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 5 of 109
Found at i:1499480 original size:30 final size:31
Alignment explanation
Indices: 1499446--1499529 Score: 154
Period size: 30 Copynumber: 2.8 Consensus size: 31
1499436 CCAATATCTC
1499446 GATACCCATATCTTTGACTTTCCAATT-TTT
1 GATACCCATATCTTTGACTTTCCAATTATTT
1499476 GATACCCATATCTTTGACTTTCC-ATTATTT
1 GATACCCATATCTTTGACTTTCCAATTATTT
1499506 GATACCCATATCTTTGACTTTCCA
1 GATACCCATATCTTTGACTTTCCA
1499530 TAAATATGGA
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
29 3 0.06
30 49 0.94
ACGTcount: A:0.24, C:0.25, G:0.07, T:0.44
Consensus pattern (31 bp):
GATACCCATATCTTTGACTTTCCAATTATTT
Found at i:1499491 original size:15 final size:15
Alignment explanation
Indices: 1499446--1499522 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
1499436 CCAATATCTC
1499446 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
1499461 GACTTTCCA-ATTTTT
1 GA-TACCCATATCTTT
1499476 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
1499491 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
1499506 GATACCCATATCTTT
1 GATACCCATATCTTT
1499521 GA
1 GA
1499523 CTTTCCATAA
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.20
15 28 0.61
16 9 0.20
ACGTcount: A:0.25, C:0.23, G:0.08, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:1500733 original size:32 final size:32
Alignment explanation
Indices: 1500693--1500757 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1500683 TCATGGAGTT
1500693 AGGCAAAATACAATACATTAGAGTTTTAATAC
1 AGGCAAAATACAATACATTAGAGTTTTAATAC
*
1500725 AGGCAAAATACAATGCATTAGAGTTTTAATAC
1 AGGCAAAATACAATACATTAGAGTTTTAATAC
1500757 A
1 A
1500758 ATTAAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (32 bp):
AGGCAAAATACAATACATTAGAGTTTTAATAC
Found at i:1502644 original size:5 final size:5
Alignment explanation
Indices: 1502634--1502661 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1502624 TGAAATATAC
1502634 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
1502662 ATATTATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:1512210 original size:18 final size:19
Alignment explanation
Indices: 1512187--1512225 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
1512177 TAAAAAGTTG
1512187 AAATAAA-ATCTAAT-TTAA
1 AAATAAATA-CTAATATTAA
1512205 AAATAAATACTAATATTAA
1 AAATAAATACTAATATTAA
1512224 AA
1 AA
1512226 GTATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATAAATACTAATATTAA
Found at i:1512345 original size:16 final size:16
Alignment explanation
Indices: 1512316--1512354 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1512306 AAATCGAGAA
1512316 AAAAAATAAATGAAACT
1 AAAAAATAAATGAAA-T
*
1512333 AAAAAA-AATTGAAAT
1 AAAAAATAAATGAAAT
1512348 AAAAAAT
1 AAAAAAT
1512355 TTGAGGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 7 0.35
16 7 0.35
17 6 0.30
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAAAATAAATGAAAT
Found at i:1520055 original size:252 final size:253
Alignment explanation
Indices: 1519598--1520116 Score: 1015
Period size: 252 Copynumber: 2.1 Consensus size: 253
1519588 CTTAAATATA
*
1519598 TATATATATTTT-ATTCTAAGTGTTTTATTGAATTAGTGTCACCCATCAACCGAGCATCAATTCA
1 TATATAAATTTTAATTCTAAGTGTTTTATTGAATTAGTGTCACCCATCAACCGAGCATCAATTCA
1519662 GTTATGAAATTATTAAAATACCCTATCATATATAAATTAAGCTATATCTTTATAAATGTGTTTTG
66 GTTATGAAATTATTAAAATACCCTATCATATATAAATTAAGCTATATCTTTATAAATGTGTTTTG
1519727 TCTTTTTATATAATAAATCAATAAAAATTGATCATAATGAAATTTAAATCTAAAACACCATACAT
131 TCTTTTTATATAATAAATCAATAAAAATTGATCATAATGAAATTTAAATCTAAAACACCATACAT
1519792 GATAAACAATTAACTTTATTACTATAGTCTAATTATTAATTTATTTTTCTGTAATTTT
196 GATAAACAATTAACTTTATTACTATAGTCTAATTATTAATTTATTTTTCTGTAATTTT
1519850 TATA-AAATTTTAATTCTAAGTGTTTTATTGAATTAGTGTCACCCATCAACCGAGCATCAATTCA
1 TATATAAATTTTAATTCTAAGTGTTTTATTGAATTAGTGTCACCCATCAACCGAGCATCAATTCA
1519914 GTTATGAAATTATTAAAATACCCTATCATATATAAATTAAGCTATATCTTTATAAATGTGTTTTG
66 GTTATGAAATTATTAAAATACCCTATCATATATAAATTAAGCTATATCTTTATAAATGTGTTTTG
1519979 TCTTTTTATATAATAAATCAATAAAAATTGATCATAATGAAATTTAAATCTAAAACACCATACAT
131 TCTTTTTATATAATAAATCAATAAAAATTGATCATAATGAAATTTAAATCTAAAACACCATACAT
1520044 GATAAACAATTAACTTTATTACTATAGTCTAATTATTAATTTATTTTTCTGTAATTTT
196 GATAAACAATTAACTTTATTACTATAGTCTAATTATTAATTTATTTTTCTGTAATTTT
1520102 TATATAAATTTTAAT
1 TATATAAATTTTAAT
1520117 AAATATATTT
Statistics
Matches: 264, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
251 6 0.02
252 248 0.94
253 10 0.04
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (253 bp):
TATATAAATTTTAATTCTAAGTGTTTTATTGAATTAGTGTCACCCATCAACCGAGCATCAATTCA
GTTATGAAATTATTAAAATACCCTATCATATATAAATTAAGCTATATCTTTATAAATGTGTTTTG
TCTTTTTATATAATAAATCAATAAAAATTGATCATAATGAAATTTAAATCTAAAACACCATACAT
GATAAACAATTAACTTTATTACTATAGTCTAATTATTAATTTATTTTTCTGTAATTTT
Found at i:1521402 original size:73 final size:74
Alignment explanation
Indices: 1521312--1521458 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 74
1521302 ATCAAAACAA
1521312 TTGAATAAATTATTGAAACATTTTTATCTATTGTTTGATAATGTCAACCGATTTGTTACTAT-AT
1 TTGAATAAATTATTGAAACATTTTTATCTATTGTTTGATAATGTCAACCGATTTGTTACTATAAT
1521376 ATTAAAATT
66 ATTAAAATT
1521385 TTGAATAAATTATTGAAACATTTTTATCTATTGTTTGATAATGTCAACCGATTTGTTACTATAAT
1 TTGAATAAATTATTGAAACATTTTTATCTATTGTTTGATAATGTCAACCGATTTGTTACTATAAT
1521450 ATTAAAATT
66 ATTAAAATT
1521459 AATTAATTTA
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 62 0.85
74 11 0.15
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (74 bp):
TTGAATAAATTATTGAAACATTTTTATCTATTGTTTGATAATGTCAACCGATTTGTTACTATAAT
ATTAAAATT
Found at i:1522348 original size:90 final size:91
Alignment explanation
Indices: 1522190--1522375 Score: 356
Period size: 90 Copynumber: 2.1 Consensus size: 91
1522180 TTTTATTATA
*
1522190 AAATGGTCAACCCTAATCTTGTTTATGAAATCTAAAAATCCTACCGGTAGTGTATCAATTATTTT
1 AAATTGTCAACCCTAATCTTGTTTATGAAATCTAAAAATCCTACCGGTAGTGTATCAATTATTTT
1522255 ATTAAGTATCATGGTGCTTT-TGTTT
66 ATTAAGTATCATGGTGCTTTATGTTT
1522280 AAATTGTCAACCCTAATCTTGTTTATGAAATCTAAAAATCCTACCGGTAGTGTATCAATTATTTT
1 AAATTGTCAACCCTAATCTTGTTTATGAAATCTAAAAATCCTACCGGTAGTGTATCAATTATTTT
1522345 ATTAAGTATCATGGTGCTTTATGTTT
66 ATTAAGTATCATGGTGCTTTATGTTT
1522371 AAATT
1 AAATT
1522376 TTATTATGCA
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
90 84 0.89
91 10 0.11
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.41
Consensus pattern (91 bp):
AAATTGTCAACCCTAATCTTGTTTATGAAATCTAAAAATCCTACCGGTAGTGTATCAATTATTTT
ATTAAGTATCATGGTGCTTTATGTTT
Found at i:1523360 original size:16 final size:16
Alignment explanation
Indices: 1523326--1523378 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
1523316 ATGGCATCAG
1523326 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
1523342 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* *
1523358 TCATACCATACTCAAT
1 TCATGCAATACTCAAT
1523374 TCATG
1 TCATG
1523379 AGTATAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:1523644 original size:41 final size:41
Alignment explanation
Indices: 1523567--1523707 Score: 157
Period size: 41 Copynumber: 3.6 Consensus size: 41
1523557 ACCAGTTTGG
* * * *
1523567 CACCCAATGCCTCATCGGAT-AATTCGAAGTAGTAAATTGA
1 CACCCAGTGTCTCATCGAATAAATCCGAAGTAGTAAATTGA
1523607 CACCCAGTGTCTCATCGAATAAATCCGAAGTAGTAAATTGA
1 CACCCAGTGTCTCATCGAATAAATCCGAAGTAGTAAATTGA
* * ** *
1523648 CACACAGTATCTCATCGGTTAAA-CCG-A--AGTAAATTGG
1 CACCCAGTGTCTCATCGAATAAATCCGAAGTAGTAAATTGA
*
1523685 CACCCAGTGTCTCATCGATTAAA
1 CACCCAGTGTCTCATCGAATAAA
1523708 CCAATAAACC
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
37 29 0.33
39 1 0.01
40 20 0.23
41 38 0.43
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (41 bp):
CACCCAGTGTCTCATCGAATAAATCCGAAGTAGTAAATTGA
Found at i:1524350 original size:20 final size:19
Alignment explanation
Indices: 1524298--1524346 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1524288 TAAACTAAAT
*
1524298 TTAACTCCCT-ATTTTTGC
1 TTAAATCCCTAATTTTTGC
1524316 TTAAATCCCTAATTTTTGC
1 TTAAATCCCTAATTTTTGC
1524335 TTAAATCCCTAA
1 TTAAATCCCTAA
1524347 ATTTCAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 9 0.31
19 20 0.69
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.45
Consensus pattern (19 bp):
TTAAATCCCTAATTTTTGC
Found at i:1524675 original size:24 final size:24
Alignment explanation
Indices: 1524647--1524699 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1524637 CTTTCTTTCC
1524647 TTTCTGTTTCGTTTTATTCCTTTA
1 TTTCTGTTTCGTTTTATTCCTTTA
* * *
1524671 TTTCTGTTTCGTTTTGTTTCTTTC
1 TTTCTGTTTCGTTTTATTCCTTTA
1524695 TTTCT
1 TTTCT
1524700 TTATTCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.04, C:0.17, G:0.09, T:0.70
Consensus pattern (24 bp):
TTTCTGTTTCGTTTTATTCCTTTA
Found at i:1527750 original size:14 final size:15
Alignment explanation
Indices: 1527726--1527759 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1527716 AGCTGGCGGA
1527726 GTTTATAAAATAGTT
1 GTTTATAAAATAGTT
*
1527741 GTTT-TAAAATATTT
1 GTTTATAAAATAGTT
1527755 GTTTA
1 GTTTA
1527760 ACTTTACAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
GTTTATAAAATAGTT
Found at i:1528493 original size:21 final size:22
Alignment explanation
Indices: 1528460--1528502 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1528450 CATCTACCAT
*
1528460 ATCACTCCGGA-TTGTAAATAA
1 ATCACTCCGGATTTGCAAATAA
* *
1528481 ATCACTGCTGATTTGCAAATAA
1 ATCACTCCGGATTTGCAAATAA
1528503 TTGCCACTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (22 bp):
ATCACTCCGGATTTGCAAATAA
Found at i:1528839 original size:27 final size:28
Alignment explanation
Indices: 1528786--1528839 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
1528776 TAGATATGGG
1528786 AAATATATATAGTTTTATAAAAATATTA
1 AAATATATATAGTTTTATAAAAATATTA
*
1528814 AAATATA-ATA-TTTTAATAAATATATT
1 AAATATATATAGTTTT-ATAAAAATATT
1528840 TATCTTAANN
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 13 0.54
28 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AAATATATATAGTTTTATAAAAATATTA
Found at i:1531654 original size:2 final size:2
Alignment explanation
Indices: 1531647--1531675 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1531637 TAATCAGAAC
1531647 AT AT 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 AT AT A
1531676 CACAATACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1531735 original size:2 final size:2
Alignment explanation
Indices: 1531728--1531755 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1531718 TAAACAGAAC
1531728 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
1531756 GCACATATGC
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:1536496 original size:22 final size:23
Alignment explanation
Indices: 1536465--1536508 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1536455 ACATCACTAA
* *
1536465 TAAAATAATATTTTTA-AAAAAG
1 TAAAAAAATAATTTTAGAAAAAG
1536487 TAAAAAAATAATTTTAGAAAAA
1 TAAAAAAATAATTTTAGAAAAA
1536509 AAAATGATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (23 bp):
TAAAAAAATAATTTTAGAAAAAG
Found at i:1537889 original size:22 final size:23
Alignment explanation
Indices: 1537849--1537894 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1537839 ATAATATTTA
** *
1537849 AACAATAACAACACCAAAATAAT
1 AACAATAACAACAAAAAAAAAAT
1537872 AACAA-AACAACAAAAAAAAAAT
1 AACAATAACAACAAAAAAAAAAT
1537894 A
1 A
1537895 GCAGTTTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.74, C:0.17, G:0.00, T:0.09
Consensus pattern (23 bp):
AACAATAACAACAAAAAAAAAAT
Found at i:1549417 original size:111 final size:111
Alignment explanation
Indices: 1549290--1549495 Score: 313
Period size: 111 Copynumber: 1.9 Consensus size: 111
1549280 ACATTATGAA
** * *
1549290 CAACAGAGATACTGTTTCTGTCCTCCATGTTTGCAGGCTCAGAAGAAACCTTATCGAGTTCAGGA
1 CAACAGAGATACTGTTTCCATCCTCCATGGTTGCAGGCTCAGAAGAAACCTTATCAAGTTCAGGA
*
1549355 GCAGCTTCTTCTGATCGATTTTCACTATCATCTGAAATGTTATTAG
66 GCAGATTCTTCTGATCGATTTTCACTATCATCTGAAATGTTATTAG
* * * *
1549401 CAACAGAGATATTGTTTCCATCCTCCTTGGTTGCAGGCTCGGAAGAAACGTTATCAAGTTCAGGA
1 CAACAGAGATACTGTTTCCATCCTCCATGGTTGCAGGCTCAGAAGAAACCTTATCAAGTTCAGGA
* *
1549466 GCAGATTCTTCTGATTGATTTTCGCTATCA
66 GCAGATTCTTCTGATCGATTTTCACTATCA
1549496 CGAGTTCCTT
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
111 84 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (111 bp):
CAACAGAGATACTGTTTCCATCCTCCATGGTTGCAGGCTCAGAAGAAACCTTATCAAGTTCAGGA
GCAGATTCTTCTGATCGATTTTCACTATCATCTGAAATGTTATTAG
Found at i:1556084 original size:20 final size:20
Alignment explanation
Indices: 1556043--1556084 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1556033 TATAAAAATA
*
1556043 ATTATTTTTATTTATTTCAT
1 ATTATTTTTAATTATTTCAT
1556063 ATTATATTTTAATTATTT-AT
1 ATTAT-TTTTAATTATTTCAT
1556083 AT
1 AT
1556085 NNNNNNNNNN
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTATTTTTAATTATTTCAT
Found at i:1559082 original size:29 final size:29
Alignment explanation
Indices: 1559050--1559110 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
1559040 ACTCGATTCA
1559050 AAAAAATTCAAATCAAATTAGAATTGATT
1 AAAAAATTCAAATCAAATTAGAATTGATT
* *
1559079 AAAAAATTCGAGTCAAATTAGAATTGATT
1 AAAAAATTCAAATCAAATTAGAATTGATT
1559108 AAA
1 AAA
1559111 TAGGACTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.30
Consensus pattern (29 bp):
AAAAAATTCAAATCAAATTAGAATTGATT
Found at i:1561950 original size:534 final size:535
Alignment explanation
Indices: 1560942--1562010 Score: 2131
Period size: 534 Copynumber: 2.0 Consensus size: 535
1560932 AAACAACAGC
1560942 ACCATGACAATTCATGTATACTTCATTTTTTTTTGTAAATATTTATGATTTTTTAAAATATTATC
1 ACCATGACAATTCATGTATACTTCATTTTTTTTTGTAAATATTTATGATTTTTTAAAATATTATC
1561007 ATATAAGACAAATAGCGACATGCTAACATGAAGTATACATGGATTTTCATGTAAGTTGTCACGCC
66 ATATAAGACAAATAGCGACATGCTAACATGAAGTATACATGGATTTTCATGTAAGTTGTCACGCC
1561072 ATCATCTAAAAAATTAGTGTTTTAATCAAGATTTCTGTTAAAAGAACGTTTTGACTTATTTTAAA
131 ATCATCTAAAAAATTAGTGTTTTAATCAAGATTTCTGTTAAAAGAACGTTTTGACTTATTTTAAA
1561137 AGATTAATAACCAAATTTAACTAAAAAAGTCAAATTAATAAAAGATGTAAACGTTAAAAGCTAAA
196 AGATTAATAACCAAATTTAACTAAAAAAGTCAAATTAATAAAAGATGTAAACGTTAAAAGCTAAA
1561202 TTTGATATTATCCGGGATGAAATATTGATTGGTTGTTGTTGCTAAATTTGAGAGTTTGTAAGAGA
261 TTTGATATTATCCGGGATGAAATATTGATTGGTTGTTGTTGCTAAATTTGAGAGTTTGTAAGAGA
1561267 GGATATTAAGGAATAAGTATGATATTAATGATGATGGCAGTCTTGACCTTATATAAATAATTGAT
326 GGATATTAAGGAATAAGTATGATATTAATGATGATGGCAGTCTTGACCTTATATAAATAATTGAT
1561332 TAGATTCTCTTTTTGTCATCATTTTAATGGGTAATTAGTGCTTCATTTAGTCACTTTAAATCATG
391 TAGATTCTCTTTTTGTCATCATTTTAATGGGTAATTAGTGCTTCATTTAGTCACTTTAAATCATG
1561397 TTTAAAATTTGTTCCTATAAATTAATTTCAGTTTCATTAAATTTTTAGTACTATATATATATATA
456 TTTAAAATTTGTTCCTATAAATTAATTTCAGTTTCATTAAATTTTTAGTACTATATATATATATA
1561462 TATA-ATATTTCAAT
521 TATATATATTTCAAT
1561476 ACCATGACAATTCATGTATACTTCATTTTTTTTTGTAAATATTTATGATTTTTTAAAATATTATC
1 ACCATGACAATTCATGTATACTTCATTTTTTTTTGTAAATATTTATGATTTTTTAAAATATTATC
1561541 ATATAAGACAAATAGCGACATGCTAACATGAAGTATACATGGATTTTCATGTAAGTTGTCACGCC
66 ATATAAGACAAATAGCGACATGCTAACATGAAGTATACATGGATTTTCATGTAAGTTGTCACGCC
1561606 ATCATCTAAAAAATTAGTGTTTTAATCAAGATTTCTGTTAAAAGAACGTTTTGACTTATTTTAAA
131 ATCATCTAAAAAATTAGTGTTTTAATCAAGATTTCTGTTAAAAGAACGTTTTGACTTATTTTAAA
1561671 AGATTAATAACCAAATTTAACTAAAAAAGTCAAATTAATAAAAGATGTAAACGTTAAAAGCTAAA
196 AGATTAATAACCAAATTTAACTAAAAAAGTCAAATTAATAAAAGATGTAAACGTTAAAAGCTAAA
1561736 TTTGATATTATCCGGGATGAAATATTGATTGGTTGTTGTTGCTAAATTTGAGAGTTTGTAAGAGA
261 TTTGATATTATCCGGGATGAAATATTGATTGGTTGTTGTTGCTAAATTTGAGAGTTTGTAAGAGA
1561801 GGATATTAAGGAATAAGTATGATATTAATGATGATGGCAGTCTTGACCTTATATAAATAATTGAT
326 GGATATTAAGGAATAAGTATGATATTAATGATGATGGCAGTCTTGACCTTATATAAATAATTGAT
1561866 TAGATTCTCTTTTTGTCATCATTTTAATGGGTAATTAGTGCTTCATTTAGTCACTTTAAATCATG
391 TAGATTCTCTTTTTGTCATCATTTTAATGGGTAATTAGTGCTTCATTTAGTCACTTTAAATCATG
1561931 TTTAAAATTTGTTCCTATAAATTAATTTCAGTTTCATTAAATTTTTAGTACTATATATATATATA
456 TTTAAAATTTGTTCCTATAAATTAATTTCAGTTTCATTAAATTTTTAGTACTATATATATATATA
1561996 TATATATATTTCAAT
521 TATATATATTTCAAT
1562011 TTCATTAATT
Statistics
Matches: 534, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
534 524 0.98
535 10 0.02
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (535 bp):
ACCATGACAATTCATGTATACTTCATTTTTTTTTGTAAATATTTATGATTTTTTAAAATATTATC
ATATAAGACAAATAGCGACATGCTAACATGAAGTATACATGGATTTTCATGTAAGTTGTCACGCC
ATCATCTAAAAAATTAGTGTTTTAATCAAGATTTCTGTTAAAAGAACGTTTTGACTTATTTTAAA
AGATTAATAACCAAATTTAACTAAAAAAGTCAAATTAATAAAAGATGTAAACGTTAAAAGCTAAA
TTTGATATTATCCGGGATGAAATATTGATTGGTTGTTGTTGCTAAATTTGAGAGTTTGTAAGAGA
GGATATTAAGGAATAAGTATGATATTAATGATGATGGCAGTCTTGACCTTATATAAATAATTGAT
TAGATTCTCTTTTTGTCATCATTTTAATGGGTAATTAGTGCTTCATTTAGTCACTTTAAATCATG
TTTAAAATTTGTTCCTATAAATTAATTTCAGTTTCATTAAATTTTTAGTACTATATATATATATA
TATATATATTTCAAT
Found at i:1563023 original size:18 final size:18
Alignment explanation
Indices: 1562997--1563034 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1562987 ACTTTTTAAC
*
1562997 TTTTAAATAT-TTTTTAT
1 TTTTAAATATATTTTGAT
1563014 TTTTAGAATATATTTTGAT
1 TTTTA-AATATATTTTGAT
1563033 TT
1 TT
1563035 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTAAATATATTTTGAT
Found at i:1565270 original size:15 final size:17
Alignment explanation
Indices: 1565250--1565287 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1565240 AATAAATAAC
1565250 ATAAATTT-AA-TAAAA
1 ATAAATTTGAAGTAAAA
1565265 ATAAATTTGAAGTAAAA
1 ATAAATTTGAAGTAAAA
1565282 ATAAAT
1 ATAAAT
1565288 GAAACTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.38
16 2 0.10
17 11 0.52
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
ATAAATTTGAAGTAAAA
Found at i:1571090 original size:23 final size:24
Alignment explanation
Indices: 1571046--1571090 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1571036 CAAACCCAAA
* **
1571046 TTTCACCACATGACAATGCAACTC
1 TTTCACCACATGAAAACCCAACTC
1571070 TTTC-CCACATGAAAACCCAAC
1 TTTCACCACATGAAAACCCAAC
1571091 ATTTCTGTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.36, C:0.36, G:0.07, T:0.22
Consensus pattern (24 bp):
TTTCACCACATGAAAACCCAACTC
Found at i:1585067 original size:22 final size:22
Alignment explanation
Indices: 1585041--1585091 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1585031 GTTCGAATAG
*
1585041 TTTAATTACTTAAATAAAAAAA
1 TTTAATTAATTAAATAAAAAAA
* * * *
1585063 TTTAAATAATTTAATGACAAAA
1 TTTAATTAATTAAATAAAAAAA
1585085 TTTAATT
1 TTTAATT
1585092 TTTTAATTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTAATTAATTAAATAAAAAAA
Found at i:1585099 original size:13 final size:14
Alignment explanation
Indices: 1585083--1585111 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1585073 TTAATGACAA
1585083 AATT-TAATTTTTT
1 AATTGTAATTTTTT
1585096 AATTGTAATTTTTT
1 AATTGTAATTTTTT
1585110 AA
1 AA
1585112 AATTGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
AATTGTAATTTTTT
Found at i:1589652 original size:31 final size:31
Alignment explanation
Indices: 1589617--1589678 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1589607 TTACAAAATG
**
1589617 ATCACTAAATTGTTCAAAAGTTTTCATTTAA
1 ATCACTAAATTACTCAAAAGTTTTCATTTAA
* *
1589648 ATCACTAAATTACTCAAAATTTTTTATTTAA
1 ATCACTAAATTACTCAAAAGTTTTCATTTAA
1589679 GTCATTGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (31 bp):
ATCACTAAATTACTCAAAAGTTTTCATTTAA
Found at i:1593235 original size:15 final size:15
Alignment explanation
Indices: 1593217--1593253 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1593207 CGCAAGCTAC
1593217 TGAAGAATGAAACCG
1 TGAAGAATGAAACCG
*
1593232 TGAAGAATGAAATCG
1 TGAAGAATGAAACCG
1593247 TGGAAGA
1 T-GAAGA
1593254 TGCTTCTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.46, C:0.08, G:0.30, T:0.16
Consensus pattern (15 bp):
TGAAGAATGAAACCG
Found at i:1593785 original size:22 final size:23
Alignment explanation
Indices: 1593751--1593794 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1593741 CTTTCTTCTC
*
1593751 AAAAAATAAAGAAAAAATAAAAT
1 AAAAAATAAAGAAAAAAAAAAAT
*
1593774 AAAAAA-AGAGAAAAAAAAAAA
1 AAAAAATAAAGAAAAAAAAAAA
1593795 AACAGCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (23 bp):
AAAAAATAAAGAAAAAAAAAAAT
Found at i:1593787 original size:20 final size:18
Alignment explanation
Indices: 1593751--1593796 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
1593741 CTTTCTTCTC
*
1593751 AAAAAATAAAGAAAAAATA
1 AAAAAAAAAAGAAAAAA-A
1593770 AAATAAAAAAAGAGAAAAAA
1 AAA-AAAAAAAGA-AAAAAA
1593790 AAAAAAA
1 AAAAAAA
1593797 CAGCACTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 12 0.50
21 5 0.21
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAAAA
Found at i:1599173 original size:110 final size:111
Alignment explanation
Indices: 1598980--1599199 Score: 433
Period size: 110 Copynumber: 2.0 Consensus size: 111
1598970 GAAGGGGATG
1598980 GGAGAGGATTTTGTTCCAAAAGACAAGCCATAGAAAACTTAATAGTGGAGGCCAAAGACATTGCT
1 GGAGAGGATTTTGTTCCAAAAGACAAGCCATAGAAAACTTAATAGTGGAGGCCAAAGACATTGCT
1599045 ACTCAGTTTTAGAGAAAAGCACAAAAAGGGAACT-GCCCACAGTCC
66 ACTCAGTTTTAGAGAAAAGCACAAAAAGGGAACTGGCCCACAGTCC
1599090 GGAGAGGATTTTGTTCCAAAAGACAAGCCATAGAAAACTTAATAGTGGAGGCCAAAGACATTGCT
1 GGAGAGGATTTTGTTCCAAAAGACAAGCCATAGAAAACTTAATAGTGGAGGCCAAAGACATTGCT
1599155 ACTCAGTTTTAGAGAAAAGCACAAAAAGGGAACTGGCCCACAGTC
66 ACTCAGTTTTAGAGAAAAGCACAAAAAGGGAACTGGCCCACAGTC
1599200 TGTGTACCTG
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
110 99 0.91
111 10 0.09
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (111 bp):
GGAGAGGATTTTGTTCCAAAAGACAAGCCATAGAAAACTTAATAGTGGAGGCCAAAGACATTGCT
ACTCAGTTTTAGAGAAAAGCACAAAAAGGGAACTGGCCCACAGTCC
Found at i:1600500 original size:22 final size:23
Alignment explanation
Indices: 1600456--1600504 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1600446 GAAAGATCTA
1600456 AAACAAAGTTGAATCAAAAACTG
1 AAACAAAGTTGAATCAAAAACTG
1600479 AAACAAAGTTGAATC-AAAACTG
1 AAACAAAGTTGAATCAAAAACTG
1600501 AAAC
1 AAAC
1600505 TTTAGATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.16
Consensus pattern (23 bp):
AAACAAAGTTGAATCAAAAACTG
Found at i:1611061 original size:4 final size:4
Alignment explanation
Indices: 1611044--1611092 Score: 89
Period size: 4 Copynumber: 12.2 Consensus size: 4
1611034 GTTAGAATGA
*
1611044 ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1611092 A
1 A
1611093 TACATATGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:1611120 original size:14 final size:14
Alignment explanation
Indices: 1611101--1611130 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1611091 TATACATATG
1611101 TGTGTGTGTGTGTA
1 TGTGTGTGTGTGTA
1611115 TGTGTGTGTGTGTA
1 TGTGTGTGTGTGTA
1611129 TG
1 TG
1611131 CAAGGTCACC
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:0.07, C:0.00, G:0.43, T:0.50
Consensus pattern (14 bp):
TGTGTGTGTGTGTA
Found at i:1613004 original size:17 final size:17
Alignment explanation
Indices: 1612978--1613011 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1612968 ATATAATATA
1612978 TATATAGTTTTAGTATT
1 TATATAGTTTTAGTATT
* *
1612995 TATATTGTTTTATTATT
1 TATATAGTTTTAGTATT
1613012 ATTTATCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (17 bp):
TATATAGTTTTAGTATT
Found at i:1618845 original size:20 final size:20
Alignment explanation
Indices: 1618817--1618854 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1618807 TGCTCTGGGT
1618817 GAGAA-TTTTGCTGGCATGTG
1 GAGAATTTTTG-TGGCATGTG
*
1618837 GAGAGTTTTTGTGGCATG
1 GAGAATTTTTGTGGCATG
1618855 AATCTTGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.18, C:0.08, G:0.37, T:0.37
Consensus pattern (20 bp):
GAGAATTTTTGTGGCATGTG
Found at i:1619168 original size:29 final size:30
Alignment explanation
Indices: 1619136--1619193 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1619126 TTAATCCAAT
*
1619136 GTACAATATC-ATATACA-AACTTTGATTTG
1 GTACAAT-TCTATATACACAACTTTAATTTG
*
1619165 GTACAATTCTATATATACAACTTTAATTT
1 GTACAATTCTATATACACAACTTTAATTT
1619194 CGATTCAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 13 0.52
30 10 0.40
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (30 bp):
GTACAATTCTATATACACAACTTTAATTTG
Found at i:1619946 original size:13 final size:13
Alignment explanation
Indices: 1619928--1619962 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1619918 TTGTCAATAC
1619928 AAAAACAAAAAAA
1 AAAAACAAAAAAA
1619941 AAAAACAAAAAAA
1 AAAAACAAAAAAA
1619954 AAAAACAAA
1 AAAAACAAA
1619963 TTACACATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAA
Found at i:1623800 original size:20 final size:20
Alignment explanation
Indices: 1623763--1623805 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1623753 AAATTTACTA
* *
1623763 TAAAATAAATTGATTTTTTT
1 TAAAAAAAATTGATTTTTAT
1623783 TAAAAAAAATT-ATGTTTTAT
1 TAAAAAAAATTGAT-TTTTAT
1623803 TAA
1 TAA
1623806 CAAGGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TAAAAAAAATTGATTTTTAT
Found at i:1625094 original size:143 final size:143
Alignment explanation
Indices: 1624781--1625094 Score: 359
Period size: 143 Copynumber: 2.2 Consensus size: 143
1624771 TAATCCCTTA
* * ** * * *
1624781 AAAATTATAAATATATTGACTATTAAAATTGTGAAATTGCACTTTTACTATCATTAAAAATTTAC
1 AAAATTAAAAATATAATGAAAAATAAAATTGTGAAATTGCACTTTTACTATCATTAAAAAATCAC
*
1624846 AATTTAATTTCGAGATCCCATAAAAAAAATTTCTGACTTCGCCCCTGGTTATATTATTTGATTAT
66 AATTTAATTTCGAGATCCCATAAAAAAAATTTCTGACTTCGCCCCTGGTTATATCATTTGATTAT
1624911 ATTTTAATTTTCT
131 ATTTTAATTTTCT
** * ** * *
1624924 AAAATTATGAATATATTGACTATTAAAATTGTGAAATTGCACTTTTACTATTA-TAAAAAATCAC
1 AAAATTAAAAATATAATGAAAAATAAAATTGTGAAATTGCACTTTTACTATCATTAAAAAATCAC
* ** *
1624988 AATTTAATTTCGAGATCCCCT-AAAAAAATTTCTGACTTTTCCTCT-GTATATATACCATTTTGA
66 AATTTAATTTCGAGATCCCATAAAAAAAATTTCTGACTTCGCCCCTGGT-TATAT--CA-TTTGA
*
1625051 TTATATTTTAGTTTTTCT
127 TTATATTTTA-ATTTTCT
*
1625069 AAATTTAAAAAT-TAAT-AAAAATAAAA
1 AAAATTAAAAATATAATGAAAAATAAAA
1625095 ATATTGTAGG
Statistics
Matches: 149, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
140 2 0.01
141 26 0.17
142 29 0.19
143 59 0.40
144 18 0.12
145 15 0.10
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (143 bp):
AAAATTAAAAATATAATGAAAAATAAAATTGTGAAATTGCACTTTTACTATCATTAAAAAATCAC
AATTTAATTTCGAGATCCCATAAAAAAAATTTCTGACTTCGCCCCTGGTTATATCATTTGATTAT
ATTTTAATTTTCT
Found at i:1634767 original size:20 final size:21
Alignment explanation
Indices: 1634742--1634780 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1634732 ATATAATTTC
*
1634742 ATTTAAT-GAATATTATTTTT
1 ATTTAATAAAATATTATTTTT
1634762 ATTTAATAAAATATTATTT
1 ATTTAATAAAATATTATTT
1634781 ATACAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
ATTTAATAAAATATTATTTTT
Found at i:1634966 original size:18 final size:18
Alignment explanation
Indices: 1634939--1634977 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1634929 TATTTTAGTT
* *
1634939 TTGAAAACTGTTGTTTTC
1 TTGAAAACTGTGGGTTTC
*
1634957 TTGAAGACTGTGGGTTTC
1 TTGAAAACTGTGGGTTTC
1634975 TTG
1 TTG
1634978 CATGCATGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (18 bp):
TTGAAAACTGTGGGTTTC
Found at i:1635974 original size:28 final size:28
Alignment explanation
Indices: 1635937--1636000 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
1635927 GATTTAGTTA
*
1635937 ATTAAATTAGT-TTCTTTATTATTAAATT
1 ATTAAATTAGTCTT-TATATTATTAAATT
* *
1635965 ATTAATTTAGTCTTTATATTATTAAATAA
1 ATTAAATTAGTCTTTATATTATTAAAT-T
1635994 ATTAAAT
1 ATTAAAT
1636001 ATTTACTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 22 0.73
29 8 0.27
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (28 bp):
ATTAAATTAGTCTTTATATTATTAAATT
Found at i:1637530 original size:2 final size:2
Alignment explanation
Indices: 1637523--1637549 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1637513 ATCTTTTTAA
1637523 AT 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 AT A
1637550 CACATTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1639467 original size:7 final size:7
Alignment explanation
Indices: 1639457--1639484 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1639447 TTCTATGACG
1639457 CGCCGCC
1 CGCCGCC
1639464 CGCCGCC
1 CGCCGCC
1639471 CGCCGCC
1 CGCCGCC
1639478 CGCCGCC
1 CGCCGCC
1639485 GGGTACTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.71, G:0.29, T:0.00
Consensus pattern (7 bp):
CGCCGCC
Found at i:1644736 original size:10 final size:10
Alignment explanation
Indices: 1644723--1644757 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1644713 ATAAAATGAC
*
1644723 TAAAAAGTCA
1 TAAAAAGTTA
1644733 TAAAAAGTTA
1 TAAAAAGTTA
1644743 TAAAAA-TTA
1 TAAAAAGTTA
1644752 TAAAAA
1 TAAAAA
1644758 ATTAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (10 bp):
TAAAAAGTTA
Found at i:1644768 original size:17 final size:18
Alignment explanation
Indices: 1644743--1644784 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
1644733 TAAAAAGTTA
*
1644743 TAAAAATTATAAAAA-AT
1 TAAAAATTAGAAAAACAT
*
1644760 TAAATATTAGAAAAACAT
1 TAAAAATTAGAAAAACAT
1644778 TAAAAAT
1 TAAAAAT
1644785 ATTAAAATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAATTAGAAAAACAT
Found at i:1647984 original size:19 final size:19
Alignment explanation
Indices: 1647947--1648006 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1647937 CTTATTAAAC
1647947 TTAT-AAAA-TATAAAAAAA
1 TTATAAAAACTAT-AAAAAA
* *
1647965 TTATAAAAATTATAATAAA
1 TTATAAAAACTATAAAAAA
*
1647984 TCTA-ATAAACTATAAAAAA
1 T-TATAAAAACTATAAAAAA
1648003 TTAT
1 TTAT
1648007 GGAACTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 6 0.18
19 23 0.68
20 5 0.15
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TTATAAAAACTATAAAAAA
Found at i:1648414 original size:19 final size:17
Alignment explanation
Indices: 1648390--1648426 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1648380 CATCCAGTTC
1648390 AATTAAATAAAATATTAAA
1 AATTAAA-AAAA-ATTAAA
1648409 AATTAAAAAAAATTAAA
1 AATTAAAAAAAATTAAA
1648426 A
1 A
1648427 TCGGTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 4 0.22
19 7 0.39
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATTAAAAAAAATTAAA
Found at i:1660499 original size:11 final size:11
Alignment explanation
Indices: 1660479--1660508 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1660469 TAAAAAATAA
1660479 AAAAAGTATTTT
1 AAAAA-TATTTT
1660491 AAAAATATTTT
1 AAAAATATTTT
1660502 AAAAATA
1 AAAAATA
1660509 AAAAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1674775 original size:21 final size:23
Alignment explanation
Indices: 1674749--1674790 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1674739 TAAGTTATTT
1674749 TAAAA-TTATAAAAA-TTATAAA
1 TAAAATTTATAAAAACTTATAAA
1674770 TAAAATTTATAAAAACTTATA
1 TAAAATTTATAAAAACTTATA
1674791 TATTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAAATTTATAAAAACTTATAAA
Found at i:1674926 original size:13 final size:13
Alignment explanation
Indices: 1674890--1674931 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1674880 TCTGTATTGT
1674890 TTTTTTTAATAAA
1 TTTTTTTAATAAA
* **
1674903 ATAATTT-ATAAA
1 TTTTTTTAATAAA
1674915 TTTTTTTAATAAA
1 TTTTTTTAATAAA
1674928 TTTT
1 TTTT
1674932 GTATATAGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTTTTAATAAA
Found at i:1682736 original size:9 final size:9
Alignment explanation
Indices: 1682722--1682824 Score: 134
Period size: 9 Copynumber: 11.4 Consensus size: 9
1682712 TTTGGTTAAA
1682722 AATTAACCG
1 AATTAACCG
*
1682731 AATTAACCA
1 AATTAACCG
1682740 AATTAACCG
1 AATTAACCG
*
1682749 AATTACCCG
1 AATTAACCG
*
1682758 ACTTAACCG
1 AATTAACCG
*
1682767 AATTACCCG
1 AATTAACCG
1682776 AATTAACCG
1 AATTAACCG
*
1682785 AATTACCCG
1 AATTAACCG
*
1682794 AATTACCCG
1 AATTAACCG
*
1682803 AATTAACCA
1 AATTAACCG
*
1682812 AATTAACCT
1 AATTAACCG
1682821 AATT
1 AATT
1682825 GAATCATACA
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 82 1.00
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:1682874 original size:6 final size:6
Alignment explanation
Indices: 1682863--1682891 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1682853 ACTTTTATAC
1682863 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1682892 AATTTTATTT
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:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:1682915 original size:20 final size:20
Alignment explanation
Indices: 1682863--1682904 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
1682853 ACTTTTATAC
1682863 TTTAGTTTTAG--TTTTAGT
1 TTTAGTTTTAGAATTTTAGT
*
1682881 TTTAGTTTTAGAATTTTATT
1 TTTAGTTTTAGAATTTTAGT
1682901 TTTA
1 TTTA
1682905 TTTATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
20 10 0.48
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTAGTTTTAGAATTTTAGT
Found at i:1688326 original size:78 final size:79
Alignment explanation
Indices: 1688218--1688375 Score: 230
Period size: 78 Copynumber: 2.0 Consensus size: 79
1688208 AATTCAAAGA
**
1688218 AAAATAAAGTTAAAGAAGAAAGGGTTTCAACAGATTGAGGTAGG-AGGCGGTTGTG-ACAGTTAT
1 AAAATAAAGTTAAAGAAGAAAGGGTTTCAACAGATTGAGGT-GGAAGGCGACTGTGCACAGTTAT
* *
1688281 GAAGAGGATGCACAT
65 CAAGAGGACGCACAT
**
1688296 AAAATAAAGTTAAAGAAGATGGGGTTTCAACAGATTGAGGTGGAAGGCGACTGTGCCACAGTTAT
1 AAAATAAAGTTAAAGAAGAAAGGGTTTCAACAGATTGAGGTGGAAGGCGACTGTG-CACAGTTAT
1688361 CAAGAGGACGCACAT
65 CAAGAGGACGCACAT
1688376 CATGTAAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
77 2 0.03
78 48 0.68
80 21 0.30
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.21
Consensus pattern (79 bp):
AAAATAAAGTTAAAGAAGAAAGGGTTTCAACAGATTGAGGTGGAAGGCGACTGTGCACAGTTATC
AAGAGGACGCACAT
Found at i:1706921 original size:112 final size:111
Alignment explanation
Indices: 1706713--1707189 Score: 537
Period size: 111 Copynumber: 4.4 Consensus size: 111
1706703 AAATTTATTT
* * * * *
1706713 TTTGGGTGCTGGCTTGTCAATGGCCGGCACCC--TAC-A-GTAAAAAAAAA-GTTTC-CTTTTTT
1 TTTGGGTGCTGGCCTGTCAATGTCCGGCACCCAGTACAATTTAAAAAAAAATTTTTCTTTTTTTT
* * * *
1706772 --T-TCAGAATAAGATATAAATATACG--AAAAAGTAAAAAAAAAA
66 CGTGTCAGAGTCAGATATAATTATACGAAAAAAATTAAAAAAAAAA
1706813 TTT-GGTGCTGGCCTGTCAATGTCCGGCACCCAGTACAATTTAAAAAAAATATTTTTTTTCTTTT
1 TTTGGGTGCTGGCCTGTCAATGTCCGGCACCCAGTACAATTTAAAAAAAA-A---TTTTTCTTTT
*
1706877 TTTTCGTGTAAGAGTCAGATATAATTATACG-AAAAAA-T-AAAAAAAAA
62 TTTTCGTGTCAGAGTCAGATATAATTATACGAAAAAAATTAAAAAAAAAA
1706924 -TTGGGTGCTGGCCTGTCAAT-TGCCGGCACCCAGTACAATTTAAAAAAAAATTCTTT-TTTTTT
1 TTTGGGTGCTGGCCTGTCAATGT-CCGGCACCCAGTACAATTTAAAAAAAAATT-TTTCTTTTTT
* *
1706986 TCCGTGTCAGAGTCAGATATAATTATACGAAAAAAATTAAAAAAAAATT
64 TTCGTGTCAGAGTCAGATATAATTATACGAAAAAAATTAAAAAAAAA-A
* *
1707035 TTTGGGTGCTGCCCTGTCAATGGT-CGGCACCCAGTACAATTTTTAAAAAAAA--TTTCTTTTTT
1 TTTGGGTGCTGGCCTGTCAAT-GTCCGGCACCCAGTACAA-TTTAAAAAAAAATTTTTCTTTTTT
**
1707097 TTCGTGTCAGAGTCAGATATAATTATACGAAAAAAATTAAAAAAAATTTTT
64 TTCGTGTCAGAGTCAGATATAATTATACGAAAAAAATTAAAAAAAA---AA
* *
1707148 TTTGGGTGCTGGCCTGTCATTGGCCGGCACCCAGTACAATTT
1 TTTGGGTGCTGGCCTGTCAATGTCCGGCACCCAGTACAATTT
1707190 TTTTTAAAAA
Statistics
Matches: 328, Mismatches: 19, Indels: 48
0.83 0.05 0.12
Matches are distributed among these distances:
99 26 0.08
100 3 0.01
101 3 0.01
102 1 0.00
103 9 0.03
104 1 0.00
107 35 0.11
108 13 0.04
109 7 0.02
110 15 0.05
111 105 0.32
112 58 0.18
113 51 0.16
114 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (111 bp):
TTTGGGTGCTGGCCTGTCAATGTCCGGCACCCAGTACAATTTAAAAAAAAATTTTTCTTTTTTTT
CGTGTCAGAGTCAGATATAATTATACGAAAAAAATTAAAAAAAAAA
Found at i:1707317 original size:54 final size:56
Alignment explanation
Indices: 1707258--1707378 Score: 183
Period size: 54 Copynumber: 2.2 Consensus size: 56
1707248 CCAGCACTCA
* *
1707258 AATTTTTTTTTATTTTTCTCGTATATTTATATCTGACTCTGACACG-AAAAAAAAG
1 AATTTTTTTTTATTTTTCTCCTATAATTATATCTGACTCTGACACGAAAAAAAAAG
* * *
1707313 -ATTTTTTTTAATTTTTTTCCTATAATTATATCTGACTCTGACTCGAAAAAAAAAG
1 AATTTTTTTTTATTTTTCTCCTATAATTATATCTGACTCTGACACGAAAAAAAAAG
1707368 AATTTTTTTTT
1 AATTTTTTTTT
1707379 TAAAATTGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
54 40 0.69
55 9 0.16
56 9 0.16
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (56 bp):
AATTTTTTTTTATTTTTCTCCTATAATTATATCTGACTCTGACACGAAAAAAAAAG
Found at i:1707539 original size:114 final size:109
Alignment explanation
Indices: 1707313--1707597 Score: 391
Period size: 109 Copynumber: 2.6 Consensus size: 109
1707303 GAAAAAAAAG
* *
1707313 ATTTTTTTTAATTTTTTTCCTATAATTATATCTGACTCTGACTCGAAAAAAAAAGAATTTTTTTT
1 ATTTTTTTT-ATTTTTTTCGTATAATTATATCTGACTCTGACACGAAAAAAAAAGAATTTTTTTT
1707378 TTAAAATTGTACTGGGTGCCGGCCATTGACAGGCCAAAACCCAAA
65 TTAAAATTGTACTGGGTGCCGGCCATTGACAGGCCAAAACCCAAA
1707423 ATTTTTTTTATTTTTTTCGTATAATTATATCTGACTCTGACACGAAAAAAAAAGAAAAATATATA
1 ATTTTTTTTATTTTTTTCGTATAATTATATCTGACTCTGACACGAAAAAAAAAG---AAT-T-T-
**
1707488 TTTTTTT-AAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA
60 TTTTTTTAAAATTGTACTGGGTGCCGGCCATTGACAGGCCAAAACCCAAA
* * * * *
1707537 A-TTTTTTTACTTTTTTCGTATATTTATATCTTATTCTG--AC-AAAAAAAAGGAATTTTTTTTT
1 ATTTTTTTTATTTTTTTCGTATAATTATATCTGACTCTGACACGAAAAAAAAAGAATTTTTTTTT
1707598 ACTGTAAAAA
Statistics
Matches: 160, Mismatches: 9, Indels: 18
0.86 0.05 0.10
Matches are distributed among these distances:
104 6 0.04
105 1 0.01
106 1 0.01
107 3 0.02
109 43 0.27
110 18 0.11
111 2 0.01
112 3 0.02
113 34 0.21
114 42 0.26
115 7 0.04
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (109 bp):
ATTTTTTTTATTTTTTTCGTATAATTATATCTGACTCTGACACGAAAAAAAAAGAATTTTTTTTT
TAAAATTGTACTGGGTGCCGGCCATTGACAGGCCAAAACCCAAA
Found at i:1714157 original size:2 final size:2
Alignment explanation
Indices: 1714150--1714202 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
1714140 AAAACTGTAA
* * *
1714150 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1714192 AC AC AT AT AT A
1 AT AT AT AT AT A
1714203 CTGACCTGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1715568 original size:42 final size:42
Alignment explanation
Indices: 1715522--1715612 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
1715512 TTAAGCATAA
1715522 ATAATTTAAA-AGTTTTTATTATATATTTAATTTCCATAAAAT
1 ATAATTTAAACA-TTTTTATTATATATTTAATTTCCATAAAAT
1715564 ATAATTTAAACATTTTTATTATATATTTAATTTCCATAAAAT
1 ATAATTTAAACATTTTTATTATATATTTAATTTCCATAAAAT
1715606 ATAATTT
1 ATAATTT
1715613 TCAATCCGGC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 47 0.98
43 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (42 bp):
ATAATTTAAACATTTTTATTATATATTTAATTTCCATAAAAT
Found at i:1717742 original size:52 final size:52
Alignment explanation
Indices: 1717686--1717876 Score: 321
Period size: 52 Copynumber: 3.7 Consensus size: 52
1717676 TTGTCTCTTA
1717686 GTGAAGCATGCATATGGTGTTTGACATTCCATAGGCATTTATTCTTATCTCG
1 GTGAAGCATGCATATGGTGTTTGACATTCCATAGGCATTTATTCTTATCTCG
1717738 GTGAAGCATGCATATGGTGTTTGACATTCCATAGGCATTTATTCTTATCTCG
1 GTGAAGCATGCATATGGTGTTTGACATTCCATAGGCATTTATTCTTATCTCG
** * *
1717790 GTGAAGCATGCATATGGTGTTTGACATTCCATAGGCATGAATTCTTATCCCT
1 GTGAAGCATGCATATGGTGTTTGACATTCCATAGGCATTTATTCTTATCTCG
*
1717842 GTGAAGCTTGCATATGGTGTTTGTA-ATTCCATAGG
1 GTGAAGCATGCATATGGTGTTTG-ACATTCCATAGG
1717877 TGTGTTTTAT
Statistics
Matches: 133, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
52 132 0.99
53 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (52 bp):
GTGAAGCATGCATATGGTGTTTGACATTCCATAGGCATTTATTCTTATCTCG
Found at i:1724166 original size:50 final size:51
Alignment explanation
Indices: 1724040--1724174 Score: 200
Period size: 51 Copynumber: 2.7 Consensus size: 51
1724030 TGTCTGCGAA
* * * * *
1724040 CACGTGTGCAGTACTAAGTGCAGGCTACTATGTGAACCGGAAGGCCTTGGT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGAACCGGAAAGCCTTGAT
*
1724091 CACGTGTGTAGTACTAAGTGTAGGCTACTACGTGAACCGGAAAG-CTTGAT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGAACCGGAAAGCCTTGAT
*
1724141 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTG
1724175 TATCGAATGA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 37 0.48
51 40 0.52
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (51 bp):
CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGAACCGGAAAGCCTTGAT
Found at i:1728686 original size:27 final size:26
Alignment explanation
Indices: 1728650--1728700 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
1728640 GAATATAAAG
*
1728650 GGGGTTGGTAATTGCTGATTTCCCCAA
1 GGGGTTGGTAAGTGCTGA-TTCCCCAA
1728677 GGGGTTGGTAAGTGCTGATTCCCC
1 GGGGTTGGTAAGTGCTGATTCCCC
1728701 GAATCATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.16, C:0.20, G:0.33, T:0.31
Consensus pattern (26 bp):
GGGGTTGGTAAGTGCTGATTCCCCAA
Found at i:1728722 original size:33 final size:33
Alignment explanation
Indices: 1728679--1728844 Score: 188
Period size: 33 Copynumber: 4.7 Consensus size: 33
1728669 TTCCCCAAGG
*
1728679 GGTTGGTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
1728712 GGTTGCTAAGTGCTGATTCCACCGTATCTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
1728754 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
1728787 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
1728820 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
1728845 GTAACAGATA
Statistics
Matches: 115, Mismatches: 8, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
33 70 0.61
34 10 0.09
36 2 0.02
37 2 0.02
38 2 0.02
39 2 0.02
41 6 0.05
42 21 0.18
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:1730890 original size:28 final size:28
Alignment explanation
Indices: 1730847--1730909 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
1730837 GTTCGAATGG
1730847 ATTGATAAATGTCAACTAAGTTTTGAGAA
1 ATTGA-AAATGTCAACTAAGTTTTGAGAA
1730876 ATTGAAAATGTCAACTAAGTTTTGAGAA
1 ATTGAAAATGTCAACTAAGTTTTGAGAA
1730904 ATTGAA
1 ATTGAA
1730910 GGCATTATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 29 0.85
29 5 0.15
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.33
Consensus pattern (28 bp):
ATTGAAAATGTCAACTAAGTTTTGAGAA
Found at i:1731896 original size:26 final size:26
Alignment explanation
Indices: 1731816--1731896 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
1731806 TGCGAACACG
*
1731816 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCCACTA
* * * *
1731842 CGTGTA-T-CGATAAAT-AATGGTCAC-A
1 TGTGTAGTAC--TAAGTGCA-GGCCACTA
1731867 TGTGTAGTACTAAGTGCAGGCCACTA
1 TGTGTAGTACTAAGTGCAGGCCACTA
1731893 TGTG
1 TGTG
1731897 AACTGGAAGG
Statistics
Matches: 39, Mismatches: 9, Indels: 14
0.63 0.15 0.23
Matches are distributed among these distances:
24 1 0.03
25 17 0.44
26 20 0.51
27 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGCAGGCCACTA
Found at i:1731980 original size:50 final size:50
Alignment explanation
Indices: 1731812--1731997 Score: 185
Period size: 51 Copynumber: 3.7 Consensus size: 50
1731802 TGTCTGCGAA
* * *** *
1731812 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGA-AAAGCTTGAT
* * * * * *
1731863 CACATGTGTAGTACTAAGTGCAGGCCACTATGTGAACTGGAAGGCCTT-ATT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAAAAG-CTTGA-T
* * *
1731914 CACGTGTGTAGTACTATGTGTAGGCAACTACGTGAACCGAAAAGCTTGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAAAAGCTTGAT
* *
1731964 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTG
1731998 TATCGGATGA
Statistics
Matches: 110, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
50 38 0.35
51 72 0.65
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (50 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAACCGAAAAGCTTGAT
Found at i:1737145 original size:25 final size:26
Alignment explanation
Indices: 1737117--1737182 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
1737107 ACCATTTCAC
1737117 TATTATATTACTATTATTTTATTG-T
1 TATTATATTACTATTATTTTATTGTT
* *
1737142 TATTGTATAACT-TATATTTTATTGTT
1 TATTATATTACTAT-TATTTTATTGTT
*
1737168 TATTTTATTACTATT
1 TATTATATTACTATT
1737183 TTAGAGACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
24 1 0.03
25 20 0.59
26 12 0.35
27 1 0.03
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (26 bp):
TATTATATTACTATTATTTTATTGTT
Found at i:1744976 original size:4 final size:4
Alignment explanation
Indices: 1744967--1744992 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1744957 CATCAAAGCA
1744967 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
1744993 GAGCTGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1746365 original size:21 final size:21
Alignment explanation
Indices: 1746335--1746374 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1746325 TGAGTTTGGG
1746335 ATTCGAGATTCAGGATTCTAA
1 ATTCGAGATTCAGGATTCTAA
* *
1746356 ATTCGGGATTCAGGGTTCT
1 ATTCGAGATTCAGGATTCT
1746375 GGAATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (21 bp):
ATTCGAGATTCAGGATTCTAA
Found at i:1746611 original size:15 final size:16
Alignment explanation
Indices: 1746593--1746622 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1746583 TAAAGGACTA
1746593 AAAAATAAA-AATTAC
1 AAAAATAAATAATTAC
1746608 AAAAATAAATAATTA
1 AAAAATAAATAATTA
1746623 ACCAAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATAAATAATTAC
Found at i:1746898 original size:31 final size:31
Alignment explanation
Indices: 1746860--1746925 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
1746850 ATTATCTCAA
* *
1746860 ACTTTTTT-ATCCAATTAGATACCTGAATTTG
1 ACTTTTTTGATCAAATT-GATACATGAATTTG
* *
1746891 ACTTTTTTGTTCAAATTGATGCATGAATTTG
1 ACTTTTTTGATCAAATTGATACATGAATTTG
1746922 ACTT
1 ACTT
1746926 CATAGTTCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (31 bp):
ACTTTTTTGATCAAATTGATACATGAATTTG
Found at i:1751506 original size:27 final size:27
Alignment explanation
Indices: 1751476--1751527 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1751466 TTCGAGTTTG
*
1751476 AGGTTCATGATTTAGA-ATTTAGGGTCA
1 AGGTTCAGGA-TTAGAGATTTAGGGTCA
*
1751503 AGGTTCGGGATTAGAGATTTAGGGT
1 AGGTTCAGGATTAGAGATTTAGGGT
1751528 AAAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.27, C:0.06, G:0.33, T:0.35
Consensus pattern (27 bp):
AGGTTCAGGATTAGAGATTTAGGGTCA
Found at i:1759962 original size:2 final size:2
Alignment explanation
Indices: 1759955--1759984 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1759945 TTTATCTGAA
1759955 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
1759985 GAAAATCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1761977 original size:12 final size:12
Alignment explanation
Indices: 1761960--1761989 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1761950 TAATAATTAC
1761960 ATACATACATAT
1 ATACATACATAT
*
1761972 ATACATATATAT
1 ATACATACATAT
1761984 ATACAT
1 ATACAT
1761990 GTTACACATG
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:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (12 bp):
ATACATACATAT
Found at i:1762471 original size:2 final size:2
Alignment explanation
Indices: 1762464--1762499 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1762454 AATGCAGCTT
*
1762464 TA TA TA TA TA CA TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1762500 GCACTCCACC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1762487 original size:15 final size:15
Alignment explanation
Indices: 1762467--1762496 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1762457 GCAGCTTTAT
1762467 ATATATACATATATA
1 ATATATACATATATA
*
1762482 ATATATATATATATA
1 ATATATACATATATA
1762497 TATGCACTCC
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:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATATACATATATA
Found at i:1762487 original size:17 final size:17
Alignment explanation
Indices: 1762465--1762498 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1762455 ATGCAGCTTT
1762465 ATATATATACATATATA
1 ATATATATACATATATA
*
1762482 ATATATATATATATATA
1 ATATATATACATATATA
1762499 TGCACTCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATATATACATATATA
Found at i:1769931 original size:1 final size:1
Alignment explanation
Indices: 1769925--1769956 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
1769915 CTTTGGTGTT
*
1769925 GGGGGGGGGGGGGGGGGGNGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1769957 AGAGAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:1774175 original size:12 final size:12
Alignment explanation
Indices: 1774158--1774182 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1774148 AAATTAGTCG
1774158 TTCTAGTTGAAT
1 TTCTAGTTGAAT
1774170 TTCTAGTTGAAT
1 TTCTAGTTGAAT
1774182 T
1 T
1774183 AACATTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (12 bp):
TTCTAGTTGAAT
Found at i:1782456 original size:19 final size:21
Alignment explanation
Indices: 1782434--1782477 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
1782424 CTTTAGCTCT
*
1782434 TTCTCTC-TCGATTCT-TTTC
1 TTCTCTCTTAGATTCTATTTC
1782453 TTCT-TCTTAGATTCTATTTC
1 TTCTCTCTTAGATTCTATTTC
1782473 TTCTC
1 TTCTC
1782478 GAGAACATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 2 0.10
19 11 0.52
20 8 0.38
ACGTcount: A:0.09, C:0.27, G:0.05, T:0.59
Consensus pattern (21 bp):
TTCTCTCTTAGATTCTATTTC
Found at i:1787393 original size:19 final size:21
Alignment explanation
Indices: 1787371--1787414 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
1787361 CTTTAGCTCT
1787371 TTCTCTC-TAGATTCT-TTTC
1 TTCTCTCTTAGATTCTATTTC
1787390 TTCT-TCTTAGATTCTATTTC
1 TTCTCTCTTAGATTCTATTTC
1787410 TTCTC
1 TTCTC
1787415 GAGAACATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.09
19 12 0.55
20 8 0.36
ACGTcount: A:0.11, C:0.25, G:0.05, T:0.59
Consensus pattern (21 bp):
TTCTCTCTTAGATTCTATTTC
Found at i:1788773 original size:21 final size:22
Alignment explanation
Indices: 1788747--1788790 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1788737 TATCATATGT
*
1788747 TTATTTAATAT-TCTTTGTAAG
1 TTATTTAAAATGTCTTTGTAAG
*
1788768 TTATTTAAAATGTTTTTGTAAG
1 TTATTTAAAATGTCTTTGTAAG
1788790 T
1 T
1788791 AAAATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (22 bp):
TTATTTAAAATGTCTTTGTAAG
Found at i:1789222 original size:34 final size:34
Alignment explanation
Indices: 1789158--1789227 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
1789148 TCGAGGGAAA
** *
1789158 AGTTATAAAGTGACCTTTCTTGAAATGAGATAAT
1 AGTTATAAAGTGACCTTTCTCCAAACGAGATAAT
1789192 AGTTATAAAGTGACCTTT-TCCAAGACGAGATAAT
1 AGTTATAAAGTGACCTTTCTCCAA-ACGAGATAAT
1789226 AG
1 AG
1789228 AGTTTCGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 3 0.09
34 29 0.91
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (34 bp):
AGTTATAAAGTGACCTTTCTCCAAACGAGATAAT
Found at i:1791472 original size:10 final size:11
Alignment explanation
Indices: 1791444--1791471 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1791434 AATTAATTAT
1791444 TAAAAAATTCA
1 TAAAAAATTCA
1791455 TAAAAAATTCA
1 TAAAAAATTCA
1791466 TAAAAA
1 TAAAAA
1791472 TATTTAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (11 bp):
TAAAAAATTCA
Found at i:1797615 original size:22 final size:24
Alignment explanation
Indices: 1797589--1797632 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1797579 GAAAAATATT
1797589 AAATAT-A-TATTTTTTATTTTTA
1 AAATATAATTATTTTTTATTTTTA
*
1797611 AAATATAATTGTTTTTTATTTT
1 AAATATAATTATTTTTTATTTT
1797633 AAGTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 1 0.05
24 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
AAATATAATTATTTTTTATTTTTA
Found at i:1799610 original size:17 final size:16
Alignment explanation
Indices: 1799569--1799611 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1799559 TTTTTACGAA
1799569 TTTTTTAA-TTTTAAT
1 TTTTTTAATTTTTAAT
*
1799584 TTGATTTAATTTTTAAT
1 TT-TTTTAATTTTTAAT
1799601 TTTTTATAATT
1 TTTTT-TAATT
1799612 ATTTGTTGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 7 0.30
17 14 0.61
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTTTTAATTTTTAAT
Found at i:1799898 original size:21 final size:20
Alignment explanation
Indices: 1799869--1799925 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 20
1799859 AATAAAGAAA
1799869 AAAATATTTTCA-ATTTATTT
1 AAAATATTTT-ATATTTATTT
1799889 AAAATAATTTTATATTTA--T
1 AAAAT-ATTTTATATTTATTT
* *
1799908 AAAATATTATAAATTTAT
1 AAAATATTTTATATTTAT
1799926 ATAGTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 10 0.31
19 6 0.19
20 6 0.19
21 10 0.31
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAATATTTTATATTTATTT
Found at i:1800707 original size:17 final size:16
Alignment explanation
Indices: 1800685--1800717 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
1800675 AATATTTGGC
1800685 AATAATAATTAATTTAA
1 AATAATAA-TAATTTAA
1800702 AATAATAATAATTTAA
1 AATAATAATAATTTAA
1800718 TGAGCATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAATAATTTAA
Found at i:1801973 original size:22 final size:24
Alignment explanation
Indices: 1801946--1801989 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
1801936 CATTTTGTCA
1801946 ATTTTAACTT-TTAT-TCAAAAAC
1 ATTTTAACTTGTTATATCAAAAAC
*
1801968 ATTTTAATTTGTTATATCAAAA
1 ATTTTAACTTGTTATATCAAAA
1801990 CATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTTTAACTTGTTATATCAAAAAC
Found at i:1804755 original size:345 final size:347
Alignment explanation
Indices: 1804111--1804803 Score: 1372
Period size: 345 Copynumber: 2.0 Consensus size: 347
1804101 GTTAATAAAA
1804111 TATTTATATTAATATATCATTTTTATAATGATTAAAATTTTAAATTTTTATATAAAATAAATTAT
1 TATTTATATTAATATATCATTTTTATAATGATTAAAATTTTAAATTTTTATATAAAATAAATTAT
1804176 TAAAGTGTAAAAACCATATAAAATAATATTAAATATGTTAATTGTTGTCATTATAACATCTTCAA
66 TAAAGTGTAAAAACCATATAAAATAATATTAAATATGTTAATTGTTGTCATTATAACATCTTCAA
1804241 AATTCGTGAATTCAAACGTACGTATTGTCAACTTCCTTCATTAATGGCCGTACTCAGCTATCCCC
131 AATTCGTGAATTCAAACGTACGTATTGTCAACTTCCTTCATTAATGGCCGTACTCAGCTATCCCC
1804306 AAGCTAGAAAAATTGGGAAAATAACTAAACTATAGAAATTAGGTATTTTCATAGCTAGAGACAAC
196 AAGCTAGAAAAATTGGGAAAATAACTAAACTATAGAAATTAGGTATTTTCATAGCTAGAGACAAC
1804371 CTTGACTAGTTATAGTAATCATGTGGTGGAAAAAGAAAATTTAATCAATAATTTAATGGAAAAAC
261 CTTGACTAGTTATAGTAATCATGTGGTGGAAAAAGAAAATTTAATCAATAATTTAATGGAAAAAC
1804436 TTTATTTTTTTCAATTTTTTTT
326 TTTATTTTTTTCAATTTTTTTT
1804458 TATTTATATT-A-ATATCATTTTTATAATGATTAAAATTTTAAATTTTTATATAAAATAAATTAT
1 TATTTATATTAATATATCATTTTTATAATGATTAAAATTTTAAATTTTTATATAAAATAAATTAT
1804521 TAAAGTGTAAAAACCATATAAAATAATATTAAATATGTTAATTGTTGTCATTATAACATCTTCAA
66 TAAAGTGTAAAAACCATATAAAATAATATTAAATATGTTAATTGTTGTCATTATAACATCTTCAA
1804586 AATTCGTGAATTCAAACGTACGTATTGTCAACTTCCTTCATTAATGGCCGTACTCAGCTATCCCC
131 AATTCGTGAATTCAAACGTACGTATTGTCAACTTCCTTCATTAATGGCCGTACTCAGCTATCCCC
1804651 AAGCTAGAAAAATTGGGAAAATAACTAAACTATAGAAATTAGGTATTTTCATAGCTAGAGACAAC
196 AAGCTAGAAAAATTGGGAAAATAACTAAACTATAGAAATTAGGTATTTTCATAGCTAGAGACAAC
1804716 CTTGACTAGTTATAGTAATCATGTGGTGGAAAAAGAAAATTTAATCAATAATTTAATGGAAAAAC
261 CTTGACTAGTTATAGTAATCATGTGGTGGAAAAAGAAAATTTAATCAATAATTTAATGGAAAAAC
1804781 TTTATTTTTTTCAATTTTTTTT
326 TTTATTTTTTTCAATTTTTTTT
1804803 T
1 T
1804804 TCAATTTTCA
Statistics
Matches: 346, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
345 335 0.97
346 1 0.00
347 10 0.03
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (347 bp):
TATTTATATTAATATATCATTTTTATAATGATTAAAATTTTAAATTTTTATATAAAATAAATTAT
TAAAGTGTAAAAACCATATAAAATAATATTAAATATGTTAATTGTTGTCATTATAACATCTTCAA
AATTCGTGAATTCAAACGTACGTATTGTCAACTTCCTTCATTAATGGCCGTACTCAGCTATCCCC
AAGCTAGAAAAATTGGGAAAATAACTAAACTATAGAAATTAGGTATTTTCATAGCTAGAGACAAC
CTTGACTAGTTATAGTAATCATGTGGTGGAAAAAGAAAATTTAATCAATAATTTAATGGAAAAAC
TTTATTTTTTTCAATTTTTTTT
Found at i:1804803 original size:13 final size:13
Alignment explanation
Indices: 1804785--1804811 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1804775 AAAAACTTTA
1804785 TTTTTTTCAATTT
1 TTTTTTTCAATTT
1804798 TTTTTTTCAATTT
1 TTTTTTTCAATTT
1804811 T
1 T
1804812 CAATTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTTTCAATTT
Found at i:1804833 original size:16 final size:17
Alignment explanation
Indices: 1804814--1804846 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1804804 TCAATTTTCA
1804814 ATTTTTCT-AAAACTTT
1 ATTTTTCTGAAAACTTT
*
1804830 ATTTTTTTGAAAACTTT
1 ATTTTTCTGAAAACTTT
1804847 TATATATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTTCTGAAAACTTT
Found at i:1809393 original size:24 final size:24
Alignment explanation
Indices: 1809348--1809393 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1809338 ATAACATGGA
*
1809348 CTGAGTTTATTTGGAAACGATTGG
1 CTGAGTTTATCTGGAAACGATTGG
1809372 CTGAGTTTATCTGGCAAA-GATT
1 CTGAGTTTATCTGG-AAACGATT
1809394 TTTTGCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (24 bp):
CTGAGTTTATCTGGAAACGATTGG
Found at i:1810490 original size:17 final size:17
Alignment explanation
Indices: 1810465--1810497 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1810455 TAATTTTGTT
*
1810465 TTTATTTTGGGTTGGGG
1 TTTAATTTGGGTTGGGG
1810482 TTTAATTTGGGTTGGG
1 TTTAATTTGGGTTGGG
1810498 TTTTTGAAAA
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:0.09, C:0.00, G:0.39, T:0.52
Consensus pattern (17 bp):
TTTAATTTGGGTTGGGG
Found at i:1817774 original size:9 final size:9
Alignment explanation
Indices: 1817760--1817813 Score: 56
Period size: 9 Copynumber: 5.7 Consensus size: 9
1817750 AAAATATTTT
1817760 TAAAAATTA
1 TAAAAATTA
1817769 TAAAAAATTA
1 T-AAAAATTA
*
1817779 TTAAAATTA
1 TAAAAATTA
1817788 TAAGAAAAATTA
1 T---AAAAATTA
1817800 T-AAAATTA
1 TAAAAATTA
1817808 TAAAAA
1 TAAAAA
1817814 ACTAAACTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.21
9 13 0.34
10 9 0.24
12 8 0.21
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:1817776 original size:10 final size:10
Alignment explanation
Indices: 1817761--1817814 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
1817751 AAATATTTTT
1817761 AAAAATTATA
1 AAAAATTATA
1817771 AAAAATTAT-
1 AAAAATTATA
*
1817780 TAAAATTATAA
1 AAAAATTAT-A
1817791 GAAAAATTAT-
1 -AAAAATTATA
1817801 -AAAATTATA
1 AAAAATTATA
1817810 AAAAA
1 AAAAA
1817815 CTAAACTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.22
9 8 0.22
10 13 0.35
12 8 0.22
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:1817782 original size:20 final size:20
Alignment explanation
Indices: 1817749--1817814 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
1817739 AACTTAAAAA
*
1817749 AAAAATATTTTTAAAAATTAT
1 AAAAA-ATTATTAAAAATTAT
1817770 AAAAAATTATT-AAAATTAT
1 AAAAAATTATTAAAAATTAT
1817789 AAGAAAA--ATTATAAAATTAT
1 AA-AAAATTATTA-AAAATTAT
1817809 AAAAAA
1 AAAAAA
1817815 CTAAACTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 3 0.07
19 14 0.34
20 19 0.46
21 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAAAATTATTAAAAATTAT
Found at i:1818381 original size:9 final size:10
Alignment explanation
Indices: 1818366--1818390 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1818356 AAGTTTTAAT
1818366 AATTTTTTAC
1 AATTTTTTAC
1818376 AATTTTTTAC
1 AATTTTTTAC
1818386 AATTT
1 AATTT
1818391 CTAATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (10 bp):
AATTTTTTAC
Found at i:1818409 original size:35 final size:36
Alignment explanation
Indices: 1818369--1818445 Score: 122
Period size: 35 Copynumber: 2.1 Consensus size: 36
1818359 TTTTAATAAT
1818369 TTTTTACAATT-TTTTACAATTTCTAATAA-TTTATA
1 TTTTTAC-ATTATTTTACAATTTCTAATAATTTTATA
1818404 TTTTTACATTATTTTACAATTTCTAATAATTTTTATA
1 TTTTTACATTATTTTACAATTTCTAATAA-TTTTATA
1818441 TTTTT
1 TTTTT
1818446 TTATAATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
34 3 0.08
35 25 0.64
37 11 0.28
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (36 bp):
TTTTTACATTATTTTACAATTTCTAATAATTTTATA
Found at i:1818435 original size:18 final size:18
Alignment explanation
Indices: 1818380--1818436 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
1818370 TTTTACAATT
1818380 TTTTACAATTTCTAATAA
1 TTTTACAATTTCTAATAA
* * *
1818398 -TTTA-TATTTTTACATTA
1 TTTTACAATTTCTA-ATAA
1818415 TTTTACAATTTCTAATAA
1 TTTTACAATTTCTAATAA
1818433 TTTT
1 TTTT
1818437 TATATTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 11 0.37
19 6 0.20
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTACAATTTCTAATAA
Found at i:1818443 original size:18 final size:17
Alignment explanation
Indices: 1818387--1818458 Score: 56
Period size: 19 Copynumber: 4.1 Consensus size: 17
1818377 ATTTTTTACA
1818387 ATTTCTAATAA-TTTAT
1 ATTTCTAATAATTTTAT
* * *
1818403 ATTTTTACATTATTTTACA
1 ATTTCTA-ATAATTTTA-T
1818422 ATTTCTAATAATTTTTAT
1 ATTTCTAATAA-TTTTAT
* *
1818440 ATTTTTTTATAATTTTAT
1 A-TTTCTAATAATTTTAT
1818458 A
1 A
1818459 GAATTCTAGC
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
16 6 0.14
17 3 0.07
18 15 0.35
19 19 0.44
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTCTAATAATTTTAT
Found at i:1818463 original size:29 final size:29
Alignment explanation
Indices: 1818403--1818463 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1818393 AATAATTTAT
*
1818403 ATTTTTACATTATTTTACAATTTCTAATA
1 ATTTTTACATTATTTTACAATTTCTAAGA
* * *
1818432 ATTTTTATATTTTTTTATAATTT-TATAGA
1 ATTTTTACATTATTTTACAATTTCTA-AGA
1818461 ATT
1 ATT
1818464 CTAGCATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTACATTATTTTACAATTTCTAAGA
Found at i:1818537 original size:11 final size:11
Alignment explanation
Indices: 1818523--1818548 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1818513 ATATTTTGTA
1818523 TTTTTAATAAT
1 TTTTTAATAAT
1818534 TTTTTAATAAT
1 TTTTTAATAAT
1818545 TTTT
1 TTTT
1818549 AGAGATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:1818546 original size:28 final size:27
Alignment explanation
Indices: 1818495--1818547 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
1818485 AAAATATATC
*
1818495 ATTTTTATAATTTTATTTATATTTTGT
1 ATTTTTATAATTTTATTAATATTTTGT
1818522 ATTTTTAATAATTTT-TTAATAATTTT
1 ATTTTT-ATAATTTTATTAAT-ATTTT
1818548 TAGAGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (27 bp):
ATTTTTATAATTTTATTAATATTTTGT
Found at i:1832040 original size:7 final size:7
Alignment explanation
Indices: 1832030--1832060 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1832020 ATTTCCCCTC
1832030 CCCATTT
1 CCCATTT
1832037 CCCATTT
1 CCCATTT
1832044 CCCATTT
1 CCCATTT
1832051 CCCATTT
1 CCCATTT
1832058 CCC
1 CCC
1832061 TAAGCCCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.48, G:0.00, T:0.39
Consensus pattern (7 bp):
CCCATTT
Found at i:1832042 original size:20 final size:21
Alignment explanation
Indices: 1832013--1832060 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1832003 TTTTAAATAA
*
1832013 ATTTCTCATTTCCC-CTCCCC
1 ATTTCCCATTTCCCACTCCCC
* *
1832033 ATTTCCCATTTCCCATTTCCC
1 ATTTCCCATTTCCCACTCCCC
1832054 ATTTCCC
1 ATTTCCC
1832061 TAAGCCCGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.12, C:0.46, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTCCCATTTCCCACTCCCC
Found at i:1832129 original size:15 final size:15
Alignment explanation
Indices: 1832105--1832160 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
1832095 CCCTTTTTTT
1832105 ATTTTT-ATTTTAAA
1 ATTTTTAATTTTAAA
* *
1832119 ATTTTTAATTTTTAT
1 ATTTTTAATTTTAAA
**
1832134 ATTTCAAATTTTAAA
1 ATTTTTAATTTTAAA
1832149 A--TTTAATTTTAA
1 ATTTTTAATTTTAA
1832161 TTATTAGTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
13 9 0.27
14 6 0.18
15 18 0.55
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTTAATTTTAAA
Found at i:1832129 original size:21 final size:21
Alignment explanation
Indices: 1832099--1832160 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1832089 CCTCCTCCCT
*
1832099 TTTTTTATTTTTATTTTAAAA
1 TTTTTAATTTTTATTTTAAAA
*
1832120 TTTTTAATTTTTATATTTCAAA
1 TTTTTAATTTTTAT-TTTAAAA
* * *
1832142 TTTTAAAATTTAATTTTAA
1 TTTTTAATTTTTATTTTAA
1832161 TTATTAGTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTAATTTTTATTTTAAAA
Found at i:1834084 original size:2 final size:2
Alignment explanation
Indices: 1834077--1834119 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1834067 TCGAAAATCT
1834077 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1834119 T
1 T
1834120 TAAAAAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1838365 original size:37 final size:37
Alignment explanation
Indices: 1838224--1838365 Score: 146
Period size: 37 Copynumber: 3.8 Consensus size: 37
1838214 TATTTTTGGT
* * *
1838224 TGGACAAGCTCTTATGAGC-ATCTAGCGTGTTATCGAG
1 TGGACTAGCTCTTACGAGCAAT-TGGCGTGTTATCGAG
*
1838261 TGGACTAGCTCTT-CGGAGCAATTGGCGTGTTATTGAG
1 TGGACTAGCTCTTAC-GAGCAATTGGCGTGTTATCGAG
* * * *
1838298 TGGACTAGCTCTTTA-GAGTAATTAGTGTGTTATCGAA
1 TGGACTAGCTC-TTACGAGCAATTGGCGTGTTATCGAG
* *
1838335 TGGATTAGCTCTTACTAGCAATTGGCGTGTT
1 TGGACTAGCTCTTACGAGCAATTGGCGTGTT
1838366 TCACTTGGAA
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
36 3 0.03
37 79 0.92
38 4 0.05
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (37 bp):
TGGACTAGCTCTTACGAGCAATTGGCGTGTTATCGAG
Found at i:1859726 original size:23 final size:23
Alignment explanation
Indices: 1859700--1859746 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1859690 GTGAAAATAT
1859700 GACACAAATATTTGTTAGCTATA
1 GACACAAATATTTGTTAGCTATA
1859723 GACACAAATATTTGTTAGCTATA
1 GACACAAATATTTGTTAGCTATA
1859746 G
1 G
1859747 TGGTTATGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (23 bp):
GACACAAATATTTGTTAGCTATA
Found at i:1876451 original size:2 final size:2
Alignment explanation
Indices: 1876444--1876473 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1876434 CATTTGATTG
1876444 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
1876474 GGAAACATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1877353 original size:13 final size:14
Alignment explanation
Indices: 1877335--1877363 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1877325 CACAATTCAT
1877335 TTAATATTT-TATA
1 TTAATATTTATATA
1877348 TTAATATTTATATA
1 TTAATATTTATATA
1877362 TT
1 TT
1877364 TTTATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAATATTTATATA
Found at i:1877380 original size:23 final size:20
Alignment explanation
Indices: 1877333--1877381 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
1877323 TTCACAATTC
1877333 ATTTAATATTTTATATTAAT
1 ATTTAATATTTTATATTAAT
1877353 ATTTATATATTTTTATTATTAAT
1 ATTTA-ATA-TTTTA-TATTAAT
*
1877376 TTTTAA
1 ATTTAA
1877382 AAAATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 5 0.20
21 3 0.12
22 6 0.24
23 11 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTAATATTTTATATTAAT
Found at i:1877815 original size:17 final size:17
Alignment explanation
Indices: 1877793--1877826 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1877783 GTCAATCCTG
1877793 TGTTTATCATTAGAGAA
1 TGTTTATCATTAGAGAA
1877810 TGTTTATCATTAGAGAA
1 TGTTTATCATTAGAGAA
1877827 GAGGTTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (17 bp):
TGTTTATCATTAGAGAA
Done.