Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024258.1 Corchorus olitorius cultivar O-4 contig24291, 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: 8262
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Found at i:1275 original size:50 final size:50
Alignment explanation
Indices: 1211--1327 Score: 198
Period size: 50 Copynumber: 2.3 Consensus size: 50
1201 GAATCAACTT
* *
1211 CTTTGAATTGTCTTCCAATCCAATATTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATCCAATATTAAAAGGACCGTCTTCCACTTATC
* *
1261 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCACTTATC
1 CTTTGAACTGTCTTCCAATCCAATATTAAAAGGACCGTCTTCCACTTATC
1311 CTTTGAACTGTCTTCCA
1 CTTTGAACTGTCTTCCA
1328 CTTATCCTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATCCAATATTAAAAGGACCGTCTTCCACTTATC
Found at i:1323 original size:23 final size:23
Alignment explanation
Indices: 1247--1400 Score: 123
Period size: 23 Copynumber: 6.3 Consensus size: 23
1237 TAAAAGGACC
*
1247 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCACTTATCCTTTGAACT
* * * *
1270 GTCTTCCAATTCAAT-CTTAAAAGGACC
1 GTCTTCCACTT--ATCCTT---TGAACT
1297 GTCTTCCACTTATCCTTTGAACT
1 GTCTTCCACTTATCCTTTGAACT
1320 GTCTTCCACTTATCCTTTGAACT
1 GTCTTCCACTTATCCTTTGAACT
* * * *
1343 GTCTTCCAATTCAAT-CTTAAAAGGACC
1 GTCTTCCACTT--ATCCTT---TGAACT
1370 GTCTTCCACTTATCCTTTGAACT
1 GTCTTCCACTTATCCTTTGAACT
1393 GTCTTCCA
1 GTCTTCCA
1401 ATTCAATCTT
Statistics
Matches: 102, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
23 56 0.55
24 6 0.06
25 8 0.08
26 6 0.06
27 26 0.25
ACGTcount: A:0.22, C:0.29, G:0.10, T:0.38
Consensus pattern (23 bp):
GTCTTCCACTTATCCTTTGAACT
Found at i:1343 original size:73 final size:73
Alignment explanation
Indices: 1247--1400 Score: 299
Period size: 73 Copynumber: 2.1 Consensus size: 73
1237 TAAAAGGACC
*
1247 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCACTTATCC
1 GTCTTCCACTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCACTTATCC
1312 TTTGAACT
66 TTTGAACT
1320 GTCTTCCACTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCACTTATCC
1 GTCTTCCACTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCACTTATCC
1385 TTTGAACT
66 TTTGAACT
1393 GTCTTCCA
1 GTCTTCCA
1401 ATTCAATCTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 80 1.00
ACGTcount: A:0.22, C:0.29, G:0.10, T:0.38
Consensus pattern (73 bp):
GTCTTCCACTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCACTTATCC
TTTGAACT
Found at i:1374 original size:50 final size:50
Alignment explanation
Indices: 1320--1453 Score: 250
Period size: 50 Copynumber: 2.7 Consensus size: 50
1310 CCTTTGAACT
1320 GTCTTCCACTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
1 GTCTTCCACTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
1370 GTCTTCCACTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
1 GTCTTCCACTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
* *
1420 GTCTCCCGCTTATCCTTTGAACTGTCTTCCAATT
1 GTCTTCCACTTATCCTTTGAACTGTCTTCCAATT
1454 GGCTTCTGGA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.37
Consensus pattern (50 bp):
GTCTTCCACTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACC
Found at i:1432 original size:123 final size:123
Alignment explanation
Indices: 1211--1450 Score: 426
Period size: 123 Copynumber: 2.0 Consensus size: 123
1201 GAATCAACTT
* *
1211 CTTTGAATTGTCTTCCAATCCAATATTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTTC
1 CTTTGAACTGTCTTCCAATCCAATATTAAAAGGACCGTCTTCCACTTATCCTTTGAACTGTCTTC
*
1276 CAATTCAATCTTAAAAGGACCGTCTTCCACTTATCCTTTGAACTGTCTTCCACTTATC
66 CAATTCAATCTTAAAAGGACCGTCTCCCACTTATCCTTTGAACTGTCTTCCACTTATC
* *
1334 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCACTTATCCTTTGAACTGTCTTC
1 CTTTGAACTGTCTTCCAATCCAATATTAAAAGGACCGTCTTCCACTTATCCTTTGAACTGTCTTC
*
1399 CAATTCAATCTTAAAAGGACCGTCTCCCGCTTATCCTTTGAACTGTCTTCCA
66 CAATTCAATCTTAAAAGGACCGTCTCCCACTTATCCTTTGAACTGTCTTCCA
1451 ATTGGCTTCT
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
123 111 1.00
ACGTcount: A:0.24, C:0.28, G:0.11, T:0.37
Consensus pattern (123 bp):
CTTTGAACTGTCTTCCAATCCAATATTAAAAGGACCGTCTTCCACTTATCCTTTGAACTGTCTTC
CAATTCAATCTTAAAAGGACCGTCTCCCACTTATCCTTTGAACTGTCTTCCACTTATC
Found at i:1667 original size:64 final size:64
Alignment explanation
Indices: 1540--1772 Score: 304
Period size: 64 Copynumber: 3.6 Consensus size: 64
1530 GGTGCATCTT
* *
1540 TTAACAAGATCGTCTTCCGATCAACTTCTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTACTT
1 TTAACAAGATCGTCTTCCGATCAAC-T-TCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTT
*
1605 T
64 C
* *
1606 TTAACAAGATCGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTC
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTC
* * * * * * *
1670 TTGACAAGATCGTCTTCCGATCAACTCCTTAAAACTCTTAAGAAACCATCTCCCGGTGTACTTC
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTC
* * * *
1734 TTGACGAGATCGTCTTCCAATCAACATCTGAAAATTCTT
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTCTT
1773 TCTAGCAAAC
Statistics
Matches: 148, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
64 123 0.83
65 1 0.01
66 24 0.16
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (64 bp):
TTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTC
Found at i:1924 original size:67 final size:67
Alignment explanation
Indices: 1739--1925 Score: 320
Period size: 67 Copynumber: 2.8 Consensus size: 67
1729 ACTTCTTGAC
* * *
1739 GAGATCGTCTTCCAATCAACATCTGAAAATTCTTTCTAGCAAACTGTCTTCCGATGTATTCCTTA
1 GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACTGTCTTCTGATGTATTCCTTA
1804 AT
66 AT
* *
1806 GAGATTGTCTTCCAATCAAAATTTGAAAATTCTTTCTAGCAAACTATCTTCTGATGTATTCCTTA
1 GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACTGTCTTCTGATGTATTCCTTA
1871 AT
66 AT
*
1873 GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCTG
1 GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACTGTCTTCTG
1926 GATCATCTTT
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 112 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (67 bp):
GAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACTGTCTTCTGATGTATTCCTTA
AT
Found at i:3541 original size:6 final size:7
Alignment explanation
Indices: 3526--3565 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
3516 CTAGAGCTCG
3526 TTCTTTT
1 TTCTTTT
3533 TTC-TTT
1 TTCTTTT
3539 TTCTTTT
1 TTCTTTT
3546 TTCTTTT
1 TTCTTTT
3553 TTCTTTT
1 TTCTTTT
3560 TTCTTT
1 TTCTTT
3566 CATTCTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.19
7 26 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTCTTTT
Found at i:3544 original size:13 final size:13
Alignment explanation
Indices: 3526--3565 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
3516 CTAGAGCTCG
3526 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
3539 TTCTTTTTTCTTTT
1 TTCTTTTTTC-TTT
3553 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
3566 CATTCTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTCTTTTTTCTTT
Found at i:3551 original size:20 final size:21
Alignment explanation
Indices: 3526--3583 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
3516 CTAGAGCTCG
3526 TTCTTTTTTC-TTTTTCTTTT
1 TTCTTTTTTCTTTTTTCTTTT
*
3546 TTCTTTTTTCTTTTTTCTTTCA
1 TTCTTTTTTCTTTTTTCTTT-T
*
3568 TTCTTCATTTCTTTTT
1 TTCTT-TTTTCTTTTT
3584 GACTAGTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 10 0.30
21 9 0.27
22 5 0.15
23 9 0.27
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (21 bp):
TTCTTTTTTCTTTTTTCTTTT
Found at i:6519 original size:20 final size:19
Alignment explanation
Indices: 6483--6520 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6473 ACACAACACG
*
6483 AAAAGCAGGGTTAAGCAAT
1 AAAAGCAGGGATAAGCAAT
6502 AAAAGCAGGGAATAAGCAA
1 AAAAGCAGGG-ATAAGCAA
6521 CAATAAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.11, G:0.26, T:0.11
Consensus pattern (19 bp):
AAAAGCAGGGATAAGCAAT
Done.