Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold127
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: 4281254
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 3 of 26
Found at i:518411 original size:5 final size:5
Alignment explanation
Indices: 518401--518452 Score: 95
Period size: 5 Copynumber: 10.4 Consensus size: 5
518391 TTCGGAATCA
*
518401 ATTAT ATTAT ATTAT ATTAT TTTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
518451 AT
1 AT
518453 AGATTAATCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTAT
Found at i:519993 original size:16 final size:18
Alignment explanation
Indices: 519961--519994 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
519951 TATTATAATG
519961 AATATTAAATACATAAAA
1 AATATTAAATACATAAAA
519979 AATA-TAAAT-CATAAAA
1 AATATTAAATACATAAAA
519995 TAAAAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
AATATTAAATACATAAAA
Found at i:523285 original size:20 final size:21
Alignment explanation
Indices: 523250--523301 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
523240 TGTTTCCATA
*
523250 ATTTTATTATAATTAAT-ATAT-
1 ATTTTAATA-AATTAATAAT-TG
523271 ATTTTAATAAATTAATAATTG
1 ATTTTAATAAATTAATAATTG
523292 ATTTTAATAA
1 ATTTTAATAA
523302 TATAATTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTTAATAAATTAATAATTG
Found at i:528960 original size:2 final size:2
Alignment explanation
Indices: 528953--528977 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
528943 CAACAAGAAA
528953 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
528978 CAGTCTTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:529194 original size:2 final size:2
Alignment explanation
Indices: 529183--529212 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
529173 TGAAAATAAC
529183 AT AT -T 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 A
529213 AATTGATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:529769 original size:16 final size:18
Alignment explanation
Indices: 529750--529789 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
529740 TTTAAAATAA
529750 AAATATTATAAA-TT-TT
1 AAATATTATAAATTTATT
529766 AAAT-TT-TAAATTTATT
1 AAATATTATAAATTTATT
529782 AAATATTA
1 AAATATTA
529790 ATTAATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 4 0.20
15 4 0.20
16 10 0.50
17 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATATTATAAATTTATT
Found at i:531678 original size:30 final size:31
Alignment explanation
Indices: 531643--531701 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
531633 AGATTGTTTA
531643 ATATTTTAATTTTTA-AAGTTAATTTATATT
1 ATATTTTAATTTTTATAAGTTAATTTATATT
* * *
531673 ATATTTTTATTTTTATAATTTTATTTATA
1 ATATTTTAATTTTTATAAGTTAATTTATA
531702 AAATTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (31 bp):
ATATTTTAATTTTTATAAGTTAATTTATATT
Found at i:532554 original size:19 final size:19
Alignment explanation
Indices: 532530--532568 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
532520 TAATCCTACA
532530 TTTTTAATT-ATATTAAATT
1 TTTTTAATTAAT-TTAAATT
*
532549 TTTTTATTTAATTTAAATT
1 TTTTTAATTAATTTAAATT
532568 T
1 T
532569 AATTTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTAATTAATTTAAATT
Found at i:532887 original size:3 final size:3
Alignment explanation
Indices: 532879--532919 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
532869 TTTCAACCAA
532879 TAT TAT 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
532920 ATTTCGTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:533219 original size:20 final size:21
Alignment explanation
Indices: 533196--533240 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
533186 ATAAGTTTGG
* *
533196 TTTAGTT-TAAATTATTTTTA
1 TTTAGTTAAAAATAATTTTTA
533216 TTTAGTTAAAAATAATTTTTA
1 TTTAGTTAAAAATAATTTTTA
533237 TTTA
1 TTTA
533241 AATTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTAGTTAAAAATAATTTTTA
Found at i:534171 original size:2 final size:2
Alignment explanation
Indices: 534164--534201 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
534154 TTAGAATGTG
534164 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
534202 CATGTATGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:543860 original size:2 final size:2
Alignment explanation
Indices: 543853--543888 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
543843 AAATGTTAAA
543853 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
543889 CTTCTAATTA
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:545191 original size:5 final size:5
Alignment explanation
Indices: 545181--545205 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
545171 TCGTGGATTC
545181 GACTA GACTA GACTA GACTA GACTA
1 GACTA GACTA GACTA GACTA GACTA
545206 CAGGCATCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
GACTA
Found at i:545436 original size:18 final size:19
Alignment explanation
Indices: 545423--545459 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
545413 ATAAAATAAG
545423 ATATAA-TATAAAAATATA
1 ATATAAGTATAAAAATATA
545441 ATATAAGTATAAAAATATA
1 ATATAAGTATAAAAATATA
545460 TTAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
ATATAAGTATAAAAATATA
Found at i:545453 original size:19 final size:18
Alignment explanation
Indices: 545423--545564 Score: 76
Period size: 18 Copynumber: 7.7 Consensus size: 18
545413 ATAAAATAAG
545423 ATATAATATAAAAATATA
1 ATATAATATAAAAATATA
545441 ATATAAGTATAAAAATATA
1 ATATAA-TATAAAAATATA
* * * *
545460 TTAAAATTTATATAATATAA
1 ATATAATATA-AAAATAT-A
* *
545480 ATTATTATCATATCAAAAT-TT
1 A-TA-TA--ATATAAAAATATA
545501 ATATAA-ATATAAAATATA
1 ATATAATATA-AAAATATA
* * * *
545519 AT-TAAAATTATAATATT
1 ATATAATATAAAAATATA
* *
545536 ATAAAATAAAAAAATATA
1 ATATAATATAAAAATATA
545554 ATATAA-ATAAA
1 ATATAATATAAA
545565 TTAATTATTA
Statistics
Matches: 90, Mismatches: 23, Indels: 23
0.66 0.17 0.17
Matches are distributed among these distances:
16 2 0.02
17 21 0.23
18 28 0.31
19 24 0.27
20 3 0.03
21 3 0.03
22 2 0.02
23 4 0.04
24 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (18 bp):
ATATAATATAAAAATATA
Found at i:545478 original size:27 final size:27
Alignment explanation
Indices: 545441--545541 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 27
545431 TAAAAATATA
545441 ATATAAGTATAAAAATATATTAAAATTT
1 ATATAA-TATAAAAATATATTAAAATTT
*
545469 ATATAATATAAATTATTATCATATCAAAATTT
1 ATATAATATAAA--A--AT-ATATTAAAATTT
545501 ATATAA-ATATAAAATATAATTAAAA-TT
1 ATATAATATA-AAAATAT-ATTAAAATTT
*
545528 ATAATATTATAAAA
1 AT-ATAATATAAAA
545542 TAAAAAAATA
Statistics
Matches: 61, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
27 12 0.20
28 20 0.33
29 4 0.07
30 1 0.02
31 5 0.08
32 19 0.31
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (27 bp):
ATATAATATAAAAATATATTAAAATTT
Found at i:545514 original size:17 final size:17
Alignment explanation
Indices: 545461--545515 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
545451 AAAAATATAT
545461 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
*
545477 T-AAA-TTAT-TATCATA
1 TAAAATTTATATA-AATA
545492 TCAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
545510 TAAAAT
1 TAAAAT
545516 ATAATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 1 0.03
14 4 0.13
15 7 0.23
16 1 0.03
17 8 0.26
18 8 0.26
19 2 0.06
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:545565 original size:23 final size:23
Alignment explanation
Indices: 545501--545564 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
545491 ATCAAAATTT
545501 ATATAA-AT-ATAAAATATAATTAAA
1 ATATAATATAATAAAATA-AA--AAA
*
545525 ATTATAATATTATAAAATAAAAAA
1 A-TATAATATAATAAAATAAAAAA
545549 ATATAATATAAATAAA
1 ATATAATAT-AATAAA
545565 TTAATTATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
23 8 0.23
24 10 0.29
25 5 0.14
26 4 0.11
27 8 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATAATATAATAAAATAAAAAA
Found at i:546339 original size:24 final size:25
Alignment explanation
Indices: 546307--546370 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 25
546297 AAATGTATTG
* *
546307 TATTATATTTATTATATTAT-TTT-
1 TATTTTATTTAATATATTATGTTTA
* *
546330 TATGTTTATTAAATGTATTATGTTTA
1 TAT-TTTATTTAATATATTATGTTTA
*
546356 TATTTTATTTTATAT
1 TATTTTATTTAATAT
546371 GGTGCATAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
23 3 0.10
24 13 0.42
25 12 0.39
26 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (25 bp):
TATTTTATTTAATATATTATGTTTA
Found at i:546381 original size:38 final size:38
Alignment explanation
Indices: 546305--546381 Score: 86
Period size: 38 Copynumber: 2.0 Consensus size: 38
546295 ATAAATGTAT
**
546305 TGTATTATATTTATTATATTATTTTTATGTTTATTAAA
1 TGTATTATATTTATTATATTATTTTTATGTGCATTAAA
* *
546343 TGTATTATGTTTA-TATTTTATTTTATATGGTGCA-TAAA
1 TGTATTATATTTATTATATTATTTT-TAT-GTGCATTAAA
546381 T
1 T
546382 TACCAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
37 10 0.30
38 20 0.61
39 3 0.09
ACGTcount: A:0.30, C:0.01, G:0.09, T:0.60
Consensus pattern (38 bp):
TGTATTATATTTATTATATTATTTTTATGTGCATTAAA
Found at i:548684 original size:2 final size:2
Alignment explanation
Indices: 548677--548721 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
548667 GGAGTCGTAG
548677 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
548719 AT A
1 AT A
548722 AAATAGACAT
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:551449 original size:15 final size:17
Alignment explanation
Indices: 551419--551450 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
551409 CTTGAATTCC
551419 TTCACAGTCTCTTCTTT
1 TTCACAGTCTCTTCTTT
551436 TTCACAG-C-CTTCTTT
1 TTCACAGTCTCTTCTTT
551451 GATCCCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.12, C:0.31, G:0.06, T:0.50
Consensus pattern (17 bp):
TTCACAGTCTCTTCTTT
Found at i:555397 original size:24 final size:23
Alignment explanation
Indices: 555357--555425 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 23
555347 TTAAATAAAA
*
555357 ATATAATATATTATTAAATAGATT
1 ATATTATAT-TTATTAAATAGATT
**
555381 ATATTA-ATTATATTTAAATTTATT
1 ATATTATATT-TA-TTAAATAGATT
555405 ATATTATATTTATTAAATAGA
1 ATATTATATTTATTAAATAGA
555426 ATTTATTTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 1 0.03
23 11 0.30
24 22 0.59
25 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
ATATTATATTTATTAAATAGATT
Found at i:555581 original size:4 final size:4
Alignment explanation
Indices: 555574--555610 Score: 65
Period size: 4 Copynumber: 9.0 Consensus size: 4
555564 TGGGGCCTGC
555574 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CCTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT
555611 TTGGCCTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:556227 original size:22 final size:24
Alignment explanation
Indices: 556201--556299 Score: 77
Period size: 22 Copynumber: 4.3 Consensus size: 24
556191 TCTTTTTTTT
556201 ATTATTAT-TAAATATAAAT-TTA
1 ATTATTATATAAATATAAATATTA
* *
556223 ATTATTACTTATAAATAT-AATTTTC
1 ATTATTA--TATAAATATAAATATTA
* *
556248 ATAATT-TATAAA-ATAAATCTTA
1 ATTATTATATAAATATAAATATTA
556270 CA-TA-TATATAAATATAAATATTA
1 -ATTATTATATAAATATAAATATTA
*
556293 ATAATTA
1 ATTATTA
556300 ATGTCTTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
21 3 0.05
22 26 0.43
23 11 0.18
24 6 0.10
25 14 0.23
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTATTATATAAATATAAATATTA
Found at i:556228 original size:19 final size:19
Alignment explanation
Indices: 556204--556244 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
556194 TTTTTTTATT
*
556204 ATTATTAAATATAAATTTA
1 ATTATTAAATATAAATATA
**
556223 ATTATTACTTATAAATATA
1 ATTATTAAATATAAATATA
556242 ATT
1 ATT
556245 TTCATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTATTAAATATAAATATA
Found at i:556273 original size:23 final size:22
Alignment explanation
Indices: 556231--556298 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
556221 TAATTATTAC
*
556231 TTAT-AAATATAATTTTCATAAT
1 TTATAAAATA-AATTTACATAAT
556253 TTATAAAATAAATCTTACAT-AT
1 TTATAAAATAAAT-TTACATAAT
*
556275 ATATAAATATAAATATTA-ATAAT
1 TTATAAA-ATAAAT-TTACATAAT
556298 T
1 T
556299 AATGTCTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 17 0.45
23 21 0.55
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATAAAATAAATTTACATAAT
Found at i:556633 original size:26 final size:27
Alignment explanation
Indices: 556586--556637 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
556576 CGATTTATAT
*
556586 AATTATTTTAAAAATAATTAAATTTAA
1 AATTATTTTAAAAATAAATAAATTTAA
556613 AATT-TTTTAATAAA-AAATAAATTTA
1 AATTATTTTAA-AAATAAATAAATTTA
556638 TTATTTATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATTATTTTAAAAATAAATAAATTTAA
Found at i:556702 original size:21 final size:21
Alignment explanation
Indices: 556655--556710 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
556645 TGTAAAATAG
*
556655 TATAATTAAGTTTAAAATATAA
1 TATATTTAA-TTTAAAATATAA
*
556677 AATATTTAATTTAATAATA-AA
1 TATATTTAATTTAA-AATATAA
*
556698 TATATTTATTTTA
1 TATATTTAATTTA
556711 TGATCACATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TATATTTAATTTAAAATATAA
Found at i:556999 original size:16 final size:16
Alignment explanation
Indices: 556953--557003 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
556943 TGATATTTTA
*
556953 ATTATAAATATAATAAAT
1 ATTATAAATAT--TAATT
*
556971 ATTAT-TATAATTAATT
1 ATTATAAAT-ATTAATT
556987 ATTATAAATATTAATT
1 ATTATAAATATTAATT
557003 A
1 A
557004 AATTAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 17 0.61
17 4 0.14
18 7 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATAAATATTAATT
Found at i:557020 original size:25 final size:25
Alignment explanation
Indices: 556962--557020 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
556952 AATTATAAAT
*
556962 ATAATAAATATTATTATAATTAATT
1 ATAATAAATATTATTATAATTAATA
*
556987 ATTATAAATATTAATTA-AATTAATA
1 ATAATAAATATT-ATTATAATTAATA
*
557012 ATAAAAAAT
1 ATAATAAAT
557021 TGAAATCACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATAAATATTATTATAATTAATA
Found at i:558151 original size:23 final size:23
Alignment explanation
Indices: 558108--558152 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
558098 TATATTTCAC
*
558108 ATAATCAATACACATTACATTAT
1 ATAATCAATACACAGTACATTAT
*
558131 ATAAT-AATACATAGTATCATTA
1 ATAATCAATACACAGTA-CATTA
558153 GCTTTAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAATCAATACACAGTACATTAT
Found at i:563018 original size:21 final size:21
Alignment explanation
Indices: 562968--563043 Score: 59
Period size: 20 Copynumber: 3.7 Consensus size: 21
562958 TTTAATATGA
* *
562968 TATATTTTAAATACATAAATA-
1 TATATTTTTAATATA-AAATAT
*
562989 -ATATATTTAATATAAAATAT
1 TATATTTTTAATATAAAATAT
* *
563009 TATATTTTT-ATTTAAAATTT
1 TATATTTTTAATATAAAATAT
*
563029 TGATATGTTTAATAT
1 T-ATATTTTTAATAT
563044 TTTAAATTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.12
20 21 0.49
21 14 0.33
22 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (21 bp):
TATATTTTTAATATAAAATAT
Found at i:577366 original size:21 final size:20
Alignment explanation
Indices: 577346--577396 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
577336 ATAAATTTTA
577346 AATTATAAATTAA-TTAATTT
1 AATT-TAAATTAATTTAATTT
*
577366 AATTTAATTTAATTTAATTTT
1 AATTTAAATTAATTTAA-TTT
577387 AATTTAAATT
1 AATTTAAATT
577397 CATATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 8 0.30
21 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTAAATTAATTTAATTT
Found at i:577369 original size:5 final size:5
Alignment explanation
Indices: 577355--577393 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
577345 AAATTATAAA
577355 TTAA- TTAAT TTAAT TTAAT TTAAT TTAATT TTAAT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA-T TTAAT TTAA
577394 ATTCATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.12
5 24 0.73
6 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:577371 original size:26 final size:22
Alignment explanation
Indices: 577334--577396 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
577324 TAAAAATAAA
*
577334 AAATAAATTTTAAATTATAAA-TT
1 AAATTAATTTT-AATT-TAAATTT
577357 -AATTAA-TTTAATTT-AATTT
1 AAATTAATTTTAATTTAAATTT
*
577376 AATTTAATTTTAATTTAAATT
1 AAATTAATTTTAATTTAAATT
577397 CATATTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 2 0.06
19 3 0.09
20 9 0.26
21 11 0.32
22 9 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATTAATTTTAATTTAAATTT
Found at i:577377 original size:15 final size:16
Alignment explanation
Indices: 577355--577393 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
577345 AAATTATAAA
577355 TTAA-TTAATTTAA-T
1 TTAATTTAATTTAATT
577369 TTAATTTAATTTAATT
1 TTAATTTAATTTAATT
577385 TTAATTTAA
1 TTAATTTAA
577394 ATTCATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 4 0.17
15 9 0.39
16 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAATTTAATTTAATT
Found at i:577406 original size:21 final size:20
Alignment explanation
Indices: 577340--577407 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
577330 TAAAAAATAA
577340 ATTTTAAATTATAAATTA-ATT
1 ATTTT-AATT-TAAATTATATT
* *
577361 AATTTAATTTAATTTA-ATTT
1 ATTTTAATTTAAATTATA-TT
577381 AATTTTAATTTAAATTCATATT
1 -ATTTTAATTTAAATT-ATATT
577403 ATTTT
1 ATTTT
577408 TTATATCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.18
20 6 0.15
21 22 0.56
22 3 0.08
23 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTTAATTTAAATTATATT
Found at i:578118 original size:29 final size:27
Alignment explanation
Indices: 578082--578138 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
578072 TTAATATAAT
578082 TATTTATATATATTAATATTTAAAAATA
1 TATTTATATATA-TAATATTTAAAAATA
* *
578110 TATTATATATATATAGTATTTGAAAATA
1 TATT-TATATATATAATATTTAAAAATA
578138 T
1 T
578139 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
TATTTATATATATAATATTTAAAAATA
Found at i:593973 original size:171 final size:171
Alignment explanation
Indices: 593688--594029 Score: 684
Period size: 171 Copynumber: 2.0 Consensus size: 171
593678 GCCATGTCCT
593688 TATCTTTGCTTCTCAGTTCCATTAACTCTGACTTTTCTAATGTAAACCTTGATCTAAGTCTTGAT
1 TATCTTTGCTTCTCAGTTCCATTAACTCTGACTTTTCTAATGTAAACCTTGATCTAAGTCTTGAT
593753 CTTAACCGCCCTCTATTAAGACTAATACACCAGGTCTTGCTGATTATTTTTTTCTTAAACCAAGT
66 CTTAACCGCCCTCTATTAAGACTAATACACCAGGTCTTGCTGATTATTTTTTTCTTAAACCAAGT
593818 GGAAAAATTTTCCTTGAAGTATTTTCAACCCTATTTAATTC
131 GGAAAAATTTTCCTTGAAGTATTTTCAACCCTATTTAATTC
593859 TATCTTTGCTTCTCAGTTCCATTAACTCTGACTTTTCTAATGTAAACCTTGATCTAAGTCTTGAT
1 TATCTTTGCTTCTCAGTTCCATTAACTCTGACTTTTCTAATGTAAACCTTGATCTAAGTCTTGAT
593924 CTTAACCGCCCTCTATTAAGACTAATACACCAGGTCTTGCTGATTATTTTTTTCTTAAACCAAGT
66 CTTAACCGCCCTCTATTAAGACTAATACACCAGGTCTTGCTGATTATTTTTTTCTTAAACCAAGT
593989 GGAAAAATTTTCCTTGAAGTATTTTCAACCCTATTTAATTC
131 GGAAAAATTTTCCTTGAAGTATTTTCAACCCTATTTAATTC
594030 ACCACCATCT
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
171 171 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (171 bp):
TATCTTTGCTTCTCAGTTCCATTAACTCTGACTTTTCTAATGTAAACCTTGATCTAAGTCTTGAT
CTTAACCGCCCTCTATTAAGACTAATACACCAGGTCTTGCTGATTATTTTTTTCTTAAACCAAGT
GGAAAAATTTTCCTTGAAGTATTTTCAACCCTATTTAATTC
Found at i:594504 original size:13 final size:13
Alignment explanation
Indices: 594486--594510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
594476 CCTCCCTAAC
594486 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
594499 TCTTTTTTTTTT
1 TCTTTTTTTTTT
594511 GTGATGACTA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:596456 original size:25 final size:23
Alignment explanation
Indices: 596386--596458 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 23
596376 ATTAAAACTA
596386 TAAATATTAAAAT-TAATTAATTT
1 TAAATA-TAAAATATAATTAATTT
**
596409 TAAATATACGTATATAATTAATTT
1 TAAATATA-AAATATAATTAATTT
*
596433 ATCAAATATAAAATATAATGAATTT
1 -T-AAATATAAAATATAATTAATTT
596458 T
1 T
596459 TACGCAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
22 2 0.05
23 8 0.20
24 11 0.27
25 13 0.32
26 7 0.17
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (23 bp):
TAAATATAAAATATAATTAATTT
Found at i:596686 original size:3 final size:3
Alignment explanation
Indices: 596678--596711 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
596668 CAATTCAACA
*
596678 ATC ATC ATC AT- ATC ATC ATC GTC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
596712 TCTCGTGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:599565 original size:2 final size:2
Alignment explanation
Indices: 599515--599557 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
599505 AATTTCTCGT
599515 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
599557 T
1 T
599558 CTTATATACG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:601655 original size:2 final size:2
Alignment explanation
Indices: 601648--601688 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
601638 GTGGTGGAGG
601648 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
601689 TTTATCTTTC
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:604157 original size:6 final size:6
Alignment explanation
Indices: 604146--604213 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
604136 GAATAATTAA
*
604146 TATATT TATA-T TATATT TATATAT TTTA-T TATATT TATAATT T-TATT
1 TATATT TATATT TATATT TATAT-T TATATT TATATT TAT-ATT TATATT
**
604193 TA-AAA TAT-TT TATATT TATAT
1 TATATT TATATT TATATT TATAT
604214 AAATTTTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
5 19 0.39
6 22 0.45
7 8 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TATATT
Found at i:604168 original size:8 final size:8
Alignment explanation
Indices: 604157--604214 Score: 52
Period size: 7 Copynumber: 7.5 Consensus size: 8
604147 ATATTTATAT
604157 TATATTTA
1 TATATTTA
604165 TATATTTTA
1 TATA-TTTA
604174 TTATATTTA
1 -TATATTTA
604183 TA-ATTT-
1 TATATTTA
*
604189 TAT-TTAA
1 TATATTTA
*
604196 AATATTT-
1 TATATTTA
604203 TATATTTA
1 TATATTTA
604211 TATA
1 TATA
604215 AATTTTAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
6 4 0.10
7 12 0.30
8 12 0.30
9 8 0.20
10 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTTA
Found at i:604177 original size:18 final size:18
Alignment explanation
Indices: 604145--604245 Score: 83
Period size: 18 Copynumber: 5.9 Consensus size: 18
604135 TGAATAATTA
604145 ATATATTTATATTATATTT
1 ATATATTT-TATTATATTT
604164 ATATATTTTATTATATTT
1 ATATATTTTATTATATTT
604182 ATA-ATTTTATT-TA---
1 ATATATTTTATTATATTT
*
604195 AAATATTTTA-TAT-TTAT
1 ATATATTTTATTATATT-T
* * *
604212 ATAAATTTTAATATATTG
1 ATATATTTTATTATATTT
604230 ATA-ATTTTTATTATAT
1 ATATA-TTTTATTATAT
604246 AAATTATAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 19
0.74 0.05 0.21
Matches are distributed among these distances:
13 3 0.04
14 7 0.10
16 2 0.03
17 17 0.25
18 29 0.43
19 10 0.15
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
ATATATTTTATTATATTT
Found at i:604204 original size:31 final size:29
Alignment explanation
Indices: 604145--604221 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 29
604135 TGAATAATTA
* *
604145 ATATATTTAT-ATTATATTTATATATTTT
1 ATATATTTATAATTTTATTTAAATATTTT
604173 ATTATATTTATAATTTTATTTAAAATATTTT
1 A-TATATTTATAATTTTATTT-AAATATTTT
604204 ATAT-TTATATAAATTTTA
1 ATATATT-TAT-AATTTTA
604222 ATATATTGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 1 0.02
29 11 0.26
30 14 0.33
31 16 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
ATATATTTATAATTTTATTTAAATATTTT
Found at i:604263 original size:27 final size:28
Alignment explanation
Indices: 604193--604274 Score: 78
Period size: 32 Copynumber: 2.8 Consensus size: 28
604183 TAATTTTATT
* *
604193 TAAAATAT-TTTATATTTATATAAATTT
1 TAAAATATATTTTTATTTATATAAATTA
604220 TAATATATTGATAATTTTTA-TTATATAAATTA
1 TAA-A-A-T-AT-ATTTTTATTTATATAAATTA
604252 TAAAATATATTTTTTATTTATAT
1 TAAAATATA-TTTTTATTTATAT
604275 TATATTTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
27 4 0.09
28 9 0.20
29 8 0.18
30 2 0.04
31 3 0.07
32 14 0.31
33 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (28 bp):
TAAAATATATTTTTATTTATATAAATTA
Found at i:604276 original size:34 final size:32
Alignment explanation
Indices: 604201--604279 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 32
604191 TTTAAAATAT
*
604201 TTTATATTTATATAAATTTTAATATATTGATAA
1 TTTATA-TTATATAAATTTAAATATATTGATAA
* ** *
604234 TTTTTATTATATAAATTATAAAATATATTTTTTA
1 TTTATATTATATAAATT-T-AAATATATTGATAA
604268 TTTATATTATAT
1 TTTATATTATAT
604280 TTTTATACCT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 11 0.29
33 6 0.16
34 21 0.55
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (32 bp):
TTTATATTATATAAATTTAAATATATTGATAA
Found at i:608554 original size:5 final size:5
Alignment explanation
Indices: 608510--608582 Score: 55
Period size: 5 Copynumber: 15.0 Consensus size: 5
608500 AATATAATAC
* * *
608510 ATATT A-ATT ATATTT AAATT AT-TT ATATC GTATT -TATT ATATT ATTATT
1 ATATT ATATT ATA-TT ATATT ATATT ATATT ATATT ATATT ATATT A-TATT
* *
608559 ATATT TTATT -TAAT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
608583 TTTAATAATT
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
4 15 0.28
5 30 0.56
6 9 0.17
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:608568 original size:16 final size:16
Alignment explanation
Indices: 608540--608603 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
608530 ATTTATATCG
*
608540 TATT-TATTATATTAT
1 TATTATATTTTATTAT
608555 TATTATATTTTATTTAAT
1 TATTATATTTTA-TT-AT
*
608573 ATATTATATTTT-TAAT
1 -TATTATATTTTATTAT
*
608589 AATTAATATTTTATT
1 TATT-ATATTTTATT
608604 TATCTTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
15 7 0.18
16 15 0.38
17 4 0.10
18 2 0.05
19 11 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTATATTTTATTAT
Found at i:608579 original size:19 final size:19
Alignment explanation
Indices: 608555--608605 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
608545 ATTATATTAT
608555 TATTATATTTTATTTAATA
1 TATTATATTTTATTTAATA
608574 TATTATA--TT-TTTAATA
1 TATTATATTTTATTTAATA
608590 -ATTAATATTTTATTTA
1 TATT-ATATTTTATTTA
608606 TCTTTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 3 0.11
16 10 0.36
17 2 0.07
18 2 0.07
19 11 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTATATTTTATTTAATA
Found at i:609388 original size:18 final size:19
Alignment explanation
Indices: 609365--609404 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
609355 TGATTTAGTG
609365 AATAATAT-TTTTTATTAA
1 AATAATATATTTTTATTAA
*
609383 AATAATATATTTTTATTTA
1 AATAATATATTTTTATTAA
609402 AAT
1 AAT
609405 TTAATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATAATATATTTTTATTAA
Found at i:609688 original size:10 final size:11
Alignment explanation
Indices: 609658--609697 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
609648 TTTTTATTGA
609658 TATATTAATTAT
1 TATATTAATT-T
609670 TATATTAATTT
1 TATATTAATTT
609681 TA-ATTAATTT
1 TATATTAATTT
*
609691 TTTATTA
1 TATATTA
609698 TAATTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.35
11 7 0.27
12 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTAATTT
Found at i:610722 original size:29 final size:28
Alignment explanation
Indices: 610668--610726 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
610658 AAATTAAAAT
* *
610668 ATATTTTTATAATTAAATTTATATTTAA
1 ATATTTTTATAATTAAATTAAAATTTAA
610696 ATATTTTTATATATTAAA-TAAGAATTTAA
1 ATATTTTTATA-ATTAAATTAA-AATTTAA
610725 AT
1 AT
610727 TGAAACAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
ATATTTTTATAATTAAATTAAAATTTAA
Found at i:611133 original size:4 final size:4
Alignment explanation
Indices: 611124--611154 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
611114 AAATATAAAT
611124 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
611155 TAGAACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:620223 original size:2 final size:2
Alignment explanation
Indices: 620218--620249 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
620208 AAAAAACTTG
620218 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
620250 ATGGCAAGGG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:621776 original size:173 final size:173
Alignment explanation
Indices: 621487--621824 Score: 464
Period size: 173 Copynumber: 2.0 Consensus size: 173
621477 TGGCTTTTGA
* * * * *
621487 ATATATAGTAAATTGTATTTGACGCATTGTGAGAGTGCTCGTCTATAAATCGATAAATTTTACAT
1 ATATATAGTAAATTGTATTTGACGCATTGTGACAATGCTCATCTATAAATCGATAAACTTTACAA
* * *
621552 TGATACATTATTAATAAATAAATATATATTTTTTTTCTAAAATAACAAATAATTATACCTTTAAA
66 TGACACATCATTAACAAATAAATATATATTTTTTTTCTAAAATAACAAATAATTATACCTTTAAA
* * *
621617 TAAGTGAATTAAGGTAATTCACTATCAATGTTTAGGTCTATAC
131 TAAGTAAATTAAGATAACTCACTATCAATGTTTAGGTCTATAC
* * * * *
621660 ATATATAGTAAATTGTATTTGATGCATTGTGACAATGTTCATGTATATATTGATAAACTTTACAA
1 ATATATAGTAAATTGTATTTGACGCATTGTGACAATGCTCATCTATAAATCGATAAACTTTACAA
* ** *
621725 TGACACATCATTAACAAATATATATTATAGTTTTTTTT-T-AAATAACAAATAATTATATTTTTT
66 TGACACATCATTAACAAATAAATA-TATA-TTTTTTTTCTAAAATAACAAATAATTATACCTTTA
621788 AATAAGTAAATTAAGATAACTCACTATCAATGTTTAG
129 AATAAGTAAATTAAGATAACTCACTATCAATGTTTAG
621825 ATTTATATAT
Statistics
Matches: 143, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
173 130 0.91
174 5 0.03
175 8 0.06
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (173 bp):
ATATATAGTAAATTGTATTTGACGCATTGTGACAATGCTCATCTATAAATCGATAAACTTTACAA
TGACACATCATTAACAAATAAATATATATTTTTTTTCTAAAATAACAAATAATTATACCTTTAAA
TAAGTAAATTAAGATAACTCACTATCAATGTTTAGGTCTATAC
Found at i:622970 original size:14 final size:13
Alignment explanation
Indices: 622951--622986 Score: 63
Period size: 14 Copynumber: 2.7 Consensus size: 13
622941 AATTTAAAAT
622951 TTAATTAAATTAA
1 TTAATTAAATTAA
622964 TTGAATTAAATTAA
1 TT-AATTAAATTAA
622978 TTAATTAAA
1 TTAATTAAA
622987 AAAATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
TTAATTAAATTAA
Found at i:623099 original size:23 final size:23
Alignment explanation
Indices: 623052--623100 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
623042 TTAAAATATA
*
623052 AATTATTTATATTATTATACAAC
1 AATTATTTATATTAGTATACAAC
623075 AATTATTGTATATT-GTAT-CATAC
1 AATTATT-TATATTAGTATACA-AC
623098 AAT
1 AAT
623101 ATAATATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 2 0.09
23 15 0.65
24 6 0.26
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (23 bp):
AATTATTTATATTAGTATACAAC
Found at i:623248 original size:20 final size:20
Alignment explanation
Indices: 623204--623251 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
623194 TAAAAAAATC
*
623204 AATTAATTTTATTATTTAAT
1 AATTAATTTTAATATTTAAT
*
623224 TATTAATTTTAAATATTTAA-
1 AATTAATTTT-AATATTTAAT
623244 AATTAATT
1 AATTAATT
623252 AAATTAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTAATTTTAATATTTAAT
Found at i:623255 original size:9 final size:9
Alignment explanation
Indices: 623243--623316 Score: 68
Period size: 9 Copynumber: 8.8 Consensus size: 9
623233 TAAATATTTA
623243 AAATTAATT
1 AAATTAATT
623252 AAATTAATT
1 AAATTAATT
*
623261 AAATAAATT
1 AAATTAATT
*
623270 -AA-TAACT
1 AAATTAATT
623277 AAATTAATT
1 AAATTAATT
*
623286 -ATTTAA--
1 AAATTAATT
623292 AAATTAATT
1 AAATTAATT
* *
623301 CAATCAATT
1 AAATTAATT
623310 AAATTAA
1 AAATTAA
623317 CTCAAATATT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
7 8 0.16
8 9 0.18
9 33 0.66
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (9 bp):
AAATTAATT
Found at i:623281 original size:12 final size:12
Alignment explanation
Indices: 623251--623284 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
623241 TAAAATTAAT
623251 TAAATTAATTAAA
1 TAAATTAA-TAAA
*
623264 TAAATTAATAAC
1 TAAATTAATAAA
623276 TAAATTAAT
1 TAAATTAAT
623285 TATTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAATTAATAAA
Found at i:623777 original size:23 final size:23
Alignment explanation
Indices: 623747--623791 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
623737 ATGTAATTAT
623747 TTTTAAAATTT-AATATTTAATAA
1 TTTTAAAATTTAAAT-TTTAATAA
623770 TTTTAAAATTTAAATTTTAATA
1 TTTTAAAATTTAAATTTTAATA
623792 TTTATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAAAATTTAAATTTTAATAA
Found at i:623808 original size:14 final size:14
Alignment explanation
Indices: 623748--623802 Score: 65
Period size: 14 Copynumber: 3.7 Consensus size: 14
623738 TGTAATTATT
*
623748 TTTAAAATTTAATA
1 TTTAAATTTTAATA
*
623762 TTTAATAATTTTAAAA
1 TTT-A-AATTTTAATA
623778 TTTAAATTTTAATA
1 TTTAAATTTTAATA
623792 TTTATAATTTT
1 TTTA-AATTTT
623803 TTATTTTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 16 0.46
15 8 0.23
16 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAAATTTTAATA
Found at i:623815 original size:30 final size:30
Alignment explanation
Indices: 623747--623815 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
623737 ATGTAATTAT
* **
623747 TTTTAAAATTTAATATTTAATAATTTTAAA
1 TTTTAAATTTTAATATTTAATAATTTTTTA
*
623777 ATTTAAATTTTAATATTT-ATAATTTTTTA
1 TTTTAAATTTTAATATTTAATAATTTTTTA
623806 TTTTCAAATT
1 TTTT-AAATT
623816 ATAAACTCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTTAAATTTTAATATTTAATAATTTTTTA
Found at i:626401 original size:22 final size:23
Alignment explanation
Indices: 626373--626420 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
626363 TTAGTAATTT
626373 TTTTAATA-ATATAAAATTTAAA
1 TTTTAATATATATAAAATTTAAA
* **
626395 TTTTAATATTTATAATTTTTAAA
1 TTTTAATATATATAAAATTTAAA
626418 TTT
1 TTT
626421 ATTTATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTAATATATATAAAATTTAAA
Found at i:626411 original size:15 final size:15
Alignment explanation
Indices: 626386--626422 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
626376 TAATAATATA
626386 AAATTTA-AA-TTTT
1 AAATTTATAATTTTT
626399 AATATTTATAATTTTT
1 AA-ATTTATAATTTTT
626415 AAATTTAT
1 AAATTTAT
626423 TTATAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 5 0.24
15 8 0.38
16 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATTTATAATTTTT
Found at i:628445 original size:29 final size:30
Alignment explanation
Indices: 628400--628460 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
628390 TATCTCATAA
*
628400 TTTAAATATTTATATTATATTT-ATATATT
1 TTTAAATATTTATATTATATTTAAAATATT
628429 TTTAAATA-TTATAATTATATTTAAAATATT
1 TTTAAATATTTAT-ATTATATTTAAAATATT
628459 TT
1 TT
628461 ATATTTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 4 0.14
29 17 0.59
30 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTAAATATTTATATTATATTTAAAATATT
Found at i:628874 original size:15 final size:17
Alignment explanation
Indices: 628849--628884 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
628839 TTTGTATTTT
628849 ATTTGATAAAAAAAT-A
1 ATTTGATAAAAAAATGA
628865 ATTT-ATAAAAAAATGA
1 ATTTGATAAAAAAATGA
628881 ATTT
1 ATTT
628885 TGAATCGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
ATTTGATAAAAAAATGA
Found at i:636395 original size:36 final size:36
Alignment explanation
Indices: 636324--636395 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
636314 ACCTATATAT
**
636324 GACATTCTCCTACTAGAATACAGTTTCATGCTGCAC
1 GACATTCTCCTACTAGAATACAGTTTCATAATGCAC
* *
636360 GACATTCTCCTACTAGTATACAGTTTCGTAATGCAC
1 GACATTCTCCTACTAGAATACAGTTTCATAATGCAC
636396 TAGCAAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (36 bp):
GACATTCTCCTACTAGAATACAGTTTCATAATGCAC
Found at i:640618 original size:16 final size:16
Alignment explanation
Indices: 640581--640639 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
640571 TTTTTTAAAA
*
640581 AATTTTAAATTGATAA-
1 AATTTT-AATTTATAAT
*
640597 AA-TTTAATTTATACT
1 AATTTTAATTTATAAT
*
640612 AATTTTATTTTATAAT
1 AATTTTAATTTATAAT
*
640628 ATTTTTAATTTA
1 AATTTTAATTTA
640640 ATTTTTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 7 0.20
15 5 0.14
16 23 0.66
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
AATTTTAATTTATAAT
Found at i:640872 original size:1 final size:1
Alignment explanation
Indices: 640866--640893 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
640856 GTTTCATTAG
640866 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
640894 CACGCGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:645137 original size:24 final size:24
Alignment explanation
Indices: 645102--645158 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
645092 AGACCAAGTA
*
645102 GCTGTTGCTGCTGATGATGGTGTT
1 GCTGTTGCTGCTGATCATGGTGTT
* * * *
645126 GCTGTTGTTGCTGCTCTTGTTGTT
1 GCTGTTGCTGCTGATCATGGTGTT
645150 GCTGTTGCT
1 GCTGTTGCT
645159 TTAAAACTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.04, C:0.16, G:0.33, T:0.47
Consensus pattern (24 bp):
GCTGTTGCTGCTGATCATGGTGTT
Found at i:646829 original size:2 final size:2
Alignment explanation
Indices: 646822--646854 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
646812 GTGAACATAC
646822 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
646855 AGTTAGGTTG
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:646977 original size:13 final size:13
Alignment explanation
Indices: 646956--646985 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
646946 AAAGTAAAAT
*
646956 AAATTTTTTTTAA
1 AAATATTTTTTAA
646969 AAATATTTTTTAA
1 AAATATTTTTTAA
646982 AAAT
1 AAAT
646986 TTTAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AAATATTTTTTAA
Found at i:648844 original size:2 final size:2
Alignment explanation
Indices: 648832--648864 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
648822 AGAAAGACAT
*
648832 TA TA TA CA 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
648865 GCCAAGGTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:649226 original size:4 final size:4
Alignment explanation
Indices: 649217--649243 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
649207 ATATTCGTAC
649217 AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AAT
649244 CTAATAGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:651061 original size:12 final size:12
Alignment explanation
Indices: 651044--651074 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
651034 ATTAATTTTG
651044 CACCCCCCCCCC
1 CACCCCCCCCCC
651056 CACCCCCCCCCC
1 CACCCCCCCCCC
651068 C-CCCCCC
1 CACCCCCC
651075 AAAACCCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.06, C:0.94, G:0.00, T:0.00
Consensus pattern (12 bp):
CACCCCCCCCCC
Found at i:653741 original size:2 final size:2
Alignment explanation
Indices: 653734--653769 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
653724 AATAAAAATA
653734 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
653770 CAGGAATAAC
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:658448 original size:17 final size:17
Alignment explanation
Indices: 658426--658459 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
658416 AAAAGATACG
658426 TTAAAATGTTCACAGTA
1 TTAAAATGTTCACAGTA
658443 TTAAAATGTTCACAGTA
1 TTAAAATGTTCACAGTA
658460 GGAATTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TTAAAATGTTCACAGTA
Found at i:660283 original size:21 final size:20
Alignment explanation
Indices: 660259--660307 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
660249 CGATTATGAA
660259 TTAAAAAAAATTATTGATAAT
1 TTAAAAAAAA-TATTGATAAT
* * *
660280 TTAATAAAAATATTTATTAT
1 TTAAAAAAAATATTGATAAT
660300 TTAAAAAA
1 TTAAAAAA
660308 TTAAAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TTAAAAAAAATATTGATAAT
Found at i:660487 original size:1 final size:1
Alignment explanation
Indices: 660481--660505 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
660471 AACCCTTCGG
660481 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
660506 GAACATGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:672235 original size:2 final size:2
Alignment explanation
Indices: 672200--672226 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
672190 AACAGGTGAG
672200 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
672227 CGTATATATT
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:673734 original size:30 final size:28
Alignment explanation
Indices: 673700--673768 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 28
673690 AAATAATTTA
673700 ATTTAAATAAAATTTTAA-AATAATAAAAAT
1 ATTTAAATAAAA-TTTAATAAT-A-AAAAAT
* *
673730 ATTTATTAATTAAATTTAATTATAAAAAAT
1 ATTTA--AATAAAATTTAATAATAAAAAAT
673760 ATTTAAATA
1 ATTTAAATA
673769 TTAATATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
28 3 0.09
30 16 0.48
31 6 0.18
32 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATTTAAATAAAATTTAATAATAAAAAAT
Found at i:673734 original size:35 final size:35
Alignment explanation
Indices: 673664--673734 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 35
673654 AATTAGATTA
* **
673664 AATTTAAGATAAAATTTTTATAATTTAAATAATTT
1 AATTTAAGATAAAATTTTAATAATAAAAATAATTT
673699 AATTTAA-ATAAAATTTTAAAATAATAAAAAT-ATTT
1 AATTTAAGATAAAATTTT--AATAATAAAAATAATTT
673734 A
1 A
673735 TTAATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
34 10 0.32
35 12 0.39
36 9 0.29
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (35 bp):
AATTTAAGATAAAATTTTAATAATAAAAATAATTT
Found at i:676083 original size:22 final size:24
Alignment explanation
Indices: 676043--676092 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
676033 CTCGTGAAAA
676043 AAAAAGAAGAAACCAAAAACAG-C
1 AAAAAGAAGAAACCAAAAACAGAC
*
676066 AAAAAGAAG-AACTC-AAAAGAGAC
1 AAAAAGAAGAAAC-CAAAAACAGAC
676089 AAAA
1 AAAA
676093 GCTACATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.70, C:0.14, G:0.14, T:0.02
Consensus pattern (24 bp):
AAAAAGAAGAAACCAAAAACAGAC
Found at i:679636 original size:18 final size:18
Alignment explanation
Indices: 679612--679653 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
679602 CACTCCCTGG
679612 ATCATCTTCATCCTCCTC
1 ATCATCTTCATCCTCCTC
* *
679630 TTCATCTTCCTCCTCCTC
1 ATCATCTTCATCCTCCTC
679648 ATCATC
1 ATCATC
679654 GGACTCCGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.14, C:0.45, G:0.00, T:0.40
Consensus pattern (18 bp):
ATCATCTTCATCCTCCTC
Found at i:684090 original size:16 final size:16
Alignment explanation
Indices: 684059--684097 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
684049 TTAAGTAAAA
684059 AATATATAAATTTATAT
1 AATAT-TAAATTTATAT
*
684076 AATATTAATTTTATAT
1 AATATTAAATTTATAT
684092 AA-ATTA
1 AATATTA
684098 TATAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATTAAATTTATAT
Found at i:684104 original size:25 final size:25
Alignment explanation
Indices: 684061--684109 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
684051 AAGTAAAAAA
684061 TATATAAATTTATATAATATTAATTT
1 TATATAAATTTATATAATA-TAATTT
684087 TATATAAA-TTATATAATATAATT
1 TATATAAATTTATATAATATAATT
684110 AACTTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.22
25 10 0.43
26 8 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TATATAAATTTATATAATATAATTT
Found at i:684238 original size:23 final size:23
Alignment explanation
Indices: 684212--684262 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
684202 AATGTAAGGA
684212 TTAAAATATATT-AATATTATAAT
1 TTAAAATATATTAAATATT-TAAT
*
684235 TT-AAATTTATTAAATATTTAAT
1 TTAAAATATATTAAATATTTAAT
684257 TTAAAA
1 TTAAAA
684263 ATAATTATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAAAATATATTAAATATTTAAT
Found at i:684269 original size:23 final size:23
Alignment explanation
Indices: 684212--684269 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
684202 AATGTAAGGA
684212 TTAAAATATATT-AATATTATAAT
1 TTAAAATA-ATTAAATATTATAAT
* *
684235 TTAAATTTATTAAATATT-TAAT
1 TTAAAATAATTAAATATTATAAT
684257 TTAAAAATAATTA
1 TT-AAAATAATTA
684270 TACTTGTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAAATAATTAAATATTATAAT
Found at i:686749 original size:18 final size:19
Alignment explanation
Indices: 686713--686750 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
686703 AAGATAATAG
* *
686713 TTAAGGTTTTTATATTAAT
1 TTAAGGTTTTTAGAGTAAT
686732 TTAA-GTTTTTAGAGTAAT
1 TTAAGGTTTTTAGAGTAAT
686750 T
1 T
686751 GAAGACCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TTAAGGTTTTTAGAGTAAT
Found at i:689180 original size:3 final size:3
Alignment explanation
Indices: 689172--689203 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
689162 CACACACACA
689172 AAT AAT AAT AAT AAT AAT AAT AA- AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
689204 TACAAGAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:691116 original size:17 final size:17
Alignment explanation
Indices: 691086--691118 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
691076 ATAGAAACAA
691086 ACAAACAAACACCAAAC
1 ACAAACAAACACCAAAC
691103 ACAAGACAAA-ACCAAA
1 ACAA-ACAAACACCAAA
691119 ACTCTCTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.67, C:0.30, G:0.03, T:0.00
Consensus pattern (17 bp):
ACAAACAAACACCAAAC
Found at i:693044 original size:22 final size:22
Alignment explanation
Indices: 693008--693053 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
692998 TACTTTTCAA
*
693008 ATTAAAAATAATAAATAACATT
1 ATTAAAAATAATAAAGAACATT
*
693030 ATTAAAAA-AATTAAAGAATATT
1 ATTAAAAATAA-TAAAGAACATT
693052 AT
1 AT
693054 CTGAGTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
ATTAAAAATAATAAAGAACATT
Found at i:693275 original size:16 final size:18
Alignment explanation
Indices: 693244--693277 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
693234 CAAAATTTTT
693244 TAATATTATATAAATATA
1 TAATATTATATAAATATA
693262 TAATATT-T-TAAATATA
1 TAATATTATATAAATATA
693278 ATTATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATATTATATAAATATA
Found at i:697362 original size:2 final size:2
Alignment explanation
Indices: 697355--697385 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
697345 TTTCACTACA
697355 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 A
697386 AACTAAAGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:698499 original size:35 final size:35
Alignment explanation
Indices: 698435--698501 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
698425 TGTAAGTATG
*
698435 ATATTTTAAATAAATATAAAATATGTATAAATAAA
1 ATATTTTAAATAAATATAAAATATATATAAATAAA
*
698470 ATATTTTTAATAAATATAAAA-ATAATATAAAT
1 ATATTTTAAATAAATATAAAATAT-ATATAAAT
698502 TTATTAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 2 0.07
35 27 0.93
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (35 bp):
ATATTTTAAATAAATATAAAATATATATAAATAAA
Found at i:698597 original size:24 final size:24
Alignment explanation
Indices: 698532--698597 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 24
698522 AAATTTAATA
*
698532 TAATAATTTTATAAATATTA-TTTT
1 TAAT-ATTTTATAATTATTATTTTT
*
698556 T-ATA-TTTATAATTTTTATTTATT
1 TAATATTTTATAATTATTATTT-TT
698579 TAATATTTTAT-ATTATTAT
1 TAATATTTTATAATTATTAT
698598 ATTTGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
21 11 0.31
22 3 0.09
23 5 0.14
24 11 0.31
25 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TAATATTTTATAATTATTATTTTT
Found at i:698599 original size:15 final size:15
Alignment explanation
Indices: 698537--698601 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
698527 TAATATAATA
*
698537 ATTTTATAAATATTAT
1 ATTTTAT-ATTATTAT
*
698553 -TTTTATATTTATAAT
1 ATTTTATA-TTATTAT
698568 -TTTTAT-TTATTTAAT
1 ATTTTATATTA-TT-AT
698583 ATTTTATATTATTAT
1 ATTTTATATTATTAT
698598 ATTT
1 ATTT
698602 GTAAAATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
13 3 0.07
14 2 0.05
15 25 0.61
16 8 0.20
17 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTATATTATTAT
Found at i:699174 original size:19 final size:18
Alignment explanation
Indices: 699133--699186 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
699123 ATACAGTAAT
*
699133 AAAATTTAAA-TTTACTTA
1 AAAATTTAAATTTTA-TGA
699151 AAAATTTAAATTTTATGA
1 AAAATTTAAATTTTATGA
*
699169 ATAAATATTAATTTTTAT
1 A-AAAT-TTAAATTTTAT
699187 CGTTCATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 13 0.42
19 8 0.26
20 10 0.32
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
AAAATTTAAATTTTATGA
Found at i:701074 original size:17 final size:17
Alignment explanation
Indices: 701054--701095 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
701044 TATATACTTA
701054 AAATATTATA-AATATTT
1 AAATATTATACAA-ATTT
701071 AAATA-TATACCAAATTT
1 AAATATTATA-CAAATTT
701088 AAATATTA
1 AAATATTA
701096 AACATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATTATACAAATTT
Found at i:704548 original size:23 final size:23
Alignment explanation
Indices: 704521--704565 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
704511 TAAACATAAA
*
704521 TTTTAATATAA-AATTAAATTTAT
1 TTTTAATA-AATAAATAAATTTAT
*
704544 TTTTATTAAATAAATAAATTTA
1 TTTTAATAAATAAATAAATTTA
704566 AATAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTAATAAATAAATAAATTTAT
Found at i:711134 original size:14 final size:15
Alignment explanation
Indices: 711100--711134 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
711090 TATATTTTTT
711100 ATTTTTTATTTTAAA
1 ATTTTTTATTTTAAA
711115 ATTTTTTATTTTAAA
1 ATTTTTTATTTTAAA
711130 ATTTT
1 ATTTT
711135 ATGGTTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTATTTTAAA
Found at i:714509 original size:15 final size:15
Alignment explanation
Indices: 714482--714523 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
714472 AAATAGTATC
714482 ATTTATATTA-TTTTA
1 ATTTAT-TTATTTTTA
714497 TATTTATTTATTTTTA
1 -ATTTATTTATTTTTA
*
714513 ATTTTTTTATT
1 ATTTATTTATT
714524 GATATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTATTTATTTTTA
Found at i:715966 original size:12 final size:12
Alignment explanation
Indices: 715938--715978 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
715928 TATTGCTTTC
715938 AATATATATA-T
1 AATATATATATT
715949 ATATATATATATT
1 A-ATATATATATT
715962 AATATCA-ATATT
1 AATAT-ATATATT
715974 AATAT
1 AATAT
715979 TAATATTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.04
12 23 0.85
13 3 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
AATATATATATT
Found at i:717025 original size:13 final size:13
Alignment explanation
Indices: 717007--717035 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
716997 AACCTTTTGT
717007 TGATAATTTGTAA
1 TGATAATTTGTAA
717020 TGATAATTTGTAA
1 TGATAATTTGTAA
717033 TGA
1 TGA
717036 AGATGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (13 bp):
TGATAATTTGTAA
Found at i:720010 original size:20 final size:19
Alignment explanation
Indices: 719982--720060 Score: 77
Period size: 20 Copynumber: 4.1 Consensus size: 19
719972 TTAAAAAAAA
* *
719982 TTACTTAATATGATTACAT
1 TTACCTAATATAATTACAT
720001 TTGACCTAATATAATTACAT
1 TT-ACCTAATATAATTACAT
** *
720021 TTAAATAATATAATTATAT
1 TTACCTAATATAATTACAT
* *
720040 TAAACCTAATATGATTACAT
1 T-TACCTAATATAATTACAT
720060 T
1 T
720061 CGAATCATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 17 0.35
20 31 0.65
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (19 bp):
TTACCTAATATAATTACAT
Found at i:720076 original size:39 final size:39
Alignment explanation
Indices: 719987--720076 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
719977 AAAAATTACT
* ** *
719987 TAATATGATTACATTTGACCTAATATAATTACATTTAAA
1 TAATATGATTATATTAAACCTAATATAATTACATTCAAA
* * *
720026 TAATATAATTATATTAAACCTAATATGATTACATTCGAA
1 TAATATGATTATATTAAACCTAATATAATTACATTCAAA
*
720065 TCATATGATTAT
1 TAATATGATTAT
720077 TCAAACATTC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (39 bp):
TAATATGATTATATTAAACCTAATATAATTACATTCAAA
Found at i:720894 original size:20 final size:20
Alignment explanation
Indices: 720869--720909 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
720859 AAAAAAGTTC
*
720869 ACCTAATATAATTACATTCA
1 ACCTAACATAATTACATTCA
*
720889 ACCTAACATGATTACATTCA
1 ACCTAACATAATTACATTCA
720909 A
1 A
720910 ATCATATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.32
Consensus pattern (20 bp):
ACCTAACATAATTACATTCA
Found at i:720926 original size:17 final size:19
Alignment explanation
Indices: 720904--720947 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
720894 ACATGATTAC
720904 ATTCAAAT-C-ATATGATT
1 ATTCAAATACAATATGATT
720921 ATTCAAATAACAATATGATT
1 ATTCAAAT-ACAATATGATT
720941 ATTCAAA
1 ATTCAAA
720948 CATTCAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.33
19 1 0.04
20 15 0.62
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (19 bp):
ATTCAAATACAATATGATT
Found at i:724353 original size:14 final size:14
Alignment explanation
Indices: 724334--724364 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
724324 TCCATGCCTT
*
724334 TTTTTTTTTTGAAA
1 TTTTTTTTTTAAAA
724348 TTTTTTTTTTAAAA
1 TTTTTTTTTTAAAA
724362 TTT
1 TTT
724365 AAAATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTTAAAA
Found at i:724457 original size:15 final size:15
Alignment explanation
Indices: 724431--724464 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
724421 ATATAGTTTG
724431 AATTTTTGTATCTATA
1 AATTTTTGTATCT-TA
724447 AATTTTT-TATCTTA
1 AATTTTTGTATCTTA
724461 AATT
1 AATT
724465 ATGAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 5 0.28
16 7 0.39
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (15 bp):
AATTTTTGTATCTTA
Found at i:724978 original size:16 final size:16
Alignment explanation
Indices: 724957--724999 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
724947 ATTTTTTTAT
*
724957 TTAAATTTGAATTAAA
1 TTAAATTTAAATTAAA
*
724973 TTAAATTTAAATTAAC
1 TTAAATTTAAATTAAA
*
724989 TTAAAATTAAA
1 TTAAATTTAAA
725000 AAAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:725670 original size:185 final size:185
Alignment explanation
Indices: 725355--725723 Score: 630
Period size: 185 Copynumber: 2.0 Consensus size: 185
725345 GTGGGTTATT
*
725355 CTTCCAAAACATATAATAGTAGCACAATAATTTAAAGAGACTATCCAAATACAATTAAAACTGAA
1 CTTCCAAAACAGATAATAGTAGCACAATAATTTAAAGAGACTATCCAAATACAATTAAAACTGAA
*
725420 ACATAACAGATTAGCACATTAATTGAGCAAATGCTTTAGAAGAGGAACCATTGTTGTTCCAAGCT
66 ACATAACAGATTAGCACATTAATTGAGCAAATGCTTTAGAAGAGGAACCATTGTTATTCCAAGCT
* * *
725485 TTTTCAGCACTGAGTTTGAGATCCTTGAGTCTGGCCCTCAGTGCATGCCCTTCAG
131 TTTTCAGCACTCAATTTGAGATCCTTGACTCTGGCCCTCAGTGCATGCCCTTCAG
* *
725540 CTTCCAAAACAGATAATAGTAGCACAATAATTTTAAGAGACTATCCAAATACAATTAAAACTGAT
1 CTTCCAAAACAGATAATAGTAGCACAATAATTTAAAGAGACTATCCAAATACAATTAAAACTGAA
* * * *
725605 ACGTAACAGATTAGCACATTAATTGAGCAAATGCTTTATAAGAGGAACCATTTTTATTGCAAGCT
66 ACATAACAGATTAGCACATTAATTGAGCAAATGCTTTAGAAGAGGAACCATTGTTATTCCAAGCT
*
725670 TTTTCAGCACTCAATTTGAGATCCTTGACTCTGGCCCTCATTGCATGCCCTTCA
131 TTTTCAGCACTCAATTTGAGATCCTTGACTCTGGCCCTCAGTGCATGCCCTTCA
725724 TCATCCACCA
Statistics
Matches: 172, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
185 172 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (185 bp):
CTTCCAAAACAGATAATAGTAGCACAATAATTTAAAGAGACTATCCAAATACAATTAAAACTGAA
ACATAACAGATTAGCACATTAATTGAGCAAATGCTTTAGAAGAGGAACCATTGTTATTCCAAGCT
TTTTCAGCACTCAATTTGAGATCCTTGACTCTGGCCCTCAGTGCATGCCCTTCAG
Found at i:727508 original size:19 final size:19
Alignment explanation
Indices: 727475--727534 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
727465 TTTAAATTGA
727475 TTTAATTTAAA-TTAATAT
1 TTTAATTTAAATTTAATAT
*
727493 TTTTATTTAAATTTAAT-T
1 TTTAATTTAAATTTAATAT
* *
727511 TTAAAATATAAATTTAATAT
1 TT-TAATTTAAATTTAATAT
727531 TTTA
1 TTTA
727535 TTAAAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 13 0.38
19 18 0.53
20 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAATTTAAATTTAATAT
Found at i:728440 original size:17 final size:17
Alignment explanation
Indices: 728394--728440 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
728384 TTATACATTT
728394 AATATATATTA-ATTTTA
1 AATATAT-TTATATTTTA
*
728411 AA-ATGATTGATATTTTA
1 AATAT-ATTTATATTTTA
728428 AATATATTTATAT
1 AATATATTTATAT
728441 ATTATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 4 0.16
17 19 0.76
18 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
AATATATTTATATTTTA
Done.