATAA
1 TAATAAATAA
13542037 TGAGTAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.37
21 11 0.41
22 6 0.22
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (20 bp):
TAATAAATAAAAATACAAAC
Found at i:13542010 original size:15 final size:13
Alignment explanation
Indices: 13541984--13542036 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
13541974 TAAAATACGT
13541984 AAATAATAAATAA
1 AAATAATAAATAA
13541997 AAATAATACTAATAA
1 AAATAATA--AATAA
13542012 AAATAA-AAATACA
1 AAATAATAAATA-A
*
13542025 AACTAA-AAATAA
1 AAATAATAAATAA
13542037 TGAGTAAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
12 5 0.14
13 19 0.53
14 1 0.03
15 11 0.31
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAATAAATAA
Found at i:13542029 original size:22 final size:22
Alignment explanation
Indices: 13541985--13542036 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
13541975 AAAATACGTA
*
13541985 AATAATAAATAAAAATAATACT
1 AATAATAAATAAAAATAAAACT
13542007 AATAA-AAATAAAAATACAAACT
1 AATAATAAATAAAAATA-AAACT
*
13542029 AAAAATAA
1 AATAATAA
13542037 TGAGTAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 13 0.50
23 2 0.08
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (22 bp):
AATAATAAATAAAAATAAAACT
Found at i:13542266 original size:5 final size:4
Alignment explanation
Indices: 13542247--13542340 Score: 54
Period size: 4 Copynumber: 22.8 Consensus size: 4
13542237 GAAGCAGAAG
*
13542247 AATA ACATA AATA AAGTA AA-A AATA AATA GAAAA AATA GAA-A AAT-
1 AATA A-ATA AATA AA-TA AATA AATA AATA -AATA AATA -AATA AATA
* *
13542292 AATA AATA TATA ATATA AA-A ATATA AA-A AATAA AAAA AATA AACTA
1 AATA AATA AATA A-ATA AATA A-ATA AATA AAT-A AATA AATA AA-TA
13542338 AAT
1 AAT
13542341 GGGGAAAAAG
Statistics
Matches: 71, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
3 13 0.18
4 32 0.45
5 26 0.37
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:13542313 original size:15 final size:15
Alignment explanation
Indices: 13542271--13542327 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
13542261 AGTAAAAAAT
*
13542271 AAATAGAAAAAATAGAA
1 AAATA-AAAATATA-AA
*
13542288 AAATAATAAATATATA
1 AAATAA-AAATATAAA
*
13542304 ATATAAAAATATAAA
1 AAATAAAAATATAAA
13542319 AAATAAAAA
1 AAATAAAAA
13542328 AAATAAACTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 16 0.47
16 7 0.21
17 11 0.32
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (15 bp):
AAATAAAAATATAAA
Found at i:13542317 original size:8 final size:8
Alignment explanation
Indices: 13542278--13542327 Score: 52
Period size: 7 Copynumber: 6.6 Consensus size: 8
13542268 AATAAATAGA
*
13542278 AAAAATAG
1 AAAAATAT
13542286 AAAAATA-
1 AAAAATAT
*
13542293 ATAAATAT
1 AAAAATAT
*
13542301 -ATAATAT
1 AAAAATAT
13542308 AAAAATAT
1 AAAAATAT
13542316 AAAAA-AT
1 AAAAATAT
13542323 AAAAA
1 AAAAA
13542328 AAATAAACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 18 0.50
8 18 0.50
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (8 bp):
AAAAATAT
Found at i:13542317 original size:24 final size:24
Alignment explanation
Indices: 13542264--13542332 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
13542254 TAAATAAAGT
13542264 AAAA-AATAAATAGAAAAAATAGA
1 AAAATAATAAATAGAAAAAATAGA
* * *
13542287 AAAATAATAAATATATAATATA-A
1 AAAATAATAAATAGAAAAAATAGA
* *
13542310 AAATATAAAAAATAAAAAAAATA
1 AAA-ATAATAAATAGAAAAAATA
13542333 AACTAAATGG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 8 0.22
24 29 0.78
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (24 bp):
AAAATAATAAATAGAAAAAATAGA
Found at i:13542333 original size:9 final size:9
Alignment explanation
Indices: 13542265--13542334 Score: 52
Period size: 9 Copynumber: 7.3 Consensus size: 9
13542255 AAATAAAGTA
13542265 AAAAATAAAT
1 AAAAA-AAAT
*
13542275 AGAAAAAAT
1 AAAAAAAAT
13542284 AGAAAAATAAT
1 A-AAAAA-AAT
*
13542295 AAATATATAAT
1 AAA-A-AAAAT
*
13542306 -ATAAAAAT
1 AAAAAAAAT
*
13542314 ATAAAAAAT
1 AAAAAAAAT
13542323 AAAAAAAAT
1 AAAAAAAAT
13542332 AAA
1 AAA
13542335 CTAAATGGGG
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
8 4 0.09
9 23 0.49
10 11 0.23
11 8 0.17
12 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:13552454 original size:14 final size:14
Alignment explanation
Indices: 13552435--13552464 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
13552425 AACTTCAATT
13552435 ATCATATTTTTAAA
1 ATCATATTTTTAAA
13552449 ATCATATTTTTAAA
1 ATCATATTTTTAAA
13552463 AT
1 AT
13552465 ATGAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
ATCATATTTTTAAA
Found at i:13554527 original size:47 final size:47
Alignment explanation
Indices: 13554448--13554674 Score: 258
Period size: 47 Copynumber: 4.8 Consensus size: 47
13554438 GGATGTGACA
* *
13554448 CACCTGCTTGACCAGTGGTTTATCCACAACGTATCTTAGTCGACAGT
1 CACCTGCTCGACCAGTGGTTTATCCACAACGTATTTTAGTCGACAGT
** * * *
13554495 CATATGTTCTACCAGTGGTTTATCCACTACGTATTTTAGTC-AGCAGT
1 CACCTGCTCGACCAGTGGTTTATCCACAACGTATTTTAGTCGA-CAGT
* * * *
13554542 CACCTACTCGACCAATGGTTTATCCACAACTTATTTTAATCGACAGT
1 CACCTGCTCGACCAGTGGTTTATCCACAACGTATTTTAGTCGACAGT
* * *
13554589 CACCTGGTCGACCAGTGGTTTATCCATAACGTATTTTAGTCTACAGT
1 CACCTGCTCGACCAGTGGTTTATCCACAACGTATTTTAGTCGACAGT
* * * * * *
13554636 CACCTTCTCAACTAATGGTATATCCACAATGTATTTTAG
1 CACCTGCTCGACCAGTGGTTTATCCACAACGTATTTTAG
13554675 CAACTTTTAT
Statistics
Matches: 147, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
46 1 0.01
47 145 0.99
48 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (47 bp):
CACCTGCTCGACCAGTGGTTTATCCACAACGTATTTTAGTCGACAGT
Found at i:13558612 original size:27 final size:28
Alignment explanation
Indices: 13558574--13558628 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
13558564 TTTAGCTCGG
13558574 GTGCTTTTCT-AAAATAGGTTAAGTTTT
1 GTGCTTTTCTAAAAATAGGTTAAGTTTT
13558601 GTGCTTTTCTAAAAATAGGTTAAGTTTT
1 GTGCTTTTCTAAAAATAGGTTAAGTTTT
13558629 CTTTTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.47
Consensus pattern (28 bp):
GTGCTTTTCTAAAAATAGGTTAAGTTTT
Found at i:13559593 original size:21 final size:21
Alignment explanation
Indices: 13559551--13559618 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
13559541 CTCCTGCTGG
* ***
13559551 TTAGGGTTTTGGGTTTTTGTT
1 TTAGGGTTTAGGGTTAGGGTT
13559572 TTAGGGTTTAGGGTTAGGGTTT
1 TTAGGGTTTAGGGTTAGGG-TT
** *
13559594 TATAGTTTTTAGGTTTAGGGTT
1 T-TAGGGTTTAGGGTTAGGGTT
13559616 TTA
1 TTA
13559619 AAGAAAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 17 0.45
22 6 0.16
23 15 0.39
ACGTcount: A:0.13, C:0.00, G:0.32, T:0.54
Consensus pattern (21 bp):
TTAGGGTTTAGGGTTAGGGTT
Found at i:13559744 original size:96 final size:94
Alignment explanation
Indices: 13559606--13559779 Score: 233
Period size: 96 Copynumber: 1.8 Consensus size: 94
13559596 TAGTTTTTAG
* *
13559606 GTTTAGGGTTTTAAAGAAAAAATTAAATAAATAAGGGATTAGGGTTTA-TTAATTAAATTAATTA
1 GTTTAGGGTTTTAAAGAAAAAATCAAATAAATAAGGGATTAGGG-TTACTTAACTAAATTAATTA
* *
13559670 TAAATTTTTCAAAATTGGATTAGGTTTCAT
65 AAAATTTTTAAAAATTGGATTAGGTTTCAT
* * * * *
13559700 GTTTATGGTTTTTAAAGAAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGACTAAATTAATT
1 GTTTA-GGGTTTTAAAG-AAAAAATCAAATAAATAAGGGATTAGGGTTACTTAACTAAATTAATT
13559765 AAAAATTTTTAAAAA
64 AAAAATTTTTAAAAA
13559780 ATCAGATTAG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
94 5 0.07
95 13 0.19
96 50 0.74
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.40
Consensus pattern (94 bp):
GTTTAGGGTTTTAAAGAAAAAATCAAATAAATAAGGGATTAGGGTTACTTAACTAAATTAATTAA
AAATTTTTAAAAATTGGATTAGGTTTCAT
Found at i:13560002 original size:126 final size:126
Alignment explanation
Indices: 13559806--13560101 Score: 475
Period size: 126 Copynumber: 2.3 Consensus size: 126
13559796 GTGTTAATTT
*
13559806 AAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGAAGAC
1 AAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGAC
* * *
13559871 GTTTCTGAGCCAATAGTGTCAAAAACGCTTTAAGCAATATGCTTCGTCAGCAAAAGTACTG
66 ATTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTCGTCAGCAAAAGTACTG
* * * * *
13559932 AAAGAAGCTCCCACGTGGACGCACTTTTGCTATAGTAGCTCCTGAAAAAATAATTTCGAGTAGGC
1 AAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGAC
* ** *
13559997 ATTTCTGAGCAAATAGTGTCAAAAATGCTTTAAGCTGGATGCTTTGTCAGCAAAAGTACTG
66 ATTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTCGTCAGCAAAAGTACTG
13560058 AAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGCTCCTG
1 AAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGCTCCTG
13560102 TTTGGCCTGA
Statistics
Matches: 154, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 154 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (126 bp):
AAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGAC
ATTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTCGTCAGCAAAAGTACTG
Found at i:13562276 original size:21 final size:21
Alignment explanation
Indices: 13562252--13562299 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
13562242 GCGGGGGTTG
*
13562252 TGGTTGCTTCGGTA-GGGATTC
1 TGGTTGCTCCGGTAGGGGA-TC
*
13562273 TGGTTCCTCCGGTAGGGGATC
1 TGGTTGCTCCGGTAGGGGATC
13562294 TGGTTG
1 TGGTTG
13562300 TCGGTGTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.08, C:0.17, G:0.40, T:0.35
Consensus pattern (21 bp):
TGGTTGCTCCGGTAGGGGATC
Found at i:13563188 original size:7 final size:7
Alignment explanation
Indices: 13563176--13563200 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13563166 TATTAGTTAT
13563176 ATACATA
1 ATACATA
13563183 ATACATA
1 ATACATA
13563190 ATACATA
1 ATACATA
13563197 ATAC
1 ATAC
13563201 TAAATACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACATA
Found at i:13563290 original size:25 final size:21
Alignment explanation
Indices: 13563244--13563285 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
13563234 CAATTTTATT
13563244 TAATACTTACTTGTGCTTCCG
1 TAATACTTACTTGTGCTTCCG
13563265 TAATACTTACTTGTGCTTCCG
1 TAATACTTACTTGTGCTTCCG
13563286 ACCGTTGGTC
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:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (21 bp):
TAATACTTACTTGTGCTTCCG
Found at i:13564382 original size:11 final size:11
Alignment explanation
Indices: 13564368--13564437 Score: 81
Period size: 11 Copynumber: 6.4 Consensus size: 11
13564358 AGCTTTTTTA
13564368 AGAGGAATTTG
1 AGAGGAATTTG
*
13564379 AGAGGAAATTG
1 AGAGGAATTTG
*
13564390 AAAGGAATTTG
1 AGAGGAATTTG
13564401 AGAGGAATTTG
1 AGAGGAATTTG
13564412 AGA-GAATATTG
1 AGAGGAAT-TTG
*
13564423 -GAGAGAAATTG
1 AGAG-GAATTTG
13564434 AGAG
1 AGAG
13564438 AAAGGATTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
10 6 0.12
11 38 0.76
12 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (11 bp):
AGAGGAATTTG
Found at i:13564435 original size:33 final size:33
Alignment explanation
Indices: 13564368--13564437 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
13564358 AGCTTTTTTA
*
13564368 AGAGGAATTTGAGAGGAAATTGAAAGGAATTTG
1 AGAGGAATTTGAGAGGAAATTGAAAGGAAATTG
*
13564401 AGAGGAATTTGAGA-GAATATTG-GAGAGAAATTG
1 AGAGGAATTTGAGAGGAA-ATTGAAAG-GAAATTG
13564434 AGAG
1 AGAG
13564438 AAAGGATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 5 0.15
33 28 0.85
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (33 bp):
AGAGGAATTTGAGAGGAAATTGAAAGGAAATTG
Found at i:13570440 original size:2 final size:2
Alignment explanation
Indices: 13570433--13570458 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13570423 TTTTGGAAGG
13570433 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13570459 GCATAAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13571388 original size:27 final size:29
Alignment explanation
Indices: 13571344--13571401 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
13571334 GATTCAAATT
13571344 TTTAGGGAGGAAAATAAGGGA-TTTAGGG
1 TTTAGGGAGGAAAATAAGGGATTTTAGGG
*
13571372 TTTAGGGA-TAAAATAAGGGATTTTAGGG
1 TTTAGGGAGGAAAATAAGGGATTTTAGGG
13571400 TT
1 TT
13571402 ATGGTTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (29 bp):
TTTAGGGAGGAAAATAAGGGATTTTAGGG
Found at i:13572944 original size:9 final size:9
Alignment explanation
Indices: 13572930--13572962 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
13572920 TGTAACTAAT
13572930 GAAAATGGG
1 GAAAATGGG
13572939 GAAAAT-GG
1 GAAAATGGG
13572947 GAAAATGGG
1 GAAAATGGG
*
13572956 AAAAATG
1 GAAAATG
13572963 AGAATGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.52, C:0.00, G:0.36, T:0.12
Consensus pattern (9 bp):
GAAAATGGG
Found at i:13572950 original size:8 final size:8
Alignment explanation
Indices: 13572930--13572959 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
13572920 TGTAACTAAT
13572930 GAAAATGGG
1 GAAAAT-GG
13572939 GAAAATGG
1 GAAAATGG
13572947 GAAAATGG
1 GAAAATGG
13572955 GAAAA
1 GAAAA
13572960 ATGAGAATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.37, T:0.10
Consensus pattern (8 bp):
GAAAATGG
Found at i:13572952 original size:17 final size:17
Alignment explanation
Indices: 13572930--13572962 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13572920 TGTAACTAAT
*
13572930 GAAAATGGGGAAAATGG
1 GAAAATGGGAAAAATGG
13572947 GAAAATGGGAAAAATG
1 GAAAATGGGAAAAATG
13572963 AGAATGCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.36, T:0.12
Consensus pattern (17 bp):
GAAAATGGGAAAAATGG
Found at i:13591731 original size:15 final size:15
Alignment explanation
Indices: 13591707--13591742 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
13591697 AAAATTATAA
13591707 AAAT-AAAAAATATT
1 AAATAAAAAAATATT
13591721 AAATAAAAAAATATT
1 AAATAAAAAAATATT
13591736 AAA-AAAA
1 AAATAAAA
13591743 GTTCATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AAATAAAAAAATATT
Found at i:13592148 original size:19 final size:21
Alignment explanation
Indices: 13592120--13592168 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
13592110 GTTTTTTTAC
*
13592120 TAAAATAATA-CAAAAGAA-A
1 TAAAAAAATACCAAAAGAATA
*
13592139 TAAAAAAATACCAAAATAATA
1 TAAAAAAATACCAAAAGAATA
13592160 TACAAAAAA
1 TA-AAAAAA
13592169 ATTATTTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 7 0.28
21 3 0.12
22 6 0.24
ACGTcount: A:0.73, C:0.08, G:0.02, T:0.16
Consensus pattern (21 bp):
TAAAAAAATACCAAAAGAATA
Found at i:13592262 original size:27 final size:27
Alignment explanation
Indices: 13592222--13592287 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
13592212 GGTAATGGAA
* * *
13592222 TGGCGGCACCGGTGGTGCCTTTCTCAT
1 TGGCGGCACAGGTGGTGCCATTCCCAT
13592249 TGGCGGCACAGGTGGTGCCATTCCCAT
1 TGGCGGCACAGGTGGTGCCATTCCCAT
13592276 TGGCGGCACAGG
1 TGGCGGCACAGG
13592288 ACTAAAATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.12, C:0.29, G:0.36, T:0.23
Consensus pattern (27 bp):
TGGCGGCACAGGTGGTGCCATTCCCAT
Found at i:13592860 original size:19 final size:19
Alignment explanation
Indices: 13592815--13592861 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
13592805 AAATTATAAT
* *
13592815 TATTTTTAAATTTATAAAA
1 TATTTTTATATATATAAAA
*
13592834 -AGTATTTATATATATAAAA
1 TA-TTTTTATATATATAAAA
13592853 TATTTTTAT
1 TATTTTTAT
13592862 TTAATTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.05
19 20 0.91
20 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TATTTTTATATATATAAAA
Found at i:13593826 original size:27 final size:27
Alignment explanation
Indices: 13593788--13593850 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
13593778 TTTTAGTCCT
* *
13593788 GTGCCGCCAATGGGAATGGCACCACCG
1 GTGCCGCCAATGAGAAAGGCACCACCG
13593815 GTGCCGCCAATGAGAAAGGCACCACCG
1 GTGCCGCCAATGAGAAAGGCACCACCG
13593842 GTGCCGCCA
1 GTGCCGCCA
13593851 TTCCATTACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.24, C:0.35, G:0.32, T:0.10
Consensus pattern (27 bp):
GTGCCGCCAATGAGAAAGGCACCACCG
Found at i:13593945 original size:19 final size:21
Alignment explanation
Indices: 13593904--13593952 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
13593894 GGTAAATTAT
13593904 TTTTTTGTATATTATTTTAGTA
1 TTTTTT-TATATTATTTTAGTA
*
13593926 TTTTTTTAT-TTCTTTT-GTA
1 TTTTTTTATATTATTTTAGTA
*
13593945 TTATTTTA
1 TTTTTTTA
13593953 ATAAAAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 6 0.24
21 3 0.12
22 6 0.24
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTTTTTATATTATTTTAGTA
Found at i:13594202 original size:24 final size:23
Alignment explanation
Indices: 13594162--13594224 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
13594152 TAGGTAAAAT
13594162 AAATAAAAAATATTAAAAATATAAG
1 AAATAAAAAA-A-TAAAAATATAAG
* *
13594187 CAAATAAAAAAATAAATATATGAG
1 -AAATAAAAAAATAAAAATATAAG
* *
13594211 AAAGAGAAAAATAA
1 AAATAAAAAAATAA
13594225 CAAAAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 12 0.36
24 10 0.30
25 1 0.03
26 10 0.30
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (23 bp):
AAATAAAAAAATAAAAATATAAG
Found at i:13610052 original size:43 final size:42
Alignment explanation
Indices: 13609948--13610073 Score: 137
Period size: 43 Copynumber: 3.0 Consensus size: 42
13609938 GGTGTGATTT
* * * * *
13609948 CATGTAAGACTATGTCTGAGACATTGACATCGATATGAGATTA
1 CATGTAAGACCATGTCTGGGACA-TGGCATCGATATGTGATAA
* *
13609991 CGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATGTGATAA
1 CATGTAAGACCATGTCTGGGACA-TGGCATCGATATGTGATAA
* * *
13610034 CATGTAAGACCATATCTGGGATATGGCAT-TATATGTGATA
1 CATGTAAGACCATGTCTGGGACATGGCATCGATATGTGATA
13610074 TATGTGTTTC
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
41 10 0.14
42 6 0.09
43 54 0.77
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (42 bp):
CATGTAAGACCATGTCTGGGACATGGCATCGATATGTGATAA
Found at i:13614361 original size:122 final size:123
Alignment explanation
Indices: 13614144--13614389 Score: 485
Period size: 122 Copynumber: 2.0 Consensus size: 123
13614134 AAATTAGGTT
13614144 AGTAGAATCGAGTAATTAAGTCGTGAGCACGAGAGATAGAGAGATATCACAATTAGAGTTGTAGA
1 AGTAGAATCGAGTAATTAAGTCGTGAGCACGAGAGATAGAGAGATATCACAATTAGAGTTGTAGA
13614209 AAATAAAATAAAATAAAATATAATAATTAGGTTATTAAATATATATTT-TATAGATTA
66 AAATAAAATAAAATAAAATATAATAATTAGGTTATTAAATATATATTTGTATAGATTA
13614266 AGTAGAATCGAGTAATTAAGTCGTGAGCACGAGAGATAGAGAGATATCACAATTAGAGTTGTAGA
1 AGTAGAATCGAGTAATTAAGTCGTGAGCACGAGAGATAGAGAGATATCACAATTAGAGTTGTAGA
13614331 AAATAAAATAAAATAAAATATAATAATTAGGTTATTAAATATATATTTGTATAGATTA
66 AAATAAAATAAAATAAAATATAATAATTAGGTTATTAAATATATATTTGTATAGATTA
13614389 A
1 A
13614390 AATGAAATGT
Statistics
Matches: 123, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 113 0.92
123 10 0.08
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (123 bp):
AGTAGAATCGAGTAATTAAGTCGTGAGCACGAGAGATAGAGAGATATCACAATTAGAGTTGTAGA
AAATAAAATAAAATAAAATATAATAATTAGGTTATTAAATATATATTTGTATAGATTA
Found at i:13615567 original size:17 final size:17
Alignment explanation
Indices: 13615547--13615589 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
13615537 CTATACTATG
*
13615547 ATGCGAACCCATGTTAT
1 ATGCGAACCAATGTTAT
*
13615564 ATGCAAACCAATGTTAT
1 ATGCGAACCAATGTTAT
13615581 ATGCGAACC
1 ATGCGAACC
13615590 TATATTATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (17 bp):
ATGCGAACCAATGTTAT
Found at i:13615597 original size:17 final size:17
Alignment explanation
Indices: 13615537--13615597 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
13615527 TACGTGTGAA
*
13615537 CTATACTATGATGCGAAC
1 CTATATTAT-ATGCGAAC
* * *
13615555 CCATGTTATATGCAAAC
1 CTATATTATATGCGAAC
* *
13615572 CAATGTTATATGCGAAC
1 CTATATTATATGCGAAC
13615589 CTATATTAT
1 CTATATTAT
13615598 GTGCAAACTA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 29 0.83
18 6 0.17
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (17 bp):
CTATATTATATGCGAAC
Found at i:13615661 original size:34 final size:34
Alignment explanation
Indices: 13615620--13615699 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 34
13615610 CTGTGATCCT
* * *
13615620 AACCTATGTTATGTGTGAATTATTCTGTTATGCG
1 AACCTATGTTATGTATGAATTATGCTGATATGCG
** *
13615654 ATTCTATGTTATGTATGACTTATGCTGATATGCG
1 AACCTATGTTATGTATGAATTATGCTGATATGCG
13615688 AACCTATGTTAT
1 AACCTATGTTAT
13615700 TAGCAAACTA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (34 bp):
AACCTATGTTATGTATGAATTATGCTGATATGCG
Found at i:13615733 original size:15 final size:15
Alignment explanation
Indices: 13615679--13615786 Score: 71
Period size: 15 Copynumber: 7.1 Consensus size: 15
13615669 TGACTTATGC
13615679 TGATA-TGCGAACCTA
1 TGATATTGCGAA-CTA
* *
13615694 TGTTATTAGCAAACTA
1 TGATATT-GCGAACTA
*
13615710 TCA-ATTGCGAACTA
1 TGATATTGCGAACTA
* *
13615724 TGATATTGCGAGCTC
1 TGATATTGCGAACTA
* *
13615739 TGCTAAATTGAGAAC-A
1 TG--ATATTGCGAACTA
*
13615755 GTGATATTGAGAACTA
1 -TGATATTGCGAACTA
13615771 TGA-ATTGCGAACTA
1 TGATATTGCGAACTA
13615785 TG
1 TG
13615787 CTATATTATG
Statistics
Matches: 72, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
14 21 0.29
15 31 0.43
16 6 0.08
17 14 0.19
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (15 bp):
TGATATTGCGAACTA
Found at i:13623256 original size:3 final size:3
Alignment explanation
Indices: 13623248--13623286 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
13623238 CTGAAAGAGG
13623248 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
13623287 CTTAAGTGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:13634643 original size:9 final size:9
Alignment explanation
Indices: 13634613--13634658 Score: 53
Period size: 8 Copynumber: 5.4 Consensus size: 9
13634603 AATGAAAACG
13634613 TAAAT-AAA
1 TAAATAAAA
13634621 TAAAT-AAA
1 TAAATAAAA
13634629 TAAATAAAA
1 TAAATAAAA
*
13634638 TGAATAAAA
1 TAAATAAAA
*
13634647 TATA-AAAA
1 TAAATAAAA
13634655 TAAA
1 TAAA
13634659 AANNNNNNNN
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 20 0.61
9 13 0.39
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (9 bp):
TAAATAAAA
Found at i:13637318 original size:15 final size:15
Alignment explanation
Indices: 13637295--13637330 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
13637285 CTAAGTAGCA
*
13637295 GTTTAGGTTTTGGGT
1 GTTTGGGTTTTGGGT
13637310 GTTTGGGTTTTGGGT
1 GTTTGGGTTTTGGGT
13637325 -TTTGGG
1 GTTTGGG
13637331 CCCCGAGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.03, C:0.00, G:0.44, T:0.53
Consensus pattern (15 bp):
GTTTGGGTTTTGGGT
Found at i:13637323 original size:7 final size:7
Alignment explanation
Indices: 13637300--13637330 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
13637290 TAGCAGTTTA
13637300 GGTTTTG
1 GGTTTTG
13637307 GGTGTTTG
1 GGT-TTTG
13637315 GGTTTTG
1 GGTTTTG
13637322 GGTTTTG
1 GGTTTTG
13637329 GG
1 GG
13637331 CCCCGAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (7 bp):
GGTTTTG
Found at i:13651710 original size:15 final size:16
Alignment explanation
Indices: 13651678--13651715 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
13651668 AATACTAATT
*
13651678 TTAAAATTTATAGAAA
1 TTAAAATTGATAGAAA
13651694 TTAAAATTGAT-GAAA
1 TTAAAATTGATAGAAA
13651709 TTAAAAT
1 TTAAAAT
13651716 ACAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (16 bp):
TTAAAATTGATAGAAA
Found at i:13654991 original size:21 final size:21
Alignment explanation
Indices: 13654955--13655026 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
13654945 TAAAACAACA
13654955 GTTTCTCCCCTCGTTCTTGTTG
1 GTTTCT-CCCTCGTTCTTGTTG
*
13654977 GTTTCTCCCTTGTTCTTGTTG
1 GTTTCTCCCTCGTTCTTGTTG
*
13654998 GTTTCTCCCTCGTTTTTGTTG
1 GTTTCTCCCTCGTTCTTGTTG
13655019 GTTTCTCC
1 GTTTCTCC
13655027 TCTCTTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 41 0.87
22 6 0.13
ACGTcount: A:0.00, C:0.28, G:0.18, T:0.54
Consensus pattern (21 bp):
GTTTCTCCCTCGTTCTTGTTG
Found at i:13655046 original size:22 final size:21
Alignment explanation
Indices: 13654955--13655037 Score: 112
Period size: 21 Copynumber: 3.9 Consensus size: 21
13654945 TAAAACAACA
*
13654955 GTTTCTCCCCTCGTTCTTGTTG
1 GTTTCT-CCCTCGTTTTTGTTG
* *
13654977 GTTTCTCCCTTGTTCTTGTTG
1 GTTTCTCCCTCGTTTTTGTTG
13654998 GTTTCTCCCTCGTTTTTGTTG
1 GTTTCTCCCTCGTTTTTGTTG
*
13655019 GTTTCTCCTCTCTTTTTTG
1 GTTTCTCC-CTCGTTTTTG
13655038 CTTTGTTCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
21 41 0.73
22 15 0.27
ACGTcount: A:0.00, C:0.27, G:0.17, T:0.57
Consensus pattern (21 bp):
GTTTCTCCCTCGTTTTTGTTG
Found at i:13656889 original size:62 final size:62
Alignment explanation
Indices: 13656806--13657100 Score: 464
Period size: 62 Copynumber: 4.7 Consensus size: 62
13656796 TGGAGGTGGA
13656806 TTGGGACTTTGATCGGTGGAAGAGGGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGGGT
1 TTGGGACTTTGATCGGTGGAAGAGGGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGGGT
* *
13656868 TTGGAACTTTGATCAGTGGAAGAGGGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGGGT
1 TTGGGACTTTGATCGGTGGAAGAGGGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGGGT
* * *
13656930 TTGGGACTTTGATTGGTGGAAGAGGGGAAATGGGAATGTGAAATGGGAGGAGGGCAGGGGGT
1 TTGGGACTTTGATCGGTGGAAGAGGGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGGGT
* * * * *
13656992 TTGGGACTTTGATCAGTGGAAGAGGGGAAATGGGAATGGGGAAATTGCACTGAGGGCACAGGGT
1 TTGGGACTTTGATCGGTGGAAGAGGGGAAATGGGAAT-GGGAAATGGGA-GGAGGGCACGGGGT
*
13657056 TTGGGACTTTGATCGGTGAAAGAGGGGAAATGGGAATGGGGAAAT
1 TTGGGACTTTGATCGGTGGAAGAGGGGAAATGGGAAT-GGGAAAT
13657101 TGCACTGTAT
Statistics
Matches: 214, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
62 152 0.71
63 8 0.04
64 54 0.25
ACGTcount: A:0.28, C:0.06, G:0.46, T:0.20
Consensus pattern (62 bp):
TTGGGACTTTGATCGGTGGAAGAGGGGAAATGGGAATGGGAAATGGGAGGAGGGCACGGGGT
Found at i:13664112 original size:78 final size:78
Alignment explanation
Indices: 13664018--13664206 Score: 297
Period size: 78 Copynumber: 2.4 Consensus size: 78
13664008 ATATACATTG
*
13664018 CATATGTGTTATTATTAGTTTCGAATCTTACATTTCATTATTTTAGCGTTTTGATAAATTACTTA
1 CATATGTGTTATTATTAGTTTCGAATCTTACATTTCATTATTTAAGCGTTTTGATAAATTACTTA
* *
13664083 AGTAAATTGTATT
66 AATAAATTGTACT
* * * * * *
13664096 CATATATGATATTATTAGTTTCAAATCTTACATTTTATTATTTAAGTGTTTTGATAATTTACTTA
1 CATATGTGTTATTATTAGTTTCGAATCTTACATTTCATTATTTAAGCGTTTTGATAAATTACTTA
13664161 AATAAATTGTACT
66 AATAAATTGTACT
13664174 CATATGTGTTATTATTAGTTTCGAATCTTACAT
1 CATATGTGTTATTATTAGTTTCGAATCTTACAT
13664207 ACTTAAAACA
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 99 1.00
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50
Consensus pattern (78 bp):
CATATGTGTTATTATTAGTTTCGAATCTTACATTTCATTATTTAAGCGTTTTGATAAATTACTTA
AATAAATTGTACT
Found at i:13665343 original size:19 final size:19
Alignment explanation
Indices: 13665319--13665360 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
13665309 AGCAATTATA
13665319 TTTATGAATGGTAGGAATT
1 TTTATGAATGGTAGGAATT
*
13665338 TTTATGAATTGTAGGAATT
1 TTTATGAATGGTAGGAATT
13665357 TTTA
1 TTTA
13665361 GTTTTTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (19 bp):
TTTATGAATGGTAGGAATT
Found at i:13667465 original size:61 final size:61
Alignment explanation
Indices: 13667347--13667470 Score: 167
Period size: 61 Copynumber: 2.0 Consensus size: 61
13667337 AACAATTAAC
* * * **
13667347 TTATTGAATTTTTTAGAATTAAAACTAAATTGACAAATTTTATAAATTTTGAAGGCTAAAT
1 TTATTGAATTTTTTAGAATTAAAACTAAAATGAAAAAATTTATAAACATTGAAGGCTAAAT
* * **
13667408 TTATTGAATTTTTTAGAATTCAAACTAAAATGAAAAAATTTGTAAACATTGGGGGCTAAAT
1 TTATTGAATTTTTTAGAATTAAAACTAAAATGAAAAAATTTATAAACATTGAAGGCTAAAT
13667469 TT
1 TT
13667471 GTTATTATAC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (61 bp):
TTATTGAATTTTTTAGAATTAAAACTAAAATGAAAAAATTTATAAACATTGAAGGCTAAAT
Found at i:13667688 original size:22 final size:20
Alignment explanation
Indices: 13667644--13667688 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
13667634 AAAATTACTC
*
13667644 ATAATGTGAGATTATCAAAA
1 ATAATGTGAGATAATCAAAA
*
13667664 ATAATGTGAGACTAAATTAAAA
1 ATAATGTGAGA-T-AATCAAAA
13667686 ATA
1 ATA
13667689 TTAATTTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 1 0.05
22 9 0.43
ACGTcount: A:0.53, C:0.04, G:0.13, T:0.29
Consensus pattern (20 bp):
ATAATGTGAGATAATCAAAA
Found at i:13674902 original size:44 final size:43
Alignment explanation
Indices: 13674852--13675275 Score: 226
Period size: 44 Copynumber: 9.7 Consensus size: 43
13674842 TCGCATCTAG
* *
13674852 TCTTATCTCCCTGAAGTTGCACTGGAGCAGACTAAGTAAGCAAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAA
* * * * *
13674896 TCTTATC-CTCCTAAAGTTACAATGGGGCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAA
* * *
13674941 CCTTATCTCCCTGAAGTTGCAGTGGAGCAG-GTTA-AAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AA
* * * * * * **
13674985 TCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAA-AATCTTGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC--AAA
* * * * * * *
13675029 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAA
* *
13675069 TCTTATCTCCCTGAAGTTGCACTGGAGCAGACTAAGTAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAA
* * *
13675113 TCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGAAGCAAA
* * * * *
13675157 ACATTATCTCCCTGAAGTTGCAGTGGAACAG-GTTA-AAGCCGATAG
1 TC-TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AA
* * *
13675202 TCCTATCTCCCTGAAGTTGCAGTGGAGC-GAATTAA-AATCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ACTAAGAAGCA-A-A
* *
13675246 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
13675276 TCGCATCTAG
Statistics
Matches: 288, Mismatches: 67, Indels: 51
0.71 0.17 0.13
Matches are distributed among these distances:
40 20 0.07
41 8 0.03
42 9 0.03
43 20 0.07
44 162 0.56
45 67 0.23
46 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAA
Found at i:13675208 original size:217 final size:217
Alignment explanation
Indices: 13674823--13675318 Score: 814
Period size: 217 Copynumber: 2.3 Consensus size: 217
13674813 CCTTACCACT
*
13674823 TGAAATTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCACTGGAGCAGACTAAG
1 TGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCACTGGAGCAGACTAAG
* *
13674888 TAAGCAACTCTTATCCTCCTAAAGTTACAATGGGGCAGACTGAAGATGGCAAACCTTATCTCCCT
66 TAAGCAACTCTTATCCTCCTAAAGTTACAATGGGGCAGACTGAAGATGGAAAACATTATCTCCCT
* * *
13674953 GAAGTTGCAGTGGAGCAGGTTAAAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATT
131 GAAGTTGCAGTGGAACAGGTTAAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGAATT
***
13675018 AAAATCTTGGATCTTATCTCTC
196 AAAATCACAGATCTTATCTCTC
13675040 TGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCACTGGAGCAGACTAAG
1 TGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCACTGGAGCAGACTAAG
* * * *
13675105 TAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGAAAACATTATCTCCCT
66 TAAGCAACTCTTATCCTCCTAAAGTTACAATGGGGCAGACTGAAGATGGAAAACATTATCTCCCT
* *
13675170 GAAGTTGCAGTGGAACAGGTTAAAGCCGATAGTCCTATCTCCCTGAAGTTGCAGTGGAGCGAATT
131 GAAGTTGCAGTGGAACAGGTTAAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGAATT
13675235 AAAATCACAGATCTTATCTCTC
196 AAAATCACAGATCTTATCTCTC
* * *
13675257 TGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGACA-TTGCAGTGGAGTAGACT
1 TGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGA-AGTTGCACTGGAGCAGACT
13675319 GTAGCACTAG
Statistics
Matches: 260, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
217 259 1.00
218 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (217 bp):
TGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCACTGGAGCAGACTAAG
TAAGCAACTCTTATCCTCCTAAAGTTACAATGGGGCAGACTGAAGATGGAAAACATTATCTCCCT
GAAGTTGCAGTGGAACAGGTTAAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGAATT
AAAATCACAGATCTTATCTCTC
Found at i:13675877 original size:18 final size:17
Alignment explanation
Indices: 13675856--13675890 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13675846 TGCATTTTCG
13675856 TTTTACTATTTATTTTAT
1 TTTTACTATTT-TTTTAT
*
13675874 TTTTATTATTTTTTTAT
1 TTTTACTATTTTTTTAT
13675891 ATACTGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTACTATTTTTTTAT
Found at i:13676687 original size:9 final size:9
Alignment explanation
Indices: 13676647--13676710 Score: 65
Period size: 9 Copynumber: 6.8 Consensus size: 9
13676637 CAATTTAGTA
13676647 TTTTTTTAT
1 TTTTTTTAT
13676656 TATTTTTTAT
1 T-TTTTTTAT
* *
13676666 GTAATTATTAT
1 -T-TTTTTTAT
13676677 TTTTTTTAT
1 TTTTTTTAT
13676686 TTTTTTTAT
1 TTTTTTTAT
**
13676695 TTTTTTCCT
1 TTTTTTTAT
13676704 TTTTTTT
1 TTTTTTT
13676711 CTAACAAATG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
9 29 0.63
10 9 0.20
11 8 0.17
ACGTcount: A:0.14, C:0.03, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:13678002 original size:19 final size:19
Alignment explanation
Indices: 13677978--13678018 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
13677968 TAAATTAAAG
13677978 ATAGAAAA-AAATAAACTAA
1 ATAGAAAATAAATAAA-TAA
*
13677997 ATAGAAAATATATAAATAA
1 ATAGAAAATAAATAAATAA
13678016 ATA
1 ATA
13678019 ATAATGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (19 bp):
ATAGAAAATAAATAAATAA
Found at i:13678330 original size:6 final size:7
Alignment explanation
Indices: 13678308--13678337 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
13678298 TTTATTTGTT
*
13678308 AAATGAA
1 AAATTAA
13678315 AAATTAA
1 AAATTAA
13678322 AAATTAA
1 AAATTAA
13678329 AAATTAA
1 AAATTAA
13678336 AA
1 AA
13678338 GTTTTACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (7 bp):
AAATTAA
Found at i:13679299 original size:34 final size:34
Alignment explanation
Indices: 13679256--13679323 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
13679246 ACATAACCAT
13679256 TTCCATATGAATGTGTACCTATATAAAGTGGTAA
1 TTCCATATGAATGTGTACCTATATAAAGTGGTAA
13679290 TTCCATATGAATGTGTACCTATATAAAGTGGTAA
1 TTCCATATGAATGTGTACCTATATAAAGTGGTAA
13679324 ATTAATTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (34 bp):
TTCCATATGAATGTGTACCTATATAAAGTGGTAA
Found at i:13681523 original size:105 final size:105
Alignment explanation
Indices: 13681308--13681512 Score: 311
Period size: 105 Copynumber: 2.0 Consensus size: 105
13681298 CGTAAATATC
* **
13681308 ATATTTAATATTTATGGACACGGTTTATGAAAATAGGGTTCCAAAATCGCATTTTCTAACACCAC
1 ATATTTAATATTTATGGACACAGTTTACAAAAATAGGGTTCCAAAATCGCATTTTCTAACACCAC
* * * *
13681373 TGAAAACCAGGTCATTACAGATATACAGACAACAACATAG
66 TAAAAACCAGGTCATTACAAATACACAAACAACAACATAG
*** *
13681413 ATATTTAATATTTATGGACACAGTTTACAAAAATAGGGTTTTGAAATGGCATTTTCTAACACCAC
1 ATATTTAATATTTATGGACACAGTTTACAAAAATAGGGTTCCAAAATCGCATTTTCTAACACCAC
13681478 TAAAAACCAGGTCATTACAAATACACAAACAACAA
66 TAAAAACCAGGTCATTACAAATACACAAACAACAA
13681513 TATTGGTATT
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 89 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.28
Consensus pattern (105 bp):
ATATTTAATATTTATGGACACAGTTTACAAAAATAGGGTTCCAAAATCGCATTTTCTAACACCAC
TAAAAACCAGGTCATTACAAATACACAAACAACAACATAG
Found at i:13681808 original size:28 final size:29
Alignment explanation
Indices: 13681777--13681840 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
13681767 AAAAGAATAT
*
13681777 AAAAATTACAAATAATTATTAAAATTA-A
1 AAAAATTAAAAATAATTATTAAAATTATA
* * *
13681805 AAAAATAAAAAATAATTATTCAAATTATT
1 AAAAATTAAAAATAATTATTAAAATTATA
13681834 AAAAATT
1 AAAAATT
13681841 TATAAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 24 0.80
29 6 0.20
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (29 bp):
AAAAATTAAAAATAATTATTAAAATTATA
Done.