Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013783.1 Corchorus olitorius cultivar O-4 contig13816, 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: 24636
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:67 original size:31 final size:30
Alignment explanation
Indices: 32--105 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
22 TTATAAATTT
* *
32 GGACTCAATTGAC-CCAATTTGATAGGTAAAG
1 GGACTCAATTGACACAAATTTCA-A-GTAAAG
*
63 GGACTCAATTGACATCAAATTTCAAGTAGAG
1 GGACTCAATTGACA-CAAATTTCAAGTAAAG
94 GGACTCAATTGA
1 GGACTCAATTGA
106 TAGTTTTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 30 0.79
32 1 0.03
33 7 0.18
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (30 bp):
GGACTCAATTGACACAAATTTCAAGTAAAG
Found at i:148 original size:27 final size:29
Alignment explanation
Indices: 89--148 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
79 AAATTTCAAG
*
89 TAGAGGGACTCAATTGATAGTTTTTGTAA
1 TAGAGGGACTCAATTGAGAGTTTTTGTAA
118 TAGAGGGA-TCAAATTGAGA-TTTTTGT-A
1 TAGAGGGACTC-AATTGAGAGTTTTTGTAA
145 TAGA
1 TAGA
149 TAAAAGGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 5 0.17
28 9 0.31
29 15 0.52
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (29 bp):
TAGAGGGACTCAATTGAGAGTTTTTGTAA
Found at i:1182 original size:20 final size:20
Alignment explanation
Indices: 1157--1195 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1147 TTTTGTTTGG
1157 CCATAAGCCCATCTCTCATT
1 CCATAAGCCCATCTCTCATT
1177 CCATAAGCCCATCTCTCAT
1 CCATAAGCCCATCTCTCAT
1196 ATCTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.41, G:0.05, T:0.28
Consensus pattern (20 bp):
CCATAAGCCCATCTCTCATT
Found at i:1288 original size:13 final size:13
Alignment explanation
Indices: 1272--1315 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
1262 GAAATTGAAG
1272 CGAAGACTGAAAA
1 CGAAGACTGAAAA
* *
1285 CGAAGATTG-AAC
1 CGAAGACTGAAAA
1297 CGAAGACTGAAAA
1 CGAAGACTGAAAA
1310 CGAAGA
1 CGAAGA
1316 AAATGCTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.50, C:0.16, G:0.25, T:0.09
Consensus pattern (13 bp):
CGAAGACTGAAAA
Found at i:1294 original size:25 final size:25
Alignment explanation
Indices: 1265--1315 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1255 AAAGCCGGAA
*
1265 ATTGAAGCGAAGACTGAAAACGAAG
1 ATTGAACCGAAGACTGAAAACGAAG
1290 ATTGAACCGAAGACTGAAAACGAAG
1 ATTGAACCGAAGACTGAAAACGAAG
1315 A
1 A
1316 AAATGCTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.25, T:0.12
Consensus pattern (25 bp):
ATTGAACCGAAGACTGAAAACGAAG
Found at i:1300 original size:12 final size:12
Alignment explanation
Indices: 1267--1315 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
1257 AGCCGGAAAT
*
1267 TGAAGCGAAGAC
1 TGAAACGAAGAC
*
1279 TGAAAACGAAGAT
1 TG-AAACGAAGAC
*
1292 TGAACCGAAGAC
1 TGAAACGAAGAC
1304 TGAAAACGAAGA
1 TG-AAACGAAGA
1316 AAATGCTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 12 0.40
13 18 0.60
ACGTcount: A:0.49, C:0.14, G:0.27, T:0.10
Consensus pattern (12 bp):
TGAAACGAAGAC
Found at i:7135 original size:2 final size:2
Alignment explanation
Indices: 7128--7152 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7118 TTGCAAAATT
7128 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
7153 CACGTGATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13058 original size:54 final size:52
Alignment explanation
Indices: 12926--13477 Score: 423
Period size: 54 Copynumber: 10.3 Consensus size: 52
12916 TTCAAACTTG
* * * **
12926 AACTTCTTAAATAACCGCACTAGATCATTTAAGATGCAAC-CTCGATCA-CGGAA
1 AACTTCTTGAATGACCGCACTGGATCATTGGAGAT-CAACTCT-GATCATC-GAA
* * ** *
12979 ACCTTTCTTGGAGTGACCATACTGGATCAAATTGGAGATCAACTCTGATCATCGGA
1 AAC-TTCTT-GAATGACCGCACTGGATC--ATTGGAGATCAACTCTGATCATCGAA
* * *
13035 AACTTCTTGAAGGACCACACTGGATCATCTGGAGATCAACTCTGATCTTCGAA
1 AACTTCTTGAATGACCGCACTGGATCAT-TGGAGATCAACTCTGATCATCGAA
** * * *
13088 AACTTCTTGAAATGACCATACCGGATCATCTGAAGATCAACTCTGATCTTCGAA
1 AACTTCTTG-AATGACCGCACTGGATCAT-TGGAGATCAACTCTGATCATCGAA
* * ** * * * *
13142 AATTTCTTGAAACGATAGCACCGGATCATCTGGAGATCAACTTTGATCTTTGAA
1 AACTTCTTG-AATGACCGCACTGGATCAT-TGGAGATCAACTCTGATCATCGAA
* * * *
13196 AACTTCTAGGAA-GAACCGCACTGGACCTTTTGGAGATCAACTCTGATCATCAAA
1 AACTTCT-TGAATG-ACCGCACTGGATC-ATTGGAGATCAACTCTGATCATCGAA
* *
13250 AACTTCTTGGAATGACCGCACGGGATCATCT-GAGGATCAACTCTAATCAT--AA
1 AACTTCTT-GAATGACCGCACTGGATCAT-TGGA-GATCAACTCTGATCATCGAA
* * * * *
13302 AACTTCTTGGAATGACCGCACTGGATCTTTGGTGATCAACTCTGACCATTGCA
1 AACTTCTT-GAATGACCGCACTGGATCATTGGAGATCAACTCTGATCATCGAA
* * * * * * *
13355 AACTTCTTGGAATAACCGCACTAGACCTTTTGGGGATCAACTCTGACCATTGAA
1 AACTTCTT-GAATGACCGCACTGGATC-ATTGGAGATCAACTCTGATCATCGAA
* * *
13409 AACTTCTTGGAATGACCGCACTGGATCTTTTGGAGATCAACTCTGACCATTGAA
1 AACTTCTT-GAATGACCGCACTGGATC-ATTGGAGATCAACTCTGATCATCGAA
13463 AACTTCTTGGAATGA
1 AACTTCTT-GAATGA
13478 GATCAACTCT
Statistics
Matches: 420, Mismatches: 60, Indels: 37
0.81 0.12 0.07
Matches are distributed among these distances:
51 15 0.04
52 32 0.08
53 62 0.15
54 268 0.64
55 20 0.05
56 13 0.03
57 10 0.02
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (52 bp):
AACTTCTTGAATGACCGCACTGGATCATTGGAGATCAACTCTGATCATCGAA
Found at i:13415 original size:213 final size:215
Alignment explanation
Indices: 13010--13477 Score: 543
Period size: 213 Copynumber: 2.2 Consensus size: 215
13000 CTGGATCAAA
* * *
13010 TTGGAGATCAACTCTGATCATCGGAAACTTCTT-GAAGGACCACACTGGATCATCTGGAGATCAA
1 TTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCACACGGGATCATCTGGAGATCAA
* * * *
13074 CTCTGATCTTCGAAAACTTCTTGAAATGACCATACCGGATCATCTGAAGATCAACTCTGATCTTC
66 CTCTAATCATC-AAAACTTCTTGAAATGACCACACCGGATCATCTGAAGATCAACTCTGACCTTC
* * * * * * * *
13139 GAAAATTTCTTGAAACGATAGCACCGGATCATCTGGAGATCAACTTTGATCTTTGAAAACTTCTA
130 GAAAACTTCTTGAAACAACAGCACCAGACCATCTGGAGATCAACTCTGACCATTGAAAACTTCTA
13204 GGAA-GAACCGCACTGGACCTT
195 GGAATG-ACCGCACTGGACCTT
* *
13225 TTGGAGATCAACTCTGATCATCAAAAACTTCTTGGAATGACCGCACGGGATCATCT-GAGGATCA
1 TTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCACACGGGATCATCTGGA-GATCA
* * * * **
13289 ACTCTAATCAT-AAAACTTCTTGGAATGACCGCACTGGATC-TTTGGTGATCAACTCTGACCATT
65 ACTCTAATCATCAAAACTTCTTGAAATGACCACACCGGATCATCTGAAGATCAACTCTGACC-TT
* * * * * * * *
13352 -GCAAACTTCTTGGAATAACCGCACTAGACCTTTTGGGGATCAACTCTGACCATTGAAAACTTCT
129 CGAAAACTTCTTGAAACAACAGCACCAGACCATCTGGAGATCAACTCTGACCATTGAAAACTTCT
* *
13416 TGGAATGACCGCACTGGATCTT
194 AGGAATGACCGCACTGGACCTT
* *
13438 TTGGAGATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 TTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAATGA
13478 GATCAACTCT
Statistics
Matches: 213, Mismatches: 36, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
213 119 0.56
214 28 0.13
215 33 0.15
216 33 0.15
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (215 bp):
TTGGAGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCACACGGGATCATCTGGAGATCAA
CTCTAATCATCAAAACTTCTTGAAATGACCACACCGGATCATCTGAAGATCAACTCTGACCTTCG
AAAACTTCTTGAAACAACAGCACCAGACCATCTGGAGATCAACTCTGACCATTGAAAACTTCTAG
GAATGACCGCACTGGACCTT
Found at i:13472 original size:108 final size:108
Alignment explanation
Indices: 12983--13477 Score: 520
Period size: 108 Copynumber: 4.6 Consensus size: 108
12973 ACGGAAACCT
* ** * * * *
12983 TTCTTGGAGTGACCATACTGGATCAAATTGGAGATCAACTCTGATCATCGGAAACTTCTT-GAAG
1 TTCTTGGAATGACCGCACTGGATC-ATTTGGAGATCAACTCTGATCATTGAAAACTTCTTGGAAT
*
13047 GACCACACTGGATCATCTGGAGATCAACTCTGATC-TTCGAAAAC
65 GACCGCACTGGATCATCTGGAGATCAACTCTGATCATT-GAAAAC
* ** * * * * * *
13091 TTCTTGAAATGACCATACCGGATCATCTGAAGATCAACTCTGATC-TTCGAAAATTTCTTGAAAC
1 TTCTTGGAATGACCGCACTGGATCATTTGGAGATCAACTCTGATCATT-GAAAACTTCTTGGAAT
** * * *
13155 GATAGCACCGGATCATCTGGAGATCAACTTTGATCTTTGAAAAC
65 GACCGCACTGGATCATCTGGAGATCAACTCTGATCATTGAAAAC
* * * **
13199 TTCTAGGAA-GAACCGCACTGGACCTTTTGGAGATCAACTCTGATCATCAAAAACTTCTTGGAAT
1 TTCTTGGAATG-ACCGCACTGGATCATTTGGAGATCAACTCTGATCATTGAAAACTTCTTGGAAT
* *
13263 GACCGCACGGGATCATCT-GAGGATCAACTCTAATCA-T-AAAAC
65 GACCGCACTGGATCATCTGGA-GATCAACTCTGATCATTGAAAAC
* * * *
13305 TTCTTGGAATGACCGCACTGGATC-TTTGGTGATCAACTCTGACCATTGCAAACTTCTTGGAATA
1 TTCTTGGAATGACCGCACTGGATCATTTGGAGATCAACTCTGATCATTGAAAACTTCTTGGAATG
* * * * * *
13369 ACCGCACTAGACCTTTTGGGGATCAACTCTGACCATTGAAAAC
66 ACCGCACTGGATCATCTGGAGATCAACTCTGATCATTGAAAAC
* *
13412 TTCTTGGAATGACCGCACTGGATCTTTTGGAGATCAACTCTGACCATTGAAAACTTCTTGGAATG
1 TTCTTGGAATGACCGCACTGGATCATTTGGAGATCAACTCTGATCATTGAAAACTTCTTGGAATG
13477 A
66 A
13478 GATCAACTCT
Statistics
Matches: 321, Mismatches: 55, Indels: 22
0.81 0.14 0.06
Matches are distributed among these distances:
105 59 0.18
106 28 0.09
107 61 0.19
108 170 0.53
109 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (108 bp):
TTCTTGGAATGACCGCACTGGATCATTTGGAGATCAACTCTGATCATTGAAAACTTCTTGGAATG
ACCGCACTGGATCATCTGGAGATCAACTCTGATCATTGAAAAC
Found at i:13485 original size:35 final size:35
Alignment explanation
Indices: 13441--14211 Score: 940
Period size: 35 Copynumber: 21.3 Consensus size: 35
13431 GGATCTTTTG
* ** *
13441 GAGATCAACTCTGACCATTGAAAACTTCTTGGAAT
1 GAGATCAACTCTGATCATAAAAAACTTCTTGAAAT
13476 GAGATCAACTCTGATCATAAAAAAAAACTTCTTGAAAT
1 GAGATCAACTCTGATCAT---AAAAAACTTCTTGAAAT
*
13514 GAGATCAACTCTGATCATCAAAAACTTCTTGAAATT
1 GAGATCAACTCTGATCATAAAAAACTTCTTGAAA-T
* *
13550 AACGAGATC-ACTCTGATCATCAAAAACTTCTTGAAAG
1 ---GAGATCAACTCTGATCATAAAAAACTTCTTGAAAT
*
13587 GAGATCAACTCTGATCATAAAAAACTTCTTGAAAC
1 GAGATCAACTCTGATCATAAAAAACTTCTTGAAAT
**
13622 GAGATCAACTCTGATCATCGAAAACTTCTT-AGAAT
1 GAGATCAACTCTGATCATAAAAAACTTCTTGA-AAT
**
13657 GAGATCAACTCTGATCATCGAAAACTTCTTGAAAT
1 GAGATCAACTCTGATCATAAAAAACTTCTTGAAAT
*
13692 GAGATCAACTCTGATCA-ACGAAAACTTCTTGAAA-
1 GAGATCAACTCTGATCATA-AAAAACTTCTTGAAAT
*
13726 GAAGATCAACTCTGATCATAAAAAACTTCTTGGAAT
1 G-AGATCAACTCTGATCATAAAAAACTTCTTGAAAT
* *
13762 GAGATCAACTCTGATCATAAAAAAAAATTTCTTGAAAC
1 GAGATCAACTCTGATCAT---AAAAAACTTCTTGAAAT
*
13800 GAGATCAACTCTGATCATCAAAAAAAAAACTTCTTGAAAC
1 GAGATCAACTCTGATCAT-----AAAAAACTTCTTGAAAT
* *
13840 GAGATCAACTCTGATCAATAAAAAAAATTCTTGAAAG
1 GAGATCAACTCTGATC-AT-AAAAAACTTCTTGAAAT
*
13877 GAGATCAACTCTGATCATAAAAAAAACCTTCTTGAAAG
1 GAGATCAACTCTGATCAT--AAAAAA-CTTCTTGAAAT
* *
13915 GNGATCAACTCTGATCATAAAAAACTTCTTGAAAC
1 GAGATCAACTCTGATCATAAAAAACTTCTTGAAAT
*
13950 GAGATCAACTCTGATCATAAAAAAAGCTTCTTGAAAG
1 GAGATCAACTCTGATCAT-AAAAAA-CTTCTTGAAAT
**
13987 GAGATCAACTCTGATCATCGAAAACTTCTTGAAAT
1 GAGATCAACTCTGATCATAAAAAACTTCTTGAAAT
* * *
14022 GAGATCAACTTTGATCA-ACGAAAACTTCTTGAAAG
1 GAGATCAACTCTGATCATA-AAAAACTTCTTGAAAT
*
14057 GAGATCAACTCTGATCATAAAAAACTTCTTGGAAT
1 GAGATCAACTCTGATCATAAAAAACTTCTTGAAAT
*
14092 GAGATCAACTCTGATCATAAAAAAAACTTCTTGAAAC
1 GAGATCAACTCTGATCAT--AAAAAACTTCTTGAAAT
*
14129 GAGATCAACTCTGATCATAAAAAAAACTTCTTGAAAC
1 GAGATCAACTCTGATCAT--AAAAAACTTCTTGAAAT
*
14166 GAGATCAACTCTGATCATAAAAAAACTTCTTGAAAG
1 GAGATCAACTCTGATCAT-AAAAAACTTCTTGAAAT
14202 GAGATCAACT
1 GAGATCAACT
14212 TAGATCTCTG
Statistics
Matches: 670, Mismatches: 38, Indels: 55
0.88 0.05 0.07
Matches are distributed among these distances:
34 8 0.01
35 314 0.47
36 50 0.07
37 137 0.20
38 118 0.18
39 6 0.01
40 35 0.05
41 2 0.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (35 bp):
GAGATCAACTCTGATCATAAAAAACTTCTTGAAAT
Found at i:15419 original size:39 final size:40
Alignment explanation
Indices: 15346--15421 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
15336 TTGAAAAACA
* ** *
15346 TTTTTCTTTTGAAAAGATTGCACTTTGAGGGAAAAAAGTC
1 TTTTTATTTTGAAAAGATCACACTTTGAGAGAAAAAAGTC
*
15386 TTTTTATTTTGAAAAGATCACAGTTTGA-AGAAAAAA
1 TTTTTATTTTGAAAAGATCACACTTTGAGAGAAAAAA
15422 AAAATTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 7 0.23
40 24 0.77
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (40 bp):
TTTTTATTTTGAAAAGATCACACTTTGAGAGAAAAAAGTC
Found at i:15651 original size:26 final size:27
Alignment explanation
Indices: 15600--15666 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 27
15590 TCCCTTCCTC
*
15600 CATCTTTTGCATTTTCAACTTCTTTCTT
1 CATCTTTT-CTTTTTCAACTTCTTTCTT
*
15628 -TTCTTTTCTTTTTCAA-TTCTTTTCTT
1 CATCTTTTCTTTTTCAACTTC-TTTCTT
15654 CAT-TTTTCTTTTT
1 CATCTTTTCTTTTT
15667 TTCTTTCCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 3 0.09
26 24 0.71
27 7 0.21
ACGTcount: A:0.10, C:0.21, G:0.01, T:0.67
Consensus pattern (27 bp):
CATCTTTTCTTTTTCAACTTCTTTCTT
Found at i:19471 original size:29 final size:30
Alignment explanation
Indices: 19425--19485 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
19415 CCAAATCCAA
* *
19425 AATAAGAAAAAAAACTTTAATCTGAATTAT
1 AATAAGAAAAAAAACTTTAATCTAAATAAT
19455 AATAA-AAAAAAAACTTTAATCTAAATAAT
1 AATAAGAAAAAAAACTTTAATCTAAATAAT
19484 AA
1 AA
19486 CCAAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (30 bp):
AATAAGAAAAAAAACTTTAATCTAAATAAT
Found at i:19491 original size:29 final size:29
Alignment explanation
Indices: 19431--19496 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
19421 CCAAAATAAG
* * *
19431 AAAAAAAACTTTAATCTGAATTATAATAA
1 AAAAAAAACTTTAATCTAAATAATAACAA
*
19460 AAAAAAAACTTTAATCTAAATAATAACCA
1 AAAAAAAACTTTAATCTAAATAATAACAA
*
19489 AAAGAAAA
1 AAAAAAAA
19497 GATGCTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (29 bp):
AAAAAAAACTTTAATCTAAATAATAACAA
Done.