Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008113.1 Hibiscus syriacus cultivar Beakdansim tig00110652_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: 992058
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 1 of 5
Found at i:4320 original size:21 final size:20
Alignment explanation
Indices: 4294--4362 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 20
4284 TGAATCGGGT
*
4294 TCTTGAACGGTGGGAGGAACC
1 TCTTGAACGGTGGGAGG-GCC
* **
4315 TCTTGAACGATGACAGGGCC
1 TCTTGAACGGTGGGAGGGCC
*
4335 TCTTGAAAGGTGGGAGGGGCC
1 TCTTGAACGGTGGGA-GGGCC
4356 TCTTGAA
1 TCTTGAA
4363 GGACTATAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 13 0.33
21 26 0.67
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (20 bp):
TCTTGAACGGTGGGAGGGCC
Found at i:4376 original size:21 final size:21
Alignment explanation
Indices: 4352--4408 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
4342 AGGTGGGAGG
*
4352 GGCCTCTTGAAGGACTAT-AGA
1 GGCCTCTTGAACGA-TATGAGA
4373 GGCCTCTTGAACGATATGAGA
1 GGCCTCTTGAACGATATGAGA
4394 GGCCTCTTGAACGAT
1 GGCCTCTTGAACGAT
4409 GATAGGTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.09
21 31 0.91
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (21 bp):
GGCCTCTTGAACGATATGAGA
Found at i:4730 original size:21 final size:21
Alignment explanation
Indices: 4706--4785 Score: 142
Period size: 21 Copynumber: 3.8 Consensus size: 21
4696 GTAGAGCGGC
*
4706 TACCTCATCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
*
4727 TACCTCACCACGTAAAATAGA
1 TACCTCACCACGTAAAGTAGA
4748 TACCTCACCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
4769 TACCTCACCACGTAAAG
1 TACCTCACCACGTAAAG
4786 AACCATTGTC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (21 bp):
TACCTCACCACGTAAAGTAGA
Found at i:4824 original size:21 final size:21
Alignment explanation
Indices: 4705--4843 Score: 63
Period size: 21 Copynumber: 6.6 Consensus size: 21
4695 CGTAGAGCGG
* *
4705 CTACCTCATCACGTAAAGTA-G
1 CTACCTCACCACGTAAAG-ACC
* **
4726 ATACCTCACCACGTAAA-ATAG
1 CTACCTCACCACGTAAAGA-CC
* *
4747 ATACCTCACCACGTAAAGTA-G
1 CTACCTCACCACGTAAAG-ACC
* *
4768 ATACCTCACCACGTAAAGAAC
1 CTACCTCACCACGTAAAGACC
** * *
4789 C-ATTGTCATCGCGTAAA-ACC
1 CTA-CCTCACCACGTAAAGACC
4809 TCTACCTCACCACGTAAAGACC
1 -CTACCTCACCACGTAAAGACC
* *
4831 GTACCTCATCACG
1 CTACCTCACCACG
4844 CCATGCACCA
Statistics
Matches: 94, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.01
20 4 0.04
21 84 0.89
22 4 0.04
23 1 0.01
ACGTcount: A:0.35, C:0.32, G:0.12, T:0.20
Consensus pattern (21 bp):
CTACCTCACCACGTAAAGACC
Found at i:4869 original size:63 final size:63
Alignment explanation
Indices: 4748--4869 Score: 140
Period size: 63 Copynumber: 1.9 Consensus size: 63
4738 GTAAAATAGA
* * *
4748 TACCTCACCACGTAAAGTAGATACCTCACCACGTAAAGAACCATTGTCATCGCGTAAAACCTC
1 TACCTCACCACGTAAAGTAGATACCTCACCACGCAAAGAACCATTGTCATCACATAAAACCTC
* * * * *
4811 TACCTCACCACGTAAAG-ACCG-TACCTCATCACGCCATGCACCATTGTCGTCACATAAAA
1 TACCTCACCACGTAAAGTA--GATACCTCACCACGCAAAGAACCATTGTCATCACATAAAA
4870 TATTGACCTC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
62 1 0.02
63 47 0.96
64 1 0.02
ACGTcount: A:0.34, C:0.34, G:0.12, T:0.20
Consensus pattern (63 bp):
TACCTCACCACGTAAAGTAGATACCTCACCACGCAAAGAACCATTGTCATCACATAAAACCTC
Found at i:4884 original size:21 final size:21
Alignment explanation
Indices: 4860--4905 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4850 ACCATTGTCG
* *
4860 TCACATAAAATATTGACCTCC
1 TCACACAAAATATTGACCTCA
* *
4881 TCACGCAAAGTATTGACCTCA
1 TCACACAAAATATTGACCTCA
4902 TCAC
1 TCAC
4906 GTAACTCCCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (21 bp):
TCACACAAAATATTGACCTCA
Found at i:6610 original size:19 final size:20
Alignment explanation
Indices: 6580--6618 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
6570 AATAGTTTCT
6580 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACGC
6600 GAAAC-TAAAATCGCAACGC
1 GAAACTTAAAATCGCAACGC
6619 AATTTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACGC
Found at i:7015 original size:20 final size:21
Alignment explanation
Indices: 6990--7033 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
6980 TCTGAGAGAT
6990 GGAGATA-GACGGATTTCGTC
1 GGAGATAGGACGGATTTCGTC
7010 GGAGATAGGGACGGATTTCGTC
1 GGAGATA-GGACGGATTTCGTC
7032 GG
1 GG
7034 CGATGGAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.32
22 15 0.68
ACGTcount: A:0.23, C:0.14, G:0.41, T:0.23
Consensus pattern (21 bp):
GGAGATAGGACGGATTTCGTC
Found at i:7231 original size:20 final size:20
Alignment explanation
Indices: 7206--7250 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
7196 CGCGCATTGT
*
7206 GAATTTGACTTCTGTGTTGC
1 GAATTTGACTTATGTGTTGC
7226 GAATTTGACTTATGTGTTGC
1 GAATTTGACTTATGTGTTGC
7246 GAATT
1 GAATT
7251 ACAAATTCTC
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:0.20, C:0.11, G:0.24, T:0.44
Consensus pattern (20 bp):
GAATTTGACTTATGTGTTGC
Found at i:7264 original size:20 final size:20
Alignment explanation
Indices: 7241--7290 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
7231 TGACTTATGT
*
7241 GTTGCGAATTACAAATTCTC
1 GTTGCGAATTACAAATTCGC
* * *
7261 GTTGTGATTTACAGATTCGC
1 GTTGCGAATTACAAATTCGC
7281 GTTGCGAATT
1 GTTGCGAATT
7291 TGGAAAATCG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:7301 original size:21 final size:21
Alignment explanation
Indices: 7283--7326 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
7273 AGATTCGCGT
7283 TGCGAATTTGGAAAATCGCAA
1 TGCGAATTTGGAAAATCGCAA
* *
7304 AGCGAATTCGGAAAATCGCAA
1 TGCGAATTTGGAAAATCGCAA
7325 TG
1 TG
7327 TGATTTACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (21 bp):
TGCGAATTTGGAAAATCGCAA
Found at i:12196 original size:21 final size:22
Alignment explanation
Indices: 12155--12196 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
12145 AAATTATTAT
*
12155 ATAATTTATATATCTTTTATTC
1 ATAATTTATATATCTTATATTC
*
12177 ATAATTTAT-TTTCTTATATT
1 ATAATTTATATATCTTATATT
12197 TTATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (22 bp):
ATAATTTATATATCTTATATTC
Found at i:12267 original size:11 final size:11
Alignment explanation
Indices: 12251--12275 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12241 CACCATCATA
12251 ATATTTTTAAT
1 ATATTTTTAAT
12262 ATATTTTTAAT
1 ATATTTTTAAT
12273 ATA
1 ATA
12276 GATCCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTTTTAAT
Found at i:19087 original size:3 final size:3
Alignment explanation
Indices: 19079--19136 Score: 107
Period size: 3 Copynumber: 19.0 Consensus size: 3
19069 GACTCTACGA
19079 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19127 AAT ATAT AAT
1 AAT A-AT AAT
19137 CAGGGGACAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:27313 original size:23 final size:23
Alignment explanation
Indices: 27280--27338 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
27270 GAAAAAAAAC
**
27280 GAAAAATGTGTCACAAAGGTAGA
1 GAAAAATGTGTCACAAAGACAGA
* * *
27303 GAAAAACGTGTCATAAAGACGGA
1 GAAAAATGTGTCACAAAGACAGA
27326 GAAAAATGTGTCA
1 GAAAAATGTGTCA
27339 AACAATAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.25, T:0.17
Consensus pattern (23 bp):
GAAAAATGTGTCACAAAGACAGA
Found at i:30519 original size:23 final size:23
Alignment explanation
Indices: 30467--30525 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
30457 CTCGTATAAA
*
30467 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
30490 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
30513 TGCACCGTAGTGC
1 TGCACCGAAGTGC
30526 TATATAAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:37428 original size:23 final size:23
Alignment explanation
Indices: 37397--37447 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
37387 CATATAAATG
*
37397 CACCAAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
* * *
37420 CACCGAAGTGTCTCGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTA
37443 CACCG
1 CACCG
37448 TAGTTCTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTA
Found at i:38508 original size:18 final size:17
Alignment explanation
Indices: 38485--38536 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
38475 CGACCCATTT
38485 ACCCGTTGACCCGACCTG
1 ACCCGTTGACCCGACC-G
*
38503 ACCCGTTGACCCAAACCG
1 ACCCGTTGACCC-GACCG
*
38521 ACCCGTTGATCCGACC
1 ACCCGTTGACCCGACC
38537 CGTTGACCGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 3 0.10
18 24 0.80
19 3 0.10
ACGTcount: A:0.21, C:0.44, G:0.19, T:0.15
Consensus pattern (17 bp):
ACCCGTTGACCCGACCG
Found at i:38536 original size:13 final size:13
Alignment explanation
Indices: 38518--38542 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38508 TTGACCCAAA
38518 CCGACCCGTTGAT
1 CCGACCCGTTGAT
38531 CCGACCCGTTGA
1 CCGACCCGTTGA
38543 CCGGTGTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
CCGACCCGTTGAT
Found at i:38644 original size:59 final size:58
Alignment explanation
Indices: 38545--38659 Score: 160
Period size: 59 Copynumber: 2.0 Consensus size: 58
38535 CCCGTTGACC
* * **
38545 GGTGTTATTCTGGGAATTAATTCGAAATGGGTGCTATTTTGGTAATTTTTTCAAAAAAA
1 GGTGATATTCTGAGAATTAATTCGAAATGGGTGCTATTTTGG-AATTAATTCAAAAAAA
*
38604 GGTGATATTCTGAGAATTAATTCGAAAT-TGTGCTATTTTTGGAATTAATTCAAAAA
1 GGTGATATTCTGAGAATTAATTCGAAATGGGTGCTA-TTTTGGAATTAATTCAAAAA
38660 GGTGCTATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 18 0.36
59 32 0.64
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (58 bp):
GGTGATATTCTGAGAATTAATTCGAAATGGGTGCTATTTTGGAATTAATTCAAAAAAA
Found at i:38649 original size:28 final size:27
Alignment explanation
Indices: 38557--38678 Score: 100
Period size: 28 Copynumber: 4.3 Consensus size: 27
38547 TGTTATTCTG
**
38557 GGAATTAATTCGAAATGGGTGCTATTTT
1 GGAATTAATTC-AAAAAGGTGCTATTTT
** * *
38585 GGTAATTTTTTCAAAAAAAGGTGATATTCT
1 GG-AATTAATTC--AAAAAGGTGCTATTTT
* **
38615 GAGAATTAATTCGAAATTGTGCTATTTTT
1 G-GAATTAATTCAAAAAGGTGCTA-TTTT
38644 GGAATTAATTCAAAAAGGTGCTATTTT
1 GGAATTAATTCAAAAAGGTGCTATTTT
38671 GGTAATTA
1 GG-AATTA
38679 TTTTTTAAAA
Statistics
Matches: 72, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
27 6 0.08
28 34 0.47
29 11 0.15
30 20 0.28
31 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.40
Consensus pattern (27 bp):
GGAATTAATTCAAAAAGGTGCTATTTT
Found at i:45799 original size:21 final size:21
Alignment explanation
Indices: 45773--45813 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
45763 GAATGCTGGA
45773 AACCGGTTTTGACCAGTTTTG
1 AACCGGTTTTGACCAGTTTTG
* *
45794 AACCGGTTTTTACCGGTTTT
1 AACCGGTTTTGACCAGTTTT
45814 ACCGGTCACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (21 bp):
AACCGGTTTTGACCAGTTTTG
Found at i:45815 original size:9 final size:10
Alignment explanation
Indices: 45774--45819 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
45764 AATGCTGGAA
45774 ACCGGTTTTG
1 ACCGGTTTTG
*
45784 ACCAGTTTTG
1 ACCGGTTTTG
*
45794 AACCGGTTTTT
1 -ACCGGTTTTG
45805 ACCGGTTTT-
1 ACCGGTTTTG
45814 ACCGGT
1 ACCGGT
45820 CACGATCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 6 0.19
10 18 0.56
11 8 0.25
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:45982 original size:28 final size:28
Alignment explanation
Indices: 45856--46011 Score: 100
Period size: 28 Copynumber: 5.4 Consensus size: 28
45846 CCCGTTGACC
* * **
45856 GGTGTTATTCTGGGAATAAATTTGAAATG
1 GGTGCTATT-TGGGAATTAATTTGAAAAA
* **
45885 GGTGCTATTTTGGTAATTTTTTTTCGAAAAA
1 GGTGCTA-TTTGGGAA-TTAATTT-GAAAAA
* * *
45916 GGTGATATTATGGGAATTAATTCG-AAAT
1 GGTGCTATT-TGGGAATTAATTTGAAAAA
* *
45944 TGTGCTAATTTGGGAATTAATTTGAAAAG
1 GGTGCT-ATTTGGGAATTAATTTGAAAAA
* *
45973 GGTGCTATTTTGGTAATT-ATTTTAAAAA
1 GGTGCTA-TTTGGGAATTAATTTGAAAAA
*
46001 AGTGCTATTTG
1 GGTGCTATTTG
46012 TGTAAAATGT
Statistics
Matches: 98, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
27 4 0.04
28 35 0.36
29 32 0.33
30 12 0.12
31 15 0.15
ACGTcount: A:0.31, C:0.04, G:0.23, T:0.42
Consensus pattern (28 bp):
GGTGCTATTTGGGAATTAATTTGAAAAA
Found at i:47938 original size:64 final size:64
Alignment explanation
Indices: 47870--47991 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
47860 GCATAAATCC
* * * * * *
47870 CATTCGATGTTTGTATTTTAAGGGGGTGTATCGATGCACTACTTGTGCATCGATACACTGATGG
1 CATTCGATATTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTGATGG
* *
47934 CATTCGATATTTTTATTTTAAAGGAGTGCATCGATACACTTCATGTGCATCGATACAC
1 CATTCGATATTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACAC
47992 CTTGAACAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (64 bp):
CATTCGATATTTGTATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTGATGG
Found at i:48956 original size:45 final size:45
Alignment explanation
Indices: 48878--48963 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
48868 ATAATTTAGA
** *
48878 TTTCAAAATCAGTTCATCAGTAAATTCATAAAACGTCAGTAAAGG
1 TTTCAAAATCAGTTCATCACCAAATTCATAAAACATCAGTAAAGG
* *
48923 TTTCAAAATCAGTTCATTACCAAATT-GTGAAAACATCAGTA
1 TTTCAAAATCAGTTCATCACCAAATTCAT-AAAACATCAGTA
48964 GTGTTTTTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (45 bp):
TTTCAAAATCAGTTCATCACCAAATTCATAAAACATCAGTAAAGG
Found at i:50146 original size:19 final size:19
Alignment explanation
Indices: 50070--50138 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
50060 GGTTAACTCT
*
50070 GGTCAAAGTCAA-TGAGTCA
1 GGTCAAAGTCAACAG-GTCA
*
50089 GGTCAAAGTCAACAGGTCG
1 GGTCAAAGTCAACAGGTCA
*
50108 GGTCAAAGTCAACGGGTCA
1 GGTCAAAGTCAACAGGTCA
50127 GGTCAAAGTCAA
1 GGTCAAAGTCAA
50139 TATGTCAGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 44 0.98
20 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.17
Consensus pattern (19 bp):
GGTCAAAGTCAACAGGTCA
Found at i:53774 original size:30 final size:30
Alignment explanation
Indices: 53740--53829 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
53730 TCTAACCCAT
* *
53740 TGACC-TTGACCCGAACCATTGACTTTGACA
1 TGACCGTTGACACG-ACCATTAACTTTGACA
* * *
53770 TGACCGCTGACATGCCCATTAACTTTGACA
1 TGACCGTTGACACGACCATTAACTTTGACA
* * *
53800 TGACCGTTGACATGGCCATTGACTGTTGAC
1 TGACCGTTGACACGACCATTAACT-TTGAC
53830 CTACCCGTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 40 0.80
31 10 0.20
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (30 bp):
TGACCGTTGACACGACCATTAACTTTGACA
Found at i:54746 original size:27 final size:27
Alignment explanation
Indices: 54716--54778 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
54706 TAAATTATTG
*
54716 AAATACCCTTGAACTGTA-AAATAACCA
1 AAATACCCCTGAACTG-AGAAATAACCA
* * *
54743 AAATACCCCTGAAGTGAGAAATGACCT
1 AAATACCCCTGAACTGAGAAATAACCA
54770 AAATACCCC
1 AAATACCCC
54779 CAAGCTCTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.19
Consensus pattern (27 bp):
AAATACCCCTGAACTGAGAAATAACCA
Found at i:55928 original size:32 final size:32
Alignment explanation
Indices: 55856--55961 Score: 108
Period size: 32 Copynumber: 3.3 Consensus size: 32
55846 CTTGGGTGGC
* *
55856 TCTAAGGCCCCAAGGCA-TTTCCTTAGGTAGGC
1 TCTAAGGCCCCAAGGTACTTT-CTTAGGTAGGT
* *
55888 TCTAAGGCCCCAAGGTACTTTCTTGGGTATGT
1 TCTAAGGCCCCAAGGTACTTTCTTAGGTAGGT
* * *
55920 TCTTAGGCCCTAAGATACTATT-TTAGGTAGGT
1 TCTAAGGCCCCAAGGTACT-TTCTTAGGTAGGT
*
55952 TCTCAGGCCC
1 TCTAAGGCCC
55962 TAAAATATTC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 57 0.92
33 5 0.08
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (32 bp):
TCTAAGGCCCCAAGGTACTTTCTTAGGTAGGT
Found at i:61025 original size:20 final size:21
Alignment explanation
Indices: 61000--61092 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
60990 TTTTCCCAAT
*
61000 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
61020 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
61041 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
61061 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
61082 TCGCAATGCGA
1 TCGCAATGCGA
61093 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:61107 original size:41 final size:41
Alignment explanation
Indices: 61000--61092 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
60990 TTTTCCCAAT
61000 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
61041 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
61082 TCGCAATGCGA
1 TCGCAATGCGA
61093 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:61127 original size:21 final size:20
Alignment explanation
Indices: 61078--61128 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
61068 GCGAATTGGG
* *
61078 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
61098 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
61119 AAAATCGCAA
1 AAAATCGCAA
61129 CGAGATACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:61148 original size:20 final size:21
Alignment explanation
Indices: 61123--61170 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
61113 TAATAAAAAA
*
61123 TCGCAACGA-GATACTTACTT
1 TCGCAACGACGATACTGACTT
61143 TCGCAAC-ACGATACTGACTT
1 TCGCAACGACGATACTGACTT
61163 TCGCAACG
1 TCGCAACG
61171 CAATTTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (21 bp):
TCGCAACGACGATACTGACTT
Found at i:61155 original size:41 final size:41
Alignment explanation
Indices: 61078--61155 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
61068 GCGAATTGGG
* * **
61078 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
61119 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
61156 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:61726 original size:19 final size:19
Alignment explanation
Indices: 61688--61754 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
61678 TTCGAGAATG
*
61688 AAAATCGCAACGTGGAAATA
1 AAAATCGCAACG-CGAAATA
**
61708 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
61727 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
61746 AAAATCGCA
1 AAAATCGCA
61755 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:61796 original size:20 final size:19
Alignment explanation
Indices: 61750--61913 Score: 118
Period size: 20 Copynumber: 9.1 Consensus size: 19
61740 GAAACCAAAA
*
61750 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
61769 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
61788 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
61808 TCGCGTTGCAATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
61824 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
61841 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
61855 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
61872 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
61892 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
61912 TC
1 TC
61914 AACCAAAAGA
Statistics
Matches: 115, Mismatches: 15, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
12 8 0.07
14 12 0.10
15 1 0.01
16 1 0.01
17 4 0.03
18 1 0.01
19 39 0.34
20 48 0.42
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:61831 original size:39 final size:39
Alignment explanation
Indices: 61755--61831 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
61745 CAAAATCGCA
* * **
61755 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCAATTTCTAGGTCGCGG
61794 TTGCGATTTTCATTTCGCGTTGCAATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCAATT-TCTAGGTCGCG
61832 ATAGTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCAATTTCTAGGTCGCGG
Found at i:61840 original size:33 final size:31
Alignment explanation
Indices: 61803--61888 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
61793 GTTGCGATTT
*
61803 TCATTTCGCGTTGCAATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCAA-T-TCTCGTCGCGATAG
* *
61836 TCATTTCGCGTTGCGATTCTCGTTGCGATAG
1 TCATTTCGCGTTGCAATTCTCGTCGCGATAG
*
61867 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCAATTCTC
61889 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
31 18 0.37
32 16 0.33
33 15 0.31
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.38
Consensus pattern (31 bp):
TCATTTCGCGTTGCAATTCTCGTCGCGATAG
Found at i:61867 original size:31 final size:31
Alignment explanation
Indices: 61793--61888 Score: 120
Period size: 33 Copynumber: 3.0 Consensus size: 31
61783 TTATTTCGCG
** * *
61793 GTTGCGATTTTCATTTCGCGTTGCAATTGTCTG
1 GTTGCGATAGTCATTTCGCGTTGCGA-T-TCTC
*
61826 GTCGCGATAGTCATTTCGCGTTGCGATTCTC
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTC
61857 GTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 GTTGCGATAGTCATTT-CGCGTTGCGATTCTC
61889 ATTATCTCGT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 18 0.32
32 16 0.29
33 22 0.39
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (31 bp):
GTTGCGATAGTCATTTCGCGTTGCGATTCTC
Found at i:63985 original size:21 final size:21
Alignment explanation
Indices: 63961--64027 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
63951 TCATTCCTCG
63961 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCATTCA
* * ** * * *
63982 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCATTCA
64003 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
64024 AGAG
1 AGAG
64028 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 14, Indels: 3
0.65 0.29 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:63985 original size:42 final size:42
Alignment explanation
Indices: 63905--64027 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
63895 GCCCGACTCG
* * * * * * *
63905 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
63947 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
* * * *
63989 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
64028 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.06
42 62 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:66857 original size:20 final size:19
Alignment explanation
Indices: 66822--66888 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
66812 GAAACTTAAA
66822 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
66841 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
66861 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
66880 ATCGCAACG
1 ATCGCAACG
66889 ACAAATCGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:66916 original size:31 final size:33
Alignment explanation
Indices: 66861--66938 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
66851 GGAAATGGCT
*
66861 ATCGCAATGCGAAATGAAAATCGCAACGAC-AA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
66893 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
66925 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
66939 CACAAATCGC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 13 0.30
32 31 0.70
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:66967 original size:19 final size:17
Alignment explanation
Indices: 66945--67040 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
66935 GAAACACAAA
66945 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
66964 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
66980 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
66996 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
67012 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
67029 TCGCATTGCGAT
1 TCGC-TTGCGAT
67041 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:66986 original size:14 final size:14
Alignment explanation
Indices: 66967--67024 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
66957 TTTCATTTCG
66967 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
66981 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
66997 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
67013 CGTTGCGATTTT
1 CGTTGCGATTTT
67025 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:67031 original size:33 final size:33
Alignment explanation
Indices: 66950--67040 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
66940 ACAAATCGCA
66950 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
66983 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
67015 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
67041 AGCCATTTCC
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:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:67059 original size:20 final size:19
Alignment explanation
Indices: 67025--67079 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
67015 TTGCGATTTT
*
67025 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
67044 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
67064 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
67080 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:67575 original size:18 final size:18
Alignment explanation
Indices: 67549--67593 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
67539 GTCGATCAGA
*
67549 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
67567 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
67585 TGATGGCTC
1 TGATGGCTC
67594 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:69234 original size:22 final size:22
Alignment explanation
Indices: 69209--69252 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
69199 GATTTAGATA
69209 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
69231 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
69253 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:69465 original size:20 final size:20
Alignment explanation
Indices: 69440--69533 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
69430 GATTATGTAT
69440 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
69460 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
69480 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
69501 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
69521 TATCGCATTGCGA
1 TATCGCGTTGCGA
69534 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:69534 original size:20 final size:20
Alignment explanation
Indices: 69420--69534 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
69410 CGCTTTGAAA
*
69420 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
69441 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
69461 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
69481 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
69502 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
69522 ATCGCATTGCGAT
1 ATCGCATTGCGAT
69535 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:69555 original size:41 final size:41
Alignment explanation
Indices: 69462--69596 Score: 121
Period size: 41 Copynumber: 3.3 Consensus size: 41
69452 AAAGTCAGTA
* * * * *
69462 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* *
69502 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* ** * * *
69544 TCGCGTTGCGAT-TTACTTATTCGAATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCTCAAT
69585 TCGCGTTGCGAT
1 TCGCGTTGCGAT
69597 TTACTTATTC
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 3 0.04
41 71 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
Found at i:69572 original size:20 final size:20
Alignment explanation
Indices: 69523--69612 Score: 90
Period size: 21 Copynumber: 4.4 Consensus size: 20
69513 ATAGTCAGTA
* *
69523 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-TAT
*
69544 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* * **
69564 TCGAATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
69585 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
69605 TCGCATTG
1 TCGCATTG
69613 TGAATTGGGA
Statistics
Matches: 54, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 24 0.44
21 30 0.56
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:69597 original size:41 final size:41
Alignment explanation
Indices: 69527--69618 Score: 148
Period size: 41 Copynumber: 2.2 Consensus size: 41
69517 TCAGTATCGC
* *
69527 ATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTATTCGA
1 ATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGA
*
69568 ATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGC
1 ATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGA
*
69609 ATTGTGAATT
1 ATTGCGAATT
69619 GGGAAAATCG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (41 bp):
ATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCGA
Found at i:70516 original size:59 final size:59
Alignment explanation
Indices: 70444--70558 Score: 230
Period size: 59 Copynumber: 1.9 Consensus size: 59
70434 TTTATATCTT
70444 TAAAATTTTCCTTTATATTTGAATGATCATATCATATATCTAATGTCCTAAACCTTCTA
1 TAAAATTTTCCTTTATATTTGAATGATCATATCATATATCTAATGTCCTAAACCTTCTA
70503 TAAAATTTTCCTTTATATTTGAATGATCATATCATATATCTAATGTCCTAAACCTT
1 TAAAATTTTCCTTTATATTTGAATGATCATATCATATATCTAATGTCCTAAACCTT
70559 TAAAAGATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.44
Consensus pattern (59 bp):
TAAAATTTTCCTTTATATTTGAATGATCATATCATATATCTAATGTCCTAAACCTTCTA
Found at i:85180 original size:42 final size:42
Alignment explanation
Indices: 85121--85220 Score: 200
Period size: 42 Copynumber: 2.4 Consensus size: 42
85111 AAATACCCAA
85121 GTTTCTATTACTTGGCCTCCTTCGTTTTTGGTTGCATTTTCT
1 GTTTCTATTACTTGGCCTCCTTCGTTTTTGGTTGCATTTTCT
85163 GTTTCTATTACTTGGCCTCCTTCGTTTTTGGTTGCATTTTCT
1 GTTTCTATTACTTGGCCTCCTTCGTTTTTGGTTGCATTTTCT
85205 GTTTCTATTACTTGGC
1 GTTTCTATTACTTGGC
85221 ATTTAGCTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.08, C:0.21, G:0.17, T:0.54
Consensus pattern (42 bp):
GTTTCTATTACTTGGCCTCCTTCGTTTTTGGTTGCATTTTCT
Found at i:85223 original size:23 final size:23
Alignment explanation
Indices: 85154--85224 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
85144 GTTTTTGGTT
85154 GCATTTTCTGTTTCTATTACTTG
1 GCATTTTCTGTTTCTATTACTTG
* * **
85177 GCCTCCTTC-G-TT-T-TTGGTT-
1 GCAT-TTTCTGTTTCTATTACTTG
85196 GCATTTTCTGTTTCTATTACTTG
1 GCATTTTCTGTTTCTATTACTTG
85219 GCATTT
1 GCATTT
85225 AGCTTTGCCA
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
18 3 0.09
19 4 0.12
20 6 0.18
21 2 0.06
22 6 0.18
23 10 0.29
24 3 0.09
ACGTcount: A:0.10, C:0.20, G:0.15, T:0.55
Consensus pattern (23 bp):
GCATTTTCTGTTTCTATTACTTG
Found at i:90323 original size:20 final size:21
Alignment explanation
Indices: 90298--90350 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
90288 GACTAACAAA
90298 TTCGCAACGCGAACTTC-AAT
1 TTCGCAACGCGAACTTCTAAT
* **
90318 TTCGCAACTC-AGTTTCTAAT
1 TTCGCAACGCGAACTTCTAAT
90338 TTCGCAACGCGAA
1 TTCGCAACGCGAA
90351 TCTGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.15
20 21 0.81
21 1 0.04
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (21 bp):
TTCGCAACGCGAACTTCTAAT
Found at i:90362 original size:20 final size:21
Alignment explanation
Indices: 90338--90390 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
90328 AGTTTCTAAT
*
90338 TTCGCAACGCGAATCTGTAAA
1 TTCGCAACGCGAATCTGGAAA
*** *
90359 -TCGCGTTGCGAATTTGGAAA
1 TTCGCAACGCGAATCTGGAAA
90379 TTCGCAACGCGA
1 TTCGCAACGCGA
90391 TAGTCAAATT
Statistics
Matches: 23, Mismatches: 8, Indels: 2
0.70 0.24 0.06
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
TTCGCAACGCGAATCTGGAAA
Found at i:90401 original size:20 final size:19
Alignment explanation
Indices: 90376--90426 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
90366 GCGAATTTGG
*
90376 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACGC-AAAGTC
**
90396 AAATTCGCAATACAAAGTC
1 AAATTCGCAACGCAAAGTC
90415 AAATTCGCAACG
1 AAATTCGCAACG
90427 AGAATTTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.20
Consensus pattern (19 bp):
AAATTCGCAACGCAAAGTC
Found at i:91361 original size:24 final size:24
Alignment explanation
Indices: 91334--91387 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 24
91324 GTATTCGAAA
91334 TTTGATCTTGGTCAATAC-CTGGAT
1 TTTGATCTTGGTCAATACTC-GGAT
91358 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAT
91382 TTTGAT
1 TTTGAT
91388 GATATGATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAT
Found at i:91570 original size:3 final size:3
Alignment explanation
Indices: 91562--91592 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
91552 ATATAACCCT
*
91562 GAA GAA GAA GAA GAA GAA TAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
91593 TCCCTGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:94008 original size:20 final size:20
Alignment explanation
Indices: 93985--94118 Score: 102
Period size: 20 Copynumber: 7.0 Consensus size: 20
93975 AATCGCAAAC
93985 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
94005 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
* * * **
94025 TGAATTTGACTATCAC--AA
1 CGAATTTGACTTTCGCGTTG
* *
94043 CG--CTT-A-TTTCGCATTG
1 CGAATTTGACTTTCGCGTTG
94059 CGAATTT-ACCTTTCGCGTTG
1 CGAATTTGA-CTTTCGCGTTG
* *
94079 CAAATTTGACTATCGCGTTG
1 CGAATTTGACTTTCGCGTTG
* * *
94099 CAAATTTGTCTATCGCGTTG
1 CGAATTTGACTTTCGCGTTG
94119 TACATTATTT
Statistics
Matches: 91, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
14 4 0.04
15 1 0.01
16 4 0.04
18 4 0.04
20 77 0.85
21 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:94539 original size:24 final size:25
Alignment explanation
Indices: 94512--94566 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
94502 TTTCAAATTC
*
94512 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
* *
94536 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
94560 ATTTCAA
1 ATTTCAA
94567 TATAAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 20 0.77
25 2 0.08
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (25 bp):
ATTTCAAATGTCAATTGGAGTTTGA
Found at i:94552 original size:18 final size:18
Alignment explanation
Indices: 94531--94567 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
94521 GTAATTGGAG
94531 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
94549 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
94567 T
1 T
94568 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:94574 original size:24 final size:24
Alignment explanation
Indices: 94523--94575 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
94513 TTTCATATGT
* * *
94523 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
94547 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
94571 AATTT
1 AATTT
94576 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:94920 original size:39 final size:39
Alignment explanation
Indices: 94877--94963 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
94867 TCCGATGCTC
94877 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
94916 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
94955 ATCAAAATC
1 ATCAAAATC
94964 TACAACTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:95170 original size:19 final size:20
Alignment explanation
Indices: 95146--95183 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
95136 GATCAATGCG
95146 AAAGTC-AATTCGCAACGCA
1 AAAGTCAAATTCGCAACGCA
*
95165 AAAGTCAAATTCGTAACGC
1 AAAGTCAAATTCGCAACGC
95184 GAAATAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAGTCAAATTCGCAACGCA
Found at i:95450 original size:66 final size:60
Alignment explanation
Indices: 95370--95509 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 60
95360 TTTTAGAAAC
*
95370 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATT----AAAC-AAAAAATAAATCTTATTTACACAT-AAATT
95435 A
60 A
* * *
95436 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATAAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAAAAATAAATCTTATTTACACATAAATTA
95496 AACAAATCAACTTT
1 AACAAATCAACTTT
95510 CAATGTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
60 20 0.29
61 21 0.30
62 3 0.04
66 26 0.37
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAAAAATAAATCTTATTTACACATAAATTA
Found at i:96907 original size:21 final size:21
Alignment explanation
Indices: 96883--96981 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
96873 GTGGGTGTGA
* *
96883 CCTCTTTAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
96904 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
96925 CTTCTTTG-ATGATGAGAGAGG
1 CCTC-TTGAACGATGAGAGGGG
*
96946 CCTCTTGAACGAT-AGAAGGCG
1 CCTCTTGAACGATGAG-AGGGG
*
96967 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
96982 TAGGTGCATC
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 5 0.08
21 51 0.85
22 4 0.07
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.25
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:96931 original size:42 final size:42
Alignment explanation
Indices: 96863--96956 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
96853 GTGAATCGGG
* * *
96863 CTCTTGAACGGTGGGTGTGACCTCTTTAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTTAACGATGACAGAGGC
* * * * *
96905 CTCTTGAACGGTGGGAGGGGCTTCTTTGATGATGAGAGAGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTTAACGATGACAGAGGC
96947 CTCTTGAACG
1 CTCTTGAACG
96957 ATAGAAGGCG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.19, C:0.19, G:0.35, T:0.27
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTTAACGATGACAGAGGC
Found at i:96979 original size:42 final size:42
Alignment explanation
Indices: 96883--96981 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 42
96873 GTGGGTGTGA
* * * * * * *
96883 CCTCTTTAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGACAGAGGCCTCTTGAACGATAGAAGGCG
* *
96925 CTTCTTTG-ATGATGAGAGAGGCCTCTTGAACGATAGAAGGCG
1 CCTC-TTGAATGATGACAGAGGCCTCTTGAACGATAGAAGGCG
96967 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
96982 TAGGTGCATC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
41 3 0.07
42 40 0.89
43 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.25
Consensus pattern (42 bp):
CCTCTTGAATGATGACAGAGGCCTCTTGAACGATAGAAGGCG
Found at i:99667 original size:20 final size:20
Alignment explanation
Indices: 99642--99754 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
99632 GCGTAAAAAC
99642 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
99662 ATTTGACTATCGCGTTACGA
1 ATTTGACTTTCGCGTTGCGA
*
99682 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
* *
99701 ATTT-ACAAATTCGCGTTGCAA
1 ATTTGAC--TTTCGCGTTGCGA
* *
99722 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
99742 ATTTGACTATCGC
1 ATTTGACTTTCGC
99755 AATGCGATTT
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
18 2 0.03
19 6 0.08
20 56 0.77
21 7 0.10
22 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:99687 original size:40 final size:40
Alignment explanation
Indices: 99642--99754 Score: 133
Period size: 40 Copynumber: 2.8 Consensus size: 40
99632 GCGTAAAAAC
* *
99642 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTACGA
1 ATTTGACTTTCGTGTTGCGAATTTGACTATCGCGTTACAA
* *
99682 ATTTGAC-TTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCAA
1 ATTTGACTTTC-GTGTTGCGAATTTGAC-TA-TCGCGTTACAA
*
99722 ATTTGACTTTTGTGTTGCGAATTTGACTATCGC
1 ATTTGACTTTCGTGTTGCGAATTTGACTATCGC
99755 AATGCGATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
38 2 0.03
39 8 0.13
40 42 0.69
41 7 0.11
42 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (40 bp):
ATTTGACTTTCGTGTTGCGAATTTGACTATCGCGTTACAA
Found at i:99725 original size:60 final size:60
Alignment explanation
Indices: 99650--99778 Score: 161
Period size: 60 Copynumber: 2.1 Consensus size: 60
99640 ACATTTGACT
* ***
99650 TTCGCGTTGCGAATTTGACTATCGCGTTACGAATTTGACT-TCTGTGTTGCGATTTACAAA
1 TTCGCGTTGCAAATTTGACTATCGCGTTACGAATTTGACTATC-GCAATGCGATTTACAAA
* * * * *
99710 TTCGCGTTGCAAATTTGACTTTTGTGTTGCGAATTTGACTATCGCAATGCGATTTACATA
1 TTCGCGTTGCAAATTTGACTATCGCGTTACGAATTTGACTATCGCAATGCGATTTACAAA
99770 TTCGCGTTG
1 TTCGCGTTG
99779 TGAAATTGGA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 57 0.97
61 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (60 bp):
TTCGCGTTGCAAATTTGACTATCGCGTTACGAATTTGACTATCGCAATGCGATTTACAAA
Found at i:111716 original size:30 final size:32
Alignment explanation
Indices: 111662--111721 Score: 81
Period size: 30 Copynumber: 1.9 Consensus size: 32
111652 TTTAAATAGG
111662 TTTTAGTATTTTAATTAAGTTTTAGGATATTAC
1 TTTTAGTATTTTAATTAAGTTTTAGG-TATTAC
*
111695 TTTTA-TATTTT-ATT-TGTTTTAGGTATT
1 TTTTAGTATTTTAATTAAGTTTTAGGTATT
111722 TTAGTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 4 0.15
30 8 0.31
31 3 0.12
32 6 0.23
33 5 0.19
ACGTcount: A:0.25, C:0.02, G:0.12, T:0.62
Consensus pattern (32 bp):
TTTTAGTATTTTAATTAAGTTTTAGGTATTAC
Found at i:112026 original size:12 final size:12
Alignment explanation
Indices: 112009--112038 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
111999 TCTTTCAAGC
112009 CGAAGGCTAAAG
1 CGAAGGCTAAAG
112021 CGAAGGCTAAAG
1 CGAAGGCTAAAG
112033 CGAAGG
1 CGAAGG
112039 TTCAATTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.37, T:0.07
Consensus pattern (12 bp):
CGAAGGCTAAAG
Found at i:112448 original size:18 final size:18
Alignment explanation
Indices: 112420--112467 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
112410 AATTTCTTTA
112420 ATTTGTTTATTTAATTAATT
1 ATTT-TTTATTTAATT-ATT
*
112440 -TTTTTTATTTAATTCTT
1 ATTTTTTATTTAATTATT
112457 ATTTTTTATTT
1 ATTTTTTATTT
112468 TAAAAACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 2 0.08
18 21 0.81
19 3 0.12
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:113964 original size:752 final size:747
Alignment explanation
Indices: 112504--114007 Score: 2566
Period size: 752 Copynumber: 2.0 Consensus size: 747
112494 TTTATATTTA
112504 TTACTATTAATATTTATTATTATATTATTTTTCCTTTTATATTATTTATTTTATTTTAATATATC
1 TTACTATTAATATTTATTATTATATTATTTTTCCTTTTATATTATTTATTTTATTTTAATATATC
* * *
112569 TTTTCAACTTCTTCTGGAATTCTATCTTTTCTTAAAATCAATAAACAGTTTTACTAAATCACAAA
66 TTTTCAACTTCATCTGGAATTCTATCTTTTCTTAAAATCAAGAAACAATTTTACTAAATCACAAA
* *
112634 AACCATAGTCCCCGTTGATCGACCCTGCTTCTCTATACTACATTTTCCTTTTTATTTATTAAAAG
131 AACCATAGTCCCCGTGGATCGACACTGCTTCTCTATACTACATTTTCCTTTTTATTTATTAAAAG
*
112699 CCAAGAATTATTTTGATAGCAAAACAACGGTTATCAAATTGGCGCCGTTGTCGGGGACTAACGAC
196 CCAAGAATTATTTTGATAGCAAAACAACGGTTATCAAATTGGCGCCGTTGCCGGGGACTAACGAC
112764 AAATACTAATTTATTTTTCTAGTTTTTTATTTATGACCATAAAGAACCTAGGTGAATTAGTAGAT
261 AAATACTAATTTATTTTTCTAG-TTTTTATTTATGACCATAAAGAACCTAGGTGAATTAGTAGAT
* *
112829 CTAGATCCATAGATCGAAGCACGAGCACGAAGAATCCACGCACAAACGCTTCGAGAAAAGAGAAA
325 CTAGATCCATAGATCGAAACACGAGCACGAAGAATCCACGCACAAACGCTTCGAGAAAACAGAAA
* *
112894 AAGACAAGAAGAACAAGAGCATAAATCAGAAACAAAATCAAATCCGGACTCTGAAGCAGACGCAT
390 AAAACAAGAAGAACAAGAGCATAAATCAGAAAAAAAATCAAATCCGGACTCTGAAGCAGACGCAT
* *
112959 ACAACATTCTGATGGAAGAACAAACGATCCGAGAGCTAGCCACAGCTCCTGTCACTCAGACGCCA
455 ACAACATTCTGATGGAAGAACAAACGATCCAAGAGCTAGCCACAGCTCCTATCACTCAGACGCCA
113024 TTATGCATTAATTTTCCTAGTGGCAAGACTCCATTTCAATTAAAGACGGGACTCATTCATCTTCT
520 TTATGCATTAATTTTCCTAGTGGCAAGACTCCATTTCAATTAAAGACGGGACTCATTCATCTTCT
* * *
113089 TCCCACTTTCTATGGCTTTCCCACTGAATATCCGTACAAACACTTGTTGGAATTCCACATGGTTT
585 TCCCACTTTCCACGGCTTTCCCACTGAAGATCCGTACAAACACTTGTTGGAATTCCACATGGTTT
* * * *
113154 ACACTAGTATGAAACCACAGGGAGTTATCGGAGATCAAATTAAATTGAGAGTTTTCCCTTTTTCT
650 ACACTAGCATAAAACCACAGGGAGTTACCGGAGATCAAATTAAATTGAGAGCTTTCCCTTTTTCT
*
113219 TTAGCCGATTTGGCTAAAGATTGATTATTTCAT
715 TTAGCCGACTTGGCTAAAGATTGATTATTTCAT
* *
113252 TTACTATTAATATTTATTATTATATTATTTTTTTTTCTTTTTTATTATTTATTTTATTTTAATAT
1 TTACTATTAATATTTATTATTATATTA---TTTTTCCTTTTATATTATTTATTTTATTTTAATAT
*
113317 ATCTTTTCAACTTCATCTGGAATTCTATCTTTTCTTAAAATCAAGAAGCAATTTTACTAAATCAC
63 ATCTTTTCAACTTCATCTGGAATTCTATCTTTTCTTAAAATCAAGAAACAATTTTACTAAATCAC
* *
113382 AAAAACCATAGTCCCTGTGGATCGACACTGCTTCTCTATACTACCTTTTCCTTTTTATTTATTAA
128 AAAAACCATAGTCCCCGTGGATCGACACTGCTTCTCTATACTACATTTTCCTTTTTATTTATTAA
* * * *
113447 GAAGCCAAGAATTATTTTGATAGCAAAACGACGGTTATTAAATTGGTGTCGTTGCCGGGGACTAA
193 -AAGCCAAGAATTATTTTGATAGCAAAACAACGGTTATCAAATTGGCGCCGTTGCCGGGGACTAA
113512 C-ATCAAATACTAATTTATTTTTCTAG-TTTTATTTATGACCATAAAGAACCTAGGTGAATTAGT
257 CGA-CAAATACTAATTTATTTTTCTAGTTTTTATTTATGACCATAAAGAACCTAGGTGAATTAGT
* *
113575 AGATCTAGATCCGA-AGATCGAAACACGAGCATGAAGAATCTACGCACAAACGCTTCGAGAAAAC
321 AGATCTAGATCC-ATAGATCGAAACACGAGCACGAAGAATCCACGCACAAACGCTTCGAGAAAAC
113639 AGAAAAAAACAAGAAGAACAAGAGCATAAATCAGAAAAAAAAAATCAAATCCGGACTCTGAAGCA
385 AGAAAAAAACAAGAAGAACAAGAGCATAAATCAG--AAAAAAAATCAAATCCGGACTCTGAAGCA
* *
113704 TACGCATATAACATT-TCGATGGAAGAACAAACGATCCAAGAGCTAGCCACAGCTCCTATCACTC
448 GACGCATACAACATTCT-GATGGAAGAACAAACGATCCAAGAGCTAGCCACAGCTCCTATCACTC
*
113768 AGACGCCATTATGCATTAATTTTCCTAGTGGCGAGACTCCATTTCAATTAAAGACGGGACTCATT
512 AGACGCCATTATGCATTAATTTTCCTAGTGGCAAGACTCCATTTCAATTAAAGACGGGACTCATT
113833 CATCTTCTTCCCACTTTCCACGGCTTTCCCACTGAAGATCCGTACAAACACTTGTTGGAATTCCA
577 CATCTTCTTCCCACTTTCCACGGCTTTCCCACTGAAGATCCGTACAAACACTTGTTGGAATTCCA
*
113898 CATGGTTTGCACTAGCATAAAACCACAGGGAGTTACCGGAGATCAAATTAAATTGAGAGCTTTCC
642 CATGGTTTACACTAGCATAAAACCACAGGGAGTTACCGGAGATCAAATTAAATTGAGAGCTTTCC
*
113963 CTTTTTCTTTAGCCGACTTGGCTAAAGATTGATTATTTTAT
707 CTTTTTCTTTAGCCGACTTGGCTAAAGATTGATTATTTCAT
114004 TTAC
1 TTAC
114008 CTCCAAATTT
Statistics
Matches: 711, Mismatches: 36, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
748 27 0.04
750 128 0.18
751 158 0.22
752 398 0.56
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (747 bp):
TTACTATTAATATTTATTATTATATTATTTTTCCTTTTATATTATTTATTTTATTTTAATATATC
TTTTCAACTTCATCTGGAATTCTATCTTTTCTTAAAATCAAGAAACAATTTTACTAAATCACAAA
AACCATAGTCCCCGTGGATCGACACTGCTTCTCTATACTACATTTTCCTTTTTATTTATTAAAAG
CCAAGAATTATTTTGATAGCAAAACAACGGTTATCAAATTGGCGCCGTTGCCGGGGACTAACGAC
AAATACTAATTTATTTTTCTAGTTTTTATTTATGACCATAAAGAACCTAGGTGAATTAGTAGATC
TAGATCCATAGATCGAAACACGAGCACGAAGAATCCACGCACAAACGCTTCGAGAAAACAGAAAA
AAACAAGAAGAACAAGAGCATAAATCAGAAAAAAAATCAAATCCGGACTCTGAAGCAGACGCATA
CAACATTCTGATGGAAGAACAAACGATCCAAGAGCTAGCCACAGCTCCTATCACTCAGACGCCAT
TATGCATTAATTTTCCTAGTGGCAAGACTCCATTTCAATTAAAGACGGGACTCATTCATCTTCTT
CCCACTTTCCACGGCTTTCCCACTGAAGATCCGTACAAACACTTGTTGGAATTCCACATGGTTTA
CACTAGCATAAAACCACAGGGAGTTACCGGAGATCAAATTAAATTGAGAGCTTTCCCTTTTTCTT
TAGCCGACTTGGCTAAAGATTGATTATTTCAT
Found at i:116142 original size:5 final size:5
Alignment explanation
Indices: 116124--116176 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
116114 ACCCATTTCG
* **
116124 TTTTA TTTTCA TTTTA -TTTA TTTCA TTCCA -TTTA TTTTA TTTTA TTTTA
1 TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
116173 TTTT
1 TTTT
116177 TAATTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 6 0.15
5 30 0.73
6 5 0.12
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:116149 original size:14 final size:14
Alignment explanation
Indices: 116125--116175 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
116115 CCCATTTCGT
116125 TTTATTTTCATTTTA
1 TTTA-TTTCATTTTA
**
116140 TTTATTTCATTCCA
1 TTTATTTCATTTTA
*
116154 TTTATTTTATTTTA
1 TTTATTTCATTTTA
116168 TTTTATTT
1 -TTTATTT
116176 TTAATTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATTTCATTTTA
Found at i:117970 original size:64 final size:64
Alignment explanation
Indices: 117896--118015 Score: 197
Period size: 64 Copynumber: 1.9 Consensus size: 64
117886 ATTTTATTTG
117896 TTTTAGGTATTTTAGTTTAAATAGGGTTT-AGTATTTTAATTAGGATTTAAAATATTATATTATT
1 TTTTAGGTATTTTAGTTTAAATA-GGTTTAAGTATTTTAATTAGGATTTAAAATATTATATTATT
* * *
117960 TTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTAAGATATT
1 TTTTAGGTATTTTAGTTTAAATAGGTTTAAGTATTTTAATTAGGATTTAAAATATT
118016 TTAGCTTGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
63 4 0.08
64 48 0.92
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (64 bp):
TTTTAGGTATTTTAGTTTAAATAGGTTTAAGTATTTTAATTAGGATTTAAAATATTATATTATT
Found at i:118641 original size:18 final size:18
Alignment explanation
Indices: 118595--118643 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
118585 AATCTCTTTA
118595 ATTTGTTTATTTAATCATT
1 ATTT-TTTATTTAATCATT
*
118614 TTTCTTTTATTTAATTC-TT
1 ATT-TTTTATTTAA-TCATT
118633 ATTTTTTATTT
1 ATTTTTTATTT
118644 TAAAAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.31
19 15 0.58
20 3 0.12
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTTATTTAATCATT
Found at i:118713 original size:15 final size:15
Alignment explanation
Indices: 118675--118734 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 15
118665 CTCTTTTATA
118675 TTTATTACTATTAATATT
1 TTTATTA-TATT-AT-TT
118693 TATTATTATATTATTT
1 T-TTATTATATTATTT
*
118709 TTTATT-TTTTATTT
1 TTTATTATATTATTT
*
118723 ATTTATTTTATT
1 -TTTATTATATT
118735 TTAATATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 7 0.19
15 11 0.30
16 6 0.16
17 2 0.05
18 5 0.14
19 6 0.16
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTATATTATTT
Found at i:118714 original size:22 final size:20
Alignment explanation
Indices: 118689--118735 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
118679 TTACTATTAA
*
118689 TATTTATTATTATATTATTTTT
1 TATTTATTATT-TATT-TATTT
*
118711 TATTTTTTATTTATTTATTT
1 TATTTATTATTTATTTATTT
118731 TATTT
1 TATTT
118736 TAATATATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 4 0.17
22 10 0.43
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (20 bp):
TATTTATTATTTATTTATTT
Found at i:118737 original size:18 final size:18
Alignment explanation
Indices: 118668--118737 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
118658 AAAAATTCTC
*
118668 TTTTATATTTATTACTATTAA
1 TTTTAT-TTTATT--TATTTA
118689 TATTTATTATTATATTATTT-
1 T-TTTATT-TTAT-TTATTTA
*
118709 TTTATTTTTTATTTATTTA
1 TTT-TATTTTATTTATTTA
118728 TTTTATTTTA
1 TTTTATTTTA
118738 ATATATCTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
18 12 0.29
19 9 0.22
20 4 0.10
21 6 0.15
22 9 0.22
23 1 0.02
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTTTATTTATTTA
Found at i:124852 original size:31 final size:31
Alignment explanation
Indices: 124806--124872 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
124796 TTGGAGACCA
*
124806 TATTACAAACAGACTAAATGTTAGGGGACTG
1 TATTGCAAACAGACTAAATGTTAGGGGACTG
* * *
124837 TATTGCAAACGGACTAAATGTTGGGGGATTG
1 TATTGCAAACAGACTAAATGTTAGGGGACTG
124868 TATTG
1 TATTG
124873 TAAGTTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (31 bp):
TATTGCAAACAGACTAAATGTTAGGGGACTG
Found at i:126393 original size:38 final size:38
Alignment explanation
Indices: 126339--126487 Score: 169
Period size: 38 Copynumber: 4.0 Consensus size: 38
126329 TAGATGTACA
* * *
126339 TTCCATATTTGGAAACCATAATTGACACCCAAAAAAAG
1 TTCCATATGTGTAAACCATAATTCACACCCAAAAAAAG
* * *
126377 TTCCATATGTGTAAACCATAGTTCACACCCGAAAATAG
1 TTCCATATGTGTAAACCATAATTCACACCCAAAAAAAG
* *
126415 CTCTATATGTGTAAACCATAATTCACACCCAAAATAAAG
1 TTCCATATGTGTAAACCATAATTCACACCCAAAA-AAAG
* * *
126454 -TCC--ACGTGTAAACCATATTTAACACCCAAAAAAA
1 TTCCATATGTGTAAACCATAATTCACACCCAAAAAAA
126488 ACTCGAAGCA
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
35 3 0.03
36 25 0.26
38 64 0.67
39 3 0.03
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.24
Consensus pattern (38 bp):
TTCCATATGTGTAAACCATAATTCACACCCAAAAAAAG
Found at i:128711 original size:63 final size:64
Alignment explanation
Indices: 128644--128802 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 64
128634 TGCACTAAGA
* * * * * *
128644 GTGCATCGATGCATCAAGTGTATTCGATGTTTCA-AATAGCCAGAGTGCATCGATACATGGCT-G
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAACCACAGTACATCGATACATGG-TAG
* * *
128707 GTGCATCGATGCATCAAATGCATTCGATGGTTTCATAAAAACCTCAGTACATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGAT-GTTTCATAAAAACCACAGTACATCGATACATGGTAG
*
128772 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
128803 CAATTTAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
63 26 0.31
64 10 0.12
65 47 0.57
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAACCACAGTACATCGATACATGGTAG
Found at i:129288 original size:2 final size:2
Alignment explanation
Indices: 129281--129310 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
129271 GCCAATTGAT
129281 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
129311 GCTTAAGCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:129474 original size:2 final size:2
Alignment explanation
Indices: 129467--129499 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
129457 ATCAAACCAA
129467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
129500 ATAAGTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:131505 original size:23 final size:22
Alignment explanation
Indices: 131475--131554 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
131465 GCATGACCCT
131475 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
131497 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
131519 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
131541 ATGCATCAATGCAC
1 GTGCATCGATGCAC
131555 TGTTAGGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 15 0.33
22 15 0.33
23 16 0.35
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:131529 original size:44 final size:42
Alignment explanation
Indices: 131479--131573 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
131469 GACCCTGTGC
* **
131479 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCAATGCA-CTGTCA-GGTGT
*
131523 ATCGATGCACATTCAAGGATGCATCAATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCAATGCACTGTCAGGTGT
131565 ATCGATGCA
1 ATCGATGCA
131574 TGAAGCACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 16 0.35
43 12 0.26
44 18 0.39
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.27
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCAATGCACTGTCAGGTGT
Found at i:131531 original size:21 final size:20
Alignment explanation
Indices: 131475--131573 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 20
131465 GCATGACCCT
131475 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTC-A-G
* *
131497 CGTGCATCGGTGCACCTTCATG
1 -GTGCATCGATGCACATTCA-G
*
131519 GTGTATCGATGCACATTCAAG
1 GTGCATCGATGCACATTC-AG
* *
131540 GATGCATCAATGCAC-TGTTAG
1 G-TGCATCGATGCACAT-TCAG
*
131561 GTGTATCGATGCA
1 GTGCATCGATGCA
131574 TGAAGCACAA
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
20 10 0.16
21 21 0.34
22 15 0.24
23 16 0.26
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (20 bp):
GTGCATCGATGCACATTCAG
Found at i:137289 original size:21 final size:23
Alignment explanation
Indices: 137263--137314 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
137253 TGGGAATCGA
137263 TCCCCCCATG-A-GGGAACCAAT
1 TCCCCCCATGAAGGGGAACCAAT
** *
137284 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCATGAAGGGGAACCAAT
137307 TCCCCCCA
1 TCCCCCCA
137315 CATGGGAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 15 0.62
ACGTcount: A:0.23, C:0.40, G:0.19, T:0.17
Consensus pattern (23 bp):
TCCCCCCATGAAGGGGAACCAAT
Found at i:144508 original size:21 final size:21
Alignment explanation
Indices: 144484--144525 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
144474 GAGTTTATTT
*
144484 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTTAAAACA
144505 TCATTTTTATATTTTAAAACA
1 TCATTTTTATATTTTAAAACA
144526 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (21 bp):
TCATTTTTATATTTTAAAACA
Found at i:146502 original size:18 final size:17
Alignment explanation
Indices: 146448--146496 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
146438 TTGGACCCTT
* *
146448 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
146466 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
146484 AGTGCATTCGATG
1 AGTGCA-TCGATG
146497 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:146601 original size:65 final size:64
Alignment explanation
Indices: 146468--146624 Score: 178
Period size: 65 Copynumber: 2.5 Consensus size: 64
146458 TGCACTAAGA
* * * *
146468 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGTATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAAACCCAGAGTGCATCGATGCATGGCTG
*
146532 GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAAACCTCA-A-TGCATCGATGCATGG-
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAAAACC-CAGAGTGCATCGATGCATGGC
*
146594 TAT
63 T-G
* *
146597 GTGCATCCATGCATGAAATGCA-TCGATG
1 GTGCATCGATGCATCAAATGCATTCGATG
146625 CATGGATTGG
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
64 33 0.41
65 39 0.49
66 6 0.08
67 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAAACCCAGAGTGCATCGATGCATGGCTG
Found at i:146603 original size:19 final size:18
Alignment explanation
Indices: 146577--146630 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
146567 TAAAAACCTC
146577 AATGCATCGATGCATGGTA
1 AATGCATCGATGCATGG-A
** *
146596 TGTGCATCCATGCAT-GA
1 AATGCATCGATGCATGGA
146613 AATGCATCGATGCATGGA
1 AATGCATCGATGCATGGA
146631 TTGGTAAATC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 13 0.46
18 3 0.11
19 12 0.43
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (18 bp):
AATGCATCGATGCATGGA
Found at i:147370 original size:23 final size:23
Alignment explanation
Indices: 147352--147412 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
147342 CTCGTATAAA
147352 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
147375 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
147398 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
147413 TATAAGATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:150028 original size:30 final size:30
Alignment explanation
Indices: 149992--150059 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
149982 CAACAGTTAC
* * *
149992 GTTGGGGGCCATATTGTAAATGGACTAACT
1 GTTGGGGGCCATATTGCAAACGGACTAAAT
150022 GTTGGGGGCCATATTGCAAACGGACTAAAT
1 GTTGGGGGCCATATTGCAAACGGACTAAAT
*
150052 GTTAGGGG
1 GTTGGGGG
150060 ATTGTATTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.26, C:0.13, G:0.34, T:0.26
Consensus pattern (30 bp):
GTTGGGGGCCATATTGCAAACGGACTAAAT
Found at i:153980 original size:9 final size:9
Alignment explanation
Indices: 153968--154001 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
153958 GAATTCAGTT
153968 AATTAACCG
1 AATTAACCG
*
153977 AATTAATCG
1 AATTAACCG
153986 AATTAACCG
1 AATTAACCG
153995 AAATTAA
1 -AATTAA
154002 ATTTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:154393 original size:183 final size:181
Alignment explanation
Indices: 154007--154393 Score: 582
Period size: 183 Copynumber: 2.1 Consensus size: 181
153997 ATTAAATTTT
* *
154007 AAATATTATATATATTATATATAACATATGGACTCAATCCAAATCATTTAAAACCCAATTAATAA
1 AAATATT-TA-ATTTTATATATAACATATGGACTCAACCCAAATCATTTAAAACCCAATTAATAA
*
154072 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
64 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
* * * *
154137 TATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTTAATTAAA
129 TATTTTATAATTATATATTATTTAAATTAATTATAAAATGTTTTTGAATTAAA
*
154190 AAATATTAAATATATTATATATAACATATGGACT-AAGCCCAAA-CTATTTAAAACCCAATTAAT
1 AAATATTTAAT-T-TTATATATAACATATGGACTCAA-CCCAAATC-ATTTAAAACCCAATTAAT
* *
154253 AATTTAAGATCTAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAAT
62 AATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAA-TTATATAAAAT
154318 TTTTATTTTATAATTTATATATTATTTAAATTAATTATAAAAAT-TTTTTGAATTAAA
126 TTTTATTTTATAA-TTATATATTATTTAAATTAATTAT-AAAATGTTTTTGAATTAAA
154375 AAATATTTAATTTTATATA
1 AAATATTTAATTTTATATA
154394 AATTAGAAAA
Statistics
Matches: 186, Mismatches: 11, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
181 2 0.01
182 4 0.02
183 109 0.59
184 23 0.12
185 44 0.24
186 4 0.02
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (181 bp):
AAATATTTAATTTTATATATAACATATGGACTCAACCCAAATCATTTAAAACCCAATTAATAATT
TAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTTTA
TTTTATAATTATATATTATTTAAATTAATTATAAAATGTTTTTGAATTAAA
Found at i:155283 original size:6 final size:6
Alignment explanation
Indices: 155272--155305 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
155262 TAATTTCTCA
*
155272 ATTTTC ATTTTC ATTTTC ATTTTC ACTTTC -TTTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
155306 TTCTTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 3 0.12
6 23 0.88
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTTC
Found at i:156995 original size:20 final size:20
Alignment explanation
Indices: 156951--157223 Score: 165
Period size: 20 Copynumber: 13.5 Consensus size: 20
156941 AATGACCAAC
156951 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
*
156970 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
156990 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
*
157010 AAAATTGCAACG-G--TCAAAAG
1 AAAATCGCAACGCGATTC---AG
157030 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* * **
157052 AGAATCGCAATGCGAGCCA-
1 AAAATCGCAACGCGATTCAG
*
157071 AAGAATCGCAATGCGATTCCA-
1 AA-AATCGCAACGCGATT-CAG
* *
157092 AGAATCGCAATGCGATCTTC-G
1 AAAATCGCAACGCGA--TTCAG
*
157113 AAGAATCGCAATGCGATTCA-
1 AA-AATCGCAACGCGATTCAG
*
157133 AAGAATCGCAACGCGATTGAG
1 AA-AATCGCAACGCGATTCAG
*
157154 AAAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTCAG
157174 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* * *
157194 AGAATCGCAAAGCGATTGAG
1 AAAATCGCAACGCGATTCAG
157214 AAAATCGCAA
1 AAAATCGCAA
157224 TACGATTCCA
Statistics
Matches: 208, Mismatches: 24, Indels: 43
0.76 0.09 0.16
Matches are distributed among these distances:
18 2 0.01
19 20 0.10
20 144 0.69
21 11 0.05
22 28 0.13
23 1 0.00
25 1 0.00
26 1 0.00
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:157087 original size:42 final size:41
Alignment explanation
Indices: 157032--157148 Score: 155
Period size: 42 Copynumber: 2.8 Consensus size: 41
157022 GTCAAAAGAA
*
157032 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGC-CAAAG
1 AATCGCAATGCGA--TTCCAAGAATCGCAATGCGAGCTCAAAG
* *
157074 AATCGCAATGCGATTCCAAGAATCGCAATGCGATCTTCGAAG
1 AATCGCAATGCGATTCCAAGAATCGCAATGCGAGC-TCAAAG
* *
157116 AATCGCAATGCGATTCAAAGAATCGCAACGCGA
1 AATCGCAATGCGATTCCAAGAATCGCAATGCGA
157149 TTGAGAAAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
40 21 0.31
42 47 0.69
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (41 bp):
AATCGCAATGCGATTCCAAGAATCGCAATGCGAGCTCAAAG
Found at i:157101 original size:62 final size:62
Alignment explanation
Indices: 157028--157243 Score: 228
Period size: 62 Copynumber: 3.5 Consensus size: 62
157018 AACGGTCAAA
*
157028 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCAAAGAATCGCAATGCGATTCC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCAAAGAATCGCAACGCGATT-C
* * * ** *
157091 A-AGAATCGCAATGCGATCTTCGAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCAAAGAATCGCAACGCGATTC
*** * * * *
157152 AGAAAATCGCAACGCGAT-TGAGAA-AATCGCAACGCGATTCC-AAGAATCGCAAAGCGATTG
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGA-GCCAAAGAATCGCAACGCGATTC
**
157212 AGAAAATCGCAATACGA--TTCCAAGAATCGCAA
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAA
157244 AACGGCAAAA
Statistics
Matches: 131, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
59 3 0.02
60 53 0.40
61 7 0.05
62 67 0.51
63 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (62 bp):
AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCAAAGAATCGCAACGCGATTC
Found at i:157239 original size:20 final size:20
Alignment explanation
Indices: 157032--157243 Score: 189
Period size: 20 Copynumber: 10.4 Consensus size: 20
157022 GTCAAAAGAA
*
157032 AATCGCAACGCGATCTTCCAAG
1 AATCGCAATGCGA--TTCCAAG
*
157054 AATCGCAATGCGA-GCCAAAG
1 AATCGCAATGCGATTCC-AAG
157074 AATCGCAATGCGATTCCAAG
1 AATCGCAATGCGATTCCAAG
*
157094 AATCGCAATGCGATCTTCGAAG
1 AATCGCAATGCGA--TTCCAAG
*
157116 AATCGCAATGCGATTCAAAG
1 AATCGCAATGCGATTCCAAG
* * *
157136 AATCGCAACGCGATT-GAGAA
1 AATCGCAATGCGATTCCA-AG
* * *
157156 AATCGCAACGCGATT-GAGAA
1 AATCGCAATGCGATTCCA-AG
*
157176 AATCGCAACGCGATTCCAAG
1 AATCGCAATGCGATTCCAAG
* * *
157196 AATCGCAAAGCGATT-GAGAA
1 AATCGCAATGCGATTCCA-AG
*
157216 AATCGCAATACGATTCCAAG
1 AATCGCAATGCGATTCCAAG
157236 AATCGCAA
1 AATCGCAA
157244 AACGGCAAAA
Statistics
Matches: 165, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.02
20 126 0.76
21 4 0.02
22 31 0.19
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (20 bp):
AATCGCAATGCGATTCCAAG
Found at i:157365 original size:6 final size:6
Alignment explanation
Indices: 157354--157410 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
157344 GACACGTATT
157354 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
157402 ACCACG ACC
1 ACCACG ACC
157411 CGAGACGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:158181 original size:6 final size:6
Alignment explanation
Indices: 158170--158238 Score: 138
Period size: 6 Copynumber: 11.5 Consensus size: 6
158160 TCTCGTCTCG
158170 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
158218 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
158239 AATACGTGTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:158374 original size:20 final size:20
Alignment explanation
Indices: 158349--158478 Score: 138
Period size: 20 Copynumber: 6.4 Consensus size: 20
158339 TTTTGCCGTT
158349 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
** *
158369 TTGCGATT-TTCTCAATCGCA
1 TTGCGATTCTT-GGAATCGCG
*
158389 TTGCGATTCCTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
158409 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
* *
158429 TTGCGATTCTTTGAATCGCA
1 TTGCGATTCTTGGAATCGCG
158449 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-A-ATCGCG
158471 TTGCGATT
1 TTGCGATT
158479 TTCTTTTGAC
Statistics
Matches: 90, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.03
20 70 0.78
21 4 0.04
22 13 0.14
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCG
Found at i:158396 original size:40 final size:40
Alignment explanation
Indices: 158349--158456 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
158339 TTTTGCCGTT
158349 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
* *
158389 TTGCGATTCCTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
* *
158429 TTGCGATTCTTTGAATCGCATTGCGATT
1 TTGCGATTCTTGGAATCGCGTTGCGATT
158457 CTTGGAAGAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
Found at i:158446 original size:60 final size:62
Alignment explanation
Indices: 158362--158482 Score: 194
Period size: 60 Copynumber: 2.0 Consensus size: 62
158352 CGATTCTTGG
158362 AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGG-A-ATCGCGTTGCGATTTTCTC
1 AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCTC
* *
158422 AATCGCGTTGCGATTCTT-TGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 AATCGCGTTGCGATT-TTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCT
158483 TTTGACCGTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
60 35 0.62
61 3 0.05
62 18 0.32
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.37
Consensus pattern (62 bp):
AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCTC
Found at i:158538 original size:20 final size:19
Alignment explanation
Indices: 158362--158540 Score: 112
Period size: 20 Copynumber: 8.9 Consensus size: 19
158352 CGATTCTTGG
158362 AATCGCGTTGCGATTTTCT
1 AATCGCGTTGCGATTTTCT
* *
158381 CAATCGCATTGCGA-TTCCT
1 -AATCGCGTTGCGATTTTCT
158400 GGAATCGCGTTGCGATTTTCT
1 --AATCGCGTTGCGATTTTCT
158421 CAATCGCGTTGCGATTCTT-T
1 -AATCGCGTTGCGATT-TTCT
* **
158441 GAATCGCATTGCGATTCTTGGA
1 -AATCGCGTTGCGATT-TT-CT
158463 AGATCGCGTTGCGATTTTCT
1 A-ATCGCGTTGCGATTTTCT
* *
158483 -TTTGACCGTTGCGATTTTCT
1 AATCG--CGTTGCGATTTTCT
** * * *
158503 TTTCAACATTGTGATTTTCT
1 AATC-GCGTTGCGATTTTCT
158523 AAATCGCGTTGCGATTTT
1 -AATCGCGTTGCGATTTT
158541 TGTTTCGCAT
Statistics
Matches: 125, Mismatches: 23, Indels: 22
0.74 0.14 0.13
Matches are distributed among these distances:
18 2 0.02
19 4 0.03
20 93 0.74
21 13 0.10
22 13 0.10
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (19 bp):
AATCGCGTTGCGATTTTCT
Found at i:158669 original size:16 final size:15
Alignment explanation
Indices: 158643--158682 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
158633 GATTTTCTCT
*
158643 TTAAAAA-ATTAGTTA
1 TTAAAAATATTA-TCA
158658 TTAAAAATATTATCA
1 TTAAAAATATTATCA
158673 TTAAAAATAT
1 TTAAAAATAT
158683 ATTAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (15 bp):
TTAAAAATATTATCA
Found at i:158771 original size:11 final size:11
Alignment explanation
Indices: 158750--158817 Score: 61
Period size: 11 Copynumber: 6.3 Consensus size: 11
158740 TAGTTGTATT
158750 ATATAATTTTTA
1 ATAT-ATTTTTA
158762 ATATATTTTTA
1 ATATATTTTTA
158773 A-A-ATTTTATA
1 ATATATTTT-TA
***
158783 AT-TATCAATA
1 ATATATTTTTA
*
158793 ATGTATTTTTA
1 ATATATTTTTA
158804 ATATATTTTTA
1 ATATATTTTTA
158815 ATA
1 ATA
158818 ATGTAATTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
9 5 0.11
10 8 0.18
11 28 0.62
12 4 0.09
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
ATATATTTTTA
Found at i:163970 original size:23 final size:22
Alignment explanation
Indices: 163944--164007 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
163934 CAGCTCATAT
163944 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
163967 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
163990 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
164008 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:164150 original size:103 final size:103
Alignment explanation
Indices: 164023--164240 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
164013 TAATGTCCAT
*
164023 AAGGACCACATATAATTCCTTAAGAATCATATGCATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATAATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
164088 GACCTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
164126 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATAATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
164191 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
164229 AAGGACCACATA
1 AAGGACCACATA
164241 GACCCTCTAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATAATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:164794 original size:64 final size:67
Alignment explanation
Indices: 164689--164812 Score: 193
Period size: 64 Copynumber: 1.9 Consensus size: 67
164679 ATTTTCATCT
164689 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
164754 TA
66 TA
* *
164756 TTTAATGG-GG-ATGCATCGATTCACT-C-CTTATGCATCGATGCATAAATCCTATTCGAT
1 TTTAATGGAGGTATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGAT
164813 TTTTTCTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
63 1 0.02
64 29 0.54
65 14 0.26
66 2 0.04
67 8 0.15
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTG
TA
Done.