Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007070.1 Hibiscus syriacus cultivar Beakdansim tig00018398_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: 124905
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1881 original size:12 final size:12
Alignment explanation
Indices: 1864--1888 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1854 TCTTCGGGGA
1864 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1876 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1888 C
1 C
1889 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2100 original size:24 final size:23
Alignment explanation
Indices: 2061--2106 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2051 CTGAAACATC
2061 ATCAAATCCGTGTATTGACCAAT
1 ATCAAATCCGTGTATTGACCAAT
2084 ATCAAAGTCCG-GATATTGACCAA
1 ATCAAA-TCCGTG-TATTGACCAA
2107 GACCAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (23 bp):
ATCAAATCCGTGTATTGACCAAT
Found at i:2807 original size:20 final size:20
Alignment explanation
Indices: 2779--2988 Score: 228
Period size: 20 Copynumber: 10.5 Consensus size: 20
2769 AAATTTCAGT
* * * *
2779 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2799 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2819 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2839 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2859 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2879 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2899 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2919 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2939 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2959 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
2979 GTTGCGATTT
1 GTTGCGATTT
2989 TGGAAAATCG
Statistics
Matches: 165, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.02
20 159 0.96
21 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:3005 original size:21 final size:21
Alignment explanation
Indices: 2975--3057 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
2965 ATTTATGTGT
*
2975 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2996 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3017 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
3038 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3058 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3297 original size:30 final size:30
Alignment explanation
Indices: 3219--3330 Score: 86
Period size: 29 Copynumber: 3.7 Consensus size: 30
3209 TATTTGACAT
* * **
3219 AAAATACCTTAGGTA-TCTATTTTGAAGTAA
1 AAAATACTTTAAGTACT-TATTTTGAAAAAA
*
3249 AAGATAACTTTATA-TACTTATTTTGAAAAAA
1 AAAAT-ACTTTA-AGTACTTATTTTGAAAAAA
** *
3280 AAAATACTTTAAGTACTTA-AATGAAAAAG
1 AAAATACTTTAAGTACTTATTTTGAAAAAA
**
3309 AGTATACTTTAAGTACTTATTT
1 AAAATACTTTAAGTACTTATTT
3331 GTTAATATAA
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
29 25 0.39
30 16 0.25
31 22 0.34
32 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.38
Consensus pattern (30 bp):
AAAATACTTTAAGTACTTATTTTGAAAAAA
Found at i:8916 original size:149 final size:149
Alignment explanation
Indices: 8646--8951 Score: 603
Period size: 149 Copynumber: 2.1 Consensus size: 149
8636 TCTGATTTAT
8646 AAAATGATAATGGAGAACTCAGTGCCTACACTTGTAATCCTAAGGAGATCCTATTTCGGTTACAA
1 AAAATGATAATGGAGAACTCAGTGCCTACACTTGTAATCCTAAGGAGATCCTATTTCGGTTACAA
*
8711 TTGGTGTATAGAGCCTAAGTTTAAAGCCTAACCTTCTGTGTCCTGCTTCCTTTTAACCACTCGAA
66 TTGGTGTATAGAGCCTAAGTTTAAAGCCTAACCTTCTGTGTCCCGCTTCCTTTTAACCACTCGAA
8776 AAACAGAGCATTTAAAAAC
131 AAACAGAGCATTTAAAAAC
8795 AAAATGATAATGGAGAACTCAGTGCCTACACTTGTAATCCTAAGGAGATCCTATTTCGGTTACAA
1 AAAATGATAATGGAGAACTCAGTGCCTACACTTGTAATCCTAAGGAGATCCTATTTCGGTTACAA
8860 TTGGTGTATAGAGCCTAAGTTTAAAGCCTAACCTTCTGTGTCCCGCTTCCTTTTAACCACTCGAA
66 TTGGTGTATAGAGCCTAAGTTTAAAGCCTAACCTTCTGTGTCCCGCTTCCTTTTAACCACTCGAA
8925 AAACAGAGCATTTAAAAAC
131 AAACAGAGCATTTAAAAAC
8944 AAAATGAT
1 AAAATGAT
8952 TTCGTCATTA
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 156 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (149 bp):
AAAATGATAATGGAGAACTCAGTGCCTACACTTGTAATCCTAAGGAGATCCTATTTCGGTTACAA
TTGGTGTATAGAGCCTAAGTTTAAAGCCTAACCTTCTGTGTCCCGCTTCCTTTTAACCACTCGAA
AAACAGAGCATTTAAAAAC
Found at i:27812 original size:21 final size:22
Alignment explanation
Indices: 27766--27814 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
27756 TAGACGGATT
*
27766 TCGTCGGAGATGGGGACATATT
1 TCGTCGGAGATGGGGACATATG
27788 TCGTCGGAGAT-GGGAC-TGATG
1 TCGTCGGAGATGGGGACAT-ATG
27809 TCGTCG
1 TCGTCG
27815 TAGAGAGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.52
22 11 0.44
ACGTcount: A:0.18, C:0.16, G:0.39, T:0.27
Consensus pattern (22 bp):
TCGTCGGAGATGGGGACATATG
Found at i:27990 original size:20 final size:20
Alignment explanation
Indices: 27962--28007 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
27952 TAAACGCGCT
*
27962 TTGCCAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
*
27982 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
28002 TTGCGA
1 TTGCGA
28008 TTTACATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:28045 original size:20 final size:20
Alignment explanation
Indices: 28015--28072 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
28005 CGATTTACAT
*
28015 ATTCGCCTTGCGAATTTGGAA
1 ATTCGCGTTGCGAATTTGG-A
* *
28036 ATT-GGGTTGCGAAATTGGA
1 ATTCGCGTTGCGAATTTGGA
*
28055 GTTCGCGTTGCGAATTTG
1 ATTCGCGTTGCGAATTTG
28073 TTGGTCATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 3 0.10
20 24 0.80
21 3 0.10
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (20 bp):
ATTCGCGTTGCGAATTTGGA
Found at i:32322 original size:23 final size:23
Alignment explanation
Indices: 32290--32339 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
32280 GGATTTTGCA
*
32290 GATACCCATAATTCGGGTAATTG
1 GATACCCATAATTCGGGTAATCG
*
32313 GATACTCATAATTCGGGTAATCG
1 GATACCCATAATTCGGGTAATCG
32336 GATA
1 GATA
32340 TTCGGTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (23 bp):
GATACCCATAATTCGGGTAATCG
Found at i:36493 original size:108 final size:108
Alignment explanation
Indices: 36359--36704 Score: 539
Period size: 108 Copynumber: 3.2 Consensus size: 108
36349 GGAGTATGGA
* *
36359 ACTCGAATAATCTTTAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGATCCACAATC
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGATCCACAATC
* *
36424 TTCATCAATCGTGTCTGCCCCCTATTTCTTCAGAAAGTATAAG
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
36467 ACTCGAACAACCTTCAACAATCGCGTCTCCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGATCCACAATC
36532 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
36575 ACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTTAGAGAGTATAAGACTCGAACAA
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAA
* * *
36640 TCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
64 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
36685 ACTCGAACAATCTTCAACAA
1 ACTCGAACAATCTTCAACAA
36705 ATGGGTTCGC
Statistics
Matches: 216, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
108 150 0.69
109 1 0.00
110 65 0.30
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (108 bp):
ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGATCCACAATC
TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:36509 original size:55 final size:55
Alignment explanation
Indices: 36359--36704 Score: 520
Period size: 55 Copynumber: 6.4 Consensus size: 55
36349 GGAGTATGGA
* *
36359 ACTCGAATAATCTTTAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
36414 A-TC-CACAATCTTCATCAATCGTGTCTGCCCCCTATTTCTTCAGAAAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
36467 ACTCGAACAACCTTCAACAATCGCGTCTCCCCCCTATATCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
36522 AC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
36575 ACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTTAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
36630 ACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
36685 ACTCGAACAATCTTCAACAA
1 ACTCGAACAATCTTCAACAA
36705 ATGGGTTCGC
Statistics
Matches: 262, Mismatches: 25, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
53 92 0.35
54 6 0.02
55 164 0.63
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:36725 original size:55 final size:54
Alignment explanation
Indices: 36326--36995 Score: 373
Period size: 55 Copynumber: 12.6 Consensus size: 54
36316 TCTAAAAATA
* * * *
36326 GGTTCGCTCCCTATTGCTTCCA-AGGAGTAT-GGAACTCGAATAATCTTTAACAATCG
1 GGTTCGCTCCCTATTTCTT-CAGA-GAGTATAAG-ACTCGAACAATCTTCAACAAT-G
* * * *
36382 CG-TCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTTCATCAAT-
1 GGTTC-GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATG
* * * *
36433 CGTGTCTGCCCCCTATTTCTTCAGAAAGTATAAGACTCGAACAACCTTCAACAATCG
1 GGT-TC-GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT-G
* * * * *
36490 CGTCTC-CCCCCTATATCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCG
1 GGT-TCGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAT-G
* * *
36543 CG-TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTG
1 GGTTC-GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATG
* * * *
36598 CG-TCTGCCCCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAACGATTG
1 GGTTC-GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATG
* *
36653 CG-TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAATG
1 GGTTC-GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATG
* * * * ** * *
36708 GGTTCGCTCCCTTTTTCTTTAGGGAGTAT-AGAACTC-AAAAATCTTCTTCTTACG
1 GGTTCGCTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAAC-AATG
* * * * * *
36762 GGTTCGCTCCTTCTCTCTTTAAAGAGTAT-AGAACTCGAAC-ATCTTC-A-AACG
1 GGTTCGCTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATG
* * * * * * *
36813 GGTTCGCTCCTTCTTTCATTAAG-GAGTAT-GGAACTCGGA-TATCTTC-ACACT-
1 GGTTCGCTCCCTATTTC-TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATG
* * *
36864 GGTTCGCTCCCTCTTTC-TCTAGGGAGTAT-AGAACTCGAACATCTCTTC-AC---G
1 GGTTCGCTCCCTATTTCTTC-AGAGAGTATAAG-ACTCGAACA-ATCTTCAACAATG
* * *
36915 GGTTCGCTCCCTCTTTC-TCTAGGGAGTAT-GGAACTCGAAC-ATCTTCAAC--TG
1 GGTTCGCTCCCTATTTCTTC-AGAGAGTATAAG-ACTCGAACAATCTTCAACAATG
* *
36966 GGTTCGCTCCCTCTTTCTTCAGGGAGTATA
1 GGTTCGCTCCCTATTTCTTCAGAGAGTATA
36996 GAAATCAAAA
Statistics
Matches: 525, Mismatches: 60, Indels: 62
0.81 0.09 0.10
Matches are distributed among these distances:
49 6 0.01
50 4 0.01
51 140 0.27
52 6 0.01
53 93 0.18
54 57 0.11
55 195 0.37
56 19 0.04
57 5 0.01
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (54 bp):
GGTTCGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATG
Found at i:36725 original size:110 final size:108
Alignment explanation
Indices: 36359--36753 Score: 496
Period size: 108 Copynumber: 3.6 Consensus size: 108
36349 GGAGTATGGA
* * *
36359 ACTCGAATAATCTTTAACAATCGCG-TCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TCCACAA
1 ACTCGAACAATCTTCAACAAT-GCGTTC-GCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAA
* *
36422 TCTTCATCAATCGTGTCTGCCCCCTATTTCTTCAGAAAGTATAAG
64 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
36467 ACTCGAACAACCTTCAACAATCGCGTCTC-CCCCCTATATCTTCAGAGAGTATAAGAC-CCACAA
1 ACTCGAACAATCTTCAACAAT-GCGT-TCGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAA
36530 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
64 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
36575 ACTCGAACAATCTTCAACGATTGCG-TCTGCCCCCTATTTCTTTAGAGAGTATAAGACTCGAACA
1 ACTCGAACAATCTTCAAC-AATGCGTTC-GCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACA
* * *
36639 ATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
63 ATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * * *
36685 ACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTTTTTCTTTAGGGAGTAT-AGAACTCAAAAA
1 ACTCGAACAATCTTCAAC-AATGCGTTCGCCCCCTATTTCTTCAGAGAGTATAAG-ACTCAACAA
36749 TCTTC
64 TCTTC
36754 TTCTTACGGG
Statistics
Matches: 256, Mismatches: 21, Indels: 19
0.86 0.07 0.06
Matches are distributed among these distances:
106 2 0.01
108 143 0.56
109 14 0.05
110 95 0.37
111 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.30
Consensus pattern (108 bp):
ACTCGAACAATCTTCAACAATGCGTTCGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATC
TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:36840 original size:51 final size:50
Alignment explanation
Indices: 36666--37211 Score: 404
Period size: 51 Copynumber: 10.4 Consensus size: 50
36656 CTGCCCCCTA
* *
36666 TTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTT-
1 TTTCTTAAG-GAGTATAGA-ACTCGAAC-ATCTT---CAAACGGGTTCGCT-CCTTC
* * * **
36721 TTTCTTTAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCTTC
1 TTTC-TTAAGGAGTATAGAACTC--GAA-CATCTTCAAACGGGTTCGCTCCTTC
* *
36775 TCTCTTTAAAGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTC
1 TTTC-TTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTC
* * * * * *
36826 TTTCATTAAGGAGTATGGAACTCGGATATCTTCACACTGGTTCGCTCCCTC
1 TTTC-TTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTC
* *
36877 TTTCTCTAGGGAGTATAGAACTCGAACATCTCTTC--ACGGGTTCGCTCCCTC
1 TTTCT-TAAGGAGTATAGAACTCGAACA--TCTTCAAACGGGTTCGCTCCTTC
* * *
36928 TTTCTCTAGGGAGTATGGAACTCGAACATCTTC-AACTGGGTTCGCTCCCTC
1 TTTCT-TAAGGAGTATAGAACTCGAACATCTTCAAAC-GGGTTCGCTCCTTC
* * * * **
36979 TTTCTTCAGGGAGTATAGAAATCAAAAATCTTCTTCTTACGGGTTCGCTCCTTC
1 TTTCTT-AAGGAGTATAGAACTC--GAA-CATCTTCAAACGGGTTCGCTCCTTC
*
37033 TCTAT-TTAAAGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTTCC-TC
1 T-T-TCTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGC-TCCTTC
* * * ** *
37084 TTTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTTCTTC
1 TTTCTTAAGG-AGTATAGAACTC--GAA-CATCTTCAAACGGGTTCGCTCCTTC
* * * * *
37138 TTTCATTAAGGAGTATGGAACTCGGATATCTTCATACGGGTTCGCTCCCTC
1 TTTC-TTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTC
* *
37189 TTTCTCTAGGGAGTATGGAACTC
1 TTTCT-TAAGGAGTATAGAACTC
37212 AAATAATCTT
Statistics
Matches: 405, Mismatches: 59, Indels: 58
0.78 0.11 0.11
Matches are distributed among these distances:
49 6 0.01
50 10 0.02
51 232 0.57
52 8 0.02
53 15 0.04
54 97 0.24
55 25 0.06
56 5 0.01
57 6 0.01
58 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (50 bp):
TTTCTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTC
Found at i:36848 original size:105 final size:104
Alignment explanation
Indices: 36676--37211 Score: 427
Period size: 105 Copynumber: 5.1 Consensus size: 104
36666 TTTCTTCAGA
* * * *
36676 GAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTT-TTTCTTTAGGGAGTATAG
1 GAGTATAGA-ACTCGAAC-ATCTT---CAAACGGGTTCGCT-CCTTCTTTCATTAAGGAGTATGG
* * * * *
36739 AACTCAAAAATCTTCTTCTTACGGGTTCGCTCCTTCTCTCTTTAAA
60 AACTCGAAAATCTTCTAC-TACGGGTTCGCTCCCTCTTTCTTTAAG
36785 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCATTAAGGAGTATGGAACTCG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCATTAAGGAGTATGGAACTCG
* * * * *
36850 GATATCTTC-AC-ACTGGTTCGCTCCCTCTTTCTCTAGG
66 AAAATCTTCTACTACGGGTTCGCTCCCTCTTTCTTTAAG
* *
36887 GAGTATAGAACTCGAACATCTCTTC--ACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAAC
1 GAGTATAGAACTCGAACA--TCTTCAAACGGGTTCGCTCCTTCTTTCAT-TAAGGAGTATGGAAC
* * * *
36949 TCGAACATCTTCAACT--GGGTTCGCTCCCTCTTTCTTCAGG
63 TCGAAAATCTTCTACTACGGGTTCGCTCCCTCTTTCTTTAAG
* * * ** * * *
36989 GAGTATAGAAATCAAAAATCTTCTTCTTACGGGTTCGCTCCTTCTCT-ATTTAAAGAGTATAGAA
1 GAGTATAGAACTC--GAA-CATCTTCAAACGGGTTCGCTCCTTCTTTCA-TTAAGGAGTATGGAA
* * * *
37053 CTCGAACATCTTC-A-AACGGGTTCGCTTCCTCTTTC-TTCAG
62 CTCGAAAATCTTCTACTACGGGTTCGCTCCCTCTTTCTTTAAG
* * ** *
37093 GAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTTCTTCTTTCATTAAGGAGTATGGAA
1 G-AGTATAGAACTC--GAA-CATCTTCAAACGGGTTCGCTCCTTCTTTCATTAAGGAGTATGGAA
* * * *
37158 CTCGGATATCTTC-A-TACGGGTTCGCTCCCTCTTTCTCTAGG
62 CTCGAAAATCTTCTACTACGGGTTCGCTCCCTCTTTCTTTAAG
*
37199 GAGTATGGAACTC
1 GAGTATAGAACTC
37212 AAATAATCTT
Statistics
Matches: 361, Mismatches: 47, Indels: 42
0.80 0.10 0.09
Matches are distributed among these distances:
101 1 0.00
102 114 0.32
103 7 0.02
104 16 0.04
105 197 0.55
106 5 0.01
108 5 0.01
109 15 0.04
110 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (104 bp):
GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCATTAAGGAGTATGGAACTCG
AAAATCTTCTACTACGGGTTCGCTCCCTCTTTCTTTAAG
Found at i:36887 original size:156 final size:152
Alignment explanation
Indices: 36707--37222 Score: 536
Period size: 156 Copynumber: 3.3 Consensus size: 152
36697 TTCAACAAAT
* *
36707 GGGTTCGCTCCCTTTTTCTTTAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAAAATCTTCTTC--ACGGGTTCGCTCC
* *
36772 TTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCATTAAGG
64 -TCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC-AACGGGTTCGCTCCTTCTTTCATTAAGG
36837 AGTATGGAACTCGGATATCTTCACAC
127 AGTATGGAACTCGGATATCTTCACAC
* * *
36863 TGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATC-TCTTCACGGGTTCGCTCCCT
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAAAATCTTCTTCACGGGTTCGCT-CCT
* * * * *
36927 CTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAACTGGGTTCGCTCCCTCTTTC-TTCAGGGA
65 CTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAC-GGGTTCGCTCCTTCTTTCATT-AAGGA
* * ** * *
36991 GTATAGAAATCAAAAATCTTCTTCTTAC
128 GTATGGAACTCGGATATCTTC-AC--AC
* * * * ** * * **
37019 GGGTTCGCTCCTTCTCTATTTAAAGAGTATAGAACTCGAACATCTTC-AAACGGGTTCGCTTCCT
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAAAATCTTCTTCACGGGTTCGC-TCCT
* * * * *
37083 CTTTC-TTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTTCTTCTTTCATTAA
65 CTTTCTTTAAGG-AGTATAGAACTC--GAA-CATCTTC-AACGGGTTCGCTCCTTCTTTCATTAA
*
37147 GGAGTATGGAACTCGGATATCTTCATAC
125 GGAGTATGGAACTCGGATATCTTCACAC
*
37175 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAAATAATCTTC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAA-AATCTTC
37223 ATTTGCTTCA
Statistics
Matches: 292, Mismatches: 53, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
152 5 0.02
153 78 0.27
154 3 0.01
155 8 0.03
156 141 0.48
157 9 0.03
158 2 0.01
159 42 0.14
160 4 0.01
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.34
Consensus pattern (152 bp):
GGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAAAATCTTCTTCACGGGTTCGCTCCTC
TTTCTTTAAGGAGTATAGAACTCGAACATCTTCAACGGGTTCGCTCCTTCTTTCATTAAGGAGTA
TGGAACTCGGATATCTTCACAC
Found at i:37212 original size:105 final size:104
Alignment explanation
Indices: 36759--37222 Score: 543
Period size: 105 Copynumber: 4.5 Consensus size: 104
36749 TCTTCTTCTT
* * * ** * * **
36759 ACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTC--GAA-CATCTTCAAACGGGTTCGCT
1 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCT
* *
36821 CCTTCTTTCATTAAGGAGTATGGAACTCGGATATCTTCA
66 CCTTCTTTCATTAAGGAGTATGGAACTCGAACATCTTCA
* * *
36860 CACTGGTTCGCTCCCTCTTTC-TCTAGGGAGTATAGAACTCGAACATC-TCTTC--ACGGGTTCG
1 -ACGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCG
* *
36921 CTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAACATCTTCA
64 CTCCTTCTTTCAT-TAAGGAGTATGGAACTCGAACATCTTCA
*
36962 ACTGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAAATCAAAAATCTTCTTCTTACGGGTTCGC
1 AC-GGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGC
* * *
37027 TCCTTCTCT-ATTTAAAGAGTATAGAACTCGAACATCTTCAA
65 TCCTTCTTTCA-TTAAGGAGTATGGAACTCGAACATCTTC-A
* *
37068 ACGGGTTCGCTTCCTCTTTCTTCAGGAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCT
1 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCT
* * *
37133 TCTTCTTTCATTAAGGAGTATGGAACTCGGATATCTTCA
66 CCTTCTTTCATTAAGGAGTATGGAACTCGAACATCTTCA
*
37172 TACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCAAATAATCTTC
1 -ACGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCAAA-AATCTTC
37223 ATTTGCTTCA
Statistics
Matches: 312, Mismatches: 33, Indels: 30
0.83 0.09 0.08
Matches are distributed among these distances:
101 4 0.01
102 112 0.36
103 7 0.02
104 9 0.03
105 168 0.54
106 12 0.04
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (104 bp):
ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCT
CCTTCTTTCATTAAGGAGTATGGAACTCGAACATCTTCA
Found at i:37655 original size:36 final size:36
Alignment explanation
Indices: 37628--37783 Score: 222
Period size: 36 Copynumber: 4.3 Consensus size: 36
37618 ACTACTTTTT
* *
37628 GGTGAAGACTTAAGATGGTTTGCTTCACTACTCTCT
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
*
37664 GGTGAAGACTTATGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
* * * *
37700 GGTGAAGGCTTCAGATTGATTGCTTCACTATTCTCC
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
* *
37736 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
*
37772 GGTGAAGGCTTA
1 GGTGAAGACTTA
37784 GGATTGACTT
Statistics
Matches: 109, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 109 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (36 bp):
GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
Found at i:46838 original size:2 final size:2
Alignment explanation
Indices: 46831--46861 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46821 GATTGAAGAA
46831 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 A
46862 AATTCAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48912 original size:15 final size:15
Alignment explanation
Indices: 48894--49027 Score: 106
Period size: 15 Copynumber: 8.5 Consensus size: 15
48884 CTTCTCTTCC
*
48894 TCTTTCTTGGGTTCT
1 TCTTTCTTTGGTTCT
*
48909 TCTTTCTTTGGCTCT
1 TCTTTCTTTGGTTCT
* * *
48924 TCCTTCTTAGGCTCT
1 TCTTTCTTTGGTTCT
48939 TCTTTCTTTGGTTCCT
1 TCTTTCTTTGGTT-CT
* *
48955 CTCCCTTCTTGGGTTCT
1 -T-CTTTCTTTGGTTCT
48972 TCTTTCTTTGGTTCCT
1 TCTTTCTTTGGTT-CT
* *
48988 CCTGTTTCTTGGGTTCT
1 --TCTTTCTTTGGTTCT
* * *
49005 TCCTTCTTTGGCTCC
1 TCTTTCTTTGGTTCT
49020 TCTTTCTT
1 TCTTTCTT
49028 CTCTGGTTCC
Statistics
Matches: 94, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
15 63 0.67
16 5 0.05
17 5 0.05
18 21 0.22
ACGTcount: A:0.01, C:0.28, G:0.15, T:0.56
Consensus pattern (15 bp):
TCTTTCTTTGGTTCT
Found at i:48956 original size:18 final size:18
Alignment explanation
Indices: 48935--49038 Score: 69
Period size: 18 Copynumber: 6.1 Consensus size: 18
48925 CCTTCTTAGG
48935 CTCTTCTTTCTTTGGTTC
1 CTCTTCTTTCTTTGGTTC
* * *
48953 CTCTCCCTTC-TTGGGT-
1 CTCTTCTTTCTTTGGTTC
48969 -TCTTCTTTCTTTGGTTC
1 CTCTTCTTTCTTTGGTTC
* * *
48986 CTCCTGTTTC-TTGGGT-
1 CTCTTCTTTCTTTGGTTC
* *
49002 -TCTTCCTTCTTTGGCTC
1 CTCTTCTTTCTTTGGTTC
*
49019 CTCTT-TCTTCTCTGGTTC
1 CTCTTCT-TTCTTTGGTTC
49037 CT
1 CT
49039 TTGCTGGTCC
Statistics
Matches: 63, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
15 13 0.21
16 10 0.16
17 10 0.16
18 30 0.48
ACGTcount: A:0.00, C:0.31, G:0.14, T:0.55
Consensus pattern (18 bp):
CTCTTCTTTCTTTGGTTC
Found at i:49036 original size:33 final size:33
Alignment explanation
Indices: 48897--49029 Score: 164
Period size: 33 Copynumber: 4.1 Consensus size: 33
48887 CTCTTCCTCT
48897 TTCTTGGGTTCTTCTTTCTTTGG---CTCTTCC
1 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
* * *
48927 TTCTTAGGCTCTTCTTTCTTTGGTTCCTCTCCC
1 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
* **
48960 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCCTGT
1 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
* * *
48993 TTCTTGGGTTCTTCCTTCTTTGGCTCCTCTTTC
1 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
49026 TTCT
1 TTCT
49030 CTGGTTCCTT
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
30 21 0.24
33 65 0.76
ACGTcount: A:0.01, C:0.29, G:0.15, T:0.56
Consensus pattern (33 bp):
TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
Found at i:51256 original size:152 final size:153
Alignment explanation
Indices: 50974--51287 Score: 513
Period size: 152 Copynumber: 2.1 Consensus size: 153
50964 ACATCATGCT
*
50974 CACATAATTTCTAATTGAAATTAGGTTTAGGTGAGAGTTATGACCCCCACTAATTTAGGGTATAA
1 CACA-AATTTCTAATTGAAATTAGGTTTAGGTGAGAGTTATGACCCCCACTAATTTAGAGTATAA
*
51039 TAAAAATAAATTAATTAAATGCAACTGCACTATTTTGGACAACAATTTCAATTAGAAACTATGTA
65 TAAAAATAAATTAATTAAATGCAACTACACTATTTTGGACAACAATTTCAATTAGAAACTATGTA
*
51104 AGTACAATATTGGTCTCTTTAGTA
130 AGCACAATATTGGTCTCTTTAGTA
*
51128 CACAAATTTCTAATTGAAATTAGGTTTAGGTGGGAGTTATGA-CCCCACTAATTTAGAGTATAAT
1 CACAAATTTCTAATTGAAATTAGGTTTAGGTGAGAGTTATGACCCCCACTAATTTAGAGTATAAT
* * * *
51192 AAAAATAAATTAATTAAATGCAACTACACTGTTTTGGATAATAATTTCAATTAGAAATTATGTAA
66 AAAAATAAATTAATTAAATGCAACTACACTATTTTGGACAACAATTTCAATTAGAAACTATGTAA
* *
51257 GCACAATGTTGGTTTCTTTAGTA
131 GCACAATATTGGTCTCTTTAGTA
*
51280 AACAAATT
1 CACAAATT
51288 CAATGTTTGG
Statistics
Matches: 149, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
152 108 0.72
153 37 0.25
154 4 0.03
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (153 bp):
CACAAATTTCTAATTGAAATTAGGTTTAGGTGAGAGTTATGACCCCCACTAATTTAGAGTATAAT
AAAAATAAATTAATTAAATGCAACTACACTATTTTGGACAACAATTTCAATTAGAAACTATGTAA
GCACAATATTGGTCTCTTTAGTA
Found at i:51497 original size:14 final size:14
Alignment explanation
Indices: 51478--51506 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
51468 ATATGACAGA
51478 CGCCCATATTTTTT
1 CGCCCATATTTTTT
51492 CGCCCATATTTTTT
1 CGCCCATATTTTTT
51506 C
1 C
51507 ACTTGTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.31, G:0.07, T:0.48
Consensus pattern (14 bp):
CGCCCATATTTTTT
Found at i:55993 original size:18 final size:18
Alignment explanation
Indices: 55947--55993 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
55937 TTCTCTTTCG
*
55947 TTTTACTTTACGTTTTTA
1 TTTTACTTTATGTTTTTA
55965 TTTTACTTTATGTTTTTA
1 TTTTACTTTATGTTTTTA
55983 TTTTACTTTAT
1 TTTTACTTTAT
55994 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTTACTTTATGTTTTTA
Found at i:57018 original size:70 final size:70
Alignment explanation
Indices: 56905--57051 Score: 267
Period size: 70 Copynumber: 2.1 Consensus size: 70
56895 TATCTTTAAA
*
56905 ACACATAGCATGTTACCTCATTAAAAGTCTTAACAAGAAAATTCGATGAAACATAATCTCAATTA
1 ACACATAGCATGTTACCTCATTAAAAGTCTTAACAAGAAAATTCAATGAAACATAATCTCAATTA
56970 AGAGT
66 AGAGT
*
56975 ACACATAGCATGTTACCTCATTAAAAGTCTTAACAAGAAAATTCAATGAAACATAATCTCGATTA
1 ACACATAGCATGTTACCTCATTAAAAGTCTTAACAAGAAAATTCAATGAAACATAATCTCAATTA
*
57040 TGAGT
66 AGAGT
57045 ACACATA
1 ACACATA
57052 TTTTTAATAC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (70 bp):
ACACATAGCATGTTACCTCATTAAAAGTCTTAACAAGAAAATTCAATGAAACATAATCTCAATTA
AGAGT
Found at i:57855 original size:28 final size:28
Alignment explanation
Indices: 57820--57885 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
57810 TGTTAATAAC
57820 ATAAAATTTTCTAATAGAATAAAAACAA
1 ATAAAATTTTCTAATAGAATAAAAACAA
57848 ATAAAATTTTCTAATAGAATAAAAACAA
1 ATAAAATTTTCTAATAGAATAAAAACAA
57876 ATAAAATTTT
1 ATAAAATTTT
57886 AAAGTGGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (28 bp):
ATAAAATTTTCTAATAGAATAAAAACAA
Found at i:64246 original size:16 final size:18
Alignment explanation
Indices: 64214--64247 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
64204 TATTAATGTA
64214 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
64232 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
64248 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:65402 original size:35 final size:35
Alignment explanation
Indices: 65352--65427 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
65342 AATTGAATTT
* * *
65352 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAAAATGA
*
65387 AATTGAATTACTTTGGAAATTGGGGTTTAAAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAAAATGA
65422 AATTGA
1 AATTGA
65428 GGATTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAAAATGA
Found at i:69876 original size:184 final size:184
Alignment explanation
Indices: 69567--69926 Score: 720
Period size: 184 Copynumber: 2.0 Consensus size: 184
69557 AATCTTCCAC
69567 CTTTACTTGGGTAAGATTCTCTTGTCTCTTCGCTTCATCAAATGGATTCTCCTCATCCTCTCCTC
1 CTTTACTTGGGTAAGATTCTCTTGTCTCTTCGCTTCATCAAATGGATTCTCCTCATCCTCTCCTC
69632 AAATGTCCGCCCAATCCCATTTATCTCTTCTCTATCACACCAACTTAGGCCTCGGCTACTCCATC
66 AAATGTCCGCCCAATCCCATTTATCTCTTCTCTATCACACCAACTTAGGCCTCGGCTACTCCATC
69697 GCCGTCGCTCTTGGTTTCCTCCTCCTCCTCTCTATTATCCTCCTTGTCTCTTCG
131 GCCGTCGCTCTTGGTTTCCTCCTCCTCCTCTCTATTATCCTCCTTGTCTCTTCG
69751 CTTTACTTGGGTAAGATTCTCTTGTCTCTTCGCTTCATCAAATGGATTCTCCTCATCCTCTCCTC
1 CTTTACTTGGGTAAGATTCTCTTGTCTCTTCGCTTCATCAAATGGATTCTCCTCATCCTCTCCTC
69816 AAATGTCCGCCCAATCCCATTTATCTCTTCTCTATCACACCAACTTAGGCCTCGGCTACTCCATC
66 AAATGTCCGCCCAATCCCATTTATCTCTTCTCTATCACACCAACTTAGGCCTCGGCTACTCCATC
69881 GCCGTCGCTCTTGGTTTCCTCCTCCTCCTCTCTATTATCCTCCTTG
131 GCCGTCGCTCTTGGTTTCCTCCTCCTCCTCTCTATTATCCTCCTTG
69927 CTTCCTACAT
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 176 1.00
ACGTcount: A:0.15, C:0.36, G:0.11, T:0.37
Consensus pattern (184 bp):
CTTTACTTGGGTAAGATTCTCTTGTCTCTTCGCTTCATCAAATGGATTCTCCTCATCCTCTCCTC
AAATGTCCGCCCAATCCCATTTATCTCTTCTCTATCACACCAACTTAGGCCTCGGCTACTCCATC
GCCGTCGCTCTTGGTTTCCTCCTCCTCCTCTCTATTATCCTCCTTGTCTCTTCG
Found at i:79516 original size:47 final size:47
Alignment explanation
Indices: 79462--79556 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
79452 ATATATAGAG
* *
79462 ATAGTCTTTTAATTGAGGGAAGATTATTGAGCCATTAAACTATTACT
1 ATAGTCTTTTAATTGAGGAAAGATTATTGAACCATTAAACTATTACT
*
79509 ATAGTCTTTTAATTGAGGAAAGATTATTGAATCATTAAACTATTACT
1 ATAGTCTTTTAATTGAGGAAAGATTATTGAACCATTAAACTATTACT
79556 A
1 A
79557 AAAGTGGTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (47 bp):
ATAGTCTTTTAATTGAGGAAAGATTATTGAACCATTAAACTATTACT
Found at i:79812 original size:15 final size:15
Alignment explanation
Indices: 79789--79818 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
79779 ACATTACCCT
*
79789 CCCCGCATCCGCCCG
1 CCCCACATCCGCCCG
79804 CCCCACATCCGCCCG
1 CCCCACATCCGCCCG
79819 TCCAGCTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.67, G:0.17, T:0.07
Consensus pattern (15 bp):
CCCCACATCCGCCCG
Found at i:81270 original size:2 final size:2
Alignment explanation
Indices: 81263--81300 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
81253 TTTAAAACTA
81263 AT AT AT AT AT 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 AT AT AT AT AT
81301 TTAAAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82984 original size:23 final size:23
Alignment explanation
Indices: 82953--83014 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
82943 ATACAGAGAA
*
82953 AAACATGTCATAAAGGCAAAGAT
1 AAACATGTCATAAAGACAAAGAT
* *
82976 AAACGTGTCAAAAAGACAAAGAT
1 AAACATGTCATAAAGACAAAGAT
82999 AAACATGTCATAAAGA
1 AAACATGTCATAAAGA
83015 TATAGAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.55, C:0.13, G:0.16, T:0.16
Consensus pattern (23 bp):
AAACATGTCATAAAGACAAAGAT
Found at i:83703 original size:15 final size:16
Alignment explanation
Indices: 83685--83723 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
83675 TATATTCAAT
*
83685 TTTTTAGTATT-TTTA
1 TTTTTAATATTGTTTA
83700 TTTTTAATATTGTTTA
1 TTTTTAATATTGTTTA
*
83716 TATTTAAT
1 TTTTTAAT
83724 TTTTTGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTTTAATATTGTTTA
Found at i:83715 original size:16 final size:15
Alignment explanation
Indices: 83685--83728 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
83675 TATATTCAAT
*
83685 TTTTTAGTATTTTTA
1 TTTTTAATATTTTTA
83700 TTTTTAATATTGTTTA
1 TTTTTAATATT-TTTA
*
83716 TATTTAAT-TTTTT
1 TTTTTAATATTTTT
83729 GAATACATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 3 0.12
15 12 0.46
16 11 0.42
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (15 bp):
TTTTTAATATTTTTA
Found at i:84404 original size:18 final size:18
Alignment explanation
Indices: 84381--84428 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
84371 AAATTGTCCT
*
84381 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
84399 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
84416 TATTTATATATTT
1 TA-TTATATATTT
84429 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:85310 original size:18 final size:18
Alignment explanation
Indices: 85287--85339 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
85277 CTAATCAATC
85287 ATTTATATATTTT-ATAAT
1 ATTTATATATTTTCAT-AT
85305 ATTTAT-TACTTTTCATAT
1 ATTTATATA-TTTTCATAT
85323 ATTTATA-ATATTTCATA
1 ATTTATATAT-TTTCATA
85340 CATCTTACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.10
18 26 0.84
19 2 0.06
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTATATATTTTCATAT
Found at i:90034 original size:22 final size:22
Alignment explanation
Indices: 89984--90036 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
89974 CCAACTTTTG
* *
89984 AAATTTTATTATTTTTAATACT
1 AAATTTTATTATTATAAATACT
* * *
90006 GATTTTTATTATTATAAATATT
1 AAATTTTATTATTATAAATACT
90028 AAATTTTAT
1 AAATTTTAT
90037 GTTAAGTAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
AAATTTTATTATTATAAATACT
Found at i:108050 original size:25 final size:25
Alignment explanation
Indices: 108021--108068 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
108011 ACTTATTTTA
*
108021 TAGGCTTTCTTCCAACTAAAGTTAC
1 TAGGCTTTCTTCCAAATAAAGTTAC
*
108046 TAGGCTTTCTTGCAAATAAAGTT
1 TAGGCTTTCTTCCAAATAAAGTT
108069 TTTCATTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (25 bp):
TAGGCTTTCTTCCAAATAAAGTTAC
Found at i:113487 original size:74 final size:76
Alignment explanation
Indices: 113338--113489 Score: 184
Period size: 74 Copynumber: 2.0 Consensus size: 76
113328 TGAAACGGGT
* * * * *
113338 ACAAATAAAATTTCAAGGTGGGCACCGTCCGTAAAATAAGTAACTAATCGAATAAAACTTAAATT
1 ACAAATAAAATTTCAAGGTGGACACCGTCAGTAAAATAAGTAACTAAACGAAGAAAAATTAAATT
*
113403 TCAGGGTGGAC
66 TCAGGATGGAC
* * **
113414 ACAAA-AAAATTT-AAGGTGGACACCTTCAGTAAAATTAGTAACTAAACGAAGAAAAATTGGA-T
1 ACAAATAAAATTTCAAGGTGGACACCGTCAGTAAAATAAGTAACTAAACGAAGAAAAATTAAATT
113476 TCTAGGATGGAC
66 TC-AGGATGGAC
113488 AC
1 AC
113490 GTGCCACCTT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
73 3 0.05
74 50 0.77
75 7 0.11
76 5 0.08
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.23
Consensus pattern (76 bp):
ACAAATAAAATTTCAAGGTGGACACCGTCAGTAAAATAAGTAACTAAACGAAGAAAAATTAAATT
TCAGGATGGAC
Found at i:117868 original size:18 final size:18
Alignment explanation
Indices: 117847--117911 Score: 112
Period size: 18 Copynumber: 3.6 Consensus size: 18
117837 TACGTGGACC
*
117847 TACGGGATATAGTGGTCT
1 TACGGGACATAGTGGTCT
117865 TACGGGACATAGTGGTCT
1 TACGGGACATAGTGGTCT
*
117883 TACGGGACATAGTGGTCC
1 TACGGGACATAGTGGTCT
117901 TACGGGACATA
1 TACGGGACATA
117912 TGTGTTCTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (18 bp):
TACGGGACATAGTGGTCT
Found at i:117921 original size:18 final size:17
Alignment explanation
Indices: 117846--117922 Score: 100
Period size: 18 Copynumber: 4.3 Consensus size: 17
117836 CTACGTGGAC
*
117846 CTACGGGATATAGTGGT
1 CTACGGGACATAGTGGT
117863 CTTACGGGACATAGTGGT
1 C-TACGGGACATAGTGGT
117881 CTTACGGGACATAGTGGT
1 C-TACGGGACATAGTGGT
*
117899 CCTACGGGACATATGTGTT
1 -CTACGGGACATA-GTGGT
117918 CTACG
1 CTACG
117923 TGGTCCTACG
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
17 1 0.02
18 49 0.89
19 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (17 bp):
CTACGGGACATAGTGGT
Found at i:117950 original size:28 final size:28
Alignment explanation
Indices: 117894--117950 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
117884 ACGGGACATA
*
117894 GTGGTCCTACGGGACATATGTGTTCTAC
1 GTGGTCCTACGGGACATATGTGGTCTAC
117922 GTGGTCCTACGGGACATA-GTGGTCGTAC
1 GTGGTCCTACGGGACATATGTGGTC-TAC
117950 G
1 G
117951 GGACAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.18, C:0.21, G:0.33, T:0.28
Consensus pattern (28 bp):
GTGGTCCTACGGGACATATGTGGTCTAC
Found at i:120338 original size:34 final size:34
Alignment explanation
Indices: 120300--120369 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
120290 AAATGAAATA
120300 AACAGTAAGTCAATCAAGCTAGAAACTTTAACCG
1 AACAGTAAGTCAATCAAGCTAGAAACTTTAACCG
120334 AACAGTAAGTCAATCAAGCTAGAAACTTTAACCG
1 AACAGTAAGTCAATCAAGCTAGAAACTTTAACCG
120368 AA
1 AA
120370 AAAAGGTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (34 bp):
AACAGTAAGTCAATCAAGCTAGAAACTTTAACCG
Done.