Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168195.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_431, 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: 27090
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Found at i:837 original size:30 final size:28
Alignment explanation
Indices: 734--837 Score: 83
Period size: 30 Copynumber: 3.7 Consensus size: 28
724 ACTAATATAT
734 TAATAATAA-TATATAT-TA-AT-TTTA
1 TAATAATAATTATATATATATATATTTA
* *
758 TAATAAAAATTATAAATAGTATATAATTTA
1 TAATAATAATTATATATA-TATAT-ATTTA
* *
788 TAGCTTAGTAATTAT-TATATATATATTTA
1 TA--ATAATAATTATATATATATATATTTA
817 TTAATAATAATTCATATATAT
1 -TAATAATAATT-ATATATAT
838 TGTTTTTATA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
24 8 0.13
25 6 0.10
27 2 0.03
28 9 0.15
29 7 0.11
30 18 0.30
31 3 0.05
32 8 0.13
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (28 bp):
TAATAATAATTATATATATATATATTTA
Found at i:1543 original size:22 final size:22
Alignment explanation
Indices: 1501--1545 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1491 TTATATATAT
* *
1501 TAAATATAAAATATTTTAATTA
1 TAAATATAAAATATATAAATTA
1523 TAAAT-TAAAATAATATAAATTA
1 TAAATATAAAAT-ATATAAATTA
1545 T
1 T
1546 TACTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATATAAAATATATAAATTA
Found at i:1760 original size:13 final size:13
Alignment explanation
Indices: 1742--1864 Score: 57
Period size: 13 Copynumber: 9.8 Consensus size: 13
1732 TTTACAATAA
1742 ATATAATATAATT
1 ATATAATATAATT
*
1755 ATAT-A-ACAATT
1 ATATAATATAATT
**
1766 ATATGACA-ATTGTT
1 ATAT-A-ATATAATT
* *
1780 ATCTAATGTAATT
1 ATATAATATAATT
*
1793 ATA-ATATTTAATT
1 ATATA-ATATAATT
1806 ATAGTAATA-AATT
1 ATA-TAATATAATT
**
1819 ATATTCTATAATT
1 ATATAATATAATT
*
1832 -TAATATTATAATT
1 AT-ATAATATAATT
1845 -TATAATA-AATT
1 ATATAATATAATT
1856 ATA-AATATA
1 ATATAATATA
1865 TAAAATTTAA
Statistics
Matches: 83, Mismatches: 16, Indels: 23
0.68 0.13 0.19
Matches are distributed among these distances:
11 17 0.20
12 15 0.18
13 41 0.49
14 9 0.11
15 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (13 bp):
ATATAATATAATT
Found at i:2015 original size:22 final size:22
Alignment explanation
Indices: 1955--2026 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
1945 TTATAATTTG
* *
1955 TAATTAGTACA-AACTAGTTAAT
1 TAATTAGTATATAAATA-TTAAT
1977 TAATTAGTATATAAATATTAAT
1 TAATTAGTATATAAATATTAAT
* *
1999 TAATTA-TAGTATTAATAATAAT
1 TAATTAGTA-TATAAATATTAAT
*
2021 TTATTA
1 TAATTA
2027 ATTCAAATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
21 2 0.05
22 37 0.86
23 4 0.09
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (22 bp):
TAATTAGTATATAAATATTAAT
Found at i:2814 original size:27 final size:29
Alignment explanation
Indices: 2750--2823 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 29
2740 TAAAATATTG
* *
2750 AAATAACATAATATTAATAAAATTTAATT
1 AAATAATATAATATTAATAAAATTTAAAT
*
2779 AAATAATATAATATT-AT-AATTTTAAAT
1 AAATAATATAATATTAATAAAATTTAAAT
*
2806 -AAT-ATATATTATTCAATA
1 AAATAATATAATATT-AATA
2824 GATCAAGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 9 0.24
26 3 0.08
27 10 0.26
28 2 0.05
29 14 0.37
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (29 bp):
AAATAATATAATATTAATAAAATTTAAAT
Found at i:3149 original size:31 final size:31
Alignment explanation
Indices: 3049--3150 Score: 75
Period size: 31 Copynumber: 3.2 Consensus size: 31
3039 TTAGTAAATG
* *
3049 TAATTAATTATTATATACTAT-TTGATAATAATTT
1 TAATTAA-TATT-TATACTATAAT-ATAA-AATAT
* * **
3083 TAATTAATATTTTATTATTAAAATATTTAA-A-
1 TAATTAATA-TTTA-TACTATAATATAAAATAT
3114 TAATTAATATTTATACTATAATATAAAATAT
1 TAATTAATATTTATACTATAATATAAAATAT
3145 TAATTA
1 TAATTA
3151 TGTTAAATAT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
29 11 0.21
30 5 0.09
31 15 0.28
33 6 0.11
34 15 0.28
35 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (31 bp):
TAATTAATATTTATACTATAATATAAAATAT
Found at i:3889 original size:23 final size:25
Alignment explanation
Indices: 3863--3921 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 25
3853 TTTAAATATT
3863 AAATTATATTTATTTCA-AATT-AA
1 AAATTATATTTATTTCATAATTCAA
* *
3886 AAATAATATTTATTTGATAATTCAA
1 AAATTATATTTATTTCATAATTCAA
*
3911 AAATTAAATTT
1 AAATTATATTT
3922 GTTGATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 15 0.50
24 4 0.13
25 11 0.37
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (25 bp):
AAATTATATTTATTTCATAATTCAA
Found at i:4146 original size:22 final size:22
Alignment explanation
Indices: 4127--4170 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
4117 TAGCTAATAG
4127 TATAA-ATAATTAGTTATAATTA
1 TATAACAT-ATTAGTTATAATTA
4149 TATAACATATTAGTT-T-ATTA
1 TATAACATATTAGTTATAATTA
4169 TA
1 TA
4171 AATTGAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
21 1 0.05
22 12 0.57
23 2 0.10
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (22 bp):
TATAACATATTAGTTATAATTA
Found at i:4254 original size:21 final size:20
Alignment explanation
Indices: 4216--4263 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
4206 ATTAATACTA
*
4216 TTAT-AATATTTTAAATAAC
1 TTATAAATATTTAAAATAAC
*
4235 TTATAAATAGTTTAAAATAAT
1 TTATAAATA-TTTAAAATAAC
4256 TTATAAAT
1 TTATAAAT
4264 TATTAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.16
20 4 0.16
21 17 0.68
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
TTATAAATATTTAAAATAAC
Found at i:4258 original size:10 final size:11
Alignment explanation
Indices: 4223--4275 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
4213 CTATTATAAT
4223 ATTT-TAAATA
1 ATTTATAAATA
*
4233 ACTTATAAATA
1 ATTTATAAATA
*
4244 GTTTA-AAATA
1 ATTTATAAATA
*
4254 ATTTATAAATT
1 ATTTATAAATA
*
4265 ATTAATAAATA
1 ATTTATAAATA
4276 TTAATATTAG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 12 0.35
11 22 0.65
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (11 bp):
ATTTATAAATA
Found at i:4492 original size:24 final size:23
Alignment explanation
Indices: 4435--4520 Score: 79
Period size: 24 Copynumber: 3.7 Consensus size: 23
4425 ATAACTTGAT
*
4435 TAAT-AATATAATCATATTTT-A
1 TAATAAATATAATTATATTTTAA
4456 TAATAATATTATAATTATATTTTAGA
1 TAATAA-A-TATAATTATATTTTA-A
* *
4482 TATTAAATATAAATATATTTTAA
1 TAATAAATATAATTATATTTTAA
* *
4505 -AATATATCTAATTATA
1 TAATAAATATAATTATA
4521 AAATATTTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
21 4 0.08
22 13 0.25
23 2 0.04
24 27 0.51
25 1 0.02
26 6 0.11
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (23 bp):
TAATAAATATAATTATATTTTAA
Found at i:4520 original size:28 final size:27
Alignment explanation
Indices: 4481--4542 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
4471 TATATTTTAG
*
4481 ATATTAAATATAAATATATTTTA-AAAT
1 ATATTAAATATAAA-ATATTTAACAAAT
*
4508 ATATCTAATTATAAAATATTTAACAAAT
1 ATAT-TAAATATAAAATATTTAACAAAT
*
4536 ATTTTAA
1 ATATTAA
4543 TAATAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 14 0.47
28 16 0.53
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATTAAATATAAAATATTTAACAAAT
Found at i:4543 original size:27 final size:28
Alignment explanation
Indices: 4484--4548 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
4474 ATTTTAGATA
* *
4484 TTAAATATAAATATATTTTAAAATATAT
1 TTAATTATAAATATATTTAAAAATATAT
*
4512 CTAATTATAAA-ATATTTAACAAATAT-T
1 TTAATTATAAATATATTTAA-AAATATAT
*
4539 TTAATAATAA
1 TTAATTATAA
4549 TTATCAAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (28 bp):
TTAATTATAAATATATTTAAAAATATAT
Found at i:4647 original size:21 final size:21
Alignment explanation
Indices: 4618--4659 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4608 TTAAGTCTCA
*
4618 TTTATTTATATAA-TTAAAATT
1 TTTACTTAT-TAATTTAAAATT
4639 TTTACTTATTAATTTAAAATT
1 TTTACTTATTAATTTAAAATT
4660 AAAATAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTACTTATTAATTTAAAATT
Found at i:4692 original size:16 final size:16
Alignment explanation
Indices: 4671--4704 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4661 AAATAATTGT
4671 TATAATTAAATAATAA
1 TATAATTAAATAATAA
* *
4687 TATAATTTAATTATAA
1 TATAATTAAATAATAA
4703 TA
1 TA
4705 AATAAACAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TATAATTAAATAATAA
Found at i:4715 original size:22 final size:23
Alignment explanation
Indices: 4673--4726 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
4663 ATAATTGTTA
*
4673 TAATTA-AAT-AATAATATAATT
1 TAATTATAATAAATAATACAATT
4694 TAATTATAATAAATAA-ACAATT
1 TAATTATAATAAATAATACAATT
* *
4716 AAAATATAATA
1 TAATTATAATA
4727 TTAATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 17 0.61
23 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TAATTATAATAAATAATACAATT
Found at i:5056 original size:14 final size:15
Alignment explanation
Indices: 5037--5070 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5027 CCAAAATAAA
*
5037 AATAATTATTTAA-T
1 AATAATTATTAAATT
5051 AATAATTATTAAATT
1 AATAATTATTAAATT
5066 AATAA
1 AATAA
5071 ACAATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATAATTATTAAATT
Found at i:6930 original size:22 final size:25
Alignment explanation
Indices: 6883--6931 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
6873 TATGTATAAT
*
6883 ATTAATAATATTATAATTAATTAAA
1 ATTAATAATATTATAATTAATCAAA
6908 ATTAATAATA-TATAA-T-ATCAAA
1 ATTAATAATATTATAATTAATCAAA
6930 AT
1 AT
6932 GATTTGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 1 0.04
24 5 0.22
25 10 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
ATTAATAATATTATAATTAATCAAA
Found at i:7539 original size:22 final size:23
Alignment explanation
Indices: 7468--7539 Score: 67
Period size: 28 Copynumber: 2.9 Consensus size: 23
7458 GAATGTTAAT
7468 AAAATTATATTATATTATT-TCATC
1 AAAATTATATTA-ATTATTAT-ATC
7492 AAAATTATTATATAATTAAATATATATC
1 AAAATTA-TAT-TAATT--AT-TATATC
7520 AAAATTATATTAATT-TTATA
1 AAAATTATATTAATTATTATA
7540 ATATATTGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
22 4 0.10
23 1 0.02
24 7 0.17
25 6 0.14
26 7 0.17
27 5 0.12
28 11 0.26
29 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATTATATTAATTATTATATC
Found at i:8602 original size:14 final size:15
Alignment explanation
Indices: 8559--8603 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
8549 TTATTAATTA
8559 TAAATTAATTGATAAT
1 TAAATTAATT-ATAAT
*
8575 TAAATTTATT-TAAT
1 TAAATTAATTATAAT
8589 T-AATTAATTATAAT
1 TAAATTAATTATAAT
8603 T
1 T
8604 GTATAGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 7 0.27
14 10 0.38
16 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TAAATTAATTATAAT
Found at i:8843 original size:19 final size:19
Alignment explanation
Indices: 8819--8888 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 19
8809 ATTTATAATT
8819 ATTTATTAATTATGAATAA
1 ATTTATTAATTATGAATAA
****
8838 ATTTATTAGATTGCCTATAA
1 ATTTATTA-ATTATGAATAA
8858 ATTTATATAATTATGTAATATA
1 ATTTAT-TAATTATG-AATA-A
8880 ATTATATTA
1 ATT-TATTA
8889 CATAACAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 8 0.21
20 16 0.42
21 5 0.13
22 6 0.16
23 3 0.08
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (19 bp):
ATTTATTAATTATGAATAA
Found at i:8935 original size:18 final size:18
Alignment explanation
Indices: 8896--8937 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
8886 TTACATAACA
* *
8896 AATAGTTTATTTTTTATT
1 AATAATTTATTTTTAATT
8914 -ATAATTTATTTTTAATT
1 AATAATTTATTTTTAATT
8931 AATAATT
1 AATAATT
8938 AATATTTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
AATAATTTATTTTTAATT
Found at i:9578 original size:16 final size:17
Alignment explanation
Indices: 9557--9589 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9547 TAGTGATTAG
9557 AAATAG-ATAATTATTC
1 AAATAGCATAATTATTC
9573 AAATAGTCATAATTATT
1 AAATAG-CATAATTATT
9590 TATACTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (17 bp):
AAATAGCATAATTATTC
Found at i:9926 original size:180 final size:176
Alignment explanation
Indices: 9337--9936 Score: 620
Period size: 177 Copynumber: 3.4 Consensus size: 176
9327 AATAAATATT
* * * * ** *
9337 AAATTGTGTCATGAGAAAACAAAAAGTCATAACAATTTGAAATAAATAATTGTTCAAATAGTCAT
1 AAATTGTTTTATGACAAAACAAAAGGTCATAATGATTTGAAATAAATAATTATTCAAATAGTCAT
* * * *
9402 AATTATTTAAACTTATTCA-ATAAATAGATTTATTTTTTAAATCTTTTACTTATTAGTTGTCTAA
66 AATTATTTAAACTT-GTCAGATAAATAGATTCATTTTTTAAATC-TTTACTTATTAATT-TCAAA
* * * *
9466 ATATTAATAAATTTGTATAATTTTATTTGAAATAAGCTTGTATGAATAGAA
128 ATATTAATAAATTAGTATTA-TTTATTTCAAATAAGC-TGTATGAACAGAA
* * * * * * *
9517 AATTTTGTTTTAGGGCAAAACAAAAGGTTATAGTGATTAGAAATAGATAATTATTCAAATAGTCA
1 AA-ATTGTTTTATGACAAAACAAAAGGTCATAATGATTTGAAATAAATAATTATTCAAATAGTCA
* ** * * *
9582 TAATTATTTATACTTGTTTGATAAATACATTCATTTTTTAAATC--T-CTTATTAATTTTTAGAA
65 TAATTATTTAAACTTGTCAGATAAATAGATTCATTTTTTAAATCTTTACTTATTAA-TTTCAAAA
* *
9644 TATTAATAAAATAGAATTATATTATTTCAAATAAGCTAGTAT-AGACAGAA
129 TATTAATAAATTAGTATTAT-TTATTTCAAATAAGCT-GTATGA-ACAGAA
* * *
9694 ACAATTGTTTTGTGATAAAACAAAAGGTCATAATGATTTGAAATAGATAATTATTCAAATAGTCA
1 A-AATTGTTTTATGACAAAACAAAAGGTCATAATGATTTGAAATAAATAATTATTCAAATAGTCA
* ** * *
9759 TAACTATTTGCA-TTGGTCAGGCT-AATTGATTCATTTTTTAAATCTATTACTTATTAATTTCAA
65 TAATTATTTAAACTT-GTCA-GATAAATAGATTCATTTTTTAAATCT-TTACTTATTAATTTCAA
*
9822 AATATTGATAAATTAGTATTACTTTATTTCAAATAAGACTGTATGAACAGAA
127 AATATTAATAAATTAGTATTA-TTTATTTCAAATAAG-CTGTATGAACAGAA
* * *
9874 ATAATTATTTTATGACAATACAAATGGTCATAATGATTTGAAATAAATAATTATTCAAATAGT
1 A-AATTGTTTTATGACAAAACAAAAGGTCATAATGATTTGAAATAAATAATTATTCAAATAGT
9937 TTTACTTTTT
Statistics
Matches: 346, Mismatches: 58, Indels: 32
0.79 0.13 0.07
Matches are distributed among these distances:
176 5 0.01
177 133 0.38
178 6 0.02
180 106 0.31
181 96 0.28
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (176 bp):
AAATTGTTTTATGACAAAACAAAAGGTCATAATGATTTGAAATAAATAATTATTCAAATAGTCAT
AATTATTTAAACTTGTCAGATAAATAGATTCATTTTTTAAATCTTTACTTATTAATTTCAAAATA
TTAATAAATTAGTATTATTTATTTCAAATAAGCTGTATGAACAGAA
Found at i:10031 original size:146 final size:144
Alignment explanation
Indices: 9812--10082 Score: 348
Period size: 146 Copynumber: 1.9 Consensus size: 144
9802 CTATTACTTA
* * * * *
9812 TTAATTTCAAAATATTGATAAATTAGTATTACTTTATTTCAAATAAGACTGTATGAACAGAAATA
1 TTAATTTCAAAATATTAATAAATTAATATTACTTTATTTCAAACAAGACTGTATGAACAAAAACA
** *
9877 ATTATTTTATGAC-AATACAAATGGTCATAATGATTTGAAATAAATAATTATTCAAATAGTTTTA
66 ATTATTTTATGACAAATA-AAAT-AACATAACGATTTGAAATAAATAATTATTCAAATAGTTTTA
9941 CTTTTTAAATTTCTTC
129 CTTTTTAAATTTCTTC
* * * *
9957 TTAATTTTCAAAATATTAATAAATTAATATTATTTTATTTCGAACAA-ACTTTTATGTACAAAAA
1 TTAA-TTTCAAAATATTAATAAATTAATATTACTTTATTTCAAACAAGAC-TGTATGAACAAAAA
* * *
10021 CATTTGTTTTATGACAAAATAAAATAACATAACGATTTGAAATAGATAATTATTCAAATAGT
64 CAATTATTTTATGAC-AAATAAAATAACATAACGATTTGAAATAAATAATTATTCAAATAGT
10083 CATAATTATT
Statistics
Matches: 107, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
145 6 0.06
146 93 0.87
147 4 0.04
148 4 0.04
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (144 bp):
TTAATTTCAAAATATTAATAAATTAATATTACTTTATTTCAAACAAGACTGTATGAACAAAAACA
ATTATTTTATGACAAATAAAATAACATAACGATTTGAAATAAATAATTATTCAAATAGTTTTACT
TTTTAAATTTCTTC
Found at i:10081 original size:16 final size:17
Alignment explanation
Indices: 10060--10092 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
10050 TAACGATTTG
10060 AAATAG-ATAATTATTC
1 AAATAGCATAATTATTC
10076 AAATAGTCATAATTATT
1 AAATAG-CATAATTATT
10093 TGAACTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (17 bp):
AAATAGCATAATTATTC
Found at i:10217 original size:326 final size:325
Alignment explanation
Indices: 9616--10261 Score: 755
Period size: 326 Copynumber: 2.0 Consensus size: 325
9606 ATACATTCAT
* * * *
9616 TTTTTAAATCTCTTATTAATTTTTAGAATATTAATAAAATAGAATTATATTATTTCAAATAAGCT
1 TTTTTAAATCTCTTATTAATTTTCAAAATATTAATAAAATAGAATTATATTATTTCAAACAAACT
* * * ** *
9681 AGTATAGACAGAAACAATTGTTTTGTGATAAAACAAAAGGTCATAATGATTTGAAATAGATAATT
66 AGTATAGACAAAAACAATTGTTTTATGACAAAACAAAAGAACATAACGATTTGAAATAGATAATT
* * * **
9746 ATTCAAATAGTCATAACTATTTGCATTGGTCAGGCTAATTGATTCATTTTTTAAATCTATTACTT
131 ATTCAAATAGTCATAACTATTTGAACTGGTCAGGCAAATAAATTCATTTTTTAAATCTATTACTT
* * *
9811 ATTAATTTCAAAATATTGATAAATTAGTATTACTTTATTTCAAATAAGACTGTATGAACAGAAAT
196 ATTAATTTCAAAATATTAATAAATTAGTATTACTTTATTTCAAATAAGAC-GTAAGAACAGAAAA
* * * * *
9876 AATTATTTTATGACAATACAAATGGTCATAATGATTTGAAATAAATAATTATTCAAATAGTTTTA
260 AATTATTTAATGACAAAACAAAAGGTCAAAATGATTTGAAATAAAGAATTATTCAAATAGTTTTA
9941 C
325 C
* * * * *
9942 TTTTTAAATTTCTTCTTAATTTTCAAAATATTAATAAATTA-ATATTATTTTATTTCGAACAAAC
1 TTTTTAAATCTCTTATTAATTTTCAAAATATTAATAAAATAGA-ATTATATTATTTCAAACAAAC
** * * *
10006 TTTTAT-GTACAAAAACATTTGTTTTATGACAAAATAAAATAACATAACGATTTGAAATAGATAA
65 TAGTATAG-ACAAAAACAATTGTTTTATGACAAAACAAAAGAACATAACGATTTGAAATAGATAA
* * * * *
10070 TTATTCAAATAGTCATAATTATTTGAACT-GTTAGGCAAACTAAATT-GTTTTTTAAATCTCTTG
129 TTATTCAAATAGTCATAACTATTTGAACTGGTCAGGCAAA-TAAATTCATTTTTTAAATCTATTA
** * * *
10133 CTTATTAAGTTTTGAAATATTAATAAATTTGTTTTACTTTATTTCGAATAAGTTAC-TAAGAA-A
193 CTTATTAA-TTTCAAAATATTAATAAATTAGTATTACTTTATTTCAAATAAG--ACGTAAGAACA
* * * *
10196 TGAAAAAATTGTTTAATGACAAAACAAAAGGTCAAAATTATTTGAAATAAAGAATTGTTCATATA
255 -GAAAAAATTATTTAATGACAAAACAAAAGGTCAAAATGATTTGAAATAAAGAATTATTCAAATA
10261 G
319 G
10262 CCTTAAATAT
Statistics
Matches: 266, Mismatches: 47, Indels: 14
0.81 0.14 0.04
Matches are distributed among these distances:
325 33 0.12
326 231 0.87
328 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.41
Consensus pattern (325 bp):
TTTTTAAATCTCTTATTAATTTTCAAAATATTAATAAAATAGAATTATATTATTTCAAACAAACT
AGTATAGACAAAAACAATTGTTTTATGACAAAACAAAAGAACATAACGATTTGAAATAGATAATT
ATTCAAATAGTCATAACTATTTGAACTGGTCAGGCAAATAAATTCATTTTTTAAATCTATTACTT
ATTAATTTCAAAATATTAATAAATTAGTATTACTTTATTTCAAATAAGACGTAAGAACAGAAAAA
ATTATTTAATGACAAAACAAAAGGTCAAAATGATTTGAAATAAAGAATTATTCAAATAGTTTTAC
Found at i:10388 original size:180 final size:177
Alignment explanation
Indices: 9957--10422 Score: 434
Period size: 180 Copynumber: 2.6 Consensus size: 177
9947 AAATTTCTTC
* * *
9957 TTAATTTTCAAAATATTAATAAATTAATATTATTTTATTTCGAACAAACTTTTATGTACAA-AAA
1 TTAATTTT-AAAATATTAATAAATTAGTATTATTTTATTTCGAA-TAACTTCTATG-A-AAGAAA
* * * *** * * * *
10021 CATTTGTTTTATGACAAAATAAAATAACATAACGATTTGAAATAGATAATTATTCAAATAGTCAT
62 AAATTGTTTTATGACAAAACAAAAGGTCAAAACGATTTGAAATAAAGAATTATTCAAATAGCCAT
* * *
10086 AATTATTTGAACTGTTAGGCAAACTAAATTGTTTTTTAAATCTCTTGCTTA
127 AAATATTTGAACTGTTAGGCAAACTAAATTATTTTTTAAATCTCTTACTTA
* * * * * *
10137 TTAAGTTTTGAAATATTAATAAATTTGTTTTACTTTATTTCGAATAAGTTACTAAGAAATGAAAA
1 TTAA-TTTTAAAATATTAATAAATTAGTATTATTTTATTTCGAATAACTT-CTATGAAA-GAAAA
* ** * * *
10202 AATTGTTTAATGACAAAACAAAAGGTCAAAATTATTTGAAATAAAGAATTGTTCATATAGCCTTA
63 AATTGTTTTATGACAAAACAAAAGGTCAAAACGATTTGAAATAAAGAATTATTCAAATAGCCATA
* *
10267 AATATTTGAACTAGTTTA-GTAAAC-AAATTTATTTTTTAAATCTCTTATTTA
128 AATATTTGAACT-G-TTAGGCAAACTAAA-TTATTTTTTAAATCTCTTACTTA
* * * * *
10318 TTAATTTTAAAATATTATTATATTAGTATTATTTTATTTCGAATGAACTTGTGTGAATAGAAATA
1 TTAATTTTAAAATATTAATAAATTAGTATTATTTTATTTCGAAT-AACTTCTATGAA-AGAAAAA
* * * * * *
10383 ATTGTTTTATAAGATAACAAAAGGTTATAACAATTTGAAA
64 ATTGTTTTATGACAAAACAAAAGGTCAAAACGATTTGAAA
10423 AGACAAAATG
Statistics
Matches: 228, Mismatches: 49, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
178 2 0.01
179 5 0.02
180 179 0.79
181 39 0.17
182 3 0.01
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.41
Consensus pattern (177 bp):
TTAATTTTAAAATATTAATAAATTAGTATTATTTTATTTCGAATAACTTCTATGAAAGAAAAAAT
TGTTTTATGACAAAACAAAAGGTCAAAACGATTTGAAATAAAGAATTATTCAAATAGCCATAAAT
ATTTGAACTGTTAGGCAAACTAAATTATTTTTTAAATCTCTTACTTA
Found at i:10565 original size:45 final size:43
Alignment explanation
Indices: 10508--10633 Score: 112
Period size: 46 Copynumber: 2.8 Consensus size: 43
10498 CAAATAGAGG
10508 AAAAAGATATAAAA-TATGAAAGATGAAAAATAAAATAAAAGTTAAT
1 AAAAAGATATAAAATTAT-AAAGA--AAAAATAAAA-AAAAGTTAAT
* *
10554 AAAAA-ATATAAAATTATAAAGAAGAAATAAAAAAAAGTGTGAAC
1 AAAAAGATATAAAATTATAAAGAAAAAATAAAAAAAAGT-T-AAT
* ** **
10598 AAAAAGATTTAAGAAAAAGCAAGAAAAAATAAAAAA
1 AAAAAGATATAA-AATTATAAAGAAAAAATAAAAAA
10634 CGAAAATACA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
42 6 0.09
43 10 0.15
44 7 0.10
45 18 0.27
46 26 0.39
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.17
Consensus pattern (43 bp):
AAAAAGATATAAAATTATAAAGAAAAAATAAAAAAAAGTTAAT
Found at i:10583 original size:19 final size:19
Alignment explanation
Indices: 10534--10585 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
10524 TGAAAGATGA
10534 AAAATAAAATAAAAGTTAAT
1 AAAA-AAAATAAAAGTTAAT
*
10554 AAAAAATATAAAA-TT-AT
1 AAAAAAAATAAAAGTTAAT
10571 AAAGAAGAAATAAAA
1 AAA-AA-AAATAAAA
10586 AAAAGTGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 5 0.18
18 4 0.14
19 15 0.54
20 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (19 bp):
AAAAAAAATAAAAGTTAAT
Found at i:10950 original size:24 final size:25
Alignment explanation
Indices: 10918--10969 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
10908 AACTATAAAT
10918 AAAGAAAGAAAATAAAAAAAGA-AA
1 AAAGAAAGAAAATAAAAAAAGACAA
* *
10942 AAAGTAAGAAAATAAAAAAGGACAA
1 AAAGAAAGAAAATAAAAAAAGACAA
10967 AAA
1 AAA
10970 TTGAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (25 bp):
AAAGAAAGAAAATAAAAAAAGACAA
Found at i:11339 original size:6 final size:7
Alignment explanation
Indices: 11314--11366 Score: 54
Period size: 7 Copynumber: 7.0 Consensus size: 7
11304 AAAAATAGCA
11314 AAAAAAT
1 AAAAAAT
11321 AAGAAAAT
1 AA-AAAAT
11329 AAAAAAT
1 AAAAAAT
11336 AAAAAAGATT
1 -AAAAA-A-T
11346 CAAAAAAT
1 -AAAAAAT
11354 -AAAAAT
1 AAAAAAT
11360 AAAAAAT
1 AAAAAAT
11367 TTTAAACTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
6 6 0.15
7 13 0.32
8 13 0.32
9 2 0.05
10 6 0.15
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:11340 original size:24 final size:25
Alignment explanation
Indices: 11303--11365 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 25
11293 TACAAAGTAG
11303 AAAAAATAGCAAAAA-AAT-AAGAAAAT
1 AAAAAATA--AAAAAGAATCAA-AAAAT
*
11329 AAAAAATAAAAAAGATTCAAAAAAT
1 AAAAAATAAAAAAGAATCAAAAAAT
11354 -AAAAATAAAAAA
1 AAAAAATAAAAAA
11366 TTTTAAACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
24 17 0.50
25 7 0.21
26 10 0.29
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (25 bp):
AAAAAATAAAAAAGAATCAAAAAAT
Found at i:11571 original size:25 final size:24
Alignment explanation
Indices: 11516--11571 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 24
11506 TTAGCGAATC
11516 AAAAAAATATAAAAAGACAAAATG
1 AAAAAAATATAAAAAGACAAAATG
* * * *
11540 AATAAAAATTTCAAAATATAAAATG
1 AA-AAAAATATAAAAAGACAAAATG
*
11565 GAAAAAA
1 AAAAAAA
11572 CTTTTAGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (24 bp):
AAAAAAATATAAAAAGACAAAATG
Found at i:11785 original size:14 final size:14
Alignment explanation
Indices: 11766--11794 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11756 ATAAAATTTG
11766 AGAAAAAAATAAAA
1 AGAAAAAAATAAAA
11780 AGAAAAAAATAAAA
1 AGAAAAAAATAAAA
11794 A
1 A
11795 ATGAAGAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (14 bp):
AGAAAAAAATAAAA
Found at i:11903 original size:16 final size:17
Alignment explanation
Indices: 11879--11913 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
11869 AACAAAAAAA
*
11879 AAAATGGAGAAAAATTT
1 AAAATGGAGAAAAAGTT
11896 AAAA-GGAGAAAAAGTT
1 AAAATGGAGAAAAAGTT
11912 AA
1 AA
11914 TGAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (17 bp):
AAAATGGAGAAAAAGTT
Found at i:12534 original size:9 final size:8
Alignment explanation
Indices: 12520--12567 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
12510 AAAAAATAGC
12520 AAAAAAAT
1 AAAAAAAT
*
12528 AAGAAAAT
1 AAAAAAAT
12536 AAAAAAAAT
1 -AAAAAAAT
12545 AAAAAAGATT
1 AAAAAA-A-T
*
12555 CAAAAAAT
1 AAAAAAAT
12563 AAAAA
1 AAAAA
12568 TAAAAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 18 0.55
9 9 0.27
10 6 0.18
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:12956 original size:22 final size:21
Alignment explanation
Indices: 12931--12971 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
12921 AAAAGCAAGA
12931 AAAAAATAAAAAATGAAAATAC
1 AAAAAATAAAAAAT-AAAATAC
* *
12953 AAAATATATAAAATAAAAT
1 AAAAAATAAAAAATAAAAT
12972 TTGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAATAC
Found at i:12999 original size:19 final size:19
Alignment explanation
Indices: 12962--13015 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
12952 CAAAATATAT
**
12962 AAAATAAAATTTG-AGAAA
1 AAAATAAAAAATGAAGAAA
*
12980 AAACATGAAAAA-GAAGAAA
1 AAA-ATAAAAAATGAAGAAA
12999 AAAATAAAAAATGAAGA
1 AAAATAAAAAATGAAGA
13016 GGGAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.72, C:0.02, G:0.13, T:0.13
Consensus pattern (19 bp):
AAAATAAAAAATGAAGAAA
Found at i:13265 original size:13 final size:12
Alignment explanation
Indices: 13247--13356 Score: 61
Period size: 13 Copynumber: 9.1 Consensus size: 12
13237 ATGAAACTAT
13247 AAATAAAGAAAGA
1 AAATAAA-AAAGA
*
13260 AAATAAAAAATAA
1 AAATAAAAAA-GA
13273 AAATAAAATAAGA
1 AAATAAAA-AAGA
13286 AAA-AAATTAAAGCA
1 AAATAAA--AAAG-A
*
13300 AAAGAAAAAAG-
1 AAATAAAAAAGA
*
13311 --ATAAATAAAGC
1 AAATAAA-AAAGA
*
13322 ACA-AAAAAAGA
1 AAATAAAAAAGA
**
13333 AAA-AAGTAAGA
1 AAATAAAAAAGA
13344 AAATAAAAAAGA
1 AAATAAAAAAGA
13356 A
1 A
13357 CAAAAATTGA
Statistics
Matches: 77, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
9 4 0.05
10 4 0.05
11 15 0.19
12 16 0.21
13 28 0.36
14 7 0.09
15 3 0.04
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (12 bp):
AAATAAAAAAGA
Found at i:13282 original size:11 final size:11
Alignment explanation
Indices: 13264--13363 Score: 53
Period size: 11 Copynumber: 8.6 Consensus size: 11
13254 GAAAGAAAAT
13264 AAAAAATAA-A
1 AAAAAATAAGA
13274 AATAAAATAAGA
1 AA-AAAATAAGA
13286 AAAAAATTAAAGCA
1 AAAAAA-T-AAG-A
*
13300 AAAGAAAAAAGA
1 AAA-AAATAAGA
* *
13312 TAAATA-AAGCA
1 AAAAAATAAG-A
*
13323 CAAAAA-AAGA
1 AAAAAATAAGA
*
13333 AAAAAGTAAGA
1 AAAAAATAAGA
*
13344 AAATAAAAAAGA
1 AAA-AAATAAGA
13356 ACAAAAAT
1 A-AAAAAT
13364 TGAATAAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
10 10 0.14
11 28 0.40
12 17 0.24
13 8 0.11
14 4 0.06
15 3 0.04
ACGTcount: A:0.77, C:0.04, G:0.09, T:0.10
Consensus pattern (11 bp):
AAAAAATAAGA
Found at i:13687 original size:18 final size:19
Alignment explanation
Indices: 13664--13700 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
13654 TTATAATTTA
*
13664 ATAAATATTAT-ATAATAT
1 ATAAATACTATAATAATAT
13682 ATAAATACTATAATAATAT
1 ATAAATACTATAATAATAT
13701 TATATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAAATACTATAATAATAT
Found at i:13722 original size:15 final size:16
Alignment explanation
Indices: 13694--13726 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
13684 AAATACTATA
*
13694 ATAATATTATATTATT
1 ATAATATTAGATTATT
13710 ATAA-ATTAGATTATT
1 ATAATATTAGATTATT
13725 AT
1 AT
13727 TTAATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
ATAATATTAGATTATT
Found at i:13743 original size:35 final size:34
Alignment explanation
Indices: 13704--13769 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 34
13694 ATAATATTAT
*
13704 ATTATTATAA-ATTAGATTATTATTTAATTATAACA
1 ATTATTATAATATTA-ATTAAT-TTTAATTATAACA
* *
13739 ATTATTTTAATTTTAATTAATTTTAATTATA
1 ATTATTATAATATTAATTAATTTTAATTATA
13770 TAAATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.37
35 14 0.52
36 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (34 bp):
ATTATTATAATATTAATTAATTTTAATTATAACA
Found at i:13797 original size:23 final size:24
Alignment explanation
Indices: 13771--13824 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
13761 TTAATTATAT
13771 AAATAAAT-TAGATT-TAATATTTA
1 AAATAAATATAGATTATAATA-TTA
* *
13794 AAATTAATATATATTATAATATTA
1 AAATAAATATAGATTATAATATTA
13818 AATATAA
1 AA-ATAA
13825 CTAGTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 7 0.28
24 10 0.40
25 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAATAAATATAGATTATAATATTA
Found at i:13849 original size:25 final size:24
Alignment explanation
Indices: 13812--13872 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
13802 ATATATTATA
13812 ATATTAAATATAACTAGTAAAAAT
1 ATATTAAATATAACTAGTAAAAAT
* * *
13836 ATATTTAATAATAATTATTAAAATAT
1 ATATTAAAT-ATAACTAGTAAAA-AT
* *
13862 TTGTTAAATAT
1 ATATTAAATAT
13873 TTTGAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 8 0.28
25 13 0.45
26 8 0.28
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (24 bp):
ATATTAAATATAACTAGTAAAAAT
Found at i:15224 original size:14 final size:15
Alignment explanation
Indices: 15205--15242 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
15195 TTAATTGAAT
15205 ATTATT-TTAGTATA
1 ATTATTATTAGTATA
15219 ATTATTTTATTAGTATA
1 ATTA--TTATTAGTATA
15236 ATTATTA
1 ATTATTA
15243 ATAATAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.19
15 3 0.14
16 2 0.10
17 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (15 bp):
ATTATTATTAGTATA
Found at i:15520 original size:13 final size:13
Alignment explanation
Indices: 15490--15554 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 13
15480 TTATATCAAG
*
15490 TTATATAATATAAT
1 TTATATTATAT-AT
15504 TTATATTATATAT
1 TTATATTATATAT
*
15517 TTATAATTCATATTT
1 TTAT-ATT-ATATAT
*
15532 TTAATATTAAATAGT
1 TT-ATATTATATA-T
15547 TT-TATTAT
1 TTATATTAT
15555 TTGTTTAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 11 0.26
14 16 0.38
15 13 0.31
16 2 0.05
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (13 bp):
TTATATTATATAT
Found at i:15811 original size:17 final size:18
Alignment explanation
Indices: 15785--15843 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
15775 GAGTAAATTT
*
15785 ATTTAATTATCTAT-TAA
1 ATTTATTTATCTATATAA
*
15802 ATTTATTTATCTTTATAA
1 ATTTATTTATCTATATAA
*
15820 ATTATATTATAACTAGTATAA
1 ATT-TATT-TATCTA-TATAA
15841 ATT
1 ATT
15844 AATAGTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 12 0.35
18 6 0.18
19 4 0.12
20 4 0.12
21 8 0.24
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTATTTATCTATATAA
Found at i:16146 original size:19 final size:19
Alignment explanation
Indices: 16118--16169 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
16108 TATTCAATTA
*
16118 TTAA-AATTATTTATCTAT
1 TTAATAATTATTAATCTAT
* *
16136 TTATTAATTATTAATTTAT
1 TTAATAATTATTAATCTAT
*
16155 TTAATAATTAATAAT
1 TTAATAATTATTAAT
16170 TAATACATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 3 0.11
19 25 0.89
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAATAATTATTAATCTAT
Found at i:16518 original size:20 final size:19
Alignment explanation
Indices: 16470--16523 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
16460 ATTAAAGATT
*
16470 AATATAATAATTTATATTATA
1 AATATAATAA-GT-TATTATA
*
16491 ATTATAATTAAGTTATTATA
1 AATATAA-TAAGTTATTATA
*
16511 AATCTAATAAGTT
1 AATATAATAAGTT
16524 TAGATAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 6 0.21
20 12 0.43
21 7 0.25
22 3 0.11
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
AATATAATAAGTTATTATA
Found at i:16961 original size:17 final size:17
Alignment explanation
Indices: 16939--16990 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 17
16929 ATAAAATTAA
16939 TATTATTATATAATATT
1 TATTATTATATAATATT
16956 TATTATATTATAATAAATATT
1 TA-T-TATTAT-AT-AATATT
*
16977 TAATATTATATAAT
1 TATTATTATATAAT
16991 TAAATAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 5 0.17
18 3 0.10
19 12 0.40
20 2 0.07
21 8 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTATTATATAATATT
Found at i:16975 original size:26 final size:25
Alignment explanation
Indices: 16949--16999 Score: 59
Period size: 28 Copynumber: 1.9 Consensus size: 25
16939 TATTATTATA
16949 TAATATT-TATTATATTATAATAAATATT
1 TAATATTATA-TA-ATTA-AATAAATA-T
16977 TAATATTATATAATTAAATAAAT
1 TAATATTATATAATTAAATAAAT
17000 TAAATATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 7 0.32
27 4 0.18
28 9 0.41
29 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAATATTATATAATTAAATAAATAT
Found at i:17067 original size:14 final size:14
Alignment explanation
Indices: 17031--17068 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
17021 CATTTACTTA
17031 TTAATTATTATAAT
1 TTAATTATTATAAT
*
17045 TTAACTATTAT-AT
1 TTAATTATTATAAT
17058 TTAATTTATTA
1 TTAA-TTATTA
17069 ACATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
TTAATTATTATAAT
Found at i:17556 original size:18 final size:17
Alignment explanation
Indices: 17514--17552 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
17504 TATTATAAGG
17514 ATTTTAATTTTAATATT
1 ATTTTAATTTTAATATT
17531 ATTTTAATTATTAAT-TT
1 ATTTTAATT-TTAATATT
17548 ATTTT
1 ATTTT
17553 TAATATGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTAATTTTAATATT
Found at i:18708 original size:29 final size:27
Alignment explanation
Indices: 18667--18722 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
18657 AATATTTGTT
**
18667 TATAAATCTAATAAGTAATTTATAATTAC
1 TATAAATAAAATAA-TAA-TTATAATTAC
*
18696 TATAAATAAAATAATAATTATATTTAC
1 TATAAATAAAATAATAATTATAATTAC
18723 AAATAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.38
28 3 0.12
29 12 0.50
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (27 bp):
TATAAATAAAATAATAATTATAATTAC
Found at i:18804 original size:16 final size:16
Alignment explanation
Indices: 18779--18836 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
18769 CAATTACTAA
*
18779 ATATAGTTTATAATAT
1 ATATAATTTATAATAT
18795 ATATAATTTAATAAATATT
1 ATATAATTT-AT-AATA-T
*
18814 ATATAATATATAA-AT
1 ATATAATTTATAATAT
18829 ACTATAAT
1 A-TATAAT
18837 AATATTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 2 0.06
16 15 0.42
17 4 0.11
18 6 0.17
19 9 0.25
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
ATATAATTTATAATAT
Found at i:18806 original size:14 final size:14
Alignment explanation
Indices: 18787--18829 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
18777 AAATATAGTT
18787 TATAATATATATAA
1 TATAATATATATAA
* * *
18801 TTTAATAAATATTA
1 TATAATATATATAA
18815 TATAATATATA-AA
1 TATAATATATATAA
18828 TA
1 TA
18830 CTATAATAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 3 0.13
14 20 0.87
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATAATATATATAA
Found at i:18818 original size:19 final size:17
Alignment explanation
Indices: 18790--18841 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 17
18780 TATAGTTTAT
*
18790 AATATATATAATTTAATA
1 AATATATATAATAT-ATA
18808 AATATTATATAATATATA
1 AATA-TATATAATATATA
18826 AATACTATAATAATAT
1 AATA-TAT-ATAATAT
18842 TACATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATATATAATATATA
Found at i:18863 original size:15 final size:16
Alignment explanation
Indices: 18835--18867 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
18825 AAATACTATA
18835 ATAATATTACATTATT
1 ATAATATTACATTATT
*
18851 ATAA-ATTAGATTATT
1 ATAATATTACATTATT
18866 AT
1 AT
18868 TTAATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
ATAATATTACATTATT
Found at i:18884 original size:35 final size:34
Alignment explanation
Indices: 18845--18910 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 34
18835 ATAATATTAC
*
18845 ATTATTATAA-ATTAGATTATTATTTAATTATAACA
1 ATTATTATAATATTA-ATTAAT-TTTAATTATAACA
* *
18880 ATTATTTTAATTTTAATTAATTTTAATTATA
1 ATTATTATAATATTAATTAATTTTAATTATA
18911 TAAATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.37
35 14 0.52
36 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (34 bp):
ATTATTATAATATTAATTAATTTTAATTATAACA
Found at i:18938 original size:23 final size:24
Alignment explanation
Indices: 18912--18965 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
18902 TTAATTATAT
18912 AAATAAAT-TAGATT-TAATATTTA
1 AAATAAATATAGATTATAATA-TTA
* *
18935 AAATTAATATATATTATAATATTA
1 AAATAAATATAGATTATAATATTA
18959 AATATAA
1 AA-ATAA
18966 CTAGTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 7 0.28
24 10 0.40
25 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAATAAATATAGATTATAATATTA
Found at i:18990 original size:25 final size:24
Alignment explanation
Indices: 18953--19013 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
18943 ATATATTATA
18953 ATATTAAATATAACTAGTAAAAAT
1 ATATTAAATATAACTAGTAAAAAT
* * *
18977 ATATTTAATAATAATTATTAAAATAT
1 ATATTAAAT-ATAACTAGTAAAA-AT
* *
19003 TTGTTAAATAT
1 ATATTAAATAT
19014 TTTGAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 8 0.28
25 13 0.45
26 8 0.28
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (24 bp):
ATATTAAATATAACTAGTAAAAAT
Found at i:19642 original size:16 final size:17
Alignment explanation
Indices: 19610--19643 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19600 TAAAAATGTC
19610 ATAATAATTCGAAATGG
1 ATAATAATTCGAAATGG
*
19627 ATAATAGTTC-AAATGG
1 ATAATAATTCGAAATGG
19643 A
1 A
19644 CATGACTATT
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:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (17 bp):
ATAATAATTCGAAATGG
Found at i:20929 original size:17 final size:17
Alignment explanation
Indices: 20871--20936 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
20861 TATTAATATA
*
20871 AATTAA-AATAAT-TTT
1 AATTAATAATATTATTT
*
20886 AATT-TTAATATTA--T
1 AATTAATAATATTATTT
* *
20900 AATTTAATTATATTGTTT
1 AA-TTAATAATATTATTT
20918 AATTAATAATATTATTT
1 AATTAATAATATTATTT
20935 AA
1 AA
20937 ATAAAATAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
14 3 0.08
15 11 0.29
16 6 0.16
17 15 0.39
18 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTAATAATATTATTT
Found at i:21256 original size:180 final size:181
Alignment explanation
Indices: 20949--21373 Score: 427
Period size: 180 Copynumber: 2.4 Consensus size: 181
20939 AAAATAATTT
* * ** * * *
20949 AAACAATTTTTTTATGACAAAACAAAAATTCATAATGA-TTTGAATAGATAATTGTTTAAATGGC
1 AAACAATTATTTTATGATAAAACAAAAGGTCATAATGATTTTAAATAGATAATTGTTTAAATAGT
* * * **
21013 CATAACTATTTGAATTGATTCGATAAACTGATTTATGTTTTAAATCTCTAACTTATTAATTTTTA
66 AAAAAATATTTGAATTGATTCGATAAACTGATTTATGTTTTAAATCTCTAACTTAACAATTTTT-
* *
21078 T-AATATTAATAAAGTAATATTATTTTATTTCAG-ATAAACTTTTATGAACTG
130 TGAATATTAATAAAGTAATATTATTTTATTT-AGAATAAACATGTATGAACTG
* *
21129 AAACAATTATTTTATGATAAAATATAAGGTCATAATGATTTTAAATAGATAATTGTTTAAATAGT
1 AAACAATTATTTTATGATAAAACAAAAGGTCATAATGATTTTAAATAGATAATTGTTTAAATAGT
* * *
21194 AAAAAATATTTGAACTTG-TTC-AGTAAA-TAGATTT-T-TTTTCTAATTTCTTACTTAACAATT
66 AAAAAATATTTGAA-TTGATTCGA-TAAACT-GATTTATGTTTT-AAATCTCTAACTTAACAATT
* * * * * * **
21254 TTTTGAATGTTAATAAATTAGTGTTATTTTATTTTGAATAAGCATGTATGAGTTG
127 TTTTGAATATTAATAAAGTAATATTATTTTATTTAGAATAAACATGTATGAACTG
* * * * * *
21309 AAGCAATTATTTTATGATTAAACAAAAGGTCAAAACGATTTGAAATGGATAATTGTTCT-AATAG
1 AAACAATTATTTTATGATAAAACAAAAGGTCATAATGATTTTAAATAGATAATTGTT-TAAATAG
21373 T
65 T
21374 CTTAATTATT
Statistics
Matches: 202, Mismatches: 35, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
179 6 0.03
180 146 0.72
181 47 0.23
182 3 0.01
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (181 bp):
AAACAATTATTTTATGATAAAACAAAAGGTCATAATGATTTTAAATAGATAATTGTTTAAATAGT
AAAAAATATTTGAATTGATTCGATAAACTGATTTATGTTTTAAATCTCTAACTTAACAATTTTTT
GAATATTAATAAAGTAATATTATTTTATTTAGAATAAACATGTATGAACTG
Found at i:21439 original size:13 final size:12
Alignment explanation
Indices: 21412--21444 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
21402 AATAATTATA
21412 ATTAT-TAAATT
1 ATTATATAAATT
21423 ATTATATAAATTT
1 ATTATATAAA-TT
21436 ATTATATAA
1 ATTATATAA
21445 TAACATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 4 0.20
13 11 0.55
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTATATAAATT
Found at i:21568 original size:11 final size:10
Alignment explanation
Indices: 21551--21608 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
21541 AATTTTTATT
21551 ATTATAATAA
1 ATTATAATAA
*
21561 ACTTATAATTAT
1 A-TTATAA-TAA
21573 ATTATAATAA
1 ATTATAATAA
21583 ATTAATAATGAA
1 ATT-ATAAT-AA
21595 ATTA-ATATAA
1 ATTATA-ATAA
21605 ATTA
1 ATTA
21609 ATTATTATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
10 13 0.32
11 20 0.49
12 8 0.20
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (10 bp):
ATTATAATAA
Found at i:21575 original size:22 final size:22
Alignment explanation
Indices: 21527--21628 Score: 86
Period size: 22 Copynumber: 4.6 Consensus size: 22
21517 ATTTTATTAG
**
21527 TATATT-TAAT-AATTAATTTT
1 TATATTATAATAAATTAATAAT
21547 TATTATTATAATAAACTT-ATAAT
1 TA-TATTATAATAAA-TTAATAAT
21570 TATATTATAATAAATTAATAAT
1 TATATTATAATAAATTAATAAT
* * *
21592 GAAATTA-ATATAAATTAATTAT
1 TATATTATA-ATAAATTAATAAT
21614 TATAATTAATAATAA
1 TAT-ATT-ATAATAA
21629 TATAATATTA
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.03
21 7 0.11
22 39 0.59
23 10 0.15
24 7 0.11
25 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (22 bp):
TATATTATAATAAATTAATAAT
Found at i:22070 original size:6 final size:6
Alignment explanation
Indices: 22035--22128 Score: 52
Period size: 6 Copynumber: 15.2 Consensus size: 6
22025 TAATATTTAG
** * *
22035 TATAAT TATCGT TATAAT TAATATT ATATAAT TATAAT TA-ACT GTATAAT
1 TATAAT TATAAT TATAAT T-ATAAT -TATAAT TATAAT TATAAT -TATAAT
*
22085 TAATAAAT T-TAAT TATTAAT T-TAAA T-TAAT TATAAT TATTAAT T
1 T-AT-AAT TATAAT TA-TAAT TATAAT TATAAT TATAAT TA-TAAT T
22129 TAACTAATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
5 14 0.21
6 27 0.40
7 22 0.32
8 5 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
TATAAT
Found at i:22111 original size:18 final size:18
Alignment explanation
Indices: 22061--22131 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 18
22051 ATTAATATTA
22061 TATAATTAT-AA-TTAACT
1 TATAATTATAAATTTAA-T
22078 GTATAATTAATAAATTTAAT
1 -TATAATT-ATAAATTTAAT
22098 TATTAATT-TAAA-TTAAT
1 TA-TAATTATAAATTTAAT
*
22115 TATAATTATTAATTTAA
1 TATAATTATAAATTTAA
22132 CTAATTTTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
16 5 0.11
17 10 0.22
18 15 0.33
19 4 0.09
20 8 0.17
21 4 0.09
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (18 bp):
TATAATTATAAATTTAAT
Found at i:22115 original size:17 final size:17
Alignment explanation
Indices: 22088--22144 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
22078 GTATAATTAA
22088 TAAATTTAATTATTAATT
1 TAAATTTAATTA-TAATT
22106 TAAA-TTAATTATAATT
1 TAAATTTAATTATAATT
* * *
22122 ATTAATTTAACTA-ATTT
1 -TAAATTTAATTATAATT
22139 TAAATT
1 TAAATT
22145 GTTTATATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.30
17 13 0.39
18 10 0.30
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATTTAATTATAATT
Found at i:22144 original size:23 final size:23
Alignment explanation
Indices: 22090--22137 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
22080 ATAATTAATA
*
22090 AATT-TAATTATTAATTTAAATT
1 AATTATAATTATTAATTTAAACT
22112 AATTATAATTATTAATTT-AACT
1 AATTATAATTATTAATTTAAACT
22134 AATT
1 AATT
22138 TTAAATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTATAATTATTAATTTAAACT
Found at i:22336 original size:23 final size:21
Alignment explanation
Indices: 22289--22341 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
22279 TTAAGTTAAC
22289 TTAAAT-ATATAAATTTATAA
1 TTAAATAATATAAATTTATAA
* *
22309 GTAAATAATATTAGAATTTATAT
1 TTAAATAATA-TA-AATTTATAA
22332 TTAAAATAAT
1 TT-AAATAAT
22342 TGATATTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 5 0.19
21 3 0.12
22 2 0.08
23 9 0.35
24 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
TTAAATAATATAAATTTATAA
Found at i:23054 original size:13 final size:13
Alignment explanation
Indices: 23016--23055 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
23006 ATATTAATCA
*
23016 AATATAATTAGTT
1 AATATAATTATTT
*
23029 AATATAATAATTT
1 AATATAATTATTT
*
23042 AATATTATTATTT
1 AATATAATTATTT
23055 A
1 A
23056 TCAATAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
AATATAATTATTT
Found at i:23122 original size:15 final size:16
Alignment explanation
Indices: 23097--23135 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
23087 TATTATTTGA
23097 AATAGTTATTAATA-TT
1 AATA-TTATTAATAGTT
23113 AATATTATTAATAGTT
1 AATATTATTAATAGTT
23129 AA-ATTAT
1 AATATTAT
23136 ATATTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
AATATTATTAATAGTT
Found at i:23130 original size:22 final size:21
Alignment explanation
Indices: 23105--23146 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
23095 GAAATAGTTA
23105 TTAATATTA-ATATTATTAATAG
1 TTAA-ATTATATATTA-TAATAG
23127 TTAAATTATATATTATAATA
1 TTAAATTATATATTATAATA
23147 AATTACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTAAATTATATATTATAATAG
Found at i:23342 original size:25 final size:24
Alignment explanation
Indices: 23280--23347 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
23270 TAATTTATCA
* *
23280 TTAATTT-TATAATATTAATTAAT
1 TTAATTTATATTATAATAATTAAT
*
23303 TATAAAATTAT-TTATAATAATTATAT
1 T-T-AATTTATATTATAATAATTA-AT
*
23329 TTAATTTATATTATTATAA
1 TTAATTTATATTATAATAA
23348 GATATTAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
23 1 0.03
24 7 0.20
25 23 0.66
26 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAATTTATATTATAATAATTAAT
Found at i:23554 original size:18 final size:17
Alignment explanation
Indices: 23533--23566 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23523 CATTTATTAA
*
23533 TATAATCTAATTTAATAG
1 TATAATC-AAATTAATAG
23551 TATAATCAAATTAATA
1 TATAATCAAATTAATA
23567 ATCTGATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (17 bp):
TATAATCAAATTAATAG
Found at i:23655 original size:9 final size:9
Alignment explanation
Indices: 23613--23670 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
23603 ATATAACAAT
23613 TATTAATAA
1 TATTAATAA
*
23622 TA-T-ATAG
1 TATTAATAA
23629 TATTATATATA
1 TATTA-ATA-A
*
23640 AATTAATAA
1 TATTAATAA
23649 TATTAATAA
1 TATTAATAA
23658 TA-TAATTAA
1 TATTAA-TAA
23667 TATT
1 TATT
23671 TGATTGATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
7 5 0.13
8 5 0.13
9 18 0.46
10 7 0.18
11 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (9 bp):
TATTAATAA
Found at i:24573 original size:20 final size:20
Alignment explanation
Indices: 24550--24603 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
24540 CATGTATATT
*
24550 ATATTATATTTA-AATATAAA
1 ATATTATAATTATAAT-TAAA
*
24570 ATATTTTAATTATAATTAAA
1 ATATTATAATTATAATTAAA
*
24590 ATAATATAAATTAT
1 ATATTAT-AATTAT
24604 TACTATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTATAATTATAATTAAA
Found at i:24808 original size:13 final size:13
Alignment explanation
Indices: 24792--24915 Score: 57
Period size: 13 Copynumber: 9.8 Consensus size: 13
24782 GTTACAAATA
24792 ATATAATATAATT
1 ATATAATATAATT
*
24805 ATAT-A-ACAATT
1 ATATAATATAATT
**
24816 ATATGACA-ATTGTT
1 ATAT-A-ATATAATT
* *
24830 ATCTAATGTAATT
1 ATATAATATAATT
*
24843 ATA-ATATTTAATT
1 ATATA-ATATAATT
24856 ATAGTAATA-AATT
1 ATA-TAATATAATT
**
24869 ATATTCTATAATTT
1 ATATAATATAA-TT
* *
24883 AAATATTATAATT
1 ATATAATATAATT
24896 -TATAATA-AATT
1 ATATAATATAATT
24907 ATA-AATATA
1 ATATAATATA
24916 TAAATTTTAA
Statistics
Matches: 82, Mismatches: 18, Indels: 23
0.67 0.15 0.19
Matches are distributed among these distances:
11 17 0.21
12 14 0.17
13 31 0.38
14 19 0.23
15 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (13 bp):
ATATAATATAATT
Found at i:24917 original size:25 final size:25
Alignment explanation
Indices: 24876--24932 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
24866 ATTATATTCT
24876 ATAATT-TAAATATTAT-AATTTATA
1 ATAATTATAAATATTATAAATTT-TA
24900 ATAAATTATAAATA-TATAAATTTTA
1 AT-AATTATAAATATTATAAATTTTA
24925 ATAATTAT
1 ATAATTAT
24933 TATTTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 8 0.27
25 11 0.37
26 11 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATAATTATAAATATTATAAATTTTA
Found at i:24925 original size:41 final size:38
Alignment explanation
Indices: 24838--24938 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 38
24828 TTATCTAATG
* *
24838 TAATTATAATATT-TAATTATAGTAATAAATTATATTCTA
1 TAATT-TAATATTATAATT-TAGTAATAAATTATAATATA
24877 TAATTTAAATATTATAATTTA-TAATAAATTATAAATATA
1 TAATTT-AATATTATAATTTAGTAATAAATTAT-AATATA
*
24916 TAAATTTTAATAATTATTATTTA
1 T-AA-TTTAAT-ATTATAATTTA
24939 ATAAACAACC
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
38 12 0.23
39 18 0.34
40 10 0.19
41 13 0.25
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (38 bp):
TAATTTAATATTATAATTTAGTAATAAATTATAATATA
Found at i:26100 original size:22 final size:22
Alignment explanation
Indices: 26058--26102 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
26048 TTAATTATTG
*
26058 TTATTAATTAATATTAGTTAAT
1 TTATTAATTAACATTAGTTAAT
26080 TTATTAATTAACATTTA-TTAAT
1 TTATTAATTAACA-TTAGTTAAT
26102 T
1 T
26103 AGTAAATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTATTAATTAACATTAGTTAAT
Found at i:26202 original size:27 final size:29
Alignment explanation
Indices: 26146--26210 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
26136 ATAATAATTT
*
26146 TAATTAATATTTATTATTAAAATATTTAAA
1 TAATTAATATTTATTACTAAAATA-TTAAA
* *
26176 TAATTAATATTTA-TACTATAATATAAAA
1 TAATTAATATTTATTACTAAAATATTAAA
26204 T-ATTAAT
1 TAATTAAT
26211 TATGTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 6 0.19
28 5 0.16
29 8 0.25
30 13 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
TAATTAATATTTATTACTAAAATATTAAA
Found at i:26584 original size:13 final size:14
Alignment explanation
Indices: 26558--26591 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
26548 AATGATATTA
26558 TTATTAAATATAAAT
1 TTATT-AATATAAAT
26573 TTATTAAT-TAAAT
1 TTATTAATATAAAT
26586 TTATTA
1 TTATTA
26592 TTATTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 3 0.16
15 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATTAATATAAAT
Found at i:26977 original size:23 final size:24
Alignment explanation
Indices: 26951--26999 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
26941 TTTAATTTCA
*
26951 AATT-AAAAA-TAATATTTTTTGAT
1 AATTCAAAAATTAA-ATTTGTTGAT
26974 AATTCAAAAATTAAATTTGTTGAT
1 AATTCAAAAATTAAATTTGTTGAT
26998 AA
1 AA
27000 ATAATTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 16 0.70
25 3 0.13
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (24 bp):
AATTCAAAAATTAAATTTGTTGAT
Done.