Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006262.1 Corchorus olitorius cultivar O-4 contig06287, 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, 696
Length: 1160
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Found at i:66 original size:37 final size:38
Alignment explanation
Indices: 9--146 Score: 120
Period size: 37 Copynumber: 3.7 Consensus size: 38
1 TTTAGATT
* * *
9 CCTGTTTAGGTTTCTTATC-AAATCCTTATTTAAGGTC
1 CCTGTTTAGGTGTCTCATCAAAATCCTTATTTAAGGTA
* * ** *
46 CCTGTTTAGGTGTCTCATCAAAAT-CTTGTTCAAAATT
1 CCTGTTTAGGTGTCTCATCAAAATCCTTATTTAAGGTA
* * * *
83 CATGTTTAGGTTTCTTAT-TAAATCCTTATTTAAGGTA
1 CCTGTTTAGGTGTCTCATCAAAATCCTTATTTAAGGTA
* * *
120 CTTGTTTAGCTGTCTCTTCAAAATCCT
1 CCTGTTTAGGTGTCTCATCAAAATCCT
147 AGTTTAGGTT
Statistics
Matches: 76, Mismatches: 22, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
36 4 0.05
37 61 0.80
38 11 0.14
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (38 bp):
CCTGTTTAGGTGTCTCATCAAAATCCTTATTTAAGGTA
Found at i:134 original size:74 final size:74
Alignment explanation
Indices: 6--144 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 74
1 TTTAG
* * *
6 ATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATC
1 ATTCATGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTGTTTAGCTGTCTCATCAAAATC
71 TTGTTCAAA
66 TTGTTCAAA
* * *
80 ATTCATGTTTAGGTTTCTTATTAAATCCTTATTTAAGGTACTTGTTTAGCTGTCTCTTCAAAATC
1 ATTCATGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTGTTTAGCTGTCTCATCAAAATC
145 CTAGTTTAGG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.45
Consensus pattern (74 bp):
ATTCATGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTGTTTAGCTGTCTCATCAAAATC
TTGTTCAAA
Found at i:209 original size:18 final size:16
Alignment explanation
Indices: 167--209 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
157 TCTTATCAAA
167 ATTTTGTTCAAAATCC
1 ATTTTGTTCAAAATCC
183 ATTTCTTGTTCAAAATTCC
1 A-TT-TTGTTCAAAA-TCC
202 TATTTTGT
1 -ATTTTGT
210 GTTTAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 2 0.09
18 14 0.61
19 5 0.22
20 1 0.04
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (16 bp):
ATTTTGTTCAAAATCC
Found at i:212 original size:20 final size:19
Alignment explanation
Indices: 170--206 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
160 TATCAAAATT
170 TTGTTCAAAA-TCCATTTC
1 TTGTTCAAAATTCCATTTC
188 TTGTTCAAAATTCCTATTT
1 TTGTTCAAAATTCC-ATTT
207 TGTGTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 3 0.18
20 4 0.24
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (19 bp):
TTGTTCAAAATTCCATTTC
Found at i:323 original size:54 final size:54
Alignment explanation
Indices: 241--500 Score: 348
Period size: 54 Copynumber: 4.8 Consensus size: 54
231 TCTCTCTAGA
**
241 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGCTTTT-AGAGGTCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAG-TTTTCAGAAATCT
*
295 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCT
*
349 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGCTTTT-AGAAGTCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAG-TTTTCAGAAATCT
* * * * *
403 AAGTTGATCTTCAGACGACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCT
* * *
457 AAGTTGATCTTAA-AGTGATCTAGTGTGGTCATTCCA-AGAAGTTT
1 AAGTTGATCTTAAGA-TGACCCAGTGTGGTC-TTTCATAGAAGTTT
501 ACGATGATCA
Statistics
Matches: 187, Mismatches: 14, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
53 9 0.05
54 169 0.90
55 9 0.05
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (54 bp):
AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCT
Found at i:497 original size:108 final size:108
Alignment explanation
Indices: 241--486 Score: 395
Period size: 108 Copynumber: 2.3 Consensus size: 108
231 TCTCTCTAGA
*
241 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGCTTTTAGAGGTCTAAGTTGATCTT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGCTTTTAGAAGTCTAAGTTGATCTT
* * * *
306 AAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
66 AAGACGACCCAGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
349 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGCTTTTAGAAGTCTAAGTTGATCTT
1 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGCTTTTAGAAGTCTAAGTTGATCTT
* *
414 CAGACGACCCTGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
66 AAGACGACCCAGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
* *
457 AAGTTGATCTTAA-AGTGATCTAGTGTGGTC
1 AAGTTGATCTTAAGA-TGACCCAGTGTGGTC
487 ATTCCAAGAA
Statistics
Matches: 128, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
107 1 0.01
108 127 0.99
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.35
Consensus pattern (108 bp):
AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGCTTTTAGAAGTCTAAGTTGATCTT
AAGACGACCCAGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
Found at i:646 original size:33 final size:33
Alignment explanation
Indices: 604--681 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
594 ATTAATTAAG
* * * *
604 AAGTTCAAAATTTGCATTTCATTTCAAAATTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
637 AAGTTCAAAATCTGCATATCATATCAAAACTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
670 AAGTTCAAAATC
1 AAGTTCAAAATC
682 CACAGTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (33 bp):
AAGTTCAAAATCTGCATATCATATCAAAACTCA
Found at i:846 original size:7 final size:7
Alignment explanation
Indices: 834--1160 Score: 636
Period size: 7 Copynumber: 46.7 Consensus size: 7
824 CCAAATAGGC
834 AATTCAA
1 AATTCAA
841 AATTCAA
1 AATTCAA
848 AATTCAA
1 AATTCAA
855 AATTCAA
1 AATTCAA
862 AATTCAA
1 AATTCAA
869 AATTCAA
1 AATTCAA
876 AATTCAA
1 AATTCAA
883 AATTCAA
1 AATTCAA
890 AATTCAA
1 AATTCAA
897 AATTCAA
1 AATTCAA
904 AATTCAA
1 AATTCAA
911 AATTCAA
1 AATTCAA
918 AATTCAA
1 AATTCAA
925 AATTCAA
1 AATTCAA
932 AATTCAA
1 AATTCAA
939 AATTCAA
1 AATTCAA
946 AATTCAA
1 AATTCAA
953 AATTCAA
1 AATTCAA
960 AATTCAA
1 AATTCAA
967 AATTCAA
1 AATTCAA
974 AATTCAA
1 AATTCAA
*
981 AATCCAA
1 AATTCAA
988 AATTCAA
1 AATTCAA
995 AATTCAA
1 AATTCAA
1002 AATTCAA
1 AATTCAA
1009 AATTCAA
1 AATTCAA
1016 AATTCAA
1 AATTCAA
1023 AATTCAA
1 AATTCAA
1030 AATTCAA
1 AATTCAA
1037 AATTCAA
1 AATTCAA
1044 AATTCAA
1 AATTCAA
1051 AATTCAA
1 AATTCAA
1058 AATTCAA
1 AATTCAA
1065 AATTCAA
1 AATTCAA
1072 AATTCAA
1 AATTCAA
1079 AATTCAA
1 AATTCAA
1086 AATTCAA
1 AATTCAA
1093 AATTCAA
1 AATTCAA
*
1100 AACTCAA
1 AATTCAA
1107 AATTCAA
1 AATTCAA
1114 AATTCAA
1 AATTCAA
1121 AATTCAA
1 AATTCAA
1128 AATTCAA
1 AATTCAA
1135 AATTCAA
1 AATTCAA
1142 AATTCAA
1 AATTCAA
1149 AATTCAA
1 AATTCAA
1156 AATTC
1 AATTC
Statistics
Matches: 316, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 316 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (7 bp):
AATTCAA
Done.