Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006057.1 Hibiscus syriacus cultivar Beakdansim tig00014329_pilon, 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: 118152
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3892 original size:29 final size:29
Alignment explanation
Indices: 3850--3906 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
3840 AGTGTTGGCC
*
3850 GTAGGTCGTCATGCACTCCGGGCAACCTT
1 GTAGGTCATCATGCACTCCGGGCAACCTT
*
3879 GTAGGTCATCATGCACTCCGGGCGACCT
1 GTAGGTCATCATGCACTCCGGGCAACCT
3907 ACCCTTGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.23
Consensus pattern (29 bp):
GTAGGTCATCATGCACTCCGGGCAACCTT
Found at i:3998 original size:29 final size:29
Alignment explanation
Indices: 3965--4020 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
3955 TCCCAACACA
*
3965 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
3994 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
4021 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.38, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:4065 original size:33 final size:33
Alignment explanation
Indices: 4024--4117 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
4014 GCGACCTACC
*
4024 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCGCATAG
4057 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * * * *
4090 CTCGGTCGGATGGCCTCGAATGCTCTCG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCG
4118 GATGGCCTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 2 0.04
33 52 0.96
ACGTcount: A:0.10, C:0.38, G:0.27, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:5190 original size:2 final size:2
Alignment explanation
Indices: 5183--5215 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5173 TACTTTACCC
5183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5216 CATTGAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6547 original size:3 final size:3
Alignment explanation
Indices: 6539--6563 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6529 ACAAATTTAT
6539 CAA CAA CAA CAA CAA CAA CAA CAA C
1 CAA CAA CAA CAA CAA CAA CAA CAA C
6564 CTATTCTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:7109 original size:2 final size:2
Alignment explanation
Indices: 7102--7129 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7092 GGGTTAAGCA
7102 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7130 TGATTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11648 original size:29 final size:28
Alignment explanation
Indices: 11615--11704 Score: 92
Period size: 33 Copynumber: 3.0 Consensus size: 28
11605 CTTTTTCATT
11615 TAAGTACCTAAAGTATTTTTTGGTCAAAA
1 TAAGTACCTAAAGTATTTTTT-GTCAAAA
*
11644 TAAGTACCTAAGGTTAATTTTTTTTTGTCAAAA
1 TAAGTACCTAAAG-T-A---TTTTTTGTCAAAA
*
11677 TAAGTACTTCAAA-TATTTTTTGTCAAAA
1 TAAGTACCT-AAAGTATTTTTTGTCAAAA
11705 GTATTCAAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
28 13 0.25
29 12 0.23
30 1 0.02
31 2 0.04
32 1 0.02
33 15 0.29
34 8 0.15
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (28 bp):
TAAGTACCTAAAGTATTTTTTGTCAAAA
Found at i:11719 original size:24 final size:26
Alignment explanation
Indices: 11663--11719 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
11653 AAGGTTAATT
11663 TTTTTTTGTCAAAATAAGTACTTCAAA
1 TTTTTTTGTC-AAATAAGTACTTCAAA
11690 TATTTTTTGTC-AA-AAGTA-TTCAAA
1 T-TTTTTTGTCAAATAAGTACTTCAAA
*
11714 CTTTTT
1 TTTTTT
11720 AATGTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 5 0.18
24 6 0.21
25 5 0.18
26 2 0.07
27 1 0.04
28 9 0.32
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (26 bp):
TTTTTTTGTCAAATAAGTACTTCAAA
Found at i:12129 original size:14 final size:14
Alignment explanation
Indices: 12110--12144 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
12100 ATGGATATAG
12110 TAAAATAAATAAAA
1 TAAAATAAATAAAA
12124 TAAAATAAATAAAA
1 TAAAATAAATAAAA
*
12138 TAGAATA
1 TAAAATA
12145 TTTTTTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
TAAAATAAATAAAA
Found at i:15720 original size:12 final size:12
Alignment explanation
Indices: 15703--15727 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15693 TTTTATTTTA
15703 TTGATTTTATAT
1 TTGATTTTATAT
15715 TTGATTTTATAT
1 TTGATTTTATAT
15727 T
1 T
15728 CCTTATTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTGATTTTATAT
Found at i:16672 original size:76 final size:75
Alignment explanation
Indices: 16566--16725 Score: 302
Period size: 76 Copynumber: 2.1 Consensus size: 75
16556 AATTTTATGT
16566 AATATAAAAGTGTACCCTAACTTCTCTATATATTTATATATATTATATGGGAAAGTAAAGTTGAG
1 AATATAAAAGTGTACCCTAACTTCTCTATATATTTATATATATTATATGGGAAAGTAAAGTTGA-
16631 GGATCCTTTGC
65 GGATCCTTTGC
16642 AATATAAAAGTGTACCCTAACTTCTCTATATATTTATATATATTATATGGGAAAGTAAAGTTGAG
1 AATATAAAAGTGTACCCTAACTTCTCTATATATTTATATATATTATATGGGAAAGTAAAGTTGAG
*
16707 GATCCTTTGT
66 GATCCTTTGC
16717 AATATAAAA
1 AATATAAAA
16726 TACCCTAAAC
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
75 19 0.23
76 64 0.77
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (75 bp):
AATATAAAAGTGTACCCTAACTTCTCTATATATTTATATATATTATATGGGAAAGTAAAGTTGAG
GATCCTTTGC
Found at i:20342 original size:9 final size:10
Alignment explanation
Indices: 20315--20346 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
20305 GGATCATTCC
20315 TCCTTTTCTTT
1 TCCTTTT-TTT
20326 TCCTTTTTTT
1 TCCTTTTTTT
20336 TCCTTTTTTT
1 TCCTTTTTTT
20346 T
1 T
20347 TAATTTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TCCTTTTTTT
Found at i:20347 original size:11 final size:11
Alignment explanation
Indices: 20315--20347 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
20305 GGATCATTCC
*
20315 TCCTTTTCTTT
1 TCCTTTTTTTT
20326 TCC-TTTTTTT
1 TCCTTTTTTTT
20336 TCCTTTTTTTT
1 TCCTTTTTTTT
20347 T
1 T
20348 AATTTAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TCCTTTTTTTT
Found at i:23481 original size:20 final size:20
Alignment explanation
Indices: 23456--23494 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23446 AAGTGGCATG
23456 ATTGATAAAATTAAAATATA
1 ATTGATAAAATTAAAATATA
**
23476 ATTGATAAGCTTAAAATAT
1 ATTGATAAAATTAAAATAT
23495 CTAGAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (20 bp):
ATTGATAAAATTAAAATATA
Found at i:25462 original size:13 final size:13
Alignment explanation
Indices: 25444--25473 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25434 CAAATATTTT
*
25444 AAAATTAAAAATA
1 AAAATTAAAAACA
25457 AAAATTAAAAACA
1 AAAATTAAAAACA
25470 AAAA
1 AAAA
25474 GACATCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAATTAAAAACA
Found at i:31265 original size:20 final size:19
Alignment explanation
Indices: 31222--31265 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
31212 CTTCTGATTT
31222 TTTTTCTGTTTTATTATAA
1 TTTTTCTGTTTTATTATAA
* * *
31241 CTTTTCTTGTTTTCTTATAG
1 TTTTTC-TGTTTTATTATAA
31261 TTTTT
1 TTTTT
31266 TAATTCTGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.14, C:0.09, G:0.07, T:0.70
Consensus pattern (19 bp):
TTTTTCTGTTTTATTATAA
Found at i:43122 original size:6 final size:6
Alignment explanation
Indices: 43111--43207 Score: 167
Period size: 6 Copynumber: 16.2 Consensus size: 6
43101 GACACGTATT
43111 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* * *
43159 ACCACG ACCTCG ACCTCG ACCACA ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
43207 A
1 A
43208 GCCGAGCCGA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 87 1.00
ACGTcount: A:0.33, C:0.49, G:0.15, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:43215 original size:5 final size:5
Alignment explanation
Indices: 43205--43243 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
43195 ACCACGACCA
* * *
43205 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
43244 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:49121 original size:6 final size:6
Alignment explanation
Indices: 49110--49188 Score: 140
Period size: 6 Copynumber: 13.2 Consensus size: 6
49100 GACACGTATT
* *
49110 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
49158 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
49189 GCCGAGCCGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:49196 original size:5 final size:5
Alignment explanation
Indices: 49186--49224 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
49176 ACCACGACCA
* * *
49186 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
49225 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:50182 original size:432 final size:434
Alignment explanation
Indices: 49359--50429 Score: 1357
Period size: 432 Copynumber: 2.4 Consensus size: 434
49349 ATTACCAACA
* *
49359 ATCCTCACGTTGTTTCAAACTAAATTCAAGATCTCGAAGACGCTCTTTCGAAGCCTTTTCTTTCA
1 ATCCTCACGTTGTTTCAAACTAAATTCAAGATCTTGAAGACGCTCTTTCGAAGCCTTTTCTTCCA
49424 ACTCAAACTCCATAAATCGCTTCTCGAAACTCTTCTCTTTCAGCACGAATTGCTCTTCTTTCAAC
66 ACTCAAACTCCATAAATCGCTTCTCGAAACTCTTCTCTTTCAGC-CGAATTGCTCTTCTTTCAAC
*
49489 TCATACTCTCTCAAGCTTTTCTCCAAGTCTTTCTCCTTCAATTCAACTTCCTCCAACTTATCTTT
130 TCATA--CTCTCAAG------T-CAAGTCTTTCTCCTTCAATCCAACTTCCTCCAACTTATCTTT
* ** * * *
49554 CACTAATTCCTCCATTGACTTAACCTCATTCTGCCATTGTGTCACGCTAAATTCAAGATCTCGAA
186 CACTAATTCCTCAACCGACTTAACCTCATCCTGCCATTGTGTCACACTAAACTCAAGATCTCGAA
* **
49619 GACGCTCCTTGGAAGTTTTTTCTTCCAACTCAAACTCCATAAATCGCTTCTCGAAAATCTTCTCT
251 GACGCTCCTTCGAAGCCTTTTCTTCCAACTCAAACTCCATAAATCGCTTCTCGAAAATCTTCTCT
* * *
49684 TTGAGCTCGAATTGCTCTTCTTTCAACTCACACTCTCTCAAGCATTTCTCCAAGTCTTTCTCCTT
316 TTGAGCCCGAATTGCTCTTCTTTCAACTCACACTCTCTCAAGCATCTCTCCAAATCTTTCTCCTT
* * *
49749 CAATCCAACTTCCTCCAACTTATCTTTTAGCAATTTCTCAACCCACTTAACCTT
381 CAATCCAACTTCATCCAACTTATCTTTTACCAATTTCTCAACCCACTTAACCTC
* * * * * *
49803 ATCCTCACATTGTATCAGACTAAATTCAAGACCTTGAAGACGCTCTTTGGAAGCTTTTTCTTCCA
1 ATCCTCACGTTGTTTCAAACTAAATTCAAGATCTTGAAGACGCTCTTTCGAAGCCTTTTCTTCCA
* * * * *
49868 ACTCATACTCCGTAAATCGCTTGTCGAAACTCTTCTCTCTCAGTCTGAATTGCTCTTCTTTCAAC
66 ACTCAAACTCCATAAATCGCTTCTCGAAACTCTTCTCTTTCAG-CCGAATTGCTCTTCTTTCAAC
* *
49933 TCGTACTC-C-AG-CAAG-CATTTTTCCTTCAATCCAACTTCCTCCAACTTATCTTCTGC-C-AA
130 TCATACTCTCAAGTCAAGTC-TTTCTCCTTCAATCCAACTTCCTCCAACTTATCTT-T-CACTAA
* * *
49992 TTTCTCAACCGACTTAACCTCATCCT-CACGTTGTTTCACACTAAACTCAAGATCTCGAAGACGC
192 TTCCTCAACCGACTTAACCTCATCCTGC-CATTGTGTCACACTAAACTCAAGATCTCGAAGACGC
* * * *
50056 TCTTTCGAAGCCTTTTCTTCCAACTCAAACTCCATAAATTGCTTCTTGAAACTCTTCTCTTTCGA
256 TCCTTCGAAGCCTTTTCTTCCAACTCAAACTCCATAAATCGCTTCTCGAAAATCTTCTCTTT-GA
* * * *
50121 -CCCGAATTGCTCTTCTTTCGATTCATACTCTCTCAAGCATCTCTCCAAATCTTTTTCCTTCAAT
320 GCCCGAATTGCTCTTCTTTCAACTCACACTCTCTCAAGCATCTCTCCAAATCTTTCTCCTTCAAT
* * *
50185 CCAACTTCATCCAACTTATCTTTTACCAATTTCTCCATCGACTTAACCTC
385 CCAACTTCATCCAACTTATCTTTTACCAATTTCTCAACCCACTTAACCTC
* * * * *
50235 ATCCTCACGTTGTTTCACACTAAACTCTAGATCTTGAATACGCTCTTTCAAAGCCTTTTCTTCCA
1 ATCCTCACGTTGTTTCAAACTAAATTCAAGATCTTGAAGACGCTCTTTCGAAGCCTTTTCTTCCA
* * *
50300 ACTCAAACTCCATAAACCGCTTTTCGAAACTCTTCTCTTTCGACCCGAATTGCTCTTCTTTCAAC
66 ACTCAAACTCCATAAATCGCTTCTCGAAACTCTTCTCTTTC-AGCCGAATTGCTCTTCTTTCAAC
* *
50365 TCATACTCTCTCAAGCATCTGTTCAATTCTTTCTCTTTCAATCCAACTTCCTCCAACTTATCTTT
130 TCATA--CTCTC-A--A---G-TCAAGTCTTTCTCCTTCAATCCAACTTCCTCCAACTTATCTTT
50430 TACCGATTTC
Statistics
Matches: 541, Mismatches: 66, Indels: 41
0.83 0.10 0.06
Matches are distributed among these distances:
431 2 0.00
432 363 0.67
433 5 0.01
434 4 0.01
435 1 0.00
439 1 0.00
440 2 0.00
441 1 0.00
442 4 0.01
443 1 0.00
444 155 0.29
445 2 0.00
ACGTcount: A:0.24, C:0.31, G:0.08, T:0.36
Consensus pattern (434 bp):
ATCCTCACGTTGTTTCAAACTAAATTCAAGATCTTGAAGACGCTCTTTCGAAGCCTTTTCTTCCA
ACTCAAACTCCATAAATCGCTTCTCGAAACTCTTCTCTTTCAGCCGAATTGCTCTTCTTTCAACT
CATACTCTCAAGTCAAGTCTTTCTCCTTCAATCCAACTTCCTCCAACTTATCTTTCACTAATTCC
TCAACCGACTTAACCTCATCCTGCCATTGTGTCACACTAAACTCAAGATCTCGAAGACGCTCCTT
CGAAGCCTTTTCTTCCAACTCAAACTCCATAAATCGCTTCTCGAAAATCTTCTCTTTGAGCCCGA
ATTGCTCTTCTTTCAACTCACACTCTCTCAAGCATCTCTCCAAATCTTTCTCCTTCAATCCAACT
TCATCCAACTTATCTTTTACCAATTTCTCAACCCACTTAACCTC
Found at i:50430 original size:222 final size:223
Alignment explanation
Indices: 49359--50448 Score: 1442
Period size: 222 Copynumber: 5.0 Consensus size: 223
49349 ATTACCAACA
* *
49359 ATCCTCACGTTGTTTCAAACTAAATTCAAGATCTCGAAGACGCTCTTTCGAAGCCTTTTCTTTCA
1 ATCCTCACGTTGTTTCACACTAAATTCAAGATCTCGAAGACGCTCTTTCGAAGCCTTTTCTTCCA
*
49424 ACTCAAACTCCATAAATCGCTTCTCGAAACTCTTCTCTTTC-AGCACGAATTGCTCTTCTTTCAA
66 ACTCAAACTCCATAAATCGCTTCTCGAAACTCTTCTCTTTCGAGCCCGAATTGCTCTTCTTTCAA
* * *
49488 CTCATACTCTCTCAAGCTTTTCTCCAAGTCTTTCTCCTTCAATTCAACTTCCTCCAACTTATCTT
131 CTCATACTCTCTCAAGCATCTCTCCAAGTCTTTCTCCTTCAATCCAACTTCCTCCAACTTATCTT
* * * *
49553 TCACTAATTCCTCCATTGACTTAACCTC
196 TTACCAATTTCTCCATCGACTTAACCTC
* * * * * * **
49581 ATTCTGC-CATTGTGTCACGCTAAATTCAAGATCTCGAAGACGCTCCTTGGAAGTTTTTTCTTCC
1 ATCCT-CACGTTGTTTCACACTAAATTCAAGATCTCGAAGACGCTCTTTCGAAGCCTTTTCTTCC
* *
49645 AACTCAAACTCCATAAATCGCTTCTCGAAAATCTTCTCTTT-GAGCTCGAATTGCTCTTCTTTCA
65 AACTCAAACTCCATAAATCGCTTCTCGAAACTCTTCTCTTTCGAGCCCGAATTGCTCTTCTTTCA
* *
49709 ACTCACACTCTCTCAAGCATTTCTCCAAGTCTTTCTCCTTCAATCCAACTTCCTCCAACTTATCT
130 ACTCATACTCTCTCAAGCATCTCTCCAAGTCTTTCTCCTTCAATCCAACTTCCTCCAACTTATCT
* * * * *
49774 TTTAGCAATTTCTCAACCCACTTAACCTT
195 TTTACCAATTTCTCCATCGACTTAACCTC
* * * * * * *
49803 ATCCTCACATTGTATCAGACTAAATTCAAGACCTTGAAGACGCTCTTTGGAAGCTTTTTCTTCCA
1 ATCCTCACGTTGTTTCACACTAAATTCAAGATCTCGAAGACGCTCTTTCGAAGCCTTTTCTTCCA
* * * * * *
49868 ACTCATACTCCGTAAATCGCTTGTCGAAACTCTTCTCTCTC-AGTCTGAATTGCTCTTCTTTCAA
66 ACTCAAACTCCATAAATCGCTTCTCGAAACTCTTCTCTTTCGAGCCCGAATTGCTCTTCTTTCAA
* **
49932 CTCGTA--CTC-C-AGCA----AGC-A-T-TTT-TCCTTCAATCCAACTTCCTCCAACTTATCTT
131 CTCATACTCTCTCAAGCATCTCTCCAAGTCTTTCTCCTTCAATCCAACTTCCTCCAACTTATCTT
* * * *
49985 CTGCCAATTTCTCAACCGACTTAACCTC
196 TTACCAATTTCTCCATCGACTTAACCTC
*
50013 ATCCTCACGTTGTTTCACACTAAACTCAAGATCTCGAAGACGCTCTTTCGAAGCCTTTTCTTCCA
1 ATCCTCACGTTGTTTCACACTAAATTCAAGATCTCGAAGACGCTCTTTCGAAGCCTTTTCTTCCA
* * *
50078 ACTCAAACTCCATAAATTGCTTCTTGAAACTCTTCTCTTTCGA-CCCGAATTGCTCTTCTTTCGA
66 ACTCAAACTCCATAAATCGCTTCTCGAAACTCTTCTCTTTCGAGCCCGAATTGCTCTTCTTTCAA
* * * *
50142 TTCATACTCTCTCAAGCATCTCTCCAAATCTTTTTCCTTCAATCCAACTTCATCCAACTTATCTT
131 CTCATACTCTCTCAAGCATCTCTCCAAGTCTTTCTCCTTCAATCCAACTTCCTCCAACTTATCTT
50207 TTACCAATTTCTCCATCGACTTAACCTC
196 TTACCAATTTCTCCATCGACTTAACCTC
* * * * *
50235 ATCCTCACGTTGTTTCACACTAAACTCTAGATCTTGAATACGCTCTTTCAAAGCCTTTTCTTCCA
1 ATCCTCACGTTGTTTCACACTAAATTCAAGATCTCGAAGACGCTCTTTCGAAGCCTTTTCTTCCA
* *
50300 ACTCAAACTCCATAAACCGCTTTTCGAAACTCTTCTCTTTCGA-CCCGAATTGCTCTTCTTTCAA
66 ACTCAAACTCCATAAATCGCTTCTCGAAACTCTTCTCTTTCGAGCCCGAATTGCTCTTCTTTCAA
* * * *
50364 CTCATACTCTCTCAAGCATCTGTTCAATTCTTTCTCTTTCAATCCAACTTCCTCCAACTTATCTT
131 CTCATACTCTCTCAAGCATCTCTCCAAGTCTTTCTCCTTCAATCCAACTTCCTCCAACTTATCTT
*
50429 TTACCGATTTCTCCATCGAC
196 TTACCAATTTCTCCATCGAC
50449 GACACCTCTT
Statistics
Matches: 759, Mismatches: 92, Indels: 34
0.86 0.10 0.04
Matches are distributed among these distances:
210 168 0.22
211 4 0.01
212 4 0.01
213 2 0.00
214 5 0.01
218 5 0.01
219 2 0.00
220 4 0.01
221 4 0.01
222 560 0.74
223 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.08, T:0.36
Consensus pattern (223 bp):
ATCCTCACGTTGTTTCACACTAAATTCAAGATCTCGAAGACGCTCTTTCGAAGCCTTTTCTTCCA
ACTCAAACTCCATAAATCGCTTCTCGAAACTCTTCTCTTTCGAGCCCGAATTGCTCTTCTTTCAA
CTCATACTCTCTCAAGCATCTCTCCAAGTCTTTCTCCTTCAATCCAACTTCCTCCAACTTATCTT
TTACCAATTTCTCCATCGACTTAACCTC
Found at i:56197 original size:31 final size:31
Alignment explanation
Indices: 56159--56252 Score: 163
Period size: 31 Copynumber: 3.0 Consensus size: 31
56149 AGGGTCGAGG
56159 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
56190 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
56221 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
56252 G
1 G
56253 GTCCTTCAGG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:57188 original size:21 final size:21
Alignment explanation
Indices: 57162--57203 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
57152 CCAGAATGGG
* *
57162 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACACCTTCATA
57183 GGGAATCGATACACCTTCATA
1 GGGAATCGATACACCTTCATA
57204 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACACCTTCATA
Found at i:57338 original size:19 final size:19
Alignment explanation
Indices: 57310--57375 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
57300 AGCCTCGGGG
*
57310 TACTGTTCAAACAGTGATT
1 TACTGTTCAAACAGTAATT
* *
57329 TACTGCTCAAATAGTAATT
1 TACTGTTCAAACAGTAATT
* *
57348 TACTGTTCAAATAGTAAAT
1 TACTGTTCAAACAGTAATT
*
57367 TACTATTCA
1 TACTGTTCA
57376 TAAAAACATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TACTGTTCAAACAGTAATT
Found at i:57472 original size:29 final size:31
Alignment explanation
Indices: 57440--57499 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
57430 AAATTTTGAA
*
57440 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
57469 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
57500 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:59659 original size:3 final size:3
Alignment explanation
Indices: 59645--59688 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
59635 AGAGATATTC
*
59645 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
59689 ATGTACGAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:60986 original size:31 final size:31
Alignment explanation
Indices: 60948--61041 Score: 154
Period size: 31 Copynumber: 3.0 Consensus size: 31
60938 AGGGTCGAGG
60948 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
60979 GTTTACCTATGTTCTTCGGGACATATTGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
61010 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
61041 G
1 G
61042 GTCCTTCAGG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:66551 original size:47 final size:47
Alignment explanation
Indices: 66484--66623 Score: 226
Period size: 49 Copynumber: 2.9 Consensus size: 47
66474 AATCATATCT
* *
66484 TACTATTTAAAACTTAAAAATTAAATTAATGCTTAAATATATATATA
1 TACTATTCAAAACTTTAAAATTAAATTAATGCTTAAATATATATATA
*
66531 TATTATTCAAAACTTTAAAATTAAATTAATGCTTAAATATGTATATATA
1 TACTATTCAAAACTTTAAAATTAAATTAATGCTTAAATA--TATATATA
*
66580 TACTATTCAAAACTTTAAAATTAAATTAATGCTTATATATATAT
1 TACTATTCAAAACTTTAAAATTAAATTAATGCTTAAATATATAT
66624 TTTGAAAGTG
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
47 41 0.48
49 45 0.52
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (47 bp):
TACTATTCAAAACTTTAAAATTAAATTAATGCTTAAATATATATATA
Found at i:74167 original size:2 final size:2
Alignment explanation
Indices: 74160--74191 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
74150 TACATACGTG
74160 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74192 CCGACATGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76752 original size:4 final size:4
Alignment explanation
Indices: 76743--76818 Score: 75
Period size: 4 Copynumber: 18.8 Consensus size: 4
76733 AGCAATCAGA
* *
76743 ATAC ATAC ATGC -TAC ACAC ATAC ATAC ATTA- ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A-TAC ATAC ATAC ATAC ATAC
* *
76790 ATAC ACACGC ATGC ATAC ATAC ATAC ATA
1 ATAC ATA--C ATAC ATAC ATAC ATAC ATA
76819 TATATATTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
3 4 0.07
4 51 0.86
5 2 0.03
6 2 0.03
ACGTcount: A:0.46, C:0.26, G:0.04, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:86954 original size:30 final size:30
Alignment explanation
Indices: 86920--86979 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
86910 AATGCAATTA
86920 AATCTCATGTTCTATGAAGTTATCAAACGT
1 AATCTCATGTTCTATGAAGTTATCAAACGT
*
86950 AATCTCATTTTCTATGAAGTTATCAAACGT
1 AATCTCATGTTCTATGAAGTTATCAAACGT
86980 CATTGCTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (30 bp):
AATCTCATGTTCTATGAAGTTATCAAACGT
Found at i:99406 original size:2 final size:2
Alignment explanation
Indices: 99399--99425 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
99389 TGCTAGGAGG
99399 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
99426 GCCATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:99955 original size:31 final size:31
Alignment explanation
Indices: 99920--100001 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
99910 AGTTCTGGGA
99920 ATTATAAAATCATCATTAAACTT-ATTAAATT
1 ATTATAAAAT-ATCATTAAACTTCATTAAATT
** *
99951 ATTATAGTATAACATTAAACTTCATTAAATT
1 ATTATAAAATATCATTAAACTTCATTAAATT
* *
99982 AGTACAAAATGATCATTAAA
1 ATTATAAAAT-ATCATTAAA
100002 ATTTATCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 11 0.27
31 22 0.54
32 8 0.20
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.38
Consensus pattern (31 bp):
ATTATAAAATATCATTAAACTTCATTAAATT
Found at i:102250 original size:31 final size:31
Alignment explanation
Indices: 102212--102336 Score: 146
Period size: 31 Copynumber: 4.0 Consensus size: 31
102202 GATCCTCGGC
* *
102212 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
**
102243 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
102274 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
102305 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
102337 TACCCTCAAC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
30 3 0.04
31 50 0.63
32 23 0.29
33 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:111028 original size:31 final size:31
Alignment explanation
Indices: 110984--111044 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
110974 GTGAGATGTT
110984 TGAACAATATGTTTTCTGAACTATGATTGTC
1 TGAACAATATGTTTTCTGAACTATGATTGTC
* * * *
111015 TGAACGATGTGTTTTCTTAACTGTGATTGT
1 TGAACAATATGTTTTCTGAACTATGATTGT
111045 TAGTATTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (31 bp):
TGAACAATATGTTTTCTGAACTATGATTGTC
Found at i:112782 original size:41 final size:41
Alignment explanation
Indices: 112724--112862 Score: 185
Period size: 41 Copynumber: 3.4 Consensus size: 41
112714 AGCAAATTCG
* *
112724 CGTTGCGATTTTTCATTTCGCTTTGCGATAGTCCA-AGTTGT
1 CGTTGCGATTTTCCATTTCGC-TTGCGATAGTCTACAGTTGT
112765 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCATTTCGC-TTGCGATAGTCTACAGTTGT
*
112807 CGTTGCGA-TTTCCAAATTCG-TTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC-ATTTCGCTTGCGATAGTCTACAGTTGT
*
112847 CATTGCGAATTTTCCA
1 CGTTGCG-ATTTTCCA
112863 AATTCGCAAC
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
40 26 0.29
41 39 0.44
42 24 0.27
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCATTTCGCTTGCGATAGTCTACAGTTGT
Found at i:112790 original size:20 final size:20
Alignment explanation
Indices: 112720--112793 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
112710 GTATAGCAAA
*
112720 TTCGCGTTGCGATTTTTCAT
1 TTCGCGTTGCGATTTTCCAT
* ** *
112740 TTCGCTTTGCGATAGTCCAAG
1 TTCGCGTTGCGATTTTCC-AT
112761 TT-GTCGTTGCGATTTTCCAT
1 TTCG-CGTTGCGATTTTCCAT
112781 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
112794 AGTCTACAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:112950 original size:21 final size:21
Alignment explanation
Indices: 112924--112980 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
112914 TGCGAAAACA
112924 AAATTCGCGTTGCGATTTTCC
1 AAATTCGCGTTGCGATTTTCC
112945 AAATTCGCGTTGCGATTTTCC
1 AAATTCGCGTTGCGATTTTCC
112966 AAATTCGCGTTGCGA
1 AAATTCGCGTTGCGA
112981 AAGTCAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (21 bp):
AAATTCGCGTTGCGATTTTCC
Found at i:112990 original size:20 final size:21
Alignment explanation
Indices: 112910--112993 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
112900 ATAGGTAATA
* *
112910 GCGTTGCGAAA-ACAAAATTC
1 GCGTTGCGAAATTCCAAATTC
**
112930 GCGTTGCGATTTTCCAAATTC
1 GCGTTGCGAAATTCCAAATTC
**
112951 GCGTTGCGATTTTCCAAATTC
1 GCGTTGCGAAATTCCAAATTC
*
112972 GCGTTGCGAAAGT-CAAATTC
1 GCGTTGCGAAATTCCAAATTC
112992 GC
1 GC
112994 AACTCGAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 18 0.32
21 38 0.68
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (21 bp):
GCGTTGCGAAATTCCAAATTC
Found at i:113053 original size:63 final size:63
Alignment explanation
Indices: 112862--113305 Score: 333
Period size: 63 Copynumber: 7.1 Consensus size: 63
112852 CGAATTTTCC
*
112862 AAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAA-TAGCGTTGCGAAAACA
1 AAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGCGAAAACG
** * * ** * * * **** * *
112924 AAATTCGC-GTTGCGATTTTC-CAA-ATTCGCGTT-GCGATTTTCCAAATTCGCGTTGCGAAAGT
1 AAATTCGCAACT-CGAATTTCTCAACCTT--AATTACCTATATAGGTAATTAGCGTTGCGAAA-A
112985 C-
62 CG
*
112986 AAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGCGAAAATG
1 AAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGCGAAAACG
** * * **** * * ***
113049 AAATTCGC-GTTGCGATTTTC-CAA-ATTCGCAACGCGA-A-A-GTCAAATTCGCAACGCGAATT
1 AAATTCGCAACT-CGAATTTCTCAACCTTAATTAC-CTATATAGGT--AATTAGCGTTGCGAA--
** *
113108 CTCC
60 AACG
*
113112 AAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGTGAAAACG
1 AAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGCGAAAACG
* * *
113175 AAATTCGCAACACGAATTTCACAACGC-TAATTACCTATATAGGTAATTAGTGTTGCGAAAACG
1 AAATTCGCAACTCGAATTTCTCAAC-CTTAATTACCTATATAGGTAATTAGCGTTGCGAAAACG
* *
113238 AAATTAGCAGCTCGAATTTCTCAACCTTAATTACCTATAT--GTAATTAGCGTTGCGAAAACG
1 AAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGCGAAAACG
113299 AAATTCG
1 AAATTCG
113306 TGTTGCGATT
Statistics
Matches: 283, Mismatches: 75, Indels: 49
0.70 0.18 0.12
Matches are distributed among these distances:
59 2 0.01
60 3 0.01
61 52 0.18
62 53 0.19
63 146 0.52
64 9 0.03
65 15 0.05
66 1 0.00
67 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (63 bp):
AAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGCGAAAACG
Found at i:113097 original size:41 final size:42
Alignment explanation
Indices: 113040--113127 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
113030 AATTAGCGTT
* *** *
113040 GCGAAAATGAAATTCGCGTTGCG-ATTTTCCAAATTCGCAAC
1 GCGAAAATCAAATTCGCAACGCGAATTCTCCAAATTCGCAAC
*
113081 GCGAAAGTCAAATTCGCAACGCGAATTCTCCAAATTCGCAAC
1 GCGAAAATCAAATTCGCAACGCGAATTCTCCAAATTCGCAAC
*
113123 TCGAA
1 GCGAA
113128 TTTCTCAACC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 18 0.46
42 21 0.54
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (42 bp):
GCGAAAATCAAATTCGCAACGCGAATTCTCCAAATTCGCAAC
Found at i:113116 original size:250 final size:251
Alignment explanation
Indices: 112851--113372 Score: 675
Period size: 250 Copynumber: 2.1 Consensus size: 251
112841 AGTTGTCATT
*
112851 GCGAATTTTCCAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAA-TAGCGTT
1 GCGAATTCTCCAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTT
**** * * * * * *
112915 GCGAAAACAAAATTCGCGTTGCGATTTTC-CAAATTCGC-GTT-GCGATTTTCCAAATTCGCGTT
66 GCGAAAACAAAATTCGCAACACGAATTTCAC-AA--CGCAATTACCGATATACCAAATTAGCGTT
* *
112977 GCGAAAGTC-AAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTG
128 GCGAAA-ACGAAATTAGCAACTCGAATTTCTCAACCTTAATTACCTATAT--GTAATTAGCGTTG
* *
113041 CGAAAATGAAATTCGCGTTGCGATTTTCCAAATTCGCAACGCGAA-AGT-CAAATTCGCAAC
190 CGAAAACGAAATTCGCGTTGCGATTTTCCAAATTCGCAACGCGAATACTCCAAATTCGCAAC
113101 GCGAATTCTCCAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTT
1 GCGAATTCTCCAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTT
* * * *** *
113166 GTGAAAACGAAATTCGCAACACGAATTTCACAACGCTAATTACCTATATAGGTAATTAGTGTTGC
66 GCGAAAACAAAATTCGCAACACGAATTTCACAACGC-AATTACCGATATACCAAATTAGCGTTGC
*
113231 GAAAACGAAATTAGCAGCTCGAATTTCTCAACCTTAATTACCTATATGTAATTAGCGTTGCGAAA
130 GAAAACGAAATTAGCAACTCGAATTTCTCAACCTTAATTACCTATATGTAATTAGCGTTGCGAAA
* * *
113296 ACGAAATTCGTGTTGCGATTTTCCAAATTCGCAACGTGAATTCTCCAAATTCGCAAC
195 ACGAAATTCGCGTTGCGATTTTCCAAATTCGCAACGCGAATACTCCAAATTCGCAAC
*
113353 GCGAA--CTCCAATTTCGCAAC
1 GCGAATTCTCCAAATTCGCAAC
113373 CCAGTTTCCA
Statistics
Matches: 237, Mismatches: 27, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
249 3 0.01
250 125 0.53
251 35 0.15
252 74 0.31
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (251 bp):
GCGAATTCTCCAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTT
GCGAAAACAAAATTCGCAACACGAATTTCACAACGCAATTACCGATATACCAAATTAGCGTTGCG
AAAACGAAATTAGCAACTCGAATTTCTCAACCTTAATTACCTATATGTAATTAGCGTTGCGAAAA
CGAAATTCGCGTTGCGATTTTCCAAATTCGCAACGCGAATACTCCAAATTCGCAAC
Found at i:113117 original size:22 final size:22
Alignment explanation
Indices: 113067--113129 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
113057 GTTGCGATTT
**
113067 TCCAAATTCGCAACGCGAA-AG
1 TCCAAATTCGCAACGCGAATTC
113088 T-CAAATTCGCAACGCGAATTC
1 TCCAAATTCGCAACGCGAATTC
*
113109 TCCAAATTCGCAACTCGAATT
1 TCCAAATTCGCAACGCGAATT
113130 TCTCAACCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 17 0.46
21 2 0.05
22 18 0.49
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.22
Consensus pattern (22 bp):
TCCAAATTCGCAACGCGAATTC
Found at i:113156 original size:126 final size:126
Alignment explanation
Indices: 112859--113372 Score: 543
Period size: 126 Copynumber: 4.1 Consensus size: 126
112849 TTGCGAATTT
112859 TCCAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAA-TAGCGTTGCGAAAAC
1 TCCAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGCGAAAAC
* *** ** *** *
112923 AAAATTCGCGTTGCGATTTTCCAAATTCGCGTTGCG-ATTTTCCAAATTCGCGTTGCGAAAG
66 GAAATTCGCGTTGCGATTTTCCAAATTCGCAACGCGAATAGTCCAAATTCGCAACGCG-AAC
*
112984 T-CAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGCGAAAAT
1 TCCAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGCGAAAAC
113048 GAAATTCGCGTTGCGATTTTCCAAATTCGCAACGCGAA-AGT-CAAATTCGCAACGCGAATTC
66 GAAATTCGCGTTGCGATTTTCCAAATTCGCAACGCGAATAGTCCAAATTCGCAACGCGAA--C
*
113109 TCCAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGTGAAAAC
1 TCCAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGCGAAAAC
**** * * * ****
113174 GAAATTCGCAACACGAATTT-CACAA--CGCTAATTAC-CTATATAGGT---AATTAGTGTTGCG
66 GAAATTCGCGTTGCGATTTTCCA-AATTCGC--A--ACGCGA-ATA-GTCCAAATTCGCAACGCG
*
113232 AAA
124 AAC
* * * *
113235 ACGAAATTAGCAGCTCGAATTTCTCAACCTTAATTACCTATAT--GTAATTAGCGTTGCGAAAAC
1 TCCAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGCGAAAAC
* * **
113298 GAAATTCGTGTTGCGATTTTCCAAATTCGCAACGTGAATTCTCCAAATTCGCAACGCGAAC
66 GAAATTCGCGTTGCGATTTTCCAAATTCGCAACGCGAATAGTCCAAATTCGCAACGCGAAC
*
113359 TCCAATTTCGCAAC
1 TCCAAATTCGCAAC
113373 CCAGTTTCCA
Statistics
Matches: 318, Mismatches: 51, Indels: 41
0.78 0.12 0.10
Matches are distributed among these distances:
121 1 0.00
122 4 0.01
123 3 0.01
124 117 0.37
125 53 0.17
126 122 0.38
127 2 0.01
128 13 0.04
129 1 0.00
130 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (126 bp):
TCCAAATTCGCAACTCGAATTTCTCAACCTTAATTACCTATATAGGTAATTAGCGTTGCGAAAAC
GAAATTCGCGTTGCGATTTTCCAAATTCGCAACGCGAATAGTCCAAATTCGCAACGCGAAC
Found at i:113345 original size:22 final size:21
Alignment explanation
Indices: 113310--113463 Score: 120
Period size: 20 Copynumber: 7.4 Consensus size: 21
113300 AATTCGTGTT
*
113310 GCGATTTTCCAAATTCGCAAC
1 GCGAATTTCCAAATTCGCAAC
*
113331 GTGAATTCTCCAAATTCGCAAC
1 GCGAATT-TCCAAATTCGCAAC
* *
113353 GCGAA-CTCCAATTTCGCAAC
1 GCGAATTTCCAAATTCGCAAC
* * * *
113373 -CCAGTTTCCAATTTCGCTAC
1 GCGAATTTCCAAATTCGCAAC
113393 GCGGAATTT-CAAATTCGCAAC
1 GC-GAATTTCCAAATTCGCAAC
* **
113414 GTGAAGAGT-CAAATTCGCAAC
1 GCGAA-TTTCCAAATTCGCAAC
**
113435 GCGAAAGT-CAAATTCGCAAC
1 GCGAATTTCCAAATTCGCAAC
*
113455 TCGAATTTC
1 GCGAATTTC
113464 GTAACTCGAA
Statistics
Matches: 107, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.02
20 49 0.46
21 34 0.32
22 22 0.21
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (21 bp):
GCGAATTTCCAAATTCGCAAC
Found at i:113369 original size:42 final size:41
Alignment explanation
Indices: 113317--113463 Score: 122
Period size: 41 Copynumber: 3.6 Consensus size: 41
113307 GTTGCGATTT
113317 TCCAAATTCGCAACGTGAATTCTCCAAATTCGCAACGCGAAC
1 TCCAAATTCGCAACGTGAATT-TCCAAATTCGCAACGCGAAC
* ** * * * *
113359 TCCAATTTCGCAAC-CCAGTTTCCAATTTCGCTACGCGGAAT
1 TCCAAATTCGCAACGTGAATTTCCAAATTCGCAACGC-GAAC
* ** *
113400 TTCAAATTCGCAACGTGAAGAGT-CAAATTCGCAACGCGAAAG
1 TCCAAATTCGCAACGTGAA-TTTCCAAATTCGCAACGCG-AAC
113442 T-CAAATTCGCAAC-TCGAATTTC
1 TCCAAATTCGCAACGT-GAATTTC
113464 GTAACTCGAA
Statistics
Matches: 80, Mismatches: 19, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
40 16 0.20
41 34 0.43
42 29 0.36
43 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (41 bp):
TCCAAATTCGCAACGTGAATTTCCAAATTCGCAACGCGAAC
Found at i:113469 original size:14 final size:14
Alignment explanation
Indices: 113447--113481 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
113437 GAAAGTCAAA
113447 TTCGCAACTCGAAT
1 TTCGCAACTCGAAT
*
113461 TTCGTAACTCGAAT
1 TTCGCAACTCGAAT
113475 TTCGCAA
1 TTCGCAA
113482 AGCGAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (14 bp):
TTCGCAACTCGAAT
Found at i:113751 original size:21 final size:21
Alignment explanation
Indices: 113687--113756 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
113677 TTTGGAAAAT
* *
113687 TCGCAATGACAACTGTAGACTA
1 TCGCAACGACAACT-TGGACTA
* **
113709 TCGCAACG--AATTTGGAAAA
1 TCGCAACGACAACTTGGACTA
113728 TCGCAACGACAACTTGGACTA
1 TCGCAACGACAACTTGGACTA
113749 TCGCAACG
1 TCGCAACG
113757 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
19 12 0.32
20 3 0.08
21 16 0.42
22 7 0.18
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (21 bp):
TCGCAACGACAACTTGGACTA
Found at i:113767 original size:40 final size:41
Alignment explanation
Indices: 113679--113855 Score: 148
Period size: 41 Copynumber: 4.3 Consensus size: 41
113669 GTTGCGAATT
* * *
113679 TGGAAAATTCGCAATGACAACTGTAGACTATCGCAA--CGAATT
1 TGGAAAA-TCGCAACGACAACT-TGGACTATCGCAACGCGAA-A
113721 TGGAAAATCGCAACGACAACTTGGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTTGGACTATCGCAACGCGAAA
* * ** *
113762 TGAAAAATCGCAACG-CGAA-ATGGAAAATCGCAACGTGAAA
1 TGGAAAATCGCAACGAC-AACTTGGACTATCGCAACGCGAAA
** ** * *
113802 TGGAAAATCGCAACG-CGATTTTCAACAATCGCAACACGAAA
1 TGGAAAATCGCAACGAC-AACTTGGACTATCGCAACGCGAAA
113843 TGGAAAATCGCAA
1 TGGAAAATCGCAA
113856 TGCGATTTTC
Statistics
Matches: 115, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
40 47 0.41
41 57 0.50
42 11 0.10
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (41 bp):
TGGAAAATCGCAACGACAACTTGGACTATCGCAACGCGAAA
Found at i:113769 original size:41 final size:41
Alignment explanation
Indices: 113681--113816 Score: 127
Period size: 40 Copynumber: 3.3 Consensus size: 41
113671 TGCGAATTTG
* * * *
113681 GAAAATTCGCAATGACAACTGTAGACTATCGCAA--CGAATTT
1 GAAAAATCGCAACGACAACT-TGGACTATCGCAACGCGAA-AT
*
113722 GGAAAATCGCAACGACAACTTGGACTATCGCAACGCGAAAT
1 GAAAAATCGCAACGACAACTTGGACTATCGCAACGCGAAAT
* ** *
113763 GAAAAATCGCAACG-CGAA-ATGGAAAATCGCAACGTGAAAT
1 GAAAAATCGCAACGAC-AACTTGGACTATCGCAACGCGAAAT
*
113803 GGAAAATCGCAACG
1 GAAAAATCGCAACG
113817 CGATTTTCAA
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
40 44 0.54
41 33 0.41
42 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.16
Consensus pattern (41 bp):
GAAAAATCGCAACGACAACTTGGACTATCGCAACGCGAAAT
Found at i:113773 original size:20 final size:20
Alignment explanation
Indices: 113721--113860 Score: 147
Period size: 20 Copynumber: 6.9 Consensus size: 20
113711 GCAACGAATT
*
113721 TGGAAAATCGCAACGAC-AACT
1 TGGAAAATCGCAACG-CGAA-A
**
113742 TGGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
*
113762 TGAAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
*
113782 TGGAAAATCGCAACGTGAAA
1 TGGAAAATCGCAACGCGAAA
**
113802 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAA
** *
113822 TTCAACAATCGCAACACGAAA
1 TGGAA-AATCGCAACGCGAAA
*
113843 TGGAAAATCGCAATGCGA
1 TGGAAAATCGCAACGCGA
113861 TTTTCAACTA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
20 67 0.69
21 30 0.31
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.15
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:113790 original size:61 final size:61
Alignment explanation
Indices: 113721--113855 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
113711 GCAACGAATT
* ** * *
113721 TGGAAAATCGCAACGACAACTTGGACTATCGCAACGCGA-AATGAAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAA-ATGGAAAATCGCAACGCGATAATCAAAAATCGCAACACGAAA
** ** *
113782 TGGAAAATCGCAACGTGAAATGGAAAATCGCAACGCGATTTTCAACAATCGCAACACGAAA
1 TGGAAAATCGCAACGACAAATGGAAAATCGCAACGCGATAATCAAAAATCGCAACACGAAA
113843 TGGAAAATCGCAA
1 TGGAAAATCGCAA
113856 TGCGATTTTC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 16 0.25
61 47 0.75
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.15
Consensus pattern (61 bp):
TGGAAAATCGCAACGACAAATGGAAAATCGCAACGCGATAATCAAAAATCGCAACACGAAA
Found at i:113832 original size:41 final size:41
Alignment explanation
Indices: 113748--113885 Score: 188
Period size: 41 Copynumber: 3.4 Consensus size: 41
113738 AACTTGGACT
* ** **
113748 ATCGCAACGCGAAATGAAAAATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACA
*
113788 ATCGCAACGTGAAATGGAAAATCGCAACGCGATTTTCAACA
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACA
* * *
113829 ATCGCAACACGAAATGGAAAATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACA
113870 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
113886 CAACGCGAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 33 0.38
41 53 0.62
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACA
Found at i:113833 original size:21 final size:21
Alignment explanation
Indices: 113807--113881 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
113797 TGAAATGGAA
113807 AATCGCAACGCGATTTTCAAC
1 AATCGCAACGCGATTTTCAAC
* ** **
113828 AATCGCAACACGAAATGGAA-
1 AATCGCAACGCGATTTTCAAC
*
113848 AATCGCAATGCGATTTTCAAC
1 AATCGCAACGCGATTTTCAAC
*
113869 TATCGCAACGCGA
1 AATCGCAACGCGA
113882 AATGCAACGC
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCAAC
Done.