Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 4 of 145
Found at i:1258910 original size:20 final size:20
Alignment explanation
Indices: 1258861--1258910 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1258851 AACTTAGCTC
*
1258861 TTAACATTTATATTTTTTTAA
1 TTAA-ATTTTTATTTTTTTAA
* *
1258882 TTTAGTTTTTATTTTTTTAA
1 TTAAATTTTTATTTTTTTAA
1258902 TTAAATTTT
1 TTAAATTTT
1258911 ACCTCCATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TTAAATTTTTATTTTTTTAA
Found at i:1266407 original size:8 final size:8
Alignment explanation
Indices: 1266394--1266426 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
1266384 GGATTTAGGT
1266394 TTATTTTA
1 TTATTTTA
1266402 TTATTTTA
1 TTATTTTA
1266410 TTATTTTA
1 TTATTTTA
1266418 TTATTTTA
1 TTATTTTA
1266426 T
1 T
1266427 CAATTACGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTTTA
Found at i:1271894 original size:22 final size:21
Alignment explanation
Indices: 1271869--1271912 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1271859 TTCGATTTTT
1271869 AGTTCAAAGTAATTTTATGTTG
1 AGTTCAAAGTAATTTTA-GTTG
* **
1271891 AGTTGAATTTAATTTTAGTTG
1 AGTTCAAAGTAATTTTAGTTG
1271912 A
1 A
1271913 TCAGATATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (21 bp):
AGTTCAAAGTAATTTTAGTTG
Found at i:1271983 original size:17 final size:18
Alignment explanation
Indices: 1271963--1271998 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1271953 TATAAATTCT
1271963 TTAAAAATATA-TATTAA
1 TTAAAAATATATTATTAA
*
1271980 TTAAAATTATATTATTAA
1 TTAAAAATATATTATTAA
1271998 T
1 T
1271999 ATGTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAAATATATTATTAA
Found at i:1272107 original size:22 final size:22
Alignment explanation
Indices: 1272079--1272124 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1272069 ACCAAATATT
*
1272079 TAAAATTATTTTTTTTAAATCA
1 TAAAATTATTTTTCTTAAATCA
1272101 TAAAATTATTTTTCTTAAATCA
1 TAAAATTATTTTTCTTAAATCA
1272123 TA
1 TA
1272125 TTAACAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAAATTATTTTTCTTAAATCA
Found at i:1275029 original size:28 final size:28
Alignment explanation
Indices: 1274989--1275050 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
1274979 TCAATCTGTG
1274989 TTAAATTTTTCTCTCTTAAAGCTTAAGC
1 TTAAATTTTTCTCTCTTAAAGCTTAAGC
1275017 TTAAATTTTTCTCTCTTAAAGCTTAAGC
1 TTAAATTTTTCTCTCTTAAAGCTTAAGC
1275045 TTAAAT
1 TTAAAT
1275051 GTGCTAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (28 bp):
TTAAATTTTTCTCTCTTAAAGCTTAAGC
Found at i:1276032 original size:15 final size:15
Alignment explanation
Indices: 1276012--1276041 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1276002 TGATTTTGAT
1276012 ATTTTAAAATTTAAA
1 ATTTTAAAATTTAAA
*
1276027 ATTTTAATATTTAAA
1 ATTTTAAAATTTAAA
1276042 TAAAAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTAAAATTTAAA
Found at i:1285512 original size:3 final size:3
Alignment explanation
Indices: 1285504--1285542 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1285494 ATTTTTCCAA
1285504 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1285543 GTGATCTAAG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1288979 original size:83 final size:84
Alignment explanation
Indices: 1288892--1289048 Score: 246
Period size: 84 Copynumber: 1.9 Consensus size: 84
1288882 AGGGGGGCTA
* * *
1288892 AAGTGCAATTTTACTATATGTTAGTTTATAATTTCT-T-TATTTATAAGAGGACTGAATTGAAAA
1 AAGTGCAATTTCACTATATATTAATTTATAATTT-TATCTATTTATAAGAGGACTGAATTGAAAA
1288955 TTTTTCATTTGGGGTGGTCG
65 TTTTTCATTTGGGGTGGTCG
* *
1288975 AAGTGCAATTTCACTATATATTAATTTATAGTTTTATCTATTTATAAGAGGACTGAATTGAAATT
1 AAGTGCAATTTCACTATATATTAATTTATAATTTTATCTATTTATAAGAGGACTGAATTGAAAAT
1289040 TTTTCATTT
66 TTTTCATTT
1289049 TCCCCTGCCT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
82 1 0.01
83 31 0.46
84 35 0.52
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (84 bp):
AAGTGCAATTTCACTATATATTAATTTATAATTTTATCTATTTATAAGAGGACTGAATTGAAAAT
TTTTCATTTGGGGTGGTCG
Found at i:1295281 original size:16 final size:16
Alignment explanation
Indices: 1295262--1295306 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1295252 ACACAAAATT
1295262 AAAATAATCCAAACCC
1 AAAATAATCCAAACCC
* ***
1295278 AAAATAATCTAAATTT
1 AAAATAATCCAAACCC
1295294 AAAATAATCCAAA
1 AAAATAATCCAAA
1295307 ACTTTGAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.18, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATAATCCAAACCC
Found at i:1295969 original size:8 final size:8
Alignment explanation
Indices: 1295956--1295985 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1295946 TTTTATGCCC
*
1295956 TTTAAATT
1 TTTAAAAT
1295964 TTTAAAAT
1 TTTAAAAT
1295972 TTTAAAAT
1 TTTAAAAT
1295980 TTTAAA
1 TTTAAA
1295986 TTAGTAAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTAAAAT
Found at i:1313512 original size:31 final size:31
Alignment explanation
Indices: 1313471--1313539 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
1313461 GTAACAAAAT
* *
1313471 AGTCATTGAACTACTT-GAAA-ATTTTCATTTA
1 AGTCACTGAACTA-TTCGAAATATCTT-ATTTA
1313502 AGTCACTGAACTATTCGAAATATCTTATTTA
1 AGTCACTGAACTATTCGAAATATCTTATTTA
*
1313533 AGGCACT
1 AGTCACT
1313540 AGCCTATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 2 0.06
31 27 0.82
32 4 0.12
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (31 bp):
AGTCACTGAACTATTCGAAATATCTTATTTA
Found at i:1316458 original size:83 final size:83
Alignment explanation
Indices: 1316371--1316629 Score: 244
Period size: 83 Copynumber: 3.1 Consensus size: 83
1316361 TTAATAGTTG
1316371 GAGTTGTGAGAATTATATATTTAAAAATAATTATAATTTAATTTAAAATTATTAAATAAAAATAT
1 GAGTTGTGAGAATTATATATTTAAAAATAATTATAATTTAATTTAAAATTATTAAATAAAAATAT
1316436 TATTTTGATTTTAAAATA
66 TATTTTGATTTTAAAATA
* * * * ** * * * **
1316454 GAGTTAT--TACTTGA-ATAGTTTCATCATATACTA-AATTCACATTTAAAAATAAAAAAGTTAA
1 GAGTTGTGAGAATT-ATATA-TTTAAAAATA-ATTATAATTTA-ATTTAAAATTATTAAA--TAA
* *
1316515 AAACTAATTATAATTT-A--TTAATAGTTG
60 AAA-T-ATTAT--TTTGATTTTAA-A-ATA
1316542 GAGTTGTGAGAATTATATATTTAAAAATAATTATAATTTAATTTAAAATTATTAAATAAAAATAT
1 GAGTTGTGAGAATTATATATTTAAAAATAATTATAATTTAATTTAAAATTATTAAATAAAAATAT
1316607 TATTTTGATTTTAAAATA
66 TATTTTGATTTTAAAATA
1316625 GAGTT
1 GAGTT
1316630 ATTACTTGAA
Statistics
Matches: 131, Mismatches: 26, Indels: 38
0.67 0.13 0.19
Matches are distributed among these distances:
81 6 0.05
82 16 0.12
83 29 0.22
84 6 0.05
85 11 0.08
86 11 0.08
87 6 0.05
88 24 0.18
89 16 0.12
90 6 0.05
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (83 bp):
GAGTTGTGAGAATTATATATTTAAAAATAATTATAATTTAATTTAAAATTATTAAATAAAAATAT
TATTTTGATTTTAAAATA
Found at i:1316501 original size:171 final size:172
Alignment explanation
Indices: 1316300--1316642 Score: 679
Period size: 171 Copynumber: 2.0 Consensus size: 172
1316290 ATTTTTTATT
1316300 TTTCATCATATTACTAAATTCACATTTAAAAATAAAAAAGTTAAAAACTAATTATAATTTATTAA
1 TTTCATCATATTACTAAATTCACATTTAAAAATAAAAAAGTTAAAAACTAATTATAATTTATTAA
1316365 TAGTTGGAGTTGTGAGAATTATATATTTAAAAATAATTATAATTTAATTTAAAATTATTAAATAA
66 TAGTTGGAGTTGTGAGAATTATATATTTAAAAATAATTATAATTTAATTTAAAATTATTAAATAA
1316430 AAATATTATTTTGATTTTAAAATAGAGTTATTACTTGAATAG
131 AAATATTATTTTGATTTTAAAATAGAGTTATTACTTGAATAG
1316472 TTTCATCATA-TACTAAATTCACATTTAAAAATAAAAAAGTTAAAAACTAATTATAATTTATTAA
1 TTTCATCATATTACTAAATTCACATTTAAAAATAAAAAAGTTAAAAACTAATTATAATTTATTAA
1316536 TAGTTGGAGTTGTGAGAATTATATATTTAAAAATAATTATAATTTAATTTAAAATTATTAAATAA
66 TAGTTGGAGTTGTGAGAATTATATATTTAAAAATAATTATAATTTAATTTAAAATTATTAAATAA
1316601 AAATATTATTTTGATTTTAAAATAGAGTTATTACTTGAATAG
131 AAATATTATTTTGATTTTAAAATAGAGTTATTACTTGAATAG
1316643 AATCTAAGCA
Statistics
Matches: 171, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
171 161 0.94
172 10 0.06
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42
Consensus pattern (172 bp):
TTTCATCATATTACTAAATTCACATTTAAAAATAAAAAAGTTAAAAACTAATTATAATTTATTAA
TAGTTGGAGTTGTGAGAATTATATATTTAAAAATAATTATAATTTAATTTAAAATTATTAAATAA
AAATATTATTTTGATTTTAAAATAGAGTTATTACTTGAATAG
Found at i:1328859 original size:9 final size:9
Alignment explanation
Indices: 1328845--1328930 Score: 93
Period size: 9 Copynumber: 9.4 Consensus size: 9
1328835 TTTGATTAAA
1328845 AATTACCCG
1 AATTACCCG
1328854 AATTACCCG
1 AATTACCCG
1328863 AATTACCCG
1 AATTACCCG
*
1328872 AATTAACCG
1 AATTACCCG
* *
1328881 AATTAACAG
1 AATTACCCG
*
1328890 AATTAACCG
1 AATTACCCG
1328899 AATTA-CCG
1 AATTACCCG
*
1328907 AAAAATACCCG
1 --AATTACCCG
*
1328918 AATTACCTG
1 AATTACCCG
1328927 AATT
1 AATT
1328931 TTTTTATTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
8 3 0.04
9 58 0.85
10 4 0.06
11 3 0.04
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:1333817 original size:2 final size:2
Alignment explanation
Indices: 1333810--1333834 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1333800 ATACTTTAAT
1333810 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 T
1333835 TACTTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1335067 original size:2 final size:2
Alignment explanation
Indices: 1335060--1335090 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1335050 GCTGCCATCT
1335060 TA TA 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 T
1335091 TATCATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1337998 original size:25 final size:25
Alignment explanation
Indices: 1337970--1338043 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 25
1337960 AGGCTCCAAC
1337970 CTGAACTTAACTAAAAGAATATAAT
1 CTGAACTTAACTAAAAGAATATAAT
* * ** *
1337995 CTGAACCTAA--AAAAG-CTCCAAC
1 CTGAACTTAACTAAAAGAATATAAT
*
1338017 CTGAACTTAGCTAAAAGAATATAAT
1 CTGAACTTAACTAAAAGAATATAAT
1338042 CT
1 CT
1338044 TCAAAATTAG
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
22 11 0.31
23 5 0.14
24 5 0.14
25 14 0.40
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.24
Consensus pattern (25 bp):
CTGAACTTAACTAAAAGAATATAAT
Found at i:1338013 original size:47 final size:47
Alignment explanation
Indices: 1337944--1338043 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 47
1337934 CAAACCTAGG
*
1337944 TAATCTGAACCTAAAAAGGCTCCAACCTGAACTTAACTAAAAGAATA
1 TAATCTGAACCTAAAAAAGCTCCAACCTGAACTTAACTAAAAGAATA
*
1337991 TAATCTGAACCTAAAAAAGCTCCAACCTGAACTTAGCTAAAAGAATA
1 TAATCTGAACCTAAAAAAGCTCCAACCTGAACTTAACTAAAAGAATA
1338038 TAATCT
1 TAATCT
1338044 TCAAAATTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (47 bp):
TAATCTGAACCTAAAAAAGCTCCAACCTGAACTTAACTAAAAGAATA
Found at i:1338020 original size:22 final size:22
Alignment explanation
Indices: 1337948--1338022 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
1337938 CCTAGGTAAT
*
1337948 CTGAACCTAAAAAGGCTCCAAC
1 CTGAACCTAAAAAAGCTCCAAC
* * ** *
1337970 CTGAACTTAACTAAAAGAATATAAT
1 CTGAACCTAA--AAAAG-CTCCAAC
1337995 CTGAACCTAAAAAAGCTCCAAC
1 CTGAACCTAAAAAAGCTCCAAC
1338017 CTGAAC
1 CTGAAC
1338023 TTAGCTAAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 4 0.10
25 12 0.31
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.19
Consensus pattern (22 bp):
CTGAACCTAAAAAAGCTCCAAC
Found at i:1340772 original size:39 final size:41
Alignment explanation
Indices: 1340710--1340798 Score: 130
Period size: 39 Copynumber: 2.2 Consensus size: 41
1340700 TGAAAAGTAT
*
1340710 TTATATT-AAAAACACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
*
1340750 TTATATTAAAAAACAC-A-AATAAATATAATAATTATTTTA
1 TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
*
1340789 TTACATTAAA
1 TTATATTAAA
1340799 TATAATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 29 0.64
40 8 0.18
41 8 0.18
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (41 bp):
TTATATTAAAAAACACTACAATAAATATAATAAATATTTTA
Found at i:1342053 original size:52 final size:52
Alignment explanation
Indices: 1341956--1342054 Score: 117
Period size: 52 Copynumber: 1.9 Consensus size: 52
1341946 AAAATAAAAA
* *
1341956 ACTCAAGCCTTAAACCTACCCTGACCCCAATTGACTCAATCCAAAAAGGAAT
1 ACTCAAGCCTTAAACCTACCCTGACCCCAATTAACCCAATCCAAAAAGGAAT
* * * * * * *
1342008 ACTCAAGCGTTAGACCTGCCCTGATCTCAATTAACCCGATTCAAAAA
1 ACTCAAGCCTTAAACCTACCCTGACCCCAATTAACCCAATCCAAAAA
1342055 ATAAAAATTG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 38 1.00
ACGTcount: A:0.36, C:0.31, G:0.11, T:0.21
Consensus pattern (52 bp):
ACTCAAGCCTTAAACCTACCCTGACCCCAATTAACCCAATCCAAAAAGGAAT
Found at i:1345443 original size:3 final size:3
Alignment explanation
Indices: 1345437--1345462 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1345427 ATTAAAAACC
1345437 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1345463 ATAAACATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1346722 original size:29 final size:30
Alignment explanation
Indices: 1346655--1346722 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
1346645 ATTTGCAATT
* * *
1346655 ATTTGATTCTTTTTAATAGTATAGAGACTAC
1 ATTTGA-TCTATTTAATAATAAAGAGACTAC
*
1346686 A-TTAATCTATTTAATAATAAAGAGACTA-
1 ATTTGATCTATTTAATAATAAAGAGACTAC
1346714 ATTTGATCT
1 ATTTGATCT
1346723 GGTCCCTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 1 0.03
29 26 0.84
30 3 0.10
31 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (30 bp):
ATTTGATCTATTTAATAATAAAGAGACTAC
Found at i:1351693 original size:29 final size:28
Alignment explanation
Indices: 1351630--1351685 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
1351620 TATACATGCT
*
1351630 AAACATTTAATAATTTTTTATTATATAAA
1 AAACATTTAAT-ATTTTTTATTATAAAAA
1351659 AAACATTTAATATTTTTT-TTA-AAAAA
1 AAACATTTAATATTTTTTATTATAAAAA
1351685 A
1 A
1351686 TCCAACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 5 0.19
27 3 0.12
28 7 0.27
29 11 0.42
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (28 bp):
AAACATTTAATATTTTTTATTATAAAAA
Found at i:1357514 original size:15 final size:17
Alignment explanation
Indices: 1357477--1357514 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1357467 TAGAAATTAA
1357477 AATATTCAAATCTGTAT
1 AATATTCAAATCTGTAT
*
1357494 ATTATTCAAAT-T-TAT
1 AATATTCAAATCTGTAT
1357509 AATATT
1 AATATT
1357515 TAAAATTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (17 bp):
AATATTCAAATCTGTAT
Found at i:1363305 original size:19 final size:21
Alignment explanation
Indices: 1363264--1363305 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
1363254 AAATTATGTG
*
1363264 AAAATAGTTTAATTTTAATAT
1 AAAATAGTTTAATTTTAACAT
*
1363285 AAAATA-TTT-ATTTTTACAT
1 AAAATAGTTTAATTTTAACAT
1363304 AA
1 AA
1363306 GAAATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATAGTTTAATTTTAACAT
Found at i:1363816 original size:7 final size:6
Alignment explanation
Indices: 1363803--1363835 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
1363793 GGGTTTTAGT
1363803 TAAAAA TAAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA T-AAAAA TAAAAA TAAAAA TAAAAA TA
1363836 TTTATTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:1363877 original size:108 final size:102
Alignment explanation
Indices: 1363700--1363891 Score: 258
Period size: 108 Copynumber: 1.8 Consensus size: 102
1363690 TTAAAGTATT
* * * * **
1363700 TTAAAATTAAAAAATAAAAATAAAAATTATATATTTATTATATTCGGGCCGGGCCGGGCTCGGGC
1 TTAAAAATAAAAAATAAAAATAAAAATAAAATATTTATTATATTCGGGCCGAGCCGGGCTCAAGC
*
1363765 CAAAAAAGTGGTGCCCGAGGCCCGGCCCGGGTTTTAG
66 CAAAAAAGTGGAGCCCGAGGCCCGGCCCGGGTTTTAG
1363802 TTAAAAATAAAAAATAAAAATAAAAATAAAAATATTTATTATATTCGGGTCGGGCTGAGCCGGGC
1 TTAAAAATAAAAAATAAAAATAAAAAT-AAAATATTTATTATATTCGGG-C---C-GAGCCGGGC
*
1363867 TCAAGCCAAAAAAGTTGAGCCCGAG
60 TCAAGCCAAAAAAGTGGAGCCCGAG
1363892 CTCATATTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
102 26 0.34
103 19 0.25
104 1 0.01
107 1 0.01
108 29 0.38
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (102 bp):
TTAAAAATAAAAAATAAAAATAAAAATAAAATATTTATTATATTCGGGCCGAGCCGGGCTCAAGC
CAAAAAAGTGGAGCCCGAGGCCCGGCCCGGGTTTTAG
Found at i:1375316 original size:30 final size:31
Alignment explanation
Indices: 1375258--1375316 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1375248 CTCTATTAAA
*
1375258 AAAGAGTAAATTAGTCTTTGTATGTTAAATC
1 AAAGAGTAAATTAATCTTTGTATGTTAAATC
* *
1375289 AAAGAGTAAATTAAT-TTTTTCTGTTAAA
1 AAAGAGTAAATTAATCTTTGTATGTTAAA
1375317 AATTCTATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (31 bp):
AAAGAGTAAATTAATCTTTGTATGTTAAATC
Found at i:1375848 original size:6 final size:6
Alignment explanation
Indices: 1375837--1375861 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1375827 TCAGGTTCCC
1375837 ACATAT ACATAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT A
1375862 TGTATGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ACATAT
Found at i:1376122 original size:66 final size:66
Alignment explanation
Indices: 1376016--1376202 Score: 331
Period size: 66 Copynumber: 2.8 Consensus size: 66
1376006 GAAAGGAAAA
*
1376016 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACA-AAGA
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATC-AAAGAAGA
1376080 GG
65 GG
*
1376082 AAAGAGAAAATAACCTCATTCATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCAAAGAAGAG
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCAAAGAAGAG
1376147 G
66 G
*
1376148 AAAGAGAATATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCAT
1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCAT
1376203 TCTCAAAATG
Statistics
Matches: 116, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
65 2 0.02
66 114 0.98
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (66 bp):
AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCAAAGAAGAG
G
Found at i:1378841 original size:29 final size:28
Alignment explanation
Indices: 1378788--1378845 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
1378778 GTAAATTTTA
1378788 CATTTTAGTCTCTAAAAATAGAATAAAAT
1 CATTTTAGTCTCTAAAAATA-AATAAAAT
*
1378817 CATTTTAGTCCTTTTAAAAAT-AATAAAAT
1 CATTTTAGT-C-TCTAAAAATAAATAAAAT
1378846 TATAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 17 0.65
30 1 0.04
31 8 0.31
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (28 bp):
CATTTTAGTCTCTAAAAATAAATAAAAT
Found at i:1378878 original size:23 final size:22
Alignment explanation
Indices: 1378828--1378878 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
1378818 ATTTTAGTCC
*
1378828 TTTTAAAAATAATAAAATTATA
1 TTTTAAAAATAATAAAATTACA
** *
1378850 AATTAATAAATGATAAAATTACA
1 TTTTAA-AAATAATAAAATTACA
1378873 TTTTAA
1 TTTTAA
1378879 CATCTCAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TTTTAAAAATAATAAAATTACA
Found at i:1380171 original size:27 final size:27
Alignment explanation
Indices: 1380139--1380192 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1380129 AGAAATTTTA
1380139 AATTTAACCAAGTTCAAGTTATTAATT
1 AATTTAACCAAGTTCAAGTTATTAATT
** *
1380166 AATTTAATGAAGTTGAAGTTATTAATT
1 AATTTAACCAAGTTCAAGTTATTAATT
1380193 TTTAATAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.43
Consensus pattern (27 bp):
AATTTAACCAAGTTCAAGTTATTAATT
Found at i:1382305 original size:4 final size:4
Alignment explanation
Indices: 1382296--1382323 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1382286 ACATATATAG
1382296 AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1382324 GTATGATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:1388329 original size:27 final size:27
Alignment explanation
Indices: 1388275--1388337 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
1388265 TAAATTTCAA
*
1388275 AATTATATATAAACTTTAATTTAATGT
1 AATTATACATAAACTTTAATTTAATGT
**
1388302 ACA-TATACATAAACTTTAATTTGGTGT
1 A-ATTATACATAAACTTTAATTTAATGT
1388329 AATTATACA
1 AATTATACA
1388338 CGTAAAACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 29 0.94
28 1 0.03
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (27 bp):
AATTATACATAAACTTTAATTTAATGT
Found at i:1394080 original size:43 final size:42
Alignment explanation
Indices: 1394032--1394116 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
1394022 TGATTACCCA
* *
1394032 TTTCTCGTTTTTTTAAATTATATTGGAAATCGCTGAGTTTATC
1 TTTCTCCTTTTTCT-AATTATATTGGAAATCGCTGAGTTTATC
* *
1394075 TTTCTCCTTTTTCTGATTATATTGGGAATCGCTGAGTTTATC
1 TTTCTCCTTTTTCTAATTATATTGGAAATCGCTGAGTTTATC
1394117 GACTTAGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
42 26 0.68
43 12 0.32
ACGTcount: A:0.20, C:0.14, G:0.15, T:0.51
Consensus pattern (42 bp):
TTTCTCCTTTTTCTAATTATATTGGAAATCGCTGAGTTTATC
Found at i:1396677 original size:13 final size:13
Alignment explanation
Indices: 1396638--1396681 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
1396628 CTGAAAATTT
1396638 TTTTATGGGAAAA
1 TTTTATGGGAAAA
1396651 TTTTGCAT-GGAAAA
1 TTTT--ATGGGAAAA
1396665 TTTTATGGGAAAA
1 TTTTATGGGAAAA
1396678 TTTT
1 TTTT
1396682 TCTCCAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.07
13 14 0.50
14 10 0.36
15 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.43
Consensus pattern (13 bp):
TTTTATGGGAAAA
Found at i:1396682 original size:14 final size:14
Alignment explanation
Indices: 1396637--1396682 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1396627 TCTGAAAATT
1396637 TTTTTATGGGAAAA
1 TTTTTATGGGAAAA
*
1396651 TTTTGCAT-GGAAAA
1 TTTT-TATGGGAAAA
1396665 -TTTTATGGGAAAA
1 TTTTTATGGGAAAA
1396678 TTTTT
1 TTTTT
1396683 CTCCAGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.07
13 9 0.33
14 14 0.52
15 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (14 bp):
TTTTTATGGGAAAA
Found at i:1401754 original size:177 final size:177
Alignment explanation
Indices: 1401423--1401754 Score: 486
Period size: 177 Copynumber: 1.9 Consensus size: 177
1401413 TTTAGTATGC
* * *
1401423 AATCCCTAATAAACCTCGAAACAGTCTTTTGTATGGTATTGACGCAATGTATAGTTTACAGTTCT
1 AATCCCGAATAAACCTCGAAACAGTCTTTTGAATGGTATTGACACAATGTATAGTTTACAGTTCT
* * * * *
1401488 TTGACTCGATCATACGATGAGGCCATCTAACTTCACCGAGAATATTGTAAAAGTAACCACCTTGG
66 TTGACTCGAACAAACAATGAGGCCATCTAACTTCACCGAGAATATGGTAAAAGAAACCACCTTGG
* * *
1401553 ATGACAGAAGTTGTATTGAAAAAGTTCAACTCGACCGCCAGTATCCA
131 ACGACAGAAGTCGTATTCAAAAAGTTCAACTCGACCGCCAGTATCCA
** * * *
1401600 AATCCCGAATAAACCTCGAGGCGGTCTTTTGAATGGTATTGACACAATGTATGGTTTACAGTTTT
1 AATCCCGAATAAACCTCGAAACAGTCTTTTGAATGGTATTGACACAATGTATAGTTTACAGTTCT
* *
1401665 TTGACTCGAAGAAACAATGAGGCTATCTAACTTCACCGAGAATATGGTAAAAGAAACCACCTTGG
66 TTGACTCGAACAAACAATGAGGCCATCTAACTTCACCGAGAATATGGTAAAAGAAACCACCTTGG
1401730 ACGACAGAAAGTCGTA-TCAAAAAGT
131 ACGACAG-AAGTCGTATTCAAAAAGT
1401755 CTAAAAAACT
Statistics
Matches: 136, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
177 129 0.95
178 7 0.05
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (177 bp):
AATCCCGAATAAACCTCGAAACAGTCTTTTGAATGGTATTGACACAATGTATAGTTTACAGTTCT
TTGACTCGAACAAACAATGAGGCCATCTAACTTCACCGAGAATATGGTAAAAGAAACCACCTTGG
ACGACAGAAGTCGTATTCAAAAAGTTCAACTCGACCGCCAGTATCCA
Found at i:1402897 original size:19 final size:20
Alignment explanation
Indices: 1402873--1402928 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
1402863 TCGTTTTTAA
1402873 GTATTTTCCGTCAAAATC-C
1 GTATTTTCCGTCAAAATCAC
*
1402892 GTATTTTCCATCAAAATTCAC
1 GTATTTTCCGTCAAAA-TCAC
*
1402913 -CATTTTCCGTCAAAAT
1 GTATTTTCCGTCAAAAT
1402929 TCGCCATCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.50
20 15 0.47
21 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (20 bp):
GTATTTTCCGTCAAAATCAC
Found at i:1402919 original size:20 final size:20
Alignment explanation
Indices: 1402894--1402935 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1402884 CAAAATCCGT
1402894 ATTTTCCATCAAAATTCACC
1 ATTTTCCATCAAAATTCACC
* *
1402914 ATTTTCCGTCAAAATTCGCC
1 ATTTTCCATCAAAATTCACC
1402934 AT
1 AT
1402936 CAATATGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.36
Consensus pattern (20 bp):
ATTTTCCATCAAAATTCACC
Found at i:1403704 original size:57 final size:56
Alignment explanation
Indices: 1403622--1403731 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 56
1403612 CTGGTCAAAC
* * *
1403622 TTTATAATTAGTATCTTTATTTTACTCAACTTATAAATTTAGTCCCTTATTTTAAAT
1 TTTATAATTAGTACCTGTATCTTACTCAACTTATAAATTTAGTCCCTT-TTTTAAAT
*
1403679 TTTATAATTAGTCCCTGTATCTTACTCAACTTATAAATTTAGTCCCTTTTTTA
1 TTTATAATTAGTACCTGTATCTTACTCAACTTATAAATTTAGTCCCTTTTTTA
1403732 TTAGTTTACC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
56 5 0.10
57 44 0.90
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (56 bp):
TTTATAATTAGTACCTGTATCTTACTCAACTTATAAATTTAGTCCCTTTTTTAAAT
Found at i:1403722 original size:31 final size:29
Alignment explanation
Indices: 1403642--1403731 Score: 98
Period size: 26 Copynumber: 3.1 Consensus size: 29
1403632 GTATCTTTAT
1403642 TTTACTCAACTTATAAATTTAGTCCCTTA
1 TTTACTCAACTTATAAATTTAGTCCCTTA
* *
1403671 TTT--T-AAATTTTATAA-TTAGTCCCTGTA
1 TTTACTCAACTTATA-AATTTAGTCCCT-TA
*
1403698 TCTTACTCAACTTATAAATTTAGTCCCTTT
1 T-TTACTCAACTTATAAATTTAGTCCCTTA
1403728 TTTA
1 TTTA
1403732 TTAGTTTACC
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
26 15 0.31
27 6 0.12
28 2 0.04
29 6 0.12
30 5 0.10
31 15 0.31
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (29 bp):
TTTACTCAACTTATAAATTTAGTCCCTTA
Found at i:1407883 original size:33 final size:33
Alignment explanation
Indices: 1407841--1407907 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1407831 TAAAACAACG
1407841 CAACTTTAATATAACACCACAAGAAACCTAATA
1 CAACTTTAATATAACACCACAAGAAACCTAATA
1407874 CAACTTTAATATAACACCACAAGAAACCTAATA
1 CAACTTTAATATAACACCACAAGAAACCTAATA
1407907 C
1 C
1407908 TTACCAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.51, C:0.25, G:0.03, T:0.21
Consensus pattern (33 bp):
CAACTTTAATATAACACCACAAGAAACCTAATA
Found at i:1409270 original size:14 final size:14
Alignment explanation
Indices: 1409251--1409279 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1409241 GAGAGAAATC
1409251 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
1409265 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
1409279 T
1 T
1409280 ACTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:1410976 original size:16 final size:18
Alignment explanation
Indices: 1410955--1410988 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1410945 AAATTTTTTT
1410955 TAAAAAA-AT-TATAATA
1 TAAAAAATATATATAATA
1410971 TAAAAAATATATATAATA
1 TAAAAAATATATATAATA
1410989 CTTCAAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAAATATATATAATA
Found at i:1416425 original size:22 final size:22
Alignment explanation
Indices: 1416400--1416445 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1416390 AGCTTTAAAA
*
1416400 TTCACTTTGATACCTGAGCTTT
1 TTCAATTTGATACCTGAGCTTT
* *
1416422 TTCAATTTGATACTTGAGTTTT
1 TTCAATTTGATACCTGAGCTTT
1416444 TT
1 TT
1416446 TTCTCCTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (22 bp):
TTCAATTTGATACCTGAGCTTT
Found at i:1441573 original size:12 final size:12
Alignment explanation
Indices: 1441558--1441587 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1441548 AATTGAGAGG
*
1441558 TTAATTTTTTAA
1 TTAATTTGTTAA
1441570 TTAATTTGTTAA
1 TTAATTTGTTAA
1441582 TTAATT
1 TTAATT
1441588 GATGCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (12 bp):
TTAATTTGTTAA
Found at i:1447318 original size:19 final size:21
Alignment explanation
Indices: 1447281--1447324 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 21
1447271 TTTCTTAGAT
1447281 TTACTGGCATTTAATTTATTC
1 TTACTGGCATTTAATTTATTC
1447302 TTACTGGCA-TT-ATTTATTC
1 TTACTGGCATTTAATTTATTC
1447321 TTAC
1 TTAC
1447325 ATGCAGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 12 0.52
20 2 0.09
21 9 0.39
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (21 bp):
TTACTGGCATTTAATTTATTC
Found at i:1448835 original size:16 final size:15
Alignment explanation
Indices: 1448814--1448847 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1448804 GAACATTTTA
1448814 ATTTTTTA-ATATAT
1 ATTTTTTATATATAT
1448828 ATATTTTTATATATAT
1 AT-TTTTTATATATAT
1448844 ATTT
1 ATTT
1448848 GATTTACAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.11
15 8 0.44
16 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTTTATATATAT
Found at i:1448839 original size:14 final size:15
Alignment explanation
Indices: 1448816--1448847 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1448806 ACATTTTAAT
1448816 TTTTTAATATATATA
1 TTTTTAATATATATA
1448831 TTTTT-ATATATATA
1 TTTTTAATATATATA
1448845 TTT
1 TTT
1448848 GATTTACAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAATATATATA
Found at i:1456020 original size:23 final size:23
Alignment explanation
Indices: 1455929--1456023 Score: 127
Period size: 23 Copynumber: 4.1 Consensus size: 23
1455919 TGTGTATCCT
* * *
1455929 TTCATATTCAAGCCTCTTAACTT
1 TTCATATTCAAGTCTCTTCACTC
* * *
1455952 TTCATCTACAAGTCTCTTCACTA
1 TTCATATTCAAGTCTCTTCACTC
*
1455975 TTCATATTCAAGTCTTTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
1455998 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
1456021 TTC
1 TTC
1456024 TAACTTTTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.23, C:0.28, G:0.04, T:0.44
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTC
Found at i:1461306 original size:23 final size:23
Alignment explanation
Indices: 1461216--1461309 Score: 125
Period size: 23 Copynumber: 4.1 Consensus size: 23
1461206 GTGTATCCTG
* * *
1461216 TCATATTCAAGCCTCTTAACTTT
1 TCATATTCAAGTCTCTTCACTCT
* *
1461239 TCATCTTCAAGTCTCTTCACTAT
1 TCATATTCAAGTCTCTTCACTCT
* *
1461262 TCATATTTAAGTCTTTTCACTCT
1 TCATATTCAAGTCTCTTCACTCT
1461285 TCATATTCAAGTCTCTTCACTCT
1 TCATATTCAAGTCTCTTCACTCT
1461308 TC
1 TC
1461310 TAACTTTTCA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.22, C:0.28, G:0.04, T:0.46
Consensus pattern (23 bp):
TCATATTCAAGTCTCTTCACTCT
Found at i:1471785 original size:26 final size:26
Alignment explanation
Indices: 1471732--1471787 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
1471722 CGATATATGA
1471732 CTCTTTGTGAGCTTTTCGATTAAAGG
1 CTCTTTGTGAGCTTTTCGATTAAAGG
*
1471758 CTCTTTGTGAGC-TTTCTGATTAATGG
1 CTCTTTGTGAGCTTTTC-GATTAAAGG
1471784 CTCT
1 CTCT
1471788 CCGGAGCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (26 bp):
CTCTTTGTGAGCTTTTCGATTAAAGG
Found at i:1471794 original size:25 final size:25
Alignment explanation
Indices: 1471740--1471860 Score: 63
Period size: 25 Copynumber: 4.9 Consensus size: 25
1471730 GACTCTTTGT
* **
1471740 GAGCTTT-TCGATTAAAGGCTCTTTG
1 GAGCTTTCT-GATTAATGGCTCTCCG
1471765 TGAGCTTTCTGATTAATGGCTCTCCG
1 -GAGCTTTCTGATTAATGGCTCTCCG
* * * * **
1471791 GAGCTTCCCGA-T-ATAGCTCGCTT
1 GAGCTTTCTGATTAATGGCTCTCCG
* *
1471814 GAAC-TTCTCGA-TATATGGCTATCCG
1 GAGCTTTCT-GATTA-ATGGCTCTCCG
*
1471839 GAGCTTCCTGATTAATGGCTCT
1 GAGCTTTCTGATTAATGGCTCT
1471861 TCAGAGCTAC
Statistics
Matches: 69, Mismatches: 20, Indels: 13
0.68 0.20 0.13
Matches are distributed among these distances:
22 2 0.03
23 13 0.19
24 1 0.01
25 27 0.39
26 25 0.36
27 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (25 bp):
GAGCTTTCTGATTAATGGCTCTCCG
Found at i:1474236 original size:23 final size:23
Alignment explanation
Indices: 1474205--1474249 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1474195 CAAAATTAAT
* *
1474205 AAAATAAATAATAAAATAATGAG
1 AAAAGAAATAAAAAAATAATGAG
1474228 AAAAGAAATAAAAAAATAATGA
1 AAAAGAAATAAAAAAATAATGA
1474250 CAATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAGAAATAAAAAAATAATGAG
Found at i:1484402 original size:2 final size:2
Alignment explanation
Indices: 1484397--1484421 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1484387 ACACACATAC
1484397 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1484422 GCTAATTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1484969 original size:2 final size:2
Alignment explanation
Indices: 1484962--1484993 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1484952 TATAGGGATC
1484962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1484994 TACTCCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1487016 original size:2 final size:2
Alignment explanation
Indices: 1487005--1487038 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1486995 TTCTTAATTA
1487005 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1487039 TTGGACCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1487463 original size:2 final size:2
Alignment explanation
Indices: 1487456--1487483 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1487446 NNNNNNNTGC
1487456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1487484 TATTCCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1488159 original size:2 final size:2
Alignment explanation
Indices: 1488152--1488179 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1488142 NNNNNNNNNN
1488152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1488180 TACTCCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1490459 original size:45 final size:45
Alignment explanation
Indices: 1490409--1490494 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
1490399 TCCTTGCTGC
*
1490409 GTATAAATAATTAATAATAAATGCTATATAATTTAGTTAAAATTA
1 GTATAAATAATTAATAATAAATACTATATAATTTAGTTAAAATTA
* * *
1490454 GTATAAGTAATTTATAATAAATATTATATAATTTAGTTAAA
1 GTATAAATAATTAATAATAAATACTATATAATTTAGTTAAA
1490495 TATATAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.42
Consensus pattern (45 bp):
GTATAAATAATTAATAATAAATACTATATAATTTAGTTAAAATTA
Found at i:1490496 original size:20 final size:20
Alignment explanation
Indices: 1490433--1490497 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 20
1490423 TAATAAATGC
*
1490433 TATATAATTTAGTTAAAATTAG
1 TATATAATTTAGTT-AAA-TAT
1490455 TATAAGTAATTTA-TAATAAATAT
1 TAT-A-TAATTTAGT--TAAATAT
1490478 TATATAATTTAGTTAAATAT
1 TATATAATTTAGTTAAATAT
1490498 ATAATAAGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
20 7 0.19
21 7 0.19
22 5 0.14
23 7 0.19
24 10 0.27
25 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (20 bp):
TATATAATTTAGTTAAATAT
Found at i:1490504 original size:20 final size:20
Alignment explanation
Indices: 1490436--1490504 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 20
1490426 TAAATGCTAT
1490436 ATAATTTAGTTAAAATTAGTATA
1 ATAATTTAGTT-AAA-TA-TATA
1490459 AGTAATTTA-TAATAAATAT-TA
1 A-TAATTTAGT--TAAATATATA
1490480 TATAATTTAGTTAAATATATA
1 -ATAATTTAGTTAAATATATA
1490501 ATAA
1 ATAA
1490505 GTCAAAATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
20 11 0.28
21 11 0.28
22 3 0.08
23 4 0.10
24 10 0.25
25 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (20 bp):
ATAATTTAGTTAAATATATA
Found at i:1494846 original size:24 final size:24
Alignment explanation
Indices: 1494783--1494834 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1494773 TTTCTAGAAG
* * *
1494783 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
1494807 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
1494831 ATTT
1 ATTT
1494835 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:1496496 original size:26 final size:26
Alignment explanation
Indices: 1496440--1496489 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1496430 AACAGAATAA
* *
1496440 ACAAAACACAAACCATGATAGTGTAG
1 ACAAAACAAAAACCACGATAGTGTAG
*
1496466 ACAAAACAAAAACTACGATAGTGT
1 ACAAAACAAAAACCACGATAGTGT
1496490 GGTCAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.18, G:0.14, T:0.16
Consensus pattern (26 bp):
ACAAAACAAAAACCACGATAGTGTAG
Found at i:1501893 original size:21 final size:24
Alignment explanation
Indices: 1501868--1501921 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 24
1501858 TGATGATTTA
1501868 AAATTAAAAT-TA-AATT-ATATC
1 AAATTAAAATATATAATTAATATC
1501889 AAATTAAAATATATTAATTAAATATC
1 AAATTAAAATATA-TAATT-AATATC
1501915 AAATTAA
1 AAATTAA
1501922 TTATAGTACG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 10 0.36
22 2 0.07
24 4 0.14
26 12 0.43
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
AAATTAAAATATATAATTAATATC
Found at i:1503416 original size:14 final size:15
Alignment explanation
Indices: 1503397--1503429 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1503387 TGTATAAAAT
*
1503397 AAAT-AAAGTAATAA
1 AAATAAAAGAAATAA
1503411 AAATAAAAGAAATAA
1 AAATAAAAGAAATAA
1503426 AAAT
1 AAAT
1503430 GCTAGATGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
AAATAAAAGAAATAA
Found at i:1509051 original size:61 final size:61
Alignment explanation
Indices: 1508977--1509099 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
1508967 AATGCTTCAT
* *
1508977 TTGTTTTTCTTTTCAAAGATTTTTCTTTTCTTAAATTACTTATCTTATTCTTATATATATA
1 TTGTTTTTATTTTCAAAGATTTTTCTTTTCTTAAATTACTTATCTTATACTTATATATATA
1509038 TTGTTTTTATTTTCAAAGATTTTTCTTTTCTTAAATTACTTATCTTATACTTATATATATA
1 TTGTTTTTATTTTCAAAGATTTTTCTTTTCTTAAATTACTTATCTTATACTTATATATATA
1509099 T
1 T
1509100 ATATATGTAC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.60
Consensus pattern (61 bp):
TTGTTTTTATTTTCAAAGATTTTTCTTTTCTTAAATTACTTATCTTATACTTATATATATA
Found at i:1509121 original size:61 final size:61
Alignment explanation
Indices: 1508989--1509113 Score: 180
Period size: 61 Copynumber: 2.0 Consensus size: 61
1508979 GTTTTTCTTT
* * * * **
1508989 TCAAAGATTTTTCTTTTCTTAAATTACTTATCTTATTCTTATATATATATTGTTTTTATTT
1 TCAAAGATTTTTCTTTTCTTAAATTACTTATCTTATACTTATATATATATTATATGTATCA
1509050 TCAAAGATTTTTCTTTTCTTAAATTACTTATCTTATACTTATATATATATATATATGTA-CA
1 TCAAAGATTTTTCTTTTCTTAAATTACTTATCTTATACTTATATATATAT-TATATGTATCA
1509111 TCA
1 TCA
1509114 TTTATTTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 52 0.91
62 5 0.09
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.55
Consensus pattern (61 bp):
TCAAAGATTTTTCTTTTCTTAAATTACTTATCTTATACTTATATATATATTATATGTATCA
Found at i:1510315 original size:19 final size:21
Alignment explanation
Indices: 1510286--1510332 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1510276 ATTTAACCTC
*
1510286 AAACTCAAACCCT-GAA-CCT
1 AAACCCAAACCCTCGAATCCT
*
1510305 GAACCCAAACCCTCGAATCCT
1 AAACCCAAACCCTCGAATCCT
1510326 AAACCCA
1 AAACCCA
1510333 TCAGGGTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 11 0.48
20 3 0.13
21 9 0.39
ACGTcount: A:0.40, C:0.40, G:0.06, T:0.13
Consensus pattern (21 bp):
AAACCCAAACCCTCGAATCCT
Found at i:1510357 original size:21 final size:21
Alignment explanation
Indices: 1510333--1510395 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
1510323 CCTAAACCCA
*
1510333 TCAGGGTTCGAGGTTTAAGAT
1 TCAGGGTTCAAGGTTTAAGAT
* *
1510354 TCA-GGTTTAAGGTTTACGAT
1 TCAGGGTTCAAGGTTTAAGAT
* *
1510374 TCAGAGTTCAAGGTTTTAGAT
1 TCAGGGTTCAAGGTTTAAGAT
1510395 T
1 T
1510396 TGAGGTTCAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (21 bp):
TCAGGGTTCAAGGTTTAAGAT
Found at i:1510366 original size:20 final size:21
Alignment explanation
Indices: 1510333--1510395 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1510323 CCTAAACCCA
* *
1510333 TCAGGGTTCGAGGTTTAAGAT
1 TCAGAGTTCAAGGTTTAAGAT
* *
1510354 TCAG-GTTTAAGGTTTACGAT
1 TCAGAGTTCAAGGTTTAAGAT
*
1510374 TCAGAGTTCAAGGTTTTAGAT
1 TCAGAGTTCAAGGTTTAAGAT
1510395 T
1 T
1510396 TGAGGTTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 17 0.49
21 18 0.51
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (21 bp):
TCAGAGTTCAAGGTTTAAGAT
Found at i:1510403 original size:21 final size:20
Alignment explanation
Indices: 1510337--1510409 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
1510327 AACCCATCAG
* *
1510337 GGTTCGAGGTTTAAGATTCA
1 GGTTCAAGGTTTTAGATTCA
*
1510357 GGTTTAAGG-TTTACGATTCA
1 GGTTCAAGGTTTTA-GATTCA
*
1510377 GAGTTCAAGGTTTTAGATTTGA
1 G-GTTCAAGGTTTTAGA-TTCA
*
1510399 GGTTCATGGTT
1 GGTTCAAGGTT
1510410 CAAGGTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 3 0.07
20 14 0.33
21 18 0.42
22 8 0.19
ACGTcount: A:0.23, C:0.08, G:0.29, T:0.40
Consensus pattern (20 bp):
GGTTCAAGGTTTTAGATTCA
Found at i:1511455 original size:16 final size:17
Alignment explanation
Indices: 1511426--1511463 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
1511416 AATGCTAATG
1511426 ACAATCGAACTAAAACT
1 ACAATCGAACTAAAACT
1511443 -CAATC-AACATAAAACT
1 ACAATCGAAC-TAAAACT
1511459 ACAAT
1 ACAAT
1511464 TTTTAAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.16
16 12 0.63
17 4 0.21
ACGTcount: A:0.55, C:0.24, G:0.03, T:0.18
Consensus pattern (17 bp):
ACAATCGAACTAAAACT
Found at i:1512158 original size:4 final size:4
Alignment explanation
Indices: 1512149--1512200 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
1512139 CGAGCCTTTG
*
1512149 TTTA TTTA TTTA TTT- TATTA TTT- TTTA -TTA -TTA TTT- TTTA TTCA
1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1512193 TTTA TTTA
1 TTTA TTTA
1512201 GTACTCCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
3 13 0.32
4 27 0.66
5 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:1512167 original size:13 final size:12
Alignment explanation
Indices: 1512149--1512199 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
1512139 CGAGCCTTTG
1512149 TTTATTTATTTAT
1 TTTA-TTATTTAT
1512162 TTTATTA-TT-T
1 TTTATTATTTAT
*
1512172 TTTATTATTATTT
1 TTTATTATT-TAT
1512185 TTTATTCATTTAT
1 TTTATT-ATTTAT
1512198 TT
1 TT
1512200 AGTACTCCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 8 0.24
11 3 0.09
12 4 0.12
13 15 0.45
14 3 0.09
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTATTTAT
Found at i:1512176 original size:10 final size:11
Alignment explanation
Indices: 1512158--1512195 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
1512148 GTTTATTTAT
1512158 TTATTTTATTA
1 TTATTTTATTA
1512169 TT-TTTTATTA
1 TTATTTTATTA
1512179 TTATTTT-TTA
1 TTATTTTATTA
1512189 TTCATTT
1 TT-ATTT
1512196 ATTTAGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:1514058 original size:114 final size:114
Alignment explanation
Indices: 1513927--1514155 Score: 449
Period size: 114 Copynumber: 2.0 Consensus size: 114
1513917 TCCGAAGAAC
*
1513927 TCGAATTGAACAAAATTTAATCAAATTTGATCATAGAAAATTTAATAATTAGTTTGGTTAAATTC
1 TCGAATTGAAAAAAATTTAATCAAATTTGATCATAGAAAATTTAATAATTAGTTTGGTTAAATTC
1513992 AATTATTAGTCATATATTAAGCGTACAGTGTCAATTTACTTCATATATA
66 AATTATTAGTCATATATTAAGCGTACAGTGTCAATTTACTTCATATATA
1514041 TCGAATTGAAAAAAATTTAATCAAATTTGATCATAGAAAATTTAATAATTAGTTTGGTTAAATTC
1 TCGAATTGAAAAAAATTTAATCAAATTTGATCATAGAAAATTTAATAATTAGTTTGGTTAAATTC
1514106 AATTATTAGTCATATATTAAGCGTACAGTGTCAATTTACTTCATATATA
66 AATTATTAGTCATATATTAAGCGTACAGTGTCAATTTACTTCATATATA
1514155 T
1 T
1514156 TCTCCAATTG
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (114 bp):
TCGAATTGAAAAAAATTTAATCAAATTTGATCATAGAAAATTTAATAATTAGTTTGGTTAAATTC
AATTATTAGTCATATATTAAGCGTACAGTGTCAATTTACTTCATATATA
Found at i:1526972 original size:19 final size:19
Alignment explanation
Indices: 1526929--1526978 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1526919 TTAAATTATT
1526929 AAAAATAAAAATATAGAAA
1 AAAAATAAAAATATAGAAA
** * *
1526948 TTAAATAAAAATTTATAAA
1 AAAAATAAAAATATAGAAA
1526967 AAAAATACAAAA
1 AAAAATA-AAAA
1526979 ACTTATAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAAATAAAAATATAGAAA
Found at i:1528278 original size:26 final size:26
Alignment explanation
Indices: 1528226--1528278 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1528216 TAAATCCTAA
* *
1528226 ATTATAAAAATAATATTTTATAAATG
1 ATTATAAAAATAATATCTGATAAATG
* * *
1528252 ATTATTAAAATTATATCTGATATATG
1 ATTATAAAAATAATATCTGATAAATG
1528278 A
1 A
1528279 AATTATTAGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (26 bp):
ATTATAAAAATAATATCTGATAAATG
Found at i:1528885 original size:10 final size:10
Alignment explanation
Indices: 1528872--1528901 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1528862 ATACTTGCAG
1528872 ATACATATAT
1 ATACATATAT
1528882 ATACATATAT
1 ATACATATAT
1528892 ATACATATAT
1 ATACATATAT
1528902 GTCTATATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (10 bp):
ATACATATAT
Found at i:1531248 original size:16 final size:16
Alignment explanation
Indices: 1531227--1531271 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1531217 TTTATATTCA
1531227 AGTTTAGATCATTTCAG
1 AGTTTAGATCATTT-AG
1531244 A-TTTAGATCGA-TTAG
1 AGTTTAGATC-ATTTAG
1531259 AGTTTAGATCATT
1 AGTTTAGATCATT
1531272 CAAGTTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 4 0.16
16 19 0.76
17 2 0.08
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (16 bp):
AGTTTAGATCATTTAG
Found at i:1546679 original size:4 final size:4
Alignment explanation
Indices: 1546670--1546699 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1546660 TATTAAAAGT
1546670 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
1546700 TGATTTGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:1547754 original size:3 final size:3
Alignment explanation
Indices: 1547746--1547771 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1547736 TTATCAGACA
1547746 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1547772 ATTCAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1548580 original size:17 final size:18
Alignment explanation
Indices: 1548560--1548596 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1548550 TTCTCATTTT
1548560 TTAAAAAATTA-ATAAAA
1 TTAAAAAATTATATAAAA
1548577 TT-AAAAATTATATAAAA
1 TTAAAAAATTATATAAAA
1548594 TTA
1 TTA
1548597 TTAGTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAAAAATTATATAAAA
Found at i:1560146 original size:15 final size:15
Alignment explanation
Indices: 1560126--1560158 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1560116 TGGTAACTAA
1560126 TCTGTGAAGATGCAT
1 TCTGTGAAGATGCAT
1560141 TCTGTGAAGATGCAT
1 TCTGTGAAGATGCAT
1560156 TCT
1 TCT
1560159 TTGGTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36
Consensus pattern (15 bp):
TCTGTGAAGATGCAT
Found at i:1574506 original size:19 final size:20
Alignment explanation
Indices: 1574471--1574514 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1574461 ATTTAAACTA
*
1574471 AATTTTATAACTATTTT-AT
1 AATTTTATAAATATTTTAAT
1574490 AATTTTATAAA-ATTTTTAAT
1 AATTTTATAAATA-TTTTAAT
1574510 AATTT
1 AATTT
1574515 ATTTCATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 14 0.64
20 7 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTTTATAAATATTTTAAT
Found at i:1576021 original size:199 final size:197
Alignment explanation
Indices: 1575663--1576268 Score: 864
Period size: 198 Copynumber: 3.1 Consensus size: 197
1575653 AAGCCCCCCT
* * **
1575663 GGTACTTCCTTTTTTGA-TGATTTTCTAAATTACCTGTAAACCTGAACTAATTAAATTTGATGAT
1 GGTACTT-CTTTTTTGACAG-TTTTCTAAACTACCTGTAAACCCAAACTAATTAAATTTGATGAT
* * *
1575727 ATTATGTACTTAA-TCGTGCTAGAATCCACAATCTCCAAGTTGCTGCAATAGCAATGCTTGAATA
64 ATTACGCACTTAAGT-GTGCTCGAATCCACAATCTCCAAGTTGCTGCAATAGCAATGCTTGAATA
*
1575791 ATTTGAAATTTGGGTTATTGG-TTTCCTGTGTAAACATTAGAGGAACCCTCT-TTTTGAAGTAGA
128 ATTTGAAA-TTGGGTTATTGGTTTTGCTGTGT-AACATTAGAGGAA-CCT-TATTTTGAAGTAGA
1575854 ACGATGGTC
189 ACGATGGTC
* * *
1575863 AGTACTTCTTTTTTGACAGTTTTCTAAACTACCCGTAAACCCAAACTAATTAAATTTGATGATAC
1 GGTACTTCTTTTTTGACAGTTTTCTAAACTACCTGTAAACCCAAACTAATTAAATTTGATGATAT
* * *
1575928 TACACACTTAAGTGTGCTCGAATCCACAACCTCCAAGTTGCTGCAATAGCTATGCTTGAATAATT
66 TACGCACTTAAGTGTGCTCGAATCCACAATCTCCAAGTTGCTGCAATAGCAATGCTTGAATAATT
*
1575993 TGAAATTGGGTTTTTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAACGATGG
131 TGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAACGATGG
1576058 TC
196 TC
* * *
1576060 GGTAATTCTTTTTTTTTGACA--ATTCTAAACTACCTGTAAACCCAAGCTAATTAAATTTGATGA
1 GGT-A--CTTCTTTTTTGACAGTTTTCTAAACTACCTGTAAACCCAAACTAATTAAATTTGATGA
* * **
1576123 TATTACGCAGTTAAGCGTGCTCGAATCCACAATCTCTGAGTTGCTGCAATAGCAATGCTTGAATA
63 TATTACGCACTTAAGTGTGCTCGAATCCACAATCTCCAAGTTGCTGCAATAGCAATGCTTGAATA
1576188 ATTTGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAACGA
128 ATTTGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAACGA
**
1576253 CAGTC
193 TGGTC
1576258 GGTACTTCTTT
1 GGTACTTCTTT
1576269 ATAGAGGCTT
Statistics
Matches: 367, Mismatches: 32, Indels: 19
0.88 0.08 0.05
Matches are distributed among these distances:
195 6 0.02
196 1 0.00
197 27 0.07
198 191 0.52
199 121 0.33
200 21 0.06
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (197 bp):
GGTACTTCTTTTTTGACAGTTTTCTAAACTACCTGTAAACCCAAACTAATTAAATTTGATGATAT
TACGCACTTAAGTGTGCTCGAATCCACAATCTCCAAGTTGCTGCAATAGCAATGCTTGAATAATT
TGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGAGGAACCTTATTTTGAAGTAGAACGATGG
TC
Found at i:1580566 original size:29 final size:29
Alignment explanation
Indices: 1580519--1580577 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1580509 ATAAAAAGAT
* * *
1580519 TTCATTAAATAGTATAGGGGTTAAATTGA
1 TTCATTAAATAATAGAGGGGCTAAATTGA
* *
1580548 TTCATTTAATAATAGAGGGGCTAATTTGA
1 TTCATTAAATAATAGAGGGGCTAAATTGA
1580577 T
1 T
1580578 ACGGTCCCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (29 bp):
TTCATTAAATAATAGAGGGGCTAAATTGA
Found at i:1581196 original size:16 final size:17
Alignment explanation
Indices: 1581175--1581212 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1581165 TAAGATCTAT
*
1581175 TAAAAT-AATTTAAACC
1 TAAAATAAATCTAAACC
1581191 TAAAATAAATCTAAACC
1 TAAAATAAATCTAAACC
1581208 -AAAAT
1 TAAAAT
1581213 TTTCAAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAATAAATCTAAACC
Found at i:1584280 original size:23 final size:22
Alignment explanation
Indices: 1584237--1584294 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
1584227 AAAGGGTATC
* *
1584237 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
1584258 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
1584281 TACATATCATATCT
1 TACAAATCATATCT
1584295 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:1584310 original size:21 final size:21
Alignment explanation
Indices: 1584284--1584345 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1584274 CTAAGATTAC
1584284 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
*
1584305 ATATCATATCTAGGATTGC--
1 ATATCATATCTAAGATTGCAT
1584324 ATATC-TATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
1584344 AT
1 AT
1584346 CCTCAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
18 12 0.32
19 5 0.14
20 2 0.05
21 18 0.49
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:1586028 original size:16 final size:15
Alignment explanation
Indices: 1586010--1586051 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
1586000 TAAATTCTCA
1586010 AAAAATAAAAAATTC
1 AAAAATAAAAAATTC
*
1586025 AAAAATATATAAATTC
1 AAAAATA-AAAAATTC
1586041 AAAAATAAAAA
1 AAAAATAAAAA
1586052 TATTAAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATAAAAAATTC
Found at i:1586281 original size:17 final size:19
Alignment explanation
Indices: 1586259--1586297 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1586249 TAAAACTCTT
*
1586259 AAAAATT-T-TATTTTAAA
1 AAAAATTATATATATTAAA
1586276 AAAAATTATATATATTAAA
1 AAAAATTATATATATTAAA
1586295 AAA
1 AAA
1586298 TACTTCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTATATATATTAAA
Found at i:1587664 original size:19 final size:17
Alignment explanation
Indices: 1587628--1587666 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
1587618 TACAGCGACT
*
1587628 AAATGACATTGTAATAA
1 AAATGACATTGAAATAA
1587645 AAATGACATTTTGAAATAA
1 AAATGACA--TTGAAATAA
1587664 AAA
1 AAA
1587667 AAATATTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
19 11 0.58
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.28
Consensus pattern (17 bp):
AAATGACATTGAAATAA
Found at i:1589865 original size:181 final size:177
Alignment explanation
Indices: 1589563--1590126 Score: 599
Period size: 180 Copynumber: 3.1 Consensus size: 177
1589553 GTTTCTTTCA
* * *
1589563 AATTT-TCATTGCAATGCATAAGTAGAGCAAGCTGT-TAACTAACAATGTGCATCGTGATCGATC
1 AATTTCTCAGTGCAATGCATAAGTAGAGGAAGCTGTGTAACTAACAATGTACATCGTGATCGATC
* ** * *
1589626 ATTGTTGATCAATTTGCGTGCTATTTTTTAAATCTGATTTAAG-TATTTTT-TCAATTTTTTAAG
66 ATTGTTGATCAATTTGCATGCTA-TTTTT-AAT-TTTTTTAAGTTTTTTTTGTTAATTTTTTAAG
**
1589689 AGAAAAGG-GAGAAAAAAGAGGAATAGTGTTTTTTTTTTTTGCTTCTTTATTCC
128 -GAAAAGGAG-GAAAAAAGAGGAATAGTGTTGATTTTTTTT-CTTCTTTATT-C
* *
1589742 AATTTCTCAGTGCAATGCATGAGTAGAGGAAGCTGTGTAACTAACAGTGTACATCGTGATCGATC
1 AATTTCTCAGTGCAATGCATAAGTAGAGGAAGCTGTGTAACTAACAATGTACATCGTGATCGATC
*
1589807 ATTGTTTATCAATTTGCATGCTATTTTTAATTTTTTTAAAGTTTTTTTTGTTAA-TTTTTAATGG
66 ATTGTTGATCAATTTGCATGCTATTTTTAATTTTTTT-AAGTTTTTTTTGTTAATTTTTTAA-GG
* *
1589871 AAAAAGAGGAAAAAAGAGGAATAGTGTTGATTTTTCTTCTTCTTTATTTC
129 AAAAGGAGGAAAAAAGAGGAATAGTGTTGATTTTTTTTCTTCTTTA-TTC
* * * * *
1589921 AATTTCTAAGTGCAATGCATAAGCAGAGGAAGCCGTG--AGTAACAATGTACATCGTGATCTATC
1 AATTTCTCAGTGCAATGCATAAGTAGAGGAAGCTGTGTAACTAACAATGTACATCGTGATCGATC
* * ***
1589984 ATTGTCGATCAAGTTGCATGCTA-TTTT-ATTTTATTCTCTCTTTTTTATCTGTTTTTAAAATTT
66 ATTGTTGATCAATTTGCATGCTATTTTTAATTTT-TT-TAAGTTTTTT-T-TG---TT--AA-TT
* *
1590047 TTTTAAGGGAAAAGGAGGAAAAAAAGAGGAATAGTGTTGATTCTTTTTCCTCTTTAATTC
121 TTTTAA-GGAAAAGGAGG-AAAAAAGAGGAATAGTGTTGATTTTTTTTCTTCTTT-ATTC
*
1590107 AATTTCTCAGTGTAATGCAT
1 AATTTCTCAGTGCAATGCAT
1590127 GAGTGCATTG
Statistics
Matches: 329, Mismatches: 35, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
175 5 0.02
176 12 0.04
177 45 0.14
178 6 0.02
179 53 0.16
180 80 0.24
181 54 0.16
183 2 0.01
185 17 0.05
186 54 0.16
187 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.41
Consensus pattern (177 bp):
AATTTCTCAGTGCAATGCATAAGTAGAGGAAGCTGTGTAACTAACAATGTACATCGTGATCGATC
ATTGTTGATCAATTTGCATGCTATTTTTAATTTTTTTAAGTTTTTTTTGTTAATTTTTTAAGGAA
AAGGAGGAAAAAAGAGGAATAGTGTTGATTTTTTTTCTTCTTTATTC
Found at i:1593316 original size:13 final size:14
Alignment explanation
Indices: 1593293--1593329 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
1593283 TGCATGTATG
1593293 TATGCATGTATATA
1 TATGCATGTATATA
*
1593307 TATG-ATGTATATG
1 TATGCATGTATATA
1593320 TATGCATGTA
1 TATGCATGTA
1593330 ATCAACCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (14 bp):
TATGCATGTATATA
Found at i:1600422 original size:25 final size:25
Alignment explanation
Indices: 1600394--1600483 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 25
1600384 CCAAATATCG
1600394 GGAAGCTCAAGAGAGATGTTAACTA
1 GGAAGCTCAAGAGAGATGTTAACTA
* * * *
1600419 GGAATCTCATGAGAGTCAAG-TATC-A
1 GGAAGCTCAAGAGAG--ATGTTAACTA
* *
1600444 AGAAGCTCAAGAGAGCTGTTAACTA
1 GGAAGCTCAAGAGAGATGTTAACTA
* *
1600469 GGAATCTCATGAGAG
1 GGAAGCTCAAGAGAG
1600484 TCAAGTATCA
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
23 1 0.02
24 3 0.06
25 39 0.81
26 3 0.06
27 2 0.04
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (25 bp):
GGAAGCTCAAGAGAGATGTTAACTA
Found at i:1600502 original size:25 final size:25
Alignment explanation
Indices: 1600424--1600508 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
1600414 AACTAGGAAT
*
1600424 CTCATGAGAGTCAAGTATCAAGAAG
1 CTCAAGAGAGTCAAGTATCAAGAAG
* * * *
1600449 CTCAAGAGAG-C-TGTTAACTAGGAAT
1 CTCAAGAGAGTCAAG-TATC-AAGAAG
*
1600474 CTCATGAGAGTCAAGTATCAAGAAG
1 CTCAAGAGAGTCAAGTATCAAGAAG
1600499 CTCAAGAGAG
1 CTCAAGAGAG
1600509 CTGTGGTACG
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
23 1 0.02
24 4 0.09
25 35 0.78
26 4 0.09
27 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (25 bp):
CTCAAGAGAGTCAAGTATCAAGAAG
Found at i:1600509 original size:50 final size:50
Alignment explanation
Indices: 1600395--1600512 Score: 227
Period size: 50 Copynumber: 2.4 Consensus size: 50
1600385 CAAATATCGG
*
1600395 GAAGCTCAAGAGAGATGTTAACTAGGAATCTCATGAGAGTCAAGTATCAA
1 GAAGCTCAAGAGAGCTGTTAACTAGGAATCTCATGAGAGTCAAGTATCAA
1600445 GAAGCTCAAGAGAGCTGTTAACTAGGAATCTCATGAGAGTCAAGTATCAA
1 GAAGCTCAAGAGAGCTGTTAACTAGGAATCTCATGAGAGTCAAGTATCAA
1600495 GAAGCTCAAGAGAGCTGT
1 GAAGCTCAAGAGAGCTGT
1600513 GGTACGTCTG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.21
Consensus pattern (50 bp):
GAAGCTCAAGAGAGCTGTTAACTAGGAATCTCATGAGAGTCAAGTATCAA
Found at i:1603551 original size:13 final size:14
Alignment explanation
Indices: 1603519--1603552 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1603509 GTTTGTTTCA
1603519 CTGAAAATGAATTT
1 CTGAAAATGAATTT
*
1603533 CGGAAAATG-ATTT
1 CTGAAAATGAATTT
1603546 CTGAAAA
1 CTGAAAA
1603553 ATGACTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (14 bp):
CTGAAAATGAATTT
Found at i:1603584 original size:19 final size:20
Alignment explanation
Indices: 1603543--1603587 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1603533 CGGAAAATGA
*
1603543 TTTCTGAAAAATGACTTATT
1 TTTCTGAAAAATGACTAATT
1603563 TTTCTGAAAAA-G-CTAATAT
1 TTTCTGAAAAATGACTAAT-T
1603582 TTTCTG
1 TTTCTG
1603588 GTGTTTGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 8 0.35
20 11 0.48
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (20 bp):
TTTCTGAAAAATGACTAATT
Found at i:1614757 original size:13 final size:13
Alignment explanation
Indices: 1614739--1614789 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
1614729 AAATTATAAA
1614739 ATTATAAAAAAAT
1 ATTATAAAAAAAT
*
1614752 ATTAT-AAAGAAT
1 ATTATAAAAAAAT
*
1614764 A-TATAAAAAATTT
1 ATTATAAAAAA-AT
*
1614777 ATTTTAAAAAAAT
1 ATTATAAAAAAAT
1614790 CCAAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
11 3 0.10
12 11 0.37
13 8 0.27
14 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
ATTATAAAAAAAT
Found at i:1614757 original size:21 final size:23
Alignment explanation
Indices: 1614731--1614778 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1614721 TTTTTAGAAA
*
1614731 ATTATAAA-ATTATA-AAAAAAT
1 ATTATAAAGAATATATAAAAAAT
1614752 ATTATAAAGAATATATAAAAAAT
1 ATTATAAAGAATATATAAAAAAT
1614775 -TTAT
1 ATTAT
1614779 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
ATTATAAAGAATATATAAAAAAT
Found at i:1616772 original size:5 final size:5
Alignment explanation
Indices: 1616762--1616786 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1616752 CCGACCCCTG
1616762 CCCGA CCCGA CCCGA CCCGA CCCGA
1 CCCGA CCCGA CCCGA CCCGA CCCGA
1616787 ATATAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
CCCGA
Found at i:1616827 original size:13 final size:13
Alignment explanation
Indices: 1616795--1616828 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1616785 GAATATAATA
1616795 AATTTATATTTTTT
1 AATTT-TATTTTTT
*
1616809 ATTTTTATTTTTT
1 AATTTTATTTTTT
1616822 AATTTTA
1 AATTTTA
1616829 AAATACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
AATTTTATTTTTT
Found at i:1617491 original size:37 final size:37
Alignment explanation
Indices: 1617441--1617550 Score: 130
Period size: 37 Copynumber: 3.0 Consensus size: 37
1617431 CCTGGAAGAT
* * * *
1617441 AAAAGACGGAGATGAACAATAATGATTCTTTGCAAAG
1 AAAACACGAAGATGAACAGTAATGATTCTCTGCAAAG
* * *
1617478 AAAACACGAAGATGAATAGCAATGATTCCCTGCAAAG
1 AAAACACGAAGATGAACAGTAATGATTCTCTGCAAAG
* * *
1617515 AAAATACGAAGATGAACAGTAATCATTCTCTACAAA
1 AAAACACGAAGATGAACAGTAATGATTCTCTGCAAA
1617551 AATTCTCTCA
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.20
Consensus pattern (37 bp):
AAAACACGAAGATGAACAGTAATGATTCTCTGCAAAG
Found at i:1628970 original size:12 final size:12
Alignment explanation
Indices: 1628948--1628982 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1628938 AGGAAGAGTA
1628948 GAGAGAAAAAATC
1 GAGA-AAAAAATC
*
1628961 GAGAAAAAAATT
1 GAGAAAAAAATC
1628973 GAGAAAAAAA
1 GAGAAAAAAA
1628983 AATATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.09
Consensus pattern (12 bp):
GAGAAAAAAATC
Found at i:1629269 original size:33 final size:33
Alignment explanation
Indices: 1629225--1629300 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
1629215 CCATTCAGTG
* *
1629225 AATTATTTTTTCACTATCACTACTATCAAGTTA
1 AATTTTTTTTTCACTATCACTACAATCAAGTTA
*
1629258 AATTTTTTTTTCACTATTACTACAATCAAGTTA
1 AATTTTTTTTTCACTATCACTACAATCAAGTTA
*
1629291 AAATTTTTTT
1 AATTTTTTTT
1629301 AATAGGTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.50
Consensus pattern (33 bp):
AATTTTTTTTTCACTATCACTACAATCAAGTTA
Found at i:1629314 original size:21 final size:22
Alignment explanation
Indices: 1629290--1629339 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1629280 CAATCAAGTT
1629290 AAAATTTTTTTAATAGG-TGAA
1 AAAATTTTTTTAATAGGTTGAA
**
1629311 AAAA-TAATTTAATAGGTTGAA
1 AAAATTTTTTTAATAGGTTGAA
*
1629332 AATATTTT
1 AAAATTTT
1629340 AACTGGTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
20 10 0.45
21 11 0.50
22 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (22 bp):
AAAATTTTTTTAATAGGTTGAA
Found at i:1629340 original size:19 final size:19
Alignment explanation
Indices: 1629297--1629341 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1629287 GTTAAAATTT
1629297 TTTTAATAGGTGAAAAAATA
1 TTTTAATAGGTG-AAAAATA
*
1629317 ATTTAATAGGTTG-AAAATA
1 TTTTAATAGG-TGAAAAATA
1629336 TTTTAA
1 TTTTAA
1629342 CTGGTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 11 0.50
20 9 0.41
21 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTTAATAGGTGAAAAATA
Found at i:1646778 original size:23 final size:23
Alignment explanation
Indices: 1646752--1646806 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1646742 ATGTCGCCAG
*
1646752 GTCGTGACGCCAAGCATCACGCC
1 GTCGAGACGCCAAGCATCACGCC
1646775 GTCGAGACGCCAAGCATCACGCC
1 GTCGAGACGCCAAGCATCACGCC
1646798 GTCGAGACG
1 GTCGAGACG
1646807 ACGGTTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.36, G:0.29, T:0.11
Consensus pattern (23 bp):
GTCGAGACGCCAAGCATCACGCC
Found at i:1648203 original size:16 final size:15
Alignment explanation
Indices: 1648182--1648211 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1648172 CCTTTTTTTA
1648182 TTTATTCATTTAATTG
1 TTTATTCA-TTAATTG
1648198 TTTATTCATTAATT
1 TTTATTCATTAATT
1648212 ATTCTTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (15 bp):
TTTATTCATTAATTG
Found at i:1649405 original size:19 final size:21
Alignment explanation
Indices: 1649366--1649405 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1649356 TTGATGAAAC
1649366 AAGAAGTTTAAAAACTCAATT
1 AAGAAGTTTAAAAACTCAATT
*
1649387 AAGAA-TTTAGAAA-TCAATT
1 AAGAAGTTTAAAAACTCAATT
1649406 TGATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
AAGAAGTTTAAAAACTCAATT
Found at i:1652048 original size:27 final size:27
Alignment explanation
Indices: 1652018--1652079 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
1652008 CCTGTCAGGT
**
1652018 AGGCGCCACTAATTGTGCCTCATAGGG
1 AGGCGCCACTAAAAGTGCCTCATAGGG
*
1652045 AGGCGCCATTAAAAGTGCCTCATAGGG
1 AGGCGCCACTAAAAGTGCCTCATAGGG
1652072 AGGCGCCA
1 AGGCGCCA
1652080 ATGGATGCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.26, C:0.26, G:0.31, T:0.18
Consensus pattern (27 bp):
AGGCGCCACTAAAAGTGCCTCATAGGG
Found at i:1652241 original size:3 final size:3
Alignment explanation
Indices: 1652235--1652281 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
1652225 GAGAGAAAGG
*
1652235 AGA AGA AG- AGA AGA AGA AGA AGA AGA AGA AG- AGA AGA AGA GGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1652281 A
1 A
1652282 AGAAAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1652245 original size:17 final size:17
Alignment explanation
Indices: 1652223--1652275 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
1652213 GAGAAAAAAA
1652223 AAGAGAGAAAGGAGAAG
1 AAGAGAGAAAGGAGAAG
*
1652240 AAGAGA-AGAAGAAGAAG
1 AAGAGAGA-AAGGAGAAG
1652257 AAGA-AG-AA-GAGAAG
1 AAGAGAGAAAGGAGAAG
1652271 AAGAG
1 AAGAG
1652276 GAAGAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 9 0.29
15 2 0.06
16 2 0.06
17 18 0.58
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (17 bp):
AAGAGAGAAAGGAGAAG
Done.