Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_10793
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, 898
Length: 1497
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.27
Found at i:1336 original size:21 final size:21
Alignment explanation
Indices: 1000--1383 Score: 203
Period size: 21 Copynumber: 18.0 Consensus size: 21
990 AAAACCTCCC
* *
1000 GTTCACTCACCACCACCACAA
1 GTTCACTCTCCACCACCACCA
* * * *
1021 GTTCTCTCCCCTCCACCACCC
1 GTTCACTCTCCACCACCACCA
* *
1042 G-TCTACTCACCACCACCACAACCT
1 GTTC-ACTCTCCACCA-C-C-ACCA
* *
1066 GTTCGCTCCCCTCCACCTCCACCA
1 GTTCACT---CTCCACCACCACCA
* * *
1090 GTTCAATCACCACCACCACCG
1 GTTCACTCTCCACCACCACCA
*
1111 GTTCACTCCCCTCCACCTCCACCA
1 GTTCACT---CTCCACCACCACCA
* *
1135 GTTCAATCACCACCACCACCA
1 GTTCACTCTCCACCACCACCA
* * * *
1156 GTTCGCTCCCCTCCACCACCC
1 GTTCACTCTCCACCACCACCA
*
1177 G-TCTACTCTCCACCTCCACCA
1 GTTC-ACTCTCCACCACCACCA
*
1198 GTTCAATCTCCACCACCACCA
1 GTTCACTCTCCACCACCACCA
* * * *
1219 GTTCTCTCCCCTCCACCACCC
1 GTTCACTCTCCACCACCACCA
* *
1240 GTCTC-CTTTCCACCTCCACCA
1 GT-TCACTCTCCACCACCACCA
*
1261 GTTCAATCTCCACCACCACCA
1 GTTCACTCTCCACCACCACCA
* * * *
1282 GTTCTCTCCCCTCCACCACCC
1 GTTCACTCTCCACCACCACCA
*
1303 GTCTC-CT-TCCCACCTCCACCA
1 GT-TCACTCT-CCACCACCACCA
* *
1324 GTTCA--AT-CACCACCACCC
1 GTTCACTCTCCACCACCACCA
1342 G-TCTACTCTCCA-CATCCACCA
1 GTTC-ACTCTCCACCA-CCACCA
* * *
1363 GTTCAATCACAACCACCACCA
1 GTTCACTCTCCACCACCACCA
1384 ACTTCACCTC
Statistics
Matches: 271, Mismatches: 66, Indels: 52
0.70 0.17 0.13
Matches are distributed among these distances:
17 2 0.01
18 11 0.04
20 12 0.04
21 193 0.71
22 11 0.04
23 1 0.00
24 31 0.11
25 3 0.01
26 1 0.00
27 6 0.02
ACGTcount: A:0.21, C:0.53, G:0.05, T:0.20
Consensus pattern (21 bp):
GTTCACTCTCCACCACCACCA
Found at i:1337 original size:39 final size:39
Alignment explanation
Indices: 1294--1379 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
1284 TCTCTCCCCT
* *
1294 CCACCACCCGTCTCCT-TCCCACCTCCACCAGTTCAATCA
1 CCACCACCCGTCTACTCT-CCACATCCACCAGTTCAATCA
1333 CCACCACCCGTCTACTCTCCACATCCACCAGTTCAATCA
1 CCACCACCCGTCTACTCTCCACATCCACCAGTTCAATCA
*
1372 CAACCACC
1 CCACCACC
1380 ACCAACTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 42 0.98
40 1 0.02
ACGTcount: A:0.24, C:0.52, G:0.05, T:0.19
Consensus pattern (39 bp):
CCACCACCCGTCTACTCTCCACATCCACCAGTTCAATCA
Found at i:1360 original size:126 final size:125
Alignment explanation
Indices: 1000--1362 Score: 383
Period size: 126 Copynumber: 2.8 Consensus size: 125
990 AAAACCTCCC
* * * * *
1000 GTTCACTCACCACCACCACAAGTTCTCTCCCCTCCACCACCCGTCTACTCACCACCACCACAACC
1 GTTCAATCACCACCACCACCAGTTCGCTCCCCTCCACCACCCGTCTACTCTCCACC-TC-C-ACC
* ** * ** * **
1065 TGTTCGCTCCCCTCCACCTCCACCAGTTCAATCACCA-CCACCACCGGTTCACTCCCCTCCACCT
63 AG-T---TCAACTCCACCACCACCAGTTCTCTC-CCATCCACCACCCG-T--CTCCTTTCCACCT
1129 CCACCA
120 CCACCA
1135 GTTCAATCACCACCACCACCAGTTCGCTCCCCTCCACCACCCGTCTACTCTCCACCTCCACCAGT
1 GTTCAATCACCACCACCACCAGTTCGCTCCCCTCCACCACCCGTCTACTCTCCACCTCCACCAGT
*
1200 TCAATCTCCACCACCACCAGTTCTCTCCCCTCCACCACCCGTCTCCTTTCCACCTCCACCA
66 TCAA-CTCCACCACCACCAGTTCTCTCCCATCCACCACCCGTCTCCTTTCCACCTCCACCA
* * *
1261 GTTCAATCTCCACCACCACCAGTTCTCTCCCCTCCACCACCCGTCTCCT-TCCCACCTCCACCAG
1 GTTCAATCACCACCACCACCAGTTCGCTCCCCTCCACCACCCGTCTACTCT-CCACCTCCACCAG
*
1325 TTCAA-T-CACCACCACCCGTCTACTCTCCACATCCACCA
65 TTCAACTCCACCACCACCAGT-T-CTCTCC-CATCCACCA
1363 GTTCAATCAC
Statistics
Matches: 202, Mismatches: 20, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
123 12 0.06
124 2 0.01
125 7 0.03
126 89 0.44
128 5 0.02
129 28 0.14
131 1 0.00
132 4 0.02
133 1 0.00
134 1 0.00
135 52 0.26
ACGTcount: A:0.20, C:0.54, G:0.06, T:0.20
Consensus pattern (125 bp):
GTTCAATCACCACCACCACCAGTTCGCTCCCCTCCACCACCCGTCTACTCTCCACCTCCACCAGT
TCAACTCCACCACCACCAGTTCTCTCCCATCCACCACCCGTCTCCTTTCCACCTCCACCA
Found at i:1362 original size:63 final size:62
Alignment explanation
Indices: 1123--1340 Score: 343
Period size: 63 Copynumber: 3.5 Consensus size: 62
1113 TCACTCCCCT
* * *
1123 CCACCTCCACCAGTTCAATCACCACCACCACCAGTTCGCTCCCCTCCACCACCCGTCTAC-TC
1 CCACCTCCACCAGTTCAA-CTCCACCACCACCAGTTCTCTCCCCTCCACCACCCGTCTCCTTC
*
1185 TCCACCTCCACCAGTTCAATCTCCACCACCACCAGTTCTCTCCCCTCCACCACCCGTCTCCTTT
1 -CCACCTCCACCAGTTCAA-CTCCACCACCACCAGTTCTCTCCCCTCCACCACCCGTCTCCTTC
1249 CCACCTCCACCAGTTCAATCTCCACCACCACCAGTTCTCTCCCCTCCACCACCCGTCTCCTTC
1 CCACCTCCACCAGTTCAA-CTCCACCACCACCAGTTCTCTCCCCTCCACCACCCGTCTCCTTC
1312 CCACCTCCACCAGTTCAA-T-CACCACCACC
1 CCACCTCCACCAGTTCAACTCCACCACCACC
1341 CGTCTACTCT
Statistics
Matches: 149, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
60 10 0.07
61 1 0.01
63 137 0.92
64 1 0.01
ACGTcount: A:0.20, C:0.55, G:0.05, T:0.21
Consensus pattern (62 bp):
CCACCTCCACCAGTTCAACTCCACCACCACCAGTTCTCTCCCCTCCACCACCCGTCTCCTTC
Done.