Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024695.1 Corchorus olitorius cultivar O-4 contig24728, 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: 42705
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:4183 original size:43 final size:43
Alignment explanation
Indices: 4136--4469 Score: 398
Period size: 43 Copynumber: 7.9 Consensus size: 43
4126 TGCCATAAGG
**
4136 AGAAATGCTTCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
1 AGAAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
* *
4179 AGAAATGCCCCTGTGTTATATATGTGTTTGGGGACTTTATAAT
1 AGAAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
*
4222 AG--ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
1 AGAAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
** *
4263 AGAGTTGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATAT
1 AGAAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-AT
*
4306 AG--ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
1 AGAAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
* * *
4347 A-AAGGTACCCCTGTGTTATATATGTGTTTGGGGAC-TTG-AAT
1 AGAA-ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
* ** * * *
4388 ATAGGTGCCTCTGTGTTACATATGTGTTTGAGGACTTTTGGAAT
1 AGAAATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGTAAT
*
4432 AGAGATGCCCCTGTGTTATATATGTGTTTG-GAGACTTT
1 AGAAATGCCCCTGTGTTATATATGTGTTTGAG-GACTTT
4470 TGGTTATTTG
Statistics
Matches: 253, Mismatches: 26, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
41 104 0.41
42 6 0.02
43 111 0.44
44 32 0.13
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.41
Consensus pattern (43 bp):
AGAAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAAT
Found at i:4240 original size:84 final size:84
Alignment explanation
Indices: 4140--4469 Score: 504
Period size: 84 Copynumber: 3.9 Consensus size: 84
4130 ATAAGGAGAA
*
4140 ATGCTTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAAATGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAAATGCCCCTGTGTTATATATGTG
4205 TTTGGGGACTTTATAATAG
66 TTTGGGGACTTTATAATAG
**
4224 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAAATGCCCCTGTGTTATATATGTG
4289 TTTGGGGACTTTGAT-ATAG
66 TTTGGGGACTTT-ATAATAG
* *
4308 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATA-AAGGTACCCCTGTGTTATATATGT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAA-ATGCCCCTGTGTTATATATGT
*
4372 GTTTGGGGACTTGA-ATATAG
65 GTTTGGGGACTTTATA-ATAG
* * * *
4392 GTGCCTCTGTGTTACATATGTGTTTGAGGACTTTTGGAATAGAGATGCCCCTGTGTTATATATGT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAAATGCCCCTGTGTTATATATGT
*
4457 GTTTGGAGACTTT
65 GTTTGGGGACTTT
4470 TGGTTATTTG
Statistics
Matches: 225, Mismatches: 15, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
83 2 0.01
84 182 0.81
85 40 0.18
86 1 0.00
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (84 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAAATGCCCCTGTGTTATATATGTG
TTTGGGGACTTTATAATAG
Found at i:7157 original size:30 final size:31
Alignment explanation
Indices: 7099--7173 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 31
7089 CGTTTCTATT
*
7099 TTTAGGCTCAAATTGGTCAACTTTTGAAAGA
1 TTTAGACTCAAATTGGTCAACTTTTGAAAGA
7130 TTTAGACTCAAATTGAG-CAAC-TTTGAAAGA
1 TTTAGACTCAAATTG-GTCAACTTTTGAAAGA
*
7160 TTTAAACTCAAATT
1 TTTAGACTCAAATT
7174 CGTGGCTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 22 0.54
31 18 0.44
32 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (31 bp):
TTTAGACTCAAATTGGTCAACTTTTGAAAGA
Found at i:8123 original size:14 final size:13
Alignment explanation
Indices: 8099--8129 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
8089 CAATTTATAA
8099 AATAAATAAATAT
1 AATAAATAAATAT
8112 AATAATATAAATAT
1 AATAA-ATAAATAT
8126 AATA
1 AATA
8130 TACTATACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAAATAAATAT
Found at i:9442 original size:14 final size:12
Alignment explanation
Indices: 9400--9483 Score: 61
Period size: 12 Copynumber: 7.2 Consensus size: 12
9390 TAACCGTTTA
9400 ATAATTATATAT
1 ATAATTATATAT
*
9412 ATTATTATATAT
1 ATAATTATATAT
*
9424 GTAATTATATAT
1 ATAATTATATAT
9436 ACCTAA-TAT-TAT
1 A--TAATTATATAT
9448 -T--TTATATAT
1 ATAATTATATAT
*
9457 ATATATAATATAT
1 ATA-ATTATATAT
* *
9470 TTAATTATAAAT
1 ATAATTATATAT
9482 AT
1 AT
9484 TACTAAACTG
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
8 3 0.05
9 4 0.07
10 1 0.02
12 32 0.58
13 12 0.22
14 3 0.05
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (12 bp):
ATAATTATATAT
Found at i:9478 original size:21 final size:22
Alignment explanation
Indices: 9401--9478 Score: 77
Period size: 24 Copynumber: 3.4 Consensus size: 22
9391 AACCGTTTAA
* *
9401 TAATTATATATATTATTATATATG
1 TAATTATATATACTA--ATATATT
9425 TAATTATATATACCTAATATTATT
1 TAATTATATATA-CTAATA-TATT
*
9449 TTATATATATATA-TAATATATT
1 TAAT-TATATATACTAATATATT
9471 TAATTATA
1 TAATTATA
9479 AATATTACTA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
21 4 0.09
22 7 0.15
23 8 0.17
24 18 0.38
25 10 0.21
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (22 bp):
TAATTATATATACTAATATATT
Found at i:11506 original size:19 final size:19
Alignment explanation
Indices: 11484--11563 Score: 56
Period size: 19 Copynumber: 4.2 Consensus size: 19
11474 TTAATTTTTG
11484 GTGTATTATCATTTGATTA
1 GTGTATTATCATTTGATTA
* *
11503 GTGTTATTAGT-GTTT-ATTG
1 GTG-TATTA-TCATTTGATTA
**
11522 GTACATTATCATTTGATTA
1 GTGTATTATCATTTGATTA
****
11541 ACACATTATCATTTGATTA
1 GTGTATTATCATTTGATTA
11560 GTGT
1 GTGT
11564 TGATGATTAA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
17 1 0.02
18 7 0.16
19 28 0.62
20 8 0.18
21 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.50
Consensus pattern (19 bp):
GTGTATTATCATTTGATTA
Found at i:28855 original size:13 final size:13
Alignment explanation
Indices: 28834--28866 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
28824 AAATAAAACG
28834 AAAACGAAAAA-A
1 AAAACGAAAAATA
28846 AAAACAGAAAAATA
1 AAAAC-GAAAAATA
28860 AAAACGA
1 AAAACGA
28867 TGCCAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.26
13 8 0.42
14 6 0.32
ACGTcount: A:0.79, C:0.09, G:0.09, T:0.03
Consensus pattern (13 bp):
AAAACGAAAAATA
Found at i:31074 original size:15 final size:14
Alignment explanation
Indices: 31030--31081 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
31020 TTAAATTCCG
31030 GTAATTTCAATGTAA
1 GTAATTTCAAT-TAA
* *
31045 GTTATTTACATTTAA
1 GTAATTT-CAATTAA
31060 GTAATTTCAGATTAA
1 GTAATTTCA-ATTAA
31075 GGTAATT
1 -GTAATT
31082 GCATTTGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 2 0.07
15 19 0.63
16 9 0.30
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (14 bp):
GTAATTTCAATTAA
Found at i:31087 original size:30 final size:30
Alignment explanation
Indices: 31030--31087 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
31020 TTAAATTCCG
* *
31030 GTAATTTCAATGTAAGTTATTTACATTTAA
1 GTAATTTCAATGTAAGGTAATTACATTTAA
*
31060 GTAATTTCAGAT-TAAGGTAATTGCATTT
1 GTAATTTCA-ATGTAAGGTAATTACATTT
31088 GATTGATGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (30 bp):
GTAATTTCAATGTAAGGTAATTACATTTAA
Found at i:32091 original size:29 final size:31
Alignment explanation
Indices: 32040--32097 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
32030 GGTCACTAAC
32040 ACATCACACACACTAAGAGGAGGCCCAATGT
1 ACATCACACACACTAAGAGGAGGCCCAATGT
32071 ACATCACACACACTAA-A-GAGGCCCAAT
1 ACATCACACACACTAAGAGGAGGCCCAAT
32098 ACATTTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 10 0.37
30 1 0.04
31 16 0.59
ACGTcount: A:0.41, C:0.31, G:0.16, T:0.12
Consensus pattern (31 bp):
ACATCACACACACTAAGAGGAGGCCCAATGT
Found at i:37639 original size:18 final size:18
Alignment explanation
Indices: 37616--37650 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
37606 CACAAACAAC
*
37616 TTCAAATACTCAACCTCT
1 TTCAAACACTCAACCTCT
37634 TTCAAACACTCAACCTC
1 TTCAAACACTCAACCTC
37651 ATTCTTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (18 bp):
TTCAAACACTCAACCTCT
Found at i:41599 original size:26 final size:25
Alignment explanation
Indices: 41568--41619 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
41558 TTTTTCAAAT
41568 ATATTTCTAA-ATTGTCATTATTAAAA
1 ATATTT-TAATATT-TCATTATTAAAA
41594 ATATTTTAATTATTTCATTATTAAAA
1 ATATTTTAA-TATTTCATTATTAAAA
41620 TAATGGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 3 0.12
26 18 0.75
27 3 0.12
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (25 bp):
ATATTTTAATATTTCATTATTAAAA
Found at i:42333 original size:6 final size:6
Alignment explanation
Indices: 42322--42354 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
42312 AATTTAGAAA
42322 TATATC TATATC --TATC TATATC TATATC TATAT
1 TATATC TATATC TATATC TATATC TATATC TATAT
42355 AGAACAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.16
6 21 0.84
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (6 bp):
TATATC
Found at i:42341 original size:16 final size:16
Alignment explanation
Indices: 42322--42352 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
42312 AATTTAGAAA
42322 TATATCTATATCTATC
1 TATATCTATATCTATC
42338 TATATCTATATCTAT
1 TATATCTATATCTAT
42353 ATAGAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATCTATATCTATC
Done.