Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018176.1 Corchorus olitorius cultivar O-4 contig18209, 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: 71973
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:612 original size:334 final size:333
Alignment explanation
Indices: 2--1477 Score: 1757
Period size: 334 Copynumber: 4.5 Consensus size: 333
1 G
* * *
2 TTTCGATTTAATCCGAAATTAATTCAGATAAAATTGGAAAAATGATATTGGAAGCGTGAAAAGTT
1 TTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACGATATTGGAAGCGTGAAAAGCT
* * *
67 CTTCACTCTTTTTGTCGTAGAATTATATATATTTTATGAGTATTGTGGCTAAAAATTTAGGTAAA
66 CTTCATTCTTTTTGTCGTAGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTTAGGAAAA
* *
132 ATCTTTTGGGTCAATTTTTTGCAAAAATTATAGCCGAAATCGAATACTAACCATCACAGTTTTTG
131 ATCTTTCGGGTCAATTTTTTGCAAAATTTA-AGCCGAAATCGAATACTAACCATCACAGTTTTTG
* * *
197 GCTAAAAAACGCGTCCCGGGGCCCCAACTCAGTTTTGCATGATTTTTGCCGCTATGACTCCTTGA
195 GCTAAAAAACGCGTCCCGGGACCCCAACTCAGTTTTGCATGATTTTTGCCGCCAAGACTCCTTGA
*
262 AATATCTATATTCATCTAAACAAATCTCCGCCAGATTGCATTTAAGGATTTGTTTTTACGAGCAT
260 AATATCTATATTCATCTAAACAAATCTCCGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCAT
327 CTAAATCAT
325 CTAAATCAT
* *
336 ATTTCGATTTAATCAGAAATTAATTCATATAAAATTGGAAAAACTATATTGGAAGCGTGAAAAGC
1 -TTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACGATATTGGAAGCGTGAAAAGC
* **
401 TCTTCATTCTTTTTGTCGTAGAATTATATATTTTTT-TGAGTATTGTTGCTCTAAATTTAGGAAA
65 TCTTCATTCTTTTTGTCGTAGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTTAGGAAA
* * **
465 AATCTTTCGTGTCAATTTTTTTGCAAAATTTAAGCCGATATCGTGTACTAACCATCACAGTTTTT
130 AATCTTTCGGGTCAA-TTTTTTGCAAAATTTAAGCCGAAATCGAATACTAACCATCACAGTTTTT
* * ** *** * * *
530 GGCTAAAAAACGTGTTCTTGGACCCCGGTTCAGTTTTGCATAATTTTTGACACCAAGACTCCTTG
194 GGCTAAAAAACGCGTCCCGGGACCCCAACTCAGTTTTGCATGATTTTTGCCGCCAAGACTCCTTG
* * * * *
595 AAATATCTATATTCATCTAACCAAATCTCTGCAATG-TTGGATTTAAGAATTCGTTTTTACGAGC
259 AAATATCTATATTCATCTAAACAAATCTCCGCCA-GATTGGATTTAAGGATTTGTTTTTACGAGC
659 ATCTAAATCAT
323 ATCTAAATCAT
* * * *
670 GTTTAGATTTAATCAGAAATTAATTCAGATAAAATTGGAAGAACAATATTGGAAGCATGAAAAGC
1 -TTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACGATATTGGAAGCGTGAAAAGC
* *
735 TCTTCATTATTTTTGTCGTAGAATTATATATTTTTTATAAGTATCT-TGGCTAAAAATTTAGGAA
65 TCTTCATTCTTTTTGTCGTAGAATTATATATTTTTTATGAGTAT-TGTGGCTAAAAATTTAGGAA
* * *
799 AAATATTTCGGGTCAATTTATTGCAAAATTGT-AGCCGAAATTGAATACTAACCATCACAGTTTT
129 AAATCTTTCGGGTCAATTTTTTGCAAAATT-TAAGCCGAAATCGAATACTAACCATCACAGTTTT
* * * *
863 TGGCTAAAAAACGCGTCCCGGGGCCCCAACTCAGTTTTGTATGATTTTTGCCGCTATGACTCCTT
193 TGGCTAAAAAACGCGTCCCGGGACCCCAACTCAGTTTTGCATGATTTTTGCCGCCAAGACTCCTT
* * * *
928 CAAATATCTTTATTCATCTAAACAAATCTCCGCCAGATTGGATTTAAAGATTTCTTTTTACGAGC
258 GAAATATCTATATTCATCTAAACAAATCTCCGCCAGATTGGATTTAAGGATTTGTTTTTACGAGC
* *
993 ATTTGAATCAT
323 ATCTAAATCAT
* * * *
1004 TATTCGATTTAATTAGAAATTAGTTCAGATAAAATTGGGAAAACGATATTGGAAGCGTGAAAAGT
1 T-TTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACGATATTGGAAGCGTGAAAAGC
* * * *
1069 TCTTCATTTTTTTTGGCATTA-AATTATATATTTTTTATGAGTATTGTGGCTAAAAATTTAAGAA
65 TCTTCATTCTTTTTGTC-GTAGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTTAGGAA
* * * *
1133 AAATC-TTCAGGTCAA-TTTTTGCAAAATTTTAA-CCGAAATCG--T-GT-A-CTTCACGGTTTT
129 AAATCTTTCGGGTCAATTTTTTGCAAAA-TTTAAGCCGAAATCGAATACTAACCATCACAGTTTT
* * * * *** * * * **
1190 TTGCT-AAAAACGCGT-TCTGAAGTGTCGACTCAATTTTGCATGATTTTTGGCGCCAAGACTAAT
193 TGGCTAAAAAACGCGTCCCGGGA-CCCCAACTCAGTTTTGCATGATTTTTGCCGCCAAGACTCCT
** ** * *
1253 TGAAATATCTATATTCATCTAATTAAATCTTAGCCACATTGGATTGAAGGATTTGTTTTTACGAG
257 TGAAATATCTATATTCATCTAAACAAATCTCCGCCAGATTGGATTTAAGGATTTGTTTTTACGAG
* * *
1318 CATCAGAAACCGGT
322 CATC-TAAATC-AT
* * * * ** * * *
1332 TTT-GATATAATTAGAAATTAATTC-GAAAAAATAGGAAAAACGATATTATAAGCGTAAAAATCC
1 TTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACGATATTGGAAGCGTGAAAAGCT
* * * * * *
1395 CTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGACTAAAAATTGA-GAAAA
66 CTTCATTCTTTTTGTCGTAGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTTAGGAAAA
* *
1459 ATCATTC-GGTCAATCTTTT
131 ATCTTTCGGGTCAATTTTTT
1478 AAATTTTTAA
Statistics
Matches: 976, Mismatches: 148, Indels: 44
0.84 0.13 0.04
Matches are distributed among these distances:
324 15 0.02
325 90 0.09
326 117 0.12
327 19 0.02
328 3 0.00
329 1 0.00
330 1 0.00
332 19 0.02
333 15 0.02
334 548 0.56
335 147 0.15
336 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (333 bp):
TTTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACGATATTGGAAGCGTGAAAAGCT
CTTCATTCTTTTTGTCGTAGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTTAGGAAAA
ATCTTTCGGGTCAATTTTTTGCAAAATTTAAGCCGAAATCGAATACTAACCATCACAGTTTTTGG
CTAAAAAACGCGTCCCGGGACCCCAACTCAGTTTTGCATGATTTTTGCCGCCAAGACTCCTTGAA
ATATCTATATTCATCTAAACAAATCTCCGCCAGATTGGATTTAAGGATTTGTTTTTACGAGCATC
TAAATCAT
Found at i:3100 original size:42 final size:42
Alignment explanation
Indices: 3027--3107 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
3017 GTTGATGGAG
* * * *
3027 TTGCTCCTCACCATCGGTACTAACTTCTTTGTCCTGATGTAA
1 TTGCTCCTCACCATCGATACCAACATCTTTGTCCCGATGTAA
*
3069 TTGCTCGTCACCATCGATACCAATCAT-TTTGTCCCGATG
1 TTGCTCCTCACCATCGATACCAA-CATCTTTGTCCCGATG
3108 GAAAGCGTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.36
Consensus pattern (42 bp):
TTGCTCCTCACCATCGATACCAACATCTTTGTCCCGATGTAA
Found at i:3119 original size:15 final size:15
Alignment explanation
Indices: 3099--3168 Score: 79
Period size: 15 Copynumber: 4.6 Consensus size: 15
3089 CAATCATTTT
3099 GTCCCGATGGAAAGC
1 GTCCCGATGGAAAGC
3114 GTCCCGATGGAAAGC
1 GTCCCGATGGAAAGC
*
3129 GTCCTGAT-GATAAGTC
1 GTCCCGATGGA-AAG-C
* * *
3145 ATCCTGATGGAAAGT
1 GTCCCGATGGAAAGC
3160 GTCCCGATG
1 GTCCCGATG
3169 ATATAAGTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
14 2 0.04
15 32 0.68
16 11 0.23
17 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (15 bp):
GTCCCGATGGAAAGC
Found at i:5460 original size:179 final size:181
Alignment explanation
Indices: 5157--5489 Score: 634
Period size: 179 Copynumber: 1.8 Consensus size: 181
5147 GATCCGGACA
5157 ATGAAAAGGTGAGATGTTGGTGCTAAATGCCATGGACAGGTCCCAACATCCACTCCATCATCTAC
1 ATGAAAAGGTGAGATGTTGGTGCTAAATGCCATGGACAGGTCCCAACATCCACTCCA-CATCTAC
*
5222 CAAATGCTCCAAATTCTAATTGGTTTGGGATAATGCTTTACCCTGCACTAGATTGATTTCAGGTA
65 CAAATGCTCCAAATTCTAATTGGTTTGGGATAATGCTTTACCCTGCACTAGATTGATTTCAGGAA
5287 CCAACCTATTTATACAAAAATATAAATTCTAATGCTCCAAATTCTAATTGCC
130 CCAACCTATTTATACAAAAATATAAATTCTAATGCTCCAAATTCTAATTGCC
5339 ATGAAAAGGTGAGATGTTGGTGCTAAATGCCATGGACAGGTCCCAACATCCACT-C-CATCTACC
1 ATGAAAAGGTGAGATGTTGGTGCTAAATGCCATGGACAGGTCCCAACATCCACTCCACATCTACC
5402 AAATGCTCCAAATTCTAATTGGTTTGGGATAATGCTTTACCCTGCACTAGATTGATTTCAGGAAC
66 AAATGCTCCAAATTCTAATTGGTTTGGGATAATGCTTTACCCTGCACTAGATTGATTTCAGGAAC
5467 CAACCTATTTATACAAAAATATA
131 CAACCTATTTATACAAAAATATA
5490 TCTATATATA
Statistics
Matches: 150, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
179 95 0.63
181 1 0.01
182 54 0.36
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (181 bp):
ATGAAAAGGTGAGATGTTGGTGCTAAATGCCATGGACAGGTCCCAACATCCACTCCACATCTACC
AAATGCTCCAAATTCTAATTGGTTTGGGATAATGCTTTACCCTGCACTAGATTGATTTCAGGAAC
CAACCTATTTATACAAAAATATAAATTCTAATGCTCCAAATTCTAATTGCC
Found at i:29211 original size:21 final size:20
Alignment explanation
Indices: 29163--29211 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
29153 TGTTTCCCAT
*
29163 ATATATATATAACGATAAAA
1 ATATATATATAAAGATAAAA
*
29183 ATAGTATATATAAAGCATGAAA
1 ATA-TATATATAAAG-ATAAAA
*
29205 TTATATA
1 ATATATA
29212 AGAGCGCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 14 0.58
22 7 0.29
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (20 bp):
ATATATATATAAAGATAAAA
Found at i:30379 original size:4 final size:4
Alignment explanation
Indices: 30370--30401 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
30360 ATAATGAGTA
30370 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
30402 ATTCCTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:48279 original size:48 final size:48
Alignment explanation
Indices: 48204--48312 Score: 184
Period size: 48 Copynumber: 2.3 Consensus size: 48
48194 ATCTATAATC
*
48204 TCTTTAATTCCCCAATTTAGAATCTTTTAGGTTTAATTGATCATGGTT
1 TCTTTAATTCCCAAATTTAGAATCTTTTAGGTTTAATTGATCATGGTT
*
48252 T-TTGTAATTCTCAAATTTAGAATCTTTTAGGTTTAATTGATCATGGTT
1 TCTT-TAATTCCCAAATTTAGAATCTTTTAGGTTTAATTGATCATGGTT
48300 TCTTTAATTCCCA
1 TCTTTAATTCCCA
48313 TTAGGAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
47 2 0.04
48 52 0.93
49 2 0.04
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.49
Consensus pattern (48 bp):
TCTTTAATTCCCAAATTTAGAATCTTTTAGGTTTAATTGATCATGGTT
Found at i:64648 original size:24 final size:23
Alignment explanation
Indices: 64613--64658 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
64603 TTTAAATATT
64613 TTTTAAAATAAA-CTTTGAAAAA
1 TTTTAAAATAAATCTTTGAAAAA
*
64635 TTTTAAAACTTAAATTTTTGAAAA
1 TTTTAAAA--TAAATCTTTGAAAA
64659 CATATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
24 4 0.20
25 8 0.40
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (23 bp):
TTTTAAAATAAATCTTTGAAAAA
Found at i:65381 original size:4 final size:4
Alignment explanation
Indices: 65372--65398 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
65362 TTTTGCTTAA
65372 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
65399 TTTAAGGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:66016 original size:19 final size:21
Alignment explanation
Indices: 65986--66049 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
65976 TTGACACTGT
*
65986 TTAGCAACTGTACAGATGAGA
1 TTAGCTACTGTACAGATGAGA
* *
66007 TTA-C-ACTGTACATATTAGA
1 TTAGCTACTGTACAGATGAGA
*
66026 TTAGCTACTGTATAGATGAGA
1 TTAGCTACTGTACAGATGAGA
66047 TTA
1 TTA
66050 TTAGAGCAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.44
20 2 0.06
21 18 0.50
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (21 bp):
TTAGCTACTGTACAGATGAGA
Found at i:67799 original size:19 final size:20
Alignment explanation
Indices: 67775--67832 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 20
67765 ATGTTTGGCA
67775 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* * *
67794 ACTGTACATATTAGATTAGGT
1 ACTGTACAGATGAGATTA-GC
67815 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
67833 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:68167 original size:14 final size:15
Alignment explanation
Indices: 68149--68189 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
68139 ATATGTCAAC
68149 ATATACAGAATATAT
1 ATATACAGAATATAT
*
68164 -TATA-AAATATATAT
1 ATATACAGA-ATATAT
68178 ATATACAGAATA
1 ATATACAGAATA
68190 AAAAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 6
0.72 0.07 0.21
Matches are distributed among these distances:
13 2 0.10
14 10 0.48
15 7 0.33
16 2 0.10
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (15 bp):
ATATACAGAATATAT
Done.