Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013899.1 Corchorus olitorius cultivar O-4 contig13932, 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: 38563
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6291 original size:3 final size:3
Alignment explanation
Indices: 6278--6341 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
6268 ATATATATAT
6278 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6325 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
6342 GAGGAATTCC
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6738 original size:116 final size:116
Alignment explanation
Indices: 6534--6759 Score: 416
Period size: 116 Copynumber: 1.9 Consensus size: 116
6524 AGCAAAACCC
*
6534 AATAATAATATATAATATCTTTGAATAACAACTAGTCAACGCATGGAACTTATTAGAGGCAGATT
1 AATAATAATATATAATATCTTTGAATAACAACTAGTCAACGCATGGAACTTATTAGAGACAGATT
*
6599 AGTAAAATTGCTTGTAATCGAATTATTACCCTCATTTTAAAAAAATATAAT
66 AGTAAAATTGCTTGTAATCGAATTATTACCCTCATTTAAAAAAAATATAAT
*
6650 AATAATAATATATAATATCTTTGAATAACAACTAGTCAACTCATGGAACTTATTAGAGACAGATT
1 AATAATAATATATAATATCTTTGAATAACAACTAGTCAACGCATGGAACTTATTAGAGACAGATT
*
6715 AGTAAAATTGCTTTTAATCGAATTATTACCCTCATTTAAAAAAAA
66 AGTAAAATTGCTTGTAATCGAATTATTACCCTCATTTAAAAAAAA
6760 AAATTGTACT
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 106 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (116 bp):
AATAATAATATATAATATCTTTGAATAACAACTAGTCAACGCATGGAACTTATTAGAGACAGATT
AGTAAAATTGCTTGTAATCGAATTATTACCCTCATTTAAAAAAAATATAAT
Found at i:9291 original size:22 final size:22
Alignment explanation
Indices: 9266--9311 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
9256 TAACTCACTC
9266 GAGTTCGATTTGGAGAAAATTT
1 GAGTTCGATTTGGAGAAAATTT
9288 GAGTTCGATTTGGAGAAAATTT
1 GAGTTCGATTTGGAGAAAATTT
9310 GA
1 GA
9312 ATTTGACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (22 bp):
GAGTTCGATTTGGAGAAAATTT
Found at i:9322 original size:22 final size:22
Alignment explanation
Indices: 9269--9322 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
9259 CTCACTCGAG
* *
9269 TTCGATTTGGAGAAAATTTGAG
1 TTCGACTTGGAGAAAATTTGAA
*
9291 TTCGATTTGGAGAAAATTTGAA
1 TTCGACTTGGAGAAAATTTGAA
*
9313 TTTGACTTGG
1 TTCGACTTGG
9323 TCACCGTCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.39
Consensus pattern (22 bp):
TTCGACTTGGAGAAAATTTGAA
Found at i:9421 original size:18 final size:18
Alignment explanation
Indices: 9386--9419 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9376 GGTATACACA
9386 TATATATATACATTAAAT
1 TATATATATACATTAAAT
*
9404 TATATATTTA-ATTAAA
1 TATATATATACATTAAA
9420 ATATTACCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TATATATATACATTAAAT
Found at i:10732 original size:31 final size:31
Alignment explanation
Indices: 10694--10758 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
10684 CACACAATGA
*
10694 CATCAATTAGCTTGTTGATCCAGTATTTTTC
1 CATCAATTAGCTTGTTGATCCAGCATTTTTC
10725 CATCAATTAGCTTGTTGATCCAGCATTTTTC
1 CATCAATTAGCTTGTTGATCCAGCATTTTTC
10756 CAT
1 CAT
10759 AAAGCTGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (31 bp):
CATCAATTAGCTTGTTGATCCAGCATTTTTC
Found at i:11215 original size:68 final size:68
Alignment explanation
Indices: 11102--11237 Score: 184
Period size: 68 Copynumber: 2.0 Consensus size: 68
11092 CCACAACAAG
* * * *
11102 CCATGATTGTCGATGGGTCTTGCATCTAAGAATTATAGAATTTTACAGTTTTAAATGGTAGGGAT
1 CCATGATTGTCGATGGGTCATGCATCTAAAAATTATAGAAATTTACAATTTTAAATGGTAGGGAT
11167 TGT
66 TGT
* * * *
11170 CCATGATTGTGGAT-GGTCATGGATCTAATAAATTATAGAAATTTACAATTTTAATTGGTTGGGA
1 CCATGATTGTCGATGGGTCATGCATCTAA-AAATTATAGAAATTTACAATTTTAAATGGTAGGGA
11234 TTGT
65 TTGT
11238 TTTGAATGGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
67 12 0.20
68 47 0.80
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (68 bp):
CCATGATTGTCGATGGGTCATGCATCTAAAAATTATAGAAATTTACAATTTTAAATGGTAGGGAT
TGT
Found at i:17546 original size:13 final size:13
Alignment explanation
Indices: 17528--17552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17518 TTAGAATTTC
17528 AAATAATATTTAT
1 AAATAATATTTAT
17541 AAATAATATTTA
1 AAATAATATTTA
17553 CAACAATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:23581 original size:20 final size:21
Alignment explanation
Indices: 23556--23601 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
23546 TCCTATATGA
*
23556 TTAATA-ATATTTTAATTTTC
1 TTAATATATATTTGAATTTTC
23576 TTAATATATATTTGAATTTTC
1 TTAATATATATTTGAATTTTC
23597 TTAAT
1 TTAAT
23602 TTGGATTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTAATATATATTTGAATTTTC
Found at i:23609 original size:21 final size:21
Alignment explanation
Indices: 23556--23610 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
23546 TCCTATATGA
* *
23556 TTAATA-ATATTTTAATTTTC
1 TTAATATAGATTTGAATTTTC
*
23576 TTAATATATATTTGAATTTTC
1 TTAATATAGATTTGAATTTTC
* *
23597 TTAATTTGGATTTG
1 TTAATATAGATTTG
23611 GTTAAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 6 0.20
21 24 0.80
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (21 bp):
TTAATATAGATTTGAATTTTC
Found at i:23635 original size:135 final size:134
Alignment explanation
Indices: 23364--23636 Score: 304
Period size: 135 Copynumber: 2.0 Consensus size: 134
23354 TCTTTGGGCG
* * *
23364 AATTAATTAATAATTTTATCTTCTTAACATACCTAGCAACGTACTCTTCTTAGATGATTAATATT
1 AATTAATTAATAATTTTATCTTCCTAACATACCTACCAACGTACTCTTCTTAGATGAATAATATT
* *
23429 TGAATTTCTTTAACATACATTATAATTTTTCTTAATGTGGATTTGACTAAATATTATTAATCTTT
66 TGAATTTCTTTAACATACATTATAATTTTTCTTAATGTGGATTTGACTAAATATTATTAA-CATA
**
23494 GGGTA
130 AAGTA
* * *
23499 AATTAATTAATATTTTTATTTTCCTAACATACCTACCAACGTACTCTTCCTATATGATTAATAAT
1 AATTAATTAATAATTTTATCTTCCTAACATACCTACCAACGTACTCTT-CT-TA-GATGAATAAT
* * * * **
23564 ATTTTAATTT-TCTTAATATATATT-TGAA-TTTTCTTAATTTGGATTTGGTTAAATATT-TTAG
63 ATTTGAATTTCT-TTAACATACATTAT-AATTTTTCTTAATGTGGATTTGACTAAATATTATTA-
23625 A-ATAAAGTA
125 ACATAAAGTA
23634 AAT
1 AAT
23637 AAAATATAAT
Statistics
Matches: 116, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
135 51 0.44
136 5 0.04
137 31 0.27
138 29 0.25
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (134 bp):
AATTAATTAATAATTTTATCTTCCTAACATACCTACCAACGTACTCTTCTTAGATGAATAATATT
TGAATTTCTTTAACATACATTATAATTTTTCTTAATGTGGATTTGACTAAATATTATTAACATAA
AGTA
Found at i:23773 original size:15 final size:16
Alignment explanation
Indices: 23753--23787 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
23743 ATTGATCATC
*
23753 GAAA-TTTGCATATAA
1 GAAATTTTGCACATAA
23768 GAAATTTTGCACATAA
1 GAAATTTTGCACATAA
23784 GAAA
1 GAAA
23788 ATTGTAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.29
Consensus pattern (16 bp):
GAAATTTTGCACATAA
Found at i:26105 original size:2 final size:2
Alignment explanation
Indices: 26098--26131 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
26088 AAACAATAAT
26098 TA TA TA TA 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 TA TA TA TA
26132 GTGATAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33024 original size:27 final size:28
Alignment explanation
Indices: 32957--33031 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
32947 CAGTGAACTT
* **
32957 AAAATGACCAAAATGCCCCTGAATGTGC
1 AAAATGACCAAAATACCCCTGAACATGC
*
32985 AAAATGACCAAAATACCCCTGGACATGC
1 AAAATGACCAAAATACCCCTGAACATGC
*
33013 -AAATGACTAAAATACCCCT
1 AAAATGACCAAAATACCCCT
33032 AGGTGACCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 18 0.43
28 24 0.57
ACGTcount: A:0.43, C:0.27, G:0.13, T:0.17
Consensus pattern (28 bp):
AAAATGACCAAAATACCCCTGAACATGC
Found at i:34321 original size:25 final size:27
Alignment explanation
Indices: 34288--34357 Score: 99
Period size: 25 Copynumber: 2.7 Consensus size: 27
34278 TAAAAATTCA
34288 CCAGGGGCATTTTGGTCA-TTTTCACC
1 CCAGGGGCATTTTGGTCATTTTTCACC
* **
34314 TC-GGGGCATTTTGGTCATTTTTTGCC
1 CCAGGGGCATTTTGGTCATTTTTCACC
34340 CCAGGGGCATTTTGGTCA
1 CCAGGGGCATTTTGGTCA
34358 AAATTACTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 15 0.39
26 8 0.21
27 15 0.39
ACGTcount: A:0.13, C:0.23, G:0.27, T:0.37
Consensus pattern (27 bp):
CCAGGGGCATTTTGGTCATTTTTCACC
Found at i:35494 original size:21 final size:21
Alignment explanation
Indices: 35468--35514 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
35458 TCAGAGTAAC
*
35468 AATAAACTGCAATG-AGCAAGG
1 AATAAACTGCAAAGCAGCAA-G
*
35489 AATAAAGTGCAAAGCAGCAAG
1 AATAAACTGCAAAGCAGCAAG
35510 AATAA
1 AATAA
35515 GAGACAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.53, C:0.13, G:0.21, T:0.13
Consensus pattern (21 bp):
AATAAACTGCAAAGCAGCAAG
Found at i:38309 original size:47 final size:47
Alignment explanation
Indices: 38240--38563 Score: 589
Period size: 47 Copynumber: 6.9 Consensus size: 47
38230 AATTTTAAAC
38240 TAAAAGAAG-AGAAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAG
1 TAAAAGAAGAAGAA-ATTAGTTTAATTCTAGGTAATTAAACTAAGTAG
38287 TAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAG
1 TAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAG
* *
38334 TAAAAGAAGAAGAAATTAGTTTAATTCTGGGTAATCAAACTAAGTAG
1 TAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAG
*
38381 TAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATCAAACTAAGTAG
1 TAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAG
38428 TAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAG
1 TAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAG
38475 TAAAAGAAGAAGAAATTAG-TTAATTCTAGGTAATTAAACTAAGTAG
1 TAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAG
*
38521 TAAAAAAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
1 TAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
Statistics
Matches: 270, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
46 45 0.17
47 221 0.82
48 4 0.01
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29
Consensus pattern (47 bp):
TAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAG
Done.