Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011917.1 Corchorus olitorius cultivar O-4 contig11950, 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, 840
Length: 1400
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Found at i:571 original size:154 final size:154
Alignment explanation
Indices: 1--1400 Score: 1967
Period size: 154 Copynumber: 9.1 Consensus size: 154
*
1 ACACTTTTTATTTTGGTATCTATCGGGGCCCGACTTAGTTCCGTTTTGTAATCGTCTTCGATTTG
1 ACACTTTTTATTTTGG-ATCTATCGGGGCCC-A-TTAGTTACGTTTTG-AATCGTCTTCGATTTG
* *
66 GTCAACCCTCAATGC-TTTCTATCCATTGTTTATGGCTTAACTATAATCATTTTGGTGAGATTAG
62 G-CAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAG
130 TCCAGTT-TGAAG-TTTTAGCTCATTTGGA
126 TCCA-TTGTGAAGTTTTTAGCTCATTTGGA
*
158 ACAC-TTTTATTTTGGATCTATCGGGGCCCATTAGTTTCGTTTTGAATCGTCTTCGATTTGGCAA
1 ACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAA
* * * *
222 CCCTCAATGCTTTTCCTTCCATTGTTTATGGCGTAACTGTAATCATTTTGATGAGATTAGTCC-T
66 CCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAT
*
286 CTGTGAAGTTTTTAGCTCATTTGCA
131 -TGTGAAGTTTTTAGCTCATTTGGA
** * * *
311 ACACTTTTTATTTTGGGGCCAATCGGGGCCCATTTTAGTGACGTTTTTAATCGTCTTCGATTTGG
1 ACACTTTTTATTTT-GGATCTATCGGGGCCCA--TTAGTTACGTTTTGAATCGTCTTCGATTTGG
* *
376 CAACCCTCAATCCTTTTCTTTCGATTGTTTATGG-CTAAACTATAATCATTTTGGTGAGATTAGT
63 CAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCT-AACTATAATCATTTTGGTGAGATTAGT
*
440 CCATTGTGAAGTTTTTAGCTAATTTGGA
127 CCATTGTGAAGTTTTTAGCTCATTTGGA
* *
468 ACACTTTTTATTTTGGATCTATCGGGGCGCATTAGTTTCGTTTTGAATCGTCTTCGATTTGGCAA
1 ACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAA
533 CCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC-T
66 CCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAT
*
597 CTGTGAAGTTTTTAGCTCATTTGCA
131 -TGTGAAGTTTTTAGCTCATTTGGA
** * * *
622 ACACTTTTTATTTTGGGCCAATCGGGGCCCATTTTAGTGACGTTTTGAATCGTCTTCGATTTGTC
1 ACACTTTTTATTTTGGATCTATCGGGGCCCA--TTAGTTACGTTTTGAATCGTCTTCGATTTGGC
* * *
687 AACCCTCAATGCTTTTCTTTCCATTGTTTATGTCGTAACTGTAATCATTTTGGTGAGATTAGTCC
64 AACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
*
752 -TCTGTGAAGGTTTTAGCTCATTTGGA
129 AT-TGTGAAGTTTTTAGCTCATTTGGA
* *
778 ACACTTTTTATTTTGGATCTATCGGGGCCCATTATTTCCGTTTTGAATCGTCTTCGATTTGGCAA
1 ACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAA
* *
843 CCCTCAATGC-TTTCTTTCCATTGTTTATGGCCTAACTA-AATCATTTTGGTCAGATTAGTCCAC
66 CCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAT
*
906 TGTGAAGTTTTTAGCTAATTTGGA
131 TGTGAAGTTTTTAGCTCATTTGGA
* * * *
930 ACAATTTTTATTTTGTG-CCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
1 ACACTTTTTATTTTG-GATCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCA
*
994 ACCCT-ATATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAAATTAGTCC
65 ACCCTCA-ATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCC
* *
1058 ATTGTGAAGTTTTTAGCTAAATTGGA
129 ATTGTGAAGTTTTTAGCTCATTTGGA
* *
1084 ACACTTTTTATTTTAGG-CCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
1 ACACTTTTTATTTT-GGATCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCA
* * * *
1148 ATCGTCAATGCTTTTCTTTCTATTGTTTATGGCCTAACTATAATAATTTTGGTGAGATTAGTCCA
65 ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCA
*
1213 CTGTGAAGTTTTTAGCTCATTTGGA
130 TTGTGAAGTTTTTAGCTCATTTGGA
* *
1238 ACACTTGTTATTTTGG-TCCTAT----GCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCA
1 ACACTTTTTATTTTGGAT-CTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCA
* ** * *
1298 ACCCTCACTGC-TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTGTTTATG-GCTTAATCC
65 ACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT-TTGGTGAGATTAGTCC
* *
1361 ATTGTGAAGTTTTTAGCTAAATTGGA
129 ATTGTGAAGTTTTTAGCTCATTTGGA
1387 ACACTTTTTATTTT
1 ACACTTTTTATTTT
Statistics
Matches: 1125, Mismatches: 95, Indels: 54
0.88 0.07 0.04
Matches are distributed among these distances:
149 77 0.07
150 49 0.04
151 15 0.01
152 180 0.16
153 89 0.08
154 388 0.34
155 32 0.03
156 168 0.15
157 126 0.11
158 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (154 bp):
ACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAA
CCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAT
TGTGAAGTTTTTAGCTCATTTGGA
Found at i:716 original size:310 final size:307
Alignment explanation
Indices: 1--1400 Score: 2058
Period size: 310 Copynumber: 4.5 Consensus size: 307
**
1 ACACTTTTTATTTTGGTATCTATCGGGGCCCGACTTAGTTCCGTTTTGTAATCGTCTTCGATTTG
1 ACACTTTTTATTTTGG-GCCTATCGGGGCCC-A-TTAGTTCCGTTTTG-AATCGTCTTCGATTTG
*
66 GTCAACCCTCAATGC-TTTCTATCCATTGTTTATGGCTTAACTATAATCATTTTGGTGAGATTAG
62 G-CAACCCTCAATGCTTTTCTTTCCATTGTTTATGGC-TAACTATAATCATTTTGGTGAGATTAG
*
130 TCCAGTT-TGAAG-TTTTAGCTCATTTGGAACAC-TTTTATTTTGGATCTATCGGGGCCCATTAG
125 TCCA-TTGTGAAGTTTTTAGCTAATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCCATTAG
* *
192 TTTCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCCTTCCATTGTTTATGGCGTA
189 TTTCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTA
* * *
257 ACTGTAATCATTTTGATGAGATTAGTCCTCTGTGAAGTTTTTAGCTCATTTGCA
254 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGCA
* ** *
311 ACACTTTTTATTTTGGGGCCAATCGGGGCCCATTTTAGTGACGTTTTTAATCGTCTTCGATTTGG
1 ACACTTTTTATTTT-GGGCCTATCGGGGCCCA--TTAGTTCCGTTTTGAATCGTCTTCGATTTGG
* *
376 CAACCCTCAATCCTTTTCTTTCGATTGTTTATGGCTAAACTATAATCATTTTGGTGAGATTAGTC
63 CAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCT-AACTATAATCATTTTGGTGAGATTAGTC
*
441 CATTGTGAAGTTTTTAGCTAATTTGGAACACTTTTTATTTTGGATCTATCGGGGCGCATTAGTTT
127 CATTGTGAAGTTTTTAGCTAATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTT
506 CGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
192 CGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
*
571 ATAATCATTTTGGTGAGATTAGTCCTCTGTGAAGTTTTTAGCTCATTTGCA
257 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGCA
* ** *
622 ACACTTTTTATTTTGGGCCAATCGGGGCCCATTTTAGTGACGTTTTGAATCGTCTTCGATTTGTC
1 ACACTTTTTATTTTGGGCCTATCGGGGCCCA--TTAGTTCCGTTTTGAATCGTCTTCGATTTGGC
* *
687 AACCCTCAATGCTTTTCTTTCCATTGTTTATGTCGTAACTGTAATCATTTTGGTGAGATTAGTCC
64 AACCCTCAATGCTTTTCTTTCCATTGTTTATGGC-TAACTATAATCATTTTGGTGAGATTAGTCC
* *
752 -TCTGTGAAGGTTTTAGCTCATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCCATTA-TTT
128 AT-TGTGAAGTTTTTAGCTAATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTT
815 CCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGC-TTTCTTTCCATTGTTTATGGCCTAAC
192 -CGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
* * *
879 TA-AATCATTTTGGTCAGATTAGTCCACTGTGAAGTTTTTAGCTAATTTGGA
256 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGCA
* * *
930 ACAATTTTTATTTTGTGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAA
1 ACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAA
*
995 CCCT-ATATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAAATTAGTCCA
66 CCCTCA-ATGCTTTTCTTTCCATTGTTTATGG-CTAACTATAATCATTTTGGTGAGATTAGTCCA
* * **
1059 TTGTGAAGTTTTTAGCTAAATTGGAACACTTTTTATTTTAGG-CCTATCGGGGCCCATTAGTGAC
129 TTGTGAAGTTTTTAGCTAATTTGGAACACTTTTTATTTT-GGATCTATCGGGGCCCATTAGTTTC
* * *
1123 GTTTTGAATCGTCTTCGATTTGGCAATCGTCAATGCTTTTCTTTCTATTGTTTATGGCCTAACTA
193 GTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
* *
1188 TAATAATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGA
258 TAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGCA
* *
1238 ACACTTGTTATTTTGGTCCTAT----GCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAA
1 ACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAA
* ** * *
1299 CCCTCACTGC-TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTGTTTATG-GCTTAATCCA
66 CCCTCAATGCTTTTCTTTCCATTGTTTATGG-CTAACTATAATCATT-TTGGTGAGATTAGTCCA
*
1362 TTGTGAAGTTTTTAGCTAAATTGGAACACTTTTTATTTT
129 TTGTGAAGTTTTTAGCTAATTTGGAACACTTTTTATTTT
Statistics
Matches: 1009, Mismatches: 62, Indels: 45
0.90 0.06 0.04
Matches are distributed among these distances:
303 82 0.08
304 49 0.05
305 2 0.00
306 173 0.17
307 32 0.03
308 151 0.15
309 104 0.10
310 255 0.25
311 161 0.16
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (307 bp):
ACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAA
CCCTCAATGCTTTTCTTTCCATTGTTTATGGCTAACTATAATCATTTTGGTGAGATTAGTCCATT
GTGAAGTTTTTAGCTAATTTGGAACACTTTTTATTTTGGATCTATCGGGGCCCATTAGTTTCGTT
TTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
TCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGCA
Done.