Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013761.1 Corchorus olitorius cultivar O-4 contig13794, 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: 33582
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:306 original size:16 final size:16
Alignment explanation
Indices: 285--315 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
275 AAGAAATAGG
285 CAATCAATCAAAGCAA
1 CAATCAATCAAAGCAA
301 CAATCAATCAAAGCA
1 CAATCAATCAAAGCA
316 TGCAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.26, G:0.06, T:0.13
Consensus pattern (16 bp):
CAATCAATCAAAGCAA
Found at i:2269 original size:31 final size:28
Alignment explanation
Indices: 2223--2311 Score: 101
Period size: 27 Copynumber: 3.1 Consensus size: 28
2213 AAACACAAAA
2223 CAAAAATATTTTTTTTTTTA-AATTAAAAGCG
1 CAAAAAT-TTTTTTTTTTTAGAA--AAAA-CG
2254 CAAAGAATTTTTTTTTTTTAGAAAAAACG
1 CAAA-AATTTTTTTTTTTTAGAAAAAACG
* *
2283 CAGAAA-TTTTTTTTTTTAGAGAAAACG
1 CAAAAATTTTTTTTTTTTAGAAAAAACG
2310 CA
1 CA
2312 GAGACTAAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
27 22 0.41
28 2 0.04
29 5 0.09
30 4 0.07
31 16 0.30
32 5 0.09
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (28 bp):
CAAAAATTTTTTTTTTTTAGAAAAAACG
Found at i:2574 original size:15 final size:16
Alignment explanation
Indices: 2554--2593 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
2544 AGAGGTTGAA
2554 AGAAAACAATTAAAC-
1 AGAAAACAATTAAACT
2569 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
2585 AGAAAACAA
1 AGAAAACAA
2594 AGCAAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.68, C:0.12, G:0.07, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:7400 original size:31 final size:30
Alignment explanation
Indices: 7359--7461 Score: 113
Period size: 31 Copynumber: 3.5 Consensus size: 30
7349 CACTACCATT
7359 TAAAACCGTTGGATGTGGGCTTAATTTAAA
1 TAAAACCGTTGGATGTGGGCTTAATTTAAA
* ** * *
7389 TAACAACCGTTGGATATAAG--TAGTGTAAA
1 TAA-AACCGTTGGATGTGGGCTTAATTTAAA
7418 -AAAACCGTTGGATGTGGGCTTAATTTAAA
1 TAAAACCGTTGGATGTGGGCTTAATTTAAA
*
7447 TAAGAATCGTTGGAT
1 TAA-AACCGTTGGAT
7462 ATAGGTAGTG
Statistics
Matches: 57, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
27 13 0.23
28 2 0.04
29 14 0.25
30 5 0.09
31 23 0.40
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (30 bp):
TAAAACCGTTGGATGTGGGCTTAATTTAAA
Found at i:7458 original size:58 final size:58
Alignment explanation
Indices: 7360--7478 Score: 211
Period size: 58 Copynumber: 2.1 Consensus size: 58
7350 ACTACCATTT
7360 AAAACCGTTGGATGTGGGCTTAATTTAAATAACAACCGTTGGATATAAGTAGTGTAAA
1 AAAACCGTTGGATGTGGGCTTAATTTAAATAACAACCGTTGGATATAAGTAGTGTAAA
* * *
7418 AAAACCGTTGGATGTGGGCTTAATTTAAATAAGAATCGTTGGATATAGGTAGTGTAAA
1 AAAACCGTTGGATGTGGGCTTAATTTAAATAACAACCGTTGGATATAAGTAGTGTAAA
7476 AAA
1 AAA
7479 GTAGTATGAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (58 bp):
AAAACCGTTGGATGTGGGCTTAATTTAAATAACAACCGTTGGATATAAGTAGTGTAAA
Found at i:7691 original size:25 final size:25
Alignment explanation
Indices: 7657--7707 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
7647 AGTTTAGAAC
*
7657 TAATTTACTCAAACGAAATCTCGAG
1 TAATTCACTCAAACGAAATCTCGAG
*
7682 TAATTCACTCAAATGAAATCTCGAG
1 TAATTCACTCAAACGAAATCTCGAG
7707 T
1 T
7708 TCAAGACTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (25 bp):
TAATTCACTCAAACGAAATCTCGAG
Found at i:9084 original size:2 final size:2
Alignment explanation
Indices: 9077--9145 Score: 74
Period size: 2 Copynumber: 36.5 Consensus size: 2
9067 GACCGACATA
* * * *
9077 AT AT AT AT -T AT AT TT AT TT AT TT AT AT AT AT -T AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9117 AT -T AT AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9146 AGAAATCTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
1 4 0.07
2 51 0.93
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
AT
Found at i:9106 original size:23 final size:25
Alignment explanation
Indices: 9074--9144 Score: 101
Period size: 23 Copynumber: 2.9 Consensus size: 25
9064 CCCGACCGAC
9074 ATAATATATATTATATTTAT-TTAT
1 ATAATATATATTATATTTATATTAT
*
9098 -TTATATATATTATATTTATATTAT
1 ATAATATATATTATATTTATATTAT
*
9122 ATAATATATATATATATATATAT
1 ATAATATATAT-TATATTTATAT
9145 AAGAAATCTG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
23 18 0.44
24 4 0.10
25 9 0.22
26 10 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATAATATATATTATATTTATATTAT
Found at i:16148 original size:13 final size:13
Alignment explanation
Indices: 16130--16161 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16120 TATTTTATTT
*
16130 AAATAAAAGAACA
1 AAATAAAAGAAAA
16143 AAATAAAAGAAAA
1 AAATAAAAGAAAA
16156 AAATAA
1 AAATAA
16162 CTTTATTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.09
Consensus pattern (13 bp):
AAATAAAAGAAAA
Found at i:16633 original size:19 final size:19
Alignment explanation
Indices: 16609--16645 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16599 CTGTTTGGCA
*
16609 ACTGTACGGATAAGATTAC
1 ACTGTACAGATAAGATTAC
*
16628 ACTGTACAGATTAGATTA
1 ACTGTACAGATAAGATTA
16646 GGTATTGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (19 bp):
ACTGTACAGATAAGATTAC
Found at i:16895 original size:36 final size:36
Alignment explanation
Indices: 16848--16922 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
16838 TACCCTTGCT
16848 ATTCTAATCCACGTTTAGTAATTTTAAGACTGTTTC
1 ATTCTAATCCACGTTTAGTAATTTTAAGACTGTTTC
16884 ATTCTAATCCACGTTTAGTAATTTTAAGACTGTTTC
1 ATTCTAATCCACGTTTAGTAATTTTAAGACTGTTTC
16920 ATT
1 ATT
16923 TCATTATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.45
Consensus pattern (36 bp):
ATTCTAATCCACGTTTAGTAATTTTAAGACTGTTTC
Found at i:17890 original size:60 final size:60
Alignment explanation
Indices: 17824--17952 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
17814 TGTATGCAAC
** * *
17824 AATGCTCAATTTGGGA-CTCATACTTTTAATTTTATTAAATAAGGCCCTAA-GTTATGTGAA
1 AATGCTCAATTCAGGATC-CATACTTTGAATTTGATTAAATAAGGCCCTAACG-TATGTGAA
* * * * *
17884 AGTGCTCAATTCAGGATCCATGCTTTGAATTTGGTTAAATAGGGTCCTAACGTATGTGAA
1 AATGCTCAATTCAGGATCCATACTTTGAATTTGATTAAATAAGGCCCTAACGTATGTGAA
17944 AATGCTCAA
1 AATGCTCAA
17953 ATAAGGATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
60 55 0.96
61 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Consensus pattern (60 bp):
AATGCTCAATTCAGGATCCATACTTTGAATTTGATTAAATAAGGCCCTAACGTATGTGAA
Found at i:18164 original size:61 final size:61
Alignment explanation
Indices: 18007--18168 Score: 168
Period size: 63 Copynumber: 2.6 Consensus size: 61
17997 GCCATGCCTT
* * * *
18007 TATTTGAGCATTTTCGCATATGTTAGGGTCCTATTTAACCAAATTAAAAGTACGGGCTCTAA
1 TATTTGAGCATTTTCGCATACGTTA-GGACCTATTTGACCAAATTAAAAGCACGGGCTCTAA
* * * * *
18069 TTATTTGAGTATTTTCTCATACATTAGGACCCTATTTGAGCAAATTTAAAAGCATGGGC-CTTAA
1 -TATTTGAGCATTTTCGCATACGTTAGGA-CCTATTTGACCAAA-TTAAAAGCACGGGCTC-TAA
18133 -A-TTGAGCATTTTCGCATACGTTAGAGACCTATTTGA
1 TATTTGAGCATTTTCGCATACGTTAG-GACCTATTTGA
18169 ACAATTAGCC
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
61 29 0.35
62 5 0.06
63 34 0.41
64 15 0.18
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (61 bp):
TATTTGAGCATTTTCGCATACGTTAGGACCTATTTGACCAAATTAAAAGCACGGGCTCTAA
Found at i:20405 original size:166 final size:167
Alignment explanation
Indices: 20127--20458 Score: 621
Period size: 166 Copynumber: 2.0 Consensus size: 167
20117 TATTTATTTA
20127 CATAATTTTAAAAAGTTAAATATTTAATTTACAATATTTTTCTATAATTAATAAAAAAAGTTCAA
1 CATAATTTTAAAAAGTTAAATATTTAATTTACAATATTTTTCTATAATTAATAAAAAAAGTTCAA
20192 TGACTAAAAAGGATGCTGATTAAAAAATTATAATACTAAGGGTATTTATAAAATTTCCCAATTAA
66 TGACTAAAAAGGATGCTGATTAAAAAATTATAATACTAAGGGTATTTATAAAATTTCCCAATTAA
20257 AATTTTTGAGTTCGTGATTTTATATAATAGTAAGATG
131 AATTTTTGAGTTCGTGATTTTATATAATAGTAAGATG
20294 CATAATTTTAAAAAGTTAAATATTTAATTTACAATATTTTTCTATAATTAAT-AAAAAAGTTCAA
1 CATAATTTTAAAAAGTTAAATATTTAATTTACAATATTTTTCTATAATTAATAAAAAAAGTTCAA
* * * *
20358 TGAGTAAAAAGGATGTTGATTAAAAAATTATAATACTAAGGGTATTTATGAAATTTCCCAATTAG
66 TGACTAAAAAGGATGCTGATTAAAAAATTATAATACTAAGGGTATTTATAAAATTTCCCAATTAA
20423 AATTTTTGAGTTCGTGATTTTATATAATAGTAAGAT
131 AATTTTTGAGTTCGTGATTTTATATAATAGTAAGAT
20459 ATATATAATT
Statistics
Matches: 161, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
166 109 0.68
167 52 0.32
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (167 bp):
CATAATTTTAAAAAGTTAAATATTTAATTTACAATATTTTTCTATAATTAATAAAAAAAGTTCAA
TGACTAAAAAGGATGCTGATTAAAAAATTATAATACTAAGGGTATTTATAAAATTTCCCAATTAA
AATTTTTGAGTTCGTGATTTTATATAATAGTAAGATG
Found at i:26394 original size:21 final size:21
Alignment explanation
Indices: 26370--26439 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
26360 ATTCAATTGA
26370 AACTCAAGAACCCTAATTATG
1 AACTCAAGAACCCTAATTATG
26391 AACTCAAGAACCCTAATTATG
1 AACTCAAGAACCCTAATTATG
* *
26412 AACTCAAGAAACCTAATTTTG
1 AACTCAAGAACCCTAATTATG
*
26433 AATTCAA
1 AACTCAA
26440 TGAGCTCCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (21 bp):
AACTCAAGAACCCTAATTATG
Found at i:28950 original size:21 final size:21
Alignment explanation
Indices: 28926--28966 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28916 TGCAAACCTT
28926 TTGGATTCAAGTGGTACAAAA
1 TTGGATTCAAGTGGTACAAAA
* *
28947 TTGGATTTAAGTGGTTCAAA
1 TTGGATTCAAGTGGTACAAA
28967 TTAGGGTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (21 bp):
TTGGATTCAAGTGGTACAAAA
Done.