Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013853.1 Corchorus olitorius cultivar O-4 contig13886, 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: 1844
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Found at i:822 original size:16 final size:17
Alignment explanation
Indices: 779--823 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
769 CCATGATGAG
*
779 TCCTTGGCGCATCACTT
1 TCCTTGGCGCATCACCT
796 TCCTTGGCGCATCACCT
1 TCCTTGGCGCATCACCT
*
813 T-CTTGCCGCAT
1 TCCTTGGCGCAT
824 ATGCACATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.11, C:0.38, G:0.18, T:0.33
Consensus pattern (17 bp):
TCCTTGGCGCATCACCT
Found at i:1274 original size:153 final size:154
Alignment explanation
Indices: 844--1844 Score: 1494
Period size: 154 Copynumber: 6.5 Consensus size: 154
834 TCTCCATGAT
* * *
844 CTCATTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGATCCGTTTTGAATTGTCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTC
*
909 GATTTGCCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
66 GATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
* *
974 ATTTGTCCGCTGTGAAGTTTTTAG
131 ATTAGTCCACTGTGAAGTTTTTAG
* *
998 CTAATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTG
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTC
1063 GATTTGGCAACCCTCAATGC--TTCATGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTG
66 GATTTGGCAACCCTCAATGCTTTTC-T-TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTG
1126 AGATTAGTCCACTGTGAAGTTTTTAG
129 AGATTAGTCCACTGTGAAGTTTTTAG
* * * *** *
1152 CTCATTTGGAACAGTTGTTA-TTTGGGTCTATAGGGGCCCATTAGTGATGTTTTGAATCGCCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTC
*
1216 GATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCC-AACATATAATTATTTTGGTGA
66 GATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC-TATAATCATTTTGGTGA
*
1280 GATTAGTCCACAGTGAAGTTTTTAG
130 GATTAGTCCACTGTGAAGTTTTTAG
* * *
1305 CTCATTTGGAACAATTGTTATTTTGGGTCTATCGGAGCCCATTAGTTCCGTTTTGAATCGTCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTC
* * * ** *
1370 GATTTGTCAAACCTCAATACTTCACGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
66 GATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
1435 ATTAGTCCACTGTGAAGTTTTTAG
131 ATTAGTCCACTGTGAAGTTTTTAG
* * *
1459 CTAATTT-GAACACTTGTTATTTTGGGCCTATCAGGGCCCTTTAGTTCCGTTTTGAATCGTCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTC
1523 GATTTGGCAACCCTCAATGCTTTT-TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
66 GATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
* *
1587 ATTAGTCCACTGTGAAGTTTTAAT
131 ATTAGTCCACTGTGAAGTTTTTAG
* * * *
1611 CTCATTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAGTCATCATC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTC
** * * *
1676 GATTTGGCAACAATCAATGCATTACTTTACATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
66 GATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
*
1741 ATTAGTCCACTGTGAAGTTTTTAA
131 ATTAGTCCACTGTGAAGTTTTTAG
* * * *** *
1765 CTCATTTGGAACAGTTGTTA-TTTGGGTCTATAGGGGCCCATTAGTGATGTTTTGAATCGCCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTC
1829 GATTTGGCAACCCTCA
66 GATTTGGCAACCCTCA
Statistics
Matches: 763, Mismatches: 75, Indels: 19
0.89 0.09 0.02
Matches are distributed among these distances:
152 73 0.10
153 325 0.43
154 359 0.47
155 6 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
CTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTC
GATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
ATTAGTCCACTGTGAAGTTTTTAG
Found at i:1431 original size:307 final size:308
Alignment explanation
Indices: 844--1844 Score: 1536
Period size: 307 Copynumber: 3.3 Consensus size: 308
834 TCTCCATGAT
* * * *
844 CTCATTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTA--GATCCGTTTTGAATTGTCT
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGAT--GTTTTGAATCGCCT
*
907 TCGATTTGCCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTG
64 TCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTG
* * *
972 AGATTTGTCCGCTGTGAAGTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
129 AGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCC
* * *
1037 CATTAGTTCCGTTTTGAATCGTCTTGGATTTGGCAACCCTCAATGCTTCATGTTCCATTGTTTAT
194 CATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTCACGTTCCATTGTTTAT
1102 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
259 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
* *
1152 CTCATTTGGAACAGTTGTTA-TTTGGGTCTATAGGGGCCCATTAGTGATGTTTTGAATCGCCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGATGTTTTGAATCGCCTTC
*
1216 GATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCC-AACATATAATTATTTTGGTGA
66 GATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC-TATAATCATTTTGGTGA
* * * *
1280 GATTAGTCCACAGTGAAGTTTTTAGCTCATTTGGAACAATTGTTATTTTGGGTCTATCGGAGCCC
130 GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCC
* *
1345 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGTCAAACCTCAATACTTCACGTTCCATTGTTTATG
195 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTCACGTTCCATTGTTTATG
1410 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
260 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
* * *** *
1459 CTAATTT-GAACACTTGTTATTTTGGGCCTATCA-GGGCCCTTTAGTTCCGTTTTGAATCGTCTT
1 CTCATTTGGAACACTTGTTATTTTGGGCCTAT-AGGGGCCCATTAGTGATGTTTTGAATCGCCTT
1522 CGATTTGGCAACCCTCAATGCTTTT-TTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGA
65 CGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGA
* * *
1586 GATTAGTCCACTGTGAAGTTTTAATCTCATTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCC
130 GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCC
* * * * * *
1651 ATTAGTTCCGTTTTGAGTCATCATCGATTTGGC-AACAATCAATGCATT-ACTTTACATTGTTTA
195 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC-CTCAATGC-TTCACGTTCCATTGTTTA
*
1714 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAA
258 TGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
* *
1765 CTCATTTGGAACAGTTGTTA-TTTGGGTCTATAGGGGCCCATTAGTGATGTTTTGAATCGCCTTC
1 CTCATTTGGAACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGATGTTTTGAATCGCCTTC
1829 GATTTGGCAACCCTCA
66 GATTTGGCAACCCTCA
Statistics
Matches: 630, Mismatches: 53, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
305 4 0.01
306 262 0.42
307 342 0.54
308 19 0.03
309 3 0.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (308 bp):
CTCATTTGGAACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGTGATGTTTTGAATCGCCTTC
GATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG
ATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCA
TTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTCACGTTCCATTGTTTATGG
CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAG
Done.