Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 100 of 208
Found at i:30027730 original size:44 final size:44
Alignment explanation
Indices: 30027667--30027786 Score: 186
Period size: 44 Copynumber: 2.7 Consensus size: 44
30027657 TGGTAAATTT
* *
30027667 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGATTC
* *
30027711 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATATTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGATTC
* *
30027755 AACCTGCTCCACTGCAACTTCAAGGAGATAAG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAG
30027787 GTTTGATATG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 70 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGATTC
Found at i:30027946 original size:50 final size:50
Alignment explanation
Indices: 30027875--30028621 Score: 349
Period size: 50 Copynumber: 15.1 Consensus size: 50
30027865 TACGATGTCG
* ** * *
30027875 GGGAAGCAAGATTCGTTGTTGTAGCTTTAATCTGCTTCACTGCACTACCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
* * * * * * * * *
30027925 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCT-TTTAAATTACAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTT-CACTGCACTGCCA
* * * *
30027975 GGGAA-CAAGATTCGCCGTTGTAGCTTCAATTTGATCCACTGCA-TCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACT-GCCA
* * * * * * * * *
30028024 GGAAAGTAAGATTCGCCCTTGCAGCTTCAATCTTCTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
* * * * * *
30028074 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCGCCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
* * * * * *
30028124 GGGAAGTAAGATTCGCTGTTGTGGCTTCAACCT--TTAACTGCGA-TGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGC-ACTGCCA
* * * *
30028172 GGGAA-TAAGATTTGTCGTTGTAGCTTTAATCTG-TTCCACTGCACCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTT-CACTGCACTGCCA
*** ** * * * *
30028221 GGGAAGTAAGATTCGCCGTTACGGCTTCAATCTTTTTAATTGCAATGTC-
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
* * * * * *
30028270 GGGGAGACAAGATTCACTGTTGTGGCTTCAATCTGCTCCACTGCACTGCCA
1 GGGAAG-TAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
** * ** * * *
30028321 GGGAAGTAAGATTCGCCGTTGCGGGTTCAATCT--TT---TAAAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
** * *
30028366 GGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGGTCCACTGCA-TCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACT-GCCA
* * ** * * * * *
30028416 GGAAAGTAAGATTCACCGTTGCGGCTTCAATCT-CTTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGC-TTCACTGCACTGCCA
** * * * * * ** *
30028466 GGGAAACAAAATTCACTGTCGTAACTTCAATCTAATCCACTGCA-TCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACT-GCCA
* * ** ** * * * * *
30028516 GGAAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
* * * * * *
30028566 GGGAAGCAAGATTCACCGTCGTAACTTTAATCTGCTCCACTGCACTGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
30028616 GGGAAG
1 GGGAAG
30028622 GTAATTTCAT
Statistics
Matches: 494, Mismatches: 179, Indels: 48
0.69 0.25 0.07
Matches are distributed among these distances:
45 33 0.07
47 22 0.04
48 18 0.04
49 54 0.11
50 357 0.72
51 10 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGCTTCACTGCACTGCCA
Found at i:30028131 original size:100 final size:99
Alignment explanation
Indices: 30027869--30028621 Score: 901
Period size: 100 Copynumber: 7.6 Consensus size: 99
30027859 TTAAACTACG
*** * * **
30027869 ATGTCGGGGAAGCAAGATTCGTTGTTGTAGCTTTAATCTGCTTCACTGCACTACCAGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
* * *
30027934 GATTCACCGTTGTGGCTTCAATCTTTTAAATTACA
66 GATTCGCCGTTGCGGCTTCAATCTTTT-AATTGCA
* * * * *
30027969 ATGTCGGGGAA-CAAGATTCGCCGTTGTAGCTTCAATTTGATCCACTGCATCGCCAGGAAAGTAA
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
* *
30028033 GATTCGCCCTTGCAGCTTCAATCTTCTTAATTGCA
66 GATTCGCCGTTGCGGCTTCAATCTT-TTAATTGCA
* *
30028068 ATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCGCCGCCAGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
* * * * *
30028133 GATTCGCTGTTGTGGCTTCAA-CCTTTAACTGCG
66 GATTCGCCGTTGCGGCTTCAATCTTTTAATTGCA
* *** * *
30028166 ATGTCGGGGAA-TAAGATTTGTCGTTGTAGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
*
30028230 GATTCGCCGTTACGGCTTCAATCTTTTTAATTGCA
66 GATTCGCCGTTGCGGCTTCAATC-TTTTAATTGCA
* * *
30028265 ATGTCGGGG-AGACAAGATTCACTGTTGTGGCTTCAATCTGCTCCACTGCACTGCCAGGGAAGTA
1 ATGTCGGGGAAG-CAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTA
*
30028329 AGATTCGCCGTTGCGGGTTCAATCTTTTAA----A
65 AGATTCGCCGTTGCGGCTTCAATCTTTTAATTGCA
* * * * *
30028360 ATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGGTCCACTGCATCGCCAGGAAAGTAA
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
*
30028425 GATTCACCGTTGCGGCTTCAATCTCTTTAATTGCA
66 GATTCGCCGTTGCGGCTTCAATCT-TTTAATTGCA
* * * * * ** * *
30028460 ATGTCGGGGAAACAAAATTCACTGTCGTAACTTCAATCTAATCCACTGCATCGCCAGGAAAGTAA
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
*
30028525 GATTCACCGTTGCGGCTTCAATCTTTTTAATTGCA
66 GATTCGCCGTTGCGGCTTCAATC-TTTTAATTGCA
* * * *
30028560 ATGTCGGGGAAGCAAGATTCACCGTCGTAACTTTAATCTGCTCCACTGCACTGCCAGGGAAG
1 ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAG
30028622 GTAATTTCAT
Statistics
Matches: 560, Mismatches: 80, Indels: 26
0.84 0.12 0.04
Matches are distributed among these distances:
95 78 0.14
96 6 0.01
97 63 0.11
98 20 0.04
99 106 0.19
100 286 0.51
101 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (99 bp):
ATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAA
GATTCGCCGTTGCGGCTTCAATCTTTTAATTGCA
Found at i:30028448 original size:392 final size:397
Alignment explanation
Indices: 30027869--30028621 Score: 1072
Period size: 392 Copynumber: 1.9 Consensus size: 397
30027859 TTAAACTACG
** * *
30027869 ATGTCGGGGAAGCAAGATTCGTTGTTGTAGCTTTAATCTGCTTCACTGCACTACCAGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGCTCCACTGCACTACCAGGGAAGTAA
*
30027934 GATTCACCGTTGTGGCTTCAATCTTTTAAATTACAATGTCGGGGAACAAGATTCGCCGTTGTAGC
66 GATTCACCGTTGCGGCTTCAATCTTTT-AA-TACAATGTCGGGGAACAAGATTCGCCGTTGTAGC
* *
30027999 TTCAATTTGATCCACTGCATCGCCAGGAAAGTAAGATTCGCCCTTGCAGCTTCAATCT-TCTTAA
129 TTCAATCTGATCCACTGCATCGCCAGGAAAGTAAGATTCACCCTTGCAGCTTCAATCTCT-TTAA
* * * ** * *
30028063 TTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCGCCGCCAGGGA
193 TTGCAATGTCGGGGAAACAAAATTCACCGTCGTAACTTCAATCTAATCCACTGCACCGCCAGGAA
* * * * * ***
30028128 AGTAAGATTCGCTGTTGTGGCTTCAA-C-CTTTAACTGCGATGTCGGGGAA-TAAGATTTGTCGT
258 AGTAAGATTCACCGTTGCGGCTTCAATCTCTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGT
* * *
30028190 TGTAGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTACGGCTTCAATCTT
323 CGTAACTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTACGGCTTCAATCTT
30028255 TTTAATTGCA
388 TTTAATTGCA
* *
30028265 ATGTCGGGG-AGACAAGATTCACTGTTGTGGCTTCAATCTGCTCCACTGCACTGCCAGGGAAGTA
1 ATGTCGGGGAAG-CAAGATTCACTGTTGTAGCTTCAATCTGCTCCACTGCACTACCAGGGAAGTA
* *
30028329 AGATTCGCCGTTGCGGGTTCAATCTTTT-A-A-AATGTCGGGGAAACAAGATTCGCCGTTGTAGC
65 AGATTCACCGTTGCGGCTTCAATCTTTTAATACAATGTCGGGG-AACAAGATTCGCCGTTGTAGC
* * *
30028391 TTCAATCTGGTCCACTGCATCGCCAGGAAAGTAAGATTCACCGTTGCGGCTTCAATCTCTTTAAT
129 TTCAATCTGATCCACTGCATCGCCAGGAAAGTAAGATTCACCCTTGCAGCTTCAATCTCTTTAAT
* *
30028456 TGCAATGTCGGGGAAACAAAATTCACTGTCGTAACTTCAATCTAATCCACTGCATCGCCAGGAAA
194 TGCAATGTCGGGGAAACAAAATTCACCGTCGTAACTTCAATCTAATCCACTGCACCGCCAGGAAA
* *
30028521 GTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTC
259 GTAAGATTCACCGTTGCGGCTTCAATCTCTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTC
*
30028586 GTAACTTTAATCTGCTCCACTGCACTGCCAGGGAAG
324 GTAACTTTAATCTGCTCCACTGCACCGCCAGGGAAG
30028622 GTAATTTCAT
Statistics
Matches: 314, Mismatches: 37, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
391 10 0.03
392 158 0.50
393 2 0.01
394 20 0.06
395 44 0.14
396 80 0.25
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (397 bp):
ATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATCTGCTCCACTGCACTACCAGGGAAGTAA
GATTCACCGTTGCGGCTTCAATCTTTTAATACAATGTCGGGGAACAAGATTCGCCGTTGTAGCTT
CAATCTGATCCACTGCATCGCCAGGAAAGTAAGATTCACCCTTGCAGCTTCAATCTCTTTAATTG
CAATGTCGGGGAAACAAAATTCACCGTCGTAACTTCAATCTAATCCACTGCACCGCCAGGAAAGT
AAGATTCACCGTTGCGGCTTCAATCTCTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTCGT
AACTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTACGGCTTCAATCTTTTT
AATTGCA
Found at i:30028954 original size:24 final size:24
Alignment explanation
Indices: 30028922--30028967 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
30028912 TTGCCCCCAC
*
30028922 TGTAATCTTCAAGGTTCAATCCGT
1 TGTAATCTTCAAGGTTAAATCCGT
*
30028946 TGTAATCTTTAAGGTTAAATCC
1 TGTAATCTTCAAGGTTAAATCC
30028968 ACGGTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (24 bp):
TGTAATCTTCAAGGTTAAATCCGT
Found at i:30028974 original size:24 final size:24
Alignment explanation
Indices: 30028918--30028975 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
30028908 CGGATTGCCC
*
30028918 CCACTGTAATCTTCAAGGTTCAAT
1 CCACTGTAATCTTCAAGGTTAAAT
** *
30028942 CCGTTGTAATCTTTAAGGTTAAAT
1 CCACTGTAATCTTCAAGGTTAAAT
*
30028966 CCACGGTAAT
1 CCACTGTAAT
30028976 TTTGGGACAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (24 bp):
CCACTGTAATCTTCAAGGTTAAAT
Found at i:30032025 original size:14 final size:15
Alignment explanation
Indices: 30031998--30032026 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30031988 ATGCACCTTC
30031998 ACATACATTGAATCT
1 ACATACATTGAATCT
30032013 ACATACA-TGAATCT
1 ACATACATTGAATCT
30032027 GCCCAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (15 bp):
ACATACATTGAATCT
Found at i:30033414 original size:13 final size:13
Alignment explanation
Indices: 30033396--30033421 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30033386 CTATGTATGA
30033396 ACTAAGACACATT
1 ACTAAGACACATT
30033409 ACTAAGACACATT
1 ACTAAGACACATT
30033422 TAAACTCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
ACTAAGACACATT
Found at i:30033517 original size:17 final size:18
Alignment explanation
Indices: 30033485--30033521 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
30033475 TGTTGAGCTG
30033485 AACTTAATTAAATTAACT
1 AACTTAATTAAATTAACT
*
30033503 AACTT-ATTTAATTAACT
1 AACTTAATTAAATTAACT
30033520 AA
1 AA
30033522 GTTTATTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
AACTTAATTAAATTAACT
Found at i:30036307 original size:19 final size:20
Alignment explanation
Indices: 30036278--30036329 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
30036268 CACTTCGTGA
* *
30036278 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
30036297 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
30036317 AAATG-AATGCAAA
1 AAATGTAATGCAAA
30036330 AAGAGACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:30038671 original size:18 final size:20
Alignment explanation
Indices: 30038636--30038676 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
30038626 ATGTATAAGC
30038636 ATGTGTATTAATTAAAATGT
1 ATGTGTATTAATTAAAATGT
30038656 ATGTGTATT-A-TAAAATGT
1 ATGTGTATTAATTAAAATGT
30038674 ATG
1 ATG
30038677 CATGTATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 11 0.52
19 1 0.05
20 9 0.43
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (20 bp):
ATGTGTATTAATTAAAATGT
Found at i:30042054 original size:22 final size:22
Alignment explanation
Indices: 30042002--30042065 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
30041992 TATTTGGGAA
* *
30042002 TTGGTACGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
30042024 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
30042046 TTGGTACGAAATGGAAATGG
1 TTGGTACGAAATGGTAATGG
30042066 TTCAGAAAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:30074275 original size:12 final size:11
Alignment explanation
Indices: 30074268--30074300 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
30074258 TTAAATTAAG
30074268 TAAAAAATAAA
1 TAAAAAATAAA
30074279 TAAATAAATAAA
1 TAAA-AAATAAA
30074291 T-AAAAATAAA
1 TAAAAAATAAA
30074301 ACTTTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 6 0.29
12 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:30076057 original size:18 final size:17
Alignment explanation
Indices: 30076036--30076073 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
30076026 AAAAATCAAG
30076036 AAAAAAAATCGAAAAGAA
1 AAAAAAAATCGAAAA-AA
*
30076054 AAAAAAAATTGAAAAAA
1 AAAAAAAATCGAAAAAA
30076071 AAA
1 AAA
30076074 TTGCATACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAAAAATCGAAAAAA
Found at i:30088150 original size:13 final size:12
Alignment explanation
Indices: 30088132--30088172 Score: 52
Period size: 10 Copynumber: 3.6 Consensus size: 12
30088122 CGTGAGCGAG
30088132 AAAAGAACATTGA
1 AAAAGAA-ATTGA
30088145 AAAAGAAATTG-
1 AAAAGAAATTGA
30088156 -AAAGAAA-TGA
1 AAAAGAAATTGA
30088166 AAAAGAA
1 AAAAGAA
30088173 GAAGAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.08
10 7 0.27
11 6 0.23
12 4 0.15
13 7 0.27
ACGTcount: A:0.68, C:0.02, G:0.17, T:0.12
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:30088332 original size:33 final size:33
Alignment explanation
Indices: 30088263--30088334 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
30088253 AGAAAACGAA
*
30088263 AGTGGAAAAGAAAAAGAGCCTGAAAAGAAATCG
1 AGTGAAAAAGAAAAAGAGCCTGAAAAGAAATCG
* **
30088296 AGTGAAAAAGAAAGAGAGTTTGTAAAAGAAAT-G
1 AGTGAAAAAGAAAAAGAGCCTG-AAAAGAAATCG
30088329 AGTGAA
1 AGTGAA
30088335 GAGAGTAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 25 0.74
34 9 0.26
ACGTcount: A:0.54, C:0.04, G:0.28, T:0.14
Consensus pattern (33 bp):
AGTGAAAAAGAAAAAGAGCCTGAAAAGAAATCG
Found at i:30116896 original size:23 final size:21
Alignment explanation
Indices: 30116869--30116919 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
30116859 GAATATTTAC
* *
30116869 ATAAAAAATTAAACTGATTAAAA
1 ATAAAAAA-TAAA-TAAATAAAA
30116892 ATAAATAAATAAATAAATAAAA
1 ATAAA-AAATAAATAAATAAAA
30116914 ATAAAA
1 ATAAAA
30116920 CTTTACAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 12 0.48
23 9 0.36
24 3 0.12
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (21 bp):
ATAAAAAATAAATAAATAAAA
Found at i:30120650 original size:16 final size:16
Alignment explanation
Indices: 30120618--30120653 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
30120608 CCGTATGCAA
30120618 TTTTTTTTCCAATTTT
1 TTTTTTTTCCAATTTT
*
30120634 TTTTCTTTTCGAATTTT
1 TTTT-TTTTCCAATTTT
30120651 TTT
1 TTT
30120654 GACTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTTTTTCCAATTTT
Found at i:30120664 original size:12 final size:12
Alignment explanation
Indices: 30120634--30120677 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
30120624 TTCCAATTTT
30120634 TTTTCTTTTCGAA
1 TTTT-TTTTCGAA
*
30120647 -TTTTTTT-GAC
1 TTTTTTTTCGAA
30120657 TTTTTTTTCGAA
1 TTTTTTTTCGAA
30120669 TTTTTTTTC
1 TTTTTTTTC
30120678 TAAGCTACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.07
11 11 0.41
12 14 0.52
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:30124489 original size:573 final size:573
Alignment explanation
Indices: 30123401--30124536 Score: 2236
Period size: 573 Copynumber: 2.0 Consensus size: 573
30123391 TGTTGAGTGT
30123401 TTATTTTTGCAGGTTTTTGGAAAATGTCTAGGTGATATTGACCATAATGATGTCTATGACATGTT
1 TTATTTTTGCAGGTTTTTGGAAAATGTCTAGGTGATATTGACCATAATGATGTCTATGACATGTT
30123466 TCAAAAACTCCAACAACAATTAGATGAACACGCTGCCACACTTCGAACCTTGAGTACCGCTTTCA
66 TCAAAAACTCCAACAACAATTAGATGAACACGCTGCCACACTTCGAACCTTGAGTACCGCTTTCA
30123531 ATGAGGTGAGATTGAATCAAGATCCTCATTATCGGGATCCAATTACAGAAGATAGGGATAACCCA
131 ATGAGGTGAGATTGAATCAAGATCCTCATTATCGGGATCCAATTACAGAAGATAGGGATAACCCA
30123596 CCTCCTGCTCATAGACGCGGTCCTCGACGTGTCCCTAGAACTGATGCTGATTTTCATGATCGTGG
196 CCTCCTGCTCATAGACGCGGTCCTCGACGTGTCCCTAGAACTGATGCTGATTTTCATGATCGTGG
30123661 GCAACCCTCCTTGGCAAAACCGAAGTTCACAATTCCCCAATTTCGTGGTAAGAATGATCCAGAAG
261 GCAACCCTCCTTGGCAAAACCGAAGTTCACAATTCCCCAATTTCGTGGTAAGAATGATCCAGAAG
30123726 CTTATTGTGAATGAGAATCTAAGATTGAACTAATGTTTAGGTATTATAAATGTCCGGATGATGAG
326 CTTATTGTGAATGAGAATCTAAGATTGAACTAATGTTTAGGTATTATAAATGTCCGGATGATGAG
30123791 AAAGTTGTGTTAGCAACGCTGGAATTTTTAGATTATGCATTAAGTTGGTGGACTCAACTTGGGGT
391 AAAGTTGTGTTAGCAACGCTGGAATTTTTAGATTATGCATTAAGTTGGTGGACTCAACTTGGGGT
*
30123856 AAATCGTCATCGGAATTATGAAGGTGAGATTTCGACATGGGAGGAGTTGAAACAAATTATGCGAA
456 AAATCGTCATCGGAATTATGAAGGTGAGATTTCGACATGGGAGGAGTTGAAACAAATTATGCAAA
30123921 AAAGGCTTGTTCCACCTCACTACTATAGGGAGATTAAAACAAATTAAAACAAA
521 AAAGGCTTGTTCCACCTCACTACTATAGGGAGATTAAAACAAATTAAAACAAA
30123974 TTATTTTTGCAGGTTTTTGGAAAATGTCTAGGTGATATTGACCATAATGATGTCTATGACATGTT
1 TTATTTTTGCAGGTTTTTGGAAAATGTCTAGGTGATATTGACCATAATGATGTCTATGACATGTT
*
30124039 TCAAAAACTCCAACAACAATTAGATGAACACGCTGCCACACTTCGAACCTTGAGTACTGCTTTCA
66 TCAAAAACTCCAACAACAATTAGATGAACACGCTGCCACACTTCGAACCTTGAGTACCGCTTTCA
30124104 ATGAGGTGAGATTGAATCAAGATCCTCATTATCGGGATCCAATTACAGAAGATAGGGATAACCCA
131 ATGAGGTGAGATTGAATCAAGATCCTCATTATCGGGATCCAATTACAGAAGATAGGGATAACCCA
30124169 CCTCCTGCTCATAGACGCGGTCCTCGACGTGTCCCTAGAACTGATGCTGATTTTCATGATCGTGG
196 CCTCCTGCTCATAGACGCGGTCCTCGACGTGTCCCTAGAACTGATGCTGATTTTCATGATCGTGG
30124234 GCAACCCTCCTTGGCAAAACCGAAGTTCACAATTCCCCAATTTCGTGGTAAGAATGATCCAGAAG
261 GCAACCCTCCTTGGCAAAACCGAAGTTCACAATTCCCCAATTTCGTGGTAAGAATGATCCAGAAG
*
30124299 CTTATTGTGAATGGGAATCTAAGATTGAACTAATGTTTAGGTATTATAAATGTCCGGATGATGAG
326 CTTATTGTGAATGAGAATCTAAGATTGAACTAATGTTTAGGTATTATAAATGTCCGGATGATGAG
30124364 AAAGTTGTGTTAGCAACGCTGGAATTTTTAGATTATGCATTAAGTTGGTGGACTCAACTTGGGGT
391 AAAGTTGTGTTAGCAACGCTGGAATTTTTAGATTATGCATTAAGTTGGTGGACTCAACTTGGGGT
*
30124429 AAATCGTCATCGGAATTATGAATGTGAGATTTCGACATGGGAGGAGTTGAAACAAATTATGCAAA
456 AAATCGTCATCGGAATTATGAAGGTGAGATTTCGACATGGGAGGAGTTGAAACAAATTATGCAAA
30124494 AAAGGCTTGTTCCACCTCACTACTATAGGGAGATTAAAACAAA
521 AAAGGCTTGTTCCACCTCACTACTATAGGGAGATTAAAACAAA
30124537 GCTTAGAAGA
Statistics
Matches: 559, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
573 559 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (573 bp):
TTATTTTTGCAGGTTTTTGGAAAATGTCTAGGTGATATTGACCATAATGATGTCTATGACATGTT
TCAAAAACTCCAACAACAATTAGATGAACACGCTGCCACACTTCGAACCTTGAGTACCGCTTTCA
ATGAGGTGAGATTGAATCAAGATCCTCATTATCGGGATCCAATTACAGAAGATAGGGATAACCCA
CCTCCTGCTCATAGACGCGGTCCTCGACGTGTCCCTAGAACTGATGCTGATTTTCATGATCGTGG
GCAACCCTCCTTGGCAAAACCGAAGTTCACAATTCCCCAATTTCGTGGTAAGAATGATCCAGAAG
CTTATTGTGAATGAGAATCTAAGATTGAACTAATGTTTAGGTATTATAAATGTCCGGATGATGAG
AAAGTTGTGTTAGCAACGCTGGAATTTTTAGATTATGCATTAAGTTGGTGGACTCAACTTGGGGT
AAATCGTCATCGGAATTATGAAGGTGAGATTTCGACATGGGAGGAGTTGAAACAAATTATGCAAA
AAAGGCTTGTTCCACCTCACTACTATAGGGAGATTAAAACAAATTAAAACAAA
Found at i:30126046 original size:19 final size:20
Alignment explanation
Indices: 30126022--30126060 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
30126012 TGCATGCATC
*
30126022 ATAGGTTCAA-TGAGCTCAA
1 ATAGGTGCAATTGAGCTCAA
*
30126041 ATAGGTGGAATTGAGCTCAA
1 ATAGGTGCAATTGAGCTCAA
30126061 GTGAGCTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.26
Consensus pattern (20 bp):
ATAGGTGCAATTGAGCTCAA
Found at i:30136376 original size:29 final size:29
Alignment explanation
Indices: 30136342--30136414 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
30136332 ATGTATTAGT
* *
30136342 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
30136371 TTAGGACATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
30136400 TTAGGACATATTTAA
1 TTAGGACATATTTAA
30136415 TAATATCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:30137269 original size:10 final size:10
Alignment explanation
Indices: 30137254--30137292 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
30137244 TAGTTTCTCG
30137254 AAAAAAATTC
1 AAAAAAATTC
*
30137264 AAAAAAATTTGA
1 AAAAAAA-TT-C
30137276 AAAAAAATTC
1 AAAAAAATTC
30137286 AAAAAAA
1 AAAAAAA
30137293 ATTTGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 14 0.56
11 4 0.16
12 7 0.28
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:30137270 original size:11 final size:11
Alignment explanation
Indices: 30137254--30137305 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
30137244 TAGTTTCTCG
30137254 AAAAAAATTCA
1 AAAAAAATTCA
* *
30137265 AAAAAATTTGA
1 AAAAAAATTCA
30137276 AAAAAAATTCA
1 AAAAAAATTCA
*
30137287 AAAAAAATTTGA
1 AAAAAAA-TTCA
30137299 AAAAAAA
1 AAAAAAA
30137306 ACTAGTTTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:30137279 original size:12 final size:12
Alignment explanation
Indices: 30137264--30137305 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
30137254 AAAAAAATTC
30137264 AAAAAAATTTGA
1 AAAAAAATTTGA
*
30137276 AAAAAAA-TTCA
1 AAAAAAATTTGA
30137287 AAAAAAATTTGA
1 AAAAAAATTTGA
30137299 AAAAAAA
1 AAAAAAA
30137306 ACTAGTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:30137282 original size:22 final size:23
Alignment explanation
Indices: 30137254--30137305 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
30137244 TAGTTTCTCG
30137254 AAAAAAATTC-AAAAAAATTTGA
1 AAAAAAATTCAAAAAAAATTTGA
30137276 AAAAAAATTCAAAAAAAATTTGA
1 AAAAAAATTCAAAAAAAATTTGA
30137299 AAAAAAA
1 AAAAAAA
30137306 ACTAGTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (23 bp):
AAAAAAATTCAAAAAAAATTTGA
Found at i:30137368 original size:14 final size:13
Alignment explanation
Indices: 30137347--30137395 Score: 89
Period size: 13 Copynumber: 3.7 Consensus size: 13
30137337 TATCAAGTTG
30137347 TGAAAAAAAAATT
1 TGAAAAAAAAATT
30137360 TGAAAAAAAAATT
1 TGAAAAAAAAATT
30137373 TGAAAAAAAAATT
1 TGAAAAAAAAATT
30137386 GTGAAAAAAA
1 -TGAAAAAAA
30137396 GAGAGAGCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 26 0.74
14 9 0.26
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.20
Consensus pattern (13 bp):
TGAAAAAAAAATT
Found at i:30138344 original size:18 final size:17
Alignment explanation
Indices: 30138323--30138367 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
30138313 GAGTGACGAG
30138323 AGAAAAATAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
30138341 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
30138359 AGAGAAAAA
1 AGA-AAAAA
30138368 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.13, T:0.09
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:30148151 original size:20 final size:20
Alignment explanation
Indices: 30148128--30148192 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
30148118 AGTTTTTCCC
* *
30148128 AGCTCGATTTAGCTTACATG
1 AGCTCAATTTAGCTTACTTG
* ***
30148148 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTTACTTG
*
30148168 AGCTCAATTTAGCTTACTTT
1 AGCTCAATTTAGCTTACTTG
30148188 AGCTC
1 AGCTC
30148193 GTTTGAGCTT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTG
Found at i:30151056 original size:13 final size:13
Alignment explanation
Indices: 30151038--30151073 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
30151028 AATCTGATTG
30151038 TTTAATGTGTTAC
1 TTTAATGTGTTAC
30151051 TTTAATGTGTTAC
1 TTTAATGTGTTAC
30151064 TTTAATGTGT
1 TTTAATGTGT
30151074 CTAAACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (13 bp):
TTTAATGTGTTAC
Found at i:30156971 original size:22 final size:22
Alignment explanation
Indices: 30156940--30157004 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
30156930 ACCTTTTTGA
*
30156940 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
30156963 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
30156985 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
30157005 TTCCTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.28
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:30191991 original size:11 final size:12
Alignment explanation
Indices: 30191965--30191996 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
30191955 TGTGATATAT
*
30191965 AAAACAAGTTCA
1 AAAAAAAGTTCA
30191977 AAAAAAAGTTCA
1 AAAAAAAGTTCA
30191989 AAAAAAAG
1 AAAAAAAG
30191997 GTTGTANNNN
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.12
Consensus pattern (12 bp):
AAAAAAAGTTCA
Found at i:30192854 original size:22 final size:22
Alignment explanation
Indices: 30192811--30192875 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
30192801 CCTTTTTGAA
*
30192811 CCATTTCCATTTTCGTACCAAAT
1 CCATTACCA-TTTCGTACCAAAT
**
30192834 CCATTACCATTTCGTTTCAAAT
1 CCATTACCATTTCGTACCAAAT
* * *
30192856 CCCTTACCGTTTCATACCAA
1 CCATTACCATTTCGTACCAA
30192876 TTCCCAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.26, C:0.32, G:0.05, T:0.37
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:30196508 original size:15 final size:15
Alignment explanation
Indices: 30196488--30196542 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
30196478 GCTCTCATCA
*
30196488 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
30196503 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
30196518 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
30196532 TTCTTTT-TCTC
1 TTCTTTTCTCTC
30196543 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:30198575 original size:18 final size:18
Alignment explanation
Indices: 30198552--30198587 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
30198542 TTTCAATCAC
*
30198552 TTTTTTTT-AATTCTGAA
1 TTTTTTTTCAATACTGAA
30198569 TTTTTTTTCAATACTGAA
1 TTTTTTTTCAATACTGAA
30198587 T
1 T
30198588 ACACAAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (18 bp):
TTTTTTTTCAATACTGAA
Found at i:30198638 original size:13 final size:13
Alignment explanation
Indices: 30198620--30198663 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
30198610 GAATACAAAC
30198620 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
*
30198633 TTTTTTTTCGAA-
1 TTTTTTTTTGAAT
30198645 -TTTTTTTTG-AT
1 TTTTTTTTTGAAT
30198656 TTTTTTTT
1 TTTTTTTT
30198664 ACAATCTCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 1 0.04
11 8 0.30
12 7 0.26
13 11 0.41
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:30200016 original size:50 final size:50
Alignment explanation
Indices: 30199957--30200062 Score: 203
Period size: 50 Copynumber: 2.1 Consensus size: 50
30199947 AGCTGATTCT
30199957 AACTAACACAACTAATTAAATTTATTCAAAATAAATATAATCAGCTCCTTG
1 AACT-ACACAACTAATTAAATTTATTCAAAATAAATATAATCAGCTCCTTG
30200008 AACTACACAACTAATTAAATTTATTCAAAATAAATATAATCAGCTCCTTG
1 AACTACACAACTAATTAAATTTATTCAAAATAAATATAATCAGCTCCTTG
30200058 AACTA
1 AACTA
30200063 ATTAAGTGCC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 51 0.93
51 4 0.07
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (50 bp):
AACTACACAACTAATTAAATTTATTCAAAATAAATATAATCAGCTCCTTG
Found at i:30203991 original size:22 final size:22
Alignment explanation
Indices: 30203939--30204002 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
30203929 TATTTGGGAA
* *
30203939 TTGGTACGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
30203961 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
30203983 TTGGTACGAAATGGAAATGG
1 TTGGTACGAAATGGTAATGG
30204003 TTCAAAAAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:30205092 original size:10 final size:10
Alignment explanation
Indices: 30205077--30205118 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
30205067 TTTGCAAGTT
30205077 TTGAGCTAAA
1 TTGAGCTAAA
* *
30205087 TTGAGCTGAT
1 TTGAGCTAAA
*
30205097 TTGAGCT-CA
1 TTGAGCTAAA
30205106 TTGAGCTAAA
1 TTGAGCTAAA
30205116 TTG
1 TTG
30205119 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:30208422 original size:11 final size:10
Alignment explanation
Indices: 30208388--30208421 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
30208378 GAAGAAGAGG
30208388 AAATTCGAAAA
1 AAATTC-AAAA
30208399 AAATTCAAAA
1 AAATTCAAAA
30208409 AAATTCAAAA
1 AAATTCAAAA
30208419 AAA
1 AAA
30208422 AAGAGTGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.74
11 6 0.26
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.18
Consensus pattern (10 bp):
AAATTCAAAA
Found at i:30209590 original size:11 final size:12
Alignment explanation
Indices: 30209564--30209595 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
30209554 TGTGATATAT
*
30209564 AAAACAAGTTCA
1 AAAAAAAGTTCA
30209576 AAAAAAAGTTCA
1 AAAAAAAGTTCA
30209588 AAAAAAAG
1 AAAAAAAG
30209596 GTTGTATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.12
Consensus pattern (12 bp):
AAAAAAAGTTCA
Found at i:30209698 original size:11 final size:10
Alignment explanation
Indices: 30209664--30209697 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
30209654 GAAGAAGAGG
30209664 AAATTCGAAAA
1 AAATTC-AAAA
30209675 AAATTCAAAA
1 AAATTCAAAA
30209685 AAATTCAAAA
1 AAATTCAAAA
30209695 AAA
1 AAA
30209698 AAGAGTGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.74
11 6 0.26
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.18
Consensus pattern (10 bp):
AAATTCAAAA
Found at i:30239864 original size:11 final size:11
Alignment explanation
Indices: 30239848--30239875 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
30239838 TTTAATTAGG
30239848 TGTTTTAAATA
1 TGTTTTAAATA
30239859 TGTTTTAAATA
1 TGTTTTAAATA
30239870 TGTTTT
1 TGTTTT
30239876 GTTAATGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (11 bp):
TGTTTTAAATA
Found at i:30239998 original size:41 final size:41
Alignment explanation
Indices: 30239941--30240048 Score: 189
Period size: 41 Copynumber: 2.6 Consensus size: 41
30239931 TTTAATATGT
* *
30239941 CGAATTTAATGCTGCCACTACATGTTATAAATGTGTCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
30239982 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
*
30240023 CGAATTTAATGCTGCTACTACATGTT
1 CGAATTTAATGCTGCCACTACATGTT
30240049 TGGCCGAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
Found at i:30241616 original size:11 final size:11
Alignment explanation
Indices: 30241600--30241640 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
30241590 CGAGATTGTA
30241600 AAAAAAATTTG
1 AAAAAAATTTG
**
30241611 AAAAAAATTCAA
1 AAAAAAATT-TG
30241623 AAAAAAATTTG
1 AAAAAAATTTG
30241634 AAAAAAA
1 AAAAAAA
30241641 AGTTTGTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (11 bp):
AAAAAAATTTG
Found at i:30241616 original size:12 final size:12
Alignment explanation
Indices: 30241599--30241646 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
30241589 ACGAGATTGT
30241599 AAAAAAAATTTG
1 AAAAAAAATTTG
**
30241611 -AAAAAAATTCA
1 AAAAAAAATTTG
30241622 AAAAAAAATTTG
1 AAAAAAAATTTG
30241634 AAAAAAAAGTTTG
1 AAAAAAAA-TTTG
30241647 TATTCAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 9 0.30
12 17 0.57
13 4 0.13
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAAAAAATTTG
Found at i:30242589 original size:15 final size:16
Alignment explanation
Indices: 30242569--30242600 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
30242559 AGAAAATGAA
30242569 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
30242584 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
30242600 A
1 A
30242601 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:30267855 original size:10 final size:10
Alignment explanation
Indices: 30267840--30267901 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
30267830 TTTGAACCAT
*
30267840 TACCAATTCG
1 TACCAATTCA
*
30267850 TACCAAATACCA
1 TACC-AAT-TCA
*
30267862 TACCATTTCA
1 TACCAATTCA
30267872 TACCAATTCCA
1 TACCAATT-CA
* *
30267883 TACCATTTCG
1 TACCAATTCA
30267893 TACCAATTC
1 TACCAATTC
30267902 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:30267885 original size:21 final size:21
Alignment explanation
Indices: 30267840--30267902 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
30267830 TTTGAACCAT
* *
30267840 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
30267862 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
30267883 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
30267903 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:30268245 original size:13 final size:13
Alignment explanation
Indices: 30268227--30268268 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 13
30268217 AAAAAAATTC
30268227 AAAATCGAAAAAA
1 AAAATCGAAAAAA
30268240 AAAATC--AAAAA
1 AAAATCGAAAAAA
*
30268251 AAAATTGAAAAGAA
1 AAAATCGAAAA-AA
30268265 AAAA
1 AAAA
30268269 ATTGCATACG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 10 0.40
13 9 0.36
14 6 0.24
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.10
Consensus pattern (13 bp):
AAAATCGAAAAAA
Found at i:30268250 original size:20 final size:19
Alignment explanation
Indices: 30268212--30268249 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
30268202 AAAAAAGAGT
*
30268212 TCGAAAAAAAAATTCAAAA
1 TCGAAAAAAAAAATCAAAA
30268231 TCGAAAAAAAAAATCAAAA
1 TCGAAAAAAAAAATCAAAA
30268250 AAAAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.71, C:0.11, G:0.05, T:0.13
Consensus pattern (19 bp):
TCGAAAAAAAAAATCAAAA
Found at i:30297743 original size:11 final size:12
Alignment explanation
Indices: 30297727--30297751 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30297717 TTCTTTTCAA
30297727 TTTTTTTGATTT
1 TTTTTTTGATTT
30297739 TTTTTTTGATTT
1 TTTTTTTGATTT
30297751 T
1 T
30297752 GAATTTTTTT
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:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (12 bp):
TTTTTTTGATTT
Found at i:30298079 original size:23 final size:23
Alignment explanation
Indices: 30298044--30298155 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
30298034 CGGTTTTGGG
* *
30298044 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
30298067 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
30298090 TTTGGTACGAATTGGTAAGGTGA
1 TTTGGTACGAAATGGTAATGCGA
* *
30298113 TTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
*
30298136 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
30298156 GTTCAAAAAG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATGCGA
Found at i:30298106 original size:46 final size:46
Alignment explanation
Indices: 30298044--30298155 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
30298034 CGGTTTTGGG
*
30298044 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
* * *
30298090 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
*
30298136 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
30298156 GTTCAAAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
Found at i:30305806 original size:14 final size:14
Alignment explanation
Indices: 30305787--30305846 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
30305777 TTCTTAGATA
30305787 TTTTAATTACTTAG
1 TTTTAATTACTTAG
*
30305801 TTTTAATTTAATTATG
1 TTTTAA-TTACTTA-G
*
30305817 TTTTAATTCCTATAG
1 TTTTAATTACT-TAG
*
30305832 -CTTAATTACTT-G
1 TTTTAATTACTTAG
30305844 TTT
1 TTT
30305847 GAATGTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
12 1 0.03
13 2 0.06
14 14 0.39
15 10 0.28
16 9 0.25
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.58
Consensus pattern (14 bp):
TTTTAATTACTTAG
Found at i:30305821 original size:16 final size:15
Alignment explanation
Indices: 30305787--30305824 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
30305777 TTCTTAGATA
*
30305787 TTTTAA-TTACTTAG
1 TTTTAATTTAATTAG
30305801 TTTTAATTTAATTATG
1 TTTTAATTTAATTA-G
30305817 TTTTAATT
1 TTTTAATT
30305825 CCTATAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 6 0.29
16 9 0.43
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (15 bp):
TTTTAATTTAATTAG
Found at i:30322762 original size:33 final size:33
Alignment explanation
Indices: 30322724--30322786 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
30322714 GATTACTCAC
30322724 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
30322757 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
30322787 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:30322813 original size:14 final size:15
Alignment explanation
Indices: 30322789--30322868 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 15
30322779 TCTCTTTCAA
*
30322789 TTTCTTTTTTCACTT
1 TTTCTTTTTTCAATT
30322804 TTTC-TTTTTCAATT
1 TTTCTTTTTTCAATT
30322818 TTT-TTTCATTCTCAA--
1 TTTCTTT--TT-TCAATT
30322833 TTTC-TTTTTCAA-T
1 TTTCTTTTTTCAATT
30322846 TTTCTTTTCTTC-A-T
1 TTTCTTTT-TTCAATT
30322860 TTTCTTTTT
1 TTTCTTTTT
30322869 CTCTCACTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
12 4 0.07
13 7 0.12
14 27 0.48
15 12 0.21
16 2 0.04
17 4 0.07
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCTTTTTTCAATT
Found at i:30322813 original size:27 final size:27
Alignment explanation
Indices: 30322783--30322869 Score: 97
Period size: 27 Copynumber: 3.1 Consensus size: 27
30322773 TCAAGCTCTC
30322783 TTTCAATTTCTTTT-TTCACTTTTTCTT
1 TTTCAATTTCTTTTCTTCAC-TTTTCTT
* * *
30322810 TTTCAATTTTTTTTCATTCTCAATTTCTT
1 TTTCAATTTCTTTTC-TTCAC-TTTTCTT
30322839 TTTCAATTTTCTTTTCTTCA-TTTTCTT
1 TTTCAA-TTTCTTTTCTTCACTTTTCTT
30322866 TTTC
1 TTTC
30322870 TCTCACTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
27 23 0.46
29 19 0.38
30 8 0.16
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTCAATTTCTTTTCTTCACTTTTCTT
Found at i:30322853 original size:12 final size:12
Alignment explanation
Indices: 30322765--30322962 Score: 69
Period size: 12 Copynumber: 16.9 Consensus size: 12
30322755 TTTTCACTTG
30322765 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
30322776 AGCTCTCTTTCA
1 ATTTCTTTTTCA
30322788 ATTTCTTTTTTCA
1 ATTTC-TTTTTCA
*
30322801 CTTTTTCTTTTTCA
1 --ATTTCTTTTTCA
30322815 ATTT-TTTTTC-
1 ATTTCTTTTTCA
30322825 A-TTC----TCA
1 ATTTCTTTTTCA
30322832 ATTTCTTTTTCA
1 ATTTCTTTTTCA
30322844 ATTTTCTTTTCTTCA
1 A-TTTC-TTT-TTCA
* *
30322859 TTTTCTTTTTCT
1 ATTTCTTTTTCA
* ** *
30322871 CTCACTTTTTCG
1 ATTTCTTTTTCA
30322883 ATTTCTTTTTC-
1 ATTTCTTTTTCA
* ** *
30322894 TTTTGCAATTTCT
1 ATTT-CTTTTTCA
* *
30322907 TTTTCTTTTTCG
1 ATTTCTTTTTCA
*
30322919 TTTTCTTTTT--
1 ATTTCTTTTTCA
* *
30322929 GTTT-TCTTTCA
1 ATTTCTTTTTCA
30322940 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
30322952 ATCTCTTTTTC
1 ATTTCTTTTTC
30322963 CTTTTCTCGC
Statistics
Matches: 140, Mismatches: 28, Indels: 37
0.68 0.14 0.18
Matches are distributed among these distances:
6 2 0.01
7 1 0.01
8 3 0.02
9 6 0.04
10 4 0.03
11 15 0.11
12 70 0.50
13 17 0.12
14 14 0.10
15 8 0.06
ACGTcount: A:0.11, C:0.20, G:0.03, T:0.67
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:30322928 original size:18 final size:18
Alignment explanation
Indices: 30322801--30322968 Score: 85
Period size: 18 Copynumber: 9.4 Consensus size: 18
30322791 TCTTTTTTCA
* **
30322801 CTTTTTCTTTTTCAATTT
1 CTTTTTCATTTTCTTTTT
* **
30322819 -TTTTTCATTCTCAATTT
1 CTTTTTCATTTTCTTTTT
30322836 CTTTTTCAATTTTCTTTTCTT
1 CTTTTTC-ATTTTC-TTT-TT
* * * **
30322857 CATTTTCTTTTTCTCTCA
1 CTTTTTCATTTTCTTTTT
30322875 CTTTTTCGA-TTTCTTTTT
1 CTTTTTC-ATTTTCTTTTT
* *
30322893 CTTTTGCAATTTCTTTTT
1 CTTTTTCATTTTCTTTTT
*
30322911 CTTTTTCGTTTTCTTTTT
1 CTTTTTCATTTTCTTTTT
* **
30322929 -GTTTTC--TTTCAATTT
1 CTTTTTCATTTTCTTTTT
* *
30322944 CTTTTTCAATCTCTTTTT
1 CTTTTTCATTTTCTTTTT
*
30322962 CCTTTTC
1 CTTTTTC
30322969 TCGCTCAATG
Statistics
Matches: 114, Mismatches: 27, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
15 7 0.06
16 5 0.04
17 21 0.18
18 60 0.53
19 7 0.06
20 6 0.05
21 8 0.07
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.68
Consensus pattern (18 bp):
CTTTTTCATTTTCTTTTT
Found at i:30322950 original size:6 final size:6
Alignment explanation
Indices: 30322801--30322937 Score: 71
Period size: 6 Copynumber: 22.7 Consensus size: 6
30322791 TCTTTTTTCA
** * * ** *
30322801 CTTTTT CTTTTT CAATTT -TTTTT CATTCT CAATTT CTTTTT CAATTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT
* * ** ** *
30322849 CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT CGATTT CTTTTT CTTTTG
1 C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
** * *
30322899 CAATTT CTTTTT CTTTTT CGTTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
30322938 CAATTTCTTT
Statistics
Matches: 92, Mismatches: 35, Indels: 8
0.68 0.26 0.06
Matches are distributed among these distances:
5 7 0.08
6 73 0.79
7 9 0.10
8 3 0.03
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:30324029 original size:11 final size:11
Alignment explanation
Indices: 30324005--30324045 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
30323995 TGTCACTTCT
*
30324005 TTTTTTTTC-C
1 TTTTTTTTCGA
30324015 TTTTTTTTCGA
1 TTTTTTTTCGA
30324026 TTTTTTTT-GAA
1 TTTTTTTTCG-A
30324037 TTTTTTTTC
1 TTTTTTTTC
30324046 TGAATTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.07, C:0.10, G:0.05, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:30334441 original size:12 final size:12
Alignment explanation
Indices: 30334399--30334449 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
30334389 TCAATTTTTC
30334399 TTTTCTTTTCG-A
1 TTTT-TTTTCGAA
*
30334411 TTTTTTTTCTTAAA
1 TTTTTTTTC--GAA
30334425 TTTTTTTTTCGAA
1 -TTTTTTTTCGAA
30334438 TTTTTTTTCGAA
1 TTTTTTTTCGAA
30334450 ACTACAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 5 0.15
12 16 0.48
13 2 0.06
14 1 0.03
15 9 0.27
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.69
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:30346226 original size:41 final size:41
Alignment explanation
Indices: 30346164--30346258 Score: 181
Period size: 41 Copynumber: 2.3 Consensus size: 41
30346154 TTCGTAGCTA
30346164 AATGCTGCTACCTACATGTTATAAATATGTCTGGACGAATTT
1 AATGCTGCTA-CTACATGTTATAAATATGTCTGGACGAATTT
30346206 AATGCTGCTACTACATGTTATAAATATGTCTGGACGAATTT
1 AATGCTGCTACTACATGTTATAAATATGTCTGGACGAATTT
30346247 AATGCTGCTACT
1 AATGCTGCTACT
30346259 TAATGTGTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 43 0.81
42 10 0.19
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (41 bp):
AATGCTGCTACTACATGTTATAAATATGTCTGGACGAATTT
Found at i:30346749 original size:30 final size:32
Alignment explanation
Indices: 30346694--30346763 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
30346684 AAATGTCCCC
* *
30346694 TTCACACACTAAGGCCTTTCAATTTCGTGT-G
1 TTCACACACTAAGGCCTATCAATTTCCTGTAG
*
30346725 TTCACACAC-AAGGCCTGATC-ATTTCCTTTAG
1 TTCACACACTAAGGCCT-ATCAATTTCCTGTAG
30346756 TTCACACA
1 TTCACACA
30346764 TAGAAACGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 14 0.41
31 20 0.59
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.33
Consensus pattern (32 bp):
TTCACACACTAAGGCCTATCAATTTCCTGTAG
Found at i:30347709 original size:18 final size:18
Alignment explanation
Indices: 30347667--30347709 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
30347657 TATTTCATCT
*
30347667 ATTGTAATTGAAAAAAAA
1 ATTGAAATTGAAAAAAAA
**
30347685 AAGGAAATTGAAAAAAAA
1 ATTGAAATTGAAAAAAAA
30347703 ATTGAAA
1 ATTGAAA
30347710 AAAAAGGTAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.21
Consensus pattern (18 bp):
ATTGAAATTGAAAAAAAA
Found at i:30347712 original size:11 final size:12
Alignment explanation
Indices: 30347689--30347714 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30347679 AAAAAAAAGG
30347689 AAATTGAAAAAA
1 AAATTGAAAAAA
30347701 AAATTGAAAAAA
1 AAATTGAAAAAA
30347713 AA
1 AA
30347715 GGTACGAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (12 bp):
AAATTGAAAAAA
Found at i:30348645 original size:18 final size:18
Alignment explanation
Indices: 30348589--30348648 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
30348579 AAAAAGTGCG
30348589 AGAAAAAGAAATCGAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
30348610 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
30348628 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
30348646 AGA
1 AGA
30348649 GAGTGAGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:30353770 original size:20 final size:19
Alignment explanation
Indices: 30353735--30353772 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
30353725 AGCTAATAAC
30353735 GAGCTCAATGAACTGAATT
1 GAGCTCAATGAACTGAATT
*
30353754 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAACTGAAT
30353773 CAAAAATGTT
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:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAACTGAATT
Found at i:30369445 original size:41 final size:41
Alignment explanation
Indices: 30369388--30369495 Score: 189
Period size: 41 Copynumber: 2.6 Consensus size: 41
30369378 TTTAATATGT
* *
30369388 CGAATTTAATGCTGCCACTACATGTTATAAATGTGTCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
30369429 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
*
30369470 CGAATTTAATGCTGCTACTACATGTT
1 CGAATTTAATGCTGCCACTACATGTT
30369496 TGGCCGAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
Found at i:30370707 original size:36 final size:36
Alignment explanation
Indices: 30370667--30370740 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
30370657 CCTGTTTTTG
30370667 TTATAAGACATATATAATATGCACATTCAACTATCA
1 TTATAAGACATATATAATATGCACATTCAACTATCA
*
30370703 TTATAAGACATTTATAATATGCACATTCAACTATCA
1 TTATAAGACATATATAATATGCACATTCAACTATCA
30370739 TT
1 TT
30370741 TCCATTTCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.36
Consensus pattern (36 bp):
TTATAAGACATATATAATATGCACATTCAACTATCA
Found at i:30372532 original size:50 final size:51
Alignment explanation
Indices: 30372423--30372553 Score: 158
Period size: 50 Copynumber: 2.5 Consensus size: 51
30372413 ATGACAAATG
* * *
30372423 AGTTACTTAATGCAAGACTTAATTTAATGATGCAGACTTAAACTAACATGGG
1 AGTTACATAATGCATGACTT-ATTTAATGATGCAGACTTAAACTAACATGGA
* *
30372475 AGTTACATAATGCATGACATTATTT-ATGATGCATACTT-AACTAGCATGGA
1 AGTTACATAATGCATGAC-TTATTTAATGATGCAGACTTAAACTAACATGGA
* *
30372525 AGTTACATAATGCATAACTTTATTAAATG
1 AGTTACATAATGCATGAC-TTATTTAATG
30372554 CAGAACATAC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
50 32 0.46
51 15 0.22
52 20 0.29
53 2 0.03
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (51 bp):
AGTTACATAATGCATGACTTATTTAATGATGCAGACTTAAACTAACATGGA
Found at i:30374301 original size:19 final size:19
Alignment explanation
Indices: 30374265--30374301 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
30374255 AAATGAGTTT
* *
30374265 ATTGAGCTAGTTCGAGCTC
1 ATTGAGCTACTTCCAGCTC
30374284 ATTGAGCTACTTCCAGCT
1 ATTGAGCTACTTCCAGCT
30374302 TGCAAACACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (19 bp):
ATTGAGCTACTTCCAGCTC
Found at i:30401722 original size:19 final size:19
Alignment explanation
Indices: 30401691--30401728 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
30401681 AATTTCAATC
30401691 TCTTTTCCAA-TTTTGTTT
1 TCTTTTCCAATTTTTGTTT
*
30401709 TCTTTTTCACATTTTTGTTT
1 TCTTTTCCA-ATTTTTGTTT
30401729 ACTCTCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.68
Consensus pattern (19 bp):
TCTTTTCCAATTTTTGTTT
Found at i:30405345 original size:21 final size:21
Alignment explanation
Indices: 30405284--30405346 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
30405274 TTTGAACTAT
*
30405284 TACCAATTCGTACCAAATACCA
1 TACCAATTCGTACC-AATTCCA
* * *
30405306 TACCATTTCATACCGATTCCA
1 TACCAATTCGTACCAATTCCA
* *
30405327 TACCAGTTCGCACCAATTCC
1 TACCAATTCGTACCAATTCC
30405347 CAGATACCTC
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.32, C:0.35, G:0.06, T:0.27
Consensus pattern (21 bp):
TACCAATTCGTACCAATTCCA
Found at i:30417248 original size:18 final size:19
Alignment explanation
Indices: 30417225--30417268 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
30417215 AGACCGTATA
*
30417225 CAATTTTTTT-CTTTTTTT
1 CAATTTTTTTGATTTTTTT
30417243 CAATTTTTTTGATTTTTTT
1 CAATTTTTTTGATTTTTTT
*
30417262 CGATTTT
1 CAATTTT
30417269 CTTTTTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.73
Consensus pattern (19 bp):
CAATTTTTTTGATTTTTTT
Found at i:30417252 original size:19 final size:19
Alignment explanation
Indices: 30417228--30417273 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
30417218 CCGTATACAA
*
30417228 TTTTTTTCTTTTTTTCAAT
1 TTTTTTTATTTTTTTCAAT
* *
30417247 TTTTTTGATTTTTTTCGAT
1 TTTTTTTATTTTTTTCAAT
30417266 TTTCTTTT
1 TTT-TTTT
30417274 TCAAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTTTTATTTTTTTCAAT
Found at i:30417257 original size:9 final size:10
Alignment explanation
Indices: 30417227--30417268 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
30417217 ACCGTATACA
30417227 ATTTTTTTC-
1 ATTTTTTTCG
*
30417236 -TTTTTTTCA
1 ATTTTTTTCG
30417245 ATTTTTTT-G
1 ATTTTTTTCG
30417254 ATTTTTTTCG
1 ATTTTTTTCG
30417264 ATTTT
1 ATTTT
30417269 CTTTTTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 8 0.28
9 8 0.28
10 13 0.45
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (10 bp):
ATTTTTTTCG
Found at i:30419595 original size:25 final size:25
Alignment explanation
Indices: 30419552--30419599 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
30419542 CGAGCTATGA
*
30419552 ATCGGTATGCTTACTCGAGCTGTAG
1 ATCGGTATGCTTACACGAGCTGTAG
30419577 ATCGGTATGCTCT-CACGAGCTGT
1 ATCGGTATGCT-TACACGAGCTGT
30419600 GGAGTATCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (25 bp):
ATCGGTATGCTTACACGAGCTGTAG
Found at i:30420160 original size:9 final size:9
Alignment explanation
Indices: 30420146--30420175 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
30420136 TAATTCAATT
30420146 TTAGTTAAA
1 TTAGTTAAA
30420155 TTAGTTAAA
1 TTAGTTAAA
30420164 TTAGTTAAA
1 TTAGTTAAA
30420173 TTA
1 TTA
30420176 TGTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (9 bp):
TTAGTTAAA
Found at i:30420323 original size:25 final size:25
Alignment explanation
Indices: 30420290--30420362 Score: 103
Period size: 25 Copynumber: 2.9 Consensus size: 25
30420280 AATATATGAT
*
30420290 TTAAATTGGTCTTAGTTTAGACGAA
1 TTAAATTGGTCTTAGTTTAGACAAA
*
30420315 TTAAATTGGACTTAGTTGT-GACAAA
1 TTAAATTGGTCTTAGTT-TAGACAAA
*
30420340 TTAAATTGGTCTTAGTTCAGACA
1 TTAAATTGGTCTTAGTTTAGACA
30420363 CCTTAATTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 41 0.98
26 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (25 bp):
TTAAATTGGTCTTAGTTTAGACAAA
Found at i:30425434 original size:21 final size:21
Alignment explanation
Indices: 30425391--30425434 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
30425381 ACACACTCAG
* *
30425391 CTTAATTGAGCTATTAATGAA
1 CTTAATTAAGCTATTAATAAA
30425412 CTTAATTAAGCTAATTAA-AAA
1 CTTAATTAAGCT-ATTAATAAA
30425433 CT
1 CT
30425435 ACAAGGCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (21 bp):
CTTAATTAAGCTATTAATAAA
Found at i:30429235 original size:20 final size:19
Alignment explanation
Indices: 30429180--30429224 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
30429170 CATTTCATTG
*
30429180 AGCTCCAATTAGCTCATTTCC
1 AGCTCC-ATGAGCTCATTT-C
*
30429201 AGCTCCATGAACTCATTTC
1 AGCTCCATGAGCTCATTTC
30429220 AGCTC
1 AGCTC
30429225 ATTTGAGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.31
Consensus pattern (19 bp):
AGCTCCATGAGCTCATTTC
Found at i:30432536 original size:25 final size:25
Alignment explanation
Indices: 30432508--30432580 Score: 103
Period size: 25 Copynumber: 2.9 Consensus size: 25
30432498 AATATATGAT
*
30432508 TTAAATTGGTCTTAGTTTAGACGAA
1 TTAAATTGGTCTTAGTTTAGACAAA
*
30432533 TTAAATTGGACTTAGTTGTA-ACAAA
1 TTAAATTGGTCTTAGTT-TAGACAAA
*
30432558 TTAAATTGGTCTTAGTTCAGACA
1 TTAAATTGGTCTTAGTTTAGACA
30432581 CCTTAATTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.02
25 39 0.93
26 2 0.05
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (25 bp):
TTAAATTGGTCTTAGTTTAGACAAA
Found at i:30438225 original size:19 final size:20
Alignment explanation
Indices: 30438190--30438227 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
30438180 CAAGTTGACT
30438190 TTAGCTCAATTTCAGCTCCC
1 TTAGCTCAATTTCAGCTCCC
*
30438210 TTAGCTC-ATTTTAGCTCC
1 TTAGCTCAATTTCAGCTCC
30438228 AATCAGCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.18, C:0.32, G:0.11, T:0.39
Consensus pattern (20 bp):
TTAGCTCAATTTCAGCTCCC
Found at i:30440095 original size:52 final size:52
Alignment explanation
Indices: 30440012--30440112 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
30440002 TAAGGAAACG
* *
30440012 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
30440064 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
30440113 TATGTGCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:30441738 original size:17 final size:17
Alignment explanation
Indices: 30441718--30441773 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 17
30441708 TCTCTTTTCA
30441718 TTCTCTTTTTTTGAATT
1 TTCTCTTTTTTTGAATT
*
30441735 TTCTTTCTTTTTTTCAATT
1 TTC--TCTTTTTTTGAATT
*
30441754 TTCT-TTTCTTTTGTATT
1 TTCTCTTT-TTTTGAATT
30441771 TTC
1 TTC
30441774 GCTCTTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.09
17 14 0.42
19 16 0.48
ACGTcount: A:0.09, C:0.14, G:0.04, T:0.73
Consensus pattern (17 bp):
TTCTCTTTTTTTGAATT
Found at i:30441745 original size:19 final size:20
Alignment explanation
Indices: 30441721--30441765 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
30441711 CTTTTCATTC
*
30441721 TCTTTTTTTGAATTTTC-TT
1 TCTTTTTTTCAATTTTCTTT
30441740 TCTTTTTTTCAATTTTCTTT
1 TCTTTTTTTCAATTTTCTTT
30441760 TCTTTT
1 TCTTTT
30441766 GTATTTTCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.76
Consensus pattern (20 bp):
TCTTTTTTTCAATTTTCTTT
Found at i:30441748 original size:20 final size:20
Alignment explanation
Indices: 30441712--30441765 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
30441702 TCTCGCTCTC
* *
30441712 TTTTCATTCTCTTTTTTTGAA
1 TTTTCTTTCT-TTTTTTTCAA
30441733 TTTTCTTTC-TTTTTTTCAA
1 TTTTCTTTCTTTTTTTTCAA
30441752 TTTTCTTTTCTTTT
1 TTTTC-TTTCTTTT
30441766 GTATTTTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 14 0.48
20 4 0.14
21 11 0.38
ACGTcount: A:0.09, C:0.15, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTCTTTCTTTTTTTTCAA
Found at i:30444009 original size:17 final size:17
Alignment explanation
Indices: 30443987--30444025 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
30443977 CCGTATGCAA
30443987 TTTTTTTCTTTC-AATT
1 TTTTTTTCTTTCGAATT
30444003 TTTTTTTCTTTCGAATT
1 TTTTTTTCTTTCGAATT
30444020 TTTTTT
1 TTTTTT
30444026 GTTTTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTTTTCTTTCGAATT
Found at i:30444030 original size:21 final size:21
Alignment explanation
Indices: 30444001--30444047 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
30443991 TTTCTTTCAA
30444001 TTTTT-TTTTCTTTCGAATTT
1 TTTTTGTTTTCTTTCGAATTT
*
30444021 TTTTTGTTTTTTTTCGAATTT
1 TTTTTGTTTTCTTTCGAATTT
30444042 TTTTTG
1 TTTTTG
30444048 AACTCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.77
Consensus pattern (21 bp):
TTTTTGTTTTCTTTCGAATTT
Found at i:30444046 original size:12 final size:11
Alignment explanation
Indices: 30444005--30444059 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 11
30443995 TTTCAATTTT
30444005 TTTTTCTTTCGAA
1 TTTTT-TTT-GAA
30444018 TTTTTTTTG--
1 TTTTTTTTGAA
30444027 TTTTTTTTCGAA
1 TTTTTTTT-GAA
30444039 TTTTTTTTGAA
1 TTTTTTTTGAA
30444050 CTCTTTTTTT
1 -T-TTTTTTT
30444060 TTTTACGTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.22
10 1 0.03
11 4 0.11
12 12 0.32
13 12 0.32
ACGTcount: A:0.11, C:0.09, G:0.07, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:30444365 original size:23 final size:23
Alignment explanation
Indices: 30444337--30444440 Score: 111
Period size: 23 Copynumber: 4.5 Consensus size: 23
30444327 GGGTTTGTTA
**
30444337 CGAAATGGTAATGTGATTTGGTT
1 CGAAATGGTAATACGATTTGGTT
* *
30444360 CAAAATGGTAATACGATTTGGTA
1 CGAAATGGTAATACGATTTGGTT
* ***
30444383 CGAACTGGTAAGGTGATTTGGTT
1 CGAAATGGTAATACGATTTGGTT
30444406 CGAAATGGTAATACGATTTGGTAT
1 CGAAATGGTAATACGATTTGGT-T
*
30444430 -GAAATGTTAAT
1 CGAAATGGTAAT
30444441 GGTTCAAAAA
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
23 64 0.98
24 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.35
Consensus pattern (23 bp):
CGAAATGGTAATACGATTTGGTT
Found at i:30444392 original size:46 final size:46
Alignment explanation
Indices: 30444330--30444435 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
30444320 CGGTTTTGGG
* *
30444330 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
* *
30444376 TTTGGTACGAACTGGTAAGGTGATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
*
30444422 TTTGGTATGAAATG
1 TTTGGTACGAAATG
30444436 TTAATGGTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
Found at i:30456198 original size:27 final size:27
Alignment explanation
Indices: 30456160--30456218 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
30456150 AATAAACACC
30456160 AAAAATATATTTTAAAAATAAAAAAAT
1 AAAAATATATTTTAAAAATAAAAAAAT
30456187 AAAAATATATTTTAAAAATAAAAAAAT
1 AAAAATATATTTTAAAAATAAAAAAAT
30456214 AAAAA
1 AAAAA
30456219 AATAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAAATATATTTTAAAAATAAAAAAAT
Found at i:30456205 original size:19 final size:19
Alignment explanation
Indices: 30456181--30456250 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
30456171 TTAAAAATAA
*
30456181 AAAAATAAAAATATATTTT
1 AAAAATAAAAAAATATTTT
*
30456200 AAAAATAAAAAAATA---A
1 AAAAATAAAAAAATATTTT
30456216 AAAAATAAAAAAATATTTT
1 AAAAATAAAAAAATATTTT
*
30456235 AAAATTAAAAAAATAT
1 AAAAATAAAAAAATAT
30456251 ATATTTATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
16 15 0.34
19 29 0.66
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATAAAAAAATATTTT
Found at i:30456219 original size:35 final size:35
Alignment explanation
Indices: 30456173--30456249 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
30456163 AATATATTTT
*
30456173 AAAAATAAAAAAATAAAAATATATTTTAAAAATAA
1 AAAAATAAAAAAATAAAAAAATATTTTAAAAATAA
*
30456208 AAAAATAAAAAAATAAAAAAATATTTTAAAATTAA
1 AAAAATAAAAAAATAAAAAAATATTTTAAAAATAA
30456243 AAAAATA
1 AAAAATA
30456250 TATATTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (35 bp):
AAAAATAAAAAAATAAAAAAATATTTTAAAAATAA
Found at i:30456246 original size:8 final size:8
Alignment explanation
Indices: 30456173--30456230 Score: 71
Period size: 8 Copynumber: 6.9 Consensus size: 8
30456163 AATATATTTT
30456173 AAAAATAA
1 AAAAATAA
30456181 AAAAATAA
1 AAAAATAA
**
30456189 AAATATATTTT
1 AAA-A-A-TAA
30456200 AAAAATAA
1 AAAAATAA
30456208 AAAAATAA
1 AAAAATAA
30456216 AAAAATAA
1 AAAAATAA
30456224 AAAAATA
1 AAAAATA
30456231 TTTTAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
8 35 0.81
9 2 0.05
10 2 0.05
11 4 0.09
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAA
Found at i:30464979 original size:20 final size:20
Alignment explanation
Indices: 30464932--30464980 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
30464922 GACGAGCTGA
* * *
30464932 AAGTAAGCTAAATTGAGCTC
1 AAGTGAGCTAAAATAAGCTC
**
30464952 AAACGAGCTAAAATAAGCTC
1 AAGTGAGCTAAAATAAGCTC
30464972 AAGTGAGCT
1 AAGTGAGCT
30464981 GATTTGAGCT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGTGAGCTAAAATAAGCTC
Found at i:30464979 original size:30 final size:31
Alignment explanation
Indices: 30464923--30464980 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
30464913 GATAAAAGAG
* *
30464923 ACGAGCTGAAAGTAAGCTAAATTGAGCTCAA
1 ACGAGCTGAAAATAAGCTAAAGTGAGCTCAA
*
30464954 ACGAGCT-AAAATAAGCTCAAGTGAGCT
1 ACGAGCTGAAAATAAGCTAAAGTGAGCT
30464981 GATTTGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.19
Consensus pattern (31 bp):
ACGAGCTGAAAATAAGCTAAAGTGAGCTCAA
Found at i:30468244 original size:14 final size:14
Alignment explanation
Indices: 30468225--30468253 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
30468215 TAGTACATTA
30468225 GCCTTGCATGACTT
1 GCCTTGCATGACTT
30468239 GCCTTGCATGACTT
1 GCCTTGCATGACTT
30468253 G
1 G
30468254 TAAGATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.28, G:0.24, T:0.34
Consensus pattern (14 bp):
GCCTTGCATGACTT
Found at i:30468584 original size:13 final size:13
Alignment explanation
Indices: 30468554--30468594 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
30468544 ATTGGAACAT
*
30468554 TTTACTTT-TTAT
1 TTTACTTTGTTAA
30468566 TTTACTTTGTTAA
1 TTTACTTTGTTAA
*
30468579 TTTACTTAGTTAA
1 TTTACTTTGTTAA
30468592 TTT
1 TTT
30468595 TTAGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (13 bp):
TTTACTTTGTTAA
Found at i:30469455 original size:14 final size:14
Alignment explanation
Indices: 30469436--30469462 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30469426 TAGTTAAATT
30469436 AGTTAATTAATTTA
1 AGTTAATTAATTTA
30469450 AGTTAATTAATTT
1 AGTTAATTAATTT
30469463 GTTAAAAATC
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
AGTTAATTAATTTA
Found at i:30469590 original size:28 final size:27
Alignment explanation
Indices: 30469506--30469590 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 27
30469496 AATGTGTTTC
* *
30469506 ATTGCATG-CTTTAATATGTCATAGCT
1 ATTGCATGTTTTTAATATGTCCTAGCT
* * *
30469532 ATTGCATGTTATTAAT-TTTTCTAAGCCT
1 ATTGCATGTTTTTAATATGTCCT-AG-CT
*
30469560 ATTGCATGTTTTTTAATATGTCCTAGTT
1 ATTGCATG-TTTTTAATATGTCCTAGCT
30469588 ATT
1 ATT
30469591 ACATAGCATA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
26 11 0.24
27 7 0.16
28 14 0.31
29 9 0.20
30 4 0.09
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (27 bp):
ATTGCATGTTTTTAATATGTCCTAGCT
Found at i:30479108 original size:132 final size:132
Alignment explanation
Indices: 30478871--30479132 Score: 434
Period size: 132 Copynumber: 2.0 Consensus size: 132
30478861 TAAGGCCTTG
* * * *
30478871 CTAATGAAGTCTTGAATGATTCCATTTAGTTTCATACGGATTTGCCTGGCCTTTGACCTTGTTAT
1 CTAATGAAGTCTTGAACGATTCCATTTAGTTTCATACGCATTTGCCTAGCCTTTGACCTCGTTAT
* *
30478936 TGGGCCTTGTGGTAATTTGAGCCCATCACGTCCTTGAGCTTGAATTGGGCCTTTGTGACTCGTAT
66 TAGGCCTTGTGGTAATTTGAGCCCATCACATCCTTGAGCTTGAATTGGGCCTTTGTGACTCGTAT
30479001 CA
131 CA
*
30479003 CTAATGAAGTCTTGAACGGTTCCATTTAGTTTCATACGCATTTGCCTAGCCTTTGACCTCGTTAT
1 CTAATGAAGTCTTGAACGATTCCATTTAGTTTCATACGCATTTGCCTAGCCTTTGACCTCGTTAT
* * *
30479068 TAGGCCTTGTGGTAATTTGAGCCCATCACATTCTTGAGCTTGAGTTGGGCCTTTGTGTCTCGTAT
66 TAGGCCTTGTGGTAATTTGAGCCCATCACATCCTTGAGCTTGAATTGGGCCTTTGTGACTCGTAT
30479133 TATTTCCCTC
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 120 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (132 bp):
CTAATGAAGTCTTGAACGATTCCATTTAGTTTCATACGCATTTGCCTAGCCTTTGACCTCGTTAT
TAGGCCTTGTGGTAATTTGAGCCCATCACATCCTTGAGCTTGAATTGGGCCTTTGTGACTCGTAT
CA
Found at i:30497504 original size:46 final size:46
Alignment explanation
Indices: 30497437--30497529 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
30497427 GGGATTGATT
30497437 TAAGTTATAGGTAGGCTAAAAGAAACAAGGATGATTTGACTAAGTG
1 TAAGTTATAGGTAGGCTAAAAGAAACAAGGATGATTTGACTAAGTG
30497483 TAAGTTATAGGTAGGCTAAAAGAAACAAGGATGATTTGACTAAGTG
1 TAAGTTATAGGTAGGCTAAAAGAAACAAGGATGATTTGACTAAGTG
30497529 T
1 T
30497530 GGCATGAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.06, G:0.26, T:0.27
Consensus pattern (46 bp):
TAAGTTATAGGTAGGCTAAAAGAAACAAGGATGATTTGACTAAGTG
Found at i:30497660 original size:18 final size:18
Alignment explanation
Indices: 30497620--30497661 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
30497610 ACACAATCAC
30497620 TTTTTTTTTAATTCACGA
1 TTTTTTTTTAATTCACGA
*
30497638 ATTTTTTTTAATTCAC--
1 TTTTTTTTTAATTCACGA
30497654 TTTTTTTT
1 TTTTTTTT
30497662 AAGTTTCGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 7 0.32
18 15 0.68
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTTTTTAATTCACGA
Found at i:30501916 original size:23 final size:23
Alignment explanation
Indices: 30501884--30501995 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
30501874 CTTTTTGAAC
* *
30501884 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
30501907 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
30501930 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
30501953 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
30501976 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
30501996 CCCAAAACCG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:30501960 original size:46 final size:46
Alignment explanation
Indices: 30501884--30501995 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
30501874 CTTTTTGAAC
* *
30501884 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
30501930 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
30501976 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
30501996 CCCAAAACCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:30502299 original size:15 final size:13
Alignment explanation
Indices: 30502279--30502312 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
30502269 AGAGAGTTCG
*
30502279 AAAAAAAAATTCA
1 AAAAAAAAAATCA
30502292 AAATAAAAAAATCA
1 AAA-AAAAAAATCA
30502306 AAAAAAA
1 AAAAAAA
30502313 TTAAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAAAAATCA
Found at i:30502308 original size:25 final size:25
Alignment explanation
Indices: 30502280--30502327 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
30502270 GAGAGTTCGA
* *
30502280 AAAAAAAATTCAAAATAAAAAAATC
1 AAAAAAAATTAAAAAGAAAAAAATC
30502305 AAAAAAAATTAAAAAGAAAAAAA
1 AAAAAAAATTAAAAAGAAAAAAA
30502328 AAATTGCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.12
Consensus pattern (25 bp):
AAAAAAAATTAAAAAGAAAAAAATC
Found at i:30507749 original size:18 final size:18
Alignment explanation
Indices: 30507728--30507787 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
30507718 GACCTCACTC
30507728 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
30507746 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
30507764 TCTTTTCTTTCGATTTCTTTT
1 TC-TTT-TTT-GATTTCTTTT
30507785 TCT
1 TCT
30507788 CGCACTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 17 0.52
19 3 0.09
20 3 0.09
21 10 0.30
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:30508632 original size:28 final size:29
Alignment explanation
Indices: 30508594--30508648 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
30508584 AAAAGACTTT
*
30508594 TCACTTTTTTTTACTTG-ATTTTTTTTGC
1 TCACTTCTTTTTACTTGAATTTTTTTTGC
**
30508622 TCACTTCTTTTTTTTTGAATTTTTTTT
1 TCACTTCTTTTTACTTGAATTTTTTTT
30508649 ACTTCGTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.11, C:0.13, G:0.05, T:0.71
Consensus pattern (29 bp):
TCACTTCTTTTTACTTGAATTTTTTTTGC
Found at i:30508676 original size:12 final size:12
Alignment explanation
Indices: 30508659--30508684 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
30508649 ACTTCGTACA
30508659 TTTTTTTTCAAT
1 TTTTTTTTCAAT
30508671 TTTTTTTTCAAT
1 TTTTTTTTCAAT
30508683 TT
1 TT
30508685 CCTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:30509646 original size:31 final size:31
Alignment explanation
Indices: 30509610--30509679 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
30509600 ACCGTTTCTA
* *
30509610 TGTGTGAACTAAAGGAAA-TGATCAGGCCTT-G
1 TGTGTGAAC-AAACGAAATTGA-AAGGCCTTAG
*
30509641 TGTGTGAACACACGAAATTGAAAGGCCTTAG
1 TGTGTGAACAAACGAAATTGAAAGGCCTTAG
30509672 TGTGTGAA
1 TGTGTGAA
30509680 GGGGACATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.26
Consensus pattern (31 bp):
TGTGTGAACAAACGAAATTGAAAGGCCTTAG
Found at i:30510163 original size:41 final size:41
Alignment explanation
Indices: 30510115--30510209 Score: 190
Period size: 41 Copynumber: 2.3 Consensus size: 41
30510105 AAACACATTA
30510115 AGTAGCAGCATTAAATTCGTCCAGACATATTTATAACATGT
1 AGTAGCAGCATTAAATTCGTCCAGACATATTTATAACATGT
30510156 AGTAGCAGCATTAAATTCGTCCAGACATATTTATAACATGT
1 AGTAGCAGCATTAAATTCGTCCAGACATATTTATAACATGT
30510197 AGTAGCAGCATTA
1 AGTAGCAGCATTA
30510210 GCTACGAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (41 bp):
AGTAGCAGCATTAAATTCGTCCAGACATATTTATAACATGT
Found at i:30523386 original size:10 final size:10
Alignment explanation
Indices: 30523371--30523432 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
30523361 TTTGAACCAT
*
30523371 TACCAATTCG
1 TACCAATTCA
*
30523381 TACCAAATACCA
1 TACC-AAT-TCA
*
30523393 TACCATTTCA
1 TACCAATTCA
30523403 TACCAATTCCA
1 TACCAATT-CA
* *
30523414 TACCATTTCG
1 TACCAATTCA
30523424 TACCAATTC
1 TACCAATTC
30523433 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:30523416 original size:21 final size:21
Alignment explanation
Indices: 30523371--30523433 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
30523361 TTTGAACCAT
* *
30523371 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
30523393 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
30523414 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
30523434 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:30527160 original size:31 final size:31
Alignment explanation
Indices: 30527124--30527193 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
30527114 ACCGTTTCTA
* *
30527124 TGTGTGAACTAAAGGAAA-TGATCAGGCCTT-G
1 TGTGTGAAC-AAACGAAATTGA-AAGGCCTTAG
*
30527155 TGTGTGAACACACGAAATTGAAAGGCCTTAG
1 TGTGTGAACAAACGAAATTGAAAGGCCTTAG
30527186 TGTGTGAA
1 TGTGTGAA
30527194 GGGAACATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.26
Consensus pattern (31 bp):
TGTGTGAACAAACGAAATTGAAAGGCCTTAG
Done.