Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_22108
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: 1731
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Found at i:586 original size:48 final size:48
Alignment explanation
Indices: 509--1518 Score: 570
Period size: 48 Copynumber: 20.9 Consensus size: 48
499 ATCATTCAGA
* * * * *
509 ATACAAATTGC-CAGCAGCTTTTCCCTGGGAGTTCAAGCCAAGGAACGA
1 ATACAAATT-CACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* * * * *
557 ACACAAATTCAAAACAGTTTTTCATTGGGAGTTCAAGTCAAGAAATGG
1 ATACAAATTCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
*
605 ATACAAA-TCGACAACAGTTTTTTC-CTGGGAGTTCAAGTCAAGGAATGG
1 ATACAAATTC-ACAACAG-TTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* *
653 ATACAAATCCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGGATGG
1 ATACAAATTCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* **** * *** ** * * *
701 ATACAAATCCACAACA-TCCACCAC-AGTTCTTCACTCC--CGCA--C
1 ATACAAATTCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* * * * * *
743 A-AC--ATCCACCACAGTTCTTCACTAGAAGTTCAAGCCAAGGGATGG
1 ATACAAATTCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* *
788 ATACAAA-TC-C--C-----TTCACTGGGAGTTCAATCCAAGGGATGG
1 ATACAAATTCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* * *
827 ATACAAATCTACAACATCCACCACAGTTATTCACTGGGAGTTCAATCCAAGGGATGG
1 ATACAAAT-T----CA--CA--ACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* * *
884 ATACAAATCCACAAC---TTTTCAATGAGAAG-TCAAGCCAAGGAATGGATACG
1 ATACAAATTCACAACAGTTTTTCACTG-GGAGTTCAAGCCAAGGAAT-G----G
* * * * *
934 AATCCACAACATCCACCACAGTTCTTCACTGGGAGTTCAATCCAAGGGATGG
1 -AT--ACAA-ATTCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* * *
986 ATACAAATCCACAACATTTTTTCACTAGGAGTTCAAGCCAAGGAATGG
1 ATACAAATTCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* * * * *
1034 ATACAAATCCACAACACCCACCACAGTTCTTCACTGGGAGTTCAATCCAAGGGACGG
1 ATACAAAT-----TCA--CA--ACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* * *
1091 ATACAAATCCACAACAGTTTTTCACTAGGAGTTCAATCCAAAGG-ATGG
1 ATACAAATTCACAACAGTTTTTCACTGGGAGTTCAAGCC-AAGGAATGG
* * * *
1139 ATACAAATCCACAACAGCTTTTCCCTGAGAAG-TCAAGCCAAGGAATGG
1 ATACAAATTCACAACAGTTTTTCACTG-GGAGTTCAAGCCAAGGAATGG
* * * * * * * *
1187 ATACAAATCCGCAACAATTTTTCACCGAGAGCTCAATCCAAGGGATGG
1 ATACAAATTCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* * * * * *
1235 ATAGAAATCCACGACAGCTTTTCCCTGAGAAG-TCAAGCCAAGGAATGG
1 ATACAAATTCACAACAGTTTTTCACTG-GGAGTTCAAGCCAAGGAATGG
* * * * * *
1283 ATACAAATCCGCAACGGTTTTTCACTGGGAGGTCAATCCAAGGGATGG
1 ATACAAATTCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* * * * *
1331 ATACAAATCCACAACAGTTTTTCACTAGGACTTCAATCCAAGGGATGG
1 ATACAAATTCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* * * * * *
1379 ATAGAAATCCACGACAGCTTTTCCCTGAGAAG-TCAAGCCAAGGAATGG
1 ATACAAATTCACAACAGTTTTTCACTG-GGAGTTCAAGCCAAGGAATGG
* * * *
1427 ATACAAATCCACAACAGTTTTTCACTGGAAGTTCAATCCAAGGGATGG
1 ATACAAATTCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
* * * *
1475 ATA-GAAGTC-CATCATTGTTTTTCATTGGGAGTTCAAGCCAAGGA
1 ATACAAATTCACAACA--GTTTTTCACTGGGAGTTCAAGCCAAGGA
1519 GGGACTCCTA
Statistics
Matches: 760, Mismatches: 137, Indels: 130
0.74 0.13 0.13
Matches are distributed among these distances:
39 41 0.05
40 5 0.01
41 11 0.01
42 1 0.00
43 2 0.00
44 3 0.00
45 21 0.03
46 18 0.02
47 30 0.04
48 479 0.63
49 22 0.03
50 5 0.01
51 4 0.01
52 6 0.01
53 6 0.01
54 8 0.01
55 2 0.00
56 4 0.01
57 92 0.12
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (48 bp):
ATACAAATTCACAACAGTTTTTCACTGGGAGTTCAAGCCAAGGAATGG
Found at i:673 original size:96 final size:95
Alignment explanation
Indices: 527--1518 Score: 665
Period size: 96 Copynumber: 10.3 Consensus size: 95
517 TGCCAGCAGC
* * * * * * *
527 TTTTCCCTGGGAGTTCAAGCCAAGGAACGAACACAAATTCAAAACAGTTTTTCATTGGGAGTTCA
1 TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACAGTTTTTCACTGGGAGTTCA
** *
592 AGTCAAGAAATGGATACAAATCGACAACAGTT
66 AGTCAAGGGATGGATACAAATCCACAACA--T
*
624 TTTTC-CTGGGAGTTCAAGTCAAGGAATGGATACAAATCCACAACAGTTTTTCACTGGGAGTTCA
1 TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACAGTTTTTCACTGGGAGTTCA
*
688 AGCCAAGGGATGGATACAAATCCACAACAT
66 AGTCAAGGGATGGATACAAATCCACAACAT
**** * *** ** * * * * * * *
718 CCACCAC-AGTTCTTCACTCC--CGCA--CA-AC--ATCCACCACAGTTCTTCACTAGAAGTTCA
1 TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACAGTTTTTCACTGGGAGTTCA
*
775 AGCCAAGGGATGGATACAAAT-C-C--C--
66 AGTCAAGGGATGGATACAAATCCACAACAT
* * *
799 --TTCACTGGGAGTTCAATCCAAGGGATGGATACAAATCTACAACATCCACCACAGTTATTCACT
1 TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAA--T-C--CA--CA--ACAGTTTTTCACT
862 GGGAGTTCAA-TCCAAGGGATGGATACAAATCCACAAC--
57 GGGAGTTCAAGT-CAAGGGATGGATACAAATCCACAACAT
* * * *
899 TTTTCAATGAGAAG-TCAAGCCAAGGAATGGATACGAATCCACAACATCCACCACAGTTCTTCAC
1 TTTTCACTG-GGAGTTCAAGCCAAGGAAT-G----G-AT--ACAA-ATCCACAACAGTTTTTCAC
963 TGGGAGTTCAA-TCCAAGGGATGGATACAAATCCACAACATT
56 TGGGAGTTCAAGT-CAAGGGATGGATACAAATCCACAACA-T
* *
1004 TTTTCACTAGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACACCCACCACAGTTCTTCACT
1 TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAAT---C--CA--CA--ACAGTTTTTCACT
*
1069 GGGAGTTCAA-TCCAAGGGACGGATACAAATCCACAACAGT
57 GGGAGTTCAAGT-CAAGGGATGGATACAAATCCACAACA-T
* * * * *
1109 TTTTCACTAGGAGTTCAATCCAAAGG-ATGGATACAAATCCACAACAGCTTTTCCCTGAGAAG-T
1 TTTTCACTGGGAGTTCAAGCC-AAGGAATGGATACAAATCCACAACAGTTTTTCACTG-GGAGTT
* * *
1172 CAAGCCAAGGAATGGATACAAATCCGCAACAAT
64 CAAGTCAAGGGATGGATACAAATCCACAAC-AT
* * * * * * * * * *
1205 TTTTCACCGAGAGCTCAATCCAAGGGATGGATAGAAATCCACGACAGCTTTTCCCTGAGAAG-TC
1 TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACAGTTTTTCACTG-GGAGTTC
* * * *
1269 AAGCCAAGGAATGGATACAAATCCGCAACGGT
65 AAGTCAAGGGATGGATACAAATCCACAAC-AT
* * * * *
1301 TTTTCACTGGGAGGTCAATCCAAGGGATGGATACAAATCCACAACAGTTTTTCACTAGGACTTCA
1 TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACAGTTTTTCACTGGGAGTTCA
* * *
1366 A-TCCAAGGGATGGATAGAAATCCACGACAGC
66 AGT-CAAGGGATGGATACAAATCCACAACA-T
* * *
1397 TTTTCCCTGAGAAG-TCAAGCCAAGGAATGGATACAAATCCACAACAGTTTTTCACTGGAAGTTC
1 TTTTCACTG-GGAGTTCAAGCCAAGGAATGGATACAAATCCACAACAGTTTTTCACTGGGAGTTC
* * ***
1461 AA-TCCAAGGGATGGATAGAAGTCCATCATTGT
65 AAGT-CAAGGGATGGATACAAATCCA-CAACAT
*
1493 TTTTCATTGGGAGTTCAAGCCAAGGA
1 TTTTCACTGGGAGTTCAAGCCAAGGA
1519 GGGACTCCTA
Statistics
Matches: 730, Mismatches: 106, Indels: 119
0.76 0.11 0.12
Matches are distributed among these distances:
79 3 0.00
80 8 0.01
82 2 0.00
83 1 0.00
84 1 0.00
85 3 0.00
86 1 0.00
87 47 0.06
89 3 0.00
90 2 0.00
92 4 0.01
94 9 0.01
95 10 0.01
96 408 0.56
97 18 0.02
98 3 0.00
99 3 0.00
100 4 0.01
101 2 0.00
102 68 0.09
103 5 0.01
104 5 0.01
105 104 0.14
106 6 0.01
107 1 0.00
108 3 0.00
109 1 0.00
110 4 0.01
111 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (95 bp):
TTTTCACTGGGAGTTCAAGCCAAGGAATGGATACAAATCCACAACAGTTTTTCACTGGGAGTTCA
AGTCAAGGGATGGATACAAATCCACAACAT
Found at i:813 original size:39 final size:39
Alignment explanation
Indices: 759--835 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
749 CACCACAGTT
759 CTTCACTAGAAGTTCAAGCCAAGGGATGGATACAAATCC
1 CTTCACTAGAAGTTCAAGCCAAGGGATGGATACAAATCC
* * *
798 CTTCACTGGGAGTTCAATCCAAGGGATGGATACAAATC
1 CTTCACTAGAAGTTCAAGCCAAGGGATGGATACAAATC
836 TACAACATCC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (39 bp):
CTTCACTAGAAGTTCAAGCCAAGGGATGGATACAAATCC
Done.