Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007015.1 Corchorus capsularis cultivar CVL-1 contig07036, 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: 17398
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Found at i:96 original size:38 final size:38
Alignment explanation
Indices: 1--298 Score: 249
Period size: 38 Copynumber: 7.8 Consensus size: 38
* * *
1 AGGTCATCTTTCAGCAGTTATCGAAGA-TGGCTGGAAA-
1 AGGTCATCTTTCAGAAGTTATC-AAAATTGACTGGAAAC
* * * *
38 AGGTCATCTTTCTGAAGTTATCAAAATCGATTGGAAAT
1 AGGTCATCTTTCAGAAGTTATCAAAATTGACTGGAAAC
* * * * *
76 AGGTAATTTTTCAGAAGTTATCAAAGTTGATTAGAAAC
1 AGGTCATCTTTCAGAAGTTATCAAAATTGACTGGAAAC
* * ** * *
114 AAGTCATCTTTCAGCAGTTATTGAAGTTGGCTGGAAAC
1 AGGTCATCTTTCAGAAGTTATCAAAATTGACTGGAAAC
** *
152 AGGTCATCTTTCAGATCTTATCGAAATTGACTGGAAAC
1 AGGTCATCTTTCAGAAGTTATCAAAATTGACTGGAAAC
* * * *
190 AGGTCATCTTTTAGAAGTTATCAAAATCGACTAGAAAT
1 AGGTCATCTTTCAGAAGTTATCAAAATTGACTGGAAAC
* * * ** *
228 ATGTCATTTTTCAGAAGTTATCAAAGTTTTCTTGAAAC
1 AGGTCATCTTTCAGAAGTTATCAAAATTGACTGGAAAC
* * * *
266 ATGTCATCTTTAAAAAGTTATCAACAATCGACT
1 AGGTCATCTTTCAGAAGTTATCAA-AATTGACT
299 ATGGATTGGT
Statistics
Matches: 206, Mismatches: 52, Indels: 4
0.79 0.20 0.02
Matches are distributed among these distances:
36 3 0.01
37 27 0.13
38 172 0.83
39 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (38 bp):
AGGTCATCTTTCAGAAGTTATCAAAATTGACTGGAAAC
Found at i:207 original size:114 final size:114
Alignment explanation
Indices: 3--298 Score: 335
Period size: 114 Copynumber: 2.6 Consensus size: 114
1 AG
* * *
3 GTCATCTTTCAGCAGTTATCGAAGATGGCTGGAAA-AGGTCATCTTTCTGAAGTTATCAAAATCG
1 GTCATCTTTCAGCAGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTCAGAACTTATCAAAATCG
* * * * *
67 ATTGGAAATAGGTAATTTTTCAGAAGTTATCAAAGTTGATTAGAAACAA
66 ACTGGAAACAGGTAATTTTTCAGAAGTTATCAAAATCGACTAGAAACAA
* * * *
116 GTCATCTTTCAGCAGTTATTGAAGTTGGCTGGAAACAGGTCATCTTTCAGATCTTATCGAAATTG
1 GTCATCTTTCAGCAGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTCAGAACTTATCAAAATCG
* * *
181 ACTGGAAACAGGTCATCTTTT-AGAAGTTATCAAAATCGACTAGAAATAT
66 ACTGGAAACAGGTAAT-TTTTCAGAAGTTATCAAAATCGACTAGAAACAA
* * * ** * * * * *
230 GTCATTTTTCAGAAGTTATCAAAGTTTTCTTGAAACATGTCATCTTTAAAAAGTTATCAACAATC
1 GTCATCTTTCAGCAGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTCAGAACTTATCAA-AATC
295 GACT
65 GACT
299 ATGGATTGGT
Statistics
Matches: 151, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
113 33 0.22
114 107 0.71
115 11 0.07
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (114 bp):
GTCATCTTTCAGCAGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTCAGAACTTATCAAAATCG
ACTGGAAACAGGTAATTTTTCAGAAGTTATCAAAATCGACTAGAAACAA
Found at i:2942 original size:13 final size:14
Alignment explanation
Indices: 2924--2952 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2914 GAAAAAATTT
2924 AAAAAAGGG-ATAA
1 AAAAAAGGGAATAA
2937 AAAAAAGGGAATAA
1 AAAAAAGGGAATAA
2951 AA
1 AA
2953 GGTTTAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (14 bp):
AAAAAAGGGAATAA
Found at i:7784 original size:16 final size:18
Alignment explanation
Indices: 7750--7784 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7740 TCCTCTTGTC
7750 ATGAAAACACTTCTTTTT
1 ATGAAAACACTTCTTTTT
7768 ATGAAAACA-TT-TTTTT
1 ATGAAAACACTTCTTTTT
7784 A
1 A
7785 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGAAAACACTTCTTTTT
Found at i:11837 original size:16 final size:16
Alignment explanation
Indices: 11816--11846 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11806 CCCTTAGCCT
*
11816 AAAACTAGAGAAAAGC
1 AAAACTAAAGAAAAGC
11832 AAAACTAAAGAAAAG
1 AAAACTAAAGAAAAG
11847 TAGAAGAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.10, G:0.16, T:0.06
Consensus pattern (16 bp):
AAAACTAAAGAAAAGC
Found at i:14577 original size:2 final size:2
Alignment explanation
Indices: 14570--14626 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
14560 TTTTGCCAAT
* * *
14570 TA TA TA TA TA TT TA TA TT TA TA TT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
14612 AA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA T
14627 TGTTCAGGTC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:15068 original size:14 final size:13
Alignment explanation
Indices: 15039--15074 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
15029 GAGTCATAAG
15039 TTTTC-AAAATAT
1 TTTTCAAAAATAT
15051 TTTTCAAAAATGAT
1 TTTTCAAAAAT-AT
15065 TTTTCAAAAA
1 TTTTCAAAAA
15075 AAAAAGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.23
13 5 0.23
14 12 0.55
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (13 bp):
TTTTCAAAAATAT
Found at i:16771 original size:38 final size:38
Alignment explanation
Indices: 16720--17184 Score: 349
Period size: 38 Copynumber: 12.2 Consensus size: 38
16710 AACTCAAAGA
16720 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTAAC
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTAAC
* * * * *
16758 AGTTATCGAAGTTGACTAGAAACAGTTCATCTTTCAGC
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTAAC
* *
16796 AGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTTAGA-
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTA-AC
* * * *
16834 AGTTATCAAAATTGACTAGAAACAGGTCATCTTTCAGC
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTAAC
* * * * *
16872 AGTTACCGAAGTTGACAGGAAAACAGGTCATCTTTCAGC
1 AGTTATCAAAGTTGACTGG-AAACAGGTCATCTTTTAAC
* * * *
16911 AGTTATCGAAGATGGCTGGAAA-AGGTCATCTTTCTGA-
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTT-TAAC
* * * * *
16948 AGTTATCAAAATCGATTGGAAATAGGTAAT-TTTTCAGA-
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTT-A-AC
* * * * *
16986 AGTTATCAAAGTTGATTAGAAACAAGTCATCTTTCAGC
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTAAC
** * *
17024 AGTTATTGAAGTTGGCTGGAAACAGGTCATCTTTCAGATC
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTA-A-C
17064 --TTATCGAAA-TTGACTGGAAACAGGTCATCTTTTAGA-
1 AGTTATC-AAAGTTGACTGGAAACAGGTCATCTTTTA-AC
* * * * *
17100 AGTTATCAAAATCGACTAGAAATATGTCAT-TTTTCAGA-
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTT-A-AC
** * * * *
17138 AGTTATCAAAGTTTTCTTGAAACATGTCATCTTTAAAA
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTAAC
17176 AGTTATCAA
1 AGTTATCAA
17185 CAATCGACTA
Statistics
Matches: 343, Mismatches: 66, Indels: 36
0.77 0.15 0.08
Matches are distributed among these distances:
36 1 0.00
37 38 0.11
38 261 0.76
39 42 0.12
40 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (38 bp):
AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTAAC
Found at i:16849 original size:76 final size:76
Alignment explanation
Indices: 16720--17171 Score: 437
Period size: 76 Copynumber: 5.9 Consensus size: 76
16710 AACTCAAAGA
* * *
16720 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTA-ACAGTTATCGAAGTTGACTAGAAACAGT
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTAGA-AGTTATCAAAATTGACTAGAAACAGG
16784 TCATCTTTCAGC
65 TCATCTTTCAGC
* *
16796 AGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTTAGAAGTTATCAAAATTGACTAGAAACAGGT
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTAGAAGTTATCAAAATTGACTAGAAACAGGT
16861 CATCTTTCAGC
66 CATCTTTCAGC
* * * * * * * *
16872 AGTTACCGAAGTTGACAGGAAAACAGGTCATCTTTCAGCAGTTATCGAAGA-TGGCTGGAAA-AG
1 AGTTATCAAAGTTGACTGG-AAACAGGTCATCTTTTAGAAGTTATC-AAAATTGACTAGAAACAG
* *
16935 GTCATCTTTCTGA
64 GTCATCTTTCAGC
* * * * * * * *
16948 AGTTATCAAAATCGATTGGAAATAGGTAAT-TTTTCAGAAGTTATCAAAGTTGATTAGAAACAAG
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTT-AGAAGTTATCAAAATTGACTAGAAACAGG
17012 TCATCTTTCAGC
65 TCATCTTTCAGC
** * * ** * *
17024 AGTTATTGAAGTTGGCTGGAAACAGGTCATCTTTCAGATCTTATCGAAATTGACTGGAAACAGGT
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTAGAAGTTATCAAAATTGACTAGAAACAGGT
* *
17089 CATCTTTTAGA
66 CATCTTTCAGC
* * * * * * ** * *
17100 AGTTATCAAAATCGACTAGAAATATGTCAT-TTTTCAGAAGTTATCAAAGTTTTCTTGAAACATG
1 AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTT-AGAAGTTATCAAAATTGACTAGAAACAGG
17164 TCATCTTT
65 TCATCTTT
17172 AAAAAGTTAT
Statistics
Matches: 300, Mismatches: 68, Indels: 16
0.78 0.18 0.04
Matches are distributed among these distances:
74 5 0.02
75 28 0.09
76 228 0.76
77 36 0.12
78 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Consensus pattern (76 bp):
AGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTAGAAGTTATCAAAATTGACTAGAAACAGGT
CATCTTTCAGC
Found at i:16937 original size:114 final size:113
Alignment explanation
Indices: 16717--17193 Score: 537
Period size: 114 Copynumber: 4.2 Consensus size: 113
16707 TCAAACTCAA
* *
16717 AGAAGTTATCAAAGTTGACTGGAAACAGGTCATCTTTTA-ACAGTTATCGAAGTTGACTAGAAAC
1 AGAAGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGA-AGTTATCGAAGTTGAC-AGAAAC
*
16781 AGTTCATCTTTCAGCAGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTT
64 AGGTCATCTTTCAGCAGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTT
* * *
16831 AGAAGTTATCAAAATTGACTAGAAACAGGTCATCTTTCAGCAGTTACCGAAGTTGACAGGAAAAC
1 AGAAGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGAAGTTATCGAAGTTGACA-G-AAAC
*
16896 AGGTCATCTTTCAGCAGTTATCGAAGATGGCTGGAAA-AGGTCATCTTTCT
64 AGGTCATCTTTCAGCAGTTATCGAAGTTGGCTGGAAACAGGTCATCTTT-T
* * * * * * *
16946 -GAAGTTATCAAAATCGATTGGAAATAGGTAATTTTTCAGAAGTTATCAAAGTTGATTAGAAACA
1 AGAAGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGAAGTTATCGAAGTTGA-CAGAAACA
* * *
17010 AGTCATCTTTCAGCAGTTATTGAAGTTGGCTGGAAACAGGTCATCTTTC
65 GGTCATCTTTCAGCAGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTT
** * * * * * *
17059 AGATCTTATCGAAATTGACTGGAAACAGGTCATCTTTTAGAAGTTATCAAAATCGACTAGAAATA
1 AGAAGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGAAGTTATCGAAGTTGAC-AGAAACA
* * * * ** * * *
17124 TGTCATTTTTCAGAAGTTATCAAAGTTTTCTTGAAACATGTCATCTTTA
65 GGTCATCTTTCAGCAGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTT
* *
17173 AAAAGTTATCAACAATCGACT
1 AGAAGTTATCAA-AATTGACT
17194 ATGGATTGGT
Statistics
Matches: 305, Mismatches: 49, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
113 39 0.13
114 218 0.71
115 48 0.16
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (113 bp):
AGAAGTTATCAAAATTGACTGGAAACAGGTCATCTTTCAGAAGTTATCGAAGTTGACAGAAACAG
GTCATCTTTCAGCAGTTATCGAAGTTGGCTGGAAACAGGTCATCTTTT
Done.