Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_D_gene_10025156
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: 1815
ACGTcount: A:0.23, C:0.47, G:0.05, T:0.25
Found at i:260 original size:48 final size:48
Alignment explanation
Indices: 193--1468 Score: 1447
Period size: 48 Copynumber: 26.6 Consensus size: 48
183 ACCACCATCC
* * *
193 TATGCCTACAAGTCCCCACCTCCACCATCTCCTTCACCACCTCCTCCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
** * * * * * *
241 TACATCTACAAATCTCCACCTCCACCATCTCATTCGCCTCCACCACCC
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* * *
289 TATGTCTACAAGTCGCCACCTCCACCATCTGCC-TCACCACCCCCACCT
1 TATGTCTACAAGTCCCCACCTCCACCATCT-CCTTCACCTCCTCCACCT
* * * * *
337 TATGTCTACAAGTCCCCACCTCCACTATCTCCGTCATCACCTCCTCCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* * * *
385 TATGTCTACAAGTCCCCACCTCCACCGTCTCCCTCACCTCCCCCACCC
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* * * *
433 TATGTCTACAAGTCCCCACCTCCACCATCTCCCTCACCACCACCTCCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
** * * * * *
481 TACATCTACAAGTCACCTCCTCCACCATCTCCTTCGCCTCCTCCTCCA
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
** * * *
529 TACATCTACAAATCCCCACCTCCACCATCTCCTTCACCTCCCCCACCA
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* *
577 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCACCTCCCCCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
** * * *
625 TATAACTACAAGTCCCCACCTCCACCATCTCCCTCACCACCTCCTCCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
** * * * * * *
673 TACATTTATAAGTCTCCACCACCACCATCTCATTCACCTCCTCCACCA
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* * * * *
721 TATGTTTACAAGTCTCCACCACCACCATCTCCTTCACTTCCTCCACCA
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* *
769 TATGTCTACAAGTCCCCACCTCCTCCATCTCCTTCACCTCCCCCACCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* *
817 TATGTCTACAAGTCCCCACCTCCACCATCTCATTCACCTCCTCCTCCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* * * *
865 TATGTTTACAAGTCTCCACCTCCACCATCTCCTTCACCACCTCCCCCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
** * * *
913 TACATCTACAAGTCCCCACCTCCACCATCTCCATCACCACCTCCTCCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
** * * * * * * *
961 TACATTTATAAGTCTCCACCACCACCATCTCATTCACCTCATCCACCA
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* * * * *
1009 TATGTTTACAAGTCTCCACCTCCACCATCTCATTCACCTCCACCACCA
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* * *
1057 TATGTCTACAAGTCCCCACCTCCTCTATCTCCTTCACCTCCCCCACCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* * * *
1105 TATGTCTACAAGTCCCCACCTCCTCCATCTCCGTCACCACCTCCTCCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* * * *
1153 TATGTCTACAAGTCCCCACCTCCACCGTCTCCCTCACCTCCCCCACCC
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* * * * *
1201 TACGTCTATAAGTCCCCACCTCCACCATCTCCCTCACCTCCCCCACCC
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* * * *
1249 TACGTCTACAAGTCCCCACCTCCACCATCTCCCTCACCACCTCCACCC
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* *
1297 TATGTGTACAAGTCCCCACCTCCACCATCTCCTTCACCACCTCCACCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
* * *
1345 TATGTTTACAAATCACCACCTCCACCATCTCCTTCACCTCCTCCACCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
*** * * * *
1393 TACACCTACAAGTCACCACCTCCACCATCTCCCTCACCACCTCCTCCT
1 TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
** *
1441 TACATCTACAAGTCACCACCTCCACCAT
1 TATGTCTACAAGTCCCCACCTCCACCAT
1469 ATGTCTACAA
Statistics
Matches: 1066, Mismatches: 160, Indels: 4
0.87 0.13 0.00
Matches are distributed among these distances:
47 2 0.00
48 1063 1.00
49 1 0.00
ACGTcount: A:0.21, C:0.50, G:0.04, T:0.25
Consensus pattern (48 bp):
TATGTCTACAAGTCCCCACCTCCACCATCTCCTTCACCTCCTCCACCT
Found at i:355 original size:27 final size:26
Alignment explanation
Indices: 287--458 Score: 86
Period size: 21 Copynumber: 7.1 Consensus size: 26
277 CCTCCACCAC
*
287 CCTATGTCTACAAGTCGCCACCTCCA
1 CCTATGTCTACAAGTCCCCACCTCCA
* * * *
313 CC-A--TCTGC--CTCACCACCCCCA
1 CCTATGTCTACAAGTCCCCACCTCCA
334 CCTTATGTCTACAAGTCCCCACCTCCA
1 CC-TATGTCTACAAGTCCCCACCTCCA
* ** *
361 -CTA--TCT-C-CGTCATCACCTCCT
1 CCTATGTCTACAAGTCCCCACCTCCA
382 CCTTATGTCTACAAGTCCCCACCTCCA
1 CC-TATGTCTACAAGTCCCCACCTCCA
** * * *
409 CC---GTCT-C-CCTCACCTCCCCCA
1 CCTATGTCTACAAGTCCCCACCTCCA
430 CCCTATGTCTACAAGTCCCCACCTCCA
1 -CCTATGTCTACAAGTCCCCACCTCCA
457 CC
1 CC
459 ATCTCCCTCA
Statistics
Matches: 102, Mismatches: 26, Indels: 36
0.62 0.16 0.22
Matches are distributed among these distances:
21 31 0.30
22 5 0.05
23 14 0.14
25 14 0.14
26 7 0.07
27 31 0.30
ACGTcount: A:0.19, C:0.51, G:0.07, T:0.23
Consensus pattern (26 bp):
CCTATGTCTACAAGTCCCCACCTCCA
Found at i:406 original size:24 final size:24
Alignment explanation
Indices: 334--407 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
324 ACCACCCCCA
334 CCTTATGTCTACAAGTCCCCACCT
1 CCTTATGTCTACAAGTCCCCACCT
* * * *
358 CCACTATCTCCGT-C-A-TCACCTCCT
1 CC-TTATGT-C-TACAAGTCCCCACCT
382 CCTTATGTCTACAAGTCCCCACCT
1 CCTTATGTCTACAAGTCCCCACCT
406 CC
1 CC
408 ACCGTCTCCC
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
21 1 0.03
22 2 0.06
23 5 0.14
24 20 0.56
25 5 0.14
26 2 0.06
27 1 0.03
ACGTcount: A:0.19, C:0.46, G:0.07, T:0.28
Consensus pattern (24 bp):
CCTTATGTCTACAAGTCCCCACCT
Found at i:790 original size:27 final size:27
Alignment explanation
Indices: 760--844 Score: 74
Period size: 27 Copynumber: 3.4 Consensus size: 27
750 TCCTTCACTT
760 CCTCCACCATATGTCTACAAGTCCCCA
1 CCTCCACCATATGTCTACAAGTCCCCA
* * * * *
787 CCTCCTCCATCT-CCTTC-A--CCTC-
1 CCTCCACCATATGTCTACAAGTCCCCA
*
809 CC-CCACCTTATGTCTACAAGTCCCCA
1 CCTCCACCATATGTCTACAAGTCCCCA
835 CCTCCACCAT
1 CCTCCACCAT
845 CTCATTCACC
Statistics
Matches: 40, Mismatches: 12, Indels: 12
0.62 0.19 0.19
Matches are distributed among these distances:
21 6 0.15
22 5 0.12
23 4 0.10
25 4 0.10
26 5 0.12
27 16 0.40
ACGTcount: A:0.20, C:0.51, G:0.05, T:0.25
Consensus pattern (27 bp):
CCTCCACCATATGTCTACAAGTCCCCA
Found at i:953 original size:21 final size:21
Alignment explanation
Indices: 880--956 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 21
870 TTACAAGTCT
*
880 CCACCTCCACCATCTCCTTCA
1 CCACCTCCACCATCTCCATCA
* * *
901 CCACCTCCCCCTTACATCTACAAGTCC
1 CCACCT-CCAC---CATCT-CCA-TCA
928 CCACCTCCACCATCTCCATCA
1 CCACCTCCACCATCTCCATCA
949 CCACCTCC
1 CCACCTCC
957 TCCTTACATT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
21 16 0.37
22 5 0.12
23 5 0.12
25 5 0.12
26 4 0.09
27 8 0.19
ACGTcount: A:0.21, C:0.57, G:0.01, T:0.21
Consensus pattern (21 bp):
CCACCTCCACCATCTCCATCA
Found at i:1173 original size:27 final size:27
Alignment explanation
Indices: 1102--1175 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 27
1092 ACCTCCCCCA
1102 CCTTATGTCTACAAGTCCCCACCTCCT
1 CCTTATGTCTACAAGTCCCCACCTCCT
* *
1129 CC--A--TCT-C-CGTCACCACCTCCT
1 CCTTATGTCTACAAGTCCCCACCTCCT
1150 CCTTATGTCTACAAGTCCCCACCTCC
1 CCTTATGTCTACAAGTCCCCACCTCC
1176 ACCGTCTCCC
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
21 14 0.38
22 1 0.03
23 4 0.11
25 4 0.11
26 1 0.03
27 13 0.35
ACGTcount: A:0.18, C:0.49, G:0.07, T:0.27
Consensus pattern (27 bp):
CCTTATGTCTACAAGTCCCCACCTCCT
Found at i:1196 original size:27 final size:27
Alignment explanation
Indices: 1166--1247 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 27
1156 GTCTACAAGT
1166 CCCCACCTCCACCGTCTCCCTCACCTC
1 CCCCACCTCCACCGTCTCCCTCACCTC
* * **
1193 CCCCACC-CTA-CGTCT--AT-AAGT-
1 CCCCACCTCCACCGTCTCCCTCACCTC
*
1214 CCCCACCTCCACCATCTCCCTCACCTC
1 CCCCACCTCCACCGTCTCCCTCACCTC
1241 CCCCACC
1 CCCCACC
1248 CTACGTCTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 12
0.66 0.15 0.20
Matches are distributed among these distances:
21 7 0.17
22 4 0.10
23 5 0.12
25 6 0.15
26 4 0.10
27 14 0.35
ACGTcount: A:0.16, C:0.62, G:0.04, T:0.18
Consensus pattern (27 bp):
CCCCACCTCCACCGTCTCCCTCACCTC
Found at i:1273 original size:27 final size:26
Alignment explanation
Indices: 1243--1322 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 26
1233 CTCACCTCCC
1243 CCACCCTACGTCTACAAGTCCCCACCT
1 CCACCCTA-GTCTACAAGTCCCCACCT
** *
1270 CCA-CC-A-TCT-C-CCTCACCACCT
1 CCACCCTAGTCTACAAGTCCCCACCT
*
1291 CCACCCTATGTGTACAAGTCCCCACCT
1 CCACCCTA-GTCTACAAGTCCCCACCT
1318 CCACC
1 CCACC
1323 ATCTCCTTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
21 11 0.28
22 3 0.08
23 4 0.10
25 3 0.08
26 3 0.08
27 16 0.40
ACGTcount: A:0.21, C:0.54, G:0.06, T:0.19
Consensus pattern (26 bp):
CCACCCTAGTCTACAAGTCCCCACCT
Found at i:1408 original size:27 final size:27
Alignment explanation
Indices: 1378--1735 Score: 140
Period size: 27 Copynumber: 14.6 Consensus size: 27
1368 ACCATCTCCT
* *
1378 TCACCTCCTCCACCTTACACCTACAAG
1 TCACCACCTCCACCATACACCTACAAG
*
1405 TCACCACCTCCACCAT-CTCC--C---
1 TCACCACCTCCACCATACACCTACAAG
* * *
1426 TCACCACCTCCTCCTTACATCTACAAG
1 TCACCACCTCCACCATACACCTACAAG
***
1453 TCACCACCTCCACCATATGTCTACAAG
1 TCACCACCTCCACCATACACCTACAAG
* *
1480 TCTCCACCTCCACCAT-CTCC--C---
1 TCACCACCTCCACCATACACCTACAAG
* **** *
1501 TCACCACCTCCACCTTATGTTTACAAA
1 TCACCACCTCCACCATACACCTACAAG
*
1528 TCACCACCTCCACCAT-CTCC--C---
1 TCACCACCTCCACCATACACCTACAAG
* * *
1549 TCACCACCTCCTCCTTACATCTACAAG
1 TCACCACCTCCACCATACACCTACAAG
*
1576 TCACCACCTCCACCAT-CTCC--C---
1 TCACCACCTCCACCATACACCTACAAG
***
1597 TCACCACCTCCACCATATGTCTACAAG
1 TCACCACCTCCACCATACACCTACAAG
* *
1624 TCTCCACCTCCACCAT-CTCC--C---
1 TCACCACCTCCACCATACACCTACAAG
***
1645 TCACCACCTCCACCATATGTCTACAAG
1 TCACCACCTCCACCATACACCTACAAG
* *
1672 TCTCCACCTCCACCAT-C-TCT-C---
1 TCACCACCTCCACCATACACCTACAAG
***
1693 TCACCACCTCCACCATATGTCTACAAG
1 TCACCACCTCCACCATACACCTACAAG
*
1720 TCCCCACCTCCACCAT
1 TCACCACCTCCACCAT
1736 TTTCCCCATC
Statistics
Matches: 245, Mismatches: 50, Indels: 72
0.67 0.14 0.20
Matches are distributed among these distances:
21 88 0.36
22 6 0.02
23 3 0.01
24 12 0.05
25 3 0.01
26 7 0.03
27 126 0.51
ACGTcount: A:0.24, C:0.50, G:0.03, T:0.23
Consensus pattern (27 bp):
TCACCACCTCCACCATACACCTACAAG
Found at i:1457 original size:123 final size:123
Alignment explanation
Indices: 1330--1591 Score: 425
Period size: 123 Copynumber: 2.1 Consensus size: 123
1320 ACCATCTCCT
* * * *
1330 TCACCACCTCCACCTTATGTTTACAAATCACCACCTCCACCATCTCCTTCACCTCCTCCACCTTA
1 TCACCACCTCCACCATATGTCTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCACCTTA
*
1395 CACCTACAAGTCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACATCTACAAG
66 CACCTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACATCTACAAG
* *
1453 TCACCACCTCCACCATATGTCTACAAGTCTCCACCTCCACCATCTCCCTCACCACCTCCACCTTA
1 TCACCACCTCCACCATATGTCTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCACCTTA
****
1518 TGTTTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACATCTACAAG
66 CACCTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACATCTACAAG
1576 TCACCACCTCCACCAT
1 TCACCACCTCCACCAT
1592 CTCCCTCACC
Statistics
Matches: 128, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 128 1.00
ACGTcount: A:0.24, C:0.49, G:0.03, T:0.24
Consensus pattern (123 bp):
TCACCACCTCCACCATATGTCTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCACCTTA
CACCTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACATCTACAAG
Found at i:1505 original size:48 final size:48
Alignment explanation
Indices: 1453--1793 Score: 531
Period size: 48 Copynumber: 7.1 Consensus size: 48
1443 CATCTACAAG
*
1453 TCACCACCTCCACCATATGTCTACAAGTCTCCACCTCCACCATCTCCC
1 TCACCACCTCCACCATATGTCTACAAGTCACCACCTCCACCATCTCCC
* * *
1501 TCACCACCTCCACCTTATGTTTACAAATCACCACCTCCACCATCTCCC
1 TCACCACCTCCACCATATGTCTACAAGTCACCACCTCCACCATCTCCC
* * **
1549 TCACCACCTCCTCCTTACATCTACAAGTCACCACCTCCACCATCTCCC
1 TCACCACCTCCACCATATGTCTACAAGTCACCACCTCCACCATCTCCC
*
1597 TCACCACCTCCACCATATGTCTACAAGTCTCCACCTCCACCATCTCCC
1 TCACCACCTCCACCATATGTCTACAAGTCACCACCTCCACCATCTCCC
* *
1645 TCACCACCTCCACCATATGTCTACAAGTCTCCACCTCCACCATCTCTC
1 TCACCACCTCCACCATATGTCTACAAGTCACCACCTCCACCATCTCCC
* *
1693 TCACCACCTCCACCATATGTCTACAAGTCCCCACCTCCACCATTTTCCC
1 TCACCACCTCCACCATATGTCTACAAGTCACCACCTCCACCA-TCTCCC
* *
1742 -CATCACCTCCACCATATGTCTACAAGTCACCACCTCCACCATCTCCA
1 TCACCACCTCCACCATATGTCTACAAGTCACCACCTCCACCATCTCCC
1789 TCACC
1 TCACC
1794 TTCTCCTCCT
Statistics
Matches: 268, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
47 4 0.01
48 260 0.97
49 4 0.01
ACGTcount: A:0.24, C:0.49, G:0.04, T:0.23
Consensus pattern (48 bp):
TCACCACCTCCACCATATGTCTACAAGTCACCACCTCCACCATCTCCC
Found at i:1505 original size:96 final size:95
Alignment explanation
Indices: 1405--1793 Score: 331
Period size: 96 Copynumber: 4.1 Consensus size: 95
1395 CACCTACAAG
* *
1405 TCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTA-CATCTACAAGTCACCACCTCCACCAT
1 TCACCACCTCCACCATCTCCCTCACCACCTCCACCTTACCATCT-C-ACTCACCACCTCCACCAT
1469 ATGTCTACAAGTCTCCACCTCCACCATCTCCC
64 ATGTCTACAAGTCTCCACCTCCACCATCTCCC
* * ** * * * * * * * *
1501 TCACCACCTCCACCTTAT-GTTTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCTCCTT
1 TCACCACCTCCACCATCTCCCTCAC-CACCTCCACCT-TACCATCTCACTCACCACCTCCACCAT
** *
1565 ACATCTACAAGTCACCACCTCCACCATCTCCC
64 ATGTCTACAAGTCTCCACCTCCACCATCTCCC
* ** * * * *
1597 TCACCACCTCCACCATATGTCT-ACAAGTCTCCACCTCCACCATCTCCCTCACCACCTCCACCAT
1 TCACCACCTCCACCATCTCCCTCACCA-CCTCCACCT-TACCATCTCACTCACCACCTCCACCAT
*
1661 ATGTCTACAAGTCTCCACCTCCACCATCTCTC
64 ATGTCTACAAGTCTCCACCTCCACCATCTCCC
* ** * * * * *
1693 TCACCACCTCCACCATATGTCT-ACAAGTCC-CCACCTCCACCATTTTC-CCCATCACCTCCACC
1 TCACCACCTCCACCATCTCCCTCACCA--CCTCCACCT-TACCA-TCTCACTCACCACCTCCACC
* *
1755 ATATGTCTACAAGTCACCACCTCCACCATCTCCA
62 ATATGTCTACAAGTCTCCACCTCCACCATCTCCC
1789 TCACC
1 TCACC
1794 TTCTCCTCCT
Statistics
Matches: 251, Mismatches: 35, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
95 5 0.02
96 234 0.93
97 7 0.03
98 5 0.02
ACGTcount: A:0.24, C:0.50, G:0.03, T:0.23
Consensus pattern (95 bp):
TCACCACCTCCACCATCTCCCTCACCACCTCCACCTTACCATCTCACTCACCACCTCCACCATAT
GTCTACAAGTCTCCACCTCCACCATCTCCC
Found at i:1517 original size:75 final size:75
Alignment explanation
Indices: 1398--1687 Score: 301
Period size: 75 Copynumber: 3.9 Consensus size: 75
1388 CACCTTACAC
* *
1398 CTACAAGTCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACATCTACAAGTCACCACCTC
1 CTACAAGTCTCCACCTCCACCATCTCCCTCACCACCTCCACCTTACATCTACAAGTCACCACCTC
1463 CACCATATGT
66 CACCATATGT
** * *
1473 CTACAAGTCTCCACCTCCACCATCTCCCTCACCACCTCCACCTTATGTTTACAAATCACCACCTC
1 CTACAAGTCTCCACCTCCACCATCTCCCTCACCACCTCCACCTTACATCTACAAGTCACCACCTC
* **
1538 CACCATCTCC
66 CACCATATGT
* * * * ** **
1548 CTCACCA-CCTCCTCCT-TA-CATCTACAAGTCACCACCTCCA-C---CATCT-C-CCTCACCAC
1 CT-ACAAGTCTCCACCTCCACCATCT-C-CCTCACCACCTCCACCTTACATCTACAAGTCACCAC
1604 CTCCACCATATGT
63 CTCCACCATATGT
* ** *
1617 CTACAAGTCTCCACCTCCACCATCTCCCTCACCACCTCCACCATATGTCTACAAGTCTCCACCTC
1 CTACAAGTCTCCACCTCCACCATCTCCCTCACCACCTCCACCTTACATCTACAAGTCACCACCTC
1682 CACCAT
66 CACCAT
1688 CTCTCTCACC
Statistics
Matches: 169, Mismatches: 34, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
68 3 0.02
69 38 0.22
70 4 0.02
71 7 0.04
73 8 0.05
74 4 0.02
75 102 0.60
76 3 0.02
ACGTcount: A:0.24, C:0.49, G:0.03, T:0.23
Consensus pattern (75 bp):
CTACAAGTCTCCACCTCCACCATCTCCCTCACCACCTCCACCTTACATCTACAAGTCACCACCTC
CACCATATGT
Found at i:1592 original size:171 final size:171
Alignment explanation
Indices: 1282--1639 Score: 599
Period size: 171 Copynumber: 2.1 Consensus size: 171
1272 ACCATCTCCC
* * *
1282 TCACCACCTCCACCCTATGTGTACAAGTCCCCACCTCCACCATCTCCTTCACCACCTCCACCTTA
1 TCACCACCTCCACCATATGTCTACAAGTCCCCACCTCCACCATCTCCCTCACCACCTCCACCTTA
* *
1347 TGTTTACAAATCACCACCTCCACCATCTCCTTCACCTCCTCCACCTTACACCTACAAGTCACCAC
66 TGTTTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCACCTTACACCTACAAGTCACCAC
* *
1412 CTCCACCATCTCCCTCACCACCTCCTCCTTACATCTACAAG
131 CTCCACCATCTCCCTCACCACCTCCACCATACATCTACAAG
*
1453 TCACCACCTCCACCATATGTCTACAAGTCTCCACCTCCACCATCTCCCTCACCACCTCCACCTTA
1 TCACCACCTCCACCATATGTCTACAAGTCCCCACCTCCACCATCTCCCTCACCACCTCCACCTTA
* *
1518 TGTTTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCTCCTTACATCTACAAGTCACCAC
66 TGTTTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCACCTTACACCTACAAGTCACCAC
**
1583 CTCCACCATCTCCCTCACCACCTCCACCATATGTCTACAAG
131 CTCCACCATCTCCCTCACCACCTCCACCATACATCTACAAG
*
1624 TCTCCACCTCCACCAT
1 TCACCACCTCCACCAT
1640 CTCCCTCACC
Statistics
Matches: 174, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
171 174 1.00
ACGTcount: A:0.24, C:0.49, G:0.03, T:0.24
Consensus pattern (171 bp):
TCACCACCTCCACCATATGTCTACAAGTCCCCACCTCCACCATCTCCCTCACCACCTCCACCTTA
TGTTTACAAATCACCACCTCCACCATCTCCCTCACCACCTCCACCTTACACCTACAAGTCACCAC
CTCCACCATCTCCCTCACCACCTCCACCATACATCTACAAG
Done.