Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold426
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: 634051
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 6 of 6
Found at i:525616 original size:34 final size:33
Alignment explanation
Indices: 525573--525641 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
525563 CCAGATGGAT
**
525573 TATTTATTT-AAATTTTAAAATTTAAGTAAAAAA
1 TATTTATTTAAAAAATT-AAATTTAAGTAAAAAA
*
525606 TATTATATTTAAAAAATTAAATTTAATTAAAAAA
1 TATT-TATTTAAAAAATTAAATTTAAGTAAAAAA
525640 TA
1 TA
525642 AATTAAACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 4 0.13
34 22 0.71
35 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (33 bp):
TATTTATTTAAAAAATTAAATTTAAGTAAAAAA
Found at i:525787 original size:30 final size:32
Alignment explanation
Indices: 525730--525794 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
525720 ATTTTTATTT
* *
525730 TTATATATTATATAATTTTTATCATATAAA-A
1 TTATATATTATATAATTATTATAATATAAACA
525761 TTATATA-TATAT-ATGTATTATAATATAAACA
1 TTATATATTATATAAT-TATTATAATATAAACA
525792 TTA
1 TTA
525795 GAAGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 2 0.07
30 17 0.57
31 11 0.37
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (32 bp):
TTATATATTATATAATTATTATAATATAAACA
Found at i:537315 original size:41 final size:41
Alignment explanation
Indices: 537209--537316 Score: 121
Period size: 43 Copynumber: 2.6 Consensus size: 41
537199 AGTTTAGAAT
*
537209 AAATTTTTATTTAAATTTTAA-AAATTTTAAAATTAAATAACA
1 AAATTTTTATTT-AATTTTAATTAATTTT-AAATTAAATAACA
* * *
537251 AATTTTTAATATTTAATTTTAATTAATTATT-ATTTAAATAATA
1 AAATTTT--TATTTAATTTTAATTAATT-TTAAATTAAATAACA
537294 AAATTTTTATTTAATTTTAATTA
1 AAATTTTTATTTAATTTTAATTA
537317 TAAAAATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
41 16 0.28
42 6 0.11
43 24 0.42
44 9 0.16
45 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (41 bp):
AAATTTTTATTTAATTTTAATTAATTTTAAATTAAATAACA
Found at i:537681 original size:20 final size:20
Alignment explanation
Indices: 537652--537713 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
537642 AACTGTGTAT
*
537652 TAAATCAAATATTATATTAA
1 TAAATAAAATATTATATTAA
537672 TAAATAAAAT-TTATA-TAA
1 TAAATAAAATATTATATTAA
*
537690 T--ATAAATTATATTAAATTAA
1 TAAATAAA--ATATTATATTAA
537710 TAAA
1 TAAA
537714 ATTTTTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 5 0.15
18 6 0.18
19 9 0.26
20 13 0.38
22 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATAAAATATTATATTAA
Found at i:537879 original size:13 final size:14
Alignment explanation
Indices: 537863--537896 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
537853 ATTATCAAAT
537863 AAAATTATT-TATA
1 AAAATTATTCTATA
*
537876 AAAAATATTCTATA
1 AAAATTATTCTATA
537890 AAAATTA
1 AAAATTA
537897 AATTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATTATTCTATA
Found at i:542533 original size:25 final size:25
Alignment explanation
Indices: 542498--542551 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
542488 CTCAAGATTT
*
542498 TTCTTCGATATAATCATTAGGGAAA
1 TTCTTCAATATAATCATTAGGGAAA
542523 TTCTTCAATATAATCATTAGGGAAA
1 TTCTTCAATATAATCATTAGGGAAA
542548 TTCT
1 TTCT
542552 ATTCACAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (25 bp):
TTCTTCAATATAATCATTAGGGAAA
Found at i:548916 original size:13 final size:14
Alignment explanation
Indices: 548893--548921 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
548883 ATCAAAAAAA
548893 ATTATTCTATTAAT
1 ATTATTCTATTAAT
548907 ATTATT-TATTAAT
1 ATTATTCTATTAAT
548920 AT
1 AT
548922 GAAAATTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATTCTATTAAT
Found at i:549704 original size:13 final size:13
Alignment explanation
Indices: 549686--549710 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
549676 TACTTTTGTT
549686 TAATTGAATTTTA
1 TAATTGAATTTTA
549699 TAATTGAATTTT
1 TAATTGAATTTT
549711 GATTTTTGAT
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:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
TAATTGAATTTTA
Found at i:550594 original size:7 final size:7
Alignment explanation
Indices: 550584--550644 Score: 70
Period size: 7 Copynumber: 8.1 Consensus size: 7
550574 GATTTTAATT
550584 TTTTTTA
1 TTTTTTA
550591 TTTTTTA
1 TTTTTTA
550598 TTTTTTAA
1 TTTTTT-A
550606 TTTTTATA
1 TTTTT-TA
550614 GTTTTTTA
1 -TTTTTTA
550622 -TTTTTA
1 TTTTTTA
550628 TCGTTTTTA
1 T--TTTTTA
550637 TTTTTTA
1 TTTTTTA
550644 T
1 T
550645 AATTACATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
6 6 0.12
7 20 0.42
8 9 0.19
9 13 0.27
ACGTcount: A:0.16, C:0.02, G:0.03, T:0.79
Consensus pattern (7 bp):
TTTTTTA
Found at i:550601 original size:15 final size:15
Alignment explanation
Indices: 550583--550644 Score: 72
Period size: 15 Copynumber: 4.1 Consensus size: 15
550573 AGATTTTAAT
550583 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
*
550598 TTTTTTAATTTTTATA
1 TTTTTTTATTTTT-TA
*
550614 GTTTTTTA-TTTTTA
1 TTTTTTTATTTTTTA
*
550628 TCGTTTTTATTTTTTA
1 T-TTTTTTATTTTTTA
550644 T
1 T
550645 AATTACATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 2 0.05
15 22 0.56
16 15 0.38
ACGTcount: A:0.16, C:0.02, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTTTTATTTTTTA
Found at i:550605 original size:24 final size:24
Alignment explanation
Indices: 550576--550644 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 24
550566 TGATAGAAGA
550576 TTTTAATTTTTTTTATTTTTTATT
1 TTTTAATTTTTTTTATTTTTTATT
*
550600 TTTTAA-TTTTTATAGTTTTTTA-T
1 TTTTAATTTTTTTTA-TTTTTTATT
**
550623 TTTT-ATCGTTTTTATTTTTTAT
1 TTTTAATTTTTTTTATTTTTTAT
550645 AATTACATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 8 0.21
23 17 0.45
24 13 0.34
ACGTcount: A:0.17, C:0.01, G:0.03, T:0.78
Consensus pattern (24 bp):
TTTTAATTTTTTTTATTTTTTATT
Found at i:550635 original size:32 final size:31
Alignment explanation
Indices: 550584--550645 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
550574 GATTTTAATT
550584 TTTTTTATTTTTTATTTTTTAATTTTTATAG
1 TTTTTTATTTTTTATTTTTTAATTTTTATAG
*
550615 TTTTTTA-TTTTTATCGTTTTTATTTTTTATA
1 TTTTTTATTTTTTAT--TTTTTAATTTTTATA
550646 ATTACATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.25
31 7 0.25
32 14 0.50
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (31 bp):
TTTTTTATTTTTTATTTTTTAATTTTTATAG
Found at i:550642 original size:8 final size:8
Alignment explanation
Indices: 550583--550626 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
550573 AGATTTTAAT
550583 TTTTTTTA
1 TTTTTTTA
550591 -TTTTTTA
1 TTTTTTTA
*
550598 TTTTTTAA
1 TTTTTTTA
*
550606 TTTTTATA
1 TTTTTTTA
*
550614 GTTTTTTA
1 TTTTTTTA
550622 TTTTT
1 TTTTT
550627 ATCGTTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:550794 original size:15 final size:15
Alignment explanation
Indices: 550757--550803 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
550747 TTTGTTTAAA
*
550757 AAAATTT-TAACTATT
1 AAAATTTATAA-TTTT
550772 AAATATTTATAATTTT
1 AAA-ATTTATAATTTT
*
550788 AAAATTTATATTTTT
1 AAAATTTATAATTTT
550803 A
1 A
550804 CATAAAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 15 0.54
16 10 0.36
17 3 0.11
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
AAAATTTATAATTTT
Found at i:551879 original size:19 final size:19
Alignment explanation
Indices: 551824--551896 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
551814 ATCGATTCAT
*
551824 TTAAATACAATAT-TAAATA
1 TTAAATAAAATATAT-AATA
* *
551843 TTAAAAAATAAT-TTTAATA
1 TTAAATAA-AATATATAATA
551862 TTAAATAAAATATAT-A-A
1 TTAAATAAAATATATAATA
551879 TT-AATAAAAATATATAAT
1 TTAAAT-AAAATATATAAT
551897 TCACTTAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
16 3 0.07
17 12 0.27
18 5 0.11
19 20 0.45
20 4 0.09
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAATAAAATATATAATA
Found at i:559561 original size:20 final size:20
Alignment explanation
Indices: 559538--559585 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
559528 TATTAATAAA
559538 ATATTAAAAATATATATTTT
1 ATATTAAAAATATATATTTT
* *
559558 ATATT-AATATATATTTTTT
1 ATATTAAAAATATATATTTT
559577 ATAATTAAA
1 AT-ATTAAA
559586 TTTAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 14 0.58
20 8 0.33
21 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTAAAAATATATATTTT
Found at i:559940 original size:10 final size:10
Alignment explanation
Indices: 559925--559950 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
559915 TATTATTTAT
559925 ATTATTAAAA
1 ATTATTAAAA
559935 ATTATTAAAA
1 ATTATTAAAA
559945 ATTATT
1 ATTATT
559951 TTTATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATTATTAAAA
Found at i:560347 original size:14 final size:13
Alignment explanation
Indices: 560294--560349 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
560284 TTTAAATACG
560294 ATATAAT-TAAATA
1 ATATAATATAAA-A
* * *
560307 ATAAAAAATTAAA
1 ATATAATATAAAA
560320 ATATAATATAAAA
1 ATATAATATAAAA
*
560333 ATATGATATTAAAA
1 ATATAATA-TAAAA
560347 ATA
1 ATA
560350 AAGTTAGATT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
13 23 0.68
14 11 0.32
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (13 bp):
ATATAATATAAAA
Found at i:560402 original size:19 final size:19
Alignment explanation
Indices: 560378--560430 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
560368 TATCAAAATC
560378 TATATAAATATGATTATGA
1 TATATAAATATGATTATGA
* * *
560397 TATATAGATCTGA-CA--A
1 TATATAAATATGATTATGA
560413 TAT-TAAATATGATTATGA
1 TATATAAATATGATTATGA
560431 AAATATAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 7
0.66 0.16 0.18
Matches are distributed among these distances:
15 7 0.28
16 5 0.20
18 2 0.08
19 11 0.44
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (19 bp):
TATATAAATATGATTATGA
Found at i:561409 original size:3 final size:3
Alignment explanation
Indices: 561401--561438 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
561391 TTAGGACAGG
561401 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 TA
561439 CCATAATTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:561507 original size:3 final size:3
Alignment explanation
Indices: 561499--561557 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
561489 ACTTAATTCA
561499 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
561547 ATT ATT ATT AT
1 ATT ATT ATT AT
561558 AATTTGTAGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:562655 original size:17 final size:18
Alignment explanation
Indices: 562621--562658 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
562611 AATGTTTCAA
562621 ATTTTATTTTTTATAAAT
1 ATTTTATTTTTTATAAAT
562639 ATTTTATTTTTTA-AAAT
1 ATTTTATTTTTTATAAAT
562656 ATT
1 ATT
562659 ATCAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTATTTTTTATAAAT
Found at i:562724 original size:2 final size:2
Alignment explanation
Indices: 562712--562747 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
562702 AAACTTTATG
*
562712 TA TA CA 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
562748 AACGAAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:563738 original size:16 final size:16
Alignment explanation
Indices: 563707--563752 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
563697 TTATCAAATT
* *
563707 TTATTGATTAAATTAA
1 TTATTAATTAATTTAA
*
563723 TTTTTAATTAATTTAA
1 TTATTAATTAATTTAA
*
563739 TTATTACTTAATTT
1 TTATTAATTAATTT
563753 TAACCGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
TTATTAATTAATTTAA
Found at i:564285 original size:16 final size:15
Alignment explanation
Indices: 564255--564311 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
564245 TTTTTTCAAA
564255 ATTTTATTTAAATTT
1 ATTTTATTTAAATTT
*
564270 ATTTTAATTTAGATTT
1 ATTTT-ATTTAAATTT
* *
564286 GAGTTGATTCGTAAATTT
1 -ATTTTATT--TAAATTT
564304 ATTTTATT
1 ATTTTATT
564312 ATTTAAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
15 5 0.16
16 12 0.38
17 9 0.28
18 6 0.19
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.60
Consensus pattern (15 bp):
ATTTTATTTAAATTT
Found at i:565436 original size:22 final size:21
Alignment explanation
Indices: 565392--565437 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
565382 AATTAAATTA
*
565392 AATTTAAATAAATATTTTTTT
1 AATTTAAATAAATATTTTATT
565413 AATTTAAATTAAAT-TATTTATT
1 AATTTAAA-TAAATAT-TTTATT
565435 AAT
1 AAT
565438 AAATTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTTAAATAAATATTTTATT
Found at i:567225 original size:21 final size:21
Alignment explanation
Indices: 567166--567227 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
567156 TAAAATAGAA
*
567166 ATATTTT-A-AAAAATCGATT
1 ATATTTTAAGAAAAATCAATT
* * *
567185 -TTTTTTAAGAGAGATCAATT
1 ATATTTTAAGAAAAATCAATT
*
567205 ATATTTTAAGAAAAATTAATT
1 ATATTTTAAGAAAAATCAATT
567226 AT
1 AT
567228 TTTATATATA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 5 0.16
19 1 0.03
20 8 0.25
21 18 0.56
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (21 bp):
ATATTTTAAGAAAAATCAATT
Found at i:568039 original size:3 final size:3
Alignment explanation
Indices: 568033--568067 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
568023 CAACTTAATA
568033 TAT TATT TAT TATT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TA-T TAT TAT TAT TAT TAT TAT TAT
568068 CACTGTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 24 0.80
4 6 0.20
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:568045 original size:7 final size:7
Alignment explanation
Indices: 568033--568065 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
568023 CAACTTAATA
568033 TATTATT
1 TATTATT
568040 TATTATT
1 TATTATT
568047 TATTA-T
1 TATTATT
568053 TATTA-T
1 TATTATT
568059 TATTATT
1 TATTATT
568066 ATCACTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TATTATT
Found at i:568316 original size:23 final size:24
Alignment explanation
Indices: 568280--568324 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
568270 ATAACATTAC
*
568280 AATATTAATATAATATATTTAATA
1 AATATTAAGATAATATATTTAATA
568304 AATA-TAAGATAATATATTTAA
1 AATATTAAGATAATATATTTAA
568325 ATATAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
AATATTAAGATAATATATTTAATA
Found at i:568328 original size:33 final size:33
Alignment explanation
Indices: 568291--568362 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
568281 ATATTAATAT
* *
568291 AATATATTTAATA-AATATAAGATAATATATTTA
1 AATATAATTAATACAAT-TAAGATAATACATTTA
* *
568324 AATATAATTAATACAATTAATATGATACATTTA
1 AATATAATTAATACAATTAAGATAATACATTTA
568357 AATATA
1 AATATA
568363 CGTATTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 31 0.91
34 3 0.09
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (33 bp):
AATATAATTAATACAATTAAGATAATACATTTA
Found at i:568960 original size:16 final size:16
Alignment explanation
Indices: 568939--568969 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
568929 TAAATGAAAA
568939 AAATTAAATTTGTTTT
1 AAATTAAATTTGTTTT
*
568955 AAATTAGATTTGTTT
1 AAATTAAATTTGTTT
568970 AAGGGTTAAT
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:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
AAATTAAATTTGTTTT
Found at i:569192 original size:15 final size:17
Alignment explanation
Indices: 569152--569193 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
569142 AAGGGAGATC
*
569152 AATTATATTTTACGAGA
1 AATTAAATTTTACGAGA
*
569169 AATTAAATTTT-CGATA
1 AATTAAATTTTACGAGA
569185 AA-TAAATTT
1 AATTAAATTT
569194 GGATCAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 7 0.30
16 6 0.26
17 10 0.43
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (17 bp):
AATTAAATTTTACGAGA
Found at i:570037 original size:10 final size:10
Alignment explanation
Indices: 570022--570047 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
570012 ATAAATCTTT
570022 TATATATCAA
1 TATATATCAA
570032 TATATATCAA
1 TATATATCAA
570042 TATATA
1 TATATA
570048 ATATTAACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (10 bp):
TATATATCAA
Found at i:570566 original size:24 final size:24
Alignment explanation
Indices: 570539--570612 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
570529 AGAAATATAT
* *
570539 AATATATATTATATATGTTTAATA
1 AATATATAATATATATATTTAATA
*
570563 AATATAAAATA-ATATTATTTAATA
1 AATATATAATATATA-TATTTAATA
570587 AA-AT-TAATATA-ATATTTAATA
1 AATATATAATATATATATTTAATA
*
570608 TATAT
1 AATAT
570613 TATATTTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 10 0.24
22 7 0.17
23 6 0.14
24 19 0.45
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
AATATATAATATATATATTTAATA
Found at i:570604 original size:21 final size:18
Alignment explanation
Indices: 570566--570626 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
570556 TTTAATAAAT
570566 ATAAAATAATATTATTTA
1 ATAAAATAATATTATTTA
570584 ATAAAATTAATATAATATTTA
1 ATAAAA-TAATAT--TATTTA
* *
570605 AT-ATATATTA-TATTTA
1 ATAAAATAATATTATTTA
570621 ATAAAA
1 ATAAAA
570627 AAGTATAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
16 8 0.22
17 2 0.06
18 6 0.17
19 10 0.28
20 2 0.06
21 8 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAAATAATATTATTTA
Found at i:570617 original size:16 final size:16
Alignment explanation
Indices: 570593--570623 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
570583 AATAAAATTA
570593 ATATAATATTTAATAT
1 ATATAATATTTAATAT
*
570609 ATATTATATTTAATA
1 ATATAATATTTAATA
570624 AAAAAGTATA
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:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATATTTAATAT
Found at i:575979 original size:24 final size:24
Alignment explanation
Indices: 575952--576004 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
575942 TCTATCGAAT
*
575952 AATTATTTTATATATTAAT-TATAA
1 AATTATTTTATAT-TTAATAAATAA
*
575976 AA-T-TTTTATATTTTATAAATAA
1 AATTATTTTATATTTAATAAATAA
575998 AATTATT
1 AATTATT
576005 AAAATAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 4 0.17
22 14 0.58
23 2 0.08
24 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTATTTTATATTTAATAAATAA
Found at i:580733 original size:16 final size:16
Alignment explanation
Indices: 580708--580752 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
580698 TATTTGATGT
*
580708 TTAAAATTTTTTAATA
1 TTAAAATTTTATAATA
* *
580724 TTAAATTTTTATAATT
1 TTAAAATTTTATAATA
*
580740 TTAAAAATTTATA
1 TTAAAATTTTATA
580753 TCTATATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAAAATTTTATAATA
Found at i:583363 original size:31 final size:27
Alignment explanation
Indices: 583306--583364 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 27
583296 TAATTATTAT
583306 TTAATAATAAAATATATTTTATTTAAA
1 TTAATAATAAAATATATTTTATTTAAA
*
583333 TTAATTATAATAATAATATTTTAATATTAAA
1 TTAATAATAA-AAT-ATATTTT-AT-TTAAA
583364 T
1 T
583365 AGTAAAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 9 0.33
28 3 0.11
29 7 0.26
30 2 0.07
31 6 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TTAATAATAAAATATATTTTATTTAAA
Found at i:585105 original size:25 final size:24
Alignment explanation
Indices: 585056--585105 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
585046 TTTTTAATTC
* *
585056 AATTAAAAATGAATAAAATAGGTA
1 AATTAAAAATAAATAAAAAAGGTA
*
585080 AATTAAAAATAAAATAAAAAATGTA
1 AATTAAAAAT-AAATAAAAAAGGTA
585105 A
1 A
585106 GATGAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (24 bp):
AATTAAAAATAAATAAAAAAGGTA
Found at i:585833 original size:17 final size:16
Alignment explanation
Indices: 585807--585838 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
585797 TTTAATCTCT
585807 TAAAAAATTAAAATTC
1 TAAAAAATTAAAATTC
585823 TAAATAAATTAAAATT
1 TAAA-AAATTAAAATT
585839 TTAATTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAAAATTAAAATTC
Found at i:586414 original size:14 final size:13
Alignment explanation
Indices: 586382--586414 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
586372 AATTAATCTT
586382 AATT-TTAAAATA
1 AATTATTAAAATA
586394 AATTATTAAAATA
1 AATTATTAAAATA
586407 ATATTATT
1 A-ATTATT
586415 TTAAGATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 9 0.47
14 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTATTAAAATA
Found at i:586417 original size:29 final size:29
Alignment explanation
Indices: 586368--586445 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
586358 TGAGACATTA
* *
586368 ATTAAATTAATCTTAATTTTAAAATAAATT
1 ATTAAAATAATATT-ATTTTAAAATAAATT
* * *
586398 ATTAAAATAATATTATTTTAAGATTATTT
1 ATTAAAATAATATTATTTTAAAATAAATT
* *
586427 ATCAAAATATTATTATTTT
1 ATTAAAATAATATTATTTT
586446 GCTCGCATGA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 29 0.71
30 12 0.29
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (29 bp):
ATTAAAATAATATTATTTTAAAATAAATT
Found at i:587454 original size:29 final size:29
Alignment explanation
Indices: 587411--587474 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
587401 ATTATGCAAG
587411 TAAAATAATAGTATTTTAATAAATAATTT
1 TAAAATAATAGTATTTTAATAAATAATTT
* * *
587440 TAAAATAATATTATTTTAATAATTTATTT
1 TAAAATAATAGTATTTTAATAAATAATTT
587469 TAAAAT
1 TAAAAT
587475 TAAAATTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TAAAATAATAGTATTTTAATAAATAATTT
Found at i:587460 original size:14 final size:14
Alignment explanation
Indices: 587414--587471 Score: 66
Period size: 13 Copynumber: 4.1 Consensus size: 14
587404 ATGCAAGTAA
*
587414 AATAATAGTATTTT
1 AATAATATTATTTT
*
587428 AATAA-ATAATTTT
1 AATAATATTATTTT
587441 AAAATAATATTATTTT
1 --AATAATATTATTTT
587457 AATAAT-TTATTTT
1 AATAATATTATTTT
587470 AA
1 AA
587472 AATTAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 15 0.39
14 11 0.29
15 5 0.13
16 7 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
AATAATATTATTTT
Found at i:587682 original size:16 final size:15
Alignment explanation
Indices: 587652--587692 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
587642 AATATAATTT
*
587652 TTTAAATTAATTTAAA
1 TTTAAA-TAACTTAAA
587668 TTTAATATAACTTAAA
1 TTTAA-ATAACTTAAA
587684 TTTAAATAA
1 TTTAAATAA
587693 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 18 0.78
17 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAAATAACTTAAA
Found at i:588010 original size:18 final size:19
Alignment explanation
Indices: 587979--588020 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
587969 GTTTAAGATA
**
587979 ATTTA-AATTATTTATTTT
1 ATTTATAATTATTTAGGTT
587997 ATTTATAATT-TTTAGGTT
1 ATTTATAATTATTTAGGTT
588015 ATTTAT
1 ATTTAT
588021 TTTATTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
ATTTATAATTATTTAGGTT
Found at i:599029 original size:2 final size:2
Alignment explanation
Indices: 599024--599048 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
599014 AATTAAGGCC
599024 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 T
599049 TTGGTGACTG
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:599362 original size:2 final size:2
Alignment explanation
Indices: 599355--599410 Score: 53
Period size: 2 Copynumber: 28.5 Consensus size: 2
599345 ATCAACTATG
* * *
599355 AT AT AT AT AT AT AT AT AT AT A- AA AT AT AA AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
599396 AT -T AT CAT TT AT AT A
1 AT AT AT -AT AT AT AT A
599411 ATAAAAATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:599704 original size:17 final size:17
Alignment explanation
Indices: 599684--599727 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
599674 ATAATTTTAG
599684 TATATATAATATGCATA
1 TATATATAATATGCATA
*
599701 TATATA-AAGTATGTATA
1 TATATATAA-TATGCATA
599718 TATATATAAT
1 TATATATAAT
599728 TTTATTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (17 bp):
TATATATAATATGCATA
Found at i:599767 original size:20 final size:20
Alignment explanation
Indices: 599743--599800 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
599733 TATCTGTATT
599743 TAATATATATTAAAAATATAA
1 TAATATAT-TTAAAAATATAA
*
599764 -AATAT-TTTAAAAATAAAA
1 TAATATATTTAAAAATATAA
599782 TAATA-ATTTTAAAAA-ATAA
1 TAATATA-TTTAAAAATATAA
599801 GTAGGGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 11 0.34
19 8 0.25
20 13 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATATATTTAAAAATATAA
Found at i:599773 original size:18 final size:19
Alignment explanation
Indices: 599743--599800 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
599733 TATCTGTATT
*
599743 TAAT-ATATATTAAAAATA
1 TAATAATATTTTAAAAATA
599761 TAA-AATATTTTAAAAATA
1 TAATAATATTTTAAAAATA
*
599779 AAATAATAATTTTAAAAA-A
1 TAATAAT-ATTTTAAAAATA
599798 TAA
1 TAA
599801 GTAGGGTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 18 0.53
19 6 0.18
20 10 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAATAATATTTTAAAAATA
Found at i:600433 original size:21 final size:21
Alignment explanation
Indices: 600409--600561 Score: 80
Period size: 21 Copynumber: 7.3 Consensus size: 21
600399 AAATTTGTAG
600409 TCAAAATTATATTTAAGGTTA
1 TCAAAATTATATTTAAGGTTA
600430 TCAAAATTATA-TTAATGGTTA
1 TCAAAATTATATTTAA-GGTTA
* * * * *
600451 ACAATATTGTATTAAAAGTTA
1 TCAAAATTATATTTAAGGTTA
*
600472 TCAAAGTATTATA---AAGCTTA
1 TCAAA--ATTATATTTAAGGTTA
* * ** ***
600492 TGAAAATCATATCCAAAACTA
1 TCAAAATTATATTTAAGGTTA
* * *
600513 TCGAAATAATATTAAAGGTTA
1 TCAAAATTATATTTAAGGTTA
* *
600534 TTAAAATTATATTTAAAGTTA
1 TCAAAATTATATTTAAGGTTA
*
600555 TTAAAAT
1 TCAAAAT
600562 CATACCAAAT
Statistics
Matches: 97, Mismatches: 28, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
18 5 0.05
20 13 0.13
21 71 0.73
22 3 0.03
23 5 0.05
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (21 bp):
TCAAAATTATATTTAAGGTTA
Found at i:600603 original size:42 final size:40
Alignment explanation
Indices: 600531--600628 Score: 90
Period size: 42 Copynumber: 2.4 Consensus size: 40
600521 ATATTAAAGG
* * **
600531 TTATTAAAATTATATTTAAAGTTATTAAAATCATACCAAAT
1 TTATCAAAATTATTTTTAAAGTTAAAAAAATCAT-CCAAAT
* *
600572 ATTATCAAAATTATTTTTAATA-TTAAAAAAATTATCGAAAT
1 -TTATCAAAATTATTTTTAA-AGTTAAAAAAATCATCCAAAT
600613 TATATCAAAAGTTATT
1 T-TATCAAAA-TTATT
600629 AAAATTATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
40 1 0.02
41 13 0.28
42 32 0.68
43 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (40 bp):
TTATCAAAATTATTTTTAAAGTTAAAAAAATCATCCAAAT
Found at i:600622 original size:21 final size:21
Alignment explanation
Indices: 600598--600687 Score: 92
Period size: 21 Copynumber: 4.3 Consensus size: 21
600588 TTAATATTAA
*
600598 AAAAATTATCGAAATTATATC
1 AAAAATTATCAAAATTATATC
* *
600619 AAAAGTTATTAAAATTATATC
1 AAAAATTATCAAAATTATATC
*
600640 AAAAATTA-CTAAAATTATATA
1 AAAAATTATC-AAAATTATATC
* * * *
600661 AAAAATGATTAAAATTAGATA
1 AAAAATTATCAAAATTATATC
600682 AAAAAT
1 AAAAAT
600688 ATATATCATT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (21 bp):
AAAAATTATCAAAATTATATC
Found at i:600662 original size:10 final size:10
Alignment explanation
Indices: 600609--600663 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 10
600599 AAAATTATCG
600609 AAATTATATCA
1 AAATTATAT-A
600620 AAAGTTAT-TA
1 AAA-TTATATA
600630 AAATTATATCAA
1 AAATTATAT--A
*
600642 AAATTA-CTA
1 AAATTATATA
600651 AAATTATATA
1 AAATTATATA
600661 AAA
1 AAA
600664 AATGATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
9 11 0.30
10 10 0.27
11 5 0.14
12 11 0.30
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (10 bp):
AAATTATATA
Found at i:600675 original size:72 final size:72
Alignment explanation
Indices: 600537--600677 Score: 158
Period size: 72 Copynumber: 2.0 Consensus size: 72
600527 AAGGTTATTA
** * * ** * *
600537 AAATTATATTTAAAGTTATTAAAATCATACCAAATATTATCAAAATTATTTTTAATATTAAAAAA
1 AAATTATATCAAAAGTTATTAAAATCATACCAAAAATTATCAAAATTATATAAAAAATGAAAAAA
600602 ATTATCG
66 ATTATCG
* * **
600609 AAATTATATCAAAAGTTATTAAAATTATATCAAAAATTA-CTAAAATTATATAAAAAATGATTAA
1 AAATTATATCAAAAGTTATTAAAATCATACCAAAAATTATC-AAAATTATATAAAAAATGAAAAA
600673 AATTA
65 AATTA
600678 GATAAAAAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
71 1 0.02
72 55 0.98
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.38
Consensus pattern (72 bp):
AAATTATATCAAAAGTTATTAAAATCATACCAAAAATTATCAAAATTATATAAAAAATGAAAAAA
ATTATCG
Found at i:600675 original size:93 final size:93
Alignment explanation
Indices: 600506--600677 Score: 218
Period size: 93 Copynumber: 1.8 Consensus size: 93
600496 AATCATATCC
* * ** * * *
600506 AAAACTATCGAAATAATATTAAAGGTTATTAAAATTATATTTAAAGTTATTAAAATCATACCAAA
1 AAAACTATCGAAATAATATCAAAAGTTATTAAAATTATATCAAAAATTACTAAAATCATACAAAA
* *
600571 TATTATCAAAATTATTTTTAATATTAAA
66 AATGATCAAAATTATTTTTAATATTAAA
* * * *
600599 AAAATTATCGAAATTATATCAAAAGTTATTAAAATTATATCAAAAATTACTAAAATTATATAAAA
1 AAAACTATCGAAATAATATCAAAAGTTATTAAAATTATATCAAAAATTACTAAAATCATACAAAA
*
600664 AATGATTAAAATTA
66 AATGATCAAAATTA
600678 GATAAAAAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
93 65 1.00
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (93 bp):
AAAACTATCGAAATAATATCAAAAGTTATTAAAATTATATCAAAAATTACTAAAATCATACAAAA
AATGATCAAAATTATTTTTAATATTAAA
Found at i:601111 original size:30 final size:29
Alignment explanation
Indices: 601054--601108 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
601044 TTAGATCTAA
*
601054 TATATTTATATATTTTATTATATTATAAT
1 TATATTTAAATATTTTATTATATTATAAT
601083 TATATTTAAAATATTTTA-TAT-TTATA
1 TATATTT-AAATATTTTATTATATTATA
601109 TAAATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 5 0.21
29 10 0.42
30 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TATATTTAAATATTTTATTATATTATAAT
Found at i:601354 original size:27 final size:29
Alignment explanation
Indices: 601316--601386 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 29
601306 AATTTTAAAA
*
601316 AAATAAT-TAACATATCAAAATATA-TAT
1 AAATAATATAACATATAAAAATATATTAT
601343 AAAT-ATATAACATATAAAAATATATTAT
1 AAATAATATAACATATAAAAATATATTAT
*
601371 ATATAATATAA-ATATA
1 AAATAATATAACATATA
601387 TGAATTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
26 2 0.05
27 20 0.51
28 11 0.28
29 6 0.15
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (29 bp):
AAATAATATAACATATAAAAATATATTAT
Found at i:601374 original size:17 final size:17
Alignment explanation
Indices: 601334--601376 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
601324 AACATATCAA
*
601334 AATATATATAAATATAT
1 AATATATAAAAATATAT
*
601351 AACATATAAAAATATAT
1 AATATATAAAAATATAT
*
601368 TATATATAA
1 AATATATAA
601377 TATAAATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATATAAAAATATAT
Found at i:601386 original size:15 final size:16
Alignment explanation
Indices: 601334--601387 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
601324 AACATATCAA
601334 AATATATATAAATATAT
1 AATATATAT-AATATAT
* *
601351 AACATATA-AAAATAT
1 AATATATATAATATAT
*
601366 ATTATATATAATATA-
1 AATATATATAATATAT
601381 AATATAT
1 AATATAT
601388 GAATTATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 18 0.60
16 5 0.17
17 7 0.23
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATATATAATATAT
Found at i:601884 original size:2 final size:2
Alignment explanation
Indices: 601879--601905 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
601869 TTCATAAATT
601879 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
601906 GCAAACGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:604196 original size:19 final size:21
Alignment explanation
Indices: 604174--604218 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
604164 TTTTTATATT
*
604174 AATATTTAGAT-AT-AAATTA
1 AATATTTAGATGATAAAAATA
604193 AATA--TAGATGATAAAAATA
1 AATATTTAGATGATAAAAATA
604212 AATATTT
1 AATATTT
604219 TAAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
17 5 0.24
18 2 0.10
19 13 0.62
21 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
AATATTTAGATGATAAAAATA
Found at i:605124 original size:30 final size:32
Alignment explanation
Indices: 605067--605133 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
605057 ACGATTGAAT
* * *
605067 ATATAAATATTTTAAAATATATATAATATAAA
1 ATATTAATATATTAAAATATATATAATAAAAA
*
605099 TTATTAATATATTAAAAT-T-TATAATAAAAA
1 ATATTAATATATTAAAATATATATAATAAAAA
605129 ATATT
1 ATATT
605134 TTAAATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 14 0.47
31 1 0.03
32 15 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATTAATATATTAAAATATATATAATAAAAA
Found at i:605405 original size:30 final size:30
Alignment explanation
Indices: 605369--605425 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
605359 TTAATATGAT
605369 AATAATTAAATAATATAA-AT-AAATATAAAA
1 AATAATT-AA-AATATAATATAAAATATAAAA
605399 AATAATTAAAATATAATATAAAATATA
1 AATAATTAAAATATAATATAAAATATA
605426 TATGATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 7 0.28
29 4 0.16
30 14 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (30 bp):
AATAATTAAAATATAATATAAAATATAAAA
Found at i:605408 original size:21 final size:21
Alignment explanation
Indices: 605376--605444 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 21
605366 GATAATAATT
605376 AAATAATATAAATAAATATAAA
1 AAATAAT-TAAATAAATATAAA
605398 AAATAATTAAAATATAATATAAA
1 AAATAATT-AAATA-AATATAAA
* * *
605421 ATATATATGATAT-AATATAAA
1 AAATA-ATTAAATAAATATAAA
605442 AAA
1 AAA
605445 ATAACATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 11 0.28
22 12 0.30
23 15 0.38
24 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (21 bp):
AAATAATTAAATAAATATAAA
Found at i:605420 original size:23 final size:22
Alignment explanation
Indices: 605376--605444 Score: 79
Period size: 21 Copynumber: 3.1 Consensus size: 22
605366 GATAATAATT
605376 AAATAATATAAATA-AATATAAA
1 AAATAATA-AAATATAATATAAA
605398 AAATAATTAAAATATAATATAAA
1 AAATAA-TAAAATATAATATAAA
* **
605421 ATAT-ATATGATATAATATAAA
1 AAATAATAAAATATAATATAAA
605442 AAA
1 AAA
605445 ATAACATGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 16 0.39
22 12 0.29
23 13 0.32
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (22 bp):
AAATAATAAAATATAATATAAA
Found at i:605437 original size:14 final size:12
Alignment explanation
Indices: 605378--605442 Score: 70
Period size: 11 Copynumber: 5.9 Consensus size: 12
605368 TAATAATTAA
605378 ATAATAT-AAAT
1 ATAATATAAAAT
*
605389 A-AATATAAAAA
1 ATAATATAAAAT
605400 ATAAT-TAAAAT
1 ATAATATAAAAT
605411 ATAATATAAAAT
1 ATAATATAAAAT
*
605423 AT-ATAT--GAT
1 ATAATATAAAAT
605432 ATAATATAAAA
1 ATAATATAAAA
605443 AAATAACATG
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
9 4 0.09
10 9 0.20
11 19 0.43
12 12 0.27
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:605457 original size:24 final size:23
Alignment explanation
Indices: 605408--605466 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
605398 AAATAATTAA
* *
605408 AATATAATAT-AAAATATATATG
1 AATATAATATAAAAAAATACATG
605430 -ATATAATATAAAAAAATAACATG
1 AATATAATATAAAAAAAT-ACATG
* *
605453 AATATGATACAAAA
1 AATATAATATAAAA
605467 TTATAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 9 0.30
22 6 0.20
23 4 0.13
24 11 0.37
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (23 bp):
AATATAATATAAAAAAATACATG
Found at i:605457 original size:63 final size:64
Alignment explanation
Indices: 605362--605483 Score: 144
Period size: 63 Copynumber: 1.9 Consensus size: 64
605352 ATATTTTTTA
*
605362 ATATGATAATAATTAAATAATATAAATAAATAT-AAAAAATAATTA-AAATATAATATAAAATAT
1 ATATGATAATAATTAAATAAAATAAATAAATATGAAAAAA-AATTATAAATATAATATAAAATAT
* * * *
605425 ATATGAT-ATAATATAAA-AAAATAACATGAATATGATACAAAATTATAAATATATTATAA
1 ATATGATAATAAT-TAAATAAAATAA-ATAAATATGAAAAAAAATTATAAATATAATATAA
605484 TATTTTATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
62 11 0.22
63 23 0.46
64 16 0.32
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (64 bp):
ATATGATAATAATTAAATAAAATAAATAAATATGAAAAAAAATTATAAATATAATATAAAATAT
Found at i:605965 original size:10 final size:10
Alignment explanation
Indices: 605950--605988 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
605940 TAAATATTTA
*
605950 ACATATAAAG
1 ACATATATAG
*
605960 ACATATATAT
1 ACATATATAG
*
605970 ATATATATAG
1 ACATATATAG
605980 ACATATATA
1 ACATATATA
605989 TATATATAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (10 bp):
ACATATATAG
Found at i:605969 original size:2 final size:2
Alignment explanation
Indices: 605962--605996 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
605952 ATATAAAGAC
* *
605962 AT AT AT AT AT AT AT AT AG AC 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 A
605997 GATTGGAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:605981 original size:20 final size:20
Alignment explanation
Indices: 605952--605996 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
605942 AATATTTAAC
605952 ATATAAAGACATATATATAT
1 ATATAAAGACATATATATAT
*
605972 ATATATAGACATATATATAT
1 ATATAAAGACATATATATAT
605992 ATATA
1 ATATA
605997 GATTGGAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
ATATAAAGACATATATATAT
Found at i:605985 original size:18 final size:18
Alignment explanation
Indices: 605964--605998 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
605954 ATAAAGACAT
605964 ATATATATATATATAGAC
1 ATATATATATATATAGAC
605982 ATATATATATATATAGA
1 ATATATATATATATAGA
605999 TTGGAAGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (18 bp):
ATATATATATATATAGAC
Found at i:606992 original size:22 final size:22
Alignment explanation
Indices: 606967--607009 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
606957 AATAATAAAA
606967 ATATTTTTAT-ATTAATATTTAT
1 ATATTTTTATAATTAA-ATTTAT
606989 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
607010 AATAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:607474 original size:68 final size:69
Alignment explanation
Indices: 607378--607508 Score: 219
Period size: 68 Copynumber: 1.9 Consensus size: 69
607368 AATTAAACCA
* *
607378 AAAATAGACCTAAACATAAAATTTAAAATTTTTTAAATCAAGACTCAAATTTTACCCGCAAACAA
1 AAAATAAACCTAAACATAAAATTTAAAATCTTTTAAATCAAGACTCAAATTTTACCCGCAAACAA
607443 ATTG
66 ATTG
* *
607447 AAAATAAACCT-AACATAAAATTTAAAATCTTTTAAATCAAGGCTCAAATTTTACCCGTAAAC
1 AAAATAAACCTAAACATAAAATTTAAAATCTTTTAAATCAAGACTCAAATTTTACCCGCAAAC
607509 GTCTTTACTT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
68 48 0.83
69 10 0.17
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (69 bp):
AAAATAAACCTAAACATAAAATTTAAAATCTTTTAAATCAAGACTCAAATTTTACCCGCAAACAA
ATTG
Found at i:608942 original size:14 final size:15
Alignment explanation
Indices: 608922--608961 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
608912 AGATACGAAT
*
608922 TTTAAAATTTTTAAA
1 TTTAAAATTTTAAAA
* *
608937 TTAAAAAATTTAAAA
1 TTTAAAATTTTAAAA
608952 TTTAAAATTT
1 TTTAAAATTT
608962 AAATTTATTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAAATTTTAAAA
Found at i:608967 original size:6 final size:7
Alignment explanation
Indices: 608922--608968 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
608912 AGATACGAAT
608922 TTTAAAA
1 TTTAAAA
*
608929 TTTTTAAA
1 -TTTAAAA
*
608937 TTAAAAAA
1 TT-TAAAA
608945 TTTAAAA
1 TTTAAAA
608952 TTTAAAA
1 TTTAAAA
608959 TTT-AAA
1 TTTAAAA
608965 TTTA
1 TTTA
608969 TTGGATCTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
6 6 0.18
7 16 0.48
8 11 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TTTAAAA
Found at i:609764 original size:14 final size:14
Alignment explanation
Indices: 609745--609771 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
609735 ATTAATATTT
609745 AAAATATATTTAAC
1 AAAATATATTTAAC
609759 AAAATATATTTAA
1 AAAATATATTTAA
609772 AATAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATATATTTAAC
Found at i:611015 original size:21 final size:21
Alignment explanation
Indices: 610998--611072 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
610988 TAAAATAAAT
610998 TTTTAATATTTTTTAATAATAA
1 TTTTAA-ATTTTTTAATAATAA
*
611020 TTTTAAATTTTTGAATGGAATTAA
1 TTTTAAATTTTTTAAT--AA-TAA
* *
611044 ATTTAAA-TTTTT-ATAAAAA
1 TTTTAAATTTTTTAATAATAA
611063 TTTTAAATTT
1 TTTTAAATTT
611073 ACAAATTGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 8 0.18
20 4 0.09
21 9 0.20
22 8 0.18
23 6 0.14
24 9 0.20
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
TTTTAAATTTTTTAATAATAA
Found at i:612003 original size:8 final size:8
Alignment explanation
Indices: 611990--612040 Score: 58
Period size: 8 Copynumber: 6.9 Consensus size: 8
611980 GGTAAGACGG
611990 AAAAAATT
1 AAAAAATT
611998 AAAAAAATT
1 -AAAAAATT
612007 --AAAA--
1 AAAAAATT
612011 AAAAAATT
1 AAAAAATT
612019 AAAAAATT
1 AAAAAATT
612027 -AAAAATT
1 AAAAAATT
612034 AAAAAAT
1 AAAAAAT
612041 ATTTTTTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
6 8 0.22
7 7 0.19
8 14 0.38
9 8 0.22
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAAATT
Found at i:612004 original size:9 final size:9
Alignment explanation
Indices: 611990--612039 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
611980 GGTAAGACGG
611990 AAAAAATTA
1 AAAAAATTA
611999 AAAAAATTAAAA
1 AAAAAATT---A
612011 AAAAAATT-
1 AAAAAATTA
612019 AAAAAATT-
1 AAAAAATTA
612027 -AAAAATTA
1 AAAAAATTA
612035 AAAAA
1 AAAAA
612040 TATTTTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 7 0.19
8 8 0.22
9 12 0.33
12 9 0.25
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATTA
Found at i:612010 original size:7 final size:7
Alignment explanation
Indices: 612000--612038 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
611990 AAAAAATTAA
612000 AAAAATT
1 AAAAATT
612007 AAAAA--
1 AAAAATT
612012 AAAAATT
1 AAAAATT
612019 AAAAAATT
1 -AAAAATT
612027 AAAAATT
1 AAAAATT
612034 AAAAA
1 AAAAA
612039 ATATTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
7 17 0.59
8 7 0.24
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAAATT
Found at i:612037 original size:21 final size:21
Alignment explanation
Indices: 611990--612031 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
611980 GGTAAGACGG
611990 AAAAAATTAAAAAAATTAAAA
1 AAAAAATTAAAAAAATTAAAA
612011 AAAAAATT-AAAAAATTAAAA
1 AAAAAATTAAAAAAATTAAAA
612031 A
1 A
612032 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (21 bp):
AAAAAATTAAAAAAATTAAAA
Found at i:612188 original size:18 final size:17
Alignment explanation
Indices: 612161--612199 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
612151 TTATATTTAT
*
612161 TAAAATTTAAAATAAAAA
1 TAAAAATTAAAA-AAAAA
*
612179 TAAAAATTAAAAAATAA
1 TAAAAATTAAAAAAAAA
612196 TAAA
1 TAAA
612200 TAATATTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAATTAAAAAAAAA
Found at i:612687 original size:17 final size:17
Alignment explanation
Indices: 612661--612708 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
612651 GATATCAAAT
612661 ATTTTTATTTATTT-TA
1 ATTTTTATTTATTTCTA
* *
612677 ATTTTTAATTTTTTTCTT
1 ATTTTT-ATTTATTTCTA
612695 ATTTTTATTTATTT
1 ATTTTTATTTATTT
612709 GTGTAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 6 0.22
17 14 0.52
18 7 0.26
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (17 bp):
ATTTTTATTTATTTCTA
Found at i:613035 original size:16 final size:16
Alignment explanation
Indices: 613014--613063 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
613004 TTAAAGGTTG
613014 AATTTAATTTTTTATT
1 AATTTAATTTTTTATT
*
613030 AATTTAATTTTATT-TG
1 AATTTAATTTT-TTATT
613046 AA-TTAATTTTTTA-T
1 AATTTAATTTTTTATT
613060 AATT
1 AATT
613064 AGAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 14 0.48
17 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
AATTTAATTTTTTATT
Found at i:615452 original size:13 final size:13
Alignment explanation
Indices: 615434--615458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
615424 TAATTATTTT
615434 TTAAAATAAAAAA
1 TTAAAATAAAAAA
615447 TTAAAATAAAAA
1 TTAAAATAAAAA
615459 TAAAAAGGGT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TTAAAATAAAAAA
Found at i:615611 original size:135 final size:130
Alignment explanation
Indices: 615368--615724 Score: 478
Period size: 134 Copynumber: 2.8 Consensus size: 130
615358 TATTATTTTT
* *
615368 AATAAAAAATAATATTTGATTAAGTTTAAAAAAATTACATTAATAAATTAAAATATT-A--ATTA
1 AATAAAAAATAATATTTAATTAAGTTT-AAAAAATTACATTAGTAAATTAAAATATTAATTATTA
* *
615430 T-TTTTTAAAATAAAAAA--TTAAAAT--AAAAATAAAAAGGGTTTATTATTATTATGTTTTAAT
65 TGTTTTTAAAATAAAAAATTTTAAAATAAAAAAATAAAAAAGGTTTATTATTATAAT-TTTTAAT
615490 AA
129 AA
*
615492 AATTAAAAATAATATTTAATTAAGTTTAAAAAATTACATTAGTAAATTAAAATATTAATTATTAT
1 AATAAAAAATAATATTTAATTAAGTTTAAAAAATTACATTAGTAAATTAAAATATTAATTATTAT
*
615557 GCTTTTATAAAAATAAAAAATTTTAAAATAAAAAAATAAAAAAAGGTTTTTTATTATAATTTTTA
66 G-TTTT-T-AAAATAAAAAATTTTAAAATAAAAAAAT-AAAAAAGGTTTATTATTATAATTTTTA
615622 ATAA
127 ATAA
* * * * *
615626 AATAAAAAATAATATTTAATCAAGTTTAAAAATTTTATATTAGCAAATTAAAATATTATTTATTA
1 AATAAAAAATAATATTTAATTAAGTTTAAAAA-ATTACATTAGTAAATTAAAATATTAATTATTA
* *
615691 TGTTTTTAAAATAAATAATTTTAAATTAAAAAAA
65 TGTTTTTAAAATAAAAAATTTTAAAATAAAAAAA
615725 ATTTTTATTA
Statistics
Matches: 206, Mismatches: 14, Indels: 18
0.87 0.06 0.08
Matches are distributed among these distances:
123 28 0.14
124 26 0.13
126 5 0.02
128 4 0.02
129 1 0.00
130 11 0.05
132 32 0.16
133 1 0.00
134 49 0.24
135 49 0.24
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (130 bp):
AATAAAAAATAATATTTAATTAAGTTTAAAAAATTACATTAGTAAATTAAAATATTAATTATTAT
GTTTTTAAAATAAAAAATTTTAAAATAAAAAAATAAAAAAGGTTTATTATTATAATTTTTAATAA
Found at i:616057 original size:35 final size:36
Alignment explanation
Indices: 616000--616091 Score: 98
Period size: 35 Copynumber: 2.5 Consensus size: 36
615990 AAGATATGAC
* * *
616000 TAATATATAAAATTTTTCTTAGATTTTAAAAGATAT
1 TAATATATAAAATTTTTATTAGAATATAAAAGATAT
*
616036 TAAT-TAT-AAATTATTTATTAGAATATAAAAGATGTGAC
1 TAATATATAAAATT-TTTATTAGAATATAAAAGA--T-AT
616074 TAATATATAAAATTTTTA
1 TAATATATAAAATTTTTA
616092 GCATTTTTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
34 5 0.11
35 19 0.41
36 4 0.09
37 1 0.02
38 5 0.11
39 7 0.15
40 5 0.11
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (36 bp):
TAATATATAAAATTTTTATTAGAATATAAAAGATAT
Found at i:616668 original size:92 final size:93
Alignment explanation
Indices: 616452--616893 Score: 302
Period size: 92 Copynumber: 4.9 Consensus size: 93
616442 AATGCATAGA
* * **
616452 TTGTAAATGTCAGATTACAAGGATTAAACTAATACATGAATTATATTTGAGAGTCGAATTTTTTT
1 TTGTAAATGTCAGATTACAAGGATTAAACTAATACATAAATTATATATGAGAAACGAATTTTTTT
*
616517 TTATAAAAAAAAAAGAAAAGTTGATTAG
66 ATATAAAAAAAAAAGAAAAGTTGATTAG
* * * * * *
616545 TTGTAAATGTCAAACTACAAGGATTAGACTAATGCATAAATTATATATGATAAACGGATTTTTTT
1 TTGTAAATGTCAGATTACAAGGATTAAACTAATACATAAATTATATATGAGAAACGAATTTTTTT
616610 AT-TAAAAAAAAAAGAAAAGTT-ATTTGAG
66 ATATAAAAAAAAAAGAAAAGTTGA-TT-AG
* * * * * * *
616638 -TGTAAATATTAGATTGCAAGGGTTAAACTAATACATTAATTATATCA-AAGAATC-ATATTTTT
1 TTGTAAATGTCAGATTACAAGGATTAAACTAATACATAAATTATAT-ATGAGAAACGA-ATTTTT
616700 TTAT-T------AAAA-AAAAGTTGATTAAG
64 TTATATAAAAAAAAAAGAAAAGTTGATT-AG
* * * ** * * * *
616723 -TATAAATGTCAGACTGCAAATATTAGACTAATGCATAAATTATATTTGAGAATCGAATTCTTTT
1 TTGTAAATGTCAGATTACAAGGATTAAACTAATACATAAATTATATATGAGAAACGAATT-TTTT
*
616787 T-TAT----AGAAAA-AAAAGTTGATT-G
65 TATATAAAAAAAAAAGAAAAGTTGATTAG
* * * * * * *
616809 ATTGTGAATGTCAGACTGA-AAGGATTAGACTAATGCATGAATTATATCTGA-AAAGCGGATTCT
1 -TTGTAAATGTCAGA-TTACAAGGATTAAACTAATACATAAATTATATATGAGAAA-CGAATT-T
616872 TTTT-TATAGAAAAAAAAAGAAA
62 TTTTATATA-AAAAAAAAAGAAA
616894 GACTGCAAGG
Statistics
Matches: 279, Mismatches: 49, Indels: 41
0.76 0.13 0.11
Matches are distributed among these distances:
85 56 0.20
86 13 0.05
87 2 0.01
88 68 0.24
91 1 0.00
92 72 0.26
93 64 0.23
94 3 0.01
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (93 bp):
TTGTAAATGTCAGATTACAAGGATTAAACTAATACATAAATTATATATGAGAAACGAATTTTTTT
ATATAAAAAAAAAAGAAAAGTTGATTAG
Found at i:616823 original size:88 final size:88
Alignment explanation
Indices: 616450--616890 Score: 363
Period size: 88 Copynumber: 4.9 Consensus size: 88
616440 ATAATGCATA
* * * * * * * *
616450 GATTGTAAATGTCAGATTACAAGGATTAAACTAATACATGAATTATATTTGAGAGTCGAATTTTT
1 GATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATAAATTATATCTGAGAATCGAATTCTT
616515 TTTTATAAAAAAAAAAGAAAAGTTGATT
66 TTTTAT----AAAAAA-AAAAGTTGATT
* * * * * * *
616543 -AGTTGTAAATGTCAAACTACAAGGATTAGACTAATGCATAAATTATATATGATAAACGGATTTT
1 GA-TTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATAAATTATATCTGAGAATCGAATTCT
*
616607 TTTATTAAAAAAAAAAGAAAAGTT-ATTT
65 TTT-TT--ATAAAAAA-AAAAGTTGA-TT
* * * * * * * * **
616635 GAGTGTAAATATTAGATTGCAAGGGTTAAACTAATACATTAATTATATCAAAGAATC--ATAT-T
1 GATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATAAATTATATCTGAGAATCGAAT-TCT
*
616697 TTTTTAT-TAAAAAAAAGTTGATT
65 TTTTTATAAAAAAAAAAGTTGATT
* * * ** *
616720 AAGTATAAATGTCAGACTGCAAATATTAGACTAATGCATAAATTATATTTGAGAATCGAATTCTT
1 GATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATAAATTATATCTGAGAATCGAATTCTT
*
616785 TTTTATAGAAAAAAAAGTTGATT
66 TTTTATAAAAAAAAAAGTTGATT
* * * * * *
616808 GATTGTGAATGTCAGACTGAAAGGATTAGACTAATGCATGAATTATATCTGAAAAGCGGATTCTT
1 GATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATAAATTATATCTGAGAATCGAATTCTT
616873 TTTTATAGAAAAAAAAAG
66 TTTTATA-AAAAAAAAAG
616891 AAAGACTGCA
Statistics
Matches: 279, Mismatches: 56, Indels: 30
0.76 0.15 0.08
Matches are distributed among these distances:
85 52 0.19
86 6 0.02
87 11 0.04
88 75 0.27
89 11 0.04
90 6 0.02
91 2 0.01
92 57 0.20
93 56 0.20
94 2 0.01
96 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (88 bp):
GATTGTAAATGTCAGACTGCAAGGATTAGACTAATGCATAAATTATATCTGAGAATCGAATTCTT
TTTTATAAAAAAAAAAGTTGATT
Found at i:616908 original size:72 final size:70
Alignment explanation
Indices: 616821--616958 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 70
616811 TGTGAATGTC
* * *
616821 AGACTGAAAGGATTAGACTAATGCATGAATTATATCTGAAAAGCGGATTCTTTTTTATAGAAAAA
1 AGACTGAAAGGATTAGACTAATACATGAATTATATCTG-AAAGCGGATTCTTCTTAATA-AAAAA
616886 AAAAGAA
64 AAAAGAA
* * *
616893 AGACTGCAAGGATTAGACTAATACATGAATTTTATCTGAAATCGGATTCTTCTTAATAAAAAAAA
1 AGACTGAAAGGATTAGACTAATACATGAATTATATCTGAAAGCGGATTCTTCTTAATAAAAAAAA
616958 A
66 A
616959 GTTGATTGAG
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 8 0.13
71 17 0.28
72 35 0.58
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (70 bp):
AGACTGAAAGGATTAGACTAATACATGAATTATATCTGAAAGCGGATTCTTCTTAATAAAAAAAA
AAGAA
Found at i:617083 original size:91 final size:91
Alignment explanation
Indices: 616893--617317 Score: 480
Period size: 86 Copynumber: 4.8 Consensus size: 91
616883 AAAAAAAGAA
* * *
616893 AGACTGCAAGGATTAGACTAATACATGAATTTTATCTGA-AATCGGATTCTTCTTA-AT---AAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTT-TTATATAAAAAA
* *
616953 AA-AAAAGTTGATTGAGTGTAAATGTT
65 AAGAAAAGTTGATTGAGTGTAAATATC
* *
616979 AGACTGTAAGGATTAGACTAATGCATGAATTATATCAGAGAATCAGATTCTTTTATATAAAAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTATATAAAAAAA
* *
617044 AGAAAAGTTGATTGAGTGTAAATGTT
66 AGAAAAGTTGATTGAGTGTAAATATC
* * * *
617070 AGACTGCAGGGATTAGACTAATGCATAAATTATATCAGAGAATCACATTCGTTTT-TATAGAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTC-TTTTATATA-AAAA
* * *
617134 AAAGAAAAATTGATTAAGTATAAATATC
64 AAAGAAAAGTTGATTGAGTGTAAATATC
** * * *
617162 AGACTGCAAATATTAGACTAATGCATGAATTATATTTGAGAATCAGATTCTTTTTTATAGAAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTATATAAAAAAA
**
617227 AGTTAA-TTGATT--GTG--AATATC
66 AGAAAAGTTGATTGAGTGTAAATATC
* * * *
617248 AGACTGAAAGGATTAGACTAATGCATAAATTATATCTGAGAATC-GAATTCTTTTTTATAGAAAA
1 AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAG-ATTCTTTTATATAAAAAA
617312 AAGAAA
65 AAGAAA
617318 GACCGTAAGG
Statistics
Matches: 297, Mismatches: 32, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
85 1 0.00
86 105 0.35
87 13 0.04
88 2 0.01
90 11 0.04
91 87 0.29
92 78 0.26
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.32
Consensus pattern (91 bp):
AGACTGCAAGGATTAGACTAATGCATGAATTATATCTGAGAATCAGATTCTTTTATATAAAAAAA
AGAAAAGTTGATTGAGTGTAAATATC
Found at i:617195 original size:183 final size:177
Alignment explanation
Indices: 616893--617317 Score: 493
Period size: 183 Copynumber: 2.4 Consensus size: 177
616883 AAAAAAAGAA
* * * * * * * *
616893 AGACTGCAAGGATTAGACTAATACATGAATTTTATCTGA-AATCGGATTC-TTCTTA-A-TAAAA
1 AGACTGAAAGGATTAGACTAATGCATAAATTATATCAGAGAATCGAATTCGTTTTTATAGAAAAA
* * * * * * *
616954 A-AAAAGTTGATTGAGTGTAAATGTTAGACTGTAAGGATTAGACTAATGCATGAATTATATCAGA
66 AGAAAAATTGATTAAGTATAAATATCAGACTGCAAAGATTAGACTAATGCATGAATTATATCAGA
* *
617018 GAATCAGATTCTTTTATATAAAAAAAAGAAAAGTTGATTGAGTGTAAATGTT
131 GAATCAGATTCTTTTATATAAAAAAAAGAAAA-TTGATT--GTG--AATATC
* *
617070 AGACTGCAGGGATTAGACTAATGCATAAATTATATCAGAGAATC-ACATTCGTTTTTATAGAAAA
1 AGACTGAAAGGATTAGACTAATGCATAAATTATATCAGAGAATCGA-ATTCGTTTTTATAG-AAA
* **
617134 AAAGAAAAATTGATTAAGTATAAATATCAGACTGCAAATATTAGACTAATGCATGAATTATATTT
64 AAAGAAAAATTGATTAAGTATAAATATCAGACTGCAAAGATTAGACTAATGCATGAATTATATCA
* * **
617199 GAGAATCAGATTCTTTTTTATAGAAAAAAGTTAATTGATTGTGAATATC
129 GAGAATCAGATTCTTTTATATAAAAAAAAGAAAATTGATTGTGAATATC
* *
617248 AGACTGAAAGGATTAGACTAATGCATAAATTATATCTGAGAATCGAATTCTTTTTTATAGAAAAA
1 AGACTGAAAGGATTAGACTAATGCATAAATTATATCAGAGAATCGAATTCGTTTTTATAGAAAAA
617313 AGAAA
66 AGAAA
617318 GACCGTAAGG
Statistics
Matches: 212, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
177 44 0.21
178 66 0.31
179 6 0.03
180 4 0.02
182 11 0.05
183 81 0.38
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.32
Consensus pattern (177 bp):
AGACTGAAAGGATTAGACTAATGCATAAATTATATCAGAGAATCGAATTCGTTTTTATAGAAAAA
AGAAAAATTGATTAAGTATAAATATCAGACTGCAAAGATTAGACTAATGCATGAATTATATCAGA
GAATCAGATTCTTTTATATAAAAAAAAGAAAATTGATTGTGAATATC
Found at i:621468 original size:112 final size:111
Alignment explanation
Indices: 621206--621496 Score: 388
Period size: 112 Copynumber: 2.7 Consensus size: 111
621196 TAAATATTAT
* *
621206 TTTTTAAATTTGTTGATGTAAA--TTTTTAAATTTAATTAAATATTATTTTTTATTTTATT-AAA
1 TTTTT-AATTTGTTAATGTAAATTTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAA
621268 A-AATAATTAAAAAAAACTTTTTATTTTTATAAAAATAATAATTAATA
65 ATAATAATT-AAAAAAACTTTTTATTTTTATAAAAATAATAATTAATA
*
621315 TTTTTAATTTGTTAATGT-AATTTTTTAAAACTTAATTAAATATTATTTTTTATTTTATTAAAAA
1 TTTTTAATTTGTTAATGTAAATTTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAA
* ** *
621379 TAATAATTATAAACCCTTTTTATTTTTATTTTTAAAA-AATAATTAATA
66 TAATAATTAAAAAAACTTTTTATTTTTA---TAAAAATAATAATTAATA
*
621427 -TTTTAATTTGTTAATGTAAATTTTTTTAAACTTAATCAAATATTATTTTTTA--TTA--AAAAA
1 TTTTTAATTTGTTAATGTAAATTTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAA
621487 TAATAATTAA
66 TAATAATTAA
621497 TACATCATTA
Statistics
Matches: 164, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
107 2 0.01
108 26 0.16
109 40 0.24
110 24 0.15
111 24 0.15
112 43 0.26
113 5 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (111 bp):
TTTTTAATTTGTTAATGTAAATTTTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAA
TAATAATTAAAAAAACTTTTTATTTTTATAAAAATAATAATTAATA
Found at i:622074 original size:12 final size:12
Alignment explanation
Indices: 622057--622083 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
622047 GCATGAAATA
622057 TAATGATTGAAT
1 TAATGATTGAAT
622069 TAATGATTGAAT
1 TAATGATTGAAT
622081 TAA
1 TAA
622084 AAATACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (12 bp):
TAATGATTGAAT
Found at i:624125 original size:22 final size:22
Alignment explanation
Indices: 624077--624125 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
624067 CAAGATTTAT
624077 ATATATTCATTTAAATAATAAA
1 ATATATTCATTTAAATAATAAA
* *
624099 A-ATATTTATTTAAA-ATTTAAA
1 ATATATTCATTTAAATA-ATAAA
624120 ATATAT
1 ATATAT
624126 AATTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATATTCATTTAAATAATAAA
Found at i:624525 original size:18 final size:18
Alignment explanation
Indices: 624502--624537 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
624492 TTATTAACAC
624502 TATCATTATTAATAAAAT
1 TATCATTATTAATAAAAT
*
624520 TATCATTATTAATGAAAT
1 TATCATTATTAATAAAAT
624538 ATAATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (18 bp):
TATCATTATTAATAAAAT
Found at i:625090 original size:2 final size:2
Alignment explanation
Indices: 625083--625111 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
625073 AATTTTACAT
625083 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 T
625112 CTCTCTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.