Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01936.F1
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: 6155
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Found at i:4936 original size:21 final size:21
Alignment explanation
Indices: 4811--4955 Score: 148
Period size: 21 Copynumber: 6.9 Consensus size: 21
4801 TCTCCTACGT
*
4811 CATCCCCTGGTTACAG-CCCA
1 CATCTCCTGGTTACAGTCCCA
* **
4831 TCATCTCCTGGATACAGTCCGT
1 -CATCTCCTGGTTACAGTCCCA
* *
4853 CATCACCTGGTTACAGTCCTA
1 CATCTCCTGGTTACAGTCCCA
* *
4874 CCTCTCCTGGTTACAGTCCTA
1 CATCTCCTGGTTACAGTCCCA
*
4895 CATCTCCTGGGTACAGTCCCA
1 CATCTCCTGGTTACAGTCCCA
* *
4916 CCTCTCCTGGTTACAGCCCCA
1 CATCTCCTGGTTACAGTCCCA
* **
4937 CATCACCTACTTACAGTCC
1 CATCTCCTGGTTACAGTCC
4956 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:4940 original size:42 final size:42
Alignment explanation
Indices: 4811--4955 Score: 166
Period size: 42 Copynumber: 3.5 Consensus size: 42
4801 TCTCCTACGT
* * * **
4811 CATCCCCTGGTTACAG-CCCATCATCTCCTGGATACAGTCCGT
1 CATCACCTGGTTACAGTCCCA-CCTCTCCTGGTTACAGTCCCA
* *
4853 CATCACCTGGTTACAGTCCTACCTCTCCTGGTTACAGTCCTA
1 CATCACCTGGTTACAGTCCCACCTCTCCTGGTTACAGTCCCA
* * *
4895 CATCTCCTGGGTACAGTCCCACCTCTCCTGGTTACAGCCCCA
1 CATCACCTGGTTACAGTCCCACCTCTCCTGGTTACAGTCCCA
**
4937 CATCACCTACTTACAGTCC
1 CATCACCTGGTTACAGTCC
4956 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:4951 original size:63 final size:63
Alignment explanation
Indices: 4832--4976 Score: 157
Period size: 63 Copynumber: 2.3 Consensus size: 63
4822 TACAGCCCAT
** * * * * **
4832 CATCTCCTGGATACAGTCCGTCATCACCTGGTTACAGTCCTACCTCTCCTGGTTACAGTCCTA
1 CATCTCCTGGATACAGTCCCACATCACCTGGTTACAGCCCCACATCACCTACTTACAGTCCTA
* * *
4895 CATCTCCTGGGTACAGTCCCACCTCTCCTGGTTACAGCCCCACATCACCTACTTACAGTCCTA
1 CATCTCCTGGATACAGTCCCACATCACCTGGTTACAGCCCCACATCACCTACTTACAGTCCTA
* *
4958 GC-TCACCAGGATACAGTCC
1 -CATCTCCTGGATACAGTCC
4977 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:5050 original size:21 final size:21
Alignment explanation
Indices: 5020--5099 Score: 106
Period size: 21 Copynumber: 3.8 Consensus size: 21
5010 ATATTCTCCA
* * *
5020 ACCTCACCAAGCTATAGCCCT
1 ACCTCTCCAAGTTACAGCCCT
5041 ACCTCTCCAAGTTACAGCCCT
1 ACCTCTCCAAGTTACAGCCCT
* *
5062 ACATCTCCAAGTTACAGTCCT
1 ACCTCTCCAAGTTACAGCCCT
*
5083 ACTTCTCCAAGTTACAG
1 ACCTCTCCAAGTTACAG
5100 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:5100 original size:21 final size:21
Alignment explanation
Indices: 5038--5108 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
5028 AAGCTATAGC
* *
5038 CCTACCTCTCCAAGTTACAGC
1 CCTACATCTCCAAGTTACAGT
5059 CCTACATCTCCAAGTTACAGT
1 CCTACATCTCCAAGTTACAGT
*
5080 CCTACTTCTCCAAGTTACAGT
1 CCTACATCTCCAAGTTACAGT
*
5101 CCCACATC
1 CCTACATC
5109 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:5122 original size:21 final size:21
Alignment explanation
Indices: 5095--5154 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
5085 TTCTCCAAGT
*
5095 TACAGTCCCACATCCCCCAGC
1 TACAGTCCCACATCACCCAGC
* *
5116 TATAGTCCCACTTCACCCAGC
1 TACAGTCCCACATCACCCAGC
* *
5137 TACAGCCCCACTTCACCC
1 TACAGTCCCACATCACCC
5155 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:5123 original size:42 final size:41
Alignment explanation
Indices: 5026--5144 Score: 130
Period size: 42 Copynumber: 2.9 Consensus size: 41
5016 TCCAACCTCA
* * *
5026 CCAAGCTATAGCCCTACCTCTCCAAGTTACAGCCCTACATCT
1 CCAAGCTATAGTCCTACTTCTCCAAGTTACAGCCC-ACATCC
* *
5068 CCAAGTTACAGTCCTACTTCTCCAAGTTACAGTCCCACATCC
1 CCAAGCTATAGTCCTACTTCTCCAAGTTACAG-CCCACATCC
* * * * *
5110 CCCAGCTATAGTCCCACTTCACCCAGCTACAGCCC
1 CCAAGCTATAGTCCTACTTCTCCAAGTTACAGCCC
5145 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:5162 original size:42 final size:41
Alignment explanation
Indices: 5116--5228 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 41
5106 ATCCCCCAGC
*
5116 TATAGTCCCACTTCACCCAGC-TACAGCCCCACTTCACCCGTA
1 TATAG-CCCACTTCA-CCAGCATACAGCCCCACTTCACCCGCA
* * *
5158 TATAGCCCTACCTCACCAGCATATAGCCCCACTTCACCTGCA
1 TATAGCCC-ACTTCACCAGCATACAGCCCCACTTCACCCGCA
* * *
5200 TACAGCCCCACTTCTCCATCATACAGCCC
1 TATAG-CCCACTTCACCAGCATACAGCCC
5229 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:5164 original size:21 final size:21
Alignment explanation
Indices: 5116--5213 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 21
5106 ATCCCCCAGC
*
5116 TATAGTCCCACTTCACCCAGC-
1 TATAGCCCCACTTCACCC-GCA
* *
5137 TACAGCCCCACTTCACCCGTA
1 TATAGCCCCACTTCACCCGCA
* * *
5158 TATAGCCCTACCTCACCAGCA
1 TATAGCCCCACTTCACCCGCA
*
5179 TATAGCCCCACTTCACCTGCA
1 TATAGCCCCACTTCACCCGCA
*
5200 TACAGCCCCACTTC
1 TATAGCCCCACTTC
5214 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:5222 original size:21 final size:21
Alignment explanation
Indices: 5137--5318 Score: 107
Period size: 21 Copynumber: 8.7 Consensus size: 21
5127 TTCACCCAGC
* *
5137 TACAGCCCCACTTCACCCGT-A
1 TACAGCCCCACTTC-TCCATCA
* * * * *
5158 TATAGCCCTACCTCACCAGCA
1 TACAGCCCCACTTCTCCATCA
* *
5179 TATAGCCCCACTTCACC-TGCA
1 TACAGCCCCACTTCTCCAT-CA
5200 TACAGCCCCACTTCTCCATCA
1 TACAGCCCCACTTCTCCATCA
* * *
5221 TACAGCCCTACATCTCCATCG
1 TACAGCCCCACTTCTCCATCA
* * * *
5242 TACAGCCCGACATCTCCTTCG
1 TACAGCCCCACTTCTCCATCA
* * * *
5263 TACAGCCCTACTTCACCGTCC
1 TACAGCCCCACTTCTCCATCA
* * *
5284 TATAGCCCCACATCTCCTTCA
1 TACAGCCCCACTTCTCCATCA
* *
5305 TATAGCCCTACTTC
1 TACAGCCCCACTTC
5319 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:5246 original size:42 final size:42
Alignment explanation
Indices: 5200--5343 Score: 153
Period size: 42 Copynumber: 3.4 Consensus size: 42
5190 TTCACCTGCA
* * * *
5200 TACAGCCCCACTTCTCCATCATACAGCCCTACATCTCCATCG
1 TACAGCCCCACATCTCCTTCATACAGCCCTACATCACCATCC
* * * *
5242 TACAGCCCGACATCTCCTTCGTACAGCCCTACTTCACCGTCC
1 TACAGCCCCACATCTCCTTCATACAGCCCTACATCACCATCC
* * * ** *
5284 TATAGCCCCACATCTCCTTCATATAGCCCTACTTCACCCGCT
1 TACAGCCCCACATCTCCTTCATACAGCCCTACATCACCATCC
*
5326 TATAGCCCCACATCTCCT
1 TACAGCCCCACATCTCCT
5344 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:5249 original size:63 final size:62
Alignment explanation
Indices: 5116--5342 Score: 195
Period size: 63 Copynumber: 3.6 Consensus size: 62
5106 ATCCCCCAGC
* * * * * *
5116 TATAGTCCCACTTCACCCAGCTACAGCCCCACTTCACCCGT-ATATAGCCCTACCTCACCAGCA
1 TATAGCCCCACTTCA-CCTGCTACAGCCCCACTTC-TCCGTCATATAGCCCTACATCTCCATCA
* * *
5179 TATAGCCCCACTTCACCTGCATACAGCCCCACTTCTCCATCATACAGCCCTACATCTCCATCG
1 TATAGCCCCACTTCACCTGC-TACAGCCCCACTTCTCCGTCATATAGCCCTACATCTCCATCA
* * * * * * * * * *
5242 TACAGCCCGACATCTCCTTCGTACAGCCCTACTTCACCGTCCTATAGCCCCACATCTCCTTCA
1 TATAGCCCCACTTCACCTGC-TACAGCCCCACTTCTCCGTCATATAGCCCTACATCTCCATCA
* * * *
5305 TATAGCCCTACTTCACCCGCTTATAGCCCCACATCTCC
1 TATAGCCCCACTTCACCTGC-TACAGCCCCACTTCTCC
5343 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:5363 original size:42 final size:42
Alignment explanation
Indices: 5137--5363 Score: 109
Period size: 42 Copynumber: 5.4 Consensus size: 42
5127 TTCACCCAGC
* * * * * *
5137 TACAGCCCCACTTCACCCG-TATATAGCCCTACCTCACCAGCA
1 TACAGCCCAACCTCACCCGCT-TATAGCCCCACATCTCCTGCA
* * * * * * *
5179 TATAGCCCCACTTCACCTGCATACAGCCCCACTTCTCCAT-CA
1 TACAGCCCAACCTCACCCGCTTATAGCCCCACATCTCC-TGCA
* * * ** * * * * *
5221 TACAGCCCTACATCTCCATCGTACAGCCCGACATCTCCTTCG
1 TACAGCCCAACCTCACCCGCTTATAGCCCCACATCTCCTGCA
* * * *
5263 TACAGCCCTACTTCA-CCGTCCTATAGCCCCACATCTCCTTCA
1 TACAGCCCAACCTCACCCG-CTTATAGCCCCACATCTCCTGCA
* * * **
5305 TATAGCCCTACTTCACCCGCTTATAGCCCCACATCTCCTGGG
1 TACAGCCCAACCTCACCCGCTTATAGCCCCACATCTCCTGCA
*
5347 TACAGTCCAACCTCACC
1 TACAGCCCAACCTCACC
5364 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:5363 original size:84 final size:84
Alignment explanation
Indices: 5203--5363 Score: 187
Period size: 84 Copynumber: 1.9 Consensus size: 84
5193 ACCTGCATAC
* * * * *
5203 AGCCCCACTTCTCCATCATACAGCCCTACATCTCCATCGTACAGCCCGACATCTCCTTCGTACAG
1 AGCCCCACATCTCCATCATACAGCCCTACATCACCAGCGTACAGCCCCACATCTCCTGCGTACAG
* *
5268 CCCTACTTCACCGTCCTAT
66 CCCAACCTCACCGTCCTAT
* * * * * * *
5287 AGCCCCACATCTCCTTCATATAGCCCTACTTCACCCGCTTATAGCCCCACATCTCCTGGGTACAG
1 AGCCCCACATCTCCATCATACAGCCCTACATCACCAGCGTACAGCCCCACATCTCCTGCGTACAG
*
5352 TCCAACCTCACC
66 CCCAACCTCACC
5364 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:5373 original size:21 final size:21
Alignment explanation
Indices: 5347--5413 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
5337 ATCTCCTGGG
5347 TACAGTCCAACCTCACCAAGT
1 TACAGTCCAACCTCACCAAGT
* * *
5368 TACAGTCCCACATCACCAAGC
1 TACAGTCCAACCTCACCAAGT
* * * *
5389 TATAGCCCTACCTCTCCAAGT
1 TACAGTCCAACCTCACCAAGT
5410 TACA
1 TACA
5414 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.