Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold376
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: 900718
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 6
Found at i:317938 original size:20 final size:20
Alignment explanation
Indices: 317913--317951 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
317903 CATTTTAGAC
317913 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
317933 ATGTATCGATACATTCACT
1 ATGTATCGATACATTCACT
317952 ACTTGCATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:317963 original size:21 final size:20
Alignment explanation
Indices: 317917--317966 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
317907 TTAGACATGT
*
317917 ATCGATACATTCACTTATGT
1 ATCGATACATTCACTTATGC
317937 ATCGATACATTCAC-TACTTGC
1 ATCGATACATTCACTTA--TGC
317958 ATCGATACA
1 ATCGATACA
317967 AATTGTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.07
20 14 0.52
21 11 0.41
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (20 bp):
ATCGATACATTCACTTATGC
Found at i:321851 original size:52 final size:50
Alignment explanation
Indices: 321795--321933 Score: 179
Period size: 51 Copynumber: 2.7 Consensus size: 50
321785 ATTTGCCTGC
* * *
321795 ATGTATCGATAAATTGAAGAATGTATCGATACATTTGTGTCAAAAACCCAGA
1 ATGTATTGATAAA-TAAAGAATGTATCGATACATTTGAGTC-AAAACCCAGA
* *
321847 ATGTATTGATATAGTAAAGAATGTATCGATACATTTGAGTCAAAACCTAGA
1 ATGTATTGATA-AATAAAGAATGTATCGATACATTTGAGTCAAAACCCAGA
* *
321898 ATGTATTGATACAACAAAAAATGTATCGATACATTT
1 ATGTATTGATA-AATAAAGAATGTATCGATACATTT
321934 TCCTTTCAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
51 41 0.53
52 35 0.45
53 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.31
Consensus pattern (50 bp):
ATGTATTGATAAATAAAGAATGTATCGATACATTTGAGTCAAAACCCAGA
Found at i:322012 original size:20 final size:20
Alignment explanation
Indices: 321969--322042 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
321959 GACATGGTCT
*
321969 TGTATCGATACATTTCA-AACA
1 TGTATCGATACA-TTCACTA-A
*
321990 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACTAA
*
322010 TGTATAGATACATTCACTAA
1 TGTATCGATACATTCACTAA
322030 TTGTATCGATACA
1 -TGTATCGATACA
322043 AATTATAGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 23 0.50
21 23 0.50
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTCACTAA
Found at i:322040 original size:21 final size:21
Alignment explanation
Indices: 321968--322042 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
321958 CGACATGGTC
321968 TTGTATCGATACATTTCA--AA
1 TTGTATCGATACA-TTCACTAA
* *
321988 CATGTATCGATACATTCACTTA
1 -TTGTATCGATACATTCACTAA
*
322010 -TGTATAGATACATTCACTAA
1 TTGTATCGATACATTCACTAA
322030 TTGTATCGATACA
1 TTGTATCGATACA
322043 AATTATAGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
20 22 0.48
21 23 0.50
22 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (21 bp):
TTGTATCGATACATTCACTAA
Found at i:322898 original size:13 final size:13
Alignment explanation
Indices: 322880--322906 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
322870 ACATTATGTT
322880 TTGTATCGATACA
1 TTGTATCGATACA
322893 TTGTATCGATACA
1 TTGTATCGATACA
322906 T
1 T
322907 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:323013 original size:33 final size:33
Alignment explanation
Indices: 322955--323023 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
322945 CTACCACTAT
*
322955 TTGTATCGATACATGGTACAATGTATCAATACA
1 TTGTATCGATACATGATACAATGTATCAATACA
* *
322988 TTGTATCGATACATGATGA-ATTGTATCGATACA
1 TTGTATCGATACATGAT-ACAATGTATCAATACA
323021 TTG
1 TTG
323024 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATGTATCAATACA
Found at i:324542 original size:19 final size:19
Alignment explanation
Indices: 324517--324573 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
324507 TTGTATCAAT
*
324517 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
324536 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
*
324555 ACAATTATATCGATACATG
1 AC-ATTGTATCGATACATG
324574 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:324643 original size:13 final size:13
Alignment explanation
Indices: 324625--324670 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
324615 TAGGATATTA
324625 TATCGATACATTG
1 TATCGATACATTG
324638 TATCGATACA-TG
1 TATCGATACATTG
324650 -AT-G--A-ATTG
1 TATCGATACATTG
324658 TATCGATACATTG
1 TATCGATACATTG
324671 CTTATAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
7 1 0.04
8 3 0.11
9 2 0.07
10 2 0.07
11 2 0.07
12 3 0.11
13 14 0.52
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:324644 original size:33 final size:33
Alignment explanation
Indices: 324602--324670 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
324592 CTACCACTGT
324602 TTGTATCGATACAT-AGGATATTATATCGATACA
1 TTGTATCGATACATGAGGA-ATTATATCGATACA
* *
324635 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGAGGAATTATATCGATACA
324668 TTG
1 TTG
324671 CTTATAATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGAGGAATTATATCGATACA
Found at i:327173 original size:17 final size:17
Alignment explanation
Indices: 327151--327184 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
327141 ATTATGTCGT
327151 CTAAATCTATTTGGGGA
1 CTAAATCTATTTGGGGA
327168 CTAAATCTATTTGGGGA
1 CTAAATCTATTTGGGGA
327185 GATGGTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (17 bp):
CTAAATCTATTTGGGGA
Found at i:331949 original size:26 final size:26
Alignment explanation
Indices: 331919--331972 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
331909 CTTAGAAGTG
*
331919 GAAAACTTCATTCTACAGTGTTCTTA
1 GAAAACTTCATTCTACAATGTTCTTA
*
331945 GAAAACTTCATTCTATAATGTTCTTA
1 GAAAACTTCATTCTACAATGTTCTTA
331971 GA
1 GA
331973 GAATGTATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (26 bp):
GAAAACTTCATTCTACAATGTTCTTA
Found at i:337642 original size:13 final size:13
Alignment explanation
Indices: 337624--337651 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
337614 ATACAAAGAT
337624 CAATGTATCGATA
1 CAATGTATCGATA
337637 CAATGTATCGATA
1 CAATGTATCGATA
337650 CA
1 CA
337652 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:337728 original size:19 final size:19
Alignment explanation
Indices: 337704--337789 Score: 85
Period size: 19 Copynumber: 4.7 Consensus size: 19
337694 AGCGATACAT
337704 TGTATCGATACAATACTTA
1 TGTATCGATACAATACTTA
337723 TGTATCGATAC---A-TTA
1 TGTATCGATACAATACTTA
*
337738 --TATCGATACAACACTTA
1 TGTATCGATACAATACTTA
*
337755 TGTATCGATACAATTACATGTT
1 TGTATCGATACAA-TAC-T-TA
337777 TGTATCGATACAA
1 TGTATCGATACAA
337790 ATTGTTGAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
13 9 0.16
15 3 0.05
16 2 0.04
17 3 0.05
19 22 0.39
20 2 0.04
21 1 0.02
22 14 0.25
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAATACTTA
Found at i:337742 original size:32 final size:32
Alignment explanation
Indices: 337696--337766 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
337686 AGCTTCGTAG
* *
337696 CGATACATTGTATCGATACAATACTTATGTAT
1 CGATACATTATATCGATACAACACTTATGTAT
337728 CGATACATTATATCGATACAACACTTATGTAT
1 CGATACATTATATCGATACAACACTTATGTAT
337760 CGATACA
1 CGATACA
337767 ATTACATGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (32 bp):
CGATACATTATATCGATACAACACTTATGTAT
Found at i:342981 original size:20 final size:19
Alignment explanation
Indices: 342952--343026 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
342942 AAAAAGACAT
342952 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* * *
342971 GAATATATCGATATATTCATA
1 -AATGTATCGATACATTGA-A
* *
342992 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
343012 AATGTATCGATACAT
1 AATGTATCGATACAT
343027 CTTGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:346792 original size:4 final size:4
Alignment explanation
Indices: 346783--346809 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
346773 ACAGATGGCT
346783 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
346810 TTATTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:349148 original size:20 final size:21
Alignment explanation
Indices: 349123--349197 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 21
349113 AATTTTTGAT
349123 AATATTTTTATGTAAT-TAAA
1 AATATTTTTATGTAATATAAA
* * *
349143 AATATTTATATATAATATAAT
1 AATATTTTTATGTAATATAAA
*
349164 AGTAATTTATGTATGTTAATATAAA
1 AAT-ATTT-T-TATG-TAATATAAA
349189 AATATTTTT
1 AATATTTTT
349198 TAATATTTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
20 14 0.33
21 5 0.12
22 5 0.12
23 1 0.02
24 7 0.17
25 10 0.24
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
AATATTTTTATGTAATATAAA
Found at i:349268 original size:6 final size:5
Alignment explanation
Indices: 349255--349303 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
349245 AAATATTTTA
*
349255 AATAT AATTAT AATAT AATAA AATAT -ATA- AATAT AATAT AA-AT -ATAT
1 AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
349302 AA
1 AA
349304 ATTTATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 1 0.03
4 10 0.27
5 21 0.57
6 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:349271 original size:11 final size:11
Alignment explanation
Indices: 349234--349300 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 11
349224 ATCTAAATTT
349234 ATATAATTATA
1 ATATAATTATA
* *
349245 AAAT-ATTTTAA
1 ATATAATTAT-A
349256 ATATAATTATA
1 ATATAATTATA
* *
349267 ATATAATAAAA
1 ATATAATTATA
*
349278 TATATAAATATA
1 -ATATAATTATA
*
349290 ATATAAATATA
1 ATATAATTATA
349301 TAAATTTATT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
10 4 0.09
11 28 0.64
12 12 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATATAATTATA
Found at i:349298 original size:29 final size:29
Alignment explanation
Indices: 349235--349304 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
349225 TCTAAATTTA
*
349235 TATAAT-TATAAAATATTTTAAATATAAT
1 TATAATATATAAAATATTATAAATATAAT
349263 TATAATATAATAAAATA-TATAAATATAA-
1 TATAATAT-ATAAAATATTATAAATATAAT
349291 TATAAATATATAAA
1 TAT-AATATATAAA
349305 TTTATTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
28 14 0.37
29 16 0.42
30 8 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
TATAATATATAAAATATTATAAATATAAT
Found at i:354183 original size:13 final size:13
Alignment explanation
Indices: 354165--354190 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
354155 CAATTTTTTG
354165 TGTATCGATACAT
1 TGTATCGATACAT
354178 TGTATCGATACAT
1 TGTATCGATACAT
354191 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:354202 original size:32 final size:33
Alignment explanation
Indices: 354145--354208 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
354135 TACAAGCCAA
**
354145 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
354178 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
354209 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:354285 original size:20 final size:21
Alignment explanation
Indices: 354238--354292 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
354228 AATCCCAATG
* *
354238 ACATGTATCGATACATCTTTT
1 ACATGTATCGATACATCTGTA
*
354259 TCATGTATCGATACAT-TGTA
1 ACATGTATCGATACATCTGTA
354279 ACATGTATCGATAC
1 ACATGTATCGATAC
354293 TTTGAATTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (21 bp):
ACATGTATCGATACATCTGTA
Found at i:356314 original size:21 final size:20
Alignment explanation
Indices: 356285--356327 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
356275 GTCTAGTATA
* *
356285 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
356306 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
356326 GG
1 GG
356328 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:362098 original size:52 final size:52
Alignment explanation
Indices: 362020--362168 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 52
362010 CGAAATATGA
362020 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
** *
362072 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
** ** *
362124 AAATTTGCCTGCATGTATTAATACAAAGATTAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACA
362169 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 86 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
Found at i:362175 original size:13 final size:13
Alignment explanation
Indices: 362157--362181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
362147 CAAAGATTAG
362157 TGTATCGATACAA
1 TGTATCGATACAA
362170 TGTATCGATACA
1 TGTATCGATACA
362182 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:362261 original size:13 final size:13
Alignment explanation
Indices: 362243--362267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
362233 AAAAAAAATA
362243 TGTATCGATACAT
1 TGTATCGATACAT
362256 TGTATCGATACA
1 TGTATCGATACA
362268 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:366578 original size:13 final size:13
Alignment explanation
Indices: 366560--366585 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
366550 CAATTTTTTG
366560 TGTATCGATACAT
1 TGTATCGATACAT
366573 TGTATCGATACAT
1 TGTATCGATACAT
366586 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:366597 original size:32 final size:33
Alignment explanation
Indices: 366540--366603 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
366530 TACAAGCCAA
**
366540 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
366573 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
366604 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:370628 original size:8 final size:8
Alignment explanation
Indices: 370615--370640 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
370605 ATTTGATTAA
370615 ATTTTGTG
1 ATTTTGTG
370623 ATTTTGTG
1 ATTTTGTG
370631 ATTTTGTG
1 ATTTTGTG
370639 AT
1 AT
370641 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:371323 original size:20 final size:21
Alignment explanation
Indices: 371293--371332 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
371283 TCTAGGCAGC
371293 ACCCACCAGGTCGCGACCGGT
1 ACCCACCAGGTCGCGACCGGT
371314 ACCC-CCAGGTCGCGACCGG
1 ACCCACCAGGTCGCGACCGG
371333 GCAGCCCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.17, C:0.45, G:0.30, T:0.07
Consensus pattern (21 bp):
ACCCACCAGGTCGCGACCGGT
Found at i:372732 original size:22 final size:22
Alignment explanation
Indices: 372701--372745 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
372691 AGAAATTGTT
372701 AAATTATTTGATTAAGGGGGAG
1 AAATTATTTGATTAAGGGGGAG
*
372723 AAATTTTTTGATTAAGGGGGAG
1 AAATTATTTGATTAAGGGGGAG
372745 A
1 A
372746 GACAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (22 bp):
AAATTATTTGATTAAGGGGGAG
Found at i:373431 original size:13 final size:13
Alignment explanation
Indices: 373413--373438 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
373403 ACACACATTA
373413 TGTATCGATACAT
1 TGTATCGATACAT
373426 TGTATCGATACAT
1 TGTATCGATACAT
373439 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:373454 original size:33 final size:32
Alignment explanation
Indices: 373393--373460 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
373383 CCTTAACTGT
**
373393 TTGTATCGATACACACATTATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
373425 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
373458 TTG
1 TTG
373461 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:374222 original size:13 final size:13
Alignment explanation
Indices: 374204--374230 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
374194 AGCTTTCACT
374204 TTGTATCGATACA
1 TTGTATCGATACA
374217 TTGTATCGATACA
1 TTGTATCGATACA
374230 T
1 T
374231 GGACAATTGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:374321 original size:33 final size:33
Alignment explanation
Indices: 374284--374349 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
374274 CACTATTTGT
*
374284 ATCGATACATGGT-ACAATGTATCAATACATTGC
1 ATCGATACATGATGA-AATGTATCAATACATTGC
* *
374317 ATCGATACATGATGAATTGTATCGATACATTGC
1 ATCGATACATGATGAAATGTATCAATACATTGC
374350 TTATAACGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (33 bp):
ATCGATACATGATGAAATGTATCAATACATTGC
Found at i:376587 original size:21 final size:20
Alignment explanation
Indices: 376553--376595 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
376543 ATATTAAAAG
*
376553 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAA-GAA
376574 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAATG-AAAACAAGAA
376594 TT
1 TT
376596 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TTAGCTAATGAAAACAAGAA
Found at i:376594 original size:20 final size:21
Alignment explanation
Indices: 376553--376595 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
376543 ATATTAAAAG
*
376553 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
376574 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
376594 TT
1 TT
376596 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:383026 original size:13 final size:13
Alignment explanation
Indices: 383008--383034 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
382998 ACATTATGCT
383008 TTGTATCGATACA
1 TTGTATCGATACA
383021 TTGTATCGATACA
1 TTGTATCGATACA
383034 T
1 T
383035 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:383143 original size:33 final size:33
Alignment explanation
Indices: 383083--383151 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
383073 TTACCACTGT
*
383083 TTGTATCGATACATAGGATATTATATCGATACA
1 TTGTATCGAGACATAGGATATTATATCGATACA
* *
383116 TTGTATCGAGACATGATGA-ATTGTATCGATACA
1 TTGTATCGAGACAT-AGGATATTATATCGATACA
383149 TTG
1 TTG
383152 CTTATAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGAGACATAGGATATTATATCGATACA
Found at i:387851 original size:32 final size:32
Alignment explanation
Indices: 387788--387851 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
387778 TTTGAAGCAA
*
387788 TGTATCGATAGAATTCATCATGTATCCATACAT
1 TGTATCGATACAATTCA-CATGTATCCATACAT
*
387821 TGTATCGATACAATTGC-CATGTATCGATACA
1 TGTATCGATACAATT-CACATGTATCCATACA
387852 AACAGTGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 13 0.46
33 14 0.50
34 1 0.04
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (32 bp):
TGTATCGATACAATTCACATGTATCCATACAT
Found at i:388238 original size:20 final size:20
Alignment explanation
Indices: 388215--388287 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
388205 ACAATTCAAA
388215 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
388235 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
388256 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
388276 GTATCGATACAT
1 GTATCGATACAT
388288 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:388258 original size:21 final size:21
Alignment explanation
Indices: 388232--388308 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
388222 TACATGTTGC
388232 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
388253 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
388273 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
388293 GGATGTATCGATACAT
1 -AATGTATCGATACAT
388309 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:388266 original size:41 final size:41
Alignment explanation
Indices: 388215--388308 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
388205 ACAATTCAAA
388215 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
388256 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
388297 GTATCGATACAT
1 GTATCGATACAT
388309 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:388365 original size:13 final size:13
Alignment explanation
Indices: 388347--388372 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
388337 TACAGCAAGT
388347 ATGTATCGATACA
1 ATGTATCGATACA
388360 ATGTATCGATACA
1 ATGTATCGATACA
388373 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:392454 original size:15 final size:15
Alignment explanation
Indices: 392434--392464 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
392424 TAAAAATGTC
*
392434 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
392449 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
392464 C
1 C
392465 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:394561 original size:13 final size:13
Alignment explanation
Indices: 394543--394581 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
394533 ACATTTTTCC
394543 TTGTATCGATACA
1 TTGTATCGATACA
394556 TTGTATCGATACA
1 TTGTATCGATACA
*
394569 CTGTATCGATACA
1 TTGTATCGATACA
394582 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:397038 original size:20 final size:20
Alignment explanation
Indices: 397015--397087 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
397005 ACAATTCAAA
397015 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
397035 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
397056 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
397076 GTATCGATACAT
1 GTATCGATACAT
397088 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:397058 original size:21 final size:21
Alignment explanation
Indices: 397032--397108 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
397022 TACATGTTGC
397032 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
397053 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
397073 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
397093 GGATGTATCGATACAT
1 -AATGTATCGATACAT
397109 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:397066 original size:41 final size:41
Alignment explanation
Indices: 397015--397108 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
397005 ACAATTCAAA
397015 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
397056 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
397097 GTATCGATACAT
1 GTATCGATACAT
397109 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:397165 original size:13 final size:13
Alignment explanation
Indices: 397147--397172 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
397137 TACAGCAAGT
397147 ATGTATCGATACA
1 ATGTATCGATACA
397160 ATGTATCGATACA
1 ATGTATCGATACA
397173 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:406463 original size:22 final size:22
Alignment explanation
Indices: 406438--406484 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
406428 GACCTTTGAG
406438 TCCGATGGTATTTGAAATATTT
1 TCCGATGGTATTTGAAATATTT
*
406460 TCCGATGGTATTTGAATTATTT
1 TCCGATGGTATTTGAAATATTT
406482 TCC
1 TCC
406485 AATGCCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (22 bp):
TCCGATGGTATTTGAAATATTT
Found at i:407460 original size:20 final size:20
Alignment explanation
Indices: 407435--407489 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
407425 CTACTAGTTT
***
407435 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTAAA
*
407455 CATGTATTGATACAA-TAAA
1 CATGTATCGATACAATTAAA
407474 CATGTATCGATACAAT
1 CATGTATCGATACAAT
407490 GTATCGATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTAAA
Found at i:407493 original size:13 final size:13
Alignment explanation
Indices: 407475--407501 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
407465 TACAATAAAC
407475 ATGTATCGATACA
1 ATGTATCGATACA
407488 ATGTATCGATACA
1 ATGTATCGATACA
407501 A
1 A
407502 AGCGTAAGGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:409359 original size:21 final size:20
Alignment explanation
Indices: 409326--409398 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
409316 TACTAATAGA
*
409326 TGTATCGACACATTCATGTAG
1 TGTATCGATACATT-ATGTAG
* * *
409347 TGTATTGATACATTGTGTAT
1 TGTATCGATACATTATGTAG
409367 TGTATCGATACATTATGATA-
1 TGTATCGATACATTATG-TAG
*
409387 TGTATCAATACA
1 TGTATCGATACA
409399 GATGAGGGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 30 0.68
21 14 0.32
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTATGTAG
Found at i:409441 original size:112 final size:112
Alignment explanation
Indices: 409233--409472 Score: 270
Period size: 112 Copynumber: 2.1 Consensus size: 112
409223 TACATTTTAA
* * *
409233 GATGTATCTG-TACATTTTGTATTGTTTCGATACATTTTGATATATATCAAAACAAACAAGGGTT
1 GATGTAT-TGATACATTGTGTATTGTATCGATACATTATGATATATATCAAAACAAACAAGGGTT
* * * *
409297 TTAGGATTTCTTTAGCTACTACTAATAGATGTATCGACACATTCATGT
65 TTAAGATTTCCTTAGCTACTACCAACAGATGTATCGACACATTCATGT
* * * **
409345 -AGTGTATTGATACATTGTGTATTGTATCGATACATTATGATATGTATCAATACAGATGAGGGTT
1 GA-TGTATTGATACATTGTGTATTGTATCGATACATTATGATATATATCAAAACAAACAAGGGTT
* * * * *
409409 TTAAGATTTCCTTA-CTTACTACCAGCATATGTATTGATACATTTATGT
65 TTAAGATTTCCTTAGC-TACTACCAACAGATGTATCGACACATTCATGT
*
409457 GATGTATTGACACATT
1 GATGTATTGATACATT
409473 CAATCTTGAA
Statistics
Matches: 106, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
111 4 0.04
112 101 0.95
113 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.40
Consensus pattern (112 bp):
GATGTATTGATACATTGTGTATTGTATCGATACATTATGATATATATCAAAACAAACAAGGGTTT
TAAGATTTCCTTAGCTACTACCAACAGATGTATCGACACATTCATGT
Found at i:419060 original size:52 final size:52
Alignment explanation
Indices: 419004--419190 Score: 211
Period size: 52 Copynumber: 3.6 Consensus size: 52
418994 ATAATATCAA
* *
419004 AATTTTCTCCATCGGGGATACTCCAACTCCGTTTTTTATTTCCAAAATATTG
1 AATTTTCACCATCGGGGATACTCCAACCCCGTTTTTTATTTCCAAAATATTG
** * * *
419056 AATTTTCACCATTAGGGATACTCCAA--CC-TAATTTT-TTTCTAAAATATTAA
1 AATTTTCACCATCGGGGATACTCCAACCCCGT-TTTTTATTTCCAAAATATT-G
* * *
419106 AATTTTCACCACCGGAGATACTCCAACCCCGTTTTTTATTTTCAAAATATTG
1 AATTTTCACCATCGGGGATACTCCAACCCCGTTTTTTATTTCCAAAATATTG
* * *
419158 ACTTTGCACCATTGGGGATACTCCAACCCCGTT
1 AATTTTCACCATCGGGGATACTCCAACCCCGTT
419191 ATATCCGAGG
Statistics
Matches: 110, Mismatches: 19, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
49 13 0.12
50 28 0.25
52 57 0.52
53 12 0.11
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (52 bp):
AATTTTCACCATCGGGGATACTCCAACCCCGTTTTTTATTTCCAAAATATTG
Found at i:419176 original size:102 final size:102
Alignment explanation
Indices: 418996--419185 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
418986 TCACTTTTAT
* * * *
418996 AATATCAAAATTTTCTCCATCGGGGATACTCCAACTCCGTTTTTTATTTCCAAAATATTGAATTT
1 AATATCAAAATTTTCACCACCGGAGATACTCCAACCCCGTTTTTTATTTCCAAAATATTGAATTT
*
419061 TCACCATTAGGGATACTCCAACCTAATTTTTTTCTAA
66 GCACCATTAGGGATACTCCAACCTAATTTTTTTCTAA
* * *
419098 AATATTAAAATTTTCACCACCGGAGATACTCCAACCCCGTTTTTTATTTTCAAAATATTGACTTT
1 AATATCAAAATTTTCACCACCGGAGATACTCCAACCCCGTTTTTTATTTCCAAAATATTGAATTT
*
419163 GCACCATTGGGGATACTCCAACC
66 GCACCATTAGGGATACTCCAACC
419186 CCGTTATATC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 79 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (102 bp):
AATATCAAAATTTTCACCACCGGAGATACTCCAACCCCGTTTTTTATTTCCAAAATATTGAATTT
GCACCATTAGGGATACTCCAACCTAATTTTTTTCTAA
Found at i:419440 original size:79 final size:77
Alignment explanation
Indices: 419122--419735 Score: 478
Period size: 79 Copynumber: 7.8 Consensus size: 77
419112 CACCACCGGA
* * * * * *
419122 GATACTCCAACCCCGTTTTTTATTTTCAAAATATT-GACTTTGCACCATTGGGGATACTCCAACC
1 GATACTCCAACCCC-ATTTTTATTTTCAAAATATTAAAATTTTCATC--TCGGGATACTCCAACC
* *
419186 CCGTTATATCCGAGGG
63 CCGTTATTTTCGA-GG
*
419202 GATACTCCAA--CC--TTTT-TTTTCAAAATATTAAAATTTTCATATCGAGGATACTCCAACCCC
1 GATACTCCAACCCCATTTTTATTTTCAAAATATTAAAATTTTCATCTCG-GGATACTCCAACCCC
419262 GTTATTTTCGAAGG
65 GTTATTTTCG-AGG
* * * * *
419276 GATACTCCAACCCCATTTTTGTTTCCAAAATATTAAATTTTTTCATTTCGGTGATACTGCAACCC
1 GATACTCCAACCCCATTTTTATTTTCAAAATATTAAA-ATTTTCATCTCGG-GATACTCCAACCC
*
419341 CGTTATTTTCTAAGG
64 CGTTATTTTC-GAGG
** *
419356 GATACTCCAACCCCGCTTTTATTTTCAAAATATTAAAATTTTCATCTCAGGGATACTCTAACCCC
1 GATACTCCAACCCCATTTTTATTTTCAAAATATTAAAATTTTCATCTC-GGGATACTCCAACCCC
*
419421 ATTATTTTCGAGG
65 GTTATTTTCGAGG
* * * * * *
419434 GAATACTCCAATCCCATTTTTATTTCCAAAATATT-GATTTTTCACCATTGGAGATACTCCAACC
1 G-ATACTCCAACCCCATTTTTATTTTCAAAATATTAAAATTTTCATC-TCGG-GATACTCCAACC
*
419498 CCGTTATTTCCGAGGG
63 CCGTTATTTTCGA-GG
* * *
419514 GATATTCCAACTCTATTTTTATTTTCAAAAT-TTAAAATTTTTCATCTCGAGGATACTCCAACCC
1 GATACTCCAACCCCATTTTTATTTTCAAAATATTAAAA-TTTTCATCTCG-GGATACTCCAACCC
**
419578 TATTA-TTTCTGAGG
64 CGTTATTTTC-GAGG
* * * * ** * *
419592 AGATACTCTAACCCTATTTTTATTTCCAAAGTA-TCGATTTTTCA-CGATTAGGGATACTCCAAC
1 -GATACTCCAACCCCATTTTTATTTTCAAAATATTAAAATTTTCATC---TCGGGATACTCCAAC
* * * *
419655 CCCATCA-CTTCTAAGGG
62 CCCGTTATTTTC-GA-GG
* * * * **
419672 GATACTCCAACCCCGTTTTCACTTCCAAAATATTAATTTTTTTCATCTCGAGGATACTCCAACC
1 GATACTCCAACCCCATTTTTATTTTCAAAATATTAA-AATTTTCATCTCG-GGATACTCCAACC
419736 TTGATTTTCA
Statistics
Matches: 435, Mismatches: 69, Indels: 60
0.77 0.12 0.11
Matches are distributed among these distances:
73 2 0.00
74 48 0.11
75 11 0.03
76 2 0.00
77 1 0.00
78 33 0.08
79 221 0.51
80 109 0.25
81 7 0.02
82 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.36
Consensus pattern (77 bp):
GATACTCCAACCCCATTTTTATTTTCAAAATATTAAAATTTTCATCTCGGGATACTCCAACCCCG
TTATTTTCGAGG
Found at i:419440 original size:159 final size:156
Alignment explanation
Indices: 419123--419735 Score: 649
Period size: 158 Copynumber: 3.9 Consensus size: 156
419113 ACCACCGGAG
* * * *
419123 ATACTCCAACCCCGTTTTTTATTTTCAAAATATTGACTTTGCACCATTGGGGATACTCCAACCCC
1 ATACTCCAACCCC-ATTTTTATTTCCAAAATATTGATTTTTCA-CATT-GGGATACTCCAACCCC
* * *
419188 GTTATATCCGAGGGGATACTCCAA---C-CTTTT-TTTTCAAAATATTAAAATTTTCATATCGAG
63 GTTATTTCCGAAGGGATACTCCAACCCCGCTTTTATTTTCAAAATATTAAAATTTTCATCTCGAG
*
419248 GATACTCCAACCCCGTTATTTTCGAAGGG-
128 GATACTCCAACCCCATTATTTTCG-AGGGA
* * * *
419277 ATACTCCAACCCCATTTTTGTTTCCAAAATATTAAATTTTTTCA-TTTCGGTGATACTGCAACCC
1 ATACTCCAACCCCATTTTTATTTCCAAAATATT-GA-TTTTTCACATT-GG-GATACTCCAACCC
* *
419341 CGTTATTTTCTAAGGGATACTCCAACCCCGCTTTTATTTTCAAAATATTAAAATTTTCATCTC-A
62 CGTTATTTCCGAAGGGATACTCCAACCCCGCTTTTATTTTCAAAATATTAAAATTTTCATCTCGA
*
419405 GGGATACTCTAACCCCATTATTTTCGAGGGA
127 -GGATACTCCAACCCCATTATTTTCGAGGGA
*
419436 ATACTCCAATCCCATTTTTATTTCCAAAATATTGATTTTTCACCATTGGAGATACTCCAACCCCG
1 ATACTCCAACCCCATTTTTATTTCCAAAATATTGATTTTTCA-CATTGG-GATACTCCAACCCCG
* * * ***
419501 TTATTTCCGAGGGGATATTCCAACTCTATTTTTATTTTCAAAAT-TTAAAATTTTTCATCTCGAG
64 TTATTTCCGAAGGGATACTCCAACCCCGCTTTTATTTTCAAAATATTAAAA-TTTTCATCTCGAG
*
419565 GATACTCCAACCCTATTA-TTTCTGA-GGA
128 GATACTCCAACCCCATTATTTTC-GAGGGA
* * * *
419593 GATACTCTAACCCTATTTTTATTTCCAAAGTATCGATTTTTCACGATTAGGGATACTCCAACCCC
1 -ATACTCCAACCCCATTTTTATTTCCAAAATATTGATTTTTCAC-ATT-GGGATACTCCAACCCC
* * * * * * **
419658 ATCACTT-CTAAGGGGATACTCCAACCCCG-TTTTCACTTCCAAAATATTAATTTTTTTCATCTC
63 GTTATTTCCGAA-GGGATACTCCAACCCCGCTTTT-ATTTTCAAAATATTAA-AATTTTCATCTC
419721 GAGGATACTCCAACC
125 GAGGATACTCCAACC
419736 TTGATTTTCA
Statistics
Matches: 387, Mismatches: 50, Indels: 39
0.81 0.11 0.08
Matches are distributed among these distances:
153 21 0.05
154 47 0.12
155 5 0.01
157 28 0.07
158 172 0.44
159 114 0.29
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.36
Consensus pattern (156 bp):
ATACTCCAACCCCATTTTTATTTCCAAAATATTGATTTTTCACATTGGGATACTCCAACCCCGTT
ATTTCCGAAGGGATACTCCAACCCCGCTTTTATTTTCAAAATATTAAAATTTTCATCTCGAGGAT
ACTCCAACCCCATTATTTTCGAGGGA
Found at i:433059 original size:20 final size:20
Alignment explanation
Indices: 433016--433061 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
433006 AAATCTTTTG
433016 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
433037 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
433057 CAAAA
1 CAAAA
433062 CTAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:435497 original size:13 final size:13
Alignment explanation
Indices: 435479--435504 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
435469 ACACCAAAGT
435479 ATGTATCGATACA
1 ATGTATCGATACA
435492 ATGTATCGATACA
1 ATGTATCGATACA
435505 TAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:436425 original size:79 final size:79
Alignment explanation
Indices: 436291--436519 Score: 255
Period size: 79 Copynumber: 2.9 Consensus size: 79
436281 TTGTTTTTAA
* * * * *
436291 GGGATACTCCAA-CCTCGTTTTTATTTCTAAAATATTTATTTTTAACCATCAAGGATACTCCAAC
1 GGGATACTCCAACCCT-GTTTTTATTTCCAAAATATTAATTTTTCACCATCGAGGATACTTCAAC
* *
436355 CCCATTATTTTCGAG
65 CCAATCATTTTCGAG
* *
436370 GGGATACTCCAACCCTGTTTTTATTTCCAAAACATTAATTTTTCACCATCGAGGATACTTTAACC
1 GGGATACTCCAACCCTGTTTTTATTTCCAAAATATTAATTTTTCACCATCGAGGATACTTCAACC
*
436435 CAATCATTTTTGAG
66 CAATCATTTTCGAG
* * * * * * *
436449 GAGATACTCCAACCCCGTTTTCACTTCCAAAGTATTAAATTTTTTCATC-TCGGGGATACTTCAA
1 GGGATACTCCAACCCTGTTTTTATTTCCAAAATATT-AA-TTTTTCACCATCGAGGATACTTCAA
436513 CCTCAAT
64 CC-CAAT
436520 TTTCACCAAA
Statistics
Matches: 127, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
79 95 0.75
80 20 0.16
81 12 0.09
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (79 bp):
GGGATACTCCAACCCTGTTTTTATTTCCAAAATATTAATTTTTCACCATCGAGGATACTTCAACC
CAATCATTTTCGAG
Found at i:439102 original size:159 final size:159
Alignment explanation
Indices: 438813--439551 Score: 676
Period size: 159 Copynumber: 4.7 Consensus size: 159
438803 ATATCAATTT
* * * * *
438813 TTTTTAACCATCGAGGATACTCCAACCCCATCATTTTCGAATGGATACTCCAACCCCATTTTTAC
1 TTTTTCACCATCGGGGATACTCCAACCCCATTATTTTTGAAGGGATACTCCAACCCCATTTTTAC
* *
438878 TTCCAAAATATCAAA-CTTTCACCATCGGGGATAC-TCGAACCCCATCATTTCCGAAGGGATACT
66 TTCCAAAATATCAAATTTTTCACCATCGGGGATACTTC-AACCCCATTATTTCCG-AGGGATACT
*** ***
438941 CCAACCTTGTTTTTACTTCCAAAATAGCGAA
129 CCAACCCCATTTTTACTTCCAAAATATTAAA
* * **
438972 TTTTTTACCATCGGGGATACTCCAA-CACATTATTTTTGAAGGGATACTCCAACCCGGTTTTTAC
1 TTTTTCACCATCGGGGATACTCCAACCCCATTATTTTTGAAGGGATACTCCAACCCCATTTTTAC
* * *
439036 TTCCAAAATATCAAATTTTTCATCATCGGGGTTACTTCAACCCTATTATTTCCGAGGGGATACTC
66 TTCCAAAATATCAAATTTTTCACCATCGGGGATACTTCAACCCCATTATTTCCGA-GGGATACTC
439101 CAACCCCATTTTTCACTTCCAAAATATTAAA
130 CAACCCCATTTTT-ACTTCCAAAATATTAAA
* * * * *** * * *
439132 ATTTTCATC-TCGGTGATACTCTAACCTTGTTA-TTTTCAAGGGGATACTGCAACCCTATTTTTA
1 TTTTTCACCATCGGGGATACTCCAACCCCATTATTTTTGAA-GGGATACTCCAACCCCATTTTTA
* * * * * ** *
439195 TTTCTAAAATATC-GATATTTCACCATCGGGGATAC-TCTAACCCCGTTATTTCTTAGGGATATT
65 CTTCCAAAATATCAAATTTTTCACCATCGGGGATACTTC-AACCCCATTATTTCCGAGGGATACT
* * *
439258 CCAACCGCGTTTTTATTTCCAAAATATTAAA
129 CCAACCCCATTTTTACTTCCAAAATATTAAA
* * * * * * * *
439289 ATTTTCATC-TCGGGGATACTCCAACCCCGTTGTTTTCG-AGGGATACTCTAACCCCGTTTTTAT
1 TTTTTCACCATCGGGGATACTCCAACCCCATTATTTTTGAAGGGATACTCCAACCCCATTTTTAC
* ** * ** * ** *
439352 TTCTAAAATAT-TGATTTTTTACCATCAAGGATACTCCAACCCTGTTATTTTCGATGGGATACTC
66 TTCCAAAATATCAAATTTTTCACCATCGGGGATACTTCAACCCCATTATTTCCGA-GGGATACTC
* * * *
439416 CAACCCTATTTTTATTTCCAAAACATT-GA
130 CAACCCCATTTTTACTTCCAAAATATTAAA
* * *
439445 TTTTTCACCATCGAGGATACTCCAACCCCATCATTTTTG-AGGAGATACTCCAACCCCATTTTCA
1 TTTTTCACCATCGGGGATACTCCAACCCCATTATTTTTGAAGG-GATACTCCAACCCCATTTTTA
* * * *
439509 CTTCCAAAGTATTAAATTTTTTCATC-TTGGGGATACTTCAACC
65 CTTCCAAAATATCAAA-TTTTTCACCATCGGGGATACTTCAACC
439552 TCGATTTTCA
Statistics
Matches: 473, Mismatches: 92, Indels: 30
0.79 0.15 0.05
Matches are distributed among these distances:
156 70 0.15
157 103 0.22
158 100 0.21
159 136 0.29
160 64 0.14
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (159 bp):
TTTTTCACCATCGGGGATACTCCAACCCCATTATTTTTGAAGGGATACTCCAACCCCATTTTTAC
TTCCAAAATATCAAATTTTTCACCATCGGGGATACTTCAACCCCATTATTTCCGAGGGATACTCC
AACCCCATTTTTACTTCCAAAATATTAAA
Found at i:439165 original size:80 final size:80
Alignment explanation
Indices: 438821--439551 Score: 647
Period size: 79 Copynumber: 9.2 Consensus size: 80
438811 TTTTTTTAAC
* * **
438821 CATCGAGGATACTCCAACCCCATCATTTTCGAATGGATACTCCAACCCCATTTTTACTTCCAAAA
1 CATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCATTTTTACTTCCAAAA
* * *
438886 TATCAAA-CTTTCAC
66 TATTAAATTTTTCAT
* * * * ***
438900 CATCGGGGATACTCGAACCCCATCATTTCCGAAGGGATACTCCAACCTTGTTTTTACTTCCAAAA
1 CATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCATTTTTACTTCCAAAA
*** * *
438965 TAGCGAATTTTTTAC
66 TATTAAATTTTTCAT
* * * **
438980 CATCGGGGATACTCCAA-CACATTATTTTTGAAGGGATACTCCAACCCGGTTTTTACTTCCAAAA
1 CATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCATTTTTACTTCCAAAA
*
439044 TATCAAATTTTTCAT
66 TATTAAATTTTTCAT
* * * *
439059 CATCGGGGTTACTTCAACCCTATTATTTCCGAGGGGATACTCCAACCCCATTTTTCACTTCCAAA
1 CATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCATTTTT-ACTTCCAAA
*
439124 ATATTAAAATTTTCAT
65 ATATTAAATTTTTCAT
* * *** * * * * *
439140 C-TCGGTGATACTCTAACCTTGTTATTTTCAAGGGGATACTGCAACCCTATTTTTATTTCTAAAA
1 CATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCATTTTTACTTCCAAAA
** * *
439204 TA-TCGATATTTCAC
66 TATTAAATTTTTCAT
* * * * * * *
439218 CATCGGGGATACTCTAACCCCGTTA-TTTCTTA-GGGATATTCCAACCGCGTTTTTATTTCCAAA
1 CATCGGGGATACTCCAACCCCATTATTTTC-GAGGGGATACTCCAACCCCATTTTTACTTCCAAA
*
439281 ATATTAAAATTTTCAT
65 ATATTAAATTTTTCAT
* * * * * *
439297 C-TCGGGGATACTCCAACCCCGTTGTTTTCGA-GGGATACTCTAACCCCGTTTTTATTTCTAAAA
1 CATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCATTTTTACTTCCAAAA
* * *
439360 TATT-GATTTTTTAC
66 TATTAAATTTTTCAT
** ** * * *
439374 CATCAAGGATACTCCAACCCTGTTATTTTCGATGGGATACTCCAACCCTATTTTTATTTCCAAAA
1 CATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCATTTTTACTTCCAAAA
* * *
439439 CATT-GATTTTTCAC
66 TATTAAATTTTTCAT
* * * * * *
439453 CATCGAGGATACTCCAACCCCATCATTTTTGAGGAGATACTCCAACCCCATTTTCACTTCCAAAG
1 CATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCATTTTTACTTCCAAAA
439518 TATTAAATTTTTTCAT
66 TATTAAA-TTTTTCAT
* *
439534 C-TTGGGGATACTTCAACC
1 CATCGGGGATACTCCAACC
439552 TCGATTTTCA
Statistics
Matches: 538, Mismatches: 103, Indels: 21
0.81 0.16 0.03
Matches are distributed among these distances:
77 7 0.01
78 120 0.22
79 270 0.50
80 109 0.20
81 32 0.06
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (80 bp):
CATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCATTTTTACTTCCAAAA
TATTAAATTTTTCAT
Found at i:442494 original size:107 final size:107
Alignment explanation
Indices: 442308--442531 Score: 385
Period size: 107 Copynumber: 2.1 Consensus size: 107
442298 TTGATATCTC
* * *
442308 TTTAAAACCATAAGCAGCATAAGCATATTTTTTCTAGCAATGATCTACATAAATGGTTATTAGAG
1 TTTAAAACCATAAGCAGCATAAGCATATTTTCTCTAGCAATGATCTACACAAATGGCTATTAGAG
*
442373 CATTCATGATGTCTAATGGTTCTTTAATGCTAGTCAGAAGTT
66 CATTCATGATGTCTAATGGTTCTTTAATGCTAGTCAAAAGTT
* *
442415 TTTAAAACCATAAGCAGCATAAGCATCTTTTCTCTAGCGATGATCTACACAAATGGCTATTAGAG
1 TTTAAAACCATAAGCAGCATAAGCATATTTTCTCTAGCAATGATCTACACAAATGGCTATTAGAG
442480 CATTCATGATGTCTAATGGTTCTTTAATGCTAGTCAAAAGTT
66 CATTCATGATGTCTAATGGTTCTTTAATGCTAGTCAAAAGTT
442522 TTTAGAAACC
1 TTTA-AAACC
442532 TTAACCAAAA
Statistics
Matches: 110, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 105 0.95
108 5 0.05
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (107 bp):
TTTAAAACCATAAGCAGCATAAGCATATTTTCTCTAGCAATGATCTACACAAATGGCTATTAGAG
CATTCATGATGTCTAATGGTTCTTTAATGCTAGTCAAAAGTT
Found at i:442821 original size:11 final size:11
Alignment explanation
Indices: 442797--442834 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
442787 CAATTTTACT
442797 TTATGTAAAT-A
1 TTAT-TAAATAA
442808 TTATTAAATAA
1 TTATTAAATAA
*
442819 TTATCAAATAA
1 TTATTAAATAA
442830 TTATT
1 TTATT
442835 TAATTTGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (11 bp):
TTATTAAATAA
Found at i:446221 original size:96 final size:96
Alignment explanation
Indices: 446102--446320 Score: 291
Period size: 97 Copynumber: 2.3 Consensus size: 96
446092 TTGAAAAACG
* * *
446102 AGGTTGGAGTA-TCCCTTCGGAGGAATGGGGTTG-GGTGTCC-CTGATGATGGCAATTTAAGTGA
1 AGGTTGGAGTATTCCC-TCGGAGGAATGGGGTTGAAGTGTCCTC-GATGATGACAATATAAGTGA
*
446164 GAATAAGATTTAAACTTTGATGTGTTAAAAAGC
64 GAATAAGATTTAAAATTTGATGTGTTAAAAAGC
*
446197 AAGGTTGGAGTATTCCCTCGGAGGAATGGGGTTGAAGTGTCCTCGATGGTGACAATATAAGTGAG
1 -AGGTTGGAGTATTCCCTCGGAGGAATGGGGTTGAAGTGTCCTCGATGATGACAATATAAGTGAG
*
446262 AATAAGATTTAAAATTTGATGTGTTTAAAAGC
65 AATAAGATTTAAAATTTGATGTGTTAAAAAGC
* * * *
446294 GGGATTGAAGTATCCCCTCAGAGGAAT
1 AGG-TTGGAGTATTCCCTCGGAGGAAT
446321 AGGTTTAGAG
Statistics
Matches: 109, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
96 30 0.28
97 78 0.72
98 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.29
Consensus pattern (96 bp):
AGGTTGGAGTATTCCCTCGGAGGAATGGGGTTGAAGTGTCCTCGATGATGACAATATAAGTGAGA
ATAAGATTTAAAATTTGATGTGTTAAAAAGC
Found at i:457047 original size:17 final size:17
Alignment explanation
Indices: 457025--457057 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
457015 TCATGGAAAC
457025 ATGTTAAGATCACTAAT
1 ATGTTAAGATCACTAAT
457042 ATGTTAAGATCACTAA
1 ATGTTAAGATCACTAA
457058 AATGATGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (17 bp):
ATGTTAAGATCACTAAT
Found at i:458630 original size:19 final size:19
Alignment explanation
Indices: 458606--458658 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
458596 TTTTAACGAT
458606 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
458625 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
458644 TTGTATCGATACATA
1 TTGTATCGATACATA
458659 TGAAGCTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:458718 original size:13 final size:13
Alignment explanation
Indices: 458700--458724 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
458690 ATTACTCAAA
458700 TGTATCGATACAT
1 TGTATCGATACAT
458713 TGTATCGATACA
1 TGTATCGATACA
458725 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:458776 original size:52 final size:52
Alignment explanation
Indices: 458733--458858 Score: 225
Period size: 52 Copynumber: 2.4 Consensus size: 52
458723 CACTGATCTT
*
458733 TGTATCGATACACGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
458785 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATTGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
458837 TGTATCGATACATGCAGGCAAA
1 TGTATCGATACATGCAGGCAAA
458859 ATTTCATATT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:462489 original size:3 final size:3
Alignment explanation
Indices: 462481--462507 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
462471 TGATCATTTG
462481 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
462508 CATGGTGTAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:462771 original size:22 final size:20
Alignment explanation
Indices: 462745--462791 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
462735 TACCTCTTTG
462745 TTTCTATTTCTTCTCTATTTT
1 TTTCTATTTCTTCTCT-TTTT
* *
462766 CTTTCTCTTTCTTTTCTTTTT
1 -TTTCTATTTCTTCTCTTTTT
462787 TTTCT
1 TTTCT
462792 TTTTTTAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 4 0.17
22 14 0.61
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTCTATTTCTTCTCTTTTT
Found at i:462781 original size:11 final size:10
Alignment explanation
Indices: 462725--462797 Score: 51
Period size: 11 Copynumber: 6.8 Consensus size: 10
462715 AAGCCAGCCT
462725 TATTTTTTTC
1 TATTTTTTTC
462735 TACCTCTTTGTTTC
1 TA--T-TTT-TTTC
*
462749 TATTTCTTCTC
1 TATTT-TTTTC
462760 TATTTTCTTTC
1 TATTTT-TTTC
*
462771 TCTTTCTTTTC
1 TATTT-TTTTC
462782 T-TTTTTTTC
1 TATTTTTTTC
462791 T-TTTTTT
1 TATTTTTT
462798 AGTTGAACCT
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
9 12 0.23
10 6 0.11
11 22 0.42
12 4 0.08
13 3 0.06
14 6 0.11
ACGTcount: A:0.05, C:0.19, G:0.01, T:0.74
Consensus pattern (10 bp):
TATTTTTTTC
Found at i:464541 original size:57 final size:57
Alignment explanation
Indices: 464335--464940 Score: 667
Period size: 57 Copynumber: 10.6 Consensus size: 57
464325 CCAACTTCTA
* * *
464335 TGGGC-TTTGAAAAGGGTTGCCACTAACTTGTGGGCTTTGAAAAGG-TGCCATTGACTTG
1 TGGGCTTTTG-AAA-GGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTG
* * * * *
464393 TTGGCTTTTGAAAGG-TACCACTGAGTTGTTGGCTTTTGAAAGG-TGCCATTGACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGC-TTTGAAAGGATGCCACTGACTTG
* * * *
464449 TGGGC-TTTGAAAGGATACCATTGACTTGTGGGCTTTGAAAGGATACCATTGACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTG
* * **
464505 TGGGCTTTTGAAAGGATGCCATTGACTTGTGAGCTTTCGAAAGGATGCCACAAACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTT-GAAAGGATGCCACTGACTTG
* * * * * ***
464563 TGGG-TTTGGAAAGGATGGCACTGACTCGTGGGCTTTTGAAAAGATGCTACTGACCCA
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGC-TTTGAAAGGATGCCACTGACTTG
** * * * *
464620 TGGGCTTTAAAAAGGATGCCACTAACTTGTAGGCTTTGAAA-GAGGCCACTAACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTG
* * * *
464676 T-GGATTTTGAAAGGATGCCACTGACTCGTGGGCTTTAAAAAGGATGCCACTAACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTT-GAAAGGATGCCACTGACTTG
*
464733 TGGGC-TTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTG
* * * *
464789 TGGGC-TTTGAAAAGATGCCACTAACTTATGGGCTTTTGAAAGGATGCCACTGACTTA
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGC-TTTGAAAGGATGCCACTGACTTG
* *
464846 TGGGCTTTTGAAAGGATGCCACTGACTTATGGGCTTTAAAAAGGATGCCACTGACTTG
1 TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTT-GAAAGGATGCCACTGACTTG
*
464904 TGGGC-TTTAAAATGGATGCCACTGACTTGTGGGCTTT
1 TGGGCTTTTGAAA-GGATGCCACTGACTTGTGGGCTTT
464941 AAAAAAGGTC
Statistics
Matches: 469, Mismatches: 64, Indels: 30
0.83 0.11 0.05
Matches are distributed among these distances:
55 47 0.10
56 128 0.27
57 163 0.35
58 127 0.27
59 4 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (57 bp):
TGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTG
Found at i:464862 original size:284 final size:284
Alignment explanation
Indices: 464334--464945 Score: 793
Period size: 284 Copynumber: 2.2 Consensus size: 284
464324 ACCAACTTCT
* * * * *
464334 ATGGGCTTTGAAAAGGGTTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCATTGACTTGTTGGCT
1 ATGGGCTTT-AAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTAACTTGTTGGAT
* * * ** * *
464399 TTTGAAAGGTACCACTGAGTTGTTGGCTTTTGAAAGGTGCCATTGACTTGTGGGCTTTGAAAGGA
65 TTTGAAAGGTACCACTGACTCGTGGGCTTTAAAAAGGTGCCACTAACTTGTGGGCTTTGAAAGGA
* * * *
464464 TACCATTGACTTGTGGGCTTTGAAAGGATACCATTGACTTGTGGGCTTTTGAAAGGATGCCATTG
130 TACCATTGACTTGTGGGCTTTGAAAGGATACCACTGACTTGTGGGCTTTTGAAAAGATGCCACTA
* * * *
464529 ACTTGTGAGCTTTCGAAAGGATGCCACAAACTTGTGGGTTTGGAAAGGATGGCACTGACTCGTGG
195 ACTTATGAGCTTTCGAAAGGATGCCACAAACTTATGGGTTTGGAAAGGATGCCACTGACTCATGG
* *
464594 GCTTTTGAAAA-GATGCTACTGACCC
260 GC-TTTAAAAAGGATGCCACTGACCC
*
464619 ATGGGCTTTAAAAAGGATGCCACTAACTTGTAGGCTTTG-AAAGAG-GCCACTAACTTG-TGGAT
1 ATGGGCTTTAAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAG-GTGCCACTAACTTGTTGGAT
*
464681 TTTGAAAGGATGCCACTGACTCGTGGGCTTTAAAAAGGATGCCACTAACTTGTGGGCTTTGAAAG
65 TTTGAAAGG-TACCACTGACTCGTGGGCTTTAAAAAGG-TGCCACTAACTTGTGGGCTTTGAAAG
* *
464746 GATGCCATTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC-TTTGAAAAGATGCCAC
128 GATACCATTGACTTGTGGGCTTTGAAAGGATACCACTGACTTGTGGGCTTTTGAAAAGATGCCAC
* * ** * *
464810 TAACTTATGGGCTTTTGAAAGGATGCCACTGACTTATGGGCTTTTGAAAGGATGCCACTGACTTA
193 TAACTTATGAGCTTTCGAAAGGATGCCACAAACTTATGGG-TTTGGAAAGGATGCCACTGACTCA
**
464875 TGGGCTTTAAAAAGGATGCCACTGACTT
257 TGGGCTTTAAAAAGGATGCCACTGACCC
* * * *
464903 GTGGGCTTTAAAATGGATGCCACTGACTTGTGGGCTTTAAAAA
1 ATGGGCTTTAAAAAGGATGCCACTAACTTGTGGGCTTTGAAAA
464946 AGGTCATATT
Statistics
Matches: 282, Mismatches: 39, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
282 13 0.05
283 90 0.32
284 167 0.59
285 12 0.04
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (284 bp):
ATGGGCTTTAAAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTAACTTGTTGGATT
TTGAAAGGTACCACTGACTCGTGGGCTTTAAAAAGGTGCCACTAACTTGTGGGCTTTGAAAGGAT
ACCATTGACTTGTGGGCTTTGAAAGGATACCACTGACTTGTGGGCTTTTGAAAAGATGCCACTAA
CTTATGAGCTTTCGAAAGGATGCCACAAACTTATGGGTTTGGAAAGGATGCCACTGACTCATGGG
CTTTAAAAAGGATGCCACTGACCC
Found at i:464944 original size:29 final size:28
Alignment explanation
Indices: 464335--464940 Score: 673
Period size: 28 Copynumber: 21.3 Consensus size: 28
464325 CCAACTTCTA
* *
464335 TGGGCTTTGAAAAGGGTTGCCACTAACTTG
1 TGGGCTTTG-AAA-GGATGCCACTGACTTG
*
464365 TGGGCTTTGAAAAGG-TGCCATTGACTTG
1 TGGGCTTTG-AAAGGATGCCACTGACTTG
* * *
464393 TTGGCTTTTGAAAGG-TACCACTGAGTTG
1 TGGGC-TTTGAAAGGATGCCACTGACTTG
* *
464421 TTGGCTTTTGAAAGG-TGCCATTGACTTG
1 TGGGC-TTTGAAAGGATGCCACTGACTTG
* *
464449 TGGGCTTTGAAAGGATACCATTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* *
464477 TGGGCTTTGAAAGGATACCATTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
*
464505 TGGGCTTTTGAAAGGATGCCATTGACTTG
1 TGGGC-TTTGAAAGGATGCCACTGACTTG
* **
464534 TGAGCTTTCGAAAGGATGCCACAAACTTG
1 TGGGCTTT-GAAAGGATGCCACTGACTTG
* *
464563 TGGG-TTTGGAAAGGATGGCACTGACTCG
1 TGGGCTTT-GAAAGGATGCCACTGACTTG
* * ***
464591 TGGGCTTTTGAAAAGATGCTACTGACCCA
1 TGGGC-TTTGAAAGGATGCCACTGACTTG
* *
464620 TGGGCTTTAAAAAGGATGCCACTAACTTG
1 TGGGCTTT-GAAAGGATGCCACTGACTTG
* * *
464649 TAGGCTTTGAAA-GAGGCCACTAACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
** *
464676 TGGATTTTGAAAGGATGCCACTGACTCG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* *
464704 TGGGCTTTAAAAAGGATGCCACTAACTTG
1 TGGGCTTT-GAAAGGATGCCACTGACTTG
*
464733 TGGGCTTTGAAAGGATGCCATTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
464761 TGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAGGATGCCACTGACTTG
* * *
464789 TGGGCTTTGAAAAGATGCCACTAACTTA
1 TGGGCTTTGAAAGGATGCCACTGACTTG
*
464817 TGGGCTTTTGAAAGGATGCCACTGACTTA
1 TGGGC-TTTGAAAGGATGCCACTGACTTG
*
464846 TGGGCTTTTGAAAGGATGCCACTGACTTA
1 TGGGC-TTTGAAAGGATGCCACTGACTTG
*
464875 TGGGCTTTAAAAAGGATGCCACTGACTTG
1 TGGGCTTT-GAAAGGATGCCACTGACTTG
*
464904 TGGGCTTTAAAATGGATGCCACTGACTTG
1 TGGGCTTTGAAA-GGATGCCACTGACTTG
464933 TGGGCTTT
1 TGGGCTTT
464941 AAAAAAGGTC
Statistics
Matches: 505, Mismatches: 59, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
27 32 0.06
28 235 0.47
29 222 0.44
30 16 0.03
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (28 bp):
TGGGCTTTGAAAGGATGCCACTGACTTG
Found at i:465027 original size:27 final size:26
Alignment explanation
Indices: 464959--465027 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
464949 TCATATTGAC
464959 GAAAATTTCTTGAC-AAAGTTTCCGAT
1 GAAAA-TTCTTGACAAAAGTTTCCGAT
* * *
464985 GAACATTCTCGACAAAAG-TTCTTGAT
1 GAAAATTCTTGACAAAAGTTTC-CGAT
465011 GATAAATTCTTGACAAA
1 GA-AAATTCTTGACAAA
465028 TGGTAAATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 10 0.29
26 13 0.37
27 12 0.34
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (26 bp):
GAAAATTCTTGACAAAAGTTTCCGAT
Found at i:466227 original size:13 final size:13
Alignment explanation
Indices: 466211--466248 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
466201 TTTTTTGTTT
466211 GTTTATTTTTTT-G
1 GTTT-TTTTTTTAG
466224 GTTTTTTTTTTAG
1 GTTTTTTTTTTAG
*
466237 CTTTTTTTTTTA
1 GTTTTTTTTTTA
466249 TTTCTTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.08, C:0.03, G:0.11, T:0.79
Consensus pattern (13 bp):
GTTTTTTTTTTAG
Found at i:466231 original size:12 final size:11
Alignment explanation
Indices: 466201--466276 Score: 73
Period size: 12 Copynumber: 6.6 Consensus size: 11
466191 TAGACCCTTC
*
466201 TTTTTTGTTTG
1 TTTTTTTTTTG
466212 TTTATTTTTTTGG
1 TTT-TTTTTTT-G
466225 TTTTTTTTTTAG
1 TTTTTTTTTT-G
*
466237 CTTTTTTTTT-
1 TTTTTTTTTTG
* *
466247 TATTTCTTTTG
1 TTTTTTTTTTG
466258 TTTTTTTTTTCG
1 TTTTTTTTTT-G
466270 TTTTTTT
1 TTTTTTT
466277 ATACGAAGGA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
10 7 0.13
11 11 0.21
12 31 0.58
13 4 0.08
ACGTcount: A:0.04, C:0.04, G:0.09, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:466249 original size:33 final size:33
Alignment explanation
Indices: 466203--466276 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
466193 GACCCTTCTT
466203 TTTTGTTTGTTTATTT-TTTTGGTTTTTTTTTTAG
1 TTTT-TTTGTTTATTTCTTTT-GTTTTTTTTTTAG
*
466237 CTTTTTTT-TTTATTTCTTTTGTTTTTTTTTTCG
1 -TTTTTTTGTTTATTTCTTTTGTTTTTTTTTTAG
466270 TTTTTTT
1 TTTTTTT
466277 ATACGAAGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
32 7 0.19
33 19 0.51
34 7 0.19
35 4 0.11
ACGTcount: A:0.04, C:0.04, G:0.09, T:0.82
Consensus pattern (33 bp):
TTTTTTTGTTTATTTCTTTTGTTTTTTTTTTAG
Found at i:473212 original size:21 final size:20
Alignment explanation
Indices: 473182--473220 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
473172 GTTAGGACCT
473182 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
*
473203 TGTATTGATACATTTAGA
1 TGTATCGATACATTTAGA
473221 CAAAAATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:477851 original size:49 final size:49
Alignment explanation
Indices: 477798--478032 Score: 228
Period size: 49 Copynumber: 4.8 Consensus size: 49
477788 TAATATGCTA
* * * * *
477798 ATTCAAGGCCAACGATATCGGACTTAAAGATAAAGGTACCAATGCACTG
1 ATTCAAGGCCAGCGATATCGGACTTAAAGATGAAGATGCCAATGCGCTG
* * *
477847 ATTCAAGACCAGCGATATCGGACTTAAAGATGATGATGCCAATACGCTG
1 ATTCAAGGCCAGCGATATCGGACTTAAAGATGAAGATGCCAATGCGCTG
* *
477896 ATTCAAGGCCAGCGATATCGGACTTAAAGATGAACATGCCAATGTGCTG
1 ATTCAAGGCCAGCGATATCGGACTTAAAGATGAAGATGCCAATGCGCTG
* * * * * *
477945 ATTCAAGGCTAGCGACATTTGGTCTTAAAG--GCAAGGTGCCAATAG-GTTG
1 ATTCAAGGCCAGCGATA-TCGGACTTAAAGATG-AAGATGCCAAT-GCGCTG
* * * *
477994 ATTCCAGGCTAGCGATATTGGACTT--AGAAGAAGATGCCA
1 ATTCAAGGCCAGCGATATCGGACTTAAAGATGAAGATGCCA
478033 CCAACTTGTG
Statistics
Matches: 157, Mismatches: 24, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
46 2 0.01
47 8 0.05
48 9 0.06
49 127 0.81
50 11 0.07
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (49 bp):
ATTCAAGGCCAGCGATATCGGACTTAAAGATGAAGATGCCAATGCGCTG
Found at i:478130 original size:57 final size:55
Alignment explanation
Indices: 478023--478240 Score: 199
Period size: 57 Copynumber: 3.8 Consensus size: 55
478013 GGACTTAGAA
** *
478023 GAAGATGCCACCAACTTGTGTGGTCTTTTAA-AATGATGCCACTGACTTGTGGGCTTTTT
1 GAAGATGCCACTGACTTGTG-GG-C-TTTAAGAA-GGTGCCACTGA-TTGTGGGCTTTTT
* * *
478082 GAAGGTTGCCA-TCGACTTGTGGGCTTTGAGAAGGTGCCACTAAGTTGTGGGC-TTTT
1 GAA-GATGCCACT-GACTTGTGGGCTTTAAGAAGGTGCCACTGA-TTGTGGGCTTTTT
** * **
478138 GAAAAGATGCCACTGACTTGTGGGCTTTTTGATGGTTGCCACTGATTCGTGGGCTTTAA
1 G--AAGATGCCACTGACTTGTGGGCTTTAAGAAGG-TGCCACTGATT-GTGGGCTTTTT
*
478197 GAAGATGCCACTGACTTGTGGGCTTTAAGAAGATGCCACTGATT
1 GAAGATGCCACTGACTTGTGGGCTTTAAGAAGGTGCCACTGATT
478241 AACTTGTGGG
Statistics
Matches: 132, Mismatches: 18, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
56 16 0.12
57 75 0.57
58 20 0.15
59 8 0.06
60 13 0.10
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (55 bp):
GAAGATGCCACTGACTTGTGGGCTTTAAGAAGGTGCCACTGATTGTGGGCTTTTT
Found at i:478169 original size:86 final size:85
Alignment explanation
Indices: 478021--478238 Score: 298
Period size: 86 Copynumber: 2.5 Consensus size: 85
478011 TTGGACTTAG
*
478021 AAGAAGATGCCACCAACTTGTGTGGTCTTTTAAAATGATGCCACTGACTTGTGGGCTTTTTGAAG
1 AAGAAGATGCCACTAACTTGTG-GG-CTTTTAAAA-GATGCCACTGACTTGTGGGCTTTTTGAAG
478086 GTTGCCA-TCGACTT-GTGGGCTTT
63 GTTGCCACT-GA-TTCGTGGGCTTT
* * * *
478109 GAGAAGGTGCCACTAAGTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTTTGATGGT
1 AAGAAGATGCCACTAACTTGTGGGCTTTT-AAAAGATGCCACTGACTTGTGGGCTTTTTGAAGGT
478174 TGCCACTGATTCGTGGGCTTT
65 TGCCACTGATTCGTGGGCTTT
*
478195 AAGAAGATGCCACTGACTTGTGGGC-TTTAAGAAGATGCCACTGA
1 AAGAAGATGCCACTAACTTGTGGGCTTTTAA-AAGATGCCACTGA
478239 TTAACTTGTG
Statistics
Matches: 117, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
84 2 0.02
85 18 0.15
86 72 0.62
87 7 0.06
88 18 0.15
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.32
Consensus pattern (85 bp):
AAGAAGATGCCACTAACTTGTGGGCTTTTAAAAGATGCCACTGACTTGTGGGCTTTTTGAAGGTT
GCCACTGATTCGTGGGCTTT
Found at i:478253 original size:32 final size:28
Alignment explanation
Indices: 478021--478238 Score: 201
Period size: 29 Copynumber: 7.6 Consensus size: 28
478011 TTGGACTTAG
**
478021 AAGAAGATGCCACCAACTTGTGTGGTCTTTT
1 AAGAAGATGCCACTGACTTGTG-GG-C-TTT
478052 AA-AATGATGCCACTGACTTGTGGGCTTT
1 AAGAA-GATGCCACTGACTTGTGGGCTTT
** *
478080 TTGAAGGTTGCCA-TCGACTTGTGGGCTTT
1 AAGAA-GATGCCACT-GACTTGTGGGCTTT
* * * *
478109 GAGAAGGTGCCACTAAGTTGTGGGCTTTT
1 AAGAAGATGCCACTGACTTGTGGGC-TTT
478138 GAA-AAGATGCCACTGACTTGTGGGCTTT
1 -AAGAAGATGCCACTGACTTGTGGGCTTT
** * *
478166 TTGATGGTTGCCACTGA-TTCGTGGGCTTT
1 AAGA-AGATGCCACTGACTT-GTGGGCTTT
478195 AAGAAGATGCCACTGACTTGTGGGCTTT
1 AAGAAGATGCCACTGACTTGTGGGCTTT
478223 AAGAAGATGCCACTGA
1 AAGAAGATGCCACTGA
478239 TTAACTTGTG
Statistics
Matches: 154, Mismatches: 23, Indels: 23
0.77 0.12 0.12
Matches are distributed among these distances:
28 60 0.39
29 72 0.47
30 5 0.03
31 17 0.11
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.32
Consensus pattern (28 bp):
AAGAAGATGCCACTGACTTGTGGGCTTT
Found at i:479072 original size:50 final size:50
Alignment explanation
Indices: 478997--479096 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
478987 AATTATTCTC
478997 CCGACATTGGAAGGCTTTGTCAACAATCTAGAGGCTGTTTGCCTGATTTG
1 CCGACATTGGAAGGCTTTGTCAACAATCTAGAGGCTGTTTGCCTGATTTG
479047 CCGACATTGGAAGGCTTTGTCAACAATCTAGAGGCTGTTTGCCTGATTTG
1 CCGACATTGGAAGGCTTTGTCAACAATCTAGAGGCTGTTTGCCTGATTTG
479097 GTTTACTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (50 bp):
CCGACATTGGAAGGCTTTGTCAACAATCTAGAGGCTGTTTGCCTGATTTG
Found at i:492993 original size:9 final size:9
Alignment explanation
Indices: 492979--493009 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
492969 AAATGACTTC
492979 AAATCATCA
1 AAATCATCA
492988 AAATCATCA
1 AAATCATCA
492997 AAATCATCA
1 AAATCATCA
493006 AAAT
1 AAAT
493010 AATCCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATCATCA
Found at i:502364 original size:97 final size:97
Alignment explanation
Indices: 502193--502530 Score: 532
Period size: 97 Copynumber: 3.5 Consensus size: 97
502183 TTGAAAAACT
* * * *
502193 GAGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTCAAGTGAG
1 GAGGTTGGAGTATCCCCTCGGAGGAATAGGGTTGAAGTGTCCCCGATGGTGACAATTTAAGTGAG
*
502258 AATAAGATTTAAACTTTGATGTGTTTAAGAGC
66 AATAAGATTTAAACTTTGATGTGTTTAAAAGC
502290 GAGGTTGGAGTATCCCCTCGGAGGAATAGGGTTGAAGTGTCCCCGATGGTGACAATTTAAGTGAG
1 GAGGTTGGAGTATCCCCTCGGAGGAATAGGGTTGAAGTGTCCCCGATGGTGACAATTTAAGTGAG
*
502355 AATACGATTTAAACTTTGATGTGTTTAAAAGC
66 AATAAGATTTAAACTTTGATGTGTTTAAAAGC
* **
502387 GTGGTTGGAGTATCCCCTCTCAGGAATAGGGTTGAAGTGTCCCCGATGGTGACAATTTAAGTGAG
1 GAGGTTGGAGTATCCCCTCGGAGGAATAGGGTTGAAGTGTCCCCGATGGTGACAATTTAAGTGAG
*
502452 AATAAGATTTAAACTTTGATGTGTTTAAAAGT
66 AATAAGATTTAAACTTTGATGTGTTTAAAAGC
* * * * * *
502484 GGGGTTAGAGTATCCACTCGAAGGAATAGGGTTGGAGTATCCCCGAT
1 GAGGTTGGAGTATCCCCTCGGAGGAATAGGGTTGAAGTGTCCCCGAT
502531 AAATAAAATT
Statistics
Matches: 223, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 223 1.00
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.29
Consensus pattern (97 bp):
GAGGTTGGAGTATCCCCTCGGAGGAATAGGGTTGAAGTGTCCCCGATGGTGACAATTTAAGTGAG
AATAAGATTTAAACTTTGATGTGTTTAAAAGC
Found at i:510424 original size:23 final size:22
Alignment explanation
Indices: 510397--510439 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
510387 GTAAATATAA
510397 TTAAATAATTATCAAATAATTAT
1 TTAAATAATTAT-AAATAATTAT
*
510420 TTAAATTATTATAAATAATT
1 TTAAATAATTATAAATAATT
510440 TTGACCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAATAATTATAAATAATTAT
Found at i:511808 original size:20 final size:20
Alignment explanation
Indices: 511783--511853 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
511773 TGAACTTAAA
511783 GTATCGATACATTTATGGAT
1 GTATCGATACATTTATGGAT
* *
511803 GTATCGATACA-TTCTGTATT
1 GTATCGATACATTTATGGA-T
511823 GTATCGATACATTCTCAT-G-T
1 GTATCGATACATT-T-ATGGAT
511843 GTATCGATACA
1 GTATCGATACA
511854 AAAGAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.12
20 35 0.81
21 1 0.02
22 1 0.02
23 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (20 bp):
GTATCGATACATTTATGGAT
Found at i:511948 original size:21 final size:21
Alignment explanation
Indices: 511890--511948 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
511880 CTGCCAACAA
*
511890 AATGTATCGATACATTCACAT
1 AATGTATCGATACATTTACAT
511911 AATGTATCGATACATTTACAT
1 AATGTATCGATACATTTACAT
511932 AATGTATCGATACATTT
1 AATGTATCGATACATTT
511949 TCATTTGTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTACAT
Found at i:512029 original size:21 final size:21
Alignment explanation
Indices: 512000--512042 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
511990 GCTACTGCCA
*
512000 ACAAAATGTATCTATACATTC
1 ACAAAATGTATCGATACATTC
*
512021 ACAAGATGTATCGATACATTC
1 ACAAAATGTATCGATACATTC
512042 A
1 A
512043 ATCCTTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (21 bp):
ACAAAATGTATCGATACATTC
Found at i:512387 original size:20 final size:20
Alignment explanation
Indices: 512362--512400 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
512352 TATTTGTTTC
512362 GATACAAAAGTAAATGTATT
1 GATACAAAAGTAAATGTATT
* *
512382 GATACATAAGTGAATGTAT
1 GATACAAAAGTAAATGTAT
512401 CAATACATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (20 bp):
GATACAAAAGTAAATGTATT
Found at i:512406 original size:20 final size:20
Alignment explanation
Indices: 512363--512408 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
512353 ATTTGTTTCG
* **
512363 ATACAAAAGTAAATGTATTG
1 ATACATAAGTAAATGTATCA
*
512383 ATACATAAGTGAATGTATCA
1 ATACATAAGTAAATGTATCA
512403 ATACAT
1 ATACAT
512409 GTTTGAAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (20 bp):
ATACATAAGTAAATGTATCA
Found at i:516428 original size:11 final size:10
Alignment explanation
Indices: 516412--516439 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
516402 ATTGGCAAGG
516412 AAAAAAAGAA
1 AAAAAAAGAA
516422 AAAAAAAGAA
1 AAAAAAAGAA
516432 AAAAAAAG
1 AAAAAAAG
516440 CCTAGTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:518578 original size:305 final size:306
Alignment explanation
Indices: 518026--518638 Score: 1021
Period size: 305 Copynumber: 2.0 Consensus size: 306
518016 CCAAGCTAAA
*
518026 GACATTGCTAGAGCAACCATATGAGATATATAAAGGTTTATAAACATATACTCAAGGTGCAGTCA
1 GACATTGCTAGAGCAACCATATGAGATATATAAAGGTTTATAAACATACACTCAAGGTGCAGTCA
* * * *
518091 TTAGGCCAAGTTCACCTCTAATGGTGCAAAATCTATCCTTGTGAAGAGGTTTAGTGAAAATATCA
66 TTAGGCCAAGTTCACCTCTAATGCTACAAAATCTATCATTGTCAAGAGGTTTAGTGAAAATATCA
* * *
518156 GCTAATTGAAGCAAGATGTCAACAAATTCAAGCACAATGTCACCTTTTTGAACATGGTCTCTAAT
131 GCTAATTGAAGCAAGACGTCAACAAATTCAAGCACAATCTCACCTTTTTAAACATGGTCTCTAAT
* *
518221 GAAATGATGTCTTATTTCAATGTGCTTAGTTCTAGAGTGTTGAATCAGATTTTTGGTAAGACAAA
196 GAAATGATGTATTATTTCAATGTGCTTAGTTCTAGAGTATTGAATCAGATTTTTGGTAAGACAAA
* *
518286 TGGCACTAGTATTGTCACATTTAATAGGAATATGATCCATGGTAAG
261 TGGCACTAGTATTGTCACATTTAACAGGAATATGATCCATGGCAAG
* * * * *
518332 GACATTGCTAGAGCTAGCATATGAGATATATCAAGGTTTATAAACATACACTCAAGGTGTA-TTA
1 GACATTGCTAGAGCAACCATATGAGATATATAAAGGTTTATAAACATACACTCAAGGTGCAGTCA
518396 TTAGGCCAAGTTCACCTCTAATGCTACAAAATCTATCATTGTCAAGAGGTTTAGTGAAAATATCA
66 TTAGGCCAAGTTCACCTCTAATGCTACAAAATCTATCATTGTCAAGAGGTTTAGTGAAAATATCA
* *
518461 GCTAATTGATGCAAGACGTCAACAAATTCAAGCACAATCTCACTTTTTTAAACATGGTCTCTAAT
131 GCTAATTGAAGCAAGACGTCAACAAATTCAAGCACAATCTCACCTTTTTAAACATGGTCTCTAAT
* *
518526 GAAATGATGTATTATTTCTATGTGCTTAGTTCTAGAGTATTGAATCAGATTTTTGGTAAGCCAAA
196 GAAATGATGTATTATTTCAATGTGCTTAGTTCTAGAGTATTGAATCAGATTTTTGGTAAGACAAA
*
518591 TGGCACTAGTATTGTCACATTTAACAGGAATATGATCTATGGCAAG
261 TGGCACTAGTATTGTCACATTTAACAGGAATATGATCCATGGCAAG
518637 GA
1 GA
518639 AAACTTGCTA
Statistics
Matches: 285, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
305 229 0.80
306 56 0.20
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (306 bp):
GACATTGCTAGAGCAACCATATGAGATATATAAAGGTTTATAAACATACACTCAAGGTGCAGTCA
TTAGGCCAAGTTCACCTCTAATGCTACAAAATCTATCATTGTCAAGAGGTTTAGTGAAAATATCA
GCTAATTGAAGCAAGACGTCAACAAATTCAAGCACAATCTCACCTTTTTAAACATGGTCTCTAAT
GAAATGATGTATTATTTCAATGTGCTTAGTTCTAGAGTATTGAATCAGATTTTTGGTAAGACAAA
TGGCACTAGTATTGTCACATTTAACAGGAATATGATCCATGGCAAG
Found at i:519017 original size:82 final size:82
Alignment explanation
Indices: 518908--519086 Score: 279
Period size: 82 Copynumber: 2.2 Consensus size: 82
518898 TTTTCACAAT
* *
518908 TTGTATCGATACATTATTCATTATATCGATACATTGTATCGATACTTTCTGGGTTTACCCAGATG
1 TTGTATCGATACATTATTCATTATATCGATACATTGTATCGATACATTCTGGATTTACCCAGATG
518973 TATCGATACATTTTGCA
66 TATCGATACATTTTGCA
* * *
518990 TTGTATCGATACATTGCTT-GTTGTATCGATACATTGTATCGATACATTCTGGATTTACCCAGAT
1 TTGTATCGATACATT-ATTCATTATATCGATACATTGTATCGATACATTCTGGATTTACCCAGAT
*
519054 GTATTGATACATTTTGCA
65 GTATCGATACATTTTGCA
*
519072 ATGTATCGATACATT
1 TTGTATCGATACATT
519087 CAGGCATTTT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
82 87 0.98
83 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (82 bp):
TTGTATCGATACATTATTCATTATATCGATACATTGTATCGATACATTCTGGATTTACCCAGATG
TATCGATACATTTTGCA
Found at i:519025 original size:20 final size:20
Alignment explanation
Indices: 518971--519026 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
518961 TTTACCCAGA
518971 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGTTG-AT
518991 TGTATCGATACATTGCTTG-T
1 TGTATCGATACATTG-TTGAT
519011 TGTATCGATACATTGT
1 TGTATCGATACATTGT
519027 ATCGATACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.03
20 30 0.88
22 3 0.09
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTGTTGAT
Found at i:519028 original size:13 final size:13
Alignment explanation
Indices: 519010--519037 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
519000 ACATTGCTTG
519010 TTGTATCGATACA
1 TTGTATCGATACA
519023 TTGTATCGATACA
1 TTGTATCGATACA
519036 TT
1 TT
519038 CTGGATTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:521593 original size:28 final size:28
Alignment explanation
Indices: 521550--521622 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
521540 TTTCACAATT
* * * **
521550 GGGGATA-TTCAACCCCGTTATTTTATC
1 GGGGATACTCCAACCCCGTTACTTCAGA
*
521577 GGGGATACTCCAACCCCGTTACTTCCGA
1 GGGGATACTCCAACCCCGTTACTTCAGA
521605 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
521623 ACTTTATATC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 7 0.18
28 32 0.82
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.25
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTACTTCAGA
Found at i:521718 original size:28 final size:28
Alignment explanation
Indices: 521658--521727 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
521648 TTTCATAATC
*
521658 GGGGGTACTCCAACCTGTTATTTCGTCGA
1 GGGGATACTCCAACCTGTTATTTC-TCGA
*
521687 --GGATACTCCAATCTCGTTATTT-TCGA
1 GGGGATACTCCAACCT-GTTATTTCTCGA
521713 GGGGATACTCCAACC
1 GGGGATACTCCAACC
521728 CCAATTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
26 4 0.11
27 12 0.34
28 19 0.54
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (28 bp):
GGGGATACTCCAACCTGTTATTTCTCGA
Found at i:521774 original size:51 final size:51
Alignment explanation
Indices: 521714--521831 Score: 177
Period size: 51 Copynumber: 2.3 Consensus size: 51
521704 TATTTTCGAG
* *
521714 GGGATACTCCAACCCCAATTTTATTTCTAAAATACCAATTT-TCCACAA-TC
1 GGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTCT-CACAATTC
*
521764 AGGGATACTCCAACTCCAATTTTATTTCCAAAACACCAATTTCTCACAATTC
1 -GGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTCTCACAATTC
521816 GGGATACTCCAACCCC
1 GGGATACTCCAACCCC
521832 GGGCTTATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
51 58 0.95
52 3 0.05
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.29
Consensus pattern (51 bp):
GGGATACTCCAACCCCAATTTTATTTCCAAAACACCAATTTCTCACAATTC
Found at i:521840 original size:51 final size:49
Alignment explanation
Indices: 521714--521882 Score: 176
Period size: 51 Copynumber: 3.3 Consensus size: 49
521704 TATTTTCGAG
*
521714 GGGATACTCCAACCCCAATTTTATTTCTAAAATACCAATTTTCCACAATC
1 GGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTTT-CACAATC
* *
521764 AGGGATACTCCAACTCCAATTTTATTTCCAAAACACCAATTTCTCACAATTC
1 -GGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTT-TCACAA-TC
**** * ** * *
521816 GGGATACTCCAACCCCGGGCTTATTTCTAAAGCATTGATTTTTCATAATC
1 GGGATACTCCAACCCCAATTTTATTTCTAAAACA-CCAATTTTCACAATC
521866 GAGGATACTCCAACCCC
1 G-GGATACTCCAACCCC
521883 GTTATTTTTG
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
50 3 0.03
51 90 0.90
52 7 0.07
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.30
Consensus pattern (49 bp):
GGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTCACAATC
Found at i:534166 original size:1 final size:1
Alignment explanation
Indices: 534162--534231 Score: 68
Period size: 1 Copynumber: 70.0 Consensus size: 1
534152 ATTCTTTTTC
* * * * * * * *
534162 AAAAAAACAAAAAAAAACAAAAAAATAAAAAAATAAAAAAACAAAAAAAAACAAAAAACAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
534227 AAAAA
1 AAAAA
534232 GAGAAAAGAA
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.89, C:0.07, G:0.01, T:0.03
Consensus pattern (1 bp):
A
Found at i:534177 original size:10 final size:10
Alignment explanation
Indices: 534162--534231 Score: 77
Period size: 10 Copynumber: 6.5 Consensus size: 10
534152 ATTCTTTTTC
534162 AAAAAAACAA
1 AAAAAAACAA
534172 AAAAAAACAAAA
1 AAAAAAAC--AA
*
534184 AAATAAAAAAA
1 AAA-AAAACAA
534195 TAAAAAAACAA
1 -AAAAAAACAA
534206 AAAAAAACAA
1 AAAAAAACAA
*
534216 AAAACAAAGAA
1 AAAA-AAACAA
534227 AAAAA
1 AAAAA
534232 GAGAAAAGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
10 23 0.44
11 17 0.33
12 8 0.15
13 4 0.08
ACGTcount: A:0.89, C:0.07, G:0.01, T:0.03
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:534185 original size:17 final size:17
Alignment explanation
Indices: 534163--534230 Score: 95
Period size: 17 Copynumber: 3.9 Consensus size: 17
534153 TTCTTTTTCA
534163 AAAAAACAAAAAAAAAC
1 AAAAAACAAAAAAAAAC
534180 AAAAAA-ATAAAAAAATA-
1 AAAAAACA-AAAAAAA-AC
534197 AAAAAACAAAAAAAAAC
1 AAAAAACAAAAAAAAAC
534214 AAAAAACAAAGAAAAAA
1 AAAAAACAAA-AAAAAA
534231 AGAGAAAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
16 2 0.04
17 36 0.78
18 8 0.17
ACGTcount: A:0.88, C:0.07, G:0.01, T:0.03
Consensus pattern (17 bp):
AAAAAACAAAAAAAAAC
Found at i:534191 original size:24 final size:24
Alignment explanation
Indices: 534163--534228 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 24
534153 TTCTTTTTCA
*
534163 AAAAAACAAAAAAAAACAAAAAAAT
1 AAAAAA-ATAAAAAAACAAAAAAAT
*
534188 AAAAAAATAAAAAAACAAAAAAAA
1 AAAAAAATAAAAAAACAAAAAAAT
*
534212 ACAAAAAACAAAGAAAA
1 A-AAAAAATAAA-AAAA
534229 AAAGAGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.47
25 15 0.42
26 4 0.11
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.03
Consensus pattern (24 bp):
AAAAAAATAAAAAAACAAAAAAAT
Found at i:534236 original size:10 final size:9
Alignment explanation
Indices: 534162--534246 Score: 61
Period size: 9 Copynumber: 9.1 Consensus size: 9
534152 ATTCTTTTTC
*
534162 AAAAAAACA
1 AAAAAAAGA
534171 AAAAAAA-A
1 AAAAAAAGA
*
534179 CAAAAAAATA
1 -AAAAAAAGA
534189 AAAAAATA-A
1 AAAAAA-AGA
534198 AAAAACAA-A
1 AAAAA-AAGA
534207 AAAAAACA-A
1 AAAAAA-AGA
534216 AAAACAAAGA
1 AAAA-AAAGA
534226 AAAAAAGAGA
1 AAAAAA-AGA
534236 AAAGAAAAGA
1 AAA-AAAAGA
534246 A
1 A
534247 CCTGCTTAAG
Statistics
Matches: 67, Mismatches: 0, Indels: 17
0.80 0.00 0.20
Matches are distributed among these distances:
8 2 0.03
9 42 0.63
10 20 0.30
11 3 0.04
ACGTcount: A:0.86, C:0.06, G:0.06, T:0.02
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:534238 original size:8 final size:8
Alignment explanation
Indices: 534172--534243 Score: 53
Period size: 8 Copynumber: 9.5 Consensus size: 8
534162 AAAAAAACAA
*
534172 AAAAAAAC
1 AAAAAAAG
*
534180 AAAAAAAT
1 AAAAAAAG
*
534188 AAAAAAAT
1 AAAAAAAG
534196 AAAAAAA-
1 AAAAAAAG
*
534203 CAAAAAA-
1 AAAAAAAG
*
534210 AAACAAA-
1 AAAAAAAG
*
534217 AAACAAAG
1 AAAAAAAG
534225 AAAAAAAG
1 AAAAAAAG
*
534233 -AGAAAAG
1 AAAAAAAG
534240 AAAA
1 AAAA
534244 GAACCTGCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
7 24 0.44
8 31 0.56
ACGTcount: A:0.86, C:0.06, G:0.06, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:534982 original size:61 final size:61
Alignment explanation
Indices: 534880--535194 Score: 306
Period size: 61 Copynumber: 5.2 Consensus size: 61
534870 TCTCCTGCAT
* * * *
534880 ACAAGTTGGTGGCATTTTTCTAGTCCTCAAAGAGCACGACGCCTTTTCCTTTTAAAGCCCAT
1 ACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCAC
* * *
534942 ACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGTAGGACGCC-TTT-C----AAAGCCCAC
1 ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCAC
* * * * *
534997 ACAAGTTGGTGGCATTTCCCAGTCTTTAAAGAGTAGGATG-CTTTCTCCTTTTAAAGACCAC
1 ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTT-TCCTTTTAAAGCCCAC
* ** * * *
535058 TCAAGTTGGTGGCACCTTACAGTCCTCAAAGAGCAGGATG-TTTTTCTCTTTGCAAAGCCCAC
1 ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTTC-CTTT-TAAAGCCCAC
* ** * *
535120 ACAAGTTGGTGGTACCTTCCAGTCTTCAAAGAGCAGGATGCCTTTT-GTTTTCAAAGCCCAC
1 ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCAC
*
535181 ACGAGTTGGTGGCA
1 ACAAGTTGGTGGCA
535195 GTCCTCAAAG
Statistics
Matches: 213, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
54 1 0.00
55 45 0.21
56 1 0.00
57 1 0.00
59 1 0.00
60 5 0.02
61 97 0.46
62 58 0.27
63 4 0.02
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (61 bp):
ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCAC
Found at i:535158 original size:123 final size:116
Alignment explanation
Indices: 534880--535194 Score: 316
Period size: 116 Copynumber: 2.6 Consensus size: 116
534870 TCTCCTGCAT
* * * * * *
534880 ACAAGTTGGTGGCATTTTTCTAGTCCTCAAAGAGCACGACGCCTTTTCCTTTTAAAGCCCA-TAC
1 ACAAGTTGGTGGCA-CTTCCCAGTCTTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACT-C
* * *
534944 AAGTTGGTGGCATTTTCTAGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCAC
64 AAGTTGGTGGCACTTACTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
* * * *
534997 ACAAGTTGGTGGCATTTCCCAGTCTTTAAAGAGTAGGATG-CTTTCTCCTTTTAAAGACCACTCA
1 ACAAGTTGGTGGCACTTCCCAGTCTTCAAAGAGCAGGATGCCTTT-TCCTTTTAAAGCCCACTCA
*
535061 AGTTGGTGGCACCTTAC-AGTCCTCAAAGAGCAGGATGTTTTTCTCTTTGCAAAGCCCAC
65 AGTTGGTGGCA-CTTACTAGTCCTCAAAGAGCAGGACG-----C-CTTT-CAAAGCCCAC
* * *
535120 ACAAGTTGGTGGTACCTT-CCAGTCTTCAAAGAGCAGGATGCCTTTT-GTTTTCAAAGCCCACAC
1 ACAAGTTGGTGGCA-CTTCCCAGTCTTCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACTC
*
535183 GAGTTGGTGGCA
64 AAGTTGGTGGCA
535195 GTCCTCAAAG
Statistics
Matches: 165, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
115 4 0.02
116 64 0.39
117 18 0.11
121 1 0.01
122 8 0.05
123 64 0.39
124 6 0.04
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (116 bp):
ACAAGTTGGTGGCACTTCCCAGTCTTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACTCAA
GTTGGTGGCACTTACTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
Found at i:535377 original size:43 final size:42
Alignment explanation
Indices: 535195--535379 Score: 168
Period size: 43 Copynumber: 4.4 Consensus size: 42
535185 GTTGGTGGCA
*
535195 GTCCTCAAAGAGCAGGACGC-C--T-TTTT-CTTTTCTCCTTT
1 GTCCTCAAA-AGCAGGACGCACTTTATTTTCCTTTTTTCCTTT
* * * * *
535233 ATTCTCAAAGAGCAGGACACACTTCA-TTCCCTTTTTTCCCTTT
1 GTCCTCAAA-AGCAGGACGCACTTTATTTTCCTTTTTT-CCTTT
* *
535276 GGTCCTCAAAGAGCAGGACGCACTTTATTTTCC-TCTTTCTTTT
1 -GTCCTCAAA-AGCAGGACGCACTTTATTTTCCTTTTTTCCTTT
* *
535319 GTCCTCAAAAAGCAGGACGCATTTTGTTTTCCTTTTTTCCTTT
1 GTCCTC-AAAAGCAGGACGCACTTTATTTTCCTTTTTTCCTTT
535362 GTCCTCGAAAAGCAGGAC
1 GTCCTC-AAAAGCAGGAC
535380 ATACTCTTTT
Statistics
Matches: 119, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
38 17 0.14
39 1 0.01
41 2 0.02
42 32 0.27
43 37 0.31
44 26 0.22
45 4 0.03
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (42 bp):
GTCCTCAAAAGCAGGACGCACTTTATTTTCCTTTTTTCCTTT
Found at i:535391 original size:42 final size:43
Alignment explanation
Indices: 535195--535396 Score: 154
Period size: 42 Copynumber: 4.8 Consensus size: 43
535185 GTTGGTGGCA
* *
535195 GTCCTCAAAGAGCAGG--ACGC-CT-TTTT-CTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGACACACTCTATTTTCCTTTTTTCCTTT
* * *
535233 ATTCTCAAAGAGCAGGACACACT-TCA-TTCCCTTTTTTCCCTTT
1 GTCCTCAAAGAGCAGGACACACTCT-ATTTTCCTTTTTT-CCTTT
* * * *
535276 GGTCCTCAAAGAGCAGGACGCACTTTATTTTCC-TCTTTCTTTT
1 -GTCCTCAAAGAGCAGGACACACTCTATTTTCCTTTTTTCCTTT
* * * * *
535319 GTCCTCAAAAAGCAGGACGCATTTTGTTTTCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACACTCTATTTTCCTTTTTTCCTTT
*
535362 GTCCTCGAAA-AGCAGGACATACTCT-TTTTCACTTT
1 GTCCTC-AAAGAGCAGGACACACTCTATTTTC-CTTT
535397 ATTCTTAAGA
Statistics
Matches: 131, Mismatches: 20, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
38 14 0.11
40 4 0.03
41 2 0.02
42 40 0.31
43 38 0.29
44 28 0.21
45 5 0.04
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACACACTCTATTTTCCTTTTTTCCTTT
Found at i:536120 original size:29 final size:29
Alignment explanation
Indices: 536078--536182 Score: 120
Period size: 29 Copynumber: 3.5 Consensus size: 29
536068 CATTGTTCAT
536078 TGTATCGATACATTCTGGATTTAACCAGA
1 TGTATCGATACATTCTGGATTTAACCAGA
* * * * *
536107 TGTATCGATACATTTTGCATTATATCGATACA
1 TGTATCGATACATTCTGGATT-TAAC--CAGA
*
536139 TTGTATCGATACATTCTGGATTTACCCAGA
1 -TGTATCGATACATTCTGGATTTAACCAGA
536169 TGTATCGATACATT
1 TGTATCGATACATT
536183 TTACAATATA
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
29 33 0.53
30 5 0.08
32 5 0.08
33 19 0.31
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (29 bp):
TGTATCGATACATTCTGGATTTAACCAGA
Found at i:536145 original size:13 final size:13
Alignment explanation
Indices: 536124--536153 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
536114 ATACATTTTG
536124 CATTATATCGATA
1 CATTATATCGATA
*
536137 CATTGTATCGATA
1 CATTATATCGATA
536150 CATT
1 CATT
536154 CTGGATTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:536172 original size:62 final size:62
Alignment explanation
Indices: 536075--536201 Score: 227
Period size: 62 Copynumber: 2.0 Consensus size: 62
536065 ATACATTGTT
* *
536075 CATTGTATCGATACATTCTGGATTTAACCAGATGTATCGATACATTTTGCATTATATCGATA
1 CATTGTATCGATACATTCTGGATTTAACCAGATGTATCGATACATTTTACAATATATCGATA
*
536137 CATTGTATCGATACATTCTGGATTTACCCAGATGTATCGATACATTTTACAATATATCGATA
1 CATTGTATCGATACATTCTGGATTTAACCAGATGTATCGATACATTTTACAATATATCGATA
536199 CAT
1 CAT
536202 CCAGGCATTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (62 bp):
CATTGTATCGATACATTCTGGATTTAACCAGATGTATCGATACATTTTACAATATATCGATA
Found at i:538693 original size:28 final size:28
Alignment explanation
Indices: 538652--538722 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
538642 CACACTTGGA
* * *
538652 GATACTTCGACCCTGTTATTTCAT-CGGG
1 GATACTCCAACCCTGTTATTTC-TGAGGG
*
538680 GATCCTCCAACCCTGTTATTTCTGAGGG
1 GATACTCCAACCCTGTTATTTCTGAGGG
538708 GATACTCCAACCCTG
1 GATACTCCAACCCTG
538723 GCTCTATATC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.31
Consensus pattern (28 bp):
GATACTCCAACCCTGTTATTTCTGAGGG
Done.