Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022432.1 Corchorus olitorius cultivar O-4 contig22465, 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: 111819
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:13741 original size:2 final size:2
Alignment explanation
Indices: 13736--13761 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13726 ATATATCACG
13736 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
13762 GTTGTGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15152 original size:40 final size:40
Alignment explanation
Indices: 15096--15175 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
15086 ATACTTCTAT
*
15096 TAATTATAGACCATTTATATCTGAAAAATTCAATTTCAAA
1 TAATTATAGACAATTTATATCTGAAAAATTCAATTTCAAA
*
15136 TAATTATAGACAATTTATATCTGAAAATTTCAATTTCAAA
1 TAATTATAGACAATTTATATCTGAAAAATTCAATTTCAAA
15176 AGAATCCGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (40 bp):
TAATTATAGACAATTTATATCTGAAAAATTCAATTTCAAA
Found at i:19331 original size:5 final size:5
Alignment explanation
Indices: 19321--19379 Score: 109
Period size: 5 Copynumber: 11.8 Consensus size: 5
19311 GCAACTCTTA
19321 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
19371 TATAC TATA
1 TATAT TATA
19380 ACAAAACAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 53 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:20528 original size:438 final size:430
Alignment explanation
Indices: 19688--20532 Score: 1219
Period size: 438 Copynumber: 1.9 Consensus size: 430
19678 TATTTATTTT
* * * *
19688 TCCGATTAAGGTGATTGAGGTGTTTATTAAAAGGTAATTTCATGATTTACAACTTTCATGAAGGA
1 TCCGACTAAGGTGATTCAGGTGTCTATTAAAAGGTAATTTCATGATATACAACTTTCATGAAGGA
* *
19753 CTCAAAAGCCAATTTTTATGTTTCAATTCAAAAAAATACTTCCAAAATTTGGTGCTTTTGATTGC
66 CTCAAAAGCCAATTTTTATATTTCAATTAAAAAAAATACTTCCAAAATTTGGTGCTTTTGATTGC
*
19818 CGGTATATTAAATATCATATAATTTTCGATCCACATGTCCGATTAATGTTATTCAAGTGTCGTTA
131 CGGTATATTAAATACCATATAATTTTCGATCCACATGTCCGATTAA-GTTATTCAAGTGTCGTTA
* *
19883 AAAGGTTATTGCATGATCTACTACTTTCATGAAGTACCCGAAAGCTAAATTTGATCTACGAGTTT
195 AAAGGTTATTGCATGATCTACGACTTTCATGAAGTACCCGAAAGCTAAATTTGATCTACAAGTTT
* * *
19948 CATTAAGAGTTCAAAAGGGAATTTTTATGTTTCAAGATCCATTAACAAACATTTTCTTATTTGGA
260 CATTAAGAGTTCAAAAGGGAAATTGTATGTTTCAAGATCCATCAACAAACATTTTCTTATTTGGA
* * * *
20013 TTATTTATCAAATGACCCTTATATTTTTCTACTTTATACTACTTAGTCCTTTACTAATTCTATCT
325 TTATTTATCAAATGACCATCATACTTTTCTACTTTATACTACTTAGTCCTTTACAAATTCTATCT
20078 TAATCAATTTAACGCTTAAGCTTTAGTTTTTTTTTCAATTG
390 TAATCAATTTAACGCTTAAGCTTTAGTTTTTTTTTCAATTG
* *
20119 TCCGACTAAGGTGATTCAGGTGTCTATTAAAAGGTAATTTTATGATATACAACTTTCATGAAGTA
1 TCCGACTAAGGTGATTCAGGTGTCTATTAAAAGGTAATTTCATGATATACAACTTTCATGAAGGA
* * *
20184 CTCAAAAGCCAATTTTTATATTTCAATTGAAAAAAAAAATGCTTCCCAAATTTGTTAG-TTTTGA
66 CTCAAAAGCCAATTTTTATATTTCAATT---AAAAAAAATACTTCCAAAATTTGGT-GCTTTTGA
* * * * *
20248 TTGCCGGTTTATTTAATACCATATAATTTTGGATTCACATGTCCGATTCGAA-TTATTTAAGTGT
127 TTGCCGGTATATTAAATACCATATAATTTTCGATCCACATGTCCGATT--AAGTTATTCAAGTG-
* * * * * *
20312 TGGTTACAAGGTTATTGCGTGATCTACGACTTTCATGGAGTCCCCGGAAGCTAAATTTGATCTAC
189 TCGTTAAAAGGTTATTGCATGATCTACGACTTTCATGAAGTACCCGAAAGCTAAATTTGATCTAC
* *
20377 AAGTTTTATTAAG-GCTTCAAAGGGGAAAATTGTATGTTTCAAGATCTCCATCAACAAACATTTT
254 AAGTTTCATTAAGAG-TTCAAAAGGG-AAATTGTATGTTTCAAGA--TCCATCAACAAACATTTT
* *
20441 CTTATTTGGATTATTTATCAAATGACCATCATGCTTTTCTACTTTATACTACTTAGTTCTTTACA
315 CTTATTTGGATTATTTATCAAATGACCATCATACTTTTCTACTTTATACTACTTAGTCCTTTACA
* *
20506 AATTCTATCTTACTCGATTTAACGCTT
380 AATTCTATCTTAATCAATTTAACGCTT
20533 CGGTTTTTTG
Statistics
Matches: 365, Mismatches: 38, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
431 86 0.24
434 81 0.22
435 79 0.22
436 18 0.05
438 101 0.28
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (430 bp):
TCCGACTAAGGTGATTCAGGTGTCTATTAAAAGGTAATTTCATGATATACAACTTTCATGAAGGA
CTCAAAAGCCAATTTTTATATTTCAATTAAAAAAAATACTTCCAAAATTTGGTGCTTTTGATTGC
CGGTATATTAAATACCATATAATTTTCGATCCACATGTCCGATTAAGTTATTCAAGTGTCGTTAA
AAGGTTATTGCATGATCTACGACTTTCATGAAGTACCCGAAAGCTAAATTTGATCTACAAGTTTC
ATTAAGAGTTCAAAAGGGAAATTGTATGTTTCAAGATCCATCAACAAACATTTTCTTATTTGGAT
TATTTATCAAATGACCATCATACTTTTCTACTTTATACTACTTAGTCCTTTACAAATTCTATCTT
AATCAATTTAACGCTTAAGCTTTAGTTTTTTTTTCAATTG
Found at i:22255 original size:2 final size:2
Alignment explanation
Indices: 22248--22277 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
22238 TCATATCAGA
*
22248 AT AT AT AT AA 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
22278 TTTTTGATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22697 original size:25 final size:26
Alignment explanation
Indices: 22654--22709 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
22644 ATAAATTAAG
22654 GATTTTTTTCTGAGAAAAATATCATA
1 GATTTTTTTCTGAGAAAAATATCATA
*
22680 GATTTTTTTTTGAG-AAAATATCATA
1 GATTTTTTTCTGAGAAAAATATCATA
*
22705 AATTT
1 GATTT
22710 AATCGTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (26 bp):
GATTTTTTTCTGAGAAAAATATCATA
Found at i:24845 original size:23 final size:22
Alignment explanation
Indices: 24815--24857 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
24805 AGTGTATTAG
*
24815 TATATATATTAATTAGTATTTCT
1 TATATATATAAATTAG-ATTTCT
24838 TATATATATAAATTAGATTT
1 TATATATATAAATTAGATTT
24858 TAAAACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (22 bp):
TATATATATAAATTAGATTTCT
Found at i:27258 original size:2 final size:2
Alignment explanation
Indices: 27251--27289 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
27241 GGGACTCATT
27251 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27290 TCCATGTTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27453 original size:17 final size:17
Alignment explanation
Indices: 27428--27461 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27418 TCTTATATGC
27428 AAAGATATTCTAATTTT
1 AAAGATATTCTAATTTT
*
27445 AAAGGTATTCTAATTTT
1 AAAGATATTCTAATTTT
27462 GGAAAATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (17 bp):
AAAGATATTCTAATTTT
Found at i:41569 original size:3 final size:3
Alignment explanation
Indices: 41561--41588 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
41551 AAGGACAAAT
41561 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
41589 TGAAAGGTTC
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:43718 original size:41 final size:41
Alignment explanation
Indices: 43661--43754 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
43651 GACTAAGGTA
*
43661 ATCACATTGGATTCACATTGGATCCGAATCAGTATTCGGTT
1 ATCACATTGGACTCACATTGGATCCGAATCAGTATTCGGTT
43702 ATCACATTGGACTCACATTGGATCCGAATCAGTATTCGGTT
1 ATCACATTGGACTCACATTGGATCCGAATCAGTATTCGGTT
43743 ATCACATTGGAC
1 ATCACATTGGAC
43755 CGGTTCTCGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (41 bp):
ATCACATTGGACTCACATTGGATCCGAATCAGTATTCGGTT
Found at i:54923 original size:42 final size:43
Alignment explanation
Indices: 54864--54968 Score: 122
Period size: 43 Copynumber: 2.5 Consensus size: 43
54854 CATAAGATAA
* * * *
54864 ATTGGGCCATGCAGCCCATA-GGTATGGAATGAATGGAGACTT
1 ATTGGGCCACGCAGCCCACATGGTATGGAATAAATGGAGAATT
** * *
54906 ATTGGGCCACGCAGCCCACATTTTATGGTATAAATGGGGAATT
1 ATTGGGCCACGCAGCCCACATGGTATGGAATAAATGGAGAATT
*
54949 GTTGGGCCACGCAGCCCACA
1 ATTGGGCCACGCAGCCCACA
54969 CCTATGGTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 18 0.34
43 35 0.66
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (43 bp):
ATTGGGCCACGCAGCCCACATGGTATGGAATAAATGGAGAATT
Found at i:54954 original size:43 final size:44
Alignment explanation
Indices: 54907--55004 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 44
54897 TGGAGACTTA
**
54907 TTGGGCCACGCAGCCCACATTTTATGGTA-TA-AATGGGGAATTG
1 TTGGGCCACGCAGCCCACA-CCTATGGTATTATAATGGGGAATTG
54950 TTGGGCCACGCAGCCCACACCTATGGTATTATTAATGGGGAATTG
1 TTGGGCCACGCAGCCCACACCTATGGTATTA-TAATGGGGAATTG
54995 TTGGGCCACG
1 TTGGGCCACG
55005 GATATTGGCT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
42 7 0.14
43 21 0.42
45 22 0.44
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (44 bp):
TTGGGCCACGCAGCCCACACCTATGGTATTATAATGGGGAATTG
Found at i:61329 original size:2 final size:2
Alignment explanation
Indices: 61316--61354 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
61306 GTTTATGTTC
*
61316 TG TG TT TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
61355 TGTTTTGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:69189 original size:144 final size:141
Alignment explanation
Indices: 68905--69194 Score: 526
Period size: 144 Copynumber: 2.0 Consensus size: 141
68895 ATCCTTACCT
68905 GATCAGGGCACAAAGCAGCAATTTTCAGATATAAAAAGTTTGAAAGGTGAAAAGGATATAATTTT
1 GATCAGGGCACAAAGCAGCAATTTTCAGATATAAAAAGTTTGAAAGGTGAAAAGGATATAATTTT
* *
68970 TAAACAGTGAAAAGGTTCAAAATTATTCCACGCCCAATAAGTGCTTTTTTACTTTTAGTTTTGGC
66 TAAACAGTGAAAAGGTTCAAAATTATACCACGCCCAATAAGTGCTTCTTTACTTTTAGTTTTGGC
69035 TTCATCCAGTA
131 TTCATCCAGTA
69046 GATCAGGGCACAAAGCAGCAATTTTCAGATATAAAAAGTTTGAAAGGTGAAAAGGATATAATTTT
1 GATCAGGGCACAAAGCAGCAATTTTCAGATATAAAAAGTTTGAAAGGTGAAAAGGATATAATTTT
*
69111 TAAACAACAGTGAAAAGGTTCAAAATTATACCACGCGCAATAAGTGCTTCTTTACTTTTAGTTTT
66 T--A-AACAGTGAAAAGGTTCAAAATTATACCACGCCCAATAAGTGCTTCTTTACTTTTAGTTTT
69176 GGCTTCATCCAGTA
128 GGCTTCATCCAGTA
69190 GATCA
1 GATCA
69195 ACTAATCGAA
Statistics
Matches: 143, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
141 66 0.46
143 1 0.01
144 76 0.53
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (141 bp):
GATCAGGGCACAAAGCAGCAATTTTCAGATATAAAAAGTTTGAAAGGTGAAAAGGATATAATTTT
TAAACAGTGAAAAGGTTCAAAATTATACCACGCCCAATAAGTGCTTCTTTACTTTTAGTTTTGGC
TTCATCCAGTA
Found at i:72042 original size:102 final size:102
Alignment explanation
Indices: 71861--72047 Score: 297
Period size: 102 Copynumber: 1.8 Consensus size: 102
71851 TCATGGCAAA
*
71861 ACTAATTATCATATGTTGTTTTGATTCAATTCAAAGTAAAGAAATTCAAAAGAACTCATTAACGG
1 ACTAATTATCATATGTTGTTTTGATT--ATTCAAAGTAAAGAAATTCAAAAGAACTCATTAAAGG
* *
71926 AGCAAGGACTACTCATGGAAAACTTCTTCTTTACCTCTC
64 AACAAGGACGACTCATGGAAAACTTCTTCTTTACCTCTC
71965 ACTAATTATCATCA-GTTGTTTTGATT-TTCAAAGTAAAAGAAATTCAAAAGAACTCATTAAAGG
1 ACTAATTATCAT-ATGTTGTTTTGATTATTCAAAGT-AAAGAAATTCAAAAGAACTCATTAAAGG
72028 AACAAGGACGACTCATGGAA
64 AACAAGGACGACTCATGGAA
72048 CTTCTTTACC
Statistics
Matches: 78, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
101 8 0.10
102 45 0.58
104 24 0.31
105 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (102 bp):
ACTAATTATCATATGTTGTTTTGATTATTCAAAGTAAAGAAATTCAAAAGAACTCATTAAAGGAA
CAAGGACGACTCATGGAAAACTTCTTCTTTACCTCTC
Found at i:106537 original size:24 final size:24
Alignment explanation
Indices: 106484--106530 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
106474 TAAAAAAGAA
106484 ACATTATTAATTTTTATTAATTAT
1 ACATTATTAATTTTTATTAATTAT
*
106508 ATATTATT-ATTGTTTATT-ATTAT
1 ACATTATTAATT-TTTATTAATTAT
106531 GCCATTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
ACATTATTAATTTTTATTAATTAT
Found at i:107291 original size:11 final size:11
Alignment explanation
Indices: 107275--107301 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
107265 TATAGTGTTA
107275 AAAAAAAAAAG
1 AAAAAAAAAAG
107286 AAAAAAAAAAG
1 AAAAAAAAAAG
107297 AAAAA
1 AAAAA
107302 GAGTTTCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:111180 original size:2 final size:2
Alignment explanation
Indices: 111173--111198 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
111163 TATTTGATGA
111173 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
111199 TATTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.