Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 7 of 18
Found at i:993453 original size:2 final size:2
Alignment explanation
Indices: 993446--993475 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
993436 CTATGAATTT
993446 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
993476 ATGCCTCATT
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:1000245 original size:2 final size:2
Alignment explanation
Indices: 1000238--1000270 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1000228 ATCAATTTTC
1000238 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 T
1000271 TTAAAGAGAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1000533 original size:19 final size:19
Alignment explanation
Indices: 1000505--1000545 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1000495 TATTTAATAA
1000505 AATTTAAATAA-AAATATTT
1 AATTTAAATAATAAAT-TTT
*
1000524 AATTTTAATAATAAATTTT
1 AATTTAAATAATAAATTTT
1000543 AAT
1 AAT
1000546 AAAAAAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTTAAATAATAAATTTT
Found at i:1001639 original size:16 final size:15
Alignment explanation
Indices: 1001618--1001667 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
1001608 AAAAAATAAT
1001618 TATAATATCAAAATTA
1 TATAATATC-AAATTA
1001634 TATAATAT-AAATTA
1 TATAATATCAAATTA
1001648 T-TAATTTATCAAATTA
1 TATAA--TATCAAATTA
1001664 TATA
1 TATA
1001668 TAAATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 3 0.10
16 15 0.50
17 2 0.07
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (15 bp):
TATAATATCAAATTA
Found at i:1001643 original size:27 final size:25
Alignment explanation
Indices: 1001613--1001681 Score: 68
Period size: 30 Copynumber: 2.5 Consensus size: 25
1001603 TTTCAAAAAA
1001613 ATAATTATAATATCAAAATTATATAAT
1 ATAATTATAATATC-AAATTATAT-AT
1001640 ATAAATTATTAATTTATCAAATTATATAT
1 AT-AATTA-TAA--TATCAAATTATATAT
1001669 A-AATATATAATAT
1 ATAAT-TATAATAT
1001682 ATTAAAACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
25 3 0.08
27 8 0.22
28 7 0.19
29 6 0.16
30 9 0.24
31 4 0.11
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (25 bp):
ATAATTATAATATCAAATTATATAT
Found at i:1006448 original size:19 final size:19
Alignment explanation
Indices: 1006405--1006448 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 19
1006395 CGGACTGGTT
1006405 TCAAGTTTCTGCCAGGACTA
1 TCAAG-TTCTGCCAGGACTA
1006425 T-AAGTTCTG-CAGGACTAA
1 TCAAGTTCTGCCAGGACT-A
1006443 TCAAGT
1 TCAAGT
1006449 AAGTTTCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.32
18 7 0.32
19 7 0.32
20 1 0.05
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (19 bp):
TCAAGTTCTGCCAGGACTA
Found at i:1009918 original size:67 final size:67
Alignment explanation
Indices: 1009830--1009959 Score: 215
Period size: 67 Copynumber: 1.9 Consensus size: 67
1009820 TTATTTATTT
* * * *
1009830 ATTTATGCTTAAGTATATAGTATAACATTATTTAATTTCAATCCATCATAATAATATTAATTAAT
1 ATTTATGCATAAGCATATAGTATAACATTATTTAATCTCAATCCATCACAATAATATTAATTAAT
1009895 TA
66 TA
*
1009897 ATTTATGCATAAGCATATAGTATAACATTATTTAATCTCAATTCATCACAATAATATTAATTA
1 ATTTATGCATAAGCATATAGTATAACATTATTTAATCTCAATCCATCACAATAATATTAATTA
1009960 GTCAATTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (67 bp):
ATTTATGCATAAGCATATAGTATAACATTATTTAATCTCAATCCATCACAATAATATTAATTAAT
TA
Found at i:1010389 original size:22 final size:23
Alignment explanation
Indices: 1010359--1010405 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1010349 AAAATCGTAA
*
1010359 TTTATTAATCA-ATATAAATTTT
1 TTTAATAATCAGATATAAATTTT
* *
1010381 TTTAATAATGAGATTTAAATTTT
1 TTTAATAATCAGATATAAATTTT
1010404 TT
1 TT
1010406 AATCTATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTAATAATCAGATATAAATTTT
Found at i:1016542 original size:3 final size:3
Alignment explanation
Indices: 1016534--1016559 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1016524 AGTCTACAGT
1016534 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1016560 TTGACTTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1021814 original size:21 final size:21
Alignment explanation
Indices: 1021790--1021832 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1021780 GGGTTGAAAA
* * *
1021790 TAAAAATCAAACATAAATATT
1 TAAAAATAAAAAATAAAAATT
1021811 TAAAAATAAAAAATAAAAATT
1 TAAAAATAAAAAATAAAAATT
1021832 T
1 T
1021833 GAGTAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAATAAAAAATAAAAATT
Found at i:1023458 original size:16 final size:17
Alignment explanation
Indices: 1023425--1023460 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1023415 TAATTTTTAA
*
1023425 TATTTAATATATATAAT
1 TATTAAATATATATAAT
1023442 TATTAAATA-ATATAAT
1 TATTAAATATATATAAT
1023458 TAT
1 TAT
1023461 AAAGTACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAAATATATATAAT
Found at i:1024407 original size:3 final size:3
Alignment explanation
Indices: 1024399--1024441 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1024389 TTATTTGAGC
1024399 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1024442 GCCACTTTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1028504 original size:24 final size:24
Alignment explanation
Indices: 1028453--1028507 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1028443 CATCTTCATG
* *
1028453 ATCATCATCTTCATCATCAGAAAT
1 ATCATCATCTTCATCACCAGAAAC
*
1028477 ATCATCATCTTCAATCACCA-AAGC
1 ATCATCATCTTC-ATCACCAGAAAC
1028501 ATCATCA
1 ATCATCA
1028508 ATCTCCACAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (24 bp):
ATCATCATCTTCATCACCAGAAAC
Found at i:1030496 original size:30 final size:30
Alignment explanation
Indices: 1030460--1030551 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
1030450 AAGAGACTAT
1030460 AACTACCAATAAACGAAGAGATAACCAAGG
1 AACTACCAATAAACGAAGAGATAACCAAGG
** * *
1030490 AACTACC-ATCTGAC-AAGAG---A-CTA-T
1 AACTACCAAT-AAACGAAGAGATAACCAAGG
1030514 AACTACCAATAAACGAAGAGATAACCAAGG
1 AACTACCAATAAACGAAGAGATAACCAAGG
1030544 AACTACCA
1 AACTACCA
1030552 TCTGAAAAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
24 9 0.20
25 9 0.20
26 1 0.02
28 1 0.02
29 9 0.20
30 17 0.37
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.13
Consensus pattern (30 bp):
AACTACCAATAAACGAAGAGATAACCAAGG
Found at i:1030505 original size:54 final size:54
Alignment explanation
Indices: 1030447--1030561 Score: 221
Period size: 54 Copynumber: 2.1 Consensus size: 54
1030437 TCATGGTAAA
1030447 GACAAGAGACTATAACTACCAATAAACGAAGAGATAACCAAGGAACTACCATCT
1 GACAAGAGACTATAACTACCAATAAACGAAGAGATAACCAAGGAACTACCATCT
1030501 GACAAGAGACTATAACTACCAATAAACGAAGAGATAACCAAGGAACTACCATCT
1 GACAAGAGACTATAACTACCAATAAACGAAGAGATAACCAAGGAACTACCATCT
*
1030555 GAAAAGA
1 GACAAGA
1030562 AAACTTACCT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.14
Consensus pattern (54 bp):
GACAAGAGACTATAACTACCAATAAACGAAGAGATAACCAAGGAACTACCATCT
Found at i:1035446 original size:12 final size:13
Alignment explanation
Indices: 1035423--1035451 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1035413 TGCATGTAAC
1035423 TTAAATTTTAAAT
1 TTAAATTTTAAAT
1035436 TTAAA-TTTAAAT
1 TTAAATTTTAAAT
1035448 TTAA
1 TTAA
1035452 TTAATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAATTTTAAAT
Found at i:1035989 original size:18 final size:18
Alignment explanation
Indices: 1035950--1035995 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
1035940 TATTTTTAAT
*
1035950 ATATATAAAAATAATATG
1 ATATATAAAAATAATATA
1035968 ATATATAAAATATAAT-TA
1 ATATATAAAA-ATAATATA
1035986 ATATAATAAA
1 ATAT-ATAAA
1035996 TTTGATGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
ATATATAAAAATAATATA
Found at i:1035996 original size:18 final size:18
Alignment explanation
Indices: 1035945--1035996 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1035935 TATAATATTT
*
1035945 TTAATATATATAAAAATAA
1 TTAATATA-ATAAATATAA
*
1035964 TATGATAT-ATAAAATATAA
1 T-TAATATAAT-AAATATAA
1035983 TTAATATAATAAAT
1 TTAATATAATAAAT
1035997 TTGATGCATG
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
18 11 0.41
19 11 0.41
20 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TTAATATAATAAATATAA
Found at i:1036476 original size:18 final size:18
Alignment explanation
Indices: 1036450--1036487 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1036440 TTAAATGTGA
*
1036450 AATTTTTTATCAAAATTT
1 AATTGTTTATCAAAATTT
1036468 AATTGTTTATCAAAATTT
1 AATTGTTTATCAAAATTT
1036486 AA
1 AA
1036488 AAAATGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTGTTTATCAAAATTT
Found at i:1038075 original size:5 final size:5
Alignment explanation
Indices: 1038065--1038098 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1038055 CACTATCCTA
*
1038065 GATAT GATAT GAGAT GATAT GATAT GATAAT GAT
1 GATAT GATAT GATAT GATAT GATAT GAT-AT GAT
1038099 TCTAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (5 bp):
GATAT
Found at i:1043620 original size:4 final size:4
Alignment explanation
Indices: 1043613--1043641 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1043603 GCCAAAAGGA
1043613 AGGT AGGT AGGT AGGT AGGT AGGT AGGT A
1 AGGT AGGT AGGT AGGT AGGT AGGT AGGT A
1043642 CGTAACGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.24
Consensus pattern (4 bp):
AGGT
Found at i:1044849 original size:2 final size:2
Alignment explanation
Indices: 1044842--1044868 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1044832 TCTAGAAACC
1044842 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1044869 ATGCATGATG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1045922 original size:6 final size:6
Alignment explanation
Indices: 1045911--1045940 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1045901 TACTTCTAAA
*
1045911 TTCTAT TTCTAT TTCTAT TTCTAT ATCTAT
1 TTCTAT TTCTAT TTCTAT TTCTAT TTCTAT
1045941 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (6 bp):
TTCTAT
Found at i:1046337 original size:2 final size:2
Alignment explanation
Indices: 1046330--1046359 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1046320 ACAAGTAAGC
*
1046330 CT CT CT CT CT AT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1046360 TCAATCTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1046874 original size:3 final size:3
Alignment explanation
Indices: 1046868--1046899 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1046858 CTGCTGCAAC
*
1046868 CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
1046900 ACAGTGGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.34, G:0.28, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1048025 original size:27 final size:26
Alignment explanation
Indices: 1047994--1048060 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
1047984 TTGAAATTTC
*
1047994 TAAAT-TTAAATTATGACTAAATATAA
1 TAAATATT-AATTATAACTAAATATAA
* *
1048020 TCAAATATTAATTATAATTAATTATAA
1 T-AAATATTAATTATAACTAAATATAA
*
1048047 TAAATATTGATTAT
1 TAAATATTAATTAT
1048061 TATAAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 13 0.37
27 20 0.57
28 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (26 bp):
TAAATATTAATTATAACTAAATATAA
Found at i:1048059 original size:26 final size:27
Alignment explanation
Indices: 1048002--1048069 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
1047992 TCTAAATTTA
*
1048002 AATTATGACTAAA-TATAATCAAATATT
1 AATTAT-AATAAATTATAATCAAATATT
*
1048029 AATTATAATTAATTATAAT-AAATATT
1 AATTATAATAAATTATAATCAAATATT
* *
1048055 GATTATTATAAATTA
1 AATTATAATAAATTA
1048070 AAACCCACTC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 23 0.66
27 12 0.34
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (27 bp):
AATTATAATAAATTATAATCAAATATT
Found at i:1048618 original size:2 final size:2
Alignment explanation
Indices: 1048611--1048638 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1048601 TGTTCTAGAA
1048611 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
1048639 TAGAGTCCAC
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:1049741 original size:2 final size:2
Alignment explanation
Indices: 1049734--1049759 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1049724 ATAATAATTA
1049734 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
1049760 TCTTATTGAG
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:1057140 original size:18 final size:19
Alignment explanation
Indices: 1057117--1057158 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
1057107 AGATTAGATT
1057117 ATTTATTTAAAATTT-AAA
1 ATTTATTTAAAATTTAAAA
*
1057135 ATTTATTTAATATTTAAAA
1 ATTTATTTAAAATTTAAAA
1057154 ATTTA
1 ATTTA
1057159 AATAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTATTTAAAATTTAAAA
Found at i:1057395 original size:17 final size:18
Alignment explanation
Indices: 1057373--1057406 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1057363 AAAAATTTGT
1057373 AAAAATT-AAATTTTAAA
1 AAAAATTAAAATTTTAAA
1057390 AAAAATTAAAATTTTAA
1 AAAAATTAAAATTTTAA
1057407 GATATGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATTAAAATTTTAAA
Found at i:1059515 original size:22 final size:22
Alignment explanation
Indices: 1059487--1059532 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1059477 AAAAGAATAC
1059487 TAGGTGAGAATTGAATAAATTT
1 TAGGTGAGAATTGAATAAATTT
*
1059509 TAGGTGAGAATTGAATAAGTTT
1 TAGGTGAGAATTGAATAAATTT
1059531 TA
1 TA
1059533 TATATATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (22 bp):
TAGGTGAGAATTGAATAAATTT
Found at i:1059773 original size:21 final size:20
Alignment explanation
Indices: 1059724--1059792 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
1059714 ACTTACATAA
1059724 AAAATTATCAAAATC-AT-C
1 AAAATTATCAAAATCAATCC
*
1059742 AAAGATAATCAAAATCAATCC
1 AAA-ATTATCAAAATCAATCC
* *
1059763 AAATATTATCAAATTCACATCG
1 AAA-ATTATCAAAATCA-ATCC
1059785 AAAATTAT
1 AAAATTAT
1059793 TAAGATTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
18 3 0.07
19 11 0.26
20 2 0.05
21 20 0.48
22 6 0.14
ACGTcount: A:0.54, C:0.16, G:0.03, T:0.28
Consensus pattern (20 bp):
AAAATTATCAAAATCAATCC
Found at i:1060326 original size:15 final size:15
Alignment explanation
Indices: 1060308--1060347 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1060298 AATTTAAAGG
1060308 ATAAAATTATTTTTA
1 ATAAAATTATTTTTA
*
1060323 ATAATATTTATTTTTA
1 ATAA-AATTATTTTTA
*
1060339 ATATAATTA
1 ATAAAATTA
1060348 AAATAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAAAATTATTTTTA
Found at i:1060400 original size:21 final size:23
Alignment explanation
Indices: 1060354--1060401 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
1060344 ATTAAAATAA
**
1060354 AAAATATTTTTTATTTTACCTTT
1 AAAATATTTTTTATTTTACCAGT
1060377 AAAAT-TTTTTTATTTTA-CAGT
1 AAAATATTTTTTATTTTACCAGT
1060398 AAAA
1 AAAA
1060402 GTTGCAGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 12 0.52
23 5 0.22
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (23 bp):
AAAATATTTTTTATTTTACCAGT
Found at i:1060759 original size:2 final size:2
Alignment explanation
Indices: 1060752--1060778 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1060742 TTCAATTATT
1060752 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1060779 TTAGGGATAT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1068165 original size:2 final size:2
Alignment explanation
Indices: 1068158--1068188 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1068148 TCATCTTCCT
1068158 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 T
1068189 TTTGACTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1072906 original size:17 final size:17
Alignment explanation
Indices: 1072884--1072921 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1072874 TTTAATAGTT
1072884 TTAAAAAATATT-TATAA
1 TTAAAAAATATTATA-AA
*
1072901 TTAAAATATATTATAAA
1 TTAAAAAATATTATAAA
1072918 TTAA
1 TTAA
1072922 GTTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAAAAATATTATAAA
Found at i:1072908 original size:15 final size:17
Alignment explanation
Indices: 1072888--1072921 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1072878 ATAGTTTTAA
1072888 AAAATAT-TTAT-AATT
1 AAAATATATTATAAATT
1072903 AAAATATATTATAAATT
1 AAAATATATTATAAATT
1072920 AA
1 AA
1072922 GTTTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 4 0.24
17 6 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATATATTATAAATT
Found at i:1073571 original size:150 final size:150
Alignment explanation
Indices: 1073291--1073579 Score: 461
Period size: 150 Copynumber: 1.9 Consensus size: 150
1073281 TAATTCCATA
* * * *
1073291 TCCTTTTATCATAAGTAAAGATTATAAACAAATTTTCTGGCAGTGTGGACTTGTCACTAAATTAA
1 TCCTTTAATCATAAGTAAAGATTATAAACAAATTTTCTGGCAATGTGAACTTGCCACTAAATTAA
* * * * * *
1073356 ATGCAATGTATTAAACTTTATTGAAGAAATAAGTAATTTTTGTTGGATTGTGTACATATAGATAT
66 ACGCAAAGTATTAAACTTTATTGAAGAAATAAGTAATTTTGGTTGGATTGGGTACAAATAAATAT
1073421 ACCATTTAACATAACTTTTG
131 ACCATTTAACATAACTTTTG
*
1073441 TCCTTTAATCGTAAGTAAAGATTATAAACAAATTTTCTGGCAATGTGAACTTGCCACTAAATTAA
1 TCCTTTAATCATAAGTAAAGATTATAAACAAATTTTCTGGCAATGTGAACTTGCCACTAAATTAA
* *
1073506 GCGCAAAGTATTAAACTTTATTGAAGAAATAAGTAATTTTGGTTGGATTGGGTGCAAATAAATAT
66 ACGCAAAGTATTAAACTTTATTGAAGAAATAAGTAATTTTGGTTGGATTGGGTACAAATAAATAT
1073571 ACCATTTAA
131 ACCATTTAA
1073580 TTAATTTTTT
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
150 126 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (150 bp):
TCCTTTAATCATAAGTAAAGATTATAAACAAATTTTCTGGCAATGTGAACTTGCCACTAAATTAA
ACGCAAAGTATTAAACTTTATTGAAGAAATAAGTAATTTTGGTTGGATTGGGTACAAATAAATAT
ACCATTTAACATAACTTTTG
Found at i:1073880 original size:10 final size:11
Alignment explanation
Indices: 1073855--1073879 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1073845 TTATATGTTA
1073855 TTTTAATTATT
1 TTTTAATTATT
1073866 TTTTAATTATT
1 TTTTAATTATT
1073877 TTT
1 TTT
1073880 ATGTTTTATA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTAATTATT
Found at i:1078306 original size:3 final size:3
Alignment explanation
Indices: 1078298--1078327 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1078288 TGATATCTAT
1078298 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1078328 GATATGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1079445 original size:3 final size:3
Alignment explanation
Indices: 1079437--1079476 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1079427 TATCACACCT
1079437 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1079477 CCAGATCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1079642 original size:16 final size:15
Alignment explanation
Indices: 1079620--1079659 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
1079610 CGATAATAAA
*
1079620 ATTAATATTATTTGT
1 ATTAATAATATTTGT
1079635 ATTTAATAATATTTGT
1 A-TTAATAATATTTGT
1079651 ATTAATAAT
1 ATTAATAAT
1079660 GATGTCGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (15 bp):
ATTAATAATATTTGT
Found at i:1081799 original size:24 final size:25
Alignment explanation
Indices: 1081770--1081821 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1081760 ATGTCAATAT
* *
1081770 TAAATATATTAGTT-GAATATGATA
1 TAAATATAATAATTAGAATATGATA
*
1081794 TAAATATAATAATTATAATATGATA
1 TAAATATAATAATTAGAATATGATA
1081819 TAA
1 TAA
1081822 TTTATATGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (25 bp):
TAAATATAATAATTAGAATATGATA
Found at i:1081821 original size:16 final size:16
Alignment explanation
Indices: 1081802--1081843 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1081792 TATAAATATA
1081802 ATAATTATAATATGAT
1 ATAATTATAATATGAT
1081818 ATAATT-T-ATATGAT
1 ATAATTATAATATGAT
1081832 A-AATTATTAATA
1 ATAATTA-TAATA
1081844 ATTAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
15 2 0.09
16 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (16 bp):
ATAATTATAATATGAT
Found at i:1086175 original size:23 final size:23
Alignment explanation
Indices: 1086121--1086175 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1086111 TTTAAATTAA
1086121 ATTA-AATTAAA--TTTTATTTT
1 ATTATAATTAAATTTTTTATTTT
*
1086141 ATTTTAATTAAATTTTTTATTTT
1 ATTATAATTAAATTTTTTATTTT
1086164 -TTATAATATAAA
1 ATTATAAT-TAAA
1086176 AATAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 3 0.10
21 7 0.24
22 6 0.21
23 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTATAATTAAATTTTTTATTTT
Found at i:1086314 original size:11 final size:12
Alignment explanation
Indices: 1086280--1086320 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
1086270 TAAAAAATAA
*
1086280 AATTTAA-AATC
1 AATTTAATATTC
1086291 AATTTAATATTC
1 AATTTAATATTC
1086303 AATTTAAT-TTC
1 AATTTAATATTC
*
1086314 AACTTAA
1 AATTTAA
1086321 ATTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTTAATATTC
Found at i:1086663 original size:21 final size:21
Alignment explanation
Indices: 1086619--1086659 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1086609 TAATAATTAA
**
1086619 AATTATTAAAATTTAATCATT
1 AATTATTAAAATTTAAAAATT
1086640 AATTATTAAAA-TTAAAAATT
1 AATTATTAAAATTTAAAAATT
1086660 TAATACTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTATTAAAATTTAAAAATT
Found at i:1089865 original size:2 final size:2
Alignment explanation
Indices: 1089853--1089896 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
1089843 TTTAATAATA
* *
1089853 AT AT AT A- AT AT AT A- AT AT GT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1089893 AT AT
1 AT AT
1089897 GTGTGTGTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1090359 original size:27 final size:26
Alignment explanation
Indices: 1090314--1090384 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
1090304 TTTAAAATTT
1090314 ATATATATAAAT-TATAAAT-TTATTAA
1 ATATATATAAATATA-AAATATT-TTAA
1090340 ATTATATATAAATATAAAATATTTTAA
1 A-TATATATAAATATAAAATATTTTAA
1090367 ATATAATAATAAA-ATAAA
1 ATAT-AT-ATAAATATAAA
1090385 CTATAAATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
26 4 0.10
27 27 0.68
28 9 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATATATAAATATAAAATATTTTAA
Found at i:1094027 original size:30 final size:27
Alignment explanation
Indices: 1093957--1094028 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 27
1093947 AAAAATATAA
1093957 TTTAAATATAAATATAAATAATTAAATT
1 TTTAAA-ATAAATATAAATAATTAAATT
*
1093985 TTTAAAATTAAATATAAAATTAATT-TATT
1 TTTAAAA-TAAATAT-AAA-TAATTAAATT
1094014 TTTATTAAATAAATA
1 TTTA--AAATAAATA
1094029 AATTTAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 1 0.03
28 13 0.34
29 10 0.26
30 11 0.29
31 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TTTAAAATAAATATAAATAATTAAATT
Found at i:1098768 original size:22 final size:21
Alignment explanation
Indices: 1098736--1098922 Score: 89
Period size: 21 Copynumber: 8.9 Consensus size: 21
1098726 CTAAAATTGT
1098736 TTAAAAATTATCAAAAATTACA
1 TTAAAAATTATC-AAAATTACA
* * *
1098758 TTAAAACTTATCAATATTATA
1 TTAAAAATTATCAAAATTACA
* * * *
1098779 TTAAAAATTTTTACAATTATA
1 TTAAAAATTATCAAAATTACA
* *
1098800 TCT-AAAGTTATCAAAATTA-T
1 T-TAAAAATTATCAAAATTACA
**
1098820 TTAAAAATAATAAAAAAATTACA
1 TTAAAAAT--TATCAAAATTACA
* **
1098843 TTAAGACA-TA-CTAAAATTGTA
1 TTAA-AAATTATC-AAAATTACA
* * *
1098864 TCAAATATTAT-TAAATTA-A
1 TTAAAAATTATCAAAATTACA
*
1098883 TTTAAAATTTATCAAAATTACA
1 -TTAAAAATTATCAAAATTACA
* *
1098905 TTAAAACTTACCAAAATT
1 TTAAAAATTATCAAAATT
1098923 GTATCAAAAG
Statistics
Matches: 122, Mismatches: 31, Indels: 25
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.02
20 20 0.16
21 72 0.59
22 22 0.18
23 4 0.03
24 2 0.02
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (21 bp):
TTAAAAATTATCAAAATTACA
Found at i:1098881 original size:84 final size:84
Alignment explanation
Indices: 1098728--1098902 Score: 194
Period size: 84 Copynumber: 2.1 Consensus size: 84
1098718 ACTACTTACT
* * * * * * *
1098728 AAAATTGTTTAAAAATTATCAAAAATTACATTAAAACTTATCAATATTATATTAAAAATTTTTAC
1 AAAATTATTTAAAAATAATAAAAAATTACATTAAAACATATCAAAATTATATCAAAAATTATTAC
1098793 AATTATATCT-AAAGTTATC
66 AATTA-ATCTAAAAGTTATC
* * *
1098812 AAAATTATTTAAAAATAATAAAAAAATTACATTAAGACATA-CTAAAATTGTATCAAATATTATT
1 AAAATTATTTAAAAATAAT-AAAAAATTACATTAAAACATATC-AAAATTATATCAAAAATTATT
* *
1098876 A-AATTAATTTAAAATTTATC
64 ACAATTAATCTAAAAGTTATC
1098896 AAAATTA
1 AAAATTA
1098903 CATTAAAACT
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
83 3 0.04
84 38 0.50
85 35 0.46
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (84 bp):
AAAATTATTTAAAAATAATAAAAAATTACATTAAAACATATCAAAATTATATCAAAAATTATTAC
AATTAATCTAAAAGTTATC
Found at i:1099069 original size:21 final size:21
Alignment explanation
Indices: 1099015--1099082 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
1099005 TGTATAAACT
1099015 AAAATTACATTAAAAA-TACC
1 AAAATTACATTAAAAATTACC
** *
1099035 AAAATT-GTTTAAAAATTATC
1 AAAATTACATTAAAAATTACC
*
1099055 AAAATTACATTAAAACTTACC
1 AAAATTACATTAAAAATTACC
1099076 AAAATTA
1 AAAATTA
1099083 TATCAAAAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 7 0.18
20 15 0.38
21 17 0.44
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (21 bp):
AAAATTACATTAAAAATTACC
Found at i:1099076 original size:159 final size:159
Alignment explanation
Indices: 1098883--1099190 Score: 553
Period size: 159 Copynumber: 1.9 Consensus size: 159
1098873 ATTAAATTAA
* *
1098883 TTTAAAATTTATCAAAATTACATTAAAACTTACCAAAATTGTATCAAAAGTCATAAATATTAATT
1 TTTAAAAATTATCAAAATTACATTAAAACTTACCAAAATTATATCAAAAGTCATAAATATTAATT
* *
1098948 TTAAGGTTAGCAAAATATTAAAAAAAATACCAAAATTGCATAAAGTGTTATCAAAATTGTATAAA
66 TTAAGGTTAGCAAAATATTAAAAAAAATACCAAAATTACATAAAATGTTATCAAAATTGTATAAA
1099013 CTAAAATTACATTAAAAATACCAAAATTG
131 CTAAAATTACATTAAAAATACCAAAATTG
*
1099042 TTTAAAAATTATCAAAATTACATTAAAACTTACCAAAATTATATCAAAAGTTATAAATATTAATT
1 TTTAAAAATTATCAAAATTACATTAAAACTTACCAAAATTATATCAAAAGTCATAAATATTAATT
* *
1099107 TTAAGGTTAGCAAAATATTATAAAAATTACCAAAATTACATAAAATGTTATCAAAATTGTATAAA
66 TTAAGGTTAGCAAAATATTAAAAAAAATACCAAAATTACATAAAATGTTATCAAAATTGTATAAA
1099172 CTAAAATTACATTAAAAAT
131 CTAAAATTACATTAAAAAT
1099191 TATTAAAATG
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
159 142 1.00
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.33
Consensus pattern (159 bp):
TTTAAAAATTATCAAAATTACATTAAAACTTACCAAAATTATATCAAAAGTCATAAATATTAATT
TTAAGGTTAGCAAAATATTAAAAAAAATACCAAAATTACATAAAATGTTATCAAAATTGTATAAA
CTAAAATTACATTAAAAATACCAAAATTG
Found at i:1099090 original size:21 final size:21
Alignment explanation
Indices: 1099015--1099090 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
1099005 TGTATAAACT
*
1099015 AAAATTACATTAAAAA-TACC
1 AAAATTATATTAAAAATTACC
* *
1099035 AAAATTGT-TTAAAAATTATC
1 AAAATTATATTAAAAATTACC
* *
1099055 AAAATTACATTAAAACTTACC
1 AAAATTATATTAAAAATTACC
*
1099076 AAAATTATATCAAAA
1 AAAATTATATTAAAA
1099091 GTTATAAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 7 0.16
20 15 0.33
21 23 0.51
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (21 bp):
AAAATTATATTAAAAATTACC
Found at i:1099163 original size:41 final size:41
Alignment explanation
Indices: 1098885--1099171 Score: 152
Period size: 41 Copynumber: 7.1 Consensus size: 41
1098875 TAAATTAATT
* * *
1098885 TAAAATTTATCAAAATTACATTAAAACTTACCAAAATTGTA
1 TAAAAATTACCAAAATTACATTAAAAGTTACCAAAATTGTA
* * * * * *
1098926 TCAAAAGT-CATAAATATTA-ATTTTAAGGTTAGCAAAATAT-TA
1 TAAAAATTAC-CAAA-ATTACA-TTAAAAGTTACCAAAAT-TGTA
* * * * *
1098968 AAAAAAATACCAAAATTGCA-TAAAGTGTTATCAAAATTGTA
1 TAAAAATTACCAAAATTACATTAAA-AGTTACCAAAATTGTA
* * *
1099009 T---AA--ACTAAAATTACATTAAAA-ATACCAAAATTGTT
1 TAAAAATTACCAAAATTACATTAAAAGTTACCAAAATTGTA
* * *
1099044 TAAAAATTATCAAAATTACATTAAAACTTACCAAAATTATA
1 TAAAAATTACCAAAATTACATTAAAAGTTACCAAAATTGTA
* * * * *
1099085 TCAAAAGTTA-TAAATATTA-ATTTTAAGGTTAGCAAAATAT-TA
1 T-AAAAATTACCAAA-ATTACA-TTAAAAGTTACCAAAAT-TGTA
*
1099127 TAAAAATTACCAAAATTACA-TAAAATGTTATCAAAATTGTA
1 TAAAAATTACCAAAATTACATTAAAA-GTTACCAAAATTGTA
1099168 TAAA
1 TAAA
1099172 CTAAAATTAC
Statistics
Matches: 183, Mismatches: 40, Indels: 46
0.68 0.15 0.17
Matches are distributed among these distances:
35 12 0.07
36 10 0.05
37 4 0.02
38 4 0.02
40 24 0.13
41 67 0.37
42 59 0.32
43 3 0.02
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (41 bp):
TAAAAATTACCAAAATTACATTAAAAGTTACCAAAATTGTA
Found at i:1099170 original size:21 final size:19
Alignment explanation
Indices: 1099031--1099171 Score: 50
Period size: 21 Copynumber: 6.8 Consensus size: 19
1099021 ACATTAAAAA
* *
1099031 TACCAAAATTGTTTAAAAAT
1 TACCAAAATT-TATAAAAGT
* * *
1099051 TATCAAAATTACATTAAAACT
1 TACCAAAATT-TA-TAAAAGT
1099072 TACCAAAATTATATCAAAAGT
1 TACCAAAATT-TAT-AAAAGT
* * * *
1099093 TA-TAAATATTAATTTTAAGGT
1 TACCAAA-ATT--TATAAAAGT
* *
1099114 TAGCAAAATATTATAAAAAT
1 TACCAAAAT-TTATAAAAGT
*
1099134 TACCAAAATTACATAAAATGT
1 TACCAAAATT-TATAAAA-GT
*
1099155 TATCAAAATTGTATAAA
1 TACCAAAATT-TATAAA
1099172 CTAAAATTAC
Statistics
Matches: 90, Mismatches: 23, Indels: 15
0.70 0.18 0.12
Matches are distributed among these distances:
19 1 0.01
20 32 0.36
21 50 0.56
22 7 0.08
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (19 bp):
TACCAAAATTTATAAAAGT
Found at i:1099215 original size:21 final size:21
Alignment explanation
Indices: 1099191--1099237 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
1099181 CATTAAAAAT
*
1099191 TATTAAAATGATATTAAAGCC
1 TATTAAAATCATATTAAAGCC
*
1099212 TATT-AAATCATATTAAAGGC
1 TATTAAAATCATATTAAAGCC
1099232 TATTAA
1 TATTAA
1099238 TATATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (21 bp):
TATTAAAATCATATTAAAGCC
Found at i:1099313 original size:11 final size:10
Alignment explanation
Indices: 1099289--1099327 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
1099279 ACATGTTATT
*
1099289 TATTTATTAT
1 TATTTATTAA
1099299 TATTTATTAGA
1 TATTTATTA-A
1099310 TATTTATTATA
1 TATTTATTA-A
1099321 TATTTAT
1 TATTTAT
1099328 GTCAACACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (10 bp):
TATTTATTAA
Found at i:1099489 original size:21 final size:21
Alignment explanation
Indices: 1099459--1099559 Score: 105
Period size: 21 Copynumber: 4.8 Consensus size: 21
1099449 AAATTAAAAA
1099459 ATTATCAAAATTATATCAAAG
1 ATTATCAAAATTATATCAAAG
* * *
1099480 ATTATTAAAATAATATTAAAG
1 ATTATCAAAATTATATCAAAG
*
1099501 GTTATCAAAAATTATATCAAAG
1 ATTATC-AAAATTATATCAAAG
** * *
1099523 GCTATTAAAATTACATCAAA-
1 ATTATCAAAATTATATCAAAG
1099543 AGTTATCAAAATTATAT
1 A-TTATCAAAATTATAT
1099560 ATAAAATTAC
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
21 47 0.73
22 17 0.27
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (21 bp):
ATTATCAAAATTATATCAAAG
Found at i:1099498 original size:43 final size:42
Alignment explanation
Indices: 1099455--1099602 Score: 163
Period size: 43 Copynumber: 3.5 Consensus size: 42
1099445 AATTAAATTA
*
1099455 AAAAATTATCAAAATTATATCAAAGATTATTAAAATAATATT
1 AAAAGTTATCAAAATTATATCAAAGATTATTAAAATAATATT
* ** * * *
1099497 AAAGGTTATCAAAAATTATATCAAAGGCTATTAAAATTACATC
1 AAAAGTTATC-AAAATTATATCAAAGATTATTAAAATAATATT
* * *
1099540 AAAAGTTATCAAAATTATAT-ATAAAATTACTAAAATAATTTT
1 AAAAGTTATCAAAATTATATCA-AAGATTATTAAAATAATATT
*
1099582 AAAAGTTATCATATATTATAT
1 AAAAGTTATCA-AAATTATAT
1099603 TATATAAAAG
Statistics
Matches: 86, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
41 1 0.01
42 41 0.48
43 44 0.51
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.36
Consensus pattern (42 bp):
AAAAGTTATCAAAATTATATCAAAGATTATTAAAATAATATT
Found at i:1099948 original size:21 final size:21
Alignment explanation
Indices: 1099924--1099977 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1099914 GTTACTAAAC
*
1099924 TTATATCAAACGTCATCAAAA
1 TTATATCAAACATCATCAAAA
* * *
1099945 TTATATTAAAAATCATCAATA
1 TTATATCAAACATCATCAAAA
1099966 TTATATCAAACA
1 TTATATCAAACA
1099978 CAATTGATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (21 bp):
TTATATCAAACATCATCAAAA
Found at i:1103491 original size:2 final size:2
Alignment explanation
Indices: 1103478--1103512 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1103468 TTCAAAGTAT
*
1103478 TA TA TG 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 T
1103513 TTATTTAGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1110258 original size:16 final size:16
Alignment explanation
Indices: 1110234--1110285 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
1110224 ATAAATAATT
1110234 TTAAT-ATAATATAAA
1 TTAATAATAATATAAA
1110249 TTAATAATAATATAAAAA
1 TTAATAATAATAT--AAA
1110267 TATAATAATAA-ATAAA
1 T-TAATAATAATATAAA
1110283 TTA
1 TTA
1110286 TTTATCATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
15 7 0.21
16 11 0.33
18 6 0.18
19 9 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAATAATAATATAAA
Found at i:1110916 original size:30 final size:26
Alignment explanation
Indices: 1110863--1110919 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 26
1110853 ATAAAAAATT
*
1110863 AATATATTATTTTTTAATTTAATTAA
1 AATATATTATTTTTTAATCTAATTAA
1110889 AATATATTATATTTGTTATACTCTAATTAA
1 AATATATTAT-TTT-TTA-A-TCTAATTAA
1110919 A
1 A
1110920 TTTTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 10 0.38
27 3 0.12
28 3 0.12
29 1 0.04
30 9 0.35
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (26 bp):
AATATATTATTTTTTAATCTAATTAA
Found at i:1111326 original size:25 final size:27
Alignment explanation
Indices: 1111296--1111346 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
1111286 ACTTTAAGAG
1111296 ATTATATT-AATAAT-ATTAAATAAAA
1 ATTATATTAAATAATAATTAAATAAAA
1111321 ATTATATTAAAATAATAATTAAATAA
1 ATTATATT-AAATAATAATTAAATAA
1111347 TTTTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.35
27 6 0.26
28 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
ATTATATTAAATAATAATTAAATAAAA
Found at i:1111329 original size:16 final size:17
Alignment explanation
Indices: 1111308--1111341 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1111298 TATATTAATA
1111308 ATATT-AAATAAAAATT
1 ATATTAAAATAAAAATT
*
1111324 ATATTAAAATAATAATT
1 ATATTAAAATAAAAATT
1111341 A
1 A
1111342 AATAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATTAAAATAAAAATT
Found at i:1112696 original size:15 final size:15
Alignment explanation
Indices: 1112650--1112696 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1112640 AATATTATTT
1112650 TTTAAATATATAAAA-A
1 TTTAAA-ATA-AAAATA
* *
1112666 TTTAAAATATATATA
1 TTTAAAATAAAAATA
1112681 TTTAAAATAAAAATA
1 TTTAAAATAAAAATA
1112696 T
1 T
1112697 AATTTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 2 0.08
15 18 0.69
16 6 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTAAAATAAAAATA
Found at i:1112909 original size:3 final size:3
Alignment explanation
Indices: 1112903--1112929 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1112893 TCCACCACAA
1112903 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1112930 GGTAAGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1114234 original size:19 final size:20
Alignment explanation
Indices: 1114181--1114235 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
1114171 AATTTTAATT
1114181 TTAATCTTAAATATTTAAAATA
1 TTAAT-TTAAAT-TTTAAAATA
* * *
1114203 TTAATATATATTTTAATATA
1 TTAATTTAAATTTTAAAATA
1114223 TT-ATTTAAATTTT
1 TTAATTTAAATTTT
1114236 TTTTGAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 9 0.32
20 10 0.36
21 4 0.14
22 5 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATTTAAATTTTAAAATA
Found at i:1121319 original size:6 final size:6
Alignment explanation
Indices: 1121308--1121431 Score: 51
Period size: 6 Copynumber: 20.0 Consensus size: 6
1121298 TCGTACTAAC
* * *
1121308 AATATA AATAT- AATAAA AATAATTA AAT-T- ATTATA AATA-A TAATATT
1 AATATA AATATA AATATA AAT-A-TA AATATA AATATA AATATA -AATATA
* * * * *
1121355 AATATGA CATATA AATATA TAATATA AATATA TTAAAATT TATATA AAAATA
1 AATAT-A AATATA AATATA -AATATA AATATA --AATATA AATATA AATATA
*
1121407 AATATA ACATA-A AAAATA ATATATA
1 AATATA A-ATATA AATATA A-ATATA
1121432 TGAATTTTCA
Statistics
Matches: 86, Mismatches: 18, Indels: 27
0.66 0.14 0.21
Matches are distributed among these distances:
4 2 0.02
5 9 0.10
6 49 0.57
7 18 0.21
8 8 0.09
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (6 bp):
AATATA
Found at i:1121374 original size:15 final size:13
Alignment explanation
Indices: 1121339--1121387 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1121329 ATTAAATTAT
1121339 TATAAATA-ATAA
1 TATAAATATATAA
* *
1121351 TATTAATATGA-CA
1 TATAAATAT-ATAA
1121364 TATAAATATATAA
1 TATAAATATATAA
1121377 TATAAATATAT
1 TATAAATATAT
1121388 TAAAATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 8 0.27
13 21 0.70
14 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
TATAAATATATAA
Found at i:1121431 original size:58 final size:56
Alignment explanation
Indices: 1121315--1121432 Score: 125
Period size: 57 Copynumber: 2.1 Consensus size: 56
1121305 AACAATATAA
* * * *
1121315 ATATAATAAAAATAATTAAATTATTATAAATAATAATATTAATATGACATATAAAT
1 ATATAATAAAAATAATTAAATTATTATAAATAATAATATTAACATAAAAAATAAAT
*
1121371 ATATAATATAAATATATTAAAATT-TATATAAA-AATAA-ATATAACATAAAAAATAATAT
1 ATATAATAAAAATA-ATT-AAATTAT-TATAAATAATAATAT-TAACATAAAAAATAA-AT
1121429 ATAT
1 ATAT
1121433 GAATTTTCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
56 15 0.29
57 20 0.38
58 17 0.33
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (56 bp):
ATATAATAAAAATAATTAAATTATTATAAATAATAATATTAACATAAAAAATAAAT
Found at i:1133194 original size:15 final size:16
Alignment explanation
Indices: 1133174--1133205 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1133164 TCAAATAATG
1133174 ATTTTTA-TATTTTAA
1 ATTTTTATTATTTTAA
1133189 ATTTTTATTATTTTAA
1 ATTTTTATTATTTTAA
1133205 A
1 A
1133206 AATAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTTATTATTTTAA
Found at i:1134787 original size:33 final size:33
Alignment explanation
Indices: 1134735--1134820 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
1134725 CGTACCGCCG
* * *
1134735 CCGCCACCACTACCGCCACCATATCTACCTCCA
1 CCGCCACCGCCACCCCCACCATATCTACCTCCA
* * *
1134768 CCGCCGCCGCCACCTCCACCATATCTGCCTCCA
1 CCGCCACCGCCACCCCCACCATATCTACCTCCA
1134801 CCGCCACCGCCACCCCCACC
1 CCGCCACCGCCACCCCCACC
1134821 GCCACCCTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.19, C:0.60, G:0.09, T:0.12
Consensus pattern (33 bp):
CCGCCACCGCCACCCCCACCATATCTACCTCCA
Found at i:1134819 original size:12 final size:12
Alignment explanation
Indices: 1134798--1134827 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1134788 ATATCTGCCT
*
1134798 CCACCGCCACCG
1 CCACCCCCACCG
1134810 CCACCCCCACCG
1 CCACCCCCACCG
1134822 CCACCC
1 CCACCC
1134828 TGTCCACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.73, G:0.10, T:0.00
Consensus pattern (12 bp):
CCACCCCCACCG
Found at i:1134975 original size:15 final size:15
Alignment explanation
Indices: 1134924--1134976 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1134914 TCTCCTTCCT
*
1134924 CCTCCACCATACCCA
1 CCTCCACCATAACCA
* *
1134939 CCGCCACCATATCCA
1 CCTCCACCATAACCA
* * *
1134954 ACACCACCATAACCT
1 CCTCCACCATAACCA
1134969 CCTCCACC
1 CCTCCACC
1134977 GCCTCGTCCG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.28, C:0.57, G:0.02, T:0.13
Consensus pattern (15 bp):
CCTCCACCATAACCA
Found at i:1137237 original size:22 final size:21
Alignment explanation
Indices: 1137167--1137239 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
1137157 TTATATTTAC
* *
1137167 TTATATTTAAATTTATGTCATATT
1 TTATATTTAAA-ATAT-TTATA-T
*
1137191 TTATATATTAAAATA-TTATAA
1 TTATAT-TTAAAATATTTATAT
1137212 TTATATTTAAAATATTTTATAT
1 TTATATTTAAAATA-TTTATAT
1137234 TTATAT
1 TTATAT
1137240 AAATTTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
20 8 0.19
21 6 0.14
22 15 0.36
24 8 0.19
25 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (21 bp):
TTATATTTAAAATATTTATAT
Found at i:1137242 original size:20 final size:19
Alignment explanation
Indices: 1137186--1137242 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 19
1137176 AATTTATGTC
1137186 ATATTTTATA--TATTAAA
1 ATATTTTATATTTATTAAA
*
1137203 ATATTATA-ATTATATTTAAA
1 ATATTTTATATT-TA-TTAAA
1137223 ATATTTTATATTTATATAAA
1 ATATTTTATATTTAT-TAAA
1137243 TTTTAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 1 0.03
17 7 0.22
19 3 0.09
20 18 0.56
21 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTTTATATTTATTAAA
Found at i:1138442 original size:13 final size:13
Alignment explanation
Indices: 1138407--1138448 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1138397 TTAATTTAAT
* *
1138407 ATAAAATTAAAAA
1 ATAAAAATATAAA
1138420 ATAAAAATATAAA
1 ATAAAAATATAAA
*
1138433 ATAAAAATATATA
1 ATAAAAATATAAA
1138446 ATA
1 ATA
1138449 TATTAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAAAAATATAAA
Found at i:1138476 original size:19 final size:19
Alignment explanation
Indices: 1138440--1138483 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1138430 AAAATAAAAA
*
1138440 TATATAATATATTAATATT
1 TATATAATATAATAATATT
1138459 TATATAATATAA-ATATATT
1 TATATAATATAATA-ATATT
1138478 TCATAT
1 T-ATAT
1138484 GAATTATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 17 0.77
20 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATAATATAATAATATT
Found at i:1148874 original size:24 final size:24
Alignment explanation
Indices: 1148820--1148878 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
1148810 TTTTTAAAAT
** * *
1148820 ATTATAATTTTTTATAATGGATAT
1 ATTATAATAATTTATAATAGATAC
**
1148844 ACGATAATAATTTATAATAGATAC
1 ATTATAATAATTTATAATAGATAC
1148868 ATTATAATAAT
1 ATTATAATAAT
1148879 CTTAATTAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (24 bp):
ATTATAATAATTTATAATAGATAC
Found at i:1150150 original size:16 final size:15
Alignment explanation
Indices: 1150106--1150152 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
1150096 TCAAATAAGT
1150106 TATTTTGTATAAAATAA
1 TATTTT-TATAAAA-AA
*
1150123 TATTTTTTTAAAAAA
1 TATTTTTATAAAAAA
1150138 TATTTATTATAAAAA
1 TATTT-TTATAAAAA
1150153 CAAAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 7 0.26
16 14 0.52
17 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
TATTTTTATAAAAAA
Found at i:1153642 original size:2 final size:2
Alignment explanation
Indices: 1153635--1153679 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1153625 AAACAAACTA
*
1153635 AC AC AC AC AC AC AC AC AC AC AC AC GC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1153677 AC A
1 AC A
1153680 TATATATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.49, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1153684 original size:2 final size:2
Alignment explanation
Indices: 1153679--1153708 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1153669 ACACACACAC
1153679 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
1153709 TAATAAACGT
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:1154982 original size:26 final size:26
Alignment explanation
Indices: 1154953--1155005 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
1154943 TTTCTTAGCA
*
1154953 TGAAAAACTAATATTA-CTATTATAAT
1 TGAAAAACTAATA-TAGCTATTAGAAT
1154979 TGAAAAACTAATATAGCTATTAGAAT
1 TGAAAAACTAATATAGCTATTAGAAT
1155005 T
1 T
1155006 AAGAGAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (26 bp):
TGAAAAACTAATATAGCTATTAGAAT
Found at i:1160261 original size:56 final size:54
Alignment explanation
Indices: 1160199--1160313 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
1160189 AAATTTCAAA
**
1160199 AATAAAGTCTAAAACGATTAAATTATATATAA-AATTTATATATAATCTCACGAATC
1 AATAAAGTCTAAAACGATT-AATTAT-TATAATAAGAT-TATATAATCTCACGAATC
* *
1160255 AATAAAGTCTAAAACGATTAATTCTTTTAATAAGATTATATAATCTCACGAATC
1 AATAAAGTCTAAAACGATTAATTATTATAATAAGATTATATAATCTCACGAATC
1160309 AATAA
1 AATAA
1160314 TGTATAGTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
54 27 0.50
55 8 0.15
56 19 0.35
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (54 bp):
AATAAAGTCTAAAACGATTAATTATTATAATAAGATTATATAATCTCACGAATC
Found at i:1160812 original size:26 final size:27
Alignment explanation
Indices: 1160783--1160837 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
1160773 ACGAGATTGG
1160783 TTAAATATTATT-TATTTATAATT-TTT
1 TTAAATATTATTATATTTAT-ATTATTT
* *
1160809 TT-AATTTTTTTATATTTATATTATTT
1 TTAAATATTATTATATTTATATTATTT
1160835 TTA
1 TTA
1160838 CTAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (27 bp):
TTAAATATTATTATATTTATATTATTT
Found at i:1160989 original size:18 final size:18
Alignment explanation
Indices: 1160963--1161021 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
1160953 TATATTTTTG
*
1160963 TATTTAATAAAAATAATA
1 TATTAAATAAAAATAATA
*
1160981 TATTAAATATAAATAAT-
1 TATTAAATAAAAATAATA
1160998 T-TT-AA-AAAAATAA-A
1 TATTAAATAAAAATAATA
*
1161012 AATTAAATAA
1 TATTAAATAA
1161022 TTATTAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
14 7 0.21
15 4 0.12
16 4 0.12
17 3 0.09
18 15 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TATTAAATAAAAATAATA
Found at i:1161008 original size:14 final size:15
Alignment explanation
Indices: 1160963--1161010 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 15
1160953 TATATTTTTG
1160963 TATTTAATAAAAATAA
1 TATTTAA-AAAAATAA
1160979 TATATTAAATATAAATAA
1 TAT-TTAAA-A-AAATAA
1160997 T-TTTAAAAAAATAA
1 TATTTAAAAAAATAA
1161011 AAATTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 6 0.21
15 1 0.03
16 9 0.31
17 6 0.21
18 7 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TATTTAAAAAAATAA
Found at i:1163416 original size:16 final size:16
Alignment explanation
Indices: 1163395--1163444 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1163385 TGAGGTCGGA
1163395 TTATTTTTATTTTAAG
1 TTATTTTTATTTTAAG
*
1163411 TTA-TTTTA--GTAA-
1 TTATTTTTATTTTAAG
1163423 -TATTTTTATTTTAAG
1 TTATTTTTATTTTAAG
1163438 TTATTTT
1 TTATTTT
1163445 AGTAATATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
11 2 0.07
12 5 0.19
13 3 0.11
14 3 0.11
15 5 0.19
16 9 0.33
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TTATTTTTATTTTAAG
Found at i:1163428 original size:27 final size:27
Alignment explanation
Indices: 1163396--1163452 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1163386 GAGGTCGGAT
1163396 TATTTTTATTTTAAGTTATTTTAGTAA
1 TATTTTTATTTTAAGTTATTTTAGTAA
1163423 TATTTTTATTTTAAGTTATTTTAGTAA
1 TATTTTTATTTTAAGTTATTTTAGTAA
1163450 TAT
1 TAT
1163453 GTGAATCGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (27 bp):
TATTTTTATTTTAAGTTATTTTAGTAA
Found at i:1167253 original size:222 final size:224
Alignment explanation
Indices: 1166807--1167257 Score: 782
Period size: 222 Copynumber: 2.0 Consensus size: 224
1166797 AGTAGATTAA
1166807 TTAAAATTTTTTAATTTAAATAACAAAACTAATTATTATATATTTAGTATAAGTAAACATGGTTC
1 TTAAAATTTTTTAATTTAAATAACAAAACTAATTATTATATATTTAGTATAAGTAAACATGGTTC
1166872 AGTCATTATATTTAATAATTACTTTCTTTAAAAGTTTTATAATAAAATATATAATGTCTTTGGAT
66 AGTCATTATATTTAATAATTACTTTCTTTAAAAGTTTTATAATAAAATATATAATGTCTTTGGAT
* *
1166937 ACAATTCTTAAATTTTTCAAAACCTAAGAAAAAAATAATAAAAATGACAGAATAAAAATAAGTTA
131 ACAATCCTTAAATTTTTCAAAACCTAAGAAAAAAATAATAAAAACGACAGAATAAAAATAAGTTA
*
1167002 TTTTACAAATAATAAATTATCGTATATGT
196 TTCTACAAATAATAAATTATCGTATATGT
* *
1167031 TTAAAATTTTTTAATTTAAATAACAAAACTAATTATTATATATTTAGTATAGGTGAACATGGTTC
1 TTAAAATTTTTTAATTTAAATAACAAAACTAATTATTATATATTTAGTATAAGTAAACATGGTTC
* *
1167096 AGTCATTATATTTAATAATTA-TTTTTCTTAAAGGTTTTATAATAAAATA-A-AATGTCTTTGGA
66 AGTCATTATATTTAATAATTACTTTCT-TTAAAAGTTTTATAATAAAATATATAATGTCTTTGGA
* *
1167158 TACAATCCTTAAATTTTTTAAAACCTAAGAAAAATATAATAAAAACGACAGAATAAAAATAAGTT
130 TACAATCCTTAAATTTTTCAAAACCTAAGAAAAAAATAATAAAAACGACAGAATAAAAATAAGTT
*
1167223 ATTCTACAGATAATAAATTATCGTATATGT
195 ATTCTACAAATAATAAATTATCGTATATGT
1167253 TTAAA
1 TTAAA
1167258 TACTTATTGT
Statistics
Matches: 216, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
222 106 0.49
223 5 0.02
224 105 0.49
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (224 bp):
TTAAAATTTTTTAATTTAAATAACAAAACTAATTATTATATATTTAGTATAAGTAAACATGGTTC
AGTCATTATATTTAATAATTACTTTCTTTAAAAGTTTTATAATAAAATATATAATGTCTTTGGAT
ACAATCCTTAAATTTTTCAAAACCTAAGAAAAAAATAATAAAAACGACAGAATAAAAATAAGTTA
TTCTACAAATAATAAATTATCGTATATGT
Found at i:1169329 original size:3 final size:3
Alignment explanation
Indices: 1169321--1169347 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1169311 CTGTCTGATG
1169321 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1169348 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1171957 original size:82 final size:85
Alignment explanation
Indices: 1171800--1171957 Score: 232
Period size: 82 Copynumber: 1.9 Consensus size: 85
1171790 TTCATTTTCC
* *
1171800 CTTTACAATTCCTTATATGAATATGATCGTAAAAAAAAAAGACTGTCTTTGATAGCTTAAACATA
1 CTTTACAATTCCTTATATGAATATGATCGTAAAAAAAAAAGACTGTCTTTAATAACTTAAACATA
1171865 AGCATTTTAAAAAATTTTTT
66 AGCATTTTAAAAAATTTTTT
* * * *
1171885 CTTTGCAATTCTTTATATGAATATGA-C-TATAAAAAAAA-ACTGTCTTTAATAATTTAAACATA
1 CTTTACAATTCCTTATATGAATATGATCGTAAAAAAAAAAGACTGTCTTTAATAACTTAAACATA
*
1171947 AGTATTTTAAA
66 AGCATTTTAAA
1171958 TTTTTTTCTC
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
82 31 0.47
83 10 0.15
84 1 0.02
85 24 0.36
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (85 bp):
CTTTACAATTCCTTATATGAATATGATCGTAAAAAAAAAAGACTGTCTTTAATAACTTAAACATA
AGCATTTTAAAAAATTTTTT
Found at i:1174961 original size:152 final size:150
Alignment explanation
Indices: 1174454--1175028 Score: 473
Period size: 155 Copynumber: 3.8 Consensus size: 150
1174444 ACCCATCTTT
* * * * * * * * *
1174454 GGCATAAAAGCGGACCCGATGACAACTTAAAAATCGATTCTAAAAAATTACCAAGATGCCCCTA-
1 GGCATAAAAGCGAACCCGGTAATAACCTAAGACTCGGTTCTAAAAAATTACCAAAATGCCCCTAG
* * * *
1174518 AGAGATACTCTCGACATAGAAGTACTTGATACTCCTAAAGGACTTAAAAAGGATAAAAAATTGGA
66 GGA-ATACTTTCGACGTAGAAGTACCTGATAC-CCTAAAGGACTTAAAAA-GATAAAAAA--GGA
*
1174583 TGAACCTATCTTAAA-TACCACCTTC
126 TGAACCTATCCTAAATTA-CACCTTC
* ** * * * *
1174608 AGCATAAAAGC-AGACCCGGCGACAACCTAAGACACGGTTATAAAAAATTATCCAAAATACCCCT
1 GGCATAAAAGCGA-ACCCGGTAATAACCTAAGACTCGGTTCTAAAAAATTA-CCAAAATGCCCCT
** * *
1174672 AGAGG-ATACTTTTAACGTAGAAGTTCCCGATACCCTTAAAGGACTTAAAAAAGATAAAAATAGG
64 AG-GGAATACTTTCGACGTAGAAGTACCTGATACCC-TAAAGGACTT-AAAAAGATAAAAA-AGG
* * *
1174736 ATGAACATATCCTAAATATTCACTTTC
125 ATGAACCTATCCTAAAT-TACACCTTC
* * * **
1174763 GGCATAAAAGCGAACTCGGTAATAACCTAAAACTCGGTTTTAAAAAATTACCAAAATGCCTTGTA
1 GGCATAAAAGCGAACCCGGTAATAACCTAAGACTCGGTTCTAAAAAATTACCAAAATGCC-CCTA
*
1174828 GGGAATACTTTCGACGTAGAAGTACCTGATATCCCTAAAGGACTTAAAAAG-TATAAAAGGATGA
65 GGGAATACTTTCGACGTAGAAGTACCTGATA-CCCTAAAGGACTTAAAAAGATAAAAAAGGATGA
1174892 ACCTATCCTAAATGTACACCTTC
129 ACCTATCCTAAAT-TACACCTTC
* * * * * ** * * * *
1174915 GGCGTAGAAGCGAACCCAGTAATAACTTAGGACTTAGTTCTAAAAAAATA-CAAAGATACTCATA
1 GGCATAAAAGCGAACCCGGTAATAACCTAAGACTCGGTTCTAAAAAATTACCAAA-ATGCCCCTA
* * * *
1174979 -GGAGATACCTTCGACGTAAAAGTA-CTCAATACTCCTAAAAGACTTAAAAA
65 GGGA-ATACTTTCGACGTAGAAGTACCT-GATAC-CCTAAAGGACTTAAAAA
1175029 AAATTGGTAA
Statistics
Matches: 341, Mismatches: 63, Indels: 37
0.77 0.14 0.08
Matches are distributed among these distances:
150 6 0.02
151 43 0.13
152 68 0.20
153 5 0.01
154 74 0.22
155 133 0.39
156 11 0.03
157 1 0.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (150 bp):
GGCATAAAAGCGAACCCGGTAATAACCTAAGACTCGGTTCTAAAAAATTACCAAAATGCCCCTAG
GGAATACTTTCGACGTAGAAGTACCTGATACCCTAAAGGACTTAAAAAGATAAAAAAGGATGAAC
CTATCCTAAATTACACCTTC
Found at i:1175975 original size:2 final size:2
Alignment explanation
Indices: 1175968--1175994 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1175958 ATATAAACAT
1175968 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
1175995 TAACAAGAAA
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:1176503 original size:14 final size:13
Alignment explanation
Indices: 1176469--1176524 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
1176459 TCATTTTTTC
*
1176469 TTTTTTTTATTCCT
1 TTTTTTTTA-TCTT
*
1176483 TTCTTTTTATGCTT
1 TTTTTTTTAT-CTT
1176497 TTTTTTTTA-CTT
1 TTTTTTTTATCTT
*
1176509 TTTTTCTT-TCTT
1 TTTTTTTTATCTT
1176521 TTTT
1 TTTT
1176525 ACTTTTCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 17 0.47
13 1 0.03
14 18 0.50
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTTTTTATCTT
Found at i:1176509 original size:12 final size:11
Alignment explanation
Indices: 1176462--1176524 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 11
1176452 ATTTCCATCA
1176462 TTTTTTCTTTT
1 TTTTTTCTTTT
1176473 TTTTATTCCTTTCT
1 TTTT-TT-CTTT-T
*
1176487 TTTTATGCTTTT
1 TTTT-TTCTTTT
1176499 TTTTTTACTTTT
1 TTTTTT-CTTTT
1176511 TTTCTTTCTTTT
1 TTT-TTTCTTTT
1176523 TT
1 TT
1176525 ACTTTTCATT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
11 5 0.11
12 22 0.49
13 11 0.24
14 7 0.16
ACGTcount: A:0.05, C:0.13, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:1177110 original size:168 final size:165
Alignment explanation
Indices: 1176821--1177122 Score: 426
Period size: 168 Copynumber: 1.8 Consensus size: 165
1176811 TGTCATGCGT
* * *
1176821 AAAAATTTACTGGAATAAAAAATACCGTATTTCGAAAAAAAGAGTTTCATGGAAAAAATCTAAAA
1 AAAAATTTACAGGAATAAAAAATACCGTATTTCGAAAAAAAGAGTTTCAAGGAAAAAATCAAAAA
* * * * *
1176886 TTCATGAAAATAAATAATTTTTTAAAAACTGAATTAATATGAAATAAATGATAATATTTGATA-A
66 CTCATGAAAATAAATAAATTTTTAAAAACTGAATCAATAGGAAATAAATAATAATATTTGA-AGA
1176950 ATTTTAAAAATTGAAAATCGAGAAAAATCCTCTCAA
130 ATTTTAAAAATTGAAAATCGAGAAAAATCCTCTCAA
* * *
1176986 AAAAATTTACAGGAGTATAAAATACTGTATTTCGAAAAAAATGGAGTTTCAAGGAAAAAAATCAA
1 AAAAATTTACAGGAATAAAAAATACCGTATTTCGAAAAAAA--GAGTTTCAAGG-AAAAAATCAA
* * * *
1177051 AAACTCATGAAAATAAATAAATTTTTGAAAACTGAATCGATGGGAATTAAATAATAATATTTGAA
63 AAACTCATGAAAATAAATAAATTTTTAAAAACTGAATCAATAGGAAATAAATAATAATATTTGAA
1177116 GAATTTT
128 GAATTTT
1177123 GATGTTTGAA
Statistics
Matches: 118, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
165 37 0.31
167 11 0.09
168 70 0.59
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (165 bp):
AAAAATTTACAGGAATAAAAAATACCGTATTTCGAAAAAAAGAGTTTCAAGGAAAAAATCAAAAA
CTCATGAAAATAAATAAATTTTTAAAAACTGAATCAATAGGAAATAAATAATAATATTTGAAGAA
TTTTAAAAATTGAAAATCGAGAAAAATCCTCTCAA
Found at i:1180375 original size:18 final size:19
Alignment explanation
Indices: 1180347--1180382 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1180337 ATATATTTTT
1180347 TATATTTAAATAAAAATAA
1 TATATTTAAATAAAAATAA
*
1180366 TATA-TTAAATATAAATA
1 TATATTTAAATAAAAATA
1180383 TTTTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATATTTAAATAAAAATAA
Found at i:1183461 original size:13 final size:13
Alignment explanation
Indices: 1183443--1183480 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1183433 TAAAAATTAA
1183443 ATTATAAATATTT
1 ATTATAAATATTT
1183456 ATTAT-AATATTT
1 ATTATAAATATTT
* *
1183468 ATAATAAAAATTT
1 ATTATAAATATTT
1183481 CACGAGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTATAAATATTT
Found at i:1183524 original size:27 final size:28
Alignment explanation
Indices: 1183494--1183547 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1183484 GAGATTAGCT
1183494 AAAGATTATT-TATTTATAATT-TTTTTG
1 AAAGATTATTATATTTAT-ATTATTTTTG
* *
1183521 AAAGTTTCTTATATTTATATTATTTTT
1 AAAGATTATTATATTTATATTATTTTT
1183548 ATTAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (28 bp):
AAAGATTATTATATTTATATTATTTTTG
Found at i:1183879 original size:6 final size:6
Alignment explanation
Indices: 1183868--1183895 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1183858 TCTAGATAAT
1183868 ATTTTC ATTTTC ATTTTC ATTTTC ATTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTT
1183896 CTGCATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTC
Found at i:1186837 original size:17 final size:18
Alignment explanation
Indices: 1186817--1186850 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1186807 ATTAAAAATC
*
1186817 TATT-TAATCGATTTTAG
1 TATTATAATAGATTTTAG
1186834 TATTATAATAGATTTTA
1 TATTATAATAGATTTTA
1186851 TCGATCGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (18 bp):
TATTATAATAGATTTTAG
Found at i:1194416 original size:51 final size:51
Alignment explanation
Indices: 1194309--1194416 Score: 112
Period size: 50 Copynumber: 2.1 Consensus size: 51
1194299 AAAGAGTTTA
* *** *
1194309 TATATTATTAATAAATTTAAATTTATATATTTTTATTGAAGTAAATAATAT
1 TATATTATTAATAAATTAAAATTTATATATTTTTAAAAAAGTAAATAAAAT
* * *
1194360 CATATTATT-ATAAA-TAAAATTATATATTTTTTTAAAAAATTATAATAAAAT
1 TATATTATTAATAAATTAAAATT-TATATATTTTTAAAAAAGTA-AATAAAAT
1194411 TATATT
1 TATATT
1194417 TTTTAATTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
49 6 0.13
50 20 0.43
51 20 0.43
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (51 bp):
TATATTATTAATAAATTAAAATTTATATATTTTTAAAAAAGTAAATAAAAT
Found at i:1194701 original size:16 final size:16
Alignment explanation
Indices: 1194673--1194722 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
1194663 TGTAGGGCTC
*
1194673 ATATTTTTATTATTTTT
1 ATATTTTT-TTATTTTG
*
1194690 ATATTTTTTTATATTG
1 ATATTTTTTTATTTTG
1194706 ATAATTTATTTTATTTT
1 AT-ATTT-TTTTATTTT
1194723 ATGTATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 8 0.29
17 12 0.43
18 8 0.29
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
ATATTTTTTTATTTTG
Found at i:1194704 original size:18 final size:18
Alignment explanation
Indices: 1194676--1194734 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
1194666 AGGGCTCATA
1194676 TTTTTATTATTTTTATATT
1 TTTTTA-TATTTTTATATT
**
1194695 TTTTTATATTGATA-ATT
1 TTTTTATATTTTTATATT
1194712 TATTTTAT-TTTATGTATATT
1 T-TTTTATATTT-T-TATATT
1194732 TTT
1 TTT
1194735 AAATATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 6 0.19
18 12 0.38
19 10 0.31
20 4 0.12
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (18 bp):
TTTTTATATTTTTATATT
Found at i:1196251 original size:27 final size:29
Alignment explanation
Indices: 1196221--1196280 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
1196211 ATTTTAATTT
*
1196221 TAAATTTATTTATTA-AATATT-TTTAAA
1 TAAATTTATTAATTATAATATTATTTAAA
* *
1196248 TAAATTTATTAATTATAATTTTATTTAAT
1 TAAATTTATTAATTATAATATTATTTAAA
1196277 TAAA
1 TAAA
1196281 AATTTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 14 0.50
28 5 0.18
29 9 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TAAATTTATTAATTATAATATTATTTAAA
Found at i:1196675 original size:3 final size:3
Alignment explanation
Indices: 1196660--1196698 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
1196650 CATCCAAACA
* *
1196660 AAT AAT AAC AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1196699 TATTATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1197592 original size:14 final size:14
Alignment explanation
Indices: 1197573--1197600 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1197563 GAGAAGAGCC
1197573 AAGAATGTGAATAT
1 AAGAATGTGAATAT
1197587 AAGAATGTGAATAT
1 AAGAATGTGAATAT
1197601 GGGCGAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
AAGAATGTGAATAT
Found at i:1198585 original size:50 final size:52
Alignment explanation
Indices: 1198484--1198587 Score: 194
Period size: 50 Copynumber: 2.0 Consensus size: 52
1198474 TGGGAGGGGG
1198484 CTGTCAGAGCCTTATCCCTCAAATTTTCTGTAAGACTTGTCAAATGATTTAT
1 CTGTCAGAGCCTTATCCCTCAAATTTTCTGTAAGACTTGTCAAATGATTTAT
1198536 CTGTCAGAGCCTTATCCCTC-AATTTTCT-TAAGACTTGTCAAATGATTTAT
1 CTGTCAGAGCCTTATCCCTCAAATTTTCTGTAAGACTTGTCAAATGATTTAT
1198586 CT
1 CT
1198588 CTTCGTTTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 24 0.46
51 8 0.15
52 20 0.38
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.39
Consensus pattern (52 bp):
CTGTCAGAGCCTTATCCCTCAAATTTTCTGTAAGACTTGTCAAATGATTTAT
Found at i:1199607 original size:3 final size:3
Alignment explanation
Indices: 1199599--1199630 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1199589 TTATTTATGT
1199599 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1199631 TAGTACTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1200240 original size:16 final size:15
Alignment explanation
Indices: 1200221--1200266 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
1200211 TTTAGATTAT
1200221 ATTTAATATATTAATA
1 ATTTAATATATTAA-A
1200237 ATTT-ATA-ATATAAA
1 ATTTAATATAT-TAAA
1200251 ATATTAATATATTAAA
1 AT-TTAATATATTAAA
1200267 TATATATCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 5 0.19
15 8 0.31
16 11 0.42
17 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTTAATATATTAAA
Found at i:1200267 original size:15 final size:15
Alignment explanation
Indices: 1200223--1200269 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1200213 TAGATTATAT
1200223 TTAATATATT-AATAA
1 TTAATATATTAAAT-A
* *
1200238 TTTATAATATAAAATA
1 TTAAT-ATATTAAATA
1200254 TTAATATATTAAATA
1 TTAATATATTAAATA
1200269 T
1 T
1200270 ATATCTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 14 0.54
16 9 0.35
17 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATATATTAAATA
Found at i:1200705 original size:3 final size:3
Alignment explanation
Indices: 1200697--1200736 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1200687 CTTTGATGTG
1200697 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1200737 AATACTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1201019 original size:3 final size:3
Alignment explanation
Indices: 1201006--1201047 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1200996 CATCCAAACC
*
1201006 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1201048 TATAGAAGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1205465 original size:42 final size:41
Alignment explanation
Indices: 1205387--1205478 Score: 98
Period size: 42 Copynumber: 2.3 Consensus size: 41
1205377 TGTAATTTAG
* * * *
1205387 ATATAATTTTTATATTTAAAATTTATGTCACGTAATAAATTT
1 ATATTATTTTTAGATATAAAATTTATGTCACATAAT-AATTT
* * *
1205429 ATATTATTTTTAGATATAATATTTATGTTATATAATAATTT
1 ATATTATTTTTAGATATAAAATTTATGTCACATAATAATTT
1205470 -TATT-TTTTT
1 ATATTATTTTT
1205479 CACATAAAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
39 5 0.12
40 4 0.09
41 5 0.12
42 29 0.67
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (41 bp):
ATATTATTTTTAGATATAAAATTTATGTCACATAATAATTT
Done.