Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017957.1 Corchorus olitorius cultivar O-4 contig17990, 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: 26959
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:1053 original size:30 final size:30
Alignment explanation
Indices: 1008--1118 Score: 177
Period size: 30 Copynumber: 3.7 Consensus size: 30
998 CGGTGAAACG
* **
1008 CAAATCGCCGGTGGATTAGCCATTTCTGAC
1 CAAATCGCCGATGGATTAGCCATTGGTGAC
*
1038 CAAATTGCCGATGGATTAGCCATTGGTGAC
1 CAAATCGCCGATGGATTAGCCATTGGTGAC
1068 CAAATCGCCGATGGATTAGCCATTGGTGAC
1 CAAATCGCCGATGGATTAGCCATTGGTGAC
*
1098 CAAATCGCCGGTGGATTAGCC
1 CAAATCGCCGATGGATTAGCC
1119 GGTGAAACGC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.24
Consensus pattern (30 bp):
CAAATCGCCGATGGATTAGCCATTGGTGAC
Found at i:1195 original size:15 final size:15
Alignment explanation
Indices: 1177--1206 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1167 GCTAGCTCAG
1177 CAGAAGAACCACCGT
1 CAGAAGAACCACCGT
1192 CAGAAGAACCACCGT
1 CAGAAGAACCACCGT
1207 GATCATTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.33, G:0.20, T:0.07
Consensus pattern (15 bp):
CAGAAGAACCACCGT
Found at i:4157 original size:22 final size:23
Alignment explanation
Indices: 4132--4177 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
4122 TAATAGCCAC
4132 ACACAATTAAT-ATATAAT-TAAA
1 ACACAATTAATCATA-AATATAAA
*
4154 ACACACTTAATCATAAATATAAA
1 ACACAATTAATCATAAATATAAA
4177 A
1 A
4178 ATAGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (23 bp):
ACACAATTAATCATAAATATAAA
Found at i:5086 original size:15 final size:15
Alignment explanation
Indices: 5066--5095 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5056 AGAATCTTAA
5066 TTTCTATAGAAGAAT
1 TTTCTATAGAAGAAT
*
5081 TTTCTATAGTAGAAT
1 TTTCTATAGAAGAAT
5096 ATATGCACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (15 bp):
TTTCTATAGAAGAAT
Found at i:5209 original size:188 final size:191
Alignment explanation
Indices: 4886--5243 Score: 598
Period size: 188 Copynumber: 1.9 Consensus size: 191
4876 CTTTCCACCT
* *
4886 GAAGATTTTTCTATAGTAGAATATATGCACCTCACCCACCCAACATTTAGAAGTTTGTGGACCAA
1 GAAGAATTTTCTATAGTAGAATATATGCACCTCACCCACCCAACATTTAAAAGTTTGTGGACCAA
* *
4951 AGGAAGATTAGCATTTTGCAATTTGATTTCATTTCTAGCTCTTTTTCTTTCCACTAAAAGAAAC-
66 AGGAAAATTAGCATTTTGCAATTTGATTTCATTTCTAACTCTTTTTCTTTCCACTAAAAGAAACA
5015 AAAAAAAAAA-GTT-ATTCAATCATTTCCCTTGCCATTTTGAAAGAATCTTAATTTCTATA
131 AAAAAAAAAATGTTGATTCAATCATTTCCCTTGCCATTTTGAAAGAATCTTAATTTCTATA
5074 GAAGAATTTTCTATAGTAGAATATATGCACCTCA-CCACCCAACATTTAAAAGTTTGTGGACCAA
1 GAAGAATTTTCTATAGTAGAATATATGCACCTCACCCACCCAACATTTAAAAGTTTGTGGACCAA
* *
5138 AGGAAAATTATCATTTTGCAATTTGATCTTCATTTCTAACTCTTTTTCTTTCCACTAAAAGAACC
66 AGGAAAATTAGCATTTTGCAATTTGAT-TTCATTTCTAACTCTTTTTCTTTCCACTAAAAGAAAC
*
5203 AAAAAAAAAAATTGGTTGATTCAATCGTTTCCCTTGCCATT
130 AAAAAAAAAAA-T-GTTGATTCAATCATTTCCCTTGCCATT
5244 GAGAGAATCT
Statistics
Matches: 157, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
187 54 0.34
188 68 0.43
189 10 0.06
192 3 0.02
193 22 0.14
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (191 bp):
GAAGAATTTTCTATAGTAGAATATATGCACCTCACCCACCCAACATTTAAAAGTTTGTGGACCAA
AGGAAAATTAGCATTTTGCAATTTGATTTCATTTCTAACTCTTTTTCTTTCCACTAAAAGAAACA
AAAAAAAAAATGTTGATTCAATCATTTCCCTTGCCATTTTGAAAGAATCTTAATTTCTATA
Found at i:12328 original size:24 final size:23
Alignment explanation
Indices: 12293--12338 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
12283 ATCATCTGTT
*
12293 TAATTGTATACT-TAATTTTGAC
1 TAATTGTATACTCGAATTTTGAC
12315 TAATTGTACTTACTCGAATTTTGA
1 TAATTGTA--TACTCGAATTTTGA
12339 TTTCCGTGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
24 4 0.20
25 8 0.40
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (23 bp):
TAATTGTATACTCGAATTTTGAC
Found at i:25111 original size:166 final size:160
Alignment explanation
Indices: 24895--25215 Score: 444
Period size: 166 Copynumber: 2.0 Consensus size: 160
24885 ATGACTAGCT
* * * * *
24895 TATTACCCCTGCGCATCCGCGTTAGGTTTTTTTGATTTCTGCACAAAGAATTTTAATTTTAAGAA
1 TATTACCCCTGCACATACGCGTCAGATTTTTTTGATTTCCGCACAAAGAATTTTAATTTTAAGAA
** * * *
24960 GGAAAACATGGTATAAGGGTTTTTAATTTGAAATGGGAGAAAACCTTGAATAAACAAATAGAGAT
66 GGAAAACATGACATAAAGGTTTTTAATTTG---T-GGAGAAAACATTGAATAAACAAAGAGAGAT
25025 ATTAATTCAAGTGAAAAATATTAATTGTAACTGGA
127 ATTAATTCAAGTG-AAAATATTAATTGTAACTGGA
* *
25060 TATTATCCCTGCACATACGCGTCAGAATTTTTTTGATTTCCGCGCAAAGAATTTTAATTTTAAGA
1 TATTACCCCTGCACATACGCGTCAG-ATTTTTTTGATTTCCGCACAAAGAATTTTAATTTTAAGA
* * * *
25125 AGGAAAATATGACATAAAGGTTTTTAATTTGTTGATAAAACATTGAATAAACAAAGAGAGCTATT
65 AGGAAAACATGACATAAAGGTTTTTAATTTGTGGAGAAAACATTGAATAAACAAAGAGAGATATT
25190 AATTCAAGTGAAAATATTAATTGTAA
130 AATTCAAGTGAAAATATTAATTGTAA
25216 TACTATCTCA
Statistics
Matches: 139, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
161 16 0.12
162 38 0.27
163 1 0.01
165 21 0.15
166 63 0.45
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.34
Consensus pattern (160 bp):
TATTACCCCTGCACATACGCGTCAGATTTTTTTGATTTCCGCACAAAGAATTTTAATTTTAAGAA
GGAAAACATGACATAAAGGTTTTTAATTTGTGGAGAAAACATTGAATAAACAAAGAGAGATATTA
ATTCAAGTGAAAATATTAATTGTAACTGGA
Found at i:25725 original size:39 final size:39
Alignment explanation
Indices: 25667--25783 Score: 207
Period size: 39 Copynumber: 3.0 Consensus size: 39
25657 GCAGTTTGAG
*
25667 GATAACTTTAATAGTAAGGTATAAATAAATAAAATATAA
1 GATAACTTTAATAGTAAGGTATAGATAAATAAAATATAA
*
25706 GATCACTTTAATAGTAAGGTATAGATAAATAAAATATAA
1 GATAACTTTAATAGTAAGGTATAGATAAATAAAATATAA
*
25745 GATAACTGTAATAGTAAGGTATAGATAAATAAAATATAA
1 GATAACTTTAATAGTAAGGTATAGATAAATAAAATATAA
25784 TTGTAATATT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.30
Consensus pattern (39 bp):
GATAACTTTAATAGTAAGGTATAGATAAATAAAATATAA
Found at i:25741 original size:23 final size:23
Alignment explanation
Indices: 25715--25780 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
25705 AGATCACTTT
25715 AATAGTAAGGTATAGATAAATAA
1 AATAGTAAGGTATAGATAAATAA
*
25738 AATA-TAA-G-ATA-ACT--GT--
1 AATAGTAAGGTATAGA-TAAATAA
25754 AATAGTAAGGTATAGATAAATAA
1 AATAGTAAGGTATAGATAAATAA
25777 AATA
1 AATA
25781 TAATTGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 18
0.62 0.04 0.35
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 2 0.06
19 5 0.16
20 5 0.16
21 2 0.06
22 3 0.09
23 8 0.25
ACGTcount: A:0.56, C:0.02, G:0.15, T:0.27
Consensus pattern (23 bp):
AATAGTAAGGTATAGATAAATAA
Done.