Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 3 of 292
Found at i:730992 original size:29 final size:28
Alignment explanation
Indices: 730956--731040 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 28
730946 AAATATACAT
730956 AATA-ATATATAAAATATAATATTAAAA
1 AATATATATATAAAATATAATATTAAAA
*
730983 ACATATATATATATATATATATAATA-T-GAA
1 A-ATATATATATA-A-A-ATATAATATTAAAA
*
731013 AATATATATATATAATATAATATTAAAA
1 AATATATATATAAAATATAATATTAAAA
731041 TATTTACAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
26 8 0.17
27 3 0.06
28 5 0.10
29 18 0.38
30 4 0.08
31 2 0.04
32 8 0.17
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (28 bp):
AATATATATATAAAATATAATATTAAAA
Found at i:731009 original size:37 final size:36
Alignment explanation
Indices: 730933--731009 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 36
730923 CTTCACAAAT
*
730933 ATATATATACTAAAAATATACATAATAATATATAAA
1 ATATATATACTAAAAACATACATAATAATATATAAA
* * *
730969 ATATA-ATATTAAAAACATATATATATATATATATATA
1 ATATATATACTAAAAACATACATA-ATA-ATATATAAA
731006 ATAT
1 ATAT
731010 GAAAATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 15 0.43
36 8 0.23
37 12 0.34
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (36 bp):
ATATATATACTAAAAACATACATAATAATATATAAA
Found at i:731009 original size:58 final size:58
Alignment explanation
Indices: 730931--731040 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
730921 TACTTCACAA
730931 ATATATATATACTAAAAATAT-ACATAATA-ATATATAAAATATAATATTAAAAACATAT
1 ATATATATATACTAAAAATATGA-A-AATATATATATAAAATATAATATTAAAAACATAT
* *
730989 ATATATATATA-TATATAATATGAAAATATATATATATAATATAATATTAAAA
1 ATATATATATACTA-AAAATATGAAAATATATATATAAAATATAATATTAAAA
731041 TATTTACAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
57 6 0.13
58 40 0.85
59 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (58 bp):
ATATATATATACTAAAAATATGAAAATATATATATAAAATATAATATTAAAAACATAT
Found at i:731056 original size:26 final size:25
Alignment explanation
Indices: 730989--731070 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 25
730979 AAAAACATAT
* * *
730989 ATATATATATATATATAATATGAAA
1 ATATATAAAAATATATAATATTAAA
* *
731014 ATATATATATATAATATAATATTAAA
1 ATATATAAAAAT-ATATAATATTAAA
*
731040 ATATTTACAAAATATATACATATTAGAA
1 ATATATA-AAAATATATA-ATATTA-AA
731068 ATA
1 ATA
731071 AAAAAAAACG
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
25 12 0.24
26 23 0.47
27 9 0.18
28 5 0.10
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (25 bp):
ATATATAAAAATATATAATATTAAA
Found at i:731119 original size:2 final size:2
Alignment explanation
Indices: 731103--731165 Score: 65
Period size: 2 Copynumber: 32.0 Consensus size: 2
731093 GCTACATAAG
* * * * * *
731103 TA TA TA CA TA AA TA TA T- TA AA TA CA TA TA CA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
731144 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
731166 AAATTATGCA
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:731345 original size:9 final size:9
Alignment explanation
Indices: 731315--731346 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
731305 ACACTACTAC
731315 ATATAATAA
1 ATATAATAA
*
731324 ATACAATAA
1 ATATAATAA
731333 ATATAATAA
1 ATATAATAA
731342 ATATA
1 ATATA
731347 TAGAGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (9 bp):
ATATAATAA
Found at i:731874 original size:7 final size:7
Alignment explanation
Indices: 731862--731896 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
731852 AAGAGAGGAA
731862 AGGGGAG
1 AGGGGAG
731869 AGGGGAG
1 AGGGGAG
*
731876 AGGAGAG
1 AGGGGAG
731883 AGGGGAG
1 AGGGGAG
731890 AAGGGGA
1 -AGGGGA
731897 TTTCCGGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (7 bp):
AGGGGAG
Found at i:732030 original size:2 final size:2
Alignment explanation
Indices: 732019--732060 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
732009 TTTTATGTGT
*
732019 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
732060 T
1 T
732061 GAGAAACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:733354 original size:78 final size:74
Alignment explanation
Indices: 733126--733466 Score: 417
Period size: 74 Copynumber: 4.6 Consensus size: 74
733116 ACGTGAGCCA
*
733126 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAATATTGAAATTAACTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAATATTGAAATTACCTCAG
*
733191 CGTGTCCTA
66 CGTGTCCTG
* *
733200 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCGACAAATAGAATATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAATATTGAAATTACCTCAG
*
733265 CTTGTCCTG
66 CGTGTCCTG
* *
733274 AGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTTTTGACAAACAGAATATTGAAATCACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGACAAACAGAATATTGAAATTACC
*
733339 TCAACGTGTCCTG
62 TCAGCGTGTCCTG
* * *
733352 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTT----AACA-AA-ATTGAAAATACCTCAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAATATTGAAATTACCTCAG
* * *
733411 CTTATCTTG
66 CGTGTCCTG
* ** * * *
733420 AGGCTCAGCTCATTTCTCGCAATATGAGTCGAATTTTGA-AAATAGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAA
733467 ATAAAAACAT
Statistics
Matches: 234, Mismatches: 25, Indels: 18
0.84 0.09 0.06
Matches are distributed among these distances:
68 51 0.22
69 2 0.01
70 4 0.02
71 3 0.01
72 2 0.01
74 105 0.45
78 67 0.29
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (74 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAATATTGAAATTACCTCAG
CGTGTCCTG
Found at i:734308 original size:44 final size:43
Alignment explanation
Indices: 734244--734364 Score: 140
Period size: 43 Copynumber: 2.8 Consensus size: 43
734234 TTGTCTCATT
* *
734244 AAAATGCCCTTTT-GGGTTTTCATCC-TAATCTTTTGTGTTAATC
1 AAAACGCCCTTTTCGGGTTTTCA-CCTTAATCCTTT-TGTTAATC
* *
734287 AAAACGCCCTTTTCGGGTTTTCACCTTGATCCTTTTGTTCATC
1 AAAACGCCCTTTTCGGGTTTTCACCTTAATCCTTTTGTTAATC
* * *
734330 AAGACTCCCTTTTCGGGTTTTCACCTTGAT-CTTTT
1 AAAACGCCCTTTTCGGGTTTTCACCTTAATCCTTTT
734365 CCTTCTTCTT
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
42 5 0.07
43 49 0.70
44 16 0.23
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.45
Consensus pattern (43 bp):
AAAACGCCCTTTTCGGGTTTTCACCTTAATCCTTTTGTTAATC
Found at i:741811 original size:4 final size:4
Alignment explanation
Indices: 741802--741838 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
741792 ATGGGATATG
* *
741802 GAAT GAAT GAAT GAAT GAAT GAAT GCAT AAAT GAAT G
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT G
741839 TTAGTCATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.24
Consensus pattern (4 bp):
GAAT
Found at i:745641 original size:31 final size:30
Alignment explanation
Indices: 745586--745653 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 30
745576 TAAATGTAAT
*
745586 AATA-ATATATACACAATATGGTA-TTAAA
1 AATATATATATACACAATATAGTATTTAAA
* *
745614 AATATATATATATACATATAATAGTATTTAAG
1 AATATATATATACACA-AT-ATAGTATTTAAA
745646 AATATATA
1 AATATATA
745654 CATAGAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 4 0.12
29 10 0.30
30 2 0.06
31 5 0.15
32 12 0.36
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (30 bp):
AATATATATATACACAATATAGTATTTAAA
Found at i:746066 original size:24 final size:24
Alignment explanation
Indices: 746033--746085 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
746023 TATAAAATGT
*
746033 AATATTAAAAACATATATATATAA
1 AATATGAAAAACATATATATATAA
* *
746057 TATATGAAAAATATATATATATAA
1 AATATGAAAAACATATATATATAA
746081 AATAT
1 AATAT
746086 AATATTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
AATATGAAAAACATATATATATAA
Found at i:746076 original size:15 final size:14
Alignment explanation
Indices: 746051--746098 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
746041 AAACATATAT
746051 ATATAATATATGAAAA
1 ATAT-ATATAT-AAAA
746067 ATATATATATATAAA
1 ATATATATATA-AAA
*
746082 ATATA-ATATTAAA
1 ATATATATATAAAA
746095 ATAT
1 ATAT
746099 TTACAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 7 0.23
14 5 0.17
15 14 0.47
16 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
ATATATATATAAAA
Found at i:746096 original size:13 final size:14
Alignment explanation
Indices: 746017--746098 Score: 70
Period size: 13 Copynumber: 6.1 Consensus size: 14
746007 AATATACATA
746017 ATAATATATAAAAT
1 ATAATATATAAAAT
*
746031 GTAATAT-TAAAA-
1 ATAATATATAAAAT
*
746043 A-CATATAT---AT
1 ATAATATATAAAAT
746053 ATAATATATGAAAAAT
1 ATAATATAT--AAAAT
746069 ATATATATATAAAAT
1 ATA-ATATATAAAAT
746084 ATAATAT-TAAAAT
1 ATAATATATAAAAT
746097 AT
1 AT
746099 TTACAAAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
9 1 0.02
10 1 0.02
11 10 0.18
12 1 0.02
13 13 0.24
14 10 0.18
15 8 0.15
16 5 0.09
17 6 0.11
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (14 bp):
ATAATATATAAAAT
Found at i:746098 original size:24 final size:24
Alignment explanation
Indices: 746020--746110 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 24
746010 ATACATAATA
*
746020 ATATATAAAATGTAATATTAAAAACAT
1 ATATATAAAATATAATATT--AAA-AT
* * *
746047 ATATATATAATATATGAAAAAT-ATAT
1 ATATATA-AA-ATAT-AATATTAAAAT
746073 ATATATAAAATATAATATTAAAAT
1 ATATATAAAATATAATATTAAAAT
* *
746097 ATTTACAAAATATA
1 ATATATAAAATATA
746111 TACATATTAG
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
23 4 0.08
24 19 0.37
25 2 0.04
26 9 0.18
27 8 0.16
28 2 0.04
29 3 0.06
30 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
ATATATAAAATATAATATTAAAAT
Found at i:746185 original size:23 final size:22
Alignment explanation
Indices: 746159--746201 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
746149 CTACATAAGT
746159 ATATACATAAATATATTAAATAC
1 ATATACATAAATATA-TAAATAC
*
746182 ATATACATATATATATAAAT
1 ATATACATAAATATATAAAT
746202 TATGCACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (22 bp):
ATATACATAAATATATAAATAC
Found at i:746358 original size:9 final size:9
Alignment explanation
Indices: 746344--746406 Score: 65
Period size: 9 Copynumber: 6.7 Consensus size: 9
746334 TATACACTAC
746344 TAAATATAA
1 TAAATATAA
*
746353 TAAATACAA
1 TAAATATAA
746362 TAAATATAA
1 TAAATATAA
746371 TAAATAT-A
1 TAAATATAA
746379 TAGAGATTATAA
1 TA-A-A-TATAA
*
746391 TTAATAATAA
1 TAAAT-ATAA
746401 TAAATA
1 TAAATA
746407 ATAGAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
8 3 0.07
9 26 0.58
10 10 0.22
11 4 0.09
12 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (9 bp):
TAAATATAA
Found at i:746428 original size:20 final size:21
Alignment explanation
Indices: 746393--746446 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
746383 GATTATAATT
* *
746393 AATAATAATAAATAA-TAGAA
1 AATAATAACAAGTAATTAGAA
*
746413 AATAATAACAAGTAATTTGAA
1 AATAATAACAAGTAATTAGAA
746434 AATAA-AAC-AGTAA
1 AATAATAACAAGTAA
746447 ACTAACACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.17
20 16 0.53
21 9 0.30
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (21 bp):
AATAATAACAAGTAATTAGAA
Found at i:757741 original size:340 final size:340
Alignment explanation
Indices: 757121--758481 Score: 2614
Period size: 340 Copynumber: 4.0 Consensus size: 340
757111 TTGTGGTCAT
*
757121 GCATTTTGGCCATTTGGTTCAACAAAGAGAAACTGTAAGCTTATGTGGATGCATGTTACACTATT
1 GCATTTTGGCCATTTGGTTCAACAAAGAGAAACCGTAAGCTTATGTGGATGCATGTTACACTATT
757186 GAGACACAAAAGGCAATTTACAAAGAAGCCGTTAATCCAATTAAAGGTCAAATCTCATGGCCAGC
66 GAGACACAAAAGGCAATTTACAAAGAAGCCGTTAATCCAATTAAAGGTCAAATCTCATGGCCAGC
757251 ATCTACTTACAACCCAAATCCTCCGATTGTGAAAAAACAGCCAGATAGACCTAAAACTTTTTTTG
131 ATCTACTTACAACCCAAATCCTCCGATTGTGAAAAAACAGCCAGATAGACCTAAAACTTTTTTTG
757316 GCCGTATATAATATACTTATTTATGACAAATCTGGTAAAAAGAGCAAATTGAAAACAATACCATT
196 GCCGTATATAATATACTTATTTATGACAAATCTGGTAAAAAGAGCAAATTGAAAACAATACCATT
757381 AACTTTGAATGAAAAGAACAAAATCCACAACCGCTTTATACAATATTGTCGAAAGAACATACAGA
261 AACTTTGAATGAAAAGAACAAAATCCACAACCGCTTTATACAATATTGTCGAAAGAACATACAGA
*
757446 CTTATAACATAAAGA
326 CTTATAACATATAGA
*
757461 GCATTTTGGCCATTTGGTCCAACAAAGAGAAACCGTAAGCTTATGTGGATGCATGTTACACTATT
1 GCATTTTGGCCATTTGGTTCAACAAAGAGAAACCGTAAGCTTATGTGGATGCATGTTACACTATT
*
757526 AAGACACAAAAGGCAATTTACAAAGAAGCCGTTAATCCAATTAAAGGTCAAATCTCATGGCCAGC
66 GAGACACAAAAGGCAATTTACAAAGAAGCCGTTAATCCAATTAAAGGTCAAATCTCATGGCCAGC
*
757591 ATCTACTTACAACCCAAATCCTCCGATTGTGAAAAAACAACCAGATAGACCTAAAACTTTTTTTG
131 ATCTACTTACAACCCAAATCCTCCGATTGTGAAAAAACAGCCAGATAGACCTAAAACTTTTTTTG
757656 GCCGTATATAATATACTTATTTATGACAAATCTGGTAAAAAGAGCAAATTGAAAACAATACCATT
196 GCCGTATATAATATACTTATTTATGACAAATCTGGTAAAAAGAGCAAATTGAAAACAATACCATT
757721 AACTTTGAATGAAAAGAACAAAATCCACAACCGCTTTATACAATATTGTCGAAAGAACATACAGA
261 AACTTTGAATGAAAAGAACAAAATCCACAACCGCTTTATACAATATTGTCGAAAGAACATACAGA
757786 CTTATAACATATAGA
326 CTTATAACATATAGA
* *
757801 GCAATTTGGCCATTTGGTTCAACAAAGAGAAACTGTAAGCTTATGTGGATGCATGTTACACTATT
1 GCATTTTGGCCATTTGGTTCAACAAAGAGAAACCGTAAGCTTATGTGGATGCATGTTACACTATT
757866 GAGACACAAAAGGCAATTTACAAAGAAGCCGTTAATCCAATTAAAGGTCAAATCTCATGGCCAGC
66 GAGACACAAAAGGCAATTTACAAAGAAGCCGTTAATCCAATTAAAGGTCAAATCTCATGGCCAGC
757931 ATCTACTTACAACCCAAATCCTCCGATTGTGAAAAAACAGCCAGATAGACCTAAAACTTTTTTTG
131 ATCTACTTACAACCCAAATCCTCCGATTGTGAAAAAACAGCCAGATAGACCTAAAACTTTTTTTG
*
757996 GCCGTATATAATATACTTATTTATGACAAATCTGGTAAAAAGAGCAAATTGGAAACAATACCATT
196 GCCGTATATAATATACTTATTTATGACAAATCTGGTAAAAAGAGCAAATTGAAAACAATACCATT
758061 AACTTTGAATGAAAAGAACAAAATCCACAACCGCTTTATACAATATTGTCGAAAGAACATACAGA
261 AACTTTGAATGAAAAGAACAAAATCCACAACCGCTTTATACAATATTGTCGAAAGAACATACAGA
758126 CTTATAACATATAGA
326 CTTATAACATATAGA
758141 GCATTTTGGCCATTTGGTTCAACAAAGAGAAACCGTAAGCTTATGTGGATGCATGTTACACTATT
1 GCATTTTGGCCATTTGGTTCAACAAAGAGAAACCGTAAGCTTATGTGGATGCATGTTACACTATT
*
758206 GAGACACAAAAGGCAATTTACAAAGAAGCCGTTAATCCAATTAAAGGTCAAATCTCTTGGCCAGC
66 GAGACACAAAAGGCAATTTACAAAGAAGCCGTTAATCCAATTAAAGGTCAAATCTCATGGCCAGC
758271 ATCTACTTACAACCCAAATCCTCCGATTGTGAAAAAACAGCCAGATAGACCTAAAACTTTTTTTT
131 ATCTACTTACAACCCAAATCCTCCGATTGTGAAAAAACAGCCAGATAGACCTAAAAC-TTTTTTT
* *
758336 GGCTGTATATAATATACTTATTTATGACAAATCTGGTAAAAAGAGCAAATTGGAAACAATACCAT
195 GGCCGTATATAATATACTTATTTATGACAAATCTGGTAAAAAGAGCAAATTGAAAACAATACCAT
758401 TAACTTTGAATGAAAAGAACAAAATCCACAACCGCTTTATACAATATTGTCGAAAGAACATACAG
260 TAACTTTGAATGAAAAGAACAAAATCCACAACCGCTTTATACAATATTGTCGAAAGAACATACAG
758466 ACTTATAACATATAGA
325 ACTTATAACATATAGA
758482 TGTGGGCTTG
Statistics
Matches: 1005, Mismatches: 15, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
340 853 0.85
341 152 0.15
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (340 bp):
GCATTTTGGCCATTTGGTTCAACAAAGAGAAACCGTAAGCTTATGTGGATGCATGTTACACTATT
GAGACACAAAAGGCAATTTACAAAGAAGCCGTTAATCCAATTAAAGGTCAAATCTCATGGCCAGC
ATCTACTTACAACCCAAATCCTCCGATTGTGAAAAAACAGCCAGATAGACCTAAAACTTTTTTTG
GCCGTATATAATATACTTATTTATGACAAATCTGGTAAAAAGAGCAAATTGAAAACAATACCATT
AACTTTGAATGAAAAGAACAAAATCCACAACCGCTTTATACAATATTGTCGAAAGAACATACAGA
CTTATAACATATAGA
Found at i:762206 original size:10 final size:10
Alignment explanation
Indices: 762193--762234 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
762183 AAATGTTATA
762193 AAAAAATATT
1 AAAAAATATT
*
762203 AAAAAATAAT
1 AAAAAATATT
*
762213 AAAAATTA-T
1 AAAAAATATT
762222 AAAAAAT-TT
1 AAAAAATATT
762231 AAAA
1 AAAA
762235 GCAACAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 12 0.43
10 16 0.57
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAAATATT
Found at i:762218 original size:19 final size:18
Alignment explanation
Indices: 762190--762228 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
762180 TTAAAATGTT
762190 ATAAAAAAA-TATTAAAAA
1 ATAAAAAAATTA-TAAAAA
762208 ATAATAAAAATTATAAAAA
1 ATAA-AAAAATTATAAAAA
762227 AT
1 AT
762229 TTAAAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 13 0.68
20 2 0.11
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAAAAAAATTATAAAAA
Found at i:762421 original size:2 final size:2
Alignment explanation
Indices: 762414--762458 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
762404 TAAAAAGATA
762414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
762456 AT A
1 AT A
762459 ATTATTTTTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:771757 original size:17 final size:16
Alignment explanation
Indices: 771737--771797 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
771727 AATAAAAAAA
771737 TTATAATTTTAAATTTT
1 TTATAATTTT-AATTTT
*
771754 TTATAAATTT-A-TTT
1 TTATAATTTTAATTTT
*
771768 TTATAATTTTTATGTTT
1 TTATAATTTTAAT-TTT
771785 TTAATAATTTTAA
1 TT-ATAATTTTAA
771798 GCTTTAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 12 0.32
15 2 0.05
17 14 0.38
18 9 0.24
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTATAATTTTAATTTT
Found at i:771786 original size:31 final size:32
Alignment explanation
Indices: 771737--771796 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
771727 AATAAAAAAA
771737 TTATAATTTTAAATTTTTT-ATAAATTTATTT
1 TTATAATTTTAAATTTTTTAATAAATTTATTT
* *
771768 TTATAATTTT-TATGTTTTTAATAATTTTA
1 TTATAATTTTAAAT-TTTTTAATAAATTTA
771797 AGCTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 2 0.08
31 15 0.60
32 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (32 bp):
TTATAATTTTAAATTTTTTAATAAATTTATTT
Found at i:772984 original size:27 final size:27
Alignment explanation
Indices: 772953--773006 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
772943 AGTATTTTAA
* *
772953 AATTTATTAAATTATAAATTTATATTT
1 AATTTATTAAATAATAAAATTATATTT
*
772980 AATTTTTTAAATAATAAAATTATATTT
1 AATTTATTAAATAATAAAATTATATTT
773007 TTACCCATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
AATTTATTAAATAATAAAATTATATTT
Found at i:774664 original size:19 final size:20
Alignment explanation
Indices: 774632--774669 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
774622 TAGGATAGCA
774632 AAAAAACGAGAAA-TGGGCC
1 AAAAAACGAGAAATTGGGCC
* *
774651 AAAAAAGGATAAATTGGGC
1 AAAAAACGAGAAATTGGGC
774670 TTAAAACAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.53, C:0.11, G:0.26, T:0.11
Consensus pattern (20 bp):
AAAAAACGAGAAATTGGGCC
Found at i:775912 original size:16 final size:16
Alignment explanation
Indices: 775891--775922 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
775881 TTTAGCCATT
775891 ATTTTGTTTTTATTTA
1 ATTTTGTTTTTATTTA
775907 ATTTTGTTTTTATTTA
1 ATTTTGTTTTTATTTA
775923 CTAAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (16 bp):
ATTTTGTTTTTATTTA
Found at i:782419 original size:15 final size:15
Alignment explanation
Indices: 782399--782431 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
782389 CTAATATGGG
782399 TATGTAATATAG-ATA
1 TATGT-ATATAGAATA
782414 TATGTATATAGAATA
1 TATGTATATAGAATA
782429 TAT
1 TAT
782432 TTAAAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (15 bp):
TATGTATATAGAATA
Found at i:782519 original size:12 final size:12
Alignment explanation
Indices: 782502--782527 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
782492 ACACTAAATA
782502 ACATATAATAAT
1 ACATATAATAAT
782514 ACATATAATAAT
1 ACATATAATAAT
782526 AC
1 AC
782528 TAAAATCGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (12 bp):
ACATATAATAAT
Found at i:784176 original size:15 final size:15
Alignment explanation
Indices: 784158--784190 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
784148 TTCATTTTAA
784158 ATATATTCTATA-TAC
1 ATATA-TCTATATTAC
784173 ATATATCTATATTAC
1 ATATATCTATATTAC
784188 ATA
1 ATA
784191 CCCATATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATCTATATTAC
Found at i:796569 original size:72 final size:72
Alignment explanation
Indices: 796447--796639 Score: 228
Period size: 72 Copynumber: 2.6 Consensus size: 72
796437 GAGTTAAGCC
* ** * * *
796447 TTTTTATTTTTGTTTTTCAAAATCAACTCATATTGTTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGAT
796512 GAGGT-A
66 GAGGTAA
**
796518 TTTTCAATTTTTGTGTTTT-AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTT-AATTTTTGT-TTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
796582 ATGAGGTAA
64 ATGAGGTAA
*
796591 TTTTAATTTCTGTTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTG
1 TTTTAATTTTTGTTTTTC-----AAAATCAACTCATATTGCGAGAGGTG
796640 GATTGAACCT
Statistics
Matches: 102, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
71 8 0.08
72 61 0.60
73 9 0.09
77 24 0.24
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (72 bp):
TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGAT
GAGGTAA
Found at i:796856 original size:130 final size:128
Alignment explanation
Indices: 796545--796866 Score: 470
Period size: 130 Copynumber: 2.5 Consensus size: 128
796535 TTAATTTCAA
*
796545 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTT-AATTTCTGTTTTTC
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGT-ATTTTCAATTTCTGTTTGTC
796609 AAAAAAAAATCAACTCATATTGCGAGAGGTGGATTGAACCTTTTAATTTCTGCTTTTTCAAAAGC
65 ---AAAAAATCAACTCATATTGCGAGAGGTGGATTGAACCTTTTAATTTCTGCTTTTTCAAAAGC
796674 AG
127 AG
*
796676 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTAATTTCAATTTCTGTTTGTC-
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTATTTTCAATTTCTGTTTGTCA
* * * *
796740 AAGAATCAACTCATGTTGCGAGAGGTGGGTTGAACCTTTTAATTTCTG-TTGTTTCAAAAAAATC
66 AAAAATCAACTCATATTGCGAGAGGTGGATTGAACCTTTTAATTTCTGCTT-TTTC---AAAAGC
796804 AG
127 AG
* * *
796806 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGACGAGGTATTTTCAATTTTTGTTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTATTTTCAATTTCTGTTT
796867 TCATTATTAT
Statistics
Matches: 176, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
126 2 0.01
127 49 0.28
130 68 0.39
131 57 0.32
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (128 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGATGAGGTATTTTCAATTTCTGTTTGTCA
AAAAATCAACTCATATTGCGAGAGGTGGATTGAACCTTTTAATTTCTGCTTTTTCAAAAGCAG
Found at i:799619 original size:12 final size:12
Alignment explanation
Indices: 799602--799627 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
799592 TGCGATTTTA
799602 GTATTATTATAT
1 GTATTATTATAT
799614 GTATTATTATAT
1 GTATTATTATAT
799626 GT
1 GT
799628 TATTTAGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (12 bp):
GTATTATTATAT
Found at i:799716 original size:15 final size:15
Alignment explanation
Indices: 799698--799730 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
799688 TTCATTTTAA
799698 ATATATTCTATA-TAC
1 ATATA-TCTATATTAC
799713 ATATATCTATATTAC
1 ATATATCTATATTAC
799728 ATA
1 ATA
799731 CCCATATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATCTATATTAC
Found at i:803481 original size:15 final size:15
Alignment explanation
Indices: 803461--803492 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
803451 CATTTCACTA
*
803461 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
803476 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
803491 TT
1 TT
803493 TTCGTGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:805326 original size:25 final size:25
Alignment explanation
Indices: 805298--805362 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
805288 CTGAGTAACA
* *
805298 GGAAACTCATACGAGTTGTATATCT
1 GGAAGCTCATACGAGTTGCATATCT
805323 GGAAGCTCATACGAGTTGCATATCT
1 GGAAGCTCATACGAGTTGCATATCT
* *
805348 AGAAGCTCTTACGAG
1 GGAAGCTCATACGAG
805363 CAAAATATCG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (25 bp):
GGAAGCTCATACGAGTTGCATATCT
Found at i:805370 original size:25 final size:25
Alignment explanation
Indices: 805342--805413 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
805332 TACGAGTTGC
* *
805342 ATATCTAGAAGCTC-TTACGAGCAAA
1 ATATCGAGAAGCTCATGA-GAGCAAA
*
805367 ATATCGAGAAGCTCATGAGAGCTAA
1 ATATCGAGAAGCTCATGAGAGCAAA
*
805392 ATATCGAGAAGCTCAAGAGAGC
1 ATATCGAGAAGCTCATGAGAGC
805414 TGTGGTATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 40 0.95
26 2 0.05
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.19
Consensus pattern (25 bp):
ATATCGAGAAGCTCATGAGAGCAAA
Found at i:815312 original size:2 final size:2
Alignment explanation
Indices: 815305--815343 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
815295 GCCATATACT
815305 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
815344 CAAAATGTAT
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:816118 original size:73 final size:73
Alignment explanation
Indices: 816041--816203 Score: 166
Period size: 73 Copynumber: 2.2 Consensus size: 73
816031 TGTATAATGG
* ** * *
816041 GAAGCTCAAAAGAGCCATA-ATCAAGAAGCTCATGTGAGCCAATAACGAGTAGCTCTGAAGAGCC
1 GAAGCTCAAAAGAGCCATATATCAAGAAGCTCAAGCAAGCC-ATAACGAGAAGCTCCGAAGAGCC
816105 ATTAATCAA
65 ATTAATCAA
*** * ** * * *
816114 GAAGCTCCGGATAGCCATATATCGGGAAGTTCAAGCAAGCCATATCGGGAAGCTCCGAAGAGCCA
1 GAAGCTCAAAAGAGCCATATATCAAGAAGCTCAAGCAAGCCATAACGAGAAGCTCCGAAGAGCCA
*
816179 TTAATCAG
66 TTAATCAA
816187 GAAGCTCACAAAGAGCC
1 GAAGCTCA-AAAGAGCC
816204 TTTAATCGGG
Statistics
Matches: 69, Mismatches: 19, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
73 49 0.71
74 20 0.29
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (73 bp):
GAAGCTCAAAAGAGCCATATATCAAGAAGCTCAAGCAAGCCATAACGAGAAGCTCCGAAGAGCCA
TTAATCAA
Found at i:816142 original size:25 final size:25
Alignment explanation
Indices: 816091--816239 Score: 105
Period size: 25 Copynumber: 6.0 Consensus size: 25
816081 AATAACGAGT
* **
816091 AGCTCTGAAGAGCCAT-TAATCAAGA
1 AGCTCCGAAGAGCCATAT-ATCGGGA
* *
816116 AGCTCCGGATAGCCATATATCGGGA
1 AGCTCCGAAGAGCCATATATCGGGA
*
816141 AG-TTC-AAGCAAGCC--ATATCGGGA
1 AGCTCCGAAG--AGCCATATATCGGGA
*
816164 AGCTCCGAAGAGCCAT-TAATCAGGA
1 AGCTCCGAAGAGCCATAT-ATCGGGA
* *
816189 AGCTCACAAAGAGCC-TTTAATCGGGA
1 AGCTC-CGAAGAGCCATAT-ATCGGGA
*
816215 AGCTCCAAAGAGCCATATATCGGGA
1 AGCTCCGAAGAGCCATATATCGGGA
816240 CACTCATAAG
Statistics
Matches: 100, Mismatches: 13, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
23 16 0.16
24 5 0.05
25 55 0.55
26 24 0.24
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATATATCGGGA
Found at i:819694 original size:29 final size:26
Alignment explanation
Indices: 819651--819708 Score: 89
Period size: 29 Copynumber: 2.1 Consensus size: 26
819641 AGATTACAAA
819651 ATCATATATTCAAGATTGCATATCAT
1 ATCATATATTCAAGATTGCATATCAT
819677 ATCATATCATATCTAAGATTGCATATCAT
1 ATCATAT-AT-TC-AAGATTGCATATCAT
819706 ATC
1 ATC
819709 TAAGATTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 7 0.24
27 2 0.07
28 2 0.07
29 18 0.62
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (26 bp):
ATCATATATTCAAGATTGCATATCAT
Found at i:819703 original size:19 final size:19
Alignment explanation
Indices: 819679--819722 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
819669 CATATCATAT
819679 CATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG
819698 CATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG
819717 CATATC
1 CATATC
819723 CTTAAAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (19 bp):
CATATCATATCTAAGATTG
Found at i:820281 original size:87 final size:87
Alignment explanation
Indices: 820117--820281 Score: 199
Period size: 87 Copynumber: 1.9 Consensus size: 87
820107 ACAATACAGA
* *
820117 GATGCCAAATCATCTTAGATCTGCTTCAGCATAAACACGTGAAAGCCAAATCTGCTGTGTCTTCG
1 GATGCCAAATCATCTTAGATCTGCTTCAGCATAAACACGTGAAAGCCAAATCTGCTATGTCTTCA
*
820182 ATTTGCTCCTTGTGAACACAAG
66 ATCTGCTCCTTGTGAACACAAG
* * * ** *
820204 GATGCCAAATCATCTTGGATCTGCTTCAGTA-AAATCATC-TGAAGGTTAGATCTGCTATGTCTT
1 GATGCCAAATCATCTTAGATCTGCTTCAGCATAAA-CA-CGTGAAAGCCAAATCTGCTATGTCTT
* *
820267 TAATCTGCTTCTTGT
64 CAATCTGCTCCTTGT
820282 AAACTTATGA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
86 3 0.05
87 61 0.94
88 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (87 bp):
GATGCCAAATCATCTTAGATCTGCTTCAGCATAAACACGTGAAAGCCAAATCTGCTATGTCTTCA
ATCTGCTCCTTGTGAACACAAG
Found at i:820783 original size:205 final size:206
Alignment explanation
Indices: 820351--821494 Score: 1943
Period size: 205 Copynumber: 5.6 Consensus size: 206
820341 AAATCTGTTT
* * *
820351 CTTCGATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTTCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
* * * * *
820416 GCGAAAACCAAATCAGCTATGCCTTCGATTTGTTTCTTGTAAGCA-AAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
*
820480 GGATCTGCTTCAGT-T----ATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAA-ATG
131 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATG
820539 GAGATGCCAAA
196 GAGATGCCAAA
820550 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
820615 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAA-CTATCT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATC-ATCT
* *
820679 TGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTACGTATCTGCTCTCCGTCGAA-AT
130 TGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATAT
* *
820743 GGAGATACCAGA
195 GGAGATGCCAAA
820755 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
*
820820 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAATCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
820885 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATG
131 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATG
* *
820950 GAGACGGCAAA
196 GAGATGCCAAA
820961 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
821026 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAA-GATGCCAAATCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
821090 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATG
131 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATG
* *
821155 GAGACGGCAAA
196 GAGATGCCAAA
*
821166 CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
* *
821231 GTGAAAGCCAAATCAGCTATGACTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCACCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* **
821296 GGATCTGCTTCAGTATAAACATATGAAGGCCA-ATCTGCTATGTGTCTGCTCTCCGTCGAATATG
131 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATG
821360 GAGATGCCAAA
196 GAGATGCCAAA
* * * *
821371 CTTCGATTTGTTCTCTGACAACACAGAGATGCCAAATCATCTTAGATTTGCTTTAGCGTAAAC-C
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
821435 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATC
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATC
821495 TGCTATCTTC
Statistics
Matches: 903, Mismatches: 32, Indels: 15
0.95 0.03 0.02
Matches are distributed among these distances:
199 104 0.12
200 31 0.03
201 1 0.00
204 60 0.07
205 539 0.60
206 168 0.19
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (206 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATG
GAGATGCCAAA
Found at i:821158 original size:411 final size:412
Alignment explanation
Indices: 820351--821495 Score: 1945
Period size: 411 Copynumber: 2.8 Consensus size: 412
820341 AAATCTGTTT
* * *
820351 CTTCGATTTGTTCTCTAACAATACAGAGATGCCAAATCATCTTAGATTTTCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
* * * * *
820416 GCGAAAACCAAATCAGCTATGCCTTCGATTTGTTTCTTGTAAGCA-AAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGACTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
*
820480 GGATCTGCTTCAGT-T----ATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAA-ATG
131 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATG
820539 GAGATGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTC
196 GAGATGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTC
820604 ATCGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGC
261 ATCGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGC
820669 CAAA-CTATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTACGTATCTGCTCT
326 CAAATCTATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTACGTATCTGCTCT
* *
820733 CCGTCGAAATGGAGATACCAGA
391 CCGTCGAAATGGAGACACCAAA
820755 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
* *
820820 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAATCATCTT
66 GTGAAAGCCAAATCAGCTATGACTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
820885 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATG
131 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATG
* *
820950 GAGACGGCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTC
196 GAGATGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTC
821015 ATCGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAA-GATGC
261 ATCGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGC
* *
821079 CAAATC-ATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCT
326 CAAATCTATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTACGTATCTGCTCT
**
821143 CCGTCGAATATGGAGACGGCAAA
391 CCGTCGAA-ATGGAGACACCAAA
*
821166 CTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
*
821231 GTGAAAGCCAAATCAGCTATGACTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCACCTT
66 GTGAAAGCCAAATCAGCTATGACTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
* **
821296 GGATCTGCTTCAGTATAAACATATGAAGGCCA-ATCTGCTATGTGTCTGCTCTCCGTCGAATATG
131 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATG
* *
821360 GAGATGCCAAACTTCGATTTGTTCTCTGACAACACAGAGATGCCAAATCATCTTAGATTTGCTTT
196 GAGATGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTC
* *
821425 AGCGTAAAC-CGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGC
261 ATCGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGC
821489 CAAATCT
326 CAAATCT
821496 GCTATCTTCA
Statistics
Matches: 699, Mismatches: 31, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
404 103 0.15
405 31 0.04
406 1 0.00
409 49 0.07
410 224 0.32
411 291 0.42
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (412 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
GTGAAAGCCAAATCAGCTATGACTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTT
GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTCGAATATG
GAGATGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTC
ATCGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGC
CAAATCTATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTACGTATCTGCTCT
CCGTCGAAATGGAGACACCAAA
Found at i:821531 original size:44 final size:44
Alignment explanation
Indices: 821441--821758 Score: 234
Period size: 44 Copynumber: 7.2 Consensus size: 44
821431 AACCGTGAAA
* * * * *
821441 GCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGAT
1 GCCAAATCTGCTA--TCTTCGATTTGTTCCCTATAAACACAGGGAT
* *
821487 GCCAAATCTGCTATCTTCAACTTGTTCCCTATAAACACAGGGAT
1 GCCAAATCTGCTATCTTCGATTTGTTCCCTATAAACACAGGGAT
** ** * * * * *
821531 GCCATGT-TGAAATCTTCGATCTGCTTCGCTGTAAGCACAGGAAT
1 GCCAAATCTGCTATCTTCGATTTG-TTCCCTATAAACACAGGGAT
* * *
821575 GTCAGATCTGTTATCTTCGATTTGTTCCCTATAAACACAGGGAT
1 GCCAAATCTGCTATCTTCGATTTGTTCCCTATAAACACAGGGAT
** * * *
821619 GAAAAACCTGCTATCTTCAACTTGTTCCCTATAAACACA-GGAT
1 GCCAAATCTGCTATCTTCGATTTGTTCCCTATAAACACAGGGAT
* * * * * * * *
821662 GCC--ATGCTG-AAGTCTTTGATCTGCTTCACTGTAAGCACAAGAAT
1 GCCAAAT-CTGCTA-TCTTCGATTTG-TTCCCTATAAACACAGGGAT
*
821706 GTCAAAT-TCGCTATCTTCGATTTGTTCCCTATAAACACAGGGAT
1 GCCAAATCT-GCTATCTTCGATTTGTTCCCTATAAACACAGGGAT
821750 GCCAAATCT
1 GCCAAATCT
821759 TGTTTCTTTG
Statistics
Matches: 204, Mismatches: 57, Indels: 23
0.72 0.20 0.08
Matches are distributed among these distances:
41 2 0.01
42 10 0.05
43 28 0.14
44 125 0.61
45 24 0.12
46 15 0.07
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (44 bp):
GCCAAATCTGCTATCTTCGATTTGTTCCCTATAAACACAGGGAT
Found at i:821731 original size:131 final size:132
Alignment explanation
Indices: 821456--821750 Score: 441
Period size: 131 Copynumber: 2.2 Consensus size: 132
821446 ATCAGCTATG
* * * * ** *
821456 TCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCTGCTATCTTCAACTTGTTCCCTATAA
1 TCTTCGATTTGTTCCCTATAAACACAGGGATGAAAAACCTGCTATCTTCAACTTGTTCCCTATAA
* * * * *
821521 ACACAGGGATGCCATGTTGAAATCTTCGATCTGCTTCGCTGTAAGCACAGGAATGTCAGATCTGT
66 ACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAAGAATGTCAAATCTGC
821586 TA
131 TA
821588 TCTTCGATTTGTTCCCTATAAACACAGGGATGAAAAACCTGCTATCTTCAACTTGTTCCCTATAA
1 TCTTCGATTTGTTCCCTATAAACACAGGGATGAAAAACCTGCTATCTTCAACTTGTTCCCTATAA
* *
821653 ACACA-GGATGCCATGCTGAAGTCTTTGATCTGCTTCACTGTAAGCACAAGAATGTCAAAT-TCG
66 ACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAAGAATGTCAAATCT-G
821716 CTA
130 CTA
821719 TCTTCGATTTGTTCCCTATAAACACAGGGATG
1 TCTTCGATTTGTTCCCTATAAACACAGGGATG
821751 CCAAATCTTG
Statistics
Matches: 148, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
130 1 0.01
131 84 0.57
132 63 0.43
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (132 bp):
TCTTCGATTTGTTCCCTATAAACACAGGGATGAAAAACCTGCTATCTTCAACTTGTTCCCTATAA
ACACAGGGATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAAGAATGTCAAATCTGC
TA
Found at i:822623 original size:13 final size:11
Alignment explanation
Indices: 822607--822666 Score: 79
Period size: 10 Copynumber: 5.5 Consensus size: 11
822597 GGCCTCTCCA
822607 TTTTTCTTTTT
1 TTTTTCTTTTT
*
822618 CATTTTTCTCTTT
1 --TTTTTCTTTTT
822631 TTTTT-TTTTT
1 TTTTTCTTTTT
822641 TTTTTCTTTTT
1 TTTTTCTTTTT
822652 TTTTT-TTTTT
1 TTTTTCTTTTT
822662 TTTTT
1 TTTTT
822667 GAAATAGAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
10 19 0.43
11 15 0.34
13 10 0.23
ACGTcount: A:0.02, C:0.08, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:822631 original size:7 final size:6
Alignment explanation
Indices: 822607--822666 Score: 60
Period size: 5 Copynumber: 10.8 Consensus size: 6
822597 GGCCTCTCCA
*
822607 TTTTTC TTTTTC ATTTTTC TCTTT- TTTTT- TTTTT- TTTTTC TTTTT-
1 TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
822652 TTTTT- TTTTT- TTTTT
1 TTTTTC TTTTTC TTTTT
822667 GAAATAGAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
5 29 0.58
6 15 0.30
7 6 0.12
ACGTcount: A:0.02, C:0.08, G:0.00, T:0.90
Consensus pattern (6 bp):
TTTTTC
Found at i:822631 original size:21 final size:21
Alignment explanation
Indices: 822607--822659 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
822597 GGCCTCTCCA
*
822607 TTTTTCTTTTTCATTTTTCTC
1 TTTTTTTTTTTCATTTTTCTC
** *
822628 TTTTTTTTTTTTTTTTTTCTT
1 TTTTTTTTTTTCATTTTTCTC
822649 TTTTTTTTTTT
1 TTTTTTTTTTT
822660 TTTTTTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.02, C:0.09, G:0.00, T:0.89
Consensus pattern (21 bp):
TTTTTTTTTTTCATTTTTCTC
Found at i:822632 original size:1 final size:1
Alignment explanation
Indices: 822628--822666 Score: 69
Period size: 1 Copynumber: 39.0 Consensus size: 1
822618 CATTTTTCTC
*
822628 TTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
822667 GAAATAGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:822660 original size:21 final size:21
Alignment explanation
Indices: 822620--822666 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
822610 TTCTTTTTCA
822620 TTTTTCTCTTTTTTTTTTTTT
1 TTTTTCTCTTTTTTTTTTTTT
*
822641 TTTTTCTTTTTTTTTTTTTTT
1 TTTTTCTCTTTTTTTTTTTTT
822662 TTTTT
1 TTTTT
822667 GAAATAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (21 bp):
TTTTTCTCTTTTTTTTTTTTT
Found at i:822663 original size:19 final size:19
Alignment explanation
Indices: 822620--822664 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
822610 TTCTTTTTCA
*
822620 TTTTTCTCTTTTTTTTTTT
1 TTTTTTTCTTTTTTTTTTT
822639 TTTTTTTCTTTTTTTTTTT
1 TTTTTTTCTTTTTTTTTTT
822658 TTTTTTT
1 TTTTTTT
822665 TTGAAATAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (19 bp):
TTTTTTTCTTTTTTTTTTT
Found at i:829314 original size:19 final size:19
Alignment explanation
Indices: 829272--829332 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
829262 CATATCATAT
829272 CATATCATATCTAAGATT-
1 CATATCATATCTAAGATTG
829290 -ATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG
829308 CATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG
829327 CATATC
1 CATATC
829333 CTTAAAGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.41
19 24 0.59
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (19 bp):
CATATCATATCTAAGATTG
Found at i:856727 original size:2 final size:2
Alignment explanation
Indices: 856720--856752 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
856710 TTTGGCCACA
856720 AT AT AT 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
856753 CACATCTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:856867 original size:47 final size:47
Alignment explanation
Indices: 856816--856959 Score: 189
Period size: 47 Copynumber: 3.1 Consensus size: 47
856806 TTCTACGTTT
** **
856816 ATCACATCAGCCATTCTACCTTATCACACATATGCATATTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATATTCACATTC
* *
856863 ATCACATTGGCCATTCGGCCTTATCACACATATGAATGTTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATATTCACATTC
* * * * *
856910 ATCACATTGGCCATTAGGCCTTATCTCATATATACACATTCACATTC
1 ATCACATTGGCCATTCGGCCTTATCACACATATGCATATTCACATTC
856957 ATC
1 ATC
856960 TCATAAAATC
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 84 1.00
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
ATCACATTGGCCATTCGGCCTTATCACACATATGCATATTCACATTC
Found at i:863470 original size:5 final size:5
Alignment explanation
Indices: 863460--863516 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
863450 GTTATATATA
* * * *
863460 ATAAT ATAAT ATGAAT AAAAT ATAAG A-AAT ATAAT ATAAA ATAAT AAAAAT
1 ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT
863511 ATAAT A
1 ATAAT A
863517 AGTAATTTGC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
4 3 0.07
5 30 0.73
6 8 0.20
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (5 bp):
ATAAT
Found at i:863490 original size:14 final size:15
Alignment explanation
Indices: 863457--863514 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
863447 TAAGTTATAT
*
863457 ATAATAATATAATATGA
1 ATAA-AATATAAAAT-A
*
863474 ATAAAATATAAGA-A
1 ATAAAATATAAAATA
*
863488 ATATAATATAAAATA
1 ATAAAATATAAAATA
863503 ATAAAAATATAA
1 AT-AAAATATAA
863515 TAAGTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 12 0.34
15 3 0.09
16 16 0.46
17 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
ATAAAATATAAAATA
Found at i:863498 original size:21 final size:21
Alignment explanation
Indices: 863453--863516 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
863443 AAAATAAGTT
* * *
863453 ATATATAATAAT-ATAATATG
1 ATATAAAATAATAAAAATATA
863473 A-ATAAAAT-ATAAGAAATATA
1 ATATAAAATAATAA-AAATATA
863493 ATATAAAATAATAAAAATATA
1 ATATAAAATAATAAAAATATA
863514 ATA
1 ATA
863517 AGTAATTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.05
19 7 0.19
20 7 0.19
21 17 0.46
22 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (21 bp):
ATATAAAATAATAAAAATATA
Found at i:874747 original size:12 final size:12
Alignment explanation
Indices: 874727--874760 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
874717 GTTCTTATAT
*
874727 ATTAGATTAAAG
1 ATTAAATTAAAG
874739 ATTAAATTAAAG
1 ATTAAATTAAAG
*
874751 AGTAAATTAA
1 ATTAAATTAA
874761 TTTTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (12 bp):
ATTAAATTAAAG
Found at i:885285 original size:38 final size:38
Alignment explanation
Indices: 885205--885293 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 38
885195 AGGCTTTATG
* * * *
885205 CTGGAATTATATCCGGGTTAAATCCCACAGGCTTCGTG
1 CTGGTATTATATCCGGGTTAAATCCCACAGGCCTAGTA
*
885243 CTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAGTA
1 CTGGTATTATATCCGGGTTAAATCCCACAGGCCTAGTA
885281 CTGGTATTATATC
1 CTGGTATTATATC
885294 TGAGTTTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (38 bp):
CTGGTATTATATCCGGGTTAAATCCCACAGGCCTAGTA
Found at i:885325 original size:40 final size:38
Alignment explanation
Indices: 885203--885339 Score: 130
Period size: 38 Copynumber: 3.6 Consensus size: 38
885193 GTAGGCTTTA
* * *
885203 TGCTGGAATTATATCCGGGTTAAATCCCACAGGCTTCG
1 TGCTGGTATTATATCCGGGTTAAATCCCGCAAGCTTCG
* * *
885241 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGTATTATATCCGGGTTAAATCCCGCAAGCTTCG
* * * * *
885279 TACTGGTATTATATCTGAGTTTAAAGTCCCGTAAGTTTCG
1 TGCTGGTATTATATCCG-GGTTAAA-TCCCGCAAGCTTCG
* * *
885319 TGCTGGTGTTATGTTCGGGTT
1 TGCTGGTATTATATCCGGGTT
885340 TTATACCTCG
Statistics
Matches: 79, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
38 49 0.62
39 9 0.11
40 21 0.27
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (38 bp):
TGCTGGTATTATATCCGGGTTAAATCCCGCAAGCTTCG
Found at i:887125 original size:29 final size:28
Alignment explanation
Indices: 887092--887190 Score: 83
Period size: 29 Copynumber: 3.5 Consensus size: 28
887082 ATGGTTAGAG
*
887092 GCACTGTGTGTGCAAATTCTTTTAACCGA
1 GCACTATGTGTGCAAATTC-TTTAACCGA
** **
887121 GCACTATGTGTGCGAAA-TCGGTAATTGA
1 GCACTATGTGTGC-AAATTCTTTAACCGA
* * * *
887149 GGCACTGTGTGTGCGAATTCTTCAACCAA
1 -GCACTATGTGTGCAAATTCTTTAACCGA
887178 GCACTATGTGTGC
1 GCACTATGTGTGC
887191 GAGATCGGTC
Statistics
Matches: 53, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
28 19 0.36
29 31 0.58
30 3 0.06
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (28 bp):
GCACTATGTGTGCAAATTCTTTAACCGA
Found at i:887158 original size:58 final size:57
Alignment explanation
Indices: 887089--887199 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
887079 CGAATGGTTA
* *
887089 GAGGCACTGTGTGTGCAAATTCTTTTAACCGAGCACTATGTGTGCGAAATCGGTAATT
1 GAGGCACTGTGTGTGCAAATTC-TTCAACCAAGCACTATGTGTGCGAAATCGGTAATT
* *
887147 GAGGCACTGTGTGTGCGAATTCTTCAACCAAGCACTATGTGTGCGAGATCGGT
1 GAGGCACTGTGTGTGCAAATTCTTCAACCAAGCACTATGTGTGCGAAATCGGT
887200 CAGTGGGCAC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 28 0.57
58 21 0.43
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (57 bp):
GAGGCACTGTGTGTGCAAATTCTTCAACCAAGCACTATGTGTGCGAAATCGGTAATT
Found at i:890091 original size:38 final size:38
Alignment explanation
Indices: 890044--890170 Score: 148
Period size: 38 Copynumber: 3.3 Consensus size: 38
890034 GGCTTAAAGA
* *
890044 CCCGTAGGCTTTATGCTGGAATTATATCCGGGTTAAAT
1 CCCGCAGGCTTTATGCTGGTATTATATCCGGGTTAAAT
* *
890082 CCCGCAGGCTTTGTACTGGTATTATATCCGGGTTAAAT
1 CCCGCAGGCTTTATGCTGGTATTATATCCGGGTTAAAT
* * *
890120 CCCGCAGGC-CTAGTGCTGGTATTATATCTGAGTTTAAAGT
1 CCCGCAGGCTTTA-TGCTGGTATTATATCCG-GGTTAAA-T
*
890160 CCCGTAGGCTT
1 CCCGCAGGCTT
890171 CGTGCTGATG
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
37 1 0.01
38 58 0.78
39 6 0.08
40 9 0.12
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (38 bp):
CCCGCAGGCTTTATGCTGGTATTATATCCGGGTTAAAT
Found at i:895398 original size:46 final size:46
Alignment explanation
Indices: 895345--895446 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
895335 GGACCACAAA
*
895345 CTCCCCTTGCGAGCACACATTGGCATGTGCGAGCTGAGACCGTGAG
1 CTCCCCTTGCGAGCACACATTGGCATGTGCGAGCTGAGACCGCGAG
** * *
895391 CTCCCCTTATGAGCACCCCTTGGCATGTGCGAGCTGAGACCGCGAG
1 CTCCCCTTGCGAGCACACATTGGCATGTGCGAGCTGAGACCGCGAG
895437 CTCCCCTTGC
1 CTCCCCTTGC
895447 TGACTTCTCA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (46 bp):
CTCCCCTTGCGAGCACACATTGGCATGTGCGAGCTGAGACCGCGAG
Found at i:895642 original size:22 final size:22
Alignment explanation
Indices: 895598--895642 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
895588 TTCTATTTTG
* ** *
895598 ATCATTGAACTTTTTTTATTTA
1 ATCATTAAACTTTTTAAAATTA
895620 ATCATTAAACTTTTTAAAATTA
1 ATCATTAAACTTTTTAAAATTA
895642 A
1 A
895643 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (22 bp):
ATCATTAAACTTTTTAAAATTA
Found at i:900219 original size:14 final size:14
Alignment explanation
Indices: 900200--900226 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
900190 TGACTTTTTT
900200 TTTTTTATAAACAC
1 TTTTTTATAAACAC
900214 TTTTTTATAAACA
1 TTTTTTATAAACA
900227 TTCTAACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTTTATAAACAC
Found at i:902132 original size:29 final size:28
Alignment explanation
Indices: 902071--902146 Score: 68
Period size: 29 Copynumber: 2.8 Consensus size: 28
902061 TTACAAGTTG
* *
902071 ATTTT-ATAT-ATTATATATCATATTTA
1 ATTTTGATATAATTATATATAAAATTTA
**
902097 AACTTGATATAATTATATATAAAACTTTA
1 ATTTTGATATAATTATATATAAAA-TTTA
*
902126 ATTTTGAT-TAAATTGTATATA
1 ATTTTGATAT-AATTATATATA
902147 TATTTATTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 3 0.08
27 4 0.10
28 12 0.31
29 20 0.51
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (28 bp):
ATTTTGATATAATTATATATAAAATTTA
Found at i:907995 original size:42 final size:42
Alignment explanation
Indices: 907883--908004 Score: 156
Period size: 43 Copynumber: 2.9 Consensus size: 42
907873 TACCGTACCA
* * *
907883 ATGTCATATCTCAGATATGATCTTACATGTAATCTCGTATCG
1 ATGTCATATCTCAGATATGGTCTTACACGTAATCTCATATCG
* * * *
907925 ATGCCAATAGCCCAGTTATGGTCTTACACG-AAGTCTCATATCG
1 ATGTC-ATATCTCAGATATGGTCTTACACGTAA-TCTCATATCG
907968 ATGTCATATCTCAGATATGGTCTTACACGTAATCTCA
1 ATGTCATATCTCAGATATGGTCTTACACGTAATCTCA
908005 GTAACCCTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 32 0.48
43 34 0.52
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (42 bp):
ATGTCATATCTCAGATATGGTCTTACACGTAATCTCATATCG
Found at i:909829 original size:32 final size:32
Alignment explanation
Indices: 909793--909853 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
909783 TCATAAACTT
* *
909793 ATAAATTGATTACTTGAATTTAATAACTCGTG
1 ATAAATTAATTAATTGAATTTAATAACTCGTG
* *
909825 ATAAATTAATTAATTTAATTTGATAACTC
1 ATAAATTAATTAATTGAATTTAATAACTC
909854 ATATTGATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (32 bp):
ATAAATTAATTAATTGAATTTAATAACTCGTG
Found at i:918105 original size:22 final size:22
Alignment explanation
Indices: 918061--918105 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
918051 AATTCATGAG
**
918061 AGGTTAAGCAAAATTTTTATTA
1 AGGTTAAGCAAAATTGCTATTA
918083 AGGTTAAGCAAAATTAGCT-TTA
1 AGGTTAAGCAAAATT-GCTATTA
918105 A
1 A
918106 AATTATAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.36
Consensus pattern (22 bp):
AGGTTAAGCAAAATTGCTATTA
Found at i:920512 original size:23 final size:23
Alignment explanation
Indices: 920481--920525 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
920471 TAAAACATTA
*
920481 CAAGTAATGAGTGACATCTTAGT
1 CAAGCAATGAGTGACATCTTAGT
*
920504 CAAGCAATGAGTGACATTTTAG
1 CAAGCAATGAGTGACATCTTAG
920526 CAATGTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (23 bp):
CAAGCAATGAGTGACATCTTAGT
Found at i:922358 original size:43 final size:43
Alignment explanation
Indices: 922290--922375 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
922280 ATTTAGAATG
* *
922290 TAAGTTGTTGTCTTTAAAGGTACTAACCAAATAAGCACTTTTA
1 TAAGTTGTTGTCTTTAAAGGCACTAACAAAATAAGCACTTTTA
* * *
922333 TAAGTTGTTGTCTTTAGAGGCACTAACAAAATGAGTACTTTTA
1 TAAGTTGTTGTCTTTAAAGGCACTAACAAAATAAGCACTTTTA
922376 GACTATAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (43 bp):
TAAGTTGTTGTCTTTAAAGGCACTAACAAAATAAGCACTTTTA
Found at i:923834 original size:31 final size:32
Alignment explanation
Indices: 923792--923855 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
923782 AAAGATTTTT
923792 TTTAGGTTTTATA-T-ATTATAATAATTATTA
1 TTTAGGTTTTATATTAATTATAATAATTATTA
*
923822 TTTATGGTTTTATATTAAATTATTATAATTATTA
1 TTTA-GGTTTTATATT-AATTATAATAATTATTA
923856 ATTAACATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 4 0.14
31 9 0.31
32 1 0.03
34 15 0.52
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (32 bp):
TTTAGGTTTTATATTAATTATAATAATTATTA
Found at i:923900 original size:15 final size:14
Alignment explanation
Indices: 923874--923904 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
923864 TATGGTTTTA
923874 TATTAGATTATTAT
1 TATTAGATTATTAT
923888 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
923903 TA
1 TA
923905 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:925432 original size:21 final size:23
Alignment explanation
Indices: 925390--925432 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
925380 TAATATTCTG
925390 GGTGTGTTTGGGTTGGACATCCT
1 GGTGTGTTTGGGTTGGACATCCT
925413 GGTGTGTTTGGG-TGGA-ATCC
1 GGTGTGTTTGGGTTGGACATCC
925433 GTGTATCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 4 0.20
23 12 0.60
ACGTcount: A:0.09, C:0.12, G:0.42, T:0.37
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGACATCCT
Found at i:928611 original size:13 final size:13
Alignment explanation
Indices: 928593--928671 Score: 95
Period size: 13 Copynumber: 6.1 Consensus size: 13
928583 CTAGTTTGGC
928593 AATGCTTTTGAAA
1 AATGCTTTTGAAA
928606 AATGCTTTTGAAA
1 AATGCTTTTGAAA
* *
928619 AGTGCTTTTGAGA
1 AATGCTTTTGAAA
* *
928632 AATGCTGTGGAAA
1 AATGCTTTTGAAA
* *
928645 AGTGCTTTTGAGA
1 AATGCTTTTGAAA
*
928658 AGTGCTTTTGAAA
1 AATGCTTTTGAAA
928671 A
1 A
928672 TTTTGGTTTA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 55 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (13 bp):
AATGCTTTTGAAA
Found at i:928624 original size:26 final size:26
Alignment explanation
Indices: 928595--928671 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
928585 AGTTTGGCAA
*
928595 TGCTTTTGAAAAATGCTTTTGAAAAG
1 TGCTTTTGAGAAATGCTTTTGAAAAG
* *
928621 TGCTTTTGAGAAATGCTGTGGAAAAG
1 TGCTTTTGAGAAATGCTTTTGAAAAG
*
928647 TGCTTTTGAGAAGTGCTTTTGAAAA
1 TGCTTTTGAGAAATGCTTTTGAAAA
928672 TTTTGGTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (26 bp):
TGCTTTTGAGAAATGCTTTTGAAAAG
Found at i:941687 original size:15 final size:16
Alignment explanation
Indices: 941661--941693 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
941651 CTGGAACTGT
*
941661 TTATGACATTCATTTA
1 TTATGACATTCATGTA
941677 TTATG-CATTCATGTA
1 TTATGACATTCATGTA
941692 TT
1 TT
941694 TCTATGTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (16 bp):
TTATGACATTCATGTA
Found at i:945371 original size:17 final size:18
Alignment explanation
Indices: 945345--945389 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
945335 AGTGGTAAAA
*
945345 GAAGATGAAAAGAAG-AT
1 GAAGAAGAAAAGAAGCAT
945362 GAAGAAGAAAAGAAGCAT
1 GAAGAAGAAAAGAAGCAT
*
945380 -AAGGAGAAAA
1 GAAGAAGAAAA
945390 CGATGAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 23 0.92
18 2 0.08
ACGTcount: A:0.62, C:0.02, G:0.29, T:0.07
Consensus pattern (18 bp):
GAAGAAGAAAAGAAGCAT
Found at i:945376 original size:11 final size:11
Alignment explanation
Indices: 945341--945370 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
945331 AAGAAGTGGT
945341 AAAAGAAGATG
1 AAAAGAAGATG
945352 AAAAGAAGATG
1 AAAAGAAGATG
945363 AAGAAGAA
1 AA-AAGAA
945371 AAGAAGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (11 bp):
AAAAGAAGATG
Found at i:947448 original size:25 final size:26
Alignment explanation
Indices: 947419--947476 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 26
947409 CTTATTTTAT
*
947419 TAAATAAAA-AAATTTTAAAATATAA
1 TAAATAAAATAAATTTTAAAACATAA
*
947444 TAAATAAAATACATTTTAAAACATAA
1 TAAATAAAATAAATTTTAAAACATAA
947470 -AAATAAA
1 TAAATAAA
947477 TATTAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 16 0.53
26 14 0.47
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (26 bp):
TAAATAAAATAAATTTTAAAACATAA
Found at i:947474 original size:20 final size:20
Alignment explanation
Indices: 947449--947508 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
947439 TATAATAAAT
*
947449 AAAATACATTTTAAAACAT-A
1 AAAATA-ATATTAAAACATAA
947469 AAAATAAATATTAAAACAAATAA
1 AAAAT-AATATTAAAAC--ATAA
947492 AAAATAATATTAAAACA
1 AAAATAATATTAAAACA
947509 ATTCTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 15 0.43
21 1 0.03
22 13 0.37
23 6 0.17
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAATAATATTAAAACATAA
Found at i:947494 original size:22 final size:22
Alignment explanation
Indices: 947445--947509 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
947435 AAAATATAAT
* *
947445 AAAT-AAAATACATTTTAAAAC
1 AAATAAAAATAAATATTAAAAC
947466 --ATAAAAATAAATATTAAAAC
1 AAATAAAAATAAATATTAAAAC
947486 AAATAAAAA-ATAATATTAAAAC
1 AAATAAAAATA-AATATTAAAAC
947508 AA
1 AA
947510 TTCTTAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 2 0.05
20 15 0.39
21 1 0.03
22 20 0.53
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (22 bp):
AAATAAAAATAAATATTAAAAC
Found at i:948303 original size:17 final size:18
Alignment explanation
Indices: 948283--948321 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
948273 TGGGCGTATA
*
948283 GGCC-ACATGGGTGTGTG
1 GGCCTACATGGGTATGTG
948300 GGCCTACATGGGTATGTG
1 GGCCTACATGGGTATGTG
948318 GGCC
1 GGCC
948322 CATTATGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.13, C:0.21, G:0.44, T:0.23
Consensus pattern (18 bp):
GGCCTACATGGGTATGTG
Found at i:949543 original size:45 final size:45
Alignment explanation
Indices: 949479--949568 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
949469 GATTGAGAAT
*
949479 GTGGTTCACCGAGTCTCTA-GCTCCGATCCTATAAGTATTTTTGTA
1 GTGGTTCACCGAGTCTCTAGGAT-CGATCCTATAAGTATTTTTGTA
*
949524 GTGGTTCACCGAGTCTCTAGGATCGATCCTGTAAGTATTTTTGTA
1 GTGGTTCACCGAGTCTCTAGGATCGATCCTATAAGTATTTTTGTA
949569 CTTAGTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 40 0.95
46 2 0.05
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (45 bp):
GTGGTTCACCGAGTCTCTAGGATCGATCCTATAAGTATTTTTGTA
Found at i:962069 original size:31 final size:29
Alignment explanation
Indices: 962015--962083 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
962005 AATCAAAATT
*
962015 TCATGTACAAAATTGCACAAAATCAAAGC
1 TCATGTATAAAATTGCACAAAATCAAAGC
* * *
962044 TCATGTATACAATTGCACATTAAATCATAGT
1 TCATGTATAAAATTGCACA--AAATCAAAGC
962075 TCATGTATA
1 TCATGTATA
962084 GTTTTGGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.50
31 17 0.50
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.30
Consensus pattern (29 bp):
TCATGTATAAAATTGCACAAAATCAAAGC
Found at i:965460 original size:27 final size:27
Alignment explanation
Indices: 965436--965490 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
965426 TTAATGTCAG
*
965436 TAAAACTTTATGAGAAAACTGTGTCTA
1 TAAAACTTTATGAGAAAACGGTGTCTA
*
965463 TACAACTTTATGAGAAAACGGTGTCTA
1 TAAAACTTTATGAGAAAACGGTGTCTA
965490 T
1 T
965491 CTCTTGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (27 bp):
TAAAACTTTATGAGAAAACGGTGTCTA
Found at i:968325 original size:26 final size:26
Alignment explanation
Indices: 968289--968372 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
968279 CATGAAATTC
968289 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
968315 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
968341 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
968367 TTATCA
1 TTATCA
968373 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:969276 original size:19 final size:20
Alignment explanation
Indices: 969254--969310 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
969244 AAATTGCAAA
969254 AAAAAATT-AAAATAATTT-T
1 AAAAAATTCAAAAT-ATTTAT
*
969273 AAAAAGTTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
*
969293 -AAAAATTCTAAA-ATTTAT
1 AAAAAATTCAAAATATTTAT
969311 GTAACACCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 6 0.18
19 21 0.64
20 6 0.18
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:969285 original size:20 final size:20
Alignment explanation
Indices: 969261--969306 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
969251 AAAAAAAAAT
969261 TAAAATAATTT-TAAAAAGTTC
1 TAAAAT-ATTTATAAAAA-TTC
969282 -AAAATATTTATAAAAATTC
1 TAAAATATTTATAAAAATTC
969301 TAAAAT
1 TAAAAT
969307 TTATGTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAATATTTATAAAAATTC
Found at i:971429 original size:30 final size:31
Alignment explanation
Indices: 971372--971443 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 31
971362 AAATTATGTT
*
971372 TTTTAAAAAAT-TATAAAAGAAATTAAAAAA
1 TTTTAAAAAATATATAAAAGAAAGTAAAAAA
971402 TTCTTAAAAAATATAT-AAA-AAAGTAAAAAA
1 TT-TTAAAAAATATATAAAAGAAAGTAAAAAA
971432 TTTTAAAAAATA
1 TTTTAAAAAATA
971444 AAATAATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 10 0.26
30 14 0.36
31 12 0.31
32 3 0.08
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (31 bp):
TTTTAAAAAATATATAAAAGAAAGTAAAAAA
Found at i:971438 original size:10 final size:10
Alignment explanation
Indices: 971372--971442 Score: 58
Period size: 10 Copynumber: 7.1 Consensus size: 10
971362 AAATTATGTT
971372 TTTTAAAAAA
1 TTTTAAAAAA
*
971382 TTATAAAAGAA
1 TTTTAAAA-AA
*
971393 -ATTAAAAAA
1 TTTTAAAAAA
971402 TTCTTAAAAAA
1 TT-TTAAAAAA
*
971413 TATATAAAAAA
1 T-TTTAAAAAA
*
971424 --GTAAAAAA
1 TTTTAAAAAA
971432 TTTTAAAAAA
1 TTTTAAAAAA
971442 T
1 T
971443 AAAATAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
8 7 0.15
9 2 0.04
10 20 0.42
11 18 0.38
12 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:971854 original size:14 final size:15
Alignment explanation
Indices: 971828--971860 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
971818 TAAAAAAGTG
971828 TTAATAAAGATAATA
1 TTAATAAAGATAATA
*
971843 TTAATAAA-ATAATT
1 TTAATAAAGATAATA
971857 TTAA
1 TTAA
971861 ATTTTTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
TTAATAAAGATAATA
Found at i:972774 original size:15 final size:17
Alignment explanation
Indices: 972753--972797 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
972743 TATTTTTCTG
972753 AATTTTTTAT-ATTTAT
1 AATTTTTTATAATTTAT
972769 -A-TTTTTATAATTTAT
1 AATTTTTTATAATTTAT
*
972784 AATTTTTTAAAATT
1 AATTTTTTATAATT
972798 GATATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.28
15 7 0.28
16 1 0.04
17 10 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTTTTTATAATTTAT
Found at i:972780 original size:24 final size:27
Alignment explanation
Indices: 972731--972781 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
972721 CTTTTTTTAC
*
972731 TTTATTATTATATATTTTTCTGAATTT
1 TTTATTATTATATATTTTTATGAATTT
972758 TTTA-TATT-TATATTTTTAT-AATTT
1 TTTATTATTATATATTTTTATGAATTT
972782 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 10 0.43
26 4 0.17
27 4 0.17
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (27 bp):
TTTATTATTATATATTTTTATGAATTT
Found at i:976915 original size:16 final size:17
Alignment explanation
Indices: 976894--976926 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
976884 TTTTTTTCAG
*
976894 TTTAAAT-TCTAATTAT
1 TTTAAATGTATAATTAT
976910 TTTAAATGTATAATTAT
1 TTTAAATGTATAATTAT
976927 CACAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATGTATAATTAT
Found at i:978660 original size:60 final size:60
Alignment explanation
Indices: 978586--978698 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
978576 CAACAGTTAA
* **
978586 CAAGTTTAGGTATCAAATTGAACTTAA-AAAACTTTAGGTACCAAATTAAGAAAGAAGGGT
1 CAAGTTTAGATATCAAATTGAACAAAAGAAAAC-TTAGGTACCAAATTAAGAAAGAAGGGT
* * *
978646 CAAGTTTAGATATCAAATTGGACAAAAGAAAACTTAGGTATCAAATTAGGAAA
1 CAAGTTTAGATATCAAATTGAACAAAAGAAAACTTAGGTACCAAATTAAGAAA
978699 ATGTATTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 41 0.89
61 5 0.11
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.26
Consensus pattern (60 bp):
CAAGTTTAGATATCAAATTGAACAAAAGAAAACTTAGGTACCAAATTAAGAAAGAAGGGT
Found at i:978992 original size:21 final size:22
Alignment explanation
Indices: 978963--979003 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
978953 ATTTTAAAAA
978963 ATTACAAAATGATCATTGAACT
1 ATTACAAAATGATCATTGAACT
**
978985 ATTA-AAAATTTTCATTGAA
1 ATTACAAAATGATCATTGAA
979004 AGCTTTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (22 bp):
ATTACAAAATGATCATTGAACT
Found at i:983816 original size:31 final size:31
Alignment explanation
Indices: 983776--983880 Score: 88
Period size: 31 Copynumber: 3.3 Consensus size: 31
983766 TATAACAGAA
983776 AGACCAATTTACTTTTTGATCTAACATACAT
1 AGACCAATTTACTTTTTGATCTAACATACAT
* * * *** *
983807 AGACTAATTTGCCCATTTTTTGA-GTAA-AGGGAA
1 AGACCAATTT----ACTTTTTGATCTAACATACAT
983840 AGACCAATTTACTTTTTGATCTAACATACAT
1 AGACCAATTTACTTTTTGATCTAACATACAT
*
983871 AGACTAATTT
1 AGACCAATTT
983881 GCCCATTTTT
Statistics
Matches: 53, Mismatches: 15, Indels: 12
0.66 0.19 0.15
Matches are distributed among these distances:
29 8 0.15
30 3 0.06
31 20 0.38
33 11 0.21
34 3 0.06
35 8 0.15
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (31 bp):
AGACCAATTTACTTTTTGATCTAACATACAT
Found at i:983827 original size:35 final size:35
Alignment explanation
Indices: 983788--983893 Score: 107
Period size: 35 Copynumber: 3.2 Consensus size: 35
983778 ACCAATTTAC
983788 TTTTTGATCTAACATACATAGACTAATTTGCCCAT
1 TTTTTGATCTAACATACATAGACTAATTTGCCCAT
* *** * * *
983823 TTTTTGA-GTAA-AGGGAAAGACCAATTT----AC
1 TTTTTGATCTAACATACATAGACTAATTTGCCCAT
983852 TTTTTGATCTAACATACATAGACTAATTTGCCCAT
1 TTTTTGATCTAACATACATAGACTAATTTGCCCAT
983887 TTTTTGA
1 TTTTTGA
983894 GTAAAGGGAG
Statistics
Matches: 51, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
29 8 0.16
30 3 0.06
31 11 0.22
33 11 0.22
34 3 0.06
35 15 0.29
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (35 bp):
TTTTTGATCTAACATACATAGACTAATTTGCCCAT
Found at i:983874 original size:64 final size:64
Alignment explanation
Indices: 983773--983902 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
983763 ATTTATAACA
983773 GAAAGACCAATTTACTTTTTGATCTAACATACATAGACTAATTTGCCCATTTTTTGAGTAAAGG
1 GAAAGACCAATTTACTTTTTGATCTAACATACATAGACTAATTTGCCCATTTTTTGAGTAAAGG
983837 GAAAGACCAATTTACTTTTTGATCTAACATACATAGACTAATTTGCCCATTTTTTGAGTAAAGG
1 GAAAGACCAATTTACTTTTTGATCTAACATACATAGACTAATTTGCCCATTTTTTGAGTAAAGG
983901 GA
1 GA
983903 GCAAAATACA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (64 bp):
GAAAGACCAATTTACTTTTTGATCTAACATACATAGACTAATTTGCCCATTTTTTGAGTAAAGG
Found at i:989292 original size:29 final size:28
Alignment explanation
Indices: 989230--989292 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
989220 TGTATATTCA
*
989230 AAATTTAGTCCTTCTACTTTTATTTCAAG
1 AAATTTAGTCCCTCTACTTTTATTT-AAG
*
989259 TAATTTAGTCCCTCTACTTTTGGATTT-AG
1 AAATTTAGTCCCTCTACTTTT--ATTTAAG
989288 AAATT
1 AAATT
989293 CAAGTCCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 25 0.86
31 4 0.14
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.48
Consensus pattern (28 bp):
AAATTTAGTCCCTCTACTTTTATTTAAG
Found at i:997951 original size:26 final size:26
Alignment explanation
Indices: 997915--998024 Score: 193
Period size: 26 Copynumber: 4.2 Consensus size: 26
997905 TGATACAAAT
997915 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
997941 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
997967 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
997993 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
998019 TGATAA
1 TGATAA
998025 GAATTTCATG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:999539 original size:25 final size:27
Alignment explanation
Indices: 999497--999549 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
999487 AATTACTGTT
999497 TACCCCTAGGTGCAAAATT-ACCGAAA
1 TACCCCTAGGTGCAAAATTGACCGAAA
** *
999523 TACCCCTAGG-GTTAAATTGACCTAAA
1 TACCCCTAGGTGCAAAATTGACCGAAA
999549 T
1 T
999550 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (27 bp):
TACCCCTAGGTGCAAAATTGACCGAAA
Found at i:1005440 original size:106 final size:106
Alignment explanation
Indices: 1005255--1005559 Score: 504
Period size: 106 Copynumber: 2.9 Consensus size: 106
1005245 AACAAGTTAT
* *
1005255 ACATAGAACCCATATGAGTAGAGTCGCCGCTAATAATTTGAGTTAGGTTGGTTAGTCGCTTATTG
1 ACATAGAACCCATATGAGTAGAGTCGCCACTAATCATTTGAGTTAGGTTGGTTAGTCGCTTATTG
1005320 CCTAAAGTCTCAAAAACAAATTAAGATATTCCTTAAGCTAG
66 CCTAAAGTCTCAAAAACAAATTAAGATATTCCTTAAGCTAG
*
1005361 ACATAGAACCCATATGAGTAGAGTCGCCACTAATCATTTGAGTTAGGTTGGCTAGTCGCTTATTG
1 ACATAGAACCCATATGAGTAGAGTCGCCACTAATCATTTGAGTTAGGTTGGTTAGTCGCTTATTG
*
1005426 CCTAAAGTCTCAAAAATAAATTAAGATATTCCTTAAGCTAG
66 CCTAAAGTCTCAAAAACAAATTAAGATATTCCTTAAGCTAG
* * * **
1005467 ACATAGAACCCATATGAGTAGAGTTGCCACTAATCATTTAAGTTAGGCTGGTTAGTTACTTATTG
1 ACATAGAACCCATATGAGTAGAGTCGCCACTAATCATTTGAGTTAGGTTGGTTAGTCGCTTATTG
1005532 CCTAAAGTCTC-AAAACTAAAATTAAGAT
66 CCTAAAGTCTCAAAAAC--AAATTAAGAT
1005560 GTATCTAAGG
Statistics
Matches: 186, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
105 4 0.02
106 172 0.92
107 10 0.05
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (106 bp):
ACATAGAACCCATATGAGTAGAGTCGCCACTAATCATTTGAGTTAGGTTGGTTAGTCGCTTATTG
CCTAAAGTCTCAAAAACAAATTAAGATATTCCTTAAGCTAG
Found at i:1016095 original size:298 final size:298
Alignment explanation
Indices: 1015559--1016451 Score: 1696
Period size: 298 Copynumber: 3.0 Consensus size: 298
1015549 CAGTGACTTG
*
1015559 AAATAGAAAGGAAAAGCACCGATGCACGTGACCGAAGATGAGAATGAAATTGTGCCTGAACAAGA
1 AAATAGAAAGGAAAAGCACCGATGCACGTGACCGAAGATGAGAATGAAACTGTGCCTGAACAAGA
1015624 AGCTAAAAAGTCTGTGGACGAGAAGGAAGCACAGGAATTCTTAAAATTTATCAAGCACAGTGAGT
66 AGCTAAAAAGTCTGTGGACGAGAAGGAAGCACAGGAATTCTTAAAATTTATCAAGCACAGTGAGT
1015689 ACAATGTGGTAGAACAATTGAGTAAGCAGCCAGTACGAATCTCAGTATTATCTCTGCTGTTGAAT
131 ACAATGTGGTAGAACAATTGAGTAAGCAGCCAGTACGAATCTCAGTATTATCTCTGCTGTTGAAT
1015754 TCAGAACCACACCGGAACGCTCTGCTAAAAGTGTTAAATCAAGCTTATGTGGCAAACAATATATC
196 TCAGAACCACACCGGAACGCTCTGCTAAAAGTGTTAAATCAAGCTTATGTGGCAAACAATATATC
1015819 CGCTGAAAAACTGGATAGGTGGGTGAACAACTTGAATA
261 CGCTGAAAAACTGGATAGGTGGGTGAACAACTTGAATA
1015857 AAATAGAAAGGAAAAGCACCGATGCACGTGACCGAAGATGAGAATGAAACTGTGCCTGAACAAGA
1 AAATAGAAAGGAAAAGCACCGATGCACGTGACCGAAGATGAGAATGAAACTGTGCCTGAACAAGA
*
1015922 AGCTAAAAAGTCTGTGGACGAGAAGGAAGCACAGGGATTCTTAAAATTTATCAAGCACAGTGAGT
66 AGCTAAAAAGTCTGTGGACGAGAAGGAAGCACAGGAATTCTTAAAATTTATCAAGCACAGTGAGT
1015987 ACAATGTGGTAGAACAATTGAGTAAGCAGCCAGTACGAATCTCAGTATTATCTCTGCTGTTGAAT
131 ACAATGTGGTAGAACAATTGAGTAAGCAGCCAGTACGAATCTCAGTATTATCTCTGCTGTTGAAT
1016052 TCAGAACCACACCGGAACGCTCTGCTAAAAGTGTTAAATCAAGCTTATGTGGCAAACAATATATC
196 TCAGAACCACACCGGAACGCTCTGCTAAAAGTGTTAAATCAAGCTTATGTGGCAAACAATATATC
1016117 CGCTGAAAAACTGGATAGGTGGGTGAACAACTTGAATA
261 CGCTGAAAAACTGGATAGGTGGGTGAACAACTTGAATA
1016155 AAATAGAAAGGAAAAGCACCGATGCACGTGACCGAAGATGAGAATGAAACTGTGCCTGAACAAGA
1 AAATAGAAAGGAAAAGCACCGATGCACGTGACCGAAGATGAGAATGAAACTGTGCCTGAACAAGA
* * *
1016220 AGCTAAAAAGCCTGTGGACGAGAAGGAAGCACAGGAATTCTTAAAGTTTATCAAGCACAGTGAAT
66 AGCTAAAAAGTCTGTGGACGAGAAGGAAGCACAGGAATTCTTAAAATTTATCAAGCACAGTGAGT
* *
1016285 ACAATGTGGTAGAATAATTGAGTAAGCAGCCAGTACGAATCTCAGTATTATCTCTACTGTTGAAT
131 ACAATGTGGTAGAACAATTGAGTAAGCAGCCAGTACGAATCTCAGTATTATCTCTGCTGTTGAAT
*
1016350 TCAGAACCACATCGGAACGCTCTGCTAAAAGTGTTAAATCAAGCTTATGTGGCAAACAATATATC
196 TCAGAACCACACCGGAACGCTCTGCTAAAAGTGTTAAATCAAGCTTATGTGGCAAACAATATATC
* *
1016415 CGTTGAAAAACTAGATAGGTGGGTGAACAACTTGAAT
261 CGCTGAAAAACTGGATAGGTGGGTGAACAACTTGAAT
1016452 GCGGATAATT
Statistics
Matches: 584, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
298 584 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (298 bp):
AAATAGAAAGGAAAAGCACCGATGCACGTGACCGAAGATGAGAATGAAACTGTGCCTGAACAAGA
AGCTAAAAAGTCTGTGGACGAGAAGGAAGCACAGGAATTCTTAAAATTTATCAAGCACAGTGAGT
ACAATGTGGTAGAACAATTGAGTAAGCAGCCAGTACGAATCTCAGTATTATCTCTGCTGTTGAAT
TCAGAACCACACCGGAACGCTCTGCTAAAAGTGTTAAATCAAGCTTATGTGGCAAACAATATATC
CGCTGAAAAACTGGATAGGTGGGTGAACAACTTGAATA
Found at i:1022273 original size:127 final size:126
Alignment explanation
Indices: 1022120--1022800 Score: 873
Period size: 127 Copynumber: 5.3 Consensus size: 126
1022110 CTGTTCTCAG
* * *
1022120 AAATCGACTCATATTGCGAGAAGTGAGTTGAGCATTTTAATTTCTATTTTTCAAAAATCAACTCA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCA
1022185 TATTGCGAGAGGTGAGTTGAGCCTCGAGACACATGGAGGTATTTTCAGTTTTTATTTTTCAA
66 TATTGCGAGAGGTGAGTTGAGCCTCGAGACACAT-GAGGTATTTTCAGTTTTTATTTTTCAA
* * *
1022247 AAATCAACTTATATTGCGAGATGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTTA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCA
* * * * *
1022312 TATTGCGAGAGGTGAGTTGAGCCTC-AGGATACGCTGAGGTAATTTCA-TTTCTGTTTTTCAA
66 TATTGCGAGAGGTGAGTTGAGCCTCGA-GACAC-ATGAGGTATTTTCAGTTTTTATTTTTCAA
* * *
1022373 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTTTAAAAAATCAACTCA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCA
1022438 TATTGCGAGAGGTGAGTTGAGCCTCGAGACACATTGAGGTATTTTCAGTTTTTATTTTTCAAA
66 TATTGCGAGAGGTGAGTTGAGCCTCGAGACACA-TGAGGTATTTTCAGTTTTTATTTTTC-AA
* * *
1022501 AAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTTA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCA
* * *
1022566 TATTGCGAGAGGTGAGTTGAGCCTC-AGGATACGCTGAGGTAATATCAATTTCTGTCTTTAATTT
66 TATTGCGAGAGGTGAGTTGAGCCTCGA-GACAC-ATGAGG---TAT---TTTCAG----T--TTT
*
1022630 CTGTTTTTCAA
117 -TATTTTTCAA
* * **
1022641 AAATCAACTCATATTGCAAGAAGTAAGTTGAGTGTTTTAATTTCTGTTTTTCAAAAATCAACTCA
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCA
* *
1022706 TATTGCGAGAGGTGAGTTGAGTCTTGAGACACATTGAGGTATTTTCAGTTTTTATTTTTCAA
66 TATTGCGAGAGGTGAGTTGAGCCTCGAGACACA-TGAGGTATTTTCAGTTTTTATTTTTCAA
* * * *
1022768 AAATCAACTTATATTGTGAGAAATGAGTCGAGC
1 AAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1022801 TCAATATCGT
Statistics
Matches: 482, Mismatches: 49, Indels: 46
0.84 0.08 0.08
Matches are distributed among these distances:
126 114 0.24
127 146 0.30
128 101 0.21
130 1 0.00
131 3 0.01
134 10 0.02
137 3 0.01
138 1 0.00
140 95 0.20
141 8 0.02
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (126 bp):
AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCA
TATTGCGAGAGGTGAGTTGAGCCTCGAGACACATGAGGTATTTTCAGTTTTTATTTTTCAA
Found at i:1022438 original size:54 final size:54
Alignment explanation
Indices: 1022358--1022589 Score: 214
Period size: 54 Copynumber: 3.9 Consensus size: 54
1022348 AGGTAATTTC
*
1022358 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTA
1 ATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTA
* *
1022412 ATTTCTATTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGACACATTGA
1 ATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT---------TTTA
*
1022475 GGTATTT-TCAGTTTTTATTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTTT
1 ---ATTTCT--G---TT---TTT-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
1022539 A
54 A
* *
1022540 ATTTCTGTTTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT
1 ATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1022590 CAGGATACGC
Statistics
Matches: 149, Mismatches: 7, Indels: 44
0.75 0.04 0.22
Matches are distributed among these distances:
54 85 0.57
55 3 0.02
58 2 0.01
61 1 0.01
62 4 0.03
63 4 0.03
65 4 0.03
66 4 0.03
70 2 0.01
73 3 0.02
74 37 0.25
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (54 bp):
ATTTCTGTTTTTAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTA
Found at i:1022704 original size:54 final size:54
Alignment explanation
Indices: 1022622--1022727 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 54
1022612 AATTTCTGTC
1022622 TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAAGTAAGTTGAGTGT
1 TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAAGTAAGTTGAGTGT
* * *
1022676 TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGT
1 TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAAGTAAGTTGAGT
1022728 CTTGAGACAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (54 bp):
TTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAAGTAAGTTGAGTGT
Found at i:1026824 original size:131 final size:131
Alignment explanation
Indices: 1026631--1026891 Score: 477
Period size: 131 Copynumber: 2.0 Consensus size: 131
1026621 ATATGTGTGT
* *
1026631 TATATGACATTTTTGAATGATCTTTTGATATATTTTAAGTTCTAGAAATGTTTAGAAATGTTATG
1 TATATGACAGTTTTGAATGATCTTTTGATATATTTTAAGTTCTAAAAATGTTTAGAAATGTTATG
* *
1026696 GGATGATTGGAGATAGTTTGGACTAAATTTTTGGTGATTTGGACTTATATCAAGTCATCTGTTTG
66 GAATGATTGGAGATAGTTTGGACTAAATTTTTGGTGATTTGGACTTATATCAAGTAATCTGTTTG
1026761 C
131 C
1026762 TATATGACAGTTTTGAATGATCTTTTGATATATTTTAAGTTCTAAAAATGTTTAGAAATGTTATG
1 TATATGACAGTTTTGAATGATCTTTTGATATATTTTAAGTTCTAAAAATGTTTAGAAATGTTATG
*
1026827 GAATGATTGGAGATAGTTTGGACTTAATTTTTGGTGATTTGGACTTATATCAAGTAATCTGTTTG
66 GAATGATTGGAGATAGTTTGGACTAAATTTTTGGTGATTTGGACTTATATCAAGTAATCTGTTTG
1026892 TGGGGTTGCA
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
131 125 1.00
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.44
Consensus pattern (131 bp):
TATATGACAGTTTTGAATGATCTTTTGATATATTTTAAGTTCTAAAAATGTTTAGAAATGTTATG
GAATGATTGGAGATAGTTTGGACTAAATTTTTGGTGATTTGGACTTATATCAAGTAATCTGTTTG
C
Found at i:1030730 original size:16 final size:16
Alignment explanation
Indices: 1030709--1030739 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1030699 TTTACTATTA
*
1030709 TGTCTTTTGTATTTTT
1 TGTCTTTTATATTTTT
1030725 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
1030740 GTGTGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTT
Found at i:1031729 original size:13 final size:13
Alignment explanation
Indices: 1031711--1031736 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1031701 AGAATTGTTC
1031711 AATTAAAGAATTT
1 AATTAAAGAATTT
1031724 AATTAAAGAATTT
1 AATTAAAGAATTT
1031737 TCTTGAAATA
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
AATTAAAGAATTT
Found at i:1032311 original size:62 final size:58
Alignment explanation
Indices: 1032225--1032357 Score: 160
Period size: 62 Copynumber: 2.2 Consensus size: 58
1032215 TCCAAAAATA
* *
1032225 ATATTATTTTAAT-AGTCTAATATTAAATTAAATTTAATGTTTATCTTGTAGATAAACATT
1 ATATTATTTTAATAAGTCTAATATTAAATTAAATCTAATATTTATC-T-TA-ATAAACATT
* * * *
1032285 CTATTATTTTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTAATAAATATT
1 ATATTATTTTAATAAG-TCTAATATTAAATTAAATCTAATATTTATCTTAATAAACATT
*
1032344 ATATTAATTTAATA
1 ATATTATTTTAATA
1032358 TTAAAGTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
59 20 0.32
60 14 0.22
61 3 0.05
62 26 0.41
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.50
Consensus pattern (58 bp):
ATATTATTTTAATAAGTCTAATATTAAATTAAATCTAATATTTATCTTAATAAACATT
Found at i:1034491 original size:40 final size:39
Alignment explanation
Indices: 1034430--1034845 Score: 368
Period size: 40 Copynumber: 10.6 Consensus size: 39
1034420 AGGCACTCAA
** * *
1034430 GTGCATTCAAGGGTATTGAAGTACAAATAGGAGTACGTAT
1 GTGCATTC-AGGGTACCGAAGTACAAACAGGAGCACGTAT
* * * *
1034470 GTGCATTTGAAGGTACCGAAGT--ATA-AGGAGCATGTAT
1 GTGCA-TTCAGGGTACCGAAGTACAAACAGGAGCACGTAT
*
1034507 GTGCATTCAGGGGTACCAAAGTACAAACA--AG--C---T
1 GTGCATTCA-GGGTACCGAAGTACAAACAGGAGCACGTAT
**
1034540 GTGCATTCAGGGGTATTGAAGTACAAACAGGAGCACGTAT
1 GTGCATTCA-GGGTACCGAAGTACAAACAGGAGCACGTAT
* * * *
1034580 GTGCATTCAGGGGTTCCAAAGTACAAATAGGAGCACGCAT
1 GTGCATTCA-GGGTACCGAAGTACAAACAGGAGCACGTAT
*
1034620 GTGCATTCAAGGATACCGAAGTACAAACAGGAGCACGTAT
1 GTGCATTC-AGGGTACCGAAGTACAAACAGGAGCACGTAT
* * * *
1034660 GTGTATTCAGGGATACTGAAGTACAAACAGGAGCACTTTT
1 GTGCATTCAGGG-TACCGAAGTACAAACAGGAGCACGTAT
* * * * * *
1034700 TTGCATTTAGGGGATCGAAGTACAAACAGGAGAATGTAT
1 GTGCATTCAGGGTACCGAAGTACAAACAGGAGCACGTAT
*
1034739 GTGCATTCAGGTGGTACCGAAGTACAAATAGGAGCACGTAT
1 GTGCATTCA-G-GGTACCGAAGTACAAACAGGAGCACGTAT
* * *
1034780 ATGCGTTCAAGGGTACCGAAGTACAAACAGGAGCACATAT
1 GTGCATTC-AGGGTACCGAAGTACAAACAGGAGCACGTAT
*
1034820 GTGCATTCGGGGGTACC-AGAGTACAA
1 GTGCATTC-AGGGTACCGA-AGTACAA
1034846 TCTTGAGCAC
Statistics
Matches: 302, Mismatches: 56, Indels: 36
0.77 0.14 0.09
Matches are distributed among these distances:
33 27 0.09
35 2 0.01
36 3 0.01
37 26 0.09
38 4 0.01
39 33 0.11
40 172 0.57
41 34 0.11
42 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (39 bp):
GTGCATTCAGGGTACCGAAGTACAAACAGGAGCACGTAT
Found at i:1039278 original size:95 final size:94
Alignment explanation
Indices: 1039116--1039303 Score: 331
Period size: 95 Copynumber: 2.0 Consensus size: 94
1039106 AATCTTGACC
* *
1039116 AAACAAATATATTAGTGTCTTATCTCAATTTGGATATCTCTCAAGACATAAAGCGAATGCTAAAA
1 AAACAAATATATTAGTGTATTATCTCAATTTGGATATCTCTCAAGACATAAAGAGAATGCTAAAA
1039181 AACTCAAATAATCTTCTAGACTAATACAA
66 AACTCAAATAATCTTCTAGACTAATACAA
*
1039210 AAACAAATATATTTAGTGTATTATCTCAATTTGGATATTTCTCAAGACATAAAGAGAATGCTAAA
1 AAACAAATATA-TTAGTGTATTATCTCAATTTGGATATCTCTCAAGACATAAAGAGAATGCTAAA
*
1039275 AAACTCAAATAATCTTCTGGACTAATACA
65 AAACTCAAATAATCTTCTAGACTAATACA
1039304 GAGAAGTCAA
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
94 11 0.12
95 78 0.88
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (94 bp):
AAACAAATATATTAGTGTATTATCTCAATTTGGATATCTCTCAAGACATAAAGAGAATGCTAAAA
AACTCAAATAATCTTCTAGACTAATACAA
Found at i:1051331 original size:57 final size:58
Alignment explanation
Indices: 1051270--1051486 Score: 160
Period size: 57 Copynumber: 3.7 Consensus size: 58
1051260 AAATAAATAA
* *
1051270 ATAAATTTTATAAAAATTATTAGAAACTAATT-AAAAAGAATAAAATTTTATAAATTT
1 ATAAATTTTATAAAAATTATTAGAAACTAATTAAAAAAAAATAAAATTTTAAAAATTT
** * *
1051327 ATAAAAAATTATAAAAA-TATTAGAAATTTATTTCAAATCATAAAAAATTTAAAATTTATAAAAA
1 AT-AAATTTTATAAAAATTATTAGAAA-CTAATT--AA--A-AAAAAA--TAAAATTT-TAAAAA
1051391 TTT
56 TTT
* * **
1051394 A-AAA-TTTATAAAAATTATTAGAAATTAATT-TAAAATCATAAAATTTTAGAAAATTT
1 ATAAATTTTATAAAAATTATTAGAAACTAATTAAAAAAAAATAAAATTTTA-AAAATTT
* * *
1051450 AGAAAATTTTAT--AAACTATTAGAAACTAATTGAAAAA
1 A-TAAATTTTATAAAAATTATTAGAAACTAATTAAAAAA
1051487 CTTACTCTAA
Statistics
Matches: 129, Mismatches: 14, Indels: 33
0.73 0.08 0.19
Matches are distributed among these distances:
55 2 0.02
56 16 0.12
57 28 0.22
58 27 0.21
59 6 0.05
61 1 0.01
63 1 0.01
64 19 0.15
65 12 0.09
66 8 0.06
67 9 0.07
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.37
Consensus pattern (58 bp):
ATAAATTTTATAAAAATTATTAGAAACTAATTAAAAAAAAATAAAATTTTAAAAATTT
Found at i:1051332 original size:18 final size:18
Alignment explanation
Indices: 1051309--1051409 Score: 82
Period size: 17 Copynumber: 5.5 Consensus size: 18
1051299 ATTAAAAAGA
*
1051309 ATAAAATTTTATAAATTT
1 ATAAAAATTTATAAATTT
* **
1051327 ATAAAAAATTATAAAAAT
1 ATAAAAATTTATAAATTT
* *
1051345 ATTAGAAATTTATTTCAAA-TC
1 A-TAAAAATTTA--T-AAATTT
1051366 ATAAAAAATTTA-AAATTT
1 AT-AAAAATTTATAAATTT
1051384 ATAAAAATTTA-AAATTT
1 ATAAAAATTTATAAATTT
1051401 ATAAAAATT
1 ATAAAAATT
1051410 ATTAGAAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
17 27 0.40
18 18 0.27
19 8 0.12
20 1 0.01
21 10 0.15
22 3 0.04
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (18 bp):
ATAAAAATTTATAAATTT
Done.