Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009952.1 Corchorus olitorius cultivar O-4 contig09984, 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: 3201
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:525 original size:11 final size:11
Alignment explanation
Indices: 509--534 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
499 AGATAATTTC
509 TTTTCTTCTAG
1 TTTTCTTCTAG
520 TTTTCTTCTAG
1 TTTTCTTCTAG
531 TTTT
1 TTTT
535 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:1355 original size:15 final size:15
Alignment explanation
Indices: 1325--1366 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
1315 TTACTTTGCT
1325 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
1341 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
1356 TTGCTTTCTGT
1 TTGTTTTCTGT
1367 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:1994 original size:50 final size:50
Alignment explanation
Indices: 1919--2206 Score: 441
Period size: 50 Copynumber: 5.8 Consensus size: 50
1909 CGAATGTTTT
*
1919 GGCTTTTCGACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* *
1969 GGCTTTTCCACAAGCCAAACTCGTTTCCATACAAGTCGATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* *
2019 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* *
2069 GGCTTTTCTACAAGCCAAACTCGTTTCCATACGAGTCAATTATCGACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* * * *
2119 GGCTTCTCCACAAGCCAAACTCGTTTCCATATGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
* * * *
2169 GACTTTTCCACAAACCGAACTCATTTCCATACGAGTCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCA
2207 TTTCAAACCT
Statistics
Matches: 216, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 216 1.00
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACACA
Found at i:2398 original size:50 final size:50
Alignment explanation
Indices: 2263--2598 Score: 505
Period size: 50 Copynumber: 6.6 Consensus size: 50
2253 CATTACCTTT
* **
2263 TTTTAAAGATTGAATTGGTTGACAGTTCAAAGGATAAGCGGAAGATTGTCC
1 TTTT-AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
2314 TTTTATAGAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTA-AG-ATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
2366 TTTTAAGATTGAATTGGTGGACAGTTTAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
2416 TTTAATAGAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTA-AG-ATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
2468 TTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
2518 TTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
2568 TTTTAATATT-AGATTGG-AGTACAATTCAAAG
1 TTTTAAGATTGA-ATTGGTAG-ACAGTTCAAAG
2599 AAATTGATCG
Statistics
Matches: 267, Mismatches: 12, Indels: 13
0.91 0.04 0.04
Matches are distributed among these distances:
49 3 0.01
50 162 0.61
51 12 0.04
52 90 0.34
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:2444 original size:102 final size:102
Alignment explanation
Indices: 2263--2598 Score: 527
Period size: 102 Copynumber: 3.3 Consensus size: 102
2253 CATTACCTTT
* ** *
2263 TTTTAAAGATTGAATTGGTTGACAGTTCAAAGGATAAGCGGAAGATTGTCCTTTTATAGAATTGA
1 TTTT-AAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTAATAGAATTGA
2328 ATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
65 ATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
2366 TTTTAAGATTGAATTGGTGGACAGTTTAAAGGATAAGCGGAAGACGGTCCTTTAATAGAATTGAA
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTAATAGAATTGAA
2431 TTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
66 TTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
2468 TTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCA-AG-ATTGAA
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTAATAGAATTGAA
2531 TTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
66 TTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
2568 TTTTAATATT-AGATTGG-AGTACAATTCAAAG
1 TTTTAAGATTGA-ATTGGTAG-ACAGTTCAAAG
2599 AAATTGATCG
Statistics
Matches: 219, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
99 3 0.01
100 66 0.30
101 2 0.01
102 144 0.66
103 4 0.02
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (102 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTAATAGAATTGAA
TTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:2489 original size:27 final size:27
Alignment explanation
Indices: 2459--2539 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
2449 GATAAGCGGA
2459 AGACGGTCCTTTCAAGATTGAATTGGT
1 AGACGGTCCTTTCAAGATTGAATTGGT
* ** *
2486 AGACAG----TTCAAAGGA-T-AAGCGGA
1 AGACGGTCCTTTC-AA-GATTGAATTGGT
2509 AGACGGTCCTTTCAAGATTGAATTGGT
1 AGACGGTCCTTTCAAGATTGAATTGGT
2536 AGAC
1 AGAC
2540 AGTTCAAAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 16
0.61 0.13 0.26
Matches are distributed among these distances:
23 12 0.32
24 3 0.08
25 4 0.11
26 3 0.08
27 16 0.42
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (27 bp):
AGACGGTCCTTTCAAGATTGAATTGGT
Found at i:2541 original size:152 final size:154
Alignment explanation
Indices: 2263--2575 Score: 526
Period size: 152 Copynumber: 2.1 Consensus size: 154
2253 CATTACCTTT
* ** *
2263 TTTTAA-AGATTGAATTGGTTGACAGTTCAAAGGATAAGCGGAAGATTGTCCTTTTATAGAATTG
1 TTTTAATAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCATAGAATTG
* *
2327 AATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGTGGACAGTT
66 AATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCAAGATTGAATTGGTAGACAGTT
*
2392 TAAAGGATAAGCGGAAGACGGTCC
131 CAAAGGATAAGCGGAAGACGGTCC
2416 -TTTAATAGAATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCA-AG-ATT
1 TTTTAATAG-ATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCATAGAATT
2478 GAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCAAGATTGAATTGGTAGACAGT
65 GAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCAAGATTGAATTGGTAGACAGT
2543 TCAAAGGATAAGCGGAAGACGGTCC
130 TCAAAGGATAAGCGGAAGACGGTCC
2568 TTTTAATA
1 TTTTAATA
2576 TTAGATTGGA
Statistics
Matches: 150, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
152 95 0.63
153 11 0.07
154 44 0.29
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (154 bp):
TTTTAATAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCATAGAATTG
AATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCAAGATTGAATTGGTAGACAGTT
CAAAGGATAAGCGGAAGACGGTCC
Found at i:2615 original size:152 final size:151
Alignment explanation
Indices: 2271--2624 Score: 450
Period size: 152 Copynumber: 2.3 Consensus size: 151
2261 TTTTTTAAAG
* * * * *
2271 ATTGAATTGGTTGACAGTTCAAAGGATAAGCGGAAGATTG-TCC-TTTTATAGAATTGAATTGGT
1 ATTGAATTGGTAGACAATTCAAAGAATAAGCGGAAGA-CGATCCATTTCA-AG-ATTGAATTGGT
* * *
2334 AGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGAATTGGTGGACAGTTTAAAGGA
63 AGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCAAGATTGAATTGGTAGACAGTTCAAAGGA
2399 TAAGCGGAAGACGGTCCTTTAATAGA
128 TAAGCGGAAGACGGTCCTTTAAT--A
* * *
2425 ATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC-TTTCAAGATTGAATTGGTAGA
1 ATTGAATTGGTAGACAATTCAAAGAATAAGCGGAAGACGATCCATTTCAAGATTGAATTGGTAGA
2489 CAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAA
66 CAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAA
2554 GCGGAAGACGGTCCTTTTAAT-
131 GCGGAAGACGGTCC-TTTAATA
* * *
2575 ATT-AGATTGG-AGTACAATTCAAAGAAATTGATCGGGAGACGATCCATTTC
1 ATTGA-ATTGGTAG-ACAATTCAAAG-AA-TAAGCGGAAGACGATCCATTTC
2625 GAAGTAAAAA
Statistics
Matches: 181, Mismatches: 12, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
149 3 0.02
150 18 0.10
151 1 0.01
152 103 0.57
153 13 0.07
154 43 0.24
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (151 bp):
ATTGAATTGGTAGACAATTCAAAGAATAAGCGGAAGACGATCCATTTCAAGATTGAATTGGTAGA
CAGTTCAAAGGATAAGCGGAAGACGGTCCTTTCAAGATTGAATTGGTAGACAGTTCAAAGGATAA
GCGGAAGACGGTCCTTTAATA
Done.