Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 2 of 32
Found at i:347238 original size:20 final size:19
Alignment explanation
Indices: 347215--347292 Score: 81
Period size: 20 Copynumber: 4.1 Consensus size: 19
347205 TATTATATAA
347215 ATTTTAAATTTTTATATTTT
1 ATTTT-AATTTTTATATTTT
347235 ATTTTAA-TTTTAT-TTTT
1 ATTTTAATTTTTATATTTT
* *
347252 GATTTTTATATTATATATTTT
1 -ATTTTAAT-TTTTATATTTT
347273 ATTTTAATATTTT-TATTTT
1 ATTTTAAT-TTTTATATTTT
347292 A
1 A
347293 ATTATAATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
17 4 0.08
18 12 0.24
19 9 0.18
20 21 0.42
21 4 0.08
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (19 bp):
ATTTTAATTTTTATATTTT
Found at i:347243 original size:26 final size:24
Alignment explanation
Indices: 347103--347295 Score: 110
Period size: 24 Copynumber: 7.7 Consensus size: 24
347093 TTTAATATCA
* *
347103 TATATTTTATTTTTA-TTTATTAT
1 TATATTTTATTTTAATTTTATTTT
*
347126 TATAATTTTA-TAT-ATTTTATTTT
1 TAT-ATTTTATTTTAATTTTATTTT
* * * * *
347149 CATTACTTTAATATAATTTTTTATGTTA
1 TA-TATTTTATTTTAA--TTTTAT-TTT
347177 TATATTTTATTTTAA-TTTA-TTT
1 TATATTTTATTTTAATTTTATTTT
* * *
347199 TACCTATATTATATAAATTTTAAATTTT
1 TA--TATTTTATTTTAATTTT--ATTTT
347227 TATATTTTATTTTAATTTTATTTT
1 TATATTTTATTTTAATTTTATTTT
347251 TGAT-TTTTATATTATATATTTTATTTT
1 T-ATATTTTAT-TT-TA-ATTTTATTTT
*
347278 AATATTTTTATTTTAATT
1 TATA-TTTTATTTTAATT
347296 ATAATATTAT
Statistics
Matches: 133, Mismatches: 17, Indels: 38
0.71 0.09 0.20
Matches are distributed among these distances:
22 5 0.04
23 18 0.14
24 36 0.27
25 11 0.08
26 20 0.15
27 29 0.22
28 14 0.11
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (24 bp):
TATATTTTATTTTAATTTTATTTT
Found at i:347258 original size:7 final size:6
Alignment explanation
Indices: 347222--347291 Score: 61
Period size: 6 Copynumber: 10.8 Consensus size: 6
347212 TAAATTTTAA
* *
347222 ATTTTT ATATTTT A-TTTT AATTTT ATTTTT GATTTTT ATATTAT ATATTTT
1 ATTTTT AT-TTTT ATTTTT ATTTTT ATTTTT -ATTTTT AT-TTTT AT-TTTT
347273 ATTTTAAT ATTTTT ATTTT
1 ATTTT--T ATTTTT ATTTT
347292 AATTATAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
5 5 0.09
6 22 0.40
7 22 0.40
8 6 0.11
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (6 bp):
ATTTTT
Found at i:347261 original size:50 final size:52
Alignment explanation
Indices: 347101--347295 Score: 135
Period size: 50 Copynumber: 3.8 Consensus size: 52
347091 TTTTTAATAT
* * * *
347101 CATATATTTTATT-TTTA-TTTATTATTATAATTTTA-TAT-ATTTTATTTT-
1 CATATATTATATTATATATTTTATTTTTAT-ATTTTATTTTAATTTTATTTTA
* * *
347149 CAT-TACTT-TAATATAATTTTTTATGTTATATATTTTATTTTAA-TTTATTTTA
1 CATATA-TTATATTAT-ATATTTTAT-TTTTATATTTTATTTTAATTTTATTTTA
* *
347201 CCTATATTATA-TA-A-ATTTTAAATTTTTATATTTTATTTTAATTTTATTTTT
1 CATATATTATATTATATATTTT--ATTTTTATATTTTATTTTAATTTTATTTTA
* * *
347252 GAT-TTTTATATTATATATTTTATTTTAATATTTTTATTTTAATT
1 CATATATTATATTATATATTTTATTTTTATA-TTTTATTTTAATT
347296 ATAATATTAT
Statistics
Matches: 116, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
47 5 0.04
48 6 0.05
49 5 0.04
50 35 0.30
51 35 0.30
52 21 0.18
53 9 0.08
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (52 bp):
CATATATTATATTATATATTTTATTTTTATATTTTATTTTAATTTTATTTTA
Found at i:347303 original size:40 final size:38
Alignment explanation
Indices: 347227--347306 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
347217 TTTAAATTTT
* * *
347227 TATATTTTATTTTAATTTTATTTTTGATTTTTATATTA
1 TATATTTTATTTTAATTTTATTTTTAATTATAATATTA
*
347265 TATATTTTATTTTAATATTTTTATTTTAATTATAATATTA
1 TATATTTTATTTTAAT-TTTAT-TTTTAATTATAATATTA
347305 TA
1 TA
347307 AAATATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 16 0.44
39 4 0.11
40 16 0.44
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (38 bp):
TATATTTTATTTTAATTTTATTTTTAATTATAATATTA
Found at i:347329 original size:22 final size:23
Alignment explanation
Indices: 347286--347332 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
347276 TTAATATTTT
347286 TATTTTAATTATAATATTATAAAA
1 TATTTTAA-TATAATATTATAAAA
347310 TATTTTAA-ATAAT-TTAATAAAA
1 TATTTTAATATAATATT-ATAAAA
347332 T
1 T
347333 TGAAAGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.09
22 12 0.55
24 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTTTAATATAATATTATAAAA
Found at i:351518 original size:28 final size:27
Alignment explanation
Indices: 351486--351555 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
351476 GATTTGTAAG
* *
351486 TAACAATAACATTTTAAGTATTAAAATA
1 TAACAATAATATTTTAAATA-TAAAATA
* *
351514 TAACAA-AATATTTTTAAATATGATATA
1 TAACAATAATA-TTTTAAATATAAAATA
351541 TAACAATAATATTTT
1 TAACAATAATATTTT
351556 TTTTAACATG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (27 bp):
TAACAATAATATTTTAAATATAAAATA
Found at i:351719 original size:66 final size:67
Alignment explanation
Indices: 351604--351728 Score: 171
Period size: 66 Copynumber: 1.9 Consensus size: 67
351594 ATGACATGTA
* ** * *
351604 ACAACTTAACCATAACGTGTTACATATTTTTATACATGATATGTTACAAC-TTAACCATAATGTA
1 ACAACTTAACCATAACGTGTCACATATTTTTATACAAAACATGTAACAACTTTAACCATAATGTA
351668 TT
66 TT
* * *
351670 ACAATTTAACCATAACGTGTCACATGTTTTTGTACAAAACATGTAACAACTTTAACCAT
1 ACAACTTAACCATAACGTGTCACATATTTTTATACAAAACATGTAACAACTTTAACCAT
351729 GACGTGCAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
66 42 0.84
67 8 0.16
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (67 bp):
ACAACTTAACCATAACGTGTCACATATTTTTATACAAAACATGTAACAACTTTAACCATAATGTA
TT
Found at i:351746 original size:46 final size:45
Alignment explanation
Indices: 351670--351763 Score: 109
Period size: 46 Copynumber: 2.1 Consensus size: 45
351660 ATAATGTATT
* *
351670 ACAATTTAACCATAACGTGTCACATGTTTTTGTACAAAACATGTA
1 ACAATTTAACCATAACGTGTCACATATTTTTATACAAAACATGTA
* * * *
351715 ACAACTTTAACCATGACGTG-CAATATATTTTTATACATAACGTGTA
1 ACAA-TTTAACCATAACGTGTC-ACATATTTTTATACAAAACATGTA
351761 ACA
1 ACA
351764 TTATGACATA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
45 5 0.12
46 36 0.88
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (45 bp):
ACAATTTAACCATAACGTGTCACATATTTTTATACAAAACATGTA
Found at i:355722 original size:6 final size:6
Alignment explanation
Indices: 355711--355740 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
355701 CCAGAGAGAC
*
355711 GAGCCA GAGCCA GAGCCA GAGCCA AAGCCA
1 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA
355741 AAACCAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.33, G:0.30, T:0.00
Consensus pattern (6 bp):
GAGCCA
Found at i:370669 original size:45 final size:45
Alignment explanation
Indices: 370618--370706 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
370608 TTTTAAAATA
* *
370618 ATTTTTTTAATATTAAAAATTATTACAAAATAAATTATAATTTTTT
1 ATTTTTTAAAT-TTAAAAATTATCACAAAATAAATTATAATTTTTT
* **
370664 ATTTTTTAAATTTTAAAATTATCATTAAATAAATTATAATTTT
1 ATTTTTTAAATTTAAAAATTATCACAAAATAAATTATAATTTT
370707 GTGTAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
45 28 0.74
46 10 0.26
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (45 bp):
ATTTTTTAAATTTAAAAATTATCACAAAATAAATTATAATTTTTT
Found at i:384648 original size:27 final size:27
Alignment explanation
Indices: 384595--384649 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
384585 TAATGTTATG
* *
384595 TTTTTGATGTTTTAATTTTTTTGATAA
1 TTTTTGATATTTTAATTTTTTAGATAA
*
384622 TTTTTTATATTTTAA-TTTTTAGAATAA
1 TTTTTGATATTTTAATTTTTTAG-ATAA
384649 T
1 T
384650 GACTTTCACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.65
Consensus pattern (27 bp):
TTTTTGATATTTTAATTTTTTAGATAA
Found at i:394492 original size:12 final size:12
Alignment explanation
Indices: 394475--394504 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
394465 TAACCATTTG
*
394475 TTATAATCTGAT
1 TTATAATCCGAT
394487 TTATAATCCGAT
1 TTATAATCCGAT
394499 TTATAA
1 TTATAA
394505 AATTTAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (12 bp):
TTATAATCCGAT
Found at i:395127 original size:32 final size:32
Alignment explanation
Indices: 395068--395128 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
395058 TTAATCAAAC
*
395068 TTTTTATATTTTTATTTTAAATTAAATAAATA
1 TTTTTATATTTTTATTTTAAATCAAATAAATA
*
395100 TTTTTAT-TTTTTATTTTTGAATCAAATAA
1 TTTTTATATTTTTA-TTTTAAATCAAATAA
395129 GTTTTTACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (32 bp):
TTTTTATATTTTTATTTTAAATCAAATAAATA
Found at i:396746 original size:27 final size:27
Alignment explanation
Indices: 396716--396767 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
396706 TATGAATAAC
*
396716 AAAAT-TTTAATTTTTTATTTTTTTAAA
1 AAAATATTTAA-TTTTTACTTTTTTAAA
396743 AAAATATTTAATTTTTACTTTTTTA
1 AAAATATTTAATTTTTACTTTTTTA
396768 GTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
AAAATATTTAATTTTTACTTTTTTAAA
Found at i:398569 original size:165 final size:162
Alignment explanation
Indices: 398295--398633 Score: 599
Period size: 165 Copynumber: 2.1 Consensus size: 162
398285 GCGCTCTCTC
398295 TCTCTCTCTCTTGTTTTTCTCCTTTGGAAAGAGAGTTTGTATTTGTTTTTCTACTTTCAACAACA
1 TCTCTCTCTCTTGTTTTTCTCCTTTGGAAAGAGAGTTTGTATTTGTTTTTCTACTTTCAACAACA
*
398360 GAACCCACCACCCTTTCTCATTACTTCTTTTGTAACTGAGGCACACAGAGTAATTGAAGAGATTG
66 GAACCCACCACCCTTTCTCATTACTTCTTTTGTAACTAAGGCACACAGAGTAATTGAAGAGATTG
398425 AGAGGAGGTACAGGAAACCAAATCCAAAGACAA
131 AGAGGAGGTACAGGAAACCAAATCCAAAGAC-A
*
398458 TCAT-TCTCTCTTGTTTTTCTCCTTTGGAAAGAGAGAGTTTTTATTTGTTTTTCTACTTTCAACA
1 TC-TCTCTCTCTTGTTTTTCTCCTTTGG-AA-AGAGAGTTTGTATTTGTTTTTCTACTTTCAACA
*
398522 ACAGAACCCACCACCCTTTCTCATTACTTCTTTTGTAACTAAGGCACACAGAGTAATTGAGGAGA
63 ACAGAACCCACCACCCTTTCTCATTACTTCTTTTGTAACTAAGGCACACAGAGTAATTGAAGAGA
*
398587 TTGAGAGGAGGTACGGGAAACCAAATCCAAAGACA
128 TTGAGAGGAGGTACAGGAAACCAAATCCAAAGACA
398622 TCTCTCTCTCTT
1 TCTCTCTCTCTT
398634 TCTTTGCTGT
Statistics
Matches: 168, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
163 26 0.15
164 14 0.08
165 128 0.76
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (162 bp):
TCTCTCTCTCTTGTTTTTCTCCTTTGGAAAGAGAGTTTGTATTTGTTTTTCTACTTTCAACAACA
GAACCCACCACCCTTTCTCATTACTTCTTTTGTAACTAAGGCACACAGAGTAATTGAAGAGATTG
AGAGGAGGTACAGGAAACCAAATCCAAAGACA
Found at i:410259 original size:29 final size:28
Alignment explanation
Indices: 410214--410279 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
410204 TAAAAATTAA
410214 ATTTTTTAAAAATTTTAAATAAAT-TATT
1 ATTTTTTAAAAATTTTAAATAAATCT-TT
** *
410242 ATTTTTTAATTATATTTAATTAAATCTTT
1 ATTTTTTAAAAAT-TTTAAATAAATCTTT
410271 ATATTTTTA
1 AT-TTTTTA
410280 TTTTAAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 11 0.34
29 14 0.44
30 7 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTTTTAAAAATTTTAAATAAATCTTT
Found at i:410511 original size:21 final size:22
Alignment explanation
Indices: 410465--410512 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
410455 TGATAAGTAA
* *
410465 TATTAATTAATAATAATTAATC
1 TATTTATTAATAATAAATAATC
*
410487 -ATTTATTAATTATAAAT-ATC
1 TATTTATTAATAATAAATAATC
410507 TATTTA
1 TATTTA
410513 CTCTAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTTATTAATAATAAATAATC
Found at i:411163 original size:20 final size:20
Alignment explanation
Indices: 411126--411163 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
411116 ACTTGAGCGA
* *
411126 GCGTAGCGTAGTAGAGTAGG
1 GCGTAGCGTAGAAAAGTAGG
411146 GCGTAGCGTAGAAAAGTA
1 GCGTAGCGTAGAAAAGTA
411164 TCGGACGGAA
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:0.32, C:0.11, G:0.39, T:0.18
Consensus pattern (20 bp):
GCGTAGCGTAGAAAAGTAGG
Found at i:414071 original size:33 final size:33
Alignment explanation
Indices: 414023--414085 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
414013 TTCATGGTCA
414023 TTTTTGTTACATCTATTCAAAGAAA-ATTCATG
1 TTTTTGTTACATCTATTCAAAGAAATATTCATG
414055 TTTTTGTTTACATCTATTCAAAGAAATATTC
1 TTTTTG-TTACATCTATTCAAAGAAATATTC
414086 TGTAACTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 6 0.21
33 19 0.66
34 4 0.14
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (33 bp):
TTTTTGTTACATCTATTCAAAGAAATATTCATG
Found at i:414558 original size:3 final size:3
Alignment explanation
Indices: 414552--414585 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
414542 TTTTCTTTTC
414552 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
414586 GTGTCGCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:420229 original size:44 final size:45
Alignment explanation
Indices: 420166--420261 Score: 149
Period size: 44 Copynumber: 2.2 Consensus size: 45
420156 CAGGTTGTTC
* *
420166 TCAATTATCACTTTCTTAAATGGCACAT-TTTTTCTGGCCAAGTT
1 TCAATTAGCACTTTCTTAAATGGCACATCTTTTCCTGGCCAAGTT
*
420210 TCAATTAGCACTTTCTTAAATGGTACATCTTTTCCTGGCCAAGTT
1 TCAATTAGCACTTTCTTAAATGGCACATCTTTTCCTGGCCAAGTT
*
420255 TCGATTA
1 TCAATTA
420262 TCATTTTCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 26 0.55
45 21 0.45
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (45 bp):
TCAATTAGCACTTTCTTAAATGGCACATCTTTTCCTGGCCAAGTT
Found at i:439288 original size:6 final size:6
Alignment explanation
Indices: 439277--439303 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
439267 CACGTTTGAT
439277 CAGAAG CAGAAG CAGAAG CAGAAG CAG
1 CAGAAG CAGAAG CAGAAG CAGAAG CAG
439304 TTGGGGCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.33, T:0.00
Consensus pattern (6 bp):
CAGAAG
Found at i:447457 original size:33 final size:32
Alignment explanation
Indices: 447415--447476 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
447405 CTTGAAGGAG
447415 GAAAAGGAAGAAAAGCTTAAAGCAGCACAGCA
1 GAAAAGGAAGAAAAGCTTAAAGCAGCACAGCA
*
447447 GAAAATGGAAGAAAAGCTTACAGCAGCACA
1 GAAAA-GGAAGAAAAGCTTAAAGCAGCACA
447477 AGGGTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 5 0.18
33 23 0.82
ACGTcount: A:0.52, C:0.16, G:0.24, T:0.08
Consensus pattern (32 bp):
GAAAAGGAAGAAAAGCTTAAAGCAGCACAGCA
Found at i:452262 original size:6 final size:6
Alignment explanation
Indices: 452251--452277 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
452241 AAACATCATG
452251 TTTGCT TTTGCT TTTGCT TTTGCT TTT
1 TTTGCT TTTGCT TTTGCT TTTGCT TTT
452278 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTGCT
Found at i:460904 original size:3 final size:3
Alignment explanation
Indices: 460896--460921 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
460886 ATTAAAGCTT
460896 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
460922 TTCTTTGACC
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:461158 original size:23 final size:22
Alignment explanation
Indices: 461129--461184 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
461119 TTTTCTTTAT
461129 ATTAAATATTAAT-TTATAAAAA
1 ATTAAATATTAATATTA-AAAAA
* *
461151 ATTCAAATTTTAATATTAAATAA
1 ATT-AAATATTAATATTAAAAAA
461174 ATTAAA-ATTAA
1 ATTAAATATTAA
461185 AAAAAGAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.14
22 6 0.21
23 16 0.55
24 3 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAAATATTAATATTAAAAAA
Found at i:475524 original size:51 final size:51
Alignment explanation
Indices: 475453--475578 Score: 173
Period size: 51 Copynumber: 2.5 Consensus size: 51
475443 CAGGGCAAAA
* **
475453 GCCATGCCCCTGTGGTGGTGGTCCTGTTGGTCCACGCCG-GAAGCCGAAGCC
1 GCCATGCCCCGGTGGTGGTGGTCCTGGAGGTCCACG-CGAGAAGCCGAAGCC
* *
475504 GCCAAGCCCCGGTGGTGGTGGTCCTGGAGGTCCACGTGAGAAGCCGAAGCC
1 GCCATGCCCCGGTGGTGGTGGTCCTGGAGGTCCACGCGAGAAGCCGAAGCC
* *
475555 GCCATGCCCAGGTGGCGGTGGTCC
1 GCCATGCCCCGGTGGTGGTGGTCC
475579 AGGTGGTGGG
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
50 1 0.02
51 65 0.98
ACGTcount: A:0.13, C:0.32, G:0.38, T:0.17
Consensus pattern (51 bp):
GCCATGCCCCGGTGGTGGTGGTCCTGGAGGTCCACGCGAGAAGCCGAAGCC
Found at i:507188 original size:2 final size:2
Alignment explanation
Indices: 507181--507229 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
507171 GGTTGGTCCC
507181 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
507223 AT AT AT A
1 AT AT AT A
507230 ATAATTGATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:525635 original size:28 final size:28
Alignment explanation
Indices: 525626--525698 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 28
525616 TATTATAATT
525626 AAAA-TAAAATATATAATATAAGAATTA
1 AAAATTAAAATATATAATATAAGAATTA
*
525653 AAAATTAAAATA-A-AATA-AA-ATATAA
1 AAAATTAAAATATATAATATAAGA-ATTA
* *
525678 AAAAATAAATTATATAATATA
1 AAAATTAAAATATATAATATA
525699 GGTAAAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 1 0.03
25 15 0.39
26 5 0.13
27 9 0.24
28 8 0.21
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (28 bp):
AAAATTAAAATATATAATATAAGAATTA
Found at i:525640 original size:26 final size:26
Alignment explanation
Indices: 525611--525697 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 26
525601 TAAAAATATT
525611 TATAATATTATAATTAAAATAAAATA
1 TATAATATTATAATTAAAATAAAATA
* *
525637 TATAATATAAGAATTAAAAATTAAAATAA
1 TATAATATTATAATT-AAAA-TAAAAT-A
* * * *
525666 AATAA-AATATAA-AAAAATAAATTA
1 TATAATATTATAATTAAAATAAAATA
525690 TATAATAT
1 TATAATAT
525698 AGGTAAAACA
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
24 5 0.11
25 6 0.13
26 17 0.36
27 4 0.09
28 10 0.21
29 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (26 bp):
TATAATATTATAATTAAAATAAAATA
Found at i:525693 original size:53 final size:54
Alignment explanation
Indices: 525626--525735 Score: 154
Period size: 53 Copynumber: 2.1 Consensus size: 54
525616 TATTATAATT
525626 AAAATAAAATATATAATATAAG-AATTAA-AAATTAAAATAAAATA-AAATATAAA
1 AAAATAAAATATATAATATAAGTAA--AACAAATTAAAATAAAATATAAATATAAA
* * *
525679 AAAATAAATTATATAATATAGGTAAAACAAATTAAAATAAAATATATATATAAA
1 AAAATAAAATATATAATATAAGTAAAACAAATTAAAATAAAATATAAATATAAA
525733 AAA
1 AAA
525736 TATATTAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
52 2 0.04
53 36 0.71
54 13 0.25
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (54 bp):
AAAATAAAATATATAATATAAGTAAAACAAATTAAAATAAAATATAAATATAAA
Found at i:525735 original size:15 final size:15
Alignment explanation
Indices: 525717--525974 Score: 76
Period size: 13 Copynumber: 17.9 Consensus size: 15
525707 AAATTAAAAT
525717 AAAATATATATATAA
1 AAAATATATATATAA
*
525732 AAAATATAT-TAAAGA
1 AAAATATATATATA-A
* * *
525747 AATGAAAATAAAATATAT
1 AA--AATAT-ATATATAA
525765 AAAAT-TATA-ATAA
1 AAAATATATATATAA
*
525778 TAAATA-A-A-AT-A
1 AAAATATATATATAA
* *
525789 AAAATATATGACATTA
1 AAAATATAT-ATATAA
525805 AAAATATAT-T-TAA
1 AAAATATATATATAA
*
525818 AATATGATATTATATAA
1 AAAAT-ATA-TATATAA
*
525835 AAATTA-ATA-AT-A
1 AAAATATATATATAA
* *
525847 TAAATATGAATATATTA
1 AAAATAT--ATATATAA
*
525864 AAAATA-AAATATAA
1 AAAATATATATATAA
*
525878 AATAT-TATA-ATAA
1 AAAATATATATATAA
* *
525891 TAAATA-A-A-A-AT
1 AAAATATATATATAA
*
525902 AAAATATATGATATTA
1 AAAATATAT-ATATAA
525918 AAAATATAT-T-TAA
1 AAAATATATATATAA
*
525931 GAAATGATATTATATAA
1 AAAAT-ATA-TATATAA
*
525948 AAATTA-ATA-ATAA
1 AAAATATATATATAA
*
525961 AAAATATAAATATA
1 AAAATATATATATA
525975 TTAAACTTAT
Statistics
Matches: 176, Mismatches: 34, Indels: 66
0.64 0.12 0.24
Matches are distributed among these distances:
11 12 0.07
12 12 0.07
13 39 0.22
14 32 0.18
15 26 0.15
16 27 0.15
17 22 0.12
18 3 0.02
19 3 0.02
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AAAATATATATATAA
Found at i:525766 original size:72 final size:73
Alignment explanation
Indices: 525679--525814 Score: 172
Period size: 72 Copynumber: 1.9 Consensus size: 73
525669 AAAATATAAA
* * *
525679 AAAATAAATTATATAATA-TAGGTAA-AACAAATTAAAAT-AAAATATAT-ATATAAAAAATATA
1 AAAATAAAATATATAAAATTA--TAATAACAAA-TAAAATAAAAATATATGACATAAAAAATATA
525740 TTAAAGAAATG
63 TTAAAGAAATG
* *
525751 AAAATAAAATATATAAAATTATAATAATAAATAAAATAAAAATATATGACATTAAAAATATATT
1 AAAATAAAATATATAAAATTATAATAACAAATAAAATAAAAATATATGACATAAAAAATATATT
525815 TAAAATATGA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
71 9 0.16
72 30 0.55
73 16 0.29
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (73 bp):
AAAATAAAATATATAAAATTATAATAACAAATAAAATAAAAATATATGACATAAAAAATATATTA
AAGAAATG
Found at i:525769 original size:33 final size:32
Alignment explanation
Indices: 525713--525797 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 32
525703 AAACAAATTA
* * *
525713 AAATAAAAT-ATATATATAAAAAATATATTAAAG
1 AAATAAAATAAAATATAT-AAAATTATAAT-AAG
*
525746 AAATGAAAATAAAATATATAAAATTATAATAAT
1 AAAT-AAAATAAAATATATAAAATTATAATAAG
525779 AAATAAAATAAAAATATAT
1 AAATAAAAT-AAAATATAT
525798 GACATTAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 5 0.11
33 19 0.42
34 14 0.31
35 7 0.16
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (32 bp):
AAATAAAATAAAATATATAAAATTATAATAAG
Found at i:525784 original size:18 final size:17
Alignment explanation
Indices: 525754--525787 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
525744 AGAAATGAAA
*
525754 ATAAAATATATAAAATT
1 ATAAAATAAATAAAATT
525771 ATAATAATAAATAAAAT
1 ATAA-AATAAATAAAAT
525788 AAAAATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAATAAATAAAATT
Found at i:525834 original size:60 final size:59
Alignment explanation
Indices: 525770--525968 Score: 193
Period size: 60 Copynumber: 3.4 Consensus size: 59
525760 TATATAAAAT
* *
525770 TATAATAATAAATAAAATAAAAATATATGACATTAAAAATATATTTAAAATATGATATTA
1 TATAAAAATAAATAAAA-AAAAATATATGATATTAAAAATATATTTAAAATATGATATTA
* * * * *
525830 TATAAAAATTAAT-AATATAAATATGAAT-ATATTAAAAATAAAATATAAAATAT--TA-TA
1 TATAAAAATAAATAAAAAAAAATAT--ATGATATTAAAAAT-ATATTTAAAATATGATATTA
525887 -AT---AATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAGAA-ATGATATTA
1 TATAAAAATAAATAAAAA-AAAATATATGATATTAAAAATATATTTAA-AATATGATATTA
* *
525943 TATAAAAATTAATAATAAAAAATATA
1 TATAAAAATAAATAAAAAAAAATATA
525969 AATATATTAA
Statistics
Matches: 111, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
53 16 0.14
54 16 0.14
55 8 0.07
56 4 0.04
57 4 0.04
58 9 0.08
59 20 0.18
60 34 0.31
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (59 bp):
TATAAAAATAAATAAAAAAAAATATATGATATTAAAAATATATTTAAAATATGATATTA
Found at i:525864 original size:23 final size:22
Alignment explanation
Indices: 525829--525902 Score: 84
Period size: 21 Copynumber: 3.5 Consensus size: 22
525819 ATATGATATT
525829 ATATAAAA-ATTAATAATATAA
1 ATATAAAATATTAATAATATAA
* *
525850 ATATGAATATATTAAAAATA-AA
1 ATAT-AAAATATTAATAATATAA
525872 ATATAAAATATT-ATAATAATAA
1 ATATAAAATATTAATAAT-ATAA
525894 ATA-AAAATA
1 ATATAAAATA
525903 AAATATATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.09
21 18 0.40
22 14 0.31
23 9 0.20
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (22 bp):
ATATAAAATATTAATAATATAA
Found at i:525890 original size:113 final size:114
Alignment explanation
Indices: 525751--525979 Score: 376
Period size: 113 Copynumber: 2.0 Consensus size: 114
525741 TAAAGAAATG
525751 AAAATAAAATATATAAAATTATAATAATAAAT-AAAATAAAAATATATGACATTAAAAATATATT
1 AAAATAAAATATATAAAATTATAATAATAAATAAAAAT-AAAATATATGACATTAAAAATATATT
* *
525815 TAA-AATATGATATTATATAAAAATTAATAAT-ATAAATATGAATATATTA
65 TAAGAA-ATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
*
525864 AAAATAAAATATA-AAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATT
1 AAAATAAAATATATAAA-ATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATT
525928 TAAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
65 TAAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
525978 AA
1 AA
525980 CTTATATTTT
Statistics
Matches: 109, Mismatches: 3, Indels: 7
0.92 0.03 0.06
Matches are distributed among these distances:
112 3 0.03
113 81 0.74
114 25 0.23
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (114 bp):
AAAATAAAATATATAAAATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
Found at i:526149 original size:15 final size:15
Alignment explanation
Indices: 526129--526169 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
526119 TTTTCCTTAT
*
526129 AATCACATTGCTTGC
1 AATCACATTACTTGC
526144 AATCACATTACTTGC
1 AATCACATTACTTGC
526159 AATCACATTAC
1 AATCACATTAC
526170 CTGTAATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:526181 original size:15 final size:15
Alignment explanation
Indices: 526129--526182 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
526119 TTTTCCTTAT
* *
526129 AATCACATTGCTTGC
1 AATCACATTACCTGC
*
526144 AATCACATTACTTGC
1 AATCACATTACCTGC
*
526159 AATCACATTACCTGT
1 AATCACATTACCTGC
*
526174 AATTACATT
1 AATCACATT
526183 GCATTGTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.35
Consensus pattern (15 bp):
AATCACATTACCTGC
Found at i:526708 original size:16 final size:16
Alignment explanation
Indices: 526687--526719 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
526677 TTCATATAGA
526687 ACAATTAGA-ATAAGTG
1 ACAATTA-ATATAAGTG
526703 ACAATTAATATAAGTG
1 ACAATTAATATAAGTG
526719 A
1 A
526720 AATAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (16 bp):
ACAATTAATATAAGTG
Found at i:533752 original size:2 final size:2
Alignment explanation
Indices: 533745--533784 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
533735 TTTTCTCTTT
533745 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
533785 AAGGAAAACT
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):
TA
Found at i:544239 original size:15 final size:15
Alignment explanation
Indices: 544219--544257 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
544209 TTTACAATGC
544219 AATGTGATTACAGGT
1 AATGTGATTACAGGT
544234 AATGTGATTACAGGT
1 AATGTGATTACAGGT
544249 AATGTGATT
1 AATGTGATT
544258 GCATAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (15 bp):
AATGTGATTACAGGT
Found at i:544462 original size:60 final size:59
Alignment explanation
Indices: 544398--544588 Score: 182
Period size: 57 Copynumber: 3.3 Consensus size: 59
544388 TTAATTATTA
*
544398 AAATACAAGTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTT
1 AAATATAAGTTTAATATATTTATATTTTTTATT-TTAATTTTTATATAATATCATCTCTT
* * * *
544458 AAATAT-ATTTTTA-ATA-TTATATATTTTATTTTTATTTATTAT-T-ATA--ATCT-TAT
1 AAATATAAGTTTAATATATTTATATTTTTTATTTTAATTT-TTATATAATATCATCTCT-T
* * ** *
544511 ATATTTTATTTTTAATATATTTATATTTTTAATTTTTAATTTTTATATAATATCATCTCTT
1 A-AATATAAGTTTAATATATTTATATTTTTTA-TTTTAATTTTTATATAATATCATCTCTT
*
544572 AAATATATGTTTAATAT
1 AAATATAAGTTTAATAT
544589 CATATATTTT
Statistics
Matches: 104, Mismatches: 15, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
52 1 0.01
53 6 0.06
54 3 0.03
55 8 0.08
56 10 0.10
57 31 0.30
58 12 0.12
59 8 0.08
60 18 0.17
61 6 0.06
62 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (59 bp):
AAATATAAGTTTAATATATTTATATTTTTTATTTTAATTTTTATATAATATCATCTCTT
Found at i:544532 original size:38 final size:38
Alignment explanation
Indices: 544490--544683 Score: 91
Period size: 38 Copynumber: 5.1 Consensus size: 38
544480 ATTTTATTTT
544490 TATTTATTATTATAATCTTATATATTTTATTTTTAATA
1 TATTTATTATTATAATCTTATATATTTTATTTTTAATA
* * * *
544528 TATTTA-TATTTTTAAT-TTTTA-ATTTT-TATATAATA
1 TATTTATTA-TTATAATCTTATATATTTTATTTTTAATA
* * * * ** * *
544563 TCATCTCTTA-AATATATGTT-TAATATCATATATTTTATTTT
1 T-ATTTATTATTATA-ATCTTAT-ATATTTTAT-TTTTA-ATA
*
544604 TATTTATTATTATAATCTTATATAATTTATTTTT-AT-
1 TATTTATTATTATAATCTTATATATTTTATTTTTAATA
* * * * *
544640 TTTTTAATATATTTTTATATTATATATTTTA-TTTTAATT
1 TATTT-AT-TATTATAATCTTATATATTTTATTTTTAATA
544679 TATTT
1 TATTT
544684 TACCTATATT
Statistics
Matches: 112, Mismatches: 28, Indels: 31
0.65 0.16 0.18
Matches are distributed among these distances:
35 10 0.09
36 15 0.13
37 18 0.16
38 35 0.31
39 9 0.08
40 19 0.17
41 6 0.05
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (38 bp):
TATTTATTATTATAATCTTATATATTTTATTTTTAATA
Found at i:544547 original size:7 final size:7
Alignment explanation
Indices: 544514--544555 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
544504 ATCTTATATA
544514 TTTT-AT
1 TTTTAAT
544520 TTTTAAT
1 TTTTAAT
544527 ATATTTATAT
1 -T-TTTA-AT
544537 TTTTAAT
1 TTTTAAT
544544 TTTTAAT
1 TTTTAAT
544551 TTTTA
1 TTTTA
544556 TATAATATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.12
7 16 0.50
8 5 0.16
9 5 0.16
10 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTAAT
Found at i:544550 original size:114 final size:114
Alignment explanation
Indices: 544407--544638 Score: 419
Period size: 114 Copynumber: 2.0 Consensus size: 114
544397 AAAATACAAG
* *
544407 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATCTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTAATTATTAATTTTTATATAATATCATCTCTTAAATATATGTTTAA
* *
544472 TATTATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
66 TATCATATATTTTATTTTTATTTATTATTATAATCTTATATAATTTATT
*
544521 TTTAATATATTTATATTTTTAATTTTTAATTTTTATATAATATCATCTCTTAAATATATGTTTAA
1 TTTAATATATTTATATTTTTAATTATTAATTTTTATATAATATCATCTCTTAAATATATGTTTAA
544586 TATCATATATTTTATTTTTATTTATTATTATAATCTTATATAATTTATT
66 TATCATATATTTTATTTTTATTTATTATTATAATCTTATATAATTTATT
544635 TTTA
1 TTTA
544639 TTTTTTAATA
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (114 bp):
TTTAATATATTTATATTTTTAATTATTAATTTTTATATAATATCATCTCTTAAATATATGTTTAA
TATCATATATTTTATTTTTATTTATTATTATAATCTTATATAATTTATT
Found at i:544627 original size:33 final size:31
Alignment explanation
Indices: 544590--544673 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 31
544580 GTTTAATATC
*
544590 ATATATTTTATTTTTATTTATTATTATAATCTT
1 ATATATTTTATTTTTATTTATTAATAT-AT-TT
* *
544623 ATATAATTTATTTTTATTTTTTAATATATTT
1 ATATATTTTATTTTTATTTATTAATATATTT
* *
544654 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
544674 TAATTTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 10 0.23
32 10 0.23
33 24 0.55
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (31 bp):
ATATATTTTATTTTTATTTATTAATATATTT
Found at i:544718 original size:35 final size:32
Alignment explanation
Indices: 544655--544720 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 32
544645 AATATATTTT
544655 TATATTATATATTTTATTTTAATTTATTTTACC
1 TATATTATATATTTTATTTT-ATTTATTTTACC
544688 TATATTATATAAATTTTAATTTT-TTATATTTTA
1 TATATTATAT--ATTTT-ATTTTATT-TATTTTA
544721 TTTTATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
33 10 0.34
34 2 0.07
35 12 0.41
36 5 0.17
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (32 bp):
TATATTATATATTTTATTTTATTTATTTTACC
Found at i:544761 original size:33 final size:35
Alignment explanation
Indices: 544708--544784 Score: 103
Period size: 33 Copynumber: 2.4 Consensus size: 35
544698 AAATTTTAAT
544708 TTTTTATATT-T-TATTTTATTTT-A-ATTTTTGA
1 TTTTTATATTATATATTTTATTTTCATATTTTTGA
*
544739 TTTTTATATTATATATTTTATTTTCATATTTTTTA
1 TTTTTATATTATATATTTTATTTTCATATTTTTGA
544774 -TTTTA-ATTATA
1 TTTTTATATTATA
544785 ATGCTATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
31 10 0.24
32 1 0.02
33 17 0.41
34 6 0.15
35 7 0.17
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (35 bp):
TTTTTATATTATATATTTTATTTTCATATTTTTGA
Found at i:545081 original size:41 final size:41
Alignment explanation
Indices: 545018--545101 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
545008 ACTTCTCTTA
* * *
545018 TACCAAAGGTCATCTAAATCCCAAGTCCCTGGACAAACATT
1 TACCAAACGTCACCTAAATCCCAAATCCCTGGACAAACATT
* *
545059 TACCAAACGTCACCTAAGTCCCAAATCCGTGGACAAACATT
1 TACCAAACGTCACCTAAATCCCAAATCCCTGGACAAACATT
545100 TA
1 TA
545102 AGATTGGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.37, C:0.30, G:0.12, T:0.21
Consensus pattern (41 bp):
TACCAAACGTCACCTAAATCCCAAATCCCTGGACAAACATT
Found at i:556583 original size:30 final size:30
Alignment explanation
Indices: 556470--556579 Score: 81
Period size: 30 Copynumber: 3.9 Consensus size: 30
556460 TATTAAAATG
* * *
556470 TAATAAAATTTTTTTAAACATAGCATATAA
1 TAATAATATTTTTTTCAACATAGTATATAA
* * *
556500 CAACAATATTTTTTTCAACATA--ACAT-A
1 TAATAATATTTTTTTCAACATAGTATATAA
* * *
556527 TAAT-ATATTTTTGT--ACAT-GATGTGTAA
1 TAATAATATTTTTTTCAACATAG-TATATAA
556554 TAATAATATTTTTTTCAACATAGTAT
1 TAATAATATTTTTTTCAACATAGTAT
556580 GTAACAACCT
Statistics
Matches: 59, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
24 4 0.07
26 10 0.17
27 8 0.14
28 12 0.20
30 24 0.41
31 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (30 bp):
TAATAATATTTTTTTCAACATAGTATATAA
Found at i:556723 original size:30 final size:30
Alignment explanation
Indices: 556689--556825 Score: 107
Period size: 30 Copynumber: 4.9 Consensus size: 30
556679 TTATGACATG
*
556689 TAACAATAATATTTTTTTTAACATGATGTA
1 TAACAATAATATTTTTTTTAACATGACGTA
* * *
556719 TAAC----A-GTTTGTTTTAACCATGACGTG
1 TAACAATAATATTTTTTTTAA-CATGACGTA
*
556745 TAACAATAATATTTTTTTTAACATGATGTA
1 TAACAATAATATTTTTTTTAACATGACGTA
* * *
556775 TAAC----A-GTTTGTTTTAACCATGACGTG
1 TAACAATAATATTTTTTTTAA-CATGACGTA
556801 TAACAATAATA-TTTTTTTAACATGA
1 TAACAATAATATTTTTTTTAACATGA
556826 AATATAATAT
Statistics
Matches: 81, Mismatches: 14, Indels: 25
0.68 0.12 0.21
Matches are distributed among these distances:
25 18 0.22
26 24 0.30
29 5 0.06
30 25 0.31
31 9 0.11
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (30 bp):
TAACAATAATATTTTTTTTAACATGACGTA
Found at i:556732 original size:25 final size:26
Alignment explanation
Indices: 556704--556805 Score: 93
Period size: 26 Copynumber: 3.8 Consensus size: 26
556694 ATAATATTTT
556704 TTTTAA-CATGATGTATAACAGTTTG
1 TTTTAACCATGATGTATAACAGTTTG
* *
556729 TTTTAACCATGACGTGTAACAATAATA-TTTT
1 TTTTAACCATGA--TGT----ATAACAGTTTG
556760 TTTTAA-CATGATGTATAACAGTTTG
1 TTTTAACCATGATGTATAACAGTTTG
* *
556785 TTTTAACCATGACGTGTAACA
1 TTTTAACCATGATGTATAACA
556806 ATAATATTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
24 5 0.08
25 15 0.24
26 17 0.27
28 6 0.10
30 5 0.08
31 9 0.15
32 5 0.08
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (26 bp):
TTTTAACCATGATGTATAACAGTTTG
Found at i:556741 original size:56 final size:56
Alignment explanation
Indices: 556681--556825 Score: 274
Period size: 56 Copynumber: 2.6 Consensus size: 56
556671 GTTTTTAATT
*
556681 ATGACATGTAACAATAATATTTTTTTTAACATGATGTATAACAGTTTGTTTTAACC
1 ATGACGTGTAACAATAATATTTTTTTTAACATGATGTATAACAGTTTGTTTTAACC
556737 ATGACGTGTAACAATAATATTTTTTTTAACATGATGTATAACAGTTTGTTTTAACC
1 ATGACGTGTAACAATAATATTTTTTTTAACATGATGTATAACAGTTTGTTTTAACC
556793 ATGACGTGTAACAATAATA-TTTTTTTAACATGA
1 ATGACGTGTAACAATAATATTTTTTTTAACATGA
556826 AATATAATAT
Statistics
Matches: 88, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
55 14 0.16
56 74 0.84
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (56 bp):
ATGACGTGTAACAATAATATTTTTTTTAACATGATGTATAACAGTTTGTTTTAACC
Found at i:557131 original size:21 final size:20
Alignment explanation
Indices: 557078--557131 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
557068 TTATTTTTTA
*
557078 TTTTAAT-TAAAATTTAAAT
1 TTTTAATATTAAATTTAAAT
557097 TTTT-ATAATATAAATATTAAAT
1 TTTTAAT-AT-TAAAT-TTAAAT
557119 TTTTAATATTAAA
1 TTTTAATATTAAA
557132 ACTATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.07
19 4 0.14
20 1 0.03
21 8 0.28
22 12 0.41
23 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTAATATTAAATTTAAAT
Found at i:557570 original size:27 final size:29
Alignment explanation
Indices: 557517--557572 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
557507 AAATAATTTT
*
557517 TAAATACTTATTTTTTTACTTTCATATTA
1 TAAATACTCATTTTTTTACTTTCATATTA
*
557546 TAAATA-TCATTTTTTTA-TTTTATATTA
1 TAAATACTCATTTTTTTACTTTCATATTA
557573 AAAAATTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.36
28 10 0.40
29 6 0.24
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (29 bp):
TAAATACTCATTTTTTTACTTTCATATTA
Found at i:560323 original size:38 final size:39
Alignment explanation
Indices: 560272--560345 Score: 141
Period size: 38 Copynumber: 1.9 Consensus size: 39
560262 TGGTTTTGGT
560272 TCTAAATAATTGTTGTTCTACCTTGGTTGAT-ATAGTTG
1 TCTAAATAATTGTTGTTCTACCTTGGTTGATGATAGTTG
560310 TCTAAATAATTGTTGTTCTACCTTGGTTGATGATAG
1 TCTAAATAATTGTTGTTCTACCTTGGTTGATGATAG
560346 GTTTGAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 31 0.89
39 4 0.11
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (39 bp):
TCTAAATAATTGTTGTTCTACCTTGGTTGATGATAGTTG
Found at i:561992 original size:77 final size:77
Alignment explanation
Indices: 561900--562052 Score: 306
Period size: 77 Copynumber: 2.0 Consensus size: 77
561890 TAGATTATGA
561900 ATATTGTTATTATCTAAAAAGGGTATTTGTCCCATTAGTTGGCAGTAACCTTTTAGGGATAATAA
1 ATATTGTTATTATCTAAAAAGGGTATTTGTCCCATTAGTTGGCAGTAACCTTTTAGGGATAATAA
561965 GCCCTTTGGCAC
66 GCCCTTTGGCAC
561977 ATATTGTTATTATCTAAAAAGGGTATTTGTCCCATTAGTTGGCAGTAACCTTTTAGGGATAATAA
1 ATATTGTTATTATCTAAAAAGGGTATTTGTCCCATTAGTTGGCAGTAACCTTTTAGGGATAATAA
562042 GCCCTTTGGCA
66 GCCCTTTGGCA
562053 TCAGCTTTAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (77 bp):
ATATTGTTATTATCTAAAAAGGGTATTTGTCCCATTAGTTGGCAGTAACCTTTTAGGGATAATAA
GCCCTTTGGCAC
Found at i:585818 original size:12 final size:12
Alignment explanation
Indices: 585801--585825 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
585791 TGTGTGTCTG
585801 AGAGAGAGAGAA
1 AGAGAGAGAGAA
585813 AGAGAGAGAGAA
1 AGAGAGAGAGAA
585825 A
1 A
585826 TTATACTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAGAA
Found at i:590063 original size:33 final size:33
Alignment explanation
Indices: 590026--590460 Score: 447
Period size: 33 Copynumber: 13.2 Consensus size: 33
590016 AAGGTGGTGG
* * * *
590026 TTCAAAGGAGGGTCCAATTCAAGCACCTGCAGC
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
* * *
590059 TTCAAAAGAAGTTTCAAGTCAAGCACCTGCAGC
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
* * **
590092 TTCAAAAGAGGGTCCAATTCAAGCATCCACAGC
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
* *
590125 TTCAAATGAGGTTTCAAGTCAAGCATCTGCAGC
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
* * *
590158 TTCAAAAGAGGTTTCTAGTCAAGCAACTGCAGC
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
* * *
590191 TTCAAAAGAGGGTCCAATTCAAGCATCTGCAGT
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
* * * *
590224 TTCAGAAGAGGGTCCAATTCAAGCACCTGCAGC
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
* * *
590257 TTCAAAAGAGGTTTCAAGTCAAGCACCTGCGGC
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
** * * * *
590290 TTCAAAAGAGAATTCAACTGAAGCATCAGCACC
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
* * * * * *
590323 TTCAATAGAGGATTTAAATGAAGCATCTGCAGT
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
* *
590356 TTCAAAAGAGGGTTCAAATGAAGCATCTGCAGC
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
* * * *
590389 CTCAAAAGTGGTTTCAAGTCAAGCATCTACAGC
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
* * *
590422 TTCAAAAGAGGGCTCAAATCAAGCATCTACAGC
1 TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
590455 TTCAAA
1 TTCAAA
590461 CGAATCAGAC
Statistics
Matches: 337, Mismatches: 65, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 337 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (33 bp):
TTCAAAAGAGGGTTCAAGTCAAGCATCTGCAGC
Found at i:591238 original size:2 final size:2
Alignment explanation
Indices: 591231--591262 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
591221 CAAAGATGAT
591231 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
591263 GTTACGAGAT
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):
TA
Found at i:591721 original size:18 final size:19
Alignment explanation
Indices: 591698--591736 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
591688 GAAGTTTATG
*
591698 TAAATTATTA-ATAAAAAT
1 TAAATTAATATATAAAAAT
*
591716 TAAATTAATATATTAAAAT
1 TAAATTAATATATAAAAAT
591735 TA
1 TA
591737 GTTTGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATTAATATATAAAAAT
Found at i:592363 original size:16 final size:17
Alignment explanation
Indices: 592329--592366 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
592319 GAAAGAGTTT
**
592329 AAAGATAACAATGGGGA
1 AAAGATAACAATGAAGA
592346 AAAGAT-ACAATGAAGA
1 AAAGATAACAATGAAGA
592362 AAAGA
1 AAAGA
592367 ATGAGTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.61, C:0.05, G:0.24, T:0.11
Consensus pattern (17 bp):
AAAGATAACAATGAAGA
Found at i:597999 original size:35 final size:36
Alignment explanation
Indices: 597949--598016 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
597939 ATAAAATGAC
* *
597949 AAAATTACTCTTTATTATAATTTAGTAA-ATTAGAT
1 AAAATTACTCATTATTATAATTTAATAATATTAGAT
597984 AAAATTACTCATTATTATAATTTAATAATATTA
1 AAAATTACTCATTATTATAATTTAATAATATTA
598017 AAATTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 26 0.87
36 4 0.13
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (36 bp):
AAAATTACTCATTATTATAATTTAATAATATTAGAT
Found at i:604507 original size:21 final size:21
Alignment explanation
Indices: 604457--604507 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 21
604447 TGTTCAATTG
* *
604457 TTTTAC-T-AATGTTTTAATT
1 TTTTACATCAATGTTTCAATC
*
604476 TGTTTAAATCAATGTTTCAATC
1 T-TTTACATCAATGTTTCAATC
604498 TTTTACATCA
1 TTTTACATCA
604508 TGACTAGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 4 0.16
21 9 0.36
22 11 0.44
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (21 bp):
TTTTACATCAATGTTTCAATC
Found at i:615107 original size:24 final size:24
Alignment explanation
Indices: 615054--615107 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
615044 AACAATGTTA
* *
615054 GCTGCTTTTCCGGATTTGTTAGTT
1 GCTGCTTTTCCGAATTTGTTAGCT
* * *
615078 GTTGCTTTTTCGAATTTGTTTGCT
1 GCTGCTTTTCCGAATTTGTTAGCT
615102 GCTGCT
1 GCTGCT
615108 GCTTTTCCAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.07, C:0.17, G:0.24, T:0.52
Consensus pattern (24 bp):
GCTGCTTTTCCGAATTTGTTAGCT
Found at i:626120 original size:242 final size:243
Alignment explanation
Indices: 625648--626893 Score: 1141
Period size: 259 Copynumber: 5.0 Consensus size: 243
625638 ATTTGTGGAC
* ** *
625648 GAAGGGTGAGGTCAAGTGAAAGGCAAGTTCGGGAATATATGGATTGCTTGCTTACTCGAGCATTT
1 GAAGGATGAGGTTGAGTGAAAGGCAAGTTCGGGAATATATGGATTGCTTGCTCACTCGAGCATTT
** * *
625713 TTTTGAGGTCATTTTGCGTTTTGGAC-TTGATAT-GTTTGTCGAGTTTTATTGTATTATTTATAA
66 TTTTGAGGTCATTTTGCACTTTGGACTTTGATATAGTTTGTCGAGTTTTATTGTACTATTTATAT
625776 ATCATTTTCTTTTTCTTAGTATGTGTGTTTTTTTTTATTTATATATTTATTTTAAAAAATTTTAA
131 ATCATTTTCTTTTTCTTAGTATGTGTG--TTTTTTTATTTATATATTTATTTTAAAAAATTTTAA
* *
625841 CATATACATGTTTCTTCTATGAATGGGAGTA-GTATATTCATTTGCCAAT
194 CATATACATGTTTCTTTTATGAATGTGAGTATGTATATTCATTTGCCAAT
*
625890 GAAGGATGAGGTTGAGTGAAAGGCAAGTTCGGGAATATATGGATTGCTTGCTTACTCGAGCATTT
1 GAAGGATGAGGTTGAGTGAAAGGCAAGTTCGGGAATATATGGATTGCTTGCTCACTCGAGCATTT
** * *
625955 TTTTGAGGTCATTTTGCGTTTTGGACTTTGATAT-GTTTGTCGAGTTTTATTGTATTATTTATAA
66 TTTTGAGGTCATTTTGCACTTTGGACTTTGATATAGTTTGTCGAGTTTTATTGTACTATTTATAT
626019 ATCATTTTCTTTTTCTTAGTATGTGTGTTTTTTTATTTATATATTTATTTTAAAAAATTTTAACA
131 ATCATTTTCTTTTTCTTAGTATGTGTGTTTTTTTATTTATATATTTATTTTAAAAAATTTTAACA
* *
626084 TATACATGTTTCTTCTATGAATGGGAGTATGTATATTCATTTGCCAAT
196 TATACATGTTTCTTTTATGAATGTGAGTATGTATATTCATTTGCCAAT
* * * *
626132 GAAGGATGAGGTTGAGTGAAAGGCAAGTTCGGGAATATATTGATTGCTTGCTCGCTTGAACA-TT
1 GAAGGATGAGGTTGAGTGAAAGGCAAGTTCGGGAATATATGGATTGCTTGCTCACTCGAGCATTT
* * * * * *
626196 CTTTGCAGGTCTTTACACACTTTGCACTTTGGTATCTCT-ATCTAGTTTGTCAAGCTTTATTGTA
66 TTTTG-AGG----T---CATTTTGCACTTTGG-A-CTTTGATATAGTTTGTCGAGTTTTATTGTA
* * * * * * *
626260 CTATTAATATGTCATTCTCTTTTT-TTATGTGTGTTTCTTTTTCCTTTTATTTATATATGTATTT
121 CTATTTATATATCATTTTCTTTTTCTTA-GTATG--TGTGTTT--TTTTATTTATATAT-T-TAT
* * * * * * *
626324 TTTAAAAAAAATTTTAATATGTACGTATTTCTTTTGTGAATGTAAGTATGTATATTCATTTGTCA
179 TTT--AAAAAATTTTAACATATACATGTTTCTTTTATGAATGTGAGTATGTATATTCATTTGCCA
*
626389 AC
242 AT
** * * **
626391 GAAGGATGAGGTCAAGTGAAAGGCAAGCTT-GGGAATATATTGTTTGCTTGCTGGCTCGAGCATT
1 GAAGGATGAGGTTGAGTGAAAGGCAAG-TTCGGGAATATATGGATTGCTTGCTCACTCGAGCATT
* * * ** ** *
626455 CTTTCGAGGTCTTTTTATACTTTACACTTTGATATCTCTATTGAGTTTGTCGATTTTTATTGTAC
65 TTTTTGAGGTCATTTTGCACTTTGGACTTTG--A----TA-T-AGTTTGTCGAGTTTTATTGTAC
* * ** * * * * * **
626520 TATCTATATGTTGTTTTCTGTTTCTT--TGTGAGTGTTTTTTTATATATTTATTTATTTTTTAAA
122 TATTTATATATCATTTTCTTTTTCTTAGTATGTGTGTTTTTTTATTTATATATTTATTTTAAAAA
* * * *
626583 ATTTT-A-ATGTACATGTGTTTCTTTTATGAATGTAAGTATATATATTCATTTGCCGAT
187 ATTTTAACATATACA--TGTTTCTTTTATGAATGTGAGTATGTATATTCATTTGCCAAT
* ** * * *
626640 GAATGATGATGAGGTTGAGTGAAAGGCAAGCTCAAGAATATATCGATTGCTTGCTCCCTTGAGCA
1 GAA-G--GATGAGGTTGAGTGAAAGGCAAGTTCGGGAATATATGGATTGCTTGCTCACTCGAGCA
* * *
626705 TTTTTTTGAGGTCATTTTGCACTTTGCACTTTGGTATCTCTATCGAGGTTGTTGAGTTTTATTGT
63 TTTTTTTGAGGTCATTTTGCACTTTGGACTTT-G-A----TAT--AGTTTGTCGAGTTTTATTGT
* * * *
626770 ACTATCTATATATTATTCTT-TTTTTCTTTGTATGTGTTTCTTTTTTCTTATTTATATATTTAAT
120 ACTATTTATATATCATT-TTCTTTTTCTTAGTATGTG--T-GTTTTT-TTATTTATATATTT-AT
* * * * ** *
626834 TTTTAAAAATTTTAGCGTACATGTGTTTCTTTTGTGAATGTGAGTATGTATATTCATTTG
179 TTTAAAAAATTTTAACATATACATGTTTCTTTTATGAATGTGAGTATGTATATTCATTTG
626894 TCGACAAAAG
Statistics
Matches: 839, Mismatches: 113, Indels: 87
0.81 0.11 0.08
Matches are distributed among these distances:
241 73 0.09
242 166 0.20
243 64 0.08
246 1 0.00
247 6 0.01
248 1 0.00
249 59 0.07
250 11 0.01
251 52 0.06
252 130 0.15
253 21 0.03
254 4 0.00
255 19 0.02
256 2 0.00
257 15 0.02
258 13 0.02
259 192 0.23
260 8 0.01
261 2 0.00
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.47
Consensus pattern (243 bp):
GAAGGATGAGGTTGAGTGAAAGGCAAGTTCGGGAATATATGGATTGCTTGCTCACTCGAGCATTT
TTTTGAGGTCATTTTGCACTTTGGACTTTGATATAGTTTGTCGAGTTTTATTGTACTATTTATAT
ATCATTTTCTTTTTCTTAGTATGTGTGTTTTTTTATTTATATATTTATTTTAAAAAATTTTAACA
TATACATGTTTCTTTTATGAATGTGAGTATGTATATTCATTTGCCAAT
Found at i:627065 original size:508 final size:505
Alignment explanation
Indices: 626042--627142 Score: 1232
Period size: 508 Copynumber: 2.2 Consensus size: 505
626032 TCTTAGTATG
* * ** *
626042 TGTGTTTTTTTATTTATATATTTATTTTAAAAAATTTTAACATATACA--TGTTTCTTCTATGAA
1 TGTGTTTTTTTATATATTTATTTATTTTTTAAAATTTT-A-ATATACATGTGTTTCTTTTATGAA
** * * **
626105 TGGGAGTATGTATATTCATTTGCCAATGAAGGATGAGGTTGAGTGAAAGGCAAGTTCGGGAATAT
64 TGTAAGTATATATATTCATTTGCCAATGAAGGATGAGGTTGAGTGAAAGGCAAGCTCAAGAATAT
* *
626170 ATTGATTGCTTGCTCGCTTGAACATTCTTTGCAGGTCTTTACACACTTTGCACTTTGGTATCTCT
129 ATCGATTGCTTGCTCCCTTGAACATTCTTTGCAGGTCTTTACACACTTTGCACTTTGGTATCTCT
* *
626235 ATCTAGTTTGTCAAGCTTTATTGTACTATTAATATGTCATTCTCTTTTTTTATGTGTGTTTCTTT
194 ATCGAGGTTGTCAAGCTTTATTGTACTATTAATATGTCATTCTCTTTTTTTATGTGTGTTTCTTT
* * *
626300 TTCCTTTTATTTATATATGTATTTTTTAAAAAAAATTTTAATATGTACGTATTTCTTTTGTGAAT
259 TT-CTCTTATTTATATATGTAATTTTT--AAAAAATTTTAATACGTACGTATTTCTTTTGTGAAT
* * * * **
626365 GTAAGTATGTATATTCATTTGTCAACGAAGGATGAGGTCAAGTGAAAGGCAAGCTTGGGAATATA
321 GTAAGTATGTATATTCATTTGTCAACAAAAGATGAGG-CAAATGAAAAGCAAGCTTGAAAATATA
* * * *
626430 TTGTTTGCTTGCTGGCTCGAGCATTCTTTCGAGGTCTTTTTATACTTTACACTTTGATATCTCTA
385 TTGATTGCTTGCTGGCTCGAGCATTCTTTAGAGATCTTTTTACACTTTACACTTTGATATCTCTA
* * * * * * **
626495 TTGAGTTTGTCGATTTTTATTGTACTATCTATATGTTGTTTTCTGTTTCTTTGTGA
450 TCGAATTTATCGAGTTTTATTATACTATCTATATGTTATTTTCTGTTTCTTCATGA
*
626551 -GTGTTTTTTTATATATTTATTTATTTTTTAAAATTTTAATGTACATGTGTTTCTTTTATGAATG
1 TGTGTTTTTTTATATATTTATTTATTTTTTAAAATTTTAATATACATGTGTTTCTTTTATGAATG
*
626615 TAAGTATATATATTCATTTGCCGATGAATGATGATGAGGTTGAGTGAAAGGCAAGCTCAAGAATA
66 TAAGTATATATATTCATTTGCCAATGAA-G--GATGAGGTTGAGTGAAAGGCAAGCTCAAGAATA
* * **
626680 TATCGATTGCTTGCTCCCTTGAGCATTTTTTTG-AGGTCATTT-TGCACTTTGCACTTTGGTATC
128 TATCGATTGCTTGCTCCCTTGAACA-TTCTTTGCAGGTC-TTTACACACTTTGCACTTTGGTATC
** * *
626743 TCTATCGAGGTTGTTGAGTTTTATTGTACTATCTATATAT-T-ATTCT-TTTTTTCTTTGTATGT
191 TCTATCGAGGTTGTCAAGCTTTATTGTACTAT-TA-ATATGTCATTCTCTTTTTT-TATG--TGT
* * *
626805 GTTTCTTTTT-TCTTATTTATATATTTAATTTTT-AAAAATTTT-A-GCGTACATGTGTTTCTTT
251 GTTTCTTTTTCTCTTATTTATATATGTAATTTTTAAAAAATTTTAATACGTAC--GTATTTCTTT
* *
626866 TGTGAATGTGAGTATGTATATTCATTTGTCGACAAAAGATGAGG-AAATGAAAAGCAAGCTTGAA
314 TGTGAATGTAAGTATGTATATTCATTTGTCAACAAAAGATGAGGCAAATGAAAAGCAAGCTTGAA
* * *
626930 AATATATTGATTGCTTGCTCGCTCGCTCGAGCATTCTTTAGAGATCTTTTTGCGCTTTGCACTTT
379 AATATATTGATTGCTTGCT-G---GCTCGAGCATTCTTTAGAGATCTTTTTACACTTTACACTTT
*
626995 -AGTATTTCTATCGAATTTATCGAGTTTTATTATACTATCTATATGTTATTATT-T-TTT-TTCA
440 GA-TATCTCTATCGAATTTATCGAGTTTTATTATACTATCTATATGTTATT-TTCTGTTTCTTCA
627056 T-A
503 TGA
* * * * *
627058 TGTGTTTTATTATTATTATTATTATTATTATTTATTAAAATTTTAACATACGTGTGTTTTTTTCT
1 TGTGTTTTTTTA-TA-TA-T-TTA-T-TTATTTTTTAAAATTTTAATATACATGTGTTTCTTT-T
*
627123 GTGAATGTGAA-TATATATAT
59 ATGAATGT-AAGTATATATAT
627143 ATATATGAAC
Statistics
Matches: 501, Mismatches: 62, Indels: 52
0.81 0.10 0.08
Matches are distributed among these distances:
506 44 0.09
507 4 0.01
508 144 0.29
509 7 0.01
510 85 0.17
511 134 0.27
512 15 0.03
513 18 0.04
514 31 0.06
515 17 0.03
516 2 0.00
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (505 bp):
TGTGTTTTTTTATATATTTATTTATTTTTTAAAATTTTAATATACATGTGTTTCTTTTATGAATG
TAAGTATATATATTCATTTGCCAATGAAGGATGAGGTTGAGTGAAAGGCAAGCTCAAGAATATAT
CGATTGCTTGCTCCCTTGAACATTCTTTGCAGGTCTTTACACACTTTGCACTTTGGTATCTCTAT
CGAGGTTGTCAAGCTTTATTGTACTATTAATATGTCATTCTCTTTTTTTATGTGTGTTTCTTTTT
CTCTTATTTATATATGTAATTTTTAAAAAATTTTAATACGTACGTATTTCTTTTGTGAATGTAAG
TATGTATATTCATTTGTCAACAAAAGATGAGGCAAATGAAAAGCAAGCTTGAAAATATATTGATT
GCTTGCTGGCTCGAGCATTCTTTAGAGATCTTTTTACACTTTACACTTTGATATCTCTATCGAAT
TTATCGAGTTTTATTATACTATCTATATGTTATTTTCTGTTTCTTCATGA
Found at i:627070 original size:3 final size:3
Alignment explanation
Indices: 627064--627094 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
627054 CATATGTGTT
627064 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
627095 AAATTTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:643339 original size:12 final size:12
Alignment explanation
Indices: 643322--643347 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
643312 GAACTGAACC
643322 AGGAGAAGCTGA
1 AGGAGAAGCTGA
643334 AGGAGAAGCTGA
1 AGGAGAAGCTGA
643346 AG
1 AG
643348 AAAAATCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.42, T:0.08
Consensus pattern (12 bp):
AGGAGAAGCTGA
Found at i:650805 original size:43 final size:40
Alignment explanation
Indices: 650752--650830 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
650742 TAAAAGATTG
*
650752 TGTTTCAGAATAATGAAGCTAATAATGGCAGAGTTTTGAGAAC
1 TGTTCCAGAATAATG-AG--AATAATGGCAGAGTTTTGAGAAC
*
650795 TGTTCCAGAATAATGAGGATAATGGCAGAGTTTTGA
1 TGTTCCAGAATAATGAGAATAATGGCAGAGTTTTGA
650831 AGAAATCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 18 0.53
42 2 0.06
43 14 0.41
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.30
Consensus pattern (40 bp):
TGTTCCAGAATAATGAGAATAATGGCAGAGTTTTGAGAAC
Found at i:656785 original size:24 final size:24
Alignment explanation
Indices: 656757--656805 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
656747 GAATATCCAA
656757 ACCAGCTTTCAAAGAGAGTTTTAC
1 ACCAGCTTTCAAAGAGAGTTTTAC
656781 ACCAGCTTTCAAAGAGAGTTTTAC
1 ACCAGCTTTCAAAGAGAGTTTTAC
656805 A
1 A
656806 GATATAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (24 bp):
ACCAGCTTTCAAAGAGAGTTTTAC
Found at i:658950 original size:21 final size:21
Alignment explanation
Indices: 658926--658999 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
658916 CTTGATGCAA
658926 CCACTGCTCCAATTGATTCTT
1 CCACTGCTCCAATTGATTCTT
* *
658947 CCACGGCTCCAATTGACTCTT
1 CCACTGCTCCAATTGATTCTT
* * *
658968 CAACTGCTCTAATTGATCCTT
1 CCACTGCTCCAATTGATTCTT
*
658989 CCACTGTTCCA
1 CCACTGCTCCA
659000 TCGCTTCCAT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.34
Consensus pattern (21 bp):
CCACTGCTCCAATTGATTCTT
Found at i:659869 original size:7 final size:7
Alignment explanation
Indices: 659857--659886 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
659847 CCACATATTC
659857 TGAAATT
1 TGAAATT
659864 TGAAATT
1 TGAAATT
659871 TGAAATT
1 TGAAATT
659878 TGAGAATT
1 TGA-AATT
659886 T
1 T
659887 ATATGAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (7 bp):
TGAAATT
Found at i:663447 original size:14 final size:14
Alignment explanation
Indices: 663428--663455 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
663418 TCCAAAAAAA
663428 TTTTAATTTGATGT
1 TTTTAATTTGATGT
663442 TTTTAATTTGATGT
1 TTTTAATTTGATGT
663456 GAAGTTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (14 bp):
TTTTAATTTGATGT
Found at i:676630 original size:10 final size:10
Alignment explanation
Indices: 676614--676644 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
676604 ATCAAAATAA
676614 ATTTAATTAT
1 ATTTAATTAT
*
676624 TTTTAATTAT
1 ATTTAATTAT
676634 ATTTAATTAT
1 ATTTAATTAT
676644 A
1 A
676645 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTTAATTAT
Found at i:677635 original size:108 final size:108
Alignment explanation
Indices: 677511--677705 Score: 234
Period size: 108 Copynumber: 1.8 Consensus size: 108
677501 TTATTTATAA
* ** * * * *
677511 AATATATTGATATTTTATTGAATT-TGATTAATTTTTATGATTTTGATATTAGTTGATTAAGAGG
1 AATATATTGATATTTTACTGAATTCAAATTAATTTTT-TCATCTAGATATTAATTGATTAAGAGG
677575 GAA-CTA-TTAATTTGTTTTTAAACTTAACATTGTTTTTGATTT
65 GAACCTATTTAATTTGTTTTTAAACTTAACATTGTTTTTGATTT
* * *
677617 AATATAATATGATGTTTTACTGAATTCAAATTGATTTTTTCATCTAGGTATTAATTGATTAAGAG
1 AATAT-AT-TGATATTTTACTGAATTCAAATTAATTTTTTCATCTAGATATTAATTGATTAAGAG
**
677682 GGAACCTATTTGTTTTGTTTTTAA
64 GGAACCTATTTAATTTGTTTTTAA
677706 GCTGGAGATC
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
106 5 0.07
107 2 0.03
108 40 0.56
109 12 0.17
110 13 0.18
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (108 bp):
AATATATTGATATTTTACTGAATTCAAATTAATTTTTTCATCTAGATATTAATTGATTAAGAGGG
AACCTATTTAATTTGTTTTTAAACTTAACATTGTTTTTGATTT
Found at i:677872 original size:120 final size:122
Alignment explanation
Indices: 677663--677881 Score: 309
Period size: 120 Copynumber: 1.8 Consensus size: 122
677653 TTTTCATCTA
* * * *
677663 GGTATTAATTGATTAAGAGGGAACCTATTTGTTTTGTTTTTAAGCTGGAGATCGATTTTGGTTCA
1 GGTATTAATTGATTAAGAAGGAACCTATTAGTTTTGTTTTTAAGCTCGAGATCGATTTTGCTTCA
*
677728 ATTTAATACAATACTTTATTGAATTCAGTTAATTCAAATTGTTTTTTTTTTAATTTT
66 ATTTAATACAATACTGTATTGAATTCAGTTAATTCAAATTGTTTTTTTTTTAATTTT
* *
677785 GGTATTAATTGATTAAGAAGG-ACTCTATTAG-TTTGTTTTTAAGCTCGATATTGA-TTTGCTTC
1 GGTATTAATTGATTAAGAAGGAAC-CTATTAGTTTTGTTTTTAAGCTCGAGATCGATTTTGCTTC
* * **
677847 GATTTAATATAATACTGTATTGAATTTGGTTAATT
65 AATTTAATACAATACTGTATTGAATTCAGTTAATT
677882 TGAATTAATT
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
120 37 0.44
121 22 0.26
122 26 0.31
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.48
Consensus pattern (122 bp):
GGTATTAATTGATTAAGAAGGAACCTATTAGTTTTGTTTTTAAGCTCGAGATCGATTTTGCTTCA
ATTTAATACAATACTGTATTGAATTCAGTTAATTCAAATTGTTTTTTTTTTAATTTT
Found at i:691373 original size:17 final size:18
Alignment explanation
Indices: 691341--691375 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
691331 CGTTAACACC
691341 CTTCTCTCTCCTTTTCTT
1 CTTCTCTCTCCTTTTCTT
*
691359 CTTCT-TCTTCTTTTCTT
1 CTTCTCTCTCCTTTTCTT
691376 GGTTCGCCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (18 bp):
CTTCTCTCTCCTTTTCTT
Found at i:693163 original size:30 final size:30
Alignment explanation
Indices: 693123--693180 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
693113 ACATCCATTC
* *
693123 TTCTTTCTAAATTTTTCTCTATAATTATTT
1 TTCTTCCTAAATTTTCCTCTATAATTATTT
*
693153 TTCTTCCTAAATTTTCCTCTGTAATTAT
1 TTCTTCCTAAATTTTCCTCTATAATTAT
693181 ACCTAACAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.02, T:0.59
Consensus pattern (30 bp):
TTCTTCCTAAATTTTCCTCTATAATTATTT
Found at i:700381 original size:2 final size:2
Alignment explanation
Indices: 700369--700412 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
700359 GTTTGAATTC
* * *
700369 AT AT GT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
700411 AT
1 AT
700413 TTATCGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:701273 original size:3 final size:3
Alignment explanation
Indices: 701265--701292 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
701255 CTTTGTCATT
701265 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
701293 TACACTGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:706529 original size:2 final size:2
Alignment explanation
Indices: 706522--706550 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
706512 TTTGATAAAG
706522 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
706551 AAAACACCAT
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:718410 original size:29 final size:29
Alignment explanation
Indices: 718378--718437 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
718368 CGGTGCAATT
* *
718378 AATGAATTTAAAATGCATTGACAAAGTCA
1 AATGAATTTAAAATACATCGACAAAGTCA
* *
718407 AATGAATTTCAAATACATCGATAAAGTCA
1 AATGAATTTAAAATACATCGACAAAGTCA
718436 AA
1 AA
718438 ATTATAGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.27
Consensus pattern (29 bp):
AATGAATTTAAAATACATCGACAAAGTCA
Found at i:725433 original size:19 final size:18
Alignment explanation
Indices: 725409--725445 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
725399 AAATTTTAAT
725409 TTATTTTAATTAAAATAAA
1 TTATTTT-ATTAAAATAAA
*
725428 TTATTTTTTTAAAATAAA
1 TTATTTTATTAAAATAAA
725446 ACGAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTTTATTAAAATAAA
Found at i:740293 original size:15 final size:16
Alignment explanation
Indices: 740242--740290 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
740232 CACTCTGAAC
*
740242 TTGTTTTTATGGTACT
1 TTGTTTTTACGGTACT
740258 TTGTTTTTACGGTACT
1 TTGTTTTTACGGTACT
740274 TTGTTTTTACGGTACT
1 TTGTTTTTACGGTACT
740290 T
1 T
740291 GTTCCTAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.59
Consensus pattern (16 bp):
TTGTTTTTACGGTACT
Found at i:745135 original size:8 final size:7
Alignment explanation
Indices: 745114--745138 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
745104 GACGTCTTCA
745114 CTTCCCC
1 CTTCCCC
745121 CTTCCCC
1 CTTCCCC
745128 CTTCCCC
1 CTTCCCC
745135 CTTC
1 CTTC
745139 TTCTCAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (7 bp):
CTTCCCC
Found at i:747954 original size:21 final size:20
Alignment explanation
Indices: 747929--747968 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
747919 TGGGTTTCTT
*
747929 TCTTTCTTTGTTTCTTTTTTC
1 TCTTT-TTTGTTTCCTTTTTC
*
747950 TCTTTTTTTTTTCCTTTTT
1 TCTTTTTTGTTTCCTTTTT
747969 GGTAGCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (20 bp):
TCTTTTTTGTTTCCTTTTTC
Found at i:751239 original size:15 final size:15
Alignment explanation
Indices: 751219--751248 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
751209 TCAAATTGAC
751219 AAAAATGAAAAAATT
1 AAAAATGAAAAAATT
*
751234 AAAAATTAAAAAATT
1 AAAAATGAAAAAATT
751249 CCCAACTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAAATGAAAAAATT
Found at i:755864 original size:17 final size:17
Alignment explanation
Indices: 755827--755864 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
755817 CTCTCTCTCT
*
755827 TTTTCCTTTTCTTTTTC
1 TTTTCCTTTTCTTTTCC
755844 TTTTCC-TTTCTTTTCC
1 TTTTCCTTTTCTTTTCC
755860 ATTTT
1 -TTTT
755865 TTTTCTCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTCCTTTTCTTTTCC
Found at i:757652 original size:13 final size:13
Alignment explanation
Indices: 757634--757659 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
757624 AAGGCCACAG
757634 AGAGAGAGAGAAA
1 AGAGAGAGAGAAA
757647 AGAGAGAGAGAAA
1 AGAGAGAGAGAAA
757660 GGGTCTTTTA
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:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (13 bp):
AGAGAGAGAGAAA
Found at i:758100 original size:3 final size:3
Alignment explanation
Indices: 758080--758116 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
758070 GCCAAACCAT
* *
758080 TAG TGG TAG TAG TTG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
758117 GTTATTGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (3 bp):
TAG
Found at i:760990 original size:5 final size:5
Alignment explanation
Indices: 760973--761009 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
760963 TTACTACTAC
* *
760973 TCCTT TCCCT TCCTT TCCTT TCTTT TCCTT TCCTT TC
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TC
761010 TTGCTTTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
TCCTT
Found at i:761033 original size:15 final size:16
Alignment explanation
Indices: 761005--761042 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
760995 TTTTCCTTTC
761005 CTTTCTTGCTTTCTAT
1 CTTTCTTGCTTTCTAT
761021 CTTTCTT-CTTTCTAT
1 CTTTCTTGCTTTCTAT
761036 CTTTCTT
1 CTTTCTT
761043 TTCTCTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.05, C:0.26, G:0.03, T:0.66
Consensus pattern (16 bp):
CTTTCTTGCTTTCTAT
Found at i:761199 original size:6 final size:6
Alignment explanation
Indices: 761184--761220 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
761174 CCTTTCTAAC
*
761184 CCCACG CCCACA CCCACA CCCACA CCCACA CCCACA C
1 CCCACA CCCACA CCCACA CCCACA CCCACA CCCACA C
761221 GCACCCTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.30, C:0.68, G:0.03, T:0.00
Consensus pattern (6 bp):
CCCACA
Found at i:763840 original size:17 final size:16
Alignment explanation
Indices: 763806--763838 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
763796 GAGTAACGAT
763806 ATATTTTATTTTTTAA
1 ATATTTTATTTTTTAA
763822 ATATTTT-TTTTATTAA
1 ATATTTTATTTT-TTAA
763838 A
1 A
763839 ATTAAGTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATATTTTATTTTTTAA
Found at i:768339 original size:2 final size:2
Alignment explanation
Indices: 768332--768361 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
768322 AGAAAGTAAC
768332 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
768362 TTGTTTCAAT
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:773752 original size:5 final size:5
Alignment explanation
Indices: 773744--773770 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
773734 TTTTTCCCTC
773744 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
773771 GGGTACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:784458 original size:5 final size:6
Alignment explanation
Indices: 784444--784468 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
784434 TTTTTTCTCA
784444 TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT T
784469 ATTCTGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:784959 original size:15 final size:15
Alignment explanation
Indices: 784939--784968 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
784929 ATTCAATAAT
784939 TTAATAAATTATTTA
1 TTAATAAATTATTTA
*
784954 TTAATATATTATTTA
1 TTAATAAATTATTTA
784969 AATTCCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAATAAATTATTTA
Found at i:789044 original size:2 final size:2
Alignment explanation
Indices: 789026--789063 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
789016 TTGGACAGTA
* *
789026 AG AG GG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
789064 CGCGAGGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:801727 original size:3 final size:3
Alignment explanation
Indices: 801719--801756 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
801709 GGCGGAGGTC
*
801719 GAG GAG GAG AAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
801757 TGGATTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:821135 original size:24 final size:24
Alignment explanation
Indices: 821093--821140 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
821083 CACAGACATC
* *
821093 ACAACGCAGGTCAAATTGGGTATT
1 ACAAAGCAGGTCAAATTGGCTATT
**
821117 ACAAAGCAGGTCATGTTGGCTATT
1 ACAAAGCAGGTCAAATTGGCTATT
821141 GTAAACCATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (24 bp):
ACAAAGCAGGTCAAATTGGCTATT
Found at i:825305 original size:6 final size:6
Alignment explanation
Indices: 825296--825322 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
825286 AAATGGAGAA
825296 GATGGT GATGGT GATGGT GATGGT GAT
1 GATGGT GATGGT GATGGT GATGGT GAT
825323 TTGTCGAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.33
Consensus pattern (6 bp):
GATGGT
Found at i:825706 original size:19 final size:19
Alignment explanation
Indices: 825674--825712 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
825664 GATGATGTCA
*
825674 TTTTTTATTTATTTTATAAT
1 TTTTTTATTGATTTTA-AAT
825694 TTTTTTA-TGATTTTAAAT
1 TTTTTTATTGATTTTAAAT
825712 T
1 T
825713 ACAAAACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 7 0.39
20 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTTTATTGATTTTAAAT
Found at i:848595 original size:17 final size:17
Alignment explanation
Indices: 848564--848609 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
848554 GAAAGACTTA
848564 TTTTT-TAATTAAATAAT
1 TTTTTATAATT-AATAAT
848581 TTTTTATAATTAATAAT
1 TTTTTATAATTAATAAT
**
848598 TAATTATAATTA
1 TTTTTATAATTA
848610 CTTATAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTTATAATTAATAAT
Found at i:848606 original size:10 final size:10
Alignment explanation
Indices: 848587--848630 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
848577 TAATTTTTTA
848587 TAATTAATAAT
1 TAATT-ATAAT
848598 TAATTATAAT
1 TAATTATAAT
*
848608 TACTTATAAT
1 TAATTATAAT
848618 AATAATTATAAT
1 --TAATTATAAT
848630 T
1 T
848631 TTATATCACG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 15 0.52
11 5 0.17
12 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (10 bp):
TAATTATAAT
Found at i:852594 original size:56 final size:55
Alignment explanation
Indices: 852526--852633 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 55
852516 CCTATGCCCA
*
852526 TTGAACAGTTGGGCT-AAATTAGTTTCGTATTTGGCACAAAACTGATGAGGGTTTCT
1 TTGAAAAGTTGGGCTCAAATT-GTTTCGTATTTGGCACAAAA-TGATGAGGGTTTCT
* * * *
852582 TTGAAAAGTTGGGCTCGAGTTGTTTTGTATTTGGCCCAAAATGATGAGGGTT
1 TTGAAAAGTTGGGCTCAAATTGTTTCGTATTTGGCACAAAATGATGAGGGTT
852634 GGACTGTAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
55 11 0.24
56 32 0.70
57 3 0.07
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.36
Consensus pattern (55 bp):
TTGAAAAGTTGGGCTCAAATTGTTTCGTATTTGGCACAAAATGATGAGGGTTTCT
Found at i:871425 original size:27 final size:26
Alignment explanation
Indices: 871358--871408 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
871348 GTCGTGTCCC
*
871358 CACCTTGCTCAATTCAATGCCCCCCT
1 CACCATGCTCAATTCAATGCCCCCCT
871384 CACCATGCTCAATTCAATGCCCCCC
1 CACCATGCTCAATTCAATGCCCCCC
871409 ATTACCTGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.47, G:0.08, T:0.24
Consensus pattern (26 bp):
CACCATGCTCAATTCAATGCCCCCCT
Found at i:872307 original size:2 final size:2
Alignment explanation
Indices: 872300--872330 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
872290 TAGACTAAGC
*
872300 AT AT AT AT AA 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 A
872331 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:872335 original size:2 final size:2
Alignment explanation
Indices: 872330--872364 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
872320 ATATATATAT
872330 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
872365 TTGATAATGA
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:874415 original size:3 final size:3
Alignment explanation
Indices: 874407--874432 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
874397 GTTGAAGACA
874407 TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TG
874433 GATTCACTGT
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:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
TGT
Found at i:874527 original size:12 final size:12
Alignment explanation
Indices: 874512--874537 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
874502 GAGAAAGGGA
874512 GAGAGAGAGAAG
1 GAGAGAGAGAAG
874524 GAGAGAGAGAAG
1 GAGAGAGAGAAG
874536 GA
1 GA
874538 AAGAAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (12 bp):
GAGAGAGAGAAG
Found at i:884326 original size:8 final size:8
Alignment explanation
Indices: 884313--884342 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
884303 GATAGGCATA
884313 GAGAGAGG
1 GAGAGAGG
884321 GAGAGAGG
1 GAGAGAGG
*
884329 GAGAGAGA
1 GAGAGAGG
884337 GAGAGA
1 GAGAGA
884343 CTTATACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (8 bp):
GAGAGAGG
Found at i:906651 original size:35 final size:37
Alignment explanation
Indices: 906589--906663 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 37
906579 CAATGCACAT
* * *
906589 AAAAAGCAAGAAAAATTGGAATCAAACTATCATTGGC
1 AAAAAGCAAGAAAAATTAGAATCAAACTATAAATGGC
*
906626 AAAAA-CAAG-AAAATTAGAATGAAACTATAAATGGC
1 AAAAAGCAAGAAAAATTAGAATCAAACTATAAATGGC
906661 AAA
1 AAA
906664 TTCCACTGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 25 0.74
36 4 0.12
37 5 0.15
ACGTcount: A:0.57, C:0.11, G:0.15, T:0.17
Consensus pattern (37 bp):
AAAAAGCAAGAAAAATTAGAATCAAACTATAAATGGC
Found at i:913496 original size:21 final size:21
Alignment explanation
Indices: 913454--913493 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
913444 TTGTATATTA
913454 TTTTATTATATTTAATTTAAT
1 TTTTATTATATTTAATTTAAT
* *
913475 TTTTA-TATTTTTATTTTAA
1 TTTTATTATATTTAATTTAA
913494 ATTAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATTATATTTAATTTAAT
Found at i:915011 original size:41 final size:39
Alignment explanation
Indices: 914937--915020 Score: 98
Period size: 41 Copynumber: 2.1 Consensus size: 39
914927 TGATTTATGA
* *
914937 TTTTATATAATTATTATTTATATAAAAATTTAAATTTAT
1 TTTTATATAATAATTATTTATATAAAAATTTAAATATAT
* *
914976 TTTTATATTAATAATTAATTTTTAGTTAAAA-TTAAATATAT
1 TTTTATA-TAATAATT-ATTTATA-TAAAAATTTAAATATAT
915017 TTTT
1 TTTT
915021 GGTATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 7 0.18
40 7 0.18
41 19 0.50
42 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (39 bp):
TTTTATATAATAATTATTTATATAAAAATTTAAATATAT
Found at i:941433 original size:96 final size:94
Alignment explanation
Indices: 941322--941508 Score: 257
Period size: 96 Copynumber: 2.0 Consensus size: 94
941312 TTCTCTTTTC
* * *
941322 GACTTTATAAAAATATAAGAGTTAAATTAATTTTTTTATATAATTCAAAGACTTATTAAATATTA
1 GACTTTATAAAAATATAAGAGTTAAATTAACTTTCTTATATAATTCAAAGACTTATTAAACATTA
941387 CACTTAAAAAATTTAAAATAAAAATCTCTCT
66 CAC--AAAAAATTTAAAATAAAAATCTCTCT
* ** * * * *
941418 GACTTTATAAAAATATAAGAGTTATATTGGCTTTCTTATATAGTTCAAAGACTTATTGAGCATTG
1 GACTTTATAAAAATATAAGAGTTAAATTAACTTTCTTATATAATTCAAAGACTTATTAAACATTA
*
941483 CACAAAAAGTTTAAAATAAAAATCTC
66 CACAAAAAATTTAAAATAAAAATCTC
941509 ACTAATGTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 22 0.28
96 58 0.73
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (94 bp):
GACTTTATAAAAATATAAGAGTTAAATTAACTTTCTTATATAATTCAAAGACTTATTAAACATTA
CACAAAAAATTTAAAATAAAAATCTCTCT
Done.