Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019612.1 Corchorus olitorius cultivar O-4 contig19645, 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: 5429
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Found at i:423 original size:44 final size:44
Alignment explanation
Indices: 358--669 Score: 294
Period size: 44 Copynumber: 7.3 Consensus size: 44
348 AAACCGAAGA
* *
358 CTGTTTTCCCTCTTTCAAAAAATGCCCCTTCCCGGTCGGAAGGTCT
1 CTGTTTT--CTCTTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCT
* *
404 CTGTTTTCTCTTTCCAAAAATTCCCCTTCCTGGTTGGAAGGTC-
1 CTGTTTTCTCTTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCT
* * *
447 C---TTT-T-ATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTTT
1 CTGTTTTCTCTTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCT
*
486 CTGTTTTCTCTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTC-
1 CTGTTTTCTCTTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCT
* * *
529 CT-TATTT-AC-TTCTCAAAAATGCCCTTTCCTGGTTGGAAGGTCT
1 CTGT-TTTCTCTTTC-CAAAAATGCCCCTTCCTGGTCGGAAGGTCT
* * * * *
572 TTATTGTCT-TTTCAAAAAAATGCCCCTTCTTGGTCGGAAGGTCT
1 CTGTTTTCTCTTTC-CAAAAATGCCCCTTCCTGGTCGGAAGGTCT
* *
616 CTG-TTTCTCTTTCCAAAAATGCCCATTTCC-GATCGGAAGGTC-
1 CTGTTTTCTCTTTCCAAAAATGCCC-CTTCCTGGTCGGAAGGTCT
*
658 CAGTTTTC-CTTT
1 CTGTTTTCTCTTT
670 GATAATTCTC
Statistics
Matches: 220, Mismatches: 31, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
38 28 0.13
39 2 0.01
40 3 0.01
41 3 0.01
42 39 0.18
43 39 0.18
44 99 0.45
46 7 0.03
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (44 bp):
CTGTTTTCTCTTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCT
Found at i:512 original size:82 final size:83
Alignment explanation
Indices: 375--656 Score: 336
Period size: 82 Copynumber: 3.3 Consensus size: 83
365 CCCTCTTTCA
* *
375 AAAAATGCCCCTTCCCGGTCGGAAGGTCTCTGTTTTCTCTTTCCAAAAATTCCCCTTCCTGGTTG
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTTCTGTTTTCTCTTTCCAAAAATGCCCCTTCCTGGTTG
440 GAAGGTCC-TTTTATTCC
66 GAAGGTCCTTTTTATTCC
457 AAAAATGCCCCTTCCCGGTCGGAAGGTTTCTGTTTTCTCTTTCCAAAAATGCCCCTTCCTGGTTG
1 AAAAATGCCCCTTCCCGGTCGGAAGGTTTCTGTTTTCTCTTTCCAAAAATGCCCCTTCCTGGTTG
522 GAAGGTCCTTATTTACTTCTC
66 GAAGGTCCTT-TTTA-TTC-C
* * * * * * *
543 AAAAATGCCCTTTCCTGGTTGGAAGGTCTT-TATTGTCT-TTTCAAAAAAATGCCCCTTCTTGGT
1 AAAAATGCCCCTTCCCGGTCGGAAGGT-TTCTGTTTTCTCTTTC-CAAAAATGCCCCTTCCTGGT
* *
606 CGGAAGGTCTCTGTTTCTCTTTCC
64 TGGAAGGTC-CT-TTT-T-ATTCC
* * *
630 AAAAATGCCCATTTCCGATCGGAAGGT
1 AAAAATGCCCCTTCCCGGTCGGAAGGT
657 CCAGTTTTCC
Statistics
Matches: 174, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
82 71 0.41
83 1 0.01
84 4 0.02
85 7 0.04
86 57 0.33
87 29 0.17
88 5 0.03
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.35
Consensus pattern (83 bp):
AAAAATGCCCCTTCCCGGTCGGAAGGTTTCTGTTTTCTCTTTCCAAAAATGCCCCTTCCTGGTTG
GAAGGTCCTTTTTATTCC
Found at i:780 original size:40 final size:40
Alignment explanation
Indices: 673--1200 Score: 593
Period size: 40 Copynumber: 12.9 Consensus size: 40
663 TTCCTTTGAT
* *
673 AATTCTCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTTTA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
713 AATTCCCAAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
1 AATTCCC-AGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
* * *
754 AACTCCTAGTTTGCCCTTCC-CGATCGGAAGGTGTTG-TCA
1 AATTCCCAGTTTGCCCTTCCTC-ATCGGAAGGTGTTGTTTA
* * * *
793 GCATTCTCAGTTTGCCCTTCCCCATCGGAAGCTGTTGTTTA
1 -AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
* * *
834 AATTCTCAGTTTGCTCTTCCTTATCGGAAGGTGTTGTTTAA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTT-A
875 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
*
915 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTCGTTTTA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTTA
*
956 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TCA
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
* * * *
995 GCATTCCCTGTTTGTCCTTCCTCATCGGAAGGTATTGTTTA
1 -AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
* * *
1036 AGTTCACCAGTTTGTCCTTCCTCACCGGAAGGTGTTGTTTA
1 AATTC-CCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
* *
1077 GATTTCCAGTTTGCCCTAT-CTCATCGGAAGGTGTTGTTTAA
1 AATTCCCAGTTTGCCCT-TCCTCATCGGAAGGTGTTGTTT-A
* *
1118 AGCCCATTCTTTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGATTT-
1 A----ATTC---CCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTTA
* *
1165 CATTCCC-GTTATGCCCTT-CTCCACCGGAAGGTGTTG
1 AATTCCCAGTT-TGCCCTTCCT-CATCGGAAGGTGTTG
1201 ATTTTATTCT
Statistics
Matches: 422, Mismatches: 43, Indels: 46
0.83 0.08 0.09
Matches are distributed among these distances:
39 9 0.02
40 221 0.52
41 154 0.36
43 4 0.01
45 3 0.01
47 1 0.00
48 27 0.06
49 3 0.01
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (40 bp):
AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
Found at i:886 original size:121 final size:120
Alignment explanation
Indices: 672--1200 Score: 604
Period size: 121 Copynumber: 4.3 Consensus size: 120
662 TTTCCTTTGA
* *
672 TAATTCTCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTTTAAATTCCCAAGTTTGCCCTTCCTCA
1 TAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCC-AGTTTGCCCTTCCTCA
* *
737 TCGGAAGGTGTTGTTT-AAACTCCTAGTTTGCCCTTCC-CGATCGGAAGGTGTTG-T
65 TCGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTC-ATCGGAAGGTGTTGTT
* * * * * * *
791 CAGCATTCTCAGTTTGCCCTTCCCCATCGGAAGCTGTTGTTTAAATTCTCAGTTTGCTCTTCCTT
1 TA--ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCTC
856 ATCGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTT
64 ATCGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTT
*
913 TAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTCGTTTTAAATTCCCAGTTTGCCCTTCCTC
1 T-AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTTAAATTCCCAGTTTGCCCTTCCTC
* ** * * *
978 ATCGGAAGGTGTTG-TCAGCATTCCCTGTTTGTCCTTCCTCATCGGAAGGTATTGTT
64 ATCGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTT
* * * *
1034 TAAGTTCACCAGTTTGTCCTTCCTCACCGGAAGGTGTTGTTTAGATTTCCAGTTTGCCCTAT-CT
1 TAA-TTC-CCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCT-TCCT
* *
1098 CATCGGAAGGTGTTGTTTAAAGCCCATTCTTTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGAT
63 CATCGGAAGGTGTTGTTTAAA----ATTC---CCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-T
1163 T
120 T
* *
1164 TCATTCCC-GTTATGCCCTT-CTCCACCGGAAGGTGTTG
1 TAATTCCCAGTT-TGCCCTTCCT-CATCGGAAGGTGTTG
1201 ATTTTATTCT
Statistics
Matches: 351, Mismatches: 38, Indels: 33
0.83 0.09 0.08
Matches are distributed among these distances:
119 1 0.00
120 32 0.09
121 182 0.52
122 70 0.20
123 1 0.00
126 4 0.01
127 5 0.01
128 23 0.07
129 29 0.08
130 4 0.01
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (120 bp):
TAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCAT
CGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTT
Found at i:915 original size:81 final size:81
Alignment explanation
Indices: 673--1200 Score: 574
Period size: 81 Copynumber: 6.4 Consensus size: 81
663 TTCCTTTGAT
*
673 AATTCTCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTTT-AAATTCCCAAGTTTGCCCTTCCTCA
1 AATTCTCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAAATTCCC-AGTTTGCCCTTCCTCA
737 TCGGAAGGTGTTGTTTA
65 TCGGAAGGTGTTGTTTA
* * ** * *
754 AACTC-CTAGTTTGCCCTTCC-CGATCGGAAGGTGTTG-TCAGCATTCTCAGTTTGCCCTTCCCC
1 AATTCTC-AGTTTGCCCTTCCTC-ATCGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTC
*
816 ATCGGAAGCTGTTGTTTA
64 ATCGGAAGGTGTTGTTTA
* *
834 AATTCTCAGTTTGCTCTTCCTTATCGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCAT
1 AATTCTCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCAT
899 CGGAAGGTGTTGTTTA
66 CGGAAGGTGTTGTTTA
* * *
915 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTCGTTTTAAATTCCCAGTTTGCCCTTCCTCAT
1 AATTCTCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCAT
*
980 CGGAAGGTGTTG-TCA
66 CGGAAGGTGTTGTTTA
* * * * * * *
995 GCATTCCCTGTTTGTCCTTCCTCATCGGAAGGTATTGTTT-AAGTTCACCAGTTTGTCCTTCCTC
1 -AATTCTCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAAATTC-CCAGTTTGCCCTTCCTC
*
1059 ACCGGAAGGTGTTGTTTA
64 ATCGGAAGGTGTTGTTTA
*
1077 GATT-TCCAGTTTGCCCTAT-CTCATCGGAAGGTGTTGTTTAAAGCCCATTCTTTCCAGTTTGCC
1 AATTCT-CAGTTTGCCCT-TCCTCATCGGAAGGTGTTGTTTAAA----ATTC---CCAGTTTGCC
* *
1140 CTTCCCCACCGGAAGGTGTTGATTT-
57 CTTCCTCATCGGAAGGTGTTG-TTTA
* * *
1165 CATTC-CCGTTATGCCCTT-CTCCACCGGAAGGTGTTG
1 AATTCTCAGTT-TGCCCTTCCT-CATCGGAAGGTGTTG
1201 ATTTTATTCT
Statistics
Matches: 381, Mismatches: 44, Indels: 37
0.82 0.10 0.08
Matches are distributed among these distances:
80 71 0.19
81 240 0.63
82 5 0.01
86 3 0.01
87 7 0.02
88 52 0.14
89 3 0.01
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (81 bp):
AATTCTCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCAT
CGGAAGGTGTTGTTTA
Found at i:1201 original size:40 final size:39
Alignment explanation
Indices: 1128--1225 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 39
1118 AGCCCATTCT
1128 TTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGATTTCA
1 TTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGATTTCA
* * *
1167 TTCCCGTTATGCCCTTCTCCACCGGAAGGTGTTGATTTTA
1 TTCCAGTT-TGCCCTTCCCCACCGGAAGGTGTTGATTTCA
**
1207 TTCTTGTTTTGCCCTTCCC
1 TTCCAG-TTTGCCCTTCCC
1226 GGTCGTAAGG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
39 7 0.14
40 42 0.82
41 2 0.04
ACGTcount: A:0.12, C:0.31, G:0.18, T:0.39
Consensus pattern (39 bp):
TTCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGATTTCA
Found at i:1271 original size:48 final size:48
Alignment explanation
Indices: 1201--1346 Score: 206
Period size: 48 Copynumber: 3.0 Consensus size: 48
1191 GAAGGTGTTG
* * *
1201 ATTTTATTCTTGTTTTGCCCTTCCCGGTCGTAAGGTGTTGTCTTCAAT
1 ATTTTATTCTCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
* * *
1249 GA-TTTATTCTCGTTTTGCCCTTCCCGATTGGAAGGTGTTATTTTCAAT
1 -ATTTTATTCTCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
1297 ATTTTATTC-CAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
1 ATTTTATTCTC-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
1345 AT
1 AT
1347 CTCGTTCCTG
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
47 2 0.02
48 83 0.97
49 1 0.01
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (48 bp):
ATTTTATTCTCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT
Done.