Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2756
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: 89000
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:844 original size:16 final size:17
Alignment explanation
Indices: 819--855 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
809 GTGTTAAAAG
*
819 AAAAAGAAAATATACCT
1 AAAAAGAAAAGATACCT
836 AAAAA-AAAAGATACCT
1 AAAAAGAAAAGATACCT
852 AAAA
1 AAAA
856 CATCCAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.70, C:0.11, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAAAGAAAAGATACCT
Found at i:6419 original size:27 final size:27
Alignment explanation
Indices: 6388--6457 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
6378 ACTGATTAAG
*
6388 AATAAATTAAAAATATTT-ATTTATT-
1 AATAAATTAAAAATATTTCATCTATTA
*
6413 TATATAATGTAAAAAT-TTTCATCTATTA
1 AATA-AAT-TAAAAATATTTCATCTATTA
6441 AATAATATTAAAAATAT
1 AATAA-ATTAAAAATAT
6458 AATATATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
25 3 0.08
26 6 0.17
27 21 0.58
28 6 0.17
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (27 bp):
AATAAATTAAAAATATTTCATCTATTA
Found at i:6591 original size:2 final size:2
Alignment explanation
Indices: 6584--6608 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6574 ATGTATACAT
6584 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 T
6609 GCATAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6784 original size:2 final size:2
Alignment explanation
Indices: 6777--6806 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6767 AAATGGTCCC
6777 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
6807 TCATCATCAT
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:11271 original size:19 final size:20
Alignment explanation
Indices: 11244--11281 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11234 TTTGATCCAT
11244 AATATTTTTTAATTAAAATA
1 AATATTTTTTAATTAAAATA
*
11264 AATA-TTTTTAATTTAAAT
1 AATATTTTTTAATTAAAAT
11282 TTAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTTTTAATTAAAATA
Found at i:11488 original size:24 final size:24
Alignment explanation
Indices: 11461--11557 Score: 74
Period size: 24 Copynumber: 4.0 Consensus size: 24
11451 AAATAAGCTT
11461 AATATATATTATTTAAATAATAAA
1 AATATATATTATTTAAATAATAAA
* *
11485 AATA-ATTTTTATTTAAAT-TTAAA
1 AATATA-TATTATTTAAATAATAAA
* * *
11508 TATAAATATTAATATAAA-AATAAA
1 AATATATATT-ATTTAAATAATAAA
* * *
11532 ATTTTAATATTTTTTAAATAATAAA
1 AATAT-ATATTATTTAAATAATAAA
11557 A
1 A
11558 TAAATTTTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
23 11 0.20
24 32 0.58
25 12 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AATATATATTATTTAAATAATAAA
Found at i:16601 original size:18 final size:17
Alignment explanation
Indices: 16568--16602 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
16558 AAAAAATCAA
16568 AAAATTATATTTAATAT
1 AAAATTATATTTAATAT
*
16585 AAAATTATTTTTAA-AT
1 AAAATTATATTTAATAT
16601 AA
1 AA
16603 TAACTTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAAATTATATTTAATAT
Found at i:16813 original size:17 final size:17
Alignment explanation
Indices: 16753--16816 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 17
16743 TGCCTAGATC
16753 TAATA-ATTAAT-ATTT
1 TAATATATTAATAATTT
* *
16768 TATTATATT-ATAATTA
1 TAATATATTAATAATTT
* *
16784 T-ATTTA-TATTAATTT
1 TAATATATTAATAATTT
16799 TAATATATTAATAATTT
1 TAATATATTAATAATTT
16816 T
1 T
16817 TATTAATATA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
14 1 0.03
15 15 0.42
16 11 0.31
17 9 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATATATTAATAATTT
Found at i:16850 original size:21 final size:21
Alignment explanation
Indices: 16798--16862 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
16788 TATATTAATT
* *
16798 TTAATATATTAATAATTTTTA
1 TTAATATATTAATAATATATA
16819 TTAATATATTAA-AATATATA
1 TTAATATATTAATAATATATA
16839 TTAATATAATT-AT-ATATAATA
1 TTAATAT-ATTAATAATAT-ATA
16860 TTA
1 TTA
16863 TCAAATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 18 0.46
21 21 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATATATTAATAATATATA
Found at i:17341 original size:11 final size:10
Alignment explanation
Indices: 17327--17389 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 10
17317 TATATTAAAT
17327 AAATATAATA
1 AAATATAATA
*
17337 AAA-ATAATT
1 AAATATAATA
17346 AAATATAATA
1 AAATATAATA
*
17356 TAATATTAATA
1 AAATA-TAATA
17367 TATAATAT-ATA
1 -A-AATATAATA
*
17378 AAA-ATTATA
1 AAATATAATA
17387 AAA
1 AAA
17390 GTATTAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
8 2 0.05
9 16 0.36
10 13 0.30
11 8 0.18
12 1 0.02
13 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAATATAATA
Found at i:17354 original size:42 final size:42
Alignment explanation
Indices: 17302--17418 Score: 118
Period size: 42 Copynumber: 2.8 Consensus size: 42
17292 TTTAATAATT
*
17302 TTAAGTATAATATATTATATTAAATAAATATAATAAAAATAA
1 TTAAATATAATATATTATATTAAATAAATATAATAAAAATAA
*
17344 TTAAATATAATATA--ATATTAATATATAATAT-ATAAAAATTA
1 TTAAATATAATATATTATATTAA-ATA-AATATAATAAAAATAA
* * *
17385 TAAAAGTATTAA-ATTTTATA-TAAATATATATAAT
1 TTAAA-TA-TAATATATTATATTAAATAAATATAAT
17419 TATTAATATG
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
40 7 0.11
41 20 0.32
42 27 0.43
43 6 0.10
44 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (42 bp):
TTAAATATAATATATTATATTAAATAAATATAATAAAAATAA
Found at i:17369 original size:18 final size:17
Alignment explanation
Indices: 17326--17375 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
17316 TTATATTAAA
*
17326 TAAATATAATAAAAATAAT
1 TAAATATAAT-ATAAT-AT
17345 TAAATATAATATAATAT
1 TAAATATAATATAATAT
17362 TAATATATAATATA
1 TAA-ATATAATATA
17376 TAAAAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 5 0.17
18 14 0.48
19 10 0.34
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATATAATATAATAT
Found at i:17375 original size:5 final size:5
Alignment explanation
Indices: 17307--17368 Score: 51
Period size: 5 Copynumber: 12.8 Consensus size: 5
17297 TAATTTTAAG
* * *
17307 TATAA TATAT TATAT TA-AA TA-AA TATAA TA-AA AATAA T-TAAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-AA TATAA
17354 TATAA TATTAA TATA
1 TATAA TA-TAA TATA
17369 TAATATATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
4 11 0.23
5 31 0.65
6 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:17384 original size:21 final size:20
Alignment explanation
Indices: 17302--17384 Score: 57
Period size: 19 Copynumber: 4.2 Consensus size: 20
17292 TTTAATAATT
* * *
17302 TTAAGTATAATATAT-TATA
1 TTAAATATAATATATAAAAA
17321 TTAAATA-AATATAATAAAAA
1 TTAAATATAATAT-ATAAAAA
* *
17341 -TAATTA-AATATAATATAATA
1 TTAAATATAATAT-ATA-AAAA
17361 TTAATATATAATATATAAAAA
1 TTAA-ATATAATATATAAAAA
17382 TTA
1 TTA
17385 TAAAAGTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
18 5 0.10
19 22 0.43
20 5 0.10
21 9 0.18
22 5 0.10
23 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (20 bp):
TTAAATATAATATATAAAAA
Found at i:17386 original size:18 final size:18
Alignment explanation
Indices: 17365--17427 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
17355 ATAATATTAA
17365 TATATAATATATAAAAAT
1 TATATAATATATAAAAAT
* **
17383 TATAAAAGTAT-TAAATTT
1 TATATAA-TATATAAAAAT
*
17401 TATATAA-ATATATATAAT
1 TATATAATATATA-AAAAT
17419 TAT-TAATAT
1 TATATAATAT
17428 GATTATAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
16 2 0.06
17 5 0.15
18 24 0.71
19 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TATATAATATATAAAAAT
Found at i:17419 original size:20 final size:19
Alignment explanation
Indices: 17345--17419 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 19
17335 TAAAAATAAT
*
17345 TAAATATAATATAATATTAATA
1 TAAATAT-ATA-AAT-TTTATA
**
17367 TATAATATATAAAAATTATA
1 TA-AATATATAAATTTTATA
17387 -AAAGTAT-TAAATTTTATA
1 TAAA-TATATAAATTTTATA
17405 TAAATATATATAATT
1 TAAATATATA-AATT
17420 ATTAATATGA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
18 14 0.33
19 9 0.21
20 8 0.19
21 2 0.05
22 5 0.12
23 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (19 bp):
TAAATATATAAATTTTATA
Found at i:17468 original size:64 final size:60
Alignment explanation
Indices: 17345--17469 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 60
17335 TAAAAATAAT
* * *
17345 TAAATATAATATAATATTAATATATAATATATAAAAATTATAAAAGTATTAAATTTTATA
1 TAAATATAATATAATATTAATATATAATATATAAAAATAATAAAAGTATGAAATATTATA
* *
17405 TAAATAT-ATATAATTATTAATATGATTATAATATACAAAATAATAAAAGTATGATATGATTATA
1 TAAATATAATATAA-TATTAATAT-ATAAT-ATATA-AAAATAATAAAAGTATGAAAT-ATTATA
17469 T
1 T
17470 TATTTTTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
59 6 0.11
60 16 0.29
61 4 0.07
62 5 0.09
63 18 0.33
64 6 0.11
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (60 bp):
TAAATATAATATAATATTAATATATAATATATAAAAATAATAAAAGTATGAAATATTATA
Found at i:18859 original size:2 final size:2
Alignment explanation
Indices: 18852--18893 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
18842 ATGGTGGTGA
18852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18894 CCAATGCTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19940 original size:15 final size:15
Alignment explanation
Indices: 19922--19953 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19912 GCTGTAAAAT
19922 GCACCCATGTACTAG
1 GCACCCATGTACTAG
19937 GCACCCATGTACTAG
1 GCACCCATGTACTAG
19952 GC
1 GC
19954 TTCCCACGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.19
Consensus pattern (15 bp):
GCACCCATGTACTAG
Found at i:26281 original size:29 final size:28
Alignment explanation
Indices: 26249--26307 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
26239 TCAAAATAAG
* *
26249 AAGAAACATATTGTATTGTAAAAAAGAAA
1 AAGAAACATACTGTATTATAAAAAA-AAA
* *
26278 AAGAAACGTACTGTATTATTAAAAAAAA
1 AAGAAACATACTGTATTATAAAAAAAAA
26306 AA
1 AA
26308 CATATTGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.59, C:0.05, G:0.12, T:0.24
Consensus pattern (28 bp):
AAGAAACATACTGTATTATAAAAAAAAA
Found at i:26552 original size:22 final size:21
Alignment explanation
Indices: 26527--26568 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
26517 TATCGAACTT
26527 ATATAAAAAAGTTATCAAAATC
1 ATATAAAAAA-TTATCAAAATC
* *
26549 ATATTAACAATTATCAAAAT
1 ATATAAAAAATTATCAAAAT
26569 TCTACCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (21 bp):
ATATAAAAAATTATCAAAATC
Found at i:26703 original size:21 final size:21
Alignment explanation
Indices: 26611--26703 Score: 71
Period size: 21 Copynumber: 4.4 Consensus size: 21
26601 TAATAAAAGC
*
26611 TTATCAAAATCACATTAAAAA
1 TTATCAAAATCATATTAAAAA
* * * *
26632 CTATTAAAATTATATTAAATA
1 TTATCAAAATCATATTAAAAA
* ** **
26653 TTATCAAAATCATTTTCGATG
1 TTATCAAAATCATATTAAAAA
*
26674 TTA-CTAAAATTATATTAAAAA
1 TTATC-AAAATCATATTAAAAA
26695 TTATCAAAA
1 TTATCAAAA
26704 GTTACCAAAA
Statistics
Matches: 52, Mismatches: 18, Indels: 4
0.70 0.24 0.05
Matches are distributed among these distances:
20 1 0.02
21 50 0.96
22 1 0.02
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.38
Consensus pattern (21 bp):
TTATCAAAATCATATTAAAAA
Found at i:26714 original size:21 final size:21
Alignment explanation
Indices: 26690--26734 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
26680 AAATTATATT
26690 AAAA-ATTATCAAAAGTTACCA
1 AAAATATTA-CAAAAGTTACCA
* *
26711 AAAATATTACAGAAGTTATCA
1 AAAATATTACAAAAGTTACCA
26732 AAA
1 AAA
26735 TAATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.24
Consensus pattern (21 bp):
AAAATATTACAAAAGTTACCA
Found at i:26768 original size:12 final size:11
Alignment explanation
Indices: 26745--26785 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
26735 TAATATAAAA
26745 ATATTAAAATT
1 ATATTAAAATT
26756 ATATTATAAA-T
1 ATATTA-AAATT
*
26767 -TATCAAAATT
1 ATATTAAAATT
26777 ATATTAAAA
1 ATATTAAAA
26786 GTTAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 3 0.12
10 5 0.20
11 14 0.56
12 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATTAAAATT
Found at i:26776 original size:21 final size:20
Alignment explanation
Indices: 26726--26796 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 20
26716 ATTACAGAAG
*
26726 TTATCAAAATAATA-TAAAA
1 TTATCAAAATTATATTAAAA
* *
26745 ATATTAAAATTATATTATAAA
1 TTATCAAAATTATATTA-AAA
26766 TTATCAAAATTATATTAAAA
1 TTATCAAAATTATATTAAAA
*
26786 GTTAACAAAAT
1 -TTATCAAAAT
26797 CATGCACCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 11 0.26
20 5 0.12
21 27 0.63
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (20 bp):
TTATCAAAATTATATTAAAA
Found at i:38608 original size:22 final size:22
Alignment explanation
Indices: 38580--38626 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
38570 GATTAAATGG
38580 TGATTTGGTAGTTTAGT-ATTGT
1 TGATTTGGTAGTTT-GTCATTGT
*
38602 TGATTTGGTGGTTTGTCATTGT
1 TGATTTGGTAGTTTGTCATTGT
38624 TGA
1 TGA
38627 CTAAATGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.15, C:0.02, G:0.30, T:0.53
Consensus pattern (22 bp):
TGATTTGGTAGTTTGTCATTGT
Found at i:38650 original size:34 final size:34
Alignment explanation
Indices: 38603--38751 Score: 176
Period size: 34 Copynumber: 4.4 Consensus size: 34
38593 TAGTATTGTT
*
38603 GATTTGGTGGTTTGTCATTGTTGACTAAATGAGA
1 GATTTGGTAGTTTGTCATTGTTGACTAAATGAGA
* * *
38637 GATTTGGTAGTTTG-CTATTGTTGATTAAATGGGT
1 GATTTGGTAGTTTGTC-ATTGTTGACTAAATGAGA
* *
38671 GATTTGGTGGTTTATCATTGTTGACTAAATGAGA
1 GATTTGGTAGTTTGTCATTGTTGACTAAATGAGA
* * * *
38705 GATTTGATAGTTTGACATTGTTGATTAAAT-AGGT
1 GATTTGGTAGTTTGTCATTGTTGACTAAATGA-GA
38739 GATTTGGTAGTTT
1 GATTTGGTAGTTT
38752 TTACCAAACC
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
33 2 0.02
34 93 0.97
35 1 0.01
ACGTcount: A:0.24, C:0.04, G:0.28, T:0.44
Consensus pattern (34 bp):
GATTTGGTAGTTTGTCATTGTTGACTAAATGAGA
Found at i:38716 original size:68 final size:68
Alignment explanation
Indices: 38602--38751 Score: 248
Period size: 68 Copynumber: 2.2 Consensus size: 68
38592 TTAGTATTGT
* *
38602 TGATTTGGTGGTTTGTCATTGTTGACTAAATGAGAGATTTGGTAGTTTG-CTATTGTTGATTAAA
1 TGATTTGGTGGTTTATCATTGTTGACTAAATGAGAGATTTGATAGTTTGAC-ATTGTTGATTAAA
*
38666 TGGG
65 TAGG
38670 TGATTTGGTGGTTTATCATTGTTGACTAAATGAGAGATTTGATAGTTTGACATTGTTGATTAAAT
1 TGATTTGGTGGTTTATCATTGTTGACTAAATGAGAGATTTGATAGTTTGACATTGTTGATTAAAT
38735 AGG
66 AGG
*
38738 TGATTTGGTAGTTT
1 TGATTTGGTGGTTT
38752 TTACCAAACC
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
68 76 0.99
69 1 0.01
ACGTcount: A:0.24, C:0.04, G:0.27, T:0.45
Consensus pattern (68 bp):
TGATTTGGTGGTTTATCATTGTTGACTAAATGAGAGATTTGATAGTTTGACATTGTTGATTAAAT
AGG
Found at i:39077 original size:19 final size:18
Alignment explanation
Indices: 39052--39112 Score: 86
Period size: 19 Copynumber: 3.3 Consensus size: 18
39042 GGTTGTCGAT
39052 GTACTATTCATGTATACG
1 GTACTATTCATGTATACG
*
39070 GATACTATTCATGTATATGG
1 G-TACTATTCATGTATA-CG
*
39090 GCACTATTCATGTATACG
1 GTACTATTCATGTATACG
39108 GTACT
1 GTACT
39113 GTGCACGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.16
19 29 0.78
20 2 0.05
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (18 bp):
GTACTATTCATGTATACG
Found at i:43219 original size:22 final size:22
Alignment explanation
Indices: 43191--43237 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
43181 TGATAAATGG
43191 TGATTTGATAGTTTGCCATTGT
1 TGATTTGATAGTTTGCCATTGT
* *
43213 TGATTTGGTGGTTTGCCATTGT
1 TGATTTGATAGTTTGCCATTGT
43235 TGA
1 TGA
43238 CTAAACGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.09, G:0.28, T:0.49
Consensus pattern (22 bp):
TGATTTGATAGTTTGCCATTGT
Found at i:43261 original size:34 final size:34
Alignment explanation
Indices: 43214--43362 Score: 199
Period size: 34 Copynumber: 4.4 Consensus size: 34
43204 TGCCATTGTT
*
43214 GATTTGGTGGTTTGCCATTGTTGACTAAACGAGA
1 GATTTGGTGGTTTGCCATTGTTGACTAAATGAGA
* * *
43248 GATTTGGTAGTTTGCCATTGTTGATTAAATGAGT
1 GATTTGGTGGTTTGCCATTGTTGACTAAATGAGA
*
43282 GATTTGGTGGTTTGCCATTGTTGACTAAATGAAA
1 GATTTGGTGGTTTGCCATTGTTGACTAAATGAGA
* * * * * *
43316 GATTTAGTAGTTTGCTATTGTTGATTAAATGGGT
1 GATTTGGTGGTTTGCCATTGTTGACTAAATGAGA
43350 GATTTGGTGGTTT
1 GATTTGGTGGTTT
43363 TTACCAAACT
Statistics
Matches: 98, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 98 1.00
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (34 bp):
GATTTGGTGGTTTGCCATTGTTGACTAAATGAGA
Found at i:43326 original size:68 final size:68
Alignment explanation
Indices: 43213--43362 Score: 255
Period size: 68 Copynumber: 2.2 Consensus size: 68
43203 TTGCCATTGT
* *
43213 TGATTTGGTGGTTTGCCATTGTTGACTAAACGAGAGATTTGGTAGTTTGCCATTGTTGATTAAAT
1 TGATTTGGTGGTTTGCCATTGTTGACTAAACGAAAGATTTAGTAGTTTGCCATTGTTGATTAAAT
43278 GAG
66 GAG
* *
43281 TGATTTGGTGGTTTGCCATTGTTGACTAAATGAAAGATTTAGTAGTTTGCTATTGTTGATTAAAT
1 TGATTTGGTGGTTTGCCATTGTTGACTAAACGAAAGATTTAGTAGTTTGCCATTGTTGATTAAAT
*
43346 GGG
66 GAG
43349 TGATTTGGTGGTTT
1 TGATTTGGTGGTTT
43363 TTACCAAACT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 77 1.00
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.43
Consensus pattern (68 bp):
TGATTTGGTGGTTTGCCATTGTTGACTAAACGAAAGATTTAGTAGTTTGCCATTGTTGATTAAAT
GAG
Found at i:44190 original size:17 final size:17
Alignment explanation
Indices: 44168--44201 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44158 GTAAATTAAG
* *
44168 TATTTATATTTTTATAA
1 TATTTAAATTTATATAA
44185 TATTTAAATTTATATAA
1 TATTTAAATTTATATAA
44202 ATGTTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTAAATTTATATAA
Found at i:44513 original size:18 final size:18
Alignment explanation
Indices: 44492--44533 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
44482 AAATAACTAT
44492 AGATATTTAAATTTTTGC
1 AGATATTTAAATTTTTGC
44510 AGATATTTAAATTTTTGC
1 AGATATTTAAATTTTTGC
*
44528 AAATAT
1 AGATAT
44534 ATAAGTTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (18 bp):
AGATATTTAAATTTTTGC
Found at i:51787 original size:20 final size:19
Alignment explanation
Indices: 51764--51810 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
51754 TAAATATATT
*
51764 TAATTATATATATATTAAAA
1 TAATTATA-ATAGATTAAAA
*
51784 TAATGATAATAGATTAAAA
1 TAATTATAATAGATTAAAA
51803 -AATT-TAAT
1 TAATTATAAT
51811 TAATCGAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 3 0.12
19 10 0.42
20 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
TAATTATAATAGATTAAAA
Found at i:52558 original size:2 final size:2
Alignment explanation
Indices: 52551--52579 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52541 GGCCATGGTA
52551 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
52580 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:52584 original size:2 final size:2
Alignment explanation
Indices: 52579--52625 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
52569 TCTCTCTCTC
* * *
52579 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52621 T- TA TA
1 TA TA TA
52626 GGGTGGCTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53697 original size:12 final size:12
Alignment explanation
Indices: 53663--53710 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
53653 TTGAAATATC
53663 TGTATATTTAAAA
1 TGTATATTT-AAA
*
53676 TTTATA-TTAAA
1 TGTATATTTAAA
53687 TGTATATTTAAA
1 TGTATATTTAAA
* *
53699 TATAAATTTAAA
1 TGTATATTTAAA
53711 AATATAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 8 0.27
12 17 0.57
13 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (12 bp):
TGTATATTTAAA
Found at i:53709 original size:24 final size:24
Alignment explanation
Indices: 53663--53710 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
53653 TTGAAATATC
**
53663 TGTATATTTAAAATTTATATTAAA
1 TGTATATTTAAAATAAATATTAAA
53687 TGTATATTTAAATATAAAT-TTAAA
1 TGTATATTTAAA-ATAAATATTAAA
53711 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
TGTATATTTAAAATAAATATTAAA
Found at i:53772 original size:22 final size:20
Alignment explanation
Indices: 53735--53774 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
53725 TAAATTTTTT
*
53735 TAAATATATATTTTAAAAAA
1 TAAATATATATATTAAAAAA
53755 TAAATATATTTATATTAAAA
1 TAAATATA--TATATTAAAA
53775 TTTGAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATATATATATTAAAAAA
Found at i:54503 original size:3 final size:3
Alignment explanation
Indices: 54495--54525 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
54485 TTAAATAAAA
54495 ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
54526 CTAAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:54537 original size:52 final size:51
Alignment explanation
Indices: 54442--54541 Score: 116
Period size: 53 Copynumber: 1.9 Consensus size: 51
54432 ATATTAAAAT
*
54442 AATTATTTTAATATTAATATTTATATATTTTTATAATTAAATTTTAAATAAA
1 AATTATTTTAATATTAATATTTATATATTTCTATAATTAAA-TTTAAATAAA
* *
54494 AATTATTATTATTATTATTA-TTATATTATTATCTA-AATT-AATTTAAAT
1 AATTATT-TTAATATTAATATTTATA-TATT-TCTATAATTAAATTTAAAT
54542 TATTAAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
51 7 0.17
52 14 0.33
53 18 0.43
54 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (51 bp):
AATTATTTTAATATTAATATTTATATATTTCTATAATTAAATTTAAATAAA
Found at i:55896 original size:27 final size:28
Alignment explanation
Indices: 55860--55912 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
55850 TATAAATTTT
*
55860 AAAATATTAATA-ATTCGTATTATATAA
1 AAAATATTAATATATTCATATTATATAA
*
55887 AAAATTTTAATATATTCATATTATAT
1 AAAATATTAATATATTCATATTATAT
55913 TTATATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (28 bp):
AAAATATTAATATATTCATATTATATAA
Found at i:55921 original size:5 final size:5
Alignment explanation
Indices: 55897--55947 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
55887 AAAATTTTAA
* *
55897 TATAT TCATAT TATATT TATAT TAT-T T-TAT TATAT TATAT TGTGT TATAT
1 TATAT T-ATAT TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT
55947 T
1 T
55948 GTAACCGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 23 0.61
6 10 0.26
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (5 bp):
TATAT
Found at i:62846 original size:22 final size:22
Alignment explanation
Indices: 62820--62878 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
62810 ATAAAAATAA
62820 AAATATATTATTTGTTAATTATT
1 AAATATATTATTT-TTAATTATT
* * *
62843 -AATATTTTATTTTTATTTTTT
1 AAATATATTATTTTTAATTATT
*
62864 AAAAATATTATTTTT
1 AAATATATTATTTTT
62879 TATTTTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
AAATATATTATTTTTAATTATT
Found at i:63151 original size:22 final size:23
Alignment explanation
Indices: 63120--63174 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
63110 TTAAAATATT
* *
63120 TTAATAAAATTTTAA-TTTAATAA
1 TTAATTAAATTATAATTTTAA-AA
63143 -TAATTAAA-TATAATTTTAAAA
1 TTAATTAAATTATAATTTTAAAA
63164 TTAATTAAATT
1 TTAATTAAATT
63175 CTTGTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 6 0.22
22 20 0.74
23 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAATTAAATTATAATTTTAAAA
Found at i:63174 original size:27 final size:27
Alignment explanation
Indices: 63104--63168 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
63094 AATACATGCA
* *
63104 TTTAAATTAA-AATATTTTAATAAAAT
1 TTTAAATTAATAATAATTAAATAAAAT
* *
63130 TTTAATTTAATAATAATTAAATATAAT
1 TTTAAATTAATAATAATTAAATAAAAT
63157 TTTAAAATTAAT
1 TTT-AAATTAAT
63169 TAAATTCTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 9 0.28
27 16 0.50
28 7 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTTAAATTAATAATAATTAAATAAAAT
Found at i:64932 original size:6 final size:6
Alignment explanation
Indices: 64921--64952 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
64911 TAGATTGCAC
64921 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
64953 GGACAAGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.69, G:0.00, T:0.16
Consensus pattern (6 bp):
CCTCCA
Found at i:65077 original size:2 final size:2
Alignment explanation
Indices: 65070--65099 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
65060 AAAGACTTCG
65070 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
65100 AAGGAAAGTT
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):
TA
Found at i:65126 original size:9 final size:9
Alignment explanation
Indices: 65112--65139 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
65102 GGAAAGTTAG
65112 AAATTTGAA
1 AAATTTGAA
65121 AAATTTGAA
1 AAATTTGAA
65130 AAATTTGAA
1 AAATTTGAA
65139 A
1 A
65140 TGAAGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (9 bp):
AAATTTGAA
Found at i:68425 original size:253 final size:253
Alignment explanation
Indices: 67975--68460 Score: 755
Period size: 253 Copynumber: 1.9 Consensus size: 253
67965 AATAGTGAAG
67975 ACATCTAATGTTAGAACACCTGTAAGAATCAGAGCTGCCCAGGACTGGGCCATAGTGGATTTGAT
1 ACATCTAATGTTAGAACACCTGTAAGAATCAGAGCTGCCCAGGACTGGGCCATAGTGGATTTGAT
*
68040 TTGTGATATCATGAACCTCTGTACTCATTTCAATTCAATCAAGGCAATGTTGTGCTCTACAACTC
66 TTGTGATATCATGAACCTCTGTACTCATTTCAATTCAATCAAAGCAATGTTGTGCTCTACAACTC
* ** * *
68105 ATTTTGTGGGTTATTATCCCCTTGAGGTGTCTTGCTAGTTTTCACGTCTGTTGTGGGGTCCAAGT
131 ATTTTGTGGGTTACTATCCCCTCAAGGTGTCTTGCTACTTTTCACGCCTGTTGTGGGGTCCAAGT
68170 TTTCTTGCATCTTTTGGTCATATTATGAAATACCATTGTGATTTTGATTTGTTAGAAC
196 TTTCTTGCATCTTTTGGTCATATTATGAAATACCATTGTGATTTTGATTTGTTAGAAC
** * *
68228 ACATCTAATGTTAGAACACCTGTAAGAATTGGAGCTGCCCGGGACTGGGCCATAGT-TATTTTGA
1 ACATCTAATGTTAGAACACCTGTAAGAATCAGAGCTGCCCAGGACTGGGCCATAGTGGA-TTTGA
* *
68292 TTTGTGAT-GCTATGAACCTCTGCT-CTTATTTCAATTCAATCAAAGCAATGTTGTGCTCTACAA
65 TTTGTGATATC-ATGAACCTCTG-TACTCATTTCAATTCAATCAAAGCAATGTTGTGCTCTACAA
* * *
68355 CTCA-TTTGTGGGTTACTATCTCCTCAAGGGTGTCTTGCTACTTTTCATGCCTGTTGTGGGGTCT
128 CTCATTTTGTGGGTTACTATCCCCTCAA-GGTGTCTTGCTACTTTTCACGCCTGTTGTGGGGTCC
* *
68419 AAGTTTTCTTGTATCTTTTGGTCCTATTATGAAATACCATTG
192 AAGTTTTCTTGCATCTTTTGGTCATATTATGAAATACCATTG
68461 CATCTAGGTG
Statistics
Matches: 212, Mismatches: 17, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
252 21 0.10
253 190 0.90
254 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (253 bp):
ACATCTAATGTTAGAACACCTGTAAGAATCAGAGCTGCCCAGGACTGGGCCATAGTGGATTTGAT
TTGTGATATCATGAACCTCTGTACTCATTTCAATTCAATCAAAGCAATGTTGTGCTCTACAACTC
ATTTTGTGGGTTACTATCCCCTCAAGGTGTCTTGCTACTTTTCACGCCTGTTGTGGGGTCCAAGT
TTTCTTGCATCTTTTGGTCATATTATGAAATACCATTGTGATTTTGATTTGTTAGAAC
Found at i:70958 original size:25 final size:25
Alignment explanation
Indices: 70929--70988 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
70919 CAATATTATA
*
70929 ATCAAATGTTTACGTAGATTTAATT
1 ATCAAATATTTACGTAGATTTAATT
70954 ATCAAATATTTACGTAGATTTAATT
1 ATCAAATATTTACGTAGATTTAATT
70979 ATCAAATATT
1 ATCAAATATT
70989 ATCATAAGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.43
Consensus pattern (25 bp):
ATCAAATATTTACGTAGATTTAATT
Found at i:78191 original size:18 final size:19
Alignment explanation
Indices: 78163--78198 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
78153 TACTCTCTCT
78163 TTTTCTTCTTTTTTTTTTA
1 TTTTCTTCTTTTTTTTTTA
78182 TTTT-TTCTTTTTTTTTT
1 TTTTCTTCTTTTTTTTTT
78199 GGTTGATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (19 bp):
TTTTCTTCTTTTTTTTTTA
Found at i:80045 original size:2 final size:2
Alignment explanation
Indices: 80033--80061 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
80023 AATATTACTG
80033 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80062 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80066 original size:2 final size:2
Alignment explanation
Indices: 80061--80090 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
80051 TATATATATA
80061 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
80091 CATGGTTAAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:80543 original size:20 final size:20
Alignment explanation
Indices: 80505--80543 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
80495 GTATTTTTTT
*
80505 TATTATAATTATATTTAAAA
1 TATTATAATTATATATAAAA
80525 TATTATATATT-TATATAAA
1 TATTATA-ATTATATATAAA
80544 TTTTAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAATTATATATAAAA
Found at i:80606 original size:5 final size:5
Alignment explanation
Indices: 80564--80653 Score: 71
Period size: 5 Copynumber: 18.0 Consensus size: 5
80554 TTTATATTTA
* * * * *
80564 ATATC ATATT A-ATT TTAAT ATATT CATATA ATATTT ATATT ATTTTT
1 ATATT ATATT ATATT ATATT ATATT -ATATT ATA-TT ATATT A-TATT
80611 ATATT ATATT ATATT ATATT ATATT -TATT -T-TT AATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT -ATATT ATATT
80654 TATACCATAT
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
3 2 0.03
4 8 0.12
5 45 0.65
6 14 0.20
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:80625 original size:52 final size:49
Alignment explanation
Indices: 80496--80634 Score: 122
Period size: 52 Copynumber: 2.7 Consensus size: 49
80486 ATTTTATTAG
*
80496 TATT-TTTTT-TATTATAATTATATTTAAAATATTATATATTTATATAAATTT
1 TATTATTTTTATATTAT-ATTATA-TT--AATATTATATATTCATATAAATTT
* ** * *
80547 TAATAAATTTATATTTAATATCATATTAATTTTAATATATTCATATAATATTT
1 TATTATTTTTATA-TT-ATATTATATTAATATT-ATATATTCATATAA-ATTT
80600 ATATTATTTTTATATTATATTATATT-ATATTATAT
1 -TATTATTTTTATATTATATTATATTAATATTATAT
80635 TTATTTTTAA
Statistics
Matches: 70, Mismatches: 11, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
50 4 0.06
51 12 0.17
52 25 0.36
53 10 0.14
54 17 0.24
55 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (49 bp):
TATTATTTTTATATTATATTATATTAATATTATATATTCATATAAATTT
Found at i:80635 original size:28 final size:29
Alignment explanation
Indices: 80564--80653 Score: 75
Period size: 28 Copynumber: 3.2 Consensus size: 29
80554 TTTATATTTA
* * *
80564 ATATCATATTA-ATTTTAATATATTCATATA
1 ATATTATATTATATTTT--TATATTAATATT
80594 ATATT-TA-TATTATTTTTATATT-ATATT
1 ATATTATATTA-TATTTTTATATTAATATT
80621 ATATTATATTATATTTATT-T-TTAATATT
1 ATATTATATTATATTT-TTATATTAATATT
80649 ATATT
1 ATATT
80654 TATACCATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
27 11 0.21
28 26 0.50
29 6 0.12
30 9 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
ATATTATATTATATTTTTATATTAATATT
Found at i:80648 original size:33 final size:33
Alignment explanation
Indices: 80569--80674 Score: 112
Period size: 31 Copynumber: 3.2 Consensus size: 33
80559 ATTTAATATC
*
80569 ATATTAATTTTA-A-TATATTCATATAATATTT
1 ATATTATTTTTATATTATATTCATATAATATTT
*
80600 ATATTATTTTTATATTATATT-ATATTATA-TT
1 ATATTATTTTTATATTATATTCATATAATATTT
* **
80631 ATATTTATTTTTAATATTATATTTATACCATATTT
1 ATA-TTATTTTT-ATATTATATTCATATAATATTT
80666 CATATTATT
1 -ATATTATT
80675 AAGTCATACG
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
31 16 0.25
32 16 0.25
33 16 0.25
34 6 0.09
35 7 0.11
36 3 0.05
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (33 bp):
ATATTATTTTTATATTATATTCATATAATATTT
Found at i:80649 original size:18 final size:17
Alignment explanation
Indices: 80598--80656 Score: 79
Period size: 18 Copynumber: 3.6 Consensus size: 17
80588 CATATAATAT
80598 TTATA-TTATTTTTATA
1 TTATATTTATTTTTATA
*
80614 TTATA-TTA-TATTATA
1 TTATATTTATTTTTATA
80629 TTATATTTATTTTTAATA
1 TTATATTTATTTTT-ATA
80647 TTATATTTAT
1 TTATATTTAT
80657 ACCATATTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.29
16 11 0.29
17 3 0.08
18 13 0.34
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATATTTATTTTTATA
Found at i:80670 original size:23 final size:22
Alignment explanation
Indices: 80582--80673 Score: 89
Period size: 23 Copynumber: 4.1 Consensus size: 22
80572 TTAATTTTAA
* *
80582 TATATTCATATAATATTTATAT
1 TATATTTATATTATATTTATAT
*
80604 TATTTTTATATTATA-TTATAT
1 TATATTTATATTATATTTATAT
*
80625 TATA-TTATATTTATTTTTAATAT
1 TATATTTATA-TTATATTT-ATAT
**
80648 TATATTTATACCATATTTCATAT
1 TATATTTATATTATATTT-ATAT
80671 TAT
1 TAT
80674 TAAGTCATAC
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
20 5 0.09
21 13 0.23
22 14 0.25
23 20 0.35
24 5 0.09
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TATATTTATATTATATTTATAT
Found at i:81330 original size:2 final size:2
Alignment explanation
Indices: 81325--81369 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
81315 GAATGGAAAT
* * *
81325 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA GA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81367 TA T
1 TA T
81370 GCATTCAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:83974 original size:14 final size:14
Alignment explanation
Indices: 83932--83980 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
83922 GCTTCAGCTC
83932 AAATTAAAT-T-TT
1 AAATTAAATATATT
* *
83944 AAAAATAATTATA-T
1 -AAATTAAATATATT
83958 AAATTAAATATATT
1 AAATTAAATATATT
83972 AAATTAAAT
1 AAATTAAAT
83981 TTCAAAGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTAAATATATT
Found at i:84780 original size:159 final size:157
Alignment explanation
Indices: 84487--84802 Score: 596
Period size: 159 Copynumber: 2.0 Consensus size: 157
84477 ATTCACATTA
84487 ATTTGACTTCAGAAATGACAAAAAAGATTTTGGTCCCCACTGGGAAAGCATTTTGCCATGTTTTA
1 ATTTGACTTCAGAAATGACAAAAAAGATTTTGGTCCCCACTGGGAAAGCATTTTGCCATGTTTTA
84552 GCTTAAGAAAGAACTTCATTTTCTGATTCACCTTAGCAAATGGGTGTTGTTAAGATCCCTTTCAT
66 GCTTAAGAAAGAACTTCATTTTCTGATTCACCTTAGCAAATGGGTGTTGTTAAGATCCCTTTCA-
*
84617 TTTTTTTTTGCATTAACCAATTTCGTTT
130 ATTTTTTTTGCATTAACCAATTTCGTTT
84645 ATTTGACTTCAGAAAATGACAAAAAAGATTTTGGTCCCCACTGGGAAAGCATTTTGCCATGTTTT
1 ATTTGACTTCAG-AAATGACAAAAAAGATTTTGGTCCCCACTGGGAAAGCATTTTGCCATGTTTT
*
84710 AGCTTAAGAAAGAACTTCATTTTCTGATTCCCCTTAGCAAATGGGTGTTGTTAAGATCCCTTTCA
65 AGCTTAAGAAAGAACTTCATTTTCTGATTCACCTTAGCAAATGGGTGTTGTTAAGATCCCTTTCA
84775 ATTTTTTTTGCATTAACCAATTTCGTTT
130 ATTTTTTTTGCATTAACCAATTTCGTTT
84803 TCTCACTTTA
Statistics
Matches: 155, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
158 39 0.25
159 116 0.75
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (157 bp):
ATTTGACTTCAGAAATGACAAAAAAGATTTTGGTCCCCACTGGGAAAGCATTTTGCCATGTTTTA
GCTTAAGAAAGAACTTCATTTTCTGATTCACCTTAGCAAATGGGTGTTGTTAAGATCCCTTTCAA
TTTTTTTTGCATTAACCAATTTCGTTT
Found at i:85489 original size:16 final size:17
Alignment explanation
Indices: 85456--85488 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
85446 AACAAGAATG
85456 CCAGTAAAAAAACAAAA
1 CCAGTAAAAAAACAAAA
85473 CCAG-AAAAAGAACAAA
1 CCAGTAAAAA-AACAAA
85489 CATGAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.70, C:0.18, G:0.09, T:0.03
Consensus pattern (17 bp):
CCAGTAAAAAAACAAAA
Found at i:85988 original size:37 final size:38
Alignment explanation
Indices: 85905--85990 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 38
85895 ATTATATATT
* *
85905 TATTTAAACTTTTTAAATACATTTCTTATATTATATCA
1 TATTTATATTTTTTAAATACATTTCTTATATTATATCA
85943 TATTTATATTTTTTAAA-ACATTTCTTATATTATATCA
1 TATTTATATTTTTTAAATACATTTCTTATATTATATCA
85980 TATTTATATTT
1 TATTTATATTT
85991 CAATTATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 31 0.67
38 15 0.33
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (38 bp):
TATTTATATTTTTTAAATACATTTCTTATATTATATCA
Found at i:86585 original size:20 final size:20
Alignment explanation
Indices: 86534--86586 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
86524 AACTATGACG
*
86534 TATAAC-ATAATTTAAAAAT
1 TATAACAATAATATAAAAAT
* *
86553 TATAACAAAAATATAATAAT
1 TATAACAATAATATAAAAAT
86573 TATCAA-AATAATAT
1 TAT-AACAATAATAT
86587 GTTTAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.21
20 20 0.71
21 2 0.07
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (20 bp):
TATAACAATAATATAAAAAT
Found at i:86914 original size:41 final size:41
Alignment explanation
Indices: 86830--86907 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
86820 ATATTTATAT
* * *
86830 AATTAAAATTAAATAAAAATATTTTTTATTATTTAATGATA
1 AATTAAAATTAAATAAAAATATTATTTATCAATTAATGATA
86871 AATT-AAATTAAATAAAAAAATATTATTTA-CAATTAAT
1 AATTAAAATTAAAT--AAAAATATTATTTATCAATTAAT
86908 TTTAAATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 9 0.28
41 10 0.31
42 13 0.41
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (41 bp):
AATTAAAATTAAATAAAAATATTATTTATCAATTAATGATA
Found at i:87373 original size:2 final size:2
Alignment explanation
Indices: 87366--87402 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
87356 CCATAGTAAA
87366 AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
87403 GCTTTTCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:87896 original size:20 final size:19
Alignment explanation
Indices: 87873--87911 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
87863 TATTTTTATA
87873 ATTAAATTAAATAAAAATTT
1 ATTAAA-TAAATAAAAATTT
* *
87893 ATTATATAAATAATAATTT
1 ATTAAATAAATAAAAATTT
87912 GAATTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTAAATAAATAAAAATTT
Found at i:87935 original size:25 final size:26
Alignment explanation
Indices: 87890--87955 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 26
87880 TAAATAAAAA
* *
87890 TTTATTATATAAATAATAATTTGAAT
1 TTTATTAAATAAATAATAATTTAAAT
87916 TTTATTAAAT-AA-AATCAATTTAAA-
1 TTTATTAAATAAATAAT-AATTTAAAT
87940 -TTATTAAAATAAATAA
1 TTTATT-AAATAAATAA
87956 ATATATGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 5 0.15
24 7 0.21
25 11 0.32
26 11 0.32
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
TTTATTAAATAAATAATAATTTAAAT
Done.