Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004011.1 Hibiscus syriacus cultivar Beakdansim tig00008748_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: 243343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:2374 original size:22 final size:22
Alignment explanation
Indices: 2346--2407 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
2336 ACATCTACAT
2346 TCTTCAAAGATGATAGATTCAC
1 TCTTCAAAGATGATAGATTCAC
**
2368 TCTTCAAAGATGATAGATTCTG
1 TCTTCAAAGATGATAGATTCAC
*
2390 TTTTCAAAGATGA-AGATT
1 TCTTCAAAGATGATAGATT
2408 TATTGGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 5 0.14
22 32 0.86
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCAC
Found at i:3180 original size:122 final size:120
Alignment explanation
Indices: 2773--3217 Score: 656
Period size: 119 Copynumber: 3.7 Consensus size: 120
2763 CACTCAATGG
*
2773 ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATTTGAAGA-G--GAAGAAGTTCATA
1 ATCAACATTTCCA-G-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
2835 ATGAGAAGAACTTGTTCAACC-TTTGCTCGACTCTATCACAGAAGGAGATAGATCAGT
64 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATA-ATCAGC
*
2892 ATC-ACATTTCCAGAGGAGTTCA-AATGAGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGA-GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* *
2955 TGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCATA-AA--AGATAATCAGC
65 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAATCAGC
**
3008 ATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTTGTA
1 ATCAACATTTCC--AGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
3073 ATGAGAAGAACTTGTTCAAACCTTTTGCTTGACTCTATCACAGAAGGAGATATATCAGC
64 ATGAGAAGAACTTGTTC-AACCTTTTGCTCGACTCTATCACAGAAGGAGATA-ATCAGC
* *
3132 ATCAATATTTCCATAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
1 ATCAACATTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
*
3197 GAGAAGAACTTGTTCGACCTT
66 GAGAAGAACTTGTTCAACCTT
3218 AGCTTGATTC
Statistics
Matches: 296, Mismatches: 16, Indels: 26
0.88 0.05 0.08
Matches are distributed among these distances:
116 30 0.10
117 22 0.07
118 16 0.05
119 96 0.32
120 38 0.13
121 7 0.02
122 65 0.22
123 5 0.02
124 17 0.06
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (120 bp):
ATCAACATTTCCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAATCAGC
Found at i:3201 original size:241 final size:235
Alignment explanation
Indices: 2773--3217 Score: 714
Period size: 241 Copynumber: 1.9 Consensus size: 235
2763 CACTCAATGG
*
2773 ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATTTGAAGAGGAAGAAGTTCATAATG
1 ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGTTCATAATG
*
2838 AGAAGAACTTGTTCAACCTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGTATCACATTTCC
66 AGAAGAACTTGTTCAACCTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCATCACATTTCC
*
2903 AGAGGAGTTCAAATGAGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
131 AGAGGAGTTCAAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
2968 TTCAACCTTTTGCTCGATTCTATCATAAAAGATAATCAGC
196 TTCAACCTTTTGCTCGATTCTATCATAAAAGATAATCAGC
**
3008 ATCAACATTTCCAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTTGT
1 ATCAACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGA-G--GAAGAAGTTCAT
* *
3072 AATGAGAAGAACTTGTTCAAACCTTTTGCTTGACTCTATCACAGAAGGAGATATATCAGCATCAA
62 AATGAGAAGAACTTGTTC-AACC-TTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCATC-A
* *
3137 TATTTCCATA-GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
124 CATTTCCAGAGGAGTTCA-AATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
*
3201 AGAACTTGTTCGACCTT
188 AGAACTTGTTCAACCTT
3218 AGCTTGATTC
Statistics
Matches: 192, Mismatches: 10, Indels: 10
0.91 0.05 0.05
Matches are distributed among these distances:
235 45 0.23
236 2 0.01
238 28 0.15
239 4 0.02
240 43 0.22
241 70 0.36
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (235 bp):
ATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGCATCACATTTCC
AGAGGAGTTCAAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACCTTTTGCTCGATTCTATCATAAAAGATAATCAGC
Found at i:3337 original size:17 final size:17
Alignment explanation
Indices: 3285--3341 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
3275 ATTTTCAGAG
*
3285 GAAGTTCATAATGAGAA
1 GAAGTTCATAATAAGAA
** *
3302 GAACATCTAAAATGGAAGAA
1 GAAGTTC-ATAAT--AAGAA
3322 GAAGTTCATAATAAGAA
1 GAAGTTCATAATAAGAA
3339 GAA
1 GAA
3342 CTTGTTCAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
17 13 0.43
18 4 0.13
19 4 0.13
20 9 0.30
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (17 bp):
GAAGTTCATAATAAGAA
Found at i:3502 original size:137 final size:139
Alignment explanation
Indices: 3132--3505 Score: 455
Period size: 137 Copynumber: 2.7 Consensus size: 139
3122 ATATATCAGC
* *
3132 ATCAATATTTCCATA-GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* * * *
3196 TGAGAAGAACTTGTTCGACC-TTAGCTT-GATTCATCATCTATGGAGTTGAATGAAAGAAGAACT
66 TGAGAAGAACTTGTTCAACCTTTAG-TTAGATTCATCATCTATGAAGTTGAATCAAAGAAGAACC
3259 TCACTTGAGG
130 TCACTTGAGG
* *
3269 ATCAACATTTTCAGAGGAAGTTCATAATGAGAAGAA--CATCT-AAAATGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGG-AGTTCATAATGAGAAGAACTCATCTGAAGA-GGAAGAAGAAGTTCAT
* * * * * *
3331 AATAAGAAGAACTTGTTCAACCTTGACTTA-ATTCATTA-CATATGAAGTTGAATCAACG-A-CA
64 AATGAGAAGAACTTGTTCAACCTTTAGTTAGATTCATCATC-TATGAAGTTGAATCAAAGAAGAA
**
3392 CCTCTTTTGAGG
128 CCTCACTTGAGG
* *
3404 ATTAGCATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAG-AGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
3469 ATGAGAA-AACTTGTTCAACCTTTTGTTAGATTCATCA
65 ATGAGAAGAACTTGTTCAACCTTTAGTTAGATTCATCA
3506 CAAAACGAGA
Statistics
Matches: 201, Mismatches: 25, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
135 39 0.19
136 26 0.13
137 112 0.56
138 6 0.03
139 18 0.09
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (139 bp):
ATCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTAGTTAGATTCATCATCTATGAAGTTGAATCAAAGAAGAACCT
CACTTGAGG
Found at i:5415 original size:128 final size:132
Alignment explanation
Indices: 5170--5407 Score: 328
Period size: 128 Copynumber: 1.8 Consensus size: 132
5160 TTTTAAGGAA
** * * *
5170 AAATTATCTTATTTTTATCATTATTTATTTATTTTTTAATATTAAGAATGATGCTGTCTTAAAAC
1 AAATTATAATATTTTTATCATTATTTATTTATTTTTTAATATTAAGAATAAGGATGTCTTAAAAC
* * *
5235 AACTAGATGTCCTTTTCTGATATTTTGAAATAAATAAAATACTATATTATTTAAATTTTTTCTTA
66 AACTAGATGTCATTTTCTGATATTTTGAAATAAATAAAATACAATACTATTTAAATTTTTTCTTA
5300 GG
131 GG
*
5302 AAATTATAATATTTTTAT-ATTTATTT-TTTA-TTTTTAATATTAA-AA-AAGGATGTCTTAAAG
1 AAATTATAATATTTTTATCA-TTATTTATTTATTTTTTAATATTAAGAATAAGGATGTCTTAAAA
*
5362 CAACTAGATGTCATTTTCTGATATTTTTAAATAAAT-AAATA-AATAC
65 CAACTAGATGTCATTTTCTGATATTTTGAAATAAATAAAATACAATAC
5408 CCTATTTATA
Statistics
Matches: 95, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
126 3 0.03
127 5 0.05
128 45 0.47
129 2 0.02
130 13 0.14
131 5 0.05
132 22 0.23
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (132 bp):
AAATTATAATATTTTTATCATTATTTATTTATTTTTTAATATTAAGAATAAGGATGTCTTAAAAC
AACTAGATGTCATTTTCTGATATTTTGAAATAAATAAAATACAATACTATTTAAATTTTTTCTTA
GG
Found at i:8673 original size:20 final size:20
Alignment explanation
Indices: 8647--8714 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
8637 AATAGTTAAA
8647 TCGCAACACGAATTTTGATT
1 TCGCAACACGAATTTTGATT
* *
8667 TCACAACTCG-ATTTTCGGA-T
1 TCGCAACACGAATTTT--GATT
*
8687 TCGCAACACGAATTTTAATT
1 TCGCAACACGAATTTTGATT
8707 TCGCAACA
1 TCGCAACA
8715 GCTTTTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 6 0.15
20 26 0.67
21 7 0.18
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (20 bp):
TCGCAACACGAATTTTGATT
Found at i:8882 original size:16 final size:16
Alignment explanation
Indices: 8861--8899 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
8851 TCCCCATCTC
* *
8861 TAATTTTGTTTTTACA
1 TAATTTTATTTCTACA
*
8877 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
8893 TAATTTT
1 TAATTTT
8900 TCAATGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:11939 original size:6 final size:6
Alignment explanation
Indices: 11928--11962 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
11918 AAGAAAAAGG
* *
11928 AAATCA AAATCA AAATCG CAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
11963 CCAATCACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:11950 original size:18 final size:18
Alignment explanation
Indices: 11929--11969 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
11919 AGAAAAAGGA
*
11929 AATCAAAATCAAAATCGC
1 AATCAAAATCAAAATCCC
11947 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
11965 AATCA
1 AATCA
11970 CATCCGACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:12430 original size:20 final size:20
Alignment explanation
Indices: 12276--12424 Score: 163
Period size: 20 Copynumber: 7.5 Consensus size: 20
12266 TACACTTTCA
*
12276 CAACGCGAAAGTCAAAATTG
1 CAACGCGAAAGTCAAAATCG
* * * *
12296 TAACGCGAAAGTTAAATTTG
1 CAACGCGAAAGTCAAAATCG
*
12316 CAACGCGAAAGTCAAAACCG
1 CAACGCGAAAGTCAAAATCG
* *
12336 CAATGTGAAAGTCAAAATCG
1 CAACGCGAAAGTCAAAATCG
** *
12356 CAATACGAAAGTCAAAACCG
1 CAACGCGAAAGTCAAAATCG
* *
12376 CAACGCAAAAATCAAAATCG
1 CAACGCGAAAGTCAAAATCG
* *
12396 CAGCGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAAATCG
12416 CAACGCGAA
1 CAACGCGAA
12425 CTTCAATTTG
Statistics
Matches: 105, Mismatches: 24, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 105 1.00
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (20 bp):
CAACGCGAAAGTCAAAATCG
Found at i:12454 original size:20 final size:20
Alignment explanation
Indices: 12429--12467 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12419 CGCGAACTTC
12429 AATTTGGAACATGCGTTGCG
1 AATTTGGAACATGCGTTGCG
*
12449 AATTTGGAACATGTGTTGC
1 AATTTGGAACATGCGTTGC
12468 AAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (20 bp):
AATTTGGAACATGCGTTGCG
Found at i:12514 original size:20 final size:20
Alignment explanation
Indices: 12478--12560 Score: 94
Period size: 20 Copynumber: 4.2 Consensus size: 20
12468 AAAATTAAAG
*
12478 TTCACGTTGCGAATTTGACT
1 TTCACGTTGCGATTTTGACT
* * *
12498 TTCGCGCTGCGATTTTGATT
1 TTCACGTTGCGATTTTGACT
* *
12518 TTCACGTTGCGGTTTTAACT
1 TTCACGTTGCGATTTTGACT
**
12538 TTCATTTTGCGATTTTGACT
1 TTCACGTTGCGATTTTGACT
12558 TTC
1 TTC
12561 GCATTGTAAA
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.47
Consensus pattern (20 bp):
TTCACGTTGCGATTTTGACT
Found at i:12734 original size:20 final size:20
Alignment explanation
Indices: 12709--12843 Score: 146
Period size: 20 Copynumber: 6.8 Consensus size: 20
12699 GTTTTCCTTG
*
12709 AATTCGCAACGCGAAAATCA
1 AATTCGCAACGCGAAAGTCA
*** *
12729 AATTCGCGTTGCGAAAGACA
1 AATTCGCAACGCGAAAGTCA
*
12749 AATTCGCAACGTGAAAGTCA
1 AATTCGCAACGCGAAAGTCA
* *
12769 AAATCGCAACGAGAAAGTCAA
1 AATTCGCAACGCGAAAGTC-A
12790 AATT-GCAACGCGAAAGTCA
1 AATTCGCAACGCGAAAGTCA
* **
12809 AAATCGCAACATGAAAGTCA
1 AATTCGCAACGCGAAAGTCA
*
12829 AAATCGCAACGCGAA
1 AATTCGCAACGCGAA
12844 TTTGACTTTT
Statistics
Matches: 94, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
19 4 0.04
20 86 0.91
21 4 0.04
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.15
Consensus pattern (20 bp):
AATTCGCAACGCGAAAGTCA
Found at i:12869 original size:20 final size:20
Alignment explanation
Indices: 12839--12939 Score: 107
Period size: 20 Copynumber: 5.1 Consensus size: 20
12829 AAATCGCAAC
* *
12839 GCGAATTTGACTTTTGTGTT
1 GCGATTTTGACTTTTGCGTT
*
12859 GGGATTTTGACTTTCT-CGTT
1 GCGATTTTGACTTT-TGCGTT
* * *
12879 CCGAATTTGACTTTGGCGTT
1 GCGATTTTGACTTTTGCGTT
* *
12899 GCGATTTTGACTTTCGTGTT
1 GCGATTTTGACTTTTGCGTT
12919 GCGATTTTGAC-TTTGCGTT
1 GCGATTTTGACTTTTGCGTT
12938 GC
1 GC
12940 AAAAGTGTAC
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
19 8 0.12
20 57 0.86
21 1 0.02
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (20 bp):
GCGATTTTGACTTTTGCGTT
Found at i:12905 original size:40 final size:39
Alignment explanation
Indices: 12840--12939 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 39
12830 AATCGCAACG
* *
12840 CGAATTTGACTTTTGTGTTGGGATTTTGACTTTC-TCGTTC
1 CGAATTTGAC-TTTGCGTTGCGATTTTGACTTTCGT-GTTC
*
12880 CGAATTTGACTTTGGCGTTGCGATTTTGACTTTCGTGTTG
1 CGAATTTGACTTT-GCGTTGCGATTTTGACTTTCGTGTTC
*
12920 CGATTTTGACTTTGCGTTGC
1 CGAATTTGACTTTGCGTTGC
12940 AAAAGTGTAC
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
39 10 0.19
40 43 0.80
41 1 0.02
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (39 bp):
CGAATTTGACTTTGCGTTGCGATTTTGACTTTCGTGTTC
Found at i:13029 original size:14 final size:13
Alignment explanation
Indices: 12996--13104 Score: 66
Period size: 13 Copynumber: 8.4 Consensus size: 13
12986 GAAATTAAAC
12996 AACAAATCAATTA
1 AACAAATCAATTA
*
13009 AACAAATCAACTTT
1 AACAAATCAA-TTA
*
13023 TACAAATCAATTA
1 AACAAATCAATTA
*
13036 AAC-AAGCAA--A
1 AACAAATCAATTA
*
13046 AA-ATAA-GAATTA
1 AACA-AATCAATTA
* *
13058 TTTACACATCAATTA
1 --AACAAATCAATTA
*
13073 AACAAATCAACTTT
1 AACAAATCAA-TTA
*
13087 TACAAATCAATTA
1 AACAAATCAATTA
13100 AACAA
1 AACAA
13105 GCAAAAATAA
Statistics
Matches: 71, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
10 5 0.07
11 2 0.03
12 6 0.08
13 28 0.39
14 24 0.34
15 6 0.08
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.26
Consensus pattern (13 bp):
AACAAATCAATTA
Found at i:13143 original size:63 final size:64
Alignment explanation
Indices: 13001--13159 Score: 266
Period size: 63 Copynumber: 2.5 Consensus size: 64
12991 TAAACAACAA
13001 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACAC
1 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACAC
*** * *
13065 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAATAATTCTTATTTCCTC
1 ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACAC
13128 ATCAATTAAACAAATCAACTTTTACAAATCAA
1 ATCAATTAAACAAATCAACTTTTACAAATCAA
13160 CTTTTACAAA
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
63 48 0.53
64 42 0.47
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.29
Consensus pattern (64 bp):
ATCAATTAAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACAC
Found at i:13156 original size:14 final size:14
Alignment explanation
Indices: 13137--13173 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
13127 CATCAATTAA
13137 ACAAATCAACTTTT
1 ACAAATCAACTTTT
13151 ACAAATCAACTTTT
1 ACAAATCAACTTTT
13165 ACAAATCAA
1 ACAAATCAA
13174 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:14550 original size:21 final size:21
Alignment explanation
Indices: 14524--14642 Score: 127
Period size: 21 Copynumber: 5.7 Consensus size: 21
14514 GTGAATCTGG
* ** *
14524 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGATAGGGGC
14545 CTCTTGAACGATGATAGGGGC
1 CTCTTGAACGATGATAGGGGC
*
14566 CTCTTGAAC-AGTGGA-ATGGGC
1 CTCTTGAACGA-T-GATAGGGGC
*
14587 CTCTTGAATGATGATAGGGGC
1 CTCTTGAACGATGATAGGGGC
*
14608 CTCTTGAACGATAGA-AGAGGC
1 CTCTTGAACGAT-GATAGGGGC
14629 CTCTTGAACGATGA
1 CTCTTGAACGATGA
14643 CAGGTGAATC
Statistics
Matches: 84, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
20 5 0.06
21 74 0.88
22 5 0.06
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGATAGGGGC
Found at i:14590 original size:42 final size:40
Alignment explanation
Indices: 14524--14642 Score: 157
Period size: 42 Copynumber: 2.8 Consensus size: 40
14514 GTGAATCTGG
*
14524 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGATAGGGGC
1 CTCTTGAAC-GTGGAAGGG-CCTCTTGAACGATGATAGGGGC
*
14566 CTCTTGAACAGTGGAATGGGCCTCTTGAATGATGATAGGGGC
1 CTCTTGAAC-GTGGAA-GGGCCTCTTGAACGATGATAGGGGC
*
14608 CTCTTGAACGATAGAAGAGGCCTCTTGAACGATGA
1 CTCTTGAACG-TGGAAG-GGCCTCTTGAACGATGA
14643 CAGGTGAATC
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
41 2 0.03
42 64 0.93
43 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (40 bp):
CTCTTGAACGTGGAAGGGCCTCTTGAACGATGATAGGGGC
Found at i:15073 original size:21 final size:21
Alignment explanation
Indices: 15049--15098 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
15039 ACCATTGTAG
* *
15049 TCACGTAAAGTACCGACCTCC
1 TCACGTAAAGCACCGACCTCA
* **
15070 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCACCGACCTCA
15091 TCACGTAA
1 TCACGTAA
15099 CTCCCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:15237 original size:21 final size:21
Alignment explanation
Indices: 15213--15267 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
15203 GTGATGGAAT
*
15213 AGGTGATGGCTCTCGTTGTGG
1 AGGTGATGGCTCTCGTTATGG
* *
15234 AGGTAATGGCTCTTGTTATGG
1 AGGTGATGGCTCTCGTTATGG
*
15255 AGATGATGGCTCT
1 AGGTGATGGCTCT
15268 GGGTGTCGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.13, G:0.36, T:0.35
Consensus pattern (21 bp):
AGGTGATGGCTCTCGTTATGG
Found at i:16867 original size:20 final size:20
Alignment explanation
Indices: 16842--16886 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
16832 TTTTCGCAAT
16842 GTTGCGATTTTTATTTTCGC
1 GTTGCGATTTTTATTTTCGC
*
16862 GTTGCGATTTTTATTTTCGT
1 GTTGCGATTTTTATTTTCGC
16882 GTTGC
1 GTTGC
16887 AAATTTAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.09, C:0.13, G:0.22, T:0.56
Consensus pattern (20 bp):
GTTGCGATTTTTATTTTCGC
Found at i:17421 original size:20 final size:20
Alignment explanation
Indices: 17396--17531 Score: 100
Period size: 20 Copynumber: 6.8 Consensus size: 20
17386 TTCGAAAATA
17396 ATATTCTCGTTGCGATTTAC
1 ATATTCTCGTTGCGATTTAC
* * **
17416 ATATTCGCGTTGTGATTTTGG
1 ATATTCTCGTTGCGA-TTTAC
* *
17437 AAAATCGT-GTTGCGATTTAC
1 ATATTC-TCGTTGCGATTTAC
*
17457 ATATTATCGTTGCGATTTAC
1 ATATTCTCGTTGCGATTTAC
* *
17477 CTATTCGCGTTGCGAATTTGAC
1 ATATTCTCGTTGCG-ATTT-AC
*
17499 -T-TT-TGCATTGCGATTTAC
1 ATATTCT-CGTTGCGATTTAC
*
17517 ATATTATCGTTGCGA
1 ATATTCTCGTTGCGA
17532 ATTTGAGATC
Statistics
Matches: 88, Mismatches: 19, Indels: 18
0.70 0.15 0.14
Matches are distributed among these distances:
18 2 0.02
19 6 0.07
20 59 0.67
21 19 0.22
22 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (20 bp):
ATATTCTCGTTGCGATTTAC
Found at i:17470 original size:61 final size:60
Alignment explanation
Indices: 17396--17531 Score: 173
Period size: 61 Copynumber: 2.2 Consensus size: 60
17386 TTCGAAAATA
* * * **
17396 ATATTCTCGTTGCGATTTACATATTCGCGTTGTGATTTTGGAAAATCGTGTTGCGATTTAC
1 ATATTATCGTTGCGATTTACATATTCGCGTTGCGAATTT-GAAAATCGCATTGCGATTTAC
* *** *
17457 ATATTATCGTTGCGATTTACCTATTCGCGTTGCGAATTTGACTTTTGCATTGCGATTTAC
1 ATATTATCGTTGCGATTTACATATTCGCGTTGCGAATTTGAAAATCGCATTGCGATTTAC
17517 ATATTATCGTTGCGA
1 ATATTATCGTTGCGA
17532 ATTTGAGATC
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
60 30 0.46
61 35 0.54
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (60 bp):
ATATTATCGTTGCGATTTACATATTCGCGTTGCGAATTTGAAAATCGCATTGCGATTTAC
Found at i:18512 original size:2 final size:2
Alignment explanation
Indices: 18507--18567 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
18497 ATACGAAGAA
18507 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
* *
18549 GT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
18568 GTTAAAGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19948 original size:31 final size:31
Alignment explanation
Indices: 19912--19970 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
19902 AACTTAAAAG
* *
19912 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
19943 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
19971 ACATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:20082 original size:32 final size:32
Alignment explanation
Indices: 20014--20579 Score: 428
Period size: 32 Copynumber: 20.4 Consensus size: 32
20004 AATCAATCAA
*
20014 TATTT-AAATAAATCAATTCATACTAAT-AAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20044 TATTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20076 TATTTAAAATAAATCAAT-C---C--AT--A-
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20099 T-TTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20130 TATTTAAAATAAATCAAT---T-C--AT--A-
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20153 T-TTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
*
20184 TATTTAAAATAAATTAAT---T-C--AT--A-
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20207 T-TTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20238 TATTTAAAATAAATC-A---AT-CT-AT--A-
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20261 T-TTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20292 TATTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20324 TATTTAAAATAAATCAAT---T-C--AT--A-
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20347 T-TTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
*
20378 TATTTAAAATAAATCAATCCATAC-AACTACA-
1 TATTTAAAATAAATCAATCCATACTAA-TAAAT
* **
20409 -A--T--AATAAATCAATTCATA-TTTTAAA-
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20434 -A-------TAAATCAATCCATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20458 TATTTAAAATAAATCAAT-C---C--AT--A-
1 TATTTAAAATAAATCAATCCATACTAATAAAT
*
20481 T-TTTAAAATAAATCAATACATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20512 TATTTAAAATAAATCAATCC--AC------A-
1 TATTTAAAATAAATCAATCCATACTAATAAAT
*
20535 T-TTTAAAATAAATCAATCTATACTAATAAAT
1 TATTTAAAATAAATCAATCCATACTAATAAAT
20566 TATTTAAAATAAAT
1 TATTTAAAATAAAT
20580 TATTTTAAAA
Statistics
Matches: 439, Mismatches: 13, Indels: 166
0.71 0.02 0.27
Matches are distributed among these distances:
22 122 0.28
23 15 0.03
24 9 0.02
25 8 0.02
26 34 0.08
27 4 0.01
28 20 0.05
29 3 0.01
30 15 0.03
31 33 0.08
32 176 0.40
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
TATTTAAAATAAATCAATCCATACTAATAAAT
Found at i:20104 original size:22 final size:22
Alignment explanation
Indices: 20078--20120 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
20068 TAATAAATTA
20078 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
20100 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
20121 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:20113 original size:54 final size:54
Alignment explanation
Indices: 20046--20579 Score: 701
Period size: 54 Copynumber: 9.8 Consensus size: 54
20036 CTAATAATTA
20046 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
20100 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
20154 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTAATTCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
20208 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
20262 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-T
** * ** * ** **
20317 AATAAATTATTTAAAATAAAT-C-AATTCA-TATTTTAAAATAAATCAATCCATACTAATAAATT
1 TTTAAAATAAAT-CAATCCATACTAATAAATTA-TTTAAAATAAATCAAT-C---C--AT--A-T
* *
20379 ATTTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATTCATAT
1 -TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATAT
20428 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
20482 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCACAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
20536 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
20580 TATTTTAAAA
Statistics
Matches: 426, Mismatches: 33, Indels: 42
0.85 0.07 0.08
Matches are distributed among these distances:
48 25 0.06
49 3 0.01
50 2 0.00
52 3 0.01
53 2 0.00
54 340 0.80
55 10 0.02
56 5 0.01
58 12 0.03
60 3 0.01
62 7 0.02
63 11 0.03
64 3 0.01
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:20129 original size:22 final size:22
Alignment explanation
Indices: 20080--20128 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
20070 ATAAATTATT
**
20080 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
20102 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
20125 TAAA
1 TAAA
20129 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:20158 original size:22 final size:22
Alignment explanation
Indices: 20132--20174 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20122 TAATAAATTA
*
20132 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
20154 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
20175 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:20183 original size:22 final size:22
Alignment explanation
Indices: 20134--20182 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20124 ATAAATTATT
* **
20134 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
20156 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
20179 TAAA
1 TAAA
20183 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:20201 original size:22 final size:22
Alignment explanation
Indices: 20176--20219 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
20166 CAATCCATAC
20176 TAATAAAT-TATTTAAAATAAAT
1 TAATAAATAT-TTTAAAATAAAT
**
20198 TAATTCATATTTTAAAATAAAT
1 TAATAAATATTTTAAAATAAAT
20220 CAATCCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATAAATATTTTAAAATAAAT
Found at i:20228 original size:22 final size:22
Alignment explanation
Indices: 20186--20228 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20176 TAATAAATTA
* *
20186 TTTAAAATAAATTAATTCATAT
1 TTTAAAATAAATCAATCCATAT
20208 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
20229 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:20291 original size:22 final size:22
Alignment explanation
Indices: 20242--20290 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20232 ATAAATTATT
* **
20242 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
20264 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
20287 TAAA
1 TAAA
20291 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:20352 original size:22 final size:22
Alignment explanation
Indices: 20326--20368 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20316 TAATAAATTA
*
20326 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
20348 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
20369 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:20377 original size:22 final size:22
Alignment explanation
Indices: 20328--20376 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20318 ATAAATTATT
* **
20328 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
20350 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
20373 TAAA
1 TAAA
20377 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:20457 original size:22 final size:23
Alignment explanation
Indices: 20382--20456 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
20372 ATAAATTATT
20382 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
* **
20404 CTACAATAATAAATCAATTCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
20430 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
20453 TAAA
1 TAAA
20457 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:20486 original size:22 final size:22
Alignment explanation
Indices: 20460--20502 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
20450 TAATAAATTA
*
20460 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATACATAT
20482 TTTAAAATAAATCAATACATA
1 TTTAAAATAAATCAATACATA
20503 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATACATAT
Found at i:20511 original size:22 final size:22
Alignment explanation
Indices: 20462--20510 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20452 ATAAATTATT
* **
20462 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATACATATAA
20484 TAAAATAAATCAATACATACTAA
1 TAAAATAAATCAATACATA-TAA
20507 TAAA
1 TAAA
20511 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATACATATAA
Found at i:20588 original size:15 final size:15
Alignment explanation
Indices: 20559--20654 Score: 95
Period size: 15 Copynumber: 6.0 Consensus size: 15
20549 AATCTATACT
20559 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
20573 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
20588 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
* *
20610 AATAATTTATTTTAT
1 AATAAATTATTTTAA
20625 AATAAATTATTTTAA
1 AATAAATTATTTTAA
20640 AATAAATTATTTTAA
1 AATAAATTATTTTAA
20655 TAAATAACTA
Statistics
Matches: 70, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
14 9 0.13
15 44 0.63
17 1 0.01
18 2 0.03
19 3 0.04
20 1 0.01
22 10 0.14
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:20618 original size:47 final size:49
Alignment explanation
Indices: 20316--20646 Score: 221
Period size: 54 Copynumber: 6.5 Consensus size: 49
20306 CAATCCATAC
* * **
20316 TAATAAATTA-TTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
1 TAATAAATTATTTTAAAATAAATCAATCCATA--CT--AATAAAT-AATTTATA
*
20369 CTAATAAATTA-TTTAAAATAAATCAATCCATAC-AACTACAATAA--TAAA
1 -TAATAAATTATTTTAAAATAAATCAATCCATACTAA-TA-AATAATTTATA
** * *
20417 TCAATTCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAA
1 T-AATAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATTT-ATA
* * * *
20467 TAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAA
1 T-AATAAAT---TATTTTAAAATAAATCAATCCATACTAATAAATAATTT-ATA
* * * *
20521 TAAATCAATCCACATTTTAAAATAAATCAATCTATACTAATAAATTATTTA-A
1 T-AATAAAT---TATTTTAAAATAAATCAATCCATACTAATAAATAATTTATA
**
20573 -AATAAATTATTTTAAAATAAATCAATCCATA-TTTTATAATAATTTATTTTA
1 TAATAAATTATTTTAAAATAAATCAATCCATACTAATA-AATAATTTA---TA
20624 TAATAAATTATTTTAAAATAAAT
1 TAATAAATTATTTTAAAATAAAT
20647 TATTTTAATA
Statistics
Matches: 239, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
46 3 0.01
47 37 0.15
48 30 0.13
49 5 0.02
50 18 0.08
51 4 0.02
52 23 0.10
53 1 0.00
54 118 0.49
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (49 bp):
TAATAAATTATTTTAAAATAAATCAATCCATACTAATAAATAATTTATA
Found at i:20638 original size:30 final size:33
Alignment explanation
Indices: 20559--20675 Score: 118
Period size: 33 Copynumber: 3.6 Consensus size: 33
20549 AATCTATACT
*
20559 AATAAAT-TA-TTTAAAATAAATTATTTTAAAATA
1 AATAAATATATTTTATAATAAATTATTTT--AATA
* *
20592 AATCAATCCATATTTTATAATAATTTATTTT-AT-
1 AATAAAT--ATATTTTATAATAAATTATTTTAATA
*
20625 AATAAAT-TATTTTAAAATAAATTATTTTAATA
1 AATAAATATATTTTATAATAAATTATTTTAATA
*
20657 AATAACTATATTTTATAAT
1 AATAAATATATTTTATAAT
20676 TGTTCTTGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
30 19 0.28
31 2 0.03
32 6 0.09
33 22 0.32
34 2 0.03
36 2 0.03
37 16 0.23
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (33 bp):
AATAAATATATTTTATAATAAATTATTTTAATA
Found at i:20661 original size:69 final size:69
Alignment explanation
Indices: 20505--20654 Score: 218
Period size: 69 Copynumber: 2.2 Consensus size: 69
20495 AATACATACT
20505 AATAAATTA-TTTAAAATAAATCAATCCACATTTTAAAATAAATCAATCTATACTAATAAATTAT
1 AATAAATTATTTTAAAATAAATCAATCCACATTTTAAAATAAATCAATCTATACTAATAAATTAT
20569 TTAA
66 TTAA
* * ** *
20573 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAAT-AATTTAT-TTTA-TAATAAATTAT
1 AATAAATTATTTTAAAATAAATCAATCCACATTTTAAAATAAATCAATCTATACTAATAAATTA-
20635 TTTAA
65 TTTAA
20640 AATAAATTATTTTAA
1 AATAAATTATTTTAA
20655 TAAATAACTA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
66 10 0.13
67 23 0.31
68 14 0.19
69 28 0.37
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (69 bp):
AATAAATTATTTTAAAATAAATCAATCCACATTTTAAAATAAATCAATCTATACTAATAAATTAT
TTAA
Found at i:27772 original size:73 final size:71
Alignment explanation
Indices: 27652--27914 Score: 344
Period size: 73 Copynumber: 3.8 Consensus size: 71
27642 CATCACGTGG
* *
27652 CAAATACAAATAATGGGAGTAGTTGTGATGGCAGCTCACATAGGGTCCAAGAAGAAAATTATGAT
1 CAAATACAAACAATGGGAGTAGTTGTGATGGCAGCTCACATGGGGTCCAAGAAGAAAATTATGAT
27717 GGTACGA
66 GGTA-GA
* * * *
27724 CAAAATACAAACAATGGGAGTAGTTGTTATGGCAGCTCACATGGGGTCCAAGAAGAGAATCACGA
1 C-AAATACAAACAATGGGAGTAGTTGTGATGGCAGCTCACATGGGGTCCAAGAAGAAAATTATGA
27789 TGGTAG-
65 TGGTAGA
*
27795 C-AAT-----C-ATGGGAGTAGTTGTGATGGCAGCTCACATGGGGTCCAAGAATAAAATTATGAT
1 CAAATACAAACAATGGGAGTAGTTGTGATGGCAGCTCACATGGGGTCCAAGAAGAAAATTATGAT
*
27853 GGTGTGA
66 GGT-AGA
* * *
27860 CAAATACAAACAATTGGAGTAGTTGTAATGGCAACTCACATGGGGTCCAAGAAGA
1 CAAATACAAACAATGGGAGTAGTTGTGATGGCAGCTCACATGGGGTCCAAGAAGA
27915 GCATCACGTT
Statistics
Matches: 165, Mismatches: 16, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
63 51 0.31
64 2 0.01
65 1 0.01
66 3 0.02
69 3 0.02
71 2 0.01
72 41 0.25
73 62 0.38
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (71 bp):
CAAATACAAACAATGGGAGTAGTTGTGATGGCAGCTCACATGGGGTCCAAGAAGAAAATTATGAT
GGTAGA
Found at i:33645 original size:14 final size:14
Alignment explanation
Indices: 33626--33652 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33616 AGGGGTATCA
33626 GTACTAAAGGAACG
1 GTACTAAAGGAACG
33640 GTACTAAAGGAAC
1 GTACTAAAGGAAC
33653 AATACCGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (14 bp):
GTACTAAAGGAACG
Found at i:37655 original size:29 final size:29
Alignment explanation
Indices: 37612--37682 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
37602 ATTATTGTTT
* * *
37612 TTTATCGAATTATTACAAAAGGATCATTTAAT
1 TTTATCAAATTA-TA-AAAAGGAT-AGTTAAA
*
37644 TTTATCAAATTATAAAAATGATAGTTAAA
1 TTTATCAAATTATAAAAAGGATAGTTAAA
37673 TTTATCAAAT
1 TTTATCAAAT
37683 ATTGAAACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.43
30 7 0.20
31 2 0.06
32 11 0.31
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (29 bp):
TTTATCAAATTATAAAAAGGATAGTTAAA
Found at i:40633 original size:105 final size:105
Alignment explanation
Indices: 40451--40656 Score: 394
Period size: 105 Copynumber: 2.0 Consensus size: 105
40441 GCTGACCGGG
*
40451 GTACATGGGTCGGTGAATCAACTTCAGAGGTAAATTTTCAAGTATTACTTAGTATTATGTTTATT
1 GTACATGGGTCGGTGAATCAACTTCAGAGGTAAATTTTCAAGTATTACTTAGTATTATGTTTATG
40516 TATTTTGTTTTCATCGTCTTCCACTACTTTTATTTTCTTA
66 TATTTTGTTTTCATCGTCTTCCACTACTTTTATTTTCTTA
*
40556 GTACATGGGTCGGTGAATCAACTTCAGAGGTAAATTTTCAAGTATTACTTGGTATTATGTTTATG
1 GTACATGGGTCGGTGAATCAACTTCAGAGGTAAATTTTCAAGTATTACTTAGTATTATGTTTATG
40621 TATTTTGTTTTCATCGTCTTCCACTACTTTTATTTT
66 TATTTTGTTTTCATCGTCTTCCACTACTTTTATTTT
40657 ATTATCTCAA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 99 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (105 bp):
GTACATGGGTCGGTGAATCAACTTCAGAGGTAAATTTTCAAGTATTACTTAGTATTATGTTTATG
TATTTTGTTTTCATCGTCTTCCACTACTTTTATTTTCTTA
Found at i:43787 original size:24 final size:23
Alignment explanation
Indices: 43743--43787 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
43733 AATTTTATTA
*
43743 TGAAATATTTTCATAATATTTTC
1 TGAAATATTTACATAATATTTTC
43766 TGAAATGATTTACA-AATGATTT
1 TGAAAT-ATTTACATAAT-ATTT
43788 CGGGTATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (23 bp):
TGAAATATTTACATAATATTTTC
Found at i:45614 original size:21 final size:21
Alignment explanation
Indices: 45566--45631 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
45556 AATAATTGCA
*
45566 TTTTATTAAAGTATTATAAAAT
1 TTTTATTAAA-TTTTATAAAAT
** *
45588 AATTATTAAATTTTATCAAAT
1 TTTTATTAAATTTTATAAAAT
* *
45609 TTTTA-TAATTTTTTATTAAAT
1 TTTTATTAA-ATTTTATAAAAT
45630 TT
1 TT
45632 ATCATATTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 3 0.09
21 24 0.69
22 8 0.23
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTATTAAATTTTATAAAAT
Found at i:45640 original size:21 final size:21
Alignment explanation
Indices: 45598--45641 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
45588 AATTATTAAA
*
45598 TTTTATCAAATTTTTATAATT
1 TTTTATCAAATTTTCATAATT
*
45619 TTTTATTAAATTTATCAT-ATT
1 TTTTATCAAATTT-TCATAATT
45640 TT
1 TT
45642 AAACTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTATCAAATTTTCATAATT
Found at i:47696 original size:21 final size:22
Alignment explanation
Indices: 47670--47714 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
47660 TTTTTATAAA
47670 TATTTTTTA-AAAATAATATTT
1 TATTTTTTATAAAATAATATTT
47691 TATTTTTTATTAAAATAATATTT
1 TATTTTTTA-TAAAATAATATTT
47714 T
1 T
47715 TATAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.41
23 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTTATAAAATAATATTT
Found at i:47723 original size:23 final size:23
Alignment explanation
Indices: 47679--47725 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
47669 ATATTTTTTA
**
47679 AAAATAATATTTTATTTTTTATT
1 AAAATAATATTTTATTAATTATT
47702 AAAATAATATTTT-TATAATTATT
1 AAAATAATATTTTAT-TAATTATT
47725 A
1 A
47726 TTTATTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AAAATAATATTTTATTAATTATT
Found at i:49540 original size:21 final size:21
Alignment explanation
Indices: 49516--49625 Score: 96
Period size: 21 Copynumber: 5.2 Consensus size: 21
49506 GATGCCATCT
*
49516 CCGCAAGGGTATATGCCAAGC
1 CCGCAAGGTTATATGCCAAGC
* *
49537 CCGCAAGGTTACATGCCTAGC
1 CCGCAAGGTTATATGCCAAGC
* * *
49558 CCGCATGGTTATATTCCTAGC
1 CCGCAAGGTTATATGCCAAGC
* * *
49579 CCACAGGGGTATATGCCCAA-C
1 CCGCAAGGTTATATG-CCAAGC
* * *
49600 CCGCAAGGTTACATACCCAGC
1 CCGCAAGGTTATATGCCAAGC
49621 CCGCA
1 CCGCA
49626 GGATTCTATG
Statistics
Matches: 70, Mismatches: 17, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
20 3 0.04
21 64 0.91
22 3 0.04
ACGTcount: A:0.25, C:0.34, G:0.23, T:0.18
Consensus pattern (21 bp):
CCGCAAGGTTATATGCCAAGC
Found at i:50614 original size:20 final size:21
Alignment explanation
Indices: 50569--50615 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
50559 AAACTAACTC
* *
50569 AATTTC-ACATTCTAACATCA
1 AATTTCAACACTCCAACATCA
50589 AA-TTCAACACTCCAACAT-A
1 AATTTCAACACTCCAACATCA
50608 AATTTCAA
1 AATTTCAA
50616 GTATAGTGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTTCAACACTCCAACATCA
Found at i:51120 original size:138 final size:137
Alignment explanation
Indices: 50632--51395 Score: 995
Period size: 138 Copynumber: 5.5 Consensus size: 137
50622 TGCCATTCCG
50632 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGGAAGGCGCACCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGGAAGGCGCACCC
* * *
50697 TCTGAAACGCGCTTTAACAACATTGATGCGTCCCCTTTC-CA-ATGATAGGTACTGACATGAATA
66 -CTGAAACGCGCTTTAACCACATTGTTGCGTCCCC--TCAAACATGATAGGTACTGACATGAATA
* *
50760 GTACCTCACC
128 GTGCCCCACC
* *
50770 GAGGGACATCA-ACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGGAAGTCAC-CC
1 G-GGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGGAAGGCGCACC
** *
50833 CCTGAAACGCATTTTAACCACATTGTTGTGTCCCCTCAAACATGATAGGTACTGACATGAATAGT
65 CCTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGT
* *
50898 GCCCCGCT
130 GCCCCACC
* * *
50906 GGGAGACATCACACATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAGAGAAGGTGCACC
1 GGG-GACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGGAAGGCGCACC
* * *
50971 CCTTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAATATGATAGGTACTGACATAAATAA
65 CC-TGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAG
51036 TGCCCCACC
129 TGCCCCACC
* *
51045 AGGGGATATCA-ACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGAGAAGGCGCACC
1 -GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGGAAGGCGCACC
* * *
51109 TCCTGAAACGCGCTTTAACCATATTGATGCGTCCCCTCAAACATGATAGGTACTGATATGAATAG
65 -CCTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAG
*
51174 TGCCCCGCC
129 TGCCCCACC
* * * * * *
51183 GGGTAACATCA-ACATAATAGGGCAATTATAACATATTCTTTGA-TAAAAAATGGAATGAGTG-T
1 GGG-GACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGGAA-G-GCGCA
* * * * *
51245 CCCCTGAAACACGCTTTAACCACAATGTTGTGTCCCCTCAAACATGATAGATACTGACATAAATA
63 CCCCTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATA
** ***
51310 GTGTACTGTC
128 GTGCCCCACC
*
51320 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGGAAGGCGCGCCC
1 GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGGAAGGCGC-ACC
51385 CCTGAAACGCG
65 CCTGAAACGCG
51396 TTTTCACATG
Statistics
Matches: 548, Mismatches: 62, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
134 2 0.00
135 3 0.01
136 73 0.13
137 156 0.28
138 229 0.42
139 82 0.15
140 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (137 bp):
GGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGGAAGGCGCACCC
CTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTG
CCCCACC
Found at i:51262 original size:275 final size:273
Alignment explanation
Indices: 50629--51395 Score: 1033
Period size: 275 Copynumber: 2.8 Consensus size: 273
50619 TAGTGCCATT
* * *
50629 CCGGGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGGAAGGCGCA
1 CCGGGAGACATCACACATAATAGGGCAATTATAACATATTCTCTGA-AAAAAAAAGGAAGGTGCA
* * * *
50694 CCCTCTGAAACGCGCTTTAACAACATTGATGCGTCCCCTTTC-CAATGATAGGTACTGACATGAA
65 CCC-CTGAAACGCGCTTTAACCACATTGTTGCGTCCCC--TCAAAATGATAGGTACTGACATAAA
* *
50758 TAGTACCTCACCGAGGGACATCAACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGG
127 TAGTGCCCCACCG-GGGACATCAACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGG
* ** * *
50823 GAA-G-TCACCCCCTGAAACGCATTTTAACCACATTGTTGTGTCCCCTCAAACATGATAGGTACT
191 GAAGGCGCACCCCCTGAAACGCGCTTTAACCACATTGATGCGTCCCCTCAAACATGATAGGTACT
50886 GACATGAATAGTGCCCCG
256 GACATGAATAGTGCCCCG
* * *
50904 CTGGGAGACATCACACATAATAGGGCAATTATAACCTATTCTCTGACAAAAAAAGAGAAGGTGCA
1 CCGGGAGACATCACACATAATAGGGCAATTATAACATATTCTCTGAAAAAAAAAG-GAAGGTGCA
50969 CCCCTTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAATATGATAGGTACTGACATAAAT
65 CCCC-TGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAA-ATGATAGGTACTGACATAAAT
* * *
51034 AATGCCCCACCAGGGGATATCAACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGAG
128 AGTGCCCCACC-GGGGACATCAACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGG
* *
51099 AAGGCGCACCTCCTGAAACGCGCTTTAACCATATTGATGCGTCCCCTCAAACATGATAGGTACTG
192 AAGGCGCACCCCCTGAAACGCGCTTTAACCACATTGATGCGTCCCCTCAAACATGATAGGTACTG
*
51164 ATATGAATAGTGCCCCG
257 ACATGAATAGTGCCCCG
* * *
51181 CCGGGTA-ACATCA-ACATAATAGGGCAATTATAACATATTCTTTGATAAAAAATGGAATGAGTG
1 CCGGG-AGACATCACACATAATAGGGCAATTATAACATATTCTCTGAAAAAAAAAGGAA-G-GTG
* * * * *
51244 -TCCCCTGAAACACGCTTTAACCACAATGTTGTGTCCCCTCAAACATGATAGATACTGACATAAA
63 CACCCCTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAA-ATGATAGGTACTGACATAAA
** ***
51308 TAGTGTACTGTCGGGGACATCACACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGG
127 TAGTGCCCCACCGGGGACATCA-ACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGG
*
51373 GAAGGCGCGCCCCCTGAAACGCG
191 GAAGGCGCACCCCCTGAAACGCG
51396 TTTTCACATG
Statistics
Matches: 437, Mismatches: 44, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
273 2 0.00
274 18 0.04
275 290 0.66
276 44 0.10
277 82 0.19
278 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (273 bp):
CCGGGAGACATCACACATAATAGGGCAATTATAACATATTCTCTGAAAAAAAAAGGAAGGTGCAC
CCCTGAAACGCGCTTTAACCACATTGTTGCGTCCCCTCAAAATGATAGGTACTGACATAAATAGT
GCCCCACCGGGGACATCAACATAATAGGGCAATTATAACATATTCTCTGACAAAAAAAGGGAAGG
CGCACCCCCTGAAACGCGCTTTAACCACATTGATGCGTCCCCTCAAACATGATAGGTACTGACAT
GAATAGTGCCCCG
Found at i:72641 original size:39 final size:39
Alignment explanation
Indices: 72597--72752 Score: 172
Period size: 39 Copynumber: 4.0 Consensus size: 39
72587 ACCGCTTTTC
72597 GCAGGCTCCTCGGCTTTGTGCTCAAGGTAAGTCCTTACT
1 GCAGGCTCCTCGGCTTTGTGCTCAAGGTAAGTCCTTACT
*
72636 GCAGGCTCCTCGGCTTTATGCTCAAGGTAAGTCCTTACT
1 GCAGGCTCCTCGGCTTTGTGCTCAAGGTAAGTCCTTACT
* * * ** *
72675 GCATGATCCTCTGCTTTGTGAAC-AGGATAAGACCTTACT
1 GCAGGCTCCTCGGCTTTGTGCTCAAGG-TAAGTCCTTACT
* * ** *
72714 GTAGGCTCCCCTACTTTGTGCAT-AGGGTAAGTCCTTACT
1 GCAGGCTCCTCGGCTTTGTGC-TCAAGGTAAGTCCTTACT
72753 AGGTGTACAG
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
38 3 0.03
39 92 0.95
40 2 0.02
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.31
Consensus pattern (39 bp):
GCAGGCTCCTCGGCTTTGTGCTCAAGGTAAGTCCTTACT
Found at i:76156 original size:39 final size:39
Alignment explanation
Indices: 76102--76255 Score: 190
Period size: 39 Copynumber: 3.9 Consensus size: 39
76092 TACTGCTTCC
76102 GCAGGCTCCTC-AGCTTTGTGCTCAGGGTAAGTCCTTACT
1 GCAGGCTCCTCTA-CTTTGTGCTCAGGGTAAGTCCTTACT
*
76141 GCAGGCTCCT-TAGCTTTGTGCTCAAGGTAAGTCCTTACT
1 GCAGGCTCCTCTA-CTTTGTGCTCAGGGTAAGTCCTTACT
* * *
76180 GCAGGCTCATCTACTTTGTGCACAGGATAA-TACCTTACT
1 GCAGGCTCCTCTACTTTGTGCTCAGGGTAAGT-CCTTACT
* *
76219 GCCGGCTCCTCTACTTTGTG-TGTAGGGTAAGTCCTTA
1 GCAGGCTCCTCTACTTTGTGCT-CAGGGTAAGTCCTTA
76256 ATGGGAGTAC
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
38 1 0.01
39 96 0.96
40 3 0.03
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.32
Consensus pattern (39 bp):
GCAGGCTCCTCTACTTTGTGCTCAGGGTAAGTCCTTACT
Found at i:77109 original size:16 final size:16
Alignment explanation
Indices: 77090--77122 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
77080 TGTAACTTAT
*
77090 AAGTTAGGTAAATATC
1 AAGTCAGGTAAATATC
77106 AAGTCAGGTAAATATC
1 AAGTCAGGTAAATATC
77122 A
1 A
77123 GACCAGTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.27
Consensus pattern (16 bp):
AAGTCAGGTAAATATC
Found at i:77846 original size:20 final size:21
Alignment explanation
Indices: 77821--77913 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
77811 TTTTCCCAAT
*
77821 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
77841 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
77862 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
77882 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
77903 TCGCAATGCGA
1 TCGCAATGCGA
77914 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:77927 original size:20 final size:20
Alignment explanation
Indices: 77902--78016 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
77892 AATTGGGAAA
*
77902 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
77922 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
77943 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
77963 TTCGCAACGTGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
77983 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
78003 TTCGCAACGCGATA
1 ATCGCAACGCGATA
78017 ATACATAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:77928 original size:41 final size:41
Alignment explanation
Indices: 77821--77913 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
77811 TTTTCCCAAT
77821 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
77862 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
77903 TCGCAATGCGA
1 TCGCAATGCGA
77914 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:78037 original size:41 final size:41
Alignment explanation
Indices: 77901--78036 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 41
77891 GAATTGGGAA
* * * *
77901 AATCGCAATGCGATACTGACTATCGCAATGCGATAATACAA
1 AATCGCAACGCGATACTGACTTTCGCAACGCGATAATACAT
* * * *
77942 AATCGCAACGAGATACTTACTTTCGCAACGTGATACTGAC-T
1 AATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-ACAT
* *
77983 -TTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACAT
1 AATCGCAACGCGATACTGACTTTCGCAACGCGATAATACAT
*
78023 AATCGCAATGCGAT
1 AATCGCAACGCGAT
78037 TTTCAAAGCG
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.41
41 41 0.54
42 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (41 bp):
AATCGCAACGCGATACTGACTTTCGCAACGCGATAATACAT
Found at i:78232 original size:22 final size:22
Alignment explanation
Indices: 78204--78247 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
78194 CACTCTCTCA
*
78204 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCAGACGAAATCCGTC
*
78226 CCCATCTCAGGCGAAATCCGTC
1 CCCATCTCAGACGAAATCCGTC
78248 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.43, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCAGACGAAATCCGTC
Found at i:78564 original size:20 final size:20
Alignment explanation
Indices: 78512--78568 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
78502 GATTCTCTCA
* **
78512 TTGCGATGGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGCG
*
78532 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCG
**
78552 TTGCGATTTTCATTTTC
1 TTGCGATAGTCATTTTC
78569 AGAAACTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:79908 original size:18 final size:18
Alignment explanation
Indices: 79887--79931 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
79877 TCCACTTCGG
*
79887 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
79905 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
79923 GAGCCATCA
1 GAGCCATCA
79932 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:80467 original size:19 final size:20
Alignment explanation
Indices: 80413--80479 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
80403 TAGTTTACTT
* *
80413 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
80433 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
80453 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
80472 TCGCAACG
1 TCGCAACG
80480 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:80487 original size:14 final size:14
Alignment explanation
Indices: 80468--80525 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
80458 ATGCGAAATG
80468 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
80482 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
80498 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
80514 AAAATCGCAACG
1 AAAATCGCAACG
80526 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:80510 original size:32 final size:33
Alignment explanation
Indices: 80452--80542 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
80442 GGAAATGGCT
*
80452 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
80485 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
80517 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
80543 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:80536 original size:19 final size:19
Alignment explanation
Indices: 80413--80547 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
80403 TAGTTTACTT
* **
80413 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
80433 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
80453 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
80472 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
80486 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
80504 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
80518 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
80537 TCGCAATGCGA
1 TCGCAACGCGA
80548 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:80580 original size:14 final size:14
Alignment explanation
Indices: 80561--80616 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
80551 GTGTTTCGCA
80561 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
80575 TTGCGATTTCATTTCGCG
1 TTGCGATTT--TGT--CG
80593 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
80607 TTGTGATTTT
1 TTGCGATTTT
80617 TATTTCGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 20 0.57
16 4 0.11
18 11 0.31
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:80597 original size:32 final size:33
Alignment explanation
Indices: 80554--80632 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
80544 GCGATTTGTG
80554 TTTCGCATTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* * *
80586 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTTA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
80619 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
80633 ATCCATTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 25 0.60
33 17 0.40
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:80651 original size:20 final size:20
Alignment explanation
Indices: 80626--80672 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
80616 TTATTTCGCA
80626 TTGCGATA-TCCATTTCCGCG
1 TTGCGATAGT-CATTTCCGCG
*
80646 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTCCGCG
80666 TTGCGAT
1 TTGCGAT
80673 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:82558 original size:14 final size:14
Alignment explanation
Indices: 82539--82574 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
82529 ATTGTTTAAT
82539 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
82553 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
82567 TGATTTGT
1 TGATTTGT
82575 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:82713 original size:19 final size:19
Alignment explanation
Indices: 82691--82777 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
82681 ATCGCAATGA
82691 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
82710 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
82729 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
82748 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
82762 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
82778 TTTTCATTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 2 0.03
17 2 0.03
19 49 0.75
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:82739 original size:38 final size:33
Alignment explanation
Indices: 82662--82777 Score: 142
Period size: 33 Copynumber: 3.4 Consensus size: 33
82652 AAAACATACT
* *** *
82662 ATCGCAACGCGAAATGGCTATCGCAATGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
82695 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
82733 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
82766 ATCGCAATGCGA
1 ATCGCAATGCGA
82778 TTTTCATTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
33 38 0.52
34 1 0.01
35 1 0.01
36 2 0.03
37 1 0.01
38 30 0.41
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:82821 original size:20 final size:20
Alignment explanation
Indices: 82796--82853 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
82786 TTGCATTGTG
*
82796 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
82816 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
82836 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
82854 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:83961 original size:24 final size:24
Alignment explanation
Indices: 83910--83963 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
83900 GTATTCGAAA
* *
83910 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
* *
83934 TTTGATATTGGTCAATACATGGAT
1 TTTGATATTGGTCAATACACGGAC
83958 TTTGAT
1 TTTGAT
83964 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:84155 original size:12 final size:12
Alignment explanation
Indices: 84138--84162 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84128 ATATAATCCT
84138 GAAGAAGAAAAA
1 GAAGAAGAAAAA
84150 GAAGAAGAAAAA
1 GAAGAAGAAAAA
84162 G
1 G
84163 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:86473 original size:19 final size:19
Alignment explanation
Indices: 86451--86581 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
86441 GGAAATTACT
86451 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
86470 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
86484 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
86503 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
86517 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
86536 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
86550 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
86569 ATCGCAACGCGAA
1 ATCGCAATGCGAA
86582 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:86493 original size:33 final size:33
Alignment explanation
Indices: 86451--86577 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
86441 GGAAATTACT
86451 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
86484 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
86516 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
86550 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
86578 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:86558 original size:66 final size:66
Alignment explanation
Indices: 86452--86584 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
86442 GAAATTACTA
*
86452 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
86517 T
66 T
*
86518 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
86583 T
66 T
86584 T
1 T
86585 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:86599 original size:19 final size:19
Alignment explanation
Indices: 86577--86651 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
86567 AAATCGCAAC
*
86577 GCGAATTTAATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
*
86596 GCG-A-TTC---TCTCGTT
1 GCGAATTTCATTTCGCGTT
*
86610 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
* *
86629 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCGTT
86648 GCGA
1 GCGA
86652 TAGTACTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
14 9 0.20
16 3 0.07
17 2 0.04
18 1 0.02
19 31 0.67
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTCATTTCGCGTT
Found at i:86652 original size:19 final size:19
Alignment explanation
Indices: 86608--86652 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
86598 GATTCTCTCG
*
86608 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
86627 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
86646 TTGCGAT
1 TTGCGAT
86653 AGTACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:88245 original size:42 final size:42
Alignment explanation
Indices: 88177--88256 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
88167 CGATGACAAT
* * *
88177 GGCCTCTTGAACGGTGGGATGAGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGATGAGACTCTCGAGGAATGATAGG
* *
88219 GGCCTCTTCAACGATAGGAGTG-GACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGA-TGAGACTCTCGAGGAATGA
88257 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 30 0.94
43 2 0.06
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGATGAGACTCTCGAGGAATGATAGG
Found at i:90322 original size:19 final size:19
Alignment explanation
Indices: 90258--90427 Score: 188
Period size: 19 Copynumber: 9.1 Consensus size: 19
90248 TCTTTTGGTT
*
90258 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
90277 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
90297 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
** *
90317 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
90334 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
90350 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
90369 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
90388 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
90407 AAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
90426 GA
1 GA
90428 TTTTTGTTTC
Statistics
Matches: 130, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
14 8 0.06
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 84 0.65
20 30 0.23
21 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:90459 original size:19 final size:19
Alignment explanation
Indices: 90423--90467 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
90413 AAAATCGCAA
*
90423 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
90442 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
90461 TGCGATT
1 TGCGATT
90468 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:91046 original size:20 final size:20
Alignment explanation
Indices: 91021--91073 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
91011 GCGCTATGTA
91021 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
91041 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
91061 TATCTCGTTGCGA
1 AATCGCGTTGCGA
91074 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:91107 original size:20 final size:20
Alignment explanation
Indices: 91082--91135 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
91072 GATTTTGTAT
91082 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
91102 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
91122 TATCGCATTGCGAT
1 TATCGCATTGCGAT
91136 TTTTCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:91120 original size:61 final size:61
Alignment explanation
Indices: 91022--91138 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
91012 CGCTATGTAA
* * * * *
91022 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
91083 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
91139 TCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:91154 original size:61 final size:61
Alignment explanation
Indices: 91017--91156 Score: 160
Period size: 61 Copynumber: 2.3 Consensus size: 61
91007 AATGGCGCTA
* * * * *
91017 TGTAA-ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
* * * *
91077 TGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
91138 T-TCCAAT-TCGCGTTGCGAT
1 TGT--AATATCGCGTTGCGAT
91157 TTACTTATTC
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
60 5 0.08
61 59 0.89
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
Found at i:92835 original size:131 final size:131
Alignment explanation
Indices: 92469--92837 Score: 461
Period size: 131 Copynumber: 2.8 Consensus size: 131
92459 ATAATTTTAA
* * *
92469 GAGAGAAAACGATGACATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * * * *
92534 TTTATTTATTACTCCAATCGAAATGAAGAGATATCAATATTCCGTCTTAAGATTTAATATCGATT
66 ATAATTTATTACTCCAATCAAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATCGATT
92599 C
131 C
* * * * * * *
92600 GAGTGAAAACAATAATATCTAATGATTTCTAATCGAGAATAAATGATCTCTCGTACCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* ** *
92665 ATAATTTATTGCTCCAATCAAAATGGTGAGATATCACTATTCCGTCTTAAAAATCAATAT-TATT
66 ATAATTTATTACTCCAATCAAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATCGA-T
92729 TC
130 TC
* * * *
92731 GAGAGAAAACGGTAATATCGAATTATTTCCAATCGATAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * *
92796 ATCATTTATTACTCCAACCAAAATGAAAAGATATTACTATTC
66 ATAATTTATTACTCCAATCAAAATGAAGAGATATCACTATTC
92838 TCAGTATCGA
Statistics
Matches: 199, Mismatches: 38, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
130 1 0.01
131 198 0.99
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
ATAATTTATTACTCCAATCAAAATGAAGAGATATCACTATTCCGTCTTAAAAATCAATATCGATT
C
Found at i:93961 original size:9 final size:9
Alignment explanation
Indices: 93947--93982 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
93937 CTATGAATAC
93947 AATTTTTTT
1 AATTTTTTT
93956 AATTTTTTT
1 AATTTTTTT
93965 AATTTTCTTT
1 AATTTT-TTT
93975 -ATTTTTTT
1 AATTTTTTT
93983 TTTATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 3 0.12
9 20 0.77
10 3 0.12
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (9 bp):
AATTTTTTT
Found at i:94871 original size:3 final size:3
Alignment explanation
Indices: 94863--94908 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
94853 GCTTGAAATA
94863 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
94909 GTAGTAGTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:105328 original size:18 final size:18
Alignment explanation
Indices: 105302--105339 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
105292 CAAGTTTATC
*
105302 TTTTAGAAATTTAATTTA
1 TTTTAGAAATTCAATTTA
*
105320 TTTTCGAAATTCAATTTA
1 TTTTAGAAATTCAATTTA
105338 TT
1 TT
105340 CTTTTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTAGAAATTCAATTTA
Found at i:106560 original size:123 final size:123
Alignment explanation
Indices: 106341--107040 Score: 1228
Period size: 123 Copynumber: 5.7 Consensus size: 123
106331 CACTCAATGG
**
106341 ATCAACTTTTATAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* *
106406 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGATATAGATCAGC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
*
106464 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGATGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
*
106529 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCAATCACAGAAGGAGATAGATCAAC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
*
106587 ATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
*
106652 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGATATAGATCAAC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
106710 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* *
106775 ATGAGAAGAGCTTGCTCAACCTTTTGCATGA--CTATCACAGAAGGAGATAGATCAGC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
106831 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
106896 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
* ** * *
106954 ATCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAATG-AGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
107017 AATGAGAAGAGCTTGTTCAACCTT
65 AATGAGAAGAGCTTGTTCAACCTT
107041 GCCTTAATTC
Statistics
Matches: 553, Mismatches: 21, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
121 118 0.21
122 65 0.12
123 370 0.67
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
Found at i:107445 original size:3 final size:3
Alignment explanation
Indices: 107386--107427 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
107376 TCCATTTGAT
*
107386 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
107428 ATAAAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:108172 original size:22 final size:22
Alignment explanation
Indices: 108126--108174 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
108116 TACGGTGGTC
* *
108126 GACGATGGGGTTGACGATGGTA
1 GACGATGGGGTTGACGACGGCA
* *
108148 GACGATGGGGTTGATGGCGGCA
1 GACGATGGGGTTGACGACGGCA
108170 GACGA
1 GACGA
108175 CTGTCGGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.12, G:0.47, T:0.18
Consensus pattern (22 bp):
GACGATGGGGTTGACGACGGCA
Found at i:108856 original size:3 final size:3
Alignment explanation
Indices: 108848--108880 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
108838 AATATATTTC
108848 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
108881 TAGTCATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:109094 original size:22 final size:21
Alignment explanation
Indices: 109052--109112 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 21
109042 CCTTTTCTGA
*
109052 TATTTTTAAATAAA-TAAATATCT
1 TATTTTT--ATAAATTATATAT-T
109075 TATTTTTATAAATTATATATT
1 TATTTTTATAAATTATATATT
* *
109096 AATTTATTTTAAATTAT
1 TATTT-TTATAAATTAT
109113 TTTTAGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 10 0.30
22 16 0.48
23 7 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTTATAAATTATATATT
Found at i:125359 original size:21 final size:21
Alignment explanation
Indices: 125333--125377 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
125323 TATAATCCCA
125333 ACAGTGGTAATTTCAGCCCTT
1 ACAGTGGTAATTTCAGCCCTT
*
125354 ACAGTGTTAATTTCAGCCCTT
1 ACAGTGGTAATTTCAGCCCTT
125375 ACA
1 ACA
125378 ATTCAGTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (21 bp):
ACAGTGGTAATTTCAGCCCTT
Found at i:125457 original size:24 final size:24
Alignment explanation
Indices: 125407--125457 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
125397 TTCACCCTTA
* * *
125407 GTTCCTGCTGTTCAACAAGTTTTT
1 GTTCCTACTGTTCAACAAGTCTCT
125431 GTTCCTACTGTTCAACAAGTCTCT
1 GTTCCTACTGTTCAACAAGTCTCT
125455 GTT
1 GTT
125458 TCGCAAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.43
Consensus pattern (24 bp):
GTTCCTACTGTTCAACAAGTCTCT
Found at i:127320 original size:18 final size:19
Alignment explanation
Indices: 127299--127339 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
127289 TCTTCTACAC
*
127299 CATCAACAT-CATCATCTT
1 CATCAACATGAATCATCTT
127317 CATC-ACATGAATCATCTT
1 CATCAACATGAATCATCTT
127335 CATCA
1 CATCA
127340 TAATAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (19 bp):
CATCAACATGAATCATCTT
Found at i:129667 original size:87 final size:87
Alignment explanation
Indices: 129521--129694 Score: 267
Period size: 87 Copynumber: 2.0 Consensus size: 87
129511 TCATTTAACC
* * * * **
129521 GGAAATATTATCAAGTACAATAACATATTATGTACCGCATATATAATGTAATAGGTAGCGCTTAT
1 GGAAACATTACCAAGCACAATAACATATTAGGTACCGCATATATAACATAATAGGTAGCGCTTAT
*
129586 ATAATAAAATATGTTAATTACT
66 ATAATAAAATAGGTTAATTACT
* *
129608 GGAAACATTACCAAGCACAATAACATATTAGGTAGCGCTTATATAACATAATAGGTAGCGCTTAT
1 GGAAACATTACCAAGCACAATAACATATTAGGTACCGCATATATAACATAATAGGTAGCGCTTAT
129673 ATAATAAAATAGGTTAATTACT
66 ATAATAAAATAGGTTAATTACT
129695 TAATTTGTTA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.32
Consensus pattern (87 bp):
GGAAACATTACCAAGCACAATAACATATTAGGTACCGCATATATAACATAATAGGTAGCGCTTAT
ATAATAAAATAGGTTAATTACT
Found at i:129679 original size:21 final size:23
Alignment explanation
Indices: 129627--129686 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
129617 ACCAAGCACA
*
129627 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
129650 ATAACATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
129673 ATAATAAAATAGGT
1 ATAACATAATAGGT
129687 TAATTACTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:129811 original size:23 final size:23
Alignment explanation
Indices: 129785--129834 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
129775 ATCAAGCACA
*
129785 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
129808 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
129831 ATAA
1 ATAA
129835 TAAAATAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:129841 original size:23 final size:23
Alignment explanation
Indices: 129785--129841 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
129775 ATCAAGCACA
* *
129785 ATAACATATTAGGTAGCGCTTAT
1 ATAACAAAATAGGTAGCGCTTAT
**
129808 ATAACGTAATAGGTAGCGCTTAT
1 ATAACAAAATAGGTAGCGCTTAT
*
129831 ATAATAAAATA
1 ATAACAAAATA
129842 AGTTAATTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (23 bp):
ATAACAAAATAGGTAGCGCTTAT
Found at i:129891 original size:158 final size:158
Alignment explanation
Indices: 129598--130138 Score: 922
Period size: 158 Copynumber: 3.4 Consensus size: 158
129588 AATAAAATAT
* *
129598 GTTAATTACTGGAAACATTACCAAGCACAATAACATATTAGGTAGCGCTTATATAACATAATAGG
1 GTTAATTACTGGAAACATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGG
*
129663 TAGCGCTTATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCC
66 TAGCGCTTATATAATAAAATAAGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCC
129728 TAAAATGTTACCAAGGATAACATAAACG
131 TAAAATGTTACCAAGGATAACATAAACG
*
129756 GTTATTTACTGGAAACATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGG
1 GTTAATTACTGGAAACATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGG
129821 TAGCGCTTATATAATAAAATAAGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCC
66 TAGCGCTTATATAATAAAATAAGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCC
129886 TAAAATGTTACCAAGGATAACAT-AACTG
131 TAAAATGTTACCAAGGATAACATAAAC-G
* * * *
129914 GTTATTTACTGGAAACATTATCAAGCATAATAACATATTAGGCATCGCTTATATAACGTAATAGG
1 GTTAATTACTGGAAACATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGG
*
129979 TAGCGCTTATATAATAAAATAAGTTAATTACTTAATTTTTTATTACAACATATTAGGTAAACGCC
66 TAGCGCTTATATAATAAAATAAGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCC
* *
130044 TAAAATATTACCAAGGATAACATAACCG
131 TAAAATGTTACCAAGGATAACATAAACG
* * * * *
130072 GTTAATTACTGGAAATATTATCAAGCATAATAACATATTAGGTAGAGCTTATGTAACGTAATGGG
1 GTTAATTACTGGAAACATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGG
130137 TA
66 TA
130139 ATTACTTACT
Statistics
Matches: 364, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
157 3 0.01
158 359 0.99
159 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (158 bp):
GTTAATTACTGGAAACATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGG
TAGCGCTTATATAATAAAATAAGTTAATTACTTAATTTGTTATTACAACATATTAGGTAAACGCC
TAAAATGTTACCAAGGATAACATAAACG
Found at i:129969 original size:23 final size:23
Alignment explanation
Indices: 129943--129992 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
129933 ATCAAGCATA
* *
129943 ATAACATATTAGGCATCGCTTAT
1 ATAACATAATAGGCAGCGCTTAT
* *
129966 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGCAGCGCTTAT
129989 ATAA
1 ATAA
129993 TAAAATAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGCAGCGCTTAT
Found at i:130394 original size:2 final size:2
Alignment explanation
Indices: 130387--130446 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
130377 ATAAGTATGA
130387 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
130429 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
130447 GTGTGTGGGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:132342 original size:18 final size:18
Alignment explanation
Indices: 132319--132358 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
132309 TTCCTCATCA
*
132319 CTTCCTCCATCTTTTTTT
1 CTTCCTCCATCTTTTCTT
*
132337 CTTCCTCTATCTTTTCTT
1 CTTCCTCCATCTTTTCTT
132355 CTTC
1 CTTC
132359 ATATTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.35, G:0.00, T:0.60
Consensus pattern (18 bp):
CTTCCTCCATCTTTTCTT
Found at i:132607 original size:66 final size:64
Alignment explanation
Indices: 132467--132607 Score: 174
Period size: 66 Copynumber: 2.1 Consensus size: 64
132457 ACTCCCTTCA
* * *
132467 CCCCCATAAGTTCACCCCTCAAATCCACAACTTCCTTCACCACTCCATCAATATTTCTACCCAT
1 CCCCCTTAACTTCACCCCTCAAATCCACAACTTCCTTCACCACTCCATCAATATTTCCACCCAT
* * * * *
132531 CACCAACTTAACTTCACCCCTCAACTCCACAACTTCTTTCACCACTCCATCTATTTTTCCACCCA
1 C-CC-CCTTAACTTCACCCCTCAAATCCACAACTTCCTTCACCACTCCATCAATATTTCCACCCA
132596 CTT
64 --T
132599 CCCCCTTAA
1 CCCCCTTAA
132608 GCCTCTCCAT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
64 1 0.02
65 2 0.03
66 57 0.89
67 2 0.03
68 2 0.03
ACGTcount: A:0.26, C:0.45, G:0.01, T:0.28
Consensus pattern (64 bp):
CCCCCTTAACTTCACCCCTCAAATCCACAACTTCCTTCACCACTCCATCAATATTTCCACCCAT
Found at i:132770 original size:21 final size:21
Alignment explanation
Indices: 132746--132785 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
132736 ACCATCTCTT
132746 CTTCCTTCTCCT-CTGCCTCCA
1 CTTCC-TCTCCTGCTGCCTCCA
*
132767 CTTCCTCTTCTGCTGCCTC
1 CTTCCTCTCCTGCTGCCTC
132786 TGCCTCATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.03, C:0.50, G:0.07, T:0.40
Consensus pattern (21 bp):
CTTCCTCTCCTGCTGCCTCCA
Found at i:136296 original size:23 final size:23
Alignment explanation
Indices: 136250--136293 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
136240 ATAAATTTAT
136250 TCCTAGGGTTTTGGCCTTTTTTC
1 TCCTAGGGTTTTGGCCTTTTTTC
136273 TCCTAGGGTTTT-GCCTTTTTT
1 TCCTAGGGTTTTGGCCTTTTTT
136294 TCTACGTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.05, C:0.20, G:0.20, T:0.55
Consensus pattern (23 bp):
TCCTAGGGTTTTGGCCTTTTTTC
Found at i:138289 original size:39 final size:39
Alignment explanation
Indices: 138206--138294 Score: 133
Period size: 39 Copynumber: 2.3 Consensus size: 39
138196 AGGACTTGCA
138206 GTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATGCG
1 GTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATGCG
* * * *
138245 ATAAGGACTTTCCCTGAGCACAAAGCAGAGGAGCTTGTG
1 GTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATGCG
*
138284 GTAAGGTCTTA
1 GTAAGGACTTA
138295 TATGTCATAG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.19
Consensus pattern (39 bp):
GTAAGGACTTACCCTGAGCACAAAGCAGAGGAGCATGCG
Found at i:139664 original size:30 final size:30
Alignment explanation
Indices: 139606--139664 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
139596 TTTGGATCCG
* *
139606 AATTTAATCAAAATTTTACTTTGGTCATCA
1 AATTTAATCAAAATTTTAATTTAGTCATCA
* * *
139636 AATTTAATTAATATTTTAATTTATTCATC
1 AATTTAATCAAAATTTTAATTTAGTCATC
139665 GAAAAAAGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.49
Consensus pattern (30 bp):
AATTTAATCAAAATTTTAATTTAGTCATCA
Found at i:141818 original size:41 final size:40
Alignment explanation
Indices: 141598--142166 Score: 607
Period size: 41 Copynumber: 13.9 Consensus size: 40
141588 ATAGCGGCAT
* * * * *
141598 TTTAGCGGCGTTTTTAGAACAAACGCCGATAAATACTCGTAA
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAAGACT-GTAC
*
141640 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTGTAC
* *
141680 TTTAGTGGCGTTTTTACACAAACGCCGCTACAGACTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTGTAC
** * * *
141720 TTTAGCAGCGTTTTTAGACAAAATGCCGCTAAATACTTGTAC
1 TTTAGTGGCGTTTTTATAC-AAACGCCGCTAAAGAC-TGTAC
* * * *
141762 TTTAGTGGTGTTTTTAATACAAACACCGCTAAAGAATATAC
1 TTTAGTGGCGTTTTT-ATACAAACGCCGCTAAAGACTGTAC
* * * *
141803 TTTAGCGGCGCTTTTATACAAACGCCGCTATATACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-GTAC
* * *
141844 TTTAGTGGCATTTTTATACAAAAGCCGCTAAATACTTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGAC-TGTAC
* * *
141885 TTTAGTGGCATTTTTAATACAAACGCCGCTAAAGAATGTAT
1 TTTAGTGGCGTTTTT-ATACAAACGCCGCTAAAGACTGTAC
* * * * *
141926 TTTAGCGGTGTTTTTATATAAACGCCGCTATATACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-GTAC
* * *
141967 TTTAGTGGCGTTTTTAATACAGACGCCGCTATAGACTCGTAT
1 TTTAGTGGCGTTTTT-ATACAAACGCCGCTAAAGACT-GTAC
*
142009 TTTAGTGGCGTTTTTATACAAATGCCGCTAAAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-GTAC
* *
142050 TTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-GTAC
* * *
142091 TTTAGTGGCGTTTTTATACAAACGCCGTTATAGACTCGTAT
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-GTAC
*** *
142132 TTTAGTGGTACTTTTATACAAACGCCGCTATAGAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGAC
142167 CCATGATTTA
Statistics
Matches: 450, Mismatches: 69, Indels: 17
0.84 0.13 0.03
Matches are distributed among these distances:
40 89 0.20
41 259 0.58
42 99 0.22
43 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (40 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTGTAC
Done.