Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006887.1 Hibiscus syriacus cultivar Beakdansim tig00017571_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: 112567
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:190 original size:34 final size:32
Alignment explanation
Indices: 151--220 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
141 TTTTGTAAAG
* *
151 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCG-G-AAAAACTA
*
185 GGGAAAAGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
217 GGGA
1 GGGA
221 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1717 original size:19 final size:20
Alignment explanation
Indices: 1693--1730 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1683 TAAAGATAAT
1693 TTGATTTTGAAAG-CAAAAG
1 TTGATTTTGAAAGCCAAAAG
1712 TTGATTTTGAAAGCCAAAA
1 TTGATTTTGAAAGCCAAAA
1731 TGAAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (20 bp):
TTGATTTTGAAAGCCAAAAG
Found at i:3065 original size:31 final size:31
Alignment explanation
Indices: 2998--3057 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
2988 CAATTTAAGG
*
2998 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
3029 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
3058 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:3155 original size:19 final size:19
Alignment explanation
Indices: 3122--3188 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
3112 AATGTTTTTA
* *
3122 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
*
3141 TAAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
3160 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
3179 TGAACAGTAA
1 TGAACAGTAA
3189 CCCGAGGTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:3320 original size:21 final size:21
Alignment explanation
Indices: 3294--3335 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3284 ATTTGAATAT
*
3294 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3315 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3336 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3397 original size:21 final size:21
Alignment explanation
Indices: 3364--3403 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3354 GTTTTGCAGA
*
3364 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
3386 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
3404 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:3658 original size:34 final size:32
Alignment explanation
Indices: 3619--3688 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
3609 TTTTGTAAAG
* *
3619 GGGAAAGGTTCTAGCTTAACCCGTGTAAAAGCTA
1 GGGAAAAGTTCTAGCTTAACCCG-G-AAAAACTA
* *
3653 GGGAAAAGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGTTCTAGCTTAACCCGGAAAAACTA
3685 GGGA
1 GGGA
3689 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAACCCGGAAAAACTA
Found at i:5738 original size:99 final size:99
Alignment explanation
Indices: 5567--5765 Score: 389
Period size: 99 Copynumber: 2.0 Consensus size: 99
5557 TGTTAGGTAC
*
5567 CTTAGGGTCCCTTTGGTAACTCGTAAACAATCTGCGAATGACTGCACAAGTCTTCTGGAAAGGAT
1 CTTAGGGTCCCTTTGGTAACTCGTAAAAAATCTGCGAATGACTGCACAAGTCTTCTGGAAAGGAT
5632 TAAAGAAAAATTAAGCCATTGGGCAAATAAATGA
66 TAAAGAAAAATTAAGCCATTGGGCAAATAAATGA
5666 CTTAGGGTCCCTTTGGTAACTCGTAAAAAATCTGCGAATGACTGCACAAGTCTTCTGGAAAGGAT
1 CTTAGGGTCCCTTTGGTAACTCGTAAAAAATCTGCGAATGACTGCACAAGTCTTCTGGAAAGGAT
5731 TAAAGAAAAATTAAGCCATTGGGCAAATAAATGA
66 TAAAGAAAAATTAAGCCATTGGGCAAATAAATGA
5765 C
1 C
5766 ACAACTTGTG
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (99 bp):
CTTAGGGTCCCTTTGGTAACTCGTAAAAAATCTGCGAATGACTGCACAAGTCTTCTGGAAAGGAT
TAAAGAAAAATTAAGCCATTGGGCAAATAAATGA
Found at i:7289 original size:30 final size:30
Alignment explanation
Indices: 7254--7317 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
7244 TCTTAAACAT
*
7254 AAGTGTACTTAAATTGAATTATATTGTTTA
1 AAGTGTACTTAAATTGAATTATATGGTTTA
7284 AAGTGTACTTAAATTGAATTATATGGTTTA
1 AAGTGTACTTAAATTGAATTATATGGTTTA
7314 AAGT
1 AAGT
7318 AAGTGGCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.44
Consensus pattern (30 bp):
AAGTGTACTTAAATTGAATTATATGGTTTA
Found at i:19121 original size:17 final size:17
Alignment explanation
Indices: 19099--19133 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
19089 AATGACTATT
*
19099 TTATATTTTTTTAATAG
1 TTATATTTTTTAAATAG
19116 TTATATTTTTTAAATAG
1 TTATATTTTTTAAATAG
19133 T
1 T
19134 CAATGATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (17 bp):
TTATATTTTTTAAATAG
Found at i:24520 original size:22 final size:19
Alignment explanation
Indices: 24482--24525 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
24472 GTAGACAGGT
*
24482 AATTTTAATTTTTTTTTTA
1 AATTTTAATTTTTTTTTGA
24501 AATTGTTAATATTTTATTTTGA
1 AATT-TTAAT-TTTT-TTTTGA
24523 AAT
1 AAT
24526 CTACAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 5 0.24
21 4 0.19
22 8 0.38
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
AATTTTAATTTTTTTTTGA
Found at i:26174 original size:111 final size:110
Alignment explanation
Indices: 26036--26329 Score: 390
Period size: 111 Copynumber: 2.6 Consensus size: 110
26026 GCATGGAAAC
* * * * *
26036 TTGGAGGATCTTCATGCTGTAGGGGAAGTAGGTACCGATATGACTGAGGCAGAGGAGAACCCTGT
1 TTGGAGGATATTCATGCTGTAGAGGAAGCAGGTACAGATATG-CTGAGGCAGAGGAGGACCCTGT
*
26101 GATGGAAAGAAAAATTGTGAATAACGTGTCTGAACAAACTGAAAAT
65 GATGGAAAGAAAAATGGTGAATAACGTGTCTGAACAAACTGAAAAT
* * ** *
26147 TTGGAGGATATTCATGCTGTAGCGGAAGCAAGTATGGATATGGTCGAGGCAGAGGAGGACCCTGT
1 TTGGAGGATATTCATGCTGTAGAGGAAGCAGGTACAGATATGCT-GAGGCAGAGGAGGACCCTGT
* *
26212 GATGGAAGGAAAAATGGTGAATAATGTGTCTGAACAAACTGAAAAT
65 GATGGAAAGAAAAATGGTGAATAACGTGTCTGAACAAACTGAAAAT
* * * * * *
26258 TTGGAGGATATGCATGCTATAGAGGAAGCAGGTGCAGATACGGTTGAGGCAGAGGAGGACCCTGC
1 TTGGAGGATATTCATGCTGTAGAGGAAGCAGGTACAGATA-TGCTGAGGCAGAGGAGGACCCTGT
26323 GATGGAA
65 GATGGAA
26330 GAGGAATCGG
Statistics
Matches: 160, Mismatches: 21, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
110 1 0.01
111 157 0.98
112 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.21
Consensus pattern (110 bp):
TTGGAGGATATTCATGCTGTAGAGGAAGCAGGTACAGATATGCTGAGGCAGAGGAGGACCCTGTG
ATGGAAAGAAAAATGGTGAATAACGTGTCTGAACAAACTGAAAAT
Found at i:29821 original size:2 final size:2
Alignment explanation
Indices: 29814--29841 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29804 AGTTGCTTTG
29814 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
29842 TGCTGCTAGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:40960 original size:2 final size:2
Alignment explanation
Indices: 40953--40981 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40943 TAGAAAACAA
40953 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 A
40982 AATCAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42912 original size:6 final size:6
Alignment explanation
Indices: 42901--42942 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
42891 GACACGTATT
42901 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
42943 CGAGACGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.29, C:0.55, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:42933 original size:5 final size:5
Alignment explanation
Indices: 42905--42945 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
42895 CGTATTACCA
42905 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
42946 GACGAGACGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:43436 original size:20 final size:21
Alignment explanation
Indices: 43411--43467 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
43401 TTTGAAATAA
43411 ATCGCAACGCGAACTTCG-CT
1 ATCGCAACGCGAACTTCGACT
* *
43431 ATCGCAATGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
43452 ATCGCAACGTGAACTT
1 ATCGCAACGCGAACTT
43468 TAAATATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:53760 original size:32 final size:32
Alignment explanation
Indices: 53706--53773 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
53696 TTTATTGAAC
* * * * *
53706 AAATGAACATTAATGAATGGACTATCGAACAT
1 AAATAAACATAAACGAACGGACTACCGAACAT
*
53738 AAATAAACATAAACGAACGGACTACCGAACGT
1 AAATAAACATAAACGAACGGACTACCGAACAT
53770 AAAT
1 AAAT
53774 GAACGAACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.19
Consensus pattern (32 bp):
AAATAAACATAAACGAACGGACTACCGAACAT
Found at i:59079 original size:186 final size:186
Alignment explanation
Indices: 58872--59262 Score: 617
Period size: 186 Copynumber: 2.1 Consensus size: 186
58862 ATTAAATTTT
* * *
58872 AAATATTATATATA-TATATATAACATATGGGCTTAGCCCAAA-CTATTTAAAACTCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAATC-ATTTAAAACCCAATTAATA
* *
58935 ATTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAACTAAAAAAATTATATAAAAAT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATACTAATTAACTAAAAAAATTATATAAAAAT
* *
59000 TTTATTTTATAATTGTATATTATTTAAATTAATTGTAAACTGTTTTTTTGAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAAA
*
59057 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAATCATTTAAAACCCAGTTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAATCATTTAAAACCCAATTAATAA
* * * *
59122 TTTAAGATCCAATAATTTTTAAACTTAAATCAATACTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATACTAATTAACTAAAAAAATTATATAAAAATT
*
59187 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAAA
* *
59243 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
59263 AATTCGAAAT
Statistics
Matches: 189, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
185 21 0.11
186 167 0.88
187 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (186 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAATCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATACTAATTAACTAAAAAAATTATATAAAAATT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAAA
Found at i:59831 original size:12 final size:11
Alignment explanation
Indices: 59793--59845 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
59783 TATTTTAATC
*
59793 TTAAATTATTT
1 TTAATTTATTT
*
59804 TAAATTTATTT
1 TTAATTTATTT
*
59815 ATAATTTCATTT
1 TTAATTT-ATTT
*
59827 TTAATTTATAT
1 TTAATTTATTT
59838 TTATATTT
1 TTA-ATTT
59846 TCAAATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 20 0.59
12 14 0.41
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TTAATTTATTT
Found at i:59858 original size:25 final size:25
Alignment explanation
Indices: 59800--59855 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
59790 ATCTTAAATT
*
59800 ATTTTAAATT-TATTTATAATTTCA
1 ATTTTAATTTATATTTATAATTTCA
* *
59824 TTTTTAATTTATATTTATATTTTCAA
1 ATTTTAATTTATATTTATAATTTC-A
59850 ATTTTA
1 ATTTTA
59856 TTTTTAGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 8 0.31
25 12 0.46
26 6 0.23
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTTAATTTATATTTATAATTTCA
Found at i:71765 original size:23 final size:22
Alignment explanation
Indices: 71739--71789 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
71729 TATTCGTTTA
71739 TTTAACGTTC-GCAAATGTGTTCG
1 TTTAACGTTCAG-AAAT-TGTTCG
*
71762 TTTAATGTTCATGAAATTGTTCG
1 TTTAACGTTCA-GAAATTGTTCG
71785 TTTAA
1 TTTAA
71790 GTGTTTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 20 0.80
24 4 0.16
25 1 0.04
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (22 bp):
TTTAACGTTCAGAAATTGTTCG
Found at i:71807 original size:24 final size:23
Alignment explanation
Indices: 71751--71800 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
71741 TAACGTTCGC
*
71751 AAATGTGTTCGTTTAATGTTCATG
1 AAAT-TGTTCGTTTAATGTTCAAG
*
71775 AAATTGTTCGTTTAAGTGTTTAAG
1 AAATTGTTCGTTTAA-TGTTCAAG
71799 AA
1 AA
71801 TATGTTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (23 bp):
AAATTGTTCGTTTAATGTTCAAG
Found at i:75501 original size:2 final size:2
Alignment explanation
Indices: 75494--75524 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
75484 GTTTAATTGA
75494 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
75525 AACTAAATAT
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:76300 original size:20 final size:21
Alignment explanation
Indices: 76269--76307 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
76259 TATCTATTTA
76269 ATTTTATTTATTATTTGAAAT
1 ATTTTATTTATTATTTGAAAT
*
76290 ATTTT-TTTATTTTTTGAA
1 ATTTTATTTATTATTTGAA
76308 TAATGGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
ATTTTATTTATTATTTGAAAT
Found at i:76911 original size:59 final size:59
Alignment explanation
Indices: 76788--76918 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 59
76778 CGAGTGACTG
* * *
76788 TTTTGTAACTTTTAATAGTCGGGGACTTTAAAAAATAATGTCCTATAATCAAGAGACCA
1 TTTTGTAACTTTTAATAGTCGAGGACTTCAAAAAATAATCTCCTATAATCAAGAGACCA
* * * *
76847 TTTTGTAACTTTTAATAGTCGAAGGAC-TCAATAAAGTAATACT-CTATAGTCGAGGGACCA
1 TTTTGTAACTTTTAATAGTCG-AGGACTTCAA-AAAATAAT-CTCCTATAATCAAGAGACCA
76907 TTTGTGT-ACTTT
1 TTT-TGTAACTTT
76919 ACCCCTAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
59 24 0.39
60 33 0.54
61 4 0.07
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (59 bp):
TTTTGTAACTTTTAATAGTCGAGGACTTCAAAAAATAATCTCCTATAATCAAGAGACCA
Found at i:80976 original size:13 final size:13
Alignment explanation
Indices: 80960--80984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
80950 ATAAAATAAT
80960 AATTTATTATTAA
1 AATTTATTATTAA
80973 AATTTATTATTA
1 AATTTATTATTA
80985 TATAATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTATTATTAA
Found at i:81101 original size:29 final size:30
Alignment explanation
Indices: 81068--81151 Score: 75
Period size: 31 Copynumber: 2.8 Consensus size: 30
81058 GAGTCCCTTA
81068 ACTATTAAAAGTTATAAAATGATCCTC-CG
1 ACTATTAAAAGTTATAAAATGATCCTCTCG
* ****
81097 ACTA-TAGGAAGTTACTTTGTTGAGT-CTCTCG
1 ACTATTA-AAAGTTA-TAAAATGA-TCCTCTCG
81128 ACTATTAAAAGTTATAAAATGATC
1 ACTATTAAAAGTTATAAAATGATC
81152 ACTTGATTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 11
0.65 0.17 0.18
Matches are distributed among these distances:
28 2 0.05
29 11 0.28
30 11 0.28
31 13 0.33
32 2 0.05
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (30 bp):
ACTATTAAAAGTTATAAAATGATCCTCTCG
Found at i:81101 original size:60 final size:60
Alignment explanation
Indices: 81035--81151 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
81025 CATGGTCTCT
* *
81035 CGACTATAAGATA-TTATTTTATTGAGTCCCTTAACTATTAAAAGTTATAAAATGATCCTC
1 CGACTATAAGA-AGTTACTTTATTGAGTCCCTCAACTATTAAAAGTTATAAAATGATCCTC
* * * *
81095 CGACTATAGGAAGTTACTTTGTTGAGTCTCTCGACTATTAAAAGTTATAAAATGATC
1 CGACTATAAGAAGTTACTTTATTGAGTCCCTCAACTATTAAAAGTTATAAAATGATC
81152 ACTTGATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
59 1 0.02
60 49 0.98
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Consensus pattern (60 bp):
CGACTATAAGAAGTTACTTTATTGAGTCCCTCAACTATTAAAAGTTATAAAATGATCCTC
Found at i:82528 original size:75 final size:75
Alignment explanation
Indices: 82379--82586 Score: 256
Period size: 75 Copynumber: 2.8 Consensus size: 75
82369 CAAAGCAAAA
* * * * **
82379 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAATCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
82444 TTGGCTCCGAG
65 TTGGCTCCGAG
* *
82455 ATTTTCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
82520 TTGTTCCGAG
66 TGGCTCCGAG
* * * * *
82530 AATTCCAGTATGCTCGGAGGGAACCAATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
82587 GTTCAACGCT
Statistics
Matches: 114, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
75 83 0.73
76 31 0.27
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:88331 original size:18 final size:19
Alignment explanation
Indices: 88300--88336 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
88290 TTTTGGTGCA
88300 GAGGGAATCGATCCCCCCT
1 GAGGGAATCGATCCCCCCT
88319 GAGGGAA-CGATCCCCCCT
1 GAGGGAATCGATCCCCCCT
88337 TTGAAGGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.22, C:0.38, G:0.27, T:0.14
Consensus pattern (19 bp):
GAGGGAATCGATCCCCCCT
Found at i:91036 original size:75 final size:75
Alignment explanation
Indices: 90906--91113 Score: 240
Period size: 75 Copynumber: 2.8 Consensus size: 75
90896 CAAAGCAAAA
* * ** **
90906 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAAAAACCGATT-CCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTGAACAGT
90970 TTGGCTCCGAG
65 TTGGCTCCGAG
* * *
90981 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACTGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTGAACAGTT
* *
91046 TTGTTCCGAG
66 TGGCTCCGAG
* * * * *
91056 AATTCCAGTATGCTCGGAGGGAACCAATCCCCCCCA-AGGGGGTACCGATTCCCCCCTG
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCTG
91114 TTCAACGCTC
Statistics
Matches: 112, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
74 18 0.16
75 88 0.79
76 6 0.05
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTGAACAGTT
TGGCTCCGAG
Found at i:91878 original size:22 final size:22
Alignment explanation
Indices: 91850--91909 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
91840 GGCAAGTGAA
*
91850 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
*
91872 ATTTGTCCCGAAGGACCTTTGT
1 ATTTGTCCCGAAGGACCTATGT
* * *
91894 ATATATCTCGAAGGAC
1 ATTTGTCCCGAAGGAC
91910 TGCGTAGGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:96791 original size:22 final size:22
Alignment explanation
Indices: 96778--96828 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
96768 AATAGTTCTG
96778 AAATAAATAAATAAATGATATC
1 AAATAAATAAATAAATGATATC
*
96800 AAATAAATAAATAAATGATATT
1 AAATAAATAAATAAATGATATC
96822 AAATAAA
1 AAATAAA
96829 AATTATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (22 bp):
AAATAAATAAATAAATGATATC
Found at i:97774 original size:23 final size:24
Alignment explanation
Indices: 97727--97774 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
97717 TTAACCTCTT
*
97727 GCTTTGAGATTAGTTTTCTTTGAA
1 GCTTTGAGATTAGTTTTCTTCGAA
*
97751 GCTTTGAGATTATTTTTC-TCGAA
1 GCTTTGAGATTAGTTTTCTTCGAA
97774 G
1 G
97775 AGAAGAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.48
Consensus pattern (24 bp):
GCTTTGAGATTAGTTTTCTTCGAA
Found at i:103090 original size:213 final size:211
Alignment explanation
Indices: 102722--103401 Score: 884
Period size: 213 Copynumber: 3.2 Consensus size: 211
102712 TTTTATTATC
* *
102722 AAAGTTTAATTTTTATTTTATTTTAGTACCA-CAGTTAAAAAATTTAACTTTTGTTTCATTTTAG
1 AAAGTTTAATTTTTATTTCATTTTAGTACCACCA-TTAAAAAATTTAATTTTTGTTTCATTTTAG
* * * * **
102786 TATCGCATTCAAAATTGAATGTTATGCTTTGAAAAAAATTGAAAGTTTATGTTTTAAAACTAATC
65 TATC-CATTCAAAATTTAATGTTAAGTTTTGAAAAAAATTGAAAGTTTAAGTACTAAAAC-AATC
* *
102851 AAAACTGATAGTTTAGATACTGAACGGGTTAAGTTTTGATATGTTTTAGTACATAAACTTTCAGT
128 AAAATTGATAGTTTAGATACTGAACGGGTTAAGTTTTGATATGTTTTAGTACCTAAACTTTCAGT
* * *
102916 TCATTTCAAAACCATGCCT
193 TCTTTTCAAAATCATACCT
* **
102935 AAAGTTTAATTTTTATTTTATTTTAGTATCTTCCATTAAAAAATTTAATTTTTGTTTCATTTTAG
1 AAAGTTTAATTTTTATTTCATTTTAGTA-CCACCATTAAAAAATTTAATTTTTGTTTCATTTTAG
* *
103000 TATCCATTCAAAATTTAATGTTAAATTTTGAAAAAAATTGAAAGTTTAGGTACTAAAACGAATCA
65 TATCCATTCAAAATTTAATGTTAAGTTTTGAAAAAAATTGAAAGTTTAAGTACTAAAAC-AATCA
* * * * * *
103065 AAATTGATAGTTTAAATATTGAACGGGTTAAGTTTTGTTCTATTTTAGTACCTAAACTTTCAATT
129 AAATTGATAGTTTAGATACTGAACGGGTTAAGTTTTGATATGTTTTAGTACCTAAACTTTCAGTT
103130 CTTTTCAAAATCATACCT
194 CTTTTCAAAATCATACCT
* * *
103148 AAAGTTTAATTTTTATTTCATTTTAGTACACACCATTAAAAACTTTAATTTTTATTTCATTTTAA
1 AAAGTTTAATTTTTATTTCATTTTAGTAC-CACCATTAAAAAATTTAATTTTTGTTTCATTTTAG
** * *
103213 TAT-CATGTTCAAAATTTAACATTAAGTTTTG-AAAAAATTGAAAGTATAAGTACTAAAACAAAC
65 TATCCA--TTCAAAATTTAATGTTAAGTTTTGAAAAAAATTGAAAGTTTAAGTACTAAAACAATC
* * *
103276 TAAAATTGATAGTTTAGATACTAAACGGGTTAAATTTTGATTTGTTTTAGTACCTAAAC-TT-AG
128 -AAAATTGATAGTTTAGATACTGAACGGGTTAAGTTTTGATATGTTTTAGTACCTAAACTTTCAG
* *
103339 TTTTTTTCTAAAATCATACAT
192 TTCTTTTC-AAAATCATACCT
* *
103360 AAAATTTAATTTTTGTTTCATTTTAGTACCCACCATTAAAAA
1 AAAGTTTAATTTTTATTTCATTTTAGTA-CCACCATTAAAAA
103402 TTACAAAATG
Statistics
Matches: 413, Mismatches: 46, Indels: 17
0.87 0.10 0.04
Matches are distributed among these distances:
211 8 0.02
212 57 0.14
213 291 0.70
214 55 0.13
215 2 0.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (211 bp):
AAAGTTTAATTTTTATTTCATTTTAGTACCACCATTAAAAAATTTAATTTTTGTTTCATTTTAGT
ATCCATTCAAAATTTAATGTTAAGTTTTGAAAAAAATTGAAAGTTTAAGTACTAAAACAATCAAA
ATTGATAGTTTAGATACTGAACGGGTTAAGTTTTGATATGTTTTAGTACCTAAACTTTCAGTTCT
TTTCAAAATCATACCT
Found at i:107655 original size:67 final size:68
Alignment explanation
Indices: 107562--107697 Score: 240
Period size: 67 Copynumber: 2.0 Consensus size: 68
107552 TTAGTTTTTG
107562 TTTCATTTTAGTATCAACCATTAAATTTATTTAATAGATCATACACAATATCTAATTTTT-TTTT
1 TTTCATTTTAGTATCAACCATTAAATTTATTTAATAGATCATACA-AATATCTAATTTTTCTTTT
107626 ATTT
65 ATTT
*
107630 TTTCATTTTA-TATCAATCATTAAATTTATTTAATAGATCATACAAATATCTAATTTTTCTTTTA
1 TTTCATTTTAGTATCAACCATTAAATTTATTTAATAGATCATACAAATATCTAATTTTTCTTTTA
107694 TTT
66 TTT
107697 T
1 T
107698 AGTACACATT
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
66 14 0.21
67 42 0.64
68 10 0.15
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (68 bp):
TTTCATTTTAGTATCAACCATTAAATTTATTTAATAGATCATACAAATATCTAATTTTTCTTTTA
TTT
Found at i:107909 original size:58 final size:58
Alignment explanation
Indices: 107847--107957 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
107837 TTTTTTTAAA
* *
107847 AAAAT-TTAGCATTAAATTTTGAATAC-CTAATTATTAAAATGAAACAAAAACTATTTTT
1 AAAATATTAACATT-AATTTTGAATACTCTAA-TACTAAAATGAAACAAAAACTATTTTT
* * *
107905 AAAATATTAACGTTAATTTTGAATACTTTGATACTAAAATGAAACAAAAACTA
1 AAAATATTAACATTAATTTTGAATACTCTAATACTAAAATGAAACAAAAACTA
107958 AACGTTGGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 38 0.83
59 8 0.17
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (58 bp):
AAAATATTAACATTAATTTTGAATACTCTAATACTAAAATGAAACAAAAACTATTTTT
Found at i:108840 original size:30 final size:30
Alignment explanation
Indices: 108804--108861 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
108794 ACCATATTCA
*
108804 TCGGTCAATTGAACCGGGTTGCCGTGCTCG
1 TCGGTCAATTGAACCGGGTTGCCATGCTCG
* **
108834 TCGGTCAGTTGAATGGGGTTGCCATGCT
1 TCGGTCAATTGAACCGGGTTGCCATGCT
108862 TGTCTCTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.14, C:0.22, G:0.34, T:0.29
Consensus pattern (30 bp):
TCGGTCAATTGAACCGGGTTGCCATGCTCG
Found at i:109631 original size:32 final size:38
Alignment explanation
Indices: 109556--109633 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 38
109546 TATTTAAAGT
*
109556 TTAATTTTTATTTTCATTTTAATATCTCGATGTTAAAAG
1 TTAATTTTTATTTTCATTTT-ATATCTCGATGTTAAAAA
109595 TTAATTTTTA-TTTCA-TTT-TA-CTCG-T-TTAAAAA
1 TTAATTTTTATTTTCATTTTATATCTCGATGTTAAAAA
109627 TTAATTT
1 TTAATTT
109634 CAAGTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
32 13 0.34
33 1 0.03
34 4 0.11
35 2 0.05
37 3 0.08
38 5 0.13
39 10 0.26
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (38 bp):
TTAATTTTTATTTTCATTTTATATCTCGATGTTAAAAA
Done.