Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012251.1 Corchorus capsularis cultivar CVL-1 contig12272, 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: 2272
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:875 original size:29 final size:29
Alignment explanation
Indices: 833--889 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
823 ATGTTTATTG
*
833 ATCCAAGGCGATCTTTCTTGAGTTAATTA
1 ATCCAAGGCGATCTTTCTTCAGTTAATTA
*
862 ATCCAGGGCGATCTTTCTTCAGTTAATT
1 ATCCAAGGCGATCTTTCTTCAGTTAATT
890 TCAATTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (29 bp):
ATCCAAGGCGATCTTTCTTCAGTTAATTA
Found at i:901 original size:35 final size:35
Alignment explanation
Indices: 829--997 Score: 133
Period size: 35 Copynumber: 5.0 Consensus size: 35
819 GTTAATGTTT
* *
829 ATTGATCCAAGGCGATCTTTCTTGAGTTAA-TT--
1 ATTGATCCAGGGCGATCTTTCTTCAGTTAATTTCA
861 A---ATCCAGGGCGATCTTTCTTCAGTTAATTTCA
1 ATTGATCCAGGGCGATCTTTCTTCAGTTAATTTCA
* * *
893 ATTGATCCAGGGCGATATTTCTTGAGTTTATTTCA
1 ATTGATCCAGGGCGATCTTTCTTCAGTTAATTTCA
*
928 GTTGA-CCTAGGGC-AGTCTTTCTTCAGCTT-ATTTCA
1 ATTGATCC-AGGGCGA-TCTTTCTTCAG-TTAATTTCA
* * * * *
963 GTTGA-CCTAGGGTGGTCTTTCTCCAGTTTATTTCA
1 ATTGATCC-AGGGCGATCTTTCTTCAGTTAATTTCA
998 GAATGATCGA
Statistics
Matches: 115, Mismatches: 11, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
29 24 0.21
30 2 0.02
32 2 0.02
34 5 0.04
35 80 0.70
36 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (35 bp):
ATTGATCCAGGGCGATCTTTCTTCAGTTAATTTCA
Found at i:998 original size:35 final size:35
Alignment explanation
Indices: 866--998 Score: 160
Period size: 35 Copynumber: 3.8 Consensus size: 35
856 TAATTAATCC
* * *
866 AGGGCGATCTTTCTTCAGTTAATTTCAATTGATCC-
1 AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGA-CCT
* * *
901 AGGGCGATATTTCTTGAGTTTATTTCAGTTGACCT
1 AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCT
* *
936 AGGGCAGTCTTTCTTCAGCTTATTTCAGTTGACCT
1 AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCT
* *
971 AGGGTGGTCTTTCTCCAGTTTATTTCAG
1 AGGGCGGTCTTTCTTCAGTTTATTTCAG
999 AATGATCGAT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
34 2 0.02
35 82 0.98
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (35 bp):
AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCT
Found at i:1078 original size:70 final size:70
Alignment explanation
Indices: 987--1194 Score: 278
Period size: 70 Copynumber: 3.0 Consensus size: 70
977 GTCTTTCTCC
* *
987 AGTTTATTTCAGAATGATCGATTCAGTCGACCCACGGTGGTCTTTCTTTAGTAGTTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCACGGTGGTCTTTCTTCAGTAGTTTCCAAGTTT
1052 ATCCA
66 ATCCA
* * * *
1057 AGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCACGGTGGTCTTTCTTCAGTAGTTTCCAAGTTT
1122 ATCCA
66 ATCCA
* * * * *
1127 AGTTTATGT-AGAATGATCGATTCAGTTGACCCA-GTGCGGTTTTTCATCAGTTGTTTCC-AGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCACG-GTGGTCTTTCTTCAGTAGTTTCCAAGTT
*
1189 GATCCA
65 TATCCA
1195 GGGTGGTCTA
Statistics
Matches: 122, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
68 9 0.07
69 41 0.34
70 72 0.59
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (70 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCACGGTGGTCTTTCTTCAGTAGTTTCCAAGTTT
ATCCA
Found at i:1491 original size:63 final size:62
Alignment explanation
Indices: 1410--1642 Score: 291
Period size: 63 Copynumber: 3.8 Consensus size: 62
1400 ATTTGAGAGT
* *
1410 TTCATTCTAAAATCCTGCTTGAGTTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCATG
1 TTCATT-TCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCC-AAATCATG
*
1474 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAATCTTG
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAATCATG
* * * * *
1536 TTCATTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAG-----T-TATCAATTCTAAGTCCTG
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAATCATG
* *
1592 TTTCATTTTCAAATCCTGCTCGAGGTCTCTAGTTGAGAGTTT-TTGTTTCAA
1 -TTCA-TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA
1643 ATCTAAAGTC
Statistics
Matches: 152, Mismatches: 10, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
56 14 0.09
57 5 0.03
58 32 0.21
62 44 0.29
63 51 0.34
64 6 0.04
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (62 bp):
TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAATCATG
Found at i:1617 original size:58 final size:56
Alignment explanation
Indices: 1457--1632 Score: 208
Period size: 62 Copynumber: 3.0 Consensus size: 56
1447 GTTTCTTGTT
* * *
1457 TCAATTCCAAAATCATGTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTT
1 TCAATTCC-AAATCCTGTTCATTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAG-----T-TA
*
1520 TCAATTCCAAATCTTGTTCATTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTA
1 TCAATTCCAAATCCTGTTCATTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTA
* * *
1576 TCAATTCTAAGTCCTGTTTCATTTTCAAATCCTGCTCGAGGTCTCTAGTTGAGAGTT
1 TCAATTCCAAATCCTG-TTCA-TTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTT
1633 TTTGTTTCAA
Statistics
Matches: 104, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
56 14 0.13
57 5 0.05
58 34 0.33
62 43 0.41
63 8 0.08
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (56 bp):
TCAATTCCAAATCCTGTTCATTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTA
Done.