Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014635.1 Corchorus olitorius cultivar O-4 contig14668, 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: 53354
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:3333 original size:22 final size:22
Alignment explanation
Indices: 3289--3342 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
3279 CATTGAGGAA
*
3289 AGTGAAAGAAACTCATGAGAAG
1 AGTGAAAGAAACTCATGAAAAG
*
3311 AGTGAAAGAGACTC-TGATAAAG
1 AGTGAAAGAAACTCATGA-AAAG
3333 AG-GTAAAGAA
1 AGTG-AAAGAA
3343 GATGAGGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.50, C:0.07, G:0.28, T:0.15
Consensus pattern (22 bp):
AGTGAAAGAAACTCATGAAAAG
Found at i:3469 original size:39 final size:39
Alignment explanation
Indices: 3415--3493 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
3405 ATGTTTACGT
**
3415 TGTTTACTTGTTTAGTTACACTAACGGTAGTAAATGATG
1 TGTTTACTTGTTTAGTTACACTAACAATAGTAAATGATG
* **
3454 TGTTTAGTTGTTTAGTTATGCTAACAATAGTAAATGATG
1 TGTTTACTTGTTTAGTTACACTAACAATAGTAAATGATG
3493 T
1 T
3494 TTTGTAGATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (39 bp):
TGTTTACTTGTTTAGTTACACTAACAATAGTAAATGATG
Found at i:4729 original size:52 final size:52
Alignment explanation
Indices: 4648--4748 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
4638 CGACTTTCCC
4648 TGTGATCCAACACAACTTAAATTTAGGATTACTTAGAACACAATGTGACATT
1 TGTGATCCAACACAACTTAAATTTAGGATTACTTAGAACACAATGTGACATT
*
4700 TGTGATCCAACACAACTTAAATTTGGGATTACTTAGAACACAATGTGAC
1 TGTGATCCAACACAACTTAAATTTAGGATTACTTAGAACACAATGTGAC
4749 TATCGGGTAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Consensus pattern (52 bp):
TGTGATCCAACACAACTTAAATTTAGGATTACTTAGAACACAATGTGACATT
Found at i:16707 original size:162 final size:158
Alignment explanation
Indices: 16222--16946 Score: 925
Period size: 162 Copynumber: 4.5 Consensus size: 158
16212 AACATCTAAA
* * * *
16222 TTCTAATAGAGATAAAAATAACGGTCTTAACGATTAACTATAGTATATATTTCAAATGATTGCAC
1 TTCTAATAAAGATAAAAATAACGGTCTTAACGACTAACTATA--ATATAATTCAAATGATTGTAC
* * *
16287 ATATGATATAACTTTTTCAACGATCGATATCAACATATCTTTTTTCTTATTTGTTTATAGATAAA
64 ATATG--ATAACTTTTTCAACGATC-A-ATCAAAATATC-TTTTTCTTGTTTGTTTATAGGTAAA
* *
16352 CTTAACGGTTTTAACGCCCGACCAAAATATCTAAT
124 CTTAACGGTTTTAACGACCGACCAAAATATCTATT
* * * *
16387 TTCTAATAGAGATATAAAAATAACGGTTTTAACGACTAACTATAGTAT--TTCAAATGATTGTAT
1 TTCTAATA-A-AGATAAAAATAACGGTCTTAACGACTAACTATAATATAATTCAAATGATTGTAC
* * *
16450 ATATGATAACTTTTTCAACGATCGATCAGAATATCTTTCTCTTGTTTGTTTATAGGTAAACTTAA
64 ATATGATAACTTTTTCAACGATCAATCAAAATATCTTTTTCTTGTTTGTTTATAGGTAAACTTAA
**
16515 CGGTTTTAATAACCGACCAAAATATCTATT
129 CGGTTTTAACGACCGACCAAAATATCTATT
* * *
16545 TTCTAATAAAGATAAAGATAACGGTCTTAACGATTAACCATAATATCAATTCAAATGATTGTACA
1 TTCTAATAAAGATAAAAATAACGGTCTTAACGACTAACTATAATAT-AATTCAAATGATTGTACA
* *
16610 TATGATAACTTTTTCAACTATCAATCAAAATATCTTTTTCTTTGTTTGTTTTTATAGGTAAATTT
65 TATGATAACTTTTTCAACGATCAATCAAAATATCTTTTTC-TTGTTTG--TTTATAGGTAAACTT
*
16675 AACGGTTTAAACGACCGACCAAAATATCTATT
127 AACGGTTTTAACGACCGACCAAAATATCTATT
* * *
16707 TTCTAATAAAGATATAGATAACGGTCTTAACGACTAACCATAATATCAATTCAAATGATTGTACA
1 TTCTAATAAAGATAAAAATAACGGTCTTAACGACTAACTATAATAT-AATTCAAATGATTGTACA
* * * *
16772 TATGATAACTTTTTCAACTATCAATCAAAATATATTTTTCTTGTTTGTTTTTATAAGTAAATTTA
65 TATGATAACTTTTTCAACGATCAATCAAAATATCTTTTTCTTGTTTG--TTTATAGGTAAACTTA
*
16837 ACGGTTTTAACGACCGATCAAAATATCTATT
128 ACGGTTTTAACGACCGACCAAAATATCTATT
* * * *
16868 TTCAAATAAAGATAAAAATAACGGTCTTAACGACT-ACTGTAATATATAAATTTAAATGATTTCT
1 TTCTAATAAAGATAAAAATAACGGTCTTAACGACTAACTAT-A-ATAT-AATTCAAATGA-TTGT
16932 ACATATGATAACTTT
62 ACATATGATAACTTT
16947 AATGATCAAT
Statistics
Matches: 503, Mismatches: 46, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
156 31 0.06
157 1 0.00
158 61 0.12
159 60 0.12
160 10 0.02
161 104 0.21
162 159 0.32
163 36 0.07
165 11 0.02
167 30 0.06
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (158 bp):
TTCTAATAAAGATAAAAATAACGGTCTTAACGACTAACTATAATATAATTCAAATGATTGTACAT
ATGATAACTTTTTCAACGATCAATCAAAATATCTTTTTCTTGTTTGTTTATAGGTAAACTTAACG
GTTTTAACGACCGACCAAAATATCTATT
Found at i:16868 original size:323 final size:319
Alignment explanation
Indices: 16222--16946 Score: 958
Period size: 323 Copynumber: 2.2 Consensus size: 319
16212 AACATCTAAA
* * *
16222 TTCTAATAGAGATAAAAATAACGGTCTTAACGATTAACTATAGTATATATTTCAAATGATTGCAC
1 TTCTAATAAAGATAAAAATAACGGTCTTAACGATTAACTATA-TATATAATTCAAATGATTGTAC
*
16287 ATATGATATAACTTTTTCAACGATCGATATCAACATATCTTTTTTCTTATTTGTTTATAGATAAA
65 ATATG--ATAACTTTTTCAACGATCGATATCAAAATATCTTTTTTCTTATTTGTTTATAGATAAA
* * * *
16352 CTTAACGGTTTTAACGCCCGACCAAAATATCTAATTTCTAATAGAGATATAAAAATAACGGTTTT
128 CTTAACGGTTTAAACGACCGACCAAAATATCTAATTTCTAATAAAGATAT-AAAATAACGGTCTT
* * * * *
16417 AACGACTAACTATAGTATTTCAAATGATTGTATATATGATAACTTTTTCAACGATCGATCAGAAT
192 AACGACTAACCATAATATTTCAAATGATTGTACATATGATAACTTTTTCAACGATCAATCAAAAT
* * *
16482 ATCTTTCTCTTGTTTGTTTATAGGTAAACTTAACGGTTTTAATAACCGACCAAAATATCTATT
257 ATATTTCTCTTGTTTGTTTATAAGTAAACTTAACGGTTTTAACAACCGACCAAAATATCTATT
* *
16545 TTCTAATAAAGATAAAGATAACGGTCTTAACGATTAACCATA-ATATCAATTCAAATGATTGTAC
1 TTCTAATAAAGATAAAAATAACGGTCTTAACGATTAACTATATATAT-AATTCAAATGATTGTAC
* * *
16609 ATATGATAACTTTTTCAACTATC-A-ATCAAAATATC-TTTTTCTTTGTTTGTTTTTATAGGTAA
65 ATATGATAACTTTTTCAACGATCGATATCAAAATATCTTTTTTC-TTATTTG--TTTATAGATAA
* * *
16671 ATTTAACGGTTTAAACGACCGACCAAAATATCTATTTTCTAATAAAGATAT-AGATAACGGTCTT
127 ACTTAACGGTTTAAACGACCGACCAAAATATCTAATTTCTAATAAAGATATAAAATAACGGTCTT
*
16735 AACGACTAACCATAATATCAATTCAAATGATTGTACATATGATAACTTTTTCAACTATCAATCAA
192 AACGACTAACCATAATAT---TTCAAATGATTGTACATATGATAACTTTTTCAACGATCAATCAA
* * * *
16800 AATATATTTTTCTTGTTTGTTTTTATAAGTAAATTTAACGGTTTTAACGACCGATCAAAATATCT
254 AATATATTTCTCTTGTTTG--TTTATAAGTAAACTTAACGGTTTTAACAACCGACCAAAATATCT
16865 ATT
317 ATT
* * * * *
16868 TTCAAATAAAGATAAAAATAACGGTCTTAACGACT-ACTGTAATATATAAATTTAAATGATTTCT
1 TTCTAATAAAGATAAAAATAACGGTCTTAACGATTAACTAT-ATATAT-AATTCAAATGA-TTGT
16932 ACATATGATAACTTT
63 ACATATGATAACTTT
16947 AATGATCAAT
Statistics
Matches: 353, Mismatches: 37, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
317 6 0.02
318 43 0.12
319 1 0.00
320 73 0.21
321 61 0.17
322 23 0.07
323 114 0.32
324 14 0.04
325 18 0.05
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (319 bp):
TTCTAATAAAGATAAAAATAACGGTCTTAACGATTAACTATATATATAATTCAAATGATTGTACA
TATGATAACTTTTTCAACGATCGATATCAAAATATCTTTTTTCTTATTTGTTTATAGATAAACTT
AACGGTTTAAACGACCGACCAAAATATCTAATTTCTAATAAAGATATAAAATAACGGTCTTAACG
ACTAACCATAATATTTCAAATGATTGTACATATGATAACTTTTTCAACGATCAATCAAAATATAT
TTCTCTTGTTTGTTTATAAGTAAACTTAACGGTTTTAACAACCGACCAAAATATCTATT
Found at i:17913 original size:42 final size:42
Alignment explanation
Indices: 17842--17922 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
17832 TGATGGACCA
*
17842 AACCCAAACTGCAGATTCCCCGAGGTTTGA-TCTGGCGCCATG
1 AACCCAAACTGCACATTCCCCGAGGTTTGATTC-GGCGCCATG
* *
17884 AACCCAAACTGGACATTCCCC-ATGTTTTGATTCGGCGCC
1 AACCCAAACTGCACATTCCCCGA-GGTTTGATTCGGCGCC
17923 GCCATGTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 1 0.03
42 31 0.91
43 2 0.06
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.23
Consensus pattern (42 bp):
AACCCAAACTGCACATTCCCCGAGGTTTGATTCGGCGCCATG
Found at i:32237 original size:2 final size:2
Alignment explanation
Indices: 32232--32275 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
32222 CCTCCCCCCC
*
32232 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
32274 CT
1 CT
32276 TCTTCTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:35409 original size:86 final size:86
Alignment explanation
Indices: 35264--35520 Score: 385
Period size: 86 Copynumber: 3.0 Consensus size: 86
35254 TACCTTTTTC
* *
35264 GTGTACAAGTATACTCC-CGTTATCCGGCAGTCACAATT-AACCCGATTAAATTAATCCAAATTC
1 GTGTACAAATATAC-CCTCATTATCCGGCAGTCAC-ATTAAACCCGATTAAATTAATCCAAATTC
35327 GAGTCGCGTTGGCCCCCAAACGG
64 GAGTCGCGTTGGCCCCCAAACGG
* * * *
35350 GTGTACAAGTATACCTTTATTATCCGACAGTCACATTAAACCCGATTAAATTAATCCAAATTCGA
1 GTGTACAAATATACCCTCATTATCCGGCAGTCACATTAAACCCGATTAAATTAATCCAAATTCGA
* *
35415 GTCACATTGGCCCCCAAACGG
66 GTCGCGTTGGCCCCCAAACGG
*
35436 GTGTACAAATATACCCTCATTATCCGGCAGTCACATTAAACCCCGATTAAATTAATCCAAATTCT
1 GTGTACAAATATACCCTCATTATCCGGCAGTCACATTAAA-CCCGATTAAATTAATCCAAATTCG
35501 AGTCGCGTTGG-CCCCAAACG
65 AGTCGCGTTGGCCCCCAAACG
35521 TGGGGATGCT
Statistics
Matches: 155, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
85 4 0.03
86 119 0.77
87 32 0.21
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (86 bp):
GTGTACAAATATACCCTCATTATCCGGCAGTCACATTAAACCCGATTAAATTAATCCAAATTCGA
GTCGCGTTGGCCCCCAAACGG
Found at i:38010 original size:66 final size:66
Alignment explanation
Indices: 37928--38083 Score: 222
Period size: 66 Copynumber: 2.4 Consensus size: 66
37918 TATATCATAA
* * * * *
37928 TTCAATATAGTAATCGGATATGGACTTGGTTTAGAATCCAACACGACTTGATTATGTATGTCAGA
1 TTCAATATAGTTATCGGATACGGAATTGATTTAGAATCCAACACGACTTGACTATGTATGTCAGA
37993 G
66 G
** **
37994 TTTTATATAGTTATCGGATACGGAATTGATTTAGAATTTAACACGACTTGACTATGTATGTCAGA
1 TTCAATATAGTTATCGGATACGGAATTGATTTAGAATCCAACACGACTTGACTATGTATGTCAGA
38059 G
66 G
*
38060 TTCAATATAGTTATCAGATACGGA
1 TTCAATATAGTTATCGGATACGGA
38084 TTAGTTAATG
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 78 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (66 bp):
TTCAATATAGTTATCGGATACGGAATTGATTTAGAATCCAACACGACTTGACTATGTATGTCAGA
G
Found at i:39226 original size:64 final size:64
Alignment explanation
Indices: 39125--39253 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 64
39115 GCTACTTCCG
39125 AGTGCAAATCATAAGTACTTATAGCTTTTCCCTTAGCGAGAAATTCTCGAAACGAAGATTTTTT
1 AGTGCAAATCATAAGTACTTATAGCTTTTCCCTTAGCGAGAAATTCTCGAAACGAAGATTTTTT
* *
39189 AGTGCAAATCATGAGTACTTATAGCTTTTCCCTTAGCGGGAAATTCTCGAAACGAAGATTTTTT
1 AGTGCAAATCATAAGTACTTATAGCTTTTCCCTTAGCGAGAAATTCTCGAAACGAAGATTTTTT
39253 A
1 A
39254 AACTTGAAAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (64 bp):
AGTGCAAATCATAAGTACTTATAGCTTTTCCCTTAGCGAGAAATTCTCGAAACGAAGATTTTTT
Found at i:45648 original size:31 final size:31
Alignment explanation
Indices: 45581--45771 Score: 226
Period size: 31 Copynumber: 6.3 Consensus size: 31
45571 AAATGACATG
*
45581 TGACACGTGTC-CTTTTT-GTGCACGTGGCA
1 TGACACGTGTCACTTTTTGGTACACGTGGCA
* **
45610 TGCCACGTGTCACTTTTTGGTACACGTGGGG
1 TGACACGTGTCACTTTTTGGTACACGTGGCA
*
45641 TTACACGTGTCAC-TTTTGGTACACGTGGCA
1 TGACACGTGTCACTTTTTGGTACACGTGGCA
* * *
45671 TGACACATGTCACTTTTTGGTGCACGTGGCG
1 TGACACGTGTCACTTTTTGGTACACGTGGCA
* * * *
45702 TGACACGTATCATTTTTTGATAAACGTGGCA
1 TGACACGTGTCACTTTTTGGTACACGTGGCA
* *
45733 TGCCACATGTCACTTTTTGGTACACGTGGCA
1 TGACACGTGTCACTTTTTGGTACACGTGGCA
*
45764 TGCCACGT
1 TGACACGT
45772 CGGACACCGT
Statistics
Matches: 133, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
29 10 0.08
30 32 0.24
31 91 0.68
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (31 bp):
TGACACGTGTCACTTTTTGGTACACGTGGCA
Found at i:45682 original size:61 final size:61
Alignment explanation
Indices: 45580--45771 Score: 251
Period size: 61 Copynumber: 3.1 Consensus size: 61
45570 AAAATGACAT
* * * *
45580 GTGACACGTGTC-CTTTTTGTGCACGTGGCATGCCACGTGTCACTTTTTGGTACACGTGGG
1 GTGACACGTGTCACTTTTGGTACACGTGGCATGCCACATGTCACTTTTTGGTACACGTGGC
* * *
45640 GTTACACGTGTCACTTTTGGTACACGTGGCATGACACATGTCACTTTTTGGTGCACGTGGC
1 GTGACACGTGTCACTTTTGGTACACGTGGCATGCCACATGTCACTTTTTGGTACACGTGGC
* * * *
45701 GTGACACGTATCATTTTTTGATAAACGTGGCATGCCACATGTCACTTTTTGGTACACGTGGC
1 GTGACACGTGTCA-CTTTTGGTACACGTGGCATGCCACATGTCACTTTTTGGTACACGTGGC
* *
45763 ATGCCACGT
1 GTGACACGT
45772 CGGACACCGT
Statistics
Matches: 114, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 11 0.10
61 53 0.46
62 50 0.44
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (61 bp):
GTGACACGTGTCACTTTTGGTACACGTGGCATGCCACATGTCACTTTTTGGTACACGTGGC
Found at i:45748 original size:92 final size:91
Alignment explanation
Indices: 45581--45765 Score: 237
Period size: 92 Copynumber: 2.0 Consensus size: 91
45571 AAATGACATG
* * * * * ** *
45581 TGACACGTGTCCTTTTTGTGCACGTGGCATGCCACGTGTCACTTTTTGGTACACGTGGGGTTACA
1 TGACACATGTCCTTTTTGTGCACGTGGCATGACACGTATCACTTTTTGATAAACGTGGCATGACA
*
45646 CGTGTCAC-TTTTGGTACACGTGGCA
66 CATGTCACTTTTTGGTACACGTGGCA
* * *
45671 TGACACATGTCACTTTTTGGTGCACGTGGCGTGACACGTATCATTTTTTGATAAACGTGGCATGC
1 TGACACATGTC-CTTTTT-GTGCACGTGGCATGACACGTATCACTTTTTGATAAACGTGGCATGA
45736 CACATGTCACTTTTTGGTACACGTGGCA
64 CACATGTCACTTTTTGGTACACGTGGCA
45764 TG
1 TG
45766 CCACGTCGGA
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
90 10 0.12
91 6 0.08
92 45 0.56
93 19 0.24
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (91 bp):
TGACACATGTCCTTTTTGTGCACGTGGCATGACACGTATCACTTTTTGATAAACGTGGCATGACA
CATGTCACTTTTTGGTACACGTGGCA
Found at i:46368 original size:2 final size:2
Alignment explanation
Indices: 46363--46389 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46353 TATATATATA
46363 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
46390 ATCAAGTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:53270 original size:2 final size:2
Alignment explanation
Indices: 53221--53256 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
53211 TAATTTGCCG
53221 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53257 CTTCATAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.