Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 94 of 153
Found at i:29669176 original size:50 final size:50
Alignment explanation
Indices: 29669112--29669211 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
29669102 TTCGGTTGTT
29669112 CCGAAAGAGCGTGTCACTTGGGATTTCTTTCAGACAGAATTTCGCAAAAA
1 CCGAAAGAGCGTGTCACTTGGGATTTCTTTCAGACAGAATTTCGCAAAAA
* *
29669162 CCGAAAGAGGGTGTCACTTGGGATTTCTTTCAGACAGAGTTTCGCAAAAA
1 CCGAAAGAGCGTGTCACTTGGGATTTCTTTCAGACAGAATTTCGCAAAAA
29669212 GTATATCAGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (50 bp):
CCGAAAGAGCGTGTCACTTGGGATTTCTTTCAGACAGAATTTCGCAAAAA
Found at i:29682358 original size:51 final size:52
Alignment explanation
Indices: 29682282--29682436 Score: 208
Period size: 51 Copynumber: 3.0 Consensus size: 52
29682272 AAGATGGTTA
* *
29682282 TGGTCACATGTGTAGTACTAAGTGCAGGTTAATATGTGTACCGGATAGCT-T
1 TGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGCTAT
* * * *
29682333 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-GGTAT
1 TGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGCTAT
* * *
29682384 TGGTCACATGTGTGGTACTAAGTGTAGGCTACTATGTGTACCAGATAGC-AT
1 TGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGCTAT
29682435 TG
1 TG
29682437 ATCATAAGGG
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.02
51 86 0.97
52 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.32
Consensus pattern (52 bp):
TGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAGCTAT
Found at i:29687379 original size:21 final size:21
Alignment explanation
Indices: 29687355--29687398 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29687345 GAATCTTTAG
*
29687355 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
*
29687376 TATTTAATTATCCTTTCTATT
1 TATTTAATTATCATTTCTATT
29687397 TA
1 TA
29687399 ATTAGTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:29692636 original size:29 final size:30
Alignment explanation
Indices: 29692594--29692668 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
29692584 ACAAACGTAT
**
29692594 GAAAGATTAAAACCTTTTG-TTCAAAAAAA
1 GAAAGATTAAAACCTTTTGAAACAAAAAAA
*
29692623 GAAAGATTAAAACCTTTTGAAAGAAAAAAA
1 GAAAGATTAAAACCTTTTGAAACAAAAAAA
*
29692653 GAAAGATTGAAACCTT
1 GAAAGATTAAAACCTT
29692669 GAATTTATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 19 0.46
30 22 0.54
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.24
Consensus pattern (30 bp):
GAAAGATTAAAACCTTTTGAAACAAAAAAA
Found at i:29693606 original size:27 final size:25
Alignment explanation
Indices: 29693549--29693619 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
29693539 TAAAATTAAT
*
29693549 TTTTTAAAAATTT-AAAAATAAAAAC
1 TTTTT-AAAATTTAAAAAATAAAAAA
*
29693574 TCTTTAAAATTATAAAAAATAAAAAGA
1 TTTTTAAAATT-TAAAAAATAAAAA-A
*
29693601 TTTTTAAAATCTAAAAAAT
1 TTTTTAAAATTTAAAAAAT
29693620 TTCAAAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
24 6 0.15
25 5 0.13
26 19 0.49
27 9 0.23
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (25 bp):
TTTTTAAAATTTAAAAAATAAAAAA
Found at i:29693741 original size:19 final size:22
Alignment explanation
Indices: 29693717--29693761 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
29693707 ATTGACCCAC
*
29693717 GAACC-GG-TATAAAA-TGGTT
1 GAACCGGGCTATAAAACTAGTT
29693736 GAACCGGGCTATAAAACTAGTT
1 GAACCGGGCTATAAAACTAGTT
29693758 GAAC
1 GAAC
29693762 TAATTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 2 0.09
21 7 0.32
22 8 0.36
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (22 bp):
GAACCGGGCTATAAAACTAGTT
Found at i:29693786 original size:17 final size:16
Alignment explanation
Indices: 29693763--29693802 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
29693753 TAGTTGAACT
*
29693763 AATTTTTATATTTTTA
1 AATTTTTATAATTTTA
29693779 ATATTTTT-TAATTTTA
1 A-ATTTTTATAATTTTA
29693795 AATTTTTA
1 AATTTTTA
29693803 ATAACTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.29
16 9 0.43
17 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTTTATAATTTTA
Found at i:29697077 original size:18 final size:18
Alignment explanation
Indices: 29697045--29697096 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
29697035 TTAAAAAAAC
* *
29697045 TAGAATAATAGTACATAA
1 TAGAATAAAATTACATAA
29697063 TAGAATAAAATTACAT-A
1 TAGAATAAAATTACATAA
* *
29697080 TA-AAAAAAATTAGATAA
1 TAGAATAAAATTACATAA
29697097 ATTGCCATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 11 0.38
17 4 0.14
18 14 0.48
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.27
Consensus pattern (18 bp):
TAGAATAAAATTACATAA
Found at i:29697141 original size:9 final size:9
Alignment explanation
Indices: 29697123--29697154 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
29697113 TGCTAACGAT
29697123 AACAATAAC
1 AACAATAAC
*
29697132 AACAACAAC
1 AACAATAAC
29697141 AACAATAAC
1 AACAATAAC
29697150 AACAA
1 AACAA
29697155 ATAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.69, C:0.25, G:0.00, T:0.06
Consensus pattern (9 bp):
AACAATAAC
Found at i:29698162 original size:25 final size:25
Alignment explanation
Indices: 29698109--29698168 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
29698099 AAGAAAATCC
*
29698109 AAAAGAATGAAAGAATAATTACTCG
1 AAAAGAATGAAAGAATAATTACTCA
*
29698134 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
29698159 AAAA-AATGAA
1 AAAAGAATGAA
29698169 TGAGAAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 9 0.28
25 23 0.72
ACGTcount: A:0.58, C:0.07, G:0.17, T:0.18
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:29700458 original size:390 final size:390
Alignment explanation
Indices: 29699739--29700526 Score: 1459
Period size: 390 Copynumber: 2.0 Consensus size: 390
29699729 ATTCCAGGGA
*
29699739 ACCTTTTTGCTATCCTTATATGAGAAATTTGATGGTTTCTGAATTACGATCTTTGGTGTCACCTG
1 ACCTTTTTGCTATCATTATATGAGAAATTTGATGGTTTCTGAATTACGATCTTTGGTGTCACCTG
***
29699804 TGCCCCTACCTCGTTAATATTAGGGTGTGAGATGATAATCACAGGATGATTTACTTTCAGAATTC
66 TGCCCCTACCTCGTTAATATTAGGGCCCGAGATGATAATCACAGGATGATTTACTTTCAGAATTC
29699869 TCATCATTGACTCCGACGCGCATATGCTTCCTTTTTCCTCCGCTTCTTCATAAAACTCTATTTCT
131 TCATCATTGACTCCGACGCGCATATGCTTCCTTTTTCCTCCGCTTCTTCATAAAACTCTATTTCT
29699934 TTATTATCCATCATGCTCTGGACCAGAACTCTGAATTCTTCACATCTTTGGATTTCGTGCCCCAC
196 TTATTATCCATCATGCTCTGGACCAGAACTCTGAATTCTTCACATCTTTGGATTTCGTGCCCCAC
*
29699999 CTCATGATGGAACTCACAATAATTTTTGGTCTCACCACCTTCCTCTAAATCCAAAATGATTAACC
261 CTCATGATGGAACTCACAATAATTTTTGGTCCCACCACCTTCCTCTAAATCCAAAATGATTAACC
* *
29700064 CTCTTCTTGCCATCTCTTCCCAAACCCATTTCAAAGGGGTTTTCACTTTAGTAATATTTGCCTAG
326 CTCTTCTTGCCATCTCTTCCCAAACCCATTTCAAAGGGGTTTTCACTTCAGCAATATTTGCCTAG
*
29700129 ACCTTTTTGCTATCATTATATGAGAAATTTGCTGGTTTCTGAATTACGATCTTTGGTGTCACCTG
1 ACCTTTTTGCTATCATTATATGAGAAATTTGATGGTTTCTGAATTACGATCTTTGGTGTCACCTG
*
29700194 TGCCCCTACCTCGTTAATGTTAGGGCCCGAGATGATAATCACAGGATGATTTACTTTCAGAATTC
66 TGCCCCTACCTCGTTAATATTAGGGCCCGAGATGATAATCACAGGATGATTTACTTTCAGAATTC
29700259 TCATCATTGACTCCGACGCGCATATGCTTCCTTTTTCCTCCGCTTCTTCATAAAACTCTATTTCT
131 TCATCATTGACTCCGACGCGCATATGCTTCCTTTTTCCTCCGCTTCTTCATAAAACTCTATTTCT
29700324 TTATTATCCATCATGCTCTGGACCAGAACTCTGAATTCTTCACATCTTTGGATTTCGTGCCCCAC
196 TTATTATCCATCATGCTCTGGACCAGAACTCTGAATTCTTCACATCTTTGGATTTCGTGCCCCAC
29700389 CTCATGATGGAACTCACAATAATTTTTGGTCCCACCACCTTCCTCTAAATCCAAAATGATTAACC
261 CTCATGATGGAACTCACAATAATTTTTGGTCCCACCACCTTCCTCTAAATCCAAAATGATTAACC
* * *
29700454 CTCTTCTTGCCATCTCTTCCTAAACCCATTTCAAAGGGGTTTTCACTTCAGCAATATTTTCCTTG
326 CTCTTCTTGCCATCTCTTCCCAAACCCATTTCAAAGGGGTTTTCACTTCAGCAATATTTGCCTAG
29700519 ACTCTTTT
1 AC-CTTTT
29700527 CCCCATATTT
Statistics
Matches: 385, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
390 380 0.99
391 5 0.01
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (390 bp):
ACCTTTTTGCTATCATTATATGAGAAATTTGATGGTTTCTGAATTACGATCTTTGGTGTCACCTG
TGCCCCTACCTCGTTAATATTAGGGCCCGAGATGATAATCACAGGATGATTTACTTTCAGAATTC
TCATCATTGACTCCGACGCGCATATGCTTCCTTTTTCCTCCGCTTCTTCATAAAACTCTATTTCT
TTATTATCCATCATGCTCTGGACCAGAACTCTGAATTCTTCACATCTTTGGATTTCGTGCCCCAC
CTCATGATGGAACTCACAATAATTTTTGGTCCCACCACCTTCCTCTAAATCCAAAATGATTAACC
CTCTTCTTGCCATCTCTTCCCAAACCCATTTCAAAGGGGTTTTCACTTCAGCAATATTTGCCTAG
Found at i:29701785 original size:18 final size:18
Alignment explanation
Indices: 29701762--29701801 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29701752 ATAATATATG
29701762 ATAATAATAAAAAATAGA
1 ATAATAATAAAAAATAGA
* * *
29701780 ATAATAGTACATAATAGA
1 ATAATAATAAAAAATAGA
29701798 ATAA
1 ATAA
29701802 AATTACATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (18 bp):
ATAATAATAAAAAATAGA
Found at i:29701808 original size:18 final size:18
Alignment explanation
Indices: 29701774--29701826 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
29701764 AATAATAAAA
* *
29701774 AATAGAATAATAGTACAT
1 AATAGAATAAAATTACAT
29701792 AATAGAATAAAATTACAT
1 AATAGAATAAAATTACAT
*
29701810 -ATA-AA-AAAATTAGAT
1 AATAGAATAAAATTACAT
29701825 AA
1 AA
29701827 ATTGCCATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 9 0.29
16 3 0.10
17 3 0.10
18 16 0.52
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (18 bp):
AATAGAATAAAATTACAT
Found at i:29701867 original size:3 final size:3
Alignment explanation
Indices: 29701853--29701908 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
29701843 TGCTAACGAT
*
29701853 AAC AAT AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
29701901 AAC AAC AA
1 AAC AAC AA
29701909 ATAATAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.68, C:0.30, G:0.00, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:29707508 original size:18 final size:20
Alignment explanation
Indices: 29707471--29707515 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
29707461 TCTTTTCACG
29707471 TTCTTTTTCTTTGGGTTTTCC
1 TTCTTTTTCTTT-GGTTTTCC
*
29707492 TTCTTTTT-TTT-GTTTTCT
1 TTCTTTTTCTTTGGTTTTCC
29707510 TTCTTT
1 TTCTTT
29707516 GTTTACTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 12 0.52
20 3 0.13
21 8 0.35
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.76
Consensus pattern (20 bp):
TTCTTTTTCTTTGGTTTTCC
Found at i:29708363 original size:24 final size:24
Alignment explanation
Indices: 29708335--29708400 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
29708325 AAGCATGTAT
* *
29708335 TATATTTTTATATTTGTATATCTG
1 TATATCTTTATATTTGTATATCGG
** * *
29708359 TATATCTACACATCTGTATATCGG
1 TATATCTTTATATTTGTATATCGG
29708383 TATATCTTTAT-TTTGTAT
1 TATATCTTTATATTTGTAT
29708401 CTATATATGG
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
23 6 0.19
24 26 0.81
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.55
Consensus pattern (24 bp):
TATATCTTTATATTTGTATATCGG
Found at i:29709284 original size:12 final size:12
Alignment explanation
Indices: 29709267--29709293 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
29709257 CATACCAAAG
29709267 CATGAATTAGCA
1 CATGAATTAGCA
29709279 CATGAATTAGCA
1 CATGAATTAGCA
29709291 CAT
1 CAT
29709294 TATTAACTAA
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:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (12 bp):
CATGAATTAGCA
Found at i:29714098 original size:22 final size:22
Alignment explanation
Indices: 29714070--29714113 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
29714060 CCCACTACGA
* *
29714070 TTAACACTCCGCTCATTAGTGT
1 TTAACACTCCACTCATCAGTGT
29714092 TTAACACTCCACTCATCAGTGT
1 TTAACACTCCACTCATCAGTGT
29714114 CTCCCACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
TTAACACTCCACTCATCAGTGT
Found at i:29718718 original size:45 final size:45
Alignment explanation
Indices: 29718660--29718764 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
29718650 CACCAGTATA
**
29718660 CAGTAATCAGTAACAATAACAGTATTCAACACACAAAGTGCTGAAC
1 CAGTAA-CAGTAACAATAACAGTATTCAACACACAAAGTGCCAAAC
* ** *
29718706 CTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCAAAC
1 CAGTAACAGTAACAATAACAGTATTCAACACACAAAGTGCCAAAC
29718751 CAGTAACAGTAACA
1 CAGTAACAGTAACA
29718765 GTAGTCGGCA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 46 0.90
46 5 0.10
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (45 bp):
CAGTAACAGTAACAATAACAGTATTCAACACACAAAGTGCCAAAC
Found at i:29720165 original size:9 final size:9
Alignment explanation
Indices: 29720151--29720195 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
29720141 CATTTAAATA
29720151 AATAATTAT
1 AATAATTAT
29720160 AATAATTAT
1 AATAATTAT
29720169 AATAATTAT
1 AATAATTAT
29720178 -ATACA-TAT
1 AATA-ATTAT
*
29720186 AATATTTAT
1 AATAATTAT
29720195 A
1 A
29720196 TATATAACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
AATAATTAT
Found at i:29723266 original size:21 final size:21
Alignment explanation
Indices: 29723223--29723266 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29723213 GTTTAGTTAC
*
29723223 TTTTAATTAATCATAATTTAT
1 TTTTAATTAATCATAATTAAT
*
29723244 TTTTAATTAA-CATTTATTAAT
1 TTTTAATTAATCA-TAATTAAT
29723265 TT
1 TT
29723267 ATTTAATCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTAATTAATCATAATTAAT
Found at i:29726561 original size:19 final size:19
Alignment explanation
Indices: 29726537--29726575 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
29726527 AGGAATGAAA
29726537 GCAGTTGTGGTAGTTAGCT
1 GCAGTTGTGGTAGTTAGCT
29726556 GCAGTTGTGGTAGTTAGCT
1 GCAGTTGTGGTAGTTAGCT
29726575 G
1 G
29726576 GTATTCTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.36
Consensus pattern (19 bp):
GCAGTTGTGGTAGTTAGCT
Found at i:29733281 original size:18 final size:18
Alignment explanation
Indices: 29733260--29733298 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29733250 TTGCTTCAAC
* *
29733260 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
29733278 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
29733296 TTC
1 TTC
29733299 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:29743717 original size:21 final size:20
Alignment explanation
Indices: 29743674--29743716 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
29743664 TCACGTCAAT
29743674 AAATAATTTAAAAGTTATAA
1 AAATAATTTAAAAGTTATAA
29743694 AAATAAATTGTAAAA-TT-TAA
1 AAAT-AATT-TAAAAGTTATAA
29743714 AAA
1 AAA
29743717 AAAACATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 10 0.48
21 6 0.29
22 5 0.24
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AAATAATTTAAAAGTTATAA
Found at i:29746104 original size:24 final size:24
Alignment explanation
Indices: 29746031--29746106 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
29746021 AATCAAAGTC
** * *
29746031 AAATATATTATGTTAATAAATGCA
1 AAATATATTATACTCATAAATGCT
29746055 AAATATATTATACTCATAAATGCT
1 AAATATATTATACTCATAAATGCT
*
29746079 AAATATATTATACTCATAAATACT
1 AAATATATTATACTCATAAATGCT
29746103 AAAT
1 AAAT
29746107 CTTCTAGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTCATAAATGCT
Found at i:29746832 original size:36 final size:35
Alignment explanation
Indices: 29746780--29746856 Score: 136
Period size: 36 Copynumber: 2.2 Consensus size: 35
29746770 GTATATTAAA
*
29746780 ATTCACTGAATCGCTTTCCAATGATCTTTATCGGG
1 ATTCACTGAACCGCTTTCCAATGATCTTTATCGGG
29746815 ATTCACNTGAACCGCTTTCCAATGATCTTTATCGGG
1 ATTCAC-TGAACCGCTTTCCAATGATCTTTATCGGG
29746851 ATTCAC
1 ATTCAC
29746857 CATGTATCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 6 0.15
36 34 0.85
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.35
Consensus pattern (35 bp):
ATTCACTGAACCGCTTTCCAATGATCTTTATCGGG
Found at i:29751872 original size:21 final size:22
Alignment explanation
Indices: 29751848--29751892 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
29751838 TGGAATTTAG
29751848 GGTAATTTTAAATA-TTTTAAA
1 GGTAATTTTAAATATTTTTAAA
* **
29751869 GGTATTTTTCCATATTTTTAAA
1 GGTAATTTTAAATATTTTTAAA
29751891 GG
1 GG
29751893 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.49
Consensus pattern (22 bp):
GGTAATTTTAAATATTTTTAAA
Found at i:29756982 original size:49 final size:49
Alignment explanation
Indices: 29756925--29757028 Score: 163
Period size: 49 Copynumber: 2.1 Consensus size: 49
29756915 TCATGTGTTA
* ** * *
29756925 TAATTTTATAAAGTGTTGAGGTTTTGATTCATGATGTTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
29756974 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
29757023 TAATTT
1 TAATTT
29757029 GTTTTTTTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:29761922 original size:18 final size:18
Alignment explanation
Indices: 29761899--29761953 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
29761889 CATTCTTTTG
29761899 TCTTTACTTTCTTTTTAT
1 TCTTTACTTTCTTTTTAT
* * *
29761917 TCTTTATTTTATTCTTAT
1 TCTTTACTTTCTTTTTAT
*
29761935 T-TTTAC--TCTTTCTAT
1 TCTTTACTTTCTTTTTAT
29761950 TCTT
1 TCTT
29761954 GTATTTCATA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 7 0.24
16 2 0.07
17 4 0.14
18 16 0.55
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (18 bp):
TCTTTACTTTCTTTTTAT
Found at i:29763207 original size:107 final size:108
Alignment explanation
Indices: 29763016--29763232 Score: 373
Period size: 107 Copynumber: 2.0 Consensus size: 108
29763006 CTTTGAAGTT
* * *
29763016 TTAAGAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTT
1 TTAAAAGGATACTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
29763081 CTCGACTTTCCAAACGCGAAATATTGCCTTATTTAG-AAAATC
66 CTCGACTTTCCAAACGCGAAATATTGCCTTATTTAGAAAAATC
*
29763123 TTAAAAGGATACTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
1 TTAAAAGGATACTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
* *
29763188 CTCGATTTTCCAAATGCGAAATATTGCCTTATTTAGAAAAATC
66 CTCGACTTTCCAAACGCGAAATATTGCCTTATTTAGAAAAATC
29763231 TT
1 TT
29763233 CCTTTTGATG
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 95 0.92
108 8 0.08
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (108 bp):
TTAAAAGGATACTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
CTCGACTTTCCAAACGCGAAATATTGCCTTATTTAGAAAAATC
Found at i:29766788 original size:23 final size:23
Alignment explanation
Indices: 29766757--29766803 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
29766747 ATTTTGTTCT
29766757 TCCAAATATTGATATATTAGCTC
1 TCCAAATATTGATATATTAGCTC
*
29766780 TCCAGATATTGATATATTAGCTC
1 TCCAAATATTGATATATTAGCTC
29766803 T
1 T
29766804 TCTGGAGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (23 bp):
TCCAAATATTGATATATTAGCTC
Found at i:29767333 original size:39 final size:40
Alignment explanation
Indices: 29767225--29767345 Score: 136
Period size: 40 Copynumber: 3.0 Consensus size: 40
29767215 CGTTTGGATA
* * * * **
29767225 AAAAAACGCCGCTAAAAATCAATCATTAGTGGCGCTTTTA
1 AAAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTCC
* **
29767265 AAAAAACGCCACTAAAGATCGAGTGTTAGCGGCGCTTTCC
1 AAAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTCC
**
29767305 AAAAAACGCCACTAAAAAT-GAGCATTAGCGGCATTTTCC
1 AAAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTCC
29767344 AA
1 AA
29767346 TAAGCGTCGC
Statistics
Matches: 67, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
39 18 0.27
40 49 0.73
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (40 bp):
AAAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTCC
Found at i:29767476 original size:41 final size:41
Alignment explanation
Indices: 29767390--29767590 Score: 239
Period size: 41 Copynumber: 4.9 Consensus size: 41
29767380 GTTATCGGGG
* * * *
29767390 CTTTAGTGGTGTTTTTTAAAAGTGCCGCTAATGCTC-GGGT
1 CTTTAGCGGCGTTTTTGAAAAGCGCCGCTAATGCTCAGGGT
29767430 CTTTAGCGGCGTTTTTGAAAAGGCGCCGCTAATGCTCAGGGT
1 CTTTAGCGGCGTTTTTGAAAA-GCGCCGCTAATGCTCAGGGT
*
29767472 -TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAGGGT
1 CTTTAGCGGCG-TTTTTGAAAAGCGCCGCTAATGCTCAGGGT
* * * * *
29767513 -TTTAGCGGCATTTTTAAAAAAACACCGCTAATGCTC-GTGT
1 CTTTAGCGGCGTTTTT-GAAAAGCGCCGCTAATGCTCAGGGT
*
29767553 CTTTAGCGGCGTTTTTAGAAAAGTGCCGCTAATGCTCA
1 CTTTAGCGGCGTTTTT-GAAAAGCGCCGCTAATGCTCA
29767591 TGGCTAAACC
Statistics
Matches: 141, Mismatches: 14, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
40 26 0.18
41 102 0.72
42 13 0.09
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAGCGCCGCTAATGCTCAGGGT
Found at i:29767527 original size:82 final size:83
Alignment explanation
Indices: 29767384--29767590 Score: 271
Period size: 82 Copynumber: 2.5 Consensus size: 83
29767374 TTCTGAGTTA
* * * * *
29767384 TCGGGGCTTTAGTGGTGTTTTTT-AAAAGTGCCGCTAATGCTC-GGGTCTTTAGCGGCGTTTTTG
1 TCGGGTCTTTAGCGGCGTTTTTTAAAAAGTGCCGCTAATGCTCAGGGTCTTTAGCGGCATTTTTA
** *
29767447 AAAAGGCGCCGCTAATGC
66 AAAAAACACCGCTAATGC
*
29767465 TCAGGGT-TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAGGGT-TTTAGCGGCATTTTT
1 TC-GGGTCTTTAGCGGCGTTTTTTAAAAAGTGCCGCTAATGCTCAGGGTCTTTAGCGGCATTTTT
29767528 AAAAAAACACCGCTAATGC
65 AAAAAAACACCGCTAATGC
*
29767547 TCGTGTCTTTAGCGGCG-TTTTTAGAAAAGTGCCGCTAATGCTCA
1 TCGGGTCTTTAGCGGCGTTTTTTA-AAAAGTGCCGCTAATGCTCA
29767591 TGGCTAAACC
Statistics
Matches: 110, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
81 25 0.23
82 81 0.74
83 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (83 bp):
TCGGGTCTTTAGCGGCGTTTTTTAAAAAGTGCCGCTAATGCTCAGGGTCTTTAGCGGCATTTTTA
AAAAAACACCGCTAATGC
Found at i:29770473 original size:43 final size:43
Alignment explanation
Indices: 29770412--29770498 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
29770402 CAATGATGTA
* * *
29770412 CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
* *
29770455 CAAGATTTACTTGATTAAGAAAATGCATTGTATGTTTTATTAC
1 CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
29770498 C
1 C
29770499 TTGCATATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (43 bp):
CAAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTAC
Found at i:29770907 original size:43 final size:43
Alignment explanation
Indices: 29770765--29771031 Score: 297
Period size: 43 Copynumber: 6.3 Consensus size: 43
29770755 GATATATTTT
* * * * *
29770765 TAGCGGCTTTTGTGTGAAAAGCTCCGCTAAAGGTCA-GATCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
* * * * *
29770807 TAGCGGCGTTTATGGGAAAAGAGCCGCTAAAGGTC-TGTTCAA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
* * *
29770849 TAGCGGCATTTGTGGGAAAAGCGTCGCTAAAAGTGATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
*
29770892 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGACCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
* * *
29770935 TAGCGGCGTTTGTGTGAAAAGCGCCGCT-AAAGATCTTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAG-TCATGATCTA
* * * * * *
29770978 TAGCGGCATTTGTGTGAAAAGTGCCGCTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
29771021 TAGCGGCGTTT
1 TAGCGGCGTTT
29771032 ATTTCTAAAA
Statistics
Matches: 193, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
42 66 0.34
43 124 0.64
44 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
Found at i:29771053 original size:129 final size:128
Alignment explanation
Indices: 29770765--29771054 Score: 332
Period size: 129 Copynumber: 2.3 Consensus size: 128
29770755 GATATATTTT
* * * * * * *
29770765 TAGCGGCTTTTGTGTGAAAAGCTCCGCTAAAGGTCA-GATCTTTAGCGGCGTTTATGGGAAAAGA
1 TAGCGGCGTTTGTGCGAAAAACGCCGCTAAAAGTCATGACCTATAGCGGCGTTTATGGGAAAAGA
* * *
29770829 GCCGCTAAAGGTCTGTTCAATAGCGGCATTTGTGGGAAAAGCGTCGCTAAAAGTGATGATCTA
66 GCCGCTAAAGATCTGTTCAATAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
* * * * *
29770892 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGACCTATAGCGGCGTTTGTGTGAAAAGC
1 TAGCGGCGTTTGTGCGAAAAACGCCGCTAAAAGTCATGACCTATAGCGGCGTTTATGGGAAAAGA
* * * * * *
29770957 GCCGCTAAAGATCTTGTTCTATAGCGGCATTTGTGTGAAAAGTGCCGCTAAAGGTCTTGTTCTA
66 GCCGCTAAAGATC-TGTTCAATAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
* * *
29771021 TAGCGGCGTTTATTTCTAAAAACGCCGC-AAAAGT
1 TAGCGGCGTTT-GTGCGAAAAACGCCGCTAAAAGT
29771055 TAGCGGCGGT
Statistics
Matches: 137, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
127 32 0.23
128 35 0.26
129 59 0.43
130 11 0.08
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (128 bp):
TAGCGGCGTTTGTGCGAAAAACGCCGCTAAAAGTCATGACCTATAGCGGCGTTTATGGGAAAAGA
GCCGCTAAAGATCTGTTCAATAGCGGCATTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
Found at i:29772370 original size:38 final size:40
Alignment explanation
Indices: 29772328--29772408 Score: 112
Period size: 38 Copynumber: 2.0 Consensus size: 40
29772318 CATTTAACAC
* * *
29772328 AATAAAATATTTATTATATTTAT-TTGTG-TTTTTAATAT
1 AATAAAATACTCATTATATTTATGTAGTGCTTTTTAATAT
29772366 AATAAAATACTCATTATATTTATGGTAGTGCTTTTTAATAT
1 AATAAAATACTCATTATATTTAT-GTAGTGCTTTTTAATAT
29772407 AA
1 AA
29772409 ATGCTTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 21 0.57
40 4 0.11
41 12 0.32
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (40 bp):
AATAAAATACTCATTATATTTATGTAGTGCTTTTTAATAT
Found at i:29772915 original size:18 final size:17
Alignment explanation
Indices: 29772871--29772917 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
29772861 AGAAGGAGAG
29772871 AGAGAATAAAAATAAAA
1 AGAGAATAAAAATAAAA
*
29772888 ATA-AATTAAAGAATAAAA
1 AGAGAA-TAAA-AATAAAA
*
29772906 AGAGAGTAAAAA
1 AGAGAATAAAAA
29772918 ACCAAAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
16 2 0.08
17 8 0.33
18 13 0.54
19 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
AGAGAATAAAAATAAAA
Found at i:29793385 original size:458 final size:458
Alignment explanation
Indices: 29792528--29793921 Score: 2066
Period size: 458 Copynumber: 3.0 Consensus size: 458
29792518 AATCATTCAT
29792528 CATTCTCTCAACTCTTTTAGCTATCTTTTCCCCTTCATCATCCTTGCATAAGGATTTTAGCAATT
1 CATTCTCTCAACTCTTTTAGCTATCTTTTCCCCTTCATCATCCTTGCATAAGGATTTTAGCAATT
* * *
29792593 AAGCATCTTAAAGAACCCTTGGTCGGCCACCTTGAAGAGCCATCAACAAAGAAGCAACGCAAAGG
66 AAGCATCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAGCCATCAACAAAGGAGCAACGCAAAGA
*
29792658 AGCGAAGGAGCCTCGTCAGTCAGAGTCTTGGGTGACAACCACTTTGAATTGGGTTTAATATTTCT
131 AGCGAAGGAGCCTCGTCAGTCAGAGTCTTGGGTGACAGCCACTTTGAATTGGGTTTAATATTTCT
29792723 TTTCTTTAATTTAATATAAATATGTTTGCTATGTGTTCTTTGTTCTTGTTTACAAAAATGATAGC
196 TTTCTTTAATTTAATATAAATATGTTTGCTATGTGTTCTTTGTTCTTGTTTACAAAAATGATAGC
29792788 TTAATTTTATTTAAGCTAGGATGATTATTTTGATTAAATAATATTTATTTGATTCATGTTTATAA
261 TTAATTTTATTTAAGCTAGGATGATTATTTTGATTAAATAATATTTATTTGATTCATGTTTATAA
29792853 TGTTTGTGCATCAATCGATCATGTGTTCAATTAAAATCAAAGTCTATATTTCGTTCATACGTGAT
326 TGTTTGTGCATCAATCGATCATGTGTTCAATTAAAATCAAAGTCTATATTTCGTTCATACGTGAT
29792918 TAAAATGCACCTAAATTAGTTGAGCAACCTAACCAGACGACGGCTAATGGACGCATAATTGAAAT
391 TAAAATGCACCTAAATTAGTTGAGCAACCTAACCAGACGACGGCTAATGGACGCATAATTGAAAT
29792983 GTG
456 GTG
29792986 CATTCTCTCAACTCTTTTAGCTATCTTTTCCCCTTCATCATCCTTGCATAAGGATTTTAGCAATT
1 CATTCTCTCAACTCTTTTAGCTATCTTTTCCCCTTCATCATCCTTGCATAAGGATTTTAGCAATT
29793051 AAGCATCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAGCCATCAACAAAGGAGCAACGCAAAGA
66 AAGCATCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAGCCATCAACAAAGGAGCAACGCAAAGA
*
29793116 AGCGAAGGAGTCTCGTCAGTCAGAGTCTTGGGTGACAGCCACTTTGAATTGGGTTTAATATTTCT
131 AGCGAAGGAGCCTCGTCAGTCAGAGTCTTGGGTGACAGCCACTTTGAATTGGGTTTAATATTTCT
29793181 TTTCTTTAATTTAATATAAATATGTTTGCTATGTGTTCTTTGTTCTTGTTTACAAAAATGATAGC
196 TTTCTTTAATTTAATATAAATATGTTTGCTATGTGTTCTTTGTTCTTGTTTACAAAAATGATAGC
*
29793246 TTAATTTTATTTAAGCTAGGATGATTATTTTGATTAAATGATATTTATTTGATTCATGTTTATAA
261 TTAATTTTATTTAAGCTAGGATGATTATTTTGATTAAATAATATTTATTTGATTCATGTTTATAA
29793311 TGTTTGTGCATCAATCGATCATGTGTTCAATTAAAATCAAAGTCTATATTTCGTTCATACGTGAT
326 TGTTTGTGCATCAATCGATCATGTGTTCAATTAAAATCAAAGTCTATATTTCGTTCATACGTGAT
29793376 TAAAATGCACCTAAATTAGTTGAGCAACCTAACCAGACGACGGCTAATGGACGCATAATTGAAAT
391 TAAAATGCACCTAAATTAGTTGAGCAACCTAACCAGACGACGGCTAATGGACGCATAATTGAAAT
29793441 GTG
456 GTG
* * * ** *** * *
29793444 CATGCTCAATTTAGATCCTAACTCGATTGAATTATAGGTTCCATAACAACTCTAACCAATCTCTG
1 CAT--TC----T--CT-C-AACTC-TTTTAGCTATCTTTTCC----C--CT-TCATC-ATC-C--
* * ** * * ** *
29793509 TTATCTGCAT-A-GTTTTTAG--ATT-TGTGTGATTAAATTGTTTCAAACCTAAG-C-GTC-CC-
44 ---T-TGCATAAGGATTTTAGCAATTAAGCAT-CTTAAA--G----AACCCTTGGTCGGCCACCT
** * ** *
29793565 T-GTTA-CC-TC-AC--ACGA--ATGTGCAAAGAAGCGAATGAGCCTCGTCAGTCAGAGTCTTGG
98 TGGAGAGCCATCAACAAAGGAGCA-ACGCAAAGAAGCGAAGGAGCCTCGTCAGTCAGAGTCTTGG
*
29793622 GTGACAGCCACTTTGAATTGGGTTTAATATTTCTTTTCTTTAATTTAATATAAATATGTTTGATA
162 GTGACAGCCACTTTGAATTGGGTTTAATATTTCTTTTCTTTAATTTAATATAAATATGTTTGCTA
*
29793687 TGTGTTCTTTGTTCTTGTTTACAAAAATGATAGCTTAATTTTATTTAAGTTAGGATGATTATTTT
227 TGTGTTCTTTGTTCTTGTTTACAAAAATGATAGCTTAATTTTATTTAAGCTAGGATGATTATTTT
29793752 GATTAAATAATATTTATTTGATTCATGTTTATAATGTTTGTGCATCAATCGATCATGTGTTCAAT
292 GATTAAATAATATTTATTTGATTCATGTTTATAATGTTTGTGCATCAATCGATCATGTGTTCAAT
29793817 TAAAATCAAAGTCTATATTTCGTTCATACGTGATTAAAATGCACCTAAATTAGTTGAGCAACCTA
357 TAAAATCAAAGTCTATATTTCGTTCATACGTGATTAAAATGCACCTAAATTAGTTGAGCAACCTA
29793882 ACCAGACGACGGCTAATGGACGCATAATTGAAATGTG
422 ACCAGACGACGGCTAATGGACGCATAATTGAAATGTG
29793919 CAT
1 CAT
29793922 GCTCAATTTA
Statistics
Matches: 867, Mismatches: 35, Indels: 51
0.91 0.04 0.05
Matches are distributed among these distances:
458 455 0.52
460 2 0.00
464 1 0.00
466 1 0.00
467 1 0.00
468 5 0.01
469 10 0.01
473 1 0.00
474 1 0.00
475 335 0.39
476 6 0.01
477 3 0.00
478 3 0.00
479 4 0.00
480 10 0.01
481 2 0.00
482 9 0.01
483 4 0.00
484 7 0.01
485 1 0.00
486 6 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (458 bp):
CATTCTCTCAACTCTTTTAGCTATCTTTTCCCCTTCATCATCCTTGCATAAGGATTTTAGCAATT
AAGCATCTTAAAGAACCCTTGGTCGGCCACCTTGGAGAGCCATCAACAAAGGAGCAACGCAAAGA
AGCGAAGGAGCCTCGTCAGTCAGAGTCTTGGGTGACAGCCACTTTGAATTGGGTTTAATATTTCT
TTTCTTTAATTTAATATAAATATGTTTGCTATGTGTTCTTTGTTCTTGTTTACAAAAATGATAGC
TTAATTTTATTTAAGCTAGGATGATTATTTTGATTAAATAATATTTATTTGATTCATGTTTATAA
TGTTTGTGCATCAATCGATCATGTGTTCAATTAAAATCAAAGTCTATATTTCGTTCATACGTGAT
TAAAATGCACCTAAATTAGTTGAGCAACCTAACCAGACGACGGCTAATGGACGCATAATTGAAAT
GTG
Found at i:29793999 original size:475 final size:475
Alignment explanation
Indices: 29793109--29794057 Score: 1853
Period size: 475 Copynumber: 2.0 Consensus size: 475
29793099 AAGGAGCAAC
*
29793109 GCAAAGAAGCGAAGGAGTCTCGTCAGTCAGAGTCTTGGGTGACAGCCACTTTGAATTGGGTTTAA
1 GCAAAGAAGCGAAGGAGCCTCGTCAGTCAGAGTCTTGGGTGACAGCCACTTTGAATTGGGTTTAA
*
29793174 TATTTCTTTTCTTTAATTTAATATAAATATGTTTGCTATGTGTTCTTTGTTCTTGTTTACAAAAA
66 TATTTCTTTTCTTTAATTTAATATAAATATGTTTGATATGTGTTCTTTGTTCTTGTTTACAAAAA
*
29793239 TGATAGCTTAATTTTATTTAAGCTAGGATGATTATTTTGATTAAATGATATTTATTTGATTCATG
131 TGATAGCTTAATTTTATTTAAGCTAGGATGATTATTTTGATTAAATAATATTTATTTGATTCATG
29793304 TTTATAATGTTTGTGCATCAATCGATCATGTGTTCAATTAAAATCAAAGTCTATATTTCGTTCAT
196 TTTATAATGTTTGTGCATCAATCGATCATGTGTTCAATTAAAATCAAAGTCTATATTTCGTTCAT
29793369 ACGTGATTAAAATGCACCTAAATTAGTTGAGCAACCTAACCAGACGACGGCTAATGGACGCATAA
261 ACGTGATTAAAATGCACCTAAATTAGTTGAGCAACCTAACCAGACGACGGCTAATGGACGCATAA
29793434 TTGAAATGTGCATGCTCAATTTAGATCCTAACTCGATTGAATTATAGGTTCCATAACAACTCTAA
326 TTGAAATGTGCATGCTCAATTTAGATCCTAACTCGATTGAATTATAGGTTCCATAACAACTCTAA
29793499 CCAATCTCTGTTATCTGCATAGTTTTTAGATTTGTGTGATTAAATTGTTTCAAACCTAAGCGTCC
391 CCAATCTCTGTTATCTGCATAGTTTTTAGATTTGTGTGATTAAATTGTTTCAAACCTAAGCGTCC
29793564 CTGTTACCTCACACGAATGT
456 CTGTTACCTCACACGAATGT
*
29793584 GCAAAGAAGCGAATGAGCCTCGTCAGTCAGAGTCTTGGGTGACAGCCACTTTGAATTGGGTTTAA
1 GCAAAGAAGCGAAGGAGCCTCGTCAGTCAGAGTCTTGGGTGACAGCCACTTTGAATTGGGTTTAA
29793649 TATTTCTTTTCTTTAATTTAATATAAATATGTTTGATATGTGTTCTTTGTTCTTGTTTACAAAAA
66 TATTTCTTTTCTTTAATTTAATATAAATATGTTTGATATGTGTTCTTTGTTCTTGTTTACAAAAA
*
29793714 TGATAGCTTAATTTTATTTAAGTTAGGATGATTATTTTGATTAAATAATATTTATTTGATTCATG
131 TGATAGCTTAATTTTATTTAAGCTAGGATGATTATTTTGATTAAATAATATTTATTTGATTCATG
29793779 TTTATAATGTTTGTGCATCAATCGATCATGTGTTCAATTAAAATCAAAGTCTATATTTCGTTCAT
196 TTTATAATGTTTGTGCATCAATCGATCATGTGTTCAATTAAAATCAAAGTCTATATTTCGTTCAT
29793844 ACGTGATTAAAATGCACCTAAATTAGTTGAGCAACCTAACCAGACGACGGCTAATGGACGCATAA
261 ACGTGATTAAAATGCACCTAAATTAGTTGAGCAACCTAACCAGACGACGGCTAATGGACGCATAA
29793909 TTGAAATGTGCATGCTCAATTTAGATCCTAACTCGATTGAATTATAGGTTCCATAACAACTCTAA
326 TTGAAATGTGCATGCTCAATTTAGATCCTAACTCGATTGAATTATAGGTTCCATAACAACTCTAA
29793974 CCAATCTCTGTTATCTGCATAGTTTTTAGATTTGTGTGATTAAATTGTTTCAAACCTAAGCGTCC
391 CCAATCTCTGTTATCTGCATAGTTTTTAGATTTGTGTGATTAAATTGTTTCAAACCTAAGCGTCC
29794039 CTGTTACCTCACACGAATG
456 CTGTTACCTCACACGAATG
29794058 CTAAGAAACC
Statistics
Matches: 469, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
475 469 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (475 bp):
GCAAAGAAGCGAAGGAGCCTCGTCAGTCAGAGTCTTGGGTGACAGCCACTTTGAATTGGGTTTAA
TATTTCTTTTCTTTAATTTAATATAAATATGTTTGATATGTGTTCTTTGTTCTTGTTTACAAAAA
TGATAGCTTAATTTTATTTAAGCTAGGATGATTATTTTGATTAAATAATATTTATTTGATTCATG
TTTATAATGTTTGTGCATCAATCGATCATGTGTTCAATTAAAATCAAAGTCTATATTTCGTTCAT
ACGTGATTAAAATGCACCTAAATTAGTTGAGCAACCTAACCAGACGACGGCTAATGGACGCATAA
TTGAAATGTGCATGCTCAATTTAGATCCTAACTCGATTGAATTATAGGTTCCATAACAACTCTAA
CCAATCTCTGTTATCTGCATAGTTTTTAGATTTGTGTGATTAAATTGTTTCAAACCTAAGCGTCC
CTGTTACCTCACACGAATGT
Found at i:29795756 original size:102 final size:101
Alignment explanation
Indices: 29795575--29796552 Score: 1730
Period size: 102 Copynumber: 9.6 Consensus size: 101
29795565 TTCACTTGTC
* * * * *
29795575 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTT-ACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
*
29795640 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
65 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
* *
29795677 TTTTGTTGCAGGGAATCTCTCCTGTT-CACATCA-TTTCTTGCAGGGAGGAATCTTTCCTGTTCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTACACATTATTTTGTTGCA--G-GGAATCTTTCCTGTTCA
29795740 CATCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
63 CATCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
29795779 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTT-ACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
29795844 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
65 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
29795881 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTT-ACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
29795946 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
65 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
29795983 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTT-ACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
29796048 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
65 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
29796085 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTT-ACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
29796150 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
65 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
29796187 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTT-ACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
29796252 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
65 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
29796289 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTT-ACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
29796354 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
65 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
29796391 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTT-ACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
29796456 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
65 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
* * *
29796493 TTTTGTTGCAGGGAATCTCTCCTGTT-CACATCA-TTTCTTGCAGGGAATCTCTCCTGTTCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCA
29796553 TGTATTATTT
Statistics
Matches: 857, Mismatches: 13, Indels: 15
0.97 0.01 0.02
Matches are distributed among these distances:
99 32 0.04
100 11 0.01
101 1 0.00
102 798 0.93
103 1 0.00
104 6 0.01
105 8 0.01
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.40
Consensus pattern (101 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACAT
CATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
Found at i:29801750 original size:45 final size:45
Alignment explanation
Indices: 29801700--29801795 Score: 174
Period size: 45 Copynumber: 2.1 Consensus size: 45
29801690 TTTTGGGCTT
29801700 TGGAGTAAAGCCTTGGTATTAACTACAGAATACATGGCTTTGAAA
1 TGGAGTAAAGCCTTGGTATTAACTACAGAATACATGGCTTTGAAA
* *
29801745 TGGAGTAAAGCCTTGGTATTAACTATAGAATACATGGCTTTGATA
1 TGGAGTAAAGCCTTGGTATTAACTACAGAATACATGGCTTTGAAA
29801790 TGGAGT
1 TGGAGT
29801796 CTATAAACCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (45 bp):
TGGAGTAAAGCCTTGGTATTAACTACAGAATACATGGCTTTGAAA
Found at i:29802400 original size:40 final size:41
Alignment explanation
Indices: 29802344--29802429 Score: 156
Period size: 40 Copynumber: 2.1 Consensus size: 41
29802334 TTTGGTCAGA
*
29802344 TTCTTGGGATTGATTAGTAACAAAGCTAGCAGAAGAATTGG
1 TTCTTGGGATTGATTAGTAACAAAGCTACCAGAAGAATTGG
29802385 TTCTT-GGATTGATTAGTAACAAAGCTACCAGAAGAATTGG
1 TTCTTGGGATTGATTAGTAACAAAGCTACCAGAAGAATTGG
29802425 TTCTT
1 TTCTT
29802430 CTAAGGAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 39 0.89
41 5 0.11
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (41 bp):
TTCTTGGGATTGATTAGTAACAAAGCTACCAGAAGAATTGG
Found at i:29813657 original size:4 final size:4
Alignment explanation
Indices: 29813648--29813699 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
29813638 TGTATTCTCA
* * ** *
29813648 TATG TATG TATG TACG TACG TACA TACG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
29813696 TATG
1 TATG
29813700 CACAGAGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (4 bp):
TATG
Found at i:29816800 original size:15 final size:15
Alignment explanation
Indices: 29816780--29816831 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
29816770 ACTACAAAAC
29816780 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
29816795 ATTTATAATTGCAATAAAT
1 ATTTATTATT--AAT--AT
*
29816814 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
29816829 ATT
1 ATT
29816832 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 14 0.47
17 5 0.17
19 11 0.37
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:29816895 original size:16 final size:16
Alignment explanation
Indices: 29816864--29816900 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
29816854 ATGTGAATAA
29816864 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
29816880 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
29816896 TATTA
1 TATTA
29816901 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:29816952 original size:22 final size:22
Alignment explanation
Indices: 29816912--29816967 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
29816902 AATAAAATTG
*
29816912 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
29816932 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
29816954 TATTAATAATTTAT
1 AAATAATAAATTAT
29816968 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:29818464 original size:14 final size:15
Alignment explanation
Indices: 29818439--29818467 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29818429 ATGTGTCTCT
29818439 TTTTTTACATATTTA
1 TTTTTTACATATTTA
29818454 TTTTTTA-ATATTTA
1 TTTTTTACATATTTA
29818468 CTATGCCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTACATATTTA
Found at i:29822181 original size:36 final size:36
Alignment explanation
Indices: 29822106--29822173 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
29822096 ATTTACATAT
** *
29822106 ATTTAATTCAATATCAACAATCACGTATACTCATGA
1 ATTTAATTCAATATCAACAATCACCAACACTCATGA
*
29822142 ATTTAATTCAATA-CCACAAT-ACCAACACTCAT
1 ATTTAATTCAATATCAACAATCACCAACACTCAT
29822174 CGCAATTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 9 0.32
35 6 0.21
36 13 0.46
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.31
Consensus pattern (36 bp):
ATTTAATTCAATATCAACAATCACCAACACTCATGA
Found at i:29822192 original size:25 final size:25
Alignment explanation
Indices: 29822160--29822215 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
29822150 CAATACCACA
*
29822160 ATACCAACACTCATCGCAATTTCAC
1 ATACCAACACTCACCGCAATTTCAC
29822185 ATACCAACACTCACCGCAATTTCAC
1 ATACCAACACTCACCGCAATTTCAC
*
29822210 TTACCA
1 ATACCA
29822216 TGCATATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.36, C:0.38, G:0.04, T:0.23
Consensus pattern (25 bp):
ATACCAACACTCACCGCAATTTCAC
Found at i:29822293 original size:41 final size:41
Alignment explanation
Indices: 29822248--29822329 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
29822238 AAAAATAATT
*
29822248 ATTAGATTCGGATTATAGAAATACAAACCAGAATTCTCGAG
1 ATTAGATTCGGATTATAAAAATACAAACCAGAATTCTCGAG
*
29822289 ATTAGATTTGGATTATAAAAATACAAACCAGAATTCTCGAG
1 ATTAGATTCGGATTATAAAAATACAAACCAGAATTCTCGAG
29822330 CTACTCCTCG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (41 bp):
ATTAGATTCGGATTATAAAAATACAAACCAGAATTCTCGAG
Found at i:29822963 original size:19 final size:20
Alignment explanation
Indices: 29822928--29822965 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
29822918 CTTTTCTATC
*
29822928 TTTTGTTTCTTTTATTTCTA
1 TTTTGTTTCTATTATTTCTA
29822948 TTTTGTTT-TATTATTTCT
1 TTTTGTTTCTATTATTTCT
29822966 TTTAACTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTTGTTTCTATTATTTCTA
Found at i:29822992 original size:5 final size:5
Alignment explanation
Indices: 29822982--29823007 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29822972 TATTATTTTA
29822982 ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT A
29823008 ATATTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:29823580 original size:22 final size:22
Alignment explanation
Indices: 29823555--29823621 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
29823545 CAAATTAATC
29823555 CCAAATAGAATCAATAAAAATT
1 CCAAATAGAATCAATAAAAATT
* *
29823577 CCAAAT----T-AAAAAAAATC
1 CCAAATAGAATCAATAAAAATT
29823594 CCAAATAGAATCAATAAAAATT
1 CCAAATAGAATCAATAAAAATT
29823616 CCAAAT
1 CCAAAT
29823622 TAAAAAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
17 14 0.39
18 1 0.03
21 1 0.03
22 20 0.56
ACGTcount: A:0.60, C:0.16, G:0.03, T:0.21
Consensus pattern (22 bp):
CCAAATAGAATCAATAAAAATT
Found at i:29823592 original size:17 final size:17
Alignment explanation
Indices: 29823570--29823630 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 17
29823560 TAGAATCAAT
29823570 AAAAATTCCAAATTAAA
1 AAAAATTCCAAATTAAA
* *
29823587 AAAAATCCCAAATAGAATCAAT
1 AAAAATTCCAAAT----T-AAA
29823609 AAAAATTCCAAATTAAA
1 AAAAATTCCAAATTAAA
29823626 AAAAA
1 AAAAA
29823631 GTAACTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 19 0.54
18 1 0.03
21 1 0.03
22 14 0.40
ACGTcount: A:0.66, C:0.13, G:0.02, T:0.20
Consensus pattern (17 bp):
AAAAATTCCAAATTAAA
Found at i:29823605 original size:39 final size:39
Alignment explanation
Indices: 29823551--29823630 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
29823541 TCCACAAATT
29823551 AATCCCAAATAGAATCAATAAAAATTCCAAATTAAAAAA
1 AATCCCAAATAGAATCAATAAAAATTCCAAATTAAAAAA
29823590 AATCCCAAATAGAATCAATAAAAATTCCAAATTAAAAAA
1 AATCCCAAATAGAATCAATAAAAATTCCAAATTAAAAAA
29823629 AA
1 AA
29823631 GTAACTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.62, C:0.15, G:0.03, T:0.20
Consensus pattern (39 bp):
AATCCCAAATAGAATCAATAAAAATTCCAAATTAAAAAA
Found at i:29824944 original size:2 final size:2
Alignment explanation
Indices: 29824937--29825014 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
29824927 CGAATTCATT
29824937 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
*
29824979 CA CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
29825015 TATATATATC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.49, G:0.00, T:0.01
Consensus pattern (2 bp):
CA
Found at i:29825272 original size:39 final size:39
Alignment explanation
Indices: 29825229--29825398 Score: 223
Period size: 39 Copynumber: 4.3 Consensus size: 39
29825219 GGTCTTTAAC
** *
29825229 CCGGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * *
29825268 CCGGATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * * *
29825307 CCGGATATATTTCTAGCATATAGCCTACGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* *
29825346 CCAGATATTTTTCCAACATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
29825385 CCGGATATATTTTC
1 CCGGATAT-TTTTC
29825399 AATCTCATAC
Statistics
Matches: 116, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
39 111 0.96
40 5 0.04
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:29833180 original size:39 final size:39
Alignment explanation
Indices: 29833137--29833306 Score: 232
Period size: 39 Copynumber: 4.3 Consensus size: 39
29833127 GGTCTTTAAC
* ** *
29833137 CCGGATATTTTTCCAACACGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * *
29833176 CCGGATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * * *
29833215 CCGAATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
29833254 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
29833293 CCGGATATATTTTC
1 CCGGATAT-TTTTC
29833307 AATCTCATAC
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 113 0.96
40 5 0.04
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:29841285 original size:14 final size:14
Alignment explanation
Indices: 29841266--29841295 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29841256 GCTAACAACC
29841266 AAAAAAAAAAAGAA
1 AAAAAAAAAAAGAA
*
29841280 AAAAAAGAAAAGAA
1 AAAAAAAAAAAGAA
29841294 AA
1 AA
29841296 CTAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:29841494 original size:15 final size:16
Alignment explanation
Indices: 29841474--29841515 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
29841464 CATATTTAAA
29841474 TTTAAATTTGA-CTCC
1 TTTAAATTTGACCTCC
** *
29841489 TTTAAAAATAACCTCC
1 TTTAAATTTGACCTCC
29841505 TTTAAATTTGA
1 TTTAAATTTGA
29841516 ATATCTTGTT
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (16 bp):
TTTAAATTTGACCTCC
Found at i:29844585 original size:26 final size:26
Alignment explanation
Indices: 29844549--29844601 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
29844539 TTAGTCACAC
29844549 TTGTCTTATTCTATTCTACTTTTAAA
1 TTGTCTTATTCTATTCTACTTTTAAA
*
29844575 TTGTCTTATTCTATTTTACTTTTAAA
1 TTGTCTTATTCTATTCTACTTTTAAA
29844601 T
1 T
29844602 GGGTTGCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.13, G:0.04, T:0.60
Consensus pattern (26 bp):
TTGTCTTATTCTATTCTACTTTTAAA
Found at i:29850831 original size:24 final size:24
Alignment explanation
Indices: 29850803--29850966 Score: 97
Period size: 25 Copynumber: 6.7 Consensus size: 24
29850793 CTGTATAACG
*
29850803 GGAAGCACATAAGAGCCATAATCA
1 GGAAGCTCATAAGAGCCATAATCA
** *
29850827 GGAAGCTCATGCGAGCCAATAA-CG
1 GGAAGCTCATAAGAGCC-ATAATCA
*
29850851 GGTAGCTC-TGAAGAGCCATTAATCA
1 GGAAGCTCAT-AAGAGCCA-TAATCA
* * *
29850876 GGAAGCTC-TGGATAGCCATATATCG
1 GGAAGCTCAT-AAGAGCCATA-ATCA
* * *
29850901 GGAAGTTCA-AGTGAGCCAT-ATCG
1 GGAAGCTCATA-AGAGCCATAATCA
29850924 GGAAGCTC-TAGAGAGCCATCAATCA
1 GGAAGCTCATA-AGAGCCAT-AATCA
*
29850949 GGAAGCTCAAAAAGAGCC
1 GGAAGCTC-ATAAGAGCC
29850967 TTTAATCGAA
Statistics
Matches: 108, Mismatches: 20, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
23 22 0.20
24 32 0.30
25 47 0.44
26 6 0.06
27 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.17
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATCA
Found at i:29850884 original size:25 final size:24
Alignment explanation
Indices: 29850813--29850956 Score: 102
Period size: 25 Copynumber: 5.9 Consensus size: 24
29850803 GGAAGCACAT
29850813 AAGAGCCATAATCAGGAAGCTCATG
1 AAGAGCCATAATCAGGAAGCTC-TG
* * *
29850838 -CGAGCCAATAA-CGGGTAGCTCTG
1 AAGAGCC-ATAATCAGGAAGCTCTG
29850861 AAGAGCCATTAATCAGGAAGCTCTG
1 AAGAGCCA-TAATCAGGAAGCTCTG
* * * *
29850886 GATAGCCATATATCGGGAAG-T-TC
1 AAGAGCCATA-ATCAGGAAGCTCTG
*
29850909 AAGTGAGCCAT-ATCGGGAAGCTCT-
1 AA--GAGCCATAATCAGGAAGCTCTG
29850933 AGAGAGCCATCAATCAGGAAGCTC
1 A-AGAGCCAT-AATCAGGAAGCTC
29850957 AAAAAGAGCC
Statistics
Matches: 94, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
23 21 0.22
24 26 0.28
25 47 0.50
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (24 bp):
AAGAGCCATAATCAGGAAGCTCTG
Found at i:29850955 original size:73 final size:73
Alignment explanation
Indices: 29850816--29850956 Score: 187
Period size: 73 Copynumber: 1.9 Consensus size: 73
29850806 AGCACATAAG
* * *
29850816 AGCCATAATCAGGAAGCTCATGCGAGCCAATAACGGGTAGCTCTGAAGAGCCATTAATCAGGAAG
1 AGCCATAATCAGGAAGCTCAAGCGAGCCAATAACGGGAAGCTCTGAAGAGCCATCAATCAGGAAG
29850881 CTCTGGAT
66 CTCTGGAT
* * * *
29850889 AGCCATATATCGGGAAGTTCAAGTGAGCC-ATATCGGGAAGCTCT-AGAGAGCCATCAATCAGGA
1 AGCCATA-ATCAGGAAGCTCAAGCGAGCCAATAACGGGAAGCTCTGA-AGAGCCATCAATCAGGA
29850952 AGCTC
64 AGCTC
29850957 AAAAAGAGCC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
72 1 0.02
73 41 0.69
74 17 0.29
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (73 bp):
AGCCATAATCAGGAAGCTCAAGCGAGCCAATAACGGGAAGCTCTGAAGAGCCATCAATCAGGAAG
CTCTGGAT
Found at i:29853801 original size:19 final size:19
Alignment explanation
Indices: 29853773--29853863 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
29853763 ATAATCTTCA
29853773 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
29853792 ATGATCTGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
29853811 ATGATAT--AATCTTAGAT
1 ATGATATGCAATCTTAGAT
29853828 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
29853846 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
29853864 AGATATGATT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
16 1 0.01
17 15 0.22
18 15 0.22
19 36 0.54
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:29853805 original size:36 final size:37
Alignment explanation
Indices: 29853773--29853863 Score: 159
Period size: 35 Copynumber: 2.5 Consensus size: 37
29853763 ATAATCTTCA
29853773 ATGATATGCAATCTTAGATATGATCTGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGAT-TGCAATCTTAGAT
29853811 ATGATAT--AATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATTGCAATCTTAGAT
29853846 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
29853864 AGATATGATT
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
35 20 0.39
36 15 0.29
37 9 0.18
38 7 0.14
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.37
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATTGCAATCTTAGAT
Found at i:29853842 original size:54 final size:53
Alignment explanation
Indices: 29853761--29853863 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 53
29853751 TCATATGGAA
*
29853761 ATATAATCTTCAATGATATGCAATCTTAGATATGATCTGCAATCTTAGATATG
1 ATATAATCTTCAATGATATGCAATCTTAGATATGATATGCAATCTTAGATATG
*
29853814 ATATAATCTTAGATATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA
1 ATATAATCTT-CA-ATGATATGCAATCTTAGATATGATATGCAATCTTAGA
29853864 AGATATGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
53 10 0.22
54 31 0.67
55 5 0.11
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.38
Consensus pattern (53 bp):
ATATAATCTTCAATGATATGCAATCTTAGATATGATATGCAATCTTAGATATG
Found at i:29853889 original size:22 final size:22
Alignment explanation
Indices: 29853773--29853886 Score: 87
Period size: 19 Copynumber: 5.8 Consensus size: 22
29853763 ATAATCTTCA
29853773 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
*
29853792 ATGATCTGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
29853811 ATGATAT--AATCTTAG---AT
1 ATGATATGCAATCTTAGAAGAT
29853828 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
29853846 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
29853868 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
29853887 GATTTAATTT
Statistics
Matches: 80, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
16 1 0.01
17 13 0.16
18 13 0.16
19 33 0.41
22 8 0.10
23 12 0.15
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:29856553 original size:19 final size:19
Alignment explanation
Indices: 29856526--29856565 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29856516 GACTAGCATT
* *
29856526 TAATGTATAAATGATATAA
1 TAATATATAAAAGATATAA
*
29856545 TAATATATAAAAGATTTAA
1 TAATATATAAAAGATATAA
29856564 TA
1 TA
29856566 CCATAATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (19 bp):
TAATATATAAAAGATATAA
Found at i:29856585 original size:7 final size:7
Alignment explanation
Indices: 29856568--29856706 Score: 58
Period size: 7 Copynumber: 20.0 Consensus size: 7
29856558 ATTTAATACC
29856568 ATAAT-T
1 ATAATAT
29856574 ATAATAT
1 ATAATAT
29856581 ATAATAT
1 ATAATAT
*
29856588 AAAAGTAT
1 ATAA-TAT
*
29856596 AT-ATGT
1 ATAATAT
* *
29856602 A-AAAAA
1 ATAATAT
29856608 ATAATAT
1 ATAATAT
*
29856615 ATAATGT
1 ATAATAT
*
29856622 AT-ATAA
1 ATAATAT
29856628 ATAATA-
1 ATAATAT
* *
29856634 ACAATTT
1 ATAATAT
* *
29856641 GTGAA-AA
1 AT-AATAT
*
29856648 ATAATAA
1 ATAATAT
29856655 ATAATA-
1 ATAATAT
29856661 ATAATAT
1 ATAATAT
29856668 AAATAATAT
1 --ATAATAT
*
29856677 ATAATAAA
1 ATAAT-AT
*
29856685 ATACTTAT
1 ATA-ATAT
29856693 ATAATAT
1 ATAATAT
29856700 ATAATAT
1 ATAATAT
29856707 GAAAATAAGG
Statistics
Matches: 98, Mismatches: 22, Indels: 25
0.68 0.15 0.17
Matches are distributed among these distances:
6 26 0.27
7 50 0.51
8 14 0.14
9 8 0.08
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (7 bp):
ATAATAT
Found at i:29856671 original size:15 final size:16
Alignment explanation
Indices: 29856651--29856705 Score: 69
Period size: 15 Copynumber: 3.4 Consensus size: 16
29856641 GTGAAAAATA
29856651 ATAAATAATA-ATAAT
1 ATAAATAATATATAAT
29856666 ATAAATAATATATAAT
1 ATAAATAATATATAAT
*
29856682 A-AAATACTTATATAAT
1 ATAAATA-ATATATAAT
29856698 ATATAATA
1 ATA-AATA
29856706 TGAAAATAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
15 15 0.43
16 15 0.43
17 1 0.03
18 4 0.11
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAATAATATATAAT
Found at i:29856672 original size:9 final size:10
Alignment explanation
Indices: 29856648--29856705 Score: 57
Period size: 10 Copynumber: 5.6 Consensus size: 10
29856638 TTTGTGAAAA
29856648 ATAATAA-AT
1 ATAATAATAT
29856657 AATAATAATAT
1 -ATAATAATAT
29856668 A-AATAATAT
1 ATAATAATAT
*
29856677 ATAATAAAAT
1 ATAATAATAT
29856687 ACTTATATAATAT
1 A--TA-ATAATAT
29856700 ATAATA
1 ATAATA
29856706 TGAAAATAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 9 0.22
10 19 0.46
11 4 0.10
12 2 0.05
13 7 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAATAATAT
Found at i:29865326 original size:78 final size:78
Alignment explanation
Indices: 29865032--29865315 Score: 444
Period size: 78 Copynumber: 3.6 Consensus size: 78
29865022 CGAAGAAACA
** * * * * *
29865032 GATTTGGCATCTCCATATTCGATGGAGAGCAGATTGAAGACATAGCAGATCT-GACCTTCATTGA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAGAT-TGGACCTTCATTGA
29865096 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
* *
29865110 GATTTGGCATCTCTGTATTAGACGGGGAGCAGAACGAAGACACAACAGATTGGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAGATTGGACCTTCATTGAA
29865175 GCAGATCCAAGAT
66 GCAGATCCAAGAT
*
29865188 GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGACATAACAGATTGGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAGATTGGACCTTCATTGAA
29865253 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* *
29865266 GATTTGGCATCTCTGTATTAGATGGGGAGCAGATCGAAGACATAGCAGAT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAGAT
29865316 CTAACCTTCA
Statistics
Matches: 190, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
77 1 0.01
78 189 0.99
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAGATTGGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:29865471 original size:89 final size:89
Alignment explanation
Indices: 29865355--29865525 Score: 261
Period size: 89 Copynumber: 1.9 Consensus size: 89
29865345 ATCCAAGATG
*
29865355 ACAGATTTGGCATCTCTGTATTAGACGGAGAGCAAATCAGAGATAACAGATTTGGCATCTCTGTA
1 ACAGATTTGGCATCTCTGTATTAGACGGAGAGCAAATCAAAGATAACAGATTTGGCATCTCTGTA
29865420 TTAGACGGGGAGCAGATTGAAGAA
66 TTAGACGGGGAGCAGATTGAAGAA
* * * * * * *
29865444 ACAGATTTGGCGTCTCTGTATTGGACGGGGAGCAGATCAAAGATAGCAGATTTTGCGTCTCTGTA
1 ACAGATTTGGCATCTCTGTATTAGACGGAGAGCAAATCAAAGATAACAGATTTGGCATCTCTGTA
*
29865509 TTAGACGGGGAGTAGAT
66 TTAGACGGGGAGCAGAT
29865526 CAAAGATAGA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 73 1.00
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (89 bp):
ACAGATTTGGCATCTCTGTATTAGACGGAGAGCAAATCAAAGATAACAGATTTGGCATCTCTGTA
TTAGACGGGGAGCAGATTGAAGAA
Found at i:29865534 original size:45 final size:45
Alignment explanation
Indices: 29865266--29865539 Score: 252
Period size: 45 Copynumber: 6.1 Consensus size: 45
29865256 GATCCAAGAT
* *
29865266 GATTTGGCATCTCTGTATTAGATGGGGAGCAGATCGAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATC-AA-AGATAGCA
* ** * * * * *
29865313 GATCTAACCT-TCATGTGTTTATATC--GAAGCAGATCCAAGAT-GACA
1 GATTTGGCATCTC-TGT-ATTAGA-CGGGGAGCAGATCAAAGATAG-CA
* * * *
29865358 GATTTGGCATCTCTGTATTAGACGGAGAGCAAATCAGAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCA
** *
29865403 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAGA-AACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCA
* *
29865447 GATTTGGCGTCTCTGTATTGGACGGGGAGCAGATCAAAGATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCA
* * * *
29865492 GATTTTGCGTCTCTGTATTAGACGGGGAGTAGATCAAAGATAGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCA
29865537 GAT
1 GAT
29865540 ATCGCCTTCC
Statistics
Matches: 182, Mismatches: 36, Indels: 20
0.76 0.15 0.08
Matches are distributed among these distances:
43 1 0.01
44 45 0.25
45 109 0.60
46 5 0.03
47 18 0.10
48 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26
Consensus pattern (45 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCA
Found at i:29865918 original size:19 final size:19
Alignment explanation
Indices: 29865890--29865980 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
29865880 ATAATCTTCA
29865890 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
29865909 ATGATCTGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
29865928 ATGATAT--AATCTTAGAT
1 ATGATATGCAATCTTAGAT
29865945 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
29865963 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
29865981 AGATATGATT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
16 1 0.01
17 15 0.22
18 15 0.22
19 36 0.54
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:29865922 original size:36 final size:37
Alignment explanation
Indices: 29865890--29865980 Score: 159
Period size: 35 Copynumber: 2.5 Consensus size: 37
29865880 ATAATCTTCA
29865890 ATGATATGCAATCTTAGATATGATCTGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGAT-TGCAATCTTAGAT
29865928 ATGATAT--AATCTTAGATATGATTGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATTGCAATCTTAGAT
29865963 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
29865981 AGATATGATT
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
35 20 0.39
36 15 0.29
37 9 0.18
38 7 0.14
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.37
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATTGCAATCTTAGAT
Found at i:29865959 original size:54 final size:53
Alignment explanation
Indices: 29865878--29865980 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 53
29865868 TCATATGGAA
*
29865878 ATATAATCTTCAATGATATGCAATCTTAGATATGATCTGCAATCTTAGATATG
1 ATATAATCTTCAATGATATGCAATCTTAGATATGATATGCAATCTTAGATATG
*
29865931 ATATAATCTTAGATATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA
1 ATATAATCTT-CA-ATGATATGCAATCTTAGATATGATATGCAATCTTAGA
29865981 AGATATGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
53 10 0.22
54 31 0.67
55 5 0.11
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.38
Consensus pattern (53 bp):
ATATAATCTTCAATGATATGCAATCTTAGATATGATATGCAATCTTAGATATG
Found at i:29866006 original size:22 final size:22
Alignment explanation
Indices: 29865890--29866003 Score: 87
Period size: 19 Copynumber: 5.8 Consensus size: 22
29865880 ATAATCTTCA
29865890 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
*
29865909 ATGATCTGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
29865928 ATGATAT--AATCTTAG---AT
1 ATGATATGCAATCTTAGAAGAT
29865945 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
29865963 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
29865985 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
29866004 GATTTAATTT
Statistics
Matches: 80, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
16 1 0.01
17 13 0.16
18 13 0.16
19 33 0.41
22 8 0.10
23 12 0.15
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:29868354 original size:30 final size:30
Alignment explanation
Indices: 29868319--29868377 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
29868309 ACAATGTAGT
* *
29868319 AGCAGTAACATAGCAGAATACCTGTAATCA
1 AGCAGTAACACAACAGAATACCTGTAATCA
*
29868349 AGCAGTAACACAACATAATACCTGTAATC
1 AGCAGTAACACAACAGAATACCTGTAATC
29868378 GAACAAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (30 bp):
AGCAGTAACACAACAGAATACCTGTAATCA
Found at i:29869718 original size:26 final size:26
Alignment explanation
Indices: 29869688--29869765 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
29869678 TGGTCAAATG
29869688 TTGATATGTCTTTGAGAGTTGTCTGA
1 TTGATATGTCTTTGAGAGTTGTCTGA
* * * *
29869714 TTGATA---CTTT-TG-TTTG-GTGT
1 TTGATATGTCTTTGAGAGTTGTCTGA
*
29869734 TTGATATGTCTTTGAGAGTTGTCCGA
1 TTGATATGTCTTTGAGAGTTGTCTGA
29869760 TTGATA
1 TTGATA
29869766 CTTTTGTTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 12
0.64 0.16 0.21
Matches are distributed among these distances:
20 8 0.22
21 3 0.08
22 1 0.03
23 8 0.22
24 1 0.03
25 3 0.08
26 13 0.35
ACGTcount: A:0.18, C:0.08, G:0.26, T:0.49
Consensus pattern (26 bp):
TTGATATGTCTTTGAGAGTTGTCTGA
Found at i:29869738 original size:24 final size:24
Alignment explanation
Indices: 29869711--29869782 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 24
29869701 GAGAGTTGTC
29869711 TGATTGATACTTTTGTTTGGTGTT
1 TGATTGATACTTTTGTTTGGTGTT
*** * *
29869735 TGATATG-T-C-TTTGAGAGTTGTC
1 TGAT-TGATACTTTTGTTTGGTGTT
*
29869757 CGATTGATACTTTTGTTTGGTGTT
1 TGATTGATACTTTTGTTTGGTGTT
29869781 TG
1 TG
29869783 GCCAAATTAG
Statistics
Matches: 32, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
21 2 0.06
22 12 0.38
23 2 0.06
24 14 0.44
25 2 0.06
ACGTcount: A:0.14, C:0.07, G:0.26, T:0.53
Consensus pattern (24 bp):
TGATTGATACTTTTGTTTGGTGTT
Found at i:29869739 original size:46 final size:46
Alignment explanation
Indices: 29869688--29869782 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
29869678 TGGTCAAATG
*
29869688 TTGATATGTCTTTGAGAGTTGTCTGATTGATACTTTTGTTTGGTGT
1 TTGATATGTCTTTGAGAGTTGTCCGATTGATACTTTTGTTTGGTGT
29869734 TTGATATGTCTTTGAGAGTTGTCCGATTGATACTTTTGTTTGGTGT
1 TTGATATGTCTTTGAGAGTTGTCCGATTGATACTTTTGTTTGGTGT
29869780 TTG
1 TTG
29869783 GCCAAATTAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.15, C:0.07, G:0.26, T:0.52
Consensus pattern (46 bp):
TTGATATGTCTTTGAGAGTTGTCCGATTGATACTTTTGTTTGGTGT
Found at i:29872585 original size:10 final size:9
Alignment explanation
Indices: 29872559--29872589 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
29872549 TTGTGTGTTC
29872559 TTTATTTTA
1 TTTATTTTA
29872568 TTTATTTTA
1 TTTATTTTA
29872577 TTATATTTTA
1 TT-TATTTTA
29872587 TTT
1 TTT
29872590 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:29877820 original size:18 final size:18
Alignment explanation
Indices: 29877783--29877825 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
29877773 AAAATAAATA
* **
29877783 TTTCTTTTTTTTTTTGCT
1 TTTCTTTTTTCTTTAACT
29877801 TTTCTTTTTTCTTTAACT
1 TTTCTTTTTTCTTTAACT
29877819 TTT-TTTT
1 TTTCTTTT
29877826 CCCTTCCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTCTTTTTTCTTTAACT
Found at i:29878344 original size:26 final size:25
Alignment explanation
Indices: 29878310--29878369 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
29878300 TATCTATTAT
* *
29878310 TATATTTAATTTTAAAAAATATTTTA
1 TATAATTAATTTT-AAAAATAATTTA
*
29878336 TATAATTAATTTTACAAATAATTTA
1 TATAATTAATTTTAAAAATAATTTA
29878361 TATTAATTA
1 TA-TAATTA
29878370 CTTAAAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 12 0.40
26 18 0.60
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATAATTAATTTTAAAAATAATTTA
Found at i:29879067 original size:22 final size:22
Alignment explanation
Indices: 29879042--29879085 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29879032 ATAAAATGTT
29879042 AAAAATAATTTT-AAACATTAA
1 AAAAATAATTTTCAAACATTAA
* *
29879063 AAAAATATTTTTCTAACATTAA
1 AAAAATAATTTTCAAACATTAA
29879085 A
1 A
29879086 TTTAAAAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAATAATTTTCAAACATTAA
Found at i:29879353 original size:13 final size:14
Alignment explanation
Indices: 29879337--29879366 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29879327 GTAAAATATT
29879337 TTTC-GAAAAATGA
1 TTTCTGAAAAATGA
29879350 TTTCTGAAAAATGA
1 TTTCTGAAAAATGA
29879364 TTT
1 TTT
29879367 ACTTTTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (14 bp):
TTTCTGAAAAATGA
Found at i:29882691 original size:15 final size:15
Alignment explanation
Indices: 29882671--29882701 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29882661 CAAATTAAAC
29882671 ATTAAAATCAAACTT
1 ATTAAAATCAAACTT
29882686 ATTAAAATCAAACTT
1 ATTAAAATCAAACTT
29882701 A
1 A
29882702 AGAAGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (15 bp):
ATTAAAATCAAACTT
Found at i:29883170 original size:16 final size:15
Alignment explanation
Indices: 29883140--29883173 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
29883130 GAAAGTCTTC
*
29883140 TATTTTTATATTAAT
1 TATTTTTATAATAAT
29883155 TATTTTTAATAATAAT
1 TATTTTT-ATAATAAT
29883171 TAT
1 TAT
29883174 GAAATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTTTATAATAAT
Found at i:29894214 original size:36 final size:36
Alignment explanation
Indices: 29894173--29894241 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
29894163 TTGGCAGATA
* **
29894173 CCTTCCTAATCATCGTATCCATTTTCATCATCTATT
1 CCTTCCTAATCAGCGTAGACATTTTCATCATCTATT
29894209 CCTTCCTAATCAGCGTAGACATTTTCATCATCT
1 CCTTCCTAATCAGCGTAGACATTTTCATCATCT
29894242 TCCTTACTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.30, G:0.06, T:0.41
Consensus pattern (36 bp):
CCTTCCTAATCAGCGTAGACATTTTCATCATCTATT
Found at i:29895986 original size:49 final size:48
Alignment explanation
Indices: 29895900--29896138 Score: 264
Period size: 49 Copynumber: 4.8 Consensus size: 48
29895890 GTAGCCGAAG
*
29895900 CTATCTGGTA-AGCATAGTAGCCTGCACTTAGTACTACACATTCGACCAA
1 CTATCTGGTACA-CGTAGTAGCCTGCACTTAGTACTACACATT-GACCAA
* * *
29895949 TTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA-TTGACC-AA
* * **
29895999 CCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGATTGAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACAT-TGA-CCAA
* * * * * *
29896049 GTTATCAGGTACGCATAGTAGCCTGCACGTAGTACTACACATGCGACCAA
1 -CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACAT-TGACCAA
*
29896099 CAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
29896139 CGTGACCTCA
Statistics
Matches: 157, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
49 73 0.46
50 47 0.30
51 37 0.24
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (48 bp):
CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATTGACCAA
Found at i:29896136 original size:100 final size:99
Alignment explanation
Indices: 29895914--29896145 Score: 324
Period size: 100 Copynumber: 2.3 Consensus size: 99
29895904 CTGGTAAGCA
* * *
29895914 TAGTAGCCTGCACTTAGTACTACACAT-TCGACCAATTATCCGGTACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACATGT-GACCAATTATCAGGTACACATAGTAGCCTGCACGT
* *
29895978 AGTACTACACACGTGACCTAACCATCTGATACACG
65 AGTACTACACACGCGACCTAACAATCTGATACACG
** *
29896013 TAGTAGCCTGCACTTAGTACTACACATGTGATTGAAGTTATCAGGTACGCATAGTAGCCTGCACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCAGGTACACATAGTAGCCTGCACG
* *
29896078 TAGTACTACACATGCGACC-AACAATCTGGTACACG
64 TAGTACTACACACGCGACCTAACAATCTGATACACG
*
29896113 TAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC
29896146 TCACAATAGC
Statistics
Matches: 117, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
99 29 0.25
100 47 0.40
101 41 0.35
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACATAGTAGCCTGCACGTA
GTACTACACACGCGACCTAACAATCTGATACACG
Found at i:29897568 original size:53 final size:54
Alignment explanation
Indices: 29897483--29897588 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 54
29897473 ATTTGCTCAC
29897483 AAGACTAACCAAACCATGTTATCTTTAGACTTATCAGATCTTTATCATAGAGTA
1 AAGACTAACCAAACCATGTTATCTTTAGACTTATCAGATCTTTATCATAGAGTA
29897537 AAGA-TAACCAAACCATGTTATCTTTAGACTTATCAGATCTTTATCATAGAGT
1 AAGACTAACCAAACCATGTTATCTTTAGACTTATCAGATCTTTATCATAGAGT
29897589 TAGTTATCGA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 48 0.92
54 4 0.08
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (54 bp):
AAGACTAACCAAACCATGTTATCTTTAGACTTATCAGATCTTTATCATAGAGTA
Found at i:29899373 original size:26 final size:26
Alignment explanation
Indices: 29899344--29899421 Score: 131
Period size: 26 Copynumber: 3.0 Consensus size: 26
29899334 GCATGCCATA
29899344 TTATCTATGTTGCATTGCATTGGGTT
1 TTATCTATGTTGCATTGCATTGGGTT
* *
29899370 TTATCTATGTTGCATTGCATT-GATA
1 TTATCTATGTTGCATTGCATTGGGTT
29899395 TTATCTATGTTGCATTGCATTGGGTT
1 TTATCTATGTTGCATTGCATTGGGTT
29899421 T
1 T
29899422 AGGTTTGTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
25 23 0.49
26 24 0.51
ACGTcount: A:0.18, C:0.12, G:0.21, T:0.50
Consensus pattern (26 bp):
TTATCTATGTTGCATTGCATTGGGTT
Found at i:29899404 original size:25 final size:25
Alignment explanation
Indices: 29899341--29899416 Score: 125
Period size: 25 Copynumber: 3.0 Consensus size: 25
29899331 TGAGCATGCC
29899341 ATATTATCTATGTTGCATTGCATTGG
1 ATATTATCTATGTTGCATTGCATT-G
* *
29899367 GTTTTATCTATGTTGCATTGCATTG
1 ATATTATCTATGTTGCATTGCATTG
29899392 ATATTATCTATGTTGCATTGCATTG
1 ATATTATCTATGTTGCATTGCATTG
29899417 GGTTTAGGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
25 24 0.52
26 22 0.48
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (25 bp):
ATATTATCTATGTTGCATTGCATTG
Found at i:29902243 original size:24 final size:24
Alignment explanation
Indices: 29902216--29902261 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
29902206 GCATGCCATA
29902216 TTATCTATGTTGCATTGCATTGCT
1 TTATCTATGTTGCATTGCATTGCT
29902240 TTATCTATGTTGCATTGCATTG
1 TTATCTATGTTGCATTGCATTG
29902262 TATGTTGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.50
Consensus pattern (24 bp):
TTATCTATGTTGCATTGCATTGCT
Found at i:29902267 original size:17 final size:17
Alignment explanation
Indices: 29902245--29902278 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29902235 TTGCTTTATC
29902245 TATGTTGCATTGCATTG
1 TATGTTGCATTGCATTG
29902262 TATGTTGCATTGCATTG
1 TATGTTGCATTGCATTG
29902279 CTTTTGGGTT
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:0.18, C:0.12, G:0.24, T:0.47
Consensus pattern (17 bp):
TATGTTGCATTGCATTG
Found at i:29905085 original size:13 final size:13
Alignment explanation
Indices: 29905067--29905092 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29905057 TTAGTATGCC
29905067 GTTCTTTTTTTTT
1 GTTCTTTTTTTTT
29905080 GTTCTTTTTTTTT
1 GTTCTTTTTTTTT
29905093 ATGAAACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (13 bp):
GTTCTTTTTTTTT
Found at i:29909311 original size:18 final size:18
Alignment explanation
Indices: 29909288--29909325 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
29909278 CTATGCTAAC
29909288 ACAACTACTATTAAACAA
1 ACAACTACTATTAAACAA
*
29909306 ACAACTGCTATTAAACAA
1 ACAACTACTATTAAACAA
29909324 AC
1 AC
29909326 TATGTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.24, G:0.03, T:0.21
Consensus pattern (18 bp):
ACAACTACTATTAAACAA
Found at i:29909560 original size:17 final size:17
Alignment explanation
Indices: 29909538--29909572 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
29909528 TGAAGCCTCC
29909538 AGTAGTATCCTATTCCT
1 AGTAGTATCCTATTCCT
29909555 AGTAGTATCCTATTCCT
1 AGTAGTATCCTATTCCT
29909572 A
1 A
29909573 TGTGCATAAC
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:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (17 bp):
AGTAGTATCCTATTCCT
Found at i:29918858 original size:3 final size:3
Alignment explanation
Indices: 29918850--29918886 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
29918840 TTACATTTAA
* *
29918850 TAT TAT TAT TAC CAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
29918887 GTTTCCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:29921935 original size:3 final size:3
Alignment explanation
Indices: 29921929--29921963 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29921919 ACCATTATTA
29921929 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
29921964 TCTGTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:29928544 original size:22 final size:21
Alignment explanation
Indices: 29928516--29928559 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
29928506 TTTGCACTAC
29928516 TCTTTCCCTTGTATTCTCGAA
1 TCTTTCCCTTGTATTCTCGAA
*
29928537 NTCTTTCCCTTGTGTTCTCGAA
1 -TCTTTCCCTTGTATTCTCGAA
29928559 T
1 T
29928560 TCTCGATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.11, C:0.27, G:0.11, T:0.48
Consensus pattern (21 bp):
TCTTTCCCTTGTATTCTCGAA
Found at i:29932021 original size:18 final size:17
Alignment explanation
Indices: 29931998--29932031 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
29931988 AGTAAATTTA
29931998 GAAAAAGAAGAAGAAATC
1 GAAAAAGAAG-AGAAATC
29932016 GAAAAAGAAGAGAAAT
1 GAAAAAGAAGAGAAAT
29932032 GATGAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.68, C:0.03, G:0.24, T:0.06
Consensus pattern (17 bp):
GAAAAAGAAGAGAAATC
Found at i:29934565 original size:16 final size:15
Alignment explanation
Indices: 29934544--29934583 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
29934534 TCAGTGCTTT
*
29934544 TGTTATATGTATATTA
1 TGTTATATGAATA-TA
29934560 TGTTATATGAATATA
1 TGTTATATGAATATA
29934575 TGTATATAT
1 TGT-TATAT
29934584 ATCAATCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
TGTTATATGAATATA
Found at i:29936174 original size:7 final size:7
Alignment explanation
Indices: 29936162--29936227 Score: 64
Period size: 7 Copynumber: 9.0 Consensus size: 7
29936152 ACCTTATTTT
29936162 TATATTA
1 TATATTA
29936169 TATATTA
1 TATATTA
29936176 TATAATTA
1 TAT-ATTA
*
29936184 TTTTATTA
1 -TATATTA
29936192 TATATTA
1 TATATTA
29936199 TTTATATTA
1 --TATATTA
29936208 T-TATTA
1 TATATTA
29936214 T-TCATTA
1 TAT-ATTA
29936221 TATATTA
1 TATATTA
29936228 CTTTTCACAA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
6 7 0.14
7 26 0.51
8 9 0.18
9 9 0.18
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (7 bp):
TATATTA
Found at i:29936176 original size:18 final size:17
Alignment explanation
Indices: 29936105--29936408 Score: 68
Period size: 16 Copynumber: 17.5 Consensus size: 17
29936095 AATCTAACCC
*
29936105 TATTATTATA-TATATAT
1 TATTTTTATATTAT-TAT
*
29936122 AATTTTT-TATTATTAT
1 TATTTTTATATTATTAT
29936138 T-TGTTTTAT-TT-TTAACCT
1 TAT-TTTTATATTATT-A--T
29936156 TATTTTTATATTATATAT
1 TATTTTTATATTAT-TAT
* *
29936174 TATATAATTATTTTATTAT
1 TAT-T-TTTATATTATTAT
29936193 ATATTATTTATATTATTAT
1 -TATT-TTTATATTATTAT
*
29936212 TATTCATTATA-TATTACT
1 TATT-TTTATATTATTA-T
*** * *
29936230 T-TTCACAAAATATTAT
1 TATTTTTATATTATTAT
* *
29936246 TA-TTTTACATTGTTAT
1 TATTTTTATATTATTAT
*
29936262 TCA--TATATCATTATTA-
1 T-ATTTTTAT-ATTATTAT
29936278 TATTTTTACT-TGTATTA-
1 TATTTTTA-TAT-TATTAT
* *
29936295 TATATTTAT-TAATTAT
1 TATTTTTATATTATTAT
* *
29936311 T-TATATATATTATATAT
1 TATTTTTATATTAT-TAT
29936328 TATTTTTACATATATACTT-T
1 TATTTTT--ATAT-TA-TTAT
* * *
29936348 CATATTGTATATTATAAT
1 TAT-TTTTATATTATTAT
*
29936366 TA-TTTTATATTA-TGT
1 TATTTTTATATTATTAT
*
29936381 TATTTTTATACTATTAT
1 TATTTTTATATTATTAT
29936398 ATATATTTTAT
1 -TAT-TTTTAT
29936409 CTATATATTA
Statistics
Matches: 213, Mismatches: 38, Indels: 70
0.66 0.12 0.22
Matches are distributed among these distances:
15 17 0.08
16 54 0.25
17 50 0.23
18 34 0.16
19 30 0.14
20 20 0.09
21 7 0.03
22 1 0.00
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (17 bp):
TATTTTTATATTATTAT
Found at i:29936190 original size:23 final size:25
Alignment explanation
Indices: 29936156--29936215 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 25
29936146 TTTTTAACCT
*
29936156 TATTTTTA-TATTATATATTATATA
1 TATTATTATTATTATATATTATATA
*
29936180 -ATTATT-TTATTATATATTATTTA
1 TATTATTATTATTATATATTATATA
29936203 TATTATTATTATT
1 TATTATTATTATT
29936216 CATTATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 20 0.65
24 6 0.19
25 5 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTATTATTATTATATATTATATA
Found at i:29936192 original size:16 final size:15
Alignment explanation
Indices: 29936162--29936232 Score: 76
Period size: 16 Copynumber: 4.7 Consensus size: 15
29936152 ACCTTATTTT
*
29936162 TATATTA-TATATTA
1 TATATTATTTTATTA
29936176 TATAATTATTTTATTA
1 TAT-ATTATTTTATTA
29936192 TATATTATTTATATTA
1 TATATTATTT-TATTA
*
29936208 T-TATTA-TTCATTA
1 TATATTATTTTATTA
29936221 TATATTACTTTT
1 TATATTA-TTTT
29936233 CACAAAATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
13 5 0.10
14 10 0.21
15 16 0.33
16 17 0.35
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTATTTTATTA
Found at i:29936195 original size:25 final size:26
Alignment explanation
Indices: 29936161--29936225 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 26
29936151 AACCTTATTT
29936161 TTATATTATATATTATATAATTATTTTA
1 TTATA-TATAT-TTATATAATTATTTTA
*
29936189 TTATATATTATTTATATTATTATTATTCA
1 TTATATA-TATTTATATAATTATT-TT-A
29936218 TTATATAT
1 TTATATAT
29936226 TACTTTTCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 14 0.42
28 11 0.33
29 8 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TTATATATATTTATATAATTATTTTA
Found at i:29936305 original size:28 final size:28
Alignment explanation
Indices: 29936240--29936328 Score: 76
Period size: 28 Copynumber: 3.0 Consensus size: 28
29936230 TTTCACAAAA
29936240 TATTAT-TATTTTACATTGTTATTCATATATCAT
1 TATTATAT-TTTTAC-TTG-TATT-ATATAT--T
29936273 TATTATATTTTTACTTGTATTATATATT
1 TATTATATTTTTACTTGTATTATATATT
*
29936301 TATTA-ATTATTTA-TATATATTATATATT
1 TATTATATT-TTTACT-TGTATTATATATT
29936329 ATTTTTACAT
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
27 4 0.08
28 22 0.42
30 6 0.12
31 4 0.08
32 3 0.06
33 12 0.23
34 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (28 bp):
TATTATATTTTTACTTGTATTATATATT
Found at i:29936310 original size:32 final size:33
Alignment explanation
Indices: 29936240--29936299 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
29936230 TTTCACAAAA
29936240 TATTAT-TATTTTACATTGTTATTCATATATCAT
1 TATTATAT-TTTTACATTGTTATTCATATATCAT
29936273 TATTATATTTTTAC-TTG-TATT-ATATAT
1 TATTATATTTTTACATTGTTATTCATATAT
29936300 TTATTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 6 0.23
31 4 0.15
32 3 0.12
33 12 0.46
34 1 0.04
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (33 bp):
TATTATATTTTTACATTGTTATTCATATATCAT
Found at i:29936311 original size:11 final size:12
Alignment explanation
Indices: 29936290--29936330 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
29936280 TTTTTACTTG
29936290 TATTATA-TATT
1 TATTATATTATT
29936301 TATTA-ATTATT
1 TATTATATTATT
*
29936312 TATATATATTATA
1 TAT-TATATTATT
29936325 TATTAT
1 TATTAT
29936331 TTTTACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 1 0.04
11 12 0.46
12 5 0.19
13 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATATTATT
Found at i:29936587 original size:21 final size:23
Alignment explanation
Indices: 29936562--29936620 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
29936552 ATCATTAATT
*
29936562 ACTTATTTTATAT-TATTCTA-A
1 ACTTATTTTATATATATTATATA
29936583 ACTTATATTTATATATATTATATA
1 ACTTAT-TTTATATATATTATATA
29936607 A-TTATTTTAT-TATA
1 ACTTATTTTATATATA
29936621 AATATAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 10 0.29
22 12 0.35
23 10 0.29
24 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (23 bp):
ACTTATTTTATATATATTATATA
Found at i:29936716 original size:18 final size:19
Alignment explanation
Indices: 29936688--29936730 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
29936678 TTTTTTATTA
29936688 TATATACAATTATTATTCT
1 TATATACAATTATTATTCT
* * *
29936707 TTTATA-AATTTTTGTTCT
1 TATATACAATTATTATTCT
29936725 TATATA
1 TATATA
29936731 TTATATATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (19 bp):
TATATACAATTATTATTCT
Found at i:29948938 original size:205 final size:205
Alignment explanation
Indices: 29948563--29949320 Score: 1078
Period size: 205 Copynumber: 3.7 Consensus size: 205
29948553 GCAGATCTGG
* *
29948563 CTGAAGTAGATCCAATATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
* * *
29948628 ATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGCCATCTCTGTATTATCAGA
66 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
* *
29948693 GAACAAATCGAAGTCTGGCA-CTCCATATTCGATGGAGGGCAGACACATAGCAGATCTCACCTTC
131 GAACAAATCGAAATCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTCACCTTC
29948757 AGATGATTTCA
196 AGATGATTT-A
* * * * *
29948768 TTGAAGCAGATCCAAGATGATTTGGCATCCTTGTACTTACAAGGAACAAATCAAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
* *
29948833 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAATATGATTTGGCATCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
*
29948898 GAACAAATCGAAATCTGGCATCTCCACT-TT-GACAGAGGGCAGACACATAGCAGATC-CAACCT
131 GAACAAATCGAAATCTGGCATCTCCA-TATTCGACGGAGGGCAGACACATAGCAGATCTC-ACCT
29948960 TCAGATGATTATA
194 TCAGATGATT-TA
* * * *
29948973 CTGAAGTAGATCCAAGATGGTTTGGCATCCTTGTGCTTAGAAAGAGCAAATTGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
* * * *
29949038 ATTTGGCTTTCACATGCTTAC-ATTGAAGCAAGTCTAAAATGATTTGGCATCTCTGTATTGTTAG
66 ATTTGGCTTTCACGTGCTTACGA-TGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * * *
29949102 AGAACAAATC-AAAGTTTAGCGTCTTCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCT
130 AGAACAAATCGAAA-TCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTCACCT
*
29949166 TCAGATGATTAGA
194 TCAGATGATT-TA
* * * *
29949179 CTGAAGCAGATCTAGGATGGTTTGGTATCCTTGTGCTTACAAGGAGTAAATCGAAGACATAGCTG
1 CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
* * * *
29949244 ATTTAGTTTTCACGTGCTTACGCTGGAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
29949309 GAACAAATCGAA
131 GAACAAATCGAA
29949321 GAAGCAAATT
Statistics
Matches: 490, Mismatches: 52, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
204 6 0.01
205 310 0.63
206 171 0.35
207 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (205 bp):
CTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTG
ATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGA
GAACAAATCGAAATCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTCACCTTC
AGATGATTTA
Found at i:29950971 original size:18 final size:19
Alignment explanation
Indices: 29950922--29950995 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 19
29950912 TAACCTTATT
* *
29950922 TTTATATTATATATATTACA
1 TTTATATTATTTTTATT-CA
*
29950942 TAATTATTTTATTTTTATT-A
1 T--TTATATTATTTTTATTCA
*
29950962 TTTATATTATTATTATTCA
1 TTTATATTATTTTTATTCA
29950981 TTATATATTACTTTT
1 TT-TATATTA-TTTT
29950996 CACAAAATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
18 14 0.33
19 3 0.07
20 10 0.23
21 3 0.07
22 13 0.30
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATATTATTTTTATTCA
Done.