Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 12 of 172
Found at i:3308365 original size:19 final size:21
Alignment explanation
Indices: 3308319--3308367 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
3308309 TGTATCTTTC
3308319 ATTT-AAATTTTAAGTAAATA
1 ATTTAAAATTTTAAGTAAATA
3308339 ATTATTAAAATTTTAAGT-AAT-
1 A-T-TTAAAATTTTAAGTAAATA
3308360 ATTTAAAA
1 ATTTAAAA
3308368 GTATTTGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 6 0.23
20 2 0.08
21 2 0.08
22 5 0.19
23 11 0.42
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
ATTTAAAATTTTAAGTAAATA
Found at i:3308609 original size:37 final size:37
Alignment explanation
Indices: 3308568--3308673 Score: 101
Period size: 38 Copynumber: 2.8 Consensus size: 37
3308558 TAACCGTTGA
*
3308568 AACCCTAAACCCCA-AATCCATAACCCCTAAAT-CCCCT
1 AACCCTAAA--CCATAACCCATAACCCCTAAATCCCCCT
* *
3308605 AACCCTTAAAGCATAACCCATAACCCTTAAATCCCCCT
1 AACCC-TAAACCATAACCCATAACCCCTAAATCCCCCT
* *
3308643 AACCCCTAAAGCATAACACC-TAACCCTTAAA
1 AA-CCCTAAACCATAAC-CCATAACCCCTAAA
3308674 CCTTAAATCC
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
36 2 0.03
37 21 0.34
38 33 0.54
39 5 0.08
ACGTcount: A:0.40, C:0.41, G:0.02, T:0.18
Consensus pattern (37 bp):
AACCCTAAACCATAACCCATAACCCCTAAATCCCCCT
Found at i:3308630 original size:21 final size:20
Alignment explanation
Indices: 3308601--3308673 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 20
3308591 CCCCTAAATC
3308601 CCCTAACCCTTAAAGCATAA
1 CCCTAACCCTTAAAGCATAA
**
3308621 CCCATAACCCTT-AA--ATCC
1 CCC-TAACCCTTAAAGCATAA
*
3308639 CCCTAACCCCTAAAGCATAA
1 CCCTAACCCTTAAAGCATAA
3308659 CACCTAACCCTTAAA
1 C-CCTAACCCTTAAA
3308674 CCTTAAATCC
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
17 7 0.17
18 7 0.17
20 8 0.19
21 20 0.48
ACGTcount: A:0.38, C:0.40, G:0.03, T:0.19
Consensus pattern (20 bp):
CCCTAACCCTTAAAGCATAA
Found at i:3308653 original size:38 final size:38
Alignment explanation
Indices: 3308585--3308673 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 38
3308575 AACCCCAAAT
* *
3308585 CCATAACCCCTAAATCCCCTAACCCTTAAAGCATAAC-
1 CCATAACCCTTAAATCCCCTAACCCCTAAAGCATAACA
3308622 CCATAACCCTTAAATCCCCCTAACCCCTAAAGCATAACA
1 CCATAACCCTTAAAT-CCCCTAACCCCTAAAGCATAACA
3308661 CC-TAACCCTTAAA
1 CCATAACCCTTAAA
3308674 CCTTAAATCC
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
37 14 0.29
38 32 0.67
39 2 0.04
ACGTcount: A:0.38, C:0.40, G:0.02, T:0.19
Consensus pattern (38 bp):
CCATAACCCTTAAATCCCCTAACCCCTAAAGCATAACA
Found at i:3309129 original size:114 final size:113
Alignment explanation
Indices: 3308909--3309572 Score: 733
Period size: 114 Copynumber: 5.9 Consensus size: 113
3308899 TAAATTATTT
* * * * *
3308909 TAAATCCCTGAGCATTAGCGGCGCTTTCTTTAAAACGCCGCTAAATCCCTGAA-AGCATAGAAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAATA-TA-AGAAAA
* * * *
3308973 TGGCG-CTGTTGGGCTTA-GTTTTTCTTGCTGCGTTTTCCCAAAAACGCCGC
64 CGGCGTC-GTTGGGCTTAGGTTTTT-TTGCGGCGCTTTCTCAAAAACGCCGC
* *
3309023 TAAAGCCTTGAGCATTAGCGGCGCTTCT-TTAAAAACGCCGCTAAATCCCTGAAATATTAAG-AA
1 TAAAGCCCTGAGCATTAGCGGCGCTT-TATTAAAAACGCCGCTAAATCCCCG-AATA-TAAGAAA
*
3309086 ACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGTCGC
63 ACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
* * ** **
3309137 TAAATCCATGAGCATTAGCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCG-A-A-AAG--CTCG
1 TAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAATATAAGAAAACG
* * *
3309197 GCGTCGTTGGGCTTAGGTTTTTTTGCAGCGCTTTCTAAAAAATGCCGCC
66 GCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCG-C
* * * * * * *
3309246 AAAAGACTTGAGAATTAGCAGTGCTTTATTAAAAACGTCGCTAAATCCCCGAATGATCAA-AAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAT-AT-AAGAAAA
3309310 CGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
64 CGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
* * * * * *
3309360 TAAATCCCTGAGCATTAGCGGCACTTTATTAAAAACACTGCTAAATCCCCGAATGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAT-ATAAGAAAAC
** * *
3309425 AACGTCGTTGGGCTTAGGTTTTTTTGCAGCGTTTTCTCAAAAACGCCGC
65 GGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
* * ** *
3309474 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTGAAAACGCCGCTAAATCCCCGAA-AGCTCGGTAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAATA--TAAGAAAA
3309538 CGGCGTCGTTGGGCTTAGG-TTTTTTGCGGCGCTTT
64 CGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTT
3309573 TTGGAAATCA
Statistics
Matches: 468, Mismatches: 65, Indels: 35
0.82 0.11 0.06
Matches are distributed among these distances:
108 45 0.10
109 45 0.10
110 1 0.00
111 1 0.00
112 2 0.00
113 16 0.03
114 298 0.64
115 58 0.12
116 2 0.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (113 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAATATAAGAAAACG
GCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGC
Found at i:3311926 original size:43 final size:42
Alignment explanation
Indices: 3311878--3312106 Score: 151
Period size: 43 Copynumber: 5.4 Consensus size: 42
3311868 ATTTTTAGAA
* *
3311878 ACAAACGCCGCTCAAGGCAAGGACCTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGGCAA-GACCTTTAGCGGCGCTTTTCTC
* * * * * *
3311921 ACAAACACCACAAAAGGCCAAGATCTTTAGCGGCGCTTTTGTT
1 ACAAACGCCGCTAAAGG-CAAGACCTTTAGCGGCGCTTTTCTC
* * * *
3311964 ACAATCGCCGCTGAAGATCATGACCTTTAGCGGCGCTTTTCTC
1 ACAAACGCCGCTAAAG-GCAAGACCTTTAGCGGCGCTTTTCTC
* * ** * * **
3312007 ACAAACACTGCTAAAGATAATGACCTTTTGTGGCGCTTCAAC-C
1 ACAAACGCCGCTAAAGGCAA-GACCTTTAGCGGCGCTT-TTCTC
* * *
3312050 ACAAATGCCACTATGAA-G-AATGACCTTTAGCGACGCTTTT-TC
1 ACAAACGCCGCTA--AAGGCAA-GACCTTTAGCGGCGCTTTTCTC
3312092 ACAAACGCCGCTAAA
1 ACAAACGCCGCTAAA
3312107 AACATAACTT
Statistics
Matches: 138, Mismatches: 41, Indels: 17
0.70 0.21 0.09
Matches are distributed among these distances:
40 2 0.01
42 13 0.09
43 117 0.85
44 4 0.03
45 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (42 bp):
ACAAACGCCGCTAAAGGCAAGACCTTTAGCGGCGCTTTTCTC
Found at i:3315075 original size:118 final size:119
Alignment explanation
Indices: 3314894--3315115 Score: 299
Period size: 118 Copynumber: 1.9 Consensus size: 119
3314884 TCCTCGTTCA
*
3314894 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
3314959 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * **
3315013 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
3315075 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
3315116 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
117 4 0.04
118 66 0.73
119 20 0.22
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:3315115 original size:40 final size:40
Alignment explanation
Indices: 3314892--3315115 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
3314882 GCTCCTCGTT
* *
3314892 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
3314932 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
3314972 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
3315012 C-AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
3315050 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
3315091 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
3315116 CATCATTCAA
Statistics
Matches: 164, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
38 24 0.15
39 21 0.13
40 107 0.65
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:3322978 original size:118 final size:119
Alignment explanation
Indices: 3322797--3323018 Score: 299
Period size: 118 Copynumber: 1.9 Consensus size: 119
3322787 TCCTCGTTCA
*
3322797 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
3322862 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * **
3322916 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
3322978 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
3323019 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
117 4 0.04
118 66 0.73
119 20 0.22
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:3323018 original size:40 final size:40
Alignment explanation
Indices: 3322795--3323018 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
3322785 GCTCCTCGTT
* *
3322795 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
3322835 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
3322875 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
3322915 C-AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
3322953 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
3322994 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
3323019 CATCATTCAA
Statistics
Matches: 164, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
38 24 0.15
39 21 0.13
40 107 0.65
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:3328757 original size:13 final size:13
Alignment explanation
Indices: 3328719--3328761 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3328709 GCTCAATGCA
*
3328719 AAATTGTAATTTT
1 AAATTCTAATTTT
* * *
3328732 GAATTTTATTTTT
1 AAATTCTAATTTT
3328745 AAATTCTAATTTT
1 AAATTCTAATTTT
3328758 AAAT
1 AAAT
3328762 CAAAATAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (13 bp):
AAATTCTAATTTT
Found at i:3331780 original size:21 final size:21
Alignment explanation
Indices: 3331756--3331814 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
3331746 CACTAACTCT
*
3331756 TAACCTCTAACCCCTAATCCC
1 TAACCTCTAACCCCTAACCCC
* *
3331777 TAA-CTACTAGCCCCCAACCCC
1 TAACCT-CTAACCCCTAACCCC
*
3331798 TAACCTCTAAACCCTAA
1 TAACCTCTAACCCCTAA
3331815 ACATTATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.32, C:0.46, G:0.02, T:0.20
Consensus pattern (21 bp):
TAACCTCTAACCCCTAACCCC
Found at i:3331983 original size:14 final size:15
Alignment explanation
Indices: 3331961--3331994 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3331951 CTTAAACCAG
*
3331961 AATCCCTAAT-CCAT
1 AATCTCTAATCCCAT
3331975 AATCTCTAATCCCAT
1 AATCTCTAATCCCAT
3331990 AATCT
1 AATCT
3331995 ATAAACCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (15 bp):
AATCTCTAATCCCAT
Found at i:3332087 original size:14 final size:14
Alignment explanation
Indices: 3332042--3332078 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3332032 ATCCTAAATT
*
3332042 AACCATAAACACTA
1 AACCATATACACTA
*
3332056 AACCATATACCCTA
1 AACCATATACACTA
3332070 AACCATATA
1 AACCATATA
3332079 TATTAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (14 bp):
AACCATATACACTA
Found at i:3332242 original size:20 final size:19
Alignment explanation
Indices: 3332213--3332254 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3332203 AATGTTAATT
3332213 AATATAAATAAACAAATAA
1 AATATAAATAAACAAATAA
* *
3332232 AATAGTAAATAGACATATAA
1 AATA-TAAATAAACAAATAA
3332252 AAT
1 AAT
3332255 GTTTTTGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:3332350 original size:41 final size:41
Alignment explanation
Indices: 3332267--3332412 Score: 222
Period size: 41 Copynumber: 3.6 Consensus size: 41
3332257 TTTTGTGGCA
* *
3332267 CTTTTTCAAAAACGCCGCTAAATC-CCGAGCATTAGCGGCG
1 CTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTAGCGGCG
*
3332307 CTTTTCCAAAAACGCCGCTAAAGCTCTGAGCATTAGCGGCG
1 CTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTAGCGGCG
* * *
3332348 CTTCTTCAAAAACGCCGCTAAAGCTCTGAACATTAGCGGTG
1 CTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTAGCGGCG
*
3332389 CTTTTTCAAAAACGCTGCTAAAGC
1 CTTTTTCAAAAACGCCGCTAAAGC
3332413 CCCGAAAGGT
Statistics
Matches: 96, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 22 0.23
41 74 0.77
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (41 bp):
CTTTTTCAAAAACGCCGCTAAAGCTCTGAGCATTAGCGGCG
Found at i:3332503 original size:40 final size:41
Alignment explanation
Indices: 3332455--3332585 Score: 155
Period size: 40 Copynumber: 3.3 Consensus size: 41
3332445 TAGGTTTTTT
* *
3332455 GCGGCGCTTTTCTAAAAAACGCCACTAATGCTC-ATCTTTA
1 GCGGCGCTTTTCTAAAAAGCGCCGCTAATGCTCAATCTTTA
*
3332495 GCGGCGC-TTT-TAGAAAAGCGTCGCTAATGCTCAATCTTTA
1 GCGGCGCTTTTCTA-AAAAGCGCCGCTAATGCTCAATCTTTA
* * *
3332535 GCGACG-TTTTTTAAAAAGCGCCGCTAATGCTCGAT-TTTA
1 GCGGCGCTTTTCTAAAAAGCGCCGCTAATGCTCAATCTTTA
*
3332574 GCGGCGTTTTTC
1 GCGGCGCTTTTC
3332586 ATCCAAACGC
Statistics
Matches: 78, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
38 2 0.03
39 28 0.36
40 46 0.59
41 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (41 bp):
GCGGCGCTTTTCTAAAAAGCGCCGCTAATGCTCAATCTTTA
Found at i:3333315 original size:96 final size:97
Alignment explanation
Indices: 3333183--3333398 Score: 321
Period size: 96 Copynumber: 2.2 Consensus size: 97
3333173 AAAAAATTGC
*
3333183 ATTTATCCTTTCATAAAA-TTTAAAATTTTAACTGTTTAAATATTAAGGATAAATAATATTTTAA
1 ATTTATCCTTTCATAAAATTTTAAAATTTTAACTGTTTAAAAATTAAGGATAAATAATATTTTAA
* *
3333247 ATATTTTGA-CTATTTTTAAGGATAACATATT
66 ATATTTTGATCTAATTTTAAGGATAAAATATT
*
3333278 ATTTATCC-TTCAATAAAATTTTAAAATTTTAACTGTTTAAAAATTAAGGATAAATAATATTTTT
1 ATTTATCCTTTC-ATAAAATTTTAAAATTTTAACTGTTTAAAAATTAAGGATAAATAATATTTTA
*
3333342 AATATTTTGATTGTTTTAATTTTAAGGATAAAATATT
65 AATATTTTGA----TCTAATTTTAAGGATAAAATATT
3333379 ATTTATCCTTTCATAAAATT
1 ATTTATCCTTTCATAAAATT
3333399 CAAAAAATAT
Statistics
Matches: 108, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
94 3 0.03
95 14 0.13
96 53 0.49
101 35 0.32
102 3 0.03
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (97 bp):
ATTTATCCTTTCATAAAATTTTAAAATTTTAACTGTTTAAAAATTAAGGATAAATAATATTTTAA
ATATTTTGATCTAATTTTAAGGATAAAATATT
Found at i:3333349 original size:42 final size:43
Alignment explanation
Indices: 3333296--3333382 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 43
3333286 TTCAATAAAA
3333296 TTTTAAAATTTTAACTGTTTAAAAATTAAGGAT-AAATAATAT
1 TTTTAAAATTTTAACTGTTTAAAAATTAAGGATAAAATAATAT
* * * * ** *
3333338 TTTTAATATTTTGATTGTTTTAATTTTAAGGATAAAATATTAT
1 TTTTAAAATTTTAACTGTTTAAAAATTAAGGATAAAATAATAT
3333381 TT
1 TT
3333383 ATCCTTTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 27 0.73
43 10 0.27
ACGTcount: A:0.40, C:0.01, G:0.08, T:0.51
Consensus pattern (43 bp):
TTTTAAAATTTTAACTGTTTAAAAATTAAGGATAAAATAATAT
Found at i:3333406 original size:31 final size:31
Alignment explanation
Indices: 3333371--3333429 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
3333361 TTTTAAGGAT
*
3333371 AAAATATTATTTATCCTTTCATAAAATTCAA
1 AAAATATTATTTATCATTTCATAAAATTCAA
3333402 AAAATATTATTTATCATTTCATAAAATT
1 AAAATATTATTTATCATTTCATAAAATT
3333430 TTAAAAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (31 bp):
AAAATATTATTTATCATTTCATAAAATTCAA
Found at i:3333463 original size:124 final size:116
Alignment explanation
Indices: 3333341--3333557 Score: 294
Period size: 115 Copynumber: 1.9 Consensus size: 116
3333331 ATAATATTTT
* * *
3333341 TAATATTTTGATTGTTTTAATTTTAAGGATAAAATATTATTTATCCTTTCAT-AAAATTCAAAAA
1 TAATATTTTGACTATTTTAATTTGAAGGATAAAATATTATTTATCCTTTCATCAAAATTCAAAAA
* *
3333405 ATATTATTTATCATTTCATAAAATTTTAAAAG-TTAAAACGTTAAGGATAAA
66 ATATCATTTATCATTTCATAAAATTTTAAAAGTTTAAAA-ATTAAGGATAAA
* *
3333456 TAATATTTTGACTATTTTAATTTGAAGGATAAAATATTATTTATCCTTTCATCAAATTTTAAAAA
1 TAATATTTTGACTATTTTAATTTGAAGGATAAAATATTATTTATCCTTTCATCAAAATTCAAAAA
* * * * * *
3333521 CTATCATTTCTCTTTTCATAAATTTTTCAAATTTTAA
66 ATATCATTTATCATTTCATAAAATTTTAAAAGTTTAA
3333558 CTGTTTAAAT
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
115 49 0.56
116 35 0.40
117 4 0.05
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (116 bp):
TAATATTTTGACTATTTTAATTTGAAGGATAAAATATTATTTATCCTTTCATCAAAATTCAAAAA
ATATCATTTATCATTTCATAAAATTTTAAAAGTTTAAAAATTAAGGATAAA
Found at i:3333905 original size:14 final size:14
Alignment explanation
Indices: 3333888--3333953 Score: 71
Period size: 14 Copynumber: 4.8 Consensus size: 14
3333878 AGCCCTAAAT
*
3333888 CTTAAACCCTAAGC
1 CTTAAATCCTAAGC
* * *
3333902 CTTAAGTCTTAAAC
1 CTTAAATCCTAAGC
*
3333916 TTTAAATCCTAAGC
1 CTTAAATCCTAAGC
3333930 C-TAAATCCTAAGC
1 CTTAAATCCTAAGC
*
3333943 CCTAAATCCTA
1 CTTAAATCCTA
3333954 TGTCCTAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
13 13 0.31
14 29 0.69
ACGTcount: A:0.36, C:0.29, G:0.06, T:0.29
Consensus pattern (14 bp):
CTTAAATCCTAAGC
Found at i:3333936 original size:13 final size:14
Alignment explanation
Indices: 3333918--3333953 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
3333908 TCTTAAACTT
3333918 TAAATCCTAAG-CC
1 TAAATCCTAAGCCC
3333931 TAAATCCTAAGCCC
1 TAAATCCTAAGCCC
3333945 TAAATCCTA
1 TAAATCCTA
3333954 TGTCCTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.39, C:0.31, G:0.06, T:0.25
Consensus pattern (14 bp):
TAAATCCTAAGCCC
Found at i:3334054 original size:7 final size:7
Alignment explanation
Indices: 3334042--3334074 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
3334032 CCGAACCCCC
3334042 TAAACCT
1 TAAACCT
3334049 TAAACCT
1 TAAACCT
3334056 TAAACCT
1 TAAACCT
*
3334063 TAAGCCT
1 TAAACCT
3334070 TAAAC
1 TAAAC
3334075 TTGAATCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.27, G:0.03, T:0.27
Consensus pattern (7 bp):
TAAACCT
Found at i:3334656 original size:19 final size:19
Alignment explanation
Indices: 3334634--3334679 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
3334624 AATTTTTATG
3334634 AATTTTTAA-TTTTTTAAA
1 AATTTTTAATTTTTTTAAA
*
3334652 TAA-TTATAATTTTTTTAAA
1 -AATTTTTAATTTTTTTAAA
3334671 ATATTTTTA
1 A-ATTTTTA
3334680 GAATTTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.27
19 12 0.55
20 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AATTTTTAATTTTTTTAAA
Found at i:3334661 original size:18 final size:18
Alignment explanation
Indices: 3334616--3334666 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
3334606 GCCAGTTGTC
*
3334616 ATAATTATAATTTTTATGA
1 ATAATTATAATTTTT-TAA
*
3334635 AT--TTTTAATTTTTTAA
1 ATAATTATAATTTTTTAA
3334651 ATAATTATAATTTTTT
1 ATAATTATAATTTTTT
3334667 TAAAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 4 0.15
17 10 0.37
18 11 0.41
19 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
ATAATTATAATTTTTTAA
Found at i:3335069 original size:22 final size:22
Alignment explanation
Indices: 3335043--3335100 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 22
3335033 TAAAACATTG
*
3335043 TGAAAATTTATAAATTATTTTT
1 TGAAAATTTATAAATTATGTTT
*
3335065 TG-AAA-TTATAAAAATATGTTT
1 TGAAAATTTAT-AAATTATGTTT
3335086 T-AAAATTT-T-AATTAT
1 TGAAAATTTATAAATTAT
3335101 ATAAAACAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
19 5 0.17
20 4 0.13
21 17 0.57
22 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
TGAAAATTTATAAATTATGTTT
Found at i:3338203 original size:96 final size:96
Alignment explanation
Indices: 3338026--3338220 Score: 248
Period size: 96 Copynumber: 2.0 Consensus size: 96
3338016 CCATATTTTC
* ** * ** *
3338026 TGGTACACAAACTCCATGGTGATCACTATCAACATGATCACCGACTCTCCCCGCTAGTGGGATCA
1 TGGTACACAAACTCCATGGTGATCACTACCAACACAATCACCAACTCTCCCAACTAGTGAGATCA
*
3338091 ACGGATCATGGCTTAATGGTAGAATAGGATA
66 ACGGATAATGGCTTAATGGTAGAATAGGATA
* * *
3338122 TGGTACACAAGCTCCATGGTGATCACTACCAACACAATCACCAACTC-CCACAATTGGTGAGATC
1 TGGTACACAAACTCCATGGTGATCACTACCAACACAATCACCAACTCTCC-CAACTAGTGAGATC
* * *
3338186 AAGGGATAATGGTTTAATGGTAGAATATGATA
65 AACGGATAATGGCTTAATGGTAGAATAGGATA
3338218 TGG
1 TGG
3338221 GAGCTGCATC
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
95 2 0.02
96 82 0.98
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (96 bp):
TGGTACACAAACTCCATGGTGATCACTACCAACACAATCACCAACTCTCCCAACTAGTGAGATCA
ACGGATAATGGCTTAATGGTAGAATAGGATA
Found at i:3339343 original size:42 final size:43
Alignment explanation
Indices: 3339291--3339445 Score: 116
Period size: 42 Copynumber: 3.5 Consensus size: 43
3339281 TATTTAAATA
*
3339291 TTAAAGAT-AAATAATATTTTAAATCTTTTGACTGTTTTAATT
1 TTAAGGATAAAATAATATTTTAAATCTTTTGACTGTTTTAATT
* * * * * ** *
3339333 TTAAGAATAAAATATTATTTATCTATTCATACCATTTTAACCGTTAAAATA
1 TTAAGGATAAAATA--A--TAT-T-TT-AAATC-TTTTGACTGTTTTAATT
*
3339384 TTAAGGAT-AAATAATATTTTAAATATTTTGACTGTTTTAATT
1 TTAAGGATAAAATAATATTTTAAATCTTTTGACTGTTTTAATT
* *
3339426 TGAAGGATAAAATATTATTT
1 TTAAGGATAAAATAATATTT
3339446 ATCATTTCAT
Statistics
Matches: 83, Mismatches: 20, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
42 25 0.30
43 17 0.20
44 2 0.02
45 2 0.02
46 3 0.04
47 3 0.04
48 2 0.02
49 2 0.02
50 8 0.10
51 19 0.23
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.46
Consensus pattern (43 bp):
TTAAGGATAAAATAATATTTTAAATCTTTTGACTGTTTTAATT
Found at i:3339372 original size:93 final size:93
Alignment explanation
Indices: 3339275--3339448 Score: 285
Period size: 93 Copynumber: 1.9 Consensus size: 93
3339265 ATCTTAAAAC
* * * *
3339275 TTTAACTATTTAAATATTAAAGATAAATAATATTTTAAATCTTTTGACTGTTTTAATTTTAAGAA
1 TTTAACCATTAAAATATTAAAGATAAATAATATTTTAAATATTTTGACTGTTTTAATTTGAAGAA
3339340 TAAAATATTATTTATCTATTCATACCAT
66 TAAAATATTATTTATCTATTCATACCAT
* * *
3339368 TTTAACCGTTAAAATATTAAGGATAAATAATATTTTAAATATTTTGACTGTTTTAATTTGAAGGA
1 TTTAACCATTAAAATATTAAAGATAAATAATATTTTAAATATTTTGACTGTTTTAATTTGAAGAA
3339433 TAAAATATTATTTATC
66 TAAAATATTATTTATC
3339449 ATTTCATCAA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (93 bp):
TTTAACCATTAAAATATTAAAGATAAATAATATTTTAAATATTTTGACTGTTTTAATTTGAAGAA
TAAAATATTATTTATCTATTCATACCAT
Found at i:3339476 original size:32 final size:32
Alignment explanation
Indices: 3339440--3339502 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
3339430 GGATAAAATA
*
3339440 TTATTTATCATTTCATCAAATTTTAAAAATTG
1 TTATTTATCATTTCATAAAATTTTAAAAATTG
* * *
3339472 TTATTTCTCTTTTCATAAAATTTTCAAAATT
1 TTATTTATCATTTCATAAAATTTTAAAAATT
3339503 TAACTGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (32 bp):
TTATTTATCATTTCATAAAATTTTAAAAATTG
Found at i:3339762 original size:13 final size:14
Alignment explanation
Indices: 3339728--3339772 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
3339718 AGTGTTAACT
3339728 CTAAATCTTAAATC
1 CTAAATCTTAAATC
3339742 CTAAATCTTAACA-C
1 CTAAATCTTAA-ATC
3339756 C-AAATCTTAAATC
1 CTAAATCTTAAATC
3339769 CTAA
1 CTAA
3339773 CATTTAAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 11 0.39
14 15 0.54
15 1 0.04
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.31
Consensus pattern (14 bp):
CTAAATCTTAAATC
Found at i:3339766 original size:20 final size:20
Alignment explanation
Indices: 3339737--3339774 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3339727 TCTAAATCTT
*
3339737 AAATCCTAAATCTTAACACC
1 AAATCCTAAATCCTAACACC
*
3339757 AAATCTTAAATCCTAACA
1 AAATCCTAAATCCTAACA
3339775 TTTAAGTCAT
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:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATCCTAAATCCTAACACC
Found at i:3339879 original size:27 final size:27
Alignment explanation
Indices: 3339847--3339901 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
3339837 CCCTAAACCT
3339847 TAAATCATAAG-TCTTAAA-TCTTAAATC
1 TAAATCATAAGCTC-TAAACTC-TAAATC
*
3339874 TAAATCCTAAGCTCTAAACTCTAAATC
1 TAAATCATAAGCTCTAAACTCTAAATC
3339901 T
1 T
3339902 TGAACTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.35
Consensus pattern (27 bp):
TAAATCATAAGCTCTAAACTCTAAATC
Found at i:3339907 original size:14 final size:14
Alignment explanation
Indices: 3339890--3339940 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
3339880 CTAAGCTCTA
3339890 AACTCTAAATCTTG
1 AACTCTAAATCTTG
*
3339904 AACTTTAAAT-TATG
1 AACTCTAAATCT-TG
*
3339918 AACCCTAAATCTT-
1 AACTCTAAATCTTG
3339931 AAGCTCTAAA
1 AA-CTCTAAA
3339941 CCTAAACCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 3 0.10
14 26 0.87
15 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (14 bp):
AACTCTAAATCTTG
Found at i:3339912 original size:21 final size:20
Alignment explanation
Indices: 3339867--3339913 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
3339857 GTCTTAAATC
3339867 TTAAATCTAAATCCTAAGCT
1 TTAAATCTAAATCCTAAGCT
* *
3339887 CTAAACTCTAAATCTTGAA-CT
1 TTAAA-TCTAAATCCT-AAGCT
3339908 TTAAAT
1 TTAAAT
3339914 TATGAACCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 5 0.23
21 15 0.68
22 2 0.09
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.36
Consensus pattern (20 bp):
TTAAATCTAAATCCTAAGCT
Found at i:3339958 original size:14 final size:14
Alignment explanation
Indices: 3339941--3339983 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
3339931 AAGCTCTAAA
*
3339941 CCTAAACCTTACAC
1 CCTACACCTTACAC
*
3339955 CCTACACCCTACAC
1 CCTACACCTTACAC
3339969 CCTACACCTTACAC
1 CCTACACCTTACAC
3339983 C
1 C
3339984 TTCAACCTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.30, C:0.51, G:0.00, T:0.19
Consensus pattern (14 bp):
CCTACACCTTACAC
Found at i:3339974 original size:21 final size:21
Alignment explanation
Indices: 3339941--3339983 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3339931 AAGCTCTAAA
*
3339941 CCTAAACCTTACACCCTACAC
1 CCTAAACCCTACACCCTACAC
* *
3339962 CCTACACCCTACACCTTACAC
1 CCTAAACCCTACACCCTACAC
3339983 C
1 C
3339984 TTCAACCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.51, G:0.00, T:0.19
Consensus pattern (21 bp):
CCTAAACCCTACACCCTACAC
Found at i:3339985 original size:7 final size:7
Alignment explanation
Indices: 3339950--3339983 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
3339940 ACCTAAACCT
3339950 TACACCC
1 TACACCC
3339957 TACACCC
1 TACACCC
3339964 TACACCC
1 TACACCC
*
3339971 TACACCT
1 TACACCC
3339978 TACACC
1 TACACC
3339984 TTCAACCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (7 bp):
TACACCC
Found at i:3340725 original size:28 final size:27
Alignment explanation
Indices: 3340668--3340726 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
3340658 AAAAGTCGTT
*
3340668 TTTTTTAAATTTATCGAAATGGGCCGA
1 TTTTTTAAATTTACCGAAATGGGCCGA
* *
3340695 TTTTTTAATTATTTACCGGAATGGTCC-A
1 TTTTTTAA--ATTTACCGAAATGGGCCGA
3340723 TTTT
1 TTTT
3340727 CCATGACATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.30
28 5 0.19
29 14 0.52
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (27 bp):
TTTTTTAAATTTACCGAAATGGGCCGA
Found at i:3341035 original size:12 final size:12
Alignment explanation
Indices: 3341018--3341043 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3341008 TAATCCTCTC
3341018 AATTTCCTTCCA
1 AATTTCCTTCCA
3341030 AATTTCCTTCCA
1 AATTTCCTTCCA
3341042 AA
1 AA
3341044 ATTCTCTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTTCCTTCCA
Found at i:3341090 original size:51 final size:51
Alignment explanation
Indices: 3341016--3341136 Score: 199
Period size: 51 Copynumber: 2.4 Consensus size: 51
3341006 TCTAATCCTC
3341016 TCAATTTCCT-TCCAAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
1 TCAATTTCCTCT-C-AATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
*
3341068 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
*
3341119 TCAATTTCCCCTCAATTT
1 TCAATTTCCTCTCAATTT
3341137 TATTTTTTAA
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 54 0.82
52 11 0.17
53 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
Found at i:3341180 original size:31 final size:30
Alignment explanation
Indices: 3341137--3341203 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 30
3341127 CCCTCAATTT
*
3341137 TATTTTTTAAAATAATTTTATATTTTTCTA
1 TATTTTTTAAAATAATTTTAAATTTTTCTA
*
3341167 TATTTTTTAAAAATAATTTTAAATTTTTTTA
1 TATTTTTT-AAAATAATTTTAAATTTTTCTA
3341198 TATTTT
1 TATTTT
3341204 CATCAATGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 8 0.24
31 26 0.76
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (30 bp):
TATTTTTTAAAATAATTTTAAATTTTTCTA
Found at i:3342295 original size:7 final size:7
Alignment explanation
Indices: 3342283--3342307 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3342273 AGTCGATTGA
3342283 TATTTAG
1 TATTTAG
3342290 TATTTAG
1 TATTTAG
3342297 TATTTAG
1 TATTTAG
3342304 TATT
1 TATT
3342308 ATGTATATAA
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:3343426 original size:25 final size:25
Alignment explanation
Indices: 3343397--3343582 Score: 83
Period size: 25 Copynumber: 7.7 Consensus size: 25
3343387 TTTAAATTTA
3343397 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
** *
3343422 TTATTTGATGTAATACGCATAGAAAT
1 TTATTTGATGTAATA-AAATAGAAGT
** *
3343448 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
3343467 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
* ** *
3343493 TTATTTGATATAATAGGCATAGAAAT
1 TTATTTGATGTAATA-AAATAGAAGT
* * ** *
3343519 TT-TTTTAAGT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
*
3343538 ATTATTTGATATAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
3343564 TCTATTTGATGTAATAAAA
1 T-TATTTGATGTAATAAAA
3343583 ATCCTAATTT
Statistics
Matches: 114, Mismatches: 28, Indels: 37
0.64 0.16 0.21
Matches are distributed among these distances:
19 2 0.02
20 8 0.07
21 14 0.12
23 4 0.04
24 6 0.05
25 42 0.37
26 38 0.33
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.45
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:3343483 original size:71 final size:71
Alignment explanation
Indices: 3343395--3343579 Score: 316
Period size: 71 Copynumber: 2.6 Consensus size: 71
3343385 TATTTAAATT
*
3343395 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCAAGTTA
3343460 TTTTGA
66 TTTTGA
* * *
3343466 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATATAATAGGCATAGAAATTTTTTTAAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCAAGTTA
3343531 TTTTGA
66 TTTTGA
*
3343537 TATTATTTGATATAATAAAATAGAAGTTCTATTTGATGTAATA
1 TATTATTTGATGTAATAAAATAGAAGTT-TATTTGATGTAATA
3343580 AAAATCCTAA
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 94 0.88
72 13 0.12
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (71 bp):
TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCAAGTTA
TTTTGA
Found at i:3343564 original size:35 final size:36
Alignment explanation
Indices: 3343455--3343573 Score: 93
Period size: 35 Copynumber: 3.4 Consensus size: 36
3343445 AATTTTTTCG
*
3343455 AGTTAT-TTTGATATTATTTGATGTAATAAAATAGA
1 AGTTATATTTGATATTATTTGATATAATAAAATAGA
* ** * *** **
3343490 AGTT-TATTTGATATAATAGGCATAGAA-ATTTTTTTA
1 AGTTATATTTGATATTATTTG-ATATAATA-AAATAGA
3343526 AGTTAT-TTTGATATTATTTGATATAATAAAATAGA
1 AGTTATATTTGATATTATTTGATATAATAAAATAGA
*
3343561 AGTTCTATTTGAT
1 AGTTATATTTGAT
3343574 GTAATAAAAA
Statistics
Matches: 58, Mismatches: 20, Indels: 11
0.65 0.22 0.12
Matches are distributed among these distances:
34 1 0.02
35 28 0.48
36 28 0.48
37 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (36 bp):
AGTTATATTTGATATTATTTGATATAATAAAATAGA
Found at i:3343699 original size:30 final size:29
Alignment explanation
Indices: 3343585--3343796 Score: 354
Period size: 29 Copynumber: 7.3 Consensus size: 29
3343575 TAATAAAAAT
3343585 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
3343614 CCTAAATTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
3343643 CCTAATTTAATT-AAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
3343671 CCTAATTTAATTAAAAACCTTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
* *
3343701 CCTAATTTAATTAAAAACCTTAACCTTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
3343730 CCTAATTTAATTAAAAACCCTAAACCTTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
3343760 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
3343789 CCTAATTT
1 CCTAATTT
3343797 TACATAATTT
Statistics
Matches: 174, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
28 28 0.16
29 88 0.51
30 58 0.33
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:3343739 original size:59 final size:59
Alignment explanation
Indices: 3343585--3343796 Score: 365
Period size: 59 Copynumber: 3.6 Consensus size: 59
3343575 TAATAAAAAT
*
3343585 CCTAATTTAATTAAAAACCCTAACCCTAACCTAAATTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
*
3343643 CCTAATTTAATT-AAAACCCTAACCCTAACCTAATTTAATTAAAAACCTTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
* * *
3343701 CCTAATTTAATTAAAAACCTTAACCTTAACCTAATTTAATTAAAAACCCTAAACCTTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
3343760 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTT
1 CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTT
3343797 TACATAATTT
Statistics
Matches: 144, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
57 35 0.24
58 32 0.22
59 77 0.53
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (59 bp):
CCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAA
Found at i:3343858 original size:55 final size:52
Alignment explanation
Indices: 3343791--3343913 Score: 201
Period size: 55 Copynumber: 2.3 Consensus size: 52
3343781 AACCCTAACC
*
3343791 TAATTTTACATAATTTGATAATTTTTCTAACCATTAACACAATTTTTGGACT
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACT
*
3343843 TAAGAATTTTACATAATTTGATAATTTTACTAACCATTAACATAATTTTTGGACT
1 T---AATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACT
3343898 TAATTTTACATAATTT
1 TAATTTTACATAATTT
3343914 TACATAATGT
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
52 16 0.24
55 50 0.76
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (52 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACT
Found at i:3344653 original size:19 final size:19
Alignment explanation
Indices: 3344629--3344673 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3344619 TGCTCGCTTT
3344629 GGAAATAGCGCCACCAAAC
1 GGAAATAGCGCCACCAAAC
*
3344648 GGAAATAGCGCCGCCAAAC
1 GGAAATAGCGCCACCAAAC
*
3344667 GAAAATA
1 GGAAATA
3344674 TGTCTCTCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.27, G:0.22, T:0.07
Consensus pattern (19 bp):
GGAAATAGCGCCACCAAAC
Found at i:3347275 original size:123 final size:123
Alignment explanation
Indices: 3347052--3347397 Score: 602
Period size: 123 Copynumber: 2.8 Consensus size: 123
3347042 CAAACTTGCT
*
3347052 ACTGTAGCAAAATCACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
* * *
3347117 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATTACCA
66 GAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATATTTCTTACATGACCA
* * *
3347175 ACTGTAGCAAAATCGCGTCCACGAGGGCACAATTTCACAATTTCTTCTCAAATAGAATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
* * *
3347240 GAAGCGATTTTATACTATTTTCTTAGAAACATCAAAAAAAATATTTCTTACATGACCT
66 GAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATATTTCTTACATGACCA
3347298 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
3347363 GAAGCGATTTTATACTATTTGCTCAGAAACATCAA
66 GAAGCGATTTTATACTATTTGCTCAGAAACATCAA
3347398 CTCGAAATAA
Statistics
Matches: 208, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 208 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (123 bp):
ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
GAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATATTTCTTACATGACCA
Found at i:3348287 original size:123 final size:123
Alignment explanation
Indices: 3348124--3348469 Score: 593
Period size: 123 Copynumber: 2.8 Consensus size: 123
3348114 CAAACTTGCT
*
3348124 ACTGTAGAAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
* ** *
3348189 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATTTATTTCTTACATTACCA
66 GAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATATTTCTTACATGACCA
* *
3348247 ACTGTAGCAAAATCGCGTCCACGAGGGCACAATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
* * *
3348312 GAAGCGATTTTATACTATTTTCTTAGAAACATCAAAAAAAATATTTCTTACATGACCT
66 GAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATATTTCTTACATGACCA
*
3348370 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGTATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
3348435 GAAGCGATTTTATACTATTTGCTCAGAAACATCAA
66 GAAGCGATTTTATACTATTTGCTCAGAAACATCAA
3348470 CTCGAAATAA
Statistics
Matches: 208, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 208 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (123 bp):
ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
GAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATATTTCTTACATGACCA
Found at i:3349418 original size:123 final size:123
Alignment explanation
Indices: 3349195--3349540 Score: 620
Period size: 123 Copynumber: 2.8 Consensus size: 123
3349185 CAAACTTGCT
*
3349195 ACTGTAGCAAAATTGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
* * *
3349260 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATTACCA
66 GAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATATTTCTTACATGACCA
*
3349318 ACTGTAGCAAAATCGCGTCCACGAGGGTGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
* * *
3349383 GAAGCGATTTTATACTATTTTCTTAGAAACATCAAAAAAAATATTTCTTACATGACCT
66 GAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATATTTCTTACATGACCA
3349441 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
3349506 GAAGCGATTTTATACTATTTGCTCAGAAACATCAA
66 GAAGCGATTTTATACTATTTGCTCAGAAACATCAA
3349541 CTCGAAATAA
Statistics
Matches: 212, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 212 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (123 bp):
ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTA
GAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATATTTCTTACATGACCA
Found at i:3356325 original size:121 final size:121
Alignment explanation
Indices: 3356111--3356357 Score: 458
Period size: 121 Copynumber: 2.0 Consensus size: 121
3356101 TGGTCTGAGA
3356111 ATATGTGACACTTTTCCCCATAGAGATAATGTTTTCAGATTTTTAGTGCTAACACTACAACTACT
1 ATATGTGACACTTTTCCCCATAGAGATAATGTTTTCAGATTTTTAGTGCTAACACTACAACTACT
* *
3356176 AGTTCCAAGTCGTGTGTTGAGTGGTTCTTTTCATTTGACTTGAGCTAACGAGATGC
66 AGTTCCAAGTCATGTGTTGAGTGGTTCTTTTCATTCGACTTGAGCTAACGAGATGC
* *
3356232 ATATGTGACACTTTTCCCCATAGAGATAATGTTTTCATATTTTTAGTGCTAACACTACAACTGCT
1 ATATGTGACACTTTTCCCCATAGAGATAATGTTTTCAGATTTTTAGTGCTAACACTACAACTACT
3356297 AGTTCCAAGTCATGTGTTGAGTGGTTCTTTTCATTCGACTTGAGCTAACGAGATGC
66 AGTTCCAAGTCATGTGTTGAGTGGTTCTTTTCATTCGACTTGAGCTAACGAGATGC
3356353 ATATG
1 ATATG
3356358 CCAGAGTCTT
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (121 bp):
ATATGTGACACTTTTCCCCATAGAGATAATGTTTTCAGATTTTTAGTGCTAACACTACAACTACT
AGTTCCAAGTCATGTGTTGAGTGGTTCTTTTCATTCGACTTGAGCTAACGAGATGC
Found at i:3359631 original size:16 final size:16
Alignment explanation
Indices: 3359610--3359643 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3359600 TTTTGATAAG
*
3359610 TTAAAATAATTTTTAC
1 TTAAAATAATTTTAAC
*
3359626 TTAAAATCATTTTAAC
1 TTAAAATAATTTTAAC
3359642 TT
1 TT
3359644 GATTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAATAATTTTAAC
Found at i:3361489 original size:19 final size:19
Alignment explanation
Indices: 3361464--3361504 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3361454 AAATATACAA
3361464 ATATATAGAAAGAAAATAATT
1 ATATAT-GAAA-AAAATAATT
*
3361485 ATATATGAAAATAATAATT
1 ATATATGAAAAAAATAATT
3361504 A
1 A
3361505 CATTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 4 0.21
21 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (19 bp):
ATATATGAAAAAAATAATT
Found at i:3362309 original size:12 final size:13
Alignment explanation
Indices: 3362287--3362320 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3362277 GTATTTTAGC
*
3362287 AAAGTAAAAAATA
1 AAAGAAAAAAATA
3362300 AAAGAAAAAAATA
1 AAAGAAAAAAATA
3362313 AAAGAAAA
1 AAAGAAAA
3362321 TATAGAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAGAAAAAAATA
Found at i:3362987 original size:44 final size:45
Alignment explanation
Indices: 3362939--3363042 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 45
3362929 ACTGCAATGC
* * * * *
3362939 CAGGGAGATAGGATTTG-TTTATTTAGTCTGCCCCAGTGCAATTT
1 CAGGGAGATAAGATTTGCTTTATTGAATCTGCCCCACTACAATTT
* * * *
3362983 CAGGGGGATAAGACTTGCTTTCTTGAATCTGCTCCACTACAATTT
1 CAGGGAGATAAGATTTGCTTTATTGAATCTGCCCCACTACAATTT
*
3363028 CAAGGAGATAAGATT
1 CAGGGAGATAAGATT
3363043 CGTTGTGATC
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
44 14 0.30
45 33 0.70
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (45 bp):
CAGGGAGATAAGATTTGCTTTATTGAATCTGCCCCACTACAATTT
Found at i:3363112 original size:44 final size:44
Alignment explanation
Indices: 3363059--3363171 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
3363049 GATCTACTCT
* * *
3363059 ACTGCAACTTTAGAGAGATAAGATCTGTA-ATTTTAATCCGCTCC
1 ACTGCAACTTCAGAGAGATAAGAT-TATAGACTTTAATCCGCTCC
* * *
3363103 ACTGCAACTTCA-AGGGGAT-AGAATTATAGGCTTTAATCTGCTCC
1 ACTGCAACTTCAGA-GAGATAAG-ATTATAGACTTTAATCCGCTCC
3363147 ACTGCAACTTCAGAGAGATAAGATT
1 ACTGCAACTTCAGAGAGATAAGATT
3363172 TATATCTTCG
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
43 6 0.11
44 48 0.84
45 3 0.05
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (44 bp):
ACTGCAACTTCAGAGAGATAAGATTATAGACTTTAATCCGCTCC
Found at i:3363325 original size:88 final size:88
Alignment explanation
Indices: 3363176--3363630 Score: 709
Period size: 88 Copynumber: 5.2 Consensus size: 88
3363166 AAGATTTATA
* * *
3363176 TCTTCGATCTACTTCATGCCGATACATTAAGACAAGATCTTCTACCCTTGATCTACTTCATGCCG
1 TCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
* *
3363241 ATACATGAAAATAAGATTCTTTT
66 ATACATGAAGACAAGATTCTTTT
3363264 TCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
1 TCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
*
3363329 ATACATGAAGACAAGATCCATTTT
66 ATACATGAAGACAAGATTC-TTTT
*
3363353 T-TTCGATCTACTTCACGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
1 TCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
* *
3363417 ATACATGAAGACAAGATCCGTTT
66 ATACATGAAGACAAGATTCTTTT
* * *
3363440 TCTTTGATCTACTTCACGCCAATACATGAAGACAATATCTTCTACCTTTGATCTACTTCATGCCG
1 TCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
3363505 ATACATGAAGACAAGA-TCTGTTT
66 ATACATGAAGACAAGATTCT-TTT
* * **
3363528 TCTTCGATCTACTTCATGCCAATACATGTAGACAAGATCTGCTACCTTTGATCTACTTCACACCG
1 TCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
*
3363593 ATACATGAAGACAAGA-TCTGCTT
66 ATACATGAAGACAAGATTCT-TTT
3363616 TCTTCGATCTACTTC
1 TCTTCGATCTACTTC
3363631 GCCCACCAGT
Statistics
Matches: 344, Mismatches: 20, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
87 5 0.01
88 334 0.97
89 5 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (88 bp):
TCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTTCTACCTTTGATCTACTTCATGCCG
ATACATGAAGACAAGATTCTTTT
Found at i:3363750 original size:44 final size:44
Alignment explanation
Indices: 3363176--3364004 Score: 587
Period size: 44 Copynumber: 18.9 Consensus size: 44
3363166 AAGATTTATA
* * * * *
3363176 TCTTCGATCTACTTCATGCCGATACATTAAGACAAGATCTTCTAC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCT-T
* * * * * *
3363221 CCTT-GATCTACTTCATGCCGATACATGAAAATAAGATTCT-TTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGA-TCTGCTT
* * *
3363264 TCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTTCTA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * ***
3363308 CCTTTGATCTACTTCATGCCGATACATGAAGACAAGATCCATTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * *
3363352 TTTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTTCTA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * * *
3363396 CCTTTGATCTACTTCATGCCGATACATGAAGACAAGATCCGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * *
3363440 TCTTTGATCTACTTCACGCCAATACATGAAGACAATATCTTCTA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * *
3363484 CCTTTGATCTACTTCATGCCGATACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * *
3363528 TCTTCGATCTACTTCATGCCAATACATGTAGACAAGATCTGCTA
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * *
3363572 CCTTTGATCTACTTCACACCGATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* *** *
3363616 TCTTCGATCTACTTCGC-CCACCAGTATGGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCACGCCA--A-TACATGAAGACAAGATCTGCTT
* * * * * * * *
3363662 TCTTCAATCCACTTCGCTACCAATATAGGAAGACAGGATTTGCTT
1 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTT
* * *
3363707 TCTTCGATCTACTTGACGCTAATACATGAAGATAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * **
3363751 TCTTTGATCTACTTCGC-CACTAATACGGGAAGACAAGA-------
1 TCTTCGATCTACTTCACGC-C-AATACATGAAGACAAGATCTGCTT
* * * * * *
3363789 TCTT-GAATCCACTTC-CTACCAATATAGGAAAAC-AGTATCTACTAT
1 TCTTCG-ATCTACTTCAC-GCCAATACATGAAGACAAG-ATCTGCT-T
*
3363834 T-TTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * *** * *
3363877 TCTTTGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTGC-A
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTT
* * * * * * *
3363921 CCTTCGATCCACTTC-CTACCAATATA-GAAAGACAGGACCTGCTA
1 TCTTCGATCTACTTCAC-GCCAATACATG-AAGACAAGATCTGCTT
*
3363965 TCTTCGATCTACTTCACACCAATACATGAAGACAAGATCT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT
3364005 ACTATTTTCA
Statistics
Matches: 621, Mismatches: 131, Indels: 65
0.76 0.16 0.08
Matches are distributed among these distances:
36 2 0.00
37 13 0.02
38 13 0.02
39 1 0.00
42 2 0.00
43 29 0.05
44 446 0.72
45 78 0.13
46 34 0.05
48 3 0.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (44 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
Found at i:3363907 original size:126 final size:126
Alignment explanation
Indices: 3363563--3364004 Score: 505
Period size: 126 Copynumber: 3.4 Consensus size: 126
3363553 ATGTAGACAA
* * *
3363563 GATCTGCTACCTTT-GATCTACTTCACACCGATACATGAAGACAAGATCTGCTTTCTTCGATCTA
1 GATCTGCTA-TTTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTTGATCTA
*
3363627 CTTCGCCCACCAGTATGGGAAGACAAGATCTGCTATCTTCAATCCACTTCGCTACCAATATAGGA
65 CTTCG-CCACCAGTATGGGAAGAC-A-A---G--ATCTTGAATCCACTTC-CTACCAATATAGGA
*
3363692 AGACAG
121 AAACAG
* * * * *
3363698 GATTTGCT-TTCTTCGATCTACTTGACGCTAATACATGAAGATAAGATCTGCTTTCTTTGATCTA
1 GATCTGCTATT-TTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTTGATCTA
* * *
3363762 CTTCGCCACTAATACGGGAAGACAAGATCTTGAATCCACTTCCTACCAATATAGGAAAACAG
65 CTTCGCCACCAGTATGGGAAGACAAGATCTTGAATCCACTTCCTACCAATATAGGAAAACAG
* * * *
3363824 TATCTACTATTTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGCTTTCTTTGATCTAC
1 GATCTGCTATTTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTTGATCTAC
*
3363889 TTCGCCACCAGTATGGGAAGATAAGATC-TGCACCTTCGATCCACTTCCTACCAATATA-GAAAG
66 TTCGCCACCAGTATGGGAAGACAAGATCTTG-A------ATCCACTTCCTACCAATATAGGAAA-
3363952 ACAG
123 ACAG
* *
3363956 GACCTGCTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCT
1 GATCTGCTATTTTCGATCTACTTCACACCAATACATGAAGACAAGATCT
3364005 ACTATTTTCA
Statistics
Matches: 268, Mismatches: 28, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
125 2 0.01
126 101 0.38
127 17 0.06
129 1 0.00
131 4 0.01
132 68 0.25
133 2 0.01
134 17 0.06
135 56 0.21
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (126 bp):
GATCTGCTATTTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTTGATCTAC
TTCGCCACCAGTATGGGAAGACAAGATCTTGAATCCACTTCCTACCAATATAGGAAAACAG
Found at i:3376461 original size:19 final size:19
Alignment explanation
Indices: 3376436--3376476 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3376426 AAATATACAA
3376436 ATATATAGAAAGAAAATAATT
1 ATATAT-GAAA-AAAATAATT
*
3376457 ATATATGAAAATAATAATT
1 ATATATGAAAAAAATAATT
3376476 A
1 A
3376477 CATTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 4 0.21
21 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (19 bp):
ATATATGAAAAAAATAATT
Found at i:3377691 original size:3 final size:3
Alignment explanation
Indices: 3377685--3377717 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3377675 GAAGAAAGTA
3377685 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
3377718 GTGAATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:3378741 original size:13 final size:13
Alignment explanation
Indices: 3378717--3378761 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
3378707 AAAGCACTCC
*
3378717 TCAAAAACACTTT
1 TCAAAAATACTTT
* *
3378730 TCCACAATACTTT
1 TCAAAAATACTTT
*
3378743 TTAAAAATACTTT
1 TCAAAAATACTTT
3378756 TCAAAA
1 TCAAAA
3378762 GCAATACTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (13 bp):
TCAAAAATACTTT
Found at i:3379450 original size:27 final size:27
Alignment explanation
Indices: 3379420--3379471 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
3379410 AAAGATTGTT
*
3379420 AAAACTCTTCTAAAAG-AAAACTCAAGA
1 AAAACTCTT-GAAAAGAAAAACTCAAGA
*
3379447 AAAATTCTTGAAAAGAAAAACTCAA
1 AAAACTCTTGAAAAGAAAAACTCAA
3379472 AGAGAATTCA
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:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (27 bp):
AAAACTCTTGAAAAGAAAAACTCAAGA
Found at i:3380529 original size:115 final size:114
Alignment explanation
Indices: 3380242--3380626 Score: 379
Period size: 115 Copynumber: 3.4 Consensus size: 114
3380232 AAAATAAGCA
* * * * * *
3380242 TTAGCGGCGATTTTAATAAAGCGCCGCTAATGATCAGGGCTTTAGCGGCGTTTTCGCG-AAAACG
1 TTAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTT-GAGTAAAGCG
* * * *
3380306 CCAC-AA-AAAACCTAATCCCAGCGACGCCGTTTAATGAG-CTTCGGGGCT
65 CCGCAAAGAAAACCTAAGCCCA-CGACGCCGTTTTATGAGCCTTTGGGGCT
* * * * * * * *
3380354 TTCGCGGCGTTTGTAAGT-AAGTGCCGCTGATG-TTCCGGGCTTTTGCGGTGTTTTCAGTAAAGC
1 TTAGCGGCGTTT-TTAGTAAAGCGCCGCTAATGCTT-AGGGCTTTAGCGGCGTTTTGAGTAAAGC
* *
3380417 GCCGCAAAGAAAACCTAAGCCCACTGACGCCGTTTTCTGAGCCTTTGGGTCT
64 GCCGCAAAGAAAACCTAAGCCCAC-GACGCCGTTTTATGAGCCTTTGGGGCT
* *
3380469 TTAGTGGCGTTTTTAGTAAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTGGGTAAAGCGC
1 TTAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTGAGTAAAGCGC
** * * * *
3380534 CGCAAAG-GGACCTAAGCCCGACGATGCCGTTTTATTAGCTTTTTGGGGAT
66 CGCAAAGAAAACCTAAGCCC-ACGACGCCGTTTTATGAGC-CTTTGGGGCT
* * *
3380584 TTAGTGGTGTTTTTAGTGAAGCGCCGCTAATGCTTAGGGCTTT
1 TTAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCTTAGGGCTTT
3380627 GGTCAAAGTT
Statistics
Matches: 223, Mismatches: 39, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
111 2 0.01
112 46 0.21
113 6 0.03
114 55 0.25
115 112 0.50
116 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (114 bp):
TTAGCGGCGTTTTTAGTAAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTGAGTAAAGCGC
CGCAAAGAAAACCTAAGCCCACGACGCCGTTTTATGAGCCTTTGGGGCT
Found at i:3381922 original size:21 final size:21
Alignment explanation
Indices: 3381896--3381941 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3381886 AACTTAAAGT
*
3381896 AGAGGCGGCAGCGAGGGAAGC
1 AGAGGCGGCAGCGAGAGAAGC
* * *
3381917 AGAGGCTGTAGCGAGAGAAGT
1 AGAGGCGGCAGCGAGAGAAGC
3381938 AGAG
1 AGAG
3381942 CAGAGCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.48, T:0.07
Consensus pattern (21 bp):
AGAGGCGGCAGCGAGAGAAGC
Found at i:3382325 original size:42 final size:42
Alignment explanation
Indices: 3382259--3382545 Score: 405
Period size: 42 Copynumber: 6.8 Consensus size: 42
3382249 GTTTTTATAT
* * * * *
3382259 AAAAGTGCCGCTAACGAACATGTTCTTTAGCAGTGCTTAGAA
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* * * * *
3382301 AAAAATACCGCTAAAGAACATGTTCTTTAGAGGTGCTTAGCA
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
3382343 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAA
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-AA
*
3382386 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
3382428 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
3382470 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTA-AGA
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGA-A
* * * *
3382512 ATAAACGCCGCTAAAGAACATGATCTTTAGCGGC
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGC
3382546 ATTTTTTTCT
Statistics
Matches: 226, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
41 1 0.00
42 184 0.81
43 41 0.18
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (42 bp):
AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:3382491 original size:127 final size:126
Alignment explanation
Indices: 3382265--3382545 Score: 436
Period size: 127 Copynumber: 2.2 Consensus size: 126
3382255 ATATAAAAGT
* * *
3382265 GCCGCTAACGAACATGTTCTTTAGCAGTGCTTAGAAAAAAATACCGCTAAAGAACATGTTCTTTA
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAATACCGCTAAAGAACATGTTCTTTA
* *
3382330 GAGGTGCTTAGCAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAAC
66 GAGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTA-AAAAAAAAC
* * *
3382392 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAATGCCGCTAAAGACCATGTTCTTTA
1 GCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAATACCGCTAAAGAACATGTTCTTTA
* * * *
3382457 GCGGCGCTTAGAAAAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAGAATAAAC
66 GAGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAAAAAAAAC
*
3382518 GCCGCTAAAGAACATGATCTTTAGCGGC
1 GCCGCTAAAGAACATGTTCTTTAGCGGC
3382546 ATTTTTTTCT
Statistics
Matches: 140, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
126 33 0.24
127 107 0.76
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (126 bp):
GCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAATACCGCTAAAGAACATGTTCTTTA
GAGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAAAAAAAAC
Found at i:3382559 original size:42 final size:42
Alignment explanation
Indices: 3382513--3382593 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
3382503 CGCTTAAGAA
3382513 TAAACGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTC
1 TAAACGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTC
* * *
3382555 TAAACGCCTCTAAAGAACATGGTCTTTAGCGGCGTTTTT
1 TAAACGCCGCTAAAGAACATGATCTTTAGCGGCATTTTT
3382594 GTTTGTAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (42 bp):
TAAACGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTC
Found at i:3382568 original size:84 final size:84
Alignment explanation
Indices: 3382265--3382588 Score: 339
Period size: 84 Copynumber: 3.8 Consensus size: 84
3382255 ATATAAAAGT
* * * **
3382265 GCCGCTAACGAACATGTTCTTTAGCAGTGC--TTAGAAAAAAATACCGCTAAAGAACATGTTCTT
1 GCCGCTAAAGACCATGTTCTTTAGC-G-GCATTTAAAAAAAAACGCCGCTAAAGAACATGTTCTT
* * *
3382328 TAGAGGTGCTTAGCAAAAAAC
64 TAGCGGCGCTTAGAAAAAAAC
** *
3382349 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGACCATGTTCTTT
1 GCCGCTAAAGACCATGTTCTTTAGCGGCATTTA-AAAAAAAACGCCGCTAAAGAACATGTTCTTT
*
3382414 AGCGGCGCTTAGAAAAAAAT
65 AGCGGCGCTTAGAAAAAAAC
** * * *
3382434 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAATGCCGCTAAAGACCATGTTCTTTA
1 GCCGCTAAAGACCATGTTCTTTAGCGGCATTTAAAAAAAAACGCCGCTAAAGAACATGTTCTTTA
*
3382499 GCGGCGCTTA-AGAATAAAC
66 GCGGCGCTTAGA-AAAAAAC
* * ****** * *
3382518 GCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTCTAAACGCCTCTAAAGAACATGGTCTTTA
1 GCCGCTAAAGACCATGTTCTTTAGCGGCATTTAAAAAAAAACGCCGCTAAAGAACATGTTCTTTA
3382583 GCGGCG
66 GCGGCG
3382589 TTTTTGTTTG
Statistics
Matches: 208, Mismatches: 28, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
82 2 0.01
83 2 0.01
84 128 0.62
85 76 0.37
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.25
Consensus pattern (84 bp):
GCCGCTAAAGACCATGTTCTTTAGCGGCATTTAAAAAAAAACGCCGCTAAAGAACATGTTCTTTA
GCGGCGCTTAGAAAAAAAC
Found at i:3383824 original size:55 final size:53
Alignment explanation
Indices: 3383722--3383824 Score: 122
Period size: 55 Copynumber: 1.9 Consensus size: 53
3383712 GTTTAAGACT
* *
3383722 TTAGGTTTAGAGTTAGGGTTCATGATTTAGGTTTGGATGTTATGGTTTAGGGG
1 TTAGGTTTAGAGTTAGGGTTCATGATTTAGGTTTGCATGTTAGGGTTTAGGGG
3383775 TTAGTGTTTAAGAGTTAGGG-TCGA-GAATTTAGGTTT-CATGTTTAGGGTTT
1 TTAG-GTTT-AGAGTTAGGGTTC-ATG-ATTTAGGTTTGCATG-TTAGGGTTT
3383825 GAAGTTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
53 4 0.09
54 10 0.23
55 29 0.67
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.44
Consensus pattern (53 bp):
TTAGGTTTAGAGTTAGGGTTCATGATTTAGGTTTGCATGTTAGGGTTTAGGGG
Found at i:3383881 original size:7 final size:7
Alignment explanation
Indices: 3383871--3383896 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3383861 AGGTTTAGGG
3383871 TTTAGAA
1 TTTAGAA
3383878 TTTAGAA
1 TTTAGAA
3383885 TTTAGAA
1 TTTAGAA
3383892 TTTAG
1 TTTAG
3383897 GTGTCAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (7 bp):
TTTAGAA
Found at i:3383881 original size:14 final size:14
Alignment explanation
Indices: 3383864--3383897 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3383854 TGGTTCAAGG
*
3383864 TTTAGGGTTTAGAA
1 TTTAGGATTTAGAA
*
3383878 TTTAGAATTTAGAA
1 TTTAGGATTTAGAA
3383892 TTTAGG
1 TTTAGG
3383898 TGTCAATGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
TTTAGGATTTAGAA
Found at i:3383937 original size:13 final size:14
Alignment explanation
Indices: 3383892--3383938 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3383882 GAATTTAGAA
3383892 TTTAGGTGTCAATG
1 TTTAGGTGTCAATG
* *
3383906 TTTTGAGT-TCAAGG
1 TTTAG-GTGTCAATG
3383920 TTTAGGTGTC-ATG
1 TTTAGGTGTCAATG
3383933 TTTAGG
1 TTTAGG
3383939 GTTTGCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
13 10 0.37
14 15 0.56
15 2 0.07
ACGTcount: A:0.19, C:0.06, G:0.30, T:0.45
Consensus pattern (14 bp):
TTTAGGTGTCAATG
Found at i:3384183 original size:14 final size:15
Alignment explanation
Indices: 3384164--3384206 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
3384154 GGGCTTCGAA
* *
3384164 TTTTGAGTTTTGTG-
1 TTTTGAGTTTCGGGC
3384178 TTTTGAGTTTCGGGC
1 TTTTGAGTTTCGGGC
3384193 TTTTGAGTTTCGGG
1 TTTTGAGTTTCGGG
3384207 TTTCAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.07, C:0.07, G:0.33, T:0.53
Consensus pattern (15 bp):
TTTTGAGTTTCGGGC
Found at i:3384198 original size:15 final size:14
Alignment explanation
Indices: 3384164--3384209 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
3384154 GGGCTTCGAA
* *
3384164 TTTTGAGTTTTGTG
1 TTTTGAGTTTCGGG
3384178 TTTTGAGTTTCGGG
1 TTTTGAGTTTCGGG
3384192 CTTTTGAGTTTCGGG
1 -TTTTGAGTTTCGGG
3384207 TTT
1 TTT
3384210 CAAGTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 15 0.52
15 14 0.48
ACGTcount: A:0.07, C:0.07, G:0.30, T:0.57
Consensus pattern (14 bp):
TTTTGAGTTTCGGG
Found at i:3384277 original size:28 final size:27
Alignment explanation
Indices: 3384226--3384344 Score: 89
Period size: 28 Copynumber: 4.3 Consensus size: 27
3384216 TTTATTTAGA
**
3384226 GGTTTA-GTTTAAGGTTTTGGGGTTTAT
1 GGTTTATGTTTAATATTTT-GGGTTTAT
3384253 GGTTTATGGTTTAATATTTTGGGTTTAT
1 GGTTTAT-GTTTAATATTTTGGGTTTAT
** * *
3384281 GGTTTCAAT-TTTAAGGTTTTGGGCTTAA
1 GGTTT--ATGTTTAATATTTTGGGTTTAT
* * * *
3384309 GGTCTCATGTTTCATATTTTGGATTTAG
1 GGT-TTATGTTTAATATTTTGGGTTTAT
3384337 GGTTTATG
1 GGTTTATG
3384345 GGTTTAGGTT
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
27 12 0.17
28 47 0.65
29 11 0.15
30 2 0.03
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.51
Consensus pattern (27 bp):
GGTTTATGTTTAATATTTTGGGTTTAT
Found at i:3384298 original size:21 final size:21
Alignment explanation
Indices: 3384248--3384299 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3384238 GGTTTTGGGG
*
3384248 TTTATGGTTTATGGTTTAATA
1 TTTAAGGTTTATGGTTTAATA
**
3384269 TTTTGGGTTTATGGTTTCAAT-
1 TTTAAGGTTTATGGTTT-AATA
3384290 TTTAAGGTTT
1 TTTAAGGTTT
3384300 TGGGCTTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.58
Consensus pattern (21 bp):
TTTAAGGTTTATGGTTTAATA
Found at i:3384391 original size:49 final size:49
Alignment explanation
Indices: 3384305--3384403 Score: 116
Period size: 49 Copynumber: 2.0 Consensus size: 49
3384295 GGTTTTGGGC
*
3384305 TTAAGGTCTCATGTTTCATATTTTGGATTTAGGGTTTATGGGTTTA-GGT
1 TTAAGGTCTCATGTTTCATATTTTGGATTTAGAGTTTA-GGGTTTATGGT
*
3384354 TTAAGGAT-TCATGTTTC-TAGTTTT-GATTTTTGAGTTTAGGGTTTATGGT
1 TTAAGG-TCTCATGTTTCATA-TTTTGGA-TTTAGAGTTTAGGGTTTATGGT
3384403 T
1 T
3384404 GTTAGAATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
48 11 0.25
49 32 0.73
50 1 0.02
ACGTcount: A:0.18, C:0.05, G:0.25, T:0.52
Consensus pattern (49 bp):
TTAAGGTCTCATGTTTCATATTTTGGATTTAGAGTTTAGGGTTTATGGT
Found at i:3384865 original size:28 final size:29
Alignment explanation
Indices: 3384834--3384888 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
3384824 AGATATATAT
* *
3384834 TTTAATATTTAAGGTTTAG-GGTTCAATA
1 TTTAATATTAAAAGTTTAGTGGTTCAATA
3384862 TTTAATATTAAAAGTTTAGTGGTTCAA
1 TTTAATATTAAAAGTTTAGTGGTTCAA
3384889 CAACCACTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (29 bp):
TTTAATATTAAAAGTTTAGTGGTTCAATA
Found at i:3385418 original size:29 final size:29
Alignment explanation
Indices: 3385362--3385420 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3385352 CTATTTATTC
** ***
3385362 ATGTATTTTATCTTAATTTTTTTCACAGA
1 ATGTATTTTATCTTAATTGGTAAAACAGA
3385391 ATGTATTTTATCTTAATTGGTAAAACAGA
1 ATGTATTTTATCTTAATTGGTAAAACAGA
3385420 A
1 A
3385421 AAGGTTTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.47
Consensus pattern (29 bp):
ATGTATTTTATCTTAATTGGTAAAACAGA
Found at i:3385780 original size:17 final size:18
Alignment explanation
Indices: 3385753--3385793 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
3385743 TAAAATTTAA
*
3385753 AAAAATAATAACAAATTT
1 AAAAATAATAAAAAATTT
3385771 AAAAAT-ATAAAAAATTT
1 AAAAATAATAAAAAATTT
*
3385788 CAAAAT
1 AAAAAT
3385794 TCAATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAATAATAAAAAATTT
Found at i:3386128 original size:22 final size:23
Alignment explanation
Indices: 3386075--3386130 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
3386065 CCTGTTTTTA
* * *
3386075 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
3386098 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
3386120 ATTAAAATTAA
1 ATTAAAATTAA
3386131 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:3386143 original size:16 final size:16
Alignment explanation
Indices: 3386106--3386145 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3386096 TTAATAAAAT
* *
3386106 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
3386122 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
3386138 TAAAATTA
1 TAAAATTA
3386146 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:3386224 original size:59 final size:61
Alignment explanation
Indices: 3386155--3386334 Score: 265
Period size: 68 Copynumber: 2.9 Consensus size: 61
3386145 ATCAAATTAT
*
3386155 TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A
3386220 TTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC-A
1 -TAA-T-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
*
3386283 -AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
3386335 ACAAACTTGA
Statistics
Matches: 110, Mismatches: 2, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
59 48 0.44
60 1 0.01
61 2 0.02
63 1 0.01
66 3 0.03
67 1 0.01
68 54 0.49
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (61 bp):
TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
Found at i:3386251 original size:9 final size:9
Alignment explanation
Indices: 3386218--3386245 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3386208 TTTATCAAAT
3386218 TATTAATTG
1 TATTAATTG
3386227 TATTAATTG
1 TATTAATTG
3386236 TATTAATTG
1 TATTAATTG
3386245 T
1 T
3386246 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:3386255 original size:68 final size:68
Alignment explanation
Indices: 3386134--3386304 Score: 319
Period size: 68 Copynumber: 2.5 Consensus size: 68
3386124 AAATTAATTG
*
3386134 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
3386197 TGA
66 TGA
3386200 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
3386265 TGA
66 TGA
3386268 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
3386305 TGTAACAAAA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 26 0.25
68 76 0.75
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:3386441 original size:22 final size:24
Alignment explanation
Indices: 3386401--3386444 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3386391 AAATAAACTT
3386401 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
3386425 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
3386445 AATATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:3387511 original size:19 final size:19
Alignment explanation
Indices: 3387467--3387539 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
3387457 AGAATTTTTG
3387467 TTTTTTAAAATATTTTT-TT
1 TTTTTTAAAA-ATTTTTATT
** *
3387486 GAATTTTAAAGATTTTTATT
1 -TTTTTTAAAAATTTTTATT
3387506 TTTTTTCAAAAATTTTTATT
1 TTTTTT-AAAAATTTTTATT
*
3387526 TTATTTAAAAATTT
1 TTTTTTAAAAATTT
3387540 ATAATTTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 18 0.41
20 26 0.59
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTTTAAAAATTTTTATT
Found at i:3390238 original size:27 final size:28
Alignment explanation
Indices: 3390188--3390285 Score: 155
Period size: 28 Copynumber: 3.5 Consensus size: 28
3390178 AATAAAAAAA
*
3390188 TTACCAAAATGT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAA-TTTTTTTTAT
3390216 TTACCAAAATATATATAATTTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTTAT
*
3390244 TTACCAAAATATATAT-ATATTTTTTAT
1 TTACCAAAATATATATAATTTTTTTTAT
3390271 TTACCAAAATATATA
1 TTACCAAAATATATA
3390286 AAAAACTAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
27 25 0.37
28 37 0.55
29 5 0.07
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (28 bp):
TTACCAAAATATATATAATTTTTTTTAT
Found at i:3390462 original size:18 final size:17
Alignment explanation
Indices: 3390439--3390596 Score: 77
Period size: 18 Copynumber: 9.4 Consensus size: 17
3390429 GAATGAGAGG
3390439 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
3390457 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
3390474 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
3390490 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
** *
3390508 GGAAAGAAAAGGAAAGGGGA
1 GG-AAG-AAA-GAAAAAGAA
*
3390528 GGAAAGAAAGAAAAATAA
1 GG-AAGAAAGAAAAAGAA
*
3390546 -G--GAAAGAAAAGGAAA
1 GGAAGAAAGAAAAAG-AA
3390561 GG-AGAAGAGAAAAA-AA
1 GGAAGAA-AGAAAAAGAA
*
3390577 --AAGAAAGAATAAGAA
1 GGAAGAAAGAAAAAGAA
3390592 -GAAGA
1 GGAAGA
3390597 CGGAAGGAAG
Statistics
Matches: 111, Mismatches: 15, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
14 15 0.14
15 17 0.15
16 11 0.10
17 8 0.07
18 28 0.25
19 20 0.18
20 12 0.11
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.01
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:3390472 original size:10 final size:10
Alignment explanation
Indices: 3390441--3390512 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
3390431 ATGAGAGGGG
*
3390441 AAGAAGAAGA
1 AAGAAAAAGA
3390451 AAGAAAGGAAGA
1 AAGAAA--AAGA
3390463 AAGAAAAAGA
1 AAGAAAAAGA
* *
3390473 AGGAAAAGGA
1 AAGAAAAAGA
3390483 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
3390497 AAGAAAAAGA
1 AAGAAAAAGA
*
3390507 AGGAAA
1 AAGAAA
3390513 GAAAAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:3390472 original size:22 final size:23
Alignment explanation
Indices: 3390441--3390542 Score: 73
Period size: 24 Copynumber: 4.3 Consensus size: 23
3390431 ATGAGAGGGG
*
3390441 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
3390463 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
3390485 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
* ***
3390511 AAGAAAAGGAAAGGGGAGGAAAGA
1 AAGAAAAAGAAAGAAAAGG-AAGA
3390535 AAGAAAAA
1 AAGAAAAA
3390543 TAAGGAAAGA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
22 12 0.20
23 10 0.17
24 32 0.53
25 5 0.08
26 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:3390495 original size:38 final size:38
Alignment explanation
Indices: 3390459--3390581 Score: 168
Period size: 38 Copynumber: 3.4 Consensus size: 38
3390449 GAAAGAAAGG
3390459 AAGAAAGAAAAAGAA-G---GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
*
3390493 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
*
3390531 AAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGA--A
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
* *
3390567 GAGAAAAAAAAAGAA
1 AAGAAAGAAAAAGAA
3390582 AGAATAAGAA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
34 15 0.19
35 1 0.01
36 13 0.16
38 50 0.63
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (38 bp):
AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
Found at i:3390499 original size:28 final size:28
Alignment explanation
Indices: 3390444--3390523 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
3390434 AGAGGGGAAG
3390444 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
3390469 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G-AA--A-AGGAAAGAAAGAAA
3390503 AAGAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAGAAAAGGAAAG
3390524 GGGAGGAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 3 0.07
28 8 0.17
29 1 0.02
30 1 0.02
31 2 0.04
32 2 0.04
33 6 0.13
34 17 0.37
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:3390519 original size:10 final size:10
Alignment explanation
Indices: 3390461--3390585 Score: 82
Period size: 10 Copynumber: 12.7 Consensus size: 10
3390451 AAGAAAGGAA
*
3390461 GAAAGAAAAA
1 GAAAGAAAAG
*
3390471 GAAGGAAAAG
1 GAAAGAAAAG
* *
3390481 GAAAGGAGAG
1 GAAAGAAAAG
3390491 GAAAG-AAA-
1 GAAAGAAAAG
3390499 GAAA-AAGAAG
1 GAAAGAA-AAG
3390509 GAAAGAAAAG
1 GAAAGAAAAG
***
3390519 GAAAGGGGAG
1 GAAAGAAAAG
3390529 GAAAG-AAA-
1 GAAAGAAAAG
3390537 GAAA-AATAAG
1 GAAAGAA-AAG
3390547 GAAAGAAAAG
1 GAAAGAAAAG
*
3390557 GAAAGGAGAAG
1 GAAA-GAAAAG
* *
3390568 AGAAAAAAAAA
1 -GAAAGAAAAG
3390579 GAAAGAA
1 GAAAGAA
3390586 TAAGAAGAAG
Statistics
Matches: 89, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
8 10 0.11
9 7 0.08
10 56 0.63
11 12 0.13
12 4 0.04
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:3391336 original size:18 final size:18
Alignment explanation
Indices: 3391296--3391346 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
3391286 AAAATATATA
** *
3391296 TAATATTTTGGTATTTTTT
1 TAATATTTTATTA-TTTTG
3391315 TAATATTTTATTATTTTG
1 TAATATTTTATTATTTTG
3391333 TAATATTTTATTAT
1 TAATATTTTATTAT
3391347 GGGTTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 18 0.62
19 11 0.38
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (18 bp):
TAATATTTTATTATTTTG
Found at i:3391413 original size:28 final size:27
Alignment explanation
Indices: 3391382--3391446 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
3391372 AAATAAAAAA
3391382 TTACCAAAATAT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAA--TTTTTTTAT
*
3391410 TTACCAAAAAATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
3391437 TTACCAAAAT
1 TTACCAAAAT
3391447 GTATCAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 18 0.53
28 11 0.32
29 5 0.15
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.48
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:3392799 original size:17 final size:17
Alignment explanation
Indices: 3392777--3392813 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3392767 ATAGGGTAAG
3392777 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
3392794 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
3392811 ATG
1 ATG
3392814 ACATCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:3393782 original size:14 final size:14
Alignment explanation
Indices: 3393763--3393791 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3393753 TTTTTGTATC
3393763 AATTTAATTATTCT
1 AATTTAATTATTCT
3393777 AATTTAATTATTCT
1 AATTTAATTATTCT
3393791 A
1 A
3393792 TTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:3396199 original size:17 final size:17
Alignment explanation
Indices: 3396177--3396209 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3396167 CAATGATCGC
*
3396177 CACCACCTTCTTCTTCG
1 CACCACATTCTTCTTCG
3396194 CACCACATTCTTCTTC
1 CACCACATTCTTCTTC
3396210 ACCACCAACC
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:0.15, C:0.45, G:0.03, T:0.36
Consensus pattern (17 bp):
CACCACATTCTTCTTCG
Found at i:3396974 original size:3 final size:3
Alignment explanation
Indices: 3396966--3396991 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3396956 CTTAATACCT
3396966 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
3396992 CTATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3397178 original size:11 final size:11
Alignment explanation
Indices: 3397162--3397197 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
3397152 AAATACCTTA
3397162 TTTTTCTCTTC
1 TTTTTCTCTTC
3397173 TTTTTCTC-TC
1 TTTTTCTCTTC
3397183 -TTTTCTCTT-
1 TTTTTCTCTTC
3397192 TTTTTC
1 TTTTTC
3397198 CGCAGCACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 7 0.30
10 8 0.35
11 8 0.35
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTCTCTTC
Found at i:3397320 original size:27 final size:27
Alignment explanation
Indices: 3397301--3397381 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
3397291 TGGTTGGTAG
3397301 GACTGGTGCCGCCAACCTGGTTCCCTC
1 GACTGGTGCCGCCAACCTGGTTCCCTC
* *
3397328 GACTGGTGCCGCCAACCTGCTTCCCTT
1 GACTGGTGCCGCCAACCTGGTTCCCTC
** *
3397355 GTTTGGTGCCGCCAACCTGCTTCCCTC
1 GACTGGTGCCGCCAACCTGGTTCCCTC
3397382 CACCCAGGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.10, C:0.41, G:0.23, T:0.26
Consensus pattern (27 bp):
GACTGGTGCCGCCAACCTGGTTCCCTC
Found at i:3397436 original size:8 final size:8
Alignment explanation
Indices: 3397425--3397462 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
3397415 TTTTTTCTGG
3397425 TTTTTATT
1 TTTTTATT
3397433 TTTTTATT
1 TTTTTATT
*
3397441 TTTTTAGT
1 TTTTTATT
3397449 TTTTTAGTT
1 TTTTTA-TT
3397458 TTTTT
1 TTTTT
3397463 TGATATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (8 bp):
TTTTTATT
Found at i:3397521 original size:27 final size:27
Alignment explanation
Indices: 3397465--3397521 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
3397455 GTTTTTTTTG
**
3397465 ATATATTTTGGTAAATAAAAAATTTAT
1 ATATATTTTGGTAAATAAAAAAGGTAT
3397492 ATATATTTTGGTAAATAAAAAAAGGT-T
1 ATATATTTTGGTAAAT-AAAAAAGGTAT
3397519 ATA
1 ATA
3397522 ACATTTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (27 bp):
ATATATTTTGGTAAATAAAAAAGGTAT
Found at i:3397527 original size:28 final size:27
Alignment explanation
Indices: 3397469--3397529 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
3397459 TTTTTGATAT
* *
3397469 ATTTTGGTAAATAAAAAATTTATATAT
1 ATTTTGGTAAATAAAAAAGTTATATAC
3397496 ATTTTGGTAAATAAAAAAAGGTTATA-AC
1 ATTTTGGTAAAT-AAAAAA-GTTATATAC
3397524 ATTTTG
1 ATTTTG
3397530 ATAATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 12 0.40
28 13 0.43
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (27 bp):
ATTTTGGTAAATAAAAAAGTTATATAC
Found at i:3400025 original size:16 final size:15
Alignment explanation
Indices: 3400003--3400042 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
3399993 TACTTCAATC
3400003 AATTTTAATTTTTATA
1 AATTTTAATTTTTA-A
* *
3400019 TATTTTAAATTTTAA
1 AATTTTAATTTTTAA
3400034 AATTTTAAT
1 AATTTTAAT
3400043 CTTAATCCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTTTAATTTTTAA
Found at i:3413060 original size:18 final size:18
Alignment explanation
Indices: 3413023--3413076 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
3413013 ATAACAAAAC
*
3413023 AATTCAAAATAATTTTTAA
1 AATTCAAAAT-ATTTATAA
3413042 AATTCAAAATATTTATAA
1 AATTCAAAATATTTATAA
*
3413060 AAGTTCTAAA-ATTTATA
1 AA-TTCAAAATATTTATA
3413077 TTTTTTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:3413718 original size:19 final size:19
Alignment explanation
Indices: 3413691--3413728 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3413681 CACTGTAATG
3413691 TTGGCTTAATACCTTTCTT
1 TTGGCTTAATACCTTTCTT
*
3413710 TTGGTTTAATACCTTTCTT
1 TTGGCTTAATACCTTTCTT
3413729 GGATGAATCT
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:0.16, C:0.18, G:0.11, T:0.55
Consensus pattern (19 bp):
TTGGCTTAATACCTTTCTT
Found at i:3413978 original size:17 final size:17
Alignment explanation
Indices: 3413952--3413984 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3413942 AGCTTGCGAA
*
3413952 ATTGGGGTCATTTCAAC
1 ATTGGAGTCATTTCAAC
3413969 ATTGGAGTCATTTCAA
1 ATTGGAGTCATTTCAA
3413985 AAATAAGGAG
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:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (17 bp):
ATTGGAGTCATTTCAAC
Found at i:3417011 original size:19 final size:19
Alignment explanation
Indices: 3416989--3417025 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3416979 TAAAAATGCA
3416989 AAAAAAATCCC-TAATATTT
1 AAAAAAA-CCCATAATATTT
3417008 AAAAAAACCCATAATATT
1 AAAAAAACCCATAATATT
3417026 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAAAACCCATAATATTT
Found at i:3419849 original size:12 final size:12
Alignment explanation
Indices: 3419834--3419864 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3419824 GGAGACAAAG
3419834 AAGAAAATTGAA
1 AAGAAAATTGAA
3419846 AAGAAAATTGAA
1 AAGAAAATTGAA
3419858 AAGAAAA
1 AAGAAAA
3419865 CAATTTGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (12 bp):
AAGAAAATTGAA
Found at i:3420850 original size:24 final size:24
Alignment explanation
Indices: 3420818--3420865 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3420808 AATTTTGGAA
*
3420818 TTTCAATCTTCTCCTAGTTAAACT
1 TTTCAATCTTCTCCAAGTTAAACT
* *
3420842 TTTCTATCTTTTCCAAGTTAAACT
1 TTTCAATCTTCTCCAAGTTAAACT
3420866 CTGATTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.23, G:0.04, T:0.48
Consensus pattern (24 bp):
TTTCAATCTTCTCCAAGTTAAACT
Found at i:3424999 original size:22 final size:22
Alignment explanation
Indices: 3424960--3425004 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3424950 AAGTTGGTCC
3424960 TTAAAATTCAAAATATT-ATAT
1 TTAAAATTCAAAATATTAATAT
* *
3424981 TTAAATATTTAAAGTATTAATAT
1 TTAAA-ATTCAAAATATTAATAT
3425004 T
1 T
3425005 GTACTAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 10 0.50
23 5 0.25
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAAAATTCAAAATATTAATAT
Found at i:3435666 original size:40 final size:40
Alignment explanation
Indices: 3435603--3435694 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 40
3435593 TGTTATCTAT
* *
3435603 TAGGCTTTATGCCGATGTATTTATCAAGCTTTGTGCCTAA
1 TAGGCTTTGTGCCGATGTATTTATCAAGCTTTATGCCTAA
* *** *
3435643 TAGGCTTTGTGCC-AGTGTGTTTATTGGGCTTTATGCCTAG
1 TAGGCTTTGTGCCGA-TGTATTTATCAAGCTTTATGCCTAA
*
3435683 CAGGCTTTGTGC
1 TAGGCTTTGTGC
3435695 TGGTGTTGTC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 1 0.02
40 42 0.98
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.40
Consensus pattern (40 bp):
TAGGCTTTGTGCCGATGTATTTATCAAGCTTTATGCCTAA
Found at i:3439710 original size:29 final size:29
Alignment explanation
Indices: 3439678--3439763 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 29
3439668 TGTGGTGAAC
* * *
3439678 CTCTAAAAAGAAACACCTTTGTGGCAAAA
1 CTCTAAAAGGAAACGCCTTTATGGCAAAA
* * *
3439707 CTCTGGAAAGGTAA-GCCTTTATGGCGAAA
1 CTCT-AAAAGGAAACGCCTTTATGGCAAAA
3439736 CTCTAAAAGGAAACGCCTTTATGGCAAA
1 CTCTAAAAGGAAACGCCTTTATGGCAAA
3439764 TTTCTGTCAA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 7 0.15
29 33 0.72
30 6 0.13
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (29 bp):
CTCTAAAAGGAAACGCCTTTATGGCAAAA
Done.