Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010979.1 Corchorus olitorius cultivar O-4 contig11011, 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, 780
Length: 1300
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.42
Found at i:356 original size:153 final size:153
Alignment explanation
Indices: 1--1300 Score: 1783
Period size: 153 Copynumber: 8.4 Consensus size: 153
* *
1 GATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACGATAATCATTTTGGTGAG
1 GATTTGGCAAACTTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGAG
* * * *
66 ATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACTACTTGTTATTTTGGGCCTATTGGGGGTT
66 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC-ACTTGTTATTTT-GGCCTATCGGGGCTC
*
131 ATTAGTGAAGTTTTGAATCATCTTC
129 ATTAGTGACGTTTTGAATCATCTTC
* * *
156 GATTTGGCAAA-TCTCAATGCTTTTCCTTACATTGTGTATGGCATAACTATAATCATTTTGGTGA
1 GATTTGGCAAACT-TCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGA
*
220 GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-TCTCTATCGGGGCTC
65 GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGC-CTATCGGGGCTC
** *
284 ATTAGTTTCGTTTTGAATCGTCTTC
129 ATTAGTGACGTTTTGAATCATCTTC
* * *
309 GATTTGG-AAACGTTCGATGCTTTTTTTTCCATTGTTTATGGCCTAACTATAATCATTTT-GTGA
1 GATTTGGCAAAC-TTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGA
372 GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGAC-
65 GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTATCGGGG-CT
*
436 CATTAGTGACGTTTTGAATCATCTTA
128 CATTAGTGACGTTTTGAATCATCTTC
* * * *
462 GATTTGGCAACCTTCGATGCCTTTCTTTCCATTGTGTATGGCCTAACGATAATCATTTTGGTGAG
1 GATTTGGCAAACTTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGAG
*
527 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-TCTCTATCGGGGCTCA
66 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGC-CTATCGGGGCTCA
** *
591 TTAGTTTCGTTTTGAATCGTCTTC
130 TTAGTGACGTTTTGAATCATCTTC
* * * *
615 GATTTGG-AAACCTTCGATGCTTTTTTTTCCTACTGTTTATGGCCTAACTATAATCA-TTTGGTG
1 GATTTGGCAAA-CTTCAATGCTTTTCTTTCC-ATTGTGTATGGCCTAACTATAATCATTTTGGTG
* * *
678 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCTATTGGGGAT
64 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTATCGGGGCT
*
743 TATTAGTGACGTTTTGAATCATCTTC
128 CATTAGTGACGTTTTGAATCATCTTC
* * * *
769 GATTTGGCAAACCTCAATGCTTTTCTTTACGTTGTATATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAAACTTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGAG
* *
834 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTTGGAACACTTTGTTATTTTGGGCCTATTGGGGAT
66 ATTAGTCCACTGTGAAGTTTTTAGCTCA-TTTGGAACAC-TTGTTATTTT-GGCCTATCGGGGCT
* *
899 TATTAGTGTAAGTTTTGAATCATCTTC
128 CATTAGTG-ACGTTTTGAATCATCTTC
* * *
926 GATTTGGCAAACCTCAATGCTTTTCTTTACGTTGTGTATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAAACTTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGAG
* * * *
991 ATTAGTCCACTGTGATGTTTTTACCTCATTTGGAACACTTTTTATTTT-TCTCTATCGGGGAC-C
66 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGC-CTATCGGGG-CTC
*
1054 ATTAGTGACGTTTTGAATCGTCTTC
129 ATTAGTGACGTTTTGAATCATCTTC
* * * *
1079 GATTTGGCAACCTTCGATGCCTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAAACTTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGAG
* * * * *
1144 ATTAGTCCACAGAGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATTGGGGATTA
66 ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTATCGGGGCTCA
*
1209 TTAGTGAAGTTTTGAATCATCTTC
130 TTAGTGACGTTTTGAATCATCTTC
* * * *
1233 GATTTGGCAAACCTCAATGCTTTTTCTTTACGTTGTGTATGGCCTAACTTTAATCATTTTGGTGA
1 GATTTGGCAAACTTCAATGC-TTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGA
1298 GAT
65 GAT
Statistics
Matches: 1025, Mismatches: 94, Indels: 52
0.88 0.08 0.04
Matches are distributed among these distances:
152 61 0.06
153 409 0.40
154 246 0.24
155 159 0.16
156 43 0.04
157 107 0.10
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.42
Consensus pattern (153 bp):
GATTTGGCAAACTTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGAG
ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGCCTATCGGGGCTCAT
TAGTGACGTTTTGAATCATCTTC
Found at i:700 original size:307 final size:308
Alignment explanation
Indices: 1--1300 Score: 1813
Period size: 307 Copynumber: 4.2 Consensus size: 308
* * *
1 GATTTGGCAAACCTCAATGCTTTTCTTTCC-ATTGTGTATGGCCTAACGATAATCATTTTGGTGA
1 GATTTGGCAAACCTCAATGCTTTTTTTTCCTACTGTGTATGGCCTAACTATAATCATTTTGGTGA
* **
65 GATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACTACTTGTTATTTTGGGCCTATTGGGGGT
66 GATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAAC-ACTTGTTATTTTGGGCCTATCGGGGAC
* * * * *
130 TATTAGTGAAGTTTTGAATCATCTTCGATTTGGCAA-ATCTCAATGCTTTTCCTTACATTGTGTA
130 CATTAGTGACGTTTTGAATCATCTTCGATTTGGCAACCT-TCAATGCCTTTCTTTACATTGTGTA
*
194 TGGCATAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC
194 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC
* * ** *
259 TTGTTATTTT-TCTCTATCGGGGCTCATTAGTTTCGTTTTGAATCGTCTTC
259 TTGTTATTTTGGC-CTATCGGGGATCATTAGTTAAGTTTTGAATCATCTTC
* * * *
309 GATTTGG-AAACGTTCGATGCTTTTTTTTCC-ATTGTTTATGGCCTAACTATAATCATTTT-GTG
1 GATTTGGCAAAC-CTCAATGCTTTTTTTTCCTACTGTGTATGGCCTAACTATAATCATTTTGGTG
*
371 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGAC
65 AGATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGAC
* * *
436 CATTAGTGACGTTTTGAATCATCTTAGATTTGGCAACCTTCGATGCCTTTCTTTCCATTGTGTAT
130 CATTAGTGACGTTTTGAATCATCTTCGATTTGGCAACCTTCAATGCCTTTCTTTACATTGTGTAT
*
501 GGCCTAACGATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
195 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
* * ** *
566 TGTTATTTT-TCTCTATCGGGGCTCATTAGTTTCGTTTTGAATCGTCTTC
260 TGTTATTTTGGC-CTATCGGGGATCATTAGTTAAGTTTTGAATCATCTTC
* *
615 GATTTGG-AAACCTTCGATGCTTTTTTTTCCTACTGTTTATGGCCTAACTATAATCA-TTTGGTG
1 GATTTGGCAAACC-TCAATGCTTTTTTTTCCTACTGTGTATGGCCTAACTATAATCATTTTGGTG
* * * *
678 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTTGAACACTTGTTATTTTGGGCCTATTGGGGAT
65 AGATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGAC
* * * *
743 TATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTACGTTGTATA
130 CATTAGTGACGTTTTGAATCATCTTCGATTTGGC-AACCTTCAATGCCTTTCTTTACATTGTGTA
807 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTTGGAACA
194 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA-TTTGGAACA
* *
872 CTTTGTTATTTTGGGCCTATTGGGGATTATTAGTGTAAGTTTTGAATCATCTTC
258 C-TTGTTATTTT-GGCCTATCGGGGATCATTAGT-TAAGTTTTGAATCATCTTC
* *
926 GATTTGGCAAACCTCAATGCTTTTCTTTACGT--TGTGTATGGCCTAACTATAATCATTTTGGTG
1 GATTTGGCAAACCTCAATGCTTTT-TTTTCCTACTGTGTATGGCCTAACTATAATCATTTTGGTG
* * *
989 AGATTAGTCCACTGTGATGTTTTTACCTCATTTGGAACACTTTTTATTTT--TCTCTATCGGGGA
65 AGATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACACTTGTTATTTTGGGC-CTATCGGGGA
* * * *
1052 CCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCTTCGATGCCTTTCTTTCCATTGTTTA
129 CCATTAGTGACGTTTTGAATCATCTTCGATTTGGCAACCTTCAATGCCTTTCTTTACATTGTGTA
* *
1117 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACAGAGAAGTTTTTAGCTCATTTGGAACAC
194 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC
* * *
1182 TTGTTATTTTGGGCCTATTGGGGATTATTAGTGAAGTTTTGAATCATCTTC
259 TTGTTATTTT-GGCCTATCGGGGATCATTAGTTAAGTTTTGAATCATCTTC
* *
1233 GATTTGGCAAACCTCAATGCTTTTTCTT--TACGTTGTGTATGGCCTAACTTTAATCATTTTGGT
1 GATTTGGCAAACCTCAATGCTTTTTTTTCCTAC--TGTGTATGGCCTAACTATAATCATTTTGGT
1296 GAGAT
64 GAGAT
Statistics
Matches: 909, Mismatches: 63, Indels: 40
0.90 0.06 0.04
Matches are distributed among these distances:
304 1 0.00
306 224 0.25
307 282 0.31
308 129 0.14
309 25 0.03
310 151 0.17
311 87 0.10
312 10 0.01
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.42
Consensus pattern (308 bp):
GATTTGGCAAACCTCAATGCTTTTTTTTCCTACTGTGTATGGCCTAACTATAATCATTTTGGTGA
GATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACC
ATTAGTGACGTTTTGAATCATCTTCGATTTGGCAACCTTCAATGCCTTTCTTTACATTGTGTATG
GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
GTTATTTTGGCCTATCGGGGATCATTAGTTAAGTTTTGAATCATCTTC
Found at i:1013 original size:464 final size:461
Alignment explanation
Indices: 1--1300 Score: 1970
Period size: 464 Copynumber: 2.8 Consensus size: 461
1 GATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACGATAATCATTTTGGTGAG
1 GATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACGATAATCATTTTGGTGAG
* * *
66 ATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACTACTTGTTATTTTGGGC-CTATTGGGGGT
66 ATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAAC-ACTTGTTATTTT--TCTCTATCGGGGCT
* * * * * * * *
130 TATTAGTGAAGTTTTGAATCATCTTCGATTTGGCAAATC-TCAATGCTTTTCCTTACATTGTGTA
128 CATTAGTGACGTTTTGAATCGTCTTCGATTTGG-AAACCTTCGATGCTTTTCTTTCCATTGTTTA
*
194 TGGCATAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC
192 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACAC
* * * * ** *
259 TTGTTATTTT--TCTCTATCGGGGCTCATTAGTTTCGTTTTGAATCGTCTTCGATTTGG-AAACG
257 TTGTTATTTTGGGC-CTATTGGGGATTATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAAC-
* * * * * *
321 TTCGATGCTTTTTTTTCCATTGTTTATGGCCTAACTATAATCATTTT-GTGAGATTAGTCCACTG
320 CTCAATGCTTTTCTTTACGTTGTATATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
*
385 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTT
385 TGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGAAGTTT
450 TGAATCATCTTA
450 TGAATCATCTTA
* *
462 GATTTGGC-AACCTTCGATGCCTTTCTTTCCATTGTGTATGGCCTAACGATAATCATTTTGGTGA
1 GATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGTGTATGGCCTAACGATAATCATTTTGGTGA
*
526 GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTTCTCTATCGGGGCTCA
65 GATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACACTTGTTATTTTTCTCTATCGGGGCTCA
** * *
591 TTAGTTTCGTTTTGAATCGTCTTCGATTTGGAAACCTTCGATGCTTTTTTTTCCTACTGTTTATG
130 TTAGTGACGTTTTGAATCGTCTTCGATTTGGAAACCTTCGATGCTTTTCTTTCC-ATTGTTTATG
*
656 GCCTAACTATAATCA-TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTTGAACACTT
194 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
720 GTTATTTTGGGCCTATTGGGGATTATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCTCA
259 GTTATTTTGGGCCTATTGGGGATTATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCTCA
785 ATGCTTTTCTTTACGTTGTATATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
324 ATGCTTTTCTTTACGTTGTATATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
* **
850 GTTTTTAGCTCATTTTGGAACACTTTGTTATTTTGGGCCTATTGGGGATTATTAGTGTAAGTTTT
389 GTTTTTAGCTCA-TTTGGAACAC-TTGTTATTTTGGGCCTATCGGGGACCATTAGTG-AAGTTTT
*
915 GAATCATCTTC
451 GAATCATCTTA
* * *
926 GATTTGGCAAACCTCAATGCTTTTCTTTACGTTGTGTATGGCCTAACTATAATCATTTTGGTGAG
1 GATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACGATAATCATTTTGGTGAG
* *
991 ATTAGTCCACTGTGATGTTTTTACCTCATTTGGAACACTTTTTATTTTTCTCTATCGGGGAC-CA
66 ATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACACTTGTTATTTTTCTCTATCGGGG-CTCA
* *
1055 TTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCTTCGATGCCTTTCTTTCCATTGTTTATGG
130 TTAGTGACGTTTTGAATCGTCTTCGATTTGGAAACCTTCGATGCTTTTCTTTCCATTGTTTATGG
* *
1120 CCTAACTATAATCATTTTGGTGAGATTAGTCCACAGAGAAGTTTTTAGCTCATTTGGAACACTTG
195 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
*
1185 TTATTTTGGGCCTATTGGGGATTATTAGTGAAGTTTTGAATCATCTTCGATTTGGCAAACCTCAA
260 TTATTTTGGGCCTATTGGGGATTATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCTCAA
* *
1250 TGCTTTTTCTTTACGTTGTGTATGGCCTAACTTTAATCATTTTGGTGAGAT
325 TGC-TTTTCTTTACGTTGTATATGGCCTAACTATAATCATTTTGGTGAGAT
Statistics
Matches: 766, Mismatches: 58, Indels: 26
0.90 0.07 0.03
Matches are distributed among these distances:
458 5 0.01
459 106 0.14
460 117 0.15
461 131 0.17
462 10 0.01
463 54 0.07
464 293 0.38
465 50 0.07
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.42
Consensus pattern (461 bp):
GATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACGATAATCATTTTGGTGAG
ATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACACTTGTTATTTTTCTCTATCGGGGCTCAT
TAGTGACGTTTTGAATCGTCTTCGATTTGGAAACCTTCGATGCTTTTCTTTCCATTGTTTATGGC
CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TATTTTGGGCCTATTGGGGATTATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCTCAAT
GCTTTTCTTTACGTTGTATATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGT
TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGAAGTTTTGAATC
ATCTTA
Done.