Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 173 of 208
Found at i:55279153 original size:51 final size:51
Alignment explanation
Indices: 55279005--55279154 Score: 158
Period size: 51 Copynumber: 2.9 Consensus size: 51
55278995 AAAGCTGAAA
* * *
55279005 TGGAGCAGATTAAAGCTGAAGGTAGCAAATCCTATCTTTTTGGAGTTACAG
1 TGGAGCAGATTAAAGCTGAAGGTAGCAAATCTTATCTTTCTGGCGTTACAG
* * * ** * *
55279056 TGGAACAGATTAAAACTAAAGGTAGTGAATCTTGT-TTCCTTGGCGTTACAG
1 TGGAGCAGATTAAAGCTGAAGGTAGCAAATCTTATCTTTC-TGGCGTTACAG
* * * *
55279107 TGGAGTAGATTCAAGCTGAAGGTAGCCAATCTTATCTTTCTAGCGTTA
1 TGGAGCAGATTAAAGCTGAAGGTAGCAAATCTTATCTTTCTGGCGTTA
55279155 AAGTTGTAGA
Statistics
Matches: 77, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
50 2 0.03
51 72 0.94
52 3 0.04
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (51 bp):
TGGAGCAGATTAAAGCTGAAGGTAGCAAATCTTATCTTTCTGGCGTTACAG
Found at i:55279373 original size:130 final size:131
Alignment explanation
Indices: 55279171--55279552 Score: 391
Period size: 130 Copynumber: 2.9 Consensus size: 131
55279161 TAGAAAGCAA
* * * *
55279171 GTCTTATCCCCCTAAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTAAATTTG
1 GTCTTATCTCCCTAAAGTTGCAGTGA-GCAAACTGAAGATAACAAATCTTATCTCCCTAAAGTTG
* * * * *
55279236 CAGTGGAGCAGATTAAAGCCAA-TAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAATT
65 CAGTGGAGCAGATTAAAG-AAACCAATCCTATCTCCCTAAAGTTGCAATGGAGCGGATTAAAATG
55279300 A-G
129 ATG
* * * *
55279302 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATA-AACCAATCTTATCTCCCTGAAGTTG
1 GTCTTATCTCCCTAAAGTTGCAGT-GAGCAAACTGAAGATAACAAATCTTATCTCCCTAAAGTTG
* *
55279366 CAGTGGAGCAGATTGAAGAAACCAATTCTATCTCCCTAAAGTTGCAATGGAGCGGATTAAAATGA
65 CAGTGGAGCAGATTAAAGAAACCAATCCTATCTCCCTAAAGTTGCAATGGAGCGGATTAAAATGA
55279431 TG
130 TG
* * * * ** *
55279433 GATCTTATCTCTCTAAAGTTGCAGTAGAGCAGA-TCACG-T--CAGGTCTTATCTCCCTGAAGTT
1 G-TCTTATCTCCCTAAAGTTGCAGT-GAGCAAACTGAAGATAACAAATCTTATCTCCCTAAAGTT
* * * * * * * * *
55279494 GCAGTGGAGCATATTGAATAAACCAATCTTATCTTCCTGAAGTTGTAGTGGAGCAGATT
64 GCAGTGGAGCAGATTAAAGAAACCAATCCTATCTCCCTAAAGTTGCAATGGAGCGGATT
55279553 GAAGTTATAA
Statistics
Matches: 212, Mismatches: 34, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
129 71 0.33
130 76 0.36
131 36 0.17
132 29 0.14
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (131 bp):
GTCTTATCTCCCTAAAGTTGCAGTGAGCAAACTGAAGATAACAAATCTTATCTCCCTAAAGTTGC
AGTGGAGCAGATTAAAGAAACCAATCCTATCTCCCTAAAGTTGCAATGGAGCGGATTAAAATGAT
G
Found at i:55279504 original size:173 final size:171
Alignment explanation
Indices: 55279172--55279640 Score: 514
Period size: 173 Copynumber: 2.7 Consensus size: 171
55279162 AGAAAGCAAG
* * * * * *
55279172 TCTTATCCCCCTAAAGTTGCAGT-GAGGCAGACTGAAGATGACAAATCTTATCTCCCTAAATTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGA-GCAGATTGAAGA-AACAATTC-TATCTCCCTAAAGTTG
* * *** * * * * * * *
55279236 CAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAATTA
63 CAATGGAGCGGATTAAA-ATGATGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGA-TCAAATCA
55279301 GGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATAAACCAA
126 GGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATAAACCAA
55279347 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATTCTATCTCCCTAAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAA-CAATTCTATCTCCCTAAAGTTGCA
* **
55279412 ATGGAGCGGATTAAAATGATGGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACGTCAGGT
65 ATGGAGCGGATTAAAATGAT-GATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCAAATCAGGT
* *
55279477 CTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAATAAACCAA
129 CTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATAAACCAA
* * * * * * *
55279520 TCTTATCTTCCTGAAGTTGTAGTGGAGCAGATTGAAGTTATA-AATCCTGTCTCCTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AAACAATTCTATCTCCCTAAAGTTGC
* *
55279584 AGCA-GGA-CGGATTAAAATGATAGATCTTATCTCTCTGAAGTTGCGGTAGAGTAGATC
64 A--ATGGAGCGGATTAAAATGAT-GATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATC
55279641 GCATCAAACC
Statistics
Matches: 253, Mismatches: 34, Indels: 16
0.83 0.11 0.05
Matches are distributed among these distances:
173 150 0.59
174 61 0.24
175 40 0.16
176 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (171 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACAATTCTATCTCCCTAAAGTTGCAA
TGGAGCGGATTAAAATGATGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCAAATCAGGTCT
TATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATAAACCAA
Found at i:55279554 original size:44 final size:44
Alignment explanation
Indices: 55279172--55279555 Score: 263
Period size: 44 Copynumber: 8.8 Consensus size: 44
55279162 AGAAAGCAAG
* * * * * *
55279172 TCTTATCCCCCTAAAGTTGCAGT-GAGGCAGACTGAAGATGACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGA-GCAGATTGAATA-AACCAA
* * * ** *
55279217 TCTTATCTCCCTAAATTTGCAGTGGAGCAGATTAAAGCCAA-TAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-TAAACCAA
* * ** ** *
55279261 TCCTATCTCCCTAAAGTTGCAGTGGAGTGGATT--A-AAATTAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAACCA-A
* *
55279303 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAACCAA
*
55279347 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAACCAA
* * * ***
55279391 T-TCTATCTCCCTAAAGTTGCAATGGAGCGGATT-AA-AATGATGGA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAA--ACCAA
* * * * * *
55279435 TCTTATCTCTCTAAAGTTGCAGTAGAGCAGA-TCACGT----CAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-ATAAACCA-A
*
55279476 TCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAATAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAACCAA
* *
55279520 TCTTATCTTCCTGAAGTTGTAGTGGAGCAGATTGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
55279556 GTTATAAATC
Statistics
Matches: 269, Mismatches: 50, Indels: 41
0.75 0.14 0.11
Matches are distributed among these distances:
40 2 0.01
41 30 0.11
42 32 0.12
43 4 0.01
44 162 0.60
45 37 0.14
46 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATAAACCAA
Found at i:55279581 original size:129 final size:129
Alignment explanation
Indices: 55279217--55279585 Score: 313
Period size: 129 Copynumber: 2.9 Consensus size: 129
55279207 AGATGACAAA
* * * * * *
55279217 TCTTATCTCCCTAAATTTGCAGTGGAGCAGATTAAAGCCAA-TAATCCTATCTCCCTAAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-AAACCAATTCTATCTCCCTAAAGTTGC
* ** ** * * * * *
55279281 AGTGGAGTGGATTAAAAT--TAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATAAAC
65 AATGGAGCAGATTAAAATGATAAATCCTATCTCTCTAAAGTTGCAGTAGAGC--A--G-AT-CAC
*
55279344 --CA-A
124 GTCAGG
55279347 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATTCTATCTCCCTAAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATTCTATCTCCCTAAAGTTGCA
* ** *
55279412 ATGGAGCGGATTAAAATGATGGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACGTCAGG
66 ATGGAGCAGATTAAAATGATAAATCCTATCTCTCTAAAGTTGCAGTAGAGCAGATCACGTCAGG
* * * * *
55279476 TCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAATAAACCAA-TCTTATCTTCCTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATTC-TATCTCCCTAAAGTTGC
* * * * * *
55279540 AGTGGAGCAGATTGAAGTTATAAATCCTGTCTC-CTTGAAGTTGCAG
65 AATGGAGCAGATTAAAATGATAAATCCTATCTCTC-TAAAGTTGCAG
55279586 CAGGACGGAT
Statistics
Matches: 201, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
126 2 0.01
127 2 0.01
128 6 0.03
129 92 0.46
130 72 0.36
132 27 0.13
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATTCTATCTCCCTAAAGTTGCA
ATGGAGCAGATTAAAATGATAAATCCTATCTCTCTAAAGTTGCAGTAGAGCAGATCACGTCAGG
Found at i:55279708 original size:173 final size:173
Alignment explanation
Indices: 55279162--55279738 Score: 432
Period size: 173 Copynumber: 3.3 Consensus size: 173
55279152 TTAAAGTTGT
* * * * * * *
55279162 AGAAAGCAAGTCTTATCCCCCTAAAGTTGCAGT-GAGGCAGACTGAAGATGACAAATCTTATCTC
1 AGAAACCAA-TCTTATCTCCCTGAAGTTGTAGTGGA-GCAGATTGAAGA-AACAAATCCTATCTC
* * * *** * * * **
55279226 CCTAAATTTGCAGTGGAGCAGATTAAAGCCAATA-ATCCTATCTCCCTAAAGTTGCAGTGGAGTG
63 CCTAAAGTTGCAATGGAGCGGATTAAA-ATGATAGATCTTATCTCTCTAAAGTTGCAGTAGAGCA
* * * *** * * * * * *
55279290 GATTAAAATTAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGA
127 GA-TCACATCAAACCTTATCTCCCTGAAGTTACAATGAAACATATTGA
* * * *
55279338 ATAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATTCTATCTCCCT
1 AGAAACCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGAAACAAATCCTATCTCCCT
*
55279403 AAAGTTGCAATGGAGCGGATTAAAATGATGGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATC
66 AAAGTTGCAATGGAGCGGATTAAAATGATAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATC
* *** * * * *
55279468 ACGTCAGGTCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGA
131 ACATCAAACCTTATCTCCCTGAAGTTACAATGAAACATATTGA
* * ** * * *
55279511 ATAAACCAATCTTATCTTCCTGAAGTTGTAGTGGAGCAGATTGAAGTTATAAATCCTGTCTCCTT
1 AGAAACCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGAAACAAATCCTATCTCCCT
* * * *
55279576 GAAGTTGCAGCA-GGA-CGGATTAAAATGATAGATCTTATCTCTCTGAAGTTGCGGTAGAGTAGA
66 AAAGTTGCA--ATGGAGCGGATTAAAATGATAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGA
* *
55279639 TCGCATCAAACCTTAT-TTCCTAGATA-TTACAATGAAACA-AGTTGA
129 TCACATCAAACCTTATCTCCCT-GA-AGTTACAATGAAACATA-TTGA
** * * * *
55279684 AGCTA-CAAGTTTTATCTCCCTGAAGTTATAGTGGAGCAAACTGAAGATAACAAAT
1 AGAAACCAA-TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGA-AACAAAT
55279739 GTTCCCTCAA
Statistics
Matches: 330, Mismatches: 62, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
172 8 0.02
173 209 0.63
174 71 0.22
175 33 0.10
176 9 0.03
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (173 bp):
AGAAACCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGAAACAAATCCTATCTCCCT
AAAGTTGCAATGGAGCGGATTAAAATGATAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATC
ACATCAAACCTTATCTCCCTGAAGTTACAATGAAACATATTGA
Found at i:55281351 original size:19 final size:18
Alignment explanation
Indices: 55281305--55281352 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
55281295 ATCCTTAATT
55281305 ATATATCTAT-ATATTATA
1 ATATAT-TATAATATTATA
*
55281323 ATAATTTTATAATATTATAA
1 AT-ATATTATAATATTAT-A
55281343 ATATATTATA
1 ATATATTATA
55281353 TCATAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 5 0.20
19 17 0.68
20 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATTATAATATTATA
Found at i:55281353 original size:16 final size:15
Alignment explanation
Indices: 55281302--55281362 Score: 52
Period size: 16 Copynumber: 4.0 Consensus size: 15
55281292 TGAATCCTTA
**
55281302 ATTATATATCTATAT
1 ATTATATATAAATAT
* *
55281317 ATTATA-ATAATTTT
1 ATTATATATAAATAT
*
55281331 ATAATATTATAAATAT
1 ATTATA-TATAAATAT
55281347 ATTATATCATAAATAT
1 ATTATAT-ATAAATAT
55281363 TCTTTCAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
14 9 0.26
15 7 0.20
16 19 0.54
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATATATAAATAT
Found at i:55284161 original size:19 final size:17
Alignment explanation
Indices: 55284123--55284160 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
55284113 GATCTTTCAC
*
55284123 ATATTTTTTTTATAAAT
1 ATATTTTTTATATAAAT
55284140 ATATTTTTTAATATAAA-
1 ATATTTTTT-ATATAAAT
55284157 ATAT
1 ATAT
55284161 ACTTGTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTTTTATATAAAT
Found at i:55287945 original size:2 final size:2
Alignment explanation
Indices: 55287938--55287974 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
55287928 TCTTAGAATT
*
55287938 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55287975 TATTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:55289320 original size:24 final size:24
Alignment explanation
Indices: 55289292--55289339 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
55289282 AGCCATTGGT
55289292 GATACTATAAAAAAGAATTACGGA
1 GATACTATAAAAAAGAATTACGGA
*
55289316 GATACTATAAAAAAGGATTACGGA
1 GATACTATAAAAAAGAATTACGGA
55289340 TTCGAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.08, G:0.19, T:0.21
Consensus pattern (24 bp):
GATACTATAAAAAAGAATTACGGA
Found at i:55290083 original size:21 final size:21
Alignment explanation
Indices: 55290058--55290098 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55290048 AATATTAATT
55290058 TATCATTATTACTATTATTAC
1 TATCATTATTACTATTATTAC
**
55290079 TATCATTATTGTTATTATTA
1 TATCATTATTACTATTATTA
55290099 TTAGTAGTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (21 bp):
TATCATTATTACTATTATTAC
Found at i:55290215 original size:21 final size:21
Alignment explanation
Indices: 55290166--55290215 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
55290156 AATTTTATTC
*
55290166 TATTA-TATACTATTATTTAG
1 TATTATTATACTATTATATAG
* *
55290186 TTTTTTTATACTATTATCATA-
1 TATTATTATACTATTAT-ATAG
55290207 TATTATTAT
1 TATTATTAT
55290216 TTAAGTTTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 3 0.13
21 18 0.78
22 2 0.09
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTATTATACTATTATATAG
Found at i:55292205 original size:16 final size:16
Alignment explanation
Indices: 55292184--55292218 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
55292174 TTGTGTTTTG
*
55292184 TTTTGATTGCATGGCA
1 TTTTGACTGCATGGCA
55292200 TTTTGACTGCATGGCA
1 TTTTGACTGCATGGCA
55292216 TTT
1 TTT
55292219 CATTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (16 bp):
TTTTGACTGCATGGCA
Found at i:55296401 original size:5 final size:5
Alignment explanation
Indices: 55296391--55296426 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
55296381 TTTATTTCCA
55296391 TTATT TTATT TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT T
55296427 AGAATAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:55297193 original size:28 final size:27
Alignment explanation
Indices: 55297162--55297223 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
55297152 TGCATTGTTT
*
55297162 TTTTATGATACATATACATACGCATGGC
1 TTTTATAATACATATACATACGCAT-GC
* * * *
55297190 TTTTATAATATATATATATATGCATTC
1 TTTTATAATACATATACATACGCATGC
55297217 TTTTATA
1 TTTTATA
55297224 CAGTATACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (27 bp):
TTTTATAATACATATACATACGCATGC
Found at i:55300874 original size:36 final size:35
Alignment explanation
Indices: 55300803--55300874 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
55300793 CATTATAAAA
** *
55300803 TAAGACTAATAAAATAAAATACATACCAATTATAT
1 TAAGACTAATAAAATAAAATACATAAAAATAATAT
*
55300838 TAAGCCTATATAAAA-AAATATACATAAAAATAATAT
1 TAAGACTA-ATAAAATAAA-ATACATAAAAATAATAT
55300874 T
1 T
55300875 CGATAGATCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 10 0.32
36 21 0.68
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (35 bp):
TAAGACTAATAAAATAAAATACATAAAAATAATAT
Found at i:55300936 original size:24 final size:24
Alignment explanation
Indices: 55300894--55300979 Score: 67
Period size: 24 Copynumber: 3.7 Consensus size: 24
55300884 TAAGTAATGA
*
55300894 TATGATAAGTTTAAAATTAT-A-G
1 TATGATAAATTTAAAATTATGATG
* *
55300916 TACATGATAAATTTTACATTATGATG
1 T--ATGATAAATTTAAAATTATGATG
*
55300942 TATGATAAATTT-AAATAAT-AT-
1 TATGATAAATTTAAAATTATGATG
55300963 TAATGAT-AATTTAAAAT
1 T-ATGATAAATTTAAAAT
55300980 AATAGTATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
21 6 0.11
22 12 0.23
23 5 0.09
24 27 0.51
25 1 0.02
26 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (24 bp):
TATGATAAATTTAAAATTATGATG
Found at i:55300971 original size:22 final size:22
Alignment explanation
Indices: 55300943--55301023 Score: 101
Period size: 22 Copynumber: 3.6 Consensus size: 22
55300933 ATTATGATGT
*
55300943 ATGATAAATTTAAATAATATTA
1 ATGATAAATTTAAATAATACTA
*
55300965 ATGAT-AATTTAAAATAATAGTA
1 ATGATAAATTT-AAATAATACTA
* *
55300987 TATGATATATTAAAATAATACTA
1 -ATGATAAATTTAAATAATACTA
55301010 ATGATAAATTTAAA
1 ATGATAAATTTAAA
55301024 GCAAAGTTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.10
22 27 0.54
23 15 0.30
24 3 0.06
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.38
Consensus pattern (22 bp):
ATGATAAATTTAAATAATACTA
Found at i:55303073 original size:28 final size:28
Alignment explanation
Indices: 55303033--55303089 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
55303023 CAAATGAACT
55303033 AAATATCAACCTACATCATAAGGCACGA
1 AAATATCAACCTACATCATAAGGCACGA
55303061 AAATATCAACCTACATCATAAGGCACGA
1 AAATATCAACCTACATCATAAGGCACGA
55303089 A
1 A
55303090 GGCCAGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.25, G:0.11, T:0.18
Consensus pattern (28 bp):
AAATATCAACCTACATCATAAGGCACGA
Found at i:55304957 original size:3 final size:3
Alignment explanation
Indices: 55304951--55304986 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
55304941 TTTACACTAC
55304951 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55304987 AGCCATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:55305174 original size:16 final size:15
Alignment explanation
Indices: 55305144--55305177 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
55305134 TATACATTTT
*
55305144 TATATATTTTGTAAA
1 TATATATTATGTAAA
55305159 TATATATATATGTAAA
1 TATATAT-TATGTAAA
55305175 TAT
1 TAT
55305178 CTTAAAGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATATTATGTAAA
Found at i:55305476 original size:5 final size:5
Alignment explanation
Indices: 55305466--55305506 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
55305456 GTTGACTCGT
* * *
55305466 TTTTA TTTTA TGTTG CTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
55305507 CTTCTATTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:55305588 original size:24 final size:24
Alignment explanation
Indices: 55305544--55305591 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
55305534 CTCTTTAGCA
* *
55305544 TTTTAAAATATGTTTGTATTTTTT
1 TTTTAAAAAATGTTTGCATTTTTT
55305568 TTTTAAAAAAATGTTT-CATTTTTT
1 TTTT-AAAAAATGTTTGCATTTTTT
55305592 ATTGAAGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (24 bp):
TTTTAAAAAATGTTTGCATTTTTT
Found at i:55306911 original size:16 final size:16
Alignment explanation
Indices: 55306890--55306924 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
55306880 TTGTGTTTTG
55306890 TTTTGAATGCATGACA
1 TTTTGAATGCATGACA
*
55306906 TTTTGAATGCATGGCA
1 TTTTGAATGCATGACA
55306922 TTT
1 TTT
55306925 CATTATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (16 bp):
TTTTGAATGCATGACA
Found at i:55309683 original size:11 final size:11
Alignment explanation
Indices: 55309667--55309701 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
55309657 CAGTTCTTTC
55309667 AAAAAAATAAA
1 AAAAAAATAAA
*
55309678 AAAAAATTAAA
1 AAAAAAATAAA
*
55309689 AAATAAATAAA
1 AAAAAAATAAA
55309700 AA
1 AA
55309702 GAAAGGAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:55311758 original size:88 final size:88
Alignment explanation
Indices: 55311488--55312541 Score: 1242
Period size: 88 Copynumber: 12.0 Consensus size: 88
55311478 CCGAAGATAC
* *
55311488 CAGCCTTGTCTCCCTGGGCAGTAGTGGAGTAGGTTGAAAATAGCAGATATTGTCTTCCTGTATTG
1 CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
*
55311553 GCAGCGAAGTAGATCGAAGA-TAC
66 GCAGCGAAGTAGATCGAAGACT-T
* * * *
55311576 CAGCCTTGTCTCCTTGGGCAGTAGTGGAGTAGGCTGAAAATAG-AGATCTTGTTTTCCTGTATTG
1 CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
* *
55311640 GCAGCGAAGTAGATCGAATA-TCC
66 GCAGCGAAGTAGATCGAAGACT-T
* * *
55311663 CAACCTTGTCTCCCTGGGCAGTAGTGGAGTAGGTTGAAAATAGCATATCTTGTCTTCCTGTATTG
1 CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
*
55311728 GCATCGAAGTAGATCGAAGACTT
66 GCAGCGAAGTAGATCGAAGACTT
** * * *
55311751 CAGCCTTGTCTCTATGGGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTATATTA
1 CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
*
55311816 GCATCGAAGTAGATCGAAGACTT
66 GCAGCGAAGTAGATCGAAGACTT
** * * * *
55311839 CAGCCTTGTCTCTATGGGCAGTAGTGGAGTAGGTTGAAAATAACAGATCTTGTCTTCTTGTATTA
1 CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
* *
55311904 GCAGTGAAGTAGATCGAAGACCT
66 GCAGCGAAGTAGATCGAAGACTT
* *
55311927 CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGTAGATCTTGTCTTCCTGTATTA
1 CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
*
55311992 GCAGCGAAGTAGATCGAAGACCT
66 GCAGCGAAGTAGATCGAAGACTT
* * *
55312015 CAGCCTTGTCTCCCTGAGCAGCAATGGAGTAGGTTGAAAATAGCAGATCTTGGCTTCCTGTATTG
1 CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
* *
55312080 GCAGCGAAGTAGATCAAAGACCT
66 GCAGCGAAGTAGATCGAAGACTT
* * *
55312103 CAGCCTTGTCTCCCTAAGCAGTAGTGGAGTAGGTTAAAAATAGCATATCTTGTCTTCCTGTATTG
1 CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
* *
55312168 GCAGTGAAGTAGATCGAAGA-TAC
66 GCAGCGAAGTAGATCGAAGACT-T
* * * * * * ** *
55312191 CAGCCTTATCTCCCTAAGAAGCATTGGAGTAGGTTGAAGACGGCAGATCTTGTCTTCCTGTACTG
1 CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
*
55312256 GCAGAGAAGTAGATCGAAGGTAC--
66 GCAGCGAAGTAGATCGAA-G-ACTT
* * * * * * *
55312279 CAGCCTTATCTCCTTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATTTTGTCTTCCTGTACTG
1 CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
* **
55312344 GCAGAGAAGTAGATCGAAGACGC
66 GCAGCGAAGTAGATCGAAGACTT
* * * * * * * * *
55312367 CAGCCTTATCTCTCTGAGAAGCAGTAGAGTAGGTTGAAGATAGCAGATCTTATCTTCCTGCACTG
1 CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
* * *
55312432 GTAGTGAAGTAGATCGAAGAC-A
66 GCAGCGAAGTAGATCGAAGACTT
* * * * * ** *
55312454 CCGACCTTGCCTCCCTGGGTTTA-CAGCAGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTA
1 CAG-CCTTGTCTCCCTGAG--CAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTA
* *
55312518 CTGGCAGCGAAGCAGATCGAAGAC
63 TTGGCAGCGAAGTAGATCGAAGAC
55312542 ACCAGTCTTA
Statistics
Matches: 866, Mismatches: 89, Indels: 21
0.89 0.09 0.02
Matches are distributed among these distances:
86 2 0.00
87 83 0.10
88 720 0.83
89 59 0.07
90 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (88 bp):
CAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
GCAGCGAAGTAGATCGAAGACTT
Found at i:55311759 original size:44 final size:43
Alignment explanation
Indices: 55311711--55311849 Score: 106
Period size: 44 Copynumber: 3.2 Consensus size: 43
55311701 AATAGCATAT
55311711 CTTGTCTTCCTGTATTGGCATCGAAGTAGATCGAAGACTTCAGC
1 CTTGTCTTCCT-TATTGGCATCGAAGTAGATCGAAGACTTCAGC
* * * * * * * *
55311755 CTTGTC-T-C-TATGGGCAGTAGTGGAGTAGGTTGAA-AATAGCAGAT
1 CTTGTCTTCCTTATTGGCA-T--CGAAGTAGATCGAAGACT-TCAG-C
*
55311799 CTTGTCTTCCTATATTAGCATCGAAGTAGATCGAAGACTTCAGC
1 CTTGTCTTCCT-TATTGGCATCGAAGTAGATCGAAGACTTCAGC
55311843 CTTGTCT
1 CTTGTCT
55311850 CTATGGGCAG
Statistics
Matches: 68, Mismatches: 17, Indels: 20
0.65 0.16 0.19
Matches are distributed among these distances:
40 7 0.10
41 1 0.01
42 3 0.04
43 14 0.21
44 19 0.28
45 14 0.21
46 3 0.04
47 1 0.01
48 6 0.09
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
CTTGTCTTCCTTATTGGCATCGAAGTAGATCGAAGACTTCAGC
Found at i:55311891 original size:44 final size:44
Alignment explanation
Indices: 55311755--55311893 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 44
55311745 AGACTTCAGC
*
55311755 CTTGTCTCTATGGGCAGTAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTCTATGGGCAGTAGTGGAGTAGGTTGAAAATAACAGAT
*** * * * * * * *
55311799 CTTGTCTTCCTAT-ATTAGCA-TCGAAGTAGATCGAAGACT-TCAG-C
1 CTTGTC-T-CTATGGGCAGTAGT-GGAGTAGGTTGAA-AATAACAGAT
55311843 CTTGTCTCTATGGGCAGTAGTGGAGTAGGTTGAAAATAACAGAT
1 CTTGTCTCTATGGGCAGTAGTGGAGTAGGTTGAAAATAACAGAT
55311887 CTTGTCT
1 CTTGTCT
55311894 TCTTGTATTA
Statistics
Matches: 67, Mismatches: 20, Indels: 16
0.65 0.19 0.16
Matches are distributed among these distances:
42 6 0.09
43 17 0.25
44 21 0.31
45 17 0.25
46 6 0.09
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.32
Consensus pattern (44 bp):
CTTGTCTCTATGGGCAGTAGTGGAGTAGGTTGAAAATAACAGAT
Found at i:55311935 original size:44 final size:44
Alignment explanation
Indices: 55311887--55312113 Score: 145
Period size: 44 Copynumber: 5.2 Consensus size: 44
55311877 AATAACAGAT
*
55311887 CTTGTCTTCTTGTATTAGCAGTGAAGTAGATCGAAGACCTCAGC
1 CTTGTCTTCCTGTATTAGCAGTGAAGTAGATCGAAGACCTCAGC
* ** * * * * * ** *
55311931 CTTGTCTCCCTG-AGCAGTAGTGGAGTAGGTTGAAAATAGT-AGAT
1 CTTGTCTTCCTGTATTAGCAGTGAAGTAGATCGAAGA-CCTCAG-C
*
55311975 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAGACCTCAGC
1 CTTGTCTTCCTGTATTAGCAGTGAAGTAGATCGAAGACCTCAGC
* ** * * * * * *** *
55312019 CTTGTCTCCCTG-AGCAGCAATGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTTCCTGTATTAGCAGTGAAGTAGATCGAAGACCTCAG-C
* * * *
55312063 CTTGGCTTCCTGTATTGGCAGCGAAGTAGATCAAAGACCTCAGC
1 CTTGTCTTCCTGTATTAGCAGTGAAGTAGATCGAAGACCTCAGC
55312107 CTTGTCT
1 CTTGTCT
55312114 CCCTAAGCAG
Statistics
Matches: 123, Mismatches: 54, Indels: 12
0.65 0.29 0.06
Matches are distributed among these distances:
43 38 0.31
44 50 0.41
45 35 0.28
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29
Consensus pattern (44 bp):
CTTGTCTTCCTGTATTAGCAGTGAAGTAGATCGAAGACCTCAGC
Found at i:55313038 original size:127 final size:125
Alignment explanation
Indices: 55312839--55313151 Score: 401
Period size: 127 Copynumber: 2.5 Consensus size: 125
55312829 ATTGTAGTTA
* * * * *
55312839 AACAAATTGAAGTAAATAATCCTATCTCATTGAAGTTACAGTGGAGTGGATTAACATTAGATCTT
1 AACAGATTGAAG-AAATAATCCTATCTC-CTGAAGTTACAGTGGAGTGGATTAAAATCAGATCAT
** * *
55312904 ATCTCTCTGAAGTTGTAGAAGAGCAGATCGCATCAAATCTTATCTCCCTGAAGTTGCAGTGG
64 ATCTCTCTGAAGTTACAGAAGAGCAGATCGCATCAAATCTTATCCCCCTAAAGTTGCAGTGG
*
55312966 AACAGATTGAAGAAATCAATCCTATCTGCCTGAAGTTACAGTGGAGTGGATTAAAATCAGGTCAT
1 AACAGATTGAAGAAAT-AATCCTATCT-CCTGAAGTTACAGTGGAGTGGATTAAAATCAGATCAT
* *
55313031 ATCTCTCTGAAGTTACAGAAGAGCAGATCGCATCCAGTCTTATCCCCCTAAAGTTGCAGTGG
64 ATCTCTCTGAAGTTACAGAAGAGCAGATCGCATCAAATCTTATCCCCCTAAAGTTGCAGTGG
* ** * * * *
55313093 AGCAGACAGAAGAAAGTAATCTTATTTCCCTGAGGTTGCAGTGGAGTGGATTAAAATCA
1 AACAGATTGAAGAAA-TAATCCTATCT-CCTGAAGTTACAGTGGAGTGGATTAAAATCA
55313152 CAGATCTCAC
Statistics
Matches: 163, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
126 4 0.02
127 157 0.96
128 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (125 bp):
AACAGATTGAAGAAATAATCCTATCTCCTGAAGTTACAGTGGAGTGGATTAAAATCAGATCATAT
CTCTCTGAAGTTACAGAAGAGCAGATCGCATCAAATCTTATCCCCCTAAAGTTGCAGTGG
Found at i:55314433 original size:3 final size:3
Alignment explanation
Indices: 55314427--55314501 Score: 91
Period size: 3 Copynumber: 25.0 Consensus size: 3
55314417 TTTACACTAC
* *
55314427 TAT TAT TAT TAT TTT TAT TAT T-T TA- AAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
55314473 TAT TAT TAT TAT TAA TAT GGTAT TAT TAT
1 TAT TAT TAT TAT TAT TAT --TAT TAT TAT
55314502 AGCCATATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
2 3 0.05
3 56 0.90
5 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:55319037 original size:9 final size:9
Alignment explanation
Indices: 55319025--55319058 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
55319015 ATTTAAGCCG
55319025 TTTAAAATT
1 TTTAAAATT
*
55319034 TTTAAGATT
1 TTTAAAATT
55319043 TTTAAAA-T
1 TTTAAAATT
55319051 TTTAAAAT
1 TTTAAAAT
55319059 GATAAAGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
TTTAAAATT
Found at i:55323217 original size:112 final size:112
Alignment explanation
Indices: 55323063--55323287 Score: 398
Period size: 112 Copynumber: 2.0 Consensus size: 112
55323053 ACGTCCAAAG
* *
55323063 AAGCGAATTTTCAAAATTTCTCCTAAATTTTCTTCACATTACTCCACATAATCAATTAAGAAAAC
1 AAGCGAATTTTCAAAATTTCTCCTAAATTTTCTGCACATTACTCCACATAATCAATTAAAAAAAC
*
55323128 TTAAAAA-ATATATTTTATTAATTGCTATATATTCTTTTATTTTTAGA
66 TTAAAAATATATATTTTA-TAATTACTATATATTCTTTTATTTTTAGA
*
55323175 AAGCGAATTTTCAAAATTTCTCCTAAATTTTCTGCACATTACTCCACATAATCCATTAAAAAAAC
1 AAGCGAATTTTCAAAATTTCTCCTAAATTTTCTGCACATTACTCCACATAATCAATTAAAAAAAC
55323240 TTAAAAATATATATTTTATAATTACTATATATTCTTTTATTTTTAGA
66 TTAAAAATATATATTTTATAATTACTATATATTCTTTTATTTTTAGA
55323287 A
1 A
55323288 TAATAGTTTA
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
112 98 0.91
113 10 0.09
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.42
Consensus pattern (112 bp):
AAGCGAATTTTCAAAATTTCTCCTAAATTTTCTGCACATTACTCCACATAATCAATTAAAAAAAC
TTAAAAATATATATTTTATAATTACTATATATTCTTTTATTTTTAGA
Found at i:55336776 original size:16 final size:15
Alignment explanation
Indices: 55336732--55336777 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
55336722 TTATACCTTA
*
55336732 AAAAACAAAAAAAAAC
1 AAAAA-AAATAAAAAC
*
55336748 AAAAAATATAAAAAC
1 AAAAAAAATAAAAAC
55336763 AAAAAAAATGAAAAA
1 AAAAAAAAT-AAAAA
55336778 TCAAGATGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.85, C:0.07, G:0.02, T:0.07
Consensus pattern (15 bp):
AAAAAAAATAAAAAC
Found at i:55337856 original size:77 final size:77
Alignment explanation
Indices: 55337637--55338784 Score: 1243
Period size: 77 Copynumber: 15.0 Consensus size: 77
55337627 CAAGAATTAT
* * * * *
55337637 TTTTCAATTTCATTTTTTTTTC-AAAAATTAACTCATAATGCAAGAGGTGAGTTGAGCCTCAGG-
1 TTTTCAATTT--TTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGC
* *
55337700 TAGCACGCCGAGATA
64 CA-CACGCCGAGGTA
* * *
55337715 TTTTCAATTTTTGTTTTTTCAAAAAAATCAACTCATATTGCTAGATGTAAGTTGAGCCTTGGGCC
1 TTTTCAATTTTTGTTTTTTC-AAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCC
* *
55337780 GCACGCCGATGTA
65 ACACGCCGAGGTA
* * *
55337793 TTTTTAATTTTTATTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTAAGCCTCGGGCCA
1 TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCCA
55337858 CACGCCGAGGTA
66 CACGCCGAGGTA
**** ** * * *
55337870 TTTTCAATTTTTGTTTTTTTTTTAAATCAACTCATAACGCAAGAGGTGAGTTGAGCCTCGAGCCG
1 TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCCA
* *
55337935 TACGCCGAGATA
66 CACGCCGAGGTA
* * * *
55337947 TTTTCAATTTTCGTTTTTTTAAAAAATCAACTCATATTGCTAGATGTGAGTTGAACCTCGGGCCA
1 TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCCA
*
55338012 CACGTCGAGGTA
66 CACGCCGAGGTA
* *
55338024 TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGCCG
1 TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCCA
55338089 CACGCCGAGGTA
66 CACGCCGAGGTA
* * * * *
55338101 TTTTTAA---TT-TTTTTTAAAAAAATCAGCTTATATTGCTAGAGGTGAGTTGAGCCTCGGGCCG
1 TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCCA
*
55338162 CACACCGAGGTA
66 CACGCCGAGGTA
* * *
55338174 TTTCCAATTTTT-TGTTTTC-AAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCCG
1 TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCCA
* * *
55338237 CATGCCTAGGTG
66 CACGCCGAGGTA
* * * *
55338249 TTTTCAATTTTCT-TTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCTTCGGGTC
1 TTTTCAATTTT-TGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCC
55338313 ACACGCCGAGGTA
65 ACACGCCGAGGTA
* * *
55338326 TTTTTCAATTTATG-TTTTTCAAAAAATCAACTCATATTG-TAGAGGTGAGTTGAGCATCGGGTC
1 -TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCC
* *
55338389 ACATGTCGAGGTA
65 ACACGCCGAGGTA
** * * * *
55338402 -CATCTAAGTTTTGTTTTTTTCCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGC
1 TTTTC-AATTTTTG-TTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGC
* * *
55338466 TACACGGCGAGGCA
64 CACACGCCGAGGTA
* * * * ** *
55338480 TTTTCAATTTCTATTTTTTCAAAAAATCAACACATAATGCGGGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCCA
* *
55338545 TATGCCGAGGTA
66 CACGCCGAGGTA
* * * *
55338557 CTTTT-AATTTCTATTTTTTTTC-AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGG
1 -TTTTCAATTT-T-TGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGG
**
55338620 CTGCACGCCGAGGTA
63 CCACACGCCGAGGTA
* * * * *
55338635 TTTTCAATTTCTGTTTTTTCAAAAAATCAACACATAATG-TGAGAGGTGAGTTGAGCCTCAGGTC
1 TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCT-AGAGGTGAGTTGAGCCTCGGGCC
*
55338699 ACAAGCCGAGGTA
65 ACACGCCGAGGTA
* * * *
55338712 CTTTT-AATTTCTGTTTTTTC-AAAAATCAACTCATAATG-TGAGAAGTGAGTTGAGCCTCGGGT
1 -TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCT-AGAGGTGAGTTGAGCCTCGGGC
*
55338774 CACATGCCGAG
64 CACACGCCGAG
55338785 CGATTTTTTA
Statistics
Matches: 912, Mismatches: 136, Indels: 46
0.83 0.12 0.04
Matches are distributed among these distances:
73 64 0.07
74 4 0.00
75 66 0.07
76 112 0.12
77 478 0.52
78 178 0.20
79 10 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (77 bp):
TTTTCAATTTTTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCCA
CACGCCGAGGTA
Found at i:55339099 original size:30 final size:30
Alignment explanation
Indices: 55338979--55339115 Score: 190
Period size: 29 Copynumber: 4.7 Consensus size: 30
55338969 TAAAAAAATT
* ** *
55338979 TAAAAGTACATTTCAACCCCTAAACCTTT-
1 TAAAATTACATTTTGACCCCTAAACTTTTC
55339008 TAAAATTACATTTTGACCCCTAAACTTTTC
1 TAAAATTACATTTTGACCCCTAAACTTTTC
*
55339038 -AAAATTACATTTTGACCCCT-AACTTTCC
1 TAAAATTACATTTTGACCCCTAAACTTTTC
* *
55339066 TAAAATTATATTTTGATCCCTAAACTTTTC
1 TAAAATTACATTTTGACCCCTAAACTTTTC
55339096 TAAAATTACATTTTGACCCC
1 TAAAATTACATTTTGACCCC
55339116 AGAAGTTTTA
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
28 7 0.07
29 63 0.66
30 25 0.26
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (30 bp):
TAAAATTACATTTTGACCCCTAAACTTTTC
Found at i:55340651 original size:7 final size:7
Alignment explanation
Indices: 55340639--55340664 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55340629 TTTAATTCAA
55340639 AAATAAT
1 AAATAAT
55340646 AAATAAT
1 AAATAAT
55340653 AAATAAT
1 AAATAAT
55340660 AAATA
1 AAATA
55340665 TATTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATAAT
Found at i:55342732 original size:22 final size:21
Alignment explanation
Indices: 55342690--55342735 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
55342680 AGCACGAAAA
*
55342690 TTTTTTTAAAAAAATGAAATT
1 TTTTTTTAAAAAAACGAAATT
* *
55342711 TTTTTTTTAAAACACGAGAATT
1 TTTTTTTAAAAAAACGA-AATT
55342733 TTT
1 TTT
55342736 AAACACGGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTTTTTAAAAAAACGAAATT
Found at i:55342887 original size:96 final size:96
Alignment explanation
Indices: 55342752--55343025 Score: 258
Period size: 96 Copynumber: 2.8 Consensus size: 96
55342742 GGAAATTTCA
* * * * *
55342752 AAAACACGAAAATTTTTAAAACACGACATTTTTTGAAACACGAGAATTTTTAAA-AC-AAGACAT
1 AAAACACGAAAATTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTGAAACACGAA-A-AT
55342815 TTTTT-GAAACACAATTTTTTTCTTAAAAAATTT
64 TTTTTAGAAA-ACAATTTTTTTCTTAAAAAATTT
* *
55342848 AAAATACGAGAATTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTGAAACACGAAAATTT
1 AAAACACGAAAATTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTGAAACACGAAAATTT
*
55342913 TTTAGAAAACGA--TTTTT-TTAAAATCACCGGAGTTTTT
66 TTTAGAAAACAATTTTTTTCTTAAAA--A----A---TTT
* *
55342950 GAAAACACGAAAATCTTTAAAACACCG-AAATTTTTGAAAACACGAAGATTTTTGAAACACGAAA
1 -AAAACACGAAAATTTTTAAAACA-CGAAAATTTTT-AAAACACGAA-AATTTTGAAACACGAAA
55343014 ATTTTTT-GAAAA
62 ATTTTTTAGAAAA
55343026 TACGAAGATT
Statistics
Matches: 150, Mismatches: 12, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
93 6 0.04
94 5 0.03
95 1 0.01
96 57 0.38
97 7 0.05
98 2 0.01
99 1 0.01
102 3 0.02
103 28 0.19
104 17 0.11
105 23 0.15
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (96 bp):
AAAACACGAAAATTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTGAAACACGAAAATTT
TTTAGAAAACAATTTTTTTCTTAAAAAATTT
Found at i:55342976 original size:35 final size:35
Alignment explanation
Indices: 55342848--55343064 Score: 144
Period size: 35 Copynumber: 6.2 Consensus size: 35
55342838 TAAAAAATTT
* * *
55342848 AAAATACGAGAATTTTTAAAACA-CGAAAATTTTT-
1 AAAACACGAAAATCTTTAAAACACCG-AAATTTTTG
* *
55342882 AAAACACGAAAAT-TTTGAAACA-CGAAAATTTTTT
1 AAAACACGAAAATCTTTAAAACACCG-AAATTTTTG
** * * *
55342916 AGAAA-ACG-ATTTTTTTAAAATCACCGGAGTTTTTG
1 A-AAACACGAAAATCTTTAAAA-CACCGAAATTTTTG
55342951 AAAACACGAAAATCTTTAAAACACCGAAATTTTTG
1 AAAACACGAAAATCTTTAAAACACCGAAATTTTTG
* * *
55342986 AAAACACGAAGATTTTTGAAACA-CGAAAATTTTTTG
1 AAAACACGAAAATCTTTAAAACACCG-AAA-TTTTTG
* * * ** *
55343022 AAAATACGAAGATTTTTTTTAACACGGAAATTTTTG
1 AAAACACGAA-AATCTTTAAAACACCGAAATTTTTG
55343058 -AAACACG
1 AAAACACG
55343065 GTCATTTTTT
Statistics
Matches: 148, Mismatches: 24, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
33 21 0.14
34 26 0.18
35 56 0.38
36 32 0.22
37 12 0.08
38 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (35 bp):
AAAACACGAAAATCTTTAAAACACCGAAATTTTTG
Found at i:55342989 original size:18 final size:17
Alignment explanation
Indices: 55342713--55343229 Score: 233
Period size: 17 Copynumber: 29.9 Consensus size: 17
55342703 ATGAAATTTT
*
55342713 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGA-AA
55342731 TTTTT--AAACACGGAAA
1 TTTTTGAAAACAC-GAAA
**
55342747 -TTTCAAAAACACGAAAA
1 TTTTTGAAAACACG-AAA
*
55342764 TTTTT-AAAACACGACAT
1 TTTTTGAAAACACGA-AA
55342781 TTTTTG-AAACACGAGAA
1 TTTTTGAAAACACGA-AA
* *
55342798 TTTTT-AAAACAAGACAT
1 TTTTTGAAAACACGA-AA
*
55342815 TTTTTG-AAACAC-AATT
1 TTTTTGAAAACACGAA-A
***
55342831 TTTTTCTTAA-A--AAA
1 TTTTTGAAAACACGAAA
*
55342845 --TTT-AAAATACGAGAA
1 TTTTTGAAAACACGA-AA
55342860 TTTTT-AAAACACGAAAA
1 TTTTTGAAAACACG-AAA
55342877 TTTTT-AAAACACGAAA
1 TTTTTGAAAACACGAAA
*
55342893 ATTTTG-AAACACGAAAA
1 TTTTTGAAAACACG-AAA
* *
55342910 TTTTTTAGAAA-ACG-AT
1 TTTTTGA-AAACACGAAA
* * *
55342926 TTTTTTAAAATCACCGGAG
1 TTTTTGAAAA-CA-CGAAA
55342945 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACG-AAA
*
55342963 TCTTT-AAAACACCGAAA
1 TTTTTGAAAACA-CGAAA
55342980 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAA-A
55342998 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACG-AAA
*
55343015 TTTTTTGAAAATACGAAGA
1 -TTTTTGAAAACACGAA-A
***
55343034 TTTTTTTTAACACGGAAA
1 TTTTTGAAAACAC-GAAA
**
55343052 TTTTTG-AAACACGGTCATTT
1 TTTTTGAAAACAC-G--A-AA
55343072 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACG-AAA
* **
55343090 TTTTTGAAAGACATGATT
1 TTTTTGAAA-ACACGAAA
*
55343108 TTTTTGAAAATACGGAAA
1 TTTTTGAAAACAC-GAAA
*
55343126 TTTAT-AAAACACGAAAA
1 TTTTTGAAAACACG-AAA
*
55343143 TTTTTTCTGAAAACAAGAAAA
1 --TTTT-TGAAAACACG-AAA
*
55343164 TTTTTG-AAACACTAGAA
1 TTTTTGAAAACACGA-AA
55343181 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAA-A
*
55343198 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGA-AA
55343215 TTTTT-AAAAGCACGA
1 TTTTTGAAAA-CACGA
55343230 GGATTATTGA
Statistics
Matches: 393, Mismatches: 53, Indels: 106
0.71 0.10 0.19
Matches are distributed among these distances:
11 2 0.01
12 4 0.01
14 1 0.00
15 11 0.03
16 48 0.12
17 168 0.43
18 98 0.25
19 36 0.09
20 8 0.02
21 17 0.04
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (17 bp):
TTTTTGAAAACACGAAA
Found at i:55343072 original size:54 final size:55
Alignment explanation
Indices: 55342860--55343094 Score: 167
Period size: 54 Copynumber: 4.4 Consensus size: 55
55342850 AATACGAGAA
** *
55342860 TTTTT-AAAACACGAAAA-TTTTTAAAACACGAA-AATTTTGAAACACGAAAATT
1 TTTTTGAAAACACGAAAATTTTTTTTAACACGAAGATTTTTGAAACACGAAAATT
* * *
55342912 TTTTAG-AAA-ACG---ATTTTTTTAAAATCACCGGAG-TTTTTGAAAACACGAAAA--
1 TTTTTGAAAACACGAAAATTTTTTT-TAA-CA-CGAAGATTTTTG-AAACACGAAAATT
* ***
55342963 TCTTT-AAAACACCG-AAATTTTTGAAAACACGAAGATTTTTGAAACACGAAAA-T
1 TTTTTGAAAACA-CGAAAATTTTTTTTAACACGAAGATTTTTGAAACACGAAAATT
* * ** *
55343016 TTTTTGAAAATACGAAGATTTTTTTTAACACGGAA-ATTTTTGAAACACGGTCATTT
1 TTTTTGAAAACACGAAAATTTTTTTTAACAC-GAAGATTTTTGAAACAC-GAAAATT
55343072 TTTTTGAAAACACGAAAATTTTT
1 TTTTTGAAAACACGAAAATTTTT
55343095 GAAAGACATG
Statistics
Matches: 144, Mismatches: 20, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
48 1 0.01
49 5 0.03
50 3 0.02
51 11 0.08
52 31 0.22
53 27 0.19
54 33 0.23
55 11 0.08
56 22 0.15
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (55 bp):
TTTTTGAAAACACGAAAATTTTTTTTAACACGAAGATTTTTGAAACACGAAAATT
Found at i:55343098 original size:74 final size:74
Alignment explanation
Indices: 55342965--55343172 Score: 212
Period size: 74 Copynumber: 2.8 Consensus size: 74
55342955 CACGAAAATC
* * *
55342965 TTTAAAACACCGAAATTTTTGAAAACACGAAGA---TTTTTG-AAACACGAAAATTTTTTGAAAA
1 TTTAAAACACGGAAATTTAT-AAAACACGAAAATTTTTTTTGAAAACACGAAAA-TTTTTGAAAA
*
55343026 TACGAAGATTTT
64 GAC-AAGATTTT
* * * ***
55343038 TTT-TAACACGGAAATTTTTGAAACACGGTCATTTTTTTTGAAAACACGAAAATTTTTG-AAAGA
1 TTTAAAACACGGAAATTTATAAAACACGAAAATTTTTTTTGAAAACACGAAAATTTTTGAAAAGA
*
55343101 CATGATTTT
66 CAAGATTTT
* * *
55343110 TTTGAAAATACGGAAATTTATAAAACACGAAAATTTTTTCTGAAAACAAGAAAATTTTTGAAA
1 TTT-AAAACACGGAAATTTATAAAACACGAAAATTTTTTTTGAAAACACGAAAATTTTTGAAA
55343173 CACTAGAATT
Statistics
Matches: 111, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
71 8 0.07
72 24 0.22
73 8 0.07
74 58 0.52
75 13 0.12
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (74 bp):
TTTAAAACACGGAAATTTATAAAACACGAAAATTTTTTTTGAAAACACGAAAATTTTTGAAAAGA
CAAGATTTT
Found at i:55343186 original size:16 final size:16
Alignment explanation
Indices: 55343165--55343218 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
55343155 ACAAGAAAAT
55343165 TTTTGAAACACTAGAA
1 TTTTGAAACACTAGAA
* *
55343181 TTTTGAAAACACGAAGAT
1 TTTTG-AAACAC-TAGAA
55343199 TTTTGAAACA-TGAGAA
1 TTTTGAAACACT-AGAA
55343215 TTTT
1 TTTT
55343219 TAAAAGCACG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 12 0.39
17 11 0.35
18 8 0.26
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (16 bp):
TTTTGAAACACTAGAA
Found at i:55343415 original size:17 final size:16
Alignment explanation
Indices: 55343381--55343431 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
55343371 AAAATTATTT
55343381 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
* *
55343397 AAAATCAAATTAAATTA
1 AAAAT-AAAATAAAATA
55343414 AAAATATAAATATAAATA
1 AAAATA-AAATA-AAATA
55343432 TGCATAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.21
17 18 0.64
18 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:55343575 original size:10 final size:9
Alignment explanation
Indices: 55343560--55343618 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
55343550 ATTGAACCTC
55343560 TTTTTTCTT
1 TTTTTTCTT
55343569 GTTTTTTC-T
1 -TTTTTTCTT
55343578 TTTTTTC-T
1 TTTTTTCTT
*
55343586 TTTTCTC-T
1 TTTTTTCTT
*
55343594 CTTTTTCTT
1 TTTTTTCTT
55343603 TTTTTCTCTT
1 TTTTT-TCTT
55343613 TTTTTT
1 TTTTTT
55343619 TTGCTGGGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
8 20 0.47
9 7 0.16
10 16 0.37
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:55343583 original size:18 final size:17
Alignment explanation
Indices: 55343560--55343617 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
55343550 ATTGAACCTC
55343560 TTTTTTCTTGTTTTTTCT
1 TTTTTTCTT-TTTTTTCT
*
55343578 TTTTTTC-TTTTTCTCT
1 TTTTTTCTTTTTTTTCT
*
55343594 CTTTTTCTTTTTTTCTCT
1 TTTTTTCTTTTTTT-TCT
55343612 TTTTTT
1 TTTTTT
55343618 TTTGCTGGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
16 13 0.38
17 6 0.18
18 15 0.44
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTTTCTTTTTTTTCT
Found at i:55343589 original size:16 final size:16
Alignment explanation
Indices: 55343560--55343620 Score: 70
Period size: 16 Copynumber: 3.7 Consensus size: 16
55343550 ATTGAACCTC
55343560 TTTTTTCTTGTTTTTTCT
1 TTTTTTC-T-TTTTTTCT
*
55343578 TTTTTTCTTTTTCTCT
1 TTTTTTCTTTTTTTCT
*
55343594 CTTTTTCTTTTTTTCT
1 TTTTTTCTTTTTTTCT
55343610 CTTTTTT-TTTT
1 -TTTTTTCTTTT
55343621 GCTGGGCTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
16 25 0.66
17 6 0.16
18 7 0.18
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.84
Consensus pattern (16 bp):
TTTTTTCTTTTTTTCT
Found at i:55343766 original size:23 final size:23
Alignment explanation
Indices: 55343738--55343782 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
55343728 TGCATTTGGG
55343738 CTGCTTCTTTCTTCTTCTTTTTT
1 CTGCTTCTTTCTTCTTCTTTTTT
55343761 CTGCTTCTTTCTTCTTCTTTTT
1 CTGCTTCTTTCTTCTTCTTTTT
55343783 GCTACTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.04, T:0.69
Consensus pattern (23 bp):
CTGCTTCTTTCTTCTTCTTTTTT
Found at i:55343774 original size:20 final size:20
Alignment explanation
Indices: 55343739--55343790 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 20
55343729 GCATTTGGGC
*
55343739 TGCTTCTTTCTTCTTCTTTTTT
1 TGCTACTTTCTTCTTC--TTTT
*
55343761 CTGCTTCTTTCTTCTTCTTTT
1 -TGCTACTTTCTTCTTCTTTT
55343782 TGCTACTTT
1 TGCTACTTT
55343791 TTTTTGCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 8 0.29
21 4 0.14
23 16 0.57
ACGTcount: A:0.02, C:0.25, G:0.06, T:0.67
Consensus pattern (20 bp):
TGCTACTTTCTTCTTCTTTT
Found at i:55343928 original size:17 final size:18
Alignment explanation
Indices: 55343908--55343978 Score: 60
Period size: 17 Copynumber: 4.0 Consensus size: 18
55343898 TTTTTTATTA
55343908 TTTCTTTTCTTT-TTCTT
1 TTTCTTTTCTTTCTTCTT
55343925 TTTC-TTTCTTTCTTCTT
1 TTTCTTTTCTTTCTTCTT
**
55343942 CCTCTTTTC-TTCTTCCTT
1 TTTCTTTTCTTTCTT-CTT
*
55343960 CTTCTTCCTTC-TTCTTCTT
1 TTTCTT--TTCTTTCTTCTT
55343979 CAAAGTCTAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
16 7 0.15
17 16 0.35
18 12 0.26
19 3 0.07
20 8 0.17
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTCTTTTCTTTCTTCTT
Found at i:55343942 original size:3 final size:3
Alignment explanation
Indices: 55343909--55343979 Score: 65
Period size: 3 Copynumber: 23.0 Consensus size: 3
55343899 TTTTTATTAT
* * *
55343909 TTC TT- TTC TTT TTC TTT TTC TTTC TTTC TTC TTC CTC TT- TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC TTC TTC TTC
55343954 TTCC TTC TTC TTCC TTC TTC TTC TTC
1 TT-C TTC TTC TT-C TTC TTC TTC TTC
55343980 AAAGTCTAGC
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 4 0.07
3 40 0.70
4 13 0.23
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:55343949 original size:28 final size:28
Alignment explanation
Indices: 55343918--55343975 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
55343908 TTTCTTTTCT
* *
55343918 TTTTCTTTTTCTTTCTTTCTT-CTTCCTC
1 TTTTCTTCTTCCTTC-TTCTTCCTTCCTC
*
55343946 TTTTCTTCTTCCTTCTTCTTCCTTCTTC
1 TTTTCTTCTTCCTTCTTCTTCCTTCCTC
55343974 TT
1 TT
55343976 CTTCAAAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTTCTTCTTCCTTCTTCTTCCTTCCTC
Found at i:55343963 original size:10 final size:10
Alignment explanation
Indices: 55343948--55343976 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
55343938 TCTTCCTCTT
55343948 TTCTTCTTCC
1 TTCTTCTTCC
55343958 TTCTTCTTCC
1 TTCTTCTTCC
55343968 TTCTTCTTC
1 TTCTTCTTC
55343977 TTCAAAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:55343972 original size:34 final size:34
Alignment explanation
Indices: 55343910--55343976 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
55343900 TTTTATTATT
* * *
55343910 TCTTTTCTTTTTCTTTTTCTTTCTTTCTTCTTCC
1 TCTTTTCTTTTCCTTCTTCTTTCCTTCTTCTTCC
55343944 TCTTTTCTTCTTCCTTCTTC-TTCCTTCTTCTTC
1 TCTTTTCTT-TTCCTTCTTCTTTCCTTCTTCTTC
55343977 TTCAAAGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (34 bp):
TCTTTTCTTTTCCTTCTTCTTTCCTTCTTCTTCC
Found at i:55344070 original size:10 final size:10
Alignment explanation
Indices: 55344035--55344084 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
55344025 ACGCCGGTAC
55344035 TCTT-TCTTT
1 TCTTCTCTTT
* *
55344044 TCTTCTCCTC
1 TCTTCTCTTT
55344054 T-TTCTCTTT
1 TCTTCTCTTT
55344063 TCTTCTCTTT
1 TCTTCTCTTT
*
55344073 TCTTCTTTTT
1 TCTTCTCTTT
55344083 TC
1 TC
55344085 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:55344082 original size:19 final size:19
Alignment explanation
Indices: 55344039--55344081 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
55344029 CGGTACTCTT
55344039 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
55344058 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
55344075 TTCTTTT
1 -TCTTTT
55344082 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:55344365 original size:29 final size:29
Alignment explanation
Indices: 55344332--55344448 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
55344322 TGTAATTTTT
*
55344332 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
55344361 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
55344391 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
55344420 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
55344449 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:55344387 original size:30 final size:30
Alignment explanation
Indices: 55344347--55344448 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
55344337 ATTTAGGATT
*
55344347 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
55344377 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
55344407 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
55344437 AAAATGCAATTT
1 AAAATGAAATTT
55344449 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:55344906 original size:54 final size:54
Alignment explanation
Indices: 55344720--55345461 Score: 1182
Period size: 54 Copynumber: 14.0 Consensus size: 54
55344710 CACGTGAGCC
* *
55344720 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT--AA
*
55344775 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A--AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTAA
* *
55344826 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
55344880 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
55344934 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
55344988 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
55345042 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG------A-AAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
55345089 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAG-AA--AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
55345140 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTG-AAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
55345193 AAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
55345247 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATCAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
55345301 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAG--A--AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
* *
55345351 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
*
55345405 AAGTCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-AA
55345460 AA
1 AA
55345462 TACCTCAACG
Statistics
Matches: 647, Mismatches: 18, Indels: 44
0.91 0.03 0.06
Matches are distributed among these distances:
47 46 0.07
48 1 0.00
50 68 0.11
51 76 0.12
52 3 0.00
53 42 0.06
54 363 0.56
55 36 0.06
56 6 0.01
57 6 0.01
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (54 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
Found at i:55345247 original size:313 final size:312
Alignment explanation
Indices: 55344720--55345454 Score: 1226
Period size: 313 Copynumber: 2.3 Consensus size: 312
55344710 CACGTGAGCC
*
55344720 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AACA-AA-TT--AAAAGGCTCAAC
55344785 TCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG-AAAAAGGCTCAACTCACCTCTCGCAA
60 TCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAAAAAGGCTCAACTCACCTCTCGCAA
*
55344849 TATGAGTTGGTTTTTGAAAAATAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGGT
124 TATGAGTTGGTTTTTGAAAAATAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
55344914 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
189 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
55344979 AGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAA
254 AGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAG--A--AA
55345042 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-A-AAATTAAAAGGCTCAACTCACCT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAACAAATTAAAAGGCTCAACTCACCT
55345105 CTCGCAATATGAGTTGATTTTTGAAAAATAGAAAAAAGGCTCAACTCACCTCTCGCAATATGAGT
66 CTCGCAATATGAGTTGATTTTTGAAAAATAGAAAAAAGGCTCAACTCACCTCTCGCAATATGAGT
*
55345170 TGGTTTTTG-AAAATAGAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
131 TGGTTTTTGAAAAATAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
*
55345234 AAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATCAGAAATT
196 AAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
55345299 AAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
261 AAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
* * *
55345351 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATTAAAAGTCTCAACT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG----A-ACAAATTAAAAGGCTCAACT
*
55345416 CACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
61 CACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAA
55345455 TTGAAAATAC
Statistics
Matches: 398, Mismatches: 7, Indels: 22
0.93 0.02 0.05
Matches are distributed among these distances:
309 40 0.10
311 1 0.00
313 180 0.45
314 77 0.19
315 1 0.00
316 57 0.14
317 2 0.01
318 1 0.00
319 1 0.00
322 38 0.10
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (312 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAACAAATTAAAAGGCTCAACTCACCT
CTCGCAATATGAGTTGATTTTTGAAAAATAGAAAAAAGGCTCAACTCACCTCTCGCAATATGAGT
TGGTTTTTGAAAAATAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
AAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
AAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
Found at i:55345639 original size:72 final size:72
Alignment explanation
Indices: 55345409--55346026 Score: 1022
Period size: 72 Copynumber: 8.5 Consensus size: 72
55345399 AATTAAAAGT
** * *
55345409 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAACGTG
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAATTACCTCAACGTG
55345474 TCTTGAGG
65 TCTTGAGG
*
55345482 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCAACGTG
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTCAACGTG
55345547 TCTTGAGG
65 TCTTGAGG
55345555 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
55345620 CTTGAGG
66 CTTGAGG
*
55345627 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACA-AAATTGAAATTACCTCAACTTGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
55345691 CTTGAGG
66 CTTGAGG
* *
55345698 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCATGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
*
55345763 CCTGAGG
66 CTTGAGG
* *
55345770 CTCAACTCATTTCTCGTAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
55345835 CTTGAGG
66 CTTGAGG
*
55345842 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
55345907 CTTGAGG
66 CTTGAGG
* *
55345914 CTCAACTTATTTCTCGCAATATGAGTTGAATTTTGAGAAGCAGAAATTGAAAATTACCTCAACGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGA-AAACAGAAATTG-AAATTACCTCAACGT
*
55345979 GCCTTGAGG
64 GTCTTGAGG
** * *
55345988 CTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAA
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA
55346027 GCATAGATTG
Statistics
Matches: 517, Mismatches: 24, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
71 70 0.14
72 277 0.54
73 116 0.22
74 54 0.10
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (72 bp):
CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
CTTGAGG
Found at i:55345889 original size:216 final size:216
Alignment explanation
Indices: 55345409--55346026 Score: 1015
Period size: 215 Copynumber: 2.8 Consensus size: 216
55345399 AATTAAAAGT
** * * *
55345409 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAACGTG
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAAAAATTGAAATTACCTCAACGTG
*
55345474 TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACC
65 TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACC
* *
55345539 TCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGA
129 TCAACGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGA
55345604 AATTACCTCAACGTGTCTTGAGG
194 AATTACCTCAACGTGTCTTGAGG
*
55345627 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAC-AAAATTGAAATTACCTCAACTTGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGT
55345691 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTC
66 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTC
* * *
55345756 AGCATGTCCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGAATTTTGAAAACAAAAATTGAAA
131 AACGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAA
55345821 TTACCTCAACGTGTCTTGAGG
196 TTACCTCAACGTGTCTTGAGG
55345842 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGT
* *
55345907 CTTGAGGCTCAACTTATTTCTCGCAATATGAGTTGAATTTTGAGAAGCAGAAATTGAAAATTACC
66 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGA-AAACAGAAATTG-AAATTACC
** * *
55345972 TCAACGTG-CCTTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAA
129 TCAACGTGTCC-TGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA
55346027 GCATAGATTG
Statistics
Matches: 374, Mismatches: 22, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
215 139 0.37
216 132 0.35
217 18 0.05
218 85 0.23
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (216 bp):
CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGT
CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTC
AACGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAA
TTACCTCAACGTGTCTTGAGG
Found at i:55345899 original size:144 final size:144
Alignment explanation
Indices: 55345409--55346026 Score: 1013
Period size: 143 Copynumber: 4.3 Consensus size: 144
55345399 AATTAAAAGT
** * *
55345409 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAACGTG
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAATTACCTCAACGTG
* *
55345474 TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACC
65 TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAAAAATTGAAATTACC
55345539 TCAACGTGTCTTGAGG
129 TCAACGTGTCTTGAGG
55345555 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
55345620 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAC-AAAATTGAAATTACCTC
66 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTC
*
55345684 AACTTGTCTTGAGG
131 AACGTGTCTTGAGG
* *
55345698 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCATGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
* *
55345763 CCTGAGGCTCAACTCATTTCTCGTAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTC
66 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTC
55345828 AACGTGTCTTGAGG
131 AACGTGTCTTGAGG
*
55345842 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAACGTGT
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
* * *
55345907 CTTGAGGCTCAACTTATTTCTCGCAATATGAGTTGAATTTTGAGAAGCAGAAATTGAAAATTACC
66 CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGA-AAACAAAAATTG-AAATTACC
*
55345972 TCAACGTGCCTTGAGG
129 TCAACGTGTCTTGAGG
** * *
55345988 CTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAA
1 CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA
55346027 GCATAGATTG
Statistics
Matches: 444, Mismatches: 25, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
143 136 0.31
144 133 0.30
145 85 0.19
146 90 0.20
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (144 bp):
CTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTGT
CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTC
AACGTGTCTTGAGG
Found at i:55346057 original size:16 final size:17
Alignment explanation
Indices: 55346023--55346057 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
55346013 TTGATTTTTG
* *
55346023 AAAAGCATAGATTGAAA
1 AAAAACATAAATTGAAA
55346040 AAAAACATAAATTGAAA
1 AAAAACATAAATTGAAA
55346057 A
1 A
55346058 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (17 bp):
AAAAACATAAATTGAAA
Found at i:55346275 original size:123 final size:116
Alignment explanation
Indices: 55346041--55346353 Score: 464
Period size: 123 Copynumber: 2.6 Consensus size: 116
55346031 AGATTGAAAA
* * * * * *
55346041 AAAACATAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGT
1 AAAACATAAACTAAAAATACCTCGGC--GTG-CCCGAGGCTCAACTCACTTCTCGCAATATGAGT
55346106 TGATTTTTGAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
63 TGATTTTTGAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
*
55346160 AAAACATAAACTAAAAATACCTCGGCGTGCCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACATAAACTAAAAATACCTCGGCGTGCCC-GAGGCTCAACTCACTTCTCGCAATATGAGTTG
55346225 ATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
65 ATTTTTG------AAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
55346283 AAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
1 AAAACATAAACTAAAAATACCTCGGCGTG-CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
55346348 ATTTTT
65 ATTTTT
55346354 TTTAAAAAAA
Statistics
Matches: 178, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
116 2 0.01
117 39 0.22
119 23 0.13
123 111 0.62
124 3 0.02
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (116 bp):
AAAACATAAACTAAAAATACCTCGGCGTGCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA
TTTTTGAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
Found at i:55354784 original size:18 final size:17
Alignment explanation
Indices: 55354603--55355111 Score: 287
Period size: 17 Copynumber: 29.8 Consensus size: 17
55354593 GAAAGTTTTT
*
55354603 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAAAA
*
55354620 TTTTT-AAACACGGAAA
1 TTTTTAAAACACGAAAA
**
55354636 TTTCAAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *
55354653 TTTTTAAAACACGACAT
1 TTTTTAAAACACGAAAA
* *
55354670 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAAAA
* *
55354687 TTTTTAAAACAAG-ACA
1 TTTTTAAAACACGAAAA
*
55354703 TTTTTGAAACAC---AA
1 TTTTTAAAACACGAAAA
* **
55354717 TTTTT---TC-TTAAAA
1 TTTTTAAAACACGAAAA
* * *
55354730 -ATTTAAAATACGAGAA
1 TTTTTAAAACACGAAAA
55354746 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
55354763 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *
55354780 TTTTTGAAACACGGAAA
1 TTTTTAAAACACGAAAA
*
55354797 TTTTTAGAAA-ACG--AT
1 TTTTTA-AAACACGAAAA
* *
55354812 TTTTTAAAATCACCG-GAG
1 TTTTTAAAA-CA-CGAAAA
55354830 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
*
55354848 TCTTTAAAACACCG-AAA
1 TTTTTAAAACA-CGAAAA
*
55354865 TTTTTGAAAACACGAAGA
1 TTTTT-AAAACACGAAAA
*
55354883 -TTTTGAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *
55354899 TTTTTTGAAAATACGAAGA
1 -TTTTT-AAAACACGAAAA
** *
55354918 TTTTTTTAACACGGAAA
1 TTTTTAAAACACGAAAA
* * **
55354935 TTTTTGAAACACGGTCATT
1 TTTTTAAAACAC-G-AAAA
55354954 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
* **
55354972 TTTTTGAAAGACATG-ATT
1 TTTTT-AAA-ACACGAAAA
* *
55354990 TTTTTGAAAATACGGAAA
1 TTTTT-AAAACACGAAAA
*
55355008 TTTATAAAACACGAAAA
1 TTTTTAAAACACGAAAA
*
55355025 TTTTTTCTGAAAACAAGAAAA
1 --TTTT-T-AAAACACGAAAA
* * *
55355046 TTTTTGAAACACTAGAA
1 TTTTTAAAACACGAAAA
* *
55355063 TTTTGAAAACACGAAGA
1 TTTTTAAAACACGAAAA
* * *
55355080 TTTTTGAAACATGAGAA
1 TTTTTAAAACACGAAAA
55355097 TTTTTAAAAGCACGA
1 TTTTTAAAA-CACGA
55355112 GGATTATTGA
Statistics
Matches: 373, Mismatches: 87, Indels: 63
0.71 0.17 0.12
Matches are distributed among these distances:
11 1 0.00
12 3 0.01
13 2 0.01
14 9 0.02
15 7 0.02
16 37 0.10
17 199 0.53
18 66 0.18
19 31 0.08
20 7 0.02
21 11 0.03
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:55355006 original size:73 final size:71
Alignment explanation
Indices: 55354746--55355054 Score: 203
Period size: 70 Copynumber: 4.4 Consensus size: 71
55354736 AATACGAGAA
* * * ** *
55354746 TTTTT-AAAACACGAAAATTTTTAAAACACGAAAATTTTTGAAACACGGAAATTTTTAGAAA-AC
1 TTTTTGAAAACACGAAAATTTTTGAAAGACGAAGATTTTTTTAACACGGAAATTTATA-AAACAC
55354809 G---A-T
65 GAAAATT
* * * * * ** * *
55354812 TTTTT-AAAATCACCG-GAGTTTTTGAAAACACGAAAATCTTTAAAACACCGAAATTTTTGAAAA
1 TTTTTGAAAA-CA-CGAAAATTTTTG-AAAGACGAAGATTTTTTTAACACGGAAATTTAT-AAAA
*
55354875 CACGAAGA--
62 CACGAAAATT
* * *
55354883 -TTTTG-AAACACGAAAATTTTTTGAAAATACGAAGATTTTTTTAACACGGAAATTTTTGAAACA
1 TTTTTGAAAACACGAAAA-TTTTTG-AAAGACGAAGATTTTTTTAACACGGAAATTTATAAAACA
***
55354946 CGGTCATT
64 CGAAAATT
* *
55354954 TTTTTGAAAACACGAAAATTTTTGAAAGAC-ATGATTTTTTTGAAAATACGGAAATTTATAAAAC
1 TTTTTGAAAACACGAAAATTTTTGAAAGACGAAGATTTTTTT---AACACGGAAATTTATAAAAC
55355018 ACGAAAATT
63 ACGAAAATT
*
55355027 TTTTCTGAAAACAAGAAAATTTTTGAAA
1 TTTT-TGAAAACACGAAAATTTTTGAAA
55355055 CACTAGAATT
Statistics
Matches: 197, Mismatches: 27, Indels: 30
0.78 0.11 0.12
Matches are distributed among these distances:
66 9 0.05
67 8 0.04
68 37 0.19
69 15 0.08
70 51 0.26
71 5 0.03
72 12 0.06
73 38 0.19
74 22 0.11
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (71 bp):
TTTTTGAAAACACGAAAATTTTTGAAAGACGAAGATTTTTTTAACACGGAAATTTATAAAACACG
AAAATT
Found at i:55355068 original size:16 final size:16
Alignment explanation
Indices: 55355047--55355100 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
55355037 ACAAGAAAAT
55355047 TTTTGAAACACTAGAA
1 TTTTGAAACACTAGAA
* *
55355063 TTTTGAAAACACGAAGAT
1 TTTTG-AAACAC-TAGAA
55355081 TTTTGAAACA-TGAGAA
1 TTTTGAAACACT-AGAA
55355097 TTTT
1 TTTT
55355101 TAAAAGCACG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 12 0.39
17 11 0.35
18 8 0.26
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (16 bp):
TTTTGAAACACTAGAA
Found at i:55355296 original size:17 final size:16
Alignment explanation
Indices: 55355262--55355312 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
55355252 AAAATTATTT
55355262 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
* *
55355278 AAAATCAAATTAAATTA
1 AAAAT-AAAATAAAATA
55355295 AAAATATAAATATAAATA
1 AAAATA-AAATA-AAATA
55355313 TGCATAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.21
17 18 0.64
18 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:55355463 original size:17 final size:16
Alignment explanation
Indices: 55355441--55355494 Score: 74
Period size: 17 Copynumber: 3.3 Consensus size: 16
55355431 ATTGAACCTC
*
55355441 TTTTTCTTGTTTTTTCT
1 TTTTTCTT-TTTTCTCT
55355458 TTTTTC-TTTTTCTCT
1 TTTTTCTTTTTTCTCT
55355473 CTTTTTCTTTTTTCTCT
1 -TTTTTCTTTTTTCTCT
55355490 TTTTT
1 TTTTT
55355495 TTTGCTGGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 7 0.21
16 12 0.35
17 15 0.44
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTTTCTCT
Found at i:55355468 original size:15 final size:15
Alignment explanation
Indices: 55355450--55355494 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
55355440 CTTTTTCTTG
55355450 TTTTTTCTTTTTTCT
1 TTTTTTCTTTTTTCT
*
55355465 TTTTCTCTCTTTTTCT
1 TTTTTTCT-TTTTTCT
55355481 TTTTTCTCTTTTTT
1 TTTTT-TCTTTTTT
55355495 TTTGCTGGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 7 0.27
16 16 0.62
17 3 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTTTTCT
Found at i:55355642 original size:23 final size:23
Alignment explanation
Indices: 55355614--55355658 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
55355604 TGCATTTGGG
55355614 CTGCTTCTTTCTTCTTCTTTTTT
1 CTGCTTCTTTCTTCTTCTTTTTT
55355637 CTGCTTCTTTCTTCTTCTTTTT
1 CTGCTTCTTTCTTCTTCTTTTT
55355659 GCTACTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.04, T:0.69
Consensus pattern (23 bp):
CTGCTTCTTTCTTCTTCTTTTTT
Found at i:55355650 original size:20 final size:20
Alignment explanation
Indices: 55355615--55355675 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 20
55355605 GCATTTGGGC
*
55355615 TGCTTCTTTCTTCTTCTTTTTT
1 TGCTACTTTCTTCTTC--TTTT
*
55355637 CTGCTTCTTTCTTCTTCTTTT
1 -TGCTACTTTCTTCTTCTTTT
*
55355658 TGCTACTTT-TTTTTCTTT
1 TGCTACTTTCTTCTTCTTT
55355676 GGTTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.22
20 8 0.22
21 4 0.11
23 16 0.44
ACGTcount: A:0.02, C:0.23, G:0.05, T:0.70
Consensus pattern (20 bp):
TGCTACTTTCTTCTTCTTTT
Found at i:55355814 original size:24 final size:24
Alignment explanation
Indices: 55355794--55355853 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
55355784 CTTTTCTTTT
*
55355794 TCTTTT-TTCTTTCTTTCTTCTTCC
1 TCTTTTCTTC-TTCCTTCTTCTTCC
55355818 TCTTTTCTTCTTCCTTCTTCTTCC
1 TCTTTTCTTCTTCCTTCTTCTTCC
*
55355842 T-TCTTCTTCTTC
1 TCTTTTCTTCTTC
55355854 AAAGTCTAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 10 0.30
24 20 0.61
25 3 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (24 bp):
TCTTTTCTTCTTCCTTCTTCTTCC
Found at i:55355816 original size:3 final size:3
Alignment explanation
Indices: 55355782--55355853 Score: 62
Period size: 3 Copynumber: 24.0 Consensus size: 3
55355772 TTTTTATTAT
* *
55355782 TTC TT- TTC TTT TTC TT- TT- TTC TTTC TTTC TTC TTC CTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC TTC TTC
55355825 TTC TTCC TTC TTC TTCC TTC TTC TTC TTC
1 TTC TT-C TTC TTC TT-C TTC TTC TTC TTC
55355854 AAAGTCTAGC
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 8 0.14
3 38 0.64
4 13 0.22
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:55355821 original size:13 final size:13
Alignment explanation
Indices: 55355805--55355853 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
55355795 CTTTTTTCTT
55355805 TCTTTCTTCTTCC
1 TCTTTCTTCTTCC
55355818 TCTTTTCTTCTT-C
1 TC-TTTCTTCTTCC
55355831 -C-TTCTTCTTCC
1 TCTTTCTTCTTCC
55355842 T-TCTTCTTCTTC
1 TCT-TTCTTCTTC
55355854 AAAGTCTAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
10 8 0.26
11 1 0.03
12 1 0.03
13 12 0.39
14 9 0.29
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTTTCTTCTTCC
Found at i:55355837 original size:10 final size:10
Alignment explanation
Indices: 55355822--55355850 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
55355812 TCTTCCTCTT
55355822 TTCTTCTTCC
1 TTCTTCTTCC
55355832 TTCTTCTTCC
1 TTCTTCTTCC
55355842 TTCTTCTTC
1 TTCTTCTTC
55355851 TTCAAAGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:55355944 original size:10 final size:10
Alignment explanation
Indices: 55355909--55355958 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
55355899 ACGCCGGTAC
55355909 TCTT-TCTTT
1 TCTTCTCTTT
* *
55355918 TCTTCTCCTC
1 TCTTCTCTTT
55355928 T-TTCTCTTT
1 TCTTCTCTTT
55355937 TCTTCTCTTT
1 TCTTCTCTTT
*
55355947 TCTTCTTTTT
1 TCTTCTCTTT
55355957 TC
1 TC
55355959 CTTCGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTCTTT
Found at i:55355956 original size:19 final size:19
Alignment explanation
Indices: 55355913--55355955 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
55355903 CGGTACTCTT
55355913 TCTTTTCTTCTCCTCTTTC
1 TCTTTTCTTCTCCTCTTTC
55355932 TCTTTTCTTCT-CT-TTTC
1 TCTTTTCTTCTCCTCTTTC
55355949 TTCTTTT
1 -TCTTTT
55355956 TTCCTTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.17
18 8 0.35
19 11 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTCCTCTTTC
Found at i:55356236 original size:29 final size:29
Alignment explanation
Indices: 55356203--55356319 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
55356193 TGTAATTTTT
*
55356203 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
55356232 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
55356262 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
55356291 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
55356320 TTATTTTTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:55356258 original size:30 final size:30
Alignment explanation
Indices: 55356218--55356319 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
55356208 ATTTAGGATT
*
55356218 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
55356248 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
55356278 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
55356308 AAAATGCAATTT
1 AAAATGAAATTT
55356320 TTATTTTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:55359041 original size:20 final size:20
Alignment explanation
Indices: 55359016--55359053 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55359006 TTTCAGTAAA
*
55359016 TTTTATAATTTTTTTGAATG
1 TTTTATAATATTTTTGAATG
55359036 TTTTATAATATTTTTGAA
1 TTTTATAATATTTTTGAA
55359054 AATTTGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (20 bp):
TTTTATAATATTTTTGAATG
Found at i:55359063 original size:20 final size:20
Alignment explanation
Indices: 55359013--55359063 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
55359003 CAATTTCAGT
*
55359013 AAATTTTATAATTTTTTTGA
1 AAATTTTATAATATTTTTGA
**
55359033 ATGTTTTATAATATTTTTGA
1 AAATTTTATAATATTTTTGA
*
55359053 AAATTTGATAA
1 AAATTTTATAA
55359064 AGTTTTATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (20 bp):
AAATTTTATAATATTTTTGA
Found at i:55359085 original size:21 final size:21
Alignment explanation
Indices: 55359062--55359103 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
55359052 AAAATTTGAT
55359062 AAAGTTTTATTTATATATTTTA
1 AAAGTTTTATTTAT-TATTTTA
*
55359084 AAATTTTTATTTATTATTTT
1 AAAGTTTTATTTATTATTTT
55359104 TCTTTTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
AAAGTTTTATTTATTATTTTA
Found at i:55363412 original size:21 final size:21
Alignment explanation
Indices: 55363386--55363426 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55363376 ATCTGCTCAA
* *
55363386 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
55363407 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
55363427 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:55368469 original size:19 final size:19
Alignment explanation
Indices: 55368447--55368492 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
55368437 GAAATTATAA
*
55368447 ATATACATAAATATTTAAAAT
1 ATATA-ATAAAT-TTAAAAAT
55368468 ATATAATAAATTTAAAAAT
1 ATATAATAAATTTAAAAAT
55368487 ATATAA
1 ATATAA
55368493 ATAATAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 13 0.54
20 6 0.25
21 5 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATAATAAATTTAAAAAT
Found at i:55371985 original size:25 final size:25
Alignment explanation
Indices: 55371957--55372021 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
55371947 ACCCAGCATG
55371957 CATGAGCTTCCCATTATTCAACTCC
1 CATGAGCTTCCCATTATTCAACTCC
* *
55371982 CATGAGCTTCCTATTATTCAACTCG
1 CATGAGCTTCCCATTATTCAACTCC
* *
55372007 GAGGAGCTTCCCATT
1 CATGAGCTTCCCATT
55372022 TACTGCTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.32
Consensus pattern (25 bp):
CATGAGCTTCCCATTATTCAACTCC
Found at i:55375412 original size:6 final size:6
Alignment explanation
Indices: 55375401--55375433 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
55375391 TAGCGTATGA
*
55375401 TGAAAG TGAAAG TGAAAG TGAAGG TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
55375434 GAAATTAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.18
Consensus pattern (6 bp):
TGAAAG
Found at i:55381065 original size:20 final size:20
Alignment explanation
Indices: 55381040--55381087 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
55381030 TGTTGATGTA
55381040 TGATTGCACTCTAATGCCCC
1 TGATTGCACTCTAATGCCCC
** *
55381060 TGATTGCACTCTGGTGCCCT
1 TGATTGCACTCTAATGCCCC
55381080 TGATTGCA
1 TGATTGCA
55381088 TTTTCGTGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (20 bp):
TGATTGCACTCTAATGCCCC
Found at i:55381096 original size:20 final size:20
Alignment explanation
Indices: 55381040--55381097 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
55381030 TGTTGATGTA
**
55381040 TGATTGCACTCTAATGCCCC
1 TGATTGCACTCTCGTGCCCC
* *
55381060 TGATTGCACTCTGGTGCCCT
1 TGATTGCACTCTCGTGCCCC
* *
55381080 TGATTGCATTTTCGTGCC
1 TGATTGCACTCTCGTGCC
55381098 TCTATATGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.14, C:0.29, G:0.21, T:0.36
Consensus pattern (20 bp):
TGATTGCACTCTCGTGCCCC
Found at i:55384035 original size:33 final size:33
Alignment explanation
Indices: 55384000--55384231 Score: 171
Period size: 33 Copynumber: 7.0 Consensus size: 33
55383990 GACAATGTGT
* *
55384000 GAATTGTGTTTATATGCGAACTGAGTTATATGT
1 GAATTGTGTTTATATGCGAACTGTGTTATATGC
* * * *
55384033 GAACTGTGTGTATATGCGAACTGGGTTACATGC
1 GAATTGTGTTTATATGCGAACTGTGTTATATGC
* * *
55384066 AAATTGTGTTTATATGTGAATTGTGTTTATATGC
1 GAATTGTGTTTATATGCGAACTGTG-TTATATGC
* * * * * *
55384100 AAACTATGTTTATATG-TAAGTTGTGTTTTATGC
1 GAATTGTGTTTATATGCGAA-CTGTGTTATATGC
* ** *
55384133 GAACTAAG-TTATATGCGAACTGTGTTTATATGT
1 GAATTGTGTTTATATGCGAACTGTG-TTATATGC
* * * *
55384166 GAGTTGTGTTTATATGTGAATTGAGTTATATGC
1 GAATTGTGTTTATATGCGAACTGTGTTATATGC
* * * *
55384199 AAATAGTGTTTATATGCAAATTGTGTTTATATG
1 GAATTGTGTTTATATGCGAACTGTG-TTATATG
55384232 TTATCTGTGT
Statistics
Matches: 157, Mismatches: 36, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
32 11 0.07
33 100 0.64
34 46 0.29
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.43
Consensus pattern (33 bp):
GAATTGTGTTTATATGCGAACTGTGTTATATGC
Found at i:55384048 original size:17 final size:17
Alignment explanation
Indices: 55384004--55384231 Score: 173
Period size: 17 Copynumber: 13.7 Consensus size: 17
55383994 ATGTGTGAAT
55384004 TGTGTTTATATGCGAAC
1 TGTGTTTATATGCGAAC
* *
55384021 TGAG-TTATATGTGAAC
1 TGTGTTTATATGCGAAC
*
55384037 TGTGTGTATATGCGAAC
1 TGTGTTTATATGCGAAC
* * * *
55384054 TG-GGTTACATGCAAAT
1 TGTGTTTATATGCGAAC
* *
55384070 TGTGTTTATATGTGAAT
1 TGTGTTTATATGCGAAC
*
55384087 TGTGTTTATATGCAAAC
1 TGTGTTTATATGCGAAC
* * *
55384104 TATGTTTATATG-TAAGT
1 TGTGTTTATATGCGAA-C
55384121 TGTGTTT-TATGCGAAC
1 TGTGTTTATATGCGAAC
**
55384137 TAAG-TTATATGCGAAC
1 TGTGTTTATATGCGAAC
* **
55384153 TGTGTTTATATGTGAGT
1 TGTGTTTATATGCGAAC
* *
55384170 TGTGTTTATATGTGAAT
1 TGTGTTTATATGCGAAC
* *
55384187 TGAG-TTATATGC-AAA
1 TGTGTTTATATGCGAAC
* *
55384202 TAGTGTTTATATGCAAAT
1 T-GTGTTTATATGCGAAC
55384220 TGTGTTTATATG
1 TGTGTTTATATG
55384232 TTATCTGTGT
Statistics
Matches: 166, Mismatches: 36, Indels: 18
0.75 0.16 0.08
Matches are distributed among these distances:
15 5 0.03
16 53 0.32
17 105 0.63
18 3 0.02
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (17 bp):
TGTGTTTATATGCGAAC
Found at i:55384079 original size:50 final size:51
Alignment explanation
Indices: 55384005--55384241 Score: 227
Period size: 50 Copynumber: 4.7 Consensus size: 51
55383995 TGTGTGAATT
* * *
55384005 GTGTTTATATGCGAACTGAG-TTATATGTGAACTGTGTGTATATGCGAACT-
1 GTGTTTATATGCAAATTGTGTTTATATGTGAACTGTGT-TATATGCGAACTA
* * * *
55384055 G-GGTTACATGCAAATTGTGTTTATATGTGAATTGTGTTTATATGCAAACTA
1 GTGTTTATATGCAAATTGTGTTTATATGTGAACTGTG-TTATATGCGAACTA
* * * **
55384106 -TGTTTATATGTAAGTTGTGTTT-TATGCGAACTAAGTTATATGCGAACT-
1 GTGTTTATATGCAAATTGTGTTTATATGTGAACTGTGTTATATGCGAACTA
** * * * *
55384154 GTGTTTATATGTGAGTTGTGTTTATATGTGAATTGAGTTATATGC-AAATA
1 GTGTTTATATGCAAATTGTGTTTATATGTGAACTGTGTTATATGCGAACTA
* *
55384204 GTGTTTATATGCAAATTGTGTTTATATGTTATCTGTGT
1 GTGTTTATATGCAAATTGTGTTTATATGTGAACTGTGT
55384242 CAACGTGTGG
Statistics
Matches: 152, Mismatches: 28, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
49 49 0.32
50 85 0.56
51 18 0.12
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.44
Consensus pattern (51 bp):
GTGTTTATATGCAAATTGTGTTTATATGTGAACTGTGTTATATGCGAACTA
Found at i:55384136 original size:83 final size:83
Alignment explanation
Indices: 55383997--55384197 Score: 246
Period size: 83 Copynumber: 2.4 Consensus size: 83
55383987 TGTGACAATG
* **
55383997 TGTGAATTGTGTTTATATGCGAACTGAGTTATATGTGAACTGTGTGTATATGCGAACTGGGTTAC
1 TGTGAATTGTGTTTATATGCAAACTGAGTTATATGTGAACTGTGTGTATATGCGAACTAAGTTAC
*
55384062 ATGCAAATTGTGTTTATA
66 ATGCAAACTGTGTTTATA
* *
55384080 TGTGAATTGTGTTTATATGCAAACT-ATGTTTATATGT-AAGT-TGTGTTTTATGCGAACTAAGT
1 TGTGAATTGTGTTTATATGCAAACTGA-G-TTATATGTGAACTGTGTG-TATATGCGAACTAAGT
* *
55384142 TATATGCGAACTGTGTTTATA
63 TACATGCAAACTGTGTTTATA
* ** *
55384163 TGTGAGTTGTGTTTATATGTGAATTGAGTTATATG
1 TGTGAATTGTGTTTATATGCAAACTGAGTTATATG
55384198 CAAATAGTGT
Statistics
Matches: 102, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
82 12 0.12
83 81 0.79
84 9 0.09
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.43
Consensus pattern (83 bp):
TGTGAATTGTGTTTATATGCAAACTGAGTTATATGTGAACTGTGTGTATATGCGAACTAAGTTAC
ATGCAAACTGTGTTTATA
Found at i:55384382 original size:26 final size:26
Alignment explanation
Indices: 55384350--55384404 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
55384340 TCATATACAT
* *
55384350 GCTCTTTGTAAAGTAATTACGTGCGA
1 GCTCTTTGTAAAGTAACTAAGTGCGA
*
55384376 GCTCTTTGTAAAGTGACTAAGTGCGA
1 GCTCTTTGTAAAGTAACTAAGTGCGA
55384402 GCT
1 GCT
55384405 AGTCTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (26 bp):
GCTCTTTGTAAAGTAACTAAGTGCGA
Found at i:55390449 original size:10 final size:10
Alignment explanation
Indices: 55390432--55390502 Score: 56
Period size: 10 Copynumber: 7.3 Consensus size: 10
55390422 TTTTATCGTC
55390432 TTTT-ATAAT
1 TTTTAATAAT
*
55390441 TTCTAATAAT
1 TTTTAATAAT
*
55390451 TTTTTATAAT
1 TTTTAATAAT
* *
55390461 TTTTTACAAT
1 TTTTAATAAT
* *
55390471 ATTT-ACAAT
1 TTTTAATAAT
* *
55390480 TTCTAACAAT
1 TTTTAATAAT
55390490 TTTTAATAAT
1 TTTTAATAAT
55390500 TTT
1 TTT
55390503 ATTATTTATT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
9 10 0.20
10 41 0.80
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:55390455 original size:20 final size:20
Alignment explanation
Indices: 55390432--55390501 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
55390422 TTTTATCGTC
*
55390432 TTTTATAATTTCTAATAATT
1 TTTTATAATTTCTAACAATT
* *
55390452 TTTTATAATTTTTTACAA-T
1 TTTTATAATTTCTAACAATT
* *
55390471 ATTTACAATTTCTAACAATT
1 TTTTATAATTTCTAACAATT
*
55390491 TTTAATAATTT
1 TTTTATAATTT
55390502 TATTATTTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 15 0.38
20 24 0.62
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATAATTTCTAACAATT
Found at i:55397717 original size:21 final size:19
Alignment explanation
Indices: 55397691--55397739 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
55397681 TTTGTATGGG
55397691 CCCAAAAAAATAAGTTACAAA
1 CCCAAAAAAA-AA-TTACAAA
* *
55397712 CCCAAAATAAACATTACAAG
1 CCCAAAA-AAAAATTACAAA
55397732 CCCAAAAA
1 CCCAAAAA
55397740 TTAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.04
20 13 0.52
21 8 0.32
22 3 0.12
ACGTcount: A:0.59, C:0.24, G:0.04, T:0.12
Consensus pattern (19 bp):
CCCAAAAAAAAATTACAAA
Found at i:55403980 original size:21 final size:19
Alignment explanation
Indices: 55403954--55404002 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
55403944 TTTGTACGGG
55403954 CCCAAAAAAATAAGTTACAAA
1 CCCAAAAAAA-AA-TTACAAA
* *
55403975 CCCAAAATAAACATTACAAG
1 CCCAAAA-AAAAATTACAAA
55403995 CCCAAAAA
1 CCCAAAAA
55404003 TTAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.04
20 13 0.52
21 8 0.32
22 3 0.12
ACGTcount: A:0.59, C:0.24, G:0.04, T:0.12
Consensus pattern (19 bp):
CCCAAAAAAAAATTACAAA
Found at i:55404224 original size:3 final size:3
Alignment explanation
Indices: 55404210--55404247 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
55404200 TTGACTTTCA
*
55404210 TTG TTA TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
55404248 ATTTTTATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.29, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:55407842 original size:27 final size:27
Alignment explanation
Indices: 55407804--55407855 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
55407794 TTTATTTCAA
55407804 GGGAGTCAGCACTTAGCAACCCCTTGG
1 GGGAGTCAGCACTTAGCAACCCCTTGG
*
55407831 GGGATTCAGCACTTAGCAACCCCTT
1 GGGAGTCAGCACTTAGCAACCCCTT
55407856 TTATATTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.21
Consensus pattern (27 bp):
GGGAGTCAGCACTTAGCAACCCCTTGG
Found at i:55416138 original size:30 final size:29
Alignment explanation
Indices: 55416068--55416140 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
55416058 ACAACGTGAT
*
55416068 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATTCCA
* *
55416097 AACATAAGTGACTAAAATGTAACCTGTGCCA
1 AACATAAGTGACTAAAACGTAACAT-T-CCA
55416128 AACA-AAGTGACTA
1 AACATAAGTGACTA
55416141 TTTTGGTAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 23 0.59
30 10 0.26
31 6 0.15
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATTCCA
Found at i:55418102 original size:30 final size:31
Alignment explanation
Indices: 55418052--55418170 Score: 138
Period size: 30 Copynumber: 3.9 Consensus size: 31
55418042 CAAAAAATAA
* * *
55418052 AAAATTGCATTTTGACCCCTAAACTTTTTTT
1 AAAATTACATTTTGACCCCTAAACTTTTCTC
55418083 AAAATTACATTTT-ACCCCTAAAC-TTTCTC
1 AAAATTACATTTTGACCCCTAAACTTTTCTC
*
55418112 AAAATTACATTTTGACCTCTAAAC-TTTCTC
1 AAAATTACATTTTGACCCCTAAACTTTTCTC
** *
55418142 AAAATTATGTTTCGA-CCCTAATACTTTTC
1 AAAATTACATTTTGACCCCTAA-ACTTTTC
55418171 CTGCATTTGC
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
29 22 0.29
30 39 0.51
31 16 0.21
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (31 bp):
AAAATTACATTTTGACCCCTAAACTTTTCTC
Found at i:55418396 original size:23 final size:20
Alignment explanation
Indices: 55418365--55418415 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
55418355 AAAAACTTGC
* *
55418365 AAAAAAGAGAAAAAGAAGAGG
1 AAAAAGGAGAGAAAG-AGAGG
55418386 AAAAAGGAGAGAAAGAGAGG
1 AAAAAGGAGAGAAAGAGAGG
*
55418406 AGAAAGGAGA
1 AAAAAGGAGA
55418416 AGAAGAGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
AAAAAGGAGAGAAAGAGAGG
Found at i:55418422 original size:20 final size:20
Alignment explanation
Indices: 55418365--55418422 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
55418355 AAAAACTTGC
* *
55418365 AAAAAAGAGAAAAAGAAGAGG
1 AAAAAGGAGAAGAAG-AGAGG
55418386 AAAAAGGAG-AGAAAGAGAGG
1 AAAAAGGAGAAG-AAGAGAGG
*
55418406 AGAAAGGAGAAGAAGAG
1 AAAAAGGAGAAGAAGAG
55418423 GCCGGCCATC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (20 bp):
AAAAAGGAGAAGAAGAGAGG
Found at i:55418516 original size:19 final size:18
Alignment explanation
Indices: 55418492--55418572 Score: 64
Period size: 16 Copynumber: 4.6 Consensus size: 18
55418482 AGACCGAACG
*
55418492 GAGAAGAAGAAGGAGAAAA
1 GAGAAGAA-AAAGAGAAAA
55418511 GAGAAGAAAAAGAG-AAA
1 GAGAAGAAAAAGAGAAAA
*
55418528 GAAGAAAGGAAAAAGA-AGAA
1 G-AG-AA-GAAAAAGAGAAAA
55418548 G-GAAGAAAAAGA-AAAA
1 GAGAAGAAAAAGAGAAAA
*
55418564 AAGAA-AAAA
1 GAGAAGAAAA
55418573 TATTTTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
16 15 0.28
17 9 0.17
18 8 0.15
19 10 0.19
20 11 0.21
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
GAGAAGAAAAAGAGAAAA
Found at i:55418547 original size:21 final size:22
Alignment explanation
Indices: 55418514--55418569 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
55418504 GAGAAAAGAG
55418514 AAGAAAAAG-AGAAAGAAG-AA
1 AAGAAAAAGAAGAAAGAAGAAA
* *
55418534 AGGAAAAAGAAGAAGGAAGAAA
1 AAGAAAAAGAAGAAAGAAGAAA
55418556 AAGAAAAA-AAGAAA
1 AAGAAAAAGAAGAAA
55418570 AAATATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.27
21 13 0.43
22 9 0.30
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (22 bp):
AAGAAAAAGAAGAAAGAAGAAA
Found at i:55418568 original size:24 final size:24
Alignment explanation
Indices: 55418495--55418568 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
55418485 CCGAACGGAG
55418495 AAGAAGAAGG-AGAAAAGAGAAGAAA
1 AAGAAGAAGGAAGAAAA-AGAA-AAA
* *
55418520 AAG-AGAAAGAAG--AAAG-GAAA
1 AAGAAGAAGGAAGAAAAAGAAAAA
55418540 AAGAAGAAGGAAGAAAAAGAAAAA
1 AAGAAGAAGGAAGAAAAAGAAAAA
55418564 AAGAA
1 AAGAA
55418569 AAAATATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
20 6 0.15
21 8 0.20
22 2 0.05
23 6 0.15
24 13 0.32
25 5 0.12
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (24 bp):
AAGAAGAAGGAAGAAAAAGAAAAA
Found at i:55418571 original size:30 final size:29
Alignment explanation
Indices: 55418505--55418571 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
55418495 AAGAAGAAGG
* *
55418505 AGAAAAGAGAAGAAAAAGAGAAAGAAGAAA
1 AGAAAA-AGAAGAAAAAGAAAAAGAAAAAA
* *
55418535 GGAAAAAGAAGAAGGAAGAAAAAGAAAAAA
1 AGAAAAAGAAGAA-AAAGAAAAAGAAAAAA
55418565 AGAAAAA
1 AGAAAAA
55418572 ATATTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (29 bp):
AGAAAAAGAAGAAAAAGAAAAAGAAAAAA
Found at i:55418807 original size:41 final size:41
Alignment explanation
Indices: 55418755--55418851 Score: 167
Period size: 41 Copynumber: 2.4 Consensus size: 41
55418745 AAGCGCAGGC
*
55418755 CCAAACCAACGCCAGGCCCAACAGCAGGCCTAGCAGGCCAA
1 CCAACCCAACGCCAGGCCCAACAGCAGGCCTAGCAGGCCAA
*
55418796 CCAACCCAACGCCAGGCCCAACAGCAGGCCTAGCAGGCCAG
1 CCAACCCAACGCCAGGCCCAACAGCAGGCCTAGCAGGCCAA
*
55418837 CCAGCCCAACGCCAG
1 CCAACCCAACGCCAG
55418852 CAGCAGGCCC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.31, C:0.44, G:0.23, T:0.02
Consensus pattern (41 bp):
CCAACCCAACGCCAGGCCCAACAGCAGGCCTAGCAGGCCAA
Found at i:55418868 original size:15 final size:15
Alignment explanation
Indices: 55418850--55418894 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
55418840 GCCCAACGCC
*
55418850 AGCAGCAGGCCCAAT
1 AGCAGCAGGCCCAAA
55418865 AGCA-CAGGCCCAAA
1 AGCAGCAGGCCCAAA
55418879 AGGCAGCAGG-CCAAA
1 A-GCAGCAGGCCCAAA
55418894 A
1 A
55418895 AAAAGAAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 10 0.37
15 13 0.48
16 4 0.15
ACGTcount: A:0.40, C:0.31, G:0.27, T:0.02
Consensus pattern (15 bp):
AGCAGCAGGCCCAAA
Found at i:55418872 original size:14 final size:15
Alignment explanation
Indices: 55418850--55418890 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
55418840 GCCCAACGCC
55418850 AGCAGCAGGCCCAAT
1 AGCAGCAGGCCCAAT
*
55418865 AGCA-CAGGCCCAAA
1 AGCAGCAGGCCCAAT
55418879 AGGCAGCAGGCC
1 A-GCAGCAGGCC
55418891 AAAAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 10 0.43
15 7 0.30
16 6 0.26
ACGTcount: A:0.34, C:0.34, G:0.29, T:0.02
Consensus pattern (15 bp):
AGCAGCAGGCCCAAT
Found at i:55418914 original size:17 final size:16
Alignment explanation
Indices: 55418894--55418974 Score: 69
Period size: 17 Copynumber: 5.0 Consensus size: 16
55418884 GCAGGCCAAA
*
55418894 AAAAAGAAGAGAAAGAG
1 AAAAA-AAGAGAAAAAG
*
55418911 AAAAAAAAAGAAAAAAG
1 AAAAAAAGAG-AAAAAG
55418928 AAAAAAAGAGAAATAA-
1 AAAAAAAGAGAAA-AAG
*
55418944 AAGAAAAAAAGAAAAA-
1 AA-AAAAAGAGAAAAAG
*
55418960 AAAAGAAGA-AAAAAG
1 AAAAAAAGAGAAAAAG
55418975 GGGTTTCAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
14 5 0.09
15 5 0.09
16 13 0.24
17 31 0.57
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.01
Consensus pattern (16 bp):
AAAAAAAGAGAAAAAG
Found at i:55418914 original size:19 final size:18
Alignment explanation
Indices: 55418892--55418972 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 18
55418882 CAGCAGGCCA
*
55418892 AAAAAAAGAAGAGAAAGAG
1 AAAAAAAGAAGA-AAAAAG
55418911 AAAAAAA-AAGAAAAAAG
1 AAAAAAAGAAGAAAAAAG
55418928 AAAAAAAG-AGAAATAAAAG
1 AAAAAAAGAAG-AA-AAAAG
*
55418947 AAAAAAAGAAAAAAAAAG
1 AAAAAAAGAAGAAAAAAG
55418965 AAGAAAAA
1 AA-AAAAA
55418973 AGGGGTTTCA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
17 14 0.25
18 13 0.24
19 27 0.49
20 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (18 bp):
AAAAAAAGAAGAAAAAAG
Found at i:55418926 original size:8 final size:8
Alignment explanation
Indices: 55418913--55418961 Score: 64
Period size: 9 Copynumber: 5.9 Consensus size: 8
55418903 AGAAAGAGAA
55418913 AAAAAAAG
1 AAAAAAAG
55418921 -AAAAAAG
1 AAAAAAAG
55418928 AAAAAAAGAG
1 -AAAAAA-AG
55418938 AAATAAAAG
1 AAA-AAAAG
55418947 AAAAAAAG
1 AAAAAAAG
55418955 AAAAAAA
1 AAAAAAA
55418962 AAGAAGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.19
8 12 0.32
9 13 0.35
10 5 0.14
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:55418935 original size:27 final size:28
Alignment explanation
Indices: 55418892--55418974 Score: 107
Period size: 27 Copynumber: 3.0 Consensus size: 28
55418882 CAGCAGGCCA
*
55418892 AAAAAAAGAAGAGAAAGAGAAAAAAAAAG
1 AAAAAAAGAA-AAAAAGAGAAAAAAAAAG
*
55418921 -AAAAAAGAAAAAAAGAG-AAATAAAAG
1 AAAAAAAGAAAAAAAGAGAAAAAAAAAG
* *
55418947 AAAAAAAGAAAAAAAAAGAAGAAAAAAG
1 AAAAAAAGAAAAAAAGAGAAAAAAAAAG
55418975 GGGTTTCAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 8 0.17
27 23 0.49
28 16 0.34
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (28 bp):
AAAAAAAGAAAAAAAGAGAAAAAAAAAG
Found at i:55419367 original size:20 final size:21
Alignment explanation
Indices: 55419342--55419381 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55419332 CGGGTTTCGA
55419342 AATTTC-CGTGTCTTCAAAAT
1 AATTTCTCGTGTCTTCAAAAT
*
55419362 AATTTCTCGTGTTTTCAAAA
1 AATTTCTCGTGTCTTCAAAA
55419382 ATAAGGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (21 bp):
AATTTCTCGTGTCTTCAAAAT
Found at i:55419522 original size:17 final size:17
Alignment explanation
Indices: 55419488--55419779 Score: 194
Period size: 17 Copynumber: 16.5 Consensus size: 17
55419478 AAAAAATCAG
*
55419488 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
55419506 AAAAATTTCCGTGTTTC
1 AAAAATTTTCGTGTTTC
*
55419523 AAAAATTTTCATGTTTTC
1 AAAAATTTTCGTG-TTTC
*
55419541 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
55419559 AAAAAAATTCCAAT-TTTC
1 -AAAAATTTTC-GTGTTTC
*
55419577 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
55419595 TAAAAA-CTTCTGTGTTTC
1 -AAAAATTTTC-GTGTTTC
* *
55419613 AAAAATTTTCGTATTTT
1 AAAAATTTTCGTGTTTC
*
55419630 AAAAATTTTTGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
55419647 TAAAATTTTCGTATTTC
1 AAAAATTTTCGTGTTTC
*
55419664 AAAAATTTTCTTGTTTTC
1 AAAAATTTTCGTG-TTTC
* *
55419682 -AAATTTTTCGTATTTC
1 AAAAATTTTCGTGTTTC
* **
55419698 AAATATCCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* *
55419716 AAAAAATTTCGGTGTTTT
1 AAAAATTTTC-GTGTTTC
* *
55419734 GAAAATTTTCTTGTTTTTC
1 AAAAATTTTC--GTGTTTC
* *
55419753 AAACAAATCTCGTGTTTC
1 AAA-AATTTTCGTGTTTC
*
55419771 ATAAATTTT
1 AAAAATTTT
55419780 TGTTTTTTTT
Statistics
Matches: 207, Mismatches: 53, Indels: 29
0.72 0.18 0.10
Matches are distributed among these distances:
16 5 0.02
17 90 0.43
18 82 0.40
19 24 0.12
20 6 0.03
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.49
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Done.