Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013087.1 Corchorus olitorius cultivar O-4 contig13120, 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: 3892
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Found at i:394 original size:154 final size:154
Alignment explanation
Indices: 1--3892 Score: 3933
Period size: 154 Copynumber: 25.2 Consensus size: 154
* * * * *
1 ATTTTAGTGAGATCAGCCCTCTGTGTAAGTTTTTAGCTCTATTTGGAACACCTGTTATTTTGGGC
1 ATTTTGGTGAGATTAGTCCACTGTG-AAGTTTTTAGCTC-ATTTGGAACACTTGTTATTTTGGGC
* * * *
66 CTATCAGGGCCCATTAGTGTACGTTTTGAATCGTCTTCGATTTGGCAAACCTTAATTGGTTTTC-
64 CTATCGGGGCCCATTAGT-TCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAA-TGCTTTTCT
*
130 TTCCATAGTTTATGGACCTTAACTATAATC
127 TTCCATTGTTTATGG-CC-TAACTATAATC
160 TATTTTGGTGAGATTAGTCCACTGTGTAAGTTTTTAGCTCATTTGGAACTACTT-TTATTTTGGG
1 -ATTTTGGTGAGATTAGTCCACTGTG-AAGTTTTTAGCTCATTTGGAAC-ACTTGTTATTTTGGG
*
224 CCTATCGGGGCCCATTACTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
63 CCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
289 TCCATTGTTTATGGCCTAACTATAATC
128 TCCATTGTTTATGGCCTAACTATAATC
* *
316 ATTTTGGTGAGATTAGTGCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * * *
381 ATAGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCAATTTGGCAAAACTCAATGCTTTTCTTTCC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
446 ATTGTTTATGGCCTAACTATAATC
131 ATTGTTTATGGCCTAACTATAATC
* * *
470 ATTATGGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTCGGAACACTTGTTATTTTGGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
*
535 ATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
600 ATTGTTTA-GGACCTAACTATAATC
131 ATTGTTTATGG-CCTAACTATAATC
* * *
624 ATTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCCCATTTGGAACACTTTTTATTTTGGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
*
689 ATCGGGGCCCATTAGTTTCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
754 ATTGTTTATGGCCTAACTATAATC
131 ATTGTTTATGGCCTAACTATAATC
*
778 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTATCTCATTTGGAAC-CTTGTTATTTTGGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * *
842 ATCGGGGCCCATTAGTTCCTTTTTGAATCGTCCTCGATTTAGC-AACCATCAATGCTTTTC-TTC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTC
*
905 CATTGTTTATGGCCTAACTATAATA
130 CATTGTTTATGGCCTAACTATAATC
* * *
930 ATATTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTCTTATTTTTGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * ** * *
995 ATTGGAGCCCATTAGTGACGTATTGAATGGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
1060 ATTGTTTATGGCCTAACTATAATC
131 ATTGTTTATGGCCTAACTATAATC
* * *
1084 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACTCTTCTTATTTT-GGCTT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * ** * * ** * *
1148 ATTTGGGGTCCATTAGTGACGTATTGAATCGTATTCGATTTATCAGACCTCAATGCTTTTCATTC
66 A-TCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
1213 CATTGTTTATGGCCTAACTATAATC
130 CATTGTTTATGGCCTAACTATAATC
* *
1238 ATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * *
1303 ATCGAGGCCCATTAGTTCTGTTTTGAATCGTCTTCGAGTTGGCAAACCTCAATGCTTTTCTTTCC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
1368 ATTGTTTATGGCCTAACTATAATC
131 ATTGTTTATGGCCTAACTATAATC
**
1392 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCAGAACACTTGTTATTTTGGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* ***
1457 ATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAA---C--TG-TTTTGAATCG
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC-
** * *
1516 TC-TTCGAGT-TGG-CAAACCT-CAATGC
130 -CATT-GTTTATGGCCTAA-CTATAAT-C
** * * * * * * * * ** *
1541 -TTTTCTTTCCATTGTTTATGGCCTAACTAT-AA-TCATTTT-GGTGAGATTAGTCCAC-TGTGA
1 ATTTT-GGT-GA--GATTA-GTCC--ACTGTGAAGT--TTTTAGCTCA-TTTGGAACACTTGT-T
** *** ** ** * *
1601 AGTTTTTAG-CTCATTTTGGAACACTT-GTT-ATTTTTG-A--GCCTATCG---GGGC---CCAT
55 A-TTTTGGGCCT-ATCGGGGCCCA-TTAGTTCCGTTTTGAATCGTCT-TCGATTTGGCAAACC-T
* * *** * * *
1654 TAGTGACGTTTTGAATCGTC-TTCGATT-TGG-CAAACCT-CAAT-
115 CAATG-C-TTTTCTTTC--CATT-GTTTATGGCCTAA-CTATAATC
** * * * * * * * * **
1695 ACTTTTCTATCCATTGTTTTTATGGCCTAACTAT-AA-TCATTTT-GGTGAGATTAGTCCAC-TG
1 A-TTTT-GGT-GA--G--ATTA-GTCC--ACTGTGAAGT--TTTTAGCTCA-TTTGGAACACTTG
* ** **** * * *
1756 TGAAGTTTTTAG-CTCATTCGGAAAAC-TTA-TT--ATTTTG-A--GCCTATCG---GGGC---C
53 T-TA-TTTTGGGCCT-A-TCGGGGCCCATTAGTTCCGTTTTGAATCGTCT-TCGATTTGGCAAAC
* * *** * * * *
1807 CATTAGTGACGTTTTGAATCGACTTCGATT-TGG-CAAACCT-CAAT-
113 C-TCAATG-C-TTTTCTTTCCA-TT-GTTTATGGCCTAA-CTATAATC
** * * * * * * ** *
1851 ACTTTTCTATCCATTGTTTATGGCCTAACTAT-AA-TCATTTT-GGTGAGATTAGTCCACAGTGA
1 A-TTTT-GGT-GA--GATTA-GTCC--ACTGTGAAGT--TTTTAGCT--CATT--TGGA-A---C
* * * ** * ** ** ** * *
1913 AGTTTTTAGATGATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTTG-TTCCGT-TTT
48 ACTTGTT--AT--TTTGG-GC-C----TA-TCGGGGCCCATTAGTTCCGTTTTGAAT-CGTCTTC
* *
1976 GAATTTGTCTTCGATTTGGCAACCTTCAATGCTTTTCTTTCCATTTTTTATGGCCTAACTATAAT
101 G-ATTTG---GC-A------AACC-TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
2041 C
154 C
*
2042 ATTTTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTTGGGC
1 A-TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA-TTTTGGGC
* *
2107 CTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGACAAACCTTAATGCTTTTCTTT
64 CTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
*
2172 CCATTGTTTATGGCCGAACTATAATC
129 CCATTGTTTATGGCCTAACTATAATC
* * * *
2198 ACTTTGGTGAGATTAGTCCATTGTGAAGTTTTTAGCTCATTTGGAACACTAGTTATTATGGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * *
2263 ATCGAGGCCCATTAGTTCCGTTTTGGAA-CGTCTTCGATTTGGCAACCCTCAAAGCTTTTCTTTC
66 ATCGGGGCCCATTAGTTCCGTTTT-GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
*
2327 TATTGTTTATGGCCTAACTATAATC
130 CATTGTTTATGGCCTAACTATAATC
** * *
2352 ATTTTATTGAGATTAGTCCACTGTTAAGTTTTTAGGTCATTTGGAACTACTTG-TATTTTGGGCC
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC-ACTTGTTATTTTGGGCC
* * *
2416 TATCGGGACACATTAGTTCCG--TT-AA-----TT--A---GGCAACCCTCAATGCTTTTCTTTC
65 TATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
2468 CATTGTTTATGGCCTAACTATAATC
130 CATTGTTTATGGCCTAACTATAATC
*
2493 ATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
** * * *
2558 ATC----CCCATTAGTGACGTTTTAAATCGTCTTCGATTTGACAACCCTCAATGCTTTTCTTTCC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
*
2619 AATGTTTATGGCCTAACTATAATC
131 ATTGTTTATGGCCTAACTATAATC
* * * * * *
2643 ATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAACTCATTTGGTACACTTGTT-TTTTGGACAT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * * *
2707 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCAATTTGCCAACCCTAAATGCTTTTCTTTCC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
* *
2772 ATTGTTTATGGCCAAACAATAATC
131 ATTGTTTATGGCCTAACTATAATC
* * *
2796 ATTTTTGTGAGATTAGTCCACTGTGAAGTTTTTAGTTCATTTGGAACACTTGTTATTTTGGTCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * * *
2861 ATCGGGACCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTTAATGCTTTACTTTCC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
2926 ATTGTTTATGGCCTAACTATAATC
131 ATTGTTTATGGCCTAACTATAATC
* * * * * *
2950 ATTTTGGTCATATTAGTCCACTGTGTAGTTTTTAACTCATTCGGAACATTTGTTATTTTGGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* * *
3015 ATCGAGGCCCATTAGTTCCGTTTTGAATCGTATTCGATTTGGCAAACCTTAATGCTTTTCTTTCC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
3080 ATTGTTTATGGCCTAACTATAATC
131 ATTGTTTATGGCCTAACTATAATC
* * * *
3104 ACTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT-CTA-ATT---ACT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
** * *
3164 ATCGGGGCCCATTAGTGACG-TTTGAATCGTCTTCGATTTGGCAACCCTCAATTC-TTTCTTTCC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
3227 ATTGTTTATGGCCTAACTATAATC
131 ATTGTTTATGGCCTAACTATAATC
* *
3251 ATTTTGTTGAGATTAGTCCACAGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
3316 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC-AACCATCAATGCTTTTCTTTC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTC
*
3380 CATTGTTTATGGCATAACTATAATC
130 CATTGTTTATGGCCTAACTATAATC
* *
3405 ATTTTTGGTGAGACTAGTCCACTATGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
1 A-TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCC
3470 TATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
65 TATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTC
**
3535 CATTGTTTATGGTGTAACTATAATC
130 CATTGTTTATGGCCTAACTATAATC
* * * * *
3560 ATTTGGGTGAGATTTGTCCATTGTTAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTAGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
* *
3625 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC-AACCATCAATGCTTTACTTTA
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTC
*
3689 GATTGTTTATGGCCTAACTATAATC
130 CATTGTTTATGGCCTAACTATAATC
3714 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
1 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
** * * * *
3779 ATCGGGGCCCATTAGTGACATTTTGAATCGTCTTCAATTTCGCAACCCTCAATGCTTTTCTTTCC
66 ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
3844 ATTGTTTATGGCCTAACTATAATC
131 ATTGTTTATGGCCTAACTATAATC
* *
3868 ATTCTGGTGAGTTTAGTCCACTGTG
1 ATTTTGGTGAGATTAGTCCACTGTG
Statistics
Matches: 3254, Mismatches: 343, Indels: 276
0.84 0.09 0.07
Matches are distributed among these distances:
137 10 0.00
139 2 0.00
140 7 0.00
141 104 0.03
144 1 0.00
145 2 0.00
146 2 0.00
147 82 0.03
148 48 0.01
149 43 0.01
150 107 0.03
151 1 0.00
152 110 0.03
153 303 0.09
154 1646 0.51
155 257 0.08
156 191 0.06
157 20 0.01
158 107 0.03
159 40 0.01
160 38 0.01
161 1 0.00
162 3 0.00
163 2 0.00
164 4 0.00
167 24 0.01
168 6 0.00
170 4 0.00
171 2 0.00
172 1 0.00
173 1 0.00
174 9 0.00
175 3 0.00
176 2 0.00
177 6 0.00
179 1 0.00
180 1 0.00
181 2 0.00
182 1 0.00
183 3 0.00
184 9 0.00
185 4 0.00
186 4 0.00
187 4 0.00
188 2 0.00
189 8 0.00
190 14 0.00
191 6 0.00
192 6 0.00
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.41
Consensus pattern (154 bp):
ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCT
ATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCC
ATTGTTTATGGCCTAACTATAATC
Found at i:1509 original size:29 final size:29
Alignment explanation
Indices: 1476--1532 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1466 CATTAGTTCC
*
1476 GTTTTGAATCGTCTTCGATTTGGCAAACT
1 GTTTTGAATCGTCTTCGAGTTGGCAAACT
1505 GTTTTGAATCGTCTTCGAGTTGGCAAAC
1 GTTTTGAATCGTCTTCGAGTTGGCAAAC
1533 CTCAATGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.39
Consensus pattern (29 bp):
GTTTTGAATCGTCTTCGAGTTGGCAAACT
Done.