Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 161 of 193
Found at i:49774021 original size:18 final size:18
Alignment explanation
Indices: 49773974--49774022 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
49773964 GGTTTAAGTT
49773974 AATTCTAAATTTATTTACA
1 AATT-TAAATTTATTTACA
**
49773993 AATTTGGATTTATCTTA-A
1 AATTTAAATTTAT-TTACA
49774011 AATTTAAATTTA
1 AATTTAAATTTA
49774023 AATCAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (18 bp):
AATTTAAATTTATTTACA
Found at i:49774134 original size:14 final size:14
Alignment explanation
Indices: 49774115--49774163 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
49774105 AAGGCCCAAT
49774115 AGGCCCAATTACAA
1 AGGCCCAATTACAA
*
49774129 AGGCCCAAAT-CAA
1 AGGCCCAATTACAA
*
49774142 AGGCCCACTTACAA
1 AGGCCCAATTACAA
*
49774156 TGGCCCAA
1 AGGCCCAA
49774164 ATAGACCCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.39, C:0.33, G:0.16, T:0.12
Consensus pattern (14 bp):
AGGCCCAATTACAA
Found at i:49774709 original size:7 final size:7
Alignment explanation
Indices: 49774694--49774754 Score: 58
Period size: 7 Copynumber: 9.3 Consensus size: 7
49774684 TAAAAATATT
*
49774694 ATTAGTA
1 ATTAATA
49774701 ATTAATA
1 ATTAATA
49774708 ATT-ATA
1 ATTAATA
49774714 ATTAAT-
1 ATTAATA
* *
49774720 ATTTATG
1 ATTAATA
49774727 ATT-ATA
1 ATTAATA
*
49774733 GTTAAT-
1 ATTAATA
49774739 ATTAATA
1 ATTAATA
49774746 ATTAATA
1 ATTAATA
49774753 AT
1 AT
49774755 ATTAAAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
6 20 0.44
7 25 0.56
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (7 bp):
ATTAATA
Found at i:49774717 original size:13 final size:13
Alignment explanation
Indices: 49774694--49774754 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
49774684 TAAAAATATT
49774694 ATTAGTAATTAATA
1 ATTA-TAATTAATA
49774708 ATTATAATTAATA
1 ATTATAATTAATA
* *
49774721 TTTATGATT-ATA
1 ATTATAATTAATA
*
49774733 GTTA-ATATTAATA
1 ATTATA-ATTAATA
49774746 ATTAATAAT
1 ATT-ATAAT
49774755 ATTAAAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
12 9 0.24
13 21 0.55
14 7 0.18
15 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (13 bp):
ATTATAATTAATA
Found at i:49774749 original size:19 final size:19
Alignment explanation
Indices: 49774701--49774754 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
49774691 ATTATTAGTA
49774701 ATTAATAATTATAATTAAT
1 ATTAATAATTATAATTAAT
* * *
49774720 ATTTATGATTATAGTTAAT
1 ATTAATAATTATAATTAAT
49774739 ATTAATAATTAATAAT
1 ATTAATAATT-ATAAT
49774755 ATTAAAATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
ATTAATAATTATAATTAAT
Found at i:49775677 original size:161 final size:161
Alignment explanation
Indices: 49775507--49776004 Score: 784
Period size: 161 Copynumber: 3.1 Consensus size: 161
49775497 TCTTTTCAAT
* * *
49775507 TTAGTCCTTTGACTGTTTGACTGTACCAGAGGTTGCCACGTGTCATTTTTGGATTATTTATGCAT
1 TTAGTCCTTTGACTGTTTGATTGTACCAGAGGCTGCCACGTGTCATTTTTGGCTTATTTATGCAT
* *** * * *
49775572 TTAGTCCCTGACATTTTTGATTTATTTTAATTTAATCCTCAAATCAACTTTTATTAAATTACGAA
66 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTAAATTACGAA
49775637 ATTGGCCCAAGAATTTTTCATGGTTTATAAA
131 ATTGGCCCAAGAATTTTTCATGGTTTATAAA
* *
49775668 TTAGTCCTTTGACTGTTTGATTGTACCAGAAGCTGCCACGTCTCATTTTTGGCTTATTTATGCAT
1 TTAGTCCTTTGACTGTTTGATTGTACCAGAGGCTGCCACGTGTCATTTTTGGCTTATTTATGCAT
49775733 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTAAATTACGAA
66 TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTAAATTACGAA
49775798 ATTGGCCCAAGAA-TTTTCATGGTTTATAAA
131 ATTGGCCCAAGAATTTTTCATGGTTTATAAA
49775828 TTAGTCCTTTGACTGTTTGATTGTACCAG-GAGCTGCCACGTGTCATTTTTTGGCTTATTTATGC
1 TTAGTCCTTTGACTGTTTGATTGTACCAGAG-GCTGCCACGTGTCA-TTTTTGGCTTATTTATGC
* * *
49775892 ATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTGTTTAATTACA
64 ATTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTAAATTACG
* * * *
49775957 AAATTGGCCCAAGAATTTTTCAAGATTTACAAC
129 AAATTGGCCCAAGAATTTTTCATGGTTTATAAA
*
49775990 TTAATCCTTTGACTG
1 TTAGTCCTTTGACTG
49776005 CTAGATGCCT
Statistics
Matches: 312, Mismatches: 22, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
160 59 0.19
161 226 0.72
162 27 0.09
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (161 bp):
TTAGTCCTTTGACTGTTTGATTGTACCAGAGGCTGCCACGTGTCATTTTTGGCTTATTTATGCAT
TTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTAAATTACGAA
ATTGGCCCAAGAATTTTTCATGGTTTATAAA
Found at i:49776139 original size:29 final size:28
Alignment explanation
Indices: 49776106--49776300 Score: 112
Period size: 29 Copynumber: 6.7 Consensus size: 28
49776096 AAAGTTTTAG
*
49776106 AAAATTACCATTTTACCCTCGAATCTTCT
1 AAAATTACCATTTTACCC-CGAATCTTCA
* * **
49776135 AAAATT-CCGTTTTTAACCCCGATTTCACCA
1 AAAATTACC-ATTTT-ACCCCGA-ATCTTCA
*
49776165 AAAATTACCATTTTACCCCCGAATCTTCC
1 AAAATTACCATTTTA-CCCCGAATCTTCA
* **
49776194 AAAATT-CCATTTTTAACCCCGATTTCACCA
1 AAAATTACCA-TTTT-ACCCCGA-ATCTTCA
* **
49776224 AAAATTACCATTTTACCCCCGTATCTTTT
1 AAAATTACCATTTTA-CCCCGAATCTTCA
*
49776253 AAAATT-CCATTTTTAACCTCG-AT-TTCA
1 AAAATTACCA-TTTT-ACCCCGAATCTTCA
*
49776280 CCAAAATCACCATTTTACCCC
1 --AAAATTACCATTTTACCCC
49776301 CGGGTATCCA
Statistics
Matches: 126, Mismatches: 25, Indels: 31
0.69 0.14 0.17
Matches are distributed among these distances:
27 2 0.02
28 14 0.11
29 59 0.47
30 46 0.37
31 5 0.04
ACGTcount: A:0.31, C:0.30, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCGAATCTTCA
Found at i:49776179 original size:30 final size:29
Alignment explanation
Indices: 49776145--49776302 Score: 139
Period size: 29 Copynumber: 5.4 Consensus size: 29
49776135 AAAATTCCGT
49776145 TTTTAACCCCGATTTCACCAAAAATTACCA
1 TTTTAACCCCGATTTCACC-AAAATTACCA
*
49776175 TTTTACCCCCGAATCTT--CCAAAATT-CCA
1 TTTTAACCCCG-AT-TTCACCAAAATTACCA
49776203 TTTTTAACCCCGATTTCACCAAAAATTACCA
1 -TTTTAACCCCGATTTCACC-AAAATTACCA
* **
49776234 TTTTACCCCCGTATCTT--TTAAAATT-CCA
1 TTTTAACCCCG-AT-TTCACCAAAATTACCA
* *
49776262 TTTTTAACCTCGATTTCACCAAAATCACCA
1 -TTTTAACCCCGATTTCACCAAAATTACCA
*
49776292 TTTTACCCCCG
1 TTTTAACCCCG
49776303 GGTATCCACA
Statistics
Matches: 103, Mismatches: 12, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
27 4 0.04
28 10 0.10
29 47 0.46
30 31 0.30
31 7 0.07
32 4 0.04
ACGTcount: A:0.30, C:0.32, G:0.04, T:0.34
Consensus pattern (29 bp):
TTTTAACCCCGATTTCACCAAAATTACCA
Found at i:49776198 original size:59 final size:59
Alignment explanation
Indices: 49776106--49776302 Score: 324
Period size: 59 Copynumber: 3.4 Consensus size: 59
49776096 AAAGTTTTAG
* *
49776106 AAAATTACCATTTTACCCTCGAATCTTCTAAAATTCCGTTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
*
49776165 AAAATTACCATTTTACCCCCGAATCTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
49776224 AAAATTACCATTTTACCCCCGTATCTTTTAAAATTCCATTTTTAACCTCGATTTCACC-
1 AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
*
49776282 AAAATCACCATTTTACCCCCG
1 AAAATTACCATTTTACCCCCG
49776303 GGTATCCACA
Statistics
Matches: 130, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
58 20 0.15
59 110 0.85
ACGTcount: A:0.31, C:0.30, G:0.04, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:49781186 original size:29 final size:29
Alignment explanation
Indices: 49781128--49781186 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
49781118 GAATTAGAGG
* *
49781128 AGAGTAAAAGTTTTGGGAGAAAGTGGAAA
1 AGAGTAAAAGTTTTGGGAAAAAGTGAAAA
49781157 AGAGTAAAAGTTTTAGGGAAAAAGT-AAAA
1 AGAGTAAAAGTTTT-GGGAAAAAGTGAAAA
49781186 A
1 A
49781187 TATTTGAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.29, T:0.20
Consensus pattern (29 bp):
AGAGTAAAAGTTTTGGGAAAAAGTGAAAA
Found at i:49785633 original size:41 final size:41
Alignment explanation
Indices: 49785576--49785671 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
49785566 AAATTTTATT
49785576 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
49785617 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
49785658 TTGACAAGAATTCT
1 TTAACAAGAATTCT
49785672 CTACGAACAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.36, C:0.29, G:0.06, T:0.28
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:49785683 original size:17 final size:17
Alignment explanation
Indices: 49785661--49785699 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
49785651 CTCCACCTTG
* *
49785661 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
49785678 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
49785695 ACAAG
1 ACAAG
49785700 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:49789170 original size:2 final size:2
Alignment explanation
Indices: 49789163--49789192 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49789153 TCCATGTATA
49789163 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
49789193 AAATATGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:49798538 original size:17 final size:17
Alignment explanation
Indices: 49798513--49798545 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49798503 ATTTTGTTTT
*
49798513 TTTTTTTTTAATATTTA
1 TTTTATTTTAATATTTA
49798530 TTTTATTTTAATATTT
1 TTTTATTTTAATATTT
49798546 TACTATACCC
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTTAATATTTA
Found at i:49842819 original size:18 final size:18
Alignment explanation
Indices: 49842796--49842832 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
49842786 TTTGCTGATC
* *
49842796 CAATTGGTTTGATCAATT
1 CAATTGGTATGACCAATT
49842814 CAATTGGTATGACCAATT
1 CAATTGGTATGACCAATT
49842832 C
1 C
49842833 GACTGGTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (18 bp):
CAATTGGTATGACCAATT
Found at i:49854581 original size:49 final size:46
Alignment explanation
Indices: 49854528--49854627 Score: 128
Period size: 46 Copynumber: 2.1 Consensus size: 46
49854518 TTTTAAAAGA
*
49854528 AAAAATAGAACCACAAAAATGTGCAATACTTCAATCAATAAATTTCTTT
1 AAAAATAGAACCACAAAAAT-AG-AATACTT-AATCAATAAATTTCTTT
* ** *
49854577 AAAAATAGGACCACAAAAATAGAATACTTAATGGATAATTTTCTTT
1 AAAAATAGAACCACAAAAATAGAATACTTAATCAATAAATTTCTTT
49854623 AAAAA
1 AAAAA
49854628 AAAAAGGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 19 0.41
47 7 0.15
48 1 0.02
49 19 0.41
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (46 bp):
AAAAATAGAACCACAAAAATAGAATACTTAATCAATAAATTTCTTT
Found at i:49854630 original size:49 final size:50
Alignment explanation
Indices: 49854527--49854628 Score: 131
Period size: 49 Copynumber: 2.1 Consensus size: 50
49854517 TTTTTAAAAG
* *
49854527 AAAAAATAGAACCACAAAAATGTGCAATACTTCAATCAATAAATTTCTTT
1 AAAAAATAGGACCACAAAAATGAGCAATACTTCAATCAATAAATTTCTTT
** *
49854577 -AAAAATAGGACCACAAAAAT-AG-AATACTT-AATGGATAATTTTCTTT
1 AAAAAATAGGACCACAAAAATGAGCAATACTTCAATCAATAAATTTCTTT
49854623 AAAAAA
1 AAAAAA
49854629 AAAAGGAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
46 14 0.30
47 12 0.26
48 1 0.02
49 19 0.41
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (50 bp):
AAAAAATAGGACCACAAAAATGAGCAATACTTCAATCAATAAATTTCTTT
Found at i:49855703 original size:19 final size:19
Alignment explanation
Indices: 49855679--49855718 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
49855669 GATTAATGTT
49855679 TATGCTTTTCTATATGAGA
1 TATGCTTTTCTATATGAGA
49855698 TATGCTTTTCTATATGAGA
1 TATGCTTTTCTATATGAGA
49855717 TA
1 TA
49855719 GGTTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (19 bp):
TATGCTTTTCTATATGAGA
Found at i:49862165 original size:2 final size:2
Alignment explanation
Indices: 49862158--49862192 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
49862148 AATGAATTAA
49862158 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
49862193 CCCAATTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:49867452 original size:9 final size:9
Alignment explanation
Indices: 49867438--49867463 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
49867428 TAGCTTCGAA
49867438 TCAATTTAT
1 TCAATTTAT
49867447 TCAATTTAT
1 TCAATTTAT
49867456 TCAATTTA
1 TCAATTTA
49867464 GTCTCTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.54
Consensus pattern (9 bp):
TCAATTTAT
Found at i:49871094 original size:18 final size:20
Alignment explanation
Indices: 49871057--49871096 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
49871047 ATTTGTATAA
*
49871057 TTAATAATTTCTTTTATATT
1 TTAATAATTTCTTATATATT
49871077 TTAA-AATTT-TTATATATT
1 TTAATAATTTCTTATATATT
49871095 TT
1 TT
49871097 CTTTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTAATAATTTCTTATATATT
Found at i:49871101 original size:23 final size:23
Alignment explanation
Indices: 49871075--49871119 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
49871065 TTCTTTTATA
49871075 TTTTAAAATTTTT-ATATATTTTC
1 TTTTAAAATTTTTGA-ATATTTTC
49871098 TTTTAAAATTTTTGAATATTTT
1 TTTTAAAATTTTTGAATATTTT
49871120 TATAAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTAAAATTTTTGAATATTTTC
Found at i:49873327 original size:61 final size:61
Alignment explanation
Indices: 49873262--49873394 Score: 153
Period size: 61 Copynumber: 2.2 Consensus size: 61
49873252 ACCAAGAATT
* * ** *
49873262 AATTTATTGATTTTTTTTAAAATTAGAACT-AAATTA-AAAATTTTGTAAATTTTGATGGCTA
1 AATTTATTGA-ATTTTTTAAAATTAGAACTAAAATGACAAAA-TTTGTAAACATTGAGGGCTA
* **
49873323 AATTTATTGAATTTTTTAGAATTCTAACTAAAATGACAAAATTTGTAAACATTGAGGGCTA
1 AATTTATTGAATTTTTTAAAATTAGAACTAAAATGACAAAATTTGTAAACATTGAGGGCTA
*
49873384 ATTTTATTGAA
1 AATTTATTGAA
49873395 AATATTATAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
60 15 0.25
61 42 0.69
62 4 0.07
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (61 bp):
AATTTATTGAATTTTTTAAAATTAGAACTAAAATGACAAAATTTGTAAACATTGAGGGCTA
Found at i:49876111 original size:31 final size:31
Alignment explanation
Indices: 49876073--49876154 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
49876063 TTAATGATTA
49876073 TATTTAAATATTTAAAATATAATTTATATAC
1 TATTTAAATATTTAAAATATAATTTATATAC
*
49876104 TATTTAAAT-TTTATAAATAATAA-TTATTTAC
1 TATTTAAATATTTA-AAAT-ATAATTTATATAC
*
49876135 TA--GAAATATTTAAAAT-TAAT
1 TATTTAAATATTTAAAATATAAT
49876155 ATTTCATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
27 3 0.07
29 8 0.18
30 8 0.18
31 22 0.49
32 4 0.09
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (31 bp):
TATTTAAATATTTAAAATATAATTTATATAC
Found at i:49879370 original size:19 final size:21
Alignment explanation
Indices: 49879333--49879371 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
49879323 ATGTACCGCT
49879333 ATATAAAAGTTTGATTTAAAA
1 ATATAAAAGTTTGATTTAAAA
49879354 ATATAAAA-TTT-ATTTAAA
1 ATATAAAAGTTTGATTTAAA
49879372 TCTAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
ATATAAAAGTTTGATTTAAAA
Found at i:49881072 original size:2 final size:2
Alignment explanation
Indices: 49881065--49881091 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49881055 GCTTTCACCT
49881065 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
49881092 TTGTATTATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49881840 original size:83 final size:82
Alignment explanation
Indices: 49881692--49881848 Score: 206
Period size: 83 Copynumber: 1.9 Consensus size: 82
49881682 TCATATACCG
* * *
49881692 AGACTTCAAAACTTCAAATATCTTGCTTGATTCGGTATGCAAACATGTTTAATTATTAAAATTTT
1 AGACTTCAAAACTTCAAATATCTTGCTTGATTCGGTATGCAAACATGCTTAAGTATCAAAATTTT
49881757 CATTGACTCTGTACATCA
66 CA-TGACTCTGTACATCA
* * * * * * * *
49881775 AGACTTTAAAACTTCGAATATCTTGCTTGATTTGGTCTGCCAACGTGCTTAAGTATCGAAGTTTT
1 AGACTTCAAAACTTCAAATATCTTGCTTGATTCGGTATGCAAACATGCTTAAGTATCAAAATTTT
49881840 CATGACTCT
66 CATGACTCT
49881849 ATATCGAGCA
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
82 7 0.11
83 56 0.89
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (82 bp):
AGACTTCAAAACTTCAAATATCTTGCTTGATTCGGTATGCAAACATGCTTAAGTATCAAAATTTT
CATGACTCTGTACATCA
Found at i:49881912 original size:73 final size:70
Alignment explanation
Indices: 49881785--49881932 Score: 179
Period size: 73 Copynumber: 2.1 Consensus size: 70
49881775 AGACTTTAAA
* * * * * *
49881785 ACTTCGAATATCTTGCTTGATTTGGTCTGCCAACGTGCTTAAGTATCGAAGTTTTCATGACTCTA
1 ACTTTGAATATCTTGCTTAATCTGGTATGCCAACATGCTTAAGTATCGAAGTTTTCAAGA--CTA
49881850 TATCGAG
64 TATCGAG
* * * *
49881857 CACTTTGAATATCTTGTTTAATCTGGTATGCTAACATGCTTAATTATTGAAGTTTTCAAGACTAT
1 -ACTTTGAATATCTTGCTTAATCTGGTATGCCAACATGCTTAAGTATCGAAGTTTTCAAGACTAT
49881922 ATCGAG
65 ATCGAG
49881928 ACTTT
1 ACTTT
49881933 AGAACTTTGA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
70 5 0.08
71 10 0.15
73 50 0.77
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (70 bp):
ACTTTGAATATCTTGCTTAATCTGGTATGCCAACATGCTTAAGTATCGAAGTTTTCAAGACTATA
TCGAG
Found at i:49885314 original size:30 final size:30
Alignment explanation
Indices: 49885273--49885332 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
49885263 AAGCAGGGAG
49885273 AGGGAGAGGGAGAGGGGCCGTTCAAGATCT
1 AGGGAGAGGGAGAGGGGCCGTTCAAGATCT
* *
49885303 AGGGCGAGGGAGAGGGGTCGTTCAAGATCT
1 AGGGAGAGGGAGAGGGGCCGTTCAAGATCT
49885333 CCAGAAGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.13, G:0.47, T:0.15
Consensus pattern (30 bp):
AGGGAGAGGGAGAGGGGCCGTTCAAGATCT
Found at i:49894353 original size:6 final size:6
Alignment explanation
Indices: 49894342--49894374 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
49894332 CATCTATTTG
49894342 AATAAA AATAAA AATAAA AATAAA AATAAA AAT
1 AATAAA AATAAA AATAAA AATAAA AATAAA AAT
49894375 CTAATATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:49894514 original size:16 final size:16
Alignment explanation
Indices: 49894493--49894527 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49894483 TTTAGATACC
*
49894493 AATTTACAAATGGCCG
1 AATTTACAAATCGCCG
*
49894509 AATTTACACATCGCCG
1 AATTTACAAATCGCCG
49894525 AAT
1 AAT
49894528 CAGCTATTCC
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:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (16 bp):
AATTTACAAATCGCCG
Found at i:49898566 original size:2 final size:2
Alignment explanation
Indices: 49898559--49898593 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
49898549 TGCCCAAAAT
* *
49898559 TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49898594 TCTGTTAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:49916307 original size:24 final size:25
Alignment explanation
Indices: 49916275--49916346 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 25
49916265 ATTTTAGTTA
*
49916275 AAATATTATTACAATAAAATA-TT-T
1 AAATTTTATTA-AATAAAATATTTAT
49916299 AAATTTTATATAAA-AACAATATTTAT
1 AAATTTTAT-TAAATAA-AATATTTAT
49916325 AATATTTTATTAAATGAAAATA
1 AA-ATTTTATTAAAT-AAAATA
49916347 AGTTTTGATA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
23 2 0.05
24 14 0.35
25 4 0.10
26 7 0.17
27 11 0.28
28 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (25 bp):
AAATTTTATTAAATAAAATATTTAT
Found at i:49927398 original size:21 final size:24
Alignment explanation
Indices: 49927357--49927400 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 24
49927347 TCTGTTACTC
49927357 CCTATATTATTTGTAAATTTAATA
1 CCTATATTATTTGTAAATTTAATA
49927381 CCTATA-TATTT-T-AATTTAAT
1 CCTATATTATTTGTAAATTTAAT
49927401 CAAATTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 1 0.05
23 5 0.25
24 6 0.30
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.52
Consensus pattern (24 bp):
CCTATATTATTTGTAAATTTAATA
Found at i:49928728 original size:22 final size:23
Alignment explanation
Indices: 49928683--49928735 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
49928673 AATTATATTG
*
49928683 CTGTTTTGGTGCTGTTTTTTTTA
1 CTGTTTTGGTGCTGTTATTTTTA
*
49928706 CTGTTTTGGTGTTG-TATTTTTA
1 CTGTTTTGGTGCTGTTATTTTTA
*
49928728 CTGCTTTG
1 CTGTTTTG
49928736 ATTTTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.06, C:0.09, G:0.23, T:0.62
Consensus pattern (23 bp):
CTGTTTTGGTGCTGTTATTTTTA
Found at i:49928808 original size:12 final size:12
Alignment explanation
Indices: 49928793--49928858 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
49928783 TTTGGTGCTG
49928793 TTTTTATTGTTA
1 TTTTTATTGTTA
* *
49928805 TTTTTGTTGCTA
1 TTTTTATTGTTA
* *
49928817 TTTTTTTTATTA
1 TTTTTATTGTTA
* * *
49928829 TTTTTGTTGCTG
1 TTTTTATTGTTA
*
49928841 TTTTGA-TGTTA
1 TTTTTATTGTTA
49928852 TTTTTAT
1 TTTTTAT
49928859 GCGCTTTTAT
Statistics
Matches: 39, Mismatches: 14, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
11 8 0.21
12 31 0.79
ACGTcount: A:0.12, C:0.03, G:0.12, T:0.73
Consensus pattern (12 bp):
TTTTTATTGTTA
Found at i:49928815 original size:24 final size:24
Alignment explanation
Indices: 49928782--49928856 Score: 98
Period size: 24 Copynumber: 3.2 Consensus size: 24
49928772 TTTTTTACTA
*
49928782 TTTTGGTGCTGTTTTTATTGTTAT
1 TTTTGTTGCTGTTTTTATTGTTAT
* * *
49928806 TTTTGTTGCTATTTTTTTTATTAT
1 TTTTGTTGCTGTTTTTATTGTTAT
*
49928830 TTTTGTTGCTGTTTTGA-TGTTAT
1 TTTTGTTGCTGTTTTTATTGTTAT
49928853 TTTT
1 TTTT
49928857 ATGCGCTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 9 0.21
24 34 0.79
ACGTcount: A:0.09, C:0.04, G:0.16, T:0.71
Consensus pattern (24 bp):
TTTTGTTGCTGTTTTTATTGTTAT
Found at i:49936216 original size:21 final size:22
Alignment explanation
Indices: 49936192--49936243 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
49936182 CCAAACATTA
*
49936192 AACCCCAAACTCATAACTT-AT
1 AACCCCAAACTCATAAATTCAT
* *
49936213 AACCTCAAA-TCCTAAATTCAT
1 AACCCCAAACTCATAAATTCAT
49936234 AACCCCAAAC
1 AACCCCAAAC
49936244 CCTTAAACCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (22 bp):
AACCCCAAACTCATAAATTCAT
Found at i:49940816 original size:3 final size:3
Alignment explanation
Indices: 49940808--49940842 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
49940798 ATTTCATGTG
49940808 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
49940843 TTAATGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:49944783 original size:59 final size:57
Alignment explanation
Indices: 49944637--49944791 Score: 144
Period size: 59 Copynumber: 2.7 Consensus size: 57
49944627 ATAGGAATAA
*
49944637 AAAAATATTTTTTTG-GTGTATGCCAA-ACCAT-AGTTGACACCTCCTTTTCCAGATAC
1 AAAAATATTTTTTTGAGTGTATGCCAACA-CATGA-TCGACACCTCCTTTTCCAGATAC
* * * *
49944693 --AAATTTTTTTTTAAGTGTCTGCTAATC-CATGATCGAC-CCTCCTTTTTCCAGATACCC
1 AAAAATATTTTTTTGAGTGTATGCCAA-CACATGATCGACACCTCC-TTTTCCAGATA--C
* *
49944750 AAAAATATTTTTTTGAGTGTTTGCCAACACATGACCGACACC
1 AAAAATATTTTTTTGAGTGTATGCCAACACATGATCGACACC
49944792 CAAAATGAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
54 16 0.21
55 27 0.35
56 1 0.01
57 1 0.01
58 1 0.01
59 30 0.38
60 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (57 bp):
AAAAATATTTTTTTGAGTGTATGCCAACACATGATCGACACCTCCTTTTCCAGATAC
Found at i:49944909 original size:58 final size:58
Alignment explanation
Indices: 49944793--49944961 Score: 182
Period size: 58 Copynumber: 2.9 Consensus size: 58
49944783 ACCGACACCC
* * * * *
49944793 AAAATGAATAAAAAATTATTTTTTTGGTGTCTGCCAAGCCATAG-TAGACACCCAAAAA
1 AAAATGAATAAAAAATTAATTTTTTGGTGTTTGACAAGCAATGGCT-GACACCCAAAAA
*
49944851 AAAACGAATAAAAAAATTAATTTTTTGGTGTTTGACAAGCAATGGCTGACACCC-AAAA
1 AAAATGAAT-AAAAAATTAATTTTTTGGTGTTTGACAAGCAATGGCTGACACCCAAAAA
* * * * *
49944909 AATATGAATTAAAAAA-TAATTTTTTTGGTGTTTGATAACCAATGACCGACACC
1 AAAATGAA-TAAAAAATTAA-TTTTTTGGTGTTTGACAAGCAATGGCTGACACC
49944962 AACTTTCCCT
Statistics
Matches: 95, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
57 3 0.03
58 53 0.56
59 38 0.40
60 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (58 bp):
AAAATGAATAAAAAATTAATTTTTTGGTGTTTGACAAGCAATGGCTGACACCCAAAAA
Found at i:49945693 original size:19 final size:18
Alignment explanation
Indices: 49945650--49945693 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
49945640 TGTGAAAATG
* *
49945650 TGAAGAAATAATTATTAT
1 TGAAAAAATAAATATTAT
*
49945668 CGAAAAAATAAATATATAT
1 TGAAAAAATAAATAT-TAT
49945687 TGAAAAA
1 TGAAAAA
49945694 TAATAATCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (18 bp):
TGAAAAAATAAATATTAT
Found at i:49946008 original size:2 final size:2
Alignment explanation
Indices: 49946003--49946037 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
49945993 GTACTATATA
* *
49946003 TG TG TG TG TG TG TG TA TG TG TG TG TG TC TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
49946038 CTTTTCTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.03, G:0.43, T:0.51
Consensus pattern (2 bp):
TG
Found at i:49948984 original size:22 final size:21
Alignment explanation
Indices: 49948932--49949007 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 21
49948922 TTTAAATTCG
**
49948932 AAATTAAAATTAACAGAGTTT
1 AAATTAAAATTAATGGAGTTT
*
49948953 AAAGTAAAAATTAATGGAGTTT
1 AAA-TTAAAATTAATGGAGTTT
*
49948975 AAGATTAAAATTAATGGAGATTA
1 AA-ATTAAAATTAATGGAG-TTT
49948998 AAATTAAAAT
1 AAATTAAAAT
49949008 GGAATTTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.06
22 39 0.83
23 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.13, T:0.32
Consensus pattern (21 bp):
AAATTAAAATTAATGGAGTTT
Found at i:49949020 original size:17 final size:18
Alignment explanation
Indices: 49948976--49949021 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
49948966 ATGGAGTTTA
49948976 AGATTAAAATT--AATGG
1 AGATTAAAATTAAAATGG
49948992 AGATTAAAATTAAAATGG
1 AGATTAAAATTAAAATGG
*
49949010 A-ATTTAAATTAA
1 AGATTAAAATTAA
49949022 TTTATAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 11 0.41
17 10 0.37
18 6 0.22
ACGTcount: A:0.54, C:0.00, G:0.13, T:0.33
Consensus pattern (18 bp):
AGATTAAAATTAAAATGG
Found at i:49949127 original size:19 final size:19
Alignment explanation
Indices: 49949103--49949163 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
49949093 CTAAATTGAA
49949103 TTTGAAAATAATATACTAG
1 TTTGAAAATAATATACTAG
*
49949122 TTTGAAATTAAT-TGA--A-
1 TTTGAAAATAATAT-ACTAG
*
49949138 TTTGAAAATAAAATACTAG
1 TTTGAAAATAATATACTAG
*
49949157 TTCGAAA
1 TTTGAAA
49949164 TTAAAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
16 11 0.33
17 2 0.06
18 2 0.06
19 18 0.55
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (19 bp):
TTTGAAAATAATATACTAG
Found at i:49949137 original size:35 final size:35
Alignment explanation
Indices: 49949096--49949167 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
49949086 TATTAGTCTA
* *
49949096 AATTGAATTTGAAAATAATATACTAGTTTGAAATT
1 AATTGAATTTGAAAATAAAATACTAGTTCGAAATT
49949131 AATTGAATTTGAAAATAAAATACTAGTTCGAAATT
1 AATTGAATTTGAAAATAAAATACTAGTTCGAAATT
49949166 AA
1 AA
49949168 AATTATAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (35 bp):
AATTGAATTTGAAAATAAAATACTAGTTCGAAATT
Found at i:49949245 original size:34 final size:35
Alignment explanation
Indices: 49949207--49949273 Score: 102
Period size: 34 Copynumber: 1.9 Consensus size: 35
49949197 GAAACTGCAT
49949207 TTGAAAAGAAAATTAAA-T-GAAATTAAAATTAAAG
1 TTGAAAAGAAAATTAAATTCGAAATT-AAATTAAAG
*
49949241 TTGAAATGAAAATTAAATTCGAAATTAAATTAA
1 TTGAAAAGAAAATTAAATTCGAAATTAAATTAA
49949274 TAAAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 16 0.53
35 8 0.27
36 6 0.20
ACGTcount: A:0.58, C:0.01, G:0.10, T:0.30
Consensus pattern (35 bp):
TTGAAAAGAAAATTAAATTCGAAATTAAATTAAAG
Found at i:49949247 original size:18 final size:17
Alignment explanation
Indices: 49949215--49949273 Score: 77
Period size: 18 Copynumber: 3.5 Consensus size: 17
49949205 ATTTGAAAAG
49949215 AAAATTAAA-TGAAATT
1 AAAATTAAATTGAAATT
*
49949231 AAAATTAAAGTTGAAATG
1 AAAATTAAA-TTGAAATT
49949249 AAAATTAAATTCGAAATT
1 AAAATTAAATT-GAAATT
49949267 -AAATTAA
1 AAAATTAA
49949274 TAAAAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
16 9 0.24
17 9 0.24
18 20 0.53
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (17 bp):
AAAATTAAATTGAAATT
Found at i:49949394 original size:15 final size:16
Alignment explanation
Indices: 49949360--49949397 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
49949350 GTGTAATAAT
* *
49949360 ATAAATTTTAAAATTA
1 ATAAAGTTTAAAACTA
49949376 ATAAAGTTT-AAACTA
1 ATAAAGTTTAAAACTA
49949391 ATAAAGT
1 ATAAAGT
49949398 GTAATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (16 bp):
ATAAAGTTTAAAACTA
Found at i:49949525 original size:6 final size:6
Alignment explanation
Indices: 49949516--49949607 Score: 102
Period size: 6 Copynumber: 16.0 Consensus size: 6
49949506 TAATTTTAAA
*
49949516 TGAAAT TGAAA- TGAAAT TGAAAT TGAAAT TGAAGT TGAAA- TGAAAT
1 TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT
** * * *
49949562 TGAAAT TGAAA- TGAAAT CAAAAT TTAAAT TTAAA- TAAAAT TGAAAT
1 TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT
49949608 AATAATAAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
5 19 0.26
6 55 0.74
ACGTcount: A:0.53, C:0.01, G:0.14, T:0.32
Consensus pattern (6 bp):
TGAAAT
Found at i:49949536 original size:17 final size:17
Alignment explanation
Indices: 49949516--49949607 Score: 98
Period size: 17 Copynumber: 5.4 Consensus size: 17
49949506 TAATTTTAAA
49949516 TGAAATTGAAATGAAAT
1 TGAAATTGAAATGAAAT
*
49949533 TGAAATTGAAATTGAAGT
1 TGAAATTGAAA-TGAAAT
49949551 TGAAA-TGAAATTGAAAT
1 TGAAATTGAAA-TGAAAT
*
49949568 TGAAA-TGAAATCAAAAT
1 TGAAATTGAAAT-GAAAT
* * *
49949585 TTAAATTTAAATAAAAT
1 TGAAATTGAAATGAAAT
49949602 TGAAAT
1 TGAAAT
49949608 AATAATAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
16 1 0.02
17 50 0.76
18 15 0.23
ACGTcount: A:0.53, C:0.01, G:0.14, T:0.32
Consensus pattern (17 bp):
TGAAATTGAAATGAAAT
Found at i:49949542 original size:23 final size:23
Alignment explanation
Indices: 49949516--49949607 Score: 114
Period size: 23 Copynumber: 4.0 Consensus size: 23
49949506 TAATTTTAAA
49949516 TGAAATTGAAATGAAATTGAAAT
1 TGAAATTGAAATGAAATTGAAAT
*
49949539 TGAAATTGAAGTTGAAA-TGAAAT
1 TGAAATTGAA-ATGAAATTGAAAT
**
49949562 TGAAATTGAAATGAAATCAAAAT
1 TGAAATTGAAATGAAATTGAAAT
* * *
49949585 TTAAATTTAAATAAAATTGAAAT
1 TGAAATTGAAATGAAATTGAAAT
49949608 AATAATAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
22 5 0.09
23 48 0.83
24 5 0.09
ACGTcount: A:0.53, C:0.01, G:0.14, T:0.32
Consensus pattern (23 bp):
TGAAATTGAAATGAAATTGAAAT
Found at i:49949548 original size:29 final size:28
Alignment explanation
Indices: 49949513--49949578 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 28
49949503 ATTTAATTTT
49949513 AAATGAAATTGAAATGAAATTGAAATTG
1 AAATGAAATTGAAATGAAATTGAAATTG
*
49949541 AAATTGAAGTTGAAATGAAATTGAAATTG
1 AAA-TGAAATTGAAATGAAATTGAAATTG
49949570 AAATGAAAT
1 AAATGAAAT
49949579 CAAAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 8 0.23
29 27 0.77
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (28 bp):
AAATGAAATTGAAATGAAATTGAAATTG
Found at i:49951071 original size:20 final size:19
Alignment explanation
Indices: 49951048--49951174 Score: 74
Period size: 20 Copynumber: 6.1 Consensus size: 19
49951038 ATATTTCCGA
*
49951048 ATTTTTTAAATAATTTTTTT
1 ATTTTTGAAAT-ATTTTTTT
* *
49951068 ATTTTCGAAATATTTTTTAC
1 ATTTTTGAAATATTTTTT-T
49951088 ATTTTTGAAATATTTCTTTT
1 ATTTTTGAAATATTT-TTTT
** **
49951108 ACAAATTAAAAATCTTATATTTTTT
1 --ATTTTTGAAA---TAT-TTTTTT
*
49951133 ATATTTTCGAAATATTTTTTAC
1 AT-TTTT-GAAATATTTTTT-T
49951155 ATTTTTGAAATATTTTTTT
1 ATTTTTGAAATATTTTTTT
49951174 A
1 A
49951175 CAAATGAAAT
Statistics
Matches: 81, Mismatches: 15, Indels: 23
0.68 0.13 0.19
Matches are distributed among these distances:
19 8 0.10
20 35 0.43
21 12 0.15
22 11 0.14
23 1 0.01
24 2 0.02
25 10 0.12
26 2 0.02
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTTTTGAAATATTTTTTT
Found at i:49952752 original size:22 final size:22
Alignment explanation
Indices: 49952726--49952782 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
49952716 ACTTCCCTAT
49952726 TTTCTATTT-CTTTTAATTCTAC
1 TTTCT-TTTACTTTTAATTCTAC
* *
49952748 TTTCTTTTATTTTTAATTCT-G
1 TTTCTTTTACTTTTAATTCTAC
*
49952769 TTTCTTTTATTTTT
1 TTTCTTTTACTTTT
49952783 CCTTAGGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTCTTTTACTTTTAATTCTAC
Found at i:49952753 original size:16 final size:15
Alignment explanation
Indices: 49952727--49952756 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
49952717 CTTCCCTATT
49952727 TTCTATTTCTTTTAA
1 TTCTATTTCTTTTAA
49952742 TTCTACTTTCTTTTA
1 TTCTA-TTTCTTTTA
49952757 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCTATTTCTTTTAA
Found at i:49953765 original size:30 final size:30
Alignment explanation
Indices: 49953731--49953792 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
49953721 TTGATTTTCT
49953731 TTTCATTTATTTTTTAAATTTAATTTGTAA
1 TTTCATTTATTTTTTAAATTTAATTTGTAA
49953761 TTTCATTTATTTTTTAAATTTAATTTGTAA
1 TTTCATTTATTTTTTAAATTTAATTTGTAA
49953791 TT
1 TT
49953793 ATTATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (30 bp):
TTTCATTTATTTTTTAAATTTAATTTGTAA
Found at i:49954517 original size:61 final size:59
Alignment explanation
Indices: 49954399--49954541 Score: 146
Period size: 61 Copynumber: 2.4 Consensus size: 59
49954389 TGCCAAGTAG
* * *
49954399 CAAAAAAA-TTATTTTTTAATTCATATTTTTACGGGTTTCAGCCATTTTTTGTCAAACAC
1 CAAAAAAATTTATTTTTT-ATTCATATTTTTACGGGTGTCAGCCATTTATGGTCAAACAC
* * **
49954458 GAACAAAAATTTATTTTTTATTCGTATTATTTGTGGGTGTCAGCCATTATATGGT-AAACAC
1 CAA-AAAAATTTATTTTTTATTCATATT-TTTACGGGTGTCAGCCATT-TATGGTCAAACAC
*
49954519 CAAAATATAATTTTTTTTTTATT
1 CAAAA-A-AATTTATTTTTTATT
49954542 TTTGGGTGTC
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
59 2 0.03
60 15 0.22
61 34 0.49
62 18 0.26
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.45
Consensus pattern (59 bp):
CAAAAAAATTTATTTTTTATTCATATTTTTACGGGTGTCAGCCATTTATGGTCAAACAC
Found at i:49954642 original size:113 final size:113
Alignment explanation
Indices: 49954513--49954747 Score: 284
Period size: 113 Copynumber: 2.1 Consensus size: 113
49954503 ATTATATGGT
* ** *
49954513 AAAC-ACCAAAATATAATTTTTTT-TTTATTTTTGGGTGTCGGCCATGGGTTGACAAACACCC-A
1 AAACAACCAAAATATAATTTTTTTATTTA-TTTTAGGTGTCGGCCATAAGATGACAAACACCCGA
*
49954575 AAAAATATATTTTTGGGTATCTGGATAAAG-GGGCGTC-AGTCATGGGTTGAC
65 AAAAATA-ATTTTT-GGTAT-TGGAAAAAGAGGGCGTCGA-TCATGGGTTGAC
* * *
49954626 AGACAACCAAAA-ATAATTTTTTTATTTATTTTAGGTGTCGGTCATAAGATGGCAAACACCCGAA
1 AAACAACCAAAATATAATTTTTTTATTTATTTTAGGTGTCGGCCATAAGATGACAAACACCCGAA
* *
49954690 AAAATAATTTTTGGTATTTGAAAAAGAGGGTGTCGATCATGGGTTGAC
66 AAAATAATTTTTGGTATTGGAAAAAGAGGGCGTCGATCATGGGTTGAC
*
49954738 AAACACCCAA
1 AAACAACCAA
49954748 TTTTTTTTGG
Statistics
Matches: 105, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
111 7 0.07
112 31 0.30
113 48 0.46
114 19 0.18
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (113 bp):
AAACAACCAAAATATAATTTTTTTATTTATTTTAGGTGTCGGCCATAAGATGACAAACACCCGAA
AAAATAATTTTTGGTATTGGAAAAAGAGGGCGTCGATCATGGGTTGAC
Found at i:49956411 original size:16 final size:16
Alignment explanation
Indices: 49956392--49956428 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
49956382 TTAAAATTAG
49956392 ATTAAGAAATAATTTA
1 ATTAAGAAATAATTTA
* *
49956408 ATTAAGAATTATTTTA
1 ATTAAGAAATAATTTA
49956424 ATTAA
1 ATTAA
49956429 TTAAATGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (16 bp):
ATTAAGAAATAATTTA
Found at i:49957504 original size:12 final size:12
Alignment explanation
Indices: 49957459--49957510 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
49957449 GAAGTTTTCT
49957459 TCTATTTATCTA
1 TCTATTTATCTA
*
49957471 TCTA-CTATCTA
1 TCTATTTATCTA
*
49957482 GCTA--T-TC-A
1 TCTATTTATCTA
49957490 TCTATTTATCTA
1 TCTATTTATCTA
49957502 TCTATTTAT
1 TCTATTTAT
49957511 TCATACATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
8 4 0.12
9 2 0.06
10 2 0.06
11 11 0.33
12 14 0.42
ACGTcount: A:0.25, C:0.19, G:0.02, T:0.54
Consensus pattern (12 bp):
TCTATTTATCTA
Found at i:49961702 original size:16 final size:15
Alignment explanation
Indices: 49961681--49961732 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
49961671 GGTTTATTGG
49961681 AATTGAATAAAGTTGT
1 AATTGAATAAAG-TGT
49961697 AATTGAATAGAAGTGT
1 AATTGAATA-AAGTGT
49961713 AA-TGAAATAAAGCTGT
1 AATTG-AATAAAG-TGT
49961729 AATT
1 AATT
49961733 AGCAATTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.16
16 23 0.72
17 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.19, T:0.33
Consensus pattern (15 bp):
AATTGAATAAAGTGT
Found at i:49961970 original size:24 final size:24
Alignment explanation
Indices: 49961914--49961973 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
49961904 TTAATAAGAT
49961914 TATTATTAA-ATATAATTTAATAA
1 TATTATTAATATATAATTTAATAA
* * *
49961937 AAATAATAATATATAATTTAATAA
1 TATTATTAATATATAATTTAATAA
*
49961961 TATTTTTAATATA
1 TATTATTAATATA
49961974 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTATTAATATATAATTTAATAA
Found at i:49962230 original size:28 final size:27
Alignment explanation
Indices: 49962197--49962251 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
49962187 TAAGTATTAT
49962197 ATTCAACCAAATAAAAA-AATAATTTTCC
1 ATTCAA-CAAATAAAAATAAT-ATTTTCC
*
49962225 ATTCAATAAATAAAAATAATATTTTCC
1 ATTCAACAAATAAAAATAATATTTTCC
49962252 CAACCAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (27 bp):
ATTCAACAAATAAAAATAATATTTTCC
Found at i:49962777 original size:30 final size:31
Alignment explanation
Indices: 49962741--49962807 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
49962731 CATTTACCAT
* *
49962741 AACAGTCACT-CAATTTTC-AAAATGTGACAA
1 AACAGTCACTAAAATTATCGAAAA-GTGACAA
49962771 AACAGTCACTAAAATTATCGAAAAGTGACAA
1 AACAGTCACTAAAATTATCGAAAAGTGACAA
49962802 AACAGT
1 AACAGT
49962808 TTGGGTGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 10 0.30
31 19 0.58
32 4 0.12
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (31 bp):
AACAGTCACTAAAATTATCGAAAAGTGACAA
Found at i:49962942 original size:6 final size:6
Alignment explanation
Indices: 49962908--49962947 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
49962898 ATGCTATATC
*
49962908 CTTTTC CTTTTT CTTTTT CTTTTCAT CTTTTT CTTTTT CT
1 CTTTTT CTTTTT CTTTTT CTTTT--T CTTTTT CTTTTT CT
49962948 ATTGACGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 25 0.81
8 6 0.19
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.75
Consensus pattern (6 bp):
CTTTTT
Found at i:49966017 original size:63 final size:62
Alignment explanation
Indices: 49965882--49966288 Score: 474
Period size: 57 Copynumber: 6.8 Consensus size: 62
49965872 TCAATTTTCA
* * * * *
49965882 AACCCTAACCCCTAAACCCTAACCCCTAAACCCTAACCCCTAAACCCTAAACTCTGAACCCTG
1 AACCCTAAACCCT-AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTG
* * * * *
49965945 AA-CCTAAACCCTGAACCTTGAACCCTAAACCCTAAACCCTGAACCTTGAACCCTAAACCCTG
1 AACCCTAAACCCT-AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTG
* * *
49966007 AACCTTAAACCCTGAACCTTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTA
1 AACCCTAAACCCT-AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTG
* * * * *
49966070 AACCCTGAA-CCTAAACCCTGAACCCTGAA-CCTAAACCCTGAA-CCTAAACCCTAAACCTTG
1 AACCCTAAACCCT-AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTG
49966130 AA-CCT-AACCCTAACCCTAAACCCT-AACCCT-AACCCT-AACCCTAAACCCT-AACCCT-
1 AACCCTAAACCCTAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTG
*
49966185 AACCCTAAACCCTAAACCT-AACCCTAAACCCTAAA-CCT-AACCCTAAACCCTAAA-CCT-
1 AACCCTAAACCCTAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTG
49966242 AACCCTAAA-CCTAACCCTAAACCCTAAA-CCT-AACCCTAAACCCTAAA
1 AACCCTAAACCCTAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAA
49966289 AATTGAGATT
Statistics
Matches: 302, Mismatches: 30, Indels: 30
0.83 0.08 0.08
Matches are distributed among these distances:
55 4 0.01
56 30 0.10
57 81 0.27
58 21 0.07
59 6 0.02
60 18 0.06
61 12 0.04
62 67 0.22
63 63 0.21
ACGTcount: A:0.39, C:0.42, G:0.03, T:0.16
Consensus pattern (62 bp):
AACCCTAAACCCTAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTG
Found at i:49966246 original size:69 final size:75
Alignment explanation
Indices: 49965882--49966288 Score: 486
Period size: 69 Copynumber: 5.6 Consensus size: 75
49965872 TCAATTTTCA
* * * * *
49965882 AACCCTAACCCCTAAACCCTAACCCCTAAACCCTAACCCCTAAACCCTAAACTCTGAACCCTGAA
1 AACCCTAAACCCTAAACCCTAA-ACCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTGAA
49965947 CCTAAACCCTG
65 CCTAAACCCTG
* * * * * * *
49965958 AACCTTGAACCCTAAACCCTAAACCCTGAACCTTGAACCCTAAACCCTGAACCTTAAACCCTGAA
1 AACCCTAAACCCTAAACCCTAAA-CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTGAA
*
49966023 CCTTAAACCCTA
65 CC-TAAACCCTG
* *
49966035 AACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTGAA-CCTAAACCCTGAACCCTGAA
1 AACCCTAAACCCTAAACCCTAAA-CCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTGAA
49966099 CCTAAACCCTG
65 CCTAAACCCTG
* *
49966110 AA-CCTAAACCCTAAACCTTGAACCT-AACCCT-AACCCTAAACCCT-AACCCT-AACCCT-AAC
1 AACCCTAAACCCTAAACCCTAAACCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTGAA-
49966169 CCTAAACCCT-
65 CCTAAACCCTG
*
49966179 AACCCT-AACCCTAAACCCTAAACCT-AACCCTAAACCCTAAA-CCT-AACCCTAAACCCTAAAC
1 AACCCTAAACCCTAAACCCTAAACCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTGAAC
49966240 CT-AACCCT-
66 CTAAACCCTG
*
49966248 AAACCT-AACCCTAAACCCTAAACCT-AACCCTAAACCCTAAA
1 AACCCTAAACCCTAAACCCTAAACCTAAACCCTAAACCCTAAA
49966289 AATTGAGATT
Statistics
Matches: 294, Mismatches: 29, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
69 82 0.28
70 37 0.13
71 16 0.05
72 9 0.03
73 3 0.01
74 18 0.06
75 10 0.03
76 73 0.25
77 46 0.16
ACGTcount: A:0.39, C:0.42, G:0.03, T:0.16
Consensus pattern (75 bp):
AACCCTAAACCCTAAACCCTAAACCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTGAAC
CTAAACCCTG
Found at i:49966288 original size:7 final size:7
Alignment explanation
Indices: 49965881--49966288 Score: 464
Period size: 7 Copynumber: 61.4 Consensus size: 7
49965871 ATCAATTTTC
49965881 AAACCCT
1 AAACCCT
*
49965888 AACCCCT
1 AAACCCT
49965895 AAACCCT
1 AAACCCT
*
49965902 AACCCCT
1 AAACCCT
49965909 AAACCCT
1 AAACCCT
*
49965916 AACCCCT
1 AAACCCT
49965923 AAACCCT
1 AAACCCT
*
49965930 AAACTCT
1 AAACCCT
*
49965937 GAACCCT
1 AAACCCT
*
49965944 GAA-CCT
1 AAACCCT
49965950 AAACCCT
1 AAACCCT
* *
49965957 GAACCTT
1 AAACCCT
*
49965964 GAACCCT
1 AAACCCT
49965971 AAACCCT
1 AAACCCT
49965978 AAACCCT
1 AAACCCT
* *
49965985 GAACCTT
1 AAACCCT
*
49965992 GAACCCT
1 AAACCCT
49965999 AAACCCT
1 AAACCCT
* *
49966006 GAACCTT
1 AAACCCT
49966013 AAACCCT
1 AAACCCT
* *
49966020 GAACCTT
1 AAACCCT
49966027 AAACCCT
1 AAACCCT
49966034 AAACCCT
1 AAACCCT
49966041 AAACCCT
1 AAACCCT
49966048 AAACCCT
1 AAACCCT
49966055 AAACCCT
1 AAACCCT
49966062 AAACCCT
1 AAACCCT
49966069 AAACCCT
1 AAACCCT
*
49966076 GAA-CCT
1 AAACCCT
49966082 AAACCCT
1 AAACCCT
*
49966089 GAACCCT
1 AAACCCT
*
49966096 GAA-CCT
1 AAACCCT
49966102 AAACCCT
1 AAACCCT
*
49966109 GAA-CCT
1 AAACCCT
49966115 AAACCCT
1 AAACCCT
*
49966122 AAACCTT
1 AAACCCT
*
49966129 GAA-CCT
1 AAACCCT
49966135 -AACCCT
1 AAACCCT
49966141 -AACCCT
1 AAACCCT
49966147 AAACCCT
1 AAACCCT
49966154 -AACCCT
1 AAACCCT
49966160 -AACCCT
1 AAACCCT
49966166 -AACCCT
1 AAACCCT
49966172 AAACCCT
1 AAACCCT
49966179 -AACCCT
1 AAACCCT
49966185 -AACCCT
1 AAACCCT
49966191 AAACCCT
1 AAACCCT
49966198 AAA-CCT
1 AAACCCT
49966204 -AACCCT
1 AAACCCT
49966210 AAACCCT
1 AAACCCT
49966217 AAA-CCT
1 AAACCCT
49966223 -AACCCT
1 AAACCCT
49966229 AAACCCT
1 AAACCCT
49966236 AAA-CCT
1 AAACCCT
49966242 -AACCCT
1 AAACCCT
49966248 AAA-CCT
1 AAACCCT
49966254 -AACCCT
1 AAACCCT
49966260 AAACCCT
1 AAACCCT
49966267 AAA-CCT
1 AAACCCT
49966273 -AACCCT
1 AAACCCT
49966279 AAACCCT
1 AAACCCT
49966286 AAA
1 AAA
49966289 AATTGAGATT
Statistics
Matches: 348, Mismatches: 35, Indels: 36
0.83 0.08 0.09
Matches are distributed among these distances:
5 12 0.03
6 91 0.26
7 245 0.70
ACGTcount: A:0.39, C:0.42, G:0.03, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:49979415 original size:11 final size:9
Alignment explanation
Indices: 49979385--49979423 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
49979375 AAGATACATA
49979385 TAATATTTT
1 TAATATTTT
49979394 TAATATTTT
1 TAATATTTT
49979403 TAATATCTTT
1 TAATAT-TTT
*
49979413 TTATATTTT
1 TAATATTTT
49979422 TA
1 TA
49979424 CCCTTTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (9 bp):
TAATATTTT
Found at i:49979418 original size:19 final size:18
Alignment explanation
Indices: 49979385--49979423 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
49979375 AAGATACATA
49979385 TAATATTTTTAATATTTT
1 TAATATTTTTAATATTTT
*
49979403 TAATATCTTTTTATATTTT
1 TAATAT-TTTTAATATTTT
49979422 TA
1 TA
49979424 CCCTTTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATATTTTTAATATTTT
Found at i:49988741 original size:6 final size:6
Alignment explanation
Indices: 49988730--49988765 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
49988720 TTTTCATACG
* *
49988730 TATCAA TATCAA TATCAA TATCAA CATTAA TATCAA
1 TATCAA TATCAA TATCAA TATCAA TATCAA TATCAA
49988766 ATTTATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TATCAA
Found at i:49989955 original size:3 final size:3
Alignment explanation
Indices: 49989947--49990005 Score: 109
Period size: 3 Copynumber: 19.3 Consensus size: 3
49989937 ATGAACTATT
49989947 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
49989995 GAA GAA TGAA G
1 GAA GAA -GAA G
49990006 GGTTTAATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:50008273 original size:282 final size:282
Alignment explanation
Indices: 50007763--50008330 Score: 1010
Period size: 282 Copynumber: 2.0 Consensus size: 282
50007753 ATGATTATTA
* * * *
50007763 ATTACTCCAATTAATTGACAACATTAAGCAGACAAGCACTAGGAAATAAATACAAGTATAATACA
1 ATTACACCAATTAATTGACAACATTAAGAAGAAAAGCACTAGGAAATAAATACAAGTAAAATACA
* *
50007828 AACAAAAACAATTACATCCTGCATGAATATTCATTTGAATGCATATTGGCATTGGAAATCGATCT
66 AACAAAAACAATTACATCCTGCATGAATATTCATTTGAAGGCATATTGGCATTGGAAATCAATCT
50007893 TCTTCAAGTAATCAATAATAATTCCATAAACATGAAAGAGGAAAAAAGAATGAATGAAACAGGAA
131 TCTTCAAGTAATCAATAATAATTCCATAAACATGAAAGAGGAAAAAAGAATGAATGAAACAGGAA
50007958 TCTTTGAATTTGAAAATGCAGAATATTCCACATCCATGACATTTGGGCTATGCTTTTTAAAATTT
196 TCTTTGAATTTGAAAATGCAGAATATTCCACATCCATGACATTTGGGCTATGCTTTTTAAAATTT
50008023 CATGAAAATACCAAGAAATAAG
261 CATGAAAATACCAAGAAATAAG
50008045 ATTACACCAATTAATTGACAACATTAAGAAGAAAAGCACTAGGAAATAAATACAAGTAAAATACA
1 ATTACACCAATTAATTGACAACATTAAGAAGAAAAGCACTAGGAAATAAATACAAGTAAAATACA
* *
50008110 AACAAAAACAATTACATCCTGCATGAATATTCATTTGAAGGTATATTGGCATTGGAAGTCAATCT
66 AACAAAAACAATTACATCCTGCATGAATATTCATTTGAAGGCATATTGGCATTGGAAATCAATCT
* * *
50008175 TCTTCAAGTGATCAATAATAATTCCATAAACATGAAAGAGGAAAAAAGAATGAGTGAAACTGGAA
131 TCTTCAAGTAATCAATAATAATTCCATAAACATGAAAGAGGAAAAAAGAATGAATGAAACAGGAA
* * *
50008240 TCTTTGAATTTGAAATTTCAGAATATTCCACATCCATGACATTTGGGCTATGCTTTTTCAAATTT
196 TCTTTGAATTTGAAAATGCAGAATATTCCACATCCATGACATTTGGGCTATGCTTTTTAAAATTT
50008305 CATGAAAATACCAAGAAATAAG
261 CATGAAAATACCAAGAAATAAG
50008327 ATTA
1 ATTA
50008331 ATTCATGATA
Statistics
Matches: 272, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
282 272 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (282 bp):
ATTACACCAATTAATTGACAACATTAAGAAGAAAAGCACTAGGAAATAAATACAAGTAAAATACA
AACAAAAACAATTACATCCTGCATGAATATTCATTTGAAGGCATATTGGCATTGGAAATCAATCT
TCTTCAAGTAATCAATAATAATTCCATAAACATGAAAGAGGAAAAAAGAATGAATGAAACAGGAA
TCTTTGAATTTGAAAATGCAGAATATTCCACATCCATGACATTTGGGCTATGCTTTTTAAAATTT
CATGAAAATACCAAGAAATAAG
Found at i:50009667 original size:2 final size:2
Alignment explanation
Indices: 50009660--50009710 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
50009650 GTAAGAGCTT
50009660 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
50009702 GA GA GA GA G
1 GA GA GA GA G
50009711 GAGGCTAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:50020817 original size:24 final size:24
Alignment explanation
Indices: 50020761--50020808 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
50020751 ACTTACAAAT
*
50020761 AAAAATAAAAATATATTTATATTCAA
1 AAAAATAAAAATATATTTATAGT--A
50020787 AAAAATAAAAATATATTTATAG
1 AAAAATAAAAATATATTTATAG
50020809 GTGAAAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAAATAAAAATATATTTATAGTA
Found at i:50043766 original size:33 final size:33
Alignment explanation
Indices: 50043701--50043766 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
50043691 GTAGGTCTTA
*
50043701 TTTTTTAAAGTTAAATTTAGCCCAAAACTTTTT
1 TTTTTTAAAGTTAAATTTAGACCAAAACTTTTT
*
50043734 TTTTTTGAAAGTTAAATTT-GACCATAA-TTTTT
1 TTTTTT-AAAGTTAAATTTAGACCAAAACTTTTT
50043766 T
1 T
50043767 AGAAAAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 6 0.20
33 12 0.40
34 12 0.40
ACGTcount: A:0.32, C:0.09, G:0.08, T:0.52
Consensus pattern (33 bp):
TTTTTTAAAGTTAAATTTAGACCAAAACTTTTT
Found at i:50043908 original size:25 final size:25
Alignment explanation
Indices: 50043857--50043908 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
50043847 AACTTCTACC
**
50043857 AACTTTTTTATATTTTTTTAATATT
1 AACTTTTTTATATTTTTAAAATATT
*
50043882 AACTTTTTTATATTTTTAAAATTTT
1 AACTTTTTTATATTTTTAAAATATT
50043907 AA
1 AA
50043909 ATTATTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (25 bp):
AACTTTTTTATATTTTTAAAATATT
Found at i:50045116 original size:17 final size:15
Alignment explanation
Indices: 50045094--50045127 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
50045084 GAGGGCAACG
50045094 GGTGAGGGAGAGAGGGA
1 GGTGAGGGA-A-AGGGA
50045111 GGTGAGGGAAAGGGA
1 GGTGAGGGAAAGGGA
50045126 GG
1 GG
50045128 GGAACTTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 1 0.06
17 9 0.53
ACGTcount: A:0.29, C:0.00, G:0.65, T:0.06
Consensus pattern (15 bp):
GGTGAGGGAAAGGGA
Found at i:50053378 original size:30 final size:31
Alignment explanation
Indices: 50053317--50053378 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
50053307 AATTAACAAC
50053317 TTAGTGACTTAAATAAAAACTTTTTAATAGT
1 TTAGTGACTTAAATAAAAACTTTTTAATAGT
*
50053348 TTAGTGACTTAAAT-GAAA-TTTTTGAATAGT
1 TTAGTGACTTAAATAAAAACTTTTT-AATAGT
50053378 T
1 T
50053379 GAATGATCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
31 14 0.48
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.44
Consensus pattern (31 bp):
TTAGTGACTTAAATAAAAACTTTTTAATAGT
Found at i:50061901 original size:213 final size:214
Alignment explanation
Indices: 50061533--50061949 Score: 669
Period size: 213 Copynumber: 2.0 Consensus size: 214
50061523 TTGTTGCAAA
* * * *
50061533 CCTAATGAATGTTACTGCAGCCAGTTGCTATAATTATCGGCTATGGAAACTAGTTGAAACTGATA
1 CCTAATGAATGTTACTGCAGCCAATTGCTATAAATATCGGCTATGGAAACGAGTTGAAACTGAAA
* *
50061598 AATAGTGATTCTTAACACAGTGTTGTGGTTGCTATTTGAATCTCTTTATAATTTCTTAGTGCTAT
66 AATAGTGACTCTTAACACAGTGTTGTGGTTGCTATTTGAATCTCTCTATAATTTCTTAGTGCTAT
*
50061663 TCTCTCTTGACTGTATGCTTGGCTGC-TAAGTCCTGCTTACCCTGTTCTTGATACCTTCTATCCA
131 TCTCTCTTGACCGTATGCTTGGCTGCTTAA-TCCTGCTTACCCTGTTCTTGATACCTTCTATCCA
50061727 AATGGAATATTCATGTTTTG
195 AATGGAATATTCATGTTTTG
* *
50061747 CCTAATGAATGTTACTGCAGCCAATTGCTTTAAATATCGGCTATGGAAA-GAGTTGAAATTGAAA
1 CCTAATGAATGTTACTGCAGCCAATTGCTATAAATATCGGCTATGGAAACGAGTTGAAACTGAAA
* * * *
50061811 AATTA-TGACTCTTAACACAGTGTTGTGGTTGCTGTTTGCATCTCTCTATAATTTCTTATTGTTA
66 AA-TAGTGACTCTTAACACAGTGTTGTGGTTGCTATTTGAATCTCTCTATAATTTCTTAGTGCTA
*
50061875 TTCTCTCTTGACCGTATGTTTGGCTGCTTAATCCTGCTTACCCTGTTCTTGATACCTTCTATCCA
130 TTCTCTCTTGACCGTATGCTTGGCTGCTTAATCCTGCTTACCCTGTTCTTGATACCTTCTATCCA
50061940 AATGGAATAT
195 AATGGAATAT
50061950 GCCTCATGTA
Statistics
Matches: 187, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
213 136 0.73
214 51 0.27
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (214 bp):
CCTAATGAATGTTACTGCAGCCAATTGCTATAAATATCGGCTATGGAAACGAGTTGAAACTGAAA
AATAGTGACTCTTAACACAGTGTTGTGGTTGCTATTTGAATCTCTCTATAATTTCTTAGTGCTAT
TCTCTCTTGACCGTATGCTTGGCTGCTTAATCCTGCTTACCCTGTTCTTGATACCTTCTATCCAA
ATGGAATATTCATGTTTTG
Found at i:50070203 original size:30 final size:30
Alignment explanation
Indices: 50070167--50070227 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
50070157 ATACTATATT
50070167 TTGATATTAGTCTAATAAAATGGTAAAGAG
1 TTGATATTAGTCTAATAAAATGGTAAAGAG
50070197 TTGATATTAGTCTAATAAAATGGTAAAGAG
1 TTGATATTAGTCTAATAAAATGGTAAAGAG
50070227 T
1 T
50070228 ATATTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (30 bp):
TTGATATTAGTCTAATAAAATGGTAAAGAG
Found at i:50072001 original size:2 final size:2
Alignment explanation
Indices: 50071994--50072019 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50071984 CCTAAGGTTA
50071994 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
50072020 TATTGTGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50074177 original size:29 final size:30
Alignment explanation
Indices: 50074144--50074201 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
50074134 TGATACAATA
50074144 TGTAATT-TAATACATGA-ATTTTGATTTTG
1 TGTAATTAT-ATACATGACATTTTGATTTTG
* *
50074173 TGTAATTATATACATTACGTTTTGATTTT
1 TGTAATTATATACATGACATTTTGATTTT
50074202 AATTTAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.53
Consensus pattern (30 bp):
TGTAATTATATACATGACATTTTGATTTTG
Found at i:50082887 original size:13 final size:13
Alignment explanation
Indices: 50082869--50082898 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
50082859 CATTCAACTA
50082869 TATTCATTTTCTT
1 TATTCATTTTCTT
*
50082882 TATTCATTTTTTT
1 TATTCATTTTCTT
50082895 TATT
1 TATT
50082899 TAAAGTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (13 bp):
TATTCATTTTCTT
Found at i:50083038 original size:15 final size:17
Alignment explanation
Indices: 50083017--50083057 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
50083007 TAATCCTTTA
50083017 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
50083033 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
50083049 AAAATTATA
1 AAAATTATA
50083058 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:50094965 original size:18 final size:17
Alignment explanation
Indices: 50094926--50094970 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
50094916 TATTATTTTT
50094926 CAAAAATATTTTTGAAA
1 CAAAAATATTTTTGAAA
*
50094943 CAAAAAATATTTTTGAGA
1 C-AAAAATATTTTTGAAA
*
50094961 TAAAAATATT
1 CAAAAATATT
50094971 ACTAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (17 bp):
CAAAAATATTTTTGAAA
Found at i:50099384 original size:17 final size:17
Alignment explanation
Indices: 50099362--50099395 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
50099352 ATCCCTGACG
*
50099362 GCAATTTAACCGAGTAA
1 GCAATTTAACCAAGTAA
50099379 GCAATTTAACCAAGTAA
1 GCAATTTAACCAAGTAA
50099396 AAAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.24
Consensus pattern (17 bp):
GCAATTTAACCAAGTAA
Found at i:50111819 original size:67 final size:67
Alignment explanation
Indices: 50111739--50111872 Score: 205
Period size: 67 Copynumber: 2.0 Consensus size: 67
50111729 ATATAAACAC
* * * *
50111739 TGAGCTCTGATTTGGTGTTTAAACTGAGTCTCGTTCACTCTTTTAGTTAGTATGTTAGGTTGGTT
1 TGAGCTCTGATTTGGTGTTTAAACTGAATCTCGTTCACTCTTTTAGCTAGCATGTTAGGTTGATT
50111804 GT
66 GT
* * *
50111806 TGAGCTTTGATTTGGTGTTTGAATTGAATCTCGTTCACTCTTTTAGCTAGCATGTTAGGTTGATT
1 TGAGCTCTGATTTGGTGTTTAAACTGAATCTCGTTCACTCTTTTAGCTAGCATGTTAGGTTGATT
50111871 GT
66 GT
50111873 ACAGTGTAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.46
Consensus pattern (67 bp):
TGAGCTCTGATTTGGTGTTTAAACTGAATCTCGTTCACTCTTTTAGCTAGCATGTTAGGTTGATT
GT
Found at i:50112270 original size:5 final size:5
Alignment explanation
Indices: 50112260--50112286 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
50112250 GAAGTACACA
50112260 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
50112287 TGCTTGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:50125221 original size:18 final size:18
Alignment explanation
Indices: 50125200--50125235 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
50125190 TTTACACTAG
*
50125200 AAAAATA-ATATAAATGA
1 AAAAATACATAAAAATGA
50125217 AAAAATACATAAAAATGA
1 AAAAATACATAAAAATGA
50125235 A
1 A
50125236 GCATGTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (18 bp):
AAAAATACATAAAAATGA
Found at i:50127261 original size:7 final size:7
Alignment explanation
Indices: 50127249--50127295 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
50127239 AGAGTAATGT
50127249 AATAGAA
1 AATAGAA
50127256 AATAGAA
1 AATAGAA
50127263 AATAGAA
1 AATAGAA
50127270 AATAGAA
1 AATAGAA
50127277 AATAGAA
1 AATAGAA
50127284 AATAGAA
1 AATAGAA
*
50127291 GATAG
1 AATAG
50127296 GGCAACCGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
AATAGAA
Found at i:50128033 original size:195 final size:195
Alignment explanation
Indices: 50127689--50128078 Score: 658
Period size: 195 Copynumber: 2.0 Consensus size: 195
50127679 ATTTTTATGA
50127689 TAGTAAAAGTGTAATTTTTAAAGGATTAAATTAAAATTTTATCATTTTTAGGAGGCCAAAGTGTA
1 TAGTAAAAGTGTAATTTTTAAAGGATTAAATTAAAATTTTATCATTTTTAGGAGGCCAAAGTGTA
*
50127754 ATTTTACTTTTATTAATTTAAAATTTTAAAAAATTATAAGGGCCTAAATGAAAAAAAAATTATTT
66 ATTTTACTTTTATTAATTTAAAATTTTAAAAAATTATAAGAGCCTAAATGAAAAAAAAATTATTT
* * * *
50127819 TAAGGAGGACCAGGATCCCT-GCAAGCCCCTTTGGTTTCGCCCCTGATAAAAACCAAATTCTCAA
131 TAAGGAAGACCAAGATCCCTACCAA-CCCCTTTGATTTCGCCCCTGATAAAAACCAAATTCTCAA
50127883 T
195 T
*
50127884 TAGTAAAAGTGTAATTTTTTAAA-GATTAAATTAAAATTTTATTATTTTTAGGAGGCCAAAGTGT
1 TAGTAAAAGTGTAA-TTTTTAAAGGATTAAATTAAAATTTTATCATTTTTAGGAGGCCAAAGTGT
* **
50127948 AATTTTACTTTTATTAATTTAAAATTTTAAAAAATTATAAGAGTCTAAATGAAAAAAATTTTATT
65 AATTTTACTTTTATTAATTTAAAATTTTAAAAAATTATAAGAGCCTAAATGAAAAAAAAATTATT
*
50128013 TTAAGGAAGACCAAGATCCCTACCAACCCCTTTGATTTCGCCCCTGATAAAAATCAAATTCTCAA
130 TTAAGGAAGACCAAGATCCCTACCAACCCCTTTGATTTCGCCCCTGATAAAAACCAAATTCTCAA
50128078 T
195 T
50128079 CACTAATTAA
Statistics
Matches: 183, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
195 172 0.94
196 11 0.06
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (195 bp):
TAGTAAAAGTGTAATTTTTAAAGGATTAAATTAAAATTTTATCATTTTTAGGAGGCCAAAGTGTA
ATTTTACTTTTATTAATTTAAAATTTTAAAAAATTATAAGAGCCTAAATGAAAAAAAAATTATTT
TAAGGAAGACCAAGATCCCTACCAACCCCTTTGATTTCGCCCCTGATAAAAACCAAATTCTCAAT
Found at i:50135653 original size:9 final size:9
Alignment explanation
Indices: 50135625--50135654 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
50135615 CATCGCTCAA
50135625 TTTTCTTCT
1 TTTTCTTCT
*
50135634 TCTTCTTCT
1 TTTTCTTCT
50135643 TTTTCTTCT
1 TTTTCTTCT
50135652 TTT
1 TTT
50135655 CAATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:50136527 original size:209 final size:208
Alignment explanation
Indices: 50136286--50136699 Score: 643
Period size: 209 Copynumber: 2.0 Consensus size: 208
50136276 ATTTTAGAGG
*
50136286 TTTCAAGATTTTCATATAAATAATGAATCAAAGCTCTTACATTGTAAAATGAGTTTGATTTTGAT
1 TTTCAAGATTTTCATATAAATAATGAATCAAAGCTCATACATTGTAAAATGAGTTTGATTTTGAT
* ** *
50136351 TCATCATTTTCGCATAAACTTGAGTATTTAAC-TTAGAGGTTTCAAGATTTTCATATAAATAATG
66 TCATCATTTTCACATAAACACGAGTATTTAACATT-GAGGTTTCAACATTTTCATATAAATAATG
* * * *
50136415 AATCAAAGCTCTTACATTGTAGTATGAGTTTGATTTTGAT-TAGGAATTTTCGCCTAAACTCAGA
130 AACCAAAGCTCTTACATTGTAGCATGAGTTTGATTTTGATCT-GGAATATTCGCATAAACTC-GA
50136479 ATATTTAACTTAGAAT
193 ATATTTAACTTAGAAT
* * *
50136495 TTTCAAGGTTTTCATGTAAATAATGAATCAAAGCTCATACATTGTAGAATGAGTTTGATTTTGAT
1 TTTCAAGATTTTCATATAAATAATGAATCAAAGCTCATACATTGTAAAATGAGTTTGATTTTGAT
* *
50136560 TCATCATTTTCACATAAACACGAGTTTTTAACATTGAGGTTTCAACATTTTCATGTAAATAATGA
66 TCATCATTTTCACATAAACACGAGTATTTAACATTGAGGTTTCAACATTTTCATATAAATAATGA
* *
50136625 ACCAAAGCTCTTACATTGTAGCATGAGTTTGATTTTGATCTGTAATATTCGCATAAACTCGAGTA
131 ACCAAAGCTCTTACATTGTAGCATGAGTTTGATTTTGATCTGGAATATTCGCATAAACTCGAATA
50136690 TTTAACTTAG
196 TTTAACTTAG
50136700 TGGTTGGTGC
Statistics
Matches: 187, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
208 14 0.07
209 170 0.91
210 3 0.02
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (208 bp):
TTTCAAGATTTTCATATAAATAATGAATCAAAGCTCATACATTGTAAAATGAGTTTGATTTTGAT
TCATCATTTTCACATAAACACGAGTATTTAACATTGAGGTTTCAACATTTTCATATAAATAATGA
ACCAAAGCTCTTACATTGTAGCATGAGTTTGATTTTGATCTGGAATATTCGCATAAACTCGAATA
TTTAACTTAGAAT
Found at i:50136539 original size:105 final size:104
Alignment explanation
Indices: 50136279--50136704 Score: 588
Period size: 104 Copynumber: 4.1 Consensus size: 104
50136269 TGTTGTAATT
*
50136279 TTAGAGGTTTCAAGATTTTCATATAAATAATGAATCAAAGCTCTTACATTGTAAAATGAGTTTGA
1 TTAGAGGTTTCAAGATTTTCATATAAATAATGAATCAAAGCTCTTACATTGTAGAATGAGTTTGA
* *
50136344 TTTTGATTCATCATTTTCGCATAAACTTGAGTATTTAAC
66 TTTTGATTCATAATTTTCGCATAAACTCGAGTATTTAAC
*
50136383 TTAGAGGTTTCAAGATTTTCATATAAATAATGAATCAAAGCTCTTACATTGTAGTATGAGTTTGA
1 TTAGAGGTTTCAAGATTTTCATATAAATAATGAATCAAAGCTCTTACATTGTAGAATGAGTTTGA
* * *
50136448 TTTTGATT-AGGAATTTTCGCCTAAACTCAGAATATTTAAC
66 TTTTGATTCA-TAATTTTCGCATAAACTC-GAGTATTTAAC
** * * *
50136488 TTAGAATTTTCAAGGTTTTCATGTAAATAATGAATCAAAGCTCATACATTGTAGAATGAGTTTGA
1 TTAGAGGTTTCAAGATTTTCATATAAATAATGAATCAAAGCTCTTACATTGTAGAATGAGTTTGA
* * * *
50136553 TTTTGATTCATCATTTTCACATAAACACGAGTTTTTAAC
66 TTTTGATTCATAATTTTCGCATAAACTCGAGTATTTAAC
* * * *
50136592 ATT-GAGGTTTCAACATTTTCATGTAAATAATGAACCAAAGCTCTTACATTGTAGCATGAGTTTG
1 -TTAGAGGTTTCAAGATTTTCATATAAATAATGAATCAAAGCTCTTACATTGTAGAATGAGTTTG
* *
50136656 ATTTTGA-TCTGTAATATTCGCATAAACTCGAGTATTTAAC
65 ATTTTGATTC-ATAATTTTCGCATAAACTCGAGTATTTAAC
*
50136696 TTAGTGGTT
1 TTAGAGGTT
50136705 GGTGCATGAT
Statistics
Matches: 282, Mismatches: 34, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
103 5 0.02
104 184 0.65
105 92 0.33
106 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (104 bp):
TTAGAGGTTTCAAGATTTTCATATAAATAATGAATCAAAGCTCTTACATTGTAGAATGAGTTTGA
TTTTGATTCATAATTTTCGCATAAACTCGAGTATTTAAC
Found at i:50142650 original size:15 final size:15
Alignment explanation
Indices: 50142630--50142659 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
50142620 ATACCATTAA
*
50142630 TATTTAGACTTATTT
1 TATTTAGACTAATTT
50142645 TATTTAGACTAATTT
1 TATTTAGACTAATTT
50142660 GATAAGGTCC
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:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (15 bp):
TATTTAGACTAATTT
Found at i:50143743 original size:13 final size:13
Alignment explanation
Indices: 50143725--50143749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50143715 ATTTTACATT
50143725 TTAGGGGTGTCAG
1 TTAGGGGTGTCAG
50143738 TTAGGGGTGTCA
1 TTAGGGGTGTCA
50143750 AGCCTGTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.44, T:0.32
Consensus pattern (13 bp):
TTAGGGGTGTCAG
Found at i:50144502 original size:35 final size:32
Alignment explanation
Indices: 50144444--50144513 Score: 79
Period size: 35 Copynumber: 2.1 Consensus size: 32
50144434 ATTTGAAACG
*
50144444 TTTTATTTAAATCATTGAACTATTCAAAAGTTTTT
1 TTTTATTTAAATCAGTGAACTATT---AAGTTTTT
*
50144479 TTTTATTTAAGTCAGT-AATCTATTAAGTTTTT
1 TTTTATTTAAATCAGTGAA-CTATTAAGTTTTT
50144511 TTT
1 TTT
50144514 AAAAAAACCC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 11 0.34
34 2 0.06
35 19 0.59
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (32 bp):
TTTTATTTAAATCAGTGAACTATTAAGTTTTT
Found at i:50147430 original size:59 final size:60
Alignment explanation
Indices: 50147291--50147446 Score: 206
Period size: 59 Copynumber: 2.6 Consensus size: 60
50147281 TTTTTGGCCC
* * *
50147291 CTATAGTGAAATTCTCACTTTGACCCTTTTACTAATTTTTTTGATCATTTTGCCCCTTGCA
1 CTATAGTGAAATTCTCACTTTGACCCTTTTACT-ATTATTTTGATCACTTTGCCCCTTACA
* * * * *
50147352 CTATAATGAAATTCTCACTTTAACCATTTTACTATTATTTT-ATCACTTTGCTCCTTATA
1 CTATAGTGAAATTCTCACTTTGACCCTTTTACTATTATTTTGATCACTTTGCCCCTTACA
* *
50147411 CTATAGTAAAATTCTCACTTTGTCCCTTTTACTATT
1 CTATAGTGAAATTCTCACTTTGACCCTTTTACTATT
50147447 TTGTTCGGTT
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 45 0.55
60 7 0.09
61 30 0.37
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (60 bp):
CTATAGTGAAATTCTCACTTTGACCCTTTTACTATTATTTTGATCACTTTGCCCCTTACA
Found at i:50155708 original size:29 final size:29
Alignment explanation
Indices: 50155667--50155732 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
50155657 ATTTGACTTT
*
50155667 ATTTGATT-TTTTAATAGT-GCAAGGACTA
1 ATTTGATTCATTTAATAGTAG-AAGGACTA
* *
50155695 ATTTGATTCATTTAATAGTAGATGGATTA
1 ATTTGATTCATTTAATAGTAGAAGGACTA
50155724 ATTTGATTC
1 ATTTGATTC
50155733 GATCACTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 8 0.24
29 24 0.73
30 1 0.03
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (29 bp):
ATTTGATTCATTTAATAGTAGAAGGACTA
Found at i:50158122 original size:95 final size:96
Alignment explanation
Indices: 50157931--50158615 Score: 904
Period size: 97 Copynumber: 7.1 Consensus size: 96
50157921 TTGATCGTCC
* * * *
50157931 TCATTGCTTGGTAT-GTGTTAGCGAGTCATATTGATTTCAAAATGTTTTAGTTGTTCTTTTATTG
1 TCATTGCTTGGT-TCGTGTTAGCAAGTTATATCGATTTCAAAATGTTTTGGTTGTT-TTTTATTG
*
50157995 GCATTACGGTTCTATCTTCCTACATTCGAGTTT
64 GCATTACGGTTCCATCTTCCTACATTCGAGTTT
* * ** *
50158028 TCATTGCTTGGTTCATGTTAGCAAGTTATATCAATTTCAAAATGTTTCT-GTT-TTCCTTATTGA
1 TCATTGCTTGGTTCGTGTTAGCAAGTTATATCGATTTCAAAATGTTT-TGGTTGTTTTTTATTGG
*
50158091 CATTACGGTTCCATCTTCCTACATTCAAGTTT
65 CATTACGGTTCCATCTTCCTACATTCGAGTTT
* * * *
50158123 TCATTGCTTGGTTCTTATTAGCAAGTCATATTGATTTCAAAATGTTTTGGTTGTTTTTTTATTGG
1 TCATTGCTTGGTTCGTGTTAGCAAGTTATATCGATTTCAAAATGTTTTGGTTG-TTTTTTATTGG
*
50158188 CGTTACGGTTCCATCTTCCTACAATT-GAGTTT
65 CATTACGGTTCCATCTTCCTAC-ATTCGAGTTT
* * * *
50158220 TCATTGCTTGGTTCGTGTTAGCAAGTTATATCGGTTTCGAAATGTTTCT-G-TCTTTTTTATTGA
1 TCATTGCTTGGTTCGTGTTAGCAAGTTATATCGATTTCAAAATGTTT-TGGTTGTTTTTTATTGG
* *
50158283 CATTTCGGTTCCATCTTCCTACATTCAAGTTT
65 CATTACGGTTCCATCTTCCTACATTCGAGTTT
**
50158315 TCATTGCTTGGTTCGTGTTAGCAAGTTATATCGATTTTGGAAATGTTTTGGTTGTTTTTTATTGG
1 TCATTGCTTGGTTCGTGTTAGCAAGTTATATCGA-TTTCAAAATGTTTTGGTTGTTTTTTATTGG
*
50158380 CATTACGGTTCCATCTTCCTACATTTGAGTTGT
65 CATTACGGTTCCATCTTCCTACATTCGAGTT-T
*
50158413 T-ATTGCTTGGTTCATGTTAGCAAGTTATATCGA--TCAAAATGTTTTGGTTGCTTTTTT-TTGG
1 TCATTGCTTGGTTCGTGTTAGCAAGTTATATCGATTTCAAAATGTTTTGGTTG-TTTTTTATTGG
* * * *
50158474 CTTTATGGTTCCTTCTTCCTACATTCAAGTTT
65 CATTACGGTTCCATCTTCCTACATTCGAGTTT
*
50158506 TCATTGCTTGGTTCGTGTTAGCAAGTTATATCGATTTTCATAATGTTTTGGTTGTTTTTTATTGG
1 TCATTGCTTGGTTCGTGTTAGCAAGTTATATCGA-TTTCAAAATGTTTTGGTTGTTTTTTATTGG
* *
50158571 CATTACGGTTCCATCTTCCTACATTTGAGTTG
65 CATTACGGTTCCATCTTCCTACATTCGAGTTT
*
50158603 TCATTGGTTGGTT
1 TCATTGCTTGGTT
50158616 TTATGGTTCC
Statistics
Matches: 515, Mismatches: 55, Indels: 36
0.85 0.09 0.06
Matches are distributed among these distances:
93 2 0.00
94 80 0.16
95 156 0.30
96 23 0.04
97 247 0.48
98 7 0.01
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (96 bp):
TCATTGCTTGGTTCGTGTTAGCAAGTTATATCGATTTCAAAATGTTTTGGTTGTTTTTTATTGGC
ATTACGGTTCCATCTTCCTACATTCGAGTTT
Found at i:50158265 original size:192 final size:190
Alignment explanation
Indices: 50157931--50158615 Score: 961
Period size: 192 Copynumber: 3.6 Consensus size: 190
50157921 TTGATCGTCC
* * *
50157931 TCATTGCTTGGTAT-GTGTTAGCGAGTCATATTGA-TTTCAAAATGTTTTAGTTGTTCTTTTATT
1 TCATTGCTTGGT-TCGTGTTAGCAAGTCATATCGATTTTCAAAATGTTTTGGTTGTT-TTTTATT
*
50157994 GGCATTACGGTTCTATCTTCCTAC-ATTCGAGTTTTCATTGCTTGGTTCATGTTAGCAAGTTATA
64 GGCATTACGGTTCCATCTTCCTACAATT-GAGTTTTCATTGCTTGGTTCATGTTAGCAAGTTATA
* *
50158058 TCAATTTCAAAATGTTTCTGTTTTCCTTATTGACATTACGGTTCCATCTTCCTACATTCAAGTTT
128 TC-GTTTCAAAATGTTTCTGTTTT-TTTATTGACATTACGGTTCCATCTTCCTACATTCAAGTTT
* * *
50158123 TCATTGCTTGGTTCTTATTAGCAAGTCATATTGA-TTTCAAAATGTTTTGGTTGTTTTTTTATTG
1 TCATTGCTTGGTTCGTGTTAGCAAGTCATATCGATTTTCAAAATGTTTTGGTTG-TTTTTTATTG
* *
50158187 GCGTTACGGTTCCATCTTCCTACAATTGAGTTTTCATTGCTTGGTTCGTGTTAGCAAGTTATATC
65 GCATTACGGTTCCATCTTCCTACAATTGAGTTTTCATTGCTTGGTTCATGTTAGCAAGTTATATC
* *
50158252 GGTTTCGAAATGTTTCTGTCTTTTTTATTGACATTTCGGTTCCATCTTCCTACATTCAAGTTT
130 -GTTTCAAAATGTTTCTGT-TTTTTTATTGACATTACGGTTCCATCTTCCTACATTCAAGTTT
* **
50158315 TCATTGCTTGGTTCGTGTTAGCAAGTTATATCGATTTTGGAAATGTTTTGGTTGTTTTTTATTGG
1 TCATTGCTTGGTTCGTGTTAGCAAGTCATATCGATTTTCAAAATGTTTTGGTTGTTTTTTATTGG
*
50158380 CATTACGGTTCCATCTTCCTACATTTGAGTTGTT-ATTGCTTGGTTCATGTTAGCAAGTTATATC
66 CATTACGGTTCCATCTTCCTACAATTGAGTT-TTCATTGCTTGGTTCATGTTAGCAAGTTATATC
* * * * * *
50158444 G-ATCAAAATGTTT-TGGTTGCTTTTTTTTGGCTTTATGGTTCCTTCTTCCTACATTCAAGTTT
130 GTTTCAAAATGTTTCT-GTT--TTTTTATTGACATTACGGTTCCATCTTCCTACATTCAAGTTT
* *
50158506 TCATTGCTTGGTTCGTGTTAGCAAGTTATATCGATTTTCATAATGTTTTGGTTGTTTTTTATTGG
1 TCATTGCTTGGTTCGTGTTAGCAAGTCATATCGATTTTCAAAATGTTTTGGTTGTTTTTTATTGG
* * *
50158571 CATTACGGTTCCATCTTCCTACATTTGAGTTGTCATTGGTTGGTT
66 CATTACGGTTCCATCTTCCTACAATTGAGTTTTCATTGCTTGGTT
50158616 TTATGGTTCC
Statistics
Matches: 449, Mismatches: 34, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
189 2 0.00
190 13 0.03
191 141 0.31
192 266 0.59
193 27 0.06
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (190 bp):
TCATTGCTTGGTTCGTGTTAGCAAGTCATATCGATTTTCAAAATGTTTTGGTTGTTTTTTATTGG
CATTACGGTTCCATCTTCCTACAATTGAGTTTTCATTGCTTGGTTCATGTTAGCAAGTTATATCG
TTTCAAAATGTTTCTGTTTTTTTATTGACATTACGGTTCCATCTTCCTACATTCAAGTTT
Found at i:50165173 original size:2 final size:2
Alignment explanation
Indices: 50165166--50165200 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
50165156 TTTTAATTTT
50165166 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
50165201 TAAATTAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50169924 original size:20 final size:20
Alignment explanation
Indices: 50169887--50169924 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
50169877 CCGTTCAATA
*
50169887 AATATTTTATTCATATATAT
1 AATATTTTAATCATATATAT
50169907 AATATTTTAGATCA-ATAT
1 AATATTTTA-ATCATATAT
50169925 GTTAAAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (20 bp):
AATATTTTAATCATATATAT
Found at i:50178841 original size:91 final size:91
Alignment explanation
Indices: 50178715--50178934 Score: 264
Period size: 91 Copynumber: 2.4 Consensus size: 91
50178705 TGATATCTGC
* * * * *
50178715 ACTTTGAAAATGTCTAATCTGGTACATAAATTATCAATTTGTGCATTATTTGGCACTTCTAATTT
1 ACTTTGAAAATGTCTAATGTGGTACTTAAACTATCAATTTGTGCATTATTTGGCACCTATAATTT
** *
50178780 CACAAAATATCTGATGTAGTACTTGT
66 CACAAAATATCCAATGTAGTACTTAT
* * * *
50178806 ACTTTGAAAATGTCTAATGTGGTACTTGAACTATCAATTTGTGTATTATTTGGTACCTATACTTT
1 ACTTTGAAAATGTCTAATGTGGTACTTAAACTATCAATTTGTGCATTATTTGGCACCTATAATTT
* * * *
50178871 TATAAAATCTCCAATGTGGTACTTAT
66 CACAAAATATCCAATGTAGTACTTAT
50178897 ACTTTGAAAATGT-TCAATGTGGTA-TCTAAACTATCAAT
1 ACTTTGAAAATGTCT-AATGTGGTACT-TAAACTATCAAT
50178935 ATGCATATTA
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
90 2 0.02
91 108 0.98
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (91 bp):
ACTTTGAAAATGTCTAATGTGGTACTTAAACTATCAATTTGTGCATTATTTGGCACCTATAATTT
CACAAAATATCCAATGTAGTACTTAT
Found at i:50186806 original size:9 final size:9
Alignment explanation
Indices: 50186792--50186817 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
50186782 TTTTAGACCC
50186792 TAAAATTTA
1 TAAAATTTA
50186801 TAAAATTTA
1 TAAAATTTA
50186810 TAAAATTT
1 TAAAATTT
50186818 TAAGTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TAAAATTTA
Found at i:50193803 original size:20 final size:21
Alignment explanation
Indices: 50193760--50193808 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
50193750 TAGTTAATGA
*
50193760 ATTTGTTGTATACATTTATTCT
1 ATTTGTTG-ATACATTTATCCT
*
50193782 ATTTGTTG-TACGTTTATCCT
1 ATTTGTTGATACATTTATCCT
50193802 ATTTGTT
1 ATTTGTT
50193809 TTTCAGTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 17 0.68
22 8 0.32
ACGTcount: A:0.18, C:0.10, G:0.12, T:0.59
Consensus pattern (21 bp):
ATTTGTTGATACATTTATCCT
Found at i:50193820 original size:24 final size:25
Alignment explanation
Indices: 50193789--50193866 Score: 72
Period size: 24 Copynumber: 3.1 Consensus size: 25
50193779 TCTATTTGTT
50193789 GTACGTTTATCCTATTTGTTTTTCA
1 GTACGTTTATCCTATTTGTTTTTCA
*** *
50193814 GTA-GTTTATGGAATGTGAATTTGTT--
1 GTACGTTTATCCTATTTG--TTT-TTCA
50193839 GTACGTTTATCCTATTTGTTTTTCA
1 GTACGTTTATCCTATTTGTTTTTCA
50193864 GTA
1 GTA
50193867 AATGTAGTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
23 2 0.05
24 13 0.33
25 9 0.23
26 13 0.33
27 2 0.05
ACGTcount: A:0.19, C:0.10, G:0.18, T:0.53
Consensus pattern (25 bp):
GTACGTTTATCCTATTTGTTTTTCA
Found at i:50196913 original size:3 final size:3
Alignment explanation
Indices: 50196907--50196935 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
50196897 TAATCTGTTG
50196907 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
50196936 TGCTAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:50214977 original size:28 final size:28
Alignment explanation
Indices: 50214936--50214989 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
50214926 TAATATATAA
*
50214936 TTATTATTTCTATAAAAGAGTATTTTAC
1 TTATTATTTATATAAAAGAGTATTTTAC
* *
50214964 TTATTATTTATATAGAAGAGTCTTTT
1 TTATTATTTATATAAAAGAGTATTTT
50214990 TTTATTAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (28 bp):
TTATTATTTATATAAAAGAGTATTTTAC
Found at i:50216138 original size:28 final size:28
Alignment explanation
Indices: 50216098--50216159 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
50216088 AAATTACTCT
50216098 TTTTCTTAATTTCGT-ATCTCA-ATTTGATA
1 TTTT-TTAATTTCGTAAT-T-ATATTTGATA
50216127 TTTTTTAATTTCGTAATTATATTTGATA
1 TTTTTTAATTTCGTAATTATATTTGATA
50216155 TTTTT
1 TTTTT
50216160 CAAGTTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
27 1 0.03
28 24 0.77
29 6 0.19
ACGTcount: A:0.24, C:0.08, G:0.06, T:0.61
Consensus pattern (28 bp):
TTTTTTAATTTCGTAATTATATTTGATA
Found at i:50216223 original size:27 final size:29
Alignment explanation
Indices: 50216176--50216258 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 29
50216166 AATATTTAAT
50216176 TTTTTTGTCTC-ATTT-AGTACTTAAACATGA
1 TTTTTTGT-TCAATTTGA-TACTTAAAC-TGA
* *
50216206 -TTTTT-TT-AATTTGATACTTAATCTTA
1 TTTTTTGTTCAATTTGATACTTAAACTGA
*
50216232 TTTTTTGTTCAATTTGATACTTGAACT
1 TTTTTTGTTCAATTTGATACTTAAACT
50216259 TGTCAAAGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
26 2 0.05
27 18 0.41
28 4 0.09
29 20 0.45
ACGTcount: A:0.25, C:0.11, G:0.08, T:0.55
Consensus pattern (29 bp):
TTTTTTGTTCAATTTGATACTTAAACTGA
Found at i:50216835 original size:1 final size:1
Alignment explanation
Indices: 50216829--50216857 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
50216819 AAATACTATT
50216829 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
50216858 AATCAAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:50231483 original size:31 final size:31
Alignment explanation
Indices: 50231443--50231571 Score: 111
Period size: 31 Copynumber: 4.2 Consensus size: 31
50231433 AAGGATTTCC
* * *
50231443 AAAACTTTTGGAGGGTTTAATTAACATTTTT
1 AAAAATTTTGGAAGGTTTAATTAAAATTTTT
* * *
50231474 AAAAATTTT-GATAGGATTAA-TGATATTTTT
1 AAAAATTTTGGA-AGGTTTAATTAAAATTTTT
* *
50231504 CAAAAATATTGG-AGAGTATAATTAAAATTTTT
1 -AAAAATTTTGGAAG-GTTTAATTAAAATTTTT
* * *
50231536 AAAACTTTTGGAAGGCTTAATTAAAATTTCT
1 AAAAATTTTGGAAGGTTTAATTAAAATTTTT
50231567 AAAAA
1 AAAAA
50231572 AAGTGATGGG
Statistics
Matches: 76, Mismatches: 16, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 12 0.16
31 53 0.70
32 11 0.14
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (31 bp):
AAAAATTTTGGAAGGTTTAATTAAAATTTTT
Found at i:50231571 original size:62 final size:62
Alignment explanation
Indices: 50231428--50231572 Score: 141
Period size: 62 Copynumber: 2.3 Consensus size: 62
50231418 ATTTAGTGGC
* * * * * *
50231428 TTAATAAGGATTTC-CAAAACTTTTGGAGGGTTTAATTAACATTTTTAAAAATTTTGATAGGA
1 TTAATAA-AATTTCTCAAAAATATTGGAGAGTATAATTAAAATTTTTAAAAATTTTGATAGGA
* * * * *
50231490 TTAATGATATTTTTCAAAAATATTGGAGAGTATAATTAAAATTTTTAAAACTTTTGGA-AGGC
1 TTAATAAAATTTCTCAAAAATATTGGAGAGTATAATTAAAATTTTTAAAAATTTT-GATAGGA
*
50231552 TTAATTAAAATTTCTAAAAAA
1 TTAA-TAAAATTTCTCAAAAA
50231573 AGTGATGGGA
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
61 4 0.06
62 48 0.73
63 14 0.21
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (62 bp):
TTAATAAAATTTCTCAAAAATATTGGAGAGTATAATTAAAATTTTTAAAAATTTTGATAGGA
Found at i:50238845 original size:29 final size:29
Alignment explanation
Indices: 50238811--50238866 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
50238801 GTTTGATATT
* *
50238811 TTTAATAGTACAACGATTAAATTGATCAA
1 TTTAATAATACAACGACTAAATTGATCAA
* *
50238840 TTTAATAATACAATGACTAATTTGATC
1 TTTAATAATACAACGACTAAATTGATC
50238867 CGGTACTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (29 bp):
TTTAATAATACAACGACTAAATTGATCAA
Found at i:50244003 original size:19 final size:19
Alignment explanation
Indices: 50243979--50244016 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
50243969 TGTATTCAAG
50243979 ATAGCAAATTAATTTTGAT
1 ATAGCAAATTAATTTTGAT
50243998 ATAGCAAATTAATTTTGAT
1 ATAGCAAATTAATTTTGAT
50244017 CTTTCTAGGC
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:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (19 bp):
ATAGCAAATTAATTTTGAT
Found at i:50255365 original size:21 final size:20
Alignment explanation
Indices: 50255353--50255419 Score: 86
Period size: 19 Copynumber: 3.5 Consensus size: 20
50255343 AATTATTCTC
50255353 TAAAAAATTCAAAATATTTA
1 TAAAAAATTCAAAATATTTA
*
50255373 TAAAAATTTCAAAAT-TTT-
1 TAAAAAATTCAAAATATTTA
* *
50255391 TAAAAAATTAAAAATTTTTA
1 TAAAAAATTCAAAATATTTA
50255411 -AAAAAATTC
1 TAAAAAATTC
50255420 TAAAGAATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 13 0.32
19 14 0.34
20 14 0.34
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAAATTCAAAATATTTA
Done.