Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014828.1 Corchorus capsularis cultivar CVL-1 contig14849, 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: 43045
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:175 original size:32 final size:32
Alignment explanation
Indices: 126--201 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
116 AACGAACAAT
* *
126 ACGCCACTATTTCGCGGCG-CCTAATGAAACCA-
1 ACGCCGCTATTTAGCGGCGTCC-AATGAAA-CAG
*
158 ACGTCGCTATTTAGCGGCGTCCAATGAAACAG
1 ACGCCGCTATTTAGCGGCGTCCAATGAAACAG
190 ACGCCGCTATTT
1 ACGCCGCTATTT
202 GGGACCCCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 2 0.05
32 34 0.89
33 2 0.05
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.22
Consensus pattern (32 bp):
ACGCCGCTATTTAGCGGCGTCCAATGAAACAG
Found at i:707 original size:28 final size:28
Alignment explanation
Indices: 637--709 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
627 ATTTTCTTCC
* * *
637 TTCTCCTCTCCGTCGA-GCGCAGCGACG
1 TTCTCCTCTCCATCGATTCGCAGAGACG
* * *
664 TTCCCCTCTCAATCGATTCGCAGAGCCG
1 TTCTCCTCTCCATCGATTCGCAGAGACG
*
692 TTCTCCTCTCCTTCGATT
1 TTCTCCTCTCCATCGATT
710 TGAGACTTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 13 0.36
28 23 0.64
ACGTcount: A:0.12, C:0.40, G:0.18, T:0.30
Consensus pattern (28 bp):
TTCTCCTCTCCATCGATTCGCAGAGACG
Found at i:747 original size:6 final size:6
Alignment explanation
Indices: 736--791 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
726 ACAGTAAGTA
* * * *
736 CTTTTC CTTTTC CTTTTA CTTTTC ATTTTA CTTTT- CATTTC CTTTTC
1 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC
*
783 TTTTTC CTT
1 CTTTTC CTT
792 CCGTGAGTTC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
5 4 0.10
6 36 0.90
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (6 bp):
CTTTTC
Found at i:870 original size:14 final size:14
Alignment explanation
Indices: 851--887 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
841 TTGGGTGTAA
*
851 CCCTAATTTCCTGT
1 CCCTAATTTCATGT
865 CCCTAATTTCATGT
1 CCCTAATTTCATGT
879 CCCTAATTT
1 CCCTAATTT
888 GTAAAACCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.32, G:0.05, T:0.43
Consensus pattern (14 bp):
CCCTAATTTCATGT
Found at i:2643 original size:27 final size:27
Alignment explanation
Indices: 2607--2750 Score: 243
Period size: 27 Copynumber: 5.3 Consensus size: 27
2597 GTCTTCTCTC
*
2607 CCCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
*
2634 CCCACTTCGACCCCAGCATTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
2661 CCCACTTCGACCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
* *
2688 CCTACTTCGACCCCAGCACTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
*
2715 CCCACTTCGATCCCAGCAGTGGATCCT
1 CCCACTTCGACCCCAGCAGTGGATCCT
2742 CCCACTTCG
1 CCCACTTCG
2751 CCTATGGTGG
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 109 1.00
ACGTcount: A:0.19, C:0.44, G:0.17, T:0.21
Consensus pattern (27 bp):
CCCACTTCGACCCCAGCAGTGGATCCT
Found at i:3579 original size:17 final size:17
Alignment explanation
Indices: 3557--3591 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3547 GAAAAAGTGC
3557 ATTCTTGGTGGCACATT
1 ATTCTTGGTGGCACATT
* *
3574 ATTCTTGTTGGCATATT
1 ATTCTTGGTGGCACATT
3591 A
1 A
3592 ACATTATGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (17 bp):
ATTCTTGGTGGCACATT
Found at i:5180 original size:32 final size:32
Alignment explanation
Indices: 5119--5181 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
5109 GATATAACGT
* *
5119 TATATAGCGGCGTCTGAAGAACAAAACGCCGC
1 TATATAACGGCGTCTGAAAAACAAAACGCCGC
* *
5151 TATATAACGGCGTCTGAAAAACCAGACGCCG
1 TATATAACGGCGTCTGAAAAACAAAACGCCG
5182 TAAACTTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (32 bp):
TATATAACGGCGTCTGAAAAACAAAACGCCGC
Found at i:5286 original size:24 final size:24
Alignment explanation
Indices: 5259--5326 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
5249 CTAAATGGTA
*
5259 GCGTCTAGACGCCACTATTT-CGCG
1 GCGTCTAGACGCCACTATTTAAG-G
* *
5283 GCGTCTCGACGCCACCATTTAAGG
1 GCGTCTAGACGCCACTATTTAAGG
* *
5307 GCGTCTGGACGCCGCTATTT
1 GCGTCTAGACGCCACTATTT
5327 GCAATTTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 36 0.97
25 1 0.03
ACGTcount: A:0.16, C:0.32, G:0.26, T:0.25
Consensus pattern (24 bp):
GCGTCTAGACGCCACTATTTAAGG
Found at i:8475 original size:28 final size:26
Alignment explanation
Indices: 8395--8666 Score: 185
Period size: 28 Copynumber: 10.0 Consensus size: 26
8385 TTTACCTTCT
* *
8395 TTTTTTACTAATTACCTTTCTTAC-C
1 TTTTTTACTGATTACCTTTTTTACTC
* *
8420 TTTTTTACTGATTA-CTAGTTTTGCTC
1 TTTTTTACTGATTACCT-TTTTTACTC
*
8446 TTTTTTACTTATTACCCTTTTCTTACTC
1 TTTTTTACTGATTA-CCTTTT-TTACTC
8474 TTTTTTTTTACTGATTACACTTTTCTTA--C
1 ---TTTTTTACTGATTAC-CTTTT-TTACTC
* *
8503 -TTTTTACTGAATACCATTTTTTTACTTT
1 TTTTTTACTGATTACC--TTTTTTAC-TC
* *
8531 TTTCCTTTACTGAATACCATTTTTACTC
1 TTT--TTTACTGATTACCTTTTTTACTC
* * * *
8559 TTTTTACTACTAAATACCATTTTTACTT
1 TTTTT--TACTGATTACCTTTTTTACTC
*
8587 TTTTTTACTGATTACCATTTCTTACTC
1 TTTTTTACTGATTACC-TTTTTTACTC
* * *
8614 TTTTTTAACTGAATATCATTTTTTATTC
1 TTTTTT-ACTGATTA-CCTTTTTTACTC
*
8642 TTTTTTACTGATTACCATTTTTACT
1 TTTTTTACTGATTACCTTTTTTACT
8667 TTACTGATTA
Statistics
Matches: 198, Mismatches: 27, Indels: 43
0.74 0.10 0.16
Matches are distributed among these distances:
24 3 0.02
25 33 0.17
26 37 0.19
27 22 0.11
28 56 0.28
29 11 0.06
30 1 0.01
31 35 0.18
ACGTcount: A:0.20, C:0.19, G:0.03, T:0.58
Consensus pattern (26 bp):
TTTTTTACTGATTACCTTTTTTACTC
Found at i:8484 original size:31 final size:30
Alignment explanation
Indices: 8446--8668 Score: 99
Period size: 31 Copynumber: 8.0 Consensus size: 30
8436 AGTTTTGCTC
* *
8446 TTTTTTACTTATTACCCTTTTCTTACTCTTT
1 TTTTTTACTGATTACACTTTTCTTACT-TTT
8477 TTTTTTACTGATTACACTTTTCTTAC----
1 TTTTTTACTGATTACACTTTTCTTACTTTT
* *
8503 -TTTTTACTGAATAC-CATTTTTTTACTTTT
1 TTTTTTACTGATTACAC-TTTTCTTACTTTT
* * * *
8532 TTCCTTTACTGAATAC-CATTT-TTACTCTT
1 TT-TTTTACTGATTACACTTTTCTTACTTTT
** * * *
8561 TTTACTACTAAATAC-CATTT-TTAC--TT
1 TTTTTTACTGATTACACTTTTCTTACTTTT
* *
8587 TTTTTTACTGATTAC-CATTTCTTAC-TCT
1 TTTTTTACTGATTACACTTTTCTTACTTTT
* * *
8615 TTTTTAACTGAATATCA-TTTT-TTA--TTC
1 TTTTTTACTGATTA-CACTTTTCTTACTTTT
*
8642 TTTTTTACTGATTAC-CATTT-TTACTTT
1 TTTTTTACTGATTACACTTTTCTTACTTT
8669 ACTGATTACT
Statistics
Matches: 154, Mismatches: 24, Indels: 31
0.74 0.11 0.15
Matches are distributed among these distances:
24 1 0.01
25 21 0.14
26 25 0.16
27 17 0.11
28 36 0.23
29 13 0.08
30 4 0.03
31 37 0.24
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.58
Consensus pattern (30 bp):
TTTTTTACTGATTACACTTTTCTTACTTTT
Found at i:8528 original size:56 final size:56
Alignment explanation
Indices: 8420--8665 Score: 203
Period size: 55 Copynumber: 4.4 Consensus size: 56
8410 CTTTCTTACC
* * * * * *
8420 TTTTTTACTGATTACTAGTT-TTGCTCTTTTTTACTTATTACCCTTTTCTTACTCTTT
1 TTTTTTACTGATTACCATTTCTTAC-CTTTTTTACTGAATACCATTTT-TTACTCTTT
*
8477 TTTTTTACTGATTACACTTTTCTTA-C-TTTTTACTGAATACCATTTTTTTACT-TTT
1 TTTTTTACTGATTAC-CATTTCTTACCTTTTTTACTGAATACCA-TTTTTTACTCTTT
* * *
8532 TTCCTTTACTGAATACCATTT-TTACTCTTTTTACTACTAAATACCA-TTTTTA--C-TT
1 TT-TTTTACTGATTACCATTTCTTAC-CTTTTT--TACTGAATACCATTTTTTACTCTTT
* *
8587 TTTTTTACTGATTACCATTTCTTACTCTTTTTTAACTGAATATCATTTTTTA---TTC
1 TTTTTTACTGATTACCATTTCTTAC-CTTTTTT-ACTGAATACCATTTTTTACTCTTT
8642 TTTTTTACTGATTACCATTT-TTAC
1 TTTTTTACTGATTACCATTTCTTAC
8666 TTTACTGATT
Statistics
Matches: 159, Mismatches: 16, Indels: 31
0.77 0.08 0.15
Matches are distributed among these distances:
53 1 0.01
54 32 0.20
55 51 0.32
56 30 0.19
57 30 0.19
58 2 0.01
59 13 0.08
ACGTcount: A:0.20, C:0.18, G:0.04, T:0.58
Consensus pattern (56 bp):
TTTTTTACTGATTACCATTTCTTACCTTTTTTACTGAATACCATTTTTTACTCTTT
Found at i:8603 original size:54 final size:53
Alignment explanation
Indices: 8395--8666 Score: 236
Period size: 54 Copynumber: 5.0 Consensus size: 53
8385 TTTACCTTCT
* * * * *
8395 TTTTTTACT-AATTACC-TTTCTTAC-CTTTTTTACTGATTACTAGTTTTGCTC
1 TTTTTTACTGAA-TACCATTTTTTACTTTTTTTTACTGATTACCATTTTTACTC
* * * *
8446 TTTTTTACTTATTACCCTTTTCTTACTCTTTTTTTTTACTGATTA-CACTTTT-CT-
1 TTTTTTACTGAATACCATTTT-TTA--C-TTTTTTTTACTGATTACCATTTTTACTC
*
8500 TACTTTTTACTGAATACCATTTTTTTACTTTTTTCCTTTACTGAATACCATTTTTACTC
1 T--TTTTTACTGAATACCA-TTTTTTAC-TTTTT--TTTACTGATTACCATTTTTACTC
*
8559 TTTTTACTACTAAATACCA-TTTTTACTTTTTTTTACTGATTACCATTTCTTACTC
1 TTTTT--TACTGAATACCATTTTTTACTTTTTTTTACTGATTACCATTT-TTACTC
*
8614 TTTTTTAACTGAATATCATTTTTTA-TTCTTTTTTACTGATTACCATTTTTACT
1 TTTTTT-ACTGAATACCATTTTTTACTT-TTTTTTACTGATTACCATTTTTACT
8667 TTACTGATTA
Statistics
Matches: 186, Mismatches: 14, Indels: 39
0.78 0.06 0.16
Matches are distributed among these distances:
51 13 0.07
52 4 0.02
53 4 0.02
54 40 0.22
55 40 0.22
56 36 0.19
57 35 0.19
58 2 0.01
59 12 0.06
ACGTcount: A:0.20, C:0.19, G:0.03, T:0.58
Consensus pattern (53 bp):
TTTTTTACTGAATACCATTTTTTACTTTTTTTTACTGATTACCATTTTTACTC
Found at i:8638 original size:55 final size:53
Alignment explanation
Indices: 8420--8666 Score: 225
Period size: 56 Copynumber: 4.5 Consensus size: 53
8410 CTTTCTTACC
* * * * * * *
8420 TTTTTTACTGATTACTAGTTTTGCTCTTTTTTACTTATTACCCTTTTCTTACTCTTT
1 TTTTTTACTGATTACCATTTTTACTCTTTTTAACTGAATACCATTTT-TTA--C-TT
*
8477 TTTTTTACTGATTA-CACTTTT-CTTACTTTTT-ACTGAATACCATTTTTTTACTTT
1 TTTTTTACTGATTACCATTTTTAC-T-CTTTTTAACTGAATACCA-TTTTTTAC-TT
* *
8531 TTTCCTTTACTGAATACCATTTTTACTCTTTTTACTACTAAATACCA-TTTTTACTT
1 TTT--TTTACTGATTACCATTTTTACTCTTTTTA--ACTGAATACCATTTTTTACTT
*
8587 TTTTTTACTGATTACCATTTCTTACTCTTTTTTAACTGAATATCATTTTTTA-TT
1 TTTTTTACTGATTACCATTT-TTACTC-TTTTTAACTGAATACCATTTTTTACTT
8641 CTTTTTTACTGATTACCATTTTTACT
1 -TTTTTTACTGATTACCATTTTTACT
8667 TTACTGATTA
Statistics
Matches: 165, Mismatches: 11, Indels: 31
0.80 0.05 0.15
Matches are distributed among these distances:
54 39 0.24
55 33 0.20
56 44 0.27
57 38 0.23
58 1 0.01
59 10 0.06
ACGTcount: A:0.20, C:0.18, G:0.04, T:0.58
Consensus pattern (53 bp):
TTTTTTACTGATTACCATTTTTACTCTTTTTAACTGAATACCATTTTTTACTT
Found at i:8720 original size:36 final size:36
Alignment explanation
Indices: 8653--8862 Score: 192
Period size: 36 Copynumber: 6.1 Consensus size: 36
8643 TTTTTACTGA
* **
8653 TTACCATTTTTAC--TTTACTGATTACTATTTACTCC
1 TTACCA-TTTTACTTTTTACTGATTACTCTTTACTTT
* *
8688 TTATCATTTTACTTTTTACTGATTGCTCTTTACTTT
1 TTACCATTTTACTTTTTACTGATTACTCTTTACTTT
* * *
8724 TTACCATTTTACTATTTACTGATCAC-CATTACTTT
1 TTACCATTTTACTTTTTACTGATTACTCTTTACTTT
**
8759 TTACCATTTTACCCTTTACTGATTA--C--T-C--T
1 TTACCATTTTACTTTTTACTGATTACTCTTTACTTT
* *
8788 TTACCATTTTAC-TCTTACTGATTGCTCTTTACTTTT
1 TTACCATTTTACTTTTTACTGATTACTCTTTAC-TTT
* *
8824 TTACCATTTTACTTTTTACTCATTAC-CATTACTTT
1 TTACCATTTTACTTTTTACTGATTACTCTTTACTTT
8859 TTAC
1 TTAC
8863 TGATTACCAT
Statistics
Matches: 144, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
28 9 0.06
29 13 0.09
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 7 0.05
35 42 0.29
36 58 0.40
37 10 0.07
ACGTcount: A:0.21, C:0.22, G:0.03, T:0.53
Consensus pattern (36 bp):
TTACCATTTTACTTTTTACTGATTACTCTTTACTTT
Found at i:8720 original size:71 final size:70
Alignment explanation
Indices: 8645--8791 Score: 170
Period size: 71 Copynumber: 2.1 Consensus size: 70
8635 TTTATTCTTT
* * * **
8645 TTTACTGATTACCATTTTTAC-TTTACTGATTACTATTTACTCCTTATCATTTTACTTTTTACTG
1 TTTACTGATTACCA-TTTTACATTTACTGATCACCA-TTACTCCTTACCATTTTACCCTTTACTG
*
8709 ATTGCTC
64 ATTACTC
** **
8716 TTTACTTTTTACCATTTTACTATTTACTGATCACCATTACTTTTTACCATTTTACCCTTTACTGA
1 TTTACTGATTACCATTTTAC-ATTTACTGATCACCATTACTCCTTACCATTTTACCCTTTACTGA
8781 TTACTC
65 TTACTC
8787 TTTAC
1 TTTAC
8792 CATTTTACTC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
70 6 0.09
71 46 0.72
72 12 0.19
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.52
Consensus pattern (70 bp):
TTTACTGATTACCATTTTACATTTACTGATCACCATTACTCCTTACCATTTTACCCTTTACTGAT
TACTC
Found at i:8741 original size:22 final size:22
Alignment explanation
Indices: 8716--8800 Score: 61
Period size: 22 Copynumber: 4.0 Consensus size: 22
8706 CTGATTGCTC
8716 TTTACTTTTTACCATTTTACTA
1 TTTACTTTTTACCATTTTACTA
** * *
8738 TTTACTGATCACCA--TTACTT
1 TTTACTTTTTACCATTTTACTA
* *
8758 TTTACCATTTTACC-CTTTACTGA
1 TTTA-CTTTTTACCATTTTACT-A
*
8781 -TTACTCTTTACCATTTTACT
1 TTTACTTTTTACCATTTTACT
8801 CTTACTGATT
Statistics
Matches: 46, Mismatches: 12, Indels: 10
0.68 0.18 0.15
Matches are distributed among these distances:
20 9 0.20
21 12 0.26
22 25 0.54
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTACTTTTTACCATTTTACTA
Found at i:8778 original size:57 final size:56
Alignment explanation
Indices: 8713--8897 Score: 149
Period size: 57 Copynumber: 3.1 Consensus size: 56
8703 TTACTGATTG
*
8713 CTCTTTACTTTTTACCATTTTACTATTTACTGATCACCATTACTTTTTACCATTTTA
1 CTCTTTACTTTTTACCATTTTACT-TTTACTGATTACCATTACTTTTTACCATTTTA
* * * *
8770 CCCTTTACTGATTACTCTTTACCATTTTACTCTTACTGATTGCTCTTTACTTTTTTACCATTTTA
1 --C--T-CT--TTACTTTTTACCATTTTACTTTTACTGATTAC-CATTAC-TTTTTACCATTTTA
* ** **
8835 CTTTTTACTCATTACCA--TTACTTTTTACTGATTACCATTTCACTGATTACCATTTTA
1 CTCTTTACTTTTTACCATTTTAC-TTTTACTGATTACCA-TT-ACTTTTTACCATTTTA
8892 CTCTTT
1 CTCTTT
8898 TTAACTGAAT
Statistics
Matches: 103, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
56 5 0.05
57 30 0.29
58 14 0.14
59 1 0.01
60 1 0.01
61 2 0.02
62 2 0.02
63 10 0.10
64 24 0.23
65 14 0.14
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.52
Consensus pattern (56 bp):
CTCTTTACTTTTTACCATTTTACTTTTACTGATTACCATTACTTTTTACCATTTTA
Found at i:8801 original size:15 final size:15
Alignment explanation
Indices: 8752--8803 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
8742 CTGATCACCA
*
8752 TTACTTTTTACCATT
1 TTACTCTTTACCATT
* *
8767 TTACCCTTTA-C-TGA
1 TTACTCTTTACCAT-T
8781 TTACTCTTTACCATT
1 TTACTCTTTACCATT
8796 TTACTCTT
1 TTACTCTT
8804 ACTGATTGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
13 1 0.03
14 10 0.34
15 17 0.59
16 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.02, T:0.54
Consensus pattern (15 bp):
TTACTCTTTACCATT
Found at i:8815 original size:28 final size:29
Alignment explanation
Indices: 8751--8869 Score: 109
Period size: 28 Copynumber: 4.2 Consensus size: 29
8741 ACTGATCACC
*
8751 ATTACTTTTTACCATTTTACCCTTTACTG
1 ATTACTCTTTACCATTTTACCCTTTACTG
*
8780 ATTACTCTTTACCATTTTACTC-TTACTG
1 ATTACTCTTTACCATTTTACCCTTTACTG
* ** * *
8808 ATTGCTCTTTACTTTTTTACCATTTTACTT
1 ATTACTCTTTACCATTTTACC-CTTTACTG
* * **
8838 TTTACTCATTACCA--TTACTTTTTACTG
1 ATTACTCTTTACCATTTTACCCTTTACTG
8865 ATTAC
1 ATTAC
8870 CATTTCACTG
Statistics
Matches: 72, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
27 11 0.15
28 27 0.38
29 20 0.28
30 14 0.19
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.53
Consensus pattern (29 bp):
ATTACTCTTTACCATTTTACCCTTTACTG
Found at i:8825 original size:100 final size:100
Alignment explanation
Indices: 8681--8862 Score: 294
Period size: 100 Copynumber: 1.8 Consensus size: 100
8671 TGATTACTAT
* * *
8681 TTACTCCTTATCATTTTACTTTTTACTGATTGCTCTTTACTTTTTACCATTTTACTATTTACTGA
1 TTACTCCTTACCATTTTACTTCTTACTGATTGCTCTTTACTTTTTACCATTTTACTATTTACTCA
8746 TCACCATTACTTTTTACCATTTTACCCTTTACTGA
66 TCACCATTACTTTTTACCATTTTACCCTTTACTGA
* *
8781 TTACTCTTTACCATTTTAC-TCTTACTGATTGCTCTTTACTTTTTTACCATTTTACTTTTTACTC
1 TTACTCCTTACCATTTTACTTCTTACTGATTGCTCTTTAC-TTTTTACCATTTTACTATTTACTC
*
8845 ATTACCATTACTTTTTAC
65 ATCACCATTACTTTTTAC
8863 TGATTACCAT
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
99 19 0.25
100 56 0.75
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.53
Consensus pattern (100 bp):
TTACTCCTTACCATTTTACTTCTTACTGATTGCTCTTTACTTTTTACCATTTTACTATTTACTCA
TCACCATTACTTTTTACCATTTTACCCTTTACTGA
Found at i:8857 original size:20 final size:20
Alignment explanation
Indices: 8832--8873 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
8822 TTTTACCATT
8832 TTACTTTTTACTCATTACCA
1 TTACTTTTTACTCATTACCA
*
8852 TTACTTTTTACTGATTACCA
1 TTACTTTTTACTCATTACCA
8872 TT
1 TT
8874 TCACTGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.21, G:0.02, T:0.52
Consensus pattern (20 bp):
TTACTTTTTACTCATTACCA
Found at i:8880 original size:100 final size:100
Alignment explanation
Indices: 8681--8884 Score: 288
Period size: 100 Copynumber: 2.0 Consensus size: 100
8671 TGATTACTAT
* * *
8681 TTACTCCTTATCATTTTACTTTTTACTGATTGCTCTTTACTTTTTACCATTTTACTATTTACTGA
1 TTACTCCTTACCATTTTACTTCTTACTGATTGCTCTTTACTTTTTACCATTTTACTATTTACTCA
* *
8746 TCACCATTACTTTTTACCATTTTACCCTTTACTGA
66 TCACCATTACTTTTTACCATATTACCATTTACTGA
* *
8781 TTACTCTTTACCATTTTAC-TCTTACTGATTGCTCTTTACTTTTTTACCATTTTACTTTTTACTC
1 TTACTCCTTACCATTTTACTTCTTACTGATTGCTCTTTAC-TTTTTACCATTTTACTATTTACTC
*
8845 ATTACCATTACTTTTTA-C-TGATTACCATTTCACTGA
65 ATCACCATTACTTTTTACCAT-ATTACCATTT-ACTGA
8881 TTAC
1 TTAC
8885 CATTTTACTC
Statistics
Matches: 93, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
98 1 0.01
99 28 0.30
100 64 0.69
ACGTcount: A:0.21, C:0.23, G:0.04, T:0.52
Consensus pattern (100 bp):
TTACTCCTTACCATTTTACTTCTTACTGATTGCTCTTTACTTTTTACCATTTTACTATTTACTCA
TCACCATTACTTTTTACCATATTACCATTTACTGA
Found at i:8881 original size:15 final size:15
Alignment explanation
Indices: 8861--8889 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
8851 ATTACTTTTT
8861 ACTGATTACCATTTC
1 ACTGATTACCATTTC
8876 ACTGATTACCATTT
1 ACTGATTACCATTT
8890 TACTCTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (15 bp):
ACTGATTACCATTTC
Found at i:13047 original size:10 final size:10
Alignment explanation
Indices: 13032--13056 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13022 GTTGCTGCAC
13032 AATTCCAGAA
1 AATTCCAGAA
13042 AATTCCAGAA
1 AATTCCAGAA
13052 AATTC
1 AATTC
13057 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:17009 original size:165 final size:165
Alignment explanation
Indices: 16772--17077 Score: 594
Period size: 165 Copynumber: 1.9 Consensus size: 165
16762 AACGGAGACT
*
16772 AAAAGCATTCCAACAAGTATTATGTCCAAACTCCAATGTCTTTAATTTCTCAAGAAATGAACCAA
1 AAAAGCATTCCAACAAGTATTATGTCCAAACTCCAATGTCTTCAATTTCTCAAGAAATGAACCAA
16837 AACCAATCTTAATGGAAAAGGGAAATAAAAGGAGAATACAATGAAGAAAGTTGACTATGTAAAGG
66 AACCAATCTTAATGGAAAAGGGAAATAAAAGGAGAATACAATGAAGAAAGTTGACTATGTAAAGG
16902 AAATTAGAAAAAGAACCAAAACCAATGTCTTCAAC
131 AAATTAGAAAAAGAACCAAAACCAATGTCTTCAAC
16937 AAAAGCATTCCAACAAGTATTATGTCCAAACTCCAATGTCTTCAATTTCTCAAGAAATGAACCAA
1 AAAAGCATTCCAACAAGTATTATGTCCAAACTCCAATGTCTTCAATTTCTCAAGAAATGAACCAA
*
17002 AACCAATCTTATTGGAAAAGGGAAATAAAAGGAGAATACAATGAAGAAAGTTGACTATGTAAAGG
66 AACCAATCTTAATGGAAAAGGGAAATAAAAGGAGAATACAATGAAGAAAGTTGACTATGTAAAGG
17067 AAATTAGAAAA
131 AAATTAGAAAA
17078 TGACACAACT
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 139 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (165 bp):
AAAAGCATTCCAACAAGTATTATGTCCAAACTCCAATGTCTTCAATTTCTCAAGAAATGAACCAA
AACCAATCTTAATGGAAAAGGGAAATAAAAGGAGAATACAATGAAGAAAGTTGACTATGTAAAGG
AAATTAGAAAAAGAACCAAAACCAATGTCTTCAAC
Found at i:19893 original size:1 final size:1
Alignment explanation
Indices: 19887--19914 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
19877 TTCCATTTGA
19887 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
19915 GCATTATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:21568 original size:2 final size:2
Alignment explanation
Indices: 21552--21599 Score: 55
Period size: 2 Copynumber: 24.0 Consensus size: 2
21542 CTAGGTACAG
*
21552 TA TA TA T- TA TGA TA TA TA TA TA TA TA TGA TA TA TA GA T- TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
21594 TA TA TA
1 TA TA TA
21600 GTATGAGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 2 0.05
2 34 0.85
3 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:21577 original size:20 final size:20
Alignment explanation
Indices: 21552--21598 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 20
21542 CTAGGTACAG
21552 TATATATTATGATATAT--A-
1 TATATA-TATGATATATAGAT
21570 TATATATATGATATATAGAT
1 TATATATATGATATATAGAT
21590 TATATATAT
1 TATATATAT
21599 AGTATGAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.38
18 6 0.23
19 1 0.04
20 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (20 bp):
TATATATATGATATATAGAT
Found at i:22267 original size:18 final size:18
Alignment explanation
Indices: 22244--22284 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
22234 ACCACCAGCG
22244 GGCACCGTAGTTT-TAGTA
1 GGCACCGTAGTTTCT-GTA
22262 GGCACCGTAGTTTCTGTA
1 GGCACCGTAGTTTCTGTA
22280 GGCAC
1 GGCAC
22285 ATTTCTTGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (18 bp):
GGCACCGTAGTTTCTGTA
Found at i:25187 original size:20 final size:19
Alignment explanation
Indices: 25149--25189 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
25139 TAGTGAGATA
25149 TTAGCAATTGCTTTAATAT
1 TTAGCAATTGCTTTAATAT
* *
25168 TTAGCATATTTCTTTTATAT
1 TTAGCA-ATTGCTTTAATAT
25188 TT
1 TT
25190 CAAAATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.56
Consensus pattern (19 bp):
TTAGCAATTGCTTTAATAT
Found at i:25361 original size:32 final size:33
Alignment explanation
Indices: 25300--25367 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
25290 TTGTCACATT
* *
25300 AGTCCTTTTATTTTAGTATATGAAGTCATTTTAG
1 AGTCCTTTTATTTTAG-ACATGAAATCATTTTAG
*
25334 AGTCTTTTTATTTTAG-CATGAAATCATTTTAG
1 AGTCCTTTTATTTTAGACATGAAATCATTTTAG
25366 AG
1 AG
25368 AAATTGCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 16 0.52
34 15 0.48
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.49
Consensus pattern (33 bp):
AGTCCTTTTATTTTAGACATGAAATCATTTTAG
Found at i:29109 original size:40 final size:40
Alignment explanation
Indices: 28945--29121 Score: 128
Period size: 40 Copynumber: 4.2 Consensus size: 40
28935 TGGTACCCAG
* *
28945 TAATTAAGAG-AGGAAGTAAAAAGATTAATTAGTAAATTGA
1 TAATTAAGAGTA-AAAGTAAAAAGATTAATCAGTAAATTGA
* *
28985 TAATTAAGGAAGTAAAAGTAGTAATCAGTAATTAAAT-A-AAAGGATTGA
1 TAATTAA-G-AGTAAAAGTA--AA-AAG--ATT-AATCAGTAA--ATTGA
*** * *
29033 TAATTAAGAGGGGAAGT-AAAGGATTATTCAGTAAATTGA
1 TAATTAAGAGTAAAAGTAAAAAGATTAATCAGTAAATTGA
*
29072 TAATTAAGAGTCAAAGTAAAAAGATTAATCAGTAAATTGA
1 TAATTAAGAGTAAAAGTAAAAAGATTAATCAGTAAATTGA
*
29112 TAAATAAGAG
1 TAATTAAGAG
29122 AGGAAGTAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 28
0.71 0.11 0.19
Matches are distributed among these distances:
39 21 0.20
40 40 0.37
41 3 0.03
42 8 0.07
43 3 0.03
44 2 0.02
45 2 0.02
46 8 0.07
47 5 0.05
48 15 0.14
ACGTcount: A:0.51, C:0.02, G:0.20, T:0.27
Consensus pattern (40 bp):
TAATTAAGAGTAAAAGTAAAAAGATTAATCAGTAAATTGA
Found at i:29146 original size:40 final size:39
Alignment explanation
Indices: 29028--29133 Score: 140
Period size: 40 Copynumber: 2.7 Consensus size: 39
29018 AAATAAAAGG
* * *
29028 ATTGATAATTAAGAGGGGAAGTAAAGGATTATTCAGTAA
1 ATTGATAATTAAGAGAGGAAGTAAAAGATTAATCAGTAA
***
29067 ATTGATAATTAAGAGTCAAAGTAAAAAGATTAATCAGTAA
1 ATTGATAATTAAGAGAGGAAGT-AAAAGATTAATCAGTAA
*
29107 ATTGATAAATAAGAGAGGAAGTAAAAG
1 ATTGATAATTAAGAGAGGAAGTAAAAG
29134 TAGCAGTCAG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 24 0.42
40 33 0.58
ACGTcount: A:0.50, C:0.03, G:0.22, T:0.25
Consensus pattern (39 bp):
ATTGATAATTAAGAGAGGAAGTAAAAGATTAATCAGTAA
Found at i:29174 original size:32 final size:33
Alignment explanation
Indices: 29138--29210 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 33
29128 TAAAAGTAGC
*
29138 AGTCAGTAACTAAGGGTCAA-AGTAAAAGGA-TA
1 AGTCAGTAACTAAGAGTCAAGA-TAAAAGGATTA
*
29170 AGTCAGTAATTAAGAGTCAAGATAAAAGGATTA
1 AGTCAGTAACTAAGAGTCAAGATAAAAGGATTA
29203 A-TCAGTAA
1 AGTCAGTAA
29211 ATTGATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 33 0.89
33 4 0.11
ACGTcount: A:0.48, C:0.08, G:0.22, T:0.22
Consensus pattern (33 bp):
AGTCAGTAACTAAGAGTCAAGATAAAAGGATTA
Found at i:29378 original size:40 final size:40
Alignment explanation
Indices: 29327--29475 Score: 244
Period size: 40 Copynumber: 3.7 Consensus size: 40
29317 CAGTAGAATG
* **
29327 GAGTGAAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
29367 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
* *
29407 GAGTAAAAGCAAAAGAAGTAATCAGTAAAATGGTAGTTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
*
29447 GAGTAAATGTAAAAGAAGTAATCAGTAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAA
29476 TCAGTAAAGA
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.52, C:0.03, G:0.22, T:0.22
Consensus pattern (40 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
Found at i:29475 original size:22 final size:21
Alignment explanation
Indices: 29448--29493 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
29438 GGTAGTTAAG
29448 AGTAAAT-GTAAAAGAAGTAATC
1 AGTAAATAGT-AAAG-AGTAATC
29470 AGTAAATCAGTAAAGAGTAATC
1 AGTAAAT-AGTAAAGAGTAATC
29492 AG
1 AG
29494 CAAAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 16 0.73
23 4 0.18
24 2 0.09
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTAAATAGTAAAGAGTAATC
Found at i:29561 original size:36 final size:36
Alignment explanation
Indices: 29480--29651 Score: 197
Period size: 36 Copynumber: 4.9 Consensus size: 36
29470 AGTAAATCAG
*
29480 TAAAGAGTAATCAGCAAAGA--AAAATGGTAAAGAA
1 TAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAGAA
* * * * *
29514 TAAAGAATAATCAGGAAAGAGTTATATGGTAAAGAG
1 TAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAGAA
* * *
29550 CAAGGAGTAATCAGTAAAGAGTAAAATGGTAAAAAA
1 TAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAGAA
* *
29586 TAAAGAGTAATCAGTAAAAAGTAAAATGGTAAAGAG
1 TAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAGAA
** *
29622 TAAATTGTAATCAGTAAAGTG-AAAATGGTA
1 TAAAGAGTAATCAGTAAAGAGTAAAATGGTA
29652 TTCAGTTAAA
Statistics
Matches: 114, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
34 18 0.16
35 9 0.08
36 87 0.76
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.20
Consensus pattern (36 bp):
TAAAGAGTAATCAGTAAAGAGTAAAATGGTAAAGAA
Found at i:29588 original size:72 final size:71
Alignment explanation
Indices: 29481--29651 Score: 218
Period size: 72 Copynumber: 2.4 Consensus size: 71
29471 GTAAATCAGT
* * * * *
29481 AAAGAGTAATCAGCAAAGA-AAAATGGTAAAGAATAAAGAATAATCAGGAAAGAGTTATATGGTA
1 AAAGAGTAATCAGTAAAGAGAAAATGGTAAAAAATAAAGAATAATCAGGAAAAAGTAAAATGGTA
29545 AAGAGC
66 AAGAGC
* * *
29551 AAGGAGTAATCAGTAAAGAGTAAAATGGTAAAAAATAAAGAGTAATCAGTAAAAAGTAAAATGGT
1 AAAGAGTAATCAGTAAAGAG-AAAATGGTAAAAAATAAAGAATAATCAGGAAAAAGTAAAATGGT
*
29616 AAAGAGT
65 AAAGAGC
** *
29623 AAATTGTAATCAGTAAAGTGAAAATGGTA
1 AAAGAGTAATCAGTAAAGAGAAAATGGTA
29652 TTCAGTTAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
70 17 0.20
71 9 0.10
72 60 0.70
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.20
Consensus pattern (71 bp):
AAAGAGTAATCAGTAAAGAGAAAATGGTAAAAAATAAAGAATAATCAGGAAAAAGTAAAATGGTA
AAGAGC
Found at i:29647 original size:21 final size:21
Alignment explanation
Indices: 29614--29719 Score: 68
Period size: 26 Copynumber: 4.6 Consensus size: 21
29604 AAGTAAAATG
* *
29614 GTAAAGAGTAAATTGTAATCA
1 GTAAAGAGAAAATGGTAATCA
* *
29635 GTAAAGTGAAAATGGTATTCA
1 GTAAAGAGAAAATGGTAATCA
29656 GTTAAAAAGAGTAAAAATGGTAATCA
1 G-T--AAAGAG--AAAATGGTAATCA
* *
29682 GAAAAAAAGAGTAAAAATGGTATTCA
1 G---TAAAGAG--AAAATGGTAATCA
29708 GTAAAGAGAAAA
1 GTAAAGAGAAAA
29720 GAGTAAAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
21 22 0.32
22 1 0.01
23 6 0.09
24 5 0.07
26 34 0.50
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.23
Consensus pattern (21 bp):
GTAAAGAGAAAATGGTAATCA
Found at i:29672 original size:26 final size:26
Alignment explanation
Indices: 29643--29874 Score: 130
Period size: 26 Copynumber: 8.3 Consensus size: 26
29633 CAGTAAAGTG
*
29643 AAAATGGTATTCAGTTAAAAAGAGTA
1 AAAATGGTATTCAGTAAAAAAGAGTA
* *
29669 AAAATGGTAATCAGAAAAAAAGAGTA
1 AAAATGGTATTCAGTAAAAAAGAGTA
29695 AAAATGGTATTCAGTAAAGAGAAAAGAGTAAAA
1 AAAATGGTATTCAGT--A-A-AAAAGAGT---A
* * *
29728 AAAATCGCATTCAGTAAAAAAGGGTA
1 AAAATGGTATTCAGTAAAAAAGAGTA
* *
29754 AGAAAAGAGTAATT-AGTAAAAAAAGAGAGAA
1 A-AAATG-GT-ATTCAGT--AAAAA-AGAGTA
* * * *
29785 AAAAGGGTAATAAGTAAAAAAGAGCA
1 AAAATGGTATTCAGTAAAAAAGAGTA
* * *
29811 AAAATAGTAATCAGTAAAACAG-GTA
1 AAAATGGTATTCAGTAAAAAAGAGTA
29836 AGAAA-GGTAATT-AGTAAAAGAAGAAGGTA
1 A-AAATGGT-ATTCAGTAAAA-AAG-A-GTA
29865 GAAAATGGTA
1 -AAAATGGTA
29875 AAAAGGAAGT
Statistics
Matches: 160, Mismatches: 24, Indels: 41
0.71 0.11 0.18
Matches are distributed among these distances:
25 12 0.08
26 68 0.43
27 8 0.05
28 7 0.04
29 23 0.14
30 22 0.14
31 6 0.04
33 14 0.09
ACGTcount: A:0.57, C:0.04, G:0.22, T:0.18
Consensus pattern (26 bp):
AAAATGGTATTCAGTAAAAAAGAGTA
Found at i:29896 original size:21 final size:23
Alignment explanation
Indices: 29847--29896 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
29837 GAAAGGTAAT
29847 TAGTAAAAGAAGAAGGTAGAAAA
1 TAGTAAAAGAAGAAGGTAGAAAA
* * *
29870 TGGTAAAA-AGGAA-GTAGAATA
1 TAGTAAAAGAAGAAGGTAGAAAA
29891 TAGTAA
1 TAGTAA
29897 TCAATAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 12 0.52
22 4 0.17
23 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (23 bp):
TAGTAAAAGAAGAAGGTAGAAAA
Found at i:37109 original size:33 final size:33
Alignment explanation
Indices: 37033--37156 Score: 144
Period size: 33 Copynumber: 3.7 Consensus size: 33
37023 TAGACAAAGG
* *
37033 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-AT
** * *
37066 GTCGTTTGGCCGGTTGTAGCCGGCCATGTCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
37099 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT
37132 GTCGCGTGGCCGGTCTTGTGGCCGG
1 GTCGCGTGGCCGG--TTGTGGCCGG
37157 TGTTGCGCGG
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
32 3 0.04
33 65 0.84
35 7 0.09
36 2 0.03
ACGTcount: A:0.07, C:0.27, G:0.42, T:0.23
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
Found at i:42368 original size:7 final size:7
Alignment explanation
Indices: 42358--42400 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
42348 CCCAAACTAA
42358 AAACCCT
1 AAACCCT
42365 AAACCCT
1 AAACCCT
42372 AAACCCT
1 AAACCCT
42379 -AACCCT
1 AAACCCT
42385 AAACCCT
1 AAACCCT
42392 AAACCCT
1 AAACCCT
42399 AA
1 AA
42401 GTCTAAAGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 29 0.83
ACGTcount: A:0.44, C:0.42, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:42407 original size:20 final size:20
Alignment explanation
Indices: 42359--42400 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
42349 CCAAACTAAA
42359 AACCCTAAACCCTAAACCCT
1 AACCCTAAACCCTAAACCCT
42379 AACCCTAAACCCTAAACCCT
1 AACCCTAAACCCTAAACCCT
42399 AA
1 AA
42401 GTCTAAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (20 bp):
AACCCTAAACCCTAAACCCT
Found at i:42503 original size:9 final size:9
Alignment explanation
Indices: 42476--42509 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
42466 TGGTCGAAAA
42476 TTTTTTTAT
1 TTTTTTTAT
42485 TTTATTTTAT
1 TTT-TTTTAT
42495 TTTTTTTAT
1 TTTTTTTAT
42504 ATTTTT
1 -TTTTT
42510 CGATATAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTAT
Done.