Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015522.1 Corchorus olitorius cultivar O-4 contig15555, 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: 7557
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:4338 original size:22 final size:22
Alignment explanation
Indices: 4215--4331 Score: 85
Period size: 22 Copynumber: 5.4 Consensus size: 22
4205 CTCCAATGCA
* *
4215 GAAATATTGATAACCACACTGT
1 GAAATTTTGATAACCACACTAT
* * ** *
4237 GAAA-ATTGATAAGCTTATTAT
1 GAAATTTTGATAACCACACTAT
* * * * *
4258 TAAATTTCGATAGCCTCCCTAT
1 GAAATTTTGATAACCACACTAT
* *
4280 GAAAATTTGATAACCACAC-AGC
1 GAAATTTTGATAACCACACTA-T
4302 GAAATTTTGATAACCACACTAT
1 GAAATTTTGATAACCACACTAT
4324 GAAATTTT
1 GAAATTTT
4332 AAAAACCTCA
Statistics
Matches: 70, Mismatches: 22, Indels: 6
0.71 0.22 0.06
Matches are distributed among these distances:
21 16 0.23
22 53 0.76
23 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:4488 original size:13 final size:13
Alignment explanation
Indices: 4470--4497 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4460 CGATGATACC
4470 ATATTTTTTAAAA
1 ATATTTTTTAAAA
4483 ATATTTTTTAAAA
1 ATATTTTTTAAAA
4496 AT
1 AT
4498 CATTACTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATTTTTTAAAA
Found at i:4808 original size:22 final size:21
Alignment explanation
Indices: 4754--4795 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4744 TGGTTATCAA
*
4754 AAAATTTCATAATGAGATTAT
1 AAAATTTCATGATGAGATTAT
*
4775 AAAACTTCATGATGAGATTAT
1 AAAATTTCATGATGAGATTAT
4796 CAAGTTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (21 bp):
AAAATTTCATGATGAGATTAT
Found at i:4951 original size:22 final size:22
Alignment explanation
Indices: 4885--5073 Score: 99
Period size: 22 Copynumber: 8.7 Consensus size: 22
4875 TTGTGTGGTA
* *
4885 ATCAAAATTTCATAATAACA-TT
1 ATCAAAATTTCATAGT-GCAGTT
4907 ATCAAAATTTCATAAG-G-AGGTT
1 ATCAAAATTTCAT-AGTGCA-GTT
*
4929 ATCAAAATTTCATAGTCCAGTT
1 ATCAAAATTTCATAGTGCAGTT
* * *
4951 A-CCAAATTTTATAG-GGAGGTT
1 ATCAAAATTTCATAGTGCA-GTT
* * **
4972 ATCAAAAATTCATATTGTGGTT
1 ATCAAAATTTCATAGTGCAGTT
* *
4994 ACCAAAATTTCATAGTGCGGTT
1 ATCAAAATTTCATAGTGCAGTT
* ** *
5016 ACCAAAATTTTGTAG-GAAGGTT
1 ATCAAAATTTCATAGTGCA-GTT
*
5038 ATCAAATTTTCATCGAGTG--GTT
1 ATCAAAATTTCAT--AGTGCAGTT
5060 ATCAAAATTT-ATAG
1 ATCAAAATTTCATAG
5074 GGATAAGGTT
Statistics
Matches: 129, Mismatches: 26, Indels: 27
0.71 0.14 0.15
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 20 0.16
22 99 0.77
23 3 0.02
24 2 0.02
25 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGCAGTT
Found at i:4972 original size:43 final size:44
Alignment explanation
Indices: 4885--4985 Score: 125
Period size: 43 Copynumber: 2.3 Consensus size: 44
4875 TTGTGTGGTA
4885 ATCAAAATTTCATAATAACATTATCAAAATTTCATAAGGAGGTT
1 ATCAAAATTTCATAATAACATTATCAAAATTTCATAAGGAGGTT
* * * * *
4929 ATCAAAATTTCATAGT-CCAGTTA-CCAAATTTTATAGGGAGGTT
1 ATCAAAATTTCATAATAACA-TTATCAAAATTTCATAAGGAGGTT
*
4972 ATCAAAAATTCATA
1 ATCAAAATTTCATA
4986 TTGTGGTTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 32 0.64
44 18 0.36
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (44 bp):
ATCAAAATTTCATAATAACATTATCAAAATTTCATAAGGAGGTT
Found at i:4994 original size:65 final size:66
Alignment explanation
Indices: 4905--5073 Score: 207
Period size: 65 Copynumber: 2.6 Consensus size: 66
4895 CATAATAACA
* * *
4905 TTATCAAAATTTCATAAGGAGGTTATCAAAATTTCATAGTCCAGTTACC-AAATTTTATAGGGAG
1 TTATCAAAATTTCATAAAGTGGTTATCAAAATTTCATAGTCCAGTTACCAAAATTTTATAGGAAG
4969 G
66 G
* ** * * * *
4970 TTATCAAAAATTCATATTGTGGTTACCAAAATTTCATAGTGCGGTTACCAAAATTTTGTAGGAAG
1 TTATCAAAATTTCATAAAGTGGTTATCAAAATTTCATAGTCCAGTTACCAAAATTTTATAGGAAG
5035 G
66 G
* **
5036 TTATCAAATTTTCATCGAGTGGTTATCAAAATTT-ATAG
1 TTATCAAAATTTCATAAAGTGGTTATCAAAATTTCATAG
5074 GGATAAGGTT
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
65 46 0.52
66 42 0.48
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (66 bp):
TTATCAAAATTTCATAAAGTGGTTATCAAAATTTCATAGTCCAGTTACCAAAATTTTATAGGAAG
G
Found at i:4995 original size:43 final size:44
Alignment explanation
Indices: 4909--5022 Score: 131
Period size: 43 Copynumber: 2.6 Consensus size: 44
4899 ATAACATTAT
* *
4909 CAAAATTTCATAAGGAGGTTATCAAAATTTCATAGTCCAGTTAC
1 CAAAATTTCATAGGGAGGTTATCAAAAATTCATAGTCCAGTTAC
* * ***
4953 C-AAATTTTATAGGGAGGTTATCAAAAATTCATATTGTGGTTAC
1 CAAAATTTCATAGGGAGGTTATCAAAAATTCATAGTCCAGTTAC
* * *
4996 CAAAATTTCATAGTGCGGTTACCAAAA
1 CAAAATTTCATAGGGAGGTTATCAAAA
5023 TTTTGTAGGA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 36 0.62
44 22 0.38
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (44 bp):
CAAAATTTCATAGGGAGGTTATCAAAAATTCATAGTCCAGTTAC
Found at i:5160 original size:22 final size:22
Alignment explanation
Indices: 5128--5236 Score: 96
Period size: 22 Copynumber: 4.8 Consensus size: 22
5118 GGCATCAAAA
*
5128 GATTATTAAAATTTCATAGAGT
1 GATTATCAAAATTTCATAGAGT
*
5150 GATTATCAAAATTTCATATGTATT
1 GATTATCAAAATTTCATA-G-AGT
* * *
5174 AGGTTATTAAAATTTCATAG-GA
1 -GATTATCAAAATTTCATAGAGT
*
5196 AAGTTATCAAAATTTCATA-ATGT
1 GA-TTATCAAAATTTCATAGA-GT
*
5219 GGTTATCAAAATTTCATA
1 GATTATCAAAATTTCATA
5237 AAGAGGCTAT
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
22 48 0.70
23 2 0.03
24 3 0.04
25 16 0.23
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (22 bp):
GATTATCAAAATTTCATAGAGT
Found at i:5237 original size:22 final size:23
Alignment explanation
Indices: 5130--5250 Score: 92
Period size: 22 Copynumber: 5.3 Consensus size: 23
5120 CATCAAAAGA
* *
5130 TTATTAAAATTTCAT-A-GAGTGA
1 TTATCAAAATTTCATAATGA-TGG
5152 TTATCAAAATTTCAT-ATGTATTAGG
1 TTATCAAAATTTCATAATG-A-T-GG
* * **
5177 TTATTAAAATTTCAT-AGGAAAG
1 TTATCAAAATTTCATAATGATGG
5199 TTATCAAAATTTCATAATG-TGG
1 TTATCAAAATTTCATAATGATGG
*
5221 TTATCAAAATTTCATAAAGA-GG
1 TTATCAAAATTTCATAATGATGG
*
5243 CTATCAAA
1 TTATCAAA
5251 GAGGTTATCA
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
22 58 0.72
23 3 0.04
24 3 0.04
25 17 0.21
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTCATAATGATGG
Found at i:5394 original size:28 final size:29
Alignment explanation
Indices: 5347--5401 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
5337 GTGGTTACCA
*
5347 AAATTTCATAGTAATGTTAT-AAAATTCT
1 AAATTTCATAGTAATATTATCAAAATTCT
5375 AAATTTCATACG-AATATTATCAAAATT
1 AAATTTCATA-GTAATATTATCAAAATT
5402 TTATTGTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.40
Consensus pattern (29 bp):
AAATTTCATAGTAATATTATCAAAATTCT
Found at i:5556 original size:22 final size:22
Alignment explanation
Indices: 5252--5714 Score: 138
Period size: 22 Copynumber: 20.9 Consensus size: 22
5242 GCTATCAAAG
* *
5252 AGGTTATCAAAATTCCATAGCA
1 AGGTTATCAAAATTTCATAGGA
* * **
5274 AGGTTATTAGAATTTCATAGTT
1 AGGTTATCAAAATTTCATAGGA
* * **
5296 TGGTTATCCAAATTT--TA-TC
1 AGGTTATCAAAATTTCATAGGA
*
5315 AGGTTATTAAAGATTTCATAGTG-
1 AGGTTATCAAA-ATTTCATAG-GA
* * *
5338 TGGTTACCAAAATTTCATAGTA
1 AGGTTATCAAAATTTCATAGGA
* * *
5360 ATGTTATAAAATTCTAAATTTCATACGA
1 A-GGT-T---A-TCAAAATTTCATAGGA
** * * *
5388 ATATTATCAAAATTTTAT-TGT
1 AGGTTATCAAAATTTCATAGGA
*
5409 TGGTTATCAAAATTTCATTAGGA
1 AGGTTATCAAAATTTCA-TAGGA
** * *
5432 A-GCAATCAAAATCTCATAGAGT
1 AGGTTATCAAAATTTCATAG-GA
*
5454 A-GTTATCAAAAATTCATAGAGA
1 AGGTTATCAAAATTTCATAG-GA
* * *
5476 TCAGATTACCAAAATTGCATAGGA
1 --AGGTTATCAAAATTTCATAGGA
* * *
5500 AAGTTAT-TAAA-TTCATAATG-
1 AGGTTATCAAAATTTCAT-AGGA
*
5520 TGGTTATCAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
* *
5542 AGGTTATCAAAATTTTAAAGCG-
1 AGGTTATCAAAATTTCATAG-GA
5564 AGGTTATCAAAATTTTC-TAGTG-
1 AGGTTATCAAAA-TTTCATAG-GA
* *
5586 AGGTTATGAAAAATTTTCATATTG-
1 AGGTTAT-CAAAA-TTTCATA-GGA
* *
5610 TGGTTATTAAAATTTCATATGG-
1 AGGTTATCAAAATTTCATA-GGA
*
5632 AGGTT-TC-AAATTTCATAGTA
1 AGGTTATCAAAATTTCATAGGA
* *
5652 TGATTATCAAAATTTCATA--A
1 AGGTTATCAAAATTTCATAGGA
*
5672 AGAGCTTAGCAAAATTTCATAAGG-
1 AG-G-TTATCAAAATTTCAT-AGGA
* * *
5696 TGTTTATCGAAATTTCATA
1 AGGTTATCAAAATTTCATA
5715 ATGTTATTAT
Statistics
Matches: 323, Mismatches: 83, Indels: 71
0.68 0.17 0.15
Matches are distributed among these distances:
19 10 0.03
20 30 0.09
21 31 0.10
22 178 0.55
23 30 0.09
24 14 0.04
25 14 0.04
26 1 0.00
27 2 0.01
28 13 0.04
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:5715 original size:22 final size:22
Alignment explanation
Indices: 5655--5732 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
5645 CATAGTATGA
* *
5655 TTATCAAAATTTCATAAAGAGC
1 TTATCAAAATTTCATAAAGTGT
* *
5677 TTAGCAAAATTTCATAAGGTGT
1 TTATCAAAATTTCATAAAGTGT
* *
5699 TTATCGAAATTTCATAATGT-T
1 TTATCAAAATTTCATAAAGTGT
*
5720 ATTATCCAAATTT
1 -TTATCAAAATTT
5733 TAGAGTGTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 1 0.02
22 46 0.98
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGTGT
Found at i:5875 original size:20 final size:22
Alignment explanation
Indices: 5823--6213 Score: 121
Period size: 22 Copynumber: 18.0 Consensus size: 22
5813 TTCAAAGGAG
**
5823 GATTATCAAAATTTCATAGTTTA
1 GATTATCAAAATTTCATAG-GGA
* *
5846 G-TTTTCAAAATTTTATAGGG-
1 GATTATCAAAATTTCATAGGGA
5866 G-TTATCAAAATTTCATAGGGA
1 GATTATCAAAATTTCATAGGGA
* **
5887 GATTAACAAAATTTCATAATGA
1 GATTATCAAAATTTCATAGGGA
* *
5909 -AGTTATCGAAAA-ATCATATGGA
1 GA-TTATC-AAAATTTCATAGGGA
* * *
5931 GGTTATCGAAA-TT--T---GT
1 GATTATCAAAATTTCATAGGGA
*
5947 GATTATCAAAATTTCATAAGGA
1 GATTATCAAAATTTCATAGGGA
* * *
5969 GGTTATTAAAATTTTATAGGGA
1 GATTATCAAAATTTCATAGGGA
* * * *
5991 GGTT-TACAAAAATTTTATATGAA
1 GATTAT-C-AAAATTTCATAGGGA
* * **
6014 TGTTTATCAAAATTTTATACCGA
1 -GATTATCAAAATTTCATAGGGA
* * * * * *
6037 GGTCATTACAATTTCATAGTGT
1 GATTATCAAAATTTCATAGGGA
* ** *
6059 GATTATCAAAATTTCACAATGT
1 GATTATCAAAATTTCATAGGGA
* *
6081 GATCA-CTAAGATTTCATAGGGA
1 GATTATC-AAAATTTCATAGGGA
* * *
6103 GATTATAAAAAAGTTCATA-GTA
1 GATTAT-CAAAATTTCATAGGGA
* * * * *
6125 TGCTTACCAACATTTCACATGGA
1 -GATTATCAAAATTTCATAGGGA
* **
6148 GATTATCAAAATTTTATAGTAA
1 GATTATCAAAATTTCATAGGGA
* *
6170 TATTTTCAAAATTGT-ATAGGGA
1 GATTATCAAAATT-TCATAGGGA
*
6192 -AGTTAACAAAATTTCATAGGGA
1 GA-TTATCAAAATTTCATAGGGA
6214 TGTTCTTATA
Statistics
Matches: 268, Mismatches: 77, Indels: 47
0.68 0.20 0.12
Matches are distributed among these distances:
16 10 0.04
17 2 0.01
19 2 0.01
20 18 0.07
21 10 0.04
22 175 0.65
23 46 0.17
24 4 0.01
25 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
GATTATCAAAATTTCATAGGGA
Found at i:6006 original size:23 final size:22
Alignment explanation
Indices: 5953--6032 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
5943 TTGTGATTAT
*
5953 CAAAATTTCATAAGGAGG-TTA
1 CAAAATTTTATAAGGAGGTTTA
* *
5974 TTAAAATTTTATAGGGAGGTTTA
1 -CAAAATTTTATAAGGAGGTTTA
* * *
5997 CAAAAATTTTATATGAATGTTTA
1 C-AAAATTTTATAAGGAGGTTTA
6020 TCAAAATTTTATA
1 -CAAAATTTTATA
6033 CCGAGGTCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
22 15 0.31
23 32 0.67
24 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (22 bp):
CAAAATTTTATAAGGAGGTTTA
Found at i:6289 original size:22 final size:22
Alignment explanation
Indices: 6150--6311 Score: 64
Period size: 22 Copynumber: 7.4 Consensus size: 22
6140 CACATGGAGA
* * *
6150 TTATCAAAATTTTATAGTAATA
1 TTATCAAAATTTCATAGGAATG
*
6172 TTTTCAAAATTGT-ATAGGGAA-G
1 TTATCAAAATT-TCATA-GGAATG
* *
6194 TTAACAAAATTTCATAGGGATG
1 TTATCAAAATTTCATAGGAATG
* * * * *
6216 TTCTTATATTTTGATAGGAATG
1 TTATCAAAATTTCATAGGAATG
* ** ** * *
6238 TTTTTGAAATAACATA-GTATCA
1 TTATCAAAATTTCATAGGAAT-G
*
6260 TTAACAAAATTTCATAGGAATG
1 TTATCAAAATTTCATAGGAATG
*
6282 TTATCAAAAGTTT-ATAAGG-AGG
1 TTATCAAAA-TTTCAT-AGGAATG
6304 TTATCAAA
1 TTATCAAA
6312 CGGAGATTAT
Statistics
Matches: 100, Mismatches: 32, Indels: 16
0.68 0.22 0.11
Matches are distributed among these distances:
21 7 0.07
22 80 0.80
23 13 0.13
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGAATG
Done.