Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_21642
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, 984
Length: 1641
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Found at i:614 original size:66 final size:66
Alignment explanation
Indices: 538--980 Score: 270
Period size: 66 Copynumber: 6.7 Consensus size: 66
528 AACAGGTAAA
*
538 GCTTCTGAGTATACAGATTATGCTGCCCAGAAAGCTAAGGACGCAAAAGACACCACAGCACAAAA
1 GCTTCTGAGTATACAGATTATGCAGCCCAGAAAGCTAAGGACGCAAAAGACACCACAGCACAAAA
603 G
66 G
* * * * ** * ** * ***
604 GCTTCCGAGTATACAGACTATGCAGCACAGAAAACTAAGGGTGCAAAGGATGCTACAATG-GGGA
1 GCTTCTGAGTATACAGATTATGCAGCCCAGAAAGCTAAGGACGCAAAAGACACCAC-A-GCACAA
668 AA-
64 AAG
** * * * * * * * * *
670 GCGACTGAATATA-AGGATTATACCGCCGAGAAAGCCAAGGAGGCAAGAGATACCACAGCCCAAA
1 GCTTCTGAGTATACA-GATTATGCAGCCCAGAAAGCTAAGGACGCAAAAGACACCACAGCACAAA
734 AG
65 AG
* * *
736 GCTTCTGAGTATACAGATTACGCTA-CCCAGAAAGCTAAGGACGCAAAAGACACCACTGCACAGA
1 GCTTCTGAGTATACAGATTATGC-AGCCCAGAAAGCTAAGGACGCAAAAGACACCACAGCACAAA
800 AG
65 AG
* ** * * * * ** * ***
802 GCTTCCGAGTATACAGGCTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAATG-GGGA
1 GCTTCTGAGTATACAGATTATGCAGCCCAGAAAGCTAAGGACGCAAAAGACACCAC-A-GCACAA
866 AA-
64 AAG
** * * * * * * * * *
868 GCGGCTGAATATA-AGGATTATACAGCTCAGAAAGCCAAGGAGGCAAGAGATACTACAGCCCAAA
1 GCTTCTGAGTATACA-GATTATGCAGCCCAGAAAGCTAAGGACGCAAAAGACACCACAGCACAAA
*
932 AA
65 AG
* * *
934 GCTTCTGAGTACACAGATTATGCAGCACAGAAAGCTAAGGATGCAAA
1 GCTTCTGAGTATACAGATTATGCAGCCCAGAAAGCTAAGGACGCAAA
981 GGATGCCGCA
Statistics
Matches: 273, Mismatches: 90, Indels: 28
0.70 0.23 0.07
Matches are distributed among these distances:
64 2 0.01
65 11 0.04
66 250 0.92
67 8 0.03
68 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.15
Consensus pattern (66 bp):
GCTTCTGAGTATACAGATTATGCAGCCCAGAAAGCTAAGGACGCAAAAGACACCACAGCACAAAA
G
Found at i:878 original size:198 final size:198
Alignment explanation
Indices: 535--980 Score: 743
Period size: 198 Copynumber: 2.3 Consensus size: 198
525 TGTAACAGGT
*
535 AAAGCTTCTGAGTATACAGATTATGCTGCCCAGAAAGCTAAGGACGCAAAAGACACCACAGCACA
1 AAAGCTTCTGAGTATACAGATTATGCTACCCAGAAAGCTAAGGACGCAAAAGACACCACAGCACA
*
600 AAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAACTAAGGGTGCAAAGGATGCTACAATGG
66 AAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAATGG
*
665 GGAAAGCGACTGAATATAAGGATTATACCGC-CGAGAAAGCCAAGGAGGCAAGAGATACCACAGC
131 GGAAAGCGACTGAATATAAGGATTATACAGCTC-AGAAAGCCAAGGAGGCAAGAGATACCACAGC
729 CCAA
195 CCAA
* * *
733 AAGGCTTCTGAGTATACAGATTACGCTACCCAGAAAGCTAAGGACGCAAAAGACACCACTGCACA
1 AAAGCTTCTGAGTATACAGATTATGCTACCCAGAAAGCTAAGGACGCAAAAGACACCACAGCACA
* *
798 GAAGGCTTCCGAGTATACAGGCTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAATGG
66 AAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAATGG
* *
863 GGAAAGCGGCTGAATATAAGGATTATACAGCTCAGAAAGCCAAGGAGGCAAGAGATACTACAGCC
131 GGAAAGCGACTGAATATAAGGATTATACAGCTCAGAAAGCCAAGGAGGCAAGAGATACCACAGCC
928 CAA
196 CAA
* * *
931 AAAGCTTCTGAGTACACAGATTATGC-AGCACAGAAAGCTAAGGATGCAAA
1 AAAGCTTCTGAGTATACAGATTATGCTA-CCCAGAAAGCTAAGGACGCAAA
981 GGATGCCGCA
Statistics
Matches: 231, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
197 1 0.00
198 229 0.99
199 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (198 bp):
AAAGCTTCTGAGTATACAGATTATGCTACCCAGAAAGCTAAGGACGCAAAAGACACCACAGCACA
AAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAATGG
GGAAAGCGACTGAATATAAGGATTATACAGCTCAGAAAGCCAAGGAGGCAAGAGATACCACAGCC
CAA
Found at i:1166 original size:66 final size:66
Alignment explanation
Indices: 806--1181 Score: 234
Period size: 66 Copynumber: 5.7 Consensus size: 66
796 CAGAAGGCTT
* * * * * **
806 CCGAGTATACAGGCTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAATGGGGAAAGCG
1 CCGAGTATAAAGACTATGCAGCACAGAAAGCTAAGGAAGCAAAGGATACTACAATGGAAAAAGCG
*
871 G
66 A
* * * * * * * * ****
872 CTGAATATAAGGATTATACAGCTCAGAAAGCCAAGGAGGC-AAGAGATACTACAGCCCAAAAAGC
1 CCGAGTATAAAGACTATGCAGCACAGAAAGCTAAGGAAGCAAAG-GATACTACAATGGAAAAAGC
**
936 TT
65 GA
* * * * * * **
938 CTGAGTACACAGATTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCCGCAATTGG-AAAAGC
1 CCGAGTATAAAGACTATGCAGCACAGAAAGCTAAGGAAGCAAAGGATACTACAA-TGGAAAAAGC
1002 GA
65 GA
* * * ** * * * ** * * * *
1004 CTGAATATAAGGACTATGCAGCTGAGAAAGCCAAGGGAGCAAAGGATACGACAGCGCAGAAGGCT
1 CCGAGTATAAAGACTATGCAGCACAGAAAGCTAAGGAAGCAAAGGATACTACAATGGAAAAAGCG
*
1069 T
66 A
* * * *
1070 CCGAGTTTACAGACTACGCAGCACAGAAAGCTAAGGAAGCAAAAGATACTACAATGGAAAAAGCG
1 CCGAGTATAAAGACTATGCAGCACAGAAAGCTAAGGAAGCAAAGGATACTACAATGGAAAAAGCG
1135 A
66 A
** * * *
1136 CCGAGTATAAAGACTATGCAGCTGAAAAAGCGAAGGAAGCGAAGGA
1 CCGAGTATAAAGACTATGCAGCACAGAAAGCTAAGGAAGCAAAGGA
1182 CGTGACAGCT
Statistics
Matches: 221, Mismatches: 85, Indels: 8
0.70 0.27 0.03
Matches are distributed among these distances:
65 4 0.02
66 214 0.97
67 3 0.01
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.14
Consensus pattern (66 bp):
CCGAGTATAAAGACTATGCAGCACAGAAAGCTAAGGAAGCAAAGGATACTACAATGGAAAAAGCG
A
Found at i:1189 original size:132 final size:129
Alignment explanation
Indices: 796--1190 Score: 434
Period size: 132 Copynumber: 3.0 Consensus size: 129
786 CACCACTGCA
* *
796 CAGAAGGCTTCCGAGTATACAGGCTATGCAGCACAGAAAACTAAGGATGCAAAGGATGCTACAAT
1 CAGAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTACAAT
* * * * * *
861 GGGGAAAGCGGCTGAATATAAGGATTATACAGCTCAGAAAGCCAAGGAGGCAAGAGATACT-ACA
66 -GGAAAAGCGACTGAATATAAGGACTATGCAGCTGAGAAAGCCAAGGAAGCAAG-G--ACTGACA
925 GCC
127 GCC
* * * * * **
928 CAAAAAGCTTCTGAGTACACAGATTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCCGCAAT
1 CAGAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTACAA-
*
993 TGGAAAAGCGACTGAATATAAGGACTATGCAGCTGAGAAAGCCAAGGGAGCAAAGGA-TACGACA
65 TGGAAAAGCGACTGAATATAAGGACTATGCAGCTGAGAAAGCCAAGGAAGC-AAGGACT--GACA
*
1057 GCG
127 GCC
* * * * *
1060 CAGAAGGCTTCCGAGTTTACAGACTACGCAGCACAGAAAGCTAAGGAAGCAAAAGATACTACAAT
1 CAGAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTACAAT
* * * * *
1125 GGAAAAAGCGACCGAGTATAAAGACTATGCAGCTGAAAAAGCGAAGGAAGCGAAGGACGTGACAG
66 GG-AAAAGCGACTGAATATAAGGACTATGCAGCTGAGAAAGCCAAGGAAGC-AAGGAC-TGACAG
1190 C
128 C
1191 TGAGAAGACA
Statistics
Matches: 219, Mismatches: 36, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
129 1 0.00
130 1 0.00
131 3 0.01
132 209 0.95
133 4 0.02
134 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (129 bp):
CAGAAGGCTTCCGAGTATACAGACTATGCAGCACAGAAAGCTAAGGATGCAAAGGATGCTACAAT
GGAAAAGCGACTGAATATAAGGACTATGCAGCTGAGAAAGCCAAGGAAGCAAGGACTGACAGCC
Done.