Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023450.1 Corchorus olitorius cultivar O-4 contig23483, 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: 29575
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:159 original size:16 final size:15
Alignment explanation
Indices: 121--162 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
111 ACAGAGGTTG
*
121 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
136 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
151 ACTAGAAAACAA
1 AC-AGAAAACAA
163 AACAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:8857 original size:43 final size:43
Alignment explanation
Indices: 8796--8881 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
8786 ATCAATTAGT
8796 TTTGGTTTTTTAATACTAATTTTCATGTCTTATAAAATGTAGA
1 TTTGGTTTTTTAATACTAATTTTCATGTCTTATAAAATGTAGA
8839 TTTGGTTTTTTAATACTAATTTTCATGTCTTATAAAATGTAGA
1 TTTGGTTTTTTAATACTAATTTTCATGTCTTATAAAATGTAGA
8882 AAGTTTTACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (43 bp):
TTTGGTTTTTTAATACTAATTTTCATGTCTTATAAAATGTAGA
Found at i:11410 original size:29 final size:29
Alignment explanation
Indices: 11368--11425 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
11358 GAAAAAGGTA
11368 GTTATCAGTGTATCAAATTCAAGTCTCTT
1 GTTATCAGTGTATCAAATTCAAGTCTCTT
11397 GTTATCAGTGTATCAAATTCAAGTCTCTT
1 GTTATCAGTGTATCAAATTCAAGTCTCTT
11426 CCCTATGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (29 bp):
GTTATCAGTGTATCAAATTCAAGTCTCTT
Found at i:17521 original size:22 final size:22
Alignment explanation
Indices: 17467--17526 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
17457 TAAATAGTTT
* * *
17467 TATGAAATTTCGATAATCACCC
1 TATGAAATTTTGATAACCACCA
*
17489 TATTAAATTTTGATAACCACCA
1 TATGAAATTTTGATAACCACCA
*
17511 TATGAAATTTTCATAA
1 TATGAAATTTTGATAA
17527 TTACCTATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACCA
Found at i:17547 original size:21 final size:21
Alignment explanation
Indices: 17471--17547 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 21
17461 TAGTTTTATG
* *
17471 AAATTTCGATAATCACCCTATT
1 AAATTTTGATAATCA-CCTATA
* *
17493 AAATTTTGATAACCACCATATG
1 AAATTTTGATAATCACC-TATA
* *
17515 AAATTTTCATAATTACCTATA
1 AAATTTTGATAATCACCTATA
*
17536 AAATTGTGATAA
1 AAATTTTGATAA
17548 ATTCCATAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 15 0.33
22 30 0.67
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (21 bp):
AAATTTTGATAATCACCTATA
Found at i:17669 original size:20 final size:21
Alignment explanation
Indices: 17597--17670 Score: 55
Period size: 22 Copynumber: 3.6 Consensus size: 21
17587 AATAAACTTT
* *
17597 CCTATGAATTTTG-TAACCTT
1 CCTATGAATTTTGTTAATCTC
* *
17617 CGTAT-AATTTTTTATAATCTC
1 CCTATGAATTTTGT-TAATCTC
* *
17638 TCTGTGAGATTTTGTTAATCTC
1 CCTATGA-ATTTTGTTAATCTC
17660 CCTAT-AATTTT
1 CCTATGAATTTT
17671 TTGATACTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
19 6 0.15
20 9 0.22
21 8 0.20
22 11 0.28
23 6 0.15
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.50
Consensus pattern (21 bp):
CCTATGAATTTTGTTAATCTC
Found at i:18999 original size:10 final size:10
Alignment explanation
Indices: 18977--19023 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
18967 TAAGTTACAC
18977 TTTTTTTGG-
1 TTTTTTTGGT
18986 -TTTTTTGGTT
1 TTTTTTTGG-T
18996 TTTTTTTGGT
1 TTTTTTTGGT
*
19006 TTTTTTTGTT
1 TTTTTTTGGT
19016 TTTTTTTG
1 TTTTTTTG
19024 CAATCTAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
8 8 0.24
10 18 0.53
11 8 0.24
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (10 bp):
TTTTTTTGGT
Found at i:19001 original size:19 final size:20
Alignment explanation
Indices: 18977--19023 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
18967 TAAGTTACAC
18977 TTTTTTTGG-TTTTTTGGTT
1 TTTTTTTGGTTTTTTTGGTT
*
18996 TTTTTTTGGTTTTTTTTGTT
1 TTTTTTTGGTTTTTTTGGTT
19016 TTTTTTTG
1 TTTTTTTG
19024 CAATCTAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (20 bp):
TTTTTTTGGTTTTTTTGGTT
Found at i:19021 original size:9 final size:9
Alignment explanation
Indices: 18977--19021 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
18967 TAAGTTACAC
*
18977 TTTTTTTGG
1 TTTTTTTGT
*
18986 TTTTTTGGTT
1 TTTTTTTG-T
18996 TTTTTTTGGT
1 TTTTTTT-GT
19006 TTTTTTTGT
1 TTTTTTTGT
19015 TTTTTTT
1 TTTTTTT
19022 TGCAATCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 16 0.52
10 14 0.45
11 1 0.03
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:20773 original size:15 final size:16
Alignment explanation
Indices: 20753--20790 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
20743 CGTTCAAATG
20753 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
20768 TCGGGTCAATTCTGGGT
1 TCGGGTCAATT-TGGGT
20785 T-GGGTC
1 TCGGGTC
20791 GTTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:22043 original size:7 final size:7
Alignment explanation
Indices: 22031--22056 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
22021 TTCAAATTTA
22031 TATAACT
1 TATAACT
22038 TATAACT
1 TATAACT
22045 TATAACT
1 TATAACT
22052 TATAA
1 TATAA
22057 ATATATTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
TATAACT
Found at i:22460 original size:17 final size:16
Alignment explanation
Indices: 22416--22460 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
22406 GCCGGATTGA
22416 TTGGGTTCGGGTCATT
1 TTGGGTTCGGGTCATT
*
22432 TTGGGTTTGGGTCATT
1 TTGGGTTCGGGTCATT
22448 TTCGGGTTCGGGT
1 TT-GGGTTCGGGT
22461 ACCCAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.04, C:0.11, G:0.40, T:0.44
Consensus pattern (16 bp):
TTGGGTTCGGGTCATT
Found at i:22509 original size:17 final size:17
Alignment explanation
Indices: 22469--22509 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
22459 GTACCCAAAA
22469 TTTCGGGTCATTTCTGG
1 TTTCGGGTCATTTCTGG
*
22486 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCA-TTTCTGG
22502 TTTCGGGT
1 TTTCGGGT
22510 TGGGCGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.37, T:0.44
Consensus pattern (17 bp):
TTTCGGGTCATTTCTGG
Found at i:23037 original size:76 final size:76
Alignment explanation
Indices: 22911--23061 Score: 302
Period size: 76 Copynumber: 2.0 Consensus size: 76
22901 GCTATATATA
22911 TACATATAGGTACGTAGATCATTCGACCAATTAAGGAGTGCTTAAATTAATTTGAATCTCATTGT
1 TACATATAGGTACGTAGATCATTCGACCAATTAAGGAGTGCTTAAATTAATTTGAATCTCATTGT
22976 TTTTTTTTTTT
66 TTTTTTTTTTT
22987 TACATATAGGTACGTAGATCATTCGACCAATTAAGGAGTGCTTAAATTAATTTGAATCTCATTGT
1 TACATATAGGTACGTAGATCATTCGACCAATTAAGGAGTGCTTAAATTAATTTGAATCTCATTGT
23052 TTTTTTTTTT
66 TTTTTTTTTT
23062 ATATCATTTG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (76 bp):
TACATATAGGTACGTAGATCATTCGACCAATTAAGGAGTGCTTAAATTAATTTGAATCTCATTGT
TTTTTTTTTTT
Found at i:23505 original size:13 final size:13
Alignment explanation
Indices: 23487--23516 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
23477 GTTATATTGA
*
23487 GAAAATATTATTT
1 GAAAATATTAATT
23500 GAAAATATTAATT
1 GAAAATATTAATT
23513 GAAA
1 GAAA
23517 TGAAGGACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (13 bp):
GAAAATATTAATT
Found at i:29090 original size:11 final size:11
Alignment explanation
Indices: 29060--29115 Score: 67
Period size: 11 Copynumber: 4.8 Consensus size: 11
29050 TTATGCACCC
29060 AAAACATTTATT
1 AAAACATTTA-T
29072 AAAACATTTAT
1 AAAACATTTAT
*
29083 AAAGCATTTATAT
1 AAAACA-TT-TAT
*
29096 AAAACAGTTAT
1 AAAACATTTAT
29107 AAAACATTT
1 AAAACATTT
29116 CCTCAACGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
11 17 0.45
12 13 0.34
13 8 0.21
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.36
Consensus pattern (11 bp):
AAAACATTTAT
Found at i:29101 original size:24 final size:23
Alignment explanation
Indices: 29060--29115 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 23
29050 TTATGCACCC
*
29060 AAAACATTTATTAAAACATTTAT
1 AAAACATTTATTAAAACAGTTAT
*
29083 AAAGCATTTATATAAAACAGTTAT
1 AAAACATTTAT-TAAAACAGTTAT
29107 AAAACATTT
1 AAAACATTT
29116 CCTCAACGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.36
Consensus pattern (23 bp):
AAAACATTTATTAAAACAGTTAT
Found at i:29289 original size:20 final size:19
Alignment explanation
Indices: 29246--29289 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
29236 GAAGTGCACC
* *
29246 AAACACAAGAAAATCATTA
1 AAACCCAAGAAAATCATCA
*
29265 AAACCCAAGATAATCAATCA
1 AAACCCAAGAAAATC-ATCA
29285 AAACC
1 AAACC
29290 GGGGATCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.59, C:0.23, G:0.05, T:0.14
Consensus pattern (19 bp):
AAACCCAAGAAAATCATCA
Done.