Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022659.1 Corchorus olitorius cultivar O-4 contig22692, 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: 40183
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:220 original size:28 final size:27
Alignment explanation
Indices: 178--232 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
168 TTTTTATTTG
*
178 AGTTTGTTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTTGAGTCAGTTTCGAGTC
204 AGTTTGTTTTTTCGAGTCAGTTTCGAGTC
1 AGTTTG-TTTTT-GAGTCAGTTTCGAGTC
233 TAGTCTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 9 0.36
29 5 0.20
ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49
Consensus pattern (27 bp):
AGTTTGTTTTTGAGTCAGTTTCGAGTC
Found at i:3911 original size:11 final size:10
Alignment explanation
Indices: 3882--3927 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
3872 AGTTCGTGAC
3882 TGAAGATTAAT
1 TGAAGA-TAAT
3893 TGAAGATAATT
1 TGAAGATAA-T
3904 TGAAGAT-A-
1 TGAAGATAAT
*
3912 TGAAGATCAT
1 TGAAGATAAT
3922 TGAAGA
1 TGAAGA
3928 AAGATTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 10 0.31
11 14 0.44
ACGTcount: A:0.46, C:0.02, G:0.22, T:0.30
Consensus pattern (10 bp):
TGAAGATAAT
Found at i:4534 original size:18 final size:18
Alignment explanation
Indices: 4511--4546 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
4501 GATACAATTC
4511 TTTTCT-TCTAGTATTTAG
1 TTTTCTGTCTAGT-TTTAG
4529 TTTTCTGTCTAGTTTTAG
1 TTTTCTGTCTAGTTTTAG
4547 AAGAGGGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.61
Consensus pattern (18 bp):
TTTTCTGTCTAGTTTTAG
Found at i:7296 original size:29 final size:30
Alignment explanation
Indices: 7238--7298 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
7228 GTTCTAATTA
* *
7238 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
7268 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
7297 AT
1 AT
7299 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:8036 original size:14 final size:15
Alignment explanation
Indices: 8012--8040 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
8002 AAGTCCAATC
8012 CTTGTTTATTTATTT
1 CTTGTTTATTTATTT
8027 CTTG-TTATTTATTT
1 CTTGTTTATTTATTT
8041 TTCCTAGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
CTTGTTTATTTATTT
Found at i:11842 original size:29 final size:29
Alignment explanation
Indices: 11807--11877 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
11797 AGTTTTGTTT
11807 AAGTGTGGGTTGTGCACTTGTGTTTGCTC
1 AAGTGTGGGTTGTGCACTTGTGTTTGCTC
11836 AAGTGTGGGTTGTGCACTTGTGTTTGCTC
1 AAGTGTGGGTTGTGCACTTGTGTTTGCTC
11865 AAGTGTGGGTTGT
1 AAGTGTGGGTTGT
11878 TTGAGTGTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.11, C:0.11, G:0.37, T:0.41
Consensus pattern (29 bp):
AAGTGTGGGTTGTGCACTTGTGTTTGCTC
Found at i:16906 original size:80 final size:82
Alignment explanation
Indices: 16773--17325 Score: 511
Period size: 80 Copynumber: 6.7 Consensus size: 82
16763 CTTTATCCTA
* * *
16773 TTTGCCCTTCCTCACCGGAAGCTGTTGTCGAT-TTACCCAATTTGCCCTTCCTCACCGGAAGGTG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTATATT-CCCAGTTTGCCCTTCCTCACCGGAAGGTG
*
16837 TTGTCT-A-GTTTCCAAG
65 TTGTTTAACGTTTCCAAG
* *
16853 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTATATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGT
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTATATTCCCAGTTTGCCCTTCCTCACCGGAAGGTGT
16918 TGTTTAAGTCTGTTTTACCCAA-
66 TGTTTAA--C-G-TTT--CCAAG
* * * * *
16940 TTTGCCCTTCCCCACCAGAAGGTGTTATCTA-ATTTCCTAGTTTG-CCTTCCTCATCGGAAGGTG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTATA-TTCCCAGTTTGCCCTTCCTCACCGGAAGGTG
17003 TTGTTTAAGTCTGCTTTACCCAA-
65 TTGTTTAA--C-G-TTT--CCAAG
* * * * *
17026 TTTGGCCTTCCCCACCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCCCACCGGAAGGTGT
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTATATTCCCAGTTTGCCCTTCCTCACCGGAAGGTGT
*
17091 TGTTTAA-ATTTCC-AG
66 TGTTTAACGTTTCCAAG
* * * **
17106 TTTGCCCTTCCCCACCAGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCTCATTGGAAGGTGT
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTATATTCCCAGTTTGCCCTTCCTCACCGGAAGGTGT
*
17171 TGTTT-ACTTTTCTC-AG
66 TGTTTAACGTTTC-CAAG
* * * * *
17187 TTTGCCCTTCCTCATCGAAAGGTGTTGTCTACCTTTTCCCAGTTTGCCCTTCCCCCACTGGAAGG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTA--TATTCCCAGTTTGCCCTT-CCTCACCGGAAGG
* *
17252 TGTTGTTT-ACTTTTCCCAG
63 TGTTGTTTAACGTTTCCAAG
* ** * * *
17271 -TTGGCCTTCCTCATTGGAAGGTGTTGTTTATCATTTCTCAGTTTGCCCTCCCTCA
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTAT-A-TTCCCAGTTTGCCCTTCCTCA
17326 TCTGAGGTAT
Statistics
Matches: 409, Mismatches: 43, Indels: 40
0.83 0.09 0.08
Matches are distributed among these distances:
79 2 0.00
80 131 0.32
81 34 0.08
82 7 0.02
83 57 0.14
84 28 0.07
85 1 0.00
86 82 0.20
87 63 0.15
88 4 0.01
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.37
Consensus pattern (82 bp):
TTTGCCCTTCCTCACCGGAAGGTGTTGTCTATATTCCCAGTTTGCCCTTCCTCACCGGAAGGTGT
TGTTTAACGTTTCCAAG
Found at i:17339 original size:41 final size:42
Alignment explanation
Indices: 16755--17329 Score: 431
Period size: 40 Copynumber: 13.9 Consensus size: 42
16745 GTTGTCCAAA
* * * *
16755 GTTGTCTACTTTATCCTA-TTTGCCCTTCCTCA-CCGGAAGCT
1 GTTGTTTACTTT-TCCCAGTTTGCCCTTCCTCATCTGGAAGGT
** * * *
16796 GTTGTCGA-TTTACCCAATTTGCCCTTCCTCA-CCGGAAGGT
1 GTTGTTTACTTTTCCCAGTTTGCCCTTCCTCATCTGGAAGGT
* * * *
16836 GTTGTCTA-GTTTCCAAGTTTGCCCTTCCTCA-CCGGAAGGT
1 GTTGTTTACTTTTCCCAGTTTGCCCTTCCTCATCTGGAAGGT
*
16876 GTTGTTTA-TATTCCCAGTTTGCCCTTCCTCATC-GGAAGGT
1 GTTGTTTACTTTTCCCAGTTTGCCCTTCCTCATCTGGAAGGT
* * **
16916 GTTGTTTAAGTCTGTTTTACCCAATTTGCCCTTCCCCA-CCAGAAGGT
1 GTTGTTT-A--C--TTTT-CCCAGTTTGCCCTTCCTCATCTGGAAGGT
* * * *
16963 GTTATCTA-ATTTCCTAGTTTG-CCTTCCTCATC-GGAAGGT
1 GTTGTTTACTTTTCCCAGTTTGCCCTTCCTCATCTGGAAGGT
* * * *
17002 GTTGTTTAAGTCTGCTTTACCCAATTTGGCCTTCCCCA-CCGGAAGGT
1 GTTGTTT-A--CT--TTT-CCCAGTTTGCCCTTCCTCATCTGGAAGGT
** * *
17049 GTTGTTTA-AATTCCCAGTTTGCCCTTCCCCA-CCGGAAGGT
1 GTTGTTTACTTTTCCCAGTTTGCCCTTCCTCATCTGGAAGGT
** * **
17089 GTTGTTTAAATTT-CCAGTTTGCCCTTCCCCA-CCAGAAGGT
1 GTTGTTTACTTTTCCCAGTTTGCCCTTCCTCATCTGGAAGGT
* **
17129 GTTGTCTA-AATTCCCAGTTTGCCCTTCCTCAT-TGGAAGGT
1 GTTGTTTACTTTTCCCAGTTTGCCCTTCCTCATCTGGAAGGT
* *
17169 GTTGTTTACTTTTCTCAGTTTGCCCTTCCTCATC-GAAAGGT
1 GTTGTTTACTTTTCCCAGTTTGCCCTTCCTCATCTGGAAGGT
* *
17210 GTTGTCTACCTTTTCCCAGTTTGCCCTTCCCCCA-CTGGAAGGT
1 GTTGTTTA-CTTTTCCCAGTTTGCCCTT-CCTCATCTGGAAGGT
*
17253 GTTGTTTACTTTTCCCAG-TTGGCCTTCCTCAT-TGGAAGGT
1 GTTGTTTACTTTTCCCAGTTTGCCCTTCCTCATCTGGAAGGT
* * *
17293 GTTGTTTATCATTTCTCAGTTTGCCCTCCCTCATCTG
1 GTTGTTTA-CTTTTCCCAGTTTGCCCTTCCTCATCTG
17330 AGGTATTGTT
Statistics
Matches: 445, Mismatches: 57, Indels: 62
0.79 0.10 0.11
Matches are distributed among these distances:
39 25 0.06
40 227 0.51
41 66 0.15
42 41 0.09
43 19 0.04
45 3 0.01
46 14 0.03
47 50 0.11
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.38
Consensus pattern (42 bp):
GTTGTTTACTTTTCCCAGTTTGCCCTTCCTCATCTGGAAGGT
Found at i:19515 original size:14 final size:14
Alignment explanation
Indices: 19492--19528 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
19482 TAATGCACCC
19492 AAAACAATTTATTT
1 AAAACAATTTATTT
*
19506 AAAACCATTTA-TT
1 AAAACAATTTATTT
19519 -AAACAATTTA
1 AAAACAATTTA
19529 ATAAAACAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 9 0.43
13 2 0.10
14 10 0.48
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAACAATTTATTT
Found at i:20108 original size:26 final size:27
Alignment explanation
Indices: 20078--20151 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 27
20068 TAGGGTCACC
20078 CAAGGGCATTTTGGTCATTTTCATACT
1 CAAGGGCATTTTGGTCATTTTCATACT
* *
20105 -AAGGGCATTTTGGTCATTTGCATATT
1 CAAGGGCATTTTGGTCATTTTCATACT
* **
20131 CAGGGGCACGTTGGTCATTTT
1 CAAGGGCATTTTGGTCATTTT
20152 AAGTCCATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
26 24 0.60
27 16 0.40
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.39
Consensus pattern (27 bp):
CAAGGGCATTTTGGTCATTTTCATACT
Found at i:23603 original size:40 final size:40
Alignment explanation
Indices: 23559--23692 Score: 119
Period size: 40 Copynumber: 3.3 Consensus size: 40
23549 CCCTAGAAAG
* *
23559 TTCAATTTGGTCCTTATTTGTCTTGATTTGTGTGATTTCA
1 TTCAATTTGGTCCTTATTTGTCTTCATTTGTGTGATTTGA
** * ** * **
23599 TTCAATTCCGTCCCTGATTTAGGATTCTAGTT-ACT-ATTTGA
1 TTCAATTTGGT-CCTTATTT-GTCTTC-ATTTGTGTGATTTGA
*
23640 TTCAATTTGGTCCTTATTTTTCTTCATTTGTGTGATTTGA
1 TTCAATTTGGTCCTTATTTGTCTTCATTTGTGTGATTTGA
*
23680 TTCAATTTTGTCC
1 TTCAATTTGGTCC
23693 CTAAATTTAA
Statistics
Matches: 69, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
38 3 0.04
39 4 0.06
40 34 0.49
41 21 0.30
42 4 0.06
43 3 0.04
ACGTcount: A:0.17, C:0.16, G:0.15, T:0.52
Consensus pattern (40 bp):
TTCAATTTGGTCCTTATTTGTCTTCATTTGTGTGATTTGA
Found at i:24468 original size:38 final size:38
Alignment explanation
Indices: 24416--24489 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 38
24406 AAGAACTTTT
24416 TTTAAGTAACTCCAAAA-GAAGATTTTGGAAAATAAAAG
1 TTTAAGTAACTCCAAAATG-AGATTTTGGAAAATAAAAG
* *
24454 TTTAGGTAATTCCAAAATGAGATTTTGGAAAATAAA
1 TTTAAGTAACTCCAAAATGAGATTTTGGAAAATAAA
24490 GAAACCCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 32 0.97
39 1 0.03
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (38 bp):
TTTAAGTAACTCCAAAATGAGATTTTGGAAAATAAAAG
Found at i:26002 original size:12 final size:12
Alignment explanation
Indices: 25987--26011 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25977 TCTCTCTTTT
25987 TTTTTCCTCTTC
1 TTTTTCCTCTTC
25999 TTTTTCCTCTTC
1 TTTTTCCTCTTC
26011 T
1 T
26012 AATTCTGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTCCTCTTC
Found at i:37005 original size:1 final size:1
Alignment explanation
Indices: 36962--36993 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
36952 CGAGGTCCAC
36962 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
36994 CCGACTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39452 original size:22 final size:22
Alignment explanation
Indices: 39427--39501 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
39417 TTGAATATTT
39427 TTATGAAATTTTGATAACTACC
1 TTATGAAATTTTGATAACTACC
* * **
39449 TTATTAAATTTTGATAACCATG
1 TTATGAAATTTTGATAACTACC
*
39471 TTATGAAATTTTGATAATTTACC
1 TTATGAAATTTTGATAA-CTACC
39494 -TATGAAAT
1 TTATGAAAT
39502 ATGAAACTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
22 42 0.98
23 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (22 bp):
TTATGAAATTTTGATAACTACC
Found at i:39527 original size:29 final size:29
Alignment explanation
Indices: 39472--39530 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
39462 ATAACCATGT
* * *
39472 TATGAAATTTTGATAATTTACCTATGAAA
1 TATGAAACTTTGATAACTAACCTATGAAA
39501 TATGAAACTTTGATAACCTAACC-ATGAAA
1 TATGAAACTTTGATAA-CTAACCTATGAAA
39530 T
1 T
39531 TTTAATAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (29 bp):
TATGAAACTTTGATAACTAACCTATGAAA
Found at i:39528 original size:22 final size:22
Alignment explanation
Indices: 39501--39584 Score: 75
Period size: 21 Copynumber: 3.9 Consensus size: 22
39491 ACCTATGAAA
*
39501 TATGAAACTTTGATAACCTAACC
1 TATGAAATTTTGATAACCT-ACC
* *
39524 -ATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACCTACC
*
39546 TATGAAATTTTG-TAACCTTCC
1 TATGAAATTTTGATAACCTACC
* *
39567 TAT-TATTTTTGATAACCT
1 TATGAAATTTTGATAACCT
39585 CTCTGTGAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
20 6 0.12
21 17 0.33
22 14 0.27
23 15 0.29
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTACC
Found at i:39584 original size:21 final size:21
Alignment explanation
Indices: 39501--39569 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 21
39491 ACCTATGAAA
* *
39501 TATGAAACTTTGATAACCTAACC
1 TATGAAATTTTG-TAACCT-TCC
*
39524 -ATGAAATTTTAATAAACCTTCC
1 TATGAAATTTT-GT-AACCTTCC
39546 TATGAAATTTTGTAACCTTCC
1 TATGAAATTTTGTAACCTTCC
39567 TAT
1 TAT
39570 TATTTTTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 11 0.28
22 13 0.33
23 15 0.38
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGTAACCTTCC
Done.