Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018488.1 Corchorus olitorius cultivar O-4 contig18521, 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: 23314
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:202 original size:18 final size:19
Alignment explanation
Indices: 170--205 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
160 TAACTAGTAA
*
170 TAATAAATAATACTAATAT
1 TAATAAATAACACTAATAT
189 TAAT-AATAACACTAATA
1 TAATAAATAACACTAATA
206 ATTATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATAACACTAATAT
Found at i:264 original size:17 final size:17
Alignment explanation
Indices: 234--267 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
224 TTAATTATAT
**
234 AATAATAATCATCATAA
1 AATAATAAAAATCATAA
251 AATAATAAAAATCATAA
1 AATAATAAAAATCATAA
268 TTTTAAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAATAAAAATCATAA
Found at i:388 original size:34 final size:33
Alignment explanation
Indices: 345--428 Score: 105
Period size: 34 Copynumber: 2.5 Consensus size: 33
335 GCCTTCCGGT
*
345 GGCGCCTCTACCATGGCGGGGGCGCCCCCTAGAG
1 GGCGCCTCTACCATGGCGGGGGCACCCCC-AGAG
** *
379 GGCGCCTCTACCATGGTTGGGGCACCCCCGGAG
1 GGCGCCTCTACCATGGCGGGGGCACCCCCAGAG
* *
412 GGCGTCTCCACCATGGC
1 GGCGCCTCTACCATGGC
429 AGAGCCCGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 17 0.40
34 26 0.60
ACGTcount: A:0.12, C:0.38, G:0.36, T:0.14
Consensus pattern (33 bp):
GGCGCCTCTACCATGGCGGGGGCACCCCCAGAG
Found at i:7326 original size:24 final size:24
Alignment explanation
Indices: 7297--7358 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 24
7287 TCTTTAAAAA
*
7297 AATAATATTAATATTAATATATA-T
1 AATAATATTAATA-TAATATAAATT
7321 AATAATATATAATATAATATAAATT
1 AATAATAT-TAATATAATATAAATT
7346 AATCAA-ATTAATA
1 AAT-AATATTAATA
7359 ATTGTAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
24 21 0.62
25 11 0.32
26 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AATAATATTAATATAATATAAATT
Found at i:7348 original size:15 final size:16
Alignment explanation
Indices: 7298--7348 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 16
7288 CTTTAAAAAA
7298 ATAATATTAATATTAAT
1 ATAATA-TAATATTAAT
7315 ATATATAATAATATATAAT
1 ATA-AT-ATAATAT-TAAT
7334 ATAATATAA-ATTAAT
1 ATAATATAATATTAAT
7349 CAAATTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.13
16 2 0.06
17 7 0.23
18 10 0.32
19 8 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAATATAATATTAAT
Found at i:7515 original size:134 final size:135
Alignment explanation
Indices: 7348--7617 Score: 497
Period size: 134 Copynumber: 2.0 Consensus size: 135
7338 TATAAATTAA
*
7348 TCAAATTAATAATTGTAAATATGTCAAAACTAAGATTTAAAGAAATACGTGAATATAAATATTGA
1 TCAAATTAATAATTGTAAATATGTCAAAACTAAGATTTAAAGAAACACGTGAATATAAATATTGA
7413 GCTATATTTATGACAAGCTTTATTAGTC-ATATTAAATTCAAAGCTTAGCCTAATTCTCACAAAT
66 GCTATATTTATGACAAGCTTTATTAGTCAATATTAAATTCAAAGCTTAGCCTAATTCTCACAAAT
7477 TGTAT
131 TGTAT
*
7482 TCAACTTAATAATTGTAAATATGTCAAAACTAAGATTTAAAGAAACACGTGAATATAAATATTGA
1 TCAAATTAATAATTGTAAATATGTCAAAACTAAGATTTAAAGAAACACGTGAATATAAATATTGA
*
7547 GCTATATTTATGACAAGCTTTATTAGTCATATATTAAATTCAAAGCTTAGCCTAATTCTCGCAAA
66 GCTATATTTATGACAAGCTTTATTAGTCA-ATATTAAATTCAAAGCTTAGCCTAATTCTCACAAA
7612 TTGTAT
130 TTGTAT
7618 GCGCATCTTA
Statistics
Matches: 131, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
134 91 0.69
136 40 0.31
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.36
Consensus pattern (135 bp):
TCAAATTAATAATTGTAAATATGTCAAAACTAAGATTTAAAGAAACACGTGAATATAAATATTGA
GCTATATTTATGACAAGCTTTATTAGTCAATATTAAATTCAAAGCTTAGCCTAATTCTCACAAAT
TGTAT
Found at i:8749 original size:211 final size:211
Alignment explanation
Indices: 8385--9170 Score: 1281
Period size: 211 Copynumber: 3.7 Consensus size: 211
8375 TTATTGATAA
* *
8385 GCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATTATTTCCCATCATCCCCAAAAA
1 GCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATTATTTCTCATCATCCCCAAATA
** * * *
8450 ATCATATGCACCATCCCCAAATTCTTTAGAGATGGACATTTATTCTCATATATCCTAAATTGACT
66 ATCATATGCACCATCCCCAAATTCAATAGAGATGGACATTTTTTCTCATATACCCAAAATTGACT
*
8515 TTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCTCGTCTATATGATTTTAGTGTCATCT
131 TTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATTTTAGTGTCATCT
8580 AATAATTAAACAAAAT
196 AATAATTAAACAAAAT
8596 GCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATTATTTCTCATCATCCCCAAATA
1 GCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATTATTTCTCATCATCCCCAAATA
**
8661 ATCATATGCACCATCCCCAAATTCTTTAGAGATGGACATTTTTTCTCATATACCCAAAATTGACT
66 ATCATATGCACCATCCCCAAATTCAATAGAGATGGACATTTTTTCTCATATACCCAAAATTGACT
* *
8726 TTAAAAGGTGTTTTAATCCATATATTAATTGAATATATCCCCGTCTATATGATTTTAGTGCCATC
131 TTAAAAGGTGTTTTAATCCATATATTAATTGAATA-AACCCCGTCTATATGATTTTAGTGTCATC
*
8791 GAATAATTAAA-AAAAT
195 TAATAATTAAACAAAAT
** *
8807 GCAAAATTCAGTATCCTTAAAGTAATATACTTTATACCCAAATTGTTTCTCATCATCCCCAAATA
1 GCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATTATTTCTCATCATCCCCAAATA
* * * *
8872 ATCATATGCATCATCCTCAAATTCAATAGTA-ATTGACATTTTTTCTCATATACCCAAAATTTAC
66 ATCATATGCACCATCCCCAAATTCAATAG-AGATGGACATTTTTTCTCATATACCCAAAATTGAC
8936 TTTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATTTTAGTGTCATC
130 TTTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATTTTAGTGTCATC
9001 TAATAATTAAACAAAAT
195 TAATAATTAAACAAAAT
* *
9018 GCAAAATTCAGTATCCCCAAAGTAACATACTTTATGCCCAAATTATTTCTCATCATCCCCAAA-A
1 GCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATTATTTCTCATCATCCCCAAATA
* * * * *
9082 ACTTATATGCACCATCCCCAAATTCAATAGTGATTGCCATTATTTCTCATATACCCAAAATTGAC
66 A-TCATATGCACCATCCCCAAATTCAATAGAGATGGACATTTTTTCTCATATACCCAAAATTGAC
9147 TTTAAAAGGTGTTTTAATCCATAT
130 TTTAAAAGGTGTTTTAATCCATAT
9171 GAGAAAAAAT
Statistics
Matches: 537, Mismatches: 33, Indels: 10
0.93 0.06 0.02
Matches are distributed among these distances:
210 39 0.07
211 461 0.86
212 37 0.07
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (211 bp):
GCAAAATTCAGTATCCCCAAAGTAATATACTTTATACCCAAATTATTTCTCATCATCCCCAAATA
ATCATATGCACCATCCCCAAATTCAATAGAGATGGACATTTTTTCTCATATACCCAAAATTGACT
TTAAAAGGTGTTTTAATCCATATATTAATTGAATAAACCCCGTCTATATGATTTTAGTGTCATCT
AATAATTAAACAAAAT
Found at i:9536 original size:214 final size:212
Alignment explanation
Indices: 9167--9806 Score: 1097
Period size: 214 Copynumber: 3.0 Consensus size: 212
9157 GTTTTAATCC
9167 ATATGAGAAAAAATGTCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGAT
1 ATATGAGAAAAAATGTCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGAT
9232 GAGAAATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTA
66 GAGAAATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTA
*
9297 TTAGATGGCACTAAAATCATATAGACGAGGTTATATTCAATTAATATATGGATTATTAAACACCT
131 TTAGATGGCACTAAAATCATATAGACGGGGTTATATTCAATTAATATATGGATTA--AAACACCT
*
9362 TTGAAAGTCAATTTTGGGT
194 TTAAAAGTCAATTTTGGGT
* *
9381 ATATGAGAAAAAATGTCCATCTCTAAAGAATTTGGGGATGCTGCATACGATTATTTGGGGATGAT
1 ATATGAGAAAAAATGTCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGAT
* * *
9446 GAGAAACAATTTTGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAATCA
66 GAGAAATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTA
* *
9511 TTAGATGGCACTAAAATCATATAGACGGGGATATATTCAATTAATATATGGATTAAAAACGCCTT
131 TTAGATGGCACTAAAATCATATAGACGGGGTTATATTCAATTAATATATGGATT-AAAACACC-T
9576 TTAAAAGTCAATTTTGGGT
194 TTAAAAGTCAATTTTGGGT
*
9595 ATATGAGAACAAATGTCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTT-GGGATGAT
1 ATATGAGAAAAAATGTCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGAT
* *
9659 GA-AAATAATTTGGGAATAAAGTATATTACTTTGGGGATAATGAATTTTGCATTTTGTTTAATTA
66 GAGAAATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTA
*
9723 TTAGATGACACTAAAATCATATAGACGGGGTT-TATTCAATTAATATATGGATTAAAACACCTTT
131 TTAGATGGCACTAAAATCATATAGACGGGGTTATATTCAATTAATATATGGATTAAAACACCTTT
*
9787 TAAAGTCAATTTTGGGT
196 AAAAGTCAATTTTGGGT
9804 ATA
1 ATA
9807 CACTAACACC
Statistics
Matches: 403, Mismatches: 21, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
209 22 0.05
210 7 0.02
211 21 0.05
212 87 0.22
213 16 0.04
214 249 0.62
215 1 0.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (212 bp):
ATATGAGAAAAAATGTCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGAT
GAGAAATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTA
TTAGATGGCACTAAAATCATATAGACGGGGTTATATTCAATTAATATATGGATTAAAACACCTTT
AAAAGTCAATTTTGGGT
Found at i:10267 original size:211 final size:211
Alignment explanation
Indices: 9889--10639 Score: 1333
Period size: 211 Copynumber: 3.6 Consensus size: 211
9879 ATAAACCACA
* *
9889 ATATGAG-AAAAATGTTCATCTCTAAAGAATTTGGGGATAGTGCATATGATTATTTGGGGATGAT
1 ATATGAGAAAAAATGTCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGAT
* *
9953 GAGAAACAATTTGGGTATAAATTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTA
66 GAGAAATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTA
*
10018 TTAGATGGCACTAAAATCATATAAACGGGGTTTATTCAATTAATATATGGATTAAAACACCTTTT
131 TTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATATATGGATTAAAACACCTTTT
10083 AAAGTCAATTTTGGGT
196 AAAGTCAATTTTGGGT
* *
10099 ATGTGAGAAAAAATGTCCAACTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGAT
1 ATATGAGAAAAAATGTCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGAT
*
10164 GAGAAATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAATCA
66 GAGAAATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTA
* *
10229 TTAGATGGCACTAAAATCATATAGACGGGATATATTCAATTAATATATGGATTAAAACACCTTTT
131 TTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATATATGGATTAAAACACCTTTT
10294 AAAGTCAATTTTGGGT
196 AAAGTCAATTTTGGGT
* *
10310 ATATGAGAACAAATGTCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTAGGGATGAT
1 ATATGAGAAAAAATGTCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGAT
* *
10375 GAGATATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTTTTTAATTA
66 GAGAAATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTA
* *
10440 TTAGATGACACTAAAATCATATAGATGGGGTTTATTCAATTAATATATGGATTAAAACACCTTTT
131 TTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATATATGGATTAAAACACCTTTT
10505 AAAGTCAATTTTGGGT
196 AAAGTCAATTTTGGGT
*
10521 ATATGAGAAAAAAATATCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGA
1 ATATGAG-AAAAAATGTCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGA
10586 TGAGAAATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCAT
65 TGAGAAATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCAT
10640 ATCAATAATC
Statistics
Matches: 514, Mismatches: 25, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
210 6 0.01
211 401 0.78
212 107 0.21
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (211 bp):
ATATGAGAAAAAATGTCCATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGAT
GAGAAATAATTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAATTA
TTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATATATGGATTAAAACACCTTTT
AAAGTCAATTTTGGGT
Found at i:13980 original size:102 final size:102
Alignment explanation
Indices: 13839--14045 Score: 414
Period size: 102 Copynumber: 2.0 Consensus size: 102
13829 TCCTTTTTGA
13839 ATATTTACCCTTAGATTGGGTATAAGTCTATTATTAGGCAAAGGATTTTGAAAAGTCGCATAAGG
1 ATATTTACCCTTAGATTGGGTATAAGTCTATTATTAGGCAAAGGATTTTGAAAAGTCGCATAAGG
13904 ATTTTGAAAAGTGCTTCTGAAAAGTACTTCCACACAC
66 ATTTTGAAAAGTGCTTCTGAAAAGTACTTCCACACAC
13941 ATATTTACCCTTAGATTGGGTATAAGTCTATTATTAGGCAAAGGATTTTGAAAAGTCGCATAAGG
1 ATATTTACCCTTAGATTGGGTATAAGTCTATTATTAGGCAAAGGATTTTGAAAAGTCGCATAAGG
14006 ATTTTGAAAAGTGCTTCTGAAAAGTACTTCCACACAC
66 ATTTTGAAAAGTGCTTCTGAAAAGTACTTCCACACAC
14043 ATA
1 ATA
14046 AATATGTGTA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 105 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (102 bp):
ATATTTACCCTTAGATTGGGTATAAGTCTATTATTAGGCAAAGGATTTTGAAAAGTCGCATAAGG
ATTTTGAAAAGTGCTTCTGAAAAGTACTTCCACACAC
Found at i:21412 original size:6 final size:6
Alignment explanation
Indices: 21401--21435 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
21391 CTGTTTCCTC
21401 TTTTTG TTTTTG TTTTTTG TTTTTG TTTTT- TTTTT
1 TTTTTG TTTTTG -TTTTTG TTTTTG TTTTTG TTTTT
21436 TCTAGAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.18
6 17 0.61
7 6 0.21
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (6 bp):
TTTTTG
Found at i:21417 original size:13 final size:13
Alignment explanation
Indices: 21401--21436 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
21391 CTGTTTCCTC
21401 TTTTTGTTTTTGT
1 TTTTTGTTTTTGT
21414 TTTTTGTTTTTGT
1 TTTTTGTTTTTGT
21427 TTTTT-TTTTT
1 TTTTTGTTTTT
21437 CTAGAGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (13 bp):
TTTTTGTTTTTGT
Found at i:21423 original size:19 final size:18
Alignment explanation
Indices: 21401--21436 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
21391 CTGTTTCCTC
21401 TTTTTGTTTTTGTTTTTTG
1 TTTTTGTTTTT-TTTTTTG
21420 TTTTTGTTTTTTTTTTT
1 TTTTTGTTTTTTTTTTT
21437 CTAGAGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (18 bp):
TTTTTGTTTTTTTTTTTG
Found at i:23294 original size:1 final size:1
Alignment explanation
Indices: 23288--23314 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
23278 TTAACTATTT
23288 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.