Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 106 of 170
Found at i:32975187 original size:16 final size:16
Alignment explanation
Indices: 32975166--32975197 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
32975156 AGGAACTTTA
*
32975166 TAAAATGTGCATCGAT
1 TAAAATATGCATCGAT
32975182 TAAAATATGCATCGAT
1 TAAAATATGCATCGAT
32975198 ATGTCCTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (16 bp):
TAAAATATGCATCGAT
Found at i:32981388 original size:14 final size:15
Alignment explanation
Indices: 32981366--32981442 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
32981356 CAATCAAACA
32981366 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
32981380 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
32981395 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
32981415 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
32981429 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
32981443 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:32981407 original size:20 final size:20
Alignment explanation
Indices: 32981382--32981421 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
32981372 AATATTTTCC
*
32981382 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
32981402 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
32981422 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:32981427 original size:34 final size:35
Alignment explanation
Indices: 32981370--32981436 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
32981360 CAAACACCAG
*
32981370 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
32981405 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
32981437 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:32984156 original size:114 final size:114
Alignment explanation
Indices: 32983951--32984195 Score: 400
Period size: 114 Copynumber: 2.1 Consensus size: 114
32983941 CTTAAGTTTT
*
32983951 AATAATGGAATTGCAATATTTAGAAATTGTAATATTTTCTATAATGGATGGATGTCAAATAATAT
1 AATAATGGAATTGCAATATTTAGAAATTGTAATATTTTCTATAATAGATGGATGTCAAATAATAT
*
32984016 CTACTTTATCAAATCAAAGATCTACACATTGATTGAAACTAAAATATCG
66 CTACTTTATCAAATCAAAGATCTACACATTGATTGAAACTAAAATATCA
* *
32984065 AATAATGGAATTGCAATATTTAGAAATTGTAATATTTTCTGTAATAGATGGATGTTAAATAATAT
1 AATAATGGAATTGCAATATTTAGAAATTGTAATATTTTCTATAATAGATGGATGTCAAATAATAT
* * * * *
32984130 CTACTTTATCAAATCAAAGATGTACACATTGTTTGAGACTGAAATATTA
66 CTACTTTATCAAATCAAAGATCTACACATTGATTGAAACTAAAATATCA
*
32984179 AATAATAGAATTGCAAT
1 AATAATGGAATTGCAAT
32984196 TTTTTCTGTA
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 121 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (114 bp):
AATAATGGAATTGCAATATTTAGAAATTGTAATATTTTCTATAATAGATGGATGTCAAATAATAT
CTACTTTATCAAATCAAAGATCTACACATTGATTGAAACTAAAATATCA
Found at i:32984203 original size:98 final size:94
Alignment explanation
Indices: 32984089--32984268 Score: 270
Period size: 94 Copynumber: 1.9 Consensus size: 94
32984079 AATATTTAGA
* * *
32984089 AATTGTAATATTTTCTGTAATAGATGGATGTTAAATAATATCTACTTTATCAAATCAAAGATGTA
1 AATTGCAATATTTTCTGTAAT--A--GATGTCAAATAATATCTACCTTATCAAATCAAAGATGTA
*
32984154 CACATTGTTTGAGACTGAAATATTAAATAATAG
62 CACATTATTTGAGACTGAAATATTAAATAATAG
*
32984187 AATTGCAATTTTTTCTGTAATAGATGTCAAATAATATCTACCTTATCAAATCAAAGATGTACACA
1 AATTGCAATATTTTCTGTAATAGATGTCAAATAATATCTACCTTATCAAATCAAAGATGTACACA
*
32984252 TTATTTGAGATTGAAAT
66 TTATTTGAGACTGAAAT
32984269 CTAGAATAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 56 0.74
96 1 0.01
98 19 0.25
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (94 bp):
AATTGCAATATTTTCTGTAATAGATGTCAAATAATATCTACCTTATCAAATCAAAGATGTACACA
TTATTTGAGACTGAAATATTAAATAATAG
Found at i:32996441 original size:46 final size:47
Alignment explanation
Indices: 32996384--32996477 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
32996374 GACCCAAGCC
* *
32996384 CCGTTATAACCTAAC-AAAACCCTTTGATCTTTGCATCCGATTCTAA
1 CCGTTACAACCTAACAAAAACCCTTTGATCTTTACATCCGATTCTAA
32996430 CCGTTACAACCTAACAAAAACCCTTTGATCTTTACATCCGATTCTAA
1 CCGTTACAACCTAACAAAAACCCTTTGATCTTTACATCCGATTCTAA
32996477 C
1 C
32996478 TCTAGTGGTG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 14 0.31
47 31 0.69
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.31
Consensus pattern (47 bp):
CCGTTACAACCTAACAAAAACCCTTTGATCTTTACATCCGATTCTAA
Found at i:32997629 original size:13 final size:13
Alignment explanation
Indices: 32997611--32997635 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32997601 TAAGTTTTTT
32997611 TTATATTATTATC
1 TTATATTATTATC
32997624 TTATATTATTAT
1 TTATATTATTAT
32997636 TTAATTTCAT
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:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATATTATTATC
Found at i:33001929 original size:6 final size:6
Alignment explanation
Indices: 33001917--33001975 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
33001907 AAATATTTCA
* * * *
33001917 AAAAATG AAAATG ATAAA- AAAAAG AAAAAG AGAAGG AAAAAG -AAAAG
1 AAAAA-G AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
33001964 AAAAAG AAAAAG
1 AAAAAG AAAAAG
33001976 GAGAGGCCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
5 9 0.21
6 29 0.69
7 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:33001939 original size:30 final size:30
Alignment explanation
Indices: 33001880--33001938 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
33001870 ATCAAAAGAG
33001880 TATTTCAAAAAAATAAAAAAAATAAAAAAA
1 TATTTCAAAAAAATAAAAAAAATAAAAAAA
* **
33001910 TATTTC-AAAAAATGAAAATGATAAAAAAA
1 TATTTCAAAAAAATAAAAAAAATAAAAAAA
33001939 AGAAAAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.22
Consensus pattern (30 bp):
TATTTCAAAAAAATAAAAAAAATAAAAAAA
Found at i:33001955 original size:12 final size:11
Alignment explanation
Indices: 33001917--33001973 Score: 62
Period size: 11 Copynumber: 4.9 Consensus size: 11
33001907 AAATATTTCA
33001917 AAAAATGAAAATG
1 AAAAA-GAAAA-G
33001930 ATAAAA-AAAAG
1 A-AAAAGAAAAG
*
33001941 AAAAAGAGAAGG
1 AAAAAGA-AAAG
33001953 AAAAAGAAAAG
1 AAAAAGAAAAG
33001964 AAAAAGAAAA
1 AAAAAGAAAA
33001974 AGGAGAGGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 4 0.10
11 16 0.41
12 14 0.36
13 1 0.03
14 4 0.10
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:33003836 original size:24 final size:24
Alignment explanation
Indices: 33003799--33003860 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
33003789 TTTATGTCTC
*
33003799 AAAAGTACAGTGGATTGAACCTTG
1 AAAATTACAGTGGATTGAACCTTG
*
33003823 AAGATTACAGTGGATTGAACCTTG
1 AAAATTACAGTGGATTGAACCTTG
33003847 AAAATTACAGTGGA
1 AAAATTACAGTGGA
33003861 GGCAATCTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAATTACAGTGGATTGAACCTTG
Found at i:33004243 original size:44 final size:43
Alignment explanation
Indices: 33004186--33004709 Score: 289
Period size: 44 Copynumber: 11.8 Consensus size: 43
33004176 GAAGATGGTG
*
33004186 AATCTTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAACCAAT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAA-CAAT
* * *** *
33004230 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTTAC
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACAAT
* ** * * *
33004273 AAGTCTTTTCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAAAAC
1 AA-TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA-ACAAT
* * * * * ***
33004318 AAGTCTTATCCCCCTAAAGTTGTAGTGGGGCAGAATGAAGATGGT
1 AA-TCTTATCTCCCTGAAGTTGTAGTGGAGCAG-ATTAAAACAAT
* * * * *
33004363 GAATTTTATCTCCTTGAAGTTGTAGTGGAGCAAATTAAAGCCGAT
1 -AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA-ACAAT
* * * *** *
33004408 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTGAC
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACAAT
* * * **
33004451 AAGTTTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGATAGCG
1 AA-TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA-ACA-AT
* * * * *
33004497 AATCTTATTTCTCTGTAGTTGTAGTGGAACAGATTAAAGCTATAAAT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA---A-CAAT
* * * * ***
33004544 CACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCATGGAA-
1 ---A-ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACAAT
** **
33004589 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTACAGCCAAT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTA-AAACAAT
* * * **
33004633 AAT-TCTATCTCCTTGAAGTTGTAGTGGAGCGGATTGAAGACACC
1 AATCT-TATCTCCCTGAAGTTGTAGTGGAGCAGATT-AAAACAAT
* *
33004677 ACTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGA
33004710 CTGAAGATAG
Statistics
Matches: 364, Mismatches: 95, Indels: 42
0.73 0.19 0.08
Matches are distributed among these distances:
41 29 0.08
42 2 0.01
43 11 0.03
44 192 0.53
45 89 0.24
46 9 0.02
47 1 0.00
48 1 0.00
50 3 0.01
51 27 0.07
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACAAT
Found at i:33004490 original size:88 final size:88
Alignment explanation
Indices: 33004190--33004490 Score: 345
Period size: 88 Copynumber: 3.4 Consensus size: 88
33004180 ATGGTGAATC
* * *
33004190 TTATCTCCCTGAAGTTGTAGTAGAGCAGATTAAAACCAATAATCCTATCTCCCTGAAGTTGTAGT
1 TTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGCCAATAATCCTATCTCCCTGAAGTTGTAGT
*
33004255 GGAGCGGATTAAAGTTACAAGTCT
66 GGAGCGGATTAAAGTGACAAGT-T
** ** * * * *
33004279 TT-TCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAAAACAAGTCTTATCCCCCTAAAGTTGTAG
1 TTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGCCAATAA-TCCTATCTCCCTGAAGTTGTAG
* * * * **
33004343 TGGGGCAGAATGAAGATGGTGAA-TT
65 TGGAGCGGATTAAAG-T-GACAAGTT
* * * * *
33004368 TTATCTCCTTGAAGTTGTAGTGGAGCAAATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGCCAATAATCCTATCTCCCTGAAGTTGTAGT
33004433 GGAGCGGATTAAAGTGACAAGTT
66 GGAGCGGATTAAAGTGACAAGTT
33004456 TTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAG
1 TTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAG
33004491 ATAGCGAATC
Statistics
Matches: 167, Mismatches: 40, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
87 3 0.02
88 66 0.40
89 64 0.38
90 32 0.19
91 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (88 bp):
TTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGCCAATAATCCTATCTCCCTGAAGTTGTAGT
GGAGCGGATTAAAGTGACAAGTT
Found at i:33004533 original size:133 final size:134
Alignment explanation
Indices: 33004281--33004536 Score: 327
Period size: 133 Copynumber: 1.9 Consensus size: 134
33004271 ACAAGTCTTT
33004281 TCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAAAACAAGTCTTATCCCCCTAAAGTTGTAGTGG
1 TCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAAAACAAGTCTTATCCCCCTAAAGTTGTAGTGG
* * * * * *
33004346 GGCAGAATGAAGATGGTGAATTTTATCTCCTTGAAGTTGTAGTGGAGCAAATTAAAGCCGATAAT
66 AGCAGAATAAAGATAGCGAATCTTATCTCCTTGAAGTTGTAGTGGAACAAATTAAAGCCGATAAT
33004411 CCTA
131 CCTA
* * * ** * * *
33004415 TCTCCCTGAAGTTGCAGTGGAGCGGATTAAAG-TGACAAGTTTTATCTCCCTGAAGTTGTAGTGG
1 TCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAAAACAAGTCTTATCCCCCTAAAGTTGTAGTGG
* * * *
33004479 AGCAGACTAAAGATAGCGAATCTTAT-TTCTCTGTAGTTGTAGTGGAACAGATTAAAGC
66 AGCAGAATAAAGATAGCGAATCTTATCTCCT-TGAAGTTGTAGTGGAACAAATTAAAGC
33004537 TATAAATCAC
Statistics
Matches: 103, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
132 3 0.03
133 71 0.69
134 29 0.28
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (134 bp):
TCTCCCTGAAGTTACAGTGGAGCAGACTAAAGAAAACAAGTCTTATCCCCCTAAAGTTGTAGTGG
AGCAGAATAAAGATAGCGAATCTTATCTCCTTGAAGTTGTAGTGGAACAAATTAAAGCCGATAAT
CCTA
Found at i:33004606 original size:41 final size:42
Alignment explanation
Indices: 33004549--33004796 Score: 145
Period size: 44 Copynumber: 5.8 Consensus size: 42
33004539 TAAATCACAG
*
33004549 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATGGAA-A
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCATGGAACA
* * * *
33004590 ATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTACA-GCCAATA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-T-CATG-GAACA
* * * *
33004634 AT-TCTATCTCCTTGAAGTTGTAGTGGAGCGGAT--TGAAGACACCA
1 ATCT-TATCTCCCTGAAGTTGCAGTAGAGCAGATCATG--GA-A-CA
* * *
33004678 CTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-C-TGAAGATAGCGG
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCATG--GA-A-C-A
* * *
33004723 GTCTTATCTCTCTGAAGTTGCAGTAGAGCAGACCAT--AACA
1 ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCATGGAACA
* * *
33004763 AGTCCTATCCCCCTGAAGTTGCAGTAGGGCAGAT
1 A-TCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT
33004797 TGAATATAGC
Statistics
Matches: 164, Mismatches: 28, Indels: 30
0.74 0.13 0.14
Matches are distributed among these distances:
41 58 0.35
42 4 0.02
43 8 0.05
44 62 0.38
45 30 0.18
46 1 0.01
47 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (42 bp):
ATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCATGGAACA
Found at i:33004715 original size:44 final size:43
Alignment explanation
Indices: 33004544--33004755 Score: 157
Period size: 44 Copynumber: 4.9 Consensus size: 43
33004534 AGCTATAAAT
* *
33004544 CACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATG--GA
1 CACA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-C-TGAAGA
* * *
33004588 -A-AATCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TTACAGC
1 CACAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA-AGA
* * * * *
33004629 CAATAAT-TCTATCTCCTTGAAGTTGTAGTGGAGCGGATTGAAGA
1 C-ACAATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
*
33004673 CACCACTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
1 CA-CAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
* ** * *
33004717 TAGCGGGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGAC
1 CA-C-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
33004756 CATAACAAGT
Statistics
Matches: 134, Mismatches: 23, Indels: 21
0.75 0.13 0.12
Matches are distributed among these distances:
38 1 0.01
41 30 0.22
42 1 0.01
43 4 0.03
44 65 0.49
45 33 0.25
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (43 bp):
CACAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
Found at i:33006378 original size:13 final size:13
Alignment explanation
Indices: 33006360--33006384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33006350 TTTAAGTTTT
33006360 TTATATTATTATA
1 TTATATTATTATA
33006373 TTATATTATTAT
1 TTATATTATTAT
33006385 TTAATTTCAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATATTATTATA
Found at i:33013490 original size:45 final size:46
Alignment explanation
Indices: 33013420--33013515 Score: 124
Period size: 45 Copynumber: 2.1 Consensus size: 46
33013410 CCCTTGATCA
* *
33013420 AGTATAGATAATTAATAATAAATACTATCTAATTTAGTTAA-ATTT
1 AGTATAAATAATTAATAATAAATACTATCTAATTTAGGTAATATTT
* *
33013465 AGTATAAATAATTTAA-AATATATACTATGTAATTTAGGTAATTATTT
1 AGTATAAATAA-TTAATAATAAATACTATCTAATTTAGGTAA-TATTT
33013512 AGTA
1 AGTA
33013516 GGTCAAATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
45 32 0.73
46 4 0.09
47 8 0.18
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (46 bp):
AGTATAAATAATTAATAATAAATACTATCTAATTTAGGTAATATTT
Found at i:33017248 original size:162 final size:163
Alignment explanation
Indices: 33016980--33017293 Score: 549
Period size: 162 Copynumber: 1.9 Consensus size: 163
33016970 AAAATATTGT
* * * *
33016980 ATGTGAAACTTTGAAATTGTACCACATCATCACTTGAAAATTCATATAATTTTTTTAAATTTTCT
1 ATGTGAAACTTTGAAATTGTACCACATCATCACCTAAAAATTCATATAATATTTTTAAATTTTCA
* *
33017045 AGTGATGATGTAGCACAATCTCATAGTGCCACATCATCAAACTTTTATAGTTTTCAAGTTTGGGA
66 AGTGATGATGTAGCACAATCTCATAATGCCACATCATCAAACTTTTATAGGTTTCAAGTTTGGGA
33017110 CTAAAATGGACTCAGTTGTCAAATTTAAGTGCC
131 CTAAAATGGACTCAGTTGTCAAATTTAAGTGCC
*
33017143 ATGTGAAACTTTGAAATTGTATCACATCATCACCTAAAAATTCATAT-ATATTTTTAAATTTTCA
1 ATGTGAAACTTTGAAATTGTACCACATCATCACCTAAAAATTCATATAATATTTTTAAATTTTCA
*
33017207 AGTGATGATGTTGCACAATCTCATAATGCCACATCATCAAACTTTTATAGGTTTCAAGTTTGGGA
66 AGTGATGATGTAGCACAATCTCATAATGCCACATCATCAAACTTTTATAGGTTTCAAGTTTGGGA
33017272 CTAAAATGGACTCAGTTGTCAA
131 CTAAAATGGACTCAGTTGTCAA
33017294 GTTGGTACCT
Statistics
Matches: 143, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
162 99 0.69
163 44 0.31
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (163 bp):
ATGTGAAACTTTGAAATTGTACCACATCATCACCTAAAAATTCATATAATATTTTTAAATTTTCA
AGTGATGATGTAGCACAATCTCATAATGCCACATCATCAAACTTTTATAGGTTTCAAGTTTGGGA
CTAAAATGGACTCAGTTGTCAAATTTAAGTGCC
Found at i:33019164 original size:18 final size:18
Alignment explanation
Indices: 33019141--33019176 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
33019131 TTTTCATACT
33019141 CTTCATCATCTTCTTCTC
1 CTTCATCATCTTCTTCTC
*
33019159 CTTCATCTTCTTCTTCTC
1 CTTCATCATCTTCTTCTC
33019177 AGCATAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.39, G:0.00, T:0.53
Consensus pattern (18 bp):
CTTCATCATCTTCTTCTC
Found at i:33020819 original size:2 final size:2
Alignment explanation
Indices: 33020812--33020837 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33020802 TAATTTTCTT
33020812 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
33020838 ACACTCCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:33021488 original size:73 final size:75
Alignment explanation
Indices: 33021406--33021549 Score: 265
Period size: 73 Copynumber: 1.9 Consensus size: 75
33021396 CCACAATCTC
33021406 ATTTTATATGATTGTAAAAGAAATATATCAGATTAGACTGCAACTTGTCACATTA-TC-AATAAT
1 ATTTTATATGATTGTAAAAGAAATATATCAGATTAGACTGCAACTTGTCACATTAGTCGAATAAT
33021469 TGATTACTCT
66 TGATTACTCT
33021479 ATTTTATATGATTGTAAAAGAAATATATCAGATTAGACTGCAACTTGTCACATTAGTCGTAATAA
1 ATTTTATATGATTGTAAAAGAAATATATCAGATTAGACTGCAACTTGTCACATTAGTCG-AATAA
33021544 TTGATT
65 TTGATT
33021550 GAAACTATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
73 55 0.81
74 2 0.03
76 11 0.16
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (75 bp):
ATTTTATATGATTGTAAAAGAAATATATCAGATTAGACTGCAACTTGTCACATTAGTCGAATAAT
TGATTACTCT
Found at i:33028730 original size:83 final size:82
Alignment explanation
Indices: 33028587--33028749 Score: 211
Period size: 83 Copynumber: 2.0 Consensus size: 82
33028577 TTAGAGGGCT
* * * *
33028587 AAAGTATAATTTTACTATATATTAATTAACAATTTCTTTATTTATAAGAGGACTATATTGAAAAA
1 AAAGTACAATTTCACTATATATTAATTAACAAATTCTCTATTTATAAGAGGACTATATTG-AAAA
33028652 TTTTAATTTTAAGGGGTC
65 TTTTAATTTTAAGGGGTC
* * * *
33028670 AAAGTACAATTTCACTATATATTAATTTATAAATTCTCTATTTATAAGAGGATTGA-ATTGAAAT
1 AAAGTACAATTTCACTATATATTAATTAACAAATTCTCTATTTATAAGAGGACT-ATATTGAAAA
* *
33028734 TTTTATTTTTGAGGGG
65 TTTTAATTTTAAGGGG
33028750 CCAAGGTGTA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
82 17 0.25
83 51 0.74
84 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (82 bp):
AAAGTACAATTTCACTATATATTAATTAACAAATTCTCTATTTATAAGAGGACTATATTGAAAAT
TTTAATTTTAAGGGGTC
Found at i:33031913 original size:13 final size:13
Alignment explanation
Indices: 33031895--33031919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33031885 ACTTACAAAT
33031895 TTTTTTAAATATA
1 TTTTTTAAATATA
33031908 TTTTTTAAATAT
1 TTTTTTAAATAT
33031920 TTTCAATTCT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTAAATATA
Found at i:33036196 original size:17 final size:18
Alignment explanation
Indices: 33036174--33036208 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
33036164 CGAATTGGGC
33036174 CGTGTGGG-CCACACGGG
1 CGTGTGGGCCCACACGGG
33036191 CGTGTGGGCCCACACGGG
1 CGTGTGGGCCCACACGGG
33036209 TGAACCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.11, C:0.31, G:0.46, T:0.11
Consensus pattern (18 bp):
CGTGTGGGCCCACACGGG
Found at i:33041530 original size:34 final size:32
Alignment explanation
Indices: 33041491--33041602 Score: 116
Period size: 34 Copynumber: 3.3 Consensus size: 32
33041481 ATTATGTATT
*
33041491 TAATAGAACAATACAGTAGTAATAAATATGCTTA
1 TAATAGATCAATACAGTA-TAAT-AATATGCTTA
* *
33041525 TAATAGTTCAATACAATATCAATTAATATGCTTA
1 TAATAGATCAATACAGTAT-AA-TAATATGCTTA
* * *
33041559 TAACAGTTCAATACAGTAACAAGTAATATGCTTA
1 TAATAGATCAATACAGT-ATAA-TAATATGCTTA
33041593 TAATAGATCA
1 TAATAGATCA
33041603 GCTTAGTAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
33 1 0.02
34 63 0.95
35 2 0.03
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (32 bp):
TAATAGATCAATACAGTATAATAATATGCTTA
Found at i:33045666 original size:24 final size:26
Alignment explanation
Indices: 33045637--33045684 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
33045627 ATATCAGAGA
*
33045637 AAAATACT-ATACA-TAGTTATACTG
1 AAAATACTAATAAAGTAGTTATACTG
*
33045661 AAAATAGTAATAAAGTAGTTATAC
1 AAAATACTAATAAAGTAGTTATAC
33045685 AAAATATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 4 0.20
26 9 0.45
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.31
Consensus pattern (26 bp):
AAAATACTAATAAAGTAGTTATACTG
Found at i:33046041 original size:99 final size:99
Alignment explanation
Indices: 33045870--33046066 Score: 394
Period size: 99 Copynumber: 2.0 Consensus size: 99
33045860 TTCCTCGGAG
33045870 ACGAACAAAAGTCTACAAATCTAAACATGAAGACAATTTGGAGATTGAGCTTTACAAGCTTAGTG
1 ACGAACAAAAGTCTACAAATCTAAACATGAAGACAATTTGGAGATTGAGCTTTACAAGCTTAGTG
33045935 GTACACAACAAATCTACCATATTTCAAGCAATTC
66 GTACACAACAAATCTACCATATTTCAAGCAATTC
33045969 ACGAACAAAAGTCTACAAATCTAAACATGAAGACAATTTGGAGATTGAGCTTTACAAGCTTAGTG
1 ACGAACAAAAGTCTACAAATCTAAACATGAAGACAATTTGGAGATTGAGCTTTACAAGCTTAGTG
33046034 GTACACAACAAATCTACCATATTTCAAGCAATT
66 GTACACAACAAATCTACCATATTTCAAGCAATT
33046067 TATAAATATA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (99 bp):
ACGAACAAAAGTCTACAAATCTAAACATGAAGACAATTTGGAGATTGAGCTTTACAAGCTTAGTG
GTACACAACAAATCTACCATATTTCAAGCAATTC
Found at i:33049831 original size:31 final size:31
Alignment explanation
Indices: 33049765--33049832 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
33049755 AATTTTTTTT
* * *
33049765 ATTTTTGTGCAAATATACACATTAAAGTTTG
1 ATTTTTGTGCAAATATACACATAAAACTTTA
* *
33049796 ATTTTTGTTG-AAATATATATATAAAACTTTA
1 ATTTTTG-TGCAAATATACACATAAAACTTTA
33049827 ATTTTT
1 ATTTTT
33049833 ATTAATTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (31 bp):
ATTTTTGTGCAAATATACACATAAAACTTTA
Found at i:33054503 original size:14 final size:14
Alignment explanation
Indices: 33054484--33054513 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
33054474 TACTAAGAAC
33054484 ATTGTTAAGAATAT
1 ATTGTTAAGAATAT
33054498 ATTGTTAAGAATAT
1 ATTGTTAAGAATAT
33054512 AT
1 AT
33054514 GTCATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
ATTGTTAAGAATAT
Found at i:33060006 original size:26 final size:25
Alignment explanation
Indices: 33059952--33060006 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
33059942 ATGTATTTTG
* *
33059952 TTTTATTATCTATGATATATGCATG
1 TTTTATTATCTATGATATATACATA
33059977 TTTTATTATCTCAAT-ATATATACATA
1 TTTTATTATCT--ATGATATATACATA
33060003 TTTT
1 TTTT
33060007 GTAATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 11 0.42
26 13 0.50
27 2 0.08
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55
Consensus pattern (25 bp):
TTTTATTATCTATGATATATACATA
Found at i:33060120 original size:18 final size:18
Alignment explanation
Indices: 33060097--33060132 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
33060087 TACTACACTT
33060097 TATACC-TTATATGATTTA
1 TATACCTTTATAT-ATTTA
33060115 TATACCTTTATATATTTA
1 TATACCTTTATATATTTA
33060133 AGAACTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.33, C:0.11, G:0.03, T:0.53
Consensus pattern (18 bp):
TATACCTTTATATATTTA
Found at i:33060966 original size:17 final size:18
Alignment explanation
Indices: 33060930--33060967 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
33060920 AACTTATTGT
*
33060930 TTTAATAAAATCAGACCA
1 TTTAATAAAAACAGACCA
*
33060948 TTTATTAAAAACA-ACCA
1 TTTAATAAAAACAGACCA
33060965 TTT
1 TTT
33060968 TTTGAGGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (18 bp):
TTTAATAAAAACAGACCA
Found at i:33062988 original size:17 final size:15
Alignment explanation
Indices: 33062966--33063007 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
33062956 TTCATTTTTC
33062966 TTGTTACTTATTATTAT
1 TTGTTA-TTATTATT-T
33062983 TTGTTATT-TTATTT
1 TTGTTATTATTATTT
*
33062997 TTCTTATTATT
1 TTGTTATTATT
33063008 GTCAGTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 8 0.35
15 7 0.30
16 2 0.09
17 6 0.26
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (15 bp):
TTGTTATTATTATTT
Found at i:33063033 original size:14 final size:14
Alignment explanation
Indices: 33063014--33063047 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
33063004 TATTGTCAGT
33063014 TTTATTATCATTAG
1 TTTATTATCATTAG
* *
33063028 TTTATTATTATTTG
1 TTTATTATCATTAG
33063042 TTTATT
1 TTTATT
33063048 GTTTTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTATTATCATTAG
Found at i:33063151 original size:3 final size:3
Alignment explanation
Indices: 33063129--33063195 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
33063119 TGTTTACTCG
* * * * *
33063129 TAT TAT TTT TAAT TAG TAT TAT TAG TAT TAG TAT TAT TTT TACT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
33063176 TAT T-T TAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
33063196 TAGTACTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
2 4 0.08
3 41 0.82
4 5 0.10
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:33063185 original size:8 final size:8
Alignment explanation
Indices: 33063172--33063196 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
33063162 TTATTTTTAC
33063172 TTATTATT
1 TTATTATT
33063180 TTATTATT
1 TTATTATT
33063188 TTATTATT
1 TTATTATT
33063196 T
1 T
33063197 AGTACTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTATT
Found at i:33064734 original size:26 final size:23
Alignment explanation
Indices: 33064691--33064742 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 23
33064681 CTGATTTTAT
*
33064691 TTTTAGTTTTATTTTTTATTTTGC
1 TTTTAGTTTTAATTTTTATTTT-C
33064715 TTTTAGTTGTTTAATTTTTATTTTC
1 TTTTAG-T-TTTAATTTTTATTTTC
33064740 TTT
1 TTT
33064743 GACTTATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 5 0.20
26 14 0.56
ACGTcount: A:0.13, C:0.04, G:0.08, T:0.75
Consensus pattern (23 bp):
TTTTAGTTTTAATTTTTATTTTC
Found at i:33064761 original size:26 final size:26
Alignment explanation
Indices: 33064698--33064761 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
33064688 TATTTTTAGT
* * * *
33064698 TTTATTTTTTATTTTGCTTTTAGTTG
1 TTTAATTTTTATTTTGCTTTGACTTA
33064724 TTTAATTTTTATTTT-CTTTGACTTA
1 TTTAATTTTTATTTTGCTTTGACTTA
*
33064749 TTTCATTTATTAT
1 TTTAATTT-TTAT
33064762 CTTTTGAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.70
Consensus pattern (26 bp):
TTTAATTTTTATTTTGCTTTGACTTA
Found at i:33076308 original size:19 final size:17
Alignment explanation
Indices: 33076264--33076300 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
33076254 TTAAAACCTT
*
33076264 AAACCCTAATTCTTAAA
1 AAACCTTAATTCTTAAA
33076281 AAACCTTAATTCTTAAA
1 AAACCTTAATTCTTAAA
33076298 AAA
1 AAA
33076301 AATCTTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (17 bp):
AAACCTTAATTCTTAAA
Found at i:33076906 original size:42 final size:42
Alignment explanation
Indices: 33076858--33076942 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
33076848 GTTTTATTTT
33076858 TAATTATAGTAATTTACATAAAATAATTTTTTATTTGAATTA
1 TAATTATAGTAATTTACATAAAATAATTTTTTATTTGAATTA
33076900 TAATTATAGTAATTTACATAAAATAATTTTTTATTTGAATTA
1 TAATTATAGTAATTTACATAAAATAATTTTTTATTTGAATTA
33076942 T
1 T
33076943 TGAATATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (42 bp):
TAATTATAGTAATTTACATAAAATAATTTTTTATTTGAATTA
Found at i:33077590 original size:28 final size:28
Alignment explanation
Indices: 33077559--33077632 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 28
33077549 GAAAATTTTA
* *
33077559 TAAAAATTTGAGAAAAGCATTTAAATTT
1 TAAAATTTTGAAAAAAGCATTTAAATTT
* ** *
33077587 TAAATTTTTGAAAAAAAATATTTAGATTT
1 TAAAATTTTG-AAAAAAGCATTTAAATTT
33077616 TAAAATTTTGAAAAAAG
1 TAAAATTTTGAAAAAAG
33077633 AAAACTTAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 14 0.38
29 23 0.62
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (28 bp):
TAAAATTTTGAAAAAAGCATTTAAATTT
Found at i:33077624 original size:30 final size:28
Alignment explanation
Indices: 33077577--33077646 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
33077567 TGAGAAAAGC
33077577 ATTTAAATTTTAAATTTTTGAAAAAAAAT
1 ATTTAAATTTTAAA-TTTTGAAAAAAAAT
* *
33077606 ATTTAGATTTTAAAATTTTGAAAAAAGAAA
1 ATTTAAATTTT-AAATTTTGAAAAAA-AAT
*
33077636 ACTTAAATTTT
1 ATTTAAATTTT
33077647 CAAAATTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (28 bp):
ATTTAAATTTTAAATTTTGAAAAAAAAT
Found at i:33080891 original size:43 final size:42
Alignment explanation
Indices: 33080738--33080892 Score: 127
Period size: 43 Copynumber: 3.6 Consensus size: 42
33080728 TGATATCGTA
*
33080738 TAAGACCACATCTGGGACGTTGGCATCG-ATTTGAGATTTATGTG
1 TAAGACCACATCTGGGACGTTGGCATCGTATTTGA-A--TACGTG
** * * * * *
33080782 TAAGACCATGTCTGGGACATTGGCATCATATATGATTTCGTG
1 TAAGACCACATCTGGGACGTTGGCATCGTATTTGAATACGTG
* * *
33080824 TAAGACC-CTATTTGGGATAG-TGGCATCGTTATTTGAATACATG
1 TAAGACCAC-ATCTGGGA-CGTTGGCATCG-TATTTGAATACGTG
*
33080867 TAAGACCACGTCTGGGACGTTGGCAT
1 TAAGACCACATCTGGGACGTTGGCAT
33080893 TGTACGAGCT
Statistics
Matches: 84, Mismatches: 21, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
42 25 0.30
43 29 0.35
44 25 0.30
45 5 0.06
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (42 bp):
TAAGACCACATCTGGGACGTTGGCATCGTATTTGAATACGTG
Found at i:33084796 original size:48 final size:48
Alignment explanation
Indices: 33084740--33084833 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
33084730 AGGGAATTCT
* * *
33084740 GTTGAATCCTTTATTGTTGCG-AATT-GAGCTAACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTG-GAAATTAG-GCTAACTTAGGCATTTTTACG
*
33084788 GTTGAATCCATTATTGGTGGAAATTAGGCTGACTTAGGCATTTTTA
1 GTTGAATCCATTATTGGTGGAAATTAGGCTAACTTAGGCATTTTTA
33084834 AGCCAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 1 0.03
48 38 0.95
49 1 0.03
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGGAAATTAGGCTAACTTAGGCATTTTTACG
Found at i:33097576 original size:17 final size:17
Alignment explanation
Indices: 33097554--33097587 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
33097544 TTGTGTATGA
33097554 ACATGAGCTACAGGATG
1 ACATGAGCTACAGGATG
33097571 ACATGAGCTACAGGATG
1 ACATGAGCTACAGGATG
33097588 TTCAACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (17 bp):
ACATGAGCTACAGGATG
Found at i:33100624 original size:18 final size:18
Alignment explanation
Indices: 33100577--33100624 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
33100567 GAAAAACATA
33100577 AATAAAAATA-A-AAAAT
1 AATAAAAATATATAAAAT
*
33100593 ACATAAAAATATATAAATT
1 A-ATAAAAATATATAAAAT
33100612 AATAAAAATATAT
1 AATAAAAATATAT
33100625 TTTTTTCTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 1 0.04
17 9 0.32
18 13 0.46
19 5 0.18
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAAAAATATATAAAAT
Found at i:33102159 original size:97 final size:100
Alignment explanation
Indices: 33102046--33102254 Score: 325
Period size: 97 Copynumber: 2.1 Consensus size: 100
33102036 AAGAAAAACG
* *
33102046 AAAAAAAAATTTGGGTGCTGGCCTGACAATTGCCAGCACCCAGTACAA-TTT-AAAAAAAAA-TT
1 AAAAAAAAATTAGGGTGCTGGCCTGACAATGGCCAGCACCCAGTACAATTTTAAAAAAAAAATTT
*
33102108 TGTGTCAGAGTCAGATATCAGTATACGAAAAAAAT
66 TGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
* * * *
33102143 AAAAAAAAATTAGGGTGTTGGCCTGTCAATGGCCGGCACCTAGTACAATTTTAAAAAAAAAATTT
1 AAAAAAAAATTAGGGTGCTGGCCTGACAATGGCCAGCACCCAGTACAATTTTAAAAAAAAAATTT
33102208 TGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
66 TGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
33102243 AAAAGAAAAATT
1 AAAA-AAAAATT
33102255 TTCGTATACT
Statistics
Matches: 101, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
97 42 0.42
98 3 0.03
99 9 0.09
100 40 0.40
101 7 0.07
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.24
Consensus pattern (100 bp):
AAAAAAAAATTAGGGTGCTGGCCTGACAATGGCCAGCACCCAGTACAATTTTAAAAAAAAAATTT
TGTGTCAGAATCAGATATCAGTATACGAAAAAAAT
Found at i:33102709 original size:108 final size:108
Alignment explanation
Indices: 33102267--33102693 Score: 530
Period size: 110 Copynumber: 4.0 Consensus size: 108
33102257 CGTATACTGA
33102267 TTTTTATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAAGAAAAAAAATTTT-A
1 TTTTTATTTTTTTCGTATACTGATATCTGATTCTGACAC--AAAAAAAAAG-AAAAAAATTTTAA
* * * * **
33102331 A-TATATTGGGTGCCGGCCAATGACAGGCCTGCACCCAAAATTTTT
63 ATTGTACTGGGTGCCAGCCATTGACAGGCCAACACCCAAAATTTTT
* *** *
33102376 TTTTTATTTTTTTCGTATACTGATATTTGATTCTGACACAAAAAAAAAGAAAATTTTTTTTTAAT
1 TTTTTATTTTTTTCGTATACTGATATCTGATTCTGACACAAAAAAAAAGAAAA--AAATTTTAAA
* *
33102441 TTGTACTGGGTGCCAGCCATTGATAGGCCAGCACCCAAAATTTTT
64 TTGTACTGGGTGCCAGCCATTGACAGGCCAACACCCAAAATTTTT
* *
33102486 TTTTTATTTTTTTCATATACTGATATCTGATTCTGAGC-C--AAAAAAAGAAAAAAA-ATTAAAT
1 TTTTTATTTTTTTCGTATACTGATATCTGATTCTGA-CACAAAAAAAAAGAAAAAAATTTTAAAT
*
33102547 TGTACTGGGTGCCAGCCATTGACAGGCCAACA-CC-AATTTTTT
65 TGTACTGGGTGCCAGCCATTGACAGGCCAACACCCAAAATTTTT
33102589 TTTTTA-TTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAAGAAAAAAATTTTAAAA
1 TTTTTATTTTTTTCGTATACTGATATCTGATTCTGACAC-AAAAAAAAAGAAAAAAATTTT--AA
* * * *
33102653 ATTGTATTGGGTACCGGCCATTGACAGGCCAACACCAAAAA
63 ATTGTACTGGGTGCCAGCCATTGACAGGCCAACACCCAAAA
33102694 AAAAATTTCG
Statistics
Matches: 276, Mismatches: 28, Indels: 27
0.83 0.08 0.08
Matches are distributed among these distances:
101 1 0.00
102 29 0.11
103 13 0.05
104 2 0.01
105 50 0.18
106 6 0.02
107 10 0.04
108 49 0.18
109 40 0.14
110 75 0.27
111 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (108 bp):
TTTTTATTTTTTTCGTATACTGATATCTGATTCTGACACAAAAAAAAAGAAAAAAATTTTAAATT
GTACTGGGTGCCAGCCATTGACAGGCCAACACCCAAAATTTTT
Found at i:33106921 original size:17 final size:17
Alignment explanation
Indices: 33106901--33106948 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
33106891 AATCGCCACC
33106901 AATATTCTTTGGTTTGT
1 AATATTCTTTGGTTTGT
** *
33106918 AATATTCTGTTTATTTTT
1 AATATTCT-TTGGTTTGT
*
33106936 TATATTCTTTGGT
1 AATATTCTTTGGT
33106949 ATGCGATTGC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (17 bp):
AATATTCTTTGGTTTGT
Found at i:33107896 original size:33 final size:32
Alignment explanation
Indices: 33107859--33107971 Score: 156
Period size: 32 Copynumber: 3.5 Consensus size: 32
33107849 CGTGTGGTTC
* *
33107859 TGTGAAATGATAACAAATATCAGCTTTTCATTT
1 TGTGAAATGATAACAAATATCAAC-TTTAATTT
33107892 TGTGAAATGATAACAAAT-TACAACTTTAATTT
1 TGTGAAATGATAACAAATAT-CAACTTTAATTT
*
33107924 TGTAAAATGATAACAAATATCAACTTTAATTT
1 TGTGAAATGATAACAAATATCAACTTTAATTT
* *
33107956 TATTAAATGATAACAA
1 TGTGAAATGATAACAA
33107972 TATTCCTCTA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
32 51 0.70
33 22 0.30
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (32 bp):
TGTGAAATGATAACAAATATCAACTTTAATTT
Found at i:33109095 original size:13 final size:13
Alignment explanation
Indices: 33109077--33109111 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
33109067 ACAAGGGACA
33109077 CATGGTCGTGTCG
1 CATGGTCGTGTCG
33109090 CATGGTCGTGTCG
1 CATGGTCGTGTCG
33109103 CATGGTCGT
1 CATGGTCGT
33109112 ATGTCACACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.09, C:0.23, G:0.37, T:0.31
Consensus pattern (13 bp):
CATGGTCGTGTCG
Found at i:33109894 original size:41 final size:41
Alignment explanation
Indices: 33109848--33109935 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
33109838 GCACGTATGA
33109848 GCAATTTAGAGGTACTGAAGTACAAATAGGGGCACATAAGT
1 GCAATTTAGAGGTACTGAAGTACAAATAGGGGCACATAAGT
*
33109889 GCAATTTAGGGGTACTGAAGTACAAATAGGGGCACATAAGT
1 GCAATTTAGAGGTACTGAAGTACAAATAGGGGCACATAAGT
33109930 GCAATT
1 GCAATT
33109936 CAGGGTATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (41 bp):
GCAATTTAGAGGTACTGAAGTACAAATAGGGGCACATAAGT
Found at i:33109898 original size:21 final size:21
Alignment explanation
Indices: 33109874--33109940 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
33109864 GAAGTACAAA
33109874 TAGGGGCACATAAGTGCAATT
1 TAGGGGCACATAAGTGCAATT
* * *
33109895 TAGGGGTAC-TGAAGTACAA-A
1 TAGGGGCACAT-AAGTGCAATT
33109915 TAGGGGCACATAAGTGCAATT
1 TAGGGGCACATAAGTGCAATT
*
33109936 CAGGG
1 TAGGG
33109941 TATAATTAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.21
Consensus pattern (21 bp):
TAGGGGCACATAAGTGCAATT
Found at i:33109920 original size:20 final size:20
Alignment explanation
Indices: 33109858--33109920 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
33109848 GCAATTTAGA
33109858 GGTACTGAAGTACAAATAGG
1 GGTACTGAAGTACAAATAGG
* * *
33109878 GGCACAT-AAGTGCAATTTAGG
1 GGTAC-TGAAGTACAA-ATAGG
33109899 GGTACTGAAGTACAAATAGG
1 GGTACTGAAGTACAAATAGG
33109919 GG
1 GG
33109921 CACATAAGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.37, C:0.11, G:0.32, T:0.21
Consensus pattern (20 bp):
GGTACTGAAGTACAAATAGG
Found at i:33109929 original size:20 final size:20
Alignment explanation
Indices: 33109865--33109929 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
33109855 AGAGGTACTG
33109865 AAGTACAAATAGGGGCACAT
1 AAGTACAAATAGGGGCACAT
* * *
33109885 AAGTGCAATTTAGGGGTAC-T
1 AAGTACAA-ATAGGGGCACAT
33109905 GAAGTACAAATAGGGGCACAT
1 -AAGTACAAATAGGGGCACAT
33109926 AAGT
1 AAGT
33109930 GCAATTCAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 20 0.56
21 16 0.44
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.20
Consensus pattern (20 bp):
AAGTACAAATAGGGGCACAT
Found at i:33112119 original size:12 final size:12
Alignment explanation
Indices: 33112104--33112128 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33112094 TATTAGAATT
33112104 AATAAAGAAGAA
1 AATAAAGAAGAA
33112116 AATAAAGAAGAA
1 AATAAAGAAGAA
33112128 A
1 A
33112129 GATGGAAAGA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AATAAAGAAGAA
Found at i:33121507 original size:9 final size:9
Alignment explanation
Indices: 33121495--33121739 Score: 97
Period size: 10 Copynumber: 25.6 Consensus size: 9
33121485 AATCAGAAAA
33121495 AAAAATTAT
1 AAAAATTAT
*
33121504 AAAAATATAAA
1 AAAAAT-T-AT
33121515 AAAAATT-T
1 AAAAATTAT
33121523 AAAAAATT-T
1 -AAAAATTAT
*
33121532 AAATATTA-
1 AAAAATTAT
33121540 AAAAATATAT
1 AAAAAT-TAT
*
33121550 GAAAATTGATT
1 AAAAATT-A-T
* * *
33121561 TAAACTTTT
1 AAAAATTAT
33121570 AAAAATTAT
1 AAAAATTAT
33121579 AAAAAATTAAT
1 -AAAAATT-AT
* *
33121590 AAATACTAT
1 AAAAATTAT
33121599 CAAAAA-TAT
1 -AAAAATTAT
33121608 AATAAATCTA-
1 AA-AAAT-TAT
*
33121618 ATAAATTAT
1 AAAAATTAT
33121627 AGAAAATTAT
1 A-AAAATTAT
33121637 -AAAATTAAT
1 AAAAATT-AT
*
33121646 AAAACATATTT
1 AAAA-AT-TAT
*
33121657 AAAATTTTAT
1 AAAA-ATTAT
33121667 AAAAATGTATT
1 AAAAAT-TA-T
*
33121678 AAAATTCTAT
1 AAAAAT-TAT
*
33121688 AAAAATAAT
1 AAAAATTAT
**
33121697 AAAAACAAT
1 AAAAATTAT
*
33121706 AAAAAGTATT
1 AAAAATTA-T
*
33121716 AAAATTTAT
1 AAAAATTAT
*
33121725 ATAAAATCAT
1 A-AAAATTAT
33121735 AAAAA
1 AAAAA
33121740 ACTGAATTGA
Statistics
Matches: 180, Mismatches: 32, Indels: 48
0.69 0.12 0.18
Matches are distributed among these distances:
8 21 0.12
9 62 0.34
10 63 0.35
11 33 0.18
12 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:33121507 original size:10 final size:10
Alignment explanation
Indices: 33121494--33121640 Score: 55
Period size: 9 Copynumber: 15.4 Consensus size: 10
33121484 AAATCAGAAA
33121494 AAAAAATTAT
1 AAAAAATTAT
*
33121504 -AAAAATATAA
1 AAAAAAT-TAT
33121514 AAAAAATT-T
1 AAAAAATTAT
33121523 AAAAAATT-T
1 AAAAAATTAT
*
33121532 -AAATA-T-T
1 AAAAAATTAT
33121539 AAAAAA-TAT
1 AAAAAATTAT
*
33121548 ATGAAAATTGAT
1 A-AAAAATT-AT
** *
33121560 TTAAACTT-T
1 AAAAAATTAT
*
33121569 TAAAAATTAT
1 AAAAAATTAT
33121579 AAAAAATTA-
1 AAAAAATTAT
* *
33121588 ATAAATACTAT
1 A-AAAAATTAT
*
33121599 CAAAAA-TAT
1 AAAAAATTAT
* *
33121608 AATAAA-TCT
1 AAAAAATTAT
*
33121617 AATAAATTAT
1 AAAAAATTAT
*
33121627 AGAAAATTAT
1 AAAAAATTAT
33121637 AAAA
1 AAAA
33121641 TTAATAAAAC
Statistics
Matches: 104, Mismatches: 22, Indels: 22
0.70 0.15 0.15
Matches are distributed among these distances:
7 2 0.02
8 9 0.09
9 40 0.38
10 39 0.38
11 12 0.12
12 2 0.02
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:33121528 original size:20 final size:21
Alignment explanation
Indices: 33121472--33121534 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
33121462 TTAAAATATT
* *
33121472 AAAAACTTATAAAAATCAGAAA
1 AAAAAATTATAAAAAT-ATAAA
33121494 AAAAAATTATAAAAATATAAA
1 AAAAAATTATAAAAATATAAA
* *
33121515 AAAAATTTA-AAAAATTTAAA
1 AAAAAATTATAAAAATATAAA
33121535 TATTAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.27
21 12 0.32
22 15 0.41
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAAATTATAAAAATATAAA
Found at i:33121670 original size:21 final size:21
Alignment explanation
Indices: 33121623--33121694 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
33121613 ATCTAATAAA
33121623 TTATAGAAAAT-TA-TAAAA-T
1 TTATA-AAAATATATTAAAATT
*
33121642 TAATAAAACATAT-TTAAAATT
1 TTATAAAA-ATATATTAAAATT
*
33121663 TTATAAAAATGTATTAAAATT
1 TTATAAAAATATATTAAAATT
*
33121684 CTATAAAAATA
1 TTATAAAAATA
33121695 ATAAAAACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 3 0.07
19 6 0.14
20 9 0.21
21 25 0.58
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TTATAAAAATATATTAAAATT
Found at i:33121718 original size:19 final size:20
Alignment explanation
Indices: 33121665--33121720 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
33121655 TTAAAATTTT
* *
33121665 ATAAAAATGTATTAAAATTCT
1 ATAAAAA-GTATTAAAATACA
*
33121686 ATAAAAA-TAATAAAA-ACA
1 ATAAAAAGTATTAAAATACA
33121704 ATAAAAAGTATTAAAAT
1 ATAAAAAGTATTAAAAT
33121721 TTATATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 8 0.28
19 14 0.48
21 7 0.24
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (20 bp):
ATAAAAAGTATTAAAATACA
Found at i:33121730 original size:21 final size:20
Alignment explanation
Indices: 33121636--33121730 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
33121626 TAGAAAATTA
33121636 TAAAATTA-ATAAAACA-TATT
1 TAAAATTATATAAAA-AGTA-T
*
33121656 TAAAATTTTATAAAAATGTAT
1 TAAAATTATATAAAAA-GTAT
* *
33121677 TAAAATTCTATAAAAA-TAA
1 TAAAATTATATAAAAAGTAT
**
33121696 TAAAAACA-ATAAAAAGTAT
1 TAAAATTATATAAAAAGTAT
33121715 TAAAATTTATATAAAA
1 TAAAA-TTATATAAAA
33121731 TCATAAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
18 7 0.12
19 14 0.23
20 9 0.15
21 28 0.47
22 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (20 bp):
TAAAATTATATAAAAAGTAT
Found at i:33121741 original size:39 final size:39
Alignment explanation
Indices: 33121665--33121739 Score: 118
Period size: 38 Copynumber: 1.9 Consensus size: 39
33121655 TTAAAATTTT
33121665 ATAAAAATGTATTAAAATTCTATAAAAATAATAAAAACA
1 ATAAAAATGTATTAAAATTCTATAAAAATAATAAAAACA
*
33121704 ATAAAAA-GTATTAAAATT-TATATAAAATCATAAAAA
1 ATAAAAATGTATTAAAATTCTATA-AAAATAATAAAAA
33121740 ACTGAATTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 4 0.12
38 23 0.68
39 7 0.21
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (39 bp):
ATAAAAATGTATTAAAATTCTATAAAAATAATAAAAACA
Found at i:33122244 original size:5 final size:5
Alignment explanation
Indices: 33122234--33122263 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
33122224 TAAAGCATCA
33122234 ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC
33122264 CTTTTGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATC
Found at i:33125719 original size:28 final size:30
Alignment explanation
Indices: 33125645--33125717 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
33125635 ACAACAGACG
* **
33125645 AAGAACCTTTTGTGTTTTTTTCGGGACAAC
1 AAGAATCTTTTGTGTTTTTTTCCAGACAAC
*
33125675 AAGAATCTTTTGTGTTTTTTTCCAGACAAT
1 AAGAATCTTTTGTGTTTTTTTCCAGACAAC
33125705 AAGAATCTTTTGT
1 AAGAATCTTTTGT
33125718 TTAATCACGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (30 bp):
AAGAATCTTTTGTGTTTTTTTCCAGACAAC
Found at i:33125961 original size:46 final size:46
Alignment explanation
Indices: 33125894--33125988 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
33125884 TAAAATAACA
33125894 ATCATTTCTATCACTTAAAAATTAAATTAATTAAATTCATCACTTT
1 ATCATTTCTATCACTTAAAAATTAAATTAATTAAATTCATCACTTT
33125940 ATCATTTCTATCACTTAAAAATTAAATTAATTAAATTCATCACTTT
1 ATCATTTCTATCACTTAAAAATTAAATTAATTAAATTCATCACTTT
33125986 ATC
1 ATC
33125989 GTTAAACAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (46 bp):
ATCATTTCTATCACTTAAAAATTAAATTAATTAAATTCATCACTTT
Found at i:33127057 original size:108 final size:109
Alignment explanation
Indices: 33126704--33127128 Score: 633
Period size: 109 Copynumber: 3.9 Consensus size: 109
33126694 TGGATTAAGA
* * * * ** *
33126704 TTTAAGAGGATATTCGGCTATTTGGTCCAACGAG--AAATCGAAACCCAGCGCATTAAAGCAAGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
* *
33126767 TTTCTCGAGTTTCCAAACGCAAAACATTGCCTTATTTTGAAATC
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
* * *
33126811 TTTGAAAGGATATTTAGCTATTTGGTC-AAGCAAGAAAAATCGAAACCCAGCACATTAGGGCACG
1 TTTAAAAGGATATTTGGCTATTTGGTCGAA-CGAGAAAAATCGAAACCCAGCACATTAGGGCACG
33126875 TTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
65 TTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
*
33126920 TTTAAAAGGATATTTGGTTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
* * * *
33126985 TTTCTCGATTTTTCAAACGC-GAACATTGCCTTATGTTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
* *
33127028 TTTAAAAGGATATTTTGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGACACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
*
33127093 TTTCTCGAATTTTCAAACGCAAAACATTGCCTTATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
33127129 GAAAAAAACA
Statistics
Matches: 288, Mismatches: 25, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
106 2 0.01
107 26 0.09
108 102 0.35
109 156 0.54
110 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (109 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
Found at i:33127084 original size:217 final size:216
Alignment explanation
Indices: 33126704--33127128 Score: 647
Period size: 217 Copynumber: 2.0 Consensus size: 216
33126694 TGGATTAAGA
* *
33126704 TTTAAGAGGATATTCGGCTATTTGGTCCAACGAGAAATCGAAACCCAGCGCATTAAAGCAAGTTT
1 TTTAAAAGGATATTCGGCTATTTGGTCCAACGAGAAATCGAAACCCAGCACATTAAAGCAAGTTT
* *
33126769 TCTCGAGTTTCCAAACGCAAAACATTGCCTTATTTTGAAATCTTTGAAAGGATATTTAGCTATTT
66 TCTCGAGTTTCCAAACGCAAAACATTGCCTTATGTTGAAATCTTTAAAAGGATATTTAGCTATTT
*
33126834 GGTCAAGCAAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAA
131 GGTCAAGCAAGAAAAATCGAAACCCAGCACATTAGGACACGTTTTCTCGAATTTCCAAACGCAAA
33126899 ACATTGCCTTATTTTGAAATT
196 ACATTGCCTTATTTTGAAATT
* * * ** *
33126920 TTTAAAAGGATATTTGGTTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTCGGCTATTTGGTCCAACGAG--AAATCGAAACCCAGCACATTAAAGCAAGT
* * * * *
33126985 TTTCTCGATTTTTCAAACGC-GAACATTGCCTTATGTTGAAATTTTTAAAAGGATATTTTGCTAT
64 TTTCTCGAGTTTCCAAACGCAAAACATTGCCTTATGTTGAAATCTTTAAAAGGATATTTAGCTAT
* *
33127049 TTGGTCGAA-CGAGAAAAATCGAAACCCAGCACATTAGGACACGTTTTCTCGAATTTTCAAACGC
129 TTGGTC-AAGCAAGAAAAATCGAAACCCAGCACATTAGGACACGTTTTCTCGAATTTCCAAACGC
33127113 AAAACATTGCCTTATT
193 AAAACATTGCCTTATT
33127129 GAAAAAAACA
Statistics
Matches: 188, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
216 30 0.16
217 113 0.60
218 45 0.24
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (216 bp):
TTTAAAAGGATATTCGGCTATTTGGTCCAACGAGAAATCGAAACCCAGCACATTAAAGCAAGTTT
TCTCGAGTTTCCAAACGCAAAACATTGCCTTATGTTGAAATCTTTAAAAGGATATTTAGCTATTT
GGTCAAGCAAGAAAAATCGAAACCCAGCACATTAGGACACGTTTTCTCGAATTTCCAAACGCAAA
ACATTGCCTTATTTTGAAATT
Found at i:33129387 original size:66 final size:67
Alignment explanation
Indices: 33129303--33129429 Score: 177
Period size: 66 Copynumber: 1.9 Consensus size: 67
33129293 TGTTGTAACT
* *
33129303 TCAATCTATTTAACTGCAATGTTG-GGTAAGAAAGATTCGTCATTGTAGCTTCAATCTATTCGTG
1 TCAATCTATTTAACTGCAATGTCGAGG-AAGAAAGATTCGCCATTGTAGCTTCAATCTATTCGTG
33129367 CCC
65 CCC
* ** *
33129370 TCAATCT-TTTAATTGCAATGTCGAGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTATTC
1 TCAATCTATTTAACTGCAATGTCGAGGAAGAAAGATTCGCCATTGTAGCTTCAATCTATTC
33129430 CACTGCACCG
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
66 44 0.83
67 9 0.17
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (67 bp):
TCAATCTATTTAACTGCAATGTCGAGGAAGAAAGATTCGCCATTGTAGCTTCAATCTATTCGTGC
CC
Found at i:33129632 original size:100 final size:99
Alignment explanation
Indices: 33129368--33129722 Score: 532
Period size: 100 Copynumber: 3.6 Consensus size: 99
33129358 CTATTCGTGC
* *
33129368 CCTCAATCTTTTAATTGCAATGTCGAGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTATTCCAC
1 CCTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTATTCCAC
*
33129433 TGCACCGCC-TGAGAAGTAAGATTCGCCGTTGTGG
66 TGCACCGCCAAG-GAAGTAAGATTCGCCGTTGTGG
* * *
33129467 CCTCAATCTTTTAATTGCAATGTTGGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCAC
1 CCTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTATTCCAC
33129532 TGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
66 TGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
* * *
33129566 CCTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTACCTTTAATCTATTCCA
1 CCTCAATC-TTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTATTCCA
* * **
33129631 CTACACCGCCAGGGAAGTAAGATTCATCGTTGTGG
65 CTGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
* * *
33129666 CTTCAATCTTTTTAATTGCAATATCGGGGAAGCGAGATTCACCGTTGTAGCCTCAAT
1 CCTCAATC-TTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAAT
33129723 ATTTTAATTA
Statistics
Matches: 234, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
99 101 0.43
100 133 0.57
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (99 bp):
CCTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCACCGTTGTAGCTTCAATCTATTCCAC
TGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
Found at i:33129788 original size:149 final size:150
Alignment explanation
Indices: 33129543--33129865 Score: 454
Period size: 149 Copynumber: 2.2 Consensus size: 150
33129533 GCACCGCCAA
* * * * *
33129543 GGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCAC
1 GGAAGCAAGATTCGCCGTTGTAGCCTCAATCATTTTAATTACAATGTCGGGGAAGCAAGATGCAC
* * * *
33129608 CGTTGTACCTTTAATCTATTCCACTACACCGCCAGGGAAGTAAGA-TT-CATCGTTGTGGCTTCA
66 CGTTGTACCTTCAATCTATTCCACTACACCGCCAGAGAAGTAAGATTTGC-T-GTTGTGGCCTAA
*
33129671 ATCTTTTTAATTGCAATATCGG
129 ATCTTTTTAATTGCAATATCAG
* * *
33129693 GGAAGCGAGATTCACCGTTGTAGCCTCAAT-ATTTTAATTACAATGTCGGGGAAGCAAGATGCAT
1 GGAAGCAAGATTCGCCGTTGTAGCCTCAATCATTTTAATTACAATGTCGGGGAAGCAAGATGCAC
* * *
33129757 CGTTGTAGCTTCAATCTGTTCCACTACACCGCCTGAGAAGTAAGATTTGCTGTTGTGGCCTAAAT
66 CGTTGTACCTTCAATCTATTCCACTACACCGCCAGAGAAGTAAGATTTGCTGTTGTGGCCTAAAT
*
33129822 CTTTTTAATTGCAATGTCAG
131 CTTTTTAATTGCAATATCAG
33129842 GGAAGCAAGATTCGCCGTTGTAGC
1 GGAAGCAAGATTCGCCGTTGTAGC
33129866 TTCGATCTAC
Statistics
Matches: 152, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
149 122 0.80
150 29 0.19
151 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (150 bp):
GGAAGCAAGATTCGCCGTTGTAGCCTCAATCATTTTAATTACAATGTCGGGGAAGCAAGATGCAC
CGTTGTACCTTCAATCTATTCCACTACACCGCCAGAGAAGTAAGATTTGCTGTTGTGGCCTAAAT
CTTTTTAATTGCAATATCAG
Found at i:33129803 original size:99 final size:99
Alignment explanation
Indices: 33129700--33130008 Score: 375
Period size: 99 Copynumber: 3.1 Consensus size: 99
33129690 CGGGGAAGCG
* * * * **
33129700 AGATTCACCGTTGTAGCCTCAATATTTTAATTACAATGTCGGGGAAGCAAGATGCATCGTTGTAG
1 AGATTCACTGTTGTGGCCTCAATATTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAG
* * * *
33129765 CTTCAATCTGTTCCACTACACCGCCTGAGAAGTA
66 CTTCAATCTATTCCACTGCACCGCCAGGGAAGTA
** * * *
33129799 AGATTTGCTGTTGTGGCCTAAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTA
1 AGATTCACTGTTGTGGCCTCAAT-ATTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTA
* * *
33129864 GCTTCGATCTACTCCACTGCACCGCCAGGGAAATA
65 GCTTCAATCTATTCCACTGCACCGCCAGGGAAGTA
*** * * * *
33129899 AGATTTGTTGTTGTGGCCTCAATCTTTTAATTGCAATGTCGAGGAAGCCAGATTCGCCATTGTAG
1 AGATTCACTGTTGTGGCCTCAATATTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAG
*
33129964 CTTCAATCTATTCCACTGCACCACCAGGGAAGTA
66 CTTCAATCTATTCCACTGCACCGCCAGGGAAGTA
33129998 AGATTCACTGT
1 AGATTCACTGT
33130009 CTTCGATCTG
Statistics
Matches: 177, Mismatches: 32, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
99 93 0.53
100 84 0.47
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (99 bp):
AGATTCACTGTTGTGGCCTCAATATTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAG
CTTCAATCTATTCCACTGCACCGCCAGGGAAGTA
Found at i:33129854 original size:249 final size:248
Alignment explanation
Indices: 33129451--33129970 Score: 736
Period size: 249 Copynumber: 2.1 Consensus size: 248
33129441 CTGAGAAGTA
* * * * * * *
33129451 AGATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTTGGGGAAGCGAGATTCGCCGTTGTAG
1 AGATTCGCCGTTGTAGCCTCAATATTTTAATTACAATGTCGGGGAAGCAAGATGCACCGTTGTAG
* *
33129516 CTTCAATCTGTTCCACTGCACCGCCAAGGAAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTTAA
66 CTTCAATCTGTTCCACTACACCGCCAAGGAAGTAAGATTCGCCGTTGTGGCCTAAATCTTTTTAA
* * *
33129581 TTGCAATGTCGGGGAAGCAAGATTCACCGTTGTACCTTTAATCTATTCCACTACACCGCCAGGGA
131 TTGCAATGTCAGGGAAGCAAGATTCACCGTTGTACCTTCAATCTACTCCACTACACCGCCAGGGA
* * * *
33129646 AGTAAGATTCATCGTTGTGGCTTCAATCTTTTTAATTGCAATATCGGGGAAGCG
196 AATAAGATTCATCGTTGTGGCCTCAATC-TTTTAATTGCAATATCGAGGAAGCC
* *
33129700 AGATTCACCGTTGTAGCCTCAATATTTTAATTACAATGTCGGGGAAGCAAGATGCATCGTTGTAG
1 AGATTCGCCGTTGTAGCCTCAATATTTTAATTACAATGTCGGGGAAGCAAGATGCACCGTTGTAG
* * *
33129765 CTTCAATCTGTTCCACTACACCGCC-TGAGAAGTAAGATTTGCTGTTGTGGCCTAAATCTTTTTA
66 CTTCAATCTGTTCCACTACACCGCCAAG-GAAGTAAGATTCGCCGTTGTGGCCTAAATCTTTTTA
* * * *
33129829 ATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCGATCTACTCCACTGCACCGCCAGGG
130 ATTGCAATGTCAGGGAAGCAAGATTCACCGTTGTACCTTCAATCTACTCCACTACACCGCCAGGG
** * *
33129894 AAATAAGATTTGTTGTTGTGGCCTCAATCTTTTAATTGCAATGTCGAGGAAGCC
195 AAATAAGATTCATCGTTGTGGCCTCAATCTTTTAATTGCAATATCGAGGAAGCC
* *
33129948 AGATTCGCCATTGTAGCTTCAAT
1 AGATTCGCCGTTGTAGCCTCAAT
33129971 CTATTCCACT
Statistics
Matches: 238, Mismatches: 32, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
248 43 0.18
249 195 0.82
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (248 bp):
AGATTCGCCGTTGTAGCCTCAATATTTTAATTACAATGTCGGGGAAGCAAGATGCACCGTTGTAG
CTTCAATCTGTTCCACTACACCGCCAAGGAAGTAAGATTCGCCGTTGTGGCCTAAATCTTTTTAA
TTGCAATGTCAGGGAAGCAAGATTCACCGTTGTACCTTCAATCTACTCCACTACACCGCCAGGGA
AATAAGATTCATCGTTGTGGCCTCAATCTTTTAATTGCAATATCGAGGAAGCC
Found at i:33129861 original size:100 final size:98
Alignment explanation
Indices: 33129709--33130002 Score: 381
Period size: 100 Copynumber: 3.0 Consensus size: 98
33129699 GAGATTCACC
* * * * * **
33129709 GTTGTAGCCTCAATATTTTAATTACAATGTCGGGGAAGCAAGATGCATCGTTGTAGCTTCAATCT
1 GTTGTGGCCTAAATCTTTTAATTGCAATGTC-GGGAAGCAAGATTCGCCGTTGTAGCTTCAATCT
* * * *
33129774 GTTCCACTACACCGCCTGAGAAGTAAGATTTGCT
65 ATTCCACTGCACCGCCAGGGAAGTAAGATTTGCT
*
33129808 GTTGTGGCCTAAATCTTTTTAATTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTAGCTTCGATC
1 GTTGTGGCCTAAATC-TTTTAATTGCAATGTC-GGGAAGCAAGATTCGCCGTTGTAGCTTCAATC
* * *
33129873 TACTCCACTGCACCGCCAGGGAAATAAGATTTGTT
64 TATTCCACTGCACCGCCAGGGAAGTAAGATTTGCT
* * *
33129908 GTTGTGGCCTCAATCTTTTAATTGCAATGTCGAGGAAGCCAGATTCGCCATTGTAGCTTCAATCT
1 GTTGTGGCCTAAATCTTTTAATTGCAATGTCG-GGAAGCAAGATTCGCCGTTGTAGCTTCAATCT
*
33129973 ATTCCACTGCACCACCAGGGAAGTAAGATT
65 ATTCCACTGCACCGCCAGGGAAGTAAGATT
33130003 CACTGTCTTC
Statistics
Matches: 170, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
98 1 0.01
99 84 0.49
100 85 0.50
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (98 bp):
GTTGTGGCCTAAATCTTTTAATTGCAATGTCGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTA
TTCCACTGCACCGCCAGGGAAGTAAGATTTGCT
Found at i:33130045 original size:44 final size:44
Alignment explanation
Indices: 33129996--33130467 Score: 150
Period size: 44 Copynumber: 10.7 Consensus size: 44
33129986 ACCAGGGAAG
* *
33129996 TAAGATTCACTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 TAAGATTCACTATCTTCAATCTGCTCCACTACTGCTTAGGGAGA
* * * * * * * *** *
33130040 CAAGATTTACAACCTTCGACCTACTCTGTTATTGCTTAGGGAGA
1 TAAGATTCACTATCTTCAATCTGCTCCACTACTGCTTAGGGAGA
* * * * *
33130084 T-AGA---ACTGGTGGTTTAAATTTGCTTCC-CTACTACATT-GGGAAGA
1 TAAGATTCACT-AT--CTTCAATCTGC-TCCACTACTGC-TTAGGGA-GA
* **
33130128 TAAGATTCACTGTCTTTGATCTGCTCCACTACTGCTTAGGGAGA
1 TAAGATTCACTATCTTCAATCTGCTCCACTACTGCTTAGGGAGA
* * ** * * *
33130172 CAGGATTTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGA
1 TAAGATTCACTATCTTCAATCTGCTCCACTACTGCTTAGGGAGA
* ** * * *
33130216 TAGGATT-GGTGGT-TTAAATCTGCTTCTCCACTA-T-CTT-GGGAAGG
1 TAAGATTCACT-ATCTTCAATCTG---CTCCACTACTGCTTAGGG-AGA
* * *
33130260 TAAGATTCACCATCTTCGATCTGCTCTACTACTGCTTAGGGAGA
1 TAAGATTCACTATCTTCAATCTGCTCCACTACTGCTTAGGGAGA
* * * * * * * *
33130304 -CAGAATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGA
1 TAAGATTC-ACTATCTTCAATCTGCTCCACTACTGCTTAGGGAGA
* * ** *
33130348 TAGGATT-AATGGCTTAAATCTGCTTCTCCACTA-T-CTT-GGGAAGA
1 TAAGATTCACTATCTTCAATCTG---CTCCACTACTGCTTAGGG-AGA
* * *
33130392 TAATATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 TAAGATTCACTATCTTCAATCTGCTCCACTACTGCTTAGGGAGA
* * ** *
33130436 -CAGAATCTAAAATCTTCAATCTACTCCACTAC
1 TAAGATTC-ACTATCTTCAATCTGCTCCACTAC
33130468 AAATCAGAGA
Statistics
Matches: 300, Mismatches: 95, Indels: 66
0.65 0.21 0.14
Matches are distributed among these distances:
40 2 0.01
42 15 0.05
43 47 0.16
44 169 0.56
45 47 0.16
46 15 0.05
47 2 0.01
48 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
TAAGATTCACTATCTTCAATCTGCTCCACTACTGCTTAGGGAGA
Found at i:33130233 original size:132 final size:132
Alignment explanation
Indices: 33129990--33130467 Score: 640
Period size: 132 Copynumber: 3.6 Consensus size: 132
33129980 TGCACCACCA
** * *
33129990 GGGAAG-TAAGATTCACTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACA-AGATTTACAAC
1 GGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGA-ATCTACAAT
* *** * * * *
33130053 CTTCGACCTACTCTGTTATTGCTTAGGGAGATAGAACTGGTGGTTTAAATTTGCTTC-CCTACTA
65 CTTCAACCTACTCCACTACTGCTTAGGGAGATAGGATTGGTGGTTTAAATCTGCTTCTCC-ACTA
33130117 -CATT
129 TC-TT
** * * * *
33130121 GGGAAGATAAGATTCACTGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGGATTTGCAATC
1 GGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTACAATC
33130186 TTCAACCTACTCCACTACTGCTTAGGGAGATAGGATTGGTGGTTTAAATCTGCTTCTCCACTATC
66 TTCAACCTACTCCACTACTGCTTAGGGAGATAGGATTGGTGGTTTAAATCTGCTTCTCCACTATC
33130251 TT
131 TT
* * *
33130253 GGGAAGGTAAGATTCACCATCTTCGATCTGCTCTACTACTGCTTAGGGAGACAGAATCTGCAATC
1 GGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTACAATC
* * ** *
33130318 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAATGGCTTAAATCTGCTTCTCCACTATC
66 TTCAACCTACTCCACTACTGCTTAGGGAGATAGGATTGGTGGTTTAAATCTGCTTCTCCACTATC
33130383 TT
131 TT
* *
33130385 GGGAAGATAATATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTAAAATC
1 GGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTACAATC
*
33130450 TTCAATCTACTCCACTAC
66 TTCAACCTACTCCACTAC
33130468 AAATCAGAGA
Statistics
Matches: 312, Mismatches: 31, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
131 6 0.02
132 303 0.97
133 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (132 bp):
GGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTACAATC
TTCAACCTACTCCACTACTGCTTAGGGAGATAGGATTGGTGGTTTAAATCTGCTTCTCCACTATC
TT
Found at i:33131571 original size:4 final size:4
Alignment explanation
Indices: 33131562--33131586 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
33131552 TGGACTGAAT
33131562 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
33131587 AATAAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:33132938 original size:10 final size:10
Alignment explanation
Indices: 33132923--33132960 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
33132913 CACCTTGGCC
33132923 TCTTTTTTTT
1 TCTTTTTTTT
*
33132933 TC-TTTTTCT
1 TCTTTTTTTT
33132942 TCTTTTTTTT
1 TCTTTTTTTT
33132952 TCTCTTTTT
1 TCT-TTTTT
33132961 CCTTCTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.33
10 11 0.46
11 5 0.21
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:33132949 original size:21 final size:22
Alignment explanation
Indices: 33132925--33132966 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
33132915 CCTTGGCCTC
33132925 TTTTTTTT-TCTTTTT-CTTCT
1 TTTTTTTTCTCTTTTTCCTTCT
33132945 TTTTTTTTCTCTTTTTCCTTCT
1 TTTTTTTTCTCTTTTTCCTTCT
33132967 CTCTTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTTTTCTCTTTTTCCTTCT
Found at i:33136802 original size:109 final size:109
Alignment explanation
Indices: 33136607--33137140 Score: 811
Period size: 109 Copynumber: 4.9 Consensus size: 109
33136597 TGGATTAAGA
* * * * * ** * *
33136607 TTTAAGAGGATATTCGGCTATTTGGTCCAACGAG--AAATCGAAACCTAGCGTATTAGAGCAAGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGT
* * *
33136670 TTTCTCGAGTTTCCAAACGCAAAACATTGCCTTTTTTTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATGTTGAAATT
* * * * *
33136714 TTTGAAAGGATATTTAGCTATTTGGTCGAGCGAGAAAAACCAAAACCCAGCACATTAGGGCACGC
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGT
* *
33136779 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAAT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATGTTGAAATT
* *
33136823 TTTAAAAGGATATTTGGTTATTTGTTCGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGT
*
33136888 TCTCTCGAATTTCCAAACGCAAAACATTGCCTTATGTTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATGTTGAAATT
* * *
33136932 TTTAAAAGGATATTTGGCTATTTGGTCGAATGAGAAAAATCAAAAGCCAGCACATTAAGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGT
33136997 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATGTTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATGTTGAAATT
*
33137041 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGT
*
33137106 TTTCTCGAATTTCCAAATGCAAAACATTGCCTTAT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTAT
33137141 TGAAAAAACA
Statistics
Matches: 387, Mismatches: 38, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
107 28 0.07
109 359 0.93
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (109 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGT
TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATGTTGAAATT
Found at i:33141317 original size:6 final size:6
Alignment explanation
Indices: 33141306--33141340 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
33141296 AAGATAAACC
33141306 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA
33141341 TTATTTCTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:33145326 original size:16 final size:16
Alignment explanation
Indices: 33145298--33145357 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
33145288 GTTCCAAAGT
33145298 TTTTCCAAAATTTTAAG
1 TTTTCC-AAATTTTAAG
33145315 TTTTCCAAA-TTTAA-
1 TTTTCCAAATTTTAAG
*
33145329 TTTT-TAAATTATTTAAG
1 TTTTCCAAA-T-TTTAAG
*
33145346 TTTTCAAAATTT
1 TTTTCCAAATTT
33145358 AATCTCATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
13 3 0.08
14 4 0.11
15 5 0.14
16 10 0.28
17 11 0.31
18 3 0.08
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTTCCAAATTTTAAG
Found at i:33148697 original size:7 final size:7
Alignment explanation
Indices: 33148687--33148722 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
33148677 TATCCTGAAT
33148687 CCCAAAC
1 CCCAAAC
33148694 CCCAAAC
1 CCCAAAC
33148701 CCCAAAC
1 CCCAAAC
*
33148708 TCCAAAC
1 CCCAAAC
*
33148715 CTCAAAC
1 CCCAAAC
33148722 C
1 C
33148723 TTGAACCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.53, G:0.00, T:0.06
Consensus pattern (7 bp):
CCCAAAC
Found at i:33148760 original size:35 final size:35
Alignment explanation
Indices: 33148704--33148800 Score: 113
Period size: 35 Copynumber: 2.8 Consensus size: 35
33148694 CCCAAACCCC
*
33148704 AAACTCCAAACCTCAAACCTTGAACCTAGAATCTA
1 AAACCCCAAACCTCAAACCTTGAACCTAGAATCTA
* * * *
33148739 AAACCCCAACCCTCAAACCTTGAGCCTTGAATCTT
1 AAACCCCAAACCTCAAACCTTGAACCTAGAATCTA
* * * *
33148774 GAACCTCAAACCTCACACCCTGAACCT
1 AAACCCCAAACCTCAAACCTTGAACCT
33148801 TCCTTGAACC
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.36, C:0.37, G:0.07, T:0.20
Consensus pattern (35 bp):
AAACCCCAAACCTCAAACCTTGAACCTAGAATCTA
Found at i:33149453 original size:7 final size:7
Alignment explanation
Indices: 33149441--33149497 Score: 62
Period size: 7 Copynumber: 8.1 Consensus size: 7
33149431 CTAAATCTCA
33149441 AACCTTG
1 AACCTTG
33149448 AACCTTG
1 AACCTTG
33149455 AACCTTG
1 AACCTTG
**
33149462 AACCAAG
1 AACCTTG
33149469 AACCTTG
1 AACCTTG
**
33149476 AACC-CC
1 AACCTTG
33149482 AACCCTTG
1 AA-CCTTG
33149490 AACCTTG
1 AACCTTG
33149497 A
1 A
33149498 GCCCTAAATC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 2 0.05
7 36 0.90
8 2 0.05
ACGTcount: A:0.33, C:0.33, G:0.12, T:0.21
Consensus pattern (7 bp):
AACCTTG
Found at i:33149492 original size:21 final size:21
Alignment explanation
Indices: 33149439--33149515 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 21
33149429 TTCTAAATCT
*
33149439 CAAACCTTGAACCTTGAACCT
1 CAAACCTTGAACCTTGAACCC
** **
33149460 TGAACCAAGAACCTTGAACCC
1 CAAACCTTGAACCTTGAACCC
* *
33149481 CAACCCTTGAACCTTGAGCCC
1 CAAACCTTGAACCTTGAACCC
* *
33149502 TAAATCTTGAACCT
1 CAAACCTTGAACCT
33149516 CAAACCTCAC
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.32, C:0.34, G:0.12, T:0.22
Consensus pattern (21 bp):
CAAACCTTGAACCTTGAACCC
Found at i:33150069 original size:93 final size:94
Alignment explanation
Indices: 33149889--33150073 Score: 284
Period size: 93 Copynumber: 2.0 Consensus size: 94
33149879 TAAAATTATG
* * *
33149889 TGTAAATAACATGGAAAATTTTGCTGAAATGTCATTAAATAATTTGAAAGGGACCATAGGTGATG
1 TGTAAATAACATGGAAAATTTTGCTGAAATGTCATTAAATAATTGGAAAGAGACCATAGGTGATA
33149954 TGGTGGGAAGGATACATAAAATAATTTCT
66 TGGTGGGAAGGATACATAAAATAATTTCT
*
33149983 TGTAAGTAA-ATGGAAAATTTTGCTGAAATGTCATTAAATAATTGGAAAGAGACCAT-GGATGAT
1 TGTAAATAACATGGAAAATTTTGCTGAAATGTCATTAAATAATTGGAAAGAGACCATAGG-TGAT
* * *
33150046 ATGGTGGGAAGGGTCCATCAAATAATTT
65 ATGGTGGGAAGGATACATAAAATAATTT
33150074 TTCAGATTGA
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
92 2 0.02
93 73 0.88
94 8 0.10
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (94 bp):
TGTAAATAACATGGAAAATTTTGCTGAAATGTCATTAAATAATTGGAAAGAGACCATAGGTGATA
TGGTGGGAAGGATACATAAAATAATTTCT
Found at i:33150706 original size:15 final size:15
Alignment explanation
Indices: 33150681--33150715 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
33150671 GACTCTATTT
*
33150681 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
33150695 TAATTAATATTAAGA
1 TAATTAATATTAAGA
33150710 TAATTA
1 TAATTA
33150716 TTAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:33150731 original size:18 final size:18
Alignment explanation
Indices: 33150710--33150751 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
33150700 AATATTAAGA
33150710 TAATTATTA-AATATTATT
1 TAATT-TTAGAATATTATT
* *
33150728 TAATTTTAGGATTTTATT
1 TAATTTTAGAATATTATT
33150746 TAATTT
1 TAATTT
33150752 ATCTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TAATTTTAGAATATTATT
Found at i:33152035 original size:6 final size:7
Alignment explanation
Indices: 33152018--33152060 Score: 59
Period size: 7 Copynumber: 5.9 Consensus size: 7
33152008 TCAAGTGTAA
33152018 AAAAATT
1 AAAAATT
33152025 AAAAATT
1 AAAAATT
33152032 AAAAATT
1 AAAAATT
33152039 AAAAATAT
1 AAAAAT-T
*
33152047 CAAATATT
1 -AAAAATT
33152055 AAAAAT
1 AAAAAT
33152061 AATTATATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 25 0.78
8 2 0.06
9 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAAATT
Found at i:33152035 original size:14 final size:16
Alignment explanation
Indices: 33152018--33152061 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 16
33152008 TCAAGTGTAA
33152018 AAAAATTAAAAAT-T-
1 AAAAATTAAAAATATC
33152032 AAAAATTAAAAATATC
1 AAAAATTAAAAATATC
*
33152048 AAATATTAAAAATA
1 AAAAATTAAAAATA
33152062 ATTATATTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.48
15 1 0.04
16 13 0.48
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAATTAAAAATATC
Found at i:33152055 original size:23 final size:23
Alignment explanation
Indices: 33152015--33152060 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
33152005 GAATCAAGTG
*
33152015 TAAAAAAATTAAAAATTAAAAAT
1 TAAAAAAATCAAAAATTAAAAAT
* *
33152038 TAAAAATATCAAATATTAAAAAT
1 TAAAAAAATCAAAAATTAAAAAT
33152061 AATTATATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAAAAATCAAAAATTAAAAAT
Found at i:33155725 original size:19 final size:19
Alignment explanation
Indices: 33155701--33155756 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
33155691 TTATTTAACC
33155701 TTTAATTAAACATAATTAA
1 TTTAATTAAACATAATTAA
* *
33155720 TTTAATTAACCTTAA-TAA
1 TTTAATTAAACATAATTAA
*
33155738 TTAAAATATAAACATAATT
1 TT-TAAT-TAAACATAATT
33155757 TACATTAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 5 0.17
19 16 0.55
20 7 0.24
21 1 0.03
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTAATTAAACATAATTAA
Found at i:33164724 original size:21 final size:19
Alignment explanation
Indices: 33164684--33164728 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
33164674 CCCTAAATTT
33164684 TCAATCCCCAAACTTCAACC
1 TCAAT-CCCAAACTTCAACC
*
33164704 ATCAATCCCAAACTCTTAACC
1 -TCAATCCCAAACT-TCAACC
33164725 TCAA
1 TCAA
33164729 ACCCTAAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.22
Consensus pattern (19 bp):
TCAATCCCAAACTTCAACC
Found at i:33165417 original size:14 final size:15
Alignment explanation
Indices: 33165398--33165426 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
33165388 ATTAAAAGCT
33165398 AGATAAA-GTAAATA
1 AGATAAATGTAAATA
33165412 AGATAAATGTAAATA
1 AGATAAATGTAAATA
33165427 GACGACAGTT
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:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (15 bp):
AGATAAATGTAAATA
Found at i:33165790 original size:29 final size:28
Alignment explanation
Indices: 33165728--33165796 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
33165718 GGGCGACGCT
*
33165728 GGTTTAGGG-TTTTGAAGAAATAAATTA
1 GGTTTAGGGTTTTTGAAAAAATAAATTA
*
33165755 GGATTTAGGGTTTTTTAAAAAATAAATTA
1 GG-TTTAGGGTTTTTGAAAAAATAAATTA
*
33165784 GAGTTTACGGTTT
1 G-GTTTAGGGTTT
33165797 GAAGGGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.06
28 7 0.19
29 26 0.72
30 1 0.03
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (28 bp):
GGTTTAGGGTTTTTGAAAAAATAAATTA
Found at i:33166042 original size:29 final size:29
Alignment explanation
Indices: 33165986--33166043 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
33165976 GTGTTTTTTA
**
33165986 GCCCATTCCGATAAATAATATTTTAAATG
1 GCCCATTCCGATAAATAATATTGGAAATG
*
33166015 GCCCATTTCCG-TAAATACTATTGGAAATG
1 GCCCA-TTCCGATAAATAATATTGGAAATG
33166044 ATTTTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (29 bp):
GCCCATTCCGATAAATAATATTGGAAATG
Found at i:33178957 original size:21 final size:22
Alignment explanation
Indices: 33178931--33178971 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
33178921 GTTGTCAAGT
33178931 AAAATTAATA-ATTTTAATGTA
1 AAAATTAATAGATTTTAATGTA
*
33178952 AAAATTAATAGGTTTTAATG
1 AAAATTAATAGATTTTAATG
33178972 CACAATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (22 bp):
AAAATTAATAGATTTTAATGTA
Found at i:33179354 original size:26 final size:27
Alignment explanation
Indices: 33179300--33179363 Score: 103
Period size: 26 Copynumber: 2.4 Consensus size: 27
33179290 ATAAAAAATA
*
33179300 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAAC-ATTTTTTATTT
33179328 ACCAAAATATTATAA-ATTTTTTATTT
1 ACCAAAATATTATAACATTTTTTATTT
33179354 ACCAAAATAT
1 ACCAAAATAT
33179364 ACCAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 20 0.57
28 15 0.43
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (27 bp):
ACCAAAATATTATAACATTTTTTATTT
Found at i:33179396 original size:16 final size:17
Alignment explanation
Indices: 33179370--33179401 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
33179360 ATATACCAAA
33179370 AAAAAACAAAAACCTGC
1 AAAAAACAAAAACCTGC
33179387 AAAAAA-AAAAACCTG
1 AAAAAACAAAAACCTG
33179402 TGGCGGCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.69, C:0.19, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAAAACAAAAACCTGC
Found at i:33180043 original size:18 final size:18
Alignment explanation
Indices: 33180022--33180074 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
33180012 AGTAATAACT
*
33180022 CTATTTTAATTTAATAAA
1 CTATTCTAATTTAATAAA
*
33180040 CTATTCTCATTTAATAAA
1 CTATTCTAATTTAATAAA
33180058 C---TCTAATTTAATAAA
1 CTATTCTAATTTAATAAA
33180073 CT
1 CT
33180075 CTATTTTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 14 0.45
18 17 0.55
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (18 bp):
CTATTCTAATTTAATAAA
Found at i:33180068 original size:15 final size:15
Alignment explanation
Indices: 33180028--33180077 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
33180018 AACTCTATTT
33180028 TAATTTAATAAACTATTC
1 TAATTTAATAAAC---TC
*
33180046 TCATTTAATAAACTC
1 TAATTTAATAAACTC
33180061 TAATTTAATAAACTC
1 TAATTTAATAAACTC
33180076 TA
1 TA
33180078 TTTTGGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 18 0.60
18 12 0.40
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATTTAATAAACTC
Found at i:33180111 original size:23 final size:23
Alignment explanation
Indices: 33180085--33180201 Score: 56
Period size: 19 Copynumber: 5.2 Consensus size: 23
33180075 CTATTTTGGT
33180085 AATTTGATGAGAAGAGTTTATTA
1 AATTTGATGAGAAGAGTTTATTA
*
33180108 AA-TT-A--AAATAGAG-TTATTAA
1 AATTTGATGAGA-AGAGTTTATT-A
*
33180128 GTAATTTGATGAGAATAGTTTATTA
1 --AATTTGATGAGAAGAGTTTATTA
*
33180153 AA-TT-A--AAATAGAG-TTATTAA
1 AATTTGATGAGA-AGAGTTTATT-A
*
33180173 GTAATTTGATGAGAATAGTTTATTA
1 --AATTTGATGAGAAGAGTTTATTA
33180198 AATT
1 AATT
33180202 AAAATAGAGT
Statistics
Matches: 69, Mismatches: 7, Indels: 36
0.62 0.06 0.32
Matches are distributed among these distances:
19 14 0.20
20 9 0.13
21 2 0.03
22 8 0.12
23 12 0.17
24 2 0.03
25 8 0.12
26 14 0.20
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (23 bp):
AATTTGATGAGAAGAGTTTATTA
Found at i:33180151 original size:26 final size:26
Alignment explanation
Indices: 33180121--33180198 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
33180111 TAAAATAGAG
33180121 TTATTAAGTAATTTGATGAGAATAGT
1 TTATTAAGTAATTTGATGAGAATAGT
*
33180147 TTATT-A--AA-TT-A--A-AATAGAG
1 TTATTAAGTAATTTGATGAGAATAG-T
33180166 TTATTAAGTAATTTGATGAGAATAGT
1 TTATTAAGTAATTTGATGAGAATAGT
33180192 TTATTAA
1 TTATTAA
33180199 ATTAAAATAG
Statistics
Matches: 41, Mismatches: 2, Indels: 18
0.67 0.03 0.30
Matches are distributed among these distances:
18 5 0.12
19 6 0.15
20 1 0.02
21 1 0.02
22 4 0.10
23 4 0.10
24 1 0.02
25 1 0.02
26 13 0.32
27 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (26 bp):
TTATTAAGTAATTTGATGAGAATAGT
Found at i:33180223 original size:45 final size:45
Alignment explanation
Indices: 33180083--33180216 Score: 259
Period size: 45 Copynumber: 3.0 Consensus size: 45
33180073 CTCTATTTTG
*
33180083 GTAATTTGATGAGAAGAGTTTATTAAATTAAAATAGAGTTATTAA
1 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
33180128 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
1 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
33180173 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTA
1 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTA
33180217 CTTAATTAGA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (45 bp):
GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTAA
Found at i:33185560 original size:24 final size:24
Alignment explanation
Indices: 33185492--33185562 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
33185482 TTACAACACC
* * *
33185492 AGCTAGTGCAATT-ACATCAACATT
1 AGCTAGTGCAGTTGGCA-CAACTTT
* *
33185516 AGCTAGTGCAGTTGTCTCAACTTT
1 AGCTAGTGCAGTTGGCACAACTTT
* *
33185540 AGCTTGTGCATTTGGCACAACTT
1 AGCTAGTGCAGTTGGCACAACTT
33185563 CAGTTGATGA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 37 0.97
25 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (24 bp):
AGCTAGTGCAGTTGGCACAACTTT
Found at i:33199917 original size:13 final size:13
Alignment explanation
Indices: 33199899--33199923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33199889 TTTCATTTAG
33199899 CATTTCAAATGTT
1 CATTTCAAATGTT
33199912 CATTTCAAATGT
1 CATTTCAAATGT
33199924 CCCTTTTTAC
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:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (13 bp):
CATTTCAAATGTT
Found at i:33199964 original size:26 final size:26
Alignment explanation
Indices: 33199934--33200013 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 26
33199924 CCCTTTTTAC
33199934 ATAACTATTCATATCAACATTTTGTAT
1 ATAACTATTCATAT-AACATTTTGTAT
* **
33199961 -TAAC-ACTTTATATAACTATTTTCCAT
1 ATAACTA-TTCATATAAC-ATTTTGTAT
*
33199987 ATAACTGATTCATATGATCATTTTGTA
1 ATAACT-ATTCATAT-AACATTTTGTA
33200014 CATCTACTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
25 4 0.10
26 17 0.43
27 4 0.10
28 12 0.30
29 3 0.08
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (26 bp):
ATAACTATTCATATAACATTTTGTAT
Found at i:33199999 original size:54 final size:52
Alignment explanation
Indices: 33199934--33200062 Score: 136
Period size: 54 Copynumber: 2.4 Consensus size: 52
33199924 CCCTTTTTAC
* *
33199934 ATAACT-ATTCATATCAACATTTTGTATTAAC-ACTTTATATAACTATTTTCCAT
1 ATAACTGATTCATATCAACATTTTGTA-CAACTACTTTATATAACCA-TTT-CAT
* * *
33199987 ATAACTGATTCATATGATCATTTTGTACATCTACTTTATATAACCATTTCAT
1 ATAACTGATTCATATCAACATTTTGTACAACTACTTTATATAACCATTTCAT
* * *
33200039 ATAACCGTTTCATATTATACATTT
1 ATAACTGATTCATATCA-ACATTT
33200063 AACACACAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
52 17 0.27
53 16 0.25
54 31 0.48
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (52 bp):
ATAACTGATTCATATCAACATTTTGTACAACTACTTTATATAACCATTTCAT
Found at i:33200042 original size:13 final size:13
Alignment explanation
Indices: 33200024--33200053 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
33200014 CATCTACTTT
33200024 ATATAACCATTTC
1 ATATAACCATTTC
*
33200037 ATATAACCGTTTC
1 ATATAACCATTTC
33200050 ATAT
1 ATAT
33200054 TATACATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (13 bp):
ATATAACCATTTC
Found at i:33209860 original size:37 final size:37
Alignment explanation
Indices: 33209810--33209886 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
33209800 TATAGTACGA
33209810 AAGTAAAATAAGAGATAATTTTAAGGTTTCTTAAACT
1 AAGTAAAATAAGAGATAATTTTAAGGTTTCTTAAACT
33209847 AAGTAAAATAAGAGATAATTTTAAGGTTTCTTAAACT
1 AAGTAAAATAAGAGATAATTTTAAGGTTTCTTAAACT
33209884 AAG
1 AAG
33209887 GAAATAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (37 bp):
AAGTAAAATAAGAGATAATTTTAAGGTTTCTTAAACT
Found at i:33212955 original size:16 final size:16
Alignment explanation
Indices: 33212934--33212965 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33212924 ATTTTGTTGC
*
33212934 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
33212950 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
33212966 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:33213164 original size:46 final size:43
Alignment explanation
Indices: 33213089--33213187 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 43
33213079 AATAATAACA
*
33213089 GATACCCGGTGGATTCAGCACACAACAACCACCCTTTGTAATCAAT
1 GATA-CCGGTGGATTCAGCACACAACAACCA-CC-TTATAATCAAT
* * *
33213135 GATATCCGGTGGGA-TCAGCACATAGCAACCACCTTATAATTAAT
1 GATA-CCGGT-GGATTCAGCACACAACAACCACCTTATAATCAAT
33213179 GATACCGGT
1 GATACCGGT
33213188 TCACATAGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
43 5 0.11
44 13 0.28
45 2 0.04
46 24 0.51
47 3 0.06
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (43 bp):
GATACCGGTGGATTCAGCACACAACAACCACCTTATAATCAAT
Found at i:33213254 original size:51 final size:50
Alignment explanation
Indices: 33213193--33213383 Score: 201
Period size: 51 Copynumber: 3.8 Consensus size: 50
33213183 CCGGTTCACA
* *
33213193 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCAATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCAGTAC-CG
* * * *
33213244 TATTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTACGG
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCAGTACCG
* * * *
33213294 ATAGTAGCCTGTACATAGTACTACACATGCGACCTATCA-T-TCTAGTACTCG
1 -TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCAGTAC-CG
*
33213345 TAGTAGCCTACACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
33213384 TTCACTTTCA
Statistics
Matches: 114, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
49 4 0.04
50 39 0.34
51 68 0.60
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCAGTACCG
Found at i:33216240 original size:47 final size:48
Alignment explanation
Indices: 33216172--33216265 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 48
33216162 ATTTACATAT
** *
33216172 TGATGTCATAGCCCAGCTATGGTCTTACACAG-TAGCACATATCACAC
1 TGATGTCATAGCCCAAATATGGTCTTACACAGAAAGCACATATCACAC
* * *
33216219 TGATGTCATATCCCAAATATGGTCTTATACAGAAATCACATATCACA
1 TGATGTCATAGCCCAAATATGGTCTTACACAGAAAGCACATATCACA
33216266 TGTTGCCATG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 28 0.70
48 12 0.30
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (48 bp):
TGATGTCATAGCCCAAATATGGTCTTACACAGAAAGCACATATCACAC
Found at i:33219531 original size:102 final size:102
Alignment explanation
Indices: 33219395--33219589 Score: 302
Period size: 102 Copynumber: 1.9 Consensus size: 102
33219385 ATTTTTTCAG
* * *
33219395 AAAATATTTAATATTTCACAACTCAACATGTTCACTGTGACCGAAT-GATTTATTTTTATTTTCA
1 AAAATATTTAATATTTCACAACTCAACATATTCACTATGACCGAATGGA-TTATTTTCATTTTCA
33219459 GGGTTCAAAACAGCTTAAAAACATAAACTTATTTCCAA
65 GGGTTCAAAACAGCTTAAAAACATAAACTTATTTCCAA
* ***
33219497 AAAATATTTAGTATTTCACAACTCAACATATTCACTATGGTTGAATGGATTATTTTCATTTTCAG
1 AAAATATTTAATATTTCACAACTCAACATATTCACTATGACCGAATGGATTATTTTCATTTTCAG
*
33219562 GGTTCAAAATAGCTTAAAAACATAAACT
66 GGTTCAAAACAGCTTAAAAACATAAACT
33219590 CGTTCTTTCA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 82 0.98
103 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (102 bp):
AAAATATTTAATATTTCACAACTCAACATATTCACTATGACCGAATGGATTATTTTCATTTTCAG
GGTTCAAAACAGCTTAAAAACATAAACTTATTTCCAA
Found at i:33225849 original size:12 final size:11
Alignment explanation
Indices: 33225832--33225866 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
33225822 AACAAATCCT
33225832 CTCTCATATTTC
1 CTCTCA-ATTTC
33225844 CTCTCAA-TTC
1 CTCTCAATTTC
33225854 CTCTCAATTTC
1 CTCTCAATTTC
33225865 CT
1 CT
33225867 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:33225879 original size:22 final size:22
Alignment explanation
Indices: 33225849--33225901 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
33225839 ATTTCCTCTC
33225849 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
*
33225872 AATTCTCTCAATTTCTTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
33225894 AATTCTCT
1 AATTCTCT
33225902 TATATCCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 25 0.86
23 4 0.14
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Done.