Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018696.1 Corchorus olitorius cultivar O-4 contig18729, 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: 10576
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:1267 original size:19 final size:19
Alignment explanation
Indices: 1228--1268 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
1218 TCAGTGTTTA
1228 TTATTGCTTATTACTTGCTT
1 TTATTGCTTA-TACTTGCTT
1248 TTATTGCTTA-ACTGTGCTT
1 TTATTGCTTATACT-TGCTT
1267 TT
1 TT
1269 CATGTTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 7 0.35
20 10 0.50
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (19 bp):
TTATTGCTTATACTTGCTT
Found at i:5899 original size:23 final size:23
Alignment explanation
Indices: 5869--5924 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
5859 CAAAAATAAA
*
5869 AAAATCAATCAAT-AAATCAAAGC
1 AAAATCAA-AAATCAAATCAAAGC
*
5892 AAAATCAAAAATCAAATCAAATC
1 AAAATCAAAAATCAAATCAAAGC
5915 AAAATCAAAA
1 AAAATCAAAA
5925 GAGAATGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.66, C:0.16, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAATCAAAAATCAAATCAAAGC
Found at i:6588 original size:50 final size:50
Alignment explanation
Indices: 6513--6662 Score: 246
Period size: 50 Copynumber: 3.0 Consensus size: 50
6503 AGTTTTATAA
* *
6513 TAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAG
*
6563 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTTCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAG
* * *
6613 TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTTGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAG
6663 GACATTGAAG
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 93 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAG
Found at i:7261 original size:91 final size:91
Alignment explanation
Indices: 7093--7261 Score: 225
Period size: 91 Copynumber: 1.9 Consensus size: 91
7083 GACCAGAGTT
* * * * *
7093 ATTGGTCCTTTTTCATCAACGATCAATAAGTTTTCAGTTACAACCTAAGACTCGGAGTCATTTTT
1 ATTGGTCCTTTTTCATCAACAATCAAGAAGTTTTCAGTTACAACATAAGACTCAGAGTCATTTTC
*
7158 CAAGTTGTTTTTCAAGTTGACCGCAC
66 CAAGTGGTTTTTCAAGTTGACCGCAC
* * *
7184 ATTGGTCCTTTTTCATCATCAATCAAGAAGTTTTCAGTTACAACATCAA-ATTCAGAGTTATTTT
1 ATTGGTCCTTTTTCATCAACAATCAAGAAGTTTTCAGTTACAACAT-AAGACTCAGAGTCATTTT
7248 CCAAG-GGTATTTTC
65 CCAAGTGGT-TTTTC
7262 TTCCAAAATC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
90 2 0.03
91 63 0.94
92 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (91 bp):
ATTGGTCCTTTTTCATCAACAATCAAGAAGTTTTCAGTTACAACATAAGACTCAGAGTCATTTTC
CAAGTGGTTTTTCAAGTTGACCGCAC
Found at i:7405 original size:50 final size:50
Alignment explanation
Indices: 7330--7721 Score: 599
Period size: 50 Copynumber: 7.8 Consensus size: 50
7320 TCAGAATGCT
7330 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGT-AGATTATCAAC
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA-ATTATCAAC
7380 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC
** *
7430 ACCGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAAC
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC
* * * *
7480 ACAGGCTTTTCCACAAGCCGAACTCATTTCCATACGAGTTAATTATCAAC
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC
*
7530 ATAGGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC
* *
7580 ATGGGCTTTTCCACAAGCCAGACTCGTTTCCATACGAGTCAATTATCAAC
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC
* * *
7630 ATGGGCTTTTCCACAAGCCAAACTTGTTTCCATACGAGTCAATTTTCAAC
1 ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC
* * * *
7680 ATAGGCTTTTCCATAAGTCAAAC-CGGCTTCCATATGAGTCAA
1 ATAGGCTTTTCCACAAGCCAAACTC-GTTTCCATACGAGTCAA
7722 GCCTTACTTT
Statistics
Matches: 317, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
50 316 1.00
51 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (50 bp):
ATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAAC
Found at i:8034 original size:26 final size:27
Alignment explanation
Indices: 8005--8078 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 27
7995 AGGGTCATCT
*
8005 AGGGGCATTTTGGTCATTTT-ATATTC
1 AGGGGCATTTTGGTCATTTTCACATTC
*
8031 AGGGGCATTTTAGTCATTTTTGCACATTC
1 AGGGGCATTTTGGTCA-TTTT-CACATTC
*
8060 AGGGGTATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
8079 GTACTCCAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.37
27 4 0.10
28 3 0.07
29 19 0.46
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCACATTC
Done.