Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022318.1 Corchorus olitorius cultivar O-4 contig22351, 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, 878
Length: 1464
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Found at i:371 original size:154 final size:153
Alignment explanation
Indices: 1--1462 Score: 2202
Period size: 154 Copynumber: 9.5 Consensus size: 153
* * *
1 CCTATCAGAGACCATTAGTGACGTTTTGAATCGTCTTTGATTTGGCAAACTTCAATGCTTTTCTT
1 CCTATC-GGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
* *
66 TCCATT-TTGTACGGCCTAACTGTAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
65 TCCATTGTT-TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
130 CATTTGGAACACTTGTTA-TTTGGG
129 CATTTGGAACACTTGTTATTTTGGG
* *
154 CCTATCGGGGACCATTAGGTGACGTTTTGAATCGTCTTCGATTTGGC-AACCTTCGATGCCTTTC
1 CCTATC-GGGACCATTA-GTGACGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTC
* *
218 ATTCCATTGTTTATGGCCTAACTATTATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
63 TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGC
283 TCATTATGGAACACTTGTTATTTTGGG
128 TCATT-TGGAACACTTGTTATTTTGGG
*
310 CCTATCAGGGACCATTAGTGACGTTTTGAATTGTCTTCGATTTGGCAAACCTCAATGC-TTTCTT
1 CCTATC-GGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
* **
374 TCCATTGTTTATGGCCTAACTATAATCATTTTTGTGAGATTTTTCCACTGTGAAGTTTTTAGCTC
65 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
* **
439 TTTTGGAACACTTGTTATTTTCTG
130 ATTTGGAACACTTGTTATTTTGGG
* ** **
463 CCTATCGAGGCCCATTAGTTCCGTTTTGAATTATCTTCGATTTGGCAAAACCTCAATGCTTTTCT
1 CCTATCG-GGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AAACCTCAATGCTTTTCT
*
528 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCT
64 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
593 CATTTGGAACACTTGTTATTTTGGG
129 CATTTGGAACACTTGTTATTTTGGG
* * * * *
618 ACTATCGGGGCGCATCAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATTCTTTTCAT
1 CCTATCGGGAC-CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
* *
683 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCTACAGTGAAGTTTTTAGCTC
65 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
748 ATTTGGAACACTTGTTATTTTGGG
130 ATTTGGAACACTTGTTATTTTGGG
* *
772 CCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCAATTTGGCAAACCTCAATTCTTTTCTT
1 CCTATC-GGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
* **
837 TCCATTGTTTATGTCCTATTTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
65 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
**
902 GATTTGGAACACTTGTTATTTTCTG
130 -ATTTGGAACACTTGTTATTTTGGG
* ** **
927 CCTATCGAGGCCCATTAGTTCCGTTTTGAATTATCTTCGATTTGGCAAAACCTCAAATCGTCTTT
1 CCTATCG-GGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AAACCTC-AAT-G-CTTT
*
992 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTA
61 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
1057 GCTCATTTGGAACACTTGTTATTTTGGG
126 GCTCATTTGGAACACTTGTTATTTTGGG
* * * *
1085 ACTATCGGGGCGCATCAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACTTCAATGC-TTTCTA
1 CCTATCGGGAC-CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT-
1149 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
64 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
1214 CATTTGGAACACTTGTTATTTTGGG
129 CATTTGGAACACTTGTTATTTTGGG
* *
1239 CCAATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGG-AAACCTTCGATGCTTTTCT
1 CCTATC-GGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCT
*
1303 TTCCATTGTTTATGGCCTAACTATAATCA-TTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCT
64 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
*
1367 CATTTGGAAAACTTGTTATTTTGGG
129 CATTTGGAACACTTGTTATTTTGGG
* *
1392 CCTATC-GGACCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAACGCTTTTCTTT
1 CCTATCGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
*
1456 TCATTGT
66 CCATTGT
1463 GT
Statistics
Matches: 1197, Mismatches: 89, Indels: 48
0.90 0.07 0.04
Matches are distributed among these distances:
151 55 0.05
152 6 0.01
153 149 0.12
154 564 0.47
155 249 0.21
156 36 0.03
157 12 0.01
158 57 0.05
159 69 0.06
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (153 bp):
CCTATCGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
TTTGGAACACTTGTTATTTTGGG
Found at i:561 original size:309 final size:307
Alignment explanation
Indices: 1--1462 Score: 2215
Period size: 309 Copynumber: 4.7 Consensus size: 307
* * *
1 CCTATCAGAGACCATTAGTGACGTTTTGAATCGTCTTTGATTTGGCAAACTTCAATGCTTTTCTT
1 CCTATC-GGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
* *
66 TCCATT-TTGTACGGCCTAACTGTAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
65 TCCATTGTT-TATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
130 CATTTGGAACACTTGTTA-TTTGGGCCTATCGGGGACCATTAGGTGACGTTTTGAATCGTCTTCG
129 CATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTA-GTGACGTTTTGAATCGTCTTCG
* * * *
194 ATTTGGC-AACCTTCGATGCCTTTCATTCCATTGTTTATGGCCTAACTATTATCATTTTGGTGAG
193 ATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
258 ATTAGTCCACTGTGAAGTTTTTAGCTCATTATGGAACACTTGTTATTTTGGG
257 ATTAGTCCACTGTGAAGTTTTTAGCTCATT-TGGAACACTTGTTATTTTGGG
*
310 CCTATCAGGGACCATTAGTGACGTTTTGAATTGTCTTCGATTTGGCAAACCTCAATGC-TTTCTT
1 CCTATC-GGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
* **
374 TCCATTGTTTATGGCCTAACTATAATCATTTTTGTGAGATTTTTCCACTGTGAAGTTTTTAGCTC
65 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
* ** * * ** **
439 TTTTGGAACACTTGTTATTTTCTGCCTATCGAGGCCCATTAGTTCCGTTTTGAATTATCTTCGAT
130 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGAT
504 TTGGCAAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGAT
195 TTGGC-AAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGAT
*
569 TTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
259 TAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
* * * * *
618 ACTATCGGGGCGCATCAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATTCTTTTCAT
1 CCTATCGGGAC-CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTT
* *
683 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCTACAGTGAAGTTTTTAGCTC
65 TCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC
*
748 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCAAT
130 ATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGAT
* * **
813 TTGGCAAACCTCAATTCTTTTCTTTCCATTGTTTATGTCCTATTTATAATCATTTTGGTGAGATT
195 TTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATT
**
878 AGTCCACTGTGAAGTTTTTAGCTCGATTTGGAACACTTGTTATTTTCTG
260 AGTCCACTGTGAAGTTTTTAGCTC-ATTTGGAACACTTGTTATTTTGGG
* ** **
927 CCTATCGAGGCCCATTAGTTCCGTTTTGAATTATCTTCGATTTGGCAAAACCTCAAATCGTCTTT
1 CCTATCG-GGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AAACCTC-AAT-G-CTTT
*
992 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTA
61 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
* *
1057 GCTCATTTGGAACACTTGTTATTTTGGGACTATCGGGG-CGCATCAGTGACGTTTTGAATCGTCT
126 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGAC-CATTAGTGACGTTTTGAATCGTCT
*
1121 TCGATTTGGCAAACTTCAATGC-TTTCTATTCCATTGTTTATGGCCTAACTATAATCATTTTGGT
190 TCGATTTGGCAAACCTCAATGCTTTTCT-TTCCATTGTTTATGGCCTAACTATAATCATTTTGGT
1185 GAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
254 GAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
* *
1239 CCAATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGG-AAACCTTCGATGCTTTTCT
1 CCTATC-GGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCT
*
1303 TTCCATTGTTTATGGCCTAACTATAATCA-TTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCT
64 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
* *
1367 CATTTGGAAAACTTGTTATTTTGGGCCTATC--GGACCATTTGTGACGTTTTGAATCGTCTTCGA
129 CATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGA
* *
1430 TTTGGCAAACCTCAACGCTTTTCTTTTCATTGT
194 TTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
1463 GT
Statistics
Matches: 1046, Mismatches: 89, Indels: 40
0.89 0.08 0.03
Matches are distributed among these distances:
305 52 0.05
306 6 0.01
307 66 0.06
308 288 0.28
309 335 0.32
310 21 0.02
311 5 0.00
312 65 0.06
313 208 0.20
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (307 bp):
CCTATCGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
TTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATT
TGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA
GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGG
Found at i:1128 original size:467 final size:461
Alignment explanation
Indices: 12--1462 Score: 2326
Period size: 467 Copynumber: 3.1 Consensus size: 461
2 CTATCAGAGA
* * *
12 CCATTAGTGACGTTTTGAATCGTCTTTGATTTGGCAAACTTCAATGCTTTTCTTTCCATT-TTGT
1 CCATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTT-T
* * *
76 ACGGCCTAACTGTAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
65 ATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
* *
141 CTTGTTA-TTTGGGCCTATCGGGGAC-CATTAGGTGACGTTTTGAATCGTCTTCGATTTGGC-AA
130 CTTGTTATTTTGGGACTATCGGGG-CGCATCA-GTGACGTTTTGAATCGTCTTCGATTTGGCAAA
* *
203 CCTTCGATGCCTTTCATTCCATTGTTTATGGCCTAACTATTATCATTTTGGTGAGATTAGTCCAC
193 CC-TCAATG-CTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAC
*
268 TGTGAAGTTTTTAGCTCATTATGGAACACTTGTTATTTTGGGCCTATCAGGGACCATTAGTGACG
256 TGTGAAGTTTTTAGCTCATT-TGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACG
*
333 TTTTGAATTGTCTTCGATTTGGCAAACCTCAATGC-TTTCTTTCCATTGTTTATGGCCTAACTAT
320 TTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
* ** *
397 AATCATTTTTGTGAGATTTTTCCACTGTGAAGTTTTTAGCTCTTTTGGAACACTTGTTATTTTCT
385 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTCT
462 GCCTATCGAGGC
450 GCCTATCGAGGC
** *
474 CCATTAGTTCCGTTTTGAATTATCTTCGATTTGGCAAAACCTCAATGCTTTTCTTTCCATTGTTT
1 CCATTAGTGACGTTTTGAATCATCTTCGATTTGGC-AAACCTCAATGCTTTTCTTTCCATTGTTT
539 ATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
65 ATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
604 CTTGTTATTTTGGGACTATCGGGGCGCATCAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACC
130 CTTGTTATTTTGGGACTATCGGGGCGCATCAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACC
* * *
669 TCAATTCTTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCTACAGT
195 TCAATGC-TTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT
734 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTT
259 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTT
* * * **
799 GAATCGTCTTCAATTTGGCAAACCTCAATTCTTTTCTTTCCATTGTTTATGTCCTATTTATAATC
324 GAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
864 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCGATTTGGAACACTTGTTATTTTCTGCC
389 ATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTC-ATTTGGAACACTTGTTATTTTCTGCC
929 TATCGAGGC
453 TATCGAGGC
** *
938 CCATTAGTTCCGTTTTGAATTATCTTCGATTTGGCAAAACCTCAAATCGTCTTTTCTTTCCATTG
1 CCATTAGTGACGTTTTGAATCATCTTCGATTTGGC-AAACCTC-AAT-G-CTTTTCTTTCCATTG
1003 TTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGA
62 TTTATGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGA
1068 ACACTTGTTATTTTGGGACTATCGGGGCGCATCAGTGACGTTTTGAATCGTCTTCGATTTGGCAA
127 ACACTTGTTATTTTGGGACTATCGGGGCGCATCAGTGACGTTTTGAATCGTCTTCGATTTGGCAA
*
1133 ACTTCAATGCTTTCTATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAC
192 ACCTCAATGCTTTC-ATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAC
*
1198 TGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCAATCGGGGACCATTAGTGACGT
256 TGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGT
*
1263 TTTGAATCGTCTTCGATTTGG-AAACCTTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
321 TTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTAT
* * **
1327 AATCA-TTTGGTGAGATTAGTCCACTATGAAGTTTTTAGCTCATTTGGAAAACTTGTTATTTTGG
385 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTCT
*
1391 GCCTATC--GGA
450 GCCTATCGAGGC
* * * *
1401 CCATTTGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAACGCTTTTCTTTTCATTGT
1 CCATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
1463 GT
Statistics
Matches: 926, Mismatches: 50, Indels: 29
0.92 0.05 0.03
Matches are distributed among these distances:
459 15 0.02
460 1 0.00
461 2 0.00
462 113 0.12
463 296 0.32
464 102 0.11
465 30 0.03
466 45 0.05
467 322 0.35
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.41
Consensus pattern (461 bp):
CCATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTA
TGGCCTAACTATAATCATTTTGGTGAGATTTGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC
TTGTTATTTTGGGACTATCGGGGCGCATCAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCT
CAATGCTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
AGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGA
ATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCAT
TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTCTGCCTAT
CGAGGC
Done.