Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397269.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.1, whole genome shotgun sequence
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: 5666189
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 144833 characters in sequence are not A, C, G, or T
File 4 of 14
Found at i:1201787 original size:23 final size:24
Alignment explanation
Indices: 1201744--1201799 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
1201734 CAGGCGTCTC
*
1201744 ATTTTTTTTATTATGATTTATT-T
1 ATTTTATTTATTATGATTTATTAT
*
1201767 ATTTTATTTATTAT-TTATTATTAT
1 ATTTTATTTATTATGAT-TTATTAT
*
1201791 CTTTTATTT
1 ATTTTATTT
1201800 GGGAGAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 18 0.64
24 9 0.32
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (24 bp):
ATTTTATTTATTATGATTTATTAT
Found at i:1207408 original size:45 final size:45
Alignment explanation
Indices: 1207299--1207401 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 45
1207289 TTGGATAAAA
*
1207299 TTACATGCTATGTACAAAAACATGTTGTACGCTATAGTTAGGTTG
1 TTACATGCTATGTACAAAAACATGTTGTACGCTATAATTAGGTTG
1207344 TTACA--CATAATGTACAAAAACATG-TG-ACATGCTATAATTAGGTTG
1 TTACATGC-T-ATGTACAAAAACATGTTGTAC--GCTATAATTAGGTTG
1207389 TTACATGCTATGT
1 TTACATGCTATGT
1207402 TGAAAAAAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
43 3 0.06
44 3 0.06
45 43 0.84
46 1 0.02
47 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (45 bp):
TTACATGCTATGTACAAAAACATGTTGTACGCTATAATTAGGTTG
Found at i:1207423 original size:30 final size:31
Alignment explanation
Indices: 1207389--1207454 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1207379 AATTAGGTTG
*
1207389 TTACATGCTATGTTG-AAAAAAATACTGTTA
1 TTACATGCCATGTTGAAAAAAAATACTGTTA
* *
1207419 TTACATGCCATGTTGAAAAAAAATATTGTTG
1 TTACATGCCATGTTGAAAAAAAATACTGTTA
1207450 TTACA
1 TTACA
1207455 CGTCATGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (31 bp):
TTACATGCCATGTTGAAAAAAAATACTGTTA
Found at i:1207469 original size:31 final size:31
Alignment explanation
Indices: 1207389--1207462 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
1207379 AATTAGGTTG
* *
1207389 TTACATGCTATGTTG-AAAAAAATACTGTTA
1 TTACACGCCATGTTGAAAAAAAATACTGTTA
* * *
1207419 TTACATGCCATGTTGAAAAAAAATATTGTTG
1 TTACACGCCATGTTGAAAAAAAATACTGTTA
*
1207450 TTACACGTCATGT
1 TTACACGCCATGT
1207463 ATAAAAACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 14 0.37
31 24 0.63
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (31 bp):
TTACACGCCATGTTGAAAAAAAATACTGTTA
Found at i:1207573 original size:30 final size:30
Alignment explanation
Indices: 1207537--1207596 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1207527 ATGGTTAGGT
1207537 TGTTACACGTCATGTTA-AAAAAAATATTAC
1 TGTTACACGTCATG-TACAAAAAAATATTAC
* *
1207567 TGTTACACGTTATGTACAAAAACATATTAC
1 TGTTACACGTCATGTACAAAAAAATATTAC
1207597 ATGTCATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (30 bp):
TGTTACACGTCATGTACAAAAAAATATTAC
Found at i:1222464 original size:19 final size:19
Alignment explanation
Indices: 1222442--1222478 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1222432 CTTGGTATAA
*
1222442 TATTTAAACTTTTTTTAAT
1 TATTTAAAATTTTTTTAAT
1222461 TATTTAAAATTTTTTTAA
1 TATTTAAAATTTTTTTAA
1222479 AAAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTAAAATTTTTTTAAT
Found at i:1225494 original size:251 final size:250
Alignment explanation
Indices: 1224628--1227953 Score: 2647
Period size: 252 Copynumber: 13.3 Consensus size: 250
1224618 TAATAATTTC
* * * *
1224628 ATCATAATTCTTTTTATCCTTACTATTATTCACGCATAAATTAAAATTTGTAAGTCGTAAAATAC
1 ATCATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAATTTGTAA-TCGTAAAACAC
* * * * * * *
1224693 TTTAAACTCTAGAATAACAATTTTAATATTTAA-TTTCTCTAAAAATTATGTCTATTAGATATAC
65 TTTAAACTCGAGAATAA-AATTTAAATGTTTAATTTTCTC-AAAAATTATGTTTATTTGACATAA
* * * * **
1224757 TTGATTTGTTACGTTAAATCTCATACATTTAGGTCAATATTTTTAAAATATTTGTTTCACCTTTA
128 TTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTTAAAATGCTTGTTTCACCTTTA
* * * ** **
1224822 TAATATTTTACGTTAATTCTTACCGTTTTACATCAAGGTTTTTTAAATCCTAATTTTT
193 TAATATTTTACGTTAATTCTTACTGCTTTACGTCAAGACTTTTTAAATATTAATTTTT
* * * * *
1224880 A-CTATAATTCTTTTTATTCTTACTATTATTCACGCATAAATTAAAATTTGAAAGCTGTAAAATA
1 ATC-ATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAATTTGTAATC-GTAAAACA
* * * * * *
1224944 ATTTAAACACGAGAATAAAAAGTTAAATGTTTAATTTT-TAAAAAAATTATATTTATTAT-ATAT
64 CTTTAAACTCGAGAAT-AAAATTTAAATGTTTAATTTTCT-CAAAAATTATGTTTATT-TGACAT
** * * * ***
1225007 AATTGACTTGTTACGTTAAAACTCATACGTTTACGTCAATATTTTGAAAACATTTGTTTCACCTT
126 AATTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTTAAAATGCTTGTTTCACCTT
* ** * * * * * *
1225072 TATAATATTTTACGTAAATTCACACTGCTTTATGTCATGACTTTTCAAGTAATGATTTTT
191 TATAATATTTTACGTTAATTCTTACTGCTTTACGTCAAGACTTTTTAAATATTAATTTTT
* * * *
1225132 ATCATAATTCCTTTTATTCTTACTATTATTTATGCATAGATTAAAATTTATAAGCCGTAAAACAC
1 ATCATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAATTTGTAA-TCGTAAAACAC
* * * * * *
1225197 TTTAAACTTGAGAATCAAAAGTTAAATATTTAATTTTTTC-AAAATTATGTTTATTTCATATAAT
65 TTTAAACTCGAGAAT-AAAATTTAAATGTTTAATTTTCTCAAAAATTATGTTTATTTGACATAAT
* * * * * *
1225261 TTACTTGTTATGTTAAATTTCACACATCTACGTCACTATTTTTAAAATGCTTGTTTTACCATTAT
129 TGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTTAAAATGCTTGTTTCACCTTTAT
** * *
1225326 AATATTTTACGTTAATTCTTACTAATTTACGTCAAAATTTTTTAAATATTAATTTTT
194 AATATTTTACGTTAATTCTTACTGCTTTACGTCAAGACTTTTTAAATATTAATTTTT
* * * ** * *
1225383 ACCATAATT-TTCTTATTCTCACTATTATTCACCCATAGATTAAAATTTGTAATCTGTAAAATAT
1 ATCATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAATTTGTAATC-GTAAAACAC
* * *
1225447 TTTAAACTCGAGAATAATAATTTAAATGCTTACTTTTCTGAAAAATTATGTTTATTTGACATAAT
65 TTTAAACTCGAGAATAA-AATTTAAATGTTTAATTTTCTCAAAAATTATGTTTATTTGACATAAT
* * * * *
1225512 TAACTTTTTACGTTAAATTTCACACATTTATGTCAAT-TTTTTGAAAATGTTTGTTTCACATTTA
129 TGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTT-AAAATGCTTGTTTCACCTTTA
* * * * * * * *
1225576 TAATGTTTTATGTTAATTCCTA-TCGCTTTACATCATGACTTTTTAACTAATAATTTTC
193 TAATATTTTACGTTAATTCTTACT-GCTTTACGTCAAGACTTTTTAAATATTAATTTTT
* * * *
1225634 ATTATAATTCCTTTTA-TCATTACTATTATTCATGTATAGATTAAAATTTGTAAGTCGTAAAAAA
1 ATCATAATTCTTTTTATTC-TTACTATTATTCATGCATAGATTAAAATTTGTAA-TCGTAAAACA
* * * * *
1225698 CTTTAAGCACGAGAATAAAAAGTTGAATGTTTAATTTTTTC-AAAATTATGTTTATTTGACATAA
64 CTTTAAACTCGAGAAT-AAAATTTAAATGTTTAATTTTCTCAAAAATTATGTTTATTTGACATAA
* * ** ** * * * * *
1225762 TTGACTTGTTACATTAAATCTCACTTATTTATATCAACATTTTAAAAATTCTTGATCCACCTTTA
128 TTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTTAAAATGCTTGTTTCACCTTTA
* * *
1225827 TAATGTTTTACGTTAATTCTTACTGCTTTACGTCAAGACTTTTAAAATATTAATTTTC
193 TAATATTTTACGTTAATTCTTACTGCTTTACGTCAAGACTTTTTAAATATTAATTTTT
* * *
1225885 ATTATAATTCTTTTTA-TCATTACTATTATTCATGTATAGATTAAAATTTGTAAGTCGTAAAAAA
1 ATCATAATTCTTTTTATTC-TTACTATTATTCATGCATAGATTAAAATTTGTAA-TCGTAAAACA
* * * * *
1225949 CTTTAAGCACGAGAATTAAAAGTTGAATGTTTAATTTTTTC-AAAATTATGTTTATTTGACATAA
64 CTTTAAACTCGAGAA-TAAAATTTAAATGTTTAATTTTCTCAAAAATTATGTTTATTTGACATAA
* * * * * * * * ***
1226013 TTGATTTATTACGTTAAATTTCATAAATTTACATCAATATTTTGAAAATGTTTGTTCCTTTTTTA
128 TTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTTAAAATGCTTGTTTCACCTTTA
* * * * *
1226078 TAATATTTT-CTATTAATCCTTACCGCTTTACGTCAAGGCTCTTTAAATATTAATTTTT
193 TAATATTTTAC-GTTAATTCTTACTGCTTTACGTCAAGACTTTTTAAATATTAATTTTT
* * * ** * * * *
1226136 ATCATAATTTTTTTTATCCTTACTATTATTTACACATAAATTAGAATTTTTAAATCGTAAATCAC
1 ATCATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAATTTGT-AATCGTAAAACAC
* * *
1226201 TTTAAACAT-GAGAATAACAATTTAAATGTTTAA-TTTCTTTAAAAATTATGTTTATTAGATATA
65 TTTAAAC-TCGAGAATAA-AATTTAAATGTTTAATTTTC-TCAAAAATTATGTTTATTTGACATA
* * * * ** * * *
1226264 ATTGACTTGTTTCGTTAAGTTTCACATATTTATGTCAAT-TTTTTGAAAATATTTATTCCACATT
127 ATTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTT-AAAATGCTTGTTTCACCTT
* * * ** * * * * * ** * *
1226328 TATAATGTTTTACATTAATTTTTACTATTTTACATTATGAGTATTCT-CCTAATAATTTTC
191 TATAATATTTTACGTTAATTCTTACTGCTTTACGTCAAGACT-TTTTAAATATTAATTTTT
* * * * * *
1226388 ATCGTAATTCTTTTTA-TCTTTAGTTTTTTTC-TGCATA-AGTTAAAAATTGTAAGCGTAAAACA
1 ATCATAATTCTTTTTATTC-TTACTATTATTCATGCATAGA-TTAAAATTTGTAATCGTAAAACA
* * * ** *
1226450 TTTTAAACACGAGAATAAAAGGTTAAATGTTTAATTTTCTCAAAAATTACATTTATTTAACATAA
64 CTTTAAACTCGAGAATAAAA-TTTAAATGTTTAATTTTCTCAAAAATTATGTTTATTTGACATAA
* * * * * * * **
1226515 GTCACTTGTTACGTTCAATCTCACACATGTACGTTAATTTTTTTAAAATGCTTGTTTCATTTTTA
128 TTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTTAAAATGCTTGTTTCACCTTTA
* *
1226580 TAATGTTTTACGTTAATTCTTACTGCTTCACGTCAAGACTTTTTAAATATTAATTTTT
193 TAATATTTTACGTTAATTCTTACTGCTTTACGTCAAGACTTTTTAAATATTAATTTTT
* * * *
1226638 ATTATAATTCTTTTTATTCTTATTATTATTTATGCATAAATTAAAAATTT-TAAATCGTAAAACA
1 ATCATAATTCTTTTTATTCTTACTATTATTCATGCATAGATT-AAAATTTGT-AATCGTAAAACA
* * * *
1226702 -TTATAAA-TGCAATAATAACAATTTAAATGTTTAA-TTTCTTCAAAAATTATATTTATTAGACA
64 CTT-TAAACT-CGAGAATAA-AATTTAAATGTTTAATTTTC-TCAAAAATTATGTTTATTTGACA
* * * * * * *
1226764 TCATTGACTTGTTACGTTAAATCTCACATATTTATGTCAATACTTTTAAAATGCTTGTTCCAACT
125 TAATTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTTAAAATGCTTGTTTCACCT
* * * * * *
1226829 TTATAATATTTTATGTTAATTCTTACCGCTTT-CTATCAA-AGCTTTTTATATGTTAATTTTA
190 TTATAATATTTTACGTTAATTCTTACTGCTTTAC-GTCAAGA-CTTTTTAAATATTAATTTTT
* * * * ** * * * *
1226890 ATCGTAATTCTTTTTATCCTCATTATTGGTCATGTATGGATTAAAATTTTTAAGTTGTAAAACAC
1 ATCATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAATTTGTAA-TCGTAAAACAC
** * * * *
1226955 TTTAAACTAAAAAATAATAATTTAAATGTTTAA-TTTCTCTAAAAATTATATTTATTTGATAAAA
65 TTTAAACTCGAGAATAA-AATTTAAATGTTTAATTTTCTC-AAAAATTATGTTTATTTGACATAA
* ** * * * * * *
1227019 TTGACTTGTTTCG------TT--CAGTTTTACATCAATATTTTAAAAATGTTTATTCCACTTTTA
128 TTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTTAAAATGCTTGTTTCACCTTTA
** * * * * * ** * *
1227076 TAATATTTTACGTTAATT-TCTACTATTTTACATTATGAGTATTCT-CCTAATAATTTTC
193 TAATATTTTACGTTAATTCT-TACTGCTTTACGTCAAGACT-TTTTAAATATTAATTTTT
* * ** * * * * * * *
1227134 ATCGTAATGCTTACTA-TCTTTATTATT-TTTATGCTTA-AGTTAAAAATTGCAAGCGTAAAGCA
1 ATCATAATTCTTTTTATTC-TTACTATTATTCATGCATAGA-TTAAAATTTGTAATCGTAAAACA
* * * *
1227196 -TATTAAGCACGAGAATAAAATGTTAAATGTTTAATTTTTTCAAAAATTATGTTTATTTAACATA
64 CT-TTAAACTCGAGAATAAAAT-TTAAATGTTTAATTTTCTCAAAAATTATGTTTATTTGACATA
* * * * * * *
1227260 ATTAACTTGTTATGTTAAATTTCACATATTTACGTTAAT-TTTTTAAAAATACTTGTTCCA-TTT
127 ATTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTT-AAAATGCTTGTTTCACCTT
* *
1227323 CTATAATGTTTTACGTTAATTCTTA-TCGCTTCACGTCAAGACTTTTTAAATATTAATTTTT
191 -TATAATATTTTACGTTAATTCTTACT-GCTTTACGTCAAGACTTTTTAAATATTAATTTTT
** * * *
1227384 ATTGTAATTCTTTTTATTCTTACTATTATTCATGCATAAATTAAAATTTTTAAGTTGTAAAACAC
1 ATCATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAATTTGTAA-TCGTAAAACAC
* * * *
1227449 TATAAACTTGAGAATAACAATTTAACA-GTTTAA-TTTCTCTAAAAATTATGTTTATTGGACATC
65 TTTAAACTCGAGAATAA-AATTTAA-ATGTTTAATTTTCTC-AAAAATTATGTTTATTTGACATA
* * * * * * *
1227512 ATTGACTTGTTACTTTAAATATCACATATTTACATCAATACTTTTAAAATGCTTATTTCACTTTT
127 ATTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTTAAAATGCTTGTTTCACCTTT
* * * * * * * **
1227577 ATAATGTTTTATGTTAATTTTTACCGCTTTAAGTTAAAACTTTTTAAATGCTAA-TTTT
192 ATAATATTTTACGTTAATTCTTACTGCTTTACGTCAAGACTTTTTAAATATTAATTTTT
* * * *
1227635 AT-AGTAATTTTTTTTA-TCATCACTATTATTCATGTATAGATTAAAATTTGTAAGCCGTAAAAC
1 ATCA-TAATTCTTTTTATTC-TTACTATTATTCATGCATAGATTAAAATTTGTAA-TCGTAAAAC
* * ** *
1227698 ACTTTAAACTCGAGAATAAAAATTTAAATATTTAA-TTTCTCAATAAATTATGTTTAGTAAATAT
63 ACTTTAAACTCGAGAAT-AAAATTTAAATGTTTAATTTTCTCAA-AAATTATGTTTATTTGACAT
* * ** *
1227762 AATTGACTTGTTGCATTAAATCTT-ACACATTTATATCAATATTTTTTAAAATGCTTG-TTCAAT
126 AATTGACTTGTTACGTTAAAT-TTCACACATTTACGTCAATA-TTTTTAAAATGCTTGTTTC-AC
* * ** * * * ** * *
1227825 CTTTCTAATATTCTATATTAATTCTTAATACTTTACGTTAAGGTTTTTTAAATACTAATTTTC
188 CTTTATAATATTTTACGTTAATTCTTACTGCTTTACGTCAAGACTTTTTAAATATTAATTTTT
* * * *** * *
1227888 ATTACAATT-TTTTTATAT-TTATTATTATTCACATATAAATTAAAATTGGTAAGTCGTAAAACA
1 ATCATAATTCTTTTTAT-TCTTACTATTATTCATGCATAGATTAAAATTTGTAA-TCGTAAAACA
1227951 CTT
64 CTT
1227954 AAATATTTAA
Statistics
Matches: 2471, Mismatches: 503, Indels: 200
0.78 0.16 0.06
Matches are distributed among these distances:
241 4 0.00
242 61 0.02
243 22 0.01
244 87 0.04
245 5 0.00
246 1 0.00
248 2 0.00
249 19 0.01
250 336 0.14
251 884 0.36
252 1007 0.41
253 41 0.02
254 2 0.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (250 bp):
ATCATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAATTTGTAATCGTAAAACACT
TTAAACTCGAGAATAAAATTTAAATGTTTAATTTTCTCAAAAATTATGTTTATTTGACATAATTG
ACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTTAAAATGCTTGTTTCACCTTTATAA
TATTTTACGTTAATTCTTACTGCTTTACGTCAAGACTTTTTAAATATTAATTTTT
Found at i:1225556 original size:502 final size:501
Alignment explanation
Indices: 1224608--1227953 Score: 2796
Period size: 502 Copynumber: 6.7 Consensus size: 501
1224598 TAAATTAATA
* * * * *
1224608 ACTTTTCAATTAATAA-TTTCATCATAATTCTTTTTATCCTTACTATTATTCACGCATAAATTAA
1 ACTTTTCAAATAATAATTTTTATCATAATTCTTTTTATTCTTACTATTATTTATGCATAAATTAA
* * * * * *
1224672 AATTTGTAAGTCGTAAAATACTTTAAAC-TCTAGAATAACAATTTTAATATTTAATTTCTCTAAA
66 AATTTGTAAGTCGTAAAACACTTTAAACAT-GAGAATAA-AATTTAAATGTTTAATTT-TTTCAA
* * * * * * *
1224736 AATTATGTCTATTAGATATACTTGATTTGTTACGTTAAATCTCATACATTTAGGTCAATATTTTT
128 AATTATGTTTATTAGATATAATTGACTTGTTACGTTAAATTTCACATATTTATGTCAATATTTTT
** * * *
1224801 AAAATATTTGTTTCACCTTTATAATATTTTACGTTAATTCTTACCGTTTTACATCAAGGTTTTTT
193 AAAATGCTTGTTTCACCTTTATAATATTTTACGTTAATTCTTACTGCTTTACGTCAAGGTTTTTT
** * *
1224866 AAATCCTAATTTTTA-CTATAATTCTTTTTATTCTTACTATTATTCACGCATAAATTAAAATTTG
258 AAATATTAATTTTTATC-ATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAATTTG
* * *
1224930 AAAG-CTGTAAAATAATTTAAACACGAGAATAAAAAGTTAAATGTTTAATTTT-TAAAAAAATTA
322 TAAGTCTGTAAAACACTTTAAACACGAGAAT-AAAAGTTAAATGTTTAATTTTCT--AAAAATTA
* ** * *
1224993 TATTTATTAT-ATATAATTGACTTGTTACGTTAAAACTCATACGTTTACGTCAATATTTTGAAAA
384 TATTTATT-TGACATAATTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTGAAAA
** * ** * *
1225057 CATTTGTTTCACCTTTATAATATTTTACGTAAATTCACACTGCTTTATGTCATG
448 TGTTTGTTTCACTTTTATAATATTTTACGTAAATTCTTACTGCTTTACGTCAAG
* * * *
1225111 ACTTTTCAAGTAATGATTTTTATCATAATTCCTTTTATTCTTACTATTATTTATGCATAGATTAA
1 ACTTTTCAAATAATAATTTTTATCATAATTCTTTTTATTCTTACTATTATTTATGCATAAATTAA
* * * * *
1225176 AATTTATAAGCCGTAAAACACTTTAAACTTGAGAATCAAAAGTTAAATATTTAATTTTTTCAAAA
66 AATTTGTAAGTCGTAAAACACTTTAAACATGAGAAT-AAAATTTAAATGTTTAATTTTTTCAAAA
** * * * * * *
1225241 TTATGTTTATTTCATATAATTTACTTGTTATGTTAAATTTCACACATCTACGTCACTATTTTTAA
130 TTATGTTTATTAGATATAATTGACTTGTTACGTTAAATTTCACATATTTATGTCAATATTTTTAA
* * ** **
1225306 AATGCTTGTTTTACCATTATAATATTTTACGTTAATTCTTACTAATTTACGTCAAAATTTTTTAA
195 AATGCTTGTTTCACCTTTATAATATTTTACGTTAATTCTTACTGCTTTACGTCAAGGTTTTTTAA
* * * **
1225371 ATATTAATTTTTACCATAATT-TTCTTATTCTCACTATTATTCACCCATAGATTAAAATTTGTAA
260 ATATTAATTTTTATCATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAATTTGTAA
* * * * * * *
1225435 -TCTGTAAAATATTTTAAACTCGAGAATAATAATTTAAATGCTTACTTTTCTGAAAAATTATGTT
325 GTCTGTAAAACACTTTAAACACGAGAATAA-AAGTTAAATGTTTAATTTTCT-AAAAATTATATT
* * * *
1225499 TATTTGACATAATTAACTTTTTACGTTAAATTTCACACATTTATGTCAATTTTTTGAAAATGTTT
388 TATTTGACATAATTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTGAAAATGTTT
* * * * * * *
1225564 GTTTCACATTTATAATGTTTTATGTTAATTCCTA-TCGCTTTACATCATG
453 GTTTCACTTTTATAATATTTTACGTAAATTCTTACT-GCTTTACGTCAAG
* * * * * * * *
1225613 ACTTTTTAACTAATAATTTTCATTATAATTCCTTTTA-TCATTACTATTATTCATGTATAGATTA
1 ACTTTTCAAATAATAATTTTTATCATAATTCTTTTTATTC-TTACTATTATTTATGCATAAATTA
* * * * *
1225677 AAATTTGTAAGTCGTAAAAAACTTTAAGCACGAGAATAAAAAGTTGAATGTTTAATTTTTTCAAA
65 AAATTTGTAAGTCGTAAAACACTTTAAACATGAGAAT-AAAATTTAAATGTTTAATTTTTTCAAA
* * * * * * * *
1225742 ATTATGTTTATTTGACATAATTGACTTGTTACATTAAATCTCACTTATTTATATCAACATTTTAA
129 ATTATGTTTATTAGATATAATTGACTTGTTACGTTAAATTTCACATATTTATGTCAATATTTTTA
* * * * ** *
1225807 AAATTCTTGATCCACCTTTATAATGTTTTACGTTAATTCTTACTGCTTTACGTCAAGACTTTTAA
194 AAATGCTTGTTTCACCTTTATAATATTTTACGTTAATTCTTACTGCTTTACGTCAAGGTTTTTTA
* * *
1225872 AATATTAATTTTCATTATAATTCTTTTTA-TCATTACTATTATTCATGTATAGATTAAAATTTGT
259 AATATTAATTTTTATCATAATTCTTTTTATTC-TTACTATTATTCATGCATAGATTAAAATTTGT
* * * * * *
1225936 AAGTC-GTAAAAAACTTTAAGCACGAGAATTAAAAGTTGAATGTTTAATTTTTTCAAAATTATGT
323 AAGTCTGTAAAACACTTTAAACACGAGAA-TAAAAGTTAAATGTTTAATTTTCTAAAAATTATAT
* * * * *
1226000 TTATTTGACATAATTGATTTATTACGTTAAATTTCATAAATTTACATCAATATTTTGAAAATGTT
387 TTATTTGACATAATTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTGAAAATGTT
* ** * *
1226065 TGTTCCTTTTTTATAATATTTT-C-TATTAATCCTTACCGCTTTACGTCAAG
452 TGTTTCACTTTTATAATATTTTACGTA--AATTCTTACTGCTTTACGTCAAG
* * * * **
1226115 GCTCTTT-AAATATTAATTTTTATCATAATTTTTTTTATCCTTACTATTATTTACACATAAATTA
1 ACT-TTTCAAATAATAATTTTTATCATAATTCTTTTTATTCTTACTATTATTTATGCATAAATTA
* * * * *
1226179 GAATTTTTAAATCGTAAATCACTTTAAACATGAGAATAACAATTTAAATGTTTAATTTCTTTAAA
65 AAATTTGTAAGTCGTAAAACACTTTAAACATGAGAATAA-AATTTAAATGTTTAATTT-TTTCAA
* *
1226244 AATTATGTTTATTAGATATAATTGACTTGTTTCGTTAAGTTTCACATATTTATGTCAAT-TTTTT
128 AATTATGTTTATTAGATATAATTGACTTGTTACGTTAAATTTCACATATTTATGTCAATATTTTT
** * * * * * * ** * * * *
1226308 GAAAATATTTATTCCACATTTATAATGTTTTACATTAATTTTTACTATTTTACATTATGAGTATT
193 -AAAATGCTTGTTTCACCTTTATAATATTTTACGTTAATTCTTACTGCTTTACGTCAAG-GTTTT
* ** * * * * * * *
1226373 CT-CCTAATAATTTTCATCGTAATTCTTTTTA-TCTTTAGTTTTTTTC-TGCATA-AGTTAAAAA
256 TTAAATATTAATTTTTATCATAATTCTTTTTATTC-TTACTATTATTCATGCATAGA-TTAAAAT
*
1226434 TTGTAAG-C-GTAAAACATTTTAAACACGAGAATAAAAGGTTAAATGTTTAATTTTCTCAAAAAT
319 TTGTAAGTCTGTAAAACACTTTAAACACGAGAATAAAA-GTTAAATGTTTAATTTTCT-AAAAAT
* * * * * * * * * *
1226497 TACATTTATTTAACATAAGTCACTTGTTACGTTCAATCTCACACATGTACGTTAATTTTTTTAAA
382 TATATTTATTTGACATAATTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTGAAA
* * * * *
1226562 ATGCTTGTTTCATTTTTATAATGTTTTACGTTAATTCTTACTGCTTCACGTCAAG
447 ATGTTTGTTTCACTTTTATAATATTTTACGTAAATTCTTACTGCTTTACGTCAAG
* * * *
1226617 ACTTTTTAAATATTAATTTTTATTATAATTCTTTTTATTCTTATTATTATTTATGCATAAATTAA
1 ACTTTTCAAATAATAATTTTTATCATAATTCTTTTTATTCTTACTATTATTTATGCATAAATT-A
* * *
1226682 AAATTT-TAAATCGTAAAACA--TTATAA-ATGCAATAATAACAATTTAAATGTTTAATTTCTTC
65 AAATTTGTAAGTCGTAAAACACTTTA-AACATG--AGAATAA-AATTTAAATGTTTAATTTTTTC
* * * * *
1226743 AAAAATTATATTTATTAGACATCATTGACTTGTTACGTTAAATCTCACATATTTATGTCAATACT
126 -AAAATTATGTTTATTAGATATAATTGACTTGTTACGTTAAATTTCACATATTTATGTCAATATT
* * * * * * *
1226808 TTTAAAATGCTTGTTCCAACTTTATAATATTTTATGTTAATTCTTACCGCTTT-CTATCAAAGCT
190 TTTAAAATGCTTGTTTCACCTTTATAATATTTTACGTTAATTCTTACTGCTTTAC-GTCAAGGTT
* * * * * * * ** * *
1226872 TTTTATATGTTAATTTTAATCGTAATTCTTTTTATCCTCATTATTGGTCATGTATGGATTAAAAT
254 TTTTAAATATTAATTTTTATCATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAAT
* * * *
1226937 TTTTAAGT-TGTAAAACACTTTAAACTA-AAAAATAATAATTTAAATGTTTAATTTCTCTAAAAA
319 TTGTAAGTCTGTAAAACACTTTAAAC-ACGAGAATAA-AAGTTAAATGTTTAATTT-TCTAAAAA
* * * ** * *
1227000 TTATATTTATTTGATAAAATTGACTTGTTTCG------TT--CAGTTTTACATCAATATTTTAAA
381 TTATATTTATTTGACATAATTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTGAA
* * * ** * * *
1227057 AATGTTTATTCCACTTTTATAATATTTTACGTTAATT-TCTACTATTTTACATTATG
446 AATGTTTGTTTCACTTTTATAATATTTTACGTAAATTCT-TACTGCTTTACGTCAAG
* * *** * * * ** * * *
1227113 AGTATTCTCCTAATAATTTTCATCGTAATGCTTACTA-TCTTTATTATT-TTTATGCTTAAGTTA
1 ACTTTTCAAATAATAATTTTTATCATAATTCTTTTTATTC-TTACTATTATTTATGCATAAATTA
* * * * *
1227176 AAAATTGCAAG-CGTAAAGCA-TATTAAGCACGAGAATAAAATGTTAAATGTTTAATTTTTTCAA
65 AAATTTGTAAGTCGTAAAACACT-TTAAACATGAGAATAAAAT-TTAAATGTTTAATTTTTTC-A
* * * * *
1227239 AAATTATGTTTATTTA-ACATAATTAACTTGTTATGTTAAATTTCACATATTTACGTTAAT-TTT
127 AAATTATGTTTA-TTAGATATAATTGACTTGTTACGTTAAATTTCACATATTTATGTCAATATTT
* * * * * **
1227302 TTAAAAATACTTGTTCCA-TTTCTATAATGTTTTACGTTAATTCTTA-TCGCTTCACGTCAAGAC
191 TT-AAAATGCTTGTTTCACCTT-TATAATATTTTACGTTAATTCTTACT-GCTTTACGTCAAGGT
** *
1227365 TTTTTAAATATTAATTTTTATTGTAATTCTTTTTATTCTTACTATTATTCATGCATAAATTAAAA
253 TTTTTAAATATTAATTTTTATCATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAA
* * ** *
1227430 TTTTTAAGT-TGTAAAACACTATAAACTTGAGAATAACAATTTAACA-GTTTAATTTCTCTAAAA
318 TTTGTAAGTCTGTAAAACACTTTAAACACGAGAATAA-AAGTTAA-ATGTTTAATTT-TCTAAAA
* * * * * * *
1227493 ATTATGTTTATTGGACATCATTGACTTGTTACTTTAAATATCACATATTTACATCAATACTTTT-
380 ATTATATTTATTTGACATAATTGACTTGTTACGTTAAATTTCACACATTTACGTCAATA-TTTTG
* * * * * * * * * *
1227557 AAAATGCTTATTTCACTTTTATAATGTTTTATGTTAATTTTTACCGCTTTAAGTTAAA
444 AAAATGTTTGTTTCACTTTTATAATATTTTACGTAAATTCTTACTGCTTTACGTCAAG
* ** * * * * *
1227615 ACTTTTTAAATGCTAA-TTTTAT-AGTAATTTTTTTTA-TCATCACTATTATTCATGTATAGATT
1 ACTTTTCAAATAATAATTTTTATCA-TAATTCTTTTTATTC-TTACTATTATTTATGCATAAATT
* * *
1227677 AAAATTTGTAAGCCGTAAAACACTTTAAAC-TCGAGAATAAAAATTTAAATATTTAA-TTTCTCA
64 AAAATTTGTAAGTCGTAAAACACTTTAAACAT-GAGAAT-AAAATTTAAATGTTTAATTTTTTC-
* * * * * *
1227740 ATAAATTATGTTTAGTAAATATAATTGACTTGTTGCATTAAATCTT-ACACATTTATATCAATAT
126 A-AAATTATGTTTATTAGATATAATTGACTTGTTACGTTAAAT-TTCACATATTTATGTCAATA-
* * * ** * * *
1227804 TTTTTAAAATGCTTG-TTCAATCTTTCTAATATTCTATATTAATTCTTAATACTTTACGTTAAGG
188 TTTTTAAAATGCTTGTTTC-ACCTTTATAATATTTTACGTTAATTCTTACTGCTTTACGTCAAGG
* * * * * *** *
1227868 TTTTTTAAATACTAATTTTCATTACAATT-TTTTTATAT-TTATTATTATTCACATATAAATTAA
252 TTTTTTAAATATTAATTTTTATCATAATTCTTTTTAT-TCTTACTATTATTCATGCATAGATTAA
*
1227931 AATTGGTAAGTC-GTAAAACACTT
316 AATTTGTAAGTCTGTAAAACACTT
1227954 AAATATTTAA
Statistics
Matches: 2294, Mismatches: 464, Indels: 170
0.78 0.16 0.06
Matches are distributed among these distances:
493 9 0.00
494 268 0.12
495 23 0.01
496 96 0.04
498 1 0.00
500 13 0.01
501 80 0.03
502 1039 0.45
503 512 0.22
504 236 0.10
505 17 0.01
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (501 bp):
ACTTTTCAAATAATAATTTTTATCATAATTCTTTTTATTCTTACTATTATTTATGCATAAATTAA
AATTTGTAAGTCGTAAAACACTTTAAACATGAGAATAAAATTTAAATGTTTAATTTTTTCAAAAT
TATGTTTATTAGATATAATTGACTTGTTACGTTAAATTTCACATATTTATGTCAATATTTTTAAA
ATGCTTGTTTCACCTTTATAATATTTTACGTTAATTCTTACTGCTTTACGTCAAGGTTTTTTAAA
TATTAATTTTTATCATAATTCTTTTTATTCTTACTATTATTCATGCATAGATTAAAATTTGTAAG
TCTGTAAAACACTTTAAACACGAGAATAAAAGTTAAATGTTTAATTTTCTAAAAATTATATTTAT
TTGACATAATTGACTTGTTACGTTAAATTTCACACATTTACGTCAATATTTTGAAAATGTTTGTT
TCACTTTTATAATATTTTACGTAAATTCTTACTGCTTTACGTCAAG
Found at i:1228477 original size:68 final size:68
Alignment explanation
Indices: 1228406--1228534 Score: 204
Period size: 68 Copynumber: 1.9 Consensus size: 68
1228396 TAATTTTCAT
1228406 AAAATTTCTATTATTCTCCTTGTTAGTTTTTTCACTTTAATTAATATATTTTGGTTAATTACTTC
1 AAAATTT-TATTATTCTCCTTGTTAGTTTTTTCACTTTAATTAATATATTTTGGTTAATTACTTC
1228471 GTTA
65 GTTA
* * ** *
1228475 AAAATTTTGTTATTCTCTTTGTTAGTTTTTTTGCTTTAATTAATATTTTTTGGTTAATTA
1 AAAATTTTATTATTCTCCTTGTTAGTTTTTTCACTTTAATTAATATATTTTGGTTAATTA
1228535 ATTCCTTTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
68 48 0.87
69 7 0.13
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.58
Consensus pattern (68 bp):
AAAATTTTATTATTCTCCTTGTTAGTTTTTTCACTTTAATTAATATATTTTGGTTAATTACTTCG
TTA
Found at i:1229540 original size:17 final size:17
Alignment explanation
Indices: 1229518--1229553 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1229508 TTCACATTCA
1229518 CATGATGTAATAAAAGT
1 CATGATGTAATAAAAGT
*
1229535 CATGATGTATTAAAAGT
1 CATGATGTAATAAAAGT
1229552 CA
1 CA
1229554 AACATTGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (17 bp):
CATGATGTAATAAAAGT
Found at i:1240308 original size:167 final size:167
Alignment explanation
Indices: 1240031--1240363 Score: 576
Period size: 167 Copynumber: 2.0 Consensus size: 167
1240021 AATCTTTGGA
1240031 ACCTCTGATATTGAAAATAACAAACAAAGGCTTCCCTCACCCCTAATTAGTTATGGAATTAATCC
1 ACCTCTGATATTGAAAATAACAAACAAAGGCTTCCCTCACCCCTAATTAGTTATGGAATTAATCC
* ** * *
1240096 TGCAAGAAAATTTAGTTGTACACTTTAAAGAATTACTTCGAAGGAAACCAATAGCTTTTCAGTTG
66 TGCAAGAAAATTGAGTCATACACTTTAAAGAAATACTTAGAAGGAAACCAATAGCTTTTCAGTTG
*
1240161 TCTTTCCCCTTTGTTGCACGTTTCTTGCAGATGATGG
131 TCTTTCCCCTTTCTTGCACGTTTCTTGCAGATGATGG
* *
1240198 ACCTCTGATATTGAAAATAACAAACTAAGGCTTCCCTGACCCCTAATTAGTTATGGAATTAATCC
1 ACCTCTGATATTGAAAATAACAAACAAAGGCTTCCCTCACCCCTAATTAGTTATGGAATTAATCC
*
1240263 TGCAAGAAAATTGAGTCATACACTTTAAAGAAATAGTTAGAAGGAAACCAATAGCTTTTCAGTTG
66 TGCAAGAAAATTGAGTCATACACTTTAAAGAAATACTTAGAAGGAAACCAATAGCTTTTCAGTTG
*
1240328 TGTTTCCCCTTTCTTGCACGTTTCTTGCAGATGATG
131 TCTTTCCCCTTTCTTGCACGTTTCTTGCAGATGATG
1240364 ATGTTTCATG
Statistics
Matches: 156, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
167 156 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (167 bp):
ACCTCTGATATTGAAAATAACAAACAAAGGCTTCCCTCACCCCTAATTAGTTATGGAATTAATCC
TGCAAGAAAATTGAGTCATACACTTTAAAGAAATACTTAGAAGGAAACCAATAGCTTTTCAGTTG
TCTTTCCCCTTTCTTGCACGTTTCTTGCAGATGATGG
Found at i:1245606 original size:47 final size:47
Alignment explanation
Indices: 1245535--1245629 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 47
1245525 GTCATTGAAA
1245535 TGGGGTGTTTGACTTGTGACTGCCTAAGAGTTCAGTATCTAGCTGAT
1 TGGGGTGTTTGACTTGTGACTGCCTAAGAGTTCAGTATCTAGCTGAT
* * * *
1245582 TGGGGTTTTTGACTTGTTG-TTGCCTAAGAGTTCAGTATTTATCTGAT
1 TGGGGTGTTTGACTTG-TGACTGCCTAAGAGTTCAGTATCTAGCTGAT
1245629 T
1 T
1245630 CTGGTCTATG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 41 0.95
48 2 0.05
ACGTcount: A:0.18, C:0.13, G:0.27, T:0.42
Consensus pattern (47 bp):
TGGGGTGTTTGACTTGTGACTGCCTAAGAGTTCAGTATCTAGCTGAT
Found at i:1259070 original size:15 final size:15
Alignment explanation
Indices: 1259030--1259072 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1259020 CTTCACAATG
*
1259030 CAATATGATTACAAA
1 CAATATGATTGCAAA
*
1259045 TAATATGATTGCAAA
1 CAATATGATTGCAAA
*
1259060 CAATGTGATTGCA
1 CAATATGATTGCA
1259073 GGGAAGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (15 bp):
CAATATGATTGCAAA
Found at i:1259335 original size:33 final size:33
Alignment explanation
Indices: 1259293--1259372 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
1259283 TGTTAAATAG
*
1259293 TTTATTTTCATTTCTTATTATAATCTTGTATAT
1 TTTATTTTCATTTCTTAATATAATCTTGTATAT
* *
1259326 TTTATTTTCATTTCTTAATATAATTTTTTATAT
1 TTTATTTTCATTTCTTAATATAATCTTGTATAT
1259359 TATATATTTT-ATTT
1 T-T-TATTTTCATTT
1259373 TAATTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 31 0.74
34 5 0.12
35 6 0.14
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.66
Consensus pattern (33 bp):
TTTATTTTCATTTCTTAATATAATCTTGTATAT
Found at i:1265737 original size:2 final size:2
Alignment explanation
Indices: 1265732--1265760 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1265722 TCTCTTCTTT
1265732 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1265761 AAATGACCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1270091 original size:141 final size:141
Alignment explanation
Indices: 1269837--1270114 Score: 412
Period size: 141 Copynumber: 2.0 Consensus size: 141
1269827 GGGTTAAAGA
* * *
1269837 TGAAATGGAGTTTAGAGATGAGTAGAATTATCATAGAATGCAGGATAAACTGATATGATCTCTAG
1 TGAAATGGAATTTAGAGATGAGCAGAATTATCATAGAATGCAGCATAAACTGATATGATCTCTAG
* ** * * *
1269902 TAAGCTTTTAGATTAGAGGGTTTGATACTACATTAACCAAATGTTGCCTATGTGCATGTTATGCC
66 TAAACTTGGAGATTACAGCGTTTGATACTACATTAACCAAATGTTGCCTATGTGAATGTTATGCC
1269967 CTATGTCAGAT
131 CTATGTCAGAT
* * *
1269978 TGAAATGGAATTTAGAGATGAGCAGGATTATCTTAGAATGCAGCATAAACTGATATTATCTCTAG
1 TGAAATGGAATTTAGAGATGAGCAGAATTATCATAGAATGCAGCATAAACTGATATGATCTCTAG
** *
1270043 TAAACTTGGAGATTACAGCGTTTGATACTACATTAACCAGTTGTTGCCTATGTGAATGTTATGTC
66 TAAACTTGGAGATTACAGCGTTTGATACTACATTAACCAAATGTTGCCTATGTGAATGTTATGCC
*
1270108 CTGTGTC
131 CTATGTC
1270115 TATCTGATAC
Statistics
Matches: 121, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
141 121 1.00
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.34
Consensus pattern (141 bp):
TGAAATGGAATTTAGAGATGAGCAGAATTATCATAGAATGCAGCATAAACTGATATGATCTCTAG
TAAACTTGGAGATTACAGCGTTTGATACTACATTAACCAAATGTTGCCTATGTGAATGTTATGCC
CTATGTCAGAT
Found at i:1278533 original size:62 final size:61
Alignment explanation
Indices: 1278425--1278602 Score: 153
Period size: 62 Copynumber: 2.9 Consensus size: 61
1278415 ATTGTAGGAG
** * ** * * **
1278425 TAAAATTATAAAATTTAAAAAAAATAAAAATATGTTAGGAT-GATTTAAACATTTTATTAAGA
1 TAAAATTATAAAATTTTTAAAAAATAAAAACAAATTA-TATAAATTTAAA-ATTTTAAAAAGA
*
1278487 TAAAATTATAAAATTTTTAAAAAATAAAAACAAATTATATAAATTTAAAAATTATTAAAAATA
1 TAAAATTATAAAATTTTTAAAAAATAAAAACAAATTATATAAATTT-AAAATT-TTAAAAAGA
* * * * * *
1278550 TGAAATGATAAAATTTTTTAAAATTATAAATC-AATTATAAAAATTTAAAATTT
1 TAAAATTATAAAATTTTTAAAAAATA-AAAACAAATTATATAAATTTAAAATTT
1278603 ATTGAAGGGG
Statistics
Matches: 96, Mismatches: 16, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
61 3 0.03
62 45 0.47
63 44 0.46
64 4 0.04
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (61 bp):
TAAAATTATAAAATTTTTAAAAAATAAAAACAAATTATATAAATTTAAAATTTTAAAAAGA
Found at i:1278561 original size:26 final size:25
Alignment explanation
Indices: 1278523--1278580 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
1278513 AAAACAAATT
*
1278523 ATATAAAT-TTAAAAATTATTAAAA
1 ATATAAATGATAAAAATTATTAAAA
* *
1278547 ATATGAAATGATAAAATTTTTTAAAA
1 ATAT-AAATGATAAAAATTATTAAAA
*
1278573 TTATAAAT
1 ATATAAAT
1278581 CAATTATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 4 0.14
25 8 0.29
26 16 0.57
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (25 bp):
ATATAAATGATAAAAATTATTAAAA
Found at i:1280363 original size:21 final size:21
Alignment explanation
Indices: 1280326--1280366 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1280316 ATGGCAACAG
*
1280326 TATAATGTAGTAAATACTATA
1 TATAATGTAGAAAATACTATA
1280347 TATAATGTA-AAATATACTAT
1 TATAATGTAGAAA-ATACTAT
1280367 GATCTAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (21 bp):
TATAATGTAGAAAATACTATA
Found at i:1281109 original size:16 final size:17
Alignment explanation
Indices: 1281088--1281119 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1281078 TACTTTTCAA
1281088 ATATATATA-TTTGTAT
1 ATATATATAGTTTGTAT
1281104 ATATATATAGTTTGTA
1 ATATATATAGTTTGTA
1281120 ATTGCTACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (17 bp):
ATATATATAGTTTGTAT
Found at i:1290919 original size:3 final size:3
Alignment explanation
Indices: 1290913--1290939 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1290903 CTACTACTAC
1290913 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1290940 AAATGCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1292199 original size:2 final size:2
Alignment explanation
Indices: 1292153--1292180 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1292143 CTAAAATCGT
1292153 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1292181 AACATATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1294890 original size:12 final size:12
Alignment explanation
Indices: 1294857--1294895 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1294847 AGAAATGAAC
* *
1294857 AGAGAAAAAGAC
1 AGAGAAAGAGAG
*
1294869 AGAGAGAGAGAG
1 AGAGAAAGAGAG
1294881 AGAGAAAGAGAG
1 AGAGAAAGAGAG
1294893 AGA
1 AGA
1294896 CGGAGAGGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.59, C:0.03, G:0.38, T:0.00
Consensus pattern (12 bp):
AGAGAAAGAGAG
Found at i:1295677 original size:16 final size:17
Alignment explanation
Indices: 1295656--1295688 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1295646 AAATTTTATT
1295656 AATATTTATAAT-AAAA
1 AATATTTATAATGAAAA
*
1295672 AATATTTTTAATGAAAA
1 AATATTTATAATGAAAA
1295689 TCAATCAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AATATTTATAATGAAAA
Found at i:1295709 original size:82 final size:81
Alignment explanation
Indices: 1295600--1295835 Score: 253
Period size: 82 Copynumber: 2.9 Consensus size: 81
1295590 GAAAAAAATT
* *
1295600 ATGAAAGTCATTCAATACAATTGGAATTCTTATTTACAAAATGGATAAATTTTATTAATATTTAT
1 ATGAAAGTCATTCAATGCAATTAGAATTCTTATTTACAAAAT-GATAAATTTTATTAATATTTAT
*
1295665 AATAAAAAATATTTTTA
65 AATAAAAAATAATTTTA
* * ** *
1295682 ATGAAAATCAATCAATGCAATTAGAATTCTTATTTACACATAA-GATAAATCGTATTTATATTTA
1 ATGAAAGTCATTCAATGCAATTAGAATTCTTATTTACA-A-AATGATAAATTTTATTAATATTTA
* *
1295746 TAATGAAATATAATTTTA
64 TAATAAAAAATAATTTTA
* * * * * *
1295764 GTGAAAGGCATTCAAAGCAAGTAGAATAT-TTATTTATAAATTGA-AAATTTTTTATTAATATTT
1 ATGAAAGTCATTCAATGCAATTAGAAT-TCTTATTTACAAAATGATAAA--TTTTATTAATATTT
1295827 ATAATAAAA
63 ATAATAAAA
1295836 GTCGTTTTAT
Statistics
Matches: 126, Mismatches: 22, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
80 4 0.03
81 3 0.02
82 115 0.91
83 2 0.02
84 2 0.02
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (81 bp):
ATGAAAGTCATTCAATGCAATTAGAATTCTTATTTACAAAATGATAAATTTTATTAATATTTATA
ATAAAAAATAATTTTA
Found at i:1309872 original size:2 final size:2
Alignment explanation
Indices: 1309865--1309902 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1309855 GCCTGATACA
1309865 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1309903 TCCAGTCATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1311043 original size:46 final size:45
Alignment explanation
Indices: 1310964--1311057 Score: 125
Period size: 46 Copynumber: 2.1 Consensus size: 45
1310954 AATTCCAGAC
* * **
1310964 TAATATGGCGTAAATATATCGTGGTGATGTATTAAAGAGTTTCTTT
1 TAATATGGCATAAATATATCATGGTGACATATTAAAGAGTTT-TTT
* *
1311010 TAATCTGGCATAAATATATCATGGTGACATATTAAGGAGTTTTTT
1 TAATATGGCATAAATATATCATGGTGACATATTAAAGAGTTTTTT
1311055 TAA
1 TAA
1311058 GTCTATACAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 6 0.14
46 36 0.86
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.40
Consensus pattern (45 bp):
TAATATGGCATAAATATATCATGGTGACATATTAAAGAGTTTTTT
Found at i:1312791 original size:3 final size:3
Alignment explanation
Indices: 1312785--1312857 Score: 58
Period size: 3 Copynumber: 24.3 Consensus size: 3
1312775 GTAGTATTCG
* * * * * * *
1312785 TCT TCT TCT TCT TCC TCC TCC TCT TCT TCC TCT TCC CCT TCG TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
1312833 TCT TCT TCT TC- TCTT TCT TCC TCT T
1 TCT TCT TCT TCT TC-T TCT TCT TCT T
1312858 GCTCTGCGTC
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.93
4 2 0.04
ACGTcount: A:0.00, C:0.42, G:0.01, T:0.56
Consensus pattern (3 bp):
TCT
Found at i:1312809 original size:21 final size:21
Alignment explanation
Indices: 1312785--1312840 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
1312775 GTAGTATTCG
1312785 TCTTCTTCTTCTTCCTCC-TCC
1 TCTTCTTCTTCTTCC-CCTTCC
* *
1312806 TCTTCTTCCTCTTCCCCTTCG
1 TCTTCTTCTTCTTCCCCTTCC
1312827 TCTTCTTCTTCTTC
1 TCTTCTTCTTCTTC
1312841 TTCTCTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.00, C:0.45, G:0.02, T:0.54
Consensus pattern (21 bp):
TCTTCTTCTTCTTCCCCTTCC
Found at i:1312825 original size:15 final size:15
Alignment explanation
Indices: 1312785--1312847 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 15
1312775 GTAGTATTCG
*
1312785 TCTTCTTCTTCTTCC
1 TCTTCCTCTTCTTCC
*
1312800 TCCTCCTCTTCTTCC
1 TCTTCCTCTTCTTCC
* * *
1312815 TCTTCCCCTTCGTCT
1 TCTTCCTCTTCTTCC
*
1312830 TCTTCTTCTTCTT-C
1 TCTTCCTCTTCTTCC
1312844 TCTT
1 TCTT
1312848 TCTTCCTCTT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
14 4 0.11
15 34 0.89
ACGTcount: A:0.00, C:0.43, G:0.02, T:0.56
Consensus pattern (15 bp):
TCTTCCTCTTCTTCC
Found at i:1313540 original size:29 final size:29
Alignment explanation
Indices: 1313485--1313542 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
1313475 AATATATCTT
* * *
1313485 TTTTTATTATATTTAATTAAATATTTATA
1 TTTTTATTATAATCAAATAAATATTTATA
1313514 TTTTTATTTATAATCAAATAAAT-TTTATA
1 TTTTTA-TTATAATCAAATAAATATTTATA
1313543 ATTAATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTTATTATAATCAAATAAATATTTATA
Found at i:1322374 original size:6 final size:6
Alignment explanation
Indices: 1322365--1322399 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1322355 ACTACTACTG
* *
1322365 CTCCCA CTCCCG CTCCCA CTTCCA CTCCCA CTCCC
1 CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCCC
1322400 GCTACTCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.11, C:0.66, G:0.03, T:0.20
Consensus pattern (6 bp):
CTCCCA
Found at i:1322381 original size:12 final size:12
Alignment explanation
Indices: 1322364--1322402 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1322354 CACTACTACT
1322364 GCTCCCACTCCC
1 GCTCCCACTCCC
*
1322376 GCTCCCACTTCC
1 GCTCCCACTCCC
*
1322388 ACTCCCACTCCC
1 GCTCCCACTCCC
1322400 GCT
1 GCT
1322403 ACTCTCACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.10, C:0.62, G:0.08, T:0.21
Consensus pattern (12 bp):
GCTCCCACTCCC
Found at i:1322392 original size:24 final size:27
Alignment explanation
Indices: 1322365--1322417 Score: 85
Period size: 24 Copynumber: 2.1 Consensus size: 27
1322355 ACTACTACTG
1322365 CTCCCACTCCCGCT-C-C-CACTTCCA
1 CTCCCACTCCCGCTACTCTCACTTCCA
1322389 CTCCCACTCCCGCTACTCTCACTTCCA
1 CTCCCACTCCCGCTACTCTCACTTCCA
1322416 CT
1 CT
1322418 GCTACTGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 14 0.54
25 1 0.04
26 1 0.04
27 10 0.38
ACGTcount: A:0.13, C:0.58, G:0.04, T:0.25
Consensus pattern (27 bp):
CTCCCACTCCCGCTACTCTCACTTCCA
Found at i:1337788 original size:93 final size:93
Alignment explanation
Indices: 1337629--1337912 Score: 439
Period size: 93 Copynumber: 3.1 Consensus size: 93
1337619 CAGCACAAAC
* * *
1337629 AATGTTGTGGAACATGTCCCTCATGTTTTGGCTGTATCACTACCACTCATACCTACTTTTTGTAT
1 AATGTTGTGGAACATGTCCCTCATGTTTTGGCTGCATCACTACCACTCATATCTAGTTTTTGTAT
*
1337694 ACAGGTTTAAAGATATGAAATCATTTTT
66 ACAGGTTTAAAGAAATGAAATCATTTTT
* *
1337722 AATGTTGCT-GAACATGCCCCTCATGTTTTGGCGGCATCACTACCACTCATATCTAGTTTTTGTA
1 AATGTTG-TGGAACATGTCCCTCATGTTTTGGCTGCATCACTACCACTCATATCTAGTTTTTGTA
*
1337786 TACAGTTTTAAAGAAATGAAATCATTTTT
65 TACAGGTTTAAAGAAATGAAATCATTTTT
* *
1337815 AATGTTGTGGAACACGTCCCTCATGTTTTGGCTGCATCACTACCACTCAT-TCCCAGTTTTTGTA
1 AATGTTGTGGAACATGTCCCTCATGTTTTGGCTGCATCACTACCACTCATAT-CTAGTTTTTGTA
1337879 TACA-GTTGTAAAGAAATGAAATCATTTTT
65 TACAGGTT-TAAAGAAATGAAATCATTTTT
1337908 AATGT
1 AATGT
1337913 CTTTAACAAA
Statistics
Matches: 175, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
92 4 0.02
93 170 0.97
94 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (93 bp):
AATGTTGTGGAACATGTCCCTCATGTTTTGGCTGCATCACTACCACTCATATCTAGTTTTTGTAT
ACAGGTTTAAAGAAATGAAATCATTTTT
Found at i:1341588 original size:2 final size:2
Alignment explanation
Indices: 1341581--1341625 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1341571 AGTGTTTCAT
1341581 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1341623 TA T
1 TA T
1341626 GGGGTAAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1347073 original size:60 final size:61
Alignment explanation
Indices: 1347000--1347120 Score: 181
Period size: 61 Copynumber: 2.0 Consensus size: 61
1346990 ACGTTAAAGA
* * *
1347000 GTTTGAGATTGTTTCAAATA-CTTAGTAAAAATGAATGAGTCAAAGGCTGAGGTAAAAAAT
1 GTTTGAGACTGTTTCAAATATCTTAGTAAAAAGGAATGAGTCAAAGGCTAAGGTAAAAAAT
* * *
1347060 GTTTGAGACTGTTTCAACTATTTTAGTAAAAAGGAATGAGTTAAAGGCTAAGGTAAAAAAT
1 GTTTGAGACTGTTTCAAATATCTTAGTAAAAAGGAATGAGTCAAAGGCTAAGGTAAAAAAT
1347121 AAATAAAACT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
60 18 0.33
61 36 0.67
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (61 bp):
GTTTGAGACTGTTTCAAATATCTTAGTAAAAAGGAATGAGTCAAAGGCTAAGGTAAAAAAT
Found at i:1349064 original size:15 final size:14
Alignment explanation
Indices: 1349044--1349073 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1349034 TTTCCTTTAG
1349044 ATTTATATATTATAA
1 ATTTATATA-TATAA
1349059 ATTTATATATATAA
1 ATTTATATATATAA
1349073 A
1 A
1349074 AAAAAGGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTATATATATAA
Found at i:1349261 original size:21 final size:21
Alignment explanation
Indices: 1349142--1349261 Score: 59
Period size: 21 Copynumber: 5.6 Consensus size: 21
1349132 CACAAAATAG
* * * *
1349142 AAAGTAAATATATTTTTATTT
1 AAAGTATATATATATATATAT
* *
1349163 AAAGTACATATAGATATATACT
1 AAAGTATATATATATATATA-T
*
1349185 AAAAGTAT-TTTA-ATATATAT
1 -AAAGTATATATATATATATAT
* *
1349205 AATAGTA-AT-TATATTCTTTAT
1 AA-AGTATATATATA-TATATAT
* *
1349226 AAATGAATCTGATATATATATAT
1 AAA-GTATAT-ATATATATATAT
1349249 AAAGTATATATAT
1 AAAGTATATATAT
1349262 TAAACGACAT
Statistics
Matches: 74, Mismatches: 15, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
19 4 0.05
20 8 0.11
21 35 0.47
22 9 0.12
23 14 0.19
24 4 0.05
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (21 bp):
AAAGTATATATATATATATAT
Found at i:1349501 original size:337 final size:329
Alignment explanation
Indices: 1348756--1349612 Score: 961
Period size: 337 Copynumber: 2.6 Consensus size: 329
1348746 TATTTCAAAC
* *
1348756 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATATTAACACAAAATA-AAA-AAAATATGTT
1 ATAATTAATAATTTTATAAGTTATAA-TTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTT
*
1348819 TATATTTAAAGC---GCATATATACTCAAAGTATTTTAATATATATATACAATAGTAATTATATT
65 TATATTTAAAGCTATG-ATATATACTAAAAGTATTTT-ATATATATAT--AATAGTAATTATATT
*
1348881 TCTTATAAATGAACCCAATGTATATAAAGTATATATATTAAACGACATTACAAG---TTAATAAT
126 T-TTATAAATGAA--CAATATATATAAAGTATATATATTAAACGACATTACAAGTAATTAATAAT
* * * *
1348943 CATAGTTTTATTAATTAATTTAATTAACTATATGAGTTTGTCCTTAATTACATGAAATTAAAGAA
188 CATAGTTTCATAAATTAATTTAATTAACTATATGAGTTTATCCTTAATTACATAAAATTAAAGAA
* *
1349008 AATAACTATGTTTCAAATCTCACAACTTTCCTTTAGATTTATATATTATAAATTTATATATATAA
253 AATAACTAGGTTTCAAA---CACAAC-TTCC-TTAGATTCATATATTAT-AATTTATATATATAA
1349073 AAAAAAGGTATATATATT
312 AAAAAAGGTATATATATT
* * *
1349091 GTAATTAATAATTTTATAAGTTGTAATGTTTGTAATGTTAACACAAAATAGAAAGTAAATATATT
1 ATAATTAATAATTTTATAAGTTATAAT-TTTGTAATGTTAACACAAAATAGAAAGTAAATATGTT
*
1349156 TTTATTTAAAGTACATATAGATATATACTAAAAGTATTTTA-ATATATATAATAGTAATTATATT
65 TATATTTAAAG--C-TAT-GATATATACTAAAAGTATTTTATATATATATAATAGTAATTATATT
1349220 CTTTATAAATGAATCTGATATATATATATAAAGTATATATATTAAACGACATTACAAAGTAATTA
126 -TTTATAAATGAA-C----A-ATATATATAAAGTATATATATTAAACGACATTAC-AAGTAATTA
* *
1349285 ATAATTATAGTTTCATAAATTAATTTAATTAAGTATATGAGTTTATCCTTAATTACATAAAATTA
183 ATAATCATAGTTTCATAAATTAATTTAATTAACTATATGAGTTTATCCTTAATTACATAAAATTA
* * * *
1349350 AA-AAAATTAACTAGGTTTCAAA-ACTA-TT-C-TA-ATCTCATA-ACTTCT-CTTTA-AGTTTA
248 AAGAAAA-TAACTAGGTTTCAAACACAACTTCCTTAGAT-TCATATA-TTATAATTTATA-TATA
*
1349406 TATAAATAAAGGTATATATATT
309 TA-AAAAAAAGGTATATATATT
* * *
1349428 ATAATTAATAATTCTATAAATTATAACTTTTGTAATGTTAACATAAAATAGAAAGTAAATATGTT
1 ATAATTAATAATTTTATAAGTTATAA-TTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTT
*
1349493 TATATTTAAAG-TAT-ATATAT--TAAAAGTATTTTAGTATATATATAATTGTAATTATATTTTT
65 TATATTTAAAGCTATGATATATACTAAAAGTATTTTA-TATATATATAATAGTAATTATATTTTT
* * *
1349554 GATAAATTAACACA-ATATATAAACTATAGATATTAAA-GACATTACAAGTTAATTAATAA
129 -ATAAATGAACA-ATATATATAAAGTATATATATTAAACGACATTACAAG-TAATTAATAA
1349613 GGGTAAAATA
Statistics
Matches: 458, Mismatches: 34, Indels: 71
0.81 0.06 0.13
Matches are distributed among these distances:
323 3 0.01
324 18 0.04
325 21 0.05
326 2 0.00
329 13 0.03
330 4 0.01
331 36 0.08
333 3 0.01
334 1 0.00
335 46 0.10
336 12 0.03
337 106 0.23
338 11 0.02
339 27 0.06
340 2 0.00
341 10 0.02
342 2 0.00
343 55 0.12
344 4 0.01
346 4 0.01
347 78 0.17
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (329 bp):
ATAATTAATAATTTTATAAGTTATAATTTTGTAATGTTAACACAAAATAGAAAGTAAATATGTTT
ATATTTAAAGCTATGATATATACTAAAAGTATTTTATATATATATAATAGTAATTATATTTTTAT
AAATGAACAATATATATAAAGTATATATATTAAACGACATTACAAGTAATTAATAATCATAGTTT
CATAAATTAATTTAATTAACTATATGAGTTTATCCTTAATTACATAAAATTAAAGAAAATAACTA
GGTTTCAAACACAACTTCCTTAGATTCATATATTATAATTTATATATATAAAAAAAAGGTATATA
TATT
Found at i:1349906 original size:19 final size:19
Alignment explanation
Indices: 1349862--1349913 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
1349852 GAGTTTTTTT
1349862 TTTTAAAATTAATAAAAAA
1 TTTTAAAATTAATAAAAAA
** *
1349881 TAATAAAATT-ATATAATAA
1 TTTTAAAATTAATA-AAAAA
1349900 TTTTAAAAATTAAT
1 TTTT-AAAATTAAT
1349914 TAATGATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 3 0.12
19 14 0.56
20 6 0.24
21 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTTAAAATTAATAAAAAA
Found at i:1350281 original size:16 final size:15
Alignment explanation
Indices: 1350247--1350284 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1350237 GGTATATGTA
1350247 TTATAATTAATAATT
1 TTATAATTAATAATT
1350262 TTATAAGTT-ATAATTT
1 TTATAA-TTAATAA-TT
1350278 TTATAAT
1 TTATAAT
1350285 GCTAACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATAATTAATAATT
Found at i:1351345 original size:17 final size:17
Alignment explanation
Indices: 1351323--1351355 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1351313 TTATTTCTTA
1351323 TTTTTC-TTTCTATTTTG
1 TTTTTCATTT-TATTTTG
1351340 TTTTTCATTTTATTTT
1 TTTTTCATTTTATTTT
1351356 TTATCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTCATTTTATTTTG
Found at i:1353355 original size:20 final size:19
Alignment explanation
Indices: 1353330--1353374 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
1353320 TTTTATTTTT
1353330 AAAATTAAAAAATAATTCTA
1 AAAATTAAAAAATAATT-TA
*
1353350 AAAATTTTAAAAATAATTTA
1 AAAA-TTAAAAAATAATTTA
1353370 AAAAT
1 AAAAT
1353375 CTGGGAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 10 0.43
21 12 0.52
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTAAAAAATAATTTA
Found at i:1353373 original size:11 final size:11
Alignment explanation
Indices: 1353332--1353374 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
1353322 TTATTTTTAA
*
1353332 AATTAAAAAAT
1 AATTTAAAAAT
1353343 AATTCTAAAAAT
1 AATT-TAAAAAT
1353355 --TTTAAAAAT
1 AATTTAAAAAT
1353364 AATTTAAAAAT
1 AATTTAAAAAT
1353375 CTGGGAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
9 7 0.25
10 2 0.07
11 13 0.46
12 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
AATTTAAAAAT
Found at i:1359394 original size:19 final size:18
Alignment explanation
Indices: 1359370--1359405 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1359360 TAGTTGTTCT
*
1359370 GCATATCATACACCAAGTA
1 GCATATCAAACA-CAAGTA
1359389 GCATATCAAACACAAGT
1 GCATATCAAACACAAGT
1359406 GTTTCCTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.19
Consensus pattern (18 bp):
GCATATCAAACACAAGTA
Found at i:1360481 original size:17 final size:17
Alignment explanation
Indices: 1360458--1360509 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
1360448 AGTTGAGACC
1360458 TATCAAAAATATT-ATT
1 TATCAAAAATATTAATT
*
1360474 TAATCAAAATTATTAATT
1 T-ATCAAAAATATTAATT
1360492 TATC--AAATATTAATT
1 TATCAAAAATATTAATT
1360507 TAT
1 TAT
1360510 AAAGGTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 13 0.41
16 1 0.03
17 14 0.44
18 4 0.12
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (17 bp):
TATCAAAAATATTAATT
Found at i:1360504 original size:15 final size:16
Alignment explanation
Indices: 1360458--1360509 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 16
1360448 AGTTGAGACC
1360458 TATCAAAAATATT-ATT
1 TATC-AAAATATTAATT
1360474 TAATCAAAATTATTAATT
1 T-ATCAAAA-TATTAATT
1360492 TATC-AAATATTAATT
1 TATCAAAATATTAATT
1360507 TAT
1 TAT
1360510 AAAGGTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
15 11 0.33
16 8 0.24
17 10 0.30
18 4 0.12
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (16 bp):
TATCAAAATATTAATT
Found at i:1364340 original size:25 final size:25
Alignment explanation
Indices: 1364308--1364367 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 25
1364298 TATACAAATT
*
1364308 AAAT-TTTTCCTTAAAAAACTGATA
1 AAATGTTTTCCTTAAAAAACTAATA
* *
1364332 AAATGTTTT-CGTAAAAAAGTAATA
1 AAATGTTTTCCTTAAAAAACTAATA
*
1364356 AAATGGTTTCCT
1 AAATGTTTTCCT
1364368 ATCTCTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (25 bp):
AAATGTTTTCCTTAAAAAACTAATA
Found at i:1381556 original size:25 final size:23
Alignment explanation
Indices: 1381510--1381569 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
1381500 TAACACGATT
1381510 AAATAAA-AA-TATTTACAATTA
1 AAATAAATAATTATTTACAATTA
*
1381531 AATATAATTATATTATTTA-AATTTA
1 AA-ATAAATA-ATTATTTACAA-TTA
1381556 AAATAAATAATTAT
1 AAATAAATAATTAT
1381570 AAAAACAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 2 0.06
22 4 0.12
23 6 0.19
24 9 0.28
25 11 0.34
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATAAATAATTATTTACAATTA
Found at i:1381798 original size:18 final size:18
Alignment explanation
Indices: 1381777--1381823 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1381767 GTATACACGT
1381777 TTAAACATGATAATACAA
1 TTAAACATGATAATACAA
* * * *
1381795 TTAAACACGTTTATACAT
1 TTAAACATGATAATACAA
1381813 TTAAACATGAT
1 TTAAACATGAT
1381824 TAACATGATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (18 bp):
TTAAACATGATAATACAA
Found at i:1382340 original size:42 final size:44
Alignment explanation
Indices: 1382294--1382393 Score: 132
Period size: 42 Copynumber: 2.3 Consensus size: 44
1382284 ATAATGATAA
* * * *
1382294 ATTTATCATTTATATATTAATATT-TTAAAATAATATAT-TTTT
1 ATTTATAATTTAAATATTAACATTGTTAAAATAATAAATGTTTT
* *
1382336 ATTTATAATTTAAATATTAACATTGTTAACATATTAAATGTTTT
1 ATTTATAATTTAAATATTAACATTGTTAAAATAATAAATGTTTT
1382380 ATTTATAATTTAAA
1 ATTTATAATTTAAA
1382394 CGTTATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 21 0.42
43 11 0.22
44 18 0.36
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (44 bp):
ATTTATAATTTAAATATTAACATTGTTAAAATAATAAATGTTTT
Found at i:1382414 original size:44 final size:43
Alignment explanation
Indices: 1382318--1382422 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 43
1382308 TATTAATATT
* * * **
1382318 TTAAAATAATATATTTTTATTTATAATTTAAATATTAACATTG
1 TTAAAATATTAAATTTTTATTTATAATTTAAACATTAACATAA
* * **
1382361 TTAACATATTAAATGTTTTATTTATAATTTAAACGTTATTATAA
1 TTAAAATATTAAAT-TTTTATTTATAATTTAAACATTAACATAA
1382405 TTAAAATATTAAGATTTT
1 TTAAAATATTAA-ATTTT
1382423 ATAATAAAAC
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
43 11 0.22
44 37 0.74
45 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (43 bp):
TTAAAATATTAAATTTTTATTTATAATTTAAACATTAACATAA
Found at i:1382445 original size:22 final size:22
Alignment explanation
Indices: 1382399--1382445 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
1382389 TTAAACGTTA
*
1382399 TTATAATTAAAATATTAAGATT
1 TTATAATTAAAATATTAAGAGT
1382421 TTATAA-TAAAACTA-TATAGAGT
1 TTATAATTAAAA-TATTA-AGAGT
1382443 TTA
1 TTA
1382446 GAGAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (22 bp):
TTATAATTAAAATATTAAGAGT
Found at i:1387017 original size:18 final size:18
Alignment explanation
Indices: 1386994--1387028 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1386984 AACTCTTATA
*
1386994 ACTAATAGTTCATTAATG
1 ACTAATAATTCATTAATG
*
1387012 ACTAATAATTGATTAAT
1 ACTAATAATTCATTAAT
1387029 TATCTTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (18 bp):
ACTAATAATTCATTAATG
Found at i:1388296 original size:6 final size:6
Alignment explanation
Indices: 1388285--1388309 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1388275 TCAAACGCAA
1388285 CACAAT CACAAT CACAAT CACAAT C
1 CACAAT CACAAT CACAAT CACAAT C
1388310 GTAGAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:1404576 original size:21 final size:20
Alignment explanation
Indices: 1404550--1404592 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
1404540 TTCTCTATTC
*
1404550 TTTTTTATCTTTCTTTGTTTTT
1 TTTTTTA-CTTT-TTTCTTTTT
1404572 TTTTTTACTTTTTTCTTTTT
1 TTTTTTACTTTTTTCTTTTT
1404592 T
1 T
1404593 CTATAACTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 4 0.20
22 7 0.35
ACGTcount: A:0.05, C:0.09, G:0.02, T:0.84
Consensus pattern (20 bp):
TTTTTTACTTTTTTCTTTTT
Found at i:1404806 original size:20 final size:22
Alignment explanation
Indices: 1404757--1404807 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 22
1404747 TAACGAATTA
1404757 TATATTAACCATTCATGTGAAATCT
1 TATATTAACCATTCATGT---ATCT
1404782 TATATTAACCATTCATGT-T-T
1 TATATTAACCATTCATGTATCT
1404802 TATATT
1 TATATT
1404808 TAATATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 7 0.27
21 1 0.04
25 18 0.69
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (22 bp):
TATATTAACCATTCATGTATCT
Found at i:1408163 original size:18 final size:19
Alignment explanation
Indices: 1408113--1408164 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
1408103 TTATAATAAA
*
1408113 AAAAATATAA-TATTTATG
1 AAAAATTTAATTATTTATG
1408131 AAAAATTTATGAATTATTTAT-
1 AAAAA-TT-T-AATTATTTATG
1408152 AAAAATTTAATTA
1 AAAAATTTAATTA
1408165 AATTCTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 10 0.34
19 2 0.07
20 3 0.10
21 7 0.24
22 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
AAAAATTTAATTATTTATG
Found at i:1410399 original size:29 final size:30
Alignment explanation
Indices: 1410348--1410411 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
1410338 AAATTAAGTC
* *
1410348 TTTATATTTTTATTTTGATTTAAATAAATT
1 TTTATATTTTTATTTTAAGTTAAATAAATT
1410378 TTTATA-TTTTATTTTAAGTTAAATAAATT
1 TTTATATTTTTATTTTAAGTTAAATAAATT
1410407 TTTAT
1 TTTAT
1410412 GATTAATGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTATATTTTTATTTTAAGTTAAATAAATT
Found at i:1419421 original size:16 final size:16
Alignment explanation
Indices: 1419400--1419430 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1419390 TTACTCAAAT
1419400 TGTCATTGTCATTTTG
1 TGTCATTGTCATTTTG
1419416 TGTCATTGTCATTTT
1 TGTCATTGTCATTTT
1419431 AAGAGAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (16 bp):
TGTCATTGTCATTTTG
Found at i:1420052 original size:63 final size:64
Alignment explanation
Indices: 1419975--1420097 Score: 212
Period size: 66 Copynumber: 1.9 Consensus size: 64
1419965 TATATATATA
*
1419975 TTTGTAATATTTGATTGATTAC-GTAATAATTTTTCATATAAATAAGATTTTCAAGATTTTTTT
1 TTTGTAATATTTGATTGATTACAATAATAATTTTTCATATAAATAAGATTTTCAAGATTTTTTT
1420038 TTTGTAATATTTGATTGATTACATAATAATAATTTTTCATATAAATAAGATTTTCAAGAT
1 TTTGTAATATTTGATTGATTAC--AATAATAATTTTTCATATAAATAAGATTTTCAAGAT
1420098 ACAAATAATA
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
63 22 0.39
66 34 0.61
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.50
Consensus pattern (64 bp):
TTTGTAATATTTGATTGATTACAATAATAATTTTTCATATAAATAAGATTTTCAAGATTTTTTT
Found at i:1420403 original size:2 final size:2
Alignment explanation
Indices: 1420396--1420421 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1420386 CAAGATGATT
1420396 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1420422 CACATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1421041 original size:49 final size:48
Alignment explanation
Indices: 1420949--1421050 Score: 143
Period size: 49 Copynumber: 2.1 Consensus size: 48
1420939 TATAATTATT
* * *
1420949 TTATTATATATATTAATAATGAATATATCATTTTTGTTATTTATTGTTA
1 TTATTACATATATTAATAATAAATATATCATTATTGTTATTTATT-TTA
*
1420998 TTATTACATATATTAATAATAAATATATCA-TATTGTTATTTTATTTTG
1 TTATTACATATATTAATAATAAATATATCATTATTGTTA-TTTATTTTA
1421046 TTATT
1 TTATT
1421051 GTTTTATTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
48 14 0.29
49 34 0.71
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (48 bp):
TTATTACATATATTAATAATAAATATATCATTATTGTTATTTATTTTA
Found at i:1424468 original size:101 final size:102
Alignment explanation
Indices: 1424267--1424521 Score: 399
Period size: 101 Copynumber: 2.5 Consensus size: 102
1424257 AAGCTAAGGC
* *
1424267 CAAAGA-TGAGCAATGA-AGCTTGCAGCCAATAACATAATATCATTACAGCCAAATCATGAGCGA
1 CAAAGATTGAGCAAT-ATAGCTTGCAACCAATAATATAATATCATTACAGCCAAATCATGAGCGA
*
1424330 TAAAGCTAACGGTTGAAACGTTAATGATAAATTATGGT
65 TAAAGCTAACAGTTGAAACGTTAATGATAAATTATGGT
*
1424368 CAAAGATTGAGCGATATAGCTTGCAACCAATAATATAATATCATTACAGCCAAATCATGAGCGAT
1 CAAAGATTGAGCAATATAGCTTGCAACCAATAATATAATATCATTACAGCCAAATCATGAGCGAT
* *
1424433 -AAGCTAGCAGTTGAAATGTTAATGATAAATTATGGT
66 AAAGCTAACAGTTGAAACGTTAATGATAAATTATGGT
* * *
1424469 CAAAGATTGACCAATATAGCTTGCGACCAATAATATAATATAATTACAGCCAA
1 CAAAGATTGAGCAATATAGCTTGCAACCAATAATATAATATCATTACAGCCAA
1424522 GATATAAGCA
Statistics
Matches: 142, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
101 89 0.63
102 53 0.37
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (102 bp):
CAAAGATTGAGCAATATAGCTTGCAACCAATAATATAATATCATTACAGCCAAATCATGAGCGAT
AAAGCTAACAGTTGAAACGTTAATGATAAATTATGGT
Found at i:1431238 original size:26 final size:27
Alignment explanation
Indices: 1431199--1431252 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
1431189 ATGAGGATGA
1431199 TGTTACACGCCATGT-TAAAAAAATAT
1 TGTTACACGCCATGTATAAAAAAATAT
* *
1431225 TGTTACACGTCATGTATAAAAACATAT
1 TGTTACACGCCATGTATAAAAAAATAT
1431252 T
1 T
1431253 ATATGTCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (27 bp):
TGTTACACGCCATGTATAAAAAAATAT
Found at i:1433087 original size:26 final size:25
Alignment explanation
Indices: 1433031--1433125 Score: 70
Period size: 26 Copynumber: 3.8 Consensus size: 25
1433021 GCGTGTAATG
*
1433031 ATAATAATTTTTTTCAACATTACAT
1 ATAATAATTTTTTTCAACATAACAT
**
1433056 GGAATAACTTTTTTT-AACTATAACAT
1 ATAATAA-TTTTTTTCAAC-ATAACAT
* * *
1433082 ATAATATATTTTTGT--ACATGACGT
1 ATAATA-ATTTTTTTCAACATAACAT
*
1433106 ATAATAATATTTTTTTAACA
1 ATAATAAT-TTTTTTCAACA
1433126 CGGCATGTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
23 2 0.04
24 16 0.29
25 10 0.18
26 26 0.47
27 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.46
Consensus pattern (25 bp):
ATAATAATTTTTTTCAACATAACAT
Found at i:1433093 original size:25 final size:24
Alignment explanation
Indices: 1433031--1433120 Score: 60
Period size: 25 Copynumber: 3.6 Consensus size: 24
1433021 GCGTGTAATG
*
1433031 ATAATAAT-TTTTTTCAACATTACAT
1 ATAATAATATTTTTT--ACATAACAT
**
1433056 GGAATAACT-TTTTTTAACTATAACAT
1 ATAATAA-TATTTTTT-AC-ATAACAT
* *
1433082 ATAAT-ATATTTTTGTACATGACGT
1 ATAATAATATTTTT-TACATAACAT
1433106 ATAATAATATTTTTT
1 ATAATAATATTTTTT
1433121 TAACACGGCA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
24 12 0.23
25 24 0.45
26 17 0.32
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.48
Consensus pattern (24 bp):
ATAATAATATTTTTTACATAACAT
Found at i:1433805 original size:30 final size:30
Alignment explanation
Indices: 1433765--1433823 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1433755 AACTATTAAT
1433765 TATAACAGTTTATTTGACTCAAAATAAAAA
1 TATAACAGTTTATTTGACTCAAAATAAAAA
* *
1433795 TATAAGAGTTTATTTGATTCAAAATAAAA
1 TATAACAGTTTATTTGACTCAAAATAAAA
1433824 GATTGAATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (30 bp):
TATAACAGTTTATTTGACTCAAAATAAAAA
Found at i:1439288 original size:119 final size:122
Alignment explanation
Indices: 1439074--1439330 Score: 331
Period size: 121 Copynumber: 2.1 Consensus size: 122
1439064 CCTAAACCCA
* * * * ** *
1439074 AGGGATTGTGGCTAATTTATAAATCAGATTTCAATCTTATTTTAGAAAAAAAAAATTCAATATGA
1 AGGGATTGTGGCTAAATTATAAAACAGACTTCAATCCTATCCTAG-AAAAAAAAATTCAATACGA
* *
1439139 ATTAATGCCCAATCAAAAACCATTAAAATAATTTATAT-AAAAA-AAAGGTTAAAACG
65 ATTAACGCCCAATCAAAAACCATTAAAATAATTTATATAAAAAACAAAGCTTAAAACG
* *
1439195 TGGGATTGTGGCTAAATTATAAAACAGACTTCAATCCTATCCTAG-AAAAAAAATTCAATCCGAA
1 AGGGATTGTGGCTAAATTATAAAACAGACTTCAATCCTATCCTAGAAAAAAAAATTCAATACGAA
* * ** *
1439259 TTAACGCTCAATCAAATATTATTAAAATAATTTATGTAAAAAACAAAGCTTAAAACG
66 TTAACGCCCAATCAAAAACCATTAAAATAATTTATATAAAAAACAAAGCTTAAAACG
*
1439316 AGGGATTGTAGCTAA
1 AGGGATTGTGGCTAA
1439331 CTTTTACAAA
Statistics
Matches: 116, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
119 48 0.41
120 5 0.04
121 63 0.54
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (122 bp):
AGGGATTGTGGCTAAATTATAAAACAGACTTCAATCCTATCCTAGAAAAAAAAATTCAATACGAA
TTAACGCCCAATCAAAAACCATTAAAATAATTTATATAAAAAACAAAGCTTAAAACG
Found at i:1439406 original size:121 final size:117
Alignment explanation
Indices: 1439074--1439399 Score: 318
Period size: 121 Copynumber: 2.7 Consensus size: 117
1439064 CCTAAACCCA
* ** *
1439074 AGGGATTGTGGCTAA-TTTATAAATCAGATTTCAATCTTATTTTAGAAAAAAAAAATTCAATATG
1 AGGGATTGTGGCTAATTTTA-AAATCAGATTTCAATCTTATTCTAGAAAAAATCAA-TC-CTA--
** *
1439138 AATTAATGCCCAATCAAA-AACCATTAAAATAATTTATATAAAAAAAAGGTTAAAACG
61 AA-TAATGCCCAATCAAATAATTATTAAAATAATTTATATAAAAAAAAGCTTAAAACG
* * * * * *
1439195 TGGGATTGTGGCTAAATTATAAAA-CAGACTTCAATCCTATCCTAGAAAAAAAATTCAATCCGAA
1 AGGGATTGTGGCT-AATTTTAAAATCAGATTTCAATCTTATTCTAG--AAAAAA-TCAATCCTAA
* * * *
1439259 TTAACGCTCAATCAAAT-ATTATTAAAATAATTTATGTAAAAAACAAAGCTTAAAACG
62 ATAATGCCCAATCAAATAATTATTAAAATAATTTATAT-AAAAA-AAAGCTTAAAACG
* * *
1439316 AGGGATTGTAGCTAACTTTTACAAATCAAATTTCAATCTTATTCTAGAATAAATCAATCCTAAAT
1 AGGGATTGTGGCTAA-TTTTA-AAATCAGATTTCAATCTTATTCTAGAAAAAATCAATCCTAAAT
1439381 AATGCCCAATCAAATAATT
64 AATGCCCAATCAAATAATT
1439400 TATAAAAAAA
Statistics
Matches: 164, Mismatches: 29, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
119 30 0.18
120 31 0.19
121 64 0.39
122 9 0.05
123 28 0.17
124 2 0.01
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.30
Consensus pattern (117 bp):
AGGGATTGTGGCTAATTTTAAAATCAGATTTCAATCTTATTCTAGAAAAAATCAATCCTAAATAA
TGCCCAATCAAATAATTATTAAAATAATTTATATAAAAAAAAGCTTAAAACG
Found at i:1446867 original size:27 final size:27
Alignment explanation
Indices: 1446837--1446892 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1446827 GTGTTTGATT
** *
1446837 TTGCTTGATGGTTGAAGTGAAAGACCC
1 TTGCTTGATGGCAGAAGTAAAAGACCC
1446864 TTGCTTGATGGCAGAAGTAAAAGACCC
1 TTGCTTGATGGCAGAAGTAAAAGACCC
1446891 TT
1 TT
1446893 TGTGGCTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (27 bp):
TTGCTTGATGGCAGAAGTAAAAGACCC
Found at i:1454936 original size:23 final size:20
Alignment explanation
Indices: 1454903--1454949 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1454893 TGCCCTAAAC
1454903 TCCCCCCATTCCACCCTCTCTT
1 TCCCCCCATTCC-CCC-CTCTT
*
1454925 TCCCCCCAATTCCCTCCTCTT
1 TCCCCCC-ATTCCCCCCTCTT
1454946 TCCC
1 TCCC
1454950 TCCCTCCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 9 0.39
23 5 0.22
ACGTcount: A:0.09, C:0.60, G:0.00, T:0.32
Consensus pattern (20 bp):
TCCCCCCATTCCCCCCTCTT
Found at i:1460068 original size:1 final size:1
Alignment explanation
Indices: 1460064--1460088 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1460054 CCCCATCTCT
1460064 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
1460089 TCCCTGCCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1461454 original size:14 final size:14
Alignment explanation
Indices: 1461435--1461463 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1461425 TTATTGTGAC
1461435 CAACTATTAGGAAA
1 CAACTATTAGGAAA
1461449 CAACTATTAGGAAA
1 CAACTATTAGGAAA
1461463 C
1 C
1461464 TGACAGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (14 bp):
CAACTATTAGGAAA
Found at i:1466742 original size:2 final size:2
Alignment explanation
Indices: 1466735--1466764 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1466725 GTGAAACTCT
*
1466735 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1466765 ATACTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1467491 original size:3 final size:3
Alignment explanation
Indices: 1467483--1467510 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1467473 GTTGCTTTCC
1467483 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1467511 AATTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1469869 original size:41 final size:41
Alignment explanation
Indices: 1469812--1469894 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
1469802 CGATATGGAC
*
1469812 TGTTGCCAGTATCATTCTATATTTGGCATTAAAATTGGTTT
1 TGTTGCCAGTATCATTCTATATTGGGCATTAAAATTGGTTT
*
1469853 TGTTGCCAGTATCATTCTATATTGGGTATTAAAATTGGTTT
1 TGTTGCCAGTATCATTCTATATTGGGCATTAAAATTGGTTT
1469894 T
1 T
1469895 CATATGATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (41 bp):
TGTTGCCAGTATCATTCTATATTGGGCATTAAAATTGGTTT
Found at i:1481795 original size:63 final size:62
Alignment explanation
Indices: 1481707--1481838 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 62
1481697 TACTCCCCCA
*
1481707 AAATTTTCACAAACACTAGAACAAAGAACTGAGAACTGAAAATGGATTTTAATACGAGATCTGT
1 AAATTTTCACAAACACTAGAACAAAGAACTGAGAACTGAAAATAGA--TTAATACGAGATCTGT
* * *
1481771 AAATTTTCAC-AACAC-CGTAACAAAGAACTGAGAACTGGAAATAGATTAATACTAGATCTGT
1 AAATTTTCACAAACACTAG-AACAAAGAACTGAGAACTGAAAATAGATTAATACGAGATCTGT
*
1481832 GAATTTT
1 AAATTTT
1481839 GCCAAGAACG
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
61 21 0.34
62 1 0.02
63 30 0.48
64 10 0.16
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (62 bp):
AAATTTTCACAAACACTAGAACAAAGAACTGAGAACTGAAAATAGATTAATACGAGATCTGT
Found at i:1483646 original size:22 final size:23
Alignment explanation
Indices: 1483579--1483646 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 23
1483569 CATTTTATTT
*
1483579 TTTAAATATTAATTATTTATAAGTTA
1 TTTAAATATTAA-TA-TT-TAAGTAA
1483605 TTTAAAATATTAATATTTAA-TAA
1 TTT-AAATATTAATATTTAAGTAA
1483628 TTTAAATATTAATATTTAA
1 TTTAAATATTAATATTTAA
1483647 AATATTGATA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
22 16 0.40
23 5 0.12
24 3 0.08
25 2 0.05
26 5 0.12
27 9 0.22
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (23 bp):
TTTAAATATTAATATTTAAGTAA
Found at i:1483663 original size:16 final size:15
Alignment explanation
Indices: 1483616--1483671 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
1483606 TTAAAATATT
1483616 AATATTTAATAATTT-A
1 AATA-TTAAT-ATTTAA
1483632 AATATTAATATTTAA
1 AATATTAATATTTAA
*
1483647 AATATTGATATTTTAA
1 AATATTAATA-TTTAA
*
1483663 AATACTAAT
1 AATATTAAT
1483672 GTTTTATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.11
15 15 0.43
16 16 0.46
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
AATATTAATATTTAA
Found at i:1483676 original size:16 final size:16
Alignment explanation
Indices: 1483622--1483677 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
1483612 TATTAATATT
* *
1483622 TAATAATTT-AAATAT
1 TAATATTTTAAAATAC
*
1483637 TAATA-TTTAAAATAT
1 TAATATTTTAAAATAC
*
1483652 TGATATTTTAAAATAC
1 TAATATTTTAAAATAC
*
1483668 TAATGTTTTA
1 TAATATTTTA
1483678 TTTATAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 3 0.09
15 15 0.43
16 17 0.49
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (16 bp):
TAATATTTTAAAATAC
Found at i:1483980 original size:13 final size:13
Alignment explanation
Indices: 1483962--1483986 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1483952 TTTTAATTTT
1483962 TTCTCTATTTTCA
1 TTCTCTATTTTCA
1483975 TTCTCTATTTTC
1 TTCTCTATTTTC
1483987 TATTTATACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (13 bp):
TTCTCTATTTTCA
Found at i:1493078 original size:13 final size:13
Alignment explanation
Indices: 1493060--1493086 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1493050 AAAAGTACAC
1493060 TCAATAAAAGGTT
1 TCAATAAAAGGTT
1493073 TCAATAAAAGGTT
1 TCAATAAAAGGTT
1493086 T
1 T
1493087 GTGTTTGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (13 bp):
TCAATAAAAGGTT
Found at i:1493947 original size:35 final size:35
Alignment explanation
Indices: 1493845--1493979 Score: 103
Period size: 35 Copynumber: 3.9 Consensus size: 35
1493835 TTATTCTATA
* * * * *
1493845 TGAAATAGTGC-TCCACTTATTATAGTTGTTCTACA
1 TGAAATAGT-CTTTCACTTATTCTAATTGTTTTACG
* * * *
1493880 TGAAATAGTGC-TTCACATGTTTTAATTATTTTACG
1 TGAAATAGT-CTTTCACTTATTCTAATTGTTTTACG
* *
1493915 TGAAGTAGTCTTTCACTTATTCTAGTTGTTTTACG
1 TGAAATAGTCTTTCACTTATTCTAATTGTTTTACG
* * * *
1493950 TAAAATAATGTTTCACCTATTCTAATTGTT
1 TGAAATAGTCTTTCACTTATTCTAATTGTT
1493980 CACATTGTTC
Statistics
Matches: 79, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
34 1 0.01
35 78 0.99
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (35 bp):
TGAAATAGTCTTTCACTTATTCTAATTGTTTTACG
Found at i:1494761 original size:28 final size:28
Alignment explanation
Indices: 1494726--1494820 Score: 122
Period size: 28 Copynumber: 3.4 Consensus size: 28
1494716 CATTCTCTAT
1494726 CATGTCATTCAACTTGTCCATCATTCAC
1 CATGTCATTCAACTTGTCCATCATTCAC
* * ** *
1494754 CACGTCATTCAACTTAT--AGTGTTTCGC
1 CATGTCATTCAACTTGTCCA-TCATTCAC
1494781 CATGTCATTCAACTTGTCCATCATTCAC
1 CATGTCATTCAACTTGTCCATCATTCAC
1494809 CATGTCATTCAA
1 CATGTCATTCAA
1494821 TTTATAGTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
26 1 0.02
27 20 0.37
28 32 0.59
29 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.09, T:0.36
Consensus pattern (28 bp):
CATGTCATTCAACTTGTCCATCATTCAC
Found at i:1494795 original size:27 final size:27
Alignment explanation
Indices: 1494757--1494849 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
1494747 CATTCACCAC
1494757 GTCATTCAACTTATAGTGTTTCGCCAT
1 GTCATTCAACTTATAGTGTTTCGCCAT
* ** *
1494784 GTCATTCAACTTGTCCA-TCATTCACCAT
1 GTCATTCAACTTAT--AGTGTTTCGCCAT
*
1494812 GTCATTCAATTTATAGTGTTTCGCCAT
1 GTCATTCAACTTATAGTGTTTCGCCAT
1494839 GTCATTCAACT
1 GTCATTCAACT
1494850 CACGTCGCGT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
26 1 0.02
27 31 0.58
28 20 0.38
29 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.40
Consensus pattern (27 bp):
GTCATTCAACTTATAGTGTTTCGCCAT
Found at i:1494810 original size:55 final size:55
Alignment explanation
Indices: 1494726--1494849 Score: 230
Period size: 55 Copynumber: 2.3 Consensus size: 55
1494716 CATTCTCTAT
1494726 CATGTCATTCAACTTGTCCATCATTCACCACGTCATTCAACTTATAGTGTTTCGC
1 CATGTCATTCAACTTGTCCATCATTCACCACGTCATTCAACTTATAGTGTTTCGC
* *
1494781 CATGTCATTCAACTTGTCCATCATTCACCATGTCATTCAATTTATAGTGTTTCGC
1 CATGTCATTCAACTTGTCCATCATTCACCACGTCATTCAACTTATAGTGTTTCGC
1494836 CATGTCATTCAACT
1 CATGTCATTCAACT
1494850 CACGTCGCGT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 67 1.00
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.38
Consensus pattern (55 bp):
CATGTCATTCAACTTGTCCATCATTCACCACGTCATTCAACTTATAGTGTTTCGC
Found at i:1494956 original size:29 final size:29
Alignment explanation
Indices: 1494902--1494967 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
1494892 ACATAACTTG
*
1494902 CCACGTCATTCAACTCATGTCATGTTTCAT
1 CCACATCATTCAACTCATGTCATGTTTC-T
* *
1494932 -CACATCATTCAA-TTATGTTCGTGTTTCT
1 CCACATCATTCAACTCATG-TCATGTTTCT
1494960 CCACATCA
1 CCACATCA
1494968 CTTGCCATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.38
Consensus pattern (29 bp):
CCACATCATTCAACTCATGTCATGTTTCT
Found at i:1496206 original size:25 final size:26
Alignment explanation
Indices: 1496153--1496206 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1496143 GGGCAAAATT
*
1496153 TTTAAAATCTTTATTTATTATATATA
1 TTTAAAATCTTTATTTATTATATACA
* *
1496179 TTTAAAATTTTTATTT-TTATTTACA
1 TTTAAAATCTTTATTTATTATATACA
1496204 TTT
1 TTT
1496207 TTTAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTAAAATCTTTATTTATTATATACA
Found at i:1496243 original size:28 final size:28
Alignment explanation
Indices: 1496151--1496243 Score: 102
Period size: 28 Copynumber: 3.4 Consensus size: 28
1496141 GGGGGCAAAA
*
1496151 TTTTTAAAATCTT-TATTTATTATATA-
1 TTTTTAAAATTTTATATTTATTATATAT
* * *
1496177 TATTTAAAATTTTTATTTTTATT-TACAT
1 TTTTTAAAA-TTTTATATTTATTATATAT
1496205 TTTTTAAAAATTTTATATTTATTATATAT
1 TTTTT-AAAATTTTATATTTATTATATAT
*
1496234 TTTTTTAAAT
1 TTTTTAAAAT
1496244 GATCTCCTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
26 8 0.15
27 6 0.11
28 27 0.50
29 13 0.24
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTTAAAATTTTATATTTATTATATAT
Found at i:1496386 original size:20 final size:20
Alignment explanation
Indices: 1496352--1496396 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1496342 TTTTCCCCAC
* *
1496352 CTTTTTCTCTCTCTTTCTTTT
1 CTTTTTCTCTATCTTT-TTGT
1496373 CTTTTT-TCTATCTTTTTGT
1 CTTTTTCTCTATCTTTTTGT
1496392 CTTTT
1 CTTTT
1496397 AATTTTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 8 0.36
21 6 0.27
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.73
Consensus pattern (20 bp):
CTTTTTCTCTATCTTTTTGT
Found at i:1496570 original size:8 final size:8
Alignment explanation
Indices: 1496551--1496588 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
1496541 TTTATTTTTT
1496551 TTATTTATA
1 TTATTTA-A
1496560 TTATTTAA
1 TTATTTAA
1496568 TTATTT-A
1 TTATTTAA
1496575 TATATTTAA
1 T-TATTTAA
1496584 TTATT
1 TTATT
1496589 ATGTGAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 2 0.07
8 16 0.59
9 9 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTATTTAA
Found at i:1496582 original size:16 final size:17
Alignment explanation
Indices: 1496551--1496588 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
1496541 TTTATTTTTT
1496551 TTATTTATATTATTTAA
1 TTATTTATATTATTTAA
1496568 TTATTTATA-TATTTAA
1 TTATTTATATTATTTAA
1496584 TTATT
1 TTATT
1496589 ATGTGAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTTATATTATTTAA
Found at i:1497080 original size:26 final size:25
Alignment explanation
Indices: 1497027--1497088 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
1497017 TCATAATTTT
* *
1497027 TTAAAAATA-ATATAATTAATTATA
1 TTAAAAATATATAAAATTAATGATA
1497051 TTAAAAATATATAAAAATTAA-GATA
1 TTAAAAATATAT-AAAATTAATGATA
1497076 GTTAATAAA-ATAT
1 -TTAA-AAATATAT
1497089 TTACTTATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 9 0.28
25 5 0.16
26 15 0.47
27 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (25 bp):
TTAAAAATATATAAAATTAATGATA
Found at i:1498812 original size:24 final size:23
Alignment explanation
Indices: 1498732--1498813 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 23
1498722 TTAAACAACT
1498732 AAAA-ATTAATATTTTAAAATTTA
1 AAAATATTAATATTTT-AAATTTA
*
1498755 AAATTATATTAAAATTTT-AA-TTA
1 AAA--ATATTAATATTTTAAATTTA
* *
1498778 TAAATTTTAATATTTTAATATTTA
1 AAAATATTAATATTTTAA-ATTTA
*
1498802 AAAATAATAATA
1 AAAATATTAATA
1498814 ATAAATAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
21 11 0.24
22 1 0.02
23 9 0.20
24 14 0.30
25 1 0.02
26 10 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAATATTAATATTTTAAATTTA
Found at i:1504106 original size:23 final size:22
Alignment explanation
Indices: 1504080--1504122 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1504070 TTGATTATAA
*
1504080 ATATAATTACATTTGTATATTTT
1 ATATAATTAC-TTTCTATATTTT
1504103 ATATAATTACTTTCTATATT
1 ATATAATTACTTTCTATATT
1504123 GGATTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATAATTACTTTCTATATTTT
Found at i:1522367 original size:2 final size:2
Alignment explanation
Indices: 1522360--1522388 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1522350 TCATTTTGAT
1522360 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1522389 CCATAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1525214 original size:32 final size:32
Alignment explanation
Indices: 1525178--1525273 Score: 95
Period size: 36 Copynumber: 2.9 Consensus size: 32
1525168 ATAATCTTAT
* *
1525178 GATAAAGTATGATAGCCCGATTAATATTGTTA
1 GATAAAGCATGATAGCCCGATTAATATTGTGA
1525210 GATAAAGCATGATA-CCCAAGTCAATTAATATTGTGA
1 GATAAAGCATGATAGCCC--G---ATTAATATTGTGA
* **
1525246 GATAAAGCATGACAGCCTAATTAATATT
1 GATAAAGCATGATAGCCCGATTAATATT
1525274 ATACATAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
31 3 0.06
32 22 0.42
33 1 0.02
36 25 0.47
37 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (32 bp):
GATAAAGCATGATAGCCCGATTAATATTGTGA
Found at i:1526015 original size:2 final size:2
Alignment explanation
Indices: 1526008--1526046 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1525998 CCTATTGCTT
1526008 TA TA TA TA TA TA TA TA TA TA TA TA TA 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 TA T
1526047 TTCTCGTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1535907 original size:2 final size:2
Alignment explanation
Indices: 1535863--1535888 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1535853 GTTCTTAGTC
1535863 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1535889 CAGAAAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1538880 original size:2 final size:2
Alignment explanation
Indices: 1538873--1538901 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1538863 ATTTGAATCT
1538873 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1538902 TTAACTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1549762 original size:15 final size:15
Alignment explanation
Indices: 1549742--1549832 Score: 130
Period size: 15 Copynumber: 6.1 Consensus size: 15
1549732 ATCACAATGC
*
1549742 AATGTGATTATAAGT
1 AATGTGATTACAAGT
*
1549757 AATGTGATTGCAAGT
1 AATGTGATTACAAGT
*
1549772 AATGTGATTATAAGT
1 AATGTGATTACAAGT
*
1549787 AATGTGATTGCAAGT
1 AATGTGATTACAAGT
*
1549802 AATGTGATTACAAGC
1 AATGTGATTACAAGT
1549817 AATGTGATTAC-AGT
1 AATGTGATTACAAGT
1549831 AA
1 AA
1549833 AAATAACATT
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
14 4 0.06
15 63 0.94
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.34
Consensus pattern (15 bp):
AATGTGATTACAAGT
Found at i:1549778 original size:30 final size:30
Alignment explanation
Indices: 1549742--1549825 Score: 150
Period size: 30 Copynumber: 2.8 Consensus size: 30
1549732 ATCACAATGC
1549742 AATGTGATTATAAGTAATGTGATTGCAAGT
1 AATGTGATTATAAGTAATGTGATTGCAAGT
1549772 AATGTGATTATAAGTAATGTGATTGCAAGT
1 AATGTGATTATAAGTAATGTGATTGCAAGT
* *
1549802 AATGTGATTACAAGCAATGTGATT
1 AATGTGATTATAAGTAATGTGATT
1549826 ACAGTAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.36
Consensus pattern (30 bp):
AATGTGATTATAAGTAATGTGATTGCAAGT
Found at i:1550017 original size:27 final size:27
Alignment explanation
Indices: 1549987--1550128 Score: 89
Period size: 27 Copynumber: 5.1 Consensus size: 27
1549977 TAATATATTT
*
1549987 ATATTTTTTATTATTAATTTTTATATA
1 ATATATTTTATTATTAATTTTTATATA
* * * *
1550014 ATATCATTTCT-TAAATATATTTTTAATGTC
1 ATAT-ATTT-TATTATTA-ATTTTT-ATATA
*
1550044 ATATATTTTATT-TTTATTTATTATTATA
1 ATATATTTTATTATTAATTT-TTA-TATA
*
1550072 ATAT-TTTATATT-TT-ATATTTAATATA
1 ATATATTT-TATTATTAAT-TTTTATATA
*
1550098 TTTATATTTTATTATTAA-TTTTATATA
1 -ATATATTTTATTATTAATTTTTATATA
1550125 ATAT
1 ATAT
1550129 CATATTTTAA
Statistics
Matches: 88, Mismatches: 14, Indels: 27
0.68 0.11 0.21
Matches are distributed among these distances:
26 7 0.08
27 31 0.35
28 30 0.34
29 13 0.15
30 7 0.08
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.63
Consensus pattern (27 bp):
ATATATTTTATTATTAATTTTTATATA
Found at i:1550082 original size:7 final size:7
Alignment explanation
Indices: 1550045--1550123 Score: 69
Period size: 7 Copynumber: 11.7 Consensus size: 7
1550035 TTTAATGTCA
1550045 TATATTT
1 TATATTT
1550052 TAT-TTT
1 TATATTT
1550058 TAT-TTAT
1 TATATT-T
*
1550065 TAT-TAT
1 TATATTT
*
1550071 AATATTT
1 TATATTT
1550078 TATATTT
1 TATATTT
1550085 TATATTT
1 TATATTT
*
1550092 AATATATT
1 TATAT-TT
1550100 TATATTT
1 TATATTT
*
1550107 TAT-TAT
1 TATATTT
1550113 TA-ATTT
1 TATATTT
1550119 TATAT
1 TATAT
1550124 AATATCATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
6 19 0.32
7 34 0.58
8 6 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TATATTT
Found at i:1550082 original size:49 final size:49
Alignment explanation
Indices: 1550029--1550196 Score: 149
Period size: 49 Copynumber: 3.2 Consensus size: 49
1550019 ATTTCTTAAA
1550029 TATATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATATTT
1 TATATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATATTT
* * *
1550078 TATA-TTTTATATTTAATATATTTATATTTTATTATTAATTTTATATAATATCATATTTT
1 TATATTTTTA-ATGTCATATATTT-TA-TTT-TTATT--TATTAT-T-ATA--ATA-TTT
* * *
1550137 AAATATATTTTTAATGTCATATATTTTATTTTCATTTATTATTATAATCTTA
1 ---TATATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATATTT
1550189 TATATTTT
1 TATATTTT
1550197 ATTTTCATTT
Statistics
Matches: 95, Mismatches: 9, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
48 5 0.05
49 23 0.24
50 2 0.02
51 3 0.03
52 7 0.07
53 2 0.02
54 5 0.05
55 4 0.04
56 4 0.04
57 5 0.05
58 3 0.03
59 7 0.07
60 3 0.03
61 2 0.02
62 15 0.16
63 5 0.05
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (49 bp):
TATATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATATTT
Found at i:1550090 original size:22 final size:23
Alignment explanation
Indices: 1550052--1550114 Score: 89
Period size: 22 Copynumber: 2.9 Consensus size: 23
1550042 TCATATATTT
1550052 TATTTT-TA-TTTATTATTATAA
1 TATTTTATATTTTATTATTATAA
1550073 TATTTTATATTTTA-TATT-TAA
1 TATTTTATATTTTATTATTATAA
1550094 TATATTTATATTTTATTATTA
1 TAT-TTTATATTTTATTATTA
1550115 ATTTTATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 12 0.32
22 17 0.46
23 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTTTATATTTTATTATTATAA
Found at i:1550113 original size:58 final size:56
Alignment explanation
Indices: 1550050--1550198 Score: 139
Period size: 56 Copynumber: 2.7 Consensus size: 56
1550040 TGTCATATAT
1550050 TTTATTTTTATTTATTATTATAATATTTTATATTTTATATTTAATATAT-T--TATAT
1 TTTATTTTTATTTATTATTATAATATTTTATATTTTATATTT-ATA-ATGTCATATAT
* * * * *
1550105 TTTATTATTAATTTTATATAATATCATATTTTA-A--ATATATTTTTAATGTCATATAT
1 TTTATT-TTTA-TTTAT-TATTATAATATTTTATATTTTATATTTATAATGTCATATAT
* * *
1550161 TTTATTTTCATTTATTATTATAATCTTATATATTTTAT
1 TTTATTTTTATTTATTATTATAATATTTTATATTTTAT
1550199 TTTCATTTCT
Statistics
Matches: 74, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
53 13 0.18
54 9 0.12
55 16 0.22
56 17 0.23
57 6 0.08
58 13 0.18
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (56 bp):
TTTATTTTTATTTATTATTATAATATTTTATATTTTATATTTATAATGTCATATAT
Found at i:1550115 original size:22 final size:21
Alignment explanation
Indices: 1550055--1550124 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 21
1550045 TATATTTTAT
1550055 TTTTAT-TTATTATTA-TAATA
1 TTTTATATT-TTATTATTAATA
1550075 TTTTATATTTTA-TATTTAATA
1 TTTTATATTTTATTA-TTAATA
1550096 TATTTATATTTTATTATTAAT-
1 T-TTTATATTTTATTATTAATA
1550117 TTTATATA
1 TTT-TATA
1550125 ATATCATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
19 2 0.05
20 11 0.25
21 13 0.30
22 16 0.36
23 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATATTTTATTATTAATA
Found at i:1550133 original size:29 final size:29
Alignment explanation
Indices: 1549992--1550137 Score: 87
Period size: 29 Copynumber: 5.2 Consensus size: 29
1549982 TATTTATATT
1549992 TTTTATTATTAATTTTTATATAATATCAT-
1 TTTTATTATTAA-TTTTATATAATATCATA
* * *
1550021 TTCTTA-AATATATTTTTA-AT-GTCAT-ATA
1 TT-TTATTAT-TAATTTTATATAAT-ATCATA
* * *
1550049 TTTTATT-TTTA-TTTAT-TATTATAATA
1 TTTTATTATTAATTTTATATAATATCATA
* * *
1550075 TTTTATATTTTATATTTAATAT-AT-TTATA
1 TTTTAT-TATTA-ATTTTATATAATATCATA
1550104 TTTTATTATTAATTTTATATAATATCATA
1 TTTTATTATTAATTTTATATAATATCATA
1550133 TTTTA
1 TTTTA
1550138 AATATATTTT
Statistics
Matches: 88, Mismatches: 14, Indels: 30
0.67 0.11 0.23
Matches are distributed among these distances:
25 7 0.08
26 11 0.12
27 16 0.18
28 14 0.16
29 29 0.33
30 10 0.11
31 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (29 bp):
TTTTATTATTAATTTTATATAATATCATA
Found at i:1550139 original size:111 final size:113
Alignment explanation
Indices: 1549975--1550198 Score: 382
Period size: 111 Copynumber: 2.0 Consensus size: 113
1549965 AAAATACAAG
1549975 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
* *
1550040 TGTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATA
65 TGTCATATATTTTATTTTCATTTATTATTATAATATTATATATTTTATA
1550089 TTTAATATATTTATA-TTTTATTATTAA-TTTTATATAATATCATATT-TTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAA
*
1550151 TGTCATATATTTTATTTTCATTTATTATTATAATCTTATATATTTTAT
65 TGTCATATATTTTATTTTCATTTATTATTATAATATTATATATTTTAT
1550199 TTTCATTTCT
Statistics
Matches: 106, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
111 77 0.73
112 14 0.13
114 15 0.14
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (113 bp):
TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
GTCATATATTTTATTTTCATTTATTATTATAATATTATATATTTTATA
Found at i:1550288 original size:7 final size:7
Alignment explanation
Indices: 1550276--1550344 Score: 54
Period size: 7 Copynumber: 9.7 Consensus size: 7
1550266 AATATTAATT
1550276 TTTTATA
1 TTTTATA
1550283 TTTTATTTTA
1 TTTTA---TA
1550293 TTTTA-A
1 TTTTATA
1550299 TTTT-TA
1 TTTTATA
1550305 TTCTTATA
1 TT-TTATA
*
1550313 TTATATA
1 TTTTATA
1550320 TTTTAT-
1 TTTTATA
*
1550326 TTTAATA
1 TTTTATA
*
1550333 TTTTTTA
1 TTTTATA
1550340 TTTTA
1 TTTTA
1550345 ATTATAACAT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
6 13 0.27
7 25 0.51
8 4 0.08
10 7 0.14
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTATA
Found at i:1550311 original size:6 final size:5
Alignment explanation
Indices: 1550281--1550344 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
1550271 TAATTTTTTA
* *
1550281 TATTT TATTT TATTT TAATTTT TATTCT TATAT TA-TA TATTT TATTT
1 TATTT TATTT TATTT T-A-TTT TATT-T TATTT TATTT TATTT TATTT
*
1550328 TAATAT T-TTT TATTT TA
1 T-ATTT TATTT TATTT TA
1550345 ATTATAACAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
4 5 0.11
5 28 0.60
6 10 0.21
7 4 0.09
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:1550323 original size:20 final size:19
Alignment explanation
Indices: 1550186--1550350 Score: 81
Period size: 17 Copynumber: 9.3 Consensus size: 19
1550176 TATTATAATC
*
1550186 TTATATATTTTATTTTCATT
1 TTATATATTTTATTTT-ATA
* *
1550206 TCTTTAATATATT-TTTTATA
1 T-TAT-ATATTTTATTTTATA
1550226 TTATATATTTTATTTTA-A
1 TTATATATTTTATTTTATA
* **
1550244 -T-T-TGTTTTA-CCTATA
1 TTATATATTTTATTTTATA
** * *
1550259 TTATATA-AATA-TTAATT
1 TTATATATTTTATTTTATA
* *
1550276 TTTTATATTTTATTTTATT
1 TTATATATTTTATTTTATA
1550295 TTA-AT-TTTTATTCTTATA
1 TTATATATTTTATT-TTATA
1550313 TTATATATTTTATTTTA-A
1 TTATATATTTTATTTTATA
1550331 -TAT-T-TTTTATTTTA-A
1 TTATATATTTTATTTTATA
1550346 TTATA
1 TTATA
1550351 ACATTATAAA
Statistics
Matches: 110, Mismatches: 21, Indels: 31
0.68 0.13 0.19
Matches are distributed among these distances:
14 2 0.02
15 18 0.16
16 6 0.05
17 22 0.20
18 20 0.18
19 19 0.17
20 11 0.10
21 6 0.05
22 6 0.05
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.67
Consensus pattern (19 bp):
TTATATATTTTATTTTATA
Found at i:1552204 original size:17 final size:17
Alignment explanation
Indices: 1552178--1552211 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1552168 CAAGAAACAA
1552178 CAAACATGAGA-AAAAT
1 CAAACATGAGAGAAAAT
1552194 CAAAGCATGAGAGAAAAT
1 CAAA-CATGAGAGAAAAT
1552212 GCATATTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.59, C:0.12, G:0.18, T:0.12
Consensus pattern (17 bp):
CAAACATGAGAGAAAAT
Found at i:1554467 original size:2 final size:2
Alignment explanation
Indices: 1554455--1554487 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1554445 AATACAATAA
*
1554455 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1554488 ATGGGGTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1555363 original size:14 final size:15
Alignment explanation
Indices: 1555344--1555374 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1555334 AATGGGACTT
1555344 ATGTATTTTTT-TAA
1 ATGTATTTTTTATAA
1555358 ATGTATTTTTTATAA
1 ATGTATTTTTTATAA
1555373 AT
1 AT
1555375 TTAACGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
ATGTATTTTTTATAA
Found at i:1574900 original size:3 final size:3
Alignment explanation
Indices: 1574892--1574926 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1574882 ACGCATAACC
*
1574892 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1574927 AGTTACAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1574931 original size:12 final size:12
Alignment explanation
Indices: 1574893--1574931 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1574883 CGCATAACCA
1574893 TTATTATTATTA-
1 TTATTATTA-TAG
*
1574905 TTATTATTATTG
1 TTATTATTATAG
1574917 TTATTATTATAG
1 TTATTATTATAG
1574929 TTA
1 TTA
1574932 CAACAACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 1 0.04
12 23 0.96
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (12 bp):
TTATTATTATAG
Done.