Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005117.1 Corchorus capsularis cultivar CVL-1 contig05135, 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: 7743
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Found at i:844 original size:35 final size:35
Alignment explanation
Indices: 798--1001 Score: 329
Period size: 35 Copynumber: 5.9 Consensus size: 35
788 GATAATTAGT
*
798 AGTAATCAACTTAATTCAGGGTAATTAAGTGAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
833 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
* *
868 AGTAATCAACTTAATTCAGTGTAATTAAGTCAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
*
903 GGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
* *
938 AGTAGTCAACTTAATTCAGGATAATTAAGTAAGT-
1 AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
* *
972 AATAAGCAACTTAATTCAGGGTAATTAAGT
1 AGTAATCAACTTAATTCAGGGTAATTAAGT
1002 TTAGTAAAAA
Statistics
Matches: 156, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
34 26 0.17
35 130 0.83
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (35 bp):
AGTAATCAACTTAATTCAGGGTAATTAAGTAAGTC
Found at i:2152 original size:22 final size:22
Alignment explanation
Indices: 2082--2265 Score: 140
Period size: 22 Copynumber: 8.3 Consensus size: 22
2072 TGTCTCTATG
*
2082 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
2104 TAGTTATTATAATTTCATGATGA
1 TGGTTATCAAAATTTCAT-AGGA
* * *
2127 -GGTTATTAAAATTCCATAGTA
1 TGGTTATCAAAATTTCATAGGA
*
2148 TGGTTACCAAAATTTCATACGGA
1 TGGTTATCAAAATTTCATA-GGA
*
2171 -AGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
2192 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * *
2214 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** * *
2238 TGGTTATTGAACTTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
2260 TGGTTA
1 TGGTTA
2266 ATTATCACAA
Statistics
Matches: 129, Mismatches: 25, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
21 4 0.03
22 102 0.79
23 5 0.04
24 18 0.14
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:2197 original size:66 final size:66
Alignment explanation
Indices: 2082--2211 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 66
2072 TGTCTCTATG
* * * **
2082 TGGTTATCAAAATTTCATAAGATAGTTATTATAATTTCATGATGAGGTTATTAAAATTCCATAGT
1 TGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGATGAGGTTACCAAAATTCCATAGT
2147 A
66 A
* * *
2148 TGGTTACCAAAATTTCATACGGA-AGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCATA
1 TGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTCATGA-TGAGGTTACCAAAATTCCATA
2211 G
64 G
2212 GATCAGGTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
65 1 0.02
66 51 0.94
67 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (66 bp):
TGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGATGAGGTTACCAAAATTCCATAGT
A
Found at i:2326 original size:22 final size:21
Alignment explanation
Indices: 2301--2679 Score: 127
Period size: 22 Copynumber: 17.7 Consensus size: 21
2291 ATCAAAGAGA
*
2301 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
2323 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
2345 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
2367 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* *
2389 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
* ** * *
2411 TTAT-GAAGCTT-ATA-AAAG
1 TTATCAAAATTTCATAGGAGG
* *
2429 -TCTC--AATTTCATA-AAGAG
1 TTATCAAAATTTCATAGGAG-G
* * *
2447 -TACCAAAATTTGATAGAAGG
1 TTATCAAAATTTCATAGGAGG
*
2467 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
* *
2487 ATTATCGAAATTTCATAGAGATCAGA
1 -TTATCAAAATTTCATAG-G---AGG
* *
2513 TTATCAAAATTT-GTAGGAAGA
1 TTATCAAAATTTCATAGG-AGG
* **
2534 TTATCAAAATTTCACAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
* *
2556 TTATCAAAATTTGAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
2578 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
* *
2600 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
2622 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
2644 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
2666 TTATCAAATTTTCA
1 TTATCAAAATTTCA
2680 AAATGTGATT
Statistics
Matches: 266, Mismatches: 64, Indels: 54
0.69 0.17 0.14
Matches are distributed among these distances:
16 3 0.01
17 7 0.03
18 4 0.02
19 2 0.01
20 21 0.08
21 36 0.14
22 166 0.62
23 10 0.04
24 4 0.02
25 11 0.04
27 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:2604 original size:44 final size:44
Alignment explanation
Indices: 2511--2700 Score: 145
Period size: 44 Copynumber: 4.3 Consensus size: 44
2501 ATAGAGATCA
* * * * *
2511 GATTATCAAAATTTGTAGGA-AGATTATCAAAATTTCACAGTGTT
1 GATTATCAAAATTTGAAAGAGAGGTTATCAAAATTTCATAATG-T
* *
2555 G-TTATCAAAATTTGAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTGAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * * * *
2598 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTGAAAGAGAGGTTATCAAAATTTCATAATGT
* * * *
2642 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTGA-AAGAGAGGTTATCAAAATTTCATAATGT
2686 GATTA-CAAAAATTTG
1 GATTATC-AAAATTTG
2701 GCATAAATGC
Statistics
Matches: 111, Mismatches: 31, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
43 18 0.16
44 92 0.83
45 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTGAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:2917 original size:31 final size:31
Alignment explanation
Indices: 2882--3012 Score: 120
Period size: 31 Copynumber: 4.2 Consensus size: 31
2872 TCAAAAAGTA
** *
2882 CCACGTGGATAAAAAAGTGACACGTTGCACG
1 CCACGTGGACCAAAAAGTGACACGTGGCACG
**
2913 CCACGTGTG-TTAAAAAGTGACACGTGGCACG
1 CCACGTG-GACCAAAAAGTGACACGTGGCACG
* * * * * *
2944 TCACATGTACCAAAAAGTGATACATGACACG
1 CCACGTGGACCAAAAAGTGACACGTGGCACG
* * *
2975 CCTCGTGTACCAAAAAGTGACACGTGGCATG
1 CCACGTGGACCAAAAAGTGACACGTGGCACG
3006 CCACGTG
1 CCACGTG
3013 CACTAAAGGA
Statistics
Matches: 80, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
31 79 0.99
32 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (31 bp):
CCACGTGGACCAAAAAGTGACACGTGGCACG
Found at i:3386 original size:44 final size:44
Alignment explanation
Indices: 3338--3461 Score: 121
Period size: 44 Copynumber: 2.8 Consensus size: 44
3328 AGTTTAGTTT
* * *
3338 TCAAAATTTTATAAGAGGGTTATCAAAATTTCGTAGT-ATGTAGA
1 TCAAAATATCATAAGAGGGTTATCAAAATTTCGTAGTGAGGT-GA
* *
3382 TCAAAATATCAT-AG-GGAGATTAACAAAATTTCGTAATGAGGTGA
1 TCAAAATATCATAAGAGG-G-TTATCAAAATTTCGTAGTGAGGTGA
* * *
3426 TCAAAAAATCATAGGAAGGTTATCAAAATTT-GTAGT
1 TCAAAATATCATAAGAGGGTTATCAAAATTTCGTAGT
3462 TATCAAGATT
Statistics
Matches: 65, Mismatches: 10, Indels: 11
0.76 0.12 0.13
Matches are distributed among these distances:
42 2 0.03
43 7 0.11
44 50 0.77
45 5 0.08
46 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (44 bp):
TCAAAATATCATAAGAGGGTTATCAAAATTTCGTAGTGAGGTGA
Found at i:3511 original size:24 final size:23
Alignment explanation
Indices: 3483--3557 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
3473 CATAAGAAAG
3483 TTATCAAAATTTTAATAGGGAGGT
1 TTATCAAAATTTT-ATAGGGAGGT
* * *
3507 TTATCAAACTTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
3530 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
3552 TTATCA
1 TTATCA
3558 CACTTTCATG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 6 0.14
23 25 0.58
24 12 0.28
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:3532 original size:23 final size:23
Alignment explanation
Indices: 3461--3546 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
3451 AAATTTGTAG
* * * *
3461 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
3483 TTATCAAAATTTTAATAGGGAGGT
1 TTATCAAAATTTT-ATAGGAAGAT
*
3507 TTATCAAACTTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
3530 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
3547 CGAGGTTATC
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
22 11 0.22
23 28 0.55
24 12 0.24
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:3586 original size:22 final size:21
Alignment explanation
Indices: 3459--3587 Score: 64
Period size: 22 Copynumber: 5.8 Consensus size: 21
3449 CAAAATTTGT
* **
3459 AGTTATCAAGATTTCATAAGAA
1 AGTTATCAAAATTTCAT-AGCG
* *
3481 AGTTATCAAAATTTTAATAGGG
1 AGTTATCAAAA-TTTCATAGCG
* *
3503 AGGTTTATCAAACTTTTATAG-G
1 A-G-TTATCAAAATTTCATAGCG
3525 AAGATTTATCAAAATTTCATAGCG
1 -AG--TTATCAAAATTTCATAGCG
* * *
3549 AGGTTATCACACTTTCATGATGTG
1 A-GTTATCAAAATTTCAT-A-GCG
3573 A-TTATCAAAATTTCA
1 AGTTATCAAAATTTCA
3588 GAGTGTAATT
Statistics
Matches: 85, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
22 40 0.47
23 32 0.38
24 13 0.15
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (21 bp):
AGTTATCAAAATTTCATAGCG
Found at i:3598 original size:22 final size:22
Alignment explanation
Indices: 3530--3598 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
3520 ATAGGAAGAT
* * *
3530 TTATCAAAATTTCATAGCG-AGG
1 TTATCAAAATTTCAGAGTGTA-A
* * *
3552 TTATCACACTTTCATGA-TGTGA
1 TTATCAAAATTTCA-GAGTGTAA
3574 TTATCAAAATTTCAGAGTGTAA
1 TTATCAAAATTTCAGAGTGTAA
3596 TTA
1 TTA
3599 CTAACAATTC
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
21 2 0.06
22 32 0.91
23 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTAA
Found at i:3699 original size:23 final size:22
Alignment explanation
Indices: 3636--3701 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
3626 TATTCATAAC
*
3636 GTGGTTATCAATATATCATATG
1 GTGGTTATCAAAATATCATATG
* ** *
3658 GAGGTTATCAACCTCTCATAGTG
1 GTGGTTATCAAAATATCATA-TG
* *
3681 TTGGTTATCAAAATTTCATAT
1 GTGGTTATCAAAATATCATAT
3702 TGAGATCTTC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (22 bp):
GTGGTTATCAAAATATCATATG
Found at i:3750 original size:19 final size:19
Alignment explanation
Indices: 3726--3764 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3716 TTTCTTAGAG
*
3726 AGGTTAACAAAATTTCATA
1 AGGTTAAAAAAATTTCATA
*
3745 AGGTTAAAAAAATTTTATA
1 AGGTTAAAAAAATTTCATA
3764 A
1 A
3765 AAAGAATCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.33
Consensus pattern (19 bp):
AGGTTAAAAAAATTTCATA
Found at i:4002 original size:38 final size:36
Alignment explanation
Indices: 3928--3999 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3918 GTGCAACGCG
3928 CGTGAAAGCTAAAATTAGTGTGTATATATATATATA
1 CGTGAAAGCTAAAATTAGTGTGTATATATATATATA
3964 CGTGAAAGCTAAAATTAGTGTGTATATATATATATA
1 CGTGAAAGCTAAAATTAGTGTGTATATATATATATA
4000 TACAGTGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (36 bp):
CGTGAAAGCTAAAATTAGTGTGTATATATATATATA
Found at i:4090 original size:2 final size:2
Alignment explanation
Indices: 4083--4128 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
4073 GGAATGAAAT
* *
4083 TA TA TA TA TA TGG TT TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4125 TA TA
1 TA TA
4129 CAAACCATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5434 original size:31 final size:31
Alignment explanation
Indices: 5398--5475 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
5388 TGTAATTTTC
5398 TTGGGTCATTCGGGTTTCAGGTCATCTAGGT
1 TTGGGTCATTCGGGTTTCAGGTCATCTAGGT
* * * *
5429 TTGGGTTATCCGGGTTTCGGGTCATCTGGGT
1 TTGGGTCATTCGGGTTTCAGGTCATCTAGGT
5460 TTCGGGTCATTCGGGT
1 TT-GGGTCATTCGGGT
5476 CTTGGGTTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 29 0.73
32 11 0.28
ACGTcount: A:0.09, C:0.17, G:0.36, T:0.38
Consensus pattern (31 bp):
TTGGGTCATTCGGGTTTCAGGTCATCTAGGT
Found at i:5482 original size:16 final size:16
Alignment explanation
Indices: 5400--5475 Score: 77
Period size: 16 Copynumber: 4.8 Consensus size: 16
5390 TAATTTTCTT
5400 GGGTCATTCGGGTTTC
1 GGGTCATTCGGGTTTC
* *
5416 AGGTCA-TCTAGGTTT-
1 GGGTCATTC-GGGTTTC
* *
5431 GGGTTATCCGGGTTTC
1 GGGTCATTCGGGTTTC
5447 GGGTCA-TCTGGGTTTC
1 GGGTCATTC-GGGTTTC
5463 GGGTCATTCGGGT
1 GGGTCATTCGGGT
5476 CTTGGGTTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
15 12 0.26
16 33 0.70
17 2 0.04
ACGTcount: A:0.09, C:0.17, G:0.37, T:0.37
Consensus pattern (16 bp):
GGGTCATTCGGGTTTC
Done.