Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014538.1 Corchorus olitorius cultivar O-4 contig14571, 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: 49026
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:94 original size:35 final size:35
Alignment explanation
Indices: 29--95 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
19 GATCCTCTTT
* *
29 GATATTGGAGTTAGTAGGATATTAATGTGTTTGGA
1 GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA
* * *
64 GATATTGAAGTTAGTGGGGTTTTAAGGTGTTT
1 GATATTGAAGTTAGTAGGATATTAAGGTGTTT
96 AAACAGTGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (35 bp):
GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA
Found at i:1076 original size:22 final size:22
Alignment explanation
Indices: 937--1104 Score: 98
Period size: 22 Copynumber: 7.7 Consensus size: 22
927 GACAGAAAGA
* *
937 TTATCAAAA-ATCATAGGAAGG
1 TTATCAAAATTTCATAGGATGG
* *
958 TTA-CAAAATTTCATAGGAAAGT
1 TTATCAAAATTTCATAGG-ATGG
*
980 TTATTAAAATTTCATA--ATTAGG
1 TTATCAAAATTTCATAGGA-T-GG
* *
1002 TTATCAAAGA-TTCTTATGGA-GT
1 TTATCAAA-ATTTCATA-GGATGG
* * **
1024 TTATCACAATTTTATAGG-TAA
1 TTATCAAAATTTCATAGGATGG
* *
1045 TTATCGAAATTTCATATGATGG
1 TTATCAAAATTTCATAGGATGG
* * *
1067 TTATCAAAATTTAATAGGGTAG
1 TTATCAAAATTTCATAGGATGG
1089 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
1105 AAAATATTCA
Statistics
Matches: 110, Mismatches: 25, Indels: 23
0.70 0.16 0.15
Matches are distributed among these distances:
20 6 0.05
21 27 0.25
22 64 0.58
23 12 0.11
25 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGATGG
Found at i:6971 original size:3 final size:3
Alignment explanation
Indices: 6963--6988 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6953 GTTATTAGAG
6963 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6989 ATTGAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17335 original size:7 final size:7
Alignment explanation
Indices: 17323--17347 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17313 CAAAAGGCTC
17323 GACTCTA
1 GACTCTA
17330 GACTCTA
1 GACTCTA
17337 GACTCTA
1 GACTCTA
17344 GACT
1 GACT
17348 GAAGAGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (7 bp):
GACTCTA
Found at i:17837 original size:57 final size:57
Alignment explanation
Indices: 17749--17861 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 57
17739 CAAAACGATG
17749 TCGTTATGCACATACAGTTTAGTTATATTATATATTATTTAATTTTAATTATATATA
1 TCGTTATGCACATACAGTTTAGTTATATTATATATTATTTAATTTTAATTATATATA
* * *
17806 TCGTTTTGCACATAGAGTTTAGTTATATTATATATTTTTTAATTTTAATTATATAT
1 TCGTTATGCACATACAGTTTAGTTATATTATATATTATTTAATTTTAATTATATAT
17862 TATATATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (57 bp):
TCGTTATGCACATACAGTTTAGTTATATTATATATTATTTAATTTTAATTATATATA
Found at i:22667 original size:29 final size:29
Alignment explanation
Indices: 22625--22696 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
22615 CGGTTTTGGT
22625 TGAAACCGACCCGACTAACCCGATTGACC
1 TGAAACCGACCCGACTAACCCGATTGACC
22654 TGAAACCGACCCGACTAACCCGATTGACC
1 TGAAACCGACCCGACTAACCCGATTGACC
22683 TGAAACCGACCCGA
1 TGAAACCGACCCGA
22697 TGCTCACCCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.32, C:0.38, G:0.18, T:0.12
Consensus pattern (29 bp):
TGAAACCGACCCGACTAACCCGATTGACC
Found at i:23181 original size:15 final size:15
Alignment explanation
Indices: 23163--23194 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
23153 ACTCTTAAAA
23163 AAAATAAAAATAGAG
1 AAAATAAAAATAGAG
23178 AAAATAAAAATAGAG
1 AAAATAAAAATAGAG
23193 AA
1 AA
23195 TAGTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAATAAAAATAGAG
Found at i:33152 original size:15 final size:16
Alignment explanation
Indices: 33119--33158 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
33109 TTACTTTGCT
33119 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
33135 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
33150 TTGCTTTCT
1 TTGTTTTCT
33159 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:44285 original size:3 final size:3
Alignment explanation
Indices: 44277--44305 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
44267 TCACTCTTAA
44277 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
44306 GGTTAGTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:48225 original size:16 final size:16
Alignment explanation
Indices: 48204--48238 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
48194 TAGCACTAAA
48204 ATTTGAGAGA-TTTGGT
1 ATTTGAGAGAGTTT-GT
48220 ATTTGAGAGAGTTTGT
1 ATTTGAGAGAGTTTGT
48236 ATT
1 ATT
48239 CAACCGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.46
Consensus pattern (16 bp):
ATTTGAGAGAGTTTGT
Done.