Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013466.1 Corchorus olitorius cultivar O-4 contig13499, 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: 19101
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1264 original size:1 final size:1
Alignment explanation
Indices: 1258--1284 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1248 TCCAAGTGTT
1258 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1285 GGAGAGCTGT
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
Found at i:1638 original size:50 final size:50
Alignment explanation
Indices: 1563--1810 Score: 426
Period size: 50 Copynumber: 5.0 Consensus size: 50
1553 AGTTTTACAA
1563 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
*
1613 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGATTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
*
1663 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
*
1713 -AAAGATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTTGCTTTTCAAAG
1 TAAA-ATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* * *
1763 TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAA
1811 GGGGCATTTA
Statistics
Matches: 189, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
49 3 0.02
50 184 0.97
51 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
Found at i:2208 original size:27 final size:27
Alignment explanation
Indices: 2137--2210 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 27
2127 TCAGCATGAA
*
2137 CAAGAAAGCAA-ATTC-AAGGACAAAT
1 CAAGAAAGCAAGATTCGAAGCACAAAT
*
2162 CAAGAAGAGC-AGAAAT-GAAGCAC-AAT
1 CAAGAA-AGCAAG-ATTCGAAGCACAAAT
2188 CAAGAAAGCAAGGATTCGAAGCA
1 CAAGAAAGCAA-GATTCGAAGCA
2211 ACAGTCCAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
25 10 0.26
26 15 0.38
27 14 0.36
ACGTcount: A:0.53, C:0.16, G:0.22, T:0.09
Consensus pattern (27 bp):
CAAGAAAGCAAGATTCGAAGCACAAAT
Found at i:2473 original size:50 final size:50
Alignment explanation
Indices: 2398--2582 Score: 253
Period size: 50 Copynumber: 3.7 Consensus size: 50
2388 CGAATGTTTT
* *
2398 GGCTTTCCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATC
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* *
2448 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAATCATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
** * *
2498 GGCTTTTCCACAAGCCAAACTCGCATCCGTACGAGTCAATTATCAACATG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* * **
2548 GGCTTCTCCATAAGCCACAGTTCGTTTCCATACGA
1 GGCTTTTCCACAAGCCA-AACTCGTTTCCATACGA
2583 TACATTACCA
Statistics
Matches: 117, Mismatches: 17, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
50 105 0.90
51 12 0.10
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.26
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
Found at i:2644 original size:35 final size:35
Alignment explanation
Indices: 2598--2904 Score: 415
Period size: 35 Copynumber: 8.8 Consensus size: 35
2588 TACCATCTTC
*
2598 TCAGATGACTCGGTGTAGCATCTTCGAAGTTATAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTATAT
2633 TCAGATGACTCGGTGTAGCATCTTCAAAGTTATAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTATAT
* *
2668 TTAGATGACTCGATGTAGCATCTTCAAAGTTGA-AT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTT-ATAT
* * *
2703 TCAGATGACTCGGTGCAGCATCTTCAAAGATGA-AC
1 TCAGATGACTCGGTGTAGCATCTTCAAAG-TTATAT
* *
2738 TCAGATGACTCGGTGTAGCATCTTCAAAGTTAAAC
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTATAT
*
2773 CCAGATGACTCGGTGTAGCATCTTCAAAGTTATAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTATAT
* * *
2808 TTAGATGACTCGGTGTAGCATCTTCAAAGATGA-AC
1 TCAGATGACTCGGTGTAGCATCTTCAAAG-TTATAT
* *
2843 TCAGATGACTCAGTGTAGCATCTTCAAAG-AATAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTAT-AT
*
2878 TCAGATGACTCGGTGTAGCATCATCAA
1 TCAGATGACTCGGTGTAGCATCTTCAA
2905 TATGGACTCA
Statistics
Matches: 243, Mismatches: 23, Indels: 12
0.87 0.08 0.04
Matches are distributed among these distances:
33 1 0.00
34 2 0.01
35 236 0.97
36 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (35 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGTTATAT
Found at i:3197 original size:28 final size:28
Alignment explanation
Indices: 3164--3240 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
3154 GTAGGATCAA
3164 CTAGGGGCATTTCGGTCATTTTCAAAAT
1 CTAGGGGCATTTCGGTCATTTTCAAAAT
** * * *
3192 CTAGGGGCATTTTAGTCATTTGCACATT
1 CTAGGGGCATTTCGGTCATTTTCAAAAT
3220 C-AGGGGCA-TTCTGGTCATTTT
1 CTAGGGGCATTTC-GGTCATTTT
3241 AAGTTCACAT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.05
27 14 0.35
28 24 0.60
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (28 bp):
CTAGGGGCATTTCGGTCATTTTCAAAAT
Found at i:14146 original size:41 final size:41
Alignment explanation
Indices: 14058--14152 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
14048 TGTTTCTGTG
* * * *
14058 TTCAATATGGTCCCTGATTTAAGATTCTATTTAATATTTGC
1 TTCAATTTGGTCCCTGATTTAAGATTCTAGTCAATATTTGA
* * * * *
14099 TACAATTTAGTCCCTGATTTAGGATTCTAGTCACTATTTTA
1 TTCAATTTGGTCCCTGATTTAAGATTCTAGTCAATATTTGA
14140 TTCAATTTGGTCC
1 TTCAATTTGGTCC
14153 TTATTTTTGT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (41 bp):
TTCAATTTGGTCCCTGATTTAAGATTCTAGTCAATATTTGA
Found at i:18664 original size:23 final size:23
Alignment explanation
Indices: 18620--18665 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
18610 TTGAAATGCT
* *
18620 AACAGTTTTCTTCATCCTATTTC
1 AACAATTTTCTTCATCCAATTTC
18643 AACAATTTTCTT-ATTCCAATTTC
1 AACAATTTTCTTCA-TCCAATTTC
18666 TACACAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.26, C:0.24, G:0.02, T:0.48
Consensus pattern (23 bp):
AACAATTTTCTTCATCCAATTTC
Found at i:19067 original size:2 final size:2
Alignment explanation
Indices: 19060--19101 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19050 CATCACAATC
19060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.