Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001045.1 Hibiscus syriacus cultivar Beakdansim tig00002073_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: 77298
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3205 original size:21 final size:21
Alignment explanation
Indices: 3154--3206 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3144 ATTCTGACTA
3154 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * **
3175 TCCCGTTGCGATTTTCTTAAT
1 TCGCATTGCGATTTTCCAAAT
*
3196 TCGCAATGCGA
1 TCGCATTGCGA
3207 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:3221 original size:20 final size:20
Alignment explanation
Indices: 3196--3328 Score: 221
Period size: 20 Copynumber: 6.7 Consensus size: 20
3186 TTTTCTTAAT
3196 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
3216 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
3236 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
3256 TCACAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
3276 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
3296 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
3316 TCACAACGCGAAT
1 TCGCAATGCGAAT
3329 CTGACTATCG
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 105 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:3342 original size:20 final size:20
Alignment explanation
Indices: 3328--3397 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
3318 ACAACGCGAA
3328 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
3348 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
*
3368 TCTGACTATCGCAACGCGAT
1 TCTGACTATCGCAACGAGAT
3388 TCTGACTATC
1 TCTGACTATC
3398 ACAATACTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
TCTGACTATCGCAACGAGAT
Found at i:3363 original size:40 final size:40
Alignment explanation
Indices: 3319--3397 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
3309 ACGTAAATCA
*
3319 CAACGCGAATCTGACTATCGCAACGAGATTCTGACTATCG
1 CAACGAGAATCTGACTATCGCAACGAGATTCTGACTATCG
* *
3359 CAACGAGATTCTGACTATCGCAACGCGATTCTGACTATC
1 CAACGAGAATCTGACTATCGCAACGAGATTCTGACTATC
3398 ACAATACTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (40 bp):
CAACGAGAATCTGACTATCGCAACGAGATTCTGACTATCG
Found at i:3819 original size:33 final size:34
Alignment explanation
Indices: 3762--3837 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 34
3752 TTTAGTTTCG
3762 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
3796 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
3829 CGTTGCGAT
1 CGTTGCGAT
3838 AGTCTGTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 28 0.67
34 14 0.33
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:3836 original size:14 final size:14
Alignment explanation
Indices: 3784--3837 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
3774 CATTTTCGCA
3784 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
3798 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
3815 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
3831 TTGCGAT
1 TTGCGAT
3838 AGTCTGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:3961 original size:14 final size:14
Alignment explanation
Indices: 3942--3978 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3932 ACATCAATTA
3942 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3956 ACAAATCATCTTTT
1 ACAAATCAACATTT
3970 ACAAATCAA
1 ACAAATCAA
3979 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:5927 original size:20 final size:20
Alignment explanation
Indices: 5902--5970 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
5892 GAAACTTAAA
*
5902 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
5922 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
5942 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
5962 ATCGCAACG
1 ATCGCAACG
5971 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:6044 original size:20 final size:20
Alignment explanation
Indices: 6019--6211 Score: 216
Period size: 20 Copynumber: 10.3 Consensus size: 20
6009 CTCTCGTTGA
**
6019 GATAGTCAAATTCGCATTGC
1 GATAGTCATTTTCGCATTGC
6039 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
6059 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
6079 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
6099 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
*
6119 GAT--T--TTTTTG--TTGC
1 GATAGTCATTTTCGCATTGC
**
6133 GATTTTCA-TTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
*
6152 GAT--TC--TCTCG--TTGC
1 GATAGTCATTTTCGCATTGC
6166 GATAGTCATTTTCG-AGTTGC
1 GATAGTCATTTTCGCA-TTGC
*
6186 GATAGTTATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
6206 GATAGT
1 GATAGT
6212 AAACTATTCT
Statistics
Matches: 153, Mismatches: 7, Indels: 26
0.82 0.04 0.14
Matches are distributed among these distances:
14 14 0.09
16 12 0.08
17 6 0.04
18 5 0.03
19 7 0.05
20 108 0.71
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (20 bp):
GATAGTCATTTTCGCATTGC
Found at i:8105 original size:20 final size:20
Alignment explanation
Indices: 8082--8122 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
8072 TCTGAAACTT
8082 AAAATCACAACACGAAAATG
1 AAAATCACAACACGAAAATG
*
8102 AAAATCGCAACACGAAAATG
1 AAAATCACAACACGAAAATG
8122 A
1 A
8123 CTACCGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (20 bp):
AAAATCACAACACGAAAATG
Found at i:8137 original size:20 final size:20
Alignment explanation
Indices: 8107--8158 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
8097 AAATGAAAAT
*
8107 CGCAACACGAAAATGACTAC
1 CGCAACGCGAAAATGACTAC
* ** *
8127 CGTAACGCGAATTTGACTAT
1 CGCAACGCGAAAATGACTAC
8147 CGCAACGCGAAA
1 CGCAACGCGAAA
8159 TGAAAATCGC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.15
Consensus pattern (20 bp):
CGCAACGCGAAAATGACTAC
Found at i:8573 original size:22 final size:22
Alignment explanation
Indices: 8509--8574 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
8499 TGACCGTGAA
* *
8509 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
8531 TGATATCGTCGGAGATTGGGAC
1 TGATTTCGTCGGAGATGGGGAC
8553 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
8575 GGATGTCGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.21, C:0.15, G:0.38, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:8793 original size:20 final size:20
Alignment explanation
Indices: 8770--8822 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
8760 CGATAGTCAG
*
8770 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
8790 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
8810 ATTCGCATTGCGA
1 ATTCGCATTGCGA
8823 ATTAGGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:8864 original size:21 final size:21
Alignment explanation
Indices: 8812--8864 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
8802 ATTTACGTAT
*
8812 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
8833 TCGAAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
8854 TCGCAATGCGA
1 TCGCAATGCGA
8865 TAGTCAGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:15341 original size:26 final size:26
Alignment explanation
Indices: 15312--15395 Score: 102
Period size: 26 Copynumber: 3.3 Consensus size: 26
15302 TACTTGTTTT
15312 TCATTTATATATTATTAAACTTGATG
1 TCATTTATATATTATTAAACTTGATG
* * * *
15338 TCATTTATTTA-AAGGTAAAC-T-ATT
1 TCATTTATATATTA-TTAAACTTGATG
15362 TCATTTATATATTATTAAACTTGATG
1 TCATTTATATATTATTAAACTTGATG
15388 TCATTTAT
1 TCATTTAT
15396 TTAAGGGTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
24 17 0.37
25 4 0.09
26 25 0.54
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.50
Consensus pattern (26 bp):
TCATTTATATATTATTAAACTTGATG
Found at i:15368 original size:50 final size:50
Alignment explanation
Indices: 15310--15406 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
15300 TTTACTTGTT
15310 TTTCATTTATATATTATTAAACTTGATGTCATTTATTTAAAGGTAAACTA
1 TTTCATTTATATATTATTAAACTTGATGTCATTTATTTAAAGGTAAACTA
*
15360 TTTCATTTATATATTATTAAACTTGATGTCATTTATTTAAGGGTAAA
1 TTTCATTTATATATTATTAAACTTGATGTCATTTATTTAAAGGTAAA
15407 GTATATAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.48
Consensus pattern (50 bp):
TTTCATTTATATATTATTAAACTTGATGTCATTTATTTAAAGGTAAACTA
Found at i:15406 original size:26 final size:26
Alignment explanation
Indices: 15327--15406 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 26
15317 TATATATTAT
15327 TAAACTTGATGTCATTTATTTAAAGG
1 TAAACTTGATGTCATTTATTTAAAGG
* * * *
15353 TAAAC-T-ATTTCATTTATATATTA-T
1 TAAACTTGATGTCATTTATTTA-AAGG
*
15377 TAAACTTGATGTCATTTATTTAAGGG
1 TAAACTTGATGTCATTTATTTAAAGG
15403 TAAA
1 TAAA
15407 GTATATAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
24 17 0.41
25 3 0.07
26 21 0.51
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (26 bp):
TAAACTTGATGTCATTTATTTAAAGG
Found at i:24919 original size:17 final size:17
Alignment explanation
Indices: 24897--24930 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
24887 AATTTCCAAC
24897 TTGCCAACTTAATTTCA
1 TTGCCAACTTAATTTCA
24914 TTGCCAACTTAATTTCA
1 TTGCCAACTTAATTTCA
24931 AGCCAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (17 bp):
TTGCCAACTTAATTTCA
Found at i:30636 original size:92 final size:94
Alignment explanation
Indices: 30511--30683 Score: 296
Period size: 92 Copynumber: 1.9 Consensus size: 94
30501 GCACCAGCCA
* *
30511 GGCATAACTTATGCCACACCAAGCTACGGACTGCACCACACAGTAGAGGT-TCGTACCTCTCCTT
1 GGCATAACTTATGCCACACCAAGCCACGGACTGCACCACACAGTACAGGTATCGTACCTCTCCTT
30575 GCATTTCTTTTCTTTTCTTTTTGTTTTCG
66 GCATTTCTTTTCTTTTCTTTTTGTTTTCG
* *
30604 GGCATAAC-TATGCCACACCAAGCCACTGACTGCACCACACAGTACAGGTATCGTATCTCTCCTT
1 GGCATAACTTATGCCACACCAAGCCACGGACTGCACCACACAGTACAGGTATCGTACCTCTCCTT
30668 GCATTTCTTTTCTTTT
66 GCATTTCTTTTCTTTT
30684 TGTTTTTATG
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 38 0.51
93 37 0.49
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.34
Consensus pattern (94 bp):
GGCATAACTTATGCCACACCAAGCCACGGACTGCACCACACAGTACAGGTATCGTACCTCTCCTT
GCATTTCTTTTCTTTTCTTTTTGTTTTCG
Found at i:33001 original size:24 final size:24
Alignment explanation
Indices: 32974--33126 Score: 139
Period size: 24 Copynumber: 6.4 Consensus size: 24
32964 TATATCAAAA
* * *
32974 ATCAAATCATAATTCACGTCAAGT
1 ATCATATCATAATCCAAGTCAAGT
* *
32998 ATCATATCAAAATCCAGGTCAAGT
1 ATCATATCATAATCCAAGTCAAGT
*
33022 ATCAGATCATAATCCAAGTCAAGT
1 ATCATATCATAATCCAAGTCAAGT
* *
33046 ATCATATCAGAATCCATGTCATA-T
1 ATCATATCATAATCCAAGTCA-AGT
* * *
33070 ATCAGATCAGAATCCATGTC-AGAT
1 ATCATATCATAATCCAAGTCAAG-T
* * *
33094 ATCATAGCAGAATCCATGTCAAGT
1 ATCATATCATAATCCAAGTCAAGT
*
33118 ATCAGATCA
1 ATCATATCA
33127 GAAATCAAAT
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
22 1 0.01
24 106 0.96
25 3 0.03
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (24 bp):
ATCATATCATAATCCAAGTCAAGT
Found at i:33050 original size:48 final size:48
Alignment explanation
Indices: 32974--33126 Score: 202
Period size: 48 Copynumber: 3.2 Consensus size: 48
32964 TATATCAAAA
* * * * *
32974 ATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGTCAAGT
1 ATCAGATCATAATCCAAGTCAAGTATCATATCAGAATCCATGTCAAGT
33022 ATCAGATCATAATCCAAGTCAAGTATCATATCAGAATCCATGTCATA-T
1 ATCAGATCATAATCCAAGTCAAGTATCATATCAGAATCCATGTCA-AGT
* * *
33070 ATCAGATCAGAATCCATGTC-AGATATCATAGCAGAATCCATGTCAAGT
1 ATCAGATCATAATCCAAGTCAAG-TATCATATCAGAATCCATGTCAAGT
33118 ATCAGATCA
1 ATCAGATCA
33127 GAAATCAAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
47 3 0.03
48 90 0.96
49 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (48 bp):
ATCAGATCATAATCCAAGTCAAGTATCATATCAGAATCCATGTCAAGT
Found at i:33128 original size:24 final size:24
Alignment explanation
Indices: 32991--33129 Score: 174
Period size: 24 Copynumber: 5.8 Consensus size: 24
32981 CATAATTCAC
* * *
32991 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
* *
33015 GTCAAGTATCAGATCATAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
33039 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
33063 GTCATA-TATCAGATCAGAATCCAT
1 GTCA-AGTATCAGATCAGAATCCAT
* *
33087 GTC-AGATATCATAGCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
33111 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
33130 ATCAAATCGA
Statistics
Matches: 100, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
22 1 0.01
24 96 0.96
25 3 0.03
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:34146 original size:26 final size:26
Alignment explanation
Indices: 34117--34181 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
34107 TTTATTCTAT
*
34117 TCATTTCAGAGCTCGAGGATATCCAA
1 TCATTCCAGAGCTCGAGGATATCCAA
*
34143 TCATTCCTGAGCTCGAGGATATCCAA
1 TCATTCCAGAGCTCGAGGATATCCAA
* *
34169 TTATTCCTGAGCT
1 TCATTCCAGAGCT
34182 TGGTGATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (26 bp):
TCATTCCAGAGCTCGAGGATATCCAA
Found at i:34190 original size:26 final size:26
Alignment explanation
Indices: 34125--34181 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
34115 ATTCATTTCA
34125 GAGCTCGAGGATATCCAATCATTCCT
1 GAGCTCGAGGATATCCAATCATTCCT
*
34151 GAGCTCGAGGATATCCAATTATTCCT
1 GAGCTCGAGGATATCCAATCATTCCT
34177 GAGCT
1 GAGCT
34182 TGGTGATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (26 bp):
GAGCTCGAGGATATCCAATCATTCCT
Found at i:37544 original size:271 final size:271
Alignment explanation
Indices: 37061--37606 Score: 1092
Period size: 271 Copynumber: 2.0 Consensus size: 271
37051 GATTAAATTA
37061 ATATTATGAGTTAATCGAATTAAAGTTTTTTAAAATTTATATTAAAAGAACATTACTCTCTTTAA
1 ATATTATGAGTTAATCGAATTAAAGTTTTTTAAAATTTATATTAAAAGAACATTACTCTCTTTAA
37126 AAAAAATACCATTCCTTTTCTTTAACATACAACCATTAATTTAAAAAATAAATATTGTTATACAA
66 AAAAAATACCATTCCTTTTCTTTAACATACAACCATTAATTTAAAAAATAAATATTGTTATACAA
37191 TTCGCCGTTTATTTATATTGTGGGTGTTTATGTTGTATGAATTTTGATATAATAATTATTTTTAA
131 TTCGCCGTTTATTTATATTGTGGGTGTTTATGTTGTATGAATTTTGATATAATAATTATTTTTAA
37256 TGTAAATTTGAATCGCTAGTATATTCTTTTCATATTTGTAACCTAATAGCACTGGAACTATAATA
196 TGTAAATTTGAATCGCTAGTATATTCTTTTCATATTTGTAACCTAATAGCACTGGAACTATAATA
37321 TATATATATAT
261 TATATATATAT
37332 ATATTATGAGTTAATCGAATTAAAGTTTTTTAAAATTTATATTAAAAGAACATTACTCTCTTTAA
1 ATATTATGAGTTAATCGAATTAAAGTTTTTTAAAATTTATATTAAAAGAACATTACTCTCTTTAA
37397 AAAAAATACCATTCCTTTTCTTTAACATACAACCATTAATTTAAAAAATAAATATTGTTATACAA
66 AAAAAATACCATTCCTTTTCTTTAACATACAACCATTAATTTAAAAAATAAATATTGTTATACAA
37462 TTCGCCGTTTATTTATATTGTGGGTGTTTATGTTGTATGAATTTTGATATAATAATTATTTTTAA
131 TTCGCCGTTTATTTATATTGTGGGTGTTTATGTTGTATGAATTTTGATATAATAATTATTTTTAA
37527 TGTAAATTTGAATCGCTAGTATATTCTTTTCATATTTGTAACCTAATAGCACTGGAACTATAATA
196 TGTAAATTTGAATCGCTAGTATATTCTTTTCATATTTGTAACCTAATAGCACTGGAACTATAATA
37592 TATATATATAT
261 TATATATATAT
37603 ATAT
1 ATAT
37607 ATATATATAT
Statistics
Matches: 275, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
271 275 1.00
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (271 bp):
ATATTATGAGTTAATCGAATTAAAGTTTTTTAAAATTTATATTAAAAGAACATTACTCTCTTTAA
AAAAAATACCATTCCTTTTCTTTAACATACAACCATTAATTTAAAAAATAAATATTGTTATACAA
TTCGCCGTTTATTTATATTGTGGGTGTTTATGTTGTATGAATTTTGATATAATAATTATTTTTAA
TGTAAATTTGAATCGCTAGTATATTCTTTTCATATTTGTAACCTAATAGCACTGGAACTATAATA
TATATATATAT
Found at i:37596 original size:2 final size:2
Alignment explanation
Indices: 37585--37653 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
37575 GCACTGGAAC
37585 TA TA -A TA TA 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 TA TA TA TA TA
37626 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
37654 CTTTTAAGAA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39847 original size:31 final size:31
Alignment explanation
Indices: 39812--39894 Score: 123
Period size: 31 Copynumber: 2.7 Consensus size: 31
39802 GTGTTCAAGT
* *
39812 AATTATGTATATAATGTATTTTCTTTTATAA
1 AATTATGTATATAATATATTTTCTTTCATAA
39843 AATTATGTATATAATATATTTTCTTTCATAA
1 AATTATGTATATAATATATTTTCTTTCATAA
*
39874 AATTACGTATTATAA-ATATTT
1 AATTATGTA-TATAATATATTT
39895 CTCAAACAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
31 43 0.90
32 5 0.10
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (31 bp):
AATTATGTATATAATATATTTTCTTTCATAA
Found at i:40554 original size:17 final size:17
Alignment explanation
Indices: 40497--40555 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
40487 AATTGAGTAT
*
40497 ATTATTATAATATTTAAA
1 ATTATTATATTA-TTAAA
* * *
40515 AATATAATATTATATTAA
1 ATTATTATATTAT-TAAA
40533 A-TATTATATTATTAAA
1 ATTATTATATTATTAAA
40549 ATTATTA
1 ATTATTA
40556 ATAAATATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
16 4 0.12
17 16 0.48
18 13 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTATTATATTATTAAA
Found at i:41036 original size:3 final size:3
Alignment explanation
Indices: 41028--41053 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41018 CTTATATGTC
41028 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
41054 TTGTTGCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41355 original size:3 final size:3
Alignment explanation
Indices: 41349--41387 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
41339 GAAAGTGATG
41349 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41388 CGAAAACAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:49162 original size:21 final size:20
Alignment explanation
Indices: 49136--49181 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
49126 AGTGAATGTC
* * *
49136 AATTACAGATATTATATTGTA
1 AATTACAAATATAAAATT-TA
49157 AATTACAAATATAAAATTTA
1 AATTACAAATATAAAATTTA
49177 AATTA
1 AATTA
49182 TATTTACACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (20 bp):
AATTACAAATATAAAATTTA
Found at i:49890 original size:6 final size:6
Alignment explanation
Indices: 49879--49918 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
49869 GCGAAGGTAT
49879 GAAATA GAAATA GAAATA GAAATA GAAATA GAAATA GAAA
1 GAAATA GAAATA GAAATA GAAATA GAAATA GAAATA GAAA
49919 GATACTGCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (6 bp):
GAAATA
Found at i:56082 original size:30 final size:30
Alignment explanation
Indices: 55873--56065 Score: 359
Period size: 30 Copynumber: 6.4 Consensus size: 30
55863 TCCGAAGGAC
55873 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
55903 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
55933 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
55963 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
55993 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
56023 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
56053 CTATCCATAGGTC
1 CTATCCAGAGGTC
56066 CCGAAGAACC
Statistics
Matches: 158, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 158 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:56105 original size:31 final size:31
Alignment explanation
Indices: 56051--56143 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
56041 GATCCTCGGT
* *
56051 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
56082 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
56113 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
56144 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:60609 original size:30 final size:30
Alignment explanation
Indices: 60310--60592 Score: 566
Period size: 30 Copynumber: 9.4 Consensus size: 30
60300 TCCGAATGAC
60310 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
60340 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
60370 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
60400 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
60430 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
60460 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
60490 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
60520 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
60550 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
60580 CTATCCAGAGGTC
1 CTATCCAGAGGTC
60593 CCGAAGAACC
Statistics
Matches: 253, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 253 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:60975 original size:2 final size:2
Alignment explanation
Indices: 60968--61016 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
60958 ACAACTCAAC
60968 TA TA TA TA TA 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 TA TA TA TA TA
61010 TA TA TA T
1 TA TA TA T
61017 TGTAACATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65738 original size:23 final size:22
Alignment explanation
Indices: 65708--65753 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
65698 AATCTAACCT
* * *
65708 AGAAAATTATGTGGCATTTAAA
1 AGAAAATTAAGAGGCATTGAAA
65730 AGAATAATTAAGAGGCATTGAAA
1 AGAA-AATTAAGAGGCATTGAAA
65753 A
1 A
65754 AAATTACCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.26
Consensus pattern (22 bp):
AGAAAATTAAGAGGCATTGAAA
Found at i:72365 original size:25 final size:25
Alignment explanation
Indices: 72337--72386 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
72327 TCCCTCTGCT
72337 GTGATGGTCGTGTTTTGTTCGTGTA
1 GTGATGGTCGTGTTTTGTTCGTGTA
72362 GTGATGGTCGTGTTTTGTTCGTGTA
1 GTGATGGTCGTGTTTTGTTCGTGTA
72387 CGTGGGGGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.08, C:0.08, G:0.36, T:0.48
Consensus pattern (25 bp):
GTGATGGTCGTGTTTTGTTCGTGTA
Done.