Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024641.1 Corchorus olitorius cultivar O-4 contig24674, 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: 62047
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:523 original size:19 final size:19
Alignment explanation
Indices: 495--563 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
485 TTTTTCTACT
495 TTTATTTTATTTATTTATA
1 TTTATTTTATTTATTTATA
* * ** *
514 TTTATATTATTAATGGATT
1 TTTATTTTATTTATTTATA
533 TTTATTTTATTTATTTAT-
1 TTTATTTTATTTATTTATA
* *
551 TTTCTTTTTTTTA
1 TTTATTTTATTTA
564 CTTGTGTTTT
Statistics
Matches: 39, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
18 11 0.28
19 28 0.72
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTATTTTATTTATTTATA
Found at i:1227 original size:20 final size:20
Alignment explanation
Indices: 1202--1247 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1192 ACGGCGTTAA
1202 ATGGCAGTAACGATGCTAAC
1 ATGGCAGTAACGATGCTAAC
* *
1222 ATGGCAGTAACGGTGCTGAC
1 ATGGCAGTAACGATGCTAAC
1242 ATGGCA
1 ATGGCA
1248 ATGTCCATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (20 bp):
ATGGCAGTAACGATGCTAAC
Found at i:3266 original size:9 final size:9
Alignment explanation
Indices: 3252--3276 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3242 TGACATTCTC
3252 GTTTTAGAA
1 GTTTTAGAA
3261 GTTTTAGAA
1 GTTTTAGAA
3270 GTTTTAG
1 GTTTTAG
3277 GCATACACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (9 bp):
GTTTTAGAA
Found at i:6080 original size:19 final size:18
Alignment explanation
Indices: 6052--6095 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
6042 GTGATTTTTG
*
6052 ATAATAATTATTCAATAAA
1 ATAATTATTATTCAAT-AA
* *
6071 ATAATTATTATTTAATTA
1 ATAATTATTATTCAATAA
6089 ATAATTA
1 ATAATTA
6096 GTTAATTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTATTATTCAATAA
Found at i:7321 original size:25 final size:25
Alignment explanation
Indices: 7293--7365 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 25
7283 TATATCCTAT
7293 TTGAGTAAACATATGAAATTACTAA
1 TTGAGTAAACATATGAAATTACTAA
** **
7318 TTGA-T-CCCATAT-ATCTTA-T--
1 TTGAGTAAACATATGAAATTACTAA
7337 TTGAGTAAACATATGAAATTACTAA
1 TTGAGTAAACATATGAAATTACTAA
7362 TTGA
1 TTGA
7366 AATTACTAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
19 4 0.12
20 1 0.03
21 6 0.18
22 8 0.24
23 6 0.18
24 1 0.03
25 8 0.24
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (25 bp):
TTGAGTAAACATATGAAATTACTAA
Found at i:7345 original size:44 final size:44
Alignment explanation
Indices: 7282--7365 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
7272 TATATACTAT
7282 ATATATCCTATTTGAGTAAACATATGAAATTACTAATTGATCCC
1 ATATATCCTATTTGAGTAAACATATGAAATTACTAATTGATCCC
*
7326 ATATATCTTATTTGAGTAAACATATGAAATTACTAATTGA
1 ATATATCCTATTTGAGTAAACATATGAAATTACTAATTGA
7366 AATTACTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (44 bp):
ATATATCCTATTTGAGTAAACATATGAAATTACTAATTGATCCC
Found at i:7368 original size:13 final size:13
Alignment explanation
Indices: 7350--7378 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
7340 AGTAAACATA
7350 TGAAATTACTAAT
1 TGAAATTACTAAT
7363 TGAAATTACTAAT
1 TGAAATTACTAAT
7376 TGA
1 TGA
7379 TCCCATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (13 bp):
TGAAATTACTAAT
Found at i:7564 original size:40 final size:40
Alignment explanation
Indices: 7520--7598 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
7510 GATAACTCTA
*
7520 CTTTTTGGTCTTTTGCTAGCGGTGAATGTGAAAGCAATTG
1 CTTTTTGGTCTTTTGCTAGCGATGAATGTGAAAGCAATTG
* *
7560 CTTTTTGGTCTTTTGCTCGCGATGAATGTGAACGCAATT
1 CTTTTTGGTCTTTTGCTAGCGATGAATGTGAAAGCAATT
7599 AATTGTGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (40 bp):
CTTTTTGGTCTTTTGCTAGCGATGAATGTGAAAGCAATTG
Found at i:9374 original size:16 final size:16
Alignment explanation
Indices: 9353--9384 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9343 ACTTGATTCT
9353 TTTCCACTACTTAAGA
1 TTTCCACTACTTAAGA
9369 TTTCCACTACTTAAGA
1 TTTCCACTACTTAAGA
9385 ATTTAAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (16 bp):
TTTCCACTACTTAAGA
Found at i:9551 original size:61 final size:61
Alignment explanation
Indices: 9481--9604 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 61
9471 CGTACTTAAG
9481 AATTTAAGATTTGCATTATTCCTATTAAACCATTTTCCTTGCATTATTGATTATCAATGCT
1 AATTTAAGATTTGCATTATTCCTATTAAACCATTTTCCTTGCATTATTGATTATCAATGCT
*
9542 AATTTAAGATTTGCATTATTCCTATTCAACCATTTTCCTTGCATTATTGATTATCAATGCT
1 AATTTAAGATTTGCATTATTCCTATTAAACCATTTTCCTTGCATTATTGATTATCAATGCT
9603 AA
1 AA
9605 GCGAATCAAG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (61 bp):
AATTTAAGATTTGCATTATTCCTATTAAACCATTTTCCTTGCATTATTGATTATCAATGCT
Found at i:9598 original size:28 final size:28
Alignment explanation
Indices: 9508--9598 Score: 67
Period size: 28 Copynumber: 3.1 Consensus size: 28
9498 ATTCCTATTA
9508 AACCATTTTCCTTGCATTATTGATTATC
1 AACCATTTTCCTTGCATTATTGATTATC
* *** **
9536 AATGCTAATTTAAGATTTGCATTATT-CCTATTC
1 AA--C-CATTT--TCCTTGCATTATTGATTA-TC
9569 AACCATTTTCCTTGCATTATTGATTATC
1 AACCATTTTCCTTGCATTATTGATTATC
9597 AA
1 AA
9599 TGCTAAGCGA
Statistics
Matches: 44, Mismatches: 12, Indels: 14
0.63 0.17 0.20
Matches are distributed among these distances:
28 16 0.36
29 2 0.05
30 5 0.11
31 5 0.11
32 2 0.05
33 14 0.32
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.45
Consensus pattern (28 bp):
AACCATTTTCCTTGCATTATTGATTATC
Found at i:16415 original size:32 final size:32
Alignment explanation
Indices: 16374--16437 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
16364 GGTCGAAGCT
16374 GCATCAATGCAATGTCAAACAAATATTAATAA
1 GCATCAATGCAATGTCAAACAAATATTAATAA
16406 GCATCAATGCAATGTCAAACAAATATTAATAA
1 GCATCAATGCAATGTCAAACAAATATTAATAA
16438 ACTAAGTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (32 bp):
GCATCAATGCAATGTCAAACAAATATTAATAA
Found at i:21274 original size:203 final size:208
Alignment explanation
Indices: 20872--21276 Score: 642
Period size: 203 Copynumber: 2.0 Consensus size: 208
20862 ATTATATGGG
* *
20872 CAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGTCCTGAAGGGTGACA
1 CAAATTATACAATACACC-GCGGTCGAGTTTAGCAGACTACACAAGCGCGTCCTGAAGGGTGACA
* * * *
20937 TGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATGTGTC
65 TGTGTCATCTAGGAACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGCGTC
*
21002 AACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCAAATAATTACCCTATT
130 AACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGATGTATCAAATAATTACCCTATT
21067 AATATTTAATATGA
195 AATATTTAATATGA
* * *
21081 CAAATTATACAATACA-C-C-GTCGAGTTTAGCATACTACAC-AG-GCGTCTTGAAGGGTGATAT
1 CAAATTATACAATACACCGCGGTCGAGTTTAGCAGACTACACAAGCGCGTCCTGAAGGGTGACAT
21141 GTGTCATCTAGGAACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGCGTCA
66 GTGTCATCTAGGAACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGCGTCA
* *
21206 ACTTCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGATGTATCAAATTATTACCC-ATTT
131 ACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGATGTATCAAATAATTACCCTA-TT
21270 AATATTT
195 AATATTT
21277 TTCTTTTCTT
Statistics
Matches: 183, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
202 1 0.01
203 143 0.78
204 2 0.01
205 19 0.10
206 1 0.01
208 1 0.01
209 16 0.09
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (208 bp):
CAAATTATACAATACACCGCGGTCGAGTTTAGCAGACTACACAAGCGCGTCCTGAAGGGTGACAT
GTGTCATCTAGGAACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGCGTCA
ACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGATGTATCAAATAATTACCCTATTA
ATATTTAATATGA
Found at i:41912 original size:72 final size:71
Alignment explanation
Indices: 41815--41961 Score: 213
Period size: 72 Copynumber: 2.1 Consensus size: 71
41805 TTAATTATAC
* *
41815 AAATTAAGAAAATCAGAATAATACTTGATCCACGAAACTGCAATTTTACATCCAACAGACCCCAA
1 AAATTAAGAAAATCAAAATAATACTTGATCCACGAAAATGCAATTTTACATCCAACAGA-CCCAA
*
41880 AACTGAT
65 AACTAAT
* * * * *
41887 AAATTAAGAAAATTAAAATAGTACTTGATCCACGAAAATGTAATTTTACATCCAATAGACCCTAA
1 AAATTAAGAAAATCAAAATAATACTTGATCCACGAAAATGCAATTTTACATCCAACAGACCCAAA
41952 ACTAAT
66 ACTAAT
41958 AAAT
1 AAAT
41962 AGAATAATAA
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
71 14 0.21
72 53 0.79
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.25
Consensus pattern (71 bp):
AAATTAAGAAAATCAAAATAATACTTGATCCACGAAAATGCAATTTTACATCCAACAGACCCAAA
ACTAAT
Found at i:42119 original size:8 final size:8
Alignment explanation
Indices: 42106--42148 Score: 70
Period size: 8 Copynumber: 5.4 Consensus size: 8
42096 AAGATTTTTA
42106 AAAAAAAG
1 AAAAAAAG
42114 AAAAAAAAG
1 -AAAAAAAG
42123 AAAAAAAG
1 AAAAAAAG
42131 -AAAAAAG
1 AAAAAAAG
42138 AAAAAAAG
1 AAAAAAAG
42146 AAA
1 AAA
42149 GAAGATAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.21
8 18 0.55
9 8 0.24
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:42119 original size:9 final size:9
Alignment explanation
Indices: 42105--42151 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
42095 AAAGATTTTT
42105 AAAAAAAAG
1 AAAAAAAAG
42114 AAAAAAAAG
1 AAAAAAAAG
42123 -AAAAAAAG
1 AAAAAAAAG
42131 AAAAAAGAA-
1 AAAAAA-AAG
42140 AAAAAGAAAG
1 AAAAA-AAAG
42150 AA
1 AA
42152 GATAAGGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.24
9 21 0.62
10 5 0.15
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:42126 original size:15 final size:15
Alignment explanation
Indices: 42106--42153 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
42096 AAGATTTTTA
42106 AAAAAAAGAAAAAAAAG
1 AAAAAAAG--AAAAAAG
42123 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
*
42138 AAAAAAAGAAAGAAG
1 AAAAAAAGAAAAAAG
42153 A
1 A
42154 TAAGGTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 22 0.73
17 8 0.27
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:48751 original size:14 final size:15
Alignment explanation
Indices: 48713--48751 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
48703 AACTAGACAC
48713 ACATATTTACTTAAT
1 ACATATTTACTTAAT
48728 ATGCATATTTACTTAAT
1 A--CATATTTACTTAAT
48745 A-ATATTT
1 ACATATTT
48752 TGGATTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.27
15 1 0.05
17 15 0.68
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (15 bp):
ACATATTTACTTAAT
Found at i:49022 original size:233 final size:235
Alignment explanation
Indices: 48600--49030 Score: 642
Period size: 233 Copynumber: 1.8 Consensus size: 235
48590 GATCTTAACC
** *
48600 ATATACATCATCTAAAGATTTATATCCAATAAGCCAGATGATATTTTCTGAATATGCAGAAATAT
1 ATATACATCATCTAAAGATACATATCCAATAAGCCAGATGATATTTCCTGAATATGCAGAAATAT
* *
48665 GTTTGACTGTATGGTAATTTCTCAGCTTATGATCCTGAAACTAGACACACATATTTACTTAATAT
66 GTTTGACTGTATGGTAATTTCCCAGCTTATGATCCTGAAACTAGA-ACACA-A-TTAC-TAATAA
* **
48730 GCATATTTACTTAATAATATTTTGGATTTTGGTCATCTATCTTTAGCTGCATTCCTAAAACACTC
127 GCATATTGACTTAATAATATTTCCGATTTTGGTCATCTATCTTTAGCTGCATTCCTAAAACACTC
48795 CATATCCAATATACATAATATGTTTCTGCAATTCCTAAAACCCA
192 CATATCCAATATACATAATATGTTTCTGCAATTCCTAAAACCCA
48839 ATATACATCATCTAAAGATACATATCCAATAAGCCAGATGAGT-TTTCCTGAATGAAAATGCAGA
1 ATATACATCATCTAAAGATACATATCCAATAAGCCAGATGA-TATTTCCTGAAT----ATGCAGA
* *
48903 AATATGTTTGAGTTTATGGTAATTTCCCAGCTTATGATCCTGAAACTAG-ACAC-A-T-C-AA-A
61 AATATGTTTGACTGTATGGTAATTTCCCAGCTTATGATCCTGAAACTAGAACACAATTACTAATA
48962 AGCATATTGACTTAATAATATTTCCGATTTTGGTCATCTATCTTTAGCTGCATTCCTAAAACACT
126 AGCATATTGACTTAATAATATTTCCGATTTTGGTCATCTATCTTTAGCTGCATTCCTAAAACACT
49027 CCAT
191 CCAT
49031 CTGTATTAAG
Statistics
Matches: 177, Mismatches: 10, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
233 66 0.37
234 2 0.01
236 1 0.01
237 1 0.01
239 49 0.28
240 1 0.01
241 4 0.02
243 53 0.30
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (235 bp):
ATATACATCATCTAAAGATACATATCCAATAAGCCAGATGATATTTCCTGAATATGCAGAAATAT
GTTTGACTGTATGGTAATTTCCCAGCTTATGATCCTGAAACTAGAACACAATTACTAATAAGCAT
ATTGACTTAATAATATTTCCGATTTTGGTCATCTATCTTTAGCTGCATTCCTAAAACACTCCATA
TCCAATATACATAATATGTTTCTGCAATTCCTAAAACCCA
Done.