Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold156
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: 2697547
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 14
Found at i:475504 original size:17 final size:17
Alignment explanation
Indices: 475426--475504 Score: 52
Period size: 17 Copynumber: 4.4 Consensus size: 17
475416 TCAATTATAT
* * *
475426 ATATATAAATTATTAAT
1 ATATATAATTTAATAAA
*
475443 ATATTAAAATTTATATAAA
1 ATA-TATAATTTA-ATAAA
* *
475462 TATAAAATATTTTAAATAAA
1 -AT-ATATAATTT-AATAAA
475482 AT-TATAATTTAATAAA
1 ATATATAATTTAATAAA
475498 ATATATA
1 ATATATA
475505 TAATATAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
16 8 0.17
17 13 0.28
18 7 0.15
19 5 0.11
20 12 0.26
21 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATAATTTAATAAA
Found at i:475515 original size:17 final size:18
Alignment explanation
Indices: 475421--475518 Score: 67
Period size: 15 Copynumber: 6.1 Consensus size: 18
475411 TCGTCTCAAT
475421 TATAT-ATATAT-AAAT-
1 TATATAATATATAAAATA
*
475436 TAT-TAATATATTAAAATT
1 TATATAATATA-TAAAATA
475454 TATATAA-ATATAAAATA
1 TATATAATATATAAAATA
* *
475471 T-TTTAA-ATA-AAATTA
1 TATATAATATATAAAATA
*
475486 TA-AT-TTA-ATAAAATA
1 TATATAATATATAAAATA
475501 TATATAATATA-AAAATA
1 TATATAATATATAAAATA
475518 T
1 T
475519 GAATTATTAC
Statistics
Matches: 65, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
14 2 0.03
15 23 0.35
16 10 0.15
17 20 0.31
18 7 0.11
19 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATATAATATATAAAATA
Found at i:476273 original size:27 final size:27
Alignment explanation
Indices: 476212--476273 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
476202 TTGAAGTTTA
*
476212 AAAATAAAAAATATATTATAAATATTT
1 AAAATTAAAAATATATTATAAATATTT
* *
476239 AAATTTAAAAAT-TATT-TAATTATTAT
1 AAAATTAAAAATATATTATAAATATT-T
476265 ATAAATTAA
1 A-AAATTAA
476274 TTTAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 7 0.24
26 6 0.21
27 16 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAATTAAAAATATATTATAAATATTT
Found at i:477361 original size:5 final size:5
Alignment explanation
Indices: 477346--477384 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
477336 TTTATTAAAT
* *
477346 TTTAA -TTAA TTTAA TTTAA TTTAA ATTAA TTTAT TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
477385 AATAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTTAA
Found at i:477390 original size:20 final size:20
Alignment explanation
Indices: 477349--477390 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
477339 ATTAAATTTT
**
477349 AATTAATTTAATTTAATTTA
1 AATTAATTTAATTTAAAATA
*
477369 AATTAATTTATTTTAAAATA
1 AATTAATTTAATTTAAAATA
477389 AA
1 AA
477391 ATTTTTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTAATTTAATTTAAAATA
Found at i:477413 original size:15 final size:16
Alignment explanation
Indices: 477351--477421 Score: 60
Period size: 15 Copynumber: 4.6 Consensus size: 16
477341 TAAATTTTAA
*
477351 TTAATT-TAATTTAAT
1 TTAATTATAATTTATT
*
477366 TTAAAT-TAATTTATT
1 TTAATTATAATTTATT
* *
477381 TTAAAATAAAATTT-TT
1 TT-AATTATAATTTATT
477397 TTAATTATAATTT-TT
1 TTAATTATAATTTATT
*
477412 TTATTTATAA
1 TTAATTATAA
477422 GATTTAAGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
15 35 0.73
16 8 0.17
17 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAATTATAATTTATT
Found at i:477681 original size:3 final size:3
Alignment explanation
Indices: 477673--477699 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
477663 TTGATTTTTG
477673 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
477700 GAATACCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:483965 original size:2 final size:2
Alignment explanation
Indices: 483960--483988 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
483950 TTTTTATGGA
483960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
483989 AATACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:488421 original size:2 final size:2
Alignment explanation
Indices: 488414--488442 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
488404 AGATATTTGA
488414 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
488443 TATCTCACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:492328 original size:13 final size:14
Alignment explanation
Indices: 492310--492343 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
492300 TATTAAAATA
492310 ATATTAAT-TTTTT
1 ATATTAATATTTTT
492323 ATATTAATATTTTT
1 ATATTAATATTTTT
*
492337 ATTTTAA
1 ATATTAA
492344 ATAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATATTAATATTTTT
Found at i:496293 original size:20 final size:20
Alignment explanation
Indices: 496270--496323 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
496260 GTATTTTATT
496270 TATTTATTTATTTTGTTG-TG
1 TATTTATTTATTTT-TTGATG
* *
496290 TATTCGATTGATTTTTTGATG
1 TATT-TATTTATTTTTTGATG
*
496311 AATTTATTTATTT
1 TATTTATTTATTT
496324 ATATTCTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.20, C:0.02, G:0.13, T:0.65
Consensus pattern (20 bp):
TATTTATTTATTTTTTGATG
Found at i:508714 original size:163 final size:163
Alignment explanation
Indices: 508434--508746 Score: 572
Period size: 163 Copynumber: 1.9 Consensus size: 163
508424 GCTGGAAAAT
508434 GTACCAAATTTGTTATTTCTTGATCATTGAGATTGATATATTTGCATATATTGGAGTACAAAAAA
1 GTACCAAATTTGTTATTTCTTGATCATTGAGATTGATATATTTGCATATATTGGAGTACAAAAAA
*
508499 GAAGTAGATGTGATGGGTAGCTAGTCAATAAAAATAACTTTTTGTGCTTGTAAAAAATAATGATT
66 GAAGTAGATGTGATGGGTAGCTAGTCAATAAAAATAACTTTTTGTACTTGTAAAAAATAATGATT
508564 TCTTTTTATTTGTCAAAAATAGTTATTTCTGAA
131 TCTTTTTATTTGTCAAAAATAGTTATTTCTGAA
*
508597 GTACTAAATTTGTTATTTCTTGATCATTGAGATTGATATATTTGCATATATTGGAGTACAAAAAA
1 GTACCAAATTTGTTATTTCTTGATCATTGAGATTGATATATTTGCATATATTGGAGTACAAAAAA
* * **
508662 GAAGTAGATGTGGTGGGTAGCTAGTCAATAAAAATCACTTTTTGTACTTGTAAAAAATGGTGATT
66 GAAGTAGATGTGATGGGTAGCTAGTCAATAAAAATAACTTTTTGTACTTGTAAAAAATAATGATT
508727 TCTTTTTATTTGTCAAAAAT
131 TCTTTTTATTTGTCAAAAAT
508747 GGTGGTTCTT
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
163 144 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (163 bp):
GTACCAAATTTGTTATTTCTTGATCATTGAGATTGATATATTTGCATATATTGGAGTACAAAAAA
GAAGTAGATGTGATGGGTAGCTAGTCAATAAAAATAACTTTTTGTACTTGTAAAAAATAATGATT
TCTTTTTATTTGTCAAAAATAGTTATTTCTGAA
Found at i:508755 original size:26 final size:27
Alignment explanation
Indices: 508709--508777 Score: 95
Period size: 26 Copynumber: 2.6 Consensus size: 27
508699 CTTTTTGTAC
* *
508709 TTGTAAAAAATGGTGATTTCTTTTTAT
1 TTGTCAAAAATGGTGAGTTCTTTTTAT
*
508736 TTGTCAAAAATGGTG-GTTCTTTTTGT
1 TTGTCAAAAATGGTGAGTTCTTTTTAT
*
508762 TTGTCAAAAATAGTGA
1 TTGTCAAAAATGGTGA
508778 CTTATTGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 23 0.62
27 14 0.38
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (27 bp):
TTGTCAAAAATGGTGAGTTCTTTTTAT
Found at i:508790 original size:24 final size:25
Alignment explanation
Indices: 508735--508800 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
508725 TTTCTTTTTA
* * *
508735 TTTGTCAAAAATGGTGGTTCTTTTTG
1 TTTGTCAAAAATAGT-GTACTTATTG
508761 TTTGTCAAAAATAGTG-ACTTATTG
1 TTTGTCAAAAATAGTGTACTTATTG
*
508785 TTTGTCAAAATTAGTG
1 TTTGTCAAAAATAGTG
508801 GCTAATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
24 21 0.58
25 1 0.03
26 14 0.39
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (25 bp):
TTTGTCAAAAATAGTGTACTTATTG
Found at i:513207 original size:26 final size:27
Alignment explanation
Indices: 513149--513229 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
513139 ACAAAAACCA
* *
513149 CCTTTTGTGTTTGTCAAAAAT-AGTAGTT
1 CCTTTT-TGTTTGTAAAAAATGA-TGGTT
513177 CCTTTTTGTTTGTAAAAAATGATGGTT
1 CCTTTTTGTTTGTAAAAAATGATGGTT
* *
513204 -CTTTTTGTTTATAAAAAATGGTGGTT
1 CCTTTTTGTTTGTAAAAAATGATGGTT
513230 TGTTGTTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 24 0.50
27 17 0.35
28 7 0.15
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.48
Consensus pattern (27 bp):
CCTTTTTGTTTGTAAAAAATGATGGTT
Found at i:513235 original size:24 final size:26
Alignment explanation
Indices: 513156--513251 Score: 88
Period size: 26 Copynumber: 3.7 Consensus size: 26
513146 CCACCTTTTG
* * * *
513156 TGTTTGTCAAAAATAGTAGTTCCTTTT
1 TGTTTGTAAAAAATGGTGGTT-CTTGT
* *
513183 TGTTTGTAAAAAATGATGGTTCTTTT
1 TGTTTGTAAAAAATGGTGGTTCTTGT
*
513209 TGTTTATAAAAAATGGTGG-T-TTGT
1 TGTTTGTAAAAAATGGTGGTTCTTGT
* *
513233 TGTTTGTCAAAATTGGTGG
1 TGTTTGTAAAAAATGGTGG
513252 CTAATTTTTA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
24 19 0.32
25 1 0.02
26 22 0.37
27 17 0.29
ACGTcount: A:0.26, C:0.05, G:0.22, T:0.47
Consensus pattern (26 bp):
TGTTTGTAAAAAATGGTGGTTCTTGT
Found at i:528993 original size:2 final size:2
Alignment explanation
Indices: 528986--529018 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
528976 GATTATAAGT
528986 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
529019 TAACTGTATT
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:529739 original size:79 final size:79
Alignment explanation
Indices: 529605--529767 Score: 272
Period size: 79 Copynumber: 2.1 Consensus size: 79
529595 GCTTGTCTCC
* ** * *
529605 AGCTAAAACTAGATTAAAAATATCCCAAATGCAAGGTGCAATAGTTGTACTTAAGCTGCAATGAG
1 AGCTAAAACTAGATTAAAAACATCCCAAATGCAAGGTAAAATAGTTGTACGTAAGCTACAATGAG
*
529670 ACTTGATGCAATTT
66 ACTTGATGAAATTT
529684 AGCTAAAACTAGATTAAAAACATCCCAAATGCAAGGTAAAATAGTTGTACGTAAGCTACAATGAG
1 AGCTAAAACTAGATTAAAAACATCCCAAATGCAAGGTAAAATAGTTGTACGTAAGCTACAATGAG
529749 ACTTGATGAAATTT
66 ACTTGATGAAATTT
529763 AGCTA
1 AGCTA
529768 CCTCTCAAAG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (79 bp):
AGCTAAAACTAGATTAAAAACATCCCAAATGCAAGGTAAAATAGTTGTACGTAAGCTACAATGAG
ACTTGATGAAATTT
Found at i:534644 original size:24 final size:25
Alignment explanation
Indices: 534617--534670 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
534607 ATATAACATA
534617 AAATATTAAAAATATAAAA-A-TT-TT
1 AAATATT--AAATATAAAATATTTATT
534641 AAATA-TAAATATAAAATATTTATT
1 AAATATTAAATATAAAATATTTATT
534665 AAATAT
1 AAATAT
534671 ATCATATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 10 0.38
22 1 0.04
23 3 0.12
24 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AAATATTAAATATAAAATATTTATT
Found at i:534650 original size:21 final size:24
Alignment explanation
Indices: 534626--534671 Score: 71
Period size: 21 Copynumber: 2.0 Consensus size: 24
534616 AAAATATTAA
534626 AAATATAAAA-A-TT-TTAAATAT
1 AAATATAAAATATTTATTAAATAT
534647 AAATATAAAATATTTATTAAATAT
1 AAATATAAAATATTTATTAAATAT
534671 A
1 A
534672 TCATATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 1 0.05
23 2 0.09
24 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AAATATAAAATATTTATTAAATAT
Found at i:534677 original size:18 final size:18
Alignment explanation
Indices: 534614--534698 Score: 66
Period size: 18 Copynumber: 4.6 Consensus size: 18
534604 TAAATATAAC
534614 ATAAAATATTAA--AAAT
1 ATAAAATATTAATTAAAT
*
534630 ATAAAAATTTTAAATATAAAT
1 AT-AAAATATT-AAT-TAAAT
*
534651 ATAAAATATTTATTAAAT
1 ATAAAATATTAATTAAAT
** *
534669 ATATCATATTAATTACAT
1 ATAAAATATTAATTAAAT
*
534687 TTAAAAATATTA
1 AT-AAAATATTA
534699 CGTTATATTT
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
16 2 0.04
17 7 0.13
18 22 0.42
19 9 0.17
20 7 0.13
21 6 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAAATATTAATTAAAT
Found at i:534848 original size:2 final size:2
Alignment explanation
Indices: 534843--534869 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
534833 CCTCTCTGTG
534843 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
534870 CGACATCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:537576 original size:23 final size:23
Alignment explanation
Indices: 537550--537593 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
537540 AATTAAATGA
537550 TTATAATTTAAAAATAAAAATTT
1 TTATAATTTAAAAATAAAAATTT
* *
537573 TTATATTTTAAAAATATAAAT
1 TTATAATTTAAAAATAAAAAT
537594 ATAATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTATAATTTAAAAATAAAAATTT
Found at i:538480 original size:3 final size:3
Alignment explanation
Indices: 538472--538507 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
538462 ATCATTATTC
538472 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
538508 CTTTATCCAT
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):
TAT
Found at i:539319 original size:17 final size:17
Alignment explanation
Indices: 539268--539322 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
539258 TAATATTTTA
* *
539268 TATTAAATATAATAATA
1 TATTAAAAATAATAATT
**
539285 TATTTAATAAATTTTAATT
1 TA-TTAA-AAATAATAATT
539304 TATTAAAAATAATAATT
1 TATTAAAAATAATAATT
539321 TA
1 TA
539323 CGTAATATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 13 0.43
18 8 0.27
19 9 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTAAAAATAATAATT
Found at i:540179 original size:26 final size:28
Alignment explanation
Indices: 540127--540182 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
540117 AAAAAATTTG
540127 TTATTTATAATATATAATAAAAATTATTA
1 TTATTTATAATATAT-ATAAAAATTATTA
* *
540156 TTATTTATAA-ATAT-TAATATTTATTA
1 TTATTTATAATATATATAAAAATTATTA
540182 T
1 T
540183 AATATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.44
28 4 0.16
29 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTATTTATAATATATATAAAAATTATTA
Found at i:555571 original size:3 final size:3
Alignment explanation
Indices: 555565--555598 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
555555 CAACAACAAC
555565 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
555599 GCTTTGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:563580 original size:2 final size:2
Alignment explanation
Indices: 563573--563618 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
563563 GATGGAAAAC
563573 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
563615 AT AT
1 AT AT
563619 TACAAATTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:567996 original size:13 final size:13
Alignment explanation
Indices: 567978--568004 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
567968 AAAAAATTAC
567978 ATATTTATTTTGG
1 ATATTTATTTTGG
567991 ATATTTATTTTGG
1 ATATTTATTTTGG
568004 A
1 A
568005 AGGTGGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (13 bp):
ATATTTATTTTGG
Found at i:568600 original size:30 final size:29
Alignment explanation
Indices: 568566--568626 Score: 113
Period size: 30 Copynumber: 2.1 Consensus size: 29
568556 AGGACATATA
568566 GATAATCAATGATTAAGGAGACCAAAGCAG
1 GATAATCAATGATTAAGGAG-CCAAAGCAG
568596 GATAATCAATGATTAAGGAGCCAAAGCAG
1 GATAATCAATGATTAAGGAGCCAAAGCAG
568625 GA
1 GA
568627 ATTTGCTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.46, C:0.13, G:0.25, T:0.16
Consensus pattern (29 bp):
GATAATCAATGATTAAGGAGCCAAAGCAG
Found at i:570721 original size:54 final size:54
Alignment explanation
Indices: 570634--570748 Score: 153
Period size: 54 Copynumber: 2.1 Consensus size: 54
570624 CAAATGAGGA
*
570634 TGCAATGGGTTTCCCGTCTGCATGTGGCTGCTGAGGCCTGGCAGA-AGGAGGTGT
1 TGCAGTGGGTTTCCCGTCTGCATGTGGCTGCTGAGGCCTGGCA-ACAGGAGGTGT
* * *
570688 TGCAGTGGGTTTCCTGTCTGCCTGCT-GCTGCTGAGGCTTGGCAACAGGAGGTGT
1 TGCAGTGGGTTTCCCGTCTGCATG-TGGCTGCTGAGGCCTGGCAACAGGAGGTGT
*
570742 AGCAGTG
1 TGCAGTG
570749 CTCTTCCAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
53 1 0.02
54 52 0.96
55 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.38, T:0.27
Consensus pattern (54 bp):
TGCAGTGGGTTTCCCGTCTGCATGTGGCTGCTGAGGCCTGGCAACAGGAGGTGT
Found at i:570761 original size:54 final size:54
Alignment explanation
Indices: 570643--570764 Score: 142
Period size: 54 Copynumber: 2.3 Consensus size: 54
570633 ATGCAATGGG
* * * *
570643 TTTCCCGTCTGCATG-TGGCTGCTGAGGCCTGGCAGAAGGAGGTGTTGCAGTGGG
1 TTTCCAGTCTGCCTGCT-GCTGCTGAGGCCTGGCAGAAGGAGGTGTAGCAGTGGC
* *
570697 TTTCCTGTCTGCCTGCTGCTGCTGAGGCTTGGCA-ACAGGAGGTGTAGCAGT-GC
1 TTTCCAGTCTGCCTGCTGCTGCTGAGGCCTGGCAGA-AGGAGGTGTAGCAGTGGC
570750 TCTTCCAGTCTGCCT
1 T-TTCCAGTCTGCCT
570765 CCCGCTTCTC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
53 3 0.05
54 55 0.93
55 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.34, T:0.29
Consensus pattern (54 bp):
TTTCCAGTCTGCCTGCTGCTGCTGAGGCCTGGCAGAAGGAGGTGTAGCAGTGGC
Found at i:576032 original size:3 final size:3
Alignment explanation
Indices: 575980--576018 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
575970 TGACTTAGAA
575980 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
576019 GTTATTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:576986 original size:3 final size:3
Alignment explanation
Indices: 576980--577025 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
576970 GATGATGATG
576980 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
577026 AAGAAGTAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:577401 original size:2 final size:2
Alignment explanation
Indices: 577394--577429 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
577384 TAATTCATGC
577394 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
577430 GATAACTTTG
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:577507 original size:20 final size:20
Alignment explanation
Indices: 577482--577527 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
577472 CATATATAAA
577482 ATAAATATATTAAAAATTAT
1 ATAAATATATTAAAAATTAT
*
577502 ATAAATATATTAAAATTTAT
1 ATAAATATATTAAAAATTAT
577522 A-AAATA
1 ATAAATA
577528 ATAATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAATATATTAAAAATTAT
Found at i:577560 original size:20 final size:19
Alignment explanation
Indices: 577483--577562 Score: 73
Period size: 20 Copynumber: 4.4 Consensus size: 19
577473 ATATATAAAA
*
577483 TAAATATATTAAAAATTAT
1 TAAATATATTAAAATTTAT
577502 ATAAATATATTAAAATTTA-
1 -TAAATATATTAAAATTTAT
*
577521 TAAA-ATA--ATAA-TTAT
1 TAAATATATTAAAATTTAT
*
577536 T-AATATATTTAAATTTATT
1 TAAATATATTAAAATTTA-T
577555 TAAATATA
1 TAAATATA
577563 ATTATAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
14 5 0.10
15 7 0.14
17 5 0.10
18 7 0.14
19 2 0.04
20 23 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATATATTAAAATTTAT
Found at i:577812 original size:3 final size:3
Alignment explanation
Indices: 577804--577832 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
577794 TGGAATTAGA
577804 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
577833 CCAAGTCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:580651 original size:2 final size:2
Alignment explanation
Indices: 580644--580676 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
580634 TTGTAAGTGC
580644 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
580677 TCATAAAGAG
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:585975 original size:10 final size:10
Alignment explanation
Indices: 585962--586003 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
585952 TTTATTTTAT
585962 ATTATAAAA-A
1 ATTA-AAAATA
585972 ATTAAAAAATA
1 ATT-AAAAATA
585983 ATTAAAAATA
1 ATTAAAAATA
*
585993 AATAAAAATA
1 ATTAAAAATA
586003 A
1 A
586004 GATTCAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 24 0.83
11 5 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
ATTAAAAATA
Found at i:600460 original size:2 final size:2
Alignment explanation
Indices: 600453--600485 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
600443 CAGGGCGTGT
600453 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
600486 TGTGTTTGGT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:601434 original size:16 final size:16
Alignment explanation
Indices: 601415--601446 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
601405 TACCGGTGTT
601415 TCCACTTACCTTCTTC
1 TCCACTTACCTTCTTC
*
601431 TCCACTTACTTTCTTC
1 TCCACTTACCTTCTTC
601447 ATTCTCGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.41, G:0.00, T:0.47
Consensus pattern (16 bp):
TCCACTTACCTTCTTC
Found at i:607272 original size:18 final size:17
Alignment explanation
Indices: 607238--607272 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
607228 CCGTTCAATT
*
607238 CGAATATAAATTAAATA
1 CGAATATAAAATAAATA
607255 CGAATATAAAAATAAATA
1 CGAATAT-AAAATAAATA
607273 TTCTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.26
Consensus pattern (17 bp):
CGAATATAAAATAAATA
Found at i:614692 original size:4 final size:4
Alignment explanation
Indices: 614683--614750 Score: 61
Period size: 4 Copynumber: 16.8 Consensus size: 4
614673 GATGTGTTAT
*
614683 AAAG AAAG AAAG -AAG AAAACG AAAA AAAG -AAG AAAG AAAG AAAGG AAA-
1 AAAG AAAG AAAG AAAG -AAA-G AAAG AAAG AAAG AAAG AAAG AAA-G AAAG
*
614731 AAAA AAAG AAAAG AAAG AAA
1 AAAG AAAG -AAAG AAAG AAA
614751 AAAATTTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
3 9 0.17
4 31 0.57
5 13 0.24
6 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.21, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:614723 original size:25 final size:25
Alignment explanation
Indices: 614683--614751 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 25
614673 GATGTGTTAT
614683 AAAGAAAGAAAG-AAGAAAACGAAAA
1 AAAG-AAGAAAGAAAGAAAACGAAAA
*
614708 AAAGAAGAAAGAAAG-AAAGGAAAA
1 AAAGAAGAAAGAAAGAAAACGAAAA
*
614732 AAAAAAGAAAAGAAAGAAAA
1 AAAGAAG-AAAGAAAGAAAA
614752 AAATTTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
24 21 0.54
25 15 0.38
26 3 0.08
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.00
Consensus pattern (25 bp):
AAAGAAGAAAGAAAGAAAACGAAAA
Found at i:614740 original size:16 final size:17
Alignment explanation
Indices: 614683--614754 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 17
614673 GATGTGTTAT
614683 AAAG-AAAGAAAGAAGAA
1 AAAGAAAAGAAAGAA-AA
*
614700 AACGAAAA-AAAGAAGAAA
1 AAAGAAAAGAAAG-A-AAA
*
614718 GAAAGAAAGGAAA-AAAA
1 -AAAGAAAAGAAAGAAAA
614735 AAAGAAAAGAAAGAAAA
1 AAAGAAAAGAAAGAAAA
614752 AAA
1 AAA
614755 TTTATATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
16 11 0.24
17 17 0.38
18 7 0.16
19 7 0.16
20 3 0.07
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAAGAAAGAAAA
Found at i:614740 original size:20 final size:20
Alignment explanation
Indices: 614683--614754 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
614673 GATGTGTTAT
* *
614683 AAAGAAAGAAAGAAGAAAACG
1 AAAGAAAAAAAAAAGAAAA-G
*
614704 AAA-AAAAGAAGAAAG-AAAG
1 AAAGAAAA-AAAAAAGAAAAG
614723 AAAGGAAAAAAAAAAGAAAAG
1 AAA-GAAAAAAAAAAGAAAAG
614744 AAAGAAAAAAA
1 AAAGAAAAAAA
614755 TTTATATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
19 4 0.09
20 20 0.47
21 19 0.44
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAAAAAAGAAAAG
Found at i:614798 original size:25 final size:23
Alignment explanation
Indices: 614755--614812 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
614745 AAGAAAAAAA
*
614755 TTTATATATTAATATTTATATTATT
1 TTTATAT-TTAAAATTTATATT-TT
614780 TTTATATTTAAAATATTATATTTT
1 TTTATATTTAAAAT-TTATATTTT
*
614804 TATATATTT
1 TTTATATTT
614813 TTTATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 16 0.53
25 14 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTATATTTAAAATTTATATTTT
Found at i:614852 original size:37 final size:33
Alignment explanation
Indices: 614760--614857 Score: 110
Period size: 37 Copynumber: 2.8 Consensus size: 33
614750 AAAAATTTAT
614760 ATATTAATATTTATAT-TATTTTTATAT-TTAAA
1 ATATT-ATATTTATATATATTTTTATATATTAAA
*
614792 ATATTATATTTTTATATATTTTTTATATATTAATA
1 ATATTATATTTATATATA-TTTTTATATATTAA-A
*
614827 ATTCATTTTATTTCATATATATTTTTATATA
1 A-T-ATTATATTT-ATATATATTTTTATATA
614858 GACGTATATT
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
31 9 0.16
32 7 0.12
33 9 0.16
34 4 0.07
35 2 0.04
36 1 0.02
37 18 0.32
38 6 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (33 bp):
ATATTATATTTATATATATTTTTATATATTAAA
Found at i:615198 original size:18 final size:18
Alignment explanation
Indices: 615168--615224 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
615158 ATTCAAGAGG
615168 GAAA-AAAGAGAAAAAAA
1 GAAAGAAAGAGAAAAAAA
*
615185 GAAAGAAGGAGAAAAAAA
1 GAAAGAAAGAGAAAAAAA
615203 -ATAAGAAAGA-AAGAAAAA
1 GA-AAGAAAGAGAA-AAAAA
615221 GAAA
1 GAAA
615225 AAATTTATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
17 7 0.21
18 26 0.76
19 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (18 bp):
GAAAGAAAGAGAAAAAAA
Found at i:615208 original size:22 final size:19
Alignment explanation
Indices: 615178--615226 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
615168 GAAAAAAGAG
615178 AAAAAAAGAAAGAAGGAGAAA
1 AAAAAAAGAAAGAA--AGAAA
615199 AAAAATAAGAAAGAAAGAAA
1 AAAAA-AAGAAAGAAAGAAA
615219 AAGAAAAA
1 AA-AAAAA
615227 ATTTATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.35
21 8 0.31
22 9 0.35
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (19 bp):
AAAAAAAGAAAGAAAGAAA
Found at i:615631 original size:478 final size:465
Alignment explanation
Indices: 614703--615597 Score: 1070
Period size: 478 Copynumber: 1.9 Consensus size: 465
614693 AGAAGAAAAC
* *
614703 GAAAAAAAGAAGAAAGAAAGAAAGGAAAAAAAAAAGAAAAGAAAGAAAAAAATTTATATATTAAT
1 GAAAAAAAGAAAAAAGAAAGAAAGGAAAAAAAAAAGAAAAGAAAAAAAAAAATTTATATATTAAT
*
614768 ATTTATATTATTTTTATATTTAAAATATTATATTTTTATATATTTTTTATATATTAATAATTCAT
66 ATTTATATTATTTTTATATTTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTCAT
* * ** * *
614833 TTTATTTCATATATATTTTTATATAGACGTATATTTATATTATCTGTATATCATTTTTATGTTAT
131 TTTATTTCATACATATTTTTATAGAGACGTATATTTATACCATATGCATATCATTTTTATGTTAT
* *
614898 GTTTTAAATATTTTTTATAAATATTGTGTTTATATTTTTTTGTGTTTAAAATAAAATAAATTTAT
196 GTTTTAAATATTTTTTATAAATATCGTGATTATATTTTTTTGTGTTTAAAATAAAATAAATTTAT
* * * *
614963 ATAAATTTTTACATGTTAATTATTCATTTATCTATATTTTGATATACTCGTGTATTCATACCGTG
261 ATAAATTTGTACATGTTAATTATTCATTTATCTATATATTGATATACTCGTGTATTCATACCATA
* ** * * * * * *
615028 TTTATATTATTTTACATATCGTGTTTTAATTTTTTATATCTATCTATCTATCTATACATATATAT
326 TTAATATTATTTTACATATCGCATATTAATTTTATATATATATATATATATCTATACATATACAT
** * * * *
615093 ATATAAAATTAACTACATAAACTTATCTCGTACTGGCACATGTCACTTAATTTTTTTTTTTTTGC
391 ATATAAAATTAACTACATAAACAAATATAGTACTGACACATGTCACTTAAGTTTTTTTTTTTTGC
615158 ATTCAAGAGG
456 ATTCAAGAGG
*
615168 GAAAAAAGAGAAAAAAAGAAAGAAGGAGAAAAAAAATAAGAAAGAAAGAAAAAGAAAAAATTTAT
1 GAAAAAA-AG-AAAAAAGAAAGAAAG-GAAAAAAAA-AAG--A-AAAGAAAAA-AAAAAATTTAT
* * * *
615233 GTTTTTATATTTATGTTATTTTTTTCATATTTAAAATATTATATTTTTATATAAATTTTTTACAT
58 ATATTAATATTTATATTA--TTTTT-ATATTTAAAATATTATATTTTTATAT--ATTTTTTACAT
* * * * * * * *
615298 ATTAATGATTTATTTTATTTCATGCATATTTTTATAGATATGTATATTTGTGCCATATGCATATT
118 ATTAATAATTCATTTTATTTCATACATATTTTTATAGAGACGTATATTTATACCATATGCATATC
* * *
615363 ATTTTTATGTTATGTTTTAAATTTTTTTTTATAAATGTCGTGATTATATTTTTTTCGTATTGTTA
183 ATTTTTATGTTATGTTTTAAA-TATTTTTTATAAATATCGTGATTATATTTTTTT-GT-GT-TTA
* * * *
615428 AAGTAAAATAAATTTATATAAATTTGTACATGTTTATTATT-AGTTTATTTATATATTGATATAT
244 AAATAAAATAAATTTATATAAATTTGTACATGTTAATTATTCA-TTTATCTATATATTGATATAC
** *
615492 TCGTGTATTCATGTCATATTAATA-TATTTT-CATATTGCATATTAA-TTTATATATATATATAT
308 TCGTGTATTCATACCATATTAATATTATTTTACATATCGCATATTAATTTTATATATATATATAT
* *
615554 ATATCTATAC-T-TACA-A-ATAAAATTAATTGCATAAA-AAATATAGT
373 ATATCTATACATATACATATATAAAATTAACTACATAAACAAATATAGT
615598 GTTGATATAT
Statistics
Matches: 359, Mismatches: 53, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
465 7 0.02
466 2 0.01
467 13 0.04
468 9 0.03
469 3 0.01
471 1 0.00
472 8 0.02
473 25 0.07
474 5 0.01
475 22 0.06
476 27 0.08
477 3 0.01
478 83 0.23
479 52 0.14
480 13 0.04
481 8 0.02
482 78 0.22
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (465 bp):
GAAAAAAAGAAAAAAGAAAGAAAGGAAAAAAAAAAGAAAAGAAAAAAAAAAATTTATATATTAAT
ATTTATATTATTTTTATATTTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTCAT
TTTATTTCATACATATTTTTATAGAGACGTATATTTATACCATATGCATATCATTTTTATGTTAT
GTTTTAAATATTTTTTATAAATATCGTGATTATATTTTTTTGTGTTTAAAATAAAATAAATTTAT
ATAAATTTGTACATGTTAATTATTCATTTATCTATATATTGATATACTCGTGTATTCATACCATA
TTAATATTATTTTACATATCGCATATTAATTTTATATATATATATATATATCTATACATATACAT
ATATAAAATTAACTACATAAACAAATATAGTACTGACACATGTCACTTAAGTTTTTTTTTTTTGC
ATTCAAGAGG
Found at i:615668 original size:16 final size:16
Alignment explanation
Indices: 615647--615679 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
615637 GTAAAGATGG
615647 AAAGAAAAAAAAGAAA
1 AAAGAAAAAAAAGAAA
*
615663 AAAGAAAAGAAAGAAA
1 AAAGAAAAAAAAGAAA
615679 A
1 A
615680 GGAGAAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAGAAA
Found at i:615672 original size:21 final size:22
Alignment explanation
Indices: 615646--615698 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
615636 AGTAAAGATG
615646 GAAAGAAAAAAAAGAAAAAAGA
1 GAAAGAAAAAAAAGAAAAAAGA
* * *
615668 -AAAGAAAGAAAAGGAGAAAGA
1 GAAAGAAAAAAAAGAAAAAAGA
*
615689 GAAATAAAAA
1 GAAAGAAAAA
615699 GAAAATTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (22 bp):
GAAAGAAAAAAAAGAAAAAAGA
Found at i:615766 original size:482 final size:476
Alignment explanation
Indices: 614703--615780 Score: 1059
Period size: 478 Copynumber: 2.2 Consensus size: 476
614693 AGAAGAAAAC
* * *
614703 GAAAAAAAG-AAGAAAGAAAGAAAGGAAAAA-AA-AAAGAAA-AGAAAGAAAAAAATTTATATAT
1 GAAAAAAAGAAAG-AAG-AAGAAA--AAAAAGAAGAAAGAAAGAAAAAG-AAAAAATTTATGTGT
* * * * *
614764 TAATATTTATATTA--TTTTTATATTTAAAATATTAT-ATTTTTATATATTTTTTATATATTAAT
61 TTATATTTATGTTATTTTTTTATATTTAAAATATTATAATTTATATAAATTTTTTACATATTAAT
* * ** * *
614826 AATTCATTTTATTTCATATATATTTTTATATAGACGTATATTTATATTATCTGTATATCATTTTT
126 AATTCATTTTATTTCATACATATTTTTATAGAGACGTATATTTATACCATATGCATATCATTTTT
* *
614891 ATGTTATGTTTTAAATATTTTTTATAAATATTGTGTTTATATTTTTTTGTGTTTAAAATAAAATA
191 ATGTTATGTTTTAAATATTTTTTATAAATATCGTGATTATATTTTTTTGTGTTTAAAATAAAATA
* *
614956 AATTTATATAAATTTTTACATGTTAATTATTCATTTATCTATATTTTGATATACTCGTGTATTCA
256 AATTTATATAAATTTGTACATGTTAATTATTCATTTATCTATATATTGATATACTCGTGTATTCA
* * * ** * * * * *
615021 TACCGTGTTTATATTATTTTACATATCGTGTTTTAATTTTTTATATCTATCTATCTATCTATACA
321 TACCATATTAATATTATTTTACATATCGCATATTAATTTTATATATATATATATATATCTATACA
* ** * * * *
615086 TATATATATATAAAATTAACTACATAAACTTATCTCGTACTGGCACATGTCACTTAATTTTTTTT
386 TATACATATATAAAATTAACTACATAAACAAATATAGTACTGACACATGTCACTTAAGTTTTTTT
** * *
615151 TTTTTGCATTCAAGAGGGAAAAAAGA
451 TTTCAGCAGTAAAGAGGGAAAAAAGA
* * *
615177 GAAAAAAAGAAAGAAGGAGAAAAAAAATAAGAAAGAAAGAAAAAGAAAAAATTTATGTTTTTATA
1 GAAAAAAAGAAAGAAGAAGAAAAAAAAGAAGAAAGAAAGAAAAAGAAAAAATTTATGTGTTTATA
* *
615242 TTTATGTTATTTTTTTCATATTTAAAATATTATATTTTTATATAAATTTTTTACATATTAATGAT
66 TTTATGTTATTTTTTT-ATATTTAAAATATTATA-ATTTATATAAATTTTTTACATATTAATAAT
* * * * * * *
615307 TTATTTTATTTCATGCATATTTTTATAGATATGTATATTTGTGCCATATGCATATTATTTTTATG
129 TCATTTTATTTCATACATATTTTTATAGAGACGTATATTTATACCATATGCATATCATTTTTATG
* * * *
615372 TTATGTTTTAAATTTTTTTTTATAAATGTCGTGATTATATTTTTTTCGTATTGTTAAAGTAAAAT
194 TTATGTTTTAAA-TATTTTTTATAAATATCGTGATTATATTTTTTT-GT-GT-TTAAAATAAAAT
* * *
615437 AAATTTATATAAATTTGTACATGTTTATTATT-AGTTTATTTATATATTGATATATTCGTGTATT
255 AAATTTATATAAATTTGTACATGTTAATTATTCA-TTTATCTATATATTGATATACTCGTGTATT
** *
615501 CATGTCATATTAATA-TATTTT-CATATTGCATATTAA-TTTATATATATATATATATATCTATA
319 CATACCATATTAATATTATTTTACATATCGCATATTAATTTTATATATATATATATATATCTATA
* * ** * * *
615563 C-T-TACA-A-ATAAAATTAATTGCATAAA-AAATATAGTGTTGATATATGTCCTGCTTTTAAGT
384 CATATACATATATAAAATTAACTACATAAACAAATATAGTACTGACACATGT-C-AC--TTAAGT
* *
615623 TTTTTTTTTCAGTAGTAAAGATGGAAAGAAA-A
445 TTTTTTTTTCAGCAGTAAAGAGGGAAA-AAAGA
* * *
615655 -AAAAGAAA-AAAGAA-AAGAAAGAAAAGGAGAAAGAGAA-ATAAAA-AGAAAATTTAATGTGTT
1 GAAAA-AAAGAAAGAAGAAGAAAAAAAAGAAGAAAGA-AAGA-AAAAGAAAAAATTT-ATGTGTT
*
615715 TATATTTGTATTCGTGT-TATTTTTTATGATTTAAAATATTATTAATTTATATAATATTTTATAC
62 TATA-TT-TA-T-GT-TAT-TTTTTTAT-ATTTAAAATATTA-TAATTTATATAA-ATTTTTTAC
615779 AT
118 AT
615781 GTATATTTAT
Statistics
Matches: 496, Mismatches: 76, Indels: 55
0.79 0.12 0.09
Matches are distributed among these distances:
471 5 0.01
472 2 0.00
473 37 0.07
474 29 0.06
475 26 0.05
476 43 0.09
477 29 0.06
478 122 0.25
479 57 0.11
480 14 0.03
481 13 0.03
482 107 0.22
483 12 0.02
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (476 bp):
GAAAAAAAGAAAGAAGAAGAAAAAAAAGAAGAAAGAAAGAAAAAGAAAAAATTTATGTGTTTATA
TTTATGTTATTTTTTTATATTTAAAATATTATAATTTATATAAATTTTTTACATATTAATAATTC
ATTTTATTTCATACATATTTTTATAGAGACGTATATTTATACCATATGCATATCATTTTTATGTT
ATGTTTTAAATATTTTTTATAAATATCGTGATTATATTTTTTTGTGTTTAAAATAAAATAAATTT
ATATAAATTTGTACATGTTAATTATTCATTTATCTATATATTGATATACTCGTGTATTCATACCA
TATTAATATTATTTTACATATCGCATATTAATTTTATATATATATATATATATCTATACATATAC
ATATATAAAATTAACTACATAAACAAATATAGTACTGACACATGTCACTTAAGTTTTTTTTTTCA
GCAGTAAAGAGGGAAAAAAGA
Found at i:615843 original size:11 final size:12
Alignment explanation
Indices: 615812--615859 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
615802 TTCGTGTCAT
615812 TTATTTTTTATA
1 TTATTTTTTATA
*
615824 TTATGTTTTA-A
1 TTATTTTTTATA
615835 TTATTTTTTTATA
1 TTA-TTTTTTATA
*
615848 TCATATTTTTAT
1 TTAT-TTTTTAT
615860 TTTTCGTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 4 0.13
12 16 0.53
13 10 0.33
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (12 bp):
TTATTTTTTATA
Found at i:616095 original size:16 final size:17
Alignment explanation
Indices: 616069--616101 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
616059 ATTTTTATTA
616069 AAAATAATTAAAAATAT
1 AAAATAATTAAAAATAT
616086 AAAA-AATTAAAAATAT
1 AAAATAATTAAAAATAT
616102 CATTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAATTAAAAATAT
Found at i:616257 original size:15 final size:16
Alignment explanation
Indices: 616239--616275 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
616229 TTTATTTATA
616239 AAAAAAAGAAAAAG-G
1 AAAAAAAGAAAAAGAG
*
616254 AAAAAAATAAAAAGAG
1 AAAAAAAGAAAAAGAG
616270 AAAAAA
1 AAAAAA
616276 TTTATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (16 bp):
AAAAAAAGAAAAAGAG
Found at i:616809 original size:16 final size:17
Alignment explanation
Indices: 616782--616822 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
616772 ATTTTTAAAT
616782 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
616797 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
616814 AAATTTTAT
1 AAATTTTAT
616823 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:617178 original size:26 final size:26
Alignment explanation
Indices: 617132--617181 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
617122 TTAATATTAC
*
617132 AATAATTTTTATTTAAAAATTATAAA
1 AATAATTTTTAATTAAAAATTATAAA
*
617158 AATAATATTTTAATT-ATAATTATA
1 AATAAT-TTTTAATTAAAAATTATA
617182 TTACTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AATAATTTTTAATTAAAAATTATAAA
Found at i:620787 original size:2 final size:2
Alignment explanation
Indices: 620780--620806 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
620770 GGCTATGTAA
620780 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
620807 ATAATTACCA
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:631671 original size:21 final size:22
Alignment explanation
Indices: 631627--631674 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
631617 AAAATATTTT
*
631627 TATTTAAATTTAATTATAAAAA
1 TATTTAAATATAATTATAAAAA
631649 TATTTAAAATATAA-TAT-AAAA
1 TATTT-AAATATAATTATAAAAA
631670 TATTT
1 TATTT
631675 TTTAACAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 8 0.33
23 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTTAAATATAATTATAAAAA
Found at i:637713 original size:16 final size:17
Alignment explanation
Indices: 637689--637736 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
637679 ATTGATTGTG
637689 CTTTGTTTT-TTTTTTT
1 CTTTGTTTTATTTTTTT
* *
637705 CTTTCTTTTCTTTTTTT
1 CTTTGTTTTATTTTTTT
637722 -TTTGTTTTATTTTTT
1 CTTTGTTTTATTTTTT
637737 AACAATTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 21 0.75
17 7 0.25
ACGTcount: A:0.02, C:0.08, G:0.04, T:0.85
Consensus pattern (17 bp):
CTTTGTTTTATTTTTTT
Found at i:637734 original size:21 final size:21
Alignment explanation
Indices: 637694--637734 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
637684 TTGTGCTTTG
*
637694 TTTTTTTTTTTCTTTCTTTTC
1 TTTTTTTTTTTCTTTATTTTC
637715 TTTTTTTTTTGT-TTTATTTT
1 TTTTTTTTTT-TCTTTATTTT
637735 TTAACAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.02, C:0.07, G:0.02, T:0.88
Consensus pattern (21 bp):
TTTTTTTTTTTCTTTATTTTC
Found at i:638072 original size:30 final size:29
Alignment explanation
Indices: 638038--638102 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
638028 ATTAAAGGTA
* *
638038 TATTTAAATATAA-ATTAAATATTAAAATTT
1 TATTTAAATATAATA-AAAATA-TAAAAATT
*
638068 TATTTGAATATAATAAAAATATAAAAATT
1 TATTTAAATATAATAAAAATATAAAAATT
638097 TATTTA
1 TATTTA
638103 GATTAAGTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 12 0.40
30 17 0.57
31 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
TATTTAAATATAATAAAAATATAAAAATT
Found at i:639079 original size:2 final size:2
Alignment explanation
Indices: 639072--639096 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
639062 ATCCTAACAC
639072 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
639097 AGGGGGGGGG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:641304 original size:1 final size:1
Alignment explanation
Indices: 641298--641326 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
641288 TCCATTGTTC
641298 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
641327 TTTGGAGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:649418 original size:15 final size:17
Alignment explanation
Indices: 649398--649445 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
649388 AAGTTTTAAC
649398 TTAAATA-AAAT-AATA
1 TTAAATATAAATAAATA
*
649413 TTAAATATAATTAAATA
1 TTAAATATAAATAAATA
649430 TTAAATATATAATAAA
1 TTAAATATA-AATAAA
649446 AATAATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.25
16 3 0.11
17 13 0.46
18 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAATATAAATAAATA
Found at i:649455 original size:40 final size:41
Alignment explanation
Indices: 649404--649502 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 41
649394 TAACTTAAAT
649404 AAAATAATATTAA-ATATAATTAAATATTAAA-TATATAATA
1 AAAATAATATTAATATATAATTAAATA-TAAATTATATAATA
* *
649444 AAAATAATATTAATATTTAATTATATATAAATTTATATAATA
1 AAAATAATATTAATATATAATTAAATATAAA-TTATATAATA
*
649486 TAAAT--TATTAATATATA
1 AAAATAATATTAATATATA
649503 TTATATAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
40 28 0.54
41 11 0.21
42 13 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (41 bp):
AAAATAATATTAATATATAATTAAATATAAATTATATAATA
Found at i:649484 original size:27 final size:27
Alignment explanation
Indices: 649426--649511 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
649416 AATATAATTA
* *
649426 AATATTAAA-TATATAATAAAAATAATATT
1 AATA-TAAATTAT-TAATAAATATTATA-T
*
649455 AATATTTAATTA-TATATAAAT-TTATAT
1 AATA-TAAATTATTA-ATAAATATTATAT
*
649482 AATATAAATTATTAATATATATTATAT
1 AATATAAATTATTAATAAATATTATAT
649509 AAT
1 AAT
649512 TATCATAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
26 11 0.23
27 16 0.33
28 6 0.12
29 13 0.27
30 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AATATAAATTATTAATAAATATTATAT
Found at i:649488 original size:15 final size:14
Alignment explanation
Indices: 649426--649511 Score: 72
Period size: 14 Copynumber: 6.2 Consensus size: 14
649416 AATATAATTA
649426 AATATTAAA-TATAT
1 AATA-TAAATTATAT
* *
649440 AATAAAAATAATATT
1 AATATAAATTATA-T
*
649455 AATATTTAATTATAT
1 AATA-TAAATTATAT
*
649470 -ATA-AATTTATAT
1 AATATAAATTATAT
649482 AATATAAATTAT-T
1 AATATAAATTATAT
*
649495 AATATATATTATAT
1 AATATAAATTATAT
649509 AAT
1 AAT
649512 TATCATAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
12 7 0.12
13 18 0.32
14 20 0.35
15 6 0.11
16 6 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATAAATTATAT
Found at i:650578 original size:45 final size:47
Alignment explanation
Indices: 650525--650628 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 47
650515 ATGAAAACTG
650525 AATATATTAATATCAAATTTAAAA-ATTA-ATATATTTATAT-ATTTT
1 AATATATTAATATCAAATTTAAAATATTATATA-ATTTATATCATTTT
* * * * *
650570 ATTATATTAAAATTATATTTAAAATATTTTATAATTTATATCATTTT
1 AATATATTAATATCAAATTTAAAATATTATATAATTTATATCATTTT
650617 AATATATTAATA
1 AATATATTAATA
650629 ATTTATTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
45 20 0.41
46 11 0.22
47 18 0.37
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (47 bp):
AATATATTAATATCAAATTTAAAATATTATATAATTTATATCATTTT
Found at i:650726 original size:36 final size:34
Alignment explanation
Indices: 650642--650744 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 34
650632 TATTTTATAT
* *
650642 AAATTTTAAA-AATATATTTATATCATATATTTA
1 AAATTTTAAATATTATATTTATATAATATATTTA
650675 ATAA-TTTAAGTATATTATATTTATATAATTATATTTA
1 A-AATTTTAA--ATATTATATTTATATAA-TATATTTA
650712 AAATTATTAAATATTATAAATTTA-ATAATATAT
1 AAATT-TTAAATATTAT--ATTTATATAATATAT
650745 AAAGAAATAT
Statistics
Matches: 59, Mismatches: 2, Indels: 15
0.78 0.03 0.20
Matches are distributed among these distances:
33 6 0.10
34 2 0.03
35 1 0.02
36 27 0.46
37 14 0.24
38 9 0.15
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (34 bp):
AAATTTTAAATATTATATTTATATAATATATTTA
Found at i:651008 original size:23 final size:22
Alignment explanation
Indices: 650969--651012 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
650959 TTAAAATATT
*
650969 ATATTTATATTTAAAATATTAAC
1 ATATTTATAATTAAAAT-TTAAC
650992 ATATTTAATAATT-AAATTTAA
1 ATATTT-ATAATTAAAATTTAA
651013 TAAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 10 0.53
24 5 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATTTATAATTAAAATTTAAC
Found at i:651012 original size:13 final size:13
Alignment explanation
Indices: 650994--651024 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
650984 ATATTAACAT
*
650994 ATTTAATAATTAA
1 ATTTAATAAATAA
651007 ATTTAATAAATAA
1 ATTTAATAAATAA
651020 ATTTA
1 ATTTA
651025 CAAAAACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTTAATAAATAA
Found at i:651014 original size:28 final size:26
Alignment explanation
Indices: 650949--651014 Score: 60
Period size: 28 Copynumber: 2.4 Consensus size: 26
650939 TAAATTACTC
* *
650949 AAATTAAATATTAAAATATTATATTT
1 AAATTTAATATTAAAATATTATAATT
* *
650975 ATATTTAAAATATTAACATATTTAATAATT
1 AAATTT--AATATTAAAATA-TT-ATAATT
651005 AAATTTAATA
1 AAATTTAATA
651015 AATAAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
26 4 0.13
28 15 0.48
29 2 0.06
30 10 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATTTAATATTAAAATATTATAATT
Found at i:651251 original size:17 final size:18
Alignment explanation
Indices: 651229--651274 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
651219 AAAATATTTA
*
651229 TAATTTTTTTAAAAG-GG
1 TAATTTTTTAAAAAGAGG
*
651246 TAATTTTTAAAAAAGTAGG
1 TAATTTTTTAAAAAG-AGG
651265 TAATTTTTTA
1 TAATTTTTTA
651275 CTTTAGAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 13 0.54
19 11 0.46
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (18 bp):
TAATTTTTTAAAAAGAGG
Found at i:652772 original size:19 final size:18
Alignment explanation
Indices: 652738--652773 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
652728 TAAATAAAAG
*
652738 ATATAGTTTGATTTTATT
1 ATATAGTTTAATTTTATT
652756 ATATAGTTTTAATTTTAT
1 ATATAG-TTTAATTTTAT
652774 ATGTCTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
ATATAGTTTAATTTTATT
Found at i:654236 original size:25 final size:24
Alignment explanation
Indices: 654190--654248 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
654180 CATATTATGT
*
654190 TATTTAAAT-TTTTTATATATATA
1 TATTTAAATATTTATATATATATA
*
654213 -ATTTTAAATATTTATATTTAATATA
1 TA-TTTAAATATTTATATAT-ATATA
654238 TATTTAAATAT
1 TATTTAAATAT
654249 AAAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.03
23 7 0.23
24 7 0.23
25 14 0.47
26 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TATTTAAATATTTATATATATATA
Found at i:654319 original size:17 final size:17
Alignment explanation
Indices: 654297--654330 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
654287 TTTAAAATTT
654297 TAAATA-TATATATTAAA
1 TAAATATTAT-TATTAAA
654314 TAAATATTATTATTAAA
1 TAAATATTATTATTAAA
654331 AATTACTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATATTATTATTAAA
Found at i:655898 original size:28 final size:28
Alignment explanation
Indices: 655808--655898 Score: 67
Period size: 28 Copynumber: 3.1 Consensus size: 28
655798 CGGTGAGATC
*
655808 CTTAATGATGTTACATTTTCAAATAATA
1 CTTAATGATGTTACATTGTCAAATAATA
* * * * ** *
655836 CTTAGTTTCATGCTAGAATTGTC-TTTGAATT
1 CTTA--ATGATGTTA-CATTGTCAAAT-AATA
655867 CTTAATGATGTTACATTGTCAAATAATA
1 CTTAATGATGTTACATTGTCAAATAATA
655895 CTTA
1 CTTA
655899 GTTTCATGCT
Statistics
Matches: 43, Mismatches: 15, Indels: 10
0.63 0.22 0.15
Matches are distributed among these distances:
28 17 0.40
29 7 0.16
30 7 0.16
31 12 0.28
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (28 bp):
CTTAATGATGTTACATTGTCAAATAATA
Found at i:655900 original size:59 final size:59
Alignment explanation
Indices: 655808--655925 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
655798 CGGTGAGATC
*
655808 CTTAATGATGTTACATTTTCAAATAATACTTAGTTTCATGCTAGAATTGTCTTTGAATT
1 CTTAATGATGTTACATTGTCAAATAATACTTAGTTTCATGCTAGAATTGTCTTTGAATT
655867 CTTAATGATGTTACATTGTCAAATAATACTTAGTTTCATGCTAGAATTGTCTTTGAATT
1 CTTAATGATGTTACATTGTCAAATAATACTTAGTTTCATGCTAGAATTGTCTTTGAATT
655926 TCATGCTATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.45
Consensus pattern (59 bp):
CTTAATGATGTTACATTGTCAAATAATACTTAGTTTCATGCTAGAATTGTCTTTGAATT
Found at i:655916 original size:31 final size:31
Alignment explanation
Indices: 655826--655917 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 31
655816 TGTTACATTT
655826 TCAAATAATACTTAGTTTCATGCTAGAATTG
1 TCAAATAATACTTAGTTTCATGCTAGAATTG
** * * * * *
655857 TC-TTTGAATTCTTA--ATGATGTTA-CATTG
1 TCAAAT-AATACTTAGTTTCATGCTAGAATTG
655885 TCAAATAATACTTAGTTTCATGCTAGAATTG
1 TCAAATAATACTTAGTTTCATGCTAGAATTG
655916 TC
1 TC
655918 TTTGAATTTC
Statistics
Matches: 42, Mismatches: 14, Indels: 10
0.64 0.21 0.15
Matches are distributed among these distances:
28 13 0.31
29 7 0.17
30 7 0.17
31 15 0.36
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (31 bp):
TCAAATAATACTTAGTTTCATGCTAGAATTG
Found at i:656763 original size:25 final size:25
Alignment explanation
Indices: 656729--656778 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
656719 GATTGGCATT
656729 CCAGCAATCTACTATCATTAAGTGA
1 CCAGCAATCTACTATCATTAAGTGA
656754 CCAGCAATCTACTATCATTAAGTGA
1 CCAGCAATCTACTATCATTAAGTGA
656779 AATAGCCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (25 bp):
CCAGCAATCTACTATCATTAAGTGA
Found at i:658760 original size:21 final size:20
Alignment explanation
Indices: 658717--658761 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
658707 TTTAATGGTT
* * *
658717 GATGATTGCCATAAAAGAAA
1 GATGATTGCAACAAAACAAA
658737 GATGATTGCAACAAGAACAAA
1 GATGATTGCAACAA-AACAAA
658758 GATG
1 GATG
658762 GTACAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.18
Consensus pattern (20 bp):
GATGATTGCAACAAAACAAA
Found at i:659537 original size:13 final size:13
Alignment explanation
Indices: 659519--659545 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
659509 TTCATATATG
659519 ACATGTGAATCCA
1 ACATGTGAATCCA
659532 ACATGTGAATCCA
1 ACATGTGAATCCA
659545 A
1 A
659546 ATTCCAGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (13 bp):
ACATGTGAATCCA
Found at i:659833 original size:13 final size:14
Alignment explanation
Indices: 659815--659844 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
659805 ACAATAAATA
659815 TATTTA-ATTTTTT
1 TATTTATATTTTTT
659828 TATTTATATTTTTT
1 TATTTATATTTTTT
659842 TAT
1 TAT
659845 ATATTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTTATATTTTTT
Found at i:661132 original size:2 final size:2
Alignment explanation
Indices: 661127--661166 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
661117 TATTTTTTTA
661127 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT GAT AT A- 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
661167 CAATTTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:672758 original size:17 final size:18
Alignment explanation
Indices: 672719--672758 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
672709 GCTAATTCAA
*
672719 TTGTTAACATATGTTCTC
1 TTGTTAACATAAGTTCTC
*
672737 TTGTTATCATAAGTTC-C
1 TTGTTAACATAAGTTCTC
672754 TTGTT
1 TTGTT
672759 TTTGTTATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53
Consensus pattern (18 bp):
TTGTTAACATAAGTTCTC
Found at i:673006 original size:80 final size:80
Alignment explanation
Indices: 672889--673036 Score: 224
Period size: 80 Copynumber: 1.9 Consensus size: 80
672879 ACTGGATTTA
* * * *
672889 CATGAGTTATCCATTTGAAAATTAAGTAACTTGAAAGAGTGCTACATAGGGGTTGGATTCCACTG
1 CATGAGTTATCCATTTGAAAATTAAGGAACTTGAAAGAGAGCTAAAGAGGGGTTGGATTCCACTG
672954 TTTTGATTTTCATGC
66 TTTTGATTTTCATGC
* * * *
672969 CATGAGTTATCCATTTGAAACTTATGGAACTTGAAAGAGAGGTAAAGAGTGGTTGGATTCCACTG
1 CATGAGTTATCCATTTGAAAATTAAGGAACTTGAAAGAGAGCTAAAGAGGGGTTGGATTCCACTG
673034 TTT
66 TTT
673037 GAAGTCACGT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 60 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (80 bp):
CATGAGTTATCCATTTGAAAATTAAGGAACTTGAAAGAGAGCTAAAGAGGGGTTGGATTCCACTG
TTTTGATTTTCATGC
Found at i:674783 original size:2 final size:2
Alignment explanation
Indices: 674776--674800 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
674766 TAGTATTTTC
674776 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
674801 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:674805 original size:2 final size:2
Alignment explanation
Indices: 674800--674831 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
674790 CTCTCTCTCT
674800 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
674832 TCTCTTTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:683564 original size:17 final size:17
Alignment explanation
Indices: 683542--683579 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
683532 TACAAATATA
683542 ATTACAT-ATTTATAAAT
1 ATTACATAATTTAT-AAT
683559 ATTACATAAATTTATAAT
1 ATTACAT-AATTTATAAT
683577 ATT
1 ATT
683580 TTAAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTACATAATTTATAAT
Found at i:683883 original size:21 final size:21
Alignment explanation
Indices: 683870--683978 Score: 72
Period size: 20 Copynumber: 5.4 Consensus size: 21
683860 ATATTATCAT
683870 TATAATAAAAAATAATTAAAA
1 TATAATAAAAAATAATTAAAA
683891 TATAAT-AAAAAT-A--AAAA
1 TATAATAAAAAATAATTAAAA
** *
683908 TATAATATTAAATACTTTAAAA
1 TATAATAAAAAATA-ATTAAAA
* * *
683930 T-TTATATAATATTAATTATAAA
1 TATAATA-AAAAATAATTA-AAA
683952 TAT-AT-AAAAAT-ATATAAAA
1 TATAATAAAAAATAAT-TAAAA
683971 TATAATAA
1 TATAATAA
683979 TATTTTAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 22
0.67 0.11 0.22
Matches are distributed among these distances:
17 10 0.15
18 4 0.06
19 9 0.14
20 14 0.21
21 14 0.21
22 14 0.21
23 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (21 bp):
TATAATAAAAAATAATTAAAA
Found at i:683914 original size:11 final size:11
Alignment explanation
Indices: 683870--683903 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
683860 ATATTATCAT
683870 TATAATAAAAA
1 TATAATAAAAA
*
683881 -ATAATTAAAA
1 TATAATAAAAA
683891 TATAATAAAAA
1 TATAATAAAAA
683902 TA
1 TA
683904 AAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TATAATAAAAA
Found at i:683975 original size:17 final size:17
Alignment explanation
Indices: 683886--684010 Score: 77
Period size: 17 Copynumber: 7.6 Consensus size: 17
683876 AAAAAATAAT
*
683886 TAAAATATAATAA-AAA
1 TAAAATATAATAATATA
683902 TAAAA-AT-ATAATAT-
1 TAAAATATAATAATATA
* *
683916 TAAATACTTTAA-AATTTA
1 TAAA-A-TATAATAATATA
*
683934 TATAATAT--TAAT-TA
1 TAAAATATAATAATATA
*
683948 TAAATATATAAAAATATA
1 TAAA-ATATAATAATATA
*
683966 TAAAATATAATAATATT
1 TAAAATATAATAATATA
* * *
683983 TTAAATATTATAATATT
1 TAAAATATAATAATATA
*
684000 TTAAATATAAT
1 TAAAATATAAT
684011 TATAATTTGA
Statistics
Matches: 86, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
14 13 0.15
15 11 0.13
16 7 0.08
17 45 0.52
18 10 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATATAATAATATA
Found at i:683978 original size:10 final size:10
Alignment explanation
Indices: 683870--683978 Score: 61
Period size: 10 Copynumber: 10.8 Consensus size: 10
683860 ATATTATCAT
683870 TATAATAAAA
1 TATAATAAAA
*
683880 AATAATTAAAA
1 TATAA-TAAAA
683891 TATAATAAAA
1 TATAATAAAA
683901 -AT-A-AAAA
1 TATAATAAAA
683908 TATAATATTAAA
1 TATAATA--AAA
*
683920 TACT-TTAAAA
1 TA-TAATAAAA
* *
683930 T-TTATATAA
1 TATAATAAAA
683939 TATTAATTATAAA
1 TA-TAA-TA-AAA
683952 TAT-ATAAAA
1 TATAATAAAA
683961 -ATATATAAAA
1 TATA-ATAAAA
683971 TATAATAA
1 TATAATAA
683979 TATTTTAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 30
0.68 0.06 0.26
Matches are distributed among these distances:
7 4 0.05
8 6 0.08
9 11 0.14
10 26 0.34
11 15 0.19
12 10 0.13
13 5 0.06
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (10 bp):
TATAATAAAA
Found at i:686008 original size:9 final size:9
Alignment explanation
Indices: 685994--686025 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
685984 TATTTATTTT
685994 AATTTATTA
1 AATTTATTA
686003 AATTTATTA
1 AATTTATTA
686012 AATTTATTA
1 AATTTATTA
686021 AATTT
1 AATTT
686026 TATTTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTATTA
Found at i:688636 original size:11 final size:12
Alignment explanation
Indices: 688620--688653 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
688610 TTTACTAACT
688620 AATAAAAAAA-A
1 AATAAAAAAACA
688631 AATAAAAAAACA
1 AATAAAAAAACA
*
688643 AATTAAAAAAC
1 AATAAAAAAAC
688654 TTTAGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (12 bp):
AATAAAAAAACA
Found at i:692058 original size:2 final size:2
Alignment explanation
Indices: 692051--692091 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
692041 CAAGAGGAGG
*
692051 TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
692092 AATATATGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:698607 original size:23 final size:22
Alignment explanation
Indices: 698536--698622 Score: 60
Period size: 21 Copynumber: 4.0 Consensus size: 22
698526 TTGGTAGTCA
698536 ATTAATATAAAAT-TTTA--AAT
1 ATTAATA-AAAATATTTAGTAAT
* *
698556 AATTAATAATAAA-ATTTTGTATT
1 -ATTAATAA-AAATATTTAGTAAT
698579 ATTTAATAAGAAATATTTAGTAAT
1 A-TTAATAA-AAATATTTAGTAAT
698603 ATTAA-AAATAAT-TTTAGTAA
1 ATTAATAAA-AATATTTAGTAA
698623 AAAAATATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.02
21 22 0.41
22 6 0.11
23 16 0.30
24 9 0.17
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTAATAAAAATATTTAGTAAT
Found at i:698641 original size:12 final size:12
Alignment explanation
Indices: 698599--698641 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
698589 AAATATTTAG
698599 TAATATTAAAAA
1 TAATATTAAAAA
*
698611 TAATTTTAGTAAAA
1 TAATATTA--AAAA
*
698625 AAATATTAAAAA
1 TAATATTAAAAA
698637 TAATA
1 TAATA
698642 CTGCAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 15 0.60
14 10 0.40
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
TAATATTAAAAA
Found at i:703885 original size:21 final size:21
Alignment explanation
Indices: 703859--703901 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
703849 AATACTTTCT
703859 TGTCTAGTTTATCGTGTAGGC
1 TGTCTAGTTTATCGTGTAGGC
703880 TGTCTAGTTTATCGTGTAGGC
1 TGTCTAGTTTATCGTGTAGGC
703901 T
1 T
703902 CTTTAGCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.44
Consensus pattern (21 bp):
TGTCTAGTTTATCGTGTAGGC
Found at i:704404 original size:38 final size:37
Alignment explanation
Indices: 704330--704405 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
704320 TTCTTTACAG
* * * *
704330 ATTTTATCTTTTGGAGGATTGACGGTATACCGGCAAT
1 ATTTTATCTTTTGGAAGATTGACAGTAAACCAGCAAT
*
704367 ATTTTATCTTTTGGGAAGATTGTCAGTAAACCAGCAAT
1 ATTTTATCTTTT-GGAAGATTGACAGTAAACCAGCAAT
704405 A
1 A
704406 CAGATTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
37 12 0.36
38 21 0.64
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (37 bp):
ATTTTATCTTTTGGAAGATTGACAGTAAACCAGCAAT
Found at i:708116 original size:26 final size:26
Alignment explanation
Indices: 708066--708136 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 26
708056 CATATTTTTG
*
708066 ATAAGCATGCCA-TAGAGGTGTCAAA
1 ATAAGCATGCCATTAGAGGTGGCAAA
*
708091 ATAAGCATGCCATTGGAGGTGGCAAA
1 ATAAGCATGCCATTAGAGGTGGCAAA
* *
708117 ATTAGCATGCCATTAAAGGT
1 ATAAGCATGCCATTAGAGGT
708137 ATCTCTATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 12 0.30
26 28 0.70
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (26 bp):
ATAAGCATGCCATTAGAGGTGGCAAA
Found at i:708686 original size:6 final size:6
Alignment explanation
Indices: 708675--708710 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
708665 GATAAATAGA
708675 TAATTC TAATTC TAATTC TAATT- TAAATTC TAATTC
1 TAATTC TAATTC TAATTC TAATTC T-AATTC TAATTC
708711 CATAATGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 1 0.04
6 26 0.93
7 1 0.04
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATTC
Found at i:711976 original size:16 final size:16
Alignment explanation
Indices: 711951--711981 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
711941 CAAGATTACA
711951 TTTTAAAATTTAAATT
1 TTTTAAAATTTAAATT
*
711967 TTTTATAATTTAAAT
1 TTTTAAAATTTAAAT
711982 AAATATAATT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTAAAATTTAAATT
Found at i:712839 original size:9 final size:9
Alignment explanation
Indices: 712825--712914 Score: 81
Period size: 9 Copynumber: 9.0 Consensus size: 9
712815 AATATTAATT
712825 ATAAATTTA
1 ATAAATTTA
712834 ATAAATTTA
1 ATAAATTTA
*
712843 ATATAATTATTC
1 ATA-AA-T-TTA
712855 ATAAATTTA
1 ATAAATTTA
712864 ATAAATATTAA
1 ATAAAT-TT-A
712875 ATAAATATATTA
1 AT-AA-AT-TTA
712887 ATAAATTTA
1 ATAAATTTA
*
712896 ATAAATATTC
1 ATAAAT-TTA
712906 ATAAATTTA
1 ATAAATTTA
712915 GTAATCATAA
Statistics
Matches: 69, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
9 31 0.45
10 15 0.22
11 8 0.12
12 10 0.14
13 5 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (9 bp):
ATAAATTTA
Found at i:712867 original size:19 final size:19
Alignment explanation
Indices: 712825--712914 Score: 86
Period size: 19 Copynumber: 5.0 Consensus size: 19
712815 AATATTAATT
*
712825 ATAAAT-TTAATAAATTTA
1 ATAAATATTCATAAATTTA
712843 ATATAATTATTCATAAATTTA
1 ATA-AA-TATTCATAAATTTA
712864 ATAAATA-T--TAAA--TA
1 ATAAATATTCATAAATTTA
* *
712878 A-ATATATTAATAAATTTA
1 ATAAATATTCATAAATTTA
712896 ATAAATATTCATAAATTTA
1 ATAAATATTCATAAATTTA
712915 GTAATCATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
13 4 0.07
14 4 0.07
16 8 0.14
18 7 0.12
19 19 0.32
20 3 0.05
21 14 0.24
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAAATATTCATAAATTTA
Found at i:712896 original size:32 final size:31
Alignment explanation
Indices: 712792--712912 Score: 119
Period size: 32 Copynumber: 3.9 Consensus size: 31
712782 TAGTTAAATA
* *
712792 TAATAAATTTGTAATAAAAAATTAATAT--TAAT
1 TAATAAA-TT-TAAT-AAATATTAATATAATTAT
712824 T-ATAAATTTAATAAAT-TTAATATAATTAT
1 TAATAAATTTAATAAATATTAATATAATTAT
*
712853 TCATAAATTTAATAAATATTAA-ATAAATATAT
1 TAATAAATTTAATAAATATTAATAT-AAT-TAT
*
712885 TAATAAATTTAATAAATATTCATA-AATT
1 TAATAAATTTAATAAATATTAATATAATT
712913 TAGTAATCAT
Statistics
Matches: 78, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
27 7 0.09
28 3 0.04
29 8 0.10
30 20 0.26
31 15 0.19
32 24 0.31
33 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (31 bp):
TAATAAATTTAATAAATATTAATATAATTAT
Found at i:712900 original size:21 final size:23
Alignment explanation
Indices: 712861--712903 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
712851 ATTCATAAAT
712861 TTAATAAATATTAAATAAATATA
1 TTAATAAATATTAAATAAATATA
712884 TTAATAAAT-TT-AATAAATAT
1 TTAATAAATATTAAATAAATAT
712904 TCATAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAATAAATATTAAATAAATATA
Found at i:713825 original size:2 final size:2
Alignment explanation
Indices: 713812--713850 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
713802 TAAAACACTT
* *
713812 TA TA TC TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
713851 TCAAAAAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:719764 original size:2 final size:2
Alignment explanation
Indices: 719757--719801 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
719747 CCTAGCAAGA
719757 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
719799 AT A
1 AT A
719802 CATAGAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:719810 original size:2 final size:2
Alignment explanation
Indices: 719805--719832 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
719795 ATATATACAT
719805 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
719833 CATTGACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:722527 original size:13 final size:12
Alignment explanation
Indices: 722496--722532 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
722486 TATAAATTAA
*
722496 TTAAATTAAATT
1 TTAAATTTAATT
722508 TTAAATTTAATT
1 TTAAATTTAATT
722520 TTATAATTTAATT
1 TTA-AATTTAATT
722533 AAAATATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTAAATTTAATT
Found at i:723668 original size:3 final size:3
Alignment explanation
Indices: 723660--723688 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
723650 TTAAACACTG
723660 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
723689 CACTGAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:728016 original size:2 final size:2
Alignment explanation
Indices: 728009--728041 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
727999 TCCAGTACAA
728009 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 A
728042 AGTCTTGTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:730867 original size:2 final size:2
Alignment explanation
Indices: 730860--730905 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
730850 CATAAGAGTA
730860 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
730902 AT AT
1 AT AT
730906 GTTCCATATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:731032 original size:2 final size:2
Alignment explanation
Indices: 731027--731062 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
731017 AAAAAAATTT
731027 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
731063 ACTTAGAGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:731611 original size:26 final size:26
Alignment explanation
Indices: 731556--731616 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
731546 TTAAATAAGT
*
731556 ATTCATAATCTCTTCACTAAATAGCC
1 ATTCATAATCTCTTCACTAAATAGAC
* * * *
731582 ATTCTTAATCTCTTCACTGAATGGAG
1 ATTCATAATCTCTTCACTAAATAGAC
731608 ATTCA-AATC
1 ATTCATAATC
731617 CGATTATCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (26 bp):
ATTCATAATCTCTTCACTAAATAGAC
Done.