Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold116
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: 1263769
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 4928 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:302494 original size:16 final size:17
Alignment explanation
Indices: 302470--302501 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
302460 ATTAAATATA
302470 TTTATAAAAAAAATCAT
1 TTTATAAAAAAAATCAT
302487 TTTA-AAAAAAAATCA
1 TTTATAAAAAAAATCA
302502 GAGTCAACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TTTATAAAAAAAATCAT
Found at i:302689 original size:28 final size:30
Alignment explanation
Indices: 302634--302702 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
302624 TATATAGTGA
* *
302634 TTTAAAACAATAACATTTTGATAAATT-AT
1 TTTAAAATAATAACATTTTAATAAATTAAT
* *
302663 TTTAAAATGATAATATTTTAAT-AATTAAT
1 TTTAAAATAATAACATTTTAATAAATTAAT
302692 TTTATAAATAA
1 TTTA-AAATAA
302703 GAATAATTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 4 0.12
29 24 0.73
30 5 0.15
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTAAAATAATAACATTTTAATAAATTAAT
Found at i:303130 original size:2 final size:2
Alignment explanation
Indices: 303123--303156 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
303113 CTGTTTTTCT
303123 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
303157 AAGCTGTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:305631 original size:87 final size:87
Alignment explanation
Indices: 305482--305656 Score: 253
Period size: 87 Copynumber: 2.0 Consensus size: 87
305472 ACAACAGAAA
* *
305482 ATCTGGTCCAATATGCCGACGTAGAATGCAACTAGAACCTGCTAACTCCACAGTTCTCAATTCTC
1 ATCTGGTCCAATATGCCGACGTAGAATCCAACTAGAACCTGCAAACTCCACAGTTCTCAATTCTC
* * *
305547 ATTCTATCTGTCAGATGCATTG
66 ATTCTATATGTAAGACGCATTG
* * * *
305569 ATCTGGTCCAATATGCC-AGCGTAGAATCCAACTAGAATCTGCAAACTTCACGGTTCTTAATTCT
1 ATCTGGTCCAATATGCCGA-CGTAGAATCCAACTAGAACCTGCAAACTCCACAGTTCTCAATTCT
305633 CATTCTATATGTAAGACGCATTG
65 CATTCTATATGTAAGACGCATTG
305656 A
1 A
305657 CCAAGCCTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 1 0.01
87 77 0.99
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (87 bp):
ATCTGGTCCAATATGCCGACGTAGAATCCAACTAGAACCTGCAAACTCCACAGTTCTCAATTCTC
ATTCTATATGTAAGACGCATTG
Found at i:313271 original size:23 final size:21
Alignment explanation
Indices: 313240--313296 Score: 51
Period size: 23 Copynumber: 2.5 Consensus size: 21
313230 TATTAAATAA
*
313240 AAAATAAAATTAATTTAGAATATG
1 AAAA-AAAATTAA--TAAAATATG
313264 AAAAAAAACTTTAATAAAATATG
1 AAAAAAAA--TTAATAAAATATG
*
313287 AAATAAAATT
1 AAAAAAAATT
313297 TCCCTGACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 2 0.07
23 19 0.66
24 4 0.14
25 4 0.14
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAAAAAATTAATAAAATATG
Found at i:316509 original size:20 final size:20
Alignment explanation
Indices: 316484--316522 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
316474 TTTTTTATTT
316484 TTTAAATT-ATTATGAATTAA
1 TTTAAATTGATT-TGAATTAA
316504 TTTAAATTGATTTGAATTA
1 TTTAAATTGATTTGAATTA
316523 TCCATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTAAATTGATTTGAATTAA
Found at i:323195 original size:28 final size:25
Alignment explanation
Indices: 323134--323206 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 25
323124 TAATTATTAA
*
323134 TAATTTATTAATAAAATATTAAATTT
1 TAATTTAATAATAAAA-ATTAAATTT
*
323160 TAATTTTAATAATTAAAATTAAATTCAAT
1 TAA-TTTAATAATAAAAATTAAATT---T
*
323189 TAATTTAATTATAAAAAT
1 TAATTTAATAATAAAAAT
323207 ATTATTAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 11 0.28
27 11 0.28
28 13 0.33
29 4 0.10
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (25 bp):
TAATTTAATAATAAAAATTAAATTT
Found at i:326461 original size:16 final size:17
Alignment explanation
Indices: 326430--326472 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
326420 AAACATAATT
* *
326430 ATAAATATTATATAAAAA
1 ATAAAAATTATA-AAATA
*
326448 ATTAAAATTATAAAATA
1 ATAAAAATTATAAAATA
326465 ATAAAAAT
1 ATAAAAAT
326473 AAATCTAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAAATTATAAAATA
Found at i:330359 original size:17 final size:20
Alignment explanation
Indices: 330315--330355 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
330305 GGTGAAGTAA
330315 ATTAAAGAAAGGGAAACAAT
1 ATTAAAGAAAGGGAAACAAT
330335 ATTAAAGAAAGGGAAACAAT
1 ATTAAAGAAAGGGAAACAAT
330355 A
1 A
330356 AAGATGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.05, G:0.20, T:0.15
Consensus pattern (20 bp):
ATTAAAGAAAGGGAAACAAT
Found at i:331985 original size:13 final size:13
Alignment explanation
Indices: 331940--331986 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
331930 TTTTTATATT
*
331940 TATATTTAA-AAA
1 TATATTAAATAAA
331952 TATATTAAATATAA
1 TATATTAAATA-AA
331966 -ATATTAAATAAA
1 TATATTAAATAAA
*
331978 TATTTTAAA
1 TATATTAAA
331987 AAACAATCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 10 0.33
13 18 0.60
14 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TATATTAAATAAA
Found at i:336982 original size:6 final size:6
Alignment explanation
Indices: 336965--336995 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
336955 TCAACGAGGG
*
336965 GCCATA GTCATA GCCATA GCCATA GCCATA G
1 GCCATA GCCATA GCCATA GCCATA GCCATA G
336996 TGAATCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.19
Consensus pattern (6 bp):
GCCATA
Found at i:337469 original size:3 final size:3
Alignment explanation
Indices: 337461--337486 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
337451 ATCAAATCTT
337461 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
337487 TCAATCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:340377 original size:2 final size:2
Alignment explanation
Indices: 340370--340401 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
340360 TGTGAATGTT
*
340370 GA GA GA GA GA GA GA GA GA GA GA GA GA GT GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
340402 TTGTCATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
GA
Found at i:341447 original size:24 final size:25
Alignment explanation
Indices: 341399--341446 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
341389 TTTAAAAGTT
*
341399 TTTTTAAATAATATAAATAATTTTA
1 TTTTTAAAAAATATAAATAATTTTA
341424 TTTTTAATAAAATA-AAATAATTT
1 TTTTTAA-AAAATATAAATAATTT
341447 AAATTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTTAAAAAATATAAATAATTTTA
Found at i:341873 original size:51 final size:51
Alignment explanation
Indices: 341781--341881 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
341771 CTTAATTTTA
* * *
341781 TTAATTTTAATCTAAAATAAAAAATTTTAATTAATTTATTTAAATTTAAAT
1 TTAATTTTAATCTAAAATAAAAAATTTAAATCAATTAATTTAAATTTAAAT
* *
341832 TTAATTTTAAT-TAAAATTAATAATTTAAAATCAATTAATTTAAATTTAAA
1 TTAATTTTAATCTAAAATAAAAAATTT-AAATCAATTAATTTAAATTTAAA
341882 ATAATTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 13 0.30
51 31 0.70
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (51 bp):
TTAATTTTAATCTAAAATAAAAAATTTAAATCAATTAATTTAAATTTAAAT
Found at i:341878 original size:61 final size:61
Alignment explanation
Indices: 341823--341944 Score: 158
Period size: 61 Copynumber: 2.0 Consensus size: 61
341813 AATTTATTTA
* * *
341823 AATTT-AAAT-TTAATTTTAATTAAAATTAATAATTTAAAATCAATTAATTTAAATTTAAAAT
1 AATTTAAAATATTAAATTTAATT-AAATCAATAATTAAAAAT-AATTAATTTAAATTTAAAAT
* * *
341884 AATTTAAAATATTAAATTTAATTAACTCAATTATTAAAAATAATTAATTTAATTTTAAAAT
1 AATTTAAAATATTAAATTTAATTAAATCAATAATTAAAAATAATTAATTTAAATTTAAAAT
341945 GATACAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
61 24 0.45
62 18 0.34
63 11 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (61 bp):
AATTTAAAATATTAAATTTAATTAAATCAATAATTAAAAATAATTAATTTAAATTTAAAAT
Found at i:341888 original size:31 final size:30
Alignment explanation
Indices: 341850--341944 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 30
341840 AATTAAAATT
341850 AATAATTTAAAATCAATTAATTTAAATTTAA
1 AATAATTTAAAAT-AATTAATTTAAATTTAA
341881 AATAATTTAAAAT-ATTAAATTT-AA-TTAA
1 AATAATTTAAAATAATT-AATTTAAATTTAA
* * *
341909 CTCAATTATTAAAAATAATTAATTTAATTTTAA
1 ---AATAATTTAAAATAATTAATTTAAATTTAA
341942 AAT
1 AAT
341945 GATACAAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
28 4 0.07
29 5 0.09
30 8 0.15
31 29 0.54
32 4 0.07
33 4 0.07
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
AATAATTTAAAATAATTAATTTAAATTTAA
Found at i:341900 original size:7 final size:6
Alignment explanation
Indices: 341818--341904 Score: 51
Period size: 6 Copynumber: 15.0 Consensus size: 6
341808 TAATTAATTT
* * * * *
341818 ATTTAA ATTTAA ATTT-A ATTTTA ATTAAA ATTAATA ATTTAA A-ATCA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTA-A ATTTAA ATTTAA
*
341865 A-TT-A ATTTAA ATTTAA A-AT-A ATTTAAA ATATTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA AT-TTAA ATTTAA
341905 TTAACTCAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
4 4 0.06
5 13 0.20
6 34 0.52
7 12 0.18
8 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:342094 original size:22 final size:22
Alignment explanation
Indices: 342065--342145 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
342055 AAATTAGTAA
* * *
342065 AAATAGTATAAGATTTATTTAT
1 AAATAGTAAAAAATATATTTAT
*
342087 CAATAGTAAAAAATATATTTAT
1 AAATAGTAAAAAATATATTTAT
* *
342109 AAATAATAATTAAAA-ATATATAT
1 AAATAGTAA--AAAATATATTTAT
342132 ACAATAGTAAAAAA
1 A-AATAGTAAAAAA
342146 ATCAAAAAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 29 0.60
23 8 0.17
24 11 0.23
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (22 bp):
AAATAGTAAAAAATATATTTAT
Found at i:343341 original size:21 final size:22
Alignment explanation
Indices: 343305--343350 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
343295 ATGATGTTGG
* *
343305 AATTTGATATTTAAAATAATTA
1 AATTTGATATTTAAAAAAATAA
*
343327 AATTTTATA-TTAAAAAAATAA
1 AATTTGATATTTAAAAAAATAA
343348 AAT
1 AAT
343351 ATTCTTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTTGATATTTAAAAAAATAA
Found at i:343955 original size:22 final size:23
Alignment explanation
Indices: 343915--343957 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
343905 AAATTAAAAA
*
343915 TTAAATTTTAATATTTTTTATTT
1 TTAAATTATAATATTTTTTATTT
343938 TTAAATTATAA-ATTTTTTAT
1 TTAAATTATAATATTTTTTAT
343958 AAAAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTAAATTATAATATTTTTTATTT
Found at i:345159 original size:2 final size:2
Alignment explanation
Indices: 345152--345180 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
345142 TGGTATTACA
345152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
345181 ATGGAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:346389 original size:2 final size:2
Alignment explanation
Indices: 346382--346411 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
346372 TAGAGTTGAG
346382 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
346412 GCATATTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:346851 original size:2 final size:2
Alignment explanation
Indices: 346844--346870 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
346834 CTTCTATAGG
346844 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
346871 ATTTTTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:349631 original size:2 final size:2
Alignment explanation
Indices: 349626--349655 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
349616 GAGTTAAGCC
349626 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
349656 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:352389 original size:2 final size:2
Alignment explanation
Indices: 352384--352425 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
352374 TATATGTGTG
352384 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
352426 AGAAAAGGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:356597 original size:35 final size:36
Alignment explanation
Indices: 356512--356597 Score: 86
Period size: 35 Copynumber: 2.4 Consensus size: 36
356502 TTAAATCAAG
* *
356512 ATTAAATTATTTGAGTAAATTTAATATTGATAATTTAT
1 ATTAAA-TATTT-ATTAAATTTAATATTAATAATTTAT
** * *
356550 ATTTTA-AGTTATTAAATTTAATATTAAT-TTTTAT
1 ATTAAATATTTATTAAATTTAATATTAATAATTTAT
356584 ATTAAATATTTATT
1 ATTAAATATTTATT
356598 TTTTAAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
34 9 0.24
35 22 0.58
36 3 0.08
38 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (36 bp):
ATTAAATATTTATTAAATTTAATATTAATAATTTAT
Found at i:356617 original size:29 final size:29
Alignment explanation
Indices: 356583--356662 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
356573 TTAATTTTTA
*
356583 TATTAAATATTTATTTTTTAAAATTATAT
1 TATTAAATATTTATTTTTTAAAATTAAAT
* *
356612 TATTAAATTTTTA-TTATTAATAATTAAAT
1 TATTAAATATTTATTTTTTAA-AATTAAAT
* *
356641 TATT-TATATTAATTTTATTAAA
1 TATTAAATATTTATTTT-TTAAA
356663 TAATTTTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
28 11 0.27
29 26 0.63
30 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TATTAAATATTTATTTTTTAAAATTAAAT
Found at i:356626 original size:14 final size:14
Alignment explanation
Indices: 356558--356631 Score: 66
Period size: 14 Copynumber: 5.5 Consensus size: 14
356548 ATATTTTAAG
356558 TTATTAAA--TTTA
1 TTATTAAATTTTTA
*
356570 ATATT-AATTTTTA
1 TTATTAAATTTTTA
*
356583 -TATTAAATATTTA
1 TTATTAAATTTTTA
* * *
356596 TTTTTTAAAATTATA
1 -TTATTAAATTTTTA
356611 TTATTAAATTTTTA
1 TTATTAAATTTTTA
356625 TTATTAA
1 TTATTAA
356632 TAATTAAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
11 2 0.04
12 8 0.17
13 11 0.23
14 18 0.38
15 9 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAAATTTTTA
Found at i:356637 original size:21 final size:20
Alignment explanation
Indices: 356567--356653 Score: 72
Period size: 21 Copynumber: 4.2 Consensus size: 20
356557 GTTATTAAAT
356567 TTAAT-ATT-AATTTTTATA
1 TTAATAATTAAATTTTTATA
* * *
356585 TTAA-ATATTTATTTTTTAAAA
1 TTAATA-ATTAAATTTTT-ATA
*
356606 TTATATTATTAAATTTTTATTA
1 TTA-ATAATTAAATTTTTA-TA
356628 TTAATAATTAAATTATTTATA
1 TTAATAATTAAATT-TTTATA
356649 TTAAT
1 TTAAT
356654 TTTATTAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
18 4 0.07
19 3 0.06
20 6 0.11
21 23 0.43
22 18 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATAATTAAATTTTTATA
Found at i:356642 original size:34 final size:31
Alignment explanation
Indices: 356603--356667 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
356593 TTATTTTTTA
356603 AAATTATATTAT-TAAATTTTTATTATTAATAATT
1 AAATTAT-TTATATAAA-TTTTATTA--AATAATT
*
356637 AAATTATTTATATTAATTTTATTAAATAATT
1 AAATTATTTATATAAATTTTATTAAATAATT
356668 TTAATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 7 0.24
33 12 0.41
34 10 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
AAATTATTTATATAAATTTTATTAAATAATT
Found at i:356670 original size:24 final size:22
Alignment explanation
Indices: 356605--356670 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 22
356595 ATTTTTTAAA
356605 ATTATATTATTAAAT-TTTTATT
1 ATTA-ATTATTAAATATTTTATT
*
356627 ATTAATAATTAAAT-TATTTA-T
1 ATTAATTATTAAATAT-TTTATT
356648 ATTAATTTTATTAAATAATTTTA
1 ATTAA--TTATTAAAT-ATTTTA
356671 ATATATATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 16 0.43
22 8 0.22
23 8 0.22
24 4 0.11
25 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTAATTATTAAATATTTTATT
Found at i:356800 original size:25 final size:26
Alignment explanation
Indices: 356763--356814 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
356753 GTTTAATTTT
*
356763 TTTATTATTTAAT-AAAATTAATATAA
1 TTTATTATATAATAAAAATTAA-ATAA
356789 TTTATTA-ATAATAAAAATTAAATAA
1 TTTATTATATAATAAAAATTAAATAA
356814 T
1 T
356815 ATAATTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTATTATATAATAAAAATTAAATAA
Found at i:356823 original size:14 final size:14
Alignment explanation
Indices: 356781--356823 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
356771 TTAATAAAAT
356781 TAATATAATTTATTAA
1 TAATATAATTTA--AA
* *
356797 TAATAAAAATTAAA
1 TAATATAATTTAAA
356811 TAATATAATTTAA
1 TAATATAATTTAA
356824 TAAATTAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 13 0.57
16 10 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATATAATTTAAA
Found at i:357291 original size:2 final size:2
Alignment explanation
Indices: 357284--357315 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
357274 TTAAAAGTCA
357284 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
357316 CCCCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:365172 original size:12 final size:12
Alignment explanation
Indices: 365155--365183 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
365145 ATCTTTCCGA
365155 GAGAGAGAGAGG
1 GAGAGAGAGAGG
365167 GAGAGAGAGAGG
1 GAGAGAGAGAGG
365179 GAGAG
1 GAGAG
365184 GTGGCCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (12 bp):
GAGAGAGAGAGG
Found at i:366717 original size:33 final size:33
Alignment explanation
Indices: 366661--366725 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
366651 TGTGCCACGT
*
366661 AAATATAAATATAAAATAAATTATAAATATGTC
1 AAATATAAACATAAAATAAATTATAAATATGTC
* *
366694 AAATCATAAACAT-AAATATATTATCAATATGT
1 AAAT-ATAAACATAAAATAAATTATAAATATGT
366726 GTAATAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (33 bp):
AAATATAAACATAAAATAAATTATAAATATGTC
Found at i:367358 original size:28 final size:27
Alignment explanation
Indices: 367321--367389 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
367311 TACGGTATGT
*
367321 GATTTCAAATTTAATTT-AATTAATTTAA
1 GATTTAAAATTTAATTTAAATT--TTTAA
367349 GATTTAAAATTTAAATTTAAATTTTTAA
1 GATTTAAAATTT-AATTTAAATTTTTAA
* *
367377 TATTTATAATTTA
1 GATTTAAAATTTA
367390 TTCTCTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 1 0.03
28 26 0.72
29 5 0.14
30 4 0.11
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (27 bp):
GATTTAAAATTTAATTTAAATTTTTAA
Found at i:367359 original size:14 final size:13
Alignment explanation
Indices: 367322--367389 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 13
367312 ACGGTATGTG
*
367322 ATTTCAAATTT-A
1 ATTTAAAATTTAA
367334 ATTTAATTAATTTAA
1 ATTTAA--AATTTAA
367349 GATTTAAAATTTAA
1 -ATTTAAAATTTAA
*
367363 ATTTAAATTTTTAA
1 ATTTAAA-ATTTAA
*
367377 TATTTATAATTTA
1 -ATTTAAAATTTA
367390 TTCTCTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
12 5 0.11
13 7 0.15
14 21 0.46
15 7 0.15
16 6 0.13
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (13 bp):
ATTTAAAATTTAA
Found at i:371270 original size:13 final size:13
Alignment explanation
Indices: 371252--371284 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
371242 ATATATTTAA
371252 AATTTAAAAAGAT
1 AATTTAAAAAGAT
371265 AATTTAAAAAGAT
1 AATTTAAAAAGAT
*
371278 AAGTTAA
1 AATTTAA
371285 GCATGAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (13 bp):
AATTTAAAAAGAT
Found at i:372394 original size:13 final size:12
Alignment explanation
Indices: 372373--372407 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
372363 GAAAAAAGGG
*
372373 GAAAGAAAAAAA
1 GAAAAAAAAAAA
372385 GATAAAAAAAAAA
1 GA-AAAAAAAAAA
372398 GAAAAAAAAA
1 GAAAAAAAAA
372408 TGATAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:377889 original size:28 final size:27
Alignment explanation
Indices: 377834--377904 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
377824 GCCACCCATT
*
377834 TGTTTGTCAAAAATGATGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
*
377861 TGTTTGTAAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
377889 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
377905 AGGCTTGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.03
27 19 0.51
28 17 0.46
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:378022 original size:20 final size:20
Alignment explanation
Indices: 377999--378039 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
377989 CCCTCTCAAG
*
377999 CATCCCTCTCTTGTATCCCT
1 CATCCCTCTCTTATATCCCT
378019 CATCCCTCTCTTATATCCCT
1 CATCCCTCTCTTATATCCCT
378039 C
1 C
378040 TTCAATTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.46, G:0.02, T:0.39
Consensus pattern (20 bp):
CATCCCTCTCTTATATCCCT
Found at i:382215 original size:12 final size:12
Alignment explanation
Indices: 382198--382224 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
382188 GTAATCTTTC
382198 AAATATATAAAA
1 AAATATATAAAA
382210 AAATATATAAAA
1 AAATATATAAAA
382222 AAA
1 AAA
382225 ATTATGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAATATATAAAA
Found at i:385295 original size:43 final size:43
Alignment explanation
Indices: 385230--385317 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
385220 GTAAAAGTCA
*
385230 AATAATGTCAGAGATTTTACGAGTTCTAGATTCCCCCATTTCT
1 AATAATGTCAGAGATTTCACGAGTTCTAGATTCCCCCATTTCT
385273 AATAATGTCAGAGATTTCACGAGTTCTAGATTCCCCCATTTCT
1 AATAATGTCAGAGATTTCACGAGTTCTAGATTCCCCCATTTCT
385316 AA
1 AA
385318 CCCCCCCCCC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.35
Consensus pattern (43 bp):
AATAATGTCAGAGATTTCACGAGTTCTAGATTCCCCCATTTCT
Found at i:390083 original size:17 final size:17
Alignment explanation
Indices: 390063--390098 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
390053 GCTTGATGGA
390063 TGTTGGTGCTTATCTCG
1 TGTTGGTGCTTATCTCG
390080 TGTTGGTGCTTATCTCG
1 TGTTGGTGCTTATCTCG
390097 TG
1 TG
390099 GTCAGACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.06, C:0.17, G:0.31, T:0.47
Consensus pattern (17 bp):
TGTTGGTGCTTATCTCG
Found at i:394076 original size:29 final size:29
Alignment explanation
Indices: 394043--394105 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
394033 CGACCTTTAC
394043 TTTTAAAATAAATCATTAAAATAATATTA
1 TTTTAAAATAAATCATTAAAATAATATTA
* * *
394072 TTTTAAAATTATTTATTAAAATAATATTA
1 TTTTAAAATAAATCATTAAAATAATATTA
394101 TTTTA
1 TTTTA
394106 CTCATCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTTAAAATAAATCATTAAAATAATATTA
Found at i:394630 original size:22 final size:21
Alignment explanation
Indices: 394605--394652 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
394595 CAGCAAATGC
394605 ATTTTATATTAAAATATCTAAA
1 ATTTTATATT-AAATATCTAAA
* * *
394627 ATTTTATGTTTAATATTTAAA
1 ATTTTATATTAAATATCTAAA
394648 ATTTT
1 ATTTT
394653 TTAAAATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
ATTTTATATTAAATATCTAAA
Found at i:394740 original size:174 final size:174
Alignment explanation
Indices: 394223--394742 Score: 501
Period size: 174 Copynumber: 3.0 Consensus size: 174
394213 TTTTTTAATT
* * *
394223 TATTATTTTATAAATTT-TT--TCCTAATAAATATATTTTATTATTAAAATAT-TTAAATTATTT
1 TATTATTTTAT-AATTTGTTAATCC-AACAAATACATTTTATTATTAAAATATCTAAAATTATTT
* * * * *
394284 GATAAATATTTAAAAATTATTAAAACCTAAAATTATAG-AAAAAAAATTTTTATGCTTCAA-AAA
64 GATAAATATTTAAAAATTTTTAAAATCTAAAATTAT-GTAATAAAATTTTTTTTGCTT-AAGAAA
* * *
394347 ATATTGTATTTTAATATGAAAATATCAATATATATTTTTTTTT-GAGACC
127 CTATTGTATTTTAATACGAAAATATCAAT-T-TATTTTTTTTTCAAGACC
* * * *
394396 TATTATTTTGTAGTTTGTTAATCCAATAAATACATTTTTATTATTAATATATCTAAAATTATTTG
1 TATTATTTTATAATTTGTTAATCCAACAAATACA-TTTTATTATTAAAATATCTAAAATTATTTG
*
394461 ATAAATATTTAAAAATTTTCAAAATCTAAAATTA--T-ATAAAATGGTTTTTTTACGCTTAAGAA
65 ATAAATATTTAAAAATTTTTAAAATCTAAAATTATGTAATAAAAT--TTTTTTT--GCTTAAGAA
** * * *
394523 ACTATCATATTTTAATAC-AAAAGCATCAATTTATATATTTTTTCAAGACT
126 ACTATTGTATTTTAATACGAAAA-TATCAATTTAT-TTTTTTTTCAAGACC
* * * *
394573 TGTTATTTTATAATTTTTTAA-CCAGCAAATGCATTTTA-TATTAAAATATCTAAAATT-TTATG
1 TATTATTTTATAATTTGTTAATCCAACAAATACATTTTATTATTAAAATATCTAAAATTATT-TG
* * * * *
394635 TTTAATATTTAAAATTTTTTAAAATCTACAATTATGTAATACAAATTTTTTTTGCTTGAGAAACT
65 ATAAATATTTAAAAATTTTTAAAATCTAAAATTATGTAATA-AAATTTTTTTTGCTTAAGAAACT
* * *
394700 ATTGTATTTTAATACGAAATTTTTAATTTACTTTTTTTTTCAA
129 ATTGTATTTTAATACGAAAATATCAATTTA-TTTTTTTTTCAA
394743 AAAATTATAT
Statistics
Matches: 286, Mismatches: 40, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
172 4 0.01
173 19 0.07
174 99 0.35
175 37 0.13
176 73 0.26
177 50 0.17
178 4 0.01
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (174 bp):
TATTATTTTATAATTTGTTAATCCAACAAATACATTTTATTATTAAAATATCTAAAATTATTTGA
TAAATATTTAAAAATTTTTAAAATCTAAAATTATGTAATAAAATTTTTTTTGCTTAAGAAACTAT
TGTATTTTAATACGAAAATATCAATTTATTTTTTTTTCAAGACC
Found at i:394952 original size:30 final size:28
Alignment explanation
Indices: 394893--394952 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 28
394883 TTCATTTTAT
** *
394893 ATAATTTTAGATTTTAAAAATTTAGTGA
1 ATAATTTTAGATTTTAAAAATAAAATGA
*
394921 ATAATTTTAGATATTTTAATAATAAAATGA
1 ATAATTTTAG--ATTTTAAAAATAAAATGA
394951 AT
1 AT
394953 TTACGAGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 10 0.38
30 16 0.62
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (28 bp):
ATAATTTTAGATTTTAAAAATAAAATGA
Found at i:395325 original size:29 final size:29
Alignment explanation
Indices: 395283--395344 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
395273 TTACGTGAAC
*
395283 AAATAATATTATTTTGATAAATAATTTTA
1 AAATAATATCATTTTGATAAATAATTTTA
* *
395312 AAATAATATCATTTTGATAATTTATTTTA
1 AAATAATATCATTTTGATAAATAATTTTA
395341 AAAT
1 AAAT
395345 TAAAGTTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (29 bp):
AAATAATATCATTTTGATAAATAATTTTA
Found at i:397472 original size:25 final size:25
Alignment explanation
Indices: 397437--397493 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
397427 TTAAAATATG
397437 TTTTATAATAAATATAAATATT-TTTA
1 TTTTATAATAAA-AT-AATATTATTTA
397463 TTTT-TAATAAAATAATATTATTTA
1 TTTTATAATAAAATAATATTATTTA
*
397487 GTTTATA
1 TTTTATA
397494 TTAATATATC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 6 0.21
24 9 0.32
25 9 0.32
26 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TTTTATAATAAAATAATATTATTTA
Found at i:398384 original size:2 final size:2
Alignment explanation
Indices: 398371--398415 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
398361 TTGCTCTGCA
*
398371 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
398413 TC T
1 TC T
398416 TAAAGTACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:399807 original size:13 final size:13
Alignment explanation
Indices: 399785--399815 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
399775 ATCTAAAAAT
*
399785 ATATTGAACATAA
1 ATATTAAACATAA
399798 ATATTAAACATAA
1 ATATTAAACATAA
399811 ATATT
1 ATATT
399816 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (13 bp):
ATATTAAACATAA
Found at i:404493 original size:2 final size:2
Alignment explanation
Indices: 404488--404520 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
404478 TATATATATA
404488 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
404521 ATATATAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:404837 original size:2 final size:2
Alignment explanation
Indices: 404830--404860 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
404820 AAGGTGTGCG
404830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
404861 CATTGAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:418806 original size:50 final size:50
Alignment explanation
Indices: 418705--418954 Score: 247
Period size: 50 Copynumber: 5.0 Consensus size: 50
418695 ATTTGTTAAT
* ** * *
418705 TATTCTTCATCAATTTTTGATAATC-AAGAGAGGTGAC-GTAATTATTGAC
1 TATTCTTCACCAACCTTTGACAATCGAA-AGAGGTGACTGTAATTGTTGAC
** * *
418754 TATTCTTCACTGATCTTTGACAATCGAAAGAGATGACTGTAATTGTTGAC
1 TATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACTGTAATTGTTGAC
* * * *
418804 TATTCTTCACCAACCTTTGACAATCGAGAGAAGTGACTGTAATTATTAAC
1 TATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACTGTAATTGTTGAC
** * * *
418854 TATTCTTCACCAATTTTTGACAATAGATAGAGGTG-GTCGTAATTGTTGAC
1 TATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACT-GTAATTGTTGAC
* * * *
418904 TATTCTCCACCAACCTTTGACAATAGAGAA-AGGTGGCTGTCATTGTTGAC
1 TATTCTTCACCAACCTTTGACAATCGA-AAGAGGTGACTGTAATTGTTGAC
418954 T
1 T
418955 TTAAACAACT
Statistics
Matches: 167, Mismatches: 29, Indels: 9
0.81 0.14 0.04
Matches are distributed among these distances:
49 29 0.17
50 136 0.81
51 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (50 bp):
TATTCTTCACCAACCTTTGACAATCGAAAGAGGTGACTGTAATTGTTGAC
Found at i:418876 original size:100 final size:99
Alignment explanation
Indices: 418705--418932 Score: 287
Period size: 100 Copynumber: 2.3 Consensus size: 99
418695 ATTTGTTAAT
* ** * * * * **
418705 TATTCTTCATCAATTTTTGATAATCAAGAGAGGTGACGTAATTATTGACTATTCTTCACTGATCT
1 TATTCTTCACCAACCTTTGACAATCGAGAGAAGTGACGTAATTATTAACTATTCTTCACCAATCT
*
418770 TTGACAATCGAAAGAGATGACT-GTAATTGTTGAC
66 TTGACAATAGAAAGAGATG-CTCGTAATTGTTGAC
*
418804 TATTCTTCACCAACCTTTGACAATCGAGAGAAGTGACTGTAATTATTAACTATTCTTCACCAATT
1 TATTCTTCACCAACCTTTGACAATCGAGAGAAGTGAC-GTAATTATTAACTATTCTTCACCAATC
* * *
418869 TTTGACAATAGATAGAGGTGGTCGTAATTGTTGAC
65 TTTGACAATAGAAAGAGATGCTCGTAATTGTTGAC
* *
418904 TATTCTCCACCAACCTTTGACAATAGAGA
1 TATTCTTCACCAACCTTTGACAATCGAGA
418933 AAGGTGGCTG
Statistics
Matches: 111, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
99 32 0.29
100 79 0.71
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (99 bp):
TATTCTTCACCAACCTTTGACAATCGAGAGAAGTGACGTAATTATTAACTATTCTTCACCAATCT
TTGACAATAGAAAGAGATGCTCGTAATTGTTGAC
Found at i:421789 original size:50 final size:50
Alignment explanation
Indices: 421720--421880 Score: 241
Period size: 50 Copynumber: 3.2 Consensus size: 50
421710 TAAGTGGGAG
* * * *
421720 AATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAAGTGGCCAT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGT
* *
421770 AATTGTTGACTATTATTCACCAACCTTTGACAATAAAGAGAGGTGACCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGT
* * *
421820 AATTGTTGACTATTCTTCACTAATCTTTGACAATAGAGAGAGGTGATCGT
1 AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGT
421870 AATTGTTGACT
1 AATTGTTGACT
421881 TTAAACAACT
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 100 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
AATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCGT
Found at i:426692 original size:20 final size:20
Alignment explanation
Indices: 426667--426704 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
426657 TTTTCTTACC
* *
426667 AAAAAAGAAAAGAAAGTTAA
1 AAAAAAAAAAAAAAAGTTAA
426687 AAAAAAAAAAAAAAAGTT
1 AAAAAAAAAAAAAAAGTT
426705 GGCAGGATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAGTTAA
Found at i:428045 original size:2 final size:2
Alignment explanation
Indices: 428038--428076 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
428028 AGAAGCTTAT
*
428038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
428077 GGCATATTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:429712 original size:20 final size:20
Alignment explanation
Indices: 429665--429712 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
429655 TTAATTGGCT
*
429665 GGTTTGTGTACAAAAACAAA
1 GGTTTGTTTACAAAAACAAA
429685 GGTTTGTTTACAAAAACAAA
1 GGTTTGTTTACAAAAACAAA
429705 GGTTTGTT
1 GGTTTGTT
429713 GGTTGCGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (20 bp):
GGTTTGTTTACAAAAACAAA
Found at i:433403 original size:2 final size:2
Alignment explanation
Indices: 433396--433420 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
433386 CAGTTGAAAA
433396 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
433421 AAAACCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:433452 original size:3 final size:3
Alignment explanation
Indices: 433444--433483 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
433434 AAATCTTAAG
433444 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
433484 GGATTTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:448463 original size:21 final size:21
Alignment explanation
Indices: 448438--448479 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
448428 TCCTTGTTCA
*
448438 TGCCAGGCCTTCCAATCAAGC
1 TGCCAGGCCCTCCAATCAAGC
*
448459 TGCCAGGCCCTCCGATCAAGC
1 TGCCAGGCCCTCCAATCAAGC
448480 ACCGGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.17
Consensus pattern (21 bp):
TGCCAGGCCCTCCAATCAAGC
Found at i:448794 original size:69 final size:69
Alignment explanation
Indices: 448706--448846 Score: 228
Period size: 69 Copynumber: 2.0 Consensus size: 69
448696 GTTATATTGA
*
448706 AATCAATTACACAGCTTTTCGTCAATAAACCAGCATTTGTAATTTTAATATCGCTTCGAATAAAA
1 AATCAATTACACAGCTTTTCGTCAATAAACCAGCATTTGCAATTTTAATATCGCTTCGAATAAAA
448771 ATCG
66 ATCG
* * * *
448775 AATCAATTAGACAGTTTTTCGTCAATAAACCAGCATTTGCAATTTTAATATTGCTTCGAATACAA
1 AATCAATTACACAGCTTTTCGTCAATAAACCAGCATTTGCAATTTTAATATCGCTTCGAATAAAA
*
448840 ATGG
66 ATCG
448844 AAT
1 AAT
448847 TGAACAATGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (69 bp):
AATCAATTACACAGCTTTTCGTCAATAAACCAGCATTTGCAATTTTAATATCGCTTCGAATAAAA
ATCG
Found at i:452068 original size:4 final size:4
Alignment explanation
Indices: 452028--452058 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
452018 GCGCTCACCT
*
452028 TTTA CTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
452059 GCTATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:456797 original size:106 final size:106
Alignment explanation
Indices: 456612--456827 Score: 396
Period size: 106 Copynumber: 2.0 Consensus size: 106
456602 TACAACATGC
456612 AATTACTCGGCTATTCTATATACGTCCCAACCGAGAGAGACAATCAAGGATACAGATTGATTAGC
1 AATTACTCGGCTATTCTATATACGTCCCAACCGAGAGAGACAATCAAGGATACAGATTGATTAGC
*
456677 TTCAGAAAAATCAATTCAGGAATTAGGTGGAGTTTTAAATG
66 TTCAGAAAAATCAATTAAGGAATTAGGTGGAGTTTTAAATG
* *
456718 AATTACTCGGCTATTCTATATATGTCCCAACCGAGAGAGACAATTAAGGATACAGATTGATTAGC
1 AATTACTCGGCTATTCTATATACGTCCCAACCGAGAGAGACAATCAAGGATACAGATTGATTAGC
*
456783 TTCAGAAAATTCAATTAAGGAATTAGGTGGAGTTTTAAATG
66 TTCAGAAAAATCAATTAAGGAATTAGGTGGAGTTTTAAATG
456824 AATT
1 AATT
456828 TGGAGAGAAC
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (106 bp):
AATTACTCGGCTATTCTATATACGTCCCAACCGAGAGAGACAATCAAGGATACAGATTGATTAGC
TTCAGAAAAATCAATTAAGGAATTAGGTGGAGTTTTAAATG
Found at i:459292 original size:5 final size:5
Alignment explanation
Indices: 459282--459312 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
459272 CCCAAAAAAG
459282 ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA A
1 ATCAA ATCAA ATCAA ATCAA ATCAA ATCAA A
459313 AGAGTACAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
ATCAA
Found at i:460048 original size:18 final size:18
Alignment explanation
Indices: 460016--460058 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
460006 ATAGTATATA
*
460016 TATTTATTTTATTATTAT
1 TATTTATTTTATTATAAT
460034 TATTTATTATT-TTATAAT
1 TATTTATT-TTATTATAAT
*
460052 TTTTTAT
1 TATTTAT
460059 GAATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTATTTTATTATAAT
Found at i:460544 original size:10 final size:10
Alignment explanation
Indices: 460518--460550 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
460508 TATTTTTAAG
*
460518 TATAATATTA
1 TATAATTTTA
460528 T-TAATTTTA
1 TATAATTTTA
460537 TATAATTTTA
1 TATAATTTTA
460547 TATA
1 TATA
460551 TAATTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TATAATTTTA
Found at i:461533 original size:12 final size:12
Alignment explanation
Indices: 461500--461538 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
461490 TTAATTAATT
*
461500 ATATAATTTTTA
1 ATATAATATTTA
461512 TATAATAATATTTA
1 -AT-ATAATATTTA
461526 ATATAATATTTA
1 ATATAATATTTA
461538 A
1 A
461539 ATTTATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 11 0.46
13 4 0.17
14 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATAATATTTA
Found at i:465534 original size:21 final size:22
Alignment explanation
Indices: 465499--465543 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
465489 ATTTTTACTC
**
465499 TTTTATTTTTGTAAA-GTAAAT
1 TTTTATTTTAATAAATGTAAAT
*
465520 TTTTATTTTAATAAATTTAAAT
1 TTTTATTTTAATAAATGTAAAT
465542 TT
1 TT
465544 AAATATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTTATTTTAATAAATGTAAAT
Found at i:473541 original size:2 final size:2
Alignment explanation
Indices: 473534--473560 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
473524 TTCATTGAAT
473534 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
473561 TTTTTTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:475708 original size:30 final size:30
Alignment explanation
Indices: 475672--475732 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
475662 AACATACTTA
475672 TCAAGGTACCTTCTTTAGTCAGATATTCAC
1 TCAAGGTACCTTCTTTAGTCAGATATTCAC
475702 TCAAGGTACCTTCTTTAGTCAGATATTCAC
1 TCAAGGTACCTTCTTTAGTCAGATATTCAC
475732 T
1 T
475733 GGAATAGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (30 bp):
TCAAGGTACCTTCTTTAGTCAGATATTCAC
Found at i:482173 original size:32 final size:33
Alignment explanation
Indices: 482114--482188 Score: 109
Period size: 32 Copynumber: 2.2 Consensus size: 33
482104 TCAATTTACA
482114 ATATTATATATTTATATAAATTATTAATATATTA-
1 ATATT-TAT-TTTATATAAATTATTAATATATTAT
482148 ATAATTTATTTTATATAAATT-TTAATATATTAT
1 AT-ATTTATTTTATATAAATTATTAATATATTAT
482181 ATATTTAT
1 ATATTTAT
482189 ATAATATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
32 17 0.44
33 14 0.36
34 5 0.13
35 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
ATATTTATTTTATATAAATTATTAATATATTAT
Found at i:482205 original size:32 final size:32
Alignment explanation
Indices: 482113--482205 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 32
482103 ATCAATTTAC
*
482113 AATATTATATATTTATATAAATTATTAATATATT
1 AATATTATATATTTATATAAATT-TTAAT-TAAT
482147 AATAATT-TAT-TTTATATAAA--TT--TTAAT
1 AAT-ATTATATATTTATATAAATTTTAATTAAT
482174 -ATATTATATATTTATATAATATTTTAATTAAT
1 AATATTATATATTTATATAA-ATTTTAATTAAT
482206 TGTTTAAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
25 3 0.06
26 5 0.10
27 12 0.24
28 2 0.04
30 4 0.08
32 5 0.10
33 10 0.20
34 6 0.12
35 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
AATATTATATATTTATATAAATTTTAATTAAT
Found at i:482934 original size:2 final size:2
Alignment explanation
Indices: 482929--482960 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
482919 CATTTTTTAA
482929 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
482961 CACAAGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:483323 original size:12 final size:11
Alignment explanation
Indices: 483250--483325 Score: 64
Period size: 12 Copynumber: 6.6 Consensus size: 11
483240 TAATAATTTA
483250 TATATTTATAT
1 TATATTTATAT
*
483261 TATATTTAAAT
1 TATATTTATAT
*
483272 TATTTTTTATAT
1 TA-TATTTATAT
*
483284 TATCTTTTATAT
1 TAT-ATTTATAT
483296 ATATATTT-TAT
1 -TATATTTATAT
*
483307 CATATTTAATAT
1 TATATTT-ATAT
*
483319 AATATTT
1 TATATTT
483326 TAGCTTTGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
10 6 0.11
11 16 0.30
12 29 0.54
13 3 0.06
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTTATAT
Found at i:488791 original size:20 final size:20
Alignment explanation
Indices: 488760--488818 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
488750 AAATGAATGT
* *
488760 TATATATGTATATGTATATG
1 TATATATATATATATATATG
*
488780 TATATGTATATATATATATG
1 TATATATATATATATATATG
*
488800 TGTATATATATATATATAT
1 TATATATATATATATATAT
488819 ATATGCCTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (20 bp):
TATATATATATATATATATG
Found at i:488793 original size:2 final size:2
Alignment explanation
Indices: 488760--488822 Score: 72
Period size: 2 Copynumber: 31.5 Consensus size: 2
488750 AAATGAATGT
* * * * * *
488760 TA TA TA TG TA TA TG TA TA TG TA TA TG TA TA TA TA TA TA TG TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
488802 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
488823 GCCTGCAAGA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.51
Consensus pattern (2 bp):
TA
Found at i:491005 original size:13 final size:13
Alignment explanation
Indices: 490987--491011 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
490977 AGGTATAAAC
490987 AAATATAAAATTT
1 AAATATAAAATTT
491000 AAATATAAAATT
1 AAATATAAAATT
491012 ACATGTAATT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATATAAAATTT
Found at i:491063 original size:33 final size:32
Alignment explanation
Indices: 490999--491064 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 32
490989 ATATAAAATT
* *
490999 TAAATATAAAATTACATGTAATTTAAAATTTAA
1 TAAATATAAAA-TAAATATAATTTAAAATTTAA
491032 TAAATATAAAA-AAATATAATATTAAACATTTAA
1 TAAATATAAAATAAATATAAT-TTAAA-ATTTAA
491065 ATTAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 7 0.24
32 5 0.17
33 17 0.59
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (32 bp):
TAAATATAAAATAAATATAATTTAAAATTTAA
Found at i:491867 original size:15 final size:15
Alignment explanation
Indices: 491814--491884 Score: 69
Period size: 15 Copynumber: 4.7 Consensus size: 15
491804 TTTATCACAA
491814 TTAATTATAATAATAT
1 TTAA-TATAATAATAT
491830 TTAATAT-AT-ATAT
1 TTAATATAATAATAT
*
491843 TAAAATTATAATAATAT
1 T-TAA-TATAATAATAT
491860 TTAATATATATAAT-T
1 TTAATATA-ATAATAT
491875 TTAATA-AATA
1 TTAATATAATA
491885 TGGTATAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
13 8 0.17
14 5 0.10
15 17 0.35
16 13 0.27
17 5 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAATATAATAATAT
Found at i:492455 original size:13 final size:13
Alignment explanation
Indices: 492419--492456 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
492409 TTTTTTTATA
492419 AAAAAATTATAAT
1 AAAAAATTATAAT
*
492432 ATTAAAA-TATAAT
1 A-AAAAATTATAAT
492445 AAAAAATTATAA
1 AAAAAATTATAA
492457 ATTTTATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 4 0.19
13 13 0.62
14 4 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAATTATAAT
Found at i:492519 original size:26 final size:25
Alignment explanation
Indices: 492471--492519 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
492461 TATAGTTTAA
* *
492471 ATTTTAAATTTAATAAATTAATATT
1 ATTTTAAAATTAATAAATAAATATT
492496 ATTTTAAAATTAATAATATAAATA
1 ATTTTAAAATTAATAA-ATAAATA
492520 AATTAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTTTAAAATTAATAAATAAATATT
Found at i:492542 original size:34 final size:33
Alignment explanation
Indices: 492482--492548 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 33
492472 TTTTAAATTT
492482 AATAAATTAATATTATTTTAAAATTAATAATATA
1 AATAAATTAATATTATTTTAAAATTAAT-ATATA
*
492516 AATAAATTAA-ATTAAATTTT-ATATTAATATATA
1 AATAAATTAATATT--ATTTTAAAATTAATATATA
492549 CAAGATAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 8 0.27
34 17 0.57
35 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AATAAATTAATATTATTTTAAAATTAATATATA
Found at i:492915 original size:16 final size:16
Alignment explanation
Indices: 492890--492924 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
492880 CATGTTGTTT
492890 TAAATAT-AAAAAAAG
1 TAAATATAAAAAAAAG
492905 TAAATTATAAAAAAAAG
1 TAAA-TATAAAAAAAAG
492922 TAA
1 TAA
492925 TGTAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 3 0.17
17 11 0.61
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
TAAATATAAAAAAAAG
Found at i:494566 original size:3 final size:3
Alignment explanation
Indices: 494558--494592 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
494548 GATCAAACTT
*
494558 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
494593 CAATTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:495301 original size:2 final size:2
Alignment explanation
Indices: 495280--495319 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
495270 CAATTCATAC
*
495280 TA TA T- TA TA T- TA TT TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
495319 T
1 T
495320 GTGTTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:496912 original size:18 final size:18
Alignment explanation
Indices: 496889--496923 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
496879 GTCGCAGTTT
* *
496889 CAGCTACTGAAGCAACAG
1 CAGCTAATGAAACAACAG
496907 CAGCTAATGAAACAACA
1 CAGCTAATGAAACAACA
496924 AAATGCATCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (18 bp):
CAGCTAATGAAACAACAG
Found at i:510392 original size:36 final size:37
Alignment explanation
Indices: 510344--510418 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 37
510334 CGAGCTTCAT
* **
510344 TTTATTATTATTATTAATTTAAAATTTTATTTTATTA
1 TTTATTATTATTATTAAATTAAAAAATTATTTTATTA
510381 TTTATTA-TATTATTAAATTAAAAAATTATTTTATTA
1 TTTATTATTATTATTAAATTAAAAAATTATTTTATTA
510417 TT
1 TT
510419 AAAATAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 28 0.80
37 7 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (37 bp):
TTTATTATTATTATTAAATTAAAAAATTATTTTATTA
Found at i:510393 original size:20 final size:22
Alignment explanation
Indices: 510346--510395 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
510336 AGCTTCATTT
510346 TATTATTATTATTAATTTAAAA
1 TATTATTATTATTAATTTAAAA
* **
510368 TTTTATT-TTATT-ATTTATTA
1 TATTATTATTATTAATTTAAAA
510388 TATTATTA
1 TATTATTA
510396 AATTAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 12 0.52
21 5 0.22
22 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTATTATTATTAATTTAAAA
Found at i:515255 original size:56 final size:56
Alignment explanation
Indices: 515169--515280 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
515159 GAGTTTGCCA
515169 TAACTCAAGAATCCAACTTCGTACATGAATACGGATCTTAATTCAGGGGGACATAT
1 TAACTCAAGAATCCAACTTCGTACATGAATACGGATCTTAATTCAGGGGGACATAT
* *
515225 TAACTCAAGAATCCAACTTTGTACATGAATACGGATCTTAATTCAGGGGGAGATAT
1 TAACTCAAGAATCCAACTTCGTACATGAATACGGATCTTAATTCAGGGGGACATAT
515281 AACCCTACTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (56 bp):
TAACTCAAGAATCCAACTTCGTACATGAATACGGATCTTAATTCAGGGGGACATAT
Found at i:516573 original size:20 final size:20
Alignment explanation
Indices: 516545--516606 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
516535 ATTTTAAAAA
*
516545 ATATATTTTATTATATTTAT
1 ATATTTTTTATTATATTTAT
516565 ATATTTTTTATTATA-TTAT
1 ATATTTTTTATTATATTTAT
*
516584 ATATTTTTACATTATATTTAT
1 ATATTTTT-TATTATATTTAT
516605 AT
1 AT
516607 TTATTTTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 12 0.32
20 20 0.53
21 6 0.16
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
ATATTTTTTATTATATTTAT
Found at i:516795 original size:12 final size:11
Alignment explanation
Indices: 516776--516805 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
516766 TTCCTTCCCT
516776 TTTCCTTTCTC
1 TTTCCTTTCTC
516787 TTTCTCTTTCTC
1 TTTC-CTTTCTC
516799 TTTCCTT
1 TTTCCTT
516806 GAGGGGGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTCCTTTCTC
Found at i:518599 original size:21 final size:21
Alignment explanation
Indices: 518575--518630 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
518565 TATATTTTTC
518575 ATTAAAAATAATAATTATATT
1 ATTAAAAATAATAATTATATT
518596 ATTAAAAA-AATTTAA-TATATT
1 ATTAAAAATAA--TAATTATATT
518617 A-TAAAAAT-ATAATT
1 ATTAAAAATAATAATT
518631 TTTAAAGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
18 3 0.10
19 1 0.03
20 9 0.29
21 15 0.48
22 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAAAAATAATAATTATATT
Found at i:518622 original size:18 final size:18
Alignment explanation
Indices: 518575--518629 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
518565 TATATTTTTC
*
518575 ATTAAAAATAATAATTATATT
1 ATTAAAAA-AAT-ATAATA-T
*
518596 ATTAAAAAAATTTAATAT
1 ATTAAAAAAATATAATAT
*
518614 ATTATAAAAATATAAT
1 ATTAAAAAAATATAAT
518630 TTTTAAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 15 0.50
19 4 0.13
20 3 0.10
21 8 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTAAAAAAATATAATAT
Found at i:520585 original size:58 final size:58
Alignment explanation
Indices: 520515--520632 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
520505 CTTCTTCCAG
520515 TAAGAACAACTTTCTTTTGATTTTGCTCTTTGCTAATCTCTATCAATTATGTATCAAT
1 TAAGAACAACTTTCTTTTGATTTTGCTCTTTGCTAATCTCTATCAATTATGTATCAAT
*
520573 TAAGAACAACTTTCTTTTGATTTTTCTCTTTGCTAATCTCTATCAATTATGTATCAAT
1 TAAGAACAACTTTCTTTTGATTTTGCTCTTTGCTAATCTCTATCAATTATGTATCAAT
520631 TA
1 TA
520633 TTAGGTGAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (58 bp):
TAAGAACAACTTTCTTTTGATTTTGCTCTTTGCTAATCTCTATCAATTATGTATCAAT
Found at i:521607 original size:23 final size:24
Alignment explanation
Indices: 521573--521623 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
521563 TTATGAACAT
521573 TTTTAGTAAATAACCTCTTTTTC-
1 TTTTAGTAAATAACCTCTTTTTCA
*
521596 TTTTAGTTAATAACCTCTTTTTCA
1 TTTTAGTAAATAACCTCTTTTTCA
521620 TTTT
1 TTTT
521624 TGCAGGGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTAGTAAATAACCTCTTTTTCA
Found at i:525610 original size:19 final size:19
Alignment explanation
Indices: 525586--525635 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
525576 TTAACAAGTA
* *
525586 TTTTTAATATTTTATAAAT
1 TTTTTAATAATTTAAAAAT
525605 TTTTT-ATGAATTTAAAAAT
1 TTTTTAAT-AATTTAAAAAT
*
525624 TTTTAAATAATT
1 TTTTTAATAATT
525636 ATATTCTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 22 0.85
20 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTAATAATTTAAAAAT
Found at i:527773 original size:2 final size:2
Alignment explanation
Indices: 527766--527800 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
527756 TATCCAAATC
527766 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
527801 TTCACTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:528717 original size:3 final size:3
Alignment explanation
Indices: 528709--528733 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
528699 AAGCTTAAGG
528709 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
528734 AAGCTGTTTA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:529864 original size:21 final size:22
Alignment explanation
Indices: 529840--529883 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
529830 TAAAAATAAG
* *
529840 TAAAAT-TAATTTAATTTTATA
1 TAAAATATAAGTTAATGTTATA
529861 T-AAATATAAGTTAATGTTATA
1 TAAAATATAAGTTAATGTTATA
529882 TA
1 TA
529884 TTATTAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
TAAAATATAAGTTAATGTTATA
Found at i:532532 original size:2 final size:2
Alignment explanation
Indices: 532525--532568 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
532515 ATGTTAATTT
*
532525 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
532567 TA
1 TA
532569 GATTAAGCGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:534080 original size:19 final size:20
Alignment explanation
Indices: 534032--534080 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
534022 ATAAATTAAT
*
534032 AATATATTAAAATTTTATATA
1 AATATA-TAAAATTTTATAAA
* *
534053 AATAAATAATATTTTA-AAA
1 AATATATAAAATTTTATAAA
534072 AATATATAA
1 AATATATAA
534081 CATAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 10 0.42
20 9 0.38
21 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATATAAAATTTTATAAA
Found at i:534085 original size:28 final size:28
Alignment explanation
Indices: 534020--534086 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
534010 TATTTATATA
* **
534020 ATATAAATTAATAATATATTAAAATTTT
1 ATATAAATAAATAATATATTAAAATAAT
*
534048 ATATAAATAAATAATATTTTAAAA-AAT
1 ATATAAATAAATAATATATTAAAATAAT
534075 ATATAACATAAA
1 ATATAA-ATAAA
534087 AAATTTAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 7 0.21
28 27 0.79
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (28 bp):
ATATAAATAAATAATATATTAAAATAAT
Found at i:535186 original size:2 final size:2
Alignment explanation
Indices: 535179--535212 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
535169 GACGACCATC
* *
535179 TA TA TA TA TA TA TA TA TA TA TA TA AA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
535213 ATAAATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:535219 original size:4 final size:4
Alignment explanation
Indices: 535200--535233 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
535190 ATATATATAT
*
535200 ATAA ATAA ATATA ATAA ATAA ATAA ACAA ATAA A
1 ATAA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA A
535234 CGGTGGGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:535222 original size:17 final size:18
Alignment explanation
Indices: 535190--535225 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
535180 ATATATATAT
*
535190 ATATATATATATAAATAA
1 ATATATATAAATAAATAA
535208 ATATA-ATAAATAAATAA
1 ATATATATAAATAAATAA
535225 A
1 A
535226 CAAATAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATATATAAATAAATAA
Found at i:540624 original size:19 final size:20
Alignment explanation
Indices: 540591--540646 Score: 89
Period size: 18 Copynumber: 2.9 Consensus size: 20
540581 TCGGTAAAAC
540591 ATTAAAATTTTAATTTTAAGT
1 ATTAAAA-TTTAATTTTAAGT
540612 ATTAAAA-TTAA-TTTAAGT
1 ATTAAAATTTAATTTTAAGT
540630 ATTAAAATTTAATTTTA
1 ATTAAAATTTAATTTTA
540647 TAATTAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 14 0.42
19 8 0.24
20 4 0.12
21 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
ATTAAAATTTAATTTTAAGT
Found at i:540652 original size:19 final size:19
Alignment explanation
Indices: 540591--540653 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
540581 TCGGTAAAAC
540591 ATTAAAATTTTAATTTTA-A
1 ATTAAAA-TTTAATTTTATA
*
540610 GTATTAAAA-TTAATTTAAGT-
1 --ATTAAAATTTAATTTTA-TA
540630 ATTAAAATTTAATTTTATA
1 ATTAAAATTTAATTTTATA
540649 ATTAA
1 ATTAA
540654 TAAAAAAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 8 0.22
19 21 0.58
21 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
ATTAAAATTTAATTTTATA
Found at i:545878 original size:2 final size:2
Alignment explanation
Indices: 545871--545910 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
545861 GATGTTATTA
545871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
545911 TAACTGTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:546295 original size:22 final size:22
Alignment explanation
Indices: 546248--546300 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
546238 TATATAATTT
546248 ATATTTTAA-TTTAATTATAAA
1 ATATTTTAATTTTAATTATAAA
*
546269 CTATTTTAATTTTAA-TATAAAA
1 ATATTTTAATTTTAATTAT-AAA
546291 ATATTTTAAT
1 ATATTTTAAT
546301 ATTTTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTTTAATTTTAATTATAAA
Found at i:554619 original size:104 final size:104
Alignment explanation
Indices: 554418--554625 Score: 249
Period size: 104 Copynumber: 2.0 Consensus size: 104
554408 TGGTCTATTT
** * * * *
554418 AGTTTGTTTAATTGAAAATTAACTTAATCAAATTTAATATTAGAATCGATTGATATCAATTTTCA
1 AGTTTGTTTAATCAAAAACTAACTTAACCAAATTTAATATCAAAATCGATTGATATCAATTTTCA
* * * *
554483 AATCGAAAAAACAGAATCGATATTATGATCGATTGGTTC
66 AATCGAAAAAACAGAATCGACATCAAGATCGATCGGTTC
* *
554522 AGTTTGTTTAATCAAAAACTAATTTAACCAAATTTAGTATCAAAATCGATTGATATCAAATTTT-
1 AGTTTGTTTAATCAAAAACTAACTTAACCAAATTTAATATCAAAATCGATTGATATC-AATTTTC
* * *
554586 AAATCGAAAAAATAGAA-CTTACATCAAGGTCGATCGGTTC
65 AAATCGAAAAAACAGAATC-GACATCAAGATCGATCGGTTC
554626 GGTTGATTTT
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
103 1 0.01
104 80 0.92
105 6 0.07
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (104 bp):
AGTTTGTTTAATCAAAAACTAACTTAACCAAATTTAATATCAAAATCGATTGATATCAATTTTCA
AATCGAAAAAACAGAATCGACATCAAGATCGATCGGTTC
Found at i:554662 original size:14 final size:14
Alignment explanation
Indices: 554643--554670 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
554633 TTTTTTAATT
554643 TTAAATATATTTTA
1 TTAAATATATTTTA
554657 TTAAATATATTTTA
1 TTAAATATATTTTA
554671 AATATTAATT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:555105 original size:17 final size:16
Alignment explanation
Indices: 555059--555107 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
555049 ATTAAGTCAA
*
555059 TAAATTTAAACTATCTTT
1 TAAATTTAAA-TA-ATTT
*
555077 TATATTTAAATAATTT
1 TAAATTTAAATAATTT
555093 TAAATTATAAATAAT
1 TAAATT-TAAATAAT
555108 ATATTCAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 8 0.30
17 10 0.37
18 9 0.33
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATTTAAATAATTT
Found at i:555433 original size:34 final size:34
Alignment explanation
Indices: 555390--555458 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
555380 AAACGAATTG
555390 GGCTGTGTCGGCCCATCACCAGGTATATCAAGTA
1 GGCTGTGTCGGCCCATCACCAGGTATATCAAGTA
*
555424 GGCTGTGTCGGTCCATCACCAGGTATATCAAGTA
1 GGCTGTGTCGGCCCATCACCAGGTATATCAAGTA
555458 G
1 G
555459 CCCAAAACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (34 bp):
GGCTGTGTCGGCCCATCACCAGGTATATCAAGTA
Found at i:559499 original size:2 final size:2
Alignment explanation
Indices: 559492--559544 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
559482 GCGACCTTTT
559492 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
559534 TA TA TA TA TA T
1 TA TA TA TA TA T
559545 GTCTTTGATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:560336 original size:12 final size:12
Alignment explanation
Indices: 560318--560351 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
560308 CTACGCTAGA
560318 ATATATATATGT
1 ATATATATATGT
*
560330 GTATATATATGT
1 ATATATATATGT
560342 ATATATATAT
1 ATATATATAT
560352 AAAGTGTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
ATATATATATGT
Done.