Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022582.1 Corchorus olitorius cultivar O-4 contig22615, 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: 12845
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Found at i:3433 original size:54 final size:54
Alignment explanation
Indices: 3311--3521 Score: 307
Period size: 54 Copynumber: 3.9 Consensus size: 54
3301 GTGTTCAAAG
* *
3311 TGATCCAATGCGGTCATTCCAAGAAGTTTTTTAA-GGATCAGAGTTGATCCTCAGA
1 TGATCCAGTGCGGTCATTCCAAGAAG-TTTTCAATGG-TCAGAGTTGATCCTCAGA
* * * * *
3366 TGATCGAGTGCGGTCATTTCAAGAAGTTTTCAATGGTCATAGTTAATCCTGAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCTCAGA
*
3420 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCTTCAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCTCAGA
* *
3474 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
3522 TCGTTTCAAG
Statistics
Matches: 140, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
54 115 0.82
55 25 0.18
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (54 bp):
TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATCCTCAGA
Found at i:3534 original size:35 final size:35
Alignment explanation
Indices: 3493--3804 Score: 394
Period size: 35 Copynumber: 8.9 Consensus size: 35
3483 GCGGTCATTC
3493 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
3528 CAAGAAGTTTTCGGTGATCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* **
3563 CAGGAAGTTTTTTATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* *
3598 CAAGAAG-TTTCGGTGATCAGAGTTGATCTCCTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
* ** * *
3632 CAGGAAGTTTTTTATGATAAGAGTTGATCTCATTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTC-GTTT
* * * *
3668 CAAGATGTTTT-TATGGTCAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
3702 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
** *
3737 CAAAGAAGTTTTTTTTATGATCAGAGTTGATCTCATTT
1 C-AAGAAG--TTTTCGATGATCAGAGTTGATCTCGTTT
*
3775 CAAGAAGTTTTTGATGATCAGAGTTGATCT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCT
3805 TCACATTGAT
Statistics
Matches: 240, Mismatches: 31, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
34 42 0.17
35 148 0.62
36 18 0.08
37 6 0.03
38 26 0.11
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (35 bp):
CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
Found at i:3679 original size:104 final size:104
Alignment explanation
Indices: 3487--3804 Score: 458
Period size: 104 Copynumber: 3.0 Consensus size: 104
3477 TCCAGTGCGG
* ***
3487 TCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGGTGATCAGAGT
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTTATGATCAGAGT
* *
3552 TGATCTCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATC
66 TGATCTCATTTCAAGAAG-TTTTTATGATCAGAGTTGATC
* * * * *
3592 TCGTTTCAAGAAG-TTTCGGTGATCAGAGTTGATCTCCTTTCAGGAAGTTTTTTATGATAAGAGT
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTTATGATCAGAGT
* *
3656 TGATCTCATTTTCAAGATGTTTTTATGGTCAGAGTTGATC
66 TGATCTCA-TTTCAAGAAGTTTTTATGATCAGAGTTGATC
3696 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAAGAAGTTTTTTTTATGATCAG
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC-AAGAAG--TTTTTTATGATCAG
3761 AGTTGATCTCATTTCAAGAAGTTTTTGATGATCAGAGTTGATC
63 AGTTGATCTCATTTCAAGAAGTTTTT-ATGATCAGAGTTGATC
3804 T
1 T
3805 TCACATTGAT
Statistics
Matches: 187, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
104 83 0.44
105 45 0.24
106 5 0.03
107 14 0.07
108 40 0.21
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (104 bp):
TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTTATGATCAGAGT
TGATCTCATTTCAAGAAGTTTTTATGATCAGAGTTGATC
Found at i:4553 original size:2 final size:2
Alignment explanation
Indices: 4546--4577 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4536 TAATCTACTC
4546 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4578 CTTCATCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5232 original size:25 final size:25
Alignment explanation
Indices: 5204--5282 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 25
5194 TATTTATTCA
5204 CTATTTATTTATTTTTAACTATCAT
1 CTATTTATTTATTTTTAACTATCAT
* *
5229 CTATTTATTTACTATT---TATCA-
1 CTATTTATTTATTTTTAACTATCAT
* *
5250 --ATTTATTTATTTTTAACCATTAT
1 CTATTTATTTATTTTTAACTATCAT
5273 CTATTTATTT
1 CTATTTATTT
5283 GCTATTTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 12 0.29
22 8 0.19
25 22 0.52
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (25 bp):
CTATTTATTTATTTTTAACTATCAT
Found at i:5264 original size:44 final size:44
Alignment explanation
Indices: 5204--5424 Score: 307
Period size: 44 Copynumber: 4.9 Consensus size: 44
5194 TATTTATTCA
*
5204 CTATTTATTTATTTTTAACTATCATCTATTTATTTACTATTTAT
1 CTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTAT
* * *
5248 CAATTTATTTATTTTTAACCATTATCTATTTATTTGCTATTTAT
1 CTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTAT
* *
5292 CTTTTTATTTATTTTTAACTATTATCTATATATTTACTATTTAT
1 CTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTAT
* *
5336 CTTTTTATTTATTAATTTAACTATTATCTATTTACTTACTATTTAT
1 CTATTTATTTATT--TTTAACTATTATCTATTTATTTACTATTTAT
* * *
5382 CTATTTATTTATTAATTTAGCTATTATCTATTTAGTTATTATT
1 CTATTTATTTATT--TTTAACTATTATCTATTTATTTACTATT
5425 ATTTTTTTCA
Statistics
Matches: 160, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
44 92 0.57
46 68 0.43
ACGTcount: A:0.28, C:0.10, G:0.01, T:0.61
Consensus pattern (44 bp):
CTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTTAT
Found at i:5293 original size:19 final size:18
Alignment explanation
Indices: 5269--5391 Score: 76
Period size: 19 Copynumber: 6.8 Consensus size: 18
5259 TTTTTAACCA
5269 TTATCTATTTATTTGCTAT
1 TTATCTATTTATTT-CTAT
* * *
5288 TTATCTTTTTATTTATTT
1 TTATCTATTTATTTCTAT
* *
5306 TTAACTA-TTATCTATATAT
1 TTATCTATTTAT-T-TCTAT
*
5325 TTA-CTATTTA--TCTTT
1 TTATCTATTTATTTCTAT
* *
5340 TTATTTATTAATTTAACTA-
1 TTATCTATTTATTT--CTAT
*
5359 TTATCTATTTACTTACTAT
1 TTATCTATTTA-TTTCTAT
5378 TTATCTATTTATTT
1 TTATCTATTTATTT
5392 ATTAATTTAG
Statistics
Matches: 79, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
15 6 0.08
16 5 0.06
17 4 0.05
18 17 0.22
19 43 0.54
20 4 0.05
ACGTcount: A:0.26, C:0.10, G:0.01, T:0.63
Consensus pattern (18 bp):
TTATCTATTTATTTCTAT
Found at i:5353 original size:27 final size:26
Alignment explanation
Indices: 5323--5422 Score: 88
Period size: 27 Copynumber: 4.0 Consensus size: 26
5313 TTATCTATAT
*
5323 ATTTACTATTTATCTTTTTATTTATTA
1 ATTTACTA-TTATCTATTTATTTATTA
*
5350 ATTTAACTATTATCTATTTA---CTT-
1 ATTT-ACTATTATCTATTTATTTATTA
*
5373 A-CTA-T-TTATCTATTTATTTATTA
1 ATTTACTATTATCTATTTATTTATTA
*
5396 ATTTAGCTATTATCTATTTAGTTATTA
1 ATTTA-CTATTATCTATTTATTTATTA
5423 TTATTTTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
19 11 0.19
20 1 0.02
21 1 0.02
22 3 0.05
23 2 0.03
24 4 0.07
26 1 0.02
27 31 0.53
28 4 0.07
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60
Consensus pattern (26 bp):
ATTTACTATTATCTATTTATTTATTA
Found at i:5368 original size:15 final size:15
Alignment explanation
Indices: 5350--5428 Score: 51
Period size: 15 Copynumber: 5.3 Consensus size: 15
5340 TTATTTATTA
5350 ATTTAACTATTATCT
1 ATTTAACTATTATCT
5365 ATTTACTTACTATTTATCT
1 ATTTA---ACTA-TTATCT
5384 ATTT-A-T-TTAT-T
1 ATTTAACTATTATCT
*
5395 AATTTAGCTATTATCT
1 -ATTTAACTATTATCT
**
5411 ATTTAGTTATTAT-T
1 ATTTAACTATTATCT
5425 ATTT
1 ATTT
5429 TTTTCAGCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 19
0.72 0.03 0.26
Matches are distributed among these distances:
11 1 0.02
12 8 0.15
14 7 0.13
15 22 0.42
16 1 0.02
18 4 0.08
19 10 0.19
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (15 bp):
ATTTAACTATTATCT
Found at i:5467 original size:24 final size:24
Alignment explanation
Indices: 5437--5502 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
5427 TTTTTTCAGC
5437 TACCTATTTATCTATTATTCTCTA
1 TACCTATTTATCTATTATTCTCTA
*
5461 TATCTATTTATCTATTCA-TCTCTA
1 TACCTATTTATCTATT-ATTCTCTA
*
5485 TACCTATTT-TTTATTATT
1 TACCTATTTATCTATTATT
5503 ATTATTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 1 0.03
23 6 0.16
24 29 0.78
25 1 0.03
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (24 bp):
TACCTATTTATCTATTATTCTCTA
Found at i:7576 original size:13 final size:11
Alignment explanation
Indices: 7554--7605 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 11
7544 CCCATCAGCG
7554 AAAGAAAAAAA
1 AAAGAAAAAAA
7565 ACAAGCAAAAAAA
1 A-AAG-AAAAAAA
7578 AAAGGAAAAGAAA
1 AAA-GAAAA-AAA
7591 AAAGAAAAAAGA
1 AAAGAAAAAA-A
7603 AAA
1 AAA
7606 TGTGAAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
11 3 0.08
12 18 0.50
13 15 0.42
ACGTcount: A:0.83, C:0.04, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:8478 original size:11 final size:10
Alignment explanation
Indices: 8451--8480 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
8441 AAAAAAGAAG
8451 AAGAGGAAAA
1 AAGAGGAAAA
8461 AAGAGGAAAA
1 AAGAGGAAAA
8471 AAGAAGGAAA
1 AAG-AGGAAA
8481 TGGTAAGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AAGAGGAAAA
Found at i:9643 original size:54 final size:54
Alignment explanation
Indices: 9466--9733 Score: 288
Period size: 54 Copynumber: 4.9 Consensus size: 54
9456 CAGGTGTTTA
* * * ** *
9466 AGATGAGCCAGTGTGGTCTTTCATAGAAGTTTTTAAAAATCTA-AGTTGATCTTC
1 AGATGACCCAGTGCGGTCTTTCAAAGAAGTTTTTAATGATC-AGAGTTGATCCTC
* ** * * * *
9520 AGATGACCCTGTGTAGTCTTTCATAAGAAGTTTTCAATGATCAGAGTTAATCTTA
1 AGATGACCCAGTGCGGTCTTTCA-AAGAAGTTTTTAATGATCAGAGTTGATCCTC
* * * *
9575 AGTTGACCCCGTGCGGTCTTTCAAAGAAGTTTTTAAGGATCAGATTTGATCCTC
1 AGATGACCCAGTGCGGTCTTTCAAAGAAGTTTTTAATGATCAGAGTTGATCCTC
* * *
9629 AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAGAGTTGATCCTC
1 AGATGACCCAGTGCGGTCTTTCAAAGAAGTTTTTAATGATCAGAGTTGATCCTC
* * *
9683 AGATGATCCAGTGCGGTCGTTTC-AAGAAGTTTTCAATGATCAGAATTGATC
1 AGATGACCCAGTGCGGTC-TTTCAAAGAAGTTTTTAATGATCAGAGTTGATC
9734 TCGTTTCAAG
Statistics
Matches: 182, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
54 137 0.75
55 45 0.25
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (54 bp):
AGATGACCCAGTGCGGTCTTTCAAAGAAGTTTTTAATGATCAGAGTTGATCCTC
Found at i:10264 original size:35 final size:35
Alignment explanation
Indices: 9702--10263 Score: 727
Period size: 35 Copynumber: 15.9 Consensus size: 35
9692 AGTGCGGTCG
* * *
9702 TTTCAAGAAGTTTTCAATGATCAGAATTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
9737 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
9772 TTTCAA-AATGTTTTCGGTGATCAGAGTTGATCTCC
1 TTTCAAGAA-GTTTTCGATGATCAGAGTTGATCTCA
**
9807 TTTCAAGAAGTTTTCGATGATCAGAGTTGATAACA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
9842 TTTTAAGAAGTTTT-GATGATCAGAGTTGATCGCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* * *
9876 TTTCAAGAAATTTTTGATGATCAGAGTTGATCACA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* * *
9911 TTTTAAGAAGTTTT-GATGATCAAAGTTGATCACA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
9945 TTTCAAGAAGTTTTTGATGATCAGAGTTGATATCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
9980 TTTCAAGAAGTTTTCTATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
10015 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
10050 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
** *
10085 TTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCC
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* * *
10120 TTTTAAGAAGTTTTTG-TCGATCAGCGTTGATCTCA
1 TTTCAAGAAGTTTTCGAT-GATCAGAGTTGATCTCA
* * *
10155 TTTCAAGAAGTTTTTTCTATGGTCAGAGTTGATCTCC
1 TTTCAAGAAG--TTTTCGATGATCAGAGTTGATCTCA
** *
10192 TTTCAAGAAGTTTTTTTTTTATGATCAGAGTTGATCTTA
1 TTTCAAGAAG----TTTTCGATGATCAGAGTTGATCTCA
*
10231 TTTCAAGACGTTTTCGATGATCAGAGTTGATCT
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
10264 TCACATTGAT
Statistics
Matches: 470, Mismatches: 47, Indels: 20
0.88 0.09 0.04
Matches are distributed among these distances:
34 65 0.14
35 342 0.73
36 2 0.00
37 28 0.06
38 1 0.00
39 32 0.07
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
Found at i:11329 original size:22 final size:23
Alignment explanation
Indices: 11290--11335 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
11280 TTTTGTAATA
11290 TTTTATATTTATGATTAAGTGTG
1 TTTTATATTTATGATTAAGTGTG
*
11313 TTTTA-ATTATAT-ATTAATTGTG
1 TTTTATATT-TATGATTAAGTGTG
11335 T
1 T
11336 GTGGATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (23 bp):
TTTTATATTTATGATTAAGTGTG
Done.