Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 52 of 106
Found at i:19645497 original size:13 final size:13
Alignment explanation
Indices: 19645479--19645503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19645469 GGAAAATGGG
19645479 ATTTTATAAAATA
1 ATTTTATAAAATA
19645492 ATTTTATAAAAT
1 ATTTTATAAAAT
19645504 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:19657094 original size:37 final size:37
Alignment explanation
Indices: 19657039--19657128 Score: 171
Period size: 37 Copynumber: 2.4 Consensus size: 37
19657029 GCCAGCCAAT
*
19657039 GAAAATCAAATCACACACGATGTTGAAGCAATAAGTG
1 GAAAGTCAAATCACACACGATGTTGAAGCAATAAGTG
19657076 GAAAGTCAAATCACACACGATGTTGAAGCAATAAGTG
1 GAAAGTCAAATCACACACGATGTTGAAGCAATAAGTG
19657113 GAAAGTCAAATCACAC
1 GAAAGTCAAATCACAC
19657129 TCGGTAGCGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.18
Consensus pattern (37 bp):
GAAAGTCAAATCACACACGATGTTGAAGCAATAAGTG
Found at i:19661231 original size:24 final size:19
Alignment explanation
Indices: 19661179--19661223 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
19661169 TTCCAAAAGG
19661179 CATTTTCTTCCTCCCACTC
1 CATTTTCTTCCTCCCACTC
19661198 CATTTTCTTCCTCCCACTC
1 CATTTTCTTCCTCCCACTC
19661217 CATTTTC
1 CATTTTC
19661224 CTTTCTTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.11, C:0.44, G:0.00, T:0.44
Consensus pattern (19 bp):
CATTTTCTTCCTCCCACTC
Found at i:19672777 original size:20 final size:19
Alignment explanation
Indices: 19672749--19672786 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
19672739 TTTATAAATC
19672749 ATTTTGAAATTGAATAATG
1 ATTTTGAAATTGAATAATG
*
19672768 ATTTTAGAAATTGAGTAAT
1 ATTTT-GAAATTGAATAAT
19672787 TAGAGACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
ATTTTGAAATTGAATAATG
Found at i:19675405 original size:39 final size:39
Alignment explanation
Indices: 19675357--19675495 Score: 199
Period size: 39 Copynumber: 3.6 Consensus size: 39
19675347 GTGCCGGTAG
*
19675357 TGTGCGGTGTGGGAGAGCACA-CACCGATGATATATGCCT
1 TGTGCGGTGTGGGAGAGCACATCA-TGATGATATATGCCT
* *
19675396 TGTGCGGTGTGGGAGAGCACATGATGATGATATAAGCCT
1 TGTGCGGTGTGGGAGAGCACATCATGATGATATATGCCT
* * *
19675435 TGTGCGATGTGGGAGAGCACATTATGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATCATGATGATATATGCCT
*
19675474 TGTGCGGTGTGGGAGTGCACAT
1 TGTGCGGTGTGGGAGAGCACAT
19675496 GAGGATATTA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 89 0.99
40 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.26
Consensus pattern (39 bp):
TGTGCGGTGTGGGAGAGCACATCATGATGATATATGCCT
Found at i:19675513 original size:36 final size:36
Alignment explanation
Indices: 19675357--19675534 Score: 128
Period size: 39 Copynumber: 4.7 Consensus size: 36
19675347 GTGCCGGTAG
* *
19675357 TGTGCGGTGTGGGAGAGCACA-CACCGATGATATATGCCT-
1 TGTGCGGTGTGGGAGAGCACATGA-GGAT-AT-TA-G-CTA
*
19675396 TGTGCGGTGTGGGAGAGCACATGATGATGATATAAGCCT-
1 TGTGCGGTGTGGGAGAGCACATGA-G--GATATTAG-CTA
* * * *
19675435 TGTGCGATGTGGGAGAGCACATTATGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGAGGAT-AT-TA-GCTA
*
19675474 TGTGCGGTGTGGGAGTGCACATGAGGATATTAGCTA
1 TGTGCGGTGTGGGAGAGCACATGAGGATATTAGCTA
* * *
19675510 TGTGTGGTGTGTGAGTGCACATGAG
1 TGTGCGGTGTGGGAGAGCACATGAG
19675535 CTAAGTTGAG
Statistics
Matches: 116, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
36 29 0.25
37 4 0.03
38 4 0.03
39 72 0.62
40 2 0.02
41 2 0.02
42 3 0.03
ACGTcount: A:0.24, C:0.13, G:0.36, T:0.27
Consensus pattern (36 bp):
TGTGCGGTGTGGGAGAGCACATGAGGATATTAGCTA
Found at i:19687731 original size:2 final size:2
Alignment explanation
Indices: 19687724--19687749 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19687714 CAAAGAAGTG
19687724 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19687750 TTGTATGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19692530 original size:2 final size:2
Alignment explanation
Indices: 19692523--19692564 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19692513 CATTATGATG
19692523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19692565 TTGTTGTGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19692611 original size:19 final size:19
Alignment explanation
Indices: 19692574--19692611 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
19692564 TTTGTTGTGC
*
19692574 ATGATAATTGATATTGTGT
1 ATGATAATTGATATCGTGT
19692593 ATGATAATT-ATAATCGTGT
1 ATGATAATTGAT-ATCGTGT
19692612 GTGTGCACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (19 bp):
ATGATAATTGATATCGTGT
Found at i:19692727 original size:38 final size:37
Alignment explanation
Indices: 19692684--19692791 Score: 144
Period size: 38 Copynumber: 2.8 Consensus size: 37
19692674 ATAGTGCTCG
* *
19692684 TGTGCACGATGTGGGGGATTGTACACAATGGCACTGAT
1 TGTGCACGATCTGGGGGA-TGCACACAATGGCACTGAT
**
19692722 TGTGCACGATCTGGGGGGATGCACATGATGGCACTGAT
1 TGTGCACGATCT-GGGGGATGCACACAATGGCACTGAT
*
19692760 TGTGCACGATCTGGGGGGATGCACACGATGGC
1 TGTGCACGATCT-GGGGGATGCACACAATGGC
19692792 GTCAGCTATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 58 0.91
39 6 0.09
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (37 bp):
TGTGCACGATCTGGGGGATGCACACAATGGCACTGAT
Found at i:19694115 original size:42 final size:42
Alignment explanation
Indices: 19694064--19694182 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
19694054 ATCTCATATG
*
19694064 CAACGGCTTATGCGCACTCCCACTCACACATAGCCAGGTCAA
1 CAACGGCTTATGTGCACTCCCACTCACACATAGCCAGGTCAA
* * * *
19694106 CAAGGGCTTATGTGCACTCCCAATCACACATAGCCAGGTTAG
1 CAACGGCTTATGTGCACTCCCACTCACACATAGCCAGGTCAA
* *
19694148 CAACGGCTTATGTGCACTCCTACTCGCACATAGCC
1 CAACGGCTTATGTGCACTCCCACTCACACATAGCC
19694183 GAGCCAATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.20
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCCACTCACACATAGCCAGGTCAA
Found at i:19701786 original size:29 final size:29
Alignment explanation
Indices: 19701726--19701790 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
19701716 GTAAATTTTT
* *
19701726 AAAAATTACACTTTTACCCCCGTAAAGTA
1 AAAAATTACACTTTTACCCCCGAAAACTA
*
19701755 AAAAATTACATTTTTACCCCC-AAAACTGA
1 AAAAATTACACTTTTACCCCCGAAAACT-A
19701784 AAAAATT
1 AAAAATT
19701791 GCCCATAGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.28
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCGAAAACTA
Found at i:19703982 original size:185 final size:184
Alignment explanation
Indices: 19703670--19704038 Score: 711
Period size: 185 Copynumber: 2.0 Consensus size: 184
19703660 GCCTCTTTAT
*
19703670 GTAATCCTGTTCACTATCCCATCAATTTTTCATCACCATTACTAGACCACCATTTTTAATTTGCA
1 GTAATCCTGTTCACTATCCCATCAATTTTTCATCACCATTACTAGACCACCATTTGTAATTTGCA
19703735 ACTAGACGTATTTCCATAATACAACATAGATACAAAAATTTACAATTGTATGATCTCAAAATAAG
66 ACTAGACGTATTTCCATAATACAACATAGATACAAAAATTTACAATTGTATGATCTCAAAATAAG
19703800 GTTATTCATAGCCATCTCATAATGCCACCATCATTCCAAACTATACATGCATCG
131 GTTATTCATAGCCATCTCATAATGCCACCATCATTCCAAACTATACATGCATCG
19703854 NGTAATCCTGTTCACTATCCCATCAATTTTTCATCACCATTACTAGACCACCATTTGTAATTTGC
1 -GTAATCCTGTTCACTATCCCATCAATTTTTCATCACCATTACTAGACCACCATTTGTAATTTGC
19703919 AACTAGACGTATTTCCATAATACAACATAGATACAAAAATTTACAATTGTATGATCTCAAAATAA
65 AACTAGACGTATTTCCATAATACAACATAGATACAAAAATTTACAATTGTATGATCTCAAAATAA
*
19703984 GGTTATTCATAGCCATCTCATAATGGCACCATCATTCCAAACTATACATGCATCG
130 GGTTATTCATAGCCATCTCATAATGCCACCATCATTCCAAACTATACATGCATCG
19704039 TTAGCAAAGT
Statistics
Matches: 182, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 182 1.00
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (184 bp):
GTAATCCTGTTCACTATCCCATCAATTTTTCATCACCATTACTAGACCACCATTTGTAATTTGCA
ACTAGACGTATTTCCATAATACAACATAGATACAAAAATTTACAATTGTATGATCTCAAAATAAG
GTTATTCATAGCCATCTCATAATGCCACCATCATTCCAAACTATACATGCATCG
Found at i:19705095 original size:43 final size:43
Alignment explanation
Indices: 19705032--19705167 Score: 245
Period size: 43 Copynumber: 3.2 Consensus size: 43
19705022 TGCAATATCA
*
19705032 TCATCATCAGCTCATATGCACTCCCACACCGCACATAGCTGGG
1 TCATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGG
*
19705075 TCATCATCAGCTCATGTGCACTCTCACACCGCACATAGCTGGG
1 TCATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGG
*
19705118 TCATCATCAACTCATGTGCACTCCCACACCGCACATAGCTGGG
1 TCATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGG
19705161 TCATCAT
1 TCATCAT
19705168 TATCACACAA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 89 1.00
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.23
Consensus pattern (43 bp):
TCATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGG
Found at i:19707796 original size:34 final size:34
Alignment explanation
Indices: 19707706--19707800 Score: 95
Period size: 34 Copynumber: 2.8 Consensus size: 34
19707696 AGGGAGGAAG
* *
19707706 GAGCAGCTTGGCTAGTGATTTTTGGAGGACAAATA
1 GAGCAACTTGGCTACTGATTTTT-GAGGACAAATA
* * * *
19707741 GAGCAATTTAGTTGCTGATTTTTGAGGA-AGAATA
1 GAGCAACTTGGCTACTGATTTTTGAGGACA-AATA
*
19707775 GAGCAACTTGGCTACT-AATTTTGAGG
1 GAGCAACTTGGCTACTGATTTTTGAGG
19707801 TTGATATGAG
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
33 10 0.21
34 21 0.44
35 17 0.35
ACGTcount: A:0.29, C:0.11, G:0.28, T:0.32
Consensus pattern (34 bp):
GAGCAACTTGGCTACTGATTTTTGAGGACAAATA
Found at i:19707987 original size:13 final size:15
Alignment explanation
Indices: 19707957--19707985 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19707947 CCGACGGGAG
19707957 AGAGAAGAAAGAAAA
1 AGAGAAGAAAGAAAA
19707972 AGAG-AGAAAGAAAA
1 AGAGAAGAAAGAAAA
19707986 GAATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (15 bp):
AGAGAAGAAAGAAAA
Found at i:19710676 original size:11 final size:11
Alignment explanation
Indices: 19710643--19710677 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
19710633 CCTGGGGTTC
19710643 TTGTTCTTCCT
1 TTGTTCTTCCT
19710654 TT-TTCTTCCT
1 TTGTTCTTCCT
*
19710664 TTGTTCTTGCT
1 TTGTTCTTCCT
19710675 TTG
1 TTG
19710678 GCCGGCCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.00, C:0.23, G:0.11, T:0.66
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:19719763 original size:13 final size:13
Alignment explanation
Indices: 19719745--19719770 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19719735 AGGAGAAATT
19719745 ATGATTTTATAAA
1 ATGATTTTATAAA
19719758 ATGATTTTATAAA
1 ATGATTTTATAAA
19719771 TTTTCTGGAA
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
ATGATTTTATAAA
Found at i:19723344 original size:20 final size:20
Alignment explanation
Indices: 19723319--19723364 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
19723309 TTTGGACCCC
19723319 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
* *
19723339 ATTTGACTTATTGTAGTATG
1 ATTTGACTTATTGGAGTATA
19723359 ATTTGA
1 ATTTGA
19723365 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:19730163 original size:35 final size:34
Alignment explanation
Indices: 19730124--19730214 Score: 121
Period size: 34 Copynumber: 2.6 Consensus size: 34
19730114 AGGGAAAAAG
*
19730124 GAGTAGCTTGGCTATTGATTTTTGAAGGACA-AATA
1 GAGTAGCTTGGCTATTGATTTTTG-A-GAAAGAATA
*
19730159 GAGTAGCTTAGCTATTGATTTTTGAGAAAGAATA
1 GAGTAGCTTGGCTATTGATTTTTGAGAAAGAATA
* *
19730193 GAGCAGCTTGGCTACTGATTTT
1 GAGTAGCTTGGCTATTGATTTT
19730215 GAGGTTGATA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 3 0.06
34 24 0.48
35 23 0.46
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (34 bp):
GAGTAGCTTGGCTATTGATTTTTGAGAAAGAATA
Found at i:19730405 original size:13 final size:15
Alignment explanation
Indices: 19730375--19730412 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
19730365 TCGACGGGAG
19730375 AGAGAAGAAAGAAAA
1 AGAGAAGAAAGAAAA
19730390 AGAG-AGAAAG-AAA
1 AGAGAAGAAAGAAAA
*
19730403 AGAAAAGAAA
1 AGAGAAGAAA
19730413 AAATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 6 0.29
14 11 0.52
15 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
AGAGAAGAAAGAAAA
Found at i:19730410 original size:18 final size:19
Alignment explanation
Indices: 19730372--19730408 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
19730362 TGATCGACGG
19730372 GAGAGAGAAGAAAGAAAAA
1 GAGAGAGAAGAAAGAAAAA
19730391 GAGAGA-AAGAAAAGAAAA
1 GAGAGAGAAG-AAAGAAAA
19730409 GAAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
GAGAGAGAAGAAAGAAAAA
Found at i:19734411 original size:29 final size:30
Alignment explanation
Indices: 19734353--19734429 Score: 120
Period size: 29 Copynumber: 2.6 Consensus size: 30
19734343 CTATTTATTC
*
19734353 AAAACTAATCGAGTTAACACTTCCAAAAAA
1 AAAACTAATCGAGTAAACACTTCCAAAAAA
*
19734383 AAAACTAATCGAGTAAACTCTTCC-AAAAA
1 AAAACTAATCGAGTAAACACTTCCAAAAAA
*
19734412 AAATCTAATCGAGTAAAC
1 AAAACTAATCGAGTAAAC
19734430 CCATATTCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 22 0.50
30 22 0.50
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (30 bp):
AAAACTAATCGAGTAAACACTTCCAAAAAA
Found at i:19744351 original size:19 final size:20
Alignment explanation
Indices: 19744327--19744364 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19744317 CTATAAATAC
19744327 CTTGAA-TTTCCAGCAGCTT
1 CTTGAATTTTCCAGCAGCTT
19744346 CTTGAATTTTCCAGCAGCT
1 CTTGAATTTTCCAGCAGCT
19744365 GGTCTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (20 bp):
CTTGAATTTTCCAGCAGCTT
Found at i:19756106 original size:180 final size:178
Alignment explanation
Indices: 19755914--19756281 Score: 406
Period size: 179 Copynumber: 2.1 Consensus size: 178
19755904 TTTAATTGGA
* * * *
19755914 AATTAGATTCCTAA-TTTTATGCCACCAAATAGCTTCAAAAGAAAG-ACAAAACCGAAAT-TGCC
1 AATTAAATTCCTAAGTTTTA-GCCA-CAAAGAACTTCAAAAG--AGCACAAAACC-AAATCTACC
* **
19755976 T-CTGCAGATAAAGGTCA-CAATTTTGAATATTTTTGACAGCCCCAAA-CAACTCCTAAAATCCT
61 TCCTGCAGATAAAGATCATCAATTTTGAAT-TTTTTGA-AGAACCAAATCAACTCCTAAAATCCT
* * *
19756038 GAAAATTTATTCTGAAATAGTTCCATGAGTTATCTATCAGGATAAAGTTTAGTAGG
124 GAAAATTTATTCTGAAATAGTTACATGAGTTATATATCAGAATAAAGTTTA-TAGG
* * * *
19756094 AATTAAATTCCTAAGTTTTAGTCACAAAGAATTTCAAAAGAGCTCAAAACCAATTCTACCTCCTG
1 AATTAAATTCCTAAGTTTTAGCCACAAAGAACTTCAAAAGAGCACAAAACCAAATCTACCTCCTG
*** * * *
19756159 CAGATAAAGATCATGGTTTTTGAATTTTTTGAATAACCAAATCACCTCCTAAAATCCTGAAAGTT
66 CAGATAAAGATCATCAATTTTGAATTTTTTGAAGAACCAAATCAACTCCTAAAATCCTGAAAATT
* * * *
19756224 TATTCTGGAATATTTACATGAGTTATATATCAGAATAAATTTTATTGG
131 TATTCTGAAATAGTTACATGAGTTATATATCAGAATAAAGTTTATAGG
19756272 AATTAAATTC
1 AATTAAATTC
19756282 TTAAAGATAC
Statistics
Matches: 158, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
177 5 0.03
178 30 0.19
179 94 0.59
180 24 0.15
181 5 0.03
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (178 bp):
AATTAAATTCCTAAGTTTTAGCCACAAAGAACTTCAAAAGAGCACAAAACCAAATCTACCTCCTG
CAGATAAAGATCATCAATTTTGAATTTTTTGAAGAACCAAATCAACTCCTAAAATCCTGAAAATT
TATTCTGAAATAGTTACATGAGTTATATATCAGAATAAAGTTTATAGG
Found at i:19757629 original size:58 final size:57
Alignment explanation
Indices: 19757539--19757658 Score: 204
Period size: 58 Copynumber: 2.1 Consensus size: 57
19757529 CATAATCATC
* *
19757539 CAAAGTAGTTTGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCTATGCAATG
1 CAAAGTAGTATGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCCATGC-ATG
*
19757597 CAAAGTAGTATGCATGTGATAGATTTATTTTATGCGATTTAATAAATGCCATGCATG
1 CAAAGTAGTATGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCCATGCATG
19757654 CAAAG
1 CAAAG
19757659 ATGAGACCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
57 8 0.14
58 51 0.86
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (57 bp):
CAAAGTAGTATGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCCATGCATG
Found at i:19763468 original size:68 final size:68
Alignment explanation
Indices: 19763381--19763647 Score: 284
Period size: 68 Copynumber: 3.9 Consensus size: 68
19763371 ATTGTACATG
* * * * *
19763381 CTTAATCATCTCATGTAGTATACGAAATCTACATCATACACACATTCTCATTGCATTCATCATGC
1 CTTAATCATCTCATATAGTATATGAAATTTACATCATACACACAATCTTATTGCATTCATCATGC
19763446 ATA
66 ATA
* * * * * * * *
19763449 CTTAATCACCTTATATAGTATATGGAATTTGCATTATATACACAATCTTA-TGTCATTGATCATA
1 CTTAATCATCTCATATAGTATATGAAATTTACATCATACACACAATCTTATTG-CATTCATCATG
19763513 CATA
65 CATA
* * * * * * *
19763517 CTTAATCATCTTATATGGTATATGGAATTTGCATCATACACATATTCTTATGGCATTCATCATGC
1 CTTAATCATCTCATATAGTATATGAAATTTACATCATACACACAATCTTATTGCATTCATCATGC
19763582 ATA
66 ATA
* * * * * *
19763585 CTTAATCATCTCCTATGGTGTATGAAGTTTACATCATATACACAATCTTATTGCATTTATCAT
1 CTTAATCATCTCATATAGTATATGAAATTTACATCATACACACAATCTTATTGCATTCATCAT
19763648 ACCAAACATG
Statistics
Matches: 164, Mismatches: 33, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
67 2 0.01
68 161 0.98
69 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (68 bp):
CTTAATCATCTCATATAGTATATGAAATTTACATCATACACACAATCTTATTGCATTCATCATGC
ATA
Found at i:19763624 original size:136 final size:136
Alignment explanation
Indices: 19763375--19763649 Score: 347
Period size: 136 Copynumber: 2.0 Consensus size: 136
19763365 ACATCAATTG
* * *
19763375 TACATGCTTAATCATCTCATGTAGTATACGAAATCTACATCATACACACATTCTCATTGCATTCA
1 TACATACTTAATCATCTCATATAGTATACGAAATCTACATCATACACACATTCTCATGGCATTCA
* * *
19763440 TCATGCATACTTAATCACCTTATATAGTATATGGAATTTGCATTATATACACAATCTTA-TGTCA
66 TCATGCATACTTAATCACCTCATATAGTATATGGAATTTACATCATATACACAATCTTATTG-CA
19763504 TTGATCA
130 TTGATCA
* * * * * * * *
19763511 TACATACTTAATCATCTTATATGGTATATGGAATTTGCATCATACACATATTCTTATGGCATTCA
1 TACATACTTAATCATCTCATATAGTATACGAAATCTACATCATACACACATTCTCATGGCATTCA
* * * *
19763576 TCATGCATACTTAATCATCTCCTATGGTGTAT-GAAGTTTACATCATATACACAATCTTATTGCA
66 TCATGCATACTTAATCACCTCATATAGTATATGGAA-TTTACATCATATACACAATCTTATTGCA
*
19763640 TTTATCA
130 TTGATCA
19763647 TAC
1 TAC
19763650 CAAACATGCA
Statistics
Matches: 118, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
135 3 0.03
136 113 0.96
137 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (136 bp):
TACATACTTAATCATCTCATATAGTATACGAAATCTACATCATACACACATTCTCATGGCATTCA
TCATGCATACTTAATCACCTCATATAGTATATGGAATTTACATCATATACACAATCTTATTGCAT
TGATCA
Found at i:19766811 original size:36 final size:36
Alignment explanation
Indices: 19766761--19766944 Score: 180
Period size: 36 Copynumber: 5.1 Consensus size: 36
19766751 AGATTCTACC
*
19766761 TTTTTAACGTGATCAAGTGATAACCTTTACACTTGT
1 TTTTTAACGAGATCAAGTGATAACCTTTACACTTGT
* ** *
19766797 TTTTTAACAAGATCAAGCAATAA-CTCTTACACTTGC
1 TTTTTAACGAGATCAAGTGATAACCT-TTACACTTGT
* *
19766833 TTTTTAACGTGATCAAGTGATAACCCTTACACTT-T
1 TTTTTAACGAGATCAAGTGATAACCTTTACACTTGT
* *
19766868 CTTTTTAACGGGATCAA-TCGATAACCTTTACACTTGC
1 -TTTTTAACGAGATCAAGT-GATAACCTTTACACTTGT
* * * *
19766905 TTTTTCACAAGATCAAGTCAT-ACCTCTTACA-TTTT
1 TTTTTAACGAGATCAAGTGATAACCT-TTACACTTGT
19766940 TTTTT
1 TTTTT
19766945 CACGTGATAC
Statistics
Matches: 121, Mismatches: 20, Indels: 15
0.78 0.13 0.10
Matches are distributed among these distances:
35 14 0.12
36 105 0.87
37 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (36 bp):
TTTTTAACGAGATCAAGTGATAACCTTTACACTTGT
Found at i:19766883 original size:72 final size:70
Alignment explanation
Indices: 19766760--19766979 Score: 228
Period size: 72 Copynumber: 3.1 Consensus size: 70
19766750 AAGATTCTAC
* *
19766760 CTTTTTAACGTGATCAAGTGATAACCTTTACACTTGTTTTTTAACAAGATCAAGCAATAACTCTT
1 CTTTTTAACGTGATCAAGTGATAACCCTTACACTT-TTTTTTAACGAGATCAA-CAATAACTCTT
19766825 ACACTTG
64 ACACTTG
* *
19766832 CTTTTTAACGTGATCAAGTGATAACCCTTACACTTTCTTTTTAACGGGATCAATCGATAAC-CTT
1 CTTTTTAACGTGATCAAGTGATAACCCTTACACTTT-TTTTTAACGAGATCAA-CAATAACTC-T
19766896 TACACTTG
63 TACACTTG
* ** * * * * * *
19766904 CTTTTTCACAAGATCAAGTCAT-ACCTCTTACATTTTTTTTTCACGTGATACAACAATGACTTTT
1 CTTTTTAACGTGATCAAGTGATAACC-CTTACACTTTTTTTTAACGAGAT-CAACAATAACTCTT
* *
19766968 GCACTAG
64 ACACTTG
19766975 CTTTT
1 CTTTT
19766980 AAATAGGATC
Statistics
Matches: 126, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
71 33 0.26
72 93 0.74
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (70 bp):
CTTTTTAACGTGATCAAGTGATAACCCTTACACTTTTTTTTAACGAGATCAACAATAACTCTTAC
ACTTG
Found at i:19768673 original size:36 final size:37
Alignment explanation
Indices: 19768582--19768711 Score: 115
Period size: 36 Copynumber: 3.5 Consensus size: 37
19768572 CTGAATGTCT
* *
19768582 TTTCAAGGATCAAGCACAAC-CTCA-ACCAAAGTCATTGCC
1 TTTCAAGGATCAAGCACAACATTCACA-CAAA---AATGCC
** *
19768621 TTTTTAGGATCAAGCACAACATTTACAACAAAAATGCC
1 TTTCAAGGATCAAGCACAACATTCAC-ACAAAAATGCC
* **
19768659 -TT-AAGGATCAAGCACAACCTTCACACCTAAATGCC
1 TTTCAAGGATCAAGCACAACATTCACACAAAAATGCC
19768694 TTTCAAGGATCAAGCACA
1 TTTCAAGGATCAAGCACA
19768712 GCCTATCATG
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
35 9 0.12
36 21 0.28
37 16 0.21
38 5 0.07
39 18 0.24
40 2 0.03
41 4 0.05
42 1 0.01
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.22
Consensus pattern (37 bp):
TTTCAAGGATCAAGCACAACATTCACACAAAAATGCC
Found at i:19771348 original size:23 final size:23
Alignment explanation
Indices: 19771318--19771371 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
19771308 TACATATACT
19771318 CATCATCATCATGCACACCATCC
1 CATCATCATCATGCACACCATCC
* *
19771341 CATCATCATCATGCACACCGTCT
1 CATCATCATCATGCACACCATCC
19771364 CATCATCA
1 CATCATCA
19771372 CCAGCTCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.41, G:0.06, T:0.24
Consensus pattern (23 bp):
CATCATCATCATGCACACCATCC
Found at i:19774296 original size:21 final size:21
Alignment explanation
Indices: 19774270--19774311 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
19774260 CATTATGGAC
* *
19774270 CGTGCCATAGGACAGCGGGAT
1 CGTGCCATAAGACAACGGGAT
19774291 CGTGCCATAAGACAACGGGAT
1 CGTGCCATAAGACAACGGGAT
19774312 TGTATTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.33, T:0.14
Consensus pattern (21 bp):
CGTGCCATAAGACAACGGGAT
Found at i:19775511 original size:56 final size:56
Alignment explanation
Indices: 19775449--19775557 Score: 218
Period size: 56 Copynumber: 1.9 Consensus size: 56
19775439 ACTTTGGTAC
19775449 ATAGAGTTATTTTGACACATTTTGGGGGCTTAAGTGGTTAGACTTTTGAGATTTGG
1 ATAGAGTTATTTTGACACATTTTGGGGGCTTAAGTGGTTAGACTTTTGAGATTTGG
19775505 ATAGAGTTATTTTGACACATTTTGGGGGCTTAAGTGGTTAGACTTTTGAGATT
1 ATAGAGTTATTTTGACACATTTTGGGGGCTTAAGTGGTTAGACTTTTGAGATT
19775558 GTAAGTCCAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (56 bp):
ATAGAGTTATTTTGACACATTTTGGGGGCTTAAGTGGTTAGACTTTTGAGATTTGG
Found at i:19778619 original size:2 final size:2
Alignment explanation
Indices: 19778612--19778637 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19778602 TATTATGATG
19778612 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19778638 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19778808 original size:38 final size:39
Alignment explanation
Indices: 19778766--19778868 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 39
19778756 ATAGTGCCCG
19778766 TGTGCACGATGTGGGGGGATGTACACGAT-AG-CA-CTAA
1 TGTGCACGATGTGGGGGGATGTACACGATGAGCCAGCT-A
* * * *
19778803 TTGTGCACAATGTGGGGGGATGCACATGATGGTGCCAGCTA
1 -TGTGCACGATGTGGGGGGATGTACACGAT-GAGCCAGCTA
19778844 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
19778869 TGAGNNNNNN
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
38 26 0.47
40 24 0.44
41 3 0.05
42 2 0.04
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.23
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGGATGTACACGATGAGCCAGCTA
Found at i:19778857 original size:40 final size:38
Alignment explanation
Indices: 19778766--19778871 Score: 126
Period size: 40 Copynumber: 2.7 Consensus size: 38
19778756 ATAGTGCCCG
*
19778766 TGTGCACGATGTGGGGGGATGTACACGATAGCACTAAT
1 TGTGCACGATGTGGGGGGATGTACATGATAGCACTAAT
* * *
19778804 TGTGCACAATGTGGGGGGATGCACATGATGGTGCCAGCT-A-
1 TGTGCACGATGTGGGGGGATGTACATGAT--AG-CA-CTAAT
19778844 TGTGCACGATGTGGGGGGATGTACATGA
1 TGTGCACGATGTGGGGGGATGTACATGA
19778872 GNNNNNNNNN
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
38 26 0.45
40 27 0.47
41 3 0.05
42 2 0.03
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.24
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATAGCACTAAT
Found at i:19786934 original size:38 final size:39
Alignment explanation
Indices: 19786892--19786994 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 39
19786882 ATAGTGCCCG
19786892 TGTGCACGATGTGGGGGGATGTACACGAT-AG-CA-CTAA
1 TGTGCACGATGTGGGGGGATGTACACGATGAGCCAGCT-A
* * * *
19786929 TTGTGCACAATGTGGGGGGATGCACATGATGGTGCCAGCTA
1 -TGTGCACGATGTGGGGGGATGTACACGAT-GAGCCAGCTA
19786970 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
19786995 TGAGTCGGGA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
38 26 0.47
40 24 0.44
41 3 0.05
42 2 0.04
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.23
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGGATGTACACGATGAGCCAGCTA
Found at i:19786983 original size:40 final size:38
Alignment explanation
Indices: 19786892--19786997 Score: 126
Period size: 40 Copynumber: 2.7 Consensus size: 38
19786882 ATAGTGCCCG
*
19786892 TGTGCACGATGTGGGGGGATGTACACGATAGCACTAAT
1 TGTGCACGATGTGGGGGGATGTACATGATAGCACTAAT
* * *
19786930 TGTGCACAATGTGGGGGGATGCACATGATGGTGCCAGCT-A-
1 TGTGCACGATGTGGGGGGATGTACATGAT--AG-CA-CTAAT
19786970 TGTGCACGATGTGGGGGGATGTACATGA
1 TGTGCACGATGTGGGGGGATGTACATGA
19786998 GTCGGGAGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
38 26 0.45
40 27 0.47
41 3 0.05
42 2 0.03
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.24
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATAGCACTAAT
Found at i:19792267 original size:43 final size:42
Alignment explanation
Indices: 19792157--19792329 Score: 186
Period size: 43 Copynumber: 4.1 Consensus size: 42
19792147 GTAATGATAT
*
19792157 TGACCCGGCTATGTG-TGAGTAGGAGTGCGCATATGCCGATGA
1 TGACCCGGCTATGTGCT-AGTAGGAGTGCGCATAAGCCGATGA
* * * * *
19792199 TGACCCGACTGTGTGCGAGTAGGAGTGTGCATACGCCGATGA
1 TGACCCGGCTATGTGCTAGTAGGAGTGCGCATAAGCCGATGA
*
19792241 TTGACCCGGCTATGTGCTAGTGGGAGTGCGCATAAGCCGATGA
1 -TGACCCGGCTATGTGCTAGTAGGAGTGCGCATAAGCCGATGA
* * * * * * *
19792284 TGACTCAGCCATGTGCTAGTGGGGAGTGCACATGAGCTGATGA
1 TGACCCGGCTATGTGCTAGT-AGGAGTGCGCATAAGCCGATGA
19792327 TGA
1 TGA
19792330 TGGGAGAGTG
Statistics
Matches: 111, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
42 53 0.48
43 58 0.52
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.23
Consensus pattern (42 bp):
TGACCCGGCTATGTGCTAGTAGGAGTGCGCATAAGCCGATGA
Found at i:19804770 original size:122 final size:121
Alignment explanation
Indices: 19804548--19804793 Score: 431
Period size: 122 Copynumber: 2.0 Consensus size: 121
19804538 CTTTTAACTA
* * *
19804548 TTTTCCAGATGAGATTTTTTCACAATTGAAGAAAATGTATTTTTTGTCAGAAAAAGAAAAACGTT
1 TTTTCCAGATGAGAGTTTTTCACAATTGAAGAAAACGTAGTTTTTGTCAGAAAAAGAAAAACGTT
*
19804613 TTTCTTTTTTGCCACCACTCCCTTTGTGTGAAAGAAAAAATTGCTTATGAAGCAAT
66 TTTCTTTATTGCCACCACTCCCTTTGTGTGAAAGAAAAAATTGCTTATGAAGCAAT
19804669 TTTTCNCAGATGAGAGTTTTTCACAATTGAAGAAAACGTAGTTTTTGTCAGAAAAAGAAAAACG-
1 TTTTC-CAGATGAGAGTTTTTCACAATTGAAGAAAACGTAGTTTTTGTCAGAAAAAGAAAAACGT
19804733 TTTTCTTTCATTGCCACCACTCCCTTTGTGTGAAAGAAAAAATTGCTTATGAAGCAAT
65 TTTTCTTT-ATTGCCACCACTCCCTTTGTGTGAAAGAAAAAATTGCTTATGAAGCAAT
19804791 TTT
1 TTT
19804794 CAAGAGAGGT
Statistics
Matches: 119, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
121 13 0.11
122 106 0.89
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (121 bp):
TTTTCCAGATGAGAGTTTTTCACAATTGAAGAAAACGTAGTTTTTGTCAGAAAAAGAAAAACGTT
TTTCTTTATTGCCACCACTCCCTTTGTGTGAAAGAAAAAATTGCTTATGAAGCAAT
Found at i:19805683 original size:37 final size:37
Alignment explanation
Indices: 19805642--19805773 Score: 151
Period size: 39 Copynumber: 3.5 Consensus size: 37
19805632 TCCTCAAAGT
*
19805642 CCAGCTCTTTCTTTCTTTTTCTGCTAGCCACCACAAC
1 CCAGCTCTTTCTCTCTTTTTCTGCTAGCCACCACAAC
* * * *
19805679 CCAGCTCTTTCTCTCTTTTTTTCCATCAACCACCATAAC
1 CCAGCTCTTTCTCTCTTTTTCTGC-T-AGCCACCACAAC
*
19805718 CCAGCTCTTTCTCTCTTTTTTCCGCTAGCCACCACAAC
1 CCAGCTCTTTCTCTC-TTTTTCTGCTAGCCACCACAAC
*
19805756 CTCAACT-TTT-TCTCTTTT
1 C-CAGCTCTTTCTCTCTTTT
19805774 CCTTTCTTTC
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
36 4 0.05
37 25 0.31
38 15 0.19
39 30 0.38
40 6 0.08
ACGTcount: A:0.17, C:0.38, G:0.05, T:0.40
Consensus pattern (37 bp):
CCAGCTCTTTCTCTCTTTTTCTGCTAGCCACCACAAC
Found at i:19808002 original size:54 final size:54
Alignment explanation
Indices: 19807870--19808005 Score: 166
Period size: 54 Copynumber: 2.5 Consensus size: 54
19807860 ATTAGGATAC
* *
19807870 CACCACATCTCATCC-AGCTCATGTACATCCCCCCACATCATGCACATAACCAAA
1 CACCCCATCTCA-CCTAGCTCATGTGCATCCCCCCACATCATGCACATAACCAAA
* * * *****
19807924 CACCCCATCTCACCTAACTCATGTGCATCCCCCCACATCGTGTACATAGTTGGA
1 CACCCCATCTCACCTAGCTCATGTGCATCCCCCCACATCATGCACATAACCAAA
19807978 CACCCCATCTCACCTAGCTCATGTGCAT
1 CACCCCATCTCACCTAGCTCATGTGCAT
19808006 NCGTGCACAT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
53 2 0.03
54 68 0.97
ACGTcount: A:0.27, C:0.41, G:0.10, T:0.22
Consensus pattern (54 bp):
CACCCCATCTCACCTAGCTCATGTGCATCCCCCCACATCATGCACATAACCAAA
Found at i:19808038 original size:47 final size:48
Alignment explanation
Indices: 19807985--19808108 Score: 133
Period size: 56 Copynumber: 2.4 Consensus size: 48
19807975 GGACACCCCA
*
19807985 TCTCACCTAGCTCATGTGCAT-NCGTGCACATAGCCGGAGTCATCATG
1 TCTCACCTAGCTCATGTGCATATCGTGCACATAGCCGGAGTCATCATG
* *
19808032 TCTCACCCAGCTCATGTGGATCCCCTCATATCGTGCACATAGCCGGAGTCATCGTG
1 TCTCACCTAGCTCATGT-G-------CATATCGTGCACATAGCCGGAGTCATCATG
*
19808088 TCTCACCTGGCTCATGTGCAT
1 TCTCACCTAGCTCATGTGCAT
19808109 CCCCTTACAT
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
47 16 0.25
48 4 0.06
55 4 0.06
56 39 0.62
ACGTcount: A:0.19, C:0.32, G:0.21, T:0.27
Consensus pattern (48 bp):
TCTCACCTAGCTCATGTGCATATCGTGCACATAGCCGGAGTCATCATG
Found at i:19808069 original size:56 final size:56
Alignment explanation
Indices: 19808007--19808128 Score: 181
Period size: 56 Copynumber: 2.2 Consensus size: 56
19807997 CATGTGCATN
* *
19808007 CGTGCACATAGCCGGAGTCATCATGTCTCACCCAGCTCATGTGGATCCCCTCATAT
1 CGTGCACATAGCCGGAGTCATCATGTCTCACCCAGCTCATGTGCATCCCCTCACAT
* ** *
19808063 CGTGCACATAGCCGGAGTCATCGTGTCTCACCTGGCTCATGTGCATCCCCTTACAT
1 CGTGCACATAGCCGGAGTCATCATGTCTCACCCAGCTCATGTGCATCCCCTCACAT
*
19808119 CATGCACATA
1 CGTGCACATA
19808129 TAATGCCATC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (56 bp):
CGTGCACATAGCCGGAGTCATCATGTCTCACCCAGCTCATGTGCATCCCCTCACAT
Found at i:19809343 original size:35 final size:34
Alignment explanation
Indices: 19809266--19809462 Score: 225
Period size: 35 Copynumber: 5.7 Consensus size: 34
19809256 GCAGCCCTTG
* *
19809266 TTTTCTCTCTC-AAATTTAAAGCAAAACTTTTTCT
1 TTTTC-CTCTCAAAATTTACAGCAAAACTCTTTCT
*
19809300 TTTTCCTCTCAAAATTTATAGCAAAACTCTTTCT
1 TTTTCCTCTCAAAATTTACAGCAAAACTCTTTCT
** *
19809334 TTTTCCCTCTCAAAATTTGTAGGAAAACTCTTTCT
1 TTTT-CCTCTCAAAATTTACAGCAAAACTCTTTCT
* *
19809369 ATTTCCTACTAAAAATTTACAGCAAAACTCTTTCT
1 TTTTCCT-CTCAAAATTTACAGCAAAACTCTTTCT
* * * *
19809404 ATTTCCCTCTCAAAATTTGCAACAAAACTCTATCT
1 -TTTTCCTCTCAAAATTTACAGCAAAACTCTTTCT
*
19809439 TTTTCGTCTCAAAATTTTACAGCA
1 TTTTCCTCTCAAAA-TTTACAGCA
19809463 CAAGGCCTCT
Statistics
Matches: 139, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
33 5 0.04
34 45 0.32
35 84 0.60
36 5 0.04
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (34 bp):
TTTTCCTCTCAAAATTTACAGCAAAACTCTTTCT
Found at i:19812930 original size:22 final size:22
Alignment explanation
Indices: 19812899--19812950 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
19812889 ATTGTTTAAT
* *
19812899 TTAATCAATTAGGCCCAACAAC
1 TTAATTAATTAAGCCCAACAAC
*
19812921 TTAATTAATTAAGCCCAACAAT
1 TTAATTAATTAAGCCCAACAAC
19812943 TTAATTAA
1 TTAATTAA
19812951 ATATTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (22 bp):
TTAATTAATTAAGCCCAACAAC
Found at i:19813098 original size:36 final size:35
Alignment explanation
Indices: 19812915--19813134 Score: 216
Period size: 36 Copynumber: 6.3 Consensus size: 35
19812905 AATTAGGCCC
* * ** *
19812915 AACAACTTAATTAATTAAGCCCAACAATTTAATTA
1 AACAATTTAATTAATTAGGCCCAATGACTTAATTA
* * *
19812950 AATATTTTTAATCAATTAGGCCC--TGACTTAATTA
1 AACA-ATTTAATTAATTAGGCCCAATGACTTAATTA
* **
19812984 AACAAATTTAATCAATTAGGCCCAAAAACTTAATTA
1 AAC-AATTTAATTAATTAGGCCCAATGACTTAATTA
***
19813020 TTTAATTTAATTAATTAGGCCCAATGACTTAATTA
1 AACAATTTAATTAATTAGGCCCAATGACTTAATTA
* *
19813055 AATAATTTAATTAATTAGGCCCTAATGATTTAATTA
1 AACAATTTAATTAATTAGGCCC-AATGACTTAATTA
*
19813091 AACAATTTAATTAATTAGGCAC-A--ACTTAATTA
1 AACAATTTAATTAATTAGGCCCAATGACTTAATTA
19813123 AACAAATTTAAT
1 AAC-AATTTAAT
19813135 CAAGTGCTTA
Statistics
Matches: 155, Mismatches: 24, Indels: 14
0.80 0.12 0.07
Matches are distributed among these distances:
32 11 0.07
33 8 0.05
34 28 0.18
35 53 0.34
36 55 0.35
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.36
Consensus pattern (35 bp):
AACAATTTAATTAATTAGGCCCAATGACTTAATTA
Found at i:19815673 original size:19 final size:20
Alignment explanation
Indices: 19815641--19815678 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19815631 AAATATCTTT
19815641 TTCTTCTAGCAGCTTCTTCA
1 TTCTTCTAGCAGCTTCTTCA
*
19815661 TTCTTC-AGTAGCTTCTTC
1 TTCTTCTAGCAGCTTCTTC
19815679 TCTTTCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.13, C:0.29, G:0.11, T:0.47
Consensus pattern (20 bp):
TTCTTCTAGCAGCTTCTTCA
Found at i:19816560 original size:2 final size:2
Alignment explanation
Indices: 19816553--19816588 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19816543 NNNNNNNNNN
*
19816553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19816589 GGTATATGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19820465 original size:2 final size:2
Alignment explanation
Indices: 19820458--19820534 Score: 109
Period size: 2 Copynumber: 38.0 Consensus size: 2
19820448 TAAATCATAC
* * *
19820458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT NAA AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
*
19820501 AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19820535 TTACGAAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19821420 original size:39 final size:39
Alignment explanation
Indices: 19821356--19821471 Score: 121
Period size: 39 Copynumber: 3.1 Consensus size: 39
19821346 TCCTCAAAGT
* * *
19821356 CCAACT-TTT-TCTTTCTTTTTCCACCAGCTACCACAAC
1 CCAACTCTTTCTCTTTTTTTTTCCACCAACCACCACAAC
* * *
19821393 CCAGCTCTTTGTCTTTTTTTTTTCACCAACCACCACAAC
1 CCAACTCTTTCTCTTTTTTTTTCCACCAACCACCACAAC
* * * *
19821432 CCAACTCTTTCTC-TCTTTTTTCCGCTAGCCACCACAAC
1 CCAACTCTTTCTCTTTTTTTTTCCACCAACCACCACAAC
19821470 CC
1 CC
19821472 TAGCTTTCTC
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
37 5 0.08
38 25 0.38
39 35 0.54
ACGTcount: A:0.20, C:0.40, G:0.04, T:0.36
Consensus pattern (39 bp):
CCAACTCTTTCTCTTTTTTTTTCCACCAACCACCACAAC
Found at i:19827469 original size:40 final size:39
Alignment explanation
Indices: 19827372--19827476 Score: 124
Period size: 38 Copynumber: 2.7 Consensus size: 39
19827362 TGATACTGCC
* * * *
19827372 CATGTGCACGATATGGAGGGATGCACACGATGGCATTAA
1 CATGTGCACGATGTGGGGGGATGCACACGATGACATCAA
* *
19827411 C-TGCGCACGATGTGGGGGGATGCACACGATGAC-TCCAG
1 CATGTGCACGATGTGGGGGGATGCACACGATGACAT-CAA
19827449 CTATGTGCACGATGTGGGGGGATGCACA
1 C-ATGTGCACGATGTGGGGGGATGCACA
19827477 TGAGCTAGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
37 1 0.02
38 30 0.54
39 1 0.02
40 24 0.43
ACGTcount: A:0.25, C:0.21, G:0.35, T:0.19
Consensus pattern (39 bp):
CATGTGCACGATGTGGGGGGATGCACACGATGACATCAA
Found at i:19827509 original size:54 final size:54
Alignment explanation
Indices: 19827447--19827551 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
19827437 CGATGACTCC
*
19827447 AGCTATGTGCACGATGTGGGGGGATGCACATGAGCTAGTTGACATGGGGTGTCT
1 AGCTATGTGCACGATGTGGGGGGATGCACATGAGCTAGGTGACATGGGGTGTCT
* * * *
19827501 AGCTATGTGCACGATGTTGGGGGATGCATATGAGCTGGGTGAGATGGGGTG
1 AGCTATGTGCACGATGTGGGGGGATGCACATGAGCTAGGTGACATGGGGTG
19827552 GTATACAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.20, C:0.12, G:0.42, T:0.26
Consensus pattern (54 bp):
AGCTATGTGCACGATGTGGGGGGATGCACATGAGCTAGGTGACATGGGGTGTCT
Found at i:19828290 original size:26 final size:26
Alignment explanation
Indices: 19828254--19828304 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
19828244 AGGTGACTTT
19828254 AAGAATAGTTGATGGAATGATGAGCC
1 AAGAATAGTTGATGGAATGATGAGCC
19828280 AAGAATAGTTGATGGAATGATGAGC
1 AAGAATAGTTGATGGAATGATGAGC
19828305 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.06, G:0.31, T:0.24
Consensus pattern (26 bp):
AAGAATAGTTGATGGAATGATGAGCC
Found at i:19828822 original size:15 final size:16
Alignment explanation
Indices: 19828804--19828833 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19828794 AACCTGTTTT
19828804 TGTAAAA-CTTTGCAA
1 TGTAAAACCTTTGCAA
19828819 TGTAAAACCTTTGCA
1 TGTAAAACCTTTGCA
19828834 TGAGGTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (16 bp):
TGTAAAACCTTTGCAA
Found at i:19829111 original size:2 final size:2
Alignment explanation
Indices: 19829104--19829181 Score: 131
Period size: 2 Copynumber: 39.5 Consensus size: 2
19829094 AAAATAGTAT
**
19829104 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GN T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19829145 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19829182 TACGGAATCG
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
1 1 0.01
2 71 0.99
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19833148 original size:43 final size:42
Alignment explanation
Indices: 19833083--19833216 Score: 187
Period size: 43 Copynumber: 3.1 Consensus size: 42
19833073 ACCGTCCCAC
* *
19833083 CATCATCAGCTCATGTGTACTCCCTACTCGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCC-ACACGCACATAGCTGGGT
* *
19833126 CATCATCAGCTCATGTGCACTCCCACACCGCACATAGTTTGGT
1 CATCATCAGCTCATGTGCACTCCCACA-CGCACATAGCTGGGT
* * *
19833169 TATCATCAACTCATGTGCACTCCCACACGTACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGT
19833211 CATCAT
1 CATCAT
19833217 TATCACACAA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 19 0.24
43 61 0.76
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (42 bp):
CATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGT
Found at i:19845424 original size:13 final size:13
Alignment explanation
Indices: 19845406--19845430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19845396 GGAGAAATTG
19845406 TGATTTTATAAAA
1 TGATTTTATAAAA
19845419 TGATTTTATAAA
1 TGATTTTATAAA
19845431 TTTTCTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:19849936 original size:25 final size:25
Alignment explanation
Indices: 19849908--19849962 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
19849898 CACAACCACA
**
19849908 TATATCAACTTGTGGCCTAGCCAAG
1 TATATCAACCCGTGGCCTAGCCAAG
* *
19849933 TATATCAACCCGTGGCCTTGCCACG
1 TATATCAACCCGTGGCCTAGCCAAG
19849958 TATAT
1 TATAT
19849963 ATCATAAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (25 bp):
TATATCAACCCGTGGCCTAGCCAAG
Found at i:19855590 original size:91 final size:91
Alignment explanation
Indices: 19855431--19855717 Score: 423
Period size: 91 Copynumber: 3.0 Consensus size: 91
19855421 CCAAAACATC
19855431 TTACTTTGCCCCGATATAGCTCTATAGCACCTTTTAACTCCATAAGTTTGACTTTAATAAAATAT
1 TTACTTTGCCCCGATATAGCTCTATAGCACCTTTTAACTCCATAAGTTTGACTTTAATAAAATAT
19855496 TATTATTTTATCATGTTGAAAATATT
66 TATTATTTTATCATGTTGAAAATATT
*
19855522 TTACTTTGCCCCGATATAGCTTTATAGCACCTTTTAACTCCATAAGTTTGACTTTAATAAAATTT
1 TTACTTTGCCCCGATATAGCTCTATAGCACCTTTTAACTCCATAAGTTTGACTTTAAT--AA---
*
19855587 TATTATTTTATTATTATTTTATCATGTAGAAAATATT
61 -A--A---TATTATTATTTTATCATGTTGAAAATATT
* *
19855624 TTACTTTGCCCCGATATAGCTCTATAGCACTTTTTAACTCCATAAGTTTGACTTTAATAAAATAC
1 TTACTTTGCCCCGATATAGCTCTATAGCACCTTTTAACTCCATAAGTTTGACTTTAATAAAATAT
19855689 TATTATTTTATCATGTAT-AAAATATT
66 TATTATTTTATCATGT-TGAAAATATT
19855715 TTA
1 TTA
19855718 TTCCAAAATA
Statistics
Matches: 178, Mismatches: 6, Indels: 24
0.86 0.03 0.12
Matches are distributed among these distances:
91 86 0.48
93 2 0.01
94 1 0.01
96 1 0.01
97 1 0.01
99 1 0.01
100 2 0.01
102 84 0.47
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (91 bp):
TTACTTTGCCCCGATATAGCTCTATAGCACCTTTTAACTCCATAAGTTTGACTTTAATAAAATAT
TATTATTTTATCATGTTGAAAATATT
Found at i:19855619 original size:102 final size:102
Alignment explanation
Indices: 19855493--19855699 Score: 369
Period size: 102 Copynumber: 2.0 Consensus size: 102
19855483 TTTAATAAAA
* *
19855493 TATTATTATTTTATCATGTTGAAAATATTTTACTTTGCCCCGATATAGCTTTATAGCACCTTTTA
1 TATTATTATTTTATCATGTAGAAAATATTTTACTTTGCCCCGATATAGCTCTATAGCACCTTTTA
**
19855558 ACTCCATAAGTTTGACTTTAATAAAATTTTATTATTT
66 ACTCCATAAGTTTGACTTTAATAAAATACTATTATTT
*
19855595 TATTATTATTTTATCATGTAGAAAATATTTTACTTTGCCCCGATATAGCTCTATAGCACTTTTTA
1 TATTATTATTTTATCATGTAGAAAATATTTTACTTTGCCCCGATATAGCTCTATAGCACCTTTTA
19855660 ACTCCATAAGTTTGACTTTAATAAAATACTATTATTT
66 ACTCCATAAGTTTGACTTTAATAAAATACTATTATTT
19855697 TAT
1 TAT
19855700 CATGTATAAA
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (102 bp):
TATTATTATTTTATCATGTAGAAAATATTTTACTTTGCCCCGATATAGCTCTATAGCACCTTTTA
ACTCCATAAGTTTGACTTTAATAAAATACTATTATTT
Found at i:19856840 original size:43 final size:43
Alignment explanation
Indices: 19856792--19856879 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
19856782 TTGTGAATAG
* *
19856792 AATGCTTTAAATAGCAATTGGTGGAGTTGTATATATAAGAAAT
1 AATGCTTCAAATAGCAATTGATGGAGTTGTATATATAAGAAAT
19856835 AATGCTTCAAATAGCAATTGATGGAGTTGTATATATAAGAAAT
1 AATGCTTCAAATAGCAATTGATGGAGTTGTATATATAAGAAAT
19856878 AA
1 AA
19856880 ATGAATTTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (43 bp):
AATGCTTCAAATAGCAATTGATGGAGTTGTATATATAAGAAAT
Found at i:19870277 original size:21 final size:22
Alignment explanation
Indices: 19870252--19870292 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19870242 CTTAGGTGGA
*
19870252 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
19870273 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
19870293 AAAAAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:19870293 original size:20 final size:21
Alignment explanation
Indices: 19870252--19870296 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
19870242 CTTAGGTGGA
*
19870252 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
19870273 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
19870293 AAAA
1 AAAA
19870297 AAAGGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:19870297 original size:21 final size:20
Alignment explanation
Indices: 19870250--19870297 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
19870240 ACCTTAGGTG
*
19870250 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
19870270 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
19870292 GAAAAA
1 GAAAAA
19870298 AAGGTAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:19895886 original size:40 final size:38
Alignment explanation
Indices: 19895831--19895931 Score: 139
Period size: 38 Copynumber: 2.6 Consensus size: 38
19895821 ACCCGGCTCA
*
19895831 TGTGCATCCACCCACATCGTGCACATAGCCAGCACCATCG
1 TGTGCATCCCCCCACATCGTGCACA-A-CCAGCACCATCG
* **
19895871 TGTGCATCCCCCCACATCGTGCACAATCAGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCACAACCAGCACCATCG
*
19895909 TGTACATCCCCCCACATCGTGCA
1 TGTGCATCCCCCCACATCGTGCA
19895932 TACGGGCACT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 31 0.55
39 1 0.02
40 24 0.43
ACGTcount: A:0.23, C:0.41, G:0.17, T:0.20
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACAACCAGCACCATCG
Found at i:19895926 original size:19 final size:19
Alignment explanation
Indices: 19895866--19895929 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
19895856 TAGCCAGCAC
*
19895866 CATCGTGTGCATCCCCCCA
1 CATCGTGTACATCCCCCCA
* ****
19895885 CATCGTGCACAATCAGTGC-
1 CATCGTGTAC-ATCCCCCCA
19895904 CATCGTGTACATCCCCCCA
1 CATCGTGTACATCCCCCCA
19895923 CATCGTG
1 CATCGTG
19895930 CATACGGGCA
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 4 0.12
19 24 0.75
20 4 0.12
ACGTcount: A:0.20, C:0.41, G:0.17, T:0.22
Consensus pattern (19 bp):
CATCGTGTACATCCCCCCA
Found at i:19904762 original size:24 final size:24
Alignment explanation
Indices: 19904727--19904772 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
19904717 TTATAAATTC
19904727 TAATCTCATAAATGTTTT-TATAAT
1 TAATCTCATAAA-GTTTTGTATAAT
19904751 TAATGCTC-TAAAGTTTTGTATA
1 TAAT-CTCATAAAGTTTTGTATA
19904773 CAGATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.25
24 12 0.60
25 3 0.15
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (24 bp):
TAATCTCATAAAGTTTTGTATAAT
Found at i:19919692 original size:50 final size:50
Alignment explanation
Indices: 19919627--19919849 Score: 204
Period size: 49 Copynumber: 4.4 Consensus size: 50
19919617 CCACTATCAA
* *
19919627 GGATTCTTGCTTTTTAATGGGAAGCGATAACCT-TTACACAATCCATAACG
1 GGATTCTTTCTTTTTAATGGGAAGCGATAACCTCTTACACAATCCACAA-G
* * *
19919677 GGGTTTTTTCTTTTTAATGAGAAGCGATAA-CTCTTACACAATCCACAAG
1 GGATTCTTTCTTTTTAATGGGAAGCGATAACCTCTTACACAATCCACAAG
* * * * *
19919726 GGATTCTTTCTTTTTAATAGGAAACGAAAACCTC-TGCACGATCCACAAG
1 GGATTCTTTCTTTTTAATGGGAAGCGATAACCTCTTACACAATCCACAAG
* * * * *
19919775 GGATTCTTGCTGTTTAAAAGGATCAATG-GATAGCCT-TTACACAATCCACAAAG
1 GGATTCTTTCT-TTTTAATGG--GAA-GCGATAACCTCTTACACAATCCAC-AAG
* *
19919828 AGATTCTTACTTTTTAATGGGA
1 GGATTCTTTCTTTTTAATGGGA
19919850 TATAGCGGTA
Statistics
Matches: 137, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
49 50 0.36
50 50 0.36
52 25 0.18
53 12 0.09
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (50 bp):
GGATTCTTTCTTTTTAATGGGAAGCGATAACCTCTTACACAATCCACAAG
Found at i:19920740 original size:35 final size:35
Alignment explanation
Indices: 19920710--19920895 Score: 189
Period size: 35 Copynumber: 5.3 Consensus size: 35
19920700 TTTAATTGTT
19920710 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * * *
19920745 CAATTTAATTAATTAAGCTCAATAATTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* *
19920780 CAAATTTAATCAATTAGGCCCAATGACTTAATTAAA
1 -TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * * *
19920816 TAATTTAATTAATTAGGCCTAATGATTTAACTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * *
19920851 CAATTTAATTAATTAGG--C-ACAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
*
19920883 CAATTTTAATCAA
1 TAA-TTTAATCAA
19920896 GTGCTTGAGA
Statistics
Matches: 126, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
32 13 0.10
33 8 0.06
35 76 0.60
36 29 0.23
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (35 bp):
TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
Found at i:19920799 original size:71 final size:70
Alignment explanation
Indices: 19920711--19920888 Score: 247
Period size: 71 Copynumber: 2.6 Consensus size: 70
19920701 TTAATTGTTT
19920711 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAG-CTCAATAATTTAA
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCT-AATAATTTAA
*
19920775 TTAAAC
65 CTAAAC
* * * *
19920781 AAATTTAATCAATTAGGCCCAATGACTTAATTAAATAATTTAATTAATTAGGCCTAATGATTTAA
1 -AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCTAATAATTTAA
19920846 CTAAAC
65 CTAAAC
* *
19920852 AATTTAATTAATTAGG--C-ACAACTTAATTAAACAATTT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTT
19920889 TAATCAAGTG
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
67 17 0.18
68 1 0.01
70 15 0.15
71 62 0.64
72 2 0.02
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (70 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCTAATAATTTAAC
TAAAC
Found at i:19924554 original size:14 final size:14
Alignment explanation
Indices: 19924535--19924562 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19924525 ATCATATTCA
19924535 ACCTTTTGATCAAT
1 ACCTTTTGATCAAT
19924549 ACCTTTTGATCAAT
1 ACCTTTTGATCAAT
19924563 TGAACATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
ACCTTTTGATCAAT
Found at i:19939443 original size:11 final size:11
Alignment explanation
Indices: 19939410--19939444 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
19939400 CCTAGGGTTC
19939410 TTGTTCTTCCT
1 TTGTTCTTCCT
19939421 TT-TTCTTCCT
1 TTGTTCTTCCT
*
19939431 TTGTTCTTGCT
1 TTGTTCTTCCT
19939442 TTG
1 TTG
19939445 GCCGGCCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.00, C:0.23, G:0.11, T:0.66
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:19941861 original size:13 final size:13
Alignment explanation
Indices: 19941843--19941867 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19941833 NNNCAGAAAA
19941843 TTTATAAAATCAT
1 TTTATAAAATCAT
19941856 TTTATAAAATCA
1 TTTATAAAATCA
19941868 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:19943775 original size:17 final size:18
Alignment explanation
Indices: 19943742--19943776 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19943732 CTAATTGTAG
19943742 AGTCCTAATCATTATTAGA
1 AGTCCTAAT-ATTATTAGA
19943761 AGTCCTAAT-TTATTAG
1 AGTCCTAATATTATTAG
19943777 TAAATTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (18 bp):
AGTCCTAATATTATTAGA
Found at i:19944621 original size:180 final size:181
Alignment explanation
Indices: 19944405--19944794 Score: 532
Period size: 180 Copynumber: 2.2 Consensus size: 181
19944395 TTAATAGCCT
* * * * *
19944405 AAATCAGCTTTTTTGGCCATGAAAATTTCCAGAAATAATCCTCATTGAGCATTTTAATAAAGATA
1 AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTGAACATTTTAATAAAAATA
* ** *
19944470 ATTTTTCTGGAATTTTTCAGTATTAATTTTTAAGAGTTTCTTGTCAATTAAAACTGAAATTCATG
66 ATTTTTCTGGAATTTTTCAGAATTAATTTCCAAGACTTTCTTGTCAATTAAAACTGAAATTCATG
* *
19944535 CCAAAATAGTGAGCTGGACAGATTT-A-TATTTGCACCAATTTTCTTGCTTG
131 CCAAAACAGTGAGCTGGACAGATTTCACTATTTGCACCAA-TTTCTTGCTTA
* * *
19944585 AAATCAGCATATTTGACCATGATATTTTCCAGAAATAATCCTTATTGAACATTTTAATAAAAATA
1 AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTGAACATTTTAATAAAAATA
*
19944650 ATTTTTCTGGAATTTTTCAGAATTAATTTCCAAGACTTTCTTGTTAATTAAAACTGAAATTCATG
66 ATTTTTCTGGAATTTTTCAGAATTAATTTCCAAGACTTTCTTGTCAATTAAAACTGAAATTCATG
* * * * * *
19944715 TCATAACAGTGAGCTGGACTGCTTTCACTTTTTGCTCCAATTTCTTGCTTA
131 CCAAAACAGTGAGCTGGACAGATTTCACTATTTGCACCAATTTCTTGCTTA
* * * *
19944766 AAATCAGCCTATTTAATCATGAACATTTC
1 AAATCAGCATATTTGACCATGAAAATTTC
19944795 ATGATTTTGC
Statistics
Matches: 181, Mismatches: 27, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
180 137 0.76
181 34 0.19
182 10 0.06
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (181 bp):
AAATCAGCATATTTGACCATGAAAATTTCCAGAAATAATCCTCATTGAACATTTTAATAAAAATA
ATTTTTCTGGAATTTTTCAGAATTAATTTCCAAGACTTTCTTGTCAATTAAAACTGAAATTCATG
CCAAAACAGTGAGCTGGACAGATTTCACTATTTGCACCAATTTCTTGCTTA
Found at i:19945076 original size:19 final size:20
Alignment explanation
Indices: 19945049--19945094 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
19945039 AGGAGACAAG
*
19945049 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
19945068 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
19945087 ATAATATT
1 ATAATATT
19945095 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:19960068 original size:2 final size:2
Alignment explanation
Indices: 19960058--19960112 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
19960048 CCACACATAG
*
19960058 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19960098 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
19960113 AAAATTTGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19960154 original size:2 final size:2
Alignment explanation
Indices: 19960147--19960180 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
19960137 TTATTATAAT
19960147 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19960181 TAGACTTGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:19960167 original size:17 final size:17
Alignment explanation
Indices: 19960141--19960182 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
19960131 ANTCACTTAT
19960141 TATA-ATTATATATATA
1 TATATATTATATATATA
19960157 TATATATTATATATATA
1 TATATATTATATATATA
19960174 TATATATTA
1 TATATATTA
19960183 GACTTGGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATTATATATATA
Found at i:19960169 original size:15 final size:15
Alignment explanation
Indices: 19960149--19960178 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19960139 ATTATAATTA
19960149 TATATATATATATAT
1 TATATATATATATAT
19960164 TATATATATATATAT
1 TATATATATATATAT
19960179 ATTAGACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:19961553 original size:31 final size:31
Alignment explanation
Indices: 19961477--19961553 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
19961467 CAACATAAGG
*
19961477 TTTGCA-ATTGGATAAAACCAAATATTAAAT
1 TTTGCATATTGGATATAACCAAATATTAAAT
19961507 TTTGCATATTGGATATAACCAAATATTAAAT
1 TTTGCATATTGGATATAACCAAATATTAAAT
19961538 TTTGCATATTGGATAT
1 TTTGCATATTGGATAT
19961554 TTCTCATAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 6 0.13
31 39 0.87
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (31 bp):
TTTGCATATTGGATATAACCAAATATTAAAT
Found at i:19961862 original size:18 final size:18
Alignment explanation
Indices: 19961839--19961883 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
19961829 CAAAATTATC
* *
19961839 TTAATATAGAAATATTTT
1 TTAATATAAAAATATTTA
*
19961857 TTAATAGAAAAATATTTA
1 TTAATATAAAAATATTTA
19961875 TTAATATAA
1 TTAATATAA
19961884 TTTTTGACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
TTAATATAAAAATATTTA
Found at i:19970940 original size:32 final size:32
Alignment explanation
Indices: 19970904--19971049 Score: 143
Period size: 35 Copynumber: 4.4 Consensus size: 32
19970894 TTTATCGAGA
*
19970904 TCAACTAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* *
19970936 TCAACCACAACCTTTCACAA-TGGTTTTTCACAGGC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAAAGGC
19970971 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* * * *
19971003 TCAACCACAACCAACAACAATGGTTTTTC-ACGAGA
1 TCAACCAAAACC--CAA-AGTGGTTTTTCAAAG-GC
19971038 TCAACCAAAACC
1 TCAACCAAAACC
19971050 TAACAACTAA
Statistics
Matches: 95, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
31 2 0.02
32 37 0.39
34 5 0.05
35 49 0.52
36 2 0.02
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:19970985 original size:67 final size:67
Alignment explanation
Indices: 19970877--19971049 Score: 253
Period size: 67 Copynumber: 2.6 Consensus size: 67
19970867 GCTTAGCCAA
* *
19970877 AACCTTTCACAATAGTTTTT-ATCGAGATCAACTAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCA-CGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
19970941 CAC
65 CAC
*
19970944 AACCTTTCACAATGGTTTTTCAC-AGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCACGA-GATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
19971008 CAC
65 CAC
**
19971011 AACC-AACAACAATGGTTTTTCACGAGATCAACCAAAACC
1 AACCTTTC-ACAATGGTTTTTCACGAGATCAACCAAAACC
19971050 TAACAACTAA
Statistics
Matches: 96, Mismatches: 6, Indels: 8
0.87 0.05 0.07
Matches are distributed among these distances:
66 2 0.02
67 92 0.96
68 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTCACGAGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
AC
Found at i:19982174 original size:67 final size:67
Alignment explanation
Indices: 19982037--19982175 Score: 158
Period size: 67 Copynumber: 2.1 Consensus size: 67
19982027 GGCTTTTACT
* * * * * *
19982037 AGGCTTAGCCAAAACTTTTCACAATAGTTTTTACCGGGATCAACTAAAACCCAAAGTGATTTTTC
1 AGGCTTAACCAAAACCTTTCACAATAGTTTTTACCGGGATCAACCAAAACCCAAACTAACTTTTC
19982102 AA
66 AA
* *
19982104 AGGCTTAACCACAACCTTTCACAATGGTTTTTGA-CGGG-TCAACCAAAACCCAATAACTAACTT
1 AGGCTTAACCAAAACCTTTCACAATAGTTTTT-ACCGGGATCAACCAAAACCC-A-AACTAACTT
19982167 TTC-A
63 TTCAA
19982171 AGGCT
1 AGGCT
19982176 AAGTTAGAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
66 12 0.20
67 39 0.64
68 10 0.16
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (67 bp):
AGGCTTAACCAAAACCTTTCACAATAGTTTTTACCGGGATCAACCAAAACCCAAACTAACTTTTC
AA
Found at i:19985608 original size:20 final size:19
Alignment explanation
Indices: 19985580--19985633 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
19985570 GGTAGTAGGC
*
19985580 TCTTAGTCGACTAACCTACT
1 TCTTGGTCGACTAACCTA-T
19985600 TCTTGGTCGACTAACCTAT
1 TCTTGGTCGACTAACCTAT
19985619 TCCTTGGTCGACTAA
1 T-CTTGGTCGACTAA
19985634 GTCTTCTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (19 bp):
TCTTGGTCGACTAACCTAT
Found at i:19988841 original size:36 final size:36
Alignment explanation
Indices: 19988801--19988974 Score: 217
Period size: 36 Copynumber: 4.9 Consensus size: 36
19988791 TCTCAAGCAC
19988801 TTGATTAAAATTGTTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAAATTGTTTAATTAAGTTATTGGGCCTAA
* * *
19988837 TTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAG
1 TTGATTAAAATTGTTTAATTAAGTTATTGGGCCTAA
* * *
19988873 TTGATTAAAATTGTTTAATTAAATTGTTGGGCTTAA
1 TTGATTAAAATTGTTTAATTAAGTTATTGGGCCTAA
* * *
19988909 TTAATT-AAATTATTTAATTAAGTTATTGGGCTTAA
1 TTGATTAAAATTGTTTAATTAAGTTATTGGGCCTAA
***
19988944 TTGATT-AAATTAAATAATTAAGTTACTTGGG
1 TTGATTAAAATTGTTTAATTAAGTTA-TTGGG
19988975 TTTTTAAAGG
Statistics
Matches: 121, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
35 48 0.40
36 73 0.60
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (36 bp):
TTGATTAAAATTGTTTAATTAAGTTATTGGGCCTAA
Found at i:19990922 original size:42 final size:42
Alignment explanation
Indices: 19990875--19990986 Score: 170
Period size: 42 Copynumber: 2.6 Consensus size: 42
19990865 GTGATGATAT
19990875 TGACCCGGCTATGTGCAAGTGGGAGTGTGCATAAGCCGATGC
1 TGACCCGGCTATGTGCAAGTGGGAGTGTGCATAAGCCGATGC
*
19990917 TGACCCGGTTATGTGCAAGTGGGAGTGTGCATAAGCCGATGC
1 TGACCCGGCTATGTGCAAGTGGGAGTGTGCATAAGCCGATGC
** * *
19990959 TGACCTAGCTATGTACGAGTAGGGAGTG
1 TGACCCGGCTATGTGCAAGT-GGGAGTG
19990987 CACATGAGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 56 0.89
43 7 0.11
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (42 bp):
TGACCCGGCTATGTGCAAGTGGGAGTGTGCATAAGCCGATGC
Found at i:19993478 original size:43 final size:43
Alignment explanation
Indices: 19993421--19993534 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 43
19993411 GTAATTATAT
* * *
19993421 TGACTCGGCTATGTGCGAGTAAGGAGTGTGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAAGGAGTGAGCATAACCCG-GTGA
* *
19993464 TGACCCGGTTATGTGCAAGT-AGGAAGTGAGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAAGG-AGTGAGCATAACCCGGTGA
* * *
19993507 TGACCCAGCCATGTGCGAGTAGGGAGTG
1 TGACCCGGCTATGTGCGAGTAAGGAGTG
19993535 CGTATGAGTT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
42 4 0.07
43 52 0.90
44 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.20
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAAGGAGTGAGCATAACCCGGTGA
Found at i:19997627 original size:16 final size:17
Alignment explanation
Indices: 19997583--19997627 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
19997573 TTTCAAGATA
19997583 ATTTATAAAATCA-TTTC
1 ATTTATAAAA-CATTTTC
*
19997600 ATTTA-AACACATTTTC
1 ATTTATAAAACATTTTC
19997616 -TTTATAAAACAT
1 ATTTATAAAACAT
19997628 AAAGATTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 6 0.25
16 13 0.54
17 5 0.21
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTATAAAACATTTTC
Found at i:20008628 original size:39 final size:38
Alignment explanation
Indices: 20008502--20008677 Score: 185
Period size: 39 Copynumber: 4.6 Consensus size: 38
20008492 TCTCCCCGAC
* **
20008502 TCATGTGCACTCCCATACCGCACATTACAATATCATCA
1 TCATGTGCACTCCCACACCGCACATGGCAATATCATCA
* * * ** * *
20008540 TCAAGTGCACTCTCACACCGCACCT--CACCATCACCG
1 TCATGTGCACTCCCACACCGCACATGGCAATATCATCA
20008576 TCATGTGCACTCCCACACCGCACATGGCATATATCATCA
1 TCATGTGCACTCCCACACCGCACATGGCA-ATATCATCA
* *
20008615 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCG
1 TCATGTGCACTCCCACACCGCACATGGCA-ATATCATCA
* * *
20008654 GCATGTGCTCTCCCACGCCGCACA
1 TCATGTGCACTCCCACACCGCACA
20008678 CTACCGGCAC
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
36 29 0.25
38 23 0.20
39 64 0.55
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.22
Consensus pattern (38 bp):
TCATGTGCACTCCCACACCGCACATGGCAATATCATCA
Found at i:20008669 original size:78 final size:74
Alignment explanation
Indices: 20008503--20008677 Score: 197
Period size: 75 Copynumber: 2.3 Consensus size: 74
20008493 CTCCCCGACT
* * * * *
20008503 CATGTGCACTCCCATACCGCACATTACAATATCATCATCAAGTGCACTCTCACACCGCACCTCAC
1 CATGTGCACTCCCACACCGCACATGACAATATCATCATCAAGTGCACTCCCACACCGCACATCAA
*
20008568 CATCACCGT
66 CATCACCGG
* * *
20008577 CATGTGCACTCCCACACCGCACATGGCATATATCATCATCATGTGCTCTCCCACACCGCACATGG
1 CATGTGCACTCCCACACCGCACATGACA-ATATCATCATCAAGTGCACTCCCACACCGCACAT--
* *
20008642 CATATATCATCGG
63 CA-ACATCACCGG
* *
20008655 CATGTGCTCTCCCACGCCGCACA
1 CATGTGCACTCCCACACCGCACA
20008678 CTACCGGCAC
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
74 25 0.30
75 30 0.36
77 2 0.02
78 27 0.32
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.22
Consensus pattern (74 bp):
CATGTGCACTCCCACACCGCACATGACAATATCATCATCAAGTGCACTCCCACACCGCACATCAA
CATCACCGG
Found at i:20008701 original size:114 final size:113
Alignment explanation
Indices: 20008502--20008713 Score: 282
Period size: 114 Copynumber: 1.9 Consensus size: 113
20008492 TCTCCCCGAC
* * * *
20008502 TCATGTGCACTCCCATACCGCACATTACAATATCATCATCAAGTGCACTCTCACACCGCACCTCA
1 TCATGTGCACTCCCACACCGCACATGACAATATCATCAGCAAGTGCACTCCCACACCGCACCTCA
*
20008567 CCATCACCGTCATGTGCACTCCCACACCGCACATGGCATATATCATCA
66 CCAGCACCGTCATGTGCACTCCCACACCGCACATGGCATATATCATCA
* * * * * *
20008615 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCGGCATGTGCTCTCCCACGCCGCACACT
1 TCATGTGCACTCCCACACCGCACATGACA-ATATCATCAGCAAGTGCACTCCCACACCGCAC-CT
* *
20008680 -ACCGGCACCGTCATGTGCACTCCTACACCGCACA
64 CACCAGCACCGTCATGTGCACTCCCACACCGCACA
20008714 CGCATGGTTA
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
113 25 0.30
114 57 0.68
115 2 0.02
ACGTcount: A:0.25, C:0.40, G:0.14, T:0.21
Consensus pattern (113 bp):
TCATGTGCACTCCCACACCGCACATGACAATATCATCAGCAAGTGCACTCCCACACCGCACCTCA
CCAGCACCGTCATGTGCACTCCCACACCGCACATGGCATATATCATCA
Found at i:20011217 original size:20 final size:20
Alignment explanation
Indices: 20011192--20011244 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
20011182 TTTATATTTG
20011192 AATGTTTATTTTAAGTTAAT
1 AATGTTTATTTTAAGTTAAT
* *
20011212 AATG-TTAGTTTTACGTTATT
1 AATGTTTA-TTTTAAGTTAAT
* *
20011232 TATATTTATTTTA
1 AATGTTTATTTTA
20011245 TGTTTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 3 0.11
20 21 0.78
21 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.58
Consensus pattern (20 bp):
AATGTTTATTTTAAGTTAAT
Found at i:20011701 original size:31 final size:35
Alignment explanation
Indices: 20011630--20011708 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 35
20011620 GTGAATGTGC
* *
20011630 GGTGTGGGAGTGCACGTGACAGTGCCGTTGGTGTA
1 GGTGTGGGAGTGCACGTGACAGTGCCGATGATGTA
*
20011665 CGGTGTGGGAGTGCACGTGAC-G-G-TGATGATGT-
1 -GGTGTGGGAGTGCACGTGACAGTGCCGATGATGTA
*
20011697 GGTGTGAGAGTG
1 GGTGTGGGAGTG
20011709 TACATGATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
31 11 0.28
33 6 0.15
34 1 0.03
35 1 0.03
36 20 0.51
ACGTcount: A:0.15, C:0.11, G:0.48, T:0.25
Consensus pattern (35 bp):
GGTGTGGGAGTGCACGTGACAGTGCCGATGATGTA
Found at i:20011747 original size:33 final size:36
Alignment explanation
Indices: 20011710--20011784 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
20011700 GTGAGAGTGT
20011710 ACATGAT-ATT-T-GCCATGTGCGGTGTGGGACTGC
1 ACATGATGATTCTAGCCATGTGCGGTGTGGGACTGC
* *
20011743 ACATGATGATTCTAGCTATGTGTGGTGTGGGACTGC
1 ACATGATGATTCTAGCCATGTGCGGTGTGGGACTGC
20011779 ACATGA
1 ACATGA
20011785 CCTGATGAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 7 0.19
34 3 0.08
35 1 0.03
36 26 0.70
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.31
Consensus pattern (36 bp):
ACATGATGATTCTAGCCATGTGCGGTGTGGGACTGC
Found at i:20011839 original size:101 final size:101
Alignment explanation
Indices: 20011706--20011911 Score: 313
Period size: 101 Copynumber: 2.0 Consensus size: 101
20011696 TGGTGTGAGA
* * **
20011706 GTGTACATGATATTTGCCATGTGCGGTGTGGGACTGCACATGATGATTCTAGCTATGTGTGGTGT
1 GTGTACATGATATTTGCCATGTGCAGTATGGGACTGCACATGATGATTCTAGCTATGTGCAGTGT
*
20011771 GGGACTGCACATGACCTGATGAGCCGACAGTTGTAT
66 GAGACTGCACATGACCTGATGAGCCGACAGTTGTAT
*
20011807 GTGTACATGATATTTGCCATGTGCAGTATGGGAGTGCACATGATGATTCTAGCTATGTGCAGTGT
1 GTGTACATGATATTTGCCATGTGCAGTATGGGACTGCACATGATGATTCTAGCTATGTGCAGTGT
* * * **
20011872 GAGAGTGCACATGAGCTGATGAGCTGGTAGTTGTAT
66 GAGACTGCACATGACCTGATGAGCCGACAGTTGTAT
20011908 GTGT
1 GTGT
20011912 TGAGCCATGT
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 94 1.00
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.32
Consensus pattern (101 bp):
GTGTACATGATATTTGCCATGTGCAGTATGGGACTGCACATGATGATTCTAGCTATGTGCAGTGT
GAGACTGCACATGACCTGATGAGCCGACAGTTGTAT
Found at i:20011848 original size:33 final size:36
Alignment explanation
Indices: 20011811--20011885 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
20011801 TTGTATGTGT
*
20011811 ACATGAT-ATT-T-GCCATGTGCAGTATGGGAGTGC
1 ACATGATGATTCTAGCCATGTGCAGTATGAGAGTGC
* *
20011844 ACATGATGATTCTAGCTATGTGCAGTGTGAGAGTGC
1 ACATGATGATTCTAGCCATGTGCAGTATGAGAGTGC
20011880 ACATGA
1 ACATGA
20011886 GCTGATGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 7 0.19
34 3 0.08
35 1 0.03
36 25 0.69
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (36 bp):
ACATGATGATTCTAGCCATGTGCAGTATGAGAGTGC
Found at i:20011972 original size:2 final size:2
Alignment explanation
Indices: 20011965--20012000 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20011955 TGAATGTTTG
20011965 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20012001 CACAAAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20018958 original size:21 final size:20
Alignment explanation
Indices: 20018934--20018981 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
20018924 ATCTTACCTT
*
20018934 TTTTTCACTTGTTTCCTTGAA
1 TTTTTCACTT-TTCCCTTGAA
*
20018955 TTTTCACACTTTTCCCTTGAA
1 TTTT-TCACTTTTCCCTTGAA
20018976 TTTTTC
1 TTTTTC
20018982 CACCTAAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.15, C:0.23, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTTCACTTTTCCCTTGAA
Found at i:20018981 original size:22 final size:22
Alignment explanation
Indices: 20018939--20018979 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20018929 ACCTTTTTTT
*
20018939 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
20018961 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
20018980 TCCACCTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:20021495 original size:33 final size:34
Alignment explanation
Indices: 20021458--20021536 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 34
20021448 ACTTGGACAT
* * *
20021458 AATCAAATCACGCTCAGTGGCCAA-CCATTAG-AG
1 AATCAAATCACACACAG-GGCAAAGCCATTAGCAG
20021491 AATCAAATCACACACAGGGCAAAGCCATTAGCAG
1 AATCAAATCACACACAGGGCAAAGCCATTAGCAG
*
20021525 AGAACAAATCAC
1 A-ATCAAATCAC
20021537 TTGTGTGCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 5 0.13
33 22 0.56
34 3 0.08
35 9 0.23
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (34 bp):
AATCAAATCACACACAGGGCAAAGCCATTAGCAG
Found at i:20024819 original size:42 final size:41
Alignment explanation
Indices: 20024733--20024907 Score: 215
Period size: 42 Copynumber: 4.1 Consensus size: 41
20024723 ACCATCCCAC
* *
20024733 CATCATAAGCTCATATGCACTCCTCACTCGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCC-CAC-CGCACATAGCTGGGT
* * *
20024776 CATCATCAGCTTATGTGCACTCCACACCTCACATAGTTGGGT
1 CATCATCAGCTCATGTGCACTCC-CACCGCACATAGCTGGGT
* * *
20024818 CATCATTAGCTCATGTGCACTCCCATACGCACATAGCTAGGT
1 CATCATCAGCTCATGTGCACTCCCA-CCGCACATAGCTGGGT
* *
20024860 CATCTTCAGCTCATGTGCACTCCCACATGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCAC-CGCACATAGCTGGGT
20024902 CATCAT
1 CATCAT
20024908 TATCACATAA
Statistics
Matches: 112, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.02
42 87 0.78
43 23 0.21
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.27
Consensus pattern (41 bp):
CATCATCAGCTCATGTGCACTCCCACCGCACATAGCTGGGT
Found at i:20024876 original size:84 final size:85
Alignment explanation
Indices: 20024733--20024909 Score: 252
Period size: 84 Copynumber: 2.1 Consensus size: 85
20024723 ACCATCCCAC
* * *
20024733 CATCATAAGCTCATATGCACTCCTCACTCGCACATAGCTGGGTCATCATCAGCTTATGTGCACTC
1 CATCATTAGCTCATATGCACTCCTCACTCGCACATAGCTAGGTCATCATCAGCTCATGTGCACTC
* *
20024798 CACACCT-CACATAGTTGGGT
66 C-CACATGCACATAGCTGGGT
* *
20024818 CATCATTAGCTCATGTGCACTCC-CA-TACGCACATAGCTAGGTCATCTTCAGCTCATGTGCACT
1 CATCATTAGCTCATATGCACTCCTCACT-CGCACATAGCTAGGTCATCATCAGCTCATGTGCACT
20024881 CCCACATGCACATAGCTGGGT
65 CCCACATGCACATAGCTGGGT
20024902 CATCATTA
1 CATCATTA
20024910 TCACATAAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
83 5 0.06
84 57 0.69
85 21 0.25
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (85 bp):
CATCATTAGCTCATATGCACTCCTCACTCGCACATAGCTAGGTCATCATCAGCTCATGTGCACTC
CCACATGCACATAGCTGGGT
Found at i:20043522 original size:21 final size:21
Alignment explanation
Indices: 20043481--20043522 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20043471 AAATAGAAGG
* * *
20043481 TTTCTCGCTGCAGCGAGATTC
1 TTTCTCACTGCAGCAAAATTC
20043502 TTTCTCACTGCAGCAAAATTC
1 TTTCTCACTGCAGCAAAATTC
20043523 AGCTGATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (21 bp):
TTTCTCACTGCAGCAAAATTC
Found at i:20058378 original size:20 final size:20
Alignment explanation
Indices: 20058329--20058382 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
20058319 TATAATATTG
*
20058329 TTAATTAATT-AA-TTTAAA
1 TTAACTAATTCAATTTTAAA
* *
20058347 TGAACCATATTCAATTTTAAA
1 TTAACTA-ATTCAATTTTAAA
20058368 TTAACTAATTCAATT
1 TTAACTAATTCAATT
20058383 CCATAGACCA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 4 0.14
19 3 0.11
20 10 0.36
21 11 0.39
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (20 bp):
TTAACTAATTCAATTTTAAA
Found at i:20063943 original size:19 final size:18
Alignment explanation
Indices: 20063908--20063948 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
20063898 TTCAATAGCC
20063908 ATAAATTCATTTGATAACT
1 ATAAATTCATTTGATAA-T
20063927 ATAAATTCA-TTGAATAAT
1 ATAAATTCATTTG-ATAAT
20063945 ATAA
1 ATAA
20063949 TAACTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (18 bp):
ATAAATTCATTTGATAAT
Found at i:20067056 original size:40 final size:40
Alignment explanation
Indices: 20066961--20067066 Score: 133
Period size: 39 Copynumber: 2.7 Consensus size: 40
20066951 ATAAGAGACC
* * * * * *
20066961 AAAACAGAAGGTTTTTCACTACAGCGAAATTTCTACCCAG
1 AAAACAGAAAGTTTCTCACTGCAGCGAAATTGCAACCAAG
* *
20067001 -AAACAGAATGTTTCTCGCTGCAGCGAAATTGCAACCAAG
1 AAAACAGAAAGTTTCTCACTGCAGCGAAATTGCAACCAAG
20067040 AAAACAGAAAGTTTCTCACTGCAGCGA
1 AAAACAGAAAGTTTCTCACTGCAGCGA
20067067 GAAGCTTCAG
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 32 0.57
40 24 0.43
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (40 bp):
AAAACAGAAAGTTTCTCACTGCAGCGAAATTGCAACCAAG
Found at i:20067394 original size:22 final size:23
Alignment explanation
Indices: 20067366--20067409 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
20067356 TACATATATA
20067366 CCCATCATCATCATCA-CACCAT
1 CCCATCATCATCATCATCACCAT
20067388 CCCATCATCATCATCATCACCA
1 CCCATCATCATCATCATCACCA
20067410 GCTCATGCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.23
Consensus pattern (23 bp):
CCCATCATCATCATCATCACCAT
Found at i:20067465 original size:43 final size:43
Alignment explanation
Indices: 20067401--20067532 Score: 156
Period size: 43 Copynumber: 3.1 Consensus size: 43
20067391 ATCATCATCA
* * * ** *
20067401 TCATCACCAGCTCATGCGCACTCCCTACTCGCACATGGCTGGG
1 TCATCACCGGCTTATGAGCACTCCCTACTCGCACATAACCGGG
* *
20067444 TCATCACCGGGTTATGAGCACTCCCTACTAGCACATAACCGGG
1 TCATCACCGGCTTATGAGCACTCCCTACTCGCACATAACCGGG
* * * *
20067487 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGAG
1 TCATCACCGGCTTATGAGCACTCCCTACTCGCACATAACCGGG
20067530 TCA
1 TCA
20067533 ATATAATTAC
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (43 bp):
TCATCACCGGCTTATGAGCACTCCCTACTCGCACATAACCGGG
Found at i:20071870 original size:35 final size:35
Alignment explanation
Indices: 20071824--20071901 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
20071814 TAGTGGAACA
*
20071824 TGATTTAGGAGATAGCTTTTAGAATTATGGTTATG
1 TGATTGAGGAGATAGCTTTTAGAATTATGGTTATG
20071859 TGATTGAGGAGATAGCTTTTAGAATTATGGTTATG
1 TGATTGAGGAGATAGCTTTTAGAATTATGGTTATG
20071894 TGATTGAG
1 TGATTGAG
20071902 TTGATTGTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.41
Consensus pattern (35 bp):
TGATTGAGGAGATAGCTTTTAGAATTATGGTTATG
Found at i:20073640 original size:2 final size:2
Alignment explanation
Indices: 20073633--20073665 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
20073623 ATTATGTTGG
*
20073633 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20073666 GTTGTGCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20073806 original size:40 final size:38
Alignment explanation
Indices: 20073710--20073812 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 38
20073700 TAACCGTGTG
* * *
20073710 TGTGCATGATGTGGGGGGATGTACACGATGGCACTGAC
1 TGTGCATGATGTAGGGGGATGCACACGATGACACTGAC
* * *
20073748 TGTGCATGATGTAAGGGGATGCACACGATGACTCTGGC
1 TGTGCATGATGTAGGGGGATGCACACGATGACACTGAC
*
20073786 TATGTGCACGATGTAGGGGGATGCACA
1 --TGTGCATGATGTAGGGGGATGCACA
20073813 TGAGCTGGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 32 0.58
40 23 0.42
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (38 bp):
TGTGCATGATGTAGGGGGATGCACACGATGACACTGAC
Found at i:20077449 original size:20 final size:20
Alignment explanation
Indices: 20077424--20077472 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
20077414 GTTCAAATAG
*
20077424 AAATTTTAATAGGAATTTGA
1 AAATTTTAAGAGGAATTTGA
20077444 AAATTTTAAGAGGAATTTGA
1 AAATTTTAAGAGGAATTTGA
20077464 AAATTTTAA
1 AAATTTTAA
20077473 AACCAACAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (20 bp):
AAATTTTAAGAGGAATTTGA
Found at i:20078634 original size:26 final size:26
Alignment explanation
Indices: 20078574--20078635 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
20078564 ACCATATACC
*
20078574 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
20078600 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
20078626 CATCATCATC
1 CATCATCATC
20078636 TCATATGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.40, G:0.03, T:0.24
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:20078928 original size:42 final size:42
Alignment explanation
Indices: 20078870--20078992 Score: 228
Period size: 42 Copynumber: 2.9 Consensus size: 42
20078860 ATGGGGGCAA
* *
20078870 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
20078912 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
20078954 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGT
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGT
20078993 TCAAATCAAC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.22, C:0.34, G:0.23, T:0.21
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
Found at i:20086764 original size:20 final size:20
Alignment explanation
Indices: 20086707--20086769 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
20086697 TATATACCCA
*
20086707 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
20086726 GCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
20086746 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
20086766 TCAT
1 TCAT
20086770 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.40, G:0.05, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:20086816 original size:43 final size:43
Alignment explanation
Indices: 20086755--20086920 Score: 210
Period size: 43 Copynumber: 3.9 Consensus size: 43
20086745 CTCATCATCA
* * ** *
20086755 TCATCACCAGCTCATGCGCACTCCCTACTCGCACATGGTTGGG
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAATCGGG
*
20086798 TCATCACCGGGTTATGCGCACTCCCTACTCGCACATAATCGGG
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAATCGGG
*
20086841 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAACCGGG
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAATCGGG
* * *
20086884 TCATC-CTC-GACTTATGTGCACTCTCTACTCGCACATA
1 TCATCAC-CAG-GTTATGCGCACTCCCTACTCGCACATA
20086921 GCCGAGTCAA
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
42 2 0.02
43 108 0.98
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (43 bp):
TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAATCGGG
Done.