Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 6 of 19
Found at i:1324334 original size:17 final size:16
Alignment explanation
Indices: 1324259--1324338 Score: 69
Period size: 15 Copynumber: 5.0 Consensus size: 16
1324249 ATGCTCATAT
* *
1324259 AATATAA-AAAATTAA
1 AATATAATAATATAAA
*
1324274 AATATAATAAGATAAA
1 AATATAATAATATAAA
1324290 AA-ATAATAATATGAATA
1 AATATAATAATAT-AA-A
1324307 AGATAT-A-AATATAAA
1 A-ATATAATAATATAAA
1324322 AATATATATAATATAAA
1 AATATA-ATAATATAAA
1324339 TTATTAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
14 4 0.07
15 18 0.33
16 13 0.24
17 15 0.28
18 2 0.04
19 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (16 bp):
AATATAATAATATAAA
Found at i:1324403 original size:44 final size:45
Alignment explanation
Indices: 1324355--1324456 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
1324345 AAATGTTAAT
* *
1324355 ATTTATATAATTATATAATACGTTAAACTCGATTAT-ATA-AAAAA
1 ATTTATATAAATATATAACA-GTTAAACTCGATTATAATATAAAAA
* *
1324399 ATTTATATAAATATATAACATTTAAACTTGATTATAATATAAAAA
1 ATTTATATAAATATATAACAGTTAAACTCGATTATAATATAAAAA
**
1324444 ATAAATATAAATA
1 ATTTATATAAATA
1324457 CACATACTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 13 0.26
44 21 0.42
45 16 0.32
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (45 bp):
ATTTATATAAATATATAACAGTTAAACTCGATTATAATATAAAAA
Found at i:1331129 original size:2 final size:2
Alignment explanation
Indices: 1331124--1331158 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1331114 ATACAGACAT
* *
1331124 AC AC AC AC AC AC AC AC GC AT AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1331159 TGTATATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.46, G:0.03, T:0.03
Consensus pattern (2 bp):
AC
Found at i:1331146 original size:20 final size:20
Alignment explanation
Indices: 1331121--1331158 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1331111 TATATACAGA
1331121 CATACACACACACACACACG
1 CATACACACACACACACACG
1331141 CATACACACACACACACA
1 CATACACACACACACACA
1331159 TGTATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.45, G:0.03, T:0.05
Consensus pattern (20 bp):
CATACACACACACACACACG
Found at i:1334792 original size:2 final size:2
Alignment explanation
Indices: 1334785--1334813 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1334775 TACTTAGATT
1334785 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1334814 TTCATAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1342008 original size:10 final size:9
Alignment explanation
Indices: 1341959--1342028 Score: 52
Period size: 10 Copynumber: 7.0 Consensus size: 9
1341949 CATTATTATT
1341959 AAATATAAA
1 AAATATAAA
1341968 TATAATATATAA
1 -A-AATATA-AA
1341980 AAAT-TAATTA
1 AAATATAA--A
1341990 AAATATAAA
1 AAATATAAA
1341999 AAATAGTAAA
1 AAATA-TAAA
*
1342009 ATATAATAAA
1 AAAT-ATAAA
1342019 AATATATAAA
1 AA-ATATAAA
1342029 TATTTTAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
8 1 0.02
9 8 0.16
10 26 0.52
11 13 0.26
12 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (9 bp):
AAATATAAA
Found at i:1342020 original size:19 final size:16
Alignment explanation
Indices: 1341965--1342031 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 16
1341955 TATTAAATAT
*
1341965 AAATATAATATATAAA
1 AAATATAAAATATAAA
*
1341981 AATTAATTAAAATATAAA
1 AAAT-A-TAAAATATAAA
1341999 AAATAGTAAAATATAATAA
1 AAATA-TAAAATAT-A-AA
1342018 AAATATATAAATAT
1 AAATATA-AAATAT
1342032 TTTAAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
16 3 0.07
17 10 0.24
18 16 0.38
19 13 0.31
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (16 bp):
AAATATAAAATATAAA
Found at i:1342028 original size:20 final size:20
Alignment explanation
Indices: 1341961--1342028 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 20
1341951 TTATTATTAA
1341961 ATATAAATATAATATATAAAAAT
1 ATATAAA-AT-ATA-ATAAAAAT
1341984 -TAATTAAAATAT-A-AAAAAT
1 AT-A-TAAAATATAATAAAAAT
*
1342003 A-GTAAAATATAATAAAAAT
1 ATATAAAATATAATAAAAAT
1342022 ATATAAA
1 ATATAAA
1342029 TATTTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
17 8 0.22
18 1 0.03
19 13 0.35
20 5 0.14
22 3 0.08
23 3 0.08
24 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (20 bp):
ATATAAAATATAATAAAAAT
Found at i:1342037 original size:19 final size:19
Alignment explanation
Indices: 1341997--1342052 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
1341987 TTAAAATATA
*
1341997 AAAAATAGTA-AAATATAAT
1 AAAAATA-TATAAATATTAT
1342016 AAAAATATATAAATATT-T
1 AAAAATATATAAATATTAT
* *
1342034 TAAAATTTATATAATATTA
1 AAAAATATATA-AATATTA
1342053 ATTATTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAAATATATAAATATTAT
Found at i:1347338 original size:15 final size:15
Alignment explanation
Indices: 1347301--1347344 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1347291 ATGTTCATAT
1347301 TTATTATAATTAAATA
1 TTATTATAA-TAAATA
* *
1347317 -AAATATAATAAATA
1 TTATTATAATAAATA
1347331 TTATTATAATAAAT
1 TTATTATAATAAAT
1347345 TATAAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTATTATAATAAATA
Found at i:1347348 original size:25 final size:24
Alignment explanation
Indices: 1347309--1347356 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1347299 ATTTATTATA
*
1347309 ATTAAATAAAATATAATAAATATT
1 ATTAAATAAAATATAAAAAATATT
*
1347333 ATTATAATAAATTATAAAAAATAT
1 ATTA-AATAAAATATAAAAAATAT
1347357 AAATGATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATTAAATAAAATATAAAAAATATT
Found at i:1348230 original size:30 final size:29
Alignment explanation
Indices: 1348177--1348247 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
1348167 TAATTTGTTA
1348177 ATAAAATATTAAATTTTTAATTTTAATAAT
1 ATAAAA-ATTAAATTTTTAATTTTAATAAT
* *
1348207 -TAAAAATTAAATTTTAATTATTTTAATTAT
1 ATAAAAATTAAATTTT--TAATTTTAATAAT
*
1348237 AAAAAAATTAA
1 ATAAAAATTAA
1348248 CATCATCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 10 0.29
29 5 0.14
30 11 0.31
31 9 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATAAAAATTAAATTTTTAATTTTAATAAT
Found at i:1348233 original size:27 final size:27
Alignment explanation
Indices: 1348165--1348240 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 27
1348155 TTGATCATTA
*
1348165 TTTAATTTGTTAA-TAAAATATTAAATT
1 TTTAATTTTTTAATTAAAA-ATTAAATT
*
1348192 TTTAATTTTAATAATTAAAAATTAAA-T
1 TTTAATTTT-TTAATTAAAAATTAAATT
1348219 TTTAATTATTTTAATTATAAAA
1 TTTAATT-TTTTAATTA-AAAA
1348241 AAATTAACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 22 0.52
28 15 0.36
29 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TTTAATTTTTTAATTAAAAATTAAATT
Found at i:1349876 original size:30 final size:31
Alignment explanation
Indices: 1349840--1349897 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
1349830 ATATTATTAA
1349840 ATTATATAATATAATAAAAT-TA-ATTAAAAT
1 ATTATATAATATAA-AAAATATATATTAAAAT
1349870 ATTATATAATATAAAAAATATATATTAA
1 ATTATATAATATAAAAAATATATATTAA
1349898 TAAATGCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 5 0.19
30 16 0.62
31 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTATATAATATAAAAAATATATATTAAAAT
Found at i:1361966 original size:23 final size:23
Alignment explanation
Indices: 1361936--1361988 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1361926 ATGATTGATT
1361936 TTAATTTATCTTAATAATAGTAA
1 TTAATTTATCTTAATAATAGTAA
*
1361959 TTAATTTATCTTAATAATTGTAA
1 TTAATTTATCTTAATAATAGTAA
*
1361982 TTTATTT
1 TTAATTT
1361989 TGGTAATCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (23 bp):
TTAATTTATCTTAATAATAGTAA
Found at i:1365644 original size:46 final size:44
Alignment explanation
Indices: 1365593--1365679 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 44
1365583 AAATAAAAAA
*
1365593 TAATATAATAAA-AATATATAAATATATTAAAATTTATATAAATATT
1 TAATAT-ATAAATAATATATAAATATA-TAAAAATTAT-TAAATATT
1365639 TAATATATAAATAATATATAAATATATAAAAATTATTAAAT
1 TAATATATAAATAATATATAAATATATAAAAATTATTAAAT
1365680 CTAATCATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
44 5 0.13
45 14 0.36
46 20 0.51
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (44 bp):
TAATATATAAATAATATATAAATATATAAAAATTATTAAATATT
Found at i:1365649 original size:26 final size:28
Alignment explanation
Indices: 1365568--1365679 Score: 90
Period size: 27 Copynumber: 4.0 Consensus size: 28
1365558 TAAATATTAC
**
1365568 ATATA-AAATATAATAAA-ATAAAAAATA
1 ATATATAAATAT-ATAAATATATTAAATA
1365595 ATATAATAAAAATATATAAATATATTAAA-A
1 ATAT-AT--AAATATATAAATATATTAAATA
* *
1365625 TTTATATAAATAT-TTAATATA-TAAATA
1 -ATATATAAATATATAAATATATTAAATA
*
1365652 ATATATAAATATATAAAAATTATTAAAT
1 ATATATAAATATATAAATA-TATTAAAT
1365680 CTAATCATAA
Statistics
Matches: 68, Mismatches: 7, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
26 15 0.22
27 16 0.24
28 9 0.13
29 5 0.07
30 8 0.12
31 15 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
ATATATAAATATATAAATATATTAAATA
Found at i:1365652 original size:19 final size:20
Alignment explanation
Indices: 1365610--1365668 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
1365600 ATAAAAATAT
* * *
1365610 ATAAATATATTAAAATTTAT
1 ATAAATATATTAATATATAA
1365630 ATAAATAT-TTAATATATAA
1 ATAAATATATTAATATATAA
*
1365649 AT-AATATATAAATATATAA
1 ATAAATATATTAATATATAA
1365668 A
1 A
1365669 AATTATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 5 0.15
19 21 0.62
20 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAATATATTAATATATAA
Found at i:1365653 original size:11 final size:11
Alignment explanation
Indices: 1365590--1365671 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 11
1365580 ATAAAATAAA
1365590 AAATAATATAAT
1 AAATAATAT-AT
1365602 AAA-AATATAT
1 AAATAATATAT
1365612 AAAT-ATAT-T
1 AAATAATATAT
*
1365621 AAA-ATTTATAT
1 AAATA-ATATAT
1365632 AAATATTTAATATAT
1 -AA-A--TAATATAT
1365647 AAATAATATAT
1 AAATAATATAT
*
1365658 AAAT-ATATAA
1 AAATAATATAT
1365668 AAAT
1 AAAT
1365672 TATTAAATCT
Statistics
Matches: 58, Mismatches: 3, Indels: 20
0.72 0.04 0.25
Matches are distributed among these distances:
9 4 0.07
10 21 0.36
11 18 0.31
12 5 0.09
13 2 0.03
14 2 0.03
15 5 0.09
16 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAATAATATAT
Found at i:1365667 original size:15 final size:15
Alignment explanation
Indices: 1365557--1365667 Score: 57
Period size: 15 Copynumber: 7.8 Consensus size: 15
1365547 ATTATACAAC
1365557 ATAAATAT-TACATAT
1 ATAAATATATA-ATAT
*
1365572 A-AAATATAATAAAAT
1 ATAAATAT-ATAATAT
*
1365587 AAAAAATAATATAATA-
1 -ATAAAT-ATATAATAT
1365603 A-AAATATATAAATAT
1 ATAAATATAT-AATAT
1365618 ATTAAA-AT-T--TAT
1 A-TAAATATATAATAT
*
1365630 ATAAATATTTAATAT
1 ATAAATATATAATAT
1365645 AT--A-A-ATAATAT
1 ATAAATATATAATAT
1365656 ATAAATATATAA
1 ATAAATATATAA
1365668 AAATTATTAA
Statistics
Matches: 76, Mismatches: 3, Indels: 34
0.67 0.03 0.30
Matches are distributed among these distances:
11 12 0.16
12 7 0.09
13 7 0.09
14 15 0.20
15 16 0.21
16 5 0.07
17 12 0.16
18 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAAATATATAATAT
Found at i:1372093 original size:58 final size:58
Alignment explanation
Indices: 1372003--1372118 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
1371993 TGGGCTATGA
1372003 ACAATCTTGCAACACCCGTTGTTGATAATGAAGAATATGTGTCGATGAAATTGGTTTT
1 ACAATCTTGCAACACCCGTTGTTGATAATGAAGAATATGTGTCGATGAAATTGGTTTT
1372061 ACAATCTTGCAACACCCGTTGTTGATAATGAAGAATATGTGTCGATGAAATTGGTTTT
1 ACAATCTTGCAACACCCGTTGTTGATAATGAAGAATATGTGTCGATGAAATTGGTTTT
1372119 CTCTCTCATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (58 bp):
ACAATCTTGCAACACCCGTTGTTGATAATGAAGAATATGTGTCGATGAAATTGGTTTT
Found at i:1372530 original size:2 final size:2
Alignment explanation
Indices: 1372523--1372565 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1372513 CACTCGAAGG
1372523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1372565 A
1 A
1372566 AAATTTTGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1373177 original size:28 final size:28
Alignment explanation
Indices: 1373154--1373211 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1373144 TAATATTTTT
1373154 TAATATTTATATATATATATATATAATA
1 TAATATTTATATATATATATATATAATA
* * *
1373182 TAATATTTTTATATTTATATTTA-AATA
1 TAATATTTATATATATATATATATAATA
1373209 TAA
1 TAA
1373212 ATAAGATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TAATATTTATATATATATATATATAATA
Found at i:1373196 original size:36 final size:38
Alignment explanation
Indices: 1373144--1373215 Score: 103
Period size: 36 Copynumber: 1.9 Consensus size: 38
1373134 ATAAATTTTT
* *
1373144 TAATATTTTTTAATATTTATATATATATATATATAATA
1 TAATATTTTTTAATATTTATATATAAATATAAATAATA
*
1373182 TAATA-TTTTT-ATATTTATATTTAAATATAAATAA
1 TAATATTTTTTAATATTTATATATAAATATAAATAA
1373216 GATGTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 21 0.68
37 5 0.16
38 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (38 bp):
TAATATTTTTTAATATTTATATATAAATATAAATAATA
Found at i:1383509 original size:23 final size:23
Alignment explanation
Indices: 1383483--1383529 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1383473 AATATTCGAC
1383483 ATAAAATA-AACCTAATATAAAAA
1 ATAAAATATAA-CTAATATAAAAA
*
1383506 ATAAAATATAATTAATATAAAAA
1 ATAAAATATAACTAATATAAAAA
1383529 A
1 A
1383530 ATATAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (23 bp):
ATAAAATATAACTAATATAAAAA
Found at i:1383567 original size:22 final size:20
Alignment explanation
Indices: 1383539--1383579 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
1383529 AATATAAACA
1383539 TTAAATATAAATATATAATATT
1 TTAAATAT-AAT-TATAATATT
1383561 TTAAATATAATTATAATAT
1 TTAAATATAATTATAATAT
1383580 AAAAAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAATATAATTATAATATT
Found at i:1385528 original size:3 final size:3
Alignment explanation
Indices: 1385522--1385546 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1385512 AAAGATGTAG
1385522 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1385547 CATATCCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1385940 original size:17 final size:17
Alignment explanation
Indices: 1385914--1385946 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1385904 ACGCATCTAA
*
1385914 TAATATTTAAATATATC
1 TAATAATTAAATATATC
1385931 TAATAATTAAATATAT
1 TAATAATTAAATATAT
1385947 ACATAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATAATTAAATATATC
Found at i:1391567 original size:15 final size:15
Alignment explanation
Indices: 1391535--1391596 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
1391525 AATTATTTAA
* **
1391535 ATTAAATATTAAAAT
1 ATTAAATTTTAATTT
1391550 ATTAAATTTTAATTT
1 ATTAAATTTTAATTT
*
1391565 ATTTAATTTTTAATTT
1 A-TTAAATTTTAATTT
*
1391581 AAATATAATTTTAATT
1 -ATTA-AATTTTAATT
1391597 AATTTTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
15 13 0.34
16 15 0.39
17 10 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTAAATTTTAATTT
Found at i:1391575 original size:16 final size:16
Alignment explanation
Indices: 1391551--1391601 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1391541 TATTAAAATA
1391551 TTAAATTTTAATTTAT
1 TTAAATTTTAATTTAT
* *
1391567 TTAATTTTTAATTTAA
1 TTAAATTTTAATTTAT
* *
1391583 ATATAATTTTAATTAAT
1 TTA-AATTTTAATTTAT
1391600 TT
1 TT
1391602 TAAAAAATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAAATTTTAATTTAT
Found at i:1393075 original size:20 final size:21
Alignment explanation
Indices: 1393052--1393098 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1393042 TATTTAAAAT
1393052 TTAAATAT-TT-ATATATGAAA
1 TTAAATATGTTCATA-ATGAAA
* *
1393072 TTAAAAATGTTCATAATTAAA
1 TTAAATATGTTCATAATGAAA
1393093 TTAAAT
1 TTAAAT
1393099 TACCGTCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 7 0.32
21 12 0.55
22 3 0.14
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (21 bp):
TTAAATATGTTCATAATGAAA
Found at i:1393147 original size:29 final size:31
Alignment explanation
Indices: 1393112--1393177 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
1393102 CGTCATTAAA
1393112 ATTTTAAATT-TAAATTTATATTAAAA-T-TT
1 ATTTTAAATTATAAATTTAT-TTAAAATTATT
*
1393141 ATTTT-AATTAATTAATTTATTTAAAATTATT
1 ATTTTAAATT-ATAAATTTATTTAAAATTATT
1393172 ATTTTA
1 ATTTTA
1393178 TTTTATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
28 4 0.13
29 11 0.35
30 9 0.29
31 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
ATTTTAAATTATAAATTTATTTAAAATTATT
Found at i:1393157 original size:18 final size:18
Alignment explanation
Indices: 1393136--1393201 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
1393126 TTTATATTAA
1393136 AATTTATTTTAATTAATT
1 AATTTATTTTAATTAATT
*
1393154 AATTTATTTAAAATT-ATT
1 AATTTATTT-TAATTAATT
* **
1393172 ATTTTATTTT-ATTAAAA
1 AATTTATTTTAATTAATT
*
1393189 AATTTATATTAAT
1 AATTTATTTTAAT
1393202 ATTTATATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
16 3 0.08
17 9 0.24
18 22 0.58
19 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTTATTTTAATTAATT
Found at i:1393178 original size:36 final size:39
Alignment explanation
Indices: 1393138--1393241 Score: 108
Period size: 35 Copynumber: 2.7 Consensus size: 39
1393128 TATATTAAAA
**
1393138 TTTATTTTAATTAATTAATTTAT-TTAA-AATTAT-TAT
1 TTTATTTTAATTAAAAAATTTATATTAATAATTATATAT
*
1393174 TTTATTTT-ATTAAAAAATTTATATTAATATTTATATAT
1 TTTATTTTAATTAAAAAATTTATATTAATAATTATATAT
* *
1393212 TTATAATTTAAATTAAATAAAATTATATTA
1 TT-T-ATTTTAATTAAA-AAATTTATATTA
1393242 TTTTAATATA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
35 12 0.21
36 12 0.21
37 5 0.09
38 5 0.09
39 1 0.02
40 4 0.07
41 6 0.11
42 11 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (39 bp):
TTTATTTTAATTAAAAAATTTATATTAATAATTATATAT
Found at i:1393237 original size:22 final size:22
Alignment explanation
Indices: 1393212--1393297 Score: 57
Period size: 23 Copynumber: 3.6 Consensus size: 22
1393202 ATTTATATAT
1393212 TTATAATTTAAATTAAATAAAA
1 TTATAATTTAAATTAAATAAAA
* *
1393234 TTATATTATTTTAATATAAAAATAATA
1 TTATA--A-TTTAA-AT-TAAATAAAA
* * *
1393261 TTTTAAATTAATTTAAATAAAAA
1 TTATAATTTAAATTAAAT-AAAA
1393284 TT-TAAATTTAAATT
1 TTAT-AATTTAAATT
1393298 CCAAACTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 13
0.69 0.13 0.19
Matches are distributed among these distances:
22 10 0.21
23 14 0.29
24 5 0.10
25 6 0.12
26 2 0.04
27 11 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTATAATTTAAATTAAATAAAA
Found at i:1393292 original size:29 final size:28
Alignment explanation
Indices: 1393238--1393297 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
1393228 ATAAAATTAT
*
1393238 ATTATTTTAATATAAAAATAATATTTTAA
1 ATTAATTTAATATAAAAATAATA-TTTAA
1393267 ATTAATTTAA-ATAAAAATTTAA-ATTTAA
1 ATTAATTTAATATAAAAA--TAATATTTAA
1393295 ATT
1 ATT
1393298 CCAAACTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 15 0.54
29 10 0.36
30 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTAATTTAATATAAAAATAATATTTAA
Found at i:1397996 original size:8 final size:8
Alignment explanation
Indices: 1397983--1398049 Score: 62
Period size: 8 Copynumber: 8.1 Consensus size: 8
1397973 TATTTGTATA
1397983 ATAAAAAT
1 ATAAAAAT
1397991 ATAAAAAT
1 ATAAAAAT
***
1397999 ATAATTTT
1 ATAAAAAT
* *
1398007 TTAAATAT
1 ATAAAAAT
1398015 ATAAAAAT
1 ATAAAAAT
1398023 ATTAAAAAT
1 A-TAAAAAT
1398032 ATTAAAAAT
1 A-TAAAAAT
*
1398041 TTAAAAAT
1 ATAAAAAT
1398049 A
1 A
1398050 CTTATTTATA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
8 32 0.67
9 16 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATAAAAAT
Found at i:1398030 original size:9 final size:9
Alignment explanation
Indices: 1398009--1398049 Score: 66
Period size: 9 Copynumber: 4.6 Consensus size: 9
1397999 ATAATTTTTT
1398009 AAATATATAA
1 AAATAT-TAA
1398019 AAATATTAA
1 AAATATTAA
1398028 AAATATTAA
1 AAATATTAA
1398037 AAAT-TTAA
1 AAATATTAA
1398045 AAATA
1 AAATA
1398050 CTTATTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.27
9 16 0.53
10 6 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATATTAA
Found at i:1401559 original size:2 final size:2
Alignment explanation
Indices: 1401552--1401582 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1401542 GTACATGTAC
1401552 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1401583 ACTAGTTTAT
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:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:1403377 original size:22 final size:22
Alignment explanation
Indices: 1403345--1403398 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
1403335 TGTATTTAAA
* *
1403345 TAATAAAAAAATTATTTAAAT-T
1 TAATATAAAAA-TATATAAATAT
1403367 TAATTATAAAAATATATAAATAT
1 TAA-TATAAAAATATATAAATAT
1403390 TAATATAAA
1 TAATATAAA
1403399 TATTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATATAAAAATATATAAATAT
Found at i:1406391 original size:17 final size:18
Alignment explanation
Indices: 1406354--1406392 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1406344 TGTCAAAACT
*
1406354 GACAAGATGAAAAGGAAA
1 GACAAGATGAAAAGCAAA
*
1406372 GACAAGATGACAA-CAAA
1 GACAAGATGAAAAGCAAA
1406389 GACA
1 GACA
1406393 TGAAAGGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.59, C:0.13, G:0.23, T:0.05
Consensus pattern (18 bp):
GACAAGATGAAAAGCAAA
Found at i:1412817 original size:35 final size:35
Alignment explanation
Indices: 1412771--1412840 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1412761 GAAAACAAGC
1412771 TTTAATTAATCGGCAGAGTGGTTTGGTTTCATTGG
1 TTTAATTAATCGGCAGAGTGGTTTGGTTTCATTGG
1412806 TTTAATTAATCGGCAGAGTGGTTTGGTTTCATTGG
1 TTTAATTAATCGGCAGAGTGGTTTGGTTTCATTGG
1412841 AAGGCTCTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.09, G:0.29, T:0.43
Consensus pattern (35 bp):
TTTAATTAATCGGCAGAGTGGTTTGGTTTCATTGG
Found at i:1415359 original size:2 final size:2
Alignment explanation
Indices: 1415352--1415388 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1415342 GAGAGGGCTG
1415352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1415389 ATTTATCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1416006 original size:234 final size:226
Alignment explanation
Indices: 1415538--1415959 Score: 549
Period size: 234 Copynumber: 1.8 Consensus size: 226
1415528 AAATTTTTAT
* * * *
1415538 TATTAATAAATTAAGTTATTTACGTTAATTTTGTTAAGTAATTTTAATAAAAAAATTTGATTCAA
1 TATTAATGAATTAAGTCATTTACGTTAATTTCGTTAAATAATTTTAATAAAAAAATTTGATTCAA
** * ** *
1415603 TATGTACATATCAACTAGATATTATCTTGATTAAATGTAAAAAATAAGTCATTTATAGATATTAA
66 TACATACATATCAACTAGATATTATCTTGATAAAACATAAAAAATAAGTCATGTATAGATATTAA
* * *
1415668 GTTAGTTTTTTTATTATAATTATTTAATAGAATTAACTTGAGTGATTTAATTTATTATATCAACT
131 GTTAGTTTTTTTATTATAATTACTTAACAGAATTAACTTGAGTAATTTAATTTATTATATCAACT
* * * * * *
1415733 AGATAGTATGCATACATCACTAAATTTTTAT
196 AAAAAGTATGCATAAATCACTAAATATTAAA
1415764 TATTAATGAATTAAGTCATTTACGTTAATTTCGTTAAATAATTTTAATAAAAAAA-TTGATTCAG
1 TATTAATGAATTAAGTCATTTACGTTAATTTCGTTAAATAATTTTAATAAAAAAATTTGATTCA-
*
1415828 TATACACACATAACGTATATCAACTAGATATTATTTTGATAAAACATAAAAAATAAGTCATGTAT
65 -AT----ACAT-AC--ATATCAACTAGATATTATCTTGATAAAACATAAAAAATAAGTCATGTAT
* *
1415893 AGATATTAAGTTAGTTTTTTTTATTATAATTACTTAACATAATTAACTTGTGTAATTTAATTTAT
122 AGATATTAAGTTAG-TTTTTTTATTATAATTACTTAACAGAATTAACTTGAGTAATTTAATTTAT
1415958 TA
186 TA
1415960 ATAATAAAAA
Statistics
Matches: 170, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
225 8 0.05
226 51 0.30
227 2 0.01
231 2 0.01
232 2 0.01
234 58 0.34
235 47 0.28
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.44
Consensus pattern (226 bp):
TATTAATGAATTAAGTCATTTACGTTAATTTCGTTAAATAATTTTAATAAAAAAATTTGATTCAA
TACATACATATCAACTAGATATTATCTTGATAAAACATAAAAAATAAGTCATGTATAGATATTAA
GTTAGTTTTTTTATTATAATTACTTAACAGAATTAACTTGAGTAATTTAATTTATTATATCAACT
AAAAAGTATGCATAAATCACTAAATATTAAA
Found at i:1424563 original size:6 final size:6
Alignment explanation
Indices: 1424545--1424588 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
1424535 ACCTTCTGGC
* * *
1424545 GGAGGT GGCGGT GGAGGT GGAGGC GGTGGT GGAGGT GGAGGT GG
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GG
1424589 GGGTATCACT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.11, C:0.05, G:0.68, T:0.16
Consensus pattern (6 bp):
GGAGGT
Found at i:1429437 original size:33 final size:33
Alignment explanation
Indices: 1429393--1429458 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1429383 AAAACTAAAC
*
1429393 CCATCTTATAAGGGCCTATAGTTTGCCCAAGAG
1 CCATCTGATAAGGGCCTATAGTTTGCCCAAGAG
1429426 CCATCTGATAAGGGCCTATAGTTTGCCCAAGAG
1 CCATCTGATAAGGGCCTATAGTTTGCCCAAGAG
1429459 AGACTTCATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (33 bp):
CCATCTGATAAGGGCCTATAGTTTGCCCAAGAG
Found at i:1429583 original size:8 final size:8
Alignment explanation
Indices: 1429570--1429596 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1429560 TTAATATAAA
1429570 AAATATAT
1 AAATATAT
1429578 AAATATAT
1 AAATATAT
1429586 AAATATAT
1 AAATATAT
1429594 AAA
1 AAA
1429597 AAAATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATATAT
Found at i:1429907 original size:2 final size:2
Alignment explanation
Indices: 1429900--1429947 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1429890 CTCAACTTCA
*
1429900 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA 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
1429942 AT AT AT
1 AT AT AT
1429948 CCCTTGATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1432928 original size:33 final size:33
Alignment explanation
Indices: 1432885--1432963 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
1432875 ATTTTTAAAA
1432885 AAATTTAAAATAATATTCATATTTAATATTATT
1 AAATTTAAAATAATATTCATATTTAATATTATT
* * *
1432918 AAATTAAAAATAATATTTATTTTTAATATTATT
1 AAATTTAAAATAATATTCATATTTAATATTATT
1432951 AAATTTAAAATAA
1 AAATTTAAAATAA
1432964 AAATGATGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (33 bp):
AAATTTAAAATAATATTCATATTTAATATTATT
Found at i:1433763 original size:9 final size:9
Alignment explanation
Indices: 1433749--1433781 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
1433739 TAATTTGAAA
1433749 AAAAATAAC
1 AAAAATAAC
1433758 AAAAATAAC
1 AAAAATAAC
1433767 AAAAAATAAC
1 -AAAAATAAC
1433777 AAAAA
1 AAAAA
1433782 AATTTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAATAAC
Found at i:1433772 original size:11 final size:11
Alignment explanation
Indices: 1433747--1433808 Score: 67
Period size: 11 Copynumber: 5.9 Consensus size: 11
1433737 ATTAATTTGA
1433747 AAAAAAATAAC
1 AAAAAAATAAC
1433758 --AAAAATAAC
1 AAAAAAATAAC
1433767 -AAAAAATAAC
1 AAAAAAATAAC
***
1433777 AAAAAAATTTG
1 AAAAAAATAAC
*
1433788 AAAAAAATAAT
1 AAAAAAATAAC
1433799 AAAAAAATAA
1 AAAAAAATAA
1433809 ACCGTGGAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
9 9 0.21
10 9 0.21
11 25 0.58
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAAAAATAAC
Found at i:1433804 original size:10 final size:10
Alignment explanation
Indices: 1433748--1433782 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
1433738 TTAATTTGAA
1433748 AAAAAATAAC
1 AAAAAATAAC
1433758 -AAAAATAAC
1 AAAAAATAAC
1433767 AAAAAATAAC
1 AAAAAATAAC
1433777 AAAAAA
1 AAAAAA
1433783 ATTTGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.83, C:0.09, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAATAAC
Found at i:1434208 original size:12 final size:13
Alignment explanation
Indices: 1434177--1434221 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
1434167 GACATATATT
1434177 TTATTTTTTAAAA
1 TTATTTTTTAAAA
*
1434190 TTAATTTTTTAATA
1 TT-ATTTTTTAAAA
1434204 -TATTTTTTAAAA
1 TTATTTTTTAAAA
*
1434216 GTATTT
1 TTATTT
1434222 AGACAAAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.36
13 8 0.29
14 10 0.36
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (13 bp):
TTATTTTTTAAAA
Found at i:1435051 original size:34 final size:34
Alignment explanation
Indices: 1434996--1435211 Score: 283
Period size: 34 Copynumber: 6.4 Consensus size: 34
1434986 GTGTTTTAAG
* * *
1434996 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * * *
1435029 TGTTGATTAAATGGGTGATTTAGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
1435063 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1435096 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
1435130 TGTTGATTAAATGGGAGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1435164 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1435198 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1435212 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 39 0.24
34 123 0.76
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1435175 original size:68 final size:67
Alignment explanation
Indices: 1434996--1435211 Score: 297
Period size: 67 Copynumber: 3.2 Consensus size: 67
1434986 GTGTTTTAAG
* * * * * * *
1434996 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTAGTGGTTTGCC
1 TGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
1435061 AT
66 AT
* * * *
1435063 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
1435128 AT
66 AT
* * *
1435130 TGTTGATTAAATGGGAGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
1435195 CAT
65 CAT
1435198 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1435212 TGGTTTTTAC
Statistics
Matches: 130, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 69 0.53
68 61 0.47
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:1439679 original size:34 final size:34
Alignment explanation
Indices: 1439622--1439839 Score: 287
Period size: 34 Copynumber: 6.5 Consensus size: 34
1439612 AAGTGGGAGA
* * *
1439622 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * * *
1439655 ATTGTTGATTAAATGGGTGATTTAGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1439689 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
1439722 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1439756 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1439790 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1439824 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1439840 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 41 0.25
34 123 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1439805 original size:68 final size:67
Alignment explanation
Indices: 1439622--1439841 Score: 314
Period size: 67 Copynumber: 3.3 Consensus size: 67
1439612 AAGTGGGAGA
* * * * * *
1439622 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTAGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1439687 CC
66 CC
* * * *
1439689 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
1439754 CC
66 CC
* * *
1439756 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
1439821 GCC
65 GCC
1439824 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1439842 GTTTTTACCA
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:1440943 original size:11 final size:10
Alignment explanation
Indices: 1440913--1440952 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1440903 TTAGTGCGTA
1440913 TTATATATTT
1 TTATATATTT
*
1440923 TCAT-TATTT
1 TTATATATTT
1440932 TTATAATATTT
1 TTAT-ATATTT
1440943 TTATATATTT
1 TTATATATTT
1440953 ACATGTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 8 0.31
10 9 0.35
11 9 0.35
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATATATTT
Found at i:1440967 original size:18 final size:18
Alignment explanation
Indices: 1440944--1440985 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1440934 ATAATATTTT
1440944 TATATAT-TTACATGTATA
1 TATATATATT-CATGTATA
*
1440962 TATATATATTTATGTATA
1 TATATATATTCATGTATA
1440980 TATATA
1 TATATA
1440986 CACACATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
TATATATATTCATGTATA
Found at i:1441505 original size:2 final size:2
Alignment explanation
Indices: 1441500--1441533 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1441490 TAATATATTC
1441500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1441534 TAAGAGGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1443237 original size:37 final size:36
Alignment explanation
Indices: 1443195--1443268 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
1443185 CTTTCTTTTC
* *
1443195 TTATATAGAAAATTATGTTTT-TATGTTATATAGTTTA
1 TTATATA-AAAATTATATTTTATATATTATATA-TTTA
* *
1443232 TTATATAATAATTATATTTTATATATTTTATATTTA
1 TTATATAAAAATTATATTTTATATATTATATATTTA
1443268 T
1 T
1443269 ATAAATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 16 0.50
37 16 0.50
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (36 bp):
TTATATAAAAATTATATTTTATATATTATATATTTA
Found at i:1443249 original size:16 final size:17
Alignment explanation
Indices: 1443230--1443296 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 17
1443220 TTATATAGTT
1443230 TATTATATAATA-ATTA
1 TATTATATAATATATTA
* *
1443246 TATTTTAT-ATATTTTA
1 TATTATATAATATATTA
*
1443262 TATTTATATAA-ATTTTA
1 TA-TTATATAATATATTA
*
1443279 -ATTATAT-TTATATTA
1 TATTATATAATATATTA
1443294 TAT
1 TAT
1443297 AAATATATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 14 0.34
16 15 0.37
17 11 0.27
18 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATATAATATATTA
Found at i:1443269 original size:15 final size:15
Alignment explanation
Indices: 1443243--1443312 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
1443233 TATATAATAA
1443243 TTATATTTTATATATT
1 TTATA-TTTATATATT
1443259 TTATATTTATATAAATT
1 TTATATTTATAT--ATT
* *
1443276 TTA-ATTATATTTATA
1 TTATATT-TATATATT
**
1443291 TTATATAAATATATT
1 TTATATTTATATATT
1443306 TT-TATTT
1 TTATATTT
1443313 TATTTGTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
14 3 0.07
15 19 0.45
16 10 0.24
17 10 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATATTTATATATT
Found at i:1448782 original size:20 final size:20
Alignment explanation
Indices: 1448737--1448783 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1448727 TTTAATTATA
*
1448737 AAAATAATAATTTTAAAATT
1 AAAATAATAATTATAAAATT
**
1448757 TTAATAATAA-TATAAACATT
1 AAAATAATAATTATAAA-ATT
1448777 AAAATAA
1 AAAATAA
1448784 ATTTTTAAGT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATAATAATTATAAAATT
Found at i:1456703 original size:3 final size:3
Alignment explanation
Indices: 1456695--1456726 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1456685 GATGCTTTTG
1456695 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1456727 TTAATCTCTG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1456799 original size:26 final size:26
Alignment explanation
Indices: 1456770--1456820 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1456760 CTGCATTTGA
*
1456770 TTTTATTCTTTTCTATTCCCTTCCGC
1 TTTTATTCTTTTCTATTCCCCTCCGC
1456796 TTTTATTCTTTTCTATTCCCCTCCG
1 TTTTATTCTTTTCTATTCCCCTCCG
1456821 GTTTCGCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.08, C:0.31, G:0.04, T:0.57
Consensus pattern (26 bp):
TTTTATTCTTTTCTATTCCCCTCCGC
Found at i:1457033 original size:23 final size:22
Alignment explanation
Indices: 1457003--1457050 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1456993 AGCCCAAAAA
*
1457003 TTATTTAAAAATTAAATTTATT
1 TTATTTAAAAATTAAATTTAAT
* *
1457025 TTATATTAATATTTAAATTTAAT
1 TTAT-TTAAAAATTAAATTTAAT
1457048 TTA
1 TTA
1457051 AATAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATTTAAAAATTAAATTTAAT
Found at i:1457060 original size:16 final size:17
Alignment explanation
Indices: 1457039--1457081 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
1457029 ATTAATATTT
1457039 AAATTTA-ATTTAAATA
1 AAATTTATATTTAAATA
1457055 AAATTTTATTATTTAAATA
1 AAA-TTTA-TATTTAAATA
1457074 ATAATTTA
1 A-AATTTA
1457082 GATAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.13
17 4 0.17
19 14 0.61
20 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTTATATTTAAATA
Found at i:1457062 original size:23 final size:23
Alignment explanation
Indices: 1457014--1457060 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1457004 TATTTAAAAA
* * *
1457014 TTAAATTTATTTTATATTAATAT
1 TTAAATTTAATTTAAATAAATAT
1457037 TTAAATTTAATTTAAATAAA-AT
1 TTAAATTTAATTTAAATAAATAT
1457059 TT
1 TT
1457061 TATTATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAATTTAATTTAAATAAATAT
Found at i:1457087 original size:31 final size:30
Alignment explanation
Indices: 1457034--1457093 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
1457024 TTTATATTAA
* *
1457034 TATTTAAATTTAATTTAAATAAAATTTTAT
1 TATTTAAATATAATTTAAATAAAAATTTAT
*
1457064 TATTTAAATAATAATTTAGATAAAAATTTA
1 TATTTAAAT-ATAATTTAAATAAAAATTTA
1457094 AGGAAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
TATTTAAATATAATTTAAATAAAAATTTAT
Found at i:1457587 original size:21 final size:24
Alignment explanation
Indices: 1457562--1457613 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1457552 TATAATTAAA
1457562 TTTATATA-A-AATTTTTTTAT-T
1 TTTATATAGATAATTTTTTTATAT
*
1457583 TTTATATATGATTATTTTTTTATAT
1 TTTATATA-GATAATTTTTTTATAT
1457608 TTTATA
1 TTTATA
1457614 ATAATAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.31
23 1 0.04
24 10 0.38
25 7 0.27
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTATATAGATAATTTTTTTATAT
Found at i:1457822 original size:17 final size:16
Alignment explanation
Indices: 1457768--1457855 Score: 78
Period size: 17 Copynumber: 5.6 Consensus size: 16
1457758 TTATATGATT
1457768 ATATAATATAAAAT-A
1 ATATAATATAAAATAA
* *
1457783 ACATAA-A-AAATTAA
1 ATATAATATAAAATAA
1457797 ATAATAATATAAAATAA
1 AT-ATAATATAAAATAA
1457814 GATATAATATAAAAATAA
1 -ATATAATAT-AAAATAA
* *
1457832 AAATAATAT-AAATAT
1 ATATAATATAAAATAA
1457847 ATA-AATATA
1 ATATAATATA
1457856 TTAAAAATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
13 4 0.07
14 8 0.14
15 16 0.27
16 1 0.02
17 21 0.36
18 9 0.15
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (16 bp):
ATATAATATAAAATAA
Found at i:1457862 original size:29 final size:29
Alignment explanation
Indices: 1457830--1457885 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1457820 ATATAAAAAT
1457830 AAAAATAATATAAA-TATATAAATATATTA
1 AAAAATAA-ATAAATTATATAAATATATTA
* *
1457859 AAAATTAAATAAATTATATATATATAT
1 AAAAATAAATAAATTATATAAATATAT
1457886 ATATATATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAAATAAATAAATTATATAAATATATTA
Found at i:1457892 original size:37 final size:37
Alignment explanation
Indices: 1457768--1457893 Score: 119
Period size: 35 Copynumber: 3.6 Consensus size: 37
1457758 TTATATGATT
*
1457768 ATATAATATA-AAATA-ACATAAAAAATTAAAT-AATA
1 ATATAATATATAAATATATAT-AAAAATTAAATAAATA
1457803 ATATAA-A-ATAAGATATAATATAAAAA-T-AA-AAATA
1 ATATAATATATAA-ATAT-ATATAAAAATTAAATAAATA
*
1457837 ATATAAATATATAAATATAT-TAAAAATTAAATAAATT
1 ATAT-AATATATAAATATATATAAAAATTAAATAAATA
*
1457874 ATAT-ATATATATATATATAT
1 ATATAATATATAAATATATAT
1457894 GATATTTTAA
Statistics
Matches: 76, Mismatches: 3, Indels: 23
0.75 0.03 0.23
Matches are distributed among these distances:
33 1 0.01
34 19 0.25
35 28 0.37
36 13 0.17
37 15 0.20
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (37 bp):
ATATAATATATAAATATATATAAAAATTAAATAAATA
Found at i:1461056 original size:15 final size:14
Alignment explanation
Indices: 1461036--1461066 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
1461026 TAACTTCGTC
1461036 TTTCTTTCTTTTTTT
1 TTTCTTT-TTTTTTT
1461051 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
1461065 TT
1 TT
1461067 CTCTATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTCTTTTTTTTTT
Found at i:1461060 original size:10 final size:11
Alignment explanation
Indices: 1461040--1461064 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1461030 TTCGTCTTTC
1461040 TTTCTTTTTTT
1 TTTCTTTTTTT
1461051 TTTCTTTTTTT
1 TTTCTTTTTTT
1461062 TTT
1 TTT
1461065 TTCTCTATGA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:1461062 original size:13 final size:13
Alignment explanation
Indices: 1461044--1461068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1461034 TCTTTCTTTC
1461044 TTTTTTTTTTCTT
1 TTTTTTTTTTCTT
1461057 TTTTTTTTTTCT
1 TTTTTTTTTTCT
1461069 CTATGAAACT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:1461538 original size:14 final size:15
Alignment explanation
Indices: 1461507--1461544 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1461497 CGAATTGCAG
*
1461507 TTAT-TTTATAATAT
1 TTATATTTAAAATAT
1461521 TTATATTTAAAATAT
1 TTATATTTAAAATAT
1461536 TATATATTT
1 T-TATATTT
1461545 TTTATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 10 0.48
16 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATATTTAAAATAT
Found at i:1461597 original size:17 final size:17
Alignment explanation
Indices: 1461561--1461607 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1461551 AAAATTTTAA
* *
1461561 TATATTAATAATTTATAT
1 TATATAAAT-ATTAATAT
1461579 TATATAAATATTAATAT
1 TATATAAATATTAATAT
1461596 TAT-TATAATATT
1 TATATA-AATATT
1461608 TCATATCCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 2 0.08
17 16 0.62
18 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATAAATATTAATAT
Found at i:1469767 original size:17 final size:16
Alignment explanation
Indices: 1469742--1469794 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 16
1469732 ATTTTTTTAT
*
1469742 TATATAAATAATTATAA
1 TATAAAAATAA-TATAA
1469759 TATAAAAATAATATAA
1 TATAAAAATAATATAA
*
1469775 -AT-AAATTAATATAA
1 TATAAAAATAATATAA
1469789 TATAAA
1 TATAAA
1469795 TTATTTATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 11 0.34
15 4 0.12
16 7 0.22
17 10 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TATAAAAATAATATAA
Found at i:1469796 original size:15 final size:15
Alignment explanation
Indices: 1469743--1469797 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
1469733 TTTTTTTATT
1469743 ATATAAA-TAATTATA
1 ATATAAATTAA-TATA
*
1469758 ATATAAAAATAATATA
1 ATAT-AAATTAATATA
1469774 A-ATAAATTAATATA
1 ATATAAATTAATATA
1469788 ATATAAATTA
1 ATATAAATTA
1469798 TTTATCAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 11 0.31
15 14 0.39
16 8 0.22
17 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATAAATTAATATA
Found at i:1469827 original size:17 final size:17
Alignment explanation
Indices: 1469757--1469831 Score: 63
Period size: 16 Copynumber: 4.7 Consensus size: 17
1469747 AAATAATTAT
1469757 AATATAAAA-ATA-ATA
1 AATATAAAATATATATA
*
1469772 TAA-ATAAATTA-ATAT-
1 -AATATAAAATATATATA
* * *
1469787 AATATAAATTATTTATC
1 AATATAAAATATATATA
1469804 AAT-TAAAATATATATA
1 AATATAAAATATATATA
1469820 AATATAAAATAT
1 AATATAAAATAT
1469832 TTCTAATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 2 0.04
15 14 0.29
16 21 0.44
17 11 0.23
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATAAAATATATATA
Found at i:1469841 original size:16 final size:17
Alignment explanation
Indices: 1469768--1469842 Score: 64
Period size: 16 Copynumber: 4.4 Consensus size: 17
1469758 ATATAAAAAT
* *
1469768 AATATAAATAAATTAATA
1 AATATAAA-ATATTTATA
* *
1469786 TAATATAAATTATTTATC
1 -AATATAAAATATTTATA
*
1469804 AAT-TAAAATATATATA
1 AATATAAAATATTTATA
*
1469820 AATATAAAATATTTCT-
1 AATATAAAATATTTATA
1469836 AATATAA
1 AATATAA
1469843 TTATAATATA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
16 20 0.43
17 13 0.28
18 5 0.11
19 8 0.17
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
AATATAAAATATTTATA
Found at i:1469851 original size:11 final size:11
Alignment explanation
Indices: 1469744--1469853 Score: 59
Period size: 11 Copynumber: 9.9 Consensus size: 11
1469734 TTTTTTATTA
1469744 TATAA-ATAAT
1 TATAATATAAT
*
1469754 TATAATATAAA
1 TATAATATAAT
* *
1469765 AATAATATAAA
1 TATAATATAAT
1469776 TA-AAT-TAA-
1 TATAATATAAT
1469784 TATAATATAAAT
1 TATAATAT-AAT
*
1469796 TAT-TTATCAAT
1 TATAATAT-AAT
*
1469807 TAAAATATATATAAA
1 T---ATA-ATATAAT
* *
1469822 TATAAAATATT
1 TATAATATAAT
*
1469833 TCTAATATAAT
1 TATAATATAAT
1469844 TATAATATAA
1 TATAATATAA
1469854 AATATACGAA
Statistics
Matches: 76, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
8 2 0.03
9 6 0.08
10 9 0.12
11 45 0.59
12 6 0.08
14 2 0.03
15 3 0.04
16 3 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TATAATATAAT
Found at i:1469874 original size:27 final size:27
Alignment explanation
Indices: 1469810--1469874 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
1469800 TATCAATTAA
* * *
1469810 AATATATATA-AATATAAAATATTTCT
1 AATATAAATATAATATAAAATATTACG
*
1469836 AATATAATTATAATATAAAATA-TACG
1 AATATAAATATAATATAAAATATTACG
1469862 AATATAAGATATA
1 AATATAA-ATATA
1469875 CATCTATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 17 0.53
27 15 0.47
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (27 bp):
AATATAAATATAATATAAAATATTACG
Found at i:1473222 original size:17 final size:18
Alignment explanation
Indices: 1473200--1473234 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1473190 TTAAAATTTA
1473200 AAAAT-ATAATTAAAAAT
1 AAAATAATAATTAAAAAT
*
1473217 AAAATAATGATTAAAAAT
1 AAAATAATAATTAAAAAT
1473235 TTGAATCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATAATAATTAAAAAT
Found at i:1476907 original size:22 final size:19
Alignment explanation
Indices: 1476855--1476908 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 19
1476845 ATTTTAAAAT
1476855 TTAAATTTAATAAATATTAA
1 TTAAATTT-ATAAATATTAA
1476875 TT-AATTATATAAATAAATTAAA
1 TTAAATT-TATAAAT--ATT-AA
1476897 TTAAATTTATAA
1 TTAAATTTATAA
1476909 TACAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 10 0.34
20 3 0.10
21 3 0.10
22 9 0.31
23 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAATTTATAAATATTAA
Found at i:1477121 original size:2 final size:2
Alignment explanation
Indices: 1477114--1477147 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1477104 CTAGTTTTGA
1477114 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1477148 TGCCATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1485227 original size:26 final size:26
Alignment explanation
Indices: 1485198--1485249 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1485188 TTATGCCAAT
1485198 TCTGAATAGAAAAATTTAGCAAACTA
1 TCTGAATAGAAAAATTTAGCAAACTA
1485224 TCTGAATAGAAAAATTTAGCAAACTA
1 TCTGAATAGAAAAATTTAGCAAACTA
1485250 ACATGTAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.27
Consensus pattern (26 bp):
TCTGAATAGAAAAATTTAGCAAACTA
Found at i:1490515 original size:2 final size:2
Alignment explanation
Indices: 1490508--1490536 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1490498 GAAGGAACGA
1490508 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 T
1490537 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1495614 original size:16 final size:15
Alignment explanation
Indices: 1495585--1495638 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
1495575 AAATTATAAA
1495585 TTATATTAT-ATATAT
1 TTATATT-TCATATAT
1495600 TTATATTTCATTATATT
1 TTATATTTCA-TATA-T
*
1495617 TTATATTTTATATAT
1 TTATATTTCATATAT
1495632 ATTATAT
1 -TTATAT
1495639 CACTATTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 1 0.03
15 9 0.26
16 14 0.41
17 10 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATATTTCATATAT
Found at i:1498319 original size:2 final size:2
Alignment explanation
Indices: 1498314--1498344 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1498304 CTCTCTCTCC
1498314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1498345 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1507247 original size:12 final size:11
Alignment explanation
Indices: 1507230--1507267 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
1507220 ATATTTTATT
1507230 TAAATTTAATTA
1 TAAATTTAA-TA
1507242 TAAATTT-ATA
1 TAAATTTAATA
1507252 TAAATATTAATA
1 TAAAT-TTAATA
1507264 TAAA
1 TAAA
1507268 ATAATTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 7 0.29
11 3 0.12
12 14 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TAAATTTAATA
Found at i:1507249 original size:22 final size:22
Alignment explanation
Indices: 1507224--1507267 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1507214 AAAATAATAT
*
1507224 TTTATTTAAAT-TTAATTATAAA
1 TTTATATAAATATTAA-TATAAA
1507246 TTTATATAAATATTAATATAAA
1 TTTATATAAATATTAATATAAA
1507268 ATAATTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTATATAAATATTAATATAAA
Found at i:1508575 original size:2 final size:2
Alignment explanation
Indices: 1508568--1508593 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1508558 ACAATAATTA
1508568 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1508594 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1508598 original size:2 final size:2
Alignment explanation
Indices: 1508593--1508617 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1508583 TCTCTCTCTC
1508593 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1508618 GAATCACACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1509940 original size:18 final size:18
Alignment explanation
Indices: 1509917--1509972 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1509907 TTTCTTTTTT
*
1509917 TTTAAAAAAAAATTATAA
1 TTTAAAAAAAAATTAAAA
1509935 TTTAAAAATAAAA-TAAAA
1 TTTAAAAA-AAAATTAAAA
* *
1509953 TTTATAAATAAAATTTAAA
1 TTTA-AAAAAAAATTAAAA
1509972 T
1 T
1509973 ATTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 20 0.62
19 12 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAAAAAAAAATTAAAA
Found at i:1509963 original size:13 final size:13
Alignment explanation
Indices: 1509945--1509969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1509935 TTTAAAAATA
1509945 AAATAAAATTTAT
1 AAATAAAATTTAT
1509958 AAATAAAATTTA
1 AAATAAAATTTA
1509970 AATATTATAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATAAAATTTAT
Found at i:1509964 original size:24 final size:24
Alignment explanation
Indices: 1509919--1509965 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1509909 TCTTTTTTTT
*
1509919 TAAAAAAAAATTATAATTTAAAAA
1 TAAAAAAAAATTATAATATAAAAA
*
1509943 TAAAATAAAATTTATAA-ATAAAA
1 TAAAA-AAAAATTATAATATAAAA
1509966 TTTAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAAAAAAAATTATAATATAAAAA
Found at i:1509972 original size:24 final size:25
Alignment explanation
Indices: 1509917--1509973 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
1509907 TTTCTTTTTT
* *
1509917 TTTAAAAAAAAATTATAATTTAAAA
1 TTTAAATAAAAATTATAATATAAAA
* * *
1509942 ATAAAATAAAATTTATAA-ATAAAA
1 TTTAAATAAAAATTATAATATAAAA
1509966 TTTAAATA
1 TTTAAATA
1509974 TTATATTTTA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
TTTAAATAAAAATTATAATATAAAA
Found at i:1510184 original size:33 final size:33
Alignment explanation
Indices: 1510146--1510208 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
1510136 TGTTTGATAG
*
1510146 CAAAGCTAGGATTAGCTGTCAATTTTCTTATGT
1 CAAAGCTAGGACTAGCTGTCAATTTTCTTATGT
1510179 CAAAGCTAGGACTAGCTGTCAATTTTCTTA
1 CAAAGCTAGGACTAGCTGTCAATTTTCTTA
1510209 CAGTATCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (33 bp):
CAAAGCTAGGACTAGCTGTCAATTTTCTTATGT
Found at i:1510327 original size:2 final size:2
Alignment explanation
Indices: 1510320--1510355 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1510310 GATATGCTGC
*
1510320 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1510356 GTACATGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1511956 original size:14 final size:14
Alignment explanation
Indices: 1511920--1511968 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
1511910 AGTAAAAAAT
1511920 TATTTTAATCTT-TG
1 TATTTTAAT-TTATG
1511934 TATTATTAAATTTAT-
1 TATT-TT-AATTTATG
1511949 TATTTTAATTTATG
1 TATTTTAATTTATG
1511963 TATTTT
1 TATTTT
1511969 TAAAATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.23
14 12 0.39
15 8 0.26
16 4 0.13
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (14 bp):
TATTTTAATTTATG
Found at i:1513356 original size:6 final size:6
Alignment explanation
Indices: 1513319--1513348 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1513309 CTGACTAATG
*
1513319 CTTTCT CTTTTT CTTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
1513349 TTTCTTTTAA
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:1513695 original size:22 final size:24
Alignment explanation
Indices: 1513656--1513699 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1513646 CTGGTTTAGA
*
1513656 TTTTTATTTAGTCAATAAATAAAT
1 TTTTTATTTAGACAATAAATAAAT
1513680 TTTTTATTTA-AC-ATAAATAA
1 TTTTTATTTAGACAATAAATAA
1513700 TACTAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 1 0.05
24 10 0.53
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTTATTTAGACAATAAATAAAT
Found at i:1514508 original size:2 final size:2
Alignment explanation
Indices: 1514501--1514526 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1514491 ACAGTGAAAA
1514501 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
1514527 TTTTCAAGAC
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:1515578 original size:21 final size:22
Alignment explanation
Indices: 1515552--1515594 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1515542 TCAATAAATT
*
1515552 TTATAAATATT-AATAATTAAA
1 TTATAAAAATTAAATAATTAAA
1515573 TTATAAAAATTAAATAATTAAA
1 TTATAAAAATTAAATAATTAAA
1515595 ATATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTATAAAAATTAAATAATTAAA
Found at i:1515951 original size:32 final size:32
Alignment explanation
Indices: 1515897--1515961 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
1515887 ATTTATAATT
* * **
1515897 AATTTTTATATTTTATAATTAAATTTAATTAA
1 AATTTTTATATATAATAATTAAATCAAATTAA
1515929 AATTTTTAT-TATAATAATTTAAATCAAATTAA
1 AATTTTTATATATAATAA-TTAAATCAAATTAA
1515961 A
1 A
1515962 TTAAATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (32 bp):
AATTTTTATATATAATAATTAAATCAAATTAA
Found at i:1517847 original size:41 final size:41
Alignment explanation
Indices: 1517771--1517850 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
1517761 CCTTTTTTTC
* **
1517771 TTTTCCTTTATTATTCTATCTGAACAGAGTGTAAGAGTCTT
1 TTTTCCTTTATTATTCTATCTAAACAGAGCCTAAGAGTCTT
**
1517812 TTTTCTCTTTATTATTCTATC-AAACTTAGCCTAAGAGTC
1 TTTTC-CTTTATTATTCTATCTAAACAGAGCCTAAGAGTC
1517851 CAACACTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 18 0.55
42 15 0.45
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.46
Consensus pattern (41 bp):
TTTTCCTTTATTATTCTATCTAAACAGAGCCTAAGAGTCTT
Found at i:1518895 original size:7 final size:7
Alignment explanation
Indices: 1518885--1518928 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
1518875 AGATAAAATT
1518885 ATTTTAA
1 ATTTTAA
1518892 ATTTTAA
1 ATTTTAA
*
1518899 AATTTAA
1 ATTTTAA
*
1518906 AATTTAA
1 ATTTTAA
1518913 A-TTTAA
1 ATTTTAA
1518919 A-TTTAA
1 ATTTTAA
1518925 ATTT
1 ATTT
1518929 GAACATCTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 12 0.34
7 23 0.66
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
ATTTTAA
Found at i:1518916 original size:6 final size:6
Alignment explanation
Indices: 1518887--1518972 Score: 68
Period size: 6 Copynumber: 13.5 Consensus size: 6
1518877 ATAAAATTAT
*
1518887 TTTAAA TTTTAAAA TTTAAAA TTTAAA TTTAAA TTTAAA TTTGAACA TCTAAA
1 TTTAAA -TTT-AAA TTT-AAA TTTAAA TTTAAA TTTAAA TTT-AA-A TTTAAA
* *
1518940 --TAAA ATCATAA TTTAAA TTTAAAA TTTAAA TTT
1 TTTAAA TTTA-AA TTTAAA TTT-AAA TTTAAA TTT
1518973 TTAATGATAA
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
4 4 0.06
6 31 0.46
7 27 0.40
8 6 0.09
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:1518916 original size:13 final size:13
Alignment explanation
Indices: 1518887--1518972 Score: 66
Period size: 13 Copynumber: 6.2 Consensus size: 13
1518877 ATAAAATTAT
*
1518887 TTTAAATTTTAAAA
1 TTTAAAATTT-AAA
1518901 TTTAAAATTTAAA
1 TTTAAAATTTAAA
1518914 TTT-AAATTTAAA
1 TTTAAAATTTAAA
*
1518926 TTTGAACATCTAAATAAA
1 TTT-AAAAT-T---TAAA
* * *
1518944 ATCATAATTTAAA
1 TTTAAAATTTAAA
1518957 TTTAAAATTTAAA
1 TTTAAAATTTAAA
1518970 TTT
1 TTT
1518973 TTAATGATAA
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
12 12 0.21
13 23 0.40
14 12 0.21
15 1 0.02
16 1 0.02
17 3 0.05
18 5 0.09
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (13 bp):
TTTAAAATTTAAA
Found at i:1519134 original size:15 final size:15
Alignment explanation
Indices: 1519114--1519158 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
1519104 TATGCAACGA
1519114 ATTTATATATTATAT
1 ATTTATATATTATAT
* *
1519129 ATTTATACATAATA-
1 ATTTATATATTATAT
1519143 ATTTATATATTA-AT
1 ATTTATATATTATAT
1519157 AT
1 AT
1519159 AGATATTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
13 1 0.04
14 12 0.48
15 12 0.48
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTATATATTATAT
Found at i:1519658 original size:2 final size:2
Alignment explanation
Indices: 1519651--1519703 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
1519641 GCCATTTCAG
*
1519651 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1519693 TA TA TG TA TA T
1 TA TA TA TA TA T
1519704 CCCTGCAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1520729 original size:15 final size:15
Alignment explanation
Indices: 1520709--1520741 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1520699 GAAGGTAATT
1520709 AAAGGAAA-AGAAAGG
1 AAAGGAAAGAG-AAGG
1520724 AAAGGAAAGAGAAGG
1 AAAGGAAAGAGAAGG
1520739 AAA
1 AAA
1520742 AATTTTACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAAGGAAAGAGAAGG
Found at i:1521847 original size:3 final size:3
Alignment explanation
Indices: 1521839--1521879 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1521829 AGTCCTATTC
1521839 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1521880 GATGGATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1523410 original size:10 final size:10
Alignment explanation
Indices: 1523373--1523415 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
1523363 ACATGTATGT
1523373 ATATATATAC
1 ATATATATAC
*
1523383 ATATACATAC
1 ATATATATAC
1523393 ATACATATATAC
1 AT--ATATATAC
*
1523405 ATATATGTAC
1 ATATATATAC
1523415 A
1 A
1523416 ACCCAGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 19 0.68
12 9 0.32
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (10 bp):
ATATATATAC
Found at i:1525557 original size:27 final size:27
Alignment explanation
Indices: 1525527--1525580 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1525517 TGTAAGAAGT
1525527 TAATCAAGGACAAGGACTTCAATATTG
1 TAATCAAGGACAAGGACTTCAATATTG
1525554 TAATCAAGGACAAGGACTTCAATATTG
1 TAATCAAGGACAAGGACTTCAATATTG
1525581 AAGCTGCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (27 bp):
TAATCAAGGACAAGGACTTCAATATTG
Found at i:1527078 original size:39 final size:39
Alignment explanation
Indices: 1527035--1527112 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
1527025 TGTAACTCTA
*
1527035 GCCCTTTTCTTTTCTTTGAGCATTCATTCAGATTTGTGT
1 GCCCTTTTCTTTTCTTTGAGAATTCATTCAGATTTGTGT
1527074 GCCCTTTTCTTTTCTTTGAGAATTCATTCAGATTTGTGT
1 GCCCTTTTCTTTTCTTTGAGAATTCATTCAGATTTGTGT
1527113 TAACTTTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.14, C:0.19, G:0.15, T:0.51
Consensus pattern (39 bp):
GCCCTTTTCTTTTCTTTGAGAATTCATTCAGATTTGTGT
Found at i:1527863 original size:87 final size:87
Alignment explanation
Indices: 1527700--1527872 Score: 235
Period size: 87 Copynumber: 2.0 Consensus size: 87
1527690 CAGACCAGAC
* *
1527700 TAACATGAAATTATGGCGCAGGTCAAGAAATTTCTCGAGGCTCTGGTGAGATGGAAGAAGCTTGA
1 TAACATGAAATTATGGCGCAGGGCAAGAAATTTCTCAAGGCTCT-GT-AGATGGAAGAAGCTTGA
1527765 AGAAGCATGAAGAAAGCAGCACAG
64 AGAAGCATGAAGAAAGCAGCACAG
* *
1527789 TAACATGGAAATTATGGGCGCAGGCGCAAGAAATTTCTCAAGGCT-T-T-GATGTAAGAAGTTTG
1 TAACAT-GAAATTAT-GGCGCAGG-GCAAGAAATTTCTCAAGGCTCTGTAGATGGAAGAAGCTTG
*
1527851 AAGAAGCTTGAAGAAAGCAGCA
63 AAGAAGCATGAAGAAAGCAGCA
1527873 TAAGAGGAGT
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
87 34 0.45
89 7 0.09
90 8 0.11
91 9 0.12
92 18 0.24
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.21
Consensus pattern (87 bp):
TAACATGAAATTATGGCGCAGGGCAAGAAATTTCTCAAGGCTCTGTAGATGGAAGAAGCTTGAAG
AAGCATGAAGAAAGCAGCACAG
Done.