Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022931.1 Corchorus olitorius cultivar O-4 contig22964, 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: 56369
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1313 original size:60 final size:60
Alignment explanation
Indices: 1182--1327 Score: 154
Period size: 60 Copynumber: 2.4 Consensus size: 60
1172 TTTTTTCCAT
* * * ** *
1182 CGTTTGCGAAAATGCTTAAATAAGGGCTTAAAGAAAAAAAATGCTTAAATCAGGGCTCAA
1 CGTTTGAGAAAATGCTCAAATAAGTGCCAAAAGAAAAAAAATGCTCAAATCAGGGCTCAA
* *
1242 CGTTTGCGAAAATGCTCAAATAAGTGCCAAAAGAAAAAAAAATGCTCAAATAACA-GTC-CAA
1 CGTTTGAGAAAATGCTCAAATAAGTGCCAAAAG-AAAAAAAATGCTCAAAT--CAGGGCTCAA
*
1303 C-TTTTAGAAAATTGCTCAAATAAGT
1 CGTTTGAGAAAA-TGCTCAAATAAGT
1328 CTCTGCTGTC
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
60 37 0.50
61 33 0.45
62 2 0.03
63 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.23
Consensus pattern (60 bp):
CGTTTGAGAAAATGCTCAAATAAGTGCCAAAAGAAAAAAAATGCTCAAATCAGGGCTCAA
Found at i:1377 original size:23 final size:23
Alignment explanation
Indices: 1347--1399 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
1337 CACTGTGTGG
1347 TTATCAAAAATTCCATAAT-AAGA
1 TTATCAAAAATTCCAT-ATGAAGA
*
1370 TTATC-AAAATTTCATATGAAGA
1 TTATCAAAAATTCCATATGAAGA
1392 TTATCAAA
1 TTATCAAA
1400 TTTTCCTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 2 0.07
22 18 0.67
23 7 0.26
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (23 bp):
TTATCAAAAATTCCATATGAAGA
Found at i:2908 original size:2 final size:2
Alignment explanation
Indices: 2901--2927 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2891 AAAGTACTAG
2901 TA 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 TA T
2928 TAATGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6213 original size:23 final size:22
Alignment explanation
Indices: 6180--6230 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
6170 TATATTTTAT
*
6180 AGAAAAGGGAAAACAAGAA-AGA
1 AGAAAAAGGAAAACAA-AACAGA
*
6202 ATGAAAAAGGAAAGCAAAACAGA
1 A-GAAAAAGGAAAACAAAACAGA
6225 AGAAAA
1 AGAAAA
6231 CAGAGAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.69, C:0.06, G:0.24, T:0.02
Consensus pattern (22 bp):
AGAAAAAGGAAAACAAAACAGA
Found at i:9433 original size:6 final size:6
Alignment explanation
Indices: 9416--9450 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
9406 TTTCTAGATG
9416 TTCCCTT TTCCCT TTCCCT TTCCCT TTCCCT TTCC
1 TTCCC-T TTCCCT TTCCCT TTCCCT TTCCCT TTCC
9451 TCCTACACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
TTCCCT
Found at i:17452 original size:13 final size:14
Alignment explanation
Indices: 17429--17457 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17419 AAAATAATTT
17429 ATTTATTAATATTA
1 ATTTATTAATATTA
17443 ATTT-TTAATATTA
1 ATTTATTAATATTA
17456 AT
1 AT
17458 ACTAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTATTAATATTA
Found at i:23068 original size:5 final size:5
Alignment explanation
Indices: 23054--23087 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
23044 TAATAATAAT
23054 AAAG- AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
23088 CATGTATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:34103 original size:32 final size:32
Alignment explanation
Indices: 34065--34126 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
34055 TTATATATTC
34065 TTTAATTTTGTAAATTCAAAATATATTTCCGT
1 TTTAATTTTGTAAATTCAAAATATATTTCCGT
34097 TTTAATTTTGTAAATTCAAAATATATTTCC
1 TTTAATTTTGTAAATTCAAAATATATTTCC
34127 TTCTTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (32 bp):
TTTAATTTTGTAAATTCAAAATATATTTCCGT
Found at i:34873 original size:321 final size:321
Alignment explanation
Indices: 34291--34928 Score: 1204
Period size: 321 Copynumber: 2.0 Consensus size: 321
34281 GATTAAAGAT
34291 CAGAGCGATTTGTGGGGACTGGATCAAAGTCACACCGGAGCATTTAAATCACTGGATCCACAAGA
1 CAGAGCGATTTGTGGGGACTGGATCAAAGTCACACCGGAGCATTTAAATCACTGGATCCACAAGA
34356 TAAAGTCTTCCTAAATTAGCGCTGCAAGAGCTGTTCTTGATTGAGATTGAGAGAAAAATAACAAC
66 TAAAGTCTTCCTAAATTAGCGCTGCAAGAGCTGTTCTTGATTGAGATTGAGAGAAAAATAACAAC
*
34421 TGATTGTTATTGCTAAGAGAGAAACGCGTGTACAGTATTTTAACGACCGGAGACAAGATTGAAAC
131 TGATTGTTATTACTAAGAGAGAAACGCGTGTACAGTATTTTAACGACCGGAGACAAGATTGAAAC
* *
34486 AAGGAAATAACACTAAAAGAGTGTTCTTTTGTCCGGAGACAAGATTGACACAAGGAAATATTGAA
196 AAGGAAATAACACTAAAAGAGCGTTCTTTTGTCCGGAGACAAGATTGAAACAAGGAAATATTGAA
* *
34551 GAACAAGTAAGAACTCGTGATGAACAAGAGAAAAAACGCGGAGCTTTTGAGAGAAAAAACG
261 GAACAAATAAGAACTCGTGATAAACAAGAGAAAAAACGCGGAGCTTTTGAGAGAAAAAACG
34612 CAGAGCGATTTGTGGGGACTGGATCAAAGTCACACCGGAGCATTTAAATCACTGGATCCACAAGA
1 CAGAGCGATTTGTGGGGACTGGATCAAAGTCACACCGGAGCATTTAAATCACTGGATCCACAAGA
34677 TAAAGTCTTCCTAAATTAGCGCTGCAAGAGCTGTTCTTGATTGAGATTGAGAGAAAAATAACAAC
66 TAAAGTCTTCCTAAATTAGCGCTGCAAGAGCTGTTCTTGATTGAGATTGAGAGAAAAATAACAAC
* *
34742 TGATTGTTATTACTGAGAGAGAAACGCGTGTACAGTGTTTTAACGACCGGAGACAAGATTGAAAC
131 TGATTGTTATTACTAAGAGAGAAACGCGTGTACAGTATTTTAACGACCGGAGACAAGATTGAAAC
34807 AAGGAAATAACACTAAAAGAGCGTTCTTTTGTCCGGAGACAAGATTGAAACAAGGAAATATTGAA
196 AAGGAAATAACACTAAAAGAGCGTTCTTTTGTCCGGAGACAAGATTGAAACAAGGAAATATTGAA
*
34872 GAACAAATAAGAACTCGTGATAAACAAGAGAAAAAGCGCGGAGCTTTTGAGAGAAAA
261 GAACAAATAAGAACTCGTGATAAACAAGAGAAAAAACGCGGAGCTTTTGAGAGAAAA
34929 TAAGCACGAA
Statistics
Matches: 309, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
321 309 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (321 bp):
CAGAGCGATTTGTGGGGACTGGATCAAAGTCACACCGGAGCATTTAAATCACTGGATCCACAAGA
TAAAGTCTTCCTAAATTAGCGCTGCAAGAGCTGTTCTTGATTGAGATTGAGAGAAAAATAACAAC
TGATTGTTATTACTAAGAGAGAAACGCGTGTACAGTATTTTAACGACCGGAGACAAGATTGAAAC
AAGGAAATAACACTAAAAGAGCGTTCTTTTGTCCGGAGACAAGATTGAAACAAGGAAATATTGAA
GAACAAATAAGAACTCGTGATAAACAAGAGAAAAAACGCGGAGCTTTTGAGAGAAAAAACG
Found at i:42001 original size:19 final size:18
Alignment explanation
Indices: 41968--42003 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41958 TTGAGATAAT
41968 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
41986 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
42004 TAAGTCTTCA
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:51009 original size:35 final size:35
Alignment explanation
Indices: 50963--51034 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
50953 AGACAGAACC
*
50963 TTGCTGTGTCCCACTAGGCGTGCCAAAAAGAGATG
1 TTGCTGTGTCCCACCAGGCGTGCCAAAAAGAGATG
* *
50998 TTGCTGTGTCCCACCGGGCGTGTCAAAAAGAGATG
1 TTGCTGTGTCCCACCAGGCGTGCCAAAAAGAGATG
51033 TT
1 TT
51035 ACGCCAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (35 bp):
TTGCTGTGTCCCACCAGGCGTGCCAAAAAGAGATG
Done.