Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 43 of 125
Found at i:13260071 original size:21 final size:21
Alignment explanation
Indices: 13260037--13260104 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
13260027 ACCCATTAAG
*
13260037 CCCAAATCCTATTTAAACCAAA
1 CCCAAATTC-ATTTAAACCAAA
*
13260059 CCCACATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
13260080 CCCAAATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
13260101 CCCA
1 CCCA
13260105 TTTGAACCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
21 36 0.84
22 7 0.16
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (21 bp):
CCCAAATTCATTTAAACCAAA
Found at i:13260106 original size:15 final size:15
Alignment explanation
Indices: 13260088--13260117 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13260078 AACCCAAATT
13260088 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
13260103 CATTTGAACCAAACC
1 CATTTAAACCAAACC
13260118 AAATGAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:13260198 original size:11 final size:10
Alignment explanation
Indices: 13260154--13260201 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
13260144 AGTCAAACCA
*
13260154 TTGACCGATG
1 TTGACCGACG
* *
13260164 TTGACTGGCG
1 TTGACCGACG
*
13260174 TTGATCGACG
1 TTGACCGACG
13260184 TTGACCGACCG
1 TTGACCGA-CG
13260195 TTGACCG
1 TTGACCG
13260202 GTGTTGATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27
Consensus pattern (10 bp):
TTGACCGACG
Found at i:13260207 original size:21 final size:21
Alignment explanation
Indices: 13260183--13260222 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13260173 GTTGATCGAC
13260183 GTTGACCGACCGTTGACCGGT
1 GTTGACCGACCGTTGACCGGT
** *
13260204 GTTGATTGATCGTTGACCG
1 GTTGACCGACCGTTGACCG
13260223 TTGACTTTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.30
Consensus pattern (21 bp):
GTTGACCGACCGTTGACCGGT
Found at i:13260234 original size:20 final size:20
Alignment explanation
Indices: 13260209--13260250 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
13260199 CCGGTGTTGA
13260209 TTGATCGTTGACCGTTGACT
1 TTGATCGTTGACCGTTGACT
13260229 TTGATCGTTGACCGTTGACT
1 TTGATCGTTGACCGTTGACT
13260249 TT
1 TT
13260251 TTTGAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGATCGTTGACCGTTGACT
Found at i:13265897 original size:11 final size:11
Alignment explanation
Indices: 13265877--13265951 Score: 69
Period size: 11 Copynumber: 6.5 Consensus size: 11
13265867 AAGCCTCTTA
*
13265877 TCTTTCCTTTC
1 TCTTTTCTTTC
*
13265888 TCTTTTCTTTT
1 TCTTTTCTTTC
*
13265899 TCTCATTCATTTC
1 TCT-TTTC-TTTC
*
13265912 TTTTTTCTTTC
1 TCTTTTCTTTC
13265923 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
13265935 TATTTTCTTCC
1 TCTTTTCTTTC
13265946 TCTTTT
1 TCTTTT
13265952 AATCACACTT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
11 30 0.59
12 16 0.31
13 5 0.10
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:13265934 original size:12 final size:12
Alignment explanation
Indices: 13265879--13265943 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
13265869 GCCTCTTATC
*
13265879 TTTCCTTTCTCT
1 TTTCTTTTCTCT
13265891 TTTCTTTT-TCT
1 TTTCTTTTCTCT
* * *
13265902 CATTCATTTCTTT
1 -TTTCTTTTCTCT
13265915 TTTC-TTTCTCT
1 TTTCTTTTCTCT
*
13265926 TTTCTTTTCTAT
1 TTTCTTTTCTCT
13265938 TTTCTT
1 TTTCTT
13265944 CCTCTTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
11 13 0.30
12 28 0.65
13 2 0.05
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTCTTTTCTCT
Found at i:13266357 original size:21 final size:21
Alignment explanation
Indices: 13266321--13266388 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
13266311 ACCCATTAAG
*
13266321 CCCAAATCCTATTTAAACCAAA
1 CCCAAATTC-ATTTAAACCAAA
* *
13266343 CTCACATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
13266364 CCCAAATTCATTTAAACCAAA
1 CCCAAATTCATTTAAACCAAA
13266385 CCCA
1 CCCA
13266389 TTTGAACCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 35 0.85
22 6 0.15
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
CCCAAATTCATTTAAACCAAA
Found at i:13266390 original size:15 final size:15
Alignment explanation
Indices: 13266372--13266401 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13266362 AACCCAAATT
13266372 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
13266387 CATTTGAACCAAACC
1 CATTTAAACCAAACC
13266402 AAATGAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:13266482 original size:11 final size:10
Alignment explanation
Indices: 13266438--13266485 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
13266428 AGTCAAACCA
*
13266438 TTGACCGATG
1 TTGACCGACG
* *
13266448 TTGACTGGCG
1 TTGACCGACG
*
13266458 TTGATCGACG
1 TTGACCGACG
13266468 TTGACCGACCG
1 TTGACCGA-CG
13266479 TTGACCG
1 TTGACCG
13266486 GTGTTGATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27
Consensus pattern (10 bp):
TTGACCGACG
Found at i:13266491 original size:21 final size:21
Alignment explanation
Indices: 13266467--13266506 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13266457 GTTGATCGAC
13266467 GTTGACCGACCGTTGACCGGT
1 GTTGACCGACCGTTGACCGGT
** *
13266488 GTTGATTGATCGTTGACCG
1 GTTGACCGACCGTTGACCG
13266507 TTGACTTTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.30
Consensus pattern (21 bp):
GTTGACCGACCGTTGACCGGT
Found at i:13266518 original size:20 final size:20
Alignment explanation
Indices: 13266493--13266534 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
13266483 CCGGTGTTGA
13266493 TTGATCGTTGACCGTTGACT
1 TTGATCGTTGACCGTTGACT
13266513 TTGATCGTTGACCGTTGACT
1 TTGATCGTTGACCGTTGACT
13266533 TT
1 TT
13266535 TTTGAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGATCGTTGACCGTTGACT
Found at i:13286815 original size:112 final size:112
Alignment explanation
Indices: 13286618--13286835 Score: 359
Period size: 112 Copynumber: 1.9 Consensus size: 112
13286608 TGATGGGTTC
*
13286618 CACGAGACATGGGAACTGTTTAAGATACTATTTCGAAAAAGGCCGAATCACGGTATGGCGGAATG
1 CACGAGACATGGGAACTGCTTAAGATACTATTTCGAAAAAGGCCGAATCACGGTATGGCGGAATG
* *
13286683 GGAAGAGGAGCCCTGATGAATCGAACGTATAATGACGCTTAGGATTT
66 GCAAGAGGAGCCCTAATGAATCGAACGTATAATGACGCTTAGGATTT
*
13286730 CACGAGACATGGGAATTGCTTAAGATACTA-TTCTGAAAAA-GCTCGAATCACGGTATGGCGGAA
1 CACGAGACATGGGAACTGCTTAAGATACTATTTC-GAAAAAGGC-CGAATCACGGTATGGCGGAA
*
13286793 TGGCAGGAGGAGCCCTAATGAATCGAACGTATAATGACGCTTA
64 TGGCAAGAGGAGCCCTAATGAATCGAACGTATAATGACGCTTA
13286836 TGTGCTCATA
Statistics
Matches: 99, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
111 5 0.05
112 94 0.95
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (112 bp):
CACGAGACATGGGAACTGCTTAAGATACTATTTCGAAAAAGGCCGAATCACGGTATGGCGGAATG
GCAAGAGGAGCCCTAATGAATCGAACGTATAATGACGCTTAGGATTT
Found at i:13290340 original size:17 final size:16
Alignment explanation
Indices: 13290318--13290362 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
13290308 TGGCAATGTA
13290318 TTTCTTTTCTTTTCTCT
1 TTTCTTTTCTTTTCT-T
13290335 TTTCTTCTTC-TTTCTT
1 TTTCTT-TTCTTTTCTT
13290351 TTTC-TTTCTTTT
1 TTTCTTTTCTTTT
13290363 TGTGATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.12
15 4 0.15
16 5 0.19
17 11 0.42
18 3 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTTCTTTTCTT
Found at i:13290361 original size:10 final size:11
Alignment explanation
Indices: 13290318--13290363 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
13290308 TGGCAATGTA
13290318 TTTCTTTTCTT
1 TTTCTTTTCTT
13290329 TTCTCTTTTCTT
1 TT-TCTTTTCTT
*
13290341 CTTC-TTTCTT
1 TTTCTTTTCTT
13290351 TTTC-TTTCTT
1 TTTCTTTTCTT
13290361 TTT
1 TTT
13290364 GTGATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 18 0.56
11 4 0.12
12 10 0.31
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:13293332 original size:20 final size:20
Alignment explanation
Indices: 13293307--13293350 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
13293297 CATAAGATTT
13293307 AAAAGA-AACAAGTAAAAGTA
1 AAAAGATAA-AAGTAAAAGTA
*
13293327 AAAAGATAAAAGTAAATGTA
1 AAAAGATAAAAGTAAAAGTA
13293347 AAAA
1 AAAA
13293351 TGCGTTGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.70, C:0.02, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAAGATAAAAGTAAAAGTA
Found at i:13293338 original size:14 final size:14
Alignment explanation
Indices: 13293306--13293342 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
13293296 GCATAAGATT
13293306 TAAAAG-AAACAAG
1 TAAAAGTAAACAAG
13293319 TAAAAGTAAA-AAG
1 TAAAAGTAAACAAG
13293332 ATAAAAGTAAA
1 -TAAAAGTAAA
13293343 TGTAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.70, C:0.03, G:0.14, T:0.14
Consensus pattern (14 bp):
TAAAAGTAAACAAG
Found at i:13300843 original size:16 final size:17
Alignment explanation
Indices: 13300822--13300855 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13300812 TTTAAAACCC
13300822 TAAATA-CTAACCATTA
1 TAAATATCTAACCATTA
*
13300838 TAAATATCTAAGCATTA
1 TAAATATCTAACCATTA
13300855 T
1 T
13300856 TCTAACTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (17 bp):
TAAATATCTAACCATTA
Found at i:13303702 original size:141 final size:140
Alignment explanation
Indices: 13303442--13303704 Score: 400
Period size: 141 Copynumber: 1.9 Consensus size: 140
13303432 ATTTTTGGAG
* *
13303442 AGTGTCGGGATAGACTTGCCAACATACGCTTTAGCCAACTCTTTGTATATGGGTTGGGATATGCA
1 AGTGTCGGCATAGACTTGCCAACATACGCTTTAGCCAACTCTTTGTATAAGGGTTGGGATATGCA
* * *
13303507 TGCCTAAGACAACACTTAAATAAGAGTTCGCTTTGTTCAACACTATGCCGACACTTTTGGGGCAA
66 TGCCTAAGACAACACTTAAATAAGAGTTAGCTTTGTCCAACACTATGCCAACACTTTTGGGGCAA
13303572 CACTTTCCTA
131 CACTTTCCTA
* * *
13303582 AGTGTCGGCATAGACTTGCCGACATATGCTTTTGCCAACTCTTTTGTATAAGGGTTGGGATATGC
1 AGTGTCGGCATAGACTTGCCAACATACGCTTTAGCCAACTC-TTTGTATAAGGGTTGGGATATGC
** ** *
13303647 ATGCCTAAGGTAATGCTTAAATAAGAGTTAGCTTTGTCCAACACTATGGCAACACTTT
65 ATGCCTAAGACAACACTTAAATAAGAGTTAGCTTTGTCCAACACTATGCCAACACTTT
13303705 CCTAAGTGTT
Statistics
Matches: 109, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
140 37 0.34
141 72 0.66
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (140 bp):
AGTGTCGGCATAGACTTGCCAACATACGCTTTAGCCAACTCTTTGTATAAGGGTTGGGATATGCA
TGCCTAAGACAACACTTAAATAAGAGTTAGCTTTGTCCAACACTATGCCAACACTTTTGGGGCAA
CACTTTCCTA
Found at i:13303800 original size:126 final size:127
Alignment explanation
Indices: 13303567--13303829 Score: 413
Period size: 126 Copynumber: 2.1 Consensus size: 127
13303557 ACACTTTTGG
** * *
13303567 GGCAACACTTTCCTAAGTGTCGGCATAGACTTGCCGACATATGCTTTTGCCAACTCTTTTGTATA
1 GGCAACACTTTCCTAAGTGTCGGCATAGACTTGCCGACATACACTTTGGCCAACTCTTATGTATA
* *
13303632 AGGGTTGGGATATGCATGCCTAAGGTAATGCTTAAATAAGAGTTAGCTTTGTCCAACACTAT
66 AGGGTTGGGATATGCATGCCTAAGGCAATGCTTAAATAAGAGTTAGCTTTATCCAACACTAT
* *
13303694 GGCAACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACACTTTGGCCAACTC-TATGTATA
1 GGCAACACTTTCCTAAGTGTCGGCATAGACTTGCCGACATACACTTTGGCCAACTCTTATGTATA
* *
13303758 AGGGTTGGGATATGCATGCCTAAGGCAATGCTTAAATGAGAGTTGGCTTTATCCAACACTAT
66 AGGGTTGGGATATGCATGCCTAAGGCAATGCTTAAATAAGAGTTAGCTTTATCCAACACTAT
*
13303820 GCCAAC-CTTT
1 GGCAACACTTT
13303830 TTAAGGTTGC
Statistics
Matches: 125, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
125 4 0.03
126 70 0.56
127 51 0.41
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (127 bp):
GGCAACACTTTCCTAAGTGTCGGCATAGACTTGCCGACATACACTTTGGCCAACTCTTATGTATA
AGGGTTGGGATATGCATGCCTAAGGCAATGCTTAAATAAGAGTTAGCTTTATCCAACACTAT
Found at i:13303889 original size:38 final size:37
Alignment explanation
Indices: 13303816--13304047 Score: 274
Period size: 38 Copynumber: 6.3 Consensus size: 37
13303806 TTATCCAACA
* *
13303816 CTATGCCAACCTTTTT-AAGGTTGCCTTAAACAAGGT
1 CTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
* *
13303852 ATATCCCAACCTTTTTAAATGGTTGCCTTAGATAAGGT
1 CTATCCCAACCTTTTTAAA-GGTTGCCTTAGACAAGGT
* *
13303890 CTATCTCAACCTTTTT-AAGGTTGTCTTAGACAAGGT
1 CTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
* * *
13303926 CTATCCCAACCTTCTTTAAAGGTTGCCTCAAATAAGGT
1 CTATCCCAACCTT-TTTAAAGGTTGCCTTAGACAAGGT
* **
13303964 CTATCCCAACCTTTTTTAAAGCTTGCCTTAGACAAGAC
1 CTATCCCAACC-TTTTTAAAGGTTGCCTTAGACAAGGT
* * *
13304002 CTACCCCAACCTTTTTAAA-GTTGCCTTAGGCGA-GT
1 CTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
13304037 CTATCCCAACC
1 CTATCCCAACC
13304048 ATTCAGTAAA
Statistics
Matches: 165, Mismatches: 26, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
35 10 0.06
36 53 0.32
37 15 0.09
38 85 0.52
39 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (37 bp):
CTATCCCAACCTTTTTAAAGGTTGCCTTAGACAAGGT
Found at i:13303900 original size:74 final size:73
Alignment explanation
Indices: 13303816--13304047 Score: 288
Period size: 74 Copynumber: 3.2 Consensus size: 73
13303806 TTATCCAACA
* * *
13303816 CTATGCCAACCTTTTTAAGGTTGCCTTAAACAAGGTATATCCCAACCTTTTTAAATGGTTGCCTT
1 CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAA-GGTTGCCTT
13303881 AGATAAGGT
65 AGATAAGGT
* * *
13303890 CTATCTCAACCTTTTTAAGGTTGTCTTAGACAAGGTCTATCCCAACCTTCTTTAAAGGTTGCCTC
1 CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTT-TTTAAAGGTTGCCTT
*
13303955 AAATAAGGT
65 AGATAAGGT
* ** *
13303964 CTATCCCAACCTTTTTTAAAGCTTGCCTTAGACAAGACCTACCCCAACCTTTTTAAA-GTTGCCT
1 CTATCCCAACC-TTTTT-AAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCT
***
13304028 TAGGCGA-GT
64 TAGATAAGGT
13304037 CTATCCCAACC
1 CTATCCCAACC
13304048 ATTCAGTAAA
Statistics
Matches: 137, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
73 13 0.09
74 79 0.58
75 17 0.12
76 28 0.20
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (73 bp):
CTATCCCAACCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAAGGTTGCCTTA
GATAAGGT
Found at i:13303971 original size:112 final size:109
Alignment explanation
Indices: 13303816--13304047 Score: 295
Period size: 112 Copynumber: 2.1 Consensus size: 109
13303806 TTATCCAACA
* * *
13303816 CTATGCCAACCTTTTTAAGGTTGCCTTAAACAAGGTATATCCCAACC-TTTTTAAATGGTTGCCT
1 CTATCCCAACCTTTTTAAGGTTGCCTCAAACAAGGTATATCCCAACCTTTTTTAAA-GCTTGCCT
* ** * * * *
13303880 TAGATAAGGTCTATCTCAACCTTTTTAAGGTTGTCTTAGACAAGGT
65 TAGACAAGACCTACCCCAACCTTTTTAAAGTTGCCTTAGACAA-GT
* *
13303926 CTATCCCAACCTTCTTTAAAGGTTGCCTCAAATAAGGTCTATCCCAACCTTTTTTAAAGCTTGCC
1 CTATCCCAACCTT-TTT-AAGGTTGCCTCAAACAAGGTATATCCCAACCTTTTTTAAAGCTTGCC
* *
13303991 TTAGACAAGACCTACCCCAACCTTTTTAAAGTTGCCTTAGGCGAGT
64 TTAGACAAGACCTACCCCAACCTTTTTAAAGTTGCCTTAGACAAGT
13304037 CTATCCCAACC
1 CTATCCCAACC
13304048 ATTCAGTAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
110 12 0.11
111 16 0.15
112 69 0.66
113 8 0.08
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (109 bp):
CTATCCCAACCTTTTTAAGGTTGCCTCAAACAAGGTATATCCCAACCTTTTTTAAAGCTTGCCTT
AGACAAGACCTACCCCAACCTTTTTAAAGTTGCCTTAGACAAGT
Found at i:13304851 original size:43 final size:43
Alignment explanation
Indices: 13304768--13304852 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
13304758 AAATTATCCT
* *
13304768 TAAACCCTAAACTCATAACCCCGAACTCTAAAACTATAAACAC
1 TAAACCCCAAACTCATAACCCCAAACTCTAAAACTATAAACAC
* * *
13304811 TAAACCCCAAACTCATAATCCCAAATCTTTAAACCT-TAAACA
1 TAAACCCCAAACTCATAACCCCAAA-CTCTAAAACTATAAACA
13304853 TGAACCTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 28 0.78
44 8 0.22
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (43 bp):
TAAACCCCAAACTCATAACCCCAAACTCTAAAACTATAAACAC
Found at i:13311747 original size:21 final size:20
Alignment explanation
Indices: 13311697--13311749 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
13311687 TTGTGCTAGC
*
13311697 TCTACCAATACAAGTATGAA
1 TCTACCGATACAAGTATGAA
*
13311717 TTCTATCGATACAAGTCATGCAA
1 -TCTACCGATACAAGT-ATG-AA
13311740 -CTACCGATAC
1 TCTACCGATAC
13311750 CAAAAACTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 22 0.81
22 3 0.11
23 2 0.07
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (20 bp):
TCTACCGATACAAGTATGAA
Found at i:13317764 original size:140 final size:141
Alignment explanation
Indices: 13317511--13317793 Score: 541
Period size: 140 Copynumber: 2.0 Consensus size: 141
13317501 AACGAAGCTC
*
13317511 GAAGACAAAAGTAAAAGGTATATTTTTATTGGGTATGATGAGAAGACAAAAGCAAGAAGGTGATG
1 GAAGACAAAAGCAAAAGGTATATTTTTATTGGGTATGATGAGAAGACAAAAGCAAGAAGGTGATG
13317576 GTGAGTCGTGATGTGTGAGTAAACGAAGCAAGCGAGTGGGACTGGAATAATTCAACAAAGGTTAT
66 GTGAGTCGTGATGTGTGAGTAAACGAAGCAAGCGAGTGGGACTGGAATAATTCAACAAAGGTTAT
13317641 CATTGAAGTTG
131 CATTGAAGTTG
13317652 GAAGACAAAAGCAAAAGGTATA-TTTTATTGGGTATGATGAGAAGACAAAAGCAAGAAGGTGATG
1 GAAGACAAAAGCAAAAGGTATATTTTTATTGGGTATGATGAGAAGACAAAAGCAAGAAGGTGATG
*
13317716 GTGAGTCGTGATGTGTGAGTAAACGAAGCAAGCGAGTGGGACTGGAATAATTCGACAAAGGTTAT
66 GTGAGTCGTGATGTGTGAGTAAACGAAGCAAGCGAGTGGGACTGGAATAATTCAACAAAGGTTAT
13317781 CATTGAAGTTG
131 CATTGAAGTTG
13317792 GA
1 GA
13317794 GAATCTTCAG
Statistics
Matches: 140, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
140 119 0.85
141 21 0.15
ACGTcount: A:0.38, C:0.08, G:0.30, T:0.23
Consensus pattern (141 bp):
GAAGACAAAAGCAAAAGGTATATTTTTATTGGGTATGATGAGAAGACAAAAGCAAGAAGGTGATG
GTGAGTCGTGATGTGTGAGTAAACGAAGCAAGCGAGTGGGACTGGAATAATTCAACAAAGGTTAT
CATTGAAGTTG
Found at i:13321252 original size:25 final size:25
Alignment explanation
Indices: 13321201--13321253 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
13321191 TGTTTAATTC
* *
13321201 TATACATTGGGTTGAATGCTAGTTG
1 TATACATTCGGTTAAATGCTAGTTG
*
13321226 TATACATTTCGGTTAAATGTTAG-TG
1 TATACA-TTCGGTTAAATGCTAGTTG
13321251 TAT
1 TAT
13321254 TTTGATTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (25 bp):
TATACATTCGGTTAAATGCTAGTTG
Found at i:13321507 original size:38 final size:36
Alignment explanation
Indices: 13321417--13321792 Score: 258
Period size: 38 Copynumber: 10.1 Consensus size: 36
13321407 CTTTACATGT
* * * * * *
13321417 GTCTATCCCAACCTTTTCAAGGTTGCTTTAAAC-GG
1 GTCTATCCTAACTTTTTAAAGGTTGCCTTAGACAAG
*
13321452 GTCTAT-CTCAACCTTTTTAAAAGGTTACCTTAGACAAG
1 GTCTATCCT-AA-CTTTTT-AAAGGTTGCCTTAGACAAG
*
13321490 GTCTATCCTAACTTTTTTAAAAGGTTGTCTTAGACAAG
1 GTCTATCCTAAC-TTTTT-AAAGGTTGCCTTAGACAAG
* * *
13321528 GTTTATCCCTATCTTTTTAAATGGTTGTCTTAGACAAG
1 GTCTAT-CCTAACTTTTTAAA-GGTTGCCTTAGACAAG
* * * * ** *
13321566 ATCTATCCCAACCTTTTCAAGGTTGTTTTAGAC-AT
1 GTCTATCCTAACTTTTTAAAGGTTGCCTTAGACAAG
* *
13321601 GTCTATCCTAACCTTTTTTAAAGGTTGCCATAGATAAG
1 GTCTATCCTAA-C-TTTTTAAAGGTTGCCTTAGACAAG
* * * * * *
13321639 ATATATCCTAACCTTTTCAAGGTTGTCTTAAACAAG
1 GTCTATCCTAACTTTTTAAAGGTTGCCTTAGACAAG
* * *
13321675 GTTTAT-CTCAACCGTTTTTAGAGGTTGCCTTAGATAAG
1 GTCTATCCT-AA-C-TTTTTAAAGGTTGCCTTAGACAAG
*
13321713 GTCTATCCCAACCTTTTTTAAAAGGTTGCCTTAGACAAG
1 GTCTATCCTAA-C-TTTTT-AAAGGTTGCCTTAGACAAG
** * *
13321752 ACCTATCCCAACCTTTTTAAAGGTTGGCCTT-GACTAG
1 GTCTATCCTAA-CTTTTTAAAGGTT-GCCTTAGACAAG
13321789 GTCT
1 GTCT
13321793 TTTCCAACCC
Statistics
Matches: 270, Mismatches: 54, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
34 1 0.00
35 20 0.07
36 42 0.16
37 57 0.21
38 114 0.42
39 36 0.13
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (36 bp):
GTCTATCCTAACTTTTTAAAGGTTGCCTTAGACAAG
Found at i:13321720 original size:74 final size:72
Alignment explanation
Indices: 13321417--13321801 Score: 326
Period size: 76 Copynumber: 5.2 Consensus size: 72
13321407 CTTTACATGT
* *
13321417 GTCTATCCCAACCTTTTCAAGGTTG-CTTTAAACGGGTCTATCTCAACCTTTTTAAAAGGTTACC
1 GTCTATCCCAACCTTTTCAAGGTTGTC-TTAAACAGGTCTATCTCAACCTTTTT-AAAGGTTGCC
13321481 TTAGACAAG
64 TTAGACAAG
* * * * * * * *
13321490 GTCTATCCTAACTTTTTTAAAAGGTTGTCTTAGACAAGGTTTATCCCTATCTTTTTAAATGGTTG
1 GTCTATCCCAAC-CTTTT-CAAGGTTGTCTTAAAC-AGGTCTATCTCAACCTTTTTAAA-GGTTG
*
13321555 TCTTAGACAAG
62 CCTTAGACAAG
* * * *
13321566 ATCTATCCCAACCTTTTCAAGGTTGTTTTAGACATGTCTATC-CTAACCTTTTTTAAAGGTTGCC
1 GTCTATCCCAACCTTTTCAAGGTTGTCTTAAACAGGTCTATCTC-AACC-TTTTTAAAGGTTGCC
* *
13321630 ATAGATAAG
64 TTAGACAAG
* * * * *
13321639 ATATATCCTAACCTTTTCAAGGTTGTCTTAAACAAGGTTTATCTCAACCGTTTTTAGAGGTTGCC
1 GTCTATCCCAACCTTTTCAAGGTTGTCTTAAAC-AGGTCTATCTCAACC-TTTTTAAAGGTTGCC
*
13321704 TTAGATAAG
64 TTAGACAAG
* * * ** *
13321713 GTCTATCCCAACCTTTTTTAAAAGGTTGCCTTAGACAAGACCTATCCCAACCTTTTTAAAGGTTG
1 GTCTATCCCAACC--TTTT-CAAGGTTGTCTTAAAC-AGGTCTATCTCAACCTTTTTAAAGGTT-
*
13321778 GCCTT-GACTAG
61 GCCTTAGACAAG
* *
13321789 GTCTTTTCCAACC
1 GTCTATCCCAACC
13321802 CTTCAATAAA
Statistics
Matches: 252, Mismatches: 47, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
72 1 0.00
73 62 0.25
74 69 0.27
75 20 0.08
76 70 0.28
77 30 0.12
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (72 bp):
GTCTATCCCAACCTTTTCAAGGTTGTCTTAAACAGGTCTATCTCAACCTTTTTAAAGGTTGCCTT
AGACAAG
Found at i:13325159 original size:21 final size:21
Alignment explanation
Indices: 13325133--13325174 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13325123 TGTAAATTCA
13325133 GGTTCAACACTTGGCTCAACT
1 GGTTCAACACTTGGCTCAACT
* **
13325154 GGTTCATCTTTTGGCTCAACT
1 GGTTCAACACTTGGCTCAACT
13325175 TTTGGCTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (21 bp):
GGTTCAACACTTGGCTCAACT
Found at i:13325178 original size:12 final size:12
Alignment explanation
Indices: 13325161--13325190 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
13325151 ACTGGTTCAT
13325161 CTTTTGGCTCAA
1 CTTTTGGCTCAA
13325173 CTTTTGGCTCAA
1 CTTTTGGCTCAA
*
13325185 CGTTTG
1 CTTTTG
13325191 TAGGTTACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (12 bp):
CTTTTGGCTCAA
Found at i:13334533 original size:142 final size:142
Alignment explanation
Indices: 13334365--13334888 Score: 482
Period size: 151 Copynumber: 3.5 Consensus size: 142
13334355 AATCAAAAGT
* *
13334365 TTTCTTTTTATTAAAAAAAATCACTACTTTACTTCAAAATCAAAACTTTTATTTAGAAATAGTTA
1 TTTCTTTTT-TTAAAGAAAATCACTACTTTACTTAAAAATC-AAACTTTTATTTAGAAATAGTTA
* ** *
13334430 AAAAATTAAAATTTTG-T-TTAAAC-TTTTCTTTAAAATCACTAAAAAAACATATTTTTATTTTT
64 AAAAATCAAAATTTTGTTATTAAACTTTTTCTTTAAAATCACTAAAAAAA-ATAGATTT-TTATT
*
13334492 TTTTAAAAATCTAAGC
127 TTTTAAAAATCTAAAC
*
13334508 TTTCTTTTTTTAATGAAAATCACTACTTTACTTAAAAATCCAAACTTTTA-TTACGAAATAGTTA
1 TTTCTTTTTTTAAAGAAAATCACTACTTTACTTAAAAAT-CAAACTTTTATTTA-GAAATAGTT-
* *
13334572 AAAAAATCAAAATTTTGTTCAAAAATTTAACTTTTTCTTTAAAATGACTAAAAAAAATAGATTTT
63 AAAAAATCAAAATTTTGTT-----ATTAAACTTTTTCTTTAAAATCACTAAAAAAAATAGATTTT
*
13334637 TATTTTTTAAAAATCTAAAT
123 TATTTTTTAAAAATCTAAAC
* * * * * *
13334657 TTTCTCTTTTTAAAGAGAATCACTATTTTATTTAAAAAATCAAACTTTTATTTCGAAATAGTAAA
1 TTTCTTTTTTTAAAGAAAATCACTACTTTACTT-AAAAATCAAACTTTTATTTAGAAATAGT-TA
* * * * * *
13334722 AAAAATCAAAACTTTATATAAAAAATTGAACTTTTTCTTTAAAATAACTAAAAATATATATATTT
64 AAAAATCAAAA-TTT-TGT----TATTAAACTTTTTCTTTAAAATCACTAAAAA-AAATAGATTT
* *
13334787 TTA-TTTTTAAAAATATAAAA
122 TTATTTTTTAAAAATCTAAAC
* * * * * ** *
13334807 TTTCTCTTCTTTAAAGAAAATCACTAATTTTCATAAAAATCAAAACATTTATTTCTAAATTGTTT
1 TTTCT-TTTTTTAAAGAAAATCACTACTTTACTTAAAAATC-AAACTTTTATTTAGAAATAG-TT
*
13334872 AAAAAACCAAAACTTTT
63 AAAAAATCAAAA-TTTT
13334889 CTCAAAATCA
Statistics
Matches: 319, Mismatches: 38, Indels: 41
0.80 0.10 0.10
Matches are distributed among these distances:
141 3 0.01
142 45 0.14
143 26 0.08
144 1 0.00
149 76 0.24
150 78 0.24
151 89 0.28
152 1 0.00
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.42
Consensus pattern (142 bp):
TTTCTTTTTTTAAAGAAAATCACTACTTTACTTAAAAATCAAACTTTTATTTAGAAATAGTTAAA
AAATCAAAATTTTGTTATTAAACTTTTTCTTTAAAATCACTAAAAAAAATAGATTTTTATTTTTT
AAAAATCTAAAC
Found at i:13334643 original size:151 final size:149
Alignment explanation
Indices: 13334453--13334888 Score: 502
Period size: 151 Copynumber: 2.9 Consensus size: 149
13334443 TTGTTTAAAC
* **
13334453 TTTTCTTTAAAATCACTAAAAAAACAT-ATTTTTATTTTTTTTTAAAAATCTAAGCTTTCTTTTT
1 TTTTCTTTAAAATAACTAAAAAAA-ATAATTTTTA---TTTTTTAAAAATCTAAAATTTCTTTTT
* * *
13334517 TTAATGAAAATCACTACTTTACTTAAAAATCCAAACTTTTATTACGAAATAGTTAAAAAAATCAA
62 TTAAAGAAAATCACTAATTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAA
* * *
13334582 AATTTTGT-TCAAAAATTTAACT
127 AATTTTATATAAAAAATTGAACT
* * *
13334604 TTTTCTTTAAAATGACTAAAAAAAATAGATTTTTATTTTTTAAAAATCTAAATTTTCTCTTTTTA
1 TTTTCTTTAAAATAACTAAAAAAAATA-ATTTTTATTTTTTAAAAATCTAAAATTTCTTTTTTTA
* * * *
13334669 AAGAGAATCACTATTTTATTTAAAAAAT-CAAACTTTTATTTCGAAATAGTAAAAAAAATCAAAA
65 AAGAAAATCACTAATTTACTT-AAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAA
*
13334733 CTTTATATAAAAAATTGAACT
129 TTTTATATAAAAAATTGAACT
* * *
13334754 TTTTCTTTAAAATAACTAAAAATATATATATTTTTA-TTTTTAAAAATATAAAATTTCTCTTCTT
1 TTTTCTTTAAAATAACTAAAAA-AAATA-ATTTTTATTTTTTAAAAATCTAAAATTTCT-TTTTT
* * * * * * * *
13334818 TAAAGAAAATCACTAATTTTCATAAAAATCAAAACATTTATTTCTAAATTGTTTAAAAAACCAAA
63 TAAAGAAAATCACTAATTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAA
13334883 ACTTTT
128 A-TTTT
13334889 CTCAAAATCA
Statistics
Matches: 243, Mismatches: 34, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
149 82 0.34
150 67 0.28
151 84 0.35
152 10 0.04
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.42
Consensus pattern (149 bp):
TTTTCTTTAAAATAACTAAAAAAAATAATTTTTATTTTTTAAAAATCTAAAATTTCTTTTTTTAA
AGAAAATCACTAATTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAATT
TTATATAAAAAATTGAACT
Found at i:13334811 original size:150 final size:146
Alignment explanation
Indices: 13334453--13334887 Score: 512
Period size: 149 Copynumber: 2.9 Consensus size: 146
13334443 TTGTTTAAAC
* * * ** *
13334453 TTTTCTTTAAAATCACTAAAAAAACATATTTTTATTTTTTTTTAAAAATCTAAGCTTTCTTTTTT
1 TTTTCTTTAAAATAACTAAAAAAA-ATA-TATT-TTTATTTTTAAAAATCTAAAATTTCTCTTTT
* * *
13334518 TAATGAAAATCACTACTTTACTTAAAAATCCAAACTTTTATTACGAAATAGTTAAAAAAATCAAA
63 TAAAGAAAATCACTATTTTA-TTAAAAAT-CAAACTTTTATTTCGAAATAGTTAAAAAAATCAAA
* * * *
13334583 ATTTTGTTCAAAAATTTAACT
126 ACTTTATTAAAAAATTGAACT
* * *
13334604 TTTTCTTTAAAATGACTAAAAAAAATAGATTTTTATTTTTTAAAAATCTAAATTTTCTCTTTTTA
1 TTTTCTTTAAAATAACTAAAAAAAATATATTTTTA-TTTTTAAAAATCTAAAATTTCTCTTTTTA
* *
13334669 AAGAGAATCACTATTTTATTTAAAAAATCAAACTTTTATTTCGAAATAGTAAAAAAAATCAAAAC
65 AAGAAAATCACTATTTTA-TT-AAAAATCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAAC
13334734 TTTATATAAAAAATTGAACT
128 TTTAT-TAAAAAATTGAACT
* *
13334754 TTTTCTTTAAAATAACTAAAAATATATATATTTTTATTTTTAAAAATATAAAATTTCTCTTCTTT
1 TTTTCTTTAAAATAACTAAAAA-AAATATATTTTTATTTTTAAAAATCTAAAATTTCTCTT-TTT
* * * * *
13334819 AAAGAAAATCACTAATTTTCA-TAAAAATCAAAACATTTATTTCTAAATTGTTTAAAAAACCAAA
64 AAAGAAAATCACT-ATTTT-ATTAAAAATC-AAACTTTTATTTCGAAATAGTTAAAAAAATCAAA
13334883 ACTTT
126 ACTTT
13334888 TCTCAAAATC
Statistics
Matches: 247, Mismatches: 29, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
148 3 0.01
149 83 0.34
150 72 0.29
151 83 0.34
152 5 0.02
153 1 0.00
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.42
Consensus pattern (146 bp):
TTTTCTTTAAAATAACTAAAAAAAATATATTTTTATTTTTAAAAATCTAAAATTTCTCTTTTTAA
AGAAAATCACTATTTTATTAAAAATCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
ATTAAAAAATTGAACT
Found at i:13334819 original size:24 final size:24
Alignment explanation
Indices: 13334770--13334821 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
13334760 TTAAAATAAC
* *
13334770 TAAAAATATATATATTTTTATTTT
1 TAAAAATATATAAATTTCTATTTT
*
13334794 TAAAAATATA-AAATTTCTCTTCTT
1 TAAAAATATATAAATTTCTATT-TT
13334818 TAAA
1 TAAA
13334822 GAAAATCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAAAATATATAAATTTCTATTTT
Found at i:13349719 original size:40 final size:40
Alignment explanation
Indices: 13349645--13349720 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
13349635 TTTTTAGGGA
* * *
13349645 TTTGTTACAACGTAGACATGTTACGTCGCGACGAAGGGGG
1 TTTGTTACAACATAGACATGCTACGTCGCAACGAAGGGGG
* * *
13349685 TTTGTTGCAACATAGACATGCTATGTTGCAACGAAG
1 TTTGTTACAACATAGACATGCTACGTCGCAACGAAG
13349721 AAGGCAGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (40 bp):
TTTGTTACAACATAGACATGCTACGTCGCAACGAAGGGGG
Found at i:13358019 original size:16 final size:16
Alignment explanation
Indices: 13357998--13358033 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
13357988 AAATAATCCC
*
13357998 AAAATTACAAGTCTCA
1 AAAATTAAAAGTCTCA
*
13358014 AAAATTAAAATTCTCA
1 AAAATTAAAAGTCTCA
13358030 AAAA
1 AAAA
13358034 ACACTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (16 bp):
AAAATTAAAAGTCTCA
Found at i:13361439 original size:7 final size:7
Alignment explanation
Indices: 13361429--13361458 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
13361419 AAATACAAAT
13361429 AAACTGA
1 AAACTGA
13361436 AAACTGA
1 AAACTGA
13361443 AAACTGA
1 AAACTGA
13361450 AAACT-A
1 AAACTGA
13361456 AAA
1 AAA
13361459 GTCTAAGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (7 bp):
AAACTGA
Found at i:13363624 original size:26 final size:23
Alignment explanation
Indices: 13363578--13363625 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
13363568 AAATAAAAAT
13363578 AAAAAAAATTATCTAAAAGTTAC
1 AAAAAAAATTATCTAAAAGTTAC
*
13363601 AAAATAAAATTGTCTCAAACAGTTA
1 AAAA-AAAATTATCT-AAA-AGTTA
13363626 TTGTTCCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 9 0.43
25 3 0.14
26 5 0.24
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.27
Consensus pattern (23 bp):
AAAAAAAATTATCTAAAAGTTAC
Found at i:13364441 original size:17 final size:17
Alignment explanation
Indices: 13364419--13364454 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
13364409 AAGTAGTATA
13364419 AACAAATTTAATAGAGG
1 AACAAATTTAATAGAGG
13364436 AACAAATTTAATAGAGG
1 AACAAATTTAATAGAGG
13364453 AA
1 AA
13364455 TTGAAGTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (17 bp):
AACAAATTTAATAGAGG
Found at i:13365519 original size:26 final size:26
Alignment explanation
Indices: 13365490--13365713 Score: 279
Period size: 26 Copynumber: 8.5 Consensus size: 26
13365480 ACCGTAAACA
* *
13365490 AATAAATAGCAGGCCTTAAGCCAGTG
1 AATAAATAGCAGGCCTTGAGCCGGTG
*
13365516 AATAAATAGCAGGCCTTAAGCCGGTG
1 AATAAATAGCAGGCCTTGAGCCGGTG
**
13365542 AATAAATAGCAGGCCTCAAGCCGGTG
1 AATAAATAGCAGGCCTTGAGCCGGTG
* * * * *
13365568 AATATATAACAAGCTTTGAGCCGATG
1 AATAAATAGCAGGCCTTGAGCCGGTG
*
13365594 AATAAATAGCAGGCCATGAGCCGGTG
1 AATAAATAGCAGGCCTTGAGCCGGTG
13365620 AATATATATAGCAGGCCTTGAGCCGGTG
1 AATA-A-ATAGCAGGCCTTGAGCCGGTG
* *
13365648 AATAAATAGCAGGCCTCGAGCCGATG
1 AATAAATAGCAGGCCTTGAGCCGGTG
* *
13365674 AATAATTAGCAGG-CTTCGACCCGGTG
1 AATAAATAGCAGGCCTT-GAGCCGGTG
13365700 AATAAATAGCAGGC
1 AATAAATAGCAGGC
13365714 TTCGTGCCGG
Statistics
Matches: 171, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
25 2 0.01
26 143 0.84
27 2 0.01
28 24 0.14
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (26 bp):
AATAAATAGCAGGCCTTGAGCCGGTG
Found at i:13365725 original size:106 final size:104
Alignment explanation
Indices: 13365490--13365713 Score: 315
Period size: 106 Copynumber: 2.1 Consensus size: 104
13365480 ACCGTAAACA
* *
13365490 AATAAATAGCAGGCCTTAAGCCAGTGAATAAATAGCAGGCCTTAAGCCGGTGAATAAATAGCAGG
1 AATAAATAGCAGGCCTTGAGCCGGTGAATAAATAGCAGGCCTTAAGCCGGTGAATAAATAGCAGG
* * *
13365555 CCTCAAGCCGGTGAATATATAACAAGCTTTGAGCCGATG
66 CCTCAAGCCGATGAATATATAACAAGCTTCGACCCGATG
* *
13365594 AATAAATAGCAGGCCATGAGCCGGTGAATATATATAGCAGGCCTTGAGCCGGTGAATAAATAGCA
1 AATAAATAGCAGGCCTTGAGCCGGTGAATA-A-ATAGCAGGCCTTAAGCCGGTGAATAAATAGCA
* * * *
13365659 GGCCTCGAGCCGATGAATA-ATTAGCAGGCTTCGACCCGGTG
64 GGCCTCAAGCCGATGAATATA-TAACAAGCTTCGACCCGATG
13365700 AATAAATAGCAGGC
1 AATAAATAGCAGGC
13365714 TTCGTGCCGG
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
104 27 0.25
105 2 0.02
106 77 0.73
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (104 bp):
AATAAATAGCAGGCCTTGAGCCGGTGAATAAATAGCAGGCCTTAAGCCGGTGAATAAATAGCAGG
CCTCAAGCCGATGAATATATAACAAGCTTCGACCCGATG
Found at i:13367503 original size:16 final size:17
Alignment explanation
Indices: 13367470--13367503 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13367460 ATGAGTTAGA
*
13367470 ATAATGTTTAGATATTT
1 ATAATGGTTAGATATTT
13367487 ATAATGGTTAG-TATTT
1 ATAATGGTTAGATATTT
13367503 A
1 A
13367504 AGGTTTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATAATGGTTAGATATTT
Found at i:13367612 original size:21 final size:21
Alignment explanation
Indices: 13367588--13367627 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13367578 TGCATAAATT
*
13367588 GTAGTCGATGTCGCGACATAG
1 GTAGTAGATGTCGCGACATAG
**
13367609 GTAGTATTTGTCGCGACAT
1 GTAGTAGATGTCGCGACAT
13367628 TGCCTTCAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
GTAGTAGATGTCGCGACATAG
Found at i:13369150 original size:24 final size:24
Alignment explanation
Indices: 13369118--13369164 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
13369108 TCTTTAATTT
13369118 TCTTAAAAC-TGCATTGACATATTA
1 TCTTAAAACTTGCATT-ACATATTA
* *
13369142 TCTTCAAACTTTCATTACATATT
1 TCTTAAAACTTGCATTACATATT
13369165 CTTATTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (24 bp):
TCTTAAAACTTGCATTACATATTA
Found at i:13373618 original size:14 final size:14
Alignment explanation
Indices: 13373588--13373641 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
13373578 CATAAACCAA
13373588 AAATAAATAAGAA-AC
1 AAAT-AATAA-AATAC
13373603 AAATAATAAAATAC
1 AAATAATAAAATAC
* *
13373617 AAAAAATAAAATAA
1 AAATAATAAAATAC
13373631 AAATAA-AAAAT
1 AAATAATAAAAT
13373642 TGTATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.20
14 24 0.69
15 4 0.11
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.17
Consensus pattern (14 bp):
AAATAATAAAATAC
Found at i:13379785 original size:40 final size:39
Alignment explanation
Indices: 13379706--13379785 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
13379696 GAAATTTTTA
* * * ** *
13379706 GGGGTTTGTCGCGACGTGGACATGTATGTTGCGATGAAG
1 GGGGTTTGTCGCAACATAGACATGTATGTAACGAAGAAG
*
13379745 GGGGTTTGTTGCAACATAGACATGCTATGTAACGAAGAAG
1 GGGGTTTGTCGCAACATAGACATG-TATGTAACGAAGAAG
13379785 G
1 G
13379786 CAAATTCATG
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
39 20 0.61
40 13 0.39
ACGTcount: A:0.25, C:0.12, G:0.36, T:0.26
Consensus pattern (39 bp):
GGGGTTTGTCGCAACATAGACATGTATGTAACGAAGAAG
Found at i:13380343 original size:15 final size:15
Alignment explanation
Indices: 13380302--13380368 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
13380292 AGAAGCAAAG
* *
13380302 GAAGACGCTGAAAAA
1 GAAGAAGCTGAGAAA
*
13380317 GACACAAG-TGAGAAA
1 GA-AGAAGCTGAGAAA
*
13380332 G-AGAAGCTTGAGGAA
1 GAAGAAGC-TGAGAAA
*
13380347 GAAGAAGCAGAGAAA
1 GAAGAAGCTGAGAAA
13380362 GAAGAAG
1 GAAGAAG
13380369 AAAAAAGAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
13 4 0.10
15 28 0.68
16 9 0.22
ACGTcount: A:0.52, C:0.09, G:0.33, T:0.06
Consensus pattern (15 bp):
GAAGAAGCTGAGAAA
Found at i:13393009 original size:35 final size:35
Alignment explanation
Indices: 13392931--13393009 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
13392921 GGTGACAGGC
* *
13392931 ATGACCCTTGGGTCAATAGGGAGCAAATAAGCATC
1 ATGACCCTTGGGTCAATAGGGAGCAAATAAGAATA
* *
13392966 ATGA-CCTTGGTGTCAATAGGGAGTAAA-ACGAATA
1 ATGACCCTTGG-GTCAATAGGGAGCAAATAAGAATA
13393000 ATGACCCTTG
1 ATGACCCTTG
13393010 AAGTTCAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 14 0.37
35 24 0.63
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (35 bp):
ATGACCCTTGGGTCAATAGGGAGCAAATAAGAATA
Found at i:13395077 original size:36 final size:36
Alignment explanation
Indices: 13395037--13395219 Score: 278
Period size: 36 Copynumber: 5.1 Consensus size: 36
13395027 GTGAAAGTGG
*
13395037 ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
1 ATATGTGGGTATGTTATTCATGTCATGTGACAGTAA
* * *
13395073 ATATGT-GGTATGTTATTCATGCCATGAGATAGTAA
1 ATATGTGGGTATGTTATTCATGTCATGTGACAGTAA
13395108 ATATGTGGGTATGTTATTCATGTCATGTGACAGTAA
1 ATATGTGGGTATGTTATTCATGTCATGTGACAGTAA
* *
13395144 ATATTTGGGTATGTTATTCATGTCATGAGACAGTAA
1 ATATGTGGGTATGTTATTCATGTCATGTGACAGTAA
* * *
13395180 ATATGTGGGTATGTTATTCATTTCATGTGTCAGTGA
1 ATATGTGGGTATGTTATTCATGTCATGTGACAGTAA
13395216 ATAT
1 ATAT
13395220 ATTGTGCTAA
Statistics
Matches: 134, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
35 33 0.25
36 101 0.75
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.39
Consensus pattern (36 bp):
ATATGTGGGTATGTTATTCATGTCATGTGACAGTAA
Found at i:13395642 original size:23 final size:23
Alignment explanation
Indices: 13395612--13395658 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
13395602 ATTAAATGTG
13395612 TTAAAAGTTAATGTGATTTATGC
1 TTAAAAGTTAATGTGATTTATGC
13395635 TTAAAAGTTAATGTGATTTATGC
1 TTAAAAGTTAATGTGATTTATGC
13395658 T
1 T
13395659 CAAATGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (23 bp):
TTAAAAGTTAATGTGATTTATGC
Found at i:13395670 original size:23 final size:23
Alignment explanation
Indices: 13395621--13395675 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
13395611 GTTAAAAGTT
* **
13395621 AATGTGATTTATGCTTAAAAGTT
1 AATGTGATTTATGCTCAAAAGAG
*
13395644 AATGTGATTTATGCTCAAATGAG
1 AATGTGATTTATGCTCAAAAGAG
13395667 AATGTGATT
1 AATGTGATT
13395676 AATGTGTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (23 bp):
AATGTGATTTATGCTCAAAAGAG
Found at i:13411123 original size:29 final size:29
Alignment explanation
Indices: 13411081--13411141 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
13411071 ATACTGCTTA
* *
13411081 CAAAATATAGCGAATTGAGGTGGTATCTG
1 CAAAATATAGCGAATTGAGGTGATATCCG
13411110 CAAAATATAGCGAATTGAGGTGATATCCG
1 CAAAATATAGCGAATTGAGGTGATATCCG
13411139 CAA
1 CAA
13411142 GTATACGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (29 bp):
CAAAATATAGCGAATTGAGGTGATATCCG
Found at i:13416477 original size:20 final size:21
Alignment explanation
Indices: 13416454--13416501 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
13416444 TAGTTGTTCT
13416454 GGTAGAAGC-ATACTTGTATC
1 GGTAGAAGCTATACTTGTATC
* *
13416474 GGTAGAA-CTGTAGTTGTATC
1 GGTAGAAGCTATACTTGTATC
13416494 GGTAGAAG
1 GGTAGAAG
13416502 AGGAGTTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.29
Consensus pattern (21 bp):
GGTAGAAGCTATACTTGTATC
Found at i:13416508 original size:20 final size:20
Alignment explanation
Indices: 13416467--13416508 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
13416457 AGAAGCATAC
* *
13416467 TTGTATCGGTAGAACTGTAG
1 TTGTATCGGTAGAACAGGAG
*
13416487 TTGTATCGGTAGAAGAGGAG
1 TTGTATCGGTAGAACAGGAG
13416507 TT
1 TT
13416509 CTACTGATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.33
Consensus pattern (20 bp):
TTGTATCGGTAGAACAGGAG
Found at i:13416734 original size:20 final size:20
Alignment explanation
Indices: 13416709--13416761 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
13416699 GTCTTCGAGT
*
13416709 TATCGGTAGAAGTGGAGTTG
1 TATCGGTAGAAGTGGAGTTC
*
13416729 TATCGGTAGAAGTTGAGTTC
1 TATCGGTAGAAGTGGAGTTC
*
13416749 TACCGGTAGAAGT
1 TATCGGTAGAAGT
13416762 CTCATTGGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.30
Consensus pattern (20 bp):
TATCGGTAGAAGTGGAGTTC
Found at i:13426228 original size:41 final size:41
Alignment explanation
Indices: 13426134--13426234 Score: 159
Period size: 41 Copynumber: 2.5 Consensus size: 41
13426124 TATTTTTTAG
**
13426134 TATCCTCTTGTTGAGAATT-AAATTATCAAGTCCAGTGCCAC
1 TATCCTCTTGTTTTG-ATTAAAATTATCAAGTCCAGTGCCAC
13426175 TATCCTCTTGTTTTGATTAAAATTATCAAGTCCAGTGCCAC
1 TATCCTCTTGTTTTGATTAAAATTATCAAGTCCAGTGCCAC
*
13426216 TGTCCTCTTGTTTTGATTA
1 TATCCTCTTGTTTTGATTA
13426235 TGCTTTTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 3 0.05
41 53 0.95
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.41
Consensus pattern (41 bp):
TATCCTCTTGTTTTGATTAAAATTATCAAGTCCAGTGCCAC
Found at i:13429403 original size:23 final size:24
Alignment explanation
Indices: 13429362--13429413 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
13429352 TTTTGGTGCT
*
13429362 TTTTTTGTGCTGTTGTTGGTATTG
1 TTTTTTGTGCTGTTGTTGGTATAG
*
13429386 TTTTTTGTGCCT-TT-TTGGTGTAG
1 TTTTTTGTG-CTGTTGTTGGTATAG
13429409 TTTTT
1 TTTTT
13429414 ATGTTGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 12 0.48
24 11 0.44
25 2 0.08
ACGTcount: A:0.04, C:0.06, G:0.25, T:0.65
Consensus pattern (24 bp):
TTTTTTGTGCTGTTGTTGGTATAG
Found at i:13429413 original size:24 final size:25
Alignment explanation
Indices: 13429361--13429413 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
13429351 GTTTTGGTGC
*
13429361 TTTTTTTGTGCTGTTGTTGGTATTG
1 TTTTTTTGTGCTGTTGTTGGTATAG
*
13429386 -TTTTTTGTGCCT-TT-TTGGTGTAG
1 TTTTTTTGTG-CTGTTGTTGGTATAG
13429409 TTTTT
1 TTTTT
13429414 ATGTTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 7 0.29
24 15 0.62
25 2 0.08
ACGTcount: A:0.04, C:0.06, G:0.25, T:0.66
Consensus pattern (25 bp):
TTTTTTTGTGCTGTTGTTGGTATAG
Found at i:13432299 original size:49 final size:49
Alignment explanation
Indices: 13432227--13432324 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
13432217 TCCTATAGAG
13432227 AACATATGAAAAGCATTAAAAACATTATATTCTTACCAAAAAGAATTAT
1 AACATATGAAAAGCATTAAAAACATTATATTCTTACCAAAAAGAATTAT
* * * * *
13432276 AACATATGGAAAGTATTAAAAACATTATATTTTTTCCCAAAAGAATTAT
1 AACATATGAAAAGCATTAAAAACATTATATTCTTACCAAAAAGAATTAT
13432325 TACTACCATG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (49 bp):
AACATATGAAAAGCATTAAAAACATTATATTCTTACCAAAAAGAATTAT
Found at i:13434488 original size:91 final size:90
Alignment explanation
Indices: 13434317--13434548 Score: 261
Period size: 91 Copynumber: 2.6 Consensus size: 90
13434307 AATTTTTTTT
* * * ** * *
13434317 AAAAAGTAATTAAGTCCCTACTTTTATTTTGCACTCACTTGAATACTTAAACTTTTAAAATGAAT
1 AAAAAGCAATTAAGCCCCTACTTTT-TTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGAAT
*
13434382 CAAAAAGACCCTCAAACTTAAAAAAA
65 CAAAAAGACACTCAAACTTAAAAAAA
*
13434408 AAAAAGCAATTAAGCCCCTACTTTTCTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCAT
1 AAAAAGCAATTAAGCCCCTACTTTT-TTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGAAT
* * ****
13434473 CCAAAAAG-CATTCAAATTTTTTCAAA
65 -CAAAAAGACACTCAAACTTAAAAAAA
* *
13434499 AAAAATCAATTAAGCCCCTGA-TTGTTTTTGCACTCAATTGGGTACTTGAA
1 AAAAAGCAATTAAGCCCCT-ACTTTTTTTTGCACTCAATTGGGTACTTGAA
13434549 GCACCTTTAA
Statistics
Matches: 121, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
90 25 0.21
91 88 0.73
92 8 0.07
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (90 bp):
AAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGAATC
AAAAAGACACTCAAACTTAAAAAAA
Found at i:13434719 original size:10 final size:10
Alignment explanation
Indices: 13434648--13434724 Score: 52
Period size: 10 Copynumber: 7.9 Consensus size: 10
13434638 ATTTTATAAG
*
13434648 ATTTTTTTTA
1 ATTTTTATTA
*
13434658 ATTTTTAATA
1 ATTTTTATTA
*
13434668 AATTTTA--A
1 ATTTTTATTA
13434676 ATTTTTA-TA
1 ATTTTTATTA
*
13434685 TTTTTTTATTA
1 -ATTTTTATTA
** * *
13434696 AAATTAAATA
1 ATTTTTATTA
13434706 ATTTTTATTA
1 ATTTTTATTA
13434716 ATTTTTATT
1 ATTTTTATT
13434725 TTTTATAATT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
8 7 0.14
9 1 0.02
10 40 0.80
11 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTATTA
Found at i:13435073 original size:29 final size:30
Alignment explanation
Indices: 13435041--13435099 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
13435031 ATGATTTAAT
*
13435041 GTGCAATTGTATACATG-AAGTTTGATTTG
1 GTGCAATTGTATACATGAAAATTTGATTTG
*
13435070 GTGCAATTTTATACATGAAAATTTGATTTG
1 GTGCAATTGTATACATGAAAATTTGATTTG
13435100 ATCCAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (30 bp):
GTGCAATTGTATACATGAAAATTTGATTTG
Found at i:13435107 original size:30 final size:29
Alignment explanation
Indices: 13435044--13435107 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
13435034 ATTTAATGTG
* * *
13435044 CAATTGTATACATGAAGTTTGATTTGGTG
1 CAATTGTATACATGAAATTTGATTTGATC
*
13435073 CAATTTTATACATGAAAATTTGATTTGATC
1 CAATTGTATACATG-AAATTTGATTTGATC
13435103 CAATT
1 CAATT
13435108 ATTGTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (29 bp):
CAATTGTATACATGAAATTTGATTTGATC
Found at i:13435316 original size:29 final size:31
Alignment explanation
Indices: 13435242--13435325 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 31
13435232 ATTAAATCAA
* * * **
13435242 AATTAAAGTTTCAAGCATACATTTAAACCAC
1 AATTAAAGTTTCATGTATACAATTGCACCAC
*
13435273 AATTAAAGTTTCATGTATATAATTGCACCA-
1 AATTAAAGTTTCATGTATACAATTGCACCAC
*
13435303 AATTAGAG-TTCATGTATACAATT
1 AATTAAAGTTTCATGTATACAATT
13435326 ACACATTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
29 14 0.31
30 7 0.16
31 24 0.53
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.35
Consensus pattern (31 bp):
AATTAAAGTTTCATGTATACAATTGCACCAC
Found at i:13435476 original size:17 final size:18
Alignment explanation
Indices: 13435443--13435477 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13435433 GTAAAAAATA
*
13435443 TAAATTTAATTATTTTTT
1 TAAATTTAATAATTTTTT
13435461 TAAATTTAA-AATTTTTT
1 TAAATTTAATAATTTTTT
13435478 ACACCCTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TAAATTTAATAATTTTTT
Found at i:13439057 original size:18 final size:18
Alignment explanation
Indices: 13439034--13439076 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
13439024 GAATAGATTT
13439034 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
13439052 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
13439070 TTAATTA
1 TTAATTA
13439077 CATCTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:13441247 original size:13 final size:12
Alignment explanation
Indices: 13441219--13441253 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
13441209 AATAAAAGCC
13441219 TTTTTTTTTTCT
1 TTTTTTTTTTCT
13441231 TTTTTTTTTTCT
1 TTTTTTTTTTCT
* *
13441243 ATTTTCTTTTC
1 TTTTTTTTTTC
13441254 ACTATATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTCT
Found at i:13442016 original size:48 final size:48
Alignment explanation
Indices: 13441945--13442037 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
13441935 GAAAAAAAAT
* *
13441945 TGTCTGCAACTCTGCATTGGTCAACTTGGAATTACTATTAGGATTATC
1 TGTCTGCAACTCTGCATTAGTCAACTTGGAATTACAATTAGGATTATC
*
13441993 TGTCTGCAACTCTGCATTAGTCAACTTGGGATTACAATTAGGATT
1 TGTCTGCAACTCTGCATTAGTCAACTTGGAATTACAATTAGGATT
13442038 GGTAAATTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (48 bp):
TGTCTGCAACTCTGCATTAGTCAACTTGGAATTACAATTAGGATTATC
Found at i:13447844 original size:21 final size:21
Alignment explanation
Indices: 13447820--13447861 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
13447810 CAATTTGAGG
13447820 AAAAATAAAAGAAACAGAATT
1 AAAAATAAAAGAAACAGAATT
13447841 AAAAATAAAAGAAACAGAATT
1 AAAAATAAAAGAAACAGAATT
13447862 GAAAGAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.14
Consensus pattern (21 bp):
AAAAATAAAAGAAACAGAATT
Found at i:13450281 original size:20 final size:19
Alignment explanation
Indices: 13450252--13450295 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
13450242 TTTCCTGGAT
13450252 AAAAATAGATA-AATAAATA
1 AAAAATAGATAGAA-AAATA
13450271 AAAAATAAGATAGAAAAATA
1 AAAAAT-AGATAGAAAAATA
13450291 AAAAA
1 AAAAA
13450296 AATAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 15 0.65
21 2 0.09
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (19 bp):
AAAAATAGATAGAAAAATA
Found at i:13455948 original size:22 final size:21
Alignment explanation
Indices: 13455908--13455950 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13455898 CGATCTGAGG
*
13455908 AAAAATAAAAGAAATAGAATT
1 AAAAATAAAAGAAACAGAATT
13455929 AAAAATAAAAGAAAACAGAATT
1 AAAAATAAAAG-AAACAGAATT
13455951 GAAAGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (21 bp):
AAAAATAAAAGAAACAGAATT
Found at i:13456782 original size:19 final size:19
Alignment explanation
Indices: 13456758--13456800 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
13456748 AAACATAAAT
13456758 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
13456777 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
13456796 TAAAT
1 TAAAT
13456801 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:13457107 original size:19 final size:19
Alignment explanation
Indices: 13457083--13457125 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
13457073 AAACATAAAT
13457083 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
13457102 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
13457121 TAAAT
1 TAAAT
13457126 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:13457255 original size:325 final size:325
Alignment explanation
Indices: 13456665--13457304 Score: 1183
Period size: 325 Copynumber: 2.0 Consensus size: 325
13456655 AATCTAAATT
13456665 CTAAAAGATAAATAGAATTATATCTAACATTTAATTCCACTAATAGGATCCAATTTAAACTCTAA
1 CTAAAAGATAAATAGAATTATATCTAACATTTAATTCCACTAATAGGATCCAATTTAAACTCTAA
13456730 AGATAAATACAAAAAGATAAACATAAATTAAATACAAATTTAAATAATAAATAATATCTTAAATA
66 AGATAAATACAAAAAGATAAACATAAATTAAATACAAATTTAAATAATAAATAATATCTTAAATA
*
13456795 TTAAATCCTAATATAAAATATATTTTAAAAAATAAAATAAAATCAATTCTTTTTGTCCTATAAAC
131 TTAAATCCTAATATAAAATATATTTTAAAAAATAAAATAAAATCAAGTCTTTTTGTCCTATAAAC
* *
13456860 TCTCTCTTTTAGCATTCCATCTTCACACAACTTCAAATTCTCTTCCAAAACCATGCTTTTTGTTT
196 TCTATCTTTTAGCATTCCATCTTCACACAACTTCAAATTCTCTTCCAAAACCATGCTTTTTGTCT
*
13456925 CCAATTTATCTTCTATCACCACTTGAGTCCCTATAAAATAAAAA-ATAATAAATAACCCTAAACC
261 CCAATTTATCTTCTATCACCACTTGAGTCCCTACAAAATAAAAAGATAATAAATAACCCTAAACC
* * * *
13456989 CTAAAAGATAATTAGAATTATATTTAACATTTAATTCCCCTAATTGGATCCAATTTAAACTCTAA
1 CTAAAAGATAAATAGAATTATATCTAACATTTAATTCCACTAATAGGATCCAATTTAAACTCT-A
13457054 AAGATAAATACAAAAAGATAAACATAAATTAAATACAAATTTAAATAATAAATAATATCTTAAAT
65 AAGATAAATACAAAAAGATAAACATAAATTAAATACAAATTTAAATAATAAATAATATCTTAAAT
13457119 ATTAAATCCTAATATAAAATATATTTTAAAAAATAAAATAAAATCAAGTCTTTTTGTCCTATAAA
130 ATTAAATCCTAATATAAAATATATTTTAAAAAATAAAATAAAATCAAGTCTTTTTGTCCTATAAA
*
13457184 CTCTATCTTTTAGCATTCCTTCTTCACACAACTTCAAATTCTCTTCCAAAACCATGCTTTTTGTC
195 CTCTATCTTTTAGCATTCCATCTTCACACAACTTCAAATTCTCTTCCAAAACCATGCTTTTTGTC
13457249 TCCAATTTATCTTCTATCACCACTTGAGTCCCTACAAAATAAAAAGATAATAAATA
260 TCCAATTTATCTTCTATCACCACTTGAGTCCCTACAAAATAAAAAGATAATAAATA
13457305 GCCCAATTTA
Statistics
Matches: 305, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
324 59 0.19
325 236 0.77
326 10 0.03
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.34
Consensus pattern (325 bp):
CTAAAAGATAAATAGAATTATATCTAACATTTAATTCCACTAATAGGATCCAATTTAAACTCTAA
AGATAAATACAAAAAGATAAACATAAATTAAATACAAATTTAAATAATAAATAATATCTTAAATA
TTAAATCCTAATATAAAATATATTTTAAAAAATAAAATAAAATCAAGTCTTTTTGTCCTATAAAC
TCTATCTTTTAGCATTCCATCTTCACACAACTTCAAATTCTCTTCCAAAACCATGCTTTTTGTCT
CCAATTTATCTTCTATCACCACTTGAGTCCCTACAAAATAAAAAGATAATAAATAACCCTAAACC
Found at i:13458437 original size:42 final size:43
Alignment explanation
Indices: 13458390--13458657 Score: 364
Period size: 43 Copynumber: 6.3 Consensus size: 43
13458380 TTATTAGAAA
* * *
13458390 AAACGCCGCTATAGAACATGGTTTTTAGCGGCGC-TTTCCCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
13458432 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
13458475 AAACGCCGCTAAAGAACATGGTCTTCAGCGGCGCTTTTCACAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
13458518 AAACGCCACTAAAGAACATTG-CTTTTAGCGGCG-TTTTCCCCAC
1 AAACGCCGCTAAAGAACATGGTC-TTTAGCGGCGCTTTT-CCCAC
* * * * *
13458561 AAATGCCGCTAAAGAACATGCTCTTTAGCGGCG-GTTTCCTAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
13458603 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
13458646 AAACGCCGCTAA
1 AAACGCCGCTAA
13458658 CATTAATAAA
Statistics
Matches: 197, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
42 71 0.36
43 125 0.63
44 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
Found at i:13458549 original size:128 final size:128
Alignment explanation
Indices: 13458390--13458657 Score: 389
Period size: 128 Copynumber: 2.1 Consensus size: 128
13458380 TTATTAGAAA
* * *
13458390 AAACGCCGCTATAGAACATGGTTTTTAGCGGCGCTTT-CCCAAAAACGCCGCTAAAGAACATGGT
1 AAACGCCGCTAAAGAACATGGCTTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAGAACATGCT
* *
13458454 CTTTAGCGGCGCTTTTTCC-ACAAACGCCGCTAAAGAACATGGTCTTCAGCGGCGC-TTTTCACA
66 CTTTAGCGGCG--GTTTCCTAAAAACGCCGCTAAAGAACATGGTCTTCAGCGGCGCTTTTTC-CA
13458517 C
128 C
* * * * *
13458518 AAACGCCACTAAAGAACATTGCTTTTAGCGGCGTTTTCCCCACAAATGCCGCTAAAGAACATGCT
1 AAACGCCGCTAAAGAACATGGCTTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAGAACATGCT
*
13458583 CTTTAGCGGCGGTTTCCTAAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTCCAC
66 CTTTAGCGGCGGTTTCCTAAAAACGCCGCTAAAGAACATGGTCTTCAGCGGCGCTTTTTCCAC
13458646 AAACGCCGCTAA
1 AAACGCCGCTAA
13458658 CATTAATAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
127 5 0.04
128 80 0.64
129 40 0.32
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (128 bp):
AAACGCCGCTAAAGAACATGGCTTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAGAACATGCT
CTTTAGCGGCGGTTTCCTAAAAACGCCGCTAAAGAACATGGTCTTCAGCGGCGCTTTTTCCAC
Found at i:13462750 original size:41 final size:41
Alignment explanation
Indices: 13462688--13463010 Score: 454
Period size: 41 Copynumber: 7.9 Consensus size: 41
13462678 AAACTCAACT
* * *
13462688 TTTAGCGACGCTTTTCTATAAGCGCCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTACCATAAGCGCCGCTATTGCTCTGACC
* *
13462729 TTTAGCGGCGTTTTACCATAAGCGCCGCTATTGGTCTGACC
1 TTTAGCGGCGCTTTACCATAAGCGCCGCTATTGCTCTGACC
*
13462770 TTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTACCATAAGCGCCGCTATTGCTCTGACC
*
13462811 TTTAGCGGCGCTTGACCATAAGCGCCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTACCATAAGCGCCGCTATTGCTCTGACC
*
13462852 TTTAGCGGCGC-TTGCTCATAAGCGCCGCTATTGCTCTGACC
1 TTTAGCGGCGCTTTAC-CATAAGCGCCGCTATTGCTCTGACC
* * * *
13462893 TTTAGCGACGCTTTCCCATAAGCGCTGCTATTTCTCTGACC
1 TTTAGCGGCGCTTTACCATAAGCGCCGCTATTGCTCTGACC
* *
13462934 TTTAGCGGCGC-TTACCCATAAGCGCCGCTATTGCTC-CACT
1 TTTAGCGGCGCTTTA-CCATAAGCGCCGCTATTGCTCTGACC
* * *
13462974 TTTAGCGGCGCTTTTCTATAAGCCCCGCTATTGCTCT
1 TTTAGCGGCGCTTTACCATAAGCGCCGCTATTGCTCT
13463011 AGTTTTTGTG
Statistics
Matches: 252, Mismatches: 25, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
40 36 0.14
41 213 0.85
42 3 0.01
ACGTcount: A:0.16, C:0.31, G:0.21, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGCTTTACCATAAGCGCCGCTATTGCTCTGACC
Found at i:13462822 original size:24 final size:24
Alignment explanation
Indices: 13462790--13462904 Score: 87
Period size: 24 Copynumber: 5.4 Consensus size: 24
13462780 CTTTCCCATA
13462790 AGCGCCGCTATTGCTCTGACCTTT
1 AGCGCCGCTATTGCTCTGACCTTT
* *
13462814 AGCG--GC----GCT-TGACCATA
1 AGCGCCGCTATTGCTCTGACCTTT
13462831 AGCGCCGCTATTGCTCTGACCTTT
1 AGCGCCGCTATTGCTCTGACCTTT
* *
13462855 AGCGGCGC--TTGCTC--A---TA
1 AGCGCCGCTATTGCTCTGACCTTT
13462872 AGCGCCGCTATTGCTCTGACCTTT
1 AGCGCCGCTATTGCTCTGACCTTT
*
13462896 AGCGACGCT
1 AGCGCCGCT
13462905 TTCCCATAAG
Statistics
Matches: 68, Mismatches: 9, Indels: 28
0.65 0.09 0.27
Matches are distributed among these distances:
17 18 0.26
18 3 0.04
19 8 0.12
20 1 0.01
21 1 0.01
22 8 0.12
23 3 0.04
24 26 0.38
ACGTcount: A:0.16, C:0.32, G:0.24, T:0.28
Consensus pattern (24 bp):
AGCGCCGCTATTGCTCTGACCTTT
Found at i:13467668 original size:137 final size:137
Alignment explanation
Indices: 13467414--13467691 Score: 520
Period size: 137 Copynumber: 2.0 Consensus size: 137
13467404 GCGAATGGTG
13467414 CTCTCTTGTCGAAGTCTTATAATGAGGCTTACAAGATTATCGAGAGAATAGAAAGTAACAATTAC
1 CTCTCTTGTCGAAGTCTTATAATGAGGCTTACAAGATTATCGAGAGAATAGAAAGTAACAATTAC
* *
13467479 CAGTGGCCAACAAATTAAACAACTTCAAGAAGACAAGTAGTAGGAGTACATGAAGTAGATGCCCT
66 CAGTGGCCAACAAATTAAACAACTTCAAGAAGACAAGTAGTAGAAGTACATGAAGTAGACGCCCT
13467544 CGCTTTA
131 CGCTTTA
13467551 CTCTCTTGTCGAAGTCTTATAATGAGGCTTACAAGATTATCGAGAGAATAGAAAGTAACAATTAC
1 CTCTCTTGTCGAAGTCTTATAATGAGGCTTACAAGATTATCGAGAGAATAGAAAGTAACAATTAC
* *
13467616 CAGTGGCCAACAAATTAAACAACTTCAAGAAGACAAGTAGTTGAAGTGCATGAAGTAGACGCCCT
66 CAGTGGCCAACAAATTAAACAACTTCAAGAAGACAAGTAGTAGAAGTACATGAAGTAGACGCCCT
13467681 CGCTTTA
131 CGCTTTA
13467688 CTCT
1 CTCT
13467692 TAGCTCAGGT
Statistics
Matches: 137, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 137 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (137 bp):
CTCTCTTGTCGAAGTCTTATAATGAGGCTTACAAGATTATCGAGAGAATAGAAAGTAACAATTAC
CAGTGGCCAACAAATTAAACAACTTCAAGAAGACAAGTAGTAGAAGTACATGAAGTAGACGCCCT
CGCTTTA
Found at i:13470831 original size:23 final size:24
Alignment explanation
Indices: 13470790--13470834 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
13470780 CATAATTGTG
* *
13470790 TCCTATATTTATTGATATTTATAT
1 TCCTATATTAATTAATATTTATAT
13470814 TCCTA-ATTAATTAATATTTAT
1 TCCTATATTAATTAATATTTAT
13470835 TGACATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (24 bp):
TCCTATATTAATTAATATTTATAT
Found at i:13476045 original size:13 final size:13
Alignment explanation
Indices: 13476027--13476051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13476017 TAAGTTAAAA
13476027 ATGCTAAAAATGC
1 ATGCTAAAAATGC
13476040 ATGCTAAAAATG
1 ATGCTAAAAATG
13476052 ATAAAATGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:13485629 original size:51 final size:51
Alignment explanation
Indices: 13485510--13485747 Score: 318
Period size: 51 Copynumber: 4.6 Consensus size: 51
13485500 TTTCATTTAA
* ** * *
13485510 TACTCACGATGACA-TATAGTCATCAGACCTCTTGTTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
* * *
13485563 TACTCACGATGACACTGAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
13485614 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
13485665 TACTCACGATGACACTTAGTCATCGGACCTTTAAT-CAGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCA-TAAAGGATTCATT
* * *
13485716 TAATCATGATGACACTTAGTCATTGGACCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTT
13485748 TCGTTTATAG
Statistics
Matches: 167, Mismatches: 16, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
50 1 0.01
51 130 0.78
52 9 0.05
53 26 0.16
54 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:13492905 original size:51 final size:51
Alignment explanation
Indices: 13492775--13493003 Score: 307
Period size: 51 Copynumber: 4.5 Consensus size: 51
13492765 TTTCGTTTAA
** * *
13492775 TACTCACGATGACA-TATAGTCATCGGACCTCTTGTTCCATATTGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAATGG-ATTCATT
* * *
13492828 TACTCACGATGACAATGAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAATGGATTCATT
* *
13492879 TACTCACGATGACACTTAGTCTTCGGACCTTTAATCCGTAATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAATGGATTCATT
* * *
13492930 TACTCACGATGACATTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAATGGATTCATT
*
13492981 TACTCATGATGACACTTAGTCAT
1 TACTCACGATGACACTTAGTCAT
13493004 TGAACGTTTT
Statistics
Matches: 159, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
51 121 0.76
52 10 0.06
53 27 0.17
54 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAATGGATTCATT
Found at i:13496181 original size:25 final size:25
Alignment explanation
Indices: 13496142--13496190 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
13496132 GTAGAAGTAC
13496142 AGGGTAGAAGAGAGGTTGTTCTCTG
1 AGGGTAGAAGAGAGGTTGTTCTCTG
* *
13496167 AGGGTAGGAGTGAGGTTGTTCTCT
1 AGGGTAGAAGAGAGGTTGTTCTCT
13496191 TACTTGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.20, C:0.08, G:0.41, T:0.31
Consensus pattern (25 bp):
AGGGTAGAAGAGAGGTTGTTCTCTG
Found at i:13502445 original size:15 final size:18
Alignment explanation
Indices: 13502425--13502464 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 18
13502415 TACTGATTAT
13502425 AATTTCCTT-G-TCGAA-
1 AATTTCCTTAGCTCGAAG
13502440 AATTTCCTTAGCTCGAAG
1 AATTTCCTTAGCTCGAAG
13502458 AATTTCC
1 AATTTCC
13502465 ATATCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.41
16 1 0.05
17 5 0.23
18 7 0.32
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (18 bp):
AATTTCCTTAGCTCGAAG
Found at i:13513531 original size:23 final size:23
Alignment explanation
Indices: 13513501--13513553 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
13513491 AAATTCGAAT
13513501 TTCGAGTTAAATGAATCAAGTTG
1 TTCGAGTTAAATGAATCAAGTTG
*
13513524 TTCGAGTTAAATGAATCGAGTTG
1 TTCGAGTTAAATGAATCAAGTTG
13513547 TTCGAGT
1 TTCGAGT
13513554 CAACTCGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (23 bp):
TTCGAGTTAAATGAATCAAGTTG
Found at i:13515788 original size:6 final size:7
Alignment explanation
Indices: 13515771--13515795 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13515761 TTTGCCTGTT
13515771 TTTTTTA
1 TTTTTTA
13515778 TTTTTTA
1 TTTTTTA
13515785 TTTTTTA
1 TTTTTTA
13515792 TTTT
1 TTTT
13515796 ATGATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:13516649 original size:36 final size:36
Alignment explanation
Indices: 13516609--13516779 Score: 263
Period size: 36 Copynumber: 4.8 Consensus size: 36
13516599 AGTTCCGACA
13516609 TTATTCATGCCATGTGACAGTAAATATGTGGGCATG
1 TTATTCATGCCATGTGACAGTAAATATGTGGGCATG
* *
13516645 TTATTCATGTCAT-TAGATAGTAAATATGTGGGCATG
1 TTATTCATGCCATGT-GACAGTAAATATGTGGGCATG
* *
13516681 TTATTCATGCCATGAGACAGTAAATATGTGGGTATG
1 TTATTCATGCCATGTGACAGTAAATATGTGGGCATG
* *
13516717 TTATTCATGCCATGTGACTGAAAATATGTGGGCATG
1 TTATTCATGCCATGTGACAGTAAATATGTGGGCATG
*
13516753 TTATTCATGCCATGTGACAGTGAATAT
1 TTATTCATGCCATGTGACAGTAAATAT
13516780 ATTGTGCTAA
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
35 1 0.01
36 119 0.99
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.35
Consensus pattern (36 bp):
TTATTCATGCCATGTGACAGTAAATATGTGGGCATG
Found at i:13517133 original size:66 final size:68
Alignment explanation
Indices: 13517024--13517161 Score: 181
Period size: 66 Copynumber: 2.1 Consensus size: 68
13517014 GGGAAATAAA
* * *
13517024 GAGAGTGTTAGCTTTACGCTTCACTTTTGGGACATATTCGACTTTATGAGTC-T-TTTGGTGTGT
1 GAGAGTGTTAGCTATACGCTTCACTTATGGGACATATTCGACTTTACGAGTCATATTTGGTGTGT
*
13517087 TTG
66 TTC
* * * * *
13517090 GAGAGTGTTGGCTATATGTTTCACTTATGGGACATGTTTGACTTTACGAGTCATATTTGGTGTGT
1 GAGAGTGTTAGCTATACGCTTCACTTATGGGACATATTCGACTTTACGAGTCATATTTGGTGTGT
13517155 TTC
66 TTC
13517158 GAGA
1 GAGA
13517162 TTCGCATATC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 44 0.72
67 1 0.02
68 16 0.26
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (68 bp):
GAGAGTGTTAGCTATACGCTTCACTTATGGGACATATTCGACTTTACGAGTCATATTTGGTGTGT
TTC
Found at i:13517264 original size:23 final size:23
Alignment explanation
Indices: 13517238--13517302 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
13517228 ATTAAATGTG
13517238 TTAAATATTAATGTGATTTGCGC
1 TTAAATATTAATGTGATTTGCGC
*
13517261 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTGCGC
13517284 TTAAATATTAAATGTGATT
1 TTAAATATT-AATGTGATT
13517303 AAATGTGACT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 31 0.77
24 9 0.22
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (23 bp):
TTAAATATTAATGTGATTTGCGC
Found at i:13517305 original size:10 final size:10
Alignment explanation
Indices: 13517290--13517324 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
13517280 GTGCTTAAAT
13517290 ATTAAATGTG
1 ATTAAATGTG
13517300 ATTAAATGTG
1 ATTAAATGTG
* *
13517310 ACTAAATATG
1 ATTAAATGTG
13517320 ATTAA
1 ATTAA
13517325 TTTGTGATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (10 bp):
ATTAAATGTG
Found at i:13517363 original size:59 final size:59
Alignment explanation
Indices: 13517298--13517427 Score: 179
Period size: 59 Copynumber: 2.2 Consensus size: 59
13517288 ATATTAAATG
* * *
13517298 TGATTAAATGTGACTAAATATGATTAATTTGTGATGTCATAAATGTTGAAATATGCATA
1 TGATTAAATGTGACTAAATATGATTAATATGTGATGTCATAAATGCTAAAATATGCATA
* * * * * *
13517357 TGATTAAATGTGACTAAGTGTTATTAATATGTGATGTTATAAATGCTAAAATATTCATG
1 TGATTAAATGTGACTAAATATGATTAATATGTGATGTCATAAATGCTAAAATATGCATA
13517416 TGATTAAATGTG
1 TGATTAAATGTG
13517428 CAACAGCCTA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.40
Consensus pattern (59 bp):
TGATTAAATGTGACTAAATATGATTAATATGTGATGTCATAAATGCTAAAATATGCATA
Found at i:13535295 original size:14 final size:14
Alignment explanation
Indices: 13535276--13535307 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
13535266 GCGAAATTTC
*
13535276 TATTCTTAAGTATT
1 TATTCTTAAGCATT
13535290 TATTCTTAAGCATT
1 TATTCTTAAGCATT
13535304 TATT
1 TATT
13535308 TTTCTTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.09, G:0.06, T:0.56
Consensus pattern (14 bp):
TATTCTTAAGCATT
Found at i:13536899 original size:19 final size:19
Alignment explanation
Indices: 13536861--13536900 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
13536851 ATGAAAACCC
*
13536861 AAAATAAAAATAAAAGATA
1 AAAATAAAAATAAAAAATA
13536880 AAAAT-AAAATAAATAAATA
1 AAAATAAAAATAAA-AAATA
13536899 AA
1 AA
13536901 TATGCCTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (19 bp):
AAAATAAAAATAAAAAATA
Found at i:13536900 original size:13 final size:13
Alignment explanation
Indices: 13536864--13536888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13536854 AAAACCCAAA
13536864 ATAAAAATAAAAG
1 ATAAAAATAAAAG
13536877 ATAAAAATAAAA
1 ATAAAAATAAAA
13536889 TAAATAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
ATAAAAATAAAAG
Found at i:13537963 original size:17 final size:18
Alignment explanation
Indices: 13537941--13537994 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
13537931 CAAAGGTCAA
13537941 CGGTCAACGAGTC-GGTT
1 CGGTCAACGAGTCAGGTT
* * *
13537958 CGGTCAATGGGTCGGGTT
1 CGGTCAACGAGTCAGGTT
*
13537976 CAGTCAACGAGTCAGGTT
1 CGGTCAACGAGTCAGGTT
13537994 C
1 C
13537995 ACTTGGTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 11 0.37
18 19 0.63
ACGTcount: A:0.19, C:0.22, G:0.35, T:0.24
Consensus pattern (18 bp):
CGGTCAACGAGTCAGGTT
Found at i:13547971 original size:36 final size:36
Alignment explanation
Indices: 13547924--13547997 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
13547914 CAAGGTATTA
*
13547924 ATGAGACTCAGATAATATGGTCATCACCAAGAAAGC
1 ATGAGACTCAGATAATATGGCCATCACCAAGAAAGC
13547960 ATGAGACTCAGATAATATGGCCATCACCAAGAAAGC
1 ATGAGACTCAGATAATATGGCCATCACCAAGAAAGC
13547996 AT
1 AT
13547998 AATGCGCCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (36 bp):
ATGAGACTCAGATAATATGGCCATCACCAAGAAAGC
Found at i:13553642 original size:183 final size:178
Alignment explanation
Indices: 13553245--13553791 Score: 758
Period size: 182 Copynumber: 3.0 Consensus size: 178
13553235 TACTTAAATT
* * *
13553245 TTCGGGTAAGCATATATTTAGCCGATTTGTTTTAAGG-TTCATAAGAAATTGGGGATTTTTTTAT
1 TTCGGGTAAGCATATATTTAGCCAATTTGTTTTAGGGCTT-ATAAGAAATTGAGGATTTTTTTAT
* * * *
13553309 TTTTTTATTATTATGTCGGCTGGATTAAATTGGTGTTACAATTCATCATAGCATTAGATTTTTGA
65 TTTTTTATTATTGTGT-AGCTGGACTAAATTGGTGCTACAATTCATCATAGCATTAGATTTTTGA
* *
13553374 GTGAATTGTAGGATTTATATAATAAAAAGTCGAATTTTTTTGTGTGAATTGTA
129 GTGAATTGTAGGGTTTATATAATAAAAAGT---TTTTTTTTGTGTGAATTGTA
* *
13553427 TTCGGGTAAGCATATATGTAGTCGAA-TTGTTTTAGGGCTTATAAGAAATTGAGGATTTTTTTTT
1 TTCGGGTAAGCATATATTTAG-CCAATTTGTTTTAGGGCTTATAAGAAATTGAGGA--TTTTTTT
* * * *
13553491 ATTTTTTGATTATTGCGTTGCCTGGACTAAATTGGTGGTACAATTCATCATAGCATTAGATTTTT
63 ATTTTTTTATTATTGTGTAG-CTGGACTAAATTGGTGCTACAATTCATCATAGCATTAGATTTTT
13553556 -AGTGAATTGTAGGGTTTATATAATAAAAAGATTTTTTTTGTGTGTGAATTGTA
127 GAGTGAATTGTAGGGTTTATATAATAAAAAG-TTTTTTTT-TGTGTGAATTGTA
* *
13553609 TTCGGGGTAAGCATATATTTAGCCAATTTGTTTTAGGGCTCATAAGAAATTGATGATTTTTTTAT
1 TTC-GGGTAAGCATATATTTAGCCAATTTGTTTTAGGGCTTATAAGAAATTGAGGATTTTTTTAT
*
13553674 TTTTTTATTATTGTGTCAGTTGGACTAAATTGGTGCTACAATTCATCATAGCATTAGATTTTTGA
65 TTTTTTATTATTGTGT-AGCTGGACTAAATTGGTGCTACAATTCATCATAGCATTAGATTTTTGA
*
13553739 GTGAATTGTAGGGTATATATAATAAAAAGTTTATTTTTTTTGTGTGAATTGTA
129 GTGAATTGTAGGGTTTATATAATAAAAAG--T-TTTTTTTTGTGTGAATTGTA
13553792 GGTTGGTGGA
Statistics
Matches: 328, Mismatches: 24, Indels: 25
0.87 0.06 0.07
Matches are distributed among these distances:
181 71 0.22
182 93 0.28
183 92 0.28
184 72 0.22
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (178 bp):
TTCGGGTAAGCATATATTTAGCCAATTTGTTTTAGGGCTTATAAGAAATTGAGGATTTTTTTATT
TTTTTATTATTGTGTAGCTGGACTAAATTGGTGCTACAATTCATCATAGCATTAGATTTTTGAGT
GAATTGTAGGGTTTATATAATAAAAAGTTTTTTTTTGTGTGAATTGTA
Found at i:13555063 original size:160 final size:158
Alignment explanation
Indices: 13554667--13555126 Score: 638
Period size: 157 Copynumber: 2.9 Consensus size: 158
13554657 TATGCCATCC
* ** *
13554667 TTTTTTGGCTTCTAGTTCTCGTACTCGTACCAGACTGAGAGAAAAAAAATCATAACCCCAAATTA
1 TTTTTTGGCTTCTAGTTCTCGTACTCGTACCAGACTAAGACCAAAAAAATCATAACCCTAAATTA
* * *
13554732 GATTTAAATATTTTAGAATTGACTTTAAAAAA-TGTTTACGATATACCTATGATCCAATTGTGTT
66 GATTTAAATATTTTGGAATTGACATTAAAAAAGTGTTTACGATATACCTGTGATCCAATTGTGTT
*
13554796 AGGCTAAATGCATGGTGTCTGTTGTTAT
131 AGGCTGAATGCATGGTGTCTGTTGTTAT
* * * ** *
13554824 TTTTTTGGCTTCTAGTTCACATACTTGTACCAGGTTAAGACCAAAAAAATCAGAA-CCTCAAATT
1 TTTTTTGGCTTCTAGTTCTCGTACTCGTACCAGACTAAGACCAAAAAAATCATAACCCT-AAATT
* * * *
13554888 AGATTTAAATATTTTGGAATTTACATTAAAAAAGTGTTTATGATATACTTGTGATCCAGTTGTGT
65 AGATTTAAATATTTTGGAATTGACATTAAAAAAGTGTTTACGATATACCTGTGATCCAATTGTGT
*
13554953 TAGGCTGAATGCATGGTGTTCTGTTGTTCTT
130 TAGGCTGAATGCATGGTG-TCTGTTGTT-AT
*
13554984 TTTTTTGGCTTCTAATTCTCGTACTCGTACCAGACTAAGACCAAAAAAATCATAACCCTAAATTA
1 TTTTTTGGCTTCTAGTTCTCGTACTCGTACCAGACTAAGACCAAAAAAATCATAACCCTAAATTA
* * * * *
13555049 GATTTAAATATTTTGGAATTGACAGT-GAAAAGTGTTTACAATAGACCTGTGATCCAATTGTGTC
66 GATTTAAATATTTTGGAATTGACATTAAAAAAGTGTTTACGATATACCTGTGATCCAATTGTGTT
*
13555113 AGGTTGAATGCATG
131 AGGCTGAATGCATG
13555127 ATCTTTTGTT
Statistics
Matches: 262, Mismatches: 36, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
156 2 0.01
157 81 0.31
158 44 0.17
159 53 0.20
160 79 0.30
161 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (158 bp):
TTTTTTGGCTTCTAGTTCTCGTACTCGTACCAGACTAAGACCAAAAAAATCATAACCCTAAATTA
GATTTAAATATTTTGGAATTGACATTAAAAAAGTGTTTACGATATACCTGTGATCCAATTGTGTT
AGGCTGAATGCATGGTGTCTGTTGTTAT
Found at i:13556400 original size:57 final size:57
Alignment explanation
Indices: 13556339--13556584 Score: 300
Period size: 57 Copynumber: 4.3 Consensus size: 57
13556329 AACCCTCAAC
* * *
13556339 ACCTTCACCACTCTCACCACCTTTACTGCCAGA-AACCTCAACACTCTCCCCACCTAA
1 ACCTTCACCACCCTCACCACCTTTACTACCA-ACAACCTCAACACCCTCCCCACCTAA
* * * * * *
13556396 ACCTTCAGCACACTCACCACCTTCACAACC--CGAACCCTCACCACCCTCACCACCTAA
1 ACCTTCACCACCCTCACCACCTTTACTACCAAC-AA-CCTCAACACCCTCCCCACCTAA
* *
13556453 ACCTTCAACACCCTCACTACCTTTACTACCAACAACCTCAACACCCTCCCCACCTAA
1 ACCTTCACCACCCTCACCACCTTTACTACCAACAACCTCAACACCCTCCCCACCTAA
* * * * *
13556510 ACCTTCACCACTCTCACCACCTTTACTGCTAAGAACCTCAACACACTCCCCACCTAA
1 ACCTTCACCACCCTCACCACCTTTACTACCAACAACCTCAACACCCTCCCCACCTAA
13556567 ACCTTCACCACCCTCACC
1 ACCTTCACCACCCTCACC
13556585 CTCACAACCT
Statistics
Matches: 161, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
56 2 0.01
57 156 0.97
58 2 0.01
59 1 0.01
ACGTcount: A:0.29, C:0.50, G:0.02, T:0.19
Consensus pattern (57 bp):
ACCTTCACCACCCTCACCACCTTTACTACCAACAACCTCAACACCCTCCCCACCTAA
Found at i:13556417 original size:24 final size:23
Alignment explanation
Indices: 13556371--13556417 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
13556361 TTACTGCCAG
* *
13556371 AAACCTCAACACTCTCCCCACCT
1 AAACCTCAACACACTCACCACCT
*
13556394 AAACCTTCAGCACACTCACCACCT
1 AAACC-TCAACACACTCACCACCT
13556418 TCACAACCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.32, C:0.49, G:0.02, T:0.17
Consensus pattern (23 bp):
AAACCTCAACACACTCACCACCT
Found at i:13556455 original size:24 final size:24
Alignment explanation
Indices: 13556408--13556474 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
13556398 CTTCAGCACA
* **
13556408 CTCACCACCTTCACAACCCGAACC
1 CTCACCACCCTCACAACCTAAACC
*
13556432 CTCACCACCCTCACCACCTAAACC
1 CTCACCACCCTCACAACCTAAACC
* * *
13556456 TTCAACACCCTCACTACCT
1 CTCACCACCCTCACAACCT
13556475 TTACTACCAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.28, C:0.54, G:0.01, T:0.16
Consensus pattern (24 bp):
CTCACCACCCTCACAACCTAAACC
Found at i:13556466 original size:33 final size:33
Alignment explanation
Indices: 13556429--13556506 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
13556419 CACAACCCGA
*
13556429 ACCCTCACCACCCTCACCACCTA-AACCTTCAAC
1 ACCCTCACCACCCTCACCACCAACAACC-TCAAC
* * * *
13556462 ACCCTCACTACCTTTACTACCAACAACCTCAAC
1 ACCCTCACCACCCTCACCACCAACAACCTCAAC
*
13556495 ACCCTCCCCACC
1 ACCCTCACCACC
13556507 TAAACCTTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
33 33 0.89
34 4 0.11
ACGTcount: A:0.29, C:0.54, G:0.00, T:0.17
Consensus pattern (33 bp):
ACCCTCACCACCCTCACCACCAACAACCTCAAC
Found at i:13556593 original size:24 final size:24
Alignment explanation
Indices: 13556566--13556633 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
13556556 TCCCCACCTA
13556566 AACCTTCACCACCCTCACCCTCAC
1 AACCTTCACCACCCTCACCCTCAC
* ** ** *
13556590 AACCTTTACTGCCAGCAACCTCAC
1 AACCTTCACCACCCTCACCCTCAC
* *
13556614 CACCTTCATCACCCTCACCC
1 AACCTTCACCACCCTCACCC
13556634 GTACCACCTT
Statistics
Matches: 30, Mismatches: 14, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.53, G:0.03, T:0.19
Consensus pattern (24 bp):
AACCTTCACCACCCTCACCCTCAC
Found at i:13556670 original size:48 final size:48
Alignment explanation
Indices: 13556567--13556680 Score: 149
Period size: 48 Copynumber: 2.4 Consensus size: 48
13556557 CCCCACCTAA
* * *
13556567 ACCTTCACCACCCTCACCCTCACAACCTTTACTGCCAGCAACCTCACC
1 ACCTTCATCACCCTCACCCTCACAACCTTTACTGCCAACAACCTCAAC
* *
13556615 ACCTTCATCACCCTCACCCGT-ACCACCTTTACTTCCAACAACCTCAAC
1 ACCTTCATCACCCTCACCC-TCACAACCTTTACTGCCAACAACCTCAAC
* *
13556663 ACCTTCATAACCATCACC
1 ACCTTCATCACCCTCACC
13556681 AGAAACTTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 57 0.98
49 1 0.02
ACGTcount: A:0.27, C:0.49, G:0.03, T:0.21
Consensus pattern (48 bp):
ACCTTCATCACCCTCACCCTCACAACCTTTACTGCCAACAACCTCAAC
Found at i:13557460 original size:15 final size:15
Alignment explanation
Indices: 13557427--13557520 Score: 61
Period size: 15 Copynumber: 6.3 Consensus size: 15
13557417 ATCCAAAACC
13557427 CAAAAACCCT-AAAT
1 CAAAAACCCTAAAAT
* *
13557441 GAAAATCCCTAAAAT
1 CAAAAACCCTAAAAT
** *
13557456 CAAAAAAACTTAAA-
1 CAAAAACCCTAAAAT
*
13557470 CAAGAATCCCTAAAAT
1 CAA-AAACCCTAAAAT
13557486 CAAAAAACCCT-AAAT
1 C-AAAAACCCTAAAAT
*
13557501 -AAAAATCCCCAAAAT
1 CAAAAA-CCCTAAAAT
*
13557516 TAAAA
1 CAAAA
13557521 CCTCGAACAC
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
13 5 0.08
14 14 0.23
15 28 0.47
16 11 0.18
17 2 0.03
ACGTcount: A:0.60, C:0.22, G:0.02, T:0.16
Consensus pattern (15 bp):
CAAAAACCCTAAAAT
Found at i:13557478 original size:30 final size:30
Alignment explanation
Indices: 13557428--13557520 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 30
13557418 TCCAAAACCC
* **
13557428 AAAAACCCTAAATGAAAATCCCTAAAATCA
1 AAAAAACCTAAACAAAAATCCCTAAAATCA
* *
13557458 AAAAAACTTAAACAAGAATCCCTAAAATCA
1 AAAAAACCTAAACAAAAATCCCTAAAATCA
* * * *
13557488 AAAAACCCTAAATAAAAATCCCCAAAATTA
1 AAAAAACCTAAACAAAAATCCCTAAAATCA
13557518 AAA
1 AAA
13557521 CCTCGAACAC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.60, C:0.22, G:0.02, T:0.16
Consensus pattern (30 bp):
AAAAAACCTAAACAAAAATCCCTAAAATCA
Found at i:13568869 original size:11 final size:11
Alignment explanation
Indices: 13568853--13568877 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13568843 TAATATCATA
13568853 ATTTAATAATT
1 ATTTAATAATT
13568864 ATTTAATAATT
1 ATTTAATAATT
13568875 ATT
1 ATT
13568878 ATTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTAATAATT
Found at i:13568908 original size:21 final size:23
Alignment explanation
Indices: 13568884--13568931 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
13568874 TATTATTTCA
13568884 AAAAAATAATTTT-AT-ATTTTT
1 AAAAAATAATTTTAATAATTTTT
*
13568905 AAAATATAATTTTAATAATTTTT
1 AAAAAATAATTTTAATAATTTTT
13568928 AAAA
1 AAAA
13568932 TTATTTGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.50
22 2 0.08
23 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAAAATAATTTTAATAATTTTT
Found at i:13568908 original size:22 final size:23
Alignment explanation
Indices: 13568874--13568931 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 23
13568864 ATTTAATAAT
13568874 TATTATTTCAAAAAAATAATTTT-A
1 TATT-TTT-AAAAAAATAATTTTAA
*
13568898 TATTTTT-AAAATATAATTTTAA
1 TATTTTTAAAAAAATAATTTTAA
13568920 TAATTTTTAAAA
1 T-ATTTTTAAAA
13568932 TTATTTGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 12 0.40
22 2 0.07
23 9 0.30
24 7 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTTTTAAAAAAATAATTTTAA
Found at i:13568937 original size:21 final size:19
Alignment explanation
Indices: 13568886--13568937 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 19
13568876 TTATTTCAAA
*
13568886 AAAATAATTTTATATTTTT
1 AAAATTATTTTATATTTTT
13568905 AAAATATAATTTTAATAATTTTT
1 AAAAT-T-ATTTT-AT-ATTTTT
13568928 AAAATTATTT
1 AAAATTATTT
13568938 GCTGATGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.18
21 9 0.32
22 3 0.11
23 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAAATTATTTTATATTTTT
Found at i:13569668 original size:32 final size:32
Alignment explanation
Indices: 13569608--13569668 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
13569598 TTTGTGTGTT
* * * *
13569608 ATTGATTGTGTTAGATTTGTGGGCAGAAAAAA
1 ATTGATTGTGCTAGAGTTGTAGGAAGAAAAAA
*
13569640 ATTGTTTGTGCTAGAGTTGTAGGAAGAAA
1 ATTGATTGTGCTAGAGTTGTAGGAAGAAA
13569669 TTTTAAGAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (32 bp):
ATTGATTGTGCTAGAGTTGTAGGAAGAAAAAA
Found at i:13583940 original size:24 final size:24
Alignment explanation
Indices: 13583913--13583967 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
13583903 CAACAAAAAC
*
13583913 TTCCTCTT-TCTCTCCTTCTTTCTT
1 TTCCTCTTCTCTCTCC-TCTTCCTT
*
13583937 TTCCTCTTCTTTCTCCTCTTCCTT
1 TTCCTCTTCTCTCTCCTCTTCCTT
*
13583961 CTCCTCT
1 TTCCTCT
13583968 ATACCCACAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (24 bp):
TTCCTCTTCTCTCTCCTCTTCCTT
Found at i:13583944 original size:12 final size:12
Alignment explanation
Indices: 13583913--13583967 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
13583903 CAACAAAAAC
13583913 TTCCTCTTTC-T
1 TTCCTCTTTCTT
*
13583924 CTCCTTCTTTCTT
1 TTCC-TCTTTCTT
13583937 TTCCTC-TTCTT
1 TTCCTCTTTCTT
*
13583948 TCTCCTCTTCCTT
1 T-TCCTCTTTCTT
*
13583961 CTCCTCT
1 TTCCTCT
13583968 ATACCCACAG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
11 9 0.25
12 19 0.53
13 8 0.22
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (12 bp):
TTCCTCTTTCTT
Found at i:13590129 original size:18 final size:18
Alignment explanation
Indices: 13590108--13590150 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
13590098 AGCTGCATAC
* *
13590108 GAGCATGTGATTGCATCT
1 GAGCATGTGACTACATCT
13590126 GAGCATGTGACTACATCT
1 GAGCATGTGACTACATCT
*
13590144 GATCATG
1 GAGCATG
13590151 ATGTGCCTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (18 bp):
GAGCATGTGACTACATCT
Found at i:13593296 original size:14 final size:14
Alignment explanation
Indices: 13593279--13593305 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13593269 TTTATTTTAT
13593279 AAATAAAATAAATG
1 AAATAAAATAAATG
13593293 AAATAAAATAAAT
1 AAATAAAATAAAT
13593306 TTCCAAGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
AAATAAAATAAATG
Found at i:13594870 original size:22 final size:22
Alignment explanation
Indices: 13594832--13594874 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
13594822 TTTTAGTGTC
13594832 ATGATTCTTATTATATTTTATT
1 ATGATTCTTATTATATTTTATT
*
13594854 ATGATTACTT-TTTTATTTTAT
1 ATGATT-CTTATTATATTTTAT
13594875 GTGTGCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (22 bp):
ATGATTCTTATTATATTTTATT
Found at i:13595732 original size:29 final size:29
Alignment explanation
Indices: 13595701--13595848 Score: 122
Period size: 30 Copynumber: 5.0 Consensus size: 29
13595691 AACTTTCCAA
*
13595701 AAAGTTTGAGGGTCAAAATGCAATTTTTAA
1 AAAGTTTGAGGGTCAAAATG-AATTTTTAG
*
13595731 AAACTTT-AGGGTCAAAATGAAATTTTTAG
1 AAAGTTTGAGGGTCAAAATG-AATTTTTAG
* * *
13595760 AAAGTTTGGGGGTTAAAAATGAAGTTTTAG
1 AAAGTTTGAGGG-TCAAAATGAATTTTTAG
* * *
13595790 AAAG-TTCATGGGTCAAATTTGAATTTTTGGG
1 AAAGTTTGA-GGGTCAAA-ATGAATTTTT-AG
* *
13595821 AAAGTTTGA-GGTTAAAATATAATTTTTA
1 AAAGTTTGAGGGTCAAAAT-GAATTTTTA
13595849 AACAAAACAG
Statistics
Matches: 93, Mismatches: 18, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
29 33 0.35
30 45 0.48
31 12 0.13
32 3 0.03
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (29 bp):
AAAGTTTGAGGGTCAAAATGAATTTTTAG
Found at i:13595848 original size:60 final size:58
Alignment explanation
Indices: 13595701--13595850 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 58
13595691 AACTTTCCAA
* ** *
13595701 AAAGTTTGAGGGTCAAAATGCAATTTTTAAAAACTTTAGGGTCAAAATGAAATTTTTAG
1 AAAGTTTGA-GGTTAAAATATAATTTTTAAAAACTTCAGGGTCAAAATGAAATTTTTAG
* * * * * *
13595760 AAAGTTTGGGGGTTAAAA-ATGAAGTTTTAGAAAGTTCATGGGTCAAATTTG-AATTTTTGGG
1 AAAGTTT-GAGGTTAAAATAT-AATTTTTAAAAACTTCA-GGGTCAAA-ATGAAATTTTT-AG
13595821 AAAGTTTGAGGTTAAAATATAATTTTTAAA
1 AAAGTTTGAGGTTAAAATATAATTTTTAAA
13595851 CAAAACAGGG
Statistics
Matches: 72, Mismatches: 13, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
59 27 0.38
60 33 0.46
61 12 0.17
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (58 bp):
AAAGTTTGAGGTTAAAATATAATTTTTAAAAACTTCAGGGTCAAAATGAAATTTTTAG
Done.