Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005659.1 Hibiscus syriacus cultivar Beakdansim tig00013231_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: 115113
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:369 original size:2 final size:2
Alignment explanation
Indices: 364--388 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
354 AAAAAAATGA
364 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 A
389 ACAATGTAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:859 original size:3 final size:3
Alignment explanation
Indices: 831--895 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
821 TGCGGGGCCT
* *
831 ATA AAA ATA ATA A-A ATA AAA AT- ATA ATA ATA ATA ATA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
875 ATA A-A TATA ATA ATA A-A ATA A
1 ATA ATA -ATA ATA ATA ATA ATA A
896 ATATTTTTGT
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 7 0.13
3 41 0.79
4 4 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:860 original size:19 final size:19
Alignment explanation
Indices: 835--898 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
825 GGGCCTATAA
835 AAATAATAA-AATAAAAAT
1 AAATAATAATAATAAAAAT
*
853 ATAATAATAATAATAATAAT
1 A-AATAATAATAATAAAAAT
873 AAATAA-ATATAATAATAAAAT
1 AAATAATA-ATAAT-A-AAAAT
894 AAATA
1 AAATA
899 TTTTTGTAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 2 0.05
19 18 0.46
20 10 0.26
21 9 0.23
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAATAATAATAAAAAT
Found at i:898 original size:28 final size:31
Alignment explanation
Indices: 831--898 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 31
821 TGCGGGGCCT
831 ATAA-AAATAATAAAATAAAAATATAATAATA
1 ATAATAAATAATAAAAT-AAAATATAATAATA
862 ATAAT-AATAAT-AAAT-AAATATAATAATA
1 ATAATAAATAATAAAATAAAATATAATAATA
890 A-AATAAATA
1 ATAATAAATA
899 TTTTTGTAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
27 3 0.09
28 18 0.51
30 4 0.11
31 10 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (31 bp):
ATAATAAATAATAAAATAAAATATAATAATA
Found at i:6636 original size:23 final size:22
Alignment explanation
Indices: 6609--6662 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
6599 TTGTGTTCGG
6609 TTCGTTTATCATTTGT-AAACATA
1 TTCGTTTAT-ATTTGTCAAA-ATA
*
6632 TTCGTTTAATGTTTGTCAAAATA
1 TTCGTTT-ATATTTGTCAAAATA
6655 TTCGTTTA
1 TTCGTTTA
6663 CAGTTATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.04
23 22 0.79
24 5 0.18
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (22 bp):
TTCGTTTATATTTGTCAAAATA
Found at i:15127 original size:16 final size:17
Alignment explanation
Indices: 15106--15143 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
15096 GAAGTCAAAC
15106 AATAAAACAAACAAGA-
1 AATAAAACAAACAAGAT
*
15122 AAT-AAATAAACAAGAT
1 AATAAAACAAACAAGAT
15138 AATAAA
1 AATAAA
15144 CGAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 11 0.58
16 6 0.32
17 2 0.11
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (17 bp):
AATAAAACAAACAAGAT
Found at i:15133 original size:39 final size:39
Alignment explanation
Indices: 15102--15181 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
15092 ACATGAAGTC
15102 AAAC-AATAAAACAAACAAGAAATAAATAAACAAGATAAT
1 AAACGAATAAAACAAA-AAGAAATAAATAAACAAGATAAT
* * * *
15141 AAACGAATAAAATAAAAATAAACAAATAAACAATA-AAT
1 AAACGAATAAAACAAAAAGAAATAAATAAACAAGATAAT
15179 AAA
1 AAA
15182 TAAATAAGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 6 0.17
39 20 0.56
40 10 0.28
ACGTcount: A:0.74, C:0.09, G:0.04, T:0.14
Consensus pattern (39 bp):
AAACGAATAAAACAAAAAGAAATAAATAAACAAGATAAT
Found at i:15178 original size:19 final size:19
Alignment explanation
Indices: 15110--15188 Score: 70
Period size: 19 Copynumber: 4.1 Consensus size: 19
15100 TCAAACAATA
* * *
15110 AAACAAACAAGAAATAAAT
1 AAACAAAAAATAAACAAAT
* *
15129 AAACAAGATAATAAACGAAT
1 AAACAA-AAAATAAACAAAT
15149 AAA-ATAAAAATAAACAAAT
1 AAACA-AAAAATAAACAAAT
* *
15168 AAACAATAAATAAATAAAT
1 AAACAAAAAATAAACAAAT
15187 AA
1 AA
15189 GTAAATTAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
19 35 0.71
20 14 0.29
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.15
Consensus pattern (19 bp):
AAACAAAAAATAAACAAAT
Found at i:15697 original size:10 final size:10
Alignment explanation
Indices: 15669--15722 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
15659 AGGATTCAAA
15669 AATATAT-AT
1 AATATATAAT
*
15678 AGTA-ATAAT
1 AATATATAAT
15687 AATATATAAT
1 AATATATAAT
* *
15697 AAAATGTAAT
1 AATATATAAT
*
15707 -ATATATAAA
1 AATATATAAT
15716 AATATAT
1 AATATAT
15723 TTTGATTGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
8 2 0.06
9 14 0.40
10 19 0.54
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (10 bp):
AATATATAAT
Found at i:18237 original size:12 final size:12
Alignment explanation
Indices: 18220--18263 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
18210 ACCCACCTTA
18220 TTTTTCTTTTCT
1 TTTTTCTTTTCT
*
18232 TTTTTCTTTTGT
1 TTTTTCTTTTCT
18244 TCTTTCTCTTTTTCT
1 T-TTT-TC-TTTTCT
18259 TTTTT
1 TTTTT
18264 TTTCAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 12 0.44
13 4 0.15
14 5 0.19
15 6 0.22
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:18390 original size:76 final size:79
Alignment explanation
Indices: 18230--18390 Score: 193
Period size: 76 Copynumber: 2.1 Consensus size: 79
18220 TTTTTCTTTT
* * * *
18230 CTTTTTTCTTTTGTTCTTTCTCTTTTTCTTTTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCA
1 CTTTTTTCTTTTGTTCTTTCTCTTTTTCTCTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCA
*** *
18295 CCCTAAACGTTTTT
66 CCCTAAACGAAGTA
* *
18309 GTTTTTTGTTTT-TT-TTTC-CTTTTTCTCTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCA
1 CTTTTTTCTTTTGTTCTTTCTCTTTTTCTCTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCA
* *
18371 TCCTAAGCGAAGTA
66 CCCTAAACGAAGTA
18385 CTTTTT
1 CTTTTT
18391 GACTGCATCC
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
76 53 0.77
77 4 0.06
78 2 0.03
79 10 0.14
ACGTcount: A:0.11, C:0.21, G:0.12, T:0.56
Consensus pattern (79 bp):
CTTTTTTCTTTTGTTCTTTCTCTTTTTCTCTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCA
CCCTAAACGAAGTA
Found at i:25414 original size:16 final size:16
Alignment explanation
Indices: 25393--25427 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
25383 ATACGAATGT
25393 AAAAACATGGAAA-ATA
1 AAAAACAT-GAAATATA
25409 AAAAACATGAAATATA
1 AAAAACATGAAATATA
25425 AAA
1 AAA
25428 TGCAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.14
Consensus pattern (16 bp):
AAAAACATGAAATATA
Found at i:28732 original size:16 final size:16
Alignment explanation
Indices: 28713--28751 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
28703 TGAAGTCAAA
28713 AAATAAAACAAACAAG
1 AAATAAAACAAACAAG
*
28729 AAAT-AAATAAACAAG
1 AAATAAAACAAACAAG
28744 ATAATAAA
1 A-AATAAA
28752 CAGATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 11 0.55
16 7 0.35
17 2 0.10
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (16 bp):
AAATAAAACAAACAAG
Found at i:28786 original size:19 final size:19
Alignment explanation
Indices: 28713--28796 Score: 71
Period size: 19 Copynumber: 4.3 Consensus size: 19
28703 TGAAGTCAAA
* * *
28713 AAATAAAACAAACAAGAAAT
1 AAAT-AAACAAAAAATAAAC
*
28733 AAATAAACAAGATAATAAAC
1 AAATAAACAA-AAAATAAAC
*
28753 AGATAAA-ATAAAAATAAAC
1 AAATAAACA-AAAAATAAAC
* *
28772 AAATAAACAATAAATAAAT
1 AAATAAACAAAAAATAAAC
28791 AAATAA
1 AAATAA
28797 GTAAATTAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
19 35 0.66
20 18 0.34
ACGTcount: A:0.74, C:0.07, G:0.04, T:0.15
Consensus pattern (19 bp):
AAATAAACAAAAAATAAAC
Found at i:28843 original size:21 final size:19
Alignment explanation
Indices: 28818--28888 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 19
28808 AAGCCAAGCG
28818 AAAATAAAAAAAATGAAAAT
1 AAAATAAAAAAAAT-AAAAT
* *
28838 ACAAATACAAAAAATTAAAT
1 A-AAATAAAAAAAATAAAAT
* *
28858 AGAAT-AAAAAAATAGTAAT
1 AAAATAAAAAAAATA-AAAT
28877 AAAATAATAAAA
1 AAAATAA-AAAA
28889 TACGAAAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
18 7 0.17
19 10 0.25
20 7 0.17
21 16 0.40
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (19 bp):
AAAATAAAAAAAATAAAAT
Found at i:29022 original size:21 final size:20
Alignment explanation
Indices: 28982--29022 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
28972 CATCGAAAGT
*
28982 AAAAAAAAGGTACAGATTTG
1 AAAAAAAAGGTAAAGATTTG
*
29002 AAAAAAAAGGGTAAAGGTTTG
1 AAAAAAAA-GGTAAAGATTTG
29023 GTCAGCTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.54, C:0.02, G:0.24, T:0.20
Consensus pattern (20 bp):
AAAAAAAAGGTAAAGATTTG
Found at i:35326 original size:130 final size:130
Alignment explanation
Indices: 35185--35432 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
35175 TATTTATATA
*
35185 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
35250 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
35315 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
35380 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
35433 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:35463 original size:130 final size:129
Alignment explanation
Indices: 35199--35463 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
35189 ATTTGGTCCT
* *
35199 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
35264 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
35329 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
35394 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
35458 -A
128 CA
35459 AAATT
1 AAATT
35464 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:35920 original size:15 final size:16
Alignment explanation
Indices: 35896--35932 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
35886 TTTAATTTCT
35896 TATT-AAAAATA-AAA
1 TATTCAAAAATATAAA
35910 TATTCAAAAATATAAA
1 TATTCAAAAATATAAA
35926 TGATTCA
1 T-ATTCA
35933 TACATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
TATTCAAAAATATAAA
Found at i:36079 original size:21 final size:21
Alignment explanation
Indices: 36055--36097 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
36045 TATTACCTTA
36055 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
36076 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
36097 A
1 A
36098 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:36115 original size:35 final size:35
Alignment explanation
Indices: 36066--36151 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
36056 ATTGAAGTAT
** * *
36066 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
36101 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
36136 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
36152 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:41578 original size:19 final size:20
Alignment explanation
Indices: 41510--41579 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 20
41500 AATAGTTTCT
*
41510 GAAACTTAAAATCGCAACGC
1 GAAACTGAAAATCGCAACGC
* * *
41530 GAAAATGAAAATTGCAACGT
1 GAAACTGAAAATCGCAACGC
*
41550 GAAA-TGAAAATCGCAACAC
1 GAAACTGAAAATCGCAACGC
41569 GAAACT-AAAAT
1 GAAACTGAAAAT
41580 AGCGTTGCGA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 21 0.50
20 21 0.50
ACGTcount: A:0.51, C:0.17, G:0.16, T:0.16
Consensus pattern (20 bp):
GAAACTGAAAATCGCAACGC
Found at i:41954 original size:20 final size:21
Alignment explanation
Indices: 41929--41993 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
41919 TCTGAGAGAT
41929 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
41949 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
* * *
41971 AGAGATGGGGACGGATATCGCC
1 GGAGAT-GAGACGGATTTCGCC
41993 G
1 G
41994 TAGAGAGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 6 0.16
22 31 0.84
ACGTcount: A:0.23, C:0.17, G:0.42, T:0.18
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:41963 original size:22 final size:22
Alignment explanation
Indices: 41936--41993 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
41926 GATGGAGATA
41936 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
41958 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
41980 GACGGATATCGCCG
1 GACGGATTTCGCCG
41994 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.41, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:42166 original size:20 final size:20
Alignment explanation
Indices: 42141--42230 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
42131 TAAAAGCGAT
* *
42141 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGCG
42161 TTGCGAATTTGACTTCTGCG
1 TTGCGAATTTGACTTCTGCG
* ** *
42181 TTGGGAATTTGGA-AACTGAG
1 TTGCGAATTT-GACTTCTGCG
* *
42201 TTGCGAAATTGGAGTTC-GCG
1 TTGCG-AATTTGACTTCTGCG
42221 TTGCGAATTT
1 TTGCGAATTT
42231 ATTGGACATT
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
19 4 0.07
20 44 0.80
21 7 0.13
ACGTcount: A:0.20, C:0.12, G:0.29, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGCG
Found at i:43641 original size:27 final size:27
Alignment explanation
Indices: 43603--43664 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
43593 ATATCCTTTT
43603 TGAAATCCCATTTCATCATAAGTGTTA
1 TGAAATCCCATTTCATCATAAGTGTTA
43630 TGAAATCCCATTTCATCATAAGTGTTA
1 TGAAATCCCATTTCATCATAAGTGTTA
43657 TGAAATCC
1 TGAAATCC
43665 AAAGGAACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.35
Consensus pattern (27 bp):
TGAAATCCCATTTCATCATAAGTGTTA
Found at i:48665 original size:2 final size:2
Alignment explanation
Indices: 48658--48703 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
48648 GTATTTACAC
48658 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
48700 AT AT
1 AT AT
48704 TAATATTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49863 original size:5 final size:5
Alignment explanation
Indices: 49853--49885 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
49843 ATGACTTATC
49853 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
49886 GTTATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:51396 original size:37 final size:35
Alignment explanation
Indices: 51341--51440 Score: 103
Period size: 35 Copynumber: 2.7 Consensus size: 35
51331 TTTCGTCCTA
51341 CTAGGATTTAAACTTTAAAAAATAGGATAGAATTCTG
1 CTAGGATTTAAACTTT--AAAATAGGATAGAATTCTG
* *
51378 CTAGGA-TTCAACTCTTAAAATAGGATAGAATTTTG
1 CTAGGATTTAAACT-TTAAAATAGGATAGAATTCTG
* * *
51413 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTAGGATTTAAACT-TTAAA-ATAGGAT
51441 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
35 22 0.41
36 17 0.31
37 15 0.28
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (35 bp):
CTAGGATTTAAACTTTAAAATAGGATAGAATTCTG
Found at i:51862 original size:33 final size:32
Alignment explanation
Indices: 51796--51875 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 32
51786 ATTATTCTTG
* *
51796 TTATATATGCATATTACTTTCTATTAATTTTA
1 TTATATATGTATATTACTTTCTATTAATGTTA
* * *
51828 TTATATATGTATATATATTTTTTATTAGTGTTA
1 TTATATATGTATAT-TACTTTCTATTAATGTTA
*
51861 TTATATATATATATT
1 TTATATATGTATATT
51876 TATATATTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 14 0.34
33 27 0.66
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.59
Consensus pattern (32 bp):
TTATATATGTATATTACTTTCTATTAATGTTA
Found at i:51865 original size:21 final size:21
Alignment explanation
Indices: 51817--51866 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
51807 TATTACTTTC
51817 TATTA-ATTTTATTATATATG
1 TATTATATTTTATTATATATG
51837 TATATATATTTT-TTAT-TAGTG
1 TAT-TATATTTTATTATATA-TG
51858 TTATTATAT
1 -TATTATAT
51867 ATATATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 5 0.19
21 13 0.50
22 8 0.31
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (21 bp):
TATTATATTTTATTATATATG
Found at i:51985 original size:17 final size:17
Alignment explanation
Indices: 51939--52055 Score: 62
Period size: 18 Copynumber: 6.6 Consensus size: 17
51929 TTTTTTATTA
*
51939 TTAT-TATTTTACTTAT
1 TTATATATTTTACTTTT
* *
51955 ATATATGCTTTTACTTTT
1 TTATAT-ATTTTACTTTT
51973 TTATATATTTTACTCATTT
1 TTATATATTTTACT--TTT
*
51992 ATTATCTATTTTTA-TTTAT
1 -TTATATA-TTTTACTTT-T
*
52011 CT-TATATTTTA-TGTTT
1 TTATATATTTTACT-TTT
*
52027 TTATATTCTTTTACTTGTT
1 TTATA-TATTTTACTT-TT
*
52046 TTATTTATTT
1 TTATATATTT
52056 ATTTGCATTA
Statistics
Matches: 77, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
16 11 0.14
17 15 0.19
18 28 0.36
19 11 0.14
20 7 0.09
21 5 0.06
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.68
Consensus pattern (17 bp):
TTATATATTTTACTTTT
Found at i:57870 original size:3 final size:3
Alignment explanation
Indices: 57862--57886 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
57852 TTATATACAT
57862 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
57887 AAACTAACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:58333 original size:17 final size:18
Alignment explanation
Indices: 58296--58335 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
58286 CCTTAGCCCA
58296 GGGCAGCATGATTGAGAG
1 GGGCAGCATGATTGAGAG
* *
58314 GGGCAGTATGTTTGAG-G
1 GGGCAGCATGATTGAGAG
58331 GGGCA
1 GGGCA
58336 TGAACAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.23, C:0.10, G:0.47, T:0.20
Consensus pattern (18 bp):
GGGCAGCATGATTGAGAG
Found at i:64180 original size:85 final size:85
Alignment explanation
Indices: 64023--64218 Score: 245
Period size: 85 Copynumber: 2.3 Consensus size: 85
64013 CTAAAGTTAA
* * *
64023 CGGCATTTTTTGAACAAACGCCGCAAAAAGGTCGATATCTATAGTGACATTTTTAGAACAAACGT
1 CGGCGTTTTTTGAACAAACGCCGCAAAAAGGTCGA-ATCTATAGCGACATTTTTAGAACAAACGC
64088 CGAAAAAGGTCAGATCTATAG
65 CGAAAAAGGTCAGATCTATAG
* * * *
64109 TGGCGTTTTTGGAACAAACGCCGC-AAAAGGTCTG-ATCTATAGCGGCGTTTTT-GAATACAAAC
1 CGGCGTTTTTTGAACAAACGCCGCAAAAAGGTC-GAATCTATAGCGACATTTTTAG-A-ACAAAC
*
64171 GCCGCAAAAGGTCAGATCTATAG
63 GCCGAAAAAGGTCAGATCTATAG
*
64194 CGGCGTTTTTTAATACAAACGCCGC
1 CGGCGTTTTTTGA-ACAAACGCCGC
64219 CAAATATGCA
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
83 1 0.01
84 16 0.17
85 45 0.47
86 33 0.35
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (85 bp):
CGGCGTTTTTTGAACAAACGCCGCAAAAAGGTCGAATCTATAGCGACATTTTTAGAACAAACGCC
GAAAAAGGTCAGATCTATAG
Found at i:64183 original size:43 final size:42
Alignment explanation
Indices: 64029--64218 Score: 231
Period size: 43 Copynumber: 4.5 Consensus size: 42
64019 TTAACGGCAT
* * * *
64029 TTTTTG-AACAAACGCCGCAAAAAGGTCGATATCTATAGTGACA
1 TTTTTGAAACAAACGCCGC-AAAAGGTC-AGATCTATAGCGGCG
* * *
64072 TTTTT-AGAACAAACGTCGAAAAAGGTCAGATCTATAGTGGCG
1 TTTTTGA-AACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
* *
64114 TTTTTGGAACAAACGCCGCAAAAGGTCTGATCTATAGCGGCG
1 TTTTTGAAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
64156 TTTTTGAATACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
1 TTTTTGAA-ACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
*
64199 TTTTTTAATACAAACGCCGC
1 TTTTTGAA-ACAAACGCCGC
64219 CAAATATGCA
Statistics
Matches: 130, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
42 55 0.42
43 65 0.50
44 10 0.08
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (42 bp):
TTTTTGAAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
Found at i:65730 original size:78 final size:78
Alignment explanation
Indices: 65601--65756 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
65591 CCTCATGATT
65601 ATCCTTTCATCAATGTCTCCCATGATTTACAAAAAAGTGGGGACAACATAGAAGAGAAAATGCAA
1 ATCCTTTCATCAATGTCTCCCATGATTTACAAAAAAGTGGGGACAACATAGAAGAGAAAATGCAA
65666 TTTGTTGGATATA
66 TTTGTTGGATATA
65679 ATCCTTTCATCAATGTCTCCCATGATTTACAAAAAAGTGGGGACAACATAGAAGAGAAAATGCAA
1 ATCCTTTCATCAATGTCTCCCATGATTTACAAAAAAGTGGGGACAACATAGAAGAGAAAATGCAA
65744 TTTGTTGGATATA
66 TTTGTTGGATATA
65757 TGAACTGCAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (78 bp):
ATCCTTTCATCAATGTCTCCCATGATTTACAAAAAAGTGGGGACAACATAGAAGAGAAAATGCAA
TTTGTTGGATATA
Found at i:66527 original size:6 final size:6
Alignment explanation
Indices: 66516--66634 Score: 208
Period size: 6 Copynumber: 20.3 Consensus size: 6
66506 GACACGTATT
66516 ACCACG ACCACG ACCACG ACCACG ACCACG ACCA-- ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
66562 ACCACG ACCACG ACCACG ACCACG ACCCCG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
66610 ACCACG A-CACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG AC
66635 GAGCCGAGCC
Statistics
Matches: 108, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
4 4 0.04
5 5 0.05
6 99 0.92
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:69949 original size:11 final size:11
Alignment explanation
Indices: 69935--69977 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
69925 AAGCAAACGA
69935 TAAACGAACAC
1 TAAACGAACAC
* **
69946 TAAATGAACGT
1 TAAACGAACAC
69957 TAAACGAACAC
1 TAAACGAACAC
69968 TAAACGAACA
1 TAAACGAACA
69978 TGTTCGTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.53, C:0.21, G:0.12, T:0.14
Consensus pattern (11 bp):
TAAACGAACAC
Found at i:69955 original size:22 final size:22
Alignment explanation
Indices: 69930--69976 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
69920 TATATAAGCA
*
69930 AACGATAAACGAACACTAAATG
1 AACGATAAACGAACACTAAACG
*
69952 AACGTTAAACGAACACTAAACG
1 AACGATAAACGAACACTAAACG
69974 AAC
1 AAC
69977 ATGTTCGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.13
Consensus pattern (22 bp):
AACGATAAACGAACACTAAACG
Found at i:70918 original size:35 final size:36
Alignment explanation
Indices: 70867--70947 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 36
70857 AACACAGTTA
* *
70867 TCAATTACATTGTAAACCCCAAATT-TAAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
*
70902 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
70938 TCAATTACAT
1 TCAATTACAT
70948 GCCTAATCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 23 0.55
36 19 0.45
ACGTcount: A:0.44, C:0.22, G:0.01, T:0.32
Consensus pattern (36 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
Found at i:70940 original size:36 final size:35
Alignment explanation
Indices: 70867--70964 Score: 126
Period size: 36 Copynumber: 2.8 Consensus size: 35
70857 AACACAGTTA
* *
70867 TCAATTACATTGTAAACCCCAAATTTAAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCAAAAATACT
*
70902 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCCCAAATT-CAAAAATACT
* *
70938 TCAATTACATGCCT-AATCCCAAATTCA
1 TCAATTACAT-TCTAAACCCCAAATTCA
70965 TAATACATTC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 25 0.45
36 28 0.51
37 2 0.04
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCAAAAATACT
Found at i:71598 original size:148 final size:148
Alignment explanation
Indices: 71418--71714 Score: 454
Period size: 148 Copynumber: 2.0 Consensus size: 148
71408 AAACTATTTA
* * * * *
71418 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACATAAACTCAAA
1 AATTACAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* * *
71483 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAATTCAAATTG-AAAAAATTTTGAGTCAAC
66 AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTC-AA-TGAAAAAAATTTCGAGTCAAC
71547 TATTTTAT-AAACTGAATTG
129 TATTTTATAAAACTGAATTG
* **
71566 AATTACAATAAAATAATGTTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTGGAA
1 AATTACAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
*
71631 AATTCAATTCAATTTGAATTGATTTAAATTTTATAAACTCAATGAAAAAAATTTCGAGTCAACTA
66 AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAATGAAAAAAATTTCGAGTCAACTA
71696 TTTTATAAAACTGAATTG
131 TTTTATAAAACTGAATTG
71714 A
1 A
71715 GTATTTAGAT
Statistics
Matches: 135, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
146 2 0.01
147 27 0.20
148 106 0.79
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (148 bp):
AATTACAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAATGAAAAAAATTTCGAGTCAACTA
TTTTATAAAACTGAATTG
Found at i:73268 original size:35 final size:36
Alignment explanation
Indices: 73229--73309 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 36
73219 AACACAGTCA
*
73229 TCAATTACATTATAAA-CTCCAAATTTC-AAAATACT
1 TCAATTACATTATAAACCT-CAAATTCCAAAAATACT
* *
73264 TCAATTACATTCTAAACCTCAAATTCCAAAAATAGT
1 TCAATTACATTATAAACCTCAAATTCCAAAAATACT
*
73300 TTAATTACAT
1 TCAATTACAT
73310 GCCCAATCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 22 0.55
36 18 0.45
ACGTcount: A:0.44, C:0.20, G:0.01, T:0.35
Consensus pattern (36 bp):
TCAATTACATTATAAACCTCAAATTCCAAAAATACT
Found at i:73974 original size:145 final size:146
Alignment explanation
Indices: 73786--74073 Score: 442
Period size: 145 Copynumber: 2.0 Consensus size: 146
73776 AAACTATTTA
* *
73786 AATTAGAATCAAATATATTATAGTATTATAAATATTTATAATTAAATTTAAACATAAACT-CAAA
1 AATTAGAATCAAATATATTATAGTATGATAAATATTTATAATT-AATTTAAACAGAAACTGCAAA
* * *
73850 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAA-AATTTTGAGTCAACT
65 ATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTC-AAT-GAAAAGAAATTCGAGTCAACT
73914 ATTTTATAAAA-TGAACTG
128 ATTTTATAAAACTGAACTG
*
73932 AATTAGAATCAAATAATATTATA-TATGA-AAATATTTATAATTAATTTAAACAGAAACTGGAAA
1 AATTAGAATCAAAT-ATATTATAGTATGATAAATATTTATAATTAATTTAAACAGAAACTGCAAA
*
73995 ATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAATTAAAAGAAATTCGAGTCAACTAT
65 ATTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAATGAAAAGAAATTCGAGTCAACTAT
74060 TTTATAAAACTGAA
130 TTTATAAAACTGAA
74074 TTGAGTATTT
Statistics
Matches: 131, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
143 4 0.03
144 42 0.32
145 59 0.45
146 18 0.14
147 8 0.06
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (146 bp):
AATTAGAATCAAATATATTATAGTATGATAAATATTTATAATTAATTTAAACAGAAACTGCAAAA
TTCAATTCAATTCGAATTGATTTAAATTTTATAAACTCAATGAAAAGAAATTCGAGTCAACTATT
TTATAAAACTGAACTG
Found at i:75647 original size:35 final size:36
Alignment explanation
Indices: 75598--75676 Score: 124
Period size: 35 Copynumber: 2.2 Consensus size: 36
75588 CACAATTATT
* *
75598 AATTATATTGTAAACCCCAAATTTC-AAAATACTTC
1 AATTATATTCTAAACCCCAAATTCCAAAAATACTTC
*
75633 AATTATATTCTAAACCTCAAATTCCAAAAATACTTC
1 AATTATATTCTAAACCCCAAATTCCAAAAATACTTC
75669 AATTATAT
1 AATTATAT
75677 GTCCAATCCT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 22 0.55
36 18 0.45
ACGTcount: A:0.44, C:0.19, G:0.01, T:0.35
Consensus pattern (36 bp):
AATTATATTCTAAACCCCAAATTCCAAAAATACTTC
Found at i:75691 original size:36 final size:36
Alignment explanation
Indices: 75598--75692 Score: 113
Period size: 36 Copynumber: 2.7 Consensus size: 36
75588 CACAATTATT
** * *
75598 AATTATATTGTAAACCCCAAATTTC-AAAATACTTC
1 AATTATATTCCAAACCTCAAATTCCAAAAATACTTC
*
75633 AATTATATTCTAAACCTCAAATTCCAAAAATACTTC
1 AATTATATTCCAAACCTCAAATTCCAAAAATACTTC
*
75669 AATTATATGTCCAATCCT-AAATTC
1 AATTATAT-TCCAAACCTCAAATTC
75693 ATAATACATT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
35 22 0.42
36 24 0.45
37 7 0.13
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (36 bp):
AATTATATTCCAAACCTCAAATTCCAAAAATACTTC
Found at i:76348 original size:148 final size:147
Alignment explanation
Indices: 76155--76446 Score: 460
Period size: 148 Copynumber: 2.0 Consensus size: 147
76145 AAACTATTTA
* * *
76155 AATTTGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
** * *
76220 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCTAGTCAACT
66 AATTCAATTCAATTCGAAATGATTTAAATTTTATAAACTC-AAT-GAAAAAAATTCGAGTCAACT
76285 ATTTTAT-AAACTGAACTG
129 ATTTTATAAAACTGAACTG
**
76303 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTGGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* *
76368 AATTTAATTCAATTCGAAATGATTTAAATTTTATAAACTCAATTAAAAAAATTCGAGTCAACTAT
66 AATTCAATTCAATTCGAAATGATTTAAATTTTATAAACTCAATGAAAAAAATTCGAGTCAACTAT
76433 TTTATAAAACTGAA
131 TTTATAAAACTGAA
76447 TTGAGTATTT
Statistics
Matches: 132, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
146 24 0.18
147 11 0.08
148 97 0.73
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (147 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTCGAAATGATTTAAATTTTATAAACTCAATGAAAAAAATTCGAGTCAACTAT
TTTATAAAACTGAACTG
Found at i:86004 original size:111 final size:111
Alignment explanation
Indices: 85861--86193 Score: 603
Period size: 111 Copynumber: 3.0 Consensus size: 111
85851 ATTACAAAAA
*
85861 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAACAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
85926 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
85972 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
86037 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
* * *
86083 TTAATTTTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
86148 AATTAACACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
86194 ATGATTTCCA
Statistics
Matches: 215, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 215 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:86521 original size:50 final size:49
Alignment explanation
Indices: 86467--86591 Score: 160
Period size: 50 Copynumber: 2.5 Consensus size: 49
86457 AGATACCTAG
* * *
86467 GTATAGCACGGATCAGGGGGTGCGCTATACCTACGTGGCGCCAAATCACC
1 GTATAACACGGATCAGGGGG-GCGCTATACCCACGTGGCGCCAAATCAAC
* ** *
86517 GTATATCACGGGGCAGGGGGCGCACTATACCCACGTGGCGCCAAATCAAC
1 GTATAACACGGATCAGGGGG-GCGCTATACCCACGTGGCGCCAAATCAAC
*
86567 GTATAACACGGTTCAGGGGGGCGCT
1 GTATAACACGGATCAGGGGGGCGCT
86592 TTACTGCTAC
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
49 4 0.06
50 60 0.94
ACGTcount: A:0.24, C:0.27, G:0.32, T:0.17
Consensus pattern (49 bp):
GTATAACACGGATCAGGGGGGCGCTATACCCACGTGGCGCCAAATCAAC
Found at i:86980 original size:61 final size:60
Alignment explanation
Indices: 86809--86985 Score: 196
Period size: 60 Copynumber: 2.9 Consensus size: 60
86799 AAGTATGATT
* * * * *
86809 TTCATTTTAAATTGGTGCATAAATTTTTAAATATTTCATTTTCATCCCTAAACTATGATAG
1 TTCATTTTAAATTGGTCCACAAATTTTTAAATATTCCAATTTCATCCC-AAACTATGACAG
* * * *
86870 TT-ATTTTAAATTAGTCCTCAAATTTTTAAACATTCCAATTGCATCCCCAAAACTATGACA-
1 TTCATTTTAAATTGGTCCACAAATTTTTAAATATTCCAATTTCAT-CCC-AAACTATGACAG
* * *
86930 TTCATTCTAAATTGGTCCCCAAACTTTTTTAATATTCCAATTTCATCCCAAACTAT
1 TTCATTTTAAATTGGTCCACAAA-TTTTTAAATATTCCAATTTCATCCCAAACTAT
86986 ACACATGTAC
Statistics
Matches: 97, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
60 43 0.44
61 35 0.36
62 19 0.20
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (60 bp):
TTCATTTTAAATTGGTCCACAAATTTTTAAATATTCCAATTTCATCCCAAACTATGACAG
Found at i:103176 original size:21 final size:22
Alignment explanation
Indices: 103141--103181 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
103131 TTTTCATATT
* *
103141 ATATTATATTTTATGTAAATAA
1 ATATGATATTTTATGAAAATAA
103163 ATATGATA-TTTATGAAAAT
1 ATATGATATTTTATGAAAAT
103182 TATTTAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (22 bp):
ATATGATATTTTATGAAAATAA
Found at i:110455 original size:39 final size:39
Alignment explanation
Indices: 110373--110457 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
110363 AGAGTTGATG
* * * *
110373 TTATTACAAAGAAAAAGTATACTTTTTAAATTATTGTTTT
1 TTATTACAAAG-AAAAGTATACTTTTAAAATTACTGCTAT
110413 TTATTACAAAG-AAA-TATACTTATATAAAATTACTGCTAT
1 TTATTACAAAGAAAAGTATACTT-T-TAAAATTACTGCTAT
110452 TTATTA
1 TTATTA
110458 TAAATTGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
37 7 0.18
38 4 0.10
39 17 0.44
40 11 0.28
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (39 bp):
TTATTACAAAGAAAAGTATACTTTTAAAATTACTGCTAT
Done.