Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019977.1 Corchorus olitorius cultivar O-4 contig20010, 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: 4019
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Found at i:254 original size:118 final size:117
Alignment explanation
Indices: 28--263 Score: 368
Period size: 118 Copynumber: 2.0 Consensus size: 117
18 TATTCTATTT
* * *
28 GCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGTTATTAGT
1 GCAACCCTCAATGCTTTTCGTTCCATTGCTTATGGCCTAACTATAATCATTTTGGTGGTATTAGT
* *
93 CCACTATGAAGTTTTGTAGCTCAATTGGAACACTTTTTATTTTGGGCCTATCG
66 CCACTATGAAGTTTTGTAGATCAATTGGAACACTTGTTATTTT-GGCCTATCG
146 GCAACCCTCAATGCTTTTCGTTCCATTGCTTATGGCCTAACTATAATCATTTTGGTGAGT-TTAG
1 GCAACCCTCAATGCTTTTCGTTCCATTGCTTATGGCCTAACTATAATCATTTTGGTG-GTATTAG
* *
210 TCCACTGTGAAGTTTT-TAGATCATTTGGAACACTTGTTATTTTTGGCCTATCG
65 TCCACTATGAAGTTTTGTAGATCAATTGGAACACTTGTTA-TTTTGGCCTATCG
263 G
1 G
264 GGCCCATTAG
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
117 30 0.28
118 78 0.72
119 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (117 bp):
GCAACCCTCAATGCTTTTCGTTCCATTGCTTATGGCCTAACTATAATCATTTTGGTGGTATTAGT
CCACTATGAAGTTTTGTAGATCAATTGGAACACTTGTTATTTTGGCCTATCG
Found at i:425 original size:154 final size:153
Alignment explanation
Indices: 145--961 Score: 1341
Period size: 154 Copynumber: 5.4 Consensus size: 153
135 TGGGCCTATC
* * *
145 GGCAACCCTCAATGCTTTTCGTTCCATTGCTTATGGCCTAACTATAATCATTTTGGTGAGTTTAG
1 GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
*
210 TCCACTGTGAAGTTTTTAGATCATTTGGAACACTTGTTATTTTTGGCCTATCGGGGCCCATTAGT
66 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA-TTTTGGCCTATCGGGGCCCATTAG-
*
275 TTTC-TTTTGAATCGTCTTCGATTT
129 TTACGTTTTGAATCGTCTTCGATTT
*
299 GGCAACGCTCAATGCTTTTCTTTCCATTGTTTAT-GCCGTAACTATAATCATTTTGGTGAGATTA
1 GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCC-TAACTATAATCATTTTGGTGAGATTA
363 GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCCTATCGGGGCCCATTAG
65 GTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG-GCCTATCGGGGCCCATTAG
*
428 TGACGTTTTGAATCGTCTTCGATTT
129 TTACGTTTTGAATCGTCTTCGATTT
* *
453 GGCAACCCTCAATGCTTTTCTTTCCATTTTTTATGGCCTAACTATAATCATTTTGGTGATATTAG
1 GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
518 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGACCTATCGGGGCCCATTAGT
66 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG-CCTATCGGGGCCCATTAGT
*
583 TCCGTTTTGAAT-GATCTTCGATTT
130 TACGTTTTGAATCG-TCTTCGATTT
*
607 GGCAATCCTCAATGCTTTTCTTTCCA----TTA---CCTAACTATAATCATTTTGGTGAGATTAG
1 GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
665 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGCCTATCGGGGCCCATTAGTT
66 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGCCTATCGGGGCCCATTAGTT
* *
730 CCGTTTTGAATCATCTTCGATTT
131 ACGTTTTGAATCGTCTTCGATTT
* *
753 GGCAATCCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGGTGAGATTAG
1 GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
818 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT
66 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTATCGGGGCCCATTAGT
* *
883 GACGTTTTGAATCGTCTTCTATTT
130 TACGTTTTGAATCGTCTTCGATTT
907 -GCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
1 GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
962 GATGGCTCAA
Statistics
Matches: 627, Mismatches: 21, Indels: 31
0.92 0.03 0.05
Matches are distributed among these distances:
146 67 0.11
147 73 0.12
150 6 0.01
153 137 0.22
154 341 0.54
155 3 0.00
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (153 bp):
GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGCCTATCGGGGCCCATTAGTT
ACGTTTTGAATCGTCTTCGATTT
Found at i:831 original size:300 final size:301
Alignment explanation
Indices: 145--933 Score: 1284
Period size: 300 Copynumber: 2.6 Consensus size: 301
135 TGGGCCTATC
* * *
145 GGCAACCCTCAATGCTTTTCGTTCCATTGCTTATGGCCTAACTATAATCATTTTGGTGAGTTTAG
1 GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
*
210 TCCACTGTGAAGTTTTTAGATCATTTGGAACACTTGTTATTTTTGGCCTATCGGGGCCCATTAGT
66 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA-TTTTGGCCTATCGGGGCCCATTAG-
*
275 TTTC-TTTTGAATCGTCTTCGATTTGGCAACGCTCAATGCTTTTCTTTCCATTGTTTATGCCGTA
129 TTACGTTTTGAATCGTCTTCGATTTGGCAAC-CTCAATGCTTTTCTTTCCA----TTA-GCCGTA
339 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
188 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
*
404 TTTGAGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTT
253 TTTGAGCCTATCGGGGCCCATTAGTGACGTTTTGAATCATCTTCGATTT
* *
453 GGCAACCCTCAATGCTTTTCTTTCCATTTTTTATGGCCTAACTATAATCATTTTGGTGATATTAG
1 GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
518 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGACCTATCGGGGCCCATTAGT
66 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGG-CCTATCGGGGCCCATTAGT
*
583 TCCGTTTTGAAT-GATCTTCGATTTGGCAATCCTCAATGCTTTTCTTTCCATTA-CC-TAACTAT
130 TACGTTTTGAATCG-TCTTCGATTTGGCAA-CCTCAATGCTTTTCTTTCCATTAGCCGTAACTAT
645 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTG-
193 AATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGA
**
709 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCATCTTCGATTT
258 GCCTATCGGGGCCCATTAGTGACGTTTTGAATCATCTTCGATTT
* *
753 GGCAATCCTCAATGCTTTTCTTTCCATTGTTTATGACCTAACTATAATCATTTTGGTGAGATTAG
1 GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
818 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT
66 TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT-GGCCTATCGGGGCCCATTAGT
* *
883 GACGTTTTGAATCGTCTTCTATTT-GCAACCCTCAATGCTTTTCTTTCCATT
130 TACGTTTTGAATCGTCTTCGATTTGGCAA-CCTCAATGCTTTTCTTTCCATT
934 GTTTATGGCC
Statistics
Matches: 457, Mismatches: 18, Indels: 21
0.92 0.04 0.04
Matches are distributed among these distances:
299 26 0.06
300 183 0.40
301 74 0.16
302 2 0.00
304 3 0.01
307 10 0.02
308 158 0.35
309 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (301 bp):
GGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
TCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGCCTATCGGGGCCCATTAGTT
ACGTTTTGAATCGTCTTCGATTTGGCAACCTCAATGCTTTTCTTTCCATTAGCCGTAACTATAAT
CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGAGCC
TATCGGGGCCCATTAGTGACGTTTTGAATCATCTTCGATTT
Done.