Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 120 of 284
Found at i:39747547 original size:5 final size:5
Alignment explanation
Indices: 39747537--39747570 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
39747527 CAATTTGAGA
39747537 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
39747571 AATACACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:39749053 original size:91 final size:91
Alignment explanation
Indices: 39748898--39749175 Score: 493
Period size: 91 Copynumber: 3.1 Consensus size: 91
39748888 ACCTCTGTTC
* *
39748898 ATGTTCGTTTGCTTATTTTTAAGCTTGTTCATGTTCAGTTTGTGTTCGTTAAGAATTTCAAATTT
1 ATGTTTGTTTGTTTATTTTTAAGCTTGTTCATGTTCAGTTTGTGTTCGTTAAGAATTTCAAATTT
39748963 TTGTTCATTTTCGTTTATTTAAAATT
66 TTGTTCATTTTCGTTTATTTAAAATT
39748989 ATGTTTGTTTGTTTATTTTTAAGCTTGTTCATGTTCAGTTTGTGTTCGTTAAGAATTTCAAATTT
1 ATGTTTGTTTGTTTATTTTTAAGCTTGTTCATGTTCAGTTTGTGTTCGTTAAGAATTTCAAATTT
39749054 TTGTTCATTTTCGTTTATTTAAAATT
66 TTGTTCATTTTCGTTTATTTAAAATT
* *
39749080 ATGTTTGTTTGTTTATTTTTAAGCTTGTTCATGTTCAGTTTGTGTTCATTAAAAATTTCAAATTT
1 ATGTTTGTTTGTTTATTTTTAAGCTTGTTCATGTTCAGTTTGTGTTCGTTAAGAATTTCAAATTT
* * *
39749145 TTGTTTATGTTCGTTTATTTAAATTT
66 TTGTTCATTTTCGTTTATTTAAAATT
39749171 ATGTT
1 ATGTT
39749176 ATTTATGTTC
Statistics
Matches: 180, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 180 1.00
ACGTcount: A:0.21, C:0.08, G:0.14, T:0.57
Consensus pattern (91 bp):
ATGTTTGTTTGTTTATTTTTAAGCTTGTTCATGTTCAGTTTGTGTTCGTTAAGAATTTCAAATTT
TTGTTCATTTTCGTTTATTTAAAATT
Found at i:39749233 original size:23 final size:23
Alignment explanation
Indices: 39749201--39749255 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
39749191 TTTAATGTTC
* *
39749201 ACGAATATGTTCATTGAAC-TTAA
1 ACGAACATGTTCA-CGAACATTAA
*
39749224 TCGAACATGTTCACGAACATTAA
1 ACGAACATGTTCACGAACATTAA
39749247 ACGAACATG
1 ACGAACATG
39749256 AACATGAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (23 bp):
ACGAACATGTTCACGAACATTAA
Found at i:39749325 original size:4 final size:4
Alignment explanation
Indices: 39749318--39749347 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
39749308 CAAACAATAA
*
39749318 ATAC ATAC ATGC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
39749348 TATTTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:39750162 original size:16 final size:17
Alignment explanation
Indices: 39750141--39750175 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
39750131 TGATATTTGA
39750141 ATGATTAAAAT-TTTTT
1 ATGATTAAAATATTTTT
*
39750157 ATGATTAAATTATTTTT
1 ATGATTAAAATATTTTT
39750174 AT
1 AT
39750176 TAAAATGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
ATGATTAAAATATTTTT
Found at i:39750166 original size:15 final size:17
Alignment explanation
Indices: 39750141--39750181 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
39750131 TGATATTTGA
39750141 ATGATTAAAATT-TTTT
1 ATGATTAAAATTATTTT
39750157 ATGATT-AAATTATTTT
1 ATGATTAAAATTATTTT
39750173 -T-ATTAAAAT
1 ATGATTAAAAT
39750182 GCTTGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
ATGATTAAAATTATTTT
Found at i:39755922 original size:17 final size:16
Alignment explanation
Indices: 39755902--39755947 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
39755892 TATATATGTA
39755902 TAATAAATATATAAAAT
1 TAATAAATAT-TAAAAT
*
39755919 TAATAATTATTAAAAT
1 TAATAAATATTAAAAT
39755935 CT-ATAAA-ATTAAA
1 -TAATAAATATTAAA
39755948 CTTTTATGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 6 0.23
16 10 0.38
17 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAAATATTAAAAT
Found at i:39755934 original size:16 final size:17
Alignment explanation
Indices: 39755902--39755934 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39755892 TATATATGTA
39755902 TAATAAATATATAAAAT
1 TAATAAATATATAAAAT
*
39755919 TAATAATTAT-TAAAAT
1 TAATAAATATATAAAAT
39755935 CTATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATATATAAAAT
Found at i:39771770 original size:9 final size:9
Alignment explanation
Indices: 39771758--39771783 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
39771748 ATATAATATG
39771758 TATAAATTC
1 TATAAATTC
39771767 TATAAATTC
1 TATAAATTC
39771776 TATAAATT
1 TATAAATT
39771784 TGCAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (9 bp):
TATAAATTC
Found at i:39785487 original size:15 final size:17
Alignment explanation
Indices: 39785463--39785505 Score: 72
Period size: 15 Copynumber: 2.6 Consensus size: 17
39785453 GAACAAGGTA
39785463 TAACATTTTACAAGTC-
1 TAACATTTTACAAGTCT
39785479 TAA-ATTTTACAAGTCT
1 TAACATTTTACAAGTCT
39785495 TAACATTTTAC
1 TAACATTTTAC
39785506 TTAATCCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.48
16 6 0.24
17 7 0.28
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (17 bp):
TAACATTTTACAAGTCT
Found at i:39786231 original size:19 final size:19
Alignment explanation
Indices: 39786185--39786232 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
39786175 GTATATATTT
*
39786185 TAAA-TTTATTTAGGTAAA
1 TAAATTTTATTTACGTAAA
* *
39786203 TAAATCTTATTTACGTAGA
1 TAAATTTTATTTACGTAAA
*
39786222 TAAGTTTTATT
1 TAAATTTTATT
39786233 CATATTCTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTACGTAAA
Found at i:39786294 original size:43 final size:43
Alignment explanation
Indices: 39786241--39786338 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
39786231 TTCATATTCT
*
39786241 AGAAATATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAG
1 AGAACTATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAG
* *
39786284 AGAACTATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAG
1 AGAACTATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAG
*
39786327 GGAACTATTTTC
1 AGAACTATTTTC
39786339 CCAATTAGGA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 49 0.98
44 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (43 bp):
AGAACTATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAG
Found at i:39790726 original size:19 final size:19
Alignment explanation
Indices: 39790698--39790745 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
39790688 GTATATATTT
39790698 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
39790716 TAAATTTTATTTGGGTAGA
1 TAAATTTTATTTAGGTAGA
*
39790735 TAAGTTTTATT
1 TAAATTTTATT
39790746 CATATTCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:39790814 original size:43 final size:44
Alignment explanation
Indices: 39790755--39790852 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 44
39790745 TCATATTCTA
*
39790755 GAAA-TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAG
1 GAAACTATTTTCTATTTTATCTTTTAATAGTTTACTAGAATAAG
* * *
39790797 GGAACTATTTTCT-TTTTATGTTTTAATAGTTTATTAGAATAAG
1 GAAACTATTTTCTATTTTATCTTTTAATAGTTTACTAGAATAAG
39790840 GAAACTATTTTCT
1 GAAACTATTTTCT
39790853 CAATTAGAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.06
43 45 0.92
44 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (44 bp):
GAAACTATTTTCTATTTTATCTTTTAATAGTTTACTAGAATAAG
Found at i:39800612 original size:432 final size:432
Alignment explanation
Indices: 39799809--39800671 Score: 1645
Period size: 432 Copynumber: 2.0 Consensus size: 432
39799799 GGATGAATGG
*
39799809 GCCCACATATATCACCTTGAATACGTTCCAGAAATGTTGGAGATTCAATCCCAACTTTAGCTGGT
1 GCCCACATATATCACCTTGAATACGTTCCAGAAATGTTGGAGATTCAATCCCAACCTTAGCTGGT
39799874 GATGGTCTAATAATCAATTTTCCTTGAGAACAAGCGACACAAGATAAATCCTTGAATTCAAGAAT
66 GATGGTCTAATAATCAATTTTCCTTGAGAACAAGCGACACAAGATAAATCCTTGAATTCAAGAAT
39799939 CTTTTGGTTCTTTAATGGGTGTCCAATTGAATTCTCGATGATTTTTCGCATCATAATAGATCCGG
131 CTTTTGGTTCTTTAATGGGTGTCCAATTGAATTCTCGATGATTTTTCGCATCATAATAGATCCGG
*
39800004 GATGGCCTAATCGGTCATGCCAAATAGTAAAAGTATGAGCTTTTACAAACTTCTGGTTTGTAGTA
196 GATGGCCTAATCGGTCATGCCAAATAGTAAAAGTATGAGCTTCTACAAACTTCTGGTTTGTAGTA
39800069 ACATATGATTCAATTGCACTAATATGTGCATAATATAAACCTGATGAAAAAGCAGGTAGCCTTTC
261 ACATATGATTCAATTGCACTAATATGTGCATAATATAAACCTGATGAAAAAGCAGGTAGCCTTTC
*
39800134 CAAAATATATTTCTTTCCACATTCAACATTTGTAATATATAGATATTAAAGATTTTTCTCATTCA
326 CAAAATATATTTCTTTCCACATTCAACATTTGTAATATATAGATATTAAACATTTTTCTCATTCA
39800199 TAGTCTCAATATGATATCCATTAAGACGAATATCTTTAAAAT
391 TAGTCTCAATATGATATCCATTAAGACGAATATCTTTAAAAT
*
39800241 GCCCACATATATCACCTTGAATATGTTCCAGAAATGTTGGAGATTCAATCCCAACCTTAGCTGGT
1 GCCCACATATATCACCTTGAATACGTTCCAGAAATGTTGGAGATTCAATCCCAACCTTAGCTGGT
*
39800306 GATGGTCTAATAATCAATTTTCCTTGAGAACAAGTGACACAAGATAAATCCTTGAATTCAAGAAT
66 GATGGTCTAATAATCAATTTTCCTTGAGAACAAGCGACACAAGATAAATCCTTGAATTCAAGAAT
*
39800371 CTTTTGGTTCTTTAATGGGTGTCCAATTGAATTCTTGATGATTTTTCGCATCATAATAGATCCGG
131 CTTTTGGTTCTTTAATGGGTGTCCAATTGAATTCTCGATGATTTTTCGCATCATAATAGATCCGG
* *
39800436 GATGGCCTAATCGGTCATGCCAAATAGTAAAAGTATGTGGTTCTACAAACTTCTGGTTTGTAGTA
196 GATGGCCTAATCGGTCATGCCAAATAGTAAAAGTATGAGCTTCTACAAACTTCTGGTTTGTAGTA
39800501 ACATATGATTCAATTGCACTAATATGTGCATAATATAAACCTGATGAAAAAGCAGGTAGCCTTTC
261 ACATATGATTCAATTGCACTAATATGTGCATAATATAAACCTGATGAAAAAGCAGGTAGCCTTTC
*
39800566 CAAAATATATTTCTTTCCACATTCAACATTTGTAATATATAGATATTCAACATTTTTCTCATTCA
326 CAAAATATATTTCTTTCCACATTCAACATTTGTAATATATAGATATTAAACATTTTTCTCATTCA
39800631 TAGTCTCAATATGATATCCATTAAGACGAATATCTTTAAAA
391 TAGTCTCAATATGATATCCATTAAGACGAATATCTTTAAAA
39800672 CTCAATAAAT
Statistics
Matches: 422, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
432 422 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (432 bp):
GCCCACATATATCACCTTGAATACGTTCCAGAAATGTTGGAGATTCAATCCCAACCTTAGCTGGT
GATGGTCTAATAATCAATTTTCCTTGAGAACAAGCGACACAAGATAAATCCTTGAATTCAAGAAT
CTTTTGGTTCTTTAATGGGTGTCCAATTGAATTCTCGATGATTTTTCGCATCATAATAGATCCGG
GATGGCCTAATCGGTCATGCCAAATAGTAAAAGTATGAGCTTCTACAAACTTCTGGTTTGTAGTA
ACATATGATTCAATTGCACTAATATGTGCATAATATAAACCTGATGAAAAAGCAGGTAGCCTTTC
CAAAATATATTTCTTTCCACATTCAACATTTGTAATATATAGATATTAAACATTTTTCTCATTCA
TAGTCTCAATATGATATCCATTAAGACGAATATCTTTAAAAT
Found at i:39815319 original size:28 final size:27
Alignment explanation
Indices: 39815255--39815348 Score: 143
Period size: 27 Copynumber: 3.4 Consensus size: 27
39815245 ATATTAAGTC
* *
39815255 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
39815282 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
* *
39815310 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
39815337 CGCACACTTAGT
1 CGCACACTTAGT
39815349 CCTGCACAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
27 36 0.58
28 26 0.42
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:39825384 original size:27 final size:27
Alignment explanation
Indices: 39825354--39825531 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39825344 ATATTGAGTC
* * * *
39825354 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39825381 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39825408 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39825436 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
39825463 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
39825490 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39825517 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39825532 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:39825493 original size:82 final size:81
Alignment explanation
Indices: 39825375--39825530 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39825365 TGCTATATAA
* *
39825375 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
39825440 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39825457 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
39825521 CACTTAGTGC
65 CACTTAGTGC
39825531 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39829019 original size:30 final size:30
Alignment explanation
Indices: 39828985--39829043 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
39828975 CCATTCACTG
39828985 GTGATGGTTTTACATCAACTATGGCGGACA
1 GTGATGGTTTTACATCAACTATGGCGGACA
39829015 GTGATGGTTTTACATCAACTATGGCGGAC
1 GTGATGGTTTTACATCAACTATGGCGGAC
39829044 TTTAAATGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (30 bp):
GTGATGGTTTTACATCAACTATGGCGGACA
Found at i:39829417 original size:35 final size:35
Alignment explanation
Indices: 39829378--39829451 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
39829368 CCCTATTTAA
*
39829378 GGTG-TCACCCTAAAGGACCTATATATCATTTACAC
1 GGTGTTCACCC-AAAGGACCTATATAACATTTACAC
** *
39829413 GGTGTTGTCCCAAAGGACCTATATAACATTTACAT
1 GGTGTTCACCCAAAGGACCTATATAACATTTACAC
39829448 GGTG
1 GGTG
39829452 ATGCCCCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 30 0.88
36 4 0.12
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (35 bp):
GGTGTTCACCCAAAGGACCTATATAACATTTACAC
Found at i:39829464 original size:35 final size:35
Alignment explanation
Indices: 39829389--39829486 Score: 115
Period size: 35 Copynumber: 2.7 Consensus size: 35
39829379 GTGTCACCCT
* * * *
39829389 AAAGGACCTATATATCATTTACACGGTGTTGTCCC
1 AAAGGACCTATATAACATTTACATGGTGATGCCCC
39829424 AAAGGACCTATATAACATTTACATGGTGATGCCCC
1 AAAGGACCTATATAACATTTACATGGTGATGCCCC
* *
39829459 GAAGGACCAGTAGATAACATTTTACATG
1 AAAGGACC--TATATAACA-TTTACATG
39829487 TTGCAGCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
35 38 0.70
37 8 0.15
38 8 0.15
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (35 bp):
AAAGGACCTATATAACATTTACATGGTGATGCCCC
Found at i:39831424 original size:46 final size:46
Alignment explanation
Indices: 39831326--39831446 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 46
39831316 TATGAGATCT
* * *
39831326 AGTGTAAGACCATGTTTGGGACATGGCGTTGGCATTGAGACGAGGGAT
1 AGTGTAAGA-CATGTTTGGGACAT-GCATTGGCATTGAGACGAGAGAC
* *
39831374 AGTGTAAGACATGTTTGGGACATGCATTGGCCTCT-AGACGTA-AGCC
1 AGTGTAAGACATGTTTGGGACATGCATTGGCAT-TGAGACG-AGAGAC
39831420 AGTGTAAGACATGTTTGGGACATGCAT
1 AGTGTAAGACATGTTTGGGACATGCAT
39831447 CGACTACGAG
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
46 41 0.62
47 16 0.24
48 9 0.14
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.26
Consensus pattern (46 bp):
AGTGTAAGACATGTTTGGGACATGCATTGGCATTGAGACGAGAGAC
Found at i:39831469 original size:46 final size:45
Alignment explanation
Indices: 39831374--39831496 Score: 133
Period size: 46 Copynumber: 2.6 Consensus size: 45
39831364 GACGAGGGAT
* * *
39831374 AGTGTAAGACATGTTTGGGACATGCATTGGCCTCTAGACGTAAGCC
1 AGTGTAAGACATGTTTGGGACATGCA-TCGACTCGAGACGTAAGCC
* *
39831420 AGTGTAAGACATGTTTGGGACATGCATCGACTACGAGATG-ATAGTC
1 AGTGTAAGACATGTTTGGGACATGCATCGACT-CGAGACGTA-AGCC
39831466 AGTGTGAA-ACCATGTTTGGGACATGGCATCG
1 AGTGT-AAGA-CATGTTTGGGACAT-GCATCG
39831497 GCTTGAGATA
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
45 5 0.07
46 40 0.60
47 16 0.24
48 6 0.09
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (45 bp):
AGTGTAAGACATGTTTGGGACATGCATCGACTCGAGACGTAAGCC
Found at i:39834135 original size:54 final size:53
Alignment explanation
Indices: 39834053--39834185 Score: 221
Period size: 54 Copynumber: 2.5 Consensus size: 53
39834043 TCTTATGGCA
39834053 GGATTACCAGTCCAGGCTAAATCCCCCATATCGTAAACTCATAAAATGATGCCG
1 GGATTACCAGT-CAGGCTAAATCCCCCATATCGTAAACTCATAAAATGATGCCG
* *
39834107 GGATTACCAGTACAAGCTAAATCCCCCATATCGTAAACTCATAAAGTGATGCCG
1 GGATTACCAGT-CAGGCTAAATCCCCCATATCGTAAACTCATAAAATGATGCCG
39834161 GGATTACCAGTCTAGGCTAAATCCC
1 GGATTACCAGTC-AGGCTAAATCCC
39834186 TTATTACGAC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
53 1 0.01
54 73 0.99
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (53 bp):
GGATTACCAGTCAGGCTAAATCCCCCATATCGTAAACTCATAAAATGATGCCG
Found at i:39838320 original size:25 final size:25
Alignment explanation
Indices: 39838292--39838343 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
39838282 AGCATTCTGA
39838292 TATATGGCCCTCT-CGAGCTTCCCGT
1 TATATGGCCCT-TACGAGCTTCCCGT
**
39838317 TATATGGTTCTTACGAGCTTCCCGT
1 TATATGGCCCTTACGAGCTTCCCGT
39838342 TA
1 TA
39838344 ATAGCTCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.15, C:0.29, G:0.19, T:0.37
Consensus pattern (25 bp):
TATATGGCCCTTACGAGCTTCCCGT
Found at i:39838484 original size:26 final size:26
Alignment explanation
Indices: 39838416--39838484 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 26
39838406 CTTATAAGCG
*
39838416 TCCCGA-TATATGGCTCTTTGTGAGCT
1 TCCCGATTA-ATGGCTCTTTGGGAGCT
***
39838442 TCCCGATTAAAATCTCTTTGGGAGCT
1 TCCCGATTAATGGCTCTTTGGGAGCT
**
39838468 TCCTTATTAATGGCTCT
1 TCCCGATTAATGGCTCT
39838485 CCGGAGCTTT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
26 31 0.94
27 2 0.06
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (26 bp):
TCCCGATTAATGGCTCTTTGGGAGCT
Found at i:39839101 original size:60 final size:60
Alignment explanation
Indices: 39839037--39839152 Score: 223
Period size: 60 Copynumber: 1.9 Consensus size: 60
39839027 TGGTCAAAAC
*
39839037 ATTTCTTGGTTAACCCATGTTTAAATTTTGAAAATTTGTTGTGTTGTGAGCTTTCGGTCA
1 ATTTCTTGGTTAACCCATGTTTAAATTTTGAAAATTTGTTCTGTTGTGAGCTTTCGGTCA
39839097 ATTTCTTGGTTAACCCATGTTTAAATTTTGAAAATTTGTTCTGTTGTGAGCTTTCG
1 ATTTCTTGGTTAACCCATGTTTAAATTTTGAAAATTTGTTCTGTTGTGAGCTTTCG
39839153 ACCATGAAAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (60 bp):
ATTTCTTGGTTAACCCATGTTTAAATTTTGAAAATTTGTTCTGTTGTGAGCTTTCGGTCA
Found at i:39839551 original size:47 final size:47
Alignment explanation
Indices: 39839479--39839620 Score: 241
Period size: 47 Copynumber: 3.0 Consensus size: 47
39839469 GTTGAATTTA
*
39839479 AAGCTTGTTAAA-TTGCTCTTAATATTTCTGGATAGGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTCTGGATAAGTTACTTAGTT
39839525 AAGCTTGTTAAATTTGCTCTTAATATTTCTGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTCTGGATAAGTTACTTAGTT
* * *
39839572 AAGCTTGTTAAATTTTCCCTTATTATTTCTGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCTCTTAATATTTCTGGATAAGTTACTTAGTT
39839619 AA
1 AA
39839621 AGAAAATTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
46 12 0.13
47 79 0.87
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.46
Consensus pattern (47 bp):
AAGCTTGTTAAATTTGCTCTTAATATTTCTGGATAAGTTACTTAGTT
Found at i:39840491 original size:45 final size:44
Alignment explanation
Indices: 39840427--39840683 Score: 298
Period size: 45 Copynumber: 5.9 Consensus size: 44
39840417 CGCACAGTAT
39840427 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCGGG-CTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
39840472 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCGGG-CTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* *
39840517 TATTTGGGCTTCGAGCCTAGCAGG-TGA-AATGCCGGTGAGATAC
1 TATTCGGGCTTTGAGCCTAGCAGGCT-ATAATGCCGGTGAGATAC
* *
39840560 TATTCGGGCTTTCGAGCCTAGCAGGCTATAATGCCAGTGAAATGA-
1 TATTCGGGCTTT-GAGCCTAGCAGGCTATAATGCCGGTGAGAT-AC
* *
39840605 TA-TCGGGCTTCGAGCCTAGCAGGCGA-AATGCCGGTGA-ATGA-
1 TATTCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT-AC
* * * *
39840646 -ATTCGGGTTTTTAAACCTAGCAGGCT-GAATGCCGGTGA
1 TATTCGGG-CTTTGAGCCTAGCAGGCTATAATGCCGGTGA
39840684 TTTGATAAAA
Statistics
Matches: 190, Mismatches: 14, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
40 1 0.01
41 9 0.05
42 34 0.18
43 41 0.22
44 37 0.19
45 67 0.35
46 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.26
Consensus pattern (44 bp):
TATTCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
Found at i:39840590 original size:88 final size:86
Alignment explanation
Indices: 39840430--39840683 Score: 304
Period size: 88 Copynumber: 2.9 Consensus size: 86
39840420 ACAGTATTAT
*
39840430 TCGGGCCTTTGAGCCTAGCAGGCT-ATAATGCCGGTGAGATACTATTCGGGCCTTTGAGCCTAGC
1 TCGGG-CTTCGAGCCTAGCAGG-TGA-AATGCCGGTGAGATACTATTCGGG-CTTTGAGCCTAGC
*
39840494 AGGCTATAATGCCGGTGAGAT-ACTA
62 AGGCTATAATGCCGGTGAAATGA-TA
*
39840519 TTTGGGCTTCGAGCCTAGCAGGTGAAATGCCGGTGAGATACTATTCGGGCTTTCGAGCCTAGCAG
1 -TCGGGCTTCGAGCCTAGCAGGTGAAATGCCGGTGAGATACTATTCGGGCTTT-GAGCCTAGCAG
*
39840584 GCTATAATGCCAGTGAAATGATA
64 GCTATAATGCCGGTGAAATGATA
* * * *
39840607 TCGGGCTTCGAGCCTAGCAGGCGAAATGCCGGTGA-ATGA--ATTCGGGTTTTTAAACCTAGCAG
1 TCGGGCTTCGAGCCTAGCAGGTGAAATGCCGGTGAGAT-ACTATTCGGG-CTTTGAGCCTAGCAG
*
39840669 GCT-GAATGCCGGTGA
64 GCTATAATGCCGGTGA
39840684 TTTGATAAAA
Statistics
Matches: 148, Mismatches: 11, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
84 10 0.07
85 19 0.13
86 5 0.03
87 38 0.26
88 55 0.37
89 17 0.11
90 4 0.03
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (86 bp):
TCGGGCTTCGAGCCTAGCAGGTGAAATGCCGGTGAGATACTATTCGGGCTTTGAGCCTAGCAGGC
TATAATGCCGGTGAAATGATA
Found at i:39841022 original size:16 final size:18
Alignment explanation
Indices: 39840991--39841023 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
39840981 AACTCGTCAC
39840991 ACTATCTATCATTTTGGT
1 ACTATCTATCATTTTGGT
39841009 ACTA-CTAT-ATTTTGG
1 ACTATCTATCATTTTGG
39841024 AGCTTGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (18 bp):
ACTATCTATCATTTTGGT
Found at i:39841377 original size:24 final size:24
Alignment explanation
Indices: 39841310--39841378 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 24
39841300 ATGGCTATTT
*
39841310 AGAGCTTCCTGATTAATGGCTCTTC
1 AGAGCTTCCTGATT-ATGGCTCTGC
* * *
39841335 AGAACTACC-CATTATTGGCTC-GC
1 AGAGCTTCCTGATTA-TGGCTCTGC
39841358 ATGAGCTTCCTGATTATGGCT
1 A-GAGCTTCCTGATTATGGCT
39841379 TTTATGAGCT
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
23 3 0.09
24 20 0.59
25 11 0.32
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (24 bp):
AGAGCTTCCTGATTATGGCTCTGC
Found at i:39844556 original size:23 final size:23
Alignment explanation
Indices: 39844528--39844604 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
39844518 TGATGAACAA
*
39844528 TAAGCTCTATTGAGCTGAAACGG
1 TAAGCTCTATCGAGCTGAAACGG
* *
39844551 TAAGCTTTATCGAGCTG-AACAG
1 TAAGCTCTATCGAGCTGAAACGG
*
39844573 TAAGCTC-ATACGAGCTGAAACGA
1 TAAGCTCTAT-CGAGCTGAAACGG
*
39844596 TAAACTCTA
1 TAAGCTCTA
39844605 ATAAGCTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.05
22 17 0.39
23 24 0.55
24 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (23 bp):
TAAGCTCTATCGAGCTGAAACGG
Found at i:39844578 original size:22 final size:22
Alignment explanation
Indices: 39844521--39844591 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
39844511 CCCCACCTGA
* * *
39844521 TGAACAATAAGCTCTATTGAGC
1 TGAACAGTAAGCTTTATCGAGC
*
39844543 TGAAACGGTAAGCTTTATCGAGC
1 TG-AACAGTAAGCTTTATCGAGC
*
39844566 TGAACAGTAAGC-TCATACGAGC
1 TGAACAGTAAGCTTTAT-CGAGC
39844588 TGAA
1 TGAA
39844592 ACGATAAACT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 3 0.07
22 20 0.49
23 18 0.44
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (22 bp):
TGAACAGTAAGCTTTATCGAGC
Found at i:39845067 original size:31 final size:31
Alignment explanation
Indices: 39845031--39845089 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
39845021 AAAACATTCA
39845031 TTTTGACTAATTTACAATTTTA-TCCTTAGAC
1 TTTTGACTAATTTACAA-TTTAGTCCTTAGAC
* *
39845062 TTTTGACTACTTTGCAATTTAGTCCTTA
1 TTTTGACTAATTTACAATTTAGTCCTTA
39845090 ACACATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.49
Consensus pattern (31 bp):
TTTTGACTAATTTACAATTTAGTCCTTAGAC
Found at i:39854182 original size:22 final size:21
Alignment explanation
Indices: 39854141--39854182 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
39854131 ATTATATCTA
*
39854141 TTATAATTTATATATTAATTT
1 TTATAATTTATATATGAATTT
39854162 TTATCAATTTAGTATA-GAATT
1 TTAT-AATTTA-TATATGAATT
39854183 AGTTTTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (21 bp):
TTATAATTTATATATGAATTT
Found at i:39857457 original size:46 final size:46
Alignment explanation
Indices: 39857395--39857700 Score: 458
Period size: 46 Copynumber: 6.6 Consensus size: 46
39857385 TACATCTCTC
39857395 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAAA
39857441 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAAA
39857487 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAAA
* **
39857533 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAAA
* * * *
39857579 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTC-T---C
1 GAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATC-CATAAAA
**
39857626 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAAA
39857672 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
39857701 TGCCCAAACA
Statistics
Matches: 239, Mismatches: 12, Indels: 18
0.89 0.04 0.07
Matches are distributed among these distances:
42 1 0.00
43 8 0.03
44 1 0.00
46 192 0.80
47 28 0.12
49 1 0.00
50 7 0.03
51 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAAA
Found at i:39857719 original size:46 final size:46
Alignment explanation
Indices: 39857359--39857719 Score: 183
Period size: 46 Copynumber: 7.8 Consensus size: 46
39857349 CTATTTTATG
* * *
39857359 CAACTCAACGAGCTCGGATGCCTAGTTACATCTCT--CGAACTCGGACT
1 CAACTCAACGAGTTCGGATGCCCA--TACATC-CTAGTGAACTCGGACT
*** * **
39857406 CAACTCAACGAGTTCGGA--CATTTGCATCCATAAAAGAACTCGGACT
1 CAACTCAACGAGTTCGGATGCCCATACATCC-T-AGTGAACTCGGACT
*** * **
39857452 CAACTCAACGAGTTCGGA--CATTTGCATCCATAAAAGAACTCGGACT
1 CAACTCAACGAGTTCGGATGCCCATACATCC-T-AGTGAACTCGGACT
*** * **
39857498 CAACTCAACGAGTTCGGA--CATTTGCATCCATAAAAGAACTCGGACT
1 CAACTCAACGAGTTCGGATGCCCATACATCC-T-AGTGAACTCGGACT
* * * *
39857544 CAACTCAACGAGTTCGGACATTCGCATCCAT--AAGTGAACTCGGACT
1 CAACTCAACGAGTTCGG--ATGCCCATACATCCTAGTGAACTCGGACT
* * *
39857590 CAACTCAACGAGCTCGGATGCCTAGTTACATCTCT--CGAACTCGGACT
1 CAACTCAACGAGTTCGGATGCCCA--TACATC-CTAGTGAACTCGGACT
*** *
39857637 CAACTCAACGAGTTCGGA--CATTTGCATCCATAAGTGAACTCGGACT
1 CAACTCAACGAGTTCGGATGCCCATACATCC-T-AGTGAACTCGGACT
*
39857683 CAACTCAACGAGTTCGGATGCCCAAACATCCTAGTGA
1 CAACTCAACGAGTTCGGATGCCCATACATCCTAGTGA
39857720 CATGTCACTT
Statistics
Matches: 266, Mismatches: 29, Indels: 39
0.80 0.09 0.12
Matches are distributed among these distances:
42 2 0.01
43 12 0.05
44 4 0.02
45 4 0.02
46 186 0.70
47 46 0.17
48 7 0.03
50 5 0.02
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
CAACTCAACGAGTTCGGATGCCCATACATCCTAGTGAACTCGGACT
Found at i:39863999 original size:27 final size:27
Alignment explanation
Indices: 39863962--39864044 Score: 114
Period size: 27 Copynumber: 3.0 Consensus size: 27
39863952 AGTGCGAGCG
*
39863962 AGAAAATGAAAATGAAATTGAAAGAAA
1 AGAAAAAGAAAATGAAATTGAAAGAAA
*
39863989 AGAAAAAGAAAAAGAAATTGAAAGAAA
1 AGAAAAAGAAAATGAAATTGAAAGAAA
*
39864016 AGAAAAAGAAAAAT-ACATTGGAAAGAAA
1 AGAAAAAG-AAAATGAAATT-GAAAGAAA
39864044 A
1 A
39864045 TGAGTGAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 37 0.74
28 13 0.26
ACGTcount: A:0.70, C:0.01, G:0.18, T:0.11
Consensus pattern (27 bp):
AGAAAAAGAAAATGAAATTGAAAGAAA
Found at i:39864054 original size:33 final size:33
Alignment explanation
Indices: 39864017--39864092 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
39864007 TGAAAGAAAA
*
39864017 GAAAAAGAAAAATA-CATTGGAA-AGAAAAT-GAGT
1 GAAAAAGAAAAAGAGC-TT-GAACAG-AAATCGAGT
*
39864050 GAAAAGGAAAAAGAGCTTGAACAGAAATCGAGT
1 GAAAAAGAAAAAGAGCTTGAACAGAAATCGAGT
39864083 GAAAAAGAAA
1 GAAAAAGAAA
39864093 TGATTAAAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
32 7 0.19
33 29 0.78
34 1 0.03
ACGTcount: A:0.59, C:0.05, G:0.24, T:0.12
Consensus pattern (33 bp):
GAAAAAGAAAAAGAGCTTGAACAGAAATCGAGT
Found at i:39866465 original size:30 final size:30
Alignment explanation
Indices: 39866431--39866501 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
39866421 ACATCAGCTA
39866431 TTCACACCATGTCCATTCGGTTCAGTCATG
1 TTCACACCATGTCCATTCGGTTCAGTCATG
39866461 TTCACACCATGTCCATTCGGTTCAGTCATG
1 TTCACACCATGTCCATTCGGTTCAGTCATG
39866491 TTCACACCATG
1 TTCACACCATG
39866502 GGACCTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.32
Consensus pattern (30 bp):
TTCACACCATGTCCATTCGGTTCAGTCATG
Found at i:39869530 original size:33 final size:32
Alignment explanation
Indices: 39869492--39869573 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 32
39869482 GATTACTCTC
*
39869492 TTCACTCATTTCTTTTACAAACTATCTTTCTTT
1 TTCACTCATTTCTTTT-CAAACTATCTTTCCTT
** * * *
39869525 TTCACTCGATTTCCGTTCAAGCTCTTTTTCCTT
1 TTCACTC-ATTTCTTTTCAAACTATCTTTCCTT
39869558 TTCACTCAGTTTCTTT
1 TTCACTCA-TTTCTTT
39869574 CCAATGTCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
32 1 0.03
33 31 0.79
34 7 0.18
ACGTcount: A:0.16, C:0.27, G:0.05, T:0.52
Consensus pattern (32 bp):
TTCACTCATTTCTTTTCAAACTATCTTTCCTT
Found at i:39869605 original size:27 final size:29
Alignment explanation
Indices: 39869567--39869627 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 29
39869557 TTTCACTCAG
*
39869567 TTTCTTTCCAATGTCTTTTTCTTTTTC-T
1 TTTCTTTCCAATGTCTTTTTCATTTTCAT
*
39869595 TTTCTTT-CAATTTCTTTTTCATTTTCAT
1 TTTCTTTCCAATGTCTTTTTCATTTTCAT
39869623 TTTCT
1 TTTCT
39869628 CACTCGCACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 17 0.57
28 13 0.43
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.69
Consensus pattern (29 bp):
TTTCTTTCCAATGTCTTTTTCATTTTCAT
Found at i:39872353 original size:27 final size:27
Alignment explanation
Indices: 39872277--39872355 Score: 72
Period size: 31 Copynumber: 2.8 Consensus size: 27
39872267 AACAAGGCAC
* *
39872277 ATTAAATTTCTGTAGTAACT-AGACAT
1 ATTAAATTGCTGTACTAACTAAGACAT
*
39872303 ATTAAATGATG-TAATGAGCTAACTAAGACAT
1 ATTAAAT--TGCT-GT-A-CTAACTAAGACAT
39872334 ATTAAATTGCTGTACTAACTAA
1 ATTAAATTGCTGTACTAACTAA
39872356 AACACAATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
26 7 0.17
27 9 0.21
28 3 0.07
29 4 0.10
30 6 0.14
31 13 0.31
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (27 bp):
ATTAAATTGCTGTACTAACTAAGACAT
Found at i:39879214 original size:47 final size:47
Alignment explanation
Indices: 39879152--39879241 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 47
39879142 TAGCTCCAGC
* * *
39879152 AAAGACAAGTTTAATGTCTAGATTCAGCTGGACAAATTAAATAGTACG
1 AAAGACAAGATTAATGACTAAATTCAGCTGGA-AAATTAAATAGTACG
*
39879200 AAAGACAA-ATTAATGACTAAATTCGGCTGGAAAATTAAATAG
1 AAAGACAAGATTAATGACTAAATTCAGCTGGAAAATTAAATAG
39879242 CAGCAGCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 11 0.29
47 19 0.50
48 8 0.21
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.26
Consensus pattern (47 bp):
AAAGACAAGATTAATGACTAAATTCAGCTGGAAAATTAAATAGTACG
Found at i:39899382 original size:9 final size:9
Alignment explanation
Indices: 39899351--39899398 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
39899341 TGATGAATAA
39899351 AAAAATGAAG
1 AAAAA-GAAG
* *
39899361 ATAATGAAG
1 AAAAAGAAG
39899370 -AAAAGAAG
1 AAAAAGAAG
39899378 AAAAAGAAG
1 AAAAAGAAG
39899387 AAAAA-AAG
1 AAAAAGAAG
39899395 AAAA
1 AAAA
39899399 TGGACAGGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 13 0.39
9 17 0.52
10 3 0.09
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:39899386 original size:17 final size:17
Alignment explanation
Indices: 39899352--39899398 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
39899342 GATGAATAAA
* *
39899352 AAAATGAAGATAATGAAG
1 AAAA-GAAGAAAAAGAAG
39899370 AAAAGAAGAAAAAGAAG
1 AAAAGAAGAAAAAGAAG
*
39899387 AAAAAAAGAAAA
1 AAAAGAAGAAAA
39899399 TGGACAGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (17 bp):
AAAAGAAGAAAAAGAAG
Found at i:39900862 original size:23 final size:23
Alignment explanation
Indices: 39900836--39900901 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
39900826 TCGGTTTAGG
*
39900836 TTTGTTACGAAATGGTAATGTGA
1 TTTGTTACGAAATGGTAATGCGA
* *
39900859 TTTGGTT-CGAAATGGTATTACGA
1 TTT-GTTACGAAATGGTAATGCGA
*
39900882 TTTGGTACGAAATGGTAATG
1 TTTGTTACGAAATGGTAATG
39900902 GGTCAAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 2 0.06
23 30 0.86
24 3 0.09
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (23 bp):
TTTGTTACGAAATGGTAATGCGA
Found at i:39902316 original size:44 final size:44
Alignment explanation
Indices: 39902266--39902405 Score: 111
Period size: 44 Copynumber: 3.2 Consensus size: 44
39902256 ATATAGTAGA
*
39902266 TCTTGCCTTCCTGCACCAACAGCGAAGCAGATTGAAGACACCAG
1 TCTTGCCTTCCTGCAACAACAGCGAAGCAGATTGAAGACACCAG
* ***** * * * * * * *
39902310 TCTTGCCTCCCT-CGGTTTCAGTGGAGTAGGTTAAAGATAGCAG
1 TCTTGCCTTCCTGCAACAACAGCGAAGCAGATTGAAGACACCAG
* *
39902353 ATCTTGCCTTCCTGCAACGACAGCGAAGCAGATCGAAGACACCAG
1 -TCTTGCCTTCCTGCAACAACAGCGAAGCAGATTGAAGACACCAG
*
39902398 CCTTGCCT
1 TCTTGCCT
39902406 CCCTCAGTTG
Statistics
Matches: 66, Mismatches: 28, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
43 19 0.29
44 29 0.44
45 18 0.27
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (44 bp):
TCTTGCCTTCCTGCAACAACAGCGAAGCAGATTGAAGACACCAG
Found at i:39902420 original size:88 final size:88
Alignment explanation
Indices: 39902258--39902567 Score: 433
Period size: 88 Copynumber: 3.5 Consensus size: 88
39902248 ATCAATGAAT
* * * * *
39902258 ATAGTAGATCTTGCCTTCCTGCACCAACAGCGAAGCAGATTGAAGACACCAGTCTTGCCTCCCTC
1 ATAGCAGATCTTGCCTTCCTGCAACGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTC
* *
39902323 GGTTTCAGTGGAGTAGGTTAAAG
66 GGTTGCAGTGGAGCAGGTTAAAG
39902346 ATAGCAGATCTTGCCTTCCTGCAACGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTC
1 ATAGCAGATCTTGCCTTCCTGCAACGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTC
* *
39902411 AGTTGCAGTGGAGCAGGTTAAAA
66 GGTTGCAGTGGAGCAGGTTAAAG
* * **
39902434 ATAACAGATCTTGCCTTCCTAC-ACTGACAATGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT
1 ATAGCAGATCTTGCCTTCCTGCAAC-GACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT
* *
39902498 CGGTTGCGGTGGAGCAGGTTGAAG
65 CGGTTGCAGTGGAGCAGGTTAAAG
* * * *
39902522 ATAGTAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGTTCGAAGA
1 ATAGCAGATCTTGCCTTCCTGCAACGACAGCGAAGCAGATCGAAGA
39902568 TGGTAAGCCT
Statistics
Matches: 197, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
87 2 0.01
88 194 0.98
89 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGCAACGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTC
GGTTGCAGTGGAGCAGGTTAAAG
Found at i:39902491 original size:44 final size:43
Alignment explanation
Indices: 39902355--39902498 Score: 112
Period size: 44 Copynumber: 3.3 Consensus size: 43
39902345 GATAGCAGAT
*
39902355 CTTGCCTTCCTGCAAC-GACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCT-C-ACTGACAGTGAAGCAGATCGAAGACACCAGC
* * * * ** * * * *
39902399 CTTGCCTCCCTCAGTTG-CAGTGGAGCAGGTTAAAAATAACAGAT
1 CTTGCCTTCCTCA-CTGACAGTGAAGCAGATCGAAGACACCAG-C
*
39902443 CTTGCCTTCCTACACTGACAATGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCT-CACTGACAGTGAAGCAGATCGAAGACACCAGC
*
39902487 CTTGCCTCCCTC
1 CTTGCCTTCCTC
39902499 GGTTGCGGTG
Statistics
Matches: 72, Mismatches: 23, Indels: 11
0.68 0.22 0.10
Matches are distributed among these distances:
42 1 0.01
43 19 0.26
44 33 0.46
45 19 0.26
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.20
Consensus pattern (43 bp):
CTTGCCTTCCTCACTGACAGTGAAGCAGATCGAAGACACCAGC
Found at i:39902522 original size:43 final size:42
Alignment explanation
Indices: 39902291--39902522 Score: 122
Period size: 43 Copynumber: 5.3 Consensus size: 42
39902281 CCAACAGCGA
* * *
39902291 AGCAGATTGAAGACACCAGTCTTGCCTCCCTCGGTTTCAGTGG
1 AGCAGGTTGAAGACACCAGCCTTGCCTCCCTC-GTTGCAGTGG
* * * * * * *** * *
39902334 AGTAGGTTAAAGATAGCAGATCTTGCCTTCCTGCAACGACAGCGA
1 AGCAGGTTGAAGACACCAG-CCTTGCCTCCCT-CGTTG-CAGTGG
* *
39902379 AGCAGATCGAAGACACCAGCCTTGCCTCCCTCAGTTGCAGTGG
1 AGCAGGTTGAAGACACCAGCCTTGCCTCCCTC-GTTGCAGTGG
* * * * * * ** * *
39902422 AGCAGGTTAAAAATAACAGATCTTGCCTTCCTACACTGACAATGA
1 AGCAGGTTGAAGACACCAG-CCTTGCCTCCCT-CGTTG-CAGTGG
* * *
39902467 AGCAGATCGAAGACACCAGCCTTGCCTCCCTCGGTTGCGGTGG
1 AGCAGGTTGAAGACACCAGCCTTGCCTCCCTC-GTTGCAGTGG
39902510 AGCAGGTTGAAGA
1 AGCAGGTTGAAGA
39902523 TAGTAGATCT
Statistics
Matches: 129, Mismatches: 52, Indels: 16
0.65 0.26 0.08
Matches are distributed among these distances:
43 47 0.36
44 46 0.36
45 36 0.28
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (42 bp):
AGCAGGTTGAAGACACCAGCCTTGCCTCCCTCGTTGCAGTGG
Found at i:39902612 original size:44 final size:44
Alignment explanation
Indices: 39902563--39902774 Score: 234
Period size: 44 Copynumber: 4.8 Consensus size: 44
39902553 GAAGCAGTTC
* * * *
39902563 GAAGATGGTAAG-CCTTATCTCACTGACCAGTAGTGGAATAGGTG
1 GAAGATTGTAAGTCC-TATCTCCCTAACCAGCAGTGGAATAGGTG
*
39902607 GAAGATTGTAAGTCCTATCTCCCTAACCAGCAGTGGAATAGGTT
1 GAAGATTGTAAGTCCTATCTCCCTAACCAGCAGTGGAATAGGTG
* *
39902651 GAAGATTGTACGTCCTATCTCCCTGACCAGCAGTGGAA-AGGTG
1 GAAGATTGTAAGTCCTATCTCCCTAACCAGCAGTGGAATAGGTG
* * * **
39902694 GAAGATCGTATGTCCTATCTCCCTAAACAATAGTGGAATAGGTTG
1 GAAGATTGTAAGTCCTATCTCCCTAACCAGCAGTGGAATAGG-TG
* * *
39902739 G-AGATTGT-AGATCCTGTCTCCCTAAGCAGTAGTGGA
1 GAAGATTGTAAG-TCCTATCTCCCTAACCAGCAGTGGA
39902775 GCAGATCGAA
Statistics
Matches: 145, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
43 37 0.26
44 103 0.71
45 5 0.03
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (44 bp):
GAAGATTGTAAGTCCTATCTCCCTAACCAGCAGTGGAATAGGTG
Found at i:39902729 original size:87 final size:88
Alignment explanation
Indices: 39902578--39902761 Score: 264
Period size: 87 Copynumber: 2.1 Consensus size: 88
39902568 TGGTAAGCCT
* * * * *
39902578 TATCTCACTGACCAGTAGTGGAATAGGTGGAAGATTGTAAGTCCTATCTCCCTAACCAGCAGTGG
1 TATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATCGTAAGTCCTATCTCCCTAAACAACAGTGG
39902643 AATAGGTTGAAGATTGTACG-TCC
66 AATAGGTTGAAGATTGTA-GATCC
* *
39902666 TATCTCCCTGACCAGCAGTGGAA-AGGTGGAAGATCGTATGTCCTATCTCCCTAAACAATAGTGG
1 TATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATCGTAAGTCCTATCTCCCTAAACAACAGTGG
*
39902730 AATAGGTTGGAGATTGTAGATCC
66 AATAGGTTGAAGATTGTAGATCC
*
39902753 TGTCTCCCT
1 TATCTCCCT
39902762 AAGCAGTAGT
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
86 1 0.01
87 64 0.74
88 21 0.24
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (88 bp):
TATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATCGTAAGTCCTATCTCCCTAAACAACAGTGG
AATAGGTTGAAGATTGTAGATCC
Found at i:39906269 original size:27 final size:27
Alignment explanation
Indices: 39906233--39906310 Score: 138
Period size: 27 Copynumber: 2.9 Consensus size: 27
39906223 AACATAAAAG
39906233 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
*
39906260 GGGGTTGCTAAGTGCTGATTCCCTCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
*
39906287 GGGGTTGCTATGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
39906311 AAATCATCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.15, C:0.24, G:0.31, T:0.29
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:39906411 original size:76 final size:74
Alignment explanation
Indices: 39906285--39906540 Score: 300
Period size: 74 Copynumber: 3.4 Consensus size: 74
39906275 TGATTCCCTC
* *
39906285 AAGGGGTTGCTATGTGCTGATTCCCCAAATCATCAGTGGTTGCTAAGTGTTGATTCCACCGTGTC
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGTTGATTCCACC-TGT-
39906350 TTTGGATATG-A
64 TTTGGAT-TGAA
* **
39906361 AAGGGGTTGCTAAGTGTTGATTCCCCAAATCATCGGTGGTTGCTAAGTGTTGATTCCA-CTGTAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGTTGATTCCACCTGTTT
* *
39906425 CGGATTGTAT
66 TGGATTG-AA
* * * *
39906435 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGGTGGTTGCTAAGTGCTAATTCCACCATATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGTTGATTCCACC-T-GT
*
39906500 TTTGAATGTGCAA
64 TTTGGAT-TG-AA
39906513 AAGGGGGTTGCTAAGTGCTGATTTCCCC
1 AA-GGGGTTGCTAAGTGCTGA-TTCCCC
39906541 CAAGGGGTCA
Statistics
Matches: 154, Mismatches: 18, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
72 2 0.01
73 4 0.03
74 57 0.37
75 2 0.01
76 56 0.36
77 4 0.03
78 5 0.03
79 18 0.12
80 6 0.04
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (74 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGTTGATTCCACCTGTTT
TGGATTGAA
Found at i:39909043 original size:18 final size:19
Alignment explanation
Indices: 39909015--39909050 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39909005 CGAATCTATC
39909015 AATTGAACACGAAACAGAA
1 AATTGAACACGAAACAGAA
*
39909034 AATT-AACACGCAACAGA
1 AATTGAACACGAAACAGA
39909051 TCACAACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.56, C:0.19, G:0.14, T:0.11
Consensus pattern (19 bp):
AATTGAACACGAAACAGAA
Found at i:39918217 original size:33 final size:33
Alignment explanation
Indices: 39918175--39918301 Score: 110
Period size: 33 Copynumber: 3.6 Consensus size: 33
39918165 GATATGAAAG
* *
39918175 GGTTGCTAAGTACTGATTCCCTAAATCATCGGT
1 GGTTGCTAAGTGCTGATTCCCTAAATCATAGGT
* *
39918208 GGTTGCTAAGTGCTGATTCCACCGTAACGGATTGTATAAGT
1 GGTTGCTAAGTGCTGATT-C-CC-TAA---A-T-CATAGGT
* *
39918249 GGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCTAAATCATAGGT
**
39918282 GGTTGCTAAGTTTTGATTCC
1 GGTTGCTAAGTGCTGATTCC
39918302 ACCATATTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
33 39 0.51
34 2 0.03
35 3 0.04
36 3 0.04
38 2 0.03
39 3 0.04
40 2 0.03
41 22 0.29
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.35
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCTAAATCATAGGT
Found at i:39918284 original size:74 final size:74
Alignment explanation
Indices: 39918099--39918304 Score: 256
Period size: 74 Copynumber: 2.8 Consensus size: 74
39918089 TTCCCTCAAG
* * * * **
39918099 GGGTTGCTAAGTGATAATTCCCCAAATCATCGGTGGTTGCTAAGTGTTTATTCCACCGTGTCCTC
1 GGGTTGCTAAGTGCTGATTCCCTAAATCATCGGTGGTTGCTAAGTGTTGATTCCACCG-GTCAAC
39918164 GGATATGAAA
65 GGATATGAAA
* *
39918174 GGGTTGCTAAGTACTGATTCCCTAAATCATCGGTGGTTGCTAAGTGCTGATTCCACC-GT-AACG
1 GGGTTGCTAAGTGCTGATTCCCTAAATCATCGGTGGTTGCTAAGTGTTGATTCCACCGGTCAACG
39918237 GAT-TGTATAA
66 GATATG-A-AA
* * *
39918247 GTGGTTGCTAAGTGCTGATTCCCTGAATCATTGGTGGTTGCTAAGTTTTGATTCCACC
1 G-GGTTGCTAAGTGCTGATTCCCTAAATCATCGGTGGTTGCTAAGTGTTGATTCCACC
39918305 ATATTTTTGA
Statistics
Matches: 115, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
71 2 0.02
72 6 0.05
73 5 0.04
74 51 0.44
75 51 0.44
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (74 bp):
GGGTTGCTAAGTGCTGATTCCCTAAATCATCGGTGGTTGCTAAGTGTTGATTCCACCGGTCAACG
GATATGAAA
Found at i:39922060 original size:18 final size:18
Alignment explanation
Indices: 39921992--39922100 Score: 78
Period size: 18 Copynumber: 5.9 Consensus size: 18
39921982 TTAACATCTT
39921992 TTTCTTTTTCTTTTTTAA
1 TTTCTTTTTCTTTTTTAA
*
39922010 TTT-TCTTTTCTTCGTCTTT-T
1 TTTCT-TTTTCTT--T-TTTAA
* ** *
39922030 TTTCTCTCACTTTTTTGA
1 TTTCTTTTTCTTTTTTAA
**
39922048 TTTCTTTTTCTTTTGCAA
1 TTTCTTTTTCTTTTTTAA
* *
39922066 TTTCTTTTTCTTTTTCAC
1 TTTCTTTTTCTTTTTTAA
39922084 TTTCTTTTTCTTCTTTT
1 TTTCTTTTTCTT-TTTT
39922101 TCATTTTTAT
Statistics
Matches: 70, Mismatches: 14, Indels: 13
0.72 0.14 0.13
Matches are distributed among these distances:
17 4 0.06
18 51 0.73
19 3 0.04
20 8 0.11
21 4 0.06
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTCTTTTTCTTTTTTAA
Found at i:39922107 original size:6 final size:6
Alignment explanation
Indices: 39921988--39922095 Score: 53
Period size: 6 Copynumber: 17.7 Consensus size: 6
39921978 TTTTTTAACA
* *
39921988 TCTTTT TCTTTT TCTTTT T-TAATTT TC-TTT TCTTCGTCT T-TTTT TCTCTC
1 TCTTTT TCTTTT TCTTTT TCT--TTT TCTTTT TCTT--T-T TCTTTT TCTTTT
* * * ** **
39922038 ACTTTT T-TGATT TCTTTT TCTTTT GCAATT TCTTTT TCTTTT TCACTT
1 TCTTTT TCT-TTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
39922086 TCTTTT TCTT
1 TCTTTT TCTT
39922096 CTTTTTCATT
Statistics
Matches: 74, Mismatches: 18, Indels: 20
0.66 0.16 0.18
Matches are distributed among these distances:
5 9 0.12
6 55 0.74
7 5 0.07
8 3 0.04
9 2 0.03
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.72
Consensus pattern (6 bp):
TCTTTT
Found at i:39924235 original size:20 final size:20
Alignment explanation
Indices: 39924210--39924254 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
39924200 TAAATACACA
39924210 TAATTAAAATT-AGACACAAT
1 TAATT-AAATTAAGACACAAT
*
39924230 TAATTAAGTTAAGACACAAT
1 TAATTAAATTAAGACACAAT
39924250 TAATT
1 TAATT
39924255 CGGTTAGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (20 bp):
TAATTAAATTAAGACACAAT
Found at i:39924260 original size:20 final size:19
Alignment explanation
Indices: 39924219--39924264 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
39924209 ATAATTAAAA
39924219 TTAGACACAATTAATTAAG
1 TTAGACACAATTAATTAAG
**
39924238 TTAAGACACAATTAATTCGG
1 TT-AGACACAATTAATTAAG
39924258 TTAGACA
1 TTAGACA
39924265 AGACATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (19 bp):
TTAGACACAATTAATTAAG
Found at i:39926317 original size:17 final size:17
Alignment explanation
Indices: 39926263--39926320 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
39926253 GGAAAGTAGT
39926263 TTTGAGTGAAAATTCTC
1 TTTGAGTGAAAATTCTC
* ** * * *
39926280 TTTGAATTCAGATTTTT
1 TTTGAGTGAAAATTCTC
39926297 TTTGAGTGAAAATTCTC
1 TTTGAGTGAAAATTCTC
39926314 TTTGAGT
1 TTTGAGT
39926321 TTCTCCAAGA
Statistics
Matches: 29, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (17 bp):
TTTGAGTGAAAATTCTC
Found at i:39940791 original size:20 final size:20
Alignment explanation
Indices: 39940766--39940809 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
39940756 AAATACACAG
39940766 AATTAAAATT-AGACACAATT
1 AATT-AAATTAAGACACAATT
*
39940786 AATTAAGTTAAGACACAATT
1 AATTAAATTAAGACACAATT
39940806 AATT
1 AATT
39940810 CAGTTGGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (20 bp):
AATTAAATTAAGACACAATT
Found at i:39940814 original size:20 final size:20
Alignment explanation
Indices: 39940776--39940814 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39940766 AATTAAAATT
39940776 AGACACAATTAATTAAGTTA
1 AGACACAATTAATTAAGTTA
*
39940796 AGACACAATTAATTCAGTT
1 AGACACAATTAATTAAGTT
39940815 GGATAAGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (20 bp):
AGACACAATTAATTAAGTTA
Found at i:39942658 original size:16 final size:18
Alignment explanation
Indices: 39942639--39942672 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
39942629 CAATATAATA
39942639 TATTTT-TAATA-ACTTT
1 TATTTTATAATATACTTT
39942655 TATTTTATAATATACTTT
1 TATTTTATAATATACTTT
39942673 AAAAGCCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTATAATATACTTT
Found at i:39947828 original size:22 final size:20
Alignment explanation
Indices: 39947797--39947850 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
39947787 CAAAAAAATG
* *
39947797 ATGAATAAAAAAAATGAAGATA
1 ATGAAGAAAAAAAAAGAA-A-A
39947819 ATGAAGAAAAAAAAAGAAAA
1 ATGAAGAAAAAAAAAGAAAA
39947839 A-GAAGAAAAAAA
1 ATGAAGAAAAAAA
39947851 GAAAATGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 1 0.03
22 16 0.53
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (20 bp):
ATGAAGAAAAAAAAAGAAAA
Found at i:39947849 original size:17 final size:16
Alignment explanation
Indices: 39947822--39947855 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
39947812 GAAGATAATG
39947822 AAGAAAAAAAAAGAAA
1 AAGAAAAAAAAAGAAA
39947838 AAGAAGAAAAAAAGAAA
1 AAGAA-AAAAAAAGAAA
39947855 A
1 A
39947856 TGGACAGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAGAAA
Found at i:39949212 original size:44 final size:44
Alignment explanation
Indices: 39949164--39949389 Score: 120
Period size: 44 Copynumber: 5.1 Consensus size: 44
39949154 GACACCAGCA
* *
39949164 TTGCCTCCCTCGGTTGCAGTGGATCAGGTTGAAGATAGTAGATC
1 TTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATACTAGATC
* *** * * * * * *
39949208 TTGCCTTCCT-GCAACGACAGTGAAGCAGATCGAAGACACCAG-CC
1 TTGCCTCCCTCG-GTTG-CAGTGGAGCAGGTTGAAGATACTAGATC
* * *
39949252 TTGCCTCCCTCGGTTGCAGTGGAACAGGTTAAAAATAAC-AGATC
1 TTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGAT-ACTAGATC
* *** * * * * * *
39949296 TTGCCTTCCTAC-ACCGACACTGAAGCAGATCGAAGACACTAG-CC
1 TTGCCTCCCT-CGGTTG-CAGTGGAGCAGGTTGAAGATACTAGATC
* * *
39949340 TTACCTCTCTCGGTTGCAGTGGAGCAGGTTGAAGATAGTAGATC
1 TTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATACTAGATC
39949384 TTGCCT
1 TTGCCT
39949390 TCCTGCATCG
Statistics
Matches: 121, Mismatches: 51, Indels: 20
0.63 0.27 0.10
Matches are distributed among these distances:
43 36 0.30
44 51 0.42
45 34 0.28
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (44 bp):
TTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATACTAGATC
Found at i:39949259 original size:88 final size:88
Alignment explanation
Indices: 39949105--39949419 Score: 452
Period size: 88 Copynumber: 3.6 Consensus size: 88
39949095 AACAGATTAG
* * *
39949105 TGAATATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATTGAAGACACCAGCATTGCCT
1 TGAAGATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
39949170 CCCTCGGTTGCAGTGGATCAGGT
66 CCCTCGGTTGCAGTGGAACAGGT
* *
39949193 TGAAGATAGTAGATCTTGCCTTCCTGCAACGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAGATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
39949258 CCCTCGGTTGCAGTGGAACAGGT
66 CCCTCGGTTGCAGTGGAACAGGT
* * ** * * *
39949281 TAAAAATAACAGATCTTGCCTTCCTACACCGACA-CTGAAGCAGATCGAAGACACTAGCCTTACC
1 TGAAGATAGTAGATCTTGCCTTCCTGCACCGACAGC-GAAGCAGATCGAAGACACCAGCCTTGCC
* *
39949345 TCTCTCGGTTGCAGTGGAGCAGGT
65 TCCCTCGGTTGCAGTGGAACAGGT
* * *
39949369 TGAAGATAGTAGATCTTGCCTTCCTGCATCGATAGCGAAGCAGTTCGAAGA
1 TGAAGATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGA
39949420 TGGTAAGCCC
Statistics
Matches: 200, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
88 199 1.00
89 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.23
Consensus pattern (88 bp):
TGAAGATAGTAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTCGGTTGCAGTGGAACAGGT
Found at i:39949464 original size:44 final size:44
Alignment explanation
Indices: 39949428--39949658 Score: 306
Period size: 44 Copynumber: 5.2 Consensus size: 44
39949418 GATGGTAAGC
* *
39949428 CCTATCTCCCTGACCAGTAGTGGAATAGGTGGAAGATTGTAAGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTATGT
*
39949472 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTATGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTATGT
* * *
39949516 CCTATCTCCCTGACTAGCAGCGGAATAGAG-AGAAGATTGTATGT
1 CCTATCTCCCTGACCAGCAGTGGAATAG-GTGGAAGATTGTATGT
* *
39949560 CCTATCTCCCTAACCAGTAGTGGAATAGGTGGAAGATTGTATGT
1 CCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTATGT
* * *
39949604 CCTATCTCCTTGAACAACAGTGGAATAGGTTGG-AGATTGTA-GAT
1 CCTATCTCCCTGACCAGCAGTGGAATAGG-TGGAAGATTGTATG-T
*
39949648 CCTGTCTCCCT
1 CCTATCTCCCT
39949659 AAGCAGTAGT
Statistics
Matches: 165, Mismatches: 18, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
43 2 0.01
44 159 0.96
45 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTATGT
Found at i:39949683 original size:88 final size:87
Alignment explanation
Indices: 39949413--39949683 Score: 278
Period size: 88 Copynumber: 3.1 Consensus size: 87
39949403 GCGAAGCAGT
* * * * *
39949413 TCGAAGATGGTAAGCCCTATCTCCCTGACCAGTAGTGGAATAGGTGGAAGATTGTA-AGTCCTAT
1 TCGAAGATTGTATGTCCTATCTCCCTGAACAGCAGTGGAATAGGTGG-AGATTGTAGA-TCCTAT
* * *
39949477 CTCCCTGACCAGCAGTGGAATAGG
64 CTCCCTAACCAGTAGTGGAACAGG
* * * *
39949501 TTGAAGATTGTATGTCCTATCTCCCTG-ACTAGCAGCGGAATAGAGAGAAGATTGTATG-TCCTA
1 TCGAAGATTGTATGTCCTATCTCCCTGAAC-AGCAGTGGAATAG-GTGGAGATTGTA-GATCCTA
*
39949564 TCTCCCTAACCAGTAGTGGAATAGG
63 TCTCCCTAACCAGTAGTGGAACAGG
* * * *
39949589 TGGAAGATTGTATGTCCTATCTCCTTGAACAACAGTGGAATAGGTTGGAGATTGTAGATCCTGTC
1 TCGAAGATTGTATGTCCTATCTCCCTGAACAGCAGTGGAATAGG-TGGAGATTGTAGATCCTATC
* * * *
39949654 TCCCTAAGCAGTAGTAGAGCAGA
65 TCCCTAACCAGTAGTGGAACAGG
39949677 TCGAAGA
1 TCGAAGA
39949684 CGGCGAATCT
Statistics
Matches: 152, Mismatches: 24, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
87 3 0.02
88 145 0.95
89 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (87 bp):
TCGAAGATTGTATGTCCTATCTCCCTGAACAGCAGTGGAATAGGTGGAGATTGTAGATCCTATCT
CCCTAACCAGTAGTGGAACAGG
Found at i:39949683 original size:132 final size:134
Alignment explanation
Indices: 39949407--39949683 Score: 359
Period size: 132 Copynumber: 2.1 Consensus size: 134
39949397 TCGATAGCGA
* *
39949407 AGCAGTTCGAAGATGGTAAGCCCTATCTCCCTGACCAGTAGTGGAATAGGTGGAAGATTGTAAGT
1 AGCAGATCGAAGATGGTAAGCCCTATCTCCCTAACCAGTAGTGGAATAGGTGGAAGATTGTAAGT
* *
39949472 CCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTATGTCCTATCTCCCTGACTAGCAGC
66 CCTATCTCCCTGAACAACAGTGGAATAGGTTGAAGATTGTATGTCCTATCTCCCTGAC-AGCAGC
* *
39949537 GGAAT
130 AGAAG
* * * *
39949542 AG-AGA--GAAGATTGTATGTCCTATCTCCCTAACCAGTAGTGGAATAGGTGGAAGATTGTATGT
1 AGCAGATCGAAGATGGTAAGCCCTATCTCCCTAACCAGTAGTGGAATAGGTGGAAGATTGTAAGT
* * * *
39949604 CCTATCTCCTTGAACAACAGTGGAATAGGTTGGAGATTGTA-GATCCTGTCTCCCT-A-AGCAGT
66 CCTATCTCCCTGAACAACAGTGGAATAGGTTGAAGATTGTATG-TCCTATCTCCCTGACAGCAGC
*
39949666 AGTAG
130 AGAAG
39949671 AGCAGATCGAAGA
1 AGCAGATCGAAGA
39949684 CGGCGAATCT
Statistics
Matches: 123, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
129 9 0.07
130 3 0.02
131 2 0.02
132 105 0.85
134 2 0.02
135 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (134 bp):
AGCAGATCGAAGATGGTAAGCCCTATCTCCCTAACCAGTAGTGGAATAGGTGGAAGATTGTAAGT
CCTATCTCCCTGAACAACAGTGGAATAGGTTGAAGATTGTATGTCCTATCTCCCTGACAGCAGCA
GAAG
Found at i:39951215 original size:23 final size:21
Alignment explanation
Indices: 39951184--39951230 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
39951174 AAATCAGCCC
*
39951184 ATTGTTTTATTAATTAGTTTAAT
1 ATTGATTTATT-ATTA-TTTAAT
*
39951207 ATTGATTTATTATTATTTATT
1 ATTGATTTATTATTATTTAAT
39951228 ATT
1 ATT
39951231 TTTATTGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 4 0.18
23 10 0.45
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (21 bp):
ATTGATTTATTATTATTTAAT
Found at i:39951439 original size:18 final size:16
Alignment explanation
Indices: 39951405--39951440 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
39951395 TAATATAATA
39951405 TATTTTTAATAACTTT
1 TATTTTTAATAACTTT
39951421 TATTTTATAATATACTTT
1 TATTTT-TAATA-ACTTT
39951439 TA
1 TA
39951441 AAAGCCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTTAATAACTTT
Found at i:39953001 original size:23 final size:22
Alignment explanation
Indices: 39952970--39953012 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
39952960 GTAAGTATGC
39952970 ATGTGATTTAATATATTATTTTA
1 ATGTGATTTAATATA-TATTTTA
* *
39952993 ATGTTATTTTATATATATTT
1 ATGTGATTTAATATATATTT
39953013 CTGGGATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (22 bp):
ATGTGATTTAATATATATTTTA
Found at i:39953194 original size:33 final size:33
Alignment explanation
Indices: 39953152--39953354 Score: 120
Period size: 33 Copynumber: 5.6 Consensus size: 33
39953142 CATAAAAGGG
39953152 GGTTGCTAAGTGCTGATTCCCCAAATCATCGGT
1 GGTTGCTAAGTGCTGATTCCCCAAATCATCGGT
*** * *
39953185 GGTTGCTAAGTGCTGATTCCACCGTGTCTTTGGATATGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCAAATC-----AT-CG---GT
39953228 GGTTGCTAAGTGCTGATTCCCCAAATCATCGGT
1 GGTTGCTAAGTGCTGATTCCCCAAATCATCGGT
* * *
39953261 GGTTGCTAAGTGTTGATTCCACCATAATGGAAT-GTATAAGG
1 GGTTGCTAAGTGCTGATTCC-CCA-AAT--CATCG-----GT
** *
39953302 GGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCAAATCATCGGT
*
39953335 GGTTGGTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
39953355 ACCATATTTT
Statistics
Matches: 131, Mismatches: 19, Indels: 40
0.69 0.10 0.21
Matches are distributed among these distances:
33 60 0.46
34 7 0.05
35 3 0.02
36 2 0.02
37 6 0.05
38 1 0.01
39 5 0.04
40 2 0.02
41 20 0.15
42 4 0.03
43 21 0.16
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCAAATCATCGGT
Found at i:39953234 original size:76 final size:75
Alignment explanation
Indices: 39953145--39953436 Score: 322
Period size: 76 Copynumber: 3.8 Consensus size: 75
39953135 CATTGAACAT
39953145 AAAAGGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGT
1 AAAA-GGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACC-T
*
39953210 GTCTTTGGATATG
64 AT-TTTGGATATG
*
39953223 -AAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGTTGATTCCACC-AT
1 AAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCTAT
**
39953286 AATGGA-ATG
66 TTTGGATATG
* ** * *
39953295 TATAAGGGGTTGCTAAGTGCTGATTCCCTGAATCATTGGTGGTTGGTAAGTGCTGATTCCACCAT
1 -AAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACC-T
* *
39953360 ATTTTTGAATGTGG
64 A-TTTTGGATAT-G
* * * ** *
39953374 AAAAGAGGGTTGCTAAGTGCTGATTCCTCGACTCA-CTGGTGAATGCTAAGTGCTGAATCCACC
1 AAAAG-GGGTTGCTAAGTGCTGATTCCCCAAATCATC-GGTGGTTGCTAAGTGCTGATTCCACC
39953437 AAATAACGGT
Statistics
Matches: 182, Mismatches: 23, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
72 3 0.02
73 4 0.02
74 56 0.31
76 58 0.32
77 7 0.04
78 5 0.03
79 49 0.27
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (75 bp):
AAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCTAT
TTTGGATATG
Found at i:39964524 original size:15 final size:15
Alignment explanation
Indices: 39964487--39964537 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
39964477 TTGAGTGAGA
* *
39964487 AAAAGAAAAATAGAG
1 AAAAGAAAAAGAGTG
*
39964502 -AAACAAAAAGAGTG
1 AAAAGAAAAAGAGTG
*
39964516 AAAAGAAAAAGAATG
1 AAAAGAAAAAGAGTG
*
39964531 AACAGAA
1 AAAAGAA
39964538 TGATGAAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.71, C:0.04, G:0.20, T:0.06
Consensus pattern (15 bp):
AAAAGAAAAAGAGTG
Found at i:39971187 original size:74 final size:75
Alignment explanation
Indices: 39970994--39971203 Score: 266
Period size: 74 Copynumber: 2.8 Consensus size: 75
39970984 TGATTCCCCC
* * *
39970994 AAGGGGTTGCTAAGTGATAATTCCCCAAATCATCGGTGGTTGCTAAGTGTTTATTCCACCGTGTC
1 AAGGGGTTGCTAAGTGATGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCG-GTC
** *
39971059 TTCGGATATGA
65 AACAGATATGA
39971070 AAGGGGTTGCTAAGT-ATTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACC-GT-
1 AAGGGGTTGCTAAGTGA-TGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGGTC
39971132 AACAGAT-TGTA
65 AACAGATATG-A
* * * *
39971143 TAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTACTGATTCCACC
1 -AAGGGGTTGCTAAGTGATGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACC
39971204 ATATTTTTGA
Statistics
Matches: 120, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
72 2 0.02
73 5 0.04
74 57 0.47
75 1 0.01
76 55 0.46
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGATGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGGTCA
ACAGATATGA
Found at i:39971297 original size:33 final size:29
Alignment explanation
Indices: 39971225--39971300 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
39971215 TGTGAAAAAG
* *
39971225 GGGGTTGCTAAGTGTTGATTTCCCCCACA
1 GGGGTTGCTAAGTGATGATTCCCCCCACA
* *
39971254 GGGGTCGCTAAGTGATGATTCCCCGACTCACT
1 GGGGTTGCTAAGTGATGATTCCCC--C-CACA
39971286 GGTGGTTGCTAAGTG
1 GG-GGTTGCTAAGTG
39971301 CTGAATCCAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 21 0.55
31 1 0.03
32 5 0.13
33 11 0.29
ACGTcount: A:0.17, C:0.22, G:0.32, T:0.29
Consensus pattern (29 bp):
GGGGTTGCTAAGTGATGATTCCCCCCACA
Found at i:39974761 original size:18 final size:18
Alignment explanation
Indices: 39974740--39974801 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
39974730 TTTTCTCTCA
*
39974740 CTTTTTTGATTTCTTTTT
1 CTTTTTTAATTTCTTTTT
**
39974758 CTTTTGCAATTTCTTTTT
1 CTTTTTTAATTTCTTTTT
* *
39974776 CTTTTTCACTTTCTTTTT
1 CTTTTTTAATTTCTTTTT
39974794 CTTCTTTT
1 CTT-TTTT
39974802 TCATTTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
18 34 0.92
19 3 0.08
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (18 bp):
CTTTTTTAATTTCTTTTT
Found at i:39974801 original size:57 final size:54
Alignment explanation
Indices: 39974681--39974802 Score: 122
Period size: 57 Copynumber: 2.1 Consensus size: 54
39974671 TTTCTCTCTT
*
39974681 TTCTTTTTTATCATCTTTTTCTTTTTCAATTTTCTTTTCTTCGTCTTCTTTTTC
1 TTCTTTTTTATCATCTTTTTCTTTTGCAATTTTCTTTTCTTCGTCTTCTTTTTC
* **
39974735 TCTCACTTTTTTGAT-TTCTTTTTCTTTTGCAA-TTTCTTTTTCTTTTTCACTTTCTTTTTC
1 T-T--CTTTTTT-ATCATCTTTTTCTTTTGCAATTTTC-TTTTCTTCGT--C-TTCTTTTTC
39974795 TTCTTTTT
1 TTCTTTTT
39974803 CATTTTTATT
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
54 1 0.02
55 1 0.02
56 4 0.07
57 36 0.64
58 2 0.04
59 2 0.04
60 10 0.18
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.70
Consensus pattern (54 bp):
TTCTTTTTTATCATCTTTTTCTTTTGCAATTTTCTTTTCTTCGTCTTCTTTTTC
Found at i:39974808 original size:6 final size:6
Alignment explanation
Indices: 39974694--39974796 Score: 57
Period size: 6 Copynumber: 16.7 Consensus size: 6
39974684 TTTTTTATCA
* * * *
39974694 TCTTTT TCTTTT TCAATTT TC-TTT TCTTCGTCT TCTTTT TCTCTC ACTTTT
1 TCTTTT TCTTTT TC-TTTT TCTTTT TCTT--T-T TCTTTT TCTTTT TCTTTT
* * ** **
39974745 T-TGATT TCTTTT TCTTTT GCAATT TCTTTT TCTTTT TCACTT TCTTTT
1 TCT-TTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
39974793 TCTT
1 TCTT
39974797 CTTTTTCATT
Statistics
Matches: 71, Mismatches: 19, Indels: 14
0.68 0.18 0.13
Matches are distributed among these distances:
5 6 0.08
6 52 0.73
7 7 0.10
8 1 0.01
9 5 0.07
ACGTcount: A:0.07, C:0.20, G:0.03, T:0.70
Consensus pattern (6 bp):
TCTTTT
Found at i:39976926 original size:20 final size:20
Alignment explanation
Indices: 39976901--39976945 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
39976891 TAAATACACA
39976901 TAATTAAAATT-AGACACAAT
1 TAATT-AAATTAAGACACAAT
*
39976921 TAATTAAGTTAAGACACAAT
1 TAATTAAATTAAGACACAAT
39976941 TAATT
1 TAATT
39976946 CGGTTAGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (20 bp):
TAATTAAATTAAGACACAAT
Found at i:39976951 original size:20 final size:19
Alignment explanation
Indices: 39976910--39976955 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
39976900 ATAATTAAAA
39976910 TTAGACACAATTAATTAAG
1 TTAGACACAATTAATTAAG
**
39976929 TTAAGACACAATTAATTCGG
1 TT-AGACACAATTAATTAAG
39976949 TTAGACA
1 TTAGACA
39976956 AGACATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (19 bp):
TTAGACACAATTAATTAAG
Found at i:39979122 original size:30 final size:29
Alignment explanation
Indices: 39979088--39979144 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
39979078 TGAGCTTTAA
39979088 CGAGCTTAAAT-GAGCTCAAGTGAGCTGATT
1 CGAGC-TAAATGGAGCTCAAG-GAGCTGATT
*
39979118 CGAGCTAAATGGAGCTCGAGGAGCTGA
1 CGAGCTAAATGGAGCTCAAGGAGCTGA
39979145 AGATGAGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.30, C:0.18, G:0.32, T:0.21
Consensus pattern (29 bp):
CGAGCTAAATGGAGCTCAAGGAGCTGATT
Found at i:39982301 original size:12 final size:12
Alignment explanation
Indices: 39982284--39982308 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39982274 TAGGTTTGTG
39982284 AAATTCAAAAAA
1 AAATTCAAAAAA
39982296 AAATTCAAAAAA
1 AAATTCAAAAAA
39982308 A
1 A
39982309 TTCAAGTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:39985948 original size:116 final size:116
Alignment explanation
Indices: 39985744--39985974 Score: 462
Period size: 116 Copynumber: 2.0 Consensus size: 116
39985734 AACATTTGGA
39985744 AAAAATATTCCATGGCAACTTGATCTTTCATGAGTTTGGAAACCACATTAGGTCCTTTCGAAATC
1 AAAAATATTCCATGGCAACTTGATCTTTCATGAGTTTGGAAACCACATTAGGTCCTTTCGAAATC
39985809 TTTTACTTAGTAAATACATATTTTACTGATCCTTATTTACTAAGGGTTTCT
66 TTTTACTTAGTAAATACATATTTTACTGATCCTTATTTACTAAGGGTTTCT
39985860 AAAAATATTCCATGGCAACTTGATCTTTCATGAGTTTGGAAACCACATTAGGTCCTTTCGAAATC
1 AAAAATATTCCATGGCAACTTGATCTTTCATGAGTTTGGAAACCACATTAGGTCCTTTCGAAATC
39985925 TTTTACTTAGTAAATACATATTTTACTGATCCTTATTTACTAAGGGTTTC
66 TTTTACTTAGTAAATACATATTTTACTGATCCTTATTTACTAAGGGTTTC
39985975 CTAGCATTCG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (116 bp):
AAAAATATTCCATGGCAACTTGATCTTTCATGAGTTTGGAAACCACATTAGGTCCTTTCGAAATC
TTTTACTTAGTAAATACATATTTTACTGATCCTTATTTACTAAGGGTTTCT
Found at i:39987762 original size:20 final size:20
Alignment explanation
Indices: 39987739--39987785 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
39987729 GGGTTAAGAT
*
39987739 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
39987759 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
39987779 TGAGCTG
1 TGAGCTG
39987786 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:39989511 original size:48 final size:48
Alignment explanation
Indices: 39989456--39989561 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
39989446 TTGTCTTTTC
*
39989456 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
39989504 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
39989552 TTTCTTTTTC
1 TTTCTTTTTC
39989562 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:39989646 original size:12 final size:12
Alignment explanation
Indices: 39989611--39989727 Score: 64
Period size: 12 Copynumber: 9.8 Consensus size: 12
39989601 AATCTCACTC
39989611 TCTTTTTCAATTT
1 TCTTTTTC-ATTT
39989624 TCTTTTCTTCATTT
1 TC-TTT-TTCATTT
* *
39989638 TCTTTTTCACTC
1 TCTTTTTCATTT
*
39989650 ACTTTTTCGA-TT
1 TCTTTTTC-ATTT
39989662 TCTTTTTC-TTT
1 TCTTTTTCATTT
** *
39989673 TGCAATTTCTTTT
1 T-CTTTTTCATTT
* *
39989686 TCTTCTTCGTTT
1 TCTTTTTCATTT
*
39989698 TCTTTTT-GTTT
1 TCTTTTTCATTT
*
39989709 TC--TTTCAATT
1 TCTTTTTCATTT
39989719 TCTTTTTCA
1 TCTTTTTCA
39989728 ATCTCTTTCT
Statistics
Matches: 81, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 9 0.11
12 43 0.53
13 10 0.12
14 9 0.11
15 3 0.04
ACGTcount: A:0.09, C:0.20, G:0.03, T:0.68
Consensus pattern (12 bp):
TCTTTTTCATTT
Found at i:39989648 original size:39 final size:39
Alignment explanation
Indices: 39989605--39989745 Score: 126
Period size: 39 Copynumber: 3.5 Consensus size: 39
39989595 TTCTTCAATC
*
39989605 TCACTCTCTTTTTCAATTTTCTTTTC-TTCATTTTCTTTT
1 TCACTCTCTTTTTC-ATTTTCTTTTCTTTCAATTTCTTTT
*
39989644 TCACTCACTTTTTCGA-TTTCTTTTTCTTTTGCAATTTCTTTT
1 TCACTCTCTTTTTC-ATTTTC-TTTTC-TTT-CAATTTCTTTT
* * * *
39989686 TC-TTCTTCGTTTTCTTTTTGTTTTCTTTCAATTTCTTTT
1 TCACTC-TCTTTTTCATTTTCTTTTCTTTCAATTTCTTTT
* * *
39989725 TCAATCTCTTTCTCCTTTTCT
1 TCACTCTCTTTTTCATTTTCT
39989746 CGCTCAATGG
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
38 4 0.05
39 43 0.52
40 5 0.06
41 9 0.11
42 21 0.26
ACGTcount: A:0.09, C:0.23, G:0.03, T:0.65
Consensus pattern (39 bp):
TCACTCTCTTTTTCATTTTCTTTTCTTTCAATTTCTTTT
Found at i:39989672 original size:18 final size:18
Alignment explanation
Indices: 39989651--39989709 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
39989641 TTTTCACTCA
39989651 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
39989669 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
39989687 CTTCTTCGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
39989705 GTTTT
1 CTTTT
39989710 CTTTCAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:39990655 original size:10 final size:10
Alignment explanation
Indices: 39990640--39990677 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
39990630 TTGGGTTAAG
39990640 ATTGAGCTGA
1 ATTGAGCTGA
39990650 ATTGAGCTCGA
1 ATTGAGCT-GA
39990661 A-TGAGCTGA
1 ATTGAGCTGA
*
39990670 CTTGAGCT
1 ATTGAGCT
39990678 CGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:39990665 original size:20 final size:20
Alignment explanation
Indices: 39990642--39990688 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
39990632 GGGTTAAGAT
39990642 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* *
39990662 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
39990682 TGAGCTG
1 TGAGCTG
39990689 GAAACGAGCT
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:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:39993274 original size:7 final size:6
Alignment explanation
Indices: 39993213--39993328 Score: 74
Period size: 6 Copynumber: 19.0 Consensus size: 6
39993203 AATGAAAAAG
** *
39993213 AAGAAA AAGAAA AAGAAA GTGAAG AAGAAA AAGAAA AAGAAA AA-AAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
** * * ** * *
39993260 TTGCAA AAGAAA AA-AAA ATCGAAA AAGTGA GAGAAA AAGAAA ATGAAGAA
1 AAGAAA AAGAAA AAGAAA A-AGAAA AAGAAA AAGAAA AAGAAA AAG-A-AA
*
39993310 AAGAAA ATTGAAA AAGAAA
1 AAGAAA A-AGAAA AAGAAA
39993329 TTGAGATTGA
Statistics
Matches: 80, Mismatches: 24, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
5 7 0.09
6 58 0.73
7 11 0.14
8 4 0.05
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (6 bp):
AAGAAA
Found at i:39993337 original size:18 final size:18
Alignment explanation
Indices: 39993316--39993350 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39993306 AGAAAAGAAA
39993316 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
39993334 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
39993351 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:39999543 original size:34 final size:34
Alignment explanation
Indices: 39999505--39999580 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
39999495 AGATTTAAAT
*
39999505 AAATTAATTATTAACACTTATTTGAACTGAACTA
1 AAATTAATTACTAACACTTATTTGAACTGAACTA
* **
39999539 AAATTAATTGCTAACACTTATTTGAGTTGAACTA
1 AAATTAATTACTAACACTTATTTGAACTGAACTA
*
39999573 AAGTTAAT
1 AAATTAAT
39999581 AAACTAACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTGAACTGAACTA
Found at i:40001467 original size:13 final size:12
Alignment explanation
Indices: 40001446--40001479 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
40001436 TTCGCTTGCA
40001446 ATTTCTTTTTCT
1 ATTTCTTTTTCT
40001458 -TTTCTCTTTTCT
1 ATTTCT-TTTTCT
40001470 ATTTCTTTTT
1 ATTTCTTTTT
40001480 AACTTTCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.25
12 10 0.50
13 5 0.25
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTCTTTTTCT
Found at i:40001468 original size:42 final size:43
Alignment explanation
Indices: 40001405--40001501 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 43
40001395 TTTTCTTTGT
**
40001405 TTTCTTTTTC-TCTCACTTTTTCTATTTCTTTTTCGCTTGCAA
1 TTTCTTTTTCTTCTCACTTTTTCTATTTCTTTTTAACTTGCAA
* * * *
40001447 TTTCTTTTTCTTTTCTC-TTTTCTATTTCTTTTTAACTTTCTA
1 TTTCTTTTTCTTCTCACTTTTTCTATTTCTTTTTAACTTGCAA
40001489 TTTCTTTTTCTTC
1 TTTCTTTTTCTTC
40001502 CTCTTCATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 43 0.91
43 4 0.09
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.68
Consensus pattern (43 bp):
TTTCTTTTTCTTCTCACTTTTTCTATTTCTTTTTAACTTGCAA
Found at i:40006441 original size:18 final size:21
Alignment explanation
Indices: 40006420--40006461 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40006410 TTCCATCTCA
40006420 TTTTCAA-ATC-CTC-TTTCT
1 TTTTCAATATCACTCATTTCT
40006438 TTTTCAATATCACTCATTTCT
1 TTTTCAATATCACTCATTTCT
40006459 TTT
1 TTT
40006462 GTACTCTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 3 0.14
20 3 0.14
21 8 0.38
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTCAATATCACTCATTTCT
Found at i:40006500 original size:18 final size:18
Alignment explanation
Indices: 40006432--40006502 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 18
40006422 TTCAAATCCT
*
40006432 CTTTCTTTTTCAATATCA
1 CTTTCTTTTTCAATCTCA
*
40006450 CTCATTTCTTTTGT-ACTCTCA
1 --C-TTTCTTTT-TCAATCTCA
40006471 -TTTCTTTCTTCAATCTCA
1 CTTTCTTT-TTCAATCTCA
40006489 CTTTCTTTTTCAAT
1 CTTTCTTTTTCAAT
40006503 TTTCTTTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
17 8 0.19
18 13 0.30
19 7 0.16
20 1 0.02
21 13 0.30
22 1 0.02
ACGTcount: A:0.17, C:0.25, G:0.01, T:0.56
Consensus pattern (18 bp):
CTTTCTTTTTCAATCTCA
Found at i:40011392 original size:34 final size:33
Alignment explanation
Indices: 40011354--40011429 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 33
40011344 AGATTTAAAC
*
40011354 AAATTAATTACTAACATTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTGAGCTGAAC-A
40011388 AAATTAATTACTAACACTTATTTGAGCTGAACA
1 AAATTAATTACTAACACTTATTTGAGCTGAACA
40011421 AAAGTTAAT
1 AAA-TTAAT
40011430 AAACTAACTC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 4 0.10
34 36 0.90
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (33 bp):
AAATTAATTACTAACACTTATTTGAGCTGAACA
Found at i:40013477 original size:11 final size:11
Alignment explanation
Indices: 40013445--40013503 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
40013435 AGAAATGAGA
*
40013445 GAATGATGAAT
1 GAATGAGGAAT
40013456 G-ATGA-GAAT
1 GAATGAGGAAT
40013465 GAATGAGGAAT
1 GAATGAGGAAT
*
40013476 GATTGAGGGATGAT
1 GAATGA-GGA--AT
40013490 GAATGAAGGAAT
1 GAATG-AGGAAT
40013502 GA
1 GA
40013504 GAGGGTCTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 10 0.25
12 7 0.17
14 9 0.22
15 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.36, T:0.22
Consensus pattern (11 bp):
GAATGAGGAAT
Found at i:40014791 original size:21 final size:21
Alignment explanation
Indices: 40014765--40014816 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
40014755 TTAAGTTTAC
40014765 ATTTATTTTGCTGGAATAATT
1 ATTTATTTTGCTGGAATAATT
*
40014786 ATTTATTTGGCTGGAATAATT
1 ATTTATTTTGCTGGAATAATT
*
40014807 ATTTAATTTG
1 ATTTATTTTG
40014817 TTATTAGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.04, G:0.15, T:0.52
Consensus pattern (21 bp):
ATTTATTTTGCTGGAATAATT
Found at i:40028533 original size:20 final size:20
Alignment explanation
Indices: 40028510--40028564 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
40028500 AGTTCAATTC
40028510 AGCTCAATT-TTAGCTCAATG
1 AGCTC-ATTCTTAGCTCAATG
*
40028530 AGCTCGTTCTTAGCTCAATG
1 AGCTCATTCTTAGCTCAATG
*
40028550 AGCTCATTGTTAGCT
1 AGCTCATTCTTAGCT
40028565 TACTTTAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (20 bp):
AGCTCATTCTTAGCTCAATG
Found at i:40030523 original size:46 final size:46
Alignment explanation
Indices: 40030472--40030565 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
40030462 ATAGTGTGGC
*
40030472 GTTCATCATATACCAAGGTTCCTATCATCCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATCCTTGATAATGGGTCGAG
* *
40030518 GTTCATCATATACCAAGGTTCTTATCATTCTTGATAATGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATCCTTGATAATGGGTCGAG
40030564 GT
1 GT
40030566 CCTTTAAACC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATCCTTGATAATGGGTCGAG
Found at i:40039596 original size:39 final size:40
Alignment explanation
Indices: 40039501--40039762 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
40039491 TTGAATGATG
*
40039501 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
40039539 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
40039580 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
40039619 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
40039658 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
40039697 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
40039736 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
40039763 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:40041342 original size:33 final size:33
Alignment explanation
Indices: 40041300--40041393 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
40041290 TCTTCACACG
* * *
40041300 TTTCTTTTTCAAGCTCTCTCTCTTTTTCACTCAT
1 TTTC-TTTTCAAGCTCTCTTTCCTTTTCACTCAC
*
40041334 TTTCTTTTCAAGCTCTCTTTCCTTTTCACTCGC
1 TTTCTTTTCAAGCTCTCTTTCCTTTTCACTCAC
40041367 TTTCTTTTCAAGCTCTCTTTCCTTTTC
1 TTTCTTTTCAAGCTCTCTTTCCTTTTC
40041394 TTGCTCACAC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
33 52 0.93
34 4 0.07
ACGTcount: A:0.10, C:0.31, G:0.04, T:0.55
Consensus pattern (33 bp):
TTTCTTTTCAAGCTCTCTTTCCTTTTCACTCAC
Found at i:40041393 original size:18 final size:18
Alignment explanation
Indices: 40041300--40041393 Score: 94
Period size: 18 Copynumber: 5.6 Consensus size: 18
40041290 TCTTCACACG
*
40041300 TTTCTTTTTCAAGCTCTC
1 TTTCCTTTTCAAGCTCTC
* *
40041318 TCTCTTTTTC-A-CTCAT-
1 TTTCCTTTTCAAGCTC-TC
40041334 TTT-CTTTTCAAGCTCTC
1 TTTCCTTTTCAAGCTCTC
*
40041351 TTTCCTTTTC-A-CTCGC
1 TTTCCTTTTCAAGCTCTC
40041367 TTT-CTTTTCAAGCTCTC
1 TTTCCTTTTCAAGCTCTC
40041384 TTTCCTTTTC
1 TTTCCTTTTC
40041394 TTGCTCACAC
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
15 11 0.17
16 15 0.24
17 16 0.25
18 21 0.33
ACGTcount: A:0.10, C:0.31, G:0.04, T:0.55
Consensus pattern (18 bp):
TTTCCTTTTCAAGCTCTC
Found at i:40041431 original size:6 final size:6
Alignment explanation
Indices: 40041422--40041458 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
40041412 GCTCTCAATC
**
40041422 TCTTTT TCTTTT TCTTTT TCGATT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T
40041459 ATTTCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (6 bp):
TCTTTT
Found at i:40041432 original size:24 final size:24
Alignment explanation
Indices: 40041405--40041458 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
40041395 TGCTCACACA
40041405 CTTTTTCGCTCTCAATCTCTTTTT
1 CTTTTTCGCTCTCAATCTCTTTTT
** * * *
40041429 CTTTTTCTTTTTCGATTTCTTTTT
1 CTTTTTCGCTCTCAATCTCTTTTT
40041453 CTTTTT
1 CTTTTT
40041459 ATTTCTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.06, C:0.22, G:0.04, T:0.69
Consensus pattern (24 bp):
CTTTTTCGCTCTCAATCTCTTTTT
Found at i:40041447 original size:18 final size:16
Alignment explanation
Indices: 40041426--40041468 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 16
40041416 TCAATCTCTT
40041426 TTTCTTTTTCTTTTTCGA
1 TTTCTTTTTCTTTTT--A
40041444 TTTCTTTTTCTTTTTA
1 TTTCTTTTTCTTTTTA
40041460 TTTCTTTTT
1 TTTCTTTTT
40041469 GACTCATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 10 0.40
18 15 0.60
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTTTTA
Found at i:40065335 original size:23 final size:23
Alignment explanation
Indices: 40065305--40065349 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
40065295 CATTAAAAAC
40065305 GGGGCTTGGAATCACTTACTATT
1 GGGGCTTGGAATCACTTACTATT
40065328 GGGGCTTGGAATCACTTACTAT
1 GGGGCTTGGAATCACTTACTAT
40065350 GGAGAACCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (23 bp):
GGGGCTTGGAATCACTTACTATT
Found at i:40080601 original size:38 final size:38
Alignment explanation
Indices: 40080545--40080742 Score: 254
Period size: 38 Copynumber: 5.2 Consensus size: 38
40080535 GGCTCAAAGG
* * * *
40080545 CCCGAATATAATACCAGCACTAGGCATGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
40080583 CCAGGATATAATACCAGCACGAAGCCTGCGGGAATTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
40080621 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
40080659 CCCGGATATATTACCAGCACGAAGCCTGCAGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* * **
40080697 CCCGGATATAATTCCAGCA-TATAGCCTGCGGTCTTTAA
1 CCCGGATATAATACCAGCACGA-AGCCTGCGGGATTTAA
*
40080735 GCCGGATA
1 CCCGGATA
40080743 CAAATATCGT
Statistics
Matches: 142, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
37 1 0.01
38 141 0.99
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.21
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:40081120 original size:43 final size:43
Alignment explanation
Indices: 40081012--40081146 Score: 155
Period size: 43 Copynumber: 3.1 Consensus size: 43
40081002 ACATAACATT
**
40081012 TCATTTCACCGGCATTATAGCCTGCTAAGCTCAAAGGCTTGAATAA
1 TCATTTCACCGGCATTATAGCCTGCTAAGCTCAAA-GCCCG-AT-A
* * *
40081058 T-ATTTCACTGGCATCATAGCCTACTAAGCTCAAAGCCCGATA
1 TCATTTCACCGGCATTATAGCCTGCTAAGCTCAAAGCCCGATA
* * *
40081100 TCATTTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATTA
1 TCATTTCACCGGCATTATAGCCTGCTAAGCTCAAAGCCCGA-TA
40081144 TCA
1 TCA
40081147 CATTTCGATA
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
42 2 0.03
43 35 0.46
44 8 0.11
45 30 0.39
46 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (43 bp):
TCATTTCACCGGCATTATAGCCTGCTAAGCTCAAAGCCCGATA
Found at i:40088116 original size:26 final size:26
Alignment explanation
Indices: 40088062--40088116 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
40088052 TTTGCCACAT
* *
40088062 ATACTGATACTGGCAGCTTTGCTATG
1 ATACTGATACTGGCAGCCTTGCTACG
* *
40088088 ATACTGTTACTGGCAGCCTTGCTGCG
1 ATACTGATACTGGCAGCCTTGCTACG
40088114 ATA
1 ATA
40088117 TTGGTGTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (26 bp):
ATACTGATACTGGCAGCCTTGCTACG
Found at i:40092102 original size:29 final size:30
Alignment explanation
Indices: 40092038--40092237 Score: 96
Period size: 29 Copynumber: 6.8 Consensus size: 30
40092028 GATGGTTGAA
*
40092038 ACCATCCCTTTTTCATTAATTGATAGTCGTC
1 ACCATCCC-TTTTCATTAATTGATAGTCATC
* * *
40092069 ACCATTCCTTTTCA-TAGTTGATGGTCATC
1 ACCATCCCTTTTCATTAATTGATAGTCATC
* * * * *
40092098 TCCATCCCTTTTCA-CAATCGATAGCCA-A
1 ACCATCCCTTTTCATTAATTGATAGTCATC
* * *
40092126 AGCTATCCCTTTTCA-T-ATTCGATTG-C-TGA
1 A-CCATCCCTTTTCATTAATT-GATAGTCAT-C
* * * * * *
40092155 AGCTATCCTTTTTCATT-TTTTATGGTCGTC
1 A-CCATCCCTTTTCATTAATTGATAGTCATC
**
40092185 ACCATCCCTTTTCA-TAATTGACGGTCATC
1 ACCATCCCTTTTCATTAATTGATAGTCATC
*
40092214 ACCATCCCTTTTCA-TAATCGATAG
1 ACCATCCCTTTTCATTAATTGATAG
40092238 CCAAAGCTAT
Statistics
Matches: 130, Mismatches: 31, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
28 4 0.03
29 107 0.82
30 11 0.08
31 8 0.06
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.40
Consensus pattern (30 bp):
ACCATCCCTTTTCATTAATTGATAGTCATC
Done.