Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 128 of 250
Found at i:41303788 original size:25 final size:25
Alignment explanation
Indices: 41303760--41303853 Score: 81
Period size: 25 Copynumber: 3.8 Consensus size: 25
41303750 CTCGTATAAA
41303760 CTTATCGATTCTCAGCTCGTGAGAG
1 CTTATCGATTCTCAGCTCGTGAGAG
* *
41303785 CTTA-CTAATTCTCAGTTCGT-ATGAG
1 CTTATC-GATTCTCAGCTCGTGA-GAG
41303810 CTTAT-GATT-TACAGCTCGTGAGAG
1 CTTATCGATTCT-CAGCTCGTGAGAG
* *
41303834 CATACCGATTCAT-AGCTCGT
1 CTTATCGATTC-TCAGCTCGT
41303854 ATGAGCATAC
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
23 1 0.02
24 18 0.33
25 35 0.64
27 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (25 bp):
CTTATCGATTCTCAGCTCGTGAGAG
Found at i:41303854 original size:49 final size:50
Alignment explanation
Indices: 41303747--41303859 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 50
41303737 GGACACACCA
* * * *
41303747 CAGCTCGTATAAACTTATCGATTCTCAGCTCGTGAGAGCTTACTAATTCT
1 CAGCTCGTATGAGCTTATCGATTCTCAGCTCGTGAGAGCATACCAATTCT
* *
41303797 CAGTTCGTATGAGCTTAT-GATT-TACAGCTCGTGAGAGCATACCGATTCAT
1 CAGCTCGTATGAGCTTATCGATTCT-CAGCTCGTGAGAGCATACCAATTC-T
41303847 -AGCTCGTATGAGC
1 CAGCTCGTATGAGC
41303860 ATACATGTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
48 1 0.02
49 37 0.69
50 16 0.30
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (50 bp):
CAGCTCGTATGAGCTTATCGATTCTCAGCTCGTGAGAGCATACCAATTCT
Found at i:41306373 original size:17 final size:18
Alignment explanation
Indices: 41306351--41306384 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
41306341 AGTTGAATTG
41306351 AAATTGTG-AAATTAAAT
1 AAATTGTGAAAATTAAAT
41306368 AAATTGTGAAAATTAAA
1 AAATTGTGAAAATTAAA
41306385 ATGGAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (18 bp):
AAATTGTGAAAATTAAAT
Found at i:41307137 original size:10 final size:10
Alignment explanation
Indices: 41307110--41307162 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
41307100 TTAAATTCTA
41307110 AAAGATAAAT
1 AAAGATAAAT
41307120 ACAA-ATAAAT
1 A-AAGATAAAT
* *
41307130 AAATATAATT
1 AAAGATAAAT
**
41307140 AAAGATACTT
1 AAAGATAAAT
41307150 AAAGATAAAT
1 AAAGATAAAT
41307160 AAA
1 AAA
41307163 ATTAAATCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 2 0.06
10 32 0.89
11 2 0.06
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.25
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:41322448 original size:33 final size:33
Alignment explanation
Indices: 41322408--41322475 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
41322398 AATTAAACTA
41322408 ATTTAATAAAAGAAAACATGAAATTAAAACACT
1 ATTTAATAAAAGAAAACATGAAATTAAAACACT
41322441 ATTTAATAAAAGAAAACATGAAATTAAAACACT
1 ATTTAATAAAAGAAAACATGAAATTAAAACACT
41322474 AT
1 AT
41322476 CTTCTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.25
Consensus pattern (33 bp):
ATTTAATAAAAGAAAACATGAAATTAAAACACT
Found at i:41323413 original size:25 final size:24
Alignment explanation
Indices: 41323335--41323414 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
41323325 TACACCACGG
*
41323335 CTCGTATGAGCTTACCGATTTGTAA
1 CTCGTATGAGCTTACTGATTT-TAA
* * *
41323360 CTTGTGA-GAGCTTA-TCGATTCTCAG
1 CTCGT-ATGAGCTTACT-GATT-TTAA
41323385 CTCGTATGAGCTTACTGATTTATAA
1 CTCGTATGAGCTTACTGATTT-TAA
41323410 CTCGT
1 CTCGT
41323415 TTATTTACAT
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
24 2 0.05
25 37 0.88
26 3 0.07
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (24 bp):
CTCGTATGAGCTTACTGATTTTAA
Found at i:41326359 original size:149 final size:149
Alignment explanation
Indices: 41326147--41326453 Score: 392
Period size: 154 Copynumber: 2.0 Consensus size: 149
41326137 TAGGATAATT
41326147 TTTTTTTTAAAAAAAAGAAAGTTTAGATGTTTAAAAATAAAAATCTATTTTTTTAGTCATTTTAA
1 TTTTTTTTAAAAAAAAGAAAGTTTAGATGTTTAAAAATAAAAATCTATTTTTTTAGTCATTTTAA
* *
41326212 AAGAAA-TTTAAATTTTTTTAAAA-AAA-ATTGA-TTTTTTCAACTATTTCAAAATAAAAGCTTT
66 AAGAAAGTTTAAA--ATTTTAAAACAAAGATTGATTTTTTTCAACTATTTCAAAATAAAAACTTT
*
41326273 GATCTTTAAGAAAA-TTAGTTA
129 GATCTTTAAGAAAAGTT-GTGA
* ** * * *
41326294 TTTTTTTTAAAAAAAAGGGCAAGTTTTTTATTTTTGAAAATAAAAATCTA-TTTTTTAGTGATTT
1 TTTTTTTTAAAAAAAA--GAAAG-TTTAGATGTTTAAAAATAAAAATCTATTTTTTTAGTCATTT
* *
41326358 TAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTTCAACTATTTCAAAATAAAAA
63 TAAAAGAAAGTTTAAAATTTTAAAACAAAG-ATTGA--TTTTTTTCAACTATTTCAAAATAAAAA
41326423 CTTTGATCTTTAAGAAAAGTTGTGA
125 CTTTGATCTTTAAGAAAAGTTGTGA
41326448 TTTTTT
1 TTTTTT
41326454 AGAAGAAAAA
Statistics
Matches: 138, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
147 16 0.12
148 8 0.06
149 28 0.20
150 28 0.20
151 4 0.03
154 52 0.38
155 2 0.01
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (149 bp):
TTTTTTTTAAAAAAAAGAAAGTTTAGATGTTTAAAAATAAAAATCTATTTTTTTAGTCATTTTAA
AAGAAAGTTTAAAATTTTAAAACAAAGATTGATTTTTTTCAACTATTTCAAAATAAAAACTTTGA
TCTTTAAGAAAAGTTGTGA
Found at i:41326463 original size:154 final size:149
Alignment explanation
Indices: 41326180--41326613 Score: 391
Period size: 154 Copynumber: 2.8 Consensus size: 149
41326170 TAGATGTTTA
*
41326180 AAAATAAAAATCTATTTTTTTAGTCATTTTAAAAGAAATTTAAATTTTTTTAAAAAAAATTGATT
1 AAAATAAAAATCTATTTTTTTAGTCATTTTAAAAGAAATTTAAA-TATTTTAAAAAAAATTGATT
* * **
41326245 TTTTCAACTATTTCAAAATAAAAGCTTTGATCTTTAAGAAAATTAGTTATTTTTTTTAAAAAAAA
65 TTTTCAACTATTTCAAAATAAAAACTTTGATCTTTAAGAAAATTAGTGATTTTTTAGAAAAAAAA
41326310 GGGCAAGTTTTTTATTTTTG
130 GGGCAAGTTTTTTATTTTTG
* * *
41326330 AAAATAAAAATCTA-TTTTTTAGTGATTTTAAAGGAAAGTTTAAA-ATTTTAAAACAAAGTTTTG
1 AAAATAAAAATCTATTTTTTTAGTCATTTTAAAAGAAA-TTTAAATATTTTAAAA-AAA--ATTG
41326393 ATTTTTTTTTCAACTATTTCAAAATAAAAACTTTGATCTTTAAGAAAAGTT-GTGATTTTTTAGA
62 A---TTTTTTCAACTATTTCAAAATAAAAACTTTGATCTTTAAGAAAA-TTAGTGATTTTTT---
*
41326457 AGAAAAAAGAGAGAGAGAAAGTTTAGGATTT-TTTTT-
120 AGAAAAAA-A-AG-G-GCAAGTTT----TTTATTTTTG
* * * *
41326493 TAAA-AAAAATATGTTTTTTTAGTCATTTTAAAGGAAAAGTTTAAAT-TTTTAAAATAAAATTTT
1 AAAATAAAAATCTATTTTTTTAGTCATTTTAAAAG-AAA-TTTAAATATTTTAAAA-AAAA--TT
** * * * *
41326556 GATCCTTTTT-AACTATTTCGGAAT-ACAGCTTTGATTTTTAAGAAAAATAGTGATTTTT
61 GAT--TTTTTCAACTATTTCAAAATAAAAACTTTGATCTTTAAGAAAATTAGTGATTTTT
41326614 AAAAGAAAAC
Statistics
Matches: 236, Mismatches: 21, Indels: 43
0.79 0.07 0.14
Matches are distributed among these distances:
148 8 0.03
149 24 0.10
150 20 0.08
151 4 0.02
154 52 0.22
155 2 0.01
157 6 0.03
158 1 0.00
159 2 0.01
160 2 0.01
161 36 0.15
162 19 0.08
163 27 0.11
164 30 0.13
165 3 0.01
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (149 bp):
AAAATAAAAATCTATTTTTTTAGTCATTTTAAAAGAAATTTAAATATTTTAAAAAAAATTGATTT
TTTCAACTATTTCAAAATAAAAACTTTGATCTTTAAGAAAATTAGTGATTTTTTAGAAAAAAAAG
GGCAAGTTTTTTATTTTTG
Found at i:41326629 original size:20 final size:20
Alignment explanation
Indices: 41326584--41326641 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
41326574 CGGAATACAG
41326584 CTTTGATTTTT--AAGAAAA
1 CTTTGATTTTTAAAAGAAAA
* *
41326602 ATAGTGATTTTTAAAAGAAAA
1 CT-TTGATTTTTAAAAGAAAA
*
41326623 CTTTGATTTTGAAAA-AAAA
1 CTTTGATTTTTAAAAGAAAA
41326642 AATTGTCCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.03
19 12 0.38
20 11 0.34
21 8 0.25
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (20 bp):
CTTTGATTTTTAAAAGAAAA
Found at i:41328183 original size:4 final size:4
Alignment explanation
Indices: 41328174--41328200 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
41328164 TGCCTAAGAT
41328174 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
41328201 AATGGCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:41332162 original size:47 final size:47
Alignment explanation
Indices: 41332108--41332439 Score: 547
Period size: 47 Copynumber: 7.1 Consensus size: 47
41332098 GATTTTATGA
** * *
41332108 GATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
* *
41332155 GATGAATGTGAACATGCATATATGTGCTAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
* *
41332202 GATGAATCTGAACATGCATATGTGTGATAAGGCCGAATGACCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
41332249 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
*
41332296 GATGAATGTGAACATGCATATGTGTGCTAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
41332343 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
* ** *
41332390 GATGAATGTGAACATGCATATGTGGGATAAGGTAGAATGGCTAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
41332437 GAT
1 GAT
41332440 AAACGTGGAA
Statistics
Matches: 269, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 269 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
Found at i:41332275 original size:141 final size:141
Alignment explanation
Indices: 41332108--41332485 Score: 571
Period size: 141 Copynumber: 2.7 Consensus size: 141
41332098 GATTTTATGA
** * *
41332108 GATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
41332173 TATATGTGCTAAGGCCGAATGGCCAATGTGATGAATCTGAACATGCATATGTGTGATAAGGCCGA
66 TATATGTGCTAAGGCCGAATGGCCAATGTGATGAATCTGAACATGCATATGTGTGATAAGGCCGA
41332238 ATGACCAATGT
131 ATGACCAATGT
41332249 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
* *
41332314 TATGTGTGCTAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGA
66 TATATGTGCTAAGGCCGAATGGCCAATGTGATGAATCTGAACATGCATATGTGTGATAAGGCCGA
*
41332379 ATGGCCAATGT
131 ATGACCAATGT
* ** * * * * *
41332390 GATGAATGTGAACATGCATATGTGGGATAAGGTAGAATGGCTAATGTGATAAACGTGGAA-GTGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGT-GAACATGC
* *
41332454 ATATATGTGGCGAA-GCCGAATGGCTAATGTGA
65 ATATATGT-GCTAAGGCCGAATGGCCAATGTGA
41332486 GATATGTATG
Statistics
Matches: 217, Mismatches: 18, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
141 210 0.97
142 7 0.03
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (141 bp):
GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
TATATGTGCTAAGGCCGAATGGCCAATGTGATGAATCTGAACATGCATATGTGTGATAAGGCCGA
ATGACCAATGT
Found at i:41339698 original size:10 final size:10
Alignment explanation
Indices: 41339669--41339702 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
41339659 CTGAAAAATT
*
41339669 AAAAAAATTAA
1 AAAAAAA-TAC
41339680 AAAAAAATAC
1 AAAAAAATAC
41339690 AAAAAAATAC
1 AAAAAAATAC
41339700 AAA
1 AAA
41339703 GCGGACGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:41341380 original size:13 final size:13
Alignment explanation
Indices: 41341353--41341414 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
41341343 ACACTTAAAT
* *
41341353 TTTTTCAAAGTAC
1 TTTTTAAAAGCAC
*
41341366 TTCTTAAAAGCAC
1 TTTTTAAAAGCAC
* * *
41341379 TTTTTTACAGTAC
1 TTTTTAAAAGCAC
41341392 TTTTTAAAAGCAC
1 TTTTTAAAAGCAC
*
41341405 TTTTCAAAAG
1 TTTTTAAAAG
41341415 TAATGAAGAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (13 bp):
TTTTTAAAAGCAC
Found at i:41341390 original size:26 final size:27
Alignment explanation
Indices: 41341352--41341408 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
41341342 AACACTTAAA
41341352 TTTTTTCAAAGTACTTCTTAAAAGCAC
1 TTTTTTCAAAGTACTTCTTAAAAGCAC
* *
41341379 TTTTTT-ACAGTACTTTTTAAAAGCAC
1 TTTTTTCAAAGTACTTCTTAAAAGCAC
41341405 TTTT
1 TTTT
41341409 CAAAAGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (27 bp):
TTTTTTCAAAGTACTTCTTAAAAGCAC
Found at i:41342663 original size:3 final size:3
Alignment explanation
Indices: 41342655--41342685 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
41342645 TGTGTCCTTT
41342655 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
41342686 CCTATTCTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:41367468 original size:15 final size:15
Alignment explanation
Indices: 41367444--41367478 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41367434 ATTTTTTATT
41367444 TTTA-TTTTAATATA
1 TTTATTTTTAATATA
41367458 TTTATTTTTAATATA
1 TTTATTTTTAATATA
*
41367473 ATTATT
1 TTTATT
41367479 ATTGTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATTTTTAATATA
Found at i:41367474 original size:20 final size:19
Alignment explanation
Indices: 41367438--41367478 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
41367428 TTAGCTATTT
* *
41367438 TTTATTTTTATTTTAATATA
1 TTTATTTTTAATATAAT-TA
41367458 TTTATTTTTAATATAATTA
1 TTTATTTTTAATATAATTA
41367477 TT
1 TT
41367479 ATTGTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTTTTAATATAATTA
Found at i:41374160 original size:10 final size:10
Alignment explanation
Indices: 41374133--41374191 Score: 66
Period size: 10 Copynumber: 5.9 Consensus size: 10
41374123 TTAAATTCTA
41374133 AAAGATAAAT
1 AAAGATAAAT
*
41374143 ACAA-ATAATT
1 A-AAGATAAAT
* *
41374153 AATGATAATT
1 AAAGATAAAT
41374163 AAAGATAAAT
1 AAAGATAAAT
*
41374173 AAGGATAAAT
1 AAAGATAAAT
41374183 AAAGATAAA
1 AAAGATAAA
41374192 AGCTAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
9 1 0.02
10 38 0.93
11 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:41374190 original size:30 final size:30
Alignment explanation
Indices: 41374133--41374190 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
41374123 TTAAATTCTA
* *
41374133 AAAGATAAATACAAATAATTAATGATAATT
1 AAAGATAAATACAAATAAATAAAGATAATT
*
41374163 AAAGATAAATA-AGGATAAATAAAGATAA
1 AAAGATAAATACA-AATAAATAAAGATAA
41374191 AAGCTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (30 bp):
AAAGATAAATACAAATAAATAAAGATAATT
Found at i:41380528 original size:47 final size:45
Alignment explanation
Indices: 41380453--41380542 Score: 117
Period size: 47 Copynumber: 2.0 Consensus size: 45
41380443 TCGGCACGGA
* *
41380453 TACGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC
1 TACGTAAGAGCCAGTATAAGACCATGTCTGGGACATGGCATCGAC
* **
41380498 TTAGCGTAAGAGCCAGTATAAAACCATGTCTGGGATGTGGCATCG
1 -TA-CGTAAGAGCCAGTATAAGACCATGTCTGGGACATGGCATCG
41380543 GCATTATACC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
46 2 0.05
47 36 0.95
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (45 bp):
TACGTAAGAGCCAGTATAAGACCATGTCTGGGACATGGCATCGAC
Found at i:41383125 original size:285 final size:284
Alignment explanation
Indices: 41382616--41383186 Score: 1061
Period size: 285 Copynumber: 2.0 Consensus size: 284
41382606 TTCCTGGAAG
* *
41382616 AGTTCTGAAAGAAGTACATTAGCCAGAGGTTTATAGACTAGAAAAGAAAAGAATTTTTAGAGCCG
1 AGTTCTGAAAGAAGTACATTAGCCAGAGGTTTATAGACCAGAAAAAAAAAGAATTTTTAGAGCCG
*
41382681 AAGCAAGGTCGTAGGACGGTGACTGAGTACGAGCGTGAGTTTGTGAGACTCAGCAAATATGTACG
66 AAGCAAGGTCGTAGGACGGTGACTGAGTACGAACGTGAGTTTGTGAGACTCAGCAAATATGTACG
*
41382746 GGAGTGCGTATCTACAAAATTCATTATGTACAAAAGGTTTGAATATGGTTTGAACGAAGATATTC
131 GGAGTGCGTATCTACAAAATTCATTATGTACAAAAGGTTTGAAGATGGTTTGAACGAAGATATTC
41382811 ATCTATTAGTCGGCATCTTAGAGATAAGAGAATTTATGGTGCTCGTGGAAAGAGCATGTAAGACC
196 ATCTATTAGTCGGCATCTTAGAGATAAGAGAATTTATGGTGCTCGTGGAAAGAGCATGTAAGACC
41382876 AAGGAATTGGCCAAAGAGAAGAAA
261 AAGGAATTGGCCAAAGAGAAGAAA
41382900 AGTTCTGAAAGAAGTACATTAGCCAGAGGTTTATAGACCAGAAAAAAAAAAGAATTTTTAGAGCC
1 AGTTCTGAAAGAAGTACATTAGCCAGAGGTTTATAGACCAG-AAAAAAAAAGAATTTTTAGAGCC
41382965 GAAGCAAGGTCGTAGGACGGTGACTGAGTACGAACGTGAGTTTGTGAGACTCAGCAAATATGTAC
65 GAAGCAAGGTCGTAGGACGGTGACTGAGTACGAACGTGAGTTTGTGAGACTCAGCAAATATGTAC
41383030 GGGAGTGCGTATCTACAAAATTCATTATGTACAAAAGGTTTGAAGATGGTTTGAACGAAGATATT
130 GGGAGTGCGTATCTACAAAATTCATTATGTACAAAAGGTTTGAAGATGGTTTGAACGAAGATATT
* * * *
41383095 CATCTATTAGTTGGCATCTTGGAGATAAGAGAATTTGTGGTGCTTGTGGAAAGAGCATGTAAGAC
195 CATCTATTAGTCGGCATCTTAGAGATAAGAGAATTTATGGTGCTCGTGGAAAGAGCATGTAAGAC
41383160 CAAGGAATTGGCCAAAGAGAAGAAA
260 CAAGGAATTGGCCAAAGAGAAGAAA
41383185 AG
1 AG
41383187 AGCTGACATT
Statistics
Matches: 278, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
284 40 0.14
285 238 0.86
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (284 bp):
AGTTCTGAAAGAAGTACATTAGCCAGAGGTTTATAGACCAGAAAAAAAAAGAATTTTTAGAGCCG
AAGCAAGGTCGTAGGACGGTGACTGAGTACGAACGTGAGTTTGTGAGACTCAGCAAATATGTACG
GGAGTGCGTATCTACAAAATTCATTATGTACAAAAGGTTTGAAGATGGTTTGAACGAAGATATTC
ATCTATTAGTCGGCATCTTAGAGATAAGAGAATTTATGGTGCTCGTGGAAAGAGCATGTAAGACC
AAGGAATTGGCCAAAGAGAAGAAA
Found at i:41389229 original size:50 final size:49
Alignment explanation
Indices: 41389120--41389298 Score: 187
Period size: 47 Copynumber: 3.8 Consensus size: 49
41389110 CATCGACCTA
*
41389120 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACAT-G-GT--G
1 AGCCAATGTAAGACCATGTCTGGGACATGGCATCGGC-ACATAGCGTGAG
* * *
41389164 TGCCAATATAAGACCATGTCTAGGACATGGCATCGGCACGAATA-CGTGAG
1 AGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCAC--ATAGCGTGAG
* * *
41389214 AGTCAATGTAAGACCATGTCTGGGACATGGCAT-TG-ACTTAGCGTGAG
1 AGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCACATAGCGTGAG
* *
41389261 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCA
1 AGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCA
41389299 TTATACCCTA
Statistics
Matches: 110, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
44 10 0.09
45 15 0.14
46 10 0.09
47 38 0.35
48 5 0.05
49 2 0.02
50 30 0.27
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (49 bp):
AGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCACATAGCGTGAG
Found at i:41392960 original size:42 final size:42
Alignment explanation
Indices: 41392895--41393029 Score: 146
Period size: 42 Copynumber: 3.2 Consensus size: 42
41392885 GGCTACACAA
* * * * *
41392895 AAGCACATAAGTGTTAAATAGAAACCTGTAAGGGTTGAACGG
1 AAGCTCATAAGAGCTAAATAGAAACCTGTAAGGGTTAAACTG
* **
41392937 AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAACTG
1 AAGCTCATAAGAGCTAAATAGAAACCTGTAAGGGTTAAACTG
* * *
41392979 AAGCTCAAAAGAGCTGAATTGAAACCTAG-AAGGGTTAAACTG
1 AAGCTCATAAGAGCTAAATAGAAACCT-GTAAGGGTTAAACTG
*
41393021 AAACTCATA
1 AAGCTCATA
41393030 TGAGTTAACT
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (42 bp):
AAGCTCATAAGAGCTAAATAGAAACCTGTAAGGGTTAAACTG
Found at i:41392975 original size:21 final size:21
Alignment explanation
Indices: 41392900--41392976 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 21
41392890 CACAAAAGCA
* *
41392900 CATAAGTGTTAAATAGAAACC
1 CATAAGGGTTAAACAGAAACC
** * * * *
41392921 TGTAAGGGTTGAACGGAAGCT
1 CATAAGGGTTAAACAGAAACC
* *
41392942 CATAAGAGCTAAACAGAAACC
1 CATAAGGGTTAAACAGAAACC
41392963 CATAAGGGTTAAAC
1 CATAAGGGTTAAAC
41392977 TGAAGCTCAA
Statistics
Matches: 38, Mismatches: 18, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (21 bp):
CATAAGGGTTAAACAGAAACC
Found at i:41393036 original size:21 final size:21
Alignment explanation
Indices: 41393012--41393058 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
41393002 ACCTAGAAGG
41393012 GTTAAACTGAAACTCAT-ATGA
1 GTTAAACTGAAACTCATGA-GA
*
41393033 GTT-AACTGAAGCTCATGAGA
1 GTTAAACTGAAACTCATGAGA
41393053 GTTAAA
1 GTTAAA
41393059 TGGAAAGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (21 bp):
GTTAAACTGAAACTCATGAGA
Found at i:41400305 original size:23 final size:21
Alignment explanation
Indices: 41400246--41400310 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 21
41400236 ATATAAGTCC
41400246 AAAAAATGAAATAAAAACAACT
1 AAAAAAT-AAATAAAAACAACT
41400268 AAAATAA-AAATAAAAGCACAACT
1 AAAA-AATAAATAAAA--ACAACT
*
41400291 AAAAAATAAAAAAAAACAAC
1 AAAAAATAAATAAAAACAAC
41400311 GATTAGAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 13 0.34
22 6 0.16
23 19 0.50
ACGTcount: A:0.75, C:0.11, G:0.03, T:0.11
Consensus pattern (21 bp):
AAAAAATAAATAAAAACAACT
Found at i:41400786 original size:8 final size:8
Alignment explanation
Indices: 41400775--41400799 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
41400765 TAAATTTTGG
41400775 AATAATAA
1 AATAATAA
41400783 AATAATAA
1 AATAATAA
41400791 AATAATAA
1 AATAATAA
41400799 A
1 A
41400800 GATGACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAATAA
Found at i:41404184 original size:91 final size:91
Alignment explanation
Indices: 41404014--41404206 Score: 217
Period size: 91 Copynumber: 2.1 Consensus size: 91
41404004 TTAATTTCAG
** * **
41404014 GTACCATAATAATACACGGATTGATAGTTCAAGTACCACATTGAATATTGTCAAGGTATAAGTAC
1 GTACCA-AATAATACACAAATTGATAGTTCAAGTACCACATTAAATATTGTCAAAATATAAGTAC
*
41404079 CATATTGAACATTTTATAAAAATACAA
65 CATATTAAACATTTTATAAAAATACAA
* * * * * *
41404106 GTACTAAATAATACACAAATTGATTGTTTAAGTGCCACATTAAATATTTTTAAAATATAAAG-AC
1 GTACCAAATAATACACAAATTGATAGTTCAAGTACCACATTAAATATTGTCAAAATAT-AAGTAC
* * * *
41404170 TATATTAAAGATTTTATAAAATTACAG
65 CATATTAAACATTTTATAAAAATACAA
41404197 GTACCAAATA
1 GTACCAAATA
41404207 TTAAGAGAAA
Statistics
Matches: 83, Mismatches: 17, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
91 75 0.90
92 8 0.10
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.33
Consensus pattern (91 bp):
GTACCAAATAATACACAAATTGATAGTTCAAGTACCACATTAAATATTGTCAAAATATAAGTACC
ATATTAAACATTTTATAAAAATACAA
Found at i:41404540 original size:15 final size:15
Alignment explanation
Indices: 41404520--41404551 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41404510 ATTTTCTCGA
*
41404520 ATCGAGTTGAGTGAG
1 ATCGAGTCGAGTGAG
41404535 ATCGAGTCGAGTGAG
1 ATCGAGTCGAGTGAG
41404550 AT
1 AT
41404552 GAAATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.09, G:0.38, T:0.25
Consensus pattern (15 bp):
ATCGAGTCGAGTGAG
Found at i:41405457 original size:38 final size:37
Alignment explanation
Indices: 41405370--41405453 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 37
41405360 TTTAATTAAC
*
41405370 TTTTAAAAATTATAAAAATATTTTTTTAAAATTAAAA
1 TTTTAAAAATTATAAAAATATTATTTTAAAATTAAAA
*
41405407 TTATTAAAAATTATAAAAA-A-TATTTTAATATTTTAAAA
1 TT-TTAAAAATTATAAAAATATTATTTTAA-A-ATTAAAA
41405445 TTTTAAAAA
1 TTTTAAAAA
41405454 ATTAATTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
36 7 0.17
37 11 0.26
38 24 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (37 bp):
TTTTAAAAATTATAAAAATATTATTTTAAAATTAAAA
Found at i:41405462 original size:28 final size:29
Alignment explanation
Indices: 41405399--41405463 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
41405389 ATTTTTTTAA
41405399 AATTAAAATTATTAAAAATTATAAAAAAT
1 AATTAAAATTATTAAAAATTATAAAAAAT
* * *
41405428 ATTTTAATATT-TT-AAAATTTTAAAAAATT
1 A-ATTAAAATTATTAAAAATTATAAAAAA-T
41405457 AATTAAA
1 AATTAAA
41405464 TGTTAACATG
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
28 17 0.59
29 5 0.17
30 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AATTAAAATTATTAAAAATTATAAAAAAT
Found at i:41405745 original size:66 final size:66
Alignment explanation
Indices: 41405673--41405799 Score: 200
Period size: 66 Copynumber: 1.9 Consensus size: 66
41405663 TTTAATCTCT
* ** *
41405673 ATACTTAATTTCTAACGTAATTTGGTTCATTCATTTTATGCTGTTATTAATTAGTCCAAAAAGTA
1 ATACTTAATTTCTAACGTAATTTGGTTCATACATTTTATAATGTTATCAATTAGTCCAAAAAGTA
41405738 A
66 A
* *
41405739 ATACTTAATTTCTAATGTAATTTGGTTCATACATTTTGTAATGTTATCAATTAGTCCAAAA
1 ATACTTAATTTCTAACGTAATTTGGTTCATACATTTTATAATGTTATCAATTAGTCCAAAA
41405800 GTTATTATCA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (66 bp):
ATACTTAATTTCTAACGTAATTTGGTTCATACATTTTATAATGTTATCAATTAGTCCAAAAAGTA
A
Found at i:41423243 original size:18 final size:17
Alignment explanation
Indices: 41423222--41423263 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
41423212 AAAAATAGAT
41423222 TTATTTATATTTAATATA
1 TTATTTATATTTAA-ATA
41423240 TTATTT-TATTTAAATA
1 TTATTTATATTTAAATA
*
41423256 TAATTTAT
1 TTATTTAT
41423264 TATGTTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 8 0.36
18 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTTATATTTAAATA
Found at i:41423247 original size:23 final size:24
Alignment explanation
Indices: 41423221--41423271 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
41423211 TAAAAATAGA
* *
41423221 TTTATTTATATTTAATATATTAT-
1 TTTATTTAAATATAATATATTATG
*
41423244 TTTATTTAAATATAATTTATTATG
1 TTTATTTAAATATAATATATTATG
41423268 TTTA
1 TTTA
41423272 AGTTTAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTATTTAAATATAATATATTATG
Found at i:41423685 original size:31 final size:31
Alignment explanation
Indices: 41423650--41423709 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
41423640 AGTCACTAAT
* * *
41423650 GTTTTAGATTATTTGTATTTTGGTCACTCCC
1 GTTTTAGATCATTTCTATTTTGATCACTCCC
*
41423681 GTTTTATATCATTTCTATTTTGATCACTC
1 GTTTTAGATCATTTCTATTTTGATCACTC
41423710 TTCGTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.18, C:0.17, G:0.12, T:0.53
Consensus pattern (31 bp):
GTTTTAGATCATTTCTATTTTGATCACTCCC
Found at i:41428405 original size:26 final size:26
Alignment explanation
Indices: 41428374--41428430 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
41428364 CATTGAAGTC
**
41428374 AAACTCAAGTTTCAAATTGAAAAAAA
1 AAACTCAAGTACCAAATTGAAAAAAA
* *
41428400 AAACTCAAGTACCAAATTGAATATAA
1 AAACTCAAGTACCAAATTGAAAAAAA
41428426 AAACT
1 AAACT
41428431 ACACTTAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.56, C:0.14, G:0.07, T:0.23
Consensus pattern (26 bp):
AAACTCAAGTACCAAATTGAAAAAAA
Found at i:41429478 original size:21 final size:22
Alignment explanation
Indices: 41429448--41429492 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
41429438 ATCCATAAAT
*
41429448 AATTTCAAAAAATATAATAGTA
1 AATTTCAAAAAATATAACAGTA
*
41429470 AATTT-AAAATATATAACAGTA
1 AATTTCAAAAAATATAACAGTA
41429491 AA
1 AA
41429493 AAGATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (22 bp):
AATTTCAAAAAATATAACAGTA
Found at i:41441803 original size:18 final size:20
Alignment explanation
Indices: 41441766--41441807 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
41441756 AAAATTATGG
41441766 AAAAGTATAAATATTATTTA
1 AAAAGTATAAATATTATTTA
*
41441786 AAAATTATAAA-A-TATTTA
1 AAAAGTATAAATATTATTTA
41441804 AAAA
1 AAAA
41441808 AATGATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
20 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAGTATAAATATTATTTA
Found at i:41444332 original size:23 final size:23
Alignment explanation
Indices: 41444306--41444352 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
41444296 ATAGCCGGCT
41444306 TTTGAATCCACCATTGATAGGTA
1 TTTGAATCCACCATTGATAGGTA
41444329 TTTGAATCCACCATTGATAGGTA
1 TTTGAATCCACCATTGATAGGTA
41444352 T
1 T
41444353 CAACCAACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (23 bp):
TTTGAATCCACCATTGATAGGTA
Found at i:41445158 original size:11 final size:11
Alignment explanation
Indices: 41445119--41445157 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
41445109 CACAATAGTC
41445119 CTCTCACAATT
1 CTCTCACAATT
41445130 CTCTCACAATT
1 CTCTCACAATT
41445141 CTCTCA-AATTT
1 CTCTCACAA-TT
41445152 CTCTCA
1 CTCTCA
41445158 ATTTTTGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 2 0.07
11 25 0.93
ACGTcount: A:0.26, C:0.36, G:0.00, T:0.38
Consensus pattern (11 bp):
CTCTCACAATT
Found at i:41445175 original size:21 final size:21
Alignment explanation
Indices: 41445151--41445190 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
41445141 CTCTCAAATT
41445151 TCTC-TCAATTTTTGTCAAAGC
1 TCTCTTCAATTTTTG-CAAAGC
*
41445172 TCTCTTTAATTTTTGCAAA
1 TCTCTTCAATTTTTGCAAA
41445191 ATAGCTCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (21 bp):
TCTCTTCAATTTTTGCAAAGC
Found at i:41446349 original size:7 final size:7
Alignment explanation
Indices: 41446337--41446368 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
41446327 AGTCGTTTCA
41446337 TATTTAG
1 TATTTAG
41446344 TATTTAG
1 TATTTAG
*
41446351 TATTTAT
1 TATTTAG
41446358 TATTTAG
1 TATTTAG
41446365 TATT
1 TATT
41446369 ACGTATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (7 bp):
TATTTAG
Found at i:41447295 original size:21 final size:21
Alignment explanation
Indices: 41447271--41447328 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
41447261 CAACACCCAT
* *
41447271 AACCAGATCCCCTGCCAGAGG
1 AACCAAATCCCCTGCCAGAGC
*
41447292 AACCACAATCCCC-ACCAGAGC
1 AACCA-AATCCCCTGCCAGAGC
41447313 AACCACAA-CCCCTGCC
1 AACCA-AATCCCCTGCC
41447329 GAAAGCTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 21 0.68
22 6 0.19
ACGTcount: A:0.33, C:0.47, G:0.14, T:0.07
Consensus pattern (21 bp):
AACCAAATCCCCTGCCAGAGC
Found at i:41447647 original size:132 final size:131
Alignment explanation
Indices: 41447434--41447948 Score: 870
Period size: 132 Copynumber: 3.9 Consensus size: 131
41447424 TTTGTAGAAT
* * *
41447434 TTTTTTATATAGTTTC-ATATAATAAAATAAAAAATTATTTTTAATATTTTAATTATACTTTACT
1 TTTTTTATATAGTTTCAAT-TAATAAAAT-AAAAGTTGTTTTTAATATTTTAATTGTACTTTACT
41447498 TTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATT
64 TTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATT
41447563 TAA
129 TAA
*
41447566 TTTTTTTTATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC-TT
* *
41447631 TTTTTAATTTTATTAAAATAAATGTTCTGTTAAATTAAGCAATATTTTTTATTATTTTTATATTT
65 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATTT
41447696 AA
130 AA
*
41447698 TTTTTTATATAGTTTCAGTTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC--T
*
41447763 TTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTATTTTTATATT
64 TTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATT
41447828 TAA
129 TAA
41447831 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
* * * *
41447896 TTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGTCAATAATTTTTATTA
66 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTA
41447949 AAATAAATGT
Statistics
Matches: 364, Mismatches: 16, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
131 83 0.23
132 151 0.41
133 130 0.36
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (131 bp):
TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATTTA
A
Found at i:41447882 original size:265 final size:263
Alignment explanation
Indices: 41447434--41447948 Score: 883
Period size: 265 Copynumber: 2.0 Consensus size: 263
41447424 TTTGTAGAAT
41447434 TTTTTTATATAGTTTCATATAATAAAATAAAAAATTATTTTTAATATTTTAATTATACTTTACTT
1 TTTTTTATATAGTTTCATATAATAAAATAAAAAATTATTTTTAATATTTTAATTATACTTTACTT
*
41447499 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATTT
66 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTATTTTTATATTT
*
41447564 AATTTTTTTTATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACT
131 AATTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC-
* *
41447629 TTTTTTTAATTTTATTAAAATAAATGTTCTGTTAAATTAAG-CAATATTTTTTATTATTTTTATA
195 TTTTTTTAATTTTAATAAAATAAATGTTCTGTTAAATT-AGTCAATAATTTTTATTATTTTTATA
41447693 TTTAA
259 TTTAA
* * *
41447698 TTTTTTATATAGTTTCAGT-TAATAAAAT-AAAAGTTGTTTTTAATATTTTAATTGTACTTTACT
1 TTTTTTATATAGTTTCA-TATAATAAAATAAAAAATTATTTTTAATATTTTAATTATACTTTAC-
41447761 TTTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTATTTTTATA
64 -TTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTATTTTTATA
41447826 TTTAATTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTT
128 TTTAATTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTT
* *
41447891 ACTTTTTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGTCAATAATTTTTATTA
193 ACTTTTTTTAATTTTAATAAAATAAATGTTCTGTTAAATTAGTCAATAATTTTTATTA
41447949 AAATAAATGT
Statistics
Matches: 238, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
263 33 0.14
264 75 0.32
265 130 0.55
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (263 bp):
TTTTTTATATAGTTTCATATAATAAAATAAAAAATTATTTTTAATATTTTAATTATACTTTACTT
TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTATTTTTATATTT
AATTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACT
TTTTTTAATTTTAATAAAATAAATGTTCTGTTAAATTAGTCAATAATTTTTATTATTTTTATATT
TAA
Found at i:41447977 original size:39 final size:38
Alignment explanation
Indices: 41447902--41447986 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
41447892 CTTTTTTTAA
* * *
41447902 TTTTAATACAATAAATGTTCTTTTAAATTAGTCAATAAT
1 TTTTAATAAAATAAATGTTATTTTAAATTAGACAAT-AT
* *
41447941 TTTTATTAAAATAAATGTTATTTTGAA-TACGACAATAT
1 TTTTAATAAAATAAATGTTATTTTAAATTA-GACAATAT
41447979 TTTTAATA
1 TTTTAATA
41447987 TTTTCAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
38 11 0.28
39 28 0.72
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (38 bp):
TTTTAATAAAATAAATGTTATTTTAAATTAGACAATAT
Found at i:41447988 original size:9 final size:9
Alignment explanation
Indices: 41447974--41448004 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41447964 TGAATACGAC
41447974 AATATTTTT
1 AATATTTTT
*
41447983 AATATTTTC
1 AATATTTTT
41447992 AATATTTTT
1 AATATTTTT
41448001 AATA
1 AATA
41448005 AAACATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTT
Found at i:41450138 original size:19 final size:20
Alignment explanation
Indices: 41450110--41450148 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
41450100 AAAAAACTTT
41450110 CAAAATATAAT-TTTGTTAAA
1 CAAAATATAATATTT-TTAAA
41450130 CAAAA-ATAATATTTTTAAA
1 CAAAATATAATATTTTTAAA
41450149 TAATAAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (20 bp):
CAAAATATAATATTTTTAAA
Found at i:41450763 original size:22 final size:21
Alignment explanation
Indices: 41450738--41450788 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
41450728 CACAATAGTC
41450738 CTCTCATAATTCTCTCAAAATT
1 CTCTCA-AATTCTCTCAAAATT
*
41450760 CTCTCCAAATTCTCTCAAATTT
1 CTCT-CAAATTCTCTCAAAATT
41450782 CTCTCAA
1 CTCTCAA
41450789 TTTTTGTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 3 0.11
22 22 0.81
23 2 0.07
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.39
Consensus pattern (21 bp):
CTCTCAAATTCTCTCAAAATT
Found at i:41450773 original size:9 final size:10
Alignment explanation
Indices: 41450738--41450788 Score: 66
Period size: 11 Copynumber: 4.7 Consensus size: 10
41450728 CACAATAGTC
41450738 CTCTCATAATT
1 CTCTCA-AATT
41450749 CTCTCAAAATT
1 CTCTC-AAATT
41450760 CTCTCCAAATT
1 CTCT-CAAATT
41450771 CTCTCAAATTT
1 CTCTCAAA-TT
41450782 CTCTCAA
1 CTCTCAA
41450789 TTTTTGTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.11
11 31 0.84
12 2 0.05
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.39
Consensus pattern (10 bp):
CTCTCAAATT
Found at i:41450805 original size:21 final size:21
Alignment explanation
Indices: 41450781--41450820 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
41450771 CTCTCAAATT
41450781 TCTC-TCAATTTTTGTCAAAGC
1 TCTCTTCAATTTTTG-CAAAGC
*
41450802 TCTCTTTAATTTTTGCAAA
1 TCTCTTCAATTTTTGCAAA
41450821 ATAGCTCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (21 bp):
TCTCTTCAATTTTTGCAAAGC
Found at i:41452192 original size:265 final size:265
Alignment explanation
Indices: 41451707--41452225 Score: 896
Period size: 265 Copynumber: 2.0 Consensus size: 265
41451697 TTTTCACTTT
* *
41451707 TCATTTTTACATCATCGAGTGAACCACCCATATACATCCCCACTAATAATGAGGTAAAATTTATA
1 TCATTTTTACATCATCGAGTAAACCACCCATATACATCCCCACTAATAACGAGGTAAAATTTATA
**
41451772 TTAGATTTTACAATTATTATGTAGATTTAAAATATAATTGTATGCTAAAAAATTATTTAATTAGG
66 TTAGATTTTACAATTATTACATAGATTTAAAATATAATTGTATGCTAAAAAATTATTTAATTAGG
* *
41451837 TGGAACCATTCGGCAAGTTATGTTGGAATACCCATATCTCTTAAAGATATACGGCTTCTATTAGA
131 TGGAACCATTCGGCAAGTTATGTTGGAATACCCACATCTCTTAAAGATATACGACTTCTATTAGA
* * *
41451902 CCAACGGTCGGAAGCACAGGTAAGTATTAAATAAAATATATATACATAATAAAATAGTCGTTTCG
196 CCAACGGTCGGAAACACAAGTAAGTACTAAATAAAATATATATACATAATAAAATAGTCGTTTCG
41451967 TATAG
261 TATAG
*
41451972 TCATTTTTACATCATCGAGTAAACCACCCATATACATTCCCACTAATAACGAGGTAAAATTTATA
1 TCATTTTTACATCATCGAGTAAACCACCCATATACATCCCCACTAATAACGAGGTAAAATTTATA
41452037 TTAGATTTTACAATTATTACATAGATTTAAAATATAATTGTATGCTAAAAAATTATTTAATTAGG
66 TTAGATTTTACAATTATTACATAGATTTAAAATATAATTGTATGCTAAAAAATTATTTAATTAGG
* * * *
41452102 TGGAACCATTCGGCGAGTTATGTTGTAATACCCACATCTCTTGAAGATATATGACTTCTATTATG
131 TGGAACCATTCGGCAAGTTATGTTGGAATACCCACATCTCTTAAAGATATACGACTTCTATTA-G
41452167 -CCAACGGTCGGAAACACAAGTAAGTACTAAATAAAATATATATACATAATAAAATAGTC
195 ACCAACGGTCGGAAACACAAGTAAGTACTAAATAAAATATATATACATAATAAAATAGTC
41452226 ATTTGATATT
Statistics
Matches: 239, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
265 238 1.00
266 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (265 bp):
TCATTTTTACATCATCGAGTAAACCACCCATATACATCCCCACTAATAACGAGGTAAAATTTATA
TTAGATTTTACAATTATTACATAGATTTAAAATATAATTGTATGCTAAAAAATTATTTAATTAGG
TGGAACCATTCGGCAAGTTATGTTGGAATACCCACATCTCTTAAAGATATACGACTTCTATTAGA
CCAACGGTCGGAAACACAAGTAAGTACTAAATAAAATATATATACATAATAAAATAGTCGTTTCG
TATAG
Found at i:41452903 original size:18 final size:18
Alignment explanation
Indices: 41452880--41452917 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41452870 TGCCAGTTGC
*
41452880 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
*
41452898 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTATAT
41452916 GT
1 GT
41452918 TTTCTTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:41453171 original size:21 final size:21
Alignment explanation
Indices: 41453147--41453197 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
41453137 ATTACCAGAT
*
41453147 TCCCTGCCGGAGGAACCACAA
1 TCCCTGCCGGAGCAACCACAA
** *
41453168 TCCCCACCAGAGCAACCACAA
1 TCCCTGCCGGAGCAACCACAA
*
41453189 CCCCTGCCG
1 TCCCTGCCG
41453198 AAAGCTGAAC
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.47, G:0.18, T:0.08
Consensus pattern (21 bp):
TCCCTGCCGGAGCAACCACAA
Found at i:41453543 original size:132 final size:131
Alignment explanation
Indices: 41453303--41453798 Score: 836
Period size: 132 Copynumber: 3.8 Consensus size: 131
41453293 TTGTAGAAAT
* * *
41453303 TTTTTTATATAGTTTC-ATATAATAAAATAAAAATTATTTTTAATATTTTAATTATACTTTACTT
1 TTTTTTATATAGTTTCAAT-TAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTT
* *
41453367 TTTTTAATTTTATTAAAATAAATGTTCTTTGAAATTAGGCAATATTTTTTATTATTTTTATATTT
65 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGAAATATTTTTTATTATTTTTATATTT
41453432 AA
130 AA
41453434 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTA
1 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTT-
41453499 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGAAATATTTTTTATTATTTTTATATTT
65 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGAAATATTTTTTATTATTTTTATATTT
41453564 AA
130 AA
* *
41453566 GTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAATTT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTT-ACTT
41453631 TTTTTAATTTTATTAAAAATAAATGTTCTTTTAAATTA-GACAATATTTTTTATTA-TTTTATAT
65 TTTTTAATTTTATT-AAAATAAATGTTCTTTTAAATTAGGA-AATATTTTTTATTATTTTTATAT
41453694 TTAA
128 TTAA
*
41453698 TTTTTTATATAGTTTCAATTAATATAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
* *
41453763 TTTTAATTTTAATACAATAAATGTTCTTTTAAATTA
66 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTA
41453799 ATCAATAATT
Statistics
Matches: 348, Mismatches: 12, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
130 22 0.06
131 74 0.21
132 212 0.61
133 40 0.11
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.56
Consensus pattern (131 bp):
TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGAAATATTTTTTATTATTTTTATATTTA
A
Found at i:41453813 original size:263 final size:263
Alignment explanation
Indices: 41453304--41453815 Score: 859
Period size: 263 Copynumber: 1.9 Consensus size: 263
41453294 TGTAGAAATT
41453304 TTTTTATATAGTTTCATATAATAAAATAAAAATTATTTTTAATATTTTAATTATACTTTACTTTT
1 TTTTTATATAGTTTCATATAATAAAATAAAAATTATTTTTAATATTTTAATTATACTTTACTTTT
*
41453369 TTTAATTTTATTAAAATAAATGTTCTTTGAAATTAGGCAATATTTTTTATTATTTTTATATTTAA
66 TTTAATTTTATTAAAATAAATGTTCTTTGAAATTAGACAATATTTTTTATTATTTTTATATTTAA
41453434 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTA
131 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTA
* * *
41453499 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGAAATATTTTTTATTATTTTTATATTT
196 TTTTTAATTTTAATAAAATAAATGTTCTTTTAAATTAAGAAATAATTTTTATTATTTTTATATTT
41453564 AAG
261 AAG
* * * *
41453567 TTTTTATATAGTTTCA-ATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAATTT
1 TTTTTATATAGTTTCATA-TAATAAAATAAAAATTATTTTTAATATTTTAATTATACTTT-ACTT
*
41453631 TTTTTAATTTTATTAAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTA-TTTTATATT
64 TTTTTAATTTTATT-AAAATAAATGTTCTTTGAAATTAGACAATATTTTTTATTATTTTTATATT
*
41453695 TAATTTTTTATATAGTTTCAATTAATATAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC
128 TAATTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC
* **
41453760 TT-TTTTTAATTTTAATACAATAAATGTTCTTTTAAATTAATCAATAATTTTTATTA
193 TTATTTTTAATTTTAATAAAATAAATGTTCTTTTAAATTAAGAAATAATTTTTATTA
41453816 AAATAAATGT
Statistics
Matches: 233, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
262 1 0.00
263 102 0.44
264 92 0.39
265 38 0.16
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (263 bp):
TTTTTATATAGTTTCATATAATAAAATAAAAATTATTTTTAATATTTTAATTATACTTTACTTTT
TTTAATTTTATTAAAATAAATGTTCTTTGAAATTAGACAATATTTTTTATTATTTTTATATTTAA
TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTA
TTTTTAATTTTAATAAAATAAATGTTCTTTTAAATTAAGAAATAATTTTTATTATTTTTATATTT
AAG
Found at i:41453855 original size:9 final size:9
Alignment explanation
Indices: 41453841--41453871 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41453831 TGAATACGAC
41453841 AATATTTTT
1 AATATTTTT
*
41453850 AATATTTTC
1 AATATTTTT
41453859 AATATTTTT
1 AATATTTTT
41453868 AATA
1 AATA
41453872 AAACATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTT
Found at i:41457880 original size:20 final size:20
Alignment explanation
Indices: 41457855--41457909 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
41457845 ATAAATTTGA
*
41457855 AAAAAATAAAAAAATGATAT
1 AAAAAATAAAAAAATGACAT
* * *
41457875 AAAAAATCAAAATATTACAT
1 AAAAAATAAAAAAATGACAT
* *
41457895 AAAAATTGAAAAAAT
1 AAAAAATAAAAAAAT
41457910 ATAAATATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAAAATAAAAAAATGACAT
Found at i:41457907 original size:21 final size:21
Alignment explanation
Indices: 41457883--41457949 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
41457873 ATAAAAAATC
*
41457883 AAAATATTACATAAAAATTGA
1 AAAATATTAAATAAAAATTGA
* *
41457904 AAAA-ATATAAATATAAATTTAA
1 AAAATAT-TAAATA-AAAATTGA
*
41457926 AAAATATTATATAAAAATTGA
1 AAAATATTAAATAAAAATTGA
41457947 AAA
1 AAA
41457950 TTTTTCATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.05
21 18 0.49
22 15 0.41
23 2 0.05
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (21 bp):
AAAATATTAAATAAAAATTGA
Found at i:41457911 original size:22 final size:22
Alignment explanation
Indices: 41457883--41457949 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
41457873 ATAAAAAATC
*
41457883 AAAATATTACATAAAAATTGAA
1 AAAATATTAAATAAAAATTGAA
* *
41457905 AAAATA-TAAATATAAATTTAA
1 AAAATATTAAATAAAAATTGAA
*
41457926 AAAATATTATATAAAAATTGAA
1 AAAATATTAAATAAAAATTGAA
41457948 AA
1 AA
41457950 TTTTTCATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 18 0.47
22 20 0.53
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (22 bp):
AAAATATTAAATAAAAATTGAA
Found at i:41458446 original size:32 final size:30
Alignment explanation
Indices: 41458376--41458543 Score: 118
Period size: 29 Copynumber: 5.6 Consensus size: 30
41458366 AATTTGACCA
*
41458376 TTTTTCAATTTTATATAATA-TTTT-GATT
1 TTTTTCAATTTTATATAATATTTTTAAATT
* *
41458404 TTTTTAAATTTATACATAAATATTTTTAAATT
1 TTTTTCAATTT-TATAT-AATATTTTTAAATT
41458436 TTTTTCAATTTTTATATAATATTTTT--ATT
1 TTTTTCAA-TTTTATATAATATTTTTAAATT
** *
41458465 TTTTAAAATTTTA-ATTATATATTATT-AATT
1 TTTTTCAATTTTATA-TA-ATATTTTTAAATT
* * *
41458495 TTTTT-AATTTT-TTTAAATTTTTTTTAAAAT
1 TTTTTCAATTTTATAT-AA-TATTTTTAAATT
41458525 TTTTTCAACTATTTATATA
1 TTTTTCAA-T-TTTATATA
41458544 TTTTATATGA
Statistics
Matches: 110, Mismatches: 14, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
27 1 0.01
28 19 0.17
29 32 0.29
30 19 0.17
31 15 0.14
32 15 0.14
33 7 0.06
34 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (30 bp):
TTTTTCAATTTTATATAATATTTTTAAATT
Found at i:41458474 original size:29 final size:29
Alignment explanation
Indices: 41458376--41458507 Score: 124
Period size: 29 Copynumber: 4.4 Consensus size: 29
41458366 AATTTGACCA
* *
41458376 TTTTTCAA-TTTTATATAATATTTTGATT
1 TTTTTAAATTTTTATATAATATTTTTATT
* *
41458404 TTTTTAAATTTATACATAAATATTTTTAAATT
1 TTTTTAAATTTTTATAT-AATATTTTT--ATT
*
41458436 TTTTTCAATTTTTATATAATATTTTTATT
1 TTTTTAAATTTTTATATAATATTTTTATT
* * *
41458465 TTTTAAAATTTTAAT-TATATATTATTAATT
1 TTTTTAAATTTTTATATA-ATATT-TTTATT
*
41458495 TTTTTAATTTTTT
1 TTTTTAAATTTTT
41458508 TAAATTTTTT
Statistics
Matches: 84, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
28 9 0.11
29 26 0.31
30 23 0.27
31 9 0.11
32 17 0.20
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (29 bp):
TTTTTAAATTTTTATATAATATTTTTATT
Found at i:41458509 original size:60 final size:61
Alignment explanation
Indices: 41458376--41458506 Score: 182
Period size: 61 Copynumber: 2.2 Consensus size: 61
41458366 AATTTGACCA
* *
41458376 TTTTTCAA-TTTTATATAATATTTTGATTTTTTTAAATTTATACATAAATATTTTTAAATT
1 TTTTTCAATTTTTATATAATATTTTGATTTTTTAAAATTTATACATAAATATTATTAAATT
* *
41458436 TTTTTCAATTTTTATATAATATTTTTATTTTTTAAAATTT-TA-ATTATATATTATT-AATT
1 TTTTTCAATTTTTATATAATATTTTGATTTTTTAAAATTTATACA-TAAATATTATTAAATT
41458495 TTTTT-AATTTTT
1 TTTTTCAATTTTT
41458507 TTAAATTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
58 7 0.11
59 10 0.15
60 19 0.29
61 29 0.45
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (61 bp):
TTTTTCAATTTTTATATAATATTTTGATTTTTTAAAATTTATACATAAATATTATTAAATT
Found at i:41458516 original size:11 final size:11
Alignment explanation
Indices: 41458493--41458529 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
41458483 ATATTATTAA
41458493 TTTTTTT-AA-
1 TTTTTTTAAAT
41458502 TTTTTTTAAAT
1 TTTTTTTAAAT
41458513 TTTTTTTAAAAT
1 TTTTTTT-AAAT
41458525 TTTTT
1 TTTTT
41458530 CAACTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.28
10 2 0.08
11 7 0.28
12 9 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTTAAAT
Found at i:41459374 original size:22 final size:23
Alignment explanation
Indices: 41459347--41459391 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
41459337 TGATATCTAC
41459347 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
41459369 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
41459392 TATCATATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:41459396 original size:22 final size:21
Alignment explanation
Indices: 41459344--41459407 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
41459334 AAATGATATC
*
41459344 TACAAATCAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
41459365 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
*
41459388 TACATATCATATC-C-AAGAT
1 TACAAATCATATCTCTAAGAT
41459407 T
1 T
41459408 GCATATCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.15
20 1 0.03
21 3 0.08
22 18 0.46
23 11 0.28
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:41465574 original size:7 final size:7
Alignment explanation
Indices: 41465562--41465586 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41465552 ATTGATGTGC
41465562 TATTATT
1 TATTATT
41465569 TATTATT
1 TATTATT
41465576 TATTATT
1 TATTATT
41465583 TATT
1 TATT
41465587 TTTGTTGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTATT
Found at i:41467141 original size:22 final size:23
Alignment explanation
Indices: 41467114--41467158 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41467104 GGATATCTAC
*
41467114 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAAATTACA
*
41467136 AAATCATATCTTCTAAAATTACA
1 AAATCAAATCTTCTAAAATTACA
41467159 TATCATATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAAATTACA
Found at i:41467163 original size:22 final size:21
Alignment explanation
Indices: 41467111--41467167 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
41467101 AAAGGATATC
* *
41467111 TACAAATCAAATCTCTAAGAT
1 TACAAATCATATCTCTAAAAT
41467132 TACAAAATCATATCTTCTAAAAT
1 TAC-AAATCATATC-TCTAAAAT
*
41467155 TACATATCATATC
1 TACAAATCATATC
41467168 CAAGATTGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (21 bp):
TACAAATCATATCTCTAAAAT
Found at i:41468242 original size:16 final size:16
Alignment explanation
Indices: 41468209--41468250 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
41468199 AAAGAAAAAC
* *
41468209 AAGAGAA-GCAGAATA
1 AAGAGAAGGAAGAAGA
*
41468224 AAGAGAGGGAAGAAGA
1 AAGAGAAGGAAGAAGA
41468240 AAGAGAAGGAA
1 AAGAGAAGGAA
41468251 AAAAAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.60, C:0.02, G:0.36, T:0.02
Consensus pattern (16 bp):
AAGAGAAGGAAGAAGA
Found at i:41473417 original size:14 final size:14
Alignment explanation
Indices: 41473398--41473426 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41473388 TGGAACAAAC
41473398 TTTGTAATATAAAT
1 TTTGTAATATAAAT
41473412 TTTGTAATATAAAT
1 TTTGTAATATAAAT
41473426 T
1 T
41473427 AAATACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGTAATATAAAT
Found at i:41473447 original size:62 final size:62
Alignment explanation
Indices: 41473369--41473598 Score: 397
Period size: 62 Copynumber: 3.7 Consensus size: 62
41473359 ATTAATTGCA
* * *
41473369 ACATTACAACACTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
* *
41473431 ACATTACAATATTAAAAATTGGAATAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
*
41473493 ACATTGCAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
*
41473555 ACATTACAACATTAAAAATTGGAACAAAGTTTGTAATATAAATT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATT
41473599 AGGTACATCG
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 158 1.00
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.36
Consensus pattern (62 bp):
ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
Found at i:41473477 original size:14 final size:14
Alignment explanation
Indices: 41473454--41473488 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41473444 AAAAATTGGA
*
41473454 ATAAACTTTGTAAT
1 ATAAATTTTGTAAT
*
41473468 ATAAATTTTGTTAT
1 ATAAATTTTGTAAT
41473482 ATAAATT
1 ATAAATT
41473489 AAATACATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (14 bp):
ATAAATTTTGTAAT
Found at i:41477783 original size:72 final size:71
Alignment explanation
Indices: 41477696--41477843 Score: 217
Period size: 72 Copynumber: 2.1 Consensus size: 71
41477686 TGGACTATTA
* * *
41477696 TTAGTTTTGGTGGTTTTAG-TTTAATCATGAATTATGGCTAATTTTGGAGTTTGGTTTGTCAATT
1 TTAGTTTTGCTGG-TTTAGATTTAATCATGAATTATGACTAATTTTGGAGTTTGGTTTATCAATT
41477760 TTAGGTT
65 TTAGGTT
* **
41477767 GTTAGTTTTGCTGGTTTCGATTTAATCATGAATTATGACTAATTTTGGAGTTTGGTTTATCGGTT
1 -TTAGTTTTGCTGGTTTAGATTTAATCATGAATTATGACTAATTTTGGAGTTTGGTTTATCAATT
41477832 TTAGGTT
65 TTAGGTT
41477839 TTAGT
1 TTAGT
41477844 GATCTCGGGT
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
71 9 0.13
72 60 0.87
ACGTcount: A:0.20, C:0.05, G:0.24, T:0.51
Consensus pattern (71 bp):
TTAGTTTTGCTGGTTTAGATTTAATCATGAATTATGACTAATTTTGGAGTTTGGTTTATCAATTT
TAGGTT
Found at i:41478361 original size:13 final size:13
Alignment explanation
Indices: 41478322--41478366 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
41478312 TCAAGCATGA
*
41478322 TATTTCTGTATCTA
1 TATTT-TGTATCTG
* *
41478336 TATATTGTTTCTG
1 TATTTTGTATCTG
41478349 TATTTTGTATCTG
1 TATTTTGTATCTG
41478362 TATTT
1 TATTT
41478367 GGGGTGGAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 22 0.85
14 4 0.15
ACGTcount: A:0.18, C:0.09, G:0.11, T:0.62
Consensus pattern (13 bp):
TATTTTGTATCTG
Found at i:41481614 original size:10 final size:9
Alignment explanation
Indices: 41481594--41481667 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 9
41481584 TTTAAATTAG
41481594 AAAATTTAT
1 AAAATTTAT
41481603 AAAATCTTAT
1 AAAAT-TTAT
41481613 -AAATATTAT
1 AAAAT-TTAT
* *
41481622 AAAAATTCT
1 AAAATTTAT
*
41481631 AATAAATTAT
1 AA-AATTTAT
**
41481641 AAAAAATAT
1 AAAATTTAT
*
41481650 AAAATTAAT
1 AAAATTTAT
*
41481659 AAAACTTAT
1 AAAATTTAT
41481668 TTAAAATATT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
9 37 0.71
10 15 0.29
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAATTTAT
Found at i:41481682 original size:29 final size:29
Alignment explanation
Indices: 41481640--41481749 Score: 86
Period size: 29 Copynumber: 3.8 Consensus size: 29
41481630 TAATAAATTA
* * *
41481640 TAAAAAATATAAAATTAATAAAACTTATT
1 TAAAATATTTAAAATTAATAAAACATATT
41481669 TAAAATATTTAAAATTAGGA-AAAACAT-TT
1 TAAAATATTTAAAATTA--ATAAAACATATT
** *
41481698 TGGAAT-TCTTAAAAATAATAAAA-ATATT
1 TAAAATAT-TTAAAATTAATAAAACATATT
*
41481726 TAAAATA-TTAAAATTCATATAAAC
1 TAAAATATTTAAAATTAATA-AAAC
41481750 TTACAAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
27 13 0.21
28 14 0.22
29 29 0.46
30 6 0.10
31 1 0.02
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.35
Consensus pattern (29 bp):
TAAAATATTTAAAATTAATAAAACATATT
Found at i:41485140 original size:46 final size:44
Alignment explanation
Indices: 41484972--41485143 Score: 134
Period size: 46 Copynumber: 3.7 Consensus size: 44
41484962 TTATGAGCAC
* *
41484972 CAGTGTAAGACCATGTCTGGGACATGGCATC-AGC-ATTGAGACGAGT
1 CAGTGTAAGA-CATGTCTAGGACAT-GCATCGA-CTA-TGAGACGTGT
* *
41485018 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCT-CGAGACGTAAGT
1 -C-AGTGTAAGACATGTCTAGGACATGCATC-GACTATGAGACGT--GT
* * * ** *
41485066 CACTATAAGACATGTCCACTACATGCATCGACTATGAGATGTGT
1 CAGTGTAAGACATGTCTAGGACATGCATCGACTATGAGACGTGT
41485110 CAGTGTAAGATCATGTCTAGGACATGGCATCGAC
1 CAGTGTAAGA-CATGTCTAGGACAT-GCATCGAC
41485144 ACAGATATGC
Statistics
Matches: 99, Mismatches: 17, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
44 10 0.10
45 14 0.14
46 48 0.48
47 16 0.16
48 11 0.11
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (44 bp):
CAGTGTAAGACATGTCTAGGACATGCATCGACTATGAGACGTGT
Found at i:41490074 original size:21 final size:20
Alignment explanation
Indices: 41490036--41490078 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
41490026 TTACTCAAGG
*
41490036 GAAGCCGATTGATCCATCTAA
1 GAAGCCGATTCATCCATC-AA
41490057 GAAGCCGAATTCAT-CATCAA
1 GAAGCCG-ATTCATCCATCAA
41490077 GA
1 GA
41490079 CTGAAGATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
GAAGCCGATTCATCCATCAA
Found at i:41494056 original size:46 final size:45
Alignment explanation
Indices: 41493925--41494139 Score: 150
Period size: 46 Copynumber: 4.6 Consensus size: 45
41493915 TGTGAGCTAC
* * * * * *
41493925 TGTAAGACATGTCTGAGACATGCATGGGCCAC-ATTATGAGAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GACGAGTG-CAG
* * *
41493971 TGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACGAGTGCTAG
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGAGTGC-AG
*
41494019 TGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTAAGT-CAT
1 TGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG--AGTGCAG
* ** * * * *
41494065 TGTAAGTCATGTCCAGAACATGCATC-GACTACGAGATGTGT-CAG
1 TGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGAGTGCAG
*
41494109 TGTAAGACCATGTCTGAGACATGGCATCGGC
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGC
41494140 ACAGATATGC
Statistics
Matches: 132, Mismatches: 27, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
44 10 0.08
45 13 0.10
46 56 0.42
47 28 0.21
48 24 0.18
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (45 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGAGTGCAG
Found at i:41497267 original size:21 final size:20
Alignment explanation
Indices: 41497253--41497311 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
41497243 TTTTTATGGA
*
41497253 TTTTTATAGAATTTTAATATG
1 TTTTTATAAAATTTT-ATATG
41497274 TTTTTATAAAATTTTAAATATG
1 TTTTTATAAAATTTT--ATATG
*
41497296 -TTTTAT-TAATTTTATA
1 TTTTTATAAAATTTTATA
41497312 ATTTATTAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 3 0.09
20 6 0.17
21 20 0.57
22 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTTATAAAATTTTATATG
Found at i:41497293 original size:22 final size:21
Alignment explanation
Indices: 41497253--41497299 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
41497243 TTTTTATGGA
*
41497253 TTTTTATAGAATTTTAATATG
1 TTTTTATAAAATTTTAATATG
41497274 TTTTTATAAAATTTTAAATATG
1 TTTTTATAAAATTTT-AATATG
41497296 TTTT
1 TTTT
41497300 ATTAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (21 bp):
TTTTTATAAAATTTTAATATG
Found at i:41497344 original size:9 final size:9
Alignment explanation
Indices: 41497296--41497346 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
41497286 TTTAAATATG
41497296 TTTTATTAA-
1 TTTTA-TAAT
41497305 TTTTATAAT
1 TTTTATAAT
* *
41497314 TTATTAGATT
1 TT-TTATAAT
41497324 TTTTAT-AT
1 TTTTATAAT
41497332 TTTTATAAT
1 TTTTATAAT
41497341 TTTTAT
1 TTTTAT
41497347 GAGTCCATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 10 0.29
9 18 0.51
10 7 0.20
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (9 bp):
TTTTATAAT
Found at i:41497414 original size:17 final size:18
Alignment explanation
Indices: 41497393--41497431 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
41497383 AATTTAAATA
*
41497393 ATTTTT-TATATTTTAT-
1 ATTTTTATAAATTTTATG
41497409 ATTTTTATAAATTTTATG
1 ATTTTTATAAATTTTATG
41497427 ATTTT
1 ATTTT
41497432 AGTTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTTTTATAAATTTTATG
Found at i:41497418 original size:25 final size:25
Alignment explanation
Indices: 41497367--41497450 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 25
41497357 CAAGTTTCAT
* * **
41497367 ATTTTTAATATTTAATAATTTAAATA
1 ATTTTTTATATTTTAT-ATTTTTATA
41497393 ATTTTTTATATTTTATATTTTTATA
1 ATTTTTTATATTTTATATTTTTATA
* *
41497418 A-ATTTTATGATTTTAGT-TTTTTATG
1 ATTTTTTAT-ATTTTA-TATTTTTATA
*
41497443 ATCTTTTA
1 ATTTTTTA
41497451 ATCATTTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
24 6 0.12
25 22 0.46
26 20 0.42
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (25 bp):
ATTTTTTATATTTTATATTTTTATA
Found at i:41505379 original size:43 final size:42
Alignment explanation
Indices: 41505314--41505470 Score: 113
Period size: 44 Copynumber: 3.7 Consensus size: 42
41505304 GTATACAATG
* * *
41505314 CCAATGTCCC-GAAAGTTGTCTTACATGTAATCAAACATCGATA
1 CCAATGTCCCAGACAG-GGTCTTACATGAAATCAAACA-CGATA
* * * ** * *
41505357 CCACTGTCCTAGATAGGGTCTTACACAAAATCAAATACGATG
1 CCAATGTCCCAGACAGGGTCTTACATGAAATCAAACACGATA
* ** *
41505399 CCAATGTCCCAGACATGGTCTTACATGCAAAAT-AGAAGTCGATG
1 CCAATGTCCCAGACAGGGTCTTACATG--AAATCA-AACACGATA
41505443 CCAATGTCCCAGAC-GTGGTCTTACATGA
1 CCAATGTCCCAGACAG-GGTCTTACATGA
41505471 TAACACATAT
Statistics
Matches: 91, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
42 26 0.29
43 25 0.27
44 40 0.44
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (42 bp):
CCAATGTCCCAGACAGGGTCTTACATGAAATCAAACACGATA
Found at i:41517711 original size:259 final size:258
Alignment explanation
Indices: 41517252--41517769 Score: 840
Period size: 259 Copynumber: 2.0 Consensus size: 258
41517242 TTCCATATAG
* * * *
41517252 TTAATTAAACCTTGAATTAGGGATCTAATTGCTAACACTTCTGAATTGATTTAATTTTACCTCTC
1 TTAATTAAACCTTGAATTAGGGATCTAATTACTAACACTCCTAAATTAATTTAATTTTACCTCTC
* * * *
41517317 GGTCTCAAATTTACCAAATTAGACAAATTGGCCCAATTTACCTCTCGATCTCACTGGCTAATCTG
66 GGTCTCAAATTTACCAAATTAGACAAATTAGCCCAATTTACCTCTCGATCTCACAGCCTAACCTG
* * * * *
41517382 GGACAAATGAGTTGGTGCCCAATAAGATTACCTCTTGATCTCACTTCTCTTGATTTTCCCTTAGG
131 GGACAAATGAATTGGTGCCCAATAAGATTACATCTCGATCTCACTTATCTTGATTTTCCCTTAAG
*
41517447 GTTGTCAATCTTAAGTTTTTAAGTCTATTTGATTTAATCCTTCTACCAAAGACTAACTAAACA
196 GTTGTCAATCTTAAGTTTTTAAGTCTATTCGATTTAATCCTTCTACCAAAGACTAACTAAACA
41517510 TTAATTAAACCTTGAATTAGGGATCTAAATTACTAACACTCCTAAATTAATTTAATTTTACCTCT
1 TTAATTAAACCTTGAATTAGGGATCT-AATTACTAACACTCCTAAATTAATTTAATTTTACCTCT
* * * *
41517575 TGGTCAT-AACTTTACCAAATTAGACAAATTAGTCCAATTTATCTCTCGATCTCACAGCCTAACC
65 CGGTC-TCAAATTTACCAAATTAGACAAATTAGCCCAATTTACCTCTCGATCTCACAGCCTAACC
41517639 TGGGACAAATGAATTGGTGCCCAATAAGATTACATCTCGATCTCACTTATCTTGATTTTCCCTTA
129 TGGGACAAATGAATTGGTGCCCAATAAGATTACATCTCGATCTCACTTATCTTGATTTTCCCTTA
*
41517704 AGGTTGTCAATTTTAAGTTTTTAAGTCTATTCGATTTAATCCTTCTACCAAAGACTAACTAAACA
194 AGGTTGTCAATCTTAAGTTTTTAAGTCTATTCGATTTAATCCTTCTACCAAAGACTAACTAAACA
41517769 T
1 T
41517770 CACTTCCATT
Statistics
Matches: 239, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
258 26 0.11
259 212 0.89
260 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (258 bp):
TTAATTAAACCTTGAATTAGGGATCTAATTACTAACACTCCTAAATTAATTTAATTTTACCTCTC
GGTCTCAAATTTACCAAATTAGACAAATTAGCCCAATTTACCTCTCGATCTCACAGCCTAACCTG
GGACAAATGAATTGGTGCCCAATAAGATTACATCTCGATCTCACTTATCTTGATTTTCCCTTAAG
GTTGTCAATCTTAAGTTTTTAAGTCTATTCGATTTAATCCTTCTACCAAAGACTAACTAAACA
Found at i:41520809 original size:20 final size:20
Alignment explanation
Indices: 41520784--41520835 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
41520774 CGAAGCGCAG
41520784 GAATCCACAAATTGTTGACT
1 GAATCCACAAATTGTTGACT
* * **
41520804 GAATCCACAGAGTGTTGGTT
1 GAATCCACAAATTGTTGACT
41520824 GAATCCACAAAT
1 GAATCCACAAAT
41520836 CAGATTCCCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (20 bp):
GAATCCACAAATTGTTGACT
Found at i:41530510 original size:18 final size:17
Alignment explanation
Indices: 41530487--41530521 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
41530477 AAATAGATTT
41530487 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
41530505 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
41530522 ACCTTAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:41541176 original size:20 final size:22
Alignment explanation
Indices: 41541138--41541180 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
41541128 TTAATTAATA
41541138 TTTTAAAATTTTAAAAAATTAT
1 TTTTAAAATTTTAAAAAATTAT
41541160 TTTTAAAA-TTT-AAAAATTAT
1 TTTTAAAATTTTAAAAAATTAT
41541180 T
1 T
41541181 AAAATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 3 0.14
22 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAATTTTAAAAAATTAT
Found at i:41541184 original size:29 final size:29
Alignment explanation
Indices: 41541152--41541247 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
41541142 AAAATTTTAA
*
41541152 AAAATTATTTTTAAAATTTAAAAATTATT
1 AAAATTATTTTAAAAATTTAAAAATTATT
* * * *
41541181 AAAATTATTTAAAAAATATAAAAGTTACT
1 AAAATTATTTTAAAAATTTAAAAATTATT
* *
41541210 AAAA-AAATTTAAAAATTTTAAAAATTAATT
1 AAAATTATTTTAAAAA-TTTAAAAATT-ATT
41541240 AAATATTA
1 AAA-ATTA
41541248 ACATGTCATC
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
28 8 0.16
29 36 0.71
30 5 0.10
31 1 0.02
32 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (29 bp):
AAAATTATTTTAAAAATTTAAAAATTATT
Found at i:41541190 original size:20 final size:20
Alignment explanation
Indices: 41541167--41541247 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 20
41541157 TATTTTTAAA
*
41541167 ATTTAAAAATTATTAAAATT
1 ATTTAAAAAATATTAAAATT
41541187 ATTTAAAAAATA-TAAAAGTT
1 ATTTAAAAAATATTAAAA-TT
* * *
41541207 ACTAAAAAAAT-TTAAAAAT
1 ATTTAAAAAATATTAAAATT
*
41541226 -TTTAAAAATTAATTAAATATT
1 ATTTAAAAAAT-ATTAAA-ATT
41541247 A
1 A
41541248 ACATGTCATC
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
18 7 0.15
19 6 0.13
20 32 0.68
21 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (20 bp):
ATTTAAAAAATATTAAAATT
Found at i:41541229 original size:9 final size:9
Alignment explanation
Indices: 41541158--41541235 Score: 50
Period size: 9 Copynumber: 8.3 Consensus size: 9
41541148 TTAAAAAATT
*
41541158 ATTTTTAAA
1 ATTTTAAAA
41541167 A-TTTAAAA
1 ATTTTAAAA
41541175 ATTATTAAAA
1 ATT-TTAAAA
*
41541185 TTATTTAAAA
1 AT-TTTAAAA
* *
41541195 AATATAAAA
1 ATTTTAAAA
* *
41541204 GTTACTAAAAA
1 ATT--TTAAAA
*
41541215 AATTTAAAA
1 ATTTTAAAA
41541224 ATTTTAAAA
1 ATTTTAAAA
41541233 ATT
1 ATT
41541236 AATTAAATAT
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
8 7 0.14
9 25 0.49
10 13 0.25
11 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:41541694 original size:14 final size:15
Alignment explanation
Indices: 41541669--41541699 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
41541659 ATCCCTTACT
41541669 TTTATAATATATATA
1 TTTATAATATATATA
41541684 TTTAT-ATATATATA
1 TTTATAATATATATA
41541698 TT
1 TT
41541700 GCAAGAGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATAATATATATA
Found at i:41542288 original size:10 final size:10
Alignment explanation
Indices: 41542223--41542288 Score: 57
Period size: 10 Copynumber: 6.8 Consensus size: 10
41542213 ATTATTTAGC
41542223 TTTTTATATA
1 TTTTTATATA
41542233 TATTTTA-ATA
1 T-TTTTATATA
*
41542243 TTTTTAAATA
1 TTTTTATATA
*
41542253 -ATTTATAT-
1 TTTTTATATA
* *
41542261 TTTTTTTGTA
1 TTTTTATATA
*
41542271 TTTATATATA
1 TTTTTATATA
41542281 TTTTTATA
1 TTTTTATA
41542289 AAATTTTGGA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
9 16 0.37
10 22 0.51
11 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTTATATA
Found at i:41543809 original size:9 final size:9
Alignment explanation
Indices: 41543787--41543843 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
41543777 AAACTTATTT
41543787 TTAAAATT-
1 TTAAAATTA
*
41543795 TAAAAATTA
1 TTAAAATTA
41543804 TTAAAATTA
1 TTAAAATTA
*
41543813 TTTAAAAAGTA
1 -TT-AAAATTA
*
41543824 TAAAAATTA
1 TTAAAATTA
*
41543833 TTTAAATTA
1 TTAAAATTA
41543842 TT
1 TT
41543844 TTTAAAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
8 7 0.18
9 23 0.59
10 3 0.08
11 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (9 bp):
TTAAAATTA
Found at i:41543813 original size:29 final size:29
Alignment explanation
Indices: 41543775--41543855 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
41543765 TTCAAAAAAA
41543775 TAAAACTTATTTTTAAAATTTAAAAATTAT
1 TAAAA-TTATTTTTAAAATTTAAAAATTAT
* *
41543805 TAAAATTA-TTTAAAAAGTATAAAAATTAT
1 TAAAATTATTTTTAAAA-TTTAAAAATTAT
* *
41543834 TTAAATTATTTTTAAAAATTAA
1 TAAAATTATTTTTAAAATTTAA
41543856 TTAAATGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 7 0.16
29 24 0.56
30 12 0.28
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (29 bp):
TAAAATTATTTTTAAAATTTAAAAATTAT
Found at i:41543815 original size:20 final size:20
Alignment explanation
Indices: 41543792--41543838 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
41543782 TATTTTTAAA
* *
41543792 ATTTAAAAATTATTAAAATT
1 ATTTAAAAAGTATAAAAATT
41543812 ATTTAAAAAGTATAAAAATT
1 ATTTAAAAAGTATAAAAATT
41543832 ATTTAAA
1 ATTTAAA
41543839 TTATTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTTAAAAAGTATAAAAATT
Found at i:41544081 original size:17 final size:18
Alignment explanation
Indices: 41544059--41544092 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41544049 ATACTTATAA
41544059 TTTAAAT-TCTAATTATT
1 TTTAAATATCTAATTATT
*
41544076 TTTAAATATGTAATTAT
1 TTTAAATATCTAATTAT
41544093 CACAAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAAATATCTAATTATT
Found at i:41553690 original size:18 final size:18
Alignment explanation
Indices: 41553669--41553727 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
41553659 ATAAAAATAA
*
41553669 TTATATTAATAATATATG
1 TTATATTAATATTATATG
* *
41553687 TTATAATAATTTTATATG
1 TTATATTAATATTATATG
41553705 -TATA-T-ATATTATAT-
1 TTATATTAATATTATATG
41553719 TTATATTAA
1 TTATATTAA
41553728 ACCATTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 12 0.35
16 2 0.06
17 5 0.15
18 15 0.44
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATATTAATATTATATG
Found at i:41553880 original size:146 final size:147
Alignment explanation
Indices: 41553689--41553986 Score: 526
Period size: 146 Copynumber: 2.0 Consensus size: 147
41553679 AATATATGTT
41553689 ATAATAATTTTATATGTATATATATTATATTTATATTAAACCATTAATTTAATAACAATTAAAAT
1 ATAATAATTTTATATG-ATATATATTATATTTATATTAAACCATTAATTTAATAACAATTAAAAT
* * * *
41553754 TATTATTCAAAATTTAAAATAAAACTTACCTAAATAAGCAACCCAATCCAAATTATAAAATTTTA
65 TATTATTCAAAACTTAAAATAAAACTTACCAAAATAAGCAACCCAATCCAAACTATAAAATTCTA
41553819 AAAATTATATTTAATACA
130 AAAATTATATTTAATACA
*
41553837 ATAATAATTTTATATG-TATATATTATATTTATATTAAACCATTAATTTAATAACAATTAAACTT
1 ATAATAATTTTATATGATATATATTATATTTATATTAAACCATTAATTTAATAACAATTAAAATT
*
41553901 ATTATTCAAAACTTAAAATAAAACTTACCAAAATAAGTAACCCAATCCAAACTATAAAATTCTAA
66 ATTATTCAAAACTTAAAATAAAACTTACCAAAATAAGCAACCCAATCCAAACTATAAAATTCTAA
41553966 AAATTATATTTAATACA
131 AAATTATATTTAATACA
41553983 ATAA
1 ATAA
41553987 AACATTTATT
Statistics
Matches: 144, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
146 128 0.89
148 16 0.11
ACGTcount: A:0.50, C:0.10, G:0.01, T:0.38
Consensus pattern (147 bp):
ATAATAATTTTATATGATATATATTATATTTATATTAAACCATTAATTTAATAACAATTAAAATT
ATTATTCAAAACTTAAAATAAAACTTACCAAAATAAGCAACCCAATCCAAACTATAAAATTCTAA
AAATTATATTTAATACA
Found at i:41554025 original size:38 final size:41
Alignment explanation
Indices: 41553974--41554062 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 41
41553964 AAAAATTATA
* * * *
41553974 TTTAATACAATAAAACATTTATTATA-TTAT-TTA-TGTTT
1 TTTAATATAATAAAACATTTATGATATTTATGGTAGTATTT
*
41554012 TTTAATATAATAAAATATTTATGATATTTATGGTAGTATTT
1 TTTAATATAATAAAACATTTATGATATTTATGGTAGTATTT
41554053 TTTAATATAA
1 TTTAATATAA
41554063 ATACTTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 23 0.53
39 4 0.09
40 2 0.05
41 14 0.33
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (41 bp):
TTTAATATAATAAAACATTTATGATATTTATGGTAGTATTT
Found at i:41558721 original size:2 final size:2
Alignment explanation
Indices: 41558714--41558744 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41558704 GTTTATAGTA
41558714 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
41558745 TGAAGAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:41564068 original size:27 final size:26
Alignment explanation
Indices: 41564011--41564085 Score: 96
Period size: 26 Copynumber: 2.9 Consensus size: 26
41564001 CATATTTTCC
* *
41564011 CAAAATTTTACCAGGGTTAAAATCGT
1 CAAAATTTTACTAGGGGTAAAATCGT
* *
41564037 CAAATTTTTACTAGGGGTAAAATTGT
1 CAAAATTTTACTAGGGGTAAAATCGT
* *
41564063 CAAAATTTTGCTAAGGGTAAAAT
1 CAAAATTTTACTAGGGGTAAAAT
41564086 AGGGATGAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (26 bp):
CAAAATTTTACTAGGGGTAAAATCGT
Found at i:41578782 original size:3 final size:3
Alignment explanation
Indices: 41578774--41578806 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
41578764 TGATATATAT
41578774 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
41578807 TACAAGATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:41598218 original size:22 final size:21
Alignment explanation
Indices: 41598193--41598235 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
41598183 AATTATTAAC
*
41598193 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTTTAATT-ATTTT
*
41598215 ATAATAAATTTTGATTATTTT
1 ATAATAAATTTTAATTATTTT
41598236 CAACAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
ATAATAAATTTTAATTATTTT
Found at i:41598719 original size:42 final size:42
Alignment explanation
Indices: 41598628--41598837 Score: 163
Period size: 42 Copynumber: 5.0 Consensus size: 42
41598618 ACAGATTTAC
* * * *
41598628 AAGTTGTGTATTAATGAAGCTCCCCACATGAGCTTAAGTGAG
1 AAGTTGTGTATTAACGAAGCTCCCTACGTGAGCTTAAGTGAT
*
41598670 AAGTTGTGTATTAGA-GAAACTCCCTACGTGAGCTTAAGTGAT
1 AAGTTGTGTATTA-ACGAAGCTCCCTACGTGAGCTTAAGTGAT
* * * *
41598712 ACA-TTGTGTATCAACGAAGCTCCCTATGTAAGTTTAAGTGAT
1 A-AGTTGTGTATTAACGAAGCTCCCTACGTGAGCTTAAGTGAT
* * * * * * * * * *
41598754 AACTTATTTGTCAGCAAAGCTCCCCATGTGAGCTTAAGTGAC
1 AAGTTGTGTATTAACGAAGCTCCCTACGTGAGCTTAAGTGAT
* * * * * *
41598796 AAGTTATGTATCAGCGAAGCTCCCCAAGCGAGCTTAAGTGAT
1 AAGTTGTGTATTAACGAAGCTCCCTACGTGAGCTTAAGTGAT
41598838 GATGCTCCTC
Statistics
Matches: 139, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
41 2 0.01
42 135 0.97
43 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (42 bp):
AAGTTGTGTATTAACGAAGCTCCCTACGTGAGCTTAAGTGAT
Found at i:41602801 original size:240 final size:241
Alignment explanation
Indices: 41602340--41602951 Score: 769
Period size: 240 Copynumber: 2.5 Consensus size: 241
41602330 TTATAATCAT
* * * * * *
41602340 ATTATTAAAACTAGAAATTCTATTACA-CGTA--A-GGAAATCACAAATTTAGAACACAAATGTA
1 ATTATTAATATTAGAAATTCTATCACATCGTATGATGGAAACCACAAATTTAGAATACAAATGTG
* *
41602401 TGTTTAAAAATAACATCAAATAAATAATCAAACTATGGTTTGAAACTAATTAATAATAACACATG
66 TGTTTAAAAATAACATAAAATAAATAATGAAACTATGGTTTGAAACTAA-TAATAATAACACATG
** *
41602466 AAATATGTATGATATTAAAATGAAAAAAATTAGATCTAATTGTTTATCATGATGTTGTCATCAAT
130 AAATATGTAAAATATTAAAACGAAAAAAATTAGATCTAATTGTTTATCATGATGTTGTCATCAAT
* *
41602531 CTTCAGCCAGTGCTGAGTTAACTTGTGACACCAATTCAATCAAATAC
195 CTTCAGCCAGTGCTGAATTAACTTGTGACACCAACTCAATCAAATAC
* *
41602578 ATTTTTAATATTAGAAATTTTATCACAT-GTATG-TGGAAACCACAAATTTAGAATACAAATGTG
1 ATTATTAATATTAGAAATTCTATCACATCGTATGATGGAAACCACAAATTTAGAATACAAATGTG
41602641 TGTTTAAAAATAACATAAAATAAATAATGAAACATATGGTTTGAAACTAATAAATAATAACACAT
66 TGTTTAAAAATAACATAAAATAAATAATGAAAC-TATGGTTTGAAACTAAT-AATAATAACACAT
* *
41602706 GAAATATGTAAAATATTAAAACG-AAAAAATTTGAT-TAAATTGTTTATCAT-A-GTACTGTCGT
129 GAAATATGTAAAATATTAAAACGAAAAAAATTAGATCT-AATTGTTTATCATGATGT--TGTCAT
* * *
41602767 CAATCTTGAGTCGGTGCTGAATTAACTTGTGACACCAACTCAATCAAATAC
191 CAATCTTCAGCCAGTGCTGAATTAACTTGTGACACCAACTCAATCAAATAC
* * * *
41602818 ATTATTAATATTAGAAATTCTATCACATGCGTATGCATGTGAAAACCACATATTTAGATTGCATA
1 ATTATTAATATTAGAAATTCTATCACAT-CGTATG-ATG-G-AAACCACAAATTTAGAATACAAA
* * * * * *
41602883 GGTGTATTTATAAATAACATAACATAAATAATGAAATGTAAT-ATTTGAAACTAATAATAATAAC
62 TGTGTGTTTAAAAATAACATAAAATAAATAATGAAA-CT-ATGGTTTGAAACTAATAATAATAAC
41602947 ACATG
125 ACATG
41602952 TTTAATATGT
Statistics
Matches: 325, Mismatches: 32, Indels: 27
0.85 0.08 0.07
Matches are distributed among these distances:
238 27 0.08
239 2 0.01
240 159 0.49
241 49 0.15
242 5 0.02
244 2 0.01
245 15 0.05
246 64 0.20
247 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.32
Consensus pattern (241 bp):
ATTATTAATATTAGAAATTCTATCACATCGTATGATGGAAACCACAAATTTAGAATACAAATGTG
TGTTTAAAAATAACATAAAATAAATAATGAAACTATGGTTTGAAACTAATAATAATAACACATGA
AATATGTAAAATATTAAAACGAAAAAAATTAGATCTAATTGTTTATCATGATGTTGTCATCAATC
TTCAGCCAGTGCTGAATTAACTTGTGACACCAACTCAATCAAATAC
Found at i:41602981 original size:12 final size:12
Alignment explanation
Indices: 41602964--41602991 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41602954 TAATATGTAC
41602964 AAAACTAAAATA
1 AAAACTAAAATA
41602976 AAAACTAAAATA
1 AAAACTAAAATA
41602988 AAAA
1 AAAA
41602992 ATAGTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (12 bp):
AAAACTAAAATA
Found at i:41604305 original size:51 final size:49
Alignment explanation
Indices: 41604245--41604348 Score: 136
Period size: 51 Copynumber: 2.1 Consensus size: 49
41604235 GGATAAATAG
* * *
41604245 GAAACATTTGGAAATGACTATGGTTTTCTCCAAAATGAAAATAGAGAAAT
1 GAAACATTTGGAAACGAATATGGTTTTCTCCAAAATGAAAAT-GAAAAAT
* * *
41604295 GAAATCATTTGGAAACGAATGTGGTTTTTTCCTAAATGAAAATGAAAAAT
1 GAAA-CATTTGGAAACGAATATGGTTTTCTCCAAAATGAAAATGAAAAAT
41604345 GAAA
1 GAAA
41604349 ATGACCTGGA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 14 0.30
51 33 0.70
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (49 bp):
GAAACATTTGGAAACGAATATGGTTTTCTCCAAAATGAAAATGAAAAAT
Found at i:41604346 original size:13 final size:13
Alignment explanation
Indices: 41604328--41604352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41604318 GTTTTTTCCT
41604328 AAATGAAAATGAA
1 AAATGAAAATGAA
41604341 AAATGAAAATGA
1 AAATGAAAATGA
41604353 CCTGGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
AAATGAAAATGAA
Found at i:41604644 original size:37 final size:37
Alignment explanation
Indices: 41604603--41604678 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
41604593 AAAGTATTTG
41604603 ATTGAAAGTTAGGACAGTACTTGTAATTGGACCCGAT
1 ATTGAAAGTTAGGACAGTACTTGTAATTGGACCCGAT
41604640 ATTGAAAGTTAGGACAGTACTTGTAATTGGACCCGAT
1 ATTGAAAGTTAGGACAGTACTTGTAATTGGACCCGAT
41604677 AT
1 AT
41604679 AGAAGATGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (37 bp):
ATTGAAAGTTAGGACAGTACTTGTAATTGGACCCGAT
Found at i:41613030 original size:26 final size:26
Alignment explanation
Indices: 41612994--41613052 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
41612984 TATTCTCTTT
41612994 AAATTTTATCAGGGGCAAAATCATCA
1 AAATTTTATCAGGGGCAAAATCATCA
* * *
41613020 AAATTTTATCATGGGTAAAATCGTCA
1 AAATTTTATCAGGGGCAAAATCATCA
*
41613046 AAGTTTT
1 AAATTTT
41613053 GTTGAGGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (26 bp):
AAATTTTATCAGGGGCAAAATCATCA
Found at i:41624828 original size:56 final size:59
Alignment explanation
Indices: 41624768--41624894 Score: 134
Period size: 56 Copynumber: 2.2 Consensus size: 59
41624758 CAAAAAAATC
* * *
41624768 ACAATAATTTTAAAATTTAAAATAT-TTATAAAAATTTCAAAATTT-AAATTTT-AAAA
1 ACAATAATTTTAAAATCTAAAATATATAAAAAAAATTTCAAAATTTAAAATTTTCAAAA
** *** * * *
41624824 ACAATTCTAAAAAAATCTAAAATATATAAAAAAAATTTTAAATTTTAAAATTTTCTAAA
1 ACAATAATTTTAAAATCTAAAATATATAAAAAAAATTTCAAAATTTAAAATTTTCAAAA
41624883 ACAATAATTTTA
1 ACAATAATTTTA
41624895 GAGACATAAT
Statistics
Matches: 52, Mismatches: 16, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
56 19 0.37
57 16 0.31
58 7 0.13
59 10 0.19
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (59 bp):
ACAATAATTTTAAAATCTAAAATATATAAAAAAAATTTCAAAATTTAAAATTTTCAAAA
Found at i:41624829 original size:26 final size:27
Alignment explanation
Indices: 41624773--41624883 Score: 82
Period size: 28 Copynumber: 4.0 Consensus size: 27
41624763 AAATCACAAT
* *
41624773 AATTTTAAAATTTAAAATATTTATAAA
1 AATTTCAAAATTTAAAATATTTAAAAA
41624800 AATTTCAAAATTT-AAAT-TTTAAAAA
1 AATTTCAAAATTTAAAATATTTAAAAA
* * *
41624825 CAATTCTAAAAAAATCTAAAATATATAAAAAA
1 -AATT-T--CAAAATTTAAAATAT-TTAAAAA
* * *
41624857 AATTTTAAATTTTAAAATTTTCTAAAA
1 AATTTCAAAATTTAAAATATT-TAAAA
41624884 CAATAATTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
25 7 0.11
26 8 0.12
27 14 0.21
28 15 0.23
29 6 0.09
30 5 0.08
31 5 0.08
32 6 0.09
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTTCAAAATTTAAAATATTTAAAAA
Found at i:41627505 original size:41 final size:41
Alignment explanation
Indices: 41627460--41627542 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
41627450 TGCTTTTGTA
41627460 TTCCTATTTCAATTTGGAATTGAATTATTCTCTCTTCTCTT
1 TTCCTATTTCAATTTGGAATTGAATTATTCTCTCTTCTCTT
* * *
41627501 TTCCTATTTCCATTTGGAATTGAATTATTTTCTTTTCTCTT
1 TTCCTATTTCAATTTGGAATTGAATTATTCTCTCTTCTCTT
41627542 T
1 T
41627543 CAAATTGACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.18, C:0.18, G:0.07, T:0.57
Consensus pattern (41 bp):
TTCCTATTTCAATTTGGAATTGAATTATTCTCTCTTCTCTT
Found at i:41631789 original size:30 final size:30
Alignment explanation
Indices: 41631753--41631812 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
41631743 ATTTAATACG
*
41631753 AACTTTTGCAAAATTACATTTTTACCCCTA
1 AACTTTTGCAAAATTACACTTTTACCCCTA
* *
41631783 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTTGCAAAATTACACTTTTACCCCTA
41631813 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (30 bp):
AACTTTTGCAAAATTACACTTTTACCCCTA
Found at i:41633159 original size:21 final size:22
Alignment explanation
Indices: 41633135--41633176 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41633125 ATTTCTGTCT
41633135 ATCT-GAAGCAGCTTTCAAACA
1 ATCTCGAAGCAGCTTTCAAACA
*
41633156 ATCTCGAATCAGCTTTCAAAC
1 ATCTCGAAGCAGCTTTCAAAC
41633177 TATCCTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (22 bp):
ATCTCGAAGCAGCTTTCAAACA
Found at i:41637504 original size:30 final size:30
Alignment explanation
Indices: 41637459--41637518 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
41637449 ATTTAATACG
*
41637459 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
41637489 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
41637519 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Done.