Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009067.1 Hibiscus syriacus cultivar Beakdansim tig00112491_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2329927
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 10
Found at i:810246 original size:23 final size:23
Alignment explanation
Indices: 810220--810314 Score: 100
Period size: 23 Copynumber: 4.1 Consensus size: 23
810210 GAAGTGCCAT
* *
810220 ATAGATTTGTCCTGAAGGACCAC
1 ATAGAATTGTCCCGAAGGACCAC
* *
810243 ATAGATTTGTCCTGAAGGACCAC
1 ATAGAATTGTCCCGAAGGACCAC
* ** *
810266 GTAGAATTGTCCCGAACAACCAG
1 ATAGAATTGTCCCGAAGGACCAC
* *
810289 ATAGAATTGTCCCCAAGGACCGC
1 ATAGAATTGTCCCGAAGGACCAC
810312 ATA
1 ATA
810315 AAATCCCTCG
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (23 bp):
ATAGAATTGTCCCGAAGGACCAC
Found at i:812635 original size:15 final size:15
Alignment explanation
Indices: 812612--812689 Score: 138
Period size: 15 Copynumber: 5.2 Consensus size: 15
812602 CATAGGACTC
812612 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
812627 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
812642 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
812657 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
812672 CTACATCCCGAATGA
1 CTACATCCCGAAGGA
812687 CTA
1 CTA
812690 TTATACCCTC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 60 1.00
ACGTcount: A:0.32, C:0.33, G:0.19, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:812816 original size:29 final size:29
Alignment explanation
Indices: 812774--812847 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
812764 TTTCATATGT
*
812774 TCATGTA-CTCATGTCATTTCTTTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
812802 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
812831 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
812848 CTTCATATCA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.16
29 37 0.84
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:812903 original size:24 final size:24
Alignment explanation
Indices: 812863--812909 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
812853 TATCATGTTC
* *
812863 TCATATCACAGGTCATATTACATA
1 TCATATCACAAGTCATATCACATA
812887 TCATATCACATAG-CATATCACAT
1 TCATATCACA-AGTCATATCACAT
812910 GAACATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (24 bp):
TCATATCACAAGTCATATCACATA
Found at i:812909 original size:12 final size:12
Alignment explanation
Indices: 812876--812909 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
812866 TATCACAGGT
* *
812876 CATATTACATAT
1 CATATCACATAG
812888 CATATCACATAG
1 CATATCACATAG
812900 CATATCACAT
1 CATATCACAT
812910 GAACATATAT
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:0.41, C:0.24, G:0.03, T:0.32
Consensus pattern (12 bp):
CATATCACATAG
Found at i:813326 original size:64 final size:63
Alignment explanation
Indices: 813218--813394 Score: 221
Period size: 64 Copynumber: 2.8 Consensus size: 63
813208 TAATGAAGGT
* * ** * **
813218 ATGCATCGATGCACTATTGATGCATCGGTGCATCAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTCTT-ATGCATCGATGCATCAATTGCATTCGATGT-GTCATTATTAATGGG
* *
813282 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACT-CTTATGCATCGATGCATCAATTGCATTCGATGTGTCATTATTAATGGG
*
813346 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGT
1 ATGCATCGATGCACT-CTTATGCATCGATGCATCAATTGCATTCGATGT
813395 CTTTATTTTA
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
63 1 0.01
64 96 0.97
65 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTCTTATGCATCGATGCATCAATTGCATTCGATGTGTCATTATTAATGGG
Found at i:813415 original size:64 final size:64
Alignment explanation
Indices: 813218--813442 Score: 215
Period size: 64 Copynumber: 3.5 Consensus size: 64
813208 TAATGAAGGT
* * ** * * *** *
813218 ATGCATCGATGCACTA-TTGATGCATCGGTGCATCAAAGGTATTCGATGTAGT-ATTATTGCTGG
1 ATGCATCGATGCACTACTT-ATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGA
813281 G
64 G
* * *
813282 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** *
813346 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
** *
813409 AGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
813443 ATTCAAATAA
Statistics
Matches: 138, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
63 3 0.02
64 128 0.93
65 7 0.05
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:815437 original size:34 final size:34
Alignment explanation
Indices: 815384--815487 Score: 167
Period size: 34 Copynumber: 3.1 Consensus size: 34
815374 ACCTTACAAC
* *
815384 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
815416 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
*
815450 TTCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
815484 TCCC
1 TCCC
815488 CTTTACAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
32 7 0.11
33 5 0.08
34 54 0.82
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.32
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
Found at i:815796 original size:21 final size:21
Alignment explanation
Indices: 815771--815812 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
815761 CAGAATGAGG
*
815771 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
815792 GGGAATCGATACTCCTTCATA
1 GGGAATCGATACCCCTTCATA
815813 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:815943 original size:15 final size:15
Alignment explanation
Indices: 815919--815995 Score: 127
Period size: 15 Copynumber: 5.1 Consensus size: 15
815909 AGCCTCGGGT
815919 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
*
815934 TACGTCCCGAAGGAC
1 TACATCCCGAAGGAC
815949 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
*
815964 TACGTCCCGAAGGAC
1 TACATCCCGAAGGAC
*
815979 TACATCCTGAAGGAC
1 TACATCCCGAAGGAC
815994 TA
1 TA
815996 TTATACCCTC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 57 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:815955 original size:30 final size:30
Alignment explanation
Indices: 815919--815995 Score: 145
Period size: 30 Copynumber: 2.6 Consensus size: 30
815909 AGCCTCGGGT
815919 TACATCCCGAAGGACTACGTCCCGAAGGAC
1 TACATCCCGAAGGACTACGTCCCGAAGGAC
815949 TACATCCCGAAGGACTACGTCCCGAAGGAC
1 TACATCCCGAAGGACTACGTCCCGAAGGAC
*
815979 TACATCCTGAAGGACTA
1 TACATCCCGAAGGACTA
815996 TTATACCCTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (30 bp):
TACATCCCGAAGGACTACGTCCCGAAGGAC
Found at i:816122 original size:29 final size:29
Alignment explanation
Indices: 816080--816153 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
816070 TTTCATATGT
816080 TCATGTA-CTCATGTCATTTCTCTTGCGA
1 TCATGTAGCTCATGTCATTTCTCTTGCGA
*
816108 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGCGA
816137 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
816154 CTTCATATCA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.16
29 37 0.84
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGCGA
Found at i:816209 original size:24 final size:24
Alignment explanation
Indices: 816169--816215 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
816159 TATCATGTTC
* *
816169 TCATATCACAGGTCATATTACATA
1 TCATATCACAAGTCATATCACATA
816193 TCATATCACATAG-CATATCACAT
1 TCATATCACA-AGTCATATCACAT
816216 GAACATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (24 bp):
TCATATCACAAGTCATATCACATA
Found at i:816215 original size:12 final size:12
Alignment explanation
Indices: 816182--816215 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
816172 TATCACAGGT
* *
816182 CATATTACATAT
1 CATATCACATAG
816194 CATATCACATAG
1 CATATCACATAG
816206 CATATCACAT
1 CATATCACAT
816216 GAACATATAT
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:0.41, C:0.24, G:0.03, T:0.32
Consensus pattern (12 bp):
CATATCACATAG
Found at i:816632 original size:64 final size:64
Alignment explanation
Indices: 816524--816700 Score: 239
Period size: 64 Copynumber: 2.8 Consensus size: 64
816514 TAATGAAGGT
* * ** * **
816524 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATGT-GTCATTATTAATGGG
* * *
816588 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATGTGTCATTATTAATGGG
*
816652 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATGT
816701 CTTTATTTTA
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 1 0.01
64 98 0.99
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATCAATTGCATTCGATGTGTCATTATTAATGGG
Found at i:816721 original size:64 final size:64
Alignment explanation
Indices: 816524--816748 Score: 222
Period size: 64 Copynumber: 3.5 Consensus size: 64
816514 TAATGAAGGT
* * * ** * * *** *
816524 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
* * *
816588 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** *
816652 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
** *
816715 AGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
816749 ATTCAAATAA
Statistics
Matches: 138, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
63 3 0.02
64 130 0.94
65 5 0.04
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:820200 original size:73 final size:73
Alignment explanation
Indices: 820063--820206 Score: 200
Period size: 73 Copynumber: 2.0 Consensus size: 73
820053 ATTTTTAAGT
* * ** *
820063 TTAATAATTAAAAAATATTTTTAAACATACTTTTTTTATTTCAAATACTTTAAAATATGGTAATT
1 TTAATAATTAAAAAATATTTTTAAACATAC-TTTTTTATTTAAAAAACTCGAAAATATGATAATT
*
820128 TAGTAGGCC
65 CAGTAGGCC
*
820137 TTAATAATTAAAAAATATTTTTAAATATTA-TTTTTTATTTAAAAAACTCGAAAATATGATAATT
1 TTAATAATTAAAAAATATTTTTAAACA-TACTTTTTTATTTAAAAAACTCGAAAATATGATAATT
820201 CAGTAG
65 CAGTAG
820207 TCCCCATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
73 34 0.55
74 26 0.42
75 2 0.03
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (73 bp):
TTAATAATTAAAAAATATTTTTAAACATACTTTTTTATTTAAAAAACTCGAAAATATGATAATTC
AGTAGGCC
Found at i:821955 original size:25 final size:25
Alignment explanation
Indices: 821902--821956 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
821892 ATTTATCAAT
* * *
821902 TATATTTTAAATTTATTCTTTTATA
1 TATATTTTAAATTTATTATTATAAA
821927 -ATATTTTATAATTTA-TATTATAAA
1 TATATTTTA-AATTTATTATTATAAA
821951 TATATT
1 TATATT
821957 CATAACTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
TATATTTTAAATTTATTATTATAAA
Found at i:822032 original size:34 final size:34
Alignment explanation
Indices: 821987--822058 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
821977 GTTAGTTTTA
* * *
821987 ATAATAGAAATATGATTAATCAATAATTTTAATT
1 ATAATAAAAATATAATTAATAAATAATTTTAATT
* *
822021 ATAATAAAAATATAATTAATAAATCATTTTAGTT
1 ATAATAAAAATATAATTAATAAATAATTTTAATT
822055 ATAA
1 ATAA
822059 ATTTATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (34 bp):
ATAATAAAAATATAATTAATAAATAATTTTAATT
Found at i:822439 original size:2 final size:2
Alignment explanation
Indices: 822434--822461 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
822424 CTTTCCCTAC
822434 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
822462 GGTAATGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:830986 original size:21 final size:21
Alignment explanation
Indices: 830960--831001 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
830950 GGAATTACAA
830960 TGGCTGTAGGAATTTCAGCAG
1 TGGCTGTAGGAATTTCAGCAG
*
830981 TGGCTGTAGGATTTTCAGCAG
1 TGGCTGTAGGAATTTCAGCAG
831002 GTTTTGTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.33, T:0.31
Consensus pattern (21 bp):
TGGCTGTAGGAATTTCAGCAG
Found at i:842537 original size:16 final size:17
Alignment explanation
Indices: 842506--842543 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
842496 ATGATATACA
842506 TGAT-TATATGCATATG
1 TGATATATATGCATATG
842522 TGATATATATGC-TATG
1 TGATATATATGCATATG
*
842538 AGATAT
1 TGATAT
842544 GACCAATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.42
Consensus pattern (17 bp):
TGATATATATGCATATG
Found at i:844845 original size:2 final size:2
Alignment explanation
Indices: 844838--844875 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
844828 TATCATTGGA
844838 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
844876 GATTGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:845331 original size:2 final size:2
Alignment explanation
Indices: 845324--845360 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
845314 TATTTGGATC
845324 AT AT 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 AT AT A
845361 GGCAATGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:853918 original size:15 final size:14
Alignment explanation
Indices: 853898--853943 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
853888 GCAAAATATC
853898 ATATTTAAAAAATA
1 ATATTTAAAAAATA
853912 ATAATTTAAGAAAATA
1 AT-ATTTAA-AAAATA
*
853928 ATATATTAAAATATA
1 ATAT-TTAAAAAATA
853943 A
1 A
853944 AATATCTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.07
15 14 0.50
16 12 0.43
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
ATATTTAAAAAATA
Found at i:853948 original size:15 final size:15
Alignment explanation
Indices: 853902--853948 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
853892 AATATCATAT
853902 TTAAAAAATAATAAT-
1 TTAAAAAATAA-AATA
*
853917 TTAAGAAAATAATATA
1 TTAA-AAAATAAAATA
*
853933 TTAAAATATAAAATA
1 TTAAAAAATAAAATA
853948 T
1 T
853949 CTTAGAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
TTAAAAAATAAAATA
Found at i:854412 original size:31 final size:30
Alignment explanation
Indices: 854374--854472 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 30
854364 TTTCAATTTC
854374 ATCCCCAAACTATGCCCTTCATTCTAAATT
1 ATCCCCAAACTATGCCCTTCATTCTAAATT
* * ** * *
854404 ATCCCCCAACTTTTGGACAT--TTC-AATTT
1 ATCCCCAAAC-TATGCCCTTCATTCTAAATT
854432 CATCCCCAAACTATGCCCTTCATTCTAAATT
1 -ATCCCCAAACTATGCCCTTCATTCTAAATT
*
854463 AGTTCCCAAA
1 A-TCCCCAAA
854473 GTTTTGAACA
Statistics
Matches: 50, Mismatches: 13, Indels: 11
0.68 0.18 0.15
Matches are distributed among these distances:
28 9 0.18
29 12 0.24
30 13 0.26
31 16 0.32
ACGTcount: A:0.29, C:0.32, G:0.05, T:0.33
Consensus pattern (30 bp):
ATCCCCAAACTATGCCCTTCATTCTAAATT
Found at i:854435 original size:59 final size:59
Alignment explanation
Indices: 854332--854564 Score: 342
Period size: 59 Copynumber: 3.9 Consensus size: 59
854322 ACTATGACTG
* *
854332 TCATTCTAAATTAGTCCTCAAATTTTTGAACATTTCAATTTCATCCCCAAACTATGCCCT
1 TCATTCTAAATTAGTCCCCAAACTTTTGAACATTTCAATTTCAT-CCCAAACTATGCCCT
* *
854392 TCATTCTAAATTA-TCCCCCAACTTTTGGACATTTCAATTTCATCCCCAAACTATGCCCT
1 TCATTCTAAATTAGTCCCCAAACTTTTGAACATTTCAATTTCAT-CCCAAACTATGCCCT
* * *
854451 TCATTCTAAATTAGTTCCCAAAGTTTTGAACATTTCAATTTCATCCCAAACTATGACCT
1 TCATTCTAAATTAGTCCCCAAACTTTTGAACATTTCAATTTCATCCCAAACTATGCCCT
* * *
854510 TCATTCTAAATTAGTCCCTAAACTTTTTGAAAATTTAAATTTCATCCCAAACTAT
1 TCATTCTAAATTAGTCCCCAAAC-TTTTGAACATTTCAATTTCATCCCAAACTAT
854565 ACATATATAT
Statistics
Matches: 157, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
59 89 0.57
60 68 0.43
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (59 bp):
TCATTCTAAATTAGTCCCCAAACTTTTGAACATTTCAATTTCATCCCAAACTATGCCCT
Found at i:854443 original size:29 final size:29
Alignment explanation
Indices: 854350--854443 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
854340 AATTAGTCCT
*
854350 CAAATTTTTGAACATTTCAATTTCATCCC
1 CAAACTTTTGAACATTTCAATTTCATCCC
* ** * *
854379 CAAAC-TATGCCCTTCATTCTAAATT-ATCCC
1 CAAACTTTTGAACAT--TTC-AATTTCATCCC
* *
854409 CCAACTTTTGGACATTTCAATTTCATCCC
1 CAAACTTTTGAACATTTCAATTTCATCCC
854438 CAAACT
1 CAAACT
854444 ATGCCCTTCA
Statistics
Matches: 47, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
28 9 0.19
29 17 0.36
30 12 0.26
31 9 0.19
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.36
Consensus pattern (29 bp):
CAAACTTTTGAACATTTCAATTTCATCCC
Found at i:854480 original size:119 final size:119
Alignment explanation
Indices: 854264--854564 Score: 360
Period size: 119 Copynumber: 2.5 Consensus size: 119
854254 GTCCCCATAT
* * * * * * * * **
854264 TATGATCTTCATTTTAAGTTAGTTCCTAAA-TTTTTAAAAATTTTAATTCCATCTTTAAACTATG
1 TATGACCTTCATTCTAAATTAGTCCCCAAACTTTTTGAAAATTTAAATTTCATC-CCAAACTATG
* *
854328 -ACTGTCATTCTAAATTAGTCCTCAAATTTTTGAACATTTCAATTTCATCCCCAAAC
65 CCCT-TCATTCTAAATTAGTCCTCAAAGTTTTGAACATTTCAATTTCAT-CCCAAAC
* * * * *
854384 TATGCCCTTCATTCTAAATTA-TCCCCCAAC-TTTTGGACATTTCAATTTCATCCCCAAACTATG
1 TATGACCTTCATTCTAAATTAGTCCCCAAACTTTTTGAAAATTTAAATTTCAT-CCCAAACTATG
854447 CCCTTCATTCTAAATTAGTTCC-CAAAGTTTTGAACATTTCAATTTCATCCCAAAC
65 CCCTTCATTCTAAATTAG-TCCTCAAAGTTTTGAACATTTCAATTTCATCCCAAAC
*
854502 TATGACCTTCATTCTAAATTAGTCCCTAAACTTTTTGAAAATTTAAATTTCATCCCAAACTAT
1 TATGACCTTCATTCTAAATTAGTCCCCAAACTTTTTGAAAATTTAAATTTCATCCCAAACTAT
854565 ACATATATAT
Statistics
Matches: 153, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
118 27 0.18
119 85 0.56
120 41 0.27
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (119 bp):
TATGACCTTCATTCTAAATTAGTCCCCAAACTTTTTGAAAATTTAAATTTCATCCCAAACTATGC
CCTTCATTCTAAATTAGTCCTCAAAGTTTTGAACATTTCAATTTCATCCCAAAC
Found at i:854556 original size:60 final size:59
Alignment explanation
Indices: 854264--854564 Score: 340
Period size: 60 Copynumber: 5.1 Consensus size: 59
854254 GTCCCCATAT
* * * * * * * * **
854264 TATGATCTTCATTTTAAGTTAGTTCCTAAATTTTTAAAAATTTTAATTCCATCTTTAAAC
1 TATGACCTTCATTCTAAATTAGTCCCTAAATTTTTGAACATTTCAATTTCATC-CCAAAC
854324 TATGA-CTGTCATTCTAAATTAGT-CCTCAAATTTTTGAACATTTCAATTTCATCCCCAAAC
1 TATGACCT-TCATTCTAAATTAGTCCCT-AAATTTTTGAACATTTCAATTTCAT-CCCAAAC
* ** * *
854384 TATGCCCTTCATTCTAAATTA-TCCCCCAACTTTTGGACATTTCAATTTCATCCCCAAAC
1 TATGACCTTCATTCTAAATTAGTCCCTAAATTTTTGAACATTTCAATTTCAT-CCCAAAC
* *
854443 TATGCCCTTCATTCTAAATTAGTTCCC-AAAGTTTTGAACATTTCAATTTCATCCCAAAC
1 TATGACCTTCATTCTAAATTAG-TCCCTAAATTTTTGAACATTTCAATTTCATCCCAAAC
* *
854502 TATGACCTTCATTCTAAATTAGTCCCTAAACTTTTTGAAAATTTAAATTTCATCCCAAAC
1 TATGACCTTCATTCTAAATTAGTCCCTAAA-TTTTTGAACATTTCAATTTCATCCCAAAC
854562 TAT
1 TAT
854565 ACATATATAT
Statistics
Matches: 212, Mismatches: 20, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
58 4 0.02
59 88 0.42
60 113 0.53
61 7 0.03
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (59 bp):
TATGACCTTCATTCTAAATTAGTCCCTAAATTTTTGAACATTTCAATTTCATCCCAAAC
Found at i:854789 original size:60 final size:57
Alignment explanation
Indices: 854679--854857 Score: 164
Period size: 60 Copynumber: 3.0 Consensus size: 57
854669 TTGCATATTT
* * * **
854679 GGATGGATTTGGGGATGAAATTGGACGATTCAAAA-TTTTGGGTACCAATTTAAATTGA
1 GGATAGATTTGGGGATGAAATTGAATG-TTCAAAAGTTTAAGG-ACCAATTTAAATTGA
*
854737 GGATCATGATTTGGGGATGAAATTGAAATGTTCAAAAGTTTAAGGACTAATTTAGAA-TGA
1 GGAT-A-GATTTGGGGATGAAATTG-AATGTTCAAAAGTTTAAGGACCAATTTA-AATTGA
* ** * *
854797 GGCTAGTATTTTGAAGATGAAATTGGAATATTTAAAAGTTTAAGGACCAATTTAAATTGA
1 GGATAG-A-TTTGGGGATGAAATT-GAATGTTCAAAAGTTTAAGGACCAATTTAAATTGA
854857 G
1 G
854858 AGTCATAGTT
Statistics
Matches: 100, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
58 5 0.05
59 4 0.04
60 81 0.81
61 10 0.10
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.33
Consensus pattern (57 bp):
GGATAGATTTGGGGATGAAATTGAATGTTCAAAAGTTTAAGGACCAATTTAAATTGA
Found at i:858304 original size:18 final size:17
Alignment explanation
Indices: 858267--858313 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
858257 TATGGAATTG
858267 GATTCCAATTCCTAACA
1 GATTCCAATTCCTAACA
* *
858284 GATTCCAATTCATTCACA
1 GATTCCAATTC-CTAACA
858302 GATTCCAATTCC
1 GATTCCAATTCC
858314 CTCAGAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (17 bp):
GATTCCAATTCCTAACA
Found at i:862750 original size:21 final size:21
Alignment explanation
Indices: 862726--862766 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
862716 GGTAAAAATT
**
862726 TACCTAAAACATTAATATTTC
1 TACCTAAAACAACAATATTTC
862747 TACCTAAAACAACAATATTT
1 TACCTAAAACAACAATATTT
862767 TTTAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (21 bp):
TACCTAAAACAACAATATTTC
Found at i:862858 original size:22 final size:22
Alignment explanation
Indices: 862794--862865 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
862784 AGTGCTAAAT
*
862794 AATAACAAAA-TCGGTAGAAAAA
1 AATAACAAAACT-GATAGAAAAA
**
862816 AATAACAAAACCAATAGAAAAA
1 AATAACAAAACTGATAGAAAAA
*
862838 AATAACAAAACTGATAAAAAAA
1 AATAACAAAACTGATAGAAAAA
862860 TAATAA
1 -AATAA
862866 TATTTCTGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
22 37 0.88
23 5 0.12
ACGTcount: A:0.69, C:0.10, G:0.07, T:0.14
Consensus pattern (22 bp):
AATAACAAAACTGATAGAAAAA
Found at i:864092 original size:73 final size:72
Alignment explanation
Indices: 864007--864149 Score: 277
Period size: 73 Copynumber: 2.0 Consensus size: 72
863997 AGTTCAGATT
864007 GATCATTGAATTGTCCTCTCGTGAATCATATTACCTAGCTCTATTTATTTTTGATATAATAAGAT
1 GATCATTGAATTGTCCTCTCGTGAATCATATTACCTAGCTCTATTTA-TTTTGATATAATAAGAT
864072 TTACGATG
65 TTACGATG
864080 GATCATTGAATTGTCCTCTCGTGAATCATATTACCTAGCTCTATTTATTTTGATATAATAAGATT
1 GATCATTGAATTGTCCTCTCGTGAATCATATTACCTAGCTCTATTTATTTTGATATAATAAGATT
864145 TACGA
66 TACGA
864150 GGGGACAATT
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 23 0.33
73 47 0.67
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42
Consensus pattern (72 bp):
GATCATTGAATTGTCCTCTCGTGAATCATATTACCTAGCTCTATTTATTTTGATATAATAAGATT
TACGATG
Found at i:864505 original size:21 final size:20
Alignment explanation
Indices: 864481--864527 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
864471 AATTTAGAGT
864481 AATAATATTTAATAATAAAA
1 AATAATATTTAATAATAAAA
* **
864501 GAATATTATTTTTTAATAAAA
1 -AATAATATTTAATAATAAAA
864522 AATAAT
1 AATAAT
864528 TATATTCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AATAATATTTAATAATAAAA
Found at i:864529 original size:21 final size:23
Alignment explanation
Indices: 864493--864542 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
864483 TAATATTTAA
864493 TAATAAAAGAATATTAT-TT-TT
1 TAATAAAAGAATATTATATTCTT
864514 TAATAAAA-AATAATTATATTCTT
1 TAATAAAAGAAT-ATTATATTCTT
864537 TAATAA
1 TAATAA
864543 TTGGAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.12
21 13 0.50
22 2 0.08
23 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TAATAAAAGAATATTATATTCTT
Found at i:864533 original size:23 final size:24
Alignment explanation
Indices: 864488--864543 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
864478 AGTAATAATA
*
864488 TTTAATAATAAAAGAATATTATTT
1 TTTAATAATAAAAGAATATTATTC
*
864512 TTTAATAA-AAAATAAT-TATATTC
1 TTTAATAATAAAAGAATAT-TATTC
864535 TTTAATAAT
1 TTTAATAAT
864544 TGGAAATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 1 0.04
23 19 0.68
24 8 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TTTAATAATAAAAGAATATTATTC
Found at i:866960 original size:15 final size:15
Alignment explanation
Indices: 866940--866996 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
866930 TTCCAGAAAA
866940 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
866955 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
866970 TGAATTACTGGAATT
1 TGAATTACTGGAATT
866985 TGAATT-CTGGAA
1 TGAATTACTGGAA
866997 AATGAATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:867004 original size:29 final size:30
Alignment explanation
Indices: 866935--867005 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
866925 TGGTTTTCCA
866935 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
866965 GAAAATGAATTACTGGAATTTGAATT-CTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
866994 GAAAATGAATTA
1 GAAAATGAATTA
867006 TATTTTTGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (30 bp):
GAAAATGAATTACTGGAATTTGAATTACTG
Found at i:867018 original size:20 final size:20
Alignment explanation
Indices: 866989--867058 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
866979 GGAATTTGAA
*
866989 TTCTGGAAAATGAATTATAT
1 TTCTGGAAAATGAATTACAT
* *
867009 TTTTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
867029 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
867049 TTCTGGAAAA
1 TTCTGGAAAA
867059 CATCTGGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:867277 original size:19 final size:20
Alignment explanation
Indices: 867255--867292 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
867245 AATATTATTC
867255 ATTATTAAATATA-TAAAAA
1 ATTATTAAATATATTAAAAA
*
867274 ATTATTATATATATTAAAA
1 ATTATTAAATATATTAAAA
867293 TAAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTATTAAATATATTAAAAA
Found at i:867277 original size:26 final size:29
Alignment explanation
Indices: 867226--867281 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
867216 TTACTAAAAT
867226 ATTATTGAAATATATAAATAATATTATTC
1 ATTATTGAAATATATAAATAATATTATTC
*
867255 ATTATT-AAATATATAAAAAATTATTAT
1 ATTATTGAAATATATAAATAA-TATTAT
867282 ATATATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
ATTATTGAAATATATAAATAATATTATTC
Found at i:867293 original size:29 final size:27
Alignment explanation
Indices: 867224--867325 Score: 77
Period size: 28 Copynumber: 3.6 Consensus size: 27
867214 CTTTACTAAA
*
867224 ATAT-TATTGAAATATATAAATAATATT
1 ATATATATT-AAATATATAAAAAATATT
867251 AT-TCATTATTAAATATATAAAAAATTATT
1 ATAT-A-TATTAAATATATAAAAAA-TATT
*
867280 ATATATATTAAA-ATAAAAATATAATATCT
1 ATATATATTAAATATATAAA-A-AATAT-T
867309 -TATATTATTATAATATA
1 ATATA-TATTA-AATATA
867326 ATTGATTATT
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
26 1 0.02
27 8 0.13
28 28 0.45
29 19 0.31
30 3 0.05
31 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (27 bp):
ATATATATTAAATATATAAAAAATATT
Found at i:867363 original size:17 final size:16
Alignment explanation
Indices: 867337--867377 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
867327 TTGATTATTT
867337 TATATAATATTAAAAA
1 TATATAATATTAAAAA
*
867353 TATATATATATTATAAA
1 TATATA-ATATTAAAAA
867370 TAT-TAATA
1 TATATAATA
867378 ATATATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 3 0.13
16 8 0.35
17 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TATATAATATTAAAAA
Found at i:867397 original size:9 final size:9
Alignment explanation
Indices: 867336--867393 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
867326 ATTGATTATT
867336 TTATATAATA
1 TTATA-AATA
*
867346 TTAAAAATA
1 TTATAAATA
*
867355 -TATATATA
1 TTATAAATA
867363 TTATAAATA
1 TTATAAATA
867372 TTAATAATATA
1 TT-ATAA-ATA
*
867383 TTTTAAATA
1 TTATAAATA
867392 TT
1 TT
867394 TTAATAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
8 6 0.15
9 18 0.45
10 11 0.28
11 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTATAAATA
Found at i:867640 original size:42 final size:42
Alignment explanation
Indices: 867581--867697 Score: 225
Period size: 42 Copynumber: 2.8 Consensus size: 42
867571 ATGAATTACA
*
867581 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
867623 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
867665 TTCCGGAAAACGAATTACGTGAAACAAACACGG
1 TTCCGGAAAACGAATTACGTGAAACAAACACGG
867698 AAATTCGGGG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:868104 original size:30 final size:30
Alignment explanation
Indices: 868066--868144 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 30
868056 CATTTTTTAA
*
868066 AATATTTTCGATCATTTTTTAACGCCTAAT
1 AATATTTTCGGTCATTTTTTAACGCCTAAT
* * *
868096 AATGTTTTCGGTC-TTTCTTAACGTCTAAT
1 AATATTTTCGGTCATTTTTTAACGCCTAAT
*
868125 AATATTTTCGGTTATTTTTT
1 AATATTTTCGGTCATTTTTT
868145 TATCGATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 25 0.61
30 16 0.39
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (30 bp):
AATATTTTCGGTCATTTTTTAACGCCTAAT
Found at i:872744 original size:355 final size:355
Alignment explanation
Indices: 872093--872803 Score: 1404
Period size: 355 Copynumber: 2.0 Consensus size: 355
872083 CAATATGAAA
872093 TTCTTTATGACTTTTCCTCATTCAAAATGAATTTCGATTTTTTCCTAACATCAGGAAAAAAATGA
1 TTCTTTATGACTTTTCCTCATTCAAAATGAATTTCGATTTTTTCCTAACATCAGGAAAAAAATGA
872158 TCTCAAGTTTAAAACAAGAGATTTTAGCACAACTGAAATAGATAATTTCTTTTTTTTCCTCTACT
66 TCTCAAGTTTAAAACAAGAGATTTTAGCACAACTGAAATAGATAATTTCTTTTTTTTCCTCTACT
872223 TAGGAAAATCACTTAAAGAGATTTAATATTACAACACACTTTTAGTAGCAATAGATTATATCATA
131 TAGGAAAATCACTTAAAGAGATTTAATATTACAACACACTTTTAGTAGCAATAGATTATATCATA
872288 TACTCATTCATGATATTCAACATATTAGCCTTAAAGAGATCATCATATATTTTATTTACTATGAC
196 TACTCATTCATGATATTCAACATATTAGCCTTAAAGAGATCATCATATATTTTATTTACTATGAC
872353 TAAATTTGGTATTCACTCAACCAAATTAATCTATACTCTTTTAACTTCTGCACTAAGTTTTAAGA
261 TAAATTTGGTATTCACTCAACCAAATTAATCTATACTCTTTTAACTTCTGCACTAAGTTTTAAGA
*
872418 GTTTTTATCTTATCATCGTATTTTATAAAT
326 GTTTTTATCTTATCATAGTATTTTATAAAT
872448 TTCTTTATGACTTTTCCTCATTCAAAATGAATTTCGATTTTTTCCTAACATCAGGAAAAAAATGA
1 TTCTTTATGACTTTTCCTCATTCAAAATGAATTTCGATTTTTTCCTAACATCAGGAAAAAAATGA
872513 TCTCAAGTTTAAAACAAGAGATTTTAGCACAACTGAAATAGATAATTTCTTTTTTTTCCTCTACT
66 TCTCAAGTTTAAAACAAGAGATTTTAGCACAACTGAAATAGATAATTTCTTTTTTTTCCTCTACT
872578 TAGGAAAATCACTTAAAGAGATTTAATATTACAACACACTTTTAGTAGCAATAGATTATATCATA
131 TAGGAAAATCACTTAAAGAGATTTAATATTACAACACACTTTTAGTAGCAATAGATTATATCATA
872643 TACTCATTCATGATATTCAACATATTAGCCTTAAAGAGATCATCATATATTTTATTTACTATGAC
196 TACTCATTCATGATATTCAACATATTAGCCTTAAAGAGATCATCATATATTTTATTTACTATGAC
*
872708 TAAATTTGGTATTTACTCAACCAAATTAATCTATACTCTTTTAACTTCTGCACTAAGTTTTAAGA
261 TAAATTTGGTATTCACTCAACCAAATTAATCTATACTCTTTTAACTTCTGCACTAAGTTTTAAGA
872773 GTTTTTATCTTATCATAGTATTTTATAAAT
326 GTTTTTATCTTATCATAGTATTTTATAAAT
872803 T
1 T
872804 GGAATAGTGA
Statistics
Matches: 354, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
355 354 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (355 bp):
TTCTTTATGACTTTTCCTCATTCAAAATGAATTTCGATTTTTTCCTAACATCAGGAAAAAAATGA
TCTCAAGTTTAAAACAAGAGATTTTAGCACAACTGAAATAGATAATTTCTTTTTTTTCCTCTACT
TAGGAAAATCACTTAAAGAGATTTAATATTACAACACACTTTTAGTAGCAATAGATTATATCATA
TACTCATTCATGATATTCAACATATTAGCCTTAAAGAGATCATCATATATTTTATTTACTATGAC
TAAATTTGGTATTCACTCAACCAAATTAATCTATACTCTTTTAACTTCTGCACTAAGTTTTAAGA
GTTTTTATCTTATCATAGTATTTTATAAAT
Found at i:875220 original size:20 final size:20
Alignment explanation
Indices: 875191--875243 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
875181 GGTTGAACCG
*
875191 ACATTTGAATCCAGACTTAC
1 ACATTCGAATCCAGACTTAC
*
875211 ACATTCGAATCTAGACTTAC
1 ACATTCGAATCCAGACTTAC
875231 ACATTCGAATCCA
1 ACATTCGAATCCA
875244 ACATGTGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.28
Consensus pattern (20 bp):
ACATTCGAATCCAGACTTAC
Found at i:876865 original size:29 final size:29
Alignment explanation
Indices: 876823--876881 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
876813 TTTGAATGAA
*
876823 ATTATTCAGCGTTGAATGTTAAATCGTTC
1 ATTATTAAGCGTTGAATGTTAAATCGTTC
* *
876852 ATTATTAAGTGTTGAATGTTGAATCGTTC
1 ATTATTAAGCGTTGAATGTTAAATCGTTC
876881 A
1 A
876882 ACATTCAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (29 bp):
ATTATTAAGCGTTGAATGTTAAATCGTTC
Found at i:876984 original size:27 final size:27
Alignment explanation
Indices: 876946--877012 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
876936 TAAAACAATA
* *
876946 CTGAATGATTCAGCATAGAAGTACATT
1 CTGAATGATTCAGCACAGAAATACATT
*
876973 CTGAATAATTCAGCACAGAAATACATT
1 CTGAATGATTCAGCACAGAAATACATT
*
877000 ATGAATGATTCAG
1 CTGAATGATTCAG
877013 AGCTATTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (27 bp):
CTGAATGATTCAGCACAGAAATACATT
Found at i:882429 original size:22 final size:21
Alignment explanation
Indices: 882377--882428 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
882367 TAATCGGTGT
*
882377 AATCGGTTTCGGTTTGAAAAA
1 AATCGGTTTTGGTTTGAAAAA
882398 AATCGGTTTTGGTTTGAAAAA
1 AATCGGTTTTGGTTTGAAAAA
882419 AATCGGTTTT
1 AATCGGTTTT
882429 TTTAAAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (21 bp):
AATCGGTTTTGGTTTGAAAAA
Found at i:882536 original size:33 final size:33
Alignment explanation
Indices: 882489--882592 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
882479 ACAAAGTTTA
* * *
882489 CGAT-AATTGAAATACTTAAATATTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
882521 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
*
882554 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
882587 CGATAA
1 CGATAA
882593 TTGAAACAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 4 0.06
33 63 0.94
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTTCAAGTT
Found at i:882612 original size:21 final size:21
Alignment explanation
Indices: 882587--882628 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
882577 CTTCCAAGTT
*
882587 CGATAATTGAAACAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
*
882608 CGATAATTAAAATAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
882629 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTAAAACAAAGTTTA
Found at i:886977 original size:21 final size:20
Alignment explanation
Indices: 886891--887048 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
886881 AAATGACCAA
**
886891 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
886910 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
886930 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
886950 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
886971 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
886992 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
887012 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
887033 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
887049 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:887077 original size:20 final size:20
Alignment explanation
Indices: 887015--887284 Score: 269
Period size: 20 Copynumber: 13.5 Consensus size: 20
887005 CGATTTTCCA
* ** *
887015 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
887035 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
887055 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
887075 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
887095 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
887115 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
887135 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
887155 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
887175 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
887195 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
887215 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
887235 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
887255 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
887275 AAATCACAAC
1 AAATCGCAAC
887285 ACTGAAATTT
Statistics
Matches: 210, Mismatches: 32, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 206 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:890521 original size:19 final size:19
Alignment explanation
Indices: 890452--890621 Score: 181
Period size: 19 Copynumber: 9.7 Consensus size: 19
890442 GCAACGAGAG
890452 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
890471 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
890485 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
890505 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
890524 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
890538 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
890557 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
890576 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
890590 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
890609 AATCGCATTGCGA
1 AATCGCAATGCGA
890622 TTCTCCCGTT
Statistics
Matches: 127, Mismatches: 8, Indels: 32
0.76 0.05 0.19
Matches are distributed among these distances:
14 32 0.25
15 2 0.02
16 5 0.04
17 5 0.04
18 2 0.02
19 65 0.51
20 16 0.13
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:890575 original size:52 final size:52
Alignment explanation
Indices: 890452--890621 Score: 279
Period size: 52 Copynumber: 3.2 Consensus size: 52
890442 GCAACGAGAG
* *
890452 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
890505 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
890557 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
890609 AATCGCATTGCGA
1 AATCGCAATGCGA
890622 TTCTCCCGTT
Statistics
Matches: 112, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
52 71 0.63
53 40 0.36
54 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:890613 original size:33 final size:33
Alignment explanation
Indices: 890438--890615 Score: 161
Period size: 33 Copynumber: 5.2 Consensus size: 33
890428 CGGAAATTAC
*
890438 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
890471 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
*
890505 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
890538 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
* *
890576 AATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
890609 AATCGCA
1 AATCGCA
890616 TTGCGATTCT
Statistics
Matches: 126, Mismatches: 7, Indels: 24
0.80 0.04 0.15
Matches are distributed among these distances:
32 1 0.01
33 77 0.61
34 17 0.13
35 2 0.02
36 4 0.03
37 2 0.02
38 10 0.08
39 13 0.10
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:890670 original size:19 final size:19
Alignment explanation
Indices: 890630--890708 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
890620 GATTCTCCCG
890630 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
890650 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
890669 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
890683 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
890702 TTGCGAT
1 TTGCGAT
890709 AGTCAATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.12
16 7 0.13
17 7 0.13
19 17 0.33
20 15 0.29
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:890834 original size:14 final size:14
Alignment explanation
Indices: 890815--890851 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
890805 CATCAATTAC
890815 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
890829 ACAAATCATCTTTT
1 ACAAATCAACTTTT
890843 ACAAATCAA
1 ACAAATCAA
890852 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:892846 original size:14 final size:14
Alignment explanation
Indices: 892827--892883 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
892817 GCGAAATGAA
*
892827 AATCGCAACGACAG
1 AATCGCAACGAAAG
892841 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
892858 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
892874 AATCGCAACG
1 AATCGCAACG
892884 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:892854 original size:33 final size:33
Alignment explanation
Indices: 892808--892900 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
892798 GCGAAACCAA
*
892808 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
892841 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
892874 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
892901 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:892865 original size:19 final size:19
Alignment explanation
Indices: 892771--892905 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
892761 TAGTTTACTT
* *
892771 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
892791 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
892810 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
892829 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
892843 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
892862 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
892876 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
892895 TCGCAATGCGA
1 TCGCAACGCGA
892906 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:892923 original size:19 final size:19
Alignment explanation
Indices: 892901--893029 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
892891 AAAATCGCAA
892901 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
892920 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
892934 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
892953 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
892967 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
892986 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
893005 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
893025 TGCGA
1 TGCGA
893030 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:892943 original size:33 final size:33
Alignment explanation
Indices: 892901--892992 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
892891 AAAATCGCAA
892901 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
892934 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
892967 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
892993 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:893196 original size:93 final size:93
Alignment explanation
Indices: 893077--893638 Score: 1090
Period size: 93 Copynumber: 6.1 Consensus size: 93
893067 ATGGATTGCA
*
893077 TTAC-TTCGACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
893141 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
893169 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
893234 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
893262 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
893327 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
893355 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
893420 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
893448 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
893513 TAGCAGAATTGGCAGCAATCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
893541 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
893606 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
893634 TTACT
1 TTACT
893639 AAGCAATCTA
Statistics
Matches: 465, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 461 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:895363 original size:14 final size:14
Alignment explanation
Indices: 895344--895433 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
895334 TTGAAATGAA
895344 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
895358 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
895377 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
895391 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
895410 AATCGCAACGAGAG
1 AATCGCAACGAGAG
895424 AATCGCAACG
1 AATCGCAACG
895434 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:895376 original size:33 final size:33
Alignment explanation
Indices: 895336--895450 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
895326 TCTTTTGGTT
895336 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
895369 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
895402 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
895435 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
895451 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:895382 original size:19 final size:19
Alignment explanation
Indices: 895358--895455 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
895348 GCAACGAGAG
895358 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
895377 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
895391 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
895410 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
895424 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
895443 AATCGCAATGCGA
1 AATCGCAACGCGA
895456 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:895499 original size:33 final size:33
Alignment explanation
Indices: 895451--895531 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
895441 AAAATCGCAA
**
895451 TGCGATTTTGGTTTCGCGTTGCGATTCTCTAGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
*
895484 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
895517 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
895532 TCTCGGTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
Found at i:895519 original size:14 final size:14
Alignment explanation
Indices: 895467--895523 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
895457 TTTGGTTTCG
895467 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
895481 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
895500 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
895514 CGTTGCGATT
1 CGTTGCGATT
895524 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:895564 original size:41 final size:41
Alignment explanation
Indices: 895507--895584 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
895497 TCGCGTTGCG
*
895507 ATTCTCTCGTTGCGATTTTCATTTCTCTCGGTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGGTGCGACAGTC
*
895548 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGGTGCGAC
895585 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGGTGCGACAGTC
Found at i:895569 original size:20 final size:21
Alignment explanation
Indices: 895508--895583 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
895498 CGCGTTGCGA
895508 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* ***
895529 TTCTCTCGGTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
895549 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
895570 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
895584 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:895705 original size:33 final size:33
Alignment explanation
Indices: 895663--895733 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
895653 AATACTAACT
* *
895663 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACACGAAA
* *
895696 TGAAAATCGCAACGACAGAATCGTAACACGAAA
1 TGAAAATCGCAACGACAGAATAGCAACACGAAA
895729 TGAAA
1 TGAAA
895734 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACACGAAA
Found at i:895967 original size:22 final size:22
Alignment explanation
Indices: 895915--895969 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
895905 TGGTTGTGAG
**
895915 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
895937 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
895959 GGATTTCTTCG
1 GGATTTCTTCG
895970 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:896141 original size:20 final size:20
Alignment explanation
Indices: 896116--896269 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
896106 CTTTAAATAT
896116 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
896136 CGCGTTGCAATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
896158 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
896177 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
896197 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
896217 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
896237 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
896257 CGCGTTGCGATTT
1 CGCGTTGCGATTT
896270 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.02
20 93 0.84
21 14 0.13
22 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:896243 original size:40 final size:40
Alignment explanation
Indices: 896115--896269 Score: 177
Period size: 40 Copynumber: 3.9 Consensus size: 40
896105 GCTTTAAATA
* *
896115 TCGCGTTGCGATTTACGGATACGCGTTGCAATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
896156 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
896196 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
896236 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
896270 TGGAAAATCG
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
40 66 0.69
41 29 0.31
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:896286 original size:21 final size:21
Alignment explanation
Indices: 896256--896338 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
896246 ATTTTCATAT
*
896256 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
896277 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
896298 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
896319 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
896339 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:896329 original size:42 final size:43
Alignment explanation
Indices: 896236--896334 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
896226 ATTTATGTGT
* *
896236 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
896277 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
896319 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
896335 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:896881 original size:15 final size:15
Alignment explanation
Indices: 896861--896889 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
896851 TTTATGAATT
896861 AAAAATAATATTTTA
1 AAAAATAATATTTTA
896876 AAAAATAATATTTT
1 AAAAATAATATTTT
896890 TTCTTTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAATAATATTTTA
Found at i:907171 original size:11 final size:11
Alignment explanation
Indices: 907136--907189 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
907126 CGGTTGTAAG
907136 AAGGAAGAAAGA
1 AAGGAAG-AAGA
*
907148 AAGG-TGAAGGA
1 AAGGAAGAA-GA
907159 AAGGAAGAAGA
1 AAGGAAGAAGA
*
907170 AATGAAGAAGA
1 AAGGAAGAAGA
*
907181 AAGAAAGAA
1 AAGGAAGAA
907190 AGGTAACCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 2 0.06
11 26 0.74
12 7 0.20
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (11 bp):
AAGGAAGAAGA
Found at i:907246 original size:12 final size:12
Alignment explanation
Indices: 907225--907254 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
907215 GTTTAAATTA
*
907225 TTAGTTAGTTAG
1 TTAGTGAGTTAG
907237 TTAGTGAGTTAG
1 TTAGTGAGTTAG
907249 TTAGTG
1 TTAGTG
907255 GGCATAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (12 bp):
TTAGTGAGTTAG
Found at i:907452 original size:28 final size:26
Alignment explanation
Indices: 907384--907453 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 26
907374 TATATATGGT
*
907384 TTATTATATGTCGTTATTTTATTAAAAA
1 TTATTATATGTCG-T-TTATATTAAAAA
*
907412 ATATT-TATG--GTTTATATTAAATCAA
1 TTATTATATGTCGTTTATATTAAA--AA
907437 TTATTATATGTCGTTTA
1 TTATTATATGTCGTTTA
907454 ATTTATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
23 9 0.26
24 1 0.03
25 7 0.21
26 4 0.12
27 4 0.12
28 9 0.26
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (26 bp):
TTATTATATGTCGTTTATATTAAAAA
Found at i:909253 original size:21 final size:21
Alignment explanation
Indices: 909227--909284 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
909217 AGGGTGTCAA
*
909227 AGTGCATCTATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
909248 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
909269 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
909285 TGCACTAGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:909306 original size:22 final size:23
Alignment explanation
Indices: 909269--909325 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 23
909259 GCACCCCTGC
*
909269 AGTGCATCCATGCACC-TGCACT
1 AGTGCATCCATACACCATGCACT
*
909291 AGTGCATCGATACACCATG--C-
1 AGTGCATCCATACACCATGCACT
909311 AGTGCATCCATACAC
1 AGTGCATCCATACAC
909326 TCCATTTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 14 0.45
23 2 0.06
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (23 bp):
AGTGCATCCATACACCATGCACT
Found at i:909370 original size:20 final size:20
Alignment explanation
Indices: 909345--909417 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
909335 AATGCACTTA
909345 GTGCATCGATGCATTCTGAT
1 GTGCATCGATGCATTCTGAT
*
909365 GTGCATCGATGCATTCTGTT
1 GTGCATCGATGCATTCTGAT
* *
909385 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATTCTGAT
*
909405 GTGCATCCATGCA
1 GTGCATCGATGCA
909418 CGAAGGCTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.33
Consensus pattern (20 bp):
GTGCATCGATGCATTCTGAT
Found at i:909822 original size:34 final size:32
Alignment explanation
Indices: 909783--909852 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 32
909773 TTTTGTAAAG
* * *
909783 GGGAAATGTTATAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
909817 GGGAAAGGTTTTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
909849 GGGA
1 GGGA
909853 GTTGTAAGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 11 0.35
33 1 0.03
34 19 0.61
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.26
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:912782 original size:21 final size:21
Alignment explanation
Indices: 912756--912854 Score: 112
Period size: 21 Copynumber: 4.7 Consensus size: 21
912746 AGGGTGTCAA
912756 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCCTAC
*
912777 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
*
912798 AGTGCATCCATGCACCTGC-AC
1 AGTGCATCCATGCACC-CCTAC
* * **
912819 TAGTGCATCGATGCA-CCATGT
1 -AGTGCATCCATGCACCCCTAC
912840 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
912855 TCCATTTTGA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
20 13 0.20
21 38 0.58
22 14 0.22
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:912844 original size:42 final size:42
Alignment explanation
Indices: 912756--912854 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
912746 AGGGTGTCAA
*
912756 AGTGCATCCATGCACCCCTACAGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTACAGTGCATCCATGCACCCATGC
* * *
912798 AGTGCATCCATGCACCTGC-ACTAGTGCATCGATGCA-CCATGT
1 AGTGCATCCATGCACC-CCTAC-AGTGCATCCATGCACCCATGC
912840 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
912855 TCCATTTTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
42 37 0.73
43 14 0.27
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.21
Consensus pattern (42 bp):
AGTGCATCCATGCACCCCTACAGTGCATCCATGCACCCATGC
Found at i:912903 original size:20 final size:20
Alignment explanation
Indices: 912878--912946 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
912868 CACTTAGTGA
912878 ATCAATGCATCCTGATGTGT
1 ATCAATGCATCCTGATGTGT
* *
912898 ATCAATGCATCTTGATAT-T
1 ATCAATGCATCCTGATGTGT
* * *
912917 CATCGATGCATCCTGTTGTGC
1 -ATCAATGCATCCTGATGTGT
*
912938 ATCCATGCA
1 ATCAATGCA
912947 CGAAGGCTGC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (20 bp):
ATCAATGCATCCTGATGTGT
Found at i:913354 original size:34 final size:32
Alignment explanation
Indices: 913315--913379 Score: 94
Period size: 34 Copynumber: 2.0 Consensus size: 32
913305 TTGTAAAGGG
*
913315 GAAAGGTTCTAGCTTATCCCGTGTAAAAACTAGA
1 GAAAGGTTCTAGCTTAGCCCG-G-AAAAACTAGA
*
913349 GAAAGGTTCTAGTTTAGCCCGGAAAAACTAG
1 GAAAGGTTCTAGCTTAGCCCGGAAAAACTAG
913380 GGAGTTGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 9 0.31
33 1 0.03
34 19 0.66
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (32 bp):
GAAAGGTTCTAGCTTAGCCCGGAAAAACTAGA
Found at i:914525 original size:14 final size:14
Alignment explanation
Indices: 914506--914584 Score: 62
Period size: 14 Copynumber: 5.9 Consensus size: 14
914496 TAGTAATAAT
914506 TATTAAATCATTAG
1 TATTAAATCATTAG
*
914520 TATTAAATCATTAT
1 TATTAAATCATTAG
* *
914534 TA-TAATTTCATTAT
1 TATTAA-ATCATTAG
*
914548 TAAT-AATCATTAG
1 TATTAAATCATTAG
914561 ---TAAATCATTAG
1 TATTAAATCATTAG
914572 T-TTCAAATCATTA
1 TATT-AAATCATTA
914585 AATATTAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
10 1 0.02
11 9 0.16
13 10 0.18
14 34 0.62
15 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.46
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:914554 original size:49 final size:49
Alignment explanation
Indices: 914490--914694 Score: 156
Period size: 49 Copynumber: 4.2 Consensus size: 49
914480 TATTATTCCA
* *
914490 TATTATTAGTAATAATTATTAAATCATTAGTATTAAATCATTATTATAATT
1 TATTATTAATAAT-ATTATTAAATCATTAGTACTAAATCATTATTATAA-T
* * *
914541 TCATTATTAATAATCATTAGTAAATCATTAGT-TTCAAATCATTA-AAT-AT
1 T-ATTATTAATAAT-ATTATTAAATCATTAGTACT-AAATCATTATTATAAT
* * * * *
914590 TAATAATAAATCATTATTATCAAATCA-T--TACTAAATCATTATTATCAT
1 T-ATTATTAAT-AATATTATTAAATCATTAGTACTAAATCATTATTATAAT
* *
914638 TATTATT-A-AATCATTATTATAATGATTATTACTAAATCATTATTATAAT
1 TATTATTAATAAT-ATTATTA-AATCATTAGTACTAAATCATTATTATAAT
*
914687 GATTATTA
1 TATTATTA
914695 TCAAATCATT
Statistics
Matches: 123, Mismatches: 19, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
44 2 0.02
45 6 0.05
46 15 0.12
47 8 0.07
48 4 0.03
49 44 0.36
50 3 0.02
51 5 0.04
52 36 0.29
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (49 bp):
TATTATTAATAATATTATTAAATCATTAGTACTAAATCATTATTATAAT
Found at i:914638 original size:121 final size:120
Alignment explanation
Indices: 914510--914785 Score: 305
Period size: 121 Copynumber: 2.3 Consensus size: 120
914500 AATAATTATT
*
914510 AAATCATTAGTATTAAATCATTATTATAATTTCATTATTAAT-AATCATTAGTA-AATCATTAGT
1 AAATCATTAATATTAAATCATTATTATAA--TCATTATTAATAAATCATTAGTATAATCATTA-T
* * *
914573 T-TCAAATCATTAAATATTAATAAT-AAATCATT-ATTA-TCAAATCATTACTAAATCATT
63 TATCAAATCATT-AATA--AATAATAAAATCATTAAATATTAAAATCATTACTAAATCATC
* * * * * *
914630 ATTATCATTATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTA
1 A-AATCATTAATATTAAATCATTATTATAATCATTATTAATAAATCATTAGTATAATCATTATTA
* * *
914695 TCAAATCATTACTAAATCATAAAATCATTAAATATTAAAATCATTATTAAATCATC
65 TCAAATCATTAATAAATAATAAAATCATTAAATATTAAAATCATTACTAAATCATC
914751 AAATCATTAAATATTAAAATCATTATTA-AATCATT
1 AAATCATT-AATATT-AAATCATTATTATAATCATT
914786 TTTATGGTTA
Statistics
Matches: 132, Mismatches: 15, Indels: 17
0.80 0.09 0.10
Matches are distributed among these distances:
118 5 0.04
119 17 0.13
120 25 0.19
121 73 0.55
122 12 0.09
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (120 bp):
AAATCATTAATATTAAATCATTATTATAATCATTATTAATAAATCATTAGTATAATCATTATTAT
CAAATCATTAATAAATAATAAAATCATTAAATATTAAAATCATTACTAAATCATC
Found at i:914642 original size:34 final size:35
Alignment explanation
Indices: 914526--914668 Score: 107
Period size: 35 Copynumber: 4.0 Consensus size: 35
914516 TTAGTATTAA
* * *
914526 ATCATTATTAT-AATTTCATTATTAATAATCATTAGTAA
1 ATCATTATTATCAA-ATCATTACT-ATAATCATTA-T-T
* * *
914564 ATCATTAGTT-TCAAATCATTAAATATTAAT-AATA-A
1 ATCATTA-TTATCAAATCATT-ACTA-TAATCATTATT
914599 ATCATTATTATCAAATCATTACTA-AATCATTATT
1 ATCATTATTATCAAATCATTACTATAATCATTATT
* * *
914633 ATCATTATTATTAAATCATTATTATAATGATTATT
1 ATCATTATTATCAAATCATTACTATAATCATTATT
914668 A
1 A
914669 CTAAATCATT
Statistics
Matches: 88, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
32 3 0.03
33 3 0.03
34 27 0.31
35 28 0.32
38 17 0.19
39 10 0.11
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (35 bp):
ATCATTATTATCAAATCATTACTATAATCATTATT
Found at i:914705 original size:23 final size:24
Alignment explanation
Indices: 914622--914705 Score: 75
Period size: 26 Copynumber: 3.4 Consensus size: 24
914612 AATCATTACT
* * *
914622 AAATC-ATTATTATCATTATTATT
1 AAATCTATTATAATGATTATTATC
914645 AAATCATTATTATAATGATTATTA-C
1 AAATC--TATTATAATGATTATTATC
914670 TAAATCATTATTATAATGATTATTATC
1 -AAATC--TATTATAATGATTATTATC
914697 AAATC-ATTA
1 AAATCTATTA
914706 CTAAATCATA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
23 9 0.17
26 43 0.81
27 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.46
Consensus pattern (24 bp):
AAATCTATTATAATGATTATTATC
Found at i:914721 original size:19 final size:18
Alignment explanation
Indices: 914697--914784 Score: 80
Period size: 16 Copynumber: 4.9 Consensus size: 18
914687 GATTATTATC
914697 AAATCATTACTAAATCATA
1 AAATCATTA-TAAATCATA
914716 AAATCA-T-TAAAT-ATTA
1 AAATCATTATAAATCA-TA
*
914732 AAATCATTATTAAATCATC
1 AAATCATTA-TAAATCATA
914751 AAATCA-T-TAAAT-ATTA
1 AAATCATTATAAATCA-TA
914767 AAATCATTATTAAATCAT
1 AAATCATTA-TAAATCAT
914785 TTTTATGGTT
Statistics
Matches: 57, Mismatches: 2, Indels: 20
0.72 0.03 0.25
Matches are distributed among these distances:
15 2 0.04
16 25 0.44
17 2 0.04
18 2 0.04
19 24 0.42
20 2 0.04
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATCATTATAAATCATA
Found at i:914744 original size:12 final size:11
Alignment explanation
Indices: 914504--914785 Score: 115
Period size: 11 Copynumber: 24.3 Consensus size: 11
914494 ATTAGTAATA
914504 ATTATTAAATC
1 ATTATTAAATC
914515 ATTAGTATTAAATC
1 A-T--TATTAAATC
914529 ATTATTATAATTTC
1 ATTATTA-AA--TC
914543 ATTATTAATAATC
1 ATTATT-A-AATC
*
914556 ATTAGTAAATC
1 ATTATTAAATC
914567 ATTAGTTTCAAATC
1 ATTA--TT-AAATC
*
914581 ATTA--AATATT
1 ATTATTAA-ATC
* *
914591 AATAATAAATC
1 ATTATTAAATC
914602 ATTATTATCAAATC
1 ATTA-T-T-AAATC
*
914616 ATTACTAAATC
1 ATTATTAAATC
* *
914627 ATTATTATCATT
1 ATTATTA-AATC
914639 ATTATTAAATC
1 ATTATTAAATC
*
914650 ATTATTATAATG
1 ATTATTA-AATC
914662 ATTATTACTAAATC
1 ATTA-T--TAAATC
*
914676 ATTATTATAATG
1 ATTATTA-AATC
914688 ATTATTATCAAATC
1 ATTA-T-T-AAATC
*
914702 ATTACTAAATC
1 ATTATTAAATC
914713 A-TA--AAATC
1 ATTATTAAATC
914721 ---ATTAAAT-
1 ATTATTAAATC
914728 ATTA--AAATC
1 ATTATTAAATC
914737 ATTATTAAATC
1 ATTATTAAATC
914748 ATCAAATCATTAAAT-
1 AT----T-ATTAAATC
914763 ATTA--AAATC
1 ATTATTAAATC
914772 ATTATTAAATC
1 ATTATTAAATC
914783 ATT
1 ATT
914786 TTTATGGTTA
Statistics
Matches: 212, Mismatches: 18, Indels: 82
0.68 0.06 0.26
Matches are distributed among these distances:
6 1 0.00
8 17 0.08
9 10 0.05
10 9 0.04
11 63 0.30
12 31 0.15
13 13 0.06
14 51 0.24
15 10 0.05
16 7 0.03
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:914746 original size:35 final size:35
Alignment explanation
Indices: 914697--914784 Score: 158
Period size: 35 Copynumber: 2.5 Consensus size: 35
914687 GATTATTATC
*
914697 AAATCATTACTAAATCATAAAATCATTAAATATTA
1 AAATCATTATTAAATCATAAAATCATTAAATATTA
*
914732 AAATCATTATTAAATCATCAAATCATTAAATATTA
1 AAATCATTATTAAATCATAAAATCATTAAATATTA
914767 AAATCATTATTAAATCAT
1 AAATCATTATTAAATCAT
914785 TTTTATGGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (35 bp):
AAATCATTATTAAATCATAAAATCATTAAATATTA
Found at i:914968 original size:14 final size:14
Alignment explanation
Indices: 914951--915010 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
914941 TTATTACTCT
*
914951 ATTAGTATTAAATC
1 ATTATTATTAAATC
*
914965 ATTATTA-TAATTTC
1 ATTATTATTAA-ATC
*
914979 ATTATTACTAAATC
1 ATTATTATTAAATC
*
914993 ATTATTATCAAATC
1 ATTATTATTAAATC
915007 ATTA
1 ATTA
915011 AATATTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
13 3 0.08
14 33 0.85
15 3 0.08
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.47
Consensus pattern (14 bp):
ATTATTATTAAATC
Found at i:915061 original size:49 final size:49
Alignment explanation
Indices: 914957--915097 Score: 212
Period size: 49 Copynumber: 2.9 Consensus size: 49
914947 CTCTATTAGT
* * *
914957 ATTAAATCATT-ATTATAATTTCATTATTACTAAATCATTATTATCAAATC
1 ATTAAAT-ATTAATAATAATTTCATTATTACT-AATCATTACTACCAAATC
915007 ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTACCAAATC
1 ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTACCAAATC
* *
915056 ATTAAATATTAATAATAAATTCATTATTACTAATAATTACTA
1 ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTA
915098 AATCATTACT
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
49 59 0.69
50 26 0.31
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (49 bp):
ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTACCAAATC
Found at i:915075 original size:21 final size:21
Alignment explanation
Indices: 915051--915133 Score: 59
Period size: 21 Copynumber: 4.1 Consensus size: 21
915041 CATTACTACC
915051 AAATCATTAAATATTAATAAT
1 AAATCATTAAATATTAATAAT
*
915072 AAATTCA-T---TATTACTAAT
1 AAA-TCATTAAATATTAATAAT
* * * **
915090 -AATTACTAAATCATTACTATC
1 AAATCATTAAAT-ATTAATAAT
915111 AAATCATTAAATATTAATAAT
1 AAATCATTAAATATTAATAAT
915132 AA
1 AA
915134 TTTCATTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
16 2 0.04
17 3 0.07
18 9 0.20
20 1 0.02
21 19 0.41
22 12 0.26
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATCATTAAATATTAATAAT
Found at i:915101 original size:109 final size:101
Alignment explanation
Indices: 914957--915255 Score: 430
Period size: 109 Copynumber: 2.9 Consensus size: 101
914947 CTCTATTAGT
* *
914957 ATTAAATCATT-ATTATAATTTCA-T-TATTACTAAATCATTATTATCAAATCATTAAATATTAA
1 ATTAAAT-ATTAATAATAATTTCATTATATTACTAAATCATTACTATCAAATCATTAAATATTAA
915019 TAATAATTTCATTATTACTAATCATTACTACCAAATC
65 TAATAATTTCATTATTACTAATCATTACTACCAAATC
*
915056 ATTAAATATTAATAATAAATTCATTATTACTAATAATTACTAAATCATTACTATCAAATCATTAA
1 ATTAAATATTAATAAT-AATT--TCA-T--T-AT-ATTACTAAATCATTACTATCAAATCATTAA
915121 ATATTAATAATAATTTCATTATTACTAATCATTACTACCAAATC
58 ATATTAATAATAATTTCATTATTACTAATCATTACTACCAAATC
*
915165 ATTAAATATTAATAATAATTTCATTAT-TT-CT-AATCATTACTATCAAATTATTAAATATTAAT
1 ATTAAATATTAATAATAATTTCATTATATTACTAAATCATTACTATCAAATCATTAAATATTAAT
*
915227 AATAATTTCATTATTAATAATCATTACTA
66 AATAATTTCATTATTACTAATCATTACTA
915256 AATAATTATT
Statistics
Matches: 183, Mismatches: 6, Indels: 23
0.86 0.03 0.11
Matches are distributed among these distances:
98 61 0.33
99 13 0.07
100 6 0.03
102 4 0.02
103 1 0.01
105 1 0.01
106 3 0.02
108 5 0.03
109 89 0.49
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (101 bp):
ATTAAATATTAATAATAATTTCATTATATTACTAAATCATTACTATCAAATCATTAAATATTAAT
AATAATTTCATTATTACTAATCATTACTACCAAATC
Found at i:915105 original size:60 final size:60
Alignment explanation
Indices: 915032--915157 Score: 218
Period size: 60 Copynumber: 2.1 Consensus size: 60
915022 TAATTTCATT
915032 ATTACT-AATCATTACTACCAAATCATTAAATATTAATAATAAATTCATTATTACTAATA
1 ATTACTAAATCATTACTACCAAATCATTAAATATTAATAATAAATTCATTATTACTAATA
* * *
915091 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTACCAAATCATTAAATATTAATAATAAATTCATTATTACTAATA
915151 ATTACTA
1 ATTACTA
915158 CCAAATCATT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
59 6 0.10
60 57 0.90
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.40
Consensus pattern (60 bp):
ATTACTAAATCATTACTACCAAATCATTAAATATTAATAATAAATTCATTATTACTAATA
Found at i:915154 original size:49 final size:49
Alignment explanation
Indices: 915091--915314 Score: 285
Period size: 49 Copynumber: 4.6 Consensus size: 49
915081 ATTACTAATA
915091 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
915141 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* *
915190 ATTTCTAATCATTACTATCAAATTATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* * * * **
915239 ATTAATAATCATTACTA-AATAATTATTATAATTTTAA-ATATAAAATCATT
1 ATTACTAATCATTACTATCA-AATCATTA-AATATTAATA-ATAATTTCATT
* *
915289 ATTA--AATCATGATTATCAAATCATTA
1 ATTACTAATCATTACTATCAAATCATTA
915315 CTAAATCAAA
Statistics
Matches: 156, Mismatches: 14, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
48 17 0.11
49 113 0.72
50 26 0.17
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:915228 original size:158 final size:159
Alignment explanation
Indices: 914957--915263 Score: 501
Period size: 158 Copynumber: 1.9 Consensus size: 159
914947 CTCTATTAGT
* * *
914957 ATTAAATCATTATTATAATTTCATTATTACTAAATCATTATTATCAAATCATTAAATATTAATAA
1 ATTAAATCATTATAATAATTTCATTATTACTAAATCATTACTACCAAATCATTAAATATTAATAA
*
915022 TAATTTCATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAAATTCATTATTACT
66 TAATTTCATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAAATTCATTATTAAT
*
915087 AATAATTACTAAATCATTACTATCAAATC
131 AATAATTACTAAATAATTACTATCAAATC
915116 ATTAAAT-ATTAATAATAATTTCATTATTACT-AATCATTACTACCAAATCATTAAATATTAATA
1 ATTAAATCATT-ATAATAATTTCATTATTACTAAATCATTACTACCAAATCATTAAATATTAATA
* * * *
915179 ATAATTTCATTATTTCTAATCATTACTATCAAATTATTAAATATTAATAATAATTTCATTATTAA
65 ATAATTTCATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAAATTCATTATTAA
*
915244 TAATCATTACTAAATAATTA
130 TAATAATTACTAAATAATTA
915264 TTATAATTTT
Statistics
Matches: 137, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
158 111 0.81
159 26 0.19
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (159 bp):
ATTAAATCATTATAATAATTTCATTATTACTAAATCATTACTACCAAATCATTAAATATTAATAA
TAATTTCATTATTACTAATCATTACTACCAAATCATTAAATATTAATAATAAATTCATTATTAAT
AATAATTACTAAATAATTACTATCAAATC
Found at i:918090 original size:2 final size:2
Alignment explanation
Indices: 918078--918123 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
918068 TCATTTTCTC
*
918078 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
918120 TA TA
1 TA TA
918124 AATTTAGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:918894 original size:28 final size:28
Alignment explanation
Indices: 918863--918916 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
918853 ATAATCTAAT
918863 ATATAACTTAAACTAACAAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
918891 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
918917 ATTTATACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:918923 original size:28 final size:28
Alignment explanation
Indices: 918859--918923 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
918849 TTATATAATC
918859 TAATATATAACTTAAACTAACAAACTAA
1 TAATATATAACTTAAACTAACAAACTAA
918887 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
918915 TAATTTATA
1 TAATATATA
918924 CTAACAAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:918926 original size:21 final size:21
Alignment explanation
Indices: 918893--918941 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
918883 CTAATATAAT
918893 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
918914 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
918935 ATTAACT
1 A-TAACT
918942 AAATTTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:919076 original size:5 final size:5
Alignment explanation
Indices: 919066--919094 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
919056 TATTCTTCTT
919066 TTTCC TTTCC TTTCC TTTCC TTTCC TTTC
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTC
919095 TCTCGCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTCC
Found at i:919606 original size:29 final size:29
Alignment explanation
Indices: 919564--919639 Score: 143
Period size: 29 Copynumber: 2.6 Consensus size: 29
919554 TAGGACGCTG
*
919564 GGAGTGCATGGCGACCTACAAGGTCGCCC
1 GGAGGGCATGGCGACCTACAAGGTCGCCC
919593 GGAGGGCATGGCGACCTACAAGGTCGCCC
1 GGAGGGCATGGCGACCTACAAGGTCGCCC
919622 GGAGGGCATGGCGACCTA
1 GGAGGGCATGGCGACCTA
919640 TGTGTTGGGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.21, C:0.29, G:0.38, T:0.12
Consensus pattern (29 bp):
GGAGGGCATGGCGACCTACAAGGTCGCCC
Found at i:927570 original size:14 final size:14
Alignment explanation
Indices: 927551--927591 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
927541 CTTCTGTCTA
*
927551 TATGCAGAGATTAT
1 TATGCAGGGATTAT
927565 TATGCAGGGATTTAT
1 TATGCAGGGA-TTAT
927580 TA-GCAGGGATTA
1 TATGCAGGGATTA
927592 CTTCCCATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 3 0.12
14 16 0.64
15 6 0.24
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (14 bp):
TATGCAGGGATTAT
Found at i:933765 original size:17 final size:18
Alignment explanation
Indices: 933732--933765 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
933722 CCGTTATTAA
933732 TGAACCGTTCAGAACCGC
1 TGAACCGTTCAGAACCGC
933750 TGAACCGTTC-GAACCG
1 TGAACCGTTCAGAACCG
933766 GACCGGCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (18 bp):
TGAACCGTTCAGAACCGC
Found at i:942098 original size:18 final size:17
Alignment explanation
Indices: 942066--942099 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
942056 AATCAACTAA
*
942066 TTATTAAATTTTTTGAG
1 TTATTAAATTATTTGAG
942083 TTATTCAAATTATTTGA
1 TTATT-AAATTATTTGA
942100 TTTCTATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (17 bp):
TTATTAAATTATTTGAG
Found at i:943633 original size:20 final size:20
Alignment explanation
Indices: 943595--943634 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
943585 AATACTCACA
* *
943595 TAAAACCATAATGTCATATT
1 TAAAAACATAATGTAATATT
*
943615 TAAAAACATAATTTAATATT
1 TAAAAACATAATGTAATATT
943635 GTGATATCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (20 bp):
TAAAAACATAATGTAATATT
Found at i:944008 original size:39 final size:39
Alignment explanation
Indices: 943954--944039 Score: 154
Period size: 39 Copynumber: 2.2 Consensus size: 39
943944 GACCATCAAA
*
943954 GTTTCAATTGAATCAATTAGACCACTCAACTATTTAAAT
1 GTTTCAATTGAATCAATCAGACCACTCAACTATTTAAAT
943993 GTTTCAATTGAATCAATCAGACCACTCAACTATTTAAAT
1 GTTTCAATTGAATCAATCAGACCACTCAACTATTTAAAT
*
944032 ATTTCAAT
1 GTTTCAAT
944040 CAAGTCACCG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (39 bp):
GTTTCAATTGAATCAATCAGACCACTCAACTATTTAAAT
Done.