Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003534.1 Corchorus capsularis cultivar CVL-1 contig03542, 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, 746
Length: 1244
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Found at i:918 original size:35 final size:35
Alignment explanation
Indices: 879--1106 Score: 296
Period size: 35 Copynumber: 6.5 Consensus size: 35
869 AAATTTCTTG
* * * *
879 AAATGAGATCACCTCTAATTGTTGGAAACTACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
914 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
*
949 AAATGCGATCAACTCTGATCGTTGGAAACTTCTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
* *
984 AAATGCGATCAACTCTGATTGTTGGAAAATACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
* *
1019 AAATGCGATCAACTCTGATCGTTGGAAAATACTAA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
* * * * *
1054 AAATGCAATCAACTCTGACCTTTGAAAACTTCTTG-
1 AAATGCGATCAACTCTGATCGTTGGAAACTAC-TGA
* *
1089 GAATGAGATCAACTCTGA
1 AAATGCGATCAACTCTGA
1107 CCTCTGAAAA
Statistics
Matches: 172, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
35 171 0.99
36 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (35 bp):
AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
Found at i:1032 original size:105 final size:105
Alignment explanation
Indices: 851--1106 Score: 370
Period size: 105 Copynumber: 2.4 Consensus size: 105
841 ACTACTCTGG
* * * * * *
851 ATCAACTCTGACCATCGAAAATTTCTTGAAATGAGATCACCTCTAATTGTTGGAAACTACTGAAA
1 ATCAACTCTGACCGTTGAAAACTTCTTGAAATGAGATCAACTCTGATTGTTGGAAAATACTGAAA
* * *
916 ATGCGATCAACTCTGATCGTTGGAAACTACTGAAAATGCG
66 ATGCGATCAACTCTGATCGTTGGAAAATACTAAAAATGCA
* * *
956 ATCAACTCTGATCGTTGGAAACTTC-TGAAAATGCGATCAACTCTGATTGTTGGAAAATACTGAA
1 ATCAACTCTGACCGTTGAAAACTTCTTG-AAATGAGATCAACTCTGATTGTTGGAAAATACTGAA
1020 AATGCGATCAACTCTGATCGTTGGAAAATACTAAAAATGCA
65 AATGCGATCAACTCTGATCGTTGGAAAATACTAAAAATGCA
* *
1061 ATCAACTCTGACCTTTGAAAACTTCTTGGAATGAGATCAACTCTGA
1 ATCAACTCTGACCGTTGAAAACTTCTTGAAATGAGATCAACTCTGA
1107 CCTCTGAAAA
Statistics
Matches: 132, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
104 2 0.02
105 128 0.97
106 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (105 bp):
ATCAACTCTGACCGTTGAAAACTTCTTGAAATGAGATCAACTCTGATTGTTGGAAAATACTGAAA
ATGCGATCAACTCTGATCGTTGGAAAATACTAAAAATGCA
Found at i:1099 original size:70 final size:70
Alignment explanation
Indices: 851--1244 Score: 308
Period size: 70 Copynumber: 5.6 Consensus size: 70
841 ACTACTCTGG
* * * * * * * *
851 ATCAACTCTGACCATCGAAAATTTCTTGAAATGAGATCACCTCTAATTGTTGGAAACTACTGAAA
1 ATCAACTCTGACCTTTGAAAACTTCTTGAAATGAGATCAACTCTGATCGTTGGAAAATTCTGAAA
*
916 ATGCG
66 ATGCA
* * * * * *
921 ATCAACTCTGATCGTTGGAAACTAC-TGAAAATGCGATCAACTCTGATCGTTGGAAACTTCTGAA
1 ATCAACTCTGACCTTTGAAAACTTCTTG-AAATGAGATCAACTCTGATCGTTGGAAAATTCTGAA
*
985 AATGCG
65 AATGCA
* * * * *
991 ATCAACTCTGA-TTGTTGGAAAA-TAC-TGAAAATGCGATCAACTCTGATCGTTGGAAAATACTA
1 ATCAACTCTGACCT-TT-GAAAACTTCTTG-AAATGAGATCAACTCTGATCGTTGGAAAATTCTG
1053 AAAATGCA
63 AAAATGCA
* *
1061 ATCAACTCTGACCTTTGAAAACTTCTTGGAATGAGATCAACTCTGA-CCTCT-GAAAACTTCTTG
1 ATCAACTCTGACCTTTGAAAACTTCTTGAAATGAGATCAACTCTGATCGT-TGGAAAA-TTC-TG
*
1124 -GAATG-A
63 AAAATGCA
* * * *
1130 GATCAACTCTGACCTCTGAAAACTGCTTGGAATGAGATCAACTCTGA-CCTCT-GAAAACTTCTT
1 -ATCAACTCTGACCTTTGAAAACTTCTTGAAATGAGATCAACTCTGATCGT-TGGAAAA-TTC-T
*
1193 G-GAATG-A
62 GAAAATGCA
* * *
1200 GATCAACTCTGACCTCTGAAAACTTCTTGGAACGAGATCAACTCT
1 -ATCAACTCTGACCTTTGAAAACTTCTTGAAATGAGATCAACTCT
Statistics
Matches: 284, Mismatches: 30, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
69 15 0.05
70 261 0.92
71 8 0.03
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (70 bp):
ATCAACTCTGACCTTTGAAAACTTCTTGAAATGAGATCAACTCTGATCGTTGGAAAATTCTGAAA
ATGCA
Found at i:1107 original size:35 final size:35
Alignment explanation
Indices: 1061--1244 Score: 341
Period size: 35 Copynumber: 5.3 Consensus size: 35
1051 TAAAAATGCA
*
1061 ATCAACTCTGACCTTTGAAAACTTCTTGGAATGAG
1 ATCAACTCTGACCTCTGAAAACTTCTTGGAATGAG
1096 ATCAACTCTGACCTCTGAAAACTTCTTGGAATGAG
1 ATCAACTCTGACCTCTGAAAACTTCTTGGAATGAG
*
1131 ATCAACTCTGACCTCTGAAAACTGCTTGGAATGAG
1 ATCAACTCTGACCTCTGAAAACTTCTTGGAATGAG
1166 ATCAACTCTGACCTCTGAAAACTTCTTGGAATGAG
1 ATCAACTCTGACCTCTGAAAACTTCTTGGAATGAG
*
1201 ATCAACTCTGACCTCTGAAAACTTCTTGGAACGAG
1 ATCAACTCTGACCTCTGAAAACTTCTTGGAATGAG
1236 ATCAACTCT
1 ATCAACTCT
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 145 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (35 bp):
ATCAACTCTGACCTCTGAAAACTTCTTGGAATGAG
Found at i:1134 original size:105 final size:105
Alignment explanation
Indices: 915--1244 Score: 359
Period size: 105 Copynumber: 3.1 Consensus size: 105
905 AACTACTGAA
* * * * * * *
915 AATGCGATCAACTCTGATCGTTGGAAACTACTGAAAATGCGATCAACTCTGATCGTTGGAAACTT
1 AATGAGATCAACTCTGATCGTTGGAAAATACTAAAAATGCAATCAACTCTGACCTTTGAAAACTT
* * * * * *
980 C-TGAAAATGCGATCAACTCTGA-TTGTTGGAAAA-TAC-TGAA
66 CTTG-GAATGAGATCAACTCTGACCT-CT-GAAAACTTCTTG-G
*
1020 AATGCGATCAACTCTGATCGTTGGAAAATACTAAAAATGCAATCAACTCTGACCTTTGAAAACTT
1 AATGAGATCAACTCTGATCGTTGGAAAATACTAAAAATGCAATCAACTCTGACCTTTGAAAACTT
1085 CTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
66 CTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
* * *** *
1125 AATGAGATCAACTCTGA-CCTCT-GAAAACTGCTTGGAATG-AGATCAACTCTGACCTCTGAAAA
1 AATGAGATCAACTCTGATCGT-TGGAAAA-TACTAAAAATGCA-ATCAACTCTGACCTTTGAAAA
1187 CTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
63 CTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
*
1230 AACGAGATCAACTCT
1 AATGAGATCAACTCT
Statistics
Matches: 198, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
104 13 0.07
105 180 0.91
106 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (105 bp):
AATGAGATCAACTCTGATCGTTGGAAAATACTAAAAATGCAATCAACTCTGACCTTTGAAAACTT
CTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCTTGG
Done.