Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold288
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: 358258
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
File 3 of 3
Found at i:255224 original size:15 final size:14
Alignment explanation
Indices: 255184--255226 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
255174 AATAAATTTT
255184 TTTTATTTATAAAA
1 TTTTATTTATAAAA
* *
255198 TTTAAATT-TAAAA
1 TTTTATTTATAAAA
255211 TTTTATTTAATAAAA
1 TTTTATTT-ATAAAA
255226 T
1 T
255227 ATATCCCTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 11 0.48
14 6 0.26
15 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTATTTATAAAA
Found at i:255758 original size:18 final size:21
Alignment explanation
Indices: 255735--255792 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 21
255725 AAAAAAATAC
255735 ATTTAA-AA-ATT-TTAAAAT
1 ATTTAATAATATTATTAAAAT
255753 ATTTAATAATATTATT-AAA-
1 ATTTAATAATATTATTAAAAT
*
255772 ATTTAA-AATATTA-AAAAAT
1 ATTTAATAATATTATTAAAAT
255791 AT
1 AT
255793 ATTTTTAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
18 16 0.47
19 10 0.29
20 6 0.18
21 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTTAATAATATTATTAAAAT
Found at i:256277 original size:2 final size:2
Alignment explanation
Indices: 256266--256299 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
256256 ATTGTTGAAG
256266 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
256300 TTTTCCCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:260325 original size:2 final size:2
Alignment explanation
Indices: 260318--260351 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
260308 TCCTATGGTT
260318 TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
260352 TTTCAACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:262828 original size:10 final size:8
Alignment explanation
Indices: 262798--262823 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
262788 TATTTAAAAT
262798 ATATTAAA
1 ATATTAAA
262806 ATATTAAA
1 ATATTAAA
262814 ATATTAAA
1 ATATTAAA
262822 AT
1 AT
262824 TTATTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATTAAA
Found at i:263648 original size:30 final size:30
Alignment explanation
Indices: 263610--263741 Score: 144
Period size: 30 Copynumber: 4.5 Consensus size: 30
263600 TTATCACATA
*
263610 CAAATAAACTTTTAACTTTTAATTTATGCT
1 CAAATAAACTTTTAACTTTTAATTTATACT
* * *
263640 CATATAAAC-CTT-ACTTTTAATTTGTACT
1 CAAATAAACTTTTAACTTTTAATTTATACT
* * *
263668 CAAATAATCTTTTAATTTTTAATTTATATT
1 CAAATAAACTTTTAACTTTTAATTTATACT
* *
263698 TAAATAAACTCTTAA-TTTTAATTTATACT
1 CAAATAAACTTTTAACTTTTAATTTATACT
* *
263727 TAAATAAATTTTTAA
1 CAAATAAACTTTTAA
263742 TATAAATTAA
Statistics
Matches: 84, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
28 21 0.25
29 30 0.36
30 33 0.39
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.49
Consensus pattern (30 bp):
CAAATAAACTTTTAACTTTTAATTTATACT
Found at i:263672 original size:58 final size:59
Alignment explanation
Indices: 263610--263741 Score: 167
Period size: 58 Copynumber: 2.3 Consensus size: 59
263600 TTATCACATA
* * * *
263610 CAAATAAACTTTTAACTTTTAATTTATGCTCATATAAAC-CTTACTTTTAATTTGTACT
1 CAAATAAACTTTTAACTTTTAATTTATACTCAAATAAACTCTTAATTTTAATTTATACT
* * * *
263668 CAAATAATCTTTTAATTTTTAATTTATATTTAAATAAACTCTTAATTTTAATTTATACT
1 CAAATAAACTTTTAACTTTTAATTTATACTCAAATAAACTCTTAATTTTAATTTATACT
* *
263727 TAAATAAATTTTTAA
1 CAAATAAACTTTTAA
263742 TATAAATTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
58 33 0.53
59 29 0.47
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.49
Consensus pattern (59 bp):
CAAATAAACTTTTAACTTTTAATTTATACTCAAATAAACTCTTAATTTTAATTTATACT
Found at i:263739 original size:23 final size:23
Alignment explanation
Indices: 263681--263742 Score: 61
Period size: 29 Copynumber: 2.4 Consensus size: 23
263671 ATAATCTTTT
*
263681 AATTTTTAATTTATATTTAAATA
1 AATTTTTAATTTATACTTAAATA
263704 AACTCTTAATTTTAATTTATACTTAAATA
1 AA----T--TTTTAATTTATACTTAAATA
263733 AATTTTTAAT
1 AATTTTTAAT
263743 ATAAATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
23 9 0.28
25 1 0.03
27 1 0.03
29 21 0.66
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTTTTAATTTATACTTAAATA
Found at i:263749 original size:29 final size:29
Alignment explanation
Indices: 263688--263749 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
263678 TTTAATTTTT
* * *
263688 AATTTATATTTAAATAAACTCTTAATTTT
1 AATTTATACTTAAATAAACTCTTAATATA
* *
263717 AATTTATACTTAAATAAATTTTTAATATA
1 AATTTATACTTAAATAAACTCTTAATATA
263746 AATT
1 AATT
263750 AAAATTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (29 bp):
AATTTATACTTAAATAAACTCTTAATATA
Found at i:265032 original size:3 final size:3
Alignment explanation
Indices: 265024--265070 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
265014 CCCAGAGTTA
265024 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
265071 CAGTAATTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:270475 original size:30 final size:27
Alignment explanation
Indices: 270441--270505 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 27
270431 AAATTAGTTG
**
270441 TATAATTATAATGTAAATATGATATAAATA
1 TATAATTAT-ATCAAAATAT-ATAT-AATA
270471 TATAATTATATCAAAATATATATAATA
1 TATAATTATATCAAAATATATATAATA
270498 T-TAATTAT
1 TATAATTAT
270506 TAATATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 7 0.21
27 5 0.15
28 4 0.12
29 8 0.24
30 9 0.27
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (27 bp):
TATAATTATATCAAAATATATATAATA
Found at i:270544 original size:18 final size:19
Alignment explanation
Indices: 270485--270544 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
270475 ATTATATCAA
*
270485 AATATATATAATATTAATTATT
1 AATATTTATAATATT--TTA-T
*
270507 AATATTTA-AAAATTTATAT
1 AATATTTATAATATTT-TAT
270526 AA-ATTTATAATATTTTAT
1 AATATTTATAATATTTTAT
270544 A
1 A
270545 TAAAAAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 9 0.27
19 10 0.30
20 2 0.06
21 5 0.15
22 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTTATAATATTTTAT
Found at i:270825 original size:31 final size:32
Alignment explanation
Indices: 270784--270845 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
270774 AATATAGTAT
270784 GAATATATTAATATATTAAA-ATATATATAAAC
1 GAATATATTAATATA-TAAACATATATATAAAC
* *
270816 GAATA-ATTAATGTATAAACATTTATATAAA
1 GAATATATTAATATATAAACATATATATAAA
270846 ATTTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 4 0.15
31 18 0.67
32 5 0.19
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (32 bp):
GAATATATTAATATATAAACATATATATAAAC
Found at i:271169 original size:16 final size:15
Alignment explanation
Indices: 271142--271184 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
271132 TCTCTTTTTT
271142 CTCTCTTT-CTTTCC
1 CTCTCTTTCCTTTCC
271156 CTCTCTTCTCCTTTCC
1 CTCTCTT-TCCTTTCC
* *
271172 TTTTCTTTCCTTT
1 CTCTCTTTCCTTT
271185 TTTTTTCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.28
15 7 0.28
16 11 0.44
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (15 bp):
CTCTCTTTCCTTTCC
Found at i:272233 original size:40 final size:40
Alignment explanation
Indices: 272183--272258 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
272173 TTTAAATTTT
* * * *
272183 TTTACCGATTTAAGATTGTATTTTATGATAAAACTTAATA
1 TTTACCGATTTAAAATTATACTTAATGATAAAACTTAATA
* *
272223 TTTATCGATTTAAAATTATACTTAATGATACAACTT
1 TTTACCGATTTAAAATTATACTTAATGATAAAACTT
272259 GTAACTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (40 bp):
TTTACCGATTTAAAATTATACTTAATGATAAAACTTAATA
Found at i:277484 original size:13 final size:12
Alignment explanation
Indices: 277468--277523 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
277458 TTTTTAATGT
277468 TAATTAATATTTA
1 TAATTAA-ATTTA
277481 TAATTAAATTTA
1 TAATTAAATTTA
*
277493 -AA-TAAA--AA
1 TAATTAAATTTA
*
277501 TAA-TAATTTTA
1 TAATTAAATTTA
277512 TAATTAAATTTA
1 TAATTAAATTTA
277524 AGTTTAACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
8 1 0.03
9 5 0.14
10 4 0.11
11 6 0.17
12 12 0.34
13 7 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TAATTAAATTTA
Found at i:279195 original size:2 final size:2
Alignment explanation
Indices: 279188--279214 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
279178 AGAAGTAAGA
279188 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 A
279215 ATCCTGCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:279494 original size:116 final size:114
Alignment explanation
Indices: 279214--279552 Score: 459
Period size: 112 Copynumber: 3.0 Consensus size: 114
279204 AGAGAGAGAG
* * * * *
279214 AATCCTGCACATACTTCGTTTCGACAAAGTTTTAATGTATATAAACAATCATGCAAATGCTTGAT
1 AATCATGCACATACTTCGTTTCGGCAAAGTTTTAATGTATATGAATAATCATGCATATGCTTGAT
279279 TTCAGTGTTGAAATCCATATGTGATACG-TTATA-GTTTCAATTCAAAT
66 TTCAGTGTTGAAATCCATATGTGATACGATTATAGGTTTCAATTCAAAT
* * * * *
279326 AATCGTGCACATACTTCGTTTCAGCAAAGTTTTCATGTATATGAATAATCATGCGTATGCTCGAT
1 AATCATGCACATACTTCGTTTCGGCAAAGTTTTAATGTATATGAATAATCATGCATATGCTTGAT
*
279391 TTCAGTGTTGGAATCCATATGTGATACGATTATAGGTTTCAATTCAAAT
66 TTCAGTGTTGAAATCCATATGTGATACGATTATAGGTTTCAATTCAAAT
* * * *
279440 AATCATATGCACATACTTTGTTTTGGCAAAGCTTTAATGTACATGAATAATCATGCATATGCTTG
1 AATC--ATGCACATACTTCGTTTCGGCAAAGTTTTAATGTATATGAATAATCATGCATATGCTTG
* * * *
279505 ATTTCAATGTTGAAACCCAATATGTAATAAGATTATAGG-TTCAATTCA
64 ATTTCAGTGTTGAAATCC-ATATGTGATACGATTATAGGTTTCAATTCA
279553 TATACCTGGA
Statistics
Matches: 198, Mismatches: 24, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
112 83 0.42
113 5 0.03
114 18 0.09
116 74 0.37
117 18 0.09
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (114 bp):
AATCATGCACATACTTCGTTTCGGCAAAGTTTTAATGTATATGAATAATCATGCATATGCTTGAT
TTCAGTGTTGAAATCCATATGTGATACGATTATAGGTTTCAATTCAAAT
Found at i:280857 original size:28 final size:28
Alignment explanation
Indices: 280826--280883 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
280816 TGAATTACAT
280826 TTAAATAAAGACACATTCTGAAGAATTC
1 TTAAATAAAGACACATTCTGAAGAATTC
280854 TTAAATAAAGACACATTCTGAAGAATTC
1 TTAAATAAAGACACATTCTGAAGAATTC
280882 TT
1 TT
280884 CCAACAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (28 bp):
TTAAATAAAGACACATTCTGAAGAATTC
Found at i:282397 original size:45 final size:45
Alignment explanation
Indices: 282346--282435 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
282336 GTAGAGACAC
* *
282346 AAAAAGAGACCTACAAATACCTCCATGACAAAATGTGCTTTGATG
1 AAAAAGAGACATAAAAATACCTCCATGACAAAATGTGCTTTGATG
* *
282391 AAAAAGAGACATAAAAATGCCTCCATTACAAAATGTGCTTTGATG
1 AAAAAGAGACATAAAAATACCTCCATGACAAAATGTGCTTTGATG
282436 CAGATTACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (45 bp):
AAAAAGAGACATAAAAATACCTCCATGACAAAATGTGCTTTGATG
Found at i:285448 original size:36 final size:36
Alignment explanation
Indices: 285390--285492 Score: 93
Period size: 36 Copynumber: 2.9 Consensus size: 36
285380 AGATCCAAAC
* * * *
285390 AAAAGAAAAACTTTTAAATTAAACCCAATTCAAT-TA
1 AAAACAAAAA-TTTCAATTTAAACCCAATTCAATGCA
*
285426 AAAACTAAAAATTTCAATTTAAA-CCAATTTAATGCA
1 AAAAC-AAAAATTTCAATTTAAACCCAATTCAATGCA
* * * *
285462 AAAGCAAAATTTTCAATTTCAACTCAATTCA
1 AAAACAAAAATTTCAATTTAAACCCAATTCA
285493 GTAGGAAAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
35 24 0.44
36 25 0.46
37 5 0.09
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (36 bp):
AAAACAAAAATTTCAATTTAAACCCAATTCAATGCA
Found at i:285476 original size:35 final size:34
Alignment explanation
Indices: 285389--285492 Score: 93
Period size: 35 Copynumber: 2.9 Consensus size: 34
285379 AAGATCCAAA
* *
285389 CAAAAGAAAAACTTTT-AAATTAAACCCAATTCAAT
1 CAAAAGCAAAA-TTTTCAATTTAAA-CCAATTCAAT
* * * *
285424 TAAAAACTAAAAATTTCAATTTAAACCAATTTAAT
1 CAAAAGC-AAAATTTTCAATTTAAACCAATTCAAT
*
285459 GCAAAAGCAAAATTTTCAATTTCAACTCAATTCA
1 -CAAAAGCAAAATTTTCAATTTAAAC-CAATTCA
285493 GTAGGAAAGC
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
35 32 0.59
36 22 0.41
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (34 bp):
CAAAAGCAAAATTTTCAATTTAAACCAATTCAAT
Found at i:286208 original size:20 final size:19
Alignment explanation
Indices: 286180--286244 Score: 78
Period size: 20 Copynumber: 3.4 Consensus size: 19
286170 TTGAAGTAGA
286180 ATTTTTAAAATTATTTTCAT
1 ATTTTTAAAATTATTTT-AT
* **
286200 ATTTGTAAAATTACATTAT
1 ATTTTTAAAATTATTTTAT
286219 -TTTTTAAAATTATTTTAAT
1 ATTTTTAAAATTATTTT-AT
286238 ATTTTTA
1 ATTTTTA
286245 TCTAAAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
18 13 0.35
19 4 0.11
20 20 0.54
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTTAAAATTATTTTAT
Found at i:286319 original size:20 final size:21
Alignment explanation
Indices: 286291--286331 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
286281 TATTTTAATC
*
286291 AAACATTTAGAGTTAT-TTAG
1 AAACATTTAAAGTTATATTAG
*
286311 AAACTTTTAAAGTTATATTAG
1 AAACATTTAAAGTTATATTAG
286332 TATTTTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (21 bp):
AAACATTTAAAGTTATATTAG
Found at i:289487 original size:29 final size:29
Alignment explanation
Indices: 289443--289499 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
289433 ATATCAAGTC
289443 CTAATAAGTTCAGTTCAAAACTAGATTTT
1 CTAATAAGTTCAGTTCAAAACTAGATTTT
**
289472 CTAATAAGTTTGGTTCAAAACTAGATTT
1 CTAATAAGTTCAGTTCAAAACTAGATTT
289500 ATTAAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (29 bp):
CTAATAAGTTCAGTTCAAAACTAGATTTT
Found at i:290866 original size:32 final size:32
Alignment explanation
Indices: 290825--290889 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
290815 TTTTAGTAAC
290825 TGGTATGTTGTTTATTAAATGTATATCTCAAG
1 TGGTATGTTGTTTATTAAATGTATATCTCAAG
290857 TGGTATGTTGTTTATTAAATGTATATCTCAAG
1 TGGTATGTTGTTTATTAAATGTATATCTCAAG
290889 T
1 T
290890 CCTAATCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.06, G:0.18, T:0.48
Consensus pattern (32 bp):
TGGTATGTTGTTTATTAAATGTATATCTCAAG
Found at i:293562 original size:58 final size:59
Alignment explanation
Indices: 293453--293565 Score: 149
Period size: 58 Copynumber: 1.9 Consensus size: 59
293443 TGTCATATTC
* * *
293453 GTATCATATCTCCATTCATGACATATTTTACATAATTTTTCTTAATAATTTAATTTAAT
1 GTATCATATCTCAATTCATAACATATTTTACATAATTTTTCATAATAATTTAATTTAAT
* * *
293512 GTATCATATCTCAATTCGTAACAT-TTTTTCATAATTTGTT-ATAATGATTTAATT
1 GTATCATATCTCAATTCATAACATATTTTACATAATTT-TTCATAATAATTTAATT
293566 AAAAAATTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 24 0.51
59 23 0.49
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (59 bp):
GTATCATATCTCAATTCATAACATATTTTACATAATTTTTCATAATAATTTAATTTAAT
Found at i:293709 original size:10 final size:10
Alignment explanation
Indices: 293694--293738 Score: 63
Period size: 11 Copynumber: 4.3 Consensus size: 10
293684 TTGTCAAGAG
293694 AAAAAGAAAA
1 AAAAAGAAAA
*
293704 AAAAAGATAGA
1 AAAAAGA-AAA
293715 AAAAAGAAGAA
1 AAAAAGAA-AA
293726 AAAAAGAAAA
1 AAAAAGAAAA
293736 AAA
1 AAA
293739 TTATGTATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 13 0.42
11 18 0.58
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:294036 original size:23 final size:25
Alignment explanation
Indices: 294009--294069 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
293999 GTATTCTTAC
294009 TGTGTTTATATTATTTT-T-TATGT
1 TGTGTTTATATTATTTTATATATGT
294032 TGTGTTT-TAATT-TTTTATATATGT
1 TGTGTTTAT-ATTATTTTATATATGT
* *
294056 TGAGTTTATGTTAT
1 TGTGTTTATATTAT
294070 ATCTCAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 5 0.16
23 11 0.35
24 13 0.42
25 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.66
Consensus pattern (25 bp):
TGTGTTTATATTATTTTATATATGT
Found at i:294739 original size:28 final size:27
Alignment explanation
Indices: 294707--294796 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 27
294697 TTTATCTTAT
294707 ATTTTATATAAATTTTTTATATAATTAA
1 ATTTTATATAAATTTTTTAT-TAATTAA
* *
294735 ATTTTAACTTTAAATTTATTTATTAAAT-A
1 ATTTT-A-TATAAATTT-TTTATTAATTAA
* *
294764 TTTTTAAATAAA--TTTTATTAATTATA
1 ATTTTATATAAATTTTTTATTAATTA-A
294790 ATTTTAT
1 ATTTTAT
294797 TTAATTAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 9 0.18
25 1 0.02
26 6 0.12
27 4 0.08
28 6 0.12
29 6 0.12
30 12 0.24
31 5 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTTATATAAATTTTTTATTAATTAA
Found at i:297191 original size:19 final size:19
Alignment explanation
Indices: 297150--297192 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
297140 TGCCCAATTA
* *
297150 TATTTTTTTTATATATGTG
1 TATTTTTCTTATACATGTG
297169 TATTTTTCTTATGACATGT-
1 TATTTTTCTTAT-ACATGTG
297188 TATTT
1 TATTT
297193 GGATACATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.21, C:0.05, G:0.09, T:0.65
Consensus pattern (19 bp):
TATTTTTCTTATACATGTG
Found at i:297457 original size:21 final size:21
Alignment explanation
Indices: 297415--297454 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
297405 AATGCACAGA
297415 TAATATTTTAATATATAAAAT
1 TAATATTTTAATATATAAAAT
*
297436 TAAT-TTTTAATTTATAAAA
1 TAATATTTTAATATATAAAA
297455 ATTTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTAATATATAAAAT
Found at i:297956 original size:338 final size:332
Alignment explanation
Indices: 297458--298107 Score: 946
Period size: 338 Copynumber: 1.9 Consensus size: 332
297448 TATAAAAATT
*
297458 TATATATATTAAATAAAAATACTAATTGATAATAATTTTATTATTATATTTTAGTAATTAAACCA
1 TATATAGATTAAATAAAAATACTAATTGATAATAATTTTATTATTATATTTTAGTAATTAAACCA
* * *
297523 TTCAAATTCTACCAAAAAGAATTAAAACATAATTTAAAAATAATTAATGAAATTAATATATTATA
66 TTCAAATTCTACCAAAAAGAATTAAAACATAATTCAAAAACAATCAATGAAATTAATATATTATA
* * * * *
297588 TAAAATTCAATGAATGAGATTGAAATAAAATTAATATATTATATTATATACAATTA-ATGAAGAT
131 TAAAATTCAATGAATGAGATTGAAATAAAATTAATATATTATATTACACAAAATGACATAAAGAT
*
297652 GAATGAGATAAAATTAATTAGTTAAATTAATATTATACATTAAATTCAATGAATTATTATAATAT
196 G-ATGAGATAAAATTAATTAATTAAATTAATATTATACATTAAATTCAATGAATTATTATAATAT
* *
297717 AT-AAAAAATTTTGAAAAAAAAATCATAATAAGTATTACCATTTATGTTAAAAAAACTGCATTTT
260 ATGAAAAAATTTTG--AAAAAAATCATAATAAATATTACCATTTATGTCAAAAAAACTGCATTTT
297781 ATATAGATTA
323 ATATAGATTA
*
297791 TATATAGATTAAATGAAAAAATATTAATT-AGTAATAATTTTTATTATTATATTTTTAGTAATTA
1 TATATAGATTAAAT--AAAAATACTAATTGA-TAATAA-TTTTATTATTATA-TTTTAGTAATTA
** * **
297855 AACCATTCAAATTCTATTAAAAGGAATTAAAATGTAATTCAAAAAGCAATCAATGAAATTAATAT
61 AACCATTCAAATTCTACCAAAAAGAATTAAAACATAATTCAAAAA-CAATCAATGAAATTAATAT
* * * *
297920 ATTATATGAAATTTAATGAATGAGATTGAGATAAAATTAATATATTATATTACACAAAATGACTT
125 ATTATATAAAATTCAATGAATGAGATTGAAATAAAATTAATATATTATATTACACAAAATGACAT
* * *
297985 AAAGATGATGAGATAAAATTAATTAATTAAATTAATATTATATATTGAATTTAATGAATTATTAT
190 AAAGATGATGAGATAAAATTAATTAATTAAATTAATATTATACATTAAATTCAATGAATTATTAT
* **
298050 AATATATGAAAAATTTTTGAAAAAAATCATAATAAATATTAGTATTTATGTCAAAAAA
255 AATATATGAAAAAATTTTGAAAAAAATCATAATAAATATTACCATTTATGTCAAAAAA
298108 TTTATCTACA
Statistics
Matches: 281, Mismatches: 28, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
333 13 0.05
334 1 0.00
335 18 0.06
336 13 0.05
337 86 0.31
338 133 0.47
339 17 0.06
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.38
Consensus pattern (332 bp):
TATATAGATTAAATAAAAATACTAATTGATAATAATTTTATTATTATATTTTAGTAATTAAACCA
TTCAAATTCTACCAAAAAGAATTAAAACATAATTCAAAAACAATCAATGAAATTAATATATTATA
TAAAATTCAATGAATGAGATTGAAATAAAATTAATATATTATATTACACAAAATGACATAAAGAT
GATGAGATAAAATTAATTAATTAAATTAATATTATACATTAAATTCAATGAATTATTATAATATA
TGAAAAAATTTTGAAAAAAATCATAATAAATATTACCATTTATGTCAAAAAAACTGCATTTTATA
TAGATTA
Found at i:298410 original size:24 final size:24
Alignment explanation
Indices: 298365--298411 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
298355 TATGTTAAAA
*
298365 AAATATATTTTATATATATTATAT
1 AAATATATTTTATAAATATTATAT
*
298389 AAATATAATTTTTTAAAT-TTATA
1 AAATAT-ATTTTATAAATATTATA
298412 AATTTTACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AAATATATTTTATAAATATTATAT
Found at i:299108 original size:79 final size:77
Alignment explanation
Indices: 298970--299123 Score: 202
Period size: 79 Copynumber: 2.0 Consensus size: 77
298960 TAAAATTCAT
* * * *
298970 AATTGAAATATATTTAATTTTTACTATAAATATAAAAATAATTTTTAAAATATATTTTAAAC-TA
1 AATTGAAATATATTGAATTTTTAATATAAATATAAAAATAATTTTTAAAATAGACTTT-AACTTA
299034 AAAATATATTTTTA
65 AAAATA-ATTTTTA
* * * *
299048 AATTGAAATATATTGAGTTTTTTAATATAAATATAAAAATACTTTTTTAAGTAGACTTTAACTTA
1 AATTGAAATATATTGA-ATTTTTAATATAAATATAAAAATAATTTTTAAAATAGACTTTAACTTA
299113 AAAATAATTTT
65 AAAATAATTTT
299124 GAATATATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 23 0.35
79 43 0.65
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (77 bp):
AATTGAAATATATTGAATTTTTAATATAAATATAAAAATAATTTTTAAAATAGACTTTAACTTAA
AAATAATTTTTA
Found at i:299150 original size:27 final size:28
Alignment explanation
Indices: 299081--299163 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 28
299071 AATATAAATA
* * *
299081 TAAAAATACTTTTTTAAGTAGACTTTAACT
1 TAAAAATA--TTTTTAAATATAATTTAACT
* * *
299111 TAAAAATAATTTTGAATATATTTTAA-T
1 TAAAAATATTTTTAAATATAATTTAACT
299138 TAAAAATATTTTTAAATATAATTTAA
1 TAAAAATATTTTTAAATATAATTTAA
299164 ATTTTAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
27 24 0.53
28 13 0.29
30 8 0.18
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (28 bp):
TAAAAATATTTTTAAATATAATTTAACT
Found at i:299517 original size:30 final size:32
Alignment explanation
Indices: 299466--299525 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
299456 ATCAATTCAT
* *
299466 AAAAAATTAAATTTATTTTATAAA-AATTTGA
1 AAAAAATTAAATATATATTATAAACAATTTGA
299497 AAAAAATTAAA-ATATATTATAAACAATTT
1 AAAAAATTAAATATATATTATAAACAATTT
299526 TATTGAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (32 bp):
AAAAAATTAAATATATATTATAAACAATTTGA
Found at i:302327 original size:2 final size:2
Alignment explanation
Indices: 302320--302360 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
302310 GATGAACCCT
302320 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
302361 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:302365 original size:2 final size:2
Alignment explanation
Indices: 302360--302395 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
302350 TCTCTCTCTC
302360 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
302396 CACACACACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:303785 original size:17 final size:16
Alignment explanation
Indices: 303760--303793 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
303750 TATTAAATGA
*
303760 TTATTATTTAAATATTT
1 TTATAATTTAAA-ATTT
303777 TTATAATTTAAAATTT
1 TTATAATTTAAAATTT
303793 T
1 T
303794 ATGTAACTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATAATTTAAAATTT
Found at i:303899 original size:34 final size:35
Alignment explanation
Indices: 303861--303938 Score: 140
Period size: 35 Copynumber: 2.3 Consensus size: 35
303851 ATGAATTGAG
303861 ACATAATACAAATATAATATG-AAAAATAATTAAA
1 ACATAATACAAATATAATATGAAAAAATAATTAAA
*
303895 ACATAATACAAATATAGTATGAAAAAATAATTAAA
1 ACATAATACAAATATAATATGAAAAAATAATTAAA
303930 ACATAATAC
1 ACATAATAC
303939 CGCATAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 20 0.48
35 22 0.52
ACGTcount: A:0.63, C:0.08, G:0.04, T:0.26
Consensus pattern (35 bp):
ACATAATACAAATATAATATGAAAAAATAATTAAA
Found at i:304821 original size:4 final size:4
Alignment explanation
Indices: 304793--304842 Score: 54
Period size: 4 Copynumber: 13.2 Consensus size: 4
304783 CATAATATTT
*
304793 TAAA T-AA TAAA AAATA TAAA T-AA TAAA TAAA T-AA TAAA TAAA T-AA
1 TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
304838 TAAA T
1 TAAA T
304843 GTTTTTTTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 12 0.31
4 24 0.62
5 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:304824 original size:11 final size:11
Alignment explanation
Indices: 304808--304842 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
304798 AATAAAAAAT
304808 ATAAATAATAA
1 ATAAATAATAA
304819 ATAAATAATAA
1 ATAAATAATAA
304830 ATAAATAATAA
1 ATAAATAATAA
304841 AT
1 AT
304843 GTTTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAAATAATAA
Found at i:304873 original size:14 final size:14
Alignment explanation
Indices: 304846--304899 Score: 58
Period size: 15 Copynumber: 3.8 Consensus size: 14
304836 AATAAATGTT
304846 TTTTTCTTTCCTTTC
1 TTTTTCTTT-CTTTC
304861 TTTTTCTTTCTTTC
1 TTTTTCTTTCTTTC
*
304875 -TTTCCATTT-TTATC
1 TTTTTC-TTTCTT-TC
304889 TTTTTCTTTCT
1 TTTTTCTTTCT
304900 CTGCTGAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 6 0.18
14 13 0.39
15 14 0.42
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTCTTTCTTTC
Found at i:304884 original size:19 final size:18
Alignment explanation
Indices: 304844--304891 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
304834 ATAATAAATG
*
304844 TTTTTTTCTTTCCTTTCT
1 TTTTTTTCTTTCCTTTCA
304862 TTTTCTTTCTTT-CTTTCCA
1 TTTT-TTTCTTTCCTTT-CA
*
304881 TTTTTATCTTT
1 TTTTTTTCTTT
304892 TTCTTTCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTTCTTTCCTTTCA
Found at i:306605 original size:2 final size:2
Alignment explanation
Indices: 306600--306631 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
306590 TGGATCACAT
306600 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
306632 ACAATGTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:309461 original size:11 final size:10
Alignment explanation
Indices: 309431--309459 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
309421 TGGGTATGTT
309431 AATTTTTTTA
1 AATTTTTTTA
309441 AATTTTTTTA
1 AATTTTTTTA
309451 AATTTTTTT
1 AATTTTTTT
309460 TATATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:312132 original size:28 final size:29
Alignment explanation
Indices: 312101--312155 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
312091 TTTATTTAAA
* * *
312101 TTTAATTATTAAAAT-ATTTTTTAAATAT
1 TTTAAATAATAAAATAAATTTTTAAATAT
312129 TTTAAATAATAAAATAAATTTTTAAAT
1 TTTAAATAATAAAATAAATTTTTAAAT
312156 TCAAATCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTAAATAATAAAATAAATTTTTAAATAT
Found at i:312566 original size:2 final size:2
Alignment explanation
Indices: 312559--312588 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
312549 CACATTATTT
312559 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
312589 ATAAAATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:315781 original size:3 final size:3
Alignment explanation
Indices: 315775--315803 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
315765 TTGTTTTCAT
315775 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
315804 GTGAAATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:316151 original size:16 final size:17
Alignment explanation
Indices: 316122--316154 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
316112 AATTTAATAA
316122 ATTTGATATTTAAATTTG
1 ATTTGATA-TTAAATTTG
316140 ATTTGATA-TAAATTT
1 ATTTGATATTAAATTT
316155 TAATAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
ATTTGATATTAAATTTG
Found at i:316280 original size:35 final size:36
Alignment explanation
Indices: 316196--316282 Score: 83
Period size: 35 Copynumber: 2.5 Consensus size: 36
316186 ATTATTATTC
* * * *
316196 AAATAA-TAAGAAAAATT-ATATTTAAATTTAATTAT
1 AAATAATTAAGATAAATTAATATTTTAATAT-ATTTT
* *
316231 AAAT-ATAAATATAAATTAATATTTTAATATATTTT
1 AAATAATTAAGATAAATTAATATTTTAATATATTTT
316266 AAATAATTAA-ATAAATT
1 AAATAATTAAGATAAATT
316283 TTTAAAACAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
34 1 0.02
35 27 0.64
36 14 0.33
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (36 bp):
AAATAATTAAGATAAATTAATATTTTAATATATTTT
Found at i:316911 original size:16 final size:17
Alignment explanation
Indices: 316870--316911 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
316860 TTAATATTTA
*
316870 TAAAATTTTTAATTAAG
1 TAAAATTTATAATTAAG
*
316887 TAAAA-TTATAATT-AT
1 TAAAATTTATAATTAAG
316902 TAAAATTTAT
1 TAAAATTTAT
316912 TTTAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.27
16 11 0.50
17 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
TAAAATTTATAATTAAG
Found at i:317889 original size:15 final size:16
Alignment explanation
Indices: 317865--317894 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
317855 TAATATTTTT
317865 AATAATAAAAAATATA
1 AATAATAAAAAATATA
317881 AATAA-AAAAAATAT
1 AATAATAAAAAATAT
317895 CGCTTGGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AATAATAAAAAATATA
Found at i:318800 original size:21 final size:19
Alignment explanation
Indices: 318764--318806 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
318754 AAACATTATT
*
318764 TTAAAATAAAAGTAAAAAA
1 TTAAAATAAAAATAAAAAA
318783 TTAAAATTAAAAAATAAAAAA
1 TTAAAA-T-AAAAATAAAAAA
318804 TTA
1 TTA
318807 TTTTAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
TTAAAATAAAAATAAAAAA
Found at i:318802 original size:14 final size:13
Alignment explanation
Indices: 318766--318801 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
318756 ACATTATTTT
318766 AAAATAAAAGTAA
1 AAAATAAAAGTAA
*
318779 AAAATTAAAATTAA
1 AAAA-TAAAAGTAA
318793 AAAATAAAA
1 AAAATAAAA
318802 AATTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (13 bp):
AAAATAAAAGTAA
Found at i:319234 original size:20 final size:20
Alignment explanation
Indices: 319211--319251 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
319201 AATATGTAAA
* *
319211 ATTTTTTATAAAAATATAAT
1 ATTTTATATAAAAAAATAAT
319231 ATTTTATATAAAAAAATAAT
1 ATTTTATATAAAAAAATAAT
319251 A
1 A
319252 AAATATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTTATATAAAAAAATAAT
Found at i:319318 original size:11 final size:11
Alignment explanation
Indices: 319277--319319 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
319267 AAATTTGTTC
319277 CCTTTTTCTTT
1 CCTTTTTCTTT
* *
319288 CATTTTTTTTT
1 CCTTTTTCTTT
*
319299 TCTCTTTTCTTT
1 CCT-TTTTCTTT
319311 CCTTTTTCT
1 CCTTTTTCT
319320 AACCCACTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (11 bp):
CCTTTTTCTTT
Found at i:320365 original size:27 final size:28
Alignment explanation
Indices: 320323--320386 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
320313 ATATATGCAA
320323 TAAAAAAATTATTAATATATAAAAAT-T
1 TAAAAAAATTATTAATATATAAAAATCT
* *
320350 TATAAAAAATTA-TAATATTTAAAACTCT
1 TA-AAAAAATTATTAATATATAAAAATCT
320378 TAAAAAAAT
1 TAAAAAAAT
320387 AATGTGAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (28 bp):
TAAAAAAATTATTAATATATAAAAATCT
Found at i:321024 original size:37 final size:38
Alignment explanation
Indices: 320946--321038 Score: 95
Period size: 39 Copynumber: 2.5 Consensus size: 38
320936 ATAACACGAA
*
320946 TATAAATATATATAAA-AATATACATAAAATAAAATAAAT
1 TATAAATATATA-AAATATTATACATAAAATAAAAT-AAT
* *
320985 TATTAATATATAAAATATTTATACA-AAAATATAAT-AT
1 TATAAATATATAAAATA-TTATACATAAAATAAAATAAT
*
321022 TATAAATA-AAAAAATAT
1 TATAAATATATAAAATAT
321039 AAATATAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
35 1 0.02
36 7 0.15
37 9 0.19
38 3 0.06
39 21 0.45
40 6 0.13
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (38 bp):
TATAAATATATAAAATATTATACATAAAATAAAATAAT
Found at i:321028 original size:14 final size:14
Alignment explanation
Indices: 321011--321053 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
321001 ATTTATACAA
* *
321011 AAATATAATATTAT
1 AAATATAAAAATAT
*
321025 AAATAAAAAAATAT
1 AAATATAAAAATAT
*
321039 AAATATAAATATAT
1 AAATATAAAAATAT
321053 A
1 A
321054 TTTTTTCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATAAAAATAT
Found at i:321036 original size:36 final size:39
Alignment explanation
Indices: 320964--321038 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 39
320954 TATATAAAAA
* *
320964 TATACATAAAATAAAATAAATTATTAATATATAAAATATT
1 TATACATAAAATAAAAT-AATTATAAATATAAAAAATATT
*
321004 TATACA-AAAATATAAT-ATTATAAATA-AAAAAATAT
1 TATACATAAAATAAAATAATTATAAATATAAAAAATAT
321039 AAATATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 8 0.25
37 9 0.28
39 9 0.28
40 6 0.19
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.35
Consensus pattern (39 bp):
TATACATAAAATAAAATAATTATAAATATAAAAAATATT
Found at i:322145 original size:15 final size:13
Alignment explanation
Indices: 322119--322152 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
322109 GACATTTTTT
322119 TTATTTGTTTGAA
1 TTATTTGTTTGAA
322132 TTGATTTGGTTTGAA
1 TT-ATTT-GTTTGAA
322147 TTATTT
1 TTATTT
322153 TTTAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 8 0.42
15 9 0.47
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.62
Consensus pattern (13 bp):
TTATTTGTTTGAA
Found at i:323838 original size:20 final size:21
Alignment explanation
Indices: 323805--323843 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
323795 TTAATGAATC
*
323805 AAATAATGTCATTT-TATTAA
1 AAATAAAGTCATTTATATTAA
*
323825 AAATAAAGTTATTTATATT
1 AAATAAAGTCATTTATATT
323844 CATTATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (21 bp):
AAATAAAGTCATTTATATTAA
Found at i:327554 original size:19 final size:19
Alignment explanation
Indices: 327506--327555 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
327496 TTCTGCTTGC
*
327506 TTACATATTTTACCACTAT
1 TTACTTATTTTACCACTAT
* * *
327525 TTGCTTATTTTACCATTGT
1 TTACTTATTTTACCACTAT
*
327544 TTACTTGTTTTA
1 TTACTTATTTTA
327556 TCATGCATGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (19 bp):
TTACTTATTTTACCACTAT
Found at i:329682 original size:19 final size:19
Alignment explanation
Indices: 329660--329697 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
329650 TTAATATATC
329660 TTAAATAATAAA-TAAATTT
1 TTAAAT-ATAAATTAAATTT
*
329679 TTAAATCTAAATTAAATTT
1 TTAAATATAAATTAAATTT
329698 AAACATCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATATAAATTAAATTT
Found at i:329874 original size:17 final size:17
Alignment explanation
Indices: 329825--329876 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
329815 TTTTACTTGA
*
329825 TTTATTTAAATT-ATTA
1 TTTATTTAAATTAATTT
* *
329841 TTTATAT-AATAATATTT
1 TTTATTTAAATTA-ATTT
329858 TTTATTTAAATTAATTT
1 TTTATTTAAATTAATTT
329875 TT
1 TT
329877 AATAAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 3 0.11
16 6 0.21
17 15 0.54
18 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTATTTAAATTAATTT
Found at i:329877 original size:16 final size:16
Alignment explanation
Indices: 329825--329877 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
329815 TTTTACTTGA
329825 TTTATTTAAATT-ATT
1 TTTATTTAAATTAATT
* * *
329840 ATTTATATAATAATATTT
1 -TTTATTTAA-ATTAATT
329858 TTTATTTAAATTAATT
1 TTTATTTAAATTAATT
329874 TTTA
1 TTTA
329878 ATAAAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 17 0.59
17 10 0.34
18 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATTTAAATTAATT
Found at i:330115 original size:2 final size:2
Alignment explanation
Indices: 330108--330137 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
330098 TCCACATTAT
330108 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
330138 CAATTTGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:333175 original size:3 final size:3
Alignment explanation
Indices: 333167--333197 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
333157 TTGGTTCCAA
333167 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
333198 CTTTATACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:333626 original size:3 final size:3
Alignment explanation
Indices: 333620--333649 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
333610 ATAATAATAA
333620 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
333650 GCGAAATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:333780 original size:4 final size:4
Alignment explanation
Indices: 333771--333795 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
333761 AGATATATTT
333771 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
333796 CAAAACGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:333963 original size:3 final size:3
Alignment explanation
Indices: 333955--333994 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
333945 ATATATATGG
333955 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
333995 ATTTTGGCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:334192 original size:7 final size:7
Alignment explanation
Indices: 334180--334225 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
334170 AATTATGATA
334180 AAAATAT
1 AAAATAT
334187 AAAATAT
1 AAAATAT
334194 AAAATAT
1 AAAATAT
334201 AAAATAT
1 AAAATAT
*
334208 AAAAAAAT
1 -AAAATAT
*
334216 TAAATAT
1 AAAATAT
334223 AAA
1 AAA
334226 TACATCATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
7 28 0.82
8 6 0.18
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAATAT
Found at i:334197 original size:15 final size:15
Alignment explanation
Indices: 334177--334250 Score: 78
Period size: 15 Copynumber: 4.7 Consensus size: 15
334167 TTAAATTATG
334177 ATAAAAATATAAAAT
1 ATAAAAATATAAAAT
334192 AT-AAAATATAAAAT
1 ATAAAAATATAAAAT
* *
334206 ATAAAAAAATTAAAT
1 ATAAAAATATAAAAT
*
334221 ATAAATACATCATGAATAT
1 ATAAA-A-AT-AT-AAAAT
334240 ATAAAAATATA
1 ATAAAAATATA
334251 TATAAACATA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
14 14 0.29
15 18 0.37
16 3 0.06
17 3 0.06
18 3 0.06
19 8 0.16
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (15 bp):
ATAAAAATATAAAAT
Found at i:335410 original size:23 final size:23
Alignment explanation
Indices: 335372--335418 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
335362 TATCATCTAC
335372 TTTAATATTAATAATATA-TAAA
1 TTTAATATTAATAATATATTAAA
335394 TTTATATATT-ATCAATATATTAAA
1 TTTA-ATATTAAT-AATATATTAAA
335418 T
1 T
335419 ACATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 11 0.50
24 5 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTAATATTAATAATATATTAAA
Found at i:336127 original size:12 final size:12
Alignment explanation
Indices: 336110--336138 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
336100 TATTATTTAA
336110 AAATATTTTATT
1 AAATATTTTATT
336122 AAATATTTTATT
1 AAATATTTTATT
336134 AAATA
1 AAATA
336139 AATAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AAATATTTTATT
Found at i:337569 original size:2 final size:2
Alignment explanation
Indices: 337562--337593 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
337552 GGCTAGGCTA
337562 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
337594 GGCAATCAAA
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:345769 original size:116 final size:116
Alignment explanation
Indices: 345544--345759 Score: 296
Period size: 116 Copynumber: 1.9 Consensus size: 116
345534 CTTAGTGATT
* ** *
345544 ATGATGCATTTATATTTTTAAAATTCAATATTTTGCAAAAAAAATTAAGGCAATATTTTATGTCG
1 ATGATGCATTCATATTTTTAAAATTCAATATTTTGCAAAAAAAATTAAGGCAATATTACATGTCA
*
345609 GTATTCCTCCTAGACTTGACATAGAAAATCTTTCCCAAACTAAATCTAGAA
66 GTATTCCTCCTAGACTTGACACAGAAAATCTTTCCCAAACTAAATCTAGAA
* * *
345660 ATGATGCATTCATAGTTTTT-AAATTCAATATTTTGCAAAGAAAATTGAGGCAATATTACATGTT
1 ATGATGCATTCATA-TTTTTAAAATTCAATATTTTGCAAAAAAAATTAAGGCAATATTACATGTC
345724 AGTA-TCCTTCC-AGTACTTGACACA-AAACATCTTTCC
65 AGTATTCC-TCCTAG-ACTTGACACAGAAA-ATCTTTCC
345760 GAAGTTAAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
115 8 0.09
116 75 0.85
117 5 0.06
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (116 bp):
ATGATGCATTCATATTTTTAAAATTCAATATTTTGCAAAAAAAATTAAGGCAATATTACATGTCA
GTATTCCTCCTAGACTTGACACAGAAAATCTTTCCCAAACTAAATCTAGAA
Found at i:346940 original size:79 final size:80
Alignment explanation
Indices: 346840--347249 Score: 332
Period size: 79 Copynumber: 5.0 Consensus size: 80
346830 CTGGAGACTT
*
346840 GATTTT-CTATGAAACTCACTAAAATGACCTTAAAACACATGTCTCGATACGAAAATATCAACAT
1 GATTTTAC-ATGAAACTCACTAAAATGACCTTAAAACACATGTCTTGATACGAAAATATCAACAT
*
346904 GCTTCTAAAGACTCAG
65 GCTCCTAAAGACTCAG
* * * * * * * *
346920 G-TTTTACATGAAACTTACTAAAAGGACTTTAATACACATGTCTTAATATGAAAATACCAATATG
1 GATTTTACATGAAACTCACTAAAATGACCTTAAAACACATGTCTTGATACGAAAATATCAACATG
* * *
346984 AAAATAC-AACATGATTCTGGAG
66 ---CTCCTAA-A-GA--CT-CAG
* *
347006 ACTTGATTTT-CTATGAAACTCACTAAAATGACCTTAAAGCACATGTCTCGATACGAAAATATCA
1 ----GATTTTAC-ATGAAACTCACTAAAATGACCTTAAAACACATGTCTTGATACGAAAATATCA
*
347070 ACATGCTTCTAAAGACTC-G
61 ACATGCTCCTAAAGACTCAG
* * * * * * * * *
347089 GATTTTACATGAAACTTACTTAAAGGACTTTAATACACATGTCTTAATATGAAAATACCAATATG
1 GATTTTACATGAAACTCACTAAAATGACCTTAAAACACATGTCTTGATACGAAAATATCAACATG
***
347154 CTCCTAAAGACTTTT
66 CTCCTAAAGACTCAG
** * * **
347169 TTTTTTTCATGAAACTCACTAAAATGGCCTT--AATGCATGTCTTGATACGAAAATATCAACATG
1 GATTTTACATGAAACTCACTAAAATGACCTTAAAACACATGTCTTGATACGAAAATATCAACATG
347232 CTCCTAAAGACTC-G
66 CTCCTAAAGACTCAG
347246 GATT
1 GATT
347250 GATCACAAAA
Statistics
Matches: 254, Mismatches: 58, Indels: 39
0.72 0.17 0.11
Matches are distributed among these distances:
77 2 0.01
78 37 0.15
79 115 0.45
80 26 0.10
81 2 0.01
82 3 0.01
83 3 0.01
85 4 0.02
86 2 0.01
87 2 0.01
88 3 0.01
89 2 0.01
90 2 0.01
91 51 0.20
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.31
Consensus pattern (80 bp):
GATTTTACATGAAACTCACTAAAATGACCTTAAAACACATGTCTTGATACGAAAATATCAACATG
CTCCTAAAGACTCAG
Found at i:346981 original size:14 final size:14
Alignment explanation
Indices: 346964--346990 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
346954 CACATGTCTT
346964 AATATGAAAATACC
1 AATATGAAAATACC
346978 AATATGAAAATAC
1 AATATGAAAATAC
346991 AACATGATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (14 bp):
AATATGAAAATACC
Found at i:347097 original size:170 final size:170
Alignment explanation
Indices: 346808--347153 Score: 658
Period size: 170 Copynumber: 2.0 Consensus size: 170
346798 GACATATATT
346808 AATATGAAAATACAACATGATTCTGGAGACTTGATTTTCTATGAAACTCACTAAAATGACCTTAA
1 AATATGAAAATACAACATGATTCTGGAGACTTGATTTTCTATGAAACTCACTAAAATGACCTTAA
346873 AACACATGTCTCGATACGAAAATATCAACATGCTTCTAAAGACTCAGGTTTTACATGAAACTTAC
66 AACACATGTCTCGATACGAAAATATCAACATGCTTCTAAAGACTCAGGTTTTACATGAAACTTAC
346938 TAAAAGGACTTTAATACACATGTCTTAATATGAAAATACC
131 TAAAAGGACTTTAATACACATGTCTTAATATGAAAATACC
346978 AATATGAAAATACAACATGATTCTGGAGACTTGATTTTCTATGAAACTCACTAAAATGACCTTAA
1 AATATGAAAATACAACATGATTCTGGAGACTTGATTTTCTATGAAACTCACTAAAATGACCTTAA
*
347043 AGCACATGTCTCGATACGAAAATATCAACATGCTTCTAAAGACTC-GGATTTTACATGAAACTTA
66 AACACATGTCTCGATACGAAAATATCAACATGCTTCTAAAGACTCAGG-TTTTACATGAAACTTA
*
347107 CTTAAAGGACTTTAATACACATGTCTTAATATGAAAATACC
130 CTAAAAGGACTTTAATACACATGTCTTAATATGAAAATACC
347148 AATATG
1 AATATG
347154 CTCCTAAAGA
Statistics
Matches: 173, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
169 2 0.01
170 171 0.99
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (170 bp):
AATATGAAAATACAACATGATTCTGGAGACTTGATTTTCTATGAAACTCACTAAAATGACCTTAA
AACACATGTCTCGATACGAAAATATCAACATGCTTCTAAAGACTCAGGTTTTACATGAAACTTAC
TAAAAGGACTTTAATACACATGTCTTAATATGAAAATACC
Found at i:349085 original size:29 final size:29
Alignment explanation
Indices: 349053--349143 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
349043 AAAATTGTTA
*
349053 AAATGACTTTAGATTATGTGAAATAATCC
1 AAATGACTTTAGATTATGTGAAATAATCT
* * *
349082 AAATAACTTTA-A-AATGATAGAAATTAT-T
1 AAATGACTTTAGATTATG-T-GAAATAATCT
* *
349110 AAGATGACTTTAGATTATGTTAAATGATCT
1 AA-ATGACTTTAGATTATGTGAAATAATCT
349140 AAAT
1 AAAT
349144 AATCCTAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
27 3 0.06
28 4 0.08
29 33 0.69
30 5 0.10
31 3 0.06
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (29 bp):
AAATGACTTTAGATTATGTGAAATAATCT
Found at i:349153 original size:58 final size:58
Alignment explanation
Indices: 349044--349153 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
349034 AAAATTATGA
* *
349044 AAATTGTTAAAATGACTTTAGATTATGTGAAATAATCCAAATAACTTTAAAATGATAG
1 AAATTATTAAAATGACTTTAGATTATGTGAAATAATCCAAATAACTCTAAAATGATAG
* * * *
349102 AAATTATTAAGATGACTTTAGATTATGTTAAATGATCTAAATAA-TCCTAAAA
1 AAATTATTAAAATGACTTTAGATTATGTGAAATAATCCAAATAACT-CTAAAA
349154 GTGCACATGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 1 0.02
58 44 0.98
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.35
Consensus pattern (58 bp):
AAATTATTAAAATGACTTTAGATTATGTGAAATAATCCAAATAACTCTAAAATGATAG
Found at i:350564 original size:15 final size:16
Alignment explanation
Indices: 350546--350579 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
350536 TTATTTTAAT
350546 ATATTTA-AAAAATAA
1 ATATTTAGAAAAATAA
350561 ATATTTATGAAAAATAA
1 ATATTTA-GAAAAATAA
350578 AT
1 AT
350580 TGATTGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATATTTAGAAAAATAA
Found at i:350809 original size:2 final size:2
Alignment explanation
Indices: 350798--350835 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
350788 TTCTTCGTCT
350798 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
350836 AACTTTCTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.