Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015254.1 Kokia drynarioides strain JFW-HI SEQ_130299, whole genome shotgun sequence
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: 1276691
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 890 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:361221 original size:6 final size:5
Alignment explanation
Indices: 361180--361225 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
361170 AATACCTTTT
361180 ATTTA ATTT- -TTTA ATTTA ATTTA ATTTA ATTTA ATATTA ATATTA A
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT-TTA AT-TTA A
361226 CATTTAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.08
5 25 0.66
6 10 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:362409 original size:23 final size:24
Alignment explanation
Indices: 362365--362410 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
362355 TTTAGAGAAT
*
362365 TTTGTGTTTAAGTTTTGAGGGTTC
1 TTTGTGTTTAAGTTTCGAGGGTTC
362389 TTTGT-TTTAAGGTTTCG-GGGTT
1 TTTGTGTTTAA-GTTTCGAGGGTT
362411 TAGTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.11, C:0.04, G:0.30, T:0.54
Consensus pattern (24 bp):
TTTGTGTTTAAGTTTCGAGGGTTC
Found at i:378682 original size:47 final size:47
Alignment explanation
Indices: 378609--378706 Score: 187
Period size: 47 Copynumber: 2.1 Consensus size: 47
378599 CCAAAAAGCG
*
378609 TGTTCCGACACAGTGATACCCGTCAATAGAAGAAATTTTAATGCTAA
1 TGTTCCGACACAGTGATACCCATCAATAGAAGAAATTTTAATGCTAA
378656 TGTTCCGACACAGTGATACCCATCAATAGAAGAAATTTTAATGCTAA
1 TGTTCCGACACAGTGATACCCATCAATAGAAGAAATTTTAATGCTAA
378703 TGTT
1 TGTT
378707 ATATAAAGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (47 bp):
TGTTCCGACACAGTGATACCCATCAATAGAAGAAATTTTAATGCTAA
Found at i:386834 original size:38 final size:38
Alignment explanation
Indices: 386783--386859 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
386773 TTGCTTGGGA
386783 AAGATAGAGATGACTATACGATGGGTAAAATACTAGAT
1 AAGATAGAGATGACTATACGATGGGTAAAATACTAGAT
*
386821 AAGATAGAGATGACTATATGATGGGTAAAATACTAGAT
1 AAGATAGAGATGACTATACGATGGGTAAAATACTAGAT
386859 A
1 A
386860 CTAAGATTCG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.25
Consensus pattern (38 bp):
AAGATAGAGATGACTATACGATGGGTAAAATACTAGAT
Found at i:387630 original size:114 final size:114
Alignment explanation
Indices: 387487--387715 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
387477 TTTGTCTTGG
387487 ATAAATACATTTACGTGGCACAAAGTGCTTTTGTTTTCGGAAGGCTTATATTGGATAATGTTGTT
1 ATAAATACATTTACGTGGCACAAAGTGCTTTTGTTTTCGGAAGGCTTATATTGGATAATGTTGTT
387552 TTGACATATGAGATTCTACATACTTTAAGTCGAAAGAGAAGAGGTGGGA
66 TTGACATATGAGATTCTACATACTTTAAGTCGAAAGAGAAGAGGTGGGA
387601 ATAAATACATTTACGTGGCACAAAGTGCTTTTGTTTTCGGAAGGCTTATATTGGATAATGTTGTT
1 ATAAATACATTTACGTGGCACAAAGTGCTTTTGTTTTCGGAAGGCTTATATTGGATAATGTTGTT
387666 TTGACATATGAGATTCTACATACTTTAAGTCGAAAGAGAAGAGGTGGGA
66 TTGACATATGAGATTCTACATACTTTAAGTCGAAAGAGAAGAGGTGGGA
387715 A
1 A
387716 GGGTTCTATG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (114 bp):
ATAAATACATTTACGTGGCACAAAGTGCTTTTGTTTTCGGAAGGCTTATATTGGATAATGTTGTT
TTGACATATGAGATTCTACATACTTTAAGTCGAAAGAGAAGAGGTGGGA
Found at i:395899 original size:22 final size:23
Alignment explanation
Indices: 395859--395906 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
395849 CGTCTTTTTA
395859 GCGTATCTGTGATACCCTT-GTG
1 GCGTATCTGTGATACCCTTCGTG
*
395881 GCGTAATCTGTGAT-GCCTTCGTG
1 GCGT-ATCTGTGATACCCTTCGTG
395904 GCG
1 GCG
395907 AAATTTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.12, C:0.23, G:0.31, T:0.33
Consensus pattern (23 bp):
GCGTATCTGTGATACCCTTCGTG
Found at i:400037 original size:39 final size:39
Alignment explanation
Indices: 399974--400052 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 39
399964 CTATCATCCT
**
399974 CCTGCTCGGGAACTGCCTTTACATCATCATCTGCTACTA
1 CCTGCTCGGGAACTGCCTCCACATCATCATCTGCTACTA
*
400013 CCTGCTCGGGAA-TGGCCTCCACATCATCATCTTCTACTA
1 CCTGCTCGGGAACT-GCCTCCACATCATCATCTGCTACTA
400052 C
1 C
400053 TGCCACCGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 35 0.97
ACGTcount: A:0.20, C:0.35, G:0.15, T:0.29
Consensus pattern (39 bp):
CCTGCTCGGGAACTGCCTCCACATCATCATCTGCTACTA
Found at i:403630 original size:67 final size:67
Alignment explanation
Indices: 403522--403656 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
403512 TTGAAGAAGA
*
403522 AGAAGAAGAAAAAATTGGAAATTAAAATTATTTAATAATTTTATTATTTCAAAAAAATAATTTTA
1 AGAAGAAGAAAAAATTAGAAATTAAAATTATTTAATAATTTTATTATTTCAAAAAAATAATTTTA
403587 AT
66 AT
*
403589 AGAAGAAGAAGAAATTAGAAATTAAAATTATTTAATAATTTTATTATTTCAAAAAAATAATTTTA
1 AGAAGAAGAAAAAATTAGAAATTAAAATTATTTAATAATTTTATTATTTCAAAAAAATAATTTTA
403654 AT
66 AT
403656 A
1 A
403657 ATTTTATATT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (67 bp):
AGAAGAAGAAAAAATTAGAAATTAAAATTATTTAATAATTTTATTATTTCAAAAAAATAATTTTA
AT
Found at i:405305 original size:13 final size:13
Alignment explanation
Indices: 405289--405313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
405279 ATTTAAATTG
405289 TTTAATATGTTTC
1 TTTAATATGTTTC
405302 TTTAATATGTTT
1 TTTAATATGTTT
405314 ATATGTTTCT
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:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTAATATGTTTC
Found at i:405431 original size:16 final size:16
Alignment explanation
Indices: 405410--405440 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
405400 ATGTCTGCTG
*
405410 GTTGTTGTTTTTGTTT
1 GTTGTTGTTGTTGTTT
405426 GTTGTTGTTGTTGTT
1 GTTGTTGTTGTTGTT
405441 GATAATTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (16 bp):
GTTGTTGTTGTTGTTT
Found at i:406197 original size:33 final size:33
Alignment explanation
Indices: 406160--406263 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 33
406150 CTGGCAGTTT
* * *
406160 AGGTGTGGAGGATGTTAATGTTGCTGTTAGTGA
1 AGGTGTGGAGGGTGTTGATGTTGCTGTAAGTGA
* * **
406193 AGGTGTTGAGGGTGTTGAGGTTGCT-TAAGGTTT
1 AGGTGTGGAGGGTGTTGATGTTGCTGTAA-GTGA
* * *
406226 AGGTGTGAAGGGTGTTGATGTTACTGTCAGTGA
1 AGGTGTGGAGGGTGTTGATGTTGCTGTAAGTGA
406259 AGGTG
1 AGGTG
406264 GTGAGAGTGA
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
32 2 0.04
33 51 0.93
34 2 0.04
ACGTcount: A:0.19, C:0.04, G:0.41, T:0.36
Consensus pattern (33 bp):
AGGTGTGGAGGGTGTTGATGTTGCTGTAAGTGA
Found at i:409376 original size:19 final size:19
Alignment explanation
Indices: 409322--409379 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
409312 TATTTAGTTG
*
409322 TTTATTTTGACATTTAATTTA
1 TTTA-TTTGTCATTT-ATTTA
* * **
409343 TTGATTTTTTGTTTATTTA
1 TTTATTTGTCATTTATTTA
409362 TTTATTTGTCATTTATTT
1 TTTATTTGTCATTTATTT
409380 TCATGTCTTA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
19 19 0.68
20 6 0.21
21 3 0.11
ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69
Consensus pattern (19 bp):
TTTATTTGTCATTTATTTA
Found at i:409461 original size:15 final size:15
Alignment explanation
Indices: 409441--409478 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
409431 GCATTTAATT
409441 TTTATTTT-TTGTTTA
1 TTTATTTTATTG-TTA
409456 TTTATTTTATTGTTA
1 TTTATTTTATTGTTA
409471 TTTATTTT
1 TTTATTTT
409479 CATGTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (15 bp):
TTTATTTTATTGTTA
Found at i:409462 original size:26 final size:25
Alignment explanation
Indices: 409433--409522 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 25
409423 TTATTTTAGC
*
409433 ATTTAATTTTTATTTTTTGTTTATTT
1 ATTTAATTGTTATTTTTT-TTTATTT
* * * *
409459 ATTTTATTGTTATTTATTTTCATGTC
1 ATTTAATTGTTATTTTTTTTTAT-TT
409485 ATTTAATTGTTATCTCTTTTATTATTATTT
1 ATTTAATTGTTA--T-TTTT-TT-TTATTT
409515 ATTTAATT
1 ATTTAATT
409523 TGCATTTATA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
25 4 0.08
26 27 0.55
28 1 0.02
29 3 0.06
30 11 0.22
31 3 0.06
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (25 bp):
ATTTAATTGTTATTTTTTTTTATTT
Found at i:409514 original size:98 final size:98
Alignment explanation
Indices: 409303--409484 Score: 257
Period size: 98 Copynumber: 1.9 Consensus size: 98
409293 TCTTTTTTAT
*
409303 TATTATTTATATTTAG-TTGTTTATTTTGACATTTAATTTATTGATTTTTTGTTTATTTATTTAT
1 TATTGTTTATATTT-GTTTGTTTATTTTGACATTTAATTTATTGATTTTTTGTTTATTTATTTAT
*
409367 TTGTCATTTATTTTCATGTCTTATCCCAATTATTTT
65 TTGTCATTTATTTTCATGTCTTAT--CAATTATTTC
409403 TATTGTTTATATTTGTTTGTTTATTTT-AGCATTTAATTT-TT-ATTTTTTGTTTATTTATTT-T
1 TATTGTTTATATTTGTTTGTTTATTTTGA-CATTTAATTTATTGATTTTTTGTTTATTTATTTAT
*
409464 ATTGTTATTTATTTTCATGTC
65 -TTGTCATTTATTTTCATGTC
409485 ATTTAATTGT
Statistics
Matches: 77, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
97 1 0.01
98 38 0.49
99 4 0.05
100 34 0.44
ACGTcount: A:0.20, C:0.05, G:0.08, T:0.66
Consensus pattern (98 bp):
TATTGTTTATATTTGTTTGTTTATTTTGACATTTAATTTATTGATTTTTTGTTTATTTATTTATT
TGTCATTTATTTTCATGTCTTATCAATTATTTC
Found at i:411157 original size:4 final size:4
Alignment explanation
Indices: 411148--411177 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
411138 TTACTGCTTC
411148 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
411178 ACAAATGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:412481 original size:52 final size:51
Alignment explanation
Indices: 412419--412640 Score: 135
Period size: 52 Copynumber: 4.4 Consensus size: 51
412409 TTTTAAAAAA
*
412419 AAAGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTTAGTTATTTT
1 AAAGAAAAAGTTTA-ATTTTTAAAAATAAAAATATGTTTTTTTAGTTATTTT
* * ** * ** *
412471 AAAGAAAAAGTTTAAATTTT---AACAAAGTTTTGATTTTTTTAACTATTTCG
1 AAAGAAAAAGTTTAATTTTTAAAAATAAAAATATG-TTTTTTTAGTTATTT-T
* * * * * *
412521 AAA-TAAAAGTTTGAATTTTT--AAGT-AAAATAACGATTTTCT--TTA---A
1 AAAGAAAAAGTTT-AATTTTTAAAAATAAAAAT-ATGTTTTTTTAGTTATTTT
*
412565 AAAGGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTTAGTTATTTT
1 AAA-GAAAAAGTTTA-ATTTTTAAAAATAAAAATATGTTTTTTTAGTTATTTT
*
412618 AAATAAAAAGTTTAAATTTTTAA
1 AAAGAAAAAGTTT-AATTTTTAA
412641 CAAAGTCTTG
Statistics
Matches: 123, Mismatches: 30, Indels: 34
0.66 0.16 0.18
Matches are distributed among these distances:
44 3 0.02
45 1 0.01
46 13 0.11
48 20 0.16
49 26 0.21
50 20 0.16
51 7 0.06
52 29 0.24
53 4 0.03
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (51 bp):
AAAGAAAAAGTTTAATTTTTAAAAATAAAAATATGTTTTTTTAGTTATTTT
Found at i:412488 original size:150 final size:151
Alignment explanation
Indices: 412216--412857 Score: 871
Period size: 150 Copynumber: 4.3 Consensus size: 151
412206 TTTTAAAACA
* * *
412216 ATTTCAAAATAAAAGCTTT-GATTTTGTAAGCAAAATAATGATTTTCTTT--AAAAAAAGAGAAA
1 ATTTCGAAATAAAAG-TTTGGATTTT-TAAGTAAAATAGTGATTTTCTTTAAAAAAAAAGAGAAA
* * * * *
412278 GTTTAGATTTTTTTAAAATAAAAATCT-ATTCTTTAGTTATTTTAAA-AAAAAGTTTAAAATTTT
64 GTTTAGA-TTTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTT
412341 AACAAAGTTTTGATTTTTTTAACT
128 AACAAAGTTTTGATTTTTTTAACT
* *
412365 ATTTTGAAATAAAAGTTTGGATTTTTAGGTAAAATAGTGAATTTT-TTTAAAAAAAAAGAGAAAG
1 ATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTG-ATTTTCTTTAAAAAAAAAGAGAAAG
*
412429 TTTATATTTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAGTTTAAA-TTTTAA
65 TTTAGATTTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAA
412493 CAAAGTTTTGATTTTTTTAACT
130 CAAAGTTTTGATTTTTTTAACT
* ** *
412515 ATTTCGAAATAAAAGTTTGAATTTTTAAGTAAAATAACGATTTTCTTT---AAAAAGGAGAAAGT
1 ATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAAAAGAGAAAGT
* *
412577 TTATATTTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAATAAAAAGTTTAAATTTTTAAC
66 TTAGATTTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAC
* *
412642 AAAGTCTTGATCTTTTCTAACT
131 AAAGTTTTGAT-TTTTTTAACT
* * ***
412664 ATTTTGAAATAAAAATTTGGATTTTTAAGTAAAATAGTGA-TTT-AAAAAAAAAAAAGAGAAA-T
1 ATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAAAAGAGAAAGT
*
412726 CTTAGATTTTTAAAAAATAAAAATATG-TTTTTTAGTTATTTTAAAGAAAAAGTTAAAATTTTTA
66 -TTAGATTTTT-AAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTA
412790 ACAAAGTTTTGATTTTTTTAAACT
129 ACAAAGTTTTGATTTTTTT-AACT
* *
412814 ATTTCGAAATAAAAATTTGGATTTTTAAGTAAAGTAGTGATTTT
1 ATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTT
412858 TATTTAATCA
Statistics
Matches: 442, Mismatches: 35, Indels: 30
0.87 0.07 0.06
Matches are distributed among these distances:
147 69 0.16
148 37 0.08
149 96 0.22
150 210 0.48
151 30 0.07
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (151 bp):
ATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAAAAGAGAAAGT
TTAGATTTTTAAAAATAAAAATATGTTTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAC
AAAGTTTTGATTTTTTTAACT
Found at i:414375 original size:239 final size:238
Alignment explanation
Indices: 413882--414612 Score: 1113
Period size: 240 Copynumber: 3.0 Consensus size: 238
413872 AAATATATTA
* * * * * *
413882 AAATCATAATAATAATAAAAGATCGAATAAGTTATATATGAATTTTAATATTTCTCTTAATTCAT
1 AAATCAGAGTAATGATAAAAGATCGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTCAT
413947 TAGTAACTTTTAGGTTTTTTTTTTTTTTTTTAA-GATTCTAAAATAGAATTAATTTTAAGAATTG
66 TAGTAACTTTTAGG----------TTTTTTTAAGGATTCTAAAATAGAATTAATTTTAAGAATTG
* * *
414011 AATGTATTTTACTAAAATTATTTAGGTATCCTTTAGGGTTTTTATTAGGAGTAAAAAATCTCTAA
121 AAAGTATTTTACTAGAATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGT-AAAAATCTCTAA
*
414076 TTTAAGTTTTAAATTAGATAAGTTTGGTGAATACGTTTTAGTCAAGTTATAAGT
185 TTTAAGTTTTAAATTAGATAAGTTTGGTGAATACGTTTTAGTCAAGTTACAAGT
* *
414130 AAATCAGAGTAATGATAAAAAATCGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTTAT
1 AAATCAGAGTAATGATAAAAGATCGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTCAT
*
414195 TAGTAACTTTTAGGCTTTTTTTAAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTT
66 TAGTAACTTTTAGG-TTTTTTTAAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTT
* *
414260 TACTAGAATTATTTAGGTATCTTTTAGGATTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTT
130 TACTAGAATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTT
414325 AAATTAGATAAGTTTGGTGAATACGTTTTAGTCAAGTTACAAGT
195 AAATTAGATAAGTTTGGTGAATACGTTTTAGTCAAGTTACAAGT
*
414369 AAATCAGAGTAATGATAAAAGATCGAATAAGTTGTAGATAAATTTTAATATTTATCTTAATTCAT
1 AAATCAGAGTAATGATAAAAGATCGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTCAT
* * * *
414434 AAGTAAATTTTTTAGGTTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTTAAAGTATT
66 TAGT-AA-CTTTTAGGTTTTTTTAAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATT
*
414499 TTACTAGAATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTTTAATTTAAGTTT
129 TTACTAGAATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTT
* * *
414564 TAAATTAGATAAGTTTGGTGAACACGTCTTAGTCAAATTACAAGT
194 TAAATTAGATAAGTTTGGTGAATACGTTTTAGTCAAGTTACAAGT
414609 AAAT
1 AAAT
414613 TGGAGTCATT
Statistics
Matches: 451, Mismatches: 29, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
239 139 0.31
240 234 0.52
241 7 0.02
248 71 0.16
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (238 bp):
AAATCAGAGTAATGATAAAAGATCGAATAAGTTGTAGATAAATTTTAATATTTCTCTTAATTCAT
TAGTAACTTTTAGGTTTTTTTAAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTTT
ACTAGAATTATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTA
AATTAGATAAGTTTGGTGAATACGTTTTAGTCAAGTTACAAGT
Found at i:415721 original size:3 final size:3
Alignment explanation
Indices: 415715--415757 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
415705 TTAAAAACAT
415715 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
415758 GTAATTAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:416857 original size:30 final size:30
Alignment explanation
Indices: 416821--416960 Score: 103
Period size: 30 Copynumber: 4.7 Consensus size: 30
416811 CTCTAAATTG
*
416821 TCCAAAAATCATATTTTGACCCTCAAACTT
1 TCCAAAAATCATATTTTGACCCTCGAACTT
* * *
416851 TCCAAAAATTACATTTTGACCCCCGAACTT
1 TCCAAAAATCATATTTTGACCCTCGAACTT
*
416881 T-TAAAAATTCCAT-TTTT-ACCCTCGAACTT
1 TCCAAAAA-T-CATATTTTGACCCTCGAACTT
* * * * *
416910 TCTAAAACTTACCATGTT-ACCCTCGAAC-T
1 TCCAAAAATCA-TATTTTGACCCTCGAACTT
416939 TCCAAAAATTCA-ATTTTTGACC
1 TCCAAAAA-TCATA-TTTTGACC
416961 TTAATATTTC
Statistics
Matches: 86, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
28 2 0.02
29 28 0.33
30 55 0.64
31 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (30 bp):
TCCAAAAATCATATTTTGACCCTCGAACTT
Found at i:416896 original size:29 final size:30
Alignment explanation
Indices: 416833--417384 Score: 253
Period size: 29 Copynumber: 18.8 Consensus size: 30
416823 CAAAAATCAT
* *
416833 ATTTTGACCCTCAAACTTTCCAAAAATTAC
1 ATTTTGACCCTCGAACTTTCCAAAAATTCC
* *
416863 ATTTTGACCCCCGAACTTT-TAAAAATTCC
1 ATTTTGACCCTCGAACTTTCCAAAAATTCC
* * *
416892 ATTTTTACCCTCGAACTTTCTAAAACTTACC
1 ATTTTGACCCTCGAACTTTCCAAAAATT-CC
* *
416923 ATGTT-ACCCTCGAAC-TTCCAAAAATTCA
1 ATTTTGACCCTCGAACTTTCCAAAAATTCC
* * * *
416951 ATTTTTGA-CCT-TAATATTTCCAAAACTTAC
1 A-TTTTGACCCTCGAA-CTTTCCAAAAATTCC
* * *
416981 ATTTTAACCCCCCAAC-TTCCAAAAATTCC
1 ATTTTGACCCTCGAACTTTCCAAAAATTCC
* *
417010 ATTTTGACCCT--AATTTTTCCAAAACTTACC
1 ATTTTGACCCTCGAA-CTTTCCAAAAATT-CC
* *
417040 ATATT-ACACC-CAAAC-TTCCAAAAATTCC
1 ATTTTGAC-CCTCGAACTTTCCAAAAATTCC
** ** *
417068 ATTTTGA-CCTTTATTTTTCCAAAATTTACC
1 ATTTTGACCCTCGAACTTTCCAAAAATT-CC
* *
417098 ATTTT-ACCC-CTAAAC-TTCCAAATATTCC
1 ATTTTGACCCTC-GAACTTTCCAAAAATTCC
* * ** * * **
417126 ATTTTTAACCCT-TATTTTTCAAAAAAATAT
1 A-TTTTGACCCTCGAACTTTCCAAAAATTCC
* *
417156 ATTTTAACCC-CTAAACTTTCCAAAAATTCC
1 ATTTTGACCCTC-GAACTTTCCAAAAATTCC
*
417186 ATTTTGA-CCTCGAACTTT-CTAAAATTACC
1 ATTTTGACCCTCGAACTTTCCAAAAATT-CC
* * *
417215 ATTTT-ACCCCCAAAC-ATCCAAAAATTCC
1 ATTTTGACCCTCGAACTTTCCAAAAATTCC
** * *
417243 ATTTTGACCCT-GATTTTTCCAAAATTTACT
1 ATTTTGACCCTCGAACTTTCCAAAAATT-CC
* * *
417273 ATTTT-ATCCTCTAAC-TTCCCAAAATTCC
1 ATTTTGACCCTCGAACTTTCCAAAAATTCC
* * *
417301 ATTTTTAACCC-CGAAC-TTCCTGAAAATTATC
1 A-TTTTGACCCTCGAACTTTCC-AAAAATT-CC
* *
417332 ATTTT-ACCCTTGAAC-TTCCAAAGATTCC
1 ATTTTGACCCTCGAACTTTCCAAAAATTCC
* * *
417360 TTTTTTGA-CCTCGAAGTGTCCAAAA
1 -ATTTTGACCCTCGAACTTTCCAAAA
417385 TTACCGTTTT
Statistics
Matches: 389, Mismatches: 91, Indels: 84
0.69 0.16 0.15
Matches are distributed among these distances:
27 4 0.01
28 34 0.09
29 207 0.53
30 132 0.34
31 12 0.03
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (30 bp):
ATTTTGACCCTCGAACTTTCCAAAAATTCC
Found at i:416937 original size:59 final size:58
Alignment explanation
Indices: 416833--417399 Score: 394
Period size: 59 Copynumber: 9.7 Consensus size: 58
416823 CAAAAATCAT
* * * **
416833 ATTTTGACCCTCAAACTTTCCAAAAATTA-CATTTTGACCCCCGAACTTTTAAAAATTCC
1 ATTTTGACCCTCGAACTTTCCAAAACTTACCATTTT-A-CCCCAAACTTCCAAAAATTCC
* * * * *
416892 ATTTTTACCCTCGAACTTTCTAAAACTTACCATGTTACCCTCGAACTTCCAAAAATTCA
1 ATTTTGACCCTCGAACTTTCCAAAACTTACCATTTTACCC-CAAACTTCCAAAAATTCC
* * *
416951 ATTTTTGA-CCT-TAATATTTCCAAAACTTA-CATTTTAACCCCCCAACTTCCAAAAATTCC
1 A-TTTTGACCCTCGAA-CTTTCCAAAACTTACCATTTT-A-CCCCAAACTTCCAAAAATTCC
* *
417010 ATTTTGACCCT--AATTTTTCCAAAACTTACCATATTACACCCAAACTTCCAAAAATTCC
1 ATTTTGACCCTCGAA-CTTTCCAAAACTTACCATTTTAC-CCCAAACTTCCAAAAATTCC
** ** * *
417068 ATTTTGA-CCTTTATTTTTCCAAAATTTACCATTTTACCCCTAAACTTCCAAATATTCC
1 ATTTTGACCCTCGAACTTTCCAAAACTTACCATTTTACCCC-AAACTTCCAAAAATTCC
* * ** * ** *
417126 ATTTTTAACCCT-TATTTTTCAAAAAAATA-TATTTTAACCCCTAAACTTTCCAAAAATTCC
1 A-TTTTGACCCTCGAACTTTCCAAAACTTACCATTTT-ACCCC-AAAC-TTCCAAAAATTCC
* *
417186 ATTTTGA-CCTCGAACTTTCTAAAA-TTACCATTTTACCCCCAAACATCCAAAAATTCC
1 ATTTTGACCCTCGAACTTTCCAAAACTTACCATTTTA-CCCCAAACTTCCAAAAATTCC
** * * * * *
417243 ATTTTGACCCT-GATTTTTCCAAAATTTACTATTTTATCCTCTAACTTCCCAAAATTCC
1 ATTTTGACCCTCGAACTTTCCAAAACTTACCATTTTA-CCCCAAACTTCCAAAAATTCC
* * ** *
417301 ATTTTTAACCC-CGAAC-TTCCTGAAAA-TTATCATTTTACCCTTGAACTTCCAAAGATTCC
1 A-TTTTGACCCTCGAACTTTCC--AAAACTTACCATTTTACCC-CAAACTTCCAAAAATTCC
* * * * *
417360 TTTTTTGA-CCTCGAAGTGTCCAAAA-TTACCGTTTTGCCCC
1 -ATTTTGACCCTCGAACTTTCCAAAACTTACCATTTTACCCC
417400 CCGGGTATCC
Statistics
Matches: 416, Mismatches: 63, Indels: 60
0.77 0.12 0.11
Matches are distributed among these distances:
57 36 0.09
58 166 0.40
59 178 0.43
60 36 0.09
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (58 bp):
ATTTTGACCCTCGAACTTTCCAAAACTTACCATTTTACCCCAAACTTCCAAAAATTCC
Found at i:417056 original size:58 final size:57
Alignment explanation
Indices: 416833--417305 Score: 418
Period size: 58 Copynumber: 8.1 Consensus size: 57
416823 CAAAAATCAT
** * * **
416833 ATTTTGACCCTCAAACTTTCCAAAAATTA-CATTTTGACCCCCGAACTTTTAAAAATTCC
1 ATTTTGACCCT-AATTTTTCCAAAACTTACCATTTT-A-CCCCAAACTTCCAAAAATTCC
* * * * * *
416892 ATTTTTACCCTCGAA-CTTTCTAAAACTTACCATGTTACCCTCGAACTTCCAAAAATTCA
1 ATTTTGACCCT--AATTTTTCCAAAACTTACCATTTTACCC-CAAACTTCCAAAAATTCC
* * *
416951 ATTTTTGACCTTAATATTTCCAAAACTTA-CATTTTAACCCCCCAACTTCCAAAAATTCC
1 A-TTTTGACCCTAATTTTTCCAAAACTTACCATTTT-A-CCCCAAACTTCCAAAAATTCC
*
417010 ATTTTGACCCTAATTTTTCCAAAACTTACCATATTACACCCAAACTTCCAAAAATTCC
1 ATTTTGACCCTAATTTTTCCAAAACTTACCATTTTAC-CCCAAACTTCCAAAAATTCC
* * * *
417068 ATTTTGACCTTTATTTTTCCAAAATTTACCATTTTACCCCTAAACTTCCAAATATTCC
1 ATTTTGACCCTAATTTTTCCAAAACTTACCATTTTACCCC-AAACTTCCAAAAATTCC
* * * ** *
417126 ATTTTTAACCCTTATTTTTCAAAAAAATA-TATTTTAACCCCTAAACTTTCCAAAAATTCC
1 A-TTTTGACCCTAATTTTTCCAAAACTTACCATTTT-ACCCC-AAAC-TTCCAAAAATTCC
* * * *
417186 ATTTTGACCTCGAA-CTTTCTAAAA-TTACCATTTTACCCCCAAACATCCAAAAATTCC
1 ATTTTGACC-CTAATTTTTCCAAAACTTACCATTTTA-CCCCAAACTTCCAAAAATTCC
* * * * * *
417243 ATTTTGACCCTGATTTTTCCAAAATTTACTATTTTATCCTCTAACTTCCCAAAATTCC
1 ATTTTGACCCTAATTTTTCCAAAACTTACCATTTTA-CCCCAAACTTCCAAAAATTCC
417301 ATTTT
1 ATTTT
417306 TAACCCCGAA
Statistics
Matches: 347, Mismatches: 49, Indels: 37
0.80 0.11 0.09
Matches are distributed among these distances:
56 2 0.01
57 33 0.10
58 149 0.43
59 130 0.37
60 33 0.10
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (57 bp):
ATTTTGACCCTAATTTTTCCAAAACTTACCATTTTACCCCAAACTTCCAAAAATTCC
Found at i:417368 original size:175 final size:172
Alignment explanation
Indices: 416833--417400 Score: 554
Period size: 175 Copynumber: 3.2 Consensus size: 172
416823 CAAAAATCAT
* * **
416833 ATTTTGACCCTCAAACTTTCCAAAAATTA-CATTTTGACCCCCGAACTTTTAAAAATTCCATTTT
1 ATTTTGA-CCTCGAACTTTCC-AAAATTACCATTTT-ACCCCCAAACTTCCAAAAATTCCATTTT
* ** * * * * * * * *
416897 TACCCTCGAACTTTCTAAAACTTACCATGTTACCCTCGAACTTCCAAAAATTCAATTTTTGACCT
63 GACCCT-GATTTTTCCAAAATTTACCATTTTA-CCTCTAACTTCCCAAAATTCCATTTTTAACCC
**
416962 TAATATTTCCAAAACTTA-CATTTTAACCCCCCAACTTCCAAAAATTCC
126 TAA-ATTTCCAAAA-TTATCATTTTAACCCCTAAACTTCCAAAAATTCC
* * * *
417010 ATTTTGACC-CTAATTTTTCCAAAACTTACCATATTACACCCAAACTTCCAAAAATTCCATTTTG
1 ATTTTGACCTCGAA-CTTTCCAAAA-TTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTG
* * *
417074 ACCTTTATTTTTCCAAAATTTACCATTTTACCCCTAAACTT-CCAAATATTCCATTTTTAACCCT
64 ACCCTGATTTTTCCAAAATTTACCATTTTACCTCT-AACTTCCCAAA-ATTCCATTTTTAACCC-
** * *
417138 TATTTTTCAAAAAAATAT-ATTTTAACCCCTAAACTTTCCAAAAATTCC
126 TAAATTTC-CAAAATTATCATTTTAACCCCTAAAC-TTCCAAAAATTCC
* *
417186 ATTTTGACCTCGAACTTTCTAAAATTACCATTTTACCCCCAAACATCCAAAAATTCCATTTTGAC
1 ATTTTGACCTCGAACTTTCCAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTGAC
* **
417251 CCTGATTTTTCCAAAATTTACTATTTTATCCTCTAACTTCCCAAAATTCCATTTTTAACCCCGAA
66 CCTGATTTTTCCAAAATTTACCATTTTA-CCTCTAACTTCCCAAAATTCCATTTTTAACCCTAAA
* * * *
417316 CTTCCTGAAAATTATCATTTT-ACCCTTGAACTTCCAAAGATTCC
130 TTTCC--AAAATTATCATTTTAACCCCTAAACTTCCAAAAATTCC
* * * * *
417360 TTTTTTGACCTCGAAGTGTCCAAAATTACCGTTTTGCCCCC
1 -ATTTTGACCTCGAACTTTCCAAAATTACCATTTTACCCCC
417401 CGGGTATCCA
Statistics
Matches: 322, Mismatches: 53, Indels: 34
0.79 0.13 0.08
Matches are distributed among these distances:
174 22 0.07
175 197 0.61
176 88 0.27
177 15 0.05
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (172 bp):
ATTTTGACCTCGAACTTTCCAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTGAC
CCTGATTTTTCCAAAATTTACCATTTTACCTCTAACTTCCCAAAATTCCATTTTTAACCCTAAAT
TTCCAAAATTATCATTTTAACCCCTAAACTTCCAAAAATTCC
Found at i:420201 original size:3 final size:3
Alignment explanation
Indices: 420193--420217 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
420183 GCAGATGTTG
420193 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
420218 ATGATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:430852 original size:3 final size:3
Alignment explanation
Indices: 430838--430884 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
430828 ACCGAACTGA
*
430838 TGG TGA TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
430885 TCAGTTGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.02, C:0.00, G:0.64, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:434288 original size:26 final size:26
Alignment explanation
Indices: 434252--434306 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
434242 ACTTAGGGCT
434252 TCAAAAATTGAGCAGAGATGAGAAGA
1 TCAAAAATTGAGCAGAGATGAGAAGA
434278 TCAAAAATTGAGCAGAGATGAGAAGA
1 TCAAAAATTGAGCAGAGATGAGAAGA
434304 TCA
1 TCA
434307 TTCTTCTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.49, C:0.09, G:0.25, T:0.16
Consensus pattern (26 bp):
TCAAAAATTGAGCAGAGATGAGAAGA
Found at i:440859 original size:56 final size:55
Alignment explanation
Indices: 440731--440860 Score: 147
Period size: 55 Copynumber: 2.3 Consensus size: 55
440721 CATAGTAATC
* * *
440731 GAAGACCATATAGTGTAAGACCTAGCCAAGAGGGCTATGACATCATAGTAGGAAT
1 GAAGACCATATAGTGTAAGACCTAACCAAAAGGGCTATAACATCATAGTAGGAAT
* * *
440786 GAAGACCATATAATGTAATG-CCTAACCAAAAGGGTTATAACATCATA-TGGGGAAAT
1 GAAGACCATATAGTGTAA-GACCTAACCAAAAGGGCTATAACATCATAGT-AGG-AAT
* *
440842 GAATATCATATAGTGTAAG
1 GAAGACCATATAGTGTAAG
440861 GACTAGCGGT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
54 1 0.02
55 43 0.68
56 19 0.30
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (55 bp):
GAAGACCATATAGTGTAAGACCTAACCAAAAGGGCTATAACATCATAGTAGGAAT
Found at i:447210 original size:20 final size:20
Alignment explanation
Indices: 447173--447209 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
447163 ATTTCGTCTT
447173 TTATTTATTTATTATTTTGA
1 TTATTTATTTATTATTTTGA
447193 TTATTTA-TTATTATTTT
1 TTATTTATTTATTATTTT
447210 TCAATTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (20 bp):
TTATTTATTTATTATTTTGA
Found at i:447624 original size:21 final size:20
Alignment explanation
Indices: 447577--447624 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
447567 AAAAAGTGAT
447577 AAAAA-AGTGAAAAAAAAAA
1 AAAAATAGTGAAAAAAAAAA
447596 AAAGAATAGT-AAAAGAAAAATA
1 AAA-AATAGTGAAAA-AAAAA-A
447618 AAAAATA
1 AAAAATA
447625 TTTTGTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.12
20 6 0.24
21 12 0.48
22 4 0.16
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (20 bp):
AAAAATAGTGAAAAAAAAAA
Found at i:461555 original size:22 final size:23
Alignment explanation
Indices: 461530--461592 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
461520 TAATAGATGA
461530 AATTTAAAAAAAAATAACAT-TT
1 AATTTAAAAAAAAATAACATCTT
*
461552 AATTT-AAAGAAAATAAACATCTT
1 AATTTAAAAAAAAAT-AACATCTT
* * *
461575 TATCTAAAAAAAATTAAC
1 AATTTAAAAAAAAATAAC
461593 TCAATAGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 8 0.24
22 10 0.30
23 8 0.24
24 7 0.21
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (23 bp):
AATTTAAAAAAAAATAACATCTT
Found at i:461582 original size:23 final size:21
Alignment explanation
Indices: 461536--461588 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
461526 ATGAAATTTA
*
461536 AAAAAAAATAACATTTAATTT
1 AAAAAAAATAACATTTAATCT
* *
461557 AAAGAAAATAAACATCTTTATCT
1 AAAAAAAAT-AACAT-TTAATCT
461580 AAAAAAAAT
1 AAAAAAAAT
461589 TAACTCAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 8 0.31
22 5 0.19
23 13 0.50
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAAAAAATAACATTTAATCT
Found at i:461869 original size:14 final size:14
Alignment explanation
Indices: 461850--461877 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
461840 AAATGCAACT
461850 AGGGGTGAGTATTC
1 AGGGGTGAGTATTC
461864 AGGGGTGAGTATTC
1 AGGGGTGAGTATTC
461878 GATCGAGTCG
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:0.21, C:0.07, G:0.43, T:0.29
Consensus pattern (14 bp):
AGGGGTGAGTATTC
Found at i:464909 original size:9 final size:9
Alignment explanation
Indices: 464875--464917 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
464865 ACCATGTTTG
464875 TTTCTTTTT
1 TTTCTTTTT
* *
464884 CTCCTTTTT
1 TTTCTTTTT
* *
464893 TCTATTTTT
1 TTTCTTTTT
464902 TTTCTTTTT
1 TTTCTTTTT
464911 TTTCTTT
1 TTTCTTT
464918 ATTCGAACTC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:466080 original size:16 final size:15
Alignment explanation
Indices: 466059--466096 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
466049 CTAAAATACC
466059 AAAAATAAAAATAAGT
1 AAAAATAAAAATAA-T
466075 AAAAAT-AAAATAAT
1 AAAAATAAAAATAAT
*
466089 ATAAATAA
1 AAAAATAA
466097 TCGAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 8 0.40
16 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAAATAAAAATAAT
Found at i:472630 original size:23 final size:23
Alignment explanation
Indices: 472602--472653 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
472592 CGTCCATCCT
*
472602 TGCTGACTAG-TCCTTCTTGAAGC
1 TGCTGACTAGAT-CTTCTAGAAGC
*
472625 TGCTGACTGGATCTTCTAGAAGC
1 TGCTGACTAGATCTTCTAGAAGC
472648 TGCTGA
1 TGCTGA
472654 TTGGACGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (23 bp):
TGCTGACTAGATCTTCTAGAAGC
Found at i:472658 original size:23 final size:23
Alignment explanation
Indices: 472614--472658 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
472604 CTGACTAGTC
*
472614 CTTCTTGAAGCTGCTGACTGGAT
1 CTTCTAGAAGCTGCTGACTGGAT
*
472637 CTTCTAGAAGCTGCTGATTGGA
1 CTTCTAGAAGCTGCTGACTGGA
472659 CGCCACATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (23 bp):
CTTCTAGAAGCTGCTGACTGGAT
Found at i:474760 original size:21 final size:20
Alignment explanation
Indices: 474734--474774 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
474724 TTAGATTTGG
*
474734 TGTAATTGTTGTAATTATTCA
1 TGTAATTATTGTAATT-TTCA
*
474755 TGTAATTATTTTAATTTTCA
1 TGTAATTATTGTAATTTTCA
474775 CCCTTAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (20 bp):
TGTAATTATTGTAATTTTCA
Found at i:475546 original size:3 final size:3
Alignment explanation
Indices: 475538--475573 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
475528 TAAATGAAAG
475538 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
475574 TTGAGTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:475560 original size:17 final size:17
Alignment explanation
Indices: 475538--475570 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
475528 TAAATGAAAG
475538 AATAATAATAATAATAT
1 AATAATAATAATAATAT
475555 AATAATAATAATAATA
1 AATAATAATAATAATA
475571 ATATTGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATAATAATAT
Found at i:482746 original size:42 final size:42
Alignment explanation
Indices: 482530--482781 Score: 121
Period size: 42 Copynumber: 5.9 Consensus size: 42
482520 TGAGGGAAAG
* * * *
482530 ATACTGACACACATAGTGCATCATCAGG-CAAGCCGAAGTAATT
1 ATACTGACACATA-AGTGCATCAT-AGGATAAACCAAAGTAATT
* * * * ** *** *
482573 ATAATGGCACATGAGGTGCATCATCGGACGAACTGGAGCAATT
1 ATACTGACACAT-AAGTGCATCATAGGATAAACCAAAGTAATT
* * *** * *
482616 ATATTGTCACACAT-AGTGCATCATCGGATAAATTGAGGTAATC
1 ATACTG--ACACATAAGTGCATCATAGGATAAACCAAAGTAATT
* * * * * ** * * *
482659 ATGCTGACACATTAGTGCATTATCGAATGTACCGAAGAAAGT
1 ATACTGACACATAAGTGCATCATAGGATAAACCAAAGTAATT
*
482701 ATACTGTCACATAAGTGCATCATAGGATAAACCAAAGTAATT
1 ATACTGACACATAAGTGCATCATAGGATAAACCAAAGTAATT
* * * *
482743 ATACTGACACGTAAGTGCATTATCGGATAAACCGAAGTA
1 ATACTGACACATAAGTGCATCATAGGATAAACCAAAGTA
482782 TAAACCCATA
Statistics
Matches: 156, Mismatches: 48, Indels: 11
0.73 0.22 0.05
Matches are distributed among these distances:
41 6 0.04
42 86 0.55
43 58 0.37
44 1 0.01
45 5 0.03
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (42 bp):
ATACTGACACATAAGTGCATCATAGGATAAACCAAAGTAATT
Found at i:482777 original size:84 final size:85
Alignment explanation
Indices: 482525--482779 Score: 201
Period size: 84 Copynumber: 3.0 Consensus size: 85
482515 TACACTGAGG
* * * * * * * *
482525 GAAAG-ATACTGACACACATAGTGCATCATCAGG-CAAGCCGAAGTAATTATAATGGCACATGAG
1 GAAAGTATACTGTCACACATAGTGCATCAT-AGGATAAACCAAAGTAATCATACTGACACAT-AA
* * ** * *
482588 GTGCATCATCGGACGAACTGGA
64 GTGCATTATCGAATAAACCGAA
* * * * *** * * *
482610 GCAATTATATTGTCACACATAGTGCATCATCGGATAAATTGAGGTAATCATGCTGACACATTAGT
1 GAAAGTATACTGTCACACATAGTGCATCATAGGATAAACCAAAGTAATCATACTGACACATAAGT
**
482675 GCATTATCGAATGTACCGAA
66 GCATTATCGAATAAACCGAA
* * *
482695 GAAAGTATACTGTCACATA-AGTGCATCATAGGATAAACCAAAGTAATTATACTGACACGTAAGT
1 GAAAGTATACTGTCACACATAGTGCATCATAGGATAAACCAAAGTAATCATACTGACACATAAGT
*
482759 GCATTATCGGATAAACCGAA
66 GCATTATCGAATAAACCGAA
482779 G
1 G
482780 TATAAACCCA
Statistics
Matches: 130, Mismatches: 38, Indels: 5
0.75 0.22 0.03
Matches are distributed among these distances:
84 54 0.42
85 36 0.28
86 40 0.31
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (85 bp):
GAAAGTATACTGTCACACATAGTGCATCATAGGATAAACCAAAGTAATCATACTGACACATAAGT
GCATTATCGAATAAACCGAA
Found at i:483243 original size:18 final size:17
Alignment explanation
Indices: 483206--483244 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
483196 ATAACAAAAT
* *
483206 ATCAAATTCCATATAAA
1 ATCAAATTCAATACAAA
483223 ATCAAATTCAATTACAAA
1 ATCAAATTCAA-TACAAA
483241 ATCA
1 ATCA
483245 TGCATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (17 bp):
ATCAAATTCAATACAAA
Found at i:488475 original size:13 final size:13
Alignment explanation
Indices: 488457--488486 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
488447 GGTTATTATT
*
488457 TTATTTTTTATCA
1 TTATTTGTTATCA
488470 TTATTTGTTATCA
1 TTATTTGTTATCA
488483 TTAT
1 TTAT
488487 CATTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (13 bp):
TTATTTGTTATCA
Found at i:496236 original size:19 final size:21
Alignment explanation
Indices: 496208--496249 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
496198 GATTTTGAAT
496208 TAATTAAAATTT-G-TTTGGA
1 TAATTAAAATTTAGATTTGGA
*
496227 TAATTCAAATTTAGATTTGGA
1 TAATTAAAATTTAGATTTGGA
496248 TA
1 TA
496250 TCAACTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 1 0.05
21 8 0.40
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.45
Consensus pattern (21 bp):
TAATTAAAATTTAGATTTGGA
Found at i:496727 original size:3 final size:3
Alignment explanation
Indices: 496719--496747 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
496709 TCACGGTACC
496719 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
496748 CATCATCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:505085 original size:24 final size:24
Alignment explanation
Indices: 505053--505118 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
505043 TTTACATTTA
*
505053 CACTCGTCAATATGAGTAAGTTTT
1 CACTCGTCAACATGAGTAAGTTTT
* * *
505077 CACTGGTCAGCATGAGTACGTTTT
1 CACTCGTCAACATGAGTAAGTTTT
* * *
505101 CGCTCATCAGCATGAGTA
1 CACTCGTCAACATGAGTA
505119 CGTTACAATC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (24 bp):
CACTCGTCAACATGAGTAAGTTTT
Found at i:505119 original size:24 final size:24
Alignment explanation
Indices: 505064--505146 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
505054 ACTCGTCAAT
* **
505064 ATGAGTAAGTTTTCACTGGTCAGC
1 ATGAGTACGTTTTCACTCATCAGC
*
505088 ATGAGTACGTTTTCGCTCATCAGC
1 ATGAGTACGTTTTCACTCATCAGC
* * *
505112 ATGAGTACG-TTACAATCATCGGC
1 ATGAGTACGTTTTCACTCATCAGC
505135 ATGAGTACGTTT
1 ATGAGTACGTTT
505147 ACATTATTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
23 19 0.38
24 31 0.62
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (24 bp):
ATGAGTACGTTTTCACTCATCAGC
Found at i:505136 original size:23 final size:23
Alignment explanation
Indices: 505083--505145 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
505073 TTTTCACTGG
* **
505083 TCAGCATGAGTACGTTTTCGCTCA
1 TCAGCATGAGTACG-TTACAATCA
505107 TCAGCATGAGTACGTTACAATCA
1 TCAGCATGAGTACGTTACAATCA
*
505130 TCGGCATGAGTACGTT
1 TCAGCATGAGTACGTT
505146 TACATTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 21 0.60
24 14 0.40
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (23 bp):
TCAGCATGAGTACGTTACAATCA
Found at i:505511 original size:18 final size:20
Alignment explanation
Indices: 505472--505513 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
505462 CAACTTCAGA
*
505472 TCATGAGAAATTAAATGATT
1 TCATGACAAATTAAATGATT
505492 TCATGACAAA-TAAA-GATT
1 TCATGACAAATTAAATGATT
505510 TCAT
1 TCAT
505514 ATATTACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 4 0.19
20 9 0.43
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (20 bp):
TCATGACAAATTAAATGATT
Found at i:508208 original size:67 final size:67
Alignment explanation
Indices: 508129--508260 Score: 237
Period size: 67 Copynumber: 2.0 Consensus size: 67
508119 ATAAACACTG
* *
508129 AGCTCTGGTTTGGTGTTTGAACTGAGTCTTATTCACTCTTTTAGCTAGTATGTTAGGCTGATTGC
1 AGCTCTGATTTGGTGTTTGAACTGAGTCTCATTCACTCTTTTAGCTAGTATGTTAGGCTGATTGC
508194 TA
66 TA
*
508196 AGCTCTGATTTGGTGTTTGAACTGAGTCTCGTTCACTCTTTTAGCTAGTATGTTAGGCTGATTGC
1 AGCTCTGATTTGGTGTTTGAACTGAGTCTCATTCACTCTTTTAGCTAGTATGTTAGGCTGATTGC
508261 ATGGTGTAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.17, C:0.16, G:0.24, T:0.42
Consensus pattern (67 bp):
AGCTCTGATTTGGTGTTTGAACTGAGTCTCATTCACTCTTTTAGCTAGTATGTTAGGCTGATTGC
TA
Found at i:509448 original size:19 final size:20
Alignment explanation
Indices: 509424--509469 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
509414 CATCCAAACA
509424 CCAGAAAA-T-ATTAACTTTT
1 CCAGAAAAGTAATTAA-TTTT
*
509443 CCAGAAAAGTAATTCATTTT
1 CCAGAAAAGTAATTAATTTT
509463 CCAGAAA
1 CCAGAAA
509470 TCATTTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 12 0.50
21 4 0.17
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (20 bp):
CCAGAAAAGTAATTAATTTT
Found at i:511945 original size:21 final size:21
Alignment explanation
Indices: 511910--511985 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
511900 TATACATGCA
* *
511910 TATGTGAATTCTTTTACATGAT
1 TATGCGAACTCTTTTACATG-T
*
511932 T-TGCGAACTCTTTTAGATGT
1 TATGCGAACTCTTTTACATGT
* * *
511952 TGTGTGAACTCTTTCACATGT
1 TATGCGAACTCTTTTACATGT
*
511973 TATGCGAGCTCTT
1 TATGCGAACTCTT
511986 ATGCATGGTA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 2 0.05
21 41 0.93
22 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (21 bp):
TATGCGAACTCTTTTACATGT
Found at i:512927 original size:15 final size:14
Alignment explanation
Indices: 512907--512961 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
512897 ATCACTAGAT
512907 TGAACTGATTATATG
1 TGAACT-ATTATATG
512922 TGAACTATTGA-ATG
1 TGAACTATT-ATATG
*
512936 TAAACTAATTATGA-G
1 TGAACT-ATTAT-ATG
512951 TGAACTATTAT
1 TGAACTATTAT
512962 CTACGATCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 17 0.50
15 16 0.47
16 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (14 bp):
TGAACTATTATATG
Found at i:516673 original size:29 final size:28
Alignment explanation
Indices: 516641--516699 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
516631 TGCAAATAAA
*
516641 AATTAATTGTAAATAAA-ATAAAATTAATT
1 AATTAATAGTAAA-AAATAT-AAATTAATT
*
516670 AATTAATAGTAAAATATATAAATTAATT
1 AATTAATAGTAAAAAATATAAATTAATT
516698 AA
1 AA
516700 GATAATGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
AATTAATAGTAAAAAATATAAATTAATT
Found at i:518319 original size:58 final size:58
Alignment explanation
Indices: 518229--518338 Score: 139
Period size: 58 Copynumber: 1.9 Consensus size: 58
518219 TAGAAATAAT
* * ** *
518229 ACAGATACAGTCACAGATACACTTACAAATGCAGCCATGCCACAGATACAGTCACGTC
1 ACAGATACAGTCACAAATACAATTACAAATGCAAACATGCCACAAATACAGTCACGTC
* ** *
518287 ACAGATACAGTTACAAATACAATTACGGATGCAAACATGCTACAAATACAGT
1 ACAGATACAGTCACAAATACAATTACAAATGCAAACATGCCACAAATACAGT
518339 TACAGATGCA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 43 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (58 bp):
ACAGATACAGTCACAAATACAATTACAAATGCAAACATGCCACAAATACAGTCACGTC
Found at i:518330 original size:29 final size:29
Alignment explanation
Indices: 518298--518354 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
518288 CAGATACAGT
*
518298 TACAAATACAATTACGGATGCAAACATGC
1 TACAAATACAATTACAGATGCAAACATGC
* *
518327 TACAAATACAGTTACAGATGCAGACATG
1 TACAAATACAATTACAGATGCAAACATG
518355 ATACCCCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (29 bp):
TACAAATACAATTACAGATGCAAACATGC
Found at i:519176 original size:53 final size:53
Alignment explanation
Indices: 519081--519212 Score: 165
Period size: 53 Copynumber: 2.5 Consensus size: 53
519071 AGAATTATAT
* * * * * *
519081 ACACACACCCATGTATCAGCCCATGTTCCTCAGAACAATATACACACACCCTG
1 ACACACGCCCATGTATCAGCCCGTGTACCCCAAAACAATATACACACACCCAG
* *
519134 ACACACGCCCATATATCAGCCCGTGTACCCCAAAACAGTATACACACACCCAG
1 ACACACGCCCATGTATCAGCCCGTGTACCCCAAAACAATATACACACACCCAG
* * *
519187 ACACACGCTCATGTGTTAGCCCGTGT
1 ACACACGCCCATGTATCAGCCCGTGT
519213 GCCACACACA
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 67 1.00
ACGTcount: A:0.32, C:0.37, G:0.13, T:0.18
Consensus pattern (53 bp):
ACACACGCCCATGTATCAGCCCGTGTACCCCAAAACAATATACACACACCCAG
Found at i:519273 original size:43 final size:43
Alignment explanation
Indices: 519216--519374 Score: 237
Period size: 43 Copynumber: 3.7 Consensus size: 43
519206 CCCGTGTGCC
* *
519216 ACACACACCCTGACACACGCTCGTGTGCCTCCAAACAGTATAG
1 ACACACACCCTGACACACCCCCGTGTGCCTCCAAACAGTATAG
* * * * *
519259 ATATACACCCTGACACACGCTCGTATGCCTCCAAACAGTATAG
1 ACACACACCCTGACACACCCCCGTGTGCCTCCAAACAGTATAG
*
519302 ACACACAACCTGACACACCCCCGTGTGCCTCCAAACAGTATAG
1 ACACACACCCTGACACACCCCCGTGTGCCTCCAAACAGTATAG
519345 ACACACACCCTGGACACACCCCCGTGTGCC
1 ACACACACCCT-GACACACCCCCGTGTGCC
519375 AGCTCGTGTG
Statistics
Matches: 105, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
43 87 0.83
44 18 0.17
ACGTcount: A:0.30, C:0.39, G:0.15, T:0.16
Consensus pattern (43 bp):
ACACACACCCTGACACACCCCCGTGTGCCTCCAAACAGTATAG
Found at i:533505 original size:13 final size:13
Alignment explanation
Indices: 533446--533522 Score: 61
Period size: 14 Copynumber: 5.8 Consensus size: 13
533436 ACATCTAAGT
*
533446 AAATAAAA-AGAC
1 AAATAAAATAAAC
*
533458 AAAATAACAATAAAT
1 -AAATAA-AATAAAC
533473 AAATAAAATTAAAC
1 AAATAAAA-TAAAC
*
533487 -ACTAAAATAAAC
1 AAATAAAATAAAC
*
533499 AAAT-AAATACAC
1 AAATAAAATAAAC
533511 AAATGAAAATAA
1 AAAT-AAAATAA
533523 CAGGGGCTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
12 16 0.31
13 16 0.31
14 17 0.33
15 2 0.04
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.17
Consensus pattern (13 bp):
AAATAAAATAAAC
Found at i:533669 original size:11 final size:10
Alignment explanation
Indices: 533651--533689 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
533641 ATTAAAAATA
533651 AAATTAAACT
1 AAATTAAACT
533661 AAGATTAAACT
1 AA-ATTAAACT
*
533672 AAATTAAAAT
1 AAATTAAACT
*
533682 AAAATAAA
1 AAATTAAA
533690 AATTATAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (10 bp):
AAATTAAACT
Found at i:533691 original size:11 final size:11
Alignment explanation
Indices: 533640--533692 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
533630 TAAAGGTGCG
533640 AATTAAAAATAA
1 AATT-AAAATAA
*
533652 AATTAAACTAA
1 AATTAAAATAA
* *
533663 GATTAAACT-A
1 AATTAAAATAA
533673 AATTAAAATAA
1 AATTAAAATAA
*
533684 AATAAAAAT
1 AATTAAAAT
533693 TATAGGGACC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 8 0.23
11 23 0.66
12 4 0.11
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (11 bp):
AATTAAAATAA
Found at i:540738 original size:26 final size:26
Alignment explanation
Indices: 540704--540756 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
540694 AGTAGATAAT
540704 AGCATAATCCAAATATAAAGTTTAGA
1 AGCATAATCCAAATATAAAGTTTAGA
540730 AGCATAATCCAAATATAAAGTTTAGA
1 AGCATAATCCAAATATAAAGTTTAGA
540756 A
1 A
540757 ATTCAAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (26 bp):
AGCATAATCCAAATATAAAGTTTAGA
Found at i:540768 original size:21 final size:21
Alignment explanation
Indices: 540739--540779 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
540729 AAGCATAATC
*
540739 CAAATATAAAGTTTAGAAATT
1 CAAACATAAAGTTTAGAAATT
*
540760 CAAACATAAAGTTTATAAAT
1 CAAACATAAAGTTTAGAAAT
540780 CTAAATTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (21 bp):
CAAACATAAAGTTTAGAAATT
Found at i:549597 original size:55 final size:55
Alignment explanation
Indices: 549488--549597 Score: 157
Period size: 55 Copynumber: 2.0 Consensus size: 55
549478 TCGTCTTAAT
* * * *
549488 TGTTGAAATACTGCTTCTTTTGAATCGATTTTTTATATGTTTAAATCGATTGTTA
1 TGTTGAAATACTGCTTCTTTCGAATCGATTGTTTATATGTTTAAATCAACTGTTA
* * *
549543 TGTTGGAATATTGCTTCTTTCGAATTGATTGTTTATATGTTTAAATCAACTGTTA
1 TGTTGAAATACTGCTTCTTTCGAATCGATTGTTTATATGTTTAAATCAACTGTTA
549598 CATAGCACTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.50
Consensus pattern (55 bp):
TGTTGAAATACTGCTTCTTTCGAATCGATTGTTTATATGTTTAAATCAACTGTTA
Found at i:549975 original size:14 final size:14
Alignment explanation
Indices: 549956--549985 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
549946 TTTTTTTTTC
549956 TCCTGAACTCTAAA
1 TCCTGAACTCTAAA
*
549970 TCCTGACCTCTAAA
1 TCCTGAACTCTAAA
549984 TC
1 TC
549986 TAGAATCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (14 bp):
TCCTGAACTCTAAA
Found at i:550097 original size:14 final size:14
Alignment explanation
Indices: 550078--550116 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
550068 CCTTGAACAT
* *
550078 TAAACCTAAATCCC
1 TAAACCCAAAACCC
550092 TAAACCCAAAACCC
1 TAAACCCAAAACCC
*
550106 AAAACCCAAAA
1 TAAACCCAAAA
550117 TTGAACCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.54, C:0.36, G:0.00, T:0.10
Consensus pattern (14 bp):
TAAACCCAAAACCC
Found at i:550152 original size:48 final size:49
Alignment explanation
Indices: 550070--550185 Score: 157
Period size: 48 Copynumber: 2.4 Consensus size: 49
550060 TTGCAAACCC
* *
550070 TTGAA-CATTAAACC-TAAATCCCTAAACCCAAAACCCAAAACCCAAAA
1 TTGAACCATTGAACCTTAAATCCCTAAACACAAAACCCAAAACCCAAAA
* *
550117 TTGAACCATTGAACCTTAAATCTC-AAACACTAAACCCAAAACCCAAAA
1 TTGAACCATTGAACCTTAAATCCCTAAACACAAAACCCAAAACCCAAAA
* *
550165 TTAAACCCTTGAACCTTAAAT
1 TTGAACCATTGAACCTTAAAT
550186 TTCGAACCCA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
47 5 0.08
48 49 0.80
49 7 0.11
ACGTcount: A:0.47, C:0.29, G:0.03, T:0.20
Consensus pattern (49 bp):
TTGAACCATTGAACCTTAAATCCCTAAACACAAAACCCAAAACCCAAAA
Found at i:553267 original size:5 final size:5
Alignment explanation
Indices: 553257--553283 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
553247 TCAAGTAAGC
553257 CTCTT CTCTT CTCTT CTCTT CTCTT CT
1 CTCTT CTCTT CTCTT CTCTT CTCTT CT
553284 TCCTTCTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
CTCTT
Found at i:553366 original size:15 final size:15
Alignment explanation
Indices: 553346--553378 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
553336 NNNNNNNNNN
553346 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
*
553361 AAAAAAAGAAAAAGA
1 AAAAAAAAAAAAAGA
553376 AAA
1 AAA
553379 CCTTACGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Found at i:560579 original size:25 final size:23
Alignment explanation
Indices: 560551--560596 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
560541 GTTGGATCCA
560551 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
560576 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
560597 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:561995 original size:207 final size:207
Alignment explanation
Indices: 561640--562054 Score: 715
Period size: 207 Copynumber: 2.0 Consensus size: 207
561630 CAAATAATGA
*
561640 AATAAAGGTATAAAAACGTGAGATCCTCCAAGTACCAAGTCACCTAAATCCAAAATAGCTATAAA
1 AATAAAGGTATAAAAACGTGAGATACTCCAAGTACCAAGTCACCTAAATCCAAAATAGCTATAAA
*
561705 AGAAATTGAGGGGGAATAAGTTAAAGAGCCCAGTGTGTCACTAAAGTATAAGCAATCACAACACA
66 AGAAATTGAGGGGGAATAAGTTAAAGAGCCCAGTGTGTCACTAAAGTACAAGCAATCACAACACA
*
561770 ATATCACAGAGATTTTTCACAAAACATTTTAAAATGAACACAAAGTATCACAACTCAAATGTAAT
131 ATATCACAGAGATTTTTCACAAAACATTTTAAAATGAACACAAAATATCACAACTCAAATGTAAT
561835 AAAATCACATAC
196 AAAATCACATAC
* * * * *
561847 AATAAAGGTATAAAAATGTGAGATACTCCGAGTACCAAGTCGCCTAAATCCAATATATCTATAAA
1 AATAAAGGTATAAAAACGTGAGATACTCCAAGTACCAAGTCACCTAAATCCAAAATAGCTATAAA
* * *
561912 AGAAATTGAGGGGGAATGAGTTAAAGAGCCCAGTTTGT-ATCTAAAGTGCAAGCAATCACAACAC
66 AGAAATTGAGGGGGAATAAGTTAAAGAGCCCAGTGTGTCA-CTAAAGTACAAGCAATCACAACAC
561976 AATATCACAGAGATTTTTCACAAAACATTTTAAAATGAACACAAAATATCACAACTCAAATGTAA
130 AATATCACAGAGATTTTTCACAAAACATTTTAAAATGAACACAAAATATCACAACTCAAATGTAA
562041 TAAAATCACATAC
195 TAAAATCACATAC
562054 A
1 A
562055 TAATGCAATG
Statistics
Matches: 196, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
206 1 0.01
207 195 0.99
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (207 bp):
AATAAAGGTATAAAAACGTGAGATACTCCAAGTACCAAGTCACCTAAATCCAAAATAGCTATAAA
AGAAATTGAGGGGGAATAAGTTAAAGAGCCCAGTGTGTCACTAAAGTACAAGCAATCACAACACA
ATATCACAGAGATTTTTCACAAAACATTTTAAAATGAACACAAAATATCACAACTCAAATGTAAT
AAAATCACATAC
Found at i:565704 original size:19 final size:18
Alignment explanation
Indices: 565663--565706 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
565653 TTGCAATCCA
565663 ATTTTATTTTTTATTTTG
1 ATTTTATTTTTTATTTTG
*
565681 TTTTTATTTATTTATTATT-
1 ATTTTATTT-TTTATT-TTG
565700 ATTTTAT
1 ATTTTAT
565707 AGATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.36
19 12 0.55
20 2 0.09
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (18 bp):
ATTTTATTTTTTATTTTG
Found at i:566741 original size:30 final size:30
Alignment explanation
Indices: 566692--566801 Score: 98
Period size: 30 Copynumber: 3.7 Consensus size: 30
566682 ATTGTTTATG
* * **
566692 ACCCCCAAACTTTCCAAAAAGTAT-GTTTTA
1 ACCCCTAAATTTTCCAAAAA-TATAAATTTA
* *
566722 ACCCCTAAATTTTCTAAAAATCTAAATTTA
1 ACCCCTAAATTTTCCAAAAATATAAATTTA
* * *
566752 ACCCCTAAATTTTTCAAAAATTTAAATTTG
1 ACCCCTAAATTTTCCAAAAATATAAATTTA
* *
566782 ACCCC-ACACTTTCCAAAAAT
1 ACCCCTAAATTTTCCAAAAAT
566802 TTCGATTTGA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
29 14 0.21
30 52 0.79
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.33
Consensus pattern (30 bp):
ACCCCTAAATTTTCCAAAAATATAAATTTA
Found at i:568989 original size:31 final size:31
Alignment explanation
Indices: 568954--569027 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
568944 TGCATATGCA
* *
568954 TTCATGCATTAATAAAATTTCGCATCTCATT
1 TTCATGCATTAATAAAATTTCACATCGCATT
* ** *
568985 TTCATGCATTCATAAGGTTTTACATCGCATT
1 TTCATGCATTAATAAAATTTCACATCGCATT
569016 TTCATGCATTAA
1 TTCATGCATTAA
569028 AATTTCGAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (31 bp):
TTCATGCATTAATAAAATTTCACATCGCATT
Found at i:573705 original size:100 final size:100
Alignment explanation
Indices: 573525--573888 Score: 548
Period size: 100 Copynumber: 3.6 Consensus size: 100
573515 GATGAATCCT
* * *
573525 ATACCCCTAAAGCTATAAAGGAACGAATTGAAGCCACAATGGCAAATCTCACACACCTAAAGCTA
1 ATACCCCTAAAGCTATAGAGGAACGAATTGAAGCCACAATGGCAAATCTCATACACCTAAAGCTG
* * *
573590 TAGAGGGGTATATTGAAGCTGCAATGGCAAATCTC
66 TAGAGGGGTAGATTGAAGCCGTAATGGCAAATCTC
* * **
573625 ATACCCCTAAAGCTATAGAGGAACAAATTGAACCCGTAATGGCAAATCTCATACACCTAAAGCTG
1 ATACCCCTAAAGCTATAGAGGAACGAATTGAAGCCACAATGGCAAATCTCATACACCTAAAGCTG
*
573690 TAGAGGAGTAGATTGAAGCCGTAATGGCAAATCTC
66 TAGAGGGGTAGATTGAAGCCGTAATGGCAAATCTC
* * * *
573725 ATACCCCTAAAGTTGTAGAGGAACGAATTGAAGCCGCAATGGAAAATCTCATACACCTAAAGCTG
1 ATACCCCTAAAGCTATAGAGGAACGAATTGAAGCCACAATGGCAAATCTCATACACCTAAAGCTG
* *
573790 TAGAGGGGCAGATTGAAGCCATAATGGCAAATCTC
66 TAGAGGGGTAGATTGAAGCCGTAATGGCAAATCTC
* * *
573825 ATACCCCTAAAACTATAGAGGAATGAATTGAAGCCACAATGACAAATCTCATACACCTAAAGCT
1 ATACCCCTAAAGCTATAGAGGAACGAATTGAAGCCACAATGGCAAATCTCATACACCTAAAGCT
573889 ATTGAGGGAC
Statistics
Matches: 237, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 237 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (100 bp):
ATACCCCTAAAGCTATAGAGGAACGAATTGAAGCCACAATGGCAAATCTCATACACCTAAAGCTG
TAGAGGGGTAGATTGAAGCCGTAATGGCAAATCTC
Found at i:573923 original size:50 final size:50
Alignment explanation
Indices: 573525--573913 Score: 401
Period size: 50 Copynumber: 7.8 Consensus size: 50
573515 GATGAATCCT
* * * *
573525 ATACCCCTAAAGCTATAAAGGAAC-GAATTGAAGCCACAATGGCAAATCTC
1 ATACACCTAAAGCTATAGAGGGACAG-ATTGAAGCCGCAATGGCAAATCTC
* ** * *
573575 ACACACCTAAAGCTATAGAGGGGTATATTGAAGCTGCAATGGCAAATCTC
1 ATACACCTAAAGCTATAGAGGGACAGATTGAAGCCGCAATGGCAAATCTC
* * * * *
573625 ATACCCCTAAAGCTATAGAGGAACAAATTGAACCCGTAATGGCAAATCTC
1 ATACACCTAAAGCTATAGAGGGACAGATTGAAGCCGCAATGGCAAATCTC
* * *
573675 ATACACCTAAAGCTGTAGA-GGAGTAGATTGAAGCCGTAATGGCAAATCTC
1 ATACACCTAAAGCTATAGAGGGA-CAGATTGAAGCCGCAATGGCAAATCTC
* * * * *
573725 ATACCCCTAAAGTTGTAGAGGAAC-GAATTGAAGCCGCAATGGAAAATCTC
1 ATACACCTAAAGCTATAGAGGGACAG-ATTGAAGCCGCAATGGCAAATCTC
* * **
573775 ATACACCTAAAGCTGTAGAGGGGCAGATTGAAGCCATAATGGCAAATCTC
1 ATACACCTAAAGCTATAGAGGGACAGATTGAAGCCGCAATGGCAAATCTC
* * * *
573825 ATACCCCTAAAACTATAGA-GGA-ATGAATTGAAGCCACAATGACAAATCTC
1 ATACACCTAAAGCTATAGAGGGACA-G-ATTGAAGCCGCAATGGCAAATCTC
* * *
573875 ATACACCTAAAGCTATTGAGGGACAGATTAAAGTCGCAA
1 ATACACCTAAAGCTATAGAGGGACAGATTGAAGCCGCAA
573914 GGACGAATCT
Statistics
Matches: 281, Mismatches: 49, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
48 1 0.00
49 6 0.02
50 266 0.95
51 7 0.02
52 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (50 bp):
ATACACCTAAAGCTATAGAGGGACAGATTGAAGCCGCAATGGCAAATCTC
Found at i:573939 original size:150 final size:150
Alignment explanation
Indices: 573525--573928 Score: 476
Period size: 150 Copynumber: 2.7 Consensus size: 150
573515 GATGAATCCT
* * *
573525 ATACCCCTAAAGCTATAAAGGAACGAATTGAAGCCACAATGGCAAATCTCACACACCTAAAGCTA
1 ATACCCCTAAAGCTATAGAGGAATGAATTGAAGCCACAATGGCAAATCTCATACACCTAAAGCTA
** * * *
573590 TAGAGGGGTATATTGAAGCTGCAATGG-CAAATCTCATACCCCTAAAGCTATAGAGGAACAAATT
66 TAGAGGGACAGATTGAAGC-GCAATGGACAAATCTCATACACCTAAAGCTGTAGAGGAACAAATT
*
573654 GAACCCGTAATGGCAAATCTC
130 GAACCCATAATGGCAAATCTC
* * * ** * *
573675 ATACACCTAAAGCTGTAGAGGAGT-AGATTGAAGCCGTAATGGCAAATCTCATACCCCTAAAGTT
1 ATACCCCTAAAGCTATAGAGGAATGA-ATTGAAGCCACAATGGCAAATCTCATACACCTAAAGCT
* * ** *
573739 GTAGAGGAAC-GAATTGAAGCCGCAATGGA-AAATCTCATACACCTAAAGCTGTAGAGGGGCAGA
65 ATAGAGGGACAG-ATTGAAG-CGCAATGGACAAATCTCATACACCTAAAGCTGTAGAGGAACAAA
*
573802 TTGAAGCCATAATGGCAAATCTC
128 TTGAACCCATAATGGCAAATCTC
* *
573825 ATACCCCTAAAACTATAGAGGAATGAATTGAAGCCACAATGACAAATCTCATACACCTAAAGCTA
1 ATACCCCTAAAGCTATAGAGGAATGAATTGAAGCCACAATGGCAAATCTCATACACCTAAAGCTA
* * * *
573890 TTGAGGGACAGATTAAAGTCGCAA-GGACGAATCTTATAC
66 TAGAGGGACAGATTGAAG-CGCAATGGACAAATCTCATAC
573929 TCTTGAAGCT
Statistics
Matches: 209, Mismatches: 38, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
149 4 0.02
150 202 0.97
151 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (150 bp):
ATACCCCTAAAGCTATAGAGGAATGAATTGAAGCCACAATGGCAAATCTCATACACCTAAAGCTA
TAGAGGGACAGATTGAAGCGCAATGGACAAATCTCATACACCTAAAGCTGTAGAGGAACAAATTG
AACCCATAATGGCAAATCTC
Found at i:574001 original size:39 final size:39
Alignment explanation
Indices: 573958--574033 Score: 136
Period size: 39 Copynumber: 1.9 Consensus size: 39
573948 CGAAGTTACC
573958 ATCCAAT-CTCTTACCCCGACCATGGGGCAGATTGAAGCA
1 ATCCAATCCT-TTACCCCGACCATGGGGCAGATTGAAGCA
573997 ATCCAATCCTTTACCCCGACCATGGGGCAGATTGAAG
1 ATCCAATCCTTTACCCCGACCATGGGGCAGATTGAAG
574034 ATCATACGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 34 0.94
40 2 0.06
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (39 bp):
ATCCAATCCTTTACCCCGACCATGGGGCAGATTGAAGCA
Found at i:574559 original size:101 final size:101
Alignment explanation
Indices: 574378--574559 Score: 220
Period size: 101 Copynumber: 1.8 Consensus size: 101
574368 AGGCGAATCC
* * **
574378 TTATCTCTCTGAAGTTGCAGTAGAGCAAGATGAAACTACAAAACCAAATCCTATACCCCTGCAGT
1 TTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAACTACAAAACCAAATCATATACCCCTAAAGT
* *
574443 TGTAGTGGGTCGAATTAAAGTCATGAAAACAAATTT
66 TGCAGTGGATCGAATTAAAGTCATGAAAACAAATTT
* * ** * * * * *
574479 TTATCTCCCTGAAGTTGTAGTGGAGCAAGATGAAGTTACGATATCAAATCATATATCCTTAAAGT
1 TTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAACTACAAAACCAAATCATATACCCCTAAAGT
*
574544 TGCAGTGGATTGAATT
66 TGCAGTGGATCGAATT
574560 GAGGCTACAT
Statistics
Matches: 65, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
101 65 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (101 bp):
TTATCTCCCTGAAGTTGCAGTAGAGCAAGATGAAACTACAAAACCAAATCATATACCCCTAAAGT
TGCAGTGGATCGAATTAAAGTCATGAAAACAAATTT
Found at i:575872 original size:30 final size:30
Alignment explanation
Indices: 575838--575954 Score: 146
Period size: 30 Copynumber: 3.9 Consensus size: 30
575828 TTTGAAAACT
* *
575838 AAATTTTCCAAAAATTTGAATTTGACCCTC
1 AAATTTTCTAAAAATTTAAATTTGACCCTC
* *
575868 AAATTTTCTAAAAACTTAAATTTAACCCTC
1 AAATTTTCTAAAAATTTAAATTTGACCCTC
*
575898 AAATTTTCTAAAAATTCAAATTTGACCC-C
1 AAATTTTCTAAAAATTTAAATTTGACCCTC
* * **
575927 ACACTTTCTAAAAATTTCGATTTGACCC
1 AAATTTTCTAAAAATTTAAATTTGACCC
575955 CTGAAGTTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
29 24 0.32
30 51 0.68
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.36
Consensus pattern (30 bp):
AAATTTTCTAAAAATTTAAATTTGACCCTC
Found at i:575876 original size:60 final size:58
Alignment explanation
Indices: 575804--575942 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 58
575794 TGTTTGTGAC
* **
575804 CCCCAAACTTTCTAAAAATTATATTTTGAAAACT-AAATTTTCCAAAAATTTGAATTTGA
1 CCCCAAACTTTCTAAAAATTA-AATTT-AAAACTCAAATTTTCCAAAAATTCAAATTTGA
* ** *
575863 CCCTCAAATTTTCTAAAAACTTAAATTTAACCCTCAAATTTTCTAAAAATTCAAATTTGA
1 CCC-CAAACTTTCTAAAAA-TTAAATTTAAAACTCAAATTTTCCAAAAATTCAAATTTGA
*
575923 CCCCACACTTTCTAAAAATT
1 CCCCAAACTTTCTAAAAATT
575943 TCGATTTGAC
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
58 2 0.03
59 20 0.29
60 43 0.63
61 3 0.04
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.36
Consensus pattern (58 bp):
CCCCAAACTTTCTAAAAATTAAATTTAAAACTCAAATTTTCCAAAAATTCAAATTTGA
Found at i:577690 original size:51 final size:51
Alignment explanation
Indices: 577609--577784 Score: 210
Period size: 51 Copynumber: 3.5 Consensus size: 51
577599 GAAGGCTCTA
**
577609 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAGCAGTCCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAAGTCCG
* * *
577660 ATGAATAAGTGTCATCGTAAGTAAATGAATCCTTTACGGATTAAAAGTCCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAAGTCCG
* * * * * *
577711 ATGACTATGTGTCATTGTGAGTAAATGAATCCATGATGGATT-AAAGCTCCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAAG-TCCG
** *
577762 ATGACTTCGTGTCATTGTGAGTA
1 ATGACTAAGTGTCATCGTGAGTA
577785 TGAATTCCTA
Statistics
Matches: 110, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 4 0.04
51 106 0.96
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (51 bp):
ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATTAAAAGTCCG
Found at i:584964 original size:51 final size:50
Alignment explanation
Indices: 584899--585073 Score: 219
Period size: 51 Copynumber: 3.5 Consensus size: 50
584889 GACTAAGTCA
584899 TGAGTAAATGAATCCTTTACGGATTAGAAGTCCGATGACTAAGTGTCATCG
1 TGAGTAAATGAATCCTTTACGGATTA-AAGTCCGATGACTAAGTGTCATCG
*
584950 TGAGTAAATGAATCCTTTACGGATTAAAAGTCCGATGACCAAGTGTCATCG
1 TGAGTAAATGAATCCTTTACGGATT-AAAGTCCGATGACTAAGTGTCATCG
* * * * * **
585001 TGAGTAAATGAATTCATGATGGATTAAAGGTCTGATGACTCCGTGTCATCG
1 TGAGTAAATGAATCCTTTACGGATTAAA-GTCCGATGACTAAGTGTCATCG
*
585052 TGAGT--ATGAATTCTTATACGGA
1 TGAGTAAATGAATCCTT-TACGGA
585074 ACAAGAGGTC
Statistics
Matches: 109, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
49 9 0.08
50 7 0.06
51 92 0.84
52 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.30
Consensus pattern (50 bp):
TGAGTAAATGAATCCTTTACGGATTAAAGTCCGATGACTAAGTGTCATCG
Found at i:585101 original size:102 final size:101
Alignment explanation
Indices: 584896--585108 Score: 225
Period size: 102 Copynumber: 2.1 Consensus size: 101
584886 GATGACTAAG
* *
584896 TCATGAGTAAATGAATCCTTTACGGATTAGAAGTCCGATGACTAAGTGTCATCGTGAGTAAATGA
1 TCATGAGTAAATGAATCCATGACGGATTAGAAGTCCGATGACTAAGTGTCATCGTGAGT-AATGA
** *
584961 ATCCTTTACGGATTAAAAGTCCGATGACCAAGTGTCA
65 ATCCTTTACGGAACAAAAGTCCGATGACCAAGTATCA
* * * * **
584998 TCGTGAGTAAATGAATTCATGATGGATTA-AAGGTCTGATGACTCCGTGTCATCGTGAGT-ATGA
1 TCATGAGTAAATGAATCCATGACGGATTAGAA-GTCCGATGACTAAGTGTCATCGTGAGTAATGA
* * **
585061 ATTCTTATACGGAACAAGAGGTCCGATGATTATA-TATCA
65 ATCCTT-TACGGAACAA-AAGTCCGATGACCA-AGTATCA
585100 TCATGAGTA
1 TCATGAGTA
585109 TTAAATGAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
100 9 0.10
101 10 0.11
102 71 0.78
103 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (101 bp):
TCATGAGTAAATGAATCCATGACGGATTAGAAGTCCGATGACTAAGTGTCATCGTGAGTAATGAA
TCCTTTACGGAACAAAAGTCCGATGACCAAGTATCA
Found at i:586597 original size:81 final size:81
Alignment explanation
Indices: 586512--586672 Score: 241
Period size: 81 Copynumber: 2.0 Consensus size: 81
586502 CTCAGCCACC
* * *
586512 GCTATGGTCTATGTCACCCGCTCACGATGCTGCTCACAAAAGCTATCAAGAAACTACAACAAATG
1 GCTATAGTCTATGTCACCCACTCAAGATGCTGCTCACAAAAGCTATCAAGAAACTACAACAAATG
586577 CAGGATCTCAACCATT
66 CAGGATCTCAACCATT
* * * *
586593 GCTATAGTCTATGTTACCCACTCAAGCTGCTGCTCACACAAGCTATCAAGAAACTGCAACAAATG
1 GCTATAGTCTATGTCACCCACTCAAGATGCTGCTCACAAAAGCTATCAAGAAACTACAACAAATG
* *
586658 TAGGATCTCAGCCAT
66 CAGGATCTCAACCAT
586673 CGTAGAAGTC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (81 bp):
GCTATAGTCTATGTCACCCACTCAAGATGCTGCTCACAAAAGCTATCAAGAAACTACAACAAATG
CAGGATCTCAACCATT
Found at i:591601 original size:46 final size:45
Alignment explanation
Indices: 591540--591632 Score: 109
Period size: 46 Copynumber: 2.0 Consensus size: 45
591530 TGTAATTATT
* *
591540 TTTTTATTGAAATTT-AT-TTTAAATATATAATATTATATGTTTAAA
1 TTTTTATTGAAATTTAATATTTAAA-ATATAAT-TTATATATTGAAA
* *
591585 TTTTTATTGATTATTTAATATTTAAAATATAGTTTATATATTGAAA
1 TTTTTATTGA-AATTTAATATTTAAAATATAATTTATATATTGAAA
591631 TT
1 TT
591633 AAATTTTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 10 0.24
46 17 0.41
47 8 0.20
48 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (45 bp):
TTTTTATTGAAATTTAATATTTAAAATATAATTTATATATTGAAA
Found at i:596453 original size:28 final size:25
Alignment explanation
Indices: 596422--596482 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 25
596412 AATGATGGTT
596422 ATAAAAGAAAATGTAATAAAAAATATAA
1 ATAAAAGAAAAT-T-ATAAAAAATA-AA
*
596450 ATAAAACATAAAATTATAAAAAATAAA
1 AT-AAA-AGAAAATTATAAAAAATAAA
596477 ATAAAA
1 ATAAAA
596483 ACAAAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 1 0.03
26 3 0.10
27 4 0.13
28 12 0.40
29 4 0.13
30 6 0.20
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (25 bp):
ATAAAAGAAAATTATAAAAAATAAA
Found at i:596470 original size:15 final size:15
Alignment explanation
Indices: 596450--596497 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
596440 AAAAATATAA
596450 ATAAAACATAAAATT
1 ATAAAACATAAAATT
*
596465 ATAAAAAATAAAA-T
1 ATAAAACATAAAATT
* *
596479 A-AAAACAAAAAATA
1 ATAAAACATAAAATT
596493 ATAAA
1 ATAAA
596498 GGATGGTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 9 0.33
14 3 0.11
15 15 0.56
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAAACATAAAATT
Found at i:596478 original size:27 final size:29
Alignment explanation
Indices: 596435--596497 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
596425 AAAGAAAATG
*
596435 TAATAAAAAATATAAAT-AAAACATAAAA
1 TAATAAAAAATATAAATAAAAACAAAAAA
*
596463 TTATAAAAAATA-AAATAAAAACAAAAAA
1 TAATAAAAAATATAAATAAAAACAAAAAA
596491 TAATAAA
1 TAATAAA
596498 GGATGGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (29 bp):
TAATAAAAAATATAAATAAAAACAAAAAA
Found at i:596489 original size:12 final size:12
Alignment explanation
Indices: 596436--596493 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 12
596426 AAGAAAATGT
596436 AATAAAAAATATA
1 AATAAAAAATA-A
*
596449 AATAAAACATAAA
1 AATAAAAAAT-AA
596462 ATTATAAAAAATAA
1 A--ATAAAAAATAA
*
596476 AATAAAAACAAAA
1 AATAAAAA-ATAA
596489 AATAA
1 AATAA
596494 TAAAGGATGG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 7 0.18
13 19 0.50
14 4 0.11
15 8 0.21
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:598190 original size:15 final size:15
Alignment explanation
Indices: 598167--598197 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
598157 GTGATGGAAT
*
598167 TTGAGTCGAATCGAA
1 TTGAATCGAATCGAA
598182 TTGAATCGAATCGAA
1 TTGAATCGAATCGAA
598197 T
1 T
598198 ATATTTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (15 bp):
TTGAATCGAATCGAA
Found at i:601106 original size:10 final size:10
Alignment explanation
Indices: 601091--601115 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
601081 CACAAATTTC
601091 GAGTATGAAA
1 GAGTATGAAA
601101 GAGTATGAAA
1 GAGTATGAAA
601111 GAGTA
1 GAGTA
601116 AGGGATGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (10 bp):
GAGTATGAAA
Found at i:602257 original size:11 final size:11
Alignment explanation
Indices: 602243--602278 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
602233 ACAAAAAGTT
602243 ATAAAATAAAA
1 ATAAAATAAAA
602254 ATAAAATAAAA
1 ATAAAATAAAA
*
602265 ACAAAA-AAAA
1 ATAAAATAAAA
602275 ATAA
1 ATAA
602279 TAAAGGATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.30
11 16 0.70
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:602262 original size:16 final size:16
Alignment explanation
Indices: 602225--602278 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 16
602215 TAATAAAAAC
602225 AAAACAAAACAAAAAGTTA
1 AAAACAAAA-AAAAA--TA
*
602244 TAAAATAAAAATAAAATA
1 -AAAACAAAAA-AAAATA
602262 AAAACAAAAAAAAATA
1 AAAACAAAAAAAAATA
602278 A
1 A
602279 TAAAGGATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 7 0.23
17 9 0.29
18 2 0.06
19 1 0.03
20 12 0.39
ACGTcount: A:0.80, C:0.06, G:0.02, T:0.13
Consensus pattern (16 bp):
AAAACAAAAAAAAATA
Found at i:605587 original size:20 final size:20
Alignment explanation
Indices: 605538--605592 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
605528 TTGTGCCTAG
*
605538 TAGGCTTTGTGCCGGGTGATT
1 TAGGCTTTGTGCC-GGTAATT
* *
605559 CAAGCTTTGTGCCGGTAATT
1 TAGGCTTTGTGCCGGTAATT
605579 TAGGCTTTGTGCCG
1 TAGGCTTTGTGCCG
605593 ATGTTTTTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.13, C:0.18, G:0.33, T:0.36
Consensus pattern (20 bp):
TAGGCTTTGTGCCGGTAATT
Found at i:612540 original size:16 final size:16
Alignment explanation
Indices: 612518--612615 Score: 70
Period size: 16 Copynumber: 5.6 Consensus size: 16
612508 ATTAATCAGA
612518 CTTTGTGCCTAGTAGG
1 CTTTGTGCCTAGTAGG
* * *
612534 TTTTGTGTCGATGATTCAGG
1 CTTTGTG-C-CT-AGT-AGG
612554 CTTTGTGCCTAGTAGG
1 CTTTGTGCCTAGTAGG
*
612570 CTTTGTGCCAATGTTTTTAGG
1 CTTTGTGCCTA-G----TAGG
*
612591 CTCTGTGCCTAGTAGG
1 CTTTGTGCCTAGTAGG
612607 CTTTGTGCC
1 CTTTGTGCC
612616 GAGGACTTCA
Statistics
Matches: 63, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
16 31 0.49
17 4 0.06
18 2 0.03
19 3 0.05
20 10 0.16
21 13 0.21
ACGTcount: A:0.12, C:0.18, G:0.29, T:0.41
Consensus pattern (16 bp):
CTTTGTGCCTAGTAGG
Found at i:612565 original size:36 final size:37
Alignment explanation
Indices: 612513--612615 Score: 136
Period size: 36 Copynumber: 2.8 Consensus size: 37
612503 ATTTAATTAA
* * * *
612513 TCAGACTTTGTGCCTAGTAGGTTTTGTGTCGATG-AT
1 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCAATGTAT
*
612549 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCAATGTTT
1 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCAATGTAT
* *
612586 TTAGGCTCTGTGCCTAGTAGGCTTTGTGCC
1 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCC
612616 GAGGACTTCA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
36 30 0.51
37 29 0.49
ACGTcount: A:0.14, C:0.18, G:0.28, T:0.40
Consensus pattern (37 bp):
TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCAATGTAT
Found at i:612601 original size:37 final size:36
Alignment explanation
Indices: 612521--612615 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 36
612511 AATCAGACTT
* * * *
612521 TGTGCCTAGTAGGTTTTGTGTCGATGATTCAGGCTT
1 TGTGCCTAGTAGGCTTTGTGCCAATGATTCAGGCTC
* *
612557 TGTGCCTAGTAGGCTTTGTGCCAATGTTTTTAGGCTC
1 TGTGCCTAGTAGGCTTTGTGCCAATG-ATTCAGGCTC
612594 TGTGCCTAGTAGGCTTTGTGCC
1 TGTGCCTAGTAGGCTTTGTGCC
612616 GAGGACTTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 23 0.44
37 29 0.56
ACGTcount: A:0.13, C:0.18, G:0.29, T:0.40
Consensus pattern (36 bp):
TGTGCCTAGTAGGCTTTGTGCCAATGATTCAGGCTC
Found at i:614779 original size:30 final size:32
Alignment explanation
Indices: 614709--614782 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 32
614699 AAAAAACATA
614709 CATG-AATTTTGATTTAATGCGTAATTCTATAT
1 CATGAAATTTTGATTT-ATGCGTAATTCTATAT
* *
614741 -AT-AAATTTTGATTT-TGTGTAATTTTAT-T
1 CATGAAATTTTGATTTATGCGTAATTCTATAT
614769 CATGAAATTTTGAT
1 CATGAAATTTTGAT
614783 ATGACCTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
28 1 0.03
29 13 0.35
30 10 0.27
31 13 0.35
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.51
Consensus pattern (32 bp):
CATGAAATTTTGATTTATGCGTAATTCTATAT
Found at i:616828 original size:17 final size:19
Alignment explanation
Indices: 616794--616831 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
616784 GTGAGTTGGC
616794 ATCAAAATCTTTTAAGTTT
1 ATCAAAATCTTTTAAGTTT
616813 ATCAAAAT-TTTT-AGTTT
1 ATCAAAATCTTTTAAGTTT
616830 AT
1 AT
616832 ATTGATACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (19 bp):
ATCAAAATCTTTTAAGTTT
Found at i:619817 original size:28 final size:26
Alignment explanation
Indices: 619773--619830 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
619763 TTAAGATGAC
*
619773 TATAAAAATTTTCAATAAATAAAA-AA
1 TATAAAAATTTTAAAT-AATAAAATAA
*
619799 TATATAAAATTATTAAATATTAAAATAA
1 TATA-AAAATT-TTAAATAATAAAATAA
619827 TATA
1 TATA
619831 CTATAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.15
27 12 0.44
28 11 0.41
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
TATAAAAATTTTAAATAATAAAATAA
Found at i:625425 original size:80 final size:80
Alignment explanation
Indices: 625292--625451 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
625282 CATTGTGATT
625292 ATGGCAAATTGATAACTGAAATAAAATTGGCGACCAGCGAAGTGGTAAGTACTCTTTTTGTCATT
1 ATGGCAAATTGATAACTGAAATAAAATTGGCGACCAGCGAAGTGGTAAGTACTCTTTTTGTCATT
625357 TTTGTCAAAATACTG
66 TTTGTCAAAATACTG
* *
625372 ATGGCAAATTGATAACTGAAATAAAATTGGCGACCAGCGAAGTGGTGAGTACTCTTTTTTTCATT
1 ATGGCAAATTGATAACTGAAATAAAATTGGCGACCAGCGAAGTGGTAAGTACTCTTTTTGTCATT
625437 TTTGTCAAAATACTG
66 TTTGTCAAAATACTG
625452 CAGGGTGAGA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (80 bp):
ATGGCAAATTGATAACTGAAATAAAATTGGCGACCAGCGAAGTGGTAAGTACTCTTTTTGTCATT
TTTGTCAAAATACTG
Found at i:633646 original size:16 final size:18
Alignment explanation
Indices: 633609--633646 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
633599 GTGTCTCGTT
*
633609 AAAACCTTTACTAAGATA
1 AAAACCTTTACTAAGAAA
633627 AAAACC-TT-CTAAGAAA
1 AAAACCTTTACTAAGAAA
633643 AAAA
1 AAAA
633647 ATTTCCTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 2 0.11
18 6 0.32
ACGTcount: A:0.58, C:0.16, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAACCTTTACTAAGAAA
Found at i:643647 original size:61 final size:59
Alignment explanation
Indices: 643505--644086 Score: 563
Period size: 61 Copynumber: 9.7 Consensus size: 59
643495 AAAAATAAAT
* ** * *
643505 TTTTTTTGTATTGGCCATATAATGGCCGACACCCCTATTTATCTGATAAAAAA-ATC-AAA
1 TTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCT-TTT-TCAGATAAAAAATTTCAAAA
** *
643564 TTTTTGGGTGTTGGCCATGCAATGGTCGACACCTCCTTTTTCAGATAAAAAATTTTCAAAA
1 TTTTTTTGTGTTGGCCATGCAATGGCCGACACC-CCTTTTTCAGATAAAAAA-TTTCAAAA
* * *
643625 CTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCCTTTTCTCAGATAAAAAATTTTTAAAA
1 TTTTTTTGTGTTGGCCATGCAATGGCCGACAC-CCCTTTT-TCAGATAAAAAA-TTTCAAAA
** * *
643687 TTTTTTTGTGTTGGCCATGCAATGGCCGACACTCTTTTTTTCAGATAAAAAAATT--ACA
1 TTTTTTTGTGTTGGCCATGCAATGGCCGACAC-CCCTTTTTCAGATAAAAAATTTCAAAA
* *
643745 TTTTTTTATGTTGGCCATGCAATGGCCGACGCACCCTTTTTCAGATAAAAAAATTTCAAAA
1 TTTTTTTGTGTTGGCCATGCAATGGCCGACAC-CCCTTTTTCAGAT-AAAAAATTTCAAAA
* * * ** *
643806 ATTTTTGGTGTTGGTCATGCAATGATCGACACCCCCTTTTCTCAGATAAAAAAATTC-AAA
1 TTTTTTTGTGTTGGCCATGCAATGGCCGACA-CCCCTTTT-TCAGATAAAAAATTTCAAAA
* * * *
643866 --TATTTGTGTTGGCTATGCAATGGTCGACACTCCCTTTTTTCAGATAAAAAAATTGC---A
1 TTTTTTTGTGTTGGCCATGCAATGGCCGACAC-CCC-TTTTTCAGAT-AAAAAATTTCAAAA
*
643923 TTTTTTTGTGTTGGCCATGCAATGGCCAACACCCCCTTTTTCAGATAAAAAAATTTCAAAA
1 TTTTTTTGTGTTGGCCATGCAATGGCCGACA-CCCCTTTTTCAGAT-AAAAAATTTCAAAA
* * * * * * *
643984 TTTTTTGGTGTTAGCCATGTAATAGTCGATACCCCTTTTTCTCAGATTAAAAATTTTCAAAA
1 TTTTTTTGTGTTGGCCATGCAATGGCCGACACCCC-TTTT-TCAGA-TAAAAAATTTCAAAA
** *
644046 TTTTTTTGTGTTGGATATGCAATGGCTGACACCCTCTTTTT
1 TTTTTTTGTGTTGGCCATGCAATGGCCGACACCC-CTTTTT
644087 ATTTGGTAAA
Statistics
Matches: 437, Mismatches: 62, Indels: 46
0.80 0.11 0.08
Matches are distributed among these distances:
57 2 0.00
58 107 0.24
59 78 0.18
60 15 0.03
61 122 0.28
62 111 0.25
63 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (59 bp):
TTTTTTTGTGTTGGCCATGCAATGGCCGACACCCCTTTTTCAGATAAAAAATTTCAAAA
Found at i:643649 original size:120 final size:117
Alignment explanation
Indices: 643505--644086 Score: 544
Period size: 120 Copynumber: 4.8 Consensus size: 117
643495 AAAAATAAAT
* * ** *
643505 TTTTTTTGTATTGGCCATATAATGGCCGACAC-CCCTATTTATCTGATAAAAAAATCAAATTTTT
1 TTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCCT-TTT-TCAGATAAAAAAATCAAATTTTT
* * * *
643569 GGGTGTTGGCCATGCAATGGTCGACACCTCCTTTTTCAGATAAAAAATTTTCAAAA
64 TGGTGTTGGCCATGCAATGGCCGACACCCCCTTTTTCAGATAAAAAA-ATTC-AAA
* * *
643625 CTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCCTTTTCTCAGATAAAAAATTTTTAAAATTT
1 TTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCCTTTT-TCAGATAAAAAA---ATCAAATTT
* * ** *
643690 TTTTGTGTTGGCCATGCAATGGCCGACACTCTTTTTTTCAGATAAAAAAATT-ACA
62 TTTGGTGTTGGCCATGCAATGGCCGACACCCCCTTTTTCAGATAAAAAAATTCAAA
** * * *
643745 TTTTTTTATGTTGGCCATGCAATGGCCGACGCACCCTTTTTCAGATAAAAAAATTTCAAAAATTT
1 TTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCCTTTTTCAGATAAAAAAA--TC-AAATTTT
* **
643810 TTGGTGTTGGTCATGCAATGATCGACACCCCCTTTTCTCAGATAAAAAAATTCAAA
63 TTGGTGTTGGCCATGCAATGGCCGACACCCCCTTTT-TCAGATAAAAAAATTCAAA
* * * ***
643866 -TATTT-GTGTTGGCTATGCAATGGTCGACACTCCCTTTTTTCAGATAAAAAAATTGCATTTTTT
1 TTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCC-TTTTTCAGATAAAAAAATCAAATTTTTT
* *
643929 TGTGTTGGCCATGCAATGGCCAACACCCCCTTTTTCAGATAAAAAAATTTCAAAA
65 GGTGTTGGCCATGCAATGGCCGACACCCCCTTTTTCAGATAAAAAAA-TTC-AAA
* * * * * **
643984 TTTTTTGGTGTTAGCCATGTAATAGTCGATAC-CCCTTTTTCTCAGATTAAAAATTTTCAAAATT
1 TTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCC-TTTT-TCAGA-TAAAAA-AATC-AAATT
* ** * *
644048 TTTTTGTGTTGGATATGCAATGGCTGACACCCTCTTTTT
61 TTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTTTTT
644087 ATTTGGTAAA
Statistics
Matches: 379, Mismatches: 65, Indels: 33
0.79 0.14 0.07
Matches are distributed among these distances:
116 13 0.03
117 38 0.10
118 5 0.01
119 83 0.22
120 139 0.37
121 12 0.03
122 3 0.01
123 86 0.23
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (117 bp):
TTTTTTGGTGTTGGCCATGCAATGGCCGACACTCCCTTTTTCAGATAAAAAAATCAAATTTTTTG
GTGTTGGCCATGCAATGGCCGACACCCCCTTTTTCAGATAAAAAAATTCAAA
Found at i:644932 original size:17 final size:17
Alignment explanation
Indices: 644912--644967 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
644902 AAAAAATAAT
*
644912 AATTAGAATATACATGA
1 AATTAGAATATACAAGA
*
644929 AATTAGAA-A-A-AAAA
1 AATTAGAATATACAAGA
* *
644943 AATTAAAATATACAGGA
1 AATTAGAATATACAAGA
644960 AATTAGAA
1 AATTAGAA
644968 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
14 9 0.30
15 2 0.07
16 2 0.07
17 17 0.57
ACGTcount: A:0.62, C:0.04, G:0.11, T:0.23
Consensus pattern (17 bp):
AATTAGAATATACAAGA
Found at i:644953 original size:31 final size:33
Alignment explanation
Indices: 644902--644968 Score: 102
Period size: 31 Copynumber: 2.1 Consensus size: 33
644892 TATAAATTTT
* *
644902 AAAAAATAATAATTAGAATATACATGAAATTAG
1 AAAAAATAATAATTAAAATATACAGGAAATTAG
644935 AAAAAA-AA-AATTAAAATATACAGGAAATTAG
1 AAAAAATAATAATTAAAATATACAGGAAATTAG
644966 AAA
1 AAA
644969 TTAAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 24 0.75
32 2 0.06
33 6 0.19
ACGTcount: A:0.66, C:0.03, G:0.09, T:0.22
Consensus pattern (33 bp):
AAAAAATAATAATTAAAATATACAGGAAATTAG
Found at i:644981 original size:30 final size:30
Alignment explanation
Indices: 644918--645010 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 30
644908 TAATAATTAG
* ** *
644918 AATATACATGAAATTAGAAAAAAAAAATTAA
1 AATATACACGAAATTAG-AAATTAAATTTAA
*
644949 AATATACAGGAAATTAGAAATTAAATTTAA
1 AATATACACGAAATTAGAAATTAAATTTAA
* * * *
644979 AATAAAAACAAAATTACAAATTAAATTTAA
1 AATATACACGAAATTAGAAATTAAATTTAA
645009 AA
1 AA
645011 AGTAAACGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 37 0.70
31 16 0.30
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (30 bp):
AATATACACGAAATTAGAAATTAAATTTAA
Found at i:646106 original size:21 final size:21
Alignment explanation
Indices: 646082--646138 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
646072 ATTTTTTTTT
*
646082 TGTAAAACAATATTTCGAAAA
1 TGTAAAAAAATATTTCGAAAA
*****
646103 TGTATTTTTATATTTCGAAAA
1 TGTAAAAAAATATTTCGAAAA
646124 TGTAAAAAAATATTT
1 TGTAAAAAAATATTT
646139 GTAAAAAATA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (21 bp):
TGTAAAAAAATATTTCGAAAA
Found at i:646219 original size:20 final size:20
Alignment explanation
Indices: 646167--646212 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
646157 TTATTTTTTT
* *
646167 AAAAA-TTCGAAAATATAAA
1 AAAAATTTCAAAAATAGAAA
*
646186 AAACATTTCAAAAATAGAAA
1 AAAAATTTCAAAAATAGAAA
646206 AAAAATT
1 AAAAATT
646213 ATAAAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAAATTTCAAAAATAGAAA
Found at i:647430 original size:17 final size:17
Alignment explanation
Indices: 647404--647437 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
647394 ATAAATTTAA
*
647404 AATATGATAAAAATTGT
1 AATATAATAAAAATTGT
*
647421 AATATAATAATAATTGT
1 AATATAATAAAAATTGT
647438 TGATTTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
AATATAATAAAAATTGT
Found at i:647656 original size:87 final size:86
Alignment explanation
Indices: 647408--647980 Score: 782
Period size: 86 Copynumber: 6.6 Consensus size: 86
647398 ATTTAAAATA
* * * *
647408 TGATAAAAATTGTAATATAATAAT-A-ATTGTTGATTTAAATATTTAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
647471 TTGTCAAATCAACACATTATT
66 TTGTCAAATCAACACATTATT
647492 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
* *
647557 TTGTTAAATCAACATATTATT
66 TTGTCAAATCAACACATTATT
*
647578 TGATAAAAATTGTAATATAATAATAATATTTTTTTATTTAAATATTTAAATTTAGTAAATAATAT
1 TGATAAAAATTGTAATATAATAATAATA-TTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
*
647643 ATTGTTAAATCAACACATTATT
65 ATTGTCAAATCAACACATTATT
*
647665 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATATATAAAATTAATAA
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTT--A-A-AT----TTAGTAA
*
647730 ATAATGTATTGCCAAATCAACACATTATT
58 ATAATGTATTGTCAAATCAACACATTATT
* * *
647759 TGATAAAAATTGTAATATAATAATAATA-TTTTTATTTAAATATGTAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
*
647823 TTGTCAAATCAACATATTATT
66 TTGTCAAATCAACACATTATT
* **
647844 TGATAAAAATTGTAATATAATAAT-A-A-TTTGTACTTTAAATATGAAAATTT-GATAAATAATG
1 TGATAAAAATTGTAATATAATAATAATATTTTTTA-TTTAAATATTTAAATTTAG-TAAATAATG
* *
647905 TATTGTCAAATAAACACAATATT
64 TATTGTCAAATCAACACATTATT
* * *
647928 TGATATAAATTATAATATAATAATAATCTTTTTTATTTAAATAATGTTAAATT
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAAT-AT-TTAAATT
647981 AATTTTAAAT
Statistics
Matches: 442, Mismatches: 29, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
83 6 0.01
84 91 0.21
85 60 0.14
86 106 0.24
87 91 0.21
88 6 0.01
89 2 0.00
90 3 0.01
91 1 0.00
93 16 0.04
94 60 0.14
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (86 bp):
TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
TTGTCAAATCAACACATTATT
Found at i:647694 original size:173 final size:172
Alignment explanation
Indices: 647408--647983 Score: 799
Period size: 173 Copynumber: 3.3 Consensus size: 172
647398 ATTTAAAATA
* *
647408 TGATAAAAATTGTAATATAATAAT-A-ATTGTTGATTTAAATATTTAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAAATTAATAAATAATGTA
647471 TTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATAT
66 TTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATAT
* *
647536 TTAAATTTAGTAAATAATGTATTGTTAAATCAACATATTATT
131 TTAAATTTAGTAAATAATGTATTGTCAAATCAACACATTATT
* * *
647578 TGATAAAAATTGTAATATAATAATAATATTTTTTTATTTAAATATTTAAATTTAGTAAATAATAT
1 TGATAAAAATTGTAATATAATAATAATA-TTTTTTATTTAAATATTTAAAATTAATAAATAATGT
*
647643 ATTGTTAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATA
65 ATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATA
* *
647708 TTTAAATATATAAAATTAATAAATAATGTATTGCCAAATCAACACATTATT
130 TTT--A-A-AT----TTAGTAAATAATGTATTGTCAAATCAACACATTATT
*
647759 TGATAAAAATTGTAATATAATAATAATA-TTTTTATTTAAATATGTAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAAATTAATAAATAATGTA
* *
647823 TTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAAT-A-A-TTTGTACTTTAAATA
66 TTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATATTTTTTA-TTTAAATA
** * *
647885 TGAAAATTT-GATAAATAATGTATTGTCAAATAAACACAATATT
130 TTTAAATTTAG-TAAATAATGTATTGTCAAATCAACACATTATT
* * *
647928 TGATATAAATTATAATATAATAATAATCTTTTTTATTTAAATAATGTT-AAATTAAT
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAAT-AT-TTAAAATTAAT
647984 TTTAAATGTA
Statistics
Matches: 363, Mismatches: 27, Indels: 31
0.86 0.06 0.07
Matches are distributed among these distances:
169 56 0.15
170 37 0.10
171 11 0.03
172 2 0.01
173 100 0.28
174 1 0.00
175 2 0.01
176 6 0.02
177 12 0.03
178 1 0.00
179 75 0.21
181 60 0.17
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (172 bp):
TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAAATTAATAAATAATGTA
TTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATAT
TTAAATTTAGTAAATAATGTATTGTCAAATCAACACATTATT
Found at i:647993 original size:87 final size:84
Alignment explanation
Indices: 647408--647983 Score: 753
Period size: 87 Copynumber: 6.6 Consensus size: 84
647398 ATTTAAAATA
* *
647408 TGATAAAAATTGTAATATAATAATAA-TTGTTGATTTAAATATTTAAAATTAATAAATAATGTAT
1 TGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTT-AAATTAATAAATAATGTAT
647472 TGTCAAATCAACACATTATT
65 TGTCAAATCAACACATTATT
*
647492 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAAT-TTTTTTATTTAAATATTTAAA-TTAATAAATAATGTA
* *
647557 TTGTTAAATCAACATATTATT
64 TTGTCAAATCAACACATTATT
* *
647578 TGATAAAAATTGTAATATAATAATAATATTTTTTTATTTAAATATTTAAATTTAGTAAATAATAT
1 TGATAAAAATTGTAATATAATAAT-A-ATTTTTTTATTTAAATATTTAAA-TTAATAAATAATGT
*
647643 ATTGTTAAATCAACACATTATT
63 ATTGTCAAATCAACACATTATT
647665 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATATATAAAATTAATAA
1 TGATAAAAATTGTAATATAATAATAAT-TTTTTTATTT-AA-A--T--AT-T-T-AAATTAATAA
*
647730 ATAATGTATTGCCAAATCAACACATTATT
56 ATAATGTATTGTCAAATCAACACATTATT
* *
647759 TGATAAAAATTGTAATATAATAATAATATTTTTATTTAAATATGTAAAATTAATAAATAATGTAT
1 TGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATAT-TTAAATTAATAAATAATGTAT
*
647824 TGTCAAATCAACATATTATT
65 TGTCAAATCAACACATTATT
* ** *
647844 TGATAAAAATTGTAATATAATAATAA--TTTGTACTTTAAATATGAAAATTTGATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATTTTTTTA-TTTAAATATTTAAA-TTAATAAATAATGTA
* *
647907 TTGTCAAATAAACACAATATT
64 TTGTCAAATCAACACATTATT
* *
647928 TGATATAAATTATAATATAATAATAATCTTTTTTATTTAAATAATGTTAAATTAAT
1 TGATAAAAATTGTAATATAATAATAAT-TTTTTTATTTAAAT-AT-TTAAATTAAT
647984 TTTAAATGTA
Statistics
Matches: 442, Mismatches: 28, Indels: 41
0.86 0.05 0.08
Matches are distributed among these distances:
83 9 0.02
84 91 0.21
85 68 0.15
86 91 0.21
87 97 0.22
88 6 0.01
89 1 0.00
90 1 0.00
91 1 0.00
92 4 0.01
93 10 0.02
94 60 0.14
95 3 0.01
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (84 bp):
TGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTTAAATTAATAAATAATGTATT
GTCAAATCAACACATTATT
Found at i:648033 original size:19 final size:19
Alignment explanation
Indices: 648011--648057 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
648001 TTTCAACTTC
* *
648011 AAATTTAAAGTAGAATTTT
1 AAATTCAAAGTAGAATTCT
648030 AAATTCAAAGTAGAATTCT
1 AAATTCAAAGTAGAATTCT
648049 AAATTCAAA
1 AAATTCAAA
648058 CTTATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (19 bp):
AAATTCAAAGTAGAATTCT
Found at i:651981 original size:60 final size:61
Alignment explanation
Indices: 651860--652513 Score: 635
Period size: 60 Copynumber: 11.2 Consensus size: 61
651850 AGGGGAAGTT
* * **
651860 GGTGTCGGCCATTACATGGCCAACACCAAAAAA-TTT--AA-TTTTTTACCAAATAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGA-AAAAAGG
*
651918 GAGTGTCGGCCATTGCATGGCCAACACTAAAAAATTTTG-AATTTTTTTATCTGAAAAAAGG
1 G-GTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGG
* * * *
651979 AGTGTCAGCCATTGCATGGCCAACATCAAAAAA---TGCAAA-TTTTTTATTTGAAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTG-AAATTTTTTTATCTGAAAAAAGG
* *
652037 GGTGTCGACCATTGCAT-G----------AAAA-TTTGAAATTTTTTTATCTGAGAAAAGCG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAG-G
* * ** *
652087 GGTGTCGGTCATTGCATGACCAACATAAAAAAATTTTGAAAATTTTTTATCTG-AAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGG
** * *
652147 GAGTGTC-GCCATTGCATGGCCAACA-CAAAAAA-AATGTAATTTTTTTATCTAAAAAAAGGG
1 G-GTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAA-GG
* *
652207 GGTGTCGG----T---TGGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAGAAAATGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGA-AAAAAGG
** * * *
652262 GGTGTCAACCATTGCATGACCAACACCAAAAAATTTTGAAA-ATTTTTATCTGAAAAAGGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGG
* * * *
652322 GGTGTCGGTCATTACATGGCCAACACCAAAAAA---TGTAGTTTTTTTATCTGAAAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTG-AAAAAAGG
* * * *
652381 GGTGTCGACCATTGCATGGCCAACACAAAAAAATTTTGAAAGTTTTTTATCTGAGAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGG
* * *
652442 GGTGTCGGCCATTGCATGACCAACACTAAAAAATTTTGAAATTTTTTTATCTG-CAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGG
652502 GGTGTCGGCCAT
1 GGTGTCGGCCAT
652514 GCAAAAATTT
Statistics
Matches: 494, Mismatches: 61, Indels: 80
0.78 0.10 0.13
Matches are distributed among these distances:
47 4 0.01
48 3 0.01
49 18 0.04
50 16 0.03
53 9 0.02
54 7 0.01
55 24 0.05
56 5 0.01
57 6 0.01
58 57 0.12
59 85 0.17
60 106 0.21
61 90 0.18
62 64 0.13
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (61 bp):
GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGG
Found at i:659336 original size:52 final size:52
Alignment explanation
Indices: 659279--659404 Score: 139
Period size: 52 Copynumber: 2.4 Consensus size: 52
659269 GAAATATTAT
* * * *
659279 CAAATTACACGATG-TATAT-AATGTTAATAGTTAAATCTTTTAGATTCAAGAC
1 CAAATTA-AC-ATGATATATAAATGTTAAGAATTAAATCTTTTAAATTCAAAAC
*
659331 CAAATTAACATGATATATAAATGTTAAGAATTAAATTTTTTAAATTCAAAAC
1 CAAATTAACATGATATATAAATGTTAAGAATTAAATCTTTTAAATTCAAAAC
* * **
659383 CAAACTAATACAATATATAAAT
1 CAAATTAACATGATATATAAAT
659405 ATTGAACGTT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 3 0.05
51 7 0.11
52 53 0.84
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (52 bp):
CAAATTAACATGATATATAAATGTTAAGAATTAAATCTTTTAAATTCAAAAC
Found at i:659417 original size:52 final size:50
Alignment explanation
Indices: 659307--659417 Score: 114
Period size: 52 Copynumber: 2.1 Consensus size: 50
659297 TAATGTTAAT
* * * ** *
659307 AGTTAAATCTTTTAGATTCAAGACCAAATTAACATGATATATAAATGTTA
1 AGTTAAATCTTTTAAATTCAAAACCAAACTAACACAATATATAAATATTA
* *
659357 AGAATTAAATTTTTTAAATTCAAAACCAAACTAATACAATATATAAATATTGA
1 AG--TTAAATCTTTTAAATTCAAAACCAAACTAACACAATATATAAATATT-A
659410 ACGTTAAA
1 A-GTTAAA
659418 ATTATTATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
50 2 0.04
52 44 0.90
53 2 0.04
54 1 0.02
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (50 bp):
AGTTAAATCTTTTAAATTCAAAACCAAACTAACACAATATATAAATATTA
Done.