Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168301.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_527, 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: 23911
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Found at i:3595 original size:24 final size:24
Alignment explanation
Indices: 3545--3591 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
3535 ATTCTCACTC
*
3545 AAAGATTCTCATTTAAAACTTCTT
1 AAAGATTCTTATTTAAAACTTCTT
3569 AAAGATTCTTATTTAAAA-TTCTT
1 AAAGATTCTTATTTAAAACTTCTT
3592 TAAAAACTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (24 bp):
AAAGATTCTTATTTAAAACTTCTT
Found at i:3600 original size:35 final size:35
Alignment explanation
Indices: 3559--3630 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
3549 ATTCTCATTT
* * *
3559 AAAACTTCTTAAAGATTCTTATTTAAAATTCTTTA
1 AAAACTTCTTAAAGATTCTCATTTAAAACTCCTTA
3594 AAAACTTCTTAAAGATTCTCATTTAAAACTCCTTA
1 AAAACTTCTTAAAGATTCTCATTTAAAACTCCTTA
3629 AA
1 AA
3631 GATTATCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (35 bp):
AAAACTTCTTAAAGATTCTCATTTAAAACTCCTTA
Found at i:3628 original size:24 final size:24
Alignment explanation
Indices: 3594--3717 Score: 176
Period size: 24 Copynumber: 5.2 Consensus size: 24
3584 AAATTCTTTA
3594 AAAACTTCTTAAAGATTCTCATTT
1 AAAACTTCTTAAAGATTCTCATTT
* *
3618 AAAACTCCTTAAAGATTATCATTT
1 AAAACTTCTTAAAGATTCTCATTT
3642 AAAACTTCTTAAAGATTCTCATTT
1 AAAACTTCTTAAAGATTCTCATTT
*** * *
3666 AAAAGGCCTTATAGATTCTCACTT
1 AAAACTTCTTAAAGATTCTCATTT
*
3690 AAAACTTCTTAAAAATTCTCATTT
1 AAAACTTCTTAAAGATTCTCATTT
3714 AAAA
1 AAAA
3718 TTTTTAACAT
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 85 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (24 bp):
AAAACTTCTTAAAGATTCTCATTT
Found at i:3653 original size:48 final size:48
Alignment explanation
Indices: 3594--3717 Score: 194
Period size: 48 Copynumber: 2.6 Consensus size: 48
3584 AAATTCTTTA
* *
3594 AAAACTTCTTAAAGATTCTCATTTAAAACTCCTTAAAGATTATCATTT
1 AAAACTTCTTAAAGATTCTCATTTAAAACGCCTTAAAGATTATCACTT
* * *
3642 AAAACTTCTTAAAGATTCTCATTTAAAAGGCCTTATAGATTCTCACTT
1 AAAACTTCTTAAAGATTCTCATTTAAAACGCCTTAAAGATTATCACTT
*
3690 AAAACTTCTTAAAAATTCTCATTTAAAA
1 AAAACTTCTTAAAGATTCTCATTTAAAA
3718 TTTTTAACAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (48 bp):
AAAACTTCTTAAAGATTCTCATTTAAAACGCCTTAAAGATTATCACTT
Found at i:4965 original size:8 final size:8
Alignment explanation
Indices: 4964--5060 Score: 87
Period size: 8 Copynumber: 12.1 Consensus size: 8
4954 TTTTTACATT
4964 TTTTTTCA
1 TTTTTTCA
4972 TTTTTTCA
1 TTTTTTCA
4980 -TTTTTCA
1 TTTTTTCA
4987 TTTTTTCA
1 TTTTTTCA
* *
4995 -TCTCTCA
1 TTTTTTCA
*
5002 TTTTTTTCT
1 -TTTTTTCA
5011 TTTTTTCA
1 TTTTTTCA
5019 TCTTTCTTCA
1 T-TTT-TTCA
5029 -TTTTTCA
1 TTTTTTCA
5036 TTCTTTT--
1 TT-TTTTCA
5043 TTTTTTCAA
1 TTTTTTC-A
5052 TTTTTTCA
1 TTTTTTCA
5060 T
1 T
5061 CCATTAATGA
Statistics
Matches: 73, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
6 4 0.05
7 18 0.25
8 29 0.40
9 18 0.25
10 4 0.05
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTTTCA
Found at i:4983 original size:15 final size:15
Alignment explanation
Indices: 4965--5060 Score: 95
Period size: 15 Copynumber: 6.1 Consensus size: 15
4955 TTTTACATTT
4965 TTTTTCATTTTTTCA
1 TTTTTCATTTTTTCA
4980 TTTTTCATTTTTTCA
1 TTTTTCATTTTTTCA
* * *
4995 TCTCTCATTTTTTTCTT
1 TTTTTCA-TTTTTTC-A
5012 TTTTTCATCTTTCTTCA
1 TTTTTCAT-TTT-TTCA
*
5029 TTTTTCATTCTTTT-T
1 TTTTTCATT-TTTTCA
5044 TTTTTCAATTTTTTCA
1 TTTTTC-ATTTTTTCA
5060 T
1 T
5061 CCATTAATGA
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
15 30 0.45
16 15 0.23
17 18 0.27
18 3 0.05
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTCATTTTTTCA
Found at i:5033 original size:41 final size:40
Alignment explanation
Indices: 4963--5061 Score: 123
Period size: 41 Copynumber: 2.5 Consensus size: 40
4953 TTTTTTACAT
4963 TTTTTTTCATTTTTTCA--TTTTTCATTTTTTCATCTCTCA
1 TTTTTTTCATTTTTTCATCTTTTTCATTTTTTCAT-TCTCA
* **
5002 TTTTTTTCTTTTTTTCATCTTTCTTCA-TTTTTCATTCTTT
1 TTTTTTTCATTTTTTCATCTTT-TTCATTTTTTCATTCTCA
5042 TTTTTTTCAATTTTTTCATC
1 TTTTTTTC-ATTTTTTCATC
5062 CATTAATGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
39 16 0.31
40 11 0.21
41 21 0.40
42 4 0.08
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (40 bp):
TTTTTTTCATTTTTTCATCTTTTTCATTTTTTCATTCTCA
Found at i:8613 original size:47 final size:46
Alignment explanation
Indices: 8561--8663 Score: 131
Period size: 47 Copynumber: 2.2 Consensus size: 46
8551 TTTATTTTTT
*
8561 ATTTTTTCA-TTTCTAAATTTT-TCACCATTTGGG-CTAATTTAGAAAA
1 ATTTTTTTATTTTCTAAATTTTCT-ACCATTTGGGTCT-ATTTAG-AAA
*
8607 ATTTTTTTATTTTCTAAATTTTCTGCCATTTGGGTCTATTTAGAAA
1 ATTTTTTTATTTTCTAAATTTTCTACCATTTGGGTCTATTTAGAAA
*
8653 TTTTTTTTATT
1 ATTTTTTTATT
8664 CTTTGAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
46 21 0.41
47 27 0.53
48 3 0.06
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (46 bp):
ATTTTTTTATTTTCTAAATTTTCTACCATTTGGGTCTATTTAGAAA
Found at i:8658 original size:46 final size:47
Alignment explanation
Indices: 8561--8663 Score: 133
Period size: 46 Copynumber: 2.2 Consensus size: 47
8551 TTTATTTTTT
*
8561 ATTTTTTCA-TTTCTAAATTTTTCACCATTTGGGCTAATTTAGAAAA
1 ATTTTTTTATTTTCTAAATTTTTCACCATTTGGGCTAATTTAGAAAA
*
8607 ATTTTTTTATTTTCTAAA-TTTTCTGCCATTTGGGTCT-ATTTAG-AAA
1 ATTTTTTTATTTTCTAAATTTTTC-ACCATTTGGG-CTAATTTAGAAAA
*
8653 TTTTTTTTATT
1 ATTTTTTTATT
8664 CTTTGAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
46 26 0.51
47 23 0.45
48 2 0.04
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (47 bp):
ATTTTTTTATTTTCTAAATTTTTCACCATTTGGGCTAATTTAGAAAA
Found at i:10329 original size:18 final size:18
Alignment explanation
Indices: 10294--10490 Score: 60
Period size: 18 Copynumber: 11.0 Consensus size: 18
10284 TTATATTAAA
*
10294 TATATTAATA-AACAATAT
1 TATATTAATATAA-TATAT
10312 TATATTAATATAATATAT
1 TATATTAATATAATATAT
* * *
10330 TA-ATAAAATCTTAATAAAT
1 TATAT-TAAT-ATAATATAT
* *
10349 AATATCTTA-ATAA-ATAT
1 TATAT-TAATATAATATAT
10366 TAT-TATAA-ATAA-ATA-
1 TATAT-TAATATAATATAT
**
10381 TATACGAATA-AATTAATAT
1 TATATTAATATAA-T-ATAT
* * *
10400 TA-ATAAATAAAATTATAA
1 TATATTAATATAA-TATAT
10418 TATATTAATATAATATAT
1 TATATTAATATAATATAT
* * *
10436 CA-ATAAATAATATTATAT
1 TATATTAAT-ATAATATAT
*
10454 T-TATTAATA-AATAATAA
1 TATATTAATATAAT-ATAT
10471 TATATTAATAAATAATATAT
1 TATATTAAT--ATAATATAT
10491 AAAAAATTAT
Statistics
Matches: 131, Mismatches: 29, Indels: 36
0.67 0.15 0.18
Matches are distributed among these distances:
15 7 0.05
16 13 0.10
17 17 0.13
18 60 0.46
19 24 0.18
20 7 0.05
21 3 0.02
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (18 bp):
TATATTAATATAATATAT
Found at i:10330 original size:31 final size:29
Alignment explanation
Indices: 10274--10588 Score: 114
Period size: 31 Copynumber: 11.2 Consensus size: 29
10264 AATTTTACTT
10274 ATAAATAATATTATAT--TA-AATATATTA
1 ATAAA-AATATTATATAATATAATATATTA
10301 ATAAACAATATTATATTAATATAATATATTA
1 ATAAA-AATATTATA-TAATATAATATATTA
* *
10332 AT-AAAATCTTA-ATAA-ATAATATCTTA
1 ATAAAAATATTATATAATATAATATATTA
* *
10358 ATAAATATTATTATA-AATA-AATATATACGA
1 ATAAA-AATATTATATAATATAATATAT--TA
10388 ATAAATTAATATTA-ATAA-ATAA-A-ATT-
1 ATAAA--AATATTATATAATATAATATATTA
*
10414 AT---AATA-TAT-TAATATAATATATCA
1 ATAAAAATATTATATAATATAATATATTA
* *
10438 ATAAATAATATTATAT-TTATTAATA-AATA
1 ATAAA-AATATTATATAATA-TAATATATTA
*
10467 AT-AATATATTA-ATAA-ATAATATA-TA
1 ATAAAAATATTATATAATATAATATATTA
* *
10492 A-AAAATTATTAATTTAAT-TAATAAATATT-
1 ATAAAAATATT-ATATAATATAAT--ATATTA
* *
10521 ACAATAATA-TATGAATAA-ATAAGATATTATTA
1 ATAAAAATATTAT--ATAATAT-A-ATA-TATTA
*
10553 ATAGATAATA-TACTATTAATATAATATATTA
1 ATA-AAAATATTA-TA-TAATATAATATATTA
10584 ATAAA
1 ATAAA
10589 TAACATTAAG
Statistics
Matches: 219, Mismatches: 23, Indels: 89
0.66 0.07 0.27
Matches are distributed among these distances:
20 5 0.02
21 8 0.04
22 1 0.00
23 2 0.01
24 2 0.01
25 14 0.06
26 19 0.09
27 32 0.15
28 23 0.11
29 24 0.11
30 31 0.14
31 35 0.16
32 8 0.04
33 12 0.05
34 3 0.01
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (29 bp):
ATAAAAATATTATATAATATAATATATTA
Found at i:10465 original size:22 final size:19
Alignment explanation
Indices: 10357--10581 Score: 103
Period size: 18 Copynumber: 12.5 Consensus size: 19
10347 ATAATATCTT
10357 AATAA-ATAT-TATT-ATA
1 AATAATATATATATTAATA
**
10373 AATAA-ATATATACGAATA
1 AATAATATATATATTAATA
*
10391 AATTAATAT-TA-ATAAATA
1 AA-TAATATATATATTAATA
*
10409 AA-ATTATAATATATTAAT-
1 AATAATAT-ATATATTAATA
*
10427 -ATAATATATCA-ATAAAT-
1 AATAATATAT-ATATTAATA
* *
10444 AATATTATATTTATTAATA
1 AATAATATATATATTAATA
10463 AATAATA-ATATATTAATA
1 AATAATATATATATTAATA
** *
10481 AATAATATATA-AAAAATT
1 AATAATATATATATTAATA
*
10499 ATTAAT-T-TA-ATTAATA
1 AATAATATATATATTAATA
* *
10515 AATATTACAATAATATATGAATA
1 AATA--A-TAT-ATATATTAATA
*
10538 AATAAGATAT-TATTAATA
1 AATAATATATATATTAATA
* *
10556 GATAATATA-CTATTAAT-
1 AATAATATATATATTAATA
10573 -ATAATATAT
1 AATAATATAT
10582 TAATAAATAA
Statistics
Matches: 160, Mismatches: 27, Indels: 43
0.70 0.12 0.19
Matches are distributed among these distances:
16 30 0.19
17 11 0.07
18 80 0.50
19 21 0.13
20 5 0.03
21 1 0.01
22 2 0.01
23 10 0.06
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
AATAATATATATATTAATA
Found at i:10493 original size:146 final size:146
Alignment explanation
Indices: 10321--10596 Score: 314
Period size: 146 Copynumber: 1.9 Consensus size: 146
10311 TTATATTAAT
** * * *
10321 ATAATATATTAATAAAATCTTAATAAATAATATCTTAATAAATATTATTATAA-A-TA-AAT-AT
1 ATAATATATTAATAAAATAATAATAAAAAAT-TATTAATAAA-ATTAATA-AATATTACAATAAT
* *
10382 ATACGAATAAATTA-ATATTAATAAATAAAATTATAATA-TATTAATATAATATATCAATAAATA
63 ATACGAATAAATAAGATATT-ATAAAT-AAATAAT-ATACTATTAATATAATATATCAATAAATA
*
10445 ATATTATATTTATTAATAAATA
125 ACATTATATTTATTAATAAATA
**
10467 ATAATATATTAAT-AAATAATATATAAAAAATTATTAATTTAATTAATAAATATTACAATAATAT
1 ATAATATATTAATAAAATAATA-ATAAAAAATTATTAATAAAATTAATAAATATTACAATAATAT
* * * *
10531 ATGAATAAATAAGATATTATTAATAGATAATATACTATTAATATAATATATTAATAAATAACATT
65 ACGAATAAATAAGATATTATAAATAAATAATATACTATTAATATAATATATCAATAAATAACATT
10596 A
130 A
10597 AGAATAATAT
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
143 2 0.02
144 7 0.06
145 18 0.17
146 58 0.53
147 19 0.17
148 5 0.05
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (146 bp):
ATAATATATTAATAAAATAATAATAAAAAATTATTAATAAAATTAATAAATATTACAATAATATA
CGAATAAATAAGATATTATAAATAAATAATATACTATTAATATAATATATCAATAAATAACATTA
TATTTATTAATAAATA
Found at i:10538 original size:97 final size:91
Alignment explanation
Indices: 10410--10581 Score: 215
Period size: 97 Copynumber: 1.8 Consensus size: 91
10400 TAATAAATAA
*
10410 AATTATAATATATTAATATAATATATCAATAAATAATATTATATTTATTAATAAATAATAATA-T
1 AATTATAATATATTAATATAATATATCAATAAAT-A-A-GATA-TTATTAATAAATAAT-ATACT
10474 ATTAATAAATAATATATAAAAAATTATTAATTT
61 ATTAAT--ATAATATATAAAAAATTATTAATTT
* *
10507 AATTAATAA-ATATTACA-ATAATATATGAATAAATAAGATATTATTAATAGATAATATACTATT
1 AATT-ATAATATATTA-ATATAATATATCAATAAATAAGATATTATTAATAAATAATATACTATT
10570 AATATAATATAT
64 AATATAATATAT
10582 TAATAAATAA
Statistics
Matches: 69, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
91 9 0.13
92 3 0.04
93 21 0.30
94 3 0.04
95 1 0.01
96 1 0.01
97 26 0.38
98 5 0.07
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (91 bp):
AATTATAATATATTAATATAATATATCAATAAATAAGATATTATTAATAAATAATATACTATTAA
TATAATATATAAAAAATTATTAATTT
Found at i:10612 original size:35 final size:35
Alignment explanation
Indices: 10572--10640 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
10562 ATACTATTAA
* *
10572 TATAATATATTAATAAATAACATTAAGAATAATAT
1 TATAATATATGAATAAATAACATCAAGAATAATAT
*
10607 TATAATATATGAATAAATAATATCAAGAATAATA
1 TATAATATATGAATAAATAACATCAAGAATAATA
10641 AATAGTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (35 bp):
TATAATATATGAATAAATAACATCAAGAATAATAT
Found at i:10629 original size:15 final size:14
Alignment explanation
Indices: 10274--10628 Score: 142
Period size: 15 Copynumber: 25.2 Consensus size: 14
10264 AATTTTACTT
10274 ATAAATAATATTATA
1 ATAAATAATA-TATA
*
10289 TTAAAT-ATAT-TA
1 ATAAATAATATATA
*
10301 ATAAACAATATTATA
1 ATAAATAATA-TATA
*
10316 TTAATATAATATATTA
1 ATAA-ATAATATA-TA
*
10332 AT-AA-AATCT-TA
1 ATAAATAATATATA
*
10343 ATAAATAATATCTTA
1 ATAAATAATAT-ATA
*
10358 ATAAATATTATTATAA
1 ATAAATAATA-TAT-A
*
10374 ATAAAT-ATATACGA
1 ATAAATAATATA-TA
10388 ATAAATTAATAT-TA
1 ATAAA-TAATATATA
*
10402 ATAAATAA-A-ATT
1 ATAAATAATATATA
10414 AT-AAT-ATAT-TA
1 ATAAATAATATATA
10425 AT--ATAATATATCA
1 ATAAATAATATAT-A
10438 ATAAATAATATTATA
1 ATAAATAATA-TATA
* * * *
10453 TTTATTAATAAATA
1 ATAAATAATATATA
10467 AT-AAT-ATAT-TA
1 ATAAATAATATATA
10478 ATAAATAATATATA
1 ATAAATAATATATA
*
10492 A-AAA-ATTAT-TA
1 ATAAATAATATATA
* *
10503 ATTTAATTAATAAATA
1 A--TAAATAATATATA
*
10519 TTACAATAATATATGA
1 ATA-AATAATATAT-A
10535 ATAAATAAGATATTATTA
1 ATAAAT-A-ATA-TA-TA
*
10553 ATAGATAATATACTA
1 ATAAATAATATA-TA
*
10568 TTAATATAATATATTA
1 ATAA-ATAATATA-TA
*
10584 ATAAATAACAT-TA
1 ATAAATAATATATA
*
10597 A-GAATAATATTATA
1 ATAAATAATA-TATA
* *
10611 ATATATGAATAAATA
1 ATAAAT-AATATATA
10626 ATA
1 ATA
10629 TCAAGAATAA
Statistics
Matches: 256, Mismatches: 42, Indels: 84
0.67 0.11 0.22
Matches are distributed among these distances:
10 3 0.01
11 22 0.09
12 29 0.11
13 31 0.12
14 33 0.13
15 76 0.30
16 49 0.19
17 4 0.02
18 8 0.03
19 1 0.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (14 bp):
ATAAATAATATATA
Found at i:10695 original size:15 final size:15
Alignment explanation
Indices: 10675--10752 Score: 59
Period size: 16 Copynumber: 4.9 Consensus size: 15
10665 ATATTAATAT
10675 AATATTTTAATATTA
1 AATATTTTAATATTA
*
10690 AATATTATTATTAAATATA
1 AATATT-TTA--ATAT-TA
*
10709 AATATTTTAAT-TTT
1 AATATTTTAATATTA
*
10723 AATAATTTTAATAATA
1 AAT-ATTTTAATATTA
*
10739 AATAATTTCAATAT
1 AAT-ATTTTAATAT
10753 ATTTTAATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
14 4 0.08
15 15 0.30
16 17 0.34
18 6 0.12
19 8 0.16
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTTTAATATTA
Found at i:10703 original size:19 final size:18
Alignment explanation
Indices: 10658--10714 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
10648 TTATTTTAAG
* *
10658 TATTTTTATATTAATATAA
1 TATTTTAATATTAA-ATAT
10677 TATTTTAATATTAAATAT
1 TATTTTAATATTAAATAT
10695 TATTATTAA-ATATAAATAT
1 TATT-TTAATAT-TAAATAT
10714 T
1 T
10715 TTAATTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.26
19 25 0.74
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTTAATATTAAATAT
Found at i:10730 original size:9 final size:9
Alignment explanation
Indices: 10716--10763 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
10706 ATAAATATTT
10716 TAATTTTAA
1 TAATTTTAA
10725 TAATTTTAA
1 TAATTTTAA
*
10734 TAA--TAAA
1 TAATTTTAA
*
10741 TAATTTCAA
1 TAATTTTAA
10750 TATATTTTAA
1 TA-ATTTTAA
10760 TAAT
1 TAAT
10764 AAAAAAGGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 6 0.18
9 19 0.58
10 8 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (9 bp):
TAATTTTAA
Found at i:10738 original size:26 final size:26
Alignment explanation
Indices: 10716--10766 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
10706 ATAAATATTT
*
10716 TAATTTTAATA-ATTTTAATAATAAA
1 TAATTTCAATATATTTTAATAATAAA
10741 TAATTTCAATATATTTTAATAATAAA
1 TAATTTCAATATATTTTAATAATAAA
10767 AAAGGTGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TAATTTCAATATATTTTAATAATAAA
Found at i:14317 original size:24 final size:23
Alignment explanation
Indices: 14276--14325 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
14266 GGGAGTGAGA
* * *
14276 AAAATTTTTTAGAGATTTTTGGCG
1 AAAATTTTCTAGAAATTTCTGG-G
*
14300 AAAATTTTCTGGAAATTTCTGGG
1 AAAATTTTCTAGAAATTTCTGGG
14323 AAA
1 AAA
14326 TTTCCAGATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (23 bp):
AAAATTTTCTAGAAATTTCTGGG
Found at i:14369 original size:31 final size:32
Alignment explanation
Indices: 14334--14404 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
14324 AATTTCCAGA
*
14334 TTCCGGCGAA-AATT-CGGCGAA-ATTTGAATTT
1 TTCCGGCGAACAATTCCGGCGAACA-TTGAA-GT
14365 TTCCGGC-AACAATTCCGGCGAACATTGAAGT
1 TTCCGGCGAACAATTCCGGCGAACATTGAAGT
14396 TTCCGGCGA
1 TTCCGGCGA
14405 CCAGCCCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
30 2 0.06
31 19 0.54
32 13 0.37
33 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (32 bp):
TTCCGGCGAACAATTCCGGCGAACATTGAAGT
Found at i:14480 original size:19 final size:20
Alignment explanation
Indices: 14456--14501 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
14446 TTCCGCCAAC
14456 TTCCGGCG-AAATTTCCAGA
1 TTCCGGCGAAAATTTCCAGA
14475 TTCCGGCGAAAATTTCCAGA
1 TTCCGGCGAAAATTTCCAGA
*
14495 ATCCGGC
1 TTCCGGC
14502 ACCGGTGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (20 bp):
TTCCGGCGAAAATTTCCAGA
Found at i:14734 original size:5 final size:5
Alignment explanation
Indices: 14724--14750 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
14714 CAGCCCCCTT
14724 CGAGC CGAGC CGAGC CGAGC CGAGC CG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CG
14751 CTCCCTCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.41, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGC
Found at i:15075 original size:58 final size:55
Alignment explanation
Indices: 14942--15110 Score: 230
Period size: 58 Copynumber: 2.9 Consensus size: 55
14932 CTTAAAAGAA
* *
14942 AAATAAATTTCCAAAAAAAAAGATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTAG
1 AAATAAATTT-C--AAAAAAATATTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTAG
*
15001 AAATAAATTTCAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
1 AAATAAATTTCAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTAG
* *
15056 AAAATCGAAATTTCCAAAAAATATTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 -AAAT--AAATTTCAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
15111 CTACAAAAAA
Statistics
Matches: 102, Mismatches: 5, Indels: 7
0.89 0.04 0.06
Matches are distributed among these distances:
55 28 0.27
56 17 0.17
58 47 0.46
59 10 0.10
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.32
Consensus pattern (55 bp):
AAATAAATTTCAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTAG
Found at i:18924 original size:14 final size:13
Alignment explanation
Indices: 18896--18923 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18886 AGATATCAAC
18896 AATGAAAAAAAAA
1 AATGAAAAAAAAA
18909 AATGAAAAAAAAA
1 AATGAAAAAAAAA
18922 AA
1 AA
18924 AAAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (13 bp):
AATGAAAAAAAAA
Found at i:20156 original size:41 final size:41
Alignment explanation
Indices: 20080--20519 Score: 753
Period size: 41 Copynumber: 11.0 Consensus size: 41
20070 GTCTAGGAGT
20080 ATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
20120 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
20161 ATTTACTTTTCCAAAGTCGTGGT-CCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
20202 ATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
20241 ATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
20280 ATTTAC-TTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
20320 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
20361 ATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
20400 ATTTACTTTTCCAAAGTC---GTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
*
20439 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
20480 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
1 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
20520 TTTGGTAAAA
Statistics
Matches: 386, Mismatches: 2, Indels: 23
0.94 0.00 0.06
Matches are distributed among these distances:
38 20 0.05
39 126 0.33
40 57 0.15
41 171 0.44
42 12 0.03
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (41 bp):
ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
Found at i:20386 original size:159 final size:159
Alignment explanation
Indices: 20080--20519 Score: 821
Period size: 159 Copynumber: 2.7 Consensus size: 159
20070 GTCTAGGAGT
20080 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCC
1 ATTTACTTTTCAAAG-TCGTTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCAAAGTCGTGGTGCC
20145 TCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGT-CCTCTGTTTAGAGGAGCAATTTACT
64 TCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACT
20209 TTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCA
128 TTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCA
20241 ATTTACTTTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAGTCGTGGTGCCTC
1 ATTTACTTTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAGTCGTGGTGCCTC
20306 TGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT
66 TGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT
20371 CAAAGTCGTTGCCTCTGTTTAGAGGAGCA
131 CAAAGTCGTTGCCTCTGTTTAGAGGAGCA
20400 ATTTACTTTTCCAAAGTCG-TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCC
1 ATTTACTTTT-CAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTT-CAAAGTCGTGGTGCC
20464 TCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
64 TCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
20520 TTTGGTAAAA
Statistics
Matches: 276, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
158 12 0.04
159 140 0.51
160 109 0.39
161 15 0.05
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (159 bp):
ATTTACTTTTCAAAGTCGTTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAGTCGTGGTGCCTC
TGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT
CAAAGTCGTTGCCTCTGTTTAGAGGAGCA
Found at i:20532 original size:1 final size:1
Alignment explanation
Indices: 20526--20597 Score: 99
Period size: 1 Copynumber: 72.0 Consensus size: 1
20516 GAGCTTTGGT
* * * *
20526 AAAAAAAAAAAAACAAAAAAACAAAAAAACAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
20591 CAAAAAA
1 AAAAAAA
20598 TGTTGAGTTG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20543 original size:8 final size:8
Alignment explanation
Indices: 20526--20597 Score: 109
Period size: 7 Copynumber: 9.6 Consensus size: 8
20516 GAGCTTTGGT
20526 AAAAAA-A
1 AAAAAACA
20533 AAAAAACA
1 AAAAAACA
20541 AAAAAACA
1 AAAAAACA
20549 AAAAAACA
1 AAAAAACA
20557 AAAAAA-A
1 AAAAAACA
20564 AAAAAAC-
1 AAAAAACA
20571 AAAAAA-A
1 AAAAAACA
20578 AAAAAA-A
1 AAAAAACA
20585 AAAAAACA
1 AAAAAACA
20593 AAAAA
1 AAAAA
20598 TGTTGAGTTG
Statistics
Matches: 61, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
7 32 0.52
8 29 0.48
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:20564 original size:31 final size:29
Alignment explanation
Indices: 20526--20597 Score: 117
Period size: 31 Copynumber: 2.4 Consensus size: 29
20516 GAGCTTTGGT
20526 AAAAAAAAAAAAACAAAAAAACAAAAAAACA
1 AAAAAAAAAAAAACAAAAAAA-AAAAAAA-A
20557 AAAAAAAAAAAAACAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAACAAAAAAAAAAAAAAA
*
20586 AAAAACAAAAAA
1 AAAAAAAAAAAA
20598 TGTTGAGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 12 0.30
30 7 0.17
31 21 0.52
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAAAACAAAAAAAAAAAAAAA
Found at i:20790 original size:9 final size:10
Alignment explanation
Indices: 20776--20827 Score: 55
Period size: 9 Copynumber: 5.9 Consensus size: 10
20766 TCTTTTCTTT
20776 TGTATT-TTA
1 TGTATTATTA
20785 TGTA-T-TTA
1 TGTATTATTA
20793 T-TATTATTA
1 TGTATTATTA
20802 T-TATTATTA
1 TGTATTATTA
20811 TGTATTA-TA
1 TGTATTATTA
20820 T-TATTATT
1 TGTATTATT
20828 TATTTATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
7 2 0.05
8 11 0.28
9 21 0.54
10 5 0.13
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (10 bp):
TGTATTATTA
Found at i:20798 original size:3 final size:3
Alignment explanation
Indices: 20790--20827 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
20780 TTTTATGTAT
20790 TTA TTA TTA TTA TTA TTA TTA TGTA TTA -TA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TT
20828 TATTTATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:20810 original size:15 final size:14
Alignment explanation
Indices: 20778--20827 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 14
20768 TTTTCTTTTG
20778 TATT-TTATGTAT-T
1 TATTATTAT-TATAT
20791 TATTATTATTATTAT
1 TATTATTATTA-TAT
20806 TATTATGTATTATAT
1 TATTAT-TATTATAT
20821 TATTATT
1 TATTATT
20828 TATTTATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
13 6 0.18
14 6 0.18
15 16 0.48
16 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (14 bp):
TATTATTATTATAT
Found at i:20832 original size:4 final size:4
Alignment explanation
Indices: 20781--20927 Score: 65
Period size: 4 Copynumber: 39.2 Consensus size: 4
20771 TCTTTTGTAT
* *
20781 TTTA TGTA TTTA -TTA -TTA -TTA -TTA -TTA -TTA TGTA -TTA TATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA
*
20823 -TTA TTTA TTTA TTTA TTT- TTTG TTAATA TTTA TTGTA TTTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TT-TA TTTA TTTA TTTA
* * *
20871 TGTA TATA TATA TATT- TTTA TTT- TTTA TTT- TATTA TTT- TTT- TTTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA
*
20916 -TTA TTTA ATTA T
1 TTTA TTTA TTTA T
20928 ATATCTGATA
Statistics
Matches: 117, Mismatches: 10, Indels: 32
0.74 0.06 0.20
Matches are distributed among these distances:
3 44 0.38
4 61 0.52
5 9 0.08
6 3 0.03
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:20900 original size:68 final size:70
Alignment explanation
Indices: 20791--20922 Score: 150
Period size: 68 Copynumber: 1.9 Consensus size: 70
20781 TTTATGTATT
*
20791 TATTATTATTATTATTATTATGTATTATATTATTATTTA-TTTATTTATTTTTTGTTAATATTTA
1 TATTATTATTATTATTATTATATATTATATTATTATTTATTTTA-TTATTTTTTGTTAATATTTA
20855 TTGTATT
65 -TGTATT
* * *
20862 TATTA-T-TTATGTA-TATATATATATT-T-TTATTTTTTATTTTATTATTTTTTTTTATTATTT
1 TATTATTATTAT-TATTAT-TATATATTATATTATTATTTATTTTATTATTTTTTGTTAATATTT
20922 A
64 A
20923 ATTATATATC
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
68 27 0.50
69 12 0.22
70 10 0.19
71 5 0.09
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (70 bp):
TATTATTATTATTATTATTATATATTATATTATTATTTATTTTATTATTTTTTGTTAATATTTAT
GTATT
Found at i:20947 original size:31 final size:33
Alignment explanation
Indices: 20909--20969 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 33
20899 TTTATTATTT
20909 TTTTTTATTATT-TAATTAT-ATATCTGATATA
1 TTTTTTATTATTATAATTATAATATCTGATATA
**
20940 TTTTTTATTATTATTTTTATAATATCTGAT
1 TTTTTTATTATTATAATTATAATATCTGAT
20970 TTATCTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 12 0.46
32 5 0.19
33 9 0.35
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (33 bp):
TTTTTTATTATTATAATTATAATATCTGATATA
Found at i:20958 original size:12 final size:12
Alignment explanation
Indices: 20789--20959 Score: 59
Period size: 12 Copynumber: 13.4 Consensus size: 12
20779 ATTTTATGTA
20789 TTTATTATTATT
1 TTTATTATTATT
*
20801 ATTATTATTATGT
1 TTTATTATTAT-T
20814 ATTATATTATTATTT
1 -TT-TATTATTA-TT
*
20829 ATTTATTTATTTTT
1 -TTTA-TTATTATT
*
20843 TGTTAATATTTATTGT
1 T-TTATTA-TTA-T-T
*
20859 ATTTATTATTTATG
1 -TTTATTA-TTATT
*
20873 TATATATATATATT
1 TTTAT-TAT-TATT
*
20887 TTTATT-TTTTAT
1 TTTATTATTAT-T
20899 TTTATTATT-TT
1 TTTATTATTATT
20910 TTT-TTATTA-T
1 TTTATTATTATT
*
20920 TTAATTA-TATAT
1 TTTATTATTAT-T
* *
20932 CTGA-TA-TATTT
1 TTTATTATTA-TT
20943 TTTATTATTATT
1 TTTATTATTATT
20955 TTTAT
1 TTTAT
20960 AATATCTGAT
Statistics
Matches: 122, Mismatches: 16, Indels: 42
0.68 0.09 0.23
Matches are distributed among these distances:
10 10 0.08
11 16 0.13
12 32 0.26
13 14 0.11
14 19 0.16
15 19 0.16
16 11 0.09
17 1 0.01
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTATTATTATT
Found at i:20965 original size:33 final size:33
Alignment explanation
Indices: 20904--20969 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
20894 TTTATTTTAT
*
20904 TATTTTTTTTTATTATTTAATTATATATCTGATA
1 TATTTTTTATTATTATTT-ATTATATATCTGATA
20938 TATTTTTTATTATTATTT-TTATAATATCTGAT
1 TATTTTTTATTATTATTTATTAT-ATATCTGAT
20970 TTATCTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 4 0.13
33 9 0.30
34 17 0.57
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (33 bp):
TATTTTTTATTATTATTTATTATATATCTGATA
Found at i:21320 original size:25 final size:25
Alignment explanation
Indices: 21268--21320 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
21258 GGGAGTGAGA
* *
21268 AAAAATTTTTTAGAGATTTTTGGCG
1 AAAAATTTTTTAGAAATTTCTGGCG
*
21293 AAAAATTTTTCTGGAAATTTCTGG-G
1 AAAAATTTTT-TAGAAATTTCTGGCG
21318 AAA
1 AAA
21321 TTTCCAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.40
Consensus pattern (25 bp):
AAAAATTTTTTAGAAATTTCTGGCG
Found at i:21353 original size:30 final size:30
Alignment explanation
Indices: 21319--21380 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
21309 ATTTCTGGGA
*
21319 AATTTCCAGATTCCGGCGAA-AATTCCGGCG
1 AATTTCAAGATTCCGGC-AACAATTCCGGCG
* **
21349 AATTTGAATTTTCCGGCAACAATTCCGGCG
1 AATTTCAAGATTCCGGCAACAATTCCGGCG
21379 AA
1 AA
21381 CATTGAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (30 bp):
AATTTCAAGATTCCGGCAACAATTCCGGCG
Found at i:21393 original size:31 final size:30
Alignment explanation
Indices: 21329--21398 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
21319 AATTTCCAGA
* *
21329 TTCCGGCGAAAATTCCGGCGAATTTGAATT
1 TTCCGGCGAAAATTCCGGCGAAATTGAAGT
21359 TTCCGGC-AACAATTCCGGCGAACATTGAAGT
1 TTCCGGCGAA-AATTCCGGCGAA-ATTGAAGT
21390 TTCCGGCGA
1 TTCCGGCGA
21399 CCAGCCCAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 19 0.54
31 13 0.37
32 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (30 bp):
TTCCGGCGAAAATTCCGGCGAAATTGAAGT
Found at i:21473 original size:19 final size:20
Alignment explanation
Indices: 21449--21494 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
21439 TCCGGCCAAC
21449 TTCCGGCG-AAATTTCCAGA
1 TTCCGGCGAAAATTTCCAGA
21468 TTCCGGCGAAAATTTCCAGA
1 TTCCGGCGAAAATTTCCAGA
*
21488 ATCCGGC
1 TTCCGGC
21495 ACCGGTGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (20 bp):
TTCCGGCGAAAATTTCCAGA
Found at i:21831 original size:12 final size:11
Alignment explanation
Indices: 21811--21857 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
21801 TTTCTTTGAA
21811 TTTTT-TTTAT
1 TTTTTATTTAT
*
21821 TTCTTTGTTTAT
1 TT-TTTATTTAT
21833 TTGTTTATTTTAT
1 TT-TTTA-TTTAT
21846 TTTTTATTTAT
1 TTTTTATTTAT
21857 T
1 T
21858 AGATTAGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 2 0.06
11 9 0.28
12 14 0.44
13 7 0.22
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.81
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:21972 original size:26 final size:26
Alignment explanation
Indices: 21937--21992 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
21927 AAAAAAAGAT
21937 TTTTAGGGAAAAGTTGAAAGTATCAA
1 TTTTAGGGAAAAGTTGAAAGTATCAA
*
21963 TTTTGGGGAAAAGTTGAAAGTATCAA
1 TTTTAGGGAAAAGTTGAAAGTATCAA
21989 TTTT
1 TTTT
21993 CCTTAGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.36
Consensus pattern (26 bp):
TTTTAGGGAAAAGTTGAAAGTATCAA
Found at i:22034 original size:58 final size:59
Alignment explanation
Indices: 21962--22112 Score: 216
Period size: 58 Copynumber: 2.6 Consensus size: 59
21952 GAAAGTATCA
* * **
21962 ATTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC-AAAAAAAGGT
1 ATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAA-TTTCAAAAAAAAAAT
*
22021 -TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAGAAATAAATTTCAAAAAAAAAAT
1 ATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAAAAAAAAAT
*
22079 ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 ATTTTGA-GGAAAAGTTGAAAGTATCAATTTTCC
22113 CTCCAAAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
57 4 0.05
58 48 0.59
59 5 0.06
60 25 0.30
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.34
Consensus pattern (59 bp):
ATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCAAAAAAAAAAT
Done.