Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold37
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: 836391
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:320151 original size:21 final size:22
Alignment explanation
Indices: 320108--320152 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
320098 AAGTTAAATA
* *
320108 TAAAAATTATTTTTTTATTTTT
1 TAAAAATTATTTTTATATGTTT
*
320130 TAAAAA-TATTTTTATCTGTTT
1 TAAAAATTATTTTTATATGTTT
320151 TA
1 TA
320153 TTGTCTGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TAAAAATTATTTTTATATGTTT
Found at i:325177 original size:51 final size:51
Alignment explanation
Indices: 325027--325245 Score: 228
Period size: 51 Copynumber: 4.3 Consensus size: 51
325017 GAAATAATGA
** * * *
325027 GGTTGGAGTATCATCGATTGTGAAAAATTGGTGTTTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTG-TTTTAGAAATAAAATCGG
* * *
325079 AGTTGGAGGATCCCCGATTAAAGGAAAATT-GATGTTTT-GAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-ATGGAAAATTAG-TGTTTTAG-AAATAAAATCGG
* *
325131 GGTTGGAATATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAATCGG
* * * * **
325182 GGTTGGAGTATCCCCGATTAT-GAGAAATCAATATTTTGGAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTATGGA-AAATTAGTGTTTTAGAAATAAAATCGG
325233 GGTTGGAGTATCC
1 GGTTGGAGTATCC
325246 TTTCGGAGGT
Statistics
Matches: 141, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
50 2 0.01
51 80 0.57
52 50 0.35
53 9 0.06
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAATCGG
Found at i:325291 original size:27 final size:27
Alignment explanation
Indices: 325255--325307 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
325245 CTTTCGGAGG
*
325255 TAACGGGGTCGGAGTATCCCCGATGAT
1 TAACGGGGTCGGAGTATCCCCAATGAT
325282 TAACGGGGTCGGAGTATCCCCAATGA
1 TAACGGGGTCGGAGTATCCCCAATGA
325308 AAAATTGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.21
Consensus pattern (27 bp):
TAACGGGGTCGGAGTATCCCCAATGAT
Found at i:325427 original size:51 final size:51
Alignment explanation
Indices: 325365--325477 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
325355 AAATAACGGG
* ** *
325365 GTTGGAATATCCCCGATTGTGA-AAAGTCAGTGCTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAGAAAGTCA-TGCTTTGGAAATAAAACCGGA
* * *
325416 GTTGGAGTATCCCCGATTAAGAGAAATTGATGTTTTGGAAATAAAACCGGA
1 GTTGGAGTATCCCCGATTAAGAGAAAGTCATGCTTTGGAAATAAAACCGGA
*
325467 ATTGGAGTATC
1 GTTGGAGTATC
325478 GTTTCGAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 48 0.91
52 5 0.09
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTAAGAGAAAGTCATGCTTTGGAAATAAAACCGGA
Found at i:325551 original size:131 final size:130
Alignment explanation
Indices: 325309--325560 Score: 294
Period size: 131 Copynumber: 1.9 Consensus size: 130
325299 CCCCAATGAA
** * * *
325309 AAATTGATGTTTTAAAAATAAAACCGGGGTTGGAGTGTCCCTTCAGAAATAACGGGGTTGGAATA
1 AAATTGATGTTTTAAAAATAAAACCGGAATTGGAGTATCCCTTCAAAAATAACGGGGTCGGAATA
* * * * *
325374 TCCCCGATTGTGAAAAGTCAGTGCTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAG
66 TCCCCGATTATGAAAAGTCAATACTTTAGAAATAAAAGCGGAGTTGGAGTATCCCCGATTAAGAG
** ** *
325439 AAATTGATGTTTTGGAAATAAAACCGGAATTGGAGTATCGTTTCGAAAAATAACGGGGTCGGAGT
1 AAATTGATGTTTTAAAAATAAAACCGGAATTGGAGTATCCCTTC-AAAAATAACGGGGTCGGAAT
* *
325504 ATCCCCGATTATGAGAAA-TCAATATTTTA-AGAAT-AAAGCAGGGGTTGGAGTATCCCC
65 ATCCCCGATTATGA-AAAGTCAATACTTTAGA-AATAAAAGC-GGAGTTGGAGTATCCCC
325561 TCGAAAATAA
Statistics
Matches: 101, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
130 42 0.42
131 56 0.55
132 3 0.03
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.27
Consensus pattern (130 bp):
AAATTGATGTTTTAAAAATAAAACCGGAATTGGAGTATCCCTTCAAAAATAACGGGGTCGGAATA
TCCCCGATTATGAAAAGTCAATACTTTAGAAATAAAAGCGGAGTTGGAGTATCCCCGATTAAGAG
Found at i:325552 original size:80 final size:79
Alignment explanation
Indices: 325419--325584 Score: 190
Period size: 80 Copynumber: 2.1 Consensus size: 79
325409 AATCGGAGTT
** * * * ***
325419 GGAGTATCCCCGATTAAGAGAAATTGATGTTTTGGAAATAAAACCGGAATTGGAGTATCGTTTCG
1 GGAGTATCCCCGATTAAGAGAAATCAATATTTTAGAAATAAAACAGGAATTGGAGTATCCCCTCG
325484 AAAAATAACGGGGTC
66 -AAAATAACGGGGTC
* * **
325499 GGAGTATCCCCGATTATGAGAAATCAATATTTTA-AGAATAAAGCAGGGGTTGGAGTATCCCCTC
1 GGAGTATCCCCGATTAAGAGAAATCAATATTTTAGA-AATAAAACAGGAATTGGAGTATCCCCTC
*
325563 GAAAATAACGGGGTT
65 GAAAATAACGGGGTC
325578 GGAGTAT
1 GGAGTAT
325585 TCCGATGATT
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
79 21 0.29
80 51 0.71
ACGTcount: A:0.34, C:0.13, G:0.27, T:0.26
Consensus pattern (79 bp):
GGAGTATCCCCGATTAAGAGAAATCAATATTTTAGAAATAAAACAGGAATTGGAGTATCCCCTCG
AAAATAACGGGGTC
Found at i:325624 original size:27 final size:27
Alignment explanation
Indices: 325544--325644 Score: 143
Period size: 27 Copynumber: 3.7 Consensus size: 27
325534 GAATAAAGCA
* *
325544 GGGGTTGGAGTATCCCCTCGA-AAATAAC
1 GGGGTTGGAGTAT-CCC-CGATGATTAAC
*
325572 GGGGTTGGAGTAT-TCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGATGATTAAC
325598 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGATGATTAAC
325625 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
325645 TGTGAAAAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
25 3 0.04
26 19 0.28
27 32 0.48
28 13 0.19
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.26
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGATGATTAAC
Found at i:325743 original size:51 final size:52
Alignment explanation
Indices: 325628--325749 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 52
325618 GATTAACGGG
* * *
325628 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTGGAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTTGAAAATAAAATCGAA
*
325681 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTTGAAAATAAAATCGAA
* *
325732 GTTGGAATATCCTCGATT
1 GTTGGAGTATCCCCGATT
325750 GCGGAGAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
51 33 0.53
52 1 0.02
53 28 0.45
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.34
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTTGAAAATAAAATCGAA
Found at i:328138 original size:13 final size:13
Alignment explanation
Indices: 328120--328179 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
328110 ACAAAGATTG
328120 ATGTATCGATACA
1 ATGTATCGATACA
328133 ATGTATCGATAC-
1 ATGTATCGATACA
* *
328145 AT-T-TC-CT-TA
1 ATGTATCGATACA
328154 ATGTATCGATACA
1 ATGTATCGATACA
328167 ATGTATCGATACA
1 ATGTATCGATACA
328180 TTTCCTTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
9 3 0.08
10 3 0.08
11 3 0.08
12 3 0.08
13 26 0.68
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:328163 original size:34 final size:34
Alignment explanation
Indices: 328120--328200 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
328110 ACAAAGATTG
328120 ATGTATCGATACAATGTATCGATACATTTCCTTA
1 ATGTATCGATACAATGTATCGATACATTTCCTTA
328154 ATGTATCGATACAATGTATCGATACATTTCCTTA
1 ATGTATCGATACAATGTATCGATACATTTCCTTA
328188 ATGTATCGATACA
1 ATGTATCGATACA
328201 TTTCCTTGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.37
Consensus pattern (34 bp):
ATGTATCGATACAATGTATCGATACATTTCCTTA
Found at i:328192 original size:21 final size:21
Alignment explanation
Indices: 328166--328207 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
328156 GTATCGATAC
328166 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
328187 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
328208 GGTAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:328271 original size:13 final size:13
Alignment explanation
Indices: 328253--328277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
328243 ACAAAACTTA
328253 TGTATCGATACAT
1 TGTATCGATACAT
328266 TGTATCGATACA
1 TGTATCGATACA
328278 ACACTAATAT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:328292 original size:19 final size:21
Alignment explanation
Indices: 328268--328317 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
328258 CGATACATTG
328268 TATCGATACA-ACACT-AATA
1 TATCGATACATACACTGAATA
**
328287 TATCGATACATTTACTGAATA
1 TATCGATACATACACTGAATA
328308 TATCGATACA
1 TATCGATACA
328318 GATTATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 10 0.37
20 3 0.11
21 14 0.52
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (21 bp):
TATCGATACATACACTGAATA
Found at i:329618 original size:5 final size:5
Alignment explanation
Indices: 329608--329646 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
329598 GCTTTTACAG
*
329608 TTTGT TTTGT TTTGT TTTAT TTTAGT TTTGT TTTAGT TT
1 TTTGT TTTGT TTTGT TTTGT TTT-GT TTTGT TTT-GT TT
329647 CTTTCATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 22 0.73
6 8 0.27
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (5 bp):
TTTGT
Found at i:329637 original size:16 final size:15
Alignment explanation
Indices: 329612--329642 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
329602 TTACAGTTTG
329612 TTTTGTTTTGTTTTA
1 TTTTGTTTTGTTTTA
329627 TTTTAGTTTTGTTTTA
1 TTTT-GTTTTGTTTTA
329643 GTTTCTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.10, C:0.00, G:0.13, T:0.77
Consensus pattern (15 bp):
TTTTGTTTTGTTTTA
Found at i:329641 original size:11 final size:11
Alignment explanation
Indices: 329611--329646 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
329601 TTTACAGTTT
329611 GTTTTGTTTT-
1 GTTTTGTTTTA
*
329621 GTTTTATTTTA
1 GTTTTGTTTTA
329632 GTTTTGTTTTA
1 GTTTTGTTTTA
329643 GTTT
1 GTTT
329647 CTTTCATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.08, C:0.00, G:0.17, T:0.75
Consensus pattern (11 bp):
GTTTTGTTTTA
Found at i:340258 original size:13 final size:15
Alignment explanation
Indices: 340240--340272 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
340230 ATTTATTCAG
340240 ATATAATT-TT-AAT
1 ATATAATTGTTAAAT
340253 ATATAATTGTTAAAT
1 ATATAATTGTTAAAT
340268 ATATA
1 ATATA
340273 TAATATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 2 0.11
15 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATATAATTGTTAAAT
Found at i:340458 original size:16 final size:16
Alignment explanation
Indices: 340433--340463 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
340423 TTGGATTGAC
340433 AATAAAAAATAATAAA
1 AATAAAAAATAATAAA
*
340449 AATAATAAATAATAA
1 AATAAAAAATAATAA
340464 CGCTGTAAAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AATAAAAAATAATAAA
Found at i:340496 original size:32 final size:32
Alignment explanation
Indices: 340455--340517 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
340445 TAAAAATAAT
340455 AAATAATAACGCTGTAAAAAAAGATGGATTAA
1 AAATAATAACGCTGTAAAAAAAGATGGATTAA
340487 AAATAATAACGCTGTAAAAAAAGATGGATTA
1 AAATAATAACGCTGTAAAAAAAGATGGATTA
340518 CAGAATGGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22
Consensus pattern (32 bp):
AAATAATAACGCTGTAAAAAAAGATGGATTAA
Found at i:340506 original size:17 final size:17
Alignment explanation
Indices: 340455--340506 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
340445 TAAAAATAAT
340455 AAATAATAACGCTGTAA
1 AAATAATAACGCTGTAA
* ** *
340472 AAA-AAGATGGAT-TAA
1 AAATAATAACGCTGTAA
340487 AAATAATAACGCTGTAA
1 AAATAATAACGCTGTAA
340504 AAA
1 AAA
340507 AAGATGGATT
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
15 6 0.24
16 10 0.40
17 9 0.36
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.21
Consensus pattern (17 bp):
AAATAATAACGCTGTAA
Found at i:348677 original size:6 final size:6
Alignment explanation
Indices: 348668--348716 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
348658 TTTATTAAAA
* *
348668 AAATAT AAATAT ATA-AT AAAT-T AAATAT AATTAT -AATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
348713 AAAT
1 AAAT
348717 TATTTTATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 13 0.36
6 23 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
AAATAT
Found at i:348688 original size:11 final size:11
Alignment explanation
Indices: 348669--348714 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
348659 TTATTAAAAA
348669 AATATAAATATAT
1 AATAT-AAT-TAT
348682 AATA-AATTA-
1 AATATAATTAT
348691 AATATAATTAT
1 AATATAATTAT
*
348702 AATATAAATAT
1 AATATAATTAT
348713 AA
1 AA
348715 ATTATTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 4 0.13
10 7 0.23
11 15 0.50
13 4 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATAATTAT
Found at i:348693 original size:22 final size:23
Alignment explanation
Indices: 348668--348716 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
348658 TTTATTAAAA
348668 AAATATAAATAT-ATAATAAAT-T
1 AAATATAAATATAAT-ATAAATAT
*
348690 AAATATAATTATAATATAAATAT
1 AAATATAAATATAATATAAATAT
348713 AAAT
1 AAAT
348717 TATTTTATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAATATAAATATAATATAAATAT
Found at i:349076 original size:29 final size:28
Alignment explanation
Indices: 349009--349098 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
348999 CTTGGGCTTT
*
349009 TTTATTTTTTAAATTTATAATA---ATA
1 TTTATTTTTTAAAATTATAATATTTATA
*
349034 -TTATTTATTAAAAATTATAATTATTTATA
1 TTTATTT-TTTAAAATTATAA-TATTTATA
* *
349063 TTTATTTTTTAAAATTTTTAAAATTTATA
1 TTTATTTTTTAAAA-TTATAATATTTATA
349092 TTTATTT
1 TTTATTT
349099 ATTACTGAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
24 6 0.11
25 11 0.21
26 2 0.04
29 23 0.43
30 11 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTATTTTTTAAAATTATAATATTTATA
Found at i:349583 original size:27 final size:27
Alignment explanation
Indices: 349543--349611 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 27
349533 AAAATAAATT
349543 TATTATTTAATTTA-TAAAAAAACTGTAAA
1 TATTATTT--TTTATTAAAAAAA-TGTAAA
*
349572 T-TTATATTTTTATTTAAAAAAATTTAAA
1 TATTAT-TTTTTA-TTAAAAAAATGTAAA
349600 TATTATTTTTTA
1 TATTATTTTTTA
349612 ATAATAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
27 4 0.11
28 16 0.46
29 15 0.43
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (27 bp):
TATTATTTTTTATTAAAAAAATGTAAA
Found at i:349597 original size:22 final size:24
Alignment explanation
Indices: 349568--349633 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
349558 AAAAAAACTG
349568 TAAATTT-ATATTTTTATTTAA-AA
1 TAAATTTAATATTTTT-TTTAATAA
349591 -AAATTTAAATATTATTTTTTAATAA
1 TAAATTT-AATATT-TTTTTTAATAA
349616 TAAATTTAATATTTTTTT
1 TAAATTTAATATTTTTTT
349634 AATTTTGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
22 6 0.16
24 15 0.39
25 11 0.29
26 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TAAATTTAATATTTTTTTTAATAA
Found at i:349605 original size:29 final size:28
Alignment explanation
Indices: 349537--349611 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 28
349527 TTAATTAAAA
*
349537 TAAATTTATTATTTAATTTATAAAAAAACTG
1 TAAATTTATT-TTTTA-TT-TAAAAAAACTG
*
349568 TAAATTTATATTTTTATTTAAAAAAA-TT
1 TAAATTTAT-TTTTTATTTAAAAAAACTG
349596 TAAATATTATTTTTTA
1 TAAAT-TTATTTTTTA
349612 ATAATAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 12 0.30
29 12 0.30
30 2 0.05
31 13 0.32
32 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (28 bp):
TAAATTTATTTTTTATTTAAAAAAACTG
Found at i:349608 original size:26 final size:26
Alignment explanation
Indices: 349543--349634 Score: 64
Period size: 25 Copynumber: 3.4 Consensus size: 26
349533 AAAATAAATT
* *
349543 TATTATTTAATTTATAAAAAAACTGTAAA
1 TATTATTTTA-TT-TAAAAAAA-TTTAAA
*
349572 TTTATATTTTTATTTAAAAAAATTTAAA
1 TAT-TA-TTTTATTTAAAAAAATTTAAA
349600 TATTA-TTT-TTTAATAATAAATTT-AA
1 TATTATTTTATTTAA-AA-AAATTTAAA
*
349625 TATTTTTTTA
1 TATTATTTTA
349635 ATTTTGATTG
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
24 5 0.10
25 11 0.21
26 9 0.17
27 2 0.04
28 7 0.13
29 10 0.19
30 4 0.08
31 4 0.08
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (26 bp):
TATTATTTTATTTAAAAAAATTTAAA
Found at i:349967 original size:17 final size:17
Alignment explanation
Indices: 349940--349990 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
349930 ATTATCATTT
*
349940 TAATATTAATTTTTTTA
1 TAATATAAATTTTTTTA
* *
349957 TCATATAAA--TTATTA
1 TAATATAAATTTTTTTA
*
349972 TAATATAAGTTTTTTTA
1 TAATATAAATTTTTTTA
349989 TA
1 TA
349991 GGGTATAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
15 12 0.46
17 14 0.54
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATATAAATTTTTTTA
Found at i:351020 original size:2 final size:2
Alignment explanation
Indices: 351013--351051 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
351003 TATTTTACTG
351013 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
351052 GTAAAAGTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:351288 original size:15 final size:15
Alignment explanation
Indices: 351268--351300 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
351258 CCCCAAACTC
351268 TTTTATTCTTTTA-TT
1 TTTTATT-TTTTAGTT
351283 TTTTATTTTTTAGTT
1 TTTTATTTTTTAGTT
351298 TTT
1 TTT
351301 GTCAGAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTATTTTTTAGTT
Found at i:351439 original size:20 final size:20
Alignment explanation
Indices: 351365--351445 Score: 62
Period size: 20 Copynumber: 4.1 Consensus size: 20
351355 GATGATTTTC
*
351365 TTAATTTGA--TAATTTTAA
1 TTAATTTGATTTAATTTAAA
* * *
351383 TT-ATTTAATTAAATTTTTAA
1 TTAATTTGATTTAA-TTTAAA
*
351403 -TAATTTTATTATAAATTTAAA
1 TTAATTTGATT-T-AATTTAAA
351424 TTAATTTGATTTAATTTAAA
1 TTAATTTGATTTAATTTAAA
351444 TT
1 TT
351446 TATATTTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
17 5 0.10
18 2 0.04
19 3 0.06
20 23 0.46
21 6 0.12
22 11 0.22
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTAATTTGATTTAATTTAAA
Found at i:351448 original size:37 final size:35
Alignment explanation
Indices: 351407--351494 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 35
351397 TTTTAATAAT
*
351407 TTTATTATAAATTTAAATTAATTTGATTTAATTTAAA
1 TTTATTATAAAATTAAA--AATTTGATTTAATTTAAA
* * *
351444 TTTATATTTAATAATTAAAAATTTTATTTTATTTAAA
1 TTTAT-TATAA-AATTAAAAATTTGATTTAATTTAAA
351481 TTTAATTATAAAAT
1 TTT-ATTATAAAAT
351495 ATATAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
36 3 0.07
37 28 0.65
38 6 0.14
39 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (35 bp):
TTTATTATAAAATTAAAAATTTGATTTAATTTAAA
Found at i:351458 original size:20 final size:18
Alignment explanation
Indices: 351433--351484 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
351423 ATTAATTTGA
351433 TTTAATTTAAATTTATAT
1 TTTAATTTAAATTTATAT
*
351451 TTAATAATTAAAAATTT-TAT
1 TT--TAATT-TAAATTTATAT
351471 TTT-ATTTAAATTTA
1 TTTAATTTAAATTTA
351485 ATTATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
16 6 0.21
17 3 0.11
18 3 0.11
20 10 0.36
21 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAATTTAAATTTATAT
Found at i:351511 original size:14 final size:14
Alignment explanation
Indices: 351492--351554 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 14
351482 TTAATTATAA
351492 AATATATAAATATT
1 AATATATAAATATT
* *
351506 AATATAAAAATTTT
1 AATATATAAATATT
*
351520 AATAT-T--TTATT
1 AATATATAAATATT
*
351531 AAT-TATAAATAAT
1 AATATATAAATATT
351544 AA-ATATAAATA
1 AATATATAAATA
351555 ATATGAATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
10 1 0.03
11 7 0.18
13 13 0.34
14 17 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATAAATATT
Found at i:351715 original size:19 final size:19
Alignment explanation
Indices: 351691--351735 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
351681 TTTAATTTTA
* *
351691 AAATTTTTAAAAATTAATT
1 AAATTTTAAAAAATCAATT
*
351710 AAA-TTTAAAAAATCGATT
1 AAATTTTAAAAAATCAATT
351728 AAATTTTA
1 AAATTTTA
351736 TATAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
AAATTTTAAAAAATCAATT
Found at i:352715 original size:15 final size:16
Alignment explanation
Indices: 352697--352735 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
352687 CTATTTCTTC
*
352697 AATTTTTTCT-TCTCT
1 AATTTTTTATATCTCT
*
352712 AATTTTTTATATTTCT
1 AATTTTTTATATCTCT
352728 AATTTTTT
1 AATTTTTT
352736 GTCACTCTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (16 bp):
AATTTTTTATATCTCT
Found at i:353053 original size:20 final size:21
Alignment explanation
Indices: 353030--353077 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
353020 TGATTTAAAT
353030 TAATT-TTTTTAAAAAAATTA
1 TAATTATTTTTAAAAAAATTA
*
353050 TAATTATTTTTTAAAAAA-TA
1 TAATTATTTTTAAAAAAATTA
*
353070 TATTTATT
1 TAATTATT
353078 ATAACTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAATTATTTTTAAAAAAATTA
Found at i:353530 original size:20 final size:20
Alignment explanation
Indices: 353507--353545 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
353497 TAATAATTTT
* *
353507 TTATTAATTTATTAAATATG
1 TTATAAATTAATTAAATATG
353527 TTATAAATTAATTAAATAT
1 TTATAAATTAATTAAATAT
353546 AAATTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TTATAAATTAATTAAATATG
Found at i:353961 original size:5 final size:5
Alignment explanation
Indices: 353943--354003 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
353933 ATACGAAAAA
*
353943 ATAATT ATAAT ATATT ATAAT ATAA- A-AA- ATAAT ATATAT ATAAT ATAA-
1 ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT
353991 AT-AT ATAAAT ATA
1 ATAAT AT-AAT ATA
354004 TCAAAAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
3 4 0.09
4 7 0.15
5 23 0.49
6 13 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:353973 original size:28 final size:29
Alignment explanation
Indices: 353938--353995 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
353928 ATATGATACG
*
353938 AAAAAATAAT-TATAATATATTAT-AATAT
1 AAAAAATAATATAT-ATATAATATAAATAT
353966 AAAAAATAATATATATATAATATAAATAT
1 AAAAAATAATATATATATAATATAAATAT
353995 A
1 A
353996 TAAATATATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAAAATAATATATATATAATATAAATAT
Found at i:353988 original size:23 final size:24
Alignment explanation
Indices: 353949--354004 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
353939 AAAAATAATT
353949 ATAATATAT-TATAATATAAA-AA
1 ATAATATATATATAATATAAATAA
*
353971 ATAATATATATATAATATAAATAT
1 ATAATATATATATAATATAAATAA
353995 ATAA-ATATAT
1 ATAATATATAT
354005 CAAAAATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 9 0.29
23 17 0.55
24 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATAATATATATATAATATAAATAA
Found at i:354001 original size:28 final size:28
Alignment explanation
Indices: 353911--353995 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 28
353901 TAATTATAAT
* *
353911 ATAATTATACAATATAAATATGATACGAAAAA
1 ATAATTAT--AATAT-AATATAATA-TAAAAA
*
353943 ATAATTATAATATATTATAATATAAAAA
1 ATAATTATAATATAATATAATATAAAAA
353971 ATAA-TATATATATAATATAAATATA
1 ATAATTATA-ATATAATAT-AATATA
353996 TAAATATATC
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
27 4 0.09
28 17 0.36
29 13 0.28
30 5 0.11
32 8 0.17
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (28 bp):
ATAATTATAATATAATATAATATAAAAA
Found at i:354925 original size:20 final size:23
Alignment explanation
Indices: 354883--354925 Score: 56
Period size: 20 Copynumber: 2.0 Consensus size: 23
354873 TATATATTTT
*
354883 ATAATATTATAATTATATTTAAA
1 ATAATATTATAATTATATGTAAA
354906 ATAAT-TTAT-ATT-TATGTAAA
1 ATAATATTATAATTATATGTAAA
354926 TTTTAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 4 0.21
23 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATAATATTATAATTATATGTAAA
Found at i:354951 original size:21 final size:22
Alignment explanation
Indices: 354925--354973 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
354915 ATTTATGTAA
354925 ATTTTAA-TATATTAATAATAT
1 ATTTTAATTATATTAATAATAT
* * *
354946 ATTTTAATTATTTTTATATTAT
1 ATTTTAATTATATTAATAATAT
354968 ATTTTA
1 ATTTTA
354974 TTTTAATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTAATTATATTAATAATAT
Found at i:354976 original size:18 final size:18
Alignment explanation
Indices: 354953--354997 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
354943 TATATTTTAA
354953 TTATTTTTATATTA-TATT
1 TTATTTTTATATTACT-TT
354971 TTA-TTTTA-ATTACTTT
1 TTATTTTTATATTACTTT
354987 TTATATTTTAT
1 TTAT-TTTTAT
354998 GCATATGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 9 0.39
17 6 0.26
18 8 0.35
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTTTATATTACTTT
Found at i:355372 original size:17 final size:17
Alignment explanation
Indices: 355340--355377 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
355330 TTAAATCAAG
*
355340 TTTAAATTTTTTATTTAA
1 TTTAAATTTATTATTT-A
355358 TTTAAA-TTATTATTTA
1 TTTAAATTTATTATTTA
355374 TTTA
1 TTTA
355378 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 8 0.42
18 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTAAATTTATTATTTA
Found at i:355393 original size:20 final size:21
Alignment explanation
Indices: 355344--355398 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
355334 ATCAAGTTTA
*
355344 AATTTTTTATTTAATTTAAAT
1 AATTTTTTATTTAATTAAAAT
* *
355365 TATTATTTATTT-ATTAAAAT
1 AATTTTTTATTTAATTAAAAT
*
355385 AATTTTTTACTTAA
1 AATTTTTTATTTAA
355399 ATTTATTATA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
AATTTTTTATTTAATTAAAAT
Found at i:355443 original size:18 final size:20
Alignment explanation
Indices: 355417--355453 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
355407 TAAAAATATA
*
355417 TTAATATTA-ATTA-ATTTT
1 TTAAAATTATATTATATTTT
355435 TTAAAATTATATTATATTT
1 TTAAAATTATATTATATTT
355454 AAAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 4 0.25
20 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAAAATTATATTATATTTT
Found at i:361409 original size:20 final size:20
Alignment explanation
Indices: 361384--361422 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
361374 TTTACTGACC
361384 ATTCATATATTTATGTTATA
1 ATTCATATATTTATGTTATA
*
361404 ATTCATGTATTTATGTTAT
1 ATTCATATATTTATGTTAT
361423 GTTTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (20 bp):
ATTCATATATTTATGTTATA
Found at i:361506 original size:18 final size:20
Alignment explanation
Indices: 361462--361507 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 20
361452 ATTTAAGATA
361462 TATTATATTTATATAAATTTT
1 TATTATA-TTATATAAATTTT
*
361483 GA-TATATTA-AT-AATTTT
1 TATTATATTATATAAATTTT
361500 TATTATAT
1 TATTATAT
361508 GAATTTTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 7 0.32
18 7 0.32
19 3 0.14
20 4 0.18
21 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTATATTATATAAATTTT
Found at i:365198 original size:17 final size:17
Alignment explanation
Indices: 365176--365208 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
365166 AGATTTATAT
365176 ATTTAATTTTTAATTTA
1 ATTTAATTTTTAATTTA
*
365193 ATTTAATTTTTTATTT
1 ATTTAATTTTTAATTT
365209 TTAAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTAATTTTTAATTTA
Found at i:365651 original size:18 final size:16
Alignment explanation
Indices: 365620--365655 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
365610 ATTTTAATAA
365620 ATTAATATTTATATTT
1 ATTAATATTTATATTT
365636 ATTAATATAATTATATTT
1 ATTAATAT--TTATATTT
365654 AT
1 AT
365656 GATGCATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTAATATTTATATTT
Found at i:366956 original size:23 final size:23
Alignment explanation
Indices: 366925--366980 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
366915 GACGTCTTCC
**
366925 AGGGATTTTTTGGTTTAAGGATT
1 AGGGATTTTTTTATTTAAGGATT
*
366948 A-GGATTTTTTTATTTAGGGATT
1 AGGGATTTTTTTATTTAAGGATT
366970 AGGGATTTTTT
1 AGGGATTTTTT
366981 CTTTGGTAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 19 0.66
23 10 0.34
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (23 bp):
AGGGATTTTTTTATTTAAGGATT
Found at i:373787 original size:16 final size:16
Alignment explanation
Indices: 373763--373797 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
373753 TCGAATAAAT
* *
373763 TTTATTTTAAATTTAA
1 TTTAATTTAAACTTAA
373779 TTTAATTTAAACTTAA
1 TTTAATTTAAACTTAA
373795 TTT
1 TTT
373798 TGGTCACGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAATTTAAACTTAA
Found at i:374037 original size:2 final size:2
Alignment explanation
Indices: 374030--374061 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
374020 TAAGGGGTCG
374030 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
374062 TTAAAATAAA
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:375346 original size:15 final size:15
Alignment explanation
Indices: 375326--375358 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
375316 CACTCAAATT
375326 AATCGGGTTCATGTC
1 AATCGGGTTCATGTC
375341 AATCGGGTTCATGTC
1 AATCGGGTTCATGTC
375356 AAT
1 AAT
375359 TAGGTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (15 bp):
AATCGGGTTCATGTC
Found at i:375364 original size:15 final size:15
Alignment explanation
Indices: 375326--375364 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
375316 CACTCAAATT
*
375326 AATCGGGTTCATGTC
1 AATCAGGTTCATGTC
*
375341 AATCGGGTTCATGTC
1 AATCAGGTTCATGTC
*
375356 AATTAGGTT
1 AATCAGGTT
375365 TAAAACTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (15 bp):
AATCAGGTTCATGTC
Found at i:385223 original size:21 final size:21
Alignment explanation
Indices: 385199--385242 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
385189 GAATGAAACG
*
385199 ATGTATTGGTTGGATGGAAAA
1 ATGTATTGGTTGGATGAAAAA
**
385220 ATGTATTTTTTGGATGAAAAA
1 ATGTATTGGTTGGATGAAAAA
385241 AT
1 AT
385243 ATAACTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (21 bp):
ATGTATTGGTTGGATGAAAAA
Found at i:385251 original size:21 final size:21
Alignment explanation
Indices: 385208--385251 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
385198 GATGTATTGG
* * **
385208 TTGGATGGAAAAATGTATTTT
1 TTGGATGAAAAAATATAACTT
385229 TTGGATGAAAAAATATAACTT
1 TTGGATGAAAAAATATAACTT
385250 TT
1 TT
385252 AATAACCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (21 bp):
TTGGATGAAAAAATATAACTT
Found at i:386909 original size:2 final size:2
Alignment explanation
Indices: 386896--386934 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
386886 GTTTATTTCC
*
386896 AT AT AT AC AT AT AT AT AT AT AT AT AT A- AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
386935 AATAAAACTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:388192 original size:20 final size:20
Alignment explanation
Indices: 388152--388192 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
388142 ATTCAATATA
*
388152 TATTTAAATATAAATATAAT
1 TATTTAAATATAAATAAAAT
388172 TATTTAAATATATAA-AAAAT
1 TATTTAAATATA-AATAAAAT
388192 T
1 T
388193 TTAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTTAAATATAAATAAAAT
Found at i:389996 original size:16 final size:15
Alignment explanation
Indices: 389975--390004 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
389965 TAACAATATA
389975 TAATGTATATTAAATT
1 TAATGTAT-TTAAATT
389991 TAATGTATTTAAAT
1 TAATGTATTTAAAT
390005 AAATTATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
TAATGTATTTAAATT
Found at i:390181 original size:13 final size:13
Alignment explanation
Indices: 390163--390188 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
390153 ATTAAAAAAT
390163 ATATTTTTTATTA
1 ATATTTTTTATTA
390176 ATATTTTTTATTA
1 ATATTTTTTATTA
390189 CACTTATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATTTTTTATTA
Found at i:391368 original size:30 final size:31
Alignment explanation
Indices: 391303--391368 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
391293 GAATGAGTGT
* * *
391303 TTTTAAAATTTTAAGATATACTTTATGTTAG
1 TTTTAAAATTTTAAAATATACTTAATGTAAG
391334 TTTTAAAATTTTAAAATATA-TTAAT-TAAAG
1 TTTTAAAATTTTAAAATATACTTAATGT-AAG
391364 TTTTA
1 TTTTA
391369 TCGTACGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 11 0.35
31 19 0.61
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (31 bp):
TTTTAAAATTTTAAAATATACTTAATGTAAG
Found at i:391513 original size:16 final size:17
Alignment explanation
Indices: 391492--391547 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
391482 TAATAATTTT
391492 ATTAATA-AAAAAATTA
1 ATTAATATAAAAAATTA
*
391508 ATTAATATAAAATATTA
1 ATTAATATAAAAAATTA
* *
391525 A--AAT-TAAACATTTA
1 ATTAATATAAAAAATTA
391539 ATTAATATA
1 ATTAATATA
391548 TTTTAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
14 8 0.25
15 3 0.09
16 10 0.31
17 11 0.34
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTAATATAAAAAATTA
Found at i:391578 original size:30 final size:29
Alignment explanation
Indices: 391542--391599 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
391532 ACATTTAATT
* *
391542 AATATATTTTAAATTTAAAAATTAATATAA
1 AATATATTTAAAATTCAAAAATT-ATATAA
391572 AATATATTTAAAATTCAAAAATTATATA
1 AATATATTTAAAATTCAAAAATTATATA
391600 CGCTATTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
AATATATTTAAAATTCAAAAATTATATAA
Found at i:391996 original size:16 final size:17
Alignment explanation
Indices: 391976--392015 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
391966 AAGATATTAT
391976 AAAATAA-TAATTTTAA
1 AAAATAATTAATTTTAA
* *
391992 TAAATAATTATTTTTAA
1 AAAATAATTAATTTTAA
392009 AAAATAA
1 AAAATAA
392016 AATATTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATAATTAATTTTAA
Found at i:392138 original size:29 final size:29
Alignment explanation
Indices: 392101--392158 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
392091 GTCGTCAAAT
392101 TTTTTATACTCAATTACTTTAATAATAGC
1 TTTTTATACTCAATTACTTTAATAATAGC
392130 TTTTTATACTCAATTACTTTAATAATAGC
1 TTTTTATACTCAATTACTTTAATAATAGC
392159 ATGGATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTTTATACTCAATTACTTTAATAATAGC
Found at i:392447 original size:27 final size:28
Alignment explanation
Indices: 392395--392459 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 28
392385 ATCACTTTTC
*
392395 ATTTAATAAAAATTTATTTTTATTTAA-
1 ATTTAATAAAAATATATTTTTATTTAAT
392422 ATTTAATTATAAAATATA-TTTT-TTTAAT
1 ATTTAA-TA-AAAATATATTTTTATTTAAT
392450 ATTTTAATAA
1 A-TTTAATAA
392460 TTTTTAAGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 12 0.36
28 9 0.27
29 12 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
ATTTAATAAAAATATATTTTTATTTAAT
Found at i:395011 original size:48 final size:47
Alignment explanation
Indices: 394957--395069 Score: 138
Period size: 48 Copynumber: 2.4 Consensus size: 47
394947 TAAAAATATT
394957 AATAATTTGAATTTAATTAACTTAAATATAAAAATAATTTAAATTTAA
1 AATAATTTGAATTTAATTAACTTAAATAT-AAAATAATTTAAATTTAA
* * * * *
395005 AATAATTTAAATTCGAAATAATTTAAATATAAAATGATTTAAATTTAA
1 AATAATTTGAATT-TAATTAACTTAAATATAAAATAATTTAAATTTAA
* *
395053 ATTGATTTGAA-TTAATT
1 AATAATTTGAATTTAATT
395070 CGAAATGATT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
46 3 0.06
47 1 0.02
48 37 0.69
49 13 0.24
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (47 bp):
AATAATTTGAATTTAATTAACTTAAATATAAAATAATTTAAATTTAA
Found at i:395060 original size:16 final size:16
Alignment explanation
Indices: 394957--395053 Score: 106
Period size: 16 Copynumber: 6.1 Consensus size: 16
394947 TAAAAATATT
*
394957 AATAATTTGAATTT-A
1 AATAATTTAAATTTAA
* * *
394972 ATTAACTTAAATATAAA
1 AATAATTTAAAT-TTAA
394989 AATAATTTAAATTTAA
1 AATAATTTAAATTTAA
**
395005 AATAATTTAAATTCGA
1 AATAATTTAAATTTAA
*
395021 AATAATTTAAATATAA
1 AATAATTTAAATTTAA
*
395037 AATGATTTAAATTTAA
1 AATAATTTAAATTTAA
395053 A
1 A
395054 TTGATTTGAA
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
15 9 0.14
16 46 0.70
17 11 0.17
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Found at i:395065 original size:16 final size:16
Alignment explanation
Indices: 394987--395065 Score: 86
Period size: 16 Copynumber: 4.9 Consensus size: 16
394977 CTTAAATATA
*
394987 AAAATAATTTAAATTT
1 AAAATGATTTAAATTT
* *
395003 AAAATAATTTAAATTC
1 AAAATGATTTAAATTT
* * *
395019 GAAATAATTTAAATAT
1 AAAATGATTTAAATTT
395035 AAAATGATTTAAATTT
1 AAAATGATTTAAATTT
* *
395051 AAATTGATTTGAATT
1 AAAATGATTTAAATT
395066 AATTCGAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 54 1.00
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (16 bp):
AAAATGATTTAAATTT
Found at i:395888 original size:2 final size:2
Alignment explanation
Indices: 395881--395915 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
395871 ACAGGAACTA
395881 AT AT AT 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 AT AT AT A
395916 CTTCTTCCAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:397005 original size:19 final size:19
Alignment explanation
Indices: 396981--397021 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
396971 TTAAGTTTCC
*
396981 TTTTCCTTTTCTGTTTCTT
1 TTTTCCTTTTCTATTTCTT
397000 TTTTCCTTTTCTATTTCTT
1 TTTTCCTTTTCTATTTCTT
397019 TTT
1 TTT
397022 CTCTTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTCCTTTTCTATTTCTT
Found at i:397023 original size:31 final size:31
Alignment explanation
Indices: 396982--397042 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
396972 TAAGTTTCCT
*
396982 TTTCCTTTTCTGTTTCTTT-TTTCCTTTTCTA
1 TTTCCTTTTCTCTTTCTTTCTTT-CTTTTCTA
*
397013 TTTCTTTTTCTCTTTCTTTCTTTCTTTTCT
1 TTTCCTTTTCTCTTTCTTTCTTTCTTTTCT
397043 GTATCAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.74
Consensus pattern (31 bp):
TTTCCTTTTCTCTTTCTTTCTTTCTTTTCTA
Found at i:397027 original size:19 final size:19
Alignment explanation
Indices: 396976--397027 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
396966 TGCTGTTAAG
* *
396976 TTTCCTTTTC-CTTTTCTG
1 TTTCTTTTTCTCTTTTCTA
396994 TTTCTTTTT-TCCTTTTCTA
1 TTTCTTTTTCT-CTTTTCTA
397013 TTTCTTTTTCTCTTT
1 TTTCTTTTTCTCTTT
397028 CTTTCTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 8 0.28
19 20 0.69
20 1 0.03
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTCTTTTTCTCTTTTCTA
Found at i:397080 original size:2 final size:2
Alignment explanation
Indices: 397073--397108 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
397063 ATGGATGAGA
397073 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
397109 TAGAGCATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:401671 original size:16 final size:16
Alignment explanation
Indices: 401652--401725 Score: 112
Period size: 16 Copynumber: 4.6 Consensus size: 16
401642 AGATACAAAC
401652 TATTTTAAATTTAAAT
1 TATTTTAAATTTAAAT
* *
401668 TATTTTATATTTAATT
1 TATTTTAAATTTAAAT
401684 TATTTTAAATTTAAAT
1 TATTTTAAATTTAAAT
* *
401700 TATTTTAAATTCAATT
1 TATTTTAAATTTAAAT
401716 TATTTTAAAT
1 TATTTTAAAT
401726 GATCAGATCG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTAAATTTAAAT
Found at i:401688 original size:32 final size:32
Alignment explanation
Indices: 401652--401725 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
401642 AGATACAAAC
* *
401652 TATTTTAAATTTAAATTATTTTATATTTAATT
1 TATTTTAAATTTAAATTATTTTAAATTCAATT
401684 TATTTTAAATTTAAATTATTTTAAATTCAATT
1 TATTTTAAATTTAAATTATTTTAAATTCAATT
401716 TATTTTAAAT
1 TATTTTAAAT
401726 GATCAGATCG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (32 bp):
TATTTTAAATTTAAATTATTTTAAATTCAATT
Found at i:403464 original size:2 final size:2
Alignment explanation
Indices: 403457--403513 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
403447 CCTTCCCTGT
403457 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
403499 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
403514 TTGAGGGTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:404541 original size:21 final size:20
Alignment explanation
Indices: 404517--404588 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 20
404507 ATTCAGAATA
*
404517 TTTATTAAATATTTTTTTAAT
1 TTTA-TAAATATATTTTTAAT
404538 TTTATAAATATATTTTTATAT
1 TTTATAAATATATTTTTA-AT
* *
404559 ATTT-CAATTATAATTTTTAATT
1 -TTTATAAATAT-ATTTTTAA-T
404581 TTTATAAA
1 TTTATAAA
404589 ATTTTATCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
20 13 0.32
21 15 0.37
22 13 0.32
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATAAATATATTTTTAAT
Found at i:404603 original size:44 final size:40
Alignment explanation
Indices: 404530--404614 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 40
404520 ATTAAATATT
404530 TTTTTAATTTTATAAATATATTTTTATATATTTCAATTATAA
1 TTTTTAATTTTATAAATATATTTTTATATATTT-AATT-TAA
404572 TTTTTAATTTTTATAAA-AT-TTTATCATATATATTTAATTTAA
1 TTTTTAA-TTTTATAAATATATTT-T--TATATATTTAATTTAA
404614 T
1 T
404615 CTTGTAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
41 3 0.08
42 14 0.36
43 13 0.33
44 9 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (40 bp):
TTTTTAATTTTATAAATATATTTTTATATATTTAATTTAA
Found at i:411222 original size:2 final size:2
Alignment explanation
Indices: 411215--411247 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
411205 GATGAACTAC
411215 AT AT AT AT AT A- 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
411248 TGTACCTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:414555 original size:2 final size:2
Alignment explanation
Indices: 414548--414583 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
414538 GAAATAATCT
414548 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
414584 ACTGAGATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:415719 original size:20 final size:21
Alignment explanation
Indices: 415668--415727 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
415658 TATTTATTTT
* *
415668 TATATATATTATAAATTAATAAAT
1 TATAT-TA-TATAAATT-TTAAAA
415692 TATATTATATAAATTTTAAAA
1 TATATTATATAAATTTTAAAA
*
415713 TAT-TTATATATATTT
1 TATATTATATAAATTT
415728 AATATTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 11 0.33
21 7 0.21
22 8 0.24
23 2 0.06
24 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATATTATATAAATTTTAAAA
Found at i:415736 original size:20 final size:20
Alignment explanation
Indices: 415677--415737 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
415667 TTATATATAT
*
415677 TATAAATTAATAAATTATATTA
1 TATAAATT-TTAAATTAT-TTA
*
415699 TATAAATTTTAAAATATTTA
1 TATAAATTTTAAATTATTTA
*
415719 TATATA-TTTAATATTATTT
1 TATAAATTTTAA-ATTATTT
415738 TTTATGACGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.15
20 14 0.41
21 7 0.21
22 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATAAATTTTAAATTATTTA
Found at i:416113 original size:15 final size:17
Alignment explanation
Indices: 416072--416113 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
416062 TAGTAAAGTA
416072 TAAATTAATAAAAAATATT
1 TAAATTAAT--AAAATATT
416091 TAAATTAATAAAA-ATT
1 TAAATTAATAAAATATT
416107 T-AATTAA
1 TAAATTAA
416114 GATTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.26
16 4 0.17
17 4 0.17
19 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTAATAAAATATT
Found at i:416140 original size:15 final size:15
Alignment explanation
Indices: 416102--416150 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
416092 AAATTAATAA
416102 AAATTTAATTAAGATTT
1 AAATTTAATTAA-A-TT
* *
416119 TAATTTAATTACATT
1 AAATTTAATTAAATT
*
416134 AAATTTATTTAAATT
1 AAATTTAATTAAATT
416149 AA
1 AA
416151 TAAAAAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 16 0.59
16 1 0.04
17 10 0.37
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
AAATTTAATTAAATT
Found at i:416148 original size:20 final size:19
Alignment explanation
Indices: 416121--416180 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
416111 TAAGATTTTA
**
416121 ATTT-AATTACATTAAATTT
1 ATTTAAATTA-ATTAAAAAT
*
416140 ATTTAAATTAATAAAAAAT
1 ATTTAAATTAATTAAAAAT
416159 ATTTAAAATTAGATTAAAAAT
1 ATTT-AAATTA-ATTAAAAAT
416180 A
1 A
416181 AGATAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 14 0.41
20 11 0.32
21 9 0.26
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTTAAATTAATTAAAAAT
Found at i:416158 original size:21 final size:21
Alignment explanation
Indices: 416134--416213 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 21
416124 TAATTACATT
416134 AAATTTATTTAAATTAATAAA
1 AAATTTATTTAAATTAATAAA
416155 AAA--TATTTAAAATTAGATTAAAA
1 AAATTTATTT-AAATTA-A-T-AAA
* *
416178 ATAAGATAATTTAAATTAATAAA
1 A-AA-TTTATTTAAATTAATAAA
*
416201 AAATGTATTTAAA
1 AAATTTATTTAAA
416214 AAAATTAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
19 5 0.11
20 6 0.13
21 11 0.23
22 3 0.06
23 8 0.17
24 3 0.06
25 1 0.02
26 6 0.13
27 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
AAATTTATTTAAATTAATAAA
Found at i:418934 original size:21 final size:20
Alignment explanation
Indices: 418885--418941 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
418875 TAAATAATTT
418885 TATTTTT-AATTAATAAAAA
1 TATTTTTAAATTAATAAAAA
* * *
418904 -AATTTAAAATATTATAAAAA
1 TATTTTTAAAT-TAATAAAAA
418924 TATTTTTAAATTAA-AAAA
1 TATTTTTAAATTAATAAAA
418942 TTTATGATTC
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
18 4 0.14
19 7 0.24
20 10 0.34
21 8 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATTTTTAAATTAATAAAAA
Found at i:419226 original size:20 final size:23
Alignment explanation
Indices: 419183--419225 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
419173 TAATTCATGC
419183 ATTATATTATGAAGTTTTATTTT
1 ATTATATTATGAAGTTTTATTTT
419206 ATTATATTAT-AA-TTTTATTT
1 ATTATATTATGAAGTTTTATTT
419226 AAATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.40
22 2 0.10
23 10 0.50
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (23 bp):
ATTATATTATGAAGTTTTATTTT
Found at i:419233 original size:20 final size:23
Alignment explanation
Indices: 419185--419233 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
419175 ATTCATGCAT
* *
419185 TATATTATGAAGTTTTATTTTAT
1 TATATTATGAAGTTTTATTTAAA
419208 TATATTAT-AA-TTTTATTTAAA
1 TATATTATGAAGTTTTATTTAAA
419229 T-TATT
1 TATATT
419234 TTATATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.17
21 10 0.42
22 2 0.08
23 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
TATATTATGAAGTTTTATTTAAA
Found at i:419237 original size:22 final size:21
Alignment explanation
Indices: 419183--419246 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 21
419173 TAATTCATGC
*
419183 ATTATATTATGAAGTTTTATTTT
1 ATTATATTAT-AA-TTTTATTTA
419206 ATTATATTATAATTTTATTTAA
1 ATTATATTATAATTTTATTT-A
*
419228 ATTATTTTAT-ATTTATATT
1 ATTATATTATAATTT-TATT
419247 AATAGTAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 12 0.32
22 15 0.41
23 10 0.27
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
ATTATATTATAATTTTATTTA
Found at i:419258 original size:20 final size:22
Alignment explanation
Indices: 419235--419283 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
419225 TAAATTATTT
419235 TATATTTAT-ATTAATAGTA-A
1 TATATTTATAATTAATAGTATA
* * *
419255 TATATTAATAATTTATATTATA
1 TATATTTATAATTAATAGTATA
419277 TATATTT
1 TATATTT
419284 TAAATTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.35
21 8 0.35
22 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATATTTATAATTAATAGTATA
Found at i:419520 original size:33 final size:34
Alignment explanation
Indices: 419460--419525 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 34
419450 TTTCAAGAAA
* *
419460 TTTTCAACTTAAATAGATAATTAAATTATGATTT
1 TTTTCAACATAAATAGATAATTAAATTAAGATTT
* * *
419494 TTTTCAA-ATAAATAGGTACTTGAATTAAGATT
1 TTTTCAACATAAATAGATAATTAAATTAAGATT
419526 AATTATGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (34 bp):
TTTTCAACATAAATAGATAATTAAATTAAGATTT
Found at i:419738 original size:3 final size:3
Alignment explanation
Indices: 419730--419772 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
419720 TTAAGCTTTA
*
419730 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATTT ATTT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT A-TT ATT AT
419773 AATACAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 30 0.81
4 7 0.19
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:420292 original size:2 final size:2
Alignment explanation
Indices: 420285--420325 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
420275 CTTTTGGGTT
420285 TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC T
420326 ACTTTATCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:420401 original size:2 final size:2
Alignment explanation
Indices: 420394--420423 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
420384 TTTGAGTGCC
420394 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
420424 AAGACTTTAA
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):
TA
Found at i:428754 original size:19 final size:18
Alignment explanation
Indices: 428672--428754 Score: 53
Period size: 18 Copynumber: 4.6 Consensus size: 18
428662 GAAATATAAT
* **
428672 TAATATTATTATAATGAA
1 TAATATAATTATAAAAAA
* * *
428690 TTATATAATAATTAAAAA
1 TAATATAATTATAAAAAA
*
428708 TAA-ATACTTATAATAAAA
1 TAATATAATTATAA-AAAA
*
428726 -AATTAAAATTATAAAAAA
1 TAA-TATAATTATAAAAAA
428744 TAATGATAATT
1 TAAT-ATAATT
428755 TTATTATATT
Statistics
Matches: 47, Mismatches: 13, Indels: 9
0.68 0.19 0.13
Matches are distributed among these distances:
17 9 0.19
18 23 0.49
19 15 0.32
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.37
Consensus pattern (18 bp):
TAATATAATTATAAAAAA
Found at i:442561 original size:21 final size:22
Alignment explanation
Indices: 442535--442575 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
442525 ATCTCGTGTC
*
442535 AAAATTCAT-AATTTAAATTTT
1 AAAATTCATGAAATTAAATTTT
442556 AAAATTCATGAAATTAAATT
1 AAAATTCATGAAATTAAATT
442576 AATAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (22 bp):
AAAATTCATGAAATTAAATTTT
Found at i:442583 original size:22 final size:21
Alignment explanation
Indices: 442535--442581 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
442525 ATCTCGTGTC
* *
442535 AAAATTCATAATTTAAATTTT
1 AAAATTCATAAATTAAATTAT
442556 AAAATTCATGAAATTAAATTAAT
1 AAAATTCAT-AAATTAAATT-AT
442579 AAA
1 AAA
442582 TTAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 9 0.41
23 4 0.18
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAATTCATAAATTAAATTAT
Found at i:443338 original size:1 final size:1
Alignment explanation
Indices: 443332--443356 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
443322 TTGATTTGCC
443332 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
443357 CTGACGTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:443436 original size:15 final size:15
Alignment explanation
Indices: 443413--443448 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
443403 GGCTCAACCC
*
443413 AAAACAAAAATAAAA
1 AAAAAAAAAATAAAA
443428 AAAAAAAAAATAAAA
1 AAAAAAAAAATAAAA
443443 AAAAAA
1 AAAAAA
443449 CTCTCTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.92, C:0.03, G:0.00, T:0.06
Consensus pattern (15 bp):
AAAAAAAAAATAAAA
Found at i:445034 original size:18 final size:18
Alignment explanation
Indices: 444955--445034 Score: 55
Period size: 18 Copynumber: 4.7 Consensus size: 18
444945 TAGTAAAGTA
**
444955 TAAATTAATAAAAATATT
1 TAAATTAATAAATTTATT
*
444973 TAAATTAATAAAATTTAAT
1 TAAATTAAT-AAATTTATT
*
444992 TAAGATT--TTAATTTA-T
1 TAA-ATTAATAAATTTATT
*
445008 TACA-T--TAAATTTATT
1 TAAATTAATAAATTTATT
445023 TAAATTAATAAA
1 TAAATTAATAAA
445035 AAATATTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
14 8 0.16
15 5 0.10
16 4 0.08
17 6 0.12
18 14 0.29
19 9 0.18
20 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (18 bp):
TAAATTAATAAATTTATT
Found at i:445090 original size:21 final size:21
Alignment explanation
Indices: 445014--445093 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 21
445004 TTATTACATT
*
445014 AAATTTATTTAAATTAATAAA
1 AAATGTATTTAAATTAATAAA
445035 AAA--TATTTAAAATTAGATTAAA
1 AAATGTATTT-AAATTA-A-TAAA
*
445057 AATAAGATAATTTAAATTAATAAA
1 AA-ATG-T-ATTTAAATTAATAAA
445081 AAATGTATTTAAA
1 AAATGTATTTAAA
445094 AAAATTAATT
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
19 5 0.10
20 6 0.12
21 11 0.22
22 7 0.14
23 3 0.06
24 6 0.12
25 1 0.02
26 7 0.14
27 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
AAATGTATTTAAATTAATAAA
Found at i:445631 original size:18 final size:19
Alignment explanation
Indices: 445595--445634 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
445585 TTAACTTGTG
445595 AATAATAATTAATTAATAA
1 AATAATAATTAATTAATAA
445614 AATAAT-ATCTAA-TAATAA
1 AATAATAAT-TAATTAATAA
445632 AAT
1 AAT
445635 TAAAAACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
AATAATAATTAATTAATAA
Found at i:445901 original size:21 final size:21
Alignment explanation
Indices: 445877--445930 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
445867 CATCATCATT
*
445877 ATTTATTTATTAATTATATTA
1 ATTTATTTATTAATGATATTA
* ** *
445898 ATTTATATATTTGTGATATTT
1 ATTTATTTATTAATGATATTA
445919 ATTTATTTATTA
1 ATTTATTTATTA
445931 CACTTTGTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
ATTTATTTATTAATGATATTA
Found at i:446694 original size:27 final size:29
Alignment explanation
Indices: 446664--446717 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
446654 GATTTGGGTC
**
446664 TAATTATTATTTATTT-TTATT-TTAATT
1 TAATTATTAAATATTTATTATTATTAATT
446691 TAATTATTAAATATTTATTATTATTAA
1 TAATTATTAAATATTTATTATTATTAA
446718 AATATTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.61
28 5 0.22
29 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TAATTATTAAATATTTATTATTATTAATT
Found at i:446715 original size:17 final size:18
Alignment explanation
Indices: 446693--446726 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
446683 TTTTAATTTA
446693 ATTATT-AAATATTTATT
1 ATTATTAAAATATTTATT
446710 ATTATTAAAATATTTAT
1 ATTATTAAAATATTTAT
446727 CAACTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTAAAATATTTATT
Found at i:448041 original size:19 final size:21
Alignment explanation
Indices: 448000--448043 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
447990 CATGCATTTA
* *
448000 TATTATGAAGTTTTTTTTTAT
1 TATTATGAAGTTTTATTTAAT
448021 TATTAT-AA-TTTTATTTAAT
1 TATTATGAAGTTTTATTTAAT
448040 TATT
1 TATT
448044 TATATTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 2 0.10
21 6 0.29
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
TATTATGAAGTTTTATTTAAT
Found at i:448083 original size:17 final size:17
Alignment explanation
Indices: 448031--448155 Score: 78
Period size: 15 Copynumber: 7.9 Consensus size: 17
448021 TATTATAATT
448031 TTAT-TTAATTATTTATA
1 TTATATTAA-TATTTATA
*
448048 TTATATTAATA-GTA-A
1 TTATATTAATATTTATA
448063 -TATATTAATATTTATA
1 TTATATTAATATTTATA
*
448079 TTATA-T-ATATTTAAA
1 TTATATTAATATTTATA
* *
448094 TTATA-TATTCGTGTTAT-
1 TTATATTAAT-AT-TTATA
448111 TTATATTTAATATTTATA
1 TTATA-TTAATATTTATA
*
448129 -TATATT-GTATTTATA
1 TTATATTAATATTTATA
448144 -TA-ATT-ATATTTA
1 TTATATTAATATTTA
448156 AAATTTTCAT
Statistics
Matches: 88, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
14 19 0.22
15 27 0.31
16 7 0.08
17 24 0.27
18 8 0.09
19 3 0.03
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATATTAATATTTATA
Found at i:448545 original size:14 final size:15
Alignment explanation
Indices: 448526--448556 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
448516 TTAAGCTTTA
448526 ATTATTATTATT-TT
1 ATTATTATTATTGTT
448540 ATTATTATTATTGTT
1 ATTATTATTATTGTT
448555 AT
1 AT
448557 ATTTATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
ATTATTATTATTGTT
Found at i:449074 original size:2 final size:2
Alignment explanation
Indices: 449067--449108 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
449057 CTTTTGGGTT
449067 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- 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
449108 T
1 T
449109 ACTTTATCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:449120 original size:21 final size:21
Alignment explanation
Indices: 449067--449121 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
449057 CTTTTGGGTT
*
449067 TCTCTCTCTC-TCTCTCTCTC
1 TCTCTATCTCTTCTCTCTCTC
*
449087 TCTCTCTCTCTTCTCTCTCTC
1 TCTCTATCTCTTCTCTCTCTC
*
449108 TACTTTATC-CTTCT
1 T-CTCTATCTCTTCT
449122 TTTCATCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 10 0.32
21 16 0.52
22 5 0.16
ACGTcount: A:0.04, C:0.44, G:0.00, T:0.53
Consensus pattern (21 bp):
TCTCTATCTCTTCTCTCTCTC
Found at i:449185 original size:2 final size:2
Alignment explanation
Indices: 449178--449205 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
449168 TTGAGTGCCT
449178 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
449206 AAGCTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:457394 original size:15 final size:16
Alignment explanation
Indices: 457374--457413 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
457364 TAATAGGAAA
*
457374 TATAATTAA-TATTAT
1 TATAATTAATTATAAT
457389 TATAATTAATTATAAT
1 TATAATTAATTATAAT
*
457405 AATAATTAA
1 TATAATTAA
457414 AAATAAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAATTATAAT
Found at i:457433 original size:13 final size:13
Alignment explanation
Indices: 457374--457439 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
457364 TAATAGGAAA
*
457374 TATAATTAAT-AT
1 TATAATAAATAAT
* *
457386 TATTATAATTAAT
1 TATAATAAATAAT
457399 TATAAT-AATAAT
1 TATAATAAATAAT
* *
457411 TAAAAATAAATACT
1 T-ATAATAAATAAT
*
457425 TATAATAAAAAAT
1 TATAATAAATAAT
457438 TA
1 TA
457440 AAATTATAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
12 13 0.32
13 22 0.54
14 6 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
TATAATAAATAAT
Found at i:471393 original size:19 final size:20
Alignment explanation
Indices: 471357--471394 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
471347 ATCTCGTGTC
*
471357 TAAAATTCATATTTAAATTT
1 TAAAATTCATATTGAAATTT
471377 TAAAATTC-TATTGAAATT
1 TAAAATTCATATTGAAATT
471395 AAATTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
TAAAATTCATATTGAAATTT
Done.