Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009436.1 Corchorus capsularis cultivar CVL-1 contig09457, 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: 93025
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:5286 original size:24 final size:21
Alignment explanation
Indices: 5267--5312 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
5257 GGTTGGGCAG
5267 CCCCATAAGGTGGAACTTGGGC
1 CCCCA-AAGGTGGAACTTGGGC
* *
5289 CCCGAATGGTGGAACTTGGGC
1 CCCCAAAGGTGGAACTTGGGC
5310 CCC
1 CCC
5313 ATATCTCTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (21 bp):
CCCCAAAGGTGGAACTTGGGC
Found at i:6180 original size:22 final size:22
Alignment explanation
Indices: 6127--6173 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
6117 ATGATCTCAT
* *
6127 TATGAAATTTTGATAACCTTAC
1 TATGAAATTTTAATAACCATAC
*
6149 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTAATAACCATAC
6171 TAT
1 TAT
6174 AGAATTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTAATAACCATAC
Found at i:6460 original size:23 final size:23
Alignment explanation
Indices: 6402--6488 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 23
6392 GATAATCACA
* * *
6402 CTATGAAATTGTGAT-AACCTCG
1 CTATAAAATTTTGATAAACCTCC
*
6424 CTATGAAAAATTTTGATAAATCTTCC
1 CTAT--AAAATTTTGATAAA-CCTCC
6450 C-ATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAACCTCC
6472 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
6489 CTTTCTTATG
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
22 9 0.16
23 29 0.53
24 9 0.16
25 4 0.07
26 4 0.07
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTCC
Found at i:6544 original size:22 final size:22
Alignment explanation
Indices: 6515--6707 Score: 148
Period size: 22 Copynumber: 8.9 Consensus size: 22
6505 TGATAACTAC
*
6515 AAATTTTGATAAGCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
** **
6537 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCCCTATG
* *
6559 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
* * *
6581 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGAT-AACCTCCCTATG
*
6603 AAATTTTGATAATCCT-CTTATG
1 AAATTTTGATAA-CCTCCCTATG
* **
6625 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CCCTATG
*
6647 AAATTTTGATAACCAT-CATATG
1 AAATTTTGATAACC-TCCCTATG
*
6669 AAATTTTGATATCCTCCC--TG
1 AAATTTTGATAACCTCCCTATG
*
6689 -AATTTTGATATCCTCCCTA
1 AAATTTTGATAACCTCCCTA
6708 AATTTTGATA
Statistics
Matches: 134, Mismatches: 28, Indels: 19
0.74 0.15 0.10
Matches are distributed among these distances:
19 17 0.13
20 4 0.03
21 4 0.03
22 103 0.77
23 5 0.04
24 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:6578 original size:44 final size:44
Alignment explanation
Indices: 6386--6678 Score: 171
Period size: 44 Copynumber: 6.7 Consensus size: 44
6376 TAGTAATCAC
* * * * *
6386 AATTTTGATAATCACACTATGAAATTGTGAT-AACCTCGCTATGAAA
1 AATTTTGATAATCTCCCTATGAAATTTTGATCAACAT-ACTATG--A
* * * * *
6432 AATTTTGATAAATCTTCCC-ATAAAATTTTGATAAACCTCCCTATAA
1 AATTTTGAT-AATC-TCCCTATGAAATTTTGATCAACAT-ACTATGA
* * *
6478 AATTTTGATAA-CTTTCTTATGAAATCTTGAT-AAC-TAC----A
1 AATTTTGATAATC-TCCCTATGAAATTTTGATCAACATACTATGA
* ** * *
6516 AATTTTGATAAGCTCCCTATGATTTTTTGAT-AACCTCATTATGA
1 AATTTTGATAATCTCCCTATGAAATTTTGATCAACAT-ACTATGA
* *
6560 AATTTTGTTAATCTCCCTATGAAATTTTGATCTACATACTATGA
1 AATTTTGATAATCTCCCTATGAAATTTTGATCAACATACTATGA
* * *
6604 AATTTTGATAATC-CTCTTATGAAATTTTGA-AAACTAAACTATGA
1 AATTTTGATAATCTC-CCTATGAAATTTTGATCAAC-ATACTATGA
* *
6648 AATTTTGATAACCAT-CATATGAAATTTTGAT
1 AATTTTGATAATC-TCCCTATGAAATTTTGAT
6679 ATCCTCCCTG
Statistics
Matches: 199, Mismatches: 31, Indels: 35
0.75 0.12 0.13
Matches are distributed among these distances:
38 28 0.14
39 2 0.01
40 1 0.01
42 1 0.01
43 4 0.02
44 101 0.51
45 16 0.08
46 19 0.10
47 15 0.08
48 12 0.06
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (44 bp):
AATTTTGATAATCTCCCTATGAAATTTTGATCAACATACTATGA
Found at i:6624 original size:66 final size:67
Alignment explanation
Indices: 6540--6684 Score: 176
Period size: 66 Copynumber: 2.2 Consensus size: 67
6530 CCCTATGATT
* * ** *
6540 TTTTGATAA-CCTCATTATGAAATTTTGTTAATCT-CCCTATGAAATTTTGATCTA-CAT-ACTA
1 TTTTGATAATCCTCATTATGAAATTTTG-AAAACTAAACTATGAAATTTTGAT-AACCATCA-TA
6601 TGAAA
63 TGAAA
6606 TTTTGATAATCCTC-TTATGAAATTTTGAAAACTAAACTATGAAATTTTGATAACCATCATATGA
1 TTTTGATAATCCTCATTATGAAATTTTGAAAACTAAACTATGAAATTTTGATAACCATCATATGA
6670 AA
66 AA
6672 TTTTGAT-ATCCTC
1 TTTTGATAATCCTC
6685 CCTGAATTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
65 11 0.16
66 54 0.77
67 5 0.07
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (67 bp):
TTTTGATAATCCTCATTATGAAATTTTGAAAACTAAACTATGAAATTTTGATAACCATCATATGA
AA
Found at i:6732 original size:20 final size:20
Alignment explanation
Indices: 6667--6736 Score: 108
Period size: 19 Copynumber: 3.6 Consensus size: 20
6657 AACCATCATA
6667 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
6687 TG-AATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
* *
6706 T-AAATTTTGATATCTTCTC
1 TGAAATTTTGATATCCTCCC
6725 TGAAATTTTGAT
1 TGAAATTTTGAT
6737 TACTCCATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 34 0.74
20 12 0.26
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.46
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:6867 original size:22 final size:22
Alignment explanation
Indices: 6842--6915 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
6832 AATCACATTT
6842 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
*
6864 TGAAAATTTAATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
*
6886 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
6908 T-AAAATTT
1 TGAAAATTT
6916 TGTTGACCCC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
21 6 0.12
22 42 0.88
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:6868 original size:44 final size:44
Alignment explanation
Indices: 6818--6916 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
6808 GAAATACCAC
** *
6818 TATGAAATTTTTGTAATCACATTT-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTAATAACCAC-TTTATGAAAATTTGATAACCTCTT
* * *
6862 TATGAAAATTTAATAACCTCTTTATGAAATTTTGATAACCTCTT
1 TATGAAATTTTAATAACCACTTTATGAAAATTTGATAACCTCTT
*
6906 TATAAAATTTT
1 TATGAAATTTT
6917 GTTGACCCCT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 3 0.07
44 43 0.93
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (44 bp):
TATGAAATTTTAATAACCACTTTATGAAAATTTGATAACCTCTT
Found at i:6932 original size:44 final size:44
Alignment explanation
Indices: 6842--6943 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
6832 AATCACATTT
* * *
6842 TGAAAATTTGATAACCTCTTTATGAAAATTTAATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTATGAAAATTTAATAACCCCTCTA
** *
6886 TGAAATTTTGATAACCTCTTTAT-AAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTATGAAAA-TTTAATAACCCCTCTA
*
6930 TGAAATTCTGATAA
1 TGAAATTTTGATAA
6944 TCACAATGTG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 4 0.08
44 46 0.92
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (44 bp):
TGAAATTTTGATAACCTCTTTATGAAAATTTAATAACCCCTCTA
Found at i:6935 original size:22 final size:22
Alignment explanation
Indices: 6842--6943 Score: 87
Period size: 22 Copynumber: 4.6 Consensus size: 22
6832 AATCACATTT
* * *
6842 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * * *
6864 TGAAAATTTAATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
6886 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
6908 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
*
6930 TGAAATTCTGATAA
1 TGAAATTTTGATAA
6944 TCACAATGTG
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 68 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:7102 original size:22 final size:22
Alignment explanation
Indices: 7072--7192 Score: 83
Period size: 22 Copynumber: 5.5 Consensus size: 22
7062 AAATTGAGAC
*
7072 TTTTATAACCTTCA-TATAAAA
1 TTTTATAACCTACACTATAAAA
7093 TTTTAATAACC-ACACTATAAAA
1 TTTT-ATAACCTACACTATAAAA
* * *
7115 TTTTGATAACCT-CCCAATGAAA
1 TTTT-ATAACCTACACTATAAAA
*
7137 TATTAGTAACCT--ACTAATAAAA
1 TTTTA-TAACCTACACT-ATAAAA
*
7159 TTTTGTTAACC-ACACTATAAAA
1 TTTT-ATAACCTACACTATAAAA
*
7181 TTCGTATAACCT
1 TT-TTATAACCT
7193 CGCTATGACA
Statistics
Matches: 77, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
21 8 0.10
22 65 0.84
23 4 0.05
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (22 bp):
TTTTATAACCTACACTATAAAA
Found at i:7307 original size:24 final size:22
Alignment explanation
Indices: 7246--7429 Score: 124
Period size: 22 Copynumber: 8.3 Consensus size: 22
7236 TTGTGATGAT
* *
7246 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
7268 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* * **
7290 TAATCTGATCCTATGAAATTTTGG
1 TAA-C-CAACCTATGAAATTTTAA
*
7314 TAACC-ACACTATGAAATTTTAG
1 TAACCAAC-CTATGAAATTTTAA
**
7336 TAACC-ACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
7358 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
7380 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
7402 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
7424 TAACCA
1 TAACCA
7430 CATAGAGACA
Statistics
Matches: 136, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
21 3 0.02
22 112 0.82
23 5 0.04
24 16 0.12
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:7406 original size:66 final size:66
Alignment explanation
Indices: 7246--7431 Score: 173
Period size: 66 Copynumber: 2.8 Consensus size: 66
7236 TTGTGATGAT
* * * * *
7246 TAACCACCCTATGAAATT-TCAATAACCAACCTAAGAAATTTTAATAATCTGATC-CTATGAAAT
1 TAACCACACTATGAAATTAT-AATAACCATCCTATGAAATTTTGATAA-C-CA-CACTATGAAAT
*
7309 TTTGG
62 TTTGA
* * * *
7314 TAACCACACTATGAAATTTTAGTAACCA-CACTATGAAATTTTGGTAACCACACTATGGAATTTT
1 TAACCACACTATGAAATTATAATAACCATC-CTATGAAATTTTGATAACCACACTATGAAATTTT
7378 GA
65 GA
* * *
7380 TAACCTC-CTCATGGAATTATAATAACCATCTTATGAAATTTTGATAACCACA
1 TAACCACACT-ATGAAATTATAATAACCATCCTATGAAATTTTGATAACCACA
7432 TAGAGACAAG
Statistics
Matches: 99, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
65 3 0.03
66 54 0.55
67 3 0.03
68 38 0.38
69 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (66 bp):
TAACCACACTATGAAATTATAATAACCATCCTATGAAATTTTGATAACCACACTATGAAATTTTG
A
Found at i:7920 original size:27 final size:29
Alignment explanation
Indices: 7883--7936 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
7873 GTCTAAATTG
* *
7883 AAATTTTATAAT-T-AATTTTTAAATAAT
1 AAATTTAATAATGTCAATTTATAAATAAT
7910 AAATTTAATAATGTCAATTTATAAATA
1 AAATTTAATAATGTCAATTTATAAATA
7937 TATTTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 11 0.48
28 1 0.04
29 11 0.48
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (29 bp):
AAATTTAATAATGTCAATTTATAAATAAT
Found at i:7994 original size:26 final size:26
Alignment explanation
Indices: 7958--8008 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
7948 TGGTACAATC
* *
7958 GGAAAATATAAAGTTTTCCATTATTT
1 GGAAAACATAAAGTTTCCCATTATTT
7984 GGAAAACATAAAGTTTCCCATTATT
1 GGAAAACATAAAGTTTCCCATTATT
8009 CGTAGAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (26 bp):
GGAAAACATAAAGTTTCCCATTATTT
Found at i:9241 original size:34 final size:35
Alignment explanation
Indices: 9194--9259 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
9184 CATATAAGAC
* *
9194 GTTGGAGATAAAGACAAAA-GCAAAATTAAATACG
1 GTTGGAAACAAAGACAAAAGGCAAAATTAAATACG
9228 GTTGGAAACAAAGACAAAAGGCAAAATTAAAT
1 GTTGGAAACAAAGACAAAAGGCAAAATTAAAT
9260 GATAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.55, C:0.09, G:0.20, T:0.17
Consensus pattern (35 bp):
GTTGGAAACAAAGACAAAAGGCAAAATTAAATACG
Found at i:9980 original size:5 final size:5
Alignment explanation
Indices: 9970--9998 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
9960 CAAACAGGCT
9970 GTTTG GTTTG GTTTG GTTT- GTTTG GTTTG
1 GTTTG GTTTG GTTTG GTTTG GTTTG GTTTG
9999 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (5 bp):
GTTTG
Found at i:9994 original size:9 final size:9
Alignment explanation
Indices: 9969--10001 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
9959 GCAAACAGGC
9969 TGTTTGGTT
1 TGTTTGGTT
9978 TGGTTTGGTT
1 T-GTTTGGTT
9988 TGTTTGGTT
1 TGTTTGGTT
9997 TGTTT
1 TGTTT
10002 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (9 bp):
TGTTTGGTT
Found at i:17994 original size:26 final size:27
Alignment explanation
Indices: 17965--18015 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
17955 GAATCTTTTA
17965 TAAAGAGAT-TTGGGGTTTTTTTTTGG
1 TAAAGAGATGTTGGGGTTTTTTTTTGG
* *
17991 TAAAGAGCTGTTTGGGTTTTTTTTT
1 TAAAGAGATGTTGGGGTTTTTTTTT
18016 TGGGAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.18, C:0.02, G:0.27, T:0.53
Consensus pattern (27 bp):
TAAAGAGATGTTGGGGTTTTTTTTTGG
Found at i:19033 original size:378 final size:373
Alignment explanation
Indices: 18330--19033 Score: 1017
Period size: 378 Copynumber: 1.9 Consensus size: 373
18320 TCGAACTCAA
*** *
18330 AAATTTGTTTAAGGGGAACAAATATCAAAGCACTTGAATCGATTGATTGTTGGTTTGTGCCAAAT
1 AAATTTGTTTAAGGGGAACAAATATCAAAGCACTTGAATCGACCAATTGTTAGTTTGTGCCAAAT
18395 ACTTTCTTAGTTCATGATAGTATGCAATTTGTACAAATTAGCTATTAAGAGCAAATGTACATTGC
66 ACTTTCTTAGTTCATGATAGTATGCAATTTG-----A-TAGCTATTAAGAGCAAATGTACATTGC
*
18460 CAATTGTTATAAACTTATTCTTGATTAATTTGCTTGAAGAGATACAAAGCAAAGCAGGGGACACT
125 CAATTGTTATAAACTTATTCTTGATTAATTTGCTTGAAGAAATACAAAGCAAAGCAGGGGACACT
*
18525 TACACTAGACAAAACCCTTGTTTGGAATTGCATTCATTCCAACAATAATAAAGAAACAGGGGATA
190 TACACTAGACAAAACCCTTGTTTGGAATTACATTCATTCCAACAATAATAAAGAAACAGGGGATA
* * * ***
18590 TATGGATGTTAAACAATTCTACTAGCTTGTAGGATATTGGCAAAGAGCTGTTTGGGGTTTTTTTT
255 TATGGATGTTAAACAATTCTACTAGCTTGTAGGATATTGGCAAAGAGATATCTGCCATTTTTTTT
18655 TTTGGAGGGGAGGGGGGAATGATAGGTAATTAATTTACCCTCCATATAATAAAT
320 TTTGGAGGGGAGGGGGGAATGATAGGTAATTAATTTACCCTCCATATAATAAAT
* * *
18709 AAATTTGTTTAGGGGGAACAAATATCAAATCACTTGAATGGACCAATTGTTAG-TTGTGCCAAAT
1 AAATTTGTTTAAGGGGAACAAATATCAAAGCACTTGAATCGACCAATTGTTAGTTTGTGCCAAAT
* * *
18773 ACTTTCTTAGTTCATGCTAGTATGGAATTTG-TAGCTATTAAGAGCAATTGTACA-TGCCAATTG
66 ACTTTCTTAGTTCATGATAGTATGCAATTTGATAGCTATTAAGAGCAAATGTACATTGCCAATTG
18836 TTATTATAAACTTATTCTTGATTAATTTGCTTGAAGAAATACAGAA-CAAAGCAGGGGACACTTA
131 ---TTATAAACTTATTCTTGATTAATTTGCTTGAAGAAATACA-AAGCAAAGCAGGGGACACTTA
*
18900 CACTAGACAAAATCCTTGTTTGGAATTACATTCATTCCAACAATAATATAATAAAGAAACAGGGG
192 CACTAGACAAAACCCTTGTTTGGAATTACATTCATTCCAAC----A-ATAATAAAGAAACAGGGG
*
18965 ATATATGGATGTTAAACAATTCTACTAGCTTGTAGGAT-TT-GTAGAAGAGATATAACT-CCATT
252 ATATATGGATGTTAAACAATTCTACTAGCTTGTAGGATATTGGCA-AAGAGATAT--CTGCCATT
19027 TTTTTTT
314 TTTTTTT
19034 GTATCCCATT
Statistics
Matches: 293, Mismatches: 20, Indels: 25
0.87 0.06 0.07
Matches are distributed among these distances:
370 9 0.03
371 22 0.08
373 96 0.33
374 2 0.01
376 2 0.01
377 10 0.03
378 105 0.36
379 47 0.16
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.34
Consensus pattern (373 bp):
AAATTTGTTTAAGGGGAACAAATATCAAAGCACTTGAATCGACCAATTGTTAGTTTGTGCCAAAT
ACTTTCTTAGTTCATGATAGTATGCAATTTGATAGCTATTAAGAGCAAATGTACATTGCCAATTG
TTATAAACTTATTCTTGATTAATTTGCTTGAAGAAATACAAAGCAAAGCAGGGGACACTTACACT
AGACAAAACCCTTGTTTGGAATTACATTCATTCCAACAATAATAAAGAAACAGGGGATATATGGA
TGTTAAACAATTCTACTAGCTTGTAGGATATTGGCAAAGAGATATCTGCCATTTTTTTTTTTGGA
GGGGAGGGGGGAATGATAGGTAATTAATTTACCCTCCATATAATAAAT
Found at i:22573 original size:21 final size:21
Alignment explanation
Indices: 22547--22589 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
22537 GGTCTTAGGT
22547 TCAACTCTCACGGAATGTGAG
1 TCAACTCTCACGGAATGTGAG
22568 TCAACTCTCACGGAATGTGAG
1 TCAACTCTCACGGAATGTGAG
22589 T
1 T
22590 TTATTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (21 bp):
TCAACTCTCACGGAATGTGAG
Found at i:25480 original size:17 final size:17
Alignment explanation
Indices: 25458--25493 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
25448 ACAATCTATC
25458 TATACTATATATAAAAG
1 TATACTATATATAAAAG
25475 TATACTATATATAAAAG
1 TATACTATATATAAAAG
25492 TA
1 TA
25494 CGAGTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
TATACTATATATAAAAG
Found at i:25775 original size:109 final size:109
Alignment explanation
Indices: 25579--25853 Score: 446
Period size: 109 Copynumber: 2.5 Consensus size: 109
25569 ACTATTATAG
* *
25579 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
*
25644 TATTTTTACCAAAAATTTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
25693 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
25758 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
25802 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
25854 TAGTTTTTTT
Statistics
Matches: 156, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
108 7 0.04
109 123 0.79
110 3 0.02
111 2 0.01
114 21 0.13
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:25972 original size:24 final size:24
Alignment explanation
Indices: 25945--26027 Score: 62
Period size: 24 Copynumber: 3.3 Consensus size: 24
25935 TTAAAATTTG
25945 TTATTTTCCTAACGTGTAATTATT
1 TTATTTTCCTAACGTGTAATTATT
* * * *
25969 TTATTTGACTTATA-AT-TATTTAAATT
1 TTATTT-TCCTA-ACGTGTAATT--ATT
25995 TGTTATTTTCCTAACGTGTAATTATT
1 T--TATTTTCCTAACGTGTAATTATT
26021 TTATTTT
1 TTATTTT
26028 TTTTGTTGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
24 16 0.37
25 4 0.09
26 10 0.23
27 4 0.09
28 9 0.21
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.58
Consensus pattern (24 bp):
TTATTTTCCTAACGTGTAATTATT
Found at i:32504 original size:29 final size:29
Alignment explanation
Indices: 32446--32514 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
32436 ACCGAACCGT
****
32446 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
32475 CAAATAAGCCCCTGAACTCTTAAAAAGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
32504 CAAATAAGCCC
1 CAAATAAGCCC
32515 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Found at i:47104 original size:17 final size:17
Alignment explanation
Indices: 47082--47129 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
47072 TCAATTGAAA
*
47082 CGGTGTATTTGGTTAGT
1 CGGTGTATTCGGTTAGT
47099 CGGTGTATTCGGTTAGT
1 CGGTGTATTCGGTTAGT
*
47116 CGGTTTATTCGGTT
1 CGGTGTATTCGGTT
47130 TCAGTCTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.10, C:0.10, G:0.33, T:0.46
Consensus pattern (17 bp):
CGGTGTATTCGGTTAGT
Found at i:48955 original size:17 final size:17
Alignment explanation
Indices: 48915--48956 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
48905 CATATGTTAT
*
48915 CTAGCACCTCATGCTAC
1 CTAGTACCTCATGCTAC
*
48932 TTAGTACCTCATGCTAC
1 CTAGTACCTCATGCTAC
*
48949 CTGGTACC
1 CTAGTACC
48957 ATGAGAGAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (17 bp):
CTAGTACCTCATGCTAC
Found at i:50961 original size:34 final size:34
Alignment explanation
Indices: 50916--51000 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
50906 TTCTCCTCTC
50916 TCTCTCTCTCTCTCTCATTTTTAATCTAATCGGA
1 TCTCTCTCTCTCTCTCATTTTTAATCTAATCGGA
*
50950 TGTCTCTCTCTCTCTCATTTTTAATCTAATCGGA
1 TCTCTCTCTCTCTCTCATTTTTAATCTAATCGGA
50984 TCTCTCTCTCTCTCTCA
1 TCTCTCTCTCTCTCTCA
51001 CATTCATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.15, C:0.32, G:0.06, T:0.47
Consensus pattern (34 bp):
TCTCTCTCTCTCTCTCATTTTTAATCTAATCGGA
Found at i:50996 original size:40 final size:40
Alignment explanation
Indices: 50911--51024 Score: 152
Period size: 34 Copynumber: 3.0 Consensus size: 40
50901 TGTTCTTCTC
50911 CTCTCTCTCTCTCTCTCTCTCATTTTTAATCTAATCGGA-
1 CTCTCTCTCTCTCTCTCTCTCATTTTTAATCTAATCGGAT
*
50950 -----TGTCTCTCTCTCTCTCATTTTTAATCTAATCGGAT
1 CTCTCTCTCTCTCTCTCTCTCATTTTTAATCTAATCGGAT
*
50985 CTCTCTCTCTCTCTCACAT-TCATTTTTAATCTAATCGGAT
1 CTCTCTCTCTCTCTCTC-TCTCATTTTTAATCTAATCGGAT
51025 TTGGATAGAG
Statistics
Matches: 65, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
34 33 0.51
40 31 0.48
41 1 0.02
ACGTcount: A:0.18, C:0.30, G:0.06, T:0.46
Consensus pattern (40 bp):
CTCTCTCTCTCTCTCTCTCTCATTTTTAATCTAATCGGAT
Found at i:54580 original size:22 final size:22
Alignment explanation
Indices: 54555--54603 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
54545 AGGGTTATGG
*
54555 AAGAATGGAGGGAAGGAAGAGA
1 AAGAATGGAGAGAAGGAAGAGA
* *
54577 AAGAATGGAGAGAAGTAAGAGG
1 AAGAATGGAGAGAAGGAAGAGA
54599 AAGAA
1 AAGAA
54604 GCGGTGGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.41, T:0.06
Consensus pattern (22 bp):
AAGAATGGAGAGAAGGAAGAGA
Found at i:58216 original size:2 final size:2
Alignment explanation
Indices: 58209--58233 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58199 ACATACATAC
58209 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
58234 CTAGCTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61121 original size:19 final size:20
Alignment explanation
Indices: 61097--61134 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
61087 TGATTACTAA
61097 AAAACAATTAT-AGGTTATC
1 AAAACAATTATAAGGTTATC
61116 AAAACAATTATAAGGTTAT
1 AAAACAATTATAAGGTTAT
61135 TTATAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (20 bp):
AAAACAATTATAAGGTTATC
Found at i:63377 original size:16 final size:15
Alignment explanation
Indices: 63354--63397 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
63344 TACTGGGCTG
63354 TGTCTTCAAGATTGA
1 TGTCTTCAAGATTGA
* *
63369 TGATCTTCAAAATTGT
1 TG-TCTTCAAGATTGA
*
63385 TGTCTACAAGATT
1 TGTCTTCAAGATT
63398 TCCCTTGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (15 bp):
TGTCTTCAAGATTGA
Found at i:72458 original size:22 final size:23
Alignment explanation
Indices: 72430--72473 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
72420 CTTGACTTTT
72430 ATAAAAAAAAAA-TAAATAATAA
1 ATAAAAAAAAAAGTAAATAATAA
*
72452 ATAAAAAAAAAAGTAATTAATA
1 ATAAAAAAAAAAGTAAATAATA
72474 CTACTAGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (23 bp):
ATAAAAAAAAAAGTAAATAATAA
Found at i:80129 original size:8 final size:8
Alignment explanation
Indices: 80116--80163 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
80106 CCGCCCCACT
80116 TTTTACAC
1 TTTTACAC
*
80124 TTTTACTC
1 TTTTACAC
80132 -TTTAC-C
1 TTTTACAC
*
80138 TTTTACCC
1 TTTTACAC
80146 TTTTTACAC
1 -TTTTACAC
80155 TTTTACAC
1 TTTTACAC
80163 T
1 T
80164 GAGACTTCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 1 0.03
7 10 0.29
8 17 0.49
9 7 0.20
ACGTcount: A:0.19, C:0.27, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTTACAC
Found at i:80142 original size:14 final size:15
Alignment explanation
Indices: 80117--80160 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
80107 CGCCCCACTT
*
80117 TTTACACTTTTACTC
1 TTTACACTTTTACCC
80132 TTTAC-CTTTTACCC
1 TTTACACTTTTACCC
80146 TTTTTACACTTTTAC
1 --TTTACACTTTTAC
80161 ACTGAGACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 5 0.20
17 7 0.28
ACGTcount: A:0.18, C:0.27, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTACACTTTTACCC
Found at i:92771 original size:18 final size:19
Alignment explanation
Indices: 92730--92771 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
92720 TTGGGATGGT
*
92730 AAATTGGTAATGATAAACA
1 AAATTGGTAATGATAAAAA
92749 AAATTGG-AGATGA-AAAAA
1 AAATTGGTA-ATGATAAAAA
92767 AAATT
1 AAATT
92772 TAAGAGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.57, C:0.02, G:0.17, T:0.24
Consensus pattern (19 bp):
AAATTGGTAATGATAAAAA
Found at i:92994 original size:32 final size:32
Alignment explanation
Indices: 92894--92995 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 32
92884 CATTGAGACT
* * * *
92894 CCCCACTAGGACGGC-TCAGCCACGGCGGAGCCT
1 CCCCACTGGGGCGGCTTC-GCCACGGCAG-GCCG
* * *
92927 CCCCACTGGGGTGGCTTCACCATGGACAGGCCG
1 CCCCACTGGGGCGGCTTCGCCACGG-CAGGCCG
92960 CCCCACTGGGGCGGCTTCGCCACGGCAGGCCG
1 CCCCACTGGGGCGGCTTCGCCACGGCAGGCCG
92992 CCCC
1 CCCC
92996 GGTGGGACGG
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
32 11 0.19
33 42 0.74
34 4 0.07
ACGTcount: A:0.14, C:0.43, G:0.32, T:0.11
Consensus pattern (32 bp):
CCCCACTGGGGCGGCTTCGCCACGGCAGGCCG
Found at i:93007 original size:32 final size:33
Alignment explanation
Indices: 92894--93007 Score: 99
Period size: 33 Copynumber: 3.5 Consensus size: 33
92884 CATTGAGACT
* * *
92894 CCCCACTAGGACGGC-TCAGCCACGG-CGGAGCCT
1 CCCCACTGGGACGGCTTCA-CCACGGACAG-GCCG
** *
92927 CCCCACTGGGGTGGCTTCACCATGGACAGGCCG
1 CCCCACTGGGACGGCTTCACCACGGACAGGCCG
* *
92960 CCCCACTGGGGCGGCTTCGCCACGG-CAGGCCG
1 CCCCACTGGGACGGCTTCACCACGGACAGGCCG
**
92992 CCCCGGTGGGACGGCT
1 CCCCACTGGGACGGCT
93008 AGACCAATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
32 20 0.30
33 42 0.63
34 5 0.07
ACGTcount: A:0.13, C:0.40, G:0.35, T:0.11
Consensus pattern (33 bp):
CCCCACTGGGACGGCTTCACCACGGACAGGCCG
Done.