Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 3 of 24
Found at i:481200 original size:28 final size:27
Alignment explanation
Indices: 481163--481218 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
481153 TTATTGAGAT
481163 TTAAATAAAATTTAATTCA-ATCTGAAA
1 TTAAATAAAATTTAATT-ATATCTGAAA
*
481190 TTAAATTAAAATTTTATTATATCTGAAA
1 TTAAA-TAAAATTTAATTATATCTGAAA
481218 T
1 T
481219 CTAATCTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (27 bp):
TTAAATAAAATTTAATTATATCTGAAA
Found at i:481624 original size:2 final size:2
Alignment explanation
Indices: 481617--481656 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
481607 ATTGATTTGC
481617 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
481657 TCGGGCGGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:482485 original size:19 final size:19
Alignment explanation
Indices: 482439--482487 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
482429 TAAATTTCAG
* *
482439 TTAAAAAATTAAATTAATAT
1 TTAAAAAATT-AATAAAAAT
*
482459 TT-ATAAATTAATAAAAAT
1 TTAAAAAATTAATAAAAAT
482477 TTAAAAAATTA
1 TTAAAAAATTA
482488 TTTTTATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 9 0.38
19 13 0.54
20 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAAAATTAATAAAAAT
Found at i:482575 original size:15 final size:16
Alignment explanation
Indices: 482545--482580 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
482535 TACTTTTATT
482545 ATTAAATAATATTTAA
1 ATTAAATAATATTTAA
*
482561 ATTAAATTA-ATTTAA
1 ATTAAATAATATTTAA
482576 ATTAA
1 ATTAA
482581 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAAATAATATTTAA
Found at i:485119 original size:20 final size:20
Alignment explanation
Indices: 485096--485135 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
485086 TTGAAATTTT
485096 AATTTTAATAATTAAAATTA
1 AATTTTAATAATTAAAATTA
* *
485116 AATTTTGATAATTTAAATTA
1 AATTTTAATAATTAAAATTA
485136 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AATTTTAATAATTAAAATTA
Found at i:486701 original size:13 final size:13
Alignment explanation
Indices: 486683--486714 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
486673 GCTTTCAAAC
486683 TTTTTTCTTCTTT
1 TTTTTTCTTCTTT
*
486696 TTTTTTCTTGTTT
1 TTTTTTCTTCTTT
486709 TTTTTT
1 TTTTTT
486715 TTTTATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTCTTT
Found at i:504169 original size:22 final size:23
Alignment explanation
Indices: 504130--504172 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
504120 ATATTGATAA
504130 TAAATAAAATAATATTATTTTAT
1 TAAATAAAATAATATTATTTTAT
* *
504153 TAAA-AAAATATTTTTATTTT
1 TAAATAAAATAATATTATTTT
504173 TAAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAAATAAAATAATATTATTTTAT
Found at i:510159 original size:12 final size:12
Alignment explanation
Indices: 510142--510193 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
510132 TTAAAATATT
*
510142 TATATTTTAATA
1 TATATTTAAATA
510154 TATATTTAAATA
1 TATATTTAAATA
* *
510166 TAAATATAAA-A
1 TATATTTAAATA
*
510177 TATTTTTTAAATA
1 TA-TATTTAAATA
510190 TATA
1 TATA
510194 AAAATTTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
11 3 0.10
12 25 0.81
13 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATTTAAATA
Found at i:510210 original size:18 final size:20
Alignment explanation
Indices: 510167--510217 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
510157 ATTTAAATAT
*
510167 AAATATAAAATATTTTTTAA
1 AAATATAAAATATTTTTAAA
*
510187 ATATATAAAA-A-TTTTAAA
1 AAATATAAAATATTTTTAAA
*
510205 AAATATTAAATAT
1 AAATATAAAATAT
510218 ACAGTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 14 0.56
19 2 0.08
20 9 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATATAAAATATTTTTAAA
Found at i:510495 original size:61 final size:62
Alignment explanation
Indices: 510428--510554 Score: 238
Period size: 61 Copynumber: 2.1 Consensus size: 62
510418 TCTACTATAT
510428 AATTAATTTGAACTACATAAAAGAATGTATAATTGACACCTGTCAAAATTCTTTT-TGACAA
1 AATTAATTTGAACTACATAAAAGAATGTATAATTGACACCTGTCAAAATTCTTTTCTGACAA
*
510489 AATTAATTTGAACTACATAAAAGAATGTATAATTGACACCTGTCAAAATTCTTTTCTGTCAA
1 AATTAATTTGAACTACATAAAAGAATGTATAATTGACACCTGTCAAAATTCTTTTCTGACAA
510551 AATT
1 AATT
510555 TTTTTAGATA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 55 0.86
62 9 0.14
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.35
Consensus pattern (62 bp):
AATTAATTTGAACTACATAAAAGAATGTATAATTGACACCTGTCAAAATTCTTTTCTGACAA
Found at i:510559 original size:16 final size:16
Alignment explanation
Indices: 510528--510558 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
510518 TAATTGACAC
510528 CTGTCAAAATTCTTTT
1 CTGTCAAAATTCTTTT
510544 CTGTCAAAATT-TTTT
1 CTGTCAAAATTCTTTT
510559 TAGATATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (16 bp):
CTGTCAAAATTCTTTT
Found at i:511151 original size:267 final size:267
Alignment explanation
Indices: 510666--511200 Score: 1007
Period size: 267 Copynumber: 2.0 Consensus size: 267
510656 TCATGAAGAC
510666 GATTCTACCATTACAATTCCAGCGAGGTAATTACAATTCTTTGATCCTTCATCATTTTCCCATAA
1 GATTCTACCATTACAATTCCAGCGAGGTAATTACAATTCTTTGATCCTTCATCATTTTCCCATAA
510731 TCAATGAGTTTTTGATCCTCCAATTTCACCAAATTGCTAAGTGGTGGAACCACGAGGAAGAGGTG
66 TCAATGAGTTTTTGATCCTCCAATTTCACCAAATTGCTAAGTGGTGGAACCACGAGGAAGAGGTG
510796 AAGAAGATTCGGATGAATTCATGACATGGTTTTACGAGGGGAAGGGAATTGGATTTGCTGTGGGT
131 AAGAAGATTCGGATGAATTCATGACATGGTTTTACGAGGGGAAGGGAATTGGATTTGCTGTGGGT
510861 TTTTGGAGATTTTGTAATGCTGTGTTCTTCAAGCGTTCTTGGAGGCAATCTTACTTTCGTTTCTT
196 TTTTGGAGATTTTGTAATGCTGTGTTCTTCAAGCGTTCTTGGAGGCAATCTTACTTTCGTTTCTT
510926 GGACAAT
261 GGACAAT
* *
510933 GATTCTGCCATTACAGTTCCAGCGAGGTAATTACAATTCTTTGATCCTTCATCATTTTCCCATAA
1 GATTCTACCATTACAATTCCAGCGAGGTAATTACAATTCTTTGATCCTTCATCATTTTCCCATAA
* *
510998 TCAATGAGTTTTTGATCCTCCAATTTCACCAAATTGCTCAGTGGTGGAACCGCGAGGAAGAGGTG
66 TCAATGAGTTTTTGATCCTCCAATTTCACCAAATTGCTAAGTGGTGGAACCACGAGGAAGAGGTG
511063 AAGAAGATTCGGATGAATTCATGACATGGTTTTACGAGGGGAAGGGAATTGGATTTGCTGTGGGT
131 AAGAAGATTCGGATGAATTCATGACATGGTTTTACGAGGGGAAGGGAATTGGATTTGCTGTGGGT
* * *
511128 TTTTGGGGATTTTGTAGTGCTGTGTTCTTCAAGCGTTCTTGGAGGCAGTCTTACTTTCGTTTCTT
196 TTTTGGAGATTTTGTAATGCTGTGTTCTTCAAGCGTTCTTGGAGGCAATCTTACTTTCGTTTCTT
511193 GGACAAT
261 GGACAAT
511200 G
1 G
511201 CAAAGAATTT
Statistics
Matches: 261, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
267 261 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (267 bp):
GATTCTACCATTACAATTCCAGCGAGGTAATTACAATTCTTTGATCCTTCATCATTTTCCCATAA
TCAATGAGTTTTTGATCCTCCAATTTCACCAAATTGCTAAGTGGTGGAACCACGAGGAAGAGGTG
AAGAAGATTCGGATGAATTCATGACATGGTTTTACGAGGGGAAGGGAATTGGATTTGCTGTGGGT
TTTTGGAGATTTTGTAATGCTGTGTTCTTCAAGCGTTCTTGGAGGCAATCTTACTTTCGTTTCTT
GGACAAT
Found at i:511447 original size:166 final size:166
Alignment explanation
Indices: 511173--511495 Score: 610
Period size: 166 Copynumber: 1.9 Consensus size: 166
511163 TTCTTGGAGG
*
511173 CAGTCTTACTTTCGTTTCTTGGACAATGCAAAGAATTTGGCTTTATGTTTCAATTGCTCTGCTGA
1 CAGTCTTACTTTCGTTTCTTGGACAATGCAAAGAATTTGACTTTATGTTTCAATTGCTCTGCTGA
*
511238 AAGTAACGTTGGGGAATAAAATTAAAACTTATTTTTCATCAAATTGCAAAAGGTAAATTGCTTGA
66 AAGTAACGTTGGGGAATAAAATTAAAACTTATTTTTCATCAAATTGAAAAAGGTAAATTGCTTGA
*
511303 CTGAATTTTACTTTTGTTTCCCCTATTATTTTTCAT
131 CTGAATTTTACCTTTGTTTCCCCTATTATTTTTCAT
511339 CAGTCTTACTTTCGTTTCTTGGACAATGCAAAGAATTTGACTTTATGTTTCAATTGCTCTGCTGA
1 CAGTCTTACTTTCGTTTCTTGGACAATGCAAAGAATTTGACTTTATGTTTCAATTGCTCTGCTGA
*
511404 AAGTAACGTTGGGGAATAGAATTAAAACTTATTTTTCATCAAATTGAAAAAGGTAAATTGCTTGA
66 AAGTAACGTTGGGGAATAAAATTAAAACTTATTTTTCATCAAATTGAAAAAGGTAAATTGCTTGA
511469 CTGAATTTTACCTTTGTTTCCCCTATT
131 CTGAATTTTACCTTTGTTTCCCCTATT
511496 CTTTAAAACT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
166 153 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (166 bp):
CAGTCTTACTTTCGTTTCTTGGACAATGCAAAGAATTTGACTTTATGTTTCAATTGCTCTGCTGA
AAGTAACGTTGGGGAATAAAATTAAAACTTATTTTTCATCAAATTGAAAAAGGTAAATTGCTTGA
CTGAATTTTACCTTTGTTTCCCCTATTATTTTTCAT
Found at i:513218 original size:25 final size:24
Alignment explanation
Indices: 513190--513236 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
513180 ATCAGAAGAA
*
513190 AAGACAAAAAGATAAAGAAAAAGTT
1 AAGAAAAAAAGA-AAAGAAAAAGTT
*
513215 AAGAAAAAAAGAAAAGGAAAAG
1 AAGAAAAAAAGAAAAGAAAAAG
513237 ACAAAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.06
Consensus pattern (24 bp):
AAGAAAAAAAGAAAAGAAAAAGTT
Found at i:515400 original size:11 final size:12
Alignment explanation
Indices: 515368--515404 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
515358 CCAAATGAAT
515368 AATC-AAATGCTA
1 AATCAAAATG-TA
515380 AATCAAAATGTA
1 AATCAAAATGTA
515392 AAT-AAAATGTA
1 AATCAAAATGTA
515403 AA
1 AA
515405 CTTGAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.42
12 9 0.38
13 5 0.21
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AATCAAAATGTA
Found at i:515501 original size:19 final size:20
Alignment explanation
Indices: 515474--515534 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 20
515464 TCAGTAACTC
*
515474 AAAAGAAAAGAGAAA-AACA
1 AAAACAAAAGAGAAAGAACA
*
515493 AAAACAAAAAAGAAAGAA-A
1 AAAACAAAAGAGAAAGAACA
515512 AAAAC-AAAG-GAAAGAACA
1 AAAACAAAAGAGAAAGAACA
515530 AAAAC
1 AAAAC
515535 TAGGGAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 7 0.19
18 9 0.24
19 19 0.51
20 2 0.05
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAACAAAAGAGAAAGAACA
Found at i:515513 original size:12 final size:12
Alignment explanation
Indices: 515480--515531 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
515470 ACTCAAAAGA
*
515480 AAAGAGAAAAAC
1 AAAGAAAAAAAC
* *
515492 AAAAACAAAAAAG
1 AAAGA-AAAAAAC
515505 AAAGAAAAAAAC
1 AAAGAAAAAAAC
* *
515517 AAAGGAAAGAAC
1 AAAGAAAAAAAC
515529 AAA
1 AAA
515532 AACTAGGGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
12 23 0.72
13 9 0.28
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAC
Found at i:517950 original size:13 final size:13
Alignment explanation
Indices: 517932--517956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
517922 TCGGTTTTTG
517932 TTTCATATATTTC
1 TTTCATATATTTC
517945 TTTCATATATTT
1 TTTCATATATTT
517957 ACAATATACT
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:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTCATATATTTC
Found at i:530455 original size:11 final size:11
Alignment explanation
Indices: 530435--530489 Score: 51
Period size: 10 Copynumber: 4.9 Consensus size: 11
530425 GTTTAGGTAA
*
530435 AAAATTTATTT
1 AAAATATATTT
*
530446 AAAAAATATTATT
1 AAAATATA-T-TT
530459 AAAATATAATTT
1 AAAATAT-ATTT
530471 -AAATATATTT
1 AAAATATATTT
530481 -AAATATATT
1 AAAATATATT
530490 GATTTTGATG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 13 0.34
11 12 0.32
12 3 0.08
13 9 0.24
14 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AAAATATATTT
Found at i:530482 original size:10 final size:10
Alignment explanation
Indices: 530449--530489 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
530439 TTTATTTAAA
*
530449 AAATATTATTA
1 AAATA-TATTT
530460 AAATATAATTT
1 AAATAT-ATTT
530471 AAATATATTT
1 AAATATATTT
530481 AAATATATT
1 AAATATATT
530490 GATTTTGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 14 0.50
11 14 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
AAATATATTT
Found at i:531398 original size:17 final size:17
Alignment explanation
Indices: 531366--531399 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
531356 ATTTTTGTTT
**
531366 AATTAAATAATGAAAGG
1 AATTAAATAACAAAAGG
531383 AATTAAATAACAAAAGG
1 AATTAAATAACAAAAGG
531400 TTGATAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.21
Consensus pattern (17 bp):
AATTAAATAACAAAAGG
Found at i:531646 original size:24 final size:26
Alignment explanation
Indices: 531619--531671 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
531609 TAAATATTAA
* *
531619 TTAAAAAA-TATTTTAT-TATTATTT
1 TTAAAAAATTACTTAATATATTATTT
531643 TTAAAAAATTACTTAATATATTATTT
1 TTAAAAAATTACTTAATATATTATTT
531669 TTA
1 TTA
531672 TTAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.32
25 6 0.24
26 11 0.44
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
TTAAAAAATTACTTAATATATTATTT
Found at i:538402 original size:2 final size:2
Alignment explanation
Indices: 538395--538424 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
538385 GATATGGATC
538395 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
538425 CCAACTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:549359 original size:2 final size:2
Alignment explanation
Indices: 549352--549386 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
549342 ATTTCATCAT
549352 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
549387 ATGTATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:561073 original size:2 final size:2
Alignment explanation
Indices: 561064--561103 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
561054 GTTTTTTTCA
561064 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
561104 ATTTTTTCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:565832 original size:2 final size:2
Alignment explanation
Indices: 565825--565850 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
565815 ATTTTATGTG
565825 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
565851 AATGAATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:566446 original size:23 final size:23
Alignment explanation
Indices: 566417--566478 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
566407 TATTTTTAAT
* *
566417 TTAATTTTTAATTAAATTATTTA
1 TTAATTTTTAATTAAATGAATTA
* *
566440 TTAATTTTGAAATAAATGAATTA
1 TTAATTTTTAATTAAATGAATTA
*
566463 TGTTATTTTT-ATTAAA
1 T-TAATTTTTAATTAAA
566479 ATAAAAGAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 25 0.81
24 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
TTAATTTTTAATTAAATGAATTA
Found at i:570617 original size:3 final size:3
Alignment explanation
Indices: 570611--570646 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
570601 AATAACAACA
570611 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
570647 GATCACGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:571734 original size:48 final size:48
Alignment explanation
Indices: 571431--571733 Score: 349
Period size: 48 Copynumber: 6.3 Consensus size: 48
571421 CGGCGACCAA
* *
571431 CACTTCCTCTCCACCGCCA-CAATCCGCCGCAACTCCGCCGCCAACTAG
1 CACTCCCTCCCCACCGCCACCAA-CCGCCGCAACTCCGCCGCCAACTAG
* * *
571479 CACTCCCTCCCCACCGCCA-CAATCTGCTGCTACTCCGCCGCCAACTAG
1 CACTCCCTCCCCACCGCCACCAA-CCGCCGCAACTCCGCCGCCAACTAG
* * * * * * *
571527 CACTCCTTCCACACCGCCACCATCTGCCGCAACTGCGCCGCCAGCTGG
1 CACTCCCTCCCCACCGCCACCAACCGCCGCAACTCCGCCGCCAACTAG
* * * **
571575 CACTCCTTCCCCACCGTCGCCAGTCGCCGCAACTCCGCCGCCAACTAG
1 CACTCCCTCCCCACCGCCACCAACCGCCGCAACTCCGCCGCCAACTAG
* * * * * *
571623 CACTGCCTCCCCTCCACCACCTACCGCCACAACTCCGCCACCAACTAG
1 CACTCCCTCCCCACCGCCACCAACCGCCGCAACTCCGCCGCCAACTAG
* *
571671 TACTCCCTCCCCACCACCACCAACCGCCGCAACTCCGCCGCCAACTAG
1 CACTCCCTCCCCACCGCCACCAACCGCCGCAACTCCGCCGCCAACTAG
571719 CACTCCCTCCCCACC
1 CACTCCCTCCCCACC
571734 ATCCACCACC
Statistics
Matches: 214, Mismatches: 40, Indels: 2
0.84 0.16 0.01
Matches are distributed among these distances:
48 212 0.99
49 2 0.01
ACGTcount: A:0.19, C:0.54, G:0.13, T:0.14
Consensus pattern (48 bp):
CACTCCCTCCCCACCGCCACCAACCGCCGCAACTCCGCCGCCAACTAG
Found at i:578324 original size:3 final size:3
Alignment explanation
Indices: 578316--578341 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
578306 CCCATTTGTT
578316 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
578342 TTGTTTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:579401 original size:55 final size:55
Alignment explanation
Indices: 579318--579436 Score: 177
Period size: 55 Copynumber: 2.2 Consensus size: 55
579308 GCAGTTGACA
* * * *
579318 AGCAACAGCAGCCAGAGAGTGTCGAAGCATCTGAGTAGATATGCAACAATGCAGC
1 AGCAGCAGCAGCCAGAGAGTGTCAAAGCATCTGAATAGATATGCAACAAAGCAGC
579373 AGCAGCAGCAGCC-GTAGAGTGTCAAAGCATCTGAATAGATATGCAACAAAGCAGC
1 AGCAGCAGCAGCCAG-AGAGTGTCAAAGCATCTGAATAGATATGCAACAAAGCAGC
*
579428 GGCAGCAGC
1 AGCAGCAGC
579437 CTTACTGATA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 1 0.02
55 57 0.98
ACGTcount: A:0.36, C:0.23, G:0.28, T:0.13
Consensus pattern (55 bp):
AGCAGCAGCAGCCAGAGAGTGTCAAAGCATCTGAATAGATATGCAACAAAGCAGC
Found at i:581352 original size:2 final size:2
Alignment explanation
Indices: 581345--581369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
581335 AATACTTTTA
581345 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
581370 CACGAGTAAC
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:586470 original size:20 final size:22
Alignment explanation
Indices: 586444--586542 Score: 79
Period size: 20 Copynumber: 4.7 Consensus size: 22
586434 TATGATATTA
586444 AAATATATAATATAAATTAT-T
1 AAATATATAATATAAATTATAT
586465 -AATATATAA-A-AAATTATAT
1 AAATATATAATATAAATTATAT
* *
586484 AAATATATAATAT--TTTAAAT
1 AAATATATAATATAAATTATAT
*
586504 ATAAT-TATAATATATAAAAATATAT
1 A-AATATAT-A-ATAT-AAATTATAT
586529 AAATATA-AATATAA
1 AAATATATAATATAA
586543 TATATTAACA
Statistics
Matches: 62, Mismatches: 5, Indels: 22
0.70 0.06 0.25
Matches are distributed among these distances:
18 7 0.11
19 2 0.03
20 27 0.44
21 7 0.11
22 8 0.13
23 1 0.02
24 3 0.05
25 7 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATATATAATATAAATTATAT
Found at i:586492 original size:8 final size:8
Alignment explanation
Indices: 586395--586535 Score: 59
Period size: 7 Copynumber: 17.4 Consensus size: 8
586385 TTTAATATAA
586395 ATAT-AAT
1 ATATAAAT
586402 ATA-AAAT
1 ATATAAAT
586409 -TATAAAT
1 ATATAAAT
586416 ATGATAAAAT
1 AT-AT-AAAT
586426 AATATAATTAT
1 -ATATAA--AT
586437 GATATTAAA-
1 -ATA-TAAAT
*
586446 ATATATA-
1 ATATAAAT
586453 ATATAAAT
1 ATATAAAT
586461 -TATTAATAT
1 ATA-TAA-AT
*
586470 ATAAAAAATT
1 AT-ATAAA-T
586480 ATATAAAT
1 ATATAAAT
586488 ATAT-AAT
1 ATATAAAT
* *
586495 ATTTTAA-
1 ATATAAAT
586502 ATAT-AAT
1 ATATAAAT
586509 -TATAATAT
1 ATATAA-AT
*
586517 ATAAAAAT
1 ATATAAAT
586525 ATATAAAT
1 ATATAAAT
586533 ATA
1 ATA
586536 AATATAATAT
Statistics
Matches: 105, Mismatches: 9, Indels: 39
0.69 0.06 0.25
Matches are distributed among these distances:
6 7 0.07
7 31 0.30
8 28 0.27
9 15 0.14
10 13 0.12
11 8 0.08
12 3 0.03
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:586532 original size:45 final size:48
Alignment explanation
Indices: 586452--586540 Score: 141
Period size: 45 Copynumber: 1.9 Consensus size: 48
586442 TAAAATATAT
586452 AATATAAATTATTAATATATAAAAAATTATATAAATATATAATATTTTA
1 AATATAAATTATTAATATATAAAAAATTATATAAATATA-AATATTTTA
586501 AATAT-AATTA-TAATATAT-AAAAA-TATATAAATATAAATAT
1 AATATAAATTATTAATATATAAAAAATTATATAAATATAAATAT
586541 AATATATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
44 5 0.12
45 12 0.30
46 5 0.12
47 8 0.20
48 5 0.12
49 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (48 bp):
AATATAAATTATTAATATATAAAAAATTATATAAATATAAATATTTTA
Found at i:586555 original size:27 final size:28
Alignment explanation
Indices: 586388--586555 Score: 111
Period size: 27 Copynumber: 6.0 Consensus size: 28
586378 ATTATAGTTT
*
586388 AATATA-AATATAATATA-AAAT-TATA
1 AATATATAATATAATATATTAATATATA
*
586413 AATATGATAAAATAATATAATT-ATGATATTAA
1 AATAT-ATAATATAATAT-ATTAAT-ATA-T-A
586445 AATATATAATATAA-ATTATTAATATATA
1 AATATATAATATAATA-TATTAATATATA
* * *
586473 AA-AAATTATATAA-ATATATAATATTTTA
1 AATATATAATATAATATAT-TAATA-TATA
* *
586501 AATATA-ATTATAATATATAAAAATATATA
1 AATATATAATATAATATAT--TAATATATA
*
586530 AATATA-AATATAATATATTAACATAT
1 AATATATAATATAATATATTAATATAT
586556 TTTTAGTACT
Statistics
Matches: 114, Mismatches: 14, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
25 5 0.04
26 4 0.04
27 30 0.26
28 16 0.14
29 27 0.24
30 14 0.12
31 12 0.11
32 6 0.05
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (28 bp):
AATATATAATATAATATATTAATATATA
Found at i:588056 original size:20 final size:21
Alignment explanation
Indices: 588019--588067 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
588009 AATAGCATTA
* *
588019 AATTAAAT-TTATACTTTATT
1 AATTAATTATTATACTTTAAT
588039 AATTAATTATTATA-TTTAAT
1 AATTAATTATTATACTTTAAT
*
588059 ATTTAATTA
1 AATTAATTA
588068 AATAATCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTAATTATTATACTTTAAT
Found at i:599066 original size:4 final size:4
Alignment explanation
Indices: 599029--599059 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
599019 CTTCTAATAA
599029 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
599060 TTGTTTGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:609429 original size:14 final size:16
Alignment explanation
Indices: 609410--609447 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
609400 TGTTATGATA
609410 ATAAAATTAA-AAT-T
1 ATAAAATTAATAATAT
609424 ATAAAATTAATAATAT
1 ATAAAATTAATAATAT
*
609440 TTAAAATT
1 ATAAAATT
609448 CAACCTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
15 3 0.14
16 8 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAAAATTAATAATAT
Found at i:610775 original size:15 final size:15
Alignment explanation
Indices: 610723--610782 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
610713 TATATTTTTT
*
610723 TAATATATAAAAATA
1 TAATATATATAAATA
*
610738 -AATATAT-TAAAAA
1 TAATATATATAAATA
* *
610751 TTATAAATATAAATA
1 TAATATATATAAATA
*
610766 TAATATATATTAATA
1 TAATATATATAAATA
610781 TA
1 TA
610783 TATTATATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
13 4 0.11
14 12 0.34
15 19 0.54
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATATATATAAATA
Found at i:610789 original size:15 final size:15
Alignment explanation
Indices: 610725--610794 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
610715 TATTTTTTTA
* *
610725 ATATATAAAAATAA-
1 ATATATTAATATAAT
* *
610739 ATATATTAAAAATTAT
1 ATATATT-AATATAAT
* *
610755 AAATATAAATATAAT
1 ATATATTAATATAAT
610770 ATATATTAATAT-AT
1 ATATATTAATATAAT
610784 ATTATATTAAT
1 A-TATATTAAT
610795 TGTTTCTAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
14 9 0.20
15 31 0.69
16 5 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATATTAATATAAT
Found at i:611997 original size:23 final size:23
Alignment explanation
Indices: 611957--612006 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
611947 TAATAAAATT
*
611957 TTAAAAATTTTAAATTTAATTAAA
1 TTAAAAATTTTAAATTTAAAT-AA
*
611981 TTAAAAATTTT-ATTTTAAATAA
1 TTAAAAATTTTAAATTTAAATAA
612003 TTAA
1 TTAA
612007 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.25
23 7 0.29
24 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAAAATTTTAAATTTAAATAA
Found at i:612540 original size:57 final size:58
Alignment explanation
Indices: 612417--612540 Score: 139
Period size: 58 Copynumber: 2.1 Consensus size: 58
612407 TTATATTAAT
612417 TTTATTTGTAAAAGTATTTTTTAGTTAGATTATATAAGTTTAAATTTTATAAATATATGA
1 TTTATTT-TAAAAGTATTTTTTAGTTAGATTATATAAGTTTAAATTTTAT-AATATATGA
** ** *
612477 -AAATTTTAAATTTATTTTTTAGTT-GATTATATGAGTTTAAAATTTT-T-ATGATATGA
1 TTTATTTTAAAAGTATTTTTTAGTTAGATTATATAAGTTT-AAATTTTATAAT-ATATGA
612533 TTTATTTT
1 TTTATTTT
612541 TATTTTTAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
55 2 0.04
56 6 0.11
57 19 0.35
58 23 0.43
59 4 0.07
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (58 bp):
TTTATTTTAAAAGTATTTTTTAGTTAGATTATATAAGTTTAAATTTTATAATATATGA
Found at i:612578 original size:72 final size:73
Alignment explanation
Indices: 612481--612616 Score: 179
Period size: 72 Copynumber: 1.9 Consensus size: 73
612471 ATATGAAAAT
* * * *
612481 TTTAAATTTATTTTTTAGTTGATTATATGAGTTTAAAAT-TTTT-ATGATATGATTTATTTTTAT
1 TTTAAATTTATTTTTTAATTGATTATAAGAATTTAAAATATTTTAAAG-TATGATTTATTTTTAT
612544 TTTTAGAAG
65 TTTTAGAAG
* *
612553 TTTAAA-TTATTTTTTATATTGATTATAAGAATTTAAATTATTTTAAAGTATGTTTTATTTTTAT
1 TTTAAATTTATTTTTTA-ATTGATTATAAGAATTTAAAATATTTTAAAGTATGATTTATTTTTAT
612617 ATGTAAGATT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
71 10 0.18
72 24 0.44
73 19 0.35
74 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (73 bp):
TTTAAATTTATTTTTTAATTGATTATAAGAATTTAAAATATTTTAAAGTATGATTTATTTTTATT
TTTAGAAG
Found at i:612866 original size:67 final size:66
Alignment explanation
Indices: 612794--612921 Score: 179
Period size: 67 Copynumber: 1.9 Consensus size: 66
612784 TTATAAAAAT
* *
612794 TTAAATTTATATTTTGTT-T-TGAATATAAGAGTTTAAATTTTTAAAGTATTATTTAATTTTTAG
1 TTAAATTTAT-TTTT-TTATATGAATATAAGAGTTTAAAATTTTAAAGTATGATTT-ATTTTTAG
612857 AAGG
63 AAGG
* *
612861 TTAAATTTATTTTTTTATATGATTATAATAGTTTAAAATTTTAAAGTATGATTTATTTTTA
1 TTAAATTTATTTTTTTATATGAATATAAGAGTTTAAAATTTTAAAGTATGATTTATTTTTA
612922 AACTTTTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
65 2 0.04
66 12 0.22
67 41 0.75
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (66 bp):
TTAAATTTATTTTTTTATATGAATATAAGAGTTTAAAATTTTAAAGTATGATTTATTTTTAGAAG
G
Found at i:613414 original size:110 final size:113
Alignment explanation
Indices: 613280--613504 Score: 375
Period size: 110 Copynumber: 2.0 Consensus size: 113
613270 TTAATAGTTT
* *
613280 TAGTGACGATATCTTATAAAAATTTAAAATTTATCATTTTAGGTAATAATTTTT-AATAAAAACA
1 TAGTGACGATATCTCATAAAAATTTAAAATTTATCATTTTAGATAATAATTTTTCAATAAAAACA
613344 GAAAAATATATATTA-AAAATATTTATAAAAACACATAATTTAAAAAA
66 GAAAAATATATATTACAAAATATTTATAAAAACACATAATTTAAAAAA
*
613391 TAGTGAC-ATATCTCATAACAATTTAAAATTTATCATTTTAGATAATAATTTTTCAATAAAAACA
1 TAGTGACGATATCTCATAAAAATTTAAAATTTATCATTTTAGATAATAATTTTTCAATAAAAACA
* * *
613455 TAAAAATGTATATTACAAAATGTTTATAAAAACACATAATTTAAAAAA
66 GAAAAATATATATTACAAAATATTTATAAAAACACATAATTTAAAAAA
613503 TA
1 TA
613505 AAAAAAAATT
Statistics
Matches: 106, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
110 43 0.41
111 30 0.28
112 33 0.31
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (113 bp):
TAGTGACGATATCTCATAAAAATTTAAAATTTATCATTTTAGATAATAATTTTTCAATAAAAACA
GAAAAATATATATTACAAAATATTTATAAAAACACATAATTTAAAAAA
Found at i:628182 original size:3 final size:3
Alignment explanation
Indices: 628174--628230 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
628164 TCGCCACCAA
*
628174 CTG CTG CTG TTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
*
628222 CTG TTG CTG
1 CTG CTG CTG
628231 AGTAACTGCA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.30, G:0.33, T:0.37
Consensus pattern (3 bp):
CTG
Found at i:629385 original size:8 final size:8
Alignment explanation
Indices: 629374--629453 Score: 58
Period size: 8 Copynumber: 10.1 Consensus size: 8
629364 GCAAATTAAA
629374 TTTAAAAT
1 TTTAAAAT
*
629382 TTTAATA-
1 TTTAAAAT
*
629389 TTTATAAT
1 TTTAAAAT
*
629397 TTTAATAT
1 TTTAAAAT
*
629405 TTT-TAAT
1 TTTAAAAT
629412 ATTTATAAAT
1 -TTTA-AAAT
* *
629422 TTAAAAAA
1 TTTAAAAT
*
629430 TTTAAAAA
1 TTTAAAAT
629438 TTTAAAA-
1 TTTAAAAT
629445 TTTAAAAT
1 TTTAAAAT
629453 T
1 T
629454 ATTTTATTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
7 14 0.25
8 36 0.64
9 3 0.05
10 3 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TTTAAAAT
Found at i:629397 original size:15 final size:15
Alignment explanation
Indices: 629369--629416 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
629359 AATTAGCAAA
*
629369 TTAA-ATTTAAAATT
1 TTAATATTTATAATT
629383 TTAATATTTATAATT
1 TTAATATTTATAATT
*
629398 TTAATATTTTTAATAT
1 TTAATATTTATAAT-T
629414 TTA
1 TTA
629417 TAAATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 4 0.13
15 22 0.73
16 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATATTTATAATT
Found at i:629424 original size:15 final size:14
Alignment explanation
Indices: 629371--629453 Score: 58
Period size: 15 Copynumber: 5.4 Consensus size: 14
629361 TTAGCAAATT
629371 AAATTTAAAATTTTA
1 AAATTTAAAA-TTTA
* *
629386 ATATTTATAATTTTA
1 AAATTTA-AAATTTA
* *
629401 ATATTTTTAATATTTA
1 A-A-ATTTAAAATTTA
629417 TAAATTTAAAAAATTTAA
1 -AAATTT--AAAATTT-A
629435 AAATTTAAAATTTA
1 AAATTTAAAATTTA
629449 AAATT
1 AAATT
629454 ATTTTATTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
14 6 0.11
15 21 0.40
16 8 0.15
17 17 0.32
18 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATTTAAAATTTA
Found at i:629433 original size:24 final size:24
Alignment explanation
Indices: 629370--629467 Score: 96
Period size: 24 Copynumber: 4.1 Consensus size: 24
629360 ATTAGCAAAT
629370 TAAATTT-AAAATTTTAATATTTA
1 TAAATTTAAAAATTTTAATATTTA
* * *
629393 TAATTTTAATATTTTTAATATTTA
1 TAAATTTAAAAATTTTAATATTTA
* *
629417 TAAATTTAAAAAATTTAAAAATTTA
1 TAAATTT-AAAAATTTTAATATTTA
629442 -AAATTTAAAATTATTTT-AT-TTTA
1 TAAATTTAAAA--ATTTTAATATTTA
629465 TAA
1 TAA
629468 TAACTTTTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
23 14 0.23
24 29 0.48
25 17 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TAAATTTAAAAATTTTAATATTTA
Found at i:629836 original size:20 final size:20
Alignment explanation
Indices: 629811--629856 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
629801 TAAATAATTA
* * *
629811 TAAAATTTTAATTTTATATT
1 TAAAATTATAATTTAATAAT
629831 TAAAATTATAATTTAATAAT
1 TAAAATTATAATTTAATAAT
629851 TAAAAT
1 TAAAAT
629857 AAAAAATAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAAATTATAATTTAATAAT
Found at i:629906 original size:21 final size:20
Alignment explanation
Indices: 629853--629907 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
629843 TTAATAATTA
** *
629853 AAATAAAAAATAAAAATTTT
1 AAATAAAAAATTTAATTTTT
*
629873 AATATTAAAAATTTAATTTTT
1 AA-ATAAAAAATTTAATTTTT
629894 AAATAAAATAATTT
1 AAATAAAA-AATTT
629908 TATTATATTC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATAAAAAATTTAATTTTT
Found at i:636126 original size:43 final size:43
Alignment explanation
Indices: 636065--636151 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
636055 CACTTGCTAC
*
636065 AAGTTCATTGGTCTAAAGAAGTTAACTTGATCATCTAGTTATT
1 AAGTTCATTGATCTAAAGAAGTTAACTTGATCATCTAGTTATT
636108 AAGTTCATTGATCTAAAGAAGTTAACTTGATCATCTAGTTATT
1 AAGTTCATTGATCTAAAGAAGTTAACTTGATCATCTAGTTATT
636151 A
1 A
636152 TCTTGAACAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (43 bp):
AAGTTCATTGATCTAAAGAAGTTAACTTGATCATCTAGTTATT
Found at i:645191 original size:16 final size:16
Alignment explanation
Indices: 645170--645204 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
645160 CATTTTTAAA
645170 ATATTCATATATTTAT
1 ATATTCATATATTTAT
*
645186 ATATTCATATATTTTT
1 ATATTCATATATTTAT
645202 ATA
1 ATA
645205 CCTTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTCATATATTTAT
Found at i:645249 original size:13 final size:13
Alignment explanation
Indices: 645231--645260 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
645221 TTTATAATAT
645231 TTATATTATATAA
1 TTATATTATATAA
645244 TTATATTATATAA
1 TTATATTATATAA
645257 TTAT
1 TTAT
645261 GTTTTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATATTATATAA
Found at i:645808 original size:17 final size:16
Alignment explanation
Indices: 645782--645815 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
645772 TATGTTTAGG
645782 ATATAAATATAATAAT
1 ATATAAATATAATAAT
*
645798 ATATAAGATATTATAAT
1 ATATAA-ATATAATAAT
645815 A
1 A
645816 AGATAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
ATATAAATATAATAAT
Found at i:650297 original size:2 final size:2
Alignment explanation
Indices: 650290--650329 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
650280 CCATTATTGA
650290 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
650330 GGAGTCACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:650565 original size:2 final size:2
Alignment explanation
Indices: 650530--650554 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
650520 TTTATTGTTA
650530 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
650555 AACTCATATA
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:651068 original size:16 final size:16
Alignment explanation
Indices: 651018--651078 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
651008 GTTTATTTTT
*
651018 AAATATGATATAATTATA
1 AAATATAATATAA-TA-A
*
651036 AAATA-AA-ATAATTA
1 AAATATAATATAATAA
651050 AAATATAATATAATAA
1 AAATATAATATAATAA
651066 AAA-ATTAATATAA
1 AAATA-TAATATAA
651079 ATATAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 6 0.16
15 4 0.11
16 21 0.57
17 1 0.03
18 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
AAATATAATATAATAA
Found at i:651086 original size:27 final size:26
Alignment explanation
Indices: 651025--651091 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 26
651015 TTTAAATATG
651025 ATATAATTATAAAATAAAATAATTAAA
1 ATATAA-TATAAAATAAAATAATTAAA
651052 ATATAATATAATAA-AAAATTAA-TATAA
1 ATATAATATAA-AATAAAA-TAATTA-AA
651079 ATATAATA-AAAAT
1 ATATAATATAAAAT
651092 TTATGAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
25 2 0.06
26 13 0.36
27 21 0.58
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
ATATAATATAAAATAAAATAATTAAA
Found at i:651091 original size:21 final size:21
Alignment explanation
Indices: 651032--651092 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
651022 ATGATATAAT
*
651032 TATAAA-ATAA-AATAATTAA
1 TATAAATATAATAAAAATTAA
*
651051 AATATAATATAATAAAAAATTAA
1 TATA-AATATAAT-AAAAATTAA
651074 TATAAATATAATAAAAATT
1 TATAAATATAATAAAAATT
651093 TATGAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 11 0.31
22 8 0.23
23 11 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TATAAATATAATAAAAATTAA
Found at i:651100 original size:19 final size:21
Alignment explanation
Indices: 651037--651102 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 21
651027 ATAATTATAA
*
651037 AATAAAATAATTAAAATATAATAT
1 AATAAAA-AATT-ATATA-AATAT
651061 AATAAAAAATTAATATAAATAT
1 AATAAAAAATT-ATATAAATAT
*
651083 AAT-AAAAATT-TATGAATAT
1 AATAAAAAATTATATAAATAT
651102 A
1 A
651103 TTAAGATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.22
21 7 0.17
22 8 0.20
23 9 0.22
24 7 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AATAAAAAATTATATAAATAT
Found at i:651145 original size:12 final size:12
Alignment explanation
Indices: 651130--651156 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
651120 CAAATTATAA
651130 ATATATAAATAT
1 ATATATAAATAT
651142 ATATATAAATAT
1 ATATATAAATAT
651154 ATA
1 ATA
651157 ATACTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATAAATAT
Found at i:651164 original size:20 final size:21
Alignment explanation
Indices: 651111--651164 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
651101 TATTAAGATT
*
651111 TATATAATAC-AAATTATAAA
1 TATATAATACTATATTATAAA
651131 TATATAA-A-TATATATATAAA
1 TATATAATACTATAT-TATAAA
651151 TATATAATACTATA
1 TATATAATACTATA
651165 AATATGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 20 0.69
21 1 0.03
22 4 0.14
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
TATATAATACTATATTATAAA
Found at i:651640 original size:2 final size:2
Alignment explanation
Indices: 651633--651662 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
651623 CATCGAATAC
651633 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
651663 GCATGTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:652560 original size:18 final size:17
Alignment explanation
Indices: 652509--652560 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
652499 CATTTTTTAT
*
652509 TAATAATTAAATTTAAA
1 TAATAATTTAATTTAAA
*
652526 TAAAAAATATTAA-TTAAA
1 T-AATAAT-TTAATTTAAA
652544 TAATAATTTATATTTAA
1 TAATAATTTA-ATTTAA
652561 TTAACAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 3 0.11
17 7 0.25
18 15 0.54
19 3 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATAATTTAATTTAAA
Found at i:653487 original size:22 final size:23
Alignment explanation
Indices: 653448--653492 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
653438 ATATATTCGA
*
653448 ATATTTTATTTAATAATAAATAT
1 ATATTTTATTAAATAATAAATAT
653471 ATATTTTA-TAAATAATAAATAT
1 ATATTTTATTAAATAATAAATAT
653493 TAAAATCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTTTATTAAATAATAAATAT
Found at i:653602 original size:14 final size:13
Alignment explanation
Indices: 653558--653614 Score: 64
Period size: 14 Copynumber: 4.4 Consensus size: 13
653548 AGATGAACGT
653558 TAAATTT-ATTTA
1 TAAATTTAATTTA
*
653570 TAAATTGAA-TTA
1 TAAATTTAATTTA
*
653582 TATATTTAATTTAA
1 TAAATTTAATTT-A
653596 TAAATTTAATTTA
1 TAAATTTAATTTA
653609 TTAAAT
1 -TAAAT
653615 GAAGTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 16 0.43
13 4 0.11
14 17 0.46
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
TAAATTTAATTTA
Found at i:654565 original size:23 final size:25
Alignment explanation
Indices: 654525--654575 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
654515 TTTTATTTAT
* *
654525 ATTTAATATATTGGTAATATA-TAA
1 ATTTAATATATAGGTAATAAATTAA
*
654549 ATTTAA-ATATAGTTAATAAATTAA
1 ATTTAATATATAGGTAATAAATTAA
654573 ATT
1 ATT
654576 ATATTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (25 bp):
ATTTAATATATAGGTAATAAATTAA
Found at i:655206 original size:7 final size:7
Alignment explanation
Indices: 655171--655220 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
655161 AGCATAAACT
655171 AAAAGAA
1 AAAAGAA
655178 AAAATGAA
1 AAAA-GAA
*
655186 GAAAGAA
1 AAAAGAA
**
655193 AGGAGAA
1 AAAAGAA
655200 AAAAGAA
1 AAAAGAA
655207 AAAA-AA
1 AAAAGAA
655213 AAAA-AA
1 AAAAGAA
655219 AA
1 AA
655221 CCTAGAGTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
6 10 0.28
7 20 0.56
8 6 0.17
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:655597 original size:2 final size:2
Alignment explanation
Indices: 655590--655638 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
655580 AAAAGGTTTA
655590 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
655632 AT AT AT A
1 AT AT AT A
655639 AGCTCCTGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:656409 original size:22 final size:20
Alignment explanation
Indices: 656359--656411 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
656349 AAGATTAGTG
656359 AAAAAT-ATTTAAATATAAT
1 AAAAATAATTTAAATATAAT
656378 AAAAATTAATTATAAATATAAAT
1 AAAAA-TAATT-TAAATAT-AAT
*
656401 ATAAATAATTT
1 AAAAATAATTT
656412 TTTTTACTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 5 0.17
20 1 0.03
21 4 0.14
22 12 0.41
23 7 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATAATTTAAATATAAT
Found at i:658039 original size:17 final size:19
Alignment explanation
Indices: 658017--658058 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
658007 ATTATATTTT
658017 TATTTAA-AATTT-TATTA
1 TATTTAATAATTTATATTA
*
658034 TATTTAATAATTTATTTTA
1 TATTTAATAATTTATATTA
658053 TATTTA
1 TATTTA
658059 TATTTTCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 5 0.23
19 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTAATAATTTATATTA
Found at i:658063 original size:17 final size:18
Alignment explanation
Indices: 658005--658063 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
657995 TAATATATAT
658005 ATATTATATTTT-TATTTA
1 ATATT-TATTTTATATTTA
* *
658023 AAATTT-TATTATATTTA
1 ATATTTATTTTATATTTA
658040 ATAATTTATTTTATATTT-
1 AT-ATTTATTTTATATTTA
658058 ATATTT
1 ATATTT
658064 TCACAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
16 3 0.09
17 12 0.35
18 10 0.29
19 9 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTATTTTATATTTA
Found at i:658560 original size:2 final size:2
Alignment explanation
Indices: 658553--658588 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
658543 TTTTTAATAC
658553 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
658589 TAGTCATAGA
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:658672 original size:2 final size:2
Alignment explanation
Indices: 658665--658700 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
658655 GATAAATTTG
* *
658665 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
658701 GGGGTGTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:659149 original size:21 final size:21
Alignment explanation
Indices: 659123--659163 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
659113 AAAGAATAAA
*
659123 AAATAATTAAAT-GATGATATC
1 AAATAATAAAATAGA-GATATC
659144 AAATAATAAAATAGAGATAT
1 AAATAATAAAATAGAGATAT
659164 TTTAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (21 bp):
AAATAATAAAATAGAGATATC
Found at i:662598 original size:6 final size:6
Alignment explanation
Indices: 662554--662597 Score: 79
Period size: 6 Copynumber: 7.2 Consensus size: 6
662544 GTTTGGGGTC
662554 GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG GGTAGGG G
1 GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG GGAGGG GG-AGGG G
662598 TTCTAGGTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 32 0.86
7 5 0.14
ACGTcount: A:0.16, C:0.00, G:0.82, T:0.02
Consensus pattern (6 bp):
GGAGGG
Found at i:666223 original size:95 final size:95
Alignment explanation
Indices: 666060--666252 Score: 359
Period size: 95 Copynumber: 2.0 Consensus size: 95
666050 CTTTTTTTCC
* *
666060 TCATTAGTAATCACCTGGTGCTCCAGAACTAGAGAATGTTCTTTTACATTGACAAGGAGTTCTGA
1 TCATTAGTAATCACCTGATGCTACAGAACTAGAGAATGTTCTTTTACATTGACAAGGAGTTCTGA
666125 TTCCTGCACCATTGAAGTTCAAAATGAGAA
66 TTCCTGCACCATTGAAGTTCAAAATGAGAA
*
666155 TCATTAGTAATCACCTGATGCTACAGAACTAGAGAATGTTCTTTTACGTTGACAAGGAGTTCTGA
1 TCATTAGTAATCACCTGATGCTACAGAACTAGAGAATGTTCTTTTACATTGACAAGGAGTTCTGA
666220 TTCCTGCACCATTGAAGTTCAAAATGAGAA
66 TTCCTGCACCATTGAAGTTCAAAATGAGAA
666250 TCA
1 TCA
666253 CAAGAAGAGT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (95 bp):
TCATTAGTAATCACCTGATGCTACAGAACTAGAGAATGTTCTTTTACATTGACAAGGAGTTCTGA
TTCCTGCACCATTGAAGTTCAAAATGAGAA
Found at i:668834 original size:22 final size:24
Alignment explanation
Indices: 668809--668857 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 24
668799 TTTATAAATT
668809 TTAATACTA-TAAA-TAA-TTTATA
1 TTAATA-TATTAAATTAATTTTATA
668831 TTAATATATTAAATTAATTTTATA
1 TTAATATATTAAATTAATTTTATA
668855 TTA
1 TTA
668858 TTTTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.08
22 10 0.42
23 3 0.12
24 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAATATATTAAATTAATTTTATA
Found at i:669306 original size:17 final size:18
Alignment explanation
Indices: 669274--669307 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
669264 GCAGGTTCAG
669274 TTTTTGTTTTCTCTTTTT
1 TTTTTGTTTTCTCTTTTT
*
669292 TTTTTTTTTTC-CTTTT
1 TTTTTGTTTTCTCTTTT
669308 AAATTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (18 bp):
TTTTTGTTTTCTCTTTTT
Found at i:671395 original size:22 final size:21
Alignment explanation
Indices: 671353--671395 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
671343 ATTAATAATG
*
671353 AATAACAAAATATCATTTATT
1 AATAACAAAATATCATATATT
671374 AATAAGCAAAATTATCA-ATATT
1 AATAA-CAAAA-TATCATATATT
671396 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.35
Consensus pattern (21 bp):
AATAACAAAATATCATATATT
Found at i:673996 original size:2 final size:2
Alignment explanation
Indices: 673989--674026 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
673979 GGACATTTCA
*
673989 AT AT AT AT AT AT AT AT GT 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
674027 GTTTTCCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:675678 original size:21 final size:21
Alignment explanation
Indices: 675653--675697 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
675643 AGCCAATCAA
*
675653 TTGGCAAGC-AAGAAATCATAC
1 TTGGCAAACAAAGAAA-CATAC
675674 TTGGCAAACAGAAGAAACATAC
1 TTGGCAAACA-AAGAAACATAC
675696 TT
1 TT
675698 TATTTTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 7 0.33
23 6 0.29
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (21 bp):
TTGGCAAACAAAGAAACATAC
Found at i:678300 original size:20 final size:21
Alignment explanation
Indices: 678275--678324 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
678265 ATTGACTTGC
*
678275 TTTAATTTAAAATAGTA-ATT
1 TTTAATTTAAAATAATATATT
678295 TTTAA-TTAAAATAATATATT
1 TTTAATTTAAAATAATATATT
678315 TTT-ATTTAAA
1 TTTAATTTAAA
678325 TTTAATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTAATTTAAAATAATATATT
Found at i:678325 original size:19 final size:19
Alignment explanation
Indices: 678275--678325 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
678265 ATTGACTTGC
*
678275 TTTAATTTAAAATAGTAATT
1 TTTAATTT-AAATAATAATT
*
678295 TTTAATTAAAATAATATATT
1 TTTAATTTAAATAATA-ATT
678315 TTT-ATTTAAAT
1 TTTAATTTAAAT
678326 TTAATTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTAATTTAAATAATAATT
Found at i:678327 original size:32 final size:31
Alignment explanation
Indices: 678291--678379 Score: 78
Period size: 32 Copynumber: 2.9 Consensus size: 31
678281 TTAAAATAGT
**
678291 AATTTTTAATTAAAATAATATATTTTTATTTA
1 AATTTTTAATTAAAATAATATATAATT-TTTA
*
678323 AA--TTTAATTATAA-AATATATAATTTTTA
1 AATTTTTAATTAAAATAATATATAATTTTTA
* *
678351 ATATTTTAAATAAAAATAA-ATAATAATTT
1 A-ATTTTTAATTAAAATAATAT-ATAATTT
678380 GAGCTTGCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
28 5 0.11
29 10 0.22
30 10 0.22
31 10 0.22
32 11 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
AATTTTTAATTAAAATAATATATAATTTTTA
Found at i:678356 original size:29 final size:29
Alignment explanation
Indices: 678290--678379 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 29
678280 TTTAAAATAG
* **
678290 TAATTTTTAATTAAAATAATATATTTTTATT
1 TAATATTTAATT-AAA-AATATATAATTATT
678321 TAA-ATTTAATTATAAAATATATAATT-TT
1 TAATATTTAATTA-AAAATATATAATTATT
* * *
678349 TAATATTTTAAATAAAAATAAATAATAATT
1 TAATA-TTTAATTAAAAATATATAATTATT
678379 T
1 T
678380 GAGCTTGCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
28 5 0.10
29 22 0.45
30 19 0.39
31 3 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TAATATTTAATTAAAAATATATAATTATT
Found at i:678560 original size:15 final size:16
Alignment explanation
Indices: 678537--678591 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 16
678527 TAAATGATCT
678537 TATTTAATA-AATATA
1 TATTTAATACAATATA
* **
678552 TATTGAATATGGATATA
1 TATTTAATA-CAATATA
678569 TATTTAATACAA-ATA
1 TATTTAATACAATATA
678584 TATTTAAT
1 TATTTAAT
678592 TTTTTAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 19 0.58
16 1 0.03
17 13 0.39
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (16 bp):
TATTTAATACAATATA
Found at i:684462 original size:115 final size:111
Alignment explanation
Indices: 684265--684494 Score: 381
Period size: 115 Copynumber: 2.0 Consensus size: 111
684255 TAATAACCCA
*
684265 TATCAACCTTTGTATCTATGGTTTTGAATTTATGTGACCCTAGATAATTCAATTTCATTTTGACA
1 TATCAACCTTTGTATCTATGGTTTTGAATTTATGCGACCCTAGATAATTCAATTTCATTTTGACA
*
684330 TCTGATTGGCATAACAGCAGT-TTTTATTTGCATGAGTTATGATTT
66 TCTGATTGACATAACAGCAGTCTTTTATTTGCATGAGTTATGATTT
684375 TATCAACCTTTGTATCTATGGTTTTGAATTTATGCGACCATCCACTAGATAATTCAATTTCATTT
1 TATCAACCTTTGTATCTATGGTTTTGAATTTATGCG---A-CC-CTAGATAATTCAATTTCATTT
*
684440 TGACATCTGATTGACATGACAGCAGTCTTTTATTTGCATGAGTTATGATTT
61 TGACATCTGATTGACATAACAGCAGTCTTTTATTTGCATGAGTTATGATTT
684491 TATC
1 TATC
684495 TGCTAATTGT
Statistics
Matches: 111, Mismatches: 3, Indels: 6
0.93 0.03 0.05
Matches are distributed among these distances:
110 35 0.32
113 1 0.01
114 2 0.02
115 45 0.41
116 28 0.25
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (111 bp):
TATCAACCTTTGTATCTATGGTTTTGAATTTATGCGACCCTAGATAATTCAATTTCATTTTGACA
TCTGATTGACATAACAGCAGTCTTTTATTTGCATGAGTTATGATTT
Found at i:684828 original size:2 final size:2
Alignment explanation
Indices: 684821--684857 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
684811 AGTGTGCCAA
684821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
684858 GTTCTCTACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:689111 original size:15 final size:15
Alignment explanation
Indices: 689093--689123 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
689083 ATCCCTTTTT
689093 AAAAAAAAAAAGAAA
1 AAAAAAAAAAAGAAA
*
689108 AAAAAAAACAAGAAA
1 AAAAAAAAAAAGAAA
689123 A
1 A
689124 GGAAAGGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.90, C:0.03, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAGAAA
Found at i:690110 original size:29 final size:28
Alignment explanation
Indices: 690078--690158 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 28
690068 GAATTTTTTA
690078 AAATTTTTATATTTATATTAAATTTAAAT
1 AAATTTTTAT-TTTATATTAAATTTAAAT
*
690107 AAATTATTTTCTTTTA-ATTTATAA-TTAAAT
1 AAA-T-TTTTATTTTATA-TTA-AATTTAAAT
*
690137 AAATTTTTATTTTA-AATAAATT
1 AAATTTTTATTTTATATTAAATT
690159 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
26 2 0.05
27 3 0.07
28 10 0.23
29 5 0.11
30 17 0.39
31 7 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (28 bp):
AAATTTTTATTTTATATTAAATTTAAAT
Found at i:690167 original size:17 final size:17
Alignment explanation
Indices: 690131--690166 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
690121 TAATTTATAA
*
690131 TTAAATAAATTTTTATT
1 TTAAATAAATTTTCATT
690148 TTAAATAAATTATTCATT
1 TTAAATAAATT-TTCATT
690166 T
1 T
690167 ATATTAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAATAAATTTTCATT
Found at i:690980 original size:11 final size:11
Alignment explanation
Indices: 690964--690998 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
690954 TAATATTTTA
*
690964 AATATAATTAT
1 AATATAAATAT
*
690975 AATATAAAAAT
1 AATATAAATAT
690986 AATATAAATAT
1 AATATAAATAT
690997 AA
1 AA
690999 GAATTATTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATATAAATAT
Found at i:691970 original size:21 final size:21
Alignment explanation
Indices: 691903--691972 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
691893 TATTAATTTT
*
691903 AAATATAATTAT-ATAAATATA
1 AAATATAATTATAAT-ATTATA
691924 AAATATAGATT-TAAGTATTAT-
1 AAATATA-ATTATAA-TATTATA
*
691945 TAATATAATTATAATATTATA
1 AAATATAATTATAATATTATA
691966 AAATATA
1 AAATATA
691973 TGAAGATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
20 9 0.22
21 23 0.56
22 8 0.20
23 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
AAATATAATTATAATATTATA
Found at i:692363 original size:16 final size:16
Alignment explanation
Indices: 692342--692372 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
692332 ATTCATTTAA
*
692342 TAAATTTAATTTAAAT
1 TAAATTAAATTTAAAT
692358 TAAATTAAATTTAAA
1 TAAATTAAATTTAAA
692373 ATATTTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTAAATTTAAAT
Found at i:697987 original size:16 final size:16
Alignment explanation
Indices: 697966--698006 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
697956 CAAATTATAT
697966 TTCTTTTTCT-GTGTA
1 TTCTTTTTCTAGTGTA
*
697981 TTACTTTTTGTAGTGTA
1 TT-CTTTTTCTAGTGTA
697998 TTCTTTTTC
1 TTCTTTTTC
698007 ATTCACATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 13 0.59
17 7 0.32
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.66
Consensus pattern (16 bp):
TTCTTTTTCTAGTGTA
Found at i:703205 original size:15 final size:16
Alignment explanation
Indices: 703179--703209 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
703169 TAAACATAAT
703179 TATAATATAAAAAATA
1 TATAATATAAAAAATA
703195 TATAA-ATAAAAAATA
1 TATAATATAAAAAATA
703210 AATATACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TATAATATAAAAAATA
Found at i:703214 original size:17 final size:18
Alignment explanation
Indices: 703174--703215 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 18
703164 TATTTTAAAC
*
703174 ATAATTATAATATAAAAA
1 ATAAATATAATATAAAAA
703192 AT--ATATAA-ATAAAAA
1 ATAAATATAATATAAAAA
703207 ATAAATATA
1 ATAAATATA
703216 CTAATTGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 5 0.24
18 2 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAATATAATATAAAAA
Found at i:707642 original size:16 final size:16
Alignment explanation
Indices: 707621--707653 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
707611 GACATAAGGA
707621 AACTTCAAGAAAATCC
1 AACTTCAAGAAAATCC
707637 AACTTCAAGAAAATCC
1 AACTTCAAGAAAATCC
707653 A
1 A
707654 TACATTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.06, T:0.18
Consensus pattern (16 bp):
AACTTCAAGAAAATCC
Found at i:709998 original size:19 final size:18
Alignment explanation
Indices: 709974--710019 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
709964 AATCGTTTGG
709974 ACCCATCATC-ATGGTGTGA
1 ACCCATCATCGA-GGT-TGA
*
709993 ACCCATCCTCGAGGTTGA
1 ACCCATCATCGAGGTTGA
710011 ACCC-TCATC
1 ACCCATCATC
710020 TTCAGACTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.17
18 7 0.29
19 12 0.50
20 1 0.04
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (18 bp):
ACCCATCATCGAGGTTGA
Found at i:713227 original size:2 final size:2
Alignment explanation
Indices: 713220--713252 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
713210 TATTATTTAC
713220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
713253 GTTATCCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:714784 original size:16 final size:16
Alignment explanation
Indices: 714763--714795 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
714753 TATCACTAAA
714763 ATTTAATTTAATATTT
1 ATTTAATTTAATATTT
714779 ATTTAATTTAATATTT
1 ATTTAATTTAATATTT
714795 A
1 A
714796 ATAAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTAATTTAATATTT
Found at i:730435 original size:4 final size:4
Alignment explanation
Indices: 730421--730454 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
730411 GATTGATGGA
*
730421 TTGG ATGG TTGG TTGG TTGG TTGG TTGG TTGG TT
1 TTGG TTGG TTGG TTGG TTGG TTGG TTGG TTGG TT
730455 TTGCTATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (4 bp):
TTGG
Found at i:731831 original size:17 final size:17
Alignment explanation
Indices: 731811--731857 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
731801 TATAAATATA
731811 AATATAAAATAATTTTT
1 AATATAAAATAATTTTT
**
731828 AATATTTTAAT-ATTTTT
1 AATA-TAAAATAATTTTT
731845 AATAATAAAATAA
1 AAT-ATAAAATAA
731858 AATAATGAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATAAAATAATTTTT
Found at i:732265 original size:12 final size:12
Alignment explanation
Indices: 732248--732284 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
732238 TTGTTTTTAA
732248 ATTAAAATTATT
1 ATTAAAATTATT
732260 ATTAAAA--ATT
1 ATTAAAATTATT
732270 ATTAAAATTATT
1 ATTAAAATTATT
732282 ATT
1 ATT
732285 TTATATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.43
12 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATTAAAATTATT
Found at i:741266 original size:19 final size:19
Alignment explanation
Indices: 741242--741280 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
741232 AAAATTAAAA
741242 ATATTTTAT-ATTAATATTT
1 ATATTTTATAATTAA-ATTT
741261 ATATTTTATAATTAAATTT
1 ATATTTTATAATTAAATTT
741280 A
1 A
741281 ATTAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTTTATAATTAAATTT
Found at i:741297 original size:21 final size:22
Alignment explanation
Indices: 741268--741328 Score: 85
Period size: 20 Copynumber: 3.0 Consensus size: 22
741258 TTTATATTTT
741268 ATAA-TTAAATTTAATTAAA-A
1 ATAATTTAAATTTAATTAAATA
*
741288 ATATTTTAAA-TTAA-TAAATA
1 ATAATTTAAATTTAATTAAATA
741308 ATAATTTAAATTTAATTAAAT
1 ATAATTTAAATTTAATTAAAT
741329 TTATAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.11
20 17 0.49
21 9 0.26
22 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATTTAAATTTAATTAAATA
Found at i:744235 original size:3 final size:3
Alignment explanation
Indices: 744227--744266 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
744217 AATTATTTCT
744227 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
744267 GCCTGCTGAA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:744494 original size:14 final size:15
Alignment explanation
Indices: 744462--744494 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
744452 GAAAACTTGA
744462 AAAAAGCTAATAACT
1 AAAAAGCTAATAACT
744477 AAAAAGCTAATAAC-
1 AAAAAGCTAATAACT
744491 AAAA
1 AAAA
744495 TCTAGCTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.15
Consensus pattern (15 bp):
AAAAAGCTAATAACT
Found at i:745278 original size:35 final size:35
Alignment explanation
Indices: 745231--745312 Score: 80
Period size: 35 Copynumber: 2.3 Consensus size: 35
745221 ATTTTAATAT
*
745231 AAATA-TATTATTTAAT-TTAATTTTT-TATATATTTA
1 AAATATTA-TATTTAATATT-ATTTTTGT-TATAATTA
* *
745266 AAATATTATATTTTATATTATTTTTGTTTTAATTA
1 AAATATTATATTTAATATTATTTTTGTTATAATTA
*
745301 AAATGTTATATT
1 AAATATTATATT
745313 CTCTTCAGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 35 0.88
36 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (35 bp):
AAATATTATATTTAATATTATTTTTGTTATAATTA
Found at i:745548 original size:17 final size:15
Alignment explanation
Indices: 745508--745547 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
745498 TATTGGTCAA
745508 ATTTTTTA--ATTTT
1 ATTTTTTATTATTTT
745521 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
*
745536 A-TATTTATTATT
1 ATTTTTTATTATT
745548 AATAAAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 10 0.42
15 6 0.25
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:747056 original size:2 final size:2
Alignment explanation
Indices: 747049--747075 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
747039 TTTGATATTC
747049 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
747076 CATAGGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:747697 original size:16 final size:16
Alignment explanation
Indices: 747676--747706 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
747666 AAATCTTATT
747676 AATATTTATAATATAA
1 AATATTTATAATATAA
*
747692 AATATTTATATTATA
1 AATATTTATAATATA
747707 CAAAAACTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATTTATAATATAA
Found at i:747805 original size:18 final size:19
Alignment explanation
Indices: 747771--747806 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
747761 ATATAAATAA
*
747771 TTAAAATTTACATTAACAT
1 TTAAAATTTAAATTAACAT
747790 TTAAAA-TTAAATTAACA
1 TTAAAATTTAAATTAACA
747807 CAAACTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAATTTAAATTAACAT
Found at i:747985 original size:21 final size:22
Alignment explanation
Indices: 747943--747985 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
747933 ATAGTTAGAA
* * *
747943 TTTTTATTTATAAATTATAAAT
1 TTTTTATTAATAAATAAAAAAT
747965 TTTTTATTAAT-AATAAAAAAT
1 TTTTTATTAATAAATAAAAAAT
747986 ATTTAAAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTTATTAATAAATAAAAAAT
Found at i:748445 original size:2 final size:2
Alignment explanation
Indices: 748438--748463 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
748428 AACAAAAACA
748438 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
748464 TATCTTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:749555 original size:22 final size:22
Alignment explanation
Indices: 749530--749615 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 22
749520 AAAATTTTTA
749530 ATTTATTAATATTTTGATTATT
1 ATTTATTAATATTTTGATTATT
*
749552 ATTTATTAATATTTTTAATT-TT
1 ATTTATTAATA-TTTTGATTATT
*
749574 ATTTTATTTAATTTTAATTGAATTATT
1 A-TTTA-TTAATATT--TTG-ATTATT
749601 ATTTATTAATATTTT
1 ATTTATTAATATTTT
749616 TTATAAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
22 14 0.26
23 15 0.28
24 5 0.09
25 9 0.17
26 7 0.13
27 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTTATTAATATTTTGATTATT
Done.