Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019754.1 Corchorus olitorius cultivar O-4 contig19787, 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: 35996
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Found at i:4265 original size:17 final size:17
Alignment explanation
Indices: 4245--4293 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
4235 GTAATCTTTG
*
4245 ATCACCGGTGATCTTGC
1 ATCACTGGTGATCTTGC
4262 ATCACTGGTGATCTTGC
1 ATCACTGGTGATCTTGC
4279 ATCACTGGTGATCTT
1 ATCACTGGTGATCTT
4294 AGATTACTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.35
Consensus pattern (17 bp):
ATCACTGGTGATCTTGC
Found at i:4307 original size:34 final size:34
Alignment explanation
Indices: 4245--4309 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
4235 GTAATCTTTG
*
4245 ATCACCGGTGATCTTGCATCACTGGTGATCTTGC
1 ATCACCGGTGATCTTGCATCACTAGTGATCTTGC
* *
4279 ATCACTGGTGATCTTAG-ATTACTAGTGATCT
1 ATCACCGGTGATCTT-GCATCACTAGTGATCT
4310 GGGGGGTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (34 bp):
ATCACCGGTGATCTTGCATCACTAGTGATCTTGC
Found at i:25094 original size:19 final size:19
Alignment explanation
Indices: 25070--25108 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
25060 TTCTTATTTG
*
25070 TAACCGTTTCACCATCGTT
1 TAACCGTTTCACCACCGTT
25089 TAACCGTTTCACCACCGTT
1 TAACCGTTTCACCACCGTT
25108 T
1 T
25109 TGGGACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.36
Consensus pattern (19 bp):
TAACCGTTTCACCACCGTT
Found at i:25563 original size:21 final size:21
Alignment explanation
Indices: 25537--25594 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 21
25527 GTTGCTTTAA
25537 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGTACC
* **
25558 TAATCTAATCTGTACA--ATG
1 TAATCTCATCTGTACAGTACC
25577 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
25595 TGCCAAACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 16 0.52
21 15 0.48
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.36
Consensus pattern (21 bp):
TAATCTCATCTGTACAGTACC
Found at i:25944 original size:15 final size:15
Alignment explanation
Indices: 25924--25955 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
25914 ACATGTGCAA
*
25924 ATAAGCAAATAATAC
1 ATAAGCAAATAAGAC
25939 ATAAGCAAATAAGAC
1 ATAAGCAAATAAGAC
25954 AT
1 AT
25956 TGTCTTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.19
Consensus pattern (15 bp):
ATAAGCAAATAAGAC
Found at i:29535 original size:36 final size:36
Alignment explanation
Indices: 29483--29551 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
29473 GTACAATAGC
*
29483 TACTTTTAGTAAGGATTCTTTAACTTTAGGTTTAAA
1 TACTATTAGTAAGGATTCTTTAACTTTAGGTTTAAA
*
29519 TACTATTAGTAAGGATTTTTTAACTTTAGGTTT
1 TACTATTAGTAAGGATTCTTTAACTTTAGGTTT
29552 GTAAGAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.49
Consensus pattern (36 bp):
TACTATTAGTAAGGATTCTTTAACTTTAGGTTTAAA
Found at i:33275 original size:80 final size:82
Alignment explanation
Indices: 33172--33347 Score: 293
Period size: 80 Copynumber: 2.1 Consensus size: 82
33162 TGATGCTTCT
33172 TTGGAGAGATCTGGTTCTGGAGGCATCTTCAGGTTGGCGTTTATTTCTTTGTTGATAGT-A-AAC
1 TTGGAGAGATCTGGTTCTGGAGGCATCTTCAGGTTGGCGTTTATTTCTTTGTTGATAGTAACAAC
33235 ATGAGCAACTTAAACAA
66 ATGAGCAACTTAAACAA
33252 TTGGAGAGATCTGGTTCTGGAGGCATCTTCAGGTTGGCGTTTATTTCTTTGTTGATAGTAAACAA
1 TTGGAGAGATCTGGTTCTGGAGGCATCTTCAGGTTGGCGTTTATTTCTTTGTTGATAGT-----A
33317 ACAACATGAGCAACTTAAACAA
61 ACAACATGAGCAACTTAAACAA
33339 TTGGAGAGA
1 TTGGAGAGA
33348 ATTTGTAGTT
Statistics
Matches: 89, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
80 59 0.66
86 1 0.01
87 29 0.33
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (82 bp):
TTGGAGAGATCTGGTTCTGGAGGCATCTTCAGGTTGGCGTTTATTTCTTTGTTGATAGTAACAAC
ATGAGCAACTTAAACAA
Found at i:34085 original size:17 final size:17
Alignment explanation
Indices: 34063--34098 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34053 CATCTAGTCT
34063 CACATTGGCATCTTTTG
1 CACATTGGCATCTTTTG
**
34080 CACATTTTCATCTTTTG
1 CACATTGGCATCTTTTG
34097 CA
1 CA
34099 TACAAAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.25, G:0.11, T:0.44
Consensus pattern (17 bp):
CACATTGGCATCTTTTG
Found at i:34383 original size:28 final size:29
Alignment explanation
Indices: 34351--34407 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
34341 GCAACGTTAT
34351 TACAAAATACAAAAAGGGGA-TAGCTTTA
1 TACAAAATACAAAAAGGGGAGTAGCTTTA
34379 TACAAAATACAAAAAGGGGAGTAGCTTTA
1 TACAAAATACAAAAAGGGGAGTAGCTTTA
34408 CATTTGCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (29 bp):
TACAAAATACAAAAAGGGGAGTAGCTTTA
Done.