Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023241.1 Corchorus olitorius cultivar O-4 contig23274, 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: 15747
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:197 original size:28 final size:28
Alignment explanation
Indices: 166--227 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
156 GCAAAACAAG
* *
166 AAAAGAATTTTTTTTAAATAAAAACGCA
1 AAAACAATTTTTTTTAAAGAAAAACGCA
** **
194 AAAACTTTTTTTTTTTTAGAAAAACGCA
1 AAAACAATTTTTTTTAAAGAAAAACGCA
222 AAAACA
1 AAAACA
228 CAAAACAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (28 bp):
AAAACAATTTTTTTTAAAGAAAAACGCA
Found at i:2077 original size:21 final size:20
Alignment explanation
Indices: 2053--2103 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
2043 CAATTCTTGC
*
2053 TCTTGAAATAAATCTTCAAAG
1 TCTTCAAAT-AATCTTCAAAG
*
2074 TCTTCAAATTATCTTCAAATGG
1 TCTTCAAATAATCTTCAAA--G
2096 TCTTCAAA
1 TCTTCAAA
2104 CACGAACTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 9 0.35
21 8 0.31
22 9 0.35
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (20 bp):
TCTTCAAATAATCTTCAAAG
Found at i:2089 original size:20 final size:21
Alignment explanation
Indices: 2064--2103 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
2054 CTTGAAATAA
2064 ATCTTCAAA-GTCTTCAAATT
1 ATCTTCAAAGGTCTTCAAATT
2084 ATCTTCAAATGGTCTTCAAA
1 ATCTTCAAA-GGTCTTCAAA
2104 CACGAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (21 bp):
ATCTTCAAAGGTCTTCAAATT
Found at i:3229 original size:76 final size:73
Alignment explanation
Indices: 3095--3238 Score: 182
Period size: 76 Copynumber: 1.9 Consensus size: 73
3085 TCATCTGGAC
* * *
3095 TGTGAGCAAAGGAATGATGAGTTTTAATAAAAAATTTTCAAAATCAGTTTTAATCAAAGCTATGA
1 TGTGAGCAAAGGAATGACGAGTTTTAATAAAAAATTTTCAAAATCAATTTTAATCAAAGCCATGA
3160 TTTCAAGT
66 TTTCAAGT
** **
3168 TGTGAGCAAAGGAATGACG-GTGATTTAATCAAAAGGTGTTTCAAAATCAATTTTGGTCAAAGCC
1 TGTGAGCAAAGGAATGACGAGT--TTTAAT-AAAAAAT-TTTCAAAATCAATTTTAATCAAAGCC
3232 ATGATTT
62 ATGATTT
3239 TGAGGTGACT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
72 2 0.03
73 18 0.30
74 6 0.10
75 5 0.08
76 29 0.48
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (73 bp):
TGTGAGCAAAGGAATGACGAGTTTTAATAAAAAATTTTCAAAATCAATTTTAATCAAAGCCATGA
TTTCAAGT
Found at i:8093 original size:30 final size:30
Alignment explanation
Indices: 8057--8116 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
8047 TGGAATTGCT
* * *
8057 AATCTAAACTAAGATTATGACTAAGATGAC
1 AATCTAAACTAAAAGTATAACTAAGATGAC
8087 AATCTAAACTAAAAGTATAACTAAGATGAC
1 AATCTAAACTAAAAGTATAACTAAGATGAC
8117 CAAAGAGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (30 bp):
AATCTAAACTAAAAGTATAACTAAGATGAC
Found at i:8172 original size:29 final size:29
Alignment explanation
Indices: 8150--8245 Score: 149
Period size: 29 Copynumber: 3.3 Consensus size: 29
8140 AAATGACCAA
* *
8150 AATGCCCCTGGATATGCCGAAATTATCAT
1 AATGCCCCTAGATATGCAGAAATTATCAT
8179 AATGCCCCTAGATATGCAGAAATTATCAT
1 AATGCCCCTAGATATGCAGAAATTATCAT
*
8208 AATGCCCCTAG-TATGCAAAAAATTATCAT
1 AATGCCCCTAGATATGC-AGAAATTATCAT
8237 AATGCCCCT
1 AATGCCCCT
8246 GGACGTGCAA
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
28 5 0.08
29 58 0.92
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (29 bp):
AATGCCCCTAGATATGCAGAAATTATCAT
Found at i:8475 original size:8 final size:8
Alignment explanation
Indices: 8446--8491 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
8436 CCCAATAATA
8446 AAAAAATG
1 AAAAAATG
*
8454 AATGAAAATC
1 AA--AAAATG
8464 AAAAAATG
1 AAAAAATG
8472 AAAAAATG
1 AAAAAATG
*
8480 AAAAAAGG
1 AAAAAATG
8488 AAAA
1 AAAA
8492 TAAAGGCACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 26 0.79
10 7 0.21
ACGTcount: A:0.74, C:0.02, G:0.13, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:9612 original size:50 final size:50
Alignment explanation
Indices: 9537--9639 Score: 161
Period size: 50 Copynumber: 2.1 Consensus size: 50
9527 GAACAAGAAG
* *
9537 TTTTACAATAAGATTGCATTCCATTTGTGAGTCCGAGGTCAAAATTCGCT
1 TTTTACAATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCT
* * *
9587 TTTTATAATATGATTGCATTCCATTTGTGAGTCCAAGATCAAATTTCGCT
1 TTTTACAATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCT
9637 TTT
1 TTT
9640 CAAAAAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.41
Consensus pattern (50 bp):
TTTTACAATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCT
Done.