Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001569.1 Hibiscus syriacus cultivar Beakdansim tig00003118_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 165673
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:7949 original size:3 final size:3
Alignment explanation
Indices: 7941--7975 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
7931 GAAAATCAAC
*
7941 AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
7976 ACCAGATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:26091 original size:2 final size:2
Alignment explanation
Indices: 26084--26113 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26074 ATGTTTCTCC
26084 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
26114 GGGATAACGG
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:33422 original size:16 final size:17
Alignment explanation
Indices: 33393--33429 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
33383 AACCTTTAAT
33393 TTTTAAATTCTTTTATA
1 TTTTAAATTCTTTTATA
33410 TTTTAAATT-TTTTATA
1 TTTTAAATTCTTTTATA
33426 TTTT
1 TTTT
33430 CTATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTAAATTCTTTTATA
Found at i:33440 original size:16 final size:16
Alignment explanation
Indices: 33393--33440 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
33383 AACCTTTAAT
*
33393 TTTTAAATTCTTTTATA
1 TTTTAAATT-TATTATA
*
33410 TTTTAAATTTTTTATA
1 TTTTAAATTTATTATA
**
33426 TTTTCTATTTATTAT
1 TTTTAAATTTATTAT
33441 CTAATTTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTAAATTTATTATA
Found at i:36396 original size:26 final size:28
Alignment explanation
Indices: 36343--36400 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
36333 GAGTAAAGTT
*
36343 CAGATATTTAACAAAGAGTAAGAATTTA
1 CAGATATTTAACAAAGAATAAGAATTTA
* *
36371 CAGATA-TTAAGAAA-AATAAGAGTTTA
1 CAGATATTTAACAAAGAATAAGAATTTA
36397 CAGA
1 CAGA
36401 CATAAATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 14 0.52
27 7 0.26
28 6 0.22
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.26
Consensus pattern (28 bp):
CAGATATTTAACAAAGAATAAGAATTTA
Found at i:50540 original size:6 final size:6
Alignment explanation
Indices: 50524--50562 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
50514 TCTCGTCTCG
50524 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
50563 ATGCACATCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.00, C:0.18, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:50654 original size:22 final size:22
Alignment explanation
Indices: 50626--50700 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
50616 TCTTTTTTTA
*
50626 ACTATCGCAACGACAACCGTAG
1 ACTATCGCAACGACAACTGTAG
* *
50648 ACTATCGCAAC-A-AA-TTTGG
1 ACTATCGCAACGACAACTGTAG
**
50667 AAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
50689 ACTATCGCAACG
1 ACTATCGCAACG
50701 CGATTTTCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 11 0.27
20 3 0.07
21 3 0.07
22 24 0.59
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (22 bp):
ACTATCGCAACGACAACTGTAG
Found at i:51320 original size:12 final size:12
Alignment explanation
Indices: 51303--51331 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
51293 GAAACTAGGC
51303 ATGCTAAATTAT
1 ATGCTAAATTAT
51315 ATGCTAAATTAT
1 ATGCTAAATTAT
51327 ATGCT
1 ATGCT
51332 TCGAGATATA
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:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (12 bp):
ATGCTAAATTAT
Found at i:51688 original size:23 final size:23
Alignment explanation
Indices: 51662--51706 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
51652 TAGTCACAAT
*
51662 AATATTTTACTAATAGTAATAAA
1 AATAATTTACTAATAGTAATAAA
*
51685 AATAATTTACTGATAGTAATAA
1 AATAATTTACTAATAGTAATAA
51707 GATCCATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (23 bp):
AATAATTTACTAATAGTAATAAA
Found at i:62559 original size:31 final size:31
Alignment explanation
Indices: 62496--62565 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
62486 AAATAAGAAC
* * *
62496 TCAAATTATTCTTCTTATTATAGAGGTCGGT
1 TCAAATTATTCTTCTTATTACAAAGATCGGT
* *
62527 TCAAATTATTCTTCTTATTCCAAAGATTGGT
1 TCAAATTATTCTTCTTATTACAAAGATCGGT
62558 TCAAATTA
1 TCAAATTA
62566 ATCCCTATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.44
Consensus pattern (31 bp):
TCAAATTATTCTTCTTATTACAAAGATCGGT
Found at i:63346 original size:2 final size:2
Alignment explanation
Indices: 63339--63374 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
63329 AAATGGTTGA
63339 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
63375 GTCTCTCAAT
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:64743 original size:18 final size:17
Alignment explanation
Indices: 64711--64744 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
64701 CTTCCATAAA
*
64711 AAATAATATAAAAATTT
1 AAATAATAAAAAAATTT
64728 AAATATATAAAAAAATT
1 AAATA-ATAAAAAAATT
64745 ATTAGAGTTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATAATAAAAAAATTT
Found at i:69207 original size:20 final size:20
Alignment explanation
Indices: 69181--69236 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
69171 AAAACCTCTC
*
69181 CCAGTCTCGAGACCAATATG
1 CCAGTCTCGAAACCAATATG
* *
69201 TCAGTCTCGAAACCAGTATG
1 CCAGTCTCGAAACCAATATG
69221 CCAGTCTCGAAACCAA
1 CCAGTCTCGAAACCAA
69237 AATCCCAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (20 bp):
CCAGTCTCGAAACCAATATG
Found at i:69244 original size:20 final size:20
Alignment explanation
Indices: 69179--69244 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
69169 CCAAAACCTC
*
69179 TCCCAGTCTCGAGACCAATA
1 TCCCAGTCTCGAAACCAATA
** *
69199 TGTCAGTCTCGAAACCAGTA
1 TCCCAGTCTCGAAACCAATA
* *
69219 TGCCAGTCTCGAAACCAAAA
1 TCCCAGTCTCGAAACCAATA
69239 TCCCAG
1 TCCCAG
69245 AAGGCTTTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.20
Consensus pattern (20 bp):
TCCCAGTCTCGAAACCAATA
Found at i:69666 original size:103 final size:103
Alignment explanation
Indices: 69487--69693 Score: 396
Period size: 103 Copynumber: 2.0 Consensus size: 103
69477 GATGTTAGAA
*
69487 GACATAAAAGGGACCAAGATTCAAATGGAGAATAACAAGAAAGTCAATTGCAAGATCAAAGCAAC
1 GACATAAAAGGGACCAAGATTCAAATGGAGAATAACAAGAAAGTCAATTGCAAGATCAAACCAAC
*
69552 ATCAATAGAGTTTTAGAGCAAAAATTGTCAAATTCTTT
66 ATCAATAGAGTTTTAGAACAAAAATTGTCAAATTCTTT
69590 GACATAAAAGGGACCAAGATTCAAATGGAGAATAACAAGAAAGTCAATTGCAAGATCAAACCAAC
1 GACATAAAAGGGACCAAGATTCAAATGGAGAATAACAAGAAAGTCAATTGCAAGATCAAACCAAC
69655 ATCAATAGAGTTTTAGAACAAAAATTGTCAAATTCTTT
66 ATCAATAGAGTTTTAGAACAAAAATTGTCAAATTCTTT
69693 G
1 G
69694 TAACACACTC
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (103 bp):
GACATAAAAGGGACCAAGATTCAAATGGAGAATAACAAGAAAGTCAATTGCAAGATCAAACCAAC
ATCAATAGAGTTTTAGAACAAAAATTGTCAAATTCTTT
Found at i:72294 original size:29 final size:29
Alignment explanation
Indices: 72262--72353 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
72252 TAATGGTTTA
*
72262 TAAATTTTAAAACATTTTATATTAATTCT
1 TAAATTTTAAAACATTTTATATTAATCCT
* *** * *
72291 TAAATTATGATCTCATTTTAAATTAGTCCT
1 TAAATT-TTAAAACATTTTATATTAATCCT
* *
72321 TAAATTTTAGAATATTTTATATTAATCCT
1 TAAATTTTAAAACATTTTATATTAATCCT
72350 TAAA
1 TAAA
72354 GTATCAGTAT
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 26 0.54
30 22 0.46
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (29 bp):
TAAATTTTAAAACATTTTATATTAATCCT
Found at i:72309 original size:30 final size:30
Alignment explanation
Indices: 72274--72367 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 30
72264 AATTTTAAAA
* *
72274 CATTTTATATTAATTCTTAAATTAT-GATCT
1 CATTTTATATTAATCCTTAAATTATAGA-AT
* * *
72304 CATTTTAAATTAGTCCTTAAATTTTAGAAT
1 CATTTTATATTAATCCTTAAATTATAGAAT
* *
72334 -ATTTTATATTAATCCTTAAAGTATCAGTAT
1 CATTTTATATTAATCCTTAAATTAT-AGAAT
72364 CATT
1 CATT
72368 CCATGTTAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 20 0.39
30 26 0.51
31 5 0.10
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (30 bp):
CATTTTATATTAATCCTTAAATTATAGAAT
Found at i:72686 original size:60 final size:60
Alignment explanation
Indices: 72566--72687 Score: 138
Period size: 60 Copynumber: 2.0 Consensus size: 60
72556 GTAATCAAAA
* * * * * *
72566 TAGAATGATAATAATAGTTTGAGAATTGATACAAAATGTTTTAAAATTTATGGACAAATT
1 TAGAATGAGAATAATAATTTAAGAATTAATACAAAATATTTTAAAATTTAAGGACAAATT
* * * *
72626 TAGAATGAGAATAATAATTTAAGGATTAATATATAATATTTTAAAGTTTAAGGATC-AATT
1 TAGAATGAGAATAATAATTTAAGAATTAATACAAAATATTTTAAAATTTAAGGA-CAAATT
72686 TA
1 TA
72688 AAACAAATAT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 50 0.98
61 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.38
Consensus pattern (60 bp):
TAGAATGAGAATAATAATTTAAGAATTAATACAAAATATTTTAAAATTTAAGGACAAATT
Found at i:79454 original size:23 final size:21
Alignment explanation
Indices: 79412--79458 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
79402 GTAATTTTTT
*
79412 AATTTTTAAAGAAATAAAAATA
1 AATTTTCAAAGAAATAAAAA-A
79434 AATTTTCAACAGAAA-ACAAAAA
1 AATTTTCAA-AGAAATA-AAAAA
79456 AAT
1 AAT
79459 ATATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (21 bp):
AATTTTCAAAGAAATAAAAAA
Found at i:79468 original size:10 final size:10
Alignment explanation
Indices: 79453--79487 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
79443 CAGAAAACAA
79453 AAAAATATAT
1 AAAAATATAT
79463 AAAAATATAT
1 AAAAATATAT
* *
79473 AAAAAAAAAT
1 AAAAATATAT
79483 AAAAA
1 AAAAA
79488 AATTTAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAAATATAT
Found at i:79472 original size:12 final size:11
Alignment explanation
Indices: 79451--79489 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
79441 AACAGAAAAC
79451 AAAAAAATATA
1 AAAAAAATATA
*
79462 TAAAAATATATA
1 -AAAAAAATATA
79474 AAAAAAA-ATA
1 AAAAAAATATA
79484 AAAAAA
1 AAAAAA
79490 TTTAGAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 6 0.24
12 10 0.40
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAAAATATA
Found at i:86235 original size:22 final size:21
Alignment explanation
Indices: 86207--86265 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 21
86197 AGTTTCATAA
86207 TATAATATTTTTATTCAATTAT
1 TATAATATTTTT-TTCAATTAT
*
86229 TATAATATTGATTTTCAATTAT
1 TATAATATT-TTTTTCAATTAT
86251 TATTTAATATTTTTT
1 TA--TAATATTTTTT
86266 ATAACTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 20 0.62
23 5 0.16
24 7 0.22
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (21 bp):
TATAATATTTTTTTCAATTAT
Found at i:90835 original size:19 final size:18
Alignment explanation
Indices: 90812--90858 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
90802 GGGTTTTGGT
90812 AAAAAGATATTTAAATAA
1 AAAAAGATATTTAAATAA
*
90830 ATAAAAGAAATTTAAATAA
1 A-AAAAGATATTTAAATAA
90849 AAATAAGATA
1 AAA-AAGATA
90859 ATAAAGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAAAGATATTTAAATAA
Found at i:92217 original size:2 final size:2
Alignment explanation
Indices: 92210--92244 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
92200 TAACCCTTAT
92210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
92245 TATTTATTTA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:92310 original size:2 final size:2
Alignment explanation
Indices: 92303--92351 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
92293 ATTATTTTCC
92303 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
92345 TA TA TA T
1 TA TA TA T
92352 TATTTTTATC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:92391 original size:12 final size:12
Alignment explanation
Indices: 92374--92398 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
92364 TGTTTACTTA
92374 TTTACTATATTT
1 TTTACTATATTT
92386 TTTACTATATTT
1 TTTACTATATTT
92398 T
1 T
92399 CCTAACGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTACTATATTT
Found at i:92558 original size:22 final size:21
Alignment explanation
Indices: 92533--92579 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
92523 TTTTATTATA
92533 TTATATATACATTTTTATATTT
1 TTATATATA-ATTTTTATATTT
* *
92555 TTATATATATTTTTTATTTTT
1 TTATATATAATTTTTATATTT
92576 TTAT
1 TTAT
92580 TTTTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTATATATAATTTTTATATTT
Found at i:92573 original size:19 final size:19
Alignment explanation
Indices: 92521--92575 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
92511 TACTATTTAG
*
92521 TATTTTATTATATTATATATA
1 TATTTT-TTAT-TTTTATATA
*
92542 CATTTTTATATTTTTATATA
1 TATTTTT-TATTTTTATATA
92562 TATTTTTTATTTTT
1 TATTTTTTATTTTT
92576 TTATTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 7 0.23
20 15 0.50
21 8 0.27
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTTTATTTTTATATA
Found at i:92573 original size:27 final size:30
Alignment explanation
Indices: 92523--92605 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 30
92513 CTATTTAGTA
* * **
92523 TTTTATTATATTATATATACATTTTTATAT
1 TTTTATTATACTATTTATTTATTTTTATAT
*
92553 TTTTA-TATA-TATTT-TTTATTTTTTTAT
1 TTTTATTATACTATTTATTTATTTTTATAT
92580 TTTTATTTATACTATTTATTTATTTT
1 TTTTA-TTATACTATTTATTTATTTT
92606 CATTATGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
27 15 0.33
28 4 0.09
29 8 0.18
30 10 0.22
31 8 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (30 bp):
TTTTATTATACTATTTATTTATTTTTATAT
Found at i:92576 original size:21 final size:22
Alignment explanation
Indices: 92523--92579 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
92513 CTATTTAGTA
* *
92523 TTTTATTATATTATATATACAT
1 TTTTATTTTTTTATATATACAT
* *
92545 TTTTATATTTTTATATATA-TT
1 TTTTATTTTTTTATATATACAT
92566 TTTTATTTTTTTAT
1 TTTTATTTTTTTAT
92580 TTTTATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTATTTTTTTATATATACAT
Found at i:92586 original size:21 final size:21
Alignment explanation
Indices: 92544--92605 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
92534 TATATATACA
* * *
92544 TTTTTATATTTTTATATATAT
1 TTTTTATTTTTTTATTTTTAT
92565 TTTTTATTTTTTTATTTTTAT
1 TTTTTATTTTTTTATTTTTAT
* *
92586 TTATACTATTTATTTATTTT
1 TT-T-TTATTTTTTTATTTT
92606 CATTATGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 20 0.59
22 1 0.03
23 13 0.38
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTATTTTTTTATTTTTAT
Found at i:97337 original size:16 final size:16
Alignment explanation
Indices: 97318--97369 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
97308 GGGCAAAAAC
*
97318 AAAAAAGAAAAGAAGA
1 AAAAAAGAAAAGAACA
97334 AAAAAAGAAGAA-AACA
1 AAAAAAGAA-AAGAACA
97350 AAAAAA-AGAAAGAACA
1 AAAAAAGA-AAAGAACA
97366 AAAA
1 AAAA
97370 TCAAAAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 3 0.09
16 27 0.84
17 2 0.06
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAGAACA
Found at i:97346 original size:19 final size:17
Alignment explanation
Indices: 97311--97381 Score: 65
Period size: 18 Copynumber: 4.0 Consensus size: 17
97301 ACAAAAAGGG
97311 CAAAAACAAAAAAGAAAA
1 CAAAAA-AAAAAAGAAAA
*
97329 GAAGAAAAAAAGAAGAAAA
1 CAA-AAAAAAA-AAGAAAA
97348 CAAAAAAAAGAAAG--AA
1 CAAAAAAAA-AAAGAAAA
*
97364 CAAAAATCAAAAAGAAAA
1 CAAAAA-AAAAAAGAAAA
97382 ATGGACAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
16 12 0.27
17 2 0.05
18 17 0.39
19 13 0.30
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.01
Consensus pattern (17 bp):
CAAAAAAAAAAAGAAAA
Found at i:100199 original size:106 final size:106
Alignment explanation
Indices: 98931--100198 Score: 1899
Period size: 106 Copynumber: 12.0 Consensus size: 106
98921 ATATCGTGCC
* * * * * * *
98931 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGATTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
98996 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
99037 ACTCCAAACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
99102 AATTTTATAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
99143 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-A-ATA-AA-----C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
99200 AATTTCAGAGCCAATTTAAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
99241 ACTCAAGACAACGCAAGTTCAACTTCATGACGTAGGGACTGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
99306 AATTTCAGAGCCAATTTCAACTTTACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
99347 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * **
99412 AATTTCAGAGCCAATTTTAATTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
99453 ACTCCAGTCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
99518 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
99559 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
99624 AATTTCGGAGCCAATTTCAACTTCACAGCAAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
99665 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
99730 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
99771 ACTCCAGATAACGCAAGTTCAACTTCACGACGAATGGACCGCTAGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
99836 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
99877 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
99942 AATTTCAAAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
99983 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *** *
100048 AATTTCGGAGCCAATTTCAACTTCACAAAAAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
100089 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGGCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
100154 GATTCCAGAGCCAATTTTAACTTCAC-GAC-AGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGA-AGGATATTGG
100195 ACTC
1 ACTC
100199 GGAACAATGC
Statistics
Matches: 1058, Mismatches: 94, Indels: 20
0.90 0.08 0.02
Matches are distributed among these distances:
98 84 0.08
99 1 0.00
100 2 0.00
101 2 0.00
103 2 0.00
104 2 0.00
105 2 0.00
106 963 0.91
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:101001 original size:37 final size:37
Alignment explanation
Indices: 100949--101052 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
100939 CTTTTCGTCC
* *
100949 TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTG
* *
100986 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTG
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTG
** * *
101023 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
101053 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTG
Found at i:101465 original size:2 final size:2
Alignment explanation
Indices: 101452--101481 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
101442 CCTTATTATT
*
101452 TA TA TG 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
101482 ATTATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:101619 original size:13 final size:13
Alignment explanation
Indices: 101601--101626 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
101591 TGTTTACTTA
101601 TTTACTATATTTT
1 TTTACTATATTTT
101614 TTTACTATATTTT
1 TTTACTATATTTT
101627 CCTAACGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTACTATATTTT
Found at i:101793 original size:18 final size:18
Alignment explanation
Indices: 101757--101803 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
101747 TAGTATTTTA
*
101757 TTATATTATATATACATTT
1 TTATATT-TTTATACATTT
*
101776 TTATATTTTTATATATTT
1 TTATATTTTTATACATTT
*
101794 TTTTATTTTT
1 TTATATTTTT
101804 TTTATTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATATTTTTATACATTT
Found at i:101804 original size:10 final size:10
Alignment explanation
Indices: 101773--101818 Score: 60
Period size: 9 Copynumber: 4.8 Consensus size: 10
101763 TATATATACA
101773 TTTTTATATT
1 TTTTTATATT
*
101783 TTTATATATT
1 TTTTTATATT
101793 TTTTTAT-TT
1 TTTTTATATT
101802 TTTTTAT-TT
1 TTTTTATATT
*
101811 TATTTATA
1 TTTTTATA
101819 CTATTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
9 17 0.53
10 15 0.47
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTATATT
Found at i:101816 original size:9 final size:9
Alignment explanation
Indices: 101782--101832 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
101772 ATTTTTATAT
*
101782 TTTTATATA
1 TTTTATTTA
101791 TTTT-TTTA
1 TTTTATTTA
*
101799 TTTTTTTTA
1 TTTTATTTA
101808 TTTTATTTA
1 TTTTATTTA
**
101817 TACTATTTA
1 TTTTATTTA
101826 -TTTATTT
1 TTTTATTT
101833 TCATTATGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
8 12 0.34
9 23 0.66
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTATTTA
Found at i:101816 original size:18 final size:18
Alignment explanation
Indices: 101767--101817 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
101757 TTATATTATA
* *
101767 TATACATTTTTATATTTT
1 TATATATTTTTTTATTTT
101785 TATATATTTTTTTATTTT
1 TATATATTTTTTTATTTT
*
101803 T-TTTATTTTATTTAT
1 TATATATTTT-TTTAT
101818 ACTATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 7 0.24
18 22 0.76
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TATATATTTTTTTATTTT
Found at i:103628 original size:17 final size:17
Alignment explanation
Indices: 103606--103639 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
103596 AAAATATAAT
103606 AATTTTATTGAATGTAA
1 AATTTTATTGAATGTAA
103623 AATTTTATTGAATGTAA
1 AATTTTATTGAATGTAA
103640 TCTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
AATTTTATTGAATGTAA
Found at i:103685 original size:22 final size:23
Alignment explanation
Indices: 103660--103711 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
103650 GTTAACTTTT
*
103660 TAATATTTTTGATTAT-ATAAAA
1 TAATATTTTTAATTATAATAAAA
103682 TAATATTTTTAATTATCAATAAAA
1 TAATATTTTTAATTAT-AATAAAA
103706 -AATATT
1 TAATATT
103712 ATAAAAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 15 0.56
23 6 0.22
24 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TAATATTTTTAATTATAATAAAA
Found at i:118192 original size:2 final size:2
Alignment explanation
Indices: 118181--118214 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
118171 TATCTATACT
118181 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
118215 TATTTACTTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:123324 original size:3 final size:3
Alignment explanation
Indices: 123318--123384 Score: 75
Period size: 3 Copynumber: 23.0 Consensus size: 3
123308 TATTTATTAT
* * * *
123318 TAA TAA TAA AAA T-A TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
123365 TAA TAA -AA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
123385 AAACGAGACA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 4 0.08
3 48 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:124652 original size:10 final size:10
Alignment explanation
Indices: 124637--124711 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
124627 CATTTAATAA
124637 ATAAACGAAC
1 ATAAACGAAC
124647 ATAAACG--C
1 ATAAACGAAC
*
124655 --ACACGAAC
1 ATAAACGAAC
124663 ATAAACGAAC
1 ATAAACGAAC
* *
124673 ATGAAC-ATAA
1 ATAAACGA-AC
124683 ATGAACACGAAC
1 AT-AA-ACGAAC
124695 ATAAACGAAC
1 ATAAACGAAC
124705 ATAAACG
1 ATAAACG
124712 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 4 0.08
8 2 0.04
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:124662 original size:16 final size:16
Alignment explanation
Indices: 124641--124705 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
124631 TAATAAATAA
*
124641 ACGAACATAAACGCAC
1 ACGAACATAAACGAAC
124657 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
124673 ATGAACATAAATGAAC
1 ACGAACATAAACGAAC
124689 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
124705 A
1 A
124706 TAAACGTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.55, C:0.23, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:124978 original size:12 final size:11
Alignment explanation
Indices: 124940--124991 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
124930 TCGAGACTTG
*
124940 AGCTCGATTGA
1 AGCTCGATTCA
124951 AGCTCGATTCA
1 AGCTCGATTCA
*
124962 AGCTCAATTCTA
1 AGCTCGATTC-A
124974 AGCTCGATTCA
1 AGCTCGATTCA
124985 AGCTCGA
1 AGCTCGA
124992 CATTGCCCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
11 27 0.73
12 10 0.27
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:126100 original size:19 final size:18
Alignment explanation
Indices: 126064--126102 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
126054 TACTTAAAGT
*
126064 TAATTATACAAAATATTA
1 TAATTATACAAAAAATTA
*
126082 TAATTAATATAAAAAATTA
1 TAATT-ATACAAAAAATTA
126101 TA
1 TA
126103 TATTCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATTATACAAAAAATTA
Found at i:127089 original size:19 final size:19
Alignment explanation
Indices: 127065--127131 Score: 125
Period size: 19 Copynumber: 3.5 Consensus size: 19
127055 ATTAAATGAA
127065 CATCGATGCATAGGGAGTG
1 CATCGATGCATAGGGAGTG
127084 CATCGATGCATAGGGAGTG
1 CATCGATGCATAGGGAGTG
*
127103 CATCGATGCATAAGGAGTG
1 CATCGATGCATAGGGAGTG
127122 CATCGATGCA
1 CATCGATGCA
127132 CCTGCTTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.28, C:0.18, G:0.33, T:0.21
Consensus pattern (19 bp):
CATCGATGCATAGGGAGTG
Found at i:127767 original size:18 final size:18
Alignment explanation
Indices: 127744--127796 Score: 106
Period size: 18 Copynumber: 2.9 Consensus size: 18
127734 AGGGATTATC
127744 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
127762 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
127780 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
127797 AATATTCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:132069 original size:21 final size:21
Alignment explanation
Indices: 132039--132219 Score: 99
Period size: 21 Copynumber: 8.6 Consensus size: 21
132029 GATTTACATA
*
132039 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
132060 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
132081 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* * *
132104 TT--CATTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* * * *
132125 TT--CATTGCGATTTATTCTAAA
1 TTCGCGTTGCGA--TAGTCCAAG
132146 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
132165 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
* **
132188 TT--CGTTGTGATAGTAGAAG
1 TTCGCGTTGCGATAGTCCAAG
132207 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
132220 TTATTCCAAA
Statistics
Matches: 135, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.12
21 101 0.75
23 18 0.13
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:132112 original size:42 final size:42
Alignment explanation
Indices: 132064--132356 Score: 331
Period size: 42 Copynumber: 7.2 Consensus size: 42
132054 TCCAAGTTCG
*
132064 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* * * * *
132106 CATTGCGATTTATTCCAAATT--CATTGCGATTTATTCTAAATT
1 CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
132148 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* **
132190 CGTTGTGATAGTAGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* **
132232 CGTTGCGAT--T--TA-TTC-C----AAATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
132264 CGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
132306 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
132348 CGTTGCGAT
1 CGTTGCGAT
132357 TTATTCCAAA
Statistics
Matches: 209, Mismatches: 28, Indels: 28
0.79 0.11 0.11
Matches are distributed among these distances:
32 23 0.11
34 1 0.00
36 2 0.01
37 6 0.03
38 2 0.01
40 10 0.05
42 157 0.75
44 8 0.04
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:132235 original size:21 final size:21
Alignment explanation
Indices: 132085--132252 Score: 173
Period size: 21 Copynumber: 8.0 Consensus size: 21
132075 TCGAAGTTCG
132085 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
*
132106 CATTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
* *
132127 CATTGCGATTTATTCTAAATT
1 CGTTGCGATTTATTCCAAATT
* *
132148 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
*
132167 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAATT
* * ** *
132190 CGTTGTGA--TAGTAGAAGTT
1 CGTTGCGATTTATTCCAAATT
132209 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
132232 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
132253 TATTCCAAAT
Statistics
Matches: 123, Mismatches: 16, Indels: 16
0.79 0.10 0.10
Matches are distributed among these distances:
19 16 0.13
21 90 0.73
23 17 0.14
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:132255 original size:11 final size:11
Alignment explanation
Indices: 132239--132263 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
132229 ATTCGTTGCG
132239 ATTTATTCCAA
1 ATTTATTCCAA
132250 ATTTATTCCAA
1 ATTTATTCCAA
132261 ATT
1 ATT
132264 CGTTGCGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTATTCCAA
Found at i:132297 original size:74 final size:74
Alignment explanation
Indices: 132176--132314 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 74
132166 TCGCGTTGCG
* * * *
132176 ATTTATTCCAAGTTCGTTGTGATAGTAGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT
1 ATTTATTCCAAATTCGTTGCGATAGTACAAGTTCACGTTGCGATTTATTCCAAATTCGTTGCGAT
132241 TTATTCCAA
66 TTATTCCAA
* *
132250 ATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGCGAT
1 ATTTATTCCAAATTCGTTGCGATAGTACAAGTTCACGTTGCGATTTATTCCAAATTCGTTGCGAT
132315 AGTCGAAGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (74 bp):
ATTTATTCCAAATTCGTTGCGATAGTACAAGTTCACGTTGCGATTTATTCCAAATTCGTTGCGAT
TTATTCCAA
Found at i:132338 original size:116 final size:116
Alignment explanation
Indices: 132134--132369 Score: 427
Period size: 116 Copynumber: 2.0 Consensus size: 116
132124 ATTCATTGCG
* * *
132134 ATTTATTCTAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGTGAT
1 ATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGCGAT
132199 AGTAGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAA
66 AGTAGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAA
132250 ATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGCGAT
1 ATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGCGAT
* *
132315 AGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCGTTGCGATTTATTCCAA
66 AGTAGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAA
132366 ATTT
1 ATTT
132370 GTTGCGATAG
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (116 bp):
ATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGCGAT
AGTAGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAA
Found at i:132363 original size:63 final size:63
Alignment explanation
Indices: 132285--132419 Score: 243
Period size: 63 Copynumber: 2.1 Consensus size: 63
132275 TCCAAGTTCA
*
132285 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATT
*
132348 CGTTGCGATTTATTCCAAATTTGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATT
*
132411 CTTTGCGAT
1 CGTTGCGAT
132420 AGTCCAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 69 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (63 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATT
Found at i:132416 original size:21 final size:21
Alignment explanation
Indices: 132250--132419 Score: 109
Period size: 21 Copynumber: 8.1 Consensus size: 21
132240 TTTATTCCAA
*
132250 ATTTATTCCAAATTCGTTGCG
1 ATTTATTCTAAATTCGTTGCG
* * *
132271 A--TAGTCCAAGTTCACGTTGCG
1 ATTTATTCTAAATT--CGTTGCG
* *
132292 ATTTATTCCAAGTTCGTTGCG
1 ATTTATTCTAAATTCGTTGCG
* * *
132313 A--TAGTCGAAGTTCGCGTTGCG
1 ATTTATTCTAAATT--CGTTGCG
132334 ATTTATTCTAAATTCGTTGCG
1 ATTTATTCTAAATTCGTTGCG
* *
132355 ATTTATTCCAAATTTGTTGCG
1 ATTTATTCTAAATTCGTTGCG
* * *
132376 A--TAGTCGAAGTTCGCGTTGCG
1 ATTTATTCTAAATT--CGTTGCG
*
132397 ATTTATTCTAAATTCTTTGCG
1 ATTTATTCTAAATTCGTTGCG
132418 AT
1 AT
132420 AGTCCAAAAT
Statistics
Matches: 119, Mismatches: 18, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
19 26 0.22
21 67 0.56
23 26 0.22
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (21 bp):
ATTTATTCTAAATTCGTTGCG
Found at i:134619 original size:30 final size:31
Alignment explanation
Indices: 134542--134621 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
134532 TATCTCGTTA
*
134542 AAATTTTTAAAATTTATATATTGAAATATGTC
1 AAATTTTT-AAATTTAAATATTGAAATATGTC
* * * *
134574 AAA-ATTGATAATTTAAATATT-AAATGTGTT
1 AAATTTTTA-AATTTAAATATTGAAATATGTC
134604 AAATTTTTAAATTTAAAT
1 AAATTTTTAAATTTAAAT
134622 GAAAAAATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
30 20 0.51
31 16 0.41
32 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (31 bp):
AAATTTTTAAATTTAAATATTGAAATATGTC
Found at i:134700 original size:47 final size:47
Alignment explanation
Indices: 134591--134681 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 47
134581 ATAATTTAAA
*
134591 TATTAA-ATGTGTTAAATTTTTAAATTTAAATGAAAAAATTATATAAG
1 TATTAAGAT-TGTTAAATTTTTAAATTTAAATAAAAAAATTATATAAG
* *
134638 TATTAAGCTTGTTAAATTTTTAAATTTATATAAAAAAATTATAT
1 TATTAAGATTGTTAAATTTTTAAATTTAAATAAAAAAATTATAT
134682 GTTAGATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 39 0.98
48 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (47 bp):
TATTAAGATTGTTAAATTTTTAAATTTAAATAAAAAAATTATATAAG
Found at i:139048 original size:19 final size:19
Alignment explanation
Indices: 139012--139053 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
139002 TTATTAAAAA
139012 ATAA-AAAACATTTAAATT
1 ATAATAAAACATTTAAATT
139030 ATAATAAAA-ATTTACAATT
1 ATAATAAAACATTTA-AATT
139049 ATAAT
1 ATAAT
139054 GATTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAATAAAACATTTAAATT
Found at i:141794 original size:32 final size:31
Alignment explanation
Indices: 141756--141832 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
141746 CGGGGCTGTG
* *
141756 GGGCCTACCTAAGAACACATCTTAGGGCCGTA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
141788 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
141819 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
141833 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:145822 original size:79 final size:80
Alignment explanation
Indices: 145728--145885 Score: 214
Period size: 79 Copynumber: 2.0 Consensus size: 80
145718 GGAATTTGAT
* * * *
145728 AGAGTTTTACTCCAACTAAAACT-TATTTAATATC-TAA-AAATATATAATAATATTTTTTAAAT
1 AGAGTTTTACTCCAACCAAAACTCT-TTTAATATCAAAATAAATAGATAATAATATTGTTTAAAT
*
145790 TTATAATATTAAACCTG
65 ATA-AATATTAAACCTG
145807 AGAGTTTTACTCCAACCAAAACTCTTTTAATATCAAAATTTAAATAGATAATAATATTGTTTAAA
1 AGAGTTTTACTCCAACCAAAACTCTTTTAATATCAAAA--TAAATAGATAATAATATTGTTTAAA
145872 TATAAATATTAAAC
64 TATAAATATTAAAC
145886 ATATATTTCC
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
79 31 0.45
80 3 0.04
82 10 0.14
83 25 0.36
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (80 bp):
AGAGTTTTACTCCAACCAAAACTCTTTTAATATCAAAATAAATAGATAATAATATTGTTTAAATA
TAAATATTAAACCTG
Found at i:153804 original size:32 final size:32
Alignment explanation
Indices: 153763--153832 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
153753 AGGTGTCTAG
153763 GACATAACGACCGTTAAATTCTACCATTAAAA
1 GACATAACGACCGTTAAATTCTACCATTAAAA
153795 GACATAACGACCGTTAAATTCTACCATTAAAA
1 GACATAACGACCGTTAAATTCTACCATTAAAA
153827 GACATA
1 GACATA
153833 TGTCACGTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.24
Consensus pattern (32 bp):
GACATAACGACCGTTAAATTCTACCATTAAAA
Found at i:154891 original size:18 final size:18
Alignment explanation
Indices: 154868--154902 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
154858 ACTGAATATT
154868 TGTCCCGGAA-GACCACTA
1 TGTCCC-GAATGACCACTA
154886 TGTCCCGAATGACCACT
1 TGTCCCGAATGACCACT
154903 GATAATCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:165611 original size:15 final size:15
Alignment explanation
Indices: 165586--165632 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
165576 CCAGAAAATG
165586 TTACT-GAATTTGAA
1 TTACTGGAATTTGAA
165600 TTACTGGAATTTGAA
1 TTACTGGAATTTGAA
**
165615 TT-CTGGAAAATGAA
1 TTACTGGAATTTGAA
165629 TTAC
1 TTAC
165633 ATTCTGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (15 bp):
TTACTGGAATTTGAA
Found at i:165673 original size:20 final size:20
Alignment explanation
Indices: 165615--165673 Score: 95
Period size: 19 Copynumber: 3.0 Consensus size: 20
165605 GGAATTTGAA
165615 TTCTGGAAAATGAATTACA-
1 TTCTGGAAAATGAATTACAT
*
165634 TTCTGTAAAATGAA-TACAT
1 TTCTGGAAAATGAATTACAT
165653 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
165673 T
1 T
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 4 0.11
19 26 0.72
20 6 0.17
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Done.