Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6
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: 4312818
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 226954 characters in sequence are not A, C, G, or T
File 4 of 14
Found at i:1187333 original size:44 final size:43
Alignment explanation
Indices: 1187065--1187339 Score: 209
Period size: 44 Copynumber: 6.4 Consensus size: 43
1187055 TGAAGCTACA
* * * * * *
1187065 ATCTCCTTGAAGTTGCAGTAGAGTGGATCACA-TTA-AATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAATCTT
** * * *
1187106 ATCTCCCT-AAGGTTGCAGTGGAGCAAATTGAAGCTGATAATCCT
1 ATCTCCCTGAA-GTTGCAGTGGAGCGGATTAAAG-TAATAATCTT
*
1187150 ATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATA-ATCTT
* * * * *** *
1187194 ATCTCTCTAAAGTTGCAGTAGAGTGGATCGCA-TTA-AATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAATCTT
* * * ** *
1187235 ATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAATCCT
1 ATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAG-TAATAATCTT
*
1187279 ATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTT
1 ATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATA-ATCTT
* *
1187323 ATCTCTCTGAATTTGCA
1 ATCTCCCTGAAGTTGCA
1187340 ATAAAGTGGA
Statistics
Matches: 178, Mismatches: 46, Indels: 17
0.74 0.19 0.07
Matches are distributed among these distances:
40 2 0.01
41 50 0.28
42 1 0.01
43 12 0.07
44 111 0.62
45 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (43 bp):
ATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAATCTT
Found at i:1189588 original size:144 final size:141
Alignment explanation
Indices: 1189416--1189699 Score: 460
Period size: 144 Copynumber: 2.0 Consensus size: 141
1189406 TCAATATTTT
* *
1189416 GATTTTCTCCATACGTAACATTTATTCTAAAATTTACTTCGCATAGTATTTATTTTATTTTAAAC
1 GATTTTCTCCATACGTAACATTTATTCTAAAATGTACTTCGCAAAGTATTTATTTTATTTTAAAC
* *
1189481 TCCATTTTAATCTATTTCAAATTATTTTTTGCATATTATTTATGTTAATATTTCTATATACGCTT
66 ACCATTTTAATCTATTTC-AA--AGTTTTTGCATATTATTTATGTTAATATTTCTATATACGCTT
1189546 TATTGATTCACAAC
128 TATTGATTCACAAC
* *
1189560 GATTTTCTTCATAGGTAACATTTATTCTAAAATGTACTTCGCAAAGTATTTATTTTATTTTAAAC
1 GATTTTCTCCATACGTAACATTTATTCTAAAATGTACTTCGCAAAGTATTTATTTTATTTTAAAC
* * *
1189625 AGCATTTTAATCTATTTCAAAGTTTTTGTATATTATTTATGTTAATATTTCTATATGCGCTTTAT
66 ACCATTTTAATCTATTTCAAAGTTTTTGCATATTATTTATGTTAATATTTCTATATACGCTTTAT
1189690 TGATTCACAA
131 TGATTCACAA
1189700 TTTACATTCC
Statistics
Matches: 131, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
141 52 0.40
143 2 0.02
144 77 0.59
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.49
Consensus pattern (141 bp):
GATTTTCTCCATACGTAACATTTATTCTAAAATGTACTTCGCAAAGTATTTATTTTATTTTAAAC
ACCATTTTAATCTATTTCAAAGTTTTTGCATATTATTTATGTTAATATTTCTATATACGCTTTAT
TGATTCACAAC
Found at i:1191894 original size:28 final size:28
Alignment explanation
Indices: 1191846--1191918 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
1191836 CTCTGTGGCA
**
1191846 ATCTTTG-TAAAGGAAGCCTTTGTGGAG
1 ATCTTTGTTAAAGGAAAACTTTGTGGAG
*
1191873 ATCTTTGTTAAAGGAAAACTTTGTGGCG
1 ATCTTTGTTAAAGGAAAACTTTGTGGAG
*
1191901 ATCTTTATT-AAGGAAAAC
1 ATCTTTGTTAAAGGAAAAC
1191919 CCTTGAGGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 16 0.39
28 25 0.61
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (28 bp):
ATCTTTGTTAAAGGAAAACTTTGTGGAG
Found at i:1191967 original size:28 final size:27
Alignment explanation
Indices: 1191836--1191998 Score: 78
Period size: 28 Copynumber: 5.9 Consensus size: 27
1191826 AAAGAAATGC
* * *
1191836 CTCTGTGGCAATCTTTGTAAAGGAAGC
1 CTCTGTGGCAATCTCTATAAAGGAAGT
* * * **
1191863 CTTTGTGG-AGATCTTTGTTAAAGGAAAA
1 CTCTGTGGCA-ATCTCT-ATAAAGGAAGT
* * * * **
1191891 CTTTGTGGCGATCTTTATTAAGGAAAA
1 CTCTGTGGCAATCTCTATAAAGGAAGT
* * *
1191918 CCCTTGAGGCAATATCTATAAAGGAAGT
1 CTC-TGTGGCAATCTCTATAAAGGAAGT
** *
1191946 -TGCTGTGGTGATCTCTATTAAAAGAAGT
1 CT-CTGTGGCAATCTCTA-TAAAGGAAGT
*
1191974 CTTTGTGGCAATCTCTATAAAGGAA
1 CTCTGTGGCAATCTCTATAAAGGAA
1191999 TCCTTTGTGG
Statistics
Matches: 103, Mismatches: 26, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
26 1 0.01
27 40 0.39
28 61 0.59
29 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (27 bp):
CTCTGTGGCAATCTCTATAAAGGAAGT
Found at i:1195717 original size:21 final size:21
Alignment explanation
Indices: 1195681--1195726 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1195671 AGGTCGCCTC
*
1195681 GTAGAGATCGGAGGAGTG-GGA
1 GTAGAGATCGCAGGAG-GAGGA
*
1195702 GTAGAGATCGCCGGAGGAGGA
1 GTAGAGATCGCAGGAGGAGGA
1195723 GTAG
1 GTAG
1195727 GTCGCCTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.28, C:0.09, G:0.50, T:0.13
Consensus pattern (21 bp):
GTAGAGATCGCAGGAGGAGGA
Found at i:1197833 original size:14 final size:14
Alignment explanation
Indices: 1197788--1197838 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
1197778 GAACTTAATA
1197788 TATTTTATAATATT
1 TATTTTATAATATT
* *
1197802 TTTTTTACTTCAGT-TT
1 TATTTTA--T-AATATT
1197818 TATTTTATAATATT
1 TATTTTATAATATT
1197832 TATTTTA
1 TATTTTA
1197839 AGAATTGGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 2 0.07
14 16 0.55
16 9 0.31
17 2 0.07
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (14 bp):
TATTTTATAATATT
Found at i:1198028 original size:36 final size:36
Alignment explanation
Indices: 1197973--1198082 Score: 175
Period size: 36 Copynumber: 3.1 Consensus size: 36
1197963 TGTCACATTT
* *
1197973 ATCGCAATTGCAGGCTTAAGGGAGACTACTGCGGTC
1 ATCGCAATTGCGGGCTTAAGGGAGACTATTGCGGTC
*
1198009 ATCGCAATTGCGGGTTTAAGGGAGACTATTGCGGTC
1 ATCGCAATTGCGGGCTTAAGGGAGACTATTGCGGTC
* *
1198045 TTCGCAATTGTGGGCTTAAGGGAGACTATTGCGGTC
1 ATCGCAATTGCGGGCTTAAGGGAGACTATTGCGGTC
1198081 AT
1 AT
1198083 GGAATTTTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (36 bp):
ATCGCAATTGCGGGCTTAAGGGAGACTATTGCGGTC
Found at i:1199084 original size:55 final size:55
Alignment explanation
Indices: 1198997--1199100 Score: 154
Period size: 55 Copynumber: 1.9 Consensus size: 55
1198987 ATTCAATTAC
* *
1198997 TCTGTGGTGTCAAAATACACCTTTAATGGTTATCTGATCGATTTGCCTTTAGATA
1 TCTGTGGTGTCAAAATACACCTTTAATAGTTATCTGATCAATTTGCCTTTAGATA
** * *
1199052 TCTGTGGTGTCCTAATTCACCTTTAATAGTTATGTGATCAATTTGCCTT
1 TCTGTGGTGTCAAAATACACCTTTAATAGTTATCTGATCAATTTGCCTT
1199101 CAAATTTTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.42
Consensus pattern (55 bp):
TCTGTGGTGTCAAAATACACCTTTAATAGTTATCTGATCAATTTGCCTTTAGATA
Found at i:1201681 original size:22 final size:22
Alignment explanation
Indices: 1201650--1201703 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
1201640 GTGTGTTTGG
*
1201650 TTCGTATATATTCACAAATAAA
1 TTCGTTTATATTCACAAATAAA
1201672 TTCGTTTATATTCACAAATAAA
1 TTCGTTTATATTCACAAATAAA
1201694 TTCGTTTATA
1 TTCGTTTATA
1201704 ACATAGAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.43
Consensus pattern (22 bp):
TTCGTTTATATTCACAAATAAA
Found at i:1204881 original size:26 final size:26
Alignment explanation
Indices: 1204852--1204906 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
1204842 AAAGCCTTAG
* *
1204852 TGGCGTAATATGAAAGAAAGTATTTA
1 TGGCATAATATGAAAGAAAGCATTTA
*
1204878 TGGCATAATATGAAAGAAAGCCTTTA
1 TGGCATAATATGAAAGAAAGCATTTA
1204904 TGG
1 TGG
1204907 AAAACTTCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (26 bp):
TGGCATAATATGAAAGAAAGCATTTA
Found at i:1206083 original size:26 final size:26
Alignment explanation
Indices: 1206054--1206121 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
1206044 AACACATCAG
*
1206054 GAAAGAAAACCTTTGTGGCATAATAT
1 GAAAGAAAACCTTTGTGGCATAATAC
* *
1206080 GAAA-AAAAGCCTTTGCGGCGTAATAC
1 GAAAGAAAA-CCTTTGTGGCATAATAC
*
1206106 GAAAGAAAGCCTTTGT
1 GAAAGAAAACCTTTGT
1206122 AGTGGAATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 4 0.11
26 28 0.80
27 3 0.09
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.24
Consensus pattern (26 bp):
GAAAGAAAACCTTTGTGGCATAATAC
Found at i:1219429 original size:17 final size:17
Alignment explanation
Indices: 1219407--1219442 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1219397 TAGAATTGAG
*
1219407 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
1219424 TTGAGAAAATTAATTAA
1 TTGAGAAAATTAATTAA
1219441 TT
1 TT
1219443 TAATTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:1219806 original size:21 final size:23
Alignment explanation
Indices: 1219772--1219815 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
1219762 TGAGAATTTA
*
1219772 TTTTCTAAGTAT-A-AATTCTAT
1 TTTTCTAAGAATAACAATTCTAT
*
1219793 TTTTCTGAGAATAACAATTCTAT
1 TTTTCTAAGAATAACAATTCTAT
1219816 CAATTTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (23 bp):
TTTTCTAAGAATAACAATTCTAT
Found at i:1222961 original size:18 final size:19
Alignment explanation
Indices: 1222923--1222962 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1222913 GAAATTTTTA
*
1222923 TAAATATTTTTATATATAG
1 TAAATATTTTTATATAAAG
1222942 TAAATATTTTTATA-AAAG
1 TAAATATTTTTATATAAAG
1222960 TAA
1 TAA
1222963 CTAAATAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
TAAATATTTTTATATAAAG
Found at i:1225140 original size:14 final size:14
Alignment explanation
Indices: 1225121--1225160 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1225111 TTGATTGGCA
1225121 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
1225135 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
1225149 GGAAAATGTTTT
1 GTAAAATGTTTT
1225161 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:1225173 original size:34 final size:35
Alignment explanation
Indices: 1225129--1225195 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1225119 CAGTAAAATG
* *
1225129 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
1225163 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
1225196 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:1225182 original size:20 final size:20
Alignment explanation
Indices: 1225144--1225183 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1225134 CGTAAAATGA
**
1225144 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
1225164 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
1225184 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:1236269 original size:54 final size:54
Alignment explanation
Indices: 1236170--1236314 Score: 157
Period size: 54 Copynumber: 2.7 Consensus size: 54
1236160 GTTTAGGTGC
* * * * * * * * *
1236170 ACACGGCCTGGGACATGGGCTGCCACATGGTCGTGTGTATTAAGTCAGTGTGTT
1 ACACGGCCTAGCACACGGCCTGCGACACGGTCGTGTGTATCAAGTCAGAGAGTT
*
1236224 ACATGGCCTAGCACACGGCCTGCGACACGGTCGTGTGTCA-CAAGTCAGAGAGTT
1 ACACGGCCTAGCACACGGCCTGCGACACGGTCGTGTGT-ATCAAGTCAGAGAGTT
** *
1236278 ACACGGTGTAGCACACGGCCTGCGACACGGCCGTGTG
1 ACACGGCCTAGCACACGGCCTGCGACACGGTCGTGTG
1236315 GCCCAACTTA
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
54 75 0.99
55 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (54 bp):
ACACGGCCTAGCACACGGCCTGCGACACGGTCGTGTGTATCAAGTCAGAGAGTT
Found at i:1236407 original size:54 final size:54
Alignment explanation
Indices: 1236221--1236405 Score: 169
Period size: 54 Copynumber: 3.4 Consensus size: 54
1236211 AAGTCAGTGT
* * * *
1236221 GTTACATGGCCTAGCACACGGCCTGCGACACGGTCGTGTGTCACAA-GTCAGAGA
1 GTTACACGGCCTAGCACACGGCCTGCGACACGGCCGTGTGTCACAACTTC-GAAA
** * * * *
1236275 GTTACACGGTGTAGCACACGGCCTGCGACACGGCCGTGTGGCCCAACTTAGTAA
1 GTTACACGGCCTAGCACACGGCCTGCGACACGGCCGTGTGTCACAACTTCGAAA
** * * * *
1236329 GTTACACGGGCGGAG-ACACAGG-CTGGGACACGACCATGTGTCTCAACTTCGAAA
1 GTTACAC-GGCCTAGCACAC-GGCCTGCGACACGGCCGTGTGTCACAACTTCGAAA
1236383 GTTACACGGCCTAGTCACACGGC
1 GTTACACGGCCTAG-CACACGGC
1236406 TGTGTGTCCC
Statistics
Matches: 104, Mismatches: 21, Indels: 11
0.76 0.15 0.08
Matches are distributed among these distances:
53 5 0.05
54 87 0.84
55 12 0.12
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (54 bp):
GTTACACGGCCTAGCACACGGCCTGCGACACGGCCGTGTGTCACAACTTCGAAA
Found at i:1237695 original size:9 final size:9
Alignment explanation
Indices: 1237666--1237702 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1237656 TGAGTTTTTG
1237666 AATTCGAAT
1 AATTCGAAT
*
1237675 AACTCGAAT
1 AATTCGAAT
1237684 AATTCGAAT
1 AATTCGAAT
*
1237693 AATTCAAAT
1 AATTCGAAT
1237702 A
1 A
1237703 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1237813 original size:30 final size:30
Alignment explanation
Indices: 1237751--1237810 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1237741 AAACCTTTTT
* * *
1237751 ACTTTTCCCTCAAAACTTTTACTCCTTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCCTCCC
1237781 ACTTTCCCCCCAAAACTTTTACTCTCCTCC
1 ACTTTCCCCCCAAAACTTTTACTC-CCTCC
1237811 ACTCCCAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.20, C:0.43, G:0.00, T:0.37
Consensus pattern (30 bp):
ACTTTCCCCCCAAAACTTTTACTCCCTCCC
Found at i:1238075 original size:16 final size:16
Alignment explanation
Indices: 1238054--1238086 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1238044 CCCTATTTAC
1238054 TTTCCCTCAAAA-TTTT
1 TTTCCC-CAAAACTTTT
1238070 TTTCCCCAAAACTTTT
1 TTTCCCCAAAACTTTT
1238086 T
1 T
1238087 ATTTTCCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTCCCCAAAACTTTT
Found at i:1238085 original size:15 final size:16
Alignment explanation
Indices: 1238054--1238086 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1238044 CCCTATTTAC
*
1238054 TTTCCCTCAAAATTTT
1 TTTCCCTCAAAACTTT
1238070 TTTCCC-CAAAACTTT
1 TTTCCCTCAAAACTTT
1238085 TT
1 TT
1238087 ATTTTCCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTCCCTCAAAACTTT
Found at i:1238106 original size:19 final size:20
Alignment explanation
Indices: 1238068--1238105 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1238058 CCTCAAAATT
*
1238068 TTTTTCCCCAAAACTTTTTA
1 TTTTCCCCCAAAACTTTTTA
*
1238088 TTTTCCCCCTAAACTTTT
1 TTTTCCCCCAAAACTTTT
1238106 ACTTCTCACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTCCCCCAAAACTTTTTA
Found at i:1242723 original size:50 final size:50
Alignment explanation
Indices: 1242664--1242800 Score: 184
Period size: 50 Copynumber: 2.7 Consensus size: 50
1242654 CTTCCAATGT
* ** * *
1242664 CATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGC
1 CATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGC
* *
1242714 CATATCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAACGC
1 CATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGC
** *
1242764 CATGCCCCATACATGGTCTTACATGGGACCTCTCATA
1 CATATCCCAGACATGGTCTTACATGGGACCTCTCATA
1242801 ATCTCAATGA
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (50 bp):
CATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGC
Found at i:1246853 original size:12 final size:12
Alignment explanation
Indices: 1246826--1246860 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1246816 ATAATAATAA
1246826 TTTTAAGTGTGGAC
1 TTTTAA-TG-GGAC
1246840 TTTTAATGGGAC
1 TTTTAATGGGAC
1246852 TTTTAATGG
1 TTTTAATGG
1246861 CTCCTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 13 0.62
13 2 0.10
14 6 0.29
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.46
Consensus pattern (12 bp):
TTTTAATGGGAC
Found at i:1251922 original size:5 final size:5
Alignment explanation
Indices: 1251912--1251942 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1251902 GAGATGGAAT
1251912 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
1251943 ATATTTGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:1252594 original size:30 final size:31
Alignment explanation
Indices: 1252555--1252614 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1252545 GGAGGTGAGA
*
1252555 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
1252586 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
1252615 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:1252813 original size:9 final size:9
Alignment explanation
Indices: 1252798--1252834 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
1252788 TATAGTTTGA
1252798 TATTCGAAT
1 TATTCGAAT
*
1252807 AATTCGAAT
1 TATTCGAAT
*
1252816 TATTCGAGT
1 TATTCGAAT
1252825 TATTCGAAT
1 TATTCGAAT
1252834 T
1 T
1252835 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1253914 original size:30 final size:30
Alignment explanation
Indices: 1253880--1253946 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
1253870 AGTTGTACTA
*
1253880 AAAAAGATTAGTATTTATATT-TTTAAATTT
1 AAAAA-ATTAGTATCTATATTATTTAAATTT
* * *
1253910 AAAAATTTAGTATCTCTATTATTTTAATTT
1 AAAAAATTAGTATCTATATTATTTAAATTT
1253940 AATAAAA
1 AA-AAAA
1253947 AATTATTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 12 0.40
30 15 0.50
31 3 0.10
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (30 bp):
AAAAAATTAGTATCTATATTATTTAAATTT
Found at i:1262356 original size:39 final size:39
Alignment explanation
Indices: 1262262--1262363 Score: 143
Period size: 39 Copynumber: 2.6 Consensus size: 39
1262252 TCGAAATCCC
* * *
1262262 TATTATAATTATTGTAATTATAA-TTTACGATCGAATAT
1 TATTATAATTATTGTAATTATAATTTTACAATCAAACAT
* *
1262300 TATTATAATTATTGTAATTGTAATTTTTCAATCAAACAT
1 TATTATAATTATTGTAATTATAATTTTACAATCAAACAT
*
1262339 TATTATAATTATGGTAATTATAATT
1 TATTATAATTATTGTAATTATAATT
1262364 ATTATATTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
38 22 0.39
39 34 0.61
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (39 bp):
TATTATAATTATTGTAATTATAATTTTACAATCAAACAT
Found at i:1270289 original size:19 final size:19
Alignment explanation
Indices: 1270265--1270302 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1270255 ACCGAGAAAG
1270265 AATTACTGGCTGTAGTCTT
1 AATTACTGGCTGTAGTCTT
*
1270284 AATTACTTGCTGTAGTCTT
1 AATTACTGGCTGTAGTCTT
1270303 TGCTTTCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (19 bp):
AATTACTGGCTGTAGTCTT
Found at i:1275409 original size:8 final size:8
Alignment explanation
Indices: 1275396--1275444 Score: 71
Period size: 8 Copynumber: 6.0 Consensus size: 8
1275386 TTATTTATAT
1275396 ATATAATA
1 ATATAATA
1275404 ATATAATA
1 ATATAATA
*
1275412 TTATAATA
1 ATATAATA
*
1275420 TTATAATA
1 ATATAATA
1275428 ATATAATTA
1 ATATAA-TA
1275437 ATATAATA
1 ATATAATA
1275445 CTTATTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
8 30 0.79
9 8 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATAATA
Found at i:1279578 original size:73 final size:73
Alignment explanation
Indices: 1279459--1279677 Score: 438
Period size: 73 Copynumber: 3.0 Consensus size: 73
1279449 TCTATGCTCG
1279459 GAATGCGTATGGCTGAAAATCTAGATAGTTACCAAGGGTTACCGTTAGCCGTTAGTAGAAAAAAG
1 GAATGCGTATGGCTGAAAATCTAGATAGTTACCAAGGGTTACCGTTAGCCGTTAGTAGAAAAAAG
1279524 TCATTAGC
66 TCATTAGC
1279532 GAATGCGTATGGCTGAAAATCTAGATAGTTACCAAGGGTTACCGTTAGCCGTTAGTAGAAAAAAG
1 GAATGCGTATGGCTGAAAATCTAGATAGTTACCAAGGGTTACCGTTAGCCGTTAGTAGAAAAAAG
1279597 TCATTAGC
66 TCATTAGC
1279605 GAATGCGTATGGCTGAAAATCTAGATAGTTACCAAGGGTTACCGTTAGCCGTTAGTAGAAAAAAG
1 GAATGCGTATGGCTGAAAATCTAGATAGTTACCAAGGGTTACCGTTAGCCGTTAGTAGAAAAAAG
1279670 TCATTAGC
66 TCATTAGC
1279678 TTTTACTAAC
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 146 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (73 bp):
GAATGCGTATGGCTGAAAATCTAGATAGTTACCAAGGGTTACCGTTAGCCGTTAGTAGAAAAAAG
TCATTAGC
Found at i:1283149 original size:21 final size:21
Alignment explanation
Indices: 1283125--1283178 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1283115 GTTGTTGAGA
*
1283125 AGGAAGTTGCTGCTGTAGAAG
1 AGGAAGTTGCTGCTGAAGAAG
1283146 AGGAAGTT-CTTGCTGAAGAAG
1 AGGAAGTTGC-TGCTGAAGAAG
*
1283167 AAGAAGTTGCTG
1 AGGAAGTTGCTG
1283179 AAAATGAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.35, T:0.24
Consensus pattern (21 bp):
AGGAAGTTGCTGCTGAAGAAG
Found at i:1283649 original size:17 final size:17
Alignment explanation
Indices: 1283627--1283674 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
1283617 GATAAATATA
1283627 TATTGTCATTGCATTTT
1 TATTGTCATTGCATTTT
*
1283644 TATTGTCATTACATTTT
1 TATTGTCATTGCATTTT
* *
1283661 CA-TGTCAGTGCATT
1 TATTGTCATTGCATT
1283675 GGGGACAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.21, C:0.15, G:0.12, T:0.52
Consensus pattern (17 bp):
TATTGTCATTGCATTTT
Found at i:1314341 original size:36 final size:36
Alignment explanation
Indices: 1314301--1314383 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 36
1314291 ATCAGTTATC
1314301 CGACTAGTGCTGAGCACAATAATTTGTCGATTCGTT
1 CGACTAGTGCTGAGCACAATAATTTGTCGATTCGTT
* * * *
1314337 CGACTAGTGTTGGGCGCAATAATTTGTTGATTCGTT
1 CGACTAGTGCTGAGCACAATAATTTGTCGATTCGTT
*
1314373 CGACTTGTGCT
1 CGACTAGTGCT
1314384 AGGCACACCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (36 bp):
CGACTAGTGCTGAGCACAATAATTTGTCGATTCGTT
Found at i:1314919 original size:19 final size:19
Alignment explanation
Indices: 1314895--1314932 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1314885 AATGAAGAAA
1314895 GCTTATTCATTGAGCCTCT
1 GCTTATTCATTGAGCCTCT
1314914 GCTTATTCATTGAGCCTCT
1 GCTTATTCATTGAGCCTCT
1314933 TAGGTTGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (19 bp):
GCTTATTCATTGAGCCTCT
Found at i:1319031 original size:25 final size:25
Alignment explanation
Indices: 1318994--1319046 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1318984 GAACTATGGC
1318994 ATGCATAGGGACTTAGTCATTTTGA
1 ATGCATAGGGACTTAGTCATTTTGA
*
1319019 ATGCATAGTGACTTAGTCATTTTGA
1 ATGCATAGGGACTTAGTCATTTTGA
1319044 ATG
1 ATG
1319047 TATGTCCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (25 bp):
ATGCATAGGGACTTAGTCATTTTGA
Found at i:1322062 original size:178 final size:178
Alignment explanation
Indices: 1321763--1322118 Score: 712
Period size: 178 Copynumber: 2.0 Consensus size: 178
1321753 TGAAAATAAA
1321763 TATGCTACGAAAAGGATTAAAAGACCTACAATGTTGATTTGAAAAGCTGGGATTACTAATATTCT
1 TATGCTACGAAAAGGATTAAAAGACCTACAATGTTGATTTGAAAAGCTGGGATTACTAATATTCT
1321828 ACCCTTATTAACCAATAATGTCTCGGCAAGATCAATCTTATTCTACTACTCGAAATAATTCTATT
66 ACCCTTATTAACCAATAATGTCTCGGCAAGATCAATCTTATTCTACTACTCGAAATAATTCTATT
1321893 GTGGTCTGTTTCTTTCGAAAGCTAAACCTTGAGTTACCACACCTAGGG
131 GTGGTCTGTTTCTTTCGAAAGCTAAACCTTGAGTTACCACACCTAGGG
1321941 TATGCTACGAAAAGGATTAAAAGACCTACAATGTTGATTTGAAAAGCTGGGATTACTAATATTCT
1 TATGCTACGAAAAGGATTAAAAGACCTACAATGTTGATTTGAAAAGCTGGGATTACTAATATTCT
1322006 ACCCTTATTAACCAATAATGTCTCGGCAAGATCAATCTTATTCTACTACTCGAAATAATTCTATT
66 ACCCTTATTAACCAATAATGTCTCGGCAAGATCAATCTTATTCTACTACTCGAAATAATTCTATT
1322071 GTGGTCTGTTTCTTTCGAAAGCTAAACCTTGAGTTACCACACCTAGGG
131 GTGGTCTGTTTCTTTCGAAAGCTAAACCTTGAGTTACCACACCTAGGG
1322119 CACTATATGT
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
178 178 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (178 bp):
TATGCTACGAAAAGGATTAAAAGACCTACAATGTTGATTTGAAAAGCTGGGATTACTAATATTCT
ACCCTTATTAACCAATAATGTCTCGGCAAGATCAATCTTATTCTACTACTCGAAATAATTCTATT
GTGGTCTGTTTCTTTCGAAAGCTAAACCTTGAGTTACCACACCTAGGG
Found at i:1330928 original size:27 final size:27
Alignment explanation
Indices: 1330881--1330934 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1330871 GTGATTAAAT
1330881 AAAATCGACACAAGCAGAATTTAAAAGA
1 AAAATCGACACAAGCAGAA-TTAAAAGA
*
1330909 AAAATTGACAGCAAG-A-AATTAAAAGA
1 AAAATCGACA-CAAGCAGAATTAAAAGA
1330935 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 8 0.33
27 2 0.08
28 10 0.42
29 4 0.17
ACGTcount: A:0.59, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACACAAGCAGAATTAAAAGA
Found at i:1332838 original size:18 final size:20
Alignment explanation
Indices: 1332794--1332841 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1332784 CCACTCTCAA
1332794 TCTCTTTTTTCTCTTTTTCAT
1 TCTC-TTTTTCTCTTTTTCAT
*
1332815 TCTCTTTTTCT-TTTTTGAT
1 TCTCTTTTTCTCTTTTTCAT
1332834 T-TCTTTTT
1 TCTCTTTTT
1332842 GTGTCTTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.27
19 8 0.31
20 7 0.27
21 4 0.15
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (20 bp):
TCTCTTTTTCTCTTTTTCAT
Found at i:1334645 original size:85 final size:85
Alignment explanation
Indices: 1334502--1334670 Score: 293
Period size: 85 Copynumber: 2.0 Consensus size: 85
1334492 TCATCCAAGG
* * * *
1334502 CCTTTAATGGGCCTCTTTGGGCTGAATTTTTTCATATAAATTTATTTATAAAGTCTAAAAATTAA
1 CCTTTAATGGGCCTCTTTGGACTAAATTTTTACATAGAAATTTATTTATAAAGTCTAAAAATTAA
1334567 AACTAAGTATTTAAAGAATA
66 AACTAAGTATTTAAAGAATA
*
1334587 CCTTTATTGGGCCTCTTTGGACTAAATTTTTACATAGAAATTTATTTATAAAGTCTAAAAATTAA
1 CCTTTAATGGGCCTCTTTGGACTAAATTTTTACATAGAAATTTATTTATAAAGTCTAAAAATTAA
1334652 AACTAAGTATTTAAAGAAT
66 AACTAAGTATTTAAAGAAT
1334671 TAAAATTTTA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (85 bp):
CCTTTAATGGGCCTCTTTGGACTAAATTTTTACATAGAAATTTATTTATAAAGTCTAAAAATTAA
AACTAAGTATTTAAAGAATA
Found at i:1336298 original size:21 final size:23
Alignment explanation
Indices: 1336255--1336307 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1336245 TATTTAAAAT
*
1336255 TAATTAATTAAATTACTTGTTTAA
1 TAATAAATTAAATTA-TTGTTTAA
1336279 TAATAAATTAAATT-TT-TTTAA
1 TAATAAATTAAATTATTGTTTAA
*
1336300 TAGTAAAT
1 TAATAAAT
1336308 ATTATTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 2 0.07
24 13 0.48
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TAATAAATTAAATTATTGTTTAA
Found at i:1345053 original size:32 final size:32
Alignment explanation
Indices: 1345017--1345103 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 32
1345007 AACTTTTCCG
*
1345017 GAAAATATTTTCAGGAAATC-TGCCAAACAACA
1 GAAAATATTTTCAGCAAATCAT-CCAAACAACA
*
1345049 GAAAATATTTTACA-CAGATTCATCCAAACAACA
1 GAAAATATTTT-CAGCA-AATCATCCAAACAACA
*
1345082 GAAAATATTTTCAGTAAATCAT
1 GAAAATATTTTCAGCAAATCAT
1345104 TTTCCAGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
32 19 0.40
33 27 0.57
34 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.26
Consensus pattern (32 bp):
GAAAATATTTTCAGCAAATCATCCAAACAACA
Found at i:1345119 original size:20 final size:20
Alignment explanation
Indices: 1345094--1345133 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1345084 AAATATTTTC
1345094 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
1345114 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
1345134 TCATTTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:1346898 original size:31 final size:29
Alignment explanation
Indices: 1346834--1346898 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1346824 ATGATAACGT
** *
1346834 AAGTGACTAAAATGTAACATTTCAAACAT
1 AAGTGACTAAAATGTAACATGGCAAACAA
1346863 AAGTGACTAAAATGTAACATGAGGCAAACAA
1 AAGTGACTAAAATGTAACAT--GGCAAACAA
1346894 AAGTG
1 AAGTG
1346899 GCTATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 20 0.65
31 11 0.35
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATGGCAAACAA
Found at i:1351954 original size:20 final size:20
Alignment explanation
Indices: 1351909--1351954 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1351899 TAGGTGCAGT
*
1351909 GGTTTGCACACAGGCGTGTG
1 GGTTTTCACACAGGCGTGTG
** *
1351929 TCTTTTCACACGGGCGTGTG
1 GGTTTTCACACAGGCGTGTG
1351949 GGTTTT
1 GGTTTT
1351955 GGGGGGGTTT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.35, T:0.35
Consensus pattern (20 bp):
GGTTTTCACACAGGCGTGTG
Found at i:1355847 original size:17 final size:17
Alignment explanation
Indices: 1355825--1355859 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1355815 CTCTAATGTG
1355825 CTTCAATAGAGAGCTAT
1 CTTCAATAGAGAGCTAT
1355842 CTTCAATAGAGAGCTAT
1 CTTCAATAGAGAGCTAT
1355859 C
1 C
1355860 AATTTGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (17 bp):
CTTCAATAGAGAGCTAT
Found at i:1363979 original size:14 final size:15
Alignment explanation
Indices: 1363951--1363980 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1363941 GCAAATGAAC
1363951 AAAAAGAAAAGATAG
1 AAAAAGAAAAGATAG
1363966 AAAAAGAAAA-ATAG
1 AAAAAGAAAAGATAG
1363980 A
1 A
1363981 GTGAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
AAAAAGAAAAGATAG
Found at i:1373487 original size:25 final size:25
Alignment explanation
Indices: 1373442--1373517 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 25
1373432 CCCATAACTA
*
1373442 GTGAGAGCATACCGATCTATAGCTC
1 GTGAGAGCATACCAATCTATAGCTC
*
1373467 GTGTA-AGCATACCAATTTATAGCTC
1 GTG-AGAGCATACCAATCTATAGCTC
** *
1373492 GTGAGAGCATACTGATCTACAGCTC
1 GTGAGAGCATACCAATCTATAGCTC
1373517 G
1 G
1373518 AGTGAGAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
24 1 0.02
25 41 0.95
26 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (25 bp):
GTGAGAGCATACCAATCTATAGCTC
Found at i:1373528 original size:25 final size:25
Alignment explanation
Indices: 1373500--1373567 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 25
1373490 TCGTGAGAGC
1373500 ATACTGA-TCTACAGCTCGAGTGAGA
1 ATACTGATTC-ACAGCTCGAGTGAGA
* * *
1373525 ATACCGATTCACAGCTTGAGTGAGC
1 ATACTGATTCACAGCTCGAGTGAGA
1373550 ATACTGATTCACAGCTCG
1 ATACTGATTCACAGCTCG
1373568 TATAAGCATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 35 0.95
26 2 0.05
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (25 bp):
ATACTGATTCACAGCTCGAGTGAGA
Found at i:1373529 original size:50 final size:50
Alignment explanation
Indices: 1373442--1373567 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 50
1373432 CCCATAACTA
* * * * * *
1373442 GTGAGAGCATACCGATCTATAGCTCGTGTAAGCATACCAATTTATAGCTC
1 GTGAGAGCATACTGATCTACAGCTCGAGTAAGAATACCAATTCACAGCTC
* * *
1373492 GTGAGAGCATACTGATCTACAGCTCGAGTGAGAATACCGATTCACAGCTT
1 GTGAGAGCATACTGATCTACAGCTCGAGTAAGAATACCAATTCACAGCTC
* *
1373542 GAGTGAGCATACTGAT-TCACAGCTCG
1 GTGAGAGCATACTGATCT-ACAGCTCG
1373568 TATAAGCATA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 1 0.02
50 63 0.98
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.25
Consensus pattern (50 bp):
GTGAGAGCATACTGATCTACAGCTCGAGTAAGAATACCAATTCACAGCTC
Found at i:1373575 original size:25 final size:25
Alignment explanation
Indices: 1373446--1373578 Score: 87
Period size: 25 Copynumber: 5.3 Consensus size: 25
1373436 TAACTAGTGA
* *
1373446 GAGCATACCGA-TCTATAGCTCGTGT
1 GAGCATACCGATTC-ACAGCTCGTAT
* * * *
1373471 AAGCATACCAATTTATAGCTCGTGA-
1 GAGCATACCGATTCACAGCTCGT-AT
*
1373496 GAGCATACTGA-TCTACAGCTCG-AGT
1 GAGCATACCGATTC-ACAGCTCGTA-T
* *
1373521 GAGAATACCGATTCACAGCTTG-AGT
1 GAGCATACCGATTCACAGCTCGTA-T
*
1373546 GAGCATACTGATTCACAGCTCGTAT
1 GAGCATACCGATTCACAGCTCGTAT
*
1373571 AAGCATAC
1 GAGCATAC
1373579 ATGTACATCA
Statistics
Matches: 85, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
23 1 0.01
24 1 0.01
25 79 0.93
26 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (25 bp):
GAGCATACCGATTCACAGCTCGTAT
Found at i:1377314 original size:179 final size:179
Alignment explanation
Indices: 1376968--1377324 Score: 457
Period size: 179 Copynumber: 2.0 Consensus size: 179
1376958 GTAGAATTTT
* ** * *
1376968 CTTCTAATTCAAATGCAGTCTGATTGAGCTTTTGTTGAGCTAGCAAGGGATCAATCGGACATATA
1 CTTCTAATTCAAATGCAGTCCGATCAAGCTTTTGTTGACCTAGCAAGGGACCAATCGGACATATA
** * * *
1377033 CAATTAGACTCGAATAATTTTAATTATGTTCAGAAGTATCGTTTCGATAATTCGCAATTTACTTA
66 CAATTAGACTCGAATAATTGCAATTATGTTCAGAAGCATCGTTCCAATAATTCGCAATTTACTTA
* * * * ** *
1377098 ATTATGGAGTTAGTCCATAAGAAGTATTATGATTGAAAACTATTTATTA
131 ATCATGGAGTCAGTCCACAAGAAATACCATAATTGAAAACTATTTATTA
*
1377147 CTTCTAATTCAAATGCAGTCCGATCAAGCTTTTGTTGACCTAGCAAAGGGACCAATTGGACATAT
1 CTTCTAATTCAAATGCAGTCCGATCAAGCTTTTGTTGACCTAGC-AAGGGACCAATCGGACATAT
* * * *
1377212 ACAATTAGGCTCTAGTAATTGCAATTATGTTCAGAAGCATCGTTCCAATAATTCGCAA-TTATTT
65 ACAATTAGACTCGAATAATTGCAATTATGTTCAGAAGCATCGTTCCAATAATTCGCAATTTACTT
* * *
1377276 GATCATGTTA-TCAGTCCACAAGAAATACCATAATTGAAAACTCTTTATT
130 AATCATG-GAGTCAGTCCACAAGAAATACCATAATTGAAAACTATTTATT
1377325 GTATACTCTT
Statistics
Matches: 151, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
179 82 0.54
180 69 0.46
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (179 bp):
CTTCTAATTCAAATGCAGTCCGATCAAGCTTTTGTTGACCTAGCAAGGGACCAATCGGACATATA
CAATTAGACTCGAATAATTGCAATTATGTTCAGAAGCATCGTTCCAATAATTCGCAATTTACTTA
ATCATGGAGTCAGTCCACAAGAAATACCATAATTGAAAACTATTTATTA
Found at i:1381407 original size:21 final size:21
Alignment explanation
Indices: 1381381--1381423 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1381371 AATAACCATA
1381381 ACATATCACATAGCTTACATG
1 ACATATCACATAGCTTACATG
1381402 ACATATCACATAGCTTACATG
1 ACATATCACATAGCTTACATG
1381423 A
1 A
1381424 TGCTGAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (21 bp):
ACATATCACATAGCTTACATG
Found at i:1382785 original size:18 final size:18
Alignment explanation
Indices: 1382738--1382785 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1382728 ATTTTTTGAA
*
1382738 TTTTAAAGAGTTTTTATTT
1 TTTTAAA-ATTTTTTATTT
*
1382757 TTTTCATAATTTTTTATTT
1 TTTT-AAAATTTTTTATTT
1382776 TTTTAAAATT
1 TTTTAAAATT
1382786 ATAAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 5 0.20
19 18 0.72
20 2 0.08
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTTAAAATTTTTTATTT
Found at i:1382796 original size:20 final size:20
Alignment explanation
Indices: 1382773--1382810 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1382763 TAATTTTTTA
1382773 TTTT-TTTAAAATTATAAATT
1 TTTTATTTAAAA-TATAAATT
1382793 TTTTATTTAAAATATAAA
1 TTTTATTTAAAATATAAA
1382811 AAATGTACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTATTTAAAATATAAATT
Found at i:1387945 original size:15 final size:15
Alignment explanation
Indices: 1387925--1387961 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1387915 TGTTTGTGTT
1387925 AAATTATAGGATAAA
1 AAATTATAGGATAAA
*
1387940 AAATTATAGGTTAAA
1 AAATTATAGGATAAA
*
1387955 ATATTAT
1 AAATTAT
1387962 GTTTCTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (15 bp):
AAATTATAGGATAAA
Found at i:1390840 original size:15 final size:16
Alignment explanation
Indices: 1390805--1390839 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1390795 GAAGTAACTT
*
1390805 AAAATGAAAATTTTAA
1 AAAATGAAAATTATAA
*
1390821 AAAATGAATATTATAA
1 AAAATGAAAATTATAA
1390837 AAA
1 AAA
1390840 TATTGGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAATGAAAATTATAA
Found at i:1401951 original size:285 final size:285
Alignment explanation
Indices: 1401435--1401985 Score: 1048
Period size: 285 Copynumber: 1.9 Consensus size: 285
1401425 TGCGTAGCTA
* *
1401435 AAGCCCGATTACCTTTTGAGGGGTTAGCAGCTTCATTCACACAGTTCGCATTCACTTTACGATGA
1 AAGCCCGATTACCTTTTGAAGGGTTAGCAGCTTCATTCACACAGTTCGCATTCACTTTACGAAGA
1401500 GGCATTCTTGCTCAGTCTAAATGTACATGAGATACTGACATAGTTAAGACTTCAAACACACGTAA
66 GGCATTCTTGCTCAGTCTAAATGTACATGAGATACTGACATAGTTAAGACTTCAAACACACGTAA
1401565 CTGGGTATCCATAATTTAACAGATAGACTTGTGAACACAATTTGCCTAACACAACTTACACGTGA
131 CTGGGTATCCATAATTTAACAGATAGACTTGTGAACACAATTTGCCTAACACAACTTACACGTGA
*
1401630 ACACATTTCGCATAACTTACTTATTGGATCAAAAAGTAGTAGAGGGATGATCTGAGGCATAATCC
196 ACACATTTCGCACAACTTACTTATTGGATCAAAAAGTAGTAGAGGGATGATCTGAGGCATAATCC
1401695 TGCAAACACACGTAATCTGAGGCAT
261 TGCAAACACACGTAATCTGAGGCAT
1401720 AAGCCCGATTACCTTTTGAAGGGTTAGCAGCTTCATTCACACAGTTCGCATTCACTTTACGAAGA
1 AAGCCCGATTACCTTTTGAAGGGTTAGCAGCTTCATTCACACAGTTCGCATTCACTTTACGAAGA
* *
1401785 GGCATTCTTGCTCAGTCTAAATGTACATGAGATACTGACTTAGTTAAGACTTCAAACACATGTAA
66 GGCATTCTTGCTCAGTCTAAATGTACATGAGATACTGACATAGTTAAGACTTCAAACACACGTAA
1401850 CTGGGTATCCATAATTTAACAGATAGACTTGTGAACACAATTTGCCTAACACAACTTACACGTGA
131 CTGGGTATCCATAATTTAACAGATAGACTTGTGAACACAATTTGCCTAACACAACTTACACGTGA
*
1401915 ACACATTTCGCACAACTTACTTATTGGATTAAAAAGTAGTAGAGGGATGATCTGAGGCATAATCC
196 ACACATTTCGCACAACTTACTTATTGGATCAAAAAGTAGTAGAGGGATGATCTGAGGCATAATCC
1401980 TGCAAA
261 TGCAAA
1401986 AGATATGGTT
Statistics
Matches: 260, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
285 260 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (285 bp):
AAGCCCGATTACCTTTTGAAGGGTTAGCAGCTTCATTCACACAGTTCGCATTCACTTTACGAAGA
GGCATTCTTGCTCAGTCTAAATGTACATGAGATACTGACATAGTTAAGACTTCAAACACACGTAA
CTGGGTATCCATAATTTAACAGATAGACTTGTGAACACAATTTGCCTAACACAACTTACACGTGA
ACACATTTCGCACAACTTACTTATTGGATCAAAAAGTAGTAGAGGGATGATCTGAGGCATAATCC
TGCAAACACACGTAATCTGAGGCAT
Found at i:1411746 original size:32 final size:33
Alignment explanation
Indices: 1411705--1411790 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
1411695 AACTTTTTCG
* *
1411705 GAAAATATTTTCAAGAAATCT-GTCAAACAGCA
1 GAAAATATTTTCAAGAAATCTAATCAAACACCA
*
1411737 GAAAATATTTTACACAG--ATTTAATCAAACACCA
1 GAAAATATTTT-CA-AGAAATCTAATCAAACACCA
*
1411770 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTCAAG-AAATC
1411791 ATTTTACAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
31 2 0.05
32 15 0.35
33 22 0.51
34 4 0.09
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (33 bp):
GAAAATATTTTCAAGAAATCTAATCAAACACCA
Found at i:1411808 original size:20 final size:20
Alignment explanation
Indices: 1411783--1411822 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1411773 AATATTTTCC
*
1411783 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
1411803 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
1411823 TTATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:1411837 original size:34 final size:35
Alignment explanation
Indices: 1411771--1411837 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1411761 CAAACACCAG
*
1411771 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
1411806 AAAACATTTTCCAG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1411838 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1412986 original size:16 final size:17
Alignment explanation
Indices: 1412961--1412994 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1412951 TAATTATATT
*
1412961 ATTTTTAACAAAA-TTA
1 ATTTTAAACAAAACTTA
1412977 ATTTTAAACAAAACTTA
1 ATTTTAAACAAAACTTA
1412994 A
1 A
1412995 ATACAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTTAAACAAAACTTA
Found at i:1416096 original size:15 final size:15
Alignment explanation
Indices: 1416073--1416102 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1416063 AAAAAAAAAT
*
1416073 TGATGGGGGAGAAAG
1 TGATAGGGGAGAAAG
1416088 TGATAGGGGAGAAAG
1 TGATAGGGGAGAAAG
1416103 CCTAACGATG
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:0.37, C:0.00, G:0.50, T:0.13
Consensus pattern (15 bp):
TGATAGGGGAGAAAG
Found at i:1425202 original size:19 final size:18
Alignment explanation
Indices: 1425161--1425204 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1425151 TTGAGATATG
1425161 ATAAAATTACAAAAATAA
1 ATAAAATTACAAAAATAA
*
1425179 CTAAATATTA-AAAAATAAA
1 ATAAA-ATTACAAAAAT-AA
1425198 ATAAAAT
1 ATAAAAT
1425205 AAAATTGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
ATAAAATTACAAAAATAA
Found at i:1435118 original size:20 final size:18
Alignment explanation
Indices: 1435071--1435130 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 18
1435061 TTTTTGAAAT
1435071 TTTTATAAA-TATTTTGAA
1 TTTTA-AAATTATTTTGAA
*
1435089 TTTTAAAATTGTTTTGAA
1 TTTTAAAATTATTTTGAA
*
1435107 TTTATGAAAATTATTTTAAA
1 TTT-T-AAAATTATTTTGAA
1435127 TTTT
1 TTTT
1435131 TTTTCTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.08
18 16 0.44
19 2 0.06
20 15 0.42
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (18 bp):
TTTTAAAATTATTTTGAA
Found at i:1435307 original size:14 final size:15
Alignment explanation
Indices: 1435290--1435322 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1435280 GACTCGAATG
1435290 ATTTGAATAACTC-A
1 ATTTGAATAACTCGA
*
1435304 ATTTGATTAACTCGA
1 ATTTGAATAACTCGA
1435319 ATTT
1 ATTT
1435323 TTTTTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (15 bp):
ATTTGAATAACTCGA
Found at i:1441162 original size:19 final size:19
Alignment explanation
Indices: 1441134--1441172 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1441124 AAATAGTGAG
*
1441134 AATTTATTTT-TAAGTATA
1 AATTTATTTTCTAAGAATA
1441152 AATTCTATTTTCTAAGAATA
1 AATT-TATTTTCTAAGAATA
1441172 A
1 A
1441173 CAATTCTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:1446636 original size:2 final size:2
Alignment explanation
Indices: 1446629--1446655 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1446619 TTTGAGTTCA
1446629 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
1446656 GAATGTCGAG
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:1453080 original size:50 final size:50
Alignment explanation
Indices: 1452911--1453138 Score: 235
Period size: 50 Copynumber: 4.5 Consensus size: 50
1452901 CCGGTTCACA
** * *
1452911 TAGTAGCCTGCACATAGTACTACACATTTGACCATTTTCA-ACCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGCGACC--TATCATTCCGATACACG
* * ** * * * *
1452962 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGC-TATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGCGA-CCTATCAT-TCCGATACACG
* *
1453013 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGATACACG
* * * *
1453063 TAGTAGCCTGCACATAGTACTACACATACGACCTATCCTTTCGATATACG
1 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGATACACG
*
1453113 TAGTAGCCTGTACATAGTACTACACA
1 TAGTAGCCTGCACATAGTACTACACA
1453139 CATGACCTAG
Statistics
Matches: 148, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
50 81 0.55
51 66 0.45
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGATACACG
Found at i:1454533 original size:50 final size:50
Alignment explanation
Indices: 1454474--1454573 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
1454464 TGTTTGGATG
1454474 ACTTCATCCAAATTTATTCTCCATTATTTGGTAAATTTTATTGAATTCAT
1 ACTTCATCCAAATTTATTCTCCATTATTTGGTAAATTTTATTGAATTCAT
1454524 ACTTCATCCAAATTTATTCTCCATTATTTGGTAAATTTTATTGAATTCAT
1 ACTTCATCCAAATTTATTCTCCATTATTTGGTAAATTTTATTGAATTCAT
1454574 TGTTTGAAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48
Consensus pattern (50 bp):
ACTTCATCCAAATTTATTCTCCATTATTTGGTAAATTTTATTGAATTCAT
Found at i:1454561 original size:23 final size:23
Alignment explanation
Indices: 1454483--1454561 Score: 61
Period size: 25 Copynumber: 3.3 Consensus size: 23
1454473 GACTTCATCC
1454483 AAATTTATTCTCCATTATTTGGT
1 AAATTTATTCTCCATTATTTGGT
* * * **
1454506 AAATTTTATTGAATTCA-TACTTCAT
1 AAA-TTTATT--CTCCATTATTTGGT
1454531 CCAAATTTATTCTCCATTATTTGGT
1 --AAATTTATTCTCCATTATTTGGT
1454556 AAATTT
1 AAATTT
1454562 TATTGAATTC
Statistics
Matches: 40, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 9 0.22
24 9 0.22
25 10 0.25
26 9 0.22
27 3 0.08
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.49
Consensus pattern (23 bp):
AAATTTATTCTCCATTATTTGGT
Found at i:1458347 original size:7 final size:7
Alignment explanation
Indices: 1458335--1458359 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1458325 ATTTGATTGA
1458335 TATTTAG
1 TATTTAG
1458342 TATTTAG
1 TATTTAG
1458349 TATTTAG
1 TATTTAG
1458356 TATT
1 TATT
1458360 ATGTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:1459010 original size:18 final size:18
Alignment explanation
Indices: 1458984--1459018 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1458974 AGGTGCGGTT
*
1458984 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
1459002 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
1459019 TCCTTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:1459486 original size:43 final size:45
Alignment explanation
Indices: 1459436--1459521 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 45
1459426 ATATTTTGAA
*
1459436 TATTTTGATATTATTTTATGTAA-AAAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
*
1459479 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGA
1459522 TGTAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 22 0.56
44 12 0.31
45 5 0.13
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
Found at i:1459557 original size:23 final size:23
Alignment explanation
Indices: 1459527--1459826 Score: 249
Period size: 23 Copynumber: 12.6 Consensus size: 23
1459517 TTTGATGTAA
* *
1459527 TAAAAACCTTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
1459550 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
1459573 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
1459596 TAAAAACCCTAGCCTAACCTAATTTAAT
1 TAAAAA--C---CCTAACCTAATTTAAT
* * * *
1459624 TTAAAATCCTAACCTAATTTGTAC
1 TAAAAACCCTAACCTAATTT-AAT
* *
1459648 CAAAAACCCTAATCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
1459671 TAAAAACCCTAGCCTAACCTAATTTAAT
1 TAAAAA--C---CCTAACCTAATTTAAT
*
1459699 TAAAAACCCTAAACC---CTTAACT
1 TAAAAACCCT-AACCTAATTTAA-T
*
1459721 TAAAAACCCTAA--TAATTTGAT
1 TAAAAACCCTAACCTAATTTAAT
1459742 TAAAAACCATAGCCTAACCTAATTTAAT
1 TAAAAA-C----CCTAACCTAATTTAAT
*
1459770 TAAAAA-CCTAACTTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* *
1459792 TAAAAACCTTAAACC---CTTAAT
1 TAAAAACCCT-AACCTAATTTAAT
1459813 TAAAAACCCTAACC
1 TAAAAACCCTAACC
1459827 CTAAGCTAAT
Statistics
Matches: 229, Mismatches: 23, Indels: 53
0.75 0.08 0.17
Matches are distributed among these distances:
20 4 0.02
21 27 0.12
22 36 0.16
23 74 0.32
24 24 0.10
25 2 0.01
26 6 0.03
28 56 0.24
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:1459573 original size:28 final size:27
Alignment explanation
Indices: 1459540--1459852 Score: 152
Period size: 28 Copynumber: 12.8 Consensus size: 27
1459530 AAACCTTAGC
1459540 CTAATTTAATTAAAAACCCTAA-C---
1 CTAATTTAATTAAAAACCCTAACCTAA
1459563 CTAATTTAATTAAAAACCCTAA-C---
1 CTAATTTAATTAAAAACCCTAACCTAA
*
1459586 CTAATTTAATTAAAAACCCTAGCCTAA
1 CTAATTTAATTAAAAACCCTAACCTAA
* *
1459613 CCTAATTTAATTTAAAATCCTAACCTAA
1 -CTAATTTAATTAAAAACCCTAACCTAA
**
1459641 -T--TTGT-ACCAAAAACCCTAA--T--
1 CTAATT-TAATTAAAAACCCTAACCTAA
*
1459661 CTAATTTAATTAAAAACCCTAGCCTAA
1 CTAATTTAATTAAAAACCCTAACCTAA
1459688 CCTAATTTAATTAAAAACCCTAAACC---
1 -CTAATTTAATTAAAAACCCT-AACCTAA
1459714 C----TTAACTTAAAAACCCT-A----A
1 CTAATTTAA-TTAAAAACCCTAACCTAA
* * *
1459733 -TAATTTGATTAAAAACCATAGCCTAA
1 CTAATTTAATTAAAAACCCTAACCTAA
1459759 CCTAATTTAATTAAAAA-CCTAA-CT--
1 -CTAATTTAATTAAAAACCCTAACCTAA
*
1459783 -TAATTTAATTAAAAACCTTAAACC---
1 CTAATTTAATTAAAAACCCT-AACCTAA
1459807 C----TTAATTAAAAACCCTAACCCTAA
1 CTAATTTAATTAAAAACCCTAA-CCTAA
*
1459831 GCTAATTCAATT-AAAACCCTAA
1 -CTAATTTAATTAAAAACCCTAA
1459853 ACCCTTAACT
Statistics
Matches: 227, Mismatches: 21, Indels: 79
0.69 0.06 0.24
Matches are distributed among these distances:
20 3 0.01
21 31 0.14
22 31 0.14
23 59 0.26
24 15 0.07
25 5 0.02
26 4 0.02
27 3 0.01
28 68 0.30
29 8 0.04
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (27 bp):
CTAATTTAATTAAAAACCCTAACCTAA
Found at i:1459672 original size:75 final size:71
Alignment explanation
Indices: 1459539--1459852 Score: 327
Period size: 71 Copynumber: 4.3 Consensus size: 71
1459529 AAAACCTTAG
*
1459539 CCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACC
1 CCTAATTTAATTAAAAACCCTAACCTAATTT--TAAAAAACCCTAA-CTAATTTAATTAAAAACC
1459604 CTAGCCTAA
63 CTAGCCTAA
* *
1459613 CCTAATTTAATTTAAAATCCTAACCTAATTTGTACCAAAAACCCTAATCTAATTTAATTAAAAAC
1 CCTAATTTAATTAAAAACCCTAACCTAATTT-TA--AAAAACCCTAA-CTAATTTAATTAAAAAC
1459678 CCTAGCCTAA
62 CCTAGCCTAA
* *
1459688 CCTAATTTAATTAAAAACCCTAAACCCTTAA-CTT-AAAAACCCTAA-TAATTTGATTAAAAACC
1 CCTAATTTAATTAAAAACCCT-AA-CC-TAATTTTAAAAAACCCTAACTAATTTAATTAAAAACC
*
1459750 ATAGCCTAA
63 CTAGCCTAA
* * * **
1459759 CCTAATTTAATTAAAAA-CCTAACTTAATTTAATTAAAAACCTTAA--ACCCTTAATTAAAAACC
1 CCTAATTTAATTAAAAACCCTAACCTAATTT--TAAAAAACCCTAACTA-ATTTAATTAAAAACC
*
1459821 CTAACCCTAA
63 CT-AGCCTAA
* *
1459831 GCTAATTCAATT-AAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAA
1459853 ACCCTTAACT
Statistics
Matches: 208, Mismatches: 20, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
67 3 0.01
68 2 0.01
69 2 0.01
70 5 0.02
71 68 0.33
72 21 0.10
73 12 0.06
74 29 0.14
75 57 0.27
76 3 0.01
77 3 0.01
78 3 0.01
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.30
Consensus pattern (71 bp):
CCTAATTTAATTAAAAACCCTAACCTAATTTTAAAAAACCCTAACTAATTTAATTAAAAACCCTA
GCCTAA
Found at i:1459826 original size:20 final size:21
Alignment explanation
Indices: 1459787--1459828 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1459777 CTAACTTAAT
*
1459787 TTAATTAAAAACCTTAAACCC
1 TTAATTAAAAACCCTAAACCC
1459808 TTAATTAAAAACCCT-AACCC
1 TTAATTAAAAACCCTAAACCC
1459828 T
1 T
1459829 AAGCTAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (21 bp):
TTAATTAAAAACCCTAAACCC
Found at i:1459830 original size:50 final size:49
Alignment explanation
Indices: 1459776--1459886 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 49
1459766 TAATTAAAAA
* *
1459776 CCTAACTTAATTTAATTAAAAACCTTAAACCCTTAA-TTAAAAACCCTAAC
1 CCTAAC-TAATTCAATT-AAAACCCTAAACCCTTAACTTAAAAACCCTAAC
*
1459826 CCTAAGCTAATTCAATTAAAACCCTAAACCCTTAACTTAATAACCCTAAC
1 CCTAA-CTAATTCAATTAAAACCCTAAACCCTTAACTTAAAAACCCTAAC
*
1459876 CTTAACGTAAT
1 CCTAAC-TAAT
1459887 GTTAGATTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
49 18 0.33
50 35 0.65
51 1 0.02
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.29
Consensus pattern (49 bp):
CCTAACTAATTCAATTAAAACCCTAAACCCTTAACTTAAAAACCCTAAC
Found at i:1459880 original size:20 final size:22
Alignment explanation
Indices: 1459841--1459886 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
1459831 GCTAATTCAA
1459841 TTAA-AACCCTAAACCCTTAAC
1 TTAATAACCCTAAACCCTTAAC
1459862 TTAATAACCCT-AA-CCTTAAC
1 TTAATAACCCTAAACCCTTAAC
*
1459882 GTAAT
1 TTAAT
1459887 GTTAGATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 11 0.48
21 6 0.26
22 6 0.26
ACGTcount: A:0.41, C:0.28, G:0.02, T:0.28
Consensus pattern (22 bp):
TTAATAACCCTAAACCCTTAAC
Found at i:1460088 original size:116 final size:116
Alignment explanation
Indices: 1459884--1460100 Score: 380
Period size: 116 Copynumber: 1.9 Consensus size: 116
1459874 ACCTTAACGT
* * *
1459884 AATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATAA
1 AATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTGTACATAATTTAACAA
1459949 TTTTACTAAACATTAATACAATTTTTTGACTTAATAATTTTACATTCACAC
66 TTTTACTAAACATTAATACAATTTTTTGACTTAATAATTTTACATTCACAC
* *
1460000 AATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAATAATTGTATATAATTTAACAA
1 AATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTGTACATAATTTAACAA
*
1460065 TTTTACTAACCATTAATACAATTTTTTGACTTAATA
66 TTTTACTAAACATTAATACAATTTTTTGACTTAATA
1460101 CAATTTATCA
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 95 1.00
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (116 bp):
AATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTGTACATAATTTAACAA
TTTTACTAAACATTAATACAATTTTTTGACTTAATAATTTTACATTCACAC
Found at i:1460117 original size:17 final size:18
Alignment explanation
Indices: 1460076--1460117 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1460066 TTTACTAACC
* *
1460076 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
1460094 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
1460111 ATTAATA
1 ATTAATA
1460118 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:1463303 original size:126 final size:125
Alignment explanation
Indices: 1463003--1463480 Score: 683
Period size: 126 Copynumber: 3.8 Consensus size: 125
1462993 CCCAAACATG
* * * *
1463003 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAAAAATTCTTCTCAAATACCATCCTGC
** * * * * *
1463068 TAGAAATGATCTTATATTATTTGCTCAGAATCGTCAAAAAAA-AATATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATATTTCTTCCGTGAC
* * * * * *
1463127 CTACTGTAGCAAAAGCGCG-CTGACGAGGCCGCAATTTCACAAATTTTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGCGCGATTTCAAAAATTCTTCTCAAATACCATCCTG
1463191 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCGTGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAA-TATTTCTTCCGTGAC
*
1463253 CTACTGTAGCAAAAGCGGGTCCACGAGGGCGCGATTTCAAAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAAAAATTCTTCTCAAATACCATCCTGC
1463318 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAAATATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAT-AATATTTCTTCCGTGAC
* *
1463379 CTACTGTAGCAAAAGCGCGTCCACGATGGCACGATTTCACAAAA-TCTTCTCAAATACCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCA-AAAATTCTTCTCAAATACCATCCTG
* ** *
1463443 CTAGAAGCGATTTTATATTATTTTATCAAAAACGTCAA
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
1463481 CTCGAAATTA
Statistics
Matches: 321, Mismatches: 27, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
123 1 0.00
124 94 0.29
125 2 0.01
126 217 0.68
127 7 0.02
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCAAAAATTCTTCTCAAATACCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATATTTCTTCCGTGAC
Found at i:1465564 original size:12 final size:15
Alignment explanation
Indices: 1465527--1465566 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1465517 TATATCTCTA
1465527 TATATTGAATTCTTG
1 TATATTGAATTCTTG
1465542 TATATTGAATTCTT-
1 TATATTGAATTCTTG
1465556 T-TA-TGAATTCT
1 TATATTGAATTCT
1465567 GAATATCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 8 0.32
13 2 0.08
14 1 0.04
15 14 0.56
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (15 bp):
TATATTGAATTCTTG
Found at i:1465655 original size:13 final size:13
Alignment explanation
Indices: 1465634--1465798 Score: 84
Period size: 13 Copynumber: 12.5 Consensus size: 13
1465624 GTTAACACTT
1465634 TGAAATGGTTATA
1 TGAAATGGTTATA
* *
1465647 TGAATTGGTTATG
1 TGAAATGGTTATA
* *
1465660 TGAAATGATCATA
1 TGAAATGGTTATA
* *
1465673 AGAATTGGTTATA
1 TGAAATGGTTATA
* *
1465686 TAGAAATAGATATA
1 T-GAAATGGTTATA
* *
1465700 CGAAATGATTATA
1 TGAAATGGTTATA
*
1465713 TG-AATCAGTTATA
1 TGAAAT-GGTTATA
* * * *
1465726 CGGAAATAGATAAA
1 -TGAAATGGTTATA
**
1465740 TGAAATAATTATA
1 TGAAATGGTTATA
1465753 TG-AATCGGTTATA
1 TGAAAT-GGTTATA
**
1465766 TGGAAATAATTATA
1 T-GAAATGGTTATA
*
1465780 TGAAGT-GTTATA
1 TGAAATGGTTATA
1465792 TGAAATG
1 TGAAATG
1465799 TTTAATGGAT
Statistics
Matches: 109, Mismatches: 35, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
12 16 0.15
13 65 0.60
14 22 0.20
15 6 0.06
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (13 bp):
TGAAATGGTTATA
Found at i:1465724 original size:40 final size:40
Alignment explanation
Indices: 1465660--1465795 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 40
1465650 ATTGGTTATG
* * * *
1465660 TGAAATGATCATAAGAATTGGTTATATAGAAATAGATATA
1 TGAAATGATTATATGAATCGGTTATATGGAAATAGATATA
* * * *
1465700 CGAAATGATTATATGAATCAGTTATACGGAAATAGATAAA
1 TGAAATGATTATATGAATCGGTTATATGGAAATAGATATA
*
1465740 TGAAATAATTATATGAATCGGTTATATGGAAATA-ATTATA
1 TGAAATGATTATATGAATCGGTTATATGGAAATAGA-TATA
*
1465780 TGAAGTG-TTATATGAA
1 TGAAATGATTATATGAA
1465796 ATGTTTAATG
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
39 10 0.12
40 70 0.88
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.33
Consensus pattern (40 bp):
TGAAATGATTATATGAATCGGTTATATGGAAATAGATATA
Found at i:1469432 original size:23 final size:22
Alignment explanation
Indices: 1469389--1469432 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
1469379 TTTCAAGTCA
1469389 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
1469412 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
1469433 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:1469548 original size:23 final size:23
Alignment explanation
Indices: 1469522--1469639 Score: 182
Period size: 23 Copynumber: 5.1 Consensus size: 23
1469512 AATTAGCACT
1469522 TGAAATGTAGCCGAAGCTACCAC
1 TGAAATGTAGCCGAAGCTACCAC
*
1469545 TGAAATGTAGTCGAAGCTACCAC
1 TGAAATGTAGCCGAAGCTACCAC
* * *
1469568 TGATATGTACCCGAAGCTACCAT
1 TGAAATGTAGCCGAAGCTACCAC
*
1469591 TGAAATGTAGCCGAAGCTACCAT
1 TGAAATGTAGCCGAAGCTACCAC
*
1469614 TGATATGTAGCCGAAGCTACCAC
1 TGAAATGTAGCCGAAGCTACCAC
1469637 TGA
1 TGA
1469640 TCAATAACAC
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 86 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (23 bp):
TGAAATGTAGCCGAAGCTACCAC
Found at i:1476764 original size:19 final size:19
Alignment explanation
Indices: 1476742--1476792 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1476732 TTTTCCCGAT
1476742 TTTCCTTTCTTCTTCTTAA
1 TTTCCTTTCTTCTTCTTAA
*
1476761 TTTCCTTGTCTTCTT-TTTA
1 TTTCCTT-TCTTCTTCTTAA
1476780 TTT--TTTCTTCTTC
1 TTTCCTTTCTTCTTC
1476793 CTCCGGATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 7 0.24
17 2 0.07
19 13 0.45
20 7 0.24
ACGTcount: A:0.06, C:0.24, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTCCTTTCTTCTTCTTAA
Found at i:1479696 original size:50 final size:49
Alignment explanation
Indices: 1479641--1479936 Score: 342
Period size: 50 Copynumber: 6.0 Consensus size: 49
1479631 CATTGAGATT
1479641 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-TGAG
* *
1479691 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-TGAG
* * * * *
1479741 ATGAGAGGTCTCATGTAAGACCAAGTTTGGGACATGGCGTTGGCATCATG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATGA-G
** * *
1479791 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCATCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT-GAG
** * * *
1479841 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA-GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATG-AG
* * ** * *
1479890 AGGAAACATCTCATGTAAGACCATGTCTGGGACATGGCTTTGGCATG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATG
1479937 TTATTATCAG
Statistics
Matches: 210, Mismatches: 32, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
48 1 0.00
49 39 0.19
50 169 0.80
51 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (49 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATGAG
Found at i:1479784 original size:100 final size:98
Alignment explanation
Indices: 1479538--1479934 Score: 361
Period size: 100 Copynumber: 3.9 Consensus size: 98
1479528 NNNNNNNNNN
* * ** * *
1479538 AGAGGTCCCATGTAAGACCATGTCTGGGACATGTGGCATCGATATCGAT-ATGTGAG--CCAGTG
1 AGAGGTCCCATGTAAGACCAAGTCTGGGACA--TGGCATTGGCATAGATGA-GAG-GTCCCA-TG
* *
1479600 TAAGACCATGTCTGGGACATGGCATTAGCATCATTGAGATTATG
61 TAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
*
1479644 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCCATGTAA
1 AGAGGTCCCATGTAAGACCAAGTCTGGGACATGGCATTGGCA-T-AGATGAGAGGTCCCATGTAA
*
1479709 GACCATGTCTGGGACATGGCGTTGGCACCGAGATG
64 GACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * **
1479744 AGAGGTCTCATGTAAGACCAAGTTTGGGACATGGCGTTGGCATCATGATGAGAGGTCCCCCGTAA
1 AGAGGTCCCATGTAAGACCAAGTCTGGGACATGGCATTGGCAT-A-GATGAGAGGTCCCATGTAA
* * *
1479809 GACCATGTCTGGGACATGGCATGGGCATCGATATG
64 GACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * ** *
1479844 AGAACTCCCATGTAAGACCATA-TCTGGGATATGGCATTGGCAGTACAGGAAACATCTCATGTAA
1 AGAGGTCCCATGTAAGACCA-AGTCTGGGACATGGCATTGGCA-TAGATGAGAGGTCCCATGTAA
*
1479908 GACCATGTCTGGGACATGGCTTTGGCA
64 GACCATGTCTGGGACATGGCATTGGCA
1479935 TGTTATTATC
Statistics
Matches: 248, Mismatches: 35, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
99 38 0.15
100 124 0.50
101 2 0.01
103 3 0.01
104 8 0.03
105 3 0.01
106 66 0.27
107 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (98 bp):
AGAGGTCCCATGTAAGACCAAGTCTGGGACATGGCATTGGCATAGATGAGAGGTCCCATGTAAGA
CCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:1479871 original size:150 final size:149
Alignment explanation
Indices: 1479598--1479935 Score: 401
Period size: 150 Copynumber: 2.2 Consensus size: 149
1479588 TGTGAGCCAG
* * * *
1479598 TGTAAGACCATGTCTGGGACATGGCATTAGCATCATTGAGATTATGAGAGGTCCCATGTAAGACC
1 TGTAAGACCAAGTCTGGGACATGGCGTTGGCATCA-T--G---ATGAGAGGTCCCACGTAAGACC
* ** *
1479663 ATGTCTGGGACATGGCATTGGCACTGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGG
60 ATGTCTGGGACATGGCATGGGCACTGAGATGAGAACTCCCATGTAAGACCATATCTGGGACATGG
* * * * **
1479728 CGTTGGCACCG-AGATGAGAGGTCTCA
125 CATTGGCA--GTACAGGAAACATCTCA
* *
1479754 TGTAAGACCAAGTTTGGGACATGGCGTTGGCATCATGATGAGAGGTCCCCCGTAAGACCATGTCT
1 TGTAAGACCAAGTCTGGGACATGGCGTTGGCATCATGATGAGAGGTCCCACGTAAGACCATGTCT
* *
1479819 GGGACATGGCATGGGCA-TCGATATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTG
66 GGGACATGGCATGGGCACT-GAGATGAGAACTCCCATGTAAGACCATATCTGGGACATGGCATTG
1479883 GCAGTACAGGAAACATCTCA
130 GCAGTACAGGAAACATCTCA
* *
1479903 TGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 TGTAAGACCAAGTCTGGGACATGGCGTTGGCAT
1479936 GTTATTATCA
Statistics
Matches: 159, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
148 1 0.01
149 41 0.26
150 84 0.53
153 1 0.01
155 1 0.01
156 31 0.19
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (149 bp):
TGTAAGACCAAGTCTGGGACATGGCGTTGGCATCATGATGAGAGGTCCCACGTAAGACCATGTCT
GGGACATGGCATGGGCACTGAGATGAGAACTCCCATGTAAGACCATATCTGGGACATGGCATTGG
CAGTACAGGAAACATCTCA
Found at i:1485695 original size:27 final size:27
Alignment explanation
Indices: 1485643--1485696 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1485633 AGAATGTTAC
* *
1485643 AATTAAATTAAAAACAAAGAATATTAA
1 AATTAAAATAAAAACAAAGAAAATTAA
*
1485670 AATTAAAATAAAAA-ATAGATAAATTAA
1 AATTAAAATAAAAACAAAGA-AAATTAA
1485697 TACAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.26
Consensus pattern (27 bp):
AATTAAAATAAAAACAAAGAAAATTAA
Found at i:1489769 original size:40 final size:40
Alignment explanation
Indices: 1489721--1489821 Score: 121
Period size: 40 Copynumber: 2.5 Consensus size: 40
1489711 CATCGAGCAG
* *
1489721 TACCTACTGAATCTACTGAAACATATGCACTTTCGAGCCA
1 TACCTACTGAATCTACTGAAACATATGCACTCTCAAGCCA
* * ** * *
1489761 TACTTACTGAATCTACTAAAATGTATGCGCTCTCAAGTCA
1 TACCTACTGAATCTACTGAAACATATGCACTCTCAAGCCA
*
1489801 TACCTACTGAATCTATTGAAA
1 TACCTACTGAATCTACTGAAA
1489822 AGAATGCTCT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.31
Consensus pattern (40 bp):
TACCTACTGAATCTACTGAAACATATGCACTCTCAAGCCA
Found at i:1494260 original size:30 final size:30
Alignment explanation
Indices: 1494212--1494385 Score: 188
Period size: 30 Copynumber: 5.8 Consensus size: 30
1494202 ACGATCCTCA
*
1494212 GCTATCAAAATAATGAAAAGGGATAGCCTTG
1 GCTATC-AAATTATGAAAAGGGATAGCCTTG
* ****
1494243 GCTATCAAATTATGAAAAGGGATGGTGACG
1 GCTATCAAATTATGAAAAGGGATAGCCTTG
* * * * *
1494273 ACCATCGAATAATGAAAAGGGATAGCTTTG
1 GCTATCAAATTATGAAAAGGGATAGCCTTG
**
1494303 GCTATCAAATTATGAAAAGGGATAGTTTTG
1 GCTATCAAATTATGAAAAGGGATAGCCTTG
*
1494333 GCTATCGAATTATGAAAAGGGATAG-CTTCG
1 GCTATCAAATTATGAAAAGGGATAGCCTT-G
*
1494363 GCAATCAAATTATGAAAAGGGAT
1 GCTATCAAATTATGAAAAGGGAT
1494386 GGTGACAACC
Statistics
Matches: 118, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
29 2 0.02
30 110 0.93
31 6 0.05
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (30 bp):
GCTATCAAATTATGAAAAGGGATAGCCTTG
Found at i:1494313 original size:60 final size:60
Alignment explanation
Indices: 1494220--1494414 Score: 275
Period size: 60 Copynumber: 3.3 Consensus size: 60
1494210 CAGCTATCAA
*
1494220 AATAATGAAAAGGGATAGCCTTGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCG
1 AATAATGAAAAGGGATAGCTTTGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCG
* *** * *
1494280 AATAATGAAAAGGGATAGCTTTGGCTATCAAATTATGAAAAGGGATAGTTTTGGCTATCG
1 AATAATGAAAAGGGATAGCTTTGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCG
* * * *
1494340 AATTATGAAAAGGGATAGCTTCGGCAATCAAATTATGAAAAGGGATGGTGACAACCATC-
1 AATAATGAAAAGGGATAGCTTTGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCG
*
1494399 AACAATGAAAAGGGAT
1 AATAATGAAAAGGGAT
1494415 TATGACGACC
Statistics
Matches: 116, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 14 0.12
60 102 0.88
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (60 bp):
AATAATGAAAAGGGATAGCTTTGGCTATCAAATTATGAAAAGGGATGGTGACGACCATCG
Found at i:1494378 original size:90 final size:91
Alignment explanation
Indices: 1494212--1494385 Score: 235
Period size: 90 Copynumber: 1.9 Consensus size: 91
1494202 ACGATCCTCA
* *
1494212 GCTATCAAAATAATGAAAAGGGATAGCCTTGGCTATCAAATTATGAAAAGGGATGGTGACGACCA
1 GCTATCAAAATAATGAAAAGGGATAGCCTTGGCTATCAAATTATGAAAAGGGATGCTGACGACAA
*
1494277 TCGAATAATGAAAAGGGATAGCTTTG
66 TCAAATAATGAAAAGGGATAGCTTTG
* ** * * *
1494303 GCTATC-AAATTATGAAAAGGGATAGTTTTGGCTATCGAATTATGAAAAGGGATAGCT-TCGGCA
1 GCTATCAAAATAATGAAAAGGGATAGCCTTGGCTATCAAATTATGAAAAGGGAT-GCTGACGACA
*
1494366 ATCAAATTATGAAAAGGGAT
65 ATCAAATAATGAAAAGGGAT
1494386 GGTGACAACC
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
90 64 0.89
91 8 0.11
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (91 bp):
GCTATCAAAATAATGAAAAGGGATAGCCTTGGCTATCAAATTATGAAAAGGGATGCTGACGACAA
TCAAATAATGAAAAGGGATAGCTTTG
Found at i:1494400 original size:30 final size:30
Alignment explanation
Indices: 1494246--1494444 Score: 145
Period size: 30 Copynumber: 6.7 Consensus size: 30
1494236 AGCCTTGGCT
1494246 ATCAAATTATGAAAAGGGATGGTGACGACC
1 ATCAAATTATGAAAAGGGATGGTGACGACC
* * * ** * *
1494276 ATCGAATAATGAAAAGGGATAGCT-TTGGCT
1 ATCAAATTATGAAAAGGGAT-GGTGACGACC
* *** * *
1494306 ATCAAATTATGAAAAGGGATAGTTTTGGCT
1 ATCAAATTATGAAAAGGGATGGTGACGACC
* * * * *
1494336 ATCGAATTATGAAAAGGGATAGCT-TCGGCA
1 ATCAAATTATGAAAAGGGAT-GGTGACGACC
*
1494366 ATCAAATTATGAAAAGGGATGGTGACAACC
1 ATCAAATTATGAAAAGGGATGGTGACGACC
**
1494396 ATCAACA--ATGAAAAGGGATTATGACGACC
1 ATCAA-ATTATGAAAAGGGATGGTGACGACC
*
1494425 ATCAAATAATGAAAAGGGAT
1 ATCAAATTATGAAAAGGGAT
1494445 AGCTTCAGCT
Statistics
Matches: 137, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
28 1 0.01
29 27 0.20
30 105 0.77
31 4 0.03
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (30 bp):
ATCAAATTATGAAAAGGGATGGTGACGACC
Found at i:1494420 original size:29 final size:30
Alignment explanation
Indices: 1494374--1494444 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
1494364 CAATCAAATT
*
1494374 ATGAAAAGGGATGGTGACAACCATC-AACA
1 ATGAAAAGGGATGATGACAACCATCAAACA
* * *
1494403 ATGAAAAGGGATTATGACGACCATCAAATA
1 ATGAAAAGGGATGATGACAACCATCAAACA
1494433 ATGAAAAGGGAT
1 ATGAAAAGGGAT
1494445 AGCTTCAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 22 0.59
30 15 0.41
ACGTcount: A:0.46, C:0.13, G:0.24, T:0.17
Consensus pattern (30 bp):
ATGAAAAGGGATGATGACAACCATCAAACA
Found at i:1498771 original size:13 final size:14
Alignment explanation
Indices: 1498739--1498771 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1498729 AAGTGTTGCT
*
1498739 TGCGAGTTGTATAC
1 TGCGAGTAGTATAC
1498753 TGCGAGTAGTATA-
1 TGCGAGTAGTATAC
1498766 TGCGAG
1 TGCGAG
1498772 CTAAGAACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.30
Consensus pattern (14 bp):
TGCGAGTAGTATAC
Found at i:1499126 original size:79 final size:79
Alignment explanation
Indices: 1499040--1499238 Score: 245
Period size: 79 Copynumber: 2.5 Consensus size: 79
1499030 GTGAATTGAT
* * * * * **
1499040 ATGGAGCTACAAACTGGTGAAGTGTGAGCTATGTCCAAGCACTGCATGCGAGTTGTAAATAGAGA
1 ATGGAGCTACAAACTGGTGAAGTGTGAGCTATCTCCAAACACTACATGAGAGCTACAAATAGAGA
1499105 GCTTGCAAACTAAG
66 GCTTGCAAACTAAG
* *
1499119 ATGGAGCTACAAACTGGTGAAGTGTGAGCTGTCTCCAAACGCTACATGAGAGCTACAAATAGAGA
1 ATGGAGCTACAAACTGGTGAAGTGTGAGCTATCTCCAAACACTACATGAGAGCTACAAATAGAGA
**
1499184 GCTTGTGAACTAAG
66 GCTTGCAAACTAAG
* * * * * *
1499198 ATGGAACTACGAATTGGTGAAGTGCGAGTTCTCTCCAAACA
1 ATGGAGCTACAAACTGGTGAAGTGTGAGCTATCTCCAAACA
1499239 TTGTATGCAA
Statistics
Matches: 102, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 102 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.23
Consensus pattern (79 bp):
ATGGAGCTACAAACTGGTGAAGTGTGAGCTATCTCCAAACACTACATGAGAGCTACAAATAGAGA
GCTTGCAAACTAAG
Found at i:1502367 original size:19 final size:19
Alignment explanation
Indices: 1502343--1502380 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1502333 TTCAATTAAG
*
1502343 TCTTTCATT-AAGTGTTTTT
1 TCTTTC-TTCAAGTATTTTT
1502362 TCTTTCTTCAAGTATTTTT
1 TCTTTCTTCAAGTATTTTT
1502381 CATCTAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.16, C:0.13, G:0.08, T:0.63
Consensus pattern (19 bp):
TCTTTCTTCAAGTATTTTT
Found at i:1502417 original size:15 final size:13
Alignment explanation
Indices: 1502386--1502457 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 13
1502376 TTTTTCATCT
* *
1502386 AGTTATTTTATCA
1 AGTTTTTTTACCA
1502399 AGTTTTTAATTACCA
1 AGTTTTT--TTACCA
*
1502414 AGTTTTTTTATCA
1 AGTTTTTTTACCA
* *
1502427 AG-TTTTGTAGCA
1 AGTTTTTTTACCA
1502439 AGTTCTTTTTA--A
1 AGTT-TTTTTACCA
1502451 AGTTTTT
1 AGTTTTT
1502458 CATCAAGCCT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
11 3 0.06
12 15 0.31
13 14 0.29
14 5 0.10
15 12 0.24
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.54
Consensus pattern (13 bp):
AGTTTTTTTACCA
Found at i:1503705 original size:54 final size:54
Alignment explanation
Indices: 1503637--1503743 Score: 178
Period size: 54 Copynumber: 2.0 Consensus size: 54
1503627 CCTGAGACCA
* **
1503637 AACCACTTCCTGAAATAAAAGAAGCAGAAGACAACCTCGGTGAACCAGAAAGGG
1 AACCACTTCCTGAAACAAAAGAAGCAGAAGACAACCTCGACGAACCAGAAAGGG
*
1503691 AACCACTTCCTGAAACAAAAGAAGTAGAAGACAACCTCGACGAACCAGAAAGG
1 AACCACTTCCTGAAACAAAAGAAGCAGAAGACAACCTCGACGAACCAGAAAGG
1503744 ATGGTGAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (54 bp):
AACCACTTCCTGAAACAAAAGAAGCAGAAGACAACCTCGACGAACCAGAAAGGG
Found at i:1506849 original size:6 final size:6
Alignment explanation
Indices: 1506801--1506851 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
1506791 TTAATTTTCC
* *
1506801 TATTAT TATTATT TATTTT TACTATTT TA-TTT TATTTT CATTTT TATTTT
1 TATTTT TATT-TT TATTTT TA-T-TTT TATTTT TATTTT TATTTT TATTTT
1506851 T
1 T
1506852 GCAGGAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 5 0.13
6 22 0.58
7 6 0.16
8 5 0.13
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (6 bp):
TATTTT
Found at i:1530631 original size:138 final size:138
Alignment explanation
Indices: 1530478--1530977 Score: 801
Period size: 138 Copynumber: 3.6 Consensus size: 138
1530468 ACATATATAA
* *
1530478 AATTAATATAAGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATG
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
* *
1530543 TAAACAGTTAAATTAATTAATTTCGGTTAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
66 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
1530608 AAGAATAT
131 AAGAATAT
* * *
1530616 AATTAATATATGAATTTGATTCGTACAAAATATTAACTGTATATATATTACCAAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
* *
1530681 TAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACGTGGAAATT-A-ATT-TTTTGGA
66 TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
1530743 AAGAATAT
131 AAGAATAT
* *
1530751 AATTAATATATGAATTTGATACATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
* *
1530816 TAAACAGTTATATGT-ATTAATTTCGGTCAAAATATAAAAGATATGAAAATTAATATTCTTTTGG
66 TAAACAGTTATAT-TAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGG
*
1530880 AATGAATAT
130 AAAGAATAT
* * * *
1530889 AATTAATATATGAATTTAATTAATACAAAATATTAATAGTATATATTTTACCAAATTTATCAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
1530954 TAAACAGTTATATTAATTAATTTC
66 TAAACAGTTATATTAATTAATTTC
1530978 ACTTCTCTAT
Statistics
Matches: 332, Mismatches: 25, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
135 120 0.36
136 5 0.02
137 5 0.02
138 202 0.61
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (138 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
TAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
AAGAATAT
Found at i:1530901 original size:17 final size:17
Alignment explanation
Indices: 1530881--1530913 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1530871 TTCTTTTGGA
1530881 ATGAATATAATTAATAT
1 ATGAATATAATTAATAT
*
1530898 ATGAATTTAATTAATA
1 ATGAATATAATTAATA
1530914 CAAAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
ATGAATATAATTAATAT
Found at i:1530967 original size:273 final size:273
Alignment explanation
Indices: 1530478--1530977 Score: 833
Period size: 273 Copynumber: 1.8 Consensus size: 273
1530468 ACATATATAA
* *
1530478 AATTAATATAAGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATG
1 AATTAATATAAGAATTTGATACATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
* *
1530543 TAAACAGTTAAATTAATTAATTTCGGTTAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
66 TAAACAGTTAAATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
* **
1530608 AAGAATATAATTAATATATGAATTTGATTCGTACAAAATATTAACTGTATATATATTACCAAATT
131 AAGAATATAATTAATATATGAATTTAATTAATACAAAATATTAACTGTATATATATTACCAAATT
*
1530673 TATTAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACGTGGAAATTAATTTT
196 TATCAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACGTGGAAATTAATTTT
1530738 TTGGAAAGAATAT
261 TTGGAAAGAATAT
* *
1530751 AATTAATATATGAATTTGATACATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
1 AATTAATATAAGAATTTGATACATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
* *
1530816 TAAACAGTTATATGT-ATTAATTTCGGTCAAAATATAAAAGATATGAAAATTAATATTCTTTTGG
66 TAAACAGTTAAAT-TAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGG
* *
1530880 AATGAATATAATTAATATATGAATTTAATTAATACAAAATATTAA-TAGTATATATTTTACCAAA
130 AAAGAATATAATTAATATATGAATTTAATTAATACAAAATATTAACT-GTATATATATTACCAAA
*
1530944 TTTATCAATATAAACAGTTATATTAATTAATTTC
194 TTTATCAATATAAACAATTATATTAATTAATTTC
1530978 ACTTCTCTAT
Statistics
Matches: 210, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
272 1 0.00
273 208 0.99
274 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (273 bp):
AATTAATATAAGAATTTGATACATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATA
TAAACAGTTAAATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
AAGAATATAATTAATATATGAATTTAATTAATACAAAATATTAACTGTATATATATTACCAAATT
TATCAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACGTGGAAATTAATTTT
TTGGAAAGAATAT
Found at i:1533610 original size:34 final size:34
Alignment explanation
Indices: 1533557--1533624 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
1533547 GCACAGTTGA
*
1533557 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATTTCAGTA-CAGTG
* *
1533592 ACAGT-TTGTGCCTTAGCCCATTTCAGTACAGTG
1 ACAGTCTTGGGCCTAAGCCCATTTCAGTACAGTG
1533625 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATTTCAGTACAGTG
Found at i:1536318 original size:22 final size:22
Alignment explanation
Indices: 1536293--1536412 Score: 59
Period size: 22 Copynumber: 5.2 Consensus size: 22
1536283 ATATTAAATT
1536293 TATTATTATATATTTTTGAAAA
1 TATTATTATATATTTTTGAAAA
*
1536315 TA-T-TTATGTATTTTT--AAA
1 TATTATTATATATTTTTGAAAA
* *
1536333 TTTTATATATTATTTTTTTGTCAACAA
1 TATTAT-TA-TATATTTTTG--AA-AA
* * * *
1536360 TAATTTTTTATTTATTTATATTAAATT
1 T-A-TTATTATATATTT-T-TGAAA-A
1536387 TATTATTATATATTTTTGAAAA
1 TATTATTATATATTTTTGAAAA
1536409 TATT
1 TATT
1536413 TATGTATTTT
Statistics
Matches: 70, Mismatches: 14, Indels: 28
0.62 0.12 0.25
Matches are distributed among these distances:
18 4 0.06
19 1 0.01
20 12 0.17
21 3 0.04
22 13 0.19
23 4 0.06
24 1 0.01
25 11 0.16
26 3 0.04
27 11 0.16
28 3 0.04
29 4 0.06
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (22 bp):
TATTATTATATATTTTTGAAAA
Found at i:1536370 original size:49 final size:49
Alignment explanation
Indices: 1536223--1536376 Score: 182
Period size: 49 Copynumber: 3.2 Consensus size: 49
1536213 TTTGAAAATA
1536223 TTTATGTATTTTTAAATTTTATATATTATTTTTTTGTCAACAATAATTT
1 TTTATGTATTTTTAAATTTTATATATTATTTTTTTGTCAACAATAATTT
*
1536272 TTTATTTATTTATATTAAA-TTTAT-TATTATATATTTTTG--AA-AAT-A---
1 TTTATGTA-TT-T-TTAAATTTTATATATTAT-T-TTTTTGTCAACAATAATTT
1536317 TTTATGTATTTTTAAATTTTATATATTATTTTTTTGTCAACAATAATTT
1 TTTATGTATTTTTAAATTTTATATATTATTTTTTTGTCAACAATAATTT
*
1536366 TTTATTTATTT
1 TTTATGTATTT
1536377 ATATTAAATT
Statistics
Matches: 88, Mismatches: 3, Indels: 28
0.74 0.03 0.24
Matches are distributed among these distances:
42 11 0.12
43 7 0.08
44 10 0.11
45 10 0.11
46 1 0.01
48 1 0.01
49 20 0.23
50 10 0.11
51 7 0.08
52 11 0.12
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (49 bp):
TTTATGTATTTTTAAATTTTATATATTATTTTTTTGTCAACAATAATTT
Found at i:1536412 original size:31 final size:31
Alignment explanation
Indices: 1536377--1536438 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
1536367 TTATTTATTT
*
1536377 ATATTAAATTTATTATTATATA-T-TTTTGAAA
1 ATATT-AATGTATT-TTATATATTATTTTGAAA
*
1536408 ATATTTATGTATTTTATATATTATTTTGAAA
1 ATATTAATGTATTTTATATATTATTTTGAAA
1536439 TTTTTAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 7 0.26
30 7 0.26
31 13 0.48
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (31 bp):
ATATTAATGTATTTTATATATTATTTTGAAA
Found at i:1536443 original size:94 final size:94
Alignment explanation
Indices: 1536211--1536422 Score: 424
Period size: 94 Copynumber: 2.3 Consensus size: 94
1536201 AATTTTAATT
1536211 TTTTTGAAAATATTTATGTATTTTTAAATTTTATATATTATTTTTTTGTCAACAATAATTTTTTA
1 TTTTTGAAAATATTTATGTATTTTTAAATTTTATATATTATTTTTTTGTCAACAATAATTTTTTA
1536276 TTTATTTATATTAAATTTATTATTATATA
66 TTTATTTATATTAAATTTATTATTATATA
1536305 TTTTTGAAAATATTTATGTATTTTTAAATTTTATATATTATTTTTTTGTCAACAATAATTTTTTA
1 TTTTTGAAAATATTTATGTATTTTTAAATTTTATATATTATTTTTTTGTCAACAATAATTTTTTA
1536370 TTTATTTATATTAAATTTATTATTATATA
66 TTTATTTATATTAAATTTATTATTATATA
1536399 TTTTTGAAAATATTTATGTATTTT
1 TTTTTGAAAATATTTATGTATTTT
1536423 ATATATTATT
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 118 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (94 bp):
TTTTTGAAAATATTTATGTATTTTTAAATTTTATATATTATTTTTTTGTCAACAATAATTTTTTA
TTTATTTATATTAAATTTATTATTATATA
Found at i:1543363 original size:16 final size:16
Alignment explanation
Indices: 1543338--1543392 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
1543328 TTGGTTCGCT
*
1543338 GTAATGGAATAGAGGC
1 GTAATAGAATAGAGGC
1543354 GTAATAGAATAGAGGC
1 GTAATAGAATAGAGGC
*
1543370 GTAATGGAATAGAGGC
1 GTAATAGAATAGAGGC
1543386 GTAATAG
1 GTAATAG
1543393 CAATTCAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.40, C:0.05, G:0.35, T:0.20
Consensus pattern (16 bp):
GTAATAGAATAGAGGC
Found at i:1543421 original size:45 final size:44
Alignment explanation
Indices: 1543370--1543466 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
1543360 GAATAGAGGC
1543370 GTAATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AATT-AATGTGTTTGGTTGAAT
* * *
1543415 GTAATGGAATAGATGCGTAATAGTATTATTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAATTAATGTGTTTGGTTGAAT
*
1543459 GGAATGGA
1 GTAATGGA
1543467 GGTGTAATAG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 2 0.04
44 23 0.49
45 22 0.47
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAATTAATGTGTTTGGTTGAAT
Found at i:1546815 original size:14 final size:14
Alignment explanation
Indices: 1546790--1546824 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
1546780 AAGAAGAAGC
1546790 AGAAATATGGAGAAA
1 AGAAA-ATGGAGAAA
1546805 AGAAAATGGAGAAA
1 AGAAAATGGAGAAA
1546819 AGAAAA
1 AGAAAA
1546825 GAAATGTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.09
Consensus pattern (14 bp):
AGAAAATGGAGAAA
Found at i:1546822 original size:19 final size:18
Alignment explanation
Indices: 1546800--1546844 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
1546790 AGAAATATGG
1546800 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
1546819 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
1546836 AGAAAAGAA
1 AGAAAAGAA
1546845 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Done.