Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022460.1 Corchorus olitorius cultivar O-4 contig22493, 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: 17798
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:1281 original size:31 final size:31
Alignment explanation
Indices: 1243--1410 Score: 154
Period size: 31 Copynumber: 5.5 Consensus size: 31
1233 TCTTTTAATT
1243 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
** **
1274 TGCTCAAATAAGGGCC---CGGTCTT-TTAATT
1 TGCTCAAATAAGGGCCTAAC-GT-TTGCCAAAA
*
1303 TGCTCAAATAAGGGCCTAACATTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * **
1334 TGCTCAAATAAGGGCCCGATC-TTT--TAATT
1 TGCTCAAATAAGGG-CCTAACGTTTGCCAAAA
1363 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
1394 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
1411 GACATCGAAA
Statistics
Matches: 106, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
28 5 0.05
29 36 0.34
30 8 0.08
31 52 0.49
32 5 0.05
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:1302 original size:60 final size:60
Alignment explanation
Indices: 1187--1409 Score: 342
Period size: 60 Copynumber: 3.7 Consensus size: 60
1177 GGTAAATTGT
* * * *** *
1187 TCAAATAAGGGCCTAACG-TTGTCAAAATGCTTAAAAAAGAATCTGATCTTTTAATTTGC
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGC
*
1246 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGGTCTTTTAATTTGC
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGC
*
1306 TCAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTT-GC
1367 -CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1410 TGACATCGAA
Statistics
Matches: 151, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
59 18 0.12
60 131 0.87
61 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (60 bp):
TCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGC
Found at i:1486 original size:31 final size:29
Alignment explanation
Indices: 1451--1616 Score: 104
Period size: 31 Copynumber: 5.5 Consensus size: 29
1441 CTGATGCCAT
1451 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTT--CAAACGTTAG
* * * *
1482 GCCCTTATTTGACCAATTT-AAAAGATCAG
1 GCCCTTATTTGAGCATTTTCAAACG-TTAG
*
1511 ACCCTTATTTGAGCATTTTCAATAACGTTAG
1 GCCCTTATTTGAGCATTTTC-A-AACGTTAG
* ** * **
1542 GTCCTTATTTG-GCCAAATT-AAAAGATCGG
1 GCCCTTATTTGAG-CATTTTCAAACG-TTAG
* * *
1571 GCCCTTATTTGACCATTTTGGCAAACATTCG
1 GCCCTTATTTGAGCATTTT--CAAACGTTAG
1602 GCCCTTATTTGAGCA
1 GCCCTTATTTGAGCA
1617 ATTAGCCATA
Statistics
Matches: 100, Mismatches: 25, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
28 7 0.07
29 36 0.36
30 1 0.01
31 50 0.50
32 6 0.06
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (29 bp):
GCCCTTATTTGAGCATTTTCAAACGTTAG
Found at i:1548 original size:60 final size:59
Alignment explanation
Indices: 1452--1613 Score: 209
Period size: 60 Copynumber: 2.7 Consensus size: 59
1442 TGATGCCATG
*
1452 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAATTTAAAAGATCAGA
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
* * * *
1512 CCCTTATTTGAGCATTTT-CAATAACGTTAGGTCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTGC-A-AACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
* * *
1572 CCCTTATTTGACCATTTTGGCAAACATTCGGCCCTTATTTGA
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGGCCCTTATTTGA
1614 GCAATTAGCC
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 84 0.95
61 1 0.01
62 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (59 bp):
CCCTTATTTGAGCATTTTGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
Found at i:3314 original size:22 final size:20
Alignment explanation
Indices: 3264--3315 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3254 TGCTCGATTA
*
3264 ATGTTCGTTTAGTGTTCTTT
1 ATGTTCGTTTAATGTTCTTT
*
3284 ATTGTTCGTTTAATAGCTTGTTT
1 A-TGTTCGTTTAAT-G-TTCTTT
3307 ATGTTCGTT
1 ATGTTCGTT
3316 AATTAAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 11 0.41
22 9 0.33
23 6 0.22
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.58
Consensus pattern (20 bp):
ATGTTCGTTTAATGTTCTTT
Found at i:3478 original size:21 final size:20
Alignment explanation
Indices: 3436--3478 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
3426 TACAGTAAAT
*
3436 ATTATTAAAAATAATATGTA
1 ATTATTAAAAATAATATCTA
* *
3456 ATTATTAGAAATTAATTTCTA
1 ATTATTA-AAAATAATATCTA
3477 AT
1 AT
3479 GAAATATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (20 bp):
ATTATTAAAAATAATATCTA
Found at i:4184 original size:107 final size:110
Alignment explanation
Indices: 4003--4274 Score: 308
Period size: 109 Copynumber: 2.5 Consensus size: 110
3993 AATTTTTCAA
* * * * ** * * *
4003 ACCCTTAAAATAAAATTTTAATTTTAACTT-GGACTAAACTTGGTG-AATTAA--TTATTATATA
1 ACCCTTAAAATAAAA-ATAAAATTTAATTTGGGACTAAACTTAATGAAATTAATTTTTTTTTGTA
* *
4064 TTTTATTTCTAAAA-CCTTATAACAAT-ATTATTAAGTATGGAATTT
65 TTTTATTTCTAAAATCC-TATAACAATAATTATTAAGTATGAAATTC
*
4109 ACCCTTAAAATAAAAA-AAAA-TTAATTTGGGCCTAAACTTAATGAAATTAATTTTTTTTTGTAT
1 ACCCTTAAAATAAAAATAAAATTTAATTTGGGACTAAACTTAATGAAATTAATTTTTTTTTGTAT
* *
4172 TTTATTTCTAAAATCCTATAACAATAAATTATTAATTTTGAAATTC
66 TTTATTTCTAAAATCCTATAACAAT-AATTATTAAGTATGAAATTC
* *
4218 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTT
1 ACCCTTAAAATAAAAATAAAA-TTTAATTTGGGACTAAACTTAATGAAATTAATTTT
4275 ATATTTTATT
Statistics
Matches: 139, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
103 6 0.04
104 14 0.10
105 6 0.04
106 15 0.11
107 30 0.22
108 2 0.01
109 31 0.22
110 4 0.03
112 31 0.22
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.42
Consensus pattern (110 bp):
ACCCTTAAAATAAAAATAAAATTTAATTTGGGACTAAACTTAATGAAATTAATTTTTTTTTGTAT
TTTATTTCTAAAATCCTATAACAATAATTATTAAGTATGAAATTC
Found at i:4281 original size:107 final size:104
Alignment explanation
Indices: 4003--4291 Score: 300
Period size: 107 Copynumber: 2.7 Consensus size: 104
3993 AATTTTTCAA
* ** * * *
4003 ACCCTTAAAATAAAATTTTAATTTTAACTT-GGACTAAACTTGGTGAATTAATTATTATATATTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTG-A--AATTATTTTATATTT
* *
4067 TATTTCTAAAACCTTATAACAATATTATTAAGTATGGAATTT
63 TATTTCTAAAACCTTATAACAATATTATTAAGTATGAAATTC
* * *
4109 ACCCTTAAAATAAAAA-AAAA--TTAATTTGGGCCTAAACTTAATGAAATTAATTTTTTTTTGTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATT-A-----TTTTATA
* *
4171 TTTTATTTCTAAAATCC-TATAACAATAAATTATTAATTTTGAAATTC
60 TTTTATTTCTAAAA-CCTTATAACAAT--ATTATTAAGTATGAAATTC
4218 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTA-TTTTATATTTTA
*
4283 TTTTTAAAA
65 TTTCTAAAA
4292 GTATATAATT
Statistics
Matches: 152, Mismatches: 18, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
101 4 0.03
102 1 0.01
103 7 0.05
104 12 0.08
105 2 0.01
106 15 0.10
107 47 0.31
108 2 0.01
109 31 0.20
110 4 0.03
111 1 0.01
112 26 0.17
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.43
Consensus pattern (104 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTATTTTATATTTTAT
TTCTAAAACCTTATAACAATATTATTAAGTATGAAATTC
Found at i:4285 original size:112 final size:110
Alignment explanation
Indices: 4003--4286 Score: 336
Period size: 112 Copynumber: 2.6 Consensus size: 110
3993 AATTTTTCAA
* ** * *
4003 ACCCTTAAAATAAAATTTTAATTTTAACTT-GGACTAAACTTGGTG-AATTAATTATTATA---T
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAATT-TTATATTTT
* *
4063 ATTTTATTTCTAAAACCTTATAACAATATTATTAAGTATGGAATTT
65 ATTTTATTTCTAAAACCTTATAACAATATTATTAAGTATGAAATTC
* * *
4109 ACCCTTAAAATAAAAA-AAAA--TTAATTTGGGCCTAAACTTAATGAAATTAATTTT-TTTTTGT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAATTTTATATTT-T
* *
4170 ATTTTATTTCTAAAATCC-TATAACAATAAATTATTAATTTTGAAATTC
65 ATTTTATTTCTAAAA-CCTTATAACAAT--ATTATTAAGTATGAAATTC
*
4218 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAATTTTATATTTTA
4283 TTTT
66 TTTT
4287 TAAAAGTATA
Statistics
Matches: 149, Mismatches: 16, Indels: 20
0.81 0.09 0.11
Matches are distributed among these distances:
103 7 0.05
104 14 0.09
105 10 0.07
106 15 0.10
107 25 0.17
108 2 0.01
109 31 0.21
110 4 0.03
112 37 0.25
113 4 0.03
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (110 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAATTTTATATTTTA
TTTTATTTCTAAAACCTTATAACAATATTATTAAGTATGAAATTC
Found at i:4592 original size:34 final size:35
Alignment explanation
Indices: 4554--4620 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
4544 GATTGATTGG
4554 TTTG-TTTTTTTTTTG-GATAAATATGATTGGTTAA
1 TTTGTTTTTTTTTTTGAGAT-AATATGATTGGTTAA
*
4588 TTTGTTTTTTTTTTTGAGATAATATGTTTGGTT
1 TTTGTTTTTTTTTTTGAGATAATATGATTGGTT
4621 TGTTTGTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 4 0.13
35 23 0.77
36 3 0.10
ACGTcount: A:0.19, C:0.00, G:0.18, T:0.63
Consensus pattern (35 bp):
TTTGTTTTTTTTTTTGAGATAATATGATTGGTTAA
Found at i:4627 original size:35 final size:35
Alignment explanation
Indices: 4544--4627 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
4534 TATAAGGAGA
* *
4544 GATTGATTGGTTTG-TTTTTTTTTTGGATAAATAT
1 GATTGGTTAGTTTGTTTTTTTTTTTGGATAAATAT
*
4578 GATTGGTTAATTTGTTTTTTTTTTTGAGAT-AATAT
1 GATTGGTTAGTTTGTTTTTTTTTTTG-GATAAATAT
* *
4613 GTTTGGTTTGTTTGT
1 GATTGGTTAGTTTGT
4628 CAATAGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
34 11 0.26
35 28 0.67
36 3 0.07
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.61
Consensus pattern (35 bp):
GATTGGTTAGTTTGTTTTTTTTTTTGGATAAATAT
Found at i:6456 original size:126 final size:130
Alignment explanation
Indices: 6223--6462 Score: 389
Period size: 126 Copynumber: 1.8 Consensus size: 130
6213 TTAAAAATTC
6223 TAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATT
1 TAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-GTATAAGGATATT
*
6288 AGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAAAGTATATTTAAAATC
62 AGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAAAGTATATTTAAAATC
6353 TTTT
127 TTTT
*
6357 TAATATATATAAGTTTTTTAATTAAAATAGTACAATGGTAAAAAT-TA-TA-AA-GATATTAGAT
1 TAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGGATATTAGAT
*
6418 TTAATTAAATAAAAATTGAGTTTTTAGTTGAGTAAAACTATAAAA
66 TTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
6463 GTTTAAATAA
Statistics
Matches: 103, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
126 53 0.51
127 2 0.02
128 2 0.02
130 2 0.02
134 44 0.43
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (130 bp):
TAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGGATATTAGAT
TTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAAAGTATATTTAAAATCTTTT
Found at i:11110 original size:36 final size:37
Alignment explanation
Indices: 11063--11142 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
11053 CACATCACGC
11063 TTTACATGAGCAAAG-TTTTTTTTTTCTTTGGCATTA
1 TTTACATGAGCAAAGTTTTTTTTTTTCTTTGGCATTA
11099 TTTACATGAGCAAAGTTTTTTTTTTTCTTTGGCATTA
1 TTTACATGAGCAAAGTTTTTTTTTTTCTTTGGCATTA
11136 TTTACAT
1 TTTACAT
11143 TGAACAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 15 0.35
37 28 0.65
ACGTcount: A:0.23, C:0.11, G:0.12, T:0.54
Consensus pattern (37 bp):
TTTACATGAGCAAAGTTTTTTTTTTTCTTTGGCATTA
Done.