Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024151.1 Corchorus olitorius cultivar O-4 contig24184, 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: 43529
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:115 original size:35 final size:33
Alignment explanation
Indices: 76--175 Score: 92
Period size: 35 Copynumber: 2.8 Consensus size: 33
66 AATTTAGCTC
76 TTTCAAAATTGGGAAAGTTCCCATCAGGTTTTAGT
1 TTTC-AAATTGGGAAAGTTCCCATCA-GTTTTAGT
*
111 TTTCAATTTAGGGAAAGTTCCCGTTACTTTCAGTTTTAGT
1 TTTCAAATT-GGGAAAGTTCCC---A---TCAGTTTTAGT
* *
151 TTTCGAAGTGGGAAAGTTCCCATCA
1 TTTCAAATTGGGAAAGTTCCCATCA
176 AAAGCATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
33 3 0.06
34 4 0.07
35 16 0.30
36 1 0.02
38 1 0.02
39 12 0.22
40 14 0.26
41 3 0.06
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (33 bp):
TTTCAAATTGGGAAAGTTCCCATCAGTTTTAGT
Found at i:5036 original size:68 final size:69
Alignment explanation
Indices: 4957--5096 Score: 221
Period size: 68 Copynumber: 2.0 Consensus size: 69
4947 TTTTGCTTAA
* *
4957 AGTGCATTGTCTTTATATGTAATTTTAGCATTTGA-ATGTAATTAATAGTGTT-CCTCCATTTTT
1 AGTGCATTGTCTTTATATATAATTTTAGCA-TTGAGATGTAATTAATAGTGTTCCCACCATTTTT
5020 TTCTT
65 TTCTT
* *
5025 AGTGCATTGTCTTTATATATAATTTTAGTATTGAGATGTAATTAATGGTGTTCCCACCATTTTTT
1 AGTGCATTGTCTTTATATATAATTTTAGCATTGAGATGTAATTAATAGTGTTCCCACCATTTTTT
5090 TCTT
66 TCTT
5094 AGT
1 AGT
5097 TGTTAGTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
67 4 0.06
68 44 0.67
69 18 0.27
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.50
Consensus pattern (69 bp):
AGTGCATTGTCTTTATATATAATTTTAGCATTGAGATGTAATTAATAGTGTTCCCACCATTTTTT
TCTT
Found at i:6652 original size:16 final size:17
Alignment explanation
Indices: 6631--6664 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
6621 TTGAATAATT
*
6631 AAGGTTTA-AAAGTTTG
1 AAGGTTTAGAAAATTTG
6647 AAGGTTTAGAAAATTTG
1 AAGGTTTAGAAAATTTG
6664 A
1 A
6665 GAGAATTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (17 bp):
AAGGTTTAGAAAATTTG
Found at i:11694 original size:15 final size:15
Alignment explanation
Indices: 11648--11691 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
11638 TTATTTTTTA
*
11648 AAAATAAAAT-TCAAT
1 AAAATAAAATAT-ATT
11663 AAAATAAAATATATT
1 AAAATAAAATATATT
11678 AAAATAAAA-ATATT
1 AAAATAAAATATATT
11692 TAATTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 5 0.19
15 21 0.78
16 1 0.04
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAAAATATATT
Found at i:13748 original size:44 final size:44
Alignment explanation
Indices: 13629--13822 Score: 146
Period size: 44 Copynumber: 4.4 Consensus size: 44
13619 ATAAAGATCA
* ** * *
13629 GATTATCAAAATTT-ATA-AGAAGATTATCAAAATTTTATAGTGT
1 GATTATCAAAATTTCATAGAG-AGGTTATCAAAATTACAAAATGT
* * * * *
13672 TATTATCAAAATTTCAAAGCGAGTTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAGAGAGGTTATCAAAATTACAAAATGT
* * * *
13716 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAAA-GT
1 GATTATCAAAATTTCATAGAGAGGTTATCAAAA--TTACA-AAATGT
* * * *
13762 --TTATTAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAGAGAGGTTATCAAAATTACAAAATGT
*
13804 GATTACCAAAATTTCATAG
1 GATTATCAAAATTTCATAG
13823 TGGTATTTTT
Statistics
Matches: 116, Mismatches: 27, Indels: 15
0.73 0.17 0.09
Matches are distributed among these distances:
41 3 0.03
42 5 0.04
43 13 0.11
44 86 0.74
45 1 0.01
46 6 0.05
47 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (44 bp):
GATTATCAAAATTTCATAGAGAGGTTATCAAAATTACAAAATGT
Found at i:13787 original size:22 final size:22
Alignment explanation
Indices: 13569--13821 Score: 115
Period size: 22 Copynumber: 11.5 Consensus size: 22
13559 AAGGAGTACT
* *
13569 AAAATTTGATAGA-AGGTTATC
1 AAAATTTCATAAAGAGGTTATC
* * *
13590 -AAATCTCATATAGTGGTTATC
1 AAAATTTCATAAAGAGGTTATC
* *
13611 GAAATTTCATAAAGATCAGATTATC
1 AAAATTTCATAAAG---AGGTTATC
*
13636 AAAATTT-AT-AAGAAGATTATC
1 AAAATTTCATAAAG-AGGTTATC
* ** ***
13657 AAAATTTTATAGTGTTATTATC
1 AAAATTTCATAAAGAGGTTATC
* *
13679 AAAATTTCA-AAGCGAGTTTATC
1 AAAATTTCATAA-AGAGGTTATC
* * * *
13701 AAAATTACATAATGTGATTATC
1 AAAATTTCATAAAGAGGTTATC
* * * *
13723 AAAATTTCATAGAGGGGTCAAC
1 AAAATTTCATAAAGAGGTTATC
* * *
13745 AAAATTTTATAGAA-AGTTTATT
1 AAAATTTCATA-AAGAGGTTATC
13767 AAAATTTCATAAAGAGGTTATC
1 AAAATTTCATAAAGAGGTTATC
* * * *
13789 AAATTTTCA-AAATGTGATTACC
1 AAAATTTCATAAA-GAGGTTATC
13811 AAAATTTCATA
1 AAAATTTCATA
13822 GTGGTATTTT
Statistics
Matches: 173, Mismatches: 46, Indels: 24
0.71 0.19 0.10
Matches are distributed among these distances:
20 9 0.05
21 28 0.16
22 114 0.66
23 8 0.05
24 2 0.01
25 12 0.07
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAAAGAGGTTATC
Found at i:13863 original size:22 final size:22
Alignment explanation
Indices: 13838--14064 Score: 120
Period size: 22 Copynumber: 10.6 Consensus size: 22
13828 TTTTTGGGGA
13838 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
* * *
13860 GGTTA-CCAAA--T-A-AGGAA
1 GGTTATCAAAATTTCATAGTAT
* * *
13877 GGTTATTAAACTTT--TACTAT
1 GGTTATCAAAATTTCATAGTAT
* *
13897 GGAGTTATCAAAATTTCA-GGCA-
1 -G-GTTATCAAAATTTCATAGTAT
* *
13919 GGATATCAAAATTTCATA-TGAA
1 GGTTATCAAAATTTCATAGT-AT
*
13941 GGTTATCAAAATTTCATAGTTT
1 GGTTATCAAAATTTCATAGTAT
* * * *
13963 AGTTTTCAAAATTTCATAGGAG
1 GGTTATCAAAATTTCATAGTAT
13985 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
* *
14007 -GTAGATCAAAATTTCATAGGGA-
1 GGT-TATCAAAATTTCATA-GTAT
* * * *
14029 GATTAACAAAATTCCATAATGA-
1 GGTTATCAAAATTTCATAGT-AT
14051 GGTTATCAAAATTT
1 GGTTATCAAAATTT
14065 GTAGTTATCA
Statistics
Matches: 149, Mismatches: 40, Indels: 32
0.67 0.18 0.14
Matches are distributed among these distances:
17 8 0.05
18 3 0.02
19 1 0.01
20 17 0.11
21 9 0.06
22 106 0.71
23 5 0.03
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTAT
Found at i:13989 original size:44 final size:44
Alignment explanation
Indices: 13923--14046 Score: 153
Period size: 44 Copynumber: 2.8 Consensus size: 44
13913 CAGGCAGGAT
*
13923 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGT-T-TAG
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATGTAG
* *
13965 TTTTCAAAATTTCATAGGAGGGTTATCAAAATTTCATAGTATGTAG
1 --ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATGTAG
* * * *
14011 ATCAAAATTTCATAGGGAGATTAACAAAATTCCATA
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
14047 ATGAGGTTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 65 0.94
45 1 0.01
46 3 0.04
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.35
Consensus pattern (44 bp):
ATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTATGTAG
Found at i:14059 original size:44 final size:41
Alignment explanation
Indices: 13922--14064 Score: 133
Period size: 44 Copynumber: 3.3 Consensus size: 41
13912 TCAGGCAGGA
* *
13922 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATA-GGAGGTTATCAAAATTTCATA--ATAGT
* *
13966 TTTCAAAATTTCATAGGAGGGTTATCAAAATTTCATAGTATGT
1 TATCAAAATTTCATAGGA-GGTTATCAAAATTTCATAATA-GT
* * * *
14009 AGATCAAAATTTCATAGGGAGATTAACAAAATTCCATAATGAGGT
1 -TATCAAAATTTCATA-GGAGGTTATCAAAATTTCATAAT-A-GT
14054 TATCAAAATTT
1 TATCAAAATTT
14065 GTAGTTATCA
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
42 2 0.02
43 4 0.05
44 71 0.86
45 6 0.07
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (41 bp):
TATCAAAATTTCATAGGAGGTTATCAAAATTTCATAATAGT
Found at i:15354 original size:23 final size:24
Alignment explanation
Indices: 15326--15370 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
15316 CTTATCACAA
15326 TTTCATAG-GTAATTATCAAAAAT
1 TTTCATAGCGTAATTATCAAAAAT
**
15349 TTTCATAGCGTGGTTATCAAAA
1 TTTCATAGCGTAATTATCAAAA
15371 TTTAATAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (24 bp):
TTTCATAGCGTAATTATCAAAAAT
Found at i:15371 original size:23 final size:21
Alignment explanation
Indices: 15254--15399 Score: 102
Period size: 22 Copynumber: 6.9 Consensus size: 21
15244 TCATAGGGAA
*
15254 AGTTA-CAAAATTTTA-AGGT
1 AGTTATCAAAATTTCATAGGT
* *
15273 --TTATTAAAATTTCATAGTT
1 AGTTATCAAAATTTCATAGGT
* * *
15292 AGGTTATCAAAGTTCCATATGGA
1 A-GTTATCAAAATTTCATA-GGT
* *
15315 ACTTATCACAATTTCATAGGT
1 AGTTATCAAAATTTCATAGGT
*
15336 AATTATCAAAAATTTTCATAGCGT
1 AGTTATC-AAAA-TTTCATAG-GT
* *
15360 GGTTATCAAAATTTAATAGGGT
1 AGTTATCAAAATTTCATA-GGT
*
15382 AGTCATCAAAATTTCATA
1 AGTTATCAAAATTTCATA
15400 AAAATATTCA
Statistics
Matches: 96, Mismatches: 21, Indels: 17
0.72 0.16 0.13
Matches are distributed among these distances:
17 3 0.03
18 8 0.08
19 3 0.03
21 8 0.08
22 52 0.54
23 15 0.16
24 7 0.07
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (21 bp):
AGTTATCAAAATTTCATAGGT
Found at i:22202 original size:42 final size:42
Alignment explanation
Indices: 22155--22236 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
22145 GGGCATTTAC
22155 TCAAAGTAAAATAGGTAAAATATATAAAATTCATTACACTCA
1 TCAAAGTAAAATAGGTAAAATATATAAAATTCATTACACTCA
*
22197 TCAAAGTAAAATAGGTAAAGTATATAAAATTCATTACACT
1 TCAAAGTAAAATAGGTAAAATATATAAAATTCATTACACT
22237 AATTGGGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (42 bp):
TCAAAGTAAAATAGGTAAAATATATAAAATTCATTACACTCA
Found at i:35281 original size:38 final size:38
Alignment explanation
Indices: 35230--35328 Score: 171
Period size: 38 Copynumber: 2.6 Consensus size: 38
35220 TATTATGGAC
*
35230 CTTTATATTTTAAAGGGATGAATATTAAAGGGATGAAG
1 CTTTATATTTTAAAGGGATGAATATTAAAAGGATGAAG
* *
35268 CTTTATATTTTAAAGGAATGAGTATTAAAAGGATGAAG
1 CTTTATATTTTAAAGGGATGAATATTAAAAGGATGAAG
35306 CTTTATATTTTAAAGGGATGAAT
1 CTTTATATTTTAAAGGGATGAAT
35329 GGAGATTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 56 1.00
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.36
Consensus pattern (38 bp):
CTTTATATTTTAAAGGGATGAATATTAAAAGGATGAAG
Found at i:41229 original size:14 final size:14
Alignment explanation
Indices: 41210--41250 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
41200 GTCTTAATTG
41210 ATTTGCTGTTTTTA
1 ATTTGCTGTTTTTA
*
41224 ATTTGCTGTTTTTG
1 ATTTGCTGTTTTTA
* *
41238 AGTTCCTGTTTTT
1 ATTTGCTGTTTTT
41251 GAGTTGCTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.10, C:0.10, G:0.17, T:0.63
Consensus pattern (14 bp):
ATTTGCTGTTTTTA
Found at i:41251 original size:14 final size:14
Alignment explanation
Indices: 41215--41255 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
41205 AATTGATTTG
* * *
41215 CTGTTTTTAATTTG
1 CTGTTTTTGAGTTC
41229 CTGTTTTTGAGTTC
1 CTGTTTTTGAGTTC
41243 CTGTTTTTGAGTT
1 CTGTTTTTGAGTT
41256 GCTGGCTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.61
Consensus pattern (14 bp):
CTGTTTTTGAGTTC
Found at i:41267 original size:18 final size:15
Alignment explanation
Indices: 41214--41259 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
41204 TAATTGATTT
* *
41214 GCTGTTTTT-AATTT
1 GCTGTTTTTGAGTTC
41228 GCTGTTTTTGAGTTC
1 GCTGTTTTTGAGTTC
41243 -CTGTTTTTGAGTT-
1 GCTGTTTTTGAGTTC
41256 GCTG
1 GCTG
41260 GCTGTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 25 0.89
15 3 0.11
ACGTcount: A:0.09, C:0.11, G:0.24, T:0.57
Consensus pattern (15 bp):
GCTGTTTTTGAGTTC
Found at i:42066 original size:55 final size:55
Alignment explanation
Indices: 42005--42115 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
41995 AAGTCTTCAA
42005 AGTTAATTAATATTTAATACTTTTTTTGCCAGATTCAATGTTAATTAAATAGACT
1 AGTTAATTAATATTTAATACTTTTTTTGCCAGATTCAATGTTAATTAAATAGACT
*
42060 AGTTAATTAATATTTAATACTTTTTTTGCCATATTCAATGTTAATTAAATAGACT
1 AGTTAATTAATATTTAATACTTTTTTTGCCAGATTCAATGTTAATTAAATAGACT
42115 A
1 A
42116 TTAGTACTGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (55 bp):
AGTTAATTAATATTTAATACTTTTTTTGCCAGATTCAATGTTAATTAAATAGACT
Found at i:42844 original size:56 final size:57
Alignment explanation
Indices: 42754--42868 Score: 205
Period size: 56 Copynumber: 2.0 Consensus size: 57
42744 TATCTGTTTC
*
42754 CTTTCACACAATAAATGTTATAATAAATCATAT-CCCCCTATTTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT
*
42810 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT
42867 CT
1 CT
42869 ACAAAATAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 32 0.57
57 24 0.43
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (57 bp):
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT
Found at i:42991 original size:42 final size:42
Alignment explanation
Indices: 42932--43014 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
42922 GCTAAGGATC
*
42932 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTTCATAATTTACAAAGAATTTTCT
*
42974 ATGATTTGAGTTGAGTATTTCATAATTTACAGAGAATTTTC
1 ATGATTTGAGTTGAGTATTTCATAATTTACAAAGAATTTTC
43015 AAGACTTAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (42 bp):
ATGATTTGAGTTGAGTATTTCATAATTTACAAAGAATTTTCT
Done.