Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_01524
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: 5552
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Found at i:4656 original size:21 final size:21
Alignment explanation
Indices: 4633--4762 Score: 127
Period size: 21 Copynumber: 6.2 Consensus size: 21
4623 TCTCCCACTT
* *
4633 CATCCCCTGGTTACAGCCC-A
1 CATCTCCTGGCTACAGCCCTA
* *
4653 TCATCTCCTGGCTACAGTCCTT
1 -CATCTCCTGGCTACAGCCCTA
*
4675 CATCTCCTGGCTACAGTCCTA
1 CATCTCCTGGCTACAGCCCTA
* * *
4696 CCTCGCCTGGTTACAGCCCTA
1 CATCTCCTGGCTACAGCCCTA
*
4717 CATCTCCTGGCTACAGTCCTA
1 CATCTCCTGGCTACAGCCCTA
* * * *
4738 CCTCGCCTGGTTACAGCCCCA
1 CATCTCCTGGCTACAGCCCTA
4759 CATC
1 CATC
4763 ACCTACTTAC
Statistics
Matches: 89, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
21 89 1.00
ACGTcount: A:0.17, C:0.42, G:0.15, T:0.26
Consensus pattern (21 bp):
CATCTCCTGGCTACAGCCCTA
Found at i:4762 original size:42 final size:42
Alignment explanation
Indices: 4675--4798 Score: 169
Period size: 42 Copynumber: 3.0 Consensus size: 42
4665 TACAGTCCTT
*
4675 CATCTCCTGGCTACAGTCCTACCTCGCCTGGTTACAGCCCTA
1 CATCTCCTGGCTACAGTCCTACCTCGCCTGGTTACAGCCCCA
4717 CATCTCCTGGCTACAGTCCTACCTCGCCTGGTTACAGCCCCA
1 CATCTCCTGGCTACAGTCCTACCTCGCCTGGTTACAGCCCCA
* * ** * *
4759 CATCACCT-ACTTACAGTCCTAGTTCACCAGGTTACAGCCC
1 CATCTCCTGGC-TACAGTCCTACCTCGCCTGGTTACAGCCC
4799 AACAAGTCCA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
41 1 0.01
42 73 0.99
ACGTcount: A:0.19, C:0.40, G:0.15, T:0.25
Consensus pattern (42 bp):
CATCTCCTGGCTACAGTCCTACCTCGCCTGGTTACAGCCCCA
Found at i:4773 original size:63 final size:64
Alignment explanation
Indices: 4643--4779 Score: 161
Period size: 63 Copynumber: 2.2 Consensus size: 64
4633 CATCCCCTGG
* * * * * * **
4643 TTACAGCCC-ATCATCTCCTGGCTACAGTCCTTCATCTCCTGGCTACAGTCCTACCTCGCCTGG
1 TTACAGCCCTATCATCTCCTGGCTACAGTCCTACATCGCCTGGCTACAGCCCCACATCACCTAC
* *
4706 TTACAGCCCTA-CATCTCCTGGCTACAGTCCTACCTCGCCTGGTTACAGCCCCACATCACCTAC
1 TTACAGCCCTATCATCTCCTGGCTACAGTCCTACATCGCCTGGCTACAGCCCCACATCACCTAC
*
4769 TTACAGTCCTA
1 TTACAGCCCTA
4780 GTTCACCAGG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
63 61 0.98
64 1 0.02
ACGTcount: A:0.19, C:0.40, G:0.14, T:0.27
Consensus pattern (64 bp):
TTACAGCCCTATCATCTCCTGGCTACAGTCCTACATCGCCTGGCTACAGCCCCACATCACCTAC
Found at i:4872 original size:21 final size:21
Alignment explanation
Indices: 4845--4996 Score: 128
Period size: 21 Copynumber: 7.2 Consensus size: 21
4835 TTCTCCAACC
*
4845 TCACCAAGCTATAGCCCTACC
1 TCACCAAGCTATAGCCCTACT
* * *
4866 TCTCCAAGCTACAGCCCTACG
1 TCACCAAGCTATAGCCCTACT
* * * *
4887 TCTCCAAGTTACAGTCCTACT
1 TCACCAAGCTATAGCCCTACT
* *
4908 TCACCAAGTTATAGTCCC-ACA
1 TCACCAAGCTATAG-CCCTACT
* * * *
4929 TCTCCCAGCTATAGTCCAACT
1 TCACCAAGCTATAGCCCTACT
*
4950 TCACCAAGCTACAGCCCTACT
1 TCACCAAGCTATAGCCCTACT
*
4971 TCACC-AGCATATAGCCCAACT
1 TCACCAAGC-TATAGCCCTACT
4992 TCACC
1 TCACC
4997 TGCATACAGC
Statistics
Matches: 106, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
20 5 0.05
21 99 0.93
22 2 0.02
ACGTcount: A:0.28, C:0.39, G:0.10, T:0.23
Consensus pattern (21 bp):
TCACCAAGCTATAGCCCTACT
Found at i:4912 original size:63 final size:62
Alignment explanation
Indices: 4845--4988 Score: 164
Period size: 63 Copynumber: 2.3 Consensus size: 62
4835 TTCTCCAACC
* * * * *
4845 TCACCAAGCTATAGCCCTACCTCTCCAAGCTACAGCCCTACGTCTCCAAGTTACAGTCCTACT
1 TCACCAAGCTATAGCCC-ACATCTCCAAGCTACAGCCCAACGTCACCAAGCTACAGCCCTACT
* * * * *
4908 TCACCAAGTTATAGTCCCACATCTCCCAGCTATAGTCCAACTTCACCAAGCTACAGCCCTACT
1 TCACCAAGCTATAG-CCCACATCTCCAAGCTACAGCCCAACGTCACCAAGCTACAGCCCTACT
4971 TCACC-AGCATATAGCCCA
1 TCACCAAGC-TATAGCCCA
4989 ACTTCACCTG
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
62 6 0.09
63 59 0.87
64 3 0.04
ACGTcount: A:0.28, C:0.39, G:0.10, T:0.23
Consensus pattern (62 bp):
TCACCAAGCTATAGCCCACATCTCCAAGCTACAGCCCAACGTCACCAAGCTACAGCCCTACT
Found at i:4984 original size:42 final size:42
Alignment explanation
Indices: 4869--5143 Score: 148
Period size: 42 Copynumber: 6.5 Consensus size: 42
4859 CCCTACCTCT
* * * *
4869 CCAAGCTACAGCCCTACGTCTCCAAG-TTACAGTCCTACTTCA
1 CCAAGCTACAGCCCTACTTCTCC-AGCATACAGCCCAACTTCA
* * * * *
4911 CCAAGTTATAGTCCC-ACATCTCCCAGC-TATAGTCCAACTTCA
1 CCAAGCTACAG-CCCTACTTCT-CCAGCATACAGCCCAACTTCA
* *
4953 CCAAGCTACAGCCCTACTTCACCAGCATATAGCCCAACTTCA
1 CCAAGCTACAGCCCTACTTCTCCAGCATACAGCCCAACTTCA
* * * * *
4995 CC-TGCATACAGCCCCACTTCTCCATCATACAGCCCAACATCG
1 CCAAGC-TACAGCCCTACTTCTCCAGCATACAGCCCAACTTCA
* * * * ** * *
5037 CC-ATCATACAGTCCGACATCTCCTTCTTACAGCCCAACCTCA
1 CCAAGC-TACAGCCCTACTTCTCCAGCATACAGCCCAACTTCA
*** * * * *
5079 CCCTCCTATAGCCCTACATCTCCATCATACAGCCCTACTTC-
1 CCAAGCTACAGCCCTACTTCTCCAGCATACAGCCCAACTTCA
* * *
5120 CCCAGCATATAGCCCCACTTCTCC
1 CCAAGC-TACAGCCCTACTTCTCC
5144 CGGGTACAGT
Statistics
Matches: 186, Mismatches: 39, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
41 14 0.08
42 166 0.89
43 6 0.03
ACGTcount: A:0.26, C:0.42, G:0.09, T:0.23
Consensus pattern (42 bp):
CCAAGCTACAGCCCTACTTCTCCAGCATACAGCCCAACTTCA
Found at i:5001 original size:21 final size:22
Alignment explanation
Indices: 4944--5032 Score: 96
Period size: 21 Copynumber: 4.2 Consensus size: 22
4934 CAGCTATAGT
4944 CCAACTTCACCAAGC-TACAGC
1 CCAACTTCACCAAGCATACAGC
* *
4965 CCTACTTCACC-AGCATATAGC
1 CCAACTTCACCAAGCATACAGC
*
4986 CCAACTTCACC-TGCATACAGC
1 CCAACTTCACCAAGCATACAGC
* * *
5007 CCCACTTCTCC-ATCATACAGC
1 CCAACTTCACCAAGCATACAGC
5028 CCAAC
1 CCAAC
5033 ATCGCCATCA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 3 0.05
21 54 0.95
ACGTcount: A:0.29, C:0.44, G:0.08, T:0.19
Consensus pattern (22 bp):
CCAACTTCACCAAGCATACAGC
Found at i:5026 original size:63 final size:63
Alignment explanation
Indices: 4959--5143 Score: 172
Period size: 63 Copynumber: 2.9 Consensus size: 63
4949 TTCACCAAGC
* * *
4959 TACAGCCCTACTTCACCAGCATATAGCCCAACTTCACCTGCATACAGCCCCACTTCTCCATCA
1 TACAGCCCTACATCACCATCATACAGCCCAACTTCACCTGCATACAGCCCCACTTCTCCATCA
* * * * * * * * * * * * *
5022 TACAGCCCAACATCGCCATCATACAGTCCGACATCTCCTTCTTACAGCCCAACCTCACCCTCC
1 TACAGCCCTACATCACCATCATACAGCCCAACTTCACCTGCATACAGCCCCACTTCTCCATCA
* * * * * *
5085 TATAGCCCTACATCTCCATCATACAGCCCTACTTCCCCAGCATATAGCCCCACTTCTCC
1 TACAGCCCTACATCACCATCATACAGCCCAACTTCACCTGCATACAGCCCCACTTCTCC
5144 CGGGTACAGT
Statistics
Matches: 92, Mismatches: 30, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
63 92 1.00
ACGTcount: A:0.25, C:0.44, G:0.08, T:0.23
Consensus pattern (63 bp):
TACAGCCCTACATCACCATCATACAGCCCAACTTCACCTGCATACAGCCCCACTTCTCCATCA
Found at i:5114 original size:21 final size:21
Alignment explanation
Indices: 4959--5143 Score: 129
Period size: 21 Copynumber: 8.8 Consensus size: 21
4949 TTCACCAAGC
* * *
4959 TACAGCCCTACTTCACCAGCA
1 TACAGCCCAACTTCTCCATCA
* *
4980 TATAGCCCAACTTCACC-TGCA
1 TACAGCCCAACTTCTCCAT-CA
*
5001 TACAGCCCCACTTCTCCATCA
1 TACAGCCCAACTTCTCCATCA
* *
5022 TACAGCCCAACATCGCCATCA
1 TACAGCCCAACTTCTCCATCA
* * * * *
5043 TACAGTCCGACATCTCCTTCT
1 TACAGCCCAACTTCTCCATCA
* * * *
5064 TACAGCCCAACCTCACCCTCC
1 TACAGCCCAACTTCTCCATCA
* * *
5085 TATAGCCCTACATCTCCATCA
1 TACAGCCCAACTTCTCCATCA
* * *
5106 TACAGCCCTACTTCCCCAGCA
1 TACAGCCCAACTTCTCCATCA
* *
5127 TATAGCCCCACTTCTCC
1 TACAGCCCAACTTCTCC
5144 CGGGTACAGT
Statistics
Matches: 129, Mismatches: 33, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
21 128 0.99
22 1 0.01
ACGTcount: A:0.25, C:0.44, G:0.08, T:0.23
Consensus pattern (21 bp):
TACAGCCCAACTTCTCCATCA
Done.