Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 5 of 125
Found at i:1389462 original size:21 final size:21
Alignment explanation
Indices: 1389433--1389476 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1389423 TAAATTGTCT
*
1389433 AAATTTAAAAATTAAATAAAA
1 AAATCTAAAAATTAAATAAAA
* *
1389454 AAATCTAAATATTAAATTAAA
1 AAATCTAAAAATTAAATAAAA
1389475 AA
1 AA
1389477 TAATATATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATCTAAAAATTAAATAAAA
Found at i:1391180 original size:26 final size:26
Alignment explanation
Indices: 1391151--1391225 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
1391141 TATATCAGAC
*
1391151 ATTAATTTAATTTAAAATATTAA-AAT
1 ATTAATTTATTTTAAAA-ATTAAGAAT
1391177 ATTATATTTATTTTTTAAAAATTAAGAAT
1 ATTA-ATTTA--TTTTAAAAATTAAGAAT
* *
1391206 ATTTATGTATTTTAAAAATT
1 ATTAATTTATTTTAAAAATT
1391226 TCATATAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
26 15 0.36
27 5 0.12
28 9 0.21
29 13 0.31
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (26 bp):
ATTAATTTATTTTAAAAATTAAGAAT
Found at i:1391216 original size:28 final size:26
Alignment explanation
Indices: 1391161--1391225 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 26
1391151 ATTAATTTAA
*
1391161 TTTAAAATATTAAAATATTATATTTATTT
1 TTTAAAA-ATTAAAATATTATATGTA--T
1391190 TTTAAAAATTAAGAATATT-TATGTAT
1 TTTAAAAATTAA-AATATTATATGTAT
1391216 TTTAAAAATT
1 TTTAAAAATT
1391226 TCATATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 11 0.32
28 10 0.29
29 13 0.38
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (26 bp):
TTTAAAAATTAAAATATTATATGTAT
Found at i:1391235 original size:29 final size:25
Alignment explanation
Indices: 1391175--1391238 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 25
1391165 AAATATTAAA
*
1391175 ATATTATATTTATTTTTTAAAAATT
1 ATATAATATTTATTTTTTAAAAATT
*
1391200 A-AGAATATTTATGTATTTTAAAAATTT
1 ATATAATATTTAT-T-TTTTAAAAA-TT
1391227 CATATAATATTT
1 -ATATAATATTT
1391239 TTATAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 9 0.29
25 2 0.06
26 9 0.29
27 2 0.06
28 1 0.03
29 8 0.26
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (25 bp):
ATATAATATTTATTTTTTAAAAATT
Found at i:1391597 original size:19 final size:19
Alignment explanation
Indices: 1391567--1391667 Score: 61
Period size: 18 Copynumber: 5.3 Consensus size: 19
1391557 AAATATACAA
1391567 AAATTA-TAAAAAATATTT
1 AAATTATTAAAAAATATTT
*
1391585 AAATTATT-AAAAA-ATTA
1 AAATTATTAAAAAATATTT
*
1391602 AATATTGTT-AAAAATATTTT
1 AA-ATTATTAAAAAATA-TTT
*
1391622 AAATT-TGTAAAAATATTATTAA
1 AAATTAT-TAAAAA-A-TATT-T
*
1391644 AAATTA-TAAAATATTATTT
1 AAATTATTAAAA-AATATTT
1391663 AAATT
1 AAATT
1391668 TTGTAGAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 21
0.71 0.06 0.23
Matches are distributed among these distances:
17 5 0.08
18 22 0.33
19 11 0.17
20 12 0.18
21 8 0.12
22 8 0.12
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AAATTATTAAAAAATATTT
Found at i:1391598 original size:29 final size:30
Alignment explanation
Indices: 1391530--1391601 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
1391520 TATAAAAATT
* *
1391530 TTATT-AAAAATCATAAAAAGTATTTATAA
1 TTATTAAAAAATTATAAAAAATATTTATAA
*
1391559 ATA-TACAAAAATTATAAAAAATATTTA-AA
1 TTATTA-AAAAATTATAAAAAATATTTATAA
1391588 TTATTAAAAAATTA
1 TTATTAAAAAATTA
1391602 AATATTGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 1 0.03
29 14 0.39
30 21 0.58
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (30 bp):
TTATTAAAAAATTATAAAAAATATTTATAA
Found at i:1391618 original size:12 final size:12
Alignment explanation
Indices: 1391601--1391647 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
1391591 TTAAAAAATT
1391601 AAATATTGTTAA
1 AAATATTGTTAA
1391613 AAATATT-TT--
1 AAATATTGTTAA
1391622 AAAT-TTG-TAA
1 AAATATTGTTAA
*
1391632 AAATATTATTAA
1 AAATATTGTTAA
1391644 AAAT
1 AAAT
1391648 TATAAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
8 3 0.10
9 4 0.14
10 4 0.14
11 4 0.14
12 14 0.48
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (12 bp):
AAATATTGTTAA
Found at i:1391634 original size:20 final size:18
Alignment explanation
Indices: 1391575--1391638 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 18
1391565 AAAAATTATA
1391575 AAAAATATTTAAATTAT-T
1 AAAAATATTTAAATT-TGT
1391593 AAAAA-A-TTAAATATTGTT
1 AAAAATATTTAAAT-TTG-T
1391611 AAAAATATTTTAAATTTGT
1 AAAAATA-TTTAAATTTGT
1391630 AAAAATATT
1 AAAAATATT
1391639 ATTAAAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
16 7 0.17
17 2 0.05
18 13 0.32
19 9 0.22
20 3 0.08
21 6 0.15
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
AAAAATATTTAAATTTGT
Found at i:1391649 original size:10 final size:10
Alignment explanation
Indices: 1391530--1391690 Score: 72
Period size: 10 Copynumber: 16.4 Consensus size: 10
1391520 TATAAAAATT
1391530 TTATTAAAAA
1 TTATTAAAAA
*
1391540 TCA-TAAAAA
1 TTATTAAAAA
* *
1391549 GTATTTATAAA
1 TTA-TTAAAAA
*
1391560 -TATACAAAAA
1 TTAT-TAAAAA
1391570 TTA-TAAAAA
1 TTATTAAAAA
* *
1391579 ATATT-TAAA
1 TTATTAAAAA
1391588 TTATTAAAAA
1 TTATTAAAAA
*
1391598 --ATTAAATA
1 TTATTAAAAA
*
1391606 TTGTTAAAAA
1 TTATTAAAAA
**
1391616 -TATTTTAAA
1 TTATTAAAAA
1391625 TT-TGTAAAAATA
1 TTAT-T-AAAA-A
1391637 TTATTAAAAA
1 TTATTAAAAA
1391647 TTA-TAAAATA
1 TTATTAAAA-A
*
1391657 TTATT-TAAA
1 TTATTAAAAA
* *
1391666 TTTTGTAGAAA
1 TTAT-TAAAAA
1391677 TTATTAAAAA
1 TTATTAAAAA
1391687 TTAT
1 TTAT
1391691 GAACGAATGA
Statistics
Matches: 110, Mismatches: 24, Indels: 34
0.65 0.14 0.20
Matches are distributed among these distances:
8 7 0.06
9 38 0.35
10 40 0.36
11 20 0.18
12 4 0.04
13 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (10 bp):
TTATTAAAAA
Found at i:1393022 original size:14 final size:14
Alignment explanation
Indices: 1393005--1393046 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1392995 ATATTGAATT
1393005 CTAAATCTTGAACC
1 CTAAATCTTGAACC
* *
1393019 CTAAATCCTAAACC
1 CTAAATCTTGAACC
*
1393033 TTAAA-CTTGAACC
1 CTAAATCTTGAACC
1393046 C
1 C
1393047 CAAACTCAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.38, C:0.31, G:0.05, T:0.26
Consensus pattern (14 bp):
CTAAATCTTGAACC
Found at i:1397018 original size:28 final size:31
Alignment explanation
Indices: 1396978--1397037 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1396968 AAATTGAATC
*
1396978 AAATTAACAATTC-ATGTATAA-ATTGCACA
1 AAATTAACAATTCGATGTAAAATATTGCACA
1397007 AAATTAA-AATTCGTATGTAAAATATTGCACA
1 AAATTAACAATTCG-ATGTAAAATATTGCACA
1397038 TTGAACCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 5 0.19
29 7 0.26
30 7 0.26
31 8 0.30
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (31 bp):
AAATTAACAATTCGATGTAAAATATTGCACA
Found at i:1399146 original size:14 final size:13
Alignment explanation
Indices: 1399127--1399157 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
1399117 AAAAATGAAA
1399127 AATAATATTATGTT
1 AATAATATTAT-TT
1399141 AATAATATTATTT
1 AATAATATTATTT
1399154 AATA
1 AATA
1399158 CCTAAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (13 bp):
AATAATATTATTT
Found at i:1400963 original size:18 final size:18
Alignment explanation
Indices: 1400936--1400979 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1400926 TTTTTAAATT
* *
1400936 ATTTAAAATATACTTATA-
1 ATTTATAATATA-TAATAG
1400954 ATTTATAATATATAATAG
1 ATTTATAATATATAATAG
1400972 ATTTATAA
1 ATTTATAA
1400980 CGGTATAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTTATAATATATAATAG
Found at i:1405705 original size:8 final size:8
Alignment explanation
Indices: 1405694--1405732 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
1405684 AAATTTTTTG
1405694 AAAATTAT
1 AAAATTAT
1405702 AAAATTAT
1 AAAATTAT
1405710 AAAATTAT
1 AAAATTAT
*
1405718 ATAA-TAGT
1 AAAATTA-T
1405726 AAAATTA
1 AAAATTA
1405733 CCTTTTAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 2 0.07
8 23 0.85
9 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (8 bp):
AAAATTAT
Found at i:1410439 original size:2 final size:2
Alignment explanation
Indices: 1410432--1410459 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1410422 TGAACCAAAA
1410432 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
1410460 TATTTTTATG
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:1424485 original size:28 final size:28
Alignment explanation
Indices: 1424453--1424508 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1424443 CTATTCATGT
1424453 TTGTGAAAGCACCTATTTAAGTAAATGC
1 TTGTGAAAGCACCTATTTAAGTAAATGC
1424481 TTGTGAAAGCACCTATTTAAGTAAATGC
1 TTGTGAAAGCACCTATTTAAGTAAATGC
1424509 ACACCCATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (28 bp):
TTGTGAAAGCACCTATTTAAGTAAATGC
Found at i:1426924 original size:38 final size:38
Alignment explanation
Indices: 1426882--1426966 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
1426872 GAATCAGTTG
* * *
1426882 AACCGATTAGTCAAATTGGTCGACTGAACATACAATTA
1 AACCGATTAGCCAAATTGATCGACTGAACAGACAATTA
*
1426920 AACCGATTAGCCAAATTGATCGATTGAACAGACAATTA
1 AACCGATTAGCCAAATTGATCGACTGAACAGACAATTA
1426958 AACCGATTA
1 AACCGATTA
1426967 AACCAATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (38 bp):
AACCGATTAGCCAAATTGATCGACTGAACAGACAATTA
Found at i:1437663 original size:22 final size:21
Alignment explanation
Indices: 1437638--1437686 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
1437628 AGGCTCACTC
* * *
1437638 ATATTATTTTTTATTTTTTTAA
1 ATATTATATTATATTATTTT-A
1437660 ATATTTATATTATATTATTTTA
1 ATA-TTATATTATATTATTTTA
1437682 ATATT
1 ATATT
1437687 TAATAGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 7 0.30
23 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATATTATATTATATTATTTTA
Found at i:1441137 original size:18 final size:19
Alignment explanation
Indices: 1441110--1441154 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1441100 ATTTAATTTT
* *
1441110 ATATAATATAAATTAT-AA
1 ATATATTATAAATAATCAA
*
1441128 ATATATTATAAATAATCTA
1 ATATATTATAAATAATCAA
1441147 ATATATTA
1 ATATATTA
1441155 AATTAAGTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTATAAATAATCAA
Found at i:1444066 original size:18 final size:19
Alignment explanation
Indices: 1444025--1444061 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1444015 ATACAGTCAC
* *
1444025 AAAATTGTTTTTTAATATA
1 AAAATAGTTTTTAAATATA
1444044 AAAATAGTTTTTAAATAT
1 AAAATAGTTTTTAAATAT
1444062 TAAATCTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
AAAATAGTTTTTAAATATA
Found at i:1452164 original size:17 final size:19
Alignment explanation
Indices: 1452142--1452179 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1452132 TTGAATTGCA
1452142 TTTTAT-AA-ATTTATAAT
1 TTTTATGAATATTTATAAT
*
1452159 TTTTATGAATATTTTTAAT
1 TTTTATGAATATTTATAAT
1452178 TT
1 TT
1452180 GGGTTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTATGAATATTTATAAT
Found at i:1453061 original size:3 final size:3
Alignment explanation
Indices: 1453053--1453094 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1453043 ATCGAGTTGC
1453053 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
1453095 GGGTTTAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1456010 original size:2 final size:2
Alignment explanation
Indices: 1456003--1456035 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1455993 GACAATTCAA
1456003 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1456036 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1458831 original size:18 final size:18
Alignment explanation
Indices: 1458804--1458894 Score: 62
Period size: 18 Copynumber: 4.8 Consensus size: 18
1458794 GTCAAATATG
*
1458804 AAAATCAAATTTAATTAA
1 AAAATTAAATTTAATTAA
*
1458822 AAAATTAAATTAATAAAAGATT-G
1 AAAATTAAATT--T---A-ATTAA
1458845 AAAATTAAATTTAATTAAA
1 AAAATTAAATTTAATT-AA
1458864 AAAATTAAA-TTAA-TAA
1 AAAATTAAATTTAATTAA
*
1458880 AAATTTAAATATTAA
1 AAAATTAAAT-TTAA
1458895 AAACTAAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
16 10 0.17
17 4 0.07
18 19 0.32
19 9 0.15
20 1 0.02
21 1 0.02
23 12 0.20
24 3 0.05
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAATTAAATTTAATTAA
Found at i:1458848 original size:23 final size:21
Alignment explanation
Indices: 1458822--1458895 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 21
1458812 ATTTAATTAA
1458822 AAAATTAAATTAATAAAAGATT
1 AAAATTAAATTAATAAAA-ATT
*
1458844 GAAAATTAAATTTAAT-TAAA--
1 -AAAATTAAA-TTAATAAAAATT
1458864 AAAATTAAATTAATAAAAATTT
1 AAAATTAAATTAATAAAAA-TT
1458886 AAATATTAAA
1 AAA-ATTAAA
1458896 AACTAAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
18 5 0.12
19 12 0.28
22 4 0.09
23 17 0.40
24 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (21 bp):
AAAATTAAATTAATAAAAATT
Found at i:1458879 original size:42 final size:40
Alignment explanation
Indices: 1458797--1458895 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 40
1458787 ATTGATAGTC
*
1458797 AAATATGAAAATCAAATTTAATTAAAAAATTAAATTAATAA
1 AAAT-TGAAAATTAAATTTAATTAAAAAATTAAATTAATAA
1458838 AAGATTGAAAATTAAATTTAATTAAAAAAATTAAATTAATAA
1 AA-ATTGAAAATTAAATTTAATT-AAAAAATTAAATTAATAA
*
1458880 AAATTTAAATATTAAA
1 AAATTGAAA-ATTAAA
1458896 AACTAAATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
41 25 0.47
42 28 0.53
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (40 bp):
AAATTGAAAATTAAATTTAATTAAAAAATTAAATTAATAA
Found at i:1465014 original size:217 final size:216
Alignment explanation
Indices: 1464632--1465260 Score: 1019
Period size: 217 Copynumber: 2.9 Consensus size: 216
1464622 CAAAATTCGA
*
1464632 TTTAATATTTGAACCAACCCCACTTTGAAAAAGTAAACATTTTTTAAATAATTGATTTTTTTTAC
1 TTTAATATTTGAACCAACCTCACTTTGAAAAAGTAAACATTTTTTAAATAATTGATTTTTTTTAC
* *
1464697 AACTCATATAATATTTATAGAAGCAAATCACTGTCATGAACATACCACAAATAGACAATCCAAAT
66 AACTCATATAATATTTATAGGAGCAAATCACTGTCATGAACATACCACAAACAGACAATCCAAAT
1464762 TATTCAAACCCACAACATGAGTTGTGGGGTGAATATTTATGGTCAATAGACCATATACTAGGGTT
131 TATTCAAACCCACAACATGAGTTGT-GGGTGAATATTTATGGTCAATAGACCATATACTAGGGTT
*
1464827 TAAATGTTTATTCAGAAGTCGG
195 TAAATGTTTATTCAGAAGTCAG
*
1464849 TTTAATATTTGAACCAACCTCACTTTGAAAAAGTAAACATTTTTTAAATAATTGAGTTTTTTTAC
1 TTTAATATTTGAACCAACCTCACTTTGAAAAAGTAAACATTTTTTAAATAATTGATTTTTTTTAC
1464914 AACTCATATAATATTTATAGGAGCAAATCACTGTCATGAACATACCACAAACAGACAATCCAAAT
66 AACTCATATAATATTTATAGGAGCAAATCACTGTCATGAACATACCACAAACAGACAATCCAAAT
*
1464979 TATTCAAACCCACAACATGAGTTGTGGGATGAATATTTATGGTCAATAGACCATAAACTAGGGTT
131 TATTCAAACCCACAACATGAGTTGTGGG-TGAATATTTATGGTCAATAGACCATATACTAGGGTT
1465044 TAAATGTTTATTCAGAAGTCAG
195 TAAATGTTTATTCAGAAGTCAG
* * *
1465066 TTTAATATTTGAACCAACCTCACTTTAAAAAAATAAACATTTTTTAAATAATTAATTTTTTTTAC
1 TTTAATATTTGAACCAACCTCACTTTGAAAAAGTAAACATTTTTTAAATAATTGATTTTTTTTAC
* * * * * * * *
1465131 AACTCATAAAACATTTATAGGGGCAAATCACTG-CAATAAACACACTACAAGCAGACAATCCCAA
66 AACTCATATAATATTTATAGGAGCAAATCACTGTC-ATGAACATACCACAAACAGACAATCCAAA
* * *
1465195 TTATTCAAACCCAAAACGTG-GATTGTAGGGTGAATATTTATGGTCAATAGACCATATACTGGGG
130 TTATTCAAACCCACAACATGAG-TTGT-GGGTGAATATTTATGGTCAATAGACCATATACTAGGG
1465259 TT
193 TT
1465261 CAAAAGTTGA
Statistics
Matches: 386, Mismatches: 22, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
216 5 0.01
217 378 0.98
218 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (216 bp):
TTTAATATTTGAACCAACCTCACTTTGAAAAAGTAAACATTTTTTAAATAATTGATTTTTTTTAC
AACTCATATAATATTTATAGGAGCAAATCACTGTCATGAACATACCACAAACAGACAATCCAAAT
TATTCAAACCCACAACATGAGTTGTGGGTGAATATTTATGGTCAATAGACCATATACTAGGGTTT
AAATGTTTATTCAGAAGTCAG
Found at i:1466430 original size:2 final size:2
Alignment explanation
Indices: 1466423--1466459 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1466413 AACAGAATAG
1466423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1466460 AAAGAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1466673 original size:298 final size:298
Alignment explanation
Indices: 1466137--1466725 Score: 1178
Period size: 298 Copynumber: 2.0 Consensus size: 298
1466127 ATTATTTTAT
1466137 TATATATATATATATATATAATATAAAAGAATAAAGAAAAGAAAAGAAAGAAACAAAAGAAGAAA
1 TATATATATATATATATATAATATAAAAGAATAAAGAAAAGAAAAGAAAGAAACAAAAGAAGAAA
1466202 GAACAGAGGCTCAAACGAAACAGGGGGAGAAAGAAAAGAGAAGGAAAAAGGAAAAGGGGAAACTA
66 GAACAGAGGCTCAAACGAAACAGGGGGAGAAAGAAAAGAGAAGGAAAAAGGAAAAGGGGAAACTA
1466267 GGATTTTGAAGCTTTAATCTTTAATTGGTAAGTCAATTAAACCTTTTTCTCTTAAATTAGATGCT
131 GGATTTTGAAGCTTTAATCTTTAATTGGTAAGTCAATTAAACCTTTTTCTCTTAAATTAGATGCT
1466332 TTAGAAGATTTAGAACAAAGTTTTGATGAAATTAAGTTGAGGTCTTGGAAGTTTTAAGGTTTTTG
196 TTAGAAGATTTAGAACAAAGTTTTGATGAAATTAAGTTGAGGTCTTGGAAGTTTTAAGGTTTTTG
1466397 AACATAGTTCATGTTGAACAGAATAGTATATATATATA
261 AACATAGTTCATGTTGAACAGAATAGTATATATATATA
1466435 TATATATATATATATATATAATATAAAAGAATAAAGAAAAGAAAAGAAAGAAACAAAAGAAGAAA
1 TATATATATATATATATATAATATAAAAGAATAAAGAAAAGAAAAGAAAGAAACAAAAGAAGAAA
1466500 GAACAGAGGCTCAAACGAAACAGGGGGAGAAAGAAAAGAGAAGGAAAAAGGAAAAGGGGAAACTA
66 GAACAGAGGCTCAAACGAAACAGGGGGAGAAAGAAAAGAGAAGGAAAAAGGAAAAGGGGAAACTA
1466565 GGATTTTGAAGCTTTAATCTTTAATTGGTAAGTCAATTAAACCTTTTTCTCTTAAATTAGATGCT
131 GGATTTTGAAGCTTTAATCTTTAATTGGTAAGTCAATTAAACCTTTTTCTCTTAAATTAGATGCT
1466630 TTAGAAGATTTAGAACAAAGTTTTGATGAAATTAAGTTGAGGTCTTGGAAGTTTTAAGGTTTTTG
196 TTAGAAGATTTAGAACAAAGTTTTGATGAAATTAAGTTGAGGTCTTGGAAGTTTTAAGGTTTTTG
1466695 AACATAGTTCATGTTGAACAGAATAGTATAT
261 AACATAGTTCATGTTGAACAGAATAGTATAT
1466726 TAGGGATTTA
Statistics
Matches: 291, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
298 291 1.00
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.28
Consensus pattern (298 bp):
TATATATATATATATATATAATATAAAAGAATAAAGAAAAGAAAAGAAAGAAACAAAAGAAGAAA
GAACAGAGGCTCAAACGAAACAGGGGGAGAAAGAAAAGAGAAGGAAAAAGGAAAAGGGGAAACTA
GGATTTTGAAGCTTTAATCTTTAATTGGTAAGTCAATTAAACCTTTTTCTCTTAAATTAGATGCT
TTAGAAGATTTAGAACAAAGTTTTGATGAAATTAAGTTGAGGTCTTGGAAGTTTTAAGGTTTTTG
AACATAGTTCATGTTGAACAGAATAGTATATATATATA
Found at i:1468761 original size:17 final size:17
Alignment explanation
Indices: 1468739--1468807 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
1468729 ATTATTTAAA
*
1468739 TTATTATTTCTATTTAG
1 TTATTATTTATATTTAG
1468756 TTATTATTTATATTTAG
1 TTATTATTTATATTTAG
* *
1468773 -T-CTATTTAGAATTTA-
1 TTATTATTTA-TATTTAG
1468788 TTATTATTTA-ATTTAAG
1 TTATTATTTATATTT-AG
1468805 TTA
1 TTA
1468808 AATAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 10 0.23
16 8 0.19
17 25 0.58
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (17 bp):
TTATTATTTATATTTAG
Found at i:1469399 original size:14 final size:14
Alignment explanation
Indices: 1469382--1469409 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1469372 ATTTTAATTT
1469382 ATTTAATAATTTAA
1 ATTTAATAATTTAA
1469396 ATTTAATAATTTAA
1 ATTTAATAATTTAA
1469410 TCCAAGGATG
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:0.00, T:0.50
Consensus pattern (14 bp):
ATTTAATAATTTAA
Found at i:1469400 original size:23 final size:22
Alignment explanation
Indices: 1469368--1469410 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1469358 TATGAAATTT
* *
1469368 TTTAATTTTAATTTATTTAATAA
1 TTTAAATTTAA-TAATTTAATAA
1469391 TTTAAATTTAATAATTTAAT
1 TTTAAATTTAATAATTTAAT
1469411 CCAAGGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAAATTTAATAATTTAATAA
Found at i:1470687 original size:13 final size:13
Alignment explanation
Indices: 1470669--1470693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1470659 TACTATAAAT
1470669 CTATATTGATTTA
1 CTATATTGATTTA
1470682 CTATATTGATTT
1 CTATATTGATTT
1470694 CAACGAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (13 bp):
CTATATTGATTTA
Found at i:1471165 original size:9 final size:9
Alignment explanation
Indices: 1471151--1471214 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
1471141 ATTTATTTAT
1471151 ATATTATTA
1 ATATTATTA
1471160 ATATTATTTA
1 ATATTA-TTA
*
1471170 TATATTATTCT
1 -ATATTATT-A
1471181 ATATTATTA
1 ATATTATTA
*
1471190 ATATATTTTA
1 ATAT-TATTA
1471200 AT-TTATATA
1 ATATTAT-TA
1471209 AT-TTAT
1 ATATTAT
1471215 ATATATTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
8 2 0.04
9 19 0.41
10 19 0.41
11 6 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
ATATTATTA
Found at i:1471168 original size:20 final size:20
Alignment explanation
Indices: 1471143--1471205 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
1471133 CTTTATATAT
1471143 TTATTTATATATTATTAATA
1 TTATTTATATATTATTAATA
*
1471163 TTATTTATATATTATTCTATA
1 TTATTTATATATTATT-AATA
*
1471184 TTATTAATATATT-TTAAT-
1 TTATTTATATATTATTAATA
1471202 TTAT
1 TTAT
1471206 ATAATTTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 4 0.10
19 2 0.05
20 18 0.46
21 15 0.38
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTATATATTATTAATA
Found at i:1471172 original size:30 final size:29
Alignment explanation
Indices: 1471138--1471205 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
1471128 TTTTTCTTTA
1471138 TATATTTATTTATATATTATTAATATTATT
1 TATATTTATTTATATATTATTAATA-TATT
*
1471168 TATATATTA-TTCTATATTATTAATATATT
1 TATAT-TTATTTATATATTATTAATATATT
1471197 T-TAATTTAT
1 TAT-ATTTAT
1471206 ATAATTTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
28 4 0.12
29 7 0.21
30 20 0.59
31 3 0.09
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (29 bp):
TATATTTATTTATATATTATTAATATATT
Found at i:1471178 original size:23 final size:22
Alignment explanation
Indices: 1471138--1471222 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 22
1471128 TTTTTCTTTA
1471138 TATATTTATTTATATATTATTA-
1 TATA-TTATTTATATATTATTAT
*
1471160 -ATATTATTTATATATTATT-C
1 TATATTATTTATATATTATTAT
*
1471180 TATATTATTAATATATT-TTAATT
1 TATATTATTTATATATTATT-A-T
*
1471203 TATATAATTTATATA-TATTA
1 TATATTATTTATATATTATTA
1471223 AATATAGATA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
20 18 0.34
21 18 0.34
22 2 0.04
23 15 0.28
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATTATTTATATATTATTAT
Found at i:1471184 original size:21 final size:20
Alignment explanation
Indices: 1471138--1471218 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 20
1471128 TTTTTCTTTA
1471138 TATATTTATTTATATATTATT
1 TATA-TTATTTATATATTATT
*
1471159 AATATTATTTATATATTATT
1 TATATTATTTATATATTATT
*
1471179 CTATATTATTAATATATTTTAATT
1 -TATATTATT--TATATATT-ATT
*
1471203 TATATAATTTATATAT
1 TATATTATTTATATAT
1471219 ATTAAATATA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
20 16 0.31
21 17 0.33
23 15 0.29
24 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATTATTTATATATTATT
Found at i:1471223 original size:23 final size:22
Alignment explanation
Indices: 1471134--1471222 Score: 85
Period size: 23 Copynumber: 4.0 Consensus size: 22
1471124 GCATTTTTTC
1471134 TTTATA-TATTTATTTATATATTA
1 TTTATATTATTTA--TATATATTA
*
1471157 TTAATATTA-TT-TATATATTA
1 TTTATATTATTTATATATATTA
* *
1471177 TTCTATATTATTAATATATTTTAA
1 TT-TATATTATTTATATATATT-A
*
1471201 TTTATATAATTTATATATATTA
1 TTTATATTATTTATATATATTA
1471223 AATATAGATA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
20 11 0.20
21 6 0.11
22 2 0.04
23 30 0.56
24 5 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTATATTATTTATATATATTA
Found at i:1495364 original size:23 final size:23
Alignment explanation
Indices: 1495334--1495398 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1495324 CTCTTATATA
*
1495334 TGCTTACTGAGCTCAAAATAATT
1 TGCTTACTGAGTTCAAAATAATT
* **
1495357 TGCTTACTGATTTCGTAATAATT
1 TGCTTACTGAGTTCAAAATAATT
**
1495380 TATTTACTGAGTTCAAAAT
1 TGCTTACTGAGTTCAAAAT
1495399 TTACTTACTC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (23 bp):
TGCTTACTGAGTTCAAAATAATT
Found at i:1496964 original size:20 final size:20
Alignment explanation
Indices: 1496939--1496979 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
1496929 AAACCCGCTC
1496939 ATATTA-ATTTTTAAATATTT
1 ATATTATATTTTT-AATATTT
1496959 ATATTATATTTTTAATATTT
1 ATATTATATTTTTAATATTT
1496979 A
1 A
1496980 ACAAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTATATTTTTAATATTT
Found at i:1498826 original size:16 final size:15
Alignment explanation
Indices: 1498797--1498828 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1498787 ACTTTTGACT
1498797 TAAATATAATAGATA
1 TAAATATAATAGATA
1498812 TAAATATAGATAGATA
1 TAAATATA-ATAGATA
1498828 T
1 T
1498829 TTGTCATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (15 bp):
TAAATATAATAGATA
Found at i:1511152 original size:31 final size:31
Alignment explanation
Indices: 1511117--1511186 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1511107 ATTTGATGCA
* *
1511117 TGAGTTTTACTTAAATGTTCAATTTGGT-AT
1 TGAGTTTTACTTAAATATTCAATTAGGTAAT
* *
1511147 CTGAGTTTTAGTTCAATATTCAATTAGGTAAT
1 -TGAGTTTTACTTAAATATTCAATTAGGTAAT
1511179 TGAGTTTT
1 TGAGTTTT
1511187 TTTTTTTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (31 bp):
TGAGTTTTACTTAAATATTCAATTAGGTAAT
Found at i:1511571 original size:22 final size:22
Alignment explanation
Indices: 1511536--1511585 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
1511526 ATATTCAAAC
*
1511536 AATAATAATAAAATAGTAACAA
1 AATAATAACAAAATAGTAACAA
* * * *
1511558 CATAATAACGAAATGGTAGCAA
1 AATAATAACAAAATAGTAACAA
1511580 AATAAT
1 AATAAT
1511586 GAAAAGACAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.22
Consensus pattern (22 bp):
AATAATAACAAAATAGTAACAA
Found at i:1511732 original size:14 final size:14
Alignment explanation
Indices: 1511709--1511739 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1511699 ACATGAGACC
*
1511709 TAACCTGTTTTTTT
1 TAACCCGTTTTTTT
1511723 TAACCCGTTTTTTT
1 TAACCCGTTTTTTT
1511737 TAA
1 TAA
1511740 ACAGACTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.58
Consensus pattern (14 bp):
TAACCCGTTTTTTT
Found at i:1512291 original size:2 final size:2
Alignment explanation
Indices: 1512284--1512316 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1512274 TTTATGTAAT
1512284 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
1512317 TTGATTTTGA
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:1512708 original size:16 final size:15
Alignment explanation
Indices: 1512671--1512720 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1512661 ACTCATTTAT
*
1512671 TTATATATATATAAA
1 TTATATAAATATAAA
*
1512686 TTA-ATAAATATGTAA
1 TTATATAAATAT-AAA
1512701 TTATAT-AATA-AAA
1 TTATATAAATATAAA
1512714 TTATATA
1 TTATATA
1512721 TTTTATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 8 0.28
14 7 0.24
15 12 0.41
16 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TTATATAAATATAAA
Found at i:1512714 original size:28 final size:31
Alignment explanation
Indices: 1512653--1512716 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
1512643 TTTAATTTTT
* * *
1512653 AATTAATAACTCATTTATTTATATATATATA
1 AATTAATAAATCATGTAATTATATATATATA
1512684 AATTAATAAAT-ATGTAATTATATA-ATA-A
1 AATTAATAAATCATGTAATTATATATATATA
1512712 AATTA
1 AATTA
1512717 TATATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 6 0.20
29 3 0.10
30 11 0.37
31 10 0.33
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (31 bp):
AATTAATAAATCATGTAATTATATATATATA
Found at i:1534322 original size:2 final size:2
Alignment explanation
Indices: 1534315--1534345 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1534305 TTTTAACTTT
1534315 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 T
1534346 TTTGATTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1535125 original size:25 final size:25
Alignment explanation
Indices: 1535096--1535158 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
1535086 TTTAAAGAAA
*
1535096 TAAATATATAAATTTATTTTTATAT
1 TAAATATATAAATTTATTTGTATAT
*
1535121 TAAATAAATATAA-TTATTTGTATAT
1 TAAATATATA-AATTTATTTGTATAT
*
1535146 GAAATATATAAAT
1 TAAATATATAAAT
1535159 ATAAAATGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.06
25 28 0.88
26 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
TAAATATATAAATTTATTTGTATAT
Found at i:1536306 original size:18 final size:17
Alignment explanation
Indices: 1536264--1536307 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1536254 ATGTTCTATA
* *
1536264 ATTATTTTTTAAATAAT
1 ATTATTTTTAAAATTAT
*
1536281 ATTGTTTTTAAAATTAT
1 ATTATTTTTAAAATTAT
1536298 ATTTATTTTT
1 A-TTATTTTT
1536308 CTCTATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
ATTATTTTTAAAATTAT
Found at i:1537078 original size:31 final size:31
Alignment explanation
Indices: 1537043--1537102 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
1537033 TAGCTCCTAT
*
1537043 TTATATTCATAAAT-ATTATTGTAATTCTTGC
1 TTATATTCATAAATGATTAGTGT-ATTCTTGC
**
1537074 TTATATTTGTAAATGATTAGTGTATTCTT
1 TTATATTCATAAATGATTAGTGTATTCTT
1537103 TTTGCTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (31 bp):
TTATATTCATAAATGATTAGTGTATTCTTGC
Found at i:1537831 original size:113 final size:114
Alignment explanation
Indices: 1537633--1537865 Score: 423
Period size: 113 Copynumber: 2.1 Consensus size: 114
1537623 AAACCATGTC
* * *
1537633 GGTTTTACAGCTGGTTTGATCCACCATTGATGCCCCGTTCAAAAATAATATTGTTGGGTCTTCTG
1 GGTTTTACAGCTAGTTTGATCCACCATTGACGCCCCGTTCAAAAATAATATTGTTGGGTCTTCTA
1537698 AAAAAAGTGAGGACATTGGAGGATGCAAGGAGGAGGGAGAG-AAAAAAT
66 AAAAAAGTGAGGACATTGGAGGATGCAAGGAGGAGGGAGAGAAAAAAAT
*
1537746 GGTTTTACAGCTAGTTTGATCCACCATTGACGCCCCGTTCAAGAATAATATTGTTGGGTCTTCTA
1 GGTTTTACAGCTAGTTTGATCCACCATTGACGCCCCGTTCAAAAATAATATTGTTGGGTCTTCTA
1537811 AAAAAAGTGAGGACATTGGAGGATGCAAGGAGGAGGGAGAGAAAAAAAT
66 AAAAAAGTGAGGACATTGGAGGATGCAAGGAGGAGGGAGAGAAAAAAAT
1537860 GGTTTT
1 GGTTTT
1537866 TAGTGCTTGT
Statistics
Matches: 115, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
113 102 0.89
114 13 0.11
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (114 bp):
GGTTTTACAGCTAGTTTGATCCACCATTGACGCCCCGTTCAAAAATAATATTGTTGGGTCTTCTA
AAAAAAGTGAGGACATTGGAGGATGCAAGGAGGAGGGAGAGAAAAAAAT
Found at i:1537958 original size:16 final size:16
Alignment explanation
Indices: 1537939--1537969 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1537929 TTGGTTGTTG
*
1537939 CTTCTCATGGTTATTA
1 CTTCTCATGGCTATTA
1537955 CTTCTCATGGCTATT
1 CTTCTCATGGCTATT
1537970 GGTTTGGTTG
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:0.16, C:0.23, G:0.13, T:0.48
Consensus pattern (16 bp):
CTTCTCATGGCTATTA
Found at i:1538278 original size:13 final size:13
Alignment explanation
Indices: 1538260--1538284 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1538250 TTGCCAAATT
1538260 TGATAGGAAACTA
1 TGATAGGAAACTA
1538273 TGATAGGAAACT
1 TGATAGGAAACT
1538285 TTACAAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (13 bp):
TGATAGGAAACTA
Found at i:1538585 original size:12 final size:12
Alignment explanation
Indices: 1538568--1538602 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1538558 AGGAAACTTT
1538568 ACAAAAAGTTCA
1 ACAAAAAGTTCA
1538580 ACAAAAAGTTCA
1 ACAAAAAGTTCA
*
1538592 A-AAATAGTTCA
1 ACAAAAAGTTCA
1538603 GAACAACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.20
Consensus pattern (12 bp):
ACAAAAAGTTCA
Found at i:1539488 original size:12 final size:11
Alignment explanation
Indices: 1539470--1539526 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
1539460 ATCATTCAAT
1539470 ATAAAGCCAAC
1 ATAAAGCCAAC
1539481 ATTAAAGCCAAC
1 A-TAAAGCCAAC
*
1539493 ATAAAG-TAGAC
1 ATAAAGCCA-AC
* *
1539504 ATAAAGTCATC
1 ATAAAGCCAAC
1539515 ATAAAGCCAAC
1 ATAAAGCCAAC
1539526 A
1 A
1539527 AAACACAGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 1 0.03
11 25 0.66
12 12 0.32
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.16
Consensus pattern (11 bp):
ATAAAGCCAAC
Found at i:1541692 original size:19 final size:19
Alignment explanation
Indices: 1541663--1541718 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
1541653 CCCTAAATCC
1541663 CAAAC-AGTGTTAACATG-T
1 CAAACAAGTGTTAACA-GAT
1541681 CAAACAAGTGTTAACAGAT
1 CAAACAAGTGTTAACAGAT
*
1541700 CAAACAAATGTTAACAGAT
1 CAAACAAGTGTTAACAGAT
1541719 AAAAATGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
18 6 0.17
19 29 0.83
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.23
Consensus pattern (19 bp):
CAAACAAGTGTTAACAGAT
Found at i:1542762 original size:25 final size:24
Alignment explanation
Indices: 1542720--1542771 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
1542710 TGCTAATATC
*
1542720 ATATAAATCATTACATAAATATTAA
1 ATATAAATCATTACATAAA-AGTAA
*
1542745 ATATAAATTAGTTA-ATAAAAGTAA
1 ATATAAATCA-TTACATAAAAGTAA
1542769 ATA
1 ATA
1542772 AATAACAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 14 0.58
26 3 0.12
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATAAATCATTACATAAAAGTAA
Found at i:1544741 original size:23 final size:23
Alignment explanation
Indices: 1544710--1544813 Score: 118
Period size: 23 Copynumber: 4.5 Consensus size: 23
1544700 AAGTGCTGGG
*
1544710 AAAACAGTAAGCACACACAATGC
1 AAAACAGTAAGCACACACAGTGC
* *
1544733 AAAATAGTAAACACACACAGTGC
1 AAAACAGTAAGCACACACAGTGC
* * * *
1544756 AAATCAATAAGCACATATAGTGC
1 AAAACAGTAAGCACACACAGTGC
**
1544779 TGAACAGTAAGCACACACAGTGC
1 AAAACAGTAAGCACACACAGTGC
*
1544802 TAAACAGTAAGC
1 AAAACAGTAAGC
1544814 GCGCTAATGT
Statistics
Matches: 65, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.14
Consensus pattern (23 bp):
AAAACAGTAAGCACACACAGTGC
Found at i:1548811 original size:20 final size:21
Alignment explanation
Indices: 1548760--1548811 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
1548750 GATAATATTT
1548760 TTTATATTTTATATATTACATA
1 TTTA-ATTTTATATATTACATA
* *
1548782 TTT-ATATTATATATT-GATA
1 TTTAATTTTATATATTACATA
1548801 TTTAATTTTAT
1 TTTAATTTTAT
1548812 TGTTTAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 6 0.23
20 17 0.65
22 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTAATTTTATATATTACATA
Found at i:1549342 original size:23 final size:22
Alignment explanation
Indices: 1549297--1549350 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
1549287 AAAAAATTTA
*
1549297 ATAAATAAAAAGATATAAAAAT
1 ATAAATAATAAGATATAAAAAT
*
1549319 ATTAAATAATAAG-TTTAAATAAT
1 A-TAAATAATAAGATATAAA-AAT
1549342 ATAAATAAT
1 ATAAATAAT
1549351 TTTAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
ATAAATAATAAGATATAAAAAT
Found at i:1551112 original size:17 final size:19
Alignment explanation
Indices: 1551082--1551119 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1551072 AATATTTTTT
*
1551082 AATTTAATTTAATATT-TA
1 AATTTAATTCAATATTATA
1551100 AATTT-ATTCAATATTATA
1 AATTTAATTCAATATTATA
1551118 AA
1 AA
1551120 AATTTGGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTTAATTCAATATTATA
Found at i:1551243 original size:29 final size:28
Alignment explanation
Indices: 1551188--1551243 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
1551178 TTTTAAAAAA
* *
1551188 AATTATATTAAAAATAGATATTGAAATG
1 AATTATATAAAAAATAAATATTGAAATG
1551216 AATTAATATAAAAAATTAAATATT-AAAT
1 AATT-ATATAAAAAA-TAAATATTGAAAT
1551244 TAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 13 0.54
30 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (28 bp):
AATTATATAAAAAATAAATATTGAAATG
Found at i:1551986 original size:3 final size:3
Alignment explanation
Indices: 1551978--1552011 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1551968 CAACATGCAT
*
1551978 ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1552012 AGAAACCACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1566382 original size:20 final size:21
Alignment explanation
Indices: 1566343--1566383 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1566333 TCAAATTTAG
*
1566343 AATTTTAATATTAGTTATTTT
1 AATTTTAATATTAATTATTTT
*
1566364 AATTTTGAT-TTAATTATTTT
1 AATTTTAATATTAATTATTTT
1566384 CATTAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (21 bp):
AATTTTAATATTAATTATTTT
Found at i:1568478 original size:10 final size:10
Alignment explanation
Indices: 1568463--1568530 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 10
1568453 TTTACATCTA
1568463 TAAAAATTAT
1 TAAAAATTAT
*
1568473 TAAAAAATCAT
1 T-AAAAATTAT
*
1568484 TAAAAATATTT
1 TAAAAAT-TAT
*
1568495 ATAAAAATT-G
1 -TAAAAATTAT
1568505 TAAAAA-TAT
1 TAAAAATTAT
*
1568514 TTAAAATTA-
1 TAAAAATTAT
1568523 TAAAAATT
1 TAAAAATT
1568531 TAAATAACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
8 1 0.02
9 18 0.39
10 9 0.20
11 11 0.24
12 7 0.15
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:1568500 original size:11 final size:10
Alignment explanation
Indices: 1568463--1568519 Score: 55
Period size: 10 Copynumber: 5.5 Consensus size: 10
1568453 TTTACATCTA
1568463 TAAAAATTATT
1 TAAAAA-TATT
*
1568474 AAAAAATCA-T
1 TAAAAAT-ATT
1568484 TAAAAATATT
1 TAAAAATATT
1568494 TATAAAA-ATT
1 TA-AAAATATT
1568504 GTAAAAATATT
1 -TAAAAATATT
1568515 TAAAA
1 TAAAA
1568520 TTATAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 1 0.03
10 23 0.59
11 15 0.38
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
TAAAAATATT
Found at i:1568524 original size:27 final size:27
Alignment explanation
Indices: 1568493--1568573 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 27
1568483 TTAAAAATAT
1568493 TTATAAAAATTGTAAAAATATTTAAAA
1 TTATAAAAATTGTAAAAATATTTAAAA
**
1568520 TTATAAAAATT-TAAATAACTA-AAAAAA
1 TTATAAAAATTGTAAA-AA-TATTTAAAA
1568547 TTA-AAAAA-TGTAAACAAATATTTAAAA
1 TTATAAAAATTGT-AA-AAATATTTAAAA
1568574 ATTAAAACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
25 1 0.02
26 12 0.27
27 28 0.64
28 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
TTATAAAAATTGTAAAAATATTTAAAA
Found at i:1568560 original size:18 final size:17
Alignment explanation
Indices: 1568516--1568580 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
1568506 AAAAATATTT
*
1568516 AAAATTATAAAAATTTAA
1 AAAATTA-AAAAAATTAA
* *
1568534 ATAACTAAAAAAATTAA
1 AAAATTAAAAAAATTAA
*
1568551 AAAATGTAAACAAATATTTA
1 AAAAT-TAAA-AAA-ATTAA
1568571 AAAATTAAAA
1 AAAATTAAAA
1568581 CAAAAATCCA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 12 0.32
18 10 0.26
19 7 0.18
20 9 0.24
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.28
Consensus pattern (17 bp):
AAAATTAAAAAAATTAA
Found at i:1579794 original size:141 final size:142
Alignment explanation
Indices: 1579508--1580077 Score: 1099
Period size: 143 Copynumber: 4.0 Consensus size: 142
1579498 TATATTTAAA
1579508 TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
1 TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
1579573 TTTTTGTTCATATTAGTTTTAGAATTTGACAGTTTTTTTTCATTTTTAATTGTGTGATGGCATGT
66 TTTTTGTTCATATTAGTTTTAGAATTTGACAG-TTTTTTTCATTTTTAATTGTGTGATGGCATGT
1579638 CATTATGAGATTG
130 CATTATGAGATTG
1579651 TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
1 TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
1579716 TTTTTGTTCATATTAGTTTTAGAATTTGACAG-TTTTTTCATTTTTAATTGTGTGATGGCATGTC
66 TTTTTGTTCATATTAGTTTTAGAATTTGACAGTTTTTTTCATTTTTAATTGTGTGATGGCATGTC
1579780 ATTATGAGATTG
131 ATTATGAGATTG
1579792 TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
1 TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
1579857 TTTTTGTTCATATTAGTTTTAGAATTTGACAGTTTTTTTTCATTTTTAATTGTGTGATGGCATGT
66 TTTTTGTTCATATTAGTTTTAGAATTTGACAG-TTTTTTTCATTTTTAATTGTGTGATGGCATGT
1579922 CATTATGAGATTG
130 CATTATGAGATTG
1579935 TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
1 TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
*
1580000 TTTTTGTTCATATTAGTTTTAGAACTTGACAG-TTTTTTCATTTTTAATTGTGTGATGGCATGTC
66 TTTTTGTTCATATTAGTTTTAGAATTTGACAGTTTTTTTCATTTTTAATTGTGTGATGGCATGTC
1580064 ATTATGAGATTG
131 ATTATGAGATTG
1580076 TA
1 TA
1580078 CCACGCCGTT
Statistics
Matches: 424, Mismatches: 1, Indels: 6
0.98 0.00 0.01
Matches are distributed among these distances:
141 187 0.44
143 237 0.56
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.48
Consensus pattern (142 bp):
TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
TTTTTGTTCATATTAGTTTTAGAATTTGACAGTTTTTTTCATTTTTAATTGTGTGATGGCATGTC
ATTATGAGATTG
Found at i:1580018 original size:284 final size:284
Alignment explanation
Indices: 1579508--1580077 Score: 1131
Period size: 284 Copynumber: 2.0 Consensus size: 284
1579498 TATATTTAAA
1579508 TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
1 TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
1579573 TTTTTGTTCATATTAGTTTTAGAATTTGACAGTTTTTTTTCATTTTTAATTGTGTGATGGCATGT
66 TTTTTGTTCATATTAGTTTTAGAATTTGACAGTTTTTTTTCATTTTTAATTGTGTGATGGCATGT
1579638 CATTATGAGATTGTAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACT
131 CATTATGAGATTGTAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACT
*
1579703 TTAGTATCTATTTTTTTTGTTCATATTAGTTTTAGAATTTGACAGTTTTTTCATTTTTAATTGTG
196 TTAGTATCTATTTTTTTTGTTCATATTAGTTTTAGAACTTGACAGTTTTTTCATTTTTAATTGTG
1579768 TGATGGCATGTCATTATGAGATTG
261 TGATGGCATGTCATTATGAGATTG
1579792 TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
1 TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
1579857 TTTTTGTTCATATTAGTTTTAGAATTTGACAGTTTTTTTTCATTTTTAATTGTGTGATGGCATGT
66 TTTTTGTTCATATTAGTTTTAGAATTTGACAGTTTTTTTTCATTTTTAATTGTGTGATGGCATGT
1579922 CATTATGAGATTGTAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACT
131 CATTATGAGATTGTAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACT
1579987 TTAGTATCTATTTTTTTTGTTCATATTAGTTTTAGAACTTGACAGTTTTTTCATTTTTAATTGTG
196 TTAGTATCTATTTTTTTTGTTCATATTAGTTTTAGAACTTGACAGTTTTTTCATTTTTAATTGTG
1580052 TGATGGCATGTCATTATGAGATTG
261 TGATGGCATGTCATTATGAGATTG
1580076 TA
1 TA
1580078 CCACGCCGTT
Statistics
Matches: 285, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
284 285 1.00
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.48
Consensus pattern (284 bp):
TAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACTTTAGTATCTATTT
TTTTTGTTCATATTAGTTTTAGAATTTGACAGTTTTTTTTCATTTTTAATTGTGTGATGGCATGT
CATTATGAGATTGTAAATGTAAAAAAAATAATATTTAACCTTTAAATTTGACGAAAATTTTCACT
TTAGTATCTATTTTTTTTGTTCATATTAGTTTTAGAACTTGACAGTTTTTTCATTTTTAATTGTG
TGATGGCATGTCATTATGAGATTG
Found at i:1582102 original size:26 final size:25
Alignment explanation
Indices: 1582073--1582135 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 25
1582063 TCAATAAATA
1582073 AAAAATATATAAAATTATTAAATA-TT
1 AAAAATATATAAAA-TA-TAAATATTT
*
1582099 -AAAATA-ATATAATATAAATATTT
1 AAAAATATATAAAATATAAATATTT
* *
1582122 AAAAAAATAAAAAA
1 AAAAATATATAAAA
1582136 ATATGAGCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
22 6 0.20
23 4 0.13
24 10 0.33
25 10 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (25 bp):
AAAAATATATAAAATATAAATATTT
Found at i:1584872 original size:21 final size:21
Alignment explanation
Indices: 1584829--1584878 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1584819 GTGTGTGGAC
**
1584829 TAATTATTTTAAAAATACTATT
1 TAATT-TTTTAAAAATAAAATT
*
1584851 TAATTTTTTTAAAATAAAATT
1 TAATTTTTTAAAAATAAAATT
1584872 T-ATTTTT
1 TAATTTTT
1584879 GTTGAATGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.24
21 14 0.56
22 5 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATTTTTTAAAAATAAAATT
Found at i:1591536 original size:30 final size:32
Alignment explanation
Indices: 1591493--1591555 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
1591483 ATTGAGTTCG
*
1591493 ATTAAATTTTTA-TTTTAACTTTTTTCTCTTA
1 ATTAAATTTTTATTTTTAACTTTTTTCACTTA
*
1591524 ATTAAA-TTTTATTTTTAAGTTTTTTCACTTA
1 ATTAAATTTTTATTTTTAACTTTTTTCACTTA
1591555 A
1 A
1591556 ATTCTAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (32 bp):
ATTAAATTTTTATTTTTAACTTTTTTCACTTA
Found at i:1593390 original size:22 final size:23
Alignment explanation
Indices: 1593365--1593408 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1593355 TACCATGCTG
1593365 AAATTACAATG-TCAAATTAAAT
1 AAATTACAATGATCAAATTAAAT
*
1593387 AAATTATAATGACTCAAATTAA
1 AAATTACAATGA-TCAAATTAA
1593409 TATTTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
24 9 0.47
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.32
Consensus pattern (23 bp):
AAATTACAATGATCAAATTAAAT
Found at i:1594981 original size:25 final size:24
Alignment explanation
Indices: 1594948--1594994 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
1594938 AATGATATGA
*
1594948 GTATTTTC-ATTTTATTTTTTTTCC
1 GTATTTTCAACTTT-TTTTTTTTCC
1594972 GTATGTTTCAACTTTTTTTTTTT
1 GTAT-TTTCAACTTTTTTTTTTT
1594995 AAATGGCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 12 0.60
26 4 0.20
ACGTcount: A:0.13, C:0.11, G:0.06, T:0.70
Consensus pattern (24 bp):
GTATTTTCAACTTTTTTTTTTTCC
Found at i:1601787 original size:38 final size:38
Alignment explanation
Indices: 1601706--1601797 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 38
1601696 ATCTTGGATT
*
1601706 TTTTTATAATTTTTAAATATTTGTTTACATTTTTTAATT
1 TTTTTATAATTTTTAAATA-TTGTTTACATTTTTTAATA
1601745 TTTTTATAA-TTTTAAATA-T-TTTACAATTTTTATAGATA
1 TTTTTATAATTTTTAAATATTGTTTAC-ATTTTT-TA-ATA
*
1601783 TTTTTAATGATTTTT
1 TTTTT-ATAATTTTT
1601798 TTAACAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
35 5 0.11
36 7 0.15
37 2 0.04
38 16 0.35
39 12 0.26
40 4 0.09
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.64
Consensus pattern (38 bp):
TTTTTATAATTTTTAAATATTGTTTACATTTTTTAATA
Found at i:1601787 original size:39 final size:37
Alignment explanation
Indices: 1601703--1601776 Score: 107
Period size: 35 Copynumber: 2.0 Consensus size: 37
1601693 TGTATCTTGG
1601703 ATTTTTTTATAATTTTTAAATATTTGTTTACATTTTTTA
1 ATTTTTTTATAA-TTTTAAATA-TTGTTTACATTTTTTA
*
1601742 ATTTTTTTATAATTTTAAATA-T-TTTACAATTTTTA
1 ATTTTTTTATAATTTTAAATATTGTTTACATTTTTTA
1601777 TAGATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
35 12 0.35
36 1 0.03
38 9 0.26
39 12 0.35
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (37 bp):
ATTTTTTTATAATTTTAAATATTGTTTACATTTTTTA
Found at i:1601817 original size:9 final size:9
Alignment explanation
Indices: 1601705--1601818 Score: 61
Period size: 10 Copynumber: 11.7 Consensus size: 9
1601695 TATCTTGGAT
1601705 TTTTTTATAA
1 TTTTTTA-AA
*
1601715 TTTTTAAATA
1 TTTTTTAA-A
*
1601725 TTTGTTTACA
1 TTT-TTTAAA
*
1601735 TTTTTTAAT
1 TTTTTTAAA
1601744 TTTTTTATAA
1 TTTTTTA-AA
1601754 --TTTTAAA
1 TTTTTTAAA
*
1601761 TATTTTACAA
1 TTTTTTA-AA
*
1601771 TTTTTATAGA
1 TTTTT-TAAA
1601781 TATTTTTAATGA
1 T-TTTTTAA--A
1601793 TTTTTTTAACA
1 -TTTTTTAA-A
*
1601804 ATTTTTAAA
1 TTTTTTAAA
1601813 TTTTTT
1 TTTTTT
1601819 TGGTTCGTGG
Statistics
Matches: 81, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
7 2 0.02
8 5 0.06
9 23 0.28
10 32 0.40
11 10 0.12
12 8 0.10
13 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:1617323 original size:11 final size:11
Alignment explanation
Indices: 1617307--1617336 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1617297 TTATACTTAA
1617307 GATGAAAATGG
1 GATGAAAATGG
1617318 GATGAAAATGG
1 GATGAAAATGG
*
1617329 AATGAAAA
1 GATGAAAA
1617337 GTTTGATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (11 bp):
GATGAAAATGG
Found at i:1619083 original size:3 final size:3
Alignment explanation
Indices: 1619075--1619121 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1619065 TCCTATGAAG
1619075 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1619122 TGATGTTCAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1625882 original size:189 final size:191
Alignment explanation
Indices: 1625557--1625943 Score: 555
Period size: 189 Copynumber: 2.0 Consensus size: 191
1625547 GGATACCGAC
* ** * *
1625557 TTCTGGTCATGCCTTGTGTGACCGACAACGAGGATGAATTTTGATGTTTCCGGTATGATCATGTT
1 TTCTGGTCATGCCTTATGTGACCG---A-GAGGATGAATTTCAATGTTTCCGATATGAGCATGTT
* * * * * *
1625622 CGCGAGGGCTTAATTTAAGCGCTCGTGAATATGATCGTTTCAGTTTCATGCTTAGAAAACCAGAG
62 AGCGAGGGCTTAATTTAAGCACTCGTGAATATGATCATATCAGTTTCATACTTAGAAAACAAGAG
* *
1625687 GAATCATTAC-AATTAATTGAATGAACAGAGTTTGAACAAGCTAGAACTAGTGAACT-AGACTGA
127 GAATCATGACAAATT-ATTAAATGAACAGAGTTTGAACAAGCTAGAACTAGTGAACTGAGACTGA
1625750 T
191 T
1625751 TTCTGGTCATGCCTTATGTGACCG-GAGGATGAATTTCAATGTTTCCGATATGAGCATGTTAGCG
1 TTCTGGTCATGCCTTATGTGACCGAGAGGATGAATTTCAATGTTTCCGATATGAGCATGTTAGCG
* *
1625815 AGGGCTTAATTTAAGCATTCTTGAATATGATCATATCAGTTTCATACTTAGAAAACAAGAGGAAT
66 AGGGCTTAATTTAAGCACTCGTGAATATGATCATATCAGTTTCATACTTAGAAAACAAGAGGAAT
* *
1625880 CATGACAAATTGTTAAATGAATAGAGTTTGAACAAGCTAGAACTAGTGAACTGAGACTGAT
131 CATGACAAATTATTAAATGAACAGAGTTTGAACAAGCTAGAACTAGTGAACTGAGACTGAT
1625941 TTC
1 TTC
1625944 CCATTCCGCC
Statistics
Matches: 174, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
189 136 0.78
190 15 0.09
194 23 0.13
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (191 bp):
TTCTGGTCATGCCTTATGTGACCGAGAGGATGAATTTCAATGTTTCCGATATGAGCATGTTAGCG
AGGGCTTAATTTAAGCACTCGTGAATATGATCATATCAGTTTCATACTTAGAAAACAAGAGGAAT
CATGACAAATTATTAAATGAACAGAGTTTGAACAAGCTAGAACTAGTGAACTGAGACTGAT
Found at i:1629139 original size:13 final size:12
Alignment explanation
Indices: 1629111--1629155 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
1629101 AAACTTTTCA
*
1629111 AAAAGTACTTTT
1 AAAAGCACTTTT
1629123 AAAAGCACTTTT
1 AAAAGCACTTTT
*
1629135 GAAAAGCACTTCTC
1 -AAAAGCACTT-TT
1629149 AAAAGCA
1 AAAAGCA
1629156 ATGCTAGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.38
13 17 0.59
14 1 0.03
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (12 bp):
AAAAGCACTTTT
Found at i:1632225 original size:7 final size:7
Alignment explanation
Indices: 1632213--1632240 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1632203 AAAAACATTC
1632213 GGGACAA
1 GGGACAA
1632220 GGGACAA
1 GGGACAA
1632227 GGGACAA
1 GGGACAA
1632234 GGGACAA
1 GGGACAA
1632241 AGCATATGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.43, T:0.00
Consensus pattern (7 bp):
GGGACAA
Found at i:1643027 original size:115 final size:116
Alignment explanation
Indices: 1642900--1643164 Score: 354
Period size: 115 Copynumber: 2.3 Consensus size: 116
1642890 TTAGACTGGT
* * * *
1642900 AGATCACAATACATGAAAGTGTGTAAGTCCATATGGTTGAAGACCCATGACATAATATGATATGC
1 AGATCACGATACATGAAAGTGTATAAGTCCATATGGTTGAAGACCCACGACATAATATGATATGA
** * *
1642965 TGGTATGAATGTTCAT-GTGTAGCCTTT-GATAATGTGTAAATTGAGCTGAC
66 TGAAATGAATGTTCATGGTGTAGCCTTTCG-TAATGTGTAAATCGAACTGAC
* * *
1643015 AGATCATGATACATGAAAGTGTATAAGTCTATGTGGTTGAAGACCCACGACATAATATGATATGA
1 AGATCACGATACATGAAAGTGTATAAGTCCATATGGTTGAAGACCCACGACATAATATGATATGA
* * *
1643080 TGAAATGAATGTTCATGGTGTATCCTTTCGTAATGTGTAGATCGAACTGGC
66 TGAAATGAATGTTCATGGTGTAGCCTTTCGTAATGTGTAAATCGAACTGAC
*
1643131 AGATCACGATACATGAAATTATGTATAAGTCCAT
1 AGATCACGATACATGAAA--GTGTATAAGTCCAT
1643165 GAGGAAGAAA
Statistics
Matches: 129, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
115 72 0.56
116 44 0.34
117 1 0.01
118 12 0.09
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (116 bp):
AGATCACGATACATGAAAGTGTATAAGTCCATATGGTTGAAGACCCACGACATAATATGATATGA
TGAAATGAATGTTCATGGTGTAGCCTTTCGTAATGTGTAAATCGAACTGAC
Found at i:1643297 original size:25 final size:25
Alignment explanation
Indices: 1643219--1643283 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
1643209 GTAACACGTG
*
1643219 ATTCTGTATGTCGCCTTTGTGGAGA
1 ATTCTGTATGTTGCCTTTGTGGAGA
* * *
1643244 ATTCTGTATGTTGTCTTTGTGGTGC
1 ATTCTGTATGTTGCCTTTGTGGAGA
1643269 ATTCTGTATGTTGCC
1 ATTCTGTATGTTGCC
1643284 CTTATGGCGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.12, C:0.15, G:0.26, T:0.46
Consensus pattern (25 bp):
ATTCTGTATGTTGCCTTTGTGGAGA
Found at i:1649526 original size:10 final size:10
Alignment explanation
Indices: 1649513--1649553 Score: 66
Period size: 10 Copynumber: 4.2 Consensus size: 10
1649503 ATAAATAATT
1649513 AAAAATTATA
1 AAAAATTATA
*
1649523 AAAAATAATA
1 AAAAATTATA
1649533 AAAAATTA-A
1 AAAAATTATA
1649542 AAAAATTATA
1 AAAAATTATA
1649552 AA
1 AA
1649554 TAGTTTAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATTATA
Found at i:1649530 original size:20 final size:20
Alignment explanation
Indices: 1649500--1649553 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1649490 CAACAATAAT
*
1649500 TAAATAAATAATTAAAAATTA
1 TAAA-AAATAATAAAAAATTA
1649521 TAAAAAATAATAAAAAATTA
1 TAAAAAATAATAAAAAATTA
*
1649541 -AAAAAATTATAAA
1 TAAAAAATAATAAA
1649554 TAGTTTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 12 0.39
20 15 0.48
21 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAAAATAATAAAAAATTA
Found at i:1652357 original size:25 final size:24
Alignment explanation
Indices: 1652329--1652394 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 24
1652319 GGTTGAAATT
1652329 AAATTGTATATTTTTATAATAATAA
1 AAATT-TATATTTTTATAATAATAA
* * **
1652354 AAATAT-TA-TTTTATTATTTTAA
1 AAATTTATATTTTTATAATAATAA
*
1652376 TAATTTATATTTTTATAAT
1 AAATTTATATTTTTATAAT
1652395 TTTTAAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
22 15 0.47
23 4 0.12
24 9 0.28
25 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
AAATTTATATTTTTATAATAATAA
Found at i:1652388 original size:15 final size:16
Alignment explanation
Indices: 1652363--1652396 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1652353 AAAATATTAT
1652363 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
1652379 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
1652394 TTT
1 TTT
1652397 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:1652420 original size:46 final size:47
Alignment explanation
Indices: 1652330--1652420 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 47
1652320 GTTGAAATTA
* *
1652330 AATTGTATATTTTTATAATAATAAAAATATTATTTTATTATTTTAAT
1 AATTGTATATTTTTATAATAATAAAAATATTAATTAATTATTTTAAT
**
1652377 AATT-TATATTTTTATAATTTTTAAAAA-ATTAAATTAATT-TTTTA
1 AATTGTATATTTTTATAA-TAATAAAAATATT-AATTAATTATTTTA
1652421 TTATTTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
46 21 0.55
47 17 0.45
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (47 bp):
AATTGTATATTTTTATAATAATAAAAATATTAATTAATTATTTTAAT
Found at i:1652449 original size:31 final size:29
Alignment explanation
Indices: 1652385--1652460 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
1652375 ATAATTTATA
* *
1652385 TTTTTATAATTTTTAAAAAATTAAATTAAT
1 TTTTTATTATTTTT-AAAAATAAAATTAAT
*
1652415 TTTTTATTATTTTTAAAAGTCAAAATATAAT
1 TTTTTATTATTTTTAAAAAT-AAAAT-TAAT
*
1652446 TTTTT-TTATTATTAA
1 TTTTTATTATTTTTAA
1652461 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 5 0.12
30 26 0.65
31 9 0.22
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (29 bp):
TTTTTATTATTTTTAAAAATAAAATTAAT
Found at i:1654164 original size:25 final size:24
Alignment explanation
Indices: 1654117--1654164 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1654107 AGACATGACT
*
1654117 TATATGATATAAAGTAGTTACAAA
1 TATATGAAATAAAGTAGTTACAAA
1654141 TATATGAAATTAAAGT-GTTGACAA
1 TATATGAAA-TAAAGTAGTT-ACAA
1654165 CAATGCACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (24 bp):
TATATGAAATAAAGTAGTTACAAA
Found at i:1654342 original size:3 final size:3
Alignment explanation
Indices: 1654334--1654370 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1654324 CTTCTATTCC
1654334 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 A
1654371 ACATCTTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1658011 original size:13 final size:13
Alignment explanation
Indices: 1657993--1658057 Score: 78
Period size: 13 Copynumber: 5.1 Consensus size: 13
1657983 CTTAAACTAA
*
1657993 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
**
1658006 ACTTTTCAAAATT
1 ACTTTTCAAAAGC
1658019 ACTTTTCAAAA-C
1 ACTTTTCAAAAGC
*
1658031 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
*
1658044 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
1658057 A
1 A
1658058 ATACTAAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.22
13 36 0.78
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:1658047 original size:25 final size:26
Alignment explanation
Indices: 1657993--1658057 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
1657983 CTTAAACTAA
* **
1657993 ACTTTTCAAAAGTACTTTTCAAAATT
1 ACTTTTCAAAAGCACTTTTCAAAAGC
*
1658019 ACTTTTCAAAA-CACTTTTTAAAAGC
1 ACTTTTCAAAAGCACTTTTCAAAAGC
*
1658044 ACTTCTCAAAAGCA
1 ACTTTTCAAAAGCA
1658058 ATACTAAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 20 0.61
26 13 0.39
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (26 bp):
ACTTTTCAAAAGCACTTTTCAAAAGC
Found at i:1661817 original size:15 final size:15
Alignment explanation
Indices: 1661797--1661849 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1661787 CTTTAATTTG
1661797 ATATTTTTAATCATT
1 ATATTTTTAATCATT
1661812 ATATTTTTAA--ATT
1 ATATTTTTAATCATT
* *
1661825 ATCAATTTTAATCCTAT
1 AT-ATTTTTAATCAT-T
1661842 ATATTTTT
1 ATATTTTT
1661850 TTTAAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
15 10 0.32
16 6 0.19
17 3 0.10
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTTTTAATCATT
Found at i:1662596 original size:31 final size:28
Alignment explanation
Indices: 1662561--1662626 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
1662551 CTAATTTTAT
* *
1662561 ATTTTTTATATTTATCACATTGGTCCATATA
1 ATTTTTAATA-TTATCA-ATTGGTACAT-TA
* *
1662592 ATTTTAAATATTATTAATTGGTACATTA
1 ATTTTTAATATTATCAATTGGTACATTA
1662620 ATTTTTA
1 ATTTTTA
1662627 TAGTGGTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 8 0.27
29 9 0.30
30 5 0.17
31 8 0.27
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (28 bp):
ATTTTTAATATTATCAATTGGTACATTA
Found at i:1663068 original size:20 final size:20
Alignment explanation
Indices: 1663003--1663076 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 20
1662993 TGAAAATATT
*
1663003 TTTTAAAATATTTATAA-AA
1 TTTTAAAAAATTTATAATAA
* * *
1663022 ATTTCAAAAA-TTAT-ATAT
1 TTTTAAAAAATTTATAATAA
* *
1663040 TTTTTAAAAATATATAATAA
1 TTTTAAAAAATTTATAATAA
1663060 TTTTAAAAAATTTATAA
1 TTTTAAAAAATTTATAA
1663077 AGAATATATA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
17 1 0.02
18 13 0.31
19 10 0.24
20 18 0.43
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTAAAAAATTTATAATAA
Found at i:1673518 original size:56 final size:56
Alignment explanation
Indices: 1673430--1673612 Score: 201
Period size: 56 Copynumber: 3.2 Consensus size: 56
1673420 TACGAATAAA
* *
1673430 AAAAATATTTTTTTTGGGTGTTTGCCACCCAATGACCTACA-TCATATTTTTT-AAATTT
1 AAAAATA--TTTTTTGAGTGTTTGCCATCCAATGACCTACACT-AT-TTTTTTCAAATTT
*
1673488 AAAAATATTTTTTGAGTGTTTGCCATCCAATGGCCTACACTATTTTTTTCAAATTT
1 AAAAATATTTTTTGAGTGTTTGCCATCCAATGACCTACACTATTTTTTTCAAATTT
* * * * ** * *
1673544 AAAAATATTTTTTTAATGTTTGTCATCCAAT-AGTCTACACTACCTTTTTCAGATGT
1 AAAAATATTTTTTGAGTGTTTGCCATCCAATGA-CCTACACTATTTTTTTCAAATTT
1673600 AAAAATATTTTTT
1 AAAAATATTTTTT
1673613 TTGGATGTTT
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
55 6 0.05
56 96 0.87
57 1 0.01
58 7 0.06
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (56 bp):
AAAAATATTTTTTGAGTGTTTGCCATCCAATGACCTACACTATTTTTTTCAAATTT
Found at i:1673628 original size:58 final size:56
Alignment explanation
Indices: 1673476--1673640 Score: 188
Period size: 56 Copynumber: 2.9 Consensus size: 56
1673466 CTACATCATA
* * * * **
1673476 TTTTTTAAATTTAAAAATA-TTTTTTGAGTGTTTGCCATCCAATGGCCTACACTATT
1 TTTTTCAAATGTAAAAATATTTTTTTGA-TGTTTGTCATCCAATAGCCTACACTACC
* * *
1673532 TTTTTCAAATTTAAAAATATTTTTTTAATGTTTGTCATCCAATAGTCTACACTACC
1 TTTTTCAAATGTAAAAATATTTTTTTGATGTTTGTCATCCAATAGCCTACACTACC
* * *
1673588 TTTTTCAGATGTAAAAATATTTTTTTTGGATGTTTATCATCCAATAACCTACA
1 TTTTTCAAATGTAAAAATA-TTTTTTT-GATGTTTGTCATCCAATAGCCTACA
1673641 TCACATCTCC
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
56 58 0.62
57 14 0.15
58 21 0.23
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (56 bp):
TTTTTCAAATGTAAAAATATTTTTTTGATGTTTGTCATCCAATAGCCTACACTACC
Found at i:1673946 original size:57 final size:56
Alignment explanation
Indices: 1673863--1674218 Score: 416
Period size: 57 Copynumber: 6.3 Consensus size: 56
1673853 GTCAAATACT
* * *
1673863 CAAAAAAATATTTTTAAATTTGAAAAAAATGGTGTAAGTCATTAGGTGTCAAACAC
1 CAAAAAAATATTTTTAAATTTGAAAAAAGTGGTGTAAGCCATTAGGTGACAAACAC
* * * **
1673919 CCAAAAAATATTTTTAAATCTGAAAAAAAGTGGTGTAAGCCATTGGGTGGTAAACAC
1 CAAAAAAATATTTTTAAATTTG-AAAAAAGTGGTGTAAGCCATTAGGTGACAAACAC
* * *
1673976 TCAAAAAAATATTTTTAAATTTGAAAAATA-TGGTGTAGGCCATT-GGATGGCAAACAAT
1 -CAAAAAAATATTTTTAAATTTGAAAAA-AGTGGTGTAAGCCATTAGG-TGACAAAC-AC
* **
1674034 CAAAAAAATATTTTTAAATTT-AAAAAAGGTGATGTAAATCATTAGGTGACAAACAC
1 CAAAAAAATATTTTTAAATTTGAAAAAA-GTGGTGTAAGCCATTAGGTGACAAACAC
* * *
1674090 TCAAAAAAAATATTTTTAAATTTGAAAAATGTGGTGTAGGCCATTAGGTGGCAAACACC
1 -C-AAAAAAATATTTTTAAATTTGAAAAAAGTGGTGTAAGCCATTAGGTGACAAACA-C
* *
1674149 CAAAAAAATATTTTTAAATCTG-AAAAAGTGGTGTATGCCATT-GGATGACAAACAC
1 CAAAAAAATATTTTTAAATTTGAAAAAAGTGGTGTAAGCCATTAGG-TGACAAACAC
1674204 CAAAAAAATATTTTT
1 CAAAAAAATATTTTT
1674219 GGGACATGAA
Statistics
Matches: 259, Mismatches: 28, Indels: 27
0.82 0.09 0.09
Matches are distributed among these distances:
55 19 0.07
56 54 0.21
57 113 0.44
58 67 0.26
59 6 0.02
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (56 bp):
CAAAAAAATATTTTTAAATTTGAAAAAAGTGGTGTAAGCCATTAGGTGACAAACAC
Found at i:1673987 original size:114 final size:114
Alignment explanation
Indices: 1673855--1674218 Score: 495
Period size: 114 Copynumber: 3.2 Consensus size: 114
1673845 TGGTGTATGT
* * * * *
1673855 CAAATACTCAAAAAAATATTTTTAAATTTGAAAAAAATGGTGTAAGTCATTAGGTGTCAAACACC
1 CAAACACTCAAAAAAATATTTTTAAATTTGAAAAATATGGTGTAGGCCATTAGGTGGCAAACACC
*
1673920 CAAAAAATATTTTTAAATCTGAAAAAAAGTGGTGTAAGCCATTGGGTGG
66 CAAAAAATATTTTTAAATCTGAAAAAAAGTGGTGTAAGCCATTGGGTGA
*
1673969 TAAACACTCAAAAAAATATTTTTAAATTTGAAAAATATGGTGTAGGCCATT-GGATGGCAAACAA
1 CAAACACTCAAAAAAATATTTTTAAATTTGAAAAATATGGTGTAGGCCATTAGG-TGGCAAAC-A
* * * * * ** *
1674033 TCAAAAAAATATTTTTAAAT-TTAAAAAAGGTGATGTAAATCATTAGGTGA
64 CCCAAAAAATATTTTTAAATCTGAAAAAAAGTGGTGTAAGCCATTGGGTGA
*
1674083 CAAACACTCAAAAAAAATATTTTTAAATTTGAAAAATGTGGTGTAGGCCATTAGGTGGCAAACAC
1 CAAACACTC-AAAAAAATATTTTTAAATTTGAAAAATATGGTGTAGGCCATTAGGTGGCAAACAC
* *
1674148 CCAAAAAAATATTTTTAAATCTG--AAAAAGTGGTGTATGCCATTGGATGA
65 CC-AAAAAATATTTTTAAATCTGAAAAAAAGTGGTGTAAGCCATTGGGTGA
1674197 CAAACAC-CAAAAAAATATTTTT
1 CAAACACTCAAAAAAATATTTTT
1674219 GGGACATGAA
Statistics
Matches: 217, Mismatches: 27, Indels: 14
0.84 0.10 0.05
Matches are distributed among these distances:
112 14 0.06
113 3 0.01
114 112 0.52
115 85 0.39
116 3 0.01
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (114 bp):
CAAACACTCAAAAAAATATTTTTAAATTTGAAAAATATGGTGTAGGCCATTAGGTGGCAAACACC
CAAAAAATATTTTTAAATCTGAAAAAAAGTGGTGTAAGCCATTGGGTGA
Found at i:1675340 original size:31 final size:31
Alignment explanation
Indices: 1675277--1675343 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1675267 AATAGATTAG
* * *
1675277 TGACTTAAATAAAAACTTTTGAATAGTTCAA
1 TGACTTAAATAAAAACTTTTGAACAATACAA
*
1675308 TGACTTAAATGAAAACTTTTGAACAATACAA
1 TGACTTAAATAAAAACTTTTGAACAATACAA
1675339 TGACT
1 TGACT
1675344 ATTTTGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAACAATACAA
Found at i:1680744 original size:29 final size:29
Alignment explanation
Indices: 1680682--1680744 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
1680672 GAAAATAACG
* * *
1680682 CAGAGTGGCACCGAAGTGCAATAACAGAG
1 CAGAGTGGCAACGAAGTGCAATAACAAAA
* *
1680711 CAGAGTGGCAACGAAGTGCATTAATAAAA
1 CAGAGTGGCAACGAAGTGCAATAACAAAA
*
1680740 TAGAG
1 CAGAG
1680745 AGTGCTCTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (29 bp):
CAGAGTGGCAACGAAGTGCAATAACAAAA
Found at i:1697001 original size:2 final size:2
Alignment explanation
Indices: 1696994--1697028 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
1696984 TCTAAATAGT
1696994 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
1697029 AAAATAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1705952 original size:25 final size:23
Alignment explanation
Indices: 1705924--1705969 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1705914 TCTTTCTGTC
1705924 GAGATCAAGGATGTACTTTTTTTAG
1 GAGATCAA-GAT-TACTTTTTTTAG
* *
1705949 GAGATGAAGATTCCTTTTTTT
1 GAGATCAAGATTACTTTTTTT
1705970 TTTATCAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 3 0.16
25 7 0.37
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (23 bp):
GAGATCAAGATTACTTTTTTTAG
Found at i:1712071 original size:48 final size:48
Alignment explanation
Indices: 1711677--1712097 Score: 481
Period size: 48 Copynumber: 8.8 Consensus size: 48
1711667 CAGCCGCAGT
* * *
1711677 ACCAGGCACT-CCAATAGGAGCACCAACTCCAAGTGCAC--CGGCTGCAAC
1 ACCAGGCA-TGCCAATAGGAGCACCACCTCC-TG-GCACAGCAGCTGCAAC
* **
1711725 ACAAGGCACACCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAAC
1 ACCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAAC
**
1711773 ACCAGGCACACCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAAC
1 ACCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAAC
**
1711821 ACCAGGCACACCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAAC
1 ACCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAAC
** * ** * *
1711869 ACCAGGCACACCAGTAGGAGCACCACCTCCTGGTGCACCAACTGCAAC
1 ACCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAAC
* *
1711917 ACCCGGCATGGCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAAC
1 ACCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAAC
* * * * *
1711965 ACCAGGCATGGCAATAGGAGCACCATCTCCTGGTACATCAGCTGGAAC
1 ACCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAAC
* * * *
1712013 ACCAGGCATGCCAATAGGAGTACCACCTCCCAGG-ACATCAGTTGCAAC
1 ACCAGGCATGCCAATAGGAGCACCACCT-CCTGGCACAGCAGCTGCAAC
* * * * *
1712061 ACCAGACATGCCAATTGGAGCAACTCCTCCAGGCACA
1 ACCAGGCATGCCAATAGGAGCACCACCTCCTGGCACA
1712098 CCTGTAGAAG
Statistics
Matches: 332, Mismatches: 36, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
46 4 0.01
47 6 0.02
48 318 0.96
49 4 0.01
ACGTcount: A:0.31, C:0.37, G:0.22, T:0.11
Consensus pattern (48 bp):
ACCAGGCATGCCAATAGGAGCACCACCTCCTGGCACAGCAGCTGCAAC
Found at i:1712269 original size:39 final size:39
Alignment explanation
Indices: 1712197--1712291 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
1712187 AGGCATGGCG
*
1712197 ACAGGAGCACCACCTCCAGCAGCAAAGAAAGGCACAACA
1 ACAGGAGCACCACCTCCAGCAGCAAACAAAGGCACAACA
* * **
1712236 ACAGGAGCATCACCTCCAGCAG-AAACATCAGGCATGACA
1 ACAGGAGCACCACCTCCAGCAGCAAACA-AAGGCACAACA
* *
1712275 ACAAGAGCACCAACTCC
1 ACAGGAGCACCACCTCC
1712292 TGATGCACCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 4 0.09
39 43 0.91
ACGTcount: A:0.41, C:0.34, G:0.19, T:0.06
Consensus pattern (39 bp):
ACAGGAGCACCACCTCCAGCAGCAAACAAAGGCACAACA
Found at i:1712371 original size:48 final size:48
Alignment explanation
Indices: 1712279--1712901 Score: 224
Period size: 48 Copynumber: 12.6 Consensus size: 48
1712269 ATGACAACAA
* * * *
1712279 GAGCACCAACTCCTGATGCACCAGATGCAACACCTGGCAAGCCAATAG
1 GAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCAAGCCAATAG
* * * * *
1712327 AAGCACCACCTCCTGGTGCACCAGCTGGAAGACCAGGTACGCCAATAG
1 GAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCAAGCCAATAG
** * * * * *
1712375 GTTCACCACCTCCTGCTGCGCCAGCTGCAACAACAGGCATGCCAGTAG
1 GAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCAAGCCAATAG
* * * * * * * * *
1712423 GAGCACCACCTACTAGTGCACCGGCCAG-AAAACAAAGCATGCCAATTG
1 GAGCACCACCTCCTGGTGCACCAG-CTGCAACACCAGGCAAGCCAATAG
* ** * * * * * *
1712471 AAGCACCATGTCCCGCTGCACCAGATGCAAGACAAGGCTCA-CCAATAG
1 GAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGC-AAGCCAATAG
* *
1712519 GAGCATCAGCAGCAACACCTGGAATGTCAATGGGAGCACCAGCTGCAAC-CTCTGGC-A-CACAG
1 GAGCA-C--CA-C--CTCCT-G---G----T----GCACCAGCTGCAACAC-CAGGCAAGC-CA-
1712581 ATAG
45 ATAG
* * * *
1712585 CAGCATCAACTCCTGGTGCACCAGCTGCAACACC-GAGCACA-TCAATAG
1 GAGCACCACCTCCTGGTGCACCAGCTGCAACACCAG-GCA-AGCCAATAG
* ** * * *
1712633 GAACACCACCTCCTGGTGCACTGGCCGCAACACCAAGCACGCCAATAG
1 GAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCAAGCCAATAG
** * * *
1712681 GAGCACCACCT-CTCAATGCACCAGCTGCAACACTAGGAAAGCCAATTG
1 GAGCACCACCTCCT-GGTGCACCAGCTGCAACACCAGGCAAGCCAATAG
* * * * *
1712729 GAGCACCACTTCCTGGTGCACCAGCTGTAGCATCAGGGACA-CCAATAG
1 GAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCA-AGCCAATAG
* * * ** * * * * *
1712777 GATCATCACCTCATGGTGCAAGAGATGCAAAACCA--CACGCATCTATAC
1 GAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCAAGC--CAATAG
* * * * * * **
1712825 AAGCACCACCTCCTGATGCATCAACTGCAACAACAGGCAAACTGATAG
1 GAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCAAGCCAATAG
* *
1712873 GAGCACCACCTCCTGCTGCACCTGCTGCA
1 GAGCACCACCTCCTGGTGCACCAGCTGCA
1712902 GCAGCAACAG
Statistics
Matches: 407, Mismatches: 130, Indels: 76
0.66 0.21 0.12
Matches are distributed among these distances:
46 2 0.00
47 4 0.01
48 345 0.85
49 9 0.02
50 4 0.01
51 2 0.00
52 1 0.00
54 2 0.00
55 1 0.00
56 1 0.00
59 1 0.00
60 4 0.01
62 1 0.00
63 2 0.00
64 2 0.00
65 3 0.01
66 23 0.06
ACGTcount: A:0.31, C:0.34, G:0.21, T:0.14
Consensus pattern (48 bp):
GAGCACCACCTCCTGGTGCACCAGCTGCAACACCAGGCAAGCCAATAG
Found at i:1724136 original size:14 final size:16
Alignment explanation
Indices: 1724119--1724150 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1724109 CATTTTTAAT
1724119 TAAA-AATTTAA-ATA
1 TAAACAATTTAATATA
1724133 TAAACAATTTAATATA
1 TAAACAATTTAATATA
1724149 TA
1 TA
1724151 TATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 7 0.44
16 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAACAATTTAATATA
Found at i:1727271 original size:72 final size:72
Alignment explanation
Indices: 1727154--1727302 Score: 237
Period size: 72 Copynumber: 2.1 Consensus size: 72
1727144 ACTTGATCAC
* * *
1727154 ACCACTCAAGTTGTTTGATGACAAATGAAGTTCACGAAGGTTCACAAGATCAAAAATGGAATCTG
1 ACCACTCAAGTTGTTTGATAACAAATCAAGTTCAAGAAGGTTCACAAGATCAAAAATGGAATCTG
*
1727219 GTATTGG
66 GTATTGA
*
1727226 ACCACTCAAGTTGTTTGATAACAAATCAAG-TGAAGTAAGGTTCACAAGATCAAAAATGGAATCT
1 ACCACTCAAGTTGTTTGATAACAAATCAAGTTCAAG-AAGGTTCACAAGATCAAAAATGGAATCT
1727290 GGTATTGA
65 GGTATTGA
1727298 ACCAC
1 ACCAC
1727303 CAATGTTATT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 3 0.04
72 68 0.96
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (72 bp):
ACCACTCAAGTTGTTTGATAACAAATCAAGTTCAAGAAGGTTCACAAGATCAAAAATGGAATCTG
GTATTGA
Found at i:1729448 original size:29 final size:29
Alignment explanation
Indices: 1729406--1729461 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
1729396 AATTTGATTC
*
1729406 TTTTAAAATATTG-ATGATTAAATTTAAAA
1 TTTTAAAATATTGAAAG-TTAAATTTAAAA
1729435 TTTTAAAA-AGTTGAAAGTTAAATTTAA
1 TTTTAAAATA-TTGAAAGTTAAATTTAA
1729462 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 1 0.04
29 21 0.88
30 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (29 bp):
TTTTAAAATATTGAAAGTTAAATTTAAAA
Found at i:1733725 original size:72 final size:72
Alignment explanation
Indices: 1733639--1733859 Score: 354
Period size: 72 Copynumber: 3.1 Consensus size: 72
1733629 ACTTGATCAC
* * * *
1733639 ACCACTCAAGTTGTTTGATGACAAATGAAGCTCACG-AAGGTTCACAAGATCAAAAATGGAATCT
1 ACCACTCAAGTTGTTTGATGACAAATCAAG-TGAAGTAAGGTTCACAAGATCAAAAATGGAATCA
1733703 GGTATTGG
65 GGTATTGG
*
1733711 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATGAAAAATGGAATCAG
1 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCAAAAATGGAATCAG
*
1733776 GTATTGA
66 GTATTGG
* *
1733783 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGCTCAAAAATGGAATCGG
1 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCAAAAATGGAATCAG
1733848 GTATTGG
66 GTATTGG
1733855 ACCAC
1 ACCAC
1733860 CAATGTCATT
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
71 3 0.02
72 135 0.98
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (72 bp):
ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCAAAAATGGAATCAG
GTATTGG
Found at i:1744081 original size:31 final size:31
Alignment explanation
Indices: 1744015--1744086 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
1744005 TTAAAAAATT
* *
1744015 AATTTGACTCTTTTTCAAAAGGTTAAGGGTC
1 AATTTGACTCCTTTTCAAAAGGTTAAGAGTC
* *
1744046 AATTTGACTCCTTTT-AAAATGTTGAGAGTC
1 AATTTGACTCCTTTTCAAAAGGTTAAGAGTC
*
1744076 AAATTTAACTC
1 -AATTTGACTC
1744087 AAAAAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 12 0.34
31 23 0.66
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (31 bp):
AATTTGACTCCTTTTCAAAAGGTTAAGAGTC
Found at i:1744512 original size:16 final size:16
Alignment explanation
Indices: 1744491--1744522 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1744481 ATGCTAATGC
*
1744491 CAATCGAGTTAAGATT
1 CAATCGAATTAAGATT
1744507 CAATCGAATTAAGATT
1 CAATCGAATTAAGATT
1744523 TTTACTATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (16 bp):
CAATCGAATTAAGATT
Found at i:1747356 original size:24 final size:24
Alignment explanation
Indices: 1747328--1747374 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1747318 AAATAATTTA
* *
1747328 AAATAATCAGAGTTTAATTGAAAC
1 AAATAAACAGAGTTTAACTGAAAC
1747352 AAATAAACAGAGTTTAACTGAAA
1 AAATAAACAGAGTTTAACTGAAA
1747375 GATTATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.26
Consensus pattern (24 bp):
AAATAAACAGAGTTTAACTGAAAC
Found at i:1755923 original size:46 final size:46
Alignment explanation
Indices: 1755860--1755954 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
1755850 ATGAAAAATC
* * *
1755860 GAAATCATATATTCTTAAGTACTCTAGAGTGAACATAAGAAGAAAA
1 GAAATCATATATACTTAAGTACTCTAGAGTGAACATAAAAAAAAAA
1755906 GAAATCATATATACTTAAGTACTCTAGAGTGAACATAAAAAAAAAA
1 GAAATCATATATACTTAAGTACTCTAGAGTGAACATAAAAAAAAAA
1755952 GAA
1 GAA
1755955 GTCTTAATTG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.24
Consensus pattern (46 bp):
GAAATCATATATACTTAAGTACTCTAGAGTGAACATAAAAAAAAAA
Found at i:1759820 original size:39 final size:39
Alignment explanation
Indices: 1759771--1759850 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
1759761 AGAACAGGCA
* *
1759771 GTCATTGAATTTATACCAAAGGCCTATCCATCATAACAT
1 GTCATAGAATTTATACCAAAGGCCCATCCATCATAACAT
* ** *
1759810 GTCATAGAATTTATATCGTAGGCCCATGCATCATAACAT
1 GTCATAGAATTTATACCAAAGGCCCATCCATCATAACAT
1759849 GT
1 GT
1759851 TTGCATGTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (39 bp):
GTCATAGAATTTATACCAAAGGCCCATCCATCATAACAT
Done.