Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold495
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: 586005
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 5
Found at i:446125 original size:42 final size:41
Alignment explanation
Indices: 446043--446126 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 41
446033 TAACTTCTTA
* * * *
446043 AAAATTACTCATTTATACTTAAAAAAATTATTTTTTATTTTT
1 AAAACTACTCATTTATA-TTAAAAAAATCATTTATGATTTTT
446085 AAAACTACTCATTTAT-TTAAAAAACAATCATTTATGATTTTT
1 AAAACTACTCATTTATATT-AAAAA-AATCATTTATGATTTTT
446127 TCCCCTGGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 2 0.06
41 5 0.14
42 29 0.81
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.48
Consensus pattern (41 bp):
AAAACTACTCATTTATATTAAAAAAATCATTTATGATTTTT
Found at i:446265 original size:15 final size:15
Alignment explanation
Indices: 446225--446265 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
446215 ATTTTTATAT
446225 TTATATAAATTAATA
1 TTATATAAATTAATA
446240 -TAT-TAATAATTAATA
1 TTATAT-A-AATTAATA
446255 TTATATAAATT
1 TTATATAAATT
446266 TTAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
13 1 0.05
14 4 0.18
15 12 0.55
16 4 0.18
17 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATATAAATTAATA
Found at i:446359 original size:22 final size:22
Alignment explanation
Indices: 446326--446388 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
446316 TTTTAAATTT
446326 TTTATATTAATT-TATATTTTAA
1 TTTATATTAATTAT-TATTTTAA
*
446348 TTTAT-TTAAATTATTATTTTTTA
1 TTTATATT-AATTATTA-TTTTAA
*
446371 TTTATATTATATAATTAT
1 TTTATATTA-ATTATTAT
446389 ATTTCGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
21 2 0.06
22 11 0.32
23 13 0.38
24 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATATTAATTATTATTTTAA
Found at i:446387 original size:24 final size:24
Alignment explanation
Indices: 446222--446392 Score: 80
Period size: 24 Copynumber: 6.8 Consensus size: 24
446212 AATATTTTTA
*
446222 TATTTATATAAATTAATATATTAA-T
1 TATTTATAT-AATT-ATATTTTAATT
* * * * **
446247 AATTAATATTATATAAATTTTAAAA
1 TATTTATATAAT-TATATTTTAATT
* *
446272 TATTTTAAATAA-TATATATTAATGT
1 TA-TTTATATAATTATATTTTAAT-T
* *
446297 TATATATTATGATGTATATTTTTAAATT
1 TATTTA-TATAAT-TATA-TTTT-AATT
446325 T-TTTATATTAATTTATATTTTAATT
1 TATTTATA-TAA-TTATATTTTAATT
* * *
446350 TATTTAAATTATTAT-TTTTTATT
1 TATTTATATAATTATATTTTAATT
446373 TATATTATATAATTATATTT
1 TAT-TTATATAATTATATTT
446393 CGAATAAGAT
Statistics
Matches: 107, Mismatches: 25, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
23 10 0.09
24 34 0.32
25 24 0.22
26 17 0.16
27 13 0.12
28 6 0.06
29 3 0.03
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TATTTATATAATTATATTTTAATT
Found at i:446391 original size:19 final size:18
Alignment explanation
Indices: 446331--446392 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
446321 AATTTTTTAT
446331 ATTA-ATTTATATT-TTA
1 ATTATATTTATATTATTA
*
446347 ATT-TATTTAAATTATTA
1 ATTATATTTATATTATTA
* *
446364 TTTTTTATTTATATTATATA
1 -ATTATATTTATATTAT-TA
446384 ATTATATTT
1 ATTATATTT
446393 CGAATAAGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
16 11 0.31
17 3 0.08
18 2 0.06
19 18 0.50
20 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTATATTTATATTATTA
Found at i:446744 original size:8 final size:8
Alignment explanation
Indices: 446733--446795 Score: 60
Period size: 8 Copynumber: 7.8 Consensus size: 8
446723 ATTAATTATG
446733 AAAAATAT
1 AAAAATAT
446741 AAAAATAT
1 AAAAATAT
446749 AAAAATTAT
1 AAAAA-TAT
*
446758 AAATAATTT
1 AAA-AATAT
446767 AAAAA-AT
1 AAAAATAT
446774 -AAAATAAGT
1 AAAAAT-A-T
446783 AAAAATA-
1 AAAAATAT
446790 AAAAAT
1 AAAAAT
446796 TGTGTACAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
6 4 0.09
7 7 0.15
8 16 0.34
9 13 0.28
10 7 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (8 bp):
AAAAATAT
Found at i:446753 original size:9 final size:9
Alignment explanation
Indices: 446733--446774 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
446723 ATTAATTATG
446733 AAAAATAT-
1 AAAAATATA
446741 AAAAATATA
1 AAAAATATA
*
446750 AAAATTATA
1 AAAAATATA
* *
446759 AATAATTTA
1 AAAAATATA
446768 AAAAATA
1 AAAAATA
446775 AAATAAGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAATATA
Found at i:446755 original size:26 final size:25
Alignment explanation
Indices: 446726--446777 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
446716 ATTATTAATT
446726 AATTATGAAA-AATATAAAAATATAAA
1 AATTAT-AAATAATATAAAAA-ATAAA
*
446752 AATTATAAATAATTTAAAAAATAAA
1 AATTATAAATAATATAAAAAATAAA
446777 A
1 A
446778 TAAGTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (25 bp):
AATTATAAATAATATAAAAAATAAA
Found at i:446758 original size:17 final size:17
Alignment explanation
Indices: 446726--446796 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 17
446716 ATTATTAATT
446726 AATTATGAAAAATATAAA
1 AATTAT-AAAAATATAAA
446744 AA-TATAAAAATTATAAA
1 AATTATAAAAA-TATAAA
446761 TAATT-TAAAAA-AT-AA
1 -AATTATAAAAATATAAA
*
446776 AATAAGTAAAAATA-AAA
1 AATTA-TAAAAATATAAA
446793 AATT
1 AATT
446797 GTGTACAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
14 3 0.07
15 2 0.05
16 13 0.30
17 15 0.34
18 10 0.23
19 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
AATTATAAAAATATAAA
Found at i:447331 original size:16 final size:16
Alignment explanation
Indices: 447312--447347 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
447302 TAATAATTTT
*
447312 ATAAAAATAATATAAA
1 ATAAAAATAAAATAAA
*
447328 ATAAAAATAAAATGAA
1 ATAAAAATAAAATAAA
447344 ATAA
1 ATAA
447348 TTATAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (16 bp):
ATAAAAATAAAATAAA
Found at i:447440 original size:21 final size:21
Alignment explanation
Indices: 447389--447432 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
447379 ATATTATAAG
447389 ATTTAAA-TTTTTAATAAAAA
1 ATTTAAATTTTTTAATAAAAA
*
447409 ATTTAAATTTTTTAA-AAATA
1 ATTTAAATTTTTTAATAAAAA
447429 ATTT
1 ATTT
447433 TATATTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTAAATTTTTTAATAAAAA
Found at i:448591 original size:14 final size:14
Alignment explanation
Indices: 448543--448594 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
448533 GGTTATAATA
448543 TTTATTTTTATTTT
1 TTTATTTTTATTTT
* *
448557 TTAATTTTGATTTT
1 TTTATTTTTATTTT
* *
448571 TCCTATTTTTCTTTT
1 T-TTATTTTTATTTT
448586 TTTATTTTT
1 TTTATTTTT
448595 TTGAATTTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 20 0.67
15 10 0.33
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTATTTTTATTTT
Found at i:449006 original size:18 final size:21
Alignment explanation
Indices: 448965--449004 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
448955 AAATTTAATT
448965 ATAAAATATATAAATATTAAA
1 ATAAAATATATAAATATTAAA
*
448986 ATAAAA-ATA-AAATTTTAAA
1 ATAAAATATATAAATATTAAA
449005 TATTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAATATATAAATATTAAA
Found at i:450288 original size:18 final size:19
Alignment explanation
Indices: 450265--450303 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
450255 TATAATTATG
*
450265 ATATAATA-AAATGTATAA
1 ATATAATACAAATATATAA
450283 ATATAATACAAATATATAA
1 ATATAATACAAATATATAA
450302 AT
1 AT
450304 TTATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
ATATAATACAAATATATAA
Found at i:450689 original size:21 final size:21
Alignment explanation
Indices: 450664--450718 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
450654 TATATTTTAT
450664 ATTTAAAATTAAATAAA-AGT-
1 ATTT-AAATTAAATAAATAGTG
* *
450684 ATTTTATATTAATTAAATAGTG
1 A-TTTAAATTAAATAAATAGTG
450706 ATTTAAATTAAAT
1 ATTTAAATTAAAT
450719 TGAGCTTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 11 0.39
21 16 0.57
22 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTTAAATTAAATAAATAGTG
Found at i:451066 original size:15 final size:17
Alignment explanation
Indices: 451036--451072 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
451026 GATATAAATA
*
451036 TAAATAAAATTTTTA-T
1 TAAATAAAATTATTATT
451052 TAAAT-AAATTATTATT
1 TAAATAAAATTATTATT
451068 TAAAT
1 TAAAT
451073 CGGATTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAATAAAATTATTATT
Found at i:451678 original size:48 final size:45
Alignment explanation
Indices: 451626--451764 Score: 112
Period size: 40 Copynumber: 3.1 Consensus size: 45
451616 ATGCTGTACT
*
451626 TAATTAAATGTAAAGGTAATATTTTATTTAATTTATAATATTTATATG
1 TAATT-AATGTAAA-GTAAT-TTTTATTTAATTTATAATATTTATATA
* * * *
451674 TAATT-A-GT-AA-T-ATTTATATTAAATTTGTAATATTT-T-TT
1 TAATTAATGTAAAGTAATTTTTATTTAATTTATAATATTTATATA
* *
451712 TAATTATATGTAAAGATAATGTTTCATATAATTTATAATATTTATATA
1 TAATTA-ATGTAAAG-TAAT-TTTTATTTAATTTATAATATTTATATA
451760 TAATT
1 TAATT
451765 GATAATATTT
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
38 6 0.08
39 1 0.01
40 20 0.28
41 4 0.06
42 3 0.04
44 3 0.04
45 4 0.06
46 18 0.25
47 1 0.01
48 11 0.15
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (45 bp):
TAATTAATGTAAAGTAATTTTTATTTAATTTATAATATTTATATA
Found at i:451751 original size:66 final size:66
Alignment explanation
Indices: 451660--451807 Score: 178
Period size: 67 Copynumber: 2.2 Consensus size: 66
451650 TATTTAATTT
*
451660 ATAATATTTATATGTAA-TTAGTAATATTTATAT-TAAATTTG-TAATATTTT-TTTAATTATAT
1 ATAATATTTATA--TAATTTA-TAATATTTATATAT-AA-TTGATAATATTTTATGTAATTATAT
* *
451721 GTAAAG
61 ATAAAA
*
451727 ATAATGTTTCATATAATTTATAATATTTATATATAATTGATAATATTTTATGTAATTATATATAA
1 ATAATATTT-ATATAATTTATAATATTTATATATAATTGATAATATTTTATGTAATTATATATAA
451792 AA
65 AA
451794 ATAATATTTATATA
1 ATAATATTTATATA
451808 TAACTTGTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
65 3 0.04
66 31 0.44
67 34 0.48
68 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (66 bp):
ATAATATTTATATAATTTATAATATTTATATATAATTGATAATATTTTATGTAATTATATATAAA
A
Found at i:451762 original size:20 final size:19
Alignment explanation
Indices: 451642--451788 Score: 84
Period size: 20 Copynumber: 7.1 Consensus size: 19
451632 AATGTAAAGG
*
451642 TAATATTTTATTTAATTTA
1 TAATATTTTATATAATTTA
*
451661 TAATATTTATATGTAA-TTA
1 TAATATTT-TATATAATTTA
*
451680 GTAATA-TTTATATTAAATTTG
1 -TAATATTTTATA-T-AATTTA
*
451701 TAATATTTT-TTTAATTATA
1 TAATATTTTATATAATT-TA
451720 TGTAAAGATAATGTTTCATATAATTTA
1 --T--A-AT-AT-TTT-ATATAATTTA
*
451747 TAATATTTATATATAATTGA
1 TAATATTT-TATATAATTTA
*
451767 TAATATTTTATGTAATTATA
1 TAATATTTTATATAATT-TA
451787 TA
1 TA
451789 TAAAAATAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 35
0.70 0.06 0.24
Matches are distributed among these distances:
18 7 0.07
19 24 0.24
20 41 0.41
21 9 0.09
22 2 0.02
23 2 0.02
24 2 0.02
25 3 0.03
26 3 0.03
27 2 0.02
28 6 0.06
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (19 bp):
TAATATTTTATATAATTTA
Found at i:451824 original size:66 final size:64
Alignment explanation
Indices: 451660--451827 Score: 160
Period size: 67 Copynumber: 2.5 Consensus size: 64
451650 TATTTAATTT
* * * *
451660 ATAATATTTATATGTAATTAGTAATATTTATATTAAATTTGTAATATTTTTTTAATTATATGTAA
1 ATAATATTTATATATAATT-GTAATATATATA-T-AATTTGTAATATTTTTGTAATTATATATAA
*
451725 AG
63 AA
* * *
451727 ATAATGTTTCATATA-ATTTATAATATTTATATATAA-TTGATAATATTTTATGTAATTATATAT
1 ATAATATTT-ATATATAATTGTAATA--TATATATAATTTG-TAATATTTT-TGTAATTATATAT
451790 AAAA
61 AAAA
*
451794 ATAATATTTATATATAACTTGTAACATATATATA
1 ATAATATTTATATATAA-TTGTAATATATATATA
451828 TATATATATG
Statistics
Matches: 82, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
65 3 0.04
66 29 0.35
67 35 0.43
68 15 0.18
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (64 bp):
ATAATATTTATATATAATTGTAATATATATATAATTTGTAATATTTTTGTAATTATATATAAAA
Found at i:452493 original size:7 final size:7
Alignment explanation
Indices: 452463--452501 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
452453 TATAGTTATT
452463 ATTAAAA
1 ATTAAAA
*
452470 ATTAATA
1 ATTAAAA
*
452477 TTTAATAA
1 ATTAA-AA
452485 ATTAAAA
1 ATTAAAA
452492 ATTAAAA
1 ATTAAAA
452499 ATT
1 ATT
452502 TAAATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 22 0.81
8 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
ATTAAAA
Found at i:452504 original size:15 final size:14
Alignment explanation
Indices: 452464--452508 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
452454 ATAGTTATTA
*
452464 TTAAAAATTAATAT
1 TTAAAAATTAAAAT
*
452478 TTAATAAATTAAAAA
1 TTAA-AAATTAAAAT
*
452493 TTAAAAATTTAAAT
1 TTAAAAATTAAAAT
452507 TT
1 TT
452509 TAATATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAAAATTAAAAT
Found at i:452698 original size:28 final size:28
Alignment explanation
Indices: 452662--452719 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
452652 AAAATAGTAT
452662 AAATATTATATAAATACATGAATATATTA
1 AAATATTATATAAATA-ATGAATATATTA
* *
452691 AAAT-TTATATAAATATTTAATATATTA
1 AAATATTATATAAATAATGAATATATTA
452718 AA
1 AA
452720 TACAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 12 0.44
28 11 0.41
29 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
AAATATTATATAAATAATGAATATATTA
Found at i:454278 original size:32 final size:32
Alignment explanation
Indices: 454242--454303 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
454232 TAGAAAGGGG
* *
454242 TAATTTATATTTTAAATTATTAA-ATTTAATAT
1 TAATTTATA-TATAAATTATAAATATTTAATAT
*
454274 TAATTTTTATATAAATTATAAATATTTAAT
1 TAATTTATATATAAATTATAAATATTTAAT
454304 TTTATTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TAATTTATATATAAATTATAAATATTTAATAT
Found at i:454317 original size:24 final size:24
Alignment explanation
Indices: 454258--454334 Score: 83
Period size: 24 Copynumber: 3.2 Consensus size: 24
454248 ATATTTTAAA
454258 TTATTAAATT-T-AATATTAATTT
1 TTATTAAATTATAAATATTAATTT
454280 TTATATAAATTATAAATATTTAA-TT
1 TTAT-TAAATTATAAATA-TTAATTT
454305 TTATTAAATTAT--ATCATTAAATTT
1 TTATTAAATTATAAAT-ATT-AATTT
454329 TTATTA
1 TTATTA
454335 TTAATAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
22 8 0.17
23 9 0.19
24 17 0.35
25 10 0.21
26 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATTAAATTATAAATATTAATTT
Found at i:454337 original size:22 final size:23
Alignment explanation
Indices: 454303--454354 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 23
454293 AAATATTTAA
*
454303 TTTTATTAAATT-ATATCATTAAAT
1 TTTTATT-AATTAATA-AATTAAAT
454327 TTTTATT-ATTAATAAATTAAAT
1 TTTTATTAATTAATAAATTAAAT
454349 TATTTA
1 T-TTTA
454355 CATTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 11 0.44
23 7 0.28
24 7 0.28
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTATTAATTAATAAATTAAAT
Found at i:454359 original size:22 final size:22
Alignment explanation
Indices: 454320--454361 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
454310 AAATTATATC
*
454320 ATTAAATTTTTATTATTAATAA
1 ATTAAATTTTTATCATTAATAA
454342 ATTAAATTATTTA-CATTAAT
1 ATTAAATT-TTTATCATTAAT
454362 TTTATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTAAATTTTTATCATTAATAA
Found at i:454517 original size:23 final size:24
Alignment explanation
Indices: 454486--454543 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
454476 TTTTTCGTTA
* *
454486 AAATTATTTAATTGAATTAAT-TT
1 AAATAATTTAATTGAATTAATAAT
* *
454509 AAATAATTTAATTTATTTAATAAT
1 AAATAATTTAATTGAATTAATAAT
454533 AAA-AATTTAAT
1 AAATAATTTAAT
454544 AAAATTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AAATAATTTAATTGAATTAATAAT
Found at i:454521 original size:18 final size:17
Alignment explanation
Indices: 454494--454532 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
454484 TAAAATTATT
454494 TAATTGAATTAATTTAAA
1 TAATTGAATTAATTT-AA
* *
454512 TAATTTAATTTATTTAA
1 TAATTGAATTAATTTAA
454529 TAAT
1 TAAT
454533 AAAAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TAATTGAATTAATTTAA
Found at i:458702 original size:52 final size:52
Alignment explanation
Indices: 458641--458757 Score: 171
Period size: 52 Copynumber: 2.2 Consensus size: 52
458631 TTGAAGAATG
* *
458641 TATCAATACATTTGGGTCAAAAACTCAAAATGTATCGATACAATAAAAAATA
1 TATCAATACATTTGGGTCAAAAACTCAAAACGTATCAATACAATAAAAAATA
** * * *
458693 TATTGATACATTTGGGTTAAAAACTCAGAACGTATCAATACAATGAAAAATA
1 TATCAATACATTTGGGTCAAAAACTCAAAACGTATCAATACAATAAAAAATA
458745 TATCAATACATTT
1 TATCAATACATTT
458758 TCCTTTTAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (52 bp):
TATCAATACATTTGGGTCAAAAACTCAAAACGTATCAATACAATAAAAAATA
Found at i:462051 original size:20 final size:20
Alignment explanation
Indices: 462026--462071 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
462016 AAGAATTGAA
*
462026 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
**
462046 GAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
462066 GAGGGA
1 GAGGGA
462072 GCCTCTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.50, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:462221 original size:24 final size:27
Alignment explanation
Indices: 462153--462218 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
462143 AGCCTTCATA
*
462153 TTTGACAAATACAAAGGA-AACCACCATT
1 TTTGACAAACACAAA--ATAACCACCATT
462181 TTTGACAAACACAAAATAACCACCATT
1 TTTGACAAACACAAAATAACCACCATT
462208 TTTGACAAACA
1 TTTGACAAACA
462219 AATGGGTGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 14 0.39
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.23
Consensus pattern (27 bp):
TTTGACAAACACAAAATAACCACCATT
Found at i:466721 original size:25 final size:25
Alignment explanation
Indices: 466688--466738 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
466678 CTTGTAATAA
*
466688 AAATTAGCC-ACAAATTTTGACAAAT
1 AAATAAGCCTACAAA-TTTGACAAAT
* *
466713 AAATAAGCCTTCATATTTGACAAAT
1 AAATAAGCCTACAAATTTGACAAAT
466738 A
1 A
466739 CAAAGGAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (25 bp):
AAATAAGCCTACAAATTTGACAAAT
Found at i:466796 original size:24 final size:27
Alignment explanation
Indices: 466728--466793 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
466718 AGCCTTCATA
*
466728 TTTGACAAATACAAAGGA-AACCACCATT
1 TTTGACAAACACAAA--ATAACCACCATT
466756 TTTGACAAACACAAAATAACCACCATT
1 TTTGACAAACACAAAATAACCACCATT
466783 TTTGACAAACA
1 TTTGACAAACA
466794 AATTGGTGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 14 0.39
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.23
Consensus pattern (27 bp):
TTTGACAAACACAAAATAACCACCATT
Found at i:467109 original size:21 final size:22
Alignment explanation
Indices: 467063--467109 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
467053 CTTAAAAGTT
* *
467063 TTAATTTAAAATATTGTATCTT
1 TTAATTTAAAAAATTGTATCTA
467085 TTAATTTAAATAAATT-TAT-TA
1 TTAATTTAAA-AAATTGTATCTA
467106 TTAA
1 TTAA
467110 CATATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 5 0.23
22 13 0.59
23 4 0.18
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTTAAAAAATTGTATCTA
Found at i:467504 original size:12 final size:12
Alignment explanation
Indices: 467489--467533 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
467479 TTTAAATATA
*
467489 ATAAAATGTAAT
1 ATAAAATATAAT
*
467501 ATAAATAAATAAT
1 ATAAA-ATATAAT
467514 -TAAAATATAAT
1 ATAAAATATAAT
467525 ATAAAATAT
1 ATAAAATAT
467534 TATTATTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 6 0.21
12 17 0.61
13 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:468379 original size:15 final size:16
Alignment explanation
Indices: 468350--468382 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
468340 TCCTTCGAGC
468350 TAAAATATATAAAAAA
1 TAAAATATATAAAAAA
468366 TAAAATAT-TAAAAAA
1 TAAAATATATAAAAAA
468381 TA
1 TA
468383 TTTTTACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAATATATAAAAAA
Found at i:468770 original size:9 final size:9
Alignment explanation
Indices: 468674--468774 Score: 51
Period size: 9 Copynumber: 10.4 Consensus size: 9
468664 AGTAGATACA
468674 ATAAGAAAAT
1 ATAA-AAAAT
468684 ATGAAAAAATT
1 AT-AAAAAA-T
468695 ATAATTAAAAT
1 ATAA--AAAAT
*
468706 -TAAAAATT
1 ATAAAAAAT
* *
468714 TTAAAAATT
1 ATAAAAAAT
*
468723 AGATAAAAAT
1 ATA-AAAAAT
468733 ATAACATAAAT
1 ATAA-A-AAAT
* *
468744 ATAATATAT
1 ATAAAAAAT
* *
468753 TTAATAAAT
1 ATAAAAAAT
468762 ATAAAAAAT
1 ATAAAAAAT
468771 ATAA
1 ATAA
468775 TAATATGATA
Statistics
Matches: 72, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
8 4 0.06
9 31 0.43
10 19 0.26
11 14 0.19
12 4 0.06
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:468775 original size:18 final size:18
Alignment explanation
Indices: 468727--468777 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
468717 AAAATTAGAT
468727 AAAAATATAACATAAATATA
1 AAAAATAT-A-ATAAATATA
* * *
468747 ATATATTTAATAAATATA
1 AAAAATATAATAAATATA
468765 AAAAATATAATAA
1 AAAAATATAATAA
468778 TATGATATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 19 0.76
19 1 0.04
20 5 0.20
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATATAATAAATATA
Found at i:469812 original size:29 final size:28
Alignment explanation
Indices: 469780--469839 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
469770 ATAAAAGTAT
* *
469780 TTTGCTAAAGATATTTTTGACAGAAATAC
1 TTTGATAAAGATA-CTTTGACAGAAATAC
* *
469809 TTTGATAAAGTTACTTTGACATAAATAC
1 TTTGATAAAGATACTTTGACAGAAATAC
469837 TTT
1 TTT
469840 TGACAGGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.42
Consensus pattern (28 bp):
TTTGATAAAGATACTTTGACAGAAATAC
Found at i:469843 original size:15 final size:14
Alignment explanation
Indices: 469795--469844 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
469785 TAAAGATATT
*
469795 TTTGACAGAAATAC
1 TTTGACATAAATAC
469809 TTTG--ATAAAGTTAC
1 TTTGACATAAA--TAC
469823 TTTGACATAAATAC
1 TTTGACATAAATAC
469837 TTTTGACA
1 -TTTGACA
469845 GGTATTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
12 4 0.13
14 14 0.47
15 7 0.23
16 5 0.17
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (14 bp):
TTTGACATAAATAC
Found at i:475127 original size:14 final size:14
Alignment explanation
Indices: 475110--475202 Score: 64
Period size: 14 Copynumber: 6.5 Consensus size: 14
475100 CAGAAAATTT
*
475110 TTTGACATAGATAC
1 TTTGACAGAGATAC
*
475124 TTTGACATA-AGTAC
1 TTTGACAGAGA-TAC
* *
475138 ATTTGGCAGAGATAT
1 -TTTGACAGAGATAC
* *
475153 TTTG-CTAAAGATATT
1 TTTGAC-AGAGATA-C
*
475168 TTTGACAGAAATAC
1 TTTGACAGAGATAC
*
475182 TTTGACAGAGTTAC
1 TTTGACAGAGATAC
475196 TTTGACA
1 TTTGACA
475203 TAAGTACTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
13 2 0.03
14 41 0.64
15 19 0.30
16 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (14 bp):
TTTGACAGAGATAC
Found at i:475210 original size:14 final size:13
Alignment explanation
Indices: 475110--475219 Score: 51
Period size: 14 Copynumber: 7.7 Consensus size: 13
475100 CAGAAAATTT
*
475110 TTTGACATAGATAC
1 TTTGACAAAG-TAC
475124 TTTGACATAAGTAC
1 TTTGACA-AAGTAC
* * *
475138 ATTTGGCAGAGATAT
1 -TTTGACAAAG-TAC
*
475153 TTTG-CTAAAGATATT
1 TTTGAC-AAAG-TA-C
*
475168 TTTGACAGAAATAC
1 TTTGACA-AAGTAC
*
475182 TTTGACAGAGTTAC
1 TTTGACAAAG-TAC
475196 TTTGACATAAGTAC
1 TTTGACA-AAGTAC
475210 TTTTGACAAA
1 -TTTGACAAA
475220 TATTTTTTAG
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
13 2 0.03
14 44 0.58
15 27 0.36
16 3 0.04
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (13 bp):
TTTGACAAAGTAC
Found at i:475243 original size:72 final size:72
Alignment explanation
Indices: 475110--475277 Score: 167
Period size: 72 Copynumber: 2.3 Consensus size: 72
475100 CAGAAAATTT
* * * *
475110 TTTGACATAGATACTTTGACATAAGTACATTTGGCAGAGATATTTTGCTAAAGATATTTTTGACA
1 TTTGACAGAGATACTTTGACATAAGTACATTTGACAAAGATATTTTGCTAAAGATACTTTTGACA
475175 GAAATAC
66 GAAATAC
* * * * * *
475182 TTTGACAGAGTTACTTTGACATAAGTACTTTTGACAAATATTTTTTAGTTGAAG-TACTTTTGAC
1 TTTGACAGAGATACTTTGACATAAGTACATTTGACAAAGATATTTT-GCTAAAGATACTTTTGAC
* * *
475246 GGAGATAT
65 AGAAATAC
* * * *
475254 TTTAATAAAGATACTTTAACATAA
1 TTTGACAGAGATACTTTGACATAA
475278 CACTCTTTGG
Statistics
Matches: 77, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
72 72 0.94
73 5 0.06
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (72 bp):
TTTGACAGAGATACTTTGACATAAGTACATTTGACAAAGATATTTTGCTAAAGATACTTTTGACA
GAAATAC
Found at i:476850 original size:35 final size:36
Alignment explanation
Indices: 476783--476859 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 36
476773 AATTTTAAAC
* *
476783 TTTAAAAATAAATTTAATTAATTTATACTATC-ACT
1 TTTAAAAATAAATTTAATTAATTTATAATATCAAAT
*
476818 TTTAAAATTAACATTT-ATTAAATTTA-AATATCAAAT
1 TTTAAAAATAA-ATTTAATT-AATTTATAATATCAAAT
476854 TTTAAA
1 TTTAAA
476860 TAGCTGTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 18 0.50
36 18 0.50
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (36 bp):
TTTAAAAATAAATTTAATTAATTTATAATATCAAAT
Found at i:480036 original size:2 final size:2
Alignment explanation
Indices: 480029--480058 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
480019 TGTTTCACTC
480029 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
480059 GCAGGCTATG
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):
AT
Found at i:480192 original size:27 final size:27
Alignment explanation
Indices: 480162--480221 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
480152 ATATATTATA
*
480162 TTATATTATAATTATA-TTTAAAATATT
1 TTATATT-TAATTAAATTTTAAAATATT
* *
480189 TTATATTTATTTAAATTTTAATATATT
1 TTATATTTAATTAAATTTTAAAATATT
480216 TTATAT
1 TTATAT
480222 AAATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATATTTAATTAAATTTTAAAATATT
Found at i:480213 original size:20 final size:20
Alignment explanation
Indices: 480190--480240 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
480180 TAAAATATTT
480190 TATATTTATTTAAATTTTAA
1 TATATTTATTTAAATTTTAA
*
480210 TATATTTTATATAAATTTTAA
1 TATA-TTTATTTAAATTTTAA
*
480231 AATATTTATT
1 TATATTTATT
480241 CATATCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATTTATTTAAATTTTAA
Found at i:480269 original size:30 final size:29
Alignment explanation
Indices: 480230--480286 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
480220 ATAAATTTTA
*
480230 AAATATTTATTCATATCATATTATTTATT
1 AAATATTTATTCATATCATATCATTTATT
**
480259 AAATATTTTATTTTTATCATATCATTTA
1 AAATA-TTTATTCATATCATATCATTTA
480287 ACTGTGTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (29 bp):
AAATATTTATTCATATCATATCATTTATT
Found at i:480348 original size:25 final size:26
Alignment explanation
Indices: 480305--480354 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
480295 TAAAATTATT
480305 TATTTATAAATTTATA-TTTATTTAA
1 TATTTATAAATTTATATTTTATTTAA
*
480330 TATTTTTACAATTTA-ATTTTATTTA
1 TATTTATA-AATTTATATTTTATTTA
480355 TTATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TATTTATAAATTTATATTTTATTTAA
Found at i:480722 original size:26 final size:25
Alignment explanation
Indices: 480693--480755 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 25
480683 TTTATATTTG
480693 ATAATATTAAATATAATTACAT-AAAT
1 ATAATA-TAAATATAATTA-ATAAAAT
*
480719 ATAATATAAA-A-AATTATTAAAAT
1 ATAATATAAATATAATTAATAAAAT
480742 ATAATATAAATATA
1 ATAATATAAATATA
480756 TAAATATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
22 1 0.03
23 19 0.58
24 2 0.06
25 5 0.15
26 6 0.18
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATATAAATATAATTAATAAAAT
Found at i:480748 original size:42 final size:38
Alignment explanation
Indices: 480702--480791 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 38
480692 GATAATATTA
480702 AATATAATTACATAAATATAATATAAAAAATTATTAAAATAT
1 AATATAATTACATAAATAT--T-TAAAAAATTA-TAAAATAT
* * *
480744 AATATAAATATATAAATATTTTAAAAATTATAAAATAT
1 AATATAATTACATAAATATTTAAAAAATTATAAAATAT
*
480782 AA-ATTATTAC
1 AATATAATTAC
480792 TTGTTATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
37 5 0.12
38 10 0.24
39 9 0.21
40 1 0.02
42 17 0.40
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (38 bp):
AATATAATTACATAAATATTTAAAAAATTATAAAATAT
Found at i:480776 original size:31 final size:30
Alignment explanation
Indices: 480713--480785 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 30
480703 ATATAATTAC
480713 ATAAATAT-AATATAAAAAATTATTAAAAT
1 ATAAATATAAATATAAAAAATTATTAAAAT
*
480742 AT-AATATAAATATATAAATATT-TTAAAAATT
1 ATAAATATAAATATA-AAAAATTATT-AAAA-T
480773 ATAAAATATAAAT
1 AT-AAATATAAAT
480786 TATTACTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
28 5 0.14
29 10 0.27
30 10 0.27
31 3 0.08
33 9 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (30 bp):
ATAAATATAAATATAAAAAATTATTAAAAT
Found at i:480779 original size:19 final size:19
Alignment explanation
Indices: 480727--480783 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
480717 ATATAATATA
480727 AAAAATTATTAAAATATAAT
1 AAAAATTA-TAAAATATAAT
* **
480747 ATAAA-TATATAAATATTTT
1 AAAAATTATA-AAATATAAT
480766 AAAAATTATAAAATATAA
1 AAAAATTATAAAATATAA
480784 ATTATTACTT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 2 0.07
19 19 0.66
20 8 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTATAAAATATAAT
Found at i:483921 original size:2 final size:2
Alignment explanation
Indices: 483914--483942 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
483904 TCCAATTTAT
483914 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
483943 TTTGTATTCG
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
Found at i:485328 original size:30 final size:31
Alignment explanation
Indices: 485281--485341 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
485271 GTCAACAGGC
*
485281 CATTACATGCTTATTATATGTGCTTGGTAGT
1 CATTACATGCTTATTATATGCGCTTGGTAGT
485312 CATTACATGC-TATTATATGCGCTTGGTAGT
1 CATTACATGCTTATTATATGCGCTTGGTAGT
485342 GGATTGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.43
Consensus pattern (31 bp):
CATTACATGCTTATTATATGCGCTTGGTAGT
Found at i:490126 original size:31 final size:30
Alignment explanation
Indices: 490081--490189 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 30
490071 GTCCAATGTT
490081 AAACTTATTTTCTTTTGAATAAGTTGAAAGTC
1 AAACTT-TTTTCTTTTGAATAAG-TGAAAGTC
* * ** *
490113 AAACTTTTTTCTTTCTTAACAAGCAAAAGTT
1 AAACTTTTTTCTTT-TGAATAAGTGAAAGTC
490144 AAA-TTTATGTTCTTTTGAATAAGCTGAAAGTC
1 AAACTTT-T-TTCTTTTGAATAAG-TGAAAGTC
490176 AAACTTTTTTCTTT
1 AAACTTTTTTCTTT
490190 CTTAACAAGC
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
30 3 0.05
31 29 0.47
32 27 0.44
33 3 0.05
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (30 bp):
AAACTTTTTTCTTTTGAATAAGTGAAAGTC
Found at i:490145 original size:63 final size:63
Alignment explanation
Indices: 490056--490231 Score: 255
Period size: 63 Copynumber: 2.8 Consensus size: 63
490046 AAGTCAATTA
* * *
490056 TTTTCTTT-TTAACAGGTCCAATGTTAAACTTATTTTCTTTTGAATAAGTTGAAAGTCAAACTT
1 TTTTCTTTCTTAACAAG-CAAAAGTTAAACTTATTTTCTTTTGAATAAGTTGAAAGTCAAACTT
* * *
490119 TTTTCTTTCTTAACAAGCAAAAGTTAAATTTATGTTCTTTTGAATAAGCTGAAAGTCAAACTT
1 TTTTCTTTCTTAACAAGCAAAAGTTAAACTTATTTTCTTTTGAATAAGTTGAAAGTCAAACTT
* *
490182 TTTTCTTTCTTAACAAGCAAAAGTTAAAACTTATTTTCTTTCGAACAAGT
1 TTTTCTTTCTTAACAAGCAAAAGTT-AAACTTATTTTCTTTTGAATAAGT
490232 CAAAAATCAA
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
63 74 0.74
64 26 0.26
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (63 bp):
TTTTCTTTCTTAACAAGCAAAAGTTAAACTTATTTTCTTTTGAATAAGTTGAAAGTCAAACTT
Found at i:490229 original size:32 final size:32
Alignment explanation
Indices: 490081--490255 Score: 117
Period size: 32 Copynumber: 5.5 Consensus size: 32
490071 GTCCAATGTT
* * ** *
490081 AAACTTATTTTCTTTTGAATAAGTTGAAAG-TC
1 AAACTTATTTTCTTTCGAACAAG-CAAAAGTTA
*
490113 AAACTT-TTTTCTTTCTTAACAAGCAAAAGTT-
1 AAACTTATTTTCTTTC-GAACAAGCAAAAGTTA
* * * * * *
490144 AAATTTATGTTCTTTTGAATAAGCTGAAAG-TC
1 AAACTTATTTTCTTTCGAACAAGC-AAAAGTTA
*
490176 AAACTT-TTTTCTTTCTTAACAAGCAAAAGTTA
1 AAACTTATTTTCTTTC-GAACAAGCAAAAGTTA
* *
490208 AAACTTATTTTCTTTCGAACAAGTCAAAAATCA
1 AAACTTATTTTCTTTCGAACAAG-CAAAAGTTA
* *
490241 AAACTTGTTTCCTTT
1 AAACTTATTTTCTTT
490256 TGGATAGATC
Statistics
Matches: 111, Mismatches: 23, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
31 35 0.32
32 47 0.42
33 29 0.26
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (32 bp):
AAACTTATTTTCTTTCGAACAAGCAAAAGTTA
Found at i:491202 original size:7 final size:7
Alignment explanation
Indices: 491192--491225 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
491182 ATTTTTTATA
491192 ATTTCAT
1 ATTTCAT
491199 ATTTCAT
1 ATTTCAT
491206 ATTTCAT
1 ATTTCAT
491213 ATTTCAT
1 ATTTCAT
491220 ATTTCA
1 ATTTCA
491226 CTTGTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTTCAT
Found at i:494642 original size:51 final size:51
Alignment explanation
Indices: 494584--494687 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
494574 AATTTCAAAT
494584 CAACTTTATTCTTCCATTTGCATCTTGGAAATACCTTTTGATTCTTGCATA
1 CAACTTTATTCTTCCATTTGCATCTTGGAAATACCTTTTGATTCTTGCATA
* * *
494635 CAACTTTATTTTTCCATTTGCATCTTTGAAATACGTTTTGATTCTTGCATA
1 CAACTTTATTCTTCCATTTGCATCTTGGAAATACCTTTTGATTCTTGCATA
494686 CA
1 CA
494688 TACCTCATTC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (51 bp):
CAACTTTATTCTTCCATTTGCATCTTGGAAATACCTTTTGATTCTTGCATA
Found at i:495030 original size:2 final size:2
Alignment explanation
Indices: 495025--495059 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
495015 AAATACACAC
495025 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 A
495060 GGAATGATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:495838 original size:2 final size:2
Alignment explanation
Indices: 495831--495857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
495821 TGGAACAACC
495831 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
495858 GTACAAGATA
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:497301 original size:5 final size:5
Alignment explanation
Indices: 497291--497349 Score: 52
Period size: 5 Copynumber: 12.2 Consensus size: 5
497281 AATAATTTTA
* * *
497291 AATAT AATAT AAAAAT AATAA AATAT AA-A- AATA- AATAA AATAT AATAT
1 AATAT AATAT -AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
*
497339 AATAA AATAT A
1 AATAT AATAT A
497350 TATTTATATT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
3 2 0.05
4 6 0.14
5 32 0.73
6 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (5 bp):
AATAT
Found at i:497315 original size:16 final size:16
Alignment explanation
Indices: 497291--497349 Score: 84
Period size: 16 Copynumber: 3.7 Consensus size: 16
497281 AATAATTTTA
*
497291 AATATAATATAAAAAT
1 AATAAAATATAAAAAT
497307 AATAAAATATAAAAAT
1 AATAAAATATAAAAAT
*
497323 AAATAAAATAT-AATAT
1 -AATAAAATATAAAAAT
497339 AATAAAATATA
1 AATAAAATATA
497350 TATTTATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.26
16 19 0.49
17 10 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAAATATAAAAAT
Found at i:497319 original size:27 final size:27
Alignment explanation
Indices: 497271--497349 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 27
497261 CATATTTTGC
* * *
497271 ATATAAAATTAAT-AATTTTAAATATA
1 ATATAAAAATAATAAAATATAAATATA
*
497297 ATATAAAAATAATAAAATATAAAAATA
1 ATATAAAAATAATAAAATATAAATATA
*
497324 A-ATAAAATATAATATAATA-AAATATA
1 ATATAAAA-ATAATAAAATATAAATATA
497350 TATTTATATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 24 0.53
27 21 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
ATATAAAAATAATAAAATATAAATATA
Found at i:497770 original size:5 final size:5
Alignment explanation
Indices: 497762--497807 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
497752 TAAAATTTTA
* *
497762 AATAT AATAA AATAT AATAT AA-AT AA-AT AATTAA AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AA
497808 AATATTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 8 0.23
5 24 0.69
6 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
AATAT
Found at i:497784 original size:29 final size:26
Alignment explanation
Indices: 497759--497810 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 26
497749 ATTTAAAATT
497759 TTAAATATAATAAAATATAATAT-AAA
1 TTAAATA-AATAAAATATAATATAAAA
*
497785 -TAAATAATTAAAATATAATATAAAA
1 TTAAATAAATAAAATATAATATAAAA
497810 T
1 T
497811 ATTATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAAATAAATAAAATATAATATAAAA
Found at i:498666 original size:15 final size:16
Alignment explanation
Indices: 498637--498669 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
498627 CTCTTCGAGC
498637 TAAAATATATAAAAAA
1 TAAAATATATAAAAAA
498653 TAAAATAT-TAAAAAA
1 TAAAATATATAAAAAA
498668 TA
1 TA
498670 TTTTTACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAATATATAAAAAA
Found at i:499049 original size:18 final size:18
Alignment explanation
Indices: 499028--499081 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
499018 AAAATATAAC
*
499028 ATAAATATGATATATTTA
1 ATAAATATGATATATATA
* * *
499046 ATAAATATAAAAAATATA
1 ATAAATATGATATATATA
499064 AT-AATATGATATAGTATA
1 ATAAATATGATATA-TATA
499082 TTTATATTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
ATAAATATGATATATATA
Found at i:500046 original size:25 final size:27
Alignment explanation
Indices: 500009--500058 Score: 86
Period size: 25 Copynumber: 1.9 Consensus size: 27
499999 CACCTTATTT
500009 ATATGAATAATAAATTTATATATTTGA
1 ATATGAATAATAAATTTATATATTTGA
500036 ATAT-AAT-ATAAATTTATATATTT
1 ATATGAATAATAAATTTATATATTT
500059 TAATTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 16 0.70
26 3 0.13
27 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (27 bp):
ATATGAATAATAAATTTATATATTTGA
Found at i:500074 original size:25 final size:25
Alignment explanation
Indices: 500016--500091 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
500006 TTTATATGAA
* * *
500016 TAATAAATTTATATATTTGAA--TA
1 TAATTAATTTATATATTTTAATTTT
500039 TAATATAAATTTATATATTTTAATTTT
1 TAAT-T-AATTTATATATTTTAATTTT
500066 TAATTAATTT-TATATTTT-ATTTT
1 TAATTAATTTATATATTTTAATTTT
500089 TAA
1 TAA
500092 AAAAATATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
23 12 0.26
24 8 0.17
25 20 0.43
26 1 0.02
27 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (25 bp):
TAATTAATTTATATATTTTAATTTT
Found at i:500083 original size:24 final size:24
Alignment explanation
Indices: 500046--500091 Score: 76
Period size: 23 Copynumber: 1.9 Consensus size: 24
500036 ATATAATATA
500046 AATTTATATATTTTAATTTTTAATT
1 AATTTATATATTTT-ATTTTTAATT
500071 AATTT-TATATTTTATTTTTAA
1 AATTTATATATTTTATTTTTAA
500092 AAAAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 8 0.38
24 8 0.38
25 5 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
AATTTATATATTTTATTTTTAATT
Found at i:500127 original size:17 final size:17
Alignment explanation
Indices: 500107--500144 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
500097 TATAAATTAC
*
500107 AAATTTATATATATAAT
1 AAATTTAAATATATAAT
*
500124 AAATTTAAATATCTAAT
1 AAATTTAAATATATAAT
500141 AAAT
1 AAAT
500145 ATTTTTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTAAATATATAAT
Found at i:500201 original size:11 final size:11
Alignment explanation
Indices: 500187--500211 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
500177 GTAATATTTG
500187 AATAATAAATA
1 AATAATAAATA
500198 AATAATAAATA
1 AATAATAAATA
500209 AAT
1 AAT
500212 TTAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAATAAATA
Found at i:500232 original size:26 final size:26
Alignment explanation
Indices: 500192--500250 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 26
500182 ATTTGAATAA
500192 TAAATAAATAATAAATAAATTTAAATTT
1 TAAATAAAT-ATAAATAAATTTAAA-TT
500220 TAAATAAAT-TAAATAAATTTAAATT
1 TAAATAAATATAAATAAATTTAAATT
500245 TAAATA
1 TAAATA
500251 TTTAAAAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 8 0.26
26 14 0.45
28 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
TAAATAAATATAAATAAATTTAAATT
Found at i:500243 original size:32 final size:29
Alignment explanation
Indices: 500192--500256 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 29
500182 ATTTGAATAA
500192 TAAATAAATAATAAATAAATTTAAAT-TT
1 TAAATAAATAATAAATAAATTTAAATATT
500220 TAAATAAATTAAATAAATTTAAATTTAAATATT
1 TAAATAAA-T-AATAAA--TAAATTTAAATATT
500253 TAAA
1 TAAA
500257 AAGTTATAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
28 8 0.25
29 1 0.03
30 6 0.19
32 11 0.34
33 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAATAAATAATAAATAAATTTAAATATT
Found at i:500247 original size:16 final size:16
Alignment explanation
Indices: 500203--500250 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 16
500193 AAATAAATAA
500203 TAAATAAATTTAAATT
1 TAAATAAATTTAAATT
500219 T---TAAA--TAAA-T
1 TAAATAAATTTAAATT
500229 TAAATAAATTTAAATT
1 TAAATAAATTTAAATT
500245 TAAATA
1 TAAATA
500251 TTTAAAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
10 2 0.08
11 4 0.15
13 8 0.31
15 4 0.15
16 8 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATAAATTTAAATT
Found at i:502754 original size:50 final size:50
Alignment explanation
Indices: 502695--502903 Score: 364
Period size: 50 Copynumber: 4.2 Consensus size: 50
502685 TATACTTAGA
*
502695 GTCAACAATTATGGTCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
502745 GTCAACAATTATGGCCACCTCCCTATATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
502795 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
502845 GTCAACAATTATGGCCACCTCTCTCTATTGTTAAAGGTTGGTGAAGGATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
502895 GTCAACAAT
1 GTCAACAAT
502904 AGCAACAACT
Statistics
Matches: 152, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 152 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:507355 original size:50 final size:50
Alignment explanation
Indices: 507296--507605 Score: 512
Period size: 50 Copynumber: 6.2 Consensus size: 50
507286 TATACTTAGA
507296 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
507346 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAATACTC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
507396 AGTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 -GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
507447 GTCAACAATTATGGTCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
507497 GTCAACAATTATGGCCATCTCCCTCTATTGTCAAAGGTTGGTGAATAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
507547 GTCAATAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
507597 GTCAACAAT
1 GTCAACAAT
507606 AGCAACAACT
Statistics
Matches: 242, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
50 194 0.80
51 48 0.20
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:508745 original size:19 final size:20
Alignment explanation
Indices: 508706--508745 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
508696 AAAGAGCCGA
*
508706 TTAAAATTATATTTTTTTAT
1 TTAAAATTATATTTTTATAT
*
508726 TTAAAA-TATCTTTTTATAT
1 TTAAAATTATATTTTTATAT
508745 T
1 T
508746 ACTATTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAAAATTATATTTTTATAT
Found at i:518160 original size:20 final size:20
Alignment explanation
Indices: 518132--518206 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
518122 TTTTACCTTG
518132 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * * *
518152 ATATATCGATATATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
518172 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
518192 ATGTATCGATACATT
1 ATGTATCGATACATT
518207 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:519155 original size:22 final size:22
Alignment explanation
Indices: 519121--519174 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
519111 AGCCTTTGAC
519121 CATGCA-TTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
519142 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
519164 CATGCATTTTT
1 CATGCATTTTT
519175 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.19
22 26 0.81
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.61
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:523701 original size:15 final size:15
Alignment explanation
Indices: 523681--523710 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
523671 TATTTACTTT
523681 GAAAAATATCATTTC
1 GAAAAATATCATTTC
523696 GAAAAATATCATTTC
1 GAAAAATATCATTTC
523711 ATACCTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
GAAAAATATCATTTC
Found at i:533380 original size:23 final size:22
Alignment explanation
Indices: 533354--533415 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 22
533344 GAAAAAAATA
533354 ATAATAATTTATGTATTTATATT
1 ATAATAATTTAT-TATTTATATT
* *
533377 ATAATTATATA-T-TTTATATT
1 ATAATAATTTATTATTTATATT
*
533397 ATTATAATTATATTATTTA
1 ATAATAATT-TATTATTTA
533416 AAATATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 14 0.45
21 3 0.10
22 1 0.03
23 13 0.42
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATAATAATTTATTATTTATATT
Found at i:533407 original size:14 final size:14
Alignment explanation
Indices: 533390--533434 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 14
533380 ATTATATATT
533390 TTATATTATTATAA
1 TTATATTATTATAA
533404 TTATATTATT-TAA
1 TTATATTATTATAA
*
533417 -AATATT-TTAT-A
1 TTATATTATTATAA
533428 TTATATT
1 TTATATT
533435 TATTTATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 3 0.11
12 11 0.41
13 3 0.11
14 10 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATATTATTATAA
Found at i:533422 original size:23 final size:23
Alignment explanation
Indices: 533372--533440 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
533362 TTATGTATTT
*
533372 ATATTATAATTATA-TATTTTATA
1 ATATTATAATTATATTA-TTTAAA
*
533395 TTATTATAATTATATTATTTAAA
1 ATATTATAATTATATTATTTAAA
*
533418 ATATTTTATATTATATTTATTTA
1 ATATTATA-ATTATA-TTATTTA
533441 TATAATTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 24 0.62
24 8 0.21
25 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
ATATTATAATTATATTATTTAAA
Found at i:533454 original size:14 final size:14
Alignment explanation
Indices: 533374--533459 Score: 56
Period size: 14 Copynumber: 6.1 Consensus size: 14
533364 ATGTATTTAT
*
533374 ATTATAATTATAT-
1 ATTATATTTATATA
*
533387 ATTTTATATTATTATA
1 ATTATAT-TTA-TATA
*
533403 ATTATA-TTATTTA
1 ATTATATTTATATA
*
533416 A-AATATTTTATATTA
1 ATTATA-TTTATA-TA
533431 TATT-TATTTATATA
1 -ATTATATTTATATA
533445 ATTATATTTA-ATA
1 ATTATATTTATATA
533458 AT
1 AT
533460 ATCGAGTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
12 3 0.05
13 17 0.30
14 18 0.32
15 11 0.19
16 8 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTATATTTATATA
Found at i:533461 original size:18 final size:18
Alignment explanation
Indices: 533427--533461 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
533417 AATATTTTAT
* *
533427 ATTATATTTATTTATATA
1 ATTATATTTAATAATATA
533445 ATTATATTTAATAATAT
1 ATTATATTTAATAATAT
533462 CGAGTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATATTTAATAATATA
Found at i:533779 original size:17 final size:18
Alignment explanation
Indices: 533759--533812 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
533749 ATATTATATT
533759 TATATTTATAATTTTA-A
1 TATATTTATAATTTTATA
533776 TATATTTAATAA-TTTATA
1 TATATTT-ATAATTTTATA
*
533794 TCATATTTATATTTTTATA
1 T-ATATTTATAATTTTATA
533813 ATTAATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 11 0.34
18 9 0.28
19 12 0.38
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTTATAATTTTATA
Found at i:535293 original size:2 final size:2
Alignment explanation
Indices: 535286--535320 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
535276 CAACCACAAA
535286 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 A
535321 GTTTTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:535621 original size:3 final size:3
Alignment explanation
Indices: 535613--535668 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
535603 CATGTTGCAT
535613 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
535661 TTA TTA TT
1 TTA TTA TT
535669 TGAAAGAGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:536670 original size:22 final size:21
Alignment explanation
Indices: 536640--536682 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
536630 ATTTTATAGT
* *
536640 TTAAAATATATT-TTAAAATA
1 TTAAAAAATATTATTTAAATA
536660 TTAAAAAATATTATTTAAATA
1 TTAAAAAATATTATTTAAATA
536681 TT
1 TT
536683 TATATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAAAAATATTATTTAAATA
Found at i:537615 original size:20 final size:20
Alignment explanation
Indices: 537590--537641 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
537580 ATAACATAAA
*
537590 AATATTTTTTAAAATATTTT
1 AATATTTTTTAAAATAATTT
537610 AATA-TTTTTAATAATAATTT
1 AATATTTTTTAA-AATAATTT
*
537630 AA-GTTTTTTAAA
1 AATATTTTTTAAA
537642 CCTATGGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
AATATTTTTTAAAATAATTT
Found at i:541501 original size:2 final size:2
Alignment explanation
Indices: 541494--541526 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
541484 AAAGTTCTAC
541494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
541527 GTGTTTCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:541704 original size:2 final size:2
Alignment explanation
Indices: 541697--541729 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
541687 AAACAAAGGA
*
541697 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
541730 CACGTGTGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:544067 original size:5 final size:6
Alignment explanation
Indices: 544040--544064 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
544030 TGAAGTGATA
544040 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
544065 ATTGAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:548562 original size:25 final size:25
Alignment explanation
Indices: 548533--548619 Score: 77
Period size: 25 Copynumber: 3.3 Consensus size: 25
548523 TTTTTAAAAT
*
548533 TTTATTTCTTAACCTTCTTCAATTC
1 TTTATTTCTTAACATTCTTCAATTC
* * *
548558 TTTATTTAGTTCACTTAATCTTTCTAAATT-
1 TTTATTT-CTTAAC--ATTC-TTC--AATTC
548588 TTTATTTCTTAACATTCTTCAATTC
1 TTTATTTCTTAACATTCTTCAATTC
548613 TTTATTT
1 TTTATTT
548620 AGTTTTACTC
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
24 4 0.08
25 14 0.29
26 7 0.15
27 3 0.06
28 2 0.04
29 7 0.15
30 7 0.15
31 4 0.08
ACGTcount: A:0.23, C:0.17, G:0.01, T:0.59
Consensus pattern (25 bp):
TTTATTTCTTAACATTCTTCAATTC
Found at i:548575 original size:31 final size:29
Alignment explanation
Indices: 548533--548623 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 29
548523 TTTTTAAAAT
*
548533 TTTATTTCTTAACCTTCTTCAATTCTTTA
1 TTTAGTTCTTAACCTTCTTCAATTCTTTA
* *
548562 TTTAGTTCACTTAATCTT-TCTAAATT-TTTA
1 TTTAGTT--CTTAACCTTCT-TCAATTCTTTA
*
548592 --T--TTCTTAACATTCTTCAATTCTTTA
1 TTTAGTTCTTAACCTTCTTCAATTCTTTA
548617 TTTAGTT
1 TTTAGTT
548624 TTACTCTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 18
0.66 0.08 0.25
Matches are distributed among these distances:
24 12 0.26
25 5 0.11
26 2 0.04
27 1 0.02
28 1 0.02
29 8 0.17
30 5 0.11
31 13 0.28
ACGTcount: A:0.23, C:0.16, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTAGTTCTTAACCTTCTTCAATTCTTTA
Found at i:548597 original size:55 final size:55
Alignment explanation
Indices: 548513--548623 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
548503 TTAATACATA
* *
548513 TCACTTAATCTTTTTAAAATTTTATTTCTTAACCTTCTTCAATTCTTTATTTAGT
1 TCACTTAATCTTTCTAAAATTTTATTTCTTAACATTCTTCAATTCTTTATTTAGT
*
548568 TCACTTAATCTTTCTAAATTTTTATTTCTTAACATTCTTCAATTCTTTATTTAGT
1 TCACTTAATCTTTCTAAAATTTTATTTCTTAACATTCTTCAATTCTTTATTTAGT
548623 T
1 T
548624 TTACTCTTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.25, C:0.16, G:0.02, T:0.57
Consensus pattern (55 bp):
TCACTTAATCTTTCTAAAATTTTATTTCTTAACATTCTTCAATTCTTTATTTAGT
Found at i:549700 original size:13 final size:14
Alignment explanation
Indices: 549669--549695 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
549659 ACATCATCTG
549669 ATTTTTTATATTTT
1 ATTTTTTATATTTT
549683 ATTTTTTATATTT
1 ATTTTTTATATTT
549696 CTTTTATCTG
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
ATTTTTTATATTTT
Found at i:552123 original size:2 final size:2
Alignment explanation
Indices: 552116--552150 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
552106 TATGTTTCTG
552116 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 A
552151 CATAGTTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:556202 original size:2 final size:2
Alignment explanation
Indices: 556195--556226 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
556185 ATCACATTAC
556195 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
556227 TTGTAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:556250 original size:31 final size:29
Alignment explanation
Indices: 556206--556288 Score: 69
Period size: 31 Copynumber: 2.7 Consensus size: 29
556196 TATATATATA
*
556206 TATATATATATATATATATATTTGTAATATT
1 TATAT-TAAATATATATATATTTGTAAT-TT
* * *
556237 TATATTAAGATATACAATTATTTTTTTAATTT
1 TATATTAA-ATATA-TA-TATATTTGTAATTT
*
556269 TATTTTAAATATATA-ATATT
1 TATATTAAATATATATATATT
556289 ATATATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
28 4 0.10
30 3 0.07
31 15 0.36
32 10 0.24
33 10 0.24
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (29 bp):
TATATTAAATATATATATATTTGTAATTT
Found at i:556290 original size:33 final size:35
Alignment explanation
Indices: 556209--556292 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 35
556199 ATATATATAT
556209 ATATATATATATATATATTTGTAATATTTATATTAAG
1 ATATATA-ATAT-TATATTTGTAATATTTATATTAAG
* *
556246 ATATACAATTATT-T-TTT-TAAT-TTTATTTTAA-
1 ATATATAA-TATTATATTTGTAATATTTATATTAAG
556277 ATATATAATATTATAT
1 ATATATAATATTATAT
556293 ATTTAAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
30 4 0.10
31 8 0.20
32 10 0.24
33 4 0.10
34 3 0.07
35 1 0.02
36 2 0.05
37 9 0.22
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (35 bp):
ATATATAATATTATATTTGTAATATTTATATTAAG
Found at i:556298 original size:33 final size:35
Alignment explanation
Indices: 556207--556302 Score: 87
Period size: 33 Copynumber: 2.8 Consensus size: 35
556197 ATATATATAT
556207 ATATATATATATATATATATTTGTAATATTTATATTAAG
1 ATATATA-ATAT-TATATA-TT-TAATATTTATATTAAG
* *
556246 ATATACAATTATT-T-T-TTTAAT-TTTATTTTAA-
1 ATATATAA-TATTATATATTTAATATTTATATTAAG
556277 ATATATAATATTATATATTTAA-ATTT
1 ATATATAATATTATATATTTAATATTT
556303 GTAAAATGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
30 4 0.08
31 8 0.16
32 10 0.20
33 12 0.24
34 2 0.04
36 1 0.02
37 1 0.02
38 2 0.04
39 9 0.18
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (35 bp):
ATATATAATATTATATATTTAATATTTATATTAAG
Found at i:556752 original size:13 final size:14
Alignment explanation
Indices: 556736--556783 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
556726 AATTATTCTA
556736 TAATTATATTTT-T
1 TAATTATATTTTAT
*
556749 TAATTAAATTTATAT
1 TAATTATATTT-TAT
**
556764 TAAAAATATTTTAT
1 TAATTATATTTTAT
556778 TAATTA
1 TAATTA
556784 AATAAAAACT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
13 10 0.37
14 8 0.30
15 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTATATTTTAT
Found at i:557710 original size:16 final size:16
Alignment explanation
Indices: 557689--557719 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
557679 TAAATAAAAT
*
557689 AAATATAATATATTAA
1 AAATATAATAAATTAA
557705 AAATATAATAAATTA
1 AAATATAATAAATTA
557720 TTATTAATTA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATAATAAATTAA
Found at i:557721 original size:19 final size:20
Alignment explanation
Indices: 557684--557722 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
557674 AATCATAAAT
557684 AAAATAAATATAATATATTA
1 AAAATAAATATAATATATTA
557704 AAAATATAATA-AAT-TATTA
1 AAAATA-AATATAATATATTA
557723 TTAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATAAATATAATATATTA
Found at i:559785 original size:55 final size:55
Alignment explanation
Indices: 559716--559839 Score: 221
Period size: 55 Copynumber: 2.3 Consensus size: 55
559706 ATCAGTTGCA
* *
559716 AATAAAACAAAACATGTAAAGTACCTCCATTGTATAATCAGAGATCTTCTTTTAG
1 AATAAAAGACAACATGTAAAGTACCTCCATTGTATAATCAGAGATCTTCTTTTAG
559771 AATAAAAGACAACATGTAAAGTACCTCCATTGTATAATCAGAGATCTTCTTTTAG
1 AATAAAAGACAACATGTAAAGTACCTCCATTGTATAATCAGAGATCTTCTTTTAG
*
559826 CATAAAAGACAACA
1 AATAAAAGACAACA
559840 ATTTAAAGAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (55 bp):
AATAAAAGACAACATGTAAAGTACCTCCATTGTATAATCAGAGATCTTCTTTTAG
Found at i:561454 original size:34 final size:32
Alignment explanation
Indices: 561378--561457 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
561368 GACATGAGAA
* * *
561378 ATAATATA-AATATGAATATATCAAAATTTAT
1 ATAATATATAATTTTAACATATCAAAATTTAT
*
561409 ATAATATATAATTTTAACATATTAAAATTTAT
1 ATAATATATAATTTTAACATATCAAAATTTAT
561441 ATAAAATATATAATTTT
1 AT--AATATATAATTTT
561458 TAAACGTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
31 8 0.19
32 21 0.50
34 13 0.31
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (32 bp):
ATAATATATAATTTTAACATATCAAAATTTAT
Found at i:561636 original size:25 final size:26
Alignment explanation
Indices: 561608--561675 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 26
561598 GTAAATATCT
* * *
561608 TTATATTATTATAAATTAAATAAT-A
1 TTATATTATTAAAAATAAAAAAATAA
*
561633 TTATTTTATTAAAAATAAAAAAATAA
1 TTATATTATTAAAAATAAAAAAATAA
* *
561659 TTATATTTTTAATAATA
1 TTATATTATTAAAAATA
561676 TAACATCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TTATATTATTAAAAATAAAAAAATAA
Found at i:562364 original size:32 final size:33
Alignment explanation
Indices: 562321--562382 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
562311 TAAATTAATT
562321 TTTTTTAAATATGTTTA-ATATGA-ATATATTTAA
1 TTTTTTAAATAT-TTTATATAT-ATATATATTTAA
562354 TTTTTT-AATATTTTATATATATATATATT
1 TTTTTTAAATATTTTATATATATATATATT
562383 GAGAATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
31 5 0.19
32 16 0.59
33 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (33 bp):
TTTTTTAAATATTTTATATATATATATATTTAA
Found at i:562441 original size:13 final size:12
Alignment explanation
Indices: 562411--562454 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
562401 TTTATATTCG
*
562411 AATATATATTAA
1 AATAAATATTAA
562423 ATATAAATATCTAA
1 A-ATAAATAT-TAA
562437 AATAAATATTAA
1 AATAAATATTAA
562449 AA-AAAT
1 AATAAAT
562455 GTAAATACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 4 0.14
12 6 0.21
13 15 0.52
14 4 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
AATAAATATTAA
Found at i:564634 original size:3 final size:3
Alignment explanation
Indices: 564626--564671 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
564616 TTTCAGGTTT
564626 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
564672 ATTAAAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:566711 original size:5 final size:5
Alignment explanation
Indices: 566701--566730 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
566691 AAATAATAAT
*
566701 TTAAA TTAAA TTAAA TTAAT TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
566731 AATTTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:567122 original size:27 final size:28
Alignment explanation
Indices: 567092--567163 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
567082 ATGGCTAAAC
*
567092 TATTAAAAAAATTTTAAATTTTTA-TTA
1 TATTTAAAAAATTTTAAATTTTTATTTA
* **
567119 TATTTAACAAATTTTTTATTTTTATTTA
1 TATTTAAAAAATTTTAAATTTTTATTTA
567147 TATTTAAAAAATATTTA
1 TATTTAAAAAAT-TTTA
567164 TATCAAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 20 0.54
28 14 0.38
29 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (28 bp):
TATTTAAAAAATTTTAAATTTTTATTTA
Found at i:567221 original size:30 final size:30
Alignment explanation
Indices: 567185--567369 Score: 178
Period size: 30 Copynumber: 6.2 Consensus size: 30
567175 AAATTAAATT
* * *
567185 AAATTAATAGTTTGTTTAAGTATAAATTAA
1 AAATTAAAAATTTATTTAAGTATAAATTAA
* *
567215 AAATTAAAAATTTATTTAGGTAAAAAATTAA
1 AAATTAAAAATTTATTTAAGT-ATAAATTAA
** * *
567246 AGCTTAAAAATTTATTTAGGTAAAAATTAA
1 AAATTAAAAATTTATTTAAGTATAAATTAA
* *
567276 AAATTAAAAATTTATTTAAATATAAAATAA
1 AAATTAAAAATTTATTTAAGTATAAATTAA
*
567306 AAATTAAAAATTTATTTGAGTAT-AA-TAA
1 AAATTAAAAATTTATTTAAGTATAAATTAA
* * * *
567334 ACATATATAGATTTATTTAAATA-AAATTATA
1 AAAT-TAAAAATTTATTTAAGTATAAATTA-A
567365 AAATT
1 AAATT
567370 TAATTATTTT
Statistics
Matches: 129, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
28 6 0.05
29 18 0.14
30 74 0.57
31 31 0.24
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (30 bp):
AAATTAAAAATTTATTTAAGTATAAATTAA
Found at i:567238 original size:23 final size:23
Alignment explanation
Indices: 567212--567280 Score: 66
Period size: 31 Copynumber: 2.7 Consensus size: 23
567202 AAGTATAAAT
567212 TAAAAATTAAAAATTTATTTAGG
1 TAAAAATTAAAAATTTATTTAGG
567235 TAAAAAATTAAAGCTTAAAAATTTATTTAGG
1 T----AA--AAA--TTAAAAATTTATTTAGG
567266 TAAAAATTAAAAATT
1 TAAAAATTAAAAATT
567281 AAAAATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
23 10 0.26
25 3 0.08
27 4 0.11
29 3 0.08
31 18 0.47
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.36
Consensus pattern (23 bp):
TAAAAATTAAAAATTTATTTAGG
Found at i:567240 original size:16 final size:16
Alignment explanation
Indices: 567219--567273 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
567209 AATTAAAAAT
567219 TAAAAATTTATTTAGG
1 TAAAAATTTATTTAGG
* * *
567235 TAAAAAATTA--AAGCT
1 TAAAAATTTATTTAG-G
567250 TAAAAATTTATTTAGG
1 TAAAAATTTATTTAGG
567266 TAAAAATT
1 TAAAAATT
567274 AAAAATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
14 2 0.07
15 9 0.30
16 17 0.57
17 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (16 bp):
TAAAAATTTATTTAGG
Done.