Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019606.1 Corchorus olitorius cultivar O-4 contig19639, 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: 75503
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:8184 original size:22 final size:22
Alignment explanation
Indices: 8159--8207 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
8149 ATCAAACTAA
*
8159 CAATTAAGATTAACT-AAGAAAG
1 CAATTAAGA-AAACTAAAGAAAG
* *
8181 CAATCAAGAAAATTAAAGAAAG
1 CAATTAAGAAAACTAAAGAAAG
8203 CAATT
1 CAATT
8208 GATAAGAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.20
Consensus pattern (22 bp):
CAATTAAGAAAACTAAAGAAAG
Found at i:9519 original size:19 final size:18
Alignment explanation
Indices: 9486--9521 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9476 TTGAAATAAT
9486 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
9504 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
9522 TGAGCCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:14139 original size:17 final size:17
Alignment explanation
Indices: 14117--14149 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
14107 GCCAGTTCAT
*
14117 TCACGTGTACGTTTTAG
1 TCACGTGCACGTTTTAG
14134 TCACGTGCACGTTTTA
1 TCACGTGCACGTTTTA
14150 ATTAAGTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (17 bp):
TCACGTGCACGTTTTAG
Found at i:16327 original size:41 final size:41
Alignment explanation
Indices: 16270--16355 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
16260 GTTCAATATG
* *
16270 GTCCCTAATTTAGGATTCTATTTACTATTTGGTACAATTTA
1 GTCCCTAATTTAGGATTCTAGTTACTATTTGATACAATTTA
* * * *
16311 GTCCCTGATTTAGGATTCTGGTTACTATTTGATTCAATTTG
1 GTCCCTAATTTAGGATTCTAGTTACTATTTGATACAATTTA
16352 GTCC
1 GTCC
16356 TTGTTTTTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (41 bp):
GTCCCTAATTTAGGATTCTAGTTACTATTTGATACAATTTA
Found at i:18932 original size:28 final size:28
Alignment explanation
Indices: 18891--18971 Score: 146
Period size: 28 Copynumber: 2.9 Consensus size: 28
18881 TTGTTTTGTG
18891 TTTT-TGCGTCATATATAAAAAAAAAGT
1 TTTTCTGCGTCATATATAAAAAAAAAGT
18918 TTTTCTGCGTCATATATAAAAAAAAAGT
1 TTTTCTGCGTCATATATAAAAAAAAAGT
*
18946 TTTTCTGCGTCATAAATAAAAAAAAA
1 TTTTCTGCGTCATATATAAAAAAAAA
18972 ATTTCTTGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 4 0.08
28 48 0.92
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (28 bp):
TTTTCTGCGTCATATATAAAAAAAAAGT
Found at i:22181 original size:21 final size:21
Alignment explanation
Indices: 22156--22204 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
22146 CCATTCACCA
*
22156 TGCCATCACCGGTTAAGCCCG
1 TGCCATCACCGGCTAAGCCCG
* * *
22177 TGCCACCACCGGCTATGCCTG
1 TGCCATCACCGGCTAAGCCCG
22198 TGCCATC
1 TGCCATC
22205 GCCATTCCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.41, G:0.22, T:0.20
Consensus pattern (21 bp):
TGCCATCACCGGCTAAGCCCG
Found at i:22807 original size:22 final size:22
Alignment explanation
Indices: 22782--22827 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
22772 GTCTGCATGC
22782 ATCATAATCTTAATATGCCATA
1 ATCATAATCTTAATATGCCATA
22804 ATCATAATCTTAATATGCCATA
1 ATCATAATCTTAATATGCCATA
22826 AT
1 AT
22828 TTTTACGAAT
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:0.41, C:0.17, G:0.04, T:0.37
Consensus pattern (22 bp):
ATCATAATCTTAATATGCCATA
Found at i:25488 original size:15 final size:16
Alignment explanation
Indices: 25455--25494 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
25445 TTACTTTGCT
25455 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
25471 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
25486 TTGCTTTCT
1 TTGTTTTCT
25495 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:29272 original size:15 final size:15
Alignment explanation
Indices: 29252--29281 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29242 AAAAGTATGT
29252 GATTTGTGTTACAGG
1 GATTTGTGTTACAGG
29267 GATTTGTGTTACAGG
1 GATTTGTGTTACAGG
29282 AGGTGGCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (15 bp):
GATTTGTGTTACAGG
Found at i:37395 original size:34 final size:34
Alignment explanation
Indices: 37357--37425 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
37347 CCGAGTGAGT
37357 GGTGTTTTTCATTGCTTTAGCCTCTACCCATTTG
1 GGTGTTTTTCATTGCTTTAGCCTCTACCCATTTG
*
37391 GGTGTTTTTCATTGCTTTAGGCTCTACCCATTTG
1 GGTGTTTTTCATTGCTTTAGCCTCTACCCATTTG
37425 G
1 G
37426 TAAAGTAGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (34 bp):
GGTGTTTTTCATTGCTTTAGCCTCTACCCATTTG
Found at i:43324 original size:22 final size:21
Alignment explanation
Indices: 43272--43325 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
43262 GCTTCTTGGA
43272 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
43293 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
43312 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
43326 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:44178 original size:18 final size:18
Alignment explanation
Indices: 44155--44191 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44145 CTCCTCCATC
*
44155 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
*
44173 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTCTTTTT
44191 A
1 A
44192 ATTACCCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:46512 original size:21 final size:23
Alignment explanation
Indices: 46481--46524 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
46471 CAGAGATTTT
*
46481 TTTTGTTTTTTT-GAAAACGCAA
1 TTTTGTTTTTTTCAAAAACGCAA
46503 TTTT-TTTTTTTCAAAAACGCAA
1 TTTTGTTTTTTTCAAAAACGCAA
46525 AAACTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (23 bp):
TTTTGTTTTTTTCAAAAACGCAA
Found at i:48191 original size:22 final size:21
Alignment explanation
Indices: 48139--48192 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
48129 GCTTCTTGGA
48139 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
48160 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
48179 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
48193 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:50292 original size:12 final size:13
Alignment explanation
Indices: 50275--50303 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
50265 TTAATCTAAC
50275 TTTTTTC-TCTCT
1 TTTTTTCTTCTCT
50287 TTTTTTCTTCTCT
1 TTTTTTCTTCTCT
50300 TTTT
1 TTTT
50304 CCTTTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTCTTCTCT
Found at i:51598 original size:11 final size:11
Alignment explanation
Indices: 51577--51610 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
51567 TTTTCAACTT
51577 AGTGAATGAGAG
1 AGTG-ATGAGAG
51589 AGTGATGAGAG
1 AGTGATGAGAG
*
51600 AGAGATGAGAG
1 AGTGATGAGAG
51611 TCTGTTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (11 bp):
AGTGATGAGAG
Found at i:53433 original size:27 final size:27
Alignment explanation
Indices: 53369--53522 Score: 156
Period size: 26 Copynumber: 5.7 Consensus size: 27
53359 AGTGGACTTA
* * *
53369 AAATGACCAAAGTGCCCCTGAACT-T-A
1 AAATGACTAAAATGCCCCTGAA-TGTGC
*
53395 AAATGACCAAAATGCCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
53422 AAATGACTAAAATGCCCCTGAATGTGC
1 AAATGACTAAAATGCCCCTGAATGTGC
*
53449 AAATGACT-AAA-GCCCCCTTAATGTGC
1 AAATGACTAAAATG-CCCCTGAATGTGC
* *
53475 AAATGACTAAAACTGCCCCTAGATTTTG-
1 AAATGACTAAAA-TGCCCCT-GAATGTGC
*
53503 AAGATGACTGAAATGCCCCT
1 AA-ATGACTAAAATGCCCCT
53523 AGTTGATCCT
Statistics
Matches: 112, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
25 2 0.02
26 45 0.40
27 37 0.33
28 14 0.12
29 14 0.12
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAATGTGC
Found at i:63406 original size:22 final size:21
Alignment explanation
Indices: 63378--63431 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
63368 AAAGTTCATG
63378 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
63400 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
63419 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
63432 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:68299 original size:15 final size:16
Alignment explanation
Indices: 68270--68299 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
68260 GTATGGATTC
68270 AAATTGATCTTTTAAA
1 AAATTGATCTTTTAAA
68286 AAATTGAT-TTTTAA
1 AAATTGATCTTTTAA
68300 CTAACACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (16 bp):
AAATTGATCTTTTAAA
Found at i:68595 original size:22 final size:21
Alignment explanation
Indices: 68567--68620 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
68557 GAAATTCCTG
68567 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
68589 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
68608 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
68621 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Done.