Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011779.1 Corchorus olitorius cultivar O-4 contig11812, 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, 648
Length: 1081
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Found at i:473 original size:154 final size:154
Alignment explanation
Indices: 1--1072 Score: 1672
Period size: 154 Copynumber: 6.9 Consensus size: 154
* * *
1 TCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGAGATTAGTTCACTATGAAGTTTTTA
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
*
66 GTCTCATTTGGTAAAACTTAGTTATTTTGGGTCCGTATCGGGGACCGATTAGTGACGTTTTGTAA
66 G-CTCATTTGG-AACACTT-GTTATTTTGGG-CC-TATCGGGGACC-ATTAGTGACGTTTTG-AA
*
131 TCGTCTTCGATTTGGCAAACC-TCAATGCTTT
124 TCGTCTTCGATTTGGC-AACCTTCGATGCTTT
* *
162 TCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTTTGAAGTTTTTA
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
*
227 GCCTCATTTGGAACACGTTTTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTC
66 G-CTCATTTGGAACAC-TTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTC
* * *
292 TTCGATTTGGCAACCTTCCACGCCTT
129 TTCGATTTGGCAACCTTCGATGCTTT
* *
318 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTAGGTGAGATTAGTCCACTGTGAAGTTCTTA
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
383 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTT
66 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTT
448 CGATTTGGCAACCTTCGATGGC-TT
131 CGATTTGGCAACCTTCGAT-GCTTT
* * *
472 TCTTTCCATTGTTTTTGGCCTAACTATAACCATTTTGGTGAGATTAGTCCACTGTGATGTTTTTA
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
* *** **
537 GCTCATTTGAAACACTTGTTATTTT--GCTCTATCGGATCCCATTAGTTTCGTTTTGAATCGTCT
66 GCTCATTTGGAACACTTGTTATTTTGGGC-CTATCGGGGACCATTAGTGACGTTTTGAATCGTCT
*
600 TCGATTTGGAAACCTTCGATGCTTT
130 TCGATTTGGCAACCTTCGATGCTTT
* *
625 TCTTTCCATTGTTTATGGCCTAACTATACTCA-TTTAGTGAGATTAGTCCACTGTGAAGTTTTTA
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
*
689 GCTCATTTGTAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTT
66 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTT
*
754 CGATTTGGCAAACC-TCAATGCTTT
131 CGATTTGGC-AACCTTCGATGCTTT
* * *
778 TCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGAGATTAGTTCACTATGAAGTTTTTA
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
843 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTT
66 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTT
908 CGATTTGGCAACCTTCGATGGC-TT
131 CGATTTGGCAACCTTCGAT-GCTTT
*
932 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGCCCACTGTGAAGTTTTTA
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
* *
997 GCTCATTTGGAAAACTTGTTATTTTGGGCGTATCGGGGACCATTAGTGACGTTTTGAATCGTCTT
66 GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTT
1062 CGATTTGGCAA
131 CGATTTGGCAA
1073 TCCTCAATG
Statistics
Matches: 847, Mismatches: 53, Indels: 29
0.91 0.06 0.03
Matches are distributed among these distances:
152 58 0.07
153 162 0.19
154 401 0.47
155 22 0.03
156 87 0.10
157 15 0.02
158 11 0.01
159 2 0.00
160 14 0.02
161 75 0.09
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (154 bp):
TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
GCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTT
CGATTTGGCAACCTTCGATGCTTT
Found at i:872 original size:460 final size:463
Alignment explanation
Indices: 1--1081 Score: 1728
Period size: 460 Copynumber: 2.3 Consensus size: 463
* * *
1 TCTTTCCATTGTGTATGGCCTAACTATAATCATTTTGGTGAGATTAGTTCACTATGAAGTTTTTA
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
*
66 GTCTCATTTGGTAAAACTTAGTTATTTTGGGTCCGTATCGGGGACCGATTAGTGACGTTTTGTAA
66 G-CTCATTTGG-AAAACTT-GTTATTTT-GGT-CGTATC--GGACCCATTAGTGACGTTTTG-AA
131 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATT
123 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATT
* * *
196 TTGGTGAGATTAGTCCACTTTGAAGTTTTTAGCCTCATTTGGAACACGTTTTTATTTTGGGCCTA
188 TTAGTGAGATTAGTCCACTGTGAAGTTTTTAGCCTCATTTGGAACACGTTGTTATTTTGGGCCTA
*
261 TCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCTTCCACGCCTTTCTTTCCA
253 TCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCTTCAACGCCTTTCTTTCCA
* *
326 TTGTTTATGGCCTAACTATAATCATTTAGGTGAGATTAGTCCACTGTGAAGTTCTTAGCTCATTT
318 TTGTGTATGGCCTAACTATAATCATTTAGGTGAGATTAGTCCACTATGAAGTTCTTAGCTCATTT
391 GGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGG
383 GGAACACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGG
456 CAACCTTCGATGGCTT
448 CAACCTTCGATGGCTT
* * *
472 TCTTTCCATTGTTTTTGGCCTAACTATAACCATTTTGGTGAGATTAGTCCACTGTGATGTTTTTA
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
* **
537 GCTCATTT-GAAACACTTGTTATTTTGCTC-TATCGGATCCCATTAGTTTCGTTTTGAATCGTCT
66 GCTCATTTGGAAA-ACTTGTTATTTTGGTCGTATCGGA-CCCATTAGTGACGTTTTGAATCGTCT
* * *
600 TCGATTTGG-AAACCTTCGATGCTTTTCTTTCCATTGTTTATGGCCTAACTATACTCA-TTTAGT
129 TCGATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTAGT
*
663 GAGATTAGTCCACTGTGAAGTTTTTAG-CTCATTTGTAACAC-TTGTTATTTTGGGCCTATCGGG
193 GAGATTAGTCCACTGTGAAGTTTTTAGCCTCATTTGGAACACGTTGTTATTTTGGGCCTATCGGG
* *
726 GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGT
258 GACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AACCTTCAACGCCTTTCTTTCCATTGT
* * *
790 GTATGGCCTAACTATAATCATTTTGGTGAGATTAGTTCACTATGAAGTTTTTAGCTCATTTGGAA
322 GTATGGCCTAACTATAATCATTTAGGTGAGATTAGTCCACTATGAAGTTCTTAGCTCATTTGGAA
855 CACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAC
387 CACTTGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAC
920 CTTCGATGGCTT
452 CTTCGATGGCTT
*
932 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGCCCACTGTGAAGTTTTTA
1 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
*
997 GCTCATTTGGAAAACTTGTTATTTTGGGCGTATCGGGGA-CCATTAGTGACGTTTTGAATCGTCT
66 GCTCATTTGGAAAACTTGTTATTTTGGTCGTATC--GGACCCATTAGTGACGTTTTGAATCGTCT
*
1061 TCGATTTGGCAATCCTCAATG
129 TCGATTTGGCAAACCTCAATG
Statistics
Matches: 566, Mismatches: 35, Indels: 28
0.90 0.06 0.04
Matches are distributed among these distances:
460 297 0.52
461 62 0.11
462 40 0.07
463 62 0.11
464 15 0.03
465 4 0.01
466 1 0.00
467 2 0.00
468 11 0.02
469 5 0.01
470 7 0.01
471 60 0.11
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (463 bp):
TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTA
GCTCATTTGGAAAACTTGTTATTTTGGTCGTATCGGACCCATTAGTGACGTTTTGAATCGTCTTC
GATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTGTATGGCCTAACTATAATCATTTTAGTGAG
ATTAGTCCACTGTGAAGTTTTTAGCCTCATTTGGAACACGTTGTTATTTTGGGCCTATCGGGGAC
CATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCTTCAACGCCTTTCTTTCCATTGTGTAT
GGCCTAACTATAATCATTTAGGTGAGATTAGTCCACTATGAAGTTCTTAGCTCATTTGGAACACT
TGTTATTTTGGGCCTATCGGGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAACCTTC
GATGGCTT
Done.