Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold307
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: 622582
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 5
Found at i:138513 original size:8 final size:8
Alignment explanation
Indices: 138480--138606 Score: 70
Period size: 8 Copynumber: 15.6 Consensus size: 8
138470 AATATAATAA
138480 ATTTATAT
1 ATTTATAT
*
138488 AATTTTTAT
1 -ATTTATAT
*
138497 ATATTATTT
1 AT-TTATAT
*
138506 ATTTATTT
1 ATTTATAT
138514 ATTTATAT
1 ATTTATAT
*
138522 -TTGATAT
1 ATTTATAT
138529 ATTTATAT
1 ATTTATAT
138537 ATTTATATCAT
1 A-TT-TAT-AT
138548 ATTTATATT
1 ATTTATA-T
138557 ACTTT-TAT
1 A-TTTATAT
*
138565 A-TTATGT
1 ATTTATAT
138572 -TTTA-AT
1 ATTTATAT
138578 -TTT-TAT
1 ATTTATAT
*
138584 ATTTATTT
1 ATTTATAT
138592 ATCTATATAT
1 AT-T-TATAT
138602 ATTTA
1 ATTTA
138607 ATTTTAACTA
Statistics
Matches: 94, Mismatches: 10, Indels: 29
0.71 0.08 0.22
Matches are distributed among these distances:
6 8 0.09
7 14 0.15
8 31 0.33
9 24 0.26
10 14 0.15
11 3 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (8 bp):
ATTTATAT
Found at i:138531 original size:23 final size:23
Alignment explanation
Indices: 138295--138544 Score: 74
Period size: 23 Copynumber: 10.6 Consensus size: 23
138285 AGAAAAAAAA
* *
138295 TTATTTATTCATAT-TTATATTACT
1 TTATATATTTATATATTATA-TA-T
* *
138319 TTTTATATTTAAAATATTATATAT
1 TTATATATTT-ATATATTATATAT
138343 TTATATATTTTTTATATATTA-ATAAT
1 TTATATA---TTTATATATTATAT-AT
* * *
138369 TGATTTTATTT-TATGA--ATATTT
1 TTA-TATATTTATAT-ATTATATAT
* *
138391 TTATATATGTATATTATT-TTTAT
1 TTATATATTTATA-TATTATATAT
* * *
138414 GTTATAT-TTTAAATATTTTTTAT
1 -TTATATATTTATATATTATATAT
**
138437 AAATATTATTT-TGATATTAT-T-T
1 TTATA-TATTTAT-ATATTATATAT
* * * *
138459 TT-TATGTTTAAAATATAATAAAT
1 TTATATATTT-ATATATTATATAT
*
138482 TTATATAATTTTTATATATTATTTAT
1 TTATAT-A--TTTATATATTATATAT
*
138508 TTATTTATTTATAT-TTGATATAT
1 TTATATATTTATATATT-ATATAT
138531 TTATATATTTATAT
1 TTATATATTTATAT
138545 CATATTTATA
Statistics
Matches: 165, Mismatches: 34, Indels: 55
0.65 0.13 0.22
Matches are distributed among these distances:
20 4 0.02
21 13 0.08
22 17 0.10
23 48 0.29
24 36 0.22
25 8 0.05
26 30 0.18
27 9 0.05
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.62
Consensus pattern (23 bp):
TTATATATTTATATATTATATAT
Found at i:141478 original size:13 final size:14
Alignment explanation
Indices: 141452--141483 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
141442 TATTAAAAAT
141452 ATATTTTTATATTA
1 ATATTTTTATATTA
141466 ATATTTTTA-ATTA
1 ATATTTTTATATTA
141479 A-ATTT
1 ATATTT
141484 AAATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.22
13 5 0.28
14 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATTTTTATATTA
Found at i:141795 original size:11 final size:11
Alignment explanation
Indices: 141781--141806 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
141771 ATTATTTTTA
141781 TATTTGTAATT
1 TATTTGTAATT
141792 TATTTGTAATT
1 TATTTGTAATT
141803 TATT
1 TATT
141807 ATTTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (11 bp):
TATTTGTAATT
Found at i:142451 original size:18 final size:18
Alignment explanation
Indices: 142405--142467 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 18
142395 AATTTTTATT
142405 TTATATCAT-ATTTTTTAA
1 TTATAT-ATAATTTTTTAA
* *
142423 -TAT-TTTTATTTTTTAA
1 TTATATATAATTTTTTAA
*
142439 TTATATATAATTTTTGTTA
1 TTATATATAATTTTT-TAA
142458 TATATATATA
1 T-TATATATA
142468 TATATTTAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
15 1 0.03
16 10 0.28
17 6 0.17
18 8 0.22
19 3 0.08
20 8 0.22
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTATATATAATTTTTTAA
Found at i:142559 original size:20 final size:22
Alignment explanation
Indices: 142534--142577 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
142524 ATAAATAAAT
142534 TTTTAATAATAAT-TTTTA-TA
1 TTTTAATAATAATATTTTACTA
142554 TTTTAATAATAATATTTTACTA
1 TTTTAATAATAATATTTTACTA
142576 TT
1 TT
142578 AAAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.59
21 5 0.23
22 4 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTAATAATAATATTTTACTA
Found at i:143509 original size:10 final size:10
Alignment explanation
Indices: 143472--143508 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
143462 AAATCCTTTA
143472 ATATATACAT
1 ATATATACAT
*
143482 TTATATACAT
1 ATATATACAT
*
143492 ATATATATAT
1 ATATATACAT
143502 ATATATA
1 ATATATA
143509 TTTTATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (10 bp):
ATATATACAT
Found at i:144323 original size:15 final size:15
Alignment explanation
Indices: 144298--144340 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
144288 TAGAAAACTA
144298 AAAATTAATTAAAAAT
1 AAAA-TAATTAAAAAT
*
144314 CAAATAATT-AAAAT
1 AAAATAATTAAAAAT
*
144328 AAAAAAATTAAAA
1 AAAATAATTAAAA
144341 TTTTTTACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 12 0.52
15 8 0.35
16 3 0.13
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATAATTAAAAAT
Found at i:146512 original size:16 final size:17
Alignment explanation
Indices: 146493--146541 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
146483 TTTTTTTTTT
146493 ATTTAGG-TAATTTTAG
1 ATTTAGGTTAATTTTAG
*
146509 ATTTTGGTTAATTTTA-
1 ATTTAGGTTAATTTTAG
*
146525 AGTTTAGATT-ATTTTAG
1 A-TTTAGGTTAATTTTAG
146542 GTTCATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (17 bp):
ATTTAGGTTAATTTTAG
Found at i:147818 original size:142 final size:143
Alignment explanation
Indices: 147657--147930 Score: 363
Period size: 145 Copynumber: 1.9 Consensus size: 143
147647 TTTTTTTTTT
* * * * ** *
147657 TTTTTTTTTCGAATTTAGATCTTAGA-CTTTTTAAAATCAATTCAAGCAATTTGGAATTGGTTAC
1 TTTTATTTTCGAATTTAGATCTTAAATCTTTTTAAAATCAATCCAAACAATTTGGAATCAGCTAC
* * *
147721 AAGTAAGTTTCAAATCATAATAAGTATTAATCGTGTTAATTTT-GAGTTTTTTTATATGTGAATT
66 AAATAAGTTTCAAATCATAATAAGTATTAATCGTATT-ATTTTCAAGTTTTTTTATATGTGAATT
147785 GTTTTAAGTTTAGA
130 GTTTTAAGTTTAGA
* *
147799 TTTTATTTTCGAATTTAGATCTTAAATTTTTTTTTTAAATCAATCCAAACAATTTGGAATCAGCT
1 TTTTATTTTCGAATTTAGATCTTAAA--TCTTTTTAAAATCAATCCAAACAATTTGGAATCAGCT
* * * *
147864 ACAAATAAGTTTCATATCATAATAAGTATTTATCGTATTATTTTCAATTTTTTTTATATTTGAAT
64 ACAAATAAGTTTCAAATCATAATAAGTATTAATCGTATTATTTTCAAGTTTTTTTATATGTGAAT
147929 TG
129 TG
147931 CTCAATGATT
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
142 24 0.21
144 5 0.04
145 83 0.74
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.48
Consensus pattern (143 bp):
TTTTATTTTCGAATTTAGATCTTAAATCTTTTTAAAATCAATCCAAACAATTTGGAATCAGCTAC
AAATAAGTTTCAAATCATAATAAGTATTAATCGTATTATTTTCAAGTTTTTTTATATGTGAATTG
TTTTAAGTTTAGA
Found at i:147961 original size:14 final size:14
Alignment explanation
Indices: 147939--147972 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
147929 TGCTCAATGA
147939 TTAAATTTTTGAAT
1 TTAAATTTTTGAAT
* *
147953 TTAATTTTTTTAAT
1 TTAAATTTTTGAAT
147967 TTAAAT
1 TTAAAT
147973 CGGTGACTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TTAAATTTTTGAAT
Found at i:155670 original size:2 final size:2
Alignment explanation
Indices: 155663--155698 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
155653 TAACATTTTA
155663 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
155699 TGTTTTCTTT
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:156075 original size:23 final size:23
Alignment explanation
Indices: 156049--156092 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
156039 AATTTAAAAT
156049 TAAAATAGTAT-ATTTATTCTAAA
1 TAAAATA-TATAATTTATTCTAAA
* *
156072 TAAATTATATAATTTGTTCTA
1 TAAAATATATAATTTATTCTA
156093 TATCATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (23 bp):
TAAAATATATAATTTATTCTAAA
Found at i:157815 original size:22 final size:23
Alignment explanation
Indices: 157765--157815 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
157755 GTTTTCTTAC
* *
157765 TTAAAATGTAATTTATTAATTAT
1 TTAAAATGTAAATTAATAATTAT
*
157788 TT-AAATTTAAATTAATAA-TAT
1 TTAAAATGTAAATTAATAATTAT
157809 TTAAAAT
1 TTAAAAT
157816 AGAGTCTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.21
22 17 0.71
23 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAAAATGTAAATTAATAATTAT
Found at i:157888 original size:89 final size:87
Alignment explanation
Indices: 157744--157904 Score: 252
Period size: 86 Copynumber: 1.8 Consensus size: 87
157734 TAAAATATTA
* *
157744 AAATTAATAAAGTTTTCTTACTTAAAATGTAATTTATTAATTATTTAAATTTAAATTAAT-AATA
1 AAATTAATAAAATTTTCCTACTTAAAATGTAATTTATTAATTATTTAAATTTAAATTAATAAATA
157808 TTTAAAATAGAGTCTATTAGTT
66 TTTAAAATAGAGTCTATTAGTT
* *
157830 AAATTAATAAAATTTTCCTATTTAAATGTGTAATTATATTAATTTATTTAAATTTAAATTAATAA
1 AAATTAATAAAATTTTCCTACTTAAA-ATGTAATT-TATTAA-TTATTTAAATTTAAATTAATAA
157895 ATATTTAAAA
63 ATATTTAAAA
157905 ATAAAATCCA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
86 23 0.34
87 7 0.10
88 6 0.09
89 20 0.30
90 11 0.16
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (87 bp):
AAATTAATAAAATTTTCCTACTTAAAATGTAATTTATTAATTATTTAAATTTAAATTAATAAATA
TTTAAAATAGAGTCTATTAGTT
Found at i:158657 original size:22 final size:21
Alignment explanation
Indices: 158632--158701 Score: 54
Period size: 22 Copynumber: 3.3 Consensus size: 21
158622 ATATAATTAC
*
158632 TAAATGATGAATATAATAGTAG
1 TAAATGATCAATA-AATAGTAG
* * *
158654 TAAAAGATTAATAAAATAATAG
1 TAAATGATCAAT-AAATAGTAG
*
158676 T--ATAATCAATAACATAGTAG
1 TAAATGATCAATAA-ATAGTAG
158696 TAAATG
1 TAAATG
158702 TTTAATAACT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
19 2 0.06
20 13 0.36
22 20 0.56
23 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.30
Consensus pattern (21 bp):
TAAATGATCAATAAATAGTAG
Found at i:159366 original size:19 final size:19
Alignment explanation
Indices: 159344--159386 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
159334 AAAGTCAATA
159344 GTTTAAAAAAACATTTAAT
1 GTTTAAAAAAACATTTAAT
** *
159363 GTTTAGGAAAACGTTTAAT
1 GTTTAAAAAAACATTTAAT
159382 GTTTA
1 GTTTA
159387 TTTTGAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.40
Consensus pattern (19 bp):
GTTTAAAAAAACATTTAAT
Found at i:162201 original size:145 final size:144
Alignment explanation
Indices: 162013--162302 Score: 526
Period size: 145 Copynumber: 2.0 Consensus size: 144
162003 AATTGAAGAC
* *
162013 GTGTCTGGATTCATTGATTGAGTGAAGTTCAAAGTCAAACATGACTCAAAATTCGAGAGAGAGAA
1 GTGTCTAGATTCATTGATTGAATGAAGTTCAAAGTCAAACATGACTCAAAATTCGAGAGAGAGAA
*
162078 AATGATTCAATTTTTGATTAAAAAAAAAACGGAGTTGGAGTATCTCCTCGGAGGAATGGGGTTGG
66 AATGATTCAATTTTTGATT-AAAAAAAAACGGAGTTGGAGTATCCCCTCGGAGGAATGGGGTTGG
162143 AGTGTCCCCGATGAT
130 AGTGTCCCCGATGAT
162158 GTGTCTAGATTCATTGATTGAATGAAGTTCAAAGTCAAACATGACTCAAAATTCGAGAGAGAGAA
1 GTGTCTAGATTCATTGATTGAATGAAGTTCAAAGTCAAACATGACTCAAAATTCGAGAGAGAGAA
* *
162223 AATGATTCAATTTTTTATTGAAAAAAAACGGAGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGA
66 AATGATTCAATTTTTGATTAAAAAAAAACGGAGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGA
162288 GTGTCCCCGATGAT
131 GTGTCCCCGATGAT
162302 G
1 G
162303 ACAATTTAAG
Statistics
Matches: 140, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
144 59 0.42
145 81 0.58
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.28
Consensus pattern (144 bp):
GTGTCTAGATTCATTGATTGAATGAAGTTCAAAGTCAAACATGACTCAAAATTCGAGAGAGAGAA
AATGATTCAATTTTTGATTAAAAAAAAACGGAGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGA
GTGTCCCCGATGAT
Found at i:164601 original size:20 final size:20
Alignment explanation
Indices: 164576--164652 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
164566 GTAAAAAGAC
*
164576 AGAATGTATCGATGCATTGA
1 AGAATGTATCGATACATTGA
*
164596 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
164616 TACG--TGTATTGATACATTGA
1 -A-GAATGTATCGATACATTGA
* *
164636 AAAATGTATCAATACAT
1 AGAATGTATCGATACAT
164653 CTGGGTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
19 1 0.02
20 43 0.93
21 1 0.02
22 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:165380 original size:28 final size:28
Alignment explanation
Indices: 165261--166486 Score: 1620
Period size: 28 Copynumber: 43.4 Consensus size: 28
165251 CCGACTCGTA
* * *
165261 TGGGCTTTGAAAAGAGTTACCACTGGCTTG
1 TGGGCTTTG-AAAG-GGTGCCACTGACTTG
* *
165291 TGGGCCTTGAAACGAGTGCCACTGACTTG
1 TGGGCTTTGAAA-GGGTGCCACTGACTTG
*
165320 TGGGCTTTGAAAGGGTGCCA-TGACTTC
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
165347 TGGGCTTTGAAAGGGTGCCACTGACTCG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * *
165375 TGGGCTTTGAAAGGATGCCACTAACTCG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
165403 TGGGCTTTGAAAGGATGCCACTGACCTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
165431 TAGGCTTTGAAAGGGTGCCACAGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
165459 TGGGCTTTGAAAAGAGTGCCACTGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
**
165488 TGGGCTTTGAAAGAATGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
165516 TGGGCTTTGAAAGGATGCCACTGACTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
165544 TGGGCTTTGAAAGAAGTGCCACTAACTTG
1 TGGGCTTTGAAAG-GGTGCCACTGACTTG
*
165573 TGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
165601 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
165629 TGAGCTTTGAAAGGGTGCCATTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * *
165657 TAGGCTTTGAAAAGAGTGCCACTGACTTA
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
* *
165686 TGGGCTTTGAAAAGAGTACCACTGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
* *
165715 TGGGCTTTGAAAAGAGTGCCACTGACTTA
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
*
165744 TGGGCTTTGAAAGGGTGCCACTGACTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
165772 TGGGCTTTGAAAGGGTGCCACTAACTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
165800 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
165828 TGGGCTTTGAAAGGGTGCCATTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
** * *
165856 TGGGCTTTGAAAATAGTGCCATTGGCTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
165885 TGGGCTTTGAAAGGAGTGCCACTGACTTG
1 TGGGCTTTGAAAGG-GTGCCACTGACTTG
*
165914 TGGGCTTTGAAAGGGTGCCACTGACTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
165942 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
165970 TGGGCTTTGAAATGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
165998 TGGGCTTTGAATGGGTGCCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
166026 TGGGTTTTGAAAAGAGTGCCACTGATTTA
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
*
166055 TGGGCTTTGAAATGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
166083 TAGGCTTTGAAAGGGTGCCACT-AGCTTG
1 TGGGCTTTGAAAGGGTGCCACTGA-CTTG
*
166111 TGGGCTTTGAAAGGAGTGCCACCGACTTG
1 TGGGCTTTGAAAGG-GTGCCACTGACTTG
* *
166140 TGGGCTTTGTAAGGGTGCCACTAAC-T-
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
166166 TGGGCTTTGAAAGGAGTGCCACCGACTTG
1 TGGGCTTTGAAAGG-GTGCCACTGACTTG
* * *
166195 TGGGCTTTGTAAGGGTGCCAGTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
166223 TGGGCTTTG-AAGGATGCCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
166250 TGGGCTTTGAAGGGGTGCCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
166278 TAGGCTTTGAAAAGAGTGCCACTGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
*
166307 TGGGCTTTGAAAGGGTGCCATTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
166335 TGGGCTTTGAAAAGAGTGCCACTGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
166364 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
166392 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
166420 TGGGCTTTGAAAGGTTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
166448 TGGAC-TTAAAAGGATGCCA-TGGAGTTG
1 TGGGCTTTGAAAGGGTGCCACT-GACTTG
*
166475 TGGACTTTGAAA
1 TGGGCTTTGAAA
166487 AGAAATGCTA
Statistics
Matches: 1069, Mismatches: 108, Indels: 40
0.88 0.09 0.03
Matches are distributed among these distances:
26 14 0.01
27 84 0.08
28 648 0.61
29 313 0.29
30 10 0.01
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (28 bp):
TGGGCTTTGAAAGGGTGCCACTGACTTG
Found at i:165500 original size:57 final size:56
Alignment explanation
Indices: 165261--166486 Score: 1620
Period size: 57 Copynumber: 21.7 Consensus size: 56
165251 CCGACTCGTA
* * * * *
165261 TGGGCTTTGAAAAGAGTTACCACTGGCTTGTGGGCCTTGAAACGAGTGCCACTGACTTG
1 TGGGCTTTG-AAAG-GGTGCCACTGACTTGTGGGCTTTGAAA-GGGTGCCACTGACTTG
* *
165320 TGGGCTTTGAAAGGGTGCCA-TGACTTCTGGGCTTTGAAAGGGTGCCACTGACTCG
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * * *
165375 TGGGCTTTGAAAGGATGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGACCTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * *
165431 TAGGCTTTGAAAGGGTGCCACAGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTG
** * *
165488 TGGGCTTTGAAAGAATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * *
165544 TGGGCTTTGAAAGAAGTGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAG-GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* *
165601 TGGGCTTTGAAAGGGTGCCACTGACTTGTGAGCTTTGAAAGGGTGCCATTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * * *
165657 TAGGCTTTGAAAAGAGTGCCACTGACTTATGGGCTTTGAAAAGAGTACCACTGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTG
* * *
165715 TGGGCTTTGAAAAGAGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTGACTTA
1 TGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* *
165772 TGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* ** * *
165828 TGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTTGAAAATAGTGCCATTGGCTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTG
*
165885 TGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTA
1 TGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
*
165942 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAATGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * * * *
165998 TGGGCTTTGAATGGGTGCCACTAACTTGTGGGTTTTGAAAAGAGTGCCACTGATTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTG
* *
166055 TGGGCTTTGAAATGGTGCCACTGACTTGTAGGCTTTGAAAGGGTGCCACT-AGCTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA-CTTG
* * *
166111 TGGGCTTTGAAAGGAGTGCCACCGACTTGTGGGCTTTGTAAGGGTGCCACTAAC-T-
1 TGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
166166 TGGGCTTTGAAAGGAGTGCCACCGACTTGTGGGCTTTGTAAGGGTGCCAGTAACTTG
1 TGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
166223 TGGGCTTTG-AAGGATGCCACTAACTTGTGGGCTTTGAAGGGGTGCCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * *
166278 TAGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
*
166335 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
*
166392 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGTTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * * *
166448 TGGAC-TTAAAAGGATGCCA-TGGAGTTGTGGACTTTGAAA
1 TGGGCTTTGAAAGGGTGCCACT-GACTTGTGGGCTTTGAAA
166487 AGAAATGCTA
Statistics
Matches: 1043, Mismatches: 108, Indels: 36
0.88 0.09 0.03
Matches are distributed among these distances:
54 1 0.00
55 159 0.15
56 386 0.37
57 408 0.39
58 80 0.08
59 9 0.01
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (56 bp):
TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
Found at i:166500 original size:85 final size:84
Alignment explanation
Indices: 165261--166486 Score: 1575
Period size: 85 Copynumber: 14.5 Consensus size: 84
165251 CCGACTCGTA
* * * * *
165261 TGGGCTTTGAAAAGAGTTACCACTGGCTTGTGGGCCTTGAAACGAGTGCCACTGACTTGTGGGCT
1 TGGGCTTTG-AAAG-GATGCCACTGACTTGTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCT
*
165326 TTGAAAGGGTGCCA-TGACTTC
63 TTGAAAGGGTGCCACTGACTTG
* * * * *
165347 TGGGCTTTGAAAGGGTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTAACTCGTGGGCTTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
165412 AAAGGATGCCACTGACCTG
66 AAAGGGTGCCACTGACTTG
* * * *
165431 TAGGCTTTGAAAGGGTGCCACAGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTT
**
165496 GAAAGAATGCCACTGACTTG
65 GAAAGGGTGCCACTGACTTG
* * *
165516 TGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAGAAGTGCCACTAACTTGTGGGCTTT
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG-GGTGCCACTGACTTGTGGGCTTT
*
165581 GAAAGGATGCCACTGACTTG
65 GAAAGGGTGCCACTGACTTG
* * * *
165601 TGGGCTTTGAAAGGGTGCCACTGACTTGTGAGCTTTGAAAGGGTGCCATTGACTTGTAGGCTTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
165666 AAAAGAGTGCCACTGACTTA
66 -AAAGGGTGCCACTGACTTG
* * * *
165686 TGGGCTTTGAAAAGAGTACCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTATGGGCTT
1 TGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTT
*
165751 TGAAAGGGTGCCACTGACTTA
64 TGAAAGGGTGCCACTGACTTG
* * *
165772 TGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
*
165837 AAAGGGTGCCATTGACTTG
66 AAAGGGTGCCACTGACTTG
** * *
165856 TGGGCTTTGAAAATAGTGCCATTGGCTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTT
1 TGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTT
*
165921 TGAAAGGGTGCCACTGACTTA
64 TGAAAGGGTGCCACTGACTTG
* *
165942 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
166007 AATGGGTGCCACTAACTTG
66 AAAGGGTGCCACTGACTTG
* * * * * *
166026 TGGGTTTTGAAAAGAGTGCCACTGATTTATGGGCTTTGAAATGGTGCCACTGACTTGTAGGCTTT
1 TGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
166091 GAAAGGGTGCCACT-AGCTTG
65 GAAAGGGTGCCACTGA-CTTG
* * *
166111 TGGGCTTTGAAAGGAGTGCCACCGACTTGTGGGCTTTGTAAGGGTGCCACTAAC-T-TGGGCTTT
1 TGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
*
166174 GAAAGGAGTGCCACCGACTTG
65 GAAAGG-GTGCCACTGACTTG
* * * * * *
166195 TGGGCTTTGTAAGGGTGCCAGTAACTTGTGGGCTTTG-AAGGATGCCACTAACTTGTGGGCTTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
166259 AAGGGGTGCCACTAACTTG
66 AAAGGGTGCCACTGACTTG
* * *
166278 TAGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTT
1 TGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT
*
166343 GAAAAGAGTGCCACTGACTTG
65 G-AAAGGGTGCCACTGACTTG
*
166364 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
*
166429 AAAGGTTGCCACTGACTTG
66 AAAGGGTGCCACTGACTTG
* * * *
166448 TGGAC-TTAAAAGGATGCCA-TGGAGTTGTGGACTTTGAAA
1 TGGGCTTTGAAAGGATGCCACT-GACTTGTGGGCTTTGAAA
166487 AGAAATGCTA
Statistics
Matches: 1000, Mismatches: 122, Indels: 39
0.86 0.11 0.03
Matches are distributed among these distances:
82 15 0.01
83 115 0.12
84 271 0.27
85 435 0.44
86 140 0.14
87 24 0.02
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (84 bp):
TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
AAAGGGTGCCACTGACTTG
Found at i:174748 original size:20 final size:20
Alignment explanation
Indices: 174725--174815 Score: 112
Period size: 20 Copynumber: 4.5 Consensus size: 20
174715 AGATAGAATA
*
174725 TATCGATACAGT-AAAGAATG
1 TATCGATACATTCAAA-AATG
* *
174745 TATCGATACATTCATACATG
1 TATCGATACATTCAAAAATG
* *
174765 TATCGATACATTCATACATG
1 TATCGATACATTCAAAAATG
*
174785 TATCGATACATTGAAAAATG
1 TATCGATACATTCAAAAATG
174805 TATCGATACAT
1 TATCGATACAT
174816 CTAGGTAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (20 bp):
TATCGATACATTCAAAAATG
Found at i:174775 original size:12 final size:12
Alignment explanation
Indices: 174742--174795 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
174732 ACAGTAAAGA
174742 ATGTATCGATAC
1 ATGTATCGATAC
174754 A--T-TC-ATAC
1 ATGTATCGATAC
174762 ATGTATCGATAC
1 ATGTATCGATAC
174774 A--T-TC-ATAC
1 ATGTATCGATAC
174782 ATGTATCGATAC
1 ATGTATCGATAC
174794 AT
1 AT
174796 TGAAAAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
8 10 0.29
9 4 0.12
10 4 0.12
11 4 0.12
12 12 0.35
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:175202 original size:51 final size:52
Alignment explanation
Indices: 175104--175207 Score: 138
Period size: 51 Copynumber: 2.0 Consensus size: 52
175094 TGAAAATTTA
* * * * *
175104 ATAACTTAGTTTGTTACTCAAAATTAAGTATATATCAAATGTTTTTTA-ATT
1 ATAACTTAATTGGTTACTCAAAATTAAGTATATACCAAATATGTTTTAGATT
* *
175155 ATAACTTAATTGGTTACTCAAAATTAAGTCTATACCACATATGTTTTAGATT
1 ATAACTTAATTGGTTACTCAAAATTAAGTATATACCAAATATGTTTTAGATT
175207 A
1 A
175208 AAAGTCAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 41 0.91
52 4 0.09
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (52 bp):
ATAACTTAATTGGTTACTCAAAATTAAGTATATACCAAATATGTTTTAGATT
Found at i:175534 original size:22 final size:22
Alignment explanation
Indices: 175509--175551 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
175499 AAATATTTAT
*
175509 TAAATCATAAATAGTATAGTAA
1 TAAATCATAAATAGCATAGTAA
* *
175531 TAAATGATTAATAGCATAGTA
1 TAAATCATAAATAGCATAGTA
175552 GTGATTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.33
Consensus pattern (22 bp):
TAAATCATAAATAGCATAGTAA
Found at i:180744 original size:18 final size:17
Alignment explanation
Indices: 180693--180755 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 17
180683 ATGATTTTTT
180693 ATTTAAATTAATTTGATTTA
1 ATTTAAA-TAA-TT-ATTTA
180713 ATTTAAATAATTATTTA
1 ATTTAAATAATTATTTA
*
180730 ATTAATAAA-AATTATTTT
1 ATT--TAAATAATTATTTA
180748 ATTTAAAT
1 ATTTAAAT
180756 TTATTAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
16 4 0.10
17 8 0.21
18 13 0.33
19 7 0.18
20 7 0.18
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTAAATAATTATTTA
Found at i:180748 original size:19 final size:19
Alignment explanation
Indices: 180708--180746 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
180698 AATTAATTTG
180708 ATTTAATT--TAAATAATT
1 ATTTAATTAATAAATAATT
180725 ATTTAATTAATAAA-AATT
1 ATTTAATTAATAAATAATT
180743 ATTT
1 ATTT
180747 TATTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 8 0.40
19 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTAATTAATAAATAATT
Found at i:185298 original size:20 final size:20
Alignment explanation
Indices: 185226--185342 Score: 92
Period size: 20 Copynumber: 5.7 Consensus size: 20
185216 TTTTACCTAG
* * *
185226 ATGTATCAATACATTTTTTA
1 ATGTATCGATACATTCTTCA
* *** *
185246 ATGTATCGATGCATAGATGA
1 ATGTATCGATACATTCTTCA
*
185266 ATGTAT-TAGTACATTCTTCA
1 ATGTATCGA-TACATTCTTCA
*
185286 ATGTATCGATACATTCTACCCA
1 ATGTATCGATACATTCT--TCA
*
185308 GATGTATCGATACATTGTTCA
1 -ATGTATCGATACATTCTTCA
185329 ATGTATCGATACAT
1 ATGTATCGATACAT
185343 CTAGTTAAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
19 1 0.01
20 54 0.71
21 3 0.04
22 2 0.03
23 16 0.21
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:185377 original size:28 final size:28
Alignment explanation
Indices: 185334--185392 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
185324 GTTCAATGTA
*
185334 TCGATACATCTAGTTAAAATTGAGCATT
1 TCGATACATATAGTTAAAATTGAGCATT
*
185362 TCGATACATATGGTTAAAATTGAGCATT
1 TCGATACATATAGTTAAAATTGAGCATT
185390 TCG
1 TCG
185393 GGCCATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (28 bp):
TCGATACATATAGTTAAAATTGAGCATT
Found at i:192444 original size:23 final size:21
Alignment explanation
Indices: 192418--192489 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 21
192408 CAAAATTATG
192418 AAAAAGTCAAAAGAAAAAGCACA
1 AAAAAGTCAAAAGAAAAA-CA-A
*
192441 AAAAA-TGAAAAGAAAAACAA
1 AAAAAGTCAAAAGAAAAACAA
* *
192461 AAAAAGGTGCAAAAGTAAAATAA
1 AAAAA-GT-CAAAAGAAAAACAA
*
192484 GAAAAG
1 AAAAAG
192490 GGAACAACAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
20 6 0.15
21 2 0.05
22 13 0.32
23 20 0.49
ACGTcount: A:0.71, C:0.07, G:0.15, T:0.07
Consensus pattern (21 bp):
AAAAAGTCAAAAGAAAAACAA
Found at i:192456 original size:21 final size:21
Alignment explanation
Indices: 192426--192465 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
192416 TGAAAAAGTC
*
192426 AAAAGAAAAAGCACAAAAAATG
1 AAAAGAAAAAACA-AAAAAATG
192448 AAAAG-AAAAACAAAAAAA
1 AAAAGAAAAAACAAAAAAA
192466 GGTGCAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.80, C:0.07, G:0.10, T:0.03
Consensus pattern (21 bp):
AAAAGAAAAAACAAAAAAATG
Found at i:193944 original size:28 final size:28
Alignment explanation
Indices: 193818--194371 Score: 496
Period size: 28 Copynumber: 19.9 Consensus size: 28
193808 CAACCTTTTT
* * *
193818 CTTTTAAAGTCCACAATTCCATGGCA-A
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * * * *
193845 TTTTTTAAGTCCACAGCTCTGTAGTACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
193873 C-TTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* **
193900 C-TTTAAAGTCCATAACTTTGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
193927 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
193955 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
193983 TTTTTAAAGTCCACAACTCCATGGCA-T
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * *
194010 CTATTAAATTCCACAACTCCGTGGTA-C
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
194037 CTTTTAAAGTCCATAACTCCGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* **
194065 C-TTTAAAGTCCATAACTCCGTGGCATT
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
194092 CTTTTAAAGTCCACAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
194120 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* *
194148 CTTTTAAAATCCACAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
*
194176 CTTTT-AAGTTCACAACTCCGTGGCATCC
1 CTTTTAAAGTCCACAACTCCGTGGCA-CC
* ** * * * *
194204 TTTTTAAAACCCATAAATCAGTGGCACT
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * **
194232 CTTTCAAAG-CCTACAAATCAATGGCACC
1 CTTTTAAAGTCC-ACAACTCCGTGGCACC
* * * * *
194260 CTTTCAAAGTCCACAAGTCAGTAGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCACC
* * * *
194288 CTTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTT-AAAGTCCACAACTCCGTGGCACC
* * * * *
194317 CTTTCAAAAGTCGACAAGTCAGTGGCA-T
1 CTTT-TAAAGTCCACAACTCCGTGGCACC
* * *
194345 CTTTTCAAAGCCCACAAGTCAGTGGCA
1 CTTTT-AAAGTCCACAACTCCGTGGCA
194372 TCTTCTCAAA
Statistics
Matches: 444, Mismatches: 72, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
27 152 0.34
28 232 0.52
29 60 0.14
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (28 bp):
CTTTTAAAGTCCACAACTCCGTGGCACC
Found at i:194098 original size:165 final size:166
Alignment explanation
Indices: 193819--194349 Score: 597
Period size: 165 Copynumber: 3.2 Consensus size: 166
193809 AACCTTTTTC
* * * * * * *
193819 TTTTAAAGTCCACAATTCCATGGCAAT-TTTTTAAGTCCACAGCTCTGTAGTACCCTTTAAAGTC
1 TTTTAAAGTCCACAACTCCATGGC-ATCTTTTAAATTCCACAACTCCGTGGTACCTTTTAAAGTC
* **
193883 CACAACTCCGTGGCACCCTTTAAAGTCCATAACTTTGTGGCACCCTTTTAAAGTCCACAACTCCG
65 CATAACTCCGTGGCACCCTTTAAAGTCCATAACTCAGTGGCACCCTTTTAAAGTCCACAACTCCG
* *
193948 TGGCACCCTTTTAAAGTCCACAACTCCGTGGCA-CCT
130 TGGCATCCTTTTAAAGTCCACAACTCAGTGGCATCCT
*
193984 TTTTAAAGTCCACAACTCCATGGCATCTATTAAATTCCACAACTCCGTGGTACCTTTTAAAGTCC
1 TTTTAAAGTCCACAACTCCATGGCATCTTTTAAATTCCACAACTCCGTGGTACCTTTTAAAGTCC
* **
194049 ATAACTCCGTGGCACCCTTTAAAGTCCATAACTCCGTGGCATTCTTTTAAAGTCCACAACTCCGT
66 ATAACTCCGTGGCACCCTTTAAAGTCCATAACTCAGTGGCACCCTTTTAAAGTCCACAACTCCGT
*
194114 GGCATCCTTTTAAAGTCCACAACTCTGTGGCATCC-
131 GGCATCCTTTTAAAGTCCACAACTCAGTGGCATCCT
* * * * *
194149 TTTTAAAATCCACAACTCCGTGGCATCCTTTTAAGTT-CACAACTCCGTGGCATCCTTTTTAAAA
1 TTTTAAAGTCCACAACTCCATGGCAT-CTTTTAAATTCCACAACTCCGTGGTA-CC-TTTTAAAG
* * * * * * * * *
194213 CCCATAAATCAGTGGCACTCTTTCAAAG-CCTACAAATCAATGGCACCCTTTCAAAGTCCACAAG
63 TCCATAACTCCGTGGCACCCTTT-AAAGTCC-ATAACTCAGTGGCACCCTTTTAAAGTCCACAAC
* * * *
194277 TCAGTAGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
126 TCCGTGGCATCCTTTT-AAAGTCCACAACTCAGTGGCATCCT
** * *
194319 TTCAAAAGTCGACAAGT-CAGTGGCATCTTTT
1 TTTTAAAGTCCACAACTCCA-TGGCATCTTTT
194350 CAAAGCCCAC
Statistics
Matches: 312, Mismatches: 44, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
164 2 0.01
165 182 0.58
166 12 0.04
167 28 0.09
168 43 0.14
169 27 0.09
170 18 0.06
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (166 bp):
TTTTAAAGTCCACAACTCCATGGCATCTTTTAAATTCCACAACTCCGTGGTACCTTTTAAAGTCC
ATAACTCCGTGGCACCCTTTAAAGTCCATAACTCAGTGGCACCCTTTTAAAGTCCACAACTCCGT
GGCATCCTTTTAAAGTCCACAACTCAGTGGCATCCT
Found at i:194372 original size:28 final size:28
Alignment explanation
Indices: 193927--194843 Score: 621
Period size: 28 Copynumber: 32.6 Consensus size: 28
193917 TTGTGGCACC
* * * *
193927 CTTTT-AAAGTCCACAACTCCGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-T
* * * *
193955 CTTTT-AAAGTCCACAACTCCGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
193982 CTTTTTAAAGTCCACAACTCCA-TGGCAT
1 CTTTTCAAAGCCCACAAGT-CAGTGGCAT
* ** * * * *
194010 CTATT-AAATTCCACAACTCCGTGGTAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * * * *
194037 CTTTT-AAAGTCCATAACTCCGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * * * *
194064 CCTTT-AAAGTCCATAACTCCGTGGCATT
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-T
* * *
194092 CTTTT-AAAGTCCACAACTCCGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
194119 CCTTTT-AAAGTCCACAACTCTGTGGCAT
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAT
** * *
194147 CCTTTT-AAAATCCACAACTCCGTGGCAT
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAT
** * *
194175 CCTTTT--AAGTTCACAACTCCGTGGCAT
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * * *
194202 CCTTTTTAAAACCCATAAATCAGTGGCA-
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * * *
194230 CTCTTTCAAAGCCTACAAATCAATGGCAC
1 CT-TTTCAAAGCCCACAAGTCAGTGGCAT
* * *
194259 CCTTTCAAAGTCCACAAGTCAGTAGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
194287 CCTTTTCAAAGCCCACAAGTCAGTGGCAT
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
194316 CCTTTCAAAAGTCGACAAGTCAGTGGCAT
1 CTTTTC-AAAGCCCACAAGTCAGTGGCAT
194345 CTTTTCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * *
194373 CTTCTCAAAACCCACAAGTCGGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
194401 CTTTTCAAAGCCCATAAGTTAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * * **
194429 CTTTTCCAAGCCCACAAGTTAATGGCGC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* * * **
194457 CCTTTCAAAGCCCACAAGTTAATGTTAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
194485 CCTTTCAAAGTCCACAAGTCAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
194513 CCTTTTCAAAGCCCACAAGTCAGAGACAT
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
194542 CTTTTCAAAGCCCACAAGTCAGTTGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
*
194570 CTTTTTC-AAGCCCACAAGTTAGTGGCA-
1 C-TTTTCAAAGCCCACAAGTCAGTGGCAT
* *
194597 CATTTTCAAAGCCCATAAGTCAGTGGCAC
1 C-TTTTCAAAGCCCACAAGTCAGTGGCAT
*
194626 CTTTTTCACAGCCCACAAGTCAGTGGCA-
1 C-TTTTCAAAGCCCACAAGTCAGTGGCAT
** *
194654 CTTTTTCAAAGCTTACAAGTTCAATGGCAT
1 C-TTTTCAAAGCCCACAAG-TCAGTGGCAT
* * *
194684 CTTTTTATAGCCCACAAGTTAGTGGCA-
1 CTTTTCAAAGCCCACAAGTCAGTGGCAT
* *
194711 CATTTTTAAAGCCCACAAATCAGTGGCA-
1 C-TTTTCAAAGCCCACAAGTCAGTGGCAT
* * * *
194739 CATTCTCAAAGCCCACAAGTGAGAGGCAC
1 C-TTTTCAAAGCCCACAAGTCAGTGGCAT
* *
194768 CTTCTT-AAAGTCCACAAGTCAGCGGCAT
1 CTT-TTCAAAGCCCACAAGTCAGTGGCAT
* *
194796 CCTTTT-AAAGCCTACACAAGTCGGTGGCAA
1 -CTTTTCAAAGCC--CACAAGTCAGTGGCAT
194826 CTTTCTCTAAAGCCCACA
1 CTTT-TC-AAAGCCCACA
194844 CAAGTTGGTG
Statistics
Matches: 750, Mismatches: 113, Indels: 50
0.82 0.12 0.05
Matches are distributed among these distances:
26 1 0.00
27 105 0.14
28 469 0.63
29 150 0.20
30 19 0.03
32 6 0.01
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAT
Found at i:194581 original size:113 final size:112
Alignment explanation
Indices: 193919--194830 Score: 602
Period size: 113 Copynumber: 8.1 Consensus size: 112
193909 CCATAACTTT
* * * * * * * * *
193919 GTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAAGTCCACAACTCCGTGGCACC
1 GTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATC
* * * * * ** * **
193983 TTTTTAAAGTCCACAACTCCA-TGGCAT-CTATTAAATTCCACAACTCC
65 TTTTCAAAGCCCACAAGT-CAGTGGCATCCTTTTCAAGCCCACAAGTTA
* * * * * * * * * * *
194030 GTGGTACCTTTTAAAGTCCATAACTCCGTGGCA-CCCTTT-AAAGTCCATAACTCCGTGGCATTC
1 GTGGCACCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCA-TC
* * * * * *
194093 TTTT-AAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCT-
65 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAGCCCACAAGT-TA
* ** * * ** * *
194140 GTGGCATCCTTTTAAAATCCACAACTCCGTGGCATCCTTTT--AAGTTCACAACTCCGTGGCATC
1 GTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCAT-
* * * * * * *
194203 CTTTTTAAAACCCATAAATCAGTGGCA--CTCTTTCAAAGCCTACAAATCA
64 CTTTTCAAAGCCCACAAGTCAGTGGCATCCT-TTTC-AAGCCCACAAGTTA
* * *
194252 ATGGCACCCTTTCAAAGTCCACAAGTCAGTAGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATC
1 GTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATC
* * * *
194317 CTTTCAAAAGTCGACAAGTCAGTGGCAT-CTTTTCAAAGCCCACAAGTCA
65 TTTTC-AAAGCCCACAAGTCAGTGGCATCCTTTTC-AAGCCCACAAGTTA
* * * * *
194366 GTGGCATCTTCTCAAAACCCACAAGTCGGTGGCAT-CTTTTCAAAGCCCATAAGTTAGTGGCATC
1 GTGGCACCTT-TCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATC
* * * * *
194430 TTTTCCAAGCCCACAAGTTAATGGC-GCCCTTTCAAAGCCCACAAGTTA
65 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTC-AAGCCCACAAGTTA
* ** * * *
194478 ATGTTATCCTTTCAAAGTCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGAGACATC
1 GTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATC
* *
194543 TTTTCAAAGCCCACAAGTCAGTTGCATCTTTTTCAAGCCCACAAGTTA
65 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAGCCCACAAGTTA
* * *
194591 GTGGCACATTTTCAAAGCCCATAAGTCAGTGGCA-CCTTTTTCACAGCCCACAAGTCAGTGGCA-
1 GTGGCAC-CTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTTCAAAGCCCACAAGTCAGTGGCAT
** * *
194654 CTTTTTCAAAGCTTACAAGTTCAATGGCAT-CTTTTTATAGCCCACAAGTTA
64 C-TTTTCAAAGCCCACAAG-TCAGTGGCATCCTTTTCA-AGCCCACAAGTTA
* * * * * * * *
194705 GTGGCACATTTTTAAAGCCCACAAATCAGTGGCA-CATTCTCAAAGCCCACAAGTGAGAGGCACC
1 GTGGCAC-CTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATC
* * * **
194769 TTCTT-AAAGTCCACAAGTCAGCGGCATCCTTTTAAAGCCTACACAAGTCG
65 TT-TTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAGCC--CACAAGTTA
*
194819 GTGGCAACTTTC
1 GTGGCACCTTTC
194831 TCTAAAGCCC
Statistics
Matches: 657, Mismatches: 114, Indels: 58
0.79 0.14 0.07
Matches are distributed among these distances:
108 1 0.00
109 44 0.07
110 55 0.08
111 56 0.09
112 138 0.21
113 212 0.32
114 149 0.23
115 2 0.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (112 bp):
GTGGCACCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTCAGTGGCATCT
TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTCAAGCCCACAAGTTA
Found at i:194845 original size:32 final size:32
Alignment explanation
Indices: 194801--194863 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
194791 GGCATCCTTT
*
194801 TAAAGCCTACACAAGTCGGTGGCAACTTTCTC
1 TAAAGCCCACACAAGTCGGTGGCAACTTTCTC
* *
194833 TAAAGCCCACACAAGTTGGTGGTAACTTTCT
1 TAAAGCCCACACAAGTCGGTGGCAACTTTCT
194864 AAACCCAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (32 bp):
TAAAGCCCACACAAGTCGGTGGCAACTTTCTC
Found at i:195644 original size:22 final size:22
Alignment explanation
Indices: 195617--195660 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
195607 TTTTACCAAG
* *
195617 ATGTATCGATACATTTTTTAAT
1 ATGTATCGATACAATCTTTAAT
195639 ATGTATCGATACAATCTTTAAT
1 ATGTATCGATACAATCTTTAAT
195661 GTATTAGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (22 bp):
ATGTATCGATACAATCTTTAAT
Found at i:195768 original size:20 final size:22
Alignment explanation
Indices: 195745--195789 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
195735 TATTTTTATT
*
195745 TAAATTTAAT-TATTAA-AATA
1 TAAAATTAATATATTAATAATA
*
195765 TAAAATTAATATTTTAATAATA
1 TAAAATTAATATATTAATAATA
195787 TAA
1 TAA
195790 TAAATAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 5 0.24
22 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAAATTAATATATTAATAATA
Found at i:200299 original size:20 final size:20
Alignment explanation
Indices: 200262--200299 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
200252 TGCCTTTGAT
*
200262 CATGCTTTTTCACTATGTTC
1 CATGCTTTTTAACTATGTTC
200282 CATGCATTTTTAAC-ATGT
1 CATGC-TTTTTAACTATGT
200300 CCTCATCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (20 bp):
CATGCTTTTTAACTATGTTC
Found at i:206473 original size:63 final size:63
Alignment explanation
Indices: 206242--206462 Score: 334
Period size: 63 Copynumber: 3.5 Consensus size: 63
206232 TCGTATTTTT
* * * *
206242 TCACTATTCTCTCTACTTGCCATTAAGGCGTTGTCTCACTAAGAGACGTTAAGTGATACCAAG
1 TCACTATTCTCTCTACTCGCCATCAAGGCATTGTCTCACTAAGAGACGCTAAGTGATACCAAG
* * * * *
206305 TTAATATTCTCTCTGCTCACCATCAAGGCATTGTCTCACTAAGAGACGCTAAGTGACACCAAG
1 TCACTATTCTCTCTACTCGCCATCAAGGCATTGTCTCACTAAGAGACGCTAAGTGATACCAAG
* * *
206368 TCACTATTCTCTCTGCTCGCCATCAAGGCGTTGTCTCACTAAGAGACGCTGAGTGATACCAAG
1 TCACTATTCTCTCTACTCGCCATCAAGGCATTGTCTCACTAAGAGACGCTAAGTGATACCAAG
206431 TCACTATTCTCTCTACTCGCCATCAAGGCATT
1 TCACTATTCTCTCTACTCGCCATCAAGGCATT
206463 ACTTTACTAA
Statistics
Matches: 141, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 141 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (63 bp):
TCACTATTCTCTCTACTCGCCATCAAGGCATTGTCTCACTAAGAGACGCTAAGTGATACCAAG
Found at i:206525 original size:53 final size:53
Alignment explanation
Indices: 206419--206539 Score: 143
Period size: 53 Copynumber: 2.3 Consensus size: 53
206409 AGAGACGCTG
* * * * *
206419 AGTGATACCAAGTCACTATTCTCTCTACTCGCCATCAAGGCATTACTTTACTA
1 AGTGACACCAAGTCACTATTCTCTCTACTCGCCACCAAGACATTACCTCACTA
* * * *
206472 AGTGACACCAAGTCACTATTCTCTCTGCTTGCCACCAAGACGTTGCCTCACTA
1 AGTGACACCAAGTCACTATTCTCTCTACTCGCCACCAAGACATTACCTCACTA
**
206525 AGAAACACCAAGTCA
1 AGTGACACCAAGTCA
206540 TGCTCTCTGA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (53 bp):
AGTGACACCAAGTCACTATTCTCTCTACTCGCCACCAAGACATTACCTCACTA
Found at i:207725 original size:22 final size:21
Alignment explanation
Indices: 207674--207731 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
207664 ATTTTAAATG
**
207674 TTTATATTTTATTTTCACATT
1 TTTATATTTTATTTAAACATT
* *
207695 TCTATTATTTTATTTAAAACTTT
1 TTTA-TATTTTATTT-AAACATT
207718 TTTATATTTATATT
1 TTTATATTT-TATT
207732 ATGTTATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 3 0.10
22 15 0.52
23 11 0.38
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTATATTTTATTTAAACATT
Found at i:208308 original size:15 final size:14
Alignment explanation
Indices: 208284--208313 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
208274 TATTATAAGT
208284 AAATTAAATAAATA
1 AAATTAAATAAATA
208298 AAATGTAAATAAATA
1 AAAT-TAAATAAATA
208313 A
1 A
208314 TAAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
AAATTAAATAAATA
Found at i:211951 original size:18 final size:16
Alignment explanation
Indices: 211926--211970 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
211916 TAAACTCCAT
211926 ATTTATCTTAATGAATA
1 ATTTATC-TAATGAATA
211943 ATTTCATCTAATGAATA
1 ATTT-ATCTAATGAATA
*
211960 TAATTATCTAA
1 -ATTTATCTAA
211971 CAATTATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (16 bp):
ATTTATCTAATGAATA
Found at i:215985 original size:52 final size:52
Alignment explanation
Indices: 215900--216024 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
215890 ATATGAAAAG
* *
215900 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
215952 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
216004 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
216025 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:216037 original size:52 final size:51
Alignment explanation
Indices: 215900--216044 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
215890 ATATGAAAAG
*
215900 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
215952 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
216004 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
216045 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:216051 original size:13 final size:13
Alignment explanation
Indices: 216033--216057 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
216023 CAAAGATCAG
216033 TGTATCGATACAA
1 TGTATCGATACAA
216046 TGTATCGATACA
1 TGTATCGATACA
216058 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:216141 original size:13 final size:13
Alignment explanation
Indices: 216123--216147 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
216113 AAAAAAAATA
216123 TGTATCGATACAT
1 TGTATCGATACAT
216136 TGTATCGATACA
1 TGTATCGATACA
216148 ACATTTTATG
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:218960 original size:17 final size:17
Alignment explanation
Indices: 218935--218998 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 17
218925 CTCAAGGGAC
* *
218935 AAAATAAAATAGCAAAA
1 AAAAGAAAAAAGCAAAA
218952 AAAAGAAAAAAG-AAAA
1 AAAAGAAAAAAGCAAAA
218968 CAAAAGAGAAAAAGCATAAA
1 -AAAAGA-AAAAAGCA-AAA
218988 AAAAGAAAAAA
1 AAAAGAAAAAA
218999 AAGTAAGACG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
16 4 0.10
17 16 0.39
18 11 0.27
19 7 0.17
20 3 0.07
ACGTcount: A:0.80, C:0.05, G:0.11, T:0.05
Consensus pattern (17 bp):
AAAAGAAAAAAGCAAAA
Found at i:218972 original size:19 final size:18
Alignment explanation
Indices: 218948--218998 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
218938 ATAAAATAGC
218948 AAAAAAAAGAAAAAAG-A
1 AAAAAAAAGAAAAAAGAA
* *
218965 AAACAAAAGAGAAAAAGCA
1 AAAAAAAAGA-AAAAAGAA
*
218984 TAAAAAAAGAAAAAA
1 AAAAAAAAGAAAAAA
218999 AAGTAAGACG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 9 0.31
18 11 0.38
19 9 0.31
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAGAA
Found at i:220506 original size:165 final size:162
Alignment explanation
Indices: 220266--220670 Score: 477
Period size: 155 Copynumber: 2.5 Consensus size: 162
220256 TTTTATGACG
* *
220266 AAGGTGGGCATTTAAGATAGGTTCATCACATCCCTTTTATTAGTCTTTTTAAGTCCTTTAGGGTT
1 AAGGTGGGCATTTAAGATAGGTTCATCCCAT--C---TA-TAGTTTTTTTAAGTCCTTTAGGGTT
220331 ATCGGGATACTTTTACGTACTTTTACGTCGAAGGTATACCCATAGGGGTATTTTCATAATTTTCT
60 ATCGGG-TACTTTTACGT-C--TTACGTCGAAGGTATACCCATAGGGGTATTTTCATAATTTTCT
* * *
220396 A-AAACCGAGTCCTA-GATTGGCACCAGGTCCACTTTCATGTCG
121 AGAAA-CAAGTCCTAGGA-TGGCACCAGGTCCACTTTAATGTCA
* * *
220438 AAGGT-GGCATTTAGGATAGGTTCATCCCATCTCTAGTTTTTTTAAGTCCTTTAGGGTTGTCGGG
1 AAGGTGGGCATTTAAGATAGGTTCATCCCATCTATAGTTTTTTTAAGTCCTTTAGGGTTATCGGG
* ** *
220502 -A----TAC-TCTTACGTCGAAGGTATACCTATAGGGGTATTTTTGTAATTTTTTAGAAACAAGT
66 TACTTTTACGTCTTACGTCGAAGGTATACCCATAGGGGTATTTTCATAATTTTCTAGAAACAAGT
* *
220561 CCTAGGATGTCACCATGTCCACTTTAATGTCA
131 CCTAGGATGGCACCAGGTCCACTTTAATGTCA
* * *
220593 AAGGTGGGCATTTAAGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCCTTTAGGGATATTGG
1 AAGGTGGGCATTTAAGATAGGTTCATCCCATCTATAGTT-TTTTTAAGTCCTTTAGGGTTATCGG
220658 GTACTTTTACGTC
65 GTACTTTTACGTC
220671 GTAGGTATCT
Statistics
Matches: 203, Mismatches: 20, Indels: 29
0.81 0.08 0.12
Matches are distributed among these distances:
155 74 0.36
156 35 0.17
157 24 0.12
158 2 0.01
159 3 0.01
162 3 0.01
163 3 0.01
165 29 0.14
166 1 0.00
169 1 0.00
171 23 0.11
172 5 0.02
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (162 bp):
AAGGTGGGCATTTAAGATAGGTTCATCCCATCTATAGTTTTTTTAAGTCCTTTAGGGTTATCGGG
TACTTTTACGTCTTACGTCGAAGGTATACCCATAGGGGTATTTTCATAATTTTCTAGAAACAAGT
CCTAGGATGGCACCAGGTCCACTTTAATGTCA
Found at i:223051 original size:27 final size:27
Alignment explanation
Indices: 223000--223053 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
222990 TAGTATTTAT
* ** *
223000 TTTTTTAAATAAAATTTTAAGATTAAA
1 TTTTATAAATAAAATAATAACATTAAA
223027 TTTTATAAATAAAATAATAACATTAAA
1 TTTTATAAATAAAATAATAACATTAAA
223054 AAAATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (27 bp):
TTTTATAAATAAAATAATAACATTAAA
Found at i:223338 original size:3 final size:3
Alignment explanation
Indices: 223332--223357 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
223322 ATTATAAATA
223332 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
223358 AATATTAATT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:229284 original size:11 final size:11
Alignment explanation
Indices: 229237--229285 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
229227 TTATAAATTG
229237 TTTAAAACTCA
1 TTTAAAACTCA
229248 TTTAATAGA-TCA
1 TTTAA-A-ACTCA
* *
229260 TTTAAAGCTAA
1 TTTAAAACTCA
229271 TTTAAAACTCA
1 TTTAAAACTCA
229282 TTTA
1 TTTA
229286 TTATTCAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
11 21 0.68
12 9 0.29
13 1 0.03
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (11 bp):
TTTAAAACTCA
Found at i:229511 original size:15 final size:15
Alignment explanation
Indices: 229493--229542 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
229483 ATATTCATCT
229493 AATTTAAACAAATCA
1 AATTTAAACAAATCA
* **
229508 AATTTAAATACGTCA
1 AATTTAAACAAATCA
*
229523 AATTTTAAACAAATAA
1 AA-TTTAAACAAATCA
229539 AATT
1 AATT
229543 CGAACACAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (15 bp):
AATTTAAACAAATCA
Found at i:229541 original size:16 final size:16
Alignment explanation
Indices: 229495--229542 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
229485 ATTCATCTAA
229495 TTTAAACAAATCAAA-
1 TTTAAACAAATCAAAT
* **
229510 TTTAAATACGTCAAAT
1 TTTAAACAAATCAAAT
*
229526 TTTAAACAAATAAAAT
1 TTTAAACAAATCAAAT
229542 T
1 T
229543 CGAACACAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.33
Consensus pattern (16 bp):
TTTAAACAAATCAAAT
Found at i:229926 original size:2 final size:2
Alignment explanation
Indices: 229921--229952 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
229911 ATGTTTTTAG
229921 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
229953 CCACATGACG
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:230752 original size:2 final size:2
Alignment explanation
Indices: 230747--230780 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
230737 TTTTTCTCTG
230747 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
230781 GAAATTGGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:231181 original size:2 final size:2
Alignment explanation
Indices: 231174--231229 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
231164 ACAATCAGCA
*
231174 AT AT AT AT GT A- 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
231215 AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT
231230 GAAGGGTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:232795 original size:28 final size:27
Alignment explanation
Indices: 232736--232825 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 27
232726 CACCCATTTG
* *
232736 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
232763 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
232791 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
232816 TTTGTCAAAA
1 TTTGTCAAAA
232826 TTTGTGGCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.06
27 19 0.35
28 21 0.39
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:232904 original size:20 final size:20
Alignment explanation
Indices: 232881--232926 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
232871 AAATAGAGGC
*
232881 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
**
232901 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
232921 TCCCTC
1 TCCCTC
232927 TTCAATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:237369 original size:28 final size:27
Alignment explanation
Indices: 237310--237399 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 27
237300 CACCCATTTG
* * *
237310 TTTGTCAAAAATAGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
237337 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
237365 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
237390 TTTGTCAAAA
1 TTTGTCAAAA
237400 TTTGTGGCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
25 11 0.21
26 3 0.06
27 18 0.34
28 21 0.40
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:237478 original size:20 final size:20
Alignment explanation
Indices: 237455--237500 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
237445 AAATAGAGGC
*
237455 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
**
237475 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
237495 TCCCTC
1 TCCCTC
237501 TTCAATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:248947 original size:18 final size:20
Alignment explanation
Indices: 248915--248953 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
248905 CTAATTTTTA
*
248915 AAATATTTTAGT-AAAATTT
1 AAATATTTTAATAAAAATTT
248934 AAAT-TTTTAATAAAAATTT
1 AAATATTTTAATAAAAATTT
248953 A
1 A
248954 TTTTATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
AAATATTTTAATAAAAATTT
Found at i:248981 original size:25 final size:25
Alignment explanation
Indices: 248926--248981 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
248916 AATATTTTAG
248926 TAAAA-TTTAAATTTTTAATAAAAA
1 TAAAATTTTAAATTTTTAATAAAAA
**
248950 T-TTATTTTATAATTTTTAA-AAAAA
1 TAAAATTTTA-AATTTTTAATAAAAA
248974 TAAAATTT
1 TAAAATTT
248982 CTTTCAGCCG
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
23 1 0.04
24 11 0.44
25 13 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TAAAATTTTAAATTTTTAATAAAAA
Found at i:250400 original size:2 final size:2
Alignment explanation
Indices: 250393--250417 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
250383 TACCAATGTC
250393 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
250418 ATTTTGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:250516 original size:25 final size:24
Alignment explanation
Indices: 250448--250516 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
250438 GGTACATATG
*
250448 TATTATATTTAATAAATATAATTAA
1 TATTATATAT-ATAAATATAATTAA
* * *
250473 TATATTTATCTTTAAATATAATTAA
1 TAT-TATATATATAAATATAATTAA
250498 TATTATATATATAATATAT
1 TATTATATATATAA-ATAT
250517 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 8 0.22
25 23 0.64
26 5 0.14
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (24 bp):
TATTATATATATAAATATAATTAA
Found at i:251935 original size:15 final size:15
Alignment explanation
Indices: 251906--251934 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
251896 TTTTGAATTA
251906 AGATTGTTTAATTTT
1 AGATTGTTTAATTTT
251921 AGATTG-TTAATTTT
1 AGATTGTTTAATTTT
251935 TTTAGTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (15 bp):
AGATTGTTTAATTTT
Found at i:252812 original size:12 final size:12
Alignment explanation
Indices: 252795--252820 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
252785 ATACTTTCGG
252795 TAATATTATATT
1 TAATATTATATT
252807 TAATATTATATT
1 TAATATTATATT
252819 TA
1 TA
252821 TTATGATTAT
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:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAATATTATATT
Found at i:260376 original size:26 final size:25
Alignment explanation
Indices: 260340--260399 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
260330 ACGATTATTG
*
260340 TTAAATTTAAATTTAAATATAAATAA
1 TTAAATTTAAAATTAAATATAAA-AA
*
260366 TTAAATTTAAAATTGAATATAAAAA
1 TTAAATTTAAAATTAAATATAAAAA
*
260391 TTAATTTTA
1 TTAAATTTA
260400 TTTTTATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 10 0.32
26 21 0.68
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TTAAATTTAAAATTAAATATAAAAA
Found at i:260522 original size:18 final size:18
Alignment explanation
Indices: 260501--260552 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
260491 AATTTAAAAG
*
260501 TAATTAATAATATATTAA
1 TAATTAATAATATATAAA
*
260519 TAATTAATATTATATAAA
1 TAATTAATAATATATAAA
*
260537 T-TTTAATATATATATA
1 TAATTAATA-ATATATA
260553 TATTTATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 6 0.21
18 23 0.79
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATTAATAATATATAAA
Found at i:260557 original size:18 final size:17
Alignment explanation
Indices: 260522--260566 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
260512 ATATTAATAA
260522 TTAATATTATATAAATT
1 TTAATATTATATAAATT
*
260539 TTAATA-TATATATATAT
1 TTAATATTATATAAAT-T
260556 TT-ATATTATAT
1 TTAATATTATAT
260567 TAATGTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATATTATATAAATT
Found at i:261397 original size:20 final size:21
Alignment explanation
Indices: 261372--261411 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
261362 ATCATATATT
*
261372 TTATTTTTTATT-TATTTTTA
1 TTATTTTATATTATATTTTTA
261392 TTATTTTATATTATATTTTT
1 TTATTTTATATTATATTTTT
261412 TTAATTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (21 bp):
TTATTTTATATTATATTTTTA
Found at i:262868 original size:11 final size:11
Alignment explanation
Indices: 262850--262937 Score: 51
Period size: 11 Copynumber: 8.2 Consensus size: 11
262840 TTAATATTTT
262850 AAAT-ATATAA
1 AAATAATATAA
*
262860 AAATAATATTA
1 AAATAATATAA
* *
262871 ACATGATATAA
1 AAATAATATAA
262882 AAATTAAT-TAA
1 AAA-TAATATAA
262893 AACATAAATATAA
1 AA-AT-AATATAA
**
262906 AAA-CGTA-AA
1 AAATAATATAA
262915 AAATAAT-TAA
1 AAATAATATAA
* *
262925 ATATTATATAA
1 AAATAATATAA
262936 AA
1 AA
262938 TTATAATACT
Statistics
Matches: 57, Mismatches: 13, Indels: 15
0.67 0.15 0.18
Matches are distributed among these distances:
9 5 0.09
10 14 0.25
11 25 0.44
12 8 0.14
13 5 0.09
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (11 bp):
AAATAATATAA
Found at i:263028 original size:18 final size:18
Alignment explanation
Indices: 262993--263028 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
262983 ATATAAATTC
* *
262993 TTTTTTCTTTTTCTTTCT
1 TTTTTTCTTTTCCCTTCT
263011 TTTTTTCTTTTCCCTTCT
1 TTTTTTCTTTTCCCTTCT
263029 ATCTTTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTCTTTTCCCTTCT
Found at i:263121 original size:12 final size:12
Alignment explanation
Indices: 263104--263144 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
263094 ATTAATTATG
263104 TATAAAAATTAA
1 TATAAAAATTAA
* *
263116 TATAAATA-TGA
1 TATAAAAATTAA
263127 TATAAAAATTAA
1 TATAAAAATTAA
263139 T-TAAAA
1 TATAAAA
263145 TATAATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
TATAAAAATTAA
Found at i:263130 original size:23 final size:23
Alignment explanation
Indices: 263100--263162 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 23
263090 TCACATTAAT
263100 TATG-TATAAAAATTAATATAAA
1 TATGATATAAAAATTAATATAAA
263122 TATGATATAAAAATTAAT-TAAA
1 TATGATATAAAAATTAATATAAA
*
263144 -AT-ATAATAAAAATAAATAT
1 TATGAT-ATAAAAATTAATAT
263163 TTTTAAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 2 0.05
21 13 0.35
22 9 0.24
23 13 0.35
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (23 bp):
TATGATATAAAAATTAATATAAA
Found at i:263143 original size:11 final size:11
Alignment explanation
Indices: 263105--263161 Score: 57
Period size: 10 Copynumber: 5.3 Consensus size: 11
263095 TTAATTATGT
263105 ATAAAAAT-TA
1 ATAAAAATATA
*
263115 ATATAAATATGA
1 ATAAAAATAT-A
263127 TATAAAAAT-TA
1 -ATAAAAATATA
*
263138 ATTAAAATATA
1 ATAAAAATATA
263149 ATAAAAATA-A
1 ATAAAAATATA
263159 ATA
1 ATA
263162 TTTTTAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 18 0.46
11 12 0.31
12 2 0.05
13 7 0.18
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
ATAAAAATATA
Found at i:263170 original size:25 final size:25
Alignment explanation
Indices: 263142--263215 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 25
263132 AAATTAATTA
*
263142 AAATATAATAAAAATAAATATTTTT
1 AAATATAATAAAAATAAATATCTTT
**
263167 AAATATCATATAAATTTATAATA-CTTT
1 AAATAT-A-ATAAAAATA-AATATCTTT
263194 AAATAATAA-AAAATATAAATAT
1 AAAT-ATAATAAAA-ATAAATAT
263216 GTAATTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
25 13 0.34
26 4 0.11
27 15 0.39
28 6 0.16
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATATAATAAAAATAAATATCTTT
Found at i:266284 original size:33 final size:33
Alignment explanation
Indices: 266237--266301 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
266227 TACTTTTGAA
*
266237 ATTAATTATGTAAATACTGGTAAAATCTATGAT
1 ATTAATTATGTAAATACTGGTAAAAGCTATGAT
*
266270 ATTAATTATTTAAATACTGGTAAAAGCTATGA
1 ATTAATTATGTAAATACTGGTAAAAGCTATGA
266302 ATAATAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.38
Consensus pattern (33 bp):
ATTAATTATGTAAATACTGGTAAAAGCTATGAT
Found at i:267760 original size:2 final size:2
Alignment explanation
Indices: 267753--267792 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
267743 ACTTGCCAAG
*
267753 TC TC TC TC TC TAC TT TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC T
267793 TTCAACGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:269675 original size:16 final size:18
Alignment explanation
Indices: 269644--269678 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
269634 TTAACGTATT
269644 AAAATTTATATAAATATA
1 AAAATTTATATAAATATA
269662 AAAATTT-T-TAAATATA
1 AAAATTTATATAAATATA
269678 A
1 A
269679 TTATGACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTTATATAAATATA
Found at i:269898 original size:23 final size:21
Alignment explanation
Indices: 269870--269927 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 21
269860 ATTAAAAATC
269870 AATTTAATTTGA-AACTCATAAAA
1 AATTTAATTT-ATAACT--TAAAA
269893 AATTTAATTTATAACTTAAAA
1 AATTTAATTTATAACTTAAAA
*
269914 AATTTGAATCTATA
1 AATTT-AATTTATA
269928 TTATTATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 10 0.31
22 8 0.25
23 14 0.44
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (21 bp):
AATTTAATTTATAACTTAAAA
Found at i:271437 original size:2 final size:2
Alignment explanation
Indices: 271430--271458 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
271420 ACTAATTCAA
271430 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
271459 ATGATGTTAT
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:271670 original size:2 final size:2
Alignment explanation
Indices: 271663--271687 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
271653 TATCAACGAT
271663 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 T
271688 GAAAATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:273714 original size:20 final size:20
Alignment explanation
Indices: 273686--273730 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
273676 CCAAATTTAT
*
273686 ATAAAAATACCTTAAATAAA
1 ATAAAAATACCATAAATAAA
* * *
273706 ATAATAATACGATAAATAAT
1 ATAAAAATACCATAAATAAA
273726 ATAAA
1 ATAAA
273731 TAAGATAAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (20 bp):
ATAAAAATACCATAAATAAA
Found at i:279649 original size:21 final size:22
Alignment explanation
Indices: 279606--279654 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
279596 GAAAAAGCAA
*
279606 TCAAAGCATAAAATAGAATAAG
1 TCAAAGCATAAAATAGAACAAG
279628 TCAAA-CA-AAAATCAGAACAAG
1 TCAAAGCATAAAAT-AGAACAAG
*
279649 TTAAAG
1 TCAAAG
279655 TGTATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.16
Consensus pattern (22 bp):
TCAAAGCATAAAATAGAACAAG
Found at i:289520 original size:10 final size:10
Alignment explanation
Indices: 289505--289558 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
289495 TCTCCCCTTA
289505 CTTTTTTTTT
1 CTTTTTTTTT
289515 CTTTTTTTCTT
1 CTTTTTTT-TT
*
289526 CCTTTTTTCTT
1 -CTTTTTTTTT
*
289537 CTTTTTCTTT
1 CTTTTTTTTT
*
289547 CTTTTTTCTT
1 CTTTTTTTTT
289557 CT
1 CT
289559 CCTCCCCCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 26 0.70
11 4 0.11
12 7 0.19
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:289522 original size:11 final size:11
Alignment explanation
Indices: 289505--289558 Score: 69
Period size: 11 Copynumber: 5.2 Consensus size: 11
289495 TCTCCCCTTA
289505 CTTTTTTT-TT
1 CTTTTTTTCTT
289515 CTTTTTTTCTT
1 CTTTTTTTCTT
*
289526 CCTTTTTTCTT
1 CTTTTTTTCTT
*
289537 CTTTTTCT-TT
1 CTTTTTTTCTT
289547 C-TTTTTTCTT
1 CTTTTTTTCTT
289557 CT
1 CT
289559 CCTCCCCCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 5 0.14
10 14 0.38
11 18 0.49
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
CTTTTTTTCTT
Found at i:289531 original size:20 final size:21
Alignment explanation
Indices: 289508--289558 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
289498 CCCCTTACTT
289508 TTTTTTTCTT-TTTTTCTTCC
1 TTTTTTTCTTCTTTTTCTTCC
*
289528 -TTTTTTCTTCTTTTTCTTTC
1 TTTTTTTCTTCTTTTTCTTCC
289548 -TTTTTTCTTCT
1 TTTTTTTCTTCT
289559 CCTCCCCCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTCTTCTTTTTCTTCC
Found at i:292334 original size:20 final size:20
Alignment explanation
Indices: 292309--292422 Score: 56
Period size: 20 Copynumber: 5.5 Consensus size: 20
292299 ATTAAATAAA
292309 AATAAAATTTATTTAATTTT
1 AATAAAATTTATTTAATTTT
*
292329 AATAAATATATT-TTAAATTTAT
1 AATAAA-AT-TTATTTAATTT-T
* * *
292351 AAATAAAAATTAAATTAA-ATT
1 -AAT-AAAATTTATTTAATTTT
* * *
292372 AATATATTTTA-TTAATATCTA
1 AATAAAATTTATTTAAT-T-TT
292393 AATTAAAATTTAATTTAA-TTT
1 AA-TAAAATTT-ATTTAATTTT
292414 AATAAAATT
1 AATAAAATT
292423 AAAATTAAAC
Statistics
Matches: 69, Mismatches: 13, Indels: 24
0.65 0.12 0.23
Matches are distributed among these distances:
18 4 0.06
19 5 0.07
20 16 0.23
21 16 0.23
22 12 0.17
23 9 0.13
24 7 0.10
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAAAATTTATTTAATTTT
Found at i:292402 original size:41 final size:40
Alignment explanation
Indices: 292319--292417 Score: 101
Period size: 39 Copynumber: 2.5 Consensus size: 40
292309 AATAAAATTT
* * * *
292319 ATTTAATTTTAATAAATATATTTTAAATTTATAAATAAAA
1 ATTTAAATTAAATTAATATATTTTAAATATATAAATAAAA
* *
292359 A-TTAAATTAAATTAATATATTTTATTAATATCTAAATTAAA
1 ATTTAAATTAAATTAATATATTTTA--AATATATAAATAAAA
* *
292400 ATTTAATTTAATTTAATA
1 ATTTAAATTAAATTAATA
292418 AAATTAAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 20 0.42
40 1 0.02
41 13 0.27
42 14 0.29
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (40 bp):
ATTTAAATTAAATTAATATATTTTAAATATATAAATAAAA
Found at i:297827 original size:32 final size:32
Alignment explanation
Indices: 297791--297914 Score: 153
Period size: 32 Copynumber: 3.9 Consensus size: 32
297781 ATTTAAATGA
* * * *
297791 ATGAATGAATTTATTTAAATGAATATAGTTGG
1 ATGAATGAATGTATTTGAATGAATACATTTGG
*
297823 ATGAATGAATGTATTTGAATGAATACATTTAG
1 ATGAATGAATGTATTTGAATGAATACATTTGG
* * *
297855 ATAAATGAACGTATTTGAATGAATGCATTTGG
1 ATGAATGAATGTATTTGAATGAATACATTTGG
*
297887 ATGAATGAAT-T-TTTGAATGAATGCATTT
1 ATGAATGAATGTATTTGAATGAATACATTT
297915 AAATACTTAA
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 17 0.21
31 1 0.01
32 63 0.78
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (32 bp):
ATGAATGAATGTATTTGAATGAATACATTTGG
Found at i:297829 original size:18 final size:18
Alignment explanation
Indices: 297808--297846 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
297798 AATTTATTTA
*
297808 AATGAATATAGTTGGATG
1 AATGAATATAGTTGAATG
* *
297826 AATGAATGTATTTGAATG
1 AATGAATATAGTTGAATG
297844 AAT
1 AAT
297847 ACATTTAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (18 bp):
AATGAATATAGTTGAATG
Found at i:297841 original size:14 final size:14
Alignment explanation
Indices: 297792--297914 Score: 66
Period size: 14 Copynumber: 8.1 Consensus size: 14
297782 TTTAAATGAA
*
297792 TGAATGAATTTATT
1 TGAATGAATGTATT
* *
297806 TAAATGAATATAGTT
1 TGAATGAATGTA-TT
297821 GGATGAATGAATGTATT
1 ---TGAATGAATGTATT
**
297838 TGAATGAATACATT
1 TGAATGAATGTATT
*
297852 TAGATAAATGAACGTATT
1 T-G---AATGAATGTATT
*
297870 TGAATGAATGCATT
1 TGAATGAATGTATT
* *
297884 TGGATGAATGAATTTT
1 TGAATGAATG--TATT
*
297900 TGAATGAATGCATT
1 TGAATGAATGTATT
297914 T
1 T
297915 AAATACTTAA
Statistics
Matches: 82, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
14 45 0.55
15 3 0.04
16 11 0.13
17 3 0.04
18 20 0.24
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (14 bp):
TGAATGAATGTATT
Found at i:297879 original size:18 final size:18
Alignment explanation
Indices: 297823--297879 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
297813 ATATAGTTGG
*
297823 ATGAATGAATGTATTTGA
1 ATGAATGAACGTATTTGA
297841 ATGAAT--AC--ATTT-A
1 ATGAATGAACGTATTTGA
*
297854 GATAAATGAACGTATTTGA
1 -ATGAATGAACGTATTTGA
297873 ATGAATG
1 ATGAATG
297880 CATTTGGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 12
0.67 0.07 0.27
Matches are distributed among these distances:
13 1 0.03
14 9 0.30
16 3 0.10
18 16 0.53
19 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (18 bp):
ATGAATGAACGTATTTGA
Found at i:298733 original size:13 final size:13
Alignment explanation
Indices: 298715--298745 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
298705 ATAATTTTGA
298715 ATTTAAAAATATT
1 ATTTAAAAATATT
298728 ATTT-AAAATATT
1 ATTTAAAAATATT
298740 ATTTAA
1 ATTTAA
298746 TTCTCAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTAAAAATATT
Found at i:299542 original size:2 final size:2
Alignment explanation
Indices: 299535--299561 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
299525 TTTAAAATAG
299535 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 T
299562 TTCACTGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:300025 original size:92 final size:93
Alignment explanation
Indices: 299865--300042 Score: 295
Period size: 92 Copynumber: 1.9 Consensus size: 93
299855 ATGGAGTTAC
* *
299865 GGGTCATGATGGGAGACTCAGAACTTGCCAAGAGACACACTCTGTCACTATCTTTGCACATTTAT
1 GGGTCACGATGGGAGACTCAGAACTTGCCAAGAGACACACTCTGTCACTATCTTCGCACATTTAT
*
299930 ATGCTGTATAGTTTAG-CTTTTGCATTA
66 ATGCTGTAAAGTTTAGACTTTTGCATTA
* * *
299957 GGGTCACGATGGGAGACTCAGGACTTGCCAAGAGACACACTCTGTCATTATCTTCGCACATTTCT
1 GGGTCACGATGGGAGACTCAGAACTTGCCAAGAGACACACTCTGTCACTATCTTCGCACATTTAT
300022 ATGCTGTAAAGTTTAGACTTT
66 ATGCTGTAAAGTTTAGACTTT
300043 GTGGGCTTGT
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
92 75 0.95
93 4 0.05
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (93 bp):
GGGTCACGATGGGAGACTCAGAACTTGCCAAGAGACACACTCTGTCACTATCTTCGCACATTTAT
ATGCTGTAAAGTTTAGACTTTTGCATTA
Found at i:302132 original size:2 final size:2
Alignment explanation
Indices: 302125--302163 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
302115 TTAATTTTCC
* *
302125 AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT 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 A
302164 AACTTCAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:305489 original size:2 final size:2
Alignment explanation
Indices: 305482--305512 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
305472 CATCAAACTT
305482 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
305513 TATCAGGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:310760 original size:54 final size:54
Alignment explanation
Indices: 310701--310829 Score: 224
Period size: 54 Copynumber: 2.4 Consensus size: 54
310691 TGGAGATGGG
310701 CACTTCTAAGGTAAAGGTATATTGGTACATGCTAAA-GATTAACTTTGATTTAGC
1 CACTTCTAAGGTAAAGGTATATTGGTACATGCTAAATG-TTAACTTTGATTTAGC
310755 CACTTCTAAGGTAAAGGTATATTGGTACATGCTAAATGTTAACTTTGATTTAGC
1 CACTTCTAAGGTAAAGGTATATTGGTACATGCTAAATGTTAACTTTGATTTAGC
* *
310809 TACTTCTAAGGTACAGGTATA
1 CACTTCTAAGGTAAAGGTATA
310830 ACACTAAACA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
54 71 0.99
55 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (54 bp):
CACTTCTAAGGTAAAGGTATATTGGTACATGCTAAATGTTAACTTTGATTTAGC
Found at i:312452 original size:2 final size:2
Alignment explanation
Indices: 312445--312489 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
312435 GAATTCAAGG
312445 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
312487 AT A
1 AT A
312490 AGTTTCAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:313085 original size:19 final size:19
Alignment explanation
Indices: 313056--313092 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
313046 TATTCGTATT
313056 ATATTCATATT-ATTTTTC
1 ATATTCATATTAATTTTTC
313074 ATATTGCATATTAATTTTT
1 ATATT-CATATTAATTTTT
313093 ATGTATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (19 bp):
ATATTCATATTAATTTTTC
Found at i:313436 original size:19 final size:21
Alignment explanation
Indices: 313412--313459 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
313402 AGGAAATGAA
313412 AGAAAAAAAGA-AAACAAAG-
1 AGAAAAAAAGATAAACAAAGC
*
313431 AGAAAAAAAGATAGACAAAGC
1 AGAAAAAAAGATAAACAAAGC
313452 A-AAAAAAA
1 AGAAAAAAA
313460 TTATGTGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.42
20 14 0.54
21 1 0.04
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (21 bp):
AGAAAAAAAGATAAACAAAGC
Found at i:316211 original size:14 final size:14
Alignment explanation
Indices: 316172--316239 Score: 61
Period size: 13 Copynumber: 4.9 Consensus size: 14
316162 AAAATAAAAA
*
316172 TTATATATTATATAT
1 TTATA-ATTAAATAT
*
316187 TT-TATTTAAATAT
1 TTATAATTAAATAT
316200 TTATAATTAAATAT
1 TTATAATTAAATAT
*
316214 TT-TATTTAAA-AT
1 TTATAATTAAATAT
316226 ATTATATATTAAAT
1 -TTATA-ATTAAAT
316240 TTAAATATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
12 2 0.05
13 18 0.42
14 16 0.37
15 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATAATTAAATAT
Found at i:316286 original size:14 final size:13
Alignment explanation
Indices: 316183--316332 Score: 87
Period size: 14 Copynumber: 11.2 Consensus size: 13
316173 TATATATTAT
316183 ATATTTTATTTAA
1 ATATTTTATTTAA
*
316196 ATATTTATAATTAA
1 ATATTT-TATTTAA
316210 ATATTTTATTTAAA
1 ATATTTTATTT-AA
*
316224 ATATTATATATTAA
1 ATATTTTAT-TTAA
* *
316238 AT-TTAAATATTTTAT
1 ATATT--TTA-TTTAA
**
316253 ATATTAAATTTAAA
1 ATATTTTATTT-AA
316267 ATATTTTATTTAAA
1 ATATTTTATTT-AA
316281 ATATTTTA--T--
1 ATATTTTATTTAA
316290 ATATTTTATTTAAA
1 ATATTTTATTT-AA
*
316304 ATATTATATATT-A
1 ATATTTTAT-TTAA
*
316317 ATATTTATAATTAA
1 ATATTT-TATTTAA
316331 AT
1 AT
316333 TTAATAAAAA
Statistics
Matches: 110, Mismatches: 11, Indels: 31
0.72 0.07 0.20
Matches are distributed among these distances:
9 8 0.07
11 1 0.01
12 1 0.01
13 23 0.21
14 62 0.56
15 12 0.11
16 3 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATTTTATTTAA
Found at i:316286 original size:23 final size:23
Alignment explanation
Indices: 316216--316308 Score: 88
Period size: 23 Copynumber: 4.2 Consensus size: 23
316206 TTAAATATTT
*
316216 TATTTAAAATATTATATATT--AA
1 TATTTAAAATATTTTAT-TTAAAA
* *
316238 -ATTT-AAATATTTTATATATTAA
1 TATTTAAAATATTTTATTTA-AAA
316260 -ATTTAAAATATTTTATTTAAAA
1 TATTTAAAATATTTTATTTAAAA
* *
316282 TATTTTATATATTTTATTTAAAA
1 TATTTAAAATATTTTATTTAAAA
316305 TATT
1 TATT
316309 ATATATTAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.02
20 10 0.17
21 4 0.07
22 8 0.13
23 37 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTTAAAATATTTTATTTAAAA
Found at i:316294 original size:37 final size:39
Alignment explanation
Indices: 316208--316292 Score: 60
Period size: 34 Copynumber: 2.4 Consensus size: 39
316198 ATTTATAATT
* * *
316208 AAATATTTTATTTAAAATA-TTATATATTAA---ATTT-
1 AAATATTTTATATAAAATATTTATAAATAAATTTATTTA
* *
316242 AAATATTTTATATATTAA-ATTTA-AAAT-ATTTTATTTA
1 AAATATTTTATATA-AAATATTTATAAATAAATTTATTTA
316279 AAATATTTTATATA
1 AAATATTTTATATA
316293 TTTTATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
33 1 0.02
34 17 0.41
35 5 0.12
36 4 0.10
37 14 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (39 bp):
AAATATTTTATATAAAATATTTATAAATAAATTTATTTA
Found at i:316313 original size:23 final size:23
Alignment explanation
Indices: 316267--316314 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
316257 TAAATTTAAA
*
316267 ATATTTTATTTAAAATATTTTAT
1 ATATTTTATTTAAAATATTATAT
316290 ATATTTTATTTAAAATATTATAT
1 ATATTTTATTTAAAATATTATAT
316313 AT
1 AT
316315 TAATATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATTTTATTTAAAATATTATAT
Found at i:316353 original size:80 final size:83
Alignment explanation
Indices: 316183--316344 Score: 199
Period size: 80 Copynumber: 2.0 Consensus size: 83
316173 TATATATTAT
316183 ATATTTTATTTAAATATTTATAATTAAATATTTTATTTAAAATATTATATATTAAATTTAAATAT
1 ATATTTTATTTAAATATTTATAATT-AATATTTTATTTAAAATATTATATATTAAATTTAAATAT
** * **
316248 TTTATATATTAAATTTAAA
65 TAAATATAATAAAAATAAA
*
316267 ATATTTTATTTAAAATATTT-T-A-T-ATATTTTATTTAAAATATTATATATTAATATTTATA-A
1 ATATTTTATTT-AAATATTTATAATTAATATTTTATTTAAAATATTATATATTAA-ATTTAAATA
*
316327 TTAAATTTAATAAAAATA
64 TTAAATATAATAAAAATA
316345 TTTTATTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
80 41 0.59
81 6 0.09
82 1 0.01
83 1 0.01
84 12 0.17
85 8 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (83 bp):
ATATTTTATTTAAATATTTATAATTAATATTTTATTTAAAATATTATATATTAAATTTAAATATT
AAATATAATAAAAATAAA
Found at i:317146 original size:32 final size:32
Alignment explanation
Indices: 317108--317181 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
317098 GATAAAAGTT
317108 TAAAAGTTTATATTTAAATAATTTCTT-AATAA
1 TAAAAGTTTATATTTAAATAATTT-TTCAATAA
*
317140 TAAAAGTTTATATTTAAATAATTTTTCAATGA
1 TAAAAGTTTATATTTAAATAATTTTTCAATAA
*
317172 TAAAAATTTA
1 TAAAAGTTTA
317182 ATCAAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 2 0.05
32 37 0.95
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (32 bp):
TAAAAGTTTATATTTAAATAATTTTTCAATAA
Found at i:317971 original size:20 final size:21
Alignment explanation
Indices: 317946--318031 Score: 65
Period size: 20 Copynumber: 4.2 Consensus size: 21
317936 AAATGGATAA
317946 AAAATT-TAATTTTTATAATT
1 AAAATTATAATTTTTATAATT
*
317966 AAAATTATAA-TTTGATAATT
1 AAAATTATAATTTTTATAATT
* * *
317986 TAAATTAAAAAATTTTATAATTT
1 AAAATT-ATAATTTTTATAA-TT
* *
318009 GAAATT-T-ATTTTTA-AAAT
1 AAAATTATAATTTTTATAATT
318027 AAAAT
1 AAAAT
318032 AATTTTATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
18 5 0.09
19 2 0.04
20 26 0.49
21 6 0.11
22 7 0.13
23 7 0.13
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATTATAATTTTTATAATT
Found at i:318051 original size:9 final size:9
Alignment explanation
Indices: 318037--318078 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
318027 AAAATAATTT
318037 TATTTTTTA
1 TATTTTTTA
318046 TATTTTTTA
1 TATTTTTTA
318055 -A-TTTTTA
1 TATTTTTTA
*
318062 T-TATTTTA
1 TATTTTTTA
318070 TATTTTTTA
1 TATTTTTTA
318079 CATGTGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 6 0.21
8 7 0.25
9 15 0.54
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TATTTTTTA
Found at i:318053 original size:16 final size:17
Alignment explanation
Indices: 318034--318078 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
318024 AATAAAATAA
318034 TTTTATTTTTTA-TATT
1 TTTTATTTTTTATTATT
*
318050 TTTTAATTTTTATTATT
1 TTTTATTTTTTATTATT
*
318067 TTATATTTTTTA
1 TTTTATTTTTTA
318079 CATGTGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTTATTATT
Found at i:318060 original size:17 final size:16
Alignment explanation
Indices: 318033--318078 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
318023 AAATAAAATA
318033 ATTTT-ATTTTTTATAT
1 ATTTTAATTTTTTAT-T
*
318049 TTTTTAA-TTTTTATT
1 ATTTTAATTTTTTATT
318064 ATTTTATATTTTTTA
1 ATTTTA-ATTTTTTA
318079 CATGTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 6 0.24
16 12 0.48
17 7 0.28
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTAATTTTTTATT
Found at i:318370 original size:17 final size:17
Alignment explanation
Indices: 318343--318383 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
318333 AAAATTTAAA
*
318343 AAATAATATATTTTTATT
1 AAAT-ATATATTTATATT
318361 AAATATATATTTATATT
1 AAATATATATTTATATT
*
318378 TAATAT
1 AAATAT
318384 CTAATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATATATATTTATATT
Found at i:319377 original size:4 final size:4
Alignment explanation
Indices: 319368--319397 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
319358 ATGAAATGAT
319368 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
319398 AACTGAGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:320201 original size:43 final size:44
Alignment explanation
Indices: 320127--320211 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 44
320117 AAAAAAAAAT
* **
320127 TATAAATTTATACAATAATTATATTTCTATTATTTTATATTTTA
1 TATAAATTTATACAATAATTATATTTATATTAAATTATATTTTA
320171 TATAAATTT-TA-ATATACATT-TATTTATATTAAATTATATTT
1 TATAAATTTATACA-ATA-ATTATATTTATATTAAATTATATTT
320212 AATTTTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 1 0.03
43 23 0.64
44 12 0.33
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (44 bp):
TATAAATTTATACAATAATTATATTTATATTAAATTATATTTTA
Done.