Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014142.1 Corchorus capsularis cultivar CVL-1 contig14163, 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: 81049
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:3015 original size:16 final size:16
Alignment explanation
Indices: 2996--3032 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
2986 TTGCTATACA
2996 TTTTTTTAATTTTTAT
1 TTTTTTTAATTTTTAT
3012 TTTTTTTAATTTTTAT
1 TTTTTTTAATTTTTAT
3028 TTTTT
1 TTTTT
3033 ACCTTCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTAATTTTTAT
Found at i:5157 original size:30 final size:30
Alignment explanation
Indices: 5084--5159 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 30
5074 TTGTGTTATA
* *
5084 TGTGTTTACGGACTTTAGTATAGGTGCCTC
1 TGTGTTGAGGGACTTTAGTATAGGTGCCTC
*
5114 TGTGTTTAGGGACTTTAGTAT-GGATGCC-C
1 TGTGTTGAGGGACTTTAGTATAGG-TGCCTC
5143 TTGTGCTTGA-GGACTTT
1 -TGTG-TTGAGGGACTTT
5160 TGGGGAGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 3 0.07
30 35 0.85
31 3 0.07
ACGTcount: A:0.16, C:0.14, G:0.29, T:0.41
Consensus pattern (30 bp):
TGTGTTGAGGGACTTTAGTATAGGTGCCTC
Found at i:8205 original size:72 final size:72
Alignment explanation
Indices: 8086--8360 Score: 362
Period size: 72 Copynumber: 3.8 Consensus size: 72
8076 GGAGAACAAA
* * *
8086 GATTGTGCGAAGGACTGGC--ATGTAGGAACTACCTCGGCTACAATCGCAATGA-GGAAGATAAT
1 GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAAT-ATGGAAGATAAT
8148 CACATAAG
65 CACATAAG
* *
8156 GATTGTGCGAAGGACTGCCAAATGTGGGAATTGCCTCGGCTACAATCGCAATGAT-GAATATAAT
1 GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAAT-ATGGAAGATAAT
*
8220 CGCATAAG
65 CACATAAG
* * *
8228 GGTTGTGCAAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAA-CTGCAATATGGAAGATTAT
1 GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATC-GCAATATGGAAGATAAT
**
8292 CATGTAAG
65 CACATAAG
* * *
8300 GATTGTGCGAAGGACTGCCAGATGTGGGAACTGCTTCGGCTACAACCGCAATATGGAAGAT
1 GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATATGGAAGAT
8361 CATGGGATGG
Statistics
Matches: 181, Mismatches: 18, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
70 18 0.10
71 3 0.02
72 159 0.88
73 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (72 bp):
GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATATGGAAGATAATC
ACATAAG
Found at i:9678 original size:32 final size:32
Alignment explanation
Indices: 9586--9862 Score: 170
Period size: 26 Copynumber: 9.5 Consensus size: 32
9576 AGATTGCCCA
* * *
9586 TGTGCTTAGGGAC-TTTGA-TATAGATGCCTT
1 TGTGTTTAGGGACTTTTTAGTATAGATGCCTC
* *
9616 TGTGTTTAGGGAC---TTA-T-GA-ATGCCTT
1 TGTGTTTAGGGACTTTTTAGTATAGATGCCTC
9642 TGTGTTT-GAGGACTTTTTAGTATAGATGCCTC
1 TGTGTTTAG-GGACTTTTTAGTATAGATGCCTC
*
9674 TGTGTTTAGGGAC---TTA-T-GA-ATGCC-C
1 TGTGTTTAGGGACTTTTTAGTATAGATGCCTC
*
9699 TTGTGTTT-GAGGACTTTTTAGTATAGATGCATC
1 -TGTGTTTAG-GGACTTTTTAGTATAGATGCCTC
9732 TGTGTTTAGGGAC---TTA-TA-A-ATGCC-C
1 TGTGTTTAGGGACTTTTTAGTATAGATGCCTC
9757 TTGTGTTT-GAGGACTTTTTAGTATAGATGCCTC
1 -TGTGTTTAG-GGACTTTTTAGTATAGATGCCTC
*
9790 TGTGTTTAGGGAC---TTA-T-GA-ATGCC-C
1 TGTGTTTAGGGACTTTTTAGTATAGATGCCTC
*
9815 ATGTGTTT-GAGGACTTTTTGGTATAGATGCCTC
1 -TGTGTTTAG-GGACTTTTTAGTATAGATGCCTC
*
9848 TATGTTTAGGGACTT
1 TGTGTTTAGGGACTT
9863 ATGAATGCCC
Statistics
Matches: 196, Mismatches: 13, Indels: 74
0.69 0.05 0.26
Matches are distributed among these distances:
25 7 0.04
26 65 0.33
27 4 0.02
28 7 0.04
29 20 0.10
30 17 0.09
31 4 0.02
32 65 0.33
33 7 0.04
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.42
Consensus pattern (32 bp):
TGTGTTTAGGGACTTTTTAGTATAGATGCCTC
Found at i:9683 original size:58 final size:58
Alignment explanation
Indices: 9604--9949 Score: 584
Period size: 58 Copynumber: 6.0 Consensus size: 58
9594 GGGACTTTGA
* *
9604 TATAGATGCCTTTGTGTTTAGGGACTTATGAATGCCTTTGTGTTTGAGGACTTTTTAG
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
9662 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
* *
9720 TATAGATGCATCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAGGACTTTTTAG
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
* *
9778 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCATGTGTTTGAGGACTTTTTGG
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
* * *
9836 TATAGATGCCTCTATGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTAAA
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
* * *
9894 TAGAGACGCCTCTGTGTTTAGGGACTTATGAATGCCCTGGTGTTTGAGGACTTTTT
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTT
9950 GATAGAGGAT
Statistics
Matches: 270, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 270 1.00
ACGTcount: A:0.20, C:0.13, G:0.26, T:0.41
Consensus pattern (58 bp):
TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
Found at i:17530 original size:19 final size:20
Alignment explanation
Indices: 17500--17563 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
17490 TTGACACTGT
17500 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
*
17521 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATGAGA
* *
17540 TTAGGTACTGTACAGATGAAA
1 TTA-GCACTGTACAGATGAGA
17561 TTA
1 TTA
17564 TTAGAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:17563 original size:21 final size:19
Alignment explanation
Indices: 17506--17563 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
17496 CTGTTTAGCA
17506 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
17525 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
*
17546 ACTGTACAGATGAAATTA
1 ACTGTACAGATGAGATTA
17564 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:18428 original size:17 final size:17
Alignment explanation
Indices: 18406--18440 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
18396 ACAATAACTT
*
18406 AATGGGATTATATTCAC
1 AATGGGATTACATTCAC
18423 AATGGGATTACATTCAC
1 AATGGGATTACATTCAC
18440 A
1 A
18441 TAGCTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (17 bp):
AATGGGATTACATTCAC
Found at i:18549 original size:21 final size:21
Alignment explanation
Indices: 18525--18567 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
18515 TTAGGCTTGG
*
18525 TCAATCAATTACTTTGATTGC
1 TCAATAAATTACTTTGATTGC
18546 TCAATAAATTACTTTGATTGC
1 TCAATAAATTACTTTGATTGC
18567 T
1 T
18568 ATTGTCTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.44
Consensus pattern (21 bp):
TCAATAAATTACTTTGATTGC
Found at i:23108 original size:16 final size:16
Alignment explanation
Indices: 23087--23120 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
23077 CAATAACTTA
*
23087 ATGGGATTATATTCAC
1 ATGGGATTACATTCAC
23103 ATGGGATTACATTCAC
1 ATGGGATTACATTCAC
23119 AT
1 AT
23121 AGCTATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (16 bp):
ATGGGATTACATTCAC
Found at i:23228 original size:21 final size:21
Alignment explanation
Indices: 23204--23246 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
23194 TTAGGTATGG
*
23204 TCAATCAATTACTTTGATTGC
1 TCAATAAATTACTTTGATTGC
23225 TCAATAAATTACTTTGATTGC
1 TCAATAAATTACTTTGATTGC
23246 T
1 T
23247 ATTGTCTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.44
Consensus pattern (21 bp):
TCAATAAATTACTTTGATTGC
Found at i:25508 original size:62 final size:62
Alignment explanation
Indices: 25411--25535 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
25401 GACATCAAAG
25411 GGCCCTTGGACTGCTCTACTGGCCAAGAACATCTGCATACATGTTGACTTCTCGATTATTAT
1 GGCCCTTGGACTGCTCTACTGGCCAAGAACATCTGCATACATGTTGACTTCTCGATTATTAT
25473 GGCCCTTGGACTGCTCTACTGGCCAAGAACATCTGCATACATGTTGACTTCTCGATTATTAT
1 GGCCCTTGGACTGCTCTACTGGCCAAGAACATCTGCATACATGTTGACTTCTCGATTATTAT
25535 G
1 G
25536 AGCAAAACTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (62 bp):
GGCCCTTGGACTGCTCTACTGGCCAAGAACATCTGCATACATGTTGACTTCTCGATTATTAT
Found at i:30536 original size:26 final size:26
Alignment explanation
Indices: 30506--30613 Score: 101
Period size: 26 Copynumber: 4.0 Consensus size: 26
30496 TATTTCTTGA
30506 TTACTAATTACCATTTTTTACTCTTT
1 TTACTAATTACCATTTTTTACTCTTT
* * *
30532 GTACTGATTACCATATTTTACTCTTTT
1 TTACTAATTACCATTTTTTACTC-TTT
* * *
30559 TTACTAGTTATCCCTTTTCTTACTGTTT
1 TTACTAATTA-CCATTTT-TTACTCTTT
* *
30587 TTACTGAA-TACTACTTTTTACTCTTT
1 TTACT-AATTACCATTTTTTACTCTTT
30613 T
1 T
30614 CATTTAACTC
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
26 29 0.45
27 14 0.22
28 15 0.23
29 6 0.09
ACGTcount: A:0.20, C:0.19, G:0.05, T:0.56
Consensus pattern (26 bp):
TTACTAATTACCATTTTTTACTCTTT
Found at i:30592 original size:55 final size:53
Alignment explanation
Indices: 30506--30613 Score: 128
Period size: 55 Copynumber: 2.0 Consensus size: 53
30496 TATTTCTTGA
*
30506 TTACTAATTACCATTTTTTACTCTTTGTACTGATTACCA-TATTTTACTCTTTT
1 TTACTAATTACCATTTTTTACTCTTTGTACTGAATACCACT-TTTTACTCTTTT
* * * * *
30559 TTACTAGTTATCCCTTTTCTTACTGTTTTTACTGAATACTACTTTTTACTCTTTT
1 TTACTAATTA-CCATTTT-TTACTCTTTGTACTGAATACCACTTTTTACTCTTTT
30614 CATTTAACTC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 9 0.20
54 6 0.13
55 30 0.65
56 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.05, T:0.56
Consensus pattern (53 bp):
TTACTAATTACCATTTTTTACTCTTTGTACTGAATACCACTTTTTACTCTTTT
Found at i:30692 original size:27 final size:26
Alignment explanation
Indices: 30660--30736 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 26
30650 TCTTTTTTAT
30660 CATTTTTACCCCTTTTTACTGAAT-AC
1 CATTTTTACCCCTTTTTACT-AATCAC
* * *
30686 CACTTTTAACTCTTTTTTACTAATCAC
1 CA-TTTTTACCCCTTTTTACTAATCAC
*
30713 CATTTCTTA-CTCTTTATTACTAAT
1 CATTT-TTACCCCTTT-TTACTAAT
30737 TACTTTCTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
26 11 0.28
27 29 0.73
ACGTcount: A:0.25, C:0.25, G:0.01, T:0.49
Consensus pattern (26 bp):
CATTTTTACCCCTTTTTACTAATCAC
Found at i:30834 original size:29 final size:27
Alignment explanation
Indices: 30775--30848 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 27
30765 ATCACCATTT
30775 TTACTCATTTCTTACTCTTTTTACTGA
1 TTACTCATTTCTTACTCTTTTTACTGA
30802 TTACTC-TTTCCTTACTCTTTTTTTACTGA
1 TTACTCATTT-CTTACTC--TTTTTACTGA
30831 TTAC-CACTTT-TTACTCTT
1 TTACTCA-TTTCTTACTCTT
30849 CTTCTTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
26 5 0.12
27 13 0.31
28 7 0.17
29 14 0.33
30 3 0.07
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.57
Consensus pattern (27 bp):
TTACTCATTTCTTACTCTTTTTACTGA
Found at i:30854 original size:67 final size:66
Alignment explanation
Indices: 30713--30846 Score: 173
Period size: 66 Copynumber: 2.0 Consensus size: 66
30703 TACTAATCAC
* *
30713 CATTTCTTACTCTTTATTACTAATTACTTTCTTTTATTCTTTTTTTTTACCGATCACCATTTTTA
1 CATTTCTTACTCTTTATTACTAATTAC-TTCTTTCATTCTCTTTTTTTACCGATCACCATTTTTA
30778 CT
65 CT
* * * *
30780 CATTTCTTACTCTTT-TTACTGATTAC-TCTTTCCTTACTCTTTTTTTACTGATTACCACTTTTT
1 CATTTCTTACTCTTTATTACTAATTACTTCTTTCATT-CTCTTTTTTTACCGATCACCA-TTTTT
30843 ACT
64 ACT
30846 C
1 C
30847 TTCTTCTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
64 7 0.12
65 18 0.31
66 19 0.32
67 15 0.25
ACGTcount: A:0.18, C:0.23, G:0.02, T:0.57
Consensus pattern (66 bp):
CATTTCTTACTCTTTATTACTAATTACTTCTTTCATTCTCTTTTTTTACCGATCACCATTTTTAC
T
Found at i:31046 original size:22 final size:22
Alignment explanation
Indices: 30897--31082 Score: 119
Period size: 22 Copynumber: 8.2 Consensus size: 22
30887 TTGAATTTAA
* *
30897 TTACTGACTATCATTTTACTCT
1 TTACTGATTACCATTTTACTCT
* ** *
30919 TCACTGATTATTATTTTTTACTTTT
1 TTACTGATTACCA--TTTTAC-TCT
* *
30944 TTATTGATTACTATTTTACTC-
1 TTACTGATTACCATTTTACTCT
* *
30965 TTACTGATTACCATAACTTTTGAACCCGA
1 TTACTGATTACC---A-TTTT--ACTC-T
*
30994 TTACTGATTACCCTTTTACT-T
1 TTACTGATTACCATTTTACTCT
31015 TTACTGATTACCATTTTACTCT
1 TTACTGATTACCATTTTACTCT
*
31037 TTACTAATTACCATTTTACTCT
1 TTACTGATTACCATTTTACTCT
* * *
31059 TAACAGA-TACC-TTTTACTTT
1 TTACTGATTACCATTTTACTCT
31079 TTAC
1 TTAC
31083 CTTTTTACTT
Statistics
Matches: 131, Mismatches: 21, Indels: 26
0.74 0.12 0.15
Matches are distributed among these distances:
20 11 0.08
21 33 0.25
22 37 0.28
23 8 0.06
24 7 0.05
25 20 0.15
27 3 0.02
29 12 0.09
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (22 bp):
TTACTGATTACCATTTTACTCT
Found at i:31082 original size:7 final size:7
Alignment explanation
Indices: 31070--31118 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
31060 AACAGATACC
31070 TTTTACT
1 TTTTACT
31077 TTTTACCT
1 TTTTA-CT
31085 TTTTACT
1 TTTTACT
31092 TTTTACT
1 TTTTACT
*
31099 GTTTAC-
1 TTTTACT
*
31105 TATTACT
1 TTTTACT
*
31112 TCTTACT
1 TTTTACT
31119 AATTTCTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 4 0.11
7 25 0.69
8 7 0.19
ACGTcount: A:0.16, C:0.18, G:0.02, T:0.63
Consensus pattern (7 bp):
TTTTACT
Found at i:31090 original size:15 final size:14
Alignment explanation
Indices: 31066--31097 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
31056 TCTTAACAGA
31066 TACCTTTTACTTTT
1 TACCTTTTACTTTT
31080 TACCTTTTTACTTTT
1 TACC-TTTTACTTTT
31095 TAC
1 TAC
31098 TGTTTACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (14 bp):
TACCTTTTACTTTT
Found at i:31154 original size:22 final size:22
Alignment explanation
Indices: 31128--31188 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
31118 TAATTTCTAT
31128 TACTCTTTACTGATTATCATTC
1 TACTCTTTACTGATTATCATTC
* * *
31150 TACTCTTTACTAATTACCATTT
1 TACTCTTTACTGATTATCATTC
* *
31172 TACCCTTAACTGATTAT
1 TACTCTTTACTGATTAT
31189 ATATTTCTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.48
Consensus pattern (22 bp):
TACTCTTTACTGATTATCATTC
Found at i:31228 original size:30 final size:30
Alignment explanation
Indices: 31192--31254 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
31182 TGATTATATA
*
31192 TTTCTTATTGATCTTAATCACTGATTACTT
1 TTTCTTATTGAACTTAATCACTGATTACTT
* *
31222 TTTCTTATTGAACTTAATTACTGATTTCTT
1 TTTCTTATTGAACTTAATCACTGATTACTT
31252 TTT
1 TTT
31255 TTACTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.57
Consensus pattern (30 bp):
TTTCTTATTGAACTTAATCACTGATTACTT
Found at i:32314 original size:50 final size:50
Alignment explanation
Indices: 32172--32490 Score: 467
Period size: 50 Copynumber: 6.3 Consensus size: 50
32162 ACTTACCACC
* * * *
32172 TAAAGATTCAATTTTTATTGATAAAATTACCAAAATTTGTGATTTTGCTACT
1 TAAAGATTCAA-TTTTATTGATGAAATTACCAAAAATTGTCA-TTTACTACT
* * * * * *
32224 TTAAGATCCGATTTTTATTGATGAAATTATCAAAATTTGTCATTTGCTACT
1 TAAAGATTC-AATTTTATTGATGAAATTACCAAAAATTGTCATTTACTACT
* * *
32275 TAAAGATCCAATTTTATTGTTGAAATTACCAAAAATTGTCATTTACCACT
1 TAAAGATTCAATTTTATTGATGAAATTACCAAAAATTGTCATTTACTACT
32325 TAAAGATTCAATTTTATTGATGAAATTACCAAAAATTGTCATTTACTACT
1 TAAAGATTCAATTTTATTGATGAAATTACCAAAAATTGTCATTTACTACT
*
32375 TAAAGATTCAATTTTTATTGATGAAATTACCAAAAATTGTCATTTGCTACT
1 TAAAGATTCAA-TTTTATTGATGAAATTACCAAAAATTGTCATTTACTACT
*
32426 TAAAGATCCAATTTTATTGATGAAATTACCAAAAATTGTCATTTACTACT
1 TAAAGATTCAATTTTATTGATGAAATTACCAAAAATTGTCATTTACTACT
32476 TAAAGATTCAATTTT
1 TAAAGATTCAATTTT
32491 TATAATCAAA
Statistics
Matches: 245, Mismatches: 20, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
50 145 0.59
51 65 0.27
52 34 0.14
53 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (50 bp):
TAAAGATTCAATTTTATTGATGAAATTACCAAAAATTGTCATTTACTACT
Found at i:32409 original size:151 final size:152
Alignment explanation
Indices: 32164--32490 Score: 530
Period size: 151 Copynumber: 2.2 Consensus size: 152
32154 TACCCAAGAC
* * * * *
32164 TTACCACCTAAAGATTCAATTTTTATTGATAAAATTACCAAAATTTGTGATTTTGCTACTTTAAG
1 TTACCACTTAAAGATTCAA-TTTTATTGATAAAATTACCAAAAATTGTCATTTTACTACTTAAAG
* * *
32229 ATCCGATTTTTATTGATGAAATTATCAAAATTTGTCATTTGCTACTTAAAGATCCAATTTTATTG
65 ATCCAATTTTTATTGATGAAATTACCAAAAATTGTCATTTGCTACTTAAAGATCCAATTTTATTG
*
32294 TTGAAATTACCAAAAATTGTCAT
130 ATGAAATTACCAAAAATTGTCAT
*
32317 TTACCACTTAAAGATTCAATTTTATTGATGAAATTACCAAAAATTGTCA-TTTACTACTTAAAGA
1 TTACCACTTAAAGATTCAATTTTATTGATAAAATTACCAAAAATTGTCATTTTACTACTTAAAGA
*
32381 TTCAATTTTTATTGATGAAATTACCAAAAATTGTCATTTGCTACTTAAAGATCCAATTTTATTGA
66 TCCAATTTTTATTGATGAAATTACCAAAAATTGTCATTTGCTACTTAAAGATCCAATTTTATTGA
32446 TGAAATTACCAAAAATTGTCAT
131 TGAAATTACCAAAAATTGTCAT
*
32468 TTACTACTTAAAGATTCAATTTT
1 TTACCACTTAAAGATTCAATTTT
32491 TATAATCAAA
Statistics
Matches: 162, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
151 117 0.72
152 27 0.17
153 18 0.11
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (152 bp):
TTACCACTTAAAGATTCAATTTTATTGATAAAATTACCAAAAATTGTCATTTTACTACTTAAAGA
TCCAATTTTTATTGATGAAATTACCAAAAATTGTCATTTGCTACTTAAAGATCCAATTTTATTGA
TGAAATTACCAAAAATTGTCAT
Found at i:32410 original size:101 final size:101
Alignment explanation
Indices: 32172--32493 Score: 502
Period size: 101 Copynumber: 3.2 Consensus size: 101
32162 ACTTACCACC
* * * * *
32172 TAAAGATTCAATTTTTATTGATAAAATTACCAAAATTTGTGATTTTGCTACTTTAAGATCCGATT
1 TAAAGATTCAATTTTTATTGATGAAATTACCAAAAATTGTCA-TTTGCTACTTAAAGATCC-AAT
* * *
32237 TTTATTGATGAAATTATCAAAATTTGTCATTTGCTACT
64 TTTATTGATGAAATTACCAAAAATTGTCATTTACTACT
* * * * *
32275 TAAAGATCCAA-TTTTATTGTTGAAATTACCAAAAATTGTCATTTACCACTTAAAGATTCAATTT
1 TAAAGATTCAATTTTTATTGATGAAATTACCAAAAATTGTCATTTGCTACTTAAAGATCCAATTT
32339 TATTGATGAAATTACCAAAAATTGTCATTTACTACT
66 TATTGATGAAATTACCAAAAATTGTCATTTACTACT
32375 TAAAGATTCAATTTTTATTGATGAAATTACCAAAAATTGTCATTTGCTACTTAAAGATCCAATTT
1 TAAAGATTCAATTTTTATTGATGAAATTACCAAAAATTGTCATTTGCTACTTAAAGATCCAATTT
32440 TATTGATGAAATTACCAAAAATTGTCATTTACTACT
66 TATTGATGAAATTACCAAAAATTGTCATTTACTACT
32476 TAAAGATTCAATTTTTAT
1 TAAAGATTCAATTTTTAT
32494 AATCAAACCT
Statistics
Matches: 200, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
100 47 0.23
101 117 0.58
102 26 0.13
103 10 0.05
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (101 bp):
TAAAGATTCAATTTTTATTGATGAAATTACCAAAAATTGTCATTTGCTACTTAAAGATCCAATTT
TATTGATGAAATTACCAAAAATTGTCATTTACTACT
Found at i:34203 original size:2 final size:2
Alignment explanation
Indices: 34190--34227 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
34180 CCTTGAAAGA
*
34190 AT AT AC 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
34228 TAGGCTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:34704 original size:17 final size:18
Alignment explanation
Indices: 34682--34717 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
34672 TAAGAAGATA
34682 ATTTTTTAT-TTTATTTT
1 ATTTTTTATCTTTATTTT
*
34699 ATTTTTTATCTTTTTTTT
1 ATTTTTTATCTTTATTTT
34717 A
1 A
34718 AATAATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (18 bp):
ATTTTTTATCTTTATTTT
Found at i:37499 original size:21 final size:21
Alignment explanation
Indices: 37473--37514 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
37463 GCACAAGTGA
*
37473 CCGGCCATGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
*
37494 CCGGCCACGGGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
37515 GCCCGCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.29, G:0.36, T:0.17
Consensus pattern (21 bp):
CCGGCCACGCGACTTGGAGAT
Found at i:37566 original size:33 final size:31
Alignment explanation
Indices: 37494--37599 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 31
37484 ACTTGGAGAT
* * *
37494 CCGGCCACGGGACTTGGAGATGCCCGCGCAACA
1 CCGGCCA-AGGACATGGAGATGCCCG-GCCACA
* *
37527 CTGGCCATGCGACATGGAGATGCCCGGCCATCA
1 CCGGCCAAG-GACATGGAGATGCCCGGCCA-CA
**
37560 CCGGCCACAGGACATGGCCATGCCCGGCCACA
1 CCGGCCA-AGGACATGGAGATGCCCGGCCACA
37592 CTCGGCCA
1 C-CGGCCA
37600 CATGACTCGG
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
32 7 0.11
33 53 0.87
34 1 0.02
ACGTcount: A:0.21, C:0.39, G:0.30, T:0.10
Consensus pattern (31 bp):
CCGGCCAAGGACATGGAGATGCCCGGCCACA
Found at i:37600 original size:33 final size:32
Alignment explanation
Indices: 37537--37632 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 32
37527 CTGGCCATGC
**
37537 GACATGGAGATGCCCGGCCATCACCGGCCACAG
1 GACATGGCCATGCCCGGCCA-CACCGGCCACAG
*
37570 GACATGGCCATGCCCGGCCACACTCGGCCACAT
1 GACATGGCCATGCCCGGCCACAC-CGGCCACAG
*
37603 GAC-TCGGCCATGCCCGACCACAACCGGCCA
1 GACAT-GGCCATGCCCGGCCAC-ACCGGCCA
37633 TATGATCCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
32 4 0.07
33 50 0.89
34 2 0.04
ACGTcount: A:0.23, C:0.42, G:0.26, T:0.09
Consensus pattern (32 bp):
GACATGGCCATGCCCGGCCACACCGGCCACAG
Found at i:38549 original size:8 final size:8
Alignment explanation
Indices: 38536--38569 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
38526 CACCTTCTTG
38536 AAAAATTC
1 AAAAATTC
38544 AAAAATTC
1 AAAAATTC
*
38552 AGAAACTTC
1 A-AAAATTC
38561 AAAAATTC
1 AAAAATTC
38569 A
1 A
38570 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:44051 original size:21 final size:21
Alignment explanation
Indices: 44025--44066 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
44015 GCACAAGTGA
*
44025 CCGGCCATGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
44046 CCGGCCACGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
44067 GTACACGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.33, T:0.17
Consensus pattern (21 bp):
CCGGCCACGCGACTTGGAGAT
Found at i:44114 original size:33 final size:32
Alignment explanation
Indices: 44076--44184 Score: 121
Period size: 33 Copynumber: 3.3 Consensus size: 32
44066 TGTACACGCA
* *
44076 ACACCGGCCATGCGACATGGAGATGCCCGGCC
1 ACACCGGCCACGCGACATGGACATGCCCGGCC
*
44108 ATCACCGGCCACGCGACATGGCCATGCCCGGCC
1 A-CACCGGCCACGCGACATGGACATGCCCGGCC
** *
44141 ACACCCGGCCACATGAC-TCGGCCATGCCCGGCC
1 ACA-CCGGCCACGCGACAT-GGACATGCCCGGCC
44174 ACAACCGGCCA
1 AC-ACCGGCCA
44185 TATGATCCTT
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
32 4 0.06
33 63 0.93
34 1 0.01
ACGTcount: A:0.21, C:0.44, G:0.27, T:0.08
Consensus pattern (32 bp):
ACACCGGCCACGCGACATGGACATGCCCGGCC
Found at i:47436 original size:25 final size:27
Alignment explanation
Indices: 47407--47459 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 27
47397 CTAATTCAAT
*
47407 ATAAGAACATTTTACTT-TTT-TTATA
1 ATAAGAACACTTTACTTCTTTCTTATA
47432 ATAAGAACACTTTACTTCTTTCTTATA
1 ATAAGAACACTTTACTTCTTTCTTATA
47459 A
1 A
47460 ATATGTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 16 0.64
26 3 0.12
27 6 0.24
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (27 bp):
ATAAGAACACTTTACTTCTTTCTTATA
Found at i:47514 original size:29 final size:30
Alignment explanation
Indices: 47457--47524 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
47447 TTCTTTCTTA
* *
47457 TAAATATGTTAAAAAAACCTAACATATATAT
1 TAAA-ATGTTAAAAAAACCTAACACATATAG
* *
47488 TAAAATGTT-AAAAAAGCTTACACATATAG
1 TAAAATGTTAAAAAAACCTAACACATATAG
47517 TAAAATGT
1 TAAAATGT
47525 CATAGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 24 0.73
30 5 0.15
31 4 0.12
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (30 bp):
TAAAATGTTAAAAAAACCTAACACATATAG
Found at i:48547 original size:16 final size:16
Alignment explanation
Indices: 48510--48547 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
48500 TATTCCTCTC
*
48510 TCCTTTTTACTAACTA
1 TCCTCTTTACTAACTA
*
48526 -CCTCTTTACTAATTA
1 TCCTCTTTACTAACTA
48541 TCCTCTT
1 TCCTCTT
48548 CTTACTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (16 bp):
TCCTCTTTACTAACTA
Found at i:48645 original size:28 final size:26
Alignment explanation
Indices: 48596--48664 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 26
48586 TTTTTACTCT
48596 TTTCTTACTCT-TTTACTAATTACCC
1 TTTCTTACTCTCTTTACTAATTACCC
* *
48621 TTTCCTTACTCTCTTTCATTGATTACCAC
1 TTT-CTTACTCTCTTT-ACTAATTACC-C
48650 TTT-TTACTCTTCTTT
1 TTTCTTACTC-TCTTT
48665 TTTTCTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 3 0.08
26 8 0.22
27 9 0.24
28 13 0.35
29 4 0.11
ACGTcount: A:0.16, C:0.28, G:0.01, T:0.55
Consensus pattern (26 bp):
TTTCTTACTCTCTTTACTAATTACCC
Found at i:48759 original size:35 final size:35
Alignment explanation
Indices: 48711--48814 Score: 122
Period size: 35 Copynumber: 2.9 Consensus size: 35
48701 ACTGAACACC
48711 TTTTACTCTTTACTGATTACTCCTTACTAATTACCA
1 TTTTACTC-TTACTGATTACTCCTTACTAATTACCA
* * *
48747 TTTTGCTCTTACTGATTAC-CCTTTACTATTTATCA
1 TTTTACTCTTACTGATTACTCC-TTACTAATTACCA
* *
48782 TTCTTCCT-TTACTGATTACTCTTTACTAATTAC
1 TT-TTACTCTTACTGATTACTCCTTACTAATTAC
48815 TTTTGCCTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
34 2 0.03
35 44 0.76
36 12 0.21
ACGTcount: A:0.22, C:0.24, G:0.04, T:0.50
Consensus pattern (35 bp):
TTTTACTCTTACTGATTACTCCTTACTAATTACCA
Found at i:48868 original size:14 final size:14
Alignment explanation
Indices: 48861--48937 Score: 140
Period size: 14 Copynumber: 5.6 Consensus size: 14
48851 TTACTTTTCG
48861 CTGATTACTCTTTA
1 CTGATTACTCTTTA
48875 CTGATTACT-TTTA
1 CTGATTACTCTTTA
48888 CTGATTACTCTTTA
1 CTGATTACTCTTTA
48902 CTGATTACT-TTTA
1 CTGATTACTCTTTA
48915 CTGATTACTCTTTA
1 CTGATTACTCTTTA
48929 CTGATTACT
1 CTGATTACT
48938 ATTTTACTCT
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
13 26 0.43
14 35 0.57
ACGTcount: A:0.22, C:0.19, G:0.08, T:0.51
Consensus pattern (14 bp):
CTGATTACTCTTTA
Found at i:48875 original size:7 final size:7
Alignment explanation
Indices: 48865--48937 Score: 60
Period size: 7 Copynumber: 10.7 Consensus size: 7
48855 TTTTCGCTGA
*
48865 TTACTCT
1 TTACTGT
*
48872 TTACTGA
1 TTACTGT
48879 TTACT-T
1 TTACTGT
*
48885 TTACTGA
1 TTACTGT
*
48892 TTACTCT
1 TTACTGT
*
48899 TTACTGA
1 TTACTGT
48906 TTACT-T
1 TTACTGT
*
48912 TTACTGA
1 TTACTGT
*
48919 TTACTCT
1 TTACTGT
*
48926 TTACTGA
1 TTACTGT
48933 TTACT
1 TTACT
48938 ATTTTACTCT
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
6 10 0.20
7 40 0.80
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (7 bp):
TTACTGT
Found at i:48895 original size:27 final size:27
Alignment explanation
Indices: 48851--48937 Score: 156
Period size: 27 Copynumber: 3.2 Consensus size: 27
48841 TTTGCCATTT
*
48851 TTACTTTTCGCTGATTACTCTTTACTGA
1 TTACTTTT-ACTGATTACTCTTTACTGA
48879 TTACTTTTACTGATTACTCTTTACTGA
1 TTACTTTTACTGATTACTCTTTACTGA
48906 TTACTTTTACTGATTACTCTTTACTGA
1 TTACTTTTACTGATTACTCTTTACTGA
48933 TTACT
1 TTACT
48938 ATTTTACTCT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
27 50 0.86
28 8 0.14
ACGTcount: A:0.21, C:0.20, G:0.08, T:0.52
Consensus pattern (27 bp):
TTACTTTTACTGATTACTCTTTACTGA
Found at i:48968 original size:26 final size:25
Alignment explanation
Indices: 48932--49029 Score: 97
Period size: 26 Copynumber: 3.6 Consensus size: 25
48922 CTCTTTACTG
48932 ATTACTATTTTACTCTCTTGAATTTA
1 ATTACTATTTTACTCT-TTGAATTTA
48958 ATTACTATTTTCACTCTTTGAATTTA
1 ATTACTATTTT-ACTCTTTGAATTTA
*
48984 ATCACCATTTGTCATTTTACTCTTTGAATTTA
1 ATTA-C-----T-ATTTTACTCTTTGAATTTA
*
49016 ATTACCATTTTACT
1 ATTACTATTTTACT
49030 ATTTTACTCT
Statistics
Matches: 61, Mismatches: 3, Indels: 17
0.75 0.04 0.21
Matches are distributed among these distances:
25 8 0.13
26 23 0.38
27 6 0.10
31 1 0.02
32 18 0.30
33 5 0.08
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (25 bp):
ATTACTATTTTACTCTTTGAATTTA
Found at i:49039 original size:33 final size:33
Alignment explanation
Indices: 48959--49041 Score: 125
Period size: 32 Copynumber: 2.5 Consensus size: 33
48949 TTGAATTTAA
48959 TTACTATTTTCACTCTTTGAATTTAATCACCATT
1 TTACTATTTT-ACTCTTTGAATTTAATCACCATT
*
48993 TGT-C-ATTTTACTCTTTGAATTTAATTACCATT
1 T-TACTATTTTACTCTTTGAATTTAATCACCATT
49025 TTACTATTTTACTCTTT
1 TTACTATTTTACTCTTT
49042 ACCGATTACT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 1 0.02
32 24 0.53
33 17 0.38
34 2 0.04
35 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.04, T:0.54
Consensus pattern (33 bp):
TTACTATTTTACTCTTTGAATTTAATCACCATT
Found at i:49439 original size:38 final size:39
Alignment explanation
Indices: 49342--49439 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 39
49332 TTTGACCCTT
* * * *
49342 AATTACTGATTGCTACTTTTACTTCCTCTCTTAGTTATC
1 AATTACTGATTACTACTTTTACTTCCTCTCTTAATCACC
* * *
49381 AATTTACTAATTAATCCTTTTACTT-C-CTCTTAATCACC
1 AA-TTACTGATTACTACTTTTACTTCCTCTCTTAATCACC
49419 AATTGACTGATTACTACTTTT
1 AATT-ACTGATTACTACTTTT
49440 TATCTTTTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
37 2 0.04
38 24 0.51
39 3 0.06
40 18 0.38
ACGTcount: A:0.26, C:0.22, G:0.05, T:0.47
Consensus pattern (39 bp):
AATTACTGATTACTACTTTTACTTCCTCTCTTAATCACC
Found at i:53027 original size:35 final size:35
Alignment explanation
Indices: 52987--53117 Score: 158
Period size: 35 Copynumber: 3.7 Consensus size: 35
52977 TCCTAATATC
* *
52987 TGAAGATGCTAT-ACCAAGTCATCTGAGTCCAACTT
1 TGAAGATGCT-TCACCGAGTCATCTGATTCCAACTT
* *
53022 TGAAGACGCTTCACCGAGTCATCTGATTCAAACTT
1 TGAAGATGCTTCACCGAGTCATCTGATTCCAACTT
* *
53057 TGAAGATGCTTCACCGAGTCAACTGATTCCGA-TT
1 TGAAGATGCTTCACCGAGTCATCTGATTCCAACTT
* *
53091 TTAAGGATGCTACACCGAGTCATCTGA
1 TGAA-GATGCTTCACCGAGTCATCTGA
53118 ACCCGACCTT
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
34 6 0.07
35 77 0.93
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (35 bp):
TGAAGATGCTTCACCGAGTCATCTGATTCCAACTT
Found at i:53227 original size:18 final size:18
Alignment explanation
Indices: 53185--53220 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53175 ATGCGGGTTA
*
53185 GAATGATAATGCAATGTC
1 GAATGCTAATGCAATGTC
*
53203 GAATGCTAATGTAATGTC
1 GAATGCTAATGCAATGTC
53221 ATATGCTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (18 bp):
GAATGCTAATGCAATGTC
Found at i:63714 original size:14 final size:14
Alignment explanation
Indices: 63697--63756 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 14
63687 CCTTTGATGA
63697 TTACTCTTTACTTT
1 TTACTCTTTACTTT
*
63711 TTACTCTTTACCATT
1 TTACTCTTTA-CTTT
**
63726 TT--TCTTTACTAA
1 TTACTCTTTACTTT
63738 TTACTCTTTTACTTT
1 TTACTC-TTTACTTT
63753 TTAC
1 TTAC
63757 CATTTTACTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
12 3 0.08
13 6 0.17
14 12 0.33
15 15 0.42
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (14 bp):
TTACTCTTTACTTT
Found at i:63754 original size:27 final size:27
Alignment explanation
Indices: 63701--63826 Score: 75
Period size: 27 Copynumber: 4.7 Consensus size: 27
63691 TGATGATTAC
**
63701 TCTTTACTTTTTACTCTTTACCATTTT
1 TCTTTACTAATTACTCTTTACCATTTT
63728 TCTTTACTAATTACTCTTTTA-C-TTTT
1 TCTTTACTAATTACTC-TTTACCATTTT
* **
63754 TACCATTT--TACTTAGCTGATTA-C-TCTTT
1 T--C-TTTACTAATTA-CTCTTTACCAT-TTT
* **
63782 ACTTTACTCTTTACTCTTTACCATTTT
1 TCTTTACTAATTACTCTTTACCATTTT
*
63809 TCTTTACTGATTACTCTT
1 TCTTTACTAATTACTCTT
63827 GTCTGAATAC
Statistics
Matches: 76, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
25 3 0.04
26 11 0.14
27 48 0.63
28 11 0.14
29 3 0.04
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.57
Consensus pattern (27 bp):
TCTTTACTAATTACTCTTTACCATTTT
Found at i:63756 original size:35 final size:35
Alignment explanation
Indices: 63704--63786 Score: 109
Period size: 35 Copynumber: 2.4 Consensus size: 35
63694 TGATTACTCT
* *
63704 TTACT-TTTTACTCTTTACCATTTTTCTTTA-CTAA
1 TTACTCTTTTACTTTTTACCATTTTAC-TTAGCTAA
*
63738 TTACTCTTTTACTTTTTACCATTTTACTTAGCTGA
1 TTACTCTTTTACTTTTTACCATTTTACTTAGCTAA
63773 TTACTC-TTTACTTT
1 TTACTCTTTTACTTT
63787 ACTCTTTACT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 16 0.36
35 28 0.64
ACGTcount: A:0.19, C:0.20, G:0.02, T:0.58
Consensus pattern (35 bp):
TTACTCTTTTACTTTTTACCATTTTACTTAGCTAA
Found at i:63802 original size:14 final size:14
Alignment explanation
Indices: 63697--63975 Score: 52
Period size: 14 Copynumber: 19.8 Consensus size: 14
63687 CCTTTGATGA
*
63697 TTACTCTTTACTTT
1 TTACTCTTTACTCT
63711 TTACTCTTTAC-CAT
1 TTACTCTTTACTC-T
* **
63725 TT-TTCTTTACTAA
1 TTACTCTTTACTCT
*
63738 TTACTCTTTTACTTT
1 TTACTC-TTTACTCT
63753 TTAC-CATTTTACTTAGCT
1 TTACTC--TTTAC-T--CT
63771 GATTACTCTTTA--CT
1 --TTACTCTTTACTCT
63785 TTACTCTTTACTCT
1 TTACTCTTTACTCT
*
63799 TTAC-CATTT-TTCT
1 TTACTC-TTTACTCT
**
63812 TTACTGATTACTCT
1 TTACTCTTTACTCT
***
63826 TGT-CTGAATACTCTT
1 T-TACTCTTTACTC-T
63841 TTACT-TTT--TCT
1 TTACTCTTTACTCT
**
63852 TTACTGATTAC-CATT
1 TTACTCTTTACTC--T
* **
63867 TTACT-TTTGCTGA
1 TTACTCTTTACTCT
63880 TTACTCTTTACTCT
1 TTACTCTTTACTCT
**
63894 TTAC-CATTTTTTTCT
1 TTACTC--TTTACTCT
**
63909 TTACTGATTACTCTT
1 TTACTCTTTACTC-T
*
63924 TTACTTTTTAC-CAT
1 TTACTCTTTACTC-T
* **
63938 TT--TACTTTGCTGA
1 TTACT-CTTTACTCT
63951 TTACTCTTTACTCT
1 TTACTCTTTACTCT
63965 TTACTCTTTAC
1 TTACTCTTTAC
63976 CATTTTTTCA
Statistics
Matches: 192, Mismatches: 39, Indels: 68
0.64 0.13 0.23
Matches are distributed among these distances:
11 6 0.03
12 15 0.08
13 32 0.17
14 80 0.42
15 48 0.25
16 1 0.01
18 1 0.01
19 4 0.02
20 4 0.02
21 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (14 bp):
TTACTCTTTACTCT
Found at i:63804 original size:46 final size:48
Alignment explanation
Indices: 63728--63924 Score: 155
Period size: 46 Copynumber: 4.1 Consensus size: 48
63718 TTACCATTTT
*
63728 TCTTTACTAATTACTCTTTTACTTTTTACCATTTTAC-TTAGCTGATTAC
1 TCTTTACT-ATTACTCTTTTACTCTTTACCATTTTACTTTA-CTGATTAC
*
63777 TCTTTACT-TTACTC-TTTACTCTTTACCATTTTTCTTTACTGATTAC
1 TCTTTACTATTACTCTTTTACTCTTTACCATTTTACTTTACTGATTAC
* * *
63823 TCTTGT-CTGAATACTCTTTTACT-TTT-TC--TTTACTGATTACCAT-TTTAC
1 TCTT-TACT-ATTACTCTTTTACTCTTTACCATTTTACT--TTA-C-TGATTAC
* *
63871 T-TTTGCTGATTACTC-TTTACTCTTTACCATTTTTTTCTTTACTGATTAC
1 TCTTTACT-ATTACTCTTTTACTCTTTACCA--TTTTACTTTACTGATTAC
63920 TCTTT
1 TCTTT
63925 TACTTTTTAC
Statistics
Matches: 120, Mismatches: 10, Indels: 35
0.73 0.06 0.21
Matches are distributed among these distances:
45 5 0.04
46 39 0.32
47 28 0.23
48 16 0.13
49 21 0.17
50 6 0.05
52 5 0.04
ACGTcount: A:0.18, C:0.21, G:0.05, T:0.56
Consensus pattern (48 bp):
TCTTTACTATTACTCTTTTACTCTTTACCATTTTACTTTACTGATTAC
Found at i:63856 original size:60 final size:61
Alignment explanation
Indices: 63769--63887 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 61
63759 TTTTACTTAG
* * *
63769 CTGATTACTCTTTACTTTACTCTTTACTCTTTACCATTTTTC-TTTACTGATTACTCTTGT
1 CTGAATACTCTTTACTTTACTCTTTACTCATTACCATTTTACTTTTACTGATTACTCTTGT
* * *
63829 CTGAATACTCTTTTACTTT-TTCTTTACTGATTACCATTTTACTTTTGCTGATTACTCTT
1 CTGAATACTC-TTTACTTTACTCTTTACTCATTACCATTTTACTTTTACTGATTACTCTT
63888 TACTCTTTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
60 28 0.55
61 23 0.45
ACGTcount: A:0.18, C:0.22, G:0.06, T:0.55
Consensus pattern (61 bp):
CTGAATACTCTTTACTTTACTCTTTACTCATTACCATTTTACTTTTACTGATTACTCTTGT
Found at i:63888 original size:35 final size:35
Alignment explanation
Indices: 63849--63968 Score: 161
Period size: 35 Copynumber: 3.4 Consensus size: 35
63839 TTTTACTTTT
**
63849 TCTTTACTGATTACCATTTTACTTTTGCTGATTAC
1 TCTTTACTCTTTACCATTTTACTTTTGCTGATTAC
** *
63884 TCTTTACTCTTTACCATTTTTTTCTTTACTGATTAC
1 TCTTTACTCTTTACCATTTTACT-TTTGCTGATTAC
*
63920 TCTTTTACTTTTTACCATTTTAC-TTTGCTGATTAC
1 TC-TTTACTCTTTACCATTTTACTTTTGCTGATTAC
63955 TCTTTACTCTTTAC
1 TCTTTACTCTTTAC
63969 TCTTTACCAT
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
34 11 0.15
35 32 0.44
36 13 0.18
37 17 0.23
ACGTcount: A:0.17, C:0.22, G:0.05, T:0.56
Consensus pattern (35 bp):
TCTTTACTCTTTACCATTTTACTTTTGCTGATTAC
Found at i:63963 original size:7 final size:7
Alignment explanation
Indices: 63951--63975 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
63941 ACTTTGCTGA
63951 TTACTCT
1 TTACTCT
63958 TTACTCT
1 TTACTCT
63965 TTACTCT
1 TTACTCT
63972 TTAC
1 TTAC
63976 CATTTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (7 bp):
TTACTCT
Found at i:68668 original size:28 final size:28
Alignment explanation
Indices: 68612--68683 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
68602 GTAGATTAAG
*
68612 AATGACC-AAATACCCCCTAAATGCCAA
1 AATGACCAAAATGCCCCCTAAATGCCAA
* **
68639 AATGACCAAAATGCCCCCTAGATGTGAA
1 AATGACCAAAATGCCCCCTAAATGCCAA
68667 AATGACCAAAATGCCCC
1 AATGACCAAAATGCCCC
68684 TGGATGACCC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.42, C:0.31, G:0.12, T:0.15
Consensus pattern (28 bp):
AATGACCAAAATGCCCCCTAAATGCCAA
Found at i:71368 original size:33 final size:33
Alignment explanation
Indices: 71302--71439 Score: 228
Period size: 33 Copynumber: 4.3 Consensus size: 33
71292 TCTTTTCACG
* *
71302 CAAAACAGAATTATTTTCAATGC---CATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
71332 CAAAACAGAATTATTTGCAATGCTATGATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
71365 CAAAACAGAATTATTTGCAATGCTATGATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
*
71398 CAAAACAGAATTATTTGCAATGCTATGATCGAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
71431 CAAAACAGA
1 CAAAACAGA
71440 TTTGTTTTCA
Statistics
Matches: 102, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
30 22 0.22
33 80 0.78
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (33 bp):
CAAAACAGAATTATTTGCAATGCTATGATCAAC
Found at i:71467 original size:66 final size:66
Alignment explanation
Indices: 71302--71472 Score: 197
Period size: 66 Copynumber: 2.6 Consensus size: 66
71292 TCTTTTCACG
* * *
71302 CAAAACAGAATTATTTTCAATGCCAT---CAACCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CAAAACAGAATTATTTGCAATACAATGAGCAACCAAAACAGAATTATTTGCAATGCTATGATCAA
71364 C
66 C
* * * *
71365 CAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATGCTATGATCGA
1 CAAAACAGAATTATTTGCAATACAATGAGCAACCAAAACAGAATTATTTGCAATGCTATGATCAA
71430 C
66 C
* * * * *
71431 CAAAACAGATTTGTTTTC-ATCACAATTAGCATCCAAAACAGA
1 CAAAACAGAATTATTTGCAAT-ACAATGAGCAACCAAAACAGA
71473 TTTAGTATCA
Statistics
Matches: 93, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
63 24 0.26
65 2 0.02
66 67 0.72
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (66 bp):
CAAAACAGAATTATTTGCAATACAATGAGCAACCAAAACAGAATTATTTGCAATGCTATGATCAA
C
Found at i:71502 original size:33 final size:33
Alignment explanation
Indices: 71464--71560 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
71454 AATTAGCATC
*
71464 CAAAACAGATTTAGTATCATCACAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
* * *
71497 TAAAACAGATTTAGTGTCATTGCAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
** *
71530 CAAATTAGGTTTAGTATCATCGCAAACAACA
1 CAAAACAGATTTAGTATCATCGCAAACAACA
71561 TCTAAAAGAC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:73195 original size:8 final size:8
Alignment explanation
Indices: 73167--73200 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
73157 GAATCGGCTA
73167 TGAATTTT
1 TGAATTTT
*
73175 TGAAGTTTC
1 TGAA-TTTT
73184 TGAATTTT
1 TGAATTTT
73192 TGAATTTT
1 TGAATTTT
73200 T
1 T
73201 CAAGAAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:79118 original size:6 final size:6
Alignment explanation
Indices: 79109--79138 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
79099 AAAACAAAGC
79109 AAATCT AAATCT AAATCT AAATCT AAATCT
1 AAATCT AAATCT AAATCT AAATCT AAATCT
79139 GAAGCAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATCT
Done.