Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold547
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: 184368
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:152218 original size:20 final size:20
Alignment explanation
Indices: 152186--152239 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
152176 CCTTTACACC
152186 CAAAA-AAACAAAACAAAAAA
1 CAAAACAAA-AAAACAAAAAA
**
152206 CAAAACAAAAAAATTTAAAAA
1 CAAAACAAAAAAA-CAAAAAA
152227 -AAAACAAAAAAAC
1 CAAAACAAAAAAAC
152240 CAAGAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.81, C:0.13, G:0.00, T:0.06
Consensus pattern (20 bp):
CAAAACAAAAAAACAAAAAA
Found at i:152237 original size:12 final size:12
Alignment explanation
Indices: 152187--152238 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
152177 CTTTACACCC
152187 AAAAAAACAAAA
1 AAAAAAACAAAA
*
152199 CAAAAAACAAAA
1 AAAAAAACAAAA
***
152211 CAAAAAAATTTAA
1 -AAAAAAACAAAA
152224 AAAAAAACAAAA
1 AAAAAAACAAAA
152236 AAA
1 AAA
152239 CCAAGAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
12 23 0.74
13 8 0.26
ACGTcount: A:0.85, C:0.10, G:0.00, T:0.06
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:153519 original size:29 final size:29
Alignment explanation
Indices: 153479--154431 Score: 1180
Period size: 29 Copynumber: 32.9 Consensus size: 29
153469 TGTTCATCCC
*
153479 TTTCAAAGCCCACAAGTCAGTAGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
153508 TTTCAAAGCCCACGAGCCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
153536 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
153565 TTTCAAAGCCCAAAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153594 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
153622 TTTCAAAGCTCATAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153651 TTTCAAAGCCCACAAGTCAGT-GCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153679 TTTCAAAGCCCACAAGTCAGTGGCACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153708 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
153736 TTTCAAAGCCCACAAGTTAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153765 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
153794 TTTCAAAGCCCACAAATTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
153823 TCTCAAAGCCCACAAGTAAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153851 TTTCAAAGCCCACAATTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
153880 TTTCAAAGCCCACAAGTGAGTGGTACAC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
153908 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
153937 TTTCAAAGCTCACACGAGTCGGTGGCAACTCT
1 TTTCAAAGC-C-CACAAGTCAGTGGC-ACTCT
153969 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
153998 TTTCAAAGCCCACAAGTTAGTAGTAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154026 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154054 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
154082 TTTCAAAACCCATGCAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCT
* * *
154112 TTTCAAAGCCCACAAATGAATGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154141 TTTCAAAGCCCACAAGTCAGTGGCACTAT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
154170 TTTCAAAGCCCACAAGTTAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154198 TTTCAAAGCCCATAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
154226 TTTCAAAGCCCACGTAAATCAATGGCACCCT
1 TTTCAAAGCCCAC--AAGTCAGTGGCACTCT
*
154257 TCT-AAAGCCCACGTAAGTCAGTGGCAC-CT
1 TTTCAAAGCCCAC--AAGTCAGTGGCACTCT
* * *
154286 TTTTAAAGCCCACAAGTTAGTGGCACTCA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154315 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
154343 TTTCAAAGCCCACAAGTCAGTGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
**
154372 TTTCAAAGCCCACACGAGTTGGTGGCAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGC-ACTCT
*
154404 TTTCAAAGCCCACATAAGTTAGTGGCAC
1 TTTCAAAGCCCAC--AAGTCAGTGGCAC
154432 CATTTTAAAA
Statistics
Matches: 814, Mismatches: 84, Indels: 50
0.86 0.09 0.05
Matches are distributed among these distances:
28 300 0.37
29 366 0.45
30 83 0.10
31 23 0.03
32 41 0.05
34 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:153564 original size:57 final size:58
Alignment explanation
Indices: 153477--154431 Score: 1170
Period size: 57 Copynumber: 16.5 Consensus size: 58
153467 AATGTTCATC
* * * *
153477 CCTTTCAAAGCCCACAAGTCAGTAGCACTCTTTTCAAAGCCCACGAGCCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
153534 CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCAAAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
153592 CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCTCATAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
153649 CCTTTCAAAGCCCACAAGTCAGT-GCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
** *
153706 TTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
153763 CCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAATTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
153821 -CTTCTCAAAGCCCACAAGTAAGTGGCAC-CCTTTCAAAGCCCACAATTCAGTGGCACT
1 CCTT-TCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * *
153878 CTTTTCAAAGCCCACAAGTGAGTGGTAC-ACTTTCAAAGCCCACAAGTTAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
153935 CTTTTCAAAGCTCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGC-C-CACAAGTCAGTGGC-ACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
153996 CTTTTCAAAGCCCACAAGTTAGTAGTAC-CCTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
*
154052 CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAACCCATGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* * * *
154110 CCTTTCAAAGCCCACAAATGAATGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
** * *
154168 ATTTTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCCATAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
154225 -CTTTCAAAGCCCACGTAAATCAATGGCAC-CC-TTCTAAAGCCCACGTAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCAC--AAGTCAGTGGCACTCCTTTC-AAAGCCCAC--AAGTCAGTGGCACT
* * * *
154284 CTTTTTAAAGCCCACAAGTTAGTGGCACTCATTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
* * **
154341 CCTTTCAAAGCCCACAAGTCAGTGACACTCTTTTCAAAGCCCACACGAGTTGGTGGCAACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA--AGTCAGTGGC-ACT
* *
154402 CTTTTCAAAGCCCACATAAGTTAGTGGCAC
1 CCTTTCAAAGCCCAC--AAGTCAGTGGCAC
154432 CATTTTAAAA
Statistics
Matches: 786, Mismatches: 82, Indels: 54
0.85 0.09 0.06
Matches are distributed among these distances:
56 55 0.07
57 412 0.52
58 175 0.22
59 49 0.06
60 33 0.04
61 51 0.06
63 11 0.01
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (58 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:153624 original size:86 final size:87
Alignment explanation
Indices: 153479--154431 Score: 1189
Period size: 86 Copynumber: 11.0 Consensus size: 87
153469 TGTTCATCCC
* * * * *
153479 TTTCAAAGCCCACAAGTCAGTAGCACTCTTTTCAAAGCCCACGAGCCAGTGGCAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
153543 GCCCACAAGTCAGTGGCACTCT
66 GCCCACAAGTCAGTGGCACTCT
* * * *
153565 TTTCAAAGCCCAAAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * *
153629 GCTCATAAGTCAGTGGCACTCC
66 GCCCACAAGTCAGTGGCACTCT
*
153651 TTTCAAAGCCCACAAGTCAGT-GCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTTTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
153715 GCCCACAAGTCAGTGGCAC-CC
66 GCCCACAAGTCAGTGGCACTCT
* *
153736 TTTCAAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* *
153801 GCCCACAAATTAGTGGCACTCT
66 GCCCACAAGTCAGTGGCACTCT
* * *
153823 TCTCAAAGCCCACAAGTAAGTGGCAC-CCTTTCAAAGCCCACAATTCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * *
153887 GCCCACAAGTGAGTGGTACAC-
66 GCCCACAAGTCAGTGGCACTCT
* * * *
153908 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCTCACACGAGTCGGTGGCAACTCTTTTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC-C-CACAAGTCAGTGGC-ACTCTTTTC
153973 AAAGCCCACAAGTCAGTGGCACTCT
63 AAAGCCCACAAGTCAGTGGCACTCT
* * * *
153998 TTTCAAAGCCCACAAGTTAGTAGTAC-CCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
154061 GCCCACAAGTCAGTGGCAC-CC
66 GCCCACAAGTCAGTGGCACTCT
* * * *
154082 TTTCAAAACCCATGCAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAATGAATGGCACTCTTTTCA
1 TTTCAAAGCCCA--CAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
*
154146 AAGCCCACAAGTCAGTGGCACTAT
64 AAGCCCACAAGTCAGTGGCACTCT
* *
154170 TTTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCCATAAGTCAGTGGCACTC-TTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * *
154233 GCCCACGTAAATCAATGGCACCCT
66 GCCCAC--AAGTCAGTGGCACTCT
* * * * *
154257 TCT-AAAGCCCACGTAAGTCAGTGGCAC-CTTTTTAAAGCCCACAAGTTAGTGGCACTCATTTCA
1 TTTCAAAGCCCAC--AAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCA
*
154320 AAGCCCACAAGTCAGTGGCAC-CC
64 AAGCCCACAAGTCAGTGGCACTCT
* * **
154343 TTTCAAAGCCCACAAGTCAGTGACACTCTTTTCAAAGCCCACACGAGTTGGTGGCAACTCTTTTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA--AGTCAGTGGC-ACTCTTTTC
*
154408 AAAGCCCACATAAGTTAGTGGCAC
63 AAAGCCCAC--AAGTCAGTGGCAC
154432 CATTTTAAAA
Statistics
Matches: 761, Mismatches: 80, Indels: 47
0.86 0.09 0.05
Matches are distributed among these distances:
84 12 0.02
85 131 0.17
86 343 0.45
87 100 0.13
88 69 0.09
89 70 0.09
90 24 0.03
91 12 0.02
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (87 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
GCCCACAAGTCAGTGGCACTCT
Found at i:155018 original size:20 final size:20
Alignment explanation
Indices: 154990--155064 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
154980 TTTTACCCAG
154990 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
155010 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
155030 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
155050 ATGTATCGATACATT
1 ATGTATCGATACATT
155065 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:155050 original size:40 final size:39
Alignment explanation
Indices: 154990--155067 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
154980 TTTTACCCAG
*
154990 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
155030 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
155068 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:158536 original size:11 final size:11
Alignment explanation
Indices: 158494--158536 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
158484 GCAGGCAAAG
158494 AAAAGGAAGAAA
1 AAAAGGAA-AAA
*
158506 AAAATGAAAAA
1 AAAAGGAAAAA
*
158517 AAAAAGAAAAA
1 AAAAGGAAAAA
*
158528 GAAAGGAAA
1 AAAAGGAAA
158537 TGAGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 20 0.74
12 7 0.26
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAGGAAAAA
Found at i:158619 original size:19 final size:19
Alignment explanation
Indices: 158591--158655 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
158581 TATTATTTAA
158591 AATA-TTATAAATTTATAT
1 AATATTTATAAATTTATAT
*
158609 AATATTTATAAATATT-TTT
1 AATATTTATAAAT-TTATAT
* * *
158628 TATATTTGTATATTTATAT
1 AATATTTATAAATTTATAT
*
158647 TATATTTAT
1 AATATTTAT
158656 TTTTATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 6 0.16
19 30 0.79
20 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
AATATTTATAAATTTATAT
Found at i:158662 original size:15 final size:15
Alignment explanation
Indices: 158611--158668 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 15
158601 ATTTATATAA
*
158611 TATTTATA-AATATT
1 TATTTATATTATATT
* *
158625 T-TTTATATT-TGTA
1 TATTTATATTATATT
158638 TATTTATATTATATT
1 TATTTATATTATATT
*
158653 TATTTTTATTATATT
1 TATTTATATTATATT
158668 T
1 T
158669 TAATTAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
13 9 0.26
14 9 0.26
15 17 0.49
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTTATATTATATT
Found at i:158666 original size:20 final size:21
Alignment explanation
Indices: 158641--158681 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
158631 ATTTGTATAT
*
158641 TTATATTAT-ATTTATTTTTA
1 TTATATTATAATTAATTTTTA
*
158661 TTATATTTTAATTAATTTTTA
1 TTATATTATAATTAATTTTTA
158682 ATGTTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATATTATAATTAATTTTTA
Found at i:159526 original size:15 final size:15
Alignment explanation
Indices: 159491--159536 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
159481 AGAGAAAGAT
159491 ATGA-AAAGAAAAAA
1 ATGAGAAAGAAAAAA
**
159505 AAAAGAAA-AAGAAAA
1 ATGAGAAAGAA-AAAA
159520 ATGAGAAAGAAAAAA
1 ATGAGAAAGAAAAAA
159535 AT
1 AT
159537 TGTGTATAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
14 4 0.16
15 19 0.76
16 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (15 bp):
ATGAGAAAGAAAAAA
Found at i:159528 original size:13 final size:13
Alignment explanation
Indices: 159494--159534 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
159484 GAAAGATATG
159494 AAAAGA-AAA-AA
1 AAAAGAGAAAGAA
*
159505 AAAAGAAAAAGAA
1 AAAAGAGAAAGAA
*
159518 AAATGAGAAAGAA
1 AAAAGAGAAAGAA
159531 AAAA
1 AAAA
159535 ATTGTGTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 6 0.24
12 3 0.12
13 16 0.64
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAAGAGAAAGAA
Found at i:159623 original size:13 final size:15
Alignment explanation
Indices: 159603--159636 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
159593 ATATTCGTAA
159603 ATTTTTTTGTGTT-T
1 ATTTTTTTGTGTTAT
159617 ATTTTTTTGTGTTAT
1 ATTTTTTTGTGTTAT
159632 ATTTT
1 ATTTT
159637 AATTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (15 bp):
ATTTTTTTGTGTTAT
Found at i:159930 original size:25 final size:23
Alignment explanation
Indices: 159870--159914 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
159860 TCGTGTAACT
159870 GTATCGTGTTAATGTTATTTTTC
1 GTATCGTGTTAATGTTATTTTTC
159893 GTATCGTGTTAATGTTATTTTT
1 GTATCGTGTTAATGTTATTTTT
159915 TGTACTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.07, G:0.18, T:0.58
Consensus pattern (23 bp):
GTATCGTGTTAATGTTATTTTTC
Found at i:160340 original size:12 final size:12
Alignment explanation
Indices: 160318--160371 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
160308 CATAGGAGAG
160318 AAAGAAAAAA-A
1 AAAGAAAAAAGA
*
160329 AGAAGAGGAAAAGA
1 A-AAGA-AAAAAGA
160343 AAAGAAAAAAG-
1 AAAGAAAAAAGA
160354 -AA-AAAAAAGA
1 AAAGAAAAAAGA
160364 AAAGAAAA
1 AAAGAAAA
160372 TTTTTTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
9 7 0.20
10 2 0.06
11 3 0.09
12 13 0.37
13 8 0.23
14 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAGA
Found at i:160346 original size:5 final size:5
Alignment explanation
Indices: 160318--160371 Score: 58
Period size: 5 Copynumber: 10.6 Consensus size: 5
160308 CATAGGAGAG
*
160318 AAAGA AAA-A AAAGA AGAGGA AAAGA AAAGAAA AAAGA AAA-A AAAGA
1 AAAGA AAAGA AAAGA A-AAGA AAAGA AAAG--A AAAGA AAAGA AAAGA
160364 AAAGA AAA
1 AAAGA AAA
160372 TTTTTTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
4 8 0.19
5 25 0.60
6 4 0.10
7 5 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:160359 original size:14 final size:14
Alignment explanation
Indices: 160318--160371 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
160308 CATAGGAGAG
160318 AAAGAAAAAAAAGA
1 AAAGAAAAAAAAGA
*
160332 AGAGGAAAAGAAAAGAAA
1 A-AAGAAAA-AAAAG--A
160350 AAAGAAAAAAAAGA
1 AAAGAAAAAAAAGA
160364 AAAGAAAA
1 AAAGAAAA
160372 TTTTTTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 10 0.29
15 6 0.18
16 10 0.29
17 6 0.18
18 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAGA
Found at i:160360 original size:20 final size:22
Alignment explanation
Indices: 160318--160371 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
160308 CATAGGAGAG
**
160318 AAAGAAAA-AAAAGAAG-AGGA
1 AAAGAAAAGAAAAGAAGAAAAA
160338 AAAGAAAAGAAAA-AAGAAAAA
1 AAAGAAAAGAAAAGAAGAAAAA
160359 AAAGAAAAGAAAA
1 AAAGAAAAGAAAA
160372 TTTTTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 11 0.37
21 19 0.63
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
AAAGAAAAGAAAAGAAGAAAAA
Found at i:160484 original size:21 final size:22
Alignment explanation
Indices: 160447--160493 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
160437 CATATTAATA
* *
160447 ATTTATTTTATTTTATATAT-T
1 ATTTATTTTATTATATACATGT
160468 ATTTA-TTTATATATATACATGT
1 ATTTATTTTAT-TATATACATGT
160490 ATTT
1 ATTT
160494 GTATCATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 12 0.55
22 5 0.23
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTATTTTATTATATACATGT
Found at i:164228 original size:32 final size:34
Alignment explanation
Indices: 164147--164231 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 34
164137 AAGTGATTGT
**
164147 GAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGGTTCTATCTTAGCCCGTGAAAAAGATAGAGA
164181 GAAAGGTTCTATCTTAGCCCGTG-AAAAGATAG-G-
1 G--AGGTTCTATCTTAGCCCGTGAAAAAGATAGAGA
164214 GAGGTTTCTATCTTAGCC
1 GAGG-TTCTATCTTAGCC
164232 TTGAAAGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
31 3 0.07
32 13 0.28
33 1 0.02
34 2 0.04
35 9 0.20
36 18 0.39
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (34 bp):
GAGGTTCTATCTTAGCCCGTGAAAAAGATAGAGA
Found at i:165383 original size:20 final size:20
Alignment explanation
Indices: 165360--165432 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
165350 ACAATTCAAA
165360 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
165380 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
165401 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
165421 GTATCGATACAT
1 GTATCGATACAT
165433 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:165404 original size:21 final size:21
Alignment explanation
Indices: 165378--165453 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
165368 ACATGTTGCA
165378 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
165399 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
165419 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
165440 ATGTATCGATACAT
1 ATGTATCGATACAT
165454 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:165411 original size:41 final size:41
Alignment explanation
Indices: 165360--165453 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
165350 ACAATTCAAA
*
165360 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
165401 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
165442 GTATCGATACAT
1 GTATCGATACAT
165454 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:165510 original size:13 final size:13
Alignment explanation
Indices: 165492--165517 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
165482 TACAGCAAGT
165492 ATGTATCGATACA
1 ATGTATCGATACA
165505 ATGTATCGATACA
1 ATGTATCGATACA
165518 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:165844 original size:23 final size:22
Alignment explanation
Indices: 165818--165860 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
165808 TTTGTTTATA
165818 TTGTCATTATT-TTTCTAAGCTCT
1 TTGT-ATTATTATTTC-AAGCTCT
*
165841 TTGTATTCTTATTTCAAGCT
1 TTGTATTATTATTTCAAGCT
165861 TAAATTCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.56
Consensus pattern (22 bp):
TTGTATTATTATTTCAAGCTCT
Found at i:167763 original size:21 final size:21
Alignment explanation
Indices: 167730--167774 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
167720 TTGCAAGTTG
*
167730 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
167752 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
167772 AAA
1 AAA
167775 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:169598 original size:15 final size:15
Alignment explanation
Indices: 169578--169608 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
169568 TAAAAATGTC
*
169578 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
169593 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
169608 C
1 C
169609 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:171701 original size:20 final size:20
Alignment explanation
Indices: 171622--171701 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
171612 AATGTCCAAA
*
171622 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
171642 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
171667 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
171687 TTGTATCGATACATT
1 ATGTATCGATACATT
171702 GTATCGATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:171705 original size:13 final size:13
Alignment explanation
Indices: 171687--171725 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
171677 ACATTTTTCT
171687 TTGTATCGATACA
1 TTGTATCGATACA
*
171700 TTGTATCGATATA
1 TTGTATCGATACA
*
171713 CTGTATCGATACA
1 TTGTATCGATACA
171726 GGGTGTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:174193 original size:20 final size:20
Alignment explanation
Indices: 174170--174242 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
174160 ACAATTCAAA
174170 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
174190 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
174211 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
174231 GTATCGATACAT
1 GTATCGATACAT
174243 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:174214 original size:21 final size:21
Alignment explanation
Indices: 174188--174263 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
174178 ACATGTTGCA
174188 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
174209 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
174229 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
174250 ATGTATCGATACAT
1 ATGTATCGATACAT
174264 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:174221 original size:41 final size:41
Alignment explanation
Indices: 174170--174263 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
174160 ACAATTCAAA
*
174170 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
174211 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
174252 GTATCGATACAT
1 GTATCGATACAT
174264 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:174320 original size:13 final size:13
Alignment explanation
Indices: 174302--174327 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
174292 TACAGCAAGT
174302 ATGTATCGATACA
1 ATGTATCGATACA
174315 ATGTATCGATACA
1 ATGTATCGATACA
174328 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:174654 original size:23 final size:22
Alignment explanation
Indices: 174628--174670 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
174618 TTTGTTTATA
174628 TTGTCATTATT-TTTCTAAGCTCT
1 TTGT-ATTATTATTTC-AAGCTCT
*
174651 TTGTATTCTTATTTCAAGCT
1 TTGTATTATTATTTCAAGCT
174671 TAAATTCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.56
Consensus pattern (22 bp):
TTGTATTATTATTTCAAGCTCT
Found at i:175446 original size:20 final size:20
Alignment explanation
Indices: 175421--175555 Score: 126
Period size: 20 Copynumber: 6.6 Consensus size: 20
175411 TAACTAGATA
175421 TATCGATACATTGAACAATG
1 TATCGATACATTGAACAATG
*
175441 TATCGATACATTAAACAATG
1 TATCGATACATTGAACAATG
* * * *
175461 TATCTATACATCTGGGTAGAATA
1 TATCGATACAT-T--GAACAATG
* *
175484 TATTGATACATTGAAGAATG
1 TATCGATACATTGAACAATG
* * * *
175504 TATCGATATATTCATCCATG
1 TATCGATACATTGAACAATG
* *
175524 TATCGATAGATTGAAAAATG
1 TATCGATACATTGAACAATG
175544 TATCGATACATT
1 TATCGATACATT
175556 CGGATAAAAA
Statistics
Matches: 90, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
20 75 0.83
21 1 0.01
22 1 0.01
23 13 0.14
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (20 bp):
TATCGATACATTGAACAATG
Found at i:176255 original size:22 final size:22
Alignment explanation
Indices: 176219--176297 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 22
176209 TAAAGTCTTT
* *
176219 TTTTTAGGTAATAAATAATTAA
1 TTTTTATGTATTAAATAATTAA
176241 TTTTTATGTATTAAATAATTAA
1 TTTTTATGTATTAAATAATTAA
*
176263 TTAATATTAATG-A-AAAATAATTAA
1 TT--T-TT-ATGTATTAAATAATTAA
176287 -TTTTATGTATT
1 TTTTTATGTATT
176298 TTATTTTTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
19 3 0.06
20 3 0.06
21 1 0.02
22 22 0.47
23 1 0.02
24 11 0.23
25 3 0.06
26 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.49
Consensus pattern (22 bp):
TTTTTATGTATTAAATAATTAA
Found at i:176492 original size:25 final size:24
Alignment explanation
Indices: 176438--176493 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
176428 AATATATATT
* *
176438 TAATATTTAAATTTTGATATTAAA
1 TAATAATTAAATTTTGAAATTAAA
* *
176462 TAAATAATTAAATATTTTAAATTTAA
1 T-AATAATTAAAT-TTTGAAATTAAA
176488 TAATAA
1 TAATAA
176494 AATAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 15 0.58
26 10 0.38
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
TAATAATTAAATTTTGAAATTAAA
Found at i:178515 original size:12 final size:12
Alignment explanation
Indices: 178498--178523 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
178488 AGGAACAACC
178498 TGGCATCAGTAG
1 TGGCATCAGTAG
178510 TGGCATCAGTAG
1 TGGCATCAGTAG
178522 TG
1 TG
178524 ACAGTGGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.35, T:0.27
Consensus pattern (12 bp):
TGGCATCAGTAG
Found at i:179893 original size:15 final size:16
Alignment explanation
Indices: 179862--179894 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
179852 TGTATATAGT
179862 TATCATATGCACAACC
1 TATCATATGCACAACC
*
179878 TATCATTTGC-CAACC
1 TATCATATGCACAACC
179893 TA
1 TA
179895 CTCCCTCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (16 bp):
TATCATATGCACAACC
Found at i:182683 original size:20 final size:21
Alignment explanation
Indices: 182660--182706 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 21
182650 TATTAAAATG
182660 TATATAATATAAATT-TTTAA
1 TATATAATATAAATTATTTAA
182680 TATAT--T-TAAATTATTTAA
1 TATATAATATAAATTATTTAA
*
182698 AATATAATA
1 TATATAATA
182707 ATAATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
17 6 0.27
18 10 0.45
20 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATAATATAAATTATTTAA
Found at i:182717 original size:10 final size:9
Alignment explanation
Indices: 182681--182736 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
182671 AATTTTTAAT
*
182681 ATATTTAAA
1 ATATATAAA
* *
182690 TTATTTAAA
1 ATATATAAA
182699 ATATAATAATA
1 ATAT-ATAA-A
182710 ATATATAAA
1 ATATATAAA
182719 A-ATATATAA
1 ATATATA-AA
182728 ATATATAAA
1 ATATATAAA
182737 TTATTAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 5 0.12
9 18 0.45
10 12 0.30
11 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
ATATATAAA
Found at i:182723 original size:8 final size:8
Alignment explanation
Indices: 182643--182737 Score: 54
Period size: 8 Copynumber: 11.8 Consensus size: 8
182633 ATATTATTAC
182643 ATAAATAT
1 ATAAATAT
182651 ATTAAA-AT
1 A-TAAATAT
* *
182659 GTATATAAT
1 ATAAAT-AT
*
182668 ATAAATTT
1 ATAAATAT
*
182676 TTAATATAT
1 ATAA-ATAT
*
182685 TTAAATTAT
1 ATAAA-TAT
*
182694 TTAAA-AT
1 ATAAATAT
182701 AT-AATA-
1 ATAAATAT
182707 ATAATATAT
1 ATAA-ATAT
*
182716 AAAAATAT
1 ATAAATAT
182724 ATAAATAT
1 ATAAATAT
182732 ATAAAT
1 ATAAAT
182738 TATTAAATTA
Statistics
Matches: 68, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
6 4 0.06
7 8 0.12
8 28 0.41
9 28 0.41
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (8 bp):
ATAAATAT
Done.