Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 170 of 202
Found at i:53114853 original size:41 final size:41
Alignment explanation
Indices: 53114761--53114899 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
53114751 GCTAATCGAA
* * *
53114761 AAACACTGCAAAAGGTTAGAGCTATAGCGGCGTTTCTTCAT
1 AAACACCGCAAAAGGTTAGATCTATAGCGGCGTTTTTTCAT
** *
53114802 AAACGTCGCAAAAGGTTAGATCTATAGCGGCATTTTTTCAT
1 AAACACCGCAAAAGGTTAGATCTATAGCGGCGTTTTTTCAT
* * * * *
53114843 AAATACCGCAAAATGTTTGAGT-TGTAGCGGCGTTTTTATTAT
1 AAACACCGCAAAAGGTTAGA-TCTATAGCGGCGTTTTT-TCAT
*
53114885 AAACACTGCAAAAGG
1 AAACACCGCAAAAGG
53114900 AAGCAATAGC
Statistics
Matches: 79, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
41 63 0.80
42 16 0.20
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (41 bp):
AAACACCGCAAAAGGTTAGATCTATAGCGGCGTTTTTTCAT
Found at i:53116077 original size:5 final size:5
Alignment explanation
Indices: 53116062--53116099 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
53116052 TATCTACTTA
53116062 TTTATT TTTAT TTTAT TTTAT TTTA- TTTAT TTTAT TTT
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
53116100 TGTTTGTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.13
5 23 0.74
6 4 0.13
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:53116092 original size:9 final size:9
Alignment explanation
Indices: 53116068--53116098 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
53116058 CTTATTTATT
53116068 TTTATTTTA
1 TTTATTTTA
53116077 TTTTATTTTA
1 -TTTATTTTA
53116087 TTTATTTTA
1 TTTATTTTA
53116096 TTT
1 TTT
53116099 TTGTTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:53116092 original size:14 final size:15
Alignment explanation
Indices: 53116062--53116099 Score: 60
Period size: 14 Copynumber: 2.5 Consensus size: 15
53116052 TATCTACTTA
53116062 TTTATTTTTATTTTAT
1 TTTA-TTTTATTTTAT
53116078 TTTATTTTA-TTTAT
1 TTTATTTTATTTTAT
53116092 TTTATTTT
1 TTTATTTT
53116100 TGTTTGTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 13 0.59
15 5 0.23
16 4 0.18
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTATTTTATTTTAT
Found at i:53117069 original size:3 final size:3
Alignment explanation
Indices: 53117061--53117146 Score: 68
Period size: 3 Copynumber: 29.0 Consensus size: 3
53117051 ATATTCGCTG
* * * * *
53117061 TTA TTA TTA TCA TTC TTA TCT- TCA TTA TTA CTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
53117106 ATA TTA TTA TTA TTA TTA CTA TTG TTA TTA -TA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53117147 CAATTTATCT
Statistics
Matches: 62, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
2 2 0.03
3 59 0.95
4 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:53119490 original size:19 final size:20
Alignment explanation
Indices: 53119449--53119490 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
53119439 ATTTCTATGC
* *
53119449 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
53119469 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
53119488 CAT
1 CAT
53119491 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:53126810 original size:26 final size:26
Alignment explanation
Indices: 53126771--53126825 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
53126761 TGTTTAGAGG
53126771 GATCGCACGACTTTGAAGGTGATGAA
1 GATCGCACGACTTTGAAGGTGATGAA
*
53126797 GATCGCACGGCTTTGAAGGTGATGAA
1 GATCGCACGACTTTGAAGGTGATGAA
53126823 GAT
1 GAT
53126826 TATGGTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.15, G:0.33, T:0.24
Consensus pattern (26 bp):
GATCGCACGACTTTGAAGGTGATGAA
Found at i:53131539 original size:44 final size:42
Alignment explanation
Indices: 53131402--53132435 Score: 454
Period size: 44 Copynumber: 23.8 Consensus size: 42
53131392 CCAATGATCC
* * *
53131402 TATCTCTCTGAAGTTGCAGTGGAGCGGATTAA-AACCACAGATCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCA-AG-TCT
* * * * *
53131446 TATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
*
53131486 TACCTTCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCT
1 TATC-TCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * * * *
53131530 TATCCTCCTGAAGTTACAGT-GAGGTAAACTGAAGATGGCAAATCT
1 TAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCAAGTCT
* * *
53131575 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TCAG-AGCCGATAATCC
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCT
* * * * **
53131619 TATCTCCCTGAAGTTACAGTGGAGCGGATTAA-AACCTTGGATCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * * *
53131663 TATCTCTCTGAAGTTGCAG-AGAGAAGA-T-CGCATCTAGTCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
53131703 TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCC-TGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * **
53131747 TATCCTCCTGAAGTTACAGTGGAGCAGACTGAAGATGGCAAACCT
1 TAT-CTCCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCT
* * * *
53131792 TATCTCCCTGAAGTTGCA-TGGAGCAG-GTTA-AAGTCGATAATCC
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCT
* ** **
53131835 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA-ATCCTTGGATCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * * *
53131879 TATCTCTCTGAAGTTGCAG-AGAGTAGA-T-CGCATCTAGTCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
*
53131919 TATCTCTCTGAAGTTGCAGCGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * * * **
53131963 TATCCACCTGAAGTTACAGTGGGGCAGACTGAAGATGTCAAACCT
1 TAT-CTCCTGAAGTTGCAGTGGAGCAGACT-AAGAAG-CAAGTCT
* * * *
53132008 TATCTCCCTGAAGTTACAGTGGAGCAG-GTTA-AAGTCGATAATCCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGT-CT
53132053 ATATC-CCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 -TATCTCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* **
53132096 TATCCTCCTGAAGTTGCAGTGGTA-CAGACTGAAGATGGCAAACCT
1 TAT-CTCCTGAAGTTGCAGTGG-AGCAGACT-AAGA-AGCAAGTCT
* * * * * *
53132141 TATTTTCCTG-AGCATGCAGTGGAGCAG-GTTA-AAGCTGATAATCC
1 TA-TCTCCTGAAG-TTGCAGTGGAGCAGACTAAGAAGC--A-AGTCT
* * * * ** **
53132185 TATCCCCCTGAAGTTACAGTGGAGCGGATTAA-ATCCTTGGATCT
1 TAT-CTCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * *
53132229 TATCTCTCTGAAGTTGCAG-AGAGCAGA-TCA-CATCTAGTCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
*
53132269 TATCTTTCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATC-TCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * *
53132313 TATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAATCT
1 TAT-CTCCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCT
* * * *
53132358 TATCTCCCTGAAGTTGCAGTGGACCAGATTAA-AAGCCGATAATCC
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCT
*
53132403 TATCTCTCTGAAGTTGCAATGGAGCAGACTAAG
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAG
53132436 TAGAGCAGAT
Statistics
Matches: 761, Mismatches: 147, Indels: 162
0.71 0.14 0.15
Matches are distributed among these distances:
39 1 0.00
40 80 0.11
41 42 0.06
42 28 0.04
43 67 0.09
44 331 0.43
45 201 0.26
46 8 0.01
47 3 0.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (42 bp):
TATCTCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
Found at i:53131780 original size:217 final size:217
Alignment explanation
Indices: 53131398--53132076 Score: 1087
Period size: 217 Copynumber: 3.1 Consensus size: 217
53131388 AAAGCCAATG
* ***
53131398 ATCCTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGC
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGC
* * *
53131463 AGAGAGCAGATCGCATCTAGTCTTACCTTCC-TGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAG
66 AGAGAGAAGATCGCATCTAGTCTTATC-TCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAG
* * *
53131527 TCTTATCCTCCTGAAGTTACAGT-GAGGTAAACTGAAGATGGCAAATCTTATCTCCCTGAAGTTG
130 TCTTATCCTCCTGAAGTTACAGTGGA-GCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTG
* * * *
53131591 CAGTGGAGCAGATCAGAGCCGATA
194 CAGTGGAGCAGGTTAAAGTCGATA
*
53131615 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGC
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGC
53131680 AGAGAGAAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
66 AGAGAGAAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
53131745 CTTATCCTCCTGAAGTTACAGTGGAGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA
131 CTTATCCTCCTGAAGTTACAGTGGAGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA
53131810 -TGGAGCAGGTTAAAGTCGATA
196 GTGGAGCAGGTTAAAGTCGATA
* *
53131831 ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATCCTTGGATCTTATCTCTCTGAAGTTGC
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGC
* *
53131896 AGAGAGTAGATCGCATCTAGTCTTATCT-CTCTGAAGTTGCAGCGGAGCAGACTAAGTAAGCAAG
66 AGAGAGAAGATCGCATCTAGTCTTATCTCCT-TGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAG
* * * *
53131960 TCTTATCCACCTGAAGTTACAGTGGGGCAGACTGAAGATGTCAAACCTTATCTCCCTGAAGTTAC
130 TCTTATCCTCCTGAAGTTACAGTGGAGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGC
53132025 AGTGGAGCAGGTTAAAGTCGATA
195 AGTGGAGCAGGTTAAAGTCGATA
*
53132048 ATCCTATATCCCTGAAGTTGCAGTGGAGC
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGC
53132077 AGACTAAGTA
Statistics
Matches: 433, Mismatches: 25, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
215 2 0.00
216 203 0.47
217 226 0.52
218 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (217 bp):
ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGC
AGAGAGAAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGT
CTTATCCTCCTGAAGTTACAGTGGAGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA
GTGGAGCAGGTTAAAGTCGATA
Found at i:53132079 original size:133 final size:133
Alignment explanation
Indices: 53131926--53132209 Score: 419
Period size: 133 Copynumber: 2.1 Consensus size: 133
53131916 TCTTATCTCT
* *
53131926 CTGAAGTTGCAGCGGAGCAGACTAAGTAAGCAAGTCTTATCCACCTGAAGTTACAGTGGGGCAGA
1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCACCTGAAGTTACAGTGGGACAGA
* *
53131991 CTGAAGATGTCAAACCTTATCTCCCTGAAG-TTACAGTGGAGCAGGTTAAAG-TCGATAATCCTA
66 CTGAAGATGGCAAACCTTATCTCCCTG-AGCATACAGTGGAGCAGGTTAAAGCT-GATAATCCTA
*
53132054 TATCC
129 TACCC
* * *
53132059 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGTACAGA
1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCACCTGAAGTTACAGTGGGACAGA
* * * *
53132124 CTGAAGATGGCAAACCTTATTTTCCTGAGCATGCAGTGGAGCAGGTTAAAGCTGATAATCCTATC
66 CTGAAGATGGCAAACCTTATCTCCCTGAGCATACAGTGGAGCAGGTTAAAGCTGATAATCCTATA
53132189 CCC
131 CCC
*
53132192 CTGAAGTTACAGTGGAGC
1 CTGAAGTTGCAGTGGAGC
53132210 GGATTAAATC
Statistics
Matches: 136, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
132 2 0.01
133 133 0.98
134 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (133 bp):
CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCACCTGAAGTTACAGTGGGACAGA
CTGAAGATGGCAAACCTTATCTCCCTGAGCATACAGTGGAGCAGGTTAAAGCTGATAATCCTATA
CCC
Found at i:53132242 original size:350 final size:350
Alignment explanation
Indices: 53131711--53132442 Score: 1193
Period size: 350 Copynumber: 2.1 Consensus size: 350
53131701 CTTATCTCCT
53131711 TGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGGAGCAGAC
1 TGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGGAGCAGAC
* *
53131776 TGAAGATGGCAAACCTTATCTCCCTGAAGTTGCATGGAGCAGGTTAAAGTCGATAATCCTATCTC
66 TGAAGATGGCAAACCTTATCTCCCTGAAGATGCATGGAGCAGGTTAAAGTCGATAATCCTATCCC
* *
53131841 CCTGAAGTTGCAGTGGAGCAGATTAAATCCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGTAGA
131 CCTGAAGTTACAGTGGAGCAGATTAAATCCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGA
*
53131906 TCGCATCTAGTCTTATCTCTCTGAAGTTGCAGCGGAGCAGACTAAGTAAGCAAGTCTTATCCACC
196 TCACATCTAGTCTTATCTCTCTGAAGTTGCAGCGGAGCAGACTAAGTAAGCAAGTCTTATCCACC
* * *
53131971 TGAAGTTACAGTGGGGCAGACTGAAGATGTCAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGG
261 TGAAGTTACAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTACAGTGGACCAGA
*
53132036 TT-AAAGTCGATAATCCTATATCCC
326 TTAAAAGCCGATAATCCTATATCCC
*
53132060 TGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGTA-CAGA
1 TGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGG-AGCAGA
* *
53132124 CTGAAGATGGCAAACCTTATTTTCCTG-AGCATGCAGTGGAGCAGGTTAAAG-CTGATAATCCTA
65 CTGAAGATGGCAAACCTTATCTCCCTGAAG-ATGCA-TGGAGCAGGTTAAAGTC-GATAATCCTA
*
53132187 TCCCCCTGAAGTTACAGTGGAGCGGATTAAATCCTTGGATCTTATCTCTCTGAAGTTGCAGAGAG
127 TCCCCCTGAAGTTACAGTGGAGCAGATTAAATCCTTGGATCTTATCTCTCTGAAGTTGCAGAGAG
* *
53132252 CAGATCACATCTAGTCTTATCTTTCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC
192 CAGATCACATCTAGTCTTATCTCTCTGAAGTTGCAGCGGAGCAGACTAAGTAAGCAAGTCTTATC
* * * *
53132317 CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAC
257 CACCTGAAGTTACAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTACAGTGGAC
* *
53132382 CAGATTAAAAGCCGATAATCCTATCTCTC
322 CAGATTAAAAGCCGATAATCCTATATCCC
*
53132411 TGAAGTTGCAATGGAGCAGACTAAGTAGAGCA
1 TGAAGTTGCAGTGGAGCAGACTAAGTA-AGCA
53132443 GATCGCATCA
Statistics
Matches: 355, Mismatches: 22, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
348 2 0.01
349 91 0.26
350 213 0.60
351 45 0.13
352 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (350 bp):
TGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGGAGCAGAC
TGAAGATGGCAAACCTTATCTCCCTGAAGATGCATGGAGCAGGTTAAAGTCGATAATCCTATCCC
CCTGAAGTTACAGTGGAGCAGATTAAATCCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGA
TCACATCTAGTCTTATCTCTCTGAAGTTGCAGCGGAGCAGACTAAGTAAGCAAGTCTTATCCACC
TGAAGTTACAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTACAGTGGACCAGA
TTAAAAGCCGATAATCCTATATCCC
Found at i:53133916 original size:21 final size:22
Alignment explanation
Indices: 53133890--53133935 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
53133880 AATCTATATA
53133890 TATACATGT-ATATTTATTTTT
1 TATACATGTAATATTTATTTTT
53133911 TATACATGTACATATTTATTTTT
1 TATACATGTA-ATATTTATTTTT
53133934 TA
1 TA
53133936 ACTAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (22 bp):
TATACATGTAATATTTATTTTT
Found at i:53134420 original size:19 final size:20
Alignment explanation
Indices: 53134379--53134420 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
53134369 ATTTCTATGC
* *
53134379 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
53134399 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
53134418 CAT
1 CAT
53134421 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:53135745 original size:3 final size:3
Alignment explanation
Indices: 53135737--53135798 Score: 74
Period size: 3 Copynumber: 20.3 Consensus size: 3
53135727 ATAGGTAAGT
*
53135737 ATA ATA ATA ATAA ATA AT- ATA ATA ATA ATTA TTA AT- ATGA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA
53135783 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
53135799 CAAATAATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 4 0.08
3 41 0.79
4 7 0.13
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:53135759 original size:18 final size:18
Alignment explanation
Indices: 53135736--53135806 Score: 85
Period size: 18 Copynumber: 4.1 Consensus size: 18
53135726 TATAGGTAAG
53135736 TATAATAATAATAAATAA
1 TATAATAATAATAAATAA
* *
53135754 TATAATAATAATTATTAA
1 TATAATAATAATAAATAA
53135772 TATGAATAATAAT-AAT-A
1 TAT-AATAATAATAAATAA
*
53135789 -ATAATAATAACAAATAA
1 TATAATAATAATAAATAA
53135806 T
1 T
53135807 GCAATAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.18
16 5 0.11
17 2 0.04
18 21 0.47
19 9 0.20
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (18 bp):
TATAATAATAATAAATAA
Found at i:53137313 original size:50 final size:50
Alignment explanation
Indices: 53137259--53137842 Score: 218
Period size: 50 Copynumber: 11.7 Consensus size: 50
53137249 TTGGGGAAAC
* *
53137259 AAGATTCGCCGTTGTGACTTCAATCTATTCCACTACATCGCCAGGGAAGT
1 AAGATCCGCCGTTGTGACTTCAATCTATTCCACTGCATCGCCAGGGAAGT
** * ** * * **
53137309 AAGATCCGCCGTTGTGGTTTCAATCTTTTTAATTGCAAT-GTCAGGGAAAC
1 AAGATCCGCCGTTGTGACTTCAATCTATTCCACTGC-ATCGCCAGGGAAGT
* * * * *
53137359 CAGATCCGCCATCGT-AGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
1 AAGATCCGCCGTTGTGA-CTTCAATCTATTCCACTGCATCGCCAGGGAAGT
* * * ** * * **
53137409 AAGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAAT-GTCAGGGAAAC
1 AAGATCCGCCGTTGTGACTTCAATCTATTCCACTGC-ATCGCCAGGGAAGT
** * * *
53137459 CGGATCCGCCATCGT-AGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
1 AAGATCCGCCGTTGTGA-CTTCAATCTATTCCACTGCATCGCCAGGGAAGT
* * * * ** * *** **
53137509 AAGATCTGCCGTTGTGGCTTCAATTTTTTTAATTGCAAT-GTTGGGGAAAC
1 AAGATCCGCCGTTGTGACTTCAATCTATTCCACTGC-ATCGCCAGGGAAGT
* * * * * *
53137559 CAGATCCACCGTCGT-AGCTTCAATCTGTTCTACTGCACCGCCAGGGAAGT
1 AAGATCCGCCGTTGTGA-CTTCAATCTATTCCACTGCATCGCCAGGGAAGT
* * ** * * * * **
53137609 AAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGTAAT-GTCGGGGAAAC
1 AAGATCCGCCGTTGTGACTTCAATCTATTCCACTG-CATCGCCAGGGAAGT
* * * * *
53137659 CAGATCCGCCGTCGT-AGCTTTAATCTATTCCACTGCATCGCTAAGGAAGT
1 AAGATCCGCCGTTGTGA-CTTCAATCTATTCCACTGCATCGCCAGGGAAGT
* ** * * ** * * * **
53137709 AAGATTCGTTGTTGTGGCTTTAATCT-TTAAATTGCAAT-GTCGGGGAAAC
1 AAGATCCGCCGTTGTGACTTCAATCTATTCCACTGC-ATCGCCAGGGAAGT
* * * * * * *
53137758 CAGATCCACCGTCGT-AGCTTCAATCTGTTCCACTACACCGCCAGGGAAGC
1 AAGATCCGCCGTTGTGA-CTTCAATCTATTCCACTGCATCGCCAGGGAAGT
* * * **
53137808 AAGATTCACCGTTGTGGCTTCAATCCGTTCCACTG
1 AAGATCCGCCGTTGTGACTTCAATCTATTCCACTG
53137843 TAGTGCCAAA
Statistics
Matches: 363, Mismatches: 150, Indels: 42
0.65 0.27 0.08
Matches are distributed among these distances:
49 34 0.09
50 324 0.89
51 5 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (50 bp):
AAGATCCGCCGTTGTGACTTCAATCTATTCCACTGCATCGCCAGGGAAGT
Found at i:53137380 original size:100 final size:100
Alignment explanation
Indices: 53137226--53137832 Score: 842
Period size: 100 Copynumber: 6.1 Consensus size: 100
53137216 GGATTATTTT
* * * * *
53137226 CTTCAAT-TTGTTTAACTGCAATGTTGGGGAAACAAGATTCGCCGTTGT-GACTTCAATCTATTC
1 CTTCAATCTT-TTTAATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG-CTTCAATCTATTC
* *
53137289 CACTACATCGCCAGGGAAGTAAGATCCGCCGTTGTGG
64 CACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
* * * *
53137326 TTTCAATCTTTTTAATTGCAATGTCAGGGAAACCAGATCCGCCATCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCA
*
53137391 CTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
* * *
53137426 CTTCAATCTTTTTAATTGCAATGTCAGGGAAACCGGATCCGCCATCGTAGCTTCAATCTATTCCA
1 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCA
*
53137491 CTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
* * * * *
53137526 CTTCAATTTTTTTAATTGCAATGTTGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCTA
1 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCA
53137591 CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
* *
53137626 CTTCAATCTTTTTAATTGTAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTATTCCA
1 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCA
* * * * **
53137691 CTGCATCGCTAAGGAAGTAAGATTCGTTGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
* * * *
53137726 CTTTAATC-TTTAAATTGCAATGTCGGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCA
* * * *
53137790 CTACACCGCCAGGGAAGCAAGATTCACCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
53137825 CTTCAATC
1 CTTCAATC
53137833 CGTTCCACTG
Statistics
Matches: 453, Mismatches: 52, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
99 85 0.19
100 365 0.81
101 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (100 bp):
CTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCA
CTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
Found at i:53138173 original size:88 final size:88
Alignment explanation
Indices: 53138024--53138201 Score: 241
Period size: 88 Copynumber: 2.0 Consensus size: 88
53138014 GGCGATAAGA
* * * * * *
53138024 CTGGTATCTTCGATCTGCTTTGCTGCCAGTACAGGAAGGCAAGATCTGTCATTTTCAACCTACTC
1 CTGGTATCCTCGACCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTCATTTTCAACCTACTC
*
53138089 CACTGCTGCTCAGGGAGACAAGG
66 CACTGCTACTCAGGGAGACAAGG
* * *
53138112 CTGGTATCCTCGACCTACTTCGCTGTCAATACAGGAAGACAATATCTG-CTATTTTGAACCTACT
1 CTGGTATCCTCGACCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTC-ATTTTCAACCTACT
*
53138176 CCACTGCTACTCAGGGAGATAAGG
65 CCACTGCTACTCAGGGAGACAAGG
53138200 CT
1 CT
53138202 AAAGTTTCAC
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
87 1 0.01
88 77 0.99
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (88 bp):
CTGGTATCCTCGACCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTCATTTTCAACCTACTC
CACTGCTACTCAGGGAGACAAGG
Found at i:53139552 original size:10 final size:9
Alignment explanation
Indices: 53139500--53139560 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 9
53139490 ATCATTTTTC
*
53139500 TTTTTTCGA
1 TTTTTTTGA
**
53139509 TTTTGTTTTT
1 TTTT-TTTGA
53139519 TTTATTTTGA
1 TTT-TTTTGA
*
53139529 TATTTTTTTA
1 T-TTTTTTGA
53139539 TTTTTTTGA
1 TTTTTTTGA
53139548 CTTTTTTTGA
1 -TTTTTTTGA
53139558 TTT
1 TTT
53139561 GATTTTTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 14 0.34
10 24 0.59
11 3 0.07
ACGTcount: A:0.11, C:0.03, G:0.08, T:0.77
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:53139553 original size:19 final size:18
Alignment explanation
Indices: 53139494--53139560 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 18
53139484 TTTTTCATCA
* *
53139494 TTTTTCTTTTTTCGATTT
1 TTTTTATTTTTTTGATTT
*
53139512 TGTTTTTTTTATTTTGATATT
1 T-TTTTATTT-TTTTGAT-TT
53139533 TTTTTATTTTTTTGACTTT
1 TTTTTATTTTTTTGA-TTT
*
53139552 TTTTGATTT
1 TTTTTATTT
53139561 GATTTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.02
19 23 0.56
20 14 0.34
21 3 0.07
ACGTcount: A:0.10, C:0.04, G:0.07, T:0.78
Consensus pattern (18 bp):
TTTTTATTTTTTTGATTT
Found at i:53139579 original size:34 final size:34
Alignment explanation
Indices: 53139500--53139579 Score: 80
Period size: 33 Copynumber: 2.4 Consensus size: 34
53139490 ATCATTTTTC
*
53139500 TTTTTTC-GA-TTTTGTTTTTTTTATTTTGATAT
1 TTTTTTCAGATTTTTGTTTTTTTGATTTTGATAT
**
53139532 TTTTTT-ATTTTTTTGACTTTTTTTGA-TTTGAT-T
1 TTTTTTCAGATTTTTG--TTTTTTTGATTTTGATAT
53139565 TTTTTTCAGATTTTT
1 TTTTTTCAGATTTTT
53139580 CTTTGATTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
32 6 0.16
33 12 0.32
34 12 0.32
35 8 0.21
ACGTcount: A:0.12, C:0.04, G:0.09, T:0.75
Consensus pattern (34 bp):
TTTTTTCAGATTTTTGTTTTTTTGATTTTGATAT
Found at i:53144167 original size:27 final size:27
Alignment explanation
Indices: 53144098--53144167 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 27
53144088 ATGTATAAAC
53144098 ATATATATATATTATAAAATATGGAAAATGT
1 ATATA-ATATA-TATAAAATAT-G-AAATGT
53144129 ATA-AATAT-TATAAAATAT-AAATGT
1 ATATAATATATATAAAATATGAAATGT
53144153 ATATACATATATATA
1 ATATA-ATATATATA
53144168 TATAAACACT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
24 9 0.25
25 1 0.03
26 4 0.11
27 14 0.39
29 4 0.11
30 1 0.03
31 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (27 bp):
ATATAATATATATAAAATATGAAATGT
Found at i:53144172 original size:40 final size:38
Alignment explanation
Indices: 53144128--53144213 Score: 88
Period size: 40 Copynumber: 2.2 Consensus size: 38
53144118 ATGGAAAATG
*
53144128 TATAAATATTAT-AAAATATAAAT-GTATATACATATATATA
1 TATAAATATTATGAAAATA-AAATAATA-ATA-ATA-ATATA
* *
53144168 TATAAACACTATGAAAATAAAATAATAATAATAATATA
1 TATAAATATTATGAAAATAAAATAATAATAATAATATA
53144206 TA-AAATAT
1 TATAAATAT
53144214 GTGTATGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
37 4 0.10
38 7 0.18
39 3 0.08
40 17 0.44
41 8 0.21
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.35
Consensus pattern (38 bp):
TATAAATATTATGAAAATAAAATAATAATAATAATATA
Found at i:53144286 original size:3 final size:3
Alignment explanation
Indices: 53144278--53144373 Score: 63
Period size: 3 Copynumber: 30.3 Consensus size: 3
53144268 ATATGTAAGT
*
53144278 ATA ATA ATAA ATA AT- ATA ATA ATA ATTA TTA AT- ATGA ATA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA A-TA ATA ATA AT-A ATA ATA ATA
* * *
53144324 ATA ATAA ATA ATGCA ATA ATA ATG ATGCA ATA ACA ATA TTA ATA A-A
1 ATA AT-A ATA AT--A ATA ATA ATA AT--A ATA ATA ATA ATA ATA ATA
53144370 ATA A
1 ATA A
53144374 ACTAAAATAG
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
2 6 0.08
3 53 0.72
4 10 0.14
5 5 0.07
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53144297 original size:15 final size:15
Alignment explanation
Indices: 53144277--53144345 Score: 72
Period size: 15 Copynumber: 4.7 Consensus size: 15
53144267 TATATGTAAG
53144277 TATAATAATAAATAA
1 TATAATAATAAATAA
*
53144292 TATAATAAT-AATTA
1 TATAATAATAAATAA
*
53144306 T-TAAT-ATGAATAA
1 TATAATAATAAATAA
53144319 TAATAATAATAAATAA
1 T-ATAATAATAAATAA
**
53144335 TGCAATAATAA
1 TATAATAATAA
53144346 TGATGCAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
12 2 0.04
13 9 0.20
14 5 0.11
15 21 0.47
16 8 0.18
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (15 bp):
TATAATAATAAATAA
Found at i:53144321 original size:22 final size:24
Alignment explanation
Indices: 53144278--53144346 Score: 85
Period size: 22 Copynumber: 3.1 Consensus size: 24
53144268 ATATGTAAGT
53144278 ATAATAATAAATAAT---ATAATA
1 ATAATAATAAATAATGCAATAATA
* *
53144299 ATAATTATTAAT-ATG-AATAATA
1 ATAATAATAAATAATGCAATAATA
53144321 ATAATAATAAATAATGCAATAATA
1 ATAATAATAAATAATGCAATAATA
53144345 AT
1 AT
53144347 GATGCAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 2 0.05
21 10 0.25
22 16 0.40
23 3 0.08
24 9 0.22
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (24 bp):
ATAATAATAAATAATGCAATAATA
Found at i:53144353 original size:14 final size:15
Alignment explanation
Indices: 53144323--53144356 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
53144313 GAATAATAAT
53144323 AATAATAAATAATGC
1 AATAATAAATAATGC
*
53144338 AATAAT-AATGATGC
1 AATAATAAATAATGC
53144352 AATAA
1 AATAA
53144357 CAATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (15 bp):
AATAATAAATAATGC
Found at i:53144373 original size:43 final size:43
Alignment explanation
Indices: 53144278--53144374 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
53144268 ATATGTAAGT
* * * **
53144278 ATAATAATAAATAATATAATAATAATTATTAATATGAATAATA
1 ATAATAATAAATAATACAATAATAATGATCAATAACAATAATA
* *
53144321 ATAATAATAAATAATGCAATAATAATGATGCAATAACAATATTA
1 ATAATAATAAATAATACAATAATAATGAT-CAATAACAATAATA
53144365 ATAA-AATAAA
1 ATAATAATAAA
53144375 CTAAAATAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
43 32 0.70
44 14 0.30
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (43 bp):
ATAATAATAAATAATACAATAATAATGATCAATAACAATAATA
Found at i:53152876 original size:12 final size:12
Alignment explanation
Indices: 53152859--53152883 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53152849 AAATTGAGAC
53152859 TATCCCTTCAGA
1 TATCCCTTCAGA
53152871 TATCCCTTCAGA
1 TATCCCTTCAGA
53152883 T
1 T
53152884 TTTCTTGTCA
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:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (12 bp):
TATCCCTTCAGA
Found at i:53153700 original size:132 final size:132
Alignment explanation
Indices: 53153461--53154309 Score: 1103
Period size: 132 Copynumber: 6.5 Consensus size: 132
53153451 CGATGACAAG
* * * * *
53153461 TCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTGAATATTGTAGATCCTGTCTCTCTAAGCAGTAG
1 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTTGTCTCCCTAAGCAGTAG
* * * * *
53153526 CGGAGCAGATCAAAGACGTTGAGTCTTATCTTCCCAAAGTAGTAGGGAAACAGATTTAAGCCACC
66 CGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACT
53153591 AA
131 AA
*
53153593 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTTGTTTCCCTAAGCAGTAG
1 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTTGTCTCCCTAAGCAGTAG
* *
53153658 TGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAATGTAGTAGGGAAGCAGATTTAAGCCACT
66 CGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACT
53153723 AA
131 AA
* *
53153725 TCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTGGTCTCCCTAAGCAGTAG
1 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTTGTCTCCCTAAGCAGTAG
* * * * *
53153790 CGGAGCAGATCGAATACAGAGAATCTTATCTTCCCAAGGTAGTAGGAAAGCAGATTTAAGCCACT
66 CGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACT
53153855 AA
131 AA
* * *
53153857 TCCTATCTCCCTGAGCGGCAGTGGAGTAGGTTGAAGAATGTAGATCTGGTCTCCCTAATCAGTAG
1 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTTGTCTCCCTAAGCAGTAG
* * * * *
53153922 CGGAGCAGATCGAAGACAGTGAATCTTATCTTCCTAAGGTAGTAGGGAAGCAGATTTAGGCTACT
66 CGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACT
53153987 AA
131 AA
* *
53153989 T-CTCATCTCCCTGAGCAGCAGT-G-G-A-G-T--AG---GTAGATCTAGTCTCCCTAAGTAGTA
1 TCCT-ATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTTGTCTCCCTAAGCAGTA
* * *
53154043 GCGGAGCAGATCGAAA-ACGGTAAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAGGCTA
65 GCGGAGCAGATC-AAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCA
53154107 CTAA
129 CTAA
* * *
53154111 T-CTCATCTCCCTGAGCAACAGTGGAGTAAGTTGAAGAATGTAGATCTTGTCTCCTTAAGCAGTA
1 TCCT-ATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTTGTCTCCCTAAGCAGTA
* * * * * * *
53154175 GTGGAGTAGATAAAAAAAATGGCGAATCTTATCTTCCCAAGATAGTAGGGAAGCAGATTTAAGCC
65 GCGGAGCAGAT--CAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCC
*
53154240 ACCAA
128 ACTAA
* * * * * * *
53154245 TACTATCTCCCTGAGCAACAGTGGAGTAGGTTGAAGATTGCAGATCATGTCTCCTTGAGCAGTAG
1 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTTGTCTCCCTAAGCAGTAG
53154310 TAGAGCGGAT
Statistics
Matches: 643, Mismatches: 58, Indels: 30
0.88 0.08 0.04
Matches are distributed among these distances:
122 104 0.16
123 3 0.00
124 1 0.00
125 3 0.00
126 1 0.00
127 2 0.00
128 1 0.00
129 3 0.00
130 1 0.00
131 3 0.00
132 414 0.64
133 3 0.00
134 102 0.16
135 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (132 bp):
TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAATGTAGATCTTGTCTCCCTAAGCAGTAG
CGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACT
AA
Found at i:53154113 original size:122 final size:122
Alignment explanation
Indices: 53153896--53154275 Score: 449
Period size: 122 Copynumber: 3.0 Consensus size: 122
53153886 GTTGAAGAAT
* * * *
53153896 GTAGATCTGGTCTCCCTAA-TCAGTAGCGGAGCAGATCGAAGACAGTGAATCTTATCTTCCTAAG
1 GTAGATCTAGTCTCCCTAAGT-AGTAGCGGAGCAGATCGAAAACGGTGAATCTTATCTTCCCAAG
*
53153960 GTAGTAGGGAAGCAGATTTAGGCTACTAATCTCATCTCCCTGAGCAGCAGTGGAGTAG
65 GTAGTAGGGAAGCAGATTTAGGCTACTAATCTCATCTCCCTGAGCAACAGTGGAGTAG
*
53154018 GTAGATCTAGTCTCCCTAAGTAGTAGCGGAGCAGATCGAAAACGGTAAATCTTATCTTCCCAAGG
1 GTAGATCTAGTCTCCCTAAGTAGTAGCGGAGCAGATCGAAAACGGTGAATCTTATCTTCCCAAGG
53154083 TAGTAGGGAAGCAGATTTAGGCTACTAATCTCATCTCCCTGAGCAACAGTGGAGTAAGTTGAAG
66 TAGTAGGGAAGCAGATTTAGGCTACTAATCTCATCTCCCTGAGCAACAGT-G-G--AG-T--AG
* * * * * ** * *
53154147 AATGTAGATCTTGTCTCCTTAAGCAGTAGTGGAGTAGATAAAAAAAATGGCGAATCTTATCTTCC
1 ---GTAGATCTAGTCTCCCTAAGTAGTAGCGGAGCAGAT--CGAAAACGGTGAATCTTATCTTCC
* * * *
53154212 CAAGATAGTAGGGAAGCAGATTTAAGCCACCAATACT-ATCTCCCTGAGCAACAGTGGAGTAG
61 CAAGGTAGTAGGGAAGCAGATTTAGGCTACTAAT-CTCATCTCCCTGAGCAACAGTGGAGTAG
53154274 GT
1 GT
53154276 TGAAGATTGC
Statistics
Matches: 224, Mismatches: 20, Indels: 26
0.83 0.07 0.10
Matches are distributed among these distances:
122 107 0.48
123 2 0.01
124 3 0.01
126 2 0.01
127 3 0.01
129 3 0.01
130 2 0.01
132 32 0.14
133 1 0.00
134 67 0.30
135 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (122 bp):
GTAGATCTAGTCTCCCTAAGTAGTAGCGGAGCAGATCGAAAACGGTGAATCTTATCTTCCCAAGG
TAGTAGGGAAGCAGATTTAGGCTACTAATCTCATCTCCCTGAGCAACAGTGGAGTAG
Found at i:53154417 original size:51 final size:51
Alignment explanation
Indices: 53154335--53154448 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
53154325 ACATCGAATT
* * ** *
53154335 TTATTTCCCTGGCGTTGCAATGGAATGGATTAAAGCTGAAGGCAGCAAATC
1 TTATTTCCCTGGCATTGCAACGGAACAGATTAAAGCTGAAGGCAACAAATC
* * *
53154386 TTATTTCCCTGGCATTGTAACGGAACAGATTAAAGTTGAAGGCAACGAATC
1 TTATTTCCCTGGCATTGCAACGGAACAGATTAAAGCTGAAGGCAACAAATC
* *
53154437 TCATCTCCCTGG
1 TTATTTCCCTGG
53154449 TATTTAAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (51 bp):
TTATTTCCCTGGCATTGCAACGGAACAGATTAAAGCTGAAGGCAACAAATC
Found at i:53155174 original size:5 final size:5
Alignment explanation
Indices: 53155159--53155191 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
53155149 TATCTACTTA
53155159 TTTATT TTTAT TTTAT TTTA- TTTAT TTTAT TTT
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTT
53155192 TGTTTGTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.69
6 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:53155184 original size:14 final size:14
Alignment explanation
Indices: 53155165--53155191 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53155155 CTTATTTATT
53155165 TTTATTTTATTTTA
1 TTTATTTTATTTTA
53155179 TTTATTTTATTTT
1 TTTATTTTATTTT
53155192 TGTTTGTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:53155362 original size:22 final size:22
Alignment explanation
Indices: 53155334--53155381 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
53155324 TTCGGCCACC
53155334 GCGGACGGTGGCGCCGTCGCCG
1 GCGGACGGTGGCGCCGTCGCCG
*
53155356 GCGGACGGTGGCGTCGTCGCCG
1 GCGGACGGTGGCGCCGTCGCCG
53155378 GCGG
1 GCGG
53155382 CCGGCAGCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.04, C:0.33, G:0.52, T:0.10
Consensus pattern (22 bp):
GCGGACGGTGGCGCCGTCGCCG
Found at i:53155948 original size:20 final size:19
Alignment explanation
Indices: 53155918--53155955 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
53155908 AATCCAAGGC
*
53155918 ATTTTTTTATTTATCTATT
1 ATTTTTTTATTTACCTATT
53155937 ATTTTATTTATTTACCTAT
1 ATTTT-TTTATTTACCTAT
53155956 ACTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTTTATTTACCTATT
Found at i:53155950 original size:24 final size:24
Alignment explanation
Indices: 53155917--53155986 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
53155907 TAATCCAAGG
*
53155917 CATTTTTTTATTTATCTATTATTTT
1 CATTTATTTATTTAT-TATTATTTT
**
53155942 -ATTTATTTACCTA-TACTTATTTT
1 CATTTATTTATTTATTA-TTATTTT
53155965 CATTTA-TTATTTATTTATTATT
1 CATTTATTTATTTA-TTATTATT
53155987 ATTCCTTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
22 2 0.06
23 12 0.33
24 20 0.56
25 2 0.06
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (24 bp):
CATTTATTTATTTATTATTATTTT
Found at i:53156189 original size:3 final size:3
Alignment explanation
Indices: 53156181--53156266 Score: 68
Period size: 3 Copynumber: 29.0 Consensus size: 3
53156171 ATATTCGTTG
* * * * *
53156181 TTA TTA TTA TCA TTC TTA TCT- TCA TTA TTA CTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
53156226 ATA TTA TTA TTA TTA TTA GTA TTG TTA TTA -TA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53156267 CAATTTATCT
Statistics
Matches: 62, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
2 2 0.03
3 59 0.95
4 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:53159006 original size:59 final size:59
Alignment explanation
Indices: 53158914--53160040 Score: 1517
Period size: 59 Copynumber: 19.2 Consensus size: 59
53158904 AAAGATGGGC
* * * *
53158914 CATATTTCATAATAATTATATGAGTAATTAATTAATTTTCAATTAATTAAATAAATAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
* * * *
53158973 CATATTTTATAATAATTTTATGAATAATTAATTAATTTTTGATTAATTAAATAAATAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
* ** *
53159032 CAAATTTCATAATAATTCTACAAATAATTAATTTATTTTTGATTAATTAAATAAATAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
* ** *
53159091 CAAATTTCATAATAATTCTACAAATAATTAATTTATTTTTGATTAATTAAATAAATAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
* * *
53159150 CATATTTCATAAGAATTCTATGAATAATTTATTTA-TTTTAGATTAATTAAATAAATATT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTA-ATTAATTAAATAAATAAT
* * * *
53159209 CATATTTCATAATAATTATACGAATAATTAATTAATTTTTTATTAATTAAATAAATAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
* * * *
53159268 CATATTTTATAATAGTTTTATGAATAATTAATTCA-TTTTAGATTAATTAAATAAATAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTA-ATTAATTAAATAAATAAT
*
53159327 CATATTTCATAATAATTCTATGAATAATTAATTTA-TTTTAGATTAATTAAATAAATATT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTA-ATTAATTAAATAAATAAT
* * ** *
53159386 CATATTTCATAATAATTATATGAATAATTAATTAATTTTCGATTAATTAAATAAAAAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
* * *
53159445 CATATTTTATAATAATTTTATGAATAATTAATTTA-TTTTAGATTAATTAAATAAGTAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTA-ATTAATTAAATAAATAAT
* * *
53159504 TATATTTCATAATAATTATATGAATAATTAATTTATTTTCAATTAATTAAATAAATAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
* * *
53159563 CATATTTTATAATAATTTTATGAATAATTAATTTA-TTTTAGATTAGTTAAATAAATAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTA-ATTAATTAAATAAATAAT
* *
53159622 CATATTTCATAATAATTCTATGAATAATTAATTTA-TTTT-AGT--TTAATTAAATAA-
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
* * *
53159676 -ATATTT-ATAATAATTATACGAATAATTAA-TTATTTTTTTATTAATTAAATAAATAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTA-TTTTTAATTAATTAAATAAATAAT
* * * * *
53159733 CATATTTTATAATAATTTTATGAATAATTAATTTATTTTTGATTAATTAATTAAATAAC
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
* *
53159792 CATATCTCATAATAATTCTATGAATAATTAATTTATTTTTGATTAATTAAATAAATAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
* * *
53159851 CATATTTTATAATAATTGTAGGAATAATTAATTTA-TTTTAGATTAATTAAATAAATAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTA-ATTAATTAAATAAATAAT
* * ** *
53159910 CATATTTCATAATAATTCTATGAATAATTAATTAATTGTCGATTAATTAAATAAATATT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
* *
53159969 CATATTTCATAATAATTCTATGAATAATTTATTTATTTTTGATTAATTAAATAAATAAT
1 CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
53160028 CATATTTCATAAT
1 CATATTTCATAAT
53160041 GATTATCATA
Statistics
Matches: 955, Mismatches: 95, Indels: 36
0.88 0.09 0.03
Matches are distributed among these distances:
51 3 0.00
52 21 0.02
53 10 0.01
54 2 0.00
55 11 0.01
56 11 0.01
57 2 0.00
58 25 0.03
59 854 0.89
60 16 0.02
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (59 bp):
CATATTTCATAATAATTCTATGAATAATTAATTTATTTTTAATTAATTAAATAAATAAT
Found at i:53159019 original size:19 final size:20
Alignment explanation
Indices: 53158985--53159022 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
53158975 TATTTTATAA
53158985 TAATTTTATGAATAATTAAT
1 TAATTTTATGAATAATTAAT
*
53159005 TAATTTT-TGATTAATTAA
1 TAATTTTATGAATAATTAA
53159023 ATAAATAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TAATTTTATGAATAATTAAT
Found at i:53159116 original size:32 final size:32
Alignment explanation
Indices: 53159021--53159122 Score: 99
Period size: 32 Copynumber: 3.3 Consensus size: 32
53159011 TTGATTAATT
53159021 AAATAAATAATCAAATTTCATAATAATTCTAC
1 AAATAAATAATCAAATTTCATAATAATTCTAC
* ** * *
53159053 AAATAATTAAT-TTATTT-TTGATTAA-T-T--
1 AAATAAATAATCAAATTTCAT-AATAATTCTAC
53159080 AAATAAATAATCAAATTTCATAATAATTCTAC
1 AAATAAATAATCAAATTTCATAATAATTCTAC
*
53159112 AAATAATTAAT
1 AAATAAATAAT
53159123 TTATTTTTGA
Statistics
Matches: 52, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
27 10 0.19
28 8 0.15
29 3 0.06
30 3 0.06
31 8 0.15
32 20 0.38
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (32 bp):
AAATAAATAATCAAATTTCATAATAATTCTAC
Found at i:53159779 original size:19 final size:20
Alignment explanation
Indices: 53159747--53159784 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
53159737 TTTTATAATA
53159747 ATTTTATGAATAATTAATTT
1 ATTTTATGAATAATTAATTT
*
53159767 ATTTT-TGATTAATTAATT
1 ATTTTATGAATAATTAATT
53159785 AAATAACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTTATGAATAATTAATTT
Found at i:53165469 original size:36 final size:36
Alignment explanation
Indices: 53165422--53165506 Score: 161
Period size: 36 Copynumber: 2.4 Consensus size: 36
53165412 NNNNNNGATG
53165422 AGATAAGTATAGCACTTATCACTTTTTCACTTGATC
1 AGATAAGTATAGCACTTATCACTTTTTCACTTGATC
53165458 AGATAAGTATAGCACTTATCACTTTTTCACTTGATC
1 AGATAAGTATAGCACTTATCACTTTTTCACTTGATC
*
53165494 AGATAAGTGTAGC
1 AGATAAGTATAGC
53165507 TAAAGCTACC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (36 bp):
AGATAAGTATAGCACTTATCACTTTTTCACTTGATC
Found at i:53169169 original size:66 final size:65
Alignment explanation
Indices: 53169057--53169194 Score: 179
Period size: 66 Copynumber: 2.1 Consensus size: 65
53169047 GCAAATTGCT
* * *
53169057 CAACTTAAAGCGAAGGCAGCATCGAGAGAAGCAGAGGTTCAAAGAAAATATGAAGAACTTCAGCT
1 CAACTTAAAACGAAGGCAGCAGCGAGAGAAGCAGAGG-TCAAAGAAAATATGAAGAACTCCAGCT
53169122 A
65 A
* * * *
53169123 CAACTTAAAACGGAGGCAGCAGCTAGGGAAGCAGAGG-CAAGCAGAAAATATGACGAACTCCAGC
1 CAACTTAAAACGAAGGCAGCAGCGAGAGAAGCAGAGGTCAA--AGAAAATATGAAGAACTCCAGC
53169187 TA
64 TA
53169189 CAACTT
1 CAACTT
53169195 CAGAATATGA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
64 3 0.05
66 60 0.95
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.14
Consensus pattern (65 bp):
CAACTTAAAACGAAGGCAGCAGCGAGAGAAGCAGAGGTCAAAGAAAATATGAAGAACTCCAGCTA
Found at i:53170949 original size:20 final size:20
Alignment explanation
Indices: 53170926--53170966 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53170916 CTATTCAAAC
* *
53170926 AATATTACTTGAATAGTTAT
1 AATATTACATGAATAATTAT
*
53170946 AATATTAGATGAATAATTAT
1 AATATTACATGAATAATTAT
53170966 A
1 A
53170967 TGTCTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.41
Consensus pattern (20 bp):
AATATTACATGAATAATTAT
Found at i:53171914 original size:19 final size:20
Alignment explanation
Indices: 53171892--53171944 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
53171882 TAATTATTTC
53171892 AAATATCATTATTTTTA-GT-
1 AAATAT-ATTATTTTTATGTG
53171911 AAATATATT-TTTTATATGTG
1 AAATATATTATTTT-TATGTG
53171931 AAATAT-TTATTTTT
1 AAATATATTATTTTT
53171945 CCTCCATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.13
18 5 0.17
19 11 0.37
20 10 0.33
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.57
Consensus pattern (20 bp):
AAATATATTATTTTTATGTG
Found at i:53172156 original size:18 final size:18
Alignment explanation
Indices: 53172100--53172157 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
53172090 ATATAGGTGA
*
53172100 AAAT-ATAATGATCTTTG
1 AAATAATAATGATATTTG
* *
53172117 AAATAAT-TTAGATA--TA
1 AAATAATAAT-GATATTTG
53172133 AAATAATAATGATATTTG
1 AAATAATAATGATATTTG
53172151 AAATAAT
1 AAATAAT
53172158 TATTTGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
16 12 0.39
17 6 0.19
18 13 0.42
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (18 bp):
AAATAATAATGATATTTG
Found at i:53172170 original size:106 final size:101
Alignment explanation
Indices: 53172012--53172210 Score: 256
Period size: 106 Copynumber: 1.9 Consensus size: 101
53172002 GAAATAATTA
* * *
53172012 TTTGAAATATTTCACATATAAAAATAGTAATATTTGAAATTATTATTTTTTATAATATTAGAATT
1 TTTGAAATATTTCACATATAAAAATAATAATATTTGAAATAATTATTTTTTATAATATTAAAATT
* *
53172077 TATCATACCCGCAATATAGGTGAAAATATAATGATC
66 TAACATACCCACAATATAGGTGAAAATATAATGATC
* *
53172113 TTTGAAATAATTT-AGATATAAAATAATAATGATATTTGAAATAATTATTTGATTTTATAATATT
1 TTTGAAAT-ATTTCACATAT-AAA-AATAATAATATTTGAAATAATTA-TT--TTTTATAATATT
* *
53172177 AAAATTTAACATACCCACAATGTAGGTGGAAATA
60 AAAATTTAACATACCCACAATATAGGTGAAAATA
53172211 ATAAATATTT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
101 13 0.16
102 7 0.08
103 20 0.24
104 2 0.02
106 41 0.49
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.40
Consensus pattern (101 bp):
TTTGAAATATTTCACATATAAAAATAATAATATTTGAAATAATTATTTTTTATAATATTAAAATT
TAACATACCCACAATATAGGTGAAAATATAATGATC
Found at i:53179861 original size:23 final size:22
Alignment explanation
Indices: 53179835--53179913 Score: 77
Period size: 24 Copynumber: 3.4 Consensus size: 22
53179825 GATAATTTGT
53179835 ATATATTTTTTAATTTTAAATTA
1 ATAT-TTTTTTAATTTTAAATTA
* ** *
53179858 ATATTTTTAGTTTATTGGAAATTGT
1 ATATTTTT--TTAATTTTAAATT-A
53179883 ATATATTTTTTAATTTTAAATTA
1 ATAT-TTTTTTAATTTTAAATTA
53179906 ATATTTTT
1 ATATTTTT
53179914 AGTTTATTGG
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
22 8 0.18
23 8 0.18
24 20 0.45
25 4 0.09
26 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (22 bp):
ATATTTTTTTAATTTTAAATTA
Found at i:53179865 original size:49 final size:48
Alignment explanation
Indices: 53179809--53179920 Score: 163
Period size: 48 Copynumber: 2.3 Consensus size: 48
53179799 TTGGTTATGT
53179809 ATATTTTTAATTT-TAAGATAATTTGTATATATTTTTTAATTTTAAATTA
1 ATATTTTTAATTTATAAGA-AA-TTGTATATATTTTTTAATTTTAAATTA
* **
53179858 ATATTTTTAGTTTATTGGAAATTGTATATATTTTTTAATTTTAAATTA
1 ATATTTTTAATTTATAAGAAATTGTATATATTTTTTAATTTTAAATTA
*
53179906 ATATTTTTAGTTTAT
1 ATATTTTTAATTTAT
53179921 TGGAAATATA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
48 42 0.71
49 14 0.24
50 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (48 bp):
ATATTTTTAATTTATAAGAAATTGTATATATTTTTTAATTTTAAATTA
Found at i:53179866 original size:20 final size:20
Alignment explanation
Indices: 53179841--53179914 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 20
53179831 TTGTATATAT
53179841 TTTTTAATTTTAAATTAATA
1 TTTTTAATTTTAAATTAATA
*
53179861 TTTTTAGTTTATTGGAAATTGTATATA
1 TTTTTA-ATT-TT--AAA-T-TA-ATA
53179888 TTTTTTAATTTTAAATTAATA
1 -TTTTTAATTTTAAATTAATA
53179909 TTTTTA
1 TTTTTA
53179915 GTTTATTGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
20 12 0.27
21 5 0.11
22 4 0.09
23 1 0.02
24 6 0.14
25 1 0.02
26 4 0.09
27 5 0.11
28 6 0.14
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTTAATTTTAAATTAATA
Found at i:53179887 original size:48 final size:48
Alignment explanation
Indices: 53179831--53179927 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
53179821 TTAAGATAAT
53179831 TTGTATATATTTTTTAATTTTAAATTAATATTTTTAGTTTATTGGAAA
1 TTGTATATATTTTTTAATTTTAAATTAATATTTTTAGTTTATTGGAAA
53179879 TTGTATATATTTTTTAATTTTAAATTAATATTTTTAGTTTATTGGAAA
1 TTGTATATATTTTTTAATTTTAAATTAATATTTTTAGTTTATTGGAAA
53179927 T
1 T
53179928 ATATAAAGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (48 bp):
TTGTATATATTTTTTAATTTTAAATTAATATTTTTAGTTTATTGGAAA
Found at i:53179903 original size:24 final size:24
Alignment explanation
Indices: 53179831--53179904 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
53179821 TTAAGATAAT
53179831 TTGTATATATTTTTTAATTTTAAA
1 TTGTATATATTTTTTAATTTTAAA
* * **
53179855 TT-AATAT-TTTTAGTTTATTGGAAA
1 TTGTATATATTTT--TTAATTTTAAA
53179879 TTGTATATATTTTTTAATTTTAAA
1 TTGTATATATTTTTTAATTTTAAA
53179903 TT
1 TT
53179905 AATATTTTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
22 4 0.11
23 4 0.11
24 22 0.58
25 4 0.11
26 4 0.11
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (24 bp):
TTGTATATATTTTTTAATTTTAAA
Found at i:53179927 original size:24 final size:24
Alignment explanation
Indices: 53179852--53179927 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
53179842 TTTTAATTTT
53179852 AAATTAATATTTTTAGTTTATTGG
1 AAATTAATATTTTTAGTTTATTGG
* * **
53179876 AAATTGTATATATTTT--TTAATTTT
1 AAATT-AATAT-TTTTAGTTTATTGG
53179900 AAATTAATATTTTTAGTTTATTGG
1 AAATTAATATTTTTAGTTTATTGG
53179924 AAAT
1 AAAT
53179928 ATATAAAGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
22 4 0.10
23 4 0.10
24 24 0.60
25 4 0.10
26 4 0.10
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (24 bp):
AAATTAATATTTTTAGTTTATTGG
Found at i:53180951 original size:33 final size:34
Alignment explanation
Indices: 53180909--53180979 Score: 135
Period size: 33 Copynumber: 2.1 Consensus size: 34
53180899 GTAAAGCAAT
53180909 CTAATGGACTTGGCTTGAATTAGCCATACAT-AA
1 CTAATGGACTTGGCTTGAATTAGCCATACATAAA
53180942 CTAATGGACTTGGCTTGAATTAGCCATACATAAA
1 CTAATGGACTTGGCTTGAATTAGCCATACATAAA
53180976 CTAA
1 CTAA
53180980 ACTACGTACC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 31 0.84
34 6 0.16
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (34 bp):
CTAATGGACTTGGCTTGAATTAGCCATACATAAA
Found at i:53186051 original size:2 final size:2
Alignment explanation
Indices: 53186046--53186073 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53186036 ACGTATGTAG
53186046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53186074 TATGTGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53186398 original size:3 final size:3
Alignment explanation
Indices: 53186392--53186421 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
53186382 TATAATAATA
53186392 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53186422 CATCAGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:53187267 original size:17 final size:19
Alignment explanation
Indices: 53187231--53187269 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
53187221 GTTGCTGATA
53187231 TTTCGTTTTTTGCTGCTTG
1 TTTCGTTTTTTGCTGCTTG
*
53187250 TTTCTTTTTTTG-TG-TTG
1 TTTCGTTTTTTGCTGCTTG
53187267 TTT
1 TTT
53187270 GCAGATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 11 0.58
ACGTcount: A:0.00, C:0.10, G:0.18, T:0.72
Consensus pattern (19 bp):
TTTCGTTTTTTGCTGCTTG
Found at i:53198351 original size:68 final size:67
Alignment explanation
Indices: 53198239--53198371 Score: 214
Period size: 68 Copynumber: 2.0 Consensus size: 67
53198229 AAGCATATAT
53198239 TTAGCCAATTTGTTTTAGGGTTCATAAGAAATTAGGGATCTTTTTAGTTTGTATGATTTTTGTGT
1 TTAGCCAATTTGTTTTAGGGTTCATAAGAAATTAGGGATCTTTTTAGTTTGTATGA-TTTTGTGT
53198304 CAG
65 CAG
* * *
53198307 TTAGCCAATTTGTTTTTGGGTTCATAAGAAATT-GGAGATTTTTTTAGTTTGTTTGATTTTGTGT
1 TTAGCCAATTTGTTTTAGGGTTCATAAGAAATTAGG-GATCTTTTTAGTTTGTATGATTTTGTGT
53198371 C
65 C
53198372 GGCTGGAATA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
67 11 0.18
68 50 0.82
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.50
Consensus pattern (67 bp):
TTAGCCAATTTGTTTTAGGGTTCATAAGAAATTAGGGATCTTTTTAGTTTGTATGATTTTGTGTC
AG
Found at i:53206244 original size:96 final size:97
Alignment explanation
Indices: 53206125--53206329 Score: 254
Period size: 96 Copynumber: 2.1 Consensus size: 97
53206115 TTTAAAAAAT
* * **
53206125 TAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAATTATTTA-AAAATCAGATAAGGGT
1 TAAATTAGGGTTCAGGGTCACTTGAGTAAACTAATTAAAAATT-TTTATAAAATCAGATAAGGGT
*
53206189 TTAGAG-TTAAGGGTTTTTAAGGAAAAA-TCAAA
65 TTAGAGTTTAA-GATTTTTAAGGAAAAACTCAAA
* ** ** *
53206221 TAAACTAGGGTTCAGGGTCACTTGAGTAAACTAATTATCAATTTTTATAAAATTTGATTAGGGTT
1 TAAATTAGGGTTCAGGGTCACTTGAGTAAACTAATTAAAAATTTTTATAAAATCAGATAAGGGTT
* *
53206286 TAGGGTTTAAGATTTTTAAGTAAAAACTCAAA
66 TAGAGTTTAAGATTTTTAAGGAAAAACTCAAA
53206318 TAAATTAGGGTT
1 TAAATTAGGGTT
53206330 TGGGGTTTAG
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
95 4 0.04
96 68 0.74
97 20 0.22
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (97 bp):
TAAATTAGGGTTCAGGGTCACTTGAGTAAACTAATTAAAAATTTTTATAAAATCAGATAAGGGTT
TAGAGTTTAAGATTTTTAAGGAAAAACTCAAA
Found at i:53206599 original size:126 final size:126
Alignment explanation
Indices: 53206369--53206623 Score: 422
Period size: 126 Copynumber: 2.0 Consensus size: 126
53206359 TTGTTAATTT
* *
53206369 AAAGAAGCTCCTAGGTGGACGCGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGAC
* *
53206434 GTTTCTGAACAAATAGTGTCAAAAACGCTTTAAGAAGGATTCTTTGTCAGC-AGAAGTACTG
66 GTTTCTGAACAAATAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGCCA-CTAGAAGTACTG
* *
53206495 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTTGCTTTTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGAC
* *
53206560 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGCCACTAGAAGTACTG
66 GTTTCTGAACAAATAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGCCACTAGAAGTACTG
53206621 AAA
1 AAA
53206624 CGCTTTTGCT
Statistics
Matches: 120, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
125 1 0.01
126 119 0.99
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGAC
GTTTCTGAACAAATAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGCCACTAGAAGTACTG
Found at i:53206705 original size:108 final size:108
Alignment explanation
Indices: 53206516--53206731 Score: 380
Period size: 108 Copynumber: 2.0 Consensus size: 108
53206506 CACGTGGACG
* *
53206516 CGCTTTTGCTACAGTTGCTTTTGAAAAAATAATTTCGAGTAGACGTTTCTGAGCAAATAGTGTCA
1 CGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGACGTTTCTGAGCAAATAGTGTCA
53206581 AAAACGCTTTAAGCAGGATGCTTTGCCA-CTAGAAGTACTGAAA
66 AAAACGCTTTAAGCAGGATGCTTTGCCAGC-AGAAGTACTGAAA
*
53206624 CGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGATGTTTCTGAGCAAATAGTGTCA
1 CGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGACGTTTCTGAGCAAATAGTGTCA
*
53206689 AAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAA
66 AAAACGCTTTAAGCAGGATGCTTTGCCAGCAGAAGTACTGAAA
53206732 GAAGCTCCCA
Statistics
Matches: 103, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
108 102 0.99
109 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (108 bp):
CGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGACGTTTCTGAGCAAATAGTGTCA
AAAACGCTTTAAGCAGGATGCTTTGCCAGCAGAAGTACTGAAA
Found at i:53209989 original size:35 final size:34
Alignment explanation
Indices: 53209950--53210039 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 34
53209940 GTAAAATAAT
* * *
53209950 TTTTATTATATTAAA-AATGTATAAGTAAATTTCTA
1 TTTTATTATATGAAATAATATAGAAG--AATTTCTA
*
53209985 TTTTAGTATATGAAATAATATAGAAGAATTTCTA
1 TTTTATTATATGAAATAATATAGAAGAATTTCTA
* *
53210019 TTTTATTACATCAAATAATAT
1 TTTTATTATATGAAATAATAT
53210040 CAAAATATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
34 26 0.55
35 13 0.28
36 8 0.17
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (34 bp):
TTTTATTATATGAAATAATATAGAAGAATTTCTA
Found at i:53210478 original size:18 final size:18
Alignment explanation
Indices: 53210452--53210494 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
53210442 GGGCTAGAAA
* * *
53210452 AGGAGACATATAAGGGTT
1 AGGATACATAAAAGGGCT
53210470 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
53210488 AGGATAC
1 AGGATAC
53210495 GCACCTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.30, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:53211166 original size:13 final size:13
Alignment explanation
Indices: 53211148--53211176 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
53211138 AAATACGGGT
53211148 TATACCAATCGAC
1 TATACCAATCGAC
53211161 TATACCAATCGAC
1 TATACCAATCGAC
53211174 TAT
1 TAT
53211177 CTCATGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.28
Consensus pattern (13 bp):
TATACCAATCGAC
Found at i:53211566 original size:15 final size:15
Alignment explanation
Indices: 53211546--53211580 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
53211536 TACATTTGGT
53211546 GCTAGAACAATTATG
1 GCTAGAACAATTATG
*
53211561 GCTAG-ATAATTATG
1 GCTAGAACAATTATG
53211575 GCTAGA
1 GCTAGA
53211581 TATTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (15 bp):
GCTAGAACAATTATG
Found at i:53211573 original size:14 final size:14
Alignment explanation
Indices: 53211554--53211586 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
53211544 GTGCTAGAAC
53211554 AATTATGGCTAGAT
1 AATTATGGCTAGAT
53211568 AATTATGGCTAGAT
1 AATTATGGCTAGAT
53211582 -ATTAT
1 AATTAT
53211587 TTAATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (14 bp):
AATTATGGCTAGAT
Found at i:53212215 original size:25 final size:25
Alignment explanation
Indices: 53212185--53212267 Score: 123
Period size: 25 Copynumber: 3.3 Consensus size: 25
53212175 ATGTGTTAAA
** *
53212185 CAGAGAGCACTGACATGCTATATAT
1 CAGAGAGCACCAACGTGCTATATAT
53212210 CAGAGAGCACCAACGTGCTATATAT
1 CAGAGAGCACCAACGTGCTATATAT
53212235 CAGAGAGCACCAACGTGCTA-ATAAT
1 CAGAGAGCACCAACGTGCTATAT-AT
53212260 CAGAGAGC
1 CAGAGAGC
53212268 GCGCTAAAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
24 2 0.04
25 52 0.96
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (25 bp):
CAGAGAGCACCAACGTGCTATATAT
Found at i:53218897 original size:2 final size:2
Alignment explanation
Indices: 53218890--53218937 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
53218880 AATTCATTTC
53218890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53218932 AT AT AT
1 AT AT AT
53218938 CAAAATGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53219469 original size:25 final size:25
Alignment explanation
Indices: 53219432--53219511 Score: 108
Period size: 25 Copynumber: 3.2 Consensus size: 25
53219422 TACAGAACAT
**
53219432 AGAGCACTGACGTGCT-ATATATCAG
1 AGAGCACCAACGTGCTAATA-ATCAG
*
53219457 AGAGCACCAACGTGCTAATAATTAG
1 AGAGCACCAACGTGCTAATAATCAG
*
53219482 AGAGCACCAATGTGCTAATAATCAG
1 AGAGCACCAACGTGCTAATAATCAG
53219507 AGAGC
1 AGAGC
53219512 GCGCTAAAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
25 46 0.94
26 3 0.06
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (25 bp):
AGAGCACCAACGTGCTAATAATCAG
Found at i:53220624 original size:5 final size:5
Alignment explanation
Indices: 53220614--53220671 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
53220604 TGTATATATA
* *
53220614 ATAAT ATAAT ATAAT ATAAT A-AA- ATAAC ATACTT ATTAAGT A-AAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT A-TAA-T ATAAT
53220659 ATAAT ATAAT ATA
1 ATAAT ATAAT ATA
53220672 TATTTTAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
3 1 0.02
4 6 0.14
5 32 0.73
6 1 0.02
7 4 0.09
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:53221982 original size:14 final size:15
Alignment explanation
Indices: 53221953--53221982 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53221943 TTTACGATTT
53221953 AAAAAAAATTCAAAA
1 AAAAAAAATTCAAAA
*
53221968 AAAAAAAATTTAAAA
1 AAAAAAAATTCAAAA
53221983 CTTTTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAAAATTCAAAA
Found at i:53223877 original size:20 final size:21
Alignment explanation
Indices: 53223828--53223877 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
53223818 TTTGCTCCAT
*
53223828 TTTC-TCTTCTCTTCTCTTTC
1 TTTCGTCTTCTCCTCTCTTTC
*
53223848 TTTCGT-TTCTCCTGTCTTTC
1 TTTCGTCTTCTCCTCTCTTTC
*
53223868 -TTCTTCTTCT
1 TTTCGTCTTCT
53223878 TCTTTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 4 0.16
20 20 0.80
21 1 0.04
ACGTcount: A:0.00, C:0.32, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTCGTCTTCTCCTCTCTTTC
Found at i:53227010 original size:115 final size:118
Alignment explanation
Indices: 53226746--53227148 Score: 503
Period size: 126 Copynumber: 3.3 Consensus size: 118
53226736 AATTTAAAAT
* * *
53226746 AGCTCCCACGTGGACGC-TCTTTTGTTACAGTAACTCTTGAAAAAATAATTTCGAGAAGACGTTT
1 AGCTCCCACGTGGACGCGT-TTTTGCTACAGTAGCTCTTG--AAAATAA--TCGAG--TA--TTT
53226810 CTGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGA
57 CTGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGA
53226872 AGCTCCCACGTGGACGCGTTTTTGCTACAGTAGCTCTTCG-AAATAGA-C-A-T-TTTCTGAGCA
1 AGCTCCCACGTGGACGCGTTTTTGCTACAGTAGCTCTT-GAAAATA-ATCGAGTATTTCTGAGCA
53226932 AATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGA
64 AATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGA
* *
53226987 AGCTCCCACGTGGACACGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGACATTTC
1 AGCTCCCACGTGGACGCGTTTTTGCTACAGTAGCTCTTG--AAAATAA--TCGAGT----ATTTC
* * *
53227052 TGAGCAAATAGAGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGTAAAAGTACTGAAAGA
58 TGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGA
**
53227113 AGCTCCTTCGTGGACGCGTTTTTGCTACAGTAGCTC
1 AGCTCCCACGTGGACGCGTTTTTGCTACAGTAGCTC
53227149 CTGTTTGGTC
Statistics
Matches: 249, Mismatches: 12, Indels: 32
0.85 0.04 0.11
Matches are distributed among these distances:
114 1 0.00
115 101 0.41
116 1 0.00
117 5 0.02
119 1 0.00
120 1 0.00
121 2 0.01
122 1 0.00
124 5 0.02
125 1 0.00
126 128 0.51
127 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (118 bp):
AGCTCCCACGTGGACGCGTTTTTGCTACAGTAGCTCTTGAAAATAATCGAGTATTTCTGAGCAAA
TAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGA
Found at i:53231421 original size:7 final size:7
Alignment explanation
Indices: 53231411--53231435 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53231401 CATAATACAT
53231411 AATACTA
1 AATACTA
53231418 AATACTA
1 AATACTA
53231425 AATACTA
1 AATACTA
53231432 AATA
1 AATA
53231436 GCAATTGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:53232626 original size:11 final size:11
Alignment explanation
Indices: 53232604--53232662 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
53232594 GCTTTTTTTA
*
53232604 AGAGGAACTTG
1 AGAGGAATTTG
*
53232615 AAAGGAATTTG
1 AGAGGAATTTG
53232626 AGA-GAATATTGG
1 AGAGGAAT-TT-G
53232638 AGAGGAATTTG
1 AGAGGAATTTG
*
53232649 AGA-GAAATTG
1 AGAGGAATTTG
53232659 AGAG
1 AGAG
53232663 AAATGATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 13 0.32
11 17 0.43
12 6 0.15
13 4 0.10
ACGTcount: A:0.42, C:0.02, G:0.34, T:0.22
Consensus pattern (11 bp):
AGAGGAATTTG
Found at i:53232643 original size:23 final size:23
Alignment explanation
Indices: 53232617--53232663 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
53232607 GGAACTTGAA
53232617 AGGAATTTGAGAGAATATTG-GAG
1 AGGAATTTGAGAGAA-ATTGAGAG
53232640 AGGAATTTGAGAGAAATTGAGAG
1 AGGAATTTGAGAGAAATTGAGAG
53232663 A
1 A
53232664 AATGATTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (23 bp):
AGGAATTTGAGAGAAATTGAGAG
Found at i:53232659 original size:10 final size:10
Alignment explanation
Indices: 53232623--53232666 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
53232613 TGAAAGGAAT
53232623 TTGAGAGAATA
1 TTGAGAGAA-A
*
53232634 TTGGAGAGGAAT
1 TT-GAGA-GAAA
53232646 TTGAGAGAAA
1 TTGAGAGAAA
53232656 TTGAGAGAAA
1 TTGAGAGAAA
53232666 T
1 T
53232667 GATTTAGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
10 14 0.48
11 6 0.21
12 6 0.21
13 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:53239710 original size:5 final size:5
Alignment explanation
Indices: 53239700--53239726 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
53239690 GAACCCAAAA
53239700 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
53239727 GGCCTCCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:53240217 original size:2 final size:2
Alignment explanation
Indices: 53240210--53240238 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53240200 TTGTGGCCAA
53240210 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53240239 TAGTCATCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:53260396 original size:186 final size:186
Alignment explanation
Indices: 53260058--53260396 Score: 469
Period size: 186 Copynumber: 1.8 Consensus size: 186
53260048 TTTTGTATCA
* *
53260058 ATATTGATCTAATGATTAACTGATTGAAATGTGATGATATATGATAGCAATTGATAGTGTTTGAT
1 ATATTGATCTAATGATTAAATGATTGAAATGTGATGATATATGATAGCAATTGATAGTATTTGAT
** *
53260123 ATTTCTAAAATATGTTATAATAATAAATGTTTTATTAACTAATGTTGGAAATAATTTAGAATATA
66 ATTTCTAAAATATGTTATAATAATAAATGTCCTATTAACTAATATTGGAAATAATTTAGAATATA
*
53260188 GTCGTCATGTCATAAAGTTTATTTATTTTGAAAATTCATGATATTATTTTGAATTG
131 GTCGACATGTCATAAAGTTTATTTATTTTGAAAATTCATGATATTATTTTGAATTG
*
53260244 ATATTGATGC-AATGGTTAAATGATTGAAACT-TGATGATATATGATAGCAATTGATAGTATTTG
1 ATATTGAT-CTAATGATTAAATGATTGAAA-TGTGATGATATATGATAGCAATTGATAGTATTTG
* ** *
53260307 ATGTTTCTACGATATGTTATAATAATAAATGTCCTATTAAAC-AATATT-G-AA-AATTT-GAGT
64 ATATTTCTAAAATATGTTATAATAATAAATGTCCTATT-AACTAATATTGGAAATAATTTAGAAT
* *
53260367 ATAGTTGACATGTCATAGAA-TTTGTTTATT
128 ATAGTCGACATGTCATA-AAGTTTATTTATT
53260397 GTGATGGATA
Statistics
Matches: 136, Mismatches: 13, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
182 27 0.20
183 7 0.05
184 2 0.01
185 1 0.01
186 94 0.69
187 5 0.04
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (186 bp):
ATATTGATCTAATGATTAAATGATTGAAATGTGATGATATATGATAGCAATTGATAGTATTTGAT
ATTTCTAAAATATGTTATAATAATAAATGTCCTATTAACTAATATTGGAAATAATTTAGAATATA
GTCGACATGTCATAAAGTTTATTTATTTTGAAAATTCATGATATTATTTTGAATTG
Found at i:53266872 original size:98 final size:98
Alignment explanation
Indices: 53266752--53266944 Score: 359
Period size: 98 Copynumber: 2.0 Consensus size: 98
53266742 TAGGTCAGAA
53266752 TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATCCCTT
1 TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATCCCTT
*
53266817 TAGAATCCCAAACTCGGAATATTTCCTTTACTT
66 TAAAATCCCAAACTCGGAATATTTCCTTTACTT
* *
53266850 TAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCCTT
1 TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATCCCTT
53266915 TAAAATCCCAAACTCGGAATATTTCCTTTA
66 TAAAATCCCAAACTCGGAATATTTCCTTTA
53266945 TCATTTTTAA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (98 bp):
TAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATCCCTT
TAAAATCCCAAACTCGGAATATTTCCTTTACTT
Found at i:53267275 original size:13 final size:13
Alignment explanation
Indices: 53267257--53267289 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
53267247 AATGGCATAA
53267257 AAATAATATAAAC-
1 AAATAA-ATAAACG
53267270 AAATAAATAAACG
1 AAATAAATAAACG
53267283 AAATAAA
1 AAATAAA
53267290 AAAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (13 bp):
AAATAAATAAACG
Found at i:53267711 original size:14 final size:14
Alignment explanation
Indices: 53267692--53267729 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
53267682 AAAAATACGC
53267692 ATATGTATATATAA
1 ATATGTATATATAA
53267706 ATATGTATA-A-AA
1 ATATGTATATATAA
*
53267718 ATATATATATAT
1 ATATGTATATAT
53267730 TTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 10 0.48
13 2 0.10
14 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (14 bp):
ATATGTATATATAA
Found at i:53267721 original size:20 final size:19
Alignment explanation
Indices: 53267698--53267759 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 19
53267688 ACGCATATGT
53267698 ATATATAAATATGTATAAAA
1 ATATATAAATATGT-TAAAA
*
53267718 ATATATATATAT-TTAAAA
1 ATATATAAATATGTTAAAA
53267736 ATA-ATTAAATATG--AAAA
1 ATATA-TAAATATGTTAAAA
53267753 ATA-ATAA
1 ATATATAA
53267760 TAATAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 3 0.08
17 9 0.24
18 14 0.37
19 1 0.03
20 11 0.29
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (19 bp):
ATATATAAATATGTTAAAA
Found at i:53270915 original size:21 final size:22
Alignment explanation
Indices: 53270886--53270926 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
53270876 TTTTATTTTA
*
53270886 TTTTATTTTATGAATCTTATAG
1 TTTTATTTTAAGAATCTTATAG
*
53270908 TTTT-TTTTAAGAATTTTAT
1 TTTTATTTTAAGAATCTTAT
53270927 GAAAATTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (22 bp):
TTTTATTTTAAGAATCTTATAG
Found at i:53271392 original size:13 final size:13
Alignment explanation
Indices: 53271374--53271437 Score: 78
Period size: 13 Copynumber: 4.9 Consensus size: 13
53271364 AGTTCTTCAT
53271374 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
53271387 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
53271400 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
53271413 TGCTTTT-AAGAAG
1 TGCTTTTGAA-AAG
53271426 TGCTTTTGAAAA
1 TGCTTTTGAAAA
53271438 ATTTGAATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
12 5 0.12
13 34 0.79
14 4 0.09
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:53271411 original size:26 final size:27
Alignment explanation
Indices: 53271374--53271438 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 27
53271364 AGTTCTTCAT
* *
53271374 TGCTTTTG-AAAAGTGCTTTTGAGAAG
1 TGCTTGTGAAAAAGTGCTTTTAAGAAG
53271400 TGC-TGTGAAAAAGTGCTTTTAAGAAG
1 TGCTTGTGAAAAAGTGCTTTTAAGAAG
*
53271426 TGCTTTTGAAAAA
1 TGCTTGTGAAAAA
53271439 TTTGAATGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.09
26 23 0.68
27 8 0.24
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.35
Consensus pattern (27 bp):
TGCTTGTGAAAAAGTGCTTTTAAGAAG
Found at i:53273359 original size:297 final size:297
Alignment explanation
Indices: 53272818--53273410 Score: 1141
Period size: 297 Copynumber: 2.0 Consensus size: 297
53272808 CAACCTCTGG
*
53272818 ATTTTTGGAGCTTTACTGACCTTATTGCCTGTAAAACCAGAAAAGTTATCAGCAAGTAATAGTTA
1 ATTTTTGGAGCTTTACTGACCTTATTGCCTGCAAAACCAGAAAAGTTATCAGCAAGTAATAGTTA
53272883 CAATCAAGAAATCATCATTTTCACCAAGCCTGTATAATTCTAGCTGAAACCCAAAATCCAATATC
66 CAATCAAGAAATCATCATTTTCACCAAGCCTGTATAATTCTAGCTGAAACCCAAAATCCAATATC
53272948 CTACTTCCAGCATACACCACGCATGAGTAAATGGTAAAGCAAAACATGTTTCCAGGAATAGAAGT
131 CTACTTCCAGCATACACCACGCATGAGTAAATGGTAAAGCAAAACATGTTTCCAGGAATAGAAGT
* *
53273013 AAATAGATTGTTACAGTGTACAAGCTGCAGTGTTTGCAAAAGGCAATCATGAAAATATTGGTCAA
196 AAACAGATTGTTACAGTGTACAAGCTGCAGTGTTTGCAAAAGCCAATCATGAAAATATTGGTCAA
53273078 CAGATTGTTGCAGCACATCAAAATCTTGTTGTAAAAT
261 CAGATTGTTGCAGCACATCAAAATCTTGTTGTAAAAT
53273115 ATTTTTGGAGCTTTACTGACCTTATTGCCTGCAAAACCAGAAAAGTTATCAGCAAGTAATAGTTA
1 ATTTTTGGAGCTTTACTGACCTTATTGCCTGCAAAACCAGAAAAGTTATCAGCAAGTAATAGTTA
*
53273180 CAATCAAGAAATCATCATTTTCACCAAGCCTGTATAATTCTATCTGAAACCCAAAATCCAATATC
66 CAATCAAGAAATCATCATTTTCACCAAGCCTGTATAATTCTAGCTGAAACCCAAAATCCAATATC
*
53273245 CTACTTCCAGCATACACCACGCATGAGTAAATGGTAAAGCAAAACATGTTTCCAGGAATAGTAGT
131 CTACTTCCAGCATACACCACGCATGAGTAAATGGTAAAGCAAAACATGTTTCCAGGAATAGAAGT
53273310 AAACAGATTGTTACAGTGTACAAGCTGCAGTGTTTGCAAAAGCCAATCATGAAAATATTGGTCAA
196 AAACAGATTGTTACAGTGTACAAGCTGCAGTGTTTGCAAAAGCCAATCATGAAAATATTGGTCAA
53273375 CAGATTGTTGCAGCACATCAAAATCTTGTTGTAAAA
261 CAGATTGTTGCAGCACATCAAAATCTTGTTGTAAAA
53273411 GATTGTTGAT
Statistics
Matches: 291, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
297 291 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (297 bp):
ATTTTTGGAGCTTTACTGACCTTATTGCCTGCAAAACCAGAAAAGTTATCAGCAAGTAATAGTTA
CAATCAAGAAATCATCATTTTCACCAAGCCTGTATAATTCTAGCTGAAACCCAAAATCCAATATC
CTACTTCCAGCATACACCACGCATGAGTAAATGGTAAAGCAAAACATGTTTCCAGGAATAGAAGT
AAACAGATTGTTACAGTGTACAAGCTGCAGTGTTTGCAAAAGCCAATCATGAAAATATTGGTCAA
CAGATTGTTGCAGCACATCAAAATCTTGTTGTAAAAT
Found at i:53274449 original size:47 final size:47
Alignment explanation
Indices: 53274391--53274825 Score: 577
Period size: 47 Copynumber: 9.3 Consensus size: 47
53274381 CAATAACATG
* * * * * *
53274391 CTCAAAA-TGGACAGCATTATACATCAAATTAGACAGCTTAAATATA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* * * * * * *
53274437 CCCAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* * * * * * * *
53274484 CTCACAATTGGACAGCATTATACATCAAATTAGATAGCTTAAATATA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* *
53274531 CTCACAATTGGACAGCATTATATATTAAAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* *
53274578 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAGTATA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* * *
53274625 CCCAAAATTGGACAACATTACACATTAAAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
*
53274672 CTCAAAATTGGACAGCATTACACATTAAAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
*
53274719 CTCAAAATTGGACAGCATTACACATTAAAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
*
53274766 CTCAAAATTGGACAGCATTATACATTAAAATGGGCAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
53274813 CTCAAAA-TGGACA
1 CTCAAAATTGGACA
53274826 TCAAATTTGG
Statistics
Matches: 363, Mismatches: 25, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 12 0.03
47 351 0.97
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (47 bp):
CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
Found at i:53275844 original size:28 final size:27
Alignment explanation
Indices: 53275812--53275882 Score: 97
Period size: 28 Copynumber: 2.6 Consensus size: 27
53275802 TTAATAAGTA
** *
53275812 CGCACACTTAGTGCTTTACCCTTATACT
1 CGCACACTTAGTGCTTT-CAATTAAACT
53275840 CGCACACTTAGTGCATTTCAATTAAACT
1 CGCACACTTAGTGC-TTTCAATTAAACT
53275868 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53275883 AATCTCATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 1 0.03
28 35 0.90
29 3 0.08
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (27 bp):
CGCACACTTAGTGCTTTCAATTAAACT
Found at i:53277174 original size:27 final size:27
Alignment explanation
Indices: 53277144--53277195 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
53277134 AAGATAAGTA
*
53277144 GAGAAAGAAAGATTGAAACAAGAAAGC
1 GAGAAAGAAAGATTAAAACAAGAAAGC
*
53277171 GAGAAAGGAAGATTAAAACAAGAAA
1 GAGAAAGAAAGATTAAAACAAGAAA
53277196 AGAAACCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.62, C:0.06, G:0.25, T:0.08
Consensus pattern (27 bp):
GAGAAAGAAAGATTAAAACAAGAAAGC
Found at i:53279782 original size:19 final size:18
Alignment explanation
Indices: 53279732--53279783 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
53279722 TTTTTTCATC
*
53279732 AAAATAATTAAAAAATCTT
1 AAAAT-ATTAAAAAAACTT
*
53279751 AAAATTATAAAAAAAACTAT
1 AAAA-TATTAAAAAAACT-T
*
53279771 TAAATATTAAAAA
1 AAAATATTAAAAA
53279784 TATGAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATATTAAAAAAACTT
Found at i:53279897 original size:21 final size:19
Alignment explanation
Indices: 53279873--53279919 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
53279863 CATAAAATTA
*
53279873 ATAAAACATATTTAGAATTTT
1 ATAAAACATA-TTA-AATTCT
53279894 ATAAAAACATATTAAATTCT
1 AT-AAAACATATTAAATTCT
53279914 ATAAAA
1 ATAAAA
53279920 ATCATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 7 0.29
21 5 0.21
22 8 0.33
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAAAACATATTAAATTCT
Found at i:53279925 original size:21 final size:22
Alignment explanation
Indices: 53279875--53279925 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
53279865 TAAAATTAAT
*
53279875 AAAACATATTTAGAATTTTATA
1 AAAACATATTTAGAATTCTATA
53279897 AAAACATA-TTA-AATTCTATA
1 AAAACATATTTAGAATTCTATA
53279917 AAAATCATA
1 AAAA-CATA
53279926 AAAAGTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 12 0.44
21 7 0.26
22 8 0.30
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAACATATTTAGAATTCTATA
Found at i:53280767 original size:18 final size:19
Alignment explanation
Indices: 53280734--53280769 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
53280724 ATCATTTCAG
53280734 TATAATATTTAACTTAAAA
1 TATAATATTTAACTTAAAA
*
53280753 TATAA-ATTTATCTTAAA
1 TATAATATTTAACTTAAA
53280770 TTTCAACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAATATTTAACTTAAAA
Found at i:53296692 original size:16 final size:16
Alignment explanation
Indices: 53296664--53296709 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
53296654 AATAATAGCC
53296664 TTATATATAAAATATA
1 TTATATATAAAATATA
53296680 TTATCATAT-AAATAT-
1 TTAT-ATATAAAATATA
53296695 TTGATATA-AAAATAT
1 TT-ATATATAAAATAT
53296710 CCAAAAGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 11 0.41
16 12 0.44
17 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
TTATATATAAAATATA
Found at i:53297575 original size:20 final size:20
Alignment explanation
Indices: 53297539--53297577 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
53297529 AATTTGGTGC
*
53297539 CAAAGAAGAAAACAAAGAAT
1 CAAAGAAGAAAAAAAAGAAT
53297559 CAAAGAA-AATAAAAAAGAA
1 CAAAGAAGAA-AAAAAAGAA
53297578 AGAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.74, C:0.08, G:0.13, T:0.05
Consensus pattern (20 bp):
CAAAGAAGAAAAAAAAGAAT
Found at i:53297778 original size:22 final size:22
Alignment explanation
Indices: 53297753--53297796 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53297743 TCTGTTCTCC
53297753 TTTTCGCTATTT-TTGCTTGTTT
1 TTTTCGCT-TTTGTTGCTTGTTT
*
53297775 TTTTCTCTTTTGTTGCTTGTTT
1 TTTTCGCTTTTGTTGCTTGTTT
53297797 GTCGTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.02, C:0.14, G:0.14, T:0.70
Consensus pattern (22 bp):
TTTTCGCTTTTGTTGCTTGTTT
Found at i:53297867 original size:18 final size:18
Alignment explanation
Indices: 53297846--53297880 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53297836 GGGCGCGCAC
*
53297846 GTACGGAGGCTCGCGTGA
1 GTACAGAGGCTCGCGTGA
*
53297864 GTACAGAGGCTGGCGTG
1 GTACAGAGGCTCGCGTG
53297881 GAGCGGCTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.20, G:0.46, T:0.17
Consensus pattern (18 bp):
GTACAGAGGCTCGCGTGA
Found at i:53302723 original size:30 final size:30
Alignment explanation
Indices: 53302687--53302748 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
53302677 TGATACCAAA
53302687 TTGTAGAAAATTATTCTCAATATAAAATTG
1 TTGTAGAAAATTATTCTCAATATAAAATTG
* *
53302717 TTGTAGAAAATTGTTCTCAATGTAAAATTG
1 TTGTAGAAAATTATTCTCAATATAAAATTG
53302747 TT
1 TT
53302749 CACATTCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (30 bp):
TTGTAGAAAATTATTCTCAATATAAAATTG
Found at i:53302745 original size:17 final size:17
Alignment explanation
Indices: 53302693--53302749 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
53302683 CAAATTGTAG
* *
53302693 AAAATTATTCTCAATAT
1 AAAATTGTTCTCAATGT
*
53302710 AAAATTGTTGT--A-G-
1 AAAATTGTTCTCAATGT
53302723 AAAATTGTTCTCAATGT
1 AAAATTGTTCTCAATGT
53302740 AAAATTGTTC
1 AAAATTGTTC
53302750 ACATTCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 10 0.31
15 2 0.06
16 1 0.03
17 19 0.59
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (17 bp):
AAAATTGTTCTCAATGT
Found at i:53309878 original size:14 final size:14
Alignment explanation
Indices: 53309859--53309886 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53309849 AATCAACTAG
53309859 ATTTGAAGATCCAT
1 ATTTGAAGATCCAT
53309873 ATTTGAAGATCCAT
1 ATTTGAAGATCCAT
53309887 CTTGTGGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
ATTTGAAGATCCAT
Found at i:53313784 original size:2 final size:2
Alignment explanation
Indices: 53313777--53313801 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53313767 AGACAAAGGC
53313777 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
53313802 GTTATCACCA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:53318483 original size:17 final size:17
Alignment explanation
Indices: 53318461--53318496 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
53318451 ATTTTTTTTC
53318461 ATTTT-AAAAATACAATT
1 ATTTTAAAAAATA-AATT
53318478 ATTTTAAAAAATAAATT
1 ATTTTAAAAAATAAATT
53318495 AT
1 AT
53318497 AATATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTTAAAAAATAAATT
Found at i:53320407 original size:10 final size:11
Alignment explanation
Indices: 53320382--53320410 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
53320372 TTTAAAAATA
53320382 AAAAATATTTT
1 AAAAATATTTT
53320393 AAAAATATTTT
1 AAAAATATTTT
53320404 AAAAATA
1 AAAAATA
53320411 AAAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:53320425 original size:17 final size:17
Alignment explanation
Indices: 53320392--53320425 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53320382 AAAAATATTT
* *
53320392 TAAAAATATTTTAAAAA
1 TAAAAAAATTTAAAAAA
53320409 TAAAAAAATTTAAAAAA
1 TAAAAAAATTTAAAAAA
53320426 ATATATATTA
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):
TAAAAAAATTTAAAAAA
Found at i:53320429 original size:29 final size:29
Alignment explanation
Indices: 53320369--53320425 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
53320359 ACCAAAAATT
*
53320369 TATTTTAAAAATAAAAAATATTTTAAAAA
1 TATTTTAAAAATAAAAAATATTTAAAAAA
53320398 TATTTTAAAAATAAAAAA-ATTTAAAAAA
1 TATTTTAAAAATAAAAAATATTTAAAAAA
53320426 ATATATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
TATTTTAAAAATAAAAAATATTTAAAAAA
Found at i:53321365 original size:55 final size:55
Alignment explanation
Indices: 53321261--53321368 Score: 144
Period size: 55 Copynumber: 2.0 Consensus size: 55
53321251 AATGCGAAAG
* * * *
53321261 TCACATAATTGGGTGCTCAACCACCGGAATGAAATATACGGATTAGTGCATTGAA
1 TCACATAATTAGGTGCTCAACCACCAGAATGAAATATACGAATGAGTGCATTGAA
* * * *
53321316 TCACATCATTAGGTGCTCAACTACTAGAATGAAATATACGAATGGGTGCATTG
1 TCACATAATTAGGTGCTCAACCACCAGAATGAAATATACGAATGAGTGCATTG
53321369 GATCTGTCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (55 bp):
TCACATAATTAGGTGCTCAACCACCAGAATGAAATATACGAATGAGTGCATTGAA
Found at i:53325783 original size:16 final size:16
Alignment explanation
Indices: 53325762--53325795 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53325752 TTTATTTTAA
53325762 TATTTATATTTATATT
1 TATTTATATTTATATT
* *
53325778 TATTTATTTTTATCTT
1 TATTTATATTTATATT
53325794 TA
1 TA
53325796 AATTTGACGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTATATTTATATT
Found at i:53331565 original size:20 final size:23
Alignment explanation
Indices: 53331530--53331570 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
53331520 GTGATGGAGC
53331530 GATCATCTTGCTTGAA-AGCATT
1 GATCATCTTGCTTGAAGAGCATT
53331552 GATC-TCTT-CTTGAAGAGCA
1 GATCATCTTGCTTGAAGAGCA
53331571 GAAATGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (23 bp):
GATCATCTTGCTTGAAGAGCATT
Found at i:53335271 original size:27 final size:28
Alignment explanation
Indices: 53335224--53335276 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
53335214 CAACTTCTCT
** *
53335224 TTGAGTTTTTCTTTTTTAAGATTTTTTC
1 TTGAGTTTTTCTTTTAGAAGAGTTTTTC
53335252 TTGAG-TTTTCTTTTAGAAGAGTTTT
1 TTGAGTTTTTCTTTTAGAAGAGTTTT
53335277 AACAATCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.17, C:0.06, G:0.15, T:0.62
Consensus pattern (28 bp):
TTGAGTTTTTCTTTTAGAAGAGTTTTTC
Found at i:53337223 original size:45 final size:45
Alignment explanation
Indices: 53337174--53337262 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
53337164 TTTAGACCTT
53337174 AATTATCCTCTTAAAGAGTTGTATTATGATGAATTCAATTTACAG
1 AATTATCCTCTTAAAGAGTTGTATTATGATGAATTCAATTTACAG
53337219 AATTATCCTCTTAAAGAGTTGTATTATGATGAATTCAATTTACA
1 AATTATCCTCTTAAAGAGTTGTATTATGATGAATTCAATTTACA
53337263 AACTTTTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (45 bp):
AATTATCCTCTTAAAGAGTTGTATTATGATGAATTCAATTTACAG
Found at i:53337437 original size:14 final size:14
Alignment explanation
Indices: 53337418--53337447 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53337408 CACATTGAAA
*
53337418 AAAGAATCTATTTG
1 AAAGAATCTACTTG
53337432 AAAGAATCTACTTG
1 AAAGAATCTACTTG
53337446 AA
1 AA
53337448 TTTGTCTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (14 bp):
AAAGAATCTACTTG
Found at i:53338718 original size:21 final size:21
Alignment explanation
Indices: 53338694--53338733 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53338684 TTCTGCTCTG
*
53338694 CTCTACTTCCCTCGTTGCTAC
1 CTCTACTTCCCTCGCTGCTAC
**
53338715 CTCTGTTTCCCTCGCTGCT
1 CTCTACTTCCCTCGCTGCT
53338734 GCATGCTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.42, G:0.12, T:0.40
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCTAC
Found at i:53342203 original size:17 final size:17
Alignment explanation
Indices: 53342181--53342215 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
53342171 TATTATATCC
53342181 TTCAAATACGAACTTGA
1 TTCAAATACGAACTTGA
*
53342198 TTCAAATATGAACTTGA
1 TTCAAATACGAACTTGA
53342215 T
1 T
53342216 AAGAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (17 bp):
TTCAAATACGAACTTGA
Found at i:53343524 original size:36 final size:36
Alignment explanation
Indices: 53343477--53343551 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
53343467 TTTTAATATT
* * *
53343477 AATATGTGATATGATGTAAGAATATGGTATTGAATA
1 AATATATGATATGATATAAGAATATGATATTGAATA
53343513 AATATATGATATGATATAAGAATATGATATTGAATA
1 AATATATGATATGATATAAGAATATGATATTGAATA
53343549 AAT
1 AAT
53343552 CAAAGAAGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (36 bp):
AATATATGATATGATATAAGAATATGATATTGAATA
Found at i:53343531 original size:18 final size:19
Alignment explanation
Indices: 53343472--53343551 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 19
53343462 TTGACTTTTA
* *
53343472 ATATTAATATGTGATA-TG
1 ATATAAATATATGATATTG
* *
53343490 ATGTAAGA-ATATGGTATTG
1 ATATAA-ATATATGATATTG
53343509 A-ATAAATATATGATA-TG
1 ATATAAATATATGATATTG
53343526 ATATAAGA-ATATGATATTG
1 ATATAA-ATATATGATATTG
53343545 A-ATAAAT
1 ATATAAAT
53343552 CAAAGAAGAG
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
17 5 0.10
18 36 0.73
19 8 0.16
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (19 bp):
ATATAAATATATGATATTG
Found at i:53343539 original size:13 final size:13
Alignment explanation
Indices: 53343485--53343542 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
53343475 TTAATATGTG
*
53343485 ATATGATGTAAGA
1 ATATGATATAAGA
* *
53343498 ATATGGTAT-TGA
1 ATATGATATAAGA
* *
53343510 ATA-AATATATG-
1 ATATGATATAAGA
53343521 ATATGATATAAGA
1 ATATGATATAAGA
53343534 ATATGATAT
1 ATATGATAT
53343543 TGAATAAATC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 6 0.17
12 13 0.37
13 16 0.46
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (13 bp):
ATATGATATAAGA
Found at i:53343547 original size:12 final size:13
Alignment explanation
Indices: 53343485--53343548 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 13
53343475 TTAATATGTG
* *
53343485 ATATGATGTAAGA
1 ATATGATATATGA
*
53343498 ATATGGTAT-TGA
1 ATATGATATATGA
*
53343510 ATA-AATATATG-
1 ATATGATATATGA
*
53343521 ATATGATATAAGA
1 ATATGATATATGA
53343534 ATATGATAT-TGA
1 ATATGATATATGA
53343546 ATA
1 ATA
53343549 AATCAAAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
11 6 0.15
12 18 0.45
13 16 0.40
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (13 bp):
ATATGATATATGA
Done.