Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 8 of 195
Found at i:1506444 original size:21 final size:22
Alignment explanation
Indices: 1506408--1506456 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
1506398 CCCGAAATTA
*
1506408 ATAAAATATTATTTTTTAAAAT
1 ATAAATTATTATTTTTTAAAAT
1506430 ATAAATTATTA-TTTTTAAAAT
1 ATAAATTATTATTTTTTAAAAT
1506451 ATAAAT
1 ATAAAT
1506457 ATTTAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAATTATTATTTTTTAAAAT
Found at i:1506849 original size:13 final size:11
Alignment explanation
Indices: 1506818--1506846 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1506808 TAAATTATAA
1506818 ATAATATTTTT
1 ATAATATTTTT
1506829 ATAATATTTTT
1 ATAATATTTTT
1506840 AT-ATATT
1 ATAATATT
1506847 ATTGATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATAATATTTTT
Found at i:1507727 original size:35 final size:34
Alignment explanation
Indices: 1507687--1507761 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 34
1507677 TTTAATTTTA
* * * * *
1507687 ATTTTTAT-TATTTATAATTTTTTATTTGTAAATT
1 ATTTTTTTGTATTTATAATATTCTAGTTGT-AATG
*
1507721 ATTTTTTTGTATTTTTAATATTCTAGTTGTAATG
1 ATTTTTTTGTATTTATAATATTCTAGTTGTAATG
1507755 ATTTTTT
1 ATTTTTT
1507762 GGGTACATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 17 0.50
35 17 0.50
ACGTcount: A:0.25, C:0.01, G:0.07, T:0.67
Consensus pattern (34 bp):
ATTTTTTTGTATTTATAATATTCTAGTTGTAATG
Found at i:1508869 original size:25 final size:26
Alignment explanation
Indices: 1508833--1508889 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
1508823 AACTTTTAAT
*
1508833 TATAATTAAAT-ATTATATTTATATAA
1 TATAATTAAATAATTA-ATTAATATAA
*
1508859 T-TAATTGAATAATTAATTAATATAA
1 TATAATTAAATAATTAATTAATATAA
1508884 TATAAT
1 TATAAT
1508890 ATAATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TATAATTAAATAATTAATTAATATAA
Found at i:1508891 original size:10 final size:9
Alignment explanation
Indices: 1508828--1508902 Score: 59
Period size: 8 Copynumber: 8.1 Consensus size: 9
1508818 TTGAGAACTT
1508828 TTAATTATAA
1 TTAA-TATAA
1508838 TTAAATATTATA
1 TT-AATA-TA-A
*
1508850 TTTATATAA
1 TTAATATAA
1508859 TTAAT-TGAA
1 TTAATAT-AA
1508868 -TAAT-TAA
1 TTAATATAA
1508875 TTAATATAA
1 TTAATATAA
1508884 TATAATATAA
1 T-TAATATAA
1508894 TTAA-ATAA
1 TTAATATAA
1508902 T
1 T
1508903 CAAAATCATA
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
7 2 0.04
8 15 0.27
9 14 0.25
10 15 0.27
11 7 0.12
12 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (9 bp):
TTAATATAA
Found at i:1517928 original size:12 final size:12
Alignment explanation
Indices: 1517911--1517935 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1517901 TAAATCAATA
1517911 TAATTTTTTAAT
1 TAATTTTTTAAT
1517923 TAATTTTTTAAT
1 TAATTTTTTAAT
1517935 T
1 T
1517936 TTTAATTTCA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATTTTTTAAT
Found at i:1524133 original size:2 final size:2
Alignment explanation
Indices: 1524126--1524177 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1524116 TCAAGATATC
1524126 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1524168 GA GA GA GA GA
1 GA GA GA GA GA
1524178 CTGTTGATGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1531829 original size:21 final size:21
Alignment explanation
Indices: 1531803--1531844 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1531793 CAAGTAGTTT
1531803 TGTTGGGTATGTTGGACCCAA
1 TGTTGGGTATGTTGGACCCAA
1531824 TGTTGGGTATGTTGGACCCAA
1 TGTTGGGTATGTTGGACCCAA
1531845 GCAAATAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.33
Consensus pattern (21 bp):
TGTTGGGTATGTTGGACCCAA
Found at i:1532374 original size:20 final size:20
Alignment explanation
Indices: 1532337--1532374 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1532327 CCGATCATTA
* *
1532337 AAATTAAAAAATATTTTATT
1 AAATTAAAAAAAAATTTATT
1532357 AAATTAAAAAAAAATTTA
1 AAATTAAAAAAAAATTTA
1532375 ACATCCTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTAAAAAAAAATTTATT
Found at i:1532527 original size:26 final size:27
Alignment explanation
Indices: 1532497--1532553 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1532487 TTTCATTGTT
* * * *
1532497 ATTTTTAATTTA-TATTTTTATTATTA
1 ATTTTAAATTTATTATTATAATAATTA
1532523 ATTTTAAATTTATTATTATAATAATTA
1 ATTTTAAATTTATTATTATAATAATTA
1532550 ATTT
1 ATTT
1532554 ATTATTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTTTAAATTTATTATTATAATAATTA
Found at i:1532533 original size:20 final size:21
Alignment explanation
Indices: 1532495--1532562 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 21
1532485 TATTTCATTG
* *
1532495 TTATTTTTAA-TTTATATTT-
1 TTATTATTAATTTTAAATTTA
1532514 TTATTATTAATTTTAAATTTA
1 TTATTATTAATTTTAAATTTA
*
1532535 TTATTA-TAATAATT-AATTTA
1 TTATTATTAAT-TTTAAATTTA
1532555 TTATTATT
1 TTATTATT
1532563 TTAATCTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 9 0.21
20 24 0.57
21 9 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTATTAATTTTAAATTTA
Found at i:1532832 original size:23 final size:24
Alignment explanation
Indices: 1532787--1532832 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1532777 TCATGACAAG
* *
1532787 ATAGATAGATACAAGTAAAATAAA
1 ATAGAAAGATACAACTAAAATAAA
1532811 ATAGAAAGAT-CAACTAAAATAA
1 ATAGAAAGATACAACTAAAATAA
1532833 GTATGATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.63, C:0.07, G:0.11, T:0.20
Consensus pattern (24 bp):
ATAGAAAGATACAACTAAAATAAA
Found at i:1533414 original size:15 final size:15
Alignment explanation
Indices: 1533394--1533467 Score: 80
Period size: 15 Copynumber: 4.9 Consensus size: 15
1533384 TTTTATTAAA
*
1533394 ATTTTAAATTATATT
1 ATTTTAAATTATTTT
1533409 ATTTTAATATT-TTTT
1 ATTTTAA-ATTATTTT
1533424 A-TTTAAATTATTTTT
1 ATTTTAAATTA-TTTT
* *
1533439 ATTATATAATTATTAT
1 ATTTTA-AATTATTTT
1533455 ATTTTAAATTATT
1 ATTTTAAATTATT
1533468 AAATATAGGG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
13 3 0.06
14 5 0.10
15 23 0.46
16 14 0.28
17 5 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTTAAATTATTTT
Found at i:1533454 original size:29 final size:29
Alignment explanation
Indices: 1533396--1533454 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
1533386 TTATTAAAAT
* *
1533396 TTTAAATTATATTATTTTAATATTTTTTA
1 TTTAAATTATATTATTTTAATAATTATTA
1533425 TTTAAATTAT-TT-TTATTATATAATTATTA
1 TTTAAATTATATTATT-TTA-ATAATTATTA
1533454 T
1 T
1533455 ATTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 2 0.08
28 5 0.19
29 19 0.73
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTAAATTATATTATTTTAATAATTATTA
Found at i:1533457 original size:38 final size:35
Alignment explanation
Indices: 1533376--1533459 Score: 89
Period size: 38 Copynumber: 2.3 Consensus size: 35
1533366 ATAAAATATA
* *
1533376 TTTATAATTTTTATTAAAATTTTAAATTATATTAT
1 TTTATATTTTTTATTAAAATTTTAAATTATATAAT
*
1533411 TTTAATATTTTTTATTTAAATTATTTT-TATTATATAAT
1 TTT-ATATTTTTTA-TTAAA--ATTTTAAATTATATAAT
1533449 TATTATATTTT
1 T-TTATATTTT
1533460 AAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
35 3 0.07
36 9 0.22
37 5 0.12
38 17 0.41
39 7 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (35 bp):
TTTATATTTTTTATTAAAATTTTAAATTATATAAT
Found at i:1534676 original size:15 final size:15
Alignment explanation
Indices: 1534652--1534688 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1534642 AATACTATAA
*
1534652 TTTAATTAATTTAAT
1 TTTAAATAATTTAAT
1534667 TTTAAATAATTTAAT
1 TTTAAATAATTTAAT
*
1534682 TTAAAAT
1 TTTAAAT
1534689 TAATCAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAAATAATTTAAT
Found at i:1539692 original size:2 final size:2
Alignment explanation
Indices: 1539685--1539711 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1539675 ATTTACATGC
1539685 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
1539712 CATGTCTTCA
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:1541876 original size:18 final size:19
Alignment explanation
Indices: 1541849--1541886 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1541839 AAAAGAGCCT
*
1541849 AAAAAGAAAAG-AAGAAAA
1 AAAAAAAAAAGAAAGAAAA
1541867 AAAAAAAAAAGAAAGAAAA
1 AAAAAAAAAAGAAAGAAAA
1541886 A
1 A
1541887 TAAATTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAAAGAAAA
Found at i:1542532 original size:139 final size:142
Alignment explanation
Indices: 1542342--1542600 Score: 314
Period size: 144 Copynumber: 1.8 Consensus size: 142
1542332 TTTTATTACT
* * * * *
1542342 CTTTTCAAATCTATCATGTGATGAATTTTTTTTATTTCTGTCTACATGTGAT-A-G-TGTTAGTG
1 CTTTTCAAATCTATCATGTAATGAATTTATTTTATTTCTGTCTACACGTGATAATGATGTTAATA
* * * *
1542404 TGATCTTATTTCATATTTAATAACTATTTAATATCCTGTAATCTTATGTTAAGCATTCAACCTGA
66 TGATATTATCTCATATTTAATAAATATTTAATATCATGTAATCTTATGTTAAGCATTCAACCTGA
1542469 TTCTCTTTTGTA
131 TTCTCTTTTGTA
* *
1542481 CTTTTTAAATTTATCATGTAAT-AGATTTATTTTATTTTCAT-T-TACACGTGATGAATGTATGT
1 CTTTTCAAATCTATCATGTAATGA-ATTTATTTTA-TTTC-TGTCTACACGTGAT-AATG-ATGT
* *
1542543 TAATATGATATTATCTCATATTTAATAAATATTTAATATCATGTAGTTTTATGTTAAG
61 TAATATGATATTATCTCATATTTAATAAATATTTAATATCATGTAATCTTATGTTAAG
1542601 TATTTTACTT
Statistics
Matches: 99, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
138 1 0.01
139 37 0.37
140 5 0.05
141 2 0.02
142 1 0.01
144 53 0.54
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.49
Consensus pattern (142 bp):
CTTTTCAAATCTATCATGTAATGAATTTATTTTATTTCTGTCTACACGTGATAATGATGTTAATA
TGATATTATCTCATATTTAATAAATATTTAATATCATGTAATCTTATGTTAAGCATTCAACCTGA
TTCTCTTTTGTA
Found at i:1544657 original size:27 final size:28
Alignment explanation
Indices: 1544605--1544657 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1544595 GATTAAAAAA
**
1544605 AAACAAAAAGAGATGTTTAATTTAAAGG
1 AAACAAAAAGAGATGTTTAAGATAAAGG
*
1544633 AAACAAAAGGAGAT-TTTAAGATAAA
1 AAACAAAAAGAGATGTTTAAGATAAA
1544658 AAAAAGAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.57, C:0.04, G:0.17, T:0.23
Consensus pattern (28 bp):
AAACAAAAAGAGATGTTTAAGATAAAGG
Found at i:1546039 original size:21 final size:22
Alignment explanation
Indices: 1546010--1546061 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1546000 TTATATTATT
1546010 TAAT-AAATTTTG-TATTAAAA
1 TAATAAAATTTTGTTATTAAAA
* **
1546030 TCATAAAATTTTGTTATTTTAA
1 TAATAAAATTTTGTTATTAAAA
1546052 TAATAAAATT
1 TAATAAAATT
1546062 ATAATAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 3 0.12
21 8 0.31
22 15 0.58
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
TAATAAAATTTTGTTATTAAAA
Found at i:1554712 original size:20 final size:18
Alignment explanation
Indices: 1554671--1554733 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 18
1554661 TTTTAGTGTT
*
1554671 ATAAAAAAAATAAATAAT
1 ATAAAAAAAATAAATAAA
1554689 ATAAAAACAAATACAATAAA
1 ATAAAAA-AAATA-AATAAA
1554709 ATAAAAATGAAAT-AATAAAA
1 ATAAAAA--AAATAAAT-AAA
1554729 ATAAA
1 ATAAA
1554734 GTTTAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 7 0.18
19 8 0.21
20 20 0.51
21 4 0.10
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (18 bp):
ATAAAAAAAATAAATAAA
Found at i:1554770 original size:14 final size:14
Alignment explanation
Indices: 1554674--1554770 Score: 54
Period size: 14 Copynumber: 6.9 Consensus size: 14
1554664 TAGTGTTATA
1554674 AAAAAAATAAATAAT
1 AAAAAAATAAA-AAT
* * * *
1554689 ATAAAAACAAATAC
1 AAAAAAATAAAAAT
*
1554703 AATAAAATAAAAAT
1 AAAAAAATAAAAAT
* *
1554717 GAAATAATAAAAAT
1 AAAAAAATAAAAAT
***
1554731 -AAAGTTTAAATAAT
1 AAAAAAATAAA-AAT
*
1554745 -AAACAATAAAAAAT
1 AAAAAAAT-AAAAAT
1554759 AAAAAAATAAAA
1 AAAAAAATAAAA
1554771 TACTAATAAA
Statistics
Matches: 60, Mismatches: 19, Indels: 7
0.70 0.22 0.08
Matches are distributed among these distances:
13 7 0.12
14 35 0.58
15 18 0.30
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:1555608 original size:14 final size:14
Alignment explanation
Indices: 1555585--1555626 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1555575 TTTTCAATAT
*
1555585 TCAAATAATAAAAA
1 TCAAAAAATAAAAA
1555599 TCAAAAAATAAAAA
1 TCAAAAAATAAAAA
1555613 --ATAAAAATAAAAA
1 TCA-AAAAATAAAAA
1555626 T
1 T
1555627 GATAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 11 0.44
14 13 0.52
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (14 bp):
TCAAAAAATAAAAA
Found at i:1555618 original size:13 final size:14
Alignment explanation
Indices: 1555602--1555639 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1555592 ATAAAAATCA
1555602 AAAAATAAAAA-AT
1 AAAAATAAAAAGAT
1555615 AAAAATAAAAATGAT
1 AAAAATAAAAA-GAT
*
1555630 AAAATTAAAA
1 AAAAATAAAA
1555640 GACTATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.50
15 11 0.50
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (14 bp):
AAAAATAAAAAGAT
Found at i:1557441 original size:21 final size:21
Alignment explanation
Indices: 1557417--1557458 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1557407 TATAATAATG
1557417 TATGCGGCGATTAATGTATTA
1 TATGCGGCGATTAATGTATTA
1557438 TATGCGGCGATTAATGTATTA
1 TATGCGGCGATTAATGTATTA
1557459 CAATCTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.38
Consensus pattern (21 bp):
TATGCGGCGATTAATGTATTA
Found at i:1557472 original size:2 final size:2
Alignment explanation
Indices: 1557465--1557499 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1557455 ATTACAATCT
* *
1557465 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1557500 TCTACCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:1560745 original size:18 final size:19
Alignment explanation
Indices: 1560699--1560741 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1560689 AAAACTACTC
* *
1560699 AAAAAGTATTTTTATAATG
1 AAAAAATATTTTGATAATG
1560718 AAAAAATATTTTGA-AAT-
1 AAAAAATATTTTGATAATG
1560735 AAAAAAT
1 AAAAAAT
1560742 TATTATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 3 0.14
19 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (19 bp):
AAAAAATATTTTGATAATG
Found at i:1565042 original size:27 final size:27
Alignment explanation
Indices: 1565012--1565092 Score: 153
Period size: 27 Copynumber: 3.0 Consensus size: 27
1565002 GGCAGGATGA
1565012 TAGTTTTTATGCAATTACAGTGTGATT
1 TAGTTTTTATGCAATTACAGTGTGATT
*
1565039 TAGTTTTTATGCAATTACAGTATGATT
1 TAGTTTTTATGCAATTACAGTGTGATT
1565066 TAGTTTTTATGCAATTACAGTGTGATT
1 TAGTTTTTATGCAATTACAGTGTGATT
1565093 CGGTATTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.48
Consensus pattern (27 bp):
TAGTTTTTATGCAATTACAGTGTGATT
Found at i:1575047 original size:14 final size:15
Alignment explanation
Indices: 1575028--1575060 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1575018 TGATATTTTT
*
1575028 TTTATTT-AATTAGA
1 TTTATTTAAATTAAA
1575042 TTTATTTAAATTAAA
1 TTTATTTAAATTAAA
1575057 TTTA
1 TTTA
1575061 AATCATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTATTTAAATTAAA
Found at i:1578679 original size:11 final size:11
Alignment explanation
Indices: 1578632--1578685 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
1578622 TATTTATAAA
1578632 TTATTTAAATT
1 TTATTTAAATT
* *
1578643 TGATTTAAATA
1 TTATTTAAATT
*
1578654 TTA-TCAAATT
1 TTATTTAAATT
*
1578664 ATATTTAAATT
1 TTATTTAAATT
1578675 TTATTTTAAAT
1 TTA-TTTAAAT
1578686 AATTTAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TTATTTAAATT
Found at i:1578782 original size:31 final size:29
Alignment explanation
Indices: 1578720--1578774 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1578710 GTTTAAATAC
*
1578720 TAAAAAATTATTATTTTAATTATTTTAAT
1 TAAAAAATTATTATTTTAATTATTATAAT
*
1578749 TAAAAAATTATTATTTT-ATGATTATA
1 TAAAAAATTATTATTTTAATTATTATA
1578775 TATATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (29 bp):
TAAAAAATTATTATTTTAATTATTATAAT
Found at i:1581319 original size:1 final size:1
Alignment explanation
Indices: 1581313--1581338 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1581303 TGGGAAATTC
1581313 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
1581339 GAGATTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1592595 original size:8 final size:8
Alignment explanation
Indices: 1592582--1592697 Score: 177
Period size: 8 Copynumber: 14.8 Consensus size: 8
1592572 ATGCTTGAAA
1592582 AAAAAATG
1 AAAAAATG
1592590 AAAAAATG
1 AAAAAATG
1592598 AAAAAATG
1 AAAAAATG
1592606 -AAAAATG
1 AAAAAATG
1592613 AAAAAATG
1 AAAAAATG
1592621 AAAAAATG
1 AAAAAATG
1592629 -AAAAATG
1 AAAAAATG
1592636 -AAAAATG
1 AAAAAATG
1592643 AAAAAATG
1 AAAAAATG
1592651 AGAAAAATG
1 A-AAAAATG
1592660 AAAAAAT-
1 AAAAAATG
1592667 AAAAAATG
1 AAAAAATG
1592675 AAAAAATG
1 AAAAAATG
*
1592683 AAAATGATG
1 AAAA-AATG
1592692 AAAAAA
1 AAAAAA
1592698 GGTGAACAAT
Statistics
Matches: 101, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
7 28 0.28
8 58 0.57
9 15 0.15
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (8 bp):
AAAAAATG
Found at i:1592609 original size:15 final size:15
Alignment explanation
Indices: 1592582--1592697 Score: 162
Period size: 15 Copynumber: 7.4 Consensus size: 15
1592572 ATGCTTGAAA
1592582 AAAAAATGAAAAAATG
1 AAAAAATG-AAAAATG
1592598 AAAAAATGAAAAATG
1 AAAAAATGAAAAATG
1592613 AAAAAATGAAAAAATG
1 AAAAAATG-AAAAATG
1592629 -AAAAATGAAAAATG
1 AAAAAATGAAAAATG
1592643 AAAAAATGAGAAAAATG
1 AAAAAAT--GAAAAATG
*
1592660 AAAAAATAAAAAATG
1 AAAAAATGAAAAATG
1592675 AAAAAATGAAAATGATG
1 AAAAAATGAAAA--ATG
1592692 AAAAAA
1 AAAAAA
1592698 GGTGAACAAT
Statistics
Matches: 92, Mismatches: 2, Indels: 11
0.88 0.02 0.10
Matches are distributed among these distances:
14 7 0.08
15 46 0.50
16 15 0.16
17 24 0.26
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAAAATGAAAAATG
Found at i:1592613 original size:23 final size:23
Alignment explanation
Indices: 1592583--1592697 Score: 171
Period size: 23 Copynumber: 4.9 Consensus size: 23
1592573 TGCTTGAAAA
1592583 AAAAATGAAAAAATGAAAAAATG
1 AAAAATGAAAAAATGAAAAAATG
1592606 AAAAATGAAAAAATGAAAAAATG
1 AAAAATGAAAAAATGAAAAAATG
1592629 AAAAATG-AAAAATGAAAAAATGAG
1 AAAAATGAAAAAATGAAAAAAT--G
1592653 AAAAATGAAAAAAT-AAAAAATG
1 AAAAATGAAAAAATGAAAAAATG
*
1592675 AAAAAATGAAAATGATGAAAAAA
1 -AAAAATGAAAA-AATGAAAAAA
1592698 GGTGAACAAT
Statistics
Matches: 85, Mismatches: 1, Indels: 10
0.89 0.01 0.10
Matches are distributed among these distances:
22 15 0.18
23 41 0.48
24 17 0.20
25 12 0.14
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (23 bp):
AAAAATGAAAAAATGAAAAAATG
Found at i:1593826 original size:80 final size:80
Alignment explanation
Indices: 1593706--1594032 Score: 450
Period size: 80 Copynumber: 4.1 Consensus size: 80
1593696 ATGATTGTCA
* * *
1593706 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTC
1 AGGAGCAATTTA-CTTTCCAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAGTC
1593771 GTGGTGCCTCTGTTTAG
64 GTGGTGCCTCTGTTTAG
* * * *
1593788 AGGAGCAATTTACTTTCCAAGT-TTGTTGCCTTTGTTTAGAGGAGCAATTTACTTTTCAAGT-TT
1 AGGAGCAATTTACTTTCCAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAGTCGT
*
1593851 GTTGCCTCTGTTTAG
66 GGTGCCTCTGTTTAG
*
1593866 AGGAGCAATTTACTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAGTTC
1 AGGAGCAATTTACTTTCC-AAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAG-TC
1593931 GT--TGCCTCTGTTTAG
64 GTGGTGCCTCTGTTTAG
* *
1593946 AGGAGCAATTTACTTTTCAAGT--TCGGTGTCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAGT
1 AGGAGCAATTTACTTTCCAAGTCGT-GGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC--AAGT
1594009 CGTGGTGCCTCTGTTTAG
63 CGTGGTGCCTCTGTTTAG
1594027 AGGAGC
1 AGGAGC
1594033 TTTGGTAAAA
Statistics
Matches: 220, Mismatches: 16, Indels: 19
0.86 0.06 0.07
Matches are distributed among these distances:
77 1 0.00
78 64 0.29
79 16 0.07
80 98 0.45
81 28 0.13
82 13 0.06
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (80 bp):
AGGAGCAATTTACTTTCCAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAGTCGT
GGTGCCTCTGTTTAG
Found at i:1593829 original size:39 final size:40
Alignment explanation
Indices: 1593706--1594032 Score: 414
Period size: 39 Copynumber: 8.2 Consensus size: 40
1593696 ATGATTGTCA
* *
1593706 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTA-CTTTCCAAGTCGTGGTGCCTCTGTTTAG
* *
1593747 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTA-CTTTCCAAGTCGTGGTGCCTCTGTTTAG
* * *
1593788 AGGAGCAATTTACTTTCCAAGT-TTGTTGCCTTTGTTTAG
1 AGGAGCAATTTACTTTCCAAGTCGTGGTGCCTCTGTTTAG
* * *
1593827 AGGAGCAATTTACTTTTCAAGT-TTGTTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAGTCGTGGTGCCTCTGTTTAG
*
1593866 AGGAGCAATTTACTTTCCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTCC-AAGTCGTGGTGCCTCTGTTTAG
*
1593907 AGGAGCAATTTACTTTTCAAGTTCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAG-TCGTGGTGCCTCTGTTTAG
* *
1593946 AGGAGCAATTTACTTTTCAAGT--TCGGTGTCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAGTCGT-GGTGCCTCTGTTTAG
*
1593985 AGGAGCAATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTAC-TTTC-CAAGTCGTGGTGCCTCTGTTTAG
1594027 AGGAGC
1 AGGAGC
1594033 TTTGGTAAAA
Statistics
Matches: 259, Mismatches: 17, Indels: 19
0.88 0.06 0.06
Matches are distributed among these distances:
36 1 0.00
38 1 0.00
39 126 0.49
40 18 0.07
41 92 0.36
42 20 0.08
43 1 0.00
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (40 bp):
AGGAGCAATTTACTTTCCAAGTCGTGGTGCCTCTGTTTAG
Found at i:1593871 original size:119 final size:119
Alignment explanation
Indices: 1593706--1594032 Score: 528
Period size: 119 Copynumber: 2.7 Consensus size: 119
1593696 ATGATTGTCA
* * *
1593706 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTC
1 AGGAGCAATTTACTTTTC-AAGT-TTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
* *
1593771 GTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTTGTTGCCTTTGTTTAG
64 GTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCTCTGTTTAG
* *
1593827 AGGAGCAATTTACTTTTCAAGTTTGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGT
1 AGGAGCAATTTACTTTTCAAGTTTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT
* *
1593892 GGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAGTTCGTTGCCTCTGTTTAG
66 GGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCTCTGTTTAG
* *
1593946 AGGAGCAATTTACTTTTCAAGTTCGGTGTCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAGTCG
1 AGGAGCAATTTACTTTTCAAGTTTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTC-AAAGTCG
1594011 TGGTGCCTCTGTTTAGAGGAGC
65 TGGTGCCTCTGTTTAGAGGAGC
1594033 TTTGGTAAAA
Statistics
Matches: 191, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
119 142 0.74
120 32 0.17
121 17 0.09
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (119 bp):
AGGAGCAATTTACTTTTCAAGTTTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT
GGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAGTTCGTTGCCTCTGTTTAG
Found at i:1594056 original size:8 final size:8
Alignment explanation
Indices: 1594039--1594126 Score: 96
Period size: 8 Copynumber: 11.5 Consensus size: 8
1594029 GAGCTTTGGT
1594039 AAAA-AAA
1 AAAACAAA
1594046 AAAACAAAA
1 AAAAC-AAA
1594055 AAAACAAA
1 AAAACAAA
1594063 AAAACAAA
1 AAAACAAA
*
1594071 AAAGC-AA
1 AAAACAAA
*
1594078 AAAATAAA
1 AAAACAAA
1594086 AAAAC-AA
1 AAAACAAA
1594093 AAAA-AAA
1 AAAACAAA
*
1594100 ACAA-AAA
1 AAAACAAA
1594107 AAAACAAA
1 AAAACAAA
*
1594115 AAAACCAA
1 AAAACAAA
1594123 AAAA
1 AAAA
1594127 TGTTGAGTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
7 26 0.38
8 35 0.51
9 8 0.12
ACGTcount: A:0.88, C:0.10, G:0.01, T:0.01
Consensus pattern (8 bp):
AAAACAAA
Found at i:1594056 original size:9 final size:9
Alignment explanation
Indices: 1594042--1594126 Score: 97
Period size: 9 Copynumber: 9.7 Consensus size: 9
1594032 CTTTGGTAAA
1594042 AAAAAAAAC
1 AAAAAAAAC
1594051 AAAAAAAAC
1 AAAAAAAAC
1594060 -AAAAAAAC
1 AAAAAAAAC
*
1594068 -AAAAAAGC
1 AAAAAAAAC
1594076 AAAAAATAA-
1 AAAAAA-AAC
*
1594085 AAAAACAA-
1 AAAAAAAAC
1594093 AAAAAAAAC
1 AAAAAAAAC
1594102 AAAAAAAAAC
1 -AAAAAAAAC
*
1594112 AAAAAAACC
1 AAAAAAAAC
1594121 AAAAAA
1 AAAAAA
1594127 TGTTGAGTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
8 24 0.36
9 33 0.49
10 10 0.15
ACGTcount: A:0.87, C:0.11, G:0.01, T:0.01
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1594126 original size:1 final size:1
Alignment explanation
Indices: 1594039--1594118 Score: 79
Period size: 1 Copynumber: 80.0 Consensus size: 1
1594029 GAGCTTTGGT
* * * ** * * *
1594039 AAAAAAAAAAACAAAAAAAACAAAAAAACAAAAAAGCAAAAAATAAAAAAACAAAAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1594104 AAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAA
1594119 CCAAAAAATG
Statistics
Matches: 62, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.89, C:0.09, G:0.01, T:0.01
Consensus pattern (1 bp):
A
Found at i:1594126 original size:11 final size:10
Alignment explanation
Indices: 1594041--1594118 Score: 90
Period size: 10 Copynumber: 7.7 Consensus size: 10
1594031 GCTTTGGTAA
1594041 AAAAAAAAAC
1 AAAAAAAAAC
1594051 -AAAAAAAAC
1 AAAAAAAAAC
1594060 AAAAAAACAA-
1 AAAAAAA-AAC
1594070 AAAAGCAAAAA-
1 AAAA--AAAAAC
*
1594081 ATAAAAAAAC
1 AAAAAAAAAC
1594091 AAAAAAAAAAC
1 -AAAAAAAAAC
1594102 AAAAAAAAAC
1 AAAAAAAAAC
1594112 AAAAAAA
1 AAAAAAA
1594119 CCAAAAAATG
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
9 14 0.23
10 27 0.45
11 16 0.27
12 3 0.05
ACGTcount: A:0.88, C:0.09, G:0.01, T:0.01
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:1594342 original size:16 final size:19
Alignment explanation
Indices: 1594321--1594369 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 19
1594311 TTTTATGTAT
1594321 TGTATTATTTATT-AT-TA
1 TGTATTATTTATTAATATA
*
1594338 T-TATTATGTATTAATATA
1 TGTATTATTTATTAATATA
1594356 TGTATATATTTATT
1 TGTAT-TATTTATT
1594370 TATTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.38
17 3 0.12
18 3 0.12
19 3 0.12
20 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TGTATTATTTATTAATATA
Found at i:1595439 original size:24 final size:25
Alignment explanation
Indices: 1595393--1595439 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
1595383 GCTCCAGGTT
* *
1595393 TTTTTTTTTTTTCTCTTTCTTTGAA
1 TTTTTTTTTCTTCTCTTTATTTGAA
*
1595418 TTTTTTTTTCTT-TGTTTATTTG
1 TTTTTTTTTCTTCTCTTTATTTG
1595440 TTTATTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (25 bp):
TTTTTTTTTCTTCTCTTTATTTGAA
Found at i:1595617 original size:57 final size:57
Alignment explanation
Indices: 1595540--1596153 Score: 793
Period size: 57 Copynumber: 10.3 Consensus size: 57
1595530 AAAAATTCTA
*
1595540 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
*
1595598 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAATAAATTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTCC
* *
1595660 AATAAAAATAGTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 -A-AAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* *
1595719 AAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTT-CTTCAGAAATAAATTTCAAAAA
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATAAATTTC----C
* *
1595780 AAAAAAAATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* *
1595837 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAAA
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC---C
* * * *
1595897 AAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTAGAAATAAATTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* *
1595954 AAAAAA-AGGGTTTTCGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTCC
1 AAAAAATA---TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCC
1596015 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTCC
*
1596077 AAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 --AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1596136 AAAAAATATTTTTGGGGA
1 AAAAAATATTTTTGGGGA
1596154 TCAATTTTCC
Statistics
Matches: 493, Mismatches: 33, Indels: 61
0.84 0.06 0.10
Matches are distributed among these distances:
56 4 0.01
57 160 0.32
58 7 0.01
59 91 0.18
60 53 0.11
61 66 0.13
62 24 0.05
63 2 0.00
64 86 0.17
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (57 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
Found at i:1595857 original size:118 final size:115
Alignment explanation
Indices: 1595539--1596340 Score: 935
Period size: 118 Copynumber: 6.9 Consensus size: 115
1595529 AAAAAATTCT
*
1595539 AAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAA
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAA
*
1595604 TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGAAAAATAAATTTCC
66 TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTT-C
* *
1595660 AATAAAAATAGTTTT-GGGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAA
1 AAAAAAAATATTTTTAGGG-AAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAA
*
1595724 ATATTTTTGGAGAAAAGTTGAAAGTATCAATTTT-CTTCAGAAATAAATTTC
65 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATAAATTTC
*
1595775 AAAAAAAAAAAAATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAA
1 ---AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAA
*
1595840 AAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC
63 AAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
* * *
1595893 AAAAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTAGAAATAAATTTTCAAAA
1 --AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAA
* *
1595958 AA-AGGGTTTTCGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTC
64 AATA---TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTC
* *
1596014 -CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCCA
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTCC-
*
1596078 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
60 -AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
* * *
1596135 -CAAAAAATATTTTT---G----G--G---G-ATCAATTTTCCTCAGAAATAAATTTCAAAAAAA
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC----CAA
1596186 AAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
62 AAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC
*** * *
1596241 -AAAAAAAGGGTTTTCGAGGAAAAGTTGAAAGTATCAATTTT-CTTTGAAAATCGAAATTTCCAA
1 AAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCCAA
1596304 AAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
62 AAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1596341 TTCTACAAAA
Statistics
Matches: 603, Mismatches: 35, Indels: 89
0.83 0.05 0.12
Matches are distributed among these distances:
103 11 0.02
105 53 0.09
106 14 0.02
108 12 0.02
109 1 0.00
110 1 0.00
112 1 0.00
114 2 0.00
115 1 0.00
116 12 0.02
117 63 0.10
118 186 0.31
119 45 0.07
120 19 0.03
121 120 0.20
122 7 0.01
123 47 0.08
124 1 0.00
125 6 0.01
126 1 0.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (115 bp):
AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAA
TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC
Found at i:1596274 original size:59 final size:56
Alignment explanation
Indices: 1596153--1596340 Score: 200
Period size: 59 Copynumber: 3.2 Consensus size: 56
1596143 ATTTTTGGGG
*
1596153 ATCAATTTTCCTCAGAAATAAA-TTTCAAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGT
1 ATCAATTTTCCTTAGAAATAAATTTTC-----AAAAAA-ATTTTTGGGGAAAAGTTGAAAGT
* *
1596214 ATCAATTTTCCTTAGAAATAAATTTTCAAAAAAAGGGTTTTCGAGGAAAAGTTGAAAGT
1 ATCAATTTTCCTTAGAAATAAATTTTCAAAAAAA---TTTTTGGGGAAAAGTTGAAAGT
* *
1596273 ATCAATTTT-CTTTGAAAATCGAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGT
1 ATCAATTTTCCTTAG-AAAT--AAATTTTCAAAAAA-ATTTTTGGGGAAAAGTTGAAAGT
1596332 ATCAATTTT
1 ATCAATTTT
1596341 TTCTACAAAA
Statistics
Matches: 112, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
56 1 0.01
57 6 0.05
58 4 0.04
59 62 0.55
61 34 0.30
62 5 0.04
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (56 bp):
ATCAATTTTCCTTAGAAATAAATTTTCAAAAAAATTTTTGGGGAAAAGTTGAAAGT
Found at i:1597611 original size:20 final size:20
Alignment explanation
Indices: 1597582--1597623 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1597572 AAACAAAACT
1597582 CTAAACAAATATAAACGAAC
1 CTAAACAAATATAAACGAAC
* *
1597602 CTAAATAAATATAAATGAAC
1 CTAAACAAATATAAACGAAC
1597622 CT
1 CT
1597624 TAAAATAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.57, C:0.17, G:0.05, T:0.21
Consensus pattern (20 bp):
CTAAACAAATATAAACGAAC
Found at i:1597831 original size:13 final size:14
Alignment explanation
Indices: 1597813--1597843 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1597803 TATTATTTGT
1597813 TAAACAT-AATAAA
1 TAAACATAAATAAA
1597826 TAAACATAAATAAA
1 TAAACATAAATAAA
1597840 TAAA
1 TAAA
1597844 AACTAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACATAAATAAA
Found at i:1599023 original size:27 final size:26
Alignment explanation
Indices: 1598974--1599035 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 26
1598964 TTTTATATTT
1598974 TATATTTAA-ATAATTTTTTATAAAAA
1 TATA-TTAATATAATTTTTTATAAAAA
1599000 TATATTAATATATATTTTTTATAAAAA
1 TATATTAATATA-ATTTTTTATAAAAA
1599027 TATATTAAT
1 TATATTAAT
1599036 TTTTAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 4 0.12
26 7 0.21
27 23 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TATATTAATATAATTTTTTATAAAAA
Found at i:1599051 original size:27 final size:28
Alignment explanation
Indices: 1598983--1599065 Score: 100
Period size: 27 Copynumber: 3.0 Consensus size: 28
1598973 TTATATTTAA
1598983 ATAATTTTTTATAAAAATATATTAATAT
1 ATAATTTTTTATAAAAATATATTAATAT
*
1599011 AT-ATTTTTTATAAAAATATATTAATTT
1 ATAATTTTTTATAAAAATATATTAATAT
* *
1599038 TTAATTATTTTA-AAATAATA-ATTTATAT
1 ATAATT-TTTTATAAA-AATATATTAATAT
1599066 TATTTAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 25 0.52
28 14 0.29
29 9 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
ATAATTTTTTATAAAAATATATTAATAT
Found at i:1600119 original size:20 final size:19
Alignment explanation
Indices: 1600096--1600143 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1600086 ATAAAATATT
1600096 TTTAAAATTT-ATATATCAAA
1 TTTAAAATTTCAT-TAT-AAA
* *
1600116 TTTAACATTTCATTATAAT
1 TTTAAAATTTCATTATAAA
1600135 TTTAAAATT
1 TTTAAAATT
1600144 ATTTGTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAAATTTCATTATAAA
Found at i:1605494 original size:24 final size:24
Alignment explanation
Indices: 1605450--1605495 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1605440 TATAATTAAT
*
1605450 TAATAATATATAAATTTTATATAC
1 TAATAATATATAAATTATATATAC
1605474 TAATAATATATCAAA-TATATAT
1 TAATAATATAT-AAATTATATAT
1605496 CCTGTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATAATATATAAATTATATATAC
Found at i:1606087 original size:14 final size:15
Alignment explanation
Indices: 1606053--1606095 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1606043 ATTTATTAAA
1606053 ATAATTTTAAA-TAT
1 ATAATTTTAAATTAT
1606067 ATAATTTTAAATTAT
1 ATAATTTTAAATTAT
* *
1606082 -TTATTTTAAGTTAT
1 ATAATTTTAAATTAT
1606096 CGAATACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 23 0.88
15 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATAATTTTAAATTAT
Found at i:1606173 original size:31 final size:33
Alignment explanation
Indices: 1606138--1606201 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 33
1606128 ATTGAATAAC
*
1606138 TTATTT-ATCTTAAATT-TTTTATAA-AAAAAAA
1 TTATTTAAT-TTAAATTATTTTAAAATAAAAAAA
*
1606169 TTATTTAATTTATATTATTTTAAAATAAAAAAA
1 TTATTTAATTTAAATTATTTTAAAATAAAAAAA
1606202 ATTGTGATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 12 0.43
32 9 0.32
33 7 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (33 bp):
TTATTTAATTTAAATTATTTTAAAATAAAAAAA
Found at i:1608516 original size:4 final size:4
Alignment explanation
Indices: 1608502--1608562 Score: 52
Period size: 4 Copynumber: 15.5 Consensus size: 4
1608492 AAGCAATTTA
* * * * * *
1608502 ATAT A-AT ATAT ATAT ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
1608549 ATAT ATAT TTAT AT
1 ATAT ATAT ATAT AT
1608563 TAGAGCTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 3 0.06
4 49 0.94
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:1609263 original size:2 final size:2
Alignment explanation
Indices: 1609256--1609287 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1609246 TTGATAAAAG
1609256 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
1609288 GTAATATTTT
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:1626489 original size:284 final size:289
Alignment explanation
Indices: 1625941--1626490 Score: 763
Period size: 284 Copynumber: 1.9 Consensus size: 289
1625931 TTTGGTCATC
1625941 AAGTGTTGACAAGCAGAGCTTTCTCTCTTTCTCTCTCAATCTCTGTATCTGTATTAACCATGATC
1 AAGTGTTGACAAGCAGAGC-TTCTCTCTTTCTCTCTCAATCTCTGTATCTGTATTAACCATGATC
* * * *
1626006 TTTCAGGACATGAGATGTTTTAAGTATGTCTAGGTAATCCCTACATTTGTACCTGGTTTTGTCTC
65 TTGCAGGACATGAAATGTTTTAAGTATGTCTAAGTAATCCCTACAGTTGTACCTGGTTTTGTCTC
**
1626071 ATGTTTATTGTTATGGCTCTTTGTTGTTCTCTTTGAAAGGGTTAAAAGGAATCATATCCGCCGGT
130 ATGTTTATTGTTATGGCTCTTTGTTG------TTGAAAGGGTTAAAAGGAATCATATCCGCCACT
* * **
1626136 TGTTTCTTGTCTGATTTCCCCATTTATATGTCAGAATAATGGGTTTGAAACTTGGGAATGGTAGG
189 TGTTTCCTGTCAGATTTCCCCATTTATACATCAGAATAATGGGTTTGAAACTTGGGAATGGTAGG
1626201 AAGAAAATTGTGCTGATTCATGATGTGATTTTCAGT
254 AAGAAAATTGTGCTGATTCATGATGTGATTTTCAGT
* * * *
1626237 AAGTGTTGACAAGTAGAGC-TCT-T-TTTCTCTCTCAATCTCTGTCTCTGTCTTAACCATGATGT
1 AAGTGTTGACAAGCAGAGCTTCTCTCTTTCTCTCTCAATCTCTGTATCTGTATTAACCATGATCT
* *
1626299 TGCAGGACATGAAATGTTTTAAGTATGTCTAAGTAATCGCTACAAGTTGTACCTTGTTTTGTCTC
66 TGCAGGACATGAAATGTTTTAAGTATGTCTAAGTAATCCCTAC-AGTTGTACCTGGTTTTGTCTC
* *
1626364 ATGTTTATTGTTATGGCT-TTTCGTTG-T-AAAGGGTT-AAAGGAATCATGTCTGCCACTTGTTT
130 ATGTTTATTGTTATGGCTCTTT-GTTGTTGAAAGGGTTAAAAGGAATCATATCCGCCACTTGTTT
*** * *
1626425 CCTGTCAGATTTCCCCATTTATACATCAGAATAATGGGTTTGAGTTTTGGGAATGTTGGGAAGAA
194 CCTGTCAGATTTCCCCATTTATACATCAGAATAATGGGTTTGAAACTTGGGAATGGTAGGAAGAA
1626490 A
259 A
1626491 TTAGCTTGAT
Statistics
Matches: 229, Mismatches: 23, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
284 79 0.34
285 8 0.03
286 1 0.00
292 78 0.34
293 42 0.18
294 3 0.01
296 18 0.08
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (289 bp):
AAGTGTTGACAAGCAGAGCTTCTCTCTTTCTCTCTCAATCTCTGTATCTGTATTAACCATGATCT
TGCAGGACATGAAATGTTTTAAGTATGTCTAAGTAATCCCTACAGTTGTACCTGGTTTTGTCTCA
TGTTTATTGTTATGGCTCTTTGTTGTTGAAAGGGTTAAAAGGAATCATATCCGCCACTTGTTTCC
TGTCAGATTTCCCCATTTATACATCAGAATAATGGGTTTGAAACTTGGGAATGGTAGGAAGAAAA
TTGTGCTGATTCATGATGTGATTTTCAGT
Found at i:1632916 original size:20 final size:19
Alignment explanation
Indices: 1632891--1632948 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 19
1632881 TATTTTTTAA
1632891 TTATTTATATAATATTATAT
1 TTATTTATAT-ATATTATAT
*
1632911 TTATTTATATTTA-TATAT
1 TTATTTATATATATTATAT
1632929 TTAATTT-TATAT-TTATAT
1 TT-ATTTATATATATTATAT
1632947 TT
1 TT
1632949 TAAAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 18 0.53
19 6 0.18
20 10 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTATATATATTATAT
Found at i:1633557 original size:11 final size:12
Alignment explanation
Indices: 1633541--1633588 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
1633531 TTGATATATA
1633541 TAATTATTT-TT
1 TAATTATTTATT
1633552 TAATTATTTATT
1 TAATTATTTATT
1633564 TAATT-TTATATT
1 TAATTATT-TATT
1633576 TATATATATTTAT
1 TA-AT-TATTTAT
1633589 AGTTATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 11 0.34
12 13 0.41
13 2 0.06
14 4 0.12
15 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TAATTATTTATT
Found at i:1633577 original size:6 final size:6
Alignment explanation
Indices: 1633556--1633620 Score: 61
Period size: 6 Copynumber: 11.8 Consensus size: 6
1633546 ATTTTTTAAT
* * *
1633556 TATTTA T-TTAA T-TTTA TATTTA TA--TA TATTTA TAGTTA T-TTAA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1633599 T-TTTA TATTTA TATTTA TATTT
1 TATTTA TATTTA TATTTA TATTT
1633621 TAAAAATAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
4 4 0.08
5 15 0.31
6 30 0.61
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (6 bp):
TATTTA
Found at i:1633577 original size:16 final size:16
Alignment explanation
Indices: 1633556--1633610 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
1633546 ATTTTTTAAT
1633556 TATTTATTTAATTTTA
1 TATTTATTTAATTTTA
*
1633572 TATTTATAT-ATATTTA
1 TATTTATTTAAT-TTTA
*
1633588 TAGTTATTTAATTTTA
1 TATTTATTTAATTTTA
1633604 TATTTAT
1 TATTTAT
1633611 ATTTATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 2 0.06
16 29 0.88
17 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TATTTATTTAATTTTA
Found at i:1633608 original size:44 final size:41
Alignment explanation
Indices: 1633535--1633642 Score: 105
Period size: 44 Copynumber: 2.5 Consensus size: 41
1633525 AATCCATTGA
1633535 TATATATAATTATTTTTTAATTATTTATTTA-ATTTTATATT
1 TATATATAATTATTTTTTAATTATTTATTTATA-TTTATATT
*
1633576 TATATATATTTATAGTTATTTAATT-TTATATTTATATTTATATTT
1 TATATATAATTAT--TT-TTTAATTATT-TATTTATATTTATA-TT
* *
1633621 TAAAAATAA-TATTTTATTAATT
1 TATATATAATTATTTT-TTAATT
1633643 TTGGATCAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
41 13 0.23
42 8 0.14
43 4 0.07
44 22 0.39
45 9 0.16
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (41 bp):
TATATATAATTATTTTTTAATTATTTATTTATATTTATATT
Found at i:1633609 original size:12 final size:11
Alignment explanation
Indices: 1633539--1633620 Score: 55
Period size: 10 Copynumber: 7.6 Consensus size: 11
1633529 CATTGATATA
*
1633539 TATAATTATTT
1 TATATTTATTT
* *
1633550 TTTAATTA-TT
1 TATATTTATTT
*
1633560 TAT-TTAATTT
1 TATATTTATTT
*
1633570 TATATTTA-TA
1 TATATTTATTT
*
1633580 TATATTTATAGT
1 TATATTTAT-TT
*
1633592 TAT-TTAATTT
1 TATATTTATTT
1633602 TATATTTATATT
1 TATATTTAT-TT
1633614 TATATTT
1 TATATTT
1633621 TAAAAATAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
9 2 0.04
10 22 0.41
11 18 0.33
12 12 0.22
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (11 bp):
TATATTTATTT
Found at i:1639683 original size:2 final size:2
Alignment explanation
Indices: 1639678--1639713 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1639668 AGTGTGTGTG
* *
1639678 TA TA TA TA CA TA TA TA TA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1639714 AGAATTGTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1643171 original size:32 final size:32
Alignment explanation
Indices: 1643110--1643171 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1643100 TATAAATTCA
* *
1643110 AATTAATATATAAAAATAAAATAATAATTTTT
1 AATTAAAATATAAAAATAAAATAAAAATTTTT
*
1643142 AATTAAAATAATAAAAAT-ATATAAAAATTT
1 AATTAAAAT-ATAAAAATAAAATAAAAATTT
1643172 AAAAATTGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 18 0.69
33 8 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (32 bp):
AATTAAAATATAAAAATAAAATAAAAATTTTT
Found at i:1643425 original size:22 final size:21
Alignment explanation
Indices: 1643400--1643449 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
1643390 ATATTAAAAA
*
1643400 TTAAATTAAA-ATCATAAATAAT
1 TTAAATTAAATAT-AAAAAT-AT
1643422 TTAAATTAAATATAAAAATAT
1 TTAAATTAAATATAAAAATAT
1643443 TTAAATT
1 TTAAATT
1643450 TGATGTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 9 0.35
22 15 0.58
23 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAATTAAATATAAAAATAT
Found at i:1643432 original size:21 final size:22
Alignment explanation
Indices: 1643400--1643449 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
1643390 ATATTAAAAA
*
1643400 TTAAATTAAAATCATAAATA-AT
1 TTAAATTAAAAT-ATAAAAATAT
1643422 TTAAATT-AAATATAAAAATAT
1 TTAAATTAAAATATAAAAATAT
1643443 TTAAATT
1 TTAAATT
1643450 TGATGTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 6 0.23
21 13 0.50
22 7 0.27
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAATTAAAATATAAAAATAT
Found at i:1645052 original size:17 final size:16
Alignment explanation
Indices: 1645030--1645069 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
1645020 AAATCATAAT
1645030 TTTTTTATATTTTATTA
1 TTTTTTATATTTT-TTA
1645047 -TTTTT-TATTTTTTA
1 TTTTTTATATTTTTTA
1645061 TTTTTTATA
1 TTTTTTATA
1645070 ATCGTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.14
15 11 0.52
16 7 0.33
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTATATTTTTTA
Found at i:1645065 original size:7 final size:7
Alignment explanation
Indices: 1645031--1645068 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
1645021 AATCATAATT
1645031 TTTTTATA
1 TTTTT-TA
1645039 TTTTATTA
1 TTTT-TTA
1645047 TTTTTTA
1 TTTTTTA
1645054 TTTTTTA
1 TTTTTTA
1645061 TTTTTTA
1 TTTTTTA
1645068 T
1 T
1645069 AATCGTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 18 0.62
8 10 0.34
9 1 0.03
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTA
Found at i:1646026 original size:7 final size:7
Alignment explanation
Indices: 1646016--1646056 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
1646006 AATTAAAAAA
1646016 TTATATT
1 TTATATT
1646023 TTATATT
1 TTATATT
1646030 TTATATTT
1 TTATA-TT
1646038 TTATATT
1 TTATATT
*
1646045 TATATATA
1 T-TATATT
1646053 TTAT
1 TTAT
1646057 GATATATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 18 0.58
8 13 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTATATT
Found at i:1646035 original size:14 final size:14
Alignment explanation
Indices: 1646016--1646056 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
1646006 AATTAAAAAA
1646016 TTATATTTTATATT
1 TTATATTTTATATT
1646030 TTATATTTTTATATT
1 TTATA-TTTTATATT
*
1646045 TATATATATTAT
1 T-TATATTTTAT
1646057 GATATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 15 0.62
16 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATATTTTATATT
Found at i:1646553 original size:16 final size:16
Alignment explanation
Indices: 1646518--1646571 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
1646508 TTATGATTTG
1646518 ATTTATAAATTT-AATA
1 ATTTA-AAATTTAAATA
*
1646534 ATTTAAAATTTAAATT
1 ATTTAAAATTTAAATA
*
1646550 ATTT-AAATTCAAATA
1 ATTTAAAATTTAAATA
1646565 ATTTAAA
1 ATTTAAA
1646572 TGTCAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 19 0.58
16 14 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTAAAATTTAAATA
Found at i:1646579 original size:16 final size:15
Alignment explanation
Indices: 1646530--1646579 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
1646520 TTATAAATTT
*
1646530 AATAATTTAAAATTTA
1 AATAATTT-AAATTCA
*
1646546 AATTATTTAAATTCA
1 AATAATTTAAATTCA
1646561 AATAATTTAAATGTCA
1 AATAATTTAAAT-TCA
1646577 AAT
1 AAT
1646580 TCAAAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (15 bp):
AATAATTTAAATTCA
Found at i:1646601 original size:22 final size:22
Alignment explanation
Indices: 1646538--1646601 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
1646528 TTAATAATTT
*
1646538 AAAATTTAAATTATTTAAATTCAA
1 AAAATTTAAA-TA-TCAAATTCAA
* *
1646562 ATAATTTAAATGTCAAATTCAA
1 AAAATTTAAATATCAAATTCAA
* *
1646584 AAAATTTGAATATGAAAT
1 AAAATTTAAATATCAAAT
1646602 AAACTTAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
22 23 0.70
23 1 0.03
24 9 0.27
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (22 bp):
AAAATTTAAATATCAAATTCAA
Found at i:1647700 original size:3 final size:3
Alignment explanation
Indices: 1647692--1647716 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1647682 TGTGTATGTG
1647692 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1647717 AATTAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1657698 original size:4 final size:4
Alignment explanation
Indices: 1657689--1657713 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1657679 ATTGAAGAAA
1657689 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
1657714 GTGATTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:1666188 original size:5 final size:5
Alignment explanation
Indices: 1666178--1666220 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
1666168 TATATTTAAT
* *
1666178 AATTA AATTA AATTTA AATTT AA-TA AATTG AATTA AATTA AAT
1 AATTA AATTA AA-TTA AATTA AATTA AATTA AATTA AATTA AAT
1666221 ATTATAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 3 0.09
5 24 0.75
6 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (5 bp):
AATTA
Found at i:1666212 original size:25 final size:25
Alignment explanation
Indices: 1666171--1666248 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
1666161 TATTATATAT
*
1666171 ATTTAAT-AATTAAATTAAATTTAA
1 ATTTAATAAATTGAATTAAATTTAA
1666195 ATTTAATAAATTGAATTAAA-TTAA
1 ATTTAATAAATTGAATTAAATTTAA
* *
1666219 ATATT-ATAATTTTGAATTAATTTTAA
1 AT-TTAATAA-ATTGAATTAAATTTAA
1666245 ATTT
1 ATTT
1666249 TTTAATTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 17 0.36
25 24 0.51
26 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (25 bp):
ATTTAATAAATTGAATTAAATTTAA
Found at i:1666709 original size:7 final size:6
Alignment explanation
Indices: 1666673--1666703 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
1666663 TATTTAATAT
1666673 ATTTTA ATTTTA ATTTTA ATTTTA ATATTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA AT-TTTA
1666704 TAATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:1668268 original size:13 final size:13
Alignment explanation
Indices: 1668250--1668276 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1668240 TTTTTTGATT
1668250 GAAGGGAGGGGAA
1 GAAGGGAGGGGAA
1668263 GAAGGGAGGGGAA
1 GAAGGGAGGGGAA
1668276 G
1 G
1668277 GAAAGGAAAA
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:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (13 bp):
GAAGGGAGGGGAA
Found at i:1668916 original size:14 final size:15
Alignment explanation
Indices: 1668880--1668916 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1668870 ATCACAAACA
1668880 ATAAAAAATTATATT
1 ATAAAAAATTATATT
1668895 A-AAAAAATT-TATT
1 ATAAAAAATTATATT
*
1668908 ATAATAAAT
1 ATAAAAAAT
1668917 CATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 14 0.70
15 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAAAATTATATT
Found at i:1669056 original size:16 final size:16
Alignment explanation
Indices: 1669037--1669071 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1669027 TTTAAAAAAA
* *
1669037 TTTTCTTTTTCTTTTC
1 TTTTCCTTTCCTTTTC
1669053 TTTTCCTTTCCTTTTC
1 TTTTCCTTTCCTTTTC
1669069 TTT
1 TTT
1669072 GTAAATATTT
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:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCCTTTCCTTTTC
Found at i:1669282 original size:14 final size:16
Alignment explanation
Indices: 1669257--1669296 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
1669247 GGTTGATTCG
1669257 ATTAATTTTAAAAT-AA
1 ATTAA-TTTAAAATCAA
1669273 ATT-ATTTAAAATCAA
1 ATTAATTTAAAATCAA
1669288 ATTAATTTA
1 ATTAATTTA
1669297 TTTTTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 8 0.36
15 6 0.27
16 8 0.36
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAATTTAAAATCAA
Found at i:1669330 original size:30 final size:31
Alignment explanation
Indices: 1669272--1669330 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1669262 TTTTAAAATA
* *
1669272 AATTATTTAAAATCAAATTAATTTATTTTTT
1 AATTAATTAAAATCAAATTAATTAATTTTTT
* *
1669303 AATTAATT-AAATTAAATTTATTAATTTT
1 AATTAATTAAAATCAAATTAATTAATTTT
1669331 GAATATTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (31 bp):
AATTAATTAAAATCAAATTAATTAATTTTTT
Found at i:1679730 original size:18 final size:16
Alignment explanation
Indices: 1679696--1679729 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1679686 TTATACTTTC
*
1679696 ATATATTGTTAATAAA
1 ATATATTGTAAATAAA
1679712 ATATATTGTAAGATAAA
1 ATATATTGTAA-ATAAA
1679729 A
1 A
1679730 AAAATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (16 bp):
ATATATTGTAAATAAA
Found at i:1685486 original size:20 final size:20
Alignment explanation
Indices: 1685450--1685487 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1685440 TTTGTTACAT
*
1685450 ATTACTTATATTTTTATTAA
1 ATTACTTATATTATTATTAA
1685470 ATTACTTA-ATTAATTATT
1 ATTACTTATATT-ATTATT
1685488 TTAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTACTTATATTATTATTAA
Found at i:1685956 original size:11 final size:11
Alignment explanation
Indices: 1685918--1685956 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1685908 AATATAATTT
1685918 AAAATTTTAATA
1 AAAATTTT-ATA
*
1685930 AAAATTATATA
1 AAAATTTTATA
*
1685941 TAAATTTTATA
1 AAAATTTTATA
1685952 AAAAT
1 AAAAT
1685957 AAAAATACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATTTTATA
Found at i:1687496 original size:72 final size:71
Alignment explanation
Indices: 1687342--1687607 Score: 248
Period size: 72 Copynumber: 3.7 Consensus size: 71
1687332 TCGTCCTCAA
* * * * * * * *
1687342 GAGGATTGCCCGAATCCATTGGGAATCTAGTTTCCTTGGAGAGTTTGGATATAGTC-TGGTCTTC
1 GAGGATTGCCTGACTCAATTGGCAATCTAGTTTCTTTGAAG-GATTGGATATA-TCATTGTCTTC
1687406 ATTTTCAG
64 ATTTTCAG
* * * *
1687414 CAGGATTGCCTGACTCAATCGGGAATCTAGTTTCTTTGAAGCGATTGGATCTATCATTGTCTTCA
1 GAGGATTGCCTGACTCAATTGGCAATCTAGTTTCTTTGAAG-GATTGGATATATCATTGTCTTCA
1687479 TTTTCAG
65 TTTTCAG
* ** * * * *
1687486 GAGGATTGCCTTACTCAATTGGCAATCTAGCATCTTTGGAGTATTTGGATTTATCATTCTCTTC-
1 GAGGATTGCCTGACTCAATTGGCAATCTAGTTTCTTTGAAGGA-TTGGATATATCATTGTCTTCA
*
1687550 TTTATCTG
65 TTT-TCAG
* * * *
1687558 GAAGATTGCCTAACTCAATTGGCAATCTAGTTTCTATGAAGTATATGGAT
1 GAGGATTGCCTGACTCAATTGGCAATCTAGTTTCTTTGAAGGAT-TGGAT
1687608 CTCCGACAGT
Statistics
Matches: 162, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
71 7 0.04
72 155 0.96
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (71 bp):
GAGGATTGCCTGACTCAATTGGCAATCTAGTTTCTTTGAAGGATTGGATATATCATTGTCTTCAT
TTTCAG
Found at i:1692172 original size:17 final size:19
Alignment explanation
Indices: 1692138--1692174 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1692128 TCAAATCAAA
*
1692138 TTATAATTTTTATTAATTT
1 TTATAATTTTTATAAATTT
1692157 TTAT-ATTTTTA-AAATTT
1 TTATAATTTTTATAAATTT
1692174 T
1 T
1692175 ATACAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATAATTTTTATAAATTT
Found at i:1692480 original size:19 final size:19
Alignment explanation
Indices: 1692456--1692500 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1692446 AAATGTTTTC
1692456 AATTATTTTACT-TATTTAT
1 AATTATTTT-CTATATTTAT
*
1692475 AATTATTTTCTATATTTTT
1 AATTATTTTCTATATTTAT
1692494 AA-TATTT
1 AATTATTT
1692501 ACAAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATTTTCTATATTTAT
Found at i:1693997 original size:41 final size:40
Alignment explanation
Indices: 1693918--1693997 Score: 92
Period size: 41 Copynumber: 1.9 Consensus size: 40
1693908 AAAATACATA
*
1693918 TTTTATTTTTAATTTATTAATATGAATTATAATATAATAAT
1 TTTTATTTTTAATTTATTAATATGAA-TAAAATATAATAAT
*
1693959 TTTTATATTTTATATTTTTTAATAT-AA-AAAATAGTAATA
1 TTTTAT-TTTTA-ATTTATTAATATGAATAAAATA-TAATA
1693998 CACAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
40 5 0.15
41 11 0.32
42 7 0.21
43 11 0.32
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (40 bp):
TTTTATTTTTAATTTATTAATATGAATAAAATATAATAAT
Found at i:1694613 original size:16 final size:16
Alignment explanation
Indices: 1694583--1694648 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
1694573 ATTAATTAAT
1694583 TAATATATATATTTATA
1 TAATA-ATATATTTATA
1694600 TAATAATAT-TTT-TA
1 TAATAATATATTTATA
*
1694614 -AATATTTATATTTA-A
1 TAATA-ATATATTTATA
*
1694629 AAATAATAT-TTTATA
1 TAATAATATATTTATA
1694644 TAATA
1 TAATA
1694649 TCAAGTTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
13 4 0.10
14 9 0.22
15 15 0.37
16 8 0.20
17 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATAATATATTTATA
Found at i:1695485 original size:12 final size:13
Alignment explanation
Indices: 1695451--1695488 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
1695441 AAAATTATAT
1695451 TAAAATAACAAATA
1 TAAAATAA-AAATA
1695465 TATAAATAAAAATA
1 TA-AAATAAAAATA
1695479 -AAAATAAAAA
1 TAAAATAAAAA
1695489 AATTTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.39
13 1 0.04
14 7 0.30
15 6 0.26
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (13 bp):
TAAAATAAAAATA
Found at i:1714805 original size:19 final size:19
Alignment explanation
Indices: 1714774--1714812 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1714764 ATATACATCC
1714774 TGCAGAAACAAT-GAATTT
1 TGCAGAAACAATGGAATTT
*
1714792 TGCATGAAAGAATGGAATTT
1 TGCA-GAAACAATGGAATTT
1714812 T
1 T
1714813 CATTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 7 0.39
20 7 0.39
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.31
Consensus pattern (19 bp):
TGCAGAAACAATGGAATTT
Found at i:1718039 original size:3 final size:3
Alignment explanation
Indices: 1718033--1718057 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1718023 ATAATAATTC
1718033 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1718058 AACATTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1719060 original size:16 final size:16
Alignment explanation
Indices: 1718992--1719083 Score: 67
Period size: 16 Copynumber: 5.8 Consensus size: 16
1718982 GAGTATTTCG
* *
1718992 AATTCAAATTATGTTA
1 AATTTAAATTATTTTA
* * *
1719008 AATATGAATTGTTTTA
1 AATTTAAATTATTTTA
* * *
1719024 AATTTAAATCATATCA
1 AATTTAAATTATTTTA
* *
1719040 TATTTAAATTATTTTG
1 AATTTAAATTATTTTA
* *
1719056 AATTTGAGTTATTTTA
1 AATTTAAATTATTTTA
*
1719072 AATTCAAATTAT
1 AATTTAAATTAT
1719084 ATTGTATCTA
Statistics
Matches: 53, Mismatches: 23, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
16 53 1.00
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (16 bp):
AATTTAAATTATTTTA
Found at i:1722487 original size:2 final size:2
Alignment explanation
Indices: 1722480--1722518 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1722470 CAATGCAAGT
*
1722480 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1722519 TATCATTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1724800 original size:4 final size:4
Alignment explanation
Indices: 1724791--1724827 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
1724781 ATTCCCTGAG
*
1724791 TCTT TCTT TCTT TCTT TCTT TTTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1724828 GAAAGCTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TCTT
Found at i:1725296 original size:2 final size:2
Alignment explanation
Indices: 1725289--1725321 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1725279 CCAAAAGAAC
1725289 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 A
1725322 CAAGTCTCTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1725411 original size:7 final size:7
Alignment explanation
Indices: 1725401--1725425 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1725391 CTTCAGTTTC
1725401 TTTTCTT
1 TTTTCTT
1725408 TTTTCTT
1 TTTTCTT
1725415 TTTTCTT
1 TTTTCTT
1725422 TTTT
1 TTTT
1725426 TACTTATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:1728117 original size:16 final size:16
Alignment explanation
Indices: 1728096--1728129 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1728086 GCCTTAATAT
1728096 ATTCATGGCTAGCTGG
1 ATTCATGGCTAGCTGG
1728112 ATTCATGGCTAGCTGG
1 ATTCATGGCTAGCTGG
1728128 AT
1 AT
1728130 ATACTAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (16 bp):
ATTCATGGCTAGCTGG
Found at i:1741292 original size:16 final size:14
Alignment explanation
Indices: 1741270--1741301 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1741260 TATTTCATAC
*
1741270 AATTATTTTTAAAA
1 AATTATATTTAAAA
1741284 AATTATATTTAAAA
1 AATTATATTTAAAA
1741298 AATT
1 AATT
1741302 TAAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTATATTTAAAA
Found at i:1741308 original size:7 final size:7
Alignment explanation
Indices: 1741296--1741322 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1741286 TTATATTTAA
1741296 AAAATTT
1 AAAATTT
1741303 AAAATTT
1 AAAATTT
1741310 AAAATTT
1 AAAATTT
1741317 AAAATT
1 AAAATT
1741323 AAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAAATTT
Found at i:1742051 original size:12 final size:12
Alignment explanation
Indices: 1742034--1742067 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1742024 ACATGTTATC
*
1742034 TTAAAAAATATA
1 TTAAAAAATAAA
1742046 TT-AAAAATAAA
1 TTAAAAAATAAA
1742057 TTAAAAAATAA
1 TTAAAAAATAA
1742068 CTTTATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
TTAAAAAATAAA
Found at i:1742934 original size:3 final size:3
Alignment explanation
Indices: 1742926--1742953 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1742916 ATAGGGCAAC
1742926 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1742954 GATGGGTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1743414 original size:21 final size:21
Alignment explanation
Indices: 1743390--1743432 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1743380 TACTTTTTAA
*
1743390 ATGTATTTTGT-TTGAATGTAC
1 ATGTATTTT-TATTAAATGTAC
1743411 ATGTATTTTTATTAAATGTAC
1 ATGTATTTTTATTAAATGTAC
1743432 A
1 A
1743433 ATAATTATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (21 bp):
ATGTATTTTTATTAAATGTAC
Found at i:1743536 original size:16 final size:16
Alignment explanation
Indices: 1743517--1743566 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
1743507 TATTTTTAAA
1743517 ATTTTTTTATATTATT
1 ATTTTTTTATATTATT
*
1743533 ATTTCTTTT-TATTA-A
1 ATTT-TTTTATATTATT
*
1743548 ATATTTTTTATATTTTT
1 AT-TTTTTTATATTATT
1743565 AT
1 AT
1743567 CATTATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
15 6 0.22
16 15 0.56
17 6 0.22
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTTTATATTATT
Found at i:1743576 original size:32 final size:33
Alignment explanation
Indices: 1743506--1743576 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 33
1743496 AAAAGTAATT
*
1743506 TTATTT-TTAAAATTTTTTTATATTATTATTTC
1 TTATTTATTAAAATTTTTTTATATTATTATATC
1743538 TT-TTTATT-AAATATTTTTTATATT-TT-TATC
1 TTATTTATTAAAAT-TTTTTTATATTATTATATC
1743568 ATTATTTAT
1 -TTATTTAT
1743577 ATATACTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
30 3 0.09
31 11 0.32
32 20 0.59
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (33 bp):
TTATTTATTAAAATTTTTTTATATTATTATATC
Found at i:1744818 original size:24 final size:25
Alignment explanation
Indices: 1744777--1744825 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1744767 TTGGCATACC
* **
1744777 ATATTTTATTTACGATA-TTATTTA
1 ATATTTTATCTAAAATATTTATTTA
1744801 ATATTTTATCTAAAATATTTATTTA
1 ATATTTTATCTAAAATATTTATTTA
1744826 GTTACAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (25 bp):
ATATTTTATCTAAAATATTTATTTA
Found at i:1745993 original size:2 final size:2
Alignment explanation
Indices: 1745986--1746015 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1745976 TATAGTACTA
1745986 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
1746016 TTCTGGTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1746217 original size:20 final size:20
Alignment explanation
Indices: 1746186--1746240 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
1746176 TTGTTCTTCT
1746186 TTTTTTTCATTATTA-TATAA
1 TTTTTTT-ATTATTATTATAA
*
1746206 TTTTGTTTATTATTATTATTA
1 TTTT-TTTATTATTATTATAA
1746227 TTTTTTTATTATTA
1 TTTTTTTATTATTA
1746241 ATCTTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTTTATTATTATTATAA
Found at i:1746720 original size:51 final size:52
Alignment explanation
Indices: 1746651--1746757 Score: 139
Period size: 51 Copynumber: 2.1 Consensus size: 52
1746641 TGGGTCGTTG
** *
1746651 AAAA-TTGAAAAAGTTTAAAATTTTCGAT-TTCCATTGAATTTTTCGA-CACC
1 AAAATTTGAAAAAAATTAAAATTTTCGATGAT-CATTGAATTTTTCGACCACC
*
1746701 AAAATTTGAAAAAAATTAAAATTTTCGATGATCGTTGAATTTTTCGACCACC
1 AAAATTTGAAAAAAATTAAAATTTTCGATGATCATTGAATTTTTCGACCACC
*
1746753 GAAAT
1 AAAAT
1746758 CTGAGGATCT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
50 4 0.08
51 36 0.73
52 9 0.18
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (52 bp):
AAAATTTGAAAAAAATTAAAATTTTCGATGATCATTGAATTTTTCGACCACC
Found at i:1747065 original size:13 final size:13
Alignment explanation
Indices: 1747056--1747089 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1747046 TTCTTTTTTA
*
1747056 TTTTGATTTTGAT
1 TTTTTATTTTGAT
*
1747069 TTTTTATGTTGAT
1 TTTTTATTTTGAT
1747082 TTTTTATT
1 TTTTTATT
1747090 ATTGTTATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.74
Consensus pattern (13 bp):
TTTTTATTTTGAT
Found at i:1747065 original size:19 final size:19
Alignment explanation
Indices: 1747043--1747085 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1747033 TTTCCTCTTT
* *
1747043 TTTTTCTTTTTTATTTTGA
1 TTTTTATTTTTTATGTTGA
*
1747062 TTTTGATTTTTTATGTTGA
1 TTTTTATTTTTTATGTTGA
1747081 TTTTT
1 TTTTT
1747086 TATTATTGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.02, G:0.09, T:0.77
Consensus pattern (19 bp):
TTTTTATTTTTTATGTTGA
Found at i:1747358 original size:13 final size:12
Alignment explanation
Indices: 1747342--1747381 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 12
1747332 TTATACTAAA
1747342 AAATGAATTATTT
1 AAATGAATT-TTT
1747355 AAATGAATCTTTT
1 AAATGAAT-TTTT
1747368 AAATGTAATTTTT
1 AAATG-AATTTTT
1747381 A
1 A
1747382 GAAAAAGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (12 bp):
AAATGAATTTTT
Found at i:1748072 original size:19 final size:19
Alignment explanation
Indices: 1748050--1748094 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1748040 TTTTCTTTTT
* * *
1748050 TTTTTCTTTTTTATTTTGA
1 TTTTTATTTTTTATGTTAA
*
1748069 TTTTGATTTTTTATGTTAA
1 TTTTTATTTTTTATGTTAA
1748088 TTTTTAT
1 TTTTTAT
1748095 GTTAATTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.76
Consensus pattern (19 bp):
TTTTTATTTTTTATGTTAA
Found at i:1748091 original size:11 final size:12
Alignment explanation
Indices: 1748076--1748106 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1748066 TGATTTTGAT
1748076 TTTTTATGTTAA
1 TTTTTATGTTAA
1748088 TTTTTATGTTAA
1 TTTTTATGTTAA
1748100 TTTTTAT
1 TTTTTAT
1748107 TATTGTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (12 bp):
TTTTTATGTTAA
Found at i:1760578 original size:39 final size:39
Alignment explanation
Indices: 1760441--1760595 Score: 166
Period size: 39 Copynumber: 3.9 Consensus size: 39
1760431 TCAGATTTTT
* * * *
1760441 ATTTAAAGTTTGTTACCTTTGGTTAAATGAGCTTTTTAA
1 ATTTAAAGTTTGTTACCTTTGGTCAGAGGAGCTTTTTGA
* * * ** * * *
1760480 CATTTAAATTTTGTTGCCTCTAATCATAGAAGCCTTTTGA
1 -ATTTAAAGTTTGTTACCTTTGGTCAGAGGAGCTTTTTGA
* *
1760520 ATTTAAAGTTTGTTGCCTTTGGTGAGAGGAGCTTTTTGA
1 ATTTAAAGTTTGTTACCTTTGGTCAGAGGAGCTTTTTGA
*
1760559 ATTTAAAGTTTGTTACCTTTGGTCAGAGGAGTTTTTT
1 ATTTAAAGTTTGTTACCTTTGGTCAGAGGAGCTTTTT
1760596 TTTAATTTCA
Statistics
Matches: 93, Mismatches: 22, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
39 65 0.70
40 28 0.30
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.46
Consensus pattern (39 bp):
ATTTAAAGTTTGTTACCTTTGGTCAGAGGAGCTTTTTGA
Done.