Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021470.1 Corchorus olitorius cultivar O-4 contig21503, 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: 15430
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Found at i:2083 original size:33 final size:33
Alignment explanation
Indices: 2037--2179 Score: 142
Period size: 33 Copynumber: 4.2 Consensus size: 33
2027 AGTTGATGGC
*
2037 GATGATGAGGATGATGACGAGGATGATGACGAG
1 GATGATGATGATGATGACGAGGATGATGACGAG
* * *
2070 GATGATGATGATGATGACGAAGATGACAATGAGGAC
1 GATGATGATGATGATGACGAGGATG---ATGACGAG
*
2106 GATGATGATGATGGCGATGATGAGGATGATGACGAG
1 GATGATGATGAT---GATGACGAGGATGATGACGAG
* * * * *
2142 GATGATGACGAGGATGATGATGATGATGACGAA
1 GATGATGATGATGATGACGAGGATGATGACGAG
2175 GATGA
1 GATGA
2180 CAATGAGGAC
Statistics
Matches: 92, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
33 47 0.51
36 34 0.37
39 11 0.12
ACGTcount: A:0.35, C:0.06, G:0.38, T:0.20
Consensus pattern (33 bp):
GATGATGATGATGATGACGAGGATGATGACGAG
Found at i:2165 original size:84 final size:84
Alignment explanation
Indices: 2030--2209 Score: 351
Period size: 84 Copynumber: 2.1 Consensus size: 84
2020 GTGCTGAAGT
2030 TGATGGCGATGATGAGGATGATGACGAGGATGATGACGAGGATGATGATGATGATGACGAAGATG
1 TGATGGCGATGATGAGGATGATGACGAGGATGATGACGAGGATGATGATGATGATGACGAAGATG
2095 ACAATGAGGACGATGATGA
66 ACAATGAGGACGATGATGA
2114 TGATGGCGATGATGAGGATGATGACGAGGATGATGACGAGGATGATGATGATGATGACGAAGATG
1 TGATGGCGATGATGAGGATGATGACGAGGATGATGACGAGGATGATGATGATGATGACGAAGATG
2179 ACAATGAGGACGATGATGA
66 ACAATGAGGACGATGATGA
*
2198 TGATGGTGATGA
1 TGATGGCGATGA
2210 CCATGAGGAG
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 95 1.00
ACGTcount: A:0.34, C:0.07, G:0.38, T:0.21
Consensus pattern (84 bp):
TGATGGCGATGATGAGGATGATGACGAGGATGATGACGAGGATGATGATGATGATGACGAAGATG
ACAATGAGGACGATGATGA
Found at i:2169 original size:12 final size:12
Alignment explanation
Indices: 2037--2209 Score: 129
Period size: 12 Copynumber: 14.7 Consensus size: 12
2027 AGTTGATGGC
2037 GATGATGAGGAT
1 GATGATGAGGAT
*
2049 GATGACGAGGAT
1 GATGATGAGGAT
*
2061 GATGACGAGGAT
1 GATGATGAGGAT
*
2073 GATGATGATGAT
1 GATGATGAGGAT
* * * *
2085 GACGAAGATGAC
1 GATGATGAGGAT
* * *
2097 AATGAGGACGAT
1 GATGATGAGGAT
*
2109 GATGATGATGG-C
1 GATGATGA-GGAT
2121 GATGATGAGGAT
1 GATGATGAGGAT
*
2133 GATGACGAGGAT
1 GATGATGAGGAT
*
2145 GATGACGAGGAT
1 GATGATGAGGAT
2157 GATGAT---GAT
1 GATGATGAGGAT
* *
2166 GATGACGAAGAT
1 GATGATGAGGAT
** *
2178 GACAATGAGGAC
1 GATGATGAGGAT
*
2190 GATGATGATGAT
1 GATGATGAGGAT
*
2202 GGTGATGA
1 GATGATGA
2210 CCATGAGGAG
Statistics
Matches: 127, Mismatches: 29, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
9 8 0.06
11 2 0.02
12 116 0.91
13 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.38, T:0.21
Consensus pattern (12 bp):
GATGATGAGGAT
Found at i:2207 original size:9 final size:9
Alignment explanation
Indices: 2037--2209 Score: 121
Period size: 9 Copynumber: 19.2 Consensus size: 9
2027 AGTTGATGGC
*
2037 GATGATGAG
1 GATGATGAT
*
2046 GATGATGAC
1 GATGATGAT
*
2055 GAGGATGAT
1 GATGATGAT
* *
2064 GACGAGGAT
1 GATGATGAT
2073 GATGATGAT
1 GATGATGAT
* *
2082 GATGACGAA
1 GATGATGAT
**
2091 GATGACAAT
1 GATGATGAT
* *
2100 GAGGACGAT
1 GATGATGAT
2109 GATGATGAT
1 GATGATGAT
**
2118 GGCGATGAT
1 GATGATGAT
*
2127 GAGGATGAT
1 GATGATGAT
* *
2136 GACGAGGAT
1 GATGATGAT
* *
2145 GATGACGAG
1 GATGATGAT
2154 GATGATGAT
1 GATGATGAT
*
2163 GATGATGAC
1 GATGATGAT
* *
2172 GAAGATGAC
1 GATGATGAT
* * *
2181 AATGAGGAC
1 GATGATGAT
2190 GATGATGAT
1 GATGATGAT
*
2199 GATGGTGAT
1 GATGATGAT
2208 GA
1 GA
2210 CCATGAGGAG
Statistics
Matches: 129, Mismatches: 35, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 129 1.00
ACGTcount: A:0.35, C:0.06, G:0.38, T:0.21
Consensus pattern (9 bp):
GATGATGAT
Found at i:3462 original size:45 final size:45
Alignment explanation
Indices: 3408--3512 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
3398 AAGGCAGCCT
** * * * **
3408 TTTATTTTGTATAGGTCTTTAATTTGCCATTATCTAGACGAGGCA
1 TTTATTTTGTATAGGTCACTAACTTGCAATGATCTAGAAAAGGCA
* *
3453 TTTATTTTGTATAGATCACTAACTTGCAATGATCTAGAAAAGGCC
1 TTTATTTTGTATAGGTCACTAACTTGCAATGATCTAGAAAAGGCA
3498 TTTATTTTGTATAGG
1 TTTATTTTGTATAGG
3513 GTTTAGTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (45 bp):
TTTATTTTGTATAGGTCACTAACTTGCAATGATCTAGAAAAGGCA
Found at i:3835 original size:25 final size:24
Alignment explanation
Indices: 3784--3833 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3774 TCATAGATAG
*
3784 AATTCCGTTTTTGATTCTATTGCA
1 AATTCCGTTTTTGATTCGATTGCA
3808 AATTCCGTTTTTGATTCCGA-TGCA
1 AATTCCGTTTTTGATT-CGATTGCA
3832 AA
1 AA
3834 ATACTCAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (24 bp):
AATTCCGTTTTTGATTCGATTGCA
Found at i:8780 original size:31 final size:31
Alignment explanation
Indices: 8742--8803 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
8732 GAGTTTTGTA
*
8742 AAACTTTTGAATCGCCTATTATATCCTTATT
1 AAACTTTTGAATCGCCTATTATACCCTTATT
*
8773 AAACTTTTGAATCGTCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATTATACCCTTATT
8804 TTTCAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATTATACCCTTATT
Found at i:9024 original size:94 final size:95
Alignment explanation
Indices: 8843--9024 Score: 296
Period size: 94 Copynumber: 1.9 Consensus size: 95
8833 TTAAATTTTT
*
8843 ATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTTAATTAAATCTAATATCCTTATAACTATTT
1 ATAGTTTTACTCAACTAAAAACTCTATTTTTATTTTAATTAAATCTAATATCCTTATAACTATTT
*
8908 TATTTTTTACCATTTTACTATTTTACTTTA
66 TATTTTTTACCATATTACTATTTTACTTTA
* *
8938 ATAGTTTTACTCAACTAAAAACTCTGTTTTTA-TTTAATTAAATCTAATATCCTTATACCTATTT
1 ATAGTTTTACTCAACTAAAAACTCTATTTTTATTTTAATTAAATCTAATATCCTTATAACTATTT
*
9002 TA-TTTTTACGATATTACTTATTT
66 TATTTTTTACCATATTAC-TATTT
9025 AATTAAAAAG
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
93 13 0.16
94 38 0.47
95 30 0.37
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.52
Consensus pattern (95 bp):
ATAGTTTTACTCAACTAAAAACTCTATTTTTATTTTAATTAAATCTAATATCCTTATAACTATTT
TATTTTTTACCATATTACTATTTTACTTTA
Found at i:12927 original size:41 final size:41
Alignment explanation
Indices: 12882--12966 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
12872 CTAATAGGTA
12882 GATATGTTTTGAATTTTCAATTAGATGTTTGGGCATATAGG
1 GATATGTTTTGAATTTTCAATTAGATGTTTGGGCATATAGG
12923 GATATGTTTTGAATTTTCAATTAGATGTTTGGGCATATAGG
1 GATATGTTTTGAATTTTCAATTAGATGTTTGGGCATATAGG
12964 GAT
1 GAT
12967 TGTAATGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.44
Consensus pattern (41 bp):
GATATGTTTTGAATTTTCAATTAGATGTTTGGGCATATAGG
Found at i:12979 original size:41 final size:41
Alignment explanation
Indices: 12882--12981 Score: 148
Period size: 41 Copynumber: 2.5 Consensus size: 41
12872 CTAATAGGTA
**
12882 GATATGTTTTGAATTTTCAATTAGATGTTTGGGCATATAGG
1 GATATGTAATGAATTTTCAATTAGATGTTTGGGCATATAGG
**
12923 GATATGTTTTGAATTTTCAATTAGATGTTTGGGCATATAGG
1 GATATGTAATGAATTTTCAATTAGATGTTTGGGCATATAGG
*
12964 GAT-TGTAATGAAATTTCA
1 GATATGTAATGAATTTTCA
12982 TGCTTTGAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 12 0.21
41 44 0.79
ACGTcount: A:0.29, C:0.05, G:0.23, T:0.43
Consensus pattern (41 bp):
GATATGTAATGAATTTTCAATTAGATGTTTGGGCATATAGG
Found at i:13015 original size:55 final size:55
Alignment explanation
Indices: 12930--13087 Score: 190
Period size: 65 Copynumber: 2.7 Consensus size: 55
12920 AGGGATATGT
*
12930 TTTGAATTTTCAATTAGATGTTTGGGCATATAGGGATTGTAATGAAATTTCATGC
1 TTTGAATTCTCAATTAGATGTTTGGGCATATAGGGATTGTAATGAAATTTCATGC
* *
12985 TTTGAATTCTCAATTAGATGTTTGGCCATATAGAGATTTATTCGGATTGTAATGAAATTTCATGT
1 TTTGAATTCTCAATTAGATGTTTGGGCATAT--AG--------GGATTGTAATGAAATTTCATGC
*
13050 TTTGAATTCTCAATTAGATGTTTGGGCATATAGAGATT
1 TTTGAATTCTCAATTAGATGTTTGGGCATATAGGGATT
13088 TATTCGGATT
Statistics
Matches: 88, Mismatches: 5, Indels: 20
0.78 0.04 0.18
Matches are distributed among these distances:
55 33 0.38
57 2 0.02
63 2 0.02
65 51 0.58
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.42
Consensus pattern (55 bp):
TTTGAATTCTCAATTAGATGTTTGGGCATATAGGGATTGTAATGAAATTTCATGC
Found at i:13067 original size:65 final size:65
Alignment explanation
Indices: 12963--13363 Score: 389
Period size: 65 Copynumber: 6.3 Consensus size: 65
12953 GGGCATATAG
*
12963 GGATTGTAATGAAATTTCATGCTTTGAATTCTCAATTAGATGTTTGGCCATATAGAGATTTATTC
1 GGATTGTAATGAAATTTCATGCTTTGAATTCTCAATTAGATGTTTGGGCATATAGAGATTTATTC
*
13028 GGATTGTAATGAAATTTCATGTTTTGAATTCTCAATTAGATGTTTGGGCATATAGAGATTTATTC
1 GGATTGTAATGAAATTTCATGCTTTGAATTCTCAATTAGATGTTTGGGCATATAGAGATTTATTC
* * * * *
13093 GGATTGTAATGAAATTTGTAATG--GT-AATT-TCATGCTTTGAAT-TCT---CA-ATTAGATG-
1 GGATTGTAATGAAA-TT-TCATGCTTTGAATTCTCA--ATTAG-ATGTTTGGGCATA-TAGA-GA
*
13148 TTTGGGCATATAT
59 TTT----AT-T-C
*
13161 GGATTGTAATGGAAATTTTATGCTTTGAATTCTCAATTAGATGTTTGGGCATATAGAGATTTATT
1 GGATTGTAAT-GAAATTTCATGCTTTGAATTCTCAATTAGATGTTTGGGCATATAGAGATTTATT
13226 C
65 C
*
13227 GGATTGTAATGAAA--T-ATGCTTTGAATTCTCAATTAGATTTTTGGGC--AT----A--TA--C
1 GGATTGTAATGAAATTTCATGCTTTGAATTCTCAATTAGATGTTTGGGCATATAGAGATTTATTC
* *
13279 GGATTGTAATGAAATTTCATGCTTTGAATTCTCAATTAGATATTTAGGCATATAGAGATTTATTC
1 GGATTGTAATGAAATTTCATGCTTTGAATTCTCAATTAGATGTTTGGGCATATAGAGATTTATTC
* *
13344 GGATTCTAATAAAATTTCAT
1 GGATTGTAATGAAATTTCAT
13364 TTGTACTCAC
Statistics
Matches: 280, Mismatches: 19, Indels: 74
0.75 0.05 0.20
Matches are distributed among these distances:
52 15 0.05
54 3 0.01
55 29 0.10
56 1 0.00
57 2 0.01
60 2 0.01
61 2 0.01
62 39 0.14
63 7 0.03
64 4 0.01
65 106 0.38
66 16 0.06
67 10 0.04
68 16 0.06
69 10 0.04
70 4 0.01
71 4 0.01
72 9 0.03
73 1 0.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (65 bp):
GGATTGTAATGAAATTTCATGCTTTGAATTCTCAATTAGATGTTTGGGCATATAGAGATTTATTC
Found at i:13194 original size:56 final size:55
Alignment explanation
Indices: 13108--13338 Score: 270
Period size: 56 Copynumber: 4.0 Consensus size: 55
13098 GTAATGAAAT
*
13108 TTGTAATGGTAATTTCATGCTTTGAATTCTCAATTAGATGTTTGGGCATATATGGA
1 TTGTAATGGAAATTTCATGCTTTGAATTCTCAATTAGATGTTTGGGCATATA-GGA
*
13164 TTGTAATGGAAATTTTATGCTTTGAATTCTCAATTAGATGTTTGGGCATATAGAGA
1 TTGTAATGGAAATTTCATGCTTTGAATTCTCAATTAGATGTTTGGGCATATAG-GA
* * *
13220 TT-TATTCGGATTGTAATGAAAT-ATGCTTTGAATTCTCAATTAGATTTTTGGGCATATACGGA
1 TTGTAAT-GGA----AAT---TTCATGCTTTGAATTCTCAATTAGATGTTTGGGCATATA-GGA
* *
13282 TTGTAAT-GAAATTTCATGCTTTGAATTCTCAATTAGATATTTAGGCATATAGAGA
1 TTGTAATGGAAATTTCATGCTTTGAATTCTCAATTAGATGTTTGGGCATATAG-GA
13337 TT
1 TT
13339 TATTCGGATT
Statistics
Matches: 153, Mismatches: 9, Indels: 27
0.81 0.05 0.14
Matches are distributed among these distances:
54 2 0.01
55 42 0.27
56 57 0.37
57 3 0.02
60 3 0.02
61 2 0.01
62 39 0.25
63 5 0.03
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (55 bp):
TTGTAATGGAAATTTCATGCTTTGAATTCTCAATTAGATGTTTGGGCATATAGGA
Found at i:13312 original size:55 final size:52
Alignment explanation
Indices: 13226--13332 Score: 169
Period size: 55 Copynumber: 2.0 Consensus size: 52
13216 GAGATTTATT
* *
13226 CGGATTGTAATGAAATATGCTTTGAATTCTCAATTAGATTTTTGGGCATATA
1 CGGATTGTAATGAAATATGCTTTGAATTCTCAATTAGATATTTAGGCATATA
13278 CGGATTGTAATGAAATTTCATGCTTTGAATTCTCAATTAGATATTTAGGCATATA
1 CGGATTGTAATGAAA--T-ATGCTTTGAATTCTCAATTAGATATTTAGGCATATA
13333 GAGATTTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
52 15 0.30
54 1 0.02
55 34 0.68
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (52 bp):
CGGATTGTAATGAAATATGCTTTGAATTCTCAATTAGATATTTAGGCATATA
Found at i:13340 original size:117 final size:118
Alignment explanation
Indices: 13124--13358 Score: 400
Period size: 117 Copynumber: 2.0 Consensus size: 118
13114 TGGTAATTTC
* *
13124 ATGCTTTGAATTCTCAATTAGATGTTTGGGCATATATGGATTGTAATGGAAATTTTATGCTTTGA
1 ATGCTTTGAATTCTCAATTAGATGTTTGGGCATATACGGATTGTAATGGAAATTTCATGCTTTGA
* * * *
13189 ATTCTCAATTAGATGTTTGGGCATATAGAGATTTATTCGGATTGTAATGAAAT
66 ATTCTCAATTAGATATTTAGGCATATAGAGATTTATTCGGATTCTAATAAAAT
*
13242 ATGCTTTGAATTCTCAATTAGATTTTTGGGCATATACGGATTGTAAT-GAAATTTCATGCTTTGA
1 ATGCTTTGAATTCTCAATTAGATGTTTGGGCATATACGGATTGTAATGGAAATTTCATGCTTTGA
13306 ATTCTCAATTAGATATTTAGGCATATAGAGATTTATTCGGATTCTAATAAAAT
66 ATTCTCAATTAGATATTTAGGCATATAGAGATTTATTCGGATTCTAATAAAAT
13359 TTCATTTGTA
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
117 65 0.59
118 45 0.41
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (118 bp):
ATGCTTTGAATTCTCAATTAGATGTTTGGGCATATACGGATTGTAATGGAAATTTCATGCTTTGA
ATTCTCAATTAGATATTTAGGCATATAGAGATTTATTCGGATTCTAATAAAAT
Found at i:14271 original size:21 final size:21
Alignment explanation
Indices: 14247--14296 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
14237 ATTTTAGATG
14247 TAAT-ATATATTATTAAATAAA
1 TAATAATATATT-TTAAATAAA
14268 TAATAAATATATTTTAAAT-AA
1 TAAT-AATATATTTTAAATAAA
14289 TAAATAAT
1 T-AATAAT
14297 GAGTTGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 10 0.38
22 9 0.35
23 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATAATATATTTTAAATAAA
Found at i:15209 original size:29 final size:29
Alignment explanation
Indices: 15177--15250 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
15167 ATTTATTAGT
15177 TTGAAATTTAATTAGTTAATTATTCTTAA
1 TTGAAATTTAATTAGTTAATTATTCTTAA
*
15206 TTGAAATTTAATTAAAATTAATTATTCTTAA
1 TTGAAATTTAATT--AGTTAATTATTCTTAA
15237 TT--AATTT-ATTAGTT
1 TTGAAATTTAATTAGTT
15251 TGACTTAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 3 0.07
28 3 0.07
29 18 0.44
31 17 0.41
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (29 bp):
TTGAAATTTAATTAGTTAATTATTCTTAA
Found at i:15230 original size:31 final size:29
Alignment explanation
Indices: 15177--15238 Score: 97
Period size: 31 Copynumber: 2.1 Consensus size: 29
15167 ATTTATTAGT
*
15177 TTGAAATTTAATTAGTTAATTATTCTTAA
1 TTGAAATTTAATTAATTAATTATTCTTAA
15206 TTGAAATTTAATTAAAATTAATTATTCTTAA
1 TTGAAATTTAATT--AATTAATTATTCTTAA
15237 TT
1 TT
15239 AATTTATTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 13 0.43
31 17 0.57
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (29 bp):
TTGAAATTTAATTAATTAATTATTCTTAA
Done.