Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005875.1 Hibiscus syriacus cultivar Beakdansim tig00013805_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: 96188
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:272 original size:15 final size:15
Alignment explanation
Indices: 231--272 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
221 CCCCTACAAT
*
231 CCGAAGGACTACATC
1 CCGAAGGACTATATC
246 CCGAAGGACTATATC
1 CCGAAGGACTATATC
*
261 CCGAAAGACTAT
1 CCGAAGGACTAT
273 TATACCTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.17
Consensus pattern (15 bp):
CCGAAGGACTATATC
Found at i:832 original size:64 final size:65
Alignment explanation
Indices: 724--884 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 65
714 TAATGAACGT
* * * * **
724 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGTATTCATTATTAATGGG
* * ** *
788 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGTATTCATTATTAATGGG
*
853 ATGTATCGATGCACTACTTATGCATCGATGCA
1 ATGCATCGATGCACTACTTATGCATCGATGCA
885 TGAATTACAT
Statistics
Matches: 83, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 43 0.52
65 40 0.48
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGTATTCATTATTAATGGG
Found at i:866 original size:65 final size:64
Alignment explanation
Indices: 724--944 Score: 221
Period size: 65 Copynumber: 3.5 Consensus size: 64
714 TAATGAACGT
* * ** * * **
724 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTTATTATTAATGGG
* **
788 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTT-ATTATTAATGGG
* * * * * * *
853 ATGTATCGATGCACTACTTATGCATCGATGCATGAATTACATTTGATGTTTTTATT-TAAAAGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATG-TTTTATTATTAATGGG
* **
917 -TGCATCAATGCACTACCAATGCATCGAT
1 ATGCATCGATGCACTACTTATGCATCGAT
945 ACACCTTCAA
Statistics
Matches: 131, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
63 24 0.18
64 48 0.37
65 55 0.42
66 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTTATTATTAATGGG
Found at i:1970 original size:38 final size:39
Alignment explanation
Indices: 1916--1995 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 39
1906 TGGGAATCTA
*
1916 AAAACAATACTAGTCTATGAACACATAATCCATAATTCT
1 AAAACAATACTAGTCTATGAACACAAAATCCATAATTCT
* *
1955 AAAATAATA-TAGTCTATGAACACAAAATCCATAATTTT
1 AAAACAATACTAGTCTATGAACACAAAATCCATAATTCT
1993 AAA
1 AAA
1996 TGGTAAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 30 0.79
39 8 0.21
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29
Consensus pattern (39 bp):
AAAACAATACTAGTCTATGAACACAAAATCCATAATTCT
Found at i:16410 original size:22 final size:23
Alignment explanation
Indices: 16384--16433 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
16374 TTCACATATT
*
16384 TTAAA-TATATTCAACGTCAAAA
1 TTAAACTATATTAAACGTCAAAA
* * *
16406 TTAAACTATTTTAAATGTCTAAA
1 TTAAACTATATTAAACGTCAAAA
16429 TTAAA
1 TTAAA
16434 ATAAAGAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (23 bp):
TTAAACTATATTAAACGTCAAAA
Found at i:25700 original size:26 final size:26
Alignment explanation
Indices: 25654--25707 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
25644 CTGGTTCCAG
* *
25654 TAGTTGATTTGACCAATTGATTTAAT
1 TAGTTGATTTGACAAACTGATTTAAT
* *
25680 TAGTTGATTTGAGAAACTGATTTGAT
1 TAGTTGATTTGACAAACTGATTTAAT
25706 TA
1 TA
25708 ACTGTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (26 bp):
TAGTTGATTTGACAAACTGATTTAAT
Found at i:25910 original size:20 final size:21
Alignment explanation
Indices: 25882--25925 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
25872 TAAAAATTCC
25882 TTTAGAAAATTAGTGAAT-ATT
1 TTTAGAAAATT-GTGAATAATT
*
25903 TTTA-AAAATTTTGAATAATT
1 TTTAGAAAATTGTGAATAATT
25923 TTT
1 TTT
25926 TTTAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 12 0.57
21 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (21 bp):
TTTAGAAAATTGTGAATAATT
Found at i:30234 original size:42 final size:42
Alignment explanation
Indices: 30186--30325 Score: 147
Period size: 51 Copynumber: 3.1 Consensus size: 42
30176 CCAAATTCCC
*
30186 TTCTGCTTCTGCATCATGTTGGAGCTCTTCTATTTCTCCTCT
1 TTCTGCTTCTGCATCATGTGGGAGCTCTTCTATTTCTCCTCT
* *
30228 TTCTGCTTCTGTTGTTGCTGCATCATGTGGGAGCTCTTCTATTTCTCTTGT
1 TTCTG---C-----TT-CTGCATCATGTGGGAGCTCTTCTATTTCTCCTCT
30279 TTCTGCTTCTGCATCATGTGGGAGCTCTTGC-ATTTCTCCTGCT
1 TTCTGCTTCTGCATCATGTGGGAGCTCTT-CTATTTCTCCT-CT
30322 TTCT
1 TTCT
30326 CCATGTTGTA
Statistics
Matches: 82, Mismatches: 5, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
42 34 0.41
43 8 0.10
45 1 0.01
48 1 0.01
50 2 0.02
51 36 0.44
ACGTcount: A:0.09, C:0.26, G:0.19, T:0.47
Consensus pattern (42 bp):
TTCTGCTTCTGCATCATGTGGGAGCTCTTCTATTTCTCCTCT
Found at i:33124 original size:19 final size:20
Alignment explanation
Indices: 33100--33148 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
33090 ATGCTTAAAA
33100 TATCGATACTTGTAG-AA-AG
1 TATCGATACTT-TAGCAAGAG
* *
33119 TATCGAAACTTTTGCAAGAG
1 TATCGATACTTTAGCAAGAG
33139 TATCGATACT
1 TATCGATACT
33149 CTTGGGCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 12 0.48
20 11 0.44
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (20 bp):
TATCGATACTTTAGCAAGAG
Found at i:34713 original size:41 final size:41
Alignment explanation
Indices: 34601--34714 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 41
34591 CTAACCTATT
* * * *
34601 GCGGCTTTTGTTCAAAAACGCCACTAAAGAACGGTTCTTTT
1 GCGGCGTTTGTTCAAAAACGCCACTAAAGTACGGTTCTGTG
* ** * *
34642 GCGGCGTTTATTCCGAAACGTCACTGAAGTA-GGATTCTGTG
1 GCGGCGTTTGTTCAAAAACGCCACTAAAGTACGG-TTCTGTG
*
34683 GCGGCGTTTGTTTAAAAACGCCACTAAAGTAC
1 GCGGCGTTTGTTCAAAAACGCCACTAAAGTAC
34715 TTATCTGTAG
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
40 2 0.04
41 54 0.96
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTTCAAAAACGCCACTAAAGTACGGTTCTGTG
Found at i:38156 original size:49 final size:50
Alignment explanation
Indices: 38050--38159 Score: 125
Period size: 49 Copynumber: 2.2 Consensus size: 50
38040 TAGGGGTATA
* * *
38050 GTGCGGTGCAGGGGTTGCGCCTTTGCTTTAATTCTGACACAATTATGCAAG
1 GTGCGGTGCAGGGG-TGAGCCTTTACTTTAATTCTGACACAATTATACAAG
* * * *
38101 GCGCGGTGTAGGGG-GAGCCTTTACTTTAAGTT-TGAGACAATTATATAAG
1 GTGCGGTGCAGGGGTGAGCCTTTACTTTAA-TTCTGACACAATTATACAAG
38150 GTGCGGTGCA
1 GTGCGGTGCA
38160 TGGGCCGCGC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
49 35 0.71
50 2 0.04
51 12 0.24
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (50 bp):
GTGCGGTGCAGGGGTGAGCCTTTACTTTAATTCTGACACAATTATACAAG
Found at i:44232 original size:13 final size:12
Alignment explanation
Indices: 44211--44247 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
44201 TGCTTAATCG
44211 AAAAAAAAAATA
1 AAAAAAAAAATA
44223 AAAGAAAAAAATA
1 AAA-AAAAAAATA
*
44236 AAAATAAAAATA
1 AAAAAAAAAATA
44248 TAACGGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (12 bp):
AAAAAAAAAATA
Found at i:48694 original size:33 final size:35
Alignment explanation
Indices: 48639--48723 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
48629 AATATAATTT
*
48639 TAAATAAAACAAACTTACAATAA-G-TATTAAATGG
1 TAAATAAAA-AAAATTACAATAACGATATTAAATGG
*
48673 TAAATAAAAAAAATTACAATAACTGATATTAAATTG
1 TAAATAAAAAAAATTACAATAAC-GATATTAAATGG
*
48709 T-AATAAACAAAATTA
1 TAAATAAAAAAAATTA
48724 ATTAACAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
33 12 0.27
34 9 0.20
35 14 0.31
36 10 0.22
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.28
Consensus pattern (35 bp):
TAAATAAAAAAAATTACAATAACGATATTAAATGG
Found at i:48721 original size:35 final size:33
Alignment explanation
Indices: 48639--48723 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
48629 AATATAATTT
*
48639 TAAATAAAACAAACTTACAATAAGTATTAAATGG
1 TAAAT-AAACAAAATTACAATAAGTATTAAATGG
* *
48673 TAAATAAAAAAAATTACAATAACTGATATTAAATTG
1 TAAATAAACAAAATTACAATAA--G-TATTAAATGG
48709 T-AATAAACAAAATTA
1 TAAATAAACAAAATTA
48724 ATTAACAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
33 15 0.34
34 5 0.11
35 14 0.32
36 10 0.23
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.28
Consensus pattern (33 bp):
TAAATAAACAAAATTACAATAAGTATTAAATGG
Found at i:48829 original size:6 final size:6
Alignment explanation
Indices: 48818--48849 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
48808 AATAAACAAG
48818 TAAATA TAAATA TAAATA T-AATA -AAATA TAAA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAA
48850 AAAATGTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 8 0.33
6 16 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TAAATA
Found at i:56358 original size:2 final size:2
Alignment explanation
Indices: 56351--56376 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56341 GTCACAAGGG
56351 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
56377 CGTACAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59891 original size:12 final size:12
Alignment explanation
Indices: 59874--59902 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
59864 TACGGCATTA
59874 AGAAGAAGAAGG
1 AGAAGAAGAAGG
59886 AGAAGAAGAAGG
1 AGAAGAAGAAGG
59898 AGAAG
1 AGAAG
59903 CAAATAATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
AGAAGAAGAAGG
Found at i:68336 original size:71 final size:72
Alignment explanation
Indices: 68247--68395 Score: 291
Period size: 71 Copynumber: 2.1 Consensus size: 72
68237 TTAGGAGTAG
68247 AGTTCATACGCTTGTATATATGTTGATGATTAGCATCTCCTTCTCCCTTGTTGCAGGGTCCAGTC
1 AGTTCATACGCTTGTATATATGTTGATGATTAGCATCTCCTTCTCCCTTGTTGCAGGGTCCAGTC
68312 AAATCAT
66 AAATCAT
68319 AGTTC-TACGCTTGTATATATGTTGATGATTAGCATCTCCTTCTCCCTTGTTGCAGGGTCCAGTC
1 AGTTCATACGCTTGTATATATGTTGATGATTAGCATCTCCTTCTCCCTTGTTGCAGGGTCCAGTC
68383 AAATCAT
66 AAATCAT
68390 AGTTCA
1 AGTTCA
68396 ATATTATCAG
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
71 71 0.93
72 5 0.07
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (72 bp):
AGTTCATACGCTTGTATATATGTTGATGATTAGCATCTCCTTCTCCCTTGTTGCAGGGTCCAGTC
AAATCAT
Found at i:69934 original size:14 final size:14
Alignment explanation
Indices: 69915--69946 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
69905 GGATAAAATC
69915 ATGTTGAATCATTG
1 ATGTTGAATCATTG
69929 ATGTTGAATCATTG
1 ATGTTGAATCATTG
69943 ATGT
1 ATGT
69947 GCGTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (14 bp):
ATGTTGAATCATTG
Found at i:77432 original size:23 final size:23
Alignment explanation
Indices: 77402--77453 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
77392 TTTTTTTCAA
77402 AAGCTTTGAGAAAAAATGTTTAC
1 AAGCTTTGAGAAAAAATGTTTAC
77425 AAGCTTTGAGAAAAAATGTTTAC
1 AAGCTTTGAGAAAAAATGTTTAC
77448 AAGCTT
1 AAGCTT
77454 AATTAGGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (23 bp):
AAGCTTTGAGAAAAAATGTTTAC
Found at i:78476 original size:16 final size:17
Alignment explanation
Indices: 78450--78497 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
78440 TAGTATAACA
*
78450 AAAACCAACCCAAATTG
1 AAAATCAACCCAAATTG
* *
78467 -AAATCAACCCGAATCG
1 AAAATCAACCCAAATTG
78483 AAAAT-AACCCAAATT
1 AAAATCAACCCAAATT
78498 TAATTTACCA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.52, C:0.27, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAATCAACCCAAATTG
Found at i:87940 original size:30 final size:31
Alignment explanation
Indices: 87891--88013 Score: 189
Period size: 30 Copynumber: 4.0 Consensus size: 31
87881 CCCGAAGGAC
*
87891 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
87922 CAGTCCATATGT-CCGAAGAACGTAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
87952 CAAT-CATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
87982 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
88013 C
1 C
88014 CCTCGACCCT
Statistics
Matches: 85, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
29 7 0.08
30 40 0.47
31 37 0.44
32 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:90048 original size:245 final size:250
Alignment explanation
Indices: 89608--90173 Score: 937
Period size: 245 Copynumber: 2.3 Consensus size: 250
89598 GGGATGTTAC
89608 ATCATTACCCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTT
1 ATCATTACCCTATTATGTCACTTATGTCCCCCGAGAAC-ATTCATGTCAATACCTATTATTCCTT
*
89673 AGGGGACCTGTGACGGCGCGTTCCCGGGGGCGCCTTCCATTATTTAGTCAGAGAATATGTTATCA
65 A-GGGACCTGTGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTAGTCAGAGAATATGTTATCA
*
89738 TTACCCTATTATGTCACTTATGTCCCCCGATAACTATTCATGTCAATACTATTATTCCCTAGGGG
129 TTACCCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACTATTATTCCCTAGGGG
* *
89803 ACCGTGAAGGCGTGTTCCCGGG-G-GCGCCTTCTATTATTTTGTCAGAGAATATGTT
194 ACCGTGAAGGCGCGTTCCCGGGTGCGCGCCTTCCATTATTTTGTCAGAGAATATGTT
** * *
89858 ATCATTACCCTATTATGTCACTTATGTGTCCCGAAAAC-TT-ATGTCAATACATATTATTCCTTA
1 ATCATTACCCTATTATGTCACTTATGTCCCCCGAGAACATTCATGTCAATACCTATTATTCCTTA
*
89921 GGGACC-GTGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATT
66 GGGACCTGTGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTAGTCAGAGAATATGTTATCATT
* *
89985 ACCCTATTATGTCACTTATGTCCCCCGGGAACTATT-ATGTCAATACCTATTATTCCTTAGGGGA
131 ACCCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATA-CTATTATTCCCTAGGGGA
*
90049 CCGTGAAGGCGCGTTCCCGGGTGCGCGCCTTCCATTATTTTGTCAGATAATATGTT
195 CCGTGAAGGCGCGTTCCCGGGTGCGCGCCTTCCATTATTTTGTCAGAGAATATGTT
*
90105 ATCATTACCCTATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTT
1 ATCATTACCCTATTATGTCACTTATGTCCCCCGAGAAC-ATTCATGTCAATACCTATTATTCCTT
90170 AGGG
65 AGGG
90174 GACTTTAAAG
Statistics
Matches: 293, Mismatches: 17, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
244 9 0.03
245 127 0.43
246 7 0.02
247 86 0.29
248 2 0.01
249 2 0.01
250 60 0.20
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (250 bp):
ATCATTACCCTATTATGTCACTTATGTCCCCCGAGAACATTCATGTCAATACCTATTATTCCTTA
GGGACCTGTGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTAGTCAGAGAATATGTTATCATT
ACCCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACTATTATTCCCTAGGGGAC
CGTGAAGGCGCGTTCCCGGGTGCGCGCCTTCCATTATTTTGTCAGAGAATATGTT
Found at i:90191 original size:126 final size:125
Alignment explanation
Indices: 89608--90176 Score: 952
Period size: 126 Copynumber: 4.6 Consensus size: 125
89598 GGGATGTTAC
89608 ATCATTACCCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTT
1 ATCATTACCCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTT
* *
89673 AGGGGACCTGTGACGGCGCGTTCCCGGGGGCGCCTTCCATTATTTAGTCAGAGAATATGTT
66 AGGGGACC-GTGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTT
* *
89734 ATCATTACCCTATTATGTCACTTATGTCCCCCGATAACTATTCATGTCAATA-CTATTATTCCCT
1 ATCATTACCCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTT
* *
89798 AGGGGACCGTGAAGGCGTGTTCCCGGGGGCGCCTTCTATTATTTTGTCAGAGAATATGTT
66 AGGGGACCGTGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTT
** * *
89858 ATCATTACCCTATTATGTCACTTATGTGTCCCGAAAAC--TT-ATGTCAATACATATTATTCCTT
1 ATCATTACCCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTT
89920 A-GGGACCGTGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTT
66 AGGGGACCGTGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTT
*
89979 ATCATTACCCTATTATGTCACTTATGTCCCCCGGGAACTATT-ATGTCAATACCTATTATTCCTT
1 ATCATTACCCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTT
*
90043 AGGGGACCGTGAAGGCGCGTTCCCGGGTGCGCGCCTTCCATTATTTTGTCAGATAATATGTT
66 AGGGGACCGTGAAGGCGCGTTCCCGGG-G-GCGCCTTCCATTATTTTGTCAGAGAATATGTT
*
90105 ATCATTACCCTATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTT
1 ATCATTACCCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTT
90170 AGGGGAC
66 AGGGGAC
90177 TTTAAAGCGC
Statistics
Matches: 417, Mismatches: 19, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
121 99 0.24
122 13 0.03
123 24 0.06
124 108 0.26
125 20 0.05
126 124 0.30
127 29 0.07
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (125 bp):
ATCATTACCCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTT
AGGGGACCGTGAAGGCGCGTTCCCGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTT
Found at i:90638 original size:33 final size:34
Alignment explanation
Indices: 90601--90666 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
90591 GAATTTAATG
90601 TTAAATTTCGAATACTATAATTT-TATTTTAAAT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
* *
90634 TTAAATTTTGAATACTATAATTTGTGTTTTAAA
1 TTAAATTTCGAATACTATAATTTGTATTTTAAA
90667 AACATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 22 0.73
34 8 0.27
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.52
Consensus pattern (34 bp):
TTAAATTTCGAATACTATAATTTGTATTTTAAAT
Found at i:91209 original size:21 final size:20
Alignment explanation
Indices: 91179--91248 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
91169 GGTATAAAAC
* *
91179 CCTGCAGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
91199 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
91220 CCCTGCGGGCTAGGAATATAA
1 -CCTGCGGGCTAGGAATGTAA
91241 CCCTGCGG
1 -CCTGCGG
91249 AGATGACATA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.23, C:0.26, G:0.33, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:93027 original size:19 final size:19
Alignment explanation
Indices: 93003--93061 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
92993 AGCACAAAAA
*
93003 AAATAATTAATAAAAATTT
1 AAATAATTAATAAAAATAT
* **
93022 AAATAAATAATAATTATAT
1 AAATAATTAATAAAAATAT
*
93041 AAATATTTTAATAAAAA-AT
1 AAATA-ATTAATAAAAATAT
93060 AA
1 AA
93062 TATTTATTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
19 24 0.77
20 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAATTAATAAAAATAT
Found at i:93048 original size:27 final size:26
Alignment explanation
Indices: 93000--93062 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 26
92990 ATTAGCACAA
93000 AAAAAATAATTAATAAAAATTTAAAT
1 AAAAAATAATTAATAAAAATTTAAAT
* * *
93026 AAATAATAATTATATAAATATTTTAAT
1 AAAAAATAATTA-ATAAAAATTTAAAT
93053 AAAAAATAAT
1 AAAAAATAAT
93063 ATTTATTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 11 0.34
27 21 0.66
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAAAATAATTAATAAAAATTTAAAT
Done.