Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold212
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: 1080337
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 10
Found at i:425453 original size:15 final size:13
Alignment explanation
Indices: 425433--425480 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
425423 AAACTTAACA
425433 AAAAATTAAATTATT
1 AAAAATTAAA-TA-T
425448 AAAAATTAAATAT
1 AAAAATTAAATAT
* *
425461 AAAAATATATATTT
1 AAAAAT-TAAATAT
425475 AAAAAT
1 AAAAAT
425481 AATAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 7 0.23
14 13 0.43
15 10 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAAATTAAATAT
Found at i:425465 original size:14 final size:15
Alignment explanation
Indices: 425432--425523 Score: 59
Period size: 15 Copynumber: 6.0 Consensus size: 15
425422 AAAACTTAAC
425432 AAAAAATTAAATTAT
1 AAAAAATTAAATTAT
*
425447 TAAAAATTAAA-TAT
1 AAAAAATTAAATTAT
*
425461 -AAAAATATATATT-T
1 AAAAAAT-TAAATTAT
*
425475 AAAAATAATAAATAATAT
1 AAAAA-ATTAAAT--TAT
425493 ATAAAAA-TAAATT-T
1 A-AAAAATTAAATTAT
425507 AAATAAACTTAAATTAT
1 AAA-AAA-TTAAATTAT
425524 TTATTTATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 22
0.70 0.05 0.25
Matches are distributed among these distances:
13 8 0.13
14 12 0.20
15 20 0.33
16 7 0.11
17 7 0.11
18 3 0.05
19 4 0.07
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAAATTAAATTAT
Found at i:425473 original size:26 final size:24
Alignment explanation
Indices: 425446--425495 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
425436 AATTAAATTA
425446 TTAAAAATTAAATATAAAAATATATAT
1 TTAAAAA-T-AATA-AAAAATATATAT
*
425473 TTAAAAATAATAAATAATATATA
1 TTAAAAATAATAAAAAATATATA
425496 AAAATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 4 0.18
26 1 0.05
27 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
TTAAAAATAATAAAAAATATATAT
Found at i:425476 original size:20 final size:19
Alignment explanation
Indices: 425453--425503 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
425443 TTATTAAAAA
*
425453 TTAAATATAAAAATATATAT
1 TTAAAAATAAAAATA-ATAT
425473 TTAAAAATAATAAATAATAT
1 TTAAAAATAA-AAATAATAT
*
425493 ATAAAAATAAA
1 TTAAAAATAAA
425504 TTTAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 1 0.04
20 22 0.79
21 5 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAAATAAAAATAATAT
Found at i:425585 original size:14 final size:14
Alignment explanation
Indices: 425548--425599 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
425538 AATCAAATCT
425548 AAATTAAATTT-AA
1 AAATTAAATTTAAA
* *
425561 AATTTATATTTAAA
1 AAATTAAATTTAAA
425575 AAATTAAATTTAAA
1 AAATTAAATTTAAA
425589 TAAATATAAAT
1 -AAAT-TAAAT
425600 AATATTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 9 0.28
14 14 0.44
15 4 0.12
16 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATTAAATTTAAA
Found at i:427636 original size:18 final size:19
Alignment explanation
Indices: 427603--427639 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
427593 TATTATTTAT
*
427603 AAATTTATTAAAAATAAAA
1 AAATTAATTAAAAATAAAA
427622 AAATTAATT-AAAATAAAA
1 AAATTAATTAAAAATAAAA
427640 TGAGACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATTAATTAAAAATAAAA
Found at i:428187 original size:17 final size:17
Alignment explanation
Indices: 428154--428187 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
428144 ATCGACGTTT
* *
428154 TTTTTATTATTATTTTA
1 TTTTTATTATAACTTTA
428171 TTTTTATTATAACTTTA
1 TTTTTATTATAACTTTA
428188 AATATAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTATTATAACTTTA
Found at i:432229 original size:2 final size:2
Alignment explanation
Indices: 432222--432262 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
432212 TGCATGTACT
432222 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
432263 TCAAGGCTTT
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:432860 original size:8 final size:8
Alignment explanation
Indices: 432847--432871 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
432837 TAAGTAACAT
432847 TATATACA
1 TATATACA
432855 TATATACA
1 TATATACA
432863 TATATACA
1 TATATACA
432871 T
1 T
432872 GAGAAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (8 bp):
TATATACA
Found at i:438069 original size:12 final size:13
Alignment explanation
Indices: 438047--438075 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
438037 TCTGAGAAAG
438047 AAAGCATGAAGAA
1 AAAGCATGAAGAA
438060 AAAG-ATGAAGAA
1 AAAGCATGAAGAA
438072 AAAG
1 AAAG
438076 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.66, C:0.03, G:0.24, T:0.07
Consensus pattern (13 bp):
AAAGCATGAAGAA
Found at i:438381 original size:22 final size:22
Alignment explanation
Indices: 438356--438412 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
438346 TTAAATTACT
*
438356 TTTAAATTTA-AGATTATTTTA-G
1 TTTAAATTTATA-A-TATTTTATA
438378 TTTAAATTTATAATATTTTATA
1 TTTAAATTTATAATATTTTATA
438400 TTTAAATTT-TAAT
1 TTTAAATTTATAAT
438413 TAATAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 11 0.34
22 20 0.62
23 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
TTTAAATTTATAATATTTTATA
Found at i:438388 original size:16 final size:15
Alignment explanation
Indices: 438315--438520 Score: 88
Period size: 15 Copynumber: 13.7 Consensus size: 15
438305 AACCTTTGGA
* *
438315 TTAAATTAAATTTAAA
1 TTAAATT-ATTTTAAT
438331 TTAAATTATTTTAAT
1 TTAAATTATTTTAAT
438346 TTAAATTACTTTTAAAT
1 TTAAATTA-TTTT-AAT
*
438363 TTAAGATTATTTTAGT
1 TTAA-ATTATTTTAAT
*
438379 TTAAA-T-TTATAAT
1 TTAAATTATTTTAAT
** *
438392 ATTTTA-TATTTAAAT
1 -TTAAATTATTTTAAT
* * **
438407 TTTAATTAATAAAAT
1 TTAAATTATTTTAAT
*
438422 TT-AA-TATTTTAAA
1 TTAAATTATTTTAAT
* *
438435 TT-AATTAAATTTAAA
1 TTAAATT-ATTTTAAT
* *
438450 TTAATTTAATTTAAT
1 TTAAATTATTTTAAT
* *
438465 TTAATTTAGTTTAAT
1 TTAAATTATTTTAAT
*
438480 ATTATAATT-TATTAAAT
1 -TTA-AATTAT-TTTAAT
*
438497 TT-AATTATTTTAAA
1 TTAAATTATTTTAAT
438511 TT-AATTATTT
1 TTAAATTATTT
438521 AGATAAAATC
Statistics
Matches: 152, Mismatches: 25, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
13 14 0.09
14 30 0.20
15 60 0.39
16 25 0.16
17 19 0.12
18 4 0.03
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (15 bp):
TTAAATTATTTTAAT
Found at i:438401 original size:28 final size:28
Alignment explanation
Indices: 438370--438442 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
438360 AATTTAAGAT
* * * *
438370 TATTTTAGTTTAAATTTATAATATTTTA
1 TATTTTAATTTAAATTAATAAAATTTAA
* *
438398 TATTTAAATTTTAATTAATAAAATTTAA
1 TATTTTAATTTAAATTAATAAAATTTAA
*
438426 TATTTTAAATT-AATTAA
1 TATTTTAATTTAAATTAA
438443 ATTTAAATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
27 6 0.16
28 31 0.84
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (28 bp):
TATTTTAATTTAAATTAATAAAATTTAA
Found at i:438455 original size:10 final size:10
Alignment explanation
Indices: 438437--438516 Score: 58
Period size: 10 Copynumber: 7.8 Consensus size: 10
438427 ATTTTAAATT
438437 AATTAAATTTA
1 AATT-AATTTA
438448 AATTAATTTA
1 AATTAATTTA
*
438458 ATTTAATTTA
1 AATTAATTTA
* *
438468 ATTTAGTTTA
1 AATTAATTTA
438478 ATATTATAATTT-
1 A-A-T-TAATTTA
438490 -ATTAAATTT-
1 AATT-AATTTA
*
438499 AATTATTTTA
1 AATTAATTTA
438509 AATTAATT
1 AATTAATT
438517 ATTTAGATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
8 1 0.02
9 10 0.18
10 36 0.63
11 4 0.07
12 1 0.02
13 5 0.09
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (10 bp):
AATTAATTTA
Found at i:438568 original size:16 final size:17
Alignment explanation
Indices: 438529--438578 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
438519 TTAGATAAAA
438529 TCAAGTTTAAATCATTT
1 TCAAGTTTAAATCATTT
* *
438546 T-ACGTTTAAA-CCTTT
1 TCAAGTTTAAATCATTT
* *
438561 TCAAGTTTTAATTATTT
1 TCAAGTTTAAATCATTT
438578 T
1 T
438579 GAATTCGAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
15 5 0.20
16 15 0.60
17 5 0.20
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (17 bp):
TCAAGTTTAAATCATTT
Found at i:439448 original size:15 final size:14
Alignment explanation
Indices: 439384--439457 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 14
439374 ATCAAATTAT
*
439384 ATATAATAATTTTAA
1 ATATAATAA-TATAA
439399 ATATGATATAAATATATA
1 ATAT-A-AT-AATATA-A
439417 ATATAA-AATAT-A
1 ATATAATAATATAA
439429 ATATAATTAATATAA
1 ATATAA-TAATATAA
439444 ATATAATAAATATA
1 ATATAAT-AATATA
439458 TATTATTTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
12 7 0.14
14 11 0.22
15 17 0.34
16 2 0.04
17 6 0.12
18 7 0.14
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (14 bp):
ATATAATAATATAA
Found at i:439451 original size:25 final size:25
Alignment explanation
Indices: 439398--439485 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
439388 AATAATTTTA
* * *
439398 AATATGATATAAAT-ATATAATATAA
1 AATATAATATAATTAATATAA-ATAT
439423 AATATAATATAATTAATATAAATAT
1 AATATAATATAATTAATATAAATAT
* *
439448 AATA-AATATATATTATTTTAAATAT
1 AATATAATATA-ATTAATATAAATAT
*
439473 AATTATATTATAA
1 AA-TATAATATAA
439486 AAATTAAGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
24 6 0.11
25 33 0.62
26 9 0.17
27 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (25 bp):
AATATAATATAATTAATATAAATAT
Found at i:439814 original size:43 final size:43
Alignment explanation
Indices: 439767--439862 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 43
439757 TAATTGTTAA
* *
439767 ATAAAAATAGTATTATTAAAAA-ATATTAATGTAATGTAATAAT
1 ATAAAAATAGTATT-TTAAAAATATAATAATATAATGTAATAAT
* * * *
439810 ATAAAAAAATTATTTTAAAAATATAATAATATAATTTTATAAT
1 ATAAAAATAGTATTTTAAAAATATAATAATATAATGTAATAAT
*
439853 AAATAAAATA
1 ATA-AAAATA
439863 AAAACTTATA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
42 7 0.16
43 31 0.72
44 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (43 bp):
ATAAAAATAGTATTTTAAAAATATAATAATATAATGTAATAAT
Found at i:439838 original size:25 final size:25
Alignment explanation
Indices: 439804--439866 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
439794 AATGTAATGT
* *
439804 AATAATATAAAAAAATTATTTTAA-A
1 AATAAAATAAAAAAATT-TTATAATA
* * *
439829 AATATAATAATATAATTTTATAATA
1 AATAAAATAAAAAAATTTTATAATA
439854 AATAAAATAAAAA
1 AATAAAATAAAAA
439867 CTTATATTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AATAAAATAAAAAAATTTTATAATA
Found at i:439846 original size:22 final size:22
Alignment explanation
Indices: 439782--439848 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
439772 AATAGTATTA
* *
439782 TTAAAAA-ATATTAATGTAA-T
1 TTAAAAATATAATAATATAATT
* * * * *
439802 GTAATAATATAAAAAAATTATT
1 TTAAAAATATAATAATATAATT
439824 TTAAAAATATAATAATATAATT
1 TTAAAAATATAATAATATAATT
439846 TTA
1 TTA
439849 TAATAAATAA
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 5 0.15
21 7 0.21
22 21 0.64
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
TTAAAAATATAATAATATAATT
Found at i:441753 original size:19 final size:18
Alignment explanation
Indices: 441715--441773 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
441705 TAAAATTATT
*
441715 ATTTTTTAAATATATAAA
1 ATTTTTTAAATAAATAAA
*
441733 ATTTTTTAAAATAAATTAA
1 ATTTTTT-AAATAAATAAA
* *
441752 ATATATTTATATCAAATAAA
1 AT-TTTTTAAAT-AAATAAA
441772 AT
1 AT
441774 AGCTCATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 7 0.21
19 14 0.42
20 12 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTTTAAATAAATAAA
Found at i:447825 original size:18 final size:18
Alignment explanation
Indices: 447784--447822 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
447774 TAAAATTGAT
*
447784 TAATTTTATATATTTTTA
1 TAATTTTATATATATTTA
447802 TAATTTTATATATGATTTA
1 TAATTTTATATAT-ATTTA
447821 TA
1 TA
447823 TTTAACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TAATTTTATATATATTTA
Found at i:453823 original size:22 final size:23
Alignment explanation
Indices: 453785--453846 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 23
453775 AATCAATTGA
453785 AATAATAT-T-TTTT-TAATTAT
1 AATAATATATATTTTATAATTAT
*
453805 -ATAATTTATATTTTATAA-TAT
1 AATAATATATATTTTATAATTAT
*
453826 AATTATATATATTTTAATAAT
1 AATAATATATATTTT-ATAAT
453847 AGTTAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 6 0.18
20 1 0.03
21 7 0.21
22 15 0.45
23 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATAATATATATTTTATAATTAT
Found at i:454583 original size:15 final size:14
Alignment explanation
Indices: 454540--454582 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
454530 AGTAATATTT
454540 ATTTTATTAAATAAA
1 ATTTTA-TAAATAAA
*
454555 ATTTTA-AATTAAA
1 ATTTTATAAATAAA
454568 ATTTTATAAATAAA
1 ATTTTATAAATAAA
454582 A
1 A
454583 AATAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 12 0.48
14 7 0.28
15 6 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTTATAAATAAA
Found at i:455124 original size:31 final size:30
Alignment explanation
Indices: 455041--455151 Score: 141
Period size: 30 Copynumber: 3.7 Consensus size: 30
455031 ATATATATTT
* * *
455041 TTTATAGTTAAATAAATTATTAATTTTTAC
1 TTTATATTTAAATAAATTTTTAATTTTTAA
** * *
455071 TTGGTAATCAAATAAATTTTTAATTTTTAA
1 TTTATATTTAAATAAATTTTTAATTTTTAA
455101 TTTATATTTAAATAATATTTTTAATTTTTAA
1 TTTATATTTAAATAA-ATTTTTAATTTTTAA
*
455132 TTTATATCTAAATAAATTTT
1 TTTATATTTAAATAAATTTT
455152 AATAAATTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
30 40 0.58
31 29 0.42
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTATATTTAAATAAATTTTTAATTTTTAA
Found at i:455801 original size:2 final size:2
Alignment explanation
Indices: 455794--455819 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
455784 ATCTTCGTAC
455794 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
455820 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:456321 original size:14 final size:13
Alignment explanation
Indices: 456291--456327 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
456281 TTACAGACTC
456291 TTTTTTTATTTTA
1 TTTTTTTATTTTA
456304 TTTTATTTA-TTTA
1 TTTT-TTTATTTTA
456317 TTTTTTT-TTTT
1 TTTTTTTATTTT
456328 TGCTTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.27
13 12 0.55
14 4 0.18
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTATTTTA
Found at i:462900 original size:5 final size:5
Alignment explanation
Indices: 462890--462931 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
462880 TCTATTCAAA
* *
462890 TTAAT TTAA- TTAAT TTAA- TTAAT TTAAT TTAAA TTAAA TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
462932 AATTAATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
4 8 0.24
5 26 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (5 bp):
TTAAT
Found at i:462902 original size:4 final size:4
Alignment explanation
Indices: 462888--462994 Score: 65
Period size: 4 Copynumber: 25.0 Consensus size: 4
462878 AATCTATTCA
462888 AATT AATTT AATT AATTT AATT AATTT AATTT AAATT AAATT AA-- AATT
1 AATT AA-TT AATT AA-TT AATT AA-TT AA-TT -AATT -AATT AATT AATT
** * * * *
462936 AATT AATT ATAAA AATT ATTT ATTT AATT AATT AGATT AATT TATAA AATT
1 AATT AATT A-ATT AATT AATT AATT AATT AATT A-ATT AATT AAT-T AATT
462987 AATT AATT
1 AATT AATT
462995 TTTTAAATTT
Statistics
Matches: 84, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
2 2 0.02
4 50 0.60
5 30 0.36
6 2 0.02
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:462902 original size:9 final size:9
Alignment explanation
Indices: 462888--462995 Score: 82
Period size: 9 Copynumber: 12.0 Consensus size: 9
462878 AATCTATTCA
462888 AATTAATTT
1 AATTAATTT
462897 AATTAATTT
1 AATTAATTT
462906 AATTAATTT
1 AATTAATTT
*
462915 AATTTAAATTA
1 AA-TT-AATTT
*
462926 AATTAAAATT
1 AATT-AATTT
462936 AATTAATTAT
1 AATTAATT-T
*
462946 AA--AAATT
1 AATTAATTT
*
462953 -ATTTATTT
1 AATTAATTT
462961 AATTAA-TT
1 AATTAATTT
462969 AGATTAATTT
1 A-ATTAATTT
* *
462979 -ATAAAATT
1 AATTAATTT
462987 AATTAATTT
1 AATTAATTT
462996 TTTAAATTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
6 1 0.01
7 1 0.01
8 15 0.19
9 38 0.49
10 17 0.22
11 6 0.08
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (9 bp):
AATTAATTT
Found at i:462963 original size:51 final size:52
Alignment explanation
Indices: 462897--462994 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 52
462887 AAATTAATTT
462897 AATTAATTTAATTAATTTAATTTAAATTAA-AT-TAAAATTAATTAATTATAAA
1 AATTAATTTAATTAA-TTAA-TTAAATTAATATATAAAATTAATTAATTATAAA
* * *
462949 AATT-ATTTATTTAATTAATTAGATTAATTTATAAAATTAATTAATT
1 AATTAATTTAATTAATTAATTAAATTAATATATAAAATTAATTAATT
462995 TTTTAAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
49 8 0.20
50 5 0.12
51 24 0.59
52 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (52 bp):
AATTAATTTAATTAATTAATTAAATTAATATATAAAATTAATTAATTATAAA
Found at i:463003 original size:17 final size:18
Alignment explanation
Indices: 462929--462995 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 18
462919 TAAATTAAAT
462929 TAAAATTA-ATTAA-TTA
1 TAAAATTAGATTAATTTA
*
462945 TAAAAATT--ATTTATTTA
1 T-AAAATTAGATTAATTTA
*
462962 -ATTAATTAGATTAATTTA
1 TA-AAATTAGATTAATTTA
462980 TAAAATTA-ATTAATTT
1 TAAAATTAGATTAATTT
462996 TTTAAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
15 1 0.02
16 9 0.22
17 17 0.41
18 13 0.32
19 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (18 bp):
TAAAATTAGATTAATTTA
Found at i:463285 original size:2 final size:2
Alignment explanation
Indices: 463278--463318 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
463268 ATAATAAGGT
463278 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
463319 GCTTGTTTAC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:463514 original size:33 final size:33
Alignment explanation
Indices: 463475--463541 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
463465 GAGCTACATC
463475 TATGGAGTTATATATCTATACACTATGTTACTA
1 TATGGAGTTATATATCTATACACTATGTTACTA
463508 TATGGAGTTATATATCTATACACTATGTTACTA
1 TATGGAGTTATATATCTATACACTATGTTACTA
463541 T
1 T
463542 TTGAATGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (33 bp):
TATGGAGTTATATATCTATACACTATGTTACTA
Found at i:466260 original size:14 final size:14
Alignment explanation
Indices: 466241--466270 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
466231 ACAGAATTCA
*
466241 ATTAATATATGTAT
1 ATTAATATATATAT
466255 ATTAATATATATAT
1 ATTAATATATATAT
466269 AT
1 AT
466271 AGCGTGTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
ATTAATATATATAT
Found at i:467982 original size:14 final size:14
Alignment explanation
Indices: 467963--467989 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
467953 ATACAAATTT
467963 ATTTAAAATTTATA
1 ATTTAAAATTTATA
467977 ATTTAAAATTTAT
1 ATTTAAAATTTAT
467990 TCGAATTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAAAATTTATA
Found at i:468025 original size:29 final size:30
Alignment explanation
Indices: 467993--468074 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
467983 AATTTATTCG
467993 AATTTAATTTTATTATTTAA-TTAAAAATT
1 AATTTAATTTTATTATTTAATTTAAAAATT
*
468022 AATTTAAATTTT-TTATTTAATTTAAAATTT
1 AATTT-AATTTTATTATTTAATTTAAAAATT
468052 AA-TT-ATTTTA-TATTTAAATTTAA
1 AATTTAATTTTATTATTT-AATTTAA
468075 TTTTGAATTG
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
27 10 0.21
28 7 0.15
29 15 0.31
30 16 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
AATTTAATTTTATTATTTAATTTAAAAATT
Found at i:468056 original size:34 final size:35
Alignment explanation
Indices: 467975--468066 Score: 92
Period size: 34 Copynumber: 2.8 Consensus size: 35
467965 TTAAAATTTA
467975 TAATTTAAAATTT-ATTCGAATTT-AATTTTATTATT
1 TAATTTAAAATTTAATT--AATTTAAATTTTATTATT
468010 TAA-TT-AAA---AATTAATTTAAATTTT-TTATT
1 TAATTTAAAATTTAATTAATTTAAATTTTATTATT
* *
468039 TAATTTAAAATTTAATTATTTTATATTT
1 TAATTTAAAATTTAATTAATTTAAATTT
468067 AAATTTAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
29 13 0.27
30 8 0.17
31 6 0.12
33 3 0.06
34 15 0.31
35 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (35 bp):
TAATTTAAAATTTAATTAATTTAAATTTTATTATT
Found at i:468070 original size:21 final size:19
Alignment explanation
Indices: 468020--468089 Score: 72
Period size: 18 Copynumber: 3.6 Consensus size: 19
468010 TAATTAAAAA
*
468020 TTAATTTAAATTT-TTTAT
1 TTAATTTAAATTTAATTAT
468038 TTAATTTAAAATTTAATTATT
1 TTAATTT-AAATTTAATTA-T
468059 TTATATTTAAATTTAATT-T
1 TTA-ATTTAAATTTAATTAT
* *
468078 TGAATTGAAATT
1 TTAATTTAAATT
468090 ATTTTTAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 15 0.33
19 9 0.20
20 3 0.07
21 14 0.31
22 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTAATTTAAATTTAATTAT
Found at i:473436 original size:19 final size:19
Alignment explanation
Indices: 473412--473450 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
473402 ATAATTATAA
473412 AAATTTAA-ATTTAAATATT
1 AAATTTAATA-TTAAATATT
*
473431 AAATTTATTATTAAATATT
1 AAATTTAATATTAAATATT
473450 A
1 A
473451 TCATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTAATATTAAATATT
Found at i:474346 original size:23 final size:23
Alignment explanation
Indices: 474315--474360 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
474305 ATTAATATTT
**
474315 ATATATTTAAATTTTAATTTAAA
1 ATATATTTAAATAATAATTTAAA
*
474338 ATATTTTTAAATAATAATTTAAA
1 ATATATTTAAATAATAATTTAAA
474361 TTACAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATATTTAAATAATAATTTAAA
Found at i:481077 original size:13 final size:13
Alignment explanation
Indices: 481061--481104 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
481051 ATTATTAATT
481061 ATAATAAATATTA
1 ATAATAAATATTA
*
481074 ATAATAAATATTG
1 ATAATAAATATTA
*
481087 ATAA-AAAAATTA
1 ATAATAAATATTA
481099 A-AATAA
1 ATAATAA
481105 TAAAATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 2 0.07
12 9 0.33
13 16 0.59
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (13 bp):
ATAATAAATATTA
Found at i:487116 original size:110 final size:110
Alignment explanation
Indices: 486922--487253 Score: 619
Period size: 110 Copynumber: 3.0 Consensus size: 110
486912 TGCATTTTTA
*
486922 CAGACATTTAAAGGGTGTTTCTTCATGGATTAAGGTTCGAAATTAAACGGTGGTCAGCAAGAAGA
1 CAGACATTTAAAGGGCGTTTCTTCATGGATTAAGGTTCGAAATTAAACGGTGGTCAGCAAGAAGA
* *
486987 AAAAGGATCAACTAGAGGCCCTCATTGTAAACACTTCCAAGAAAG
66 AAAAGGATCAACTAAAGGCCCTTATTGTAAACACTTCCAAGAAAG
487032 CAGACATTTAAAGGGCGTTTCTTCATGGATTAAGGTTCGAAATTAAACGGTGGTCAGCAAGAAGA
1 CAGACATTTAAAGGGCGTTTCTTCATGGATTAAGGTTCGAAATTAAACGGTGGTCAGCAAGAAGA
487097 AAAAGGATCAACTAAAGGCCCTTATTGTAAACACTTCCAAGAAAG
66 AAAAGGATCAACTAAAGGCCCTTATTGTAAACACTTCCAAGAAAG
* *
487142 CAGACATTTAAAGGGCATTTCTTCATTGATTAAGGTTCGAAATTAAACGGTGGTCAGCAAGAAGA
1 CAGACATTTAAAGGGCGTTTCTTCATGGATTAAGGTTCGAAATTAAACGGTGGTCAGCAAGAAGA
487207 AAAAGGATCAACTAAAGGCCCTTATTGTAAACACTTCCAAGAAAG
66 AAAAGGATCAACTAAAGGCCCTTATTGTAAACACTTCCAAGAAAG
487252 CA
1 CA
487254 TTAAACCATC
Statistics
Matches: 217, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 217 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (110 bp):
CAGACATTTAAAGGGCGTTTCTTCATGGATTAAGGTTCGAAATTAAACGGTGGTCAGCAAGAAGA
AAAAGGATCAACTAAAGGCCCTTATTGTAAACACTTCCAAGAAAG
Found at i:488932 original size:17 final size:17
Alignment explanation
Indices: 488898--488930 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
488888 TCTTTAAATT
*
488898 TTTATATTTATTTAAAA
1 TTTATATTTATTAAAAA
488915 TTTATATTT-TTAAAAA
1 TTTATATTTATTAAAAA
488931 ATCAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTATATTTATTAAAAA
Found at i:490407 original size:2 final size:2
Alignment explanation
Indices: 490400--490424 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
490390 TATGATTTTG
490400 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
490425 GCTTTTTTTC
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:490837 original size:2 final size:2
Alignment explanation
Indices: 490832--490868 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
490822 TGTGTGTGTC
490832 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
490869 CTCTTTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:492984 original size:22 final size:22
Alignment explanation
Indices: 492959--493001 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
492949 ATTTTTAAAA
492959 ATATATTTAT-ATTAATATTTAT
1 ATATATTTATAATTAA-ATTTAT
*
492981 ATATTTTTATAATTAAATTTA
1 ATATATTTATAATTAAATTTA
493002 AATAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATATTTATAATTAAATTTAT
Found at i:493001 original size:34 final size:34
Alignment explanation
Indices: 492931--493001 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
492921 GTTTTGGGGA
* *
492931 TTATTTTAATATATTAATATTTTTAAAAATATAT
1 TTATATTAATATATTAATATTTTTAAAAATAAAT
* *
492965 TTATATTAATAT-TTATATATTTTTATAATTAAAT
1 TTATATTAATATATTA-ATATTTTTAAAAATAAAT
492999 TTA
1 TTA
493002 AATAAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 3 0.09
34 29 0.91
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
TTATATTAATATATTAATATTTTTAAAAATAAAT
Found at i:493364 original size:12 final size:13
Alignment explanation
Indices: 493346--493399 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 13
493336 TATACACAAA
493346 ATAAAAAAATAAT
1 ATAAAAAAATAAT
493359 -T-AAAAAATAAT
1 ATAAAAAAATAAT
493370 ATAAAATATGACATAAT
1 ATAAAA-A--A-ATAAT
493387 AT-AAAAAATAAT
1 ATAAAAAAATAAT
493399 A
1 A
493400 AAATATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
11 10 0.29
12 8 0.23
13 4 0.11
14 1 0.03
15 1 0.03
16 4 0.11
17 7 0.20
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (13 bp):
ATAAAAAAATAAT
Found at i:493376 original size:29 final size:29
Alignment explanation
Indices: 493343--493399 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
493333 TTTTATACAC
493343 AAAATAAAAAAATAAT-TAAAAAATAATAT
1 AAAAT-AAAAAATAATATAAAAAATAATAT
** *
493372 AAAATATGACATAATATAAAAAATAATA
1 AAAATAAAAAATAATATAAAAAATAATA
493400 AAATATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (29 bp):
AAAATAAAAAATAATATAAAAAATAATAT
Found at i:493442 original size:31 final size:32
Alignment explanation
Indices: 493404--493463 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
493394 ATAATAAAAT
*
493404 ATATTTTAAAATATATGT-AATATAAAAATTA
1 ATATTTTAAAATATATATAAATATAAAAATTA
*
493435 ATATTTTAAAATTTATATAAATATAAAAA
1 ATATTTTAAAATATATATAAATATAAAAA
493464 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (32 bp):
ATATTTTAAAATATATATAAATATAAAAATTA
Found at i:496663 original size:31 final size:30
Alignment explanation
Indices: 496606--496663 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
496596 ATTGTTAAAT
*
496606 ATATATAAAAATAATATAATTTTTTAATTA
1 ATATATAAAAATAATATAATTATTTAATTA
*
496636 ATATGATAAAAATATTA-AATTAATTTAA
1 ATAT-ATAAAAATAATATAATT-ATTTAA
496664 AATTTTACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
ATATATAAAAATAATATAATTATTTAATTA
Found at i:496694 original size:16 final size:16
Alignment explanation
Indices: 496673--496703 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
496663 AAATTTTACG
*
496673 TATACATATATAAAAT
1 TATACAAATATAAAAT
496689 TATACAAATATAAAA
1 TATACAAATATAAAA
496704 AATTAATTAA
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:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
TATACAAATATAAAAT
Found at i:497631 original size:2 final size:2
Alignment explanation
Indices: 497626--497662 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
497616 GACCGACGGA
497626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
497663 CATAATCCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:500235 original size:2 final size:2
Alignment explanation
Indices: 500228--500257 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
500218 TGCTGTTGTT
500228 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
500258 GTTTTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:500404 original size:9 final size:9
Alignment explanation
Indices: 500392--500416 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
500382 GAATTCTAAA
500392 AAATCTATC
1 AAATCTATC
500401 AAATCTATC
1 AAATCTATC
500410 AAATCTA
1 AAATCTA
500417 ATGAACCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATCTATC
Found at i:502717 original size:5 final size:5
Alignment explanation
Indices: 502707--502731 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
502697 GAGAACCATA
502707 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
502732 TATTTTAGGT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:503762 original size:55 final size:55
Alignment explanation
Indices: 503693--503802 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
503683 ATTTTTTATG
503693 CCATTATAAGACTATTGGATCAATAGAGTACTGAAAGCTCCATAAGGATCCTTAA
1 CCATTATAAGACTATTGGATCAATAGAGTACTGAAAGCTCCATAAGGATCCTTAA
*
503748 CCATTATAAGACTATTGGATCAATAGAGTACTGAAAGCTCCATATGGATCCTTAA
1 CCATTATAAGACTATTGGATCAATAGAGTACTGAAAGCTCCATAAGGATCCTTAA
503803 ACATCTTTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.28
Consensus pattern (55 bp):
CCATTATAAGACTATTGGATCAATAGAGTACTGAAAGCTCCATAAGGATCCTTAA
Found at i:506744 original size:18 final size:18
Alignment explanation
Indices: 506706--506749 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
506696 CAAATTTTAT
506706 ATTTTAAATATAATAAAA
1 ATTTTAAATATAATAAAA
*
506724 ATTATTAAATA-AATTAAA
1 ATT-TTAAATATAATAAAA
506742 ATTTTAAA
1 ATTTTAAA
506750 CAAGATATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 5 0.21
18 12 0.50
19 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTTAAATATAATAAAA
Found at i:508306 original size:79 final size:78
Alignment explanation
Indices: 508213--508409 Score: 223
Period size: 79 Copynumber: 2.5 Consensus size: 78
508203 ACTACGAAAG
* * *
508213 TCCAACCCCAATTTTATTTTCAAAATATCAATTTTTCATAATTGGAGATACTCTAACCCTGTTAT
1 TCCAA-CCCAATTTTATTTCCAAAATATCAATTTTTCATAATTGGAGATACTCCAACCCCGTTAT
* *
508278 TTTTGAGGGGATAC
65 TTCTGAAGGGATAC
* * * ** *
508292 TCCAACCTCGATTTTATTTCCAAAACATCGATTTTTCACCATTGGGGATACTCCAACCCCGTTAT
1 TCCAACC-CAATTTTATTTCCAAAATATCAATTTTTCATAATTGGAGATACTCCAACCCCGTTAT
508357 TTCTGAAGGGATAC
65 TTCTGAAGGGATAC
* ** * *
508371 TCCGACCCCTTTTTATCTCCAAAATATTAAATTTTTCAT
1 TCCAACCCAATTTTATTTCCAAAATA-TCAATTTTTCAT
508410 CGGGAGATGT
Statistics
Matches: 97, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
78 17 0.18
79 80 0.82
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (78 bp):
TCCAACCCAATTTTATTTCCAAAATATCAATTTTTCATAATTGGAGATACTCCAACCCCGTTATT
TCTGAAGGGATAC
Found at i:511163 original size:75 final size:75
Alignment explanation
Indices: 511036--511185 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
511026 TTTGTCCGAT
*
511036 GGCTAAGAGCGCGTGGAATGTTGAGCTTGGATTCAAGTCCAAGCATCTCATCCCTCTTTCCTAAT
1 GGCTAAGAGCGCGTGGAATGTTGAGCTTGGATTCAAGTCCAAGCATCCCATCCCTCTTTCCTAAT
511101 TTGTCATCAC
66 TTGTCATCAC
511111 GGCTAAGAGCGCGTGGAATGTTGAGCTTGGATTCAAGTCCAAGCATCCCATCCCTCTTTCCTAAT
1 GGCTAAGAGCGCGTGGAATGTTGAGCTTGGATTCAAGTCCAAGCATCCCATCCCTCTTTCCTAAT
511176 TTGTCATCAC
66 TTGTCATCAC
511186 AATATTATAT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (75 bp):
GGCTAAGAGCGCGTGGAATGTTGAGCTTGGATTCAAGTCCAAGCATCCCATCCCTCTTTCCTAAT
TTGTCATCAC
Found at i:511234 original size:11 final size:11
Alignment explanation
Indices: 511213--511288 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 11
511203 ATATGACAAA
*
511213 ATATTTATAAT
1 ATATATATAAT
*
511224 ATATATTTAAT
1 ATATATATAAT
* *
511235 TTTTATATAAT
1 ATATATATAAT
*
511246 ATAAAT-TACAT
1 ATATATATA-AT
511257 AATATATATAA-
1 -ATATATATAAT
* *
511268 ATAAAAATAAT
1 ATATATATAAT
511279 AT-TATATAAT
1 ATATATATAAT
511289 TTAAAACTAT
Statistics
Matches: 48, Mismatches: 13, Indels: 9
0.69 0.19 0.13
Matches are distributed among these distances:
10 16 0.33
11 24 0.50
12 6 0.12
13 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATATATAAT
Found at i:511365 original size:19 final size:20
Alignment explanation
Indices: 511343--511388 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
511333 AAGATTCAAC
511343 TTATTTA-TTAAATAAATTT
1 TTATTTATTTAAATAAATTT
*
511362 TTA-TTATTTAAATTAATTT
1 TTATTTATTTAAATAAATTT
511381 TTAATTTA
1 TT-ATTTA
511389 AATTATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 3 0.13
19 16 0.70
20 1 0.04
21 3 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATTTATTTAAATAAATTT
Found at i:511389 original size:17 final size:17
Alignment explanation
Indices: 511350--511424 Score: 89
Period size: 19 Copynumber: 4.2 Consensus size: 17
511340 AACTTATTTA
*
511350 TTAAATAAATTTTTATTAT
1 TTAAATTAATTTTTA--AT
511369 TTAAATTAATTTTTAAT
1 TTAAATTAATTTTTAAT
*
511386 TTAAATT-ATTTTAAAT
1 TTAAATTAATTTTTAAT
511402 ATTAAATTAATTTTTAAAT
1 -TTAAATTAATTTTT-AAT
511421 TTAA
1 TTAA
511425 TGAAATAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
16 8 0.16
17 16 0.32
18 9 0.18
19 17 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAATTAATTTTTAAT
Found at i:511830 original size:19 final size:18
Alignment explanation
Indices: 511769--511839 Score: 76
Period size: 17 Copynumber: 4.0 Consensus size: 18
511759 AATAAATTTG
*
511769 TATATTTATAT-TTATAT
1 TATATTTTTATATTATAT
*
511786 TAT-TTTTTCGTATTATAT
1 TATATTTTT-ATATTATAT
*
511804 CATA-TTTTATATTATAT
1 TATATTTTTATATTATAT
511821 TATAATTTTTATATTATAT
1 TAT-ATTTTTATATTATAT
511840 AATCTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
16 4 0.09
17 14 0.32
18 13 0.30
19 13 0.30
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (18 bp):
TATATTTTTATATTATAT
Found at i:512798 original size:28 final size:27
Alignment explanation
Indices: 512755--512823 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
512745 TTTTATATAA
* *
512755 ATTTATA-TATTCTTGTATTACTATCAT
1 ATTTATATTATTTTTGTATCA-TATCAT
* *
512782 ATTTATATTATTTTTGTGTCATATTAT
1 ATTTATATTATTTTTGTATCATATCAT
512809 ATTT-TAATTATTTTT
1 ATTTAT-ATTATTTTT
512824 TAAATTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 25 0.69
28 10 0.28
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (27 bp):
ATTTATATTATTTTTGTATCATATCAT
Found at i:512832 original size:23 final size:22
Alignment explanation
Indices: 512804--512858 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
512794 TTTGTGTCAT
* *
512804 ATTATATTTTAATTATTTTTTAA
1 ATTATATTTTAATTATATCTT-A
*
512827 ATTATATTTTTATTATATCTTA
1 ATTATATTTTAATTATATCTTA
512849 ATT-TATTTTA
1 ATTATATTTTA
512859 TATTTTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 6 0.21
22 4 0.14
23 18 0.64
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTATATTTTAATTATATCTTA
Found at i:512863 original size:11 final size:12
Alignment explanation
Indices: 512802--512862 Score: 67
Period size: 11 Copynumber: 5.4 Consensus size: 12
512792 TTTTTGTGTC
512802 ATATTATATTTT
1 ATATTATATTTT
*
512814 A-ATTATTTTTT
1 ATATTATATTTT
*
512825 AAATTATATTTT
1 ATATTATATTTT
*
512837 -TATTATATCTT
1 ATATTATATTTT
512848 A-ATT-TATTTT
1 ATATTATATTTT
512858 ATATT
1 ATATT
512863 TTATATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
10 6 0.15
11 25 0.61
12 10 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:512912 original size:13 final size:14
Alignment explanation
Indices: 512882--512941 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
512872 TTTTTATATA
*
512882 ATTAAATTTTAATT
1 ATTAAATTTTATTT
512896 -TTAAA-TTTATTT
1 ATTAAATTTTATTT
512908 ATTAAATATTT-TTT
1 ATTAAAT-TTTATTT
*
512922 AATAAATTTTATTT
1 ATTAAATTTTATTT
*
512936 AATAAA
1 ATTAAA
512942 AAATTTTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 6 0.15
13 13 0.32
14 18 0.45
15 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTAAATTTTATTT
Found at i:513351 original size:16 final size:15
Alignment explanation
Indices: 513320--513412 Score: 72
Period size: 13 Copynumber: 6.4 Consensus size: 15
513310 TTTAATATTT
513320 ATAAAATTTGTAATTAA
1 ATAAAA-TT-TAATTAA
513337 ATAAAATTATAATT-A
1 ATAAAATT-TAATTAA
*
513352 ATAAAATTTATTTAA
1 ATAAAATTTAATTAA
*
513367 A-AATATTTAA-TAA
1 ATAAAATTTAATTAA
*
513380 AT-AAATTTAA--AG
1 ATAAAATTTAATTAA
* *
513392 TTAAAATTTAATTAT
1 ATAAAATTTAATTAA
513407 ATAAAA
1 ATAAAA
513413 AATTTATATA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
12 2 0.03
13 19 0.31
14 11 0.18
15 17 0.27
16 7 0.11
17 6 0.10
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
ATAAAATTTAATTAA
Found at i:513424 original size:28 final size:27
Alignment explanation
Indices: 513337--513426 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 27
513327 TTGTAATTAA
513337 ATAAAATTATAATTAAT--AAAATTTAT
1 ATAAAATT-TAATTAATAAAAAATTTAT
* * * *
513363 TTAAAA-ATATTTAATAAATAAATTTAA
1 ATAAAATTTAATTAATAAA-AAATTTAT
513390 AGTTAAAATTTAATTATATAAAAAATTTAT
1 A--TAAAATTTAATTA-ATAAAAAATTTAT
513420 ATAAAAT
1 ATAAAAT
513427 ATAAGATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 7 0.14
26 6 0.12
27 7 0.14
28 6 0.12
29 5 0.10
30 13 0.27
31 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
ATAAAATTTAATTAATAAAAAATTTAT
Found at i:513795 original size:23 final size:23
Alignment explanation
Indices: 513743--513795 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
513733 GAAACACGAA
* *
513743 ATGAACACAACATAGAAAATAAT
1 ATGAATACAACATAAAAAATAAT
* *
513766 -TAAAATACAGCATAAAAAATAAT
1 AT-GAATACAACATAAAAAATAAT
513789 ATGAATA
1 ATGAATA
513796 TAATACAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
22 1 0.04
23 21 0.91
24 1 0.04
ACGTcount: A:0.62, C:0.09, G:0.08, T:0.21
Consensus pattern (23 bp):
ATGAATACAACATAAAAAATAAT
Found at i:514641 original size:58 final size:59
Alignment explanation
Indices: 514562--514673 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
514552 CAATTTTTTT
* * *
514562 AATTAAATCATTATAACAAATTATG-AAAAAATGTCACGAATTGAGATATGATATATTA
1 AATTAAATCATTATAAAAAATTATGTAAAAAATGTCACGAATGGAGATACGATATATTA
* * *
514620 AATTAAATTATTA-AGAAAAATTATGTAAAATATGTCATGAATGGAGATACGATA
1 AATTAAATCATTATA-AAAAATTATGTAAAAAATGTCACGAATGGAGATACGATA
514674 CGAATATGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 1 0.02
58 21 0.46
59 24 0.52
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.32
Consensus pattern (59 bp):
AATTAAATCATTATAAAAAATTATGTAAAAAATGTCACGAATGGAGATACGATATATTA
Found at i:515090 original size:22 final size:22
Alignment explanation
Indices: 515065--515107 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
515055 ATGAATTGAG
*
515065 ATATAA-TACAAACTCAACATAT
1 ATATAATTA-AAACACAACATAT
515087 ATATAATTAAAACACAACATA
1 ATATAATTAAAACACAACATA
515108 AAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (22 bp):
ATATAATTAAAACACAACATAT
Found at i:515420 original size:14 final size:13
Alignment explanation
Indices: 515401--515430 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
515391 ATATAAAATT
515401 TTTTTTTTTTTTAC
1 TTTTTTTTTTTT-C
515415 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
515428 TTT
1 TTT
515431 CTCTCCTGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:515797 original size:16 final size:17
Alignment explanation
Indices: 515778--515810 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
515768 TAAATTAAAT
515778 ATTT-AATAAAAATTTA
1 ATTTAAATAAAAATTTA
*
515794 ATTTAAATAAATATTTA
1 ATTTAAATAAAAATTTA
515811 TATTATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTAAATAAAAATTTA
Found at i:515952 original size:18 final size:18
Alignment explanation
Indices: 515931--515970 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
515921 AAAAATATTT
515931 TATTAAA-ATTAAATTAAA
1 TATTAAATATTAAATT-AA
*
515949 TATTAAATATTATATTAA
1 TATTAAATATTAAATTAA
515967 TATT
1 TATT
515971 TTTTAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATATTAAATTAA
Found at i:520201 original size:79 final size:80
Alignment explanation
Indices: 520065--520222 Score: 255
Period size: 79 Copynumber: 2.0 Consensus size: 80
520055 CTCTTGTTCT
* * *
520065 TCACCATATGAGAAGAAAGAGTTCATAGGATACAGGACTCTTGTTCCAAGTTATGTTACTTAGAG
1 TCACCACATGAGAAGAAAGAGTTCATAGGATACAGGACTCTTGTTACAAGCTATGTTACTTAGAG
520130 TTGGGTGC-GAGTGC
66 TTGGGTGCTGAGTGC
* * *
520144 TCACCACATGAGAAGAAATAGTTCATGGGATACAGGACTCTTGTTACAAGCTGTGTTACTTAGAG
1 TCACCACATGAGAAGAAAGAGTTCATAGGATACAGGACTCTTGTTACAAGCTATGTTACTTAGAG
520209 TTGGGTGCTGAGTG
66 TTGGGTGCTGAGTG
520223 TCGAACATTC
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 67 0.93
80 5 0.07
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (80 bp):
TCACCACATGAGAAGAAAGAGTTCATAGGATACAGGACTCTTGTTACAAGCTATGTTACTTAGAG
TTGGGTGCTGAGTGC
Found at i:526665 original size:14 final size:13
Alignment explanation
Indices: 526642--526675 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
526632 TCACTTCAAT
526642 AAATTTTTTAATG
1 AAATTTTTTAATG
*
526655 AAATTTATTTAATT
1 AAATTT-TTTAATG
526669 AAATTTT
1 AAATTTT
526676 ATGAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
AAATTTTTTAATG
Found at i:527990 original size:7 final size:7
Alignment explanation
Indices: 527978--528010 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
527968 CGGTGACCCA
527978 AAAAAAT
1 AAAAAAT
527985 AAAAAAT
1 AAAAAAT
527992 AAAAAAT
1 AAAAAAT
527999 AAAAAAT
1 AAAAAAT
528006 AAAAA
1 AAAAA
528011 GGAAAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:528002 original size:6 final size:6
Alignment explanation
Indices: 528000--528039 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
527990 ATAAAAAATA
* *
528000 AAAAAT AAAAAG GAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
528040 TAGTATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:528016 original size:14 final size:14
Alignment explanation
Indices: 527978--528016 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
527968 CGGTGACCCA
*
527978 AAAAAATAAAAAAT
1 AAAAAAGAAAAAAT
*
527992 AAAAAATAAAAAAT
1 AAAAAAGAAAAAAT
*
528006 AAAAAGGAAAA
1 AAAAAAGAAAA
528017 GAAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (14 bp):
AAAAAAGAAAAAAT
Found at i:528225 original size:22 final size:22
Alignment explanation
Indices: 528200--528250 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
528190 TTAAATTAAA
528200 TTAATTTAAAT-TATTATTTTAT
1 TTAATTTAAATATATT-TTTTAT
528222 TTAA-TTAAATAATATTTTTTAT
1 TTAATTTAAAT-ATATTTTTTAT
528244 TTAATTT
1 TTAATTT
528251 TAATCATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.23
22 14 0.54
23 6 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTAATTTAAATATATTTTTTAT
Found at i:529132 original size:16 final size:16
Alignment explanation
Indices: 529111--529171 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
529101 TAATATCAAC
529111 TAAAATTA-TTAAATT
1 TAAAATTATTTAAATT
529126 TATAAATTATTTAAATT
1 TA-AAATTATTTAAATT
*
529143 TAAAATAATTCT-AA-T
1 TAAAATTATT-TAAATT
*
529158 CAAAATTATTTAAA
1 TAAAATTATTTAAA
529172 ATATTAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.03
15 13 0.33
16 15 0.38
17 10 0.26
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATTATTTAAATT
Found at i:529183 original size:19 final size:19
Alignment explanation
Indices: 529159--529197 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
529149 AATTCTAATC
529159 AAAA-TTATTTAAAATATTA
1 AAAATTTATTT-AAATATTA
*
529178 AAAATTTATTTTAATATTA
1 AAAATTTATTTAAATATTA
529197 A
1 A
529198 TATTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAATTTATTTAAATATTA
Found at i:529188 original size:20 final size:18
Alignment explanation
Indices: 529112--529197 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 18
529102 AATATCAACT
529112 AAAATTA-TTAAAT-TTA
1 AAAATTATTTAAATATTA
*
529128 TAAATTATTTAAAT-TT-
1 AAAATTATTTAAATATTA
* *
529144 AAAATAATTCT--A-A-TC
1 AAAATTATT-TAAATATTA
529159 AAAATTATTTAAAATATTA
1 AAAATTATTT-AAATATTA
*
529178 AAAATTTATTTTAATATTA
1 AAAA-TTATTTAAATATTA
529197 A
1 A
529198 TATTAATATT
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
14 2 0.04
15 9 0.17
16 13 0.24
17 10 0.19
18 1 0.02
19 13 0.24
20 6 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATTATTTAAATATTA
Found at i:529266 original size:20 final size:20
Alignment explanation
Indices: 529211--529267 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
529201 TAATATTTTT
* *
529211 ATATAATTTAATTTAAATAAA
1 ATATTATTTAAATT-AATAAA
**
529232 ATATTATTTTGATTAAT-AA
1 ATATTATTTAAATTAATAAA
529251 ATAATTATTTAAATTAA
1 AT-ATTATTTAAATTAA
529268 ATTTATTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 4 0.14
20 15 0.52
21 10 0.34
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATTATTTAAATTAATAAA
Found at i:529452 original size:17 final size:17
Alignment explanation
Indices: 529425--529464 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
529415 GAAAGAGACG
529425 GAAAGAGGGAAAGGAGAA
1 GAAA-AGGGAAAGGAGAA
529443 GAAAAGGGAAAGGAGAA
1 GAAAAGGGAAAGGAGAA
529460 -AAAAG
1 GAAAAG
529465 AATTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 5 0.23
17 13 0.59
18 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (17 bp):
GAAAAGGGAAAGGAGAA
Found at i:529624 original size:38 final size:40
Alignment explanation
Indices: 529516--529624 Score: 93
Period size: 42 Copynumber: 2.7 Consensus size: 40
529506 TTATATAAAA
529516 TTTTATATATTA-ATAAT-TTATATTATATTTATTTTTATATAT
1 TTTTATAT-TTATATAATATT-TA-TATA-TTATTTTTATATAT
* * *
529558 TTTTATATTTGTATAATATTAATAATATT-TTTTTGT-TAT
1 TTTTATATTTATATAATATTTAT-ATATTATTTTTATATAT
*
529597 TTTTA-ATTTATATAAATTTTTATATATT
1 TTTTATATTTATAT-AATATTTATATATT
529625 GATAATTACT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
38 12 0.21
39 15 0.26
40 6 0.11
41 5 0.09
42 17 0.30
43 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (40 bp):
TTTTATATTTATATAATATTTATATATTATTTTTATATAT
Found at i:529639 original size:19 final size:19
Alignment explanation
Indices: 529615--529672 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 19
529605 TATATAAATT
529615 TTTATATATTGATAATTAC
1 TTTATATATTGATAATTAC
529634 -TT-TATA-T-A-AATT--
1 TTTATATATTGATAATTAC
529646 TTTATATATTGATAATTAC
1 TTTATATATTGATAATTAC
529665 TTTATATA
1 TTTATATA
529673 AATTTTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
13 2 0.06
14 8 0.25
15 2 0.06
16 2 0.06
17 8 0.25
18 2 0.06
19 8 0.25
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTATATATTGATAATTAC
Found at i:529641 original size:31 final size:31
Alignment explanation
Indices: 529603--529683 Score: 162
Period size: 31 Copynumber: 2.6 Consensus size: 31
529593 TTATTTTTAA
529603 TTTATATAAATTTTTATATATTGATAATTAC
1 TTTATATAAATTTTTATATATTGATAATTAC
529634 TTTATATAAATTTTTATATATTGATAATTAC
1 TTTATATAAATTTTTATATATTGATAATTAC
529665 TTTATATAAATTTTTATAT
1 TTTATATAAATTTTTATAT
529684 GTTTTGTGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (31 bp):
TTTATATAAATTTTTATATATTGATAATTAC
Found at i:529701 original size:98 final size:98
Alignment explanation
Indices: 529503--529706 Score: 213
Period size: 98 Copynumber: 2.1 Consensus size: 98
529493 TATATCTATA
** * *
529503 AATTTATATAAAATTTTATATATTAATAATTTATATTATATTTATTTTTATATATTTTTATATTT
1 AATTTATATAAAATTTTATATATTAATAATTTATATTATATAAATTTTTATATATTATAATATTT
* * * *
529568 GTATAATATTAATAATATTTTTTTGTTATTTTT
66 ATATAATATTAATAATATTTTTGTGTCATTATT
* *
529601 AATTTATATAAATTTTTATATATTGATAA-TTACT-TTATATAAATTTTTATATATTGATAATTA
1 AATTTATATAAAATTTTATATATTAATAATTTA-TATTATATAAATTTTTATATATT-ATAA-TA
* *
529664 CTTTATATAA-ATT-TTTATATGTTTTGTGTCA-TATT
63 -TTTATATAATATTAATAATAT-TTTTGTGTCATTATT
529699 AA-TTATAT
1 AATTTATAT
529707 TTTTATATTA
Statistics
Matches: 89, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
97 28 0.31
98 40 0.45
99 13 0.15
100 8 0.09
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (98 bp):
AATTTATATAAAATTTTATATATTAATAATTTATATTATATAAATTTTTATATATTATAATATTT
ATATAATATTAATAATATTTTTGTGTCATTATT
Found at i:530188 original size:19 final size:20
Alignment explanation
Indices: 530164--530208 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
530154 TTTAATAAAA
* *
530164 TAAAATAAATTTTAAT-TTT
1 TAAAATAAATTTAAATATAT
*
530183 TAAAATATATTTAAATATAT
1 TAAAATAAATTTAAATATAT
530203 TAAAAT
1 TAAAAT
530209 TTAATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAATAAATTTAAATATAT
Found at i:535501 original size:2 final size:2
Alignment explanation
Indices: 535490--535524 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
535480 GCATTTTTAG
535490 AT AT -T 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
535525 CTCTATGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:536764 original size:2 final size:2
Alignment explanation
Indices: 536757--536795 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
536747 GTTTGAACAA
536757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
536796 AACTTGTCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:537030 original size:6 final size:6
Alignment explanation
Indices: 537019--537082 Score: 59
Period size: 6 Copynumber: 11.7 Consensus size: 6
537009 ATAATCGATC
* *
537019 AATTTA AATTTA AA-AT- AATTTA AATTTA AAATT- -ATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
537063 AA-AT- AATTTA AATTTA AATT
1 AATTTA AATTTA AATTTA AATT
537083 GATTTGATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
4 7 0.15
5 4 0.09
6 35 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AATTTA
Found at i:537087 original size:16 final size:16
Alignment explanation
Indices: 537019--537080 Score: 115
Period size: 16 Copynumber: 3.9 Consensus size: 16
537009 ATAATCGATC
537019 AATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
537035 AATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
*
537051 TATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
537067 AATTTAAATTTAAA
1 AATTTAAATTTAAA
537081 TTGATTTGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:538197 original size:22 final size:22
Alignment explanation
Indices: 538154--538197 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
538144 ATTAAATTAT
*
538154 TAATAATAAAAAATATTTATAA
1 TAATAATAAAAAATATTAATAA
*
538176 TAATAATTTAAAAATA-TAATAA
1 TAATAA-TAAAAAATATTAATAA
538198 AAAAAGTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TAATAATAAAAAATATTAATAA
Found at i:539417 original size:22 final size:20
Alignment explanation
Indices: 539379--539428 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 20
539369 GTCAAAATAT
*
539379 ATATAAATATATAATAATACAA
1 ATATAATTATATAATAA-A-AA
539401 ATATAATTATA-ACATAAAAA
1 ATATAATTATATA-ATAAAAA
539421 ATA-AATTA
1 ATATAATTA
539429 CTTGATCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 5 0.19
21 2 0.08
22 14 0.54
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATAATTATATAATAAAAA
Found at i:539764 original size:52 final size:49
Alignment explanation
Indices: 539708--539824 Score: 114
Period size: 50 Copynumber: 2.3 Consensus size: 49
539698 TATTTTATAA
* *
539708 TTAAATTTAAATAAAAA-TATT-TTATAATTATTAAATATTAAATTAATTTAAT
1 TTAAA-TTAAATAAAAACT-TTATT-TAA-TATTAAAT-TTAAATAAATTAAAT
*
539760 TTAAA-TAAATAAAAACTTTATTTAATATTTAATTTAAATAAATTAAATTT
1 TTAAATTAAATAAAAACTTTATTTAATATTAAATTTAAATAAATTAAA--T
539810 ATTAAATTAAATAAA
1 -TTAAATTAAATAAA
539825 TAAAGAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
48 12 0.21
49 7 0.12
50 16 0.29
51 8 0.14
52 13 0.23
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (49 bp):
TTAAATTAAATAAAAACTTTATTTAATATTAAATTTAAATAAATTAAAT
Found at i:540454 original size:36 final size:38
Alignment explanation
Indices: 540414--540503 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 38
540404 TTATTTTTAT
*
540414 ATTTAAAATTATAAATATTTGA-TCATTAATTAT-TAA
1 ATTTAAAATTATAAATATTTGATTCATAAATTATATAA
* *
540450 ATTTAATAA-T-TAAATATTTTATTGATAAATTATATAA
1 ATTTAA-AATTATAAATATTTGATTCATAAATTATATAA
540487 ATTTTTAAAATTA-AAAT
1 A--TTTAAAATTATAAAT
540504 CTTATTATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
35 10 0.23
36 16 0.36
37 6 0.14
38 2 0.05
39 10 0.23
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (38 bp):
ATTTAAAATTATAAATATTTGATTCATAAATTATATAA
Found at i:541809 original size:31 final size:33
Alignment explanation
Indices: 541772--541865 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 33
541762 ATTTTCTTTT
541772 AATTTTATATTA-TATTAATATATTTTTACAT-
1 AATTTTATATTATTATTAATATATTTTTACATA
* * * *
541803 ATTTTTATA-TATTAATAATTTATTTTTATATA
1 AATTTTATATTATTATTAATATATTTTTACATA
541835 AATTTTA-ATATATTATTAATATTATTATTTA
1 AATTTTATAT-TATTATTAATA-TATT-TTTA
541866 TTTTTTGTCG
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
30 2 0.04
31 25 0.50
32 6 0.12
33 9 0.18
34 4 0.08
35 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (33 bp):
AATTTTATATTATTATTAATATATTTTTACATA
Found at i:541831 original size:52 final size:52
Alignment explanation
Indices: 541769--541867 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 52
541759 AAAATTTTCT
* * *
541769 TTTAATTTTATAT-TATATTAATATATTTTTACATATTTTTATATATTAATAA
1 TTTAATTTTATATAAATATTAATATATTATTA-ATATTATTATATATTAATAA
* * *
541821 TTTATTTTTATATAAATTTTAATATATTATTAATATTATTATTTATT
1 TTTAATTTTATATAAATATTAATATATTATTAATATTATTATATATT
541868 TTTTGTCGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
52 25 0.62
53 15 0.38
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (52 bp):
TTTAATTTTATATAAATATTAATATATTATTAATATTATTATATATTAATAA
Found at i:542262 original size:14 final size:15
Alignment explanation
Indices: 542236--542265 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
542226 GTCAATTAAT
542236 ATATTATTTATATTA
1 ATATTATTTATATTA
542251 ATATTA-TTATATTA
1 ATATTATTTATATTA
542265 A
1 A
542266 ATGTAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATTATTTATATTA
Found at i:543405 original size:2 final size:2
Alignment explanation
Indices: 543398--543445 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
543388 GCTTCAAACA
*
543398 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT -T AT TT 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
543438 AT AT AT AT
1 AT AT AT AT
543446 TGTCAACCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:546211 original size:15 final size:17
Alignment explanation
Indices: 546177--546214 Score: 53
Period size: 15 Copynumber: 2.3 Consensus size: 17
546167 TTATTAAGTT
546177 TTTAGATATAGATATATA
1 TTTA-ATATAGATATATA
546195 TTTAATATA-AT-TATA
1 TTTAATATAGATATATA
546210 TTTAA
1 TTTAA
546215 ATTTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 2 0.10
17 5 0.25
18 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TTTAATATAGATATATA
Found at i:546583 original size:26 final size:26
Alignment explanation
Indices: 546554--546607 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
546544 GATTATATTG
* *
546554 TTAATTATGTTGTTATTTATATT-ATA
1 TTAATAATGTTATTA-TTATATTGATA
*
546580 TTAATAATTTTATTATTATATTGATA
1 TTAATAATGTTATTATTATATTGATA
546606 TT
1 TT
546608 TTTTAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (26 bp):
TTAATAATGTTATTATTATATTGATA
Found at i:546608 original size:19 final size:20
Alignment explanation
Indices: 546569--546637 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
546559 TATGTTGTTA
*
546569 TTTA-TATTATATTAATAAT
1 TTTATTATTATATTGATAAT
546588 TTTATTATTATATTGAT-AT
1 TTTATTATTATATTGATAAT
* *
546607 TTT-TTAATTATATTGTTAAC
1 TTTATT-ATTATATTGATAAT
*
546627 TATATTATTAT
1 TTTATTATTAT
546638 GTTGGTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.05
19 19 0.45
20 19 0.45
21 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTATTATTATATTGATAAT
Found at i:546693 original size:19 final size:19
Alignment explanation
Indices: 546654--546699 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
546644 ATTTTTTAAA
* * *
546654 ATTAATAAAATATTATGTT
1 ATTAATAAAAGATAATATT
546673 ATTAATAAAAGATAATATT
1 ATTAATAAAAGATAATATT
546692 ATT-ATAAA
1 ATTAATAAA
546700 TATAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
ATTAATAAAAGATAATATT
Found at i:547276 original size:27 final size:26
Alignment explanation
Indices: 547246--547298 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
547236 AAAATTAGTA
547246 TTTGACTTAAATA-TAATTTTAATAAAT
1 TTTGA-TTAAATATTAATTTT-ATAAAT
**
547273 TTTGATTATTTATTAATTTTATAAAT
1 TTTGATTAAATATTAATTTTATAAAT
547299 ATCAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (26 bp):
TTTGATTAAATATTAATTTTATAAAT
Found at i:548157 original size:2 final size:2
Alignment explanation
Indices: 548150--548183 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
548140 AGTACCATAA
548150 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
548184 CTACATGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:548417 original size:27 final size:26
Alignment explanation
Indices: 548384--548468 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
548374 TAAAAAATTT
548384 ATATAATATAAATATATAATATTTTAA
1 ATATAATATAAATATATAA-ATTTTAA
*
548411 ATATAAT-TATAATA-A-AAA--AT-A
1 ATATAATATA-AATATATAAATTTTAA
548432 ATATAAATATAAATATATAAATTATTAA
1 ATAT-AATATAAATATATAAATT-TTAA
*
548460 ATTTAATAT
1 ATATAATAT
548469 TTCAATTGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 18
0.69 0.04 0.27
Matches are distributed among these distances:
21 5 0.11
22 8 0.17
23 3 0.07
24 4 0.09
25 2 0.04
26 3 0.07
27 17 0.37
28 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATAATATAAATATATAAATTTTAA
Found at i:554582 original size:20 final size:19
Alignment explanation
Indices: 554554--554594 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
554544 AACTGACAAA
554554 TTTTATTAATTCAATTTATT
1 TTTTATTAATTCAATTT-TT
* *
554574 TTTTTTTAATTTAATTTTT
1 TTTTATTAATTCAATTTTT
554593 TT
1 TT
554595 ATACAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTATTAATTCAATTTTT
Found at i:554836 original size:2 final size:2
Alignment explanation
Indices: 554831--554858 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
554821 AATATATGTC
554831 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
554859 TATGACCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:556187 original size:15 final size:16
Alignment explanation
Indices: 556167--556199 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
556157 ATATTTTTTA
556167 TAAAATA-ATTATATT
1 TAAAATATATTATATT
*
556182 TAAAATATTTTATATT
1 TAAAATATATTATATT
556198 TA
1 TA
556200 TATTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAAATATATTATATT
Found at i:556242 original size:31 final size:33
Alignment explanation
Indices: 556185--556268 Score: 93
Period size: 31 Copynumber: 2.6 Consensus size: 33
556175 TTATATTTAA
* * *
556185 AATATTTTATATTTATATTAATTTTAATATATT
1 AATAATTTATATTTATATAAATTTTAAAATATT
556218 AATAATTTATA-TTATA-AAATTTTAAAATATT
1 AATAATTTATATTTATATAAATTTTAAAATATT
*
556249 TATATATTTAT-TTTAATATA
1 AATA-ATTTATATTT-ATATA
556269 TTATAATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
31 16 0.37
32 13 0.30
33 13 0.30
34 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
AATAATTTATATTTATATAAATTTTAAAATATT
Found at i:556278 original size:27 final size:26
Alignment explanation
Indices: 556175--556281 Score: 78
Period size: 27 Copynumber: 4.0 Consensus size: 26
556165 TATAAAATAA
* *
556175 TTATATTTAAAATATTTTATATTTATAT
1 TTAT-TTTAATATATTATA-ATTTATAT
*
556203 TAATTTTAATATATTAATAATTTATAT
1 TTATTTTAATATATT-ATAATTTATAT
*
556230 TATAAAATTTTAAAATATT-T-A--TATAT
1 T-T---ATTTTAATATATTATAATTTATAT
556256 TTATTTTAATATATTATAATTATATA
1 TTATTTTAATATATTATAATT-TATA
556282 ATCAAATTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
22 12 0.19
23 1 0.02
24 1 0.02
25 1 0.02
26 6 0.10
27 23 0.37
28 6 0.10
29 1 0.02
31 12 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATTTTAATATATTATAATTTATAT
Found at i:556808 original size:2 final size:2
Alignment explanation
Indices: 556801--556828 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
556791 CGATACATAC
556801 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
556829 TTAATTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:561157 original size:30 final size:30
Alignment explanation
Indices: 561123--561180 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
561113 ACTCAAATTG
*
561123 ATAAAAATATATATTTAAAAGTTTAATTAA
1 ATAAAAATAAATATTTAAAAGTTTAATTAA
**
561153 ATAAAAATAAATATTTAAGGGTTTAATT
1 ATAAAAATAAATATTTAAAAGTTTAATT
561181 GATTGTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (30 bp):
ATAAAAATAAATATTTAAAAGTTTAATTAA
Found at i:561620 original size:20 final size:20
Alignment explanation
Indices: 561583--561621 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
561573 CTTATTATTT
*
561583 ATAAAAAAATTTAGATAAAA
1 ATAAAAAAATTAAGATAAAA
* *
561603 ATAATAAAATTAATATAAA
1 ATAAAAAAATTAAGATAAA
561622 TCAATATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
ATAAAAAAATTAAGATAAAA
Done.