Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020193.1 Corchorus olitorius cultivar O-4 contig20226, 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: 50632
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:114 original size:22 final size:22
Alignment explanation
Indices: 86--136 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
76 TAAAAGGATG
86 AATGCAAAAGATACCATGCAAA
1 AATGCAAAAGATACCATGCAAA
* *
108 AATGCAAAAGGTGCCATGCAAA
1 AATGCAAAAGATACCATGCAAA
130 AATGCAA
1 AATGCAA
137 CTATTACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.14
Consensus pattern (22 bp):
AATGCAAAAGATACCATGCAAA
Found at i:1088 original size:21 final size:21
Alignment explanation
Indices: 1062--1103 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1052 AAAATCAGAA
* * *
1062 CAAGTCTTGTCCAGATCTTGG
1 CAAGTCCTGCCCAGAACTTGG
1083 CAAGTCCTGCCCAGAACTTGG
1 CAAGTCCTGCCCAGAACTTGG
1104 GCTGTTGAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (21 bp):
CAAGTCCTGCCCAGAACTTGG
Found at i:2711 original size:30 final size:30
Alignment explanation
Indices: 2677--2763 Score: 75
Period size: 30 Copynumber: 3.2 Consensus size: 30
2667 TATATTTACA
2677 TATATACAGAATGTGATTTGCAATTTGGCT
1 TATATACAGAATGTGATTTGCAATTTGGCT
* * * *
2707 TATATATATAATAT-ATTT---A--T---A
1 TATATACAGAATGTGATTTGCAATTTGGCT
2728 TATATACAGAATGTGATTTGCAATTTGGCT
1 TATATACAGAATGTGATTTGCAATTTGGCT
2758 TATATA
1 TATATA
2764 TATAATATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 18
0.61 0.12 0.27
Matches are distributed among these distances:
21 11 0.28
22 4 0.10
24 1 0.03
25 1 0.03
26 1 0.03
27 1 0.03
29 4 0.10
30 17 0.43
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (30 bp):
TATATACAGAATGTGATTTGCAATTTGGCT
Found at i:2832 original size:53 final size:51
Alignment explanation
Indices: 2619--2818 Score: 355
Period size: 51 Copynumber: 3.9 Consensus size: 51
2609 CATTTTCATA
*
2619 TTACATATATACAGAATGGGATTTGCAATTTGGCATATATATATATAATATAT
1 TTACATATATACAGAATGTGATTTGCAATTTGGC-T-TATATATATAATATAT
2672 TTACATATATACAGAATGTGATTTGCAATTTGGCTTATATATATAATATAT
1 TTACATATATACAGAATGTGATTTGCAATTTGGCTTATATATATAATATAT
*
2723 TTATATATATACAGAATGTGATTTGCAATTTGGCTTATATATATAATATAT
1 TTACATATATACAGAATGTGATTTGCAATTTGGCTTATATATATAATATAT
*
2774 TTACATATATACAGAATGTAATTTGCAATTTGGCTTATATATATA
1 TTACATATATACAGAATGTGATTTGCAATTTGGCTTATATATATA
2819 TCTGAAGTTT
Statistics
Matches: 143, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
51 109 0.76
52 1 0.01
53 33 0.23
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (51 bp):
TTACATATATACAGAATGTGATTTGCAATTTGGCTTATATATATAATATAT
Found at i:5565 original size:13 final size:12
Alignment explanation
Indices: 5546--5582 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
5536 TGTTTGTAGT
5546 TTCTGAAATCAA
1 TTCTGAAATCAA
5558 TATCTGAAATCGAA
1 T-TCTGAAATC-AA
5572 TTCTGAAATCA
1 TTCTGAAATCA
5583 GTTTGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 18 0.78
14 3 0.13
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (12 bp):
TTCTGAAATCAA
Found at i:5614 original size:50 final size:51
Alignment explanation
Indices: 5546--5750 Score: 192
Period size: 50 Copynumber: 4.1 Consensus size: 51
5536 TGTTTGTAGT
*
5546 TTCTGAAATCAATATCTGAAATC-GAATTCTGAAATCAG-TTTGATTTT-AGA
1 TTCTGAAATCAGTATCTGAAATCAG-ATTCTGAAATCAGTTTTG-TTTTCAGA
* * ** *
5596 TTCTAAAATCAGTTTCTGATTTCAGTTTCTGAAATCAGTTTTTGTTTTCAGA
1 TTCTGAAATCAGTATCTGAAATCAGATTCTGAAATCAG-TTTTGTTTTCAGA
** * *
5648 TTCTGAAATCAG--TCTGATTTCAGTTTCTGAAATCAGTTTCTGTTTTCAAA
1 TTCTGAAATCAGTATCTGAAATCAGATTCTGAAATCAGTTT-TGTTTTCAGA
** *
5698 TTCTGAAATCAG--TCTGATTTCAGTTTCTGAAATCAGTTTCTGTTTTCAG-
1 TTCTGAAATCAGTATCTGAAATCAGATTCTGAAATCAGTTT-TGTTTTCAGA
5747 TTCT
1 TTCT
5751 ATTTCCATTT
Statistics
Matches: 141, Mismatches: 9, Indels: 11
0.88 0.06 0.07
Matches are distributed among these distances:
49 7 0.05
50 111 0.79
51 5 0.04
52 18 0.13
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (51 bp):
TTCTGAAATCAGTATCTGAAATCAGATTCTGAAATCAGTTTTGTTTTCAGA
Found at i:5620 original size:13 final size:13
Alignment explanation
Indices: 5604--5748 Score: 109
Period size: 13 Copynumber: 11.5 Consensus size: 13
5594 GATTCTAAAA
5604 TCAGTTTCTGATT
1 TCAGTTTCTGATT
**
5617 TCAGTTTCTGAAA
1 TCAGTTTCTGATT
* *
5630 TCAGTTTTTGTTT
1 TCAGTTTCTGATT
* **
5643 TCAGATTCTGAAA
1 TCAGTTTCTGATT
5656 TCAG--TCTGATT
1 TCAGTTTCTGATT
**
5667 TCAGTTTCTGAAA
1 TCAGTTTCTGATT
*
5680 TCAGTTTCTGTTT
1 TCAGTTTCTGATT
** **
5693 TCAAATTCTGAAA
1 TCAGTTTCTGATT
5706 TCAG--TCTGATT
1 TCAGTTTCTGATT
**
5717 TCAGTTTCTGAAA
1 TCAGTTTCTGATT
*
5730 TCAGTTTCTGTTT
1 TCAGTTTCTGATT
5743 TCAGTT
1 TCAGTT
5749 CTATTTCCAT
Statistics
Matches: 97, Mismatches: 31, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
11 18 0.19
13 79 0.81
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (13 bp):
TCAGTTTCTGATT
Found at i:5625 original size:26 final size:26
Alignment explanation
Indices: 5572--5748 Score: 222
Period size: 26 Copynumber: 7.0 Consensus size: 26
5562 TGAAATCGAA
* *
5572 TTCTGAAATCAG-TT-TGATTTTAGA
1 TTCTGAAATCAGTTTCTGATTTCAGT
*
5596 TTCTAAAATCAGTTTCTGATTTCAGT
1 TTCTGAAATCAGTTTCTGATTTCAGT
* * *
5622 TTCTGAAATCAGTTTTTGTTTTCAGA
1 TTCTGAAATCAGTTTCTGATTTCAGT
5648 TTCTGAAATCAG--TCTGATTTCAGT
1 TTCTGAAATCAGTTTCTGATTTCAGT
* **
5672 TTCTGAAATCAGTTTCTGTTTTCAAA
1 TTCTGAAATCAGTTTCTGATTTCAGT
5698 TTCTGAAATCAG--TCTGATTTCAGT
1 TTCTGAAATCAGTTTCTGATTTCAGT
*
5722 TTCTGAAATCAGTTTCTGTTTTCAGT
1 TTCTGAAATCAGTTTCTGATTTCAGT
5748 T
1 T
5749 CTATTTCCAT
Statistics
Matches: 130, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
24 53 0.41
25 2 0.02
26 75 0.58
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (26 bp):
TTCTGAAATCAGTTTCTGATTTCAGT
Found at i:7519 original size:35 final size:36
Alignment explanation
Indices: 7473--7841 Score: 499
Period size: 35 Copynumber: 10.5 Consensus size: 36
7463 ATTGTGATCA
* **
7473 TACACCGAGTCATCCGAGA-TCACCTTTGAAGATGC
1 TACACCGAGTCATCTGAGATTCAATTTTGAAGATGC
*
7508 TACACCGAGTCATCTG-GATTCAATTTTGAGGATGC
1 TACACCGAGTCATCTGAGATTCAATTTTGAAGATGC
*
7543 TGCACCGAGTCATCTGAG-TTCAATTTTGAAGATGC
1 TACACCGAGTCATCTGAGATTCAATTTTGAAGATGC
* * * *
7578 TGCACCGAGTCATCTGAG-TCCAATTTTGAAAATGT
1 TACACCGAGTCATCTGAGATTCAATTTTGAAGATGC
*
7613 TGCACCGAGTCATCTGAG-TTCAATTTTGAAGATGC
1 TACACCGAGTCATCTGAGATTCAATTTTGAAGATGC
*
7648 TACACCGAGTAATCTG-GATTCAATTTTGAAGATGC
1 TACACCGAGTCATCTGAGATTCAATTTTGAAGATGC
* *
7683 TGCACCGAGTCATTTG-GATTCAATTTTGAAGATGC
1 TACACCGAGTCATCTGAGATTCAATTTTGAAGATGC
*
7718 TACACCGAGTCATCTG-GATTCAATTTTTAAGATGC
1 TACACCGAGTCATCTGAGATTCAATTTTGAAGATGC
* *
7753 TACACCGAGTCATCTGA-ATTCAACTTTGGAGATGC
1 TACACCGAGTCATCTGAGATTCAATTTTGAAGATGC
*
7788 TACACCGAGTCATCTGAG-TT-AGTCTTTGAAGATGC
1 TACACCGAGTCATCTGAGATTCAAT-TTTGAAGATGC
7823 TACACCGAGTCATCTGAGA
1 TACACCGAGTCATCTGAGA
7842 AGATGGTAAT
Statistics
Matches: 301, Mismatches: 26, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
34 4 0.01
35 296 0.98
36 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (36 bp):
TACACCGAGTCATCTGAGATTCAATTTTGAAGATGC
Found at i:7936 original size:50 final size:50
Alignment explanation
Indices: 7855--8139 Score: 489
Period size: 50 Copynumber: 5.7 Consensus size: 50
7845 TGGTAATGTA
* * *
7855 TCGTATGGAAACGAACTGTGGCTTATGGAAAAGCCCATGTTGATAATTGAC
1 TCGTATGGAAACG-AGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
* *
7906 TCGTACGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
* *
7956 TCGTATGGAAACAAGTTTGGCTTGTGGAAAAGCCCATGATGATAATTGAC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
*
8006 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
8056 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
8106 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
8140 TAAGCATTCG
Statistics
Matches: 221, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
50 209 0.95
51 12 0.05
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (50 bp):
TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGAC
Found at i:8808 original size:50 final size:50
Alignment explanation
Indices: 8754--8900 Score: 186
Period size: 50 Copynumber: 2.9 Consensus size: 50
8744 CTTAAATGCC
* * *
8754 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAACTGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* * *
8804 CTTTGAAAAGCGAATTTTAATCTTGAACCCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* * * * * *
8854 TTTTCAAAAGTGAATTTTGGTCTTGAACTCATAAATGGAAAGAAATC
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATC
8901 CTGTTATAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
Found at i:9504 original size:23 final size:23
Alignment explanation
Indices: 9478--9527 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
9468 GTCAATTCTC
9478 TTTTGATTTTGA-TTTGATTTGAT
1 TTTTGATTTTGATTTTGA-TTGAT
9501 TTTTGATTTTGATTTTGATTGAT
1 TTTTGATTTTGATTTTGATTGAT
9524 TTTT
1 TTTT
9528 TTTTATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (23 bp):
TTTTGATTTTGATTTTGATTGAT
Found at i:9507 original size:7 final size:6
Alignment explanation
Indices: 9478--9520 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
9468 GTCAATTCTC
9478 TTTTGA TTTTGA -TTTGA -TTTGA TTTTTGA TTTTGA TTTTGA TT
1 TTTTGA TTTTGA TTTTGA TTTTGA -TTTTGA TTTTGA TTTTGA TT
9521 GATTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.29
6 20 0.57
7 5 0.14
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.67
Consensus pattern (6 bp):
TTTTGA
Found at i:9963 original size:22 final size:21
Alignment explanation
Indices: 9923--9966 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
9913 TCCAAGTGCC
9923 TTTATTTTCCTTTTTTCATTT
1 TTTATTTTCCTTTTTTCATTT
9944 TTTATTTT-CTTCATTTTCATTT
1 TTTATTTTCCTT--TTTTCATTT
9966 T
1 T
9967 CATTTTTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.14
21 8 0.38
22 10 0.48
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATTTTCCTTTTTTCATTT
Found at i:9965 original size:15 final size:15
Alignment explanation
Indices: 9926--9967 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
9916 AAGTGCCTTT
*
9926 ATTTTCCTTTT-TTC
1 ATTTTCATTTTCTTC
*
9940 ATTTTTTATTTTCTTC
1 A-TTTTCATTTTCTTC
9956 ATTTTCATTTTC
1 ATTTTCATTTTC
9968 ATTTTTCTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.78
16 4 0.17
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTCATTTTCTTC
Found at i:11190 original size:139 final size:138
Alignment explanation
Indices: 10941--11222 Score: 442
Period size: 139 Copynumber: 2.0 Consensus size: 138
10931 ATGTATTGCT
* *
10941 TATATGCACAAAATGTATTCATTTTCAAAAGATAAGGATAATGCAAAATAGATGCATGTAGTAAT
1 TATATGCACAAAATGCATTCATTTACAAAAGATAAGGATAATGCAAAATAGATGCATGTAGTAAT
* * * * * *
11006 GAATGGATAATGCATGACCTGTGCATGAACATATGTACAAAGGAATGGATGATGCATGGA-GGAT
66 GAAGGGAGAATGCATAACCTATGCATGAACATATATACAAAGGAATGGATGATGCA-CGATGGAT
11070 GTATGAACA
130 GTATGAACA
*
11079 TATATGCACAAAATGCA-TCTATTTACAAAAGATAAGGATAATGCAAAAATAGATGCATGTGGTA
1 TATATGCACAAAATGCATTC-ATTTACAAAAGATAAGGATAATGC-AAAATAGATGCATGTAGTA
11143 ATGAAGGGAGAATGCATAACCTATGCATGAACATATATACAAAGGAATGGATGATGCACGATGGA
64 ATGAAGGGAGAATGCATAACCTATGCATGAACATATATACAAAGGAATGGATGATGCACGATGGA
11208 TGTATGAACA
129 TGTATGAACA
11218 TATAT
1 TATAT
11223 ACAAAGACAT
Statistics
Matches: 132, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
137 2 0.02
138 41 0.31
139 89 0.67
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.26
Consensus pattern (138 bp):
TATATGCACAAAATGCATTCATTTACAAAAGATAAGGATAATGCAAAATAGATGCATGTAGTAAT
GAAGGGAGAATGCATAACCTATGCATGAACATATATACAAAGGAATGGATGATGCACGATGGATG
TATGAACA
Found at i:11216 original size:42 final size:42
Alignment explanation
Indices: 11169--11263 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
11159 TAACCTATGC
*
11169 ATGAACATATATACAAAGGA-ATGGATGATGCA-CGATGGATGT
1 ATGAACATATATACAAA-GACATGGACGATGCATCGA-GGATGT
*
11211 ATGAACATATATACAAAGACATGGACGATGCATGGAGGATGT
1 ATGAACATATATACAAAGACATGGACGATGCATCGAGGATGT
11253 ATG-ACATATAT
1 ATGAACATATAT
11264 CAATGGATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
41 10 0.20
42 37 0.76
43 2 0.04
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (42 bp):
ATGAACATATATACAAAGACATGGACGATGCATCGAGGATGT
Found at i:13603 original size:21 final size:21
Alignment explanation
Indices: 13578--13634 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
13568 AATCAGGGTC
13578 TAAATTGAATCAATTAGCAAA
1 TAAATTGAATCAATTAGCAAA
* ** *
13599 TAAA-T-ATTCCAATTAGGGAT
1 TAAATTGAAT-CAATTAGCAAA
13619 TAAATTGAATCAATTA
1 TAAATTGAATCAATTA
13635 ACGAACATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.07
20 13 0.46
21 11 0.39
22 2 0.07
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (21 bp):
TAAATTGAATCAATTAGCAAA
Found at i:13658 original size:41 final size:41
Alignment explanation
Indices: 13549--13662 Score: 103
Period size: 41 Copynumber: 2.8 Consensus size: 41
13539 AGGCCGCATA
* *
13549 AATTAA-AAATAAAATTTTAAATCAGGG-TCTAAATTGAATC
1 AATTAACAAAT-AAATATTAAATAAGGGATCTAAATTGAATC
* * *
13589 AATTAGCAAATAAATATTCCAATTAGGGAT-TAAATTGAATC
1 AATTAACAAATAAATATT-AAATAAGGGATCTAAATTGAATC
*
13630 AATTAACGAACATAAA-CTTAAATAAGGGA-CTAA
1 AATTAAC-AA-ATAAATATTAAATAAGGGATCTAA
13663 GGTGAAAACG
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
40 11 0.18
41 39 0.65
42 5 0.08
43 5 0.08
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.29
Consensus pattern (41 bp):
AATTAACAAATAAATATTAAATAAGGGATCTAAATTGAATC
Found at i:15506 original size:22 final size:22
Alignment explanation
Indices: 15478--15528 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
15468 TAAAAGGATG
15478 AATGCAAAAGATACCATGCAAA
1 AATGCAAAAGATACCATGCAAA
* *
15500 AATGCAAAAGGTGCCATGCAAA
1 AATGCAAAAGATACCATGCAAA
15522 AATGCAA
1 AATGCAA
15529 CTATTACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.14
Consensus pattern (22 bp):
AATGCAAAAGATACCATGCAAA
Found at i:15916 original size:29 final size:29
Alignment explanation
Indices: 15883--15956 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
15873 GCACTTGAAG
* **
15883 TGACCAAAATGCCCCCTAGATGTGTAAAA
1 TGACCAAAATGCCCCCTAGATATACAAAA
* *
15912 TGACCAAAATG-CCCCTGGATATACAGAA
1 TGACCAAAATGCCCCCTAGATATACAAAA
15940 TGACCAAAATGCCCCCT
1 TGACCAAAATGCCCCCT
15957 TAAGTGACCC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 23 0.59
29 16 0.41
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.19
Consensus pattern (29 bp):
TGACCAAAATGCCCCCTAGATATACAAAA
Found at i:16867 original size:17 final size:18
Alignment explanation
Indices: 16829--16865 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16819 TAAATGTGGT
16829 AATGCATGTGTAATAAAA
1 AATGCATGTGTAATAAAA
16847 AATGCATGTG-AAGTAAAA
1 AATGCATGTGTAA-TAAAA
16865 A
1 A
16866 TGAATGTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.24
Consensus pattern (18 bp):
AATGCATGTGTAATAAAA
Found at i:20044 original size:21 final size:22
Alignment explanation
Indices: 20003--20045 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19993 TGGGCTTAAT
20003 TTGGCGGTTTTACTTTAATTTA
1 TTGGCGGTTTTACTTTAATTTA
* *
20025 TTGGTGGTTTT-CTTTGATTTA
1 TTGGCGGTTTTACTTTAATTTA
20046 CCAGTTTGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.58
Consensus pattern (22 bp):
TTGGCGGTTTTACTTTAATTTA
Found at i:23053 original size:27 final size:27
Alignment explanation
Indices: 23015--23069 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
23005 TGAAGCTAGT
23015 TCTACTTTAACTTACTCTATGGATAAG
1 TCTACTTTAACTTACTCTATGGATAAG
23042 TCTACTTTAACTTACTCTATGGATAAG
1 TCTACTTTAACTTACTCTATGGATAAG
23069 T
1 T
23070 TTGCTAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (27 bp):
TCTACTTTAACTTACTCTATGGATAAG
Found at i:23421 original size:2 final size:2
Alignment explanation
Indices: 23409--23497 Score: 80
Period size: 2 Copynumber: 47.0 Consensus size: 2
23399 ATTGTGATGT
* * * *
23409 TA TA T- TA TA TA TA TA T- TA TT TA GA AA TA -A TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
23448 TG TA T- TA CA TA -A TA TA CA 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 TA TA TA TA TA TA
23488 TA TA TA TA TA
1 TA TA TA TA TA
23498 GTAATTCGGG
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
1 5 0.07
2 64 0.93
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:26537 original size:101 final size:101
Alignment explanation
Indices: 26362--26552 Score: 373
Period size: 101 Copynumber: 1.9 Consensus size: 101
26352 TCTAGTTAGG
26362 AATAAGGTTGGGAAAGTCAAGGAATTTGGTTGGGCTCAAGATGGTGTTTGGTCTTGGAATGTTCT
1 AATAAGGTTGGGAAAGTCAAGGAATTTGGTTGGGCTCAAGATGGTGTTTGGTCTTGGAATGTTCT
26427 TTTGAGAAGGAATTTATTTGATTGGCATTAGCTTGT
66 TTTGAGAAGGAATTTATTTGATTGGCATTAGCTTGT
*
26463 AATAAGGTTGGGAAAGTCAAGGAATTTGGTTGTGCTCAAGATGGTGTTTGGTCTTGGAATGTTCT
1 AATAAGGTTGGGAAAGTCAAGGAATTTGGTTGGGCTCAAGATGGTGTTTGGTCTTGGAATGTTCT
26528 TTTGAGAAGGAATTTATTTGATTGG
66 TTTGAGAAGGAATTTATTTGATTGG
26553 GAACTTCAAC
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 89 1.00
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (101 bp):
AATAAGGTTGGGAAAGTCAAGGAATTTGGTTGGGCTCAAGATGGTGTTTGGTCTTGGAATGTTCT
TTTGAGAAGGAATTTATTTGATTGGCATTAGCTTGT
Found at i:28391 original size:18 final size:18
Alignment explanation
Indices: 28365--28412 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
28355 GACTAAAATT
28365 TCTTA-TATTTTATCTTA
1 TCTTACTATTTTATCTTA
28382 TCTTACTATTTTATCTTA
1 TCTTACTATTTTATCTTA
28400 TCTTACTATTTTA
1 TCTTACTATTTTA
28413 CTATCTCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 5 0.17
18 25 0.83
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TCTTACTATTTTATCTTA
Found at i:28483 original size:35 final size:35
Alignment explanation
Indices: 28444--28515 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
28434 GTACGAACTC
28444 AAAAATCTTAATTAGTCAATTACTAAAACACCCTT
1 AAAAATCTTAATTAGTCAATTACTAAAACACCCTT
* *
28479 AAAAATCTTAATTAGTCAATTACTAAAATATCCTT
1 AAAAATCTTAATTAGTCAATTACTAAAACACCCTT
28514 AA
1 AA
28516 TATTATAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (35 bp):
AAAAATCTTAATTAGTCAATTACTAAAACACCCTT
Found at i:28704 original size:30 final size:30
Alignment explanation
Indices: 28664--28755 Score: 175
Period size: 30 Copynumber: 3.1 Consensus size: 30
28654 TATAATTTTT
*
28664 AATCATTAAACTTTTATTTATTAATTATAA
1 AATCTTTAAACTTTTATTTATTAATTATAA
28694 AATCTTTAAACTTTTATTTATTAATTATAA
1 AATCTTTAAACTTTTATTTATTAATTATAA
28724 AATCTTTAAACTTTTATTTATTAATTATAA
1 AATCTTTAAACTTTTATTTATTAATTATAA
28754 AA
1 AA
28756 AGATATTGAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (30 bp):
AATCTTTAAACTTTTATTTATTAATTATAA
Found at i:29468 original size:18 final size:18
Alignment explanation
Indices: 29447--29540 Score: 102
Period size: 18 Copynumber: 5.1 Consensus size: 18
29437 AGATTTCCTA
*
29447 TATCTTATTTTATCTTAC
1 TATCTTATCTTATCTTAC
*
29465 TATCTTATCTTATCTTAT
1 TATCTTATCTTATCTTAC
29483 TATCTTATCTTATCTTAC
1 TATCTTATCTTATCTTAC
* *
29501 TACCCTTACTATTTTATCTTAC
1 TA-TC-T--TATCTTATCTTAC
29523 TATCTTA-C-TATCTTAC
1 TATCTTATCTTATCTTAC
29539 TA
1 TA
29541 CTATATAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
16 10 0.15
18 37 0.57
19 1 0.02
20 2 0.03
21 1 0.02
22 14 0.22
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.55
Consensus pattern (18 bp):
TATCTTATCTTATCTTAC
Found at i:29470 original size:8 final size:8
Alignment explanation
Indices: 29457--29540 Score: 84
Period size: 8 Copynumber: 10.2 Consensus size: 8
29447 TATCTTATTT
29457 TATCTTAC
1 TATCTTAC
29465 TATCTTATC
1 TATCTTA-C
*
29474 TTATCTTAT
1 -TATCTTAC
29483 TATCTTATC
1 TATCTTA-C
29492 TTATCTTAC
1 -TATCTTAC
*
29501 TACCCTTAC
1 TA-TCTTAC
29510 TAT-TT--
1 TATCTTAC
29515 TATCTTAC
1 TATCTTAC
29523 TATCTTAC
1 TATCTTAC
29531 TATCTTAC
1 TATCTTAC
29539 TA
1 TA
29541 CTATATAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
5 3 0.05
6 2 0.03
7 2 0.03
8 34 0.53
9 9 0.14
10 14 0.22
ACGTcount: A:0.24, C:0.23, G:0.00, T:0.54
Consensus pattern (8 bp):
TATCTTAC
Found at i:29473 original size:5 final size:5
Alignment explanation
Indices: 29447--29499 Score: 69
Period size: 5 Copynumber: 11.4 Consensus size: 5
29437 AGATTTCCTA
*
29447 TATCT TATTT TATCT TA-C- TATCT TATCT TATCT TA--T TATCT TATCT
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT
29493 TATCT TA
1 TATCT TA
29500 CTACCCTTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 5 0.12
4 2 0.05
5 35 0.83
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (5 bp):
TATCT
Found at i:29474 original size:13 final size:13
Alignment explanation
Indices: 29456--29529 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 13
29446 ATATCTTATT
29456 TTATCTTACTATC
1 TTATCTTACTATC
*
29469 TTATCTTATCT-TA
1 TTATCTTA-CTATC
29482 TTATCTTATCTTATC
1 TTATCTTA-C-TATC
*
29497 TTACTACCCTTACTATT
1 TTA-T---CTTACTATC
29514 TTATCTTACTATC
1 TTATCTTACTATC
29527 TTA
1 TTA
29530 CTATCTTACT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
13 30 0.60
14 3 0.06
15 4 0.08
16 2 0.04
17 6 0.12
18 1 0.02
19 4 0.08
ACGTcount: A:0.23, C:0.22, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATCTTACTATC
Found at i:29520 original size:22 final size:21
Alignment explanation
Indices: 29492--29533 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
29482 TTATCTTATC
29492 TTATCTTACTACCCTTACTATT
1 TTATCTTACTA-CCTTACTATT
*
29514 TTATCTTACTATCTTACTAT
1 TTATCTTACTACCTTACTAT
29534 CTTACTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATCTTACTACCTTACTATT
Found at i:31839 original size:19 final size:19
Alignment explanation
Indices: 31815--31853 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
31805 AAATTGATTT
31815 CCACCAAACTTGAATCCCA
1 CCACCAAACTTGAATCCCA
*
31834 CCACCAGACTTGAATCCCA
1 CCACCAAACTTGAATCCCA
31853 C
1 C
31854 GTGTGACGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.44, G:0.08, T:0.15
Consensus pattern (19 bp):
CCACCAAACTTGAATCCCA
Found at i:32447 original size:41 final size:41
Alignment explanation
Indices: 32402--32480 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
32392 TATGATTCCC
32402 TTCTAAGAAAACAAAGGCCAAATTTGTTAATTTGCAGTCCT
1 TTCTAAGAAAACAAAGGCCAAATTTGTTAATTTGCAGTCCT
32443 TTCTAAGAAAACAAAGGCCAAATTTGTTAATTTGCAGT
1 TTCTAAGAAAACAAAGGCCAAATTTGTTAATTTGCAGT
32481 TCGTTACTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (41 bp):
TTCTAAGAAAACAAAGGCCAAATTTGTTAATTTGCAGTCCT
Found at i:33488 original size:36 final size:35
Alignment explanation
Indices: 33377--33502 Score: 117
Period size: 36 Copynumber: 3.4 Consensus size: 35
33367 CCATGTCATG
*
33377 CTGCCACGTCATCCATTGACCGTTGACCGAGTCAAC
1 CTGCCACATCATCCATTGACCGTTGA-CGAGTCAAC
* * *
33413 CTGCCACATCATGCTGCCATGTCATCCGTTTACCAGTCAAC
1 CTGCCACATCA---T-CCAT-TGA-CCGTTGACGAGTCAAC
* * *
33454 CTGCCACGTCATCCGTTGACCGTTGACTGGGTCAAC
1 CTGCCACATCATCCATTGACCGTTGAC-GAGTCAAC
33490 CTGCCACATCATC
1 CTGCCACATCATC
33503 TAGTTGACTT
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
35 7 0.10
36 30 0.42
37 3 0.04
38 1 0.01
39 1 0.01
40 4 0.06
41 20 0.28
42 6 0.08
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.25
Consensus pattern (35 bp):
CTGCCACATCATCCATTGACCGTTGACGAGTCAAC
Found at i:33516 original size:36 final size:36
Alignment explanation
Indices: 33448--33518 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
33438 CCGTTTACCA
* *
33448 GTCAACCTGCCACGTCATCCGTTGACCGTTGACTGG
1 GTCAACCTGCCACATCATCAGTTGACCGTTGACTGG
*
33484 GTCAACCTGCCACATCATCTAGTTGA-CTTTGACTG
1 GTCAACCTGCCACATCATC-AGTTGACCGTTGACTG
33519 TTGACTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 26 0.84
37 5 0.16
ACGTcount: A:0.20, C:0.31, G:0.21, T:0.28
Consensus pattern (36 bp):
GTCAACCTGCCACATCATCAGTTGACCGTTGACTGG
Found at i:33702 original size:18 final size:18
Alignment explanation
Indices: 33677--33784 Score: 99
Period size: 18 Copynumber: 6.4 Consensus size: 18
33667 CTATTTTCTG
33677 CCTGTTTGACCTCTTGGT
1 CCTGTTTGACCTCTTGGT
*
33695 CTTGTTTGACCTCTTGGT
1 CCTGTTTGACCTCTTGGT
33713 CCTGTTTGACC-CTTTGGT
1 CCTGTTTGACCTC-TTGGT
33731 CCTGTTT----TC-T-G-
1 CCTGTTTGACCTCTTGGT
* * *
33742 CTTGTTCGACCTCTTAGT
1 CCTGTTTGACCTCTTGGT
33760 CCTGTTTGACCT-TTCGGT
1 CCTGTTTGACCTCTT-GGT
33778 CCTGTTT
1 CCTGTTT
33785 TCTGCCTGAT
Statistics
Matches: 73, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
11 5 0.07
12 1 0.01
13 1 0.01
15 3 0.04
16 1 0.01
17 4 0.05
18 58 0.79
ACGTcount: A:0.06, C:0.27, G:0.20, T:0.47
Consensus pattern (18 bp):
CCTGTTTGACCTCTTGGT
Found at i:33733 original size:65 final size:64
Alignment explanation
Indices: 33652--33784 Score: 187
Period size: 65 Copynumber: 2.1 Consensus size: 64
33642 AGTTTGCTCC
* * *
33652 GTTTGACCTTTCGTCCTATTTTCTGCCTGTTTGACCTCTTGGTCTTGTTTGACCTCTT-GGTCCT
1 GTTTGACCTTTCGTCCTATTTTCTGCCTGTTCGACCTCTTAGTCCTGTTTGACCT-TTCGGTCCT
* * *
33716 GTTTGACCCTTTGGTCCTGTTTTCTGCTTGTTCGACCTCTTAGTCCTGTTTGACCTTTCGGTCCT
1 GTTTGA-CCTTTCGTCCTATTTTCTGCCTGTTCGACCTCTTAGTCCTGTTTGACCTTTCGGTCCT
33781 GTTT
1 GTTT
33785 TCTGCCTGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
64 8 0.13
65 53 0.87
ACGTcount: A:0.06, C:0.26, G:0.20, T:0.48
Consensus pattern (64 bp):
GTTTGACCTTTCGTCCTATTTTCTGCCTGTTCGACCTCTTAGTCCTGTTTGACCTTTCGGTCCT
Found at i:33746 original size:47 final size:47
Alignment explanation
Indices: 33695--33811 Score: 166
Period size: 47 Copynumber: 2.5 Consensus size: 47
33685 ACCTCTTGGT
33695 CTTGTTTGACCTCTTGGTCCTGTTTGACCCTTT-GGTCCTGTTTTCTG
1 CTTGTTTGACCTCTTGGTCCTGTTTGA-CCTTTCGGTCCTGTTTTCTG
* *
33742 CTTGTTCGACCTCTTAGTCCTGTTTGACCTTTCGGTCCTGTTTTCTG
1 CTTGTTTGACCTCTTGGTCCTGTTTGACCTTTCGGTCCTGTTTTCTG
* *
33789 CCTGATTGACCT-TTCGGTCCTGT
1 CTTGTTTGACCTCTT-GGTCCTGT
33812 ATTTTAGCCC
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
46 7 0.11
47 55 0.89
ACGTcount: A:0.06, C:0.27, G:0.21, T:0.46
Consensus pattern (47 bp):
CTTGTTTGACCTCTTGGTCCTGTTTGACCTTTCGGTCCTGTTTTCTG
Found at i:34477 original size:90 final size:90
Alignment explanation
Indices: 34383--34546 Score: 265
Period size: 90 Copynumber: 1.8 Consensus size: 90
34373 ACAAATATTA
* * * * *
34383 AAAAATTGGAGATTTGACTTAGTATGTAATTGTTATATGAATTCATGACTTGAGTAAGACATTAT
1 AAAAATTGAAGATTTGACTTAGTATATAATTGTTATATGAATTCATGACATGAGTAAAACATCAT
*
34448 TTTTTTTAAGCAATAACTTTTTCTT
66 TTATTTTAAGCAATAACTTTTTCTT
*
34473 AAAAATTGAAGATTTGACTTAGTATATAATTGTTATATGAATTCATGAGATGAGTAAAACATCAT
1 AAAAATTGAAGATTTGACTTAGTATATAATTGTTATATGAATTCATGACATGAGTAAAACATCAT
34538 TTATTTTAA
66 TTATTTTAA
34547 CCCCGCAAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 67 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (90 bp):
AAAAATTGAAGATTTGACTTAGTATATAATTGTTATATGAATTCATGACATGAGTAAAACATCAT
TTATTTTAAGCAATAACTTTTTCTT
Found at i:37302 original size:18 final size:18
Alignment explanation
Indices: 37281--37327 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
37271 ATCGTTTTCA
*
37281 TTTTTTTTGTGTTTTTGT
1 TTTTTTTTGTGTTTTCGT
*
37299 TTTTTATTT-CGTTTTCGT
1 TTTTT-TTTGTGTTTTCGT
37317 TTTGTTTTTGT
1 TTT-TTTTTGT
37328 TGGGTTGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.02, C:0.04, G:0.15, T:0.79
Consensus pattern (18 bp):
TTTTTTTTGTGTTTTCGT
Found at i:44504 original size:35 final size:35
Alignment explanation
Indices: 44458--44531 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
44448 ACGTGTCTTT
44458 GAAAATGGGTTTAGC-TGGGATAGAACTATGACG-CA
1 GAAAATGGGTTTAGCTTGGG-TAGAACTATGA-GACA
* *
44493 GAAAATGGGTTTGGCTTGGGTAGAAGTATGAGACA
1 GAAAATGGGTTTAGCTTGGGTAGAACTATGAGACA
44528 GAAA
1 GAAA
44532 TTGAGGAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 1 0.03
35 30 0.86
36 4 0.11
ACGTcount: A:0.35, C:0.08, G:0.34, T:0.23
Consensus pattern (35 bp):
GAAAATGGGTTTAGCTTGGGTAGAACTATGAGACA
Found at i:45224 original size:18 final size:18
Alignment explanation
Indices: 45201--45235 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
45191 GCTTTTCCTT
45201 ATACTCATTTCCAATTAA
1 ATACTCATTTCCAATTAA
45219 ATACTCATTTCCAATTA
1 ATACTCATTTCCAATTA
45236 CGTAGTGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (18 bp):
ATACTCATTTCCAATTAA
Found at i:45571 original size:36 final size:36
Alignment explanation
Indices: 45520--45595 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
45510 AGGGAGTAGT
45520 TTGG-AAAGAGTGAGATTGAATCTGGGTTATCTACC
1 TTGGTAAAGAGTGAGATTGAATCTGGGTTATCTACC
45555 TTGGTAAAGAGTGAGATTGAATCTGGGTTATCTACC
1 TTGGTAAAGAGTGAGATTGAATCTGGGTTATCTACC
45591 TTGGT
1 TTGGT
45596 CTAAAATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 4 0.10
36 36 0.90
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (36 bp):
TTGGTAAAGAGTGAGATTGAATCTGGGTTATCTACC
Found at i:48635 original size:18 final size:18
Alignment explanation
Indices: 48584--48628 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
48574 TTAAGCTCAA
48584 AATATACCATATAAATAT
1 AATATACCATATAAATAT
48602 AATATACCATATAAATAT
1 AATATACCATATAAATAT
48620 AATATACCA
1 AATATACCA
48629 CACAAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (18 bp):
AATATACCATATAAATAT
Done.