Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011907.1 Corchorus olitorius cultivar O-4 contig11940, 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: 3585
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Found at i:1174 original size:154 final size:154
Alignment explanation
Indices: 894--1845 Score: 1478
Period size: 154 Copynumber: 6.2 Consensus size: 154
884 ATTCGTATCA
*
894 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCACTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
* * * * * ** *
959 CACTTGTTATTTTGGGCATATTGAGGACCACTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAC
66 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA
*
1024 CCTCAATGCTTTTCTTTCCAATGT
131 CCTCAATGCTTTTCTTTCCATTGT
* * * *
1048 TTATGGCCTAACTATAATCATTTTAGTAAGATTAGTCCACTTTGAAGTTTTTTTG-TCATTTGGA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG-TTTTTAGCTCATTTGGA
* * ** *
1112 ACACTCGTTATTTTGGGCCTACCGGGGCCCATTAGTTCCGTTCTGAATCGTCTTCGATTTGGCAA
65 ACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAA
* *
1177 CCCTCAATGCTTTTCGTTCCATTGT
130 ACCTCAATGCTTTTCTTTCCATTGT
*
1202 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTAGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
*
1267 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAA
66 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA
1332 CCTCAATGCTTTTCTTTCCATTGT
131 CCTCAATGCTTTTCTTTCCATTGT
1356 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA-TTTTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
* *
1420 CACCTGTTATTTTAGGGCCTATCGGGGCTCTATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
66 CACTTGTTATTTT-GGGCCTATCGGGGC-CCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCA
* *
1485 AACCTCGAATGCTTTTCTTCCCGTTGT
129 AACCTC-AATGCTTTTCTTTCCATTGT
* *
1512 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTAATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
*
1577 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAA
66 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA
* *
1642 CCTCAATGCGTTTGTTTCCATTGT
131 CCTCAATGCTTTTCTTTCCATTGT
*
1666 TTATGGCCTACCTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
1 TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
* * *
1731 CACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAA
66 CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA
* *
1796 CGCT-AATGCTTTTCTTTTCATTGC
131 C-CTCAATGCTTTTCTTTCCATTGT
* *
1820 TTATTGACTAACTATAATCATTTTGG
1 TTATGGCCTAACTATAATCATTTTGG
1846 ATTTTGGGCC
Statistics
Matches: 735, Mismatches: 56, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
153 35 0.05
154 505 0.69
155 88 0.12
156 78 0.11
157 29 0.04
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
CACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAA
CCTCAATGCTTTTCTTTCCATTGT
Found at i:1925 original size:107 final size:107
Alignment explanation
Indices: 1739--1952 Score: 367
Period size: 107 Copynumber: 2.0 Consensus size: 107
1729 AACACTTGTT
1739 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACGCTAATG
1 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACGCTAATG
* *
1804 CTTTTCTTTTCATTGCTTATTGACTAACTATAATCATTTTGG
66 CTTTTCTTTTCATTGCTTATGGACTAACTATAATCATATTGG
* *
1846 ATTTTGGGCCTATTGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAAAC-CTAAT
1 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGC-AAACGCTAAT
*
1910 GCTTTTCTTTTCATTGTTTATGGACTAACTATAATCATATTGG
65 GCTTTTCTTTTCATTGCTTATGGACTAACTATAATCATATTGG
1953 TGAGATTAGT
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
107 97 0.96
108 4 0.04
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (107 bp):
ATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTCAATTCGGCAAACGCTAATG
CTTTTCTTTTCATTGCTTATGGACTAACTATAATCATATTGG
Found at i:2057 original size:261 final size:261
Alignment explanation
Indices: 1585--2106 Score: 832
Period size: 261 Copynumber: 2.0 Consensus size: 261
1575 AACACTTGTT
* *
1585 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATG
1 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTATTGAATCGTCTTCGATTCGGCAAACCTCAATG
* * * * *
1650 CGTTTGTTTCCATTGTTTATGGCCTACCTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
66 CGTTTCTTTCCATTGTTTATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTGTGAACTT
*
1715 TTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCG
131 TTTAGCTCAGTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCG
* *
1780 TCTTCAATTCGGCAAACGCT-AATGCTTTTCTTTTCATTGCTTATTGACTAACTATAATCATTTT
196 TCTTCAATTCGGCAAAC-CTCAATGCTTTTCTTTCCATTGCTTATGGACTAACTATAATCATTTT
1844 GG
260 GG
* *
1846 ATTTTGGGCCTATTGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAAACCT-AAT
1 ATTTTGGGCCTATCGAGGCCCATTAGTGACGTATTGAATCGTCTTCGATTCGGC-AAACCTCAAT
* *
1910 GCTTTTCTTTTCATTGTTTATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTGTGAACT
65 GCGTTTCTTTCCATTGTTTATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTGTGAACT
*
1975 TTTTAGCTCAGTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATC
130 TTTTAGCTCAGTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATC
* * * * *
2040 GTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCGTTGTTTATGGCCTAACTATAATCATTTT
195 GTCTTCAATTCGGCAAACCTCAATGCTTTTCTTTCCATTGCTTATGGACTAACTATAATCATTTT
2105 GG
260 GG
2107 TGAGATTAGT
Statistics
Matches: 239, Mismatches: 20, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
260 2 0.01
261 231 0.97
262 6 0.03
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (261 bp):
ATTTTGGGCCTATCGAGGCCCATTAGTGACGTATTGAATCGTCTTCGATTCGGCAAACCTCAATG
CGTTTCTTTCCATTGTTTATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTGTGAACTT
TTTAGCTCAGTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCG
TCTTCAATTCGGCAAACCTCAATGCTTTTCTTTCCATTGCTTATGGACTAACTATAATCATTTTG
G
Found at i:2126 original size:154 final size:154
Alignment explanation
Indices: 1846--3584 Score: 2627
Period size: 154 Copynumber: 11.3 Consensus size: 154
1836 ATCATTTTGG
* * *
1846 ATTTTGGGCCTATTGAGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTCGGCAAAACCT-AAT
1 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGC-AAACCTCAAT
* * *
1910 GCTTTTCTTTTCATTGTTTATGGACTAACTATAATCATATTGGTGAGATTAGTCCACTGTGAACT
65 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACT
*
1975 TTTTAGCTCAGTTGGAACACTTGTT
130 TTTTAGCTCATTTGGAACACTTGTT
2000 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
*
2065 CTTTTCTTTCCGTTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTT
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTT
2130 TTTAGCTCATTTGGAACACTTGTT
131 TTTAGCTCATTTGGAACACTTGTT
**
2154 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
* * *
2219 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATAATTTTGGTGAGATTAGTCCACTATGAAGTT
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTT
*
2284 TTTAGCTCATTTGGAACACTTCTT
131 TTTAGCTCATTTGGAACACTTGTT
* * * *
2308 ATTTTGGGCTTACCGAGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
2373 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTA
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACT-
* *
2438 TTTTAGCTCATTTGGAATACTTCTT
130 TTTTAGCTCATTTGGAACACTTGTT
* * *
2463 ATTTTGGGCCTATCGGGG-CCATTTGTGACATTATTGAATCTTCTTCGATTTGGCAAACCTCAAT
1 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTT-TTGAATCGTCTTCGATTTGGCAAACCTCAAT
*
2527 GCTTTTCTTTCCATTGTTTATGGTCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACT
65 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACT
*
2592 TTTTAGCTCATTCGGAACACTTGTT
130 TTTTAGCTCATTTGGAACACTTGTT
* * **
2617 ATTTTGGGCCTATCAGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
*
2682 CTTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCATTGTGAACT
66 C-TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACT
*
2747 TTTTAGCTCATTTGGAATACTTGTT
130 TTTTAGCTCATTTGGAACACTTGTT
* **
2772 ATTTTGGACCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
* * * * *
2837 CATTTCATTCCATTGTTTATGTCCTAACTATAATAATTTTGGTGAGATTAGTCCACTGTGAAGTT
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTT
* *
2902 TTTAGCTCATTCGGAACACTTGTC
131 TTTAGCTCATTTGGAACACTTGTT
* * * * * * ** *
2926 AATTTGGGCTTATTGGGGTCGATTAGTGACGTATTGAATCGTCTTCGATTTATCAGACCTCAATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
* * *
2991 CTTTTCATTCCATTGTTTATGACCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACCT
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTT
*
3056 TTTAGCTCAGTTGGAACACTTGTT
131 TTTAGCTCATTTGGAACACTTGTT
* * * ** * *
3080 ATTTTGAGCATATCGGGACCCATTAGTTCCGTTTTAAATCGTCTTCGATTTGGCAAACCTCAACG
1 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
* * *
3145 CTTTTCTTTCCATTGTATATGGTCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTT
* *
3210 TTTAGCTCATTTGGAATACTTCTT
131 TTTAGCTCATTTGGAACACTTGTT
** * ****
3234 ATTTTGGATCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGTTTGCCTCAATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
*
3299 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTATGAACTT
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTT
3364 TTTAGCTCATTTGGAACACTTGTT
131 TTTAGCTCATTTGGAACACTTGTT
* * * * *
3388 ATTTTGGGCCTATCGGGGCACATTAGTGACGTATTGAATCTTCTTCGAATTGGCAAGCCTCAATG
1 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
* * * * * *
3453 CTTTTGTTTCCATTGTTTATGGCCTACCTATAATCATTTTGTTTAGATTAGTCCACTTTGAAGTT
66 CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA-CT
*
3518 TTTTAGCTCATTTGGAACACCTGTT
130 TTTTAGCTCATTTGGAACACTTGTT
**
3543 ATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
1 ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGT
3585 T
Statistics
Matches: 1436, Mismatches: 143, Indels: 11
0.90 0.09 0.01
Matches are distributed among these distances:
153 6 0.00
154 1079 0.75
155 351 0.24
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
ATTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATG
CTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTT
TTTAGCTCATTTGGAACACTTGTT
Done.