Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_22158
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: 5520
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Found at i:4702 original size:21 final size:21
Alignment explanation
Indices: 4577--4721 Score: 148
Period size: 21 Copynumber: 6.9 Consensus size: 21
4567 TCTCCTACGT
*
4577 CATCCCCTGGTTACAG-CCCA
1 CATCTCCTGGTTACAGTCCCA
* **
4597 TCATCTCCTGGATACAGTCCGT
1 -CATCTCCTGGTTACAGTCCCA
* *
4619 CATCACCTGGTTACAGTCCTA
1 CATCTCCTGGTTACAGTCCCA
* *
4640 CCTCTCCTGGTTACAGTCCTA
1 CATCTCCTGGTTACAGTCCCA
*
4661 CATCTCCTGGGTACAGTCCCA
1 CATCTCCTGGTTACAGTCCCA
* *
4682 CCTCTCCTGGTTACAGCCCCA
1 CATCTCCTGGTTACAGTCCCA
* **
4703 CATCACCTACTTACAGTCC
1 CATCTCCTGGTTACAGTCC
4722 TAGCTCACCA
Statistics
Matches: 102, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
21 100 0.98
22 2 0.02
ACGTcount: A:0.19, C:0.39, G:0.14, T:0.27
Consensus pattern (21 bp):
CATCTCCTGGTTACAGTCCCA
Found at i:4706 original size:42 final size:42
Alignment explanation
Indices: 4577--4721 Score: 166
Period size: 42 Copynumber: 3.5 Consensus size: 42
4567 TCTCCTACGT
* * * **
4577 CATCCCCTGGTTACAG-CCCATCATCTCCTGGATACAGTCCGT
1 CATCACCTGGTTACAGTCCCA-CCTCTCCTGGTTACAGTCCCA
* *
4619 CATCACCTGGTTACAGTCCTACCTCTCCTGGTTACAGTCCTA
1 CATCACCTGGTTACAGTCCCACCTCTCCTGGTTACAGTCCCA
* * *
4661 CATCTCCTGGGTACAGTCCCACCTCTCCTGGTTACAGCCCCA
1 CATCACCTGGTTACAGTCCCACCTCTCCTGGTTACAGTCCCA
**
4703 CATCACCTACTTACAGTCC
1 CATCACCTGGTTACAGTCC
4722 TAGCTCACCA
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 84 0.97
43 3 0.03
ACGTcount: A:0.19, C:0.39, G:0.14, T:0.27
Consensus pattern (42 bp):
CATCACCTGGTTACAGTCCCACCTCTCCTGGTTACAGTCCCA
Found at i:4717 original size:63 final size:63
Alignment explanation
Indices: 4598--4742 Score: 157
Period size: 63 Copynumber: 2.3 Consensus size: 63
4588 TACAGCCCAT
** * * * * **
4598 CATCTCCTGGATACAGTCCGTCATCACCTGGTTACAGTCCTACCTCTCCTGGTTACAGTCCTA
1 CATCTCCTGGATACAGTCCCACATCACCTGGTTACAGCCCCACATCACCTACTTACAGTCCTA
* * *
4661 CATCTCCTGGGTACAGTCCCACCTCTCCTGGTTACAGCCCCACATCACCTACTTACAGTCCTA
1 CATCTCCTGGATACAGTCCCACATCACCTGGTTACAGCCCCACATCACCTACTTACAGTCCTA
* *
4724 GC-TCACCAGGATACAGTCC
1 -CATCTCCTGGATACAGTCC
4743 GACAAGTCCA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
63 66 0.99
64 1 0.01
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (63 bp):
CATCTCCTGGATACAGTCCCACATCACCTGGTTACAGCCCCACATCACCTACTTACAGTCCTA
Found at i:4816 original size:21 final size:21
Alignment explanation
Indices: 4786--4865 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
4776 ATATTCTCCA
* * *
4786 ACCTCACCAAGCTATAGCCCT
1 ACCTCTCCAAGTTACAGCCCT
4807 ACCTCTCCAAGTTACAGCCCT
1 ACCTCTCCAAGTTACAGCCCT
* *
4828 ACATCTCCAAGTTACAGTCCT
1 ACCTCTCCAAGTTACAGCCCT
*
4849 ACTTCTCCAAGTTACAG
1 ACCTCTCCAAGTTACAG
4866 TCCCACATCC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.28, C:0.38, G:0.10, T:0.25
Consensus pattern (21 bp):
ACCTCTCCAAGTTACAGCCCT
Found at i:4866 original size:21 final size:21
Alignment explanation
Indices: 4804--4874 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
4794 AAGCTATAGC
* *
4804 CCTACCTCTCCAAGTTACAGC
1 CCTACATCTCCAAGTTACAGT
4825 CCTACATCTCCAAGTTACAGT
1 CCTACATCTCCAAGTTACAGT
*
4846 CCTACTTCTCCAAGTTACAGT
1 CCTACATCTCCAAGTTACAGT
*
4867 CCCACATC
1 CCTACATC
4875 CCCCAGCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.25, C:0.39, G:0.08, T:0.27
Consensus pattern (21 bp):
CCTACATCTCCAAGTTACAGT
Found at i:4888 original size:21 final size:21
Alignment explanation
Indices: 4861--4920 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
4851 TTCTCCAAGT
*
4861 TACAGTCCCACATCCCCCAGC
1 TACAGTCCCACATCACCCAGC
* *
4882 TATAGTCCCACTTCACCCAGC
1 TACAGTCCCACATCACCCAGC
* *
4903 TACAGCCCCACTTCACCC
1 TACAGTCCCACATCACCC
4921 GTATATAGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.50, G:0.08, T:0.18
Consensus pattern (21 bp):
TACAGTCCCACATCACCCAGC
Found at i:4889 original size:42 final size:41
Alignment explanation
Indices: 4792--4910 Score: 130
Period size: 42 Copynumber: 2.9 Consensus size: 41
4782 TCCAACCTCA
* * *
4792 CCAAGCTATAGCCCTACCTCTCCAAGTTACAGCCCTACATCT
1 CCAAGCTATAGTCCTACTTCTCCAAGTTACAGCCC-ACATCC
* *
4834 CCAAGTTACAGTCCTACTTCTCCAAGTTACAGTCCCACATCC
1 CCAAGCTATAGTCCTACTTCTCCAAGTTACAG-CCCACATCC
* * * * *
4876 CCCAGCTATAGTCCCACTTCACCCAGCTACAGCCC
1 CCAAGCTATAGTCCTACTTCTCCAAGTTACAGCCC
4911 CACTTCACCC
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 3 0.05
42 58 0.91
43 3 0.05
ACGTcount: A:0.25, C:0.42, G:0.10, T:0.23
Consensus pattern (41 bp):
CCAAGCTATAGTCCTACTTCTCCAAGTTACAGCCCACATCC
Found at i:4928 original size:42 final size:41
Alignment explanation
Indices: 4882--4994 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 41
4872 ATCCCCCAGC
*
4882 TATAGTCCCACTTCACCCAGC-TACAGCCCCACTTCACCCGTA
1 TATAG-CCCACTTCA-CCAGCATACAGCCCCACTTCACCCGCA
* * *
4924 TATAGCCCTACCTCACCAGCATATAGCCCCACTTCACCTGCA
1 TATAGCCC-ACTTCACCAGCATACAGCCCCACTTCACCCGCA
* * *
4966 TACAGCCCCACTTCTCCATCATACAGCCC
1 TATAG-CCCACTTCACCAGCATACAGCCC
4995 TACATCTCCA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
41 8 0.14
42 48 0.81
43 3 0.05
ACGTcount: A:0.25, C:0.45, G:0.09, T:0.21
Consensus pattern (41 bp):
TATAGCCCACTTCACCAGCATACAGCCCCACTTCACCCGCA
Found at i:4930 original size:21 final size:21
Alignment explanation
Indices: 4882--4979 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 21
4872 ATCCCCCAGC
*
4882 TATAGTCCCACTTCACCCAGC-
1 TATAGCCCCACTTCACCC-GCA
* *
4903 TACAGCCCCACTTCACCCGTA
1 TATAGCCCCACTTCACCCGCA
* * *
4924 TATAGCCCTACCTCACCAGCA
1 TATAGCCCCACTTCACCCGCA
*
4945 TATAGCCCCACTTCACCTGCA
1 TATAGCCCCACTTCACCCGCA
*
4966 TACAGCCCCACTTC
1 TATAGCCCCACTTC
4980 TCCATCATAC
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 1 0.02
21 63 0.98
ACGTcount: A:0.24, C:0.45, G:0.09, T:0.21
Consensus pattern (21 bp):
TATAGCCCCACTTCACCCGCA
Found at i:4988 original size:21 final size:21
Alignment explanation
Indices: 4903--5084 Score: 107
Period size: 21 Copynumber: 8.7 Consensus size: 21
4893 TTCACCCAGC
* *
4903 TACAGCCCCACTTCACCCGT-A
1 TACAGCCCCACTTC-TCCATCA
* * * * *
4924 TATAGCCCTACCTCACCAGCA
1 TACAGCCCCACTTCTCCATCA
* *
4945 TATAGCCCCACTTCACC-TGCA
1 TACAGCCCCACTTCTCCAT-CA
4966 TACAGCCCCACTTCTCCATCA
1 TACAGCCCCACTTCTCCATCA
* * *
4987 TACAGCCCTACATCTCCATCG
1 TACAGCCCCACTTCTCCATCA
* * * *
5008 TACAGCCCGACATCTCCTTCG
1 TACAGCCCCACTTCTCCATCA
* * * *
5029 TACAGCCCTACTTCACCGTCC
1 TACAGCCCCACTTCTCCATCA
* * *
5050 TATAGCCCCACATCTCCTTCA
1 TACAGCCCCACTTCTCCATCA
* *
5071 TATAGCCCTACTTC
1 TACAGCCCCACTTC
5085 ACCCGCTTAT
Statistics
Matches: 129, Mismatches: 29, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
20 2 0.02
21 126 0.98
22 1 0.01
ACGTcount: A:0.23, C:0.44, G:0.09, T:0.24
Consensus pattern (21 bp):
TACAGCCCCACTTCTCCATCA
Found at i:5012 original size:42 final size:42
Alignment explanation
Indices: 4966--5109 Score: 153
Period size: 42 Copynumber: 3.4 Consensus size: 42
4956 TTCACCTGCA
* * * *
4966 TACAGCCCCACTTCTCCATCATACAGCCCTACATCTCCATCG
1 TACAGCCCCACATCTCCTTCATACAGCCCTACATCACCATCC
* * * *
5008 TACAGCCCGACATCTCCTTCGTACAGCCCTACTTCACCGTCC
1 TACAGCCCCACATCTCCTTCATACAGCCCTACATCACCATCC
* * * ** *
5050 TATAGCCCCACATCTCCTTCATATAGCCCTACTTCACCCGCT
1 TACAGCCCCACATCTCCTTCATACAGCCCTACATCACCATCC
*
5092 TATAGCCCCACATCTCCT
1 TACAGCCCCACATCTCCT
5110 GGGTACAGTC
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.22, C:0.44, G:0.08, T:0.26
Consensus pattern (42 bp):
TACAGCCCCACATCTCCTTCATACAGCCCTACATCACCATCC
Found at i:5015 original size:63 final size:62
Alignment explanation
Indices: 4882--5108 Score: 195
Period size: 63 Copynumber: 3.6 Consensus size: 62
4872 ATCCCCCAGC
* * * * * *
4882 TATAGTCCCACTTCACCCAGCTACAGCCCCACTTCACCCGT-ATATAGCCCTACCTCACCAGCA
1 TATAGCCCCACTTCA-CCTGCTACAGCCCCACTTC-TCCGTCATATAGCCCTACATCTCCATCA
* * *
4945 TATAGCCCCACTTCACCTGCATACAGCCCCACTTCTCCATCATACAGCCCTACATCTCCATCG
1 TATAGCCCCACTTCACCTGC-TACAGCCCCACTTCTCCGTCATATAGCCCTACATCTCCATCA
* * * * * * * * * *
5008 TACAGCCCGACATCTCCTTCGTACAGCCCTACTTCACCGTCCTATAGCCCCACATCTCCTTCA
1 TATAGCCCCACTTCACCTGC-TACAGCCCCACTTCTCCGTCATATAGCCCTACATCTCCATCA
* * * *
5071 TATAGCCCTACTTCACCCGCTTATAGCCCCACATCTCC
1 TATAGCCCCACTTCACCTGC-TACAGCCCCACTTCTCC
5109 TGGGTACAGT
Statistics
Matches: 128, Mismatches: 34, Indels: 4
0.77 0.20 0.02
Matches are distributed among these distances:
62 7 0.05
63 121 0.95
ACGTcount: A:0.23, C:0.44, G:0.09, T:0.24
Consensus pattern (62 bp):
TATAGCCCCACTTCACCTGCTACAGCCCCACTTCTCCGTCATATAGCCCTACATCTCCATCA
Found at i:5129 original size:42 final size:42
Alignment explanation
Indices: 4903--5129 Score: 109
Period size: 42 Copynumber: 5.4 Consensus size: 42
4893 TTCACCCAGC
* * * * * *
4903 TACAGCCCCACTTCACCCG-TATATAGCCCTACCTCACCAGCA
1 TACAGCCCAACCTCACCCGCT-TATAGCCCCACATCTCCTGCA
* * * * * * *
4945 TATAGCCCCACTTCACCTGCATACAGCCCCACTTCTCCAT-CA
1 TACAGCCCAACCTCACCCGCTTATAGCCCCACATCTCC-TGCA
* * * ** * * * * *
4987 TACAGCCCTACATCTCCATCGTACAGCCCGACATCTCCTTCG
1 TACAGCCCAACCTCACCCGCTTATAGCCCCACATCTCCTGCA
* * * *
5029 TACAGCCCTACTTCA-CCGTCCTATAGCCCCACATCTCCTTCA
1 TACAGCCCAACCTCACCCG-CTTATAGCCCCACATCTCCTGCA
* * * **
5071 TATAGCCCTACTTCACCCGCTTATAGCCCCACATCTCCTGGG
1 TACAGCCCAACCTCACCCGCTTATAGCCCCACATCTCCTGCA
*
5113 TACAGTCCAACCTCACC
1 TACAGCCCAACCTCACC
5130 AAGTTACAGT
Statistics
Matches: 145, Mismatches: 35, Indels: 10
0.76 0.18 0.05
Matches are distributed among these distances:
41 2 0.01
42 140 0.97
43 3 0.02
ACGTcount: A:0.23, C:0.44, G:0.10, T:0.23
Consensus pattern (42 bp):
TACAGCCCAACCTCACCCGCTTATAGCCCCACATCTCCTGCA
Found at i:5129 original size:84 final size:84
Alignment explanation
Indices: 4969--5129 Score: 187
Period size: 84 Copynumber: 1.9 Consensus size: 84
4959 ACCTGCATAC
* * * * *
4969 AGCCCCACTTCTCCATCATACAGCCCTACATCTCCATCGTACAGCCCGACATCTCCTTCGTACAG
1 AGCCCCACATCTCCATCATACAGCCCTACATCACCAGCGTACAGCCCCACATCTCCTGCGTACAG
* *
5034 CCCTACTTCACCGTCCTAT
66 CCCAACCTCACCGTCCTAT
* * * * * * *
5053 AGCCCCACATCTCCTTCATATAGCCCTACTTCACCCGCTTATAGCCCCACATCTCCTGGGTACAG
1 AGCCCCACATCTCCATCATACAGCCCTACATCACCAGCGTACAGCCCCACATCTCCTGCGTACAG
*
5118 TCCAACCTCACC
66 CCCAACCTCACC
5130 AAGTTACAGT
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
84 62 1.00
ACGTcount: A:0.22, C:0.44, G:0.10, T:0.24
Consensus pattern (84 bp):
AGCCCCACATCTCCATCATACAGCCCTACATCACCAGCGTACAGCCCCACATCTCCTGCGTACAG
CCCAACCTCACCGTCCTAT
Found at i:5139 original size:21 final size:21
Alignment explanation
Indices: 5113--5179 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
5103 ATCTCCTGGG
5113 TACAGTCCAACCTCACCAAGT
1 TACAGTCCAACCTCACCAAGT
* * *
5134 TACAGTCCCACATCACCAAGC
1 TACAGTCCAACCTCACCAAGT
* * * *
5155 TATAGCCCTACCTCTCCAAGT
1 TACAGTCCAACCTCACCAAGT
5176 TACA
1 TACA
5180 ACCCGCAGTC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.31, C:0.39, G:0.09, T:0.21
Consensus pattern (21 bp):
TACAGTCCAACCTCACCAAGT
Done.