Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 91 of 198
Found at i:29128005 original size:31 final size:31
Alignment explanation
Indices: 29127970--29128029 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
29127960 CAACAACCCA
29127970 GTGACTTAAATAAAAACTTCTAAATAGTTTG
1 GTGACTTAAATAAAAACTTCTAAATAGTTTG
* * *
29128001 GTGACTTAAATGAAAACTTTTGAATAGTT
1 GTGACTTAAATAAAAACTTCTAAATAGTT
29128030 CAATGACCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (31 bp):
GTGACTTAAATAAAAACTTCTAAATAGTTTG
Found at i:29129492 original size:33 final size:33
Alignment explanation
Indices: 29129451--29129516 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
29129441 AAGGTATGTG
29129451 ATATATATGTGTGCGTGAATGATATACTGATAA
1 ATATATATGTGTGCGTGAATGATATACTGATAA
29129484 ATATATATGTGTGCGTGAATGATATACTGATAA
1 ATATATATGTGTGCGTGAATGATATACTGATAA
29129517 TTCTGATGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (33 bp):
ATATATATGTGTGCGTGAATGATATACTGATAA
Found at i:29132714 original size:25 final size:26
Alignment explanation
Indices: 29132680--29132729 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
29132670 GATGTTGTGG
* * *
29132680 CTTTGCTTT-GTTTTTTTTTTTTTTA
1 CTTTGATTTGGTTTTTATCTTTTTTA
29132705 CTTTGATTTGGTTTTTATCTTTTTT
1 CTTTGATTTGGTTTTTATCTTTTTT
29132730 GGTTTTAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.06, C:0.08, G:0.10, T:0.76
Consensus pattern (26 bp):
CTTTGATTTGGTTTTTATCTTTTTTA
Found at i:29134183 original size:125 final size:126
Alignment explanation
Indices: 29133811--29134224 Score: 652
Period size: 126 Copynumber: 3.3 Consensus size: 126
29133801 TTTAAAAAAA
* * * * * *
29133811 CTCCCACGTGGACACTCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTTGAGAAAACGTTTCTG
1 CTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTG
29133876 AGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAG
66 AGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAG
*
29133937 CTCCTACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTG
1 CTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTG
* * **
29134002 AGAAAATAGTG-CAAAAAATGCTTTAAGCAGGACCCTTTGTCAGCAAAAGTACTGAAAGAAG
66 AGCAAATAGTGTC-AAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAG
* *
29134063 CTCCCACGTGGACGCGCTTTTGCTACAATAGCTCCT-AAAAAATAATTTCGAGTAGACGTTTCTA
1 CTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTG
* *
29134127 AGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGACAGCAAAAGTATTGAAAGAAG
66 AGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAG
* *
29134188 CTCTCACGTGGACGCGTTTTTGCTACAGTAGCTCCTG
1 CTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG
29134225 TTTGGCCTGA
Statistics
Matches: 262, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
125 114 0.44
126 148 0.56
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (126 bp):
CTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTG
AGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAG
Found at i:29137237 original size:116 final size:116
Alignment explanation
Indices: 29137033--29137243 Score: 316
Period size: 116 Copynumber: 1.8 Consensus size: 116
29137023 ACATTATTTG
* *
29137033 TATTTTATTAAATCAAATAATATGGAAATATTCAGAATATTGACTTATTTAAAAGAAAATTTATT
1 TATTTTATTAAATCAAATAATATAGAAATATTCAAAATATTGACTTATTTAAAAGAAAATTTATT
* *
29137098 TTATTAAAAATATTAAAGTAAATTACAATTACTTTATTCAAAACAGCGTTT
66 ATATTAAAAATATAAAAGTAAATTACAATTACTTTATTCAAAACAGCGTTT
* ** *
29137149 TATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTGTTATTTAAAAG-AATTTCTAT
1 TATTTTATTAAATCAAATAATATAGAAATATTCAAAATATTGACTTATTTAAAAGAAAATT-TAT
* *
29137213 TATATTAAAAATGTAAAAGTAAATTTCAATT
65 TATATTAAAAATATAAAAGTAAATTACAATT
29137244 TTATAACATG
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
115 4 0.05
116 80 0.95
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (116 bp):
TATTTTATTAAATCAAATAATATAGAAATATTCAAAATATTGACTTATTTAAAAGAAAATTTATT
ATATTAAAAATATAAAAGTAAATTACAATTACTTTATTCAAAACAGCGTTT
Found at i:29137442 original size:21 final size:21
Alignment explanation
Indices: 29137418--29137457 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29137408 TTGTCCAGCT
* *
29137418 TCCGCCGGGGGTTGTGGTTGC
1 TCCGCCGGGGATTCTGGTTGC
*
29137439 TCCGGCGGGGATTCTGGTT
1 TCCGCCGGGGATTCTGGTT
29137458 CATTCGGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.23, G:0.45, T:0.30
Consensus pattern (21 bp):
TCCGCCGGGGATTCTGGTTGC
Found at i:29137752 original size:18 final size:18
Alignment explanation
Indices: 29137725--29137762 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29137715 GAAAAGGGAA
* *
29137725 ACATATAAGGGTTAGGAT
1 ACATAAAAGGGCTAGGAT
29137743 ACATAAAAGGGCTAGGAT
1 ACATAAAAGGGCTAGGAT
29137761 AC
1 AC
29137763 GCACCTAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (18 bp):
ACATAAAAGGGCTAGGAT
Found at i:29139587 original size:11 final size:11
Alignment explanation
Indices: 29139573--29139653 Score: 94
Period size: 11 Copynumber: 7.4 Consensus size: 11
29139563 AGCTTTTTTA
29139573 AGAGGAATTTG
1 AGAGGAATTTG
*
29139584 AGAGGAAATTG
1 AGAGGAATTTG
*
29139595 AAAGGAATTTG
1 AGAGGAATTTG
29139606 AGAGGAATTTG
1 AGAGGAATTTG
*
29139617 AGAGAAATTTG
1 AGAGGAATTTG
29139628 AGA-GAATATTG
1 AGAGGAAT-TTG
*
29139639 -GAGAGAAATTG
1 AGAG-GAATTTG
29139650 AGAG
1 AGAG
29139654 AAAGGATTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
10 5 0.08
11 48 0.81
12 6 0.10
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.23
Consensus pattern (11 bp):
AGAGGAATTTG
Found at i:29139958 original size:29 final size:29
Alignment explanation
Indices: 29139893--29139958 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 29
29139883 GTTTTTGGGG
*
29139893 AAATAGGG-CCATTCCAGTAATTAATTTTT
1 AAATAGGGCCCATTCCAGTAATT-ATTTTA
* *
29139922 CAAT-GGGCCCATTTCAGTAATT-TTTTAA
1 AAATAGGGCCCATTCCAGTAATTATTTT-A
29139950 AAATAGGGC
1 AAATAGGGC
29139959 TTTTATTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
27 4 0.13
28 6 0.20
29 20 0.67
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (29 bp):
AAATAGGGCCCATTCCAGTAATTATTTTA
Found at i:29145394 original size:14 final size:16
Alignment explanation
Indices: 29145365--29145396 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
29145355 TTGAACTGGA
29145365 TTTGTCTTTGTTTGTT
1 TTTGTCTTTGTTTGTT
29145381 TTTGT-TTT-TTTGTT
1 TTTGTCTTTGTTTGTT
29145395 TT
1 TT
29145397 GGGCTTGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.81
Consensus pattern (16 bp):
TTTGTCTTTGTTTGTT
Found at i:29149802 original size:21 final size:21
Alignment explanation
Indices: 29149776--29149821 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
29149766 TTATAACAGA
* *
29149776 TACAGATCATGCTTATCATAT
1 TACAGATCATACATATCATAT
*
29149797 TACAGATCATACATATCGTAT
1 TACAGATCATACATATCATAT
29149818 TACA
1 TACA
29149822 TTTTATACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
TACAGATCATACATATCATAT
Found at i:29161573 original size:51 final size:50
Alignment explanation
Indices: 29161450--29161732 Score: 134
Period size: 51 Copynumber: 5.6 Consensus size: 50
29161440 TATCGATGAA
** * * * * *
29161450 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAG-TAATGG
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGCACCAAGAAGCT-TTGG
* * *
29161500 TCACATGTGTGGTACTAAGTGAAGGCTACTATGTGCACCAAGAAGCTTTGAG
1 -CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGCACCAAGAAGCTTTG-G
** * * * * **
29161552 CACGTGTGTAGTACTGTGTGAATGCTA-TCACGTGTC-TC-GGTAAACTACGG
1 CACGTGTGTAGTACTAAGTGAAGGCTACT-ACGTG-CACCAAG-AAGCTTTGG
* ** * * * *
29161602 TTATATGTGTAGTACTAAGTGAAGGCTACTATGTGAACTAAGAAGC-TTGAA
1 -CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGCACCAAGAAGCTTTG-G
* * *
29161653 CACGTGTGTAGTACTGAGTGAAGGCTACTACGTG-AGTCGTAA-AA-C-TTGTT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGCA--C-CAAGAAGCTTTG-G
*
29161703 CACGTGTGTAGTACTATGTGAAGGCTACTA
1 CACGTGTGTAGTACTAAGTGAAGGCTACTA
29161733 TGTAAATTGT
Statistics
Matches: 174, Mismatches: 45, Indels: 27
0.71 0.18 0.11
Matches are distributed among these distances:
49 1 0.01
50 65 0.37
51 100 0.57
52 8 0.05
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTAAGTGAAGGCTACTACGTGCACCAAGAAGCTTTGG
Found at i:29161626 original size:102 final size:100
Alignment explanation
Indices: 29161446--29161777 Score: 354
Period size: 102 Copynumber: 3.3 Consensus size: 100
29161436 TAAGTATCGA
* * * * *
29161446 TGAACACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAGTAATGGTCACATGTGTG
1 TGAACACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGGTAAAT-ACGGTTACATGTGTA
*
29161511 GTACTAAGTGAAGGCTACTATGTGCACCAAGAAGCTT
65 GTACTAAGTGAAGGCTACTATGTGAACCAAGAAGC-T
* * * *
29161548 TGAGCACGTGTGTAGTACTGTGTGAATGCTA-TCACGTGTCTCGGTAAACTACGGTTATATGTGT
1 TGAACACGTGTGTAGTACTGTGTGAAGGCTACT-ACGTGTATCGGTAAA-TACGGTTACATGTGT
*
29161612 AGTACTAAGTGAAGGCTACTATGTGAACTAAGAAGCT
64 AGTACTAAGTGAAGGCTACTATGTGAACCAAGAAGCT
* * *
29161649 TGAACACGTGTGTAGTACTGAGTGAAGGCTACTACGTG-AGTC-GTAAA-ACTTGTTCACGTGTG
1 TGAACACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTA-TCGGTAAATAC-GGTT-ACATGTG
* * **
29161711 TAGTACTATGTGAAGGCTACTATGTAAATTGTAA-AA-C-
63 TAGTACTAAGTGAAGGCTACTATGTGAA--CCAAGAAGCT
* *
29161748 TGATCACGTGTGTAGTACTATGTGAAGGCT
1 TGAACACGTGTGTAGTACTGTGTGAAGGCT
29161778 TCAACTCGGG
Statistics
Matches: 198, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
98 2 0.01
99 30 0.15
100 37 0.19
101 39 0.20
102 89 0.45
103 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (100 bp):
TGAACACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGGTAAATACGGTTACATGTGTAG
TACTAAGTGAAGGCTACTATGTGAACCAAGAAGCT
Found at i:29161673 original size:50 final size:48
Alignment explanation
Indices: 29161607--29161777 Score: 202
Period size: 50 Copynumber: 3.5 Consensus size: 48
29161597 TACGGTTATA
* *
29161607 TGTGTAGTACTAAGTGAAGGCTACTATGTGAACTAAGAAGCTTGAACACG
1 TGTGTAGTACTATGTGAAGGCTACTATGTGAACTAA-AA-CTTGATCACG
* * *
29161657 TGTGTAGTACTGA-GTGAAGGCTACTACGTGAGTCGTAAAACTTGTTCACG
1 TGTGTAGTACT-ATGTGAAGGCTACTATGTGA-AC-TAAAACTTGATCACG
* *
29161707 TGTGTAGTACTATGTGAAGGCTACTATGTAAATTGTAAAAC-TGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTATGTGAA--CTAAAACTTGATCACG
29161756 TGTGTAGTACTATGTGAAGGCT
1 TGTGTAGTACTATGTGAAGGCT
29161778 TCAACTCGGG
Statistics
Matches: 106, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
49 30 0.28
50 69 0.65
51 4 0.04
52 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.30
Consensus pattern (48 bp):
TGTGTAGTACTATGTGAAGGCTACTATGTGAACTAAAACTTGATCACG
Found at i:29172611 original size:27 final size:27
Alignment explanation
Indices: 29172570--29172628 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
29172560 AAACCCGAAT
* *
29172570 TTTTTGCTTTTGGTTTTCATTTGTTTG
1 TTTTTGCTTTAGGTTTTCATTTGTTTC
*
29172597 TTTTTGCTTTAGGTTTTCATTTTTTTC
1 TTTTTGCTTTAGGTTTTCATTTGTTTC
29172624 TTTTT
1 TTTTT
29172629 ATTGTTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.05, C:0.08, G:0.14, T:0.73
Consensus pattern (27 bp):
TTTTTGCTTTAGGTTTTCATTTGTTTC
Found at i:29177795 original size:19 final size:20
Alignment explanation
Indices: 29177742--29177803 Score: 72
Period size: 19 Copynumber: 3.1 Consensus size: 20
29177732 TGAAAAAAAT
29177742 ATAATATATAAATAATTCAAA
1 ATAATATATAAA-AATTCAAA
* *
29177763 AGAATTTATAAAAATT-AAA
1 ATAATATATAAAAATTCAAA
* *
29177782 ATAATATATTAAAATTGAAA
1 ATAATATATAAAAATTCAAA
29177802 AT
1 AT
29177804 TTTACAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 16 0.46
20 9 0.26
21 10 0.29
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (20 bp):
ATAATATATAAAAATTCAAA
Found at i:29178092 original size:27 final size:26
Alignment explanation
Indices: 29178024--29178115 Score: 72
Period size: 27 Copynumber: 3.8 Consensus size: 26
29178014 TTTTACAATT
*
29178024 TTTTAAAATTTAAATA-TATTTT--A
1 TTTTAAAATTTATATATTATTTTAAA
* *
29178047 TTTT---ATTTA-ATTTTTTTTTAAA
1 TTTTAAAATTTATATATTATTTTAAA
* *
29178069 TTTTAAAATTTTATATATTATTTTGAT
1 TTTTAAAA-TTTATATATTATTTTAAA
*
29178096 TTTTAAAATTTATATTTTAT
1 TTTTAAAATTTATATATTAT
29178116 AATTTTATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
19 2 0.04
20 10 0.19
22 5 0.09
23 4 0.07
25 1 0.02
26 15 0.28
27 17 0.31
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (26 bp):
TTTTAAAATTTATATATTATTTTAAA
Found at i:29188269 original size:39 final size:40
Alignment explanation
Indices: 29188226--29188330 Score: 104
Period size: 44 Copynumber: 2.5 Consensus size: 40
29188216 TTCCATTATG
29188226 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
29188265 CTATTACGCCTCTATTTCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTA-TTC----CATTCAACCAAACACAAGATTTA
*
29188310 CTATTACACTTCTATTCCATT
1 CTATTACACCTCTATTCCATT
29188331 ACACCTCTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
39 13 0.25
40 7 0.13
44 19 0.36
45 14 0.26
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:29188331 original size:45 final size:44
Alignment explanation
Indices: 29188243--29188333 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
29188233 ACCTCTATTC
* *
29188243 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTTCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** * *
29188287 CATTCAACCAAACAGTTGATTTGCTATTACACTTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
29188332 CA
1 CA
29188334 CCTCTAATCT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 16 0.41
45 23 0.59
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:29194678 original size:29 final size:29
Alignment explanation
Indices: 29194645--29194700 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
29194635 AAAAGCCACT
29194645 TTTTTTAAAAAATTACCGAAATGGGCCGG
1 TTTTTTAAAAAATTACCGAAATGGGCCGG
** * *
29194674 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAAAAAATTACCGAAATGGGCC
29194701 ATTTTCCCCG
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:0.29, C:0.14, G:0.20, T:0.38
Consensus pattern (29 bp):
TTTTTTAAAAAATTACCGAAATGGGCCGG
Found at i:29194956 original size:22 final size:22
Alignment explanation
Indices: 29194924--29194993 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 22
29194914 AAATTCAATA
29194924 TCAATTTCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
29194946 TCAATTCCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
* * *
29194968 TCAATTTTCTTCCAAAATTTTC
1 TCAATTTCCTTCAAAAATTCTC
29194990 TCAA
1 TCAA
29194994 ACTCTCAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.41
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:29195022 original size:30 final size:30
Alignment explanation
Indices: 29194965--29195023 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
29194955 TTCAAAAATT
* * **
29194965 CTCTCAATTTTCTTCCAAAATTTTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
29194995 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
29195024 TTTCCTTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.32, G:0.00, T:0.37
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:29195034 original size:21 final size:22
Alignment explanation
Indices: 29194995--29195036 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29194985 TTTTCTCAAA
29194995 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
29195017 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
29195037 ATCTCCAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:29195098 original size:26 final size:28
Alignment explanation
Indices: 29195068--29195132 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
29195058 TTTTTTCCCA
29195068 TTAAA-TTTCA-TTTTTTTAAGAA-AATT
1 TTAAATTTTCATTTTTTTTAA-AATAATT
*
29195094 TTAAATTTTTTATTTTTTTTAAAATAATT
1 TTAAA-TTTTCATTTTTTTTAAAATAATT
29195123 TTAAAATTTT
1 TT-AAATTTT
29195133 TAATATTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
26 5 0.15
28 6 0.18
29 19 0.58
30 3 0.09
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
TTAAATTTTCATTTTTTTTAAAATAATT
Found at i:29195130 original size:30 final size:29
Alignment explanation
Indices: 29195078--29195134 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
29195068 TTAAATTTCA
29195078 TTTTTTTAAGAAAATTTTAAATTTTTTAT
1 TTTTTTTAAGAAAATTTTAAATTTTTTAT
*
29195107 TTTTTTTAA-AATAATTTTAAAATTTTTA
1 TTTTTTTAAGAA-AATTTTAAATTTTTTA
29195135 ATATTTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTTTAAGAAAATTTTAAATTTTTTAT
Found at i:29195141 original size:29 final size:29
Alignment explanation
Indices: 29195080--29195141 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
29195070 AAATTTCATT
* * *
29195080 TTTTTAAGAAAATTTTAAATTTTTTATTT
1 TTTTTAAGAAAATTTTAAAATTTTTAATA
29195109 TTTTTAA-AATAATTTTAAAATTTTTAATA
1 TTTTTAAGAA-AATTTTAAAATTTTTAATA
29195138 TTTT
1 TTTT
29195142 CAACAATGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTAAGAAAATTTTAAAATTTTTAATA
Found at i:29195261 original size:14 final size:15
Alignment explanation
Indices: 29195232--29195265 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29195222 AAATTTTAAA
29195232 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
29195247 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
29195261 TTTTA
1 TTTTA
29195266 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:29197453 original size:33 final size:28
Alignment explanation
Indices: 29197402--29197493 Score: 175
Period size: 28 Copynumber: 3.3 Consensus size: 28
29197392 TTTTGACATT
*
29197402 ATTTGATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
29197430 ATTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
29197458 ATTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
29197486 ATTTAATT
1 ATTTAATT
29197494 NNNNNNNNNN
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.35
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACTTA
Found at i:29197727 original size:28 final size:27
Alignment explanation
Indices: 29197594--29197734 Score: 118
Period size: 23 Copynumber: 5.2 Consensus size: 27
29197584 NNNNNNNNNN
29197594 AATTAAAAACCCTAACCTAACCCTACATATTT
1 AATTAAAAACCCTAACCTAA--C--C-TATTT
29197626 AATTAAAAACCCTAACCTAA-C---TT
1 AATTAAAAACCCTAACCTAACCTATTT
*
29197649 AATTAAAAACCGTAACCTAA-C---TT
1 AATTAAAAACCCTAACCTAACCTATTT
* * *
29197672 AATTGAAATCCCTAAGCTAACCTAATTT
1 AATTAAAAACCCTAACCTAACCT-ATTT
29197700 AATTAAAAACCCTAACCCTAACCTATTT
1 AATTAAAAACCCTAA-CCTAACCTATTT
29197728 GAATTAA
1 -AATTAA
29197735 TGTAATAATT
Statistics
Matches: 94, Mismatches: 8, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
23 40 0.43
24 1 0.01
27 1 0.01
28 19 0.20
29 13 0.14
32 20 0.21
ACGTcount: A:0.45, C:0.24, G:0.03, T:0.28
Consensus pattern (27 bp):
AATTAAAAACCCTAACCTAACCTATTT
Found at i:29201230 original size:126 final size:127
Alignment explanation
Indices: 29200940--29201207 Score: 373
Period size: 126 Copynumber: 2.1 Consensus size: 127
29200930 CCACGAGGGC
* *
29200940 GCGATTTGACACTATTTGCTCAG-AAACGTC--AAAAAAAATTATTTCCTACATGACCAACTGTA
1 GCGATTTCACACTATTTGCTCAGTAAAAGTCAAAAAAAAAATTATTTCCTACATGACCAACTGTA
** * * * **
29201002 GCGGTATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 GCGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* * *
29201064 GCGATTTTATACTATTTGCTCAGTAAAAGTCAAAAAAAAAATTATTTCTTACATGACC-ACTGTA
1 GCGATTTCACACTATTTGCTCAGTAAAAGTCAAAAAAAAAATTATTTCCTACATGACCAACTGTA
* *
29201128 GCGAAATCGCGTCCACGAGGCCACTATTTCACAATTTTTTCTCAAATAGCATCCTGGTAGAA
66 GCGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
*
29201190 GCGATTTCCCACTATTTG
1 GCGATTTCACACTATTTG
29201208 ACCAGATACG
Statistics
Matches: 125, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
124 21 0.17
125 6 0.05
126 74 0.59
127 24 0.19
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (127 bp):
GCGATTTCACACTATTTGCTCAGTAAAAGTCAAAAAAAAAATTATTTCCTACATGACCAACTGTA
GCGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:29203443 original size:16 final size:16
Alignment explanation
Indices: 29203422--29203454 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29203412 TTCGCTGTAT
29203422 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
29203438 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
29203454 T
1 T
29203455 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:29203766 original size:22 final size:21
Alignment explanation
Indices: 29203741--29203792 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
29203731 TAGATATTCT
*
29203741 TAATATTAA-ATTACTAAAATCA
1 TAATATTAATACTA-TAAAAT-A
29203763 TAATATATAATACTATAAAATA
1 TAATAT-TAATACTATAAAATA
29203785 TAAT-TTAA
1 TAATATTAA
29203793 CATAATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.11
21 1 0.04
22 11 0.41
23 9 0.33
24 3 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATATTAATACTATAAAATA
Found at i:29203908 original size:119 final size:121
Alignment explanation
Indices: 29203667--29203916 Score: 432
Period size: 119 Copynumber: 2.1 Consensus size: 121
29203657 TTAATCATAT
*
29203667 TTTAACATAATTATTATTAAATATAGTTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* *
29203732 AGATATTCTTAATATTAAATTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTAATATGAAATTACTAAAATCATAATATATAATACTATAAAATATAA
*
29203788 TTTAACATAATTATTATTAAATATAATTTAA-AAATATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
29203852 AAATATTCTT-ATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTAATATGAAATTACTAAAATCATAATATATAATACTATAAAATATAA
*
29203907 TTTAAAATAA
1 TTTAACATAA
29203917 NNNNNNNNNN
Statistics
Matches: 123, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
119 52 0.42
120 41 0.33
121 30 0.24
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (121 bp):
TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTAATATGAAATTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:29211066 original size:558 final size:555
Alignment explanation
Indices: 29209834--29211515 Score: 2453
Period size: 561 Copynumber: 3.0 Consensus size: 555
29209824 CAAGAAAGAT
* * * * **
29209834 CCAACTTGGCCTTATATCACATAAGGGGTGGCAAACCTTAGTGTTTTGTGGAGGGTGTCACCGTC
1 CCAACTTGGCCTTATATCACGTAAGGGGCGACAAACCCTAGTGTTTTAAGG-GGGTGTCACCGTC
* * *
29209899 CCCTATACTATAGTTCTACTATGATATTGTATTTTTTATTAAATATTTTTATTTAATTAGACCTT
65 CCCTATACTATAGTTCTACTATAATATTGTATTTTTTATTAAATATTATTATTGAATTAGACCTT
* * * *
29209964 ATTCAAATAGATGTTATGTTGTAACACCCCTT-TCCCTGCCAGGAGACATGGCGTATATTAATCA
130 ATTCAAATAGATGTTTTGTTGTAACACCCCTTAGCCC-GTCAGGAGACATGGCGTATATCAATCA
* * * *
29210028 GCCAAATAAACCTCTCAATGGA-CTAGGGTGTTACTGATAGACTCAAA-CCTTTGGCTTAATTTA
194 GCCAAACAAA-CTCCCAACGGATCGA-GGTGTTACTGATAGACTCAAATCCTTTGGCTTAATTTA
* * *
29210091 AATCTTTGAGAAATCAGTTGCAAGGATTCTCCTTTTAGTGAAAGATCATTATTATTGGCTCATTT
257 AATCTTTGAGAAATCAGTTGTAAGG-TTCTCCTTTTAGTGAAAGACCATTATTCTTGGCTCATTT
* * *
29210156 AGTAACGTATCTTTGAAGAAAGTAATAGGAATTAATAAAGACAATCTTTAAATCATACACTGCCA
321 AGTAACGTATCCTTGAAGAAAGTAATAGGAATTAATAAAG-CAATCTTTAAATCATACTCTGTCA
*
29210221 TGTATGGCAAATACACTTAATAGAAAAGACAAGTTTGTAATATGCAAATCAAGGGAGTTT-GCGT
385 TGTATGGCAAATACACTTAATAGAAAAGGCAAGTTTGTAATATGCAAATCAAGGGAGTTTGGCGT
* * *
29210285 ACACATGTATAATAAGGGGAAGTTCTACTTTATGACAAAAACAATATAGTTGTGAGGTAAAAACA
450 ACACATGTATAATAAGGGGCAGTTCCACTTTAAGACAAAAACAATAT-GTTGTGAGGTAAAAACA
* * *
29210350 AAAGTCAAGTATAAAACATTTATATACGGCATCCGCCAACTAG
514 AAA-TTAAGTACAAAACATTTATATACGCCATCCGCCAACTAG
** * * * * *
29210393 ATAACTTGGCTTTATATCACGTAAGGGGC-ACAAATCCTAATGTTTTACGGGGGGTGTCACCATC
1 CCAACTTGGCCTTATATCACGTAAGGGGCGACAAACCCTAGTGTTTTA-AGGGGGTGTCACCGTC
*
29210457 CCCTATACTATAGTTCTACTATAATATTGCA-TTTTTATTAAATATTATTATTGAATTAGACCTT
65 CCCTATACTATAGTTCTACTATAATATTGTATTTTTTATTAAATATTATTATTGAATTAGACCTT
* *
29210521 ATTCAAATAGATGTTTTGTTGTAACACCCCTTAGCCCGTCAAGAGACATGGCGTATATCAACCAG
130 ATTCAAATAGATGTTTTGTTGTAACACCCCTTAGCCCGTCAGGAGACATGGCGTATATCAATCAG
* * *
29210586 CCAAACAAACTGCCCAACAGATCGATGTGTTATTGATAGACTCAAATCCTTTGGCTTAATTTAAA
195 CCAAACAAACT-CCCAACGGATCGAGGTGTTACTGATAGACTCAAATCCTTTGGCTTAATTTAAA
* *
29210651 TATTTGAGAAATCAGTTGTAAGAGTTCTCCTTCTAGTGAAAGACCATTATTCTTGGCTCATTTAG
259 TCTTTGAGAAATCAGTTGTAAG-GTTCTCCTTTTAGTGAAAGACCATTATTCTTGGCTCATTTAG
*
29210716 TAACGTATCCTTGAAGAAAGTAATAGGAATTAATAAATGCAATCTTTAAATCATACTCTGTCGTG
323 TAACGTATCCTTGAAGAAAGTAATAGGAATTAATAAA-GCAATCTTTAAATCATACTCTGTCATG
* *
29210781 TATGGCGAATACACTTAAAAGAAAAGGCAAGTTTGTAATATGCAAATCAAGGGAGTTTGGCGTAC
387 TATGGCAAATACACTTAATAGAAAAGGCAAGTTTGTAATATGCAAATCAAGGGAGTTTGGCGTAC
29210846 ACATGTATAATAAGGGGCAGTTCCACTTTAAGACAAAAACAATATGTTTGTG-GAGTAAAAACAA
452 ACATGTATAATAAGGGGCAGTTCCACTTTAAGACAAAAACAATATG-TTGTGAG-GTAAAAACAA
* * *
29210910 AATTAAAGTACAAAACGTTTATATATGCCATCCGTCAACTAG
515 AATT-AAGTACAAAACATTTATATACGCCATCCGCCAACTAG
* **
29210952 CCAACTTGTCCTTATATCACGTAAGGGGCGACAAACCCTAGTGTTTTAAGGGGGTGTCACCGTTT
1 CCAACTTGGCCTTATATCACGTAAGGGGCGACAAACCCTAGTGTTTTAAGGGGGTGTCACCGTCC
*
29211017 CCTGTACTATAGTTCTACTATAATATTGTAATTTTTTATTAAATATTATTATTGAATTAGACCTT
66 CCTATACTATAGTTCTACTATAATATTGT-ATTTTTTATTAAATATTATTATTGAATTAGACCTT
* * * *
29211082 ATTCAAATAGAAGTTTTGTTGTAACACCCCTTAGCCCTTCAGGAGACATGGCATATATCAATTAG
130 ATTCAAATAGATGTTTTGTTGTAACACCCCTTAGCCCGTCAGGAGACATGGCGTATATCAATCAG
* * ** *
29211147 CCAAACAAACCACCCAACGGATCGGGGCATTACTGGTAGACTCAAATCCTTTGGCTTAATTTAAA
195 CCAAACAAA-CTCCCAACGGATCGAGGTGTTACTGATAGACTCAAATCCTTTGGCTTAATTTAAA
* *
29211212 TCTTTGAGAAATCAGTTGTAATGGTTCTCTTTTTAGTGAAAGACCATTATTCTTGGCCCATTTAG
259 TCTTTGAGAAATCAGTTGTAA-GGTTCTCCTTTTAGTGAAAGACCATTATTCTTGGCTCATTTAG
29211277 TAACGTATCCTTGAAGAAAGTAATAGGAATTAATAAAGGCAATCTTTAAATCATACAT-TGTCAT
323 TAACGTATCCTTGAAGAAAGTAATAGGAATTAATAAA-GCAATCTTTAAATCATAC-TCTGTCAT
* * **
29211341 GTATGGCAAATACACTTAATAGAAAATGCAAGTTTGTAATATGCAAATTAAGGGAGTTTGGTATA
386 GTATGGCAAATACACTTAATAGAAAAGGCAAGTTTGTAATATGCAAATCAAGGGAGTTTGGCGTA
*
29211406 CACATGCATAATAAGGGGCAGTTCCACTTTAAGACAAAAACAATATGATTGTGAGGTAAAAACAA
451 CACATGTATAATAAGGGGCAGTTCCACTTTAAGACAAAAACAATATG-TTGTGAGGTAAAAACAA
* *
29211471 AAGTTAAGTACAAAACTTTTATATACGCCATCTGCCAACTAG
515 AA-TTAAGTACAAAACATTTATATACGCCATCCGCCAACTAG
29211513 CCA
1 CCA
29211516 TGCATGATAC
Statistics
Matches: 1010, Mismatches: 94, Indels: 36
0.89 0.08 0.03
Matches are distributed among these distances:
556 2 0.00
557 119 0.12
558 252 0.25
559 190 0.19
560 17 0.02
561 424 0.42
562 6 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (555 bp):
CCAACTTGGCCTTATATCACGTAAGGGGCGACAAACCCTAGTGTTTTAAGGGGGTGTCACCGTCC
CCTATACTATAGTTCTACTATAATATTGTATTTTTTATTAAATATTATTATTGAATTAGACCTTA
TTCAAATAGATGTTTTGTTGTAACACCCCTTAGCCCGTCAGGAGACATGGCGTATATCAATCAGC
CAAACAAACTCCCAACGGATCGAGGTGTTACTGATAGACTCAAATCCTTTGGCTTAATTTAAATC
TTTGAGAAATCAGTTGTAAGGTTCTCCTTTTAGTGAAAGACCATTATTCTTGGCTCATTTAGTAA
CGTATCCTTGAAGAAAGTAATAGGAATTAATAAAGCAATCTTTAAATCATACTCTGTCATGTATG
GCAAATACACTTAATAGAAAAGGCAAGTTTGTAATATGCAAATCAAGGGAGTTTGGCGTACACAT
GTATAATAAGGGGCAGTTCCACTTTAAGACAAAAACAATATGTTGTGAGGTAAAAACAAAATTAA
GTACAAAACATTTATATACGCCATCCGCCAACTAG
Found at i:29217483 original size:9 final size:9
Alignment explanation
Indices: 29217425--29217544 Score: 59
Period size: 9 Copynumber: 13.0 Consensus size: 9
29217415 GGATGCGACA
*
29217425 AAAAATGAT
1 AAAAATTAT
*
29217434 ATAAACTTAT
1 A-AAAATTAT
* *
29217444 ATATATTAT
1 AAAAATTAT
*
29217453 CAAAA-TAT
1 AAAAATTAT
* *
29217461 AAAAACCTAA
1 AAAAA-TTAT
29217471 AAAAATTAT
1 AAAAATTAT
29217480 AAAAATTAT
1 AAAAATTAT
29217489 -AAAATTAAT
1 AAAAATT-AT
*
29217498 AAAACATATGT
1 AAAA-AT-TAT
29217509 AAAATATT-T
1 AAAA-ATTAT
*
29217518 AAAATTTTAT
1 AAAA-ATTAT
*
29217528 AAAAATAAT
1 AAAAATTAT
29217537 -AAAATTAT
1 AAAAATTAT
29217545 TAAACTTTAT
Statistics
Matches: 85, Mismatches: 18, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
8 20 0.24
9 32 0.38
10 23 0.27
11 9 0.11
12 1 0.01
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:29218043 original size:9 final size:9
Alignment explanation
Indices: 29218031--29218274 Score: 69
Period size: 10 Copynumber: 26.1 Consensus size: 9
29218021 TTTTATGATT
29218031 TTTTTATAA
1 TTTTTATAA
29218040 TTTTTATAA
1 TTTTTATAA
*
29218049 GTTTATATCAA
1 -TTTTTAT-AA
*
29218060 TTTTAAT-A
1 TTTTTATAA
*
29218068 TTTTTATAG
1 TTTTTATAA
29218077 TTTTT-TAAGA
1 TTTTTAT-A-A
*
29218087 TTTTTAATACG
1 TTTTT-ATA-A
29218098 TTTTTA-AA
1 TTTTTATAA
*
29218106 TTTTAAATAA
1 TTTT-TATAA
**
29218116 AATTTATTAA
1 TTTTTA-TAA
*
29218126 -TTTCATAGA
1 TTTTTATA-A
29218135 TTTTTTATAA
1 -TTTTTATAA
*
29218145 TTAATTTTATTTGA
1 -T--TTTTA--TAA
29218159 TTTTTA-ATA
1 TTTTTATA-A
29218168 TTTTTATAA
1 TTTTTATAA
*
29218177 GTTTTAATAA
1 -TTTTTATAA
29218187 TTTTTATAAA
1 TTTTTAT-AA
*
29218197 TTTATATCAA
1 TTTTTAT-AA
*
29218207 TTTTAAT-A
1 TTTTTATAA
*
29218215 TTTTT-TAT
1 TTTTTATAA
*
29218223 TTTTTGATGA
1 TTTTT-ATAA
**
29218233 TTTTT-TTC
1 TTTTTATAA
*
29218241 TTTTTCT--
1 TTTTTATAA
29218248 TTTTTATAA
1 TTTTTATAA
*
29218257 TTTTTATGA
1 TTTTTATAA
29218266 TTTTT-TAA
1 TTTTTATAA
29218274 T
1 T
29218275 CAATTTATGA
Statistics
Matches: 175, Mismatches: 33, Indels: 55
0.67 0.13 0.21
Matches are distributed among these distances:
7 7 0.04
8 33 0.19
9 50 0.29
10 57 0.33
11 19 0.11
12 6 0.03
13 1 0.01
14 2 0.01
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29218082 original size:19 final size:21
Alignment explanation
Indices: 29218060--29218114 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
29218050 TTTATATCAA
*
29218060 TTTTAATATTTTT-ATA-GTT
1 TTTTAAGATTTTTAATACGTT
29218079 TTTTAAGATTTTTAATACG-T
1 TTTTAAGATTTTTAATACGTT
*
29218099 TTTTAA-ATTTTAAATA
1 TTTTAAGATTTTTAATA
29218115 AAATTTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 21 0.66
20 10 0.31
21 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTTAAGATTTTTAATACGTT
Found at i:29218191 original size:29 final size:27
Alignment explanation
Indices: 29218159--29218221 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 27
29218149 TTTTATTTGA
*
29218159 TTTTTAATATTTTTAT-AAGTTTTAATAAT
1 TTTTTAA-ATTTATATCAA-TTTTAAT-AT
29218188 TTTTATAAATTTATATCAATTTTAATAT
1 TTTT-TAAATTTATATCAATTTTAATAT
29218216 TTTTTA
1 TTTTTA
29218222 TTTTTTGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 2 0.06
28 6 0.19
29 18 0.58
30 5 0.16
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTTAAATTTATATCAATTTTAATAT
Found at i:29218271 original size:19 final size:19
Alignment explanation
Indices: 29218146--29218272 Score: 65
Period size: 19 Copynumber: 7.0 Consensus size: 19
29218136 TTTTTATAAT
* *
29218146 TAATTTTATTTGATTTTTAA
1 TAATTTT-TATGATTTTTTA
* * *
29218166 T-ATTTTTATAAGTTTTAA
1 TAATTTTTATGATTTTTTA
* * *
29218184 TAATTTTTATAAATTTATA
1 TAATTTTTATGATTTTTTA
*
29218203 TCAATTTTAAT-ATTTTTTA
1 T-AATTTTTATGATTTTTTA
29218222 T--TTTTTGATGATTTTTT-
1 TAATTTTT-ATGATTTTTTA
* *
29218239 T--CTTTT-T-CTTTTTTA
1 TAATTTTTATGATTTTTTA
29218254 TAATTTTTATGATTTTTTA
1 TAATTTTTATGATTTTTTA
29218273 ATCAATTTAT
Statistics
Matches: 84, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
14 6 0.07
15 2 0.02
16 4 0.05
17 11 0.13
18 18 0.21
19 34 0.40
20 9 0.11
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (19 bp):
TAATTTTTATGATTTTTTA
Found at i:29222076 original size:38 final size:38
Alignment explanation
Indices: 29222031--29222150 Score: 181
Period size: 38 Copynumber: 3.2 Consensus size: 38
29222021 TTTTGATTTT
29222031 TGCTGTTAATGGTGTTCTGATTTTGATTTTGCTGTTAA
1 TGCTGTTAATGGTGTTCTGATTTTGATTTTGCTGTTAA
29222069 TGCTGTTAATGGTGTTCTGATTTTGATTTTGCTGTTAA
1 TGCTGTTAATGGTGTTCTGATTTTGATTTTGCTGTTAA
* * *
29222107 TGCTGTTAAT-G-GTTGTGTTTTTTATTTTTGCTGTTAA
1 TGCTGTTAATGGTGTTCTGATTTTGA-TTTTGCTGTTAA
*
29222144 TGGTGTT
1 TGCTGTT
29222151 CTGTTAATGT
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
36 10 0.13
37 19 0.25
38 48 0.62
ACGTcount: A:0.14, C:0.07, G:0.24, T:0.55
Consensus pattern (38 bp):
TGCTGTTAATGGTGTTCTGATTTTGATTTTGCTGTTAA
Found at i:29222108 original size:29 final size:30
Alignment explanation
Indices: 29222018--29222075 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
29222008 ATGTTGGTTG
*
29222018 TGATTTTGATTTTTGCTGTTAATGGTGTTC
1 TGATTTTGATTTTTGCTGTTAATGCTGTTC
29222048 TGATTTTGA-TTTTGCTGTTAATGCTGTT
1 TGATTTTGATTTTTGCTGTTAATGCTGTT
29222076 AATGGTGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.14, C:0.07, G:0.22, T:0.57
Consensus pattern (30 bp):
TGATTTTGATTTTTGCTGTTAATGCTGTTC
Found at i:29222127 original size:29 final size:29
Alignment explanation
Indices: 29222069--29222128 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
29222059 TTGCTGTTAA
* * *
29222069 TGCTGTTAATGGTGTTCTGATTTTGATTT
1 TGCTGTTAATGCTGTTATGATTGTGATTT
* *
29222098 TGCTGTTAATGCTGTTAATGGTTGTGTTTT
1 TGCTGTTAATGCTGTT-ATGATTGTGATTT
29222128 T
1 T
29222129 TATTTTTGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.13, C:0.07, G:0.25, T:0.55
Consensus pattern (29 bp):
TGCTGTTAATGCTGTTATGATTGTGATTT
Found at i:29223567 original size:22 final size:22
Alignment explanation
Indices: 29223539--29223676 Score: 195
Period size: 22 Copynumber: 6.3 Consensus size: 22
29223529 TTTATTGTTC
*
29223539 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
29223561 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
29223583 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
29223605 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
29223627 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
29223649 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
29223671 AAACAT
1 AAACAT
29223677 ACTTTATTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 104 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:29223833 original size:13 final size:13
Alignment explanation
Indices: 29223777--29223900 Score: 80
Period size: 13 Copynumber: 9.5 Consensus size: 13
29223767 ATTTTAAATG
29223777 TAATATACTATTT
1 TAATATACTATTT
29223790 TAATAATA-TATTGT
1 TAAT-ATACTATT-T
29223804 T-ATGA-A--ATTT
1 TAAT-ATACTATTT
29223814 ATAATATACTATTT
1 -TAATATACTATTT
29223828 TAATATACTATTAT
1 TAATATACTATT-T
* *
29223842 AAATATAAT-TTT
1 TAATATACTATTT
* *
29223854 TAATATATTGTTT
1 TAATATACTATTT
* *
29223867 TAATATACTGTTA
1 TAATATACTATTT
* *
29223880 TAATTATATTGTTT
1 TAA-TATACTATTT
29223894 TAATATA
1 TAATATA
29223901 ATGTTTTAAC
Statistics
Matches: 92, Mismatches: 9, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
10 1 0.01
11 5 0.05
12 12 0.13
13 46 0.50
14 28 0.30
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.52
Consensus pattern (13 bp):
TAATATACTATTT
Found at i:29223868 original size:39 final size:39
Alignment explanation
Indices: 29223809--29223909 Score: 130
Period size: 39 Copynumber: 2.6 Consensus size: 39
29223799 ATTGTTATGA
* * *
29223809 AATTTATAATATACTATTTTAATATACTATTATAAATAT
1 AATTTTTAATATAATGTTTTAATATACTATTATAAATAT
* * *
29223848 AATTTTTAATATATTGTTTTAATATACTGTTATAATTAT
1 AATTTTTAATATAATGTTTTAATATACTATTATAAATAT
*
29223887 ATTGTTTTAATATAATGTTTTAA
1 AAT-TTTTAATATAATGTTTTAA
29223910 CTTTTAAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 36 0.67
40 18 0.33
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (39 bp):
AATTTTTAATATAATGTTTTAATATACTATTATAAATAT
Found at i:29223889 original size:27 final size:27
Alignment explanation
Indices: 29223857--29223941 Score: 100
Period size: 27 Copynumber: 3.1 Consensus size: 27
29223847 TAATTTTTAA
29223857 TATATTGTTTTAATATACTGTTATAAT
1 TATATTGTTTTAATATACTGTTATAAT
* *
29223884 TATATTGTTTTAATATAATGTTTTAACT
1 TATATTGTTTTAATATACTGTTATAA-T
* ** *
29223912 TTTA-AATTTTAATATACTGTTATAAA
1 TATATTGTTTTAATATACTGTTATAAT
29223938 TATA
1 TATA
29223942 CATTTAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
26 3 0.06
27 41 0.85
28 4 0.08
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (27 bp):
TATATTGTTTTAATATACTGTTATAAT
Found at i:29223905 original size:13 final size:13
Alignment explanation
Indices: 29223815--29223909 Score: 93
Period size: 13 Copynumber: 7.2 Consensus size: 13
29223805 ATGAAATTTA
*
29223815 TAATATACTATTT
1 TAATATACTGTTT
*
29223828 TAATATACTATTAT
1 TAATATACTGTT-T
* *
29223842 AAATATAAT-TTT
1 TAATATACTGTTT
*
29223854 TAATATATTGTTT
1 TAATATACTGTTT
*
29223867 TAATATACTGTTA
1 TAATATACTGTTT
*
29223880 TAATTATATTGTTT
1 TAA-TATACTGTTT
*
29223894 TAATATAATGTTT
1 TAATATACTGTTT
29223907 TAA
1 TAA
29223910 CTTTTAAATT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
12 8 0.11
13 43 0.61
14 19 0.27
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:29224359 original size:19 final size:19
Alignment explanation
Indices: 29224335--29224372 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29224325 TTAATGAGTA
29224335 TGAAAGTTCTCTCAAACGT
1 TGAAAGTTCTCTCAAACGT
29224354 TGAAAGTTCTCTCAAACGT
1 TGAAAGTTCTCTCAAACGT
29224373 CAAAAGTCTA
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:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (19 bp):
TGAAAGTTCTCTCAAACGT
Found at i:29224378 original size:19 final size:19
Alignment explanation
Indices: 29224337--29224379 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
29224327 AATGAGTATG
**
29224337 AAAGTTCTCTCAAACGTTG
1 AAAGTTCTCTCAAACGTCA
29224356 AAAGTTCTCTCAAACGTCA
1 AAAGTTCTCTCAAACGTCA
29224375 AAAGT
1 AAAGT
29224380 CTACCACTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (19 bp):
AAAGTTCTCTCAAACGTCA
Found at i:29226342 original size:33 final size:33
Alignment explanation
Indices: 29226300--29226371 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
29226290 TATTCAAATT
*
29226300 TTATATTATTTTTTCATCAATTTGATTATCTAA
1 TTATTTTATTTTTTCATCAATTTGATTATCTAA
29226333 TTATTTTATTTTTTCATCAATTTGATTATCTAA
1 TTATTTTATTTTTTCATCAATTTGATTATCTAA
29226366 TTATTT
1 TTATTT
29226372 ATTCTTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.61
Consensus pattern (33 bp):
TTATTTTATTTTTTCATCAATTTGATTATCTAA
Found at i:29226419 original size:9 final size:9
Alignment explanation
Indices: 29226405--29226441 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
29226395 GGTTGCAAAA
29226405 AGGACGATG
1 AGGACGATG
29226414 AGGACGATG
1 AGGACGATG
29226423 AGGACGATG
1 AGGACGATG
29226432 AGGACGATG
1 AGGACGATG
29226441 A
1 A
29226442 TGATGATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.43, T:0.11
Consensus pattern (9 bp):
AGGACGATG
Found at i:29227261 original size:25 final size:25
Alignment explanation
Indices: 29227227--29227274 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
29227217 TTAATATTTG
29227227 ATTGTTTGTAATTAAATTCAAATTA
1 ATTGTTTGTAATTAAATTCAAATTA
29227252 ATTGTTTGTAATTAAATTCAAAT
1 ATTGTTTGTAATTAAATTCAAAT
29227275 AAGTAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (25 bp):
ATTGTTTGTAATTAAATTCAAATTA
Found at i:29227366 original size:16 final size:16
Alignment explanation
Indices: 29227345--29227378 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29227335 ATATAAATTC
29227345 AATAACAATTAATTTT
1 AATAACAATTAATTTT
*
29227361 AATAACAATTAGTTTT
1 AATAACAATTAATTTT
29227377 AA
1 AA
29227379 CTTTTAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAACAATTAATTTT
Found at i:29228411 original size:25 final size:24
Alignment explanation
Indices: 29228365--29228461 Score: 99
Period size: 25 Copynumber: 3.9 Consensus size: 24
29228355 GATACACCAT
* *
29228365 AGCTCGT-ATGAGTTTATCGATTTGC
1 AGCTCGTGA-GAGCTTACCGATTT-C
*
29228390 AGCTCGTGAGAGCTTACTGATTCTC
1 AGCTCGTGAGAGCTTACCGATT-TC
29228415 AGCTCGT-ATGAGCTTACCGATTTAC
1 AGCTCGTGA-GAGCTTACCGATTT-C
*
29228440 AGCTCGTGAGAGCATACCGATT
1 AGCTCGTGAGAGCTTACCGATT
29228462 CATAGCTCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
24 2 0.03
25 57 0.92
26 3 0.05
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (24 bp):
AGCTCGTGAGAGCTTACCGATTTC
Found at i:29228424 original size:50 final size:50
Alignment explanation
Indices: 29228362--29228477 Score: 171
Period size: 50 Copynumber: 2.3 Consensus size: 50
29228352 GCGGATACAC
* * * * *
29228362 CATAGCTCGTATGAGTTTATCGATTTGCAGCTCGTGAGAGCTTACTGATT
1 CATAGCTCGTATGAGCTTACCGATTTACAGCTCGTGAGAGCATACCGATT
29228412 C-TCAGCTCGTATGAGCTTACCGATTTACAGCTCGTGAGAGCATACCGATT
1 CAT-AGCTCGTATGAGCTTACCGATTTACAGCTCGTGAGAGCATACCGATT
29228462 CATAGCTCGTATGAGC
1 CATAGCTCGTATGAGC
29228478 ATACATGTAC
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
49 1 0.02
50 57 0.97
51 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (50 bp):
CATAGCTCGTATGAGCTTACCGATTTACAGCTCGTGAGAGCATACCGATT
Found at i:29228468 original size:25 final size:25
Alignment explanation
Indices: 29228362--29228481 Score: 93
Period size: 25 Copynumber: 4.8 Consensus size: 25
29228352 GCGGATACAC
** *
29228362 CATAGCTCGTATGAGTTTATCGATT
1 CATAGCTCGTATGAGCATACCGATT
*** * *
29228387 TGCAGCTCGTGA-GAGCTTACTGATT
1 CATAGCTCGT-ATGAGCATACCGATT
*
29228412 C-TCAGCTCGTATGAGCTTACCGATT
1 CAT-AGCTCGTATGAGCATACCGATT
* *
29228437 TACAGCTCGTGA-GAGCATACCGATT
1 CATAGCTCGT-ATGAGCATACCGATT
29228462 CATAGCTCGTATGAGCATAC
1 CATAGCTCGTATGAGCATAC
29228482 ATGTACAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
24 2 0.03
25 71 0.95
26 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (25 bp):
CATAGCTCGTATGAGCATACCGATT
Found at i:29233705 original size:38 final size:38
Alignment explanation
Indices: 29233607--29233760 Score: 137
Period size: 38 Copynumber: 4.0 Consensus size: 38
29233597 TGATATAACA
* ** * **
29233607 CACCGGCATAAAGCCTAATAGGCACAAAGGATGATATAAT
1 CACCGGCACAAAGCCTGCTAGGCACAGAGCTTGA-AT-AT
* *
29233647 CTACCGGCACGAAGCTTGCTAGGCACAGAGCTTGAATAT
1 C-ACCGGCACAAAGCCTGCTAGGCACAGAGCTTGAATAT
* * *
29233686 CACTGGCACAAAGCCTGCTAGGCACAGAGCCTGATTAT
1 CACCGGCACAAAGCCTGCTAGGCACAGAGCTTGAATAT
* * * * *
29233724 CACCGACATAAAGTCTGCTAGGCACAAAGCTCGAATA
1 CACCGGCACAAAGCCTGCTAGGCACAGAGCTTGAATA
29233761 ACGTTACATT
Statistics
Matches: 92, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
38 61 0.66
39 3 0.03
40 3 0.03
41 25 0.27
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.18
Consensus pattern (38 bp):
CACCGGCACAAAGCCTGCTAGGCACAGAGCTTGAATAT
Found at i:29236208 original size:19 final size:17
Alignment explanation
Indices: 29236175--29236210 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
29236165 CAATATATAT
29236175 CCTTTATAGATAAACCA
1 CCTTTATAGATAAACCA
29236192 CCTTTGATAGAATAAACCA
1 CCTTT-ATAG-ATAAACCA
29236211 TAAGAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (17 bp):
CCTTTATAGATAAACCA
Found at i:29239213 original size:38 final size:38
Alignment explanation
Indices: 29239168--29239290 Score: 131
Period size: 38 Copynumber: 3.2 Consensus size: 38
29239158 AAATCTCTGA
* **
29239168 CACAAAGCCTACTAGGCACAGAGTTTGAATATCACCGG
1 CACAAAGCCTACTAGGCATAGAGCATGAATATCACCGG
* * * *
29239206 CATAAAGCTTGA-TAGGTATAGAGCACGAATATCACCGG
1 CACAAAGCCT-ACTAGGCATAGAGCATGAATATCACCGG
* * * *
29239244 TACAAAGTCTGCTAGGCATAGAGCCTGAATATCACCGG
1 CACAAAGCCTACTAGGCATAGAGCATGAATATCACCGG
29239282 CACAAAGCC
1 CACAAAGCC
29239291 CGAATATCAT
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
38 65 0.98
39 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (38 bp):
CACAAAGCCTACTAGGCATAGAGCATGAATATCACCGG
Found at i:29243864 original size:42 final size:42
Alignment explanation
Indices: 29243826--29243904 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
29243816 GTTTTTATGC
29243826 ATTTT-TCTAAAAATTTT-CAAAAATTCCAAAAATATTTTACG
1 ATTTTGTCTAAAAATTTTCCAAAAA-TCCAAAAATATTTTACG
* * **
29243867 TTTTTGTGTTTAAATTTTCCAAAAATCCAAAAATATTT
1 ATTTTGTCTAAAAATTTTCCAAAAATCCAAAAATATTT
29243905 CTTATTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.12
42 22 0.69
43 6 0.19
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (42 bp):
ATTTTGTCTAAAAATTTTCCAAAAATCCAAAAATATTTTACG
Found at i:29243921 original size:42 final size:41
Alignment explanation
Indices: 29243836--29243926 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 41
29243826 ATTTTTCTAA
**
29243836 AAATTTTCAAAAATTCCAAAAATATTTTACGTTTTTGTGTTT
1 AAATTTTCAAAAATTCCAAAAATATTTTAC-TTTTCATGTTT
*
29243878 AAATTTTCCAAAAA-TCCAAAAATATTTCTTA-TTTTCATTTTT
1 AAATTTT-CAAAAATTCCAAAAATA-TT-TTACTTTTCATGTTT
*
29243920 AATTTTT
1 AAATTTT
29243927 GTTATTGCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
42 31 0.74
43 8 0.19
44 3 0.07
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.49
Consensus pattern (41 bp):
AAATTTTCAAAAATTCCAAAAATATTTTACTTTTCATGTTT
Found at i:29244776 original size:24 final size:24
Alignment explanation
Indices: 29244744--29244802 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
29244734 TCCACATTGT
29244744 AGGAGAAATAAGAAAAGTGAGAGA
1 AGGAGAAATAAGAAAAGTGAGAGA
*
29244768 AGGAGAAATAAGAAATGTGAGAGA
1 AGGAGAAATAAGAAAAGTGAGAGA
*
29244792 ATGAGAAATAA
1 AGGAGAAATAA
29244803 TGTGGTGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.58, C:0.00, G:0.31, T:0.12
Consensus pattern (24 bp):
AGGAGAAATAAGAAAAGTGAGAGA
Found at i:29254431 original size:4 final size:4
Alignment explanation
Indices: 29254417--29254461 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
29254407 GAAAACTTAA
* * *
29254417 GTAT ATAT GTAT GTAT GTAT GCAT GTAT GTAT GTGT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
29254462 GAAATGTTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:29260241 original size:9 final size:9
Alignment explanation
Indices: 29260227--29260257 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
29260217 CTGATTACCG
29260227 TTGAAGCAT
1 TTGAAGCAT
29260236 TTGAAGCA-
1 TTGAAGCAT
29260244 TTGAAGCAT
1 TTGAAGCAT
29260253 TTGAA
1 TTGAA
29260258 ATGGAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (9 bp):
TTGAAGCAT
Found at i:29261423 original size:13 final size:13
Alignment explanation
Indices: 29261405--29261445 Score: 82
Period size: 13 Copynumber: 3.2 Consensus size: 13
29261395 AGCAAATCAG
29261405 TTTTGAGTGACTA
1 TTTTGAGTGACTA
29261418 TTTTGAGTGACTA
1 TTTTGAGTGACTA
29261431 TTTTGAGTGACTA
1 TTTTGAGTGACTA
29261444 TT
1 TT
29261446 GTAATGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.49
Consensus pattern (13 bp):
TTTTGAGTGACTA
Found at i:29261690 original size:18 final size:18
Alignment explanation
Indices: 29261667--29261701 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29261657 ATTGGTTAAA
*
29261667 ATAAAAATATTTAAATTC
1 ATAAAAATAATTAAATTC
*
29261685 ATAAAACTAATTAAATT
1 ATAAAAATAATTAAATT
29261702 ATATATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAAAATAATTAAATTC
Found at i:29262024 original size:19 final size:19
Alignment explanation
Indices: 29262000--29262036 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29261990 ATAAATTTAT
*
29262000 TTTTACATATACCTACAAA
1 TTTTACATATACCAACAAA
29262019 TTTTACATATACCAACAA
1 TTTTACATATACCAACAA
29262037 TTAATTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTTACATATACCAACAAA
Found at i:29265424 original size:15 final size:16
Alignment explanation
Indices: 29265396--29265425 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29265386 TAAATTCATA
29265396 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
29265412 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
29265426 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:29265445 original size:18 final size:17
Alignment explanation
Indices: 29265417--29265451 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29265407 ATTATTAAGA
*
29265417 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29265434 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29265452 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29265451 original size:16 final size:16
Alignment explanation
Indices: 29265417--29265470 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
29265407 ATTATTAAGA
29265417 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
29265434 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
29265450 A-TTTAA-TAATAAT-T
1 ATTTTAATTAA-AATAT
29265464 ATTTTAA
1 ATTTTAA
29265471 ATTATATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.15
15 13 0.38
16 5 0.15
17 5 0.15
18 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:29265556 original size:17 final size:17
Alignment explanation
Indices: 29265536--29265569 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29265526 ATTATTAAGA
29265536 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
29265553 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
29265570 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:29265601 original size:11 final size:11
Alignment explanation
Indices: 29265585--29265609 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29265575 AATAATTATG
29265585 TTAAAATATTA
1 TTAAAATATTA
29265596 TTAAAATATTA
1 TTAAAATATTA
29265607 TTA
1 TTA
29265610 TTCATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAAATATTA
Found at i:29265609 original size:27 final size:26
Alignment explanation
Indices: 29265520--29265611 Score: 66
Period size: 26 Copynumber: 3.5 Consensus size: 26
29265510 TTCATATAAG
*
29265520 AATATTATTA-TTAAGAATTTTATTAA
1 AATATTATTATTTAA-AATATTATTAA
* * *
29265546 ATTATATATTTTATTAAATTA-TATTTAA
1 AATAT-TATTAT-TTAAAATATTA-TTAA
29265574 TAATA--ATTATGTTAAAATATTATTAA
1 -AATATTATTAT-TTAAAATATTATTAA
29265600 AATATTATTATT
1 AATATTATTATT
29265612 CATATTAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 16
0.68 0.11 0.22
Matches are distributed among these distances:
25 4 0.08
26 20 0.40
27 13 0.26
28 6 0.12
29 7 0.14
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
AATATTATTATTTAAAATATTATTAA
Found at i:29265610 original size:120 final size:120
Alignment explanation
Indices: 29265322--29265589 Score: 504
Period size: 120 Copynumber: 2.2 Consensus size: 120
29265312 AAGTAGATTA
29265322 TAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
1 TAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
29265387 AAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATATTTTAAT
66 AAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATATTTTAAT
29265442 TAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
1 TAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
29265507 AAATTCATATAAGAATA-TTATTATTAAGAATTTTATTAAATTATATATTTT-AT
66 AAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATATTTTAAT
* *
29265560 TAAATTATATTTAATAATAATTATGTTAAA
1 TAAAATATATTTAATAATAATTATTTTAAA
29265590 ATATTATTAA
Statistics
Matches: 146, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
118 30 0.21
119 34 0.23
120 82 0.56
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (120 bp):
TAAAATATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
AAATTCATATAAGAATATTTATTATTAAGAATTTTATTAAATTATATATTTTAAT
Found at i:29267145 original size:29 final size:30
Alignment explanation
Indices: 29267093--29267150 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
29267083 ATGTTGGTTG
*
29267093 TGATTTTGATTTTTGCTGTTAATGGTGTTC
1 TGATTTTGATTTTTGCTATTAATGGTGTTC
*
29267123 TGATTTTGA-TTTTGCTATTAATGTTGTT
1 TGATTTTGATTTTTGCTATTAATGGTGTT
29267151 AATGGTGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.59
Consensus pattern (30 bp):
TGATTTTGATTTTTGCTATTAATGGTGTTC
Found at i:29267154 original size:38 final size:38
Alignment explanation
Indices: 29267106--29267194 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 38
29267096 TTTTGATTTT
* *
29267106 TGCTGTTAATGGTGTTCTGATTTTGATTTTGCTATTAA
1 TGCTGTTAATGGTGCTCTAATTTTGATTTTGCTATTAA
* * *
29267144 TGTTGTTAATGGTGCTCTAATTTTGATTTTTCTGTTAA
1 TGCTGTTAATGGTGCTCTAATTTTGATTTTGCTATTAA
29267182 TGCTGTTAATGGT
1 TGCTGTTAATGGT
29267195 TGTGTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.18, C:0.08, G:0.21, T:0.53
Consensus pattern (38 bp):
TGCTGTTAATGGTGCTCTAATTTTGATTTTGCTATTAA
Found at i:29268952 original size:39 final size:40
Alignment explanation
Indices: 29268898--29268992 Score: 129
Period size: 39 Copynumber: 2.4 Consensus size: 40
29268888 ATAAAATTTA
* *
29268898 TAATATACTATTTTAATATACTATTATAAATATACT-TTT
1 TAATATAATGTTTTAATATACTATTATAAATATACTGTTT
* * * *
29268937 TAATATATTGTTTTAATATACTGTTATAATTATATTGTTT
1 TAATATAATGTTTTAATATACTATTATAAATATACTGTTT
29268977 TAATATAATGTTTTAA
1 TAATATAATGTTTTAA
29268993 CTTTTAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
39 31 0.63
40 18 0.37
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (40 bp):
TAATATAATGTTTTAATATACTATTATAAATATACTGTTT
Found at i:29268974 original size:27 final size:27
Alignment explanation
Indices: 29268926--29269024 Score: 105
Period size: 27 Copynumber: 3.7 Consensus size: 27
29268916 TACTATTATA
*
29268926 AATATACT-TTTTAA-TATATTGTTTT
1 AATATACTGTTATAATTATATTGTTTT
29268951 AATATACTGTTATAATTATATTGTTTT
1 AATATACTGTTATAATTATATTGTTTT
* * * **
29268978 AATATAATGTTTTAACTTTTA-AATTTT
1 AATATACTGTTATAA-TTATATTGTTTT
*
29269005 AATATACTGTTATAAATATA
1 AATATACTGTTATAATTATA
29269025 CATTTAATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
25 8 0.13
26 8 0.13
27 41 0.67
28 4 0.07
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (27 bp):
AATATACTGTTATAATTATATTGTTTT
Found at i:29268989 original size:13 final size:13
Alignment explanation
Indices: 29268860--29268992 Score: 103
Period size: 13 Copynumber: 10.2 Consensus size: 13
29268850 ATTTTAAATG
29268860 TAATATACTGTTT
1 TAATATACTGTTT
*
29268873 TAATAATA-TATTGT
1 TAAT-ATACTGTT-T
* * *
29268887 T-ATAAAAT-TTA
1 TAATATACTGTTT
*
29268898 TAATATACTATTT
1 TAATATACTGTTT
*
29268911 TAATATACTATTAT
1 TAATATACTGTT-T
*
29268925 AAATATACT-TTT
1 TAATATACTGTTT
*
29268937 TAATATATTGTTT
1 TAATATACTGTTT
*
29268950 TAATATACTGTTA
1 TAATATACTGTTT
*
29268963 TAATTATATTGTTT
1 TAA-TATACTGTTT
*
29268977 TAATATAATGTTT
1 TAATATACTGTTT
29268990 TAA
1 TAA
29268993 CTTTTAAATT
Statistics
Matches: 98, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
11 1 0.01
12 17 0.17
13 55 0.56
14 25 0.26
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:29271444 original size:9 final size:9
Alignment explanation
Indices: 29271430--29271457 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29271420 GGTTGCAAAA
29271430 AGGACGATG
1 AGGACGATG
29271439 AGGACGATG
1 AGGACGATG
29271448 AGGACGATG
1 AGGACGATG
29271457 A
1 A
29271458 TGATGATGAT
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:0.36, C:0.11, G:0.43, T:0.11
Consensus pattern (9 bp):
AGGACGATG
Found at i:29272278 original size:25 final size:25
Alignment explanation
Indices: 29272244--29272291 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
29272234 TTAATATTTG
29272244 ATTGTTTGTAATTAAATTCAAATTA
1 ATTGTTTGTAATTAAATTCAAATTA
29272269 ATTGTTTGTAATTAAATTCAAAT
1 ATTGTTTGTAATTAAATTCAAAT
29272292 AAGTAATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (25 bp):
ATTGTTTGTAATTAAATTCAAATTA
Found at i:29272383 original size:16 final size:16
Alignment explanation
Indices: 29272362--29272395 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29272352 ATATAAATTC
29272362 AATAACAATTAATTTT
1 AATAACAATTAATTTT
*
29272378 AATAACAATTAGTTTT
1 AATAACAATTAATTTT
29272394 AA
1 AA
29272396 CTTTTAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAACAATTAATTTT
Found at i:29274495 original size:18 final size:19
Alignment explanation
Indices: 29274461--29274507 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
29274451 CTCACAAGTG
*
29274461 AGTTTAACATCATTA-TTTA
1 AGTTTAA-ATAATTATTTTA
*
29274480 ATTTTAAATAATTATTTTA
1 AGTTTAAATAATTATTTTA
29274499 AGTTTAAAT
1 AGTTTAAAT
29274508 TTATAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (19 bp):
AGTTTAAATAATTATTTTA
Found at i:29281262 original size:22 final size:23
Alignment explanation
Indices: 29281209--29281264 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
29281199 CCAGTTTTTA
* * *
29281209 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
29281232 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
29281254 ATTAAAATTAA
1 ATTAAAATTAA
29281265 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:29281277 original size:16 final size:16
Alignment explanation
Indices: 29281240--29281279 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29281230 TTAATAAAAT
* *
29281240 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
29281256 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
29281272 TAAAATTA
1 TAAAATTA
29281280 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:29281358 original size:59 final size:59
Alignment explanation
Indices: 29281290--29281459 Score: 313
Period size: 59 Copynumber: 2.9 Consensus size: 59
29281280 TCAAATTATT
* *
29281290 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTATCATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
29281349 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
29281408 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
29281460 ACAAACTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 108 1.00
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.45
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:29281552 original size:21 final size:20
Alignment explanation
Indices: 29281528--29281572 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
29281518 ATAAACTTAA
29281528 AATAAAAAAT-TATTATATTTT
1 AATAAAAAATATA-TATA-TTT
*
29281549 AATAATAAATATATATATTT
1 AATAAAAAATATATATATTT
29281569 AATA
1 AATA
29281573 TTTTTCGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 13 0.59
22 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATAAAAAATATATATATTT
Found at i:29284555 original size:44 final size:44
Alignment explanation
Indices: 29284449--29284746 Score: 166
Period size: 44 Copynumber: 6.6 Consensus size: 44
29284439 TTCGGTCTAT
* * * *
29284449 TCCACTGTAATCTCAGGGAGATAAGA-CC-TGA-TGCGATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCTGC
* * * *
29284490 TCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAATCTGC
* * * *
29284534 TCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTAC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAATCTGC
* * *
29284578 TCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGA--TC---CTT-TAT-T--T-CAATCTGC
* * *
29284632 TCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAAT-TCGC
1 TCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTCAATCT-GC
* * * *
29284676 TCCACTGTAATCTCAAGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTCAATCTGC
*
29284720 TCCGCTGTAATCTCAGGGAGATAAGAT
1 TCCACTGTAATCTCAGGGAGATAAGAT
29284747 TTCTGGCTTC
Statistics
Matches: 193, Mismatches: 39, Indels: 47
0.69 0.14 0.17
Matches are distributed among these distances:
40 1 0.01
41 22 0.11
42 4 0.02
43 7 0.04
44 114 0.59
45 4 0.02
46 1 0.01
47 1 0.01
48 2 0.01
49 3 0.02
51 3 0.02
52 2 0.01
53 2 0.01
54 27 0.14
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
TCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTCAATCTGC
Found at i:29284732 original size:142 final size:142
Alignment explanation
Indices: 29284476--29284762 Score: 538
Period size: 142 Copynumber: 2.0 Consensus size: 142
29284466 GAGATAAGAC
29284476 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
*
29284541 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
29284606 TCTGGCTTCAAT
131 TCTGGCTTCAAT
* *
29284618 CTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATTCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
*
29284683 TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
29284748 TCTGGCTTCAAT
131 TCTGGCTTCAAT
29284760 CTG
1 CTG
29284763 CTTCCTTACA
Statistics
Matches: 141, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAAGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:29284756 original size:44 final size:44
Alignment explanation
Indices: 29284674--29284764 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
29284664 ATTTTAATTC
*
29284674 GCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATCT
1 GCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTCAATCT
* * * *
29284718 GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCT
1 GCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTCAATCT
29284762 GCT
1 GCT
29284765 TCCTTACACT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (44 bp):
GCTCCACTGTAATCTCAAGGAGATAAGATTACTAGCTTCAATCT
Found at i:29301838 original size:25 final size:25
Alignment explanation
Indices: 29301783--29301880 Score: 96
Period size: 25 Copynumber: 4.0 Consensus size: 25
29301773 GAACACACCA
29301783 CAGCTCGT-ATGAGCTTACCGA-TCT
1 CAGCTCGTGA-GAGCTTACCGATTCT
* *
29301807 CAGCTCGTGAAAGCTTACTGATTCT
1 CAGCTCGTGAGAGCTTACCGATTCT
*
29301832 CAGCTCGT-ATGAGGTTACCGATT-T
1 CAGCTCGTGA-GAGCTTACCGATTCT
* *
29301856 CTAGCTCGTGAGAGCATACTGATTC
1 C-AGCTCGTGAGAGCTTACCGATTC
29301881 ATAACTCGTA
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
24 20 0.33
25 39 0.65
26 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (25 bp):
CAGCTCGTGAGAGCTTACCGATTCT
Found at i:29301889 original size:50 final size:49
Alignment explanation
Indices: 29301786--29301895 Score: 150
Period size: 50 Copynumber: 2.2 Consensus size: 49
29301776 CACACCACAG
* *
29301786 CTCGTATGAGCTTACCGATCTCAGCTCGTGAAAGCTTACTGATTCTCAG
1 CTCGTATGAGCTTACCGATCTCAGCTCGTGAAAGCATACTGATTCTCAA
* * *
29301835 CTCGTATGAGGTTACCGATTTCTAGCTCGTGAGAGCATACTGATTCAT-AA
1 CTCGTATGAGCTTACCGATCTC-AGCTCGTGAAAGCATACTGATTC-TCAA
29301885 CTCGTATGAGC
1 CTCGTATGAGC
29301896 ATACATGTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
49 20 0.38
50 32 0.60
51 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (49 bp):
CTCGTATGAGCTTACCGATCTCAGCTCGTGAAAGCATACTGATTCTCAA
Found at i:29302364 original size:17 final size:17
Alignment explanation
Indices: 29302334--29302368 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29302324 AGTGAATCGG
29302334 AAGCTCGTTCGAGCTAT
1 AAGCTCGTTCGAGCTAT
* *
29302351 AAGCTTGTTGGAGCTAT
1 AAGCTCGTTCGAGCTAT
29302368 A
1 A
29302369 TCACACTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (17 bp):
AAGCTCGTTCGAGCTAT
Found at i:29308197 original size:11 final size:13
Alignment explanation
Indices: 29308177--29308208 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
29308167 AATAAATTAA
29308177 TAAAATATCAT-T
1 TAAAATATCATAT
29308189 TAAAA-ATCATAT
1 TAAAATATCATAT
29308201 TAAAATAT
1 TAAAATAT
29308209 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:29310976 original size:12 final size:12
Alignment explanation
Indices: 29310959--29310983 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29310949 AAAAAATGAC
29310959 AATAATAATAAA
1 AATAATAATAAA
29310971 AATAATAATAAA
1 AATAATAATAAA
29310983 A
1 A
29310984 TGCGTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:29315179 original size:34 final size:34
Alignment explanation
Indices: 29315136--29315244 Score: 115
Period size: 34 Copynumber: 3.4 Consensus size: 34
29315126 CGTCTACTAA
29315136 AGGAATGTTGATCTACAGTTTCTTCAATATATCT
1 AGGAATGTTGATCTACAGTTTCTTCAATATATCT
* ** *
29315170 AGGAATGTTG-TACTAGAGCGTC-T-ACTA-A---
1 AGGAATGTTGAT-CTACAGTTTCTTCAATATATCT
29315198 AGGAATGTTGATCTACAGTTTCTTCAATATATCT
1 AGGAATGTTGATCTACAGTTTCTTCAATATATCT
29315232 AGGAACTGTTGAT
1 AGGAA-TGTTGAT
29315245 ACTGCTTGTC
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
28 17 0.29
29 2 0.03
30 3 0.05
31 2 0.03
32 3 0.05
33 2 0.03
34 22 0.38
35 7 0.12
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (34 bp):
AGGAATGTTGATCTACAGTTTCTTCAATATATCT
Found at i:29315212 original size:62 final size:62
Alignment explanation
Indices: 29315111--29315247 Score: 249
Period size: 62 Copynumber: 2.2 Consensus size: 62
29315101 CCATAACTTA
29315111 GAAT-TTGTACTAGAGCGTCTACTAAAGGAATGTTGATCTACAGTTTCTTCAATATATCTAG
1 GAATGTTGTACTAGAGCGTCTACTAAAGGAATGTTGATCTACAGTTTCTTCAATATATCTAG
29315172 GAATGTTGTACTAGAGCGTCTACTAAAGGAATGTTGATCTACAGTTTCTTCAATATATCTAG
1 GAATGTTGTACTAGAGCGTCTACTAAAGGAATGTTGATCTACAGTTTCTTCAATATATCTAG
29315234 GAACTGTTGATACT
1 GAA-TGTTG-TACT
29315248 GCTTGTCATG
Statistics
Matches: 73, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
61 4 0.05
62 60 0.82
63 5 0.07
64 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.36
Consensus pattern (62 bp):
GAATGTTGTACTAGAGCGTCTACTAAAGGAATGTTGATCTACAGTTTCTTCAATATATCTAG
Found at i:29324905 original size:57 final size:57
Alignment explanation
Indices: 29324836--29324943 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 57
29324826 GTCATTAGGG
* * *
29324836 TGTTACATTTTCCAGGAACTCTGTGCCAGTGATATATTTCCAAGTACTATGGAACGA
1 TGTTACAGTTTCCAAGAACTCTGTGCAAGTGATATATTTCCAAGTACTATGGAACGA
* * *
29324893 TGTTACAGTTTCCAAGCACTCTGTGCAAGTGATATATTTTCAGGTACTATG
1 TGTTACAGTTTCCAAGAACTCTGTGCAAGTGATATATTTCCAAGTACTATG
29324944 TACCGGTGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (57 bp):
TGTTACAGTTTCCAAGAACTCTGTGCAAGTGATATATTTCCAAGTACTATGGAACGA
Found at i:29324933 original size:29 final size:29
Alignment explanation
Indices: 29324842--29324933 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
29324832 AGGGTGTTAC
* *
29324842 ATTTTCCAGGAACTCTGTGCCAGTGATAT
1 ATTTTCCAAGAACTCTGTGCAAGTGATAT
* * * *
29324871 A-TTTCCAAGTACTATG-G-AACGATGTTAC
1 ATTTTCCAAGAACTCTGTGCAA-G-TGATAT
* *
29324899 AGTTTCCAAGCACTCTGTGCAAGTGATAT
1 ATTTTCCAAGAACTCTGTGCAAGTGATAT
29324928 ATTTTC
1 ATTTTC
29324934 AGGTACTATG
Statistics
Matches: 47, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
26 1 0.02
27 2 0.04
28 17 0.36
29 23 0.49
30 2 0.04
31 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (29 bp):
ATTTTCCAAGAACTCTGTGCAAGTGATAT
Found at i:29330020 original size:21 final size:21
Alignment explanation
Indices: 29329996--29330037 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
29329986 ACTTTAAAAG
29329996 TAAACATAATACAATCCAACC
1 TAAACATAATACAATCCAACC
29330017 TAAACATAATACAATCCAACC
1 TAAACATAATACAATCCAACC
29330038 AATAGCTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAACATAATACAATCCAACC
Found at i:29330574 original size:35 final size:34
Alignment explanation
Indices: 29330530--29330625 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 34
29330520 ATGTTCACCC
* *
29330530 GAGCCAGTCCCTCCAGAACACACCAATGCTCATAA
1 GAGCTAGTCCCT-CAGAACACACCAATGCTCAAAA
* *
29330565 GAGCTAGTCCAATCAAAACACACCAATGCTCAAAA
1 GAGCTAGTCC-CTCAGAACACACCAATGCTCAAAA
*
29330600 GAGCTAGTCCCTCTGAAACACACCAA
1 GAGCTAGTCCCTCAG-AACACACCAA
29330626 ACAGATAGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 2 0.04
35 49 0.94
36 1 0.02
ACGTcount: A:0.39, C:0.33, G:0.14, T:0.15
Consensus pattern (34 bp):
GAGCTAGTCCCTCAGAACACACCAATGCTCAAAA
Found at i:29334362 original size:19 final size:22
Alignment explanation
Indices: 29334315--29334364 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 22
29334305 TTTTTAATTA
29334315 AAAAATATATAAATATAACATT
1 AAAAATATATAAATATAACATT
29334337 AAAAATAT-TAAAT-TAA-ATT
1 AAAAATATATAAATATAACATT
*
29334356 AATAATATA
1 AAAAATATA
29334365 AACTAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
20 3 0.12
21 5 0.19
22 8 0.31
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAATATATAAATATAACATT
Found at i:29334373 original size:19 final size:18
Alignment explanation
Indices: 29334316--29334374 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 18
29334306 TTTTAATTAA
29334316 AAAATATATAAATATAACATT
1 AAAA-ATATAAATA-AA-ATT
*
29334337 AAAAATATTAAATTAAATT
1 AAAAATA-TAAATAAAATT
*
29334356 AATAATATAAACTAAAATT
1 AAAAATATAAA-TAAAATT
29334375 TACACTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.12
19 15 0.45
20 5 0.15
21 9 0.27
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATATAAATAAAATT
Found at i:29338759 original size:17 final size:17
Alignment explanation
Indices: 29338733--29338765 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29338723 CTGATCAAAA
*
29338733 AAAATTGTAAAAAAATT
1 AAAATCGTAAAAAAATT
29338750 AAAATCGTAAAAAAAT
1 AAAATCGTAAAAAAAT
29338766 ATTTAAAAAT
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:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAATCGTAAAAAAATT
Found at i:29338772 original size:29 final size:29
Alignment explanation
Indices: 29338729--29338839 Score: 97
Period size: 29 Copynumber: 3.8 Consensus size: 29
29338719 TGACCTGATC
*
29338729 AAAAAAA-ATTGTAAAAAAATTAAAATCGT
1 AAAAAAATATT-TAAAAAAATTAAAATTGT
*
29338758 AAAAAAATATTTAAAAATATATAAAAATTGT
1 AAAAAAATATTTAAAAA-A-ATTAAAATTGT
* **
29338789 --GAAAATATTT-AAATTATTAAAAATTGT
1 AAAAAAATATTTAAAAAAATT-AAAATTGT
29338816 AAAAAAAT-TTTAAAAAAAATTAAA
1 AAAAAAATATTT-AAAAAAATTAAA
29338840 TTTTTGTCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
26 2 0.03
27 8 0.12
28 6 0.09
29 30 0.46
30 10 0.15
31 9 0.14
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAAAAATATTTAAAAAAATTAAAATTGT
Found at i:29338773 original size:10 final size:10
Alignment explanation
Indices: 29338760--29338831 Score: 53
Period size: 9 Copynumber: 7.5 Consensus size: 10
29338750 AAAATCGTAA
29338760 AAAAATATTT
1 AAAAATATTT
*
29338770 AAAAATATAT
1 AAAAATATTT
*
29338780 AAAAAT-TGT
1 AAAAATATTT
*
29338789 GAAAATATTT
1 AAAAATATTT
*
29338799 -AAATTA-TT
1 AAAAATATTT
*
29338807 AAAAAT-TGT
1 AAAAATATTT
*
29338816 AAAAAAATTTT
1 AAAAATA-TTT
29338827 AAAAA
1 AAAAA
29338832 AAATTAAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
8 2 0.04
9 22 0.46
10 17 0.35
11 7 0.15
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (10 bp):
AAAAATATTT
Found at i:29338881 original size:19 final size:19
Alignment explanation
Indices: 29338851--29338905 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
29338841 TTTTGTCAAT
*
29338851 AATTATTAAAAATATTTTAA
1 AATTA-TAAAAAAATTTTAA
* ** *
29338871 AATTGTAAAAAGCTATTAA
1 AATTATAAAAAAATTTTAA
29338890 AATTATAAAAAAATTT
1 AATTATAAAAAAATTT
29338906 ATTTAAATAT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
AATTATAAAAAAATTTTAA
Found at i:29338901 original size:10 final size:10
Alignment explanation
Indices: 29338851--29338954 Score: 58
Period size: 10 Copynumber: 10.4 Consensus size: 10
29338841 TTTTGTCAAT
29338851 AATTATTAAA
1 AATTATTAAA
*
29338861 AA-TATTTTAA
1 AATTA-TTAAA
*
29338871 AATT-GTAAA
1 AATTATTAAA
*
29338880 AAGCTATT-AA
1 AA-TTATTAAA
*
29338890 AATTATAAAAA
1 AATTAT-TAAA
29338901 AATTTATTTAAA
1 AA-TTA-TTAAA
*
29338913 TATT-TT-AA
1 AATTATTAAA
29338921 AATTATTAAA
1 AATTATTAAA
*
29338931 AATCA-TAAA
1 AATTATTAAA
29338940 TAATTATTAAA
1 -AATTATTAAA
29338951 AATT
1 AATT
29338955 TGTAAATAAT
Statistics
Matches: 70, Mismatches: 12, Indels: 24
0.66 0.11 0.23
Matches are distributed among these distances:
8 5 0.07
9 18 0.26
10 27 0.39
11 12 0.17
12 7 0.10
13 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (10 bp):
AATTATTAAA
Found at i:29338985 original size:3 final size:3
Alignment explanation
Indices: 29338977--29339003 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29338967 ACAAACCAAA
29338977 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
29339004 AACTTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:29350790 original size:49 final size:50
Alignment explanation
Indices: 29350729--29350870 Score: 166
Period size: 56 Copynumber: 2.8 Consensus size: 50
29350719 AATAACATGC
*
29350729 CAAA-GCCATGTCCCAGACATGGTCTTACATGGGATGT-T-TCT-TGTACTG
1 CAAATGCCATGTCCCAGACATGGTCTTACATGGGATCTATATCTATG-A-TG
29350777 CAAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATG
1 CAAATGCCATGTCCCAGACATGGTCTTACATGGGA--TCT-AT-ATCT--ATGATG
*
29350833 CCAATGCCATGTCCCAGACATGGTCTTACATGGGATCT
1 CAAATGCCATGTCCCAGACATGGTCTTACATGGGATCT
29350871 CTTTACCCTA
Statistics
Matches: 82, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
48 4 0.05
49 30 0.37
51 2 0.02
53 1 0.01
54 3 0.04
55 3 0.04
56 36 0.44
57 1 0.01
58 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (50 bp):
CAAATGCCATGTCCCAGACATGGTCTTACATGGGATCTATATCTATGATG
Found at i:29351554 original size:22 final size:22
Alignment explanation
Indices: 29351521--29351581 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
29351511 GCCCGACCCG
* *
29351521 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
29351544 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
29351566 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
29351582 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:29351594 original size:16 final size:16
Alignment explanation
Indices: 29351557--29351596 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
29351547 TTAATAAAAT
* *
29351557 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
29351573 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
29351589 TAAAATTA
1 TAAAATTA
29351597 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:29351702 original size:9 final size:9
Alignment explanation
Indices: 29351669--29351696 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29351659 TTTATCAAAT
29351669 TATTAATTG
1 TATTAATTG
29351678 TATTAATTG
1 TATTAATTG
29351687 TATTAATTG
1 TATTAATTG
29351696 T
1 T
29351697 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:29351706 original size:68 final size:68
Alignment explanation
Indices: 29351585--29351794 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
29351575 AAATTAATTG
*
29351585 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
29351648 TGA
66 TGA
29351651 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
29351716 TGA
66 TGA
*
29351719 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
29351784 TGA
66 TGA
29351787 TTAGTAAA
1 TTAGTAAA
29351795 ACAAACTTGA
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 26 0.19
68 114 0.81
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:29351749 original size:9 final size:9
Alignment explanation
Indices: 29351737--29351764 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29351727 TTTATCAAAT
29351737 TATTAATTG
1 TATTAATTG
29351746 TATTAATTG
1 TATTAATTG
29351755 TATTAATTG
1 TATTAATTG
29351764 T
1 T
29351765 TGTAACAAAA
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:29351890 original size:24 final size:25
Alignment explanation
Indices: 29351861--29351907 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
29351851 AAATAAACTT
*
29351861 AAAATAAAAAACTAT-TATATTTTA
1 AAAATAAAAAAATATATATATTTTA
29351885 AAAATAAAAAAATATATATATTT
1 AAAATAAAAAAATATATATATTT
29351908 AATATTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
AAAATAAAAAAATATATATATTTTA
Found at i:29357886 original size:50 final size:50
Alignment explanation
Indices: 29357737--29358033 Score: 222
Period size: 50 Copynumber: 5.8 Consensus size: 50
29357727 GATAATAACA
* * ** * **
29357737 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTC-T-TGCAC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCT-CGG
* * * * * * * ** *
29357786 TGCAAAAGTCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
29357836 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGTGACCTCTCGTCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGG-GACCTCTCATCTCGG
* *
29357886 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * * *
29357936 TGCCAACACCATGTCCCAGACATGGTCTTACATGAGACGTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGAC--CTC-TCATCTC---GG
* * * *
29357992 CGCCAACGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
29358034 TTACCCAAAT
Statistics
Matches: 201, Mismatches: 37, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
49 37 0.18
50 115 0.57
51 3 0.01
52 3 0.01
53 7 0.03
54 3 0.01
56 33 0.16
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:29365692 original size:17 final size:17
Alignment explanation
Indices: 29365670--29365704 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
29365660 TTCAAGTCTA
29365670 ACTCGCCCATACTTTGT
1 ACTCGCCCATACTTTGT
29365687 ACTCGCCCATACTTTGT
1 ACTCGCCCATACTTTGT
29365704 A
1 A
29365705 TTCACCTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.34, G:0.11, T:0.34
Consensus pattern (17 bp):
ACTCGCCCATACTTTGT
Found at i:29365890 original size:27 final size:28
Alignment explanation
Indices: 29365852--29365926 Score: 104
Period size: 27 Copynumber: 2.8 Consensus size: 28
29365842 TAGATTTTAT
*
29365852 CATACATACTATCCA-TTCGGAGTGT-GC
1 CATACATACTATCCACTTCAGAGT-TCGC
29365879 CATACATACTAT-CACTTCAGAGTTCGC
1 CATACATACTATCCACTTCAGAGTTCGC
29365906 CATACATACTATCC-CTTCAGA
1 CATACATACTATCCACTTCAGA
29365927 TGGTTGCCAC
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
26 3 0.07
27 40 0.91
28 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (28 bp):
CATACATACTATCCACTTCAGAGTTCGC
Found at i:29366018 original size:28 final size:27
Alignment explanation
Indices: 29365959--29366083 Score: 121
Period size: 27 Copynumber: 4.6 Consensus size: 27
29365949 TTTTGTGTAC
*
29365959 GCCACGAAGGCGTTT-CTTTCATCAT-TT
1 GCCACAAAGGC-TTTCCTTTCAT-ATATT
* * *
29365986 GCCACAAAGGCTTTCCTTCCCATAGATC
1 GCCACAAAGGCTTTCCTT-TCATATATT
*
29366014 GCCACAAAGGC-TTCCATATCATATATT
1 GCCACAAAGGCTTTCC-TTTCATATATT
* *
29366041 GCCATAAAGGCTTTTCGTTTCATATATT
1 GCCACAAAGGC-TTTCCTTTCATATATT
29366069 GCCACAAAGGCTTTC
1 GCCACAAAGGCTTTC
29366084 ATTTTTTGGC
Statistics
Matches: 80, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
26 3 0.04
27 38 0.47
28 36 0.45
29 3 0.04
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (27 bp):
GCCACAAAGGCTTTCCTTTCATATATT
Done.