Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold144
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: 3311329
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
File 5 of 21
Found at i:545597 original size:23 final size:22
Alignment explanation
Indices: 545558--545615 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
545548 ATCATATTGA
*
545558 TTTTTATATT-ATGTTTTAATTCT
1 TTTTTAT-TTAATATTTTAATT-T
*
545581 TTTTTATTTAATATTTTTATTT
1 TTTTTATTTAATATTTTAATTT
545603 TTTGTATATTTAA
1 TTT-T-TATTTAA
545616 AATAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 6 0.20
23 17 0.57
24 7 0.23
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (22 bp):
TTTTTATTTAATATTTTAATTT
Found at i:546112 original size:13 final size:13
Alignment explanation
Indices: 546096--546138 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
546086 ATGCAAAGAA
*
546096 AAAATAAAAAAAT
1 AAAAGAAAAAAAT
546109 AAAAGAAAAAAAT
1 AAAAGAAAAAAAT
* * *
546122 AAGAGAGAGAAAT
1 AAAAGAAAAAAAT
546135 AAAA
1 AAAA
546139 AAATTAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (13 bp):
AAAAGAAAAAAAT
Found at i:546323 original size:693 final size:667
Alignment explanation
Indices: 545309--546683 Score: 1685
Period size: 693 Copynumber: 2.0 Consensus size: 667
545299 ATCTATACAT
* * * *
545309 ATATAAAATTAACTACATAAATAAATTTGATGTTGACACATGTTCTGTTTTCAGTTTTTTTTAAC
1 ATATAAAATTAACTACATAAATAAATCTGATGTTAACACATGTTCTGTTTTAAGTTTTTTTCAAC
*** * * * *
545374 AGTTATGAGAGAGAGAAAAATGGAAAGAAAAAAAGAAAAAAAAAGAAAAAGAGAGAAAAAAAATA
66 AACCATGAGAGAGAGAAAAATGCAAAGAAAAAAAAAAAAAAAAAGAAAAAAAAAGAAAAAAAAT-
* * ** *
545439 AAAAAAAATTAATATGTTTATATTTATATTTGTATTATTTTTTTATTATTTAAAGTATTATAAAT
130 AAAAAAAATTAAAATATTTATATTTATATTCATATTATTTTTTTATTATTTAAAATATTATAAAT
* * *
545504 TTATATAATATTGCACACATATATATTTATATATTTTTATATTGATCATATTGATTTTTATATTA
195 TTATATAATATTGCACACA-ATATATTTATACATTCTTATATTCATCATATTGATTTTTATATTA
* **
545569 TGTTTTAATTCTTTTTTATTTAATATTTTTATTTTTTGTATATTTAAAATAATATAAATTTATAT
259 TGTTTTAATTATTTTTTA-TTAATATTTTTATTTTTCATATATTTAAAATAATATAAATTTATAT
* *
545634 AAATTTTTACATATTAATTATTTGTATATGTATATTTTGACATGTTGA-TGTAATTAAAT-A-AT
323 AAATTTTTACATATTAATTATTTATATATGTATA--TTGACACG-TGAGTGTAATTAAATAATAT
* *
545696 ATTTAAAATGATAAATTCT-TAAGTTGATGTACT-ATCTATGTAAAATTCATA-CTCTATTCTAA
385 ATTTAAAATGATAAA-TCTGCAAGTTGATGTA-TGATCAATGTAAAATTCATACCT-TATTCTAA
*
545758 ATGTAAATTTAAATAAATAAATAAATATTATTTAATAAAATTTAATTTTTATTAAAAATAATTAA
447 ATATAAA-TT---TAAATAAATAAATATTATTTAATAAAATTTAATTTTTATTAAAAATAATTAA
* * *
545823 AAATATAAAAAATTAAAAATGTCATTATTTAATTTATTTTTAAATGATGTGTTTAAAATAATAAA
508 AAA-AT---AAA--AAAAAT-T-ATTAATTAATTTATTTTTAAATGATATATTTAAAATAATAAA
** *
545888 TTTTTGTATTAACTCACAAGATATTTAAATTTTACTTTTAATTTTAAATACAAACTTTAAATACA
565 TTTTTACATT-A-T------A-A-TTAAATTTTACTTTTAATTTTAAATACAAAATTTAAATACA
*
545953 TAATCATTATTTAATAAAATTTATTTTATAATTAAATTTTTATTAATA
620 TAATCATTATTTAATAAAACTTATTTTATAATTAAATTTTTATTAATA
* *
546001 ATATAAAATTAACTACATAAATAAATCTGATGTTAATACATG-TCTTGCTTTTAAGTTTTTTTCG
1 ATATAAAATTAACTACATAAATAAATCTGATGTTAACACATGTTC-TG-TTTTAAGTTTTTTTCA
* * *
546065 GCAACCATGAGGGATG-GAAAAATGCAAAGAAAAAATAAAAAAATAAAAGAAAAAAATAAGAGAG
64 ACAACCATGAGAGA-GAGAAAAATGCAAAGAAAAAA-AAAAAAA-AAAAGAAAAAAA-AAGA-AA
* * *
546129 AGAAAT-AAAAAAATTAAAATATTTATATTTATATTCATGTTA-TTTTTTATTGTTTAAAATATT
124 AAAAATAAAAAAAATTAAAATATTTATATTTATATTCATATTATTTTTTTATTATTTAAAATATT
* ** * *
546192 ATAAATTTGTATAATATTTTACAC-ATATATTTATACGTTCTTATATTCATGTCATATTTATTTT
189 ATAAATTTATATAATATTGCACACAATATATTTATACATTCTTATATTCA--TCATATTGATTTT
* *
546256 TATATTATGTTTTAATTATTTTTTA-TACATATTTTTATTTTTCATATATTTAAAGTAGTATAAA
252 TATATTATGTTTTAATTATTTTTTATTA-ATATTTTTATTTTTCATATATTTAAAATAATATAAA
* * * * *
546320 TTTATATAAATTTTTATATATTATTTATTTATTTATGTATATTGATACGTGAGTGTAATTGAATA
316 TTTATATAAATTTTTACATATTAATTATTTATATATGTATATTGACACGTGAGTGTAATTAAATA
* * * * *
546385 ATATATTTAAAATGATAGATCTGCATGTTTATGTATGATCAATTTAAAATTTATACCTTATTCTA
381 ATATATTTAAAATGATAAATCTGCAAGTTGATGTATGATCAATGTAAAATTCATACCTTATTCTA
**
546450 AATATGGATTTAAATAAATAAATATTATTTAATAAAATTTAATTTTTATTAAAAATAATTAAAAA
446 AATATAAATTTAAATAAATAAATATTATTTAATAAAATTTAATTTTTATTAAAAATAATTAAAAA
* *
546515 ATTAAAAAAATTATTAATTATTTTATTTTTAAATGATATATTTAAAATAATAAATTTTTACATTA
511 ATAAAAAAAATTATTAATTAATTTATTTTTAAATGATATATTTAAAATAATAAATTTTTACATTA
* * *
546580 TAATTAAATTTTATTTTTAATTTTAAATATAAAATTTAAATACATAATTATTATTTAATAAAACT
576 TAATTAAATTTTACTTTTAATTTTAAATACAAAATTTAAATACATAATCATTATTTAATAAAACT
546645 TATTTTATAATTAAATTTTTATTAATA
641 TATTTTATAATTAAATTTTTATTAATA
546672 ATAATTAAAATT
1 AT-A-TAAAATT
546684 TATAAAATAA
Statistics
Matches: 599, Mismatches: 66, Indels: 55
0.83 0.09 0.08
Matches are distributed among these distances:
671 86 0.14
672 2 0.00
673 8 0.01
679 1 0.00
680 1 0.00
681 46 0.08
682 1 0.00
683 6 0.01
685 2 0.00
688 2 0.00
689 55 0.09
690 3 0.01
691 18 0.03
692 71 0.12
693 161 0.27
694 85 0.14
695 42 0.07
696 3 0.01
697 6 0.01
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (667 bp):
ATATAAAATTAACTACATAAATAAATCTGATGTTAACACATGTTCTGTTTTAAGTTTTTTTCAAC
AACCATGAGAGAGAGAAAAATGCAAAGAAAAAAAAAAAAAAAAAGAAAAAAAAAGAAAAAAAATA
AAAAAAATTAAAATATTTATATTTATATTCATATTATTTTTTTATTATTTAAAATATTATAAATT
TATATAATATTGCACACAATATATTTATACATTCTTATATTCATCATATTGATTTTTATATTATG
TTTTAATTATTTTTTATTAATATTTTTATTTTTCATATATTTAAAATAATATAAATTTATATAAA
TTTTTACATATTAATTATTTATATATGTATATTGACACGTGAGTGTAATTAAATAATATATTTAA
AATGATAAATCTGCAAGTTGATGTATGATCAATGTAAAATTCATACCTTATTCTAAATATAAATT
TAAATAAATAAATATTATTTAATAAAATTTAATTTTTATTAAAAATAATTAAAAAATAAAAAAAA
TTATTAATTAATTTATTTTTAAATGATATATTTAAAATAATAAATTTTTACATTATAATTAAATT
TTACTTTTAATTTTAAATACAAAATTTAAATACATAATCATTATTTAATAAAACTTATTTTATAA
TTAAATTTTTATTAATA
Found at i:546692 original size:18 final size:21
Alignment explanation
Indices: 546651--546693 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
546641 AACTTATTTT
*
546651 ATAATTAAATTTTTATTAATA
1 ATAATTAAATATTTATTAATA
546672 ATAATTAAA-ATTTA-TAA-A
1 ATAATTAAATATTTATTAATA
546690 ATAA
1 ATAA
546694 AAAAAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 4 0.19
21 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATTAAATATTTATTAATA
Found at i:549707 original size:19 final size:20
Alignment explanation
Indices: 549673--549713 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
549663 AAAGTTAACA
*
549673 TAAAATTAAGAAAATATAAT
1 TAAAAATAAGAAAATATAAT
*
549693 TAAAAATAA-AAAATATTAT
1 TAAAAATAAGAAAATATAAT
549712 TA
1 TA
549714 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAAAATAAGAAAATATAAT
Found at i:550457 original size:21 final size:19
Alignment explanation
Indices: 550419--550457 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
550409 ATAAAAATAT
*
550419 TTTAATAATTATTTTAAAG
1 TTTAATAATTAATTTAAAG
550438 TTTATATAATTTAATTTAAA
1 TTTA-ATAA-TTAATTTAAA
550458 ATAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TTTAATAATTAATTTAAAG
Found at i:550475 original size:19 final size:20
Alignment explanation
Indices: 550451--550489 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
550441 ATATAATTTA
550451 ATTTAAAAT-AAATTTAAAT
1 ATTTAAAATGAAATTTAAAT
* *
550470 ATTTAACATGTAATTTAAAT
1 ATTTAAAATGAAATTTAAAT
550490 TAAATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
ATTTAAAATGAAATTTAAAT
Found at i:550774 original size:24 final size:22
Alignment explanation
Indices: 550716--550777 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
550706 ACAATTCATA
*
550716 TAAAAAATAAATAA-ATATTTTT
1 TAAAAATTAAA-AATATATTTTT
*
550738 TAAATATTAAAAATATATTTTT
1 TAAAAATTAAAAATATATTTTT
550760 TATAAAACTTTAAAAATA
1 TA-AAAA--TTAAAAATA
550778 AATATCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 19 0.58
23 3 0.09
25 9 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAAATTAAAAATATATTTTT
Found at i:552699 original size:17 final size:17
Alignment explanation
Indices: 552674--552707 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
552664 AGCGATGAAT
*
552674 ATAAGTATATATAATAA
1 ATAAATATATATAATAA
*
552691 ATAAATATATTTAATAA
1 ATAAATATATATAATAA
552708 TTTTTTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAAATATATATAATAA
Found at i:553778 original size:2 final size:2
Alignment explanation
Indices: 553771--553806 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
553761 ATTTGTAGTT
* *
553771 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
553807 CACACACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:555284 original size:3 final size:3
Alignment explanation
Indices: 555276--555305 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
555266 TAACACACTT
*
555276 ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
555306 TTATTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:555306 original size:6 final size:6
Alignment explanation
Indices: 555277--555340 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
555267 AACACACTTA
* * * * * *
555277 TAATAA TAATAA TAATAA TAATAT TAATAT TATTAT TATTAT TATTAT
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
* *
555325 TATTAT TATTAT TAAT
1 TAATAT TAATAT TAAT
555341 CAATATGATC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TAATAT
Found at i:555310 original size:3 final size:3
Alignment explanation
Indices: 555298--555338 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
555288 ATAATAATAA
*
555298 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
555339 ATCAATATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:555310 original size:9 final size:9
Alignment explanation
Indices: 555292--555340 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
555282 ATAATAATAA
*
555292 TAATAATAT
1 TAATATTAT
555301 TAATATTAT
1 TAATATTAT
*
555310 TATTATTAT
1 TAATATTAT
*
555319 TATTATTAT
1 TAATATTAT
*
555328 TATTATTAT
1 TAATATTAT
555337 TAAT
1 TAAT
555341 CAATATGATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TAATATTAT
Found at i:555809 original size:17 final size:19
Alignment explanation
Indices: 555780--555838 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 19
555770 AAACTGATCA
555780 AAATTTAAATTAAATTAATT
1 AAATTT-AATTAAATTAATT
555800 -AA-TTAATTAAATTTAATT
1 AAATTTAATTAAA-TTAATT
555818 AAAATTTTAATTAAATTAATT
1 -AAA-TTTAATTAAATTAATT
555839 TTAACTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.21
18 8 0.24
19 2 0.06
20 2 0.06
21 6 0.18
22 9 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTTAATTAAATTAATT
Found at i:556759 original size:2 final size:2
Alignment explanation
Indices: 556752--556794 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
556742 GTTTCAAGAT
556752 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
556794 T
1 T
556795 TTTGGTAGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:558395 original size:16 final size:18
Alignment explanation
Indices: 558374--558411 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
558364 CTTTCAGTTA
558374 TTTTGTTTT-TTTTTTT-
1 TTTTGTTTTGTTTTTTTC
558390 TTTTGTTTTGTTTTTTTC
1 TTTTGTTTTGTTTTTTTC
558408 TTTT
1 TTTT
558412 CTCTTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
17 7 0.35
18 4 0.20
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (18 bp):
TTTTGTTTTGTTTTTTTC
Found at i:562571 original size:32 final size:32
Alignment explanation
Indices: 562535--562612 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
562525 AATTTTCAAA
*
562535 TTATGAGTAATTATGTTAAATATTAATTAAAT
1 TTATGAATAATTATGTTAAATATTAATTAAAT
* * * *
562567 TTATGAATAATTTTGTTTAATATTGATTTAAT
1 TTATGAATAATTATGTTAAATATTAATTAAAT
*
562599 TTACGAATAATTAT
1 TTATGAATAATTAT
562613 ATCTAATTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.50
Consensus pattern (32 bp):
TTATGAATAATTATGTTAAATATTAATTAAAT
Found at i:575237 original size:41 final size:41
Alignment explanation
Indices: 575180--575261 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
575170 TAGCGGGTTG
575180 AGTTTAGATTCAACCCAACTCATCTTAATGCAATGTTCTTT
1 AGTTTAGATTCAACCCAACTCATCTTAATGCAATGTTCTTT
575221 AGTTTAGATTCAACCCAACTCATCTTAATGCAATGTTCTTT
1 AGTTTAGATTCAACCCAACTCATCTTAATGCAATGTTCTTT
575262 CACTAGTCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (41 bp):
AGTTTAGATTCAACCCAACTCATCTTAATGCAATGTTCTTT
Found at i:581419 original size:17 final size:17
Alignment explanation
Indices: 581372--581424 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
581362 GATGTAATTA
581372 ATTATTAATTTTTTTAT
1 ATTATTAATTTTTTTAT
* **
581389 ATTTTTAAAATTTTTAT
1 ATTATTAATTTTTTTAT
*
581406 ATTAATAATTTTTTTAT
1 ATTATTAATTTTTTTAT
581423 AT
1 AT
581425 ATATGAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATTAATTTTTTTAT
Found at i:581654 original size:9 final size:9
Alignment explanation
Indices: 581634--581676 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
581624 TTTATTAATT
581634 TAAATAAAAA
1 TAAAT-AAAA
581644 TAAATAAAA
1 TAAATAAAA
*
581653 TAAATAAAC
1 TAAATAAAA
581662 TAAAGATAAAA
1 T-AA-ATAAAA
581673 TAAA
1 TAAA
581677 AATATAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 14 0.48
10 9 0.31
11 6 0.21
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (9 bp):
TAAATAAAA
Found at i:582917 original size:20 final size:19
Alignment explanation
Indices: 582868--582917 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
582858 GTTTTTATTC
582868 AAAA-TATTTTTTAAAAAT
1 AAAATTATTTTTTAAAAAT
* *
582886 -ACATTATATTTTAAAATAT
1 AAAATTATTTTTTAAAA-AT
582905 AAAATTATTTTTT
1 AAAATTATTTTTT
582918 TTATAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 11 0.44
19 2 0.08
20 10 0.40
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATTATTTTTTAAAAAT
Found at i:583474 original size:17 final size:17
Alignment explanation
Indices: 583454--583488 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
583444 TAAAAAAATT
*
583454 TAAATATTAATATTATA
1 TAAAAATTAATATTATA
*
583471 TAAAAATTCATATTATA
1 TAAAAATTAATATTATA
583488 T
1 T
583489 CTAATATATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAAATTAATATTATA
Found at i:583607 original size:6 final size:7
Alignment explanation
Indices: 583588--583619 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
583578 TTAAGAAATT
583588 ATAAAAA
1 ATAAAAA
583595 ATAAAAA
1 ATAAAAA
583602 ATAAAAAA
1 AT-AAAAA
583610 ATAAAAA
1 ATAAAAA
583617 ATA
1 ATA
583620 CGAAGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
ATAAAAA
Found at i:583610 original size:15 final size:15
Alignment explanation
Indices: 583590--583619 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
583580 AAGAAATTAT
583590 AAAAAATAAAAAATA
1 AAAAAATAAAAAATA
583605 AAAAAATAAAAAATA
1 AAAAAATAAAAAATA
583620 CGAAGTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAATA
Found at i:584300 original size:28 final size:29
Alignment explanation
Indices: 584253--584310 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
584243 TTTCATAAAG
*
584253 TAAGGAAAAGAAAACAAAAAAAGTATGTA
1 TAAGAAAAAGAAAACAAAAAAAGTATGTA
*
584282 TAAGAAAAAGTAAAC-AAAAAAGTATGTA
1 TAAGAAAAAGAAAACAAAAAAAGTATGTA
584310 T
1 T
584311 TTATATCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.64, C:0.03, G:0.16, T:0.17
Consensus pattern (29 bp):
TAAGAAAAAGAAAACAAAAAAAGTATGTA
Found at i:588906 original size:2 final size:2
Alignment explanation
Indices: 588901--588937 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
588891 ACACACACAC
588901 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
588938 ACAAAGTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:592243 original size:21 final size:22
Alignment explanation
Indices: 592208--592249 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
592198 ATTAAATAAT
*
592208 TTTAATTTTATTATATGTAAAC
1 TTTAATTTTAATATATGTAAAC
*
592230 TTTAA-TTTAATATATTTAAA
1 TTTAATTTTAATATATGTAAA
592250 AGGCGTATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTAATTTTAATATATGTAAAC
Found at i:594489 original size:16 final size:15
Alignment explanation
Indices: 594469--594556 Score: 86
Period size: 16 Copynumber: 5.5 Consensus size: 15
594459 TTTTAATGAA
594469 TTAAATATAATTATT
1 TTAAATATAATTATT
* * *
594484 TGTAAATTTAATAAATA
1 T-TAAATATAAT-TATT
594501 TTAAATATAATTATT
1 TTAAATATAATTATT
* *
594516 TGTAAATTTAATTAATA
1 T-TAAATATAATT-ATT
594533 TTAAATATAATTATT
1 TTAAATATAATTATT
594548 TATAAATAT
1 T-TAAATAT
594557 GACAGTCATT
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
15 7 0.12
16 45 0.78
17 6 0.10
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TTAAATATAATTATT
Found at i:594569 original size:32 final size:32
Alignment explanation
Indices: 594468--594554 Score: 156
Period size: 32 Copynumber: 2.7 Consensus size: 32
594458 ATTTTAATGA
594468 ATTAAATATAATTATTTGTAAATTTAATAAAT
1 ATTAAATATAATTATTTGTAAATTTAATAAAT
*
594500 ATTAAATATAATTATTTGTAAATTTAATTAAT
1 ATTAAATATAATTATTTGTAAATTTAATAAAT
*
594532 ATTAAATATAATTATTTATAAAT
1 ATTAAATATAATTATTTGTAAAT
594555 ATGACAGTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (32 bp):
ATTAAATATAATTATTTGTAAATTTAATAAAT
Found at i:595081 original size:19 final size:20
Alignment explanation
Indices: 595037--595086 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
595027 AAACGTGATA
595037 TAAAATTATTTTAAAAAATT
1 TAAAATTATTTTAAAAAATT
* *
595057 TAAAATTTTTTTCAAAAATT
1 TAAAATTATTTTAAAAAATT
595077 TAAATATTAT
1 TAAA-ATTAT
595087 AATATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAAATTATTTTAAAAAATT
Found at i:596004 original size:3 final size:3
Alignment explanation
Indices: 595996--596020 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
595986 GAAAAAGTAG
595996 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
596021 TTTTTTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:596110 original size:3 final size:3
Alignment explanation
Indices: 596102--596133 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
596092 AAATTGTTTA
596102 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
596134 GATTTCATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:597298 original size:22 final size:20
Alignment explanation
Indices: 597258--597297 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
597248 ATACTTTATG
597258 GTCCATATATAAGAGAAAAA
1 GTCCATATATAAGAGAAAAA
597278 GTCCATATATAAGAGAAAAA
1 GTCCATATATAAGAGAAAAA
597298 ATTGAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.15, T:0.20
Consensus pattern (20 bp):
GTCCATATATAAGAGAAAAA
Found at i:598320 original size:17 final size:17
Alignment explanation
Indices: 598300--598343 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
598290 ACGATGTTGA
* *
598300 AATAAAATAGATGACCT
1 AATAAAACAGATAACCT
* *
598317 AATAGAACAGGTAACCT
1 AATAAAACAGATAACCT
598334 AATAAAACAG
1 AATAAAACAG
598344 GAAAGGGATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.18
Consensus pattern (17 bp):
AATAAAACAGATAACCT
Found at i:598582 original size:21 final size:22
Alignment explanation
Indices: 598544--598631 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 22
598534 TATTTTTTAT
* * *
598544 TATTTAAATTAATTTAAATTAA
1 TATTTATATTAATATAAATAAA
598566 TATTTATA-TAATATAAATAAA
1 TATTTATATTAATATAAATAAA
* *
598587 TTTTTAT-TTAAATTTAATTATAAAA
1 TATTTATATT-AATATAA--AT-AAA
598612 TATATATATATTAATATAAA
1 TAT-T-TATATTAATATAAA
598632 AATAATTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
21 18 0.35
22 13 0.25
24 2 0.04
25 6 0.12
26 1 0.02
27 9 0.18
28 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTATATTAATATAAATAAA
Found at i:598587 original size:35 final size:33
Alignment explanation
Indices: 598548--598631 Score: 78
Period size: 35 Copynumber: 2.4 Consensus size: 33
598538 TTTTATTATT
* *
598548 TAAATTAATTTAAATTAATATTTATATAATATAAA
1 TAAATTAATTTAAATT--TAATTATAAAATATAAA
* *
598583 TAAATTTTTATTTAAATTTAATTATAAAATATATA
1 TAAA--TTAATTTAAATTTAATTATAAAATATAAA
* *
598618 TATATTAATATAAA
1 TAAATTAATTTAAA
598632 AATAATTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
33 8 0.20
35 21 0.52
37 11 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
TAAATTAATTTAAATTTAATTATAAAATATAAA
Found at i:598643 original size:18 final size:21
Alignment explanation
Indices: 598599--598646 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 21
598589 TTTATTTAAA
598599 TTTAATTATAAAATATATATAT
1 TTTAA-TATAAAATATATATAT
*
598621 ATTAATATAAAA-ATA-AT-T
1 TTTAATATAAAATATATATAT
598639 TTTAATAT
1 TTTAATAT
598647 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 8 0.33
19 2 0.08
20 3 0.12
21 7 0.29
22 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAATATAAAATATATATAT
Found at i:599712 original size:21 final size:23
Alignment explanation
Indices: 599673--599723 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
599663 TTTATATTAA
* *
599673 ATAATATTTTTAT-TTTTTATTT
1 ATAATATTTTTATAATTTAATTT
599695 ATAAT-TTTTTATAATTTAATTT
1 ATAATATTTTTATAATTTAATTT
599717 A-AATATT
1 ATAATATT
599724 CAATTATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATAATATTTTTATAATTTAATTT
Found at i:599925 original size:18 final size:16
Alignment explanation
Indices: 599883--599930 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
599873 CACATAAACT
*
599883 TTAAAATATAATAAAA
1 TTAATATATAATAAAA
599899 TTAAT-TATAATAAAA
1 TTAATATATAATAAAA
599914 TTAAAATATATAATAAA
1 TT--AATATATAATAAA
599931 CCACTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 12 0.43
16 4 0.14
17 3 0.11
18 9 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAATATATAATAAAA
Found at i:599926 original size:15 final size:16
Alignment explanation
Indices: 599883--599923 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
599873 CACATAAACT
599883 TTAAAATATAATAAAA
1 TTAAAATATAATAAAA
*
599899 TT-AATTATAATAAAA
1 TTAAAATATAATAAAA
599914 TTAAAATATA
1 TTAAAATATA
599924 TAATAAACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAAATATAATAAAA
Found at i:602832 original size:30 final size:30
Alignment explanation
Indices: 602798--602921 Score: 103
Period size: 31 Copynumber: 4.2 Consensus size: 30
602788 GGCTTGATCA
*
602798 TATTTTAATTAACTCAAAAATTTATTTTAT
1 TATTTTAATTAACTCAAAAAATTATTTTAT
* * * * *
602828 TATTTAAAATAATATTAAAAAATTATTTCA-
1 TATTTTAATTAA-CTCAAAAAATTATTTTAT
602858 TA-TTT-ATTATACTCAAAAAATTATTTTAT
1 TATTTTAATTA-ACTCAAAAAATTATTTTAT
* * * *
602887 TATTTAAAATAATATTAAAAAATTATTTTA-
1 TATTTTAATTAA-CTCAAAAAATTATTTTAT
602917 TATTT
1 TATTT
602922 ATTATTTATA
Statistics
Matches: 73, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
28 17 0.23
29 5 0.07
30 20 0.27
31 31 0.42
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (30 bp):
TATTTTAATTAACTCAAAAAATTATTTTAT
Found at i:602872 original size:59 final size:59
Alignment explanation
Indices: 602795--602926 Score: 221
Period size: 59 Copynumber: 2.2 Consensus size: 59
602785 CTTGGCTTGA
*
602795 TCATATTTTAATTA-ACTCAAAAATTTATTTTATTATTTAAAATAATATTAAAAAATTATT
1 TCATA-TTT-ATTATACTCAAAAAATTATTTTATTATTTAAAATAATATTAAAAAATTATT
602855 TCATATTTATTATACTCAAAAAATTATTTTATTATTTAAAATAATATTAAAAAATTATT
1 TCATATTTATTATACTCAAAAAATTATTTTATTATTTAAAATAATATTAAAAAATTATT
*
602914 TTATATTTATTAT
1 TCATATTTATTAT
602927 TTATAATTAA
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
58 4 0.06
59 60 0.87
60 5 0.07
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (59 bp):
TCATATTTATTATACTCAAAAAATTATTTTATTATTTAAAATAATATTAAAAAATTATT
Found at i:602922 original size:30 final size:31
Alignment explanation
Indices: 602813--602922 Score: 140
Period size: 31 Copynumber: 3.7 Consensus size: 31
602803 TAATTAACTC
*
602813 AAAAATTTATTTTATTATTTAAAATAATATT
1 AAAAAATTATTTTATTATTTAAAATAATATT
* * *
602844 AAAAAATTATTTCA-TATTT---ATTATACTC
1 AAAAAATTATTTTATTATTTAAAATAATA-TT
602872 AAAAAATTATTTTATTATTTAAAATAATATT
1 AAAAAATTATTTTATTATTTAAAATAATATT
602903 AAAAAATTATTTTA-TATTTA
1 AAAAAATTATTTTATTATTTA
602923 TTATTTATAA
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.07
28 14 0.21
29 5 0.07
30 11 0.16
31 27 0.40
32 5 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (31 bp):
AAAAAATTATTTTATTATTTAAAATAATATT
Found at i:602953 original size:38 final size:36
Alignment explanation
Indices: 602878--602954 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 36
602868 ACTCAAAAAA
*
602878 TTATTTTATTATTTAAAATAATATTAAAAAATTATT
1 TTATTTTATTATTTAAAATAATATTAAAAAATAATT
*
602914 TTATATTTATTATTTATAATTAA-ATTTAAATAAA-AATT
1 TTAT-TTTATTATTTA-AAATAATA-TTAAA-AAATAATT
602952 TTA
1 TTA
602955 AATTATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
36 4 0.11
37 12 0.34
38 16 0.46
39 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (36 bp):
TTATTTTATTATTTAAAATAATATTAAAAAATAATT
Found at i:603262 original size:2 final size:2
Alignment explanation
Indices: 603255--603280 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
603245 TACAATTGTT
603255 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
603281 ATAGAATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:604844 original size:11 final size:11
Alignment explanation
Indices: 604740--604852 Score: 74
Period size: 11 Copynumber: 10.3 Consensus size: 11
604730 ATCAGACTCA
604740 ATAATATTAAAT
1 ATAATA-TAAAT
604752 ATAATATAATTAT
1 ATAATATAA--AT
*
604765 ATAATATAAAA
1 ATAATATAAAT
*
604776 ATAATATAAAA
1 ATAATATAAAT
604787 ATAAT-TAAAAT
1 ATAATAT-AAAT
*
604798 ATTATATAAAAT
1 ATAATAT-AAAT
* *
604810 ATGAT-TTAAT
1 ATAATATAAAT
**
604820 ACGA-A-AAA-
1 ATAATATAAAT
604828 ATAATATAAAT
1 ATAATATAAAT
*
604839 ATAATATGAAT
1 ATAATATAAAT
604850 ATA
1 ATA
604853 TTAATATTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 17
0.75 0.09 0.15
Matches are distributed among these distances:
8 2 0.02
9 3 0.04
10 10 0.12
11 41 0.49
12 16 0.19
13 11 0.13
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:604902 original size:31 final size:33
Alignment explanation
Indices: 604837--604906 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 33
604827 AATAATATAA
* * *
604837 ATATAATATGAATATATTAATATTTTAAAATTT
1 ATATAATATAAATATATTAACATATTAAAATTT
604870 ATATAATATAAAT-TATTAACATATT-AAATTT
1 ATATAATATAAATATATTAACATATTAAAATTT
604901 ATATAA
1 ATATAA
604907 AATATTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 12 0.35
32 10 0.29
33 12 0.35
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (33 bp):
ATATAATATAAATATATTAACATATTAAAATTT
Found at i:605130 original size:7 final size:7
Alignment explanation
Indices: 605108--605139 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
605098 TTTTATTTTA
605108 TTTTATT
1 TTTTATT
605115 TTGTTATT
1 TT-TTATT
605123 TTTTATT
1 TTTTATT
605130 TTTTATT
1 TTTTATT
605137 TTT
1 TTT
605140 ATTAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.84
Consensus pattern (7 bp):
TTTTATT
Found at i:605135 original size:14 final size:15
Alignment explanation
Indices: 605108--605139 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
605098 TTTTATTTTA
605108 TTTTATTTTGTTATT
1 TTTTATTTTGTTATT
605123 TTTTATTTT-TTATT
1 TTTTATTTTGTTATT
605137 TTT
1 TTT
605140 ATTAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.84
Consensus pattern (15 bp):
TTTTATTTTGTTATT
Found at i:605139 original size:13 final size:13
Alignment explanation
Indices: 605103--605142 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
605093 ATGTTTTTTA
605103 TTTTA-TTTTATT
1 TTTTATTTTTATT
605115 TTGTTATTTTTTATT
1 TT-TTA-TTTTTATT
605130 TTTTATTTTTATT
1 TTTTATTTTTATT
605143 AGAAAAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 11 0.44
14 3 0.12
15 9 0.36
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:607285 original size:11 final size:10
Alignment explanation
Indices: 607254--607284 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
607244 TTTAATTAAA
607254 AAATATTTTT
1 AAATATTTTT
607264 ATAATATTTTT
1 A-AATATTTTT
607275 AAATATTTTT
1 AAATATTTTT
607285 TCACCAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
AAATATTTTT
Found at i:611864 original size:16 final size:16
Alignment explanation
Indices: 611845--611875 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
611835 AACTAAGTCT
611845 AAACCCACAAAAAAAA
1 AAACCCACAAAAAAAA
*
611861 AAACCCGCAAAAAAA
1 AAACCCACAAAAAAA
611876 GACGTATATC
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:0.71, C:0.26, G:0.03, T:0.00
Consensus pattern (16 bp):
AAACCCACAAAAAAAA
Found at i:612178 original size:3 final size:3
Alignment explanation
Indices: 612170--612198 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
612160 AAAAATAAAA
612170 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
612199 AGAAAGAAAC
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:612413 original size:2 final size:2
Alignment explanation
Indices: 612402--612442 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
612392 TCTCCCCTTT
*
612402 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
612443 ACAGCTATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:613278 original size:42 final size:41
Alignment explanation
Indices: 613197--613279 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 41
613187 AATATATTAT
613197 ATTTAAATTTAAATTTGATAAAATTTTATGAGGTATTTAAAA
1 ATTTAAATTTAAATTTGATAAAATTTTATGA-GTATTTAAAA
* *
613239 ATTTAAATTTAGATTTAGATTTAAAA-TTTATGA-TTTTTAAA
1 ATTTAAATTTAAATTT-GA--TAAAATTTTATGAGTATTTAAA
613280 TTCATAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
42 22 0.61
43 2 0.06
44 7 0.19
45 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.48
Consensus pattern (41 bp):
ATTTAAATTTAAATTTGATAAAATTTTATGAGTATTTAAAA
Found at i:614834 original size:24 final size:24
Alignment explanation
Indices: 614807--614853 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
614797 TATAACAAAA
614807 TTAATA-TTAATTAATTTAAATAAT
1 TTAATACTT-ATTAATTTAAATAAT
**
614831 TTAATACTTATTTTTTTAAATAA
1 TTAATACTTATTAATTTAAATAA
614854 GATCTTCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAATACTTATTAATTTAAATAAT
Found at i:615217 original size:28 final size:28
Alignment explanation
Indices: 615177--615249 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
615167 TTAACGAATT
615177 TTTA-TTTTT-TTATATTATTATATT-AA
1 TTTATTTTTTATTATATTATTAT-TTAAA
* *
615203 TTTATTTTTTATTATTTTAATATTTAAA
1 TTTATTTTTTATTATATTATTATTTAAA
* *
615231 TTTATGTTTAATTA-ATTAT
1 TTTATTTTTTATTATATTAT
615250 ATTATATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 4 0.11
27 10 0.26
28 24 0.63
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (28 bp):
TTTATTTTTTATTATATTATTATTTAAA
Found at i:615218 original size:26 final size:26
Alignment explanation
Indices: 615177--615253 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
615167 TTAACGAATT
615177 TTTATTTTTT-TATATTATTATATTAA
1 TTTATTTTTTAT-TATTATTATATTAA
615203 TTTATTTTTTATTATT-TTAATATTTAAA
1 TTTATTTTTTATTATTATT-ATA-TT-AA
* *
615231 TTTATGTTTAATTA--ATTATATTA
1 TTTATTTTTTATTATTATTATATTA
615254 TATAAAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
24 1 0.02
25 4 0.09
26 20 0.45
27 5 0.11
28 14 0.32
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (26 bp):
TTTATTTTTTATTATTATTATATTAA
Found at i:615263 original size:16 final size:16
Alignment explanation
Indices: 615244--615294 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 16
615234 ATGTTTAATT
615244 AATTATATTATATAAA
1 AATTATATTATATAAA
*
615260 AATTAAATAATATAATAAA
1 AATT--ATATTAT-ATAAA
615279 AATATATATT-TATAAA
1 AAT-TATATTATATAAA
615295 GTTATAACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 9 0.31
17 1 0.03
18 10 0.34
19 8 0.28
20 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTATATTATATAAA
Found at i:618231 original size:164 final size:162
Alignment explanation
Indices: 618052--618561 Score: 629
Period size: 164 Copynumber: 3.1 Consensus size: 162
618042 AAATTCTTTT
* * *
618052 ATTTTCATTAGTTTTTGAATTTTTTTTAAAATTCTCTTTTTTTAAAAATACGAAGTTTTTTGCTC
1 ATTTTCATGAGTTTTTGAATTTTTTTTGAAATTCTCTTTTTTT-AAAATACGAAGTTTTCTGCTC
* *
618117 CGTGGATTTTTTCAAAAGGATTTTTCTTAGTTT-TAATTTTTAAAATTCATCAAACATCATTATT
65 CGTGGATTTTTTC-AAGGGATTTTTCTTGGTTTGTAATTTTTAAAATTCATCAAACATCATTATT
* * *
618181 TATTTCACATTAATTTAGTTTTAAAAAACAAACTC
129 TATTTCATATTAATTCAGTTTTAAAAAA-AAATTC
* * * *
618216 ATTTTCATAAGTTTTTGGATTTTTTCCATGAAATT-TCTATTGTTTTGAAATAC-AGAGTTTTCT
1 ATTTTCATGAGTTTTTGAATTTTTT--TTGAAATTCTCT-TT-TTTTAAAATACGA-AGTTTTCT
* * *
618279 GCTCTGTGGATTTTTTTCGAGGGGATTTTTCTTGGTTTGTAACTTTTAAAATTCATCAAACATCA
61 GCTCCGTGGA-TTTTTTC-AAGGGATTTTTCTTGGTTTGTAATTTTTAAAATTCATCAAACATCA
618344 TTATTTATTTCATATTAATTCAG-TTTAAAAAAAAATTC
124 TTATTTATTTCATATTAATTCAGTTTTAAAAAAAAATTC
* * * *
618382 ATTTTCATGAGTTTTTGAATTTTTTCTTTGAAATTCTTTTTTTTTCAAAATAGGTA-TTTTCTAC
1 ATTTTCATGAGTTTTTGAA-TTTTT-TTTGAAATTCTCTTTTTTT-AAAATACGAAGTTTTCTGC
* * * *
618446 TCCAT-AATTTTTATCGAGGAGATTTTTCTTGGTTTGAAATTTTTAAAATTCATCAAACATCATT
63 TCCGTGGATTTTT-TCAAGG-GATTTTTCTTGGTTTGTAATTTTTAAAATTCATCAAACATCATT
618510 ATTTATTTCATATTAATTCAGTTTT-AAAAAAAATTC
126 ATTTATTTCATATTAATTCAGTTTTAAAAAAAAATTC
618546 ATTTTCATGAGTTTTT
1 ATTTTCATGAGTTTTT
618562 TATTTTTCTC
Statistics
Matches: 301, Mismatches: 30, Indels: 30
0.83 0.08 0.08
Matches are distributed among these distances:
163 7 0.02
164 116 0.39
165 21 0.07
166 67 0.22
167 43 0.14
168 47 0.16
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.50
Consensus pattern (162 bp):
ATTTTCATGAGTTTTTGAATTTTTTTTGAAATTCTCTTTTTTTAAAATACGAAGTTTTCTGCTCC
GTGGATTTTTTCAAGGGATTTTTCTTGGTTTGTAATTTTTAAAATTCATCAAACATCATTATTTA
TTTCATATTAATTCAGTTTTAAAAAAAAATTC
Found at i:621633 original size:50 final size:50
Alignment explanation
Indices: 621540--621634 Score: 154
Period size: 50 Copynumber: 1.9 Consensus size: 50
621530 GCCTCCAGCA
* *
621540 GGGCATAAAAGTGAATAATAAAAACTTACGTGTTTCATAGGCTTCCAACG
1 GGGCATAAAAGTGAATAATAAAAACTTACGTATTTCACAGGCTTCCAACG
* *
621590 GGGCGTAAAAGTGAATAATAAAAACTTACGTATTTCACGGGCTTC
1 GGGCATAAAAGTGAATAATAAAAACTTACGTATTTCACAGGCTTC
621635 TATGGAGTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (50 bp):
GGGCATAAAAGTGAATAATAAAAACTTACGTATTTCACAGGCTTCCAACG
Found at i:632464 original size:17 final size:19
Alignment explanation
Indices: 632429--632466 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
632419 AAATCTAGTC
*
632429 AATACTGATAGTGTGAAAA
1 AATACTGATAGTGTAAAAA
632448 AATACT-AT-GTGTAAAAA
1 AATACTGATAGTGTAAAAA
632465 AA
1 AA
632467 AAATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 2 0.11
19 6 0.33
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (19 bp):
AATACTGATAGTGTAAAAA
Found at i:632554 original size:65 final size:66
Alignment explanation
Indices: 632460--632587 Score: 195
Period size: 65 Copynumber: 2.0 Consensus size: 66
632450 TACTATGTGT
*
632460 AAAAAAAAAATTAAAATGACAATGCTTGGATGAAAACCCAAAAGGACGTTCAGGTAAAAAAAAGT
1 AAAAAAAAAATTAAAATGACAATACTTGGATGAAAACCCAAAAGGACGTTCAGGTAAAAAAAAGT
632525 A
66 A
* * ** *
632526 AAAAAAAAAATT-TATTGACAATACTTGGATGAAAACCTGAAAGGGCGTTCAGGTAAAAAAAA
1 AAAAAAAAAATTAAAATGACAATACTTGGATGAAAACCCAAAAGGACGTTCAGGTAAAAAAAA
632588 ATCGATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
65 44 0.79
66 12 0.21
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.19
Consensus pattern (66 bp):
AAAAAAAAAATTAAAATGACAATACTTGGATGAAAACCCAAAAGGACGTTCAGGTAAAAAAAAGT
A
Found at i:633363 original size:77 final size:78
Alignment explanation
Indices: 633236--633404 Score: 223
Period size: 77 Copynumber: 2.2 Consensus size: 78
633226 AGCCCAACCG
* * * *
633236 CACATTCCTAATCATATCCTTCCTTCCCAAATACCAGATGATACTAGTGCATCCCAAGGCCAAA-
1 CACATTCCCAATCATATCCTTCCTTACCAAATACCAGATGATACTAGTGCATCACAAAGCCAAAG
633300 AGGGCACTTCCCA
66 AGGGCACTTCCCA
* * * ** * *
633313 CACATTCCCAATCATATCCTTCTTTATCAAATACTAGATGATGTTGGTGCATCATAAAGCCAAAG
1 CACATTCCCAATCATATCCTTCCTTACCAAATACCAGATGATACTAGTGCATCACAAAGCCAAAG
*
633378 GGGGCACTTCCCA
66 AGGGCACTTCCCA
633391 CACATTCCCAATCA
1 CACATTCCCAATCA
633405 CATCTCTCTT
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
77 53 0.67
78 26 0.33
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.25
Consensus pattern (78 bp):
CACATTCCCAATCATATCCTTCCTTACCAAATACCAGATGATACTAGTGCATCACAAAGCCAAAG
AGGGCACTTCCCA
Found at i:633460 original size:78 final size:77
Alignment explanation
Indices: 633236--633470 Score: 213
Period size: 78 Copynumber: 3.0 Consensus size: 77
633226 AGCCCAACCG
* * * * * * * * **
633236 CACATTCCTAATCATATCCTTCCTTCCCAAATACCAGATGATACT-AGTGCATCCCAAGGCCAAA
1 CACATTCCCAATCACATCCTTCTTTACCAAACACTAAATGATATTGA-TGCATCATAAGGCCAAA
*
633300 AGGGCACTTCCCA
65 GGGGCACTTCCCA
* * * * * * *
633313 CACATTCCCAATCATATCCTTCTTTATCAAATACTAGATGATGTTGGTGCATCATAAAGCCAAAG
1 CACATTCCCAATCACATCCTTCTTTACCAAACACTAAATGATATTGATGCATCATAAGGCCAAA-
633378 GGGGCACTTCCCA
65 GGGGCACTTCCCA
* * **
633391 CACATTCCCAATCACAT-CTCTCTTTCCCAAACACTAAATGGTATTGATGCATCATGTGGCCATA
1 CACATTCCCAATCACATCCT-TCTTTACCAAACACTAAATGATATTGATGCATCATAAGGCCA-A
*
633455 AGGGGCACATCCCA
64 AGGGGCACTTCCCA
633469 CA
1 CA
633471 GGCTCCTCGT
Statistics
Matches: 130, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
77 54 0.42
78 74 0.57
79 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.26
Consensus pattern (77 bp):
CACATTCCCAATCACATCCTTCTTTACCAAACACTAAATGATATTGATGCATCATAAGGCCAAAG
GGGCACTTCCCA
Found at i:634143 original size:43 final size:43
Alignment explanation
Indices: 633958--635165 Score: 812
Period size: 43 Copynumber: 28.5 Consensus size: 43
633948 TTCATTTTTA
* * *** * *
633958 TCTGCTCGTCGACTTAGACCTAAAAGACTTT-TTCATCATTCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* * *
634000 TCTGCCAGTCGGCTTAGACCCGAGAGA-TTT-TTTCATCAATCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTT-ATCAATCG
*
634042 TCTGCCCGTCGGCTTAGACCCGGGAGA-TTT-TTTCATCAATCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTT-ATCAATCG
* * *
634084 CCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTGTCAATCA
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* * * *
634127 TCTGCCCGTCGACTTAGACCCGAGAGACTTTCTTTATCAATTG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* ** * * * *
634170 TGTGCCCGTCAACTTAGACCCGGGAGA-ATT-TTCATCAATTG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* ** * ** *
634211 TTTGCCCGTCGGCTTAGA-CTCAAGAAACTTT-TCCATCAATCA
1 TCTGCCCGTCGGCTTAGACCT-GGGAGACTTTCTTTATCAATCG
* * **
634253 TCTGCCCATCGGCTTAGACCTGGGAGACTTCCTTTATCAATTA
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* * * * *
634296 TCTACCTGTCGACTTAGACCTGAGAGACTTCCTTTATCAATCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* ** * * *
634339 TCTGCCTGTCAACTTAGACCTGGGAGACTTCCTTTGTCAATTG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* * ** * *
634382 TCTACCCCTCGGCTTAGA-CTCGGGAGACTTT-TCCATCATTTG
1 TCTGCCCGTCGGCTTAGACCT-GGGAGACTTTCTTTATCAATCG
* * * * *
634424 TCTACCCGTTGGCTTAAACTTGGGAGACTTCCTTTATCAATCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* * * *
634467 TTTGCCCGTCAGCTTAGACCT-AGAGACTTCCTTTATCAATCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* * * *
634509 TCTGCTCGTCGGCTTAGACTTGGGAGACTTTTTTTATTAATCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* * * ** *
634552 TCTGCCCGTCAGCTTAAACCCGGGAGACTTT-TCCATCAATCA
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* * * *
634594 TCTGCCCGTCAGCTTAAACCTGGGAGACTTCCTTTATTAATCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* * *
634637 TCTGCTCGTCGGCTTAGACCCGGGAGAC-TTCTTTTTTCAATCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTC-TTTATCAATCG
* * * *
634680 TCTACTCATCGGCTTAGA-CTCGGGAGATTTTCTTTATCAATCG
1 TCTGCCCGTCGGCTTAGACCT-GGGAGACTTTCTTTATCAATCG
* * ** * * *
634723 TTTGCCCATCGATTTAGACCTGGAAGACTTCCTTTGTCAATCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* ** * * * *
634766 TTTGCTGGTCGGTTTAGACCCGGGAGACTTT-TCTATCAATGG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* * * * *
634808 TTTGCCCGTTGGCTTAGACCCGAGAGACTTTCTTTGTCAATCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* * * * * * *
634851 TCTACCCATAGACTTAGA-ATCGGGAGACTTCCTTTGTCAATCG
1 TCTGCCCGTCGGCTTAGACCT-GGGAGACTTTCTTTATCAATCG
*
634894 TCTGCCCGTCGGCTTAGACCCGGGAGACTTT-TTTATCAATCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
* ** * ** **
634936 TCTACTTGTCGGCTTAGACCCGAAAGACTTT-TCCAATCAATCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCT-TTATCAATCG
* * ** *
634979 TCTGCCCATCGGCTTAGA-CTCAGGAGACTTT-TCCATCATTCG
1 TCTGCCCGTCGGCTTAGACCT-GGGAGACTTTCTTTATCAATCG
* * *** * * * *
635021 TCTGCCCAT-GGCTCAGACCCAAGAGACTTCCTTTGTTAATCA
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
** * * * ** *
635063 TCCACTCGTCGG-TTCAAACCTAGGAGACTTT-TTTATCTTTTG
1 TCTGCCCGTCGGCTT-AGACCTGGGAGACTTTCTTTATCAATCG
* * * * * * *
635105 TCTACCCATCAGCTTAGACCCGGTAGAC-TT-TTCATCATTCG
1 TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
*
635146 TCTGCCCGTCGACTTAGACC
1 TCTGCCCGTCGGCTTAGACC
635166 CGAAAGATTT
Statistics
Matches: 920, Mismatches: 220, Indels: 53
0.77 0.18 0.04
Matches are distributed among these distances:
40 1 0.00
41 74 0.08
42 359 0.39
43 478 0.52
44 8 0.01
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.33
Consensus pattern (43 bp):
TCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTATCAATCG
Found at i:634190 original size:128 final size:127
Alignment explanation
Indices: 633997--634997 Score: 888
Period size: 128 Copynumber: 7.8 Consensus size: 127
633987 TTTTCATCAT
* * *
633997 TCGTCTGCCAGTCGGCTTAGACCCGAGAGA-TTTTTTCATCAATCGTCTGCCCGTCGGCTTAGAC
1 TCGTCTGCCCGTCGGCTTAGACCCGGGAGACTTTTTT-ATCAATCGTCTACCCGTCGGCTTAGAC
* *
634061 CCGGGAGATTTTTTCATCAATCGCCTGCCCGTCGGCTTAGACCTGGGAGACTTTCTTTGTCAA
65 CCGGGAGATTTTTTCATCAATCGTCTGCCCGTCGGCTTAGACCTGGGAGACTTCCTTTGTCAA
* * * * * * **
634124 TCATCTGCCCGTCGACTTAGACCCGAGAGACTTTCTTTATCAATTGTGTGCCCGTCAACTTAGAC
1 TCGTCTGCCCGTCGGCTTAGACCCGGGAGACTTT-TTTATCAATCGTCTACCCGTCGGCTTAGAC
* * * ** * **
634189 CCGGGAGA-ATTTTCATCAATTGTTTGCCCGTCGGCTTAGA-CTCAAGAAACTT--TTCCATCAA
65 CCGGGAGATTTTTTCATCAATCGTCTGCCCGTCGGCTTAGACCT-GGGAGACTTCCTT-TGTCAA
* * * * ** * *
634250 TCATCTGCCCATCGGCTTAGACCTGGGAGACTTCCTTTATCAATTATCTACCTGTCGACTTAGAC
1 TCGTCTGCCCGTCGGCTTAGACCCGGGAGACTT-TTTTATCAATCGTCTACCCGTCGGCTTAGAC
* * * * **
634315 CTGAGAGACTTCCTTT-ATCAATCGTCTGCCTGTCAACTTAGACCTGGGAGACTTCCTTTGTCAA
65 CCGGGAGA-TT-TTTTCATCAATCGTCTGCCCGTCGGCTTAGACCTGGGAGACTTCCTTTGTCAA
* * * * ** * * * * *
634379 TTGTCTACCCCTCGGCTTAGACTCGGGAGACTTTTCCATCATTTGTCTACCCGTTGGCTTAAACT
1 TCGTCTGCCCGTCGGCTTAGACCCGGGAGACTTTTTTATCAATCGTCTACCCGTCGGCTTAGACC
* * * * * *
634444 TGGGAGACTTCCTTT-ATCAATCGTTTGCCCGTCAGCTTAGACCT-AGAGACTTCCTTTATCAA
66 CGGGAGA-TT-TTTTCATCAATCGTCTGCCCGTCGGCTTAGACCTGGGAGACTTCCTTTGTCAA
* ** * * * *
634506 TCGTCTGCTCGTCGGCTTAGACTTGGGAGACTTTTTTTATTAATCGTCTGCCCGTCAGCTTAAAC
1 TCGTCTGCCCGTCGGCTTAGACCCGGGAGAC-TTTTTTATCAATCGTCTACCCGTCGGCTTAGAC
* * * * * * *
634571 CCGGGAGACTTTTCCATCAATCATCTGCCCGTCAGCTTAAACCTGGGAGACTTCCTTTATTAA
65 CCGGGAGATTTTTTCATCAATCGTCTGCCCGTCGGCTTAGACCTGGGAGACTTCCTTTGTCAA
* * * *
634634 TCGTCTGCTCGTCGGCTTAGACCCGGGAGACTTCTTTTTTCAATCGTCTACTCATCGGCTTAGAC
1 TCGTCTGCCCGTCGGCTTAGACCCGGGAGACTT-TTTTATCAATCGTCTACCCGTCGGCTTAGAC
* * * * ** *
634699 TCGGGAGATTTTCTTTATCAATCGTTTGCCCATCGATTTAGACCTGGAAGACTTCCTTTGTCAA
65 CCGGGAGATTTT-TTCATCAATCGTCTGCCCGTCGGCTTAGACCTGGGAGACTTCCTTTGTCAA
* ** * * * * * *
634763 TCGTTTGCTGGTCGGTTTAGACCCGGGAGACTTTTCTATCAATGGTTTGCCCGTTGGCTTAGACC
1 TCGTCTGCCCGTCGGCTTAGACCCGGGAGACTTTTTTATCAATCGTCTACCCGTCGGCTTAGACC
* * * * * * *
634828 CGAGAGACTTTCTTT-GTCAATCGTCTACCCATAGACTTAGA-ATCGGGAGACTTCCTTTGTCAA
66 CGGGAGA-TTT-TTTCATCAATCGTCTGCCCGTCGGCTTAGACCT-GGGAGACTTCCTTTGTCAA
**
634891 TCGTCTGCCCGTCGGCTTAGACCCGGGAGACTTTTTTATCAATCGTCTACTTGTCGGCTTAGACC
1 TCGTCTGCCCGTCGGCTTAGACCCGGGAGACTTTTTTATCAATCGTCTACCCGTCGGCTTAGACC
** * * *
634956 CGAAAGACTTTTCCAATCAATCGTCTGCCCATCGGCTTAGAC
66 CGGGAGATTTTTTC-ATCAATCGTCTGCCCGTCGGCTTAGAC
634998 TCAGGAGACT
Statistics
Matches: 706, Mismatches: 146, Indels: 42
0.79 0.16 0.05
Matches are distributed among these distances:
125 2 0.00
126 70 0.10
127 135 0.19
128 383 0.54
129 113 0.16
130 3 0.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (127 bp):
TCGTCTGCCCGTCGGCTTAGACCCGGGAGACTTTTTTATCAATCGTCTACCCGTCGGCTTAGACC
CGGGAGATTTTTTCATCAATCGTCTGCCCGTCGGCTTAGACCTGGGAGACTTCCTTTGTCAA
Found at i:634482 original size:85 final size:85
Alignment explanation
Indices: 633958--635054 Score: 797
Period size: 85 Copynumber: 12.9 Consensus size: 85
633948 TTCATTTTTA
* * ** * * * * * *
633958 TCTGCTCGTCGACTTAGACCTAAAAGACTTTTTCATCATTCGTCTGCCAGTCGGCTTAGACCCGA
1 TCTGCCCGTCGGCTTAGACCCGAGAGACTTTTCCATCAATCGTCTGCCCGTCGGCTTAGACCTGG
*
634023 GAGA-TT-TTTTCATCAATCG
66 GAGACTTCCTTT-ATCAATCG
* * * *
634042 TCTGCCCGTCGGCTTAGACCCGGGAGATTTTTTCATCAATCGCCTGCCCGTCGGCTTAGACCTGG
1 TCTGCCCGTCGGCTTAGACCCGAGAGACTTTTCCATCAATCGTCTGCCCGTCGGCTTAGACCTGG
* * *
634107 GAGACTTTCTTTGTCAATCA
66 GAGACTTCCTTTATCAATCG
* ** * * ** *
634127 TCTGCCCGTCGACTTAGACCCGAGAGACTTTCTTTATCAATTGTGTGCCCGTCAACTTAGACCCG
1 TCTGCCCGTCGGCTTAGACCCGAGAGACTTT-TCCATCAATCGTCTGCCCGTCGGCTTAGACCTG
* * *
634192 GGAGAATT--TTCATCAATTG
65 GGAGACTTCCTTTATCAATCG
* * * * * *
634211 TTTGCCCGTCGGCTTAGACTCAAGAAACTTTTCCATCAATCATCTGCCCATCGGCTTAGACCTGG
1 TCTGCCCGTCGGCTTAGACCCGAGAGACTTTTCCATCAATCGTCTGCCCGTCGGCTTAGACCTGG
**
634276 GAGACTTCCTTTATCAATTA
66 GAGACTTCCTTTATCAATCG
* * * * * * **
634296 TCTACCTGTCGACTTAGACCTGAGAGACTTCCTT-TATCAATCGTCTGCCTGTCAACTTAGACCT
1 TCTGCCCGTCGGCTTAGACCCGAGAGACTT--TTCCATCAATCGTCTGCCCGTCGGCTTAGACCT
* *
634360 GGGAGACTTCCTTTGTCAATTG
64 GGGAGACTTCCTTTATCAATCG
* * * * * * * * * *
634382 TCTACCCCTCGGCTTAGACTCGGGAGACTTTTCCATCATTTGTCTACCCGTTGGCTTAAACTTGG
1 TCTGCCCGTCGGCTTAGACCCGAGAGACTTTTCCATCAATCGTCTGCCCGTCGGCTTAGACCTGG
634447 GAGACTTCCTTTATCAATCG
66 GAGACTTCCTTTATCAATCG
* * * * * *
634467 TTTGCCCGTCAGCTTAGA-CCTAGAGACTTCCTT-TATCAATCGTCTGCTCGTCGGCTTAGACTT
1 TCTGCCCGTCGGCTTAGACCCGAGAGACTT--TTCCATCAATCGTCTGCCCGTCGGCTTAGACCT
** *
634530 GGGAGACTTTTTTTATTAATCG
64 GGGAGACTTCCTTTATCAATCG
* * * * * *
634552 TCTGCCCGTCAGCTTAAACCCGGGAGACTTTTCCATCAATCATCTGCCCGTCAGCTTAAACCTGG
1 TCTGCCCGTCGGCTTAGACCCGAGAGACTTTTCCATCAATCGTCTGCCCGTCGGCTTAGACCTGG
*
634617 GAGACTTCCTTTATTAATCG
66 GAGACTTCCTTTATCAATCG
* * *** * * *
634637 TCTGCTCGTCGGCTTAGACCCGGGAGACTTCTTTTTTCAATCGTCTACTCATCGGCTTAGA-CTC
1 TCTGCCCGTCGGCTTAGACCCGAGAGACTT-TTCCATCAATCGTCTGCCCGTCGGCTTAGACCT-
* *
634701 GGGAGATTTTCTTTATCAATCG
64 GGGAGACTTCCTTTATCAATCG
* * ** * ** * ** *
634723 TTTGCCCATCGATTTAGACCTG-GAAGACTTCCTT-TGTCAATCGTTTGCTGGTCGGTTTAGACC
1 TCTGCCCGTCGGCTTAGACCCGAG-AGACTT--TTCCATCAATCGTCTGCCCGTCGGCTTAGACC
* *
634786 CGGGAGACTT--TTCTATCAATGG
63 TGGGAGACTTCCTT-TATCAATCG
* * *** * * * * *
634808 TTTGCCCGTTGGCTTAGACCCGAGAGACTTTCTTTGTCAATCGTCTACCCATAGACTTAGA-ATC
1 TCTGCCCGTCGGCTTAGACCCGAGAGACTTT-TCCATCAATCGTCTGCCCGTCGGCTTAGACCT-
*
634872 GGGAGACTTCCTTTGTCAATCG
64 GGGAGACTTCCTTTATCAATCG
* ** * ** * *
634894 TCTGCCCGTCGGCTTAGACCCGGGAGACTTTTTTATCAATCGTCTACTTGTCGGCTTAGACCCGA
1 TCTGCCCGTCGGCTTAGACCCGAGAGACTTTTCCATCAATCGTCTGCCCGTCGGCTTAGACCTGG
* *
634959 AAGACTT--TTCCAATCAATCG
66 GAGACTTCCTT--TATCAATCG
* * * * * **
634979 TCTGCCCATCGGCTTAGACTC-AGGAGACTTTTCCATCATTCGTCTGCCCAT-GGCTCAGACCCA
1 TCTGCCCGTCGGCTTAGACCCGA-GAGACTTTTCCATCAATCGTCTGCCCGTCGGCTTAGACCTG
*
635042 AGAGACTTCCTTT
65 GGAGACTTCCTTT
635055 GTTAATCATC
Statistics
Matches: 797, Mismatches: 186, Indels: 60
0.76 0.18 0.06
Matches are distributed among these distances:
83 34 0.04
84 122 0.15
85 389 0.49
86 244 0.31
87 8 0.01
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (85 bp):
TCTGCCCGTCGGCTTAGACCCGAGAGACTTTTCCATCAATCGTCTGCCCGTCGGCTTAGACCTGG
GAGACTTCCTTTATCAATCG
Found at i:636589 original size:175 final size:173
Alignment explanation
Indices: 636146--636662 Score: 662
Period size: 175 Copynumber: 3.0 Consensus size: 173
636136 TATTCATTAG
* * ** * * * *
636146 TTTTTAAATTTTTTCCTTAAAATTCTCTTTTTTTCTGAAATACGGAGTTTTCTGCTCCGTAGATT
1 TTTTTGAATTTTTTCCTTGAAATTCTC-TTTTTT-TGAAATACAAAATTTTCTACTCCATAAATT
* *
636211 TTTTTGAAGGGATTTTTCTTAGTTT-TAATTTTTAAAATTCATCAAATATCATTATTTATTTCAT
64 TTTTTGAAGGGATTTTTCTCAGTTTGTAATTTTTAAAATTCATCAAACATCATTATTTATTTCAT
* *
636275 ATTAATTCAG-TTT-AAAAA-AAACTCTTTTTCATGA------G-
129 ATTAATTCAGTTTTAAAAAACAAATTCATTTTCATGAGCTTTTGA
* * * * *
636310 TTTTTGAATTTTTTTCTTGAAATTCTTTTTTTTTTAAATACAAAATTTTCTGCTCCGTAAATTTT
1 TTTTTGAATTTTTTCCTTGAAATTCTCTTTTTTTGAAATACAAAATTTTCTACTCCATAAATTTT
* * *
636375 TTTGAGGGGATTTTTCTTAGTTTGTAATTTTTAAAATTCATCAAACATCATTATTTATTTCATGT
66 TTTGAAGGGATTTTTCTCAGTTTGTAATTTTTAAAATTCATCAAACATCATTATTTATTTCATAT
*
636440 TAATTCAGTTTTAAAAAACAAATTCATTTTCATGAGTTTTTGAA
131 TAATTCAGTTTTAAAAAACAAATTCATTTTCATGAGCTTTTG-A
* ** *
636484 TTTTTGAATTTTTTCCTTGAAATTTCTCTTTTTTTGAAATACGATGTTTTGTACTCCAT-AATTT
1 TTTTTGAATTTTTTCCTTGAAA-TTCTCTTTTTTTGAAATACAAAATTTTCTACTCCATAAATTT
*
636548 TTTTCGAAGGGATTTTTCTCGGTTTGTAATTTTTAAAATTCATCAAACATCATTATTTATTTCAT
65 TTTT-GAAGGGATTTTTCTCAGTTTGTAATTTTTAAAATTCATCAAACATCATTATTTATTTCAT
*
636613 ATTAATTCAGTTTTAAAAAACAAATTCATTTTCATGGGCTTTTGA
129 ATTAATTCAGTTTTAAAAAACAAATTCATTTTCATGAGCTTTTGA
636658 TTTTT
1 TTTTT
636663 CTCCTCGAAA
Statistics
Matches: 310, Mismatches: 29, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
162 49 0.16
163 53 0.17
164 26 0.08
165 5 0.02
166 14 0.05
172 1 0.00
174 36 0.12
175 126 0.41
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.51
Consensus pattern (173 bp):
TTTTTGAATTTTTTCCTTGAAATTCTCTTTTTTTGAAATACAAAATTTTCTACTCCATAAATTTT
TTTGAAGGGATTTTTCTCAGTTTGTAATTTTTAAAATTCATCAAACATCATTATTTATTTCATAT
TAATTCAGTTTTAAAAAACAAATTCATTTTCATGAGCTTTTGA
Found at i:636803 original size:338 final size:334
Alignment explanation
Indices: 636146--636793 Score: 718
Period size: 338 Copynumber: 1.9 Consensus size: 334
636136 TATTCATTAG
* *
636146 TTTTTAAATTTTTTCCTTAAAATTCTCTTTTTTTCTGAAATACGGAGTTTTCTGCTCCGTAGATT
1 TTTTTAAATTTTTTCCTTAAAATTCTCTTTTTTTCTGAAATACGGAGTTTTCTACTCCATAGATT
* *
636211 TTTTTGAAGGGATTTTTCTTAGTTTTAATTTTTAAAATTCATCAAATATCATTATTTATTTCATA
66 TTTTTGAAGGGATTTTTCTCAGTTTTAATTTTTAAAATTCATCAAACATCATTATTTATTTCATA
* * * * *
636276 TTAATTCAGTTTAAAAAAAACTCTTTTTCATGAGTTTTTGAATTTTTTTCTTGAAATTCTTTTTT
131 TTAATTCAGTTTAAAAAAAACTCATTTTCATGAGCTTTTGAATTTTTTCCTCGAAATTCTCTTTT
*** * * **
636341 TTTTAAATACAAAATTTTCTGCTCCGTAAATTTTTTTGAGGGGATTTTTCTTAGTTTGTAATTTT
196 TCCAAAATACAAAATTTTCT-CTCCGTAAATTTTTTTGAGGAGATTTTTCTTAGTCTAAAATTTT
* * * ** **
636406 TAAAATTCATCAAACATCATTATTTATTTCATGTTAATTCAGTTTTAAAAAACAAATTCATTTTC
260 TAAAATACATCAAACATCATCATTGAACTCACATTAATTCAGTTTT---AAACAAATTCATTTTC
636471 ATGAGTTTTTGAA
322 ATGAGTTTTTGAA
* * *
636484 TTTTTGAATTTTTTCCTTGAAATT-TCTCTTTTTT-TGAAATAC-GATGTTTTGTACTCCATA-A
1 TTTTTAAATTTTTTCCTTAAAATTCTCT-TTTTTTCTGAAATACGGA-GTTTTCTACTCCATAGA
*
636545 TTTTTTTCGAAGGGATTTTTCTCGGTTTGTAATTTTTAAAATTCATCAAACATCATTATTTATTT
64 TTTTTTT-GAAGGGATTTTTCTCAGTTT-TAATTTTTAAAATTCATCAAACATCATTATTTATTT
* *
636610 CATATTAATTCAGTTTTAAAAAACAAATTCATTTTCATGGGCTTTTG-ATTTTTCTCCTCGAAAT
127 CATATTAATTCAG-TTT-AAAAA-AAACTCATTTTCATGAGCTTTTGAATTTTT-TCCTCGAAA-
* **** * *
636674 TTCTCTTTTTCCAAAATGCGGTGTTTT-TCATTTCGT-AATTTTTTTCGAGGAGA-TTTTCTTTG
187 TTCTCTTTTTCCAAAATACAAAATTTTCTC--TCCGTAAATTTTTTT-GAGGAGATTTTTC-TTA
* * ** *
636736 GTCTAAAATTTTTAAAATACATCTAATATTGTCATTGAACTCCCATTAATTCAGTTTT
248 GTCTAAAATTTTTAAAATACATCAAACATCATCATTGAACTCACATTAATTCAGTTTT
636794 GAGAAATTCA
Statistics
Matches: 256, Mismatches: 41, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
336 10 0.04
337 41 0.16
338 76 0.30
339 3 0.01
340 12 0.05
341 41 0.16
342 73 0.29
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (334 bp):
TTTTTAAATTTTTTCCTTAAAATTCTCTTTTTTTCTGAAATACGGAGTTTTCTACTCCATAGATT
TTTTTGAAGGGATTTTTCTCAGTTTTAATTTTTAAAATTCATCAAACATCATTATTTATTTCATA
TTAATTCAGTTTAAAAAAAACTCATTTTCATGAGCTTTTGAATTTTTTCCTCGAAATTCTCTTTT
TCCAAAATACAAAATTTTCTCTCCGTAAATTTTTTTGAGGAGATTTTTCTTAGTCTAAAATTTTT
AAAATACATCAAACATCATCATTGAACTCACATTAATTCAGTTTTAAACAAATTCATTTTCATGA
GTTTTTGAA
Found at i:637371 original size:22 final size:20
Alignment explanation
Indices: 637325--637362 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
637315 GGCTCCAGCT
637325 GAAAAGAGAGAAAAAAAAAA
1 GAAAAGAGAGAAAAAAAAAA
637345 GAAAAGAGA-AAGAAAAAA
1 GAAAAGAGAGAA-AAAAAA
637363 TAGGGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
GAAAAGAGAGAAAAAAAAAA
Found at i:638503 original size:128 final size:127
Alignment explanation
Indices: 638347--638576 Score: 372
Period size: 128 Copynumber: 1.8 Consensus size: 127
638337 CATTAATCGT
* *
638347 TTTTTAATCATTTATATTCTTACTGGTATCCATAGGGGTATAAAATATTTCAAAAACTTTTCATA
1 TTTTTAATCATTTATATTCTTACTGGTATCCATAGAGGTATAAAAGATTTCAAAAACTTTTCATA
*
638412 TCTTTTCGGGTATCCATTAAGGTAAGAAATGATTTTTTCAAAACACAAATAAATATCAATTA
66 TCTTTTCGAGTATCCATTAAGGTAAGAAATGATTTTTTCAAAACACAAATAAATATCAATTA
* * *
638474 TTTTTAAGTCTTTTATATTCTTA-TGGGTATCCGTAGAGGTATAAAAGATTTCAAAAACTTTTCG
1 TTTTTAA-TCATTTATATTCTTACT-GGTATCCATAGAGGTATAAAAGATTTCAAAAACTTTTCA
*
638538 TATCTTTTCGAGTATCCATTAAGGTACGAAATGATTTTT
64 TATCTTTTCGAGTATCCATTAAGGTAAGAAATGATTTTT
638577 AGAGATAATT
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
127 8 0.09
128 86 0.91
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (127 bp):
TTTTTAATCATTTATATTCTTACTGGTATCCATAGAGGTATAAAAGATTTCAAAAACTTTTCATA
TCTTTTCGAGTATCCATTAAGGTAAGAAATGATTTTTTCAAAACACAAATAAATATCAATTA
Found at i:648645 original size:52 final size:52
Alignment explanation
Indices: 648554--648668 Score: 126
Period size: 52 Copynumber: 2.2 Consensus size: 52
648544 AACAGGGCTG
* * *
648554 GAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGAGGTTA
1 GAGTATCCCCGATTATGAAAAATCGATGTTCTAAAAAATAAAACCGAGGTTA
* * ** *
648606 GAGTATCCCCGATTGTGAAAAATCCGATGCTT-T-AGAAATAAGGCCGGGGTTA
1 GAGTATCCCCGATTATGAAAAAT-CGATG-TTCTAAAAAATAAAACCGAGGTTA
648658 GAGTATCCCCG
1 GAGTATCCCCG
648669 TGAAAATAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
52 46 0.87
53 5 0.09
54 2 0.04
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.25
Consensus pattern (52 bp):
GAGTATCCCCGATTATGAAAAATCGATGTTCTAAAAAATAAAACCGAGGTTA
Found at i:648778 original size:132 final size:132
Alignment explanation
Indices: 648541--648958 Score: 543
Period size: 132 Copynumber: 3.2 Consensus size: 132
648531 TTTTGGAGAT
* * *
648541 AATAACAGGGCTGGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGAGG-TT
1 AATAACGGGGTTGGAGTATCCCCGATTATGGAAAATTGGTGTTCTAAAAAATAAAATCG-GGATT
* *
648605 AGAGTATCCCCGATTGTG-AAAAATCCGATGCTTTAGAAATAAGGCCGGGGTTAGAGTATCCCCG
65 AGAGTATCCCCGATTGTGAAAAAAT-TGATTCTTTAGAAATAAGGCCGGGGTTAGAGTATCCCCG
648669 TGAA
129 TGAA
*
648673 AATAACGGGGTTGGAGTATCCCCAATTATGGAAAATTGGTGTTCTAAAAAATAAAATCGGGATTA
1 AATAACGGGGTTGGAGTATCCCCGATTATGGAAAATTGGTGTTCTAAAAAATAAAATCGGGATTA
648738 GAGTATCCCCGATTGTGAAAAAATTGATTCTTTAGAAATAAGGCCGGGGTTAGAGTATCCCCGTG
66 GAGTATCCCCGATTGTGAAAAAATTGATTCTTTAGAAATAAGGCCGGGGTTAGAGTATCCCCGTG
648803 AA
131 AA
* *** *
648805 AATAACGGGGTTGGAGTATCCCCGATTGT-GAGAAATTGGTGTT-TTGGAACTAAAATC-GGAGT
1 AATAACGGGGTTGGAGTATCCCCGATTATGGA-AAATTGGTGTTCTAAAAAATAAAATCGGGA-T
* *** *
648867 TGGAGTATCCCCGA-T-T-AAAAAATTCG-TAT-TTTAGAAATAAAATCGGGGTTGGAGTATCCC
64 TAGAGTATCCCCGATTGTGAAAAAATT-GAT-TCTTTAGAAATAAGGCCGGGGTTAGAGTATCCC
648927 C-TCGAA
127 CGT-GAA
*
648933 AACAACGGGGTTGGAGTATCCCCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
648959 GAAAAATTGA
Statistics
Matches: 261, Mismatches: 18, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
127 1 0.00
128 65 0.25
129 3 0.01
130 4 0.02
131 28 0.11
132 154 0.59
133 6 0.02
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (132 bp):
AATAACGGGGTTGGAGTATCCCCGATTATGGAAAATTGGTGTTCTAAAAAATAAAATCGGGATTA
GAGTATCCCCGATTGTGAAAAAATTGATTCTTTAGAAATAAGGCCGGGGTTAGAGTATCCCCGTG
AA
Found at i:648912 original size:49 final size:51
Alignment explanation
Indices: 648814--648927 Score: 151
Period size: 49 Copynumber: 2.3 Consensus size: 51
648804 AAATAACGGG
* * * * * *
648814 GTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAACTAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAAAAAATTCGTATTTTAGAAATAAAATCGGA
*
648865 GTTGGAGTATCCCCGA-T-TAAAAAATTCGTATTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTGTAAAAAATTCGTATTTTAGAAATAAAATCGGA
648914 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
648928 TCGAAAACAA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 39 0.70
50 1 0.02
51 16 0.29
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTAAAAAATTCGTATTTTAGAAATAAAATCGGA
Found at i:651325 original size:20 final size:19
Alignment explanation
Indices: 651300--651373 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 19
651290 AAAATGCCTG
*
651300 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
651320 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
651340 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
651360 AATGTATCGATACA
1 AATGTATCGATACA
651374 TCTAGGTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:651430 original size:13 final size:13
Alignment explanation
Indices: 651412--651470 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
651402 ACAAAGATCG
651412 ATGTATCGATACA
1 ATGTATCGATACA
651425 ATGTATCGATAC-
1 ATGTATCGATACA
*
651437 A--T-T-GA-ATA
1 ATGTATCGATACA
651445 ATGTATCGATACA
1 ATGTATCGATACA
651458 ATGTATCGATACA
1 ATGTATCGATACA
651471 TTGAATAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
7 1 0.03
8 3 0.08
9 1 0.03
10 2 0.05
11 1 0.03
12 3 0.08
13 27 0.71
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:651434 original size:33 final size:33
Alignment explanation
Indices: 651392--651490 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
651382 AACTTCCTAG
*
651392 ATGTATCGATACAAAG-ATCGATGTATCGATACA
1 ATGTATCGATACAAAGAAT-AATGTATCGATACA
**
651425 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
**
651458 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
651491 TTTCCTTGGC
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
33 60 0.97
34 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.31
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:651449 original size:20 final size:20
Alignment explanation
Indices: 651424--651492 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
651414 GTATCGATAC
651424 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
651444 AATGTATCGATAC-------
1 AATGTATCGATACATTGAAT
651457 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
651477 AATGTATCGATACATT
1 AATGTATCGATACATT
651493 TCCTTGGCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 13 0.31
20 29 0.69
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAT
Found at i:651457 original size:53 final size:53
Alignment explanation
Indices: 651392--651492 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
651382 AACTTCCTAG
**
651392 ATGTATCGATACAAAG-ATCGATGTATCGATACAATGTATCGATACATTGAATA
1 ATGTATCGATACAAAGTATCGATACATCGA-ACAATGTATCGATACATTGAATA
* * *
651445 ATGTATCGATACAATGTATCGATACATTGAATAATGTATCGATACATT
1 ATGTATCGATACAAAGTATCGATACATCGAACAATGTATCGATACATT
651493 TCCTTGGCAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 32 0.76
54 10 0.24
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (53 bp):
ATGTATCGATACAAAGTATCGATACATCGAACAATGTATCGATACATTGAATA
Found at i:655979 original size:2 final size:2
Alignment explanation
Indices: 655972--656002 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
655962 AATCTCAATC
655972 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
656003 GCCAAGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:656309 original size:30 final size:31
Alignment explanation
Indices: 656214--656337 Score: 103
Period size: 31 Copynumber: 3.9 Consensus size: 31
656204 TTTTGATTTA
*
656214 TATAAAAATAAAT-TATTATTTTAAATAAAAAT
1 TATAAAATTAAATAT-TTA-TTTAAATAAAAAT
* * * * *
656246 TAATTTATATTAACA-AATTGTTTAAATATAAAT
1 T-A-TAAAATTAA-ATATTTATTTAAATAAAAAT
*
656279 TA-AAAATTAAA-ATTTTATTTTAATAAAAAT
1 TATAAAATTAAATA-TTTATTTAAATAAAAAT
656309 TATAAAATTAAATATTTATTTAAATAAAA
1 TATAAAATTAAATATTTATTTAAATAAAA
656338 TAAAAGTATG
Statistics
Matches: 72, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
29 2 0.03
30 21 0.29
31 23 0.32
32 3 0.04
33 14 0.19
34 8 0.11
35 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.43
Consensus pattern (31 bp):
TATAAAATTAAATATTTATTTAAATAAAAAT
Found at i:656338 original size:30 final size:29
Alignment explanation
Indices: 656266--656342 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 29
656256 TAACAAATTG
656266 TTTAAATATAAATTAAAAATTAAAATTTTA
1 TTTAAATA-AAATTAAAAATTAAAATTTTA
*
656296 TTTTAATAAAAATTATAAAATT-AAATATTTA
1 TTTAAAT-AAAATTA-AAAATTAAAAT-TTTA
656327 TTTAAATAAAA-TAAAA
1 TTTAAATAAAATTAAAA
656343 GTATGAAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 3 0.07
29 2 0.05
30 20 0.48
31 17 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TTTAAATAAAATTAAAAATTAAAATTTTA
Found at i:657785 original size:4 final size:4
Alignment explanation
Indices: 657778--657815 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
657768 TTAATTTATT
657778 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
657816 CTTGAATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:657908 original size:19 final size:18
Alignment explanation
Indices: 657884--657923 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
657874 TAGGGAAAAA
657884 AAAAAGGAAAACCAATTGT
1 AAAAA-GAAAACCAATTGT
657903 AAAAAGAAAACCAATTGT
1 AAAAAGAAAACCAATTGT
657921 AAA
1 AAA
657924 CAAGTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.15
Consensus pattern (18 bp):
AAAAAGAAAACCAATTGT
Found at i:661062 original size:2 final size:2
Alignment explanation
Indices: 661055--661086 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
661045 AGCGAGTGAG
661055 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
661087 CAAATGTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:664270 original size:2 final size:2
Alignment explanation
Indices: 664263--664303 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
664253 GCTGCAGCCA
664263 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
664304 TCAATGGCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:664660 original size:18 final size:18
Alignment explanation
Indices: 664617--664674 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
664607 TTTTATAATA
664617 AATTTATTTA-TAAA-TT
1 AATTTATTTATTAAATTT
*
664633 AAGTTATTTATTAAATTT
1 AATTTATTTATTAAATTT
* * *
664651 AATTTTTTTATTTATTTT
1 AATTTATTTATTAAATTT
664669 AATTTA
1 AATTTA
664675 AATTATTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 9 0.26
17 4 0.12
18 21 0.62
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
AATTTATTTATTAAATTT
Found at i:664683 original size:22 final size:21
Alignment explanation
Indices: 664627--664686 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
664617 AATTTATTTA
664627 TAAATTAAGTTATTTATTAAATT
1 TAAATT-A-TTATTTATTAAATT
* * *
664650 TAATTTTTTTATTTATTTTAATT
1 TAA-ATTATTATTTA-TTAAATT
664673 TAAATTATTATTTA
1 TAAATTATTATTTA
664687 ATAATAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
22 16 0.53
23 12 0.40
24 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TAAATTATTATTTATTAAATT
Found at i:664768 original size:19 final size:16
Alignment explanation
Indices: 664728--664778 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
664718 ATAATATTTG
*
664728 AAATTTTTTAATTATT
1 AAATTTTTTAATTATA
664744 AAATTTTTATATATATATA
1 AAATTTTT-TA-AT-TATA
*
664763 AAA-TTTTAAATTATA
1 AAATTTTTTAATTATA
664778 A
1 A
664779 TTTAATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 5 0.17
16 10 0.33
17 3 0.10
18 6 0.20
19 6 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATTTTTTAATTATA
Found at i:665076 original size:16 final size:17
Alignment explanation
Indices: 665057--665108 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
665047 ATTTTACTTA
665057 AATA-AAATTTTATATT
1 AATATAAATTTTATATT
*
665073 AATATTAA-TTTATATTT
1 AATATAAATTTTATA-TT
665090 AA-ATAAATTTTA-ATT
1 AATATAAATTTTATATT
665105 AATA
1 AATA
665109 ATTATATGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 4 0.13
16 16 0.53
17 10 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATAAATTTTATATT
Found at i:665964 original size:3 final size:3
Alignment explanation
Indices: 665956--665996 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
665946 CAAAAGAGTT
*
665956 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
665997 GTAGGAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:669359 original size:17 final size:18
Alignment explanation
Indices: 669308--669360 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 18
669298 ATTTTAATTT
*
669308 ATTATATTTATATTAAAA
1 ATTATATTTTTATTAAAA
* *
669326 ATTATATCATTTAATTAAAT
1 ATTATAT--TTTTATTAAAA
669346 A-TATATTTTTATTAA
1 ATTATATTTTTATTAA
669361 TTATTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 8 0.28
18 7 0.24
19 5 0.17
20 9 0.31
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATATTTTTATTAAAA
Found at i:669529 original size:13 final size:13
Alignment explanation
Indices: 669511--669535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
669501 TGCAACTCAA
669511 GAAAAAAAAAAAG
1 GAAAAAAAAAAAG
669524 GAAAAAAAAAAA
1 GAAAAAAAAAAA
669536 AACTATTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAAAG
Found at i:670245 original size:43 final size:44
Alignment explanation
Indices: 670163--670249 Score: 117
Period size: 43 Copynumber: 2.0 Consensus size: 44
670153 TAAAGTTGAT
* *
670163 TATTTATATAATAAATAATATTTTTATTTATATTTAATTATAAA
1 TATTAATATAATAAATAATATTTTAATTTATATTTAATTATAAA
670207 TATTAATATAA-AAATAAT-TTTTAATATTAT-TTTAAATTATAAA
1 TATTAATATAATAAATAATATTTTAAT-TTATATTT-AATTATAAA
670250 ATAAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
42 9 0.23
43 20 0.51
44 10 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (44 bp):
TATTAATATAATAAATAATATTTTAATTTATATTTAATTATAAA
Found at i:670505 original size:2 final size:2
Alignment explanation
Indices: 670498--670522 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
670488 TTAACCGTTG
670498 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 G
670523 TAAATATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:671424 original size:30 final size:32
Alignment explanation
Indices: 671390--671460 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
671380 TTTGAATTAC
* * *
671390 TTTTTAAA-AAAATTTATATT-AACATTTATA
1 TTTTTAAATAAAATTTAAATTAAAAATATATA
*
671420 TTTTTAAATTAAATTTAAATTAAAAATATATA
1 TTTTTAAATAAAATTTAAATTAAAAATATATA
671452 TTTATTAAA
1 TTT-TTAAA
671461 CGGTAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.24
31 10 0.29
32 11 0.32
33 5 0.15
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (32 bp):
TTTTTAAATAAAATTTAAATTAAAAATATATA
Found at i:678640 original size:12 final size:13
Alignment explanation
Indices: 678591--678664 Score: 50
Period size: 13 Copynumber: 5.9 Consensus size: 13
678581 TTTAGTATTA
*
678591 AAAAAATTAAA-TA
1 AAAAAA-TAAATTT
*
678604 AAAAAATTATATTT
1 AAAAAA-TAAATTT
678618 AAAAAATAAATTT
1 AAAAAATAAATTT
*
678631 AAACAA-AAA--T
1 AAAAAATAAATTT
* *
678641 ATAAAAT-TATTT
1 AAAAAATAAATTT
678653 AAAAAATAAATT
1 AAAAAATAAATT
678665 AAGCCTTGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
10 6 0.13
12 10 0.21
13 24 0.51
14 7 0.15
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAAATAAATTT
Found at i:678656 original size:18 final size:17
Alignment explanation
Indices: 678613--678662 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
678603 AAAAAAATTA
*
678613 TATTTAAAAAATAAATT
1 TATTTAAAAAATAAAAT
***
678630 TAAACAAAAATATAAAAT
1 TATTTAAAAA-ATAAAAT
678648 TATTTAAAAAATAAA
1 TATTTAAAAAATAAA
678663 TTAAGCCTTG
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
TATTTAAAAAATAAAAT
Found at i:678759 original size:24 final size:24
Alignment explanation
Indices: 678709--678768 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 24
678699 ACTCGATCTG
678709 TTTTTA-ATTATATAATATATTAA
1 TTTTTATATTATATAATATATTAA
678732 -TTTTATATT-TAT-ATATTATGTAA
1 TTTTTATATTATATAATA-TAT-TAA
678755 -TTTT-TATTATATAA
1 TTTTTATATTATATAA
678769 ATAAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
21 3 0.09
22 15 0.47
23 13 0.41
24 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTTATATTATATAATATATTAA
Found at i:679346 original size:27 final size:27
Alignment explanation
Indices: 679305--679376 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 27
679295 TTATTAAAAT
679305 ATAATAATATTTTTAAATTT-ATATT-TA
1 ATAATAATATTTTT--ATTTAATATTATA
679332 ATAAT-ATATATTTTATTTAATATTATA
1 ATAATAATAT-TTTTATTTAATATTATA
*
679359 ATAAAATAATAATTTTAT
1 AT--AATAATATTTTTAT
679377 CAATTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
25 4 0.11
26 9 0.24
27 13 0.34
29 9 0.24
30 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATAATAATATTTTTATTTAATATTATA
Found at i:679350 original size:19 final size:20
Alignment explanation
Indices: 679321--679358 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
679311 ATATTTTTAA
679321 ATTTATATTTAATAATATAT
1 ATTTATATTTAATAATATAT
*
679341 ATTT-TATTTAATATTATA
1 ATTTATATTTAATAATATA
679359 ATAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTATATTTAATAATATAT
Found at i:680392 original size:17 final size:18
Alignment explanation
Indices: 680367--680406 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
680357 TCTTGTGGGT
*
680367 AAAAGTTATTTT-TTAAA
1 AAAATTTATTTTGTTAAA
*
680384 AAAATTTATTTTGTTTAA
1 AAAATTTATTTTGTTAAA
680402 AAAAT
1 AAAAT
680407 AATAAGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
AAAATTTATTTTGTTAAA
Found at i:682348 original size:16 final size:16
Alignment explanation
Indices: 682324--682354 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
682314 TAAATAGATA
682324 AAAAATTTCTTAAATG
1 AAAAATTTCTTAAATG
*
682340 AAAATTTTCTTAAAT
1 AAAAATTTCTTAAAT
682355 ACTAACATGA
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:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
AAAAATTTCTTAAATG
Found at i:683420 original size:18 final size:18
Alignment explanation
Indices: 683399--683456 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
683389 AATAATTTTT
683399 ATTTTAAATTAAATTTAA
1 ATTTTAAATTAAATTTAA
*
683417 ATTTTAAAAATAATATTT-A
1 ATTTT-AAATTAA-ATTTAA
*
683436 A-TTTGAATTAAATTTTAA
1 ATTTTAAATTAAA-TTTAA
683454 ATT
1 ATT
683457 ATGAATTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
16 1 0.03
17 8 0.25
18 10 0.31
19 9 0.28
20 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTTTAAATTAAATTTAA
Found at i:684624 original size:4 final size:4
Alignment explanation
Indices: 684615--684642 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
684605 CTTGACCATA
684615 GGCT GGCT GGCT GGCT GGCT GGCT GGCT
1 GGCT GGCT GGCT GGCT GGCT GGCT GGCT
684643 TACACATTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.50, T:0.25
Consensus pattern (4 bp):
GGCT
Found at i:687583 original size:2 final size:2
Alignment explanation
Indices: 687576--687609 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
687566 AATTAAAATC
687576 AT AT AT AT AT CAT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
687610 TTGGGATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:687767 original size:31 final size:31
Alignment explanation
Indices: 687705--687769 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
687695 ACATAAGATT
* * ***
687705 AAAAATATTAAATTCATTAATAAATTTATGA
1 AAAAATATGAAACTCATTAATAAACCCATGA
687736 AAAAATATGAAACTCATTAATAAACCCATGA
1 AAAAATATGAAACTCATTAATAAACCCATGA
687767 AAA
1 AAA
687770 GTTGTTTCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.57, C:0.09, G:0.05, T:0.29
Consensus pattern (31 bp):
AAAAATATGAAACTCATTAATAAACCCATGA
Found at i:687889 original size:43 final size:41
Alignment explanation
Indices: 687834--687914 Score: 135
Period size: 43 Copynumber: 1.9 Consensus size: 41
687824 AACCATCAAC
687834 CAATAAGATAAGATAAGATGTATTTTGAACTAAAAATGAGA
1 CAATAAGATAAGATAAGATGTATTTTGAACTAAAAATGAGA
*
687875 CAATAATGAATAAGATAAGATGTATTTTGAATTAAAAATG
1 CAATAA-G-ATAAGATAAGATGTATTTTGAACTAAAAATG
687915 GAAACTAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
41 6 0.16
42 1 0.03
43 30 0.81
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.30
Consensus pattern (41 bp):
CAATAAGATAAGATAAGATGTATTTTGAACTAAAAATGAGA
Found at i:688282 original size:58 final size:55
Alignment explanation
Indices: 688175--688342 Score: 156
Period size: 58 Copynumber: 3.0 Consensus size: 55
688165 AAAAATCATC
** * * * * * *
688175 AAGATAAGATGCATGTTGAATCGAAGATTGAAACAAAAGATGAGGTAATGATTAAT
1 AAGATAAGATATATTTTGAATTGAA-AATGAAACTAAAGATGAGATAATGATCAAT
** *
688231 GTGATAAGATGTATTTTGAATTGCAAAAGTGGAAACTAAAGATGAGATAATGATCAAT
1 AAGATAAGATATATTTTGAATTG-AAAA-T-GAAACTAAAGATGAGATAATGATCAAT
* * * *
688289 AAGATAAGGTATATTTTGAATTGAAAATGAAAATCAAAGATGAAATGATGATCA
1 AAGATAAGATATATTTTGAATTGAAAATGAAACT-AAAGATGAGATAATGATCA
688343 GGTAATGGGA
Statistics
Matches: 92, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
55 5 0.05
56 37 0.40
57 7 0.08
58 43 0.47
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.27
Consensus pattern (55 bp):
AAGATAAGATATATTTTGAATTGAAAATGAAACTAAAGATGAGATAATGATCAAT
Found at i:688952 original size:56 final size:57
Alignment explanation
Indices: 688878--688990 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 57
688868 AAGCAATAAG
* * *
688878 ATAAGATAAAATGTATTTTGAATTGAAAATGAAAACT-AAAGATGAGATAATGATCA
1 ATAAGATAAAATGCATTTTGAATTGAAAATGAAAACTAAAAAATGAAATAATGATCA
* * *
688934 ATAAGATAAGATGCATTTTGAATTGAAAATGGAAATTAAAAAATGAAATAATGATCA
1 ATAAGATAAAATGCATTTTGAATTGAAAATGAAAACTAAAAAATGAAATAATGATCA
688991 GGTTAATGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
56 33 0.66
57 17 0.34
ACGTcount: A:0.52, C:0.04, G:0.16, T:0.28
Consensus pattern (57 bp):
ATAAGATAAAATGCATTTTGAATTGAAAATGAAAACTAAAAAATGAAATAATGATCA
Found at i:691384 original size:19 final size:20
Alignment explanation
Indices: 691362--691400 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
691352 AAAATTATTG
691362 TATAAA-GATATTTTTATAA
1 TATAAATGATATTTTTATAA
*
691381 TATAAATTTATATTTTTATA
1 TATAAA-TGATATTTTTATA
691401 TATTTTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TATAAATGATATTTTTATAA
Found at i:693475 original size:14 final size:15
Alignment explanation
Indices: 693456--693484 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
693446 AAACTATCTC
693456 TTTATT-TTTTAAAA
1 TTTATTATTTTAAAA
693470 TTTATTATTTTAAAA
1 TTTATTATTTTAAAA
693485 AGCAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATTATTTTAAAA
Found at i:697143 original size:20 final size:22
Alignment explanation
Indices: 697093--697147 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
697083 TTTTTTTATT
697093 TAAA-TTTAATTATAAAAATATA
1 TAAATTTTAA-TATAAAAATATA
697115 TAAATTTTAATATAAAAATA-A
1 TAAATTTTAATATAAAAATATA
*
697136 T-TATTTTAATAT
1 TAAATTTTAATAT
697148 TTTAGTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 10 0.32
21 2 0.06
22 14 0.45
23 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATTTTAATATAAAAATATA
Found at i:698608 original size:3 final size:3
Alignment explanation
Indices: 698600--698635 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
698590 TATCCACTCA
698600 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
698636 GAAATAAATA
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:700528 original size:14 final size:15
Alignment explanation
Indices: 700502--700536 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
700492 GCATACGAAG
700502 ATTTTAGTTTTTTTT
1 ATTTTAGTTTTTTTT
700517 ATTTTA-TTTTTTTT
1 ATTTTAGTTTTTTTT
700531 ATTTTA
1 ATTTTA
700537 ATTGAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (15 bp):
ATTTTAGTTTTTTTT
Found at i:703154 original size:71 final size:74
Alignment explanation
Indices: 703075--703226 Score: 229
Period size: 72 Copynumber: 2.1 Consensus size: 74
703065 TTTTTATTAT
* * * *
703075 TAATAAAATTTATCACA-TTTATAAATAAGAATTTTAATTTTATTAAAAGATTTTATTTAAA-AA
1 TAATAAAATTTATCACATTTTATAAATAAAAATTTTAATGTTATCAAAAGATTTTAGTTAAATAA
*
703138 -ATATTTTA
66 TATATTTAA
703146 TAATAAAATTTATCACATTTTATAAATAAAAATTTTAATGTTATCAAAAGATTTTAGTTAAATAA
1 TAATAAAATTTATCACATTTTATAAATAAAAATTTTAATGTTATCAAAAGATTTTAGTTAAATAA
*
703211 TTTATTTAA
66 TATATTTAA
703220 TAATAAA
1 TAATAAA
703227 TAAAAAAAGT
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 17 0.24
72 40 0.56
73 2 0.03
74 13 0.18
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (74 bp):
TAATAAAATTTATCACATTTTATAAATAAAAATTTTAATGTTATCAAAAGATTTTAGTTAAATAA
TATATTTAA
Found at i:713775 original size:16 final size:16
Alignment explanation
Indices: 713751--713804 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
713741 TGTAAAACCT
*
713751 TTAACTATTAATTTAA
1 TTAATTATTAATTTAA
*
713767 TTAATTATTAAATTAA
1 TTAATTATTAATTTAA
* *
713783 TCAATTTGATTAATTAAA
1 TTAA-TT-ATTAATTTAA
713801 TTAA
1 TTAA
713805 AAATTTTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
16 17 0.57
17 2 0.07
18 11 0.37
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (16 bp):
TTAATTATTAATTTAA
Found at i:713816 original size:22 final size:22
Alignment explanation
Indices: 713767--713817 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
713757 ATTAATTTAA
*
713767 TTAATT-ATTAAATTAATCAAT
1 TTAATTAATTAAATTAATAAAT
*
713788 TTGATTAATTAAATTAA-AAATT
1 TTAATTAATTAAATTAATAAA-T
713810 TTAATTAA
1 TTAATTAA
713818 ATATAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAATTAATTAAATTAATAAAT
Done.