Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017404.1 Corchorus olitorius cultivar O-4 contig17437, 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: 12055
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1397 original size:2 final size:2
Alignment explanation
Indices: 1390--1434 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1380 GTCTCTACAA
1390 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1432 AC A
1 AC A
1435 AACCCTTTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6097 original size:22 final size:22
Alignment explanation
Indices: 6071--6202 Score: 99
Period size: 22 Copynumber: 6.0 Consensus size: 22
6061 TAAAATTCCA
6071 ATAACCTTCGTATGAAATTTTG
1 ATAACCTTCGTATGAAATTTTG
* * * *
6093 TTAACCTCCCTAAGAAATTTTG
1 ATAACCTTCGTATGAAATTTTG
**
6115 ATAACCTTTTTATGAAATTTTG
1 ATAACCTTCGTATGAAATTTTG
* *
6137 GTAATC-TCTGTATGAAATTTTG
1 ATAACCTTC-GTATGAAATTTTG
* *
6159 ATAA--TTACACTATGAAGTTTTG
1 ATAACCTT-C-GTATGAAATTTTG
* * *
6181 ATAACCTCCATATAAAATTTTG
1 ATAACCTTCGTATGAAATTTTG
6203 GTAATAACAC
Statistics
Matches: 84, Mismatches: 21, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
21 2 0.02
22 80 0.95
23 1 0.01
24 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
ATAACCTTCGTATGAAATTTTG
Found at i:6119 original size:44 final size:44
Alignment explanation
Indices: 6071--6162 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 44
6061 TAAAATTCCA
*
6071 ATAACCTTCGTATGAAATTTTGTTAACCTCCCTAAGAAATTTTG
1 ATAACCTTCGTATGAAATTTTGGTAACCTCCCTAAGAAATTTTG
** * ** *
6115 ATAACCTTTTTATGAAATTTTGGTAATCTCTGTATGAAATTTTG
1 ATAACCTTCGTATGAAATTTTGGTAACCTCCCTAAGAAATTTTG
6159 ATAA
1 ATAA
6163 TTACACTATG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (44 bp):
ATAACCTTCGTATGAAATTTTGGTAACCTCCCTAAGAAATTTTG
Found at i:6150 original size:66 final size:66
Alignment explanation
Indices: 6080--6207 Score: 159
Period size: 66 Copynumber: 1.9 Consensus size: 66
6070 AATAACCTTC
* * *** *
6080 GTATGAAATTTTGTTAACCT-CCCTAAGAAATTTTGATAACCTTTTTATGAAATTTTGGTAATCT
1 GTATGAAATTTTGATAA-CTACACTAAGAAATTTTGATAACCTCCATATAAAATTTTGGTAATCT
6144 CT
65 CT
* * *
6146 GTATGAAATTTTGATAATTACACTATGAAGTTTTGATAACCTCCATATAAAATTTTGGTAAT
1 GTATGAAATTTTGATAACTACACTAAGAAATTTTGATAACCTCCATATAAAATTTTGGTAAT
6208 AACACTATGA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 1 0.02
66 51 0.98
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (66 bp):
GTATGAAATTTTGATAACTACACTAAGAAATTTTGATAACCTCCATATAAAATTTTGGTAATCTC
T
Found at i:6173 original size:44 final size:44
Alignment explanation
Indices: 6125--6230 Score: 133
Period size: 44 Copynumber: 2.4 Consensus size: 44
6115 ATAACCTTTT
* ** * *
6125 TATGAAATTTTGGTAATCTCTGTATGAAATTTTGATAATTACAC
1 TATGAAATTTTGATAATCTCCATATAAAATTTTGATAATAACAC
* * *
6169 TATGAAGTTTTGATAACCTCCATATAAAATTTTGGTAATAACAC
1 TATGAAATTTTGATAATCTCCATATAAAATTTTGATAATAACAC
6213 TATGAAA-TTTGATAATCT
1 TATGAAATTTTGATAATCT
6231 TCCTATGTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
43 10 0.19
44 42 0.81
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (44 bp):
TATGAAATTTTGATAATCTCCATATAAAATTTTGATAATAACAC
Found at i:6228 original size:21 final size:21
Alignment explanation
Indices: 6125--6228 Score: 79
Period size: 22 Copynumber: 4.8 Consensus size: 21
6115 ATAACCTTTT
* *
6125 TATGAAATTTTGGTAAT-CTC
1 TATGAAATTTTGATAATACAC
6145 TGTATGAAATTTTGATAATTACAC
1 --TATGAAATTTTGATAA-TACAC
* *
6169 TATGAAGTTTTGATAACCTCCA-
1 TATGAAATTTTGATAA--TACAC
* *
6191 TATAAAATTTTGGTAATAACAC
1 TATGAAATTTTGATAAT-ACAC
6213 TATGAAA-TTTGATAAT
1 TATGAAATTTTGATAAT
6229 CTTCCTATGT
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
20 1 0.02
21 10 0.15
22 49 0.74
23 4 0.06
24 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (21 bp):
TATGAAATTTTGATAATACAC
Found at i:7815 original size:3 final size:3
Alignment explanation
Indices: 7809--7870 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
7799 AAAAAAAAAT
7809 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
7857 GAA GAA GAA -AA GAA
1 GAA GAA GAA GAA GAA
7871 TAAATAATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:8191 original size:25 final size:25
Alignment explanation
Indices: 8153--8216 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
8143 AGCTTCCCAG
** *
8153 CAACGAGCACCCTGATAGCGAGCTT
1 CAACGAGCTTCCTGACAGCGAGCTT
*
8178 CAACGAGCTTCCTGGCAGCGAGCTT
1 CAACGAGCTTCCTGACAGCGAGCTT
*
8203 CACCGAGCTTCCTG
1 CAACGAGCTTCCTG
8217 GCAGTGAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.22, C:0.34, G:0.25, T:0.19
Consensus pattern (25 bp):
CAACGAGCTTCCTGACAGCGAGCTT
Found at i:8217 original size:25 final size:25
Alignment explanation
Indices: 8169--8238 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
8159 GCACCCTGAT
8169 AGCGAGCTTCAACGAGCTTCCTGGC
1 AGCGAGCTTCAACGAGCTTCCTGGC
*
8194 AGCGAGCTTCACCGAGCTTCCTGGC
1 AGCGAGCTTCAACGAGCTTCCTGGC
* * * *
8219 AGTGAGTTTCAGCGAACTTC
1 AGCGAGCTTCAACGAGCTTC
8239 ACCGAGCTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.23
Consensus pattern (25 bp):
AGCGAGCTTCAACGAGCTTCCTGGC
Found at i:8232 original size:35 final size:36
Alignment explanation
Indices: 8193--8260 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
8183 AGCTTCCTGG
*
8193 CAGCGAGCTTCACCGAGCTTCCTGGCAG-TGAGTTT
1 CAGCGAACTTCACCGAGCTTCCTGGCAGCTGAGTTT
8228 CAGCGAACTTCACCGAGCTTCCTGGCAGCTGAG
1 CAGCGAACTTCACCGAGCTTCCTGGCAGCTGAG
8261 CTCCTCTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.19, C:0.31, G:0.28, T:0.22
Consensus pattern (36 bp):
CAGCGAACTTCACCGAGCTTCCTGGCAGCTGAGTTT
Found at i:9956 original size:104 final size:103
Alignment explanation
Indices: 9775--9992 Score: 244
Period size: 104 Copynumber: 2.1 Consensus size: 103
9765 TCGTGATGTG
* * *
9775 GAAGGCTAGGTGAGATAGTGCACTACCTTCACCCTTTGGATACCTTTGCTTTATAACGCTTCGGC
1 GAAGGCTAGGTGAGATAGTGCACTACCTTCAACCTTTGGATACCTTGGCTTTATAACGCTTCGGA
* * * * *
9840 CACATCTTTAGTCGTGATGGGCTAAATCATGTGACAAC
66 CACATCTTTAGTCATGATAGACTAAACCATGGGACAAC
* * *
9878 GAAGGCTAGGTGAGAGTAGTGCGCTA-TTCTCAACCTTTGAGATATCTTGGCTTTATAACGCCTT
1 GAAGGCTAGGTGAGA-TAGTGCACTACCT-TCAACCTTTG-GATACCTTGGCTTTATAACG-CTT
* * * *
9942 -GGACTCATC-TTAGTCATGGTAGACTAAACCATGGGATAAG
62 CGGACACATCTTTAGTCATGATAGACTAAACCATGGGACAAC
9982 GAAGGCTAGGT
1 GAAGGCTAGGT
9993 AGGAGACCTT
Statistics
Matches: 96, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
103 16 0.17
104 52 0.54
105 25 0.26
106 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (103 bp):
GAAGGCTAGGTGAGATAGTGCACTACCTTCAACCTTTGGATACCTTGGCTTTATAACGCTTCGGA
CACATCTTTAGTCATGATAGACTAAACCATGGGACAAC
Found at i:11158 original size:13 final size:13
Alignment explanation
Indices: 11140--11166 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11130 TTAAAACAGA
11140 TCTTCTATTTCAT
1 TCTTCTATTTCAT
11153 TCTTCTATTTCAT
1 TCTTCTATTTCAT
11166 T
1 T
11167 TTTCCTTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTTCTATTTCAT
Found at i:11912 original size:12 final size:12
Alignment explanation
Indices: 11895--11919 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11885 ATTTACTAAT
11895 TAATATTTTGAG
1 TAATATTTTGAG
11907 TAATATTTTGAG
1 TAATATTTTGAG
11919 T
1 T
11920 TCGTACTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TAATATTTTGAG
Found at i:11946 original size:2 final size:2
Alignment explanation
Indices: 11941--11987 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
11931 TATAGTAGTA
11941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11983 AT AT A
1 AT AT A
11988 ATNTTAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.