Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010024.1 Corchorus olitorius cultivar O-4 contig10056, 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: 2218
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:858 original size:81 final size:80
Alignment explanation
Indices: 669--1041 Score: 306
Period size: 81 Copynumber: 4.6 Consensus size: 80
659 AATATATAAA
* * ** * * *
669 TCCATTCGTTAATCTCAATGTAGTATTTACTGTAAATTATTTAA-TTAACCTTGTAAATGGGAAA
1 TCCATTCGTTAAACCCAATGTAACATTTACTGCAAATTATCTAATTTAACCTTGTAAATGGG-AG
*
733 ATAGAGGGTGAGTAAG
65 AGAGAGGGTGAGTAAG
* * * ** * *
749 TCCATTCGTTAATCTCAATATAGTATTTACTGTAAATTATTTAATTTAACCTTGTAAATGGGAAG
1 TCCATTCGTTAAACCCAATGTAACATTTACTGCAAATTATCTAATTTAACCTTGTAAATGGG-AG
814 AGAGAGGGTGAGTAAG
65 AGAGAGGGTGAGTAAG
* * * * * *
830 TCCATTTGTTAAACCCAATGTAACATTTATTGCACATTACCCAATTTTTACGCTTG-AAAGTGGT
1 TCCATTCGTTAAACCCAATGTAACATTTACTGCAAATTATCTAA-TTTAAC-CTTGTAAA-TGG-
* *
894 G-GCAAAGTGGGTGAGTAAG
62 GAG-AGAGAGGGTGAGTAAG
* * * * * * *
913 TCCTTTCGTTAAACCCAATGTAACATTTACTACACATTATCTAATTTGACCTTGCAAGTAGGAG-
1 TCCATTCGTTAAACCCAATGTAACATTTACTGCAAATTATCTAATTTAACCTTGTAAATGGGAGA
* *
977 GAGATGGGATCAATAAG
66 GAGA-GGG-TGAGTAAG
* * *
994 TCCCTTCGTTAAACCCGATGTAACATTTGA-TGCATATTATCTAATTTA
1 TCCATTCGTTAAACCCAATGTAACATTT-ACTGCAAATTATCTAATTTA
1042 CCTGTACACC
Statistics
Matches: 246, Mismatches: 36, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
79 2 0.01
80 47 0.19
81 120 0.49
82 17 0.07
83 59 0.24
84 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (80 bp):
TCCATTCGTTAAACCCAATGTAACATTTACTGCAAATTATCTAATTTAACCTTGTAAATGGGAGA
GAGAGGGTGAGTAAG
Found at i:925 original size:83 final size:80
Alignment explanation
Indices: 819--1021 Score: 230
Period size: 83 Copynumber: 2.5 Consensus size: 80
809 GGAAGAGAGA
* * *
819 GGGTGAGTAAGTCCATTT-GTTAAACCCAATGTAACATTTATTGCACATTACCCAATTTTTACGC
1 GGGTGAGTAAGTCC-TTTCGTTAAACCCAATGTAACATTTACTACACATTACCCAA-TTTGAC-C
*
883 TTGAAAGT-GGTGGCAAAGT
63 TTGAAAGTAGGAGG-AAA-T
* *
902 GGGTGAGTAAGTCCTTTCGTTAAACCCAATGTAACATTTACTACACATTATCTAATTTGACCTTG
1 GGGTGAGTAAGTCCTTTCGTTAAACCCAATGTAACATTTACTACACATTACCCAATTTGACCTTG
* *
967 CAAGTAGGAGGAGAT
66 AAAGTAGGAGGAAAT
* * * *
982 GGGATCAATAAGTCCCTTCGTTAAACCCGATGTAACATTT
1 GGG-TGAGTAAGTCCTTTCGTTAAACCCAATGTAACATTT
1022 GATGCATATT
Statistics
Matches: 105, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
80 4 0.04
81 42 0.40
82 12 0.11
83 47 0.45
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (80 bp):
GGGTGAGTAAGTCCTTTCGTTAAACCCAATGTAACATTTACTACACATTACCCAATTTGACCTTG
AAAGTAGGAGGAAAT
Found at i:1175 original size:135 final size:135
Alignment explanation
Indices: 917--1178 Score: 350
Period size: 135 Copynumber: 1.9 Consensus size: 135
907 AGTAAGTCCT
*
917 TTCGTTAAACCCAATGTAACATTTACTACACATTATCTAATTTGACCTTGCAAGTAGGAGGAGAT
1 TTCGTTAAACCCAATGTAACATTTACTACACATTACCTAATTTGACCTTGCAAGTAGGAGGAGAT
* * * * * *
982 GGGATCAATAAGTCCCTTCGTTAAACCCGATGTAACATTTGATGCATATTATCTAATTTACCTGT
66 CGGATCAATAAGTCCCTTCGTTAAACCCAATGTAACATCTGATGCACATTAACGAATTTACCTGT
1047 ACACC
131 ACACC
* *
1052 TTCGTTAAACCCAATGTAACATTTACTACACATTACCTAATTT-ACCCTTGCAAGTGGGAGGCGA
1 TTCGTTAAACCCAATGTAACATTTACTACACATTACCTAATTTGA-CCTTGCAAGTAGGAGGAGA
* * * **
1116 GTCGG-TGAGTAAGTCCCTTCGTTAAACCCAATTTCGCATCT-ACTGCACATTAACGAATTTACC
65 -TCGGATCAATAAGTCCCTTCGTTAAACCCAATGTAACATCTGA-TGCACATTAACGAATTTACC
1179 CTTGCAAGTG
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
134 2 0.02
135 105 0.95
136 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (135 bp):
TTCGTTAAACCCAATGTAACATTTACTACACATTACCTAATTTGACCTTGCAAGTAGGAGGAGAT
CGGATCAATAAGTCCCTTCGTTAAACCCAATGTAACATCTGATGCACATTAACGAATTTACCTGT
ACACC
Found at i:1185 original size:81 final size:81
Alignment explanation
Indices: 1050--1672 Score: 656
Period size: 81 Copynumber: 7.6 Consensus size: 81
1040 TACCTGTACA
* * * *
1050 CCTTCGTTAAACCCAATGTAACATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGCG
1 CCTTCGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
*
1115 AGTCGGTGAGTAAGTC
66 AGTGGGTGAGTAAGTC
* * * *
1131 CCTTCGTTAAACCCAATTTCGCATCTACTGCACATTAACGAATTTACCCTTGCAAGTGGGAGGAG
1 CCTTCGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
* *
1196 AGTGGGTCAGTAACTC
66 AGTGGGTGAGTAAGTC
* * ** * * *
1212 TCTTCGTTAAACTCAATTTTTCATTAACTGCACATTACATAATTTACCCTTGCAAGTGGTAGGAG
1 CCTTCGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
*
1277 AGAGGGTGAGTAAGTC
66 AGTGGGTGAGTAAGTC
** ** * * * * * *
1293 CCTTTATTAAA-CCAATTTTTCATTTACTGTATATTGCCTAATTTGCCCTTACAAGTGGGAGGAA
1 CCTTCGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
*
1357 AGTGGGTGAGTTAGTC
66 AGTGGGTGAGTAAGTC
* ** * *
1373 CCATCGTTAAACCCAATTTTTCATTTACTGCAAATTACCTAATTTACCCTTACAAGTGGGAGGAG
1 CCTTCGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
* * **
1438 AGAGGGTGTGTAACCC
66 AGTGGGTGAGTAAGTC
* * * * **
1454 CCTTCGTTAAACCCAATGTAGCATTTATTGCACATTACTTAATTTACCATTGTTAGTGGGACTAG
1 CCTTCGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGG---AG
*
1519 AGAGAGTGTGGGTAAGTAAGTC
63 -GAGA--GTGGGTGAGTAAGTC
* * * * * **
1541 CCATCGTTAAACCTAATATAACATTTACTGCACATTACCTGATTTAAGCTTGCAAGTGGGAGGAG
1 CCTTCGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
*
1606 AGTGTGTGAGTATA-TC
66 AGTGGGTGAGTA-AGTC
* * *
1622 CCTTCGTTAAACCTAATGTGGCATTTACTGCACATTACCTAATTTACCCTT
1 CCTTCGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTT
1673 ACACTTTCGT
Statistics
Matches: 445, Mismatches: 89, Indels: 16
0.81 0.16 0.03
Matches are distributed among these distances:
80 65 0.15
81 309 0.69
82 1 0.00
83 4 0.01
84 4 0.01
85 4 0.01
87 58 0.13
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (81 bp):
CCTTCGTTAAACCCAATTTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
AGTGGGTGAGTAAGTC
Found at i:1257 original size:216 final size:217
Alignment explanation
Indices: 837--1259 Score: 507
Period size: 216 Copynumber: 1.9 Consensus size: 217
827 AAGTCCATTT
* * * *
837 GTTAAACCCAATGTAACATTTATTGCACATTACCCAATTTTTACGCTTGAAAGTGGTGGCAAAGT
1 GTTAAACCCAATGTAACATTTACTACACATTACCCAA-TTTTACCCTTGAAAGTGGAGGCAAAGT
* * * * *
902 GGGTGAGTAAGTCCTTTCGTTAAACCCAATGTAACATTTACTACACATTATCTAATTTGACCTTG
65 CGGTGAGTAAGTCCCTTCGTTAAACCCAATGTAACATCTACTACACATTAACGAATTTGACCTTG
* * * *
967 CAAGTAGGAGGAGATGGGATCAATAAGTCCCTTCGTTAAACCCGATGTAACATTTGATGCATATT
130 CAAGTAGGAGGAGATGGGATCAATAACTCCCTTCGTTAAACCCAATGTAACATTTAATGCACATT
1032 ATCTAATTTACCTGTACACCTTC
195 ATCTAATTTACCTGTACACCTTC
* * *
1055 GTTAAACCCAATGTAACATTTACTACACATTACCTAA-TTTACCCTTGCAAGTGGGAGGC-GAGT
1 GTTAAACCCAATGTAACATTTACTACACATTACCCAATTTTACCCTTGAAAGT-GGAGGCAAAGT
* ** *
1118 CGGTGAGTAAGTCCCTTCGTTAAACCCAATTTCGCATCTACTGCACATTAACGAATTT-ACCCTT
65 CGGTGAGTAAGTCCCTTCGTTAAACCCAATGTAACATCTACTACACATTAACGAATTTGA-CCTT
* * * * * **
1182 GCAAGTGGGAGGAGAGTGGG-TCAGTAACTCTCTTCGTTAAACTCAATTTTTCA-TTAACTGCAC
129 GCAAGTAGGAGGAGA-TGGGATCAATAACTCCCTTCGTTAAACCCAATGTAACATTTAA-TGCAC
1245 ATTA-CATAATTTACC
192 ATTATC-TAATTTACC
1260 CTTGCAAGTG
Statistics
Matches: 173, Mismatches: 27, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
215 5 0.03
216 125 0.72
217 9 0.05
218 34 0.20
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (217 bp):
GTTAAACCCAATGTAACATTTACTACACATTACCCAATTTTACCCTTGAAAGTGGAGGCAAAGTC
GGTGAGTAAGTCCCTTCGTTAAACCCAATGTAACATCTACTACACATTAACGAATTTGACCTTGC
AAGTAGGAGGAGATGGGATCAATAACTCCCTTCGTTAAACCCAATGTAACATTTAATGCACATTA
TCTAATTTACCTGTACACCTTC
Found at i:1418 original size:161 final size:162
Alignment explanation
Indices: 1053--1675 Score: 665
Period size: 161 Copynumber: 3.8 Consensus size: 162
1043 CTGTACACCT
* * * *
1053 TCGTTAAACCCAATGTAACATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGCGAGT
1 TCGTTAAACCCAATTTAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGA
* * * * * * *
1118 CGGTGAGTAAGTCCCTTCGTTAAACCCAATTTCGCATCTACTGCACATTAACGAATTTACCCTTG
66 GGGTGAGTAAGTCCCTTCGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTACCCTTA
* * * * *
1183 CAAGTGGGAGGAGAGTGGGTCAGTAACTCTCT
131 CAAGTGGGAGGAAAGTGGGTAAGTAAGTCCCA
* ** * * *
1215 TCGTTAAACTCAATTTTTCATTAACTGCACATTACATAATTTACCCTTGCAAGTGGTAGGAGAGA
1 TCGTTAAACCCAATTTAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGA
** * ** * * * *
1280 GGGTGAGTAAGTCCCTTTATTAAA-CCAATTTTTCATTTACTGTATATTGCCTAATTTGCCCTTA
66 GGGTGAGTAAGTCCCTTCGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTACCCTTA
* *
1344 CAAGTGGGAGGAAAGTGGGTGAGTTAGTCCCA
131 CAAGTGGGAGGAAAGTGGGTAAGTAAGTCCCA
** * *
1376 TCGTTAAACCCAATTTTTCATTTACTGCAAATTACCTAATTTACCCTTACAAGTGGGAGGAGAGA
1 TCGTTAAACCCAATTTAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGA
* ** * * * *
1441 GGGTGTGTAACCCCCTTCGTTAAACCCAATGTAGCATTTATTGCACATTACTTAATTTACCATTG
66 GGGTGAGTAAGTCCCTTCGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTACCCTTA
** *
1506 TTAGTGGGACTAGAGAGAGTGTGGGTAAGTAAGTCCCA
131 CAAGTGGG---AG-GA-A-AGTGGGTAAGTAAGTCCCA
* * * ** *
1544 TCGTTAAACCTAATATAACATTTACTGCACATTACCTGATTTAAGCTTGCAAGTGGGAGGAGAGT
1 TCGTTAAACCCAATTTAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGA
* * *
1609 GTGTGAGTATA-TCCCTTCGTTAAACCTAATGTGGCATTTACTGCACATTACCTAATTTACCCTT
66 GGGTGAGTA-AGTCCCTTCGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTACCCTT
1673 ACA
130 ACA
1676 CTTTCGTTGA
Statistics
Matches: 376, Mismatches: 77, Indels: 10
0.81 0.17 0.02
Matches are distributed among these distances:
161 134 0.36
162 111 0.30
165 2 0.01
166 2 0.01
167 1 0.00
168 125 0.33
169 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (162 bp):
TCGTTAAACCCAATTTAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGA
GGGTGAGTAAGTCCCTTCGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTACCCTTA
CAAGTGGGAGGAAAGTGGGTAAGTAAGTCCCA
Found at i:1499 original size:242 final size:247
Alignment explanation
Indices: 1056--1675 Score: 721
Period size: 242 Copynumber: 2.5 Consensus size: 247
1046 TACACCTTCG
* * * * *
1056 TTAAACCCAATGTAACATTTACTACACATTACCTAATTTACCCTTGCAAGTGGGAGGCGAGTCGG
1 TTAAACCTAATATAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGTGGG
* * * * *
1121 TGAGTAAGTCCCTTCGTTAAACCCAATTTCGCATCTACTGCACATTAACGAATTTACCCTTGCAA
66 TGAGTTAGTCCCTTCGTTAAACCCAATTTCGCATTTACTGCACATTACCTAATTTACCCTTACAA
* * * * * **
1186 GTGGGAGGAGAGTGGGTCAGTAACTCTCTTCGTTAAACTCAATTTTTCATTAACTGCACATTACA
131 GTGGGAGGAGAGAGGGTCAGTAACCCCCTTCGTTAAACCCAATGTAGCATTAACTGCACATTACA
* * * *
1251 TAATTTACCCTTGCAAGT-GG-TAG-GAGA-GAGGGTGAGTAAGTCCCTTTA
196 TAATTTACCATTGCAAGTGGGATAGAGAGAGGAGGGTAAGTAAGTCCCATCA
* ** * * * * * *
1299 TTAAACC-AATTTTTCATTTACTGTATATTGCCTAATTTGCCCTTACAAGTGGGAGGAAAGTGGG
1 TTAAACCTAATATAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGTGGG
* ** *
1363 TGAGTTAGTCCCATCGTTAAACCCAATTTTTCATTTACTGCAAATTACCTAATTTACCCTTACAA
66 TGAGTTAGTCCCTTCGTTAAACCCAATTTCGCATTTACTGCACATTACCTAATTTACCCTTACAA
** * * *
1428 GTGGGAGGAGAGAGGGTGTGTAACCCCCTTCGTTAAACCCAATGTAGCATTTATTGCACATTACT
131 GTGGGAGGAGAGAGGGTCAGTAACCCCCTTCGTTAAACCCAATGTAGCATTAACTGCACATTACA
** * *
1493 TAATTTACCATTGTTAGTGGGACTAGAGAGAGTGTGGGTAAGTAAGTCCCATCG
196 TAATTTACCATTGCAAGTGGGA-TAGAGAGAG-GAGGGTAAGTAAGTCCCATCA
* ** *
1547 TTAAACCTAATATAACATTTACTGCACATTACCTGATTTAAGCTTGCAAGTGGGAGGAGAGTGTG
1 TTAAACCTAATATAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGTGGG
* * *
1612 TGAGTATA-TCCCTTCGTTAAACCTAATGTGGCATTTACTGCACATTACCTAATTTACCCTTACA
66 TGAGT-TAGTCCCTTCGTTAAACCCAATTTCGCATTTACTGCACATTACCTAATTTACCCTTACA
1676 CTTTCGTTGA
Statistics
Matches: 309, Mismatches: 60, Indels: 10
0.82 0.16 0.03
Matches are distributed among these distances:
242 169 0.55
243 9 0.03
245 3 0.01
246 4 0.01
248 23 0.07
249 99 0.32
250 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (247 bp):
TTAAACCTAATATAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGGAGAGTGGG
TGAGTTAGTCCCTTCGTTAAACCCAATTTCGCATTTACTGCACATTACCTAATTTACCCTTACAA
GTGGGAGGAGAGAGGGTCAGTAACCCCCTTCGTTAAACCCAATGTAGCATTAACTGCACATTACA
TAATTTACCATTGCAAGTGGGATAGAGAGAGGAGGGTAAGTAAGTCCCATCA
Found at i:1835 original size:81 final size:81
Alignment explanation
Indices: 1688--1883 Score: 239
Period size: 81 Copynumber: 2.4 Consensus size: 81
1678 TTCGTTGAAT
* * * * * * *
1688 CCAATGTTGCATTTACTGCATATTACCTAATTTACCCTTGCAAGTTGGAGGGGTGTCGGTGAGTA
1 CCAATGTTGCATTTACTGCAAATTACCTAATTTAACCTTGCAAGTGGGAAGAGAGACGGTGAGTA
*
1753 AGTCCCTTTATTAAAC
66 AGTCCCATTATTAAAC
* * * * *
1769 CCAATTTTGCATTAACTGCAAATTACCTAATTTAACTTTGCAAGTGGGAAGAGAGAGGGTGGGTA
1 CCAATGTTGCATTTACTGCAAATTACCTAATTTAACCTTGCAAGTGGGAAGAGAGACGGTGAGTA
*
1834 AGTCCCATTGTTAAAC
66 AGTCCCATTATTAAAC
* * *
1850 CTAATGTAGCATTTACTGCACATTACCTAATTTA
1 CCAATGTTGCATTTACTGCAAATTACCTAATTTA
1884 CTCTTACAAT
Statistics
Matches: 96, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
81 96 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (81 bp):
CCAATGTTGCATTTACTGCAAATTACCTAATTTAACCTTGCAAGTGGGAAGAGAGACGGTGAGTA
AGTCCCATTATTAAAC
Found at i:2059 original size:54 final size:54
Alignment explanation
Indices: 1989--2091 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
1979 CGTAAGCCCT
1989 TTCGTTAAACCAAATGTAGCATTTACTGCACATTACCGAATTTACCCTTACACC
1 TTCGTTAAACCAAATGTAGCATTTACTGCACATTACCGAATTTACCCTTACACC
* * *
2043 TTCGTTAAATCC-AATGTTGCATTTATTGCACATTACCTAATTTACCCTT
1 TTCGTTAAA-CCAAATGTAGCATTTACTGCACATTACCGAATTTACCCTT
2092 GCAAGTAGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 43 0.96
55 2 0.04
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (54 bp):
TTCGTTAAACCAAATGTAGCATTTACTGCACATTACCGAATTTACCCTTACACC
Done.