Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003079.1 Hibiscus syriacus cultivar Beakdansim tig00006419_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: 96502
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1710 original size:2 final size:2
Alignment explanation
Indices: 1703--1776 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
1693 GAAAAGGAAA
1703 AT AT AT AT AT AT AT AT AT AT AT -T 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 AT AT
1744 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
1777 CATCAAGTAT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 70 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1835 original size:35 final size:33
Alignment explanation
Indices: 1767--1836 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
1757 TATATATATA
* *
1767 TATATATATACATCAAGTATTAAAAAAATAAGC
1 TATATATATACATCAAATATTAAAAAAAAAAGC
1800 TATATATATACA-CAAATATTTAAAAATAGAAAAGC
1 TATATATATACATCAAATA-TTAAAAA-A-AAAAGC
1835 TA
1 TA
1837 CCCTCTCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 5 0.16
33 19 0.59
34 1 0.03
35 7 0.22
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.30
Consensus pattern (33 bp):
TATATATATACATCAAATATTAAAAAAAAAAGC
Found at i:2040 original size:22 final size:23
Alignment explanation
Indices: 1997--2041 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1987 AAGATTTTTT
* **
1997 AAAAATAATATAATAATGAATAA
1 AAAAAGAATATAATAAAAAATAA
2020 AAAAAGAA-ATAATAAAAAATAA
1 AAAAAGAATATAATAAAAAATAA
2042 TATATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAAAGAATATAATAAAAAATAA
Found at i:2354 original size:59 final size:59
Alignment explanation
Indices: 2250--2362 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 59
2240 AAGTAAAATA
* *
2250 TTAAAGAAATATATATATATATATATAATAAAATAAAGTAAAAAAATCAAATGAAATAAT
1 TTAAAGAAATATATATACATATATATAATAAAATAAAATAAAAAAAT-AAATGAAATAAT
* *
2310 TTAAA-AAATATATATACGTATA-ATAATAACATGAATAAT-AAAAAATAAATGAA
1 TTAAAGAAATATATATACATATATATAATAAAAT-AA-AATAAAAAAATAAATGAA
2363 TAAAATATCC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
58 16 0.34
59 24 0.51
60 7 0.15
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (59 bp):
TTAAAGAAATATATATACATATATATAATAAAATAAAATAAAAAAATAAATGAAATAAT
Found at i:2779 original size:35 final size:35
Alignment explanation
Indices: 2740--2811 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
2730 CTAAAAAACC
* * *
2740 CTATTTTAGACTAGTATTTGAGTCTTAATCCAACT
1 CTATTTTAGACTAGTATTTAACTCCTAATCCAACT
*
2775 CTATTTTAGACTAGTATTTAACTCCTAATCTAACT
1 CTATTTTAGACTAGTATTTAACTCCTAATCCAACT
2810 CT
1 CT
2812 TCTTTTTGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.43
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTAACTCCTAATCCAACT
Found at i:5126 original size:14 final size:14
Alignment explanation
Indices: 5107--5153 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 14
5097 ACCGGGGTTC
5107 GACTAAAGATTAAA
1 GACTAAAGATTAAA
*
5121 GACTAAAGA--AGA
1 GACTAAAGATTAAA
5133 GACT--AGATTAAA
1 GACTAAAGATTAAA
5145 GACTAAAGA
1 GACTAAAGA
5154 AGAGGAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.11
12 12 0.44
14 12 0.44
ACGTcount: A:0.55, C:0.09, G:0.19, T:0.17
Consensus pattern (14 bp):
GACTAAAGATTAAA
Found at i:9704 original size:20 final size:20
Alignment explanation
Indices: 9675--9712 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9665 CAATACATAC
* *
9675 AAATATATACATACGAATTG
1 AAATAAATACAAACGAATTG
9695 AAATAAATACAAACGAAT
1 AAATAAATACAAACGAAT
9713 ATTCCAACCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.24
Consensus pattern (20 bp):
AAATAAATACAAACGAATTG
Found at i:9811 original size:30 final size:29
Alignment explanation
Indices: 9762--9957 Score: 119
Period size: 30 Copynumber: 6.6 Consensus size: 29
9752 AAAATTTCAT
* *
9762 GGACCAAAATAAGAAAAACAGAAACTTAAA
1 GGACTAAAAT-AGTAAAACAGAAACTTAAA
* * *
9792 GGACTAAAATGGCACAAACAGAAATTTAAA
1 GGACTAAAATAGTA-AAACAGAAACTTAAA
*
9822 -GAGCTAAAACAGTAACAACAGAAACTTAAA
1 GGA-CTAAAATAGTAA-AACAGAAACTTAAA
* * * *
9852 TGACTAAAATAATAAAAATAGAAACTTAAG
1 GGACTAAAATAGT-AAAACAGAAACTTAAA
* * * * *
9882 GGACTAATACAATAAAAACA-AACATTTAAG
1 GGACTAAAATAGT-AAAACAGAA-ACTTAAA
** * *
9912 GGACTAAAATCACAAAAATAGAAACTTAAG
1 GGACTAAAAT-AGTAAAACAGAAACTTAAA
*
9942 GGGCTAAAATAG-AAAA
1 GGACTAAAATAGTAAAA
9958 TAAAAATAAT
Statistics
Matches: 133, Mismatches: 25, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
28 4 0.03
29 8 0.06
30 114 0.86
31 7 0.05
ACGTcount: A:0.58, C:0.12, G:0.14, T:0.16
Consensus pattern (29 bp):
GGACTAAAATAGTAAAACAGAAACTTAAA
Found at i:9875 original size:60 final size:60
Alignment explanation
Indices: 9775--9950 Score: 185
Period size: 60 Copynumber: 2.9 Consensus size: 60
9765 CCAAAATAAG
** * * * * *
9775 AAAAACAGAAACTTAAAGGACTAAAATGGCACAAACAGAAATTTAAAGAGCTAAAACAGT
1 AAAAACAGAAACTTAAAGGACTAAAATAACAAAAATAGAAACTTAAAGGGCTAAAACAAT
* * * *
9835 AACAACAGAAACTTAAATGACTAAAATAATAAAAATAGAAACTT-AAGGGACTAATACAAT
1 AAAAACAGAAACTTAAAGGACTAAAATAACAAAAATAGAAACTTAAAGGG-CTAAAACAAT
* * * *
9895 AAAAACA-AACATTTAAGGGACTAAAATCACAAAAATAGAAACTTAAGGGGCTAAAA
1 AAAAACAGAA-ACTTAAAGGACTAAAATAACAAAAATAGAAACTTAAAGGGCTAAAA
9951 TAGAAAATAA
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
59 6 0.06
60 84 0.89
61 4 0.04
ACGTcount: A:0.57, C:0.12, G:0.13, T:0.17
Consensus pattern (60 bp):
AAAAACAGAAACTTAAAGGACTAAAATAACAAAAATAGAAACTTAAAGGGCTAAAACAAT
Found at i:10479 original size:2 final size:2
Alignment explanation
Indices: 10472--10520 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
10462 CCGTTTTGCC
* *
10472 AG AG AG AG AG GG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10514 AG AG AG A
1 AG AG AG A
10521 TTCAATGGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11298 original size:3 final size:3
Alignment explanation
Indices: 11290--11320 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
11280 TAATAGTTAA
11290 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
11321 TTATAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12693 original size:95 final size:95
Alignment explanation
Indices: 12561--12748 Score: 277
Period size: 95 Copynumber: 2.0 Consensus size: 95
12551 CGAAGAGGTA
* * * *
12561 GTATCAATACCTTGATAAGGGTATCAATACCAAGCAACATCGAATCTAATTTTGGTATCGATACT
1 GTATCAATACCATGATAAGGGTATCAATACCAAGCAACATCAAACCTAATTTTGGTATCGATACC
* **
12626 GGAAGGGGGTATCGGTACCATAGTATAGTT
66 GGAAGGAGGTATCAATACCATAGTATAGTT
* * * *
12656 GTATCAATACCATGGTAAGGGTATCAGTACTAGGCAACATCAAACCTAATTTTGGTATCGATACC
1 GTATCAATACCATGATAAGGGTATCAATACCAAGCAACATCAAACCTAATTTTGGTATCGATACC
12721 GGAAGGAGGTATCAATACCATAGTATAG
66 GGAAGGAGGTATCAATACCATAGTATAG
12749 AAGTATTGGT
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 82 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (95 bp):
GTATCAATACCATGATAAGGGTATCAATACCAAGCAACATCAAACCTAATTTTGGTATCGATACC
GGAAGGAGGTATCAATACCATAGTATAGTT
Found at i:13198 original size:55 final size:55
Alignment explanation
Indices: 13110--13377 Score: 326
Period size: 55 Copynumber: 4.9 Consensus size: 55
13100 CTATGTGTAC
* * *
13110 TACAAGCACTTTGTGTGCATATCCAAGGGATTCATAATGGGTTGATGAATCACCG
1 TACAAGCACTTTGTGTGCAAATCCAAGGAATTCATCATGGGTTGATGAATCACCG
* * * * *
13165 TACAAGCACTTTGTGCGCAAATACATGAAATTCATCATGGGTTGATGAATCACTG
1 TACAAGCACTTTGTGTGCAAATCCAAGGAATTCATCATGGGTTGATGAATCACCG
* * * * *
13220 TACAGGCACTTTGTGTGCGAATCCATA-GAATTAATCATAGGTTGATGAATCATCG
1 TACAAGCACTTTGTGTGCAAATCCA-AGGAATTCATCATGGGTTGATGAATCACCG
* * *
13275 TACATGCACTTTGTGTGCAAATCCACGGAATTCATCATGGGTTGATAAATCACCG
1 TACAAGCACTTTGTGTGCAAATCCAAGGAATTCATCATGGGTTGATGAATCACCG
* * * *
13330 TACAAACAC--TGTGTGCAAACCCAAGGAATTCATAATGAGTTGATGAAT
1 TACAAGCACTTTGTGTGCAAATCCAAGGAATTCATCATGGGTTGATGAAT
13378 TTCCGTATAG
Statistics
Matches: 179, Mismatches: 32, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
53 34 0.19
55 145 0.81
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (55 bp):
TACAAGCACTTTGTGTGCAAATCCAAGGAATTCATCATGGGTTGATGAATCACCG
Found at i:15312 original size:20 final size:22
Alignment explanation
Indices: 15266--15318 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
15256 CCGGAAGGGG
15266 GTATCGATACCATAGAATAGTA
1 GTATCGATACCATAGAATAGTA
* *
15288 GTATCGATACCATGGTA-AG-A
1 GTATCGATACCATAGAATAGTA
15308 GTATCGATACC
1 GTATCGATACC
15319 CGACAACATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.41
21 2 0.07
22 15 0.52
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (22 bp):
GTATCGATACCATAGAATAGTA
Found at i:15313 original size:95 final size:95
Alignment explanation
Indices: 15190--15412 Score: 281
Period size: 95 Copynumber: 2.3 Consensus size: 95
15180 TACCGACGAG
* * * * *
15190 GTAGTATCGATACCATGATAAGGGTATCGATACCA-AGCAATATCAAATCTAATTTTAGTATCGA
1 GTAGTATCGATACCATGGTAAGAGTATCGATACCAGA-CAACATCAAACCTAATTTTAGGATCGA
15254 TACCGGAAGGGGGTATCGATACCATAGAATA
65 TACCGGAAGGGGGTATCGATACCATAGAATA
* *
15285 GTAGTATCGATACCATGGTAAGAGTATCGATACCCGACAACATCAAACCTAATTTTGGGATCGAT
1 GTAGTATCGATACCATGGTAAGAGTATCGATACCAGACAACATCAAACCTAATTTTAGGATCGAT
* * *
15350 ACCGGAAGGGGGTATTGGTACCATAGTATA
66 ACCGGAAGGGGGTATCGATACCATAGAATA
* * *
15380 GAAGTATC-AGTACTC-TGGTAGGAATATCGATAC
1 GTAGTATCGA-TAC-CATGGTAAGAGTATCGATAC
15413 TCTGGATCCA
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
94 1 0.01
95 109 0.97
96 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.26
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTAAGAGTATCGATACCAGACAACATCAAACCTAATTTTAGGATCGAT
ACCGGAAGGGGGTATCGATACCATAGAATA
Found at i:15830 original size:55 final size:55
Alignment explanation
Indices: 15771--15916 Score: 161
Period size: 55 Copynumber: 2.7 Consensus size: 55
15761 TATCCTCGGG
** * *
15771 ATTCATTATGGGTTGATGAATCATTGTACAGGGACTTTGCGTGCAAA-TCCATAAA
1 ATTCATTATGGGTTGATGAATCACCGTACAGGCACTTTGCGTGCAAACT-CACAAA
* * *
15826 ATTCATCATGGGTTGATGAATCACCGTACAGGCACTTTGTGTGTAAACTCACAAA
1 ATTCATTATGGGTTGATGAATCACCGTACAGGCACTTTGCGTGCAAACTCACAAA
* ** *
15881 ATTCATCT-TGAGTTGATGAATTTCCGTATAGGCACT
1 ATTCAT-TATGGGTTGATGAATCACCGTACAGGCACT
15917 ACTTGTGCAT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
55 76 0.99
56 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (55 bp):
ATTCATTATGGGTTGATGAATCACCGTACAGGCACTTTGCGTGCAAACTCACAAA
Found at i:21172 original size:32 final size:32
Alignment explanation
Indices: 21121--21239 Score: 163
Period size: 32 Copynumber: 3.8 Consensus size: 32
21111 GTTCCTTAGA
21121 ACATAGGT-A-TACTGTCCATATGTCTCAAAAG
1 ACATAGGTAATTA-TGTCCATATGTCTCAAAAG
* *
21152 GCATAGGTAATTATGTCCATATGT-TCTGAAAG
1 ACATAGGTAATTATGTCCATATGTCTC-AAAAG
* *
21184 ACATAGGTAATTCTGTCCATATGTCCCAAAAG
1 ACATAGGTAATTATGTCCATATGTCTCAAAAG
21216 ACATAGGTAATTATGTCCATATGT
1 ACATAGGTAATTATGTCCATATGT
21240 TCCGTAGAAC
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
31 9 0.12
32 65 0.84
33 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (32 bp):
ACATAGGTAATTATGTCCATATGTCTCAAAAG
Found at i:21252 original size:32 final size:32
Alignment explanation
Indices: 21071--21257 Score: 154
Period size: 32 Copynumber: 5.9 Consensus size: 32
21061 TCTCGACAAC
* * *
21071 TGTCCATAGGTCCCGAAGAACCTAGGTAA--A
1 TGTCCATATGTTCCGAAGAACATAGGTAATTA
* **
21101 CTGTCCACATGTTCCTTAGAACATAGGT-A-TA
1 -TGTCCATATGTTCCGAAGAACATAGGTAATTA
** *
21132 CTGTCCATATGTCTCAAAAG-GCATAGGTAATTA
1 -TGTCCATATGT-TCCGAAGAACATAGGTAATTA
* *
21165 TGTCCATATGTTCTGAA-AGACATAGGTAATTC
1 TGTCCATATGTTCCGAAGA-ACATAGGTAATTA
* *
21197 TGTCCATATG-TCCCAAAAGACATAGGTAATTA
1 TGTCCATATGTTCCGAAGA-ACATAGGTAATTA
*
21229 TGTCCATATGTTCCGTAGAACATAGGTAA
1 TGTCCATATGTTCCGAAGAACATAGGTAA
21258 ACCCTCGACT
Statistics
Matches: 127, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
30 1 0.01
31 48 0.38
32 71 0.56
33 7 0.06
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (32 bp):
TGTCCATATGTTCCGAAGAACATAGGTAATTA
Found at i:21252 original size:64 final size:64
Alignment explanation
Indices: 21069--21257 Score: 226
Period size: 64 Copynumber: 3.0 Consensus size: 64
21059 AATCTCGACA
* * * * *
21069 ACTGTCCATAGGTCCC-GAAGAACCTAGGTAA--ACTGTCCACATGTTCCTTAGAACATAGGT-A
1 ACTGTCCATATGTCCCAAAAG-ACATAGGTAATTA-TGTCCATATGTTCCGTAGAACATAGGTAA
21130 T
64 T
* * * *
21131 ACTGTCCATATGTCTCAAAAGGCATAGGTAATTATGTCCATATGTTCTG-AAAGACATAGGTAAT
1 ACTGTCCATATGTCCCAAAAGACATAGGTAATTATGTCCATATGTTCCGTAGA-ACATAGGTAAT
*
21195 TCTGTCCATATGTCCCAAAAGACATAGGTAATTATGTCCATATGTTCCGTAGAACATAGGTAA
1 ACTGTCCATATGTCCCAAAAGACATAGGTAATTATGTCCATATGTTCCGTAGAACATAGGTAA
21258 ACCCTCGACT
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
62 24 0.22
63 23 0.21
64 58 0.54
65 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (64 bp):
ACTGTCCATATGTCCCAAAAGACATAGGTAATTATGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:28858 original size:34 final size:34
Alignment explanation
Indices: 28820--28900 Score: 126
Period size: 34 Copynumber: 2.4 Consensus size: 34
28810 CCATGATAAG
*
28820 GGTATCGATACCAAGCAACATCGAATCTAATTTT
1 GGTATCGATACCAAGCAACATCGAACCTAATTTT
** *
28854 GGTATCGATACCCGGCAACATCGAACCTATTTTT
1 GGTATCGATACCAAGCAACATCGAACCTAATTTT
28888 GGTATCGATACCA
1 GGTATCGATACCA
28901 GAAGGGGGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (34 bp):
GGTATCGATACCAAGCAACATCGAACCTAATTTT
Found at i:29422 original size:55 final size:54
Alignment explanation
Indices: 29330--29489 Score: 212
Period size: 55 Copynumber: 2.9 Consensus size: 54
29320 TCATGGGCCG
* * *
29330 TACAAGCACTTTGTGTGCAAATCCACAGAATTAATCATAGGTTGATGAATCACCA
1 TACATGCACTTTGTGTGCAAATCCACGGAATTCATCAT-GGTTGATGAATCACCA
*
29385 TACATGCACTTTGTGTGCAAATCCACGGAATTCATCATGGGTTGATGAATCACCG
1 TACATGCACTTTGTGTGCAAATCCACGGAATTCATCAT-GGTTGATGAATCACCA
* * * * *
29440 TACATACACTTTGTGTGCAAACCCATGAAATTCATAATGAGTTGATGAAT
1 TACATGCACTTTGTGTGCAAATCCACGGAATTCATCATG-GTTGATGAAT
29490 TTCCGTATAG
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 1 0.01
55 93 0.99
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (54 bp):
TACATGCACTTTGTGTGCAAATCCACGGAATTCATCATGGTTGATGAATCACCA
Found at i:30365 original size:38 final size:37
Alignment explanation
Indices: 30291--30430 Score: 146
Period size: 38 Copynumber: 3.8 Consensus size: 37
30281 AGAGACAAAC
* * *
30291 TTTGTTTCAAG-GTAAACGATCTCATAGATA--TTTGT
1 TTTGTTTCAAGTG-AAACAAACTCAAAGATATTTTTGT
* *
30326 TTTGTTTAAAGGGAAACAAACTCAAAGATGATTTTTGT
1 TTTGTTTCAAGTGAAACAAACTCAAAGAT-ATTTTTGT
*
30364 TTTGTTTCAAGTGAAACAAACTC-AA-ATATTTCTTTT
1 TTTGTTTCAAGTGAAACAAACTCAAAGATATTT-TTGT
*
30400 CTTTGTTTCAAGTGAAACAGACTCAAAGATA
1 -TTTGTTTCAAGTGAAACAAACTCAAAGATA
30431 AGTGTTTCAA
Statistics
Matches: 89, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
35 27 0.30
36 7 0.08
37 24 0.27
38 28 0.31
39 3 0.03
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (37 bp):
TTTGTTTCAAGTGAAACAAACTCAAAGATATTTTTGT
Found at i:30612 original size:33 final size:33
Alignment explanation
Indices: 30575--30643 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
30565 GTCGAATCCC
30575 CAAAGATACCCTAACATTCGATGTTGATTGCTT
1 CAAAGATACCCTAACATTCGATGTTGATTGCTT
* * *
30608 CAAAGATGCCGTAATATTCGATGTTGATTGCTT
1 CAAAGATACCCTAACATTCGATGTTGATTGCTT
30641 CAA
1 CAA
30644 CACTGATTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (33 bp):
CAAAGATACCCTAACATTCGATGTTGATTGCTT
Found at i:31714 original size:15 final size:15
Alignment explanation
Indices: 31696--31791 Score: 59
Period size: 15 Copynumber: 5.9 Consensus size: 15
31686 TTTTCTTTTA
31696 TTTTTTTCTCTTTGT
1 TTTTTTTCTCTTTGT
* * *
31711 TTTTATTTTTTTTCTCT
1 TTTT-TTTCTCTT-TGT
*
31728 TTACTTTTTTTCTTTGCT
1 TT--TTTTTCTCTTTG-T
31746 CTTTATTTT-TCTTTGGT
1 -TTT-TTTTCTCTTT-GT
*
31763 TCTTTTTCTCTTTGT
1 TTTTTTTCTCTTTGT
*
31778 TCTTTTTCTCTTTG
1 TTTTTTTCTCTTTG
31792 CTTTGATTTG
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
15 24 0.36
16 13 0.20
17 12 0.18
18 13 0.20
19 4 0.06
ACGTcount: A:0.03, C:0.16, G:0.06, T:0.75
Consensus pattern (15 bp):
TTTTTTTCTCTTTGT
Found at i:31720 original size:21 final size:21
Alignment explanation
Indices: 31691--31755 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 21
31681 TTGCTTTTTC
*
31691 TTTTA-TTTTTTTCTCTTTGT
1 TTTTATTTTTTTTCTCTTTAT
*
31711 TTTTATTTTTTTTCTCTTTAC
1 TTTTATTTTTTTTCTCTTTAT
* *
31732 TTTT-TTTCTTTGCTCTTTAT
1 TTTTATTTTTTTTCTCTTTAT
31752 TTTT
1 TTTT
31756 CTTTGGTTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 22 0.56
21 17 0.44
ACGTcount: A:0.06, C:0.12, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTATTTTTTTTCTCTTTAT
Found at i:31767 original size:18 final size:17
Alignment explanation
Indices: 31699--31760 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
31689 TCTTTTATTT
*
31699 TTTTCTCTTTG-TTTTTA
1 TTTT-TCTTTGCTCTTTA
31716 TTTTT-TTT-CTCTTTA
1 TTTTTCTTTGCTCTTTA
31731 CTTTTTTTCTTTGCTCTTTA
1 ---TTTTTCTTTGCTCTTTA
31751 TTTTTCTTTG
1 TTTTTCTTTG
31761 GTTCTTTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
15 8 0.21
16 1 0.03
17 14 0.37
18 5 0.13
19 3 0.08
20 7 0.18
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTTCTTTGCTCTTTA
Found at i:31789 original size:41 final size:41
Alignment explanation
Indices: 31684--31790 Score: 103
Period size: 41 Copynumber: 2.6 Consensus size: 41
31674 TCGCTCTTTG
* * **
31684 CTTTTTCTTTTATT-TTTTTCTCTTTGTTTTTATTTTTTTT
1 CTTTTTCTTTTATTCTTTTTCTCTTTATTTTTACTTTGGTT
* * *
31724 CTCTTTACTTTTTTTC-TTTGCTCTTTATTTTT-CTTTGGTT
1 CT-TTTTCTTTTATTCTTTTTCTCTTTATTTTTACTTTGGTT
*
31764 CTTTTTCTCTTTGTTCTTTTTCTCTTT
1 CTTTTTCT-TTTATTCTTTTTCTCTTT
31791 GCTTTGATTT
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
39 5 0.09
40 15 0.28
41 33 0.62
ACGTcount: A:0.04, C:0.16, G:0.05, T:0.76
Consensus pattern (41 bp):
CTTTTTCTTTTATTCTTTTTCTCTTTATTTTTACTTTGGTT
Found at i:36203 original size:3 final size:3
Alignment explanation
Indices: 36197--36280 Score: 150
Period size: 3 Copynumber: 27.7 Consensus size: 3
36187 GTAGTAGTAG
36197 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
36245 TAA TAA TAA TAA TAA TAA TAA TAA TATA TTA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA
36281 GTTTTGATAG
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
3 76 0.97
4 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:43976 original size:72 final size:73
Alignment explanation
Indices: 43852--43994 Score: 200
Period size: 72 Copynumber: 2.0 Consensus size: 73
43842 ACACAAATGT
* **
43852 GCGTCATTGAAGCCACCGTCATAAATCTCAGATGACACACAATTGTGTGTCATAAATCTATGA-A
1 GCGTCATTGAAGCCACCATCATAAATCGAAGATGACACACAATTGTGTGTCATAAATCTATGACA
43916 TCGCATTGC
66 -CGCATTGC
* * * *
43925 GCGTCATTGAAGCCCCCATCATAAAT-GAAGATGAGACACATTTGTGTGTCATAAATTTATGACA
1 GCGTCATTGAAGCCACCATCATAAATCGAAGATGACACACAATTGTGTGTCATAAATCTATGACA
43989 CGCATT
66 CGCATT
43995 TTTTACTTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
72 37 0.60
73 25 0.40
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (73 bp):
GCGTCATTGAAGCCACCATCATAAATCGAAGATGACACACAATTGTGTGTCATAAATCTATGACA
CGCATTGC
Found at i:44088 original size:2 final size:2
Alignment explanation
Indices: 44081--44105 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44071 TCGTAAATTT
44081 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
44106 TGTAAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47504 original size:30 final size:30
Alignment explanation
Indices: 47433--47504 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
47423 AATGGAGTTG
* * *
47433 AAGATACTGAGATAGGAGAGGATAGTTAGT
1 AAGATACTGGGATAGGAGAGGATAGTGAAT
47463 AAGATACTGGGATAGGAGAGGATAGTGAAT
1 AAGATACTGGGATAGGAGAGGATAGTGAAT
*
47493 AAGATAATGGGA
1 AAGATACTGGGA
47505 CATGGGAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.42, C:0.03, G:0.35, T:0.21
Consensus pattern (30 bp):
AAGATACTGGGATAGGAGAGGATAGTGAAT
Found at i:48415 original size:2 final size:2
Alignment explanation
Indices: 48408--48435 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48398 ACGTCAATAA
48408 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
48436 TGTAGATTGA
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:50982 original size:2 final size:2
Alignment explanation
Indices: 50975--51005 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
50965 ATAAAGGATA
50975 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
51006 CCTGCATTGT
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:54723 original size:24 final size:24
Alignment explanation
Indices: 54678--54723 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
54668 CAAACGAACG
* *
54678 AACATATATAAACCAACGTAAATA
1 AACATAAATAAACCAACATAAATA
**
54702 AACATAAATAAATGAACATAAA
1 AACATAAATAAACCAACATAAA
54724 ATTAATTGGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.63, C:0.13, G:0.04, T:0.20
Consensus pattern (24 bp):
AACATAAATAAACCAACATAAATA
Found at i:54943 original size:24 final size:24
Alignment explanation
Indices: 54908--54957 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
54898 GATTAGGTTG
*
54908 AATATAAGTGAACGAACATAAACA
1 AATATAAATGAACGAACATAAACA
*
54932 AATATAAATGAATGAACATAAACA
1 AATATAAATGAACGAACATAAACA
54956 AA
1 AA
54958 CAGATTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (24 bp):
AATATAAATGAACGAACATAAACA
Found at i:60175 original size:29 final size:29
Alignment explanation
Indices: 60140--60221 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
60130 AAACTAAATT
*
60140 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
60169 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
60198 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
60222 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:60583 original size:10 final size:10
Alignment explanation
Indices: 60568--60592 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
60558 CTGAGTTCTG
60568 ACGCACCGCC
1 ACGCACCGCC
60578 ACGCACCGCC
1 ACGCACCGCC
60588 ACGCA
1 ACGCA
60593 AATGGTATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.56, G:0.20, T:0.00
Consensus pattern (10 bp):
ACGCACCGCC
Found at i:61369 original size:15 final size:15
Alignment explanation
Indices: 61346--61375 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61336 ACGAGGCTGG
61346 AATTACAACAATAAC
1 AATTACAACAATAAC
*
61361 AATTCCAACAATAAC
1 AATTACAACAATAAC
61376 TATGAGAAAG
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:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:64772 original size:29 final size:29
Alignment explanation
Indices: 64737--64818 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
64727 AAACTAAATT
*
64737 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
64766 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
64795 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
64819 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:73779 original size:65 final size:64
Alignment explanation
Indices: 73692--73847 Score: 163
Period size: 65 Copynumber: 2.4 Consensus size: 64
73682 TACACTTGGG
* * *
73692 GTGCATCGGTACACT-AATTACATTCGATGTTTCAAA-AGAGCCAGGAGTGCATCGATGCATAGT
1 GTGCATCGGTACA-TAAAATACATTCGAT-TTTCAAATAAAACCAGGAGTGCATCGATGCATAGT
73755 AT
64 -T
* * * * *
73757 GTGCATTGGTACATAAAATACATTCAATTTTTAAATAAAATCAGGAGTGCATCGATGCATGGTT
1 GTGCATCGGTACATAAAATACATTCGATTTTCAAATAAAACCAGGAGTGCATCGATGCATAGTT
* ** *
73821 TTGCATCGGTACCCAAAATGCATTCGA
1 GTGCATCGGTACATAAAATACATTCGA
73848 ATTAGGGTGC
Statistics
Matches: 75, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
64 29 0.39
65 46 0.61
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATACATTCGATTTTCAAATAAAACCAGGAGTGCATCGATGCATAGTT
Found at i:74205 original size:13 final size:13
Alignment explanation
Indices: 74187--74220 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
74177 TAAGATTTTC
*
74187 TTTGAAAATCATT
1 TTTGAAAATCAGT
74200 TTTG-AAATCAGT
1 TTTGAAAATCAGT
74212 TTTGAAAAT
1 TTTGAAAAT
74221 TACTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAGT
Found at i:76577 original size:20 final size:21
Alignment explanation
Indices: 76554--76604 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
76544 TATATAGTTT
76554 TCAAAAACAACATAA-TT-AAA
1 TCAAAAACAACA-AATTTAAAA
*
76574 TCAAAAACATCAAATTTAAAA
1 TCAAAAACAACAAATTTAAAA
*
76595 ACAAAAACAA
1 TCAAAAACAA
76605 TTTTTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 2 0.08
20 13 0.50
21 11 0.42
ACGTcount: A:0.67, C:0.16, G:0.00, T:0.18
Consensus pattern (21 bp):
TCAAAAACAACAAATTTAAAA
Found at i:77071 original size:44 final size:44
Alignment explanation
Indices: 77005--77111 Score: 155
Period size: 44 Copynumber: 2.4 Consensus size: 44
76995 CGATGCACTG
*
77005 CATAGTGTATCGATGCACATTC-AAGGATTGCATCAGTGCA-TCTT
1 CATAGTGTATCGATGCACATTCAAAGGA-TGCATCAGTACACT-TT
* *
77049 CATAGTGTATCGATGCATATTCAAAGGATGCATCGGTACACTTT
1 CATAGTGTATCGATGCACATTCAAAGGATGCATCAGTACACTTT
77093 CATAGTGTATCGATGCACA
1 CATAGTGTATCGATGCACA
77112 ATGCACAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
44 51 0.89
45 6 0.11
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (44 bp):
CATAGTGTATCGATGCACATTCAAAGGATGCATCAGTACACTTT
Found at i:80760 original size:20 final size:21
Alignment explanation
Indices: 80721--80760 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
80711 GAAGCTTTAA
* *
80721 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTATTGAT
80742 GATCATC-ATTTACTATTGA
1 GATCATCAATTTACTATTGA
80761 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTATTGAT
Found at i:82903 original size:65 final size:64
Alignment explanation
Indices: 82810--82964 Score: 195
Period size: 65 Copynumber: 2.4 Consensus size: 64
82800 TACACTTGGG
* * * *
82810 GTGCATCGGTACACTAATTACATTCGATGTTTCAA-AAAATCCAAGAGTGCAGCGATGCATGGTC
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAGAAAAT-CAAGAGTACAGCGATGCATGGT-
82874 T
64 T
* * * * * *
82875 TTGCATCGTTACATAAAATGCATTCGATGTTTCAAGAAAATCAGGAGTACATCGATGTATGGTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAGAAAATCAAGAGTACAGCGATGCATGGTT
82939 GTGCATCGGTACACAAAATGCATTCG
1 GTGCATCGGTACACAAAATGCATTCG
82965 GATTAGGGTG
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 24 0.32
65 47 0.62
66 5 0.07
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAGAAAATCAAGAGTACAGCGATGCATGGTT
Found at i:87480 original size:17 final size:17
Alignment explanation
Indices: 87460--87497 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
87450 CGATACTGCC
87460 TTAGTATC-AGTACCAAT
1 TTAGTATCGA-TACCAAT
87477 TTAGTATCGATACCAAT
1 TTAGTATCGATACCAAT
87494 TTAG
1 TTAG
87498 CTTACTAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (17 bp):
TTAGTATCGATACCAAT
Found at i:89967 original size:32 final size:32
Alignment explanation
Indices: 89931--89995 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
89921 ATTAATTCTT
89931 TAGAAATTTTTTGAACAGATATTATTTTATAA
1 TAGAAATTTTTTGAACAGATATTATTTTATAA
*
89963 TAGAAATTTTTTGAACATATATTATTTTATAA
1 TAGAAATTTTTTGAACAGATATTATTTTATAA
89995 T
1 T
89996 TATCTTAGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (32 bp):
TAGAAATTTTTTGAACAGATATTATTTTATAA
Found at i:90205 original size:21 final size:21
Alignment explanation
Indices: 90166--90205 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
90156 TTAACAAAAA
*
90166 TATTAATTATTAAAGTATATT
1 TATTAATTATTAAAATATATT
90187 TATTAATT-TTAATAATATA
1 TATTAATTATTAA-AATATA
90206 ATAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TATTAATTATTAAAATATATT
Found at i:90379 original size:18 final size:18
Alignment explanation
Indices: 90358--90392 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
90348 TATTTTTACT
90358 TTATTATTATAATAATAA
1 TTATTATTATAATAATAA
90376 TTATTATTATAATAATA
1 TTATTATTATAATAATA
90393 TAATATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTATTATAATAATAA
Found at i:90380 original size:15 final size:15
Alignment explanation
Indices: 90360--90402 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
90350 TTTTTACTTT
90360 ATTATTATAATAATA
1 ATTATTATAATAATA
*
90375 ATTATTATTATAATA
1 ATTATTATAATAATA
*
90390 ATATAATATAATA
1 AT-TATTATAATA
90403 TTTTAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATTATAATAATA
Found at i:90382 original size:21 final size:21
Alignment explanation
Indices: 90358--90418 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
90348 TATTTTTACT
90358 TTATTATTATAATAATAATTA
1 TTATTATTATAATAATAATTA
*
90379 TTATTATAATAAT-ATAA-TA
1 TTATTATTATAATAATAATTA
* *
90398 -TAATATTTTAATAAATAATTA
1 TTATTATTATAAT-AATAATTA
90419 ATAGAGTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.27
19 2 0.06
20 8 0.24
21 14 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATTATTATAATAATAATTA
Found at i:90543 original size:20 final size:20
Alignment explanation
Indices: 90518--90578 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 20
90508 AATGATTTAA
90518 TTAATATTAAATAAATTATT
1 TTAATATTAAATAAATTATT
90538 TTAATATTTTAAA-AATATTATT
1 TTAATA--TTAAATAA-ATTATT
* * *
90560 TTTATAATAAATAATTTAT
1 TTAATATTAAATAAATTAT
90579 AAAATATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
20 14 0.41
21 4 0.12
22 16 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAATATTAAATAAATTATT
Found at i:92674 original size:2 final size:2
Alignment explanation
Indices: 92667--92715 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
92657 GAGATTTTAG
92667 AT AT 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 AT AT
92709 AT AT AT A
1 AT AT AT A
92716 ATAGAAACGT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:94977 original size:14 final size:13
Alignment explanation
Indices: 94958--94992 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
94948 GAAAAATGAC
*
94958 TTTTAAAAGTGTCT
1 TTTTAAAAGTG-CA
94972 TTTTAAAAGTGCA
1 TTTTAAAAGTGCA
94985 TTTTAAAA
1 TTTTAAAA
94993 TTTAATTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (13 bp):
TTTTAAAAGTGCA
Done.