Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 192 of 295
Found at i:61082195 original size:46 final size:46
Alignment explanation
Indices: 61082145--61082320 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
61082135 TGGTTGAGCA
61082145 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
61082191 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
61082236 CATCCGAACTCGTTGAGTTGAGTCCGAGTTAACTTATGGATACGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
61082284 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
61082321 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 62 0.58
47 28 0.26
48 3 0.03
50 2 0.02
51 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:61082301 original size:93 final size:93
Alignment explanation
Indices: 61082142--61082312 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
61082132 GGATGGTTGA
* * * *
61082142 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTAACTTATGGATACGAACGCCCGAACTCGTTGAGT
61082207 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
61082235 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTAACTTATGGATACGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTAACTTATGGATACGAACGCCCGAACTCGTTGAGT
*
61082300 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
61082313 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTAACTTATGGATACGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:61095373 original size:38 final size:39
Alignment explanation
Indices: 61095324--61095398 Score: 134
Period size: 38 Copynumber: 1.9 Consensus size: 39
61095314 TGGAAATTAA
61095324 TAATTTAATTGTTAATAACTG-TTTTTTTTATGGATGAT
1 TAATTTAATTGTTAATAACTGTTTTTTTTTATGGATGAT
*
61095362 TAATTTAATTGTTAATAAGTGTTTTTTTTTATGGATG
1 TAATTTAATTGTTAATAACTGTTTTTTTTTATGGATG
61095399 CCGAATGTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 20 0.57
39 15 0.43
ACGTcount: A:0.28, C:0.01, G:0.15, T:0.56
Consensus pattern (39 bp):
TAATTTAATTGTTAATAACTGTTTTTTTTTATGGATGAT
Found at i:61096925 original size:6 final size:6
Alignment explanation
Indices: 61096895--61096969 Score: 82
Period size: 6 Copynumber: 12.3 Consensus size: 6
61096885 AAGAAACATT
* * *
61096895 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCA-A GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
61096944 ATCAGA ATCAGA ATCAGA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCAGA AT
61096970 TAGGTGACAG
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
5 3 0.05
6 50 0.86
7 3 0.05
8 2 0.03
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (6 bp):
ATCAGA
Found at i:61096945 original size:37 final size:37
Alignment explanation
Indices: 61096904--61097003 Score: 128
Period size: 37 Copynumber: 2.7 Consensus size: 37
61096894 TATCAGAACT
*
61096904 AGAATCAAAATGAGAATCAGAATCAGAATCAAGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAAGTGAC
* * *
61096941 AGAATCAGAATCAGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGAATCAAGTGAC
* * * *
61096978 AGAATTAGAATCAGAATTAGTATCAG
1 AGAATCAAAATCAGAATCAGAATCAG
61097004 GTAACAGAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.20
Consensus pattern (37 bp):
AGAATCAAAATCAGAATCAGAATCAGAATCAAGTGAC
Found at i:61096953 original size:31 final size:31
Alignment explanation
Indices: 61096916--61097025 Score: 103
Period size: 31 Copynumber: 3.4 Consensus size: 31
61096906 AATCAAAATG
61096916 AGAATCAGAATCAGAATCAAGTGACAGAATC
1 AGAATCAGAATCAGAATCAAGTGACAGAATC
*
61096947 AGAATCAGAATCAGAATCAGAATTAGGTGACAGAATT
1 AGAATCAGAATCAGAATC---A--A-GTGACAGAATC
* * * *
61096984 AGAATCAGAATTAGTATCAGGTAACAGAATC
1 AGAATCAGAATCAGAATCAAGTGACAGAATC
* *
61097015 AAAATTAGAAT
1 AGAATCAGAAT
61097026 GTGAAGGCAA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
31 36 0.55
34 2 0.03
36 1 0.02
37 26 0.40
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAAGTGACAGAATC
Found at i:61097021 original size:37 final size:36
Alignment explanation
Indices: 61096904--61097025 Score: 119
Period size: 37 Copynumber: 3.5 Consensus size: 36
61096894 TATCAGAACT
* *
61096904 AGAATCAAAATGAGAATCAGAATCAGAATCAAGTGAC
1 AGAATCAAAATTAGAATCAGAATCAGAATCAGGT-AC
* * *
61096941 AGAATCAGAATCAGAATCAGAATCAGAATTAGGT--
1 AGAATCAAAATTAGAATCAGAATCAGAATCAGGTAC
* * *
61096975 -G-A-CAGAATTAGAATCAGAATTAGTATCAGGTAAC
1 AGAATCAAAATTAGAATCAGAATCAGAATCAGGT-AC
61097009 AGAATCAAAATTAGAAT
1 AGAATCAAAATTAGAAT
61097026 GTGAAGGCAA
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
31 25 0.36
32 1 0.01
33 1 0.01
35 1 0.01
36 1 0.01
37 41 0.59
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.20
Consensus pattern (36 bp):
AGAATCAAAATTAGAATCAGAATCAGAATCAGGTAC
Found at i:61098738 original size:39 final size:39
Alignment explanation
Indices: 61098621--61098830 Score: 316
Period size: 39 Copynumber: 5.3 Consensus size: 39
61098611 GCTCCTCGTT
* * *
61098621 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
61098661 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
61098701 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
61098740 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
61098779 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
61098818 CAAATGCCTTCGG
1 CAAATGCCTTCGG
61098831 ATCTTAGTCC
Statistics
Matches: 161, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 114 0.71
40 45 0.28
41 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:61098866 original size:78 final size:78
Alignment explanation
Indices: 61098621--61098882 Score: 302
Period size: 78 Copynumber: 3.3 Consensus size: 78
61098611 GCTCCTCGTT
* * * *
61098621 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGGACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCC
* * *
61098684 GGATTTAGTAACTCGCA
62 GGAATTAGTATCTAGCA
61098701 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
*
61098766 TTAGTATCTCGCA
66 TTAGTATCTAGCA
* *
61098779 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGG-GCTTAGCCCGGA
61098844 TATT-GTCA-CTTAGCA
65 -ATTAGT-ATC-TAGCA
*
61098859 C-GA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
61098883 CATCATTCAA
Statistics
Matches: 165, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
78 85 0.52
79 56 0.34
80 24 0.15
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
TTAGTATCTAGCA
Found at i:61118803 original size:15 final size:15
Alignment explanation
Indices: 61118783--61118828 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
61118773 GGAGCATGGT
61118783 AAGAAAATAATGAAA
1 AAGAAAATAATGAAA
*
61118798 AAGAAAATGATGAAGA
1 AAGAAAATAATGAA-A
*
61118814 AA-AAAA-AAGGAAA
1 AAGAAAATAATGAAA
61118827 AA
1 AA
61118829 AAGTTCTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 3 0.11
14 4 0.15
15 17 0.63
16 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (15 bp):
AAGAAAATAATGAAA
Found at i:61120270 original size:40 final size:41
Alignment explanation
Indices: 61120213--61120398 Score: 247
Period size: 40 Copynumber: 4.7 Consensus size: 41
61120203 CTAACGGGGT
* * *
61120213 TAAGTCCCGAAGACATTTGTGCTAGTGATTAAT-TCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
*
61120253 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
*
61120293 TAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
* * *
61120333 TAAGTCCCGAAGGCATTTGTGCTAGTGAC-CATATCCGGAC
1 TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
* *
61120373 TAAGACCCGAAGGC-CTTGTGCGAGTG
1 TAAGTCCCGAAGGCATTTGTGCGAGTG
61120399 GTTATTACAG
Statistics
Matches: 134, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 12 0.09
40 122 0.91
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (41 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTGACTAATATCCGGGC
Found at i:61127373 original size:20 final size:20
Alignment explanation
Indices: 61127348--61127395 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
61127338 GGTTTTGATA
*
61127348 TACATGAT-TGATATGATGTG
1 TACATGATATG-TATGATATG
61127368 TACATGATATGTATGATATG
1 TACATGATATGTATGATATG
*
61127388 CACATGAT
1 TACATGAT
61127396 GTATTCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (20 bp):
TACATGATATGTATGATATG
Found at i:61127471 original size:26 final size:24
Alignment explanation
Indices: 61127443--61127537 Score: 122
Period size: 25 Copynumber: 3.9 Consensus size: 24
61127433 AGGAAGTGCA
*
61127443 AAAAGGGC-TATGCCCCAGTTTACC
1 AAAAGGGCTTTTGCCCCAGTTTA-C
*
61127467 GAAAAGGGCTTTTGCCCCAGTTTATT
1 -AAAAGGGCTTTTGCCCCAGTTTA-C
61127493 AAAAGGGCTTTTGCCCCAGTTTATC
1 AAAAGGGCTTTTGCCCCAGTTTA-C
61127518 AAAAGGGC-TTTGCCCCAGTT
1 AAAAGGGCTTTTGCCCCAGTT
61127538 ATTAAAGAGG
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
24 12 0.18
25 40 0.62
26 13 0.20
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTTTGCCCCAGTTTAC
Found at i:61127795 original size:31 final size:31
Alignment explanation
Indices: 61127757--61127820 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
61127747 CCATTATAGT
61127757 AAAGGCTTCAGCCCAATAATATGAAATATGA
1 AAAGGCTTCAGCCCAATAATATGAAATATGA
* * **
61127788 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCAGCCCAATAATATGAAATATGA
61127819 AA
1 AA
61127821 CATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAATAATATGAAATATGA
Found at i:61132928 original size:18 final size:18
Alignment explanation
Indices: 61132905--61132944 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
61132895 TCAAGAAAGA
61132905 GTTGCGTACCTAGTATCC
1 GTTGCGTACCTAGTATCC
61132923 GTTGCGTACCTAGTATCC
1 GTTGCGTACCTAGTATCC
61132941 -TTGC
1 GTTGC
61132945 AGGTGTGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.15, C:0.28, G:0.23, T:0.35
Consensus pattern (18 bp):
GTTGCGTACCTAGTATCC
Found at i:61133374 original size:27 final size:27
Alignment explanation
Indices: 61133304--61133470 Score: 163
Period size: 27 Copynumber: 6.2 Consensus size: 27
61133294 TTTACCTAGA
* * * *
61133304 GCCCTTATGTGATAAAATGACTATATT
1 GCCCTTATATGGTAAAATGACTGTTTT
* * * *
61133331 ACCCTTATGTTGAAAAATGACTGTTTT
1 GCCCTTATATGGTAAAATGACTGTTTT
* *
61133358 GCCTTTGTATGGTAAAATGACTGTTTT
1 GCCCTTATATGGTAAAATGACTGTTTT
* *
61133385 ACCCTTATATGGTAAAATAACTGTTTT
1 GCCCTTATATGGTAAAATGACTGTTTT
* * * *
61133412 GCCTTTATGTGGTGAAATGATTGTTTT
1 GCCCTTATATGGTAAAATGACTGTTTT
* * *
61133439 TCCCTTATATGGTAAGATTACTGTTTT
1 GCCCTTATATGGTAAAATGACTGTTTT
61133466 GCCCT
1 GCCCT
61133471 ATGTGATGTA
Statistics
Matches: 110, Mismatches: 30, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 110 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (27 bp):
GCCCTTATATGGTAAAATGACTGTTTT
Found at i:61133402 original size:54 final size:54
Alignment explanation
Indices: 61133316--61133468 Score: 189
Period size: 54 Copynumber: 2.8 Consensus size: 54
61133306 CCTTATGTGA
* * * * * * *
61133316 TAAAATGACTATATTACCCTTATGTTGAAAAATGACTGTTTTGCCTTTGTATGG
1 TAAAATGACTGTTTTACCCTTATATGGTAAAATAACTGTTTTGCCTTTATATGG
*
61133370 TAAAATGACTGTTTTACCCTTATATGGTAAAATAACTGTTTTGCCTTTATGTGG
1 TAAAATGACTGTTTTACCCTTATATGGTAAAATAACTGTTTTGCCTTTATATGG
* * * * *
61133424 TGAAATGATTGTTTTTCCCTTATATGGTAAGATTACTGTTTTGCC
1 TAAAATGACTGTTTTACCCTTATATGGTAAAATAACTGTTTTGCC
61133469 CTATGTGATG
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 86 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (54 bp):
TAAAATGACTGTTTTACCCTTATATGGTAAAATAACTGTTTTGCCTTTATATGG
Found at i:61133691 original size:45 final size:45
Alignment explanation
Indices: 61133625--61133743 Score: 195
Period size: 45 Copynumber: 2.7 Consensus size: 45
61133615 AGGAAGTGTT
*
61133625 TTATACTAGCAGCTCTGCTACAAATCACTGATGGCTCTAAGCCTA
1 TTATACTGGCAGCTCTGCTACAAATCACTGATGGCTCTAAGCCTA
* *
61133670 TTATACTGGCAACTCTACTACAAATCACTGATGGCTCTAAGCCTA
1 TTATACTGGCAGCTCTGCTACAAATCACTGATGGCTCTAAGCCTA
*
61133715 TTATACTGGCAGCTCTGCTGCAAAT-ACTG
1 TTATACTGGCAGCTCTGCTACAAATCACTG
61133744 TTTAGTGCTA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
44 4 0.06
45 64 0.94
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (45 bp):
TTATACTGGCAGCTCTGCTACAAATCACTGATGGCTCTAAGCCTA
Found at i:61135275 original size:24 final size:24
Alignment explanation
Indices: 61135223--61135275 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
61135213 GAGTGTTATG
* *
61135223 TGGAGGAAATCAAGGAAAGGATGG
1 TGGAGAAAATCAAGGAAAGGATGA
* * *
61135247 GGGAGAAAATCAAGGAGAGGATTA
1 TGGAGAAAATCAAGGAAAGGATGA
61135271 TGGAG
1 TGGAG
61135276 GGATTTTAGG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.42, T:0.13
Consensus pattern (24 bp):
TGGAGAAAATCAAGGAAAGGATGA
Found at i:61146097 original size:28 final size:27
Alignment explanation
Indices: 61146048--61146145 Score: 106
Period size: 28 Copynumber: 3.5 Consensus size: 27
61146038 TATATTGAGC
* *
61146048 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
61146075 CGCACACTTTAGTGCTACGTAATCAAAT
1 CGCACAC-TTAGTGCTACATAATCAACT
* * *
61146103 CGCACACTTTAGTCCTACATAGTAAAACT
1 CGCACAC-TTAGTGCTACATAAT-CAACT
61146132 CGCACACTTAGTGC
1 CGCACACTTAGTGC
61146146 CGCTTATGTT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
27 7 0.12
28 42 0.71
29 10 0.17
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:61164060 original size:20 final size:20
Alignment explanation
Indices: 61164031--61164075 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
61164021 ATCACATGTA
* *
61164031 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
61164051 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
61164071 TTCAT
1 TTCAT
61164076 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:61167316 original size:13 final size:13
Alignment explanation
Indices: 61167298--61167349 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
61167288 AGTTTGGAAA
61167298 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
61167311 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
61167324 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
61167337 T-CTTTTGAAAAG
1 TGCTTTTGAAAAG
61167349 T
1 T
61167350 TTAGTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 10 0.29
13 25 0.71
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:61168682 original size:13 final size:13
Alignment explanation
Indices: 61168664--61168715 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
61168654 AGTTTGGAAA
61168664 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
61168677 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
61168690 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
61168703 T-CTTTTGAAAAG
1 TGCTTTTGAAAAG
61168715 T
1 T
61168716 TTAGTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 10 0.29
13 25 0.71
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:61170047 original size:13 final size:13
Alignment explanation
Indices: 61170029--61170080 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
61170019 AGTTTGGAAA
61170029 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
61170042 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
61170055 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
61170068 T-CTTTTGAAAAG
1 TGCTTTTGAAAAG
61170080 T
1 T
61170081 TTAGTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 10 0.29
13 25 0.71
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:61175935 original size:30 final size:30
Alignment explanation
Indices: 61175901--61175960 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
61175891 CCTTAACTCG
61175901 AACTTTGGCAAAATTACAATTTTGCCCCTA
1 AACTTTGGCAAAATTACAATTTTGCCCCTA
* * * **
61175931 AACTTTTGCATATTTACTCTTTTGCCCCTA
1 AACTTTGGCAAAATTACAATTTTGCCCCTA
61175961 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (30 bp):
AACTTTGGCAAAATTACAATTTTGCCCCTA
Found at i:61183067 original size:93 final size:93
Alignment explanation
Indices: 61182952--61183124 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
61182942 TGTAACCCAC
* *
61182952 CCATAAGCGAACTCAGACTCAACTCAACAAGCTCGGATGCCCAGTTACATCTCACGAACTCTGAC
1 CCATAAGCGAACTCAGACTCAACACAACAAGCTCGGATGCCCAGTTACATCTCACGAACTCGGAC
*
61183017 TCAACTCAATGAGTTCGGAGGTTCGCAT
66 TCAACTCAACGAGTTCGGAGGTTCGCAT
* * * *
61183045 CCATAAGTGAACTCGGACTCAACACAACGAGCTCGGATGCCTAGTTACATCTCACGAACTCGGAC
1 CCATAAGCGAACTCAGACTCAACACAACAAGCTCGGATGCCCAGTTACATCTCACGAACTCGGAC
61183110 TCAACTCAACGAGTT
66 TCAACTCAACGAGTT
61183125 TAGATGCCCA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (93 bp):
CCATAAGCGAACTCAGACTCAACACAACAAGCTCGGATGCCCAGTTACATCTCACGAACTCGGAC
TCAACTCAACGAGTTCGGAGGTTCGCAT
Found at i:61183132 original size:47 final size:46
Alignment explanation
Indices: 61182959--61183122 Score: 165
Period size: 47 Copynumber: 3.5 Consensus size: 46
61182949 CACCCATAAG
* *
61182959 CGAACTCAGACTCAACTCAACAAGCTCGGATGCCCAGTTACATCTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGATG-CCAGTTACATCTCA
* * * * *
61183006 CGAACTCTGACTCAACTCAATGAGTTCGGA-G---GTTCGCATCCATAA
1 CGAACTCGGACTCAACTCAACGAGCTCGGATGCCAGTT-ACAT-C-TCA
* *
61183051 GTGAACTCGGACTCAACACAACGAGCTCGGATGCCTAGTTACATCTCA
1 -CGAACTCGGACTCAACTCAACGAGCTCGGATGCC-AGTTACATCTCA
61183099 CGAACTCGGACTCAACTCAACGAG
1 CGAACTCGGACTCAACTCAACGAG
61183123 TTTAGATGCC
Statistics
Matches: 93, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 1 0.01
45 2 0.02
46 26 0.28
47 49 0.53
48 2 0.02
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.20
Consensus pattern (46 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGATGCCAGTTACATCTCA
Found at i:61186039 original size:18 final size:17
Alignment explanation
Indices: 61186001--61186050 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
61185991 GAAAAAGAGC
61186001 AAAACAAAAGAAAGTGA
1 AAAACAAAAGAAAGTGA
*
61186018 AAAAGAAAAGAAAGTG-
1 AAAACAAAAGAAAGTGA
*
61186034 GAAA-AAAAGAAAG-GA
1 AAAACAAAAGAAAGTGA
61186049 AA
1 AA
61186051 GAATGAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 1 0.03
15 10 0.34
16 3 0.10
17 15 0.52
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (17 bp):
AAAACAAAAGAAAGTGA
Found at i:61190649 original size:28 final size:28
Alignment explanation
Indices: 61190586--61190763 Score: 225
Period size: 28 Copynumber: 6.4 Consensus size: 28
61190576 ATAATAAGTC
* *
61190586 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
61190613 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
61190641 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
61190669 CTCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
61190697 CGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAATCAAACT
* * * *
61190724 CGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAA-TCAAACT
61190753 CGCACACTTAG
1 CGCACACTTAG
61190764 CGCCAATCTC
Statistics
Matches: 134, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
27 43 0.32
28 78 0.58
29 13 0.10
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:61198829 original size:28 final size:28
Alignment explanation
Indices: 61198766--61198943 Score: 234
Period size: 28 Copynumber: 6.4 Consensus size: 28
61198756 ATAATAAGTC
* *
61198766 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
61198793 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
61198821 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
61198849 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
61198877 CGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAATCAAACT
* * * *
61198904 CGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAA-TCAAACT
61198933 CGCACACTTAG
1 CGCACACTTAG
61198944 CGCCAATCTC
Statistics
Matches: 136, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
27 43 0.32
28 80 0.59
29 13 0.10
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:61202826 original size:38 final size:38
Alignment explanation
Indices: 61202784--61202895 Score: 91
Period size: 38 Copynumber: 3.2 Consensus size: 38
61202774 GCTCTCTTGT
61202784 CTACATGGGATACATCCCGTATCACACATGTGACCTAG
1 CTACATGGGATACATCCCGTATCACACATGTGACCTAG
** * * *
61202822 CTACAT-TTAT-C-TCTCACGTAGCTCTC-T-TG---T--
1 CTACATGGGATACATC-C-CGTATCACACATGTGACCTAG
61202852 CTACATGGGATACATCCCGTATCACACATGTGACCTAG
1 CTACATGGGATACATCCCGTATCACACATGTGACCTAG
61202890 CTACAT
1 CTACAT
61202896 TTATCTCTCA
Statistics
Matches: 52, Mismatches: 10, Indels: 24
0.60 0.12 0.28
Matches are distributed among these distances:
30 6 0.12
31 9 0.17
32 4 0.08
33 4 0.08
35 4 0.08
36 4 0.08
37 9 0.17
38 12 0.23
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (38 bp):
CTACATGGGATACATCCCGTATCACACATGTGACCTAG
Found at i:61202829 original size:68 final size:68
Alignment explanation
Indices: 61202736--61202961 Score: 434
Period size: 68 Copynumber: 3.3 Consensus size: 68
61202726 TTCACTTGGA
* *
61202736 ATCACTCATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
61202801 CGT
66 CGT
61202804 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
61202869 CGT
66 CGT
61202872 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
61202937 CGT
66 CGT
61202940 ATCACACATGTGACCTAGCTAC
1 ATCACACATGTGACCTAGCTAC
61202962 TATATAGTAT
Statistics
Matches: 156, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 156 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (68 bp):
ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
CGT
Found at i:61202994 original size:136 final size:135
Alignment explanation
Indices: 61202736--61202987 Score: 418
Period size: 136 Copynumber: 1.9 Consensus size: 135
61202726 TTCACTTGGA
*
61202736 ATCACTCATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
* *
61202801 CGTATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACA
66 CGTATCACACATGTGACCTAGCTACATATATATCT-ACGTAGCTCTCTTGTCTACATGGGATACA
61202866 TCCCGT
130 TCCCGT
*
61202872 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
61202937 CGTATCACACATGTGACCTAGCTACTATATAGTATCT-CGTAGC-CTTCTTGT
66 CGTATCACACATGTGACCTAGCTAC-ATATA-TATCTACGTAGCTC-TCTTGT
61202988 ACACATGATG
Statistics
Matches: 109, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
135 1 0.01
136 100 0.92
137 4 0.04
138 4 0.04
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (135 bp):
ATCACACATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
CGTATCACACATGTGACCTAGCTACATATATATCTACGTAGCTCTCTTGTCTACATGGGATACAT
CCCGT
Found at i:61203017 original size:136 final size:135
Alignment explanation
Indices: 61202742--61203029 Score: 397
Period size: 136 Copynumber: 2.1 Consensus size: 135
61202732 TGGAATCACT
*
61202742 CATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATC
1 CATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATC
* * *
61202807 ACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGT
66 ACACATGTGACCTAGCTACATATATATCT-ACGTAGCTCTCTTGTCTACATGGGATACATCCCGC
*
61202872 ATCACA
130 ACCACA
61202878 CATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATC
1 CATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATC
* *
61202943 ACACATGTGACCTAGCTACTATATAGTATCT-CGTAGC-CTTCTTGTAC-ACATGATG-TGCA-C
66 ACACATGTGACCTAGCTAC-ATATA-TATCTACGTAGCTC-TCTTGT-CTACATG-GGATACATC
* *
61203003 TCGGCACCATA
126 -CCGCACCACA
61203014 CATGTGACCTAGCTAC
1 CATGTGACCTAGCTAC
61203030 GCTCCCTCTA
Statistics
Matches: 137, Mismatches: 9, Indels: 12
0.87 0.06 0.08
Matches are distributed among these distances:
135 2 0.01
136 125 0.91
137 6 0.04
138 4 0.03
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (135 bp):
CATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTATC
ACACATGTGACCTAGCTACATATATATCTACGTAGCTCTCTTGTCTACATGGGATACATCCCGCA
CCACA
Found at i:61229689 original size:65 final size:67
Alignment explanation
Indices: 61229543--61229697 Score: 269
Period size: 65 Copynumber: 2.3 Consensus size: 67
61229533 TTCACTTGGA
* *
61229543 ATCACTCATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATTTA-CTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
61229608 CGT
65 CGT
61229611 ATCACACATGTGACCTAGCTACATTTA-TCTCACGTAGCTCTCTTGTCTACAT-GGATACATCCC
1 ATCACACATGTGACCTAGCTACATTTACTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCC
61229674 GT
66 GT
61229676 ATCACACATGTGACCTAGCTAC
1 ATCACACATGTGACCTAGCTAC
61229698 TATATAGTAT
Statistics
Matches: 85, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
65 35 0.41
66 25 0.29
68 25 0.29
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31
Consensus pattern (67 bp):
ATCACACATGTGACCTAGCTACATTTACTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCC
GT
Found at i:61231419 original size:26 final size:26
Alignment explanation
Indices: 61231390--61231442 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
61231380 TAATATATTT
*
61231390 TCGTAAAAATTTTACCATGGGTAAAA
1 TCGTAAAAATTTTACCAAGGGTAAAA
* *
61231416 TCGTCATAATTTTACCAAGGGTAAAA
1 TCGTAAAAATTTTACCAAGGGTAAAA
61231442 T
1 T
61231443 TGGGATGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (26 bp):
TCGTAAAAATTTTACCAAGGGTAAAA
Found at i:61233356 original size:38 final size:38
Alignment explanation
Indices: 61233312--61233387 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
61233302 GGTGCAAGTA
*
61233312 TACACTATCATTGACAAGTACTAAAGTGATAAGTATAT
1 TACACTATCATTGACAAGTAATAAAGTGATAAGTATAT
61233350 TACACTATCATTGACAAGTAATAAAGTGATAAGTATAT
1 TACACTATCATTGACAAGTAATAAAGTGATAAGTATAT
61233388 CGAATATCGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (38 bp):
TACACTATCATTGACAAGTAATAAAGTGATAAGTATAT
Found at i:61239676 original size:43 final size:43
Alignment explanation
Indices: 61239583--61239733 Score: 160
Period size: 43 Copynumber: 3.5 Consensus size: 43
61239573 GGTTATCGAG
* *
61239583 ATGTGATTACATGTAAGACCATGTTTGGGACATTGGCAT-TGT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCTTT
*
61239625 ACTGTGATTACATGTAAGACCATGTCTGGGATATTGGCATCTTT
1 A-TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCTTT
* * *** * * **
61239669 GTATGATTTTGTGTAAGACCCTGTCTGGGACAGTGGCATCGAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCTTT
* *
61239712 ATGTGGTAACATGTAAGACCAT
1 ATGTGATTACATGTAAGACCAT
61239734 ATCTAGGATA
Statistics
Matches: 86, Mismatches: 21, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
42 1 0.01
43 83 0.97
44 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCTTT
Found at i:61240753 original size:34 final size:34
Alignment explanation
Indices: 61240687--61240762 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
61240677 AGTAACAGTC
* * *
61240687 CAGTATCAGTGTGGACCTTAGCCCATAGCAGTAG
1 CAGTATTAATGTGGACCTTAGCCCATAGCAGTAA
* *
61240721 TAGTATTAATGTGGGCCTTAGCCCATTA-CAGTAA
1 CAGTATTAATGTGGACCTTAGCCCA-TAGCAGTAA
61240755 CAGTATTA
1 CAGTATTA
61240763 GTAATGCAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 33 0.94
35 2 0.06
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (34 bp):
CAGTATTAATGTGGACCTTAGCCCATAGCAGTAA
Found at i:61248513 original size:34 final size:34
Alignment explanation
Indices: 61248441--61248518 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
61248431 AGTAATAGAC
* * **
61248441 CAGTATCAGTGTGGGCCTTAGCCCAAAGTAGTTG
1 CAGTATCAATGTAGGCCTTAGCCCAAAGTAGTAA
*
61248475 CAGTATCAATGTAGGCCTTAGCCCATTAG-AGTAA
1 CAGTATCAATGTAGGCCTTAGCCCA-AAGTAGTAA
61248509 CAGTATCAAT
1 CAGTATCAAT
61248519 AATGCAACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
34 36 0.95
35 2 0.05
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (34 bp):
CAGTATCAATGTAGGCCTTAGCCCAAAGTAGTAA
Found at i:61254526 original size:71 final size:66
Alignment explanation
Indices: 61254393--61254528 Score: 164
Period size: 71 Copynumber: 2.0 Consensus size: 66
61254383 AGGAAGCGTT
* * * * *
61254393 CTGGTAGCCTCGCTACAATCTGGTGCCTCGCCATATATATCTGTTCTGGTGACTTCGTCACAATA
1 CTGGTAGCCTCGCTACAATCTGGTGCCCCACCATATATATCTGTTCTGGTGACCTAGCCACAATA
61254458 C
66 C
* *
61254459 CTGGTAGCCTCGCTGCAATCTGGTGGCTTCACCACACATATATATCTGTTCTGGTGGCCTAGCCA
1 CTGGTAGCCTCGCTACAATCTGGT-GC--C-CCAC-CATATATATCTGTTCTGGTGACCTAGCCA
61254524 CAATA
61 CAATA
61254529 TCTGTATCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
66 23 0.40
67 2 0.03
69 1 0.02
70 2 0.03
71 30 0.52
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.30
Consensus pattern (66 bp):
CTGGTAGCCTCGCTACAATCTGGTGCCCCACCATATATATCTGTTCTGGTGACCTAGCCACAATA
C
Found at i:61254529 original size:26 final size:27
Alignment explanation
Indices: 61254500--61254559 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
61254490 CCACACATAT
*
61254500 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
61254526 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
61254553 ATATCTG
1 ATATCTG
61254560 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:61265063 original size:62 final size:62
Alignment explanation
Indices: 61264966--61265089 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
61264956 TATCTTTGAA
61264966 AACACAGTAGCACCTTTCAACTGATCGAATAAGTCATCAATTCAAGGCAGAGGATATTTGTT
1 AACACAGTAGCACCTTTCAACTGATCGAATAAGTCATCAATTCAAGGCAGAGGATATTTGTT
61265028 AACACAGTAGCACCTTTCAACTGATCGAATAAGTCATCAATTCAAGGCAGAGGATATTTGTT
1 AACACAGTAGCACCTTTCAACTGATCGAATAAGTCATCAATTCAAGGCAGAGGATATTTGTT
61265090 CTTTATATTC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (62 bp):
AACACAGTAGCACCTTTCAACTGATCGAATAAGTCATCAATTCAAGGCAGAGGATATTTGTT
Found at i:61269713 original size:30 final size:30
Alignment explanation
Indices: 61269679--61269739 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
61269669 TCTTTAACTC
61269679 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
61269709 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
61269739 A
1 A
61269740 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:61273096 original size:18 final size:18
Alignment explanation
Indices: 61273054--61273096 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
61273044 GCCCATTCCG
* *
61273054 AAGTATATATATATACAT
1 AAGTATGTATATATACAC
61273072 ATA-TATGTATATATACAC
1 A-AGTATGTATATATACAC
61273090 AAGTATG
1 AAGTATG
61273097 CCCATTCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (18 bp):
AAGTATGTATATATACAC
Found at i:61273603 original size:56 final size:55
Alignment explanation
Indices: 61273541--61273723 Score: 208
Period size: 56 Copynumber: 3.3 Consensus size: 55
61273531 GAGATTGGCG
* *
61273541 CTAAGTGTGCGGGTTTAAATTGTGCAGCACTAAGTGTGCGA-ATTGACTATGTAGCA
1 CTAAGTGTGCGAGTTT-AATTGTG-AGCACTAAGTGTGCGAGATTGATTATGTAGCA
* * *
61273597 CTAAGTGTACGAGTTTGACTATGT-AGCACTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-AAT-TGTGAGCACTAAGTGTGCGAGATTGATTATGTAGCA
* * * * * *
61273653 CTAAGTGTGCGAGCTTGATTATGTAGAACTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAATTGTG-AGCACTAAGTGTGCGAGATTGATTATGTAGCA
61273709 CTAAGTGTGCGAGTT
1 CTAAGTGTGCGAGTT
61273724 GATTATATAG
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
54 2 0.02
55 17 0.16
56 86 0.80
57 3 0.03
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (55 bp):
CTAAGTGTGCGAGTTTAATTGTGAGCACTAAGTGTGCGAGATTGATTATGTAGCA
Found at i:61273622 original size:28 final size:28
Alignment explanation
Indices: 61273566--61273746 Score: 258
Period size: 28 Copynumber: 6.5 Consensus size: 28
61273556 TAAATTGTGC
* *
61273566 AGCACTAAGTGTGCGA-ATTGACTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
* * *
61273593 AGCACTAAGTGTACGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
61273621 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
61273649 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
* * *
61273677 AGAACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
61273705 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
61273732 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
61273747 GACTTATTAT
Statistics
Matches: 143, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
27 39 0.27
28 104 0.73
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTTGATTATGT
Found at i:61281309 original size:18 final size:18
Alignment explanation
Indices: 61281267--61281309 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
61281257 GCCCATTCCG
* *
61281267 AAGTATATATATATACAT
1 AAGTATGTATATATACAC
61281285 ATA-TATGTATATATACAC
1 A-AGTATGTATATATACAC
61281303 AAGTATG
1 AAGTATG
61281310 CCCATTCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (18 bp):
AAGTATGTATATATACAC
Found at i:61281819 original size:28 final size:28
Alignment explanation
Indices: 61281779--61281932 Score: 247
Period size: 28 Copynumber: 5.5 Consensus size: 28
61281769 TAAATTGTGC
* *
61281779 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
61281807 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
61281835 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
* *
61281863 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
61281891 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGCTTGATTATGT
*
61281918 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
61281933 GACTTATTAT
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 24 0.20
28 97 0.80
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTTGATTATGT
Found at i:61288433 original size:13 final size:13
Alignment explanation
Indices: 61288417--61288442 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61288407 AATCAATTAG
61288417 GTTAAACAAAATA
1 GTTAAACAAAATA
61288430 GTTAAACAAAATA
1 GTTAAACAAAATA
61288443 AAGGAGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
GTTAAACAAAATA
Found at i:61294226 original size:25 final size:24
Alignment explanation
Indices: 61294198--61294343 Score: 105
Period size: 25 Copynumber: 5.9 Consensus size: 24
61294188 CAAACCAAGA
*
61294198 CTTTATGGCGAGTTATCTGTAAAGC
1 CTTTGTGGCGAGTTAT-TGTAAAGC
* * *
61294223 CTTTGTGGTGAATTATTAGAAAAGC
1 CTTTGTGGCGAGTTATT-GTAAAGC
*
61294248 TTTTGTGGCGAGTTATTTGTAAAGC
1 CTTTGTGGCGAGTTA-TTGTAAAGC
* * ***
61294273 CTTTGTGGTGAATTATCAAAAAAGC
1 CTTTGTGGCGAGTTAT-TGTAAAGC
* * *
61294298 CTTTGTGGCAAATTATTAGAAAAGC
1 CTTTGTGGCGAGTTATT-GTAAAGC
* *
61294323 CTTTGTGGTGAATTATT-TAAA
1 CTTTGTGGCGAGTTATTGTAAA
61294344 AATTCTTTGT
Statistics
Matches: 96, Mismatches: 21, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
23 3 0.03
24 2 0.02
25 89 0.93
26 2 0.02
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (24 bp):
CTTTGTGGCGAGTTATTGTAAAGC
Found at i:61294260 original size:50 final size:49
Alignment explanation
Indices: 61294198--61294355 Score: 199
Period size: 50 Copynumber: 3.2 Consensus size: 49
61294188 CAAACCAAGA
* *
61294198 CTTTATGGCGAGTTATCTGTAAAGCCTTTGTGGTGAATTATTAGAAAAGC
1 CTTTGTGGCGAGTTAT-TGTAAAGCCTTTGTGGTGAATTATTAAAAAAGC
* *
61294248 TTTTGTGGCGAGTTATTTGTAAAGCCTTTGTGGTGAATTATCAAAAAAGC
1 CTTTGTGGCGAGTTA-TTGTAAAGCCTTTGTGGTGAATTATTAAAAAAGC
* * * * **
61294298 CTTTGTGGCAAATTATTAGAAAAGCCTTTGTGGTGAATTATTTAAAAATT
1 CTTTGTGGCGAGTTATT-GTAAAGCCTTTGTGGTGAATTATTAAAAAAGC
61294348 CTTTGTGG
1 CTTTGTGG
61294356 TGTATTGTAT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
49 2 0.02
50 91 0.97
51 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (49 bp):
CTTTGTGGCGAGTTATTGTAAAGCCTTTGTGGTGAATTATTAAAAAAGC
Found at i:61294345 original size:25 final size:25
Alignment explanation
Indices: 61294218--61294357 Score: 149
Period size: 25 Copynumber: 5.6 Consensus size: 25
61294208 AGTTATCTGT
61294218 AAAGCCTTTGTGGTGAATTA-TTAGA
1 AAAGCCTTTGTGGTGAATTATTTA-A
* * * **
61294243 AAAGCTTTTGTGGCGAGTTATTTGT
1 AAAGCCTTTGTGGTGAATTATTTAA
**
61294268 AAAGCCTTTGTGGTGAATTATCAAA
1 AAAGCCTTTGTGGTGAATTATTTAA
**
61294293 AAAGCCTTTGTGGCAAATTA-TTAGA
1 AAAGCCTTTGTGGTGAATTATTTA-A
61294318 AAAGCCTTTGTGGTGAATTATTTAA
1 AAAGCCTTTGTGGTGAATTATTTAA
**
61294343 AAATTCTTTGTGGTG
1 AAAGCCTTTGTGGTG
61294358 TATTGTATGG
Statistics
Matches: 92, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
24 1 0.01
25 86 0.93
26 5 0.05
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (25 bp):
AAAGCCTTTGTGGTGAATTATTTAA
Found at i:61294372 original size:75 final size:75
Alignment explanation
Indices: 61294218--61294357 Score: 199
Period size: 75 Copynumber: 1.9 Consensus size: 75
61294208 AGTTATCTGT
** * * **
61294218 AAAGCCTTTGTGGTGAATTATTAGAAAAGCTTTTGTGGCGAGTTATTTGTAAAGCCTTTGTGGTG
1 AAAGCCTTTGTGGCAAATTATTAGAAAAGCCTTTGTGGCGAATTATTTAAAAAGCCTTTGTGGTG
61294283 AATTATCAAA
66 AATTATCAAA
* **
61294293 AAAGCCTTTGTGGCAAATTATTAGAAAAGCCTTTGTGGTGAATTATTTAAAAATTCTTTGTGGTG
1 AAAGCCTTTGTGGCAAATTATTAGAAAAGCCTTTGTGGCGAATTATTTAAAAAGCCTTTGTGGTG
61294358 TATTGTATGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 56 1.00
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (75 bp):
AAAGCCTTTGTGGCAAATTATTAGAAAAGCCTTTGTGGCGAATTATTTAAAAAGCCTTTGTGGTG
AATTATCAAA
Found at i:61296060 original size:46 final size:46
Alignment explanation
Indices: 61296010--61296182 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
61296000 TGGTTGAGCA
61296010 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
61296056 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
61296101 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
61296149 CCCGAGCTCATTGGGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
61296183 AGGGCGGGTT
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.56
47 29 0.28
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:61296167 original size:93 final size:93
Alignment explanation
Indices: 61296007--61296177 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
61295997 GGATGGTTGA
* * *
61296007 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
61296072 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
61296100 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGGGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
61296165 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
61296178 ACTTAAGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:61302489 original size:46 final size:46
Alignment explanation
Indices: 61302439--61302564 Score: 234
Period size: 46 Copynumber: 2.7 Consensus size: 46
61302429 TGGTTGAGCA
61302439 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
61302485 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
61302531 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
61302565 GGGGCGGGTT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:61306228 original size:22 final size:22
Alignment explanation
Indices: 61306203--61306245 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
61306193 CATCTCAAAT
*
61306203 CAAACCACAATATACCAACTTC
1 CAAACAACAATATACCAACTTC
* *
61306225 CAAACAATAATATTCCAACTT
1 CAAACAACAATATACCAACTT
61306246 ACAACTATCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (22 bp):
CAAACAACAATATACCAACTTC
Found at i:61307037 original size:43 final size:43
Alignment explanation
Indices: 61306891--61307040 Score: 167
Period size: 43 Copynumber: 3.5 Consensus size: 43
61306881 TATCCCATAT
* * * * *
61306891 ATGGTCTTACATGTTATCA-TATATCGATGTCACTGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATA-CGATGCCAATGTCCCAGAC
* * * * *
61306934 AAGGTCTTATACGAAATCATAATACGATGCCAATGTCCCAAAC
1 ATGGTCTTACACGTAATCACAATACGATGCCAATGTCCCAGAC
* *
61306977 ATGGTCTTACACATAATCACAATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATACGATGCCAATGTCCCAGAC
*
61307020 ATGGTCTTACATGTAATCACA
1 ATGGTCTTACACGTAATCACA
61307041 TCTCGGTAAC
Statistics
Matches: 88, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
43 85 0.97
44 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCACAATACGATGCCAATGTCCCAGAC
Found at i:61320396 original size:15 final size:15
Alignment explanation
Indices: 61320376--61320405 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61320366 CAACACTTGT
61320376 GCCGAAACCACAAAA
1 GCCGAAACCACAAAA
*
61320391 GCCGAAACCTCAAAA
1 GCCGAAACCACAAAA
61320406 AATACATTAG
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:0.50, C:0.33, G:0.13, T:0.03
Consensus pattern (15 bp):
GCCGAAACCACAAAA
Found at i:61328280 original size:15 final size:15
Alignment explanation
Indices: 61328260--61328289 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61328250 CAACACTTGT
61328260 GCCGAAACCACAAAA
1 GCCGAAACCACAAAA
*
61328275 GCCGAAACCTCAAAA
1 GCCGAAACCACAAAA
61328290 AATACATTAG
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:0.50, C:0.33, G:0.13, T:0.03
Consensus pattern (15 bp):
GCCGAAACCACAAAA
Found at i:61351154 original size:15 final size:15
Alignment explanation
Indices: 61351134--61351180 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
61351124 ATCTAAACAT
61351134 ATTCAAATTAAGTTC
1 ATTCAAATTAAGTTC
*
61351149 ATTCAAA--CA--T-
1 ATTCAAATTAAGTTC
61351159 ATTCAAATTAAGTTC
1 ATTCAAATTAAGTTC
61351174 ATTCAAA
1 ATTCAAA
61351181 CATATTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
10 7 0.28
11 1 0.04
12 1 0.04
13 1 0.04
14 1 0.04
15 14 0.56
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (15 bp):
ATTCAAATTAAGTTC
Found at i:61351156 original size:25 final size:25
Alignment explanation
Indices: 61351128--61351186 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
61351118 TTCTTGATCT
61351128 AAACATATTCAAATTAAGTTCATTC
1 AAACATATTCAAATTAAGTTCATTC
61351153 AAACATATTCAAATTAAGTTCATTC
1 AAACATATTCAAATTAAGTTCATTC
61351178 AAACATATT
1 AAACATATT
61351187 TTCATTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (25 bp):
AAACATATTCAAATTAAGTTCATTC
Found at i:61354970 original size:79 final size:79
Alignment explanation
Indices: 61354839--61354999 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 79
61354829 TATTTTAAAG
61354839 AAATTCAATCTAGCAAGAATATTTCAAAAAGAAAAAAAAGGAAAAAACTAAGGCAAGAAGACAGC
1 AAATTCAATCTAGCAAGAATATTTCAAAAAGAAAAAAAAGGAAAAAACTAAGGCAAGAAGACAGC
61354904 TTCATGAAGAAGCT
66 TTCATGAAGAAGCT
*
61354918 AAATTCAATCTAGCAAGAATATTTCATAAAGAAAAAAAAGGAAAAAACTAAGGCAAGAAGACAGC
1 AAATTCAATCTAGCAAGAATATTTCAAAAAGAAAAAAAAGGAAAAAACTAAGGCAAGAAGACAGC
61354983 TTCATGAAGAAGCT
66 TTCATGAAGAAGCT
61354997 AAA
1 AAA
61355000 GACAGTGTCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.55, C:0.12, G:0.16, T:0.17
Consensus pattern (79 bp):
AAATTCAATCTAGCAAGAATATTTCAAAAAGAAAAAAAAGGAAAAAACTAAGGCAAGAAGACAGC
TTCATGAAGAAGCT
Found at i:61369402 original size:53 final size:54
Alignment explanation
Indices: 61369325--61369526 Score: 190
Period size: 53 Copynumber: 3.7 Consensus size: 54
61369315 CTTTTTAAAC
* * * *
61369325 TTACCATTGCCATGTCTTGACATGGTCTTACGTGGCATCCTTGCCTTAT-GAAG
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAG
* * * * * ** * *
61369378 TCACCATTGCCACGCCTTGGCATGGTCTTACATGGGATATTTGCCTTATCGTAG
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAG
* * * * * * *
61369432 TTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAAAAC
1 -TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAG
* *
61369487 TTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCC
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
61369527 CTAAACCCTA
Statistics
Matches: 116, Mismatches: 31, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
53 41 0.35
54 37 0.32
55 38 0.33
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (54 bp):
TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAG
Found at i:61371737 original size:15 final size:16
Alignment explanation
Indices: 61371719--61371749 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61371709 TTTAACTAAG
61371719 TAAAAT-AAAATAAAA
1 TAAAATAAAAATAAAA
61371734 TAAAATAAAAATAAAA
1 TAAAATAAAAATAAAA
61371750 GTTTCAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAATAAAAATAAAA
Found at i:61371746 original size:6 final size:5
Alignment explanation
Indices: 61371719--61371749 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
61371709 TTTAACTAAG
61371719 TAAAA TAAAA TAAAA TAAAA TAAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA
61371750 GTTTCAATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:61373707 original size:30 final size:30
Alignment explanation
Indices: 61373671--61373731 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
61373661 CACGGGTTGG
*
61373671 CACATGGGCATGTGGCCTA-CCCGTGTGGAT
1 CACATGGGCATGT-GCCCAGCCCGTGTGGAT
*
61373701 CACATGGGCGTGTGCCCAGCCCGTGTGGAT
1 CACATGGGCATGTGCCCAGCCCGTGTGGAT
61373731 C
1 C
61373732 CTGAAAACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.15, C:0.30, G:0.34, T:0.21
Consensus pattern (30 bp):
CACATGGGCATGTGCCCAGCCCGTGTGGAT
Found at i:61375504 original size:48 final size:49
Alignment explanation
Indices: 61375386--61375508 Score: 162
Period size: 49 Copynumber: 2.5 Consensus size: 49
61375376 GTCGACGCTG
* *
61375386 TGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAGGCTAATGCCA
1 TGTCCCAGACAGGTCTTACACTAGCTTTCATATATCGAGGCCAATGCCA
* *
61375435 TGTCCCAGACAGGTCTTACACTAGCTTGT-ATAT-CCTGAGGCCGATG-CA
1 TGTCCCAGACAGGTCTTACACTAGCTT-TCATATATC-GAGGCCAATGCCA
*
61375483 TGTCCCAGACATGTCTTACACTAGCT
1 TGTCCCAGACAGGTCTTACACTAGCT
61375509 CTCGTCTCAA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
48 28 0.42
49 38 0.57
50 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (49 bp):
TGTCCCAGACAGGTCTTACACTAGCTTTCATATATCGAGGCCAATGCCA
Found at i:61378092 original size:40 final size:40
Alignment explanation
Indices: 61378036--61378238 Score: 250
Period size: 40 Copynumber: 5.1 Consensus size: 40
61378026 CGGAATTCAA
* * *
61378036 CCGGATATAGCT-ACTCGCTCGAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
61378076 CCGGTTATAGTAACTCGCACAAATGCCTCCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
61378116 CCGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
61378156 ACGGATATAATAACTCGCACAATTGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
61378195 TCAGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
61378235 CCGG
1 CCGG
61378239 TTATCATCTG
Statistics
Matches: 140, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
38 1 0.01
39 32 0.23
40 107 0.76
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:61381496 original size:27 final size:27
Alignment explanation
Indices: 61381466--61381643 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
61381456 ATATTGAGTC
* * * *
61381466 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
61381493 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
61381520 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
61381548 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
61381575 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
61381602 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
61381629 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
61381644 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:61381605 original size:82 final size:81
Alignment explanation
Indices: 61381487--61381642 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
61381477 TGCTATATAA
* *
61381487 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
61381552 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
61381569 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
61381633 CACTTAGTGC
65 CACTTAGTGC
61381643 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:61389681 original size:27 final size:27
Alignment explanation
Indices: 61389651--61389828 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
61389641 ATATTGAGTC
* * * *
61389651 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
61389678 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
61389705 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
61389733 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
61389760 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
61389787 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
61389814 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
61389829 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:61389790 original size:82 final size:81
Alignment explanation
Indices: 61389672--61389827 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
61389662 TGCTATATAA
* *
61389672 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
61389737 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
61389754 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
61389818 CACTTAGTGC
65 CACTTAGTGC
61389828 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:61411662 original size:27 final size:27
Alignment explanation
Indices: 61411632--61411809 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
61411622 ATATTGAGTC
* * * *
61411632 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
61411659 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
61411686 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
61411714 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
61411741 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
61411768 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
61411795 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
61411810 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:61411771 original size:82 final size:81
Alignment explanation
Indices: 61411653--61411808 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
61411643 TGCTATATAA
* *
61411653 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
61411718 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
61411735 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
61411799 CACTTAGTGC
65 CACTTAGTGC
61411809 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:61416151 original size:47 final size:47
Alignment explanation
Indices: 61416092--61416516 Score: 638
Period size: 47 Copynumber: 9.1 Consensus size: 47
61416082 TATCACATTT
* * * *
61416092 ATACAC-T-TTCACATTCATCACATCGGCCATTAGGCCTTATCTCAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* * *
61416137 ATACACATGCTCACATTCATCACATTGGCCACTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
*
61416184 ATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* * *
61416231 ATATACATGTTTACTTTCATCACATTGGCCATTCGGCTTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* *
61416278 ATATACATGTTCACTTTCATCACATTGGCCATTCGGTCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
*
61416325 ATACACACGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* *
61416372 ATATACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAT
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* * *
61416419 ATACACCTATTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
* *
61416466 ATATACATGTTCACTTTCATCACATTGGCCATTCGGCCCTATTCACAC
1 ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTA-TCACAC
61416514 ATA
1 ATA
61416517 TACACTTTCA
Statistics
Matches: 347, Mismatches: 30, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
45 6 0.02
46 1 0.00
47 331 0.95
48 9 0.03
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.32
Consensus pattern (47 bp):
ATACACATGTTCACTTTCATCACATTGGCCATTCGGCCTTATCACAC
Found at i:61416253 original size:25 final size:25
Alignment explanation
Indices: 61416224--61416301 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
61416214 ATTCGGCCTT
*
61416224 ATCACACATATACATGTTTACTTTC
1 ATCACACATATACATGTTCACTTTC
* *** *
61416249 ATCACA-TTGGCCA--TTCGGCTTT-
1 ATCACACATATACATGTTC-ACTTTC
61416271 ATCACACATATACATGTTCACTTTC
1 ATCACACATATACATGTTCACTTTC
61416296 ATCACA
1 ATCACA
61416302 TTGGCCATTC
Statistics
Matches: 37, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
22 8 0.22
23 7 0.19
24 7 0.19
25 15 0.41
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.36
Consensus pattern (25 bp):
ATCACACATATACATGTTCACTTTC
Found at i:61416417 original size:22 final size:22
Alignment explanation
Indices: 61416390--61416464 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
61416380 GTTCACTTTC
61416390 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * *
61416412 ATCACATATACACCTATTC-ACATT
1 ATCACAT-T-GGCC-ATTCGGCCTT
61416436 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
61416459 ATCACA
1 ATCACA
61416465 CATATACATG
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 17 0.43
23 6 0.15
24 6 0.15
25 11 0.28
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.31
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:61435490 original size:33 final size:34
Alignment explanation
Indices: 61435420--61435506 Score: 133
Period size: 33 Copynumber: 2.6 Consensus size: 34
61435410 TTTCAGTTAG
61435420 GGGCCTTAGCCCATTTTCAGTAACAGCAGCAGTCT
1 GGGCCTTAGCCCA-TTTCAGTAACAGCAGCAGTCT
*
61435455 GGGCCTGAGCCCATTTCAGT-ACAG-AGGCAGTCT
1 GGGCCTTAGCCCATTTCAGTAACAGCA-GCAGTCT
61435488 GGGCCTTAGCCCATTTCAG
1 GGGCCTTAGCCCATTTCAG
61435507 CATAGTATGC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
32 1 0.02
33 29 0.59
34 7 0.14
35 12 0.24
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (34 bp):
GGGCCTTAGCCCATTTCAGTAACAGCAGCAGTCT
Found at i:61435947 original size:30 final size:30
Alignment explanation
Indices: 61435911--61435978 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
61435901 TCAGTGATAA
61435911 TGGGCCTACAACCCATATTGCGGGCCCATG
1 TGGGCCTACAACCCATATTGCGGGCCCATG
* *
61435941 TGGGCCTCCAACCCATATTGCGGGCCTATG
1 TGGGCCTACAACCCATATTGCGGGCCCATG
61435971 TGGGCCTA
1 TGGGCCTA
61435979 TACTCTCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (30 bp):
TGGGCCTACAACCCATATTGCGGGCCCATG
Found at i:61450406 original size:43 final size:42
Alignment explanation
Indices: 61450358--61450521 Score: 181
Period size: 43 Copynumber: 3.9 Consensus size: 42
61450348 ATCGAGATGT
61450358 GATTACATGTAAGACCATGTCTGGGACATTGGCATTATATTG
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTATATTG
* *
61450400 AGATTACGTGTAAGACCATGTCTGGGACATTGGCATCATTAATT-
1 -GATTACATGTAAGACCATGTCTGGGACATTGGCATTA-T-ATTG
* * * *
61450444 GATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATTGATA-TG
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATT-ATATTG
* * *
61450486 TGATAACATGTAAGACCATATCTGGGATA-TGGCATT
1 -GATTACATGTAAGACCATGTCTGGGACATTGGCATT
61450522 GTATGAGCTT
Statistics
Matches: 104, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
41 1 0.01
42 8 0.08
43 90 0.87
44 2 0.02
45 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (42 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATTATATTG
Found at i:61452080 original size:29 final size:29
Alignment explanation
Indices: 61452018--61452107 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
61452008 CACATACCTG
* * *
61452018 TATATGGGCCACTAGGCCC-AATCATATT
1 TATATGGCCCATTAGGCCCAAATCACATT
61452046 TATATGGCCCATTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
* * * * *
61452075 TTTATGGTCCATCAAGCCCAATTCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
61452104 TATA
1 TATA
61452108 GTCATGCTCA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
28 17 0.33
29 35 0.67
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATCACATT
Found at i:61455389 original size:43 final size:42
Alignment explanation
Indices: 61455319--61455435 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
61455309 ACGTAGTACT
*
61455319 GTACCAATGCCACAT-CCCAGATATGGTCTTACATG-TGATCTC
1 GTACCAATGCCA-ATACCCAGATATGGTCTTACATGAAG-TCTC
* *
61455361 GTACCAATGCCAATAGCCCAGCTATGGTCTTAGATGAAGTCTC
1 GTACCAATGCCAATA-CCCAGATATGGTCTTACATGAAGTCTC
* * *
61455404 ATATCGATGCC-ATATCCCAGATATGGTCTTAC
1 GTACCAATGCCAATA-CCCAGATATGGTCTTAC
61455436 GCGTAATCTC
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
41 2 0.03
42 30 0.48
43 30 0.48
44 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (42 bp):
GTACCAATGCCAATACCCAGATATGGTCTTACATGAAGTCTC
Found at i:61461211 original size:30 final size:29
Alignment explanation
Indices: 61461168--61461224 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
61461158 TTAATACGAG
*
61461168 CTTTGGCAAAATTACATTTTTGCCCCTAAA
1 CTTTGGCAAAATTACACTTTT-CCCCTAAA
* *
61461198 CTTTTGCATAATTACACTTTTCCCCTA
1 CTTTGGCAAAATTACACTTTTCCCCTA
61461225 TGCTCGGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.40
Consensus pattern (29 bp):
CTTTGGCAAAATTACACTTTTCCCCTAAA
Found at i:61470984 original size:49 final size:50
Alignment explanation
Indices: 61470912--61471009 Score: 164
Period size: 49 Copynumber: 2.0 Consensus size: 50
61470902 TTTAATATGT
61470912 TTAGTTTAATTAATTCAATTGTTTT-AATTTTCTTTAGTTGCGTAAATAC
1 TTAGTTTAATTAATTCAATTGTTTTGAATTTTCTTTAGTTGCGTAAATAC
*
61470961 TTAGTTTAATTAATT-AAGTTGTTTTGAATTTTCTTTAGTTGCTTAAATA
1 TTAGTTTAATTAATTCAA-TTGTTTTGAATTTTCTTTAGTTGCGTAAATA
61471010 ATTTCGGCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
48 2 0.04
49 22 0.48
50 22 0.48
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (50 bp):
TTAGTTTAATTAATTCAATTGTTTTGAATTTTCTTTAGTTGCGTAAATAC
Found at i:61474244 original size:6 final size:6
Alignment explanation
Indices: 61474233--61474280 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
61474223 AAGAGACTGT
* * * * *
61474233 AGAAAA AGAAAA AGAACA AGAAAA ATAAAG AGAAAA ATAAAA ATAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
61474281 TAAAATAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.06
Consensus pattern (6 bp):
AGAAAA
Found at i:61474256 original size:18 final size:18
Alignment explanation
Indices: 61474233--61474280 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
61474223 AAGAGACTGT
* *
61474233 AGAAAAAGAAAAAGAACA
1 AGAAAAATAAAAAGAAAA
*
61474251 AGAAAAATAAAGAGAAAA
1 AGAAAAATAAAAAGAAAA
*
61474269 ATAAAAATAAAA
1 AGAAAAATAAAA
61474281 TAAAATAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.06
Consensus pattern (18 bp):
AGAAAAATAAAAAGAAAA
Found at i:61474280 original size:5 final size:5
Alignment explanation
Indices: 61474266--61474295 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
61474256 AATAAAGAGA
61474266 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
61474296 AGGAAAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:61482595 original size:46 final size:45
Alignment explanation
Indices: 61482528--61482703 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 45
61482518 ATGTAACCTG
61482528 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCA
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCA
* * * *
61482574 TCCATAAGTGAACTCGGACTCAACTCAACAAGCTCGGATGCCTAG-T
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGCA
* *** * * *
61482620 TACATCTCTCGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCA
1 TCCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCA
*
61482667 TCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
61482704 ATGCCCAAAT
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
45 1 0.01
46 70 0.67
47 32 0.30
48 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (45 bp):
TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCA
Found at i:61482644 original size:93 final size:93
Alignment explanation
Indices: 61482537--61482708 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
61482527 GTCCATAAGT
* * *
61482537 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
61482602 CAAGCTCGGATGCCTAGTTACATCTCTC
66 CAAGCTCGGATGCCTAGTTACATCTCTC
*
61482630 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
61482695 CGAGTTCGGATGCC
66 CAAGCTCGGATGCC
61482709 CAAATATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CAAGCTCGGATGCCTAGTTACATCTCTC
Found at i:61482723 original size:46 final size:44
Alignment explanation
Indices: 61482534--61482723 Score: 109
Period size: 46 Copynumber: 4.1 Consensus size: 44
61482524 CCTGTCCATA
* ** ** **
61482534 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCC-T
* * *
61482579 AAGTGAACTCGGACTCAACTCAACAAGCTCGGATGCCTAGTTACATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CT
* * * *
61482629 --CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTC-G-GATGCCCAAATCC-T
61482672 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCT
61482719 AGTGA
1 AGTGA
61482724 CATGTCACTT
Statistics
Matches: 110, Mismatches: 19, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
42 1 0.01
43 4 0.04
44 4 0.04
45 1 0.01
46 62 0.56
47 25 0.23
48 5 0.05
49 3 0.03
50 4 0.04
51 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCT
Found at i:61484889 original size:25 final size:25
Alignment explanation
Indices: 61484861--61484933 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 25
61484851 AGCTGCCATC
61484861 TGTATGCTAGACTGGTAGCTATTAT
1 TGTATGCTAGACTGGTAGCTATTAT
* * * *
61484886 TGTAAGC-A-A-AGGT-GCCA-T-C
1 TGTATGCTAGACTGGTAGCTATTAT
61484905 TGTATGCTAGACTGGTAGCTATTAT
1 TGTATGCTAGACTGGTAGCTATTAT
61484930 TGTA
1 TGTA
61484934 AGCAAACTCT
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
19 6 0.18
20 2 0.06
21 4 0.12
22 6 0.18
23 4 0.12
24 2 0.06
25 10 0.29
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.36
Consensus pattern (25 bp):
TGTATGCTAGACTGGTAGCTATTAT
Found at i:61484917 original size:44 final size:44
Alignment explanation
Indices: 61484854--61484939 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
61484844 CTTCGTAAGC
61484854 TGCCATCTGTATGCTAGACTGGTAGCTATTATTGTAAGCAAAGG
1 TGCCATCTGTATGCTAGACTGGTAGCTATTATTGTAAGCAAAGG
61484898 TGCCATCTGTATGCTAGACTGGTAGCTATTATTGTAAGCAAA
1 TGCCATCTGTATGCTAGACTGGTAGCTATTATTGTAAGCAAA
61484940 CTCTGGTAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (44 bp):
TGCCATCTGTATGCTAGACTGGTAGCTATTATTGTAAGCAAAGG
Found at i:61486547 original size:12 final size:12
Alignment explanation
Indices: 61486526--61486555 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
61486516 CCAGAGATGT
*
61486526 TCATCGTGTTCC
1 TCATCATGTTCC
61486538 TCATCATGTTCC
1 TCATCATGTTCC
61486550 TCATCA
1 TCATCA
61486556 GTCCTTGAAT
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:0.17, C:0.33, G:0.10, T:0.40
Consensus pattern (12 bp):
TCATCATGTTCC
Found at i:61497983 original size:46 final size:46
Alignment explanation
Indices: 61497853--61498068 Score: 194
Period size: 46 Copynumber: 4.7 Consensus size: 46
61497843 AACCGTCCCA
*
61497853 ATGCTATGTCCCAGACATGGTCTTACACTAACACATC-T-T-GTA-GCCG
1 ATGC-ATGTCCCAGACAT-GTCTTACACTAGCAC-TCGTCTCG-AGGCCG
* * *
61497899 ATGCATGTCCCAGACATGTCTTATACTAGTTTA-T-GTCTCGAGGCTG
1 ATGCATGTCCCAGACATGTCTTACACTAG--CACTCGTCTCGAGGCCG
* * *
61497945 ATGCATGTCCCAAACATGTCTTACACTAGCACTCGTCTCAATGCCG
1 ATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGAGGCCG
* * * * *
61497991 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCCG
1 ATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCGT-CTCGAGGCCG
61498039 ATGCATGTCCCAGACATGTCTTACACTAGC
1 ATGCATGTCCCAGACATGTCTTACACTAGC
61498069 TCACACAAAT
Statistics
Matches: 140, Mismatches: 19, Indels: 22
0.77 0.10 0.12
Matches are distributed among these distances:
44 13 0.09
45 16 0.11
46 60 0.43
47 27 0.19
48 23 0.16
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGAGGCCG
Found at i:61498014 original size:94 final size:90
Alignment explanation
Indices: 61497822--61498068 Score: 232
Period size: 94 Copynumber: 2.7 Consensus size: 90
61497812 GGCTATCATG
* * * *
61497822 GTCTTACACTAGCTCTCA-AATAACCGTCCCAATGCTATGTCCCAGACATGGTCTTACACTAACA
1 GTCTTACACTAGCTCTCATAATGA--G-GCCGATGC-ATGTCCCAGACAT-GTCTTACACTAGCA
**
61497886 CATCTTGTAGCCGATGCATGTCCCAGACAT
61 CATCTTCAAGCCGATGCATGTCCCAGACAT
* * ** * *
61497916 GTCTTATACTAG-T-TTATGTCTCGAGGCTGATGCATGTCCCAAACATGTCTTACACTAGCAC-T
1 GTCTTACACTAGCTCTCAT-AAT-GAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCACAT
61497978 CGTCTCAATGCCGATGCCATGTCCCAGACAT
64 C-T-TCAA-GCCGATG-CATGTCCCAGACAT
* *
61498009 GGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGTCTTACACTAGC
1 -GTCTTACACTAGCTCTCATAATGAGGCCGATGCATGTCCCAGACATGTCTTACACTAGC
61498069 TCACACAAAT
Statistics
Matches: 123, Mismatches: 20, Indels: 20
0.75 0.12 0.12
Matches are distributed among these distances:
89 2 0.02
90 15 0.12
91 14 0.11
92 14 0.11
93 16 0.13
94 56 0.46
95 3 0.02
96 3 0.02
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (90 bp):
GTCTTACACTAGCTCTCATAATGAGGCCGATGCATGTCCCAGACATGTCTTACACTAGCACATCT
TCAAGCCGATGCATGTCCCAGACAT
Found at i:61504803 original size:40 final size:40
Alignment explanation
Indices: 61504745--61504926 Score: 217
Period size: 40 Copynumber: 4.5 Consensus size: 40
61504735 GTCGAATGAC
*
61504745 ATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACTAT
1 ATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACTAT
* * *
61504785 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CTAT
1 ATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACTAT
* * * * *
61504825 ATCCAGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTAT
1 ATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACTAT
*
61504865 ATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACCAT
1 ATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACTAT
*
61504905 ATCCGGGCTAAGACCCGAAGGC
1 ATCCGGGCTAAGATCCGAAGGC
61504927 CTTGTGCGAG
Statistics
Matches: 120, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 116 0.97
41 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACTAT
Found at i:61504883 original size:80 final size:79
Alignment explanation
Indices: 61504745--61504962 Score: 262
Period size: 80 Copynumber: 2.7 Consensus size: 79
61504735 GTCGAATGAC
* * * *
61504745 ATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGCAT
1 ATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAG-TCCCGAAGGCAT
* *
61504809 TTGTGCGAGTTG-CTAT
64 TTATGCGAG-TGACCAT
* *
61504825 ATCCAGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAGTCCCGAAGGCATT
*
61504890 TATGCTAGTGACCAT
65 TATGCGAGTGACCAT
* * * *
61504905 ATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCC-GGCTAAATCCCGAAG
1 ATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGTCCCGAAG
61504963 ATACTTGGGT
Statistics
Matches: 120, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
78 14 0.12
79 20 0.17
80 86 0.72
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (79 bp):
ATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGTCCCGAAGGCATTT
ATGCGAGTGACCAT
Found at i:61508871 original size:20 final size:20
Alignment explanation
Indices: 61508829--61508871 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
61508819 ATGTCCCAGA
*
61508829 CATGGTCTTACACTAGCTGT
1 CATGGTCTTACACTAGCTAT
*
61508849 CATGGTCTTACACTGGCTAT
1 CATGGTCTTACACTAGCTAT
61508869 CAT
1 CAT
61508872 CTTCGAGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (20 bp):
CATGGTCTTACACTAGCTAT
Found at i:61508954 original size:50 final size:49
Alignment explanation
Indices: 61508890--61509017 Score: 156
Period size: 50 Copynumber: 2.7 Consensus size: 49
61508880 CTTATGCCAA
* *
61508890 GTCCCAAACATGGTCTTACACTAGCTCTCACATAACCAT-CCCGATGTCAT
1 GTCCCAGACATGGTCTTACACTAGCTCTCACATAA-CATGCCCGAT-ACAT
** *
61508940 GTCCCAGACATGGTCTTACACTAGCTCT--CATAATGTGGCCGATACAT
1 GTCCCAGACATGGTCTTACACTAGCTCTCACATAACATGCCCGATACAT
*
61508987 GTCCCAGACAT-GTCTTACACTAGCTCACACA
1 GTCCCAGACATGGTCTTACACTAGCTCTCACA
61509018 AATGACCCAA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
46 15 0.22
47 15 0.22
48 12 0.17
50 27 0.39
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (49 bp):
GTCCCAGACATGGTCTTACACTAGCTCTCACATAACATGCCCGATACAT
Found at i:61511898 original size:16 final size:17
Alignment explanation
Indices: 61511852--61511900 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
61511842 TGATTTTTTT
*
61511852 TATTTTGTTATATTAGA
1 TATTTTTTTATATTAGA
**
61511869 TAAATTTTTA-ATTA-A
1 TATTTTTTTATATTAGA
61511884 TATTTTTTTATATTAGA
1 TATTTTTTTATATTAGA
61511901 AAATATATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
15 9 0.36
16 8 0.32
17 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TATTTTTTTATATTAGA
Found at i:61520858 original size:26 final size:26
Alignment explanation
Indices: 61520797--61520916 Score: 100
Period size: 26 Copynumber: 4.5 Consensus size: 26
61520787 CGAAAGTTTG
**
61520797 AAATAAATAATATACAGAAA-AAGTTTA
1 AAATAAATAATATGTA-AAATAA-TTTA
*
61520824 AAATGAATAATATGTAAAATAATTTA
1 AAATAAATAATATGTAAAATAATTTA
* * *
61520850 AGATAAATAATATAT-AAATGAGTTTA
1 AAATAAATAATATGTAAAAT-AATTTA
** *
61520876 AAATAAATGTTATGTAAAAAGAAATTTA
1 AAATAAATAATATGT-AAAA-TAATTTA
61520904 AAATAAATAATAT
1 AAATAAATAATAT
61520917 ACAAGACATT
Statistics
Matches: 73, Mismatches: 15, Indels: 9
0.75 0.15 0.09
Matches are distributed among these distances:
25 4 0.05
26 35 0.48
27 15 0.21
28 19 0.26
ACGTcount: A:0.59, C:0.01, G:0.08, T:0.32
Consensus pattern (26 bp):
AAATAAATAATATGTAAAATAATTTA
Found at i:61520890 original size:52 final size:55
Alignment explanation
Indices: 61520788--61520919 Score: 153
Period size: 54 Copynumber: 2.4 Consensus size: 55
61520778 TAATATAGGC
* *
61520788 GAAAGTTTGAAATAAATAATATACAGAAAAAGTTTAAAATGAATAATATGT-AAAA
1 GAAA-TTTAAAATAAATAATATACAGAAAAAGTTTAAAATAAATAATATGTAAAAA
* * * ** **
61520843 -TAATTTAAGATAAATAATATATA-AATGAGTTTAAAATAAATGTTATGTAAAAA
1 GAAATTTAAAATAAATAATATACAGAAAAAGTTTAAAATAAATAATATGTAAAAA
61520896 GAAATTTAAAATAAATAATATACA
1 GAAATTTAAAATAAATAATATACA
61520920 AGACATTTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
52 20 0.32
53 21 0.33
54 22 0.35
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.31
Consensus pattern (55 bp):
GAAATTTAAAATAAATAATATACAGAAAAAGTTTAAAATAAATAATATGTAAAAA
Found at i:61522308 original size:15 final size:16
Alignment explanation
Indices: 61522288--61522317 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61522278 CGGAGGTACG
61522288 TTTTATTATT-TTTCT
1 TTTTATTATTATTTCT
61522303 TTTTATTATTATTTC
1 TTTTATTATTATTTC
61522318 GTGAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTATTATTTCT
Found at i:61533281 original size:56 final size:56
Alignment explanation
Indices: 61533195--61533314 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
61533185 ACAAGGGATG
61533195 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
61533251 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
61533307 ATGGGCAA
1 ATGGGCAA
61533315 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:61534818 original size:47 final size:47
Alignment explanation
Indices: 61534764--61535308 Score: 769
Period size: 47 Copynumber: 11.6 Consensus size: 47
61534754 TATTTGAATA
* *
61534764 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
61534811 AATGTGAA-AGTGTATACATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
61534858 AATGTGAA-AGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
61534907 AATGTGAACATGCATATATGAGATAAGGTCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
61534954 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
61535001 AATGTGAACATGTGTATGTGTGATGAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
61535048 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
61535095 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
61535142 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
61535189 AATGTGAACATGCATATACGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
61535236 AATGTGAA-AGTGTAT-TATGTGATAAGGCCGGATGGCCAATGTGATG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
61535282 GATGTGGAA-GTGTATAAATGTGATAAG
1 AATGT-GAACATGTATATATGTGATAAG
61535309 TCCCGAAGGG
Statistics
Matches: 458, Mismatches: 34, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
46 38 0.08
47 375 0.82
49 44 0.10
50 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (47 bp):
AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:61540116 original size:46 final size:46
Alignment explanation
Indices: 61540049--61540269 Score: 284
Period size: 46 Copynumber: 4.8 Consensus size: 46
61540039 TGTAACCCGC
61540049 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
61540095 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * * * *
61540141 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCCGATGC-CTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCT-CG-GGCGTTCGCAT
* *** * * *
61540187 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
61540234 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
61540270 ATGCCCAAAT
Statistics
Matches: 150, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
45 1 0.01
46 115 0.77
47 32 0.21
48 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:61540236 original size:93 final size:93
Alignment explanation
Indices: 61540103--61540274 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
61540093 ATCCATAAGT
* *
61540103 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
61540168 CGAGCTCCGATGCCTAGTTACATCTCTC
66 CGAGCTCCGATGCCTAGTTACATCTCTC
* *
61540196 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
* *
61540261 CGAGTTCGGATGCC
66 CGAGCTCCGATGCC
61540275 CAAATATCCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCCGATGCCTAGTTACATCTCTC
Found at i:61544367 original size:96 final size:97
Alignment explanation
Indices: 61544202--61544394 Score: 307
Period size: 96 Copynumber: 2.0 Consensus size: 97
61544192 AAGGAGGAAT
* *
61544202 ACAATTGAGCGATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGGGTTTCCG
1 ACAATTGAGCGATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGAGTTTCCA
61544267 ATGTCCAATTAAACATCCAAATAGAG-AGAAA
66 ATGTCCAATTAAACATCCAAATAGAGAAGAAA
** * *
61544298 ACAATTGAGTTATCACCTTTTGTGCAATGTTATTGGTGTAGTTTAGAAGATCATAAGAGTTTCCA
1 ACAATTGAGCGATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGAGTTTCCA
* *
61544363 ATGTCCAATTAAATATCCAACTAGAGAAGAAA
66 ATGTCCAATTAAACATCCAAATAGAGAAGAAA
61544395 GTAAGTATGA
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
96 83 0.94
97 5 0.06
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (97 bp):
ACAATTGAGCGATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGAGTTTCCA
ATGTCCAATTAAACATCCAAATAGAGAAGAAA
Found at i:61547335 original size:43 final size:42
Alignment explanation
Indices: 61547283--61547464 Score: 136
Period size: 43 Copynumber: 4.3 Consensus size: 42
61547273 TCTGGCACTG
61547283 TAGTGCATCATCGGATAAATCGAATGAAATATTGTGGCACACA
1 TAGTGCATCATCGGATAAA-CGAATGAAATATTGTGGCACACA
* * * ** * * *
61547326 TAGTGCATCATCAGATAAGC-CATAGAAATAATACTTGCATACG
1 TAGTGCATCATCGGATAAACGAAT-GAAAT-ATTGTGGCACACA
* * * **
61547369 TAGTGCATCATCGGATTAACCGAA-GTAATAATGCTGGCACGTA
1 TAGTGCATCATCGGA-TAAACGAATGAAATATTG-TGGCACACA
* * * *
61547412 -AGTGCATCATCGGATATACAAAAGAAAATATTTTGGCACACA
1 TAGTGCATCATCGGATAAACGAATG-AAATATTGTGGCACACA
61547454 TAGTGCATCAT
1 TAGTGCATCAT
61547465 TGATTAAACC
Statistics
Matches: 103, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
41 7 0.07
42 29 0.28
43 62 0.60
44 4 0.04
45 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (42 bp):
TAGTGCATCATCGGATAAACGAATGAAATATTGTGGCACACA
Found at i:61549445 original size:17 final size:18
Alignment explanation
Indices: 61549423--61549458 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
61549413 ATACTAGGCC
61549423 GTGTGGGCC-ACACGGGT
1 GTGTGGGCCTACACGGGT
61549440 GTGTGGGCCTACACGGGT
1 GTGTGGGCCTACACGGGT
61549458 G
1 G
61549459 AACCACACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.19
Consensus pattern (18 bp):
GTGTGGGCCTACACGGGT
Found at i:61551285 original size:20 final size:21
Alignment explanation
Indices: 61551262--61551301 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
61551252 AGTTTTATTT
61551262 AATTAAATAA-AGGTTAATTA
1 AATTAAATAACAGGTTAATTA
* *
61551282 AATTAATTAACATGTTAATT
1 AATTAAATAACAGGTTAATT
61551302 TAGCTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (21 bp):
AATTAAATAACAGGTTAATTA
Found at i:61551601 original size:24 final size:24
Alignment explanation
Indices: 61551569--61551626 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
61551559 ATAATTATTC
* *
61551569 ATGAGGTAATTATATAATGCTTGT
1 ATGAGGTAAGTATATAAAGCTTGT
*
61551593 ATGAGGTAAGTGTATAAAGCTTGT
1 ATGAGGTAAGTATATAAAGCTTGT
*
61551617 ATGAGTTAAG
1 ATGAGGTAAG
61551627 ATAAGATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (24 bp):
ATGAGGTAAGTATATAAAGCTTGT
Found at i:61553450 original size:22 final size:24
Alignment explanation
Indices: 61553416--61553460 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
61553406 AATCTAAATA
*
61553416 ATTAACATCTTTAA-CT-ATTTTG
1 ATTAAAATCTTTAATCTAATTTTG
*
61553438 ATTAAAATTTTTAATCTAATTTT
1 ATTAAAATCTTTAATCTAATTTT
61553461 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 2 0.11
24 5 0.26
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTAAAATCTTTAATCTAATTTTG
Found at i:61553468 original size:24 final size:22
Alignment explanation
Indices: 61553425--61553468 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
61553415 AATTAACATC
* *
61553425 TTTAACTATTTTGATTAAAATT
1 TTTAACTATTTTAATAAAAATT
61553447 TTTAATCTAATTTTAATAAAAA
1 TTTAA-CT-ATTTTAATAAAAA
61553469 ATATCATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 2 0.11
24 11 0.61
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAACTATTTTAATAAAAATT
Found at i:61554444 original size:34 final size:32
Alignment explanation
Indices: 61554395--61554468 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 32
61554385 AGTGATATAT
** *
61554395 TTAAATTATATTAAAATTTTTATAAATTCAAAAA
1 TTAAA-TATATTAAAAAATTTAGAAATT-AAAAA
61554429 TTAGAATATATTAAAAAATTTAGAAATTAAAAA
1 TTA-AATATATTAAAAAATTTAGAAATTAAAAA
61554462 TTAAATA
1 TTAAATA
61554469 AAAATTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 4 0.11
33 8 0.22
34 22 0.61
35 2 0.06
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (32 bp):
TTAAATATATTAAAAAATTTAGAAATTAAAAA
Found at i:61554482 original size:10 final size:11
Alignment explanation
Indices: 61554456--61554484 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
61554446 ATTTAGAAAT
61554456 TAAAAATTAAA
1 TAAAAATTAAA
61554467 TAAAAATTAAA
1 TAAAAATTAAA
61554478 TAAAAAT
1 TAAAAAT
61554485 AGTTCTCCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAAAATTAAA
Found at i:61554896 original size:19 final size:19
Alignment explanation
Indices: 61554840--61554907 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
61554830 ATAAATTTAA
*
61554840 ATAATTTTATATACTTTTT
1 ATAATTTTATATAATTTTT
*
61554859 -T-ATTTTTTA-AATTGATTT
1 ATAATTTTATATAATT--TTT
*
61554877 ATAATTTTATATAGTTTTT
1 ATAATTTTATATAATTTTT
*
61554896 ATAATTCTATAT
1 ATAATTTTATAT
61554908 CTTTTTACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.08
17 7 0.18
18 4 0.10
19 15 0.38
20 7 0.18
21 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
ATAATTTTATATAATTTTT
Found at i:61554974 original size:9 final size:10
Alignment explanation
Indices: 61554953--61554988 Score: 56
Period size: 9 Copynumber: 3.6 Consensus size: 10
61554943 AAAAAATAAT
61554953 TTTTTAAATA
1 TTTTTAAATA
61554963 TTTTTAAA-A
1 TTTTTAAATA
61554972 TTTTTAAATA
1 TTTTTAAATA
61554982 GTTTTTA
1 -TTTTTA
61554989 TGATTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 9 0.38
11 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (10 bp):
TTTTTAAATA
Done.