Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, whole genome shotgun sequence
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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 9 of 125
Found at i:1299950 original size:41 final size:40
Alignment explanation
Indices: 1299893--1300146 Score: 323
Period size: 41 Copynumber: 6.2 Consensus size: 40
1299883 ATGATTGTCA
1299893 AGGAGCAATTTATTTTCCAAAGTTTCGT-TGCCTCTGTTTAG
1 AGGAGCAATTTATTTTCCAAAG--TCGTGTGCCTCTGTTTAG
*
1299934 AGGAGTAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTCCAAAGTCGT-GTGCCTCTGTTTAG
*
1299975 AGGAGCCATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTA-TTTTCCAAAGTCGT-GTGCCTCTGTTTAG
*
1300016 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTCCAAAGTCGT-GTGCCTCTGTTTAG
* * *
1300057 AGGAGCAATTTATTTTCAAAAGTCATGGTGCCTCTATTTAG
1 AGGAGCAATTTATTTTCCAAAGTCGT-GTGCCTCTGTTTAG
* * *
1300098 AGGAGCAATTTATGTTTCTCAAAGTCGTTGAGCCTTTATTTAG
1 AGGAGCAATTTAT-TTTC-CAAAGTCG-TGTGCCTCTGTTTAG
1300141 AGGAGC
1 AGGAGC
1300147 TTTGGTCATA
Statistics
Matches: 194, Mismatches: 12, Indels: 12
0.89 0.06 0.06
Matches are distributed among these distances:
39 4 0.02
40 4 0.02
41 153 0.79
42 8 0.04
43 24 0.12
44 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.38
Consensus pattern (40 bp):
AGGAGCAATTTATTTTCCAAAGTCGTGTGCCTCTGTTTAG
Found at i:1300054 original size:123 final size:124
Alignment explanation
Indices: 1299893--1300146 Score: 361
Period size: 123 Copynumber: 2.0 Consensus size: 124
1299883 ATGATTGTCA
* *
1299893 AGGAGCAATTTATTTTCCAAAGTTTCGTTGCCTCTGTTTAGAGGAGTAATTTATTTTCCAAAGTC
1 AGGAGCAATTTATTTTCCAAAG-TTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTCAAAAGTC
* * * * *
1299958 GTGGTGCCTCTGTTTAGAGGAGCCATTTA-CTTT-TCAAAGTCGTGGTGCCTCTGTTTAG
65 ATGGTGCCTCTATTTAGAGGAGCAATTTATCTTTCTCAAAGTCGTGGAGCCTCTATTTAG
*
1300016 AGGAGCAATTTATTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTCAAAAGT
1 AGGAGCAATTTATTTTCCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTCAAAAGT
* * *
1300080 CATGGTGCCTCTATTTAGAGGAGCAATTTATGTTTCTCAAAGTCGTTGAGCCTTTATTTAG
64 CATGGTGCCTCTATTTAGAGGAGCAATTTATCTTTCTCAAAGTCGTGGAGCCTCTATTTAG
1300141 AGGAGC
1 AGGAGC
1300147 TTTGGTCATA
Statistics
Matches: 116, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
121 4 0.03
123 82 0.71
124 3 0.03
125 27 0.23
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.38
Consensus pattern (124 bp):
AGGAGCAATTTATTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTCAAAAGTCA
TGGTGCCTCTATTTAGAGGAGCAATTTATCTTTCTCAAAGTCGTGGAGCCTCTATTTAG
Found at i:1300162 original size:1 final size:1
Alignment explanation
Indices: 1300156--1300220 Score: 58
Period size: 1 Copynumber: 65.0 Consensus size: 1
1300146 CTTTGGTCAT
* * * * * * * *
1300156 AAAAAAATAAAAAACAAAAAAAAAAACATAAAAAAAAACATAAAAAACAAAAAAAAAATAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1300221 TGACAATGTT
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:1300179 original size:12 final size:12
Alignment explanation
Indices: 1300158--1300219 Score: 72
Period size: 12 Copynumber: 4.9 Consensus size: 12
1300148 TTGGTCATAA
1300158 AAAAATAAAAAAC
1 AAAAA-AAAAAAC
1300171 AAAAAAAAAAAC
1 AAAAAAAAAAAC
*
1300183 ATAAAAAAAAAC
1 AAAAAAAAAAAC
1300195 ATAAAAAACAAAA-
1 A-AAAAAA-AAAAC
1300208 AAAAAATAAAAA
1 AAAAAA-AAAAA
1300220 ATGACAATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
12 28 0.64
13 12 0.27
14 4 0.09
ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:1300435 original size:19 final size:21
Alignment explanation
Indices: 1300411--1300462 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
1300401 TTCTTTTGTA
1300411 TTTTATGTATT-TTATTATT-
1 TTTTATGTATTATTATTATTC
1300430 TTTTAT-TATTATTATTATTC
1 TTTTATGTATTATTATTATTC
1300450 TTATTATGTATTA
1 TT-TTATGTATTA
1300463 ATATATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.14
19 14 0.48
20 2 0.07
21 4 0.14
22 5 0.17
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTATGTATTATTATTATTC
Found at i:1300438 original size:3 final size:3
Alignment explanation
Indices: 1300409--1300462 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
1300399 TTTTCTTTTG
*
1300409 TAT T-T TAT GTAT T-T TAT TAT T-T T-T TAT TAT TAT TAT TAT TCT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1300451 TAT TAT GTAT TA
1 TAT TAT -TAT TA
1300463 ATATATGTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 8 0.18
3 30 0.68
4 6 0.14
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1300444 original size:9 final size:8
Alignment explanation
Indices: 1300384--1300456 Score: 53
Period size: 9 Copynumber: 8.8 Consensus size: 8
1300374 TTTTATCTTG
1300384 TATTATTTT
1 TATTA-TTT
1300393 TATT-TTT
1 TATTATTT
*
1300400 T-TTCTTT
1 TATTATTT
*
1300407 T-GTATTT
1 TATTATTT
1300414 TATGTATTT
1 TAT-TATTT
1300423 TATTATTTTT
1 TATTA--TTT
1300433 TATTATTAT
1 TATTATT-T
1300442 TATTATTCT
1 TATTATT-T
1300451 TATTAT
1 TATTAT
1300457 GTATTAATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
6 2 0.04
7 13 0.24
8 4 0.07
9 27 0.50
10 8 0.15
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (8 bp):
TATTATTT
Found at i:1300461 original size:25 final size:24
Alignment explanation
Indices: 1300376--1300462 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
1300366 AATTCAATTT
* * *
1300376 TTATCTTGTATTATTTTTATTTTTT
1 TTATTTTGTATTATTATTA-TTTTA
*
1300401 TTCTTTTGTATT-TTATGTATTTTA
1 TTATTTTGTATTATTAT-TATTTTA
* *
1300425 TTATTTTTTATTATTATTATTATTC
1 TTATTTTGTATTATTATTATT-TTA
*
1300450 TTATTATGTATTA
1 TTATTTTGTATTA
1300463 ATATATGTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 21 0.42
25 29 0.58
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (24 bp):
TTATTTTGTATTATTATTATTTTA
Found at i:1301531 original size:21 final size:21
Alignment explanation
Indices: 1301502--1301542 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1301492 CTCCAAGTTT
*
1301502 TTTTTTTTATTTGTTTATTTG
1 TTTTATTTATTTGTTTATTTG
*
1301523 TTTTATTTATTTTTTTATTT
1 TTTTATTTATTTGTTTATTT
1301543 ATTTATTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (21 bp):
TTTTATTTATTTGTTTATTTG
Found at i:1301540 original size:12 final size:13
Alignment explanation
Indices: 1301515--1301546 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1301505 TTTTTATTTG
1301515 TTTATTTGTTTTA
1 TTTATTTGTTTTA
1301528 TTTATTT-TTTTA
1 TTTATTTGTTTTA
1301540 TTTATTT
1 TTTATTT
1301547 ATTAGATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTATTTGTTTTA
Found at i:1301565 original size:4 final size:4
Alignment explanation
Indices: 1301507--1301549 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
1301497 AGTTTTTTTT
* * *
1301507 TTTA TTTG TTTA TTTGT TTTA TTTA TTTT TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TT
1301550 AGATTAGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:1304314 original size:2 final size:2
Alignment explanation
Indices: 1304307--1304334 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1304297 ACACGTTACT
1304307 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1304335 ATGTAATTTT
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):
TA
Found at i:1304731 original size:3 final size:3
Alignment explanation
Indices: 1304723--1304751 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1304713 CTCAATATTA
1304723 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1304752 AATGTTGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1309339 original size:22 final size:22
Alignment explanation
Indices: 1309314--1309367 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1309304 TATTTATATA
1309314 ATATTATTTTTTA-ATATAAAT
1 ATATTATTTTTTATATATAAAT
1309335 -TA-TATTTTAATTATATATAAAT
1 ATATTATTTT--TTATATATAAAT
*
1309357 ATAATATTTTT
1 ATATTATTTTT
1309368 ATTAAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
19 6 0.21
20 2 0.07
21 3 0.11
22 9 0.32
23 2 0.07
24 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTATTTTTTATATATAAAT
Found at i:1309349 original size:18 final size:18
Alignment explanation
Indices: 1309296--1309345 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
1309286 ATTTTTAATT
1309296 TATTATAATATTT-ATATAA
1 TATTAT-AT-TTTAATATAA
*
1309315 TATTATTTTTTAATATAA
1 TATTATATTTTAATATAA
1309333 -ATTATATTTTAAT
1 TATTATATTTTAAT
1309346 TATATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 15 0.54
18 7 0.25
19 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATATTTTAATATAA
Found at i:1309358 original size:41 final size:40
Alignment explanation
Indices: 1309308--1309423 Score: 110
Period size: 42 Copynumber: 2.8 Consensus size: 40
1309298 TTATAATATT
*
1309308 TATATAATATTAT-TTTTTAATATAAATT-ATATTTTAATTA
1 TATATAATATAATATTTTT-AT-TAAATTAATATTTTAATTA
1309348 TATATAAATATAATATTTTTATTAAATTAATATTTTAAATTAA
1 TATAT-AATATAATATTTTTATTAAATTAATATTTT-AATT-A
* * * * *
1309391 AATATTACATAATAATTTTATTAATATTTATAT
1 TATATAATATAATATTTTTATTAA-ATTAATAT
1309424 ACAAATATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
40 11 0.17
41 16 0.25
42 25 0.39
43 12 0.19
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (40 bp):
TATATAATATAATATTTTTATTAAATTAATATTTTAATTA
Found at i:1309371 original size:24 final size:24
Alignment explanation
Indices: 1309294--1309371 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
1309284 TAATTTTTAA
**
1309294 TTTATTATAATATTTATATAATATT
1 TTTATTAT-ATATAAATATAATATT
*
1309319 ATTTTTTA-ATATAAAT-T-ATATT
1 -TTTATTATATATAAATATAATATT
*
1309341 TTAATTATATATAAATATAATATT
1 TTTATTATATATAAATATAATATT
1309365 TTTATTA
1 TTTATTA
1309372 AATTAATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
21 5 0.12
22 13 0.30
23 2 0.05
24 17 0.40
26 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTATTATATATAAATATAATATT
Found at i:1309389 original size:18 final size:18
Alignment explanation
Indices: 1309352--1309391 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1309342 TAATTATATA
*
1309352 TAAATATAATATTTTTAT
1 TAAATATAATATTTTAAT
1309370 TAAAT-TAATATTTTAAAT
1 TAAATATAATATTTT-AAT
1309388 TAAA
1 TAAA
1309392 ATATTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAATATAATATTTTAAT
Found at i:1310879 original size:45 final size:45
Alignment explanation
Indices: 1310828--1310918 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
1310818 AAAAATAGAA
*
1310828 AAAAAAAAACAAATGATTTACTTACAATTCTAAATTATCTAACATCC
1 AAAAAAGAA-AAA-GATTTACTTACAATTCTAAATTATCTAACATCC
*
1310875 AAAAAAGAAAAAGATTTACTTACAATTCTAAATTGTCTAACATC
1 AAAAAAGAAAAAGATTTACTTACAATTCTAAATTATCTAACATC
1310919 AAATGATTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 31 0.74
46 3 0.07
47 8 0.19
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (45 bp):
AAAAAAGAAAAAGATTTACTTACAATTCTAAATTATCTAACATCC
Found at i:1317628 original size:14 final size:14
Alignment explanation
Indices: 1317609--1317638 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1317599 TTCTACGTGC
1317609 AACAAAATAGTCAA
1 AACAAAATAGTCAA
1317623 AACAAAATAGTCAA
1 AACAAAATAGTCAA
1317637 AA
1 AA
1317639 ACCAATGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (14 bp):
AACAAAATAGTCAA
Found at i:1321792 original size:3 final size:3
Alignment explanation
Indices: 1321786--1321829 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
1321776 TTGTTGTTTT
1321786 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1321830 ACAAAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1322391 original size:30 final size:30
Alignment explanation
Indices: 1322345--1322554 Score: 145
Period size: 30 Copynumber: 7.0 Consensus size: 30
1322335 TCGTTTTCTT
* *
1322345 TAAAACCCTAAAACCCTCCAAACTCTAATAC
1 TAAAACCCT-AAACCCTCCAAACCCTAAAAC
* ***
1322376 TAAAGCCCTAAACCCTTTGAACCCTAAAAC
1 TAAAACCCTAAACCCTCCAAACCCTAAAAC
*** *
1322406 TAAAACCCTAAACCCTTTGAACCTTAAAA-
1 TAAAACCCTAAACCCTCCAAACCCTAAAAC
* * * * *
1322435 TCGAAACCTTAAAACC-CCAAACCTTAAAAT
1 T-AAAACCCTAAACCCTCCAAACCCTAAAAC
* **
1322465 TGAAACTTTAAACCCTCCAAACCCTAAAAC
1 TAAAACCCTAAACCCTCCAAACCCTAAAAC
** * *
1322495 TAAAACCCTAAACCCTTTAAACTCTAAAAT
1 TAAAACCCTAAACCCTCCAAACCCTAAAAC
* * **
1322525 TGAAACCTTAAAACCCTTTAAACCCTAAAA
1 TAAAACCCT-AAACCCTCCAAACCCTAAAA
1322555 TCGTACCATA
Statistics
Matches: 147, Mismatches: 28, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
29 23 0.16
30 97 0.66
31 27 0.18
ACGTcount: A:0.45, C:0.30, G:0.03, T:0.22
Consensus pattern (30 bp):
TAAAACCCTAAACCCTCCAAACCCTAAAAC
Found at i:1322402 original size:16 final size:16
Alignment explanation
Indices: 1322381--1322433 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1322371 AATACTAAAG
1322381 CCCTAAACCCTTTGAA
1 CCCTAAACCCTTTGAA
* **
1322397 CCCTAAA-AC-TAAAA
1 CCCTAAACCCTTTGAA
1322411 CCCTAAACCCTTTGAA
1 CCCTAAACCCTTTGAA
*
1322427 CCTTAAA
1 CCCTAAA
1322434 ATCGAAACCT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
14 10 0.36
15 2 0.07
16 16 0.57
ACGTcount: A:0.40, C:0.34, G:0.04, T:0.23
Consensus pattern (16 bp):
CCCTAAACCCTTTGAA
Found at i:1322444 original size:14 final size:14
Alignment explanation
Indices: 1322425--1322476 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1322415 AAACCCTTTG
1322425 AACCTTAAAATCGA
1 AACCTTAAAATCGA
* *
1322439 AACCTTAAAACCCCA
1 AACCTTAAAA-TCGA
*
1322454 AACCTTAAAATTGA
1 AACCTTAAAATCGA
*
1322468 AACTTTAAA
1 AACCTTAAA
1322477 CCCTCCAAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.50, C:0.23, G:0.04, T:0.23
Consensus pattern (14 bp):
AACCTTAAAATCGA
Found at i:1322458 original size:15 final size:14
Alignment explanation
Indices: 1322425--1322463 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1322415 AAACCCTTTG
* *
1322425 AACCTTAAAATCGA
1 AACCTTAAAACCCA
1322439 AACCTTAAAACCCCA
1 AACCTTAAAA-CCCA
1322454 AACCTTAAAA
1 AACCTTAAAA
1322464 TTGAAACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.51, C:0.28, G:0.03, T:0.18
Consensus pattern (14 bp):
AACCTTAAAACCCA
Found at i:1322506 original size:119 final size:120
Alignment explanation
Indices: 1322355--1322574 Score: 309
Period size: 119 Copynumber: 1.8 Consensus size: 120
1322345 TAAAACCCTA
* * * *
1322355 AAACCCTCCAAACTCTAATACTAAAGCCCTAAACCCTTTGAACCCTAAAACTAAAACCCT-AAAC
1 AAACCCTCCAAACCCTAAAACTAAAACCCTAAACCCTTTAAACCCTAAAACTAAAACCCTAAAAC
* * *
1322419 CCTTTGAACCTTAAAATCGAAACCTTAAAACC-CCAAACCTTAAAATTGAAACTTT
66 CCTTTAAACCCTAAAATCG-AACCATAAAACCTCCAAACCTTAAAATTGAAACTTT
* * * *
1322474 AAACCCTCCAAACCCTAAAACTAAAACCCTAAACCCTTTAAACTCTAAAATTGAAACCTTAAAAC
1 AAACCCTCCAAACCCTAAAACTAAAACCCTAAACCCTTTAAACCCTAAAACTAAAACCCTAAAAC
*
1322539 CCTTTAAACCCTAAAATCGTACCATAAAACCTCCAA
66 CCTTTAAACCCTAAAATCGAACCATAAAACCTCCAA
1322575 GCTCTAAAAT
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
119 62 0.71
120 25 0.29
ACGTcount: A:0.44, C:0.31, G:0.03, T:0.22
Consensus pattern (120 bp):
AAACCCTCCAAACCCTAAAACTAAAACCCTAAACCCTTTAAACCCTAAAACTAAAACCCTAAAAC
CCTTTAAACCCTAAAATCGAACCATAAAACCTCCAAACCTTAAAATTGAAACTTT
Found at i:1322580 original size:60 final size:60
Alignment explanation
Indices: 1322415--1322616 Score: 169
Period size: 60 Copynumber: 3.3 Consensus size: 60
1322405 CTAAAACCCT
* * * *
1322415 AAACCCTTTGAACCTTAAAATCGAAACCTTAAAACC-CCAAAC-CTTAAAATTGAAA-CTTT
1 AAACCCTTTAAACCCTAAAATCG-AACCATAAAACCTCCAAACTC-TAAAATTGAAACCTTA
** ** * * **
1322474 AAACCCTCCAAACCCTAAAACTAAAACCCTAAACCCTTTAAACTCTAAAATTGAAACCTTA
1 AAACCCTTTAAACCCTAAAA-TCGAACCATAAAACCTCCAAACTCTAAAATTGAAACCTTA
* * * *
1322535 AAACCCTTTAAACCCTAAAATCGTACCATAAAACCTCCAAGCTCTAAAATTAAAAACCCTA
1 AAACCCTTTAAACCCTAAAATCGAACCATAAAACCTCCAAACTCTAAAATT-GAAACCTTA
*
1322596 AAA-TCTTTAAAACCCTTAAAA
1 AAACCCTTT-AAACCC-TAAAA
1322617 CCCTAAGATT
Statistics
Matches: 112, Mismatches: 24, Indels: 11
0.76 0.16 0.07
Matches are distributed among these distances:
59 26 0.23
60 43 0.38
61 38 0.34
62 5 0.04
ACGTcount: A:0.46, C:0.28, G:0.03, T:0.23
Consensus pattern (60 bp):
AAACCCTTTAAACCCTAAAATCGAACCATAAAACCTCCAAACTCTAAAATTGAAACCTTA
Found at i:1322632 original size:26 final size:24
Alignment explanation
Indices: 1322587--1322647 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 24
1322577 TCTAAAATTA
1322587 AAAACCCTAAAATCTTTAAAACCCTT
1 AAAACCCTAAAATCTTT-AAA-CCTT
*
1322613 AAAACCCTAAGAT-TTCTAAACCTT
1 AAAACCCTAAAATCTT-TAAACCTT
1322637 -AAACCTCTAAA
1 AAAACC-CTAAA
1322648 TCCTAGACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 5 0.16
24 8 0.26
25 5 0.16
26 13 0.42
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAACCCTAAAATCTTTAAACCTT
Found at i:1322698 original size:14 final size:14
Alignment explanation
Indices: 1322676--1322705 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1322666 CCAAAATCTT
1322676 CCAAACCCTAAAAC
1 CCAAACCCTAAAAC
*
1322690 CCAAGCCCTAAAAC
1 CCAAACCCTAAAAC
1322704 CC
1 CC
1322706 TTAAAACTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.47, G:0.03, T:0.07
Consensus pattern (14 bp):
CCAAACCCTAAAAC
Found at i:1326930 original size:16 final size:17
Alignment explanation
Indices: 1326909--1326941 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1326899 TTCTTAAAAA
1326909 TAAAAATAAT-ATTATT
1 TAAAAATAATAATTATT
*
1326925 TAAAAATGATAATTATT
1 TAAAAATAATAATTATT
1326942 GGTAACTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAAAATAATAATTATT
Found at i:1327559 original size:12 final size:12
Alignment explanation
Indices: 1327538--1327608 Score: 70
Period size: 12 Copynumber: 5.6 Consensus size: 12
1327528 TTAGGGTTTC
*
1327538 GGTTTCATTTAG
1 GGTTTTATTTAG
*
1327550 GGTTTTATTTAA
1 GGTTTTATTTAG
1327562 GGTTTTAATTTTAG
1 GGTTTT-A-TTTAG
1327576 GGTTTTGATTTTAG
1 GGTTTT-A-TTTAG
* *
1327590 GATTTCATTTAG
1 GGTTTTATTTAG
1327602 GGTTTTA
1 GGTTTTA
1327609 AGTTTAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 26 0.53
13 2 0.04
14 21 0.43
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.55
Consensus pattern (12 bp):
GGTTTTATTTAG
Found at i:1327575 original size:26 final size:25
Alignment explanation
Indices: 1327544--1327608 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
1327534 TTTCGGTTTC
*
1327544 ATTTAGGGTTTTATTTAAGGTTTTA
1 ATTTAGGGTTTTATTTAAGGATTTA
* *
1327569 ATTTTAGGGTTTTGATTTTAGGATTTC
1 A-TTTAGGGTTTT-ATTTAAGGATTTA
1327596 ATTTAGGGTTTTA
1 ATTTAGGGTTTTA
1327609 AGTTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.06
26 22 0.63
27 11 0.31
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.55
Consensus pattern (25 bp):
ATTTAGGGTTTTATTTAAGGATTTA
Found at i:1334001 original size:3 final size:3
Alignment explanation
Indices: 1333995--1334027 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1333985 AAAATTGATG
1333995 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1334028 TAGAGAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1335725 original size:28 final size:27
Alignment explanation
Indices: 1335664--1335727 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
1335654 TATAATATAA
*
1335664 AAATATAAAATTAATATAATTTAAAATTT
1 AAATA-AAAATTAATATAATTT-AAATTG
*
1335693 TAATAAAAATTATATATAGATTT-AATTG
1 AAATAAAAATTA-ATATA-ATTTAAATTG
1335721 AAATAAA
1 AAATAAA
1335728 TTTTTATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 17 0.57
29 9 0.30
30 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (27 bp):
AAATAAAAATTAATATAATTTAAATTG
Found at i:1335895 original size:18 final size:20
Alignment explanation
Indices: 1335874--1335912 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1335864 AAAAATTAAA
1335874 AAATCA-AA-AATCGATTTG
1 AAATCATAATAATCGATTTG
*
1335892 AAATCATAATATTCGATTTG
1 AAATCATAATAATCGATTTG
1335912 A
1 A
1335913 TTCAAATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 2 0.11
20 10 0.56
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (20 bp):
AAATCATAATAATCGATTTG
Found at i:1348206 original size:43 final size:43
Alignment explanation
Indices: 1348145--1348227 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
1348135 GAAAACAACA
* *
1348145 GATTACTATAATACACTACAATTCAGTCTTGTATCTTTTCAGT
1 GATTACTACAATACACTACAATTCAGTCTTGTACCTTTTCAGT
1348188 GATTACTACAATACACTACAATTCAGTCTTGTACCTTTTC
1 GATTACTACAATACACTACAATTCAGTCTTGTACCTTTTC
1348228 TGCGACCAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (43 bp):
GATTACTACAATACACTACAATTCAGTCTTGTACCTTTTCAGT
Found at i:1350191 original size:13 final size:13
Alignment explanation
Indices: 1350175--1350202 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1350165 TTTCTATCTT
1350175 TTTCATTTTTTAA
1 TTTCATTTTTTAA
1350188 TTTCATTTTTTAA
1 TTTCATTTTTTAA
1350201 TT
1 TT
1350203 AATTCTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTCATTTTTTAA
Found at i:1353291 original size:13 final size:13
Alignment explanation
Indices: 1353273--1353297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1353263 TATATCTTAT
1353273 TTATATTATATTA
1 TTATATTATATTA
1353286 TTATATTATATT
1 TTATATTATATT
1353298 TTAAATCATC
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATATTATATTA
Found at i:1365740 original size:2 final size:2
Alignment explanation
Indices: 1365733--1365758 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1365723 CAAAGCTTCC
1365733 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
1365759 TTTGTAAGAA
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:1366846 original size:32 final size:33
Alignment explanation
Indices: 1366751--1366846 Score: 81
Period size: 32 Copynumber: 3.0 Consensus size: 33
1366741 CCAATAATTA
* * * *
1366751 AAAATAATTCGTACTTAAATTAATTCAAAACTG
1 AAAATGATTCGAACTTAAAATAATTCAAAAATG
* * * **
1366784 AAATTG-TTCGAA-TCTGAAATGATTTGAAAAT-
1 AAAATGATTCGAACT-TAAAATAATTCAAAAATG
1366815 AAAATGATTCGAACTTAAAATAATTCAAAAAT
1 AAAATGATTCGAACTTAAAATAATTCAAAAAT
1366847 TAACCAACAT
Statistics
Matches: 46, Mismatches: 14, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
31 6 0.13
32 35 0.76
33 5 0.11
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (33 bp):
AAAATGATTCGAACTTAAAATAATTCAAAAATG
Found at i:1367934 original size:16 final size:16
Alignment explanation
Indices: 1367915--1367974 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
1367905 CTTGAAACCA
*
1367915 AAATGGTTCAAACTTG
1 AAATGGTTCAAACTCG
* **
1367931 AAATGATTTGAACTCG
1 AAATGGTTCAAACTCG
* *
1367947 AAATGGCTCAAAATCG
1 AAATGGTTCAAACTCG
1367963 AAATGGTTCAAA
1 AAATGGTTCAAA
1367975 AAATTAATCC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (16 bp):
AAATGGTTCAAACTCG
Found at i:1368050 original size:24 final size:24
Alignment explanation
Indices: 1368002--1368052 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1367992 AATTATGCAT
**
1368002 AATAAAAACAATAAATATAGTACA
1 AATAAAAACAATAAATATAACACA
*
1368026 AATAAAAATAATAAATATAACACA
1 AATAAAAACAATAAATATAACACA
1368050 AAT
1 AAT
1368053 GATTAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.22
Consensus pattern (24 bp):
AATAAAAACAATAAATATAACACA
Found at i:1368806 original size:11 final size:11
Alignment explanation
Indices: 1368790--1368816 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1368780 AAAAATTATA
1368790 ATATTATATTT
1 ATATTATATTT
1368801 ATATTATATTT
1 ATATTATATTT
1368812 ATATT
1 ATATT
1368817 TTTTAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTATATTT
Found at i:1369021 original size:16 final size:16
Alignment explanation
Indices: 1368996--1369035 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1368986 ATCCGAATAA
* *
1368996 AAAATAATCTAAATCT
1 AAAATGATCTAAATCC
*
1369012 AAAATGATCTGAATCC
1 AAAATGATCTAAATCC
1369028 AAAATGAT
1 AAAATGAT
1369036 TCAAATTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (16 bp):
AAAATGATCTAAATCC
Found at i:1372406 original size:5 final size:5
Alignment explanation
Indices: 1372396--1372425 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1372386 AGTGTCAACA
1372396 ATTAT ATTAT ATTAT ATTAT ATTA- ATTAT A
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
1372426 AGTGTACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATTAT
Found at i:1376171 original size:17 final size:17
Alignment explanation
Indices: 1376149--1376188 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1376139 ATTGTACGAA
1376149 TAAATTAAATTAAATGT
1 TAAATTAAATTAAATGT
* * *
1376166 TAAATTCAGTTAAATTT
1 TAAATTAAATTAAATGT
1376183 TAAATT
1 TAAATT
1376189 TAAAATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (17 bp):
TAAATTAAATTAAATGT
Found at i:1381728 original size:17 final size:17
Alignment explanation
Indices: 1381697--1381749 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1381687 CACAATTTCA
*
1381697 AAACAATTCACAACTTC
1 AAACAATTAACAACTTC
* *
1381714 AAATAATTAATAACTTC
1 AAACAATTAACAACTTC
*
1381731 AAACAATTCACAACTTC
1 AAACAATTAACAACTTC
1381748 AA
1 AA
1381750 GCAAAATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (17 bp):
AAACAATTAACAACTTC
Found at i:1388572 original size:187 final size:187
Alignment explanation
Indices: 1388197--1388996 Score: 1088
Period size: 187 Copynumber: 4.3 Consensus size: 187
1388187 GTAATTTTAT
* * * *
1388197 ACTA-AAAGACGCTTTTAATAATCTAAAAAATTTTTAAAAGAAAATTATTAAAGGCGTTTGTTCT
1 ACTAGAAA-ACGCCTTTAATAATCTCAAAAATTTTTAAAAAAAAATTATTAAAGGTGTTTGTTCT
*
1388261 AAAAAAATGCCTTCAATAATTATGTAC-AAAATTAAAAGGAATTAGTGAAGGCATTTTTCTAGAA
65 AAAAAAATACCTTCAATAATTATGTACAAAAATTAAAAGGAATTAGTGAAGGCATTTTTCTAGAA
* * * * *
1388325 TAAACGCCTTCACTAATCGTCTTACAATTTGAGTAGTAGAATATTGAAGGTCTTTTTC
130 TAAACGCCTTCACTAACCATCTTAAAATTTGAGTAGTGGAATATTGAAGGTGTTTTTC
* *
1388383 ACTAGAAAACGTCTTTAATAATCTCAAAAATTTTTAAAAAGAAATTATTAAAGGTGTTTGTTCT-
1 ACTAGAAAACGCCTTTAATAATCTCAAAAATTTTTAAAAAAAAATTATTAAAGGTGTTTGTTCTA
* * * * *
1388447 AAAAAATCACCTTCAATAATTATGTACAAAAATTAAAAAGAATTATTAAAGGTATTTTTCTATAA
66 AAAAAAT-ACCTTCAATAATTATGTACAAAAATTAAAAGGAATTAGTGAAGGCATTTTTCTAGAA
* * * * * *
1388512 TAAATGCCTTTACTAACCGTCTTAAAATTTGAGTATTGGTATATTAAAGGTGTTTTTC
130 TAAACGCCTTCACTAACCATCTTAAAATTTGAGTAGTGGAATATTGAAGGTGTTTTTC
* * * ** *
1388570 ACTAGAAAACGCCTTTAATAATCTGAAAAATTTTTCAAAAAAAATTATTGAAGGCATTTGTTTTA
1 ACTAGAAAACGCCTTTAATAATCTCAAAAATTTTTAAAAAAAAATTATTAAAGGTGTTTGTTCTA
* * * *
1388635 AAAAAATACCTTCAATAATTATGTACAAAAATTATAATGAATTAGTGAAGACACTTTTCTAGAAT
66 AAAAAATACCTTCAATAATTATGTACAAAAATTAAAAGGAATTAGTGAAGGCATTTTTCTAGAAT
* * * *
1388700 AAATGCCTTCACTAACCATTTTAAAATTTGAGTAGTGAAATATTGAAGGTATTTTTC
131 AAACGCCTTCACTAACCATCTTAAAATTTGAGTAGTGGAATATTGAAGGTGTTTTTC
* *
1388757 ACTAGAAGACGCCTTTAATAATCGCAAAAA-TTTTAAAAAAAAATTATTAAAGGTGTTTGTTCTA
1 ACTAGAAAACGCCTTTAATAATCTCAAAAATTTTTAAAAAAAAATTATTAAAGGTGTTTGTTCTA
* * * *
1388821 AAAAAATACTTTCAATAATTATATACAAAAATTAAAAGGAATTAGTGAAGGCATTTTTTTGGAAT
66 AAAAAATACCTTCAATAATTATGTACAAAAATTAAAAGGAATTAGTGAAGGCATTTTTCTAGAAT
* * *
1388886 AAACGCCTTCACTAACTATC-TAAAATTTGAGTACTGGCATATTGAAGGTGTTTTTC
131 AAACGCCTTCACTAACCATCTTAAAATTTGAGTAGTGGAATATTGAAGGTGTTTTTC
* ** * *
1388942 ACTAGAAGACAACTTTAATAATTTCAAAAATTTTTAAAAAAAAATTATTGAAGGT
1 ACTAGAAAACGCCTTTAATAATCTCAAAAATTTTTAAAAAAAAATTATTAAAGGT
1388997 ATTTTTTTGG
Statistics
Matches: 536, Mismatches: 73, Indels: 10
0.87 0.12 0.02
Matches are distributed among these distances:
185 65 0.12
186 198 0.37
187 266 0.50
188 7 0.01
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (187 bp):
ACTAGAAAACGCCTTTAATAATCTCAAAAATTTTTAAAAAAAAATTATTAAAGGTGTTTGTTCTA
AAAAAATACCTTCAATAATTATGTACAAAAATTAAAAGGAATTAGTGAAGGCATTTTTCTAGAAT
AAACGCCTTCACTAACCATCTTAAAATTTGAGTAGTGGAATATTGAAGGTGTTTTTC
Found at i:1388936 original size:124 final size:122
Alignment explanation
Indices: 1388801--1389043 Score: 271
Period size: 124 Copynumber: 2.0 Consensus size: 122
1388791 AAAAAAAAAT
**
1388801 TATTAAAGGTGTTTGTT-CTA-AAAAAATACTTTCAATAATTATATACAAAAA-TT-AAAAGGAA
1 TATTAAAGGTGTTT-TTACTAGAAAAAA-ACTTT-AATAA-T-T-T-CAAAAATTTAAAAAAAAA
*
1388862 TTAGTGAAGGCATTTTTTTGGAATAAACGCCTTCACTAACTATC-TAAAATTTGAGTACTGGCA
59 TTAGTGAAGGCATTTTTTTGGAATAAACGCCTTCACTAACCATCTTAAAATTTGAGTACTGGCA
* * * *
1388925 TATTGAAGGTGTTTTTCACTAGAAGACAACTTTAATAATTTCAAAAATTTTTAAAAAAAAATTAT
1 TATTAAAGGTGTTTTT-ACTAGAAAAAAACTTTAATAATTTCAAAAA--TTTAAAAAAAAATTAG
* * *
1388990 TGAAGGTATTTTTTTGGAATAAACGCCTTCATTAACCGTCTTAAAATTTGAGTA
63 TGAAGGCATTTTTTTGGAATAAACGCCTTCACTAACCATCTTAAAATTTGAGTA
1389044 GTGGAACATT
Statistics
Matches: 101, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
120 6 0.06
121 1 0.01
122 1 0.01
123 5 0.05
124 63 0.62
125 21 0.21
126 4 0.04
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (122 bp):
TATTAAAGGTGTTTTTACTAGAAAAAAACTTTAATAATTTCAAAAATTTAAAAAAAAATTAGTGA
AGGCATTTTTTTGGAATAAACGCCTTCACTAACCATCTTAAAATTTGAGTACTGGCA
Found at i:1388985 original size:373 final size:373
Alignment explanation
Indices: 1388210--1389004 Score: 1141
Period size: 373 Copynumber: 2.1 Consensus size: 373
1388200 AAAAGACGCT
* * * * *
1388210 TTTAATAATCTAAAAAATTTTTAAAAGAAAATTATTAAAGGCGTTTGTTCTAAAAAAATGCCTTC
1 TTTAATAATCTAAAAAATTTTTAAAAAAAAATTATTGAAGGCATTTGTTTTAAAAAAATACCTTC
* *
1388275 AATAATTATGTACAAAATTAAAAGGAATTAGTGAAGGCATTTTTCTAGAATAAACGCCTTCACTA
66 AATAATTATGTACAAAATTAAAAGGAATTAGTGAAGACACTTTTCTAGAATAAACGCCTTCACTA
* * * * *
1388340 ATCGTCTTACAATTTGAGTAGTAGAATATTGAAGGTCTTTTTCACTAGAAAACGTCTTTAATAAT
131 ACCATCTTAAAATTTGAGTAGTAGAATATTGAAGGTATTTTTCACTAGAAAACGCCTTTAATAAT
* *
1388405 CTCAAAAATTTTTAAAAAGAAATTATTAAAGGTGTTTGTTCTAAAAAATCACCTTCAATAATTAT
196 CGCAAAAATTTTTAAAAAAAAATTATTAAAGGTGTTTGTTCTAAAAAATCACCTTCAATAATTAT
* * * * * * *
1388470 GTACAAAAATTAAAAAGAATTATTAAAGGTATTTTTCTATAATAAATGCCTTTACTAACCGTCTT
261 ATACAAAAATTAAAAAGAATTAGTAAAGGCATTTTTCTAGAATAAACGCCTTCACTAACCATCTT
* * **
1388535 AAAATTTGAGTATTGGTATATTAAAGGTGTTTTTCACTAGAAAACGCC
326 AAAATTTGAGTACTGGCATATTAAAGGTGTTTTTCACTAGAAAACAAC
* *
1388583 TTTAATAATCTGAAAAATTTTTCAAAAAAAATTATTGAAGGCATTTGTTTTAAAAAAATACCTTC
1 TTTAATAATCTAAAAAATTTTTAAAAAAAAATTATTGAAGGCATTTGTTTTAAAAAAATACCTTC
* * *
1388648 AATAATTATGTACAAAAATTATAATGAATTAGTGAAGACACTTTTCTAGAATAAATGCCTTCACT
66 AATAATTATGTAC-AAAATTAAAAGGAATTAGTGAAGACACTTTTCTAGAATAAACGCCTTCACT
* *
1388713 AACCATTTTAAAATTTGAGTAGT-GAAATATTGAAGGTATTTTTCACTAGAAGACGCCTTTAATA
130 AACCATCTTAAAATTTGAGTAGTAG-AATATTGAAGGTATTTTTCACTAGAAAACGCCTTTAATA
*
1388777 ATCGCAAAAA-TTTTAAAAAAAAATTATTAAAGGTGTTTGTTCTAAAAAAAT-ACTTTCAATAAT
194 ATCGCAAAAATTTTTAAAAAAAAATTATTAAAGGTGTTTGTTCT-AAAAAATCACCTTCAATAAT
* * * * *
1388840 TATATACAAAAATTAAAAGGAATTAGTGAAGGCATTTTTTTGGAATAAACGCCTTCACTAACTAT
258 TATATACAAAAATTAAAAAGAATTAGTAAAGGCATTTTTCTAGAATAAACGCCTTCACTAACCAT
* *
1388905 C-TAAAATTTGAGTACTGGCATATTGAAGGTGTTTTTCACTAGAAGACAAC
323 CTTAAAATTTGAGTACTGGCATATTAAAGGTGTTTTTCACTAGAAAACAAC
* * *
1388955 TTTAATAATTTCAAAAATTTTTAAAAAAAAATTATTGAAGGTATTT-TTTT
1 TTTAATAATCTAAAAAATTTTTAAAAAAAAATTATTGAAGGCATTTGTTTT
1389005 GGAATAAACG
Statistics
Matches: 375, Mismatches: 44, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
371 4 0.01
372 85 0.23
373 169 0.45
374 117 0.31
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.36
Consensus pattern (373 bp):
TTTAATAATCTAAAAAATTTTTAAAAAAAAATTATTGAAGGCATTTGTTTTAAAAAAATACCTTC
AATAATTATGTACAAAATTAAAAGGAATTAGTGAAGACACTTTTCTAGAATAAACGCCTTCACTA
ACCATCTTAAAATTTGAGTAGTAGAATATTGAAGGTATTTTTCACTAGAAAACGCCTTTAATAAT
CGCAAAAATTTTTAAAAAAAAATTATTAAAGGTGTTTGTTCTAAAAAATCACCTTCAATAATTAT
ATACAAAAATTAAAAAGAATTAGTAAAGGCATTTTTCTAGAATAAACGCCTTCACTAACCATCTT
AAAATTTGAGTACTGGCATATTAAAGGTGTTTTTCACTAGAAAACAAC
Found at i:1389087 original size:125 final size:124
Alignment explanation
Indices: 1388860--1389089 Score: 336
Period size: 125 Copynumber: 1.8 Consensus size: 124
1388850 AATTAAAAGG
* *
1388860 AATTAGTGAAGGCATTTTTTTGGAATAAACGCCTTCACTAACTATCTAAAATTTGAGTACTGGCA
1 AATTAGTGAAGGCATTTTTTTGGAATAAACGCCTTCACTAACCATCTAAAATTTGAGTACTGGAA
* * *
1388925 TATTGAAGGTGTTTTTCACTAGAAGACAACTTTAATAATTTCAAAAATTTTTAAAAAAA
66 CATTGAAGGTATTTTTCACTAGAAGACAACTTCAATAATTTCAAAAATTTTTAAAAAAA
* * * * *
1388984 AATTATTGAAGGTATTTTTTTGGAATAAACGCCTTCATTAACCGTCTTAAAATTTGAGTAGTGGA
1 AATTAGTGAAGGCATTTTTTTGGAATAAACGCCTTCACTAACCATC-TAAAATTTGAGTACTGGA
*
1389049 ACATTGAATGTATTTTTCACTAGAAGAC-ACATTCAATAATT
65 ACATTGAAGGTATTTTTCACTAGAAGACAAC-TTCAATAATT
1389090 CCTTTAAAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
124 43 0.46
125 50 0.54
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (124 bp):
AATTAGTGAAGGCATTTTTTTGGAATAAACGCCTTCACTAACCATCTAAAATTTGAGTACTGGAA
CATTGAAGGTATTTTTCACTAGAAGACAACTTCAATAATTTCAAAAATTTTTAAAAAAA
Found at i:1403845 original size:24 final size:24
Alignment explanation
Indices: 1403811--1403857 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1403801 TATGTAAAAT
*
1403811 TAATAATGTTGCAAAGATGTAATC
1 TAATAAAGTTGCAAAGATGTAATC
* *
1403835 TAATAAAGTTGTAGAGATGTAAT
1 TAATAAAGTTGCAAAGATGTAAT
1403858 TTAACAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (24 bp):
TAATAAAGTTGCAAAGATGTAATC
Found at i:1404267 original size:17 final size:17
Alignment explanation
Indices: 1404223--1404270 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1404213 AAAATTATAA
**
1404223 TATTATGTATTTATGTT
1 TATTATGTATTTAAATT
1404240 TATT-TGATATTTAAATT
1 TATTATG-TATTTAAATT
*
1404257 TTTTATGTATTTAA
1 TATTATGTATTTAA
1404271 TGTTATAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 2 0.08
17 22 0.85
18 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.62
Consensus pattern (17 bp):
TATTATGTATTTAAATT
Found at i:1406157 original size:2 final size:2
Alignment explanation
Indices: 1406150--1406176 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1406140 CCTCCCTTTA
1406150 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 A
1406177 ATGAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1413630 original size:1 final size:1
Alignment explanation
Indices: 1413596--1413622 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1413586 CCTTCTATTG
1413596 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1413623 AAATTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1414000 original size:55 final size:56
Alignment explanation
Indices: 1413885--1414005 Score: 129
Period size: 55 Copynumber: 2.2 Consensus size: 56
1413875 GATAAAAAAT
* * * *
1413885 AAAAAAAAAGTGTTTTGTGTTTAAGTGTTGATATGAAAATTATATATAAATTTGAT
1 AAAAAAAAAGTGTTTTGTGTTTAAATGTTGATACGAAAATTATATATAAATTTAAC
* * * * *
1413941 AAAAAAAATA-TGTTTTGTGTTTAAAT-TTGATGCGAAAATTGTGTATCAGTTTAAC
1 AAAAAAAA-AGTGTTTTGTGTTTAAATGTTGATACGAAAATTATATATAAATTTAAC
1413996 AAAAATAAAA
1 AAAAA-AAAA
1414006 AAAATATTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
55 27 0.50
56 26 0.48
57 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (56 bp):
AAAAAAAAAGTGTTTTGTGTTTAAATGTTGATACGAAAATTATATATAAATTTAAC
Found at i:1414082 original size:59 final size:58
Alignment explanation
Indices: 1413880--1414082 Score: 150
Period size: 59 Copynumber: 3.5 Consensus size: 58
1413870 AATTTGATAA
* * *
1413880 AAAATAAAAAAAAAGTGTTTTGTGTTTAAGTGTTGATATGAAAA-TTATATATAAATT-TG
1 AAAAT-AAAAAAAA-TGTTTTGTGTTTAAGTGTTGATA-CAAAATTTGTATATGAATTATG
* * * * * **
1413939 ATAA-AAAAAATATGTTTTGTGTTTAAAT-TTGATGCGAAAATTGTGTATCA-G-TTTAACA
1 AAAATAAAAAAAATGTTTTGTGTTTAAGTGTTGATAC-AAAATT-TGTAT-ATGAATT-ATG
* * *
1413997 AAAATAAAAAAAATATTTTTTATTTAAGTGTT-ATACAAAATTTGTATATGAATTAGGTG
1 AAAATAAAAAAAATGTTTTGTGTTTAAGTGTTGATACAAAATTTGTATATGAATTA--TG
*
1414056 AAAATAAAAAATATGTTTTGTGTTTAA
1 AAAATAAAAAAAATGTTTTGTGTTTAA
1414083 ATATTCATAC
Statistics
Matches: 108, Mismatches: 24, Indels: 24
0.69 0.15 0.15
Matches are distributed among these distances:
55 9 0.08
56 19 0.18
57 18 0.17
58 12 0.11
59 48 0.44
60 2 0.02
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (58 bp):
AAAATAAAAAAAATGTTTTGTGTTTAAGTGTTGATACAAAATTTGTATATGAATTATG
Found at i:1414161 original size:12 final size:12
Alignment explanation
Indices: 1414144--1414168 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1414134 TATAAAATAA
1414144 ACATGAATATAT
1 ACATGAATATAT
1414156 ACATGAATATAT
1 ACATGAATATAT
1414168 A
1 A
1414169 GAAATTGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
ACATGAATATAT
Found at i:1421747 original size:2 final size:2
Alignment explanation
Indices: 1421740--1421780 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1421730 TTATTTCAGG
1421740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1421781 AACACCTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1424033 original size:30 final size:29
Alignment explanation
Indices: 1423968--1424070 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 29
1423958 TATGTTAAAA
*
1423968 GTTTATTTAAATACAAATTAAAGTATAAT
1 GTTTATTTAAATACAAATTAAAATATAAT
* *
1423997 GATTTATTTAAATATAAATTAAAATTTAAGT
1 G-TTTATTTAAATACAAATTAAAATATAA-T
*** * *
1424028 GTTTATTTGGGTACAAA-AAAAATATTAAA
1 GTTTATTTAAATACAAATTAAAATA-TAAT
1424057 GATTTATTTAAATA
1 G-TTTATTTAAATA
1424071 TAATAAATAT
Statistics
Matches: 57, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
29 7 0.12
30 48 0.84
31 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.42
Consensus pattern (29 bp):
GTTTATTTAAATACAAATTAAAATATAAT
Found at i:1424090 original size:29 final size:28
Alignment explanation
Indices: 1424042--1424105 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
1424032 ATTTGGGTAC
* * *
1424042 AAAAAAAATATTAAAGATTTATTTAAAT
1 AAAATAAATATTAAAAATTTATCTAAAT
*
1424070 ATAATAAATATATAAAAATTTATCTAAAT
1 AAAATAAATAT-TAAAAATTTATCTAAAT
1424099 AAAATAA
1 AAAATAA
1424106 TAAAATTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 9 0.30
29 21 0.70
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAATAAATATTAAAAATTTATCTAAAT
Found at i:1425219 original size:19 final size:20
Alignment explanation
Indices: 1425197--1425244 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1425187 AACATTAATT
1425197 TACACAAATAAACA-TGATA
1 TACACAAATAAACACTGATA
** *
1425216 TACATGAAT-AACACTGCTA
1 TACACAAATAAACACTGATA
1425235 TACACAAATA
1 TACACAAATA
1425245 CATAGTAGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (20 bp):
TACACAAATAAACACTGATA
Found at i:1428829 original size:14 final size:14
Alignment explanation
Indices: 1428812--1428842 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1428802 AAATAAATAA
1428812 ATAAAAATATGAAT
1 ATAAAAATATGAAT
*
1428826 ATAAAATTATGAAT
1 ATAAAAATATGAAT
1428840 ATA
1 ATA
1428843 TAATAATCAT
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:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (14 bp):
ATAAAAATATGAAT
Found at i:1429868 original size:12 final size:12
Alignment explanation
Indices: 1429847--1429897 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
1429837 AATACTTTTT
1429847 TAAA-AAACAAA
1 TAAACAAACAAA
1429858 TAAACAAACAAA
1 TAAACAAACAAA
*
1429870 CAAACAAACAAA
1 TAAACAAACAAA
* *
1429882 TAAATAAATAAA
1 TAAACAAACAAA
1429894 TAAA
1 TAAA
1429898 ATACCAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
11 4 0.11
12 31 0.89
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (12 bp):
TAAACAAACAAA
Found at i:1429897 original size:4 final size:4
Alignment explanation
Indices: 1429851--1429881 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1429841 CTTTTTTAAA
*
1429851 AAAC AAAT AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1429882 TAAATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.77, C:0.19, G:0.00, T:0.03
Consensus pattern (4 bp):
AAAC
Found at i:1429897 original size:8 final size:8
Alignment explanation
Indices: 1429851--1429893 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
1429841 CTTTTTTAAA
1429851 AAACAAAT
1 AAACAAAT
*
1429859 AAACAAAC
1 AAACAAAT
*
1429867 AAACAAAC
1 AAACAAAT
1429875 AAACAAAT
1 AAACAAAT
*
1429883 AAATAAAT
1 AAACAAAT
1429891 AAA
1 AAA
1429894 TAAAATACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.77, C:0.14, G:0.00, T:0.09
Consensus pattern (8 bp):
AAACAAAT
Found at i:1430328 original size:19 final size:19
Alignment explanation
Indices: 1430304--1430343 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1430294 TTGTTTGCCT
1430304 AAAGTTCATCAAAAAATTC
1 AAAGTTCATCAAAAAATTC
* *
1430323 AAAGTTCATCGAAATATTC
1 AAAGTTCATCAAAAAATTC
1430342 AA
1 AA
1430344 CCAGATTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (19 bp):
AAAGTTCATCAAAAAATTC
Found at i:1430405 original size:31 final size:31
Alignment explanation
Indices: 1430363--1430431 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1430353 AGAAAACCTG
*
1430363 CCAAAACATTCAACCAACAGCAAAAAATTCA
1 CCAAAAAATTCAACCAACAGCAAAAAATTCA
** *
1430394 CCAAAAAATTCAACCGGCATCAAAAAATTCA
1 CCAAAAAATTCAACCAACAGCAAAAAATTCA
1430425 CCAAAAA
1 CCAAAAA
1430432 CTAAAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.55, C:0.28, G:0.04, T:0.13
Consensus pattern (31 bp):
CCAAAAAATTCAACCAACAGCAAAAAATTCA
Found at i:1430910 original size:21 final size:21
Alignment explanation
Indices: 1430884--1430928 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1430874 ATAAGACCCT
1430884 AAATAAATAAATAAAT-AAATA
1 AAATAAATAAA-AAATAAAATA
* *
1430905 AAATAACTAAAATATAAAATA
1 AAATAAATAAAAAATAAAATA
1430926 AAA
1 AAA
1430929 AGTAATTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAAATAAAAAATAAAATA
Found at i:1431225 original size:43 final size:43
Alignment explanation
Indices: 1431144--1431414 Score: 253
Period size: 43 Copynumber: 6.3 Consensus size: 43
1431134 CTTCCATAAG
*
1431144 CAGAGGCTC-ACAACTTTTGAAAAAATAAATACGGCTCTTCTAAA
1 CAGAGGCTCAACAAC-TTTG-AAAAATAAATAAGGCTCTTCTAAA
* *
1431188 CAGAGGCTCAACAATTTTGAAAAATAAATAAGGCTCTTTTAAA
1 CAGAGGCTCAACAACTTTGAAAAATAAATAAGGCTCTTCTAAA
* * * * ** * *
1431231 -TGAAGACTTAACAATTTTGGAAAAATAAATATTGCTCATCTAAT
1 CAG-AGGCTCAACAACTTT-GAAAAATAAATAAGGCTCTTCTAAA
* * * * *
1431275 TAAAGGCTTAACAACTTTGGAAAATAAATAAGGCTCCTCTAAA
1 CAGAGGCTCAACAACTTTGAAAAATAAATAAGGCTCTTCTAAA
* * *
1431318 CAAAGGCTCAACAACTTTGGAAACTAAATAAGG--CTTCTATAA
1 CAGAGGCTCAACAACTTTGAAAAATAAATAAGGCTCTTCTA-AA
* * * *
1431360 TCAGAGGTTCAACAACTTTGAAAAATAAATAAAGCTCCTCTAAT
1 -CAGAGGCTCAACAACTTTGAAAAATAAATAAGGCTCTTCTAAA
1431404 CAGAGGCTCAA
1 CAGAGGCTCAA
1431415 AATAAATAAA
Statistics
Matches: 187, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
41 5 0.03
42 3 0.02
43 123 0.66
44 47 0.25
45 9 0.05
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.27
Consensus pattern (43 bp):
CAGAGGCTCAACAACTTTGAAAAATAAATAAGGCTCTTCTAAA
Found at i:1431255 original size:87 final size:87
Alignment explanation
Indices: 1431153--1431402 Score: 263
Period size: 87 Copynumber: 2.9 Consensus size: 87
1431143 GCAGAGGCTC
* * *
1431153 ACAACTTTTGAAAAAATAAATACGGCTCTTCTAAACAGAGGCTCAACAATTTTGAAAAATAAATA
1 ACAA-TTTTGGAAAAATAAATAAGGCTCTTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATA
* * ** *
1431218 AGGCTCTTTTAAATGAAGACTTA
65 AGGCTCCTCTAAACAAAGACTCA
** * ** * * *
1431241 ACAATTTTGGAAAAATAAATATTGCTCATCTAATTAAAGGCTTAACAACTTTGGAAAATAAATAA
1 ACAATTTTGGAAAAATAAATAAGGCTCTTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAA
*
1431306 GGCTCCTCTAAACAAAGGCTCA
66 GGCTCCTCTAAACAAAGACTCA
* * *
1431328 ACAACTTTGG-AAACTAAATAAGG--CTTCTATAATCAGAGGTTCAACAACTTTGAAAAATAAAT
1 ACAATTTTGGAAAAATAAATAAGGCTCTTCTA-AA-CAGAGGCTCAACAACTTTGAAAAATAAAT
*
1431390 AAAGCTCCTCTAA
64 AAGGCTCCTCTAA
1431403 TCAGAGGCTC
Statistics
Matches: 132, Mismatches: 28, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
84 5 0.04
85 1 0.01
86 46 0.35
87 76 0.58
88 4 0.03
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (87 bp):
ACAATTTTGGAAAAATAAATAAGGCTCTTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAA
GGCTCCTCTAAACAAAGACTCA
Found at i:1431584 original size:16 final size:15
Alignment explanation
Indices: 1431565--1431621 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
1431555 CTTTGTAAGA
1431565 ATTCACCAAAATTTTG
1 ATTCA-CAAAATTTTG
**
1431581 ATTCTGAAAATTTTAG
1 ATTCACAAAATTTT-G
*
1431597 TTTCACAAGAA-TTTG
1 ATTCACAA-AATTTTG
1431612 ATTCACAAAA
1 ATTCACAAAA
1431622 CTTCAAATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 2 0.06
15 16 0.48
16 13 0.39
17 2 0.06
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (15 bp):
ATTCACAAAATTTTG
Found at i:1432121 original size:21 final size:21
Alignment explanation
Indices: 1432088--1432148 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1432078 CATTTTAAAT
* *
1432088 ATTCCCATTTGAAACTCAAAG
1 ATTCTCATCTGAAACTCAAAG
*
1432109 ATTCTTATCTGAAACTCAAAG
1 ATTCTCATCTGAAACTCAAAG
*
1432130 ATTCTCATTTGAAAACTCA
1 ATTCTCATCTG-AAACTCA
1432149 TAATTTTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 27 0.79
22 7 0.21
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (21 bp):
ATTCTCATCTGAAACTCAAAG
Found at i:1433269 original size:12 final size:11
Alignment explanation
Indices: 1433252--1433318 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 11
1433242 TCATTTTTTA
1433252 TTTTTTTATCTT
1 TTTTTTTAT-TT
1433264 TTTTTTTATTT
1 TTTTTTTATTT
*
1433275 TTATCTTTATCTT
1 TT-TTTTTAT-TT
1433288 TATCCTTTTT-TTAT
1 T-T--TTTTTATT-T
1433302 TTTTTTTATTT
1 TTTTTTTATTT
1433313 TTTTTT
1 TTTTTT
1433319 CATTATTGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
11 16 0.35
12 17 0.37
13 5 0.11
14 4 0.09
15 4 0.09
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:1433562 original size:22 final size:22
Alignment explanation
Indices: 1433511--1433562 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1433501 TAAAACAGGC
*
1433511 TCAAAACACATGTTTAAAGGGT
1 TCAAAACCCATGTTTAAAGGGT
1433533 TCAAAACCCATGTTTAAAGGGT
1 TCAAAACCCATGTTTAAAGGGT
1433555 TCAAAACC
1 TCAAAACC
1433563 AAATGATCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (22 bp):
TCAAAACCCATGTTTAAAGGGT
Found at i:1438901 original size:20 final size:21
Alignment explanation
Indices: 1438876--1438914 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1438866 CATAAAGACA
*
1438876 TAGATTTCTTCC-AATTTTTT
1 TAGATTTCTCCCAAATTTTTT
1438896 TAGATTTCTCCCAAATTTT
1 TAGATTTCTCCCAAATTTT
1438915 GCTCCGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.54
Consensus pattern (21 bp):
TAGATTTCTCCCAAATTTTTT
Found at i:1439280 original size:11 final size:11
Alignment explanation
Indices: 1439264--1439288 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1439254 TGATCAGAAC
1439264 AAAAAAGGAAA
1 AAAAAAGGAAA
1439275 AAAAAAGGAAA
1 AAAAAAGGAAA
1439286 AAA
1 AAA
1439289 GGAAAAAATG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAGGAAA
Found at i:1439367 original size:3 final size:3
Alignment explanation
Indices: 1439301--1439355 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
1439291 AAAAAATGAA
* * *
1439301 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT CAT CAT -AT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1439347 AAT AAT AAT
1 AAT AAT AAT
1439356 GACATTAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1439836 original size:113 final size:114
Alignment explanation
Indices: 1439594--1439876 Score: 300
Period size: 113 Copynumber: 2.5 Consensus size: 114
1439584 GATGACCAGG
* * * * * *
1439594 ACAAAACCACAAGTCAAAGTGAAGCGATCAAGA-CTAAGTCGAGGCAAAAAATGACTGGAACGAA
1 ACAAAACCACGAGTCAAAATGAAGCGACCAAGATC-AAGTCGAGGTAAAAAATGA-TGAAACAAA
* * ****
1439658 ACCACGAATCATGAGAAATAATCTAGACTGAGCCAAGATCAGATGATTGGG
64 ACCACGAATCATGAGAAATAATCTAGACTGAGCCAAAATCAGATAATCAAA
* * * * * *
1439709 ATAAAACTATGAGTCAAAATAAAGCGACCAAGATCAAGTCGAGGTAAAAAATG-TGAAATAAAAT
1 ACAAAACCACGAGTCAAAATGAAGCGACCAAGATCAAGTCGAGGTAAAAAATGATGAAACAAAAC
* * *
1439773 CACGAATCATGAGAAATAATCTGGACTGAGCTAAAATTAGATAATCAAA
66 CACGAATCATGAGAAATAATCTAGACTGAGCCAAAATCAGATAATCAAA
* * ** *
1439822 ACGAAACCACGAGTCGAAATGAAGCGACCAAGATTGAGTCGAGGTCAAAAATGAT
1 ACAAAACCACGAGTCAAAATGAAGCGACCAAGATCAAGTCGAGGTAAAAAATGAT
1439877 CTGAACAAAA
Statistics
Matches: 136, Mismatches: 30, Indels: 5
0.80 0.18 0.03
Matches are distributed among these distances:
113 91 0.67
114 1 0.01
115 43 0.32
116 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (114 bp):
ACAAAACCACGAGTCAAAATGAAGCGACCAAGATCAAGTCGAGGTAAAAAATGATGAAACAAAAC
CACGAATCATGAGAAATAATCTAGACTGAGCCAAAATCAGATAATCAAA
Found at i:1439951 original size:59 final size:59
Alignment explanation
Indices: 1439825--1439951 Score: 173
Period size: 59 Copynumber: 2.2 Consensus size: 59
1439815 AATCAAAACG
* * * *
1439825 AAACCACGAGTCGAAATGAAGCGACCAAGATTGAGTCGAGGTCAAAAATGATCTGAACA
1 AAACCACGAGTCGAAATAAAGCGACCAAGATTGAGTCGAAGTAAAAAATGATCGGAACA
* * * * *
1439884 AAATCACGAGTCGAAATAAAGTGACCAAGATTGAGTTGAAGTAAAAAATGATCGGGATA
1 AAACCACGAGTCGAAATAAAGCGACCAAGATTGAGTCGAAGTAAAAAATGATCGGAACA
1439943 AAACCACGA
1 AAACCACGA
1439952 ATGATCTAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.17
Consensus pattern (59 bp):
AAACCACGAGTCGAAATAAAGCGACCAAGATTGAGTCGAAGTAAAAAATGATCGGAACA
Found at i:1439971 original size:59 final size:59
Alignment explanation
Indices: 1439825--1439973 Score: 149
Period size: 59 Copynumber: 2.5 Consensus size: 59
1439815 AATCAAAACG
* * * * *
1439825 AAACCACGAGTCGAAATGAAGC-GACCAAGATTGAGTCGAGGTCAAAAATGATCTGAACA
1 AAACCACGAATCGAAAT-AAACTGACCAAGATTGAGTCGAAGTAAAAAATGATCGGAACA
* * * * * *
1439884 AAATCACGAGTCGAAATAAAGTGACCAAGATTGAGTTGAAGTAAAAAATGATCGGGATA
1 AAACCACGAATCGAAATAAACTGACCAAGATTGAGTCGAAGTAAAAAATGATCGGAACA
**
1439943 AAACCACGAAT-GATCTAAACTGAGCCAAGAT
1 AAACCACGAATCGAAATAAACTGA-CCAAGAT
1439974 CAAGTGACCT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
58 11 0.15
59 63 0.85
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.17
Consensus pattern (59 bp):
AAACCACGAATCGAAATAAACTGACCAAGATTGAGTCGAAGTAAAAAATGATCGGAACA
Found at i:1440897 original size:52 final size:51
Alignment explanation
Indices: 1440801--1440947 Score: 167
Period size: 52 Copynumber: 2.9 Consensus size: 51
1440791 CAAGTCACCT
* * *
1440801 TTTCAAGTTTTCAAGTTGAA--CTCTTTTTTTTCTTGGGTTCAAGCCTCCC
1 TTTCAAGTTTTCAACTTGAACCCTCTTTTTTTTTTTGGGTTTAAGCCTCCC
* **
1440850 TTTCGAGTTTTCAACTTGAACTCCTCTTTTTTTTTTTGGGTTTAAGCCTCTT
1 TTTCAAGTTTTCAACTTGAAC-CCTCTTTTTTTTTTTGGGTTTAAGCCTCCC
**
1440902 TTTTTAGTTTTCAACTTGAACACC-CTTTTTTTTTTTAGGG-TTAAGC
1 TTTCAAGTTTTCAACTTGAAC-CCTCTTTTTTTTTTT-GGGTTTAAGC
1440948 AAAGTACTTC
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
49 18 0.21
51 18 0.21
52 49 0.58
ACGTcount: A:0.16, C:0.19, G:0.14, T:0.51
Consensus pattern (51 bp):
TTTCAAGTTTTCAACTTGAACCCTCTTTTTTTTTTTGGGTTTAAGCCTCCC
Found at i:1440936 original size:53 final size:52
Alignment explanation
Indices: 1440777--1440947 Score: 163
Period size: 52 Copynumber: 3.4 Consensus size: 52
1440767 AACTCAAAGC
* * * * * * *
1440777 TTTTTCTTTGGGTCCAAGTCACCTTTTCAAGTTTTCAAGTTGAA---CTCTT
1 TTTTTTTTTGGGTTCAAGCCTCCCTTTCGAGTTTTCAACTTGAACCCCTCTT
* *
1440826 TTTTTTCTTGGGTTCAAGCCTCCCTTTCGAGTTTTCAACTTGAACTCCTCTT
1 TTTTTTTTTGGGTTCAAGCCTCCCTTTCGAGTTTTCAACTTGAACCCCTCTT
* ** **
1440878 TTTTTTTTTGGGTTTAAGCCTCTTTTTTTAGTTTTCAACTTGAACACCCT-TT
1 TTTTTTTTTGGGTTCAAGCCTCCCTTTCGAGTTTTCAACTTGAAC-CCCTCTT
*
1440930 TTTTTTTTAGGGTT-AAGC
1 TTTTTTTTTGGGTTCAAGC
1440948 AAAGTACTTC
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
49 36 0.35
51 4 0.04
52 59 0.58
53 3 0.03
ACGTcount: A:0.16, C:0.20, G:0.14, T:0.50
Consensus pattern (52 bp):
TTTTTTTTTGGGTTCAAGCCTCCCTTTCGAGTTTTCAACTTGAACCCCTCTT
Found at i:1451689 original size:7 final size:7
Alignment explanation
Indices: 1451676--1451706 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1451666 TATCTTTCAT
1451676 TTTTTTA
1 TTTTTTA
*
1451683 ATTTTTA
1 TTTTTTA
1451690 TTTTTTA
1 TTTTTTA
1451697 TTTTTTA
1 TTTTTTA
1451704 TTT
1 TTT
1451707 AAAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTA
Found at i:1456064 original size:16 final size:15
Alignment explanation
Indices: 1456027--1456066 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1456017 ACTTTTTTCC
* *
1456027 AAAAATATTTTTTTT
1 AAAAAAATTATTTTT
1456042 AAAAAAATTATTTTT
1 AAAAAAATTATTTTT
1456057 AAAGAAAATT
1 AAA-AAAATT
1456067 GATACTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
AAAAAAATTATTTTT
Found at i:1456125 original size:60 final size:59
Alignment explanation
Indices: 1455819--1456125 Score: 239
Period size: 60 Copynumber: 5.1 Consensus size: 59
1455809 TTATACAAGA
* * *
1455819 AAAATTGATACTTTTAAC-TTTTCCTTAAAAATA--TTTTCTTGATAATTTTTATCTTTAAGA
1 AAAATTGATACTTTTAACTTTTTCC-CAAAAATATTTTTTTTTGA-AATTTTTA--TTTAAGG
* * * * * *
1455879 AAAACTGATAATTTCAACTTTTTCTC-AAAATATTTTGTTTTTGAAATTTTAATTTCAAGA
1 AAAATTGATACTTTTAACTTTTTCCCAAAAATATTTT-TTTTTGAAATTTTTATTT-AAGG
** **** * *
1455939 AAAATTGATACTTTTAACTTTTT-CTTAAAATACCTTTTTTAAAAAAATTTTTGTTCTAAAAG
1 AAAATTGATACTTTTAACTTTTTCCCAAAAATA--TTTTTTTTTGAAATTTTTATT-T-AAGG
* ** * *
1456001 AAAATTGATACTTTTAACTTTTTTCCAAAAATATTTTTTTTAAAAAAATTATT-TTTAAAG
1 AAAATTGATACTTTTAACTTTTTCCCAAAAATATTTTTTTT--TGAAATTTTTATTTAAGG
* *
1456061 AAAATTGATACTTTAAACTTTTTCCCAAAAATATTTTTTTTTGGAAATTTTTATTTTAGG
1 AAAATTGATACTTTTAACTTTTTCCCAAAAATATTTTTTTTT-GAAATTTTTATTTAAGG
1456121 AAAAT
1 AAAAT
1456126 CATTGACAAA
Statistics
Matches: 200, Mismatches: 33, Indels: 28
0.77 0.13 0.11
Matches are distributed among these distances:
59 16 0.08
60 98 0.49
61 32 0.16
62 38 0.19
63 16 0.08
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.48
Consensus pattern (59 bp):
AAAATTGATACTTTTAACTTTTTCCCAAAAATATTTTTTTTTGAAATTTTTATTTAAGG
Found at i:1456204 original size:3 final size:3
Alignment explanation
Indices: 1456196--1456221 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1456186 AATAAGCATA
1456196 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1456222 ATAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1457550 original size:19 final size:18
Alignment explanation
Indices: 1457516--1457557 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1457506 AATACATGGC
*
1457516 AAAAAAAGAAAATTAAA-
1 AAAAAAACAAAATTAAAG
1457533 AAAAAAACAAAATGTTAAAG
1 AAAAAAACAAAA--TTAAAG
1457553 AAAAA
1 AAAAA
1457558 CGAGTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 11 0.52
19 5 0.24
20 5 0.24
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (18 bp):
AAAAAAACAAAATTAAAG
Found at i:1461281 original size:2 final size:2
Alignment explanation
Indices: 1461276--1461313 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1461266 TATATATGTT
*
1461276 TG TG TG AG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1461314 ATGAGAGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.00, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:1461411 original size:2 final size:2
Alignment explanation
Indices: 1461404--1461430 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1461394 TTTTACCATT
1461404 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1461431 TTTTGAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1461636 original size:2 final size:2
Alignment explanation
Indices: 1461629--1461661 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1461619 TCCAATGGTT
1461629 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
1461662 GTTATATGAT
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:1462152 original size:2 final size:2
Alignment explanation
Indices: 1462147--1462171 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1462137 GCGAGCGCGC
1462147 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 A
1462172 AATAAATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1463411 original size:8 final size:8
Alignment explanation
Indices: 1463400--1463429 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1463390 CAATTTCTTT
1463400 TTTTTTTA
1 TTTTTTTA
1463408 -TTTTTTA
1 TTTTTTTA
1463415 TTTTTTTA
1 TTTTTTTA
1463423 TTTTTTT
1 TTTTTTT
1463430 GGTAATTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1463418 original size:15 final size:15
Alignment explanation
Indices: 1463400--1463428 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1463390 CAATTTCTTT
1463400 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
1463415 TTTTTTTATTTTTT
1 TTTTTTTATTTTTT
1463429 TGGTAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTATTTTTTA
Found at i:1466512 original size:2 final size:2
Alignment explanation
Indices: 1466505--1466536 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1466495 AAATTTCTTT
1466505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1466537 AGAAAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1467415 original size:2 final size:2
Alignment explanation
Indices: 1467408--1467442 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1467398 TAAAGGAAGA
1467408 AT AT AT AT AT AT AT AT AT -T 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
1467443 TATTTTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1467431 original size:15 final size:15
Alignment explanation
Indices: 1467411--1467440 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1467401 AGGAAGAATA
1467411 TATATATATATATAT
1 TATATATATATATAT
1467426 TATATATATATATAT
1 TATATATATATATAT
1467441 ATTATTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:1467431 original size:17 final size:17
Alignment explanation
Indices: 1467409--1467445 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1467399 AAAGGAAGAA
1467409 TATATATATATATATAT
1 TATATATATATATATAT
1467426 TATATATATATATATAT
1 TATATATATATATATAT
1467443 TAT
1 TAT
1467446 TTTACAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:1467568 original size:2 final size:2
Alignment explanation
Indices: 1467561--1467624 Score: 83
Period size: 2 Copynumber: 32.0 Consensus size: 2
1467551 TTGTTATTTG
* * * *
1467561 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AC AC AC 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
*
1467603 AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1467625 GTTCCACCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1469494 original size:34 final size:34
Alignment explanation
Indices: 1469428--1469507 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
1469418 GGATTTTCAT
* *
1469428 TTTC-AAAAACTTCTAAAAGTTTTAAGAGATGCA
1 TTTCTAAAAGCTTCTAAAAGTTTTAAGAAATGCA
* * *
1469461 TTTCTAAAAGCTTCTAAATGTTTTCATAAATGCA
1 TTTCTAAAAGCTTCTAAAAGTTTTAAGAAATGCA
1469495 TTTCTAAAAGCTT
1 TTTCTAAAAGCTT
1469508 TTCTAAGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 4 0.10
34 37 0.90
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (34 bp):
TTTCTAAAAGCTTCTAAAAGTTTTAAGAAATGCA
Found at i:1469502 original size:12 final size:12
Alignment explanation
Indices: 1469456--1469513 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
1469446 GTTTTAAGAG
1469456 ATGCATTTCTAA
1 ATGCATTTCTAA
*
1469468 AAGC--TTCTAA
1 ATGCATTTCTAA
*
1469478 ATG-TTTTCATAA
1 ATGCATTTC-TAA
1469490 ATGCATTTCTAA
1 ATGCATTTCTAA
* *
1469502 AAGCTTTTCTAA
1 ATGCATTTCTAA
1469514 GTTTCTGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
10 8 0.22
11 3 0.08
12 22 0.59
13 4 0.11
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (12 bp):
ATGCATTTCTAA
Found at i:1470814 original size:27 final size:26
Alignment explanation
Indices: 1470777--1470832 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 26
1470767 TATCATGTTA
*
1470777 ATTAACAGATTTATAATTCAAATATCAC
1 ATTAACAGATTT-T-ATTCAAAAATCAC
*
1470805 ATTAA-AGATTTTTTTCAAAAATCAC
1 ATTAACAGATTTTATTCAAAAATCAC
1470830 ATT
1 ATT
1470833 GAATGTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 14 0.54
26 1 0.04
27 6 0.23
28 5 0.19
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (26 bp):
ATTAACAGATTTTATTCAAAAATCAC
Found at i:1482336 original size:17 final size:17
Alignment explanation
Indices: 1482310--1482356 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
1482300 ATGTAAATTA
*
1482310 AAATTTTAATTTTTTTT
1 AAATTATAATTTTTTTT
*
1482327 AAATTATAA-TTCTTTT
1 AAATTATAATTTTTTTT
*
1482343 ATATTAT-ATTTTTT
1 AAATTATAATTTTTT
1482357 ATGTTTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 1 0.04
16 16 0.64
17 8 0.32
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (17 bp):
AAATTATAATTTTTTTT
Found at i:1484859 original size:13 final size:13
Alignment explanation
Indices: 1484841--1484875 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1484831 TAAATGGATT
1484841 ATTTAATAAATTA
1 ATTTAATAAATTA
*
1484854 ATTTAAGAAATTA
1 ATTTAATAAATTA
1484867 ATTTAATAA
1 ATTTAATAA
1484876 CCAATGAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (13 bp):
ATTTAATAAATTA
Found at i:1485030 original size:12 final size:12
Alignment explanation
Indices: 1484960--1485030 Score: 54
Period size: 12 Copynumber: 5.6 Consensus size: 12
1484950 TGAGTTTAAT
*
1484960 TTAATTT-TATA
1 TTAATTTATTTA
1484971 TTAAATTTATTTGA
1 TT-AATTTATTT-A
1484985 TTATGATTTAATTTA
1 TTA--ATTT-ATTTA
*
1485000 TTAATTGATTTA
1 TTAATTTATTTA
*
1485012 TTTATTTATTTA
1 TTAATTTATTTA
*
1485024 ATAATTT
1 TTAATTT
1485031 TTTGTATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
11 2 0.04
12 25 0.52
13 6 0.12
14 3 0.06
15 8 0.17
16 4 0.08
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (12 bp):
TTAATTTATTTA
Found at i:1485911 original size:64 final size:65
Alignment explanation
Indices: 1485838--1485967 Score: 210
Period size: 65 Copynumber: 2.0 Consensus size: 65
1485828 TAGGTATTAT
* *
1485838 ATTTGTATGTTTTAAAACGTAAT-AATGA-ATATTATTTTATGTGTTTCTTTTAATGAAACACAG
1 ATTTGTATGTTTTAAAACATAATAAATGATA-ATTATTTTATGTGTTTCTTTTAACGAAACACAG
1485901 C
65 C
*
1485902 ATTTGTATGTTTTAAAACATAATAAATGTTAATTATTTTATGTGTTTCTTTTAACGAAACACAGC
1 ATTTGTATGTTTTAAAACATAATAAATGATAATTATTTTATGTGTTTCTTTTAACGAAACACAGC
1485967 A
1 A
1485968 CTCGTAATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
64 22 0.36
65 38 0.62
66 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (65 bp):
ATTTGTATGTTTTAAAACATAATAAATGATAATTATTTTATGTGTTTCTTTTAACGAAACACAGC
Found at i:1486434 original size:61 final size:60
Alignment explanation
Indices: 1486350--1486518 Score: 171
Period size: 61 Copynumber: 2.7 Consensus size: 60
1486340 CAATTATTAT
* *
1486350 TTTTTAAAGATAAATATAGTAATTGATTATTATAATTTATTTAAAATAATTAAATAAT-ATA
1 TTTTTAAA-ATAAATATAATAATTGATTATTGTAATTT-TTTAAAATAATTAAATAATCATA
* * * * * *
1486411 TTTTTAAAATTAAATGTAATAATT-ATTTTTTGTGATTTTTTAAAAATAATTAATTATTGCATT
1 TTTTTAAAA-TAAATATAATAATTGA-TTATTGTAATTTTTT-AAAATAATTAAATAAT-CATA
* *
1486474 TTTTTAAAGCTAAATATAATAATTGTTTATTGTAATTTTTTAAAA
1 TTTTTAAA-ATAAATATAATAATTGATTATTGTAATTTTTTAAAA
1486519 ATATGTAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 13
0.77 0.11 0.11
Matches are distributed among these distances:
60 5 0.06
61 43 0.49
62 4 0.05
63 36 0.41
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (60 bp):
TTTTTAAAATAAATATAATAATTGATTATTGTAATTTTTTAAAATAATTAAATAATCATA
Found at i:1486495 original size:63 final size:61
Alignment explanation
Indices: 1486349--1486521 Score: 190
Period size: 63 Copynumber: 2.8 Consensus size: 61
1486339 TCAATTATTA
* *
1486349 TTTTTTAAAGATAAATATAGTAATTGA-TTATTATAATTTATTT-AAAATAATTAAATAATAT
1 TTTTTTAAAGATAAATATAATAATT-ATTTATTGTAATTT-TTTAAAAATAATTAAATAATAT
* * * * * *
1486410 ATTTTTAAA-ATTAAATGTAATAATTATTTTTTGTGATTTTTTAAAAATAATTAATTATTGCAT
1 TTTTTTAAAGA-TAAATATAATAATTATTTATTGTAATTTTTTAAAAATAATTAAATAAT--AT
* *
1486473 TTTTTTAAAGCTAAATATAATAATTGTTTATTGTAATTTTTTAAAAATA
1 TTTTTTAAAGATAAATATAATAATTATTTATTGTAATTTTTTAAAAATA
1486522 TGTAAAATGC
Statistics
Matches: 92, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
60 5 0.05
61 43 0.47
63 44 0.48
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (61 bp):
TTTTTTAAAGATAAATATAATAATTATTTATTGTAATTTTTTAAAAATAATTAAATAATAT
Found at i:1493139 original size:43 final size:43
Alignment explanation
Indices: 1493056--1493142 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
1493046 GCCACTAGTA
* * *
1493056 ATTAATTGTAACCTTTAACCATTTTTAACACCCTTATAATGTG
1 ATTAATTGAAACCTTTAACCATTCTTAACACCATTATAATGTG
* *
1493099 ATTAATTGCAAACC-TTAACCATTCTTAACACTATTGTAATGTG
1 ATTAATTG-AAACCTTTAACCATTCTTAACACCATTATAATGTG
1493142 A
1 A
1493143 CTATAAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
43 34 0.89
44 4 0.11
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (43 bp):
ATTAATTGAAACCTTTAACCATTCTTAACACCATTATAATGTG
Found at i:1493529 original size:35 final size:35
Alignment explanation
Indices: 1493483--1493549 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
1493473 ATGATGTATA
* *
1493483 GGTGCATATGAGTATGTATTTGTTTGTGTTGAAAT
1 GGTGCATATGAGCATGTATTTGTTTGGGTTGAAAT
*
1493518 GGTGCATATGAGCATGTGTTTGTTTGGGTTGA
1 GGTGCATATGAGCATGTATTTGTTTGGGTTGA
1493550 GAATATTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.19, C:0.04, G:0.33, T:0.43
Consensus pattern (35 bp):
GGTGCATATGAGCATGTATTTGTTTGGGTTGAAAT
Found at i:1496533 original size:17 final size:18
Alignment explanation
Indices: 1496501--1496534 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1496491 AACAAGATTG
*
1496501 ATATATTCATAATTAAAA
1 ATATAATCATAATTAAAA
1496519 ATATAATCA-AATTAAA
1 ATATAATCATAATTAAA
1496535 TTAAATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (18 bp):
ATATAATCATAATTAAAA
Found at i:1497271 original size:19 final size:21
Alignment explanation
Indices: 1497247--1497296 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1497237 ACATGTATCC
1497247 ATAATTTTACA-TTTTTAT-A
1 ATAATTTTACATTTTTTATAA
**
1497266 ATAATTCTTTTATTTTTTATAA
1 ATAATT-TTACATTTTTTATAA
1497288 ATAATTTTA
1 ATAATTTTA
1497297 ACTTAGTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 6 0.24
20 3 0.12
21 9 0.36
22 7 0.28
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
ATAATTTTACATTTTTTATAA
Found at i:1498671 original size:77 final size:78
Alignment explanation
Indices: 1498543--1498689 Score: 244
Period size: 77 Copynumber: 1.9 Consensus size: 78
1498533 TTGTGGTTGA
*
1498543 AAGTATTGGGAATTTGAATACTAACGAGTTTAATTTTGAAATTTCAATATGTAA-ATAGTTAAAA
1 AAGTATTGGGAATTTGAATACTAACGAGTTTAATTTTGAAATTGCAATATGTAATA-AGTTAAAA
*
1498607 GTATATAAGCAGGC
65 GCATATAAGCAGGC
*
1498621 AAGTATTGGGAATTTGAA-ACTAAGGAGTTTAATTTTGAAATTGCAATATGTAATAAGTTAAAAG
1 AAGTATTGGGAATTTGAATACTAACGAGTTTAATTTTGAAATTGCAATATGTAATAAGTTAAAAG
1498685 CATAT
66 CATAT
1498690 CATCATGCAT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
77 46 0.71
78 19 0.29
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.35
Consensus pattern (78 bp):
AAGTATTGGGAATTTGAATACTAACGAGTTTAATTTTGAAATTGCAATATGTAATAAGTTAAAAG
CATATAAGCAGGC
Found at i:1509283 original size:61 final size:61
Alignment explanation
Indices: 1509198--1509313 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
1509188 AATGTGTTTT
* * * *
1509198 TTTGAGATGGATTTGTCATTTGTGGTAGTATAAAAGAGGATAAAATGAA-AAAGAACACACA
1 TTTGAGATGGAGTTGTCATATGTGGTAATATAAAAGAAGATAAAAT-AAGAAAGAACACACA
*
1509259 TTTGAGATGGAGTTGTTATATGTGGTAATATAAAAGAAGATAAAATAAGAAAGAA
1 TTTGAGATGGAGTTGTCATATGTGGTAATATAAAAGAAGATAAAATAAGAAAGAA
1509314 GTCATCTATA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 2 0.04
61 47 0.96
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.28
Consensus pattern (61 bp):
TTTGAGATGGAGTTGTCATATGTGGTAATATAAAAGAAGATAAAATAAGAAAGAACACACA
Found at i:1516376 original size:17 final size:18
Alignment explanation
Indices: 1516336--1516376 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1516326 AGAATAAGAT
*
1516336 AATTTATTTATTTGTCAA
1 AATTTATTTATTTGTAAA
*
1516354 AA-TTATTT-TTTTTAAA
1 AATTTATTTATTTGTAAA
1516370 AATTTAT
1 AATTTAT
1516377 ATAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 10 0.50
18 2 0.10
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
AATTTATTTATTTGTAAA
Found at i:1519238 original size:63 final size:63
Alignment explanation
Indices: 1519139--1519260 Score: 208
Period size: 63 Copynumber: 1.9 Consensus size: 63
1519129 GGTTGACTGT
* * *
1519139 TAGTAAACCGTTATCACTATGGTATTGACTATTGATTGTCTAAAGTCTCACTTGAGTAGGATA
1 TAGTAAACCGTTATCACCATGGAATTGACTATTGATTGTCCAAAGTCTCACTTGAGTAGGATA
*
1519202 TAGTAAACCGTTATCACCGTGGAATTGACTATTGATTGTCCAAAGTCTCACTTGAGTAG
1 TAGTAAACCGTTATCACCATGGAATTGACTATTGATTGTCCAAAGTCTCACTTGAGTAG
1519261 TATTCCTCGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (63 bp):
TAGTAAACCGTTATCACCATGGAATTGACTATTGATTGTCCAAAGTCTCACTTGAGTAGGATA
Found at i:1519590 original size:19 final size:20
Alignment explanation
Indices: 1519566--1519608 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1519556 GGTAGCACTT
* *
1519566 TAATTTTTAATA-GATTTAA
1 TAATTTTAAATATGATATAA
1519585 TAATTTTAAATATGATATAA
1 TAATTTTAAATATGATATAA
1519605 TAAT
1 TAAT
1519609 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TAATTTTAAATATGATATAA
Found at i:1520006 original size:34 final size:33
Alignment explanation
Indices: 1519968--1520040 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 33
1519958 TATTAAAAAA
1519968 ATTTTGA-GTTATTATATTTTAAAAATAAGATTT-T
1 ATTTTGATGTTATTATA-TTT--AAATAAGATTTAT
*
1520002 ATTTT-ATTTTATTATATTTAAATAAGATTTAT
1 ATTTTGATGTTATTATATTTAAATAAGATTTAT
1520034 ATTTTGA
1 ATTTTGA
1520041 ATCGTATTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
31 11 0.31
32 6 0.17
33 5 0.14
34 13 0.37
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (33 bp):
ATTTTGATGTTATTATATTTAAATAAGATTTAT
Found at i:1520028 original size:31 final size:34
Alignment explanation
Indices: 1519976--1520038 Score: 96
Period size: 31 Copynumber: 1.9 Consensus size: 34
1519966 AAATTTTGAG
1519976 TTATTATATTTTAAAAATAAGATTT-TATTTTATT
1 TTATTATATTTT-AAAATAAGATTTATATTTTATT
1520010 TTATTATA-TTT-AAATAAGATTTATATTTT
1 TTATTATATTTTAAAATAAGATTTATATTTT
1520039 GAATCGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 11 0.39
32 6 0.21
33 3 0.11
34 8 0.29
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (34 bp):
TTATTATATTTTAAAATAAGATTTATATTTTATT
Found at i:1520083 original size:16 final size:16
Alignment explanation
Indices: 1520045--1520110 Score: 60
Period size: 17 Copynumber: 4.0 Consensus size: 16
1520035 TTTTGAATCG
* *
1520045 TATTCAAATAAAATTT
1 TATTTAAATAAAAATT
*
1520061 TATTTTAAATAAAAAAT
1 TA-TTTAAATAAAAATT
*
1520078 TATTTAGATTAAAAATT
1 TATTTA-AATAAAAATT
* *
1520095 TATTTAGATATAAATT
1 TATTTAAATAAAAATT
1520111 AAAAGTTAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 13 0.32
17 27 0.68
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (16 bp):
TATTTAAATAAAAATT
Done.