Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_pilon, 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: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 18
Found at i:1469338 original size:22 final size:20
Alignment explanation
Indices: 1469310--1469374 Score: 80
Period size: 19 Copynumber: 3.2 Consensus size: 20
1469300 TAAATACAAT
1469310 AAATAATATTATTTATTATA
1 AAATAATATTATTTATTATA
*
1469330 AAACTTAATATTA-TTATTTTA
1 AAA--TAATATTATTTATTATA
*
1469351 AAATAAT-TTATTTATTATT
1 AAATAATATTATTTATTATA
1469370 AAATA
1 AAATA
1469375 TTTTTATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 3 0.08
21 10 0.26
22 8 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATAATATTATTTATTATA
Found at i:1469526 original size:23 final size:23
Alignment explanation
Indices: 1469477--1469527 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1469467 GCGTTATATT
**
1469477 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
1469500 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
1469523 ATATT
1 ATATT
1469528 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1469539 original size:19 final size:18
Alignment explanation
Indices: 1469515--1469567 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
1469505 TTAAATATCT
*
1469515 TTATTAAAATATTATTAGA
1 TTATTAAAATATTATT-CA
1469534 TTATTATATTAATATTATTCA
1 TTATTA-A--AATATTATTCA
1469555 TTATTAAATATAT
1 TTATTAAA-ATAT
1469568 AAAAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 1 0.03
19 10 0.34
20 2 0.07
21 7 0.24
22 9 0.31
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TTATTAAAATATTATTCA
Found at i:1469610 original size:30 final size:30
Alignment explanation
Indices: 1469545--1469612 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
1469535 TATTATATTA
1469545 ATATTATTCATTATTAAATATATAAAAAAT
1 ATATTATTCATTATTAAATATATAAAAAAT
*
1469575 TTATTATAT-ATTATTAAA-ATA-AAATATAAT
1 ATATTAT-TCATTATTAAATATATAAA-A-AAT
1469605 ATATTATT
1 ATATTATT
1469613 GTAATATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 3 0.09
29 5 0.15
30 24 0.73
31 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
ATATTATTCATTATTAAATATATAAAAAAT
Found at i:1469618 original size:18 final size:19
Alignment explanation
Indices: 1469597--1469642 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1469587 ATTAAAATAA
1469597 AATATAATAT-ATTATTGT
1 AATATAATATGATTATTGT
*
1469615 AATATAAT-TGATTATTTT
1 AATATAATATGATTATTGT
*
1469633 ATTATAATAT
1 AATATAATAT
1469643 TAAAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (19 bp):
AATATAATATGATTATTGT
Found at i:1469659 original size:22 final size:23
Alignment explanation
Indices: 1469632--1469678 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1469622 TTGATTATTT
1469632 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
1469654 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
1469677 TA
1 TA
1469679 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:1469665 original size:30 final size:34
Alignment explanation
Indices: 1469615--1469684 Score: 103
Period size: 32 Copynumber: 2.2 Consensus size: 34
1469605 ATATTATTGT
*
1469615 AATATAATTGATTATTTTATTAT-AATATTAA-A
1 AATATAATTGATTATATTATTATAAATATTAATA
1469647 AATATAA-T-ATTATATTATTATAAATATTAATA
1 AATATAATTGATTATATTATTATAAATATTAATA
1469679 AATATA
1 AATATA
1469685 TTTTAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
30 12 0.34
31 9 0.26
32 14 0.40
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (34 bp):
AATATAATTGATTATATTATTATAAATATTAATA
Found at i:1469683 original size:22 final size:22
Alignment explanation
Indices: 1469639--1469695 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1469629 TTTTATTATA
* *
1469639 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
1469660 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
1469682 ATATTTTAAATATT
1 ATATTATAAATATT
1469696 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:1469963 original size:41 final size:41
Alignment explanation
Indices: 1469908--1469998 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
1469898 TTCCTTCGAC
* *
1469908 CAAACACTGGAAAACATTTTCCGGAAAATGAATTACGTGAAA
1 CAAACAC-GGAAAACATTTTCCGGAAAACGAATTACATGAAA
*
1469950 CAAACACGGAAAACATTTTTCGGAAAACGAATTACATGAAA
1 CAAACACGGAAAACATTTTCCGGAAAACGAATTACATGAAA
1469991 CAAACACG
1 CAAACACG
1469999 AGATATCAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 39 0.85
42 7 0.15
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (41 bp):
CAAACACGGAAAACATTTTCCGGAAAACGAATTACATGAAA
Found at i:1471415 original size:2 final size:2
Alignment explanation
Indices: 1471408--1471452 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
1471398 TTTATTCCCT
* *
1471408 TA TA TA TA TA TA TA TG TA TA CA T- TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1471448 T- TA TA
1 TA TA TA
1471453 GCTATTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1471458 original size:24 final size:25
Alignment explanation
Indices: 1471407--1471460 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
1471397 TTTTATTCCC
1471407 TTATATATATATATATGTATACATTA
1 TTATATATATATATATGTATACA-TA
1471433 TTATATATATATATAT-TATAGC-TA
1 TTATATATATATATATGTATA-CATA
1471457 TTAT
1 TTAT
1471461 TATTTCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 6 0.22
25 4 0.15
26 17 0.63
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (25 bp):
TTATATATATATATATGTATACATA
Found at i:1471464 original size:15 final size:14
Alignment explanation
Indices: 1471429--1471478 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 14
1471419 ATATGTATAC
1471429 ATTATTATA-TATAT
1 ATTATTATACTAT-T
1471443 ATATATTATAGCTATT
1 AT-TATTATA-CTATT
1471459 ATTATT-T-CTATT
1 ATTATTATACTATT
1471471 ATTATTAT
1 ATTATTAT
1471479 TATTTTATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 11 0.34
13 1 0.03
14 3 0.09
15 11 0.34
16 3 0.09
17 3 0.09
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (14 bp):
ATTATTATACTATT
Found at i:1471556 original size:14 final size:14
Alignment explanation
Indices: 1471506--1471564 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1471496 ATATATATAT
1471506 TTTTATTTATTATCA
1 TTTTATTTATT-TCA
* *
1471521 TTCTTATATGTGTATTCT
1 TT-TTAT-T-TAT-TTCA
1471539 TTTTATTTATTTCA
1 TTTTATTTATTTCA
1471553 TTTTATTTATTT
1 TTTTATTTATTT
1471565 TCTTATTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 15 0.42
15 4 0.11
16 5 0.14
17 5 0.14
18 6 0.17
19 1 0.03
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTTATTTATTTCA
Found at i:1471746 original size:13 final size:13
Alignment explanation
Indices: 1471724--1471755 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1471714 TATGTTTTAT
1471724 TTTA-TTTTTTCC
1 TTTATTTTTTTCC
1471736 TTTATTTTTTTCC
1 TTTATTTTTTTCC
1471749 TTTATTT
1 TTTATTT
1471756 ATCCTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTTTTTCC
Found at i:1475065 original size:26 final size:28
Alignment explanation
Indices: 1475030--1475081 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
1475020 CCATTGCATA
1475030 TTTTGTATTTTATA-TTT-CATGTTTGT
1 TTTTGTATTTTATATTTTCCATGTTTGT
*
1475056 TTTTTTATTTTATATTTTCCATGTTT
1 TTTTGTATTTTATATTTTCCATGTTT
1475082 TTACATTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 13 0.57
27 3 0.13
28 7 0.30
ACGTcount: A:0.15, C:0.06, G:0.08, T:0.71
Consensus pattern (28 bp):
TTTTGTATTTTATATTTTCCATGTTTGT
Found at i:1482217 original size:9 final size:9
Alignment explanation
Indices: 1482198--1482246 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
1482188 AAGAAAAAGG
1482198 AAAAGAAAA
1 AAAAGAAAA
1482207 AGGAAA-AAAA
1 A--AAAGAAAA
*
1482217 GAAA-AAAA
1 AAAAGAAAA
1482225 AAAAGAAAA
1 AAAAGAAAA
1482234 AAAAGAAAA
1 AAAAGAAAA
1482243 AAAA
1 AAAA
1482247 TGTTTAGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 10 0.29
9 18 0.51
10 4 0.11
11 3 0.09
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:1482217 original size:21 final size:19
Alignment explanation
Indices: 1482187--1482246 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
1482177 TAAGTCGAAG
*
1482187 AAAG-AAAAAGGAAAAGAAA
1 AAAGAAAAAAAGAAAA-AAA
*
1482206 AAGGAAAAAAAGAAAAAAAA
1 AAAGAAAAAAAG-AAAAAAA
1482226 AAAGAAAAAAAAGAAAAAAA
1 AAAG-AAAAAAAGAAAAAAA
1482246 A
1 A
1482247 TGTTTAGGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 3 0.09
20 20 0.57
21 12 0.34
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAAAGAAAAAAA
Found at i:1482220 original size:20 final size:19
Alignment explanation
Indices: 1482184--1482246 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 19
1482174 TCTTAAGTCG
1482184 AAGAAAGAAAAAGGAAAAGAAA
1 AAGAAA-AAAAA-GAAAA-AAA
*
1482206 AAGGAAAAAAAGAAAAAAAAA
1 AA-GAAAAAAA-AGAAAAAAA
1482227 AAGAAAAAAAAGAAAAAAA
1 AAGAAAAAAAAGAAAAAAA
1482246 A
1 A
1482247 TGTTTAGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 5 0.14
22 10 0.27
23 5 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAAAGAAAAAAA
Found at i:1482225 original size:12 final size:12
Alignment explanation
Indices: 1482187--1482246 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
1482177 TAAGTCGAAG
**
1482187 AAAGAAAAAGGA
1 AAAGAAAAAAAA
1482199 AAAGAAAAAGGAAAA
1 AAAG-AAAA--AAAA
1482214 AAAGAAAAAAAA
1 AAAGAAAAAAAA
1482226 AAAGAAAAAAAA
1 AAAGAAAAAAAA
1482238 GAAA-AAAAA
1 -AAAGAAAAA
1482247 TGTTTAGGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 25 0.60
13 7 0.17
14 4 0.10
15 6 0.14
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:1482242 original size:27 final size:27
Alignment explanation
Indices: 1482187--1482244 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1482177 TAAGTCGAAG
** *
1482187 AAAGAAAAAGGAAAAGAAAAAGGAAAA
1 AAAGAAAAAAAAAAAGAAAAAGAAAAA
*
1482214 AAAGAAAAAAAAAAAGAAAAAAAAGAAA
1 AAAGAAAAAAAAAAAGAAAAAGAA-AAA
1482242 AAA
1 AAA
1482245 AATGTTTAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (27 bp):
AAAGAAAAAAAAAAAGAAAAAGAAAAA
Found at i:1482243 original size:6 final size:6
Alignment explanation
Indices: 1482187--1482234 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
1482177 TAAGTCGAAG
* *
1482187 AAAGAA AAAGGA AAAGAA AAAGGAAAA AAAGAA AAAAAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAA-G--AA AAAGAA AAAGAA AAAGAA AAA
1482235 AAAGAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 28 0.80
7 1 0.03
8 1 0.03
9 5 0.14
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:1485710 original size:12 final size:13
Alignment explanation
Indices: 1485695--1485726 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1485685 ATATATATAG
1485695 CTATTATTATT-T
1 CTATTATTATTAT
1485707 CTATTATTATTAT
1 CTATTATTATTAT
1485720 -TATTATT
1 CTATTATT
1485727 TTTAACGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 18 0.95
13 1 0.05
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (13 bp):
CTATTATTATTAT
Found at i:1487553 original size:2 final size:2
Alignment explanation
Indices: 1487546--1487572 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1487536 GTTTTATGGC
1487546 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
1487573 GCAGCTTCAA
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:1499651 original size:21 final size:21
Alignment explanation
Indices: 1499627--1499666 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1499617 TAATAAATTA
1499627 TATGAATATAAAAGATAAGTT
1 TATGAATATAAAAGATAAGTT
1499648 TATGAATATAAAAGATAAG
1 TATGAATATAAAAGATAAG
1499667 ATCTTTGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (21 bp):
TATGAATATAAAAGATAAGTT
Found at i:1500824 original size:23 final size:23
Alignment explanation
Indices: 1500798--1500865 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
1500788 CATCTTATAT
1500798 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* * * *
1500821 GGCACTTCGGTGCAATTCTCCGT
1 GGCACTACGGTGCATTTCTACGC
* *
1500844 GGCACTCCGGTGCATTTATACG
1 GGCACTACGGTGCATTTCTACG
1500866 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.16, C:0.29, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:1505608 original size:2 final size:2
Alignment explanation
Indices: 1505601--1505627 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1505591 ATTAAATCAT
1505601 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
1505628 CAAATGTTAA
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:1506232 original size:2 final size:2
Alignment explanation
Indices: 1506225--1506271 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
1506215 ATTATTTTGT
* * * *
1506225 TA TA TA TA TA TA TA TA TA TT TT TA T- TA TA TA TA TA TG TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1506266 TA TA TA
1 TA TA TA
1506272 GTAATATAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1506385 original size:38 final size:37
Alignment explanation
Indices: 1506304--1506662 Score: 209
Period size: 38 Copynumber: 10.1 Consensus size: 37
1506294 TTATGACAAA
* * * *
1506304 ATATAATATATAATTTTCGGAAAACGATTTTGAAAATTT
1 ATATAATATATAGTTTT-TGAAAAC-ATTTTTAAAATAT
* *
1506343 ATATATTATATAGTTTTTGAAAATATTTTT--AA-A-
1 ATATAATATATAGTTTTTGAAAACATTTTTAAAATAT
1506376 ATATAATATATAG-TTTTGAAAACA---TT----TAT
1 ATATAATATATAGTTTTTGAAAACATTTTTAAAATAT
* * *
1506405 ATAT--TGTATAGTTTTT-AAAATATTTTGAAAACT-T
1 ATATAATATATAGTTTTTGAAAACATTTTTAAAA-TAT
*
1506439 ATATAGTATATAGTTTTT-AAAACATTTTTTGAAAA-ATT
1 ATATAATATATAGTTTTTGAAAACA-TTTTT-AAAATA-T
*
1506477 ATATAATATATAG-TTTTAAAAACATTTTTGAAAA-ATT
1 ATATAATATATAGTTTTTGAAAACATTTTT-AAAATA-T
*** *
1506514 ATATAATATATAGTTTAAAAAAACATTTTTTAAAAAATT
1 ATATAATATATAGTTTTTGAAAACA-TTTTTAAAATA-T
* *
1506553 ATATAATATATAG-TTTTAAAAACATTTTTTGAAAA-CT
1 ATATAATATATAGTTTTTGAAAACA-TTTTT-AAAATAT
* *
1506590 -TAT-ATA-ATA-TTTTT-AAAACATTTTGAAAA-CT
1 ATATAATATATAGTTTTTGAAAACATTTTTAAAATAT
* *
1506621 ATATAACATATAG-TTTTGAAAACTTTTTTAAAATAT
1 ATATAATATATAGTTTTTGAAAACATTTTTAAAATAT
1506657 AATATA
1 -ATATA
1506663 TAGTTAAAAA
Statistics
Matches: 265, Mismatches: 25, Indels: 62
0.75 0.07 0.18
Matches are distributed among these distances:
27 11 0.04
28 5 0.02
29 6 0.02
30 1 0.00
31 6 0.02
32 17 0.06
33 20 0.08
34 19 0.07
35 19 0.07
36 20 0.08
37 45 0.17
38 56 0.21
39 40 0.15
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATAATATATAGTTTTTGAAAACATTTTTAAAATAT
Found at i:1506594 original size:31 final size:29
Alignment explanation
Indices: 1506558--1506625 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 29
1506548 AAATTATATA
1506558 ATATATAGTTTTAAAAACATTTTTTGAAAACTT
1 ATATATA-TTTTAAAAACA--TTTTGAAAAC-T
*
1506591 ATATAATATTTTTAAAACATTTTGAAAACT
1 ATAT-ATATTTTAAAAACATTTTGAAAACT
1506621 ATATA
1 ATATA
1506626 ACATATAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 1 0.03
30 5 0.15
31 10 0.30
33 14 0.42
34 3 0.09
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (29 bp):
ATATATATTTTAAAAACATTTTGAAAACT
Found at i:1506700 original size:36 final size:37
Alignment explanation
Indices: 1506401--1506700 Score: 242
Period size: 37 Copynumber: 8.4 Consensus size: 37
1506391 TTGAAAACAT
* * *
1506401 TTATATATTGTATAGTTTT-TAAAATA-TTTTGAAAA
1 TTATATAATATATAGTTTTAAAAAATATTTTTGAAAA
* *
1506436 CTTATATAGTATATAGTTTTTAAAACAT-TTTTTGAAAAA
1 -TTATATAATATATAG-TTTTAAAAAATATTTTTG-AAAA
*
1506475 TTATATAATATATAGTTTT-AAAAACATTTTTGAAAAA
1 TTATATAATATATAGTTTTAAAAAATATTTTTG-AAAA
* * *
1506512 TTATATAATATATAGTTTAAAAAAACATTTTTTAAAAAA
1 TTATATAATATATAGTTTTAAAAAATA-TTTTT-GAAAA
1506551 TTATATAATATATAGTTTTAAAAACAT-TTTTTGAAAA
1 TTATATAATATATAGTTTTAAAAA-ATATTTTTGAAAA
*
1506588 CTTATAT-A-ATAT--TTTT--AAAACA-TTTTGAAAA
1 -TTATATAATATATAGTTTTAAAAAATATTTTTGAAAA
* * * *
1506619 CTATATAACATATAGTTTTGAAAACT-TTTTT--AAA
1 TTATATAATATATAGTTTTAAAAAATATTTTTGAAAA
*
1506653 --ATATAATATATAG-TTAAAAAAATATTTTTG-AAA
1 TTATATAATATATAGTTTTAAAAAATATTTTTGAAAA
*
1506686 TATATATATTATATA
1 T-TATATAATATATA
1506701 AATTATATTT
Statistics
Matches: 220, Mismatches: 21, Indels: 46
0.77 0.07 0.16
Matches are distributed among these distances:
30 5 0.02
31 18 0.08
32 24 0.11
33 3 0.01
34 11 0.05
36 39 0.18
37 42 0.19
38 41 0.19
39 36 0.16
40 1 0.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (37 bp):
TTATATAATATATAGTTTTAAAAAATATTTTTGAAAA
Found at i:1506735 original size:5 final size:5
Alignment explanation
Indices: 1506725--1506782 Score: 68
Period size: 5 Copynumber: 11.8 Consensus size: 5
1506715 TATTATTATT
*
1506725 TTTTA TTTTA TTTTA TTTTA -TTCA TTTTA -TTTA TTTTAA TTTT- TTTTCA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTT-A
1506774 TTTTA TTTT
1 TTTTA TTTT
1506783 TCTTTTTTAG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
4 11 0.24
5 26 0.57
6 9 0.20
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:1506776 original size:16 final size:14
Alignment explanation
Indices: 1506717--1506783 Score: 73
Period size: 15 Copynumber: 4.6 Consensus size: 14
1506707 ATTTAGTATA
1506717 TTATTATTTTTTATT
1 TTATT-TTTTTTATT
1506732 TTATTTTATTTTA-T
1 TTATTTT-TTTTATT
* *
1506746 TCATTTTATTTATT
1 TTATTTTTTTTATT
1506760 TTAATTTTTTTTCATT
1 TT-ATTTTTTTT-ATT
1506776 TTATTTTT
1 TTATTTTT
1506784 CTTTTTTAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.09
14 11 0.25
15 24 0.55
16 5 0.11
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (14 bp):
TTATTTTTTTTATT
Found at i:1507851 original size:16 final size:16
Alignment explanation
Indices: 1507827--1507861 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1507817 CGGTCCCTCG
*
1507827 TTCATTTAATTAACTT
1 TTCAATTAATTAACTT
*
1507843 TTCAATTAATTAATTT
1 TTCAATTAATTAACTT
1507859 TTC
1 TTC
1507862 TTTTTCCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (16 bp):
TTCAATTAATTAACTT
Found at i:1507989 original size:13 final size:13
Alignment explanation
Indices: 1507973--1508002 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1507963 CGTTCCTCCC
1507973 TTTTATTTTATTT
1 TTTTATTTTATTT
*
1507986 TTTTATTTTCTTT
1 TTTTATTTTATTT
1507999 TTTT
1 TTTT
1508003 CCTCTTCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:1513433 original size:20 final size:22
Alignment explanation
Indices: 1513391--1513441 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
1513381 AGATGGAGAA
1513391 AAAAGAAGACGAAGAGAAAAGG
1 AAAAGAAGACGAAGAGAAAAGG
1513413 AAAAGAA-A-GAAGA-AAATAGG
1 AAAAGAAGACGAAGAGAAA-AGG
1513433 AAAATGAAG
1 AAAA-GAAG
1513442 GGGGAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.12
20 12 0.46
21 4 0.15
22 7 0.27
ACGTcount: A:0.67, C:0.02, G:0.27, T:0.04
Consensus pattern (22 bp):
AAAAGAAGACGAAGAGAAAAGG
Found at i:1524083 original size:87 final size:87
Alignment explanation
Indices: 1523938--1524111 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
1523928 AATTTCCCAA
1523938 CCCCCCGACCGTTCACACTCCCATCACACCCCTATATATAAATTCATTCTCAATCATTTTCATCC
1 CCCCCCGACCGTTCACACTCCCATCACACCCCTATATATAAATTCATTCTCAATCATTTTCATCC
1524003 TCTCAAATCCTCTCAACTTCTC
66 TCTCAAATCCTCTCAACTTCTC
1524025 CCCCCCGACCGTTCACACTCCCATCACACCCCTATATATAAATTCATTCTCAATCATTTTCATCC
1 CCCCCCGACCGTTCACACTCCCATCACACCCCTATATATAAATTCATTCTCAATCATTTTCATCC
1524090 TCTCAAATCCTCTCAACTTCTC
66 TCTCAAATCCTCTCAACTTCTC
1524112 TCAAATCCTC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.25, C:0.41, G:0.02, T:0.31
Consensus pattern (87 bp):
CCCCCCGACCGTTCACACTCCCATCACACCCCTATATATAAATTCATTCTCAATCATTTTCATCC
TCTCAAATCCTCTCAACTTCTC
Found at i:1524099 original size:10 final size:10
Alignment explanation
Indices: 1524086--1524125 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
1524076 AATCATTTTC
1524086 ATCCTCTCAA
1 ATCCTCTCAA
1524096 ATCCTCTCAA
1 ATCCTCTCAA
* *
1524106 CTTCTCTCAA
1 ATCCTCTCAA
1524116 ATCCTCTCAA
1 ATCCTCTCAA
1524126 CTTAAGGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.33
Consensus pattern (10 bp):
ATCCTCTCAA
Found at i:1524114 original size:20 final size:20
Alignment explanation
Indices: 1524089--1524128 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1524079 CATTTTCATC
1524089 CTCTCAAATCCTCTCAACTT
1 CTCTCAAATCCTCTCAACTT
1524109 CTCTCAAATCCTCTCAACTT
1 CTCTCAAATCCTCTCAACTT
1524129 AAGGTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.40, G:0.00, T:0.35
Consensus pattern (20 bp):
CTCTCAAATCCTCTCAACTT
Found at i:1524191 original size:13 final size:13
Alignment explanation
Indices: 1524175--1524212 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1524165 TTTTATTTAA
*
1524175 TTATTTAATTATT
1 TTATTAAATTATT
1524188 TTATTAAATTATT
1 TTATTAAATTATT
1524201 TT-TTACAATTAT
1 TTATTA-AATTAT
1524213 AAAATGGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 3 0.13
13 20 0.87
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTAAATTATT
Found at i:1531044 original size:30 final size:30
Alignment explanation
Indices: 1531008--1531258 Score: 475
Period size: 30 Copynumber: 8.4 Consensus size: 30
1530998 CGAAGGACCG
*
1531008 ATCCAGAGGTCATAAAGATCCTCGATAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1531038 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1531068 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1531098 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
*
1531128 ATCCAGAGCTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1531158 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1531188 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1531218 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
*
1531248 ATCCATAGGTC
1 ATCCAGAGGTC
1531259 CAGAAGAACC
Statistics
Matches: 217, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 217 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
ATCCAGAGGTCATAAAGATCCTCGGTAACT
Found at i:1531658 original size:2 final size:2
Alignment explanation
Indices: 1531646--1531674 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1531636 TACACAACTC
1531646 AT AT A- 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
1531675 TGTACATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1535624 original size:30 final size:30
Alignment explanation
Indices: 1535588--1535868 Score: 526
Period size: 30 Copynumber: 9.4 Consensus size: 30
1535578 CGAAGGACCG
*
1535588 ATCCAGAGGTCATAAAGATCCTCGATAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1535618 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1535648 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1535678 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1535708 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1535738 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
*
1535768 ATCCATAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
*
1535798 ATCCAGAGGTCATAAAGATCCTTGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1535828 ATCCAGAGGTCATAAAGATCCTCGGTAACT
1 ATCCAGAGGTCATAAAGATCCTCGGTAACT
*
1535858 ATCCATAGGTC
1 ATCCAGAGGTC
1535869 CAGAAGAACC
Statistics
Matches: 245, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 245 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (30 bp):
ATCCAGAGGTCATAAAGATCCTCGGTAACT
Found at i:1536270 original size:2 final size:2
Alignment explanation
Indices: 1536258--1536306 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1536248 TACACAACTC
1536258 AT AT A- 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
1536299 AT AT AT AT
1 AT AT AT AT
1536307 TGTAACATGT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1538414 original size:2 final size:2
Alignment explanation
Indices: 1538409--1538435 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1538399 CACATCCAAT
1538409 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
1538436 TTTTTTTTAA
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:1540832 original size:20 final size:21
Alignment explanation
Indices: 1540795--1540835 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1540785 TTTAGAAAAT
1540795 AAAATTCATAATTATTTTTTA
1 AAAATTCATAATTATTTTTTA
1540816 AAAATTC-TCAATT-TTTTTTA
1 AAAATTCAT-AATTATTTTTTA
1540836 TTTTTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (21 bp):
AAAATTCATAATTATTTTTTA
Found at i:1543159 original size:16 final size:17
Alignment explanation
Indices: 1543134--1543166 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1543124 ATACACATAT
1543134 TTTTTATAAAAAAATCA
1 TTTTTATAAAAAAATCA
*
1543151 TTTTT-TAAAAATATCA
1 TTTTTATAAAAAAATCA
1543167 ATATCAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTTATAAAAAAATCA
Found at i:1548516 original size:47 final size:48
Alignment explanation
Indices: 1548440--1548536 Score: 178
Period size: 47 Copynumber: 2.0 Consensus size: 48
1548430 TATATATATG
1548440 TGTGTACGTGTGTGCGTGTGTGTTAGAAGCAAAAAGAAAATGGGAGAGA
1 TGTGTACGTGTGT-CGTGTGTGTTAGAAGCAAAAAGAAAATGGGAGAGA
1548489 TGTGTACGTGTGT-GTGTGTGTTAGAAGCAAAAAGAAAATGGGAGAGA
1 TGTGTACGTGTGTCGTGTGTGTTAGAAGCAAAAAGAAAATGGGAGAGA
1548536 T
1 T
1548537 ACCTGAAGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 35 0.73
49 13 0.27
ACGTcount: A:0.33, C:0.05, G:0.36, T:0.26
Consensus pattern (48 bp):
TGTGTACGTGTGTCGTGTGTGTTAGAAGCAAAAAGAAAATGGGAGAGA
Found at i:1552843 original size:26 final size:26
Alignment explanation
Indices: 1552800--1552851 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1552790 TAATGTTAGG
1552800 AGAAAAAATAAACGAAAGCAAAATAA
1 AGAAAAAATAAACGAAAGCAAAATAA
* *
1552826 AGAAAACAATAAA-TAAAGTAAAATAA
1 AGAAAA-AATAAACGAAAGCAAAATAA
1552852 GGGGAAGCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.73, C:0.06, G:0.10, T:0.12
Consensus pattern (26 bp):
AGAAAAAATAAACGAAAGCAAAATAA
Found at i:1553286 original size:2 final size:2
Alignment explanation
Indices: 1553279--1553303 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1553269 ATATGAGAAA
1553279 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
1553304 ATAAATAAGG
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:1553345 original size:2 final size:2
Alignment explanation
Indices: 1553340--1553371 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1553330 TATAAAAATA
1553340 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
1553372 GATGTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1555633 original size:12 final size:12
Alignment explanation
Indices: 1555616--1555646 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1555606 ACTGTGAAGT
1555616 TGAAATTGGTTC
1 TGAAATTGGTTC
1555628 TGAAATTGGTTC
1 TGAAATTGGTTC
*
1555640 TAAAATT
1 TGAAATT
1555647 AGGAAGCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (12 bp):
TGAAATTGGTTC
Found at i:1567055 original size:16 final size:17
Alignment explanation
Indices: 1567036--1567069 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1567026 AAAAAAAACA
1567036 AGAAAAAG-AAAAAAAT
1 AGAAAAAGTAAAAAAAT
*
1567052 AGAACAAGTAAAAAAAT
1 AGAAAAAGTAAAAAAAT
1567069 A
1 A
1567070 ATAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (17 bp):
AGAAAAAGTAAAAAAAT
Found at i:1573006 original size:33 final size:33
Alignment explanation
Indices: 1572959--1573100 Score: 159
Period size: 33 Copynumber: 4.4 Consensus size: 33
1572949 TTCACCCTAA
*
1572959 ACCCGACCCGAATATCACACTTAAAAAAGCCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
*
1572992 ACCCGACCCAAATATCACACTT-AAAAAA----
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
* * *
1573020 TCCCGACCCGAATAGCACACTTAAAAAAATCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
* * **
1573053 ACCCGACCCGAATATCAAACTTTAAAAAACATG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
1573086 ACCCGATCCCGAATA
1 ACCCGA-CCCGAATA
1573101 CCAAAAGATT
Statistics
Matches: 91, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
28 19 0.21
29 6 0.07
32 5 0.05
33 53 0.58
34 8 0.09
ACGTcount: A:0.42, C:0.33, G:0.10, T:0.15
Consensus pattern (33 bp):
ACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:1573024 original size:28 final size:28
Alignment explanation
Indices: 1572960--1573058 Score: 119
Period size: 28 Copynumber: 3.4 Consensus size: 28
1572950 TCACCCTAAA
*
1572960 CCCGACCCGAATATCACACTTAAAAAAG
1 CCCGACCCGAATATCACACTTAAAAAAT
1572988 CCCGACCCGACCCAAATATCACACTTAAAAAAT
1 CCCGACCCG-----AATATCACACTTAAAAAAT
*
1573021 CCCGACCCGAATAGCACACTTAAAAAAAT
1 CCCGACCCGAATATCACACTT-AAAAAAT
1573050 -CCGACCCGA
1 CCCGACCCGA
1573059 CCCGAATATC
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
28 29 0.46
29 7 0.11
33 27 0.43
ACGTcount: A:0.41, C:0.35, G:0.10, T:0.13
Consensus pattern (28 bp):
CCCGACCCGAATATCACACTTAAAAAAT
Found at i:1573030 original size:61 final size:62
Alignment explanation
Indices: 1572960--1573081 Score: 192
Period size: 61 Copynumber: 2.0 Consensus size: 62
1572950 TCACCCTAAA
* * *
1572960 CCCGACCCGAATATCACACTTAAAAAAGCCCGACCCGACCCAAATATCACAC-TTAAAAAAT
1 CCCGACCCGAATAGCACACTTAAAAAAACCCGACCCGACCCAAATATCAAACTTTAAAAAAT
* *
1573021 CCCGACCCGAATAGCACACTTAAAAAAATCCGACCCGACCCGAATATCAAACTTTAAAAAA
1 CCCGACCCGAATAGCACACTTAAAAAAACCCGACCCGACCCAAATATCAAACTTTAAAAAA
1573082 CATGACCCGA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
61 47 0.85
62 8 0.15
ACGTcount: A:0.43, C:0.33, G:0.09, T:0.15
Consensus pattern (62 bp):
CCCGACCCGAATAGCACACTTAAAAAAACCCGACCCGACCCAAATATCAAACTTTAAAAAAT
Found at i:1583402 original size:21 final size:21
Alignment explanation
Indices: 1583376--1583416 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1583366 ATATGTGTTA
1583376 TATGTGGTCATTCGGGACATC
1 TATGTGGTCATTCGGGACATC
*
1583397 TATGTGGTCTTTCGGGACAT
1 TATGTGGTCATTCGGGACAT
1583417 TTCTACGCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.37
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACATC
Found at i:1583692 original size:18 final size:18
Alignment explanation
Indices: 1583669--1583712 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1583659 AAAAGATATG
*
1583669 AATGATAACAATACTAAT
1 AATGATAACAATAATAAT
*
1583687 AATGATAAGAATAATAAT
1 AATGATAACAATAATAAT
*
1583705 AAGGATAA
1 AATGATAA
1583713 TAAGATGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.25
Consensus pattern (18 bp):
AATGATAACAATAATAAT
Found at i:1588099 original size:12 final size:12
Alignment explanation
Indices: 1588082--1588185 Score: 70
Period size: 13 Copynumber: 8.7 Consensus size: 12
1588072 TAGCAATTCT
*
1588082 AATAATGATAAG
1 AATAATAATAAG
1588094 AATAATAATAAG
1 AATAATAATAAG
* *
1588106 GATAATAATATG
1 AATAATAATAAG
*
1588118 ATATAGTAATAA-
1 A-ATAATAATAAG
* *
1588130 TATAATAATAAT
1 AATAATAATAAG
* *
1588142 ATATAATTATATAT
1 A-ATAATAATA-AG
*
1588156 AATAATAATATG
1 AATAATAATAAG
*
1588168 -ATAAT-ATAAT
1 AATAATAATAAG
1588178 AATAATAA
1 AATAATAA
1588186 GATAATTGTT
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
10 3 0.04
11 19 0.27
12 22 0.31
13 24 0.34
14 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.35
Consensus pattern (12 bp):
AATAATAATAAG
Found at i:1588100 original size:3 final size:3
Alignment explanation
Indices: 1588081--1588185 Score: 85
Period size: 3 Copynumber: 36.0 Consensus size: 3
1588071 ATAGCAATTC
* * ** * *
1588081 TAA TAA TGA TAA GAA TAA TAA TAA GGA TAA TAA T-A TGA T-A TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1588127 TAA T-A TAA TAA TAA TATA TAA TTA TATA TAA TAA TAA T-A TGA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA
1588172 T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
1588186 GATAATTGTT
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
2 10 0.12
3 66 0.80
4 6 0.07
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1588129 original size:16 final size:17
Alignment explanation
Indices: 1588107--1588181 Score: 86
Period size: 16 Copynumber: 4.5 Consensus size: 17
1588097 AATAATAAGG
1588107 ATAATAATATGAT-ATA
1 ATAATAATATGATAATA
* *
1588123 GTAATAATATAATAATA
1 ATAATAATATGATAATA
1588140 ATATATAAT-T-ATATATA
1 ATA-ATAATATGATA-ATA
1588157 ATAATAATATGATAAT-
1 ATAATAATATGATAATA
1588173 ATAATAATA
1 ATAATAATA
1588182 ATAAGATAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
16 28 0.55
17 15 0.29
18 8 0.16
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (17 bp):
ATAATAATATGATAATA
Found at i:1588132 original size:11 final size:10
Alignment explanation
Indices: 1588118--1588184 Score: 80
Period size: 11 Copynumber: 6.3 Consensus size: 10
1588108 TAATAATATG
1588118 ATATAGTAATA
1 ATATA-TAATA
1588129 ATATAATAATA
1 ATAT-ATAATA
*
1588140 ATATATAATT
1 ATATATAATA
1588150 ATATATAATA
1 ATATATAATA
*
1588160 ATAATATGATA
1 AT-ATATAATA
1588171 ATATAATAATA
1 ATAT-ATAATA
1588182 ATA
1 ATA
1588185 AGATAATTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
10 18 0.37
11 30 0.61
12 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
ATATATAATA
Found at i:1588156 original size:34 final size:35
Alignment explanation
Indices: 1588095--1588180 Score: 99
Period size: 34 Copynumber: 2.5 Consensus size: 35
1588085 AATGATAAGA
* *
1588095 ATAATAATAAGGATAATAA-TATGATATAGTAATAAT
1 ATAATAATAA-TAT-ATAATTATGATATAATAATAAT
1588131 ATAATAATAATATATAATTAT-ATATAATAATAAT
1 ATAATAATAATATATAATTATGATATAATAATAAT
*
1588165 ATGATAAT-ATA-ATAAT
1 ATAATAATAATATATAAT
1588181 AATAAGATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
32 5 0.11
33 3 0.07
34 23 0.50
35 5 0.11
36 10 0.22
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (35 bp):
ATAATAATAATATATAATTATGATATAATAATAAT
Found at i:1588191 original size:8 final size:8
Alignment explanation
Indices: 1588081--1588181 Score: 73
Period size: 8 Copynumber: 12.0 Consensus size: 8
1588071 ATAGCAATTC
1588081 TAATAATGA
1 TAATAAT-A
*
1588090 TAAGAATAA
1 TAATAAT-A
*
1588099 TAATAAGGA
1 TAATAA-TA
1588108 TAATAATA
1 TAATAATA
*
1588116 TGAT-ATA
1 TAATAATA
1588123 GTAATAATA
1 -TAATAATA
1588132 TAATAATAA
1 TAATAAT-A
1588141 TATATAAT-
1 TA-ATAATA
1588149 T-ATATATAA
1 TAATA-AT-A
1588158 TAATAATA
1 TAATAATA
*
1588166 TGATAATA
1 TAATAATA
1588174 TAATAATA
1 TAATAATA
1588182 ATAAGATAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 19
0.73 0.09 0.19
Matches are distributed among these distances:
6 3 0.04
7 5 0.07
8 30 0.41
9 28 0.38
10 8 0.11
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (8 bp):
TAATAATA
Found at i:1591206 original size:20 final size:20
Alignment explanation
Indices: 1591181--1591221 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1591171 AGTTTTCATG
1591181 AAAACAAC-ATAATTAAATCA
1 AAAACAACTA-AATTAAATCA
*
1591201 AAAACATCTAAATTAAATCA
1 AAAACAACTAAATTAAATCA
1591221 A
1 A
1591222 TGATTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAACAACTAAATTAAATCA
Found at i:1591683 original size:23 final size:23
Alignment explanation
Indices: 1591653--1591696 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1591643 ATGCACTGCT
1591653 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* *
1591676 GAGTGCATCGGTGCACCTTCA
1 GAGTGCATCGATGCACATTCA
1591697 TGGTGTATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:1597560 original size:46 final size:46
Alignment explanation
Indices: 1597460--1597564 Score: 124
Period size: 46 Copynumber: 2.3 Consensus size: 46
1597450 TGCACTAAGG
* * *
1597460 GTGCATCGATGCATACAATGCATTCGATGTTTCAAACAAGCTTAGA
1 GTGCATCGATGCATAAAATACATTCGATGTTTCAAACAAGCCTAGA
** *
1597506 GTAAATCGATGCATAAAATACATTCGATGTTTTCATAA-AATCCT-GA
1 GTGCATCGATGCATAAAATACATTCGATG-TTTCA-AACAAGCCTAGA
1597552 GTGCATCGATGCA
1 GTGCATCGATGCA
1597565 CGTCGATGCA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
46 38 0.78
47 9 0.18
48 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATACATTCGATGTTTCAAACAAGCCTAGA
Found at i:1597907 original size:13 final size:13
Alignment explanation
Indices: 1597889--1597915 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1597879 TAATAATAAC
1597889 ATATATAATTAAT
1 ATATATAATTAAT
1597902 ATATATAATTAAT
1 ATATATAATTAAT
1597915 A
1 A
1597916 ACAAAAACGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATATAATTAAT
Found at i:1604093 original size:18 final size:20
Alignment explanation
Indices: 1604054--1604093 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1604044 AGGCAAAAAG
1604054 AAAACAAGTTAAGATGTATAA
1 AAAACAAGTTAAGA-GTATAA
1604075 AAAACAAG-TAAGA-TATAA
1 AAAACAAGTTAAGAGTATAA
1604093 A
1 A
1604094 GGTAAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
20 5 0.26
21 8 0.42
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (20 bp):
AAAACAAGTTAAGAGTATAA
Found at i:1611368 original size:34 final size:33
Alignment explanation
Indices: 1611327--1611429 Score: 179
Period size: 34 Copynumber: 3.0 Consensus size: 33
1611317 TACACACAAA
1611327 AAATACTTAAAACAGAATACCAAATAAGCTAAAC
1 AAATACTTAAAACAGAA-ACCAAATAAGCTAAAC
1611361 AAATACTTAAAACAGAAAACCAAATAAGCTAAAC
1 AAATACTTAAAACAG-AAACCAAATAAGCTAAAC
1611395 AAATACTTAAAACAAGAAACCAAATAAGCTAAAC
1 AAATACTTAAAAC-AGAAACCAAATAAGCTAAAC
1611429 A
1 A
1611430 TTATAGAATC
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
34 63 0.94
35 4 0.06
ACGTcount: A:0.61, C:0.17, G:0.06, T:0.16
Consensus pattern (33 bp):
AAATACTTAAAACAGAAACCAAATAAGCTAAAC
Found at i:1613367 original size:21 final size:21
Alignment explanation
Indices: 1613343--1613402 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1613333 AAAATACTTA
1613343 AAACAGAATACCAAATAAGCT
1 AAACAGAATACCAAATAAGCT
*
1613364 AAACA-AATA-C---TTA---
1 AAACAGAATACCAAATAAGCT
1613377 AAACAGAATACCAAATAAGCT
1 AAACAGAATACCAAATAAGCT
1613398 AAACA
1 AAACA
1613403 TTATAGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 16
0.62 0.04 0.34
Matches are distributed among these distances:
13 5 0.17
14 4 0.14
15 1 0.03
16 2 0.07
18 2 0.07
19 1 0.03
20 4 0.14
21 10 0.34
ACGTcount: A:0.60, C:0.18, G:0.07, T:0.15
Consensus pattern (21 bp):
AAACAGAATACCAAATAAGCT
Found at i:1613377 original size:34 final size:34
Alignment explanation
Indices: 1613334--1613402 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1613324 ACACACAGAA
1613334 AAATACTTAAAACAGAATACCAAATAAGCTAAAC
1 AAATACTTAAAACAGAATACCAAATAAGCTAAAC
1613368 AAATACTTAAAACAGAATACCAAATAAGCTAAAC
1 AAATACTTAAAACAGAATACCAAATAAGCTAAAC
1613402 A
1 A
1613403 TTATAGAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.59, C:0.17, G:0.06, T:0.17
Consensus pattern (34 bp):
AAATACTTAAAACAGAATACCAAATAAGCTAAAC
Found at i:1618203 original size:14 final size:14
Alignment explanation
Indices: 1618181--1618245 Score: 59
Period size: 14 Copynumber: 5.0 Consensus size: 14
1618171 AACGTAAACG
*
1618181 AACACAAACGAACA
1 AACATAAACGAACA
1618195 AACATAAACGAAC-
1 AACATAAACGAACA
*
1618208 -AC--AAACGAACG
1 AACATAAACGAACA
1618219 AACATAAACGAACA
1 AACATAAACGAACA
* *
1618233 TA-ATAAATGAACA
1 AACATAAACGAACA
1618246 TAAAATAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
10 8 0.19
12 4 0.09
13 10 0.23
14 21 0.49
ACGTcount: A:0.62, C:0.22, G:0.09, T:0.08
Consensus pattern (14 bp):
AACATAAACGAACA
Found at i:1618204 original size:24 final size:24
Alignment explanation
Indices: 1618175--1618232 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
1618165 TAAATGAACG
1618175 TAAACGAACACAAACGAACAAACA
1 TAAACGAACACAAACGAACAAACA
*
1618199 TAAACGAACACAAACGAACGAACA
1 TAAACGAACACAAACGAACAAACA
1618223 TAAACGAACA
1 TAAACGAACA
1618233 TAATAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.60, C:0.24, G:0.10, T:0.05
Consensus pattern (24 bp):
TAAACGAACACAAACGAACAAACA
Found at i:1622475 original size:45 final size:45
Alignment explanation
Indices: 1622411--1622500 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1622401 CCAATAAATC
1622411 TTTCTTCAACTCTTCATCGTCTGGTATCACAATTCTTTCTTTATA
1 TTTCTTCAACTCTTCATCGTCTGGTATCACAATTCTTTCTTTATA
1622456 TTTCTTCAACTCTTCATCGTCTGGTATCACAATTCTTTCTTTATA
1 TTTCTTCAACTCTTCATCGTCTGGTATCACAATTCTTTCTTTATA
1622501 ATACAATTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.20, C:0.24, G:0.07, T:0.49
Consensus pattern (45 bp):
TTTCTTCAACTCTTCATCGTCTGGTATCACAATTCTTTCTTTATA
Found at i:1626513 original size:23 final size:24
Alignment explanation
Indices: 1626482--1626539 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
1626472 GTATAATTGT
*
1626482 ACCGAAGTGCCA-CGTAGAATTAC
1 ACCGTAGTGCCAGCGTAGAATTAC
*
1626505 ACCAG-AGTG-CAGCGTAGAATTGC
1 ACC-GTAGTGCCAGCGTAGAATTAC
1626528 ACCGTAGTGCCA
1 ACCGTAGTGCCA
1626540 TATAATAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.10
23 24 0.80
24 3 0.10
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (24 bp):
ACCGTAGTGCCAGCGTAGAATTAC
Found at i:1632061 original size:17 final size:18
Alignment explanation
Indices: 1632033--1632066 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1632023 AAGTATAAAG
1632033 ATTTATTTAAAATTAATC
1 ATTTATTTAAAATTAATC
1632051 ATTTA-TTAAAATTAAT
1 ATTTATTTAAAATTAAT
1632067 TATAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTATTTAAAATTAATC
Found at i:1632178 original size:17 final size:17
Alignment explanation
Indices: 1632158--1632250 Score: 59
Period size: 17 Copynumber: 5.6 Consensus size: 17
1632148 ATTATAATTC
1632158 AATTATAATTCTATTAA
1 AATTATAATTCTATTAA
** **
1632175 AATTATAATTAAATTTT
1 AATTATAATTCTATTAA
*
1632192 AA-TA-AATT-GATTAA
1 AATTATAATTCTATTAA
** * *
1632206 TTTTAAATAAATCT-TTAT
1 AATT--ATAATTCTATTAA
1632224 AATTATAATTCTATTAA
1 AATTATAATTCTATTAA
1632241 AATTATAATT
1 AATTATAATT
1632251 TTAATATTTA
Statistics
Matches: 54, Mismatches: 16, Indels: 12
0.66 0.20 0.15
Matches are distributed among these distances:
14 3 0.06
15 5 0.09
16 9 0.17
17 29 0.54
18 8 0.15
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.48
Consensus pattern (17 bp):
AATTATAATTCTATTAA
Found at i:1632341 original size:42 final size:43
Alignment explanation
Indices: 1632292--1632382 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 43
1632282 TTTAAGTTAT
*
1632292 AATTAGGA-TTTATTTACATAATAAGTAATTTAAGTTGTTTAG
1 AATTAGGATTTTATTTACATAACAAGTAATTTAAGTTGTTTAG
* *
1632334 AATTAGGATTTTTTTTTACATAACAAGTAATTTAATTTGTTTAG
1 AATTAGGA-TTTTATTTACATAACAAGTAATTTAAGTTGTTTAG
1632378 AATTA
1 AATTA
1632383 AAAATTTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 8 0.18
44 36 0.82
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.47
Consensus pattern (43 bp):
AATTAGGATTTTATTTACATAACAAGTAATTTAAGTTGTTTAG
Found at i:1632862 original size:42 final size:41
Alignment explanation
Indices: 1632815--1632928 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 41
1632805 GCCAATTCTA
1632815 ACTTATAT-AAATTAAAAATCCTAATTCTAAACAAATTAAATT
1 ACTTATATGAAA--AAAAATCCTAATTCTAAACAAATTAAATT
* * *
1632857 ACTTATTATGTAAAAAAATCCTAATTCTAAGCAACTTAAATT
1 ACTTA-TATGAAAAAAAATCCTAATTCTAAACAAATTAAATT
* * *
1632899 ACTTATTATGTAAATAAATCCTATTTCTAA
1 ACTTA-TATGAAAAAAAATCCTAATTCTAA
1632929 CTTAAAAATC
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
42 60 0.92
43 3 0.05
44 2 0.03
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (41 bp):
ACTTATATGAAAAAAAATCCTAATTCTAAACAAATTAAATT
Found at i:1632988 original size:17 final size:17
Alignment explanation
Indices: 1632966--1633057 Score: 59
Period size: 17 Copynumber: 5.6 Consensus size: 17
1632956 TAAATATTAT
1632966 AATTATAATTTTAATAG
1 AATTATAATTTTAATAG
*
1632983 AATTATAATTAT-A-AG
1 AATTATAATTTTAATAG
* *
1632998 AATT-T-A-TTTAAAATT
1 AATTATAATTTTAATA-G
* ** **
1633013 AATTATTTATTAAAATTT
1 AATTA-TAATTTTAATAG
1633031 AATTATAATTTTAATAG
1 AATTATAATTTTAATAG
1633048 AATTATAATT
1 AATTATAATT
1633058 AAATTAAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
12 2 0.04
13 2 0.04
14 2 0.04
15 10 0.18
16 1 0.02
17 29 0.52
18 7 0.12
19 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
AATTATAATTTTAATAG
Found at i:1633022 original size:18 final size:18
Alignment explanation
Indices: 1632999--1633036 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
1632989 AATTATAAGA
1632999 ATTTATTTAAAA-TTAATT
1 ATTTA-TTAAAATTTAATT
1633017 ATTTATTAAAATTTAATT
1 ATTTATTAAAATTTAATT
1633035 AT
1 AT
1633037 AATTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTATTAAAATTTAATT
Found at i:1633159 original size:17 final size:18
Alignment explanation
Indices: 1633137--1633170 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1633127 TAAAATTATA
1633137 ATTAATTTT-AATAAATG
1 ATTAATTTTAAATAAATG
1633154 ATTAATTTTAAATAAAT
1 ATTAATTTTAAATAAAT
1633171 TCTTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTAATTTTAAATAAATG
Found at i:1635216 original size:112 final size:112
Alignment explanation
Indices: 1634879--1635565 Score: 956
Period size: 112 Copynumber: 6.1 Consensus size: 112
1634869 TTGTCGGTTT
* *
1634879 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACATG-TAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACA-GATTAAAAAATGACAAAAC
* *
1634943 CTGTCTATAAATGACAAAACAGGTAAAGCGCTACCTGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
1634991 GTGTCGATACTTTATAAAAATATATTGATCCATAACAACATAACA-AGTAAAACAAATGATAAAA
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGA-TTAAA-AAATGACAAAA
* * *
1635055 CCGATCTATAAATGACAAAACAGGTCAAGCGCTATCGGATATATTGAAA
64 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
1635104 GTGTCGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGATTAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGATTAAAAAATGACAAAACC
1635169 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
1635216 GTGTCGATACTTTATAAAAATGTATCGATCCACAACAATATAACAG-GTAAAAAATGACAAAAAC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGATTAAAAAATGACAAAACC
* *
1635280 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTAAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
1635327 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAA-AAAGTAAAAAGATAACAAAAC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGATTAAAAA-ATGACAAAAC
* *
1635391 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
1635439 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAAC--ATGTAAAAATATGACAAAA
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGAT-TAAAAA-ATGACAAAA
** * * * * *
1635502 TCC-GTCTCGAAATGATAAAACCGGTAAAGAGCTACCGAATATGTTGAAA
64 -CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1635551 GTGTCGATATTTTAT
1 GTGTCGATACTTTAT
1635566 TATAAGTATC
Statistics
Matches: 523, Mismatches: 43, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
110 1 0.00
111 111 0.21
112 309 0.59
113 101 0.19
114 1 0.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGATTAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:1635397 original size:223 final size:221
Alignment explanation
Indices: 1634879--1635565 Score: 987
Period size: 223 Copynumber: 3.1 Consensus size: 221
1634869 TTGTCGGTTT
* * * *
1634879 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAAAAGT-AAAAAATGACAAAACC
* *
1634944 TGTCTATAAATGACAAAACAGGTAAAGCGCTACCTGATATATTGAAAGTGTCGATACTTTATAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* * * * *
1635009 AATATATTGATCCATAACAACATAACAAGTAAAACAAATGATAAAACCGATCTATAAATGACAAA
130 AATATATCGATCCATAACAATATAACAAGT-AAA-AAATGACAAAAACGGTCTATAAATGACAAA
* *
1635074 ACAGGTCAAGCGCTATCGGATATATTGAAA
193 ACAGGTAAAGCGCTA-CCGATATATTGAAA
* * * *
1635104 GTGTCGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGATTAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAA-AAAGTAAAAAATGACAAAACC
1635169 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* * *
1635234 AATGTATCGATCCACAACAATATAACAGGTAAAAAATGACAAAAACGGTCTATAAATGACAAAAC
130 AATATATCGATCCATAACAATATAACAAGTAAAAAATGACAAAAACGGTCTATAAATGACAAAAC
*
1635299 AGGTAAAGCGCTACCAGATATATTAAAA
195 AGGTAAAGCGCTACC-GATATATTGAAA
*
1635327 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAAAAGTAAAAAGATAACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAAAAGTAAAAA-ATGACAAAACC
* *
1635392 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* * * ** *
1635457 AATATATCGATCCATAACAATATAACATGTAAAAATATGACAAAATCCGTCTCGAAATGATAAAA
130 AATATATCGATCCATAACAATATAACAAGTAAAAA-ATGACAAAAACGGTCTATAAATGACAAAA
* * *
1635522 CCGGTAAAGAGCTACCGAATATGTTGAAA
194 CAGGTAAAGCGCTACCG-ATATATTGAAA
*
1635551 GTGTCGATATTTTAT
1 GTGTCGATACTTTAT
1635566 TATAAGTATC
Statistics
Matches: 416, Mismatches: 41, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
222 9 0.02
223 199 0.48
224 64 0.15
225 143 0.34
226 1 0.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (221 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAAAAGTAAAAAATGACAAAACCG
GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAA
ATATATCGATCCATAACAATATAACAAGTAAAAAATGACAAAAACGGTCTATAAATGACAAAACA
GGTAAAGCGCTACCGATATATTGAAA
Found at i:1635530 original size:335 final size:336
Alignment explanation
Indices: 1634879--1635565 Score: 1047
Period size: 335 Copynumber: 2.0 Consensus size: 336
1634869 TTGTCGGTTT
* * * *
1634879 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCACAACAATATAACAGGTAAAAAAATGACAAAAAC
* * *
1634944 TGTCTATAAATGACAAAACAGGTAAAGCGCTACCTGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTAAAAGTGTCGATACTTTATAAA
* * * *
1635009 AATATATTGATCCATAACAACATAACAAGTAAAACAAATGATAAAACCGATCTATAAATGACAAA
131 AATATATCGATCCATAACAACATAAAAAGTAAAACAAATAACAAAACCGATCTATAAATGACAAA
* * *
1635074 ACAGGTCAAGCGCTATCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCAATCCATAA
196 ACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATATATCAATCCATAA
* * *
1635139 CAATATAACAGATTAAAAAATGACAAAATCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCG
261 CAATATAACAGA-TAAAAAATGACAAAATCCGTCTAGAAATGACAAAACAGGTAAAGAGCTACCG
*
1635204 GATATATTGAAA
325 AATATATTGAAA
*
1635216 GTGTCGATACTTTATAAAAATGTATCGATCCACAACAATATAACAGGT-AAAAAATGACAAAAAC
1 GTGTCGATACTTTATAAAAATATATCGATCCACAACAATATAACAGGTAAAAAAATGACAAAAAC
1635280 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTAAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTAAAAGTGTCGATACTTTATAAA
* * * *
1635345 AATGTATCGATCCATAACAATATAAAAAGTAAAA-AGATAACAAAACCGGTCTATAAATGACAAA
131 AATATATCGATCCATAACAACATAAAAAGTAAAACAAATAACAAAACCGATCTATAAATGACAAA
* * *
1635409 ACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATAAAAATATATCGATCCATAA
196 ACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATATATCAATCCATAA
* * *
1635474 CAATATAACATG-TAAAAATATGACAAAATCCGTCTCGAAATGATAAAACCGGTAAAGAGCTACC
261 CAATATAACA-GATAAAAA-ATGACAAAATCCGTCTAGAAATGACAAAACAGGTAAAGAGCTACC
*
1635538 GAATATGTTGAAA
324 GAATATATTGAAA
*
1635551 GTGTCGATATTTTAT
1 GTGTCGATACTTTAT
1635566 TATAAGTATC
Statistics
Matches: 317, Mismatches: 31, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
334 6 0.02
335 159 0.50
336 108 0.34
337 44 0.14
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (336 bp):
GTGTCGATACTTTATAAAAATATATCGATCCACAACAATATAACAGGTAAAAAAATGACAAAAAC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTAAAAGTGTCGATACTTTATAAA
AATATATCGATCCATAACAACATAAAAAGTAAAACAAATAACAAAACCGATCTATAAATGACAAA
ACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATATATCAATCCATAA
CAATATAACAGATAAAAAATGACAAAATCCGTCTAGAAATGACAAAACAGGTAAAGAGCTACCGA
ATATATTGAAA
Found at i:1635855 original size:112 final size:112
Alignment explanation
Indices: 1635624--1635859 Score: 364
Period size: 112 Copynumber: 2.1 Consensus size: 112
1635614 CAATAAAGTA
* * * *
1635624 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATAACAAAACCGAT
* *
1635689 CTATAAATGACAAAACGGGTAAAGCGCTACCGGATATATTGAAAATG
66 CTATAAATAACAAAACAGGTAAAGCGCTACCGGATATATTGAAAATG
* *
1635736 TCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATAATAAAACCGAT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATAACAAAACCGAT
* * *
1635801 CTATAAATAACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTG
66 CTATAAATAACAAAACAGGTAAAGCGCTACCGGATATATTGAAAATG
*
1635848 TTGATACTTTAT
1 TCGATACTTTAT
1635860 TATAAGTATT
Statistics
Matches: 111, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.26
Consensus pattern (112 bp):
TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATAACAAAACCGAT
CTATAAATAACAAAACAGGTAAAGCGCTACCGGATATATTGAAAATG
Found at i:1635861 original size:294 final size:294
Alignment explanation
Indices: 1635324--1636024 Score: 1089
Period size: 294 Copynumber: 2.4 Consensus size: 294
1635314 AGATATATTA
* * * *
1635324 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAAAAGTAAAAAGATAACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
1635389 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAATGTCAATACTTTAT
* * * * * *
1635454 AAAAATATATCGATCCATAACAATATAACATGTAAAAATATGACAAAATCCGTCTCGAAATGATA
131 AAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATAACAAAATCCGTCTAGAAATAACA
* * *
1635519 AAACCGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATATTTTATTATAAGTATCGGCACTTT
196 AAACAGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
1635584 TGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
261 TGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
*
1635618 AAAGTATCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
1635683 ACCGGTCTATAAATGACAAAACGGGTAAAGCGCTACCGGATATATTGAAAATGTCAATACTTTAT
66 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAATGTCAATACTTTAT
* * *
1635748 AAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATAATAAAA-CCGATCTATAAATAAC
131 AAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATAACAAAATCCG-TCTAGAAATAAC
* * * * *
1635812 AAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTTGATACTTTATTATAAGTATTGACACTT
195 AAAACAGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTT
* *
1635877 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
260 TTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
1635912 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
** * *
1635977 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGA
66 ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGA
1636025 TAGTGTCGAT
Statistics
Matches: 371, Mismatches: 35, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
293 3 0.01
294 368 0.99
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (294 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAATGTCAATACTTTAT
AAAAATATATCGATCCATAACAATATAACAAGTAAAAAAATAACAAAATCCGTCTAGAAATAACA
AAACAGGTAAAGAGCTACCGAATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
TGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
Found at i:1636046 original size:182 final size:182
Alignment explanation
Indices: 1635734--1636364 Score: 974
Period size: 182 Copynumber: 3.5 Consensus size: 182
1635724 ATATTGAAAA
* * * * *
1635734 TGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATAATAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCG
* ** * * * * *
1635799 ATCTATAAATAACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTTGATACTTTATTATA
66 GTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATATTTTATTATA
1635864 AGTATTGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAG
131 AGTATTGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAG
1635916 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCG
1635981 GTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATATTTTATTATA
66 GTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATATTTTATTATA
* * * *
1636046 AGTATCGAAACTTTTGAAATTTAAAAGAGAATAAGTTATAGCGCTAATAAAG
131 AGTATTGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAG
1636098 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCG
* * * * *** *
1636163 GTCTCGAACTGATAAAATCAGTAAAGAGCTATTAGATATGTTGAAAGTGTCGATATTTTATTATA
66 GTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATATTTTATTATA
* * * *
1636228 AGTATTGCCACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAA
131 AGTATTGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAG
* *
1636280 TGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAATATGACAAAATCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCG
*
1636345 GTCTCGAAATGATAAAACCG
66 GTCTCGAAATGACAAAACCG
1636365 ATAGTAAAAA
Statistics
Matches: 411, Mismatches: 38, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
182 411 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (182 bp):
TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCG
GTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATATTTTATTATA
AGTATTGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAG
Found at i:1637015 original size:23 final size:23
Alignment explanation
Indices: 1636986--1637033 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1636976 AAATAGATCA
*
1636986 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
1637009 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
1637032 AT
1 AT
1637034 TGTACATGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:1650132 original size:2 final size:2
Alignment explanation
Indices: 1650127--1650156 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1650117 AAAGATGACA
1650127 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1650157 ATGAAATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1653092 original size:60 final size:61
Alignment explanation
Indices: 1653023--1653202 Score: 204
Period size: 60 Copynumber: 3.0 Consensus size: 61
1653013 CATATGTCAT
*
1653023 CAAAGTATGACCTTCATTTTAAATTGGTCCCTAAACTTTTAAATATTCCAATTTCAT-ACC
1 CAAAGTATGACATTCATTTTAAATTGGTCCCTAAACTTTTAAATATTCCAATTTCATCACC
* * * * * *
1653083 TAAAGTATGA-TTATCATTTTAAATTAGT-CCTCAAACTTTTAAATATTTCAATATCATCCCC
1 CAAAGTATGACAT-TCATTTTAAATTGGTCCCT-AAACTTTTAAATATTCCAATTTCATCACC
* * * * *
1653144 CAAAATATGACATTCATTCTAAATTGGTCCCTAAATATTTTGAACATTCCAATTTCATC
1 CAAAGTATGACATTCATTTTAAATTGGTCCCTAAA-CTTTTAAATATTCCAATTTCATC
1653203 TCAAACTATA
Statistics
Matches: 98, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
59 4 0.04
60 46 0.47
61 26 0.27
62 22 0.22
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (61 bp):
CAAAGTATGACATTCATTTTAAATTGGTCCCTAAACTTTTAAATATTCCAATTTCATCACC
Found at i:1655044 original size:22 final size:20
Alignment explanation
Indices: 1655019--1655061 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
1655009 GTGTTTACGT
*
1655019 TTATATTATATACATATACATA
1 TTATACTATATAC-TATA-ATA
1655041 TTATACTATATACTATAATA
1 TTATACTATATACTATAATA
1655061 T
1 T
1655062 ACTATGAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 4 0.20
22 12 0.60
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATACTATATACTATAATA
Found at i:1655062 original size:17 final size:16
Alignment explanation
Indices: 1655026--1655066 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1655016 CGTTTATATT
1655026 ATATAC-ATATACATA
1 ATATACTATATACATA
*
1655041 TTATACTATATACTATA
1 ATATACTATATAC-ATA
1655058 ATATACTAT
1 ATATACTAT
1655067 GAGGGGCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 5 0.23
16 6 0.27
17 11 0.50
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATACTATATACATA
Found at i:1656279 original size:3 final size:3
Alignment explanation
Indices: 1656271--1656305 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1656261 TTTTATCTAT
*
1656271 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1656306 TTTTTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:1656306 original size:6 final size:6
Alignment explanation
Indices: 1656270--1656363 Score: 59
Period size: 6 Copynumber: 15.5 Consensus size: 6
1656260 CTTTTATCTA
* * * *
1656270 TTTATT ATTATT ATTATT ATTATT ATTATT TTTATT TTT-TT TTTCATTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT-A-TT
* * * *
1656319 TTTACT GTT-TT TTAATCT TAGTATT TTT-TT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTAT-T T-TTATT TTTATT TTTATT TTTATT TTT
1656364 TAGTTATTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
5 12 0.17
6 47 0.66
7 5 0.07
8 7 0.10
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:1656310 original size:9 final size:9
Alignment explanation
Indices: 1656253--1656383 Score: 50
Period size: 9 Copynumber: 13.8 Consensus size: 9
1656243 TTGCCTTTAA
1656253 TTATTTTCTT
1 TTATTTT-TT
*
1656263 TTATCTATTTA
1 TTAT-T-TTTT
* *
1656274 TTATTATTA
1 TTATTTTTT
* *
1656283 TTATTATTA
1 TTATTTTTT
*
1656292 TTATTATTT
1 TTATTTTTT
1656301 TTATTTTTT
1 TTATTTTTT
1656310 TT-TTCATTTT
1 TTATT--TTTT
*
1656320 TTACTGTTTT
1 TTA-TTTTTT
* * *
1656330 TTAATCTTA
1 TTATTTTTT
*
1656339 GTATTTTTT
1 TTATTTTTT
*
1656348 TT-TTATTT
1 TTATTTTTT
1656356 TTATTTTTT
1 TTATTTTTT
1656365 AGTTATTTTGTT
1 --TTATTTT-TT
*
1656377 CTATTTT
1 TTATTTT
1656384 AATTTAATTT
Statistics
Matches: 94, Mismatches: 17, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
8 9 0.10
9 43 0.46
10 24 0.26
11 13 0.14
12 5 0.05
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (9 bp):
TTATTTTTT
Found at i:1656370 original size:17 final size:17
Alignment explanation
Indices: 1656340--1656373 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1656330 TTAATCTTAG
**
1656340 TATTTTTTTTTTATTTT
1 TATTTTTTAGTTATTTT
1656357 TATTTTTTAGTTATTTT
1 TATTTTTTAGTTATTTT
1656374 GTTCTATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
TATTTTTTAGTTATTTT
Found at i:1659661 original size:35 final size:35
Alignment explanation
Indices: 1659605--1659677 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
1659595 CAGCATCCTG
* *
1659605 TTTTAACTTATTTTTTGAACTTTCTCATATTTCTT
1 TTTTAACTTATCTTTTAAACTTTCTCATATTTCTT
*
1659640 TTTTAACTTGTCTTTTAAACTTTCTCATATTTCTT
1 TTTTAACTTATCTTTTAAACTTTCTCATATTTCTT
1659675 TTT
1 TTT
1659678 ATAAGGTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.19, C:0.15, G:0.03, T:0.63
Consensus pattern (35 bp):
TTTTAACTTATCTTTTAAACTTTCTCATATTTCTT
Found at i:1660300 original size:99 final size:99
Alignment explanation
Indices: 1660185--1660386 Score: 332
Period size: 99 Copynumber: 2.0 Consensus size: 99
1660175 TTATAATATT
* * *
1660185 ATATGTATACAATAAAGCTTGAGCTTTCCCTCTAGAGAAATTGGTTAAACACCCCGACTTTATGG
1 ATATCTATACAATAAAGCTTGAGCTGTCCCTCCAGAGAAATTGGTTAAACACCCCGACTTTATGG
*
1660250 ATAAGATTCAGCTAGCCTGATAGAGGTGATTATA
66 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
* * * *
1660284 ATATCTATACAATAAAGCTTGAGCTGTCCCTCCAGAGCAATTGGTTGAACTCCCTGACTTTATGG
1 ATATCTATACAATAAAGCTTGAGCTGTCCCTCCAGAGAAATTGGTTAAACACCCCGACTTTATGG
1660349 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
1660383 ATAT
1 ATAT
1660387 TGAGTTGTCC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (99 bp):
ATATCTATACAATAAAGCTTGAGCTGTCCCTCCAGAGAAATTGGTTAAACACCCCGACTTTATGG
ATAAGATTCAGCTAGCCTGATAAAGGTGATTATA
Found at i:1662568 original size:85 final size:85
Alignment explanation
Indices: 1662290--1662605 Score: 370
Period size: 85 Copynumber: 3.7 Consensus size: 85
1662280 CTATTACAAT
* * ** * *
1662290 ATAACTCAAGACGAGAAGAATTATCTGTCAATAAAAACCTTCGAGTTCGATTCCATTCAACTCAA
1 ATAACTCAAGGCAAGAAGAGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGCTCAA
*
1662355 GGGAATATCAAATTTACAGC
66 GGGCATATCAAATTTACAGC
* * * * * *
1662375 ATAGCTCAAGGCGAGAAGGGGCTATATGTCAACAAAAACCTTCGAGTTTGATT-AATT-AGCTCA
1 ATAACTCAAGGCAAGAA-GAGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGCTCA
*
1662438 ATGGCATATC-AATTTACAGC
65 AGGGCATATCAAATTTACAGC
* * * * *
1662458 ATAGCTAAAGGCGAA-AAGGGCTATCTATCAGCAAAAACCTTCGAGTTCGATTCCATTCAGCTCA
1 ATAACTCAAGGC-AAGAAGAGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGCTCA
1662522 AGGGCATATCAAATTTACAGC
65 AGGGCATATCAAATTTACAGC
* * * *
1662543 ATAACTCAAGGCAAGAAGAGTTATCTGTTAACAAAAAACTGTCAAGTTCGATTCCATTCAGCT
1 ATAACTCAAGGCAAGAAGAGCTATCTGTCAACAAAAACCT-TCGAGTTCGATTCCATTCAGCT
1662606 TGATGACATA
Statistics
Matches: 195, Mismatches: 29, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
82 31 0.16
83 26 0.13
84 31 0.16
85 57 0.29
86 50 0.26
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (85 bp):
ATAACTCAAGGCAAGAAGAGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGCTCAA
GGGCATATCAAATTTACAGC
Found at i:1662616 original size:86 final size:85
Alignment explanation
Indices: 1662290--1662619 Score: 348
Period size: 86 Copynumber: 3.9 Consensus size: 85
1662280 CTATTACAAT
* * ** * *
1662290 ATAACTCAAGACGAGAAGAATTATCTGTCAATAAAAACCTTCGAGTTCGATTCCATTCAACTCAA
1 ATAACTCAAGGCAAGAAGAGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGCTCAA
1662355 GGGA-ATATCAAATTTACAGC
66 -GGACATATCAAATTTACAGC
* * * * * *
1662375 ATAGCTCAAGGCGAGAAGGGGCTATATGTCAACAAAAACCTTCGAGTTTGATT-AATT-AGCTCA
1 ATAACTCAAGGCAAGAA-GAGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGCTCA
1662438 ATGG-CATATC-AATTTACAGC
65 A-GGACATATCAAATTTACAGC
* * * * *
1662458 ATAGCTAAAGGCGAA-AAGGGCTATCTATCAGCAAAAACCTTCGAGTTCGATTCCATTCAGCTCA
1 ATAACTCAAGGC-AAGAAGAGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGCTCA
*
1662522 AGGGCATATCAAATTTACAGC
65 AGGACATATCAAATTTACAGC
* * * * **
1662543 ATAACTCAAGGCAAGAAGAGTTATCTGTTAACAAAAAACTGTCAAGTTCGATTCCATTCAGCTTG
1 ATAACTCAAGGCAAGAAGAGCTATCTGTCAACAAAAACCT-TCGAGTTCGATTCCATTCAGCTCA
*
1662608 ATGACATATCAA
65 AGGACATATCAA
1662620 CCGCATGGTA
Statistics
Matches: 205, Mismatches: 31, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
82 31 0.15
83 28 0.14
84 29 0.14
85 57 0.28
86 60 0.29
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (85 bp):
ATAACTCAAGGCAAGAAGAGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAGCTCAA
GGACATATCAAATTTACAGC
Found at i:1663297 original size:22 final size:20
Alignment explanation
Indices: 1663271--1663316 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
1663261 GATTACGTTT
*
1663271 ATATTATATTATATACATATA
1 ATATTATACTATATAC-TATA
1663292 CATATTATACTATATACTATA
1 -ATATTATACTATATACTATA
1663313 ATAT
1 ATAT
1663317 ACTATACGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 15 0.65
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTATACTATATACTATA
Found at i:1663317 original size:17 final size:16
Alignment explanation
Indices: 1663281--1663322 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
1663271 ATATTATATT
1663281 ATATAC-ATATACATA
1 ATATACTATATACATA
*
1663296 TTATACTATATACTATA
1 ATATACTATATAC-ATA
1663313 ATATACTATA
1 ATATACTATA
1663323 CGGGGCATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
17 12 0.52
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATACTATATACATA
Found at i:1663322 original size:22 final size:23
Alignment explanation
Indices: 1663270--1663323 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
1663260 TGATTACGTT
*
1663270 TATATTATATTATATACATATACA
1 TATA-TATACTATATACATATACA
1663294 TAT-TATACTATATAC-TATA-A
1 TATATATACTATATACATATACA
1663314 TATACTATAC
1 TATA-TATAC
1663324 GGGGCATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 16 0.59
24 3 0.11
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (23 bp):
TATATATACTATATACATATACA
Found at i:1665271 original size:2 final size:2
Alignment explanation
Indices: 1665264--1665308 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1665254 TAGTCACTAT
1665264 TA TA TA TA TA 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 TA TA TA TA TA
1665306 TA T
1 TA T
1665309 TATGTATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1665479 original size:20 final size:19
Alignment explanation
Indices: 1665446--1665489 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1665436 TATATATTTC
*
1665446 ATTAT-TAATAATTAGTAT
1 ATTATATAATAATTAATAT
1665464 ATTATATAATTAATTAATAT
1 ATTATATAA-TAATTAATAT
1665484 -TTATAT
1 ATTATAT
1665490 TTTTAGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 9 0.39
20 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTATATAATAATTAATAT
Found at i:1665567 original size:22 final size:21
Alignment explanation
Indices: 1665526--1665567 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1665516 TTAATTATAA
*
1665526 TAATTTTATAATTCAAATTAG
1 TAATTTTATAATTAAAATTAG
1665547 TAATATTTAT-ATTAAACATTA
1 TAAT-TTTATAATTAAA-ATTA
1665568 TTAAGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (21 bp):
TAATTTTATAATTAAAATTAG
Found at i:1671034 original size:42 final size:42
Alignment explanation
Indices: 1670965--1671079 Score: 167
Period size: 42 Copynumber: 2.7 Consensus size: 42
1670955 TAGAATGATG
*
1670965 GGGCATGATGAAGGCCCATTTCAGTCAAAAATAATCCATGTA
1 GGGCATGCTGAAGGCCCATTTCAGTCAAAAATAATCCATGTA
* * *
1671007 GGGTATGCTGAAGGCCCATTTCTGTCAAAAATAATCTATGTA
1 GGGCATGCTGAAGGCCCATTTCAGTCAAAAATAATCCATGTA
** *
1671049 GGGCATGCTGAAGGCATATTTCAGACAAAAA
1 GGGCATGCTGAAGGCCCATTTCAGTCAAAAA
1671080 AGATCCAACA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (42 bp):
GGGCATGCTGAAGGCCCATTTCAGTCAAAAATAATCCATGTA
Found at i:1671593 original size:57 final size:56
Alignment explanation
Indices: 1671496--1671606 Score: 168
Period size: 57 Copynumber: 2.0 Consensus size: 56
1671486 ACCTTATTCA
* * *
1671496 AGATCTGATTAGATGTGGAGACATGATAGGAATTAGGATAAAATCCTTTTTGTAAAG
1 AGATCTGATTAGATGTGGAGACATGAAAGGAATTAAGAT-AAATCCTTCTTGTAAAG
* *
1671553 AGATTTGATTAGATGTGGAGACGTGAAAGGAATTAAGATAAATCCTTCTTGTAA
1 AGATCTGATTAGATGTGGAGACATGAAAGGAATTAAGATAAATCCTTCTTGTAA
1671607 TGTGTTGTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 14 0.29
57 35 0.71
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (56 bp):
AGATCTGATTAGATGTGGAGACATGAAAGGAATTAAGATAAATCCTTCTTGTAAAG
Found at i:1672593 original size:42 final size:42
Alignment explanation
Indices: 1672546--1672627 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
1672536 CACGAACTTG
* * *
1672546 TAAATCCTTCGGGTCATCTGTCAGTCCTTCTAGCATGATGTT
1 TAAATCCTTCGGGTCATATGTCAGTCCTTCAAGCAAGATGTT
* *
1672588 TAAATCCTTCTGGTCATATGTCAGTCTTTCAAGCAAGATG
1 TAAATCCTTCGGGTCATATGTCAGTCCTTCAAGCAAGATG
1672628 ATAAGTCCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATATGTCAGTCCTTCAAGCAAGATGTT
Found at i:1674005 original size:2 final size:2
Alignment explanation
Indices: 1673994--1674022 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1673984 ATTTTAGTCA
1673994 AT AT -T 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
1674023 TAATTATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1675002 original size:12 final size:11
Alignment explanation
Indices: 1674991--1675067 Score: 57
Period size: 12 Copynumber: 6.5 Consensus size: 11
1674981 TTTGCCTTTA
1674991 ATTTTTATTTT
1 ATTTTTATTTT
1675002 ATTTATT-TATTT
1 ATTT-TTAT-TTT
*
1675014 ATTATTATTATT
1 ATTTTTATT-TT
*
1675026 ATTATTATTTT
1 ATTTTTATTTT
*
1675037 ATTATTTTTTTT
1 ATT-TTTATTTT
1675049 CATTTTTCATTTT
1 -ATTTTT-ATTTT
*
1675062 CTTTTT
1 ATTTTT
1675068 GTTTGTCTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
11 13 0.24
12 34 0.63
13 7 0.13
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:1675008 original size:9 final size:9
Alignment explanation
Indices: 1674994--1675054 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
1674984 GCCTTTAATT
1674994 TTTATTTTA
1 TTTATTTTA
1675003 TTTA-TTTA
1 TTTATTTTA
1675011 TTTATTATTA
1 TTTATT-TTA
1675021 -TTATTATTA
1 TTTATT-TTA
1675030 -TTATTTTA
1 TTTATTTTA
*
1675038 -TTATTTTT
1 TTTATTTTA
1675046 TTTCATTTT
1 TTT-ATTTT
1675055 TCATTTTCTT
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
8 18 0.38
9 21 0.45
10 8 0.17
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1675020 original size:3 final size:3
Alignment explanation
Indices: 1675012--1675042 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1675002 ATTTATTTAT
1675012 TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1675043 TTTTTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:1675030 original size:23 final size:23
Alignment explanation
Indices: 1674995--1675047 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1674985 CCTTTAATTT
1674995 TTATTTTATTTATT-TATTTATTA
1 TTATTTTATTTATTAT-TTTATTA
1675018 TTATTATTA-TTATTATTTTATTA
1 TTATT-TTATTTATTATTTTATTA
*
1675041 TTTTTTT
1 TTATTTT
1675048 TCATTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 2 0.07
23 21 0.78
24 4 0.15
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (23 bp):
TTATTTTATTTATTATTTTATTA
Found at i:1675122 original size:23 final size:23
Alignment explanation
Indices: 1675079--1675125 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1675069 TTTGTCTTAG
**
1675079 TTTTTTTTATCTTTTTTATTTTT
1 TTTTTTTTATCTTTTGCATTTTT
1675102 TTTTTTTTAT-TATTTGCATTTTT
1 TTTTTTTTATCT-TTTGCATTTTT
1675125 T
1 T
1675126 ACTTGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (23 bp):
TTTTTTTTATCTTTTGCATTTTT
Found at i:1675139 original size:16 final size:15
Alignment explanation
Indices: 1675090--1675152 Score: 65
Period size: 16 Copynumber: 4.1 Consensus size: 15
1675080 TTTTTTTATC
1675090 TTTTTTATT-TTTTT
1 TTTTTTATTGTTTTT
* **
1675104 TTTTTTATTATTTGCA
1 TTTTTTATTGTTT-TT
1675120 TTTTTTACTTGTTTTT
1 TTTTTTA-TTGTTTTT
*
1675136 TTTTTTACTGTTTTT
1 TTTTTTATTGTTTTT
1675151 TT
1 TT
1675153 AATCTTAGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 9 0.22
15 12 0.30
16 14 0.35
17 5 0.12
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.81
Consensus pattern (15 bp):
TTTTTTATTGTTTTT
Found at i:1675181 original size:17 final size:17
Alignment explanation
Indices: 1674991--1675181 Score: 54
Period size: 19 Copynumber: 10.5 Consensus size: 17
1674981 TTTGCCTTTA
1674991 ATTTTTATTTTATTTATTT
1 ATTTTTATTTTA-TT-TTT
*
1675010 ATTTATTATTATTATTATT
1 ATTT-TTATT-TTATTTTT
*
1675029 ATTATTTTATTATTTTTTTT
1 A-T-TTTTATT-TTATTTTT
*
1675049 CATTTTTCATTTTCTTTTT
1 -ATTTTT-ATTTTATTTTT
* *
1675068 GTTTGTCTTAGTTT-TTTTT
1 -ATT-T-TTATTTTATTTTT
*
1675087 A-TCTT-TTTTATTTTT
1 ATTTTTATTTTATTTTT
* **
1675102 -TTTTTTTTATTATTTGC
1 ATTTTTATT-TTATTTTT
*
1675119 ATTTTTTACTTGT-TTTTT
1 A-TTTTTA-TTTTATTTTT
*
1675137 -TTTTTACTGTTT-TTTTA
1 ATTTTTA-T-TTTATTTTT
*
1675154 ATCTTAGTATTTTATTTTT
1 AT-TT-TTATTTTATTTTT
1675173 ATTTTTATT
1 ATTTTTATT
1675182 ATTTCGTTTT
Statistics
Matches: 130, Mismatches: 22, Indels: 42
0.67 0.11 0.22
Matches are distributed among these distances:
14 3 0.02
15 10 0.08
16 10 0.08
17 17 0.13
18 9 0.07
19 40 0.31
20 33 0.25
21 8 0.06
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (17 bp):
ATTTTTATTTTATTTTT
Found at i:1675207 original size:22 final size:22
Alignment explanation
Indices: 1675147--1675217 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 22
1675137 TTTTTACTGT
*
1675147 TTTTTTAATCTT-AGTATTTT-A
1 TTTTTTAAT-TTAATTATTTTCA
* * *
1675168 -TTTTTATTTTTATTATTT-CG
1 TTTTTTAATTTAATTATTTTCA
1675188 TTTTTTAATTTAATTAATTTTCA
1 TTTTTTAATTTAATT-ATTTTCA
1675211 TTTTTTA
1 TTTTTTA
1675218 GTTAATCTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 2 0.05
20 13 0.33
21 12 0.31
22 4 0.10
23 8 0.21
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (22 bp):
TTTTTTAATTTAATTATTTTCA
Found at i:1679644 original size:21 final size:20
Alignment explanation
Indices: 1679613--1679652 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1679603 TTGATAAAAT
1679613 TATATTATTTTAGT-ATTTTA
1 TATATTATTTT-GTGATTTTA
1679633 TATATATATTTTGTGATTTT
1 TATAT-TATTTTGTGATTTT
1679653 TAGGTAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (20 bp):
TATATTATTTTGTGATTTTA
Done.