Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012175.1 Corchorus olitorius cultivar O-4 contig12208, 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: 38985
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Found at i:8226 original size:30 final size:30
Alignment explanation
Indices: 8190--8252 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
8180 CATCTTTAAG
8190 TCCATGATAAGTCCTT-GGCGCATCATTCCC
1 TCCATGATAAG-CCTTGGGCGCATCATTCCC
8220 TCCATGATAAGCCTTGGGCGCATCATTCCC
1 TCCATGATAAGCCTTGGGCGCATCATTCCC
8250 TCC
1 TCC
8253 CCCTTGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.19, C:0.35, G:0.17, T:0.29
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCC
Found at i:9785 original size:3 final size:3
Alignment explanation
Indices: 9777--9804 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9767 CGCCTCCCCT
9777 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
9805 AACTGAGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:15248 original size:22 final size:22
Alignment explanation
Indices: 15220--15265 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
15210 CAGAAAATCT
15220 AATTCAACC-TCTGGAGAGGTCG
1 AATTCAACCTTC-GGAGAGGTCG
*
15242 AATTCAACCTTCGTAGAGGTCG
1 AATTCAACCTTCGGAGAGGTCG
15264 AA
1 AA
15266 ACAACAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (22 bp):
AATTCAACCTTCGGAGAGGTCG
Found at i:19033 original size:20 final size:18
Alignment explanation
Indices: 19001--19047 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
18991 GGTGTTGGAG
*
19001 TATTTATTTATCTTGTTGCT
1 TATTTA-TTATCTTCTTG-T
19021 TAATTTATTATCTTCTTGT
1 T-ATTTATTATCTTCTTGT
19040 TATTTATT
1 TATTTATT
19048 TTTATTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 7 0.28
19 2 0.08
20 11 0.44
21 5 0.20
ACGTcount: A:0.19, C:0.09, G:0.06, T:0.66
Consensus pattern (18 bp):
TATTTATTATCTTCTTGT
Found at i:19435 original size:14 final size:14
Alignment explanation
Indices: 19416--19446 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
19406 TTTGTGTTTC
19416 TGATATTTTTGATG
1 TGATATTTTTGATG
19430 TGATATTTTTGATG
1 TGATATTTTTGATG
19444 TGA
1 TGA
19447 AAATAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (14 bp):
TGATATTTTTGATG
Found at i:20167 original size:35 final size:35
Alignment explanation
Indices: 20121--20194 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
20111 ACTTTTGTAA
* *
20121 GCTTTGTTGTTGGTTTGTTGATAGAGACGAACTTT
1 GCTTTGTTGTTGCTTTGTTGATAGAGAAGAACTTT
*
20156 GCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTT
1 GCTTTGTTGTTGCTTTGTTGATAGAGAAGAACTTT
20191 GCTT
1 GCTT
20195 CAGATTTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.16, C:0.09, G:0.28, T:0.46
Consensus pattern (35 bp):
GCTTTGTTGTTGCTTTGTTGATAGAGAAGAACTTT
Found at i:20233 original size:27 final size:26
Alignment explanation
Indices: 20203--20360 Score: 107
Period size: 24 Copynumber: 5.8 Consensus size: 26
20193 TTCAGATTTG
*
20203 ATTTGATGCAGAATAACTTTGCCTTGA
1 ATTTGATG-AGAAGAACTTTGCCTTGA
20230 ATTTG--GAGAAGAACTTTGCTTCAAATCT-A
1 ATTTGATGAGAAGAACTTTGC--C---T-TGA
20259 ATTTGATGGAGAAGAACTTTGCCTTGA
1 ATTTGAT-GAGAAGAACTTTGCCTTGA
20286 ATTTG--GAGAAGAACTTTGCTTCAAATCT-A
1 ATTTGATGAGAAGAACTTTGC--C---T-TGA
*
20315 CTTTGATGGAGAAGAACTTTGCCTTGA
1 ATTTGAT-GAGAAGAACTTTGCCTTGA
20342 ATTTG--GAGAAGAACTTTGC
1 ATTTGATGAGAAGAACTTTGC
20361 TTCAGATCTG
Statistics
Matches: 108, Mismatches: 3, Indels: 43
0.70 0.02 0.28
Matches are distributed among these distances:
24 40 0.37
25 1 0.01
26 4 0.04
27 18 0.17
29 13 0.12
30 4 0.04
32 28 0.26
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (26 bp):
ATTTGATGAGAAGAACTTTGCCTTGA
Found at i:20234 original size:32 final size:32
Alignment explanation
Indices: 20173--20392 Score: 100
Period size: 32 Copynumber: 7.6 Consensus size: 32
20163 TGTTGCTTTG
*
20173 TTGATGGAGAAGAACTTTGCTTCAGATTTGAT
1 TTGATGCAGAAGAACTTTGCTTCAGATTTGAT
*
20205 TTGATGCAGAATAACTTTGC--C----TTGAAT
1 TTGATGCAGAAGAACTTTGCTTCAGATTTG-AT
* * *
20232 TTG--G-AGAAGAACTTTGCTTCAAATCTAAT
1 TTGATGCAGAAGAACTTTGCTTCAGATTTGAT
*
20261 TTGATGGAGAAGAACTTTGC--C----TTGAAT
1 TTGATGCAGAAGAACTTTGCTTCAGATTTG-AT
* *
20288 TTG--G-AGAAGAACTTTGCTTCAAATCT-ACT
1 TTGATGCAGAAGAACTTTGCTTCAGATTTGA-T
*
20317 TTGATGGAGAAGAACTTTGC--C----TTGAAT
1 TTGATGCAGAAGAACTTTGCTTCAGATTTG-AT
* *
20344 TTG--G-AGAAGAACTTTGCTTCAGATCTGCT
1 TTGATGCAGAAGAACTTTGCTTCAGATTTGAT
*
20373 TTGATGGAGAAGAACTTTGC
1 TTGATGCAGAAGAACTTTGC
20393 CTTGATTTTG
Statistics
Matches: 145, Mismatches: 11, Indels: 64
0.66 0.05 0.29
Matches are distributed among these distances:
24 38 0.26
25 3 0.02
26 8 0.06
27 14 0.10
28 2 0.01
29 13 0.09
30 7 0.05
31 3 0.02
32 57 0.39
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (32 bp):
TTGATGCAGAAGAACTTTGCTTCAGATTTGAT
Found at i:20249 original size:56 final size:56
Alignment explanation
Indices: 20177--20406 Score: 372
Period size: 56 Copynumber: 4.1 Consensus size: 56
20167 GCTTTGTTGA
* * * *
20177 TGGAGAAGAACTTTGCTTCAGATTTGATTTGATGCAGAATAACTTTGCCTTGAATT
1 TGGAGAAGAACTTTGCTTCAAATCTGATTTGATGGAGAAGAACTTTGCCTTGAATT
*
20233 TGGAGAAGAACTTTGCTTCAAATCTAATTTGATGGAGAAGAACTTTGCCTTGAATT
1 TGGAGAAGAACTTTGCTTCAAATCTGATTTGATGGAGAAGAACTTTGCCTTGAATT
20289 TGGAGAAGAACTTTGCTTCAAATCT-ACTTTGATGGAGAAGAACTTTGCCTTGAATT
1 TGGAGAAGAACTTTGCTTCAAATCTGA-TTTGATGGAGAAGAACTTTGCCTTGAATT
* * *
20345 TGGAGAAGAACTTTGCTTCAGATCTGCTTTGATGGAGAAGAACTTTGCCTTGATTT
1 TGGAGAAGAACTTTGCTTCAAATCTGATTTGATGGAGAAGAACTTTGCCTTGAATT
20401 TGGAGA
1 TGGAGA
20407 GATTGCCGGG
Statistics
Matches: 164, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
55 1 0.01
56 163 0.99
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (56 bp):
TGGAGAAGAACTTTGCTTCAAATCTGATTTGATGGAGAAGAACTTTGCCTTGAATT
Found at i:20952 original size:318 final size:317
Alignment explanation
Indices: 20375--21001 Score: 1119
Period size: 318 Copynumber: 2.0 Consensus size: 317
20365 GATCTGCTTT
* *
20375 GATGGAGAAGAACTTTGCCTTGATTTTGGAGAGATTGCCGGGGTGGCTTGAAGGCTTAAAATCTC
1 GATGGAGAAGAACTTTGCCTTGAATTTGGAGAGATTGCCGGGGTGGCTTGAAGGCTCAAAATCTC
20440 TAAGGAGGCTAGGTTTTCTTTTAAAGAGAATAGGTTTTCTCCCTTTTCAGTTGTCTTCCAAAATG
66 TAAGGAGGCTAGGTTTTCTTTTAAAGAGAATAGGTTTTCTCCCTTTTCAGTTGTCTTCCAAAATG
*
20505 AGAGGTAAAAACCTCTTTATATAGAGGAGGCTAGGGTCCATTTGGTAACCCTAGTAAATTAGTAT
131 AGAGGTAAAAACCTCTTTATATAGAGGAGGCTAGAGTCCATTTGGTAACCCTAGTAAATTAGTAT
20570 TAGGCCAGTTTTAGTGGGCCAACTTAACTGCATTTTTAATTGGGCTCAAATTAGAATGTAATCCA
196 TAGGCCAGTTTTAGTGGGCCAACTTAACTGCATTTTTAATTGGGCTCAAATTAGAATGTAATCCA
20635 AATGAATTTTCTTATGGACTAAACCCAAATATTTATTTAACCAATCTAAATTGGTTA
261 AATGAATTTTCTTATGGACTAAACCCAAATATTTATTTAACCAATCTAAATTGGTTA
*
20692 GATGGAGAAGAACTTTGCCTTGAATTTGGAGAGATTGTCGGGGTGGCTTGAAGGCTCAAAATCTC
1 GATGGAGAAGAACTTTGCCTTGAATTTGGAGAGATTGCCGGGGTGGCTTGAAGGCTCAAAATCTC
* *
20757 TGAGGAGGCTAGGTTTTCTTTTGAAGAGAATAGGGTTTTCTCCCTTTTCAGTTGTCTTCCAAAAT
66 TAAGGAGGCTAGGTTTTCTTTTAAAGAGAATA-GGTTTTCTCCCTTTTCAGTTGTCTTCCAAAAT
* * * *
20822 GAGAGGTGAAGACTTCTTTATATAGAGGAGGCTAGAGTCCATTTGGTAATCCTAGTAAATTAGTA
130 GAGAGGTAAAAACCTCTTTATATAGAGGAGGCTAGAGTCCATTTGGTAACCCTAGTAAATTAGTA
* * * *
20887 TTAGGCCAGTTTTAGTGGGCCAACTTAATTGTATTTTTAATTGGGCTCAAATTAGGATTTAATCC
195 TTAGGCCAGTTTTAGTGGGCCAACTTAACTGCATTTTTAATTGGGCTCAAATTAGAATGTAATCC
20952 AAATGAATTTTCTTATGGACTAAACCCAAATATTTATTTAACCAATCTAA
260 AAATGAATTTTCTTATGGACTAAACCCAAATATTTATTTAACCAATCTAA
21002 CCAATGGTTA
Statistics
Matches: 295, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
317 92 0.31
318 203 0.69
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (317 bp):
GATGGAGAAGAACTTTGCCTTGAATTTGGAGAGATTGCCGGGGTGGCTTGAAGGCTCAAAATCTC
TAAGGAGGCTAGGTTTTCTTTTAAAGAGAATAGGTTTTCTCCCTTTTCAGTTGTCTTCCAAAATG
AGAGGTAAAAACCTCTTTATATAGAGGAGGCTAGAGTCCATTTGGTAACCCTAGTAAATTAGTAT
TAGGCCAGTTTTAGTGGGCCAACTTAACTGCATTTTTAATTGGGCTCAAATTAGAATGTAATCCA
AATGAATTTTCTTATGGACTAAACCCAAATATTTATTTAACCAATCTAAATTGGTTA
Found at i:26735 original size:24 final size:24
Alignment explanation
Indices: 26704--26789 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
26694 CTTTGACGGG
26704 GAAGAACTTTGCCTTGAATTTGGA
1 GAAGAACTTTGCCTTGAATTTGGA
**
26728 GAAGAACTTTGCTTCAGATCTGTTTTGATGGA
1 GAAGAACTTTGC--C---T-TGAATT--TGGA
26760 GAAGAACTTTGCCTTGAATTTGGA
1 GAAGAACTTTGCCTTGAATTTGGA
26784 GAAGAA
1 GAAGAA
26790 ATTTTCTTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
24 22 0.44
26 5 0.10
27 1 0.02
29 1 0.02
30 5 0.10
32 16 0.32
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.33
Consensus pattern (24 bp):
GAAGAACTTTGCCTTGAATTTGGA
Found at i:26741 original size:56 final size:56
Alignment explanation
Indices: 26674--26897 Score: 340
Period size: 56 Copynumber: 4.0 Consensus size: 56
26664 TTGTTGATGG
* *
26674 AGAACTTTGCTTCAGATCTGCTTTGACGGGGAAGAACTTTGCCTTGAATTTGGAGA
1 AGAACTTTGCTTCAGATCTGCTTTGATGGAGAAGAACTTTGCCTTGAATTTGGAGA
*
26730 AGAACTTTGCTTCAGATCTGTTTTGATGGAGAAGAACTTTGCCTTGAATTTGGAGA
1 AGAACTTTGCTTCAGATCTGCTTTGATGGAGAAGAACTTTGCCTTGAATTTGGAGA
* * * *
26786 AGAAATTTTCTTCAGATCTGCTTTGATGGAGAAGAATTTTGCCTTGAATTTGAAGA
1 AGAACTTTGCTTCAGATCTGCTTTGATGGAGAAGAACTTTGCCTTGAATTTGGAGA
* ** * *
26842 AGAGCTTTGCTTCAGATCTGCTTTGATATAGAAGAACTTTGCCATCAATTTGGAGA
1 AGAACTTTGCTTCAGATCTGCTTTGATGGAGAAGAACTTTGCCTTGAATTTGGAGA
26898 GATTGCCGGT
Statistics
Matches: 151, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 151 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (56 bp):
AGAACTTTGCTTCAGATCTGCTTTGATGGAGAAGAACTTTGCCTTGAATTTGGAGA
Found at i:26760 original size:32 final size:32
Alignment explanation
Indices: 26724--26883 Score: 102
Period size: 32 Copynumber: 5.5 Consensus size: 32
26714 GCCTTGAATT
*
26724 TGGAGAAGAACTTTGCTTCAGATCTGTTTTGA
1 TGGAGAAGAACTTTGCTTCAGATCTGATTTGA
*
26756 TGGAGAAGAACTTTGC--C---T-TGAATT--
1 TGGAGAAGAACTTTGCTTCAGATCTGATTTGA
* * *
26780 TGGAGAAGAAATTTTCTTCAGATCTGCTTTGA
1 TGGAGAAGAACTTTGCTTCAGATCTGATTTGA
*
26812 TGGAGAAGAATTTTGC--C---T-TGAATTTGA
1 TGGAGAAGAACTTTGCTTCAGATCTG-ATTTGA
* *
26839 ---AGAAGAGCTTTGCTTCAGATCTGCTTTGA
1 TGGAGAAGAACTTTGCTTCAGATCTGATTTGA
**
26868 TATAGAAGAACTTTGC
1 TGGAGAAGAACTTTGC
26884 CATCAATTTG
Statistics
Matches: 97, Mismatches: 13, Indels: 36
0.66 0.09 0.25
Matches are distributed among these distances:
24 25 0.26
26 8 0.08
27 7 0.07
29 7 0.07
30 8 0.08
32 42 0.43
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (32 bp):
TGGAGAAGAACTTTGCTTCAGATCTGATTTGA
Found at i:38764 original size:72 final size:72
Alignment explanation
Indices: 38682--38828 Score: 276
Period size: 72 Copynumber: 2.0 Consensus size: 72
38672 TTAACCATTC
* *
38682 TAAATTATCATTTATTCAATAAAATTTTTATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
1 TAAATGATCATTTATTCAATAAAATTTTCATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
38747 ATGAATA
66 ATGAATA
38754 TAAATGATCATTTATTCAATAAAATTTTCATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
1 TAAATGATCATTTATTCAATAAAATTTTCATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
38819 ATGAATA
66 ATGAATA
38826 TAA
1 TAA
38829 GTATTAAATC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.48
Consensus pattern (72 bp):
TAAATGATCATTTATTCAATAAAATTTTCATTATTGTTATAATTTTATTAAATTTGCTAAACTTC
ATGAATA
Done.