Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016135.1 Corchorus olitorius cultivar O-4 contig16168, 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: 43389
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3115 original size:20 final size:21
Alignment explanation
Indices: 3082--3128 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
3072 AAAATAAAAG
* *
3082 AAAAAATTAGAAATTTTCAAC
1 AAAAAAATAGAAATCTTCAAC
3103 AAAAAAATA-AAATCTTC-AC
1 AAAAAAATAGAAATCTTCAAC
*
3122 AAGAAAA
1 AAAAAAA
3129 GAGATGAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAAATAGAAATCTTCAAC
Found at i:14219 original size:30 final size:30
Alignment explanation
Indices: 14183--14241 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
14173 TTCGTTGAAT
*
14183 TTTTTTCTTTTT-GACTCCTTAAAATAATTC
1 TTTTTTCTTTTTAG-CTCCTCAAAATAATTC
*
14213 TTTTTTCTTTTTAGCTTCTCAAAATAATT
1 TTTTTTCTTTTTAGCTCCTCAAAATAATT
14242 TATCTTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.03, T:0.58
Consensus pattern (30 bp):
TTTTTTCTTTTTAGCTCCTCAAAATAATTC
Found at i:22027 original size:25 final size:25
Alignment explanation
Indices: 21984--22059 Score: 107
Period size: 27 Copynumber: 2.9 Consensus size: 25
21974 TATTTATTTA
21984 TTTTCATAAACCCCTTTGGGCTTTTTT
1 TTTTCATAAA-CCC-TTGGGCTTTTTT
22011 TTTTCATAAACCCTTGGGCTTTTTT
1 TTTTCATAAACCCTTGGGCTTTTTT
*
22036 TTTTCACCAAAACCCTTGGGCTTT
1 TTTTCA--TAAACCCTTGGGCTTT
22060 ATACAGCTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 18 0.39
26 3 0.07
27 25 0.54
ACGTcount: A:0.17, C:0.24, G:0.12, T:0.47
Consensus pattern (25 bp):
TTTTCATAAACCCTTGGGCTTTTTT
Found at i:22178 original size:18 final size:19
Alignment explanation
Indices: 22147--22184 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
22137 AGTTTGTGAC
22147 AGTTTTTTCTAAATG-TAT
1 AGTTTTTTCTAAATGATAT
22165 AGTTTTTT-TAAAATGATAT
1 AGTTTTTTCT-AAATGATAT
22184 A
1 A
22185 AATAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 13 0.72
19 4 0.22
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (19 bp):
AGTTTTTTCTAAATGATAT
Found at i:22338 original size:2 final size:2
Alignment explanation
Indices: 22331--22355 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22321 TTATAATTAG
22331 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22356 TATTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24555 original size:216 final size:216
Alignment explanation
Indices: 24181--24596 Score: 760
Period size: 216 Copynumber: 1.9 Consensus size: 216
24171 CCAAATAACT
*
24181 TATTCCCTCCGTTCCACTTTGAACGTGCACTTTGTGTTTGACAAAAAGTTTCTTGAAAATTGATA
1 TATTCCCTCCGTTCCACTTTGAACGTGCACTTTGTGTTTGACAAAAAGTTTCTAGAAAATTGATA
24246 TTTGTTGGTTACTTTACATTGTTTGACTTTGAATTTTGATATAAAGTAACGAGTCCCATGTAAAA
66 TTTGTTGGTTACTTTACATTGTTTGACTTTGAATTTTGATATAAAGTAACGAGTCCCATGTAAAA
*
24311 GTTAGGTTTATGTAGAATGTAAGGAGAAAAGTATTTTCCATTTTAGAAAATAGAAAAATAGTACA
131 ATTAGGTTTATGTAGAATGTAAGGAGAAAAGTATTTTCCATTTTAGAAAATAGAAAAATAGTACA
*
24376 CTACCTATAATAGAAAAAAAG
196 ATACCTATAATAGAAAAAAAG
* *
24397 TATTCCCTCCGTTCCACTTTGAGCGTGCACTTTGTGTTTGACACAAAGTTTCTAGAAAATTGATA
1 TATTCCCTCCGTTCCACTTTGAACGTGCACTTTGTGTTTGACAAAAAGTTTCTAGAAAATTGATA
* *
24462 TTTGTTGGTTACTTTACATTGTTTGACTTTGAATTTTGATATAAAGTGACGGGTCCCATGTAAAA
66 TTTGTTGGTTACTTTACATTGTTTGACTTTGAATTTTGATATAAAGTAACGAGTCCCATGTAAAA
*
24527 ATTAGGTTTATGTTGAATGTAAGGAGAAAAGTATTTTCCATTTTAGAAAATAGAAAAATAGTACA
131 ATTAGGTTTATGTAGAATGTAAGGAGAAAAGTATTTTCCATTTTAGAAAATAGAAAAATAGTACA
24592 ATACC
196 ATACC
24597 ACAAAACAGC
Statistics
Matches: 192, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
216 192 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.37
Consensus pattern (216 bp):
TATTCCCTCCGTTCCACTTTGAACGTGCACTTTGTGTTTGACAAAAAGTTTCTAGAAAATTGATA
TTTGTTGGTTACTTTACATTGTTTGACTTTGAATTTTGATATAAAGTAACGAGTCCCATGTAAAA
ATTAGGTTTATGTAGAATGTAAGGAGAAAAGTATTTTCCATTTTAGAAAATAGAAAAATAGTACA
ATACCTATAATAGAAAAAAAG
Found at i:24890 original size:33 final size:33
Alignment explanation
Indices: 24837--24927 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 33
24827 AGGAAAGTAA
* *
24837 GTGGCGTTTATA-TGAACAAACGTTCC-TATACG
1 GTGGCGTTTTTATTGAACAAACG-CCCTTATACG
*
24869 GTGGCGTTTTTATTGAACAAACGCCCTTATATG
1 GTGGCGTTTTTATTGAACAAACGCCCTTATACG
**
24902 GTGGCGTTTTGCTTGAGACAAACGCC
1 GTGGCGTTTTTATTGA-ACAAACGCC
24928 ACCATATAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
32 13 0.25
33 29 0.57
34 9 0.18
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (33 bp):
GTGGCGTTTTTATTGAACAAACGCCCTTATACG
Found at i:25423 original size:16 final size:16
Alignment explanation
Indices: 25404--25492 Score: 79
Period size: 16 Copynumber: 5.6 Consensus size: 16
25394 CGGGCTCGGG
25404 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTTTTTT
* ***
25420 CGGGCTCGGGTTAAGT
1 CGGGTTCGGGTTTTTT
*
25436 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTTTTTT
** * *
25452 CGGCCTCGGGTTATGT
1 CGGGTTCGGGTTTTTT
*
25468 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTTTTTT
*
25484 CAGGTTCGG
1 CGGGTTCGG
25493 TCTCGGGTAG
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 53 1.00
ACGTcount: A:0.07, C:0.17, G:0.39, T:0.37
Consensus pattern (16 bp):
CGGGTTCGGGTTTTTT
Found at i:25444 original size:32 final size:32
Alignment explanation
Indices: 25404--25484 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
25394 CGGGCTCGGG
* *
25404 CGGGTTCGGGTTTTTTCGGGCTCGGGTTAAGT
1 CGGGTTCGGGTATTTTCGGCCTCGGGTTAAGT
*
25436 CGGGTTCGGGTATTTTCGGCCTCGGGTTATGT
1 CGGGTTCGGGTATTTTCGGCCTCGGGTTAAGT
25468 CGGGTTCGGGTATTTTC
1 CGGGTTCGGGTATTTTC
25485 AGGTTCGGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.06, C:0.17, G:0.38, T:0.38
Consensus pattern (32 bp):
CGGGTTCGGGTATTTTCGGCCTCGGGTTAAGT
Found at i:25689 original size:13 final size:12
Alignment explanation
Indices: 25666--25731 Score: 64
Period size: 12 Copynumber: 5.3 Consensus size: 12
25656 AAGTTTATTG
25666 ATAATATATAAT
1 ATAATATATAAT
25678 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
25691 ATAACAT-TATT
1 ATAATATATAAT
25702 ATCAATATAT-AT
1 AT-AATATATAAT
25714 ATATATATATATAT
1 ATA-ATATATA-AT
25728 ATAA
1 ATAA
25732 AGATTGAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
11 6 0.14
12 20 0.45
13 13 0.30
14 5 0.11
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:25694 original size:37 final size:36
Alignment explanation
Indices: 25660--25731 Score: 78
Period size: 37 Copynumber: 1.9 Consensus size: 36
25650 TATTATAAGT
25660 TTATTGAT-AATATATA-ATATA-ATAATATAATATAACA
1 TTATT-ATCAATATATATATATATAT-ATA--ATATAACA
25697 TTATTATCAATATATATATATATATATATATATAA
1 TTATTATCAATATATATATATATATATA-ATATAA
25732 AGATTGAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
36 2 0.06
37 19 0.61
38 8 0.26
39 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (36 bp):
TTATTATCAATATATATATATATATATAATATAACA
Found at i:25713 original size:2 final size:2
Alignment explanation
Indices: 25706--25730 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25696 ATTATTATCA
25706 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
25731 AAGATTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26244 original size:15 final size:15
Alignment explanation
Indices: 26224--26253 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26214 ATTTCATGTA
26224 TTTAATTAATTATAC
1 TTTAATTAATTATAC
*
26239 TTTAATTAGTTATAC
1 TTTAATTAATTATAC
26254 GGTACTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTAATTAATTATAC
Found at i:29717 original size:20 final size:21
Alignment explanation
Indices: 29684--29723 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
29674 TCTCTAGGTA
*
29684 ATTCATCAACATAAAGCTAAT
1 ATTCATCAAAATAAAGCTAAT
29705 ATTC-TCAAAATAAAGCTAA
1 ATTCATCAAAATAAAGCTAA
29724 CATTAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.28
Consensus pattern (21 bp):
ATTCATCAAAATAAAGCTAAT
Found at i:31820 original size:24 final size:24
Alignment explanation
Indices: 31783--31829 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31773 AAACAACACA
* *
31783 CTTTTTGTACAAATCTATGTTTGAT
1 CTTTTTGTAAAAATCAAT-TTTGAT
31808 CTTTTTG-AAAAATCAATTTTGA
1 CTTTTTGTAAAAATCAATTTTGA
31830 ATGCATACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 8 0.40
25 7 0.35
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (24 bp):
CTTTTTGTAAAAATCAATTTTGAT
Found at i:32379 original size:17 final size:17
Alignment explanation
Indices: 32346--32378 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32336 CTCCTCTTGC
*
32346 ATGAAAACACTTCTTTT
1 ATGAAAACAATTCTTTT
32363 ATGAAAACAATT-TTTT
1 ATGAAAACAATTCTTTT
32379 TTTTTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (17 bp):
ATGAAAACAATTCTTTT
Done.