Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016816.1 Corchorus olitorius cultivar O-4 contig16849, 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: 32949
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7101 original size:16 final size:16
Alignment explanation
Indices: 7082--7171 Score: 58
Period size: 16 Copynumber: 5.6 Consensus size: 16
7072 ATTTAGAAAT
*
7082 ATATCTATATATCTAA
1 ATATATATATATCTAA
* *
7098 ATATATCTATATCTAT
1 ATATATATATATCTAA
* *
7114 TTATATCTA-AT-TAAA
1 ATATATATATATCT-AA
* *
7129 ATATATCTATATCTAT
1 ATATATATATATCTAA
*
7145 TTATACTATATATCTATA
1 ATATA-TATATATCTA-A
*
7163 CTATATATA
1 ATATATATA
7172 AAACTACGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
14 1 0.02
15 11 0.19
16 28 0.48
17 14 0.24
18 4 0.07
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATATATATCTAA
Found at i:8594 original size:43 final size:43
Alignment explanation
Indices: 8527--8798 Score: 141
Period size: 43 Copynumber: 6.3 Consensus size: 43
8517 GGTGTAGTTA
* * * *
8527 ATTATCAAAAATTCATTGGGGGTTATCAAAATTTAATAGTGCT
1 ATTATCAAAATTTCATAGGAGGTTATCAAAATTTAATAGTGAT
* * * *
8570 ATTATCAAAATTTCGTAGGAGGTTAACAAAATTTTATAAG-GAG
1 ATTATCAAAATTTCATAGGAGGTTATCAAAATTTAAT-AGTGAT
* * * *
8613 GTTATAAAAATTT-ATAGAGATGTTATCAAAATTTCATA-TGAT
1 ATTATCAAAATTTCATAG-GAGGTTATCAAAATTTAATAGTGAT
* * * *
8655 GGTTATCAAAATTTCATGAGGTGGTTTTCAAAATTTCATGAG-G--
1 -ATTATCAAAATTTCAT-AGGAGGTTATCAAAATTTAAT-AGTGAT
* * * * *
8698 -TTATCAAAATTTTTAAATTGAGGTTATCAAAATTTTATAGGGAGGT
1 ATTATCAAAA-TTTCATA-GGAGGTTATCAAAATTTAATAGTGA--T
* * * *
8744 -TTATAAAAATTTCATAGTGAGG-TATCACAATTTCATGGT-AT
1 ATTATCAAAATTTCATAG-GAGGTTATCAAAATTTAATAGTGAT
*
8785 GGTTATCAAAATTT
1 -ATTATCAAAATTT
8799 TATAATGTGA
Statistics
Matches: 177, Mismatches: 34, Indels: 36
0.72 0.14 0.15
Matches are distributed among these distances:
41 13 0.07
42 27 0.15
43 83 0.47
44 33 0.19
45 13 0.07
46 8 0.05
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (43 bp):
ATTATCAAAATTTCATAGGAGGTTATCAAAATTTAATAGTGAT
Found at i:8601 original size:21 final size:21
Alignment explanation
Indices: 8528--8798 Score: 210
Period size: 22 Copynumber: 12.6 Consensus size: 21
8518 GTGTAGTTAA
* * *
8528 TTATCAAAAATTCATTGGGGG
1 TTATCAAAATTTCATAGGAGG
* ***
8549 TTATCAAAATTTAATAGTGCTA
1 TTATCAAAATTTCATAG-GAGG
*
8571 TTATCAAAATTTCGTAGGAGG
1 TTATCAAAATTTCATAGGAGG
* *
8592 TTAACAAAATTTTATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
8614 TTATAAAAATTT-ATAGAGATG
1 TTATCAAAATTTCATAG-GAGG
*
8635 TTATCAAAATTTCATATGATGG
1 TTATCAAAATTTCATAGGA-GG
*
8657 TTATCAAAATTTCATGAGGTGG
1 TTATCAAAATTTCAT-AGGAGG
*
8679 TTTTCAAAATTTCAT--GAGG
1 TTATCAAAATTTCATAGGAGG
* * *
8698 TTATCAAAATTTTTAAATTGAGG
1 TTATCAAAA-TTTCATA-GGAGG
*
8721 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
*
8743 TTTATAAAAATTTCATAGTGAGG
1 -TTATCAAAATTTCATAG-GAGG
*
8766 -TATCACAATTTCAT-GGTATGG
1 TTATCAAAATTTCATAGG-A-GG
8787 TTATCAAAATTT
1 TTATCAAAATTT
8799 TATAATGTGA
Statistics
Matches: 200, Mismatches: 35, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
19 12 0.06
20 8 0.04
21 59 0.29
22 88 0.44
23 33 0.17
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.38
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:8770 original size:108 final size:107
Alignment explanation
Indices: 8571--8798 Score: 268
Period size: 108 Copynumber: 2.1 Consensus size: 107
8561 AATAGTGCTA
*
8571 TTATCAAAATTTCGTAGGAGGTTAACAAAATTTTATAAGGAGGTTATAAAAATTTATAGAGATGT
1 TTATCAAAATTTCG-AGGAGGTTAACAAAATTTTATAAGGAGGTTATAAAAATTTATAGAGAGGT
* *
8636 TATCAAAATTTCATATGATGGTTATCAAAATTTCATGAG-GTGG
65 TATAAAAATTTCATATGATGGTTATCAAAATTTCATG-GTATGG
* * * * * *
8679 TTTTCAAAATTTC-ATGAGGTTATCAAAATTTT-TAAATTGAGGTTATCAAAATTTTATAGGGAG
1 TTATCAAAATTTCGAGGAGGTTAACAAAATTTTAT-AA-GGAGGTTAT-AAAAATTTATAGAGAG
*
8742 GTTTATAAAAATTTCATAGTGA-GG-TATCACAATTTCATGGTATGG
63 G-TTATAAAAATTTCATA-TGATGGTTATCAAAATTTCATGGTATGG
8787 TTATCAAAATTT
1 TTATCAAAATTT
8799 TATAATGTGA
Statistics
Matches: 103, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
105 1 0.01
106 19 0.18
107 9 0.09
108 54 0.52
109 17 0.17
110 3 0.03
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (107 bp):
TTATCAAAATTTCGAGGAGGTTAACAAAATTTTATAAGGAGGTTATAAAAATTTATAGAGAGGTT
ATAAAAATTTCATATGATGGTTATCAAAATTTCATGGTATGG
Found at i:9312 original size:26 final size:26
Alignment explanation
Indices: 9293--9345 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
9283 TTTTATTTCT
9293 TGATTACTGATTACCATTTTTTACTC
1 TGATTACTGATTACCATTTTTTACTC
* *
9319 TGTTTACTTATTACCATTTTTTACTC
1 TGATTACTGATTACCATTTTTTACTC
9345 T
1 T
9346 TTCTAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.55
Consensus pattern (26 bp):
TGATTACTGATTACCATTTTTTACTC
Found at i:9548 original size:27 final size:26
Alignment explanation
Indices: 9472--9550 Score: 95
Period size: 27 Copynumber: 3.0 Consensus size: 26
9462 ATTACCCTTG
*
9472 CTCTTTTTACTGATTACCAATTCTTTA
1 CTCTTTTTACTGATTACC-ATTTTTTA
* *
9499 CTCTTTTTACTTATTACCCTTTTTTA
1 CTCTTTTTACTGATTACCATTTTTTA
* *
9525 CTCTTTTTTACTGGTTTCCATTTTTT
1 CTC-TTTTTACTGATTACCATTTTTT
9551 GCCTTTTCTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 9 0.20
27 35 0.80
ACGTcount: A:0.15, C:0.22, G:0.04, T:0.59
Consensus pattern (26 bp):
CTCTTTTTACTGATTACCATTTTTTA
Found at i:9582 original size:35 final size:36
Alignment explanation
Indices: 9542--9619 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 36
9532 TTACTGGTTT
* * *
9542 CCATTTTTTGC-CTTTTCTACTTTAATTATTGAATA
1 CCATTTTTTACACTTTTCTACTTTAATTACTAAATA
*
9577 CCA-TTTTTACACTTTTTTACTTTAATTACTAAATA
1 CCATTTTTTACACTTTTCTACTTTAATTACTAAATA
9612 CCATTTTT
1 CCATTTTT
9620 AATTAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 6 0.16
35 27 0.73
36 4 0.11
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.54
Consensus pattern (36 bp):
CCATTTTTTACACTTTTCTACTTTAATTACTAAATA
Found at i:9620 original size:35 final size:35
Alignment explanation
Indices: 9553--9620 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
9543 CATTTTTTGC
* *
9553 CTTTTCTACTTTAATTATTGAATACCATTTTTACA
1 CTTTTCTACTTTAATTACTAAATACCATTTTTACA
*
9588 CTTTTTTACTTTAATTACTAAATACCATTTTTA
1 CTTTTCTACTTTAATTACTAAATACCATTTTTA
9621 ATTAATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.01, T:0.53
Consensus pattern (35 bp):
CTTTTCTACTTTAATTACTAAATACCATTTTTACA
Found at i:9780 original size:20 final size:20
Alignment explanation
Indices: 9755--9834 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
9745 ACCCTTCTAC
*
9755 TGATTACTATTACTCTCTCT
1 TGATTACTATTACTCTTTCT
*
9775 TGATTACTCCTTACTCTTTAC-
1 TGATTACT-ATTACTCTTT-CT
* * *
9796 TGACTATTATTACACTTTCT
1 TGATTACTATTACTCTTTCT
*
9816 TGATTACTCTTTACTCTTT
1 TGATTACT-ATTACTCTTT
9835 ACTCTTTACT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
19 1 0.02
20 22 0.48
21 22 0.48
22 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.05, T:0.51
Consensus pattern (20 bp):
TGATTACTATTACTCTTTCT
Found at i:9807 original size:41 final size:41
Alignment explanation
Indices: 9691--9837 Score: 152
Period size: 41 Copynumber: 3.5 Consensus size: 41
9681 ATTTTTTTAC
* * * * *
9691 TGATTACTCTTTACTAC-TTACTGATTGCTATTATCATTTTAT
1 TGATTACTCTTTACT-CTTTACTGACTACTATTA-CACTCTCT
* * * *
9733 TGTTTACTCTTTACCCTTCTACTGATTACTATTACTCTCTCT
1 TGATTACTCTTTACTCTT-TACTGACTACTATTACACTCTCT
* * *
9775 TGATTACTCCTTACTCTTTACTGACTATTATTACACTTTCT
1 TGATTACTCTTTACTCTTTACTGACTACTATTACACTCTCT
9816 TGATTACTCTTTACTCTTTACT
1 TGATTACTCTTTACTCTTTACT
9838 CTTTACTGAT
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
41 41 0.47
42 33 0.38
43 14 0.16
ACGTcount: A:0.20, C:0.23, G:0.05, T:0.51
Consensus pattern (41 bp):
TGATTACTCTTTACTCTTTACTGACTACTATTACACTCTCT
Found at i:9831 original size:7 final size:7
Alignment explanation
Indices: 9819--9875 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
9809 ACTTTCTTGA
9819 TTACTCT
1 TTACTCT
9826 TTACTCT
1 TTACTCT
9833 TTACTCT
1 TTACTCT
**
9840 TTACTGA
1 TTACTCT
*
9847 TTACT-A
1 TTACTCT
*
9853 TTACCCTT
1 TTACTC-T
*
9861 TTACTGT
1 TTACTCT
9868 TTACTCT
1 TTACTCT
9875 T
1 T
9876 ACCATTTACT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
6 5 0.12
7 32 0.78
8 4 0.10
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.54
Consensus pattern (7 bp):
TTACTCT
Found at i:9843 original size:21 final size:22
Alignment explanation
Indices: 9819--9897 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 22
9809 ACTTTCTTGA
* *
9819 TTACTCTTTACTCTTTACTC-T
1 TTACTGTTTACTCTTTACCCTT
* *
9840 TTACTGATTACT-ATTACCCTT
1 TTACTGTTTACTCTTTACCCTT
*
9861 TTACTGTTTACTC-TTA-CCAT
1 TTACTGTTTACTCTTTACCCTT
* *
9881 TTACTGATTGCTCTTTA
1 TTACTGTTTACTCTTTA
9898 ACTGATTACT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 19 0.40
21 28 0.60
ACGTcount: A:0.19, C:0.24, G:0.05, T:0.52
Consensus pattern (22 bp):
TTACTGTTTACTCTTTACCCTT
Found at i:9861 original size:20 final size:20
Alignment explanation
Indices: 9833--10007 Score: 96
Period size: 21 Copynumber: 8.8 Consensus size: 20
9823 TCTTTACTCT
*
9833 TTACTCTTTACTGATTACTA
1 TTACCCTTTACTGATTACTA
* *
9853 TTACCCTTTTACTGTTTACTC
1 TTACCC-TTTACTGATTACTA
* *
9874 TTACCATTTACTGATTGC--
1 TTACCCTTTACTGATTACTA
9892 -T---CTTTAACTGATTACTA
1 TTACCCTTT-ACTGATTACTA
* **
9909 TTACTCTTTTACTGATTGTTA
1 TTAC-CCTTTACTGATTACTA
* *
9930 TTACTCTTTTACTGATTACTC
1 TTAC-CCTTTACTGATTACTA
* * *
9951 TTACCATTTACTAATTACTC
1 TTACCCTTTACTGATTACTA
* *
9971 TTACCATTT-CTTGATTACTCT
1 TTACCCTTTAC-TGATTACT-A
9992 TTACTCC-TTACTGATT
1 TTAC-CCTTTACTGATT
10008 GACCCCATTT
Statistics
Matches: 123, Mismatches: 19, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
14 3 0.02
15 8 0.07
17 1 0.01
18 1 0.01
19 1 0.01
20 45 0.37
21 59 0.48
22 5 0.04
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (20 bp):
TTACCCTTTACTGATTACTA
Found at i:9907 original size:35 final size:35
Alignment explanation
Indices: 9858--9972 Score: 113
Period size: 35 Copynumber: 3.1 Consensus size: 35
9848 TACTATTACC
*
9858 CTTTTACTGTTTACTCTTACCATTTACTGATTGCT
1 CTTTTACTGATTACTCTTACCATTTACTGATTGCT
* * *
9893 CTTTAACTGATTACTATTACTCTTTTACTGATTGTTATTACT
1 CTTTTACTGATTACTCTTAC-CATTTACTGATTG------CT
* *
9935 CTTTTACTGATTACTCTTACCATTTACTAATTACT
1 CTTTTACTGATTACTCTTACCATTTACTGATTGCT
9970 CTT
1 CTT
9973 ACCATTTCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
35 22 0.34
36 12 0.19
41 10 0.16
42 20 0.31
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.51
Consensus pattern (35 bp):
CTTTTACTGATTACTCTTACCATTTACTGATTGCT
Found at i:9916 original size:21 final size:21
Alignment explanation
Indices: 9881--10007 Score: 100
Period size: 21 Copynumber: 6.1 Consensus size: 21
9871 CTCTTACCAT
* *
9881 TTACTGATTGCTCTTTAACTGA
1 TTACT-ATTACTCTTTTACTGA
9903 TTACTATTACTCTTTTACTGA
1 TTACTATTACTCTTTTACTGA
**
9924 TTGTTATTACTCTTTTACTGA
1 TTACTATTACTCTTTTACTGA
* * *
9945 TTACTCTTAC-CATTTACTAA
1 TTACTATTACTCTTTTACTGA
* *
9965 TTACTCTTAC-CATTT-CTTGA
1 TTACTATTACTCTTTTAC-TGA
* *
9985 TTACTCTTTACTC-CTTACTGA
1 TTACT-ATTACTCTTTTACTGA
10006 TT
1 TT
10008 GACCCCATTT
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.01
20 30 0.34
21 51 0.57
22 7 0.08
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.50
Consensus pattern (21 bp):
TTACTATTACTCTTTTACTGA
Found at i:10075 original size:26 final size:26
Alignment explanation
Indices: 10046--10499 Score: 553
Period size: 26 Copynumber: 17.3 Consensus size: 26
10036 TTTAGATTTT
*
10046 TCTTTAATTACCAAATTTTC-TCTTAC
1 TCTTTAATTACCAAA-TTTCATTTTAC
*
10072 TCTTTAATTGTCC-AATTTCATTTTAC
1 TCTTTAATT-ACCAAATTTCATTTTAC
* *
10098 TCTTTAATTACCAAATTCCCTTTTAC
1 TCTTTAATTACCAAATTTCATTTTAC
* * *
10124 TCTTTAATTAACAACTTTCCTTTTAC
1 TCTTTAATTACCAAATTTCATTTTAC
*
10150 TCTTCAATTACCAAATTTCATTTTAC
1 TCTTTAATTACCAAATTTCATTTTAC
*
10176 TCTTTAATTACCAAATTTCATTTTAT
1 TCTTTAATTACCAAATTTCATTTTAC
10202 TCTTTAATTAACC-AATTTCATTTTAC
1 TCTTTAATT-ACCAAATTTCATTTTAC
***
10228 TCTTTAATTAATTAATTTCATTTTAC
1 TCTTTAATTACCAAATTTCATTTTAC
*
10254 TCTTTAATTACCCAATTTCATTTTAC
1 TCTTTAATTACCAAATTTCATTTTAC
10280 TCTTTAATTAACCAAA-TTCATTTTAC
1 TCTTTAATT-ACCAAATTTCATTTTAC
10306 TCTTTAATTAACCAAA-TTCATTTTAC
1 TCTTTAATT-ACCAAATTTCATTTTAC
10332 TCTTTAATTAACCAAA-TTCATTTTAC
1 TCTTTAATT-ACCAAATTTCATTTTAC
* *
10358 TCTTTAATTAAACAAATTTCCTTTTAC
1 TCTTTAATT-ACCAAATTTCATTTTAC
*
10385 TCTTTAATTAACCAAATTTCCTTTTAC
1 TCTTTAATT-ACCAAATTTCATTTTAC
* *
10412 TCTTTAATTAACCAAATCTCCTTTTAC
1 TCTTTAATT-ACCAAATTTCATTTTAC
*
10439 TCTTTAATTACCAAATTTCCTTTTAC
1 TCTTTAATTACCAAATTTCATTTTAC
* * * * *
10465 TTTTTGACTATCAAATTTTC-TTTAAC
1 TCTTTAATTACCAAA-TTTCATTTTAC
10491 TCTTTAATT
1 TCTTTAATT
10500 TTTCTCTCTC
Statistics
Matches: 386, Mismatches: 34, Indels: 16
0.89 0.08 0.04
Matches are distributed among these distances:
25 7 0.02
26 295 0.76
27 84 0.22
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (26 bp):
TCTTTAATTACCAAATTTCATTTTAC
Found at i:11248 original size:19 final size:19
Alignment explanation
Indices: 11228--11264 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11218 AATTAATTAT
11228 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
11246 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
11265 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:14490 original size:25 final size:25
Alignment explanation
Indices: 14462--14512 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
14452 AAATGGCCAC
14462 GGTAAATCATAAAACATGTGCAAAT
1 GGTAAATCATAAAACATGTGCAAAT
14487 GGTAAATCATAAAACATGTGCAAAT
1 GGTAAATCATAAAACATGTGCAAAT
14512 G
1 G
14513 CAATTACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (25 bp):
GGTAAATCATAAAACATGTGCAAAT
Found at i:14855 original size:22 final size:22
Alignment explanation
Indices: 14828--14891 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
14818 GGGTGTTACA
14828 GTTATCAAAATTTCATAGGGTG
1 GTTATCAAAATTTCATAGGGTG
14850 GTTATCAAAATTTCATTA-GGTG
1 GTTATCAAAATTTCA-TAGGGTG
* *
14872 GTTATTAAAATTTTATAGGG
1 GTTATCAAAATTTCATAGGG
14892 AAAGTTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.05
22 34 0.89
23 2 0.05
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGGTG
Found at i:14970 original size:22 final size:21
Alignment explanation
Indices: 14945--15011 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
14935 TATCATCATA
14945 AAAATTTAATAGTGTAATTATC
1 AAAATTTAATAGTG-AATTATC
*
14967 AAAATTTTATA-TGAAGGTTATC
1 AAAATTTAATAGTGAA--TTATC
* *
14989 GAAATTTCATAGTG-ATTATC
1 AAAATTTAATAGTGAATTATC
15009 AAA
1 AAA
15012 TTTCATGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 9 0.24
21 2 0.05
22 25 0.66
23 2 0.05
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (21 bp):
AAAATTTAATAGTGAATTATC
Found at i:22861 original size:23 final size:23
Alignment explanation
Indices: 22833--22879 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
22823 TCTGTCTAAT
22833 TTCTCTTCTCATCTTACCTCTGA
1 TTCTCTTCTCATCTTACCTCTGA
*
22856 TTCTCTTCTCATTTTACCTCTGA
1 TTCTCTTCTCATCTTACCTCTGA
22879 T
1 T
22880 CTGATTCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.32, G:0.04, T:0.51
Consensus pattern (23 bp):
TTCTCTTCTCATCTTACCTCTGA
Found at i:23024 original size:23 final size:23
Alignment explanation
Indices: 22996--23042 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
22986 ATAAAGAGAT
22996 TTCTCTTCTCATCTTACCTCTGA
1 TTCTCTTCTCATCTTACCTCTGA
*
23019 TTCTCTTCTCATTTTACCTCTGA
1 TTCTCTTCTCATCTTACCTCTGA
23042 T
1 T
23043 CTGATTCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.32, G:0.04, T:0.51
Consensus pattern (23 bp):
TTCTCTTCTCATCTTACCTCTGA
Found at i:23101 original size:163 final size:163
Alignment explanation
Indices: 22831--23159 Score: 658
Period size: 163 Copynumber: 2.0 Consensus size: 163
22821 ACTCTGTCTA
22831 ATTTCTCTTCTCATCTTACCTCTGATTCTCTTCTCATTTTACCTCTGATCTGATTCCCTATCAGA
1 ATTTCTCTTCTCATCTTACCTCTGATTCTCTTCTCATTTTACCTCTGATCTGATTCCCTATCAGA
22896 TTCTATATGATTTTCCTTTGAGATTCTTTTTTCTTTTGTTTATAAAAGAGTAAAATGGGACTATT
66 TTCTATATGATTTTCCTTTGAGATTCTTTTTTCTTTTGTTTATAAAAGAGTAAAATGGGACTATT
22961 TATCCAGCATAGACTAACAAGAATAATAAAGAG
131 TATCCAGCATAGACTAACAAGAATAATAAAGAG
22994 ATTTCTCTTCTCATCTTACCTCTGATTCTCTTCTCATTTTACCTCTGATCTGATTCCCTATCAGA
1 ATTTCTCTTCTCATCTTACCTCTGATTCTCTTCTCATTTTACCTCTGATCTGATTCCCTATCAGA
23059 TTCTATATGATTTTCCTTTGAGATTCTTTTTTCTTTTGTTTATAAAAGAGTAAAATGGGACTATT
66 TTCTATATGATTTTCCTTTGAGATTCTTTTTTCTTTTGTTTATAAAAGAGTAAAATGGGACTATT
23124 TATCCAGCATAGACTAACAAGAATAATAAAGAG
131 TATCCAGCATAGACTAACAAGAATAATAAAGAG
23157 ATT
1 ATT
23160 ATGGGTGAAC
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 166 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.43
Consensus pattern (163 bp):
ATTTCTCTTCTCATCTTACCTCTGATTCTCTTCTCATTTTACCTCTGATCTGATTCCCTATCAGA
TTCTATATGATTTTCCTTTGAGATTCTTTTTTCTTTTGTTTATAAAAGAGTAAAATGGGACTATT
TATCCAGCATAGACTAACAAGAATAATAAAGAG
Found at i:31778 original size:20 final size:20
Alignment explanation
Indices: 31753--31794 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31743 TCATTTAGTA
* *
31753 CACATCACCAGTTCAGGTGC
1 CACATCAACAATTCAGGTGC
*
31773 CACATCAAGAATTCAGGTGC
1 CACATCAACAATTCAGGTGC
31793 CA
1 CA
31795 AAAGAACAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (20 bp):
CACATCAACAATTCAGGTGC
Done.