Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017202.1 Corchorus olitorius cultivar O-4 contig17235, 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: 26828
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:486 original size:15 final size:14
Alignment explanation
Indices: 463--511 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
453 AAGGAAGCTT
*
463 TTTCCTTCCTCCCCA
1 TTTCTTTCCT-CCCA
478 TTTCTTTCCGTCCCA
1 TTTCTTTCC-TCCCA
*
493 CTTCTTTCCTTCCCA
1 TTTCTTTCC-TCCCA
508 TTTC
1 TTTC
512 CTCCATACCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 28 0.97
16 1 0.03
ACGTcount: A:0.06, C:0.45, G:0.02, T:0.47
Consensus pattern (14 bp):
TTTCTTTCCTCCCA
Found at i:1774 original size:19 final size:19
Alignment explanation
Indices: 1734--1770 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1724 AATTTTTAAG
1734 TAAAAATTTAATATATAAA
1 TAAAAATTTAATATATAAA
1753 TAAAAATTTAATAT-TAAA
1 TAAAAATTTAATATATAAA
1771 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAATTTAATATATAAA
Found at i:3493 original size:12 final size:13
Alignment explanation
Indices: 3467--3491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3457 GTTTTGTAAC
3467 TGCTTTATAAAAA
1 TGCTTTATAAAAA
3480 TGCTTTATAAAA
1 TGCTTTATAAAA
3492 TGTTTTTAAT
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
TGCTTTATAAAAA
Found at i:5696 original size:46 final size:45
Alignment explanation
Indices: 5643--5736 Score: 161
Period size: 46 Copynumber: 2.1 Consensus size: 45
5633 TAATCTCTAT
*
5643 TAATTAATGAACATAATTAAAAAGAATGAACTTTTTTTCCCTCAAA
1 TAATTAATGAACATAATTAAAAAGAATGAAC-TTTTTTCCCTAAAA
*
5689 TAATTAATGAACATGATTAAAAAGAATGAACTTTTTTCCCTAAAA
1 TAATTAATGAACATAATTAAAAAGAATGAACTTTTTTCCCTAAAA
5734 TAA
1 TAA
5737 ATCAAAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 16 0.35
46 30 0.65
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (45 bp):
TAATTAATGAACATAATTAAAAAGAATGAACTTTTTTCCCTAAAA
Found at i:11094 original size:24 final size:22
Alignment explanation
Indices: 11041--11118 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
11031 ATAACCATAT
11041 TATGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAATCACAC
* *
11063 TATGAAATTTTGATAATCTCTCCC
1 TATGAAATTTTGATAA--TCACAC
11087 TATGAAATTTTGATAA-CGACAC
1 TATGAAATTTTGATAATC-ACAC
*
11109 TATGGAATTT
1 TATGAAATTT
11119 CAAGAACTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
21 1 0.02
22 27 0.56
24 20 0.42
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAC
Found at i:11109 original size:46 final size:44
Alignment explanation
Indices: 11041--11140 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 44
11031 ATAACCATAT
** *
11041 TATGAAATTTTGATAATCACACTATGAAATTTTGATAATCTCTCCC
1 TATGAAATTTTGATAATCACACTATGAAATTTCAAGAA-CT-TCCC
*
11087 TATGAAATTTTGATAA-CGACACTATGGAATTTCAAGAACTTCCC
1 TATGAAATTTTGATAATC-ACACTATGAAATTTCAAGAACTTCCC
11131 TATGAAATTT
1 TATGAAATTT
11141 CTCGAACCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 14 0.29
45 3 0.06
46 32 0.65
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACACTATGAAATTTCAAGAACTTCCC
Found at i:11185 original size:22 final size:22
Alignment explanation
Indices: 11129--11260 Score: 83
Period size: 22 Copynumber: 6.0 Consensus size: 22
11119 CAAGAACTTC
11129 CCTATGAAATTTCTCG--AACCTT
1 CCTATGAAATTT-T-GTAAACCTT
* * *
11151 TCTATTAAATTTTGTCAACCTT
1 CCTATGAAATTTTGTAAACCTT
* *
11173 CCTATGAAATTTTGTTAACTTT
1 CCTATGAAATTTTGTAAACCTT
* **
11195 CATAT-AGAATTTT-TAAAAATT
1 CCTATGA-AATTTTGTAAACCTT
* *
11216 ACTATGAAATTTTGATAAAGCTT
1 CCTATGAAATTTTG-TAAACCTT
* *
11239 CCTATAAAATTTTTATAAACCT
1 CCTATGAAA-TTTTGTAAACCT
11261 CACTACAAAA
Statistics
Matches: 85, Mismatches: 18, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 16 0.19
22 45 0.53
23 19 0.22
24 4 0.05
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (22 bp):
CCTATGAAATTTTGTAAACCTT
Found at i:11243 original size:23 final size:23
Alignment explanation
Indices: 11216--11301 Score: 79
Period size: 23 Copynumber: 3.8 Consensus size: 23
11206 TTTAAAAATT
* *
11216 ACTATGAAATTTTGATAAAGCTTC
1 ACTATAAAATTTTGATAAA-CCTC
*
11240 -CTATAAAATTTTTATAAACCTC
1 ACTATAAAATTTTGATAAACCTC
* *
11262 ACTACAAAATTTTGAT-AATCTC
1 ACTATAAAATTTTGATAAACCTC
*
11284 -CTTGTAAAATTTTGATAA
1 AC-TATAAAATTTTGATAA
11302 CCACAAATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.02
22 20 0.39
23 30 0.59
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (23 bp):
ACTATAAAATTTTGATAAACCTC
Found at i:12401 original size:21 final size:21
Alignment explanation
Indices: 12377--12485 Score: 64
Period size: 21 Copynumber: 5.2 Consensus size: 21
12367 AATTCTCTGT
12377 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
12398 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
12419 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
12440 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
12461 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
12482 AAAT
1 AAAT
12486 CTTGATCCTT
Statistics
Matches: 60, Mismatches: 20, Indels: 16
0.62 0.21 0.17
Matches are distributed among these distances:
20 12 0.20
21 36 0.60
22 12 0.20
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:12423 original size:42 final size:42
Alignment explanation
Indices: 12364--12486 Score: 237
Period size: 42 Copynumber: 2.9 Consensus size: 42
12354 GTTAAGTCTT
*
12364 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
12406 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
12448 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
12487 TTGATCCTTA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:14103 original size:41 final size:43
Alignment explanation
Indices: 14058--14146 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 43
14048 CATTACCTGA
*
14058 ATTCTA-CTCCATCTCTAGGCAATTCATC-AAATAAAGCTAAT
1 ATTCTACCTCCATCTCTAGACAATTCATCAAAATAAAGCTAAT
*
14099 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
1 ATTCTA--CCTCCATCTCTAGACAATTCATCAAAATAAAGCTAAT
14144 ATT
1 ATT
14147 AATTATTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 6 0.14
44 20 0.48
45 16 0.38
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGACAATTCATCAAAATAAAGCTAAT
Found at i:14241 original size:32 final size:32
Alignment explanation
Indices: 14200--14264 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
14190 TACGCTGCAG
14200 TCATTTTTTAATCTTGATTGCAATTATTAAAT
1 TCATTTTTTAATCTTGATTGCAATTATTAAAT
* *
14232 TCATTTTTTAATCTTGATTGTAATTCTTAAAT
1 TCATTTTTTAATCTTGATTGCAATTATTAAAT
14264 T
1 T
14265 AATAGAATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.55
Consensus pattern (32 bp):
TCATTTTTTAATCTTGATTGCAATTATTAAAT
Found at i:15283 original size:44 final size:44
Alignment explanation
Indices: 15186--15283 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
15176 TACTTTAATA
*
15186 ATGACAATTTTATATATTTTATATAATGGCATAATTGAAATATAT
1 ATGA-AATTTTATATATTTTATATAATGGCATAATTGAAATAAAT
* *
15231 -TGGTAATTTTATATATTTTA-ATAATGGCATAATTTAAATAAACT
1 AT-GAAATTTTATATATTTTATATAATGGCATAATTGAAATAAA-T
15275 ATGAAATTT
1 ATGAAATTT
15284 CAATAACTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 20 0.43
44 24 0.52
45 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (44 bp):
ATGAAATTTTATATATTTTATATAATGGCATAATTGAAATAAAT
Found at i:16033 original size:22 final size:22
Alignment explanation
Indices: 15981--16036 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
15971 TGTGGCTACC
**
15981 AAAATTTCATAATGTGGTTATCA
1 AAAATTTCATAATGTAATTA-CA
16004 AAAATTTCATAATGTAATTA-A
1 AAAATTTCATAATGTAATTACA
16025 AAAATTTTCATA
1 AAAA-TTTCATA
16037 GAAGATAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 5 0.17
22 7 0.23
23 18 0.60
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (22 bp):
AAAATTTCATAATGTAATTACA
Found at i:16419 original size:22 final size:22
Alignment explanation
Indices: 15960--16420 Score: 186
Period size: 22 Copynumber: 20.5 Consensus size: 22
15950 CAGATTATTG
* * *
15960 AAATTTCATAGTGTGGCTACCA
1 AAATTTCATAGTGAGGTTATCA
* *
15982 AAATTTCATAATGTGGTTATCAA
1 AAATTTCATAGTGAGGTTATC-A
* * *
16005 AAATTTCATAATGTA-ATTA-AA
1 AAATTTCATAGTG-AGGTTATCA
* * *
16026 AAATTTTCATAG-AAGATAATCA
1 AAA-TTTCATAGTGAGGTTATCA
* * * *
16048 AAGTTTCATAATGTGCTTATCA
1 AAATTTCATAGTGAGGTTATCA
* * *
16070 AAATTTCATAGTGAGATTAACG
1 AAATTTCATAGTGAGGTTATCA
* *
16092 AAA-TTCTATAGGGAAGTTATCA
1 AAATTTC-ATAGTGAGGTTATCA
* * *
16114 ACATTCCATAGGGAGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
* *
16136 AAATTTCATAGT-ATGATTATCC
1 AAATTTCATAGTGA-GGTTATCA
* ****
16158 AAATTTTATAGTGTACCAAATCA
1 AAATTTCATAGTG-AGGTTATCA
** * *
16181 ACCTTTTGCAATTAATGCGG-TATTCA
1 A-AATTT-C-A-TAGTGAGGTTA-TCA
* * *
16207 AAATTTTATATTTG-GGTCATCA
1 AAATTTCATA-GTGAGGTTATCA
16229 AAATTAATATCATA-TAGAGGTTATCA
1 AAA-T--T-TCATAGT-GAGGTTATCA
* ** *
16255 CAATTTTGTAGTGTGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
* * * *
16277 AAATTTCACAGTGTGGTGACCA
1 AAATTTCATAGTGAGGTTATCA
*
16299 AAATTTCATA-AGATGGTTATCA
1 AAATTTCATAGTGA-GGTTATCA
*
16321 AAATTTCATAGTGTGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
* * *
16343 AAGTTTCACAGGGAGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
* *
16365 CAATTTCTTAGTGAGGTTATCA
1 AAATTTCATAGTGAGGTTATCA
* * *
16387 AAATAAT-ATAGCGAGATTATCA
1 AAAT-TTCATAGTGAGGTTATCA
16409 AAATTTCATAGT
1 AAATTTCATAGT
16421 AAGACTATGC
Statistics
Matches: 321, Mismatches: 89, Indels: 58
0.69 0.19 0.12
Matches are distributed among these distances:
20 1 0.00
21 20 0.06
22 234 0.73
23 32 0.10
24 5 0.02
25 7 0.02
26 18 0.06
27 4 0.01
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (22 bp):
AAATTTCATAGTGAGGTTATCA
Found at i:16847 original size:25 final size:27
Alignment explanation
Indices: 16794--16852 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
16784 GGTAAGACTA
16794 ATTTTAATAATGGCATAATTAAAATAT
1 ATTTTAATAATGGCATAATTAAAATAT
* *
16821 ATTTTGATAATGGCA-ATTTAGAAATAT
1 ATTTTAATAATGGCATAATTA-AAATAT
*
16848 TTTTT
1 ATTTT
16853 TTTTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (27 bp):
ATTTTAATAATGGCATAATTAAAATAT
Done.