Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011231.1 Kokia drynarioides strain JFW-HI SEQ_126209, whole genome shotgun sequence
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: 114891
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Warning! 90 characters in sequence are not A, C, G, or T
Found at i:3813 original size:17 final size:17
Alignment explanation
Indices: 3769--3813 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
3759 AGTAAAAGTC
3769 TTTTAATAAAATTAAGA
1 TTTTAATAAAATTAAGA
**
3786 TTTTCCT-AAATTAAGA
1 TTTTAATAAAATTAAGA
3802 TTTTAATAAAAT
1 TTTTAATAAAAT
3814 CTTTAGGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (17 bp):
TTTTAATAAAATTAAGA
Found at i:6324 original size:30 final size:30
Alignment explanation
Indices: 6241--6330 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 30
6231 ATAAGGACCA
* *
6241 AACCTTTATAAAAGTGCTTAAATGAA-GGCTA
1 AACCTTTA-AAAAGTGCTCAAAT-AAGGGCTT
* **
6272 AACCTTTCAAAA-TGAACAAATAAGGGCTT
1 AACCTTTAAAAAGTGCTCAAATAAGGGCTT
*
6301 AACCTTTAAAAAGTGCTCAAATAAGAGCTT
1 AACCTTTAAAAAGTGCTCAAATAAGGGCTT
6331 CTCAAAGGGG
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 2 0.04
29 21 0.44
30 18 0.38
31 7 0.15
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (30 bp):
AACCTTTAAAAAGTGCTCAAATAAGGGCTT
Found at i:8913 original size:21 final size:22
Alignment explanation
Indices: 8889--8936 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
8879 TTATCCAAAT
*
8889 ATTATAATCGAAA-ATTTTTAA
1 ATTATAATCAAAATATTTTTAA
*
8910 ATTATAATTAAAATATTTTTAA
1 ATTATAATCAAAATATTTTTAA
*
8932 TTTAT
1 ATTAT
8937 TTAATCTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTATAATCAAAATATTTTTAA
Found at i:9251 original size:140 final size:139
Alignment explanation
Indices: 9037--9691 Score: 811
Period size: 140 Copynumber: 4.8 Consensus size: 139
9027 ACTGGGGTAA
* * * * *
9037 ACTTGTCAACATACGTTTTGGCCAACTCTTTGTATAAGGGATGAGATATGCATGCCTAAGACAAC
1 ACTTGTCGACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAAC
* * ** *
9102 GGTTAAATAAGAGTTGACTTTGTCCAACACAATATCGACACTTTTGAGGTGACACTTTCCTAAGT
66 GCTTAAATAAGAGTTGACTTTGTCCAACACTATGCCGACACTTTTG-GGCGACACTTTCCTAAGT
9167 GTTGAGATAG
130 GTTGAGATAG
* * * **
9177 ACTTGTCGACATATGCTTTGGTCAACTCTTTGTATAAGGATTGGGATATGCATGCCTAAAACAAC
1 ACTTGTCGACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAAC
* * * * *
9242 GTTTAAATAAGAGTTGGCTTTATTCAACACTATGCCGACACTTTTGGGGCGACACTTTTCTAAGT
66 GCTTAAATAAGAGTTGACTTTGTCCAACACTATGCCGACACTTTT-GGGCGACACTTTCCTAAGT
* *
9307 GTTGGGATAA
130 GTTGAGATAG
*
9317 ACTTGTCGACATACGCTTTTGCCAACTCTTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAA
1 ACTTGTCGACATACGCTTTGGCCAACTC-TTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAA
* * *
9382 CGC-TAAATAAGAGTCGACTTTGTCCAACACTATGGCGACACTTTTGGGCCGACACTTTCTTAAG
65 CGCTTAAATAAGAGTTGACTTTGTCCAACACTATGCCGACACTTTTGGG-CGACACTTTCCTAAG
9446 TGTT-AGGATAG
129 TGTTGA-GATAG
* * *
9457 ACTTGCCGGCATACGCTTTGGCCAACACTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAAC
1 ACTTGTCGACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAAC
* *
9522 GCTTAAATAAGAATTGACTTTGTCTAACACTATGCCGACAC--TT--------C---CCTAAGTG
66 GCTTAAATAAGAGTTGACTTTGTCCAACACTATGCCGACACTTTTGGGCGACACTTTCCTAAGTG
*
9574 TTGGGATAG
131 TTGAGATAG
* * *
9583 AGTTG-CTGACATATGCTTTGGCCAACTCTTTATATAAGGGTTGGGATATGCATGCCTAAGGCAA
1 ACTTGTC-GACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAA
* *
9647 CGCTTAAATAAGAGTCGATTTTGTCCAACACTATGCCGACACTTT
65 CGCTTAAATAAGAGTTGACTTTGTCCAACACTATGCCGACACTTT
9692 CCTGAGTGTT
Statistics
Matches: 452, Mismatches: 54, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
125 1 0.00
126 109 0.24
128 1 0.00
129 1 0.00
138 2 0.00
139 42 0.09
140 260 0.58
141 36 0.08
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (139 bp):
ACTTGTCGACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAAC
GCTTAAATAAGAGTTGACTTTGTCCAACACTATGCCGACACTTTTGGGCGACACTTTCCTAAGTG
TTGAGATAG
Found at i:9503 original size:280 final size:271
Alignment explanation
Indices: 8999--9817 Score: 916
Period size: 280 Copynumber: 3.0 Consensus size: 271
8989 TCCTAAGACA
* ** * *
8999 ACACTTTTGGAGCAACACTTTTGTAAGTACTGGGGTAAACTTGTCAACATACG-TTTTGGCCAAC
1 ACACTTTTGG-GC-ACACTTTTCTAAGTGTTGGGATAAACTTGTCGACATACGCTTTT-GCCAAC
* * * * *
9063 TCTTTGTATAAGGGATGAGATATGCATGCCTAAGACAACGGTTAAATAAGAGTTGACTTTGTCCA
63 TCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAAC-GCTAAATAAGAGTCGACTTTGTCCA
* * *
9128 ACACAATATCGACACTTTTGAGG-TGACACTTTCCTAAGTGTTGAGATAGACTTGTCGACATATG
127 ACAC---ATCGACACTTTTG-GGCCGACACTTTCCTAAGTGTTG-GATAGACTTGCCGGCATATG
* ** *
9192 CTTTGGTCAACTCTTTGTATAAGGATTGGGATATGCATGCCTAAAACAACGTTTAAATAAGAGTT
187 CTTTGG-CAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTT
9257 GGCTTTATTCAACACTATGCCG
251 GGCTTT-TTCAACACTATGCCG
9279 ACACTTTTGGGGCGACACTTTTCTAAGTGTTGGGATAAACTTGTCGACATACGCTTTTGCCAACT
1 ACACTTTT-GGGC-ACACTTTTCTAAGTGTTGGGATAAACTTGTCGACATACGCTTTTGCCAACT
9344 CTTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTAAATAAGAGTCGACTTTGTCCAA
64 C-TTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTAAATAAGAGTCGACTTTGTCCAA
* *
9409 CACTATGGCGACACTTTTGGGCCGACACTTTCTTAAGTGTTAGGATAGACTTGCCGGCATACGCT
128 CAC-AT--CGACACTTTTGGGCCGACACTTTCCTAAGTGTT-GGATAGACTTGCCGGCATATGCT
* * *
9474 TTGGCCAACACTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAATTGA
189 TTGG-CAACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGG
*
9539 CTTTGTCTAACACTATGCCG
253 CTTTTTC-AACACTATGCCG
* * * *
9559 ACAC--TT-----C-C----CTAAGTGTTGGGATAGAGTTG-CTGACATATGCTTTGGCCAACTC
1 ACACTTTTGGGCACACTTTTCTAAGTGTTGGGATAAACTTGTC-GACATACGCTTTTGCCAACTC
* *
9611 TTTATATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGATTTTGTCCAAC
65 TTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGC-TAAATAAGAGTCGACTTTGTCCAAC
* *
9676 AC-T----A----T--GCCGACACTTTCCTGAGTGTTGGGATAGACTTACCGGCATATGCTTTGG
129 ACATCGACACTTTTGGGCCGACACTTTCCTAAGTGTT-GGATAGACTTGCCGGCATATGCTTTGG
* *
9730 CACACTCTTTGTATAAGAGTTGGAATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTT
193 CA-ACTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTT
* *
9795 GTCCAACACTATGCCA
257 -TTCAACACTATGCCG
9811 ACACTTT
1 ACACTTT
9818 CCTAAGTGTT
Statistics
Matches: 481, Mismatches: 44, Indels: 54
0.83 0.08 0.09
Matches are distributed among these distances:
251 2 0.00
252 116 0.24
253 1 0.00
254 2 0.00
258 1 0.00
264 1 0.00
265 39 0.08
266 64 0.13
270 1 0.00
271 1 0.00
278 5 0.01
279 4 0.01
280 203 0.42
281 41 0.09
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (271 bp):
ACACTTTTGGGCACACTTTTCTAAGTGTTGGGATAAACTTGTCGACATACGCTTTTGCCAACTCT
TTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTAAATAAGAGTCGACTTTGTCCAACAC
ATCGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGATAGACTTGCCGGCATATGCTTTGGCAA
CTCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTTTTCA
ACACTATGCCG
Found at i:9654 original size:126 final size:126
Alignment explanation
Indices: 9429--9872 Score: 656
Period size: 126 Copynumber: 3.5 Consensus size: 126
9419 ACACTTTTGG
* * * *
9429 GCCGACACTTTCTTAAGTGTTAGGATAGACTTGCCGGCATACGCTTTGGCCAACACTTTGTATAA
1 GCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAACTCTTTGTATAA
* *
9494 GGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAATTGACTTTGTCTAACACTAT
66 GGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGACTTTGTCCAACACTAT
* * * * *
9555 GCCGACACTTCCCTAAGTGTTGGGATAGAGTTGCTGACATATGCTTTGGCCAACTCTTTATATAA
1 GCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAACTCTTTGTATAA
* *
9620 GGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGATTTTGTCCAACACTAT
66 GGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGACTTTGTCCAACACTAT
* * * *
9681 GCCGACACTTTCCTGAGTGTTGGGATAGACTTACCGGCATATGCTTTGG-CACACTCTTTGTATA
1 GCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCA-ACTCTTTGTATA
* * *
9745 AGAGTTGGAATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTTGTCCAACACTAT
65 AGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGACTTTGTCCAACACTAT
* * * *
9807 GCCAACACTTTCCTAAGTGTTGGGATAGACTTGCTGACAAACGCTTTGGCCAACTCGTTGTATAA
1 GCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAACTCTTTGTATAA
9872 G
66 G
9873 AGTTAGCTAA
Statistics
Matches: 283, Mismatches: 33, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
125 2 0.01
126 279 0.99
127 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (126 bp):
GCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAACTCTTTGTATAA
GGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGACTTTGTCCAACACTAT
Found at i:11261 original size:17 final size:16
Alignment explanation
Indices: 11241--11274 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
11231 TCCCTTTTTA
11241 AATTTATTATAAGATTT
1 AATTTATTATAA-ATTT
*
11258 AATTTATTTTAAATTT
1 AATTTATTATAAATTT
11274 A
1 A
11275 CTTTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
AATTTATTATAAATTT
Found at i:11297 original size:30 final size:28
Alignment explanation
Indices: 11236--11304 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 28
11226 CTAAATCCCT
* * *
11236 TTTTAAATTTATTATAAGATTTAATTTA
1 TTTTAAATTTATTATAAAATTAAAATTA
*
11264 TTTTAAATTTACTTTTAAAATTAAAAATTA
1 TTTTAAATTTA-TTATAAAATT-AAAATTA
11294 TTTTAAATTTA
1 TTTTAAATTTA
11305 AAAAGTCCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 11 0.31
29 8 0.23
30 16 0.46
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
TTTTAAATTTATTATAAAATTAAAATTA
Found at i:12143 original size:10 final size:10
Alignment explanation
Indices: 12124--12162 Score: 71
Period size: 10 Copynumber: 4.0 Consensus size: 10
12114 ATAATGAGTT
12124 TATT-AATAA
1 TATTAAATAA
12133 TATTAAATAA
1 TATTAAATAA
12143 TATTAAATAA
1 TATTAAATAA
12153 TATTAAATAA
1 TATTAAATAA
12163 AAAAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 4 0.14
10 25 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:13341 original size:29 final size:29
Alignment explanation
Indices: 13196--13655 Score: 327
Period size: 29 Copynumber: 15.5 Consensus size: 29
13186 TAAATTGTCT
* *
13196 AAAAATTACATTTTT-GCCCCAAACTTCC
1 AAAAATTCCATTTTTACCCCCAAACTTCC
* *
13224 AAAAATTCCATTTTCGACCCCCAAAATTTCC
1 AAAAATTCCATTTT-TACCCCC-AAACTTCC
*
13255 AAAAAATTCCATTTTTACCCCAAAAACTTCC
1 -AAAAATTCCATTTTTACCCC-CAAACTTCC
* * *
13286 AACAATCCCATTTTTTCCCCCAAAACTTCC
1 AAAAATTCCATTTTTACCCCC-AAACTTCC
* * *
13316 AAAAATCCCATTTTTACCCCCTAACTTCT
1 AAAAATTCCATTTTTACCCCCAAACTTCC
*
13345 AAAAATTCCATTTTTACCCCTAAACTTCC
1 AAAAATTCCATTTTTACCCCCAAACTTCC
* *
13374 AAAAATTCCATTTTTGACCCCAAAACTTCA
1 AAAAATTCCATTTTT-ACCCCCAAACTTCC
* * *
13404 AAAAATTCCATTTTTACCCTCGAACTTCT
1 AAAAATTCCATTTTTACCCCCAAACTTCC
* ** * *
13433 AAAAATTCCATTTTCAACCCTAAAAGTCCC
1 AAAAATTCCATTTT-TACCCCCAAACTTCC
* * * * *
13463 AAAAATTACATTTCTACCCTCGAACCTCC
1 AAAAATTCCATTTTTACCCCCAAACTTCC
* *
13492 AAAAATTTCCATTTTTAACCCCAAAACTTTC
1 AAAAA-TTCCATTTTT-ACCCCCAAACTTCC
* * **
13523 AAAAATTATCA-TTTTGCCCCTGAA-TGTCC
1 AAAAATT-CCATTTTTACCCCCAAACT-TCC
* * * ***
13552 AAAAACTCTATTTTCGACCTTGAAAC-TCC
1 AAAAATTCCATTTT-TACCCCCAAACTTCC
** *
13581 AAAAATTCCATTTTTACCCCTGAA-TGTCT
1 AAAAATTCCATTTTTACCCCCAAACT-TCC
* * *
13610 AAAAATTCCATCTTTTAACCTCGAACTTCCC
1 AAAAATTCCAT-TTTTACCCCCAAACTT-CC
*
13641 CAAAATTACCATTTT
1 AAAAATT-CCATTTT
13656 GCATCGAAAA
Statistics
Matches: 338, Mismatches: 73, Indels: 39
0.75 0.16 0.09
Matches are distributed among these distances:
28 20 0.06
29 129 0.38
30 125 0.37
31 46 0.14
32 18 0.05
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCCAAACTTCC
Found at i:13394 original size:59 final size:59
Alignment explanation
Indices: 13196--13625 Score: 358
Period size: 59 Copynumber: 7.3 Consensus size: 59
13186 TAAATTGTCT
* * ** *
13196 AAAAATTACATTTTTG-CCCC-AAACTTCCAAAAATTCCATTTTCGACCCCCAAAATTTCC
1 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTT-TA-CCCCTGAACTTCC
* * * **
13255 AAAAAATTCCATTTTT-ACCCCAAAAACTTCCAACAATCCCATTTTTTCCCCCAAAACTTCC
1 -AAAAATTCCATTTTTGACCCC-AAAACTTCCAAAAATTCCA-TTTTTACCCCTGAACTTCC
* ** * *
13316 AAAAATCCCATTTTT-ACCCCCTAACTTCTAAAAATTCCATTTTTACCCCTAAACTTCC
1 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCC
* *
13374 AAAAATTCCATTTTTGACCCCAAAACTTCAAAAAATTCCATTTTTA-CCCTCGAACTTCT
1 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCT-GAACTTCC
** * * * * * *
13433 AAAAATTCCATTTTCAACCCTAAAAGTCCCAAAAATTACATTTCTA-CCCTCGAACCTCC
1 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCT-GAACTTCC
* * * *
13492 AAAAATTTCCATTTTTAACCCCAAAACTTTCAAAAATTATCA-TTTTGCCCCTGAA-TGTCC
1 AAAAA-TTCCATTTTTGACCCCAAAACTTCCAAAAATT-CCATTTTTACCCCTGAACT-TCC
* * * *** *
13552 AAAAACTCTATTTTCGACCTTGAAAC-TCCAAAAATTCCATTTTTACCCCTGAA-TGTCT
1 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACT-TCC
13610 AAAAATTCCATCTTTT
1 AAAAATTCCAT-TTTT
13626 AACCTCGAAC
Statistics
Matches: 305, Mismatches: 53, Indels: 25
0.80 0.14 0.07
Matches are distributed among these distances:
57 2 0.01
58 69 0.23
59 118 0.39
60 78 0.26
61 18 0.06
62 16 0.05
63 4 0.01
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (59 bp):
AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCC
Found at i:24516 original size:10 final size:10
Alignment explanation
Indices: 24497--24535 Score: 71
Period size: 10 Copynumber: 4.0 Consensus size: 10
24487 ATAATGAGTT
24497 TATT-AATAA
1 TATTAAATAA
24506 TATTAAATAA
1 TATTAAATAA
24516 TATTAAATAA
1 TATTAAATAA
24526 TATTAAATAA
1 TATTAAATAA
24536 AAAAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 4 0.14
10 25 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:25714 original size:29 final size:29
Alignment explanation
Indices: 25569--26028 Score: 327
Period size: 29 Copynumber: 15.5 Consensus size: 29
25559 TAAATTGTCT
* *
25569 AAAAATTACATTTTT-GCCCCAAACTTCC
1 AAAAATTCCATTTTTACCCCCAAACTTCC
* *
25597 AAAAATTCCATTTTCGACCCCCAAAATTTCC
1 AAAAATTCCATTTT-TACCCCC-AAACTTCC
*
25628 AAAAAATTCCATTTTTACCCCAAAAACTTCC
1 -AAAAATTCCATTTTTACCCC-CAAACTTCC
* * *
25659 AACAATCCCATTTTTTCCCCCAAAACTTCC
1 AAAAATTCCATTTTTACCCCC-AAACTTCC
* * *
25689 AAAAATCCCATTTTTACCCCCTAACTTCT
1 AAAAATTCCATTTTTACCCCCAAACTTCC
*
25718 AAAAATTCCATTTTTACCCCTAAACTTCC
1 AAAAATTCCATTTTTACCCCCAAACTTCC
* *
25747 AAAAATTCCATTTTTGACCCCAAAACTTCA
1 AAAAATTCCATTTTT-ACCCCCAAACTTCC
* * *
25777 AAAAATTCCATTTTTACCCTCGAACTTCT
1 AAAAATTCCATTTTTACCCCCAAACTTCC
* ** * *
25806 AAAAATTCCATTTTCAACCCTAAAAGTCCC
1 AAAAATTCCATTTT-TACCCCCAAACTTCC
* * * * *
25836 AAAAATTACATTTCTACCCTCGAACCTCC
1 AAAAATTCCATTTTTACCCCCAAACTTCC
* *
25865 AAAAATTTCCATTTTTAACCCCAAAACTTTC
1 AAAAA-TTCCATTTTT-ACCCCCAAACTTCC
* * **
25896 AAAAATTATCA-TTTTGCCCCTGAA-TGTCC
1 AAAAATT-CCATTTTTACCCCCAAACT-TCC
* * * ***
25925 AAAAACTCTATTTTCGACCTTGAAAC-TCC
1 AAAAATTCCATTTT-TACCCCCAAACTTCC
** *
25954 AAAAATTCCATTTTTACCCCTGAA-TGTCT
1 AAAAATTCCATTTTTACCCCCAAACT-TCC
* * *
25983 AAAAATTCCATCTTTTAACCTCGAACTTCCC
1 AAAAATTCCAT-TTTTACCCCCAAACTT-CC
*
26014 CAAAATTACCATTTT
1 AAAAATT-CCATTTT
26029 GCATCGAAAA
Statistics
Matches: 338, Mismatches: 73, Indels: 39
0.75 0.16 0.09
Matches are distributed among these distances:
28 20 0.06
29 129 0.38
30 125 0.37
31 46 0.14
32 18 0.05
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCCAAACTTCC
Found at i:25767 original size:59 final size:59
Alignment explanation
Indices: 25569--25998 Score: 358
Period size: 59 Copynumber: 7.3 Consensus size: 59
25559 TAAATTGTCT
* * ** *
25569 AAAAATTACATTTTTG-CCCC-AAACTTCCAAAAATTCCATTTTCGACCCCCAAAATTTCC
1 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTT-TA-CCCCTGAACTTCC
* * * **
25628 AAAAAATTCCATTTTT-ACCCCAAAAACTTCCAACAATCCCATTTTTTCCCCCAAAACTTCC
1 -AAAAATTCCATTTTTGACCCC-AAAACTTCCAAAAATTCCA-TTTTTACCCCTGAACTTCC
* ** * *
25689 AAAAATCCCATTTTT-ACCCCCTAACTTCTAAAAATTCCATTTTTACCCCTAAACTTCC
1 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCC
* *
25747 AAAAATTCCATTTTTGACCCCAAAACTTCAAAAAATTCCATTTTTA-CCCTCGAACTTCT
1 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCT-GAACTTCC
** * * * * * *
25806 AAAAATTCCATTTTCAACCCTAAAAGTCCCAAAAATTACATTTCTA-CCCTCGAACCTCC
1 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCT-GAACTTCC
* * * *
25865 AAAAATTTCCATTTTTAACCCCAAAACTTTCAAAAATTATCA-TTTTGCCCCTGAA-TGTCC
1 AAAAA-TTCCATTTTTGACCCCAAAACTTCCAAAAATT-CCATTTTTACCCCTGAACT-TCC
* * * *** *
25925 AAAAACTCTATTTTCGACCTTGAAAC-TCCAAAAATTCCATTTTTACCCCTGAA-TGTCT
1 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACT-TCC
25983 AAAAATTCCATCTTTT
1 AAAAATTCCAT-TTTT
25999 AACCTCGAAC
Statistics
Matches: 305, Mismatches: 53, Indels: 25
0.80 0.14 0.07
Matches are distributed among these distances:
57 2 0.01
58 69 0.23
59 118 0.39
60 78 0.26
61 18 0.06
62 16 0.05
63 4 0.01
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (59 bp):
AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCC
Found at i:43275 original size:50 final size:50
Alignment explanation
Indices: 43180--43410 Score: 146
Period size: 50 Copynumber: 4.6 Consensus size: 50
43170 GAATCCAGTT
* *
43180 CTAAGAAGATGTGATGGGAAAGGTTGAGGCTACAACGGTGAACCCGATAA
1 CTAAAAAGATGTGATGGGAAAGGTTGAGGCCACAACGGTGAACCCGATAA
* ** * *
43230 CTAAAAAGATGTGATGGGAAAGGTTGAGGCCGCAGTGGTGGACCCGGT-A
1 CTAAAAAGATGTGATGGGAAAGGTTGAGGCCACAACGGTGAACCCGATAA
* ** * * * *** * **
43279 CCATGAAGA-GATGAAGGG-AAGGATTGAAGCCACGACGACAAATCC-AGTTC
1 CTAAAAAGATG-TGATGGGAAAGG-TTGAGGCCACAACGGTGAACCCGA-TAA
** * * * * *
43329 CTAAGCAGATGTGATGGGAAAGGTTGAGGCCATAACGGCGAACTCGGTAC
1 CTAAAAAGATGTGATGGGAAAGGTTGAGGCCACAACGGTGAACCCGATAA
43379 CTAAGAAGAAGATGTGATGGGAAAGGTTGAGG
1 CT-A-AA-AAGATGTGATGGGAAAGGTTGAGG
43411 TCGTAACAGC
Statistics
Matches: 133, Mismatches: 38, Indels: 17
0.71 0.20 0.09
Matches are distributed among these distances:
48 5 0.04
49 26 0.20
50 72 0.54
51 6 0.05
52 1 0.01
53 23 0.17
ACGTcount: A:0.34, C:0.15, G:0.34, T:0.17
Consensus pattern (50 bp):
CTAAAAAGATGTGATGGGAAAGGTTGAGGCCACAACGGTGAACCCGATAA
Found at i:43423 original size:53 final size:53
Alignment explanation
Indices: 43335--43438 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 53
43325 GTTCCTAAGC
* *
43335 AGATGTGATGGGAAAGGTTGAGGCCATAACGGCGAACTCGGTACCTAAGAAGA
1 AGATGTGATGGGAAAGGTTGAGGCCATAACAGCGAACTCGATACCTAAGAAGA
* * *
43388 AGATGTGATGGGAAAGGTTGAGGTCGTAACAGCGAACTCGATACCTTAGAA
1 AGATGTGATGGGAAAGGTTGAGGCCATAACAGCGAACTCGATACCTAAGAA
43439 AACAAGATGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.19
Consensus pattern (53 bp):
AGATGTGATGGGAAAGGTTGAGGCCATAACAGCGAACTCGATACCTAAGAAGA
Found at i:43894 original size:41 final size:41
Alignment explanation
Indices: 43763--43882 Score: 170
Period size: 41 Copynumber: 2.9 Consensus size: 41
43753 ATCATTCAGA
* * *
43763 CTTTTACCTTTAATCAAGAAGGGCA-AATTGAAGATTTCAGT
1 CTTTTACCCTTAATCAAGAAGGGTAGAA-TGAAGATTCCAGT
* *
43804 CTTTTACCCTTAATTAAGAAGGGTAGATTGAAGATTCCAGT
1 CTTTTACCCTTAATCAAGAAGGGTAGAATGAAGATTCCAGT
*
43845 TTTTTACCCTTAATCAAGAAGGGTAGAATGAAGATTCC
1 CTTTTACCCTTAATCAAGAAGGGTAGAATGAAGATTCC
43883 GATCTCTTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
41 69 0.99
42 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (41 bp):
CTTTTACCCTTAATCAAGAAGGGTAGAATGAAGATTCCAGT
Found at i:44578 original size:208 final size:209
Alignment explanation
Indices: 43958--44875 Score: 1173
Period size: 208 Copynumber: 4.4 Consensus size: 209
43948 TGTAGTTATC
* * * * ** * *
43958 CAAAGCAATAAAACGGTCATTTTCCTGATGAGATATAGAGAAGTGGAATAAATTCGTCTTCCTGA
1 CAAAGAAATAAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTAA
** * *
44023 TGAGATACAGAGAAACAAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGT
66 TGAGATACAGAGAAGTAAATTAAAACAAGTGATGCGGCCATCTTCCTGATGAGATACAGAGAAGT
* * *
44088 AGACCAAATCGATGAAGCAAAGCTC-A-ATGGAGCAAAACTTCGAACCCCAGCTTCCTGATGAGA
131 ATACCAAATCAATGAAACAAAGCTCGATAT-GAGCAAAACTTCGAACCCCAGCTTCCTGATGAGA
44151 TACTGAGAAGCAGGT
195 TACTGAGAAGCAGGT
* * *
44166 CGAAGAAATAAAATGGTCGTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCGTCTTCCTAA
1 CAAAGAAATAAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTAA
* *** * *
44231 TGAGATACAAAGAAGTGCGTTAAAACAAGTAATGCGGCCATCGTCCTGATGAGATACAGAGAAGT
66 TGAGATACAGAGAAGTAAATTAAAACAAGTGATGCGGCCATCTTCCTGATGAGATACAGAGAAGT
* * **
44296 AAACCAAATCAATGAAACAAAGCTCGATATGAGCAAAGCTTCGAACCCCATATTCCTGATGAGAT
131 ATACCAAATCAATGAAACAAAGCTCGATATGAGCAAAACTTCGAACCCCAGCTTCCTGATGAGAT
44361 ACTGAGAAGCAGGT
196 ACTGAGAAGCAGGT
* *
44375 CGAAGAAATAAAATGGTCATCTTTCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTAA
1 CAAAGAAATAAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTAA
* * * * * *
44440 CGAAATACAGAGAAGCAAATTGAAACAA-TGATGCGACCATCTTCTTGATGAGATACAGAGAAGT
66 TGAGATACAGAGAAGTAAATTAAAACAAGTGATGCGGCCATCTTCCTGATGAGATACAGAGAAGT
* *
44504 ATACCAAATCAATGAAACAAAGCTCGATATGAGCAAAACTTTGAACCCCAGCTTCCTGATGAGGT
131 ATACCAAATCAATGAAACAAAGCTCGATATGAGCAAAACTTCGAACCCCAGCTTCCTGATGAGAT
44569 ACTGAGAAGCAGGT
196 ACTGAGAAGCAGGT
* *
44583 -AAAAATAATAAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTG
1 CAAAGA-AATAAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTA
* * * * * * * * * *
44647 GTGAGATACAAAGAAGTAGATTGAAAC-AGTGATGCGGTCGTCTTCCTAATGAAATACAAAAAAG
65 ATGAGATACAGAGAAGTAAATTAAAACAAGTGATGCGGCCATCTTCCTGATGAGATACAGAGAAG
* * * ** * *
44711 TATAACAAATCAATGAAACAAAACTCAATATGAGTGAAACTTC-AAACCCATCTTCCTGATGAGA
130 TATACCAAATCAATGAAACAAAGCTCGATATGAGCAAAACTTCGAACCCCAGCTTCCTGATGAGA
* **
44775 TATTGAGAAGTGGGT
195 TACTGAGAAGCAGGT
* * * * * *
44790 CAAAGCAATAAAAATGGTTATCTTCCTGACGAGATACAGAGAAGTGGACCAAATCTGTCTTCTTC
1 CAAAGAAAT-AAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTA
44855 ATGAGATACAGAGAAGTAAAT
65 ATGAGATACAGAGAAGTAAAT
44876 CAAATCAATG
Statistics
Matches: 618, Mismatches: 86, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
207 37 0.06
208 450 0.73
209 129 0.21
210 2 0.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (209 bp):
CAAAGAAATAAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTAA
TGAGATACAGAGAAGTAAATTAAAACAAGTGATGCGGCCATCTTCCTGATGAGATACAGAGAAGT
ATACCAAATCAATGAAACAAAGCTCGATATGAGCAAAACTTCGAACCCCAGCTTCCTGATGAGAT
ACTGAGAAGCAGGT
Found at i:44880 original size:37 final size:37
Alignment explanation
Indices: 44818--44927 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 37
44808 TATCTTCCTG
* *
44818 ACGAGATACAGAGAAGTGGACCAAATCTGTCTTCTTC
1 ACGAGATACAGAGAAGTGAATCAAATCTGTCTTCTTC
* * ** * *
44855 ATGAGATACAGAGAAGTAAATCAAATCAATGTTCTTG
1 ACGAGATACAGAGAAGTGAATCAAATCTGTCTTCTTC
*
44892 ACGAGATGCAGAGAAGTGAATCAAAT-TCGTCTTCTT
1 ACGAGATACAGAGAAGTGAATCAAATCT-GTCTTCTT
44928 AGTGAAATTC
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.26
Consensus pattern (37 bp):
ACGAGATACAGAGAAGTGAATCAAATCTGTCTTCTTC
Found at i:45935 original size:10 final size:10
Alignment explanation
Indices: 45922--45946 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
45912 CAAAAGGCAA
45922 AAAAAGAAAG
1 AAAAAGAAAG
45932 AAAAAGAAAG
1 AAAAAGAAAG
45942 AAAAA
1 AAAAA
45947 AACACCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:46762 original size:31 final size:31
Alignment explanation
Indices: 46724--46795 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
46714 CATATTTTAA
*
46724 CCCTAAACTTTC-CAAATATTACA-TTTTGCCC
1 CCCTAAACTTTCTCAAAAATTACATTTTTG--C
*
46755 CCCTAAAC-TTCTTAAAAATTACATTTTTGC
1 CCCTAAACTTTCTCAAAAATTACATTTTTGC
46785 CCCTAAACTTT
1 CCCTAAACTTT
46796 AAAATTACCG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
30 12 0.33
31 19 0.53
32 5 0.14
ACGTcount: A:0.31, C:0.29, G:0.03, T:0.38
Consensus pattern (31 bp):
CCCTAAACTTTCTCAAAAATTACATTTTTGC
Found at i:46995 original size:89 final size:87
Alignment explanation
Indices: 46874--47257 Score: 382
Period size: 89 Copynumber: 4.3 Consensus size: 87
46864 TTTTTTACCT
* * *
46874 CAAACTTTCCAAAAATTATCATTTTACCCTCGAACATCTTAAAATTACCATTTTACCATCAGATG
1 CAAACTTTCCAAAAATTACCATTTTACCCTCGAACATCTAAAAATTACCATTTTACC-CCAGATG
* *
46939 TCCAAAAATCACATTTGTGACTC
65 CCCAAAAATCACATTTTTGACTC
* * *
46962 CAAACTTTCCAAAAAATTACCATTTTACCCTCGAAAATCTTAAAATTACCATTTTACCATC-GAA
1 CAAACTTTCC-AAAAATTACCATTTTACCCTCGAACATCTAAAAATTACCATTTTACC-CCAG-A
* * *
47026 TGTCTAAAAATCACATTTTTTACTC
63 TGCCCAAAAATCACATTTTTGACTC
** * * * *
47051 TGAACTTTCCAAAAATTATCAAATTTATTCC-CGAACATCTAAAAATTATCATTTTATCCCCAGA
1 CAAACTTTCCAAAAATTA-CCATTTTA-CCCTCGAACATCTAAAAATTACCATTTTA-CCCCAGA
* *
47115 TGCCCAAAATTTACATTTTTGAC-C
63 TGCCCAAAAATCACATTTTTGACTC
* * * *
47139 CTGAACTTT-TAGAAAATTACCATTTTACCGTCGAACAT-TCAAAAATTACCATTTTACCCCTAA
1 C-AAACTTTCCA-AAAATTACCATTTTACCCTCGAACATCT-AAAAATTACCATTTTACCCC-AG
* * * * *
47202 ATGCCCTAAAATTACTTTTTTTACCC
62 ATGCCCAAAAATCACATTTTTGACTC
47228 CAAACTTTCCAAAAATTACCATTTTACCCT
1 CAAACTTTCCAAAAATTACCATTTTACCCT
47258 TGTGTGTTCA
Statistics
Matches: 249, Mismatches: 34, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
87 6 0.02
88 94 0.38
89 144 0.58
90 5 0.02
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (87 bp):
CAAACTTTCCAAAAATTACCATTTTACCCTCGAACATCTAAAAATTACCATTTTACCCCAGATGC
CCAAAAATCACATTTTTGACTC
Found at i:47157 original size:177 final size:178
Alignment explanation
Indices: 46854--47257 Score: 450
Period size: 177 Copynumber: 2.3 Consensus size: 178
46844 TCTAACTTCC
* * *
46854 AAAATTACTATTTTTTACCTCAAACTTTCCAAAAATTATCATTTTACCCTCGAACATCTTAAAAT
1 AAAATCACTATTTTTTACCTCAAACTTTCCAAAAATTATCAATTTACCCTCGAACATCTAAAAAT
* *
46919 TACCATTTTACCATCAGATGTCCAAAAATCACATTTGTGACTCCAAACTTTCCAAAAAATTACCA
66 TACCATTTTACCACCAGATGCCCAAAAATCACATTTGTGACTCCAAACTTTCCAAAAAATTACCA
*
46984 TTTTACCCTCGAAAA-TCTTAAAATTACCATTTTACCATCGAATGTCTA
131 TTTTACCCTCGAAAATTC-AAAAATTACCATTTTACCATCGAATGTCTA
* *
47032 AAAATCAC-ATTTTTTA-CTCTGAACTTTCCAAAAATTATCAAATTTATTCC-CGAACATCTAAA
1 AAAATCACTATTTTTTACCTC-AAACTTTCCAAAAATTATC-AATTTA-CCCTCGAACATCTAAA
* * * * * * *
47094 AATTATCATTTTATCC-CCAGATGCCCAAAATTTACATTTTTGAC-CCTGAACTTT-TAGAAAAT
63 AATTACCATTTTA-CCACCAGATGCCCAAAAATCACATTTGTGACTCC-AAACTTTCCAAAAAAT
* * * * *
47156 TACCATTTTACCGTCGAACATTCAAAAATTACCATTTTACC-CCTAAATGCCCT-
126 TACCATTTTACCCTCGAAAATTCAAAAATTACCATTTTACCATC-GAATG-TCTA
* * * *
47209 AAAATTACT-TTTTTTACCCCAAACTTTCCAAAAATTACCATTTTACCCT
1 AAAATCACTATTTTTTACCTCAAACTTTCCAAAAATTATCAATTTACCCT
47258 TGTGTGTTCA
Statistics
Matches: 189, Mismatches: 26, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
175 2 0.01
176 9 0.05
177 104 0.55
178 70 0.37
179 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.35
Consensus pattern (178 bp):
AAAATCACTATTTTTTACCTCAAACTTTCCAAAAATTATCAATTTACCCTCGAACATCTAAAAAT
TACCATTTTACCACCAGATGCCCAAAAATCACATTTGTGACTCCAAACTTTCCAAAAAATTACCA
TTTTACCCTCGAAAATTCAAAAATTACCATTTTACCATCGAATGTCTA
Found at i:47256 original size:29 final size:29
Alignment explanation
Indices: 46866--47256 Score: 126
Period size: 29 Copynumber: 13.3 Consensus size: 29
46856 AATTACTATT
* *
46866 TTTTACCTCAAACTTTCCAAAAATTATCA
1 TTTTACCCCAAACTTTCCAAAAATTACCA
* * **
46895 TTTTACCCTCGAAC-ATCTTAAAATTACCA
1 TTTTACCC-CAAACTTTCCAAAAATTACCA
* * * *
46924 TTTTACCATCAGA-TGTCCAAAAATCA-CA
1 TTTTACC-CCAAACTTTCCAAAAATTACCA
*
46952 TTTGTGACTCCAAACTTTCCAAAAAATTACCA
1 TTT-T-ACCCCAAACTTTCC-AAAAATTACCA
*
46984 TTTTACCCTCGAAAATCTT---AAAATTACCA
1 TTTTACCC-C-AAACT-TTCCAAAAATTACCA
* * * * *
47013 TTTTACCATCGAA-TGTCTAAAAATCA-CA
1 TTTTACC-CCAAACTTTCCAAAAATTACCA
* ** *
47041 TTTTTTACTCTGAACTTTCCAAAAATTATCAA
1 --TTTTACCCCAAACTTTCCAAAAATTA-CCA
* * * * * *
47073 ATTTATTCCCGAAC-ATCTAAAAATTATCA
1 TTTTA-CCCCAAACTTTCCAAAAATTACCA
* ** *
47102 TTTTATCCCCAGA-TGCCCAAAATTTA-CA
1 TTTTA-CCCCAAACTTTCCAAAAATTACCA
** *
47130 TTTTTGACCCTGAACTTT-TAGAAAATTACCA
1 -TTTT-ACCCCAAACTTTCCA-AAAATTACCA
* * *
47161 TTTTACCGTCGAACATT-CAAAAATTACCA
1 TTTTACC-CCAAACTTTCCAAAAATTACCA
** * **
47190 TTTTACCCCTAAA-TGCCCTAAAATTACTTT
1 TTTTACCCC-AAACTTTCCAAAAATTAC-CA
47220 TTTTACCCCAAACTTTCCAAAAATTACCA
1 TTTTACCCCAAACTTTCCAAAAATTACCA
47249 TTTTACCC
1 TTTTACCC
47257 TTGTGTGTTC
Statistics
Matches: 259, Mismatches: 71, Indels: 64
0.66 0.18 0.16
Matches are distributed among these distances:
26 1 0.00
27 1 0.00
28 12 0.05
29 135 0.52
30 82 0.32
31 16 0.06
32 10 0.04
33 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (29 bp):
TTTTACCCCAAACTTTCCAAAAATTACCA
Found at i:51209 original size:14 final size:15
Alignment explanation
Indices: 51192--51222 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
51182 AAATATGTGG
51192 ATGAAATA-ATAGAA
1 ATGAAATACATAGAA
51206 ATGAAATACATAGAA
1 ATGAAATACATAGAA
51221 AT
1 AT
51223 TTGATATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.61, C:0.03, G:0.13, T:0.23
Consensus pattern (15 bp):
ATGAAATACATAGAA
Found at i:51475 original size:29 final size:29
Alignment explanation
Indices: 51441--51929 Score: 612
Period size: 29 Copynumber: 16.7 Consensus size: 29
51431 TTTAAGGTCT
* *
51441 AAAATGGAATTTTTAGAAGTTCGGGGGTA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTA
* *
51470 AAAATGGGATTTTTGGAAATTTC-GGGATGA
1 AAAATGGGATTTTTGG-AAGTTCGGGGGT-A
51500 AAAATGGGATTTTTGGAAGTTC-GGGG-A
1 AAAATGGGATTTTTGGAAGTTCGGGGGTA
*
51527 AAAATGAGATTTTTGGAAGTTTC-GGGGTGA
1 AAAATGGGATTTTTGGAAG-TTCGGGGGT-A
*
51557 AAAATGGGATTTTTGGAAGTTTC-GGGATGA
1 AAAATGGGATTTTTGGAAG-TTCGGGGGT-A
*
51587 AAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTA
51616 AAAATGGGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTA
*
51645 AAAATGGGATTTTTGGAAGTTTC-GGGATGA
1 AAAATGGGATTTTTGGAAG-TTCGGGGGT-A
*
51675 AAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTA
*
51704 AAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTA
* ***
51733 AAAATGAGATTTTTGGAAGTTTTAGGGTGA
1 AAAATGGGATTTTTGGAAGTTCGGGGGT-A
** *
51763 AAAATGAAATTTTTGGAAGTTTGGGGGTA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTA
**
51792 AAAATGGGATTTTTGGAAGTTTAGGGGTGA
1 AAAATGGGATTTTTGGAAGTTCGGGGGT-A
**
51822 AAAATGGGATTTTTGGAAGTTTAGGGGTA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTA
*** *
51851 AAAATGGGATTTTTGGAAGTTTTAGGGTG
1 AAAATGGGATTTTTGGAAGTTCGGGGGTA
*
51880 AAAATGAGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTA
51909 AAAATGGGATTTTTGGAAGTT
1 AAAATGGGATTTTTGGAAGTT
51930 TAGGGACCTA
Statistics
Matches: 416, Mismatches: 33, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
27 19 0.05
28 7 0.02
29 236 0.57
30 154 0.37
ACGTcount: A:0.31, C:0.02, G:0.34, T:0.33
Consensus pattern (29 bp):
AAAATGGGATTTTTGGAAGTTCGGGGGTA
Found at i:51488 original size:59 final size:58
Alignment explanation
Indices: 51441--51929 Score: 571
Period size: 59 Copynumber: 8.4 Consensus size: 58
51431 TTTAAGGTCT
* * * *
51441 AAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAATTTCGGGATGA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGGG-TGA
* *
51500 AAAATGGGATTTTTGGAAGTTC-GGGG-AAAAATGAGATTTTTGGAAGTTTCGGGGTGA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTT-AGGGTGA
* *
51557 AAAATGGGATTTTTGGAAGTTTC-GGGATGAAAAATGGGATTTTTGGAAGTTCGAGGGT-A
1 AAAATGGGATTTTTGGAAG-TTCGGGGGT-AAAAATGGGATTTTTGGAAGTT-TAGGGTGA
*
51616 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGATGA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGGG-TGA
* *
51675 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTTCGAGGGT-A
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTT-TAGGGTGA
* *** ** *
51733 AAAATGAGATTTTTGGAAGTTTTAGGGTGAAAAATGAAATTTTTGGAAGTTT-GGGGGTA
1 AAAATGGGATTTTTGGAAGTTCGGGGGT-AAAAATGGGATTTTTGGAAGTTTAGGGTG-A
**
51792 AAAATGGGATTTTTGGAAGTTTAGGGGTGAAAAATGGGATTTTTGGAAGTTTAGGG-GTA
1 AAAATGGGATTTTTGGAAGTTCGGGGGT-AAAAATGGGATTTTTGGAAGTTTAGGGTG-A
*** * * * *
51851 AAAATGGGATTTTTGGAAGTTTTAGGGTGAAAATGAGATTTTTGGAAG-TTCGGGGGTA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGGGTG-A
51909 AAAATGGGATTTTTGGAAGTT
1 AAAATGGGATTTTTGGAAGTT
51930 TAGGGACCTA
Statistics
Matches: 384, Mismatches: 32, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
57 54 0.14
58 107 0.28
59 192 0.50
60 31 0.08
ACGTcount: A:0.31, C:0.02, G:0.34, T:0.33
Consensus pattern (58 bp):
AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGGGTGA
Found at i:51670 original size:88 final size:88
Alignment explanation
Indices: 51441--51935 Score: 739
Period size: 88 Copynumber: 5.6 Consensus size: 88
51431 TTTAAGGTCT
* * * *
51441 AAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAATTTCGGGATGAAAAATG
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGGGATGAAAAATG
51506 GGATTTTTGGAAGTTCG-GGG-A
66 GGATTTTTGGAAGTTCGAGGGTA
* *
51527 AAAATGAGATTTTTGGAAGTTTC-GGGGTGAAAAATGGGATTTTTGGAAGTTTCGGGATGAAAAA
1 AAAATGGGATTTTTGGAAG-TTCGGGGGT-AAAAATGGGATTTTTGGAAGTTTAGGGATGAAAAA
51591 TGGGATTTTTGGAAGTTCGAGGGTA
64 TGGGATTTTTGGAAGTTCGAGGGTA
*
51616 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTCGGGATGAAAAATG
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGGGATGAAAAATG
51681 GGATTTTTGGAAGTTCGAGGGTA
66 GGATTTTTGGAAGTTCGAGGGTA
* *
51704 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGAGATTTTTGGAAGTTTTAGGG-TGAAAAAT
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAG-TTTAGGGATGAAAAAT
** * *
51768 GAAATTTTTGGAAGTTTGGGGGTA
65 GGGATTTTTGGAAGTTCGAGGGTA
** *
51792 AAAATGGGATTTTTGGAAGTTTAGGGGTGAAAAATGGGATTTTTGGAAGTTTAGGGGT-AAAAAT
1 AAAATGGGATTTTTGGAAGTTCGGGGGT-AAAAATGGGATTTTTGGAAGTTTAGGGATGAAAAAT
** *
51856 GGGATTTTTGGAAGTTTTAGGGTG
65 GGGATTTTTGGAAGTTCGAGGGTA
*
51880 AAAATGAGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGGGA
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGGGA
51936 CCTACGAGAT
Statistics
Matches: 376, Mismatches: 25, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
86 21 0.06
87 83 0.22
88 222 0.59
89 50 0.13
ACGTcount: A:0.31, C:0.02, G:0.34, T:0.33
Consensus pattern (88 bp):
AAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTAGGGATGAAAAATG
GGATTTTTGGAAGTTCGAGGGTA
Found at i:52957 original size:14 final size:14
Alignment explanation
Indices: 52938--52973 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
52928 TTTTATTCTC
52938 ATTTAATACTTATT
1 ATTTAATACTTATT
52952 ATTTAATACTTATT
1 ATTTAATACTTATT
52966 ATTTAATA
1 ATTTAATA
52974 TTGAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTAATACTTATT
Found at i:53706 original size:17 final size:17
Alignment explanation
Indices: 53686--53768 Score: 87
Period size: 17 Copynumber: 4.9 Consensus size: 17
53676 AAATAAATTT
53686 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
* **
53703 TAAATTTAAGTTTCA-GC
1 TAAATTTAAATTT-ATAA
53720 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
* * *
53737 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
*
53754 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
53769 TGGGCCCAGA
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
16 1 0.02
17 50 0.96
18 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:53724 original size:34 final size:34
Alignment explanation
Indices: 53686--53768 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
53676 AAATAAATTT
* * **
53686 TAAATTTAAATTTATAATAAATTTAAGTTTCAGC
1 TAAATTTAAATTTATAATAAACTTAAGTTTAAAA
*
53720 TAAATTTAAATTTATAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAATAAACTTAAGTTTAAAA
*
53754 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
53769 TGGGCCCAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (34 bp):
TAAATTTAAATTTATAATAAACTTAAGTTTAAAA
Found at i:55124 original size:19 final size:19
Alignment explanation
Indices: 55076--55124 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
55066 TTTTTTAAAA
* *
55076 ATATAAATTTTGGATTTTT
1 ATATAATTTTTGAATTTTT
55095 ATA-AATATTTTGAATTTTT
1 ATATAAT-TTTTGAATTTTT
*
55114 TTATAATTTTT
1 ATATAATTTTT
55125 TTTGAGAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 20 0.80
20 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
ATATAATTTTTGAATTTTT
Found at i:62211 original size:10 final size:10
Alignment explanation
Indices: 62196--62256 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
62186 TTTAAAGTGC
62196 TAAAAATAAA
1 TAAAAATAAA
62206 T--AAA-AAA
1 TAAAAATAAA
62213 TAAAAATAAA
1 TAAAAATAAA
*
62223 AAAAAATAAA
1 TAAAAATAAA
62233 -AACAAAT-AA
1 TAA-AAATAAA
62242 TAAAAATAAA
1 TAAAAATAAA
62252 GTAAA
1 -TAAA
62257 GAACTGAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
7 4 0.09
8 3 0.07
9 11 0.26
10 21 0.49
11 4 0.09
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:62217 original size:6 final size:6
Alignment explanation
Indices: 62196--62251 Score: 64
Period size: 6 Copynumber: 9.7 Consensus size: 6
62186 TTTAAAGTGC
* *
62196 TAAAAA TAAATA -AAAAA TAAAAA T-AAAA -AAAAA TAAAAA CAAATAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAA-AA
62242 TAAAAA TAAA
1 TAAAAA TAAA
62252 GTAAAGAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 12 0.29
6 25 0.60
7 5 0.12
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (6 bp):
TAAAAA
Found at i:62221 original size:13 final size:13
Alignment explanation
Indices: 62203--62251 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
62193 TGCTAAAAAT
62203 AAATAAAAAATAA
1 AAATAAAAAATAA
62216 AAATAAAAAAAAATAA
1 AAAT---AAAAAATAA
* *
62232 AAACAAATAATAA
1 AAATAAAAAATAA
62245 AAATAAA
1 AAATAAA
62252 GTAAAGAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 18 0.60
16 12 0.40
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.14
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:62229 original size:23 final size:23
Alignment explanation
Indices: 62196--62256 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
62186 TTTAAAGTGC
*
62196 TAAAAATAAATAAAAA-ATAAAAA
1 TAAAAAAAAATAAAAACA-AAAAA
*
62219 TAAAAAAAAATAAAAACAAATAA
1 TAAAAAAAAATAAAAACAAAAAA
*
62242 TAAAAATAAAGTAAA
1 TAAAAA-AAAATAAA
62257 GAACTGAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 25 0.76
24 8 0.24
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (23 bp):
TAAAAAAAAATAAAAACAAAAAA
Found at i:64221 original size:100 final size:93
Alignment explanation
Indices: 64005--64352 Score: 315
Period size: 94 Copynumber: 3.6 Consensus size: 93
63995 AGATCATAGT
* * * * * ** *
64005 TTCATCTTGCTCCATTGCATTTTCAAGGAGATGAGA-TTCGCTATTGTAGTTTTAATCTGATACA
1 TTCATCTTGCCCCATTACATCTTCAAGGAGAT-AGACTT-GCTAATGTAGTTTCAATCCAATCCA
* *
64069 CTATAACTTCAGGGATATGGGATTTGTAGC
64 CTAGAACTTCAGGGATATAGGATTTGTAGC
* * * *
64099 TTCATCTCGCCCCATTGCATCTTCATGGAGATAGTACTTGCTAATGTAGTTTCAATCCGATCCAC
1 TTCATCTTGCCCCATTACATCTTCAAGGAGATAG-ACTTGCTAATGTAGTTTCAATCCAATCCAC
* *
64164 T-GCAACTTTAGGGTTATAAGATTTGATGTTGTAGC
65 TAG-AACTTCAGGGATAT-AG----GAT-TTGTAGC
* * * * *
64199 TTCATCTTACTCCATTACATCTTCAGGGAGATGAGATTTG-TTATCGTAGTTTCAATCCAATCCA
1 TTCATCTTGCCCCATTACATCTTCAAGGAGAT-AGACTTGCTAAT-GTAGTTTCAATCCAATCCA
*
64263 CTAGAGCTTCAGGGATATAGGATTTGTAGC
64 CTAGAACTTCAGGGATATAGGATTTGTAGC
* * * * *
64293 TTTATCTTGCCCCACTACATCTTTAAGGAGATAGGACTTGCTAATGTAATTTCATTCCAA
1 TTCATCTTGCCCCATTACATCTTCAAGGAGATA-GACTTGCTAATGTAGTTTCAATCCAA
64353 CCCGTTACAA
Statistics
Matches: 207, Mismatches: 33, Indels: 28
0.77 0.12 0.10
Matches are distributed among these distances:
93 3 0.01
94 115 0.56
95 9 0.04
99 8 0.04
100 69 0.33
101 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (93 bp):
TTCATCTTGCCCCATTACATCTTCAAGGAGATAGACTTGCTAATGTAGTTTCAATCCAATCCACT
AGAACTTCAGGGATATAGGATTTGTAGC
Found at i:64366 original size:194 final size:194
Alignment explanation
Indices: 64005--64370 Score: 480
Period size: 194 Copynumber: 1.9 Consensus size: 194
63995 AGATCATAGT
* * * * * **
64005 TTCATCTTGCTCCATTGCATTTTCAAGGAGATGAGATTCGCTATTGTAGTTTTAATCTGATACAC
1 TTCATCTTACTCCATTACATCTTCAAGGAGATGAGATTCGCTATCGTAGTTTCAATCCAATACAC
* * * * * *
64070 TATAACTTCAGGGATATGGGATTTGTAGCTTCATCTCGCCCCATTGCATCTTCATGGAGATAGTA
66 TAGAACTTCAGGGATATAGGATTTGTAGCTTCATCTCGCCCCACTACATCTTCAAGGAGATAGGA
* * * *
64135 CTTGCTAATGTAGTTTCAATCCGATCCACTGCAACTTTAGGGTTATAAGATTTGATGTTGTAGC
131 CTTGCTAATGTAATTTCAATCCAACCCACTACAACTTTAGGGTTATAAGATTTGATGTTGTAGC
* * * *
64199 TTCATCTTACTCCATTACATCTTCAGGGAGATGAGATTTGTTATCGTAGTTTCAATCCAATCCAC
1 TTCATCTTACTCCATTACATCTTCAAGGAGATGAGATTCGCTATCGTAGTTTCAATCCAATACAC
* * * *
64264 TAGAGCTTCAGGGATATAGGATTTGTAGCTTTATCTTGCCCCACTACATCTTTAAGGAGATAGGA
66 TAGAACTTCAGGGATATAGGATTTGTAGCTTCATCTCGCCCCACTACATCTTCAAGGAGATAGGA
* **
64329 CTTGCTAATGTAATTTCATTCCAACCCGTTACAACTTTAGGG
131 CTTGCTAATGTAATTTCAATCCAACCCACTACAACTTTAGGG
64371 GGATTGGAAT
Statistics
Matches: 144, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
194 144 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (194 bp):
TTCATCTTACTCCATTACATCTTCAAGGAGATGAGATTCGCTATCGTAGTTTCAATCCAATACAC
TAGAACTTCAGGGATATAGGATTTGTAGCTTCATCTCGCCCCACTACATCTTCAAGGAGATAGGA
CTTGCTAATGTAATTTCAATCCAACCCACTACAACTTTAGGGTTATAAGATTTGATGTTGTAGC
Found at i:69366 original size:12 final size:12
Alignment explanation
Indices: 69348--69379 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
69338 AATGAATGGT
69348 AAAAAATGCATG
1 AAAAAATGCATG
*
69360 CAAAAATGCATG
1 AAAAAATGCATG
69372 AAAAAATG
1 AAAAAATG
69380 TATTGATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.59, C:0.09, G:0.16, T:0.16
Consensus pattern (12 bp):
AAAAAATGCATG
Found at i:71331 original size:306 final size:306
Alignment explanation
Indices: 70778--71390 Score: 1181
Period size: 306 Copynumber: 2.0 Consensus size: 306
70768 CCTATGTTTG
*
70778 CACGAAGGTGAAGACCTCACGAAAATATAGGTATGGACATATCTCGAAAGCGATCCACTATCCTG
1 CACGAAGGTGAAGACCTCACGAAAACATAGGTATGGACATATCTCGAAAGCGATCCACTATCCTG
*
70843 CACAGAAGTAAAGACCTCACGAAGGAATAGTTTCTTACTCCCACTTAAGAAGGGTGGAGTAGAAT
66 CACAGAAGTAAAGACCTCACGAAGGAATAGTTTCTTACTCCCACTTAAGAAGGGTGGAGTAGAAC
70908 GATCATGTTATGCAATGCATATAAAAGAAAACTCTTAAACCTTCGACTCAACAACAAAATTAACA
131 GATCATGTTATGCAATGCATATAAAAGAAAACTCTTAAACCTTCGACTCAACAACAAAATTAACA
70973 CGAACATTTGTATCAAATCAACACATGAATGATGAAATACAAGGAAGGGATCACCATTTAAATTA
196 CGAACATTTGTATCAAATCAACACATGAATGATGAAATACAAGGAAGGGATCACCATTTAAATTA
*
71038 AATTGAATTCTCGATTCCAAACAAGAAGATCAAAAAGTAATCAACT
261 AATTGAATTCTCGATTCCAAACAAGAAGACCAAAAAGTAATCAACT
71084 CACGAAGGTGAAGACCTCACGAAAACATAGGTATGGACATATCTCGAAAGCGATCCACTATCCTG
1 CACGAAGGTGAAGACCTCACGAAAACATAGGTATGGACATATCTCGAAAGCGATCCACTATCCTG
*
71149 CACAGAAGTGAAGACCTCACGAAGGAATAGTTTCTTACTCCCACTTAAGAAGGGTGGAGTAGAAC
66 CACAGAAGTAAAGACCTCACGAAGGAATAGTTTCTTACTCCCACTTAAGAAGGGTGGAGTAGAAC
*
71214 GATCATGTTATGCAATGCATATAAAAGAAAATTCTTAAACCTTCGACTCAACAACAAAATTAACA
131 GATCATGTTATGCAATGCATATAAAAGAAAACTCTTAAACCTTCGACTCAACAACAAAATTAACA
71279 CGAACATTTGTATCAAATCAACACATGAATGATGAAATACAAGGAAGGGATCACCATTTAAATTA
196 CGAACATTTGTATCAAATCAACACATGAATGATGAAATACAAGGAAGGGATCACCATTTAAATTA
71344 AATTGAATTCTCGATTCCAAACAAGAAGACCAAAAAGTAATCAACT
261 AATTGAATTCTCGATTCCAAACAAGAAGACCAAAAAGTAATCAACT
71390 C
1 C
71391 GCGACTTGAC
Statistics
Matches: 302, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
306 302 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (306 bp):
CACGAAGGTGAAGACCTCACGAAAACATAGGTATGGACATATCTCGAAAGCGATCCACTATCCTG
CACAGAAGTAAAGACCTCACGAAGGAATAGTTTCTTACTCCCACTTAAGAAGGGTGGAGTAGAAC
GATCATGTTATGCAATGCATATAAAAGAAAACTCTTAAACCTTCGACTCAACAACAAAATTAACA
CGAACATTTGTATCAAATCAACACATGAATGATGAAATACAAGGAAGGGATCACCATTTAAATTA
AATTGAATTCTCGATTCCAAACAAGAAGACCAAAAAGTAATCAACT
Found at i:78350 original size:21 final size:21
Alignment explanation
Indices: 78302--78353 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
78292 CTTTGCGATG
* * **
78302 GCGAATTCTTCCTATGTACCT
1 GCGAACTCTTCCCATGTACAA
*
78323 GCAAACTCTTCCCATGTACAA
1 GCGAACTCTTCCCATGTACAA
78344 GCGAACTCTT
1 GCGAACTCTT
78354 TCCACAAACG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (21 bp):
GCGAACTCTTCCCATGTACAA
Found at i:81069 original size:13 final size:13
Alignment explanation
Indices: 81047--81108 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
81037 TTAAACCAAG
*
81047 CTTTTTAAAAATA
1 CTTTTCAAAAATA
81060 CTTTTC-AAAATCA
1 CTTTTCAAAAAT-A
* *
81073 CTTTTCCAAAGTA
1 CTTTTCAAAAATA
* **
81086 CTTTTTAAAAGCA
1 CTTTTCAAAAATA
81099 CTTTTCAAAA
1 CTTTTCAAAA
81109 TCAATGCTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
12 5 0.12
13 32 0.78
14 4 0.10
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.40
Consensus pattern (13 bp):
CTTTTCAAAAATA
Found at i:81077 original size:26 final size:26
Alignment explanation
Indices: 81047--81108 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
81037 TTAAACCAAG
* *
81047 CTTTTTAAAAATACTTTTCAAAATCA
1 CTTTTCAAAAATACTTTTCAAAAGCA
* * *
81073 CTTTTCCAAAGTACTTTTTAAAAGCA
1 CTTTTCAAAAATACTTTTCAAAAGCA
81099 CTTTTCAAAA
1 CTTTTCAAAA
81109 TCAATGCTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.40
Consensus pattern (26 bp):
CTTTTCAAAAATACTTTTCAAAAGCA
Found at i:82060 original size:122 final size:124
Alignment explanation
Indices: 81806--82060 Score: 304
Period size: 126 Copynumber: 2.1 Consensus size: 124
81796 TTTAAAAAGA
* * ** * *
81806 AAAAATCACTATTTTTCTTAAAGATCAAAGTTTTTGTTTTGAAATAATTAACAAAAAATCAAAAC
1 AAAAATCACTACTTTTCCTAAAGATCAAAACTTTTATTTCGAAATAATT-A-AAAAAATCAAAAC
**
81871 TTTGTTTTTTAAATTTAAACTTTTCCTTTTAAAATAACTAAAAACATATTTTTATTTTTTT
64 TTTGTTTTAAAAATTTAAACTTTTCCTTTTAAAATAACTAAAAACATATTTTTATTTTTTT
* *
81932 AAAAATCATTACTTTTCCTAAAGATCAAAACTTTTATTTCGAAATAGTT-AAAAAATCAAAA-TT
1 AAAAATCACTACTTTTCCTAAAGATCAAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTT
* * * *
81995 TCG-TTTAAAAATTTAAATTTTTTCC-TTTAAAATGATTAAAAAACATGTTTTTA-TTTTTT
66 T-GTTTTAAAAATTTAAA-CTTTTCCTTTTAAAATAACT-AAAAACATATTTTTATTTTTTT
82054 AAAAATC
1 AAAAATC
82061 TAAACTTTCT
Statistics
Matches: 112, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
122 38 0.34
123 33 0.29
126 41 0.37
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (124 bp):
AAAAATCACTACTTTTCCTAAAGATCAAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTT
TGTTTTAAAAATTTAAACTTTTCCTTTTAAAATAACTAAAAACATATTTTTATTTTTTT
Found at i:88915 original size:36 final size:36
Alignment explanation
Indices: 88838--88915 Score: 84
Period size: 36 Copynumber: 2.2 Consensus size: 36
88828 ATTGGATGGA
* * ** *
88838 GATGATGTCGACAAGGAAGACGATGATGATGATGAT
1 GATGATGTCGACAAGGAAGACAACGACAACGATGAT
* * *
88874 AATGATGTCGACGAGGAAGACAACGACAACGGTGAT
1 GATGATGTCGACAAGGAAGACAACGACAACGATGAT
88910 GATGAT
1 GATGAT
88916 AATCCTAACT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.32, T:0.19
Consensus pattern (36 bp):
GATGATGTCGACAAGGAAGACAACGACAACGATGAT
Found at i:91323 original size:15 final size:15
Alignment explanation
Indices: 91299--91332 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
91289 ATAAGATAGA
91299 ACAT-AATCAATGTC
1 ACATCAATCAATGTC
91313 ACATCAATCAATGTC
1 ACATCAATCAATGTC
91328 ACATC
1 ACATC
91333 TCGAAAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.41, C:0.26, G:0.06, T:0.26
Consensus pattern (15 bp):
ACATCAATCAATGTC
Found at i:100039 original size:79 final size:79
Alignment explanation
Indices: 99938--100139 Score: 307
Period size: 79 Copynumber: 2.6 Consensus size: 79
99928 AAACCTCAAA
* *
99938 TGTGAGCCTAGCTCTAGTTGGATTAACCAACAATATCCGTCAAATCCTAGCACCCAATGCCTAGC
1 TGTGAGCCCAGCTCTAGTTGGATTAACCAACAATATCCATCAAATCCTAGCACCCAATGCCTAGC
100003 GAATAAA-TCGCAAT
66 GAATAAACT-GCAAT
* * * *
100017 TGTGAGCCCAGCTCTAGTTGGATTAACCAACAATATCTATCAAATCCTGGCACCTAGTGCCTAGC
1 TGTGAGCCCAGCTCTAGTTGGATTAACCAACAATATCCATCAAATCCTAGCACCCAATGCCTAGC
*
100082 GGATAAACTGCAAT
66 GAATAAACTGCAAT
* *
100096 TGTGAGCCCAGCTCTAGTTGGATTAATCAACAATGTCCATCAAA
1 TGTGAGCCCAGCTCTAGTTGGATTAACCAACAATATCCATCAAA
100140 CAACCAATTT
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 111 0.99
80 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (79 bp):
TGTGAGCCCAGCTCTAGTTGGATTAACCAACAATATCCATCAAATCCTAGCACCCAATGCCTAGC
GAATAAACTGCAAT
Found at i:101229 original size:16 final size:13
Alignment explanation
Indices: 101199--101225 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
101189 AAACAATATC
101199 ATAATAATCCTAA
1 ATAATAATCCTAA
101212 ATAATAATCCTAA
1 ATAATAATCCTAA
101225 A
1 A
101226 AAATTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATAATCCTAA
Found at i:107645 original size:41 final size:41
Alignment explanation
Indices: 107570--107672 Score: 134
Period size: 41 Copynumber: 2.4 Consensus size: 41
107560 ATCATTTCGT
* * *
107570 ACAGTATACACACACTCGTAACCCACGCCCGTGTGCCTCAAA
1 ACAGTATACACACAC-CCTAACCCACACCAGTGTGCCTCAAA
* *
107612 ATAGTATACACACACCCTAACCCACACCAGTGTGCCTCCAA
1 ACAGTATACACACACCCTAACCCACACCAGTGTGCCTCAAA
107653 ACAGTATAGACACACACCCT
1 ACAGTAT--ACACACACCCT
107673 GTAATCACCC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 28 0.53
42 14 0.26
43 11 0.21
ACGTcount: A:0.34, C:0.38, G:0.12, T:0.17
Consensus pattern (41 bp):
ACAGTATACACACACCCTAACCCACACCAGTGTGCCTCAAA
Found at i:109129 original size:42 final size:42
Alignment explanation
Indices: 109070--109247 Score: 257
Period size: 42 Copynumber: 4.2 Consensus size: 42
109060 AGCAAAAAAG
* *
109070 AAGTAGATGGACCTCCACACCTGGACCTCTAAATGCAATCAA
1 AAGTAAATGGACCTCCACACCTGGACCTCTAAATGCAATGAA
* * *
109112 AAGTAAATGGACTTCCACTCCTGGATCTCTAAATGCAATGAA
1 AAGTAAATGGACCTCCACACCTGGACCTCTAAATGCAATGAA
* *
109154 AAGTAAATGGACCTCCACACTTGGTCCTCTAAAATGCAATGAA
1 AAGTAAATGGACCTCCACACCTGGACCTCT-AAATGCAATGAA
* * *
109197 AAATAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAA
1 AAGTAAATGGACCTCCACACCTGGACCTCTAAATGCAATGAA
109239 AAGTAAATG
1 AAGTAAATG
109248 TTTTTTATAG
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
42 82 0.67
43 40 0.33
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (42 bp):
AAGTAAATGGACCTCCACACCTGGACCTCTAAATGCAATGAA
Found at i:109227 original size:85 final size:84
Alignment explanation
Indices: 109070--109247 Score: 257
Period size: 85 Copynumber: 2.1 Consensus size: 84
109060 AGCAAAAAAG
* * * *
109070 AAGTAGATGGACCTCCACACCTGGACCTCTAAATGCAATCAAAAGTAAATGGACTTCCACTCCTG
1 AAGTAAATGGACCTCCACACCTGGACCTCTAAATGCAATCAAAAATAAATGGACCTCCACACCTG
*
109135 GATCTCTAAATGCAATGAA
66 GACCTCTAAATGCAATGAA
* * * *
109154 AAGTAAATGGACCTCCACACTTGGTCCTCTAAAATGCAATGAAAAATAAATGGACCTCCACACTT
1 AAGTAAATGGACCTCCACACCTGGACCTCT-AAATGCAATCAAAAATAAATGGACCTCCACACCT
*
109219 GGGCCTCTAAATGCAATGAA
65 GGACCTCTAAATGCAATGAA
109239 AAGTAAATG
1 AAGTAAATG
109248 TTTTTTATAG
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 27 0.33
85 56 0.67
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (84 bp):
AAGTAAATGGACCTCCACACCTGGACCTCTAAATGCAATCAAAAATAAATGGACCTCCACACCTG
GACCTCTAAATGCAATGAA
Found at i:110216 original size:18 final size:19
Alignment explanation
Indices: 110193--110228 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
110183 TTCTCTCAGT
110193 TATCTTTCTATTG-TATTA
1 TATCTTTCTATTGATATTA
*
110211 TATCTTTGTATTGATATT
1 TATCTTTCTATTGATATT
110229 TCCTCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.61
Consensus pattern (19 bp):
TATCTTTCTATTGATATTA
Found at i:111431 original size:22 final size:22
Alignment explanation
Indices: 111399--111447 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
111389 AACCACCAAT
**
111399 AATAATATGCAGTTAAATTGCC
1 AATAATATGCAGACAAATTGCC
*
111421 AATAATTTGCAGACAAATTGCC
1 AATAATATGCAGACAAATTGCC
111443 AATAA
1 AATAA
111448 GTTGAGGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (22 bp):
AATAATATGCAGACAAATTGCC
Found at i:112555 original size:80 final size:80
Alignment explanation
Indices: 112421--112578 Score: 255
Period size: 80 Copynumber: 2.0 Consensus size: 80
112411 GAAGAAAAGT
*
112421 ATGGGAGAAAATTAGGACTTAGTATCACGTCCAAAAATCGAGTTAGTAAACCAAGAGTGGA-CAT
1 ATGGGAGAAAATTAGGACTTAGTATCACATCCAAAAATCGAGTTAGTAAACCAAGAGT-GATCAT
112485 GTCCTGTTTTTGAAGA
65 GTCCTGTTTTTGAAGA
* * * *
112501 ATGGGAGAAAATTAGGACTTGGTGTCACATCCAAAAATCGAGTTAGTAATCCAAGCGTGATCATG
1 ATGGGAGAAAATTAGGACTTAGTATCACATCCAAAAATCGAGTTAGTAAACCAAGAGTGATCATG
112566 TCCTGTTTTTGAA
66 TCCTGTTTTTGAA
112579 TAAATGTTGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
79 2 0.03
80 70 0.97
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (80 bp):
ATGGGAGAAAATTAGGACTTAGTATCACATCCAAAAATCGAGTTAGTAAACCAAGAGTGATCATG
TCCTGTTTTTGAAGA
Done.