Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011016.1 Corchorus olitorius cultivar O-4 contig11049, 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, 746
Length: 1244
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Found at i:557 original size:307 final size:308
Alignment explanation
Indices: 3--1242 Score: 1872
Period size: 307 Copynumber: 4.0 Consensus size: 308
1 TA
* **
3 TTTGAATCGTGTTCGATTTGGCAAACCTCATTGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
1 TTTGAATCGTCTTCGATTTGGCAAACCTCAACGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
*
68 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
* ** *
133 CCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
131 CCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
* * * *
198 TCCATTGTTTATGACCTAACTATAATAATTATGGTGAGATAAGTCCACTGTGAACTTTTTAGCTC
196 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTC
* *
263 AGTTGGAACACTTGTTATTTT-GGCCTATCGGGGCCCATTAGTTCCGT
261 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGATCCGT
* *
310 TTTGAATCGTCTTCGATTTGGCAAACCTCAACGCTTTTCTTTCCAGTGTTTATGGTCTAACTATA
1 TTTGAATCGTCTTCGATTTGGCAAACCTCAACGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
*
375 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAATACTTGTTATTTTGGG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
*
440 CGTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
131 CCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
505 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGTCT
196 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAG-CT
*
570 CATTTGGAATACTTGTTATTTTGGGCCTATCGGGGCCCGATTAGATCCGT
260 CATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCC-ATTAGATCCGT
*
620 TTTGAATCGTCTTCGATTTGGCAAACCCTCAACGCTTTTCTTTCCTATTGTTTATGGTCTAACTA
1 TTTGAATCGTCTTCGATTTGGCAAA-CCTCAACGCTTTTCTTTCC-ATTGTTTATGGCCTAACTA
* *
685 TAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAATACTTGTTATTTTG
64 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
750 GGCCTATC-GGGCCGCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT
129 GGCCTATCGGGGCC-CATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT
* * * * * * *
814 CTTTCAATTGTTTATGGCATAACTATAATTA-TTTGGTGCGATTAGTCCACTATGAA-GTTTTAA
193 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAG
* * *
877 CTCATTCGGAACAC-TG-TA-TTT-GGCCTAAC-GGGCTCATTA-ATCCGT
258 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGATCCGT
* * * **
922 TTTGAATCGCCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAATGTTTATCACCTAACTATA
1 TTTGAATCGTCTTCGATTTGGCAAACCTCAACGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
*
987 ATCATTATGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
* * ** * * * * *
1052 CATATCGAGGCCCATTAGTTTCGTTTTAAATCGTCTTTGATTTGGCAACCCTTAATGCTTTTCTT
131 CCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
* *
1117 TCCATT-TTGTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
196 TCCATTGTT-TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
* * *
1181 CATTTGGAACACTTGTTATTTTGGGCATATCGAGGCCCATTAGTTCCGT
260 CATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGATCCGT
*
1230 TTTAAATCGTCTT
1 TTTGAATCGTCTT
1243 TG
Statistics
Matches: 850, Mismatches: 67, Indels: 31
0.90 0.07 0.03
Matches are distributed among these distances:
299 2 0.00
300 151 0.18
301 45 0.05
302 48 0.06
303 6 0.01
304 7 0.01
305 10 0.01
306 9 0.01
307 251 0.30
308 40 0.05
309 27 0.03
310 40 0.05
311 47 0.06
312 167 0.20
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (308 bp):
TTTGAATCGTCTTCGATTTGGCAAACCTCAACGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
CCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTC
ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGATCCGT
Found at i:1244 original size:154 final size:154
Alignment explanation
Indices: 3--1242 Score: 1863
Period size: 154 Copynumber: 8.1 Consensus size: 154
1 TA
* *
3 TTTGAATCGTGTTCGATTTGGCAAACCTCATTGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
1 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
*
68 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
*
133 CCTATCGGGGCTCATTAGTTCCGT
131 CCTATCGGGGCCCATTAGTTCCGT
*
157 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACTATA
1 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
* * * * *
222 ATAATTATGGTGAGATAAGTCCACTGTGAACTTTTTAGCTCAGTTGGAACACTTGTTATTTT-GG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
286 CCTATCGGGGCCCATTAGTTCCGT
131 CCTATCGGGGCCCATTAGTTCCGT
* * *
310 TTTGAATCGTCTTCGATTTGGCAAACCTCAACGCTTTTCTTTCCAGTGTTTATGGTCTAACTATA
1 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
*
375 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAATACTTGTTATTTTGGG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
* **
440 CGTATCGGGGCCCATTAGTGACGT
131 CCTATCGGGGCCCATTAGTTCCGT
*
464 ATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
1 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
* *
529 ATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGTCTCATTTGGAATACTTGTTATTTTGG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG-CTCATTTGGAACACTTGTTATTTTGG
*
594 GCCTATCGGGGCCCGATTAGATCCGT
130 GCCTATCGGGGCCC-ATTAGTTCCGT
* *
620 TTTGAATCGTCTTCGATTTGGCAAACCCTCAACGCTTTTCTTTCCTATTGTTTATGGTCTAACTA
1 TTTGAATCGTCTTCGATTTGGCAAA-CCTCAATGCTTTTCTTTCC-ATTGTTTATGGCCTAACTA
* *
685 TAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAATACTTGTTATTTTG
64 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG
**
750 GGCCTATC-GGGCCGCATTAGTGACGT
129 GGCCTATCGGGGCC-CATTAGTTCCGT
* * *
776 ATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCAATTGTTTATGGCATAACTATA
1 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
* * * * *
841 ATTA-TTTGGTGCGATTAGTCCACTATGAAG-TTTTAACTCATTCGGAACAC-TG-TA-TTT-GG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
* * *
900 CCTAAC-GGGCTCATTA-ATCCGT
131 CCTATCGGGGCCCATTAGTTCCGT
* * **
922 TTTGAATCGCCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAATGTTTATCACCTAACTATA
1 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
*
987 ATCATTATGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
66 ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
* * *
1052 CATATCGAGGCCCATTAGTTTCGT
131 CCTATCGGGGCCCATTAGTTCCGT
* * * * *
1076 TTTAAATCGTCTTTGATTTGGCAACCCTTAATGCTTTTCTTTCCATT-TTGTATGCCCTAACTAT
1 TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT-TATGGCCTAACTAT
1140 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
65 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG
* *
1205 GCATATCGAGGCCCATTAGTTCCGT
130 GCCTATCGGGGCCCATTAGTTCCGT
*
1230 TTTAAATCGTCTT
1 TTTGAATCGTCTT
1243 TG
Statistics
Matches: 987, Mismatches: 84, Indels: 30
0.90 0.08 0.03
Matches are distributed among these distances:
146 64 0.06
147 28 0.03
148 29 0.03
149 5 0.01
150 4 0.00
151 5 0.01
152 23 0.02
153 175 0.18
154 419 0.42
155 56 0.06
156 69 0.07
157 52 0.05
158 58 0.06
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
TTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATA
ATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
CCTATCGGGGCCCATTAGTTCCGT
Done.