Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 66 of 175
Found at i:19702330 original size:124 final size:122
Alignment explanation
Indices: 19702081--19702330 Score: 351
Period size: 124 Copynumber: 2.0 Consensus size: 122
19702071 TCCTAATTAT
*
19702081 ATATGTTCAATCGATCCTTCTGCTAACTTGAGATAACCAAAATTGCATGTAGAACAAATAGAAAG
1 ATATGTCCAATCGATCCTTCTGCTAACTTGAGATAACCAAAATTGCATGTAGAACAAATAGAAAG
*
19702146 AATTGAATAAAAATGAAGTAAGAGAAATAGATCACACGTATCATTATTCATAGTATTAA
66 AAATGAATAAAAATGAAGTAAGAGAAATAGATCACACGTATCATTATTCATAG--TTAA
* * * * *
19702205 ATATGTCCAATCGGTTCC-TCTGCTAGCTTGAGATAACTAGAATTGCATGTAGAACAAATAGATA
1 ATATGTCCAATC-GATCCTTCTGCTAACTTGAGATAACCAAAATTGCATGTAGAACAAATAGAAA
* *
19702269 GAAATGAATGAAAACAATGAAGTAAGATAAATAGATCACATGTATCATTATTCATAG-TAA
65 GAAATGAAT--AAA-AATGAAGTAAGAGAAATAGATCACACGTATCATTATTCATAGTTAA
19702329 AT
1 AT
19702331 GCATTTTCTT
Statistics
Matches: 113, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
124 66 0.58
125 4 0.04
126 3 0.03
127 40 0.35
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (122 bp):
ATATGTCCAATCGATCCTTCTGCTAACTTGAGATAACCAAAATTGCATGTAGAACAAATAGAAAG
AAATGAATAAAAATGAAGTAAGAGAAATAGATCACACGTATCATTATTCATAGTTAA
Found at i:19709177 original size:17 final size:17
Alignment explanation
Indices: 19709157--19709193 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19709147 TATCTAGTCA
* *
19709157 ATATTGTCCACTAGGGG
1 ATATTATCCACTAGGCG
19709174 ATATTATCCACTAGGCG
1 ATATTATCCACTAGGCG
19709191 ATA
1 ATA
19709194 CTGTTTGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (17 bp):
ATATTATCCACTAGGCG
Found at i:19709469 original size:78 final size:78
Alignment explanation
Indices: 19709340--19709493 Score: 238
Period size: 78 Copynumber: 2.0 Consensus size: 78
19709330 TCATAAGGTG
*
19709340 TGACCCTGTAGATTCTTGTAACGTTGTTAGTAATACTAGAACATTTTTAATGTTACAAGCAATAA
1 TGACCCTGTAGATTCTTGTAACGTTGTTAGTAATACTAGAACATTTTTAATGTTACAAGAAATAA
*
19709405 GTGGCGTCTAGTA
66 GTGGCATCTAGTA
* * * *
19709418 TGACCCTGTAGGTTCTTGTAATGTT-TGTAGTAATACTAGAACATTTTTAATGTTATAAGAAATG
1 TGACCCTGTAGATTCTTGTAACGTTGT-TAGTAATACTAGAACATTTTTAATGTTACAAGAAATA
19709482 AGTGGCATCTAG
65 AGTGGCATCTAG
19709494 CAACGCATCA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
77 1 0.01
78 68 0.99
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (78 bp):
TGACCCTGTAGATTCTTGTAACGTTGTTAGTAATACTAGAACATTTTTAATGTTACAAGAAATAA
GTGGCATCTAGTA
Found at i:19712078 original size:75 final size:75
Alignment explanation
Indices: 19711955--19712103 Score: 217
Period size: 75 Copynumber: 2.0 Consensus size: 75
19711945 TTTGGGTAAA
*
19711955 TCAAGAATAAGGCATGCCCACACCTTATTATTGCAGAACATCAGGAAGTACAAAATTTTTGTTCA
1 TCAAGAATAAGGCATGCCCACACCTTATTATTGCAGAACATCAAGAAGTACAAAATTTTTGTTCA
19712020 CAAAAGAAAT
66 CAAAAGAAAT
** * * * *
19712030 TCAAGAATAAGGCATGCCCATGCCTTATTATTGTAGAACATTAAGAAGTACAACATTTTTTTTCA
1 TCAAGAATAAGGCATGCCCACACCTTATTATTGCAGAACATCAAGAAGTACAAAATTTTTGTTCA
* *
19712095 TAGAAGAAA
66 CAAAAGAAA
19712104 CTCTAAAACA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (75 bp):
TCAAGAATAAGGCATGCCCACACCTTATTATTGCAGAACATCAAGAAGTACAAAATTTTTGTTCA
CAAAAGAAAT
Found at i:19712132 original size:75 final size:75
Alignment explanation
Indices: 19711955--19712133 Score: 189
Period size: 75 Copynumber: 2.4 Consensus size: 75
19711945 TTTGGGTAAA
* * * *
19711955 TCAAGAATAAGGCATGCCCACACCTTATTATTGCAGAACATCAGGAAGTACAAAATTTTTGTTCA
1 TCAAGAACAAGACATGCCCATACCTTATTATTGCAGAACATCAAGAAGTACAAAATTTTTGTTCA
*
19712020 CAAAAGAAAT
66 CAAAAGAAAC
* * * * * * *
19712030 TCAAGAATAAGGCATGCCCATGCCTTATTATTGTAGAACATTAAGAAGTACAACATTTTTTTTCA
1 TCAAGAACAAGACATGCCCATACCTTATTATTGCAGAACATCAAGAAGTACAAAATTTTTGTTCA
* *
19712095 TAGAAGAAAC
66 CAAAAGAAAC
* * *
19712105 TCTAA-AACAATACGTGCCCATAACTTATT
1 TC-AAGAACAAGACATGCCCATACCTTATT
19712134 CTTAAACTCC
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
75 85 0.98
76 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (75 bp):
TCAAGAACAAGACATGCCCATACCTTATTATTGCAGAACATCAAGAAGTACAAAATTTTTGTTCA
CAAAAGAAAC
Found at i:19717868 original size:3 final size:3
Alignment explanation
Indices: 19717860--19717884 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19717850 TGGTGACTCT
19717860 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
19717885 CAATTTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:19723391 original size:18 final size:17
Alignment explanation
Indices: 19723363--19723396 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
19723353 CATTTTTCTT
19723363 ATAATTAATTAATTTTA
1 ATAATTAATTAATTTTA
19723380 ATAATGTAATTAATTTT
1 ATAAT-TAATTAATTTT
19723397 TTATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATAATTAATTAATTTTA
Found at i:19735831 original size:44 final size:43
Alignment explanation
Indices: 19735779--19736483 Score: 284
Period size: 44 Copynumber: 16.2 Consensus size: 43
19735769 GATCGCATCT
19735779 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAACA
* **
19735823 AGTCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AACA
* * * * * **
19735868 AATCTTATCTCCTTGAGGTTGCAATGGAGCAGATTAA-AGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAC-A
* * * * * * *
19735911 TAATCCTATTTCCCTGAAGTTACAGTGGAGCAGATTAA-AATCTT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAC-A
* * * * * * *
19735955 GGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAACA
*
19735996 CGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAACA
* * * **
19736040 AGTCTTATC-CTCCTAAAGTTGCAGT-AAGGCAGACTGAATATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AACA
* * **
19736085 AATCTTATCTCCCT-AAGGTTGCAGTGGAGCAGATTAA-AGCCGA
1 AGTCTTATCTCCCTGAA-GTTGCAGTGGAGCAGACTAAGAAAC-A
* * * * * * *
19736128 TAATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAA-AACCTT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAC-A
* * * * * * *
19736172 GGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAACA
* *
19736213 AGTCTTATCTCCCTAAAGTTGCAGTAGAGCAGACTAAGTAAACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAACA
* **
19736257 AGTCTTATC-CTTCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AACA
* * * * **
19736302 AATCTTATCTCCCTGAGGTTGCAATGGAGCAGATTAA-AGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAC-A
* * * * * * *
19736345 TAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAA-AATCTT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAC-A
* * * * * * * * *
19736389 GGATCTTATCTCTCTGAAGTTGTAG-AGAGTAGA-T-CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAACA
* * * *
19736430 AGTCTTATCTCCCTGAAGCTGCATTTGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAACA
19736474 AGTCTTATCT
1 AGTCTTATCT
19736484 TTCTGAAATC
Statistics
Matches: 507, Mismatches: 110, Indels: 88
0.72 0.16 0.12
Matches are distributed among these distances:
40 59 0.12
41 27 0.05
42 20 0.04
43 34 0.07
44 269 0.53
45 90 0.18
46 8 0.02
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (43 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAACA
Found at i:19736072 original size:217 final size:217
Alignment explanation
Indices: 19735680--19736482 Score: 1363
Period size: 217 Copynumber: 3.7 Consensus size: 217
19735670 CCCTAAAGAA
* *
19735680 CAGATTAAAGCCGATAATCCTATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAACCTTGGATCTT
1 CAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTT
*
19735745 ATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
66 ATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
*
19735810 GACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGTAGTGAGGCAGACTGAAGATGGCAAATCTTA
131 GACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTA
*
19735875 TCTCCTTGAGGTTGCAATGGAG
196 TCTCCCTGAGGTTGCAATGGAG
* * * *
19735897 CAGATTAAAGCCGATAATCCTATTTCCCTGAAGTTACAGTGGAGCAGATTAAAATCTTGGATCTT
1 CAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTT
*
19735962 ATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTCGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
66 ATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * *
19736027 GACTAAGTAAACAAGTCTTATCCTCCTAAAGTTGCAGTAAGGCAGACTGAATATGGCAAATCTTA
131 GACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTA
* *
19736092 TCTCCCTAAGGTTGCAGTGGAG
196 TCTCCCTGAGGTTGCAATGGAG
*
19736114 CAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTT
1 CAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTT
* *
19736179 ATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTGCAGTAGAGCA
66 ATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
*
19736244 GACTAAGTAAACAAGTCTTATCCTTCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTA
131 GACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTA
19736309 TCTCCCTGAGGTTGCAATGGAG
196 TCTCCCTGAGGTTGCAATGGAG
* *
19736331 CAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCTTGGATCTT
1 CAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTT
* * * * *
19736396 ATCTCTCTGAAGTTGTAGAGAGTAGATCGCATCTAGTCTTATCTCCCTGAAGCTGCATTTGAGCA
66 ATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
*
19736461 GACTAAGTAAGCAAGTCTTATC
131 GACTAAGTAAACAAGTCTTATC
19736483 TTTCTGAAAT
Statistics
Matches: 547, Mismatches: 39, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
217 547 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (217 bp):
CAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTT
ATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
GACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTA
TCTCCCTGAGGTTGCAATGGAG
Found at i:19736263 original size:84 final size:85
Alignment explanation
Indices: 19735741--19736289 Score: 248
Period size: 84 Copynumber: 6.4 Consensus size: 85
19735731 AAACCTTGGA
* * * *
19735741 TCTTATCTCTCTGAAGTTGTAGAGAGCAGA-TCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTG
1 TCTTATCTCTCTGAAGTTGCAGGGAGCAGATTAGCATCTAGTCTTATCTCCCTGAAGTTGCAGTA
19735805 GAGCAGACTAAGTAAACAAG
66 GAGCAGACTAAGTAAACAAG
* * * * * * *
19735825 TCTTATC-CTCCTGAAGTTGTAGTGAGGCAGACTGAAG-ATGGCAAATCTTATCTCCTTGAGGTT
1 TCTTATCTCT-CTGAAGTTGCAGGGA-GCAGA-T-TAGCAT--CTAGTCTTATCTCCCTGAAGTT
* * * *** *
19735888 GCAATGGAGCAGATTAAAGCCGATAA-
60 GCAGTAGAGCAGACT-AAGTAAACAAG
* * * * ** * *
19735914 TCCTATTTCCCTGAAGTTACAGTGGAGCAGATTAAAATCTTGGATCTTATCTCTCTGAAGTTGCA
1 TCTTATCTCTCTGAAGTTGCAG-GGAGCAGATTAGCATC-TAG-TCTTATCTCCCTGAAGTTGCA
* * * **
19735979 G-AGAGCAGA-T-CG-CATCTCG
63 GTAGAGCAGACTAAGTAAACAAG
* * * * * *
19735998 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATC-CTCCTAAAGTTGC
1 TCTTATCTCTCTGAAGTTGCAG-GGAGCAGA-TTAG-CATCTAGTCTTATCTC-CCTGAAGTTGC
** *
19736062 AGTA-AGGCAGACTGAA-TATGGCAAA
62 AGTAGA-GCAGACT-AAGTA-AACAAG
* *** * * *
19736087 TCTTATCTCCCT-AAGGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTTCCTGAAGTTGC
1 TCTTATCTCTCTGAA-GTTGCAG-GGAGCAGATT--AGCATCTAGTCTTATCTCCCTGAAGTTGC
* * * * **
19736151 AGTGGAGCGGATTAA--AACCTTGG
62 AGTAGAGCAGACTAAGTAAAC-AAG
* * *
19736174 ATCTTATCTCTCTGAAGTTGCAGAGAGCAGA-TCGCATCTAGTCTTATCTCCCTAAAGTTGCAGT
1 -TCTTATCTCTCTGAAGTTGCAGGGAGCAGATTAGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
19736238 AGAGCAGACTAAGTAAACAAG
65 AGAGCAGACTAAGTAAACAAG
*
19736259 TCTTATC-CTTCTGAAGTTGCAGTGAGGCAGA
1 TCTTATCTC-TCTGAAGTTGCAGGGA-GCAGA
19736290 CTGAAGATGG
Statistics
Matches: 342, Mismatches: 87, Indels: 71
0.68 0.17 0.14
Matches are distributed among these distances:
83 5 0.01
84 124 0.36
85 20 0.06
86 11 0.03
87 18 0.05
88 45 0.13
89 107 0.31
90 12 0.04
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (85 bp):
TCTTATCTCTCTGAAGTTGCAGGGAGCAGATTAGCATCTAGTCTTATCTCCCTGAAGTTGCAGTA
GAGCAGACTAAGTAAACAAG
Found at i:19736861 original size:32 final size:33
Alignment explanation
Indices: 19736801--19736863 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
19736791 AACAGTCCTT
*
19736801 TTACAATAAAATGGGCCCAAAACCCAAACCCAA
1 TTACAATAAAATAGGCCCAAAACCCAAACCCAA
*
19736834 TTACAATAAAATAGGTCC-AAACCCAAACCC
1 TTACAATAAAATAGGCCCAAAACCCAAACCC
19736864 GATTTTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.48, C:0.30, G:0.08, T:0.14
Consensus pattern (33 bp):
TTACAATAAAATAGGCCCAAAACCCAAACCCAA
Found at i:19739801 original size:29 final size:30
Alignment explanation
Indices: 19739752--19739811 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
19739742 TGTTTAATCA
19739752 TATACATAAACTTTGATTTTG-TGTAATTT
1 TATACATAAACTTTGATTTTGATGTAATTT
* *
19739781 TATACATAAAATTTTGA-TTTGATTTAATTT
1 TATACAT-AAACTTTGATTTTGATGTAATTT
19739811 T
1 T
19739812 TGTAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.53
Consensus pattern (30 bp):
TATACATAAACTTTGATTTTGATGTAATTT
Found at i:19741050 original size:14 final size:14
Alignment explanation
Indices: 19741031--19741078 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
19741021 TTTGCCCGTT
19741031 TTTAGGTTTTAGGG
1 TTTAGGTTTTAGGG
19741045 TTTAGGGTTTTAGGG
1 TTTA-GGTTTTAGGG
* *
19741060 TTT-GGGTTTGGGG
1 TTTAGGTTTTAGGG
19741073 TTTAGG
1 TTTAGG
19741079 GTTAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 11 0.37
14 6 0.20
15 13 0.43
ACGTcount: A:0.10, C:0.00, G:0.42, T:0.48
Consensus pattern (14 bp):
TTTAGGTTTTAGGG
Found at i:19741073 original size:7 final size:7
Alignment explanation
Indices: 19741031--19741081 Score: 68
Period size: 7 Copynumber: 7.3 Consensus size: 7
19741021 TTTGCCCGTT
*
19741031 TTTAGGT
1 TTTAGGG
19741038 TTTAGGG
1 TTTAGGG
19741045 TTTAGGG
1 TTTAGGG
19741052 TTTTAGGG
1 -TTTAGGG
19741060 TTT-GGG
1 TTTAGGG
*
19741066 TTTGGGG
1 TTTAGGG
19741073 TTTAGGG
1 TTTAGGG
19741080 TT
1 TT
19741082 AAAAATTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 6 0.15
7 27 0.68
8 7 0.17
ACGTcount: A:0.10, C:0.00, G:0.41, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:19741349 original size:37 final size:38
Alignment explanation
Indices: 19741283--19741356 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 38
19741273 AATAAATACC
19741283 AAAAATTATTTTAAAATAAAAAGAATAAAAAAGTATTTT
1 AAAAATTATTTTAAAATAAAAAGAATAAAAAA-TATTTT
*
19741322 AAAAA-TATTTTAAAAT-TAAAGAATAAAAAATATTT
1 AAAAATTATTTTAAAATAAAAAGAATAAAAAATATTT
19741357 ATTGATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 5 0.15
37 13 0.38
38 11 0.32
39 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (38 bp):
AAAAATTATTTTAAAATAAAAAGAATAAAAAATATTTT
Found at i:19741698 original size:18 final size:19
Alignment explanation
Indices: 19741675--19741711 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
19741665 TTAGATTAGG
19741675 GTTAGGGTT-AGGGTTTTT
1 GTTAGGGTTAAGGGTTTTT
19741693 GTTAGGGTTAAGGGTTTTT
1 GTTAGGGTTAAGGGTTTTT
19741712 AAGGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.49
Consensus pattern (19 bp):
GTTAGGGTTAAGGGTTTTT
Found at i:19742045 original size:222 final size:221
Alignment explanation
Indices: 19741538--19742194 Score: 962
Period size: 212 Copynumber: 3.0 Consensus size: 221
19741528 TACTTTAAGG
*
19741538 TTTGTCAATT-AATTATTTAAAAAAATTTCAAAATTGGATTAGTTTTCGTGTTTATTATTTTTTA
1 TTTGTCAATTAAATTATTTAAAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTATTATTTTTTA
* *
19741602 AGAAAAATCAATTAAATTAGGGTTTAGAGTTACTTGAGTAATTTAATTAAAAAAATTTTAAAATT
66 AGAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAATTTAAAAATT
*
19741667 AGATTAGGGTTA-GG-----GTTAGGGTTTTTG---TTAGGGTTAAGGGTTTTTAAGGAAAAATT
131 AGATTAGGGTTAGGGTTTTTGTTAGGGTTTTTGTTTTTA-AGTTAAGGGTTTTTAAGGAAAAATT
* *
19741723 ACATAAGTTAGGGTTTAGAGTTTAGGG
195 AAATAAGTTAGGGTTTAGAGTTTAGGA
*
19741750 TTTGTCAATTAAATTATTTAAAAAATTTTC-AAATTGGATTCGTTTTCGTGTTTATTA-TTTTTA
1 TTTGTCAATTAAATTATTTAAAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTATTATTTTTTA
* *
19741813 AGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGTGTAATTTAATTTAAAAAATTTAAAAAT
66 AG-AAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAATTTAAAAAT
19741878 TAGATTAGGGTTAGGGTTTTTGTTAGGGTTTTAATGTTTTTAAGTTAAGGGTTTTTAAGG-AAAA
130 TAGATTAGGGTTAGGGTTTTTGTTAGGGTTTT--TGTTTTTAAGTTAAGGGTTTTTAAGGAAAAA
* *
19741942 TCAAATAAGTTAGGGTTTAAAGTTTAGGA
193 TTAAATAAGTTAGGGTTTAGAGTTTAGGA
* * *
19741971 TTTGTCAATTAAATTATTTATAAATTTTTCAAAATTGGATTAGTTTTCGTGCTTATTATTTTTTA
1 TTTGTCAATTAAATTATTTAAAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTATTATTTTTTA
*
19742036 AGAAAAATCAATTATATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAATTTTAAAAAT
66 AGAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAA-TTT--AAA-
* *
19742101 CAGATTAGGTTAGGGTTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTAAGGATTTTTAAGG
127 -A-ATTAGATTAGGGTTAGGGTTTTTGTTAGGGTTTT--TGTTTTTAAGTTAAGGGTTTTTAAGG
19742166 AAAAATTAAATAAGTTAGGGTTTAGAGTT
188 AAAAATTAAATAAGTTAGGGTTTAGAGTT
19742195 ATTTCCAAAT
Statistics
Matches: 399, Mismatches: 24, Indels: 27
0.89 0.05 0.06
Matches are distributed among these distances:
211 8 0.02
212 107 0.27
213 20 0.05
218 11 0.03
220 2 0.01
221 57 0.14
222 92 0.23
223 14 0.04
225 3 0.01
227 1 0.00
228 58 0.15
229 26 0.07
ACGTcount: A:0.35, C:0.03, G:0.19, T:0.44
Consensus pattern (221 bp):
TTTGTCAATTAAATTATTTAAAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTATTATTTTTTA
AGAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAATTTAAAAATT
AGATTAGGGTTAGGGTTTTTGTTAGGGTTTTTGTTTTTAAGTTAAGGGTTTTTAAGGAAAAATTA
AATAAGTTAGGGTTTAGAGTTTAGGA
Found at i:19743567 original size:18 final size:18
Alignment explanation
Indices: 19743546--19743582 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
19743536 GAAAAGGAAC
* *
19743546 CATATAAGGGTTAGGATA
1 CATAAAAGGGCTAGGATA
19743564 CATAAAAGGGCTAGGATA
1 CATAAAAGGGCTAGGATA
19743582 C
1 C
19743583 GCACCTGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.22
Consensus pattern (18 bp):
CATAAAAGGGCTAGGATA
Found at i:19745439 original size:11 final size:11
Alignment explanation
Indices: 19745420--19745515 Score: 76
Period size: 11 Copynumber: 9.0 Consensus size: 11
19745410 GGATTTAAGA
19745420 GAAATTTGAGAG
1 GAAA-TTGAGAG
19745432 GAAATTGAGAG
1 GAAATTGAGAG
* *
19745443 TAAATTGAGAT
1 GAAATTGAGAG
*
19745454 TAAA-T-AG-G
1 GAAATTGAGAG
*
19745462 G-ATTTGAGA-
1 GAAATTGAGAG
*
19745471 GAAATTTAGAAG
1 GAAATTGAG-AG
19745483 GAAATTGAGAG
1 GAAATTGAGAG
*
19745494 CAAATTGAGAG
1 GAAATTGAGAG
*
19745505 GACATTGAGAG
1 GAAATTGAGAG
19745516 AATAATAGAG
Statistics
Matches: 67, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 5 0.07
10 6 0.09
11 42 0.63
12 12 0.18
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (11 bp):
GAAATTGAGAG
Found at i:19745460 original size:51 final size:51
Alignment explanation
Indices: 19745404--19745503 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
19745394 AATAATTAAA
*
19745404 AAATAGGGATTTAAGAGAAATTT-GAGAGGAAATTGAGAGTAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
*
19745455 AAATAGGGATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
19745504 GGACATTGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 44 0.96
52 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.28, T:0.25
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:19746356 original size:30 final size:33
Alignment explanation
Indices: 19746301--19746361 Score: 92
Period size: 30 Copynumber: 1.9 Consensus size: 33
19746291 TCTAAAACAT
19746301 TTTATTATTAAATATTTATAAATTATAATATATA
1 TTTATTATTAAATA-TTATAAATTATAATATATA
19746335 TTTATTATTAAA-A-TA-AAATTATAATAT
1 TTTATTATTAAATATTATAAATTATAATAT
19746362 TAAATAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 12 0.44
31 2 0.07
33 1 0.04
34 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TTTATTATTAAATATTATAAATTATAATATATA
Found at i:19748273 original size:9 final size:9
Alignment explanation
Indices: 19748259--19748304 Score: 56
Period size: 9 Copynumber: 4.7 Consensus size: 9
19748249 GAAGATGGAT
19748259 AAATAAATA
1 AAATAAATA
19748268 AAATAAATA
1 AAATAAATA
19748277 AAATAGAATA
1 AAATA-AATA
19748287 TAAATAAGATA
1 -AAATAA-ATA
19748298 AAGATAA
1 AA-ATAA
19748305 GGCAGGAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 14 0.42
10 7 0.21
11 12 0.36
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.22
Consensus pattern (9 bp):
AAATAAATA
Found at i:19767093 original size:5 final size:5
Alignment explanation
Indices: 19767083--19767120 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
19767073 TTTTTATTCA
19767083 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
19767121 TAATCTTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:19778379 original size:18 final size:19
Alignment explanation
Indices: 19778356--19778392 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
19778346 AAACTCCATC
19778356 TCCTCATCCTC-CTTTCTT
1 TCCTCATCCTCGCTTTCTT
*
19778374 TCCTCATCTTCGCTTTCTT
1 TCCTCATCCTCGCTTTCTT
19778393 CACTTTCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.05, C:0.41, G:0.03, T:0.51
Consensus pattern (19 bp):
TCCTCATCCTCGCTTTCTT
Found at i:19788845 original size:27 final size:27
Alignment explanation
Indices: 19788815--19788880 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
19788805 CATCCAAATG
19788815 TATTTAAATGTTAATGTGGTACTATTT
1 TATTTAAATGTTAATGTGGTACTATTT
19788842 TATTTAAATGTTAATGTGGTACTATTT
1 TATTTAAATGTTAATGTGGTACTATTT
*
19788869 TATCTTATATGT
1 TAT-TTAAATGT
19788881 CAGTAAACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 30 0.81
28 7 0.19
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (27 bp):
TATTTAAATGTTAATGTGGTACTATTT
Found at i:19789114 original size:23 final size:23
Alignment explanation
Indices: 19789084--19789134 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
19789074 GATTGAGCTC
19789084 GCATTAGTTTCAAGTTTTTGGAT
1 GCATTAGTTTCAAGTTTTTGGAT
19789107 GCATTAGTTTCAAGTTTTTGGAT
1 GCATTAGTTTCAAGTTTTTGGAT
19789130 GCATT
1 GCATT
19789135 TAAGTTCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.47
Consensus pattern (23 bp):
GCATTAGTTTCAAGTTTTTGGAT
Found at i:19790075 original size:15 final size:16
Alignment explanation
Indices: 19790055--19790087 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
19790045 TGATGATTTT
19790055 AAAATAATT-TTTTAA
1 AAAATAATTATTTTAA
19790070 AAAATAATTATTTTAA
1 AAAATAATTATTTTAA
19790086 AA
1 AA
19790088 TTATTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATAATTATTTTAA
Found at i:19798881 original size:2 final size:2
Alignment explanation
Indices: 19798876--19798900 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19798866 GGTATATATA
19798876 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
19798901 ACTTAAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:19799468 original size:41 final size:41
Alignment explanation
Indices: 19799424--19799583 Score: 257
Period size: 41 Copynumber: 3.9 Consensus size: 41
19799414 CAAGTTTATT
*
19799424 GCCGGTGAAACATTTCAGACTTTAAGTCTAGCAGGCTTGAT
1 GCCGGTGAAACATTTCAGACTTTAAGTCTAGCAGGCTTGAC
* * *
19799465 GCCGGGGAAACATTTTAGACTTTAAGTTTAGCAGGCTTGAC
1 GCCGGTGAAACATTTCAGACTTTAAGTCTAGCAGGCTTGAC
*
19799506 GCCGATGAAACATTTCAGACTTTAAGTCTAGCAGGCTTGAC
1 GCCGGTGAAACATTTCAGACTTTAAGTCTAGCAGGCTTGAC
* *
19799547 GCCGGTGAAACATTTCAGACTTTATGTCTAACAGGCT
1 GCCGGTGAAACATTTCAGACTTTAAGTCTAGCAGGCT
19799584 AAGTGTCAGT
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 108 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
GCCGGTGAAACATTTCAGACTTTAAGTCTAGCAGGCTTGAC
Found at i:19800986 original size:53 final size:54
Alignment explanation
Indices: 19800904--19801013 Score: 141
Period size: 53 Copynumber: 2.1 Consensus size: 54
19800894 TCGTGGCACT
* * * * *
19800904 AAAGAATACCATATCGTGTAAGACCGTAACTGATGAGTTATGGCATCATAT-GG
1 AAAGAAGACCATATCATGTAAAACAGTAACTGAGGAGTTATGGCATCATATAGG
* * *
19800957 AAAGAAGACCATATCATGTAAAATAGTAACTGGGGGGTTATGGCATCATATAGG
1 AAAGAAGACCATATCATGTAAAACAGTAACTGAGGAGTTATGGCATCATATAGG
19801011 AAA
1 AAA
19801014 ATTTAAGAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 43 0.90
54 5 0.10
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.25
Consensus pattern (54 bp):
AAAGAAGACCATATCATGTAAAACAGTAACTGAGGAGTTATGGCATCATATAGG
Found at i:19801245 original size:57 final size:57
Alignment explanation
Indices: 19801125--19801253 Score: 152
Period size: 57 Copynumber: 2.3 Consensus size: 57
19801115 AACACTAGTA
* * * * * * *
19801125 AAAGAACAGCCTTTATGGAAAAACTCTGAAAAGACAAGCCTTTGTGGCGAACCTGTT
1 AAAGGACAACCTTTATGGAAAAACTCTAAAAAGACAAGCCTTTCTGGAGAACATATT
* *
19801182 ACAGGACAACCTTTATGGAAAAACTCTAAAAA-AGCAAGCTTTTCTGGAGAACATATT
1 AAAGGACAACCTTTATGGAAAAACTCTAAAAAGA-CAAGCCTTTCTGGAGAACATATT
*
19801239 AAAGGACAACTTTTA
1 AAAGGACAACCTTTA
19801254 AAGCAAAACT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
56 1 0.02
57 59 0.98
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (57 bp):
AAAGGACAACCTTTATGGAAAAACTCTAAAAAGACAAGCCTTTCTGGAGAACATATT
Found at i:19802733 original size:23 final size:23
Alignment explanation
Indices: 19802698--19802742 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
19802688 TGGAGTATAA
* *
19802698 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
19802721 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
19802743 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:19803362 original size:42 final size:42
Alignment explanation
Indices: 19803315--19803538 Score: 267
Period size: 42 Copynumber: 5.4 Consensus size: 42
19803305 TGCCTATCAA
19803315 GCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGCAG
1 GCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGCAG
* * * *
19803357 GCTTAATGCCGGTGAAATAATTTCAGAATTTACGTCTAGCAG
1 GCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGCAG
*
19803399 GCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAG
1 GCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGCAG
* * * *
19803441 GCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAGCAG
1 GCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGCAG
* * * * * *
19803482 GCTAAATGCCAGTG-TACTGA-ATCAGGCTTTAAGTCTAGCAA
1 GCTTAATGCCAGTGAAAC-AATATCAGACTTTACGTCTAGCAG
19803523 GC-TAAGTGCCAGTGAA
1 GCTTAA-TGCCAGTGAA
19803539 TCTGTTTAAA
Statistics
Matches: 158, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
40 4 0.03
41 58 0.37
42 96 0.61
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (42 bp):
GCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGCAG
Found at i:19803456 original size:84 final size:83
Alignment explanation
Indices: 19803315--19803495 Score: 299
Period size: 84 Copynumber: 2.2 Consensus size: 83
19803305 TGCCTATCAA
19803315 GCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATTT
1 GCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA-AATTT
*
19803380 CAGAATTTACGTCTAGCAG
65 CAGAATATACGTCTAGCAG
* *
19803399 GCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACATTTC
1 GCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAAAATTTC
* *
19803464 AGACTATATGTCTAGCAG
66 AGAATATACGTCTAGCAG
*
19803482 GCTAAATGCCAGTG
1 GCTTAATGCCAGTG
19803496 TACTGAATCA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
83 32 0.36
84 58 0.64
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (83 bp):
GCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAAAATTTC
AGAATATACGTCTAGCAG
Found at i:19809711 original size:23 final size:23
Alignment explanation
Indices: 19809676--19809720 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
19809666 TGGAGTATAA
* *
19809676 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
19809699 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
19809721 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:19810452 original size:41 final size:42
Alignment explanation
Indices: 19810286--19810465 Score: 274
Period size: 42 Copynumber: 4.3 Consensus size: 42
19810276 CAGTGCCTAT
19810286 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * *
19810328 CAGGCTTAATGCCGGTGAAATAATTTCAGAATTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
19810370 CAGGCTTAATG-CGAGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCG-GTGAAACAATATCAGACTTTACGTCTAG
* * *
19810412 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
*
19810453 CAGGCTAAATGCC
1 CAGGCTTAATGCC
19810466 AATGTACTGA
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
41 31 0.25
42 93 0.74
43 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
Found at i:19812682 original size:33 final size:32
Alignment explanation
Indices: 19812566--19812675 Score: 148
Period size: 33 Copynumber: 3.3 Consensus size: 32
19812556 TATTATCTGT
*
19812566 TGGTGTGCTGGTTGGACTAGCTCTTATGAGCA
1 TGGTGTGCTGGTTGGATTAGCTCTTATGAGCA
* *
19812598 CTGGTGTGATAGTTGGATTAGCTCTTATGAGCA
1 -TGGTGTGCTGGTTGGATTAGCTCTTATGAGCA
* *
19812631 TTGGTGTGTTGGTTGGATTAGCTCTTCTGAGCA
1 -TGGTGTGCTGGTTGGATTAGCTCTTATGAGCA
19812664 TAGGTGTGCTGG
1 T-GGTGTGCTGG
19812676 AGGGATTGCC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 1 0.01
33 67 0.99
ACGTcount: A:0.15, C:0.13, G:0.35, T:0.37
Consensus pattern (32 bp):
TGGTGTGCTGGTTGGATTAGCTCTTATGAGCA
Found at i:19816375 original size:51 final size:49
Alignment explanation
Indices: 19816242--19816427 Score: 219
Period size: 51 Copynumber: 3.7 Consensus size: 49
19816232 GTGAAAGTGA
* *
19816242 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAG-T
* * * *
19816292 AGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGCT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAG-T
* * * * *
19816342 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACATGTATCGGATAGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGT
*
19816392 GATGGTCACATGTGTAGTACTATGTGTAGGCTACTA
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
19816428 TGTGAACCGG
Statistics
Matches: 114, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
50 44 0.39
51 69 0.61
52 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGT
Found at i:19816505 original size:46 final size:44
Alignment explanation
Indices: 19816432--19816531 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 44
19816422 CTACTATGTG
*
19816432 AACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCC
1 AACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
* * *
19816475 AACCGGATATCATTGATTACAAAGGGTGGTTGTTGTGTGCTGAATCC
1 AACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
19816522 -ACCGTGTATC
1 AACCG-GTATC
19816532 TGTTACTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 6 0.12
44 11 0.23
45 2 0.04
46 24 0.50
47 5 0.10
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (44 bp):
AACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:19816701 original size:37 final size:38
Alignment explanation
Indices: 19816632--19816704 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
19816622 ATGTATGGAA
* **
19816632 TTGAATTGAATATTGACTTGAAAATGGCAAAGTGAATT
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAATT
*
19816670 TTGAATTGAATAGTGA-TTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAA
19816705 ATTATAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (38 bp):
TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAATT
Found at i:19827953 original size:17 final size:17
Alignment explanation
Indices: 19827923--19827956 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19827913 TATTAATATT
**
19827923 AATATTAATTAAAAATA
1 AATATTAAAAAAAAATA
19827940 AATATTAAAAAAAAATA
1 AATATTAAAAAAAAATA
19827957 TTTTCCCTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATATTAAAAAAAAATA
Found at i:19837797 original size:16 final size:16
Alignment explanation
Indices: 19837757--19837798 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
19837747 TTTGAATAAG
19837757 AGTTGTTCTATGGTAA
1 AGTTGTTCTATGGTAA
* *
19837773 TGTTTTTCT-TGGTAA
1 AGTTGTTCTATGGTAA
19837788 AGCTTGTTCTA
1 AG-TTGTTCTA
19837799 AATAATGACT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.19, C:0.10, G:0.21, T:0.50
Consensus pattern (16 bp):
AGTTGTTCTATGGTAA
Found at i:19839081 original size:31 final size:30
Alignment explanation
Indices: 19839046--19839105 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
19839036 GGAGGTGGGA
*
19839046 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
19839077 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
19839106 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:19839328 original size:9 final size:9
Alignment explanation
Indices: 19839314--19839350 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
19839304 TATAGTTTGA
19839314 TATTCGAAT
1 TATTCGAAT
*
19839323 TATTCGACT
1 TATTCGAAT
*
19839332 TATTCGAGT
1 TATTCGAAT
19839341 TATTCGAAT
1 TATTCGAAT
19839350 T
1 T
19839351 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19839421 original size:9 final size:9
Alignment explanation
Indices: 19839404--19839434 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19839394 TCGAGTTGAT
19839404 TCGAATAAC
1 TCGAATAAC
*
19839413 TCGATTAAC
1 TCGAATAAC
19839422 TCGAATAAC
1 TCGAATAAC
19839431 TCGA
1 TCGA
19839435 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:19839678 original size:28 final size:29
Alignment explanation
Indices: 19839629--19839683 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
19839619 TTTTTTCAAA
*
19839629 ATTTATCGAAATGGGCCAATTTTTTGATT
1 ATTTACCGAAATGGGCCAATTTTTTGATT
* *
19839658 ATTTACCGGAATGGTCC-ATTTTTTGA
1 ATTTACCGAAATGGGCCAATTTTTTGA
19839684 GAAATTGCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (29 bp):
ATTTACCGAAATGGGCCAATTTTTTGATT
Found at i:19840635 original size:31 final size:32
Alignment explanation
Indices: 19840600--19840667 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
19840590 GCCATTGATG
19840600 AAAATAT-AAAAAATTTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTTAAAATTATTTTAAA
*
19840631 AAAATATAAAAAAATTTTGAAATTATTTTAAA
1 AAAATATAAAAAAATTTTAAAATTATTTTAAA
19840663 AAAAT
1 AAAAT
19840668 GAAATTGAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 7 0.20
32 28 0.80
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (32 bp):
AAAATATAAAAAAATTTTAAAATTATTTTAAA
Found at i:19840726 original size:22 final size:21
Alignment explanation
Indices: 19840701--19840751 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
19840691 TAATATGGAT
*
19840701 TTGAGAGATTTTTGGAATGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
19840723 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGA-GATTTTGGAAGGAAA
19840745 TTGAGAG
1 TTGAGAG
19840752 TTTAAGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 24 0.89
23 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:19840768 original size:52 final size:52
Alignment explanation
Indices: 19840704--19840802 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
19840694 TATGGATTTG
* *
19840704 AGAGATTTTTGGAATGAAATTGAGAGGATTTTGGAAGGAAATTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGAGTTTA
19840756 AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGA
1 AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGA
19840803 TAGGATTTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGAGTTTA
Found at i:19840786 original size:22 final size:22
Alignment explanation
Indices: 19840756--19840802 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
19840746 TGAGAGTTTA
19840756 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
*
19840778 AGAGGATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
19840800 AGA
1 AGA
19840803 TAGGATTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:19846092 original size:30 final size:30
Alignment explanation
Indices: 19846058--19846130 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
19846048 ACAGGCTGCC
* * *
19846058 ACACGGCCATGTGTCCCACACTGTCCAATG
1 ACACGGCCATGTGCCCCACACGGTCAAATG
***
19846088 ACACGGTTGTGTGCCCCACACGGTCAAATG
1 ACACGGCCATGTGCCCCACACGGTCAAATG
*
19846118 ACACAGCCATGTG
1 ACACGGCCATGTG
19846131 ATCCTTTAAA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.19
Consensus pattern (30 bp):
ACACGGCCATGTGCCCCACACGGTCAAATG
Found at i:19846798 original size:24 final size:24
Alignment explanation
Indices: 19846771--19846848 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 24
19846761 GCCAATATGA
*
19846771 AAAGTGATAGAGGCACTATGGTGC
1 AAAGTGATAGTGGCACTATGGTGC
* **
19846795 AAAGTGATGGTGGCACTACAGTGC
1 AAAGTGATAGTGGCACTATGGTGC
* *
19846819 -AAGTGA-A-TGGTACTTTGGTGC
1 AAAGTGATAGTGGCACTATGGTGC
19846840 AAAGTGATA
1 AAAGTGATA
19846849 TCCACATGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
21 10 0.23
22 6 0.14
23 7 0.16
24 20 0.47
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (24 bp):
AAAGTGATAGTGGCACTATGGTGC
Found at i:19848169 original size:25 final size:25
Alignment explanation
Indices: 19848140--19848189 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
19848130 TGAGAAAAGA
*
19848140 AAAGTTTGAACTTGAGATAGTGAGT
1 AAAGTTTGAACTTGAGATAGCGAGT
*
19848165 AAAGTTTGAATTTGAGATAGCGAGT
1 AAAGTTTGAACTTGAGATAGCGAGT
19848190 GTTCAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (25 bp):
AAAGTTTGAACTTGAGATAGCGAGT
Found at i:19848518 original size:26 final size:26
Alignment explanation
Indices: 19848489--19848538 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
19848479 CTGTAGAGTT
19848489 AGTATAACCTAGAGGGAAGAACCAGG
1 AGTATAACCTAGAGGGAAGAACCAGG
19848515 AGTATAACCTAGAGGGAAGAACCA
1 AGTATAACCTAGAGGGAAGAACCA
19848539 TGAGACGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.28, T:0.12
Consensus pattern (26 bp):
AGTATAACCTAGAGGGAAGAACCAGG
Found at i:19872422 original size:16 final size:16
Alignment explanation
Indices: 19872401--19872447 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
19872391 TTTGTGTTTT
19872401 CTTATTTTTAACTTTA
1 CTTATTTTTAACTTTA
*
19872417 CTTATTTTATTACTTTA
1 CTTATTTT-TAACTTTA
19872434 -TTATTATTTAACTT
1 CTTATT-TTTAACTT
19872448 ATAATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.64
Consensus pattern (16 bp):
CTTATTTTTAACTTTA
Found at i:19874611 original size:20 final size:18
Alignment explanation
Indices: 19874576--19874664 Score: 55
Period size: 18 Copynumber: 5.0 Consensus size: 18
19874566 GCAAGCCTAT
*
19874576 TAAATATGACTTATTAAA
1 TAAAAATGACTTATTAAA
19874594 TAAAAATGATCTTAATTAAAA
1 TAAAAATGA-CTT-ATT-AAA
** *
19874615 TAGCAA-G-CCTATTAAA
1 TAAAAATGACTTATTAAA
19874631 T----ATGACTTATTAAA
1 TAAAAATGACTTATTAAA
19874645 TAAAAATGATCTTAATTAAA
1 TAAAAATGA-CTT-ATTAAA
19874665 ATATTATTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
12 1 0.02
13 1 0.02
14 9 0.16
16 4 0.07
17 3 0.05
18 14 0.25
19 6 0.11
20 10 0.18
21 7 0.13
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.35
Consensus pattern (18 bp):
TAAAAATGACTTATTAAA
Found at i:19874620 original size:51 final size:51
Alignment explanation
Indices: 19874565--19874667 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
19874555 GTTTCATATA
19874565 AGCAAGCCTATTAAATATGACTTATTAAATAAAAATGATCTTAATTAAAAT
1 AGCAAGCCTATTAAATATGACTTATTAAATAAAAATGATCTTAATTAAAAT
19874616 AGCAAGCCTATTAAATATGACTTATTAAATAAAAATGATCTTAATTAAAAT
1 AGCAAGCCTATTAAATATGACTTATTAAATAAAAATGATCTTAATTAAAAT
19874667 A
1 A
19874668 TTATTTCAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (51 bp):
AGCAAGCCTATTAAATATGACTTATTAAATAAAAATGATCTTAATTAAAAT
Found at i:19878856 original size:2 final size:2
Alignment explanation
Indices: 19878849--19878901 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
19878839 GCATCAAACG
19878849 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19878891 CT CT CT CT CT C
1 CT CT CT CT CT C
19878902 GGACTGAAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:19879679 original size:3 final size:3
Alignment explanation
Indices: 19879671--19879721 Score: 59
Period size: 3 Copynumber: 16.3 Consensus size: 3
19879661 TAGAACTAAA
*
19879671 AAT AAT AAT -AT AATT AAA AACCT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AA--T AAT AAT AAT AAT AAT AAT AAT AAT
19879718 AAT A
1 AAT A
19879722 TGTTCATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 2 0.05
3 35 0.83
4 3 0.07
5 2 0.05
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19880197 original size:12 final size:11
Alignment explanation
Indices: 19880167--19880218 Score: 70
Period size: 11 Copynumber: 4.6 Consensus size: 11
19880157 AAATTATATT
19880167 ATATTTATTTA
1 ATATTTATTTA
19880178 ATATTTATTTA
1 ATATTTATTTA
19880189 ATGATTTATTTA
1 AT-ATTTATTTA
19880201 ATATTCT-TTTA
1 ATATT-TATTTA
*
19880212 ACATTTA
1 ATATTTA
19880219 CATAATCTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
10 1 0.03
11 24 0.65
12 12 0.32
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (11 bp):
ATATTTATTTA
Found at i:19880335 original size:21 final size:21
Alignment explanation
Indices: 19880285--19880349 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
19880275 TATTTATAAT
*
19880285 ATATTAAAATAATTTTAATTAAA
1 ATATTAAAAT--TTTTAATAAAA
19880308 ATAATTAAAATTTTTAA-AAATA
1 AT-ATTAAAATTTTTAATAAA-A
* * *
19880330 ATATTATATTTTTTATTAAA
1 ATATTAAAATTTTTAATAAA
19880350 CAAATTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 13 0.37
22 12 0.34
23 2 0.06
24 8 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATTAAAATTTTTAATAAAA
Found at i:19880670 original size:43 final size:43
Alignment explanation
Indices: 19880562--19880680 Score: 166
Period size: 43 Copynumber: 2.8 Consensus size: 43
19880552 TAAACGGACT
* * * * *
19880562 TTTAGCGGCGCTTTTCCCATAAACGCCACTAAAGATCAAGACC
1 TTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAGACCAAAACC
* *
19880605 TTTAGCGACGCTTTTCCCACAAGCACCGCTAAAGACCAAAACC
1 TTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAGACCAAAACC
*
19880648 TTTAGCGGCGCTTTTCACACAAGCGCCGCTAAA
1 TTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAA
19880681 AATATATCTT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTCCCACAAGCGCCGCTAAAGACCAAAACC
Found at i:19880995 original size:43 final size:43
Alignment explanation
Indices: 19880947--19881037 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
19880937 ACATATGCAA
* * *
19880947 GGTAATAAAACATAGAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAACATAGAATACATTTACTTAATCAAGGAAATCTT
* **
19880990 GGTAATAAAAGATATCATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAACATAGAATACATTTACTTAATCAAGGAAATCTT
19881033 -GTAAT
1 GGTAAT
19881038 GAACTCAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 5 0.12
43 37 0.88
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (43 bp):
GGTAATAAAACATAGAATACATTTACTTAATCAAGGAAATCTT
Found at i:19885218 original size:13 final size:13
Alignment explanation
Indices: 19885200--19885227 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19885190 ATTCTTTCTC
19885200 TATTTATGAAGTT
1 TATTTATGAAGTT
19885213 TATTTATGAAGTT
1 TATTTATGAAGTT
19885226 TA
1 TA
19885228 CTTGTACAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (13 bp):
TATTTATGAAGTT
Found at i:19886624 original size:12 final size:12
Alignment explanation
Indices: 19886607--19886632 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19886597 TTTTCCAGAA
19886607 AACATTATATCG
1 AACATTATATCG
19886619 AACATTATATCG
1 AACATTATATCG
19886631 AA
1 AA
19886633 TACACAAACG
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (12 bp):
AACATTATATCG
Found at i:19887360 original size:18 final size:18
Alignment explanation
Indices: 19887337--19887394 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
19887327 ATTTGAAGGA
19887337 ATGAAGGGAGAAGAATGG
1 ATGAAGGGAGAAGAATGG
* *** *
19887355 ATGAAGGAAGCTTACTGG
1 ATGAAGGGAGAAGAATGG
*
19887373 ATGAAGGGAGAAGAATGC
1 ATGAAGGGAGAAGAATGG
19887391 ATGA
1 ATGA
19887395 GAGCTTTAGG
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.41, C:0.05, G:0.38, T:0.16
Consensus pattern (18 bp):
ATGAAGGGAGAAGAATGG
Found at i:19888181 original size:14 final size:15
Alignment explanation
Indices: 19888158--19888215 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
19888148 AATCATAAAA
*
19888158 CATAAGCCCTAAACC
1 CATAACCCCTAAACC
*
19888173 CATAACCCTTAAACC
1 CATAACCCCTAAACC
*
19888188 C-TAACCTCT-AACC
1 CATAACCCCTAAACC
*
19888201 CTTAACCCCTAAACC
1 CATAACCCCTAAACC
19888216 TTAAACCCCA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 5 0.14
14 13 0.36
15 18 0.50
ACGTcount: A:0.36, C:0.43, G:0.02, T:0.19
Consensus pattern (15 bp):
CATAACCCCTAAACC
Found at i:19888217 original size:14 final size:14
Alignment explanation
Indices: 19888164--19888243 Score: 63
Period size: 14 Copynumber: 5.6 Consensus size: 14
19888154 AAAACATAAG
*
19888164 CCCTAAACCCATAAC
1 CCCTAAA-CCTTAAC
* *
19888179 CCTTAAACCCTAAC
1 CCCTAAACCTTAAC
* *
19888193 CTCTAACCCTTAAC
1 CCCTAAACCTTAAC
19888207 CCCTAAACCTTAAAC
1 CCCTAAACCTT-AAC
* *
19888222 CCC-AACCCTTAAA
1 CCCTAAACCTTAAC
*
19888235 CCATAAACC
1 CCCTAAACC
19888244 ATAATCCATA
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
13 4 0.08
14 35 0.69
15 12 0.24
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.19
Consensus pattern (14 bp):
CCCTAAACCTTAAC
Found at i:19888228 original size:21 final size:21
Alignment explanation
Indices: 19888204--19888243 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19888194 TCTAACCCTT
*
19888204 AACCCCTAAACCTTAAACCCC
1 AACCCCTAAACCATAAACCCC
*
19888225 AACCCTTAAACCATAAACC
1 AACCCCTAAACCATAAACC
19888244 ATAATCCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (21 bp):
AACCCCTAAACCATAAACCCC
Found at i:19889118 original size:41 final size:41
Alignment explanation
Indices: 19889063--19889460 Score: 449
Period size: 41 Copynumber: 9.9 Consensus size: 41
19889053 CCTGAGCATT
* **
19889063 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGTCTGGGC
1 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGGGC
19889104 ATTAGCGGCGCTTTCCCAAAAACG-C-C---A----TGGGC
1 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGGGC
* ** * *
19889136 ATTAGCGACGCTTTCCTGAAAACGCCCCTAAAGCCATGGGC
1 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGGGC
* * *
19889177 ATTAGCGGCGCTTTACCAAAAACGTCGCTAAAGCCATGGGC
1 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGGGC
* * * *
19889218 ATTAGTGACGCTTT-CCAACAAACGCCGCTAAAGCCCTAGGA
1 ATTAGCGGCGCTTTCCCAA-AAACGCCGCTAAAGCCCTGGGC
*
19889259 ATTAGCGGCGCTTTCCCAAAAACGCCTCTAAAGCCCTGGGC
1 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGGGC
* **
19889300 ATCAGCGGCGCTTTCCCAAAAATACCGCTAAAGCCCTGGGC
1 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGGGC
*
19889341 ATTAGCGGCGCTTCCCCAAAAACGCCGCTAAAGCCCTGGGC
1 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGGGC
* * *
19889382 ATTAGTGGCGC-TTCCTCAAAAATGCCGCTAAAGCCCTGAGC
1 ATTAGCGGCGCTTTCC-CAAAAACGCCGCTAAAGCCCTGGGC
* ** * *
19889423 ATTAGTGGCGCTTTCTTAAAAATGCCGCTAAATCCCTG
1 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTG
19889461 AAAGCTCACA
Statistics
Matches: 308, Mismatches: 36, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
32 26 0.08
33 1 0.00
34 1 0.00
36 1 0.00
37 1 0.00
39 1 0.00
40 8 0.03
41 262 0.85
42 7 0.02
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGGGC
Found at i:19889140 original size:32 final size:32
Alignment explanation
Indices: 19889099--19889161 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
19889089 GCTAAAGGTC
*
19889099 TGGGCATTAGCGGCGCTTTCCCAAAAACGCCA
1 TGGGCATTAGCGACGCTTTCCCAAAAACGCCA
**
19889131 TGGGCATTAGCGACGCTTTCCTGAAAACGCC
1 TGGGCATTAGCGACGCTTTCCCAAAAACGCC
19889162 CCTAAAGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.24, C:0.30, G:0.25, T:0.21
Consensus pattern (32 bp):
TGGGCATTAGCGACGCTTTCCCAAAAACGCCA
Found at i:19889564 original size:39 final size:39
Alignment explanation
Indices: 19889513--19889628 Score: 119
Period size: 40 Copynumber: 2.9 Consensus size: 39
19889503 CGCTTTCTTG
* * * *
19889513 AAAA-CGCGGCTAATGCTTATTTTTAGCGGCGTTTTTCG
1 AAAAGCGCCGCTAATGCTTATCTTTAGTGGCGTTTTTCA
* * *
19889551 TAAAGCGCCGCTAAAT-CTCAATCTTTAGTGGCGTTTTCCA
1 AAAAGCGCCGCT-AATGCT-TATCTTTAGTGGCGTTTTTCA
*
19889591 AAAAGCGCCACTAATGCTTGATCTTTAGTGGCGTTTTT
1 AAAAGCGCCGCTAATGCTT-ATCTTTAGTGGCGTTTTT
19889629 TATCCAAACG
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
38 3 0.05
39 11 0.18
40 48 0.77
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (39 bp):
AAAAGCGCCGCTAATGCTTATCTTTAGTGGCGTTTTTCA
Found at i:19890951 original size:22 final size:22
Alignment explanation
Indices: 19890926--19890972 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
19890916 TTGAGATACT
19890926 TTTATTCACGATTATGAACTGA
1 TTTATTCACGATTATGAACTGA
*
19890948 TTTATTCATGATTATGAACTGA
1 TTTATTCACGATTATGAACTGA
19890970 TTT
1 TTT
19890973 TCTAAATACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.47
Consensus pattern (22 bp):
TTTATTCACGATTATGAACTGA
Found at i:19895234 original size:27 final size:27
Alignment explanation
Indices: 19895201--19895321 Score: 163
Period size: 27 Copynumber: 4.5 Consensus size: 27
19895191 ATGAAAGAAA
*
19895201 AGCCTTTGTGGCGAACTATAAAAGAGT
1 AGCCTTTGTGGCGAAATATAAAAGAGT
*
19895228 AGTCTTTGTGGCGAAATATAAAAGAGT
1 AGCCTTTGTGGCGAAATATAAAAGAGT
* * *
19895255 AGTCTTTGTGGCAAAATATGAAAGAGT
1 AGCCTTTGTGGCGAAATATAAAAGAGT
* *
19895282 AGCCTTTGTGGCAAAATATGAAAGA-T
1 AGCCTTTGTGGCGAAATATAAAAGAGT
*
19895308 AGCCTTTATGGCGA
1 AGCCTTTGTGGCGA
19895322 GCCCTACAAG
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
26 13 0.15
27 74 0.85
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.28
Consensus pattern (27 bp):
AGCCTTTGTGGCGAAATATAAAAGAGT
Found at i:19902249 original size:12 final size:12
Alignment explanation
Indices: 19902232--19902257 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19902222 AAAGTTACAT
19902232 GGCCTAGCACAC
1 GGCCTAGCACAC
19902244 GGCCTAGCACAC
1 GGCCTAGCACAC
19902256 GG
1 GG
19902258 GCATGTGTGG
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:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (12 bp):
GGCCTAGCACAC
Found at i:19907192 original size:18 final size:18
Alignment explanation
Indices: 19907169--19907204 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19907159 CTTACCGTAA
19907169 GAGTTAGAAAAGGTTCAC
1 GAGTTAGAAAAGGTTCAC
19907187 GAGTTAGAAAAGGTTCAC
1 GAGTTAGAAAAGGTTCAC
19907205 AATGTATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.22
Consensus pattern (18 bp):
GAGTTAGAAAAGGTTCAC
Found at i:19910883 original size:12 final size:13
Alignment explanation
Indices: 19910838--19910894 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
19910828 ACACTCAAAA
* *
19910838 TTTTCAAAAGCAA
1 TTTTCAAAAACAC
*
19910851 TTTTCTAAAACAC
1 TTTTCAAAAACAC
*
19910864 TTTTTTC-ACAACAC
1 --TTTTCAAAAACAC
19910878 TTTTCAAAAACAC
1 TTTTCAAAAACAC
19910891 TTTT
1 TTTT
19910895 TTAACTTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 5 0.14
13 20 0.56
14 6 0.17
15 5 0.14
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAACAC
Found at i:19929840 original size:32 final size:31
Alignment explanation
Indices: 19929790--19929885 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
19929780 CTTAGATAAT
19929790 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
19929821 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
19929853 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
19929884 TT
1 TT
19929886 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:19935534 original size:27 final size:27
Alignment explanation
Indices: 19935502--19935565 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 27
19935492 AAGAACATAC
19935502 TAAAAACATGTAATAGAATAAGACAAAT
1 TAAAAACATGTAATAG-ATAAGACAAAT
* * * *
19935530 TAAAAACATGTACTAGCTATGACATAT
1 TAAAAACATGTAATAGATAAGACAAAT
19935557 T-AAAACATG
1 TAAAAACATG
19935566 CATTAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 8 0.25
27 9 0.28
28 15 0.47
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (27 bp):
TAAAAACATGTAATAGATAAGACAAAT
Found at i:19937522 original size:18 final size:17
Alignment explanation
Indices: 19937501--19937558 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
19937491 GCTCTCAATC
19937501 TCTTTTTCTTTTTTGATT
1 TCTTTTTCTTTTTT-ATT
* *
19937519 TCTTTTTCTTTCATT-TC
1 TCTTTTTCTTT-TTTATT
19937536 TCTTTTTC-TTTTTATT
1 TCTTTTTCTTTTTTATT
19937552 TCTTTTT
1 TCTTTTT
19937559 GACTCATTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 2 0.06
16 10 0.29
17 9 0.26
18 11 0.32
19 2 0.06
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.78
Consensus pattern (17 bp):
TCTTTTTCTTTTTTATT
Found at i:19937566 original size:33 final size:35
Alignment explanation
Indices: 19937499--19937566 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 35
19937489 TCGCTCTCAA
**
19937499 TCTCTTTTTCTTTTTTGATTTCTTTTTCTTTCATT
1 TCTCTTTTTCTTTTTTGATTTCTTTTTCACTCATT
*
19937534 TCTCTTTTTC-TTTTT-ATTTCTTTTTGACTCATT
1 TCTCTTTTTCTTTTTTGATTTCTTTTTCACTCATT
19937567 CTTTCATTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 15 0.50
34 5 0.17
35 10 0.33
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (35 bp):
TCTCTTTTTCTTTTTTGATTTCTTTTTCACTCATT
Found at i:19939944 original size:28 final size:27
Alignment explanation
Indices: 19939912--19939971 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 27
19939902 AAGAACATAC
19939912 TAAAAACATGTAATATACTAAGACAAAT
1 TAAAAACATGTAATAT-CTAAGACAAAT
* * *
19939940 TAAAAACATGTACTATCTATGACATAT
1 TAAAAACATGTAATATCTAAGACAAAT
19939967 TAAAA
1 TAAAA
19939972 CACGCATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (27 bp):
TAAAAACATGTAATATCTAAGACAAAT
Found at i:19941113 original size:137 final size:138
Alignment explanation
Indices: 19940863--19941119 Score: 310
Period size: 137 Copynumber: 1.9 Consensus size: 138
19940853 GCTATAAGAT
* *
19940863 GGTCTGCTCACACAAGCTAATGGTCGGAATGTAAACTACACAATGCTGCTCGCACAAGATGATGA
1 GGTCTGCTCACACAAGCTAACGGTCGGAATGTAAACTACACAATGCTGCTCACACAAGATGATGA
* * * **
19940928 GTATCTATAACTAATGTCGAACCTCAGCCATCAGTAGGACATTTAGGACCAGCACCCAAAACATG
66 GTATCCATAACAAATGTCGAAACTCAGCCATCAGTAGGACATCCAGGACCAGCACCCAAAACATG
19940993 GCAACCTG
131 GCAACCTG
* * * *
19941001 GGTCTGCTCACACGAGCTGACGGTCGGAATGT-AGCTACACGATG-TCGCTCACACAA-ACTGAT
1 GGTCTGCTCACACAAGCTAACGGTCGGAATGTAAACTACACAATGCT-GCTCACACAAGA-TGAT
* *
19941063 GAGTATTCGCA-AA-AAATG-CTGAAACTTAGCCATCTGTAGGACATCCAGGACCAGCAC
64 GAGTA-TC-CATAACAAATGTC-GAAACTCAGCCATCAGTAGGACATCCAGGACCAGCAC
19941120 TTGAAATAAG
Statistics
Matches: 101, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
136 3 0.03
137 64 0.63
138 33 0.33
139 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.21
Consensus pattern (138 bp):
GGTCTGCTCACACAAGCTAACGGTCGGAATGTAAACTACACAATGCTGCTCACACAAGATGATGA
GTATCCATAACAAATGTCGAAACTCAGCCATCAGTAGGACATCCAGGACCAGCACCCAAAACATG
GCAACCTG
Found at i:19946383 original size:27 final size:27
Alignment explanation
Indices: 19946206--19946406 Score: 217
Period size: 27 Copynumber: 7.5 Consensus size: 27
19946196 TTTACCCCCA
*
19946206 TAGGGTAAAATGACCGTAATA-TCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* * * *
19946232 TAGGGTTAAATGACAGTAATACCCTTA
1 TAGGGTAAAATGACCGTAATACCCCTG
*
19946259 TAGGGTAAAATGGCCGTAATACCCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* *
19946286 TAGGGTAAAATGACTGTAATAACCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* * *
19946313 TAAGGTAAAATGACTGTAATGCCCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* * *
19946340 TAGGGTAAAATGCCCATAATACCCCTA
1 TAGGGTAAAATGACCGTAATACCCCTG
* * * *
19946367 TAGGGTTAAATGACCATAATGCCCTTG
1 TAGGGTAAAATGACCGTAATACCCCTG
*
19946394 GAGGGT-AAATGAC
1 TAGGGTAAAATGAC
19946407 TATTTTGCCC
Statistics
Matches: 146, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 26 0.18
27 120 0.82
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (27 bp):
TAGGGTAAAATGACCGTAATACCCCTG
Found at i:19946401 original size:81 final size:79
Alignment explanation
Indices: 19946198--19946407 Score: 249
Period size: 81 Copynumber: 2.6 Consensus size: 79
19946188 TTGATCGATT
* * * *
19946198 TACCCCCATAGGGTAAAATGACCGTAATATCCTGTAGGGTTAAATGACAGTAATACCCTTATAGG
1 TACCCCTATAGGGTAAAATGACCGTAATACCCTGTAGGG-TAAATGACTGTAATACCCCTATAGG
* *
19946263 GTAAAATGGCCGTAA
65 GTAAAATGCCCATAA
* * * * *
19946278 TACCCCTGTAGGGTAAAATGACTGTAATAACCCTGTAAGGTAAAATGACTGTAATGCCCCTGTAG
1 TACCCCTATAGGGTAAAATGACCGTAAT-ACCCTGTAGGGT-AAATGACTGTAATACCCCTATAG
19946343 GGTAAAATGCCCATAA
64 GGTAAAATGCCCATAA
* * * *
19946359 TACCCCTATAGGGTTAAATGACCATAATGCCCTTGGAGGGTAAATGACT
1 TACCCCTATAGGGTAAAATGACCGTAATACCC-TGTAGGGTAAATGACT
19946408 ATTTTGCCCC
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
80 37 0.34
81 72 0.66
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (79 bp):
TACCCCTATAGGGTAAAATGACCGTAATACCCTGTAGGGTAAATGACTGTAATACCCCTATAGGG
TAAAATGCCCATAA
Found at i:19946402 original size:26 final size:26
Alignment explanation
Indices: 19946206--19946432 Score: 127
Period size: 27 Copynumber: 8.5 Consensus size: 26
19946196 TTTACCCCCA
* **
19946206 TAGGGTAAAATGACCGTAAT-ATCCTG
1 TAGGGT-AAATGACCATAATGCCCCTG
* * *
19946232 TAGGGTTAAATGA-CAGTAATACCCTTA
1 TAGGG-TAAATGACCA-TAATGCCCCTG
* * *
19946259 TAGGGTAAAATGGCCGTAATACCCCTG
1 TAGGGT-AAATGACCATAATGCCCCTG
** **
19946286 TAGGGTAAAATGACTGTAATAACCCTG
1 TAGGGT-AAATGACCATAATGCCCCTG
* **
19946313 TAAGGTAAAATGACTGTAATGCCCCTG
1 TAGGGT-AAATGACCATAATGCCCCTG
* * *
19946340 TAGGGTAAAATGCCCATAATACCCCTA
1 TAGGGT-AAATGACCATAATGCCCCTG
*
19946367 TAGGGTTAAATGACCATAATGCCCTTG
1 TAGGG-TAAATGACCATAATGCCCCTG
* * **
19946394 GAGGGTAAATGACTATTTTGCCCCTCG
1 TAGGGTAAATGACCATAATGCCCCT-G
*
19946421 -AGTGTAAATGAC
1 TAGGGTAAATGAC
19946433 TGAATTTTCT
Statistics
Matches: 163, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
25 1 0.01
26 43 0.26
27 117 0.72
28 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (26 bp):
TAGGGTAAATGACCATAATGCCCCTG
Found at i:19946586 original size:27 final size:27
Alignment explanation
Indices: 19946530--19946587 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
19946520 GGAAGTATTG
* * *
19946530 TACTGGTGGCTTTGCCACAATCACTGT
1 TACTAGTGGCTTGGCCACAATCACTAT
*
19946557 TACTAGTGGCTTGGCCACGTAT-ACTAT
1 TACTAGTGGCTTGGCCAC-AATCACTAT
19946584 TACT
1 TACT
19946588 GCCAGCTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (27 bp):
TACTAGTGGCTTGGCCACAATCACTAT
Found at i:19946648 original size:32 final size:31
Alignment explanation
Indices: 19946605--19946794 Score: 218
Period size: 32 Copynumber: 6.0 Consensus size: 31
19946595 TTGTTGCGAT
19946605 GTTACTGATGGCTTTGTGCCGATCATATTATC
1 GTTACTGATGGCTTTGTGCCGATCATATTA-C
* *
19946637 GTTACTCATGGCTTTGTGTCGATCATATTAC
1 GTTACTGATGGCTTTGTGCCGATCATATTAC
19946668 TGTTACTGATGGCTTTGTGCCGATCATATTAAC
1 -GTTACTGATGGCTTTGTGCCGATCATATT-AC
* **
19946701 GTTATTGATGATTTTGTGCCGATCATATTACC
1 GTTACTGATGGCTTTGTGCCGATCATATTA-C
* * * * * *
19946733 GCTACGGATGGCTATGTTCTGATCATATCAC
1 GTTACTGATGGCTTTGTGCCGATCATATTAC
* *
19946764 TGTTACTGATGGCTTTGTTCCAATCATATTA
1 -GTTACTGATGGCTTTGTGCCGATCATATTA
19946795 TTGTACTTAT
Statistics
Matches: 132, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
31 3 0.02
32 127 0.96
33 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (31 bp):
GTTACTGATGGCTTTGTGCCGATCATATTAC
Found at i:19946774 original size:96 final size:96
Alignment explanation
Indices: 19946617--19946794 Score: 268
Period size: 96 Copynumber: 1.9 Consensus size: 96
19946607 TACTGATGGC
* * * * *
19946617 TTTGTGCCGATCATATTATCGTTACTCATGGCTTTGTGTCGATCATATTACTGTTACTGATGGCT
1 TTTGTGCCGATCATATTACCGCTACGCATGGCTATGTGTCGATCATATCACTGTTACTGATGGCT
*
19946682 TTGTGCCGATCATATTAACGTTATTGATGAT
66 TTGTGCCAATCATATTAACGTTATTGATGAT
*
19946713 TTTGTGCCGATCATATTACCGCTACGGATGGCTATGT-TCTGATCATATCACTGTTACTGATGGC
1 TTTGTGCCGATCATATTACCGCTACGCATGGCTATGTGTC-GATCATATCACTGTTACTGATGGC
*
19946777 TTTGTTCCAATCATATTA
65 TTTGTGCCAATCATATTA
19946795 TTGTACTTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 2 0.03
96 71 0.97
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (96 bp):
TTTGTGCCGATCATATTACCGCTACGCATGGCTATGTGTCGATCATATCACTGTTACTGATGGCT
TTGTGCCAATCATATTAACGTTATTGATGAT
Found at i:19946937 original size:29 final size:26
Alignment explanation
Indices: 19946868--19946930 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
19946858 CCATTCTGGC
*
19946868 TACTGGCAGCTCTGTTGTATTATTAA
1 TACTGGCAGCTCTGCTGTATTATTAA
*
19946894 TACTGGCAGCTCTGCTGTATTATTAC
1 TACTGGCAGCTCTGCTGTATTATTAA
*
19946920 TACTGGTAGCT
1 TACTGGCAGCT
19946931 ATCCTGCGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (26 bp):
TACTGGCAGCTCTGCTGTATTATTAA
Found at i:19947086 original size:28 final size:28
Alignment explanation
Indices: 19947053--19947106 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
19947043 CATACTGACA
*
19947053 CTGTA-TAGGGCTTAGGCCCACACTGTTT
1 CTGTATTAGGG-TAAGGCCCACACTGTTT
*
19947081 CTGTATTAGGGTAAGGCTCACACTGT
1 CTGTATTAGGGTAAGGCCCACACTGT
19947107 ACTGTTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (28 bp):
CTGTATTAGGGTAAGGCCCACACTGTTT
Found at i:19949269 original size:20 final size:20
Alignment explanation
Indices: 19949246--19949310 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
19949236 AAGCTCAAAC
*
19949246 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGTGAGCTAAATT
**
19949266 GAGCTAAAACGAGCTAAATT
1 GAGCTAAAGTGAGCTAAATT
* * * *
19949286 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGTGAGCTAAATT
19949306 GAGCT
1 GAGCT
19949311 GGGAAAAACT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (20 bp):
GAGCTAAAGTGAGCTAAATT
Found at i:19949278 original size:30 final size:30
Alignment explanation
Indices: 19949237--19949310 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
19949227 ACTTAAGCCA
*
19949237 AGCTCAAACGAGCTAAAGTAAGCTAAAT-TG
1 AGCTAAAACGAGCTAAAGTAAGCT-AATGTG
* *
19949267 AGCTAAAACGAGCTAAATTAAGCTCATGTG
1 AGCTAAAACGAGCTAAAGTAAGCTAATGTG
*
19949297 AGCTAAATCGAGCT
1 AGCTAAAACGAGCT
19949311 GGGAAAAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 2 0.05
30 37 0.95
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (30 bp):
AGCTAAAACGAGCTAAAGTAAGCTAATGTG
Found at i:19952202 original size:28 final size:29
Alignment explanation
Indices: 19952125--19952205 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 29
19952115 GCAAGACTTT
* **
19952125 TCACTTTTTTTTAACTTGATTTTTTTTGC
1 TCACTTTTTTTTCACTTCTTTTTTTTTGC
*
19952154 TCACTTTTTTTTC-TTTCTTTTTTTTTGC
1 TCACTTTTTTTTCACTTCTTTTTTTTTGC
19952182 TCGA-TTTTTTTTCACTT-TTTTTTT
1 TC-ACTTTTTTTTCACTTCTTTTTTT
19952206 ATTTTTTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 30 0.67
29 15 0.33
ACGTcount: A:0.09, C:0.15, G:0.05, T:0.72
Consensus pattern (29 bp):
TCACTTTTTTTTCACTTCTTTTTTTTTGC
Found at i:19953853 original size:20 final size:19
Alignment explanation
Indices: 19953830--19953894 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
19953820 AAGCTCAAAC
19953830 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
19953850 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
19953870 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
19953890 GAGCT
1 GAGCT
19953895 GGGAAAGACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:19966326 original size:20 final size:20
Alignment explanation
Indices: 19966301--19966338 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19966291 CGTAATATGA
*
19966301 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
19966321 TTTCTGTAAAATGATTTA
1 TTTCTGGAAAATGATTTA
19966339 TTGGAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:19966335 original size:34 final size:35
Alignment explanation
Indices: 19966286--19966352 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
19966276 CAGTAAAATG
* *
19966286 TTTTCCGTAATATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
* *
19966320 TTTTCTGTAAAATGATTTATTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
19966353 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.49
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:19967681 original size:27 final size:28
Alignment explanation
Indices: 19967651--19967717 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
19967641 TAATCAATTT
*
19967651 AATATCCAACAAGGTT-AAAACATA-ATC
1 AATATCCAACAA-ATTCAAAACATATATC
* *
19967678 AATATCAAACAAATTCAAGACATATATC
1 AATATCCAACAAATTCAAAACATATATC
*
19967706 AAAATCCAACAA
1 AATATCCAACAA
19967718 TCTAAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.06
27 18 0.55
28 13 0.39
ACGTcount: A:0.55, C:0.19, G:0.04, T:0.21
Consensus pattern (28 bp):
AATATCCAACAAATTCAAAACATATATC
Found at i:19969316 original size:37 final size:37
Alignment explanation
Indices: 19969266--19969337 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
19969256 CTTATTTTTT
19969266 CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
1 CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
*
19969303 CCATTATATTAGAATTCACTAACTATTTAATTAAT
1 CCATTAGATTAGAATTCACTAACTATTTAATTAAT
19969338 TATGACTAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.40
Consensus pattern (37 bp):
CCATTAGATTAGAATTCACTAACTATTTAATTAATCA
Found at i:19971362 original size:14 final size:14
Alignment explanation
Indices: 19971345--19971377 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
19971335 GTGGAGGACC
19971345 GGAGGTGGACCGGT
1 GGAGGTGGACCGGT
*
19971359 GGAGGTGGATCGGT
1 GGAGGTGGACCGGT
19971373 GGAGG
1 GGAGG
19971378 ACGGAGGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.09, G:0.61, T:0.15
Consensus pattern (14 bp):
GGAGGTGGACCGGT
Found at i:19972334 original size:21 final size:22
Alignment explanation
Indices: 19972310--19972350 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
19972300 AACTCCTGAA
*
19972310 AATAAATAACAAA-AATTAAAG
1 AATAAAAAACAAAGAATTAAAG
*
19972331 AATAAAAAATAAAGAATTAA
1 AATAAAAAACAAAGAATTAA
19972351 TTAGTAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (22 bp):
AATAAAAAACAAAGAATTAAAG
Found at i:19972347 original size:14 final size:14
Alignment explanation
Indices: 19972308--19972347 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
19972298 TAAACTCCTG
* *
19972308 AAAATAAATAACAA
1 AAAATAAAGAATAA
*
19972322 AAATTAAAGAATAA
1 AAAATAAAGAATAA
19972336 AAAATAAAGAAT
1 AAAATAAAGAAT
19972348 TAATTAGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (14 bp):
AAAATAAAGAATAA
Found at i:19972705 original size:32 final size:32
Alignment explanation
Indices: 19972669--19972733 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
19972659 ATCTAAGTAT
19972669 GATAATTAATTAAAATGTATGAGATGAATTTA
1 GATAATTAATTAAAATGTATGAGATGAATTTA
19972701 GATAATTAATTAAAATGTATGAGATGAATTTA
1 GATAATTAATTAAAATGTATGAGATGAATTTA
19972733 G
1 G
19972734 CAGCAAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (32 bp):
GATAATTAATTAAAATGTATGAGATGAATTTA
Found at i:19973033 original size:21 final size:21
Alignment explanation
Indices: 19973007--19973047 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
19972997 ATAATAGAGC
19973007 TCGTTAAAGTTATTATGAACT
1 TCGTTAAAGTTATTATGAACT
19973028 TCGTTAAAGTTATTATGAAC
1 TCGTTAAAGTTATTATGAAC
19973048 CTTTAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (21 bp):
TCGTTAAAGTTATTATGAACT
Found at i:19976090 original size:49 final size:49
Alignment explanation
Indices: 19976037--19976274 Score: 167
Period size: 49 Copynumber: 4.7 Consensus size: 49
19976027 GATAATAACA
* * * *
19976037 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCTTGTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGA-GTTCTCATAT-CG
* * *
19976086 TGCCAATGCCATATCCCAGATATGATCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGAGTTCTCATATC-G
* * * ** *
19976136 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGAGTTCTCATATC-G
** * * ** *
19976185 TGCCAACACCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGAGTTCTCAT-A--TC----G
*
19976241 TGCCATTGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
19976275 GGATCTCTTT
Statistics
Matches: 151, Mismatches: 28, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
48 4 0.03
49 76 0.50
50 39 0.26
53 2 0.01
56 30 0.20
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGAGTTCTCATATCG
Found at i:19983555 original size:50 final size:50
Alignment explanation
Indices: 19983438--19983679 Score: 211
Period size: 50 Copynumber: 4.7 Consensus size: 50
19983428 GATAATAACA
* * *
19983438 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* * * *
19983487 TACCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* ** ** * *
19983537 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGAACTCTAATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * ** *
19983587 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAATCTGAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-ATC-G----G
*
19983643 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
19983680 TCTCTTTACC
Statistics
Matches: 154, Mismatches: 30, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
48 4 0.03
49 36 0.23
50 77 0.50
51 2 0.01
52 1 0.01
56 34 0.22
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:19984680 original size:13 final size:13
Alignment explanation
Indices: 19984662--19984695 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
19984652 CCAAAATGTC
19984662 GAAATTTTTGAAT
1 GAAATTTTTGAAT
19984675 GAAATTTTTGAAT
1 GAAATTTTTGAAT
19984688 GAAATTTT
1 GAAATTTT
19984696 CATGTAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (13 bp):
GAAATTTTTGAAT
Found at i:20001311 original size:21 final size:20
Alignment explanation
Indices: 20001271--20001311 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20001261 ATTATTTGAT
*
20001271 CCTTTAAATTGAATTTTTAA
1 CCTTTAAATCGAATTTTTAA
*
20001291 CCTTTAAATCGCATATTTTAA
1 CCTTTAAATCGAAT-TTTTAA
20001312 ATAAAAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (20 bp):
CCTTTAAATCGAATTTTTAA
Found at i:20004789 original size:50 final size:51
Alignment explanation
Indices: 20004714--20004904 Score: 201
Period size: 51 Copynumber: 3.8 Consensus size: 51
20004704 GTGAAATTGC
*
20004714 TAGGTCACATGTGTAGTACTATGTGCAGGCTGCTATGTGTACTGGAATG-A
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGAATGAA
* * * **
20004764 TAGGTCACATGTGTAGTACTGTGTGCAGGCTACTATGCGTAC-CGAATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGAAT-GAA
* * * * *
20004815 TCGATCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTA-TCGG-ATGAA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACT-GGAATGAA
* * *
20004865 AATGGTCACATGTATAGTACTATGTGCAGGCTACTTTGTG
1 TA-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
20004905 AGCCGGGTAT
Statistics
Matches: 113, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
49 4 0.04
50 41 0.36
51 67 0.59
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (51 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGAATGAA
Found at i:20010045 original size:50 final size:51
Alignment explanation
Indices: 20009970--20010160 Score: 201
Period size: 51 Copynumber: 3.8 Consensus size: 51
20009960 GTGAAATTGC
*
20009970 TAGGTCACATGTGTAGTACTATGTGCAGGCTGCTATGTGTACTGGAATG-A
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGAATGAA
* * * **
20010020 TAGGTCACATGTGTAGTACTGTGTGCAGGCTACTATGCGTAC-CGAATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGAAT-GAA
* * * * *
20010071 TCGATCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTA-TCGG-ATGAA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACT-GGAATGAA
* * *
20010121 AATGGTCACATGTATAGTACTATGTGCAGGCTACTTTGTG
1 TA-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
20010161 AGCCGGGTAT
Statistics
Matches: 113, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
49 4 0.04
50 41 0.36
51 67 0.59
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (51 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGAATGAA
Found at i:20016123 original size:43 final size:43
Alignment explanation
Indices: 20016075--20016161 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
20016065 GTGAAAAAAT
20016075 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAAC
20016118 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAAC
20016161 G
1 G
20016162 TCGCGTGCCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.30, C:0.32, G:0.20, T:0.18
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAAC
Found at i:20018221 original size:21 final size:21
Alignment explanation
Indices: 20018197--20018240 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20018187 AAGTTATATA
20018197 TAAGTT-TATATATAAGTTATG
1 TAAGTTAT-TATATAAGTTATG
*
20018218 TAAGTTATTATGTAAGTTATG
1 TAAGTTATTATATAAGTTATG
20018239 TA
1 TA
20018241 TTGTGCAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (21 bp):
TAAGTTATTATATAAGTTATG
Found at i:20018228 original size:12 final size:12
Alignment explanation
Indices: 20018181--20018237 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
20018171 AACATGAAAG
20018181 TTATGTAAGTTA
1 TTATGTAAGTTA
*
20018193 -TATATAAGTT-
1 TTATGTAAGTTA
*
20018203 TATATATAAG---
1 T-TATGTAAGTTA
20018213 TTATGTAAGTTA
1 TTATGTAAGTTA
20018225 TTATGTAAGTTA
1 TTATGTAAGTTA
20018237 T
1 T
20018238 GTATTGTGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 7 0.18
10 1 0.03
11 9 0.24
12 21 0.55
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:20018306 original size:12 final size:13
Alignment explanation
Indices: 20018193--20018306 Score: 52
Period size: 12 Copynumber: 9.4 Consensus size: 13
20018183 ATGTAAGTTA
*
20018193 TATATAAGTT-TA
1 TATATAAGTTATG
20018205 TATATAAGTTATG
1 TATATAAGTTATG
20018218 ----TAAGTTAT-
1 TATATAAGTTATG
*
20018226 TATGTAAGTTATG
1 TATATAAGTTATG
* *
20018239 TATTGTGCAAGTT-TA
1 TA-TAT--AAGTTATG
*
20018254 TATATAAATT-T-
1 TATATAAGTTATG
*
20018265 TATTTAAGTTATG
1 TATATAAGTTATG
* *
20018278 TATGTAGGTT-TG
1 TATATAAGTTATG
20018290 TATATAAGTTATG
1 TATATAAGTTATG
20018303 -ATAT
1 TATAT
20018307 GATTGATAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
9 8 0.10
11 8 0.10
12 38 0.47
13 13 0.16
14 5 0.06
15 3 0.04
16 5 0.06
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (13 bp):
TATATAAGTTATG
Found at i:20018380 original size:17 final size:19
Alignment explanation
Indices: 20018346--20018386 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
20018336 GATATGGTTG
20018346 ATAAATTGTTTAAAAATAT
1 ATAAATTGTTTAAAAATAT
20018365 ATAAATT-TTTAAAATATAT
1 ATAAATTGTTTAAAA-ATAT
20018384 ATA
1 ATA
20018387 TTAAAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATAAATTGTTTAAAAATAT
Found at i:20018441 original size:24 final size:22
Alignment explanation
Indices: 20018403--20018448 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
20018393 ATGTATATAA
*
20018403 ATATTAATAAGTTATGTAAGTTAT
1 ATATTAAAAAGTTA--TAAGTTAT
*
20018427 ATATTAAAAATTTATAAGTTAT
1 ATATTAAAAAGTTATAAGTTAT
20018449 GTAAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
24 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (22 bp):
ATATTAAAAAGTTATAAGTTAT
Found at i:20018444 original size:22 final size:22
Alignment explanation
Indices: 20018381--20018448 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
20018371 TTTTAAAATA
*
20018381 TATATATTAAAAATGTAT-A--
1 TATATATTAAAAATTTATAAGT
* * *
20018400 TAAATATTAATAAGTTATGTAAGT
1 TATATATTAA-AAATT-TATAAGT
20018424 TATATATTAAAAATTTATAAGT
1 TATATATTAAAAATTTATAAGT
20018446 TAT
1 TAT
20018449 GTAAAATTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
19 9 0.24
20 3 0.08
21 2 0.05
22 10 0.27
23 4 0.11
24 9 0.24
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
TATATATTAAAAATTTATAAGT
Found at i:20023150 original size:17 final size:17
Alignment explanation
Indices: 20023128--20023177 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
20023118 TCCCAGATTT
20023128 TGATACCCATATCTTTA
1 TGATACCCATATCTTTA
* *
20023145 TGATACTCATATCTTTC
1 TGATACCCATATCTTTA
20023162 TGATACCCATATCTTT
1 TGATACCCATATCTTT
20023178 GACTTTCTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (17 bp):
TGATACCCATATCTTTA
Found at i:20030155 original size:7 final size:7
Alignment explanation
Indices: 20030145--20030197 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
20030135 CACTAACTCT
20030145 TAACCTC
1 TAACCTC
20030152 TAACCTC
1 TAACCTC
*
20030159 AAACC-C
1 TAACCTC
*
20030165 TAACCCC
1 TAACCTC
*
20030172 TAACCTT
1 TAACCTC
*
20030179 TAACCCC
1 TAACCTC
*
20030186 TAACCAC
1 TAACCTC
20030193 TAACC
1 TAACC
20030198 CTTAAACATT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
6 5 0.13
7 33 0.87
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (7 bp):
TAACCTC
Found at i:20030163 original size:14 final size:14
Alignment explanation
Indices: 20030145--20030198 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
20030135 CACTAACTCT
*
20030145 TAACCTCTAACCTC
1 TAACCTCTAACCCC
*
20030159 AAACC-CTAACCCC
1 TAACCTCTAACCCC
*
20030172 TAACCTTTAACCCC
1 TAACCTCTAACCCC
*
20030186 TAACCACTAACCC
1 TAACCTCTAACCC
20030199 TTAAACATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 11 0.33
14 22 0.67
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.20
Consensus pattern (14 bp):
TAACCTCTAACCCC
Done.