Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00158.M1
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: 4372
ACGTcount: A:0.29, C:0.38, G:0.10, T:0.23
Found at i:342 original size:48 final size:48
Alignment explanation
Indices: 269--396 Score: 166
Period size: 48 Copynumber: 2.7 Consensus size: 48
259 ATCACCTCCT
* * * * *
269 CCGCCTTATGAGTATAAGTCACCACCACCGCCTTCTCCTTCTCCACCA
1 CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTATCCACCA
* *
317 CCGCCTTATGTGTATAAATCTCCACCACCACCTTCACCTTATCCTCCA
1 CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTATCCACCA
* * *
365 CCTCCGTATGTGTACAAGTCTCCACCACCACC
1 CCGCCTTATGTGTATAAGTCTCCACCACCACC
397 ACCTAAACAT
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.22, C:0.43, G:0.09, T:0.26
Consensus pattern (48 bp):
CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTATCCACCA
Found at i:429 original size:48 final size:42
Alignment explanation
Indices: 377--487 Score: 150
Period size: 42 Copynumber: 2.5 Consensus size: 42
367 TCCGTATGTG
377 TACAAGTCTCCACCACCACCACCTAAACATGAGGAGAAGCCTTATGAA
1 TACAAGTCTCCACCACCACCACC---A-A--AGGAGAAGCCTTATGAA
*
425 TACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAG
1 TACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAA
*
467 TACAAGTCTCCACCCCCACCA
1 TACAAGTCTCCACCACCACCA
488 TCACCTTCTC
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
42 36 0.59
44 1 0.02
45 1 0.02
48 23 0.38
ACGTcount: A:0.35, C:0.36, G:0.14, T:0.15
Consensus pattern (42 bp):
TACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAA
Found at i:454 original size:42 final size:45
Alignment explanation
Indices: 377--711 Score: 193
Period size: 48 Copynumber: 7.4 Consensus size: 45
367 TCCGTATGTG
377 TACAAGTCTCCACCACCACCACCTAAACATGAGGAGAAGCCTTATGAA
1 TACAAGTCTCCACCACCACCACC--AACA-GAGGAGAAGCCTTATGAA
*
425 TACAAGTCTCCACCACCACCACC-A-A-AGGAGAAGCCTTATGAG
1 TACAAGTCTCCACCACCACCACCAACAGAGGAGAAGCCTTATGAA
* * * ******* ** *
467 TACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACCTCCTTATGAG
1 TACAAGTCTCCACCACCACCACCAAC--AGAGGAGA-AGCCTTATGAA
* * * * ***** * ** * **
515 TACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCTTACGTG
1 TACAAGTCTCCACCACCACCACCAAC-AGAGGA-GA-AGCCTTATGAA
* *
563 TACAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAAGCCGTATGAA
1 TACAAGTCTCCACCACCACCACC-AA-CA-GAGGAGAAGCCTTATGAA
* *
611 TACAAGTCTCCACCACCACCACC--GA-AGGAGAAGCCTTATGAG
1 TACAAGTCTCCACCACCACCACCAACAGAGGAGAAGCCTTATGAA
*
653 TACAAGTCTCCACCACCACCACC--GA-AGGAGAAGCCTTATGAA
1 TACAAGTCTCCACCACCACCACCAACAGAGGAGAAGCCTTATGAA
695 TACAAGTCTCCACCACC
1 TACAAGTCTCCACCACC
712 TCCATCGCCT
Statistics
Matches: 235, Mismatches: 42, Indels: 26
0.78 0.14 0.09
Matches are distributed among these distances:
42 110 0.47
44 2 0.01
45 1 0.00
47 3 0.01
48 115 0.49
49 2 0.01
50 2 0.01
ACGTcount: A:0.31, C:0.38, G:0.13, T:0.18
Consensus pattern (45 bp):
TACAAGTCTCCACCACCACCACCAACAGAGGAGAAGCCTTATGAA
Found at i:532 original size:27 final size:26
Alignment explanation
Indices: 494--582 Score: 71
Period size: 27 Copynumber: 3.5 Consensus size: 26
484 ACCATCACCT
*
494 TCTCCTCCACCTCCTTATGAGTACAAA
1 TCTCCACCACCTCCTTATG-GTACAAA
* **
521 TCTCCACCACCTCC--AT--CAC-CT
1 TCTCCACCACCTCCTTATGGTACAAA
* *
542 TCTCCACCACCTCCTTACGTGTACAAG
1 TCTCCACCACCTCCTTATG-GTACAAA
569 TCTCCACCACCTCC
1 TCTCCACCACCTCC
583 ACCAAAGCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
21 14 0.29
22 2 0.04
23 1 0.02
25 2 0.04
26 2 0.04
27 27 0.56
ACGTcount: A:0.21, C:0.47, G:0.06, T:0.26
Consensus pattern (26 bp):
TCTCCACCACCTCCTTATGGTACAAA
Found at i:596 original size:186 final size:186
Alignment explanation
Indices: 271--673 Score: 619
Period size: 186 Copynumber: 2.2 Consensus size: 186
261 CACCTCCTCC
* * * * * * *
271 GCCTTATGAGTATAAGTCACCACCACCGCCTTCTCCTTCTCCACCACCGCCTTATGTGTATAAAT
1 GCCTTATGAGTACAAGTCTCCACCACCACCATCACCTTCTCCACCACCGCCTTATGAGTACAAAT
* * *
336 CTCCACCACCACCTTCACCTTATCCTCCACCTCCGTATGTGTACAAGTCTCCACCACCACCACCT
66 CTCCACCACCACCATCACCTTATCCACCACCTCCGTACGTGTACAAGTCTCCACCACCACCACCT
*
401 AAACATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
131 AAACATGAGGAGAAGCCGTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
* * *
457 GCCTTATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAAT
1 GCCTTATGAGTACAAGTCTCCACCACCACCATCACCTTCTCCACCACCGCCTTATGAGTACAAAT
* * * *
522 CTCCACCACCTCCATCACCTTCTCCACCACCTCCTTACGTGTACAAGTCTCCACCACCTCCACC-
66 CTCCACCACCACCATCACCTTATCCACCACCTCCGTACGTGTACAAGTCTCCACCACCACCACCT
*
586 AAAGCATGAGGAGAAGCCGTATGAATACAAGTCTCCACCACCACCACCGAAGGAGAA
131 AAA-CATGAGGAGAAGCCGTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
643 GCCTTATGAGTACAAGTCTCCACCACCACCA
1 GCCTTATGAGTACAAGTCTCCACCACCACCA
674 CCGAAGGAGA
Statistics
Matches: 196, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
185 3 0.02
186 193 0.98
ACGTcount: A:0.28, C:0.39, G:0.12, T:0.21
Consensus pattern (186 bp):
GCCTTATGAGTACAAGTCTCCACCACCACCATCACCTTCTCCACCACCGCCTTATGAGTACAAAT
CTCCACCACCACCATCACCTTATCCACCACCTCCGTACGTGTACAAGTCTCCACCACCACCACCT
AAACATGAGGAGAAGCCGTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
Found at i:615 original size:48 final size:42
Alignment explanation
Indices: 594--711 Score: 218
Period size: 42 Copynumber: 2.8 Consensus size: 42
584 CCAAAGCATG
*
594 AGGAGAAGCCGTATGAATACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
*
636 AGGAGAAGCCTTATGAGTACAAGTCTCCACCACCACCACCGA
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
678 AGGAGAAGCCTTATGAATACAAGTCTCCACCACC
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACC
712 TCCATCGCCT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.35, C:0.32, G:0.19, T:0.14
Consensus pattern (42 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGA
Found at i:689 original size:228 final size:228
Alignment explanation
Indices: 408--822 Score: 697
Period size: 228 Copynumber: 1.8 Consensus size: 228
398 CCTAAACATG
*
408 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAGTACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAATACAAG
*
473 TCTCCACCCCCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATC
66 TCTCCACCACCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATC
* * * * * *
538 ACCTTCTCCACCACCTCCTTACGT-GTACAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAAG
131 ACCATCACCACCACCTCCATAC-TACTACAAGTCGCCACCACCACCACCAAAGCATGAGGAGAAG
602 CCGTATGAATACAAGTCTCCACCACCACCACCGA
195 CCGTATGAATACAAGTCTCCACCACCACCACCGA
* *
636 AGGAGAAGCCTTATGAGTACAAGTCTCCACCACCACCACCGAAGGAGAAGCCTTATGAATACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAATACAAG
* * *
701 TCTCCACCACCTCCATCGCCTTCTCCTCCACCTCCTTATGAGTATAAATCTCCACCACCTCCATC
66 TCTCCACCACCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATC
766 ACCATCACCACCACCTCCATACTACTACAAGTCGCCACCACCACCACCAAAGCATGA
131 ACCATCACCACCACCTCCATACTACTACAAGTCGCCACCACCACCACCAAAGCATGA
823 AGAACAACCA
Statistics
Matches: 173, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
227 1 0.01
228 172 0.99
ACGTcount: A:0.30, C:0.39, G:0.12, T:0.19
Consensus pattern (228 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAATACAAG
TCTCCACCACCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATC
ACCATCACCACCACCTCCATACTACTACAAGTCGCCACCACCACCACCAAAGCATGAGGAGAAGC
CGTATGAATACAAGTCTCCACCACCACCACCGA
Found at i:1054 original size:27 final size:26
Alignment explanation
Indices: 1017--1101 Score: 81
Period size: 27 Copynumber: 3.4 Consensus size: 26
1007 CCATCACCCT
1017 CACCACCACCTTACTACTATAAATCTC
1 CACCACCACCTTACTACTA-AAATCTC
*
1044 CACCACCACCTT-C-AC---CATCTC
1 CACCACCACCTTACTACTAAAATCTC
* * *
1065 CACCACCTCCTTACTACTACAAGTCCC
1 CACCACCACCTTACTACTA-AAATCTC
1092 CACCACCACC
1 CACCACCACC
1102 ACCAAAGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
21 16 0.35
22 1 0.02
23 2 0.04
25 2 0.04
26 1 0.02
27 24 0.52
ACGTcount: A:0.28, C:0.51, G:0.01, T:0.20
Consensus pattern (26 bp):
CACCACCACCTTACTACTAAAATCTC
Found at i:1193 original size:24 final size:24
Alignment explanation
Indices: 1166--1245 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 24
1156 ACCCTCACCA
*
1166 CCACCACCTTACTATTACAAGTCT
1 CCACCACCTTACTATTACAAATCT
* **
1190 CCACCACC--ACCT-TCACCATCTCCT
1 CCACCACCTTA-CTATTA-CAAAT-CT
*
1214 CCACCACCTTACTACTACAAATCT
1 CCACCACCTTACTATTACAAATCT
1238 CCACCACC
1 CCACCACC
1246 ACCCCCACAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
22 3 0.07
23 5 0.12
24 28 0.65
25 5 0.12
26 2 0.05
ACGTcount: A:0.28, C:0.49, G:0.01, T:0.23
Consensus pattern (24 bp):
CCACCACCTTACTATTACAAATCT
Found at i:1193 original size:27 final size:27
Alignment explanation
Indices: 1163--1296 Score: 105
Period size: 27 Copynumber: 5.4 Consensus size: 27
1153 ATCACCCTCA
* *
1163 CCACCACCACCTTACTATTACAAGTCT
1 CCACCACCACCTTACTACTACAAATCT
1190 CCACCACCACCTT-C-AC--C--ATCT
1 CCACCACCACCTTACTACTACAAATCT
*
1211 CCTCCACCACCTTACTACTACAAATCT
1 CCACCACCACCTTACTACTACAAATCT
** * *
1238 CCACCACCACCCCCAC-ATTAC--GTCT
1 CCACCACCA-CCTTACTACTACAAATCT
1263 -CACCACCA---TACTACTACAAATCT
1 CCACCACCACCTTACTACTACAAATCT
1286 CCACCACCACC
1 CCACCACCACC
1297 AGTGAAATCT
Statistics
Matches: 83, Mismatches: 11, Indels: 27
0.69 0.09 0.22
Matches are distributed among these distances:
20 2 0.02
21 19 0.23
22 1 0.01
23 6 0.07
24 16 0.19
25 5 0.06
26 1 0.01
27 29 0.35
28 4 0.05
ACGTcount: A:0.29, C:0.49, G:0.01, T:0.20
Consensus pattern (27 bp):
CCACCACCACCTTACTACTACAAATCT
Found at i:1246 original size:48 final size:48
Alignment explanation
Indices: 695--1297 Score: 381
Period size: 48 Copynumber: 12.4 Consensus size: 48
685 GCCTTATGAA
* * * * * *
695 TACAAGTCTCCACCACCTCCATCGCCTTCTCCTCCACCTCCTTA-TGAG
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACT-AC
* * * * * *
743 TATAAATCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* * * **** * *
791 TACAAGTCGCCACCACCACCACCAAAGCATGAAGAACAACCACCATACTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CTCCACCACCACCTTACTAC
* * * * * * * *
842 TACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* * * * * * * *
890 TACAAGTCCCCACCACCTCCGTCTCCATCACCACCTCCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* * * **** * * *
938 TACAAATCTCCACCACCACCACCAAAGCATGAAGAACAACCCCCATACTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CTCCACCACCACCTTACTAC
*
989 TACAAGTCTCCACCACCTCCATCACC--CT-CACCACCACCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* * * *
1034 TATAAATCTCCACCACCACCTTCACCATCTCCACCACCTCCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* * * **** * * *
1082 TACAAGTCCCCACCACCACCACCAAAGCATGAAGAACAACCCCCATACTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CTCCACCACCACCTTACTAC
* * * *
1133 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTAT
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* *
1181 TACAAGTCTCCACCACCACCTTCACCATCTCCTCCACCACCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
* ** ** *
1229 TACAAATCTCCACCACCACCCCCA-CAT-TACGTCTCACCACCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCT-CCAC-CACCACCTTACTAC
*
1277 TACAAATCTCCACCACCACCA
1 TACAAGTCTCCACCACCACCA
1298 GTGAAATCTC
Statistics
Matches: 437, Mismatches: 103, Indels: 30
0.77 0.18 0.05
Matches are distributed among these distances:
45 35 0.08
46 1 0.00
47 8 0.02
48 273 0.62
49 9 0.02
50 11 0.03
51 100 0.23
ACGTcount: A:0.30, C:0.47, G:0.04, T:0.19
Consensus pattern (48 bp):
TACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCTTACTAC
Found at i:1279 original size:147 final size:147
Alignment explanation
Indices: 695--1248 Score: 747
Period size: 147 Copynumber: 3.8 Consensus size: 147
685 GCCTTATGAA
* * * * * * *
695 TACAAGTCTCCACCACCTCCATCGCCTTCTCCTCCACCTCCTTA-TGAGTATAAATCTCCACCAC
1 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACT-ACTACAAATCTCCACCAC
* * * *
759 CTCCATCACCATCACCACCACCTCCATACTACTACAAGTCGCCACCACCACCACCAAAGCATGAA
65 CACCTTCACCATCACCACCACCTCCATACTACTACAAATCTCCACCACCACCACCAAAGCATGAA
*
824 GAACAACCACCATACTAC
130 GAACAACCCCCATACTAC
* * * * * * * * *
842 TACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCTTACTACTACAAGTCCCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCTCCACCACC
* * * *
907 TCCGTCTCCATCACCACCTCCTCCATACTACTACAAATCTCCACCACCACCACCAAAGCATGAAG
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAATCTCCACCACCACCACCAAAGCATGAAG
972 AACAACCCCCATACTAC
131 AACAACCCCCATACTAC
*
989 TACAAGTCTCCACCACCTCCATCACCCT---CACCACCACCTTACTACTATAAATCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCTCCACCACC
* * * *
1051 ACCTTCACCATCTCCACCACCTCCTTACTACTACAAGTCCCCACCACCACCACCAAAGCATGAAG
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAATCTCCACCACCACCACCAAAGCATGAAG
1116 AACAACCCCCATACTAC
131 AACAACCCCCATACTAC
* *
1133 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTATTACAAGTCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCTCCACCACC
* * * *
1198 ACCTTCACCATCTCCTCCACCACCTTACTACTACAAATCTCCACCACCACC
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAATCTCCACCACCACC
1249 CCCACATTAC
Statistics
Matches: 360, Mismatches: 43, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
144 131 0.36
147 228 0.63
148 1 0.00
ACGTcount: A:0.30, C:0.47, G:0.04, T:0.19
Consensus pattern (147 bp):
TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCTCCACCACC
ACCTTCACCATCACCACCACCTCCATACTACTACAAATCTCCACCACCACCACCAAAGCATGAAG
AACAACCCCCATACTAC
Found at i:1290 original size:24 final size:24
Alignment explanation
Indices: 1212--1294 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
1202 TCACCATCTC
*
1212 CTCCACCACCTTACTACTACAAAT
1 CTCCACCACCATACTACTACAAAT
** * *
1236 CTCCACCACC--ACCCCCAC-ATT
1 CTCCACCACCATACTACTACAAAT
1257 ACGTCTCACCACCATACTACTACAAAT
1 -C-TC-CACCACCATACTACTACAAAT
1284 CTCCACCACCA
1 CTCCACCACCA
1295 CCAGTGAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
21 2 0.04
22 6 0.13
23 2 0.04
24 25 0.56
25 2 0.04
26 6 0.13
27 2 0.04
ACGTcount: A:0.31, C:0.48, G:0.01, T:0.19
Consensus pattern (24 bp):
CTCCACCACCATACTACTACAAAT
Found at i:1362 original size:6 final size:6
Alignment explanation
Indices: 1351--1394 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
1341 CTCCTTACTA
* * *
1351 CCCCAC CCCCAC CCTCAC CCCCAG CCCCAC CCCCAC CCACAC CC
1 CCCCAC CCCCAC CCCCAC CCCCAC CCCCAC CCCCAC CCCCAC CC
1395 GCTCATAGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.18, C:0.77, G:0.02, T:0.02
Consensus pattern (6 bp):
CCCCAC
Found at i:1890 original size:36 final size:36
Alignment explanation
Indices: 1843--1922 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
1833 GTACTATTAT
* * *
1843 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTAC
1 AAGTCACCACCTCCACCGGCACCAACTTATGTTTAC
*
1879 AAGTCACCACCTCCACCGTCACCAACTTATGTTTAC
1 AAGTCACCACCTCCACCGGCACCAACTTATGTTTAC
1915 AAGTCACC
1 AAGTCACC
1923 TCCACCTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.25, C:0.40, G:0.10, T:0.25
Consensus pattern (36 bp):
AAGTCACCACCTCCACCGGCACCAACTTATGTTTAC
Found at i:2030 original size:114 final size:113
Alignment explanation
Indices: 1879--2150 Score: 456
Period size: 114 Copynumber: 2.4 Consensus size: 113
1869 TTATGTTTAC
* *
1879 AAGTCACCACCTCCACCG-TCACCAACTTATGTTTACAAGTCACCTCCACCTCCTGCGTACTACT
1 AAGTCTCCACCTCCACCGCTC-CC-ACTTATGTTTACAAGTCACCTCCACCTCCTACGTACTACT
* *
1943 ACAAGTCTCCACCACCACCAAAGCATGTGGAACAGCCTCCATACTACTAT
64 ACAAGTCTCCACCACCACCAAAGCATGTGGAACAACCACCATACTACTAT
*
1993 AAGTCTCCACCTCCACCAGCTCCCACTTATGTTTACAAGTCACCTCCACCTCCTATGTACTACTA
1 AAGTCTCCACCTCCACC-GCTCCCACTTATGTTTACAAGTCACCTCCACCTCCTACGTACTACTA
2058 CAAGTCTCCACCACCACCAAAGCATGTGGAACAACCACCATACTACTAT
65 CAAGTCTCCACCACCACCAAAGCATGTGGAACAACCACCATACTACTAT
2107 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACC
1 AAGTCTCCACCTCCACC-GCTCCCACTTATGTTTACAAGTCACC
2151 GCCTCCACCA
Statistics
Matches: 150, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
114 145 0.97
115 3 0.02
116 2 0.01
ACGTcount: A:0.28, C:0.39, G:0.10, T:0.23
Consensus pattern (113 bp):
AAGTCTCCACCTCCACCGCTCCCACTTATGTTTACAAGTCACCTCCACCTCCTACGTACTACTAC
AAGTCTCCACCACCACCAAAGCATGTGGAACAACCACCATACTACTAT
Found at i:2156 original size:36 final size:36
Alignment explanation
Indices: 2107--2195 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 36
2097 ATACTACTAT
* * *
2107 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* * *
2143 AAGTCACCGCCTCCACCATCGCCGACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* *
2179 AAGTCACCTCCACCACC
1 AAGTCACCACCTCCACC
2196 TGTGTACTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.22, C:0.43, G:0.11, T:0.24
Consensus pattern (36 bp):
AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
Found at i:2330 original size:48 final size:48
Alignment explanation
Indices: 2278--3772 Score: 908
Period size: 48 Copynumber: 31.2 Consensus size: 48
2268 GCAGCCCCCG
* * *
2278 TACTACTACAAGTCTCCTCCACCACCATCACCATCTCCTCCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* *
2326 TACTATTACAAGTCCCCACCACCACCAGTTCA-C-TCTCCACCACCACCA
1 TACTACTACAAGTCCCCACCACCACCA--TCACCATCTCCACCTCCACCA
* * **** ** *
2374 TACTACTACAAGTCCCCACCACCACCA-AAACATGAGGAACAACCTCCA
1 TACTACTACAAGTCCCCACCACCACCATCACCAT-CTCCACCTCCACCA
* * * * * * *
2422 TACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * ** * ** *** *
2470 TACTACTACAAATCCCCACCACCACCA-AAATATGTAGAAGAGCCCCCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCT-CCACCTCCACCA
* * * *
2518 TACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * *
2566 TACTACTACAAGTCCCCACCACCACCATCTCCATCACCACCCCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * * * *
2614 TACTATTACAAATCACCC-CCACCACCATCGCCATCTCCTCATCCACCA
1 TACTACTACAAGTC-CCCACCACCACCATCACCATCTCCACCTCCACCA
* * ** *** *
2662 TACTACTACAAGTCCCCACCACCACCGA--AACATGTAGAGGAGCCCCCA
1 TACTACTACAAGTCCCCACCACCACC-ATCACCATCTCCA-CCTCCACCA
*
2710 TACTACTACAAGTCTCCC-CCACCACCATCGA-CATCTCCTCCTCCACCA
1 TACTACTACAAGTC-CCCACCACCACCATC-ACCATCTCCACCTCCACCA
* * * * * *
2758 TACTATTACAAATCTCCTCCACCACCATCACCATCTCCTCCACCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * ** *** *
2806 TACTACTACAAGTCCCCACCACCACCGA--AACATGTAGAGGAGCCCCCA
1 TACTACTACAAGTCCCCACCACCACC-ATCACCATCTCCA-CCTCCACCA
* * * * * *
2854 TAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCACCACCA
1 TACTA-CTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * * *
2902 TACTATTACAAGTCCCCACCACCACCAGTTCA--TTCTCCATCACCACCA
1 TACTACTACAAGTCCCCACCACCACCA--TCACCATCTCCACCTCCACCA
* * *
2950 TACTACTACAAGTCTCCACCACCACCAGT--CCACTCCCCACCCCCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACCA-TCTCCACCTCCACCA
* * * * *
2998 TACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * * * ** ***
3046 TACTATTACAAGTCTCCACCACCACCA-AAACA-CGTAGAGGAGCC-CCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATC-TCCA-CCTCCACCA
* * * * * *
3093 TAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCACCACCA
1 TACTA-CTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * *
3141 TACTATTACAAGTCCCCACCACCACCAGT--TCAT-TCCCACCACCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACCATCT-CCACCTCCACCA
* * * * *
3188 TACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * * ** *** *
3236 TACTATTACAAGTCCCCACCACCACCA-AAACA-CGTAGAGAAGCCCCCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATC-TCCA-CCTCCACCA
* * * *
3284 TACATA-TACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCA
1 TAC-TACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * * *
3332 TATTATTACAAGTCCCCACCACCACCAGT--CCACTTTCCACCACCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACCA-TCTCCACCTCCACCA
* * * * * *
3380 TACTATTACAAGTCCCCTCCTCCACCATCGCCATCTCCTCCTCTACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * *
3428 TACTATTACAAATCCCCACCACCACCAGT--CCACTCTCCACCCCCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACCA-TCTCCACCTCCACCA
*
3476 TACTACTACAAATCCCCACCACCACCAGT--CCACTCTCCACCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCA-TCACCA-TCTCCACCTCCACCA
* * *
3524 TACTACTACAAATCCCCACCACCACCATC-TCATTCACCACCTCCACCA
1 TACTACTACAAGTCCCCACCACCACCATCACCA-TCTCCACCTCCACCA
* * * * * * * *
3572 TACTATTACAAATCACCC-CCACCTCCAGTGA-AAGCTCCAGCACCTACC-
1 TACTACTACAAGTC-CCCACCACCACCA-TCACCATCTCCACCTCC-ACCA
* * * * * * *
3620 TACCATTACAACTCCCCTCCTCCACCATCACCATCTCCTCCTCCCCCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
* * *
3668 TACTACTACAAATCTCCC-CCACCACCAGT--CCACTCTCCCCCACCACCA
1 TACTACTACAAGTC-CCCACCACCACCA-TCACCA-TCTCCACCTCCACCA
* * * * * * * *
3716 TACTACTACAAATCTCCACCTCCTCCATCTCCCTCACCACCTCCTCCA
1 TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
3764 TACTACTAC
1 TACTACTAC
3773 CACTCACCTC
Statistics
Matches: 1119, Mismatches: 259, Indels: 138
0.74 0.17 0.09
Matches are distributed among these distances:
45 1 0.00
46 6 0.01
47 116 0.10
48 934 0.83
49 55 0.05
50 7 0.01
ACGTcount: A:0.29, C:0.48, G:0.04, T:0.19
Consensus pattern (48 bp):
TACTACTACAAGTCCCCACCACCACCATCACCATCTCCACCTCCACCA
Found at i:2400 original size:144 final size:144
Alignment explanation
Indices: 2235--3550 Score: 1014
Period size: 144 Copynumber: 9.2 Consensus size: 144
2225 CCACTTATGT
* * *
2235 CTACAAGTCTCCACCACCACCAAAGCATGTAGAGCAGCCCCCGTACTACTACAAGTCTCCTCCAC
1 CTACAAGTCCCCACCACCACCAAAGCATGTAGAGCAGCCCCCATACTACTACAAGTCTCCACCAC
2300 CACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTCCA
66 CACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTCCA
2365 CCACCACCATACTA
131 CCACCACCATACTA
* * * * * * *
2379 CTACAAGTCCCCACCACCACCAAAACATG-AGGAACAACCTCCATACTACTACAAATCTCCTCCT
1 CTACAAGTCCCCACCACCACCAAAGCATGTA-GAGCAGCCCCCATACTACTACAAGTCTCCACCA
* * * * ** * *
2443 CCACCATCGCCATCTCCTCCACCACCATACTACTACAAATCCCCACCACCACCAAAAT-A-TGTA
65 CCACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACC-AGTTCACTCTC
* ** *
2506 GAAGAGCCCCCATACTA
129 CACCA-CCACCATACTA
* * * * * * *** ** * *
2523 CTACAAATCTCCTCCACCACCATCACCATCT-CCTCCTCCACCATACTACTACAAGTCCCCACCA
1 CTACAAGTCCCCACCACCACCA-AAGCATGTAGAGCAGCCCCCATACTACTACAAGTCTCCACCA
* * * * * *
2587 CCACCATCTCCATCACCACCCCCACCATACTATTACAAATCACCC-CCACCACCA--TCGCCATC
65 CCACCATCACCATCTCCTCCTCCACCATACTATTACAAGTC-CCCACCACCACCAGTTC-AC-TC
*
2649 TCC-TCATCCACCATACTA
127 TCCACCA-CCACCATACTA
* *
2667 CTACAAGTCCCCACCACCACCGAAA-CATGTAGAGGAGCCCCCATACTACTACAAGTCTCCCCCA
1 CTACAAGTCCCCACCACCACC-AAAGCATGTAGAGCAGCCCCCATACTACTACAAGTCTCCACCA
* * *
2731 CCACCATCGA-CATCTCCTCCTCCACCATACTATTACAAATCTCCTCCACCACCA--TCACCATC
65 CCACCATC-ACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCA-C-TC
*
2793 TCCTCCACCACCATACTA
127 TCCACCACCACCATACTA
* * *
2811 CTACAAGTCCCCACCACCACCGAAA-CATGTAGAGGAGCCCCCATAC-ATCTACAAATCTCCTCC
1 CTACAAGTCCCCACCACCACC-AAAGCATGTAGAGCAGCCCCCATACTA-CTACAAGTCTCCACC
* * *
2874 ACCACCATCGCCATCTCCTCCACCACCATACTATTACAAGTCCCCACCACCACCAGTTCATTCTC
64 ACCACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTC
*
2939 CATCACCACCATACTA
129 CACCACCACCATACTA
* *** * *** *
2955 CTACAAGTCTCCACCACCACCAGTCCA-CT-CCCCACCCCCACCATACTACTACAAGTCTCCACC
1 CTACAAGTCCCCACCACCACCAAAGCATGTAGAGCA-GCCC-CCATACTACTACAAGTCTCCACC
* * * * * * *** * *
3018 ACCACCTTCTCCCTCACCACCTCCACCATACTATTACAAGTCTCCACCACCACCAAAACAC-GTA
64 ACCACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTC
* **
3082 GAGGAGCC-CCATAC-A
129 CACCA-CCACCATACTA
* * * ** * **** * * *
3097 TCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCA-CCACCATACTATTACAAGTCCCCACC
1 -CTACAAGTCCCCACCACCACCAAAG-CATGTAGAGCAGCCCCCATACTACTACAAGTCTCCACC
* * * * * * *
3161 ACCACCAGT--TCAT-TCCCACCACCACCATACTACTACAAGTCTCCACCACCACC-TTCTCCCT
64 ACCACCA-TCACCATCT-CCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGT-TCACT
* *
3222 CACCACCTCCACCATACTA
126 CTCCACCACCACCATACTA
* * * * * *
3241 TTACAAGTCCCCACCACCACCAAAACACGTAGAGAAGCCCCCATACATA-TACAAATCTCCTCCA
1 CTACAAGTCCCCACCACCACCAAAGCATGTAGAGCAGCCCCCATAC-TACTACAAGTCTCCACCA
* * *
3305 CCACCATCACCATCTCCTCCTCCACCATATTATTACAAGTCCCCACCACCACCAGTCCACTTTCC
65 CCACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTCC
3370 ACCACCACCATACTA
130 ACCACCACCATACTA
* * * ** * *** ** ** * * *
3385 TTACAAGTCCCCTCCTCCACCATCGCCATCT-CCTCCTCTACCATACTATTACAAATCCCCACCA
1 CTACAAGTCCCCACCACCACCAAAG-CATGTAGAGCAGCCCCCATACTACTACAAGTCTCCACCA
* * * * *
3449 CCACCAGT--CCACTCTCCACCCCCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
65 CCACCA-TCACCA-TCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCT
*
3512 CCACCTCCACCATACTA
128 CCACCACCACCATACTA
*
3529 CTACAAATCCCCACCACCACCA
1 CTACAAGTCCCCACCACCACCA
3551 TCTCATTCAC
Statistics
Matches: 936, Mismatches: 191, Indels: 90
0.77 0.16 0.07
Matches are distributed among these distances:
141 1 0.00
142 49 0.05
143 130 0.14
144 726 0.78
145 23 0.02
146 7 0.01
ACGTcount: A:0.30, C:0.47, G:0.05, T:0.19
Consensus pattern (144 bp):
CTACAAGTCCCCACCACCACCAAAGCATGTAGAGCAGCCCCCATACTACTACAAGTCTCCACCAC
CACCATCACCATCTCCTCCTCCACCATACTATTACAAGTCCCCACCACCACCAGTTCACTCTCCA
CCACCACCATACTA
Found at i:2928 original size:27 final size:27
Alignment explanation
Indices: 2887--3072 Score: 113
Period size: 27 Copynumber: 7.6 Consensus size: 27
2877 ACCATCGCCA
* *
2887 TCTCCTCCACCACCATACTATTACAAG
1 TCTCCACCACCACCATACTACTACAAG
* * *
2914 TCCCCACCACCACC--AGT--T-C-AT
1 TCTCCACCACCACCATACTACTACAAG
*
2935 TCTCCATCACCACCATACTACTACAAG
1 TCTCCACCACCACCATACTACTACAAG
2962 TCTCCACCACCACCAGT-C--C-AC---
1 TCTCCACCACCACCA-TACTACTACAAG
* *
2983 TCCCCACCCCCACCATACTACTACAAG
1 TCTCCACCACCACCATACTACTACAAG
**
3010 TCTCCACCACCACC-T--T-CT-C-CC
1 TCTCCACCACCACCATACTACTACAAG
* * *
3031 TCACCACCTCCACCATACTATTACAAG
1 TCTCCACCACCACCATACTACTACAAG
3058 TCTCCACCACCACCA
1 TCTCCACCACCACCA
3073 AAACACGTAG
Statistics
Matches: 117, Mismatches: 22, Indels: 40
0.65 0.12 0.22
Matches are distributed among these distances:
20 1 0.01
21 39 0.33
22 3 0.03
23 6 0.05
24 6 0.05
25 5 0.04
26 3 0.03
27 53 0.45
28 1 0.01
ACGTcount: A:0.27, C:0.49, G:0.03, T:0.20
Consensus pattern (27 bp):
TCTCCACCACCACCATACTACTACAAG
Found at i:3167 original size:27 final size:27
Alignment explanation
Indices: 3132--3262 Score: 90
Period size: 27 Copynumber: 5.3 Consensus size: 27
3122 GCCATCTCCT
3132 CCACCACCATACTATTACAAGTCCCCA
1 CCACCACCATACTATTACAAGTCCCCA
* *
3159 CCACCACC--A--GTT-C-A-TTCCCA
1 CCACCACCATACTATTACAAGTCCCCA
* *
3179 CCACCACCATACTACTACAAGTCTCCA
1 CCACCACCATACTATTACAAGTCCCCA
* ** *
3206 CCACCACC-T--T-CT-C-CCTCACCA
1 CCACCACCATACTATTACAAGTCCCCA
*
3227 CCTCCACCATACTATTACAAGTCCCCA
1 CCACCACCATACTATTACAAGTCCCCA
3254 CCACCACCA
1 CCACCACCA
3263 AAACACGTAG
Statistics
Matches: 76, Mismatches: 15, Indels: 26
0.65 0.13 0.22
Matches are distributed among these distances:
20 13 0.17
21 13 0.17
22 4 0.05
23 4 0.05
24 3 0.04
25 3 0.04
26 3 0.04
27 33 0.43
ACGTcount: A:0.29, C:0.50, G:0.03, T:0.18
Consensus pattern (27 bp):
CCACCACCATACTATTACAAGTCCCCA
Found at i:3467 original size:21 final size:21
Alignment explanation
Indices: 3443--3523 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 21
3433 TTACAAATCC
3443 CCACCACCACCAGTCCACTCT
1 CCACCACCACCAGTCCACTCT
* *
3464 CCACCCCCACCA-TACTACTACAAATCC
1 CCACCACCACCAGT-C--C-AC---TCT
3491 CCACCACCACCAGTCCACTCT
1 CCACCACCACCAGTCCACTCT
*
3512 CCACCTCCACCA
1 CCACCACCACCA
3524 TACTACTACA
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
20 1 0.02
21 25 0.53
23 1 0.02
24 4 0.09
25 1 0.02
27 14 0.30
28 1 0.02
ACGTcount: A:0.27, C:0.57, G:0.02, T:0.14
Consensus pattern (21 bp):
CCACCACCACCAGTCCACTCT
Found at i:3494 original size:27 final size:27
Alignment explanation
Indices: 3424--3551 Score: 95
Period size: 27 Copynumber: 5.2 Consensus size: 27
3414 CTCCTCCTCT
*
3424 ACCATACTATTACAAATCCCCACCACC
1 ACCATACTACTACAAATCCCCACCACC
* *
3451 ACCAGT-C--C-AC---TCTCCACCCCC
1 ACCA-TACTACTACAAATCCCCACCACC
3472 ACCATACTACTACAAATCCCCACCACC
1 ACCATACTACTACAAATCCCCACCACC
* *
3499 ACCAGT-C--C-AC---TCTCCACCTCC
1 ACCA-TACTACTACAAATCCCCACCACC
3520 ACCATACTACTACAAATCCCCACCACC
1 ACCATACTACTACAAATCCCCACCACC
3547 ACCAT
1 ACCAT
3552 CTCATTCACC
Statistics
Matches: 76, Mismatches: 9, Indels: 32
0.65 0.08 0.27
Matches are distributed among these distances:
20 2 0.03
21 28 0.37
23 2 0.03
24 8 0.11
25 1 0.01
27 33 0.43
28 2 0.03
ACGTcount: A:0.31, C:0.51, G:0.02, T:0.16
Consensus pattern (27 bp):
ACCATACTACTACAAATCCCCACCACC
Found at i:3587 original size:27 final size:26
Alignment explanation
Indices: 3512--3588 Score: 74
Period size: 27 Copynumber: 3.1 Consensus size: 26
3502 AGTCCACTCT
*
3512 CCACCTCCACCATACTACTACAAATCC
1 CCACCTCCACCATACTA-TACAAATCA
* *
3539 CCACCACCACCAT-C--T-C-ATTCA
1 CCACCTCCACCATACTATACAAATCA
3560 CCACCTCCACCATACTATTACAAATCA
1 CCACCTCCACCATACTA-TACAAATCA
3587 CC
1 CC
3589 CCCACCTCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
21 15 0.38
22 2 0.05
23 1 0.03
25 1 0.03
26 2 0.05
27 18 0.46
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.19
Consensus pattern (26 bp):
CCACCTCCACCATACTATACAAATCA
Done.