Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 9 of 284
Found at i:2866034 original size:17 final size:17
Alignment explanation
Indices: 2866014--2866047 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2866004 ATTCACTAAT
2866014 ATAAT-ATCAATTAAATA
1 ATAATAATCAA-TAAATA
2866031 ATAATAATCAATAAATA
1 ATAATAATCAATAAATA
2866048 TCTTTTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATAATCAATAAATA
Found at i:2868312 original size:22 final size:22
Alignment explanation
Indices: 2868284--2868330 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2868274 CTATAACCAA
2868284 GTTTGAGCATTGCTTAGACTTG
1 GTTTGAGCATTGCTTAGACTTG
2868306 GTTTGAGCATTGCTTAGACTTG
1 GTTTGAGCATTGCTTAGACTTG
2868328 GTT
1 GTT
2868331 GGTGTCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.13, G:0.28, T:0.43
Consensus pattern (22 bp):
GTTTGAGCATTGCTTAGACTTG
Found at i:2868776 original size:5 final size:5
Alignment explanation
Indices: 2868766--2868803 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
2868756 TTGTGTGTTC
2868766 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
2868804 CAAAGCTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:2869572 original size:24 final size:25
Alignment explanation
Indices: 2869526--2869572 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2869516 GTTTGTGAAT
*
2869526 ATTATATTATTTATAACATATAAAA
1 ATTATATTATTTATAACACATAAAA
*
2869551 ATTATATT-TTTATAATACATAA
1 ATTATATTATTTATAACACATAA
2869573 TACTATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATATTATTTATAACACATAAAA
Found at i:2869580 original size:26 final size:25
Alignment explanation
Indices: 2869523--2869582 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
2869513 TAAGTTTGTG
*
2869523 AATATTATATTATTTATAACATATA
1 AATATTATATTATTTATAACACATA
* *
2869548 AAAATTATATT-TTTATAATACATA
1 AATATTATATTATTTATAACACATA
2869572 ATACTATTATA
1 A-A-TATTATA
2869583 ATGTAAACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 12 0.41
25 11 0.38
26 6 0.21
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (25 bp):
AATATTATATTATTTATAACACATA
Found at i:2876598 original size:12 final size:13
Alignment explanation
Indices: 2876577--2876644 Score: 77
Period size: 12 Copynumber: 5.3 Consensus size: 13
2876567 TTTGACAAAA
*
2876577 AAAAATTAAAATC
1 AAAAATCAAAATC
* *
2876590 AAAAATAAAAAACC
1 AAAAAT-CAAAATC
*
2876604 CAAAATCAAAATC
1 AAAAATCAAAATC
2876617 -AAAATCAAAATC
1 AAAAATCAAAATC
2876629 -AAAATCAAAATC
1 AAAAATCAAAATC
2876641 AAAA
1 AAAA
2876645 TTCGATTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
12 24 0.50
13 14 0.29
14 10 0.21
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATCAAAATC
Found at i:2876599 original size:18 final size:19
Alignment explanation
Indices: 2876577--2876645 Score: 79
Period size: 18 Copynumber: 3.6 Consensus size: 19
2876567 TTTGACAAAA
* *
2876577 AAAAATTAAAATCAAAAATA
1 AAAAATCAAAATC-AAAATC
*
2876597 AAAAACCCAAAATCAAAATC
1 AAAAA-TCAAAATCAAAATC
2876617 -AAAATCAAAATCAAAATC
1 AAAAATCAAAATCAAAATC
2876635 -AAAATCAAAAT
1 AAAAATCAAAAT
2876646 TCGATTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
18 24 0.55
19 4 0.09
20 10 0.23
21 6 0.14
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAATCAAAATCAAAATC
Found at i:2876613 original size:6 final size:6
Alignment explanation
Indices: 2876604--2876645 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
2876594 ATAAAAAACC
2876604 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT
2876646 TCGATTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CAAAAT
Found at i:2892595 original size:27 final size:27
Alignment explanation
Indices: 2892564--2892741 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
2892554 TAAATTGTAC
2892564 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
2892591 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2892617 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
2892645 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
2892673 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2892700 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2892727 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2892742 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:2892678 original size:82 final size:81
Alignment explanation
Indices: 2892565--2892720 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
2892555 AAATTGTACA
* *
2892565 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
2892629 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
2892646 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
2892711 TGCGAGTTGA
65 TGCGAATTGA
2892721 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:2892732 original size:82 final size:81
Alignment explanation
Indices: 2892561--2892741 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
2892551 GATTAAATTG
* *
2892561 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
2892626 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
2892642 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
2892706 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
2892724 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
2892742 GGCTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:2892752 original size:27 final size:27
Alignment explanation
Indices: 2892646--2892752 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
2892636 TGACCATGCG
* * * *
2892646 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
2892674 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
2892701 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
2892728 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
2892753 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:2895329 original size:50 final size:50
Alignment explanation
Indices: 2895229--2895340 Score: 118
Period size: 50 Copynumber: 2.2 Consensus size: 50
2895219 CAAGCATGTA
* * * **
2895229 AACGGGAAGCTCTTTCGAGCCATATGACAGAAAGATCATGTGAGTTAAGT
1 AACGGGAAGCTCTTGCGAGCCAAATGACAGAAAGATCATGAGAGCCAAGT
** *
2895279 AACGGGAAGCTCTTGCGAGCCAAAT-ATTGAGAAGTTCATGAGAGCCAAGT
1 AACGGGAAGCTCTTGCGAGCCAAATGACAGA-AAGATCATGAGAGCCAAGT
* *
2895329 ATCAGGAAGCTC
1 AACGGGAAGCTC
2895341 AAGAGAGCTG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
49 3 0.06
50 48 0.94
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (50 bp):
AACGGGAAGCTCTTGCGAGCCAAATGACAGAAAGATCATGAGAGCCAAGT
Found at i:2897355 original size:10 final size:10
Alignment explanation
Indices: 2897340--2897368 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2897330 CATTTCAAAG
2897340 CATCCCTCAA
1 CATCCCTCAA
2897350 CATCCCTCAA
1 CATCCCTCAA
2897360 CATCCCTCA
1 CATCCCTCA
2897369 TTCCACAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.52, G:0.00, T:0.21
Consensus pattern (10 bp):
CATCCCTCAA
Found at i:2900415 original size:37 final size:37
Alignment explanation
Indices: 2900374--2900447 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
2900364 AAGTTATTTT
2900374 CAGCTTTACCAGTGAAGAAATCTAAAGAGGAATTTAG
1 CAGCTTTACCAGTGAAGAAATCTAAAGAGGAATTTAG
2900411 CAGCTTTACCAGTGAAGAAATCTAAAGAGGAATTTAG
1 CAGCTTTACCAGTGAAGAAATCTAAAGAGGAATTTAG
2900448 TCGAGCCACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (37 bp):
CAGCTTTACCAGTGAAGAAATCTAAAGAGGAATTTAG
Found at i:2904575 original size:39 final size:40
Alignment explanation
Indices: 2904474--2904658 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
2904464 TTGAATGATG
* * *
2904474 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
2904513 ATCCGGACTAAGAT-CCGAAGGCATTTTTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
2904554 TCCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
2904593 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
2904632 GACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
2904659 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 34 0.28
40 79 0.65
41 9 0.07
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:2904610 original size:79 final size:79
Alignment explanation
Indices: 2904471--2904691 Score: 236
Period size: 79 Copynumber: 2.8 Consensus size: 79
2904461 TATTTGAATG
* * * * **
2904471 ATGTCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGC
1 ATGTCCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTACTATATCCGGGTTAAG-TCCGAAGGC
*
2904535 ATTTTTGCGAGATACT
64 ATTTGTGCGAGATACT
*
2904551 AAT-TCCGGGCTAAG-CCCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGC
1 -ATGTCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGGGTTAAGT-CCGAAGGC
*
2904614 ATTTGTGCGAGTTACT
64 ATTTGTGCGAGATACT
* * * *
2904630 ATGACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 ATGTCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTA-CTATATCCGGGTT-AAGTCCGAAGG
2904692 TACGTGATTT
Statistics
Matches: 120, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
78 3 0.03
79 69 0.57
80 46 0.38
81 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (79 bp):
ATGTCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGGGTTAAGTCCGAAGGCAT
TTGTGCGAGATACT
Found at i:2910007 original size:33 final size:33
Alignment explanation
Indices: 2909970--2910034 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
2909960 GGTAAAGCCA
2909970 AATGGCTAATGTGAAATATATATGAGATATGTG
1 AATGGCTAATGTGAAATATATATGAGATATGTG
2910003 AATGGCTAATGTGAAATATATATGAGATATGT
1 AATGGCTAATGTGAAATATATATGAGATATGT
2910035 ATATGTGGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (33 bp):
AATGGCTAATGTGAAATATATATGAGATATGTG
Found at i:2910038 original size:48 final size:48
Alignment explanation
Indices: 2910002--2910342 Score: 583
Period size: 48 Copynumber: 7.1 Consensus size: 48
2909992 TGAGATATGT
*
2910002 GAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCC
1 GAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCC
*
2910050 GAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCC
1 GAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCC
* * *
2910098 GAGTGGCTAATGTGAAATATATACGAGATATGTATATGTGGTAAAGCC
1 GAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCC
* * *
2910146 GAGTGGCTAATGTGAAATATGTACGAGATATGTATATGTCGTAAAGCC
1 GAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCC
* *
2910194 AAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCC
1 GAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCC
*
2910242 GAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCC
1 GAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCC
2910290 GAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCC
1 GAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCC
2910338 GAATG
1 GAATG
2910343 ACCAAATGTG
Statistics
Matches: 278, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 278 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (48 bp):
GAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCC
Found at i:2910510 original size:37 final size:37
Alignment explanation
Indices: 2910461--2910600 Score: 235
Period size: 37 Copynumber: 3.8 Consensus size: 37
2910451 GGAAATATAT
* *
2910461 TCCGGGTAAGACCCGATGACTACGTGTAGAGATTTTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
2910498 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
2910535 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
2910572 TCCAGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
2910601 GGACTATTCG
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:2917735 original size:44 final size:44
Alignment explanation
Indices: 2917687--2917837 Score: 150
Period size: 44 Copynumber: 3.5 Consensus size: 44
2917677 TATGTGTTTT
**
2917687 CGTGTAAGACCATGTCTTAGACATTGGCATCGACTTATGATTTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGACTTATGATTTA
* * *
2917731 CGTGTAAGACCACGTCTGGGACGTTGGCATC-ATCTT-TTATTT-
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGA-CTTATGATTTA
* * * * *
2917773 TGTGTAAGACCCTGTCTGGGATAGTGGCATCGA-TAATTGA-TTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGACTTA-TGATTTA
*
2917816 CATGTAAGACCATGTCTGGGAC
1 CGTGTAAGACCATGTCTGGGAC
2917838 GTTAGCATTG
Statistics
Matches: 85, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
41 1 0.01
42 27 0.32
43 27 0.32
44 30 0.35
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (44 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCGACTTATGATTTA
Found at i:2921540 original size:16 final size:17
Alignment explanation
Indices: 2921519--2921550 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2921509 AACTGAGTTG
2921519 AGAAAATT-ATTTAATT
1 AGAAAATTAATTTAATT
2921535 AGAAAATTAATTTAAT
1 AGAAAATTAATTTAAT
2921551 AAATAATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
AGAAAATTAATTTAATT
Found at i:2925519 original size:29 final size:29
Alignment explanation
Indices: 2925485--2925542 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
2925475 AGTTTAATTT
2925485 ACAAGTCTAGGGGCAAAAATGTAATTTTG
1 ACAAGTCTAGGGGCAAAAATGTAATTTTG
* *
2925514 ACAAGTTTAGGGGCAAAATTGTAATTTTG
1 ACAAGTCTAGGGGCAAAAATGTAATTTTG
2925543 CAAAAATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (29 bp):
ACAAGTCTAGGGGCAAAAATGTAATTTTG
Found at i:2930146 original size:44 final size:44
Alignment explanation
Indices: 2930093--2930184 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
2930083 CCGAAGTAAC
* *
2930093 AGTAGCAGTACGAAACACATGGTGCCTCATCAACTCGAA-GTCGA
1 AGTAACAGTACGAAACACATAGTGCCTCATCAACTC-AAGGTCGA
* ** *
2930137 AGTAACAGTACGACACTTATAGTGCCTCATCGACTCAAGGTCGA
1 AGTAACAGTACGAAACACATAGTGCCTCATCAACTCAAGGTCGA
2930181 AGTA
1 AGTA
2930185 TCCCTGAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 2 0.05
44 39 0.95
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.21
Consensus pattern (44 bp):
AGTAACAGTACGAAACACATAGTGCCTCATCAACTCAAGGTCGA
Found at i:2931623 original size:44 final size:44
Alignment explanation
Indices: 2931557--2931644 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
2931547 TGTAAAAAGA
*
2931557 AAGAGGATCTCTTTGCGTCACTCCTCTTAATGGGATGAAACCTT
1 AAGAGGATCTCTTTGCGCCACTCCTCTTAATGGGATGAAACCTT
2931601 AAGAGGATCTCTTTGCGCCACTCCTCTTAATGGGATGAAACCTT
1 AAGAGGATCTCTTTGCGCCACTCCTCTTAATGGGATGAAACCTT
2931645 CCGAGAGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (44 bp):
AAGAGGATCTCTTTGCGCCACTCCTCTTAATGGGATGAAACCTT
Found at i:2931878 original size:16 final size:16
Alignment explanation
Indices: 2931857--2931913 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
2931847 TAATATGCTT
2931857 ATAAAAATAATTAAAA
1 ATAAAAATAATTAAAA
2931873 ATAAAAAGTACATTAATTAAAA
1 AT--AAA--A-A-TAATTAAAA
*
2931895 ATAAAAATATTTAAAA
1 ATAAAAATAATTAAAA
2931911 ATA
1 ATA
2931914 TCATCAAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
16 13 0.38
17 1 0.03
18 4 0.12
20 4 0.12
21 1 0.03
22 11 0.32
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
ATAAAAATAATTAAAA
Found at i:2932629 original size:18 final size:17
Alignment explanation
Indices: 2932602--2932638 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
2932592 AATATCACAT
*
2932602 TAATACTATTATTATAA
1 TAATACTATTATTAAAA
2932619 TAATAACTATTATTAAAA
1 TAAT-ACTATTATTAAAA
2932637 TA
1 TA
2932639 TTATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATACTATTATTAAAA
Found at i:2935648 original size:168 final size:169
Alignment explanation
Indices: 2935382--2935694 Score: 416
Period size: 166 Copynumber: 1.9 Consensus size: 169
2935372 AAACACATTC
* * * * *
2935382 TAAAATTTGTTAATGTTCTGCATAAAGGATGCAACTTCACTTGTTTTTGTTTAGGAATTCTCAGT
1 TAAAATTTGTTAATGTTCTGCATAAA-GAGGCAACTGCACTTGTTTTTATTGAGGAATTCTCAGC
* **
2935447 ATGTGACAGATAACAAATCAATCATACAAATAACCTGTATTGTTAGTAATCAATTCTATTTTTGA
65 ATGTGACAGATAACAAATCAATCATACAAATAA-CT-TATCGTTAGTAATCAATTCTATAGTTGA
* *
2935512 TTTCAAGACAGTTAACCAAAGGCAATATCACTGACTTTGTTT
128 TTACAAGACACTTAACCAAAGGCAATATCACTGACTTTGTTT
* *
2935554 TAAAATTTGTTAATGTTCTGCA-AAA-AGGCAACTGCACTTGTTTTTATTGA-GAATTCTTAGCG
1 TAAAATTTGTTAATGTTCTGCATAAAGAGGCAACTGCACTTGTTTTTATTGAGGAATTCTCAGCA
* ** * * *
2935616 TGTGACAGCTTTCAGATCAATCATATAAATAACTTGTCGTTAGTAATCAATTCTATAGTTGATTA
66 TGTGACAGATAACAAATCAATCATACAAATAACTTATCGTTAGTAATCAATTCTATAGTTGATTA
2935681 CAAGACACTTAACC
131 CAAGACACTTAACC
2935695 GTGTTTCATG
Statistics
Matches: 123, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
166 39 0.32
167 2 0.02
168 36 0.29
169 21 0.17
171 3 0.02
172 22 0.18
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (169 bp):
TAAAATTTGTTAATGTTCTGCATAAAGAGGCAACTGCACTTGTTTTTATTGAGGAATTCTCAGCA
TGTGACAGATAACAAATCAATCATACAAATAACTTATCGTTAGTAATCAATTCTATAGTTGATTA
CAAGACACTTAACCAAAGGCAATATCACTGACTTTGTTT
Found at i:2940576 original size:69 final size:69
Alignment explanation
Indices: 2940465--2940737 Score: 537
Period size: 69 Copynumber: 4.0 Consensus size: 69
2940455 CAAGACTCTA
*
2940465 TCAGCCCTACCACCACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
1 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
2940530 CCTG
66 CCTG
2940534 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
1 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
2940599 CCTG
66 CCTG
2940603 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
1 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
2940668 CCTG
66 CCTG
2940672 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
1 TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
2940737 C
66 C
2940738 TTGTTTTTCC
Statistics
Matches: 203, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 203 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (69 bp):
TCAGCCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
CCTG
Found at i:2949344 original size:37 final size:40
Alignment explanation
Indices: 2949303--2949380 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 40
2949293 TTTACAATTC
*
2949303 TTATACTTGTTAAT-AATTTTTAA-TTTTTAAAAAA-AAT
1 TTATAATTGTTAATGAATTTTTAATTTTTTAAAAAATAAT
* **
2949340 TTATAATTTTTTTTGAATTTTTAATTTTTTAAAAAATAAT
1 TTATAATTGTTAATGAATTTTTAATTTTTTAAAAAATAAT
2949380 T
1 T
2949381 CAATGTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 10 0.29
38 9 0.26
39 11 0.32
40 4 0.12
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (40 bp):
TTATAATTGTTAATGAATTTTTAATTTTTTAAAAAATAAT
Found at i:2950363 original size:186 final size:184
Alignment explanation
Indices: 2950047--2950398 Score: 641
Period size: 186 Copynumber: 1.9 Consensus size: 184
2950037 ATATATGTGT
*
2950047 GCGCGCCATATAATATTTATTGTATTAATTTTGGTGAATCGATTAATTAATTACTTTTGAACTGA
1 GCGCGCCATATAATATTTATTGTATTAATTTCGGTGAATCGATTAATTAATTACTTTTGAACTGA
* *
2950112 ATTAATTGATAATTAAATTTTTAATTGATCTCGATTGAATTAATTTTAATGACCGATCGATTTAC
66 ATTAATTGATAATTAAATTTTTAATTGATCTCGATTGAATTAATTTCAATGACCGATCAATTTAC
2950177 TAAATTAATTTGATTTTAACCACACATAATATATATATATGTGTGTGTGTGAGCGC
131 TAAATTAATTTGATTTTAACCACACATAA-AT-TATATATGTGTGTGTGTGAGCGC
*
2950233 GCGCGCCATATAATATTTATTGTATTAATTTCGGTGAATTGATTAATTAATTACTTTTGAACTGA
1 GCGCGCCATATAATATTTATTGTATTAATTTCGGTGAATCGATTAATTAATTACTTTTGAACTGA
*
2950298 ATTAATTGATAATTAAATTTTTAATTGATCTTGATTGAATTAATTTCAATGACCGATCAATTTAC
66 ATTAATTGATAATTAAATTTTTAATTGATCTCGATTGAATTAATTTCAATGACCGATCAATTTAC
2950363 TAAATTAATTTGATTTTAACCACACATAAATTATAT
131 TAAATTAATTTGATTTTAACCACACATAAATTATAT
2950399 TTTAGTGTTT
Statistics
Matches: 161, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
184 5 0.03
185 2 0.01
186 154 0.96
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (184 bp):
GCGCGCCATATAATATTTATTGTATTAATTTCGGTGAATCGATTAATTAATTACTTTTGAACTGA
ATTAATTGATAATTAAATTTTTAATTGATCTCGATTGAATTAATTTCAATGACCGATCAATTTAC
TAAATTAATTTGATTTTAACCACACATAAATTATATATGTGTGTGTGTGAGCGC
Found at i:2952218 original size:33 final size:33
Alignment explanation
Indices: 2952157--2952224 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
2952147 AATAAAATTT
2952157 AAATATTTTAAATTACATTAATAATAAATAATA
1 AAATATTTTAAATTACATTAATAATAAATAATA
* * *
2952190 AAATATATTTAAATTA-TTTTATATTAAATAATA
1 AAATAT-TTTAAATTACATTAATAATAAATAATA
2952223 AA
1 AA
2952225 TAAAATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 22 0.71
34 9 0.29
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
AAATATTTTAAATTACATTAATAATAAATAATA
Found at i:2952751 original size:10 final size:10
Alignment explanation
Indices: 2952736--2952764 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2952726 TCTTTTGGCG
2952736 CTCCTTTCAT
1 CTCCTTTCAT
2952746 CTCCTTTCAT
1 CTCCTTTCAT
2952756 CTCCTTTCA
1 CTCCTTTCA
2952765 AAATATTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.41, G:0.00, T:0.48
Consensus pattern (10 bp):
CTCCTTTCAT
Found at i:2975555 original size:22 final size:23
Alignment explanation
Indices: 2975456--2975605 Score: 101
Period size: 24 Copynumber: 6.3 Consensus size: 23
2975446 GGACTCACCA
*
2975456 CAGCTCGTATGAGCTTACCGATATTT
1 CAGCTCGTATGAGCTTA-C--TGTTT
* * * *
2975482 TAGTTCGTAAGAGCTTACTATTTT
1 CAGCTCGTATGAGCTTACT-GTTT
* * *
2975506 CAGTTCAT-TGGAGCTTAATGTTT
1 CAGCTCGTAT-GAGCTTACTGTTT
2975529 CAGCTCGTATGAGCTTACTG-TT
1 CAGCTCGTATGAGCTTACTGTTT
2975551 CAGCTCGGTA-GAGCTTACTGTTTT
1 CAGCTC-GTATGAGCTTACTG-TTT
*
2975575 CAGCTC-AATAGAGCTTACTGTTCAT
1 CAGCTCGTAT-GAGCTTACTGTT--T
2975600 CAGCTC
1 CAGCTC
2975606 AAGAGGAGCT
Statistics
Matches: 101, Mismatches: 13, Indels: 21
0.75 0.10 0.16
Matches are distributed among these distances:
22 19 0.19
23 24 0.24
24 36 0.36
25 8 0.08
26 14 0.14
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (23 bp):
CAGCTCGTATGAGCTTACTGTTT
Found at i:2975586 original size:24 final size:24
Alignment explanation
Indices: 2975491--2975618 Score: 111
Period size: 24 Copynumber: 5.4 Consensus size: 24
2975481 TTAGTTCGTA
* * *
2975491 AGAGCTTACTATTTTCAGTTCATT
1 AGAGCTTACTGTTTTCAGCTCAAT
* * *
2975515 GGAGCTTAATG-TTTCAGCTC-GT
1 AGAGCTTACTGTTTTCAGCTCAAT
**
2975537 ATGAGCTTACTG--TTCAGCTCGGT
1 A-GAGCTTACTGTTTTCAGCTCAAT
2975560 AGAGCTTACTGTTTTCAGCTCAAT
1 AGAGCTTACTGTTTTCAGCTCAAT
* *
2975584 AGAGCTTACTGTTCATCAGCTCAAG
1 AGAGCTTACTGTT-TTCAGCTCAAT
2975609 AGGAGCTTAC
1 A-GAGCTTAC
2975619 CGATCATGGC
Statistics
Matches: 87, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
22 19 0.22
23 20 0.23
24 30 0.34
25 10 0.11
26 8 0.09
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (24 bp):
AGAGCTTACTGTTTTCAGCTCAAT
Found at i:2975625 original size:26 final size:25
Alignment explanation
Indices: 2975574--2975625 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
2975564 CTTACTGTTT
* * *
2975574 TCAGCTCAATAGAGCTTACTGTTCA
1 TCAGCTCAAGAGAGCTTACCGATCA
2975599 TCAGCTCAAGAGGAGCTTACCGATCA
1 TCAGCTCAAGA-GAGCTTACCGATCA
2975625 T
1 T
2975626 GGCTCGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (25 bp):
TCAGCTCAAGAGAGCTTACCGATCA
Found at i:2975743 original size:20 final size:20
Alignment explanation
Indices: 2975718--2975769 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
2975708 CAGCGGGTAC
*
2975718 AATTACTGTTTATACAGATG
1 AATTACTGTTTATACAAATG
*
2975738 AATTACAG-TT-TACAAATG
1 AATTACTGTTTATACAAATG
*
2975756 AATTATTGTTTATA
1 AATTACTGTTTATA
2975770 TGATATATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 13 0.50
19 4 0.15
20 9 0.35
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (20 bp):
AATTACTGTTTATACAAATG
Found at i:2982584 original size:55 final size:54
Alignment explanation
Indices: 2982476--2982622 Score: 163
Period size: 55 Copynumber: 2.7 Consensus size: 54
2982466 ATTAGGGTTT
* * *
2982476 AAGGATACGATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC-
1 AAGGA-ACCATGTAAGACCATGCCAAGGCATGGC-ATTGATAAGGTTTATAAGGCA
* * *
2982531 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAA-GTTACTATAAGGCA
1 AAGG-AACCATGTAAGACCATGCCAAGGCATGGCATTGATAAGGTT--TATAAGGCA
**
2982587 AAGGTCCCATGTAAGACCATGCCAAGGCATGGCATT
1 AAGGAACCATGTAAGACCATGCCAAGGCATGGCATT
2982623 AAGACCATGC
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
53 3 0.04
54 7 0.09
55 62 0.81
56 5 0.06
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (54 bp):
AAGGAACCATGTAAGACCATGCCAAGGCATGGCATTGATAAGGTTTATAAGGCA
Found at i:2982625 original size:24 final size:24
Alignment explanation
Indices: 2982598--2982646 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2982588 AGGTCCCATG
2982598 TAAGACCATGCCAAGGCATGGCAT
1 TAAGACCATGCCAAGGCATGGCAT
2982622 TAAGACCATGCCAAGGCATGGCAT
1 TAAGACCATGCCAAGGCATGGCAT
2982646 T
1 T
2982647 GGTGAGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (24 bp):
TAAGACCATGCCAAGGCATGGCAT
Found at i:2982953 original size:16 final size:16
Alignment explanation
Indices: 2982932--2982962 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2982922 ATAAATTTGA
2982932 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
2982948 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
2982963 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:2986477 original size:38 final size:38
Alignment explanation
Indices: 2986434--2986521 Score: 149
Period size: 38 Copynumber: 2.3 Consensus size: 38
2986424 CAAGGCCTGA
* * *
2986434 ATATAATACCAGTACTAGGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGGACGAAGCCTGCGGGATTTAACCCGG
2986472 ATATAATACCAGGACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGGACGAAGCCTGCGGGATTTAACCCGG
2986510 ATATAATACCAG
1 ATATAATACCAG
2986522 CATGAAGCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.22
Consensus pattern (38 bp):
ATATAATACCAGGACGAAGCCTGCGGGATTTAACCCGG
Found at i:2986529 original size:38 final size:38
Alignment explanation
Indices: 2986434--2986552 Score: 141
Period size: 38 Copynumber: 3.1 Consensus size: 38
2986424 CAAGGCCTGA
* *
2986434 ATATAATACCAGTACT-AGGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCA-TGAAGCCTGCGGGATTTAACCCGG
* *
2986472 ATATAATACCAGGACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCATGAAGCCTGCGGGATTTAACCCGG
* * *
2986510 ATATAATACCAGCATGAAGCTTGTGGGTCTTTAAGCCCGG
1 ATATAATACCAGCATGAAGCCTGCGGG-ATTTAA-CCCGG
2986550 ATA
1 ATA
2986553 CACATCAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
38 57 0.81
39 5 0.07
40 8 0.11
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (38 bp):
ATATAATACCAGCATGAAGCCTGCGGGATTTAACCCGG
Found at i:2986677 original size:38 final size:38
Alignment explanation
Indices: 2986626--2986720 Score: 127
Period size: 38 Copynumber: 2.4 Consensus size: 38
2986616 CATTTTCACT
*
2986626 GGGATTTAACCCGGATATATTACCAGCACGAAGCCTGC
1 GGGATTTAACCCGGATATAATACCAGCACGAAGCCTGC
* * *
2986664 GGGATTTAACCCGGATATAATACCAGCATGAAGCTTGT
1 GGGATTTAACCCGGATATAATACCAGCACGAAGCCTGC
*
2986702 GGGTCTTTAAGCCCGGATA
1 GGG-ATTTAA-CCCGGATA
2986721 CACATCAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
38 37 0.74
39 5 0.10
40 8 0.16
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.24
Consensus pattern (38 bp):
GGGATTTAACCCGGATATAATACCAGCACGAAGCCTGC
Found at i:2986736 original size:168 final size:168
Alignment explanation
Indices: 2986458--2986792 Score: 652
Period size: 168 Copynumber: 2.0 Consensus size: 168
2986448 CTAGGCCTGC
*
2986458 GGGATTTAACCCGGATATAATACCAGGACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGC
1 GGGATTTAACCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGC
2986523 ATGAAGCTTGTGGGTCTTTAAGCCCGGATACACATCAAATATCATGCATATTTAATCATATATTA
66 ATGAAGCTTGTGGGTCTTTAAGCCCGGATACACATCAAATATCATGCATATTTAATCATATATTA
2986588 ACACATCTCAAACACTTTTATTTCATCTCATTTTCACT
131 ACACATCTCAAACACTTTTATTTCATCTCATTTTCACT
*
2986626 GGGATTTAACCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGC
1 GGGATTTAACCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGC
2986691 ATGAAGCTTGTGGGTCTTTAAGCCCGGATACACATCAAATATCATGCATATTTAATCATATATTA
66 ATGAAGCTTGTGGGTCTTTAAGCCCGGATACACATCAAATATCATGCATATTTAATCATATATTA
2986756 ACACATCTCAAACACTTTTATTTCATCTCATTTTCAC
131 ACACATCTCAAACACTTTTATTTCATCTCATTTTCAC
2986793 ACTTAGCATT
Statistics
Matches: 165, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 165 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (168 bp):
GGGATTTAACCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGC
ATGAAGCTTGTGGGTCTTTAAGCCCGGATACACATCAAATATCATGCATATTTAATCATATATTA
ACACATCTCAAACACTTTTATTTCATCTCATTTTCACT
Found at i:2987060 original size:43 final size:44
Alignment explanation
Indices: 2986999--2987084 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 44
2986989 TAACATTTCA
*
2986999 TTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCG-ATATCG
1 TTTCACCGGCATTATAGCCTGCTAGGCCCAAAGCCCGAATATCG
*
2987042 TTTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGAATATC
1 TTTCACCGGCATTATAGCCTGCTAGGCCCAAAGCCCGAATATC
2987085 ATATTTTGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 35 0.88
44 5 0.12
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.24
Consensus pattern (44 bp):
TTTCACCGGCATTATAGCCTGCTAGGCCCAAAGCCCGAATATCG
Found at i:2991120 original size:27 final size:28
Alignment explanation
Indices: 2991036--2991133 Score: 119
Period size: 27 Copynumber: 3.5 Consensus size: 28
2991026 CATGAGATTG
* * *
2991036 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
2991065 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
2991093 GCACTAAGTGTGCGAG-TTGATTTTATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
2991120 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
2991134 GACTTAATAT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
27 23 0.37
28 21 0.33
29 19 0.30
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:2991146 original size:27 final size:27
Alignment explanation
Indices: 2991064--2991146 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
2991054 TAAATTGTTC
* *
2991064 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* * *
2991092 AGCACTAAGTGTGCGAGTTGATTTTAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
2991119 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
2991146 A
1 A
2991147 TATTTTTGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 28 0.58
28 20 0.42
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:2991453 original size:90 final size:90
Alignment explanation
Indices: 2991295--2991473 Score: 331
Period size: 90 Copynumber: 2.0 Consensus size: 90
2991285 ATGTGACAAT
*
2991295 TATAATTGAAGTCACGTACATAAGATTTATCGTGGAATAGGTGAAAGGTCGTTTAGTTGTATGAT
1 TATAATTGAAGTCACGTACATAAGATTTATCGTGGAATAGGTGAAAGGCCGTTTAGTTGTATGAT
2991360 TGTAACGAAAATAAAATGATGTATA
66 TGTAACGAAAATAAAATGATGTATA
*
2991385 TATACTTGAAGTCACGTACATAAGATTTATCGTGGAATAGGTGAAAGGCCGTTTAGTTGTATGAT
1 TATAATTGAAGTCACGTACATAAGATTTATCGTGGAATAGGTGAAAGGCCGTTTAGTTGTATGAT
*
2991450 TGTAACGAAATTAAAATGATGTAT
66 TGTAACGAAAATAAAATGATGTAT
2991474 GAAAATGCCT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (90 bp):
TATAATTGAAGTCACGTACATAAGATTTATCGTGGAATAGGTGAAAGGCCGTTTAGTTGTATGAT
TGTAACGAAAATAAAATGATGTATA
Found at i:2994455 original size:23 final size:23
Alignment explanation
Indices: 2994429--2994491 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
2994419 CGCTCTAATG
2994429 AGCTGAAACGGTAAGCTC-TATCA
1 AGCTGAAACGGTAAGCTCATA-CA
* *
2994452 AGCTG-AACAGTAAGCTCATACG
1 AGCTGAAACGGTAAGCTCATACA
* *
2994474 AGTTGAAATGGTAAGCTC
1 AGCTGAAACGGTAAGCTC
2994492 CAATGAGCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (23 bp):
AGCTGAAACGGTAAGCTCATACA
Found at i:2994481 original size:45 final size:46
Alignment explanation
Indices: 2994432--2994526 Score: 113
Period size: 47 Copynumber: 2.1 Consensus size: 46
2994422 TCTAATGAGC
* *
2994432 TGAAACGGTAAGCT-CTATCAAGCTG-AACAGTAAGCTCATACGAGT
1 TGAAACGGTAAGCTCCAAT-AAGCTGAAACAGAAAGCTCATACGAGT
* * *
2994477 TGAAATGGTAAGCTCCAATGAGCTGAAAACAGAAAGCTCTTACGAGT
1 TGAAACGGTAAGCTCCAATAAGCTG-AAACAGAAAGCTCATACGAGT
2994524 TGA
1 TGA
2994527 TATATCGATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 18 0.43
46 3 0.07
47 21 0.50
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (46 bp):
TGAAACGGTAAGCTCCAATAAGCTGAAACAGAAAGCTCATACGAGT
Found at i:2994503 original size:23 final size:21
Alignment explanation
Indices: 2994420--2994504 Score: 64
Period size: 23 Copynumber: 3.8 Consensus size: 21
2994410 CGAACAATAC
2994420 GCTCTAATGAGCTGAAACGGTAA
1 GCTC-AATGAGCTGAAA-GGTAA
* *
2994443 GCTCTATCAAGCTGAACA-GTAA
1 GCTCAAT-GAGCTGAA-AGGTAA
* *
2994465 GCTCATACGAGTTGAAATGGTAA
1 GCTCA-ATGAGCTGAAA-GGTAA
2994488 GCTCCAATGAGCTGAAA
1 GCT-CAATGAGCTGAAA
2994505 ACAGAAAGCT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
21 1 0.02
22 16 0.33
23 28 0.58
24 3 0.06
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (21 bp):
GCTCAATGAGCTGAAAGGTAA
Found at i:2997161 original size:22 final size:22
Alignment explanation
Indices: 2997143--2997195 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
2997133 CAGCTCGTAT
2997143 GAGCTTACTATTCAACTCGATA
1 GAGCTTACTATTCAACTCGATA
* * *
2997165 GAGTTTACTATTTTCAGCTCAATA
1 GAGCTTACTA--TTCAACTCGATA
2997189 GAGCTTA
1 GAGCTTA
2997196 TTGTTCATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 9 0.36
24 16 0.64
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (22 bp):
GAGCTTACTATTCAACTCGATA
Found at i:3002779 original size:29 final size:29
Alignment explanation
Indices: 3002746--3002801 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
3002736 GGACATAGTT
3002746 TTTGAATCTGTAGGATGTCAAATATGAAG
1 TTTGAATCTGTAGGATGTCAAATATGAAG
3002775 TTTGAATCTGTAGGATGTCAAATATGA
1 TTTGAATCTGTAGGATGTCAAATATGA
3002802 GTTGTTCTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (29 bp):
TTTGAATCTGTAGGATGTCAAATATGAAG
Found at i:3008366 original size:14 final size:14
Alignment explanation
Indices: 3008347--3008386 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3008337 TTGTTTGGCA
3008347 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
3008361 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
3008375 GGAAAATGTTTT
1 GTAAAATGTTTT
3008387 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:3008395 original size:20 final size:20
Alignment explanation
Indices: 3008370--3008407 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3008360 CGTAAAATGA
*
3008370 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
3008390 TTTCTGTAAAATGATTTA
1 TTTCTGGAAAATGATTTA
3008408 GTGGAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:3008399 original size:34 final size:35
Alignment explanation
Indices: 3008355--3008421 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
3008345 CAGTAAAATG
*
3008355 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
* *
3008389 TTTTCTGTAAAATGATTTAGTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
3008422 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:3008486 original size:32 final size:32
Alignment explanation
Indices: 3008411--3008487 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
3008401 TGATTTAGTG
* *
3008411 GAAAATATTTTCTGGTGTTTGGATGAATCTGT
1 GAAAATATTTTCTGCTGTTTGGATGAATCTCT
*
3008443 GTAAAATATTTTCTGCTGTTTGGCA-G-ATTTCCT
1 G-AAAATATTTTCTGCTGTTTGG-ATGAATCT-CT
3008476 GAAAATATTTTC
1 GAAAATATTTTC
3008488 CAAAAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
32 15 0.38
33 23 0.59
34 1 0.03
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.44
Consensus pattern (32 bp):
GAAAATATTTTCTGCTGTTTGGATGAATCTCT
Found at i:3010878 original size:22 final size:23
Alignment explanation
Indices: 3010852--3010895 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3010842 GCATATACTC
*
3010852 CAAACAAAAAGAGTAA-AAAAAT
1 CAAACAAAAAGAGAAATAAAAAT
*
3010874 CAAACAAATAGAGAAATAAAAA
1 CAAACAAAAAGAGAAATAAAAA
3010896 AGAAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.73, C:0.09, G:0.09, T:0.09
Consensus pattern (23 bp):
CAAACAAAAAGAGAAATAAAAAT
Found at i:3013647 original size:33 final size:33
Alignment explanation
Indices: 3013610--3013675 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
3013600 TATTTATGCG
*
3013610 TTAAATTGAAAATGATTTTTA-TATAGGGGGAGC
1 TTAAATTGAAAATGACTTTTATTA-AGGGGGAGC
3013643 TTAAATTGAAAATGACTTTTATTAAGGGGGAGC
1 TTAAATTGAAAATGACTTTTATTAAGGGGGAGC
3013676 AACCTATTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (33 bp):
TTAAATTGAAAATGACTTTTATTAAGGGGGAGC
Found at i:3016455 original size:20 final size:20
Alignment explanation
Indices: 3016430--3016475 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3016420 ATCGATCCAA
*
3016430 TATCGACACT-TTTCTTAAGG
1 TATCGACA-TATTTCCTAAGG
*
3016450 TATCGATATATTTCCTAAGG
1 TATCGACATATTTCCTAAGG
3016470 TATCGA
1 TATCGA
3016476 TATTCATGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (20 bp):
TATCGACATATTTCCTAAGG
Found at i:3016476 original size:20 final size:20
Alignment explanation
Indices: 3016440--3016478 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3016430 TATCGACACT
*
3016440 TTTCTTAAGGTATCGATATA
1 TTTCCTAAGGTATCGATATA
3016460 TTTCCTAAGGTATCGATAT
1 TTTCCTAAGGTATCGATAT
3016479 TCATGCTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
TTTCCTAAGGTATCGATATA
Found at i:3021873 original size:18 final size:20
Alignment explanation
Indices: 3021850--3021889 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
3021840 ACTTTATAAA
3021850 AATTTTT-AAAAAAATC-AT
1 AATTTTTGAAAAAAATCTAT
3021868 AATTTTTGAAAAAAATCTAT
1 AATTTTTGAAAAAAATCTAT
3021888 AA
1 AA
3021890 CATCAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 9 0.45
20 4 0.20
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (20 bp):
AATTTTTGAAAAAAATCTAT
Found at i:3022360 original size:8 final size:8
Alignment explanation
Indices: 3022349--3022376 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3022339 AAATTAAACC
3022349 AAAATTTT
1 AAAATTTT
3022357 AAAATTTT
1 AAAATTTT
3022365 AAAATTTT
1 AAAATTTT
3022373 AAAA
1 AAAA
3022377 ATATTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
AAAATTTT
Found at i:3023851 original size:12 final size:12
Alignment explanation
Indices: 3023834--3023860 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3023824 AAGTATTTTT
3023834 AAAAAGAAGAAG
1 AAAAAGAAGAAG
3023846 AAAAAGAAGAAG
1 AAAAAGAAGAAG
3023858 AAA
1 AAA
3023861 TTAAGGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:3027654 original size:19 final size:19
Alignment explanation
Indices: 3027615--3027654 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3027605 TTATAACTGC
*
3027615 TTGAAAATAAAAAATACAA
1 TTGAAAATAAAAAACACAA
3027634 TTGAAGAATAAAAAACA-AA
1 TTGAA-AATAAAAAACACAA
3027653 TT
1 TT
3027655 TTTAGGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (19 bp):
TTGAAAATAAAAAACACAA
Found at i:3029792 original size:17 final size:17
Alignment explanation
Indices: 3029770--3029805 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3029760 GATACAATAC
3029770 TTAAAATTATTAACAAA
1 TTAAAATTATTAACAAA
3029787 TTAAAATTATTAACAAA
1 TTAAAATTATTAACAAA
3029804 TT
1 TT
3029806 TTTACTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAATTATTAACAAA
Found at i:3032146 original size:20 final size:21
Alignment explanation
Indices: 3032099--3032146 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3032089 CACCCCAACA
*
3032099 AAATTTTTTATTTTGAAAAAT
1 AAATTTTTTATTTTCAAAAAT
*
3032120 AATATTTTTTA-TTTCAAAGAT
1 AA-ATTTTTTATTTTCAAAAAT
*
3032141 GAATTT
1 AAATTT
3032147 CTCATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 11 0.48
22 8 0.35
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (21 bp):
AAATTTTTTATTTTCAAAAAT
Found at i:3034531 original size:20 final size:20
Alignment explanation
Indices: 3034455--3034552 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
3034445 CAAAACATAC
* *
3034455 CAGAGAGCATCGAAATGCTAA
1 CAGAG-GCATCGAAGTGCAAA
* *
3034476 CAGAGGCATTGTAGTGCAAATA
1 CAGAGGCATCGAAGTGC-AA-A
* *
3034498 TAGAGGCATTGAAGTGCAAA
1 CAGAGGCATCGAAGTGCAAA
*
3034518 CAGGGGCATCGAAGTGCAAA
1 CAGAGGCATCGAAGTGCAAA
*
3034538 TAGAGGCATCGAAGT
1 CAGAGGCATCGAAGT
3034553 ATAATCCCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
20 40 0.62
21 8 0.12
22 16 0.25
ACGTcount: A:0.38, C:0.15, G:0.30, T:0.17
Consensus pattern (20 bp):
CAGAGGCATCGAAGTGCAAA
Found at i:3034534 original size:42 final size:40
Alignment explanation
Indices: 3034456--3034552 Score: 113
Period size: 42 Copynumber: 2.4 Consensus size: 40
3034446 AAAACATACC
* * * *
3034456 AGAGAGCATCGAAATGCTAACAGAGGCATTGTAGTGCAAATAT
1 AGAG-GCATCGAAGTGCAAACAGAGGCATCGAAGTGC-AA-AT
* *
3034499 AGAGGCATTGAAGTGCAAACAGGGGCATCGAAGTGCAAAT
1 AGAGGCATCGAAGTGCAAACAGAGGCATCGAAGTGCAAAT
3034539 AGAGGCATCGAAGT
1 AGAGGCATCGAAGT
3034553 ATAATCCCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
40 15 0.32
41 2 0.04
42 26 0.55
43 4 0.09
ACGTcount: A:0.38, C:0.14, G:0.30, T:0.18
Consensus pattern (40 bp):
AGAGGCATCGAAGTGCAAACAGAGGCATCGAAGTGCAAAT
Found at i:3047340 original size:62 final size:62
Alignment explanation
Indices: 3047243--3047366 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
3047233 AATGCATGAA
*
3047243 ATTTCTAAGTTACCCAAGCCTAGCCGAATATTTTTCTTGCCTATAGCAGCCAACATTTTCTT
1 ATTTCTAAGTTACCCAAGCCTAGCCAAATATTTTTCTTGCCTATAGCAGCCAACATTTTCTT
* * *
3047305 ATTTCTAAGTTACCCAAGCCTAGCTAAATATTTTTCTTGCCTATAGTAGCCCACATTTTCTT
1 ATTTCTAAGTTACCCAAGCCTAGCCAAATATTTTTCTTGCCTATAGCAGCCAACATTTTCTT
3047367 TCATTTCACA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.39
Consensus pattern (62 bp):
ATTTCTAAGTTACCCAAGCCTAGCCAAATATTTTTCTTGCCTATAGCAGCCAACATTTTCTT
Found at i:3055907 original size:20 final size:20
Alignment explanation
Indices: 3055869--3055907 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3055859 AATTGTCAAA
*
3055869 GCATACTGAAAATTTTGAAG
1 GCATACTGAAAATTATGAAG
3055889 GCATACT-AAAAGTTATGAA
1 GCATACTGAAAA-TTATGAA
3055908 ATATTACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (20 bp):
GCATACTGAAAATTATGAAG
Found at i:3059719 original size:40 final size:40
Alignment explanation
Indices: 3059664--3059749 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
3059654 TTTGAATAAG
* * *
3059664 AAACGCTGCCAAAGAACGAGCATTAGTGGCGCTTTTCGAA
1 AAACGCAGCCAAAGAACGAGCATTAGCGGCGCTTTTCAAA
* * *
3059704 AAACGCAGCTAAAGAACGAGCATTAGCGGTGCTTTTTAAA
1 AAACGCAGCCAAAGAACGAGCATTAGCGGCGCTTTTCAAA
3059744 AAACGC
1 AAACGC
3059750 CGCAAAACTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (40 bp):
AAACGCAGCCAAAGAACGAGCATTAGCGGCGCTTTTCAAA
Found at i:3060189 original size:76 final size:76
Alignment explanation
Indices: 3060055--3060239 Score: 253
Period size: 76 Copynumber: 2.4 Consensus size: 76
3060045 ATAAGTACAC
** * * *
3060055 CTTTAGCGGCGCTTTTTAAAAAACGCCACAAAAGAATTTTGCAAAACGCCGTCATTTTGTATTGA
1 CTTTAGCGGCGCTTTCCAAAAAACGCCACAAAAGAATTTTACAAAACGCCATCATTTTGTATTAA
3060120 GCTTTTAGTGG
66 GCTTTTAGTGG
* * **
3060131 CTTTAGAGGCGCTTTCCAAAAAACGCCGCAAAAGAATTTTACAAAACGCCATTGTTTTGTATTAA
1 CTTTAGCGGCGCTTTCCAAAAAACGCCACAAAAGAATTTTACAAAACGCCATCATTTTGTATTAA
3060196 GCTTTTAGTGG
66 GCTTTTAGTGG
*** *
3060207 CTTTAGCGGCGCTTTTTGAAAAATGCCACAAAA
1 CTTTAGCGGCGCTTTCCAAAAAACGCCACAAAA
3060240 AAATATTTCA
Statistics
Matches: 94, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 94 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (76 bp):
CTTTAGCGGCGCTTTCCAAAAAACGCCACAAAAGAATTTTACAAAACGCCATCATTTTGTATTAA
GCTTTTAGTGG
Found at i:3060556 original size:14 final size:14
Alignment explanation
Indices: 3060534--3060564 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3060524 TTAATTATCA
3060534 TTATAGTTTAGGGT
1 TTATAGTTTAGGGT
*
3060548 TTATGGTTTAGGGT
1 TTATAGTTTAGGGT
3060562 TTA
1 TTA
3060565 AAATATACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (14 bp):
TTATAGTTTAGGGT
Found at i:3064325 original size:7 final size:7
Alignment explanation
Indices: 3064313--3064385 Score: 56
Period size: 7 Copynumber: 10.0 Consensus size: 7
3064303 AATCTTCAAA
3064313 AAAATTT
1 AAAATTT
3064320 AAAATTT
1 AAAATTT
*
3064327 AAAAATTA
1 -AAAATTT
*
3064335 AAAATTA
1 AAAATTT
3064342 AAAATTT
1 AAAATTT
**
3064349 AAAAATAA
1 -AAAATTT
*
3064357 AAAACTTA
1 AAAA-TTT
3064365 AAAATTT
1 AAAATTT
*
3064372 AATATTT
1 AAAATTT
*
3064379 AATATTT
1 AAAATTT
3064386 TAATCCATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
7 39 0.70
8 17 0.30
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (7 bp):
AAAATTT
Found at i:3064331 original size:8 final size:8
Alignment explanation
Indices: 3064286--3064373 Score: 85
Period size: 7 Copynumber: 10.9 Consensus size: 8
3064276 TTTATATGAT
3064286 AATTTAAA
1 AATTTAAA
3064294 AATTATAAA
1 AATT-TAAA
3064303 AATCTTCAAAAA
1 AAT-TT---AAA
3064315 AATTT-AA
1 AATTTAAA
3064322 AATTTAAA
1 AATTTAAA
3064330 AA-TTAAA
1 AATTTAAA
3064337 AA-TTAAA
1 AATTTAAA
3064344 AATTTAAA
1 AATTTAAA
*
3064352 AA-TAAAA
1 AATTTAAA
*
3064359 AACTTAAA
1 AATTTAAA
3064367 AATTTAA
1 AATTTAA
3064374 TATTTAATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
7 27 0.39
8 25 0.36
9 8 0.12
10 1 0.01
11 2 0.03
12 6 0.09
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (8 bp):
AATTTAAA
Found at i:3064332 original size:15 final size:15
Alignment explanation
Indices: 3064312--3064380 Score: 86
Period size: 15 Copynumber: 4.7 Consensus size: 15
3064302 AAATCTTCAA
*
3064312 AAAAATTTAAAATTT
1 AAAAATTTAAAAATT
3064327 AAAAA-TTAAAAATT
1 AAAAATTTAAAAATT
*
3064341 AAAAATTTAAAAATA
1 AAAAATTTAAAAATT
*
3064356 AAAAACTTAAAAATT
1 AAAAATTTAAAAATT
* *
3064371 TAATATTTAA
1 AAAAATTTAA
3064381 TATTTTAATC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
14 13 0.28
15 33 0.72
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAATTTAAAAATT
Found at i:3069801 original size:20 final size:20
Alignment explanation
Indices: 3069761--3069802 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3069751 TGCATGAATA
**
3069761 TTTTGTGGTGTGAATGGTGG
1 TTTTGTGGTGTGAATACTGG
*
3069781 TTTTGTGGTGTGATTACTGG
1 TTTTGTGGTGTGAATACTGG
3069801 TT
1 TT
3069803 AGTAAAGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.02, G:0.38, T:0.50
Consensus pattern (20 bp):
TTTTGTGGTGTGAATACTGG
Found at i:3069924 original size:21 final size:21
Alignment explanation
Indices: 3069900--3069940 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3069890 TATTAAAGTT
3069900 AGGTTTGCAAACACTTGGGCC
1 AGGTTTGCAAACACTTGGGCC
* *
3069921 AGGTTTGCTAACTCTTGGGC
1 AGGTTTGCAAACACTTGGGC
3069941 TTGAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (21 bp):
AGGTTTGCAAACACTTGGGCC
Found at i:3075110 original size:37 final size:37
Alignment explanation
Indices: 3075060--3075139 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
3075050 CTTATTACGA
* *
3075060 AGTCTTACCCGGACATAA-TCTCCACACGAAGTTATCG
1 AGTCTTACCCGGACAAAATTC-CCACACGAAGTCATCG
*
3075097 AGTCTTACCCGGACAAAATTCCCACACGCAGTCATCG
1 AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
*
3075134 GGTCTT
1 AGTCTT
3075140 TAGAGCCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCGGACAAAATTCCCACACGAAGTCATCG
Found at i:3075329 original size:47 final size:47
Alignment explanation
Indices: 3075270--3075601 Score: 479
Period size: 47 Copynumber: 7.1 Consensus size: 47
3075260 TATCACATTT
* * * *
3075270 ATACAC-T-TTCACATTCATCACATCGGCCATTAGGCCTTATCTCAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* * *
3075315 ATACACATGCTCACATTCATCACATTGGCCACTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
*
3075362 ATACACCTGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* * *
3075409 ATATACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCTCAT
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
** * *
3075456 ATATGCATGTTCACATTCATCACATTGGCCATTCGGCCCTATTCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTA-TCACAC
3075504 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* *
3075551 ATATACATGTTCACTTTCATCACATTGGCCATTCGGCCCTATTCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTA-TCACAC
3075599 ATA
1 ATA
3075602 TACACTTTCA
Statistics
Matches: 259, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
45 6 0.02
46 1 0.00
47 202 0.78
48 50 0.19
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (47 bp):
ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
Found at i:3075559 original size:142 final size:141
Alignment explanation
Indices: 3075258--3075597 Score: 531
Period size: 142 Copynumber: 2.4 Consensus size: 141
3075248 CCCTTCGGGA
** * * *
3075258 CTTATCACATTTATACACT-TTCACATTCATCACATCGGCCATTAGGCCTTATCTCACATACACA
1 CTTATCACACATATACA-TGTTCACTTTCATCACATTGGCCATTCGGCCTTATCTCACATACACA
* *
3075322 TGCTCACATTCATCACATTGGCCACTCGGCCTTATCACACATACACCTGTTCACTTTCATCACAT
65 TGCTCACATTCATCACATTGGCCACTCGGCCCTATCACACATACACATGTTCACTTTCATCACAT
3075387 TGGCCATTCGGC
130 TGGCCATTCGGC
* **
3075399 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCTCATATATGCAT
1 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCTCACATACACAT
* *
3075464 GTTCACATTCATCACATTGGCCATTCGGCCCTATTCACACATACACATGTTCACTTTCATCACAT
66 GCTCACATTCATCACATTGGCCACTCGGCCCTA-TCACACATACACATGTTCACTTTCATCACAT
3075529 TGGCCATTCGGC
130 TGGCCATTCGGC
*
3075541 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGCCCTAT-TCACA
1 CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCTCACA
3075598 CATATACACT
Statistics
Matches: 183, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
140 1 0.01
141 89 0.49
142 93 0.51
ACGTcount: A:0.25, C:0.32, G:0.10, T:0.33
Consensus pattern (141 bp):
CTTATCACACATATACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCTCACATACACAT
GCTCACATTCATCACATTGGCCACTCGGCCCTATCACACATACACATGTTCACTTTCATCACATT
GGCCATTCGGC
Found at i:3079350 original size:27 final size:27
Alignment explanation
Indices: 3079311--3079495 Score: 228
Period size: 27 Copynumber: 6.9 Consensus size: 27
3079301 TTATCTAAGC
3079311 TAATA-CCCTGTAGGGTAAAATGACCG
1 TAATACCCCTGTAGGGTAAAATGACCG
3079337 TAATACCCCTGTAGGGTAAAATGACCG
1 TAATACCCCTGTAGGGTAAAATGACCG
* *
3079364 TAATACCCCTATAGGGTAAAATGACTG
1 TAATACCCCTGTAGGGTAAAATGACCG
* * *
3079391 TAATAACCCTGTAGGGTAAAATGATCA
1 TAATACCCCTGTAGGGTAAAATGACCG
*
3079418 TAATACCCCTGTAGGGTAAAATGACTG
1 TAATACCCCTGTAGGGTAAAATGACCG
* * * * * *
3079445 TAATGCCACTGTCGGGTAAAGTGGCTG
1 TAATACCCCTGTAGGGTAAAATGACCG
* * *
3079472 TGATACCCCTGTATGGAAAAATGA
1 TAATACCCCTGTAGGGTAAAATGA
3079496 TGAGTAGCCC
Statistics
Matches: 134, Mismatches: 24, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
26 5 0.04
27 129 0.96
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (27 bp):
TAATACCCCTGTAGGGTAAAATGACCG
Found at i:3079711 original size:27 final size:27
Alignment explanation
Indices: 3079647--3079720 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
3079637 GTACTGGTTC
3079647 ACTGTTACTGGTGGCTATGCCACAATT
1 ACTGTTACTGGTGGCTATGCCACAATT
* * *
3079674 ACTGATACTGGTGGCTTTGCCACATTT
1 ACTGTTACTGGTGGCTATGCCACAATT
* **
3079701 ACTGTTTCTGGCAGCTATGC
1 ACTGTTACTGGTGGCTATGC
3079721 TGCGTTATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (27 bp):
ACTGTTACTGGTGGCTATGCCACAATT
Found at i:3079885 original size:28 final size:29
Alignment explanation
Indices: 3079824--3079885 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
3079814 ATTACACTGT
* *
3079824 ACTGTTACTATATTGGGCTCAGGCCCACA
1 ACTGTTACTATATGGGGCTAAGGCCCACA
*
3079853 A-TGTTACTGTATGGGGCTAAGGCCCA-A
1 ACTGTTACTATATGGGGCTAAGGCCCACA
3079880 ACTGTT
1 ACTGTT
3079886 CTGATACTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 2 0.07
28 26 0.90
29 1 0.03
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (29 bp):
ACTGTTACTATATGGGGCTAAGGCCCACA
Found at i:3081810 original size:17 final size:18
Alignment explanation
Indices: 3081790--3081829 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3081780 GTTGAGAAAA
3081790 TAATTTAATTAAGT-AAT
1 TAATTTAATTAAGTAAAT
* *
3081807 TAATTTAGTTAATTAAAT
1 TAATTTAATTAAGTAAAT
3081825 TAATT
1 TAATT
3081830 AAATAAATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TAATTTAATTAAGTAAAT
Found at i:3081831 original size:13 final size:13
Alignment explanation
Indices: 3081790--3081837 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
3081780 GTTGAGAAAA
* *
3081790 TAATTTAATTAAG
1 TAATTAAATTAAT
* *
3081803 TAATTAATTTAGT
1 TAATTAAATTAAT
3081816 TAATTAAATTAAT
1 TAATTAAATTAAT
*
3081829 TAAATAAAT
1 TAATTAAAT
3081838 CGTATTTAAG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:3084610 original size:48 final size:47
Alignment explanation
Indices: 3084497--3084614 Score: 134
Period size: 46 Copynumber: 2.5 Consensus size: 47
3084487 TATGTGTGCC
* * *
3084497 AGTGTAAGACATGTCTGGGACATGCATTGGCCACATTATGAGAGCCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAAAGCCT
* *
3084544 A-TGTAAGACATGTTTGGGACATGCATCGGCCTCGAGATAT-ACAAG-CT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-ATATGA-AAGCCT
*
3084591 AGTGTAAGACTTGTCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
3084615 GCGTCAGCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
46 29 0.48
47 6 0.10
48 25 0.42
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAAAGCCT
Found at i:3084697 original size:49 final size:49
Alignment explanation
Indices: 3084634--3084758 Score: 135
Period size: 49 Copynumber: 2.6 Consensus size: 49
3084624 TGTTGTGTGT
*
3084634 CAGTGTAAGACCTGTCTGGGACATGGCATCAACACT-GATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCAAC-CTCGATAGATGAAAGC
* * * *** * **
3084683 CAGTGTAAGACCTGTTTGGGACACGACATTGGCCTCGATATATGAAATT
1 CAGTGTAAGACCTGTCTGGGACATGGCATCAACCTCGATAGATGAAAGC
*
3084732 CAGTGTAAGACCTATCTGGGACATGGC
1 CAGTGTAAGACCTGTCTGGGACATGGC
3084759 GTCGACATCT
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
48 2 0.03
49 59 0.97
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCAACCTCGATAGATGAAAGC
Found at i:3103606 original size:40 final size:40
Alignment explanation
Indices: 3103560--3103762 Score: 261
Period size: 40 Copynumber: 5.1 Consensus size: 40
3103550 ACTAAGATCT
* * *
3103560 GAAGGCATTTGTGCGAGTTG-CTATATCTGGGCTAAGTCCT
1 GAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTCCC
*
3103600 GAAGGCATTTATGCTAGTGACTATATCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
*
3103640 GAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
* *
3103680 GAAGGCATTTATGCTAGTGACAATATCCGGGCTAA-TACCC
1 GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGT-CCC
* * *
3103720 GAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCTC
1 GAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTCCC
3103759 GAAG
1 GAAG
3103763 ATACTTGGGT
Statistics
Matches: 146, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 15 0.10
40 129 0.88
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
GAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCC
Found at i:3103684 original size:80 final size:80
Alignment explanation
Indices: 3103560--3103762 Score: 295
Period size: 80 Copynumber: 2.5 Consensus size: 80
3103550 ACTAAGATCT
* * * *
3103560 GAAGGCATTTGTGCGAGTTGCTATATCTGGGCTAAGTCCTGAAGGCATTTATGCTAGTGACTATA
1 GAAGGCATTTGTGCGAGTCGCTATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACAATA
3103625 TCCGGGCTAAGT-CCC
66 TCCGGGCTAA-TACCC
*
3103640 GAAGGCATTTGTGCTAG-CGACTATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACAAT
1 GAAGGCATTTGTGCGAGTCG-CTATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACAAT
3103704 ATCCGGGCTAATACCC
65 ATCCGGGCTAATACCC
* * *
3103720 GAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATCTCGAAG
1 GAAGGCATTTGTGCGAGTCGCTATATCCGGGCTAAGTCCCGAAG
3103763 ATACTTGGGT
Statistics
Matches: 111, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
79 15 0.14
80 95 0.86
81 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.28
Consensus pattern (80 bp):
GAAGGCATTTGTGCGAGTCGCTATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACAATA
TCCGGGCTAATACCC
Found at i:3105649 original size:93 final size:93
Alignment explanation
Indices: 3105537--3105708 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
3105527 GCCCATAAGT
* * *
3105537 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
3105602 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
3105630 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
3105695 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
3105709 CAAATATCCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:3105704 original size:46 final size:46
Alignment explanation
Indices: 3105529--3105704 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
3105519 TGTAACCCGC
* * *
3105529 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
3105575 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
3105625 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
3105668 CCATAGGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
3105705 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 1 0.01
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:3108636 original size:35 final size:35
Alignment explanation
Indices: 3108590--3108661 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
3108580 CATATATATA
*
3108590 ATTATAATGCATATAATATAAATTGTAAATACCAT
1 ATTATAATGCATATAATATAAATTATAAATACCAT
*
3108625 ATTATAATGCATATAATCTAAATTATAAATACCAT
1 ATTATAATGCATATAATATAAATTATAAATACCAT
3108660 AT
1 AT
3108662 GAACTAACCT
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:0.10, G:0.04, T:0.38
Consensus pattern (35 bp):
ATTATAATGCATATAATATAAATTATAAATACCAT
Found at i:3110039 original size:59 final size:59
Alignment explanation
Indices: 3109947--3110060 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
3109937 CAGCCGGTAA
* * *
3109947 AGACCAGGACCTTTAGCGGTGCTTTTATAAAAAACGCCGCTAAATACTTGTACTTCTAG
1 AGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCTGTACTTCTAG
3110006 AGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCTGTACTT
1 AGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCTGTACTT
3110061 TAAGCGGCGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (59 bp):
AGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCTGTACTTCTAG
Found at i:3110067 original size:43 final size:42
Alignment explanation
Indices: 3110016--3110134 Score: 184
Period size: 43 Copynumber: 2.8 Consensus size: 42
3110006 AGACCAGGAC
*
3110016 CTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACCTGTA
1 CTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACATGTA
3110058 CTTTAAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACATGTA
1 CTTT-AGCGGCGCTTTTATAAAAAACGCCGCTAAAGACATGTA
* * *
3110101 CTTTTAGTGACGCTTTTTTAAAAAACGCCGCTAA
1 C-TTTAGCGGCGCTTTTATAAAAAACGCCGCTAA
3110135 TTTGCCCAGT
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
42 4 0.06
43 64 0.90
44 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTTATAAAAAACGCCGCTAAAGACATGTA
Found at i:3111042 original size:18 final size:18
Alignment explanation
Indices: 3111010--3111047 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3111000 TACAATATAG
3111010 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
3111029 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
3111046 TA
1 TA
3111048 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:3114016 original size:28 final size:28
Alignment explanation
Indices: 3113945--3114018 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 28
3113935 ATAATAAGCC
*
3113945 CGCACACTTAGTGCT-TAATAGTCGAACT
1 CGCACACTTAGTGCTAT-ATAGTCAAACT
3113973 CGCACACTTAGTGCTATAT-GATCAAACT
1 CGCACACTTAGTGCTATATAG-TCAAACT
3114001 CGCACACTTAGTGCTATA
1 CGCACACTTAGTGCTATA
3114019 CAATTTGAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
27 1 0.02
28 41 0.95
29 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAGTCAAACT
Found at i:3114037 original size:30 final size:28
Alignment explanation
Indices: 3113943--3114044 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 28
3113933 GTATAATAAG
*
3113943 CCCGCACACTTAGTGCT-TAATAGTCG-AA
1 CCCGCACACTTAGTGCTATAA-A-TTGAAA
* * *
3113971 CTCGCACACTTAGTGCTATATGA-TCAAA
1 CCCGCACACTTAGTGCTATA-AATTGAAA
*
3113999 CTCGCACACTTAGTGCTATACAATTTGAAA
1 CCCGCACACTTAGTGCTATA-AA-TTGAAA
3114029 CCCGCACACTTAGTGC
1 CCCGCACACTTAGTGC
3114045 CAATCTCATG
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
28 39 0.64
29 3 0.05
30 19 0.31
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (28 bp):
CCCGCACACTTAGTGCTATAAATTGAAA
Found at i:3120825 original size:28 final size:28
Alignment explanation
Indices: 3120778--3120859 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
3120768 ATGTCGTTGA
* * *
3120778 ATACTCAATGTCTTGCACACTAAGTGCC
1 ATACTCGATATCTCGCACACTAAGTGCC
*
3120806 ATACTCGATATCTCGTACACTAAGTGCC
1 ATACTCGATATCTCGCACACTAAGTGCC
3120834 ATACTCGATATCTCGCACACTAAGTG
1 ATACTCGATATCTCGCACACTAAGTG
3120860 TAATACATAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (28 bp):
ATACTCGATATCTCGCACACTAAGTGCC
Found at i:3120981 original size:40 final size:40
Alignment explanation
Indices: 3120846--3120990 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
3120836 ACTCGATATC
** * ** * * *
3120846 TCGCACACTAAGTGTAATACATAGCTAAAGCTATATCAAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCAATGTCGAA
* *
3120886 TCACACACTAAGTGCCATATATAGCCGAAGCTATGTCGAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCAATGTCGAA
*
3120926 TCGCACACTAAGTGCCATATATAGCCGAAGCAATGTCGAG
1 TCGCACACTAAGTGCCATATATAGCCGAAGCAATGTCGAA
*
3120966 TCGCACACTAAGTGCCACA-ATAGCC
1 TCGCACACTAAGTGCCATATATAGCC
3120991 AATTTGTCGT
Statistics
Matches: 93, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 6 0.06
40 87 0.94
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATATATAGCCGAAGCAATGTCGAA
Found at i:3129368 original size:30 final size:30
Alignment explanation
Indices: 3129334--3129393 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
3129324 ATTTAATACG
3129334 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
3129364 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
3129394 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:3139619 original size:37 final size:37
Alignment explanation
Indices: 3139560--3139668 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
3139550 AGCTCAGACG
* * *
3139560 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
3139597 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
3139634 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
3139669 ATATATTTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:3139941 original size:47 final size:47
Alignment explanation
Indices: 3139877--3141015 Score: 2035
Period size: 47 Copynumber: 24.1 Consensus size: 47
3139867 ACACGTTTCG
* * * * **
3139877 CATTAGCCATTCAGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * *
3139924 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3139971 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140018 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140065 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140112 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140159 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140206 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140253 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140300 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140347 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140394 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140441 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140488 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140535 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140582 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140629 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140676 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
***
3140723 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
*
3140774 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
3140821 CAGTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3140868 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
***
3140915 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
* *
3140966 CATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
3141013 CAT
1 CAT
3141016 AAAATCCTAA
Statistics
Matches: 1058, Mismatches: 26, Indels: 16
0.96 0.02 0.01
Matches are distributed among these distances:
47 971 0.92
51 87 0.08
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:3147040 original size:43 final size:44
Alignment explanation
Indices: 3146993--3147105 Score: 137
Period size: 42 Copynumber: 2.7 Consensus size: 44
3146983 CATCGACTTA
*
3146993 TGATTTACGTGTAAGACCATGTCTGGGACA-TCGACATTG-TATT
1 TGATTTACGTGTAAGACCATGTCTGGGACAGT-GACATCGATATT
* *
3147036 TGATTT-CGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATT
1 TGATTTACGTGTAAGACCATGTCTGGGACAGTGACATCGATATT
* *
3147079 TGA--TACATGTAAGACCATATCTGGGAC
1 TGATTTACGTGTAAGACCATGTCTGGGAC
3147106 GTTGGCATTG
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
41 1 0.02
42 46 0.75
43 14 0.23
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (44 bp):
TGATTTACGTGTAAGACCATGTCTGGGACAGTGACATCGATATT
Found at i:3147090 original size:42 final size:42
Alignment explanation
Indices: 3146959--3147113 Score: 124
Period size: 42 Copynumber: 3.7 Consensus size: 42
3146949 TGTGTTTTCG
* * *
3146959 TGTAAGACCACGTCT-GGA-TGTTGGCATCG-ACTTATGATTTACG
1 TGTAAGACCATGTCTGGGACAG-TGGCATCGTA-TT-TGA-TTACA
* * * *
3147002 TGTAAGACCATGTCTGGGACA-TCGACATTGTATTTGATTTCG
1 TGTAAGACCATGTCTGGGACAGT-GGCATCGTATTTGATTACA
*
3147044 TGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGA-TACA
1 TGTAAGACCATGTCTGGGACAGTGGCATCG-TATTTGATTACA
*
3147086 TGTAAGACCATATCTGGGAC-GTTGGCAT
1 TGTAAGACCATGTCTGGGACAG-TGGCAT
3147114 TGTACTAGTT
Statistics
Matches: 93, Mismatches: 12, Indels: 15
0.77 0.10 0.12
Matches are distributed among these distances:
41 1 0.01
42 55 0.59
43 26 0.28
44 10 0.11
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGTATTTGATTACA
Found at i:3154982 original size:17 final size:17
Alignment explanation
Indices: 3154962--3154996 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3154952 AAAGAAAAAG
*
3154962 AAAATAAAAAGCTTGCT
1 AAAAGAAAAAGCTTGCT
3154979 AAAAGAAAAAGCTTGCT
1 AAAAGAAAAAGCTTGCT
3154996 A
1 A
3154997 GGGTTTCGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.20
Consensus pattern (17 bp):
AAAAGAAAAAGCTTGCT
Found at i:3163507 original size:37 final size:37
Alignment explanation
Indices: 3163457--3163540 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 37
3163447 TACCTGTTTG
3163457 GGCTAAACCTTTAAAA-TGACATCAGGTTA-TCAGTCCA
1 GGCTAAACCTTTAAAACTG-CATCAGGTTACT-AGTCCA
*
3163494 GGCTAAACCTTTAAAACTGCATTAGGTTACTAGTCCA
1 GGCTAAACCTTTAAAACTGCATCAGGTTACTAGTCCA
3163531 GGCTAAACCT
1 GGCTAAACCT
3163541 AAGTCCCGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
37 41 0.93
38 3 0.07
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (37 bp):
GGCTAAACCTTTAAAACTGCATCAGGTTACTAGTCCA
Found at i:3166462 original size:19 final size:18
Alignment explanation
Indices: 3166432--3166473 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
3166422 AGAAGCAGCC
3166432 CACAATTTTCAT-TATTT
1 CACAATTTTCATCTATTT
3166449 CACACATTTATCATCTATTT
1 CACA-ATTT-TCATCTATTT
*
3166469 TACAA
1 CACAA
3166474 CTTATGCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.19
18 4 0.19
19 5 0.24
20 8 0.38
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.45
Consensus pattern (18 bp):
CACAATTTTCATCTATTT
Found at i:3171745 original size:79 final size:81
Alignment explanation
Indices: 3171628--3171812 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
3171618 GCTACTCGTT
* * *
3171628 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
3171692 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* * **
3171708 CAAATGCCTTCGGG-CTTAGCCTGGA-ATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
3171771 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
3171788 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
3171813 CATCATTCAA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 4 0.04
79 53 0.60
80 32 0.36
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:3171749 original size:39 final size:40
Alignment explanation
Indices: 3171628--3171812 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
3171618 GCTACTCGTT
*
3171628 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
3171668 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
3171708 CAAATGCCTTCGGG-CTTAGCCTGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
3171747 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
3171788 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
3171813 CATCATTCAA
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 76 0.62
41 13 0.11
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:3176638 original size:48 final size:46
Alignment explanation
Indices: 3176513--3176641 Score: 147
Period size: 46 Copynumber: 2.8 Consensus size: 46
3176503 CATGTAGCCA
*
3176513 ATGCAT-TCCCAGACATGTCTTACACTGGCT-TACATCTCGAGACCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCAAGACCG
* * * *
3176558 ATGTATGTCCCAGGCATTTCTTACACTAGCTCTCATCTCAATG-CCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAA-GACCG
*
3176604 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCAT
1 ATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT
3176642 AATGTGGTTG
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
45 5 0.07
46 34 0.49
47 13 0.19
48 17 0.25
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.29
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAAGACCG
Found at i:3185985 original size:41 final size:40
Alignment explanation
Indices: 3185858--3186002 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
3185848 CTCGCACAAG
* ** * * *
3185858 GCCTTCGGGTCTTAAACCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
3185898 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
3185938 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
3185979 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
3186003 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 58 0.64
41 27 0.30
42 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:3193942 original size:40 final size:40
Alignment explanation
Indices: 3193847--3194020 Score: 147
Period size: 40 Copynumber: 4.4 Consensus size: 40
3193837 AATCAAGCAT
** ** * *
3193847 CTTCGGGGTTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
3193885 CTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
3193925 CTTCGAGACTTAGCCCGGATATAGTCGCTAGCACAACTAC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
3193965 CTTC-GGATCTTAGTCCGGATGTAGTCACTTTGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCAC-TAGCACAAATGC
3194006 CTTCGGGACTTAGCC
1 CTTCGGGACTTAGCC
3194021 TAGATATCAT
Statistics
Matches: 105, Mismatches: 26, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
38 10 0.10
39 17 0.16
40 57 0.54
41 18 0.17
42 3 0.03
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:3202363 original size:43 final size:43
Alignment explanation
Indices: 3202302--3202393 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 43
3202292 CCATAGCTCA
*
3202302 TGTGAGCAACATTGTGTAGCTTAACATCCTGACCCACAACTCG
1 TGTGAGCAACATCGTGTAGCTTAACATCCTGACCCACAACTCG
* * **
3202345 TGTGAGCAATATCGTGTAGCTTAATATCCTGACTTACAACTCG
1 TGTGAGCAACATCGTGTAGCTTAACATCCTGACCCACAACTCG
3202388 TGTGAG
1 TGTGAG
3202394 AAAACTCATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (43 bp):
TGTGAGCAACATCGTGTAGCTTAACATCCTGACCCACAACTCG
Found at i:3204433 original size:21 final size:21
Alignment explanation
Indices: 3204409--3204450 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3204399 TATTTAGGTA
*
3204409 TGTTTT-AAGCTTATTTGAATG
1 TGTTTTGAAGC-TATGTGAATG
3204430 TGTTTTGAAGCTATGTGAATG
1 TGTTTTGAAGCTATGTGAATG
3204451 GTTGATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.48
Consensus pattern (21 bp):
TGTTTTGAAGCTATGTGAATG
Found at i:3207252 original size:15 final size:15
Alignment explanation
Indices: 3207232--3207273 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
3207222 TGATAACAAA
3207232 AATAATAATATAAAT
1 AATAATAATATAAAT
**
3207247 AATAATAGCATAAAT
1 AATAATAATATAAAT
*
3207262 GATAATAATATA
1 AATAATAATATA
3207274 TATGGTATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (15 bp):
AATAATAATATAAAT
Found at i:3207325 original size:15 final size:15
Alignment explanation
Indices: 3207305--3207334 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3207295 TGATAATAGA
*
3207305 AATAAAAGTATATAT
1 AATAAAAATATATAT
3207320 AATAAAAATATATAT
1 AATAAAAATATATAT
3207335 GTACGGGATA
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:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AATAAAAATATATAT
Found at i:3207460 original size:19 final size:20
Alignment explanation
Indices: 3207419--3207460 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3207409 AAATGATGTG
* *
3207419 CATGATATAATATTAATATA
1 CATGATATAATATTAAAAAA
*
3207439 CATGATATAGT-TTAAAAAA
1 CATGATATAATATTAAAAAA
3207458 CAT
1 CAT
3207461 AAACATAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (20 bp):
CATGATATAATATTAAAAAA
Found at i:3210474 original size:30 final size:30
Alignment explanation
Indices: 3210406--3210477 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
3210396 TTTAAATTAG
* **
3210406 AAATGAT-AAAATTGTATTTTAATTTTTTA
1 AAATGATAAAAATTGTAATTTAATCATTTA
3210435 AAATGATAAAAATT-TAATTTAATCATTTA
1 AAATGATAAAAATTGTAATTTAATCATTTA
*
3210464 AATATTATAAAAAT
1 AA-ATGATAAAAAT
3210478 ATAAACTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATGATAAAAATTGTAATTTAATCATTTA
Done.