Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006718.1 Hibiscus syriacus cultivar Beakdansim tig00016800_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: 152405
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:963 original size:32 final size:32
Alignment explanation
Indices: 924--989 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
914 GAATGAGATA
924 TTTAGATATTTTTAAATATTCAT-AGATATTTT
1 TTTAGATA-TTTTAAATATTCATCAGATATTTT
* **
956 TTTAGATATTTTAGATATTTTTCAGATATTTT
1 TTTAGATATTTTAAATATTCATCAGATATTTT
988 TT
1 TT
990 ATTGAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.59
Consensus pattern (32 bp):
TTTAGATATTTTAAATATTCATCAGATATTTT
Found at i:982 original size:11 final size:10
Alignment explanation
Indices: 924--988 Score: 69
Period size: 10 Copynumber: 6.3 Consensus size: 10
914 GAATGAGATA
924 TTTAGATATT
1 TTTAGATATT
*
934 TTTAAATATT
1 TTTAGATATT
**
944 CATAGATATTTT
1 TTTAGATA--TT
956 TTTAGATA-T
1 TTTAGATATT
965 TTTAGATATT
1 TTTAGATATT
975 TTTCAGATATT
1 TTT-AGATATT
986 TTT
1 TTT
989 TATTGAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
9 9 0.20
10 18 0.40
11 10 0.22
12 8 0.18
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (10 bp):
TTTAGATATT
Found at i:982 original size:20 final size:19
Alignment explanation
Indices: 919--987 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
909 GAGGTGAATG
919 AGATA-TTTAGATATTTTT
1 AGATATTTTAGATATTTTT
* *
937 AAATATTCATAGATATTTTTTT
1 AGATATT-TTAGATA--TTTTT
959 AGATATTTTAGATATTTTT
1 AGATATTTTAGATATTTTT
978 CAGATATTTT
1 -AGATATTTT
988 TTATTGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
18 4 0.10
19 6 0.14
20 15 0.36
21 6 0.14
22 11 0.26
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (19 bp):
AGATATTTTAGATATTTTT
Found at i:8109 original size:2 final size:2
Alignment explanation
Indices: 8102--8132 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8092 CCATTATTGT
8102 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
8133 GCTTTCGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:17696 original size:35 final size:35
Alignment explanation
Indices: 17645--17724 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
17635 AACACAATCA
*
17645 TCAATTACATTATAAACCCCAAATTCCAAAATGCT
1 TCAATTACATTATAAACCCCAAATTCCAAAATACT
* * *
17680 TCAATTATATTTTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTATAAACCCCAAATTCCAAAATACT
17715 TCAATTACAT
1 TCAATTACAT
17725 GGTCAATCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (35 bp):
TCAATTACATTATAAACCCCAAATTCCAAAATACT
Found at i:17738 original size:35 final size:34
Alignment explanation
Indices: 17645--17740 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 34
17635 AACACAATCA
* *
17645 TCAATTACAT-TATAAACCCCAAATTCCAAAATGCT
1 TCAATTACATGT-CAAA-CCCAAATTCCAAAATACT
* * *
17680 TCAATTATATTTTAAACCTCAAATTCCAAAATACT
1 TCAATTACATGTCAAACC-CAAATTCCAAAATACT
*
17715 TCAATTACATGGTCAATCCCAAATTC
1 TCAATTACAT-GTCAAACCCAAATTC
17741 ATAATCTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
34 2 0.04
35 44 0.85
36 6 0.12
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.32
Consensus pattern (34 bp):
TCAATTACATGTCAAACCCAAATTCCAAAATACT
Found at i:18509 original size:143 final size:142
Alignment explanation
Indices: 18220--18501 Score: 384
Period size: 143 Copynumber: 1.9 Consensus size: 142
18210 AAACTATTTA
* * *
18220 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAATAGAAACTCGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
* **** * * *
18285 AATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAATTTTTTTGAGTCAATTATTTT
66 AATTCAATTCGACTTGATTTAAATTTTAAAAACTCAAATCGAAAAAAATTCGAGTAAACTATTTT
18350 ATAAACTAAACTG
131 AT-AACTAAACTG
*
18363 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACATAAACTCGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCG--
* *
18428 AATTCAATTCAATTCGACTTGATTTAAATTTTAAAAACTCAACTTGAAAAAAATTCGAGTAAACT
64 AA---AATTCAATTCGACTTGATTTAAATTTTAAAAACTCAAATCGAAAAAAATTCGAGTAAACT
18493 ATTTTATAA
126 ATTTTATAA
18502 ACTGAATTGA
Statistics
Matches: 120, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
143 59 0.49
145 2 0.02
147 2 0.02
148 57 0.47
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (142 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
AATTCAATTCGACTTGATTTAAATTTTAAAAACTCAAATCGAAAAAAATTCGAGTAAACTATTTT
ATAACTAAACTG
Found at i:18753 original size:35 final size:35
Alignment explanation
Indices: 18660--18753 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 35
18650 AATGGATTAT
* * * *
18660 GAATTTGGGATTGAGCATGTAATTGAAGTATTTTG
1 GAATTTGGGGTTTAGAATGTAATTGAAGCATTTTG
* ** *
18695 GAATTTGAGGTTTATTATATAATTGAAGCATTTTG
1 GAATTTGGGGTTTAGAATGTAATTGAAGCATTTTG
18730 GAATTTGGGGTTTAGAATGTAATT
1 GAATTTGGGGTTTAGAATGTAATT
18754 AATGACTGTG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.43
Consensus pattern (35 bp):
GAATTTGGGGTTTAGAATGTAATTGAAGCATTTTG
Found at i:19856 original size:21 final size:21
Alignment explanation
Indices: 19830--19878 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
19820 ATATTTAGAT
19830 TATTGATT-TAATTATAAGTTA
1 TATTGATTATAATTATAA-TTA
**
19851 TATTGATTATTTTTATAATTA
1 TATTGATTATAATTATAATTA
19872 TATTGAT
1 TATTGAT
19879 AGCACTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (21 bp):
TATTGATTATAATTATAATTA
Found at i:21734 original size:2 final size:2
Alignment explanation
Indices: 21727--21765 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
21717 ATCTCTAAAT
21727 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
21766 TTAATCATGT
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:22204 original size:60 final size:60
Alignment explanation
Indices: 22140--22256 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
22130 TTCATATCTT
*** * * *
22140 TAGGGACCAA-TTAAGAATGAGTGTCATAGTTTAAGAATGAATTTGGAATGTTTAAAAGTG
1 TAGGGACCAATTTAA-AATGAAAATCATAGTTTAAGAATGAAGTTAGAATGTTCAAAAGTG
22200 TAGGGACCAATTTAAAATGAAAATCATAGTTTAAGAATGAAGTTAGAATGTTCAAAA
1 TAGGGACCAATTTAAAATGAAAATCATAGTTTAAGAATGAAGTTAGAATGTTCAAAA
22257 TTTTAGAGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 46 0.92
61 4 0.08
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (60 bp):
TAGGGACCAATTTAAAATGAAAATCATAGTTTAAGAATGAAGTTAGAATGTTCAAAAGTG
Found at i:22279 original size:60 final size:60
Alignment explanation
Indices: 22163--22280 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 60
22153 AGAATGAGTG
* * * * *
22163 TCATAGTTTAAGAATGAATTTGGAATGTTTAAAAGTGTAGGGACCAATTTAAAATGAAAA
1 TCATAGTTTAAGAATGAAGTTAGAATGTTCAAAAGTGTAGAGACCAATATAAAATGAAAA
* * ** *
22223 TCATAGTTTAAGAATGAAGTTAGAATGTTCAAAATTTTAGAGATTAATATAGAATGAA
1 TCATAGTTTAAGAATGAAGTTAGAATGTTCAAAAGTGTAGAGACCAATATAAAATGAA
22281 GATTATAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (60 bp):
TCATAGTTTAAGAATGAAGTTAGAATGTTCAAAAGTGTAGAGACCAATATAAAATGAAAA
Found at i:26850 original size:256 final size:257
Alignment explanation
Indices: 26317--27066 Score: 962
Period size: 257 Copynumber: 2.9 Consensus size: 257
26307 TTTAGGAAAT
**
26317 ACCCGACCCGAAAATGTATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC
1 ACCCGACCC-AAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC
* * ** *
26382 TATATATA-AT-TCTTTTCCAATTAAGTCACTGCTTTTATTGAAT-AAAATAATTTTT-TTA-TT
65 TATATATATATATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTATTATTT
* * * *
26442 ----TCGGATCGGATTTCTAATTCATATATTTGGGTCGGGTC-GGTGAAACTTTATTTTGGTCAG
130 CGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGG
* * ** * ** * * *
26502 GTCGGGTC-GGGTTTTTTAAGTGT--GATATTCGGGTCGGGTCGGATTCGGGTTTAGAGTGAAAA
195 GTCGGGTCTCGG--ATGGAGGT-TCCCTTGTTC---TCGGGTCGG-GTCGGG-TTAGAG-CAAAA
*
26564 ATACCCG
251 ATACCCA
*
26571 ACCCGTCCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCT
1 ACCCGACCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCT
26636 ATATATATATATATTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTTATTATT
66 ATATATATATAT-TTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATA-TTTTTTATTATT
26701 TCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCG
129 TCGGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCG
*
26766 GGTCGGGTCTCGGATGGAGGTTCCCTTGTTCTCGGGTCGGGTCGGG-TAGA-CCAAAA-ACCCA
194 GGTCGGGTCTCGGATGGAGGTTCCCTTGTTCTCGGGTCGGGTCGGGTTAGAGCAAAAATACCCA
26827 ACCCGACCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC-
1 ACCCGACCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCT
*
26891 -TGTATATA-ATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAATTTTTTATTATTT
66 ATATATATATATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAAT-ATTTTTTATTATTT
*
26954 CGGGTCGGGTCAGGTCAGGTTTCTAATTCATATATTCAGGTCGGGTCGGGTGAAACTTTATTTTG
130 CGGGTCGGGTC--G---GGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTG
*
27019 GTCGGGTCGGGTCTCGGATGGAGGTTCCCTTGTTCTCAGGTCGGGTCG
190 GTCGGGTCGGGTCTCGGATGGAGGTTCCCTTGTTCTCGGGTCGGGTCG
27067 AGAATACTAA
Statistics
Matches: 447, Mismatches: 28, Indels: 39
0.87 0.05 0.08
Matches are distributed among these distances:
252 62 0.14
253 64 0.14
254 18 0.04
255 1 0.00
256 95 0.21
257 104 0.23
258 5 0.01
259 7 0.02
260 2 0.00
261 5 0.01
262 9 0.02
263 1 0.00
264 39 0.09
265 33 0.07
266 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (257 bp):
ACCCGACCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCT
ATATATATATATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATATTTTTTATTATTTC
GGGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGG
TCGGGTCTCGGATGGAGGTTCCCTTGTTCTCGGGTCGGGTCGGGTTAGAGCAAAAATACCCA
Found at i:27456 original size:44 final size:44
Alignment explanation
Indices: 27331--27444 Score: 201
Period size: 44 Copynumber: 2.6 Consensus size: 44
27321 TCTAACATGT
* *
27331 CTGCGAACCAAACAGAATATGGAATTGGATTCCAATTCAATTTG
1 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCAATTTC
*
27375 CTGTCAACCAAACAGAATATGGAATTGGATTCCAATTCAATTTC
1 CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCAATTTC
27419 CTGCCAACCAAACAGAATATGGAATT
1 CTGCCAACCAAACAGAATATGGAATT
27445 TAATTTCAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (44 bp):
CTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCAATTTC
Found at i:30494 original size:2 final size:2
Alignment explanation
Indices: 30487--30516 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30477 TGCTTAACTT
30487 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
30517 AAAAGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30723 original size:21 final size:21
Alignment explanation
Indices: 30672--30794 Score: 71
Period size: 20 Copynumber: 6.0 Consensus size: 21
30662 CCAAATTCAG
*
30672 TTTTCAAATTCGCAACTCGAA
1 TTTTCAATTTCGCAACTCGAA
*
30693 TTTGCCAATTTCGCAACTC-AA
1 TTT-TCAATTTCGCAACTCGAA
* *
30714 TTTTCGAA-TTCGTAACTTGAA
1 TTTTC-AATTTCGCAACTCGAA
* *
30735 -TAT-AGATTTCGCAACTTGAA
1 TTTTCA-ATTTCGCAACTCGAA
**
30755 -AATCGAA-TTCGCAACTCGAA
1 TTTTC-AATTTCGCAACTCGAA
* *
30775 ATTT-AAATTCGCAACTCGAA
1 TTTTCAATTTCGCAACTCGAA
30795 ACTCAATTCA
Statistics
Matches: 82, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 50 0.61
21 14 0.17
22 14 0.17
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (21 bp):
TTTTCAATTTCGCAACTCGAA
Found at i:30765 original size:20 final size:20
Alignment explanation
Indices: 30717--30829 Score: 111
Period size: 20 Copynumber: 5.7 Consensus size: 20
30707 AACTCAATTT
* * *
30717 TCGAATTCGTAACTTGAATA
1 TCGAATTCGCAACTCGAAAA
* * *
30737 TAGATTTCGCAACTTGAAAA
1 TCGAATTCGCAACTCGAAAA
*
30757 TCGAATTCGCAACTCGAAAT
1 TCGAATTCGCAACTCGAAAA
** *
30777 TTAAATTCGCAACTCGAAAC
1 TCGAATTCGCAACTCGAAAA
* *
30797 TC-AATTCACAACTCGAGAA
1 TCGAATTCGCAACTCGAAAA
30816 TCGAATTCGCAACT
1 TCGAATTCGCAACT
30830 TAAATTTCAT
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
19 16 0.21
20 60 0.79
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (20 bp):
TCGAATTCGCAACTCGAAAA
Found at i:30809 original size:39 final size:40
Alignment explanation
Indices: 30742--30829 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 40
30732 GAATATAGAT
* * *
30742 TTCGCAACTTGAAAATCGAATTCGCAACTCGA-AATTTAAA
1 TTCGCAACTCGAAAATCGAATTCACAACTCGAGAA-TCAAA
* *
30782 TTCGCAACTCGAAACTC-AATTCACAACTCGAGAATCGAA
1 TTCGCAACTCGAAAATCGAATTCACAACTCGAGAATCAAA
30821 TTCGCAACT
1 TTCGCAACT
30830 TAAATTTCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 25 0.60
40 17 0.40
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (40 bp):
TTCGCAACTCGAAAATCGAATTCACAACTCGAGAATCAAA
Found at i:30857 original size:20 final size:20
Alignment explanation
Indices: 30834--30877 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
30824 GCAACTTAAA
30834 TTTCATTTTCGAGTTGCGAT
1 TTTCATTTTCGAGTTGCGAT
30854 TTTCATTTTCGAGTTGCGAT
1 TTTCATTTTCGAGTTGCGAT
30874 TTTC
1 TTTC
30878 GTGTTGCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.16, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCATTTTCGAGTTGCGAT
Found at i:30964 original size:40 final size:39
Alignment explanation
Indices: 30915--30992 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
30905 GAATTCCAAA
*
30915 TTCGAGTTGCGAATTCGGAAACTT-TGTTGCGAAATTGGCT
1 TTCGAGTTGCGAATTC-GAAA-TTGAGTTGCGAAATTGGCT
* *
30955 TTCGTGTTGCGAATTCGAAATTGAGTTGCGAATTTGGC
1 TTCGAGTTGCGAATTCGAAATTGAGTTGCGAAATTGGC
30993 ACTCCACCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 2 0.06
39 17 0.50
40 15 0.44
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (39 bp):
TTCGAGTTGCGAATTCGAAATTGAGTTGCGAAATTGGCT
Found at i:41388 original size:63 final size:66
Alignment explanation
Indices: 41265--41394 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 66
41255 CTTGCTTGAA
41265 TCTTGTTATCTTCAGAAACTCGAGCTTTAAAGTAGTAATCGGTTGCTTATGCAAAATTGGACAGG
1 TCTTGTTATCTTCAGAAACTCGAGCTTTAAAGTAGTAA-CGGTTGCTTATGCAAAATTGGACAGG
41330 TG
65 TG
41332 TCTTGTTATCTTCAG-AACTCGAGCTTTAAAGTAGT-A-GGTTGCTTATGCAAAATTGGACAGGT
1 TCTTGTTATCTTCAGAAACTCGAGCTTTAAAGTAGTAACGGTTGCTTATGCAAAATTGGACAGGT
41394 G
66 G
41395 CTAAATGTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
63 27 0.43
65 1 0.02
66 20 0.32
67 15 0.24
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (66 bp):
TCTTGTTATCTTCAGAAACTCGAGCTTTAAAGTAGTAACGGTTGCTTATGCAAAATTGGACAGGT
G
Found at i:42017 original size:25 final size:27
Alignment explanation
Indices: 41989--42050 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 27
41979 TTTATATTAT
41989 TTTATTATATAAA-TAAATATA-AATA
1 TTTATTATATAAATTAAATATACAATA
* * *
42014 TTTA-AATATAAATTTAATATACTATA
1 TTTATTATATAAATTAAATATACAATA
*
42040 TTAATTATATA
1 TTTATTATATA
42051 TTAAAGTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
24 7 0.24
25 11 0.38
26 6 0.21
27 5 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TTTATTATATAAATTAAATATACAATA
Found at i:42178 original size:28 final size:25
Alignment explanation
Indices: 42147--42197 Score: 66
Period size: 28 Copynumber: 1.9 Consensus size: 25
42137 TTAACCTTAA
42147 AAAACATATATCACAAGGATAATTTCGT
1 AAAACATATATC-CAA-G-TAATTTCGT
*
42175 AAAATATATATCCAAGTAATTTC
1 AAAACATATATCCAAGTAATTTC
42198 TTCCAACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 1 0.05
27 3 0.14
28 11 0.50
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (25 bp):
AAAACATATATCCAAGTAATTTCGT
Found at i:42830 original size:20 final size:20
Alignment explanation
Indices: 42790--42831 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
42780 CGGTTATACT
* * *
42790 ATCCGGTTTTAAAATATCCG
1 ATCCGGTTTAAAAAAAACCG
42810 ATCCGGTTTAAAAAAAACCG
1 ATCCGGTTTAAAAAAAACCG
42830 AT
1 AT
42832 TTTTCTCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (20 bp):
ATCCGGTTTAAAAAAAACCG
Found at i:48319 original size:2 final size:2
Alignment explanation
Indices: 48312--48338 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48302 CAATATGAAA
48312 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
48339 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:49321 original size:16 final size:16
Alignment explanation
Indices: 49300--49330 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49290 AATGATAATG
*
49300 ATATTAATTTAATTAC
1 ATATTAATTGAATTAC
49316 ATATTAATTGAATTA
1 ATATTAATTGAATTA
49331 TTCTTTGATA
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:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
ATATTAATTGAATTAC
Found at i:51024 original size:48 final size:48
Alignment explanation
Indices: 50908--51039 Score: 149
Period size: 48 Copynumber: 2.8 Consensus size: 48
50898 ATAGGTTTTT
* * * * ** *
50908 CTGATGTTGCAGTCGTTGCACCAAGAGATGTTTTTCGTATTGGTGTGC
1 CTGATGTTGCAGCCGATGCACCAGGAGATGATGCTCGTATTAGTGTGC
*
50956 CTGATGTTGCAGCC-ATTGCACCAGGAGATGGTGCTCGTATTAGTGTGC
1 CTGATGTTGCAGCCGA-TGCACCAGGAGATGATGCTCGTATTAGTGTGC
* **
51004 CTGATGTTGTAGCCGATGCACTGGGAGATGATGCTC
1 CTGATGTTGCAGCCGATGCACCAGGAGATGATGCTC
51040 CAATAGGCAT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
48 70 0.99
49 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (48 bp):
CTGATGTTGCAGCCGATGCACCAGGAGATGATGCTCGTATTAGTGTGC
Found at i:51205 original size:48 final size:48
Alignment explanation
Indices: 51153--51253 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 48
51143 ACCGATAGGC
*
51153 GGTGCTCCTATTGGATTGCATGATGTAACATCCAGTGCATAGGGAGGT
1 GGTGCTCCTATTGGATTGCATGATATAACATCCAGTGCATAGGGAGGT
* * * * * * *
51201 GGTGCTTCTATTGGCTTGCTTGATATAGCATCTAGTGTATCGGGAGGT
1 GGTGCTCCTATTGGATTGCATGATATAACATCCAGTGCATAGGGAGGT
51249 GGTGC
1 GGTGC
51254 ACTAGTTTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.33
Consensus pattern (48 bp):
GGTGCTCCTATTGGATTGCATGATATAACATCCAGTGCATAGGGAGGT
Found at i:51494 original size:39 final size:39
Alignment explanation
Indices: 51417--51496 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 39
51407 TCGTACATCG
* * * * *
51417 GAAGGTTGTGCTCCTCTTGAAATGCTTGGTGTTGCAGCT
1 GAAGGTGGTACTCCTCTTGAAATGCCTGATGTTACAGCT
* *
51456 GAAGGTGGTACTCCTTTTGACATGCCTGATGTTACAGCT
1 GAAGGTGGTACTCCTCTTGAAATGCCTGATGTTACAGCT
51495 GA
1 GA
51497 TGCTTCAGGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.34
Consensus pattern (39 bp):
GAAGGTGGTACTCCTCTTGAAATGCCTGATGTTACAGCT
Found at i:61759 original size:2 final size:2
Alignment explanation
Indices: 61752--61800 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
61742 CGGATGGAGG
61752 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61794 TA TA TA T
1 TA TA TA T
61801 TTAAAAGATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63656 original size:20 final size:20
Alignment explanation
Indices: 63631--63668 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
63621 TGTGGCTGAG
63631 TGAGAAGATTACCAACTGGT
1 TGAGAAGATTACCAACTGGT
* *
63651 TGAGAAGTTTCCCAACTG
1 TGAGAAGATTACCAACTG
63669 CATATTATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
TGAGAAGATTACCAACTGGT
Found at i:78158 original size:14 final size:14
Alignment explanation
Indices: 78130--78171 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
78120 CGGACAATTA
*
78130 AAATGAAAATAAAAT
1 AAATAAAAAT-AAAT
*
78145 TAATAAAAATAAAT
1 AAATAAAAATAAAT
78159 AAATAAAAATAAA
1 AAATAAAAATAAA
78172 CAACAACGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:78261 original size:36 final size:37
Alignment explanation
Indices: 78214--78290 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
78204 TTCTACAAAC
* *
78214 TATATAATATATA-TTTTCAAAA-GTATTTTAAAATTA
1 TATATAATATATATTTTTAAAAACGT-TTTCAAAATTA
*
78250 TATATTATATATATTTTTAAAAACGTTTTCAAAATTA
1 TATATAATATATATTTTTAAAAACGTTTTCAAAATTA
78287 TATA
1 TATA
78291 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 12 0.33
37 22 0.61
38 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (37 bp):
TATATAATATATATTTTTAAAAACGTTTTCAAAATTA
Found at i:78469 original size:35 final size:36
Alignment explanation
Indices: 78393--78543 Score: 151
Period size: 36 Copynumber: 4.1 Consensus size: 36
78383 TTTAAAAAAT
* **
78393 TATATTTATTTTAAAAATGTTTTTTAAAACCGTATAA
1 TATATTTATTTTAAAAATG-TTTTAAAAACTATATAA
* * *
78430 TATATTT-TCTTAAAAACGTTTTAAAAACTATATAT
1 TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
* *
78465 TATATTTATTTTCAAAGTGTTTTAAAAACTATATAA
1 TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
** * * *
78501 TATATAAATGTTTCAAATATGTTTTCAAAACTATATTA
1 TATATTTAT-TTT-AAAAATGTTTTAAAAACTATATAA
78539 TATAT
1 TATAT
78544 ATATGTATAT
Statistics
Matches: 93, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
35 20 0.22
36 39 0.42
37 10 0.11
38 24 0.26
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (36 bp):
TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
Found at i:78533 original size:38 final size:37
Alignment explanation
Indices: 78335--78549 Score: 139
Period size: 36 Copynumber: 5.9 Consensus size: 37
78325 TAAGTTTTTT
* * *
78335 AAAATGATTTCAAAACTATATAATATATATGT-TTTC
1 AAAATGTTTTAAAAACTATATAATATATATATGTTTC
*
78371 AAAATGTTTCTTTTTAAAAA--AT-T-ATAT-T-TAT-TTTA
1 AAAATG-----TTTTAAAAACTATATAATATATATATGTTTC
* ** *
78406 AAAATGTTTTTTAAAACCGTATAATATAT-T-T-TCTTA
1 AAAATG-TTTTAAAAACTATATAATATATATATGT-TTC
* * *
78442 AAAACGTTTTAAAAACTATATATTATATTTAT-TTTC
1 AAAATGTTTTAAAAACTATATAATATATATATGTTTC
* *
78478 AAAGTGTTTTAAAAACTATATAATATATAAATGTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATGTTTC
* *
78515 AAATATGTTTTCAAAACTATATTATATATATATGT
1 AAA-ATGTTTTAAAAACTATATAATATATATATGT
78550 ATATACAAAA
Statistics
Matches: 143, Mismatches: 21, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
31 9 0.06
33 1 0.01
34 1 0.01
35 35 0.24
36 47 0.33
37 13 0.09
38 28 0.20
39 2 0.01
41 7 0.05
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATAATATATATATGTTTC
Found at i:79407 original size:165 final size:165
Alignment explanation
Indices: 79122--79958 Score: 1387
Period size: 165 Copynumber: 5.1 Consensus size: 165
79112 TGACAAATAG
* * * * * * *
79122 CCCTTCTTGCCATGAGCTATGTTGTAAATGATATGACCC-CGCAGTTGAGTGTAATCGAACTCGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG-CCCTCGAAGCTGAGTGTAATCGAACTCGG
* *
79186 GAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAG
65 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
79251 CGTAGTCGAACTCGAAGGTCCTTTGGTCACAGATAA
130 CGTAGTCGAACTCGAAGGTCCTTTGGTCACAGATAA
*
79287 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
* *
79352 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGT
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* * *
79417 GTAATCGAACTCAAAGGTCTTTTGGTCACAGATAA
131 GTAGTCGAACTCGAAGGTCCTTTGGTCACAGATAA
* * * **
79452 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
79517 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
79582 GTAGTCGAACTCGAAGGT-C-TTGGTCACAGATAA
131 GTAGTCGAACTCGAAGGTCCTTTGGTCACAGATAA
79615 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
*
79680 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
79745 GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAA
131 GTAGTCGAACTCGAAGGTCCTTTGGTCACAGATAA
79780 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
79845 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
** * *
79910 GTAGTCGAACTCGAAGGT-C-TTGGTGGCAGGTAG
131 GTAGTCGAACTCGAAGGTCCTTTGGTCACAGATAA
*
79943 CCCTTCTGGCCTTGAG
1 CCCTTCTAGCCTTGAG
79959 CTAAGCTGCA
Statistics
Matches: 631, Mismatches: 38, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
163 181 0.29
164 3 0.00
165 447 0.71
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (165 bp):
CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTCCTTTGGTCACAGATAA
Found at i:79694 original size:328 final size:328
Alignment explanation
Indices: 79122--79958 Score: 1408
Period size: 328 Copynumber: 2.5 Consensus size: 328
79112 TGACAAATAG
* * * * * * *
79122 CCCTTCTTGCCATGAGCTATGTTGTAAATGATATGACCC-CGCAGTTGAGTGTAATCGAAC-TCG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATG-CCCTCGAAGCTGAGTGTAATCGAACTTAG
*
79185 GGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGA
65 GG-GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGA
79250 GCGTAGTCGAACTCGAAGGTCCTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
129 GCGTAGTCGAACTCGAAGGT-C-TTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA
*
79315 TGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACT
192 TGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACT
* *
79380 TAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTGGTCA
257 TAAGCTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCA
79445 CAGATAA
322 CAGATAA
* *
79452 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAGG
79517 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
79582 GTAGTCGAACTCGAAGGTCTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
131 GTAGTCGAACTCGAAGGTCTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
79647 GTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAG
196 GTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAG
* * *
79712 CTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGA
261 CTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACAGA
79777 TAA
326 TAA
* **
79780 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAGG
79845 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
** * * *
79910 GTAGTCGAACTCGAAGGTCTTGGTGGCAGGTAGCCCTTCTGGCCTTGAG
131 GTAGTCGAACTCGAAGGTCTTGGTCACAGATAACCCTTCTAGCCTTGAG
79959 CTAAGCTGCA
Statistics
Matches: 479, Mismatches: 26, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
328 342 0.71
329 4 0.01
330 129 0.27
331 4 0.01
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (328 bp):
CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAGG
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTCTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
GTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAG
CTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACAGA
TAA
Found at i:86483 original size:14 final size:14
Alignment explanation
Indices: 86455--86496 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
86445 TGGACAATTA
*
86455 AAATGAAAATAAAAT
1 AAATAAAAAT-AAAT
*
86470 TAATAAAAATAAAT
1 AAATAAAAATAAAT
86484 AAATAAAAATAAA
1 AAATAAAAATAAA
86497 CAACAACGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:86583 original size:36 final size:37
Alignment explanation
Indices: 86536--86612 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
86526 TTCTACAAAC
* *
86536 TATATAATATATA-TTTTCAAAA-GTATTTTAAAATTA
1 TATATAATATATATTTTTAAAAACGT-TTTCAAAATTA
*
86572 TATATTATATATATTTTTAAAAACGTTTTCAAAATTA
1 TATATAATATATATTTTTAAAAACGTTTTCAAAATTA
86609 TATA
1 TATA
86613 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 12 0.33
37 22 0.61
38 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (37 bp):
TATATAATATATATTTTTAAAAACGTTTTCAAAATTA
Found at i:86792 original size:35 final size:36
Alignment explanation
Indices: 86716--86866 Score: 151
Period size: 36 Copynumber: 4.1 Consensus size: 36
86706 TTTAAAAAAT
* **
86716 TATATTTATTTTAAAAATGTTTTTTAAAACCGTATAA
1 TATATTTATTTTAAAAATG-TTTTAAAAACTATATAA
* * *
86753 TATATTT-TCTTAAAAACGTTTTAAAAACTATATAT
1 TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
* *
86788 TATATTTATTTTCAAAGTGTTTTAAAAACTATATAA
1 TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
** * * *
86824 TATATAGATGTTTCAAATATGTTTTCAAAACTATATTA
1 TATATTTAT-TTT-AAAAATGTTTTAAAAACTATATAA
86862 TATAT
1 TATAT
86867 ATATGTATAT
Statistics
Matches: 93, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
35 20 0.22
36 39 0.42
37 10 0.11
38 24 0.26
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (36 bp):
TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
Found at i:86815 original size:36 final size:36
Alignment explanation
Indices: 86629--86868 Score: 143
Period size: 35 Copynumber: 6.6 Consensus size: 36
86619 AAAATGTTTT
* *
86629 TTTTTAAAACTATATATTATAAGTT-TTTT-AAAATG
1 TTTTAAAAACTATATATTAT-ATTTATTTTAAAAATG
* * * * * *
86664 ATTTCAAAACTATATAATATATATGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATTTATTTTAAAAATG
**
86700 TTTCTTTTTAAA--A-A-ATTATATTTATTTTAAAAATG
1 --T-TTTAAAAACTATATATTATATTTATTTTAAAAATG
* ** * * *
86735 TTTTTTAAAACCGTATAATATATTT-TCTTAAAAACG
1 -TTTTAAAAACTATATATTATATTTATTTTAAAAATG
* *
86771 TTTTAAAAACTATATATTATATTTATTTTCAAAGTG
1 TTTTAAAAACTATATATTATATTTATTTTAAAAATG
* ** *
86807 TTTTAAAAACTATATAATATATAGATGTTTCAAATATG
1 TTTTAAAAACTATATATTATATTTAT-TTT-AAAAATG
*
86845 TTTTCAAAACTATATTATATATAT
1 TTTTAAAAACTATA-TAT-TATAT
86869 ATGTATATAC
Statistics
Matches: 158, Mismatches: 33, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
33 7 0.04
34 4 0.03
35 58 0.37
36 47 0.30
37 12 0.08
38 17 0.11
39 8 0.05
40 5 0.03
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.47
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATTTATTTTAAAAATG
Found at i:86856 original size:38 final size:37
Alignment explanation
Indices: 86629--86872 Score: 140
Period size: 36 Copynumber: 6.8 Consensus size: 37
86619 AAAATGTTTT
* * *
86629 TTTTTAAAACTATAT-AT-TATA-AGTTTTTTAAAATG
1 TTTTAAAAACTATATAATATATATA-TGTTTCAAAATG
* * *
86664 ATTTCAAAACTATATAATATATATGT-TTTCAAAATG
1 TTTTAAAAACTATATAATATATATATGTTTCAAAATG
*
86700 TTTCTTTTTAAAAA--AT-T-ATAT-T-TAT-TTTAAAAATG
1 -----TTTTAAAAACTATATAATATATATATGTTTCAAAATG
* ** * *
86735 TTTTTTAAAACCGTATAATATAT-T-T-TCTTAAAAACG
1 -TTTTAAAAACTATATAATATATATATGT-TTCAAAATG
* * *
86771 TTTTAAAAACTATATATTATATTTAT-TTTCAAAGTG
1 TTTTAAAAACTATATAATATATATATGTTTCAAAATG
*
86807 TTTTAAAAACTATATAATATATAGATGTTTCAAATATG
1 TTTTAAAAACTATATAATATATATATGTTTCAAA-ATG
* *
86845 TTTTCAAAACTATATTATATATATATGT
1 TTTTAAAAACTATATAATATATATATGT
86873 ATATACAAAA
Statistics
Matches: 166, Mismatches: 25, Indels: 33
0.74 0.11 0.15
Matches are distributed among these distances:
31 9 0.05
33 1 0.01
34 1 0.01
35 48 0.29
36 52 0.31
37 18 0.11
38 28 0.17
39 2 0.01
41 7 0.04
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (37 bp):
TTTTAAAAACTATATAATATATATATGTTTCAAAATG
Found at i:91984 original size:22 final size:22
Alignment explanation
Indices: 91954--92005 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
91944 AAAAATTCAA
* * *
91954 TTCGACCACACGTTGTTTGGTG
1 TTCGGCCACACGTCGTTTAGTG
*
91976 TTCGGCCACATGTCGTTTAGTG
1 TTCGGCCACACGTCGTTTAGTG
*
91998 TTCAGCCA
1 TTCGGCCA
92006 ATTAATGGCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (22 bp):
TTCGGCCACACGTCGTTTAGTG
Found at i:92747 original size:32 final size:33
Alignment explanation
Indices: 92707--92773 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 33
92697 AATTAAAATA
*
92707 CAATTTAAAAATATATTAATATAATTTTCATAT
1 CAATTAAAAAATATATTAATATAATTTTCATAT
92740 CAATTAAAAAAATATATTAATATAATTTTCATAT
1 CAATT-AAAAAATATATTAATATAATTTTCATAT
92774 GAATATGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 5 0.16
34 27 0.84
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (33 bp):
CAATTAAAAAATATATTAATATAATTTTCATAT
Found at i:92773 original size:17 final size:17
Alignment explanation
Indices: 92719--92779 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
92709 ATTTAAAAAT
92719 ATATTAATATAATTTTC
1 ATATTAATATAATTTTC
* * ***
92736 ATATCAATTAAAAAAAT-
1 ATATTAA-TATAATTTTC
92753 ATATTAATATAATTTTC
1 ATATTAATATAATTTTC
*
92770 ATATGAATAT
1 ATATTAATAT
92780 GTTAAAATTT
Statistics
Matches: 31, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
16 5 0.16
17 21 0.68
18 5 0.16
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (17 bp):
ATATTAATATAATTTTC
Found at i:98657 original size:21 final size:21
Alignment explanation
Indices: 98633--98682 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
98623 ACTGGTATAT
98633 TGTATAATCTCATTAGTTGAC
1 TGTATAATCTCATTAGTTGAC
98654 TGTATAATCTCATTAGTTGAC
1 TGTATAATCTCATTAGTTGAC
98675 TGTATAAT
1 TGTATAAT
98683 ATTCACACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (21 bp):
TGTATAATCTCATTAGTTGAC
Found at i:100107 original size:19 final size:19
Alignment explanation
Indices: 100067--100107 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
100057 TTTATTAAAT
* *
100067 AATATAATTTAAAAAATCA
1 AATAAAATTTAAAAAATAA
*
100086 AATAAAATTTAAATAATAA
1 AATAAAATTTAAAAAATAA
100105 AAT
1 AAT
100108 GATATTCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAAAATTTAAAAAATAA
Found at i:107314 original size:42 final size:43
Alignment explanation
Indices: 107233--107314 Score: 96
Period size: 42 Copynumber: 1.9 Consensus size: 43
107223 AATGAAAGAT
* *
107233 CTTTCGATGAAAATGACTTAACTTTTTGATTAAAAGATTTCTC
1 CTTTCGATGAAAATGACTTAACTTTTTCATGAAAAGATTTCTC
* * *
107276 CTTTTGATGAAAA-GGCTTAA-TATTTTCATGAAAGGATTT
1 CTTTCGATGAAAATGACTTAACT-TTTTCATGAAAAGATTT
107315 AATCTTTTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
41 1 0.03
42 20 0.61
43 12 0.36
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (43 bp):
CTTTCGATGAAAATGACTTAACTTTTTCATGAAAAGATTTCTC
Found at i:113083 original size:12 final size:13
Alignment explanation
Indices: 113066--113098 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
113056 ATGGGCAAAA
*
113066 TTTGAAAACTAT-
1 TTTGAAAACAATG
113078 TTTGAAAACAATG
1 TTTGAAAACAATG
113091 TTTGAAAA
1 TTTGAAAA
113099 ATCATAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:113156 original size:18 final size:17
Alignment explanation
Indices: 113135--113171 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
113125 AACAACATAA
113135 TTAAATAAAAAAACAATT
1 TTAAA-AAAAAAACAATT
*
113153 TTAAAAATAAAACAATT
1 TTAAAAAAAAAACAATT
113170 TT
1 TT
113172 TTATTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAAAAAAAACAATT
Found at i:113591 original size:21 final size:20
Alignment explanation
Indices: 113566--113623 Score: 89
Period size: 21 Copynumber: 2.9 Consensus size: 20
113556 AAAAACCCGA
113566 TGGGTGTATCGGTACACCTG
1 TGGGTGTATCGGTACACCTG
113586 TGGGGTGTATCGGTACACCTG
1 T-GGGTGTATCGGTACACCTG
* *
113607 TGAGTGTATCGATACAC
1 TGGGTGTATCGGTACAC
113624 ATTCAAGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.43
21 20 0.57
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (20 bp):
TGGGTGTATCGGTACACCTG
Found at i:122389 original size:116 final size:118
Alignment explanation
Indices: 122184--122395 Score: 297
Period size: 117 Copynumber: 1.8 Consensus size: 118
122174 TTTCAAATCG
* * *
122184 AAAATTTCTTTTTCAATACTCTCAAAATTTATTTTTGAGAGCTTTAAATCCTTCTTCAATATTTC
1 AAAATTTCTTTTTCAATACTCTCAAAATTTATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTC
122249 ATTTTGATTTTCAAAATCCATTTTAG-TTTCTAGAAAAAGTTTGTTTAATTCA
66 ATTTTGATTTTCAAAATCCATTTTAGCTTTCTAGAAAAAGTTTGTTTAATTCA
* * *
122301 AAAATTTCTTTTTCAA-AGTTTTC-AAATTTCATTTTTGAAAGCTCTAACTCCTT-TTCAACATT
1 AAAATTTCTTTTTCAATA-CTCTCAAAATTT-ATTTTTGAAAGCTCTAAATCCTTCTTCAACATT
* * *
122363 TCATTTTGATTTTCCAAGTCTATTTTAGCTTTC
64 TCATTTTGATTTTCAAAATCCATTTTAGCTTTC
122396 AAAAGAAGAT
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
116 40 0.48
117 43 0.52
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (118 bp):
AAAATTTCTTTTTCAATACTCTCAAAATTTATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTC
ATTTTGATTTTCAAAATCCATTTTAGCTTTCTAGAAAAAGTTTGTTTAATTCA
Found at i:124796 original size:7 final size:7
Alignment explanation
Indices: 124786--124817 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
124776 AACTTGTGTG
124786 TTGTAAC
1 TTGTAAC
124793 TTGTAAC
1 TTGTAAC
*
124800 TTATAAC
1 TTGTAAC
124807 TTGTAAC
1 TTGTAAC
124814 TTGT
1 TTGT
124818 GTGTAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (7 bp):
TTGTAAC
Found at i:124853 original size:15 final size:15
Alignment explanation
Indices: 124833--124863 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
124823 ATTGTGCCTA
124833 AACTAGCCTATATAT
1 AACTAGCCTATATAT
124848 AACTAGCCTATATAT
1 AACTAGCCTATATAT
124863 A
1 A
124864 GCGAGAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (15 bp):
AACTAGCCTATATAT
Found at i:125157 original size:21 final size:21
Alignment explanation
Indices: 125131--125172 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
125121 GAGGTTAAGA
*
125131 CCTTTTGATGGAAAAACTTCT
1 CCTTTTGATGAAAAAACTTCT
*
125152 CCTTTTGATTAAAAAACTTCT
1 CCTTTTGATGAAAAAACTTCT
125173 TTTGATGAAA
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:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (21 bp):
CCTTTTGATGAAAAAACTTCT
Found at i:125219 original size:21 final size:21
Alignment explanation
Indices: 125170--125223 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
125160 TTAAAAAACT
* *
125170 TCTTTTGATGAAAGGGTTTAA
1 TCTTTTCATGAAAGGATTTAA
125191 TC-TTTCATGAAAGGATTTAA
1 TCTTTTCATGAAAGGATTTAA
125211 TCTTTTCATGAAA
1 TCTTTTCATGAAA
125224 AGAGTTGTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (21 bp):
TCTTTTCATGAAAGGATTTAA
Found at i:126675 original size:33 final size:33
Alignment explanation
Indices: 126633--126697 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
126623 GAAAGCGTTA
126633 AATATGGTTACAGGTTAGTCGTTAGCTGTATTG
1 AATATGGTTACAGGTTAGTCGTTAGCTGTATTG
*
126666 AATATGGTTACAGGTTAGTTGTTAGCTGTATT
1 AATATGGTTACAGGTTAGTCGTTAGCTGTATT
126698 CTTTTTCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.42
Consensus pattern (33 bp):
AATATGGTTACAGGTTAGTCGTTAGCTGTATTG
Found at i:131339 original size:22 final size:22
Alignment explanation
Indices: 131311--131353 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
131301 AGCAGGTTCG
*
131311 TACATACATATACATATATACA
1 TACATACATACACATATATACA
*
131333 TACATACATACATATATATAC
1 TACATACATACACATATATAC
131354 TTAGATCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.33
Consensus pattern (22 bp):
TACATACATACACATATATACA
Found at i:134821 original size:2 final size:2
Alignment explanation
Indices: 134814--134849 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
134804 TATTTTCGAG
134814 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
134850 CATAATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:140064 original size:32 final size:32
Alignment explanation
Indices: 140028--140135 Score: 83
Period size: 32 Copynumber: 3.2 Consensus size: 32
140018 GCACAAGGGC
140028 TTCTACTCTCTTTATACTGGAACAATACCAGT
1 TTCTACTCTCTTTATACTGGAACAATACCAGT
** * * * * * *
140060 TTCTACTCATGATAAAATTAGTG-CCAGAAAGCAGGT
1 TTCTACTC-TCTTTATACT-G-GAACA-ATACCA-GT
*
140096 ATCTACTCTCTTTATACTGGAACAATACCAGT
1 TTCTACTCTCTTTATACTGGAACAATACCAGT
140128 TTCTACTC
1 TTCTACTC
140136 ATGATAAAAT
Statistics
Matches: 52, Mismatches: 18, Indels: 12
0.63 0.22 0.15
Matches are distributed among these distances:
32 17 0.33
33 10 0.19
34 6 0.12
35 10 0.19
36 9 0.17
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (32 bp):
TTCTACTCTCTTTATACTGGAACAATACCAGT
Found at i:140138 original size:68 final size:68
Alignment explanation
Indices: 140029--140167 Score: 278
Period size: 68 Copynumber: 2.0 Consensus size: 68
140019 CACAAGGGCT
140029 TCTACTCTCTTTATACTGGAACAATACCAGTTTCTACTCATGATAAAATTAGTGCCAGAAAGCAG
1 TCTACTCTCTTTATACTGGAACAATACCAGTTTCTACTCATGATAAAATTAGTGCCAGAAAGCAG
140094 GTA
66 GTA
140097 TCTACTCTCTTTATACTGGAACAATACCAGTTTCTACTCATGATAAAATTAGTGCCAGAAAGCAG
1 TCTACTCTCTTTATACTGGAACAATACCAGTTTCTACTCATGATAAAATTAGTGCCAGAAAGCAG
140162 GTA
66 GTA
140165 TCT
1 TCT
140168 TCTTGTATAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (68 bp):
TCTACTCTCTTTATACTGGAACAATACCAGTTTCTACTCATGATAAAATTAGTGCCAGAAAGCAG
GTA
Found at i:140217 original size:19 final size:19
Alignment explanation
Indices: 140193--140230 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
140183 TACCTCTTTT
*
140193 GAATCTCTTGTACTCCCCA
1 GAATCTCTTCTACTCCCCA
140212 GAATCTCTTCTACTCCCCA
1 GAATCTCTTCTACTCCCCA
140231 TATCAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.39, G:0.08, T:0.32
Consensus pattern (19 bp):
GAATCTCTTCTACTCCCCA
Found at i:142449 original size:249 final size:250
Alignment explanation
Indices: 142011--142611 Score: 947
Period size: 249 Copynumber: 2.4 Consensus size: 250
142001 TTCTTGATTC
* *
142011 GTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTA
1 GTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
* * * *
142076 AGCCTTTCGAGCCAGATGATAAGTCCTTTGGGCCACCCGTCAAACCTTTGGGTAGGATGTTTACC
66 AGCCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACA
*
142141 TATGATTTTCACATGAAAATGAGAAAACAATTTTCAAAGTTTCTCATTTAATGTTCAAGAAAATG
131 TATGATTTTCACATGAAAATGAGAAAACAATTTTCAAAGCTTCTCATTTAATGTTCAAGAAAATG
*
142206 AAATTTTTGAAAAGTAAGAAG-TTTCTTACCTAGTAAATTATTTCGCACAAATTT
196 AAATTTTTGAAAAGTAAGAAGTTTTCTTACCTAGTAAATTATTTCCCACAAATTT
** * *
142260 GTAAATCCTTCGGGTCATCAATAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGATCATCTGTA
1 GTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
* *
142325 AGCCTTTCGAACTAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACA
66 AGCCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACA
*
142390 TATGATTTTCGCATGAAAATGAGAAAGAC-ATTTTCAAAGCTTCTCATTTAATGTTCAAGAAAAT
131 TATGATTTTCACATGAAAATGAGAAA-ACAATTTTCAAAGCTTCTCATTTAATGTTCAAGAAAAT
* *
142454 GAAATTTTTGAAAAGTAATAAGTTTTTTTACCTAGTAAATTATTTCCCACAAATTT
195 GAAATTTTTGAAAAGTAAGAAGTTTTCTTACCTAGTAAATTATTTCCCACAAATTT
* * * *
142510 GTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCCA-GATGTTTAAATCCTTAGGGTCATCTAT
1 GTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAG-CATGATGCTTAAATCCTTCGGGTCATCTGT
* *
142574 TAGTCTTTCGAGCAAGATGAATAAGTCCTTAGGGCCAT
65 AAGCCTTTCGAGCAAGATG-ATAAGTCCTTAGGGCCAT
142612 TTGTAAGACC
Statistics
Matches: 320, Mismatches: 28, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
249 199 0.62
250 101 0.32
251 20 0.06
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (250 bp):
GTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
AGCCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTCAAACCTTTGGGTAGGATGTTTACA
TATGATTTTCACATGAAAATGAGAAAACAATTTTCAAAGCTTCTCATTTAATGTTCAAGAAAATG
AAATTTTTGAAAAGTAAGAAGTTTTCTTACCTAGTAAATTATTTCCCACAAATTT
Found at i:142570 original size:42 final size:42
Alignment explanation
Indices: 142511--142607 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
142501 CACAAATTTG
* * * **
142511 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCCAGATGTT
1 TAAATCCTTAGGGTCATCTATCAGTCTTTCGAGCAAGATGAA
*
142553 TAAATCCTTAGGGTCATCTATTAGTCTTTCGAGCAAGATGAA
1 TAAATCCTTAGGGTCATCTATCAGTCTTTCGAGCAAGATGAA
*
142595 TAAGTCCTTAGGG
1 TAAATCCTTAGGG
142608 CCATTTGTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (42 bp):
TAAATCCTTAGGGTCATCTATCAGTCTTTCGAGCAAGATGAA
Found at i:142789 original size:3 final size:3
Alignment explanation
Indices: 142781--142833 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
142771 CTAATTATAT
* * * *
142781 TTA TTA TTA TTA TTA TTA CTA CTA TTA TTA TAA TAA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
142828 TTA TTA
1 TTA TTA
142834 CAAATAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:150363 original size:20 final size:19
Alignment explanation
Indices: 150330--150418 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 19
150320 TTTTCCAAAT
*
150330 TCGCTACGTGAATATGTAAA
1 TCGCAACGT-AATATGTAAA
150350 TCGCAACGATAATATGTAAA
1 TCGCAACG-TAATATGTAAA
* *
150370 TCGCAACGTGAAGAGGTAAA
1 TCGCAACGT-AATATGTAAA
*
150390 TCGCAACGCGAATATGTAAA
1 TCGCAACG-TAATATGTAAA
150410 TTCGCAACG
1 -TCGCAACG
150419 CGATTTTCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.02
20 49 0.83
21 9 0.15
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.22
Consensus pattern (19 bp):
TCGCAACGTAATATGTAAA
Found at i:150389 original size:40 final size:41
Alignment explanation
Indices: 150326--150418 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 41
150316 GCGATTTTCC
* * * *
150326 AAATTCGCTACGTGAATATGTAAATCGCAACGATAATATGT
1 AAATTCGCAACGTGAAGAGGTAAATCGCAACGAGAATATGT
*
150367 AAA-TCGCAACGTGAAGAGGTAAATCGCAACGCGAATATGT
1 AAATTCGCAACGTGAAGAGGTAAATCGCAACGAGAATATGT
150407 AAATTCGCAACG
1 AAATTCGCAACG
150419 CGATTTTCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 35 0.76
41 11 0.24
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (41 bp):
AAATTCGCAACGTGAAGAGGTAAATCGCAACGAGAATATGT
Found at i:150416 original size:21 final size:20
Alignment explanation
Indices: 150339--150421 Score: 112
Period size: 20 Copynumber: 4.1 Consensus size: 20
150329 TTCGCTACGT
*
150339 GAATATGTAAATCGCAACGA
1 GAATATGTAAATCGCAACGC
* *
150359 TAATATGTAAATCGCAACGT
1 GAATATGTAAATCGCAACGC
* *
150379 GAAGAGGTAAATCGCAACGC
1 GAATATGTAAATCGCAACGC
150399 GAATATGTAAATTCGCAACGC
1 GAATATGTAAA-TCGCAACGC
150420 GA
1 GA
150422 TTTTCAAATC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
20 43 0.80
21 11 0.20
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (20 bp):
GAATATGTAAATCGCAACGC
Found at i:150527 original size:57 final size:57
Alignment explanation
Indices: 150411--150558 Score: 188
Period size: 57 Copynumber: 2.6 Consensus size: 57
150401 ATATGTAAAT
* * **
150411 TCGCAACGCGATTTTCAAATCCGCAACGCCAATTACCGATATAGGTAAACAGTACTA
1 TCGCAACACGATTTTCAAATTCGCAACGCCAATTACCGATATAGGTAAACACAACTA
* * *
150468 TCGTAACACGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAATTA
1 TCGCAACACGATTTTCAAATTCGCAACGCCAATTACCGATATAGGTAAACACAACTA
* *** *
150525 TCGCAACGCGATTTTCGTTTTCGCAACGCGAATT
1 TCGCAACACGATTTTCAAATTCGCAACGCCAATT
150559 TCGCAAATCG
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 78 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (57 bp):
TCGCAACACGATTTTCAAATTCGCAACGCCAATTACCGATATAGGTAAACACAACTA
Found at i:150935 original size:20 final size:20
Alignment explanation
Indices: 150910--150958 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
150900 TCGGTAATTA
150910 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
*
150930 GCGTTGCGAATTTGAAAATT
1 GCGTTGCGAATTTGAAAATC
150950 GCGTTGCGA
1 GCGTTGCGA
150959 TAGTACTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:150972 original size:77 final size:77
Alignment explanation
Indices: 150855--151015 Score: 277
Period size: 77 Copynumber: 2.1 Consensus size: 77
150845 TGAAAATAAA
* * *
150855 GTTGCGAATTTAAAAATCGCGTTGCGATAGTAGTGTTTACCTATGTCGGTAATTAGCGTTGCGAA
1 GTTGCGAATTTAAAAATCGCGTTGCGATAGTACTATTTACCTATATCGGTAATTAGCGTTGCGAA
150920 TTTGAAAATCGC
66 TTTGAAAATCGC
* *
150932 GTTGCGAATTTGAAAATTGCGTTGCGATAGTACTATTTACCTATATCGGTAATTAGCGTTGCGAA
1 GTTGCGAATTTAAAAATCGCGTTGCGATAGTACTATTTACCTATATCGGTAATTAGCGTTGCGAA
150997 TTTGAAAATCGC
66 TTTGAAAATCGC
151009 GTTGCGA
1 GTTGCGA
151016 TAGTACTGTT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.34
Consensus pattern (77 bp):
GTTGCGAATTTAAAAATCGCGTTGCGATAGTACTATTTACCTATATCGGTAATTAGCGTTGCGAA
TTTGAAAATCGC
Found at i:150991 original size:57 final size:57
Alignment explanation
Indices: 150930--151072 Score: 259
Period size: 57 Copynumber: 2.5 Consensus size: 57
150920 TTTGAAAATC
*
150930 GCGTTGCGAATTTGAAAATTGCGTTGCGATAGTACTATTTACCTATATCGGTAATTA
1 GCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACCTATATCGGTAATTA
*
150987 GCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTA
1 GCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACCTATATCGGTAATTA
*
151044 GCGTTGCGGATTTGAAAATCGCGTTGCGA
1 GCGTTGCGAATTTGAAAATCGCGTTGCGA
151073 ATTTACATAT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 83 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (57 bp):
GCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACCTATATCGGTAATTA
Found at i:151098 original size:20 final size:20
Alignment explanation
Indices: 151062--151156 Score: 118
Period size: 20 Copynumber: 4.7 Consensus size: 20
151052 GATTTGAAAA
151062 TCGCGTTGCGAATTTACATAT
1 TCGCGTTGCG-ATTTACATAT
*
151083 TTGCGTTGCGATTTACATAT
1 TCGCGTTGCGATTTACATAT
*
151103 TCGTGTTGCGATTTACATAT
1 TCGCGTTGCGATTTACATAT
** * * *
151123 TATCTTTTCGATTTACTTAT
1 TCGCGTTGCGATTTACATAT
151143 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
151157 TGGAACCTGT
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
20 52 0.85
21 9 0.15
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (20 bp):
TCGCGTTGCGATTTACATAT
Found at i:152350 original size:20 final size:20
Alignment explanation
Indices: 152308--152351 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
152298 ATAACAACTA
* *
152308 ATTTACGGTACGACTGCATT
1 ATTTACGGTACGACTGAAAT
* *
152328 ATTTACGGTACGAGTTAAAT
1 ATTTACGGTACGACTGAAAT
152348 ATTT
1 ATTT
152352 GAATTAACAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTACGGTACGACTGAAAT
Done.