Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009287.1 Hibiscus syriacus cultivar Beakdansim tig00112980_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: 362425
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 2
Found at i:1456 original size:1 final size:1
Alignment explanation
Indices: 1450--1497 Score: 78
Period size: 1 Copynumber: 48.0 Consensus size: 1
1440 ATGCTTGAAG
* *
1450 AAAAAAAAAAAAAAAAAAAAGAGAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1498 GAAGAAGAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:1475 original size:23 final size:23
Alignment explanation
Indices: 1448--1492 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1438 TTATGCTTGA
1448 AGAAAAAAAAAAAAAAAAAAAAG
1 AGAAAAAAAAAAAAAAAAAAAAG
1471 AGAAAAAAAAAAAAAAAAAAAA
1 AGAAAAAAAAAAAAAAAAAAAA
1493 AAAAAGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (23 bp):
AGAAAAAAAAAAAAAAAAAAAAG
Found at i:1486 original size:26 final size:26
Alignment explanation
Indices: 1450--1518 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
1440 ATGCTTGAAG
*
1450 AAAAAAAAAAAAAAAAAAAAGAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAGAAA
*
1476 AAAAAAAAAAAAAAAAAAAAAAGAAG
1 AAAAAAAAAAAAAAAAAAAAAAGAAA
* * *
1502 AAGAAGAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAA
1519 GGGGTCAAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAAAAAAAAAAAAAAGAAA
Found at i:1490 original size:28 final size:29
Alignment explanation
Indices: 1450--1518 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
1440 ATGCTTGAAG
1450 AAAAAAAAAAAAAAAAAAAAG-AGAAAAA
1 AAAAAAAAAAAAAAAAAAAAGAAGAAAAA
*
1478 AAAAAAAAAAAAAAAAAAAAGAAGAAGAA
1 AAAAAAAAAAAAAAAAAAAAGAAGAAAAA
* *
1507 GAAAAGAAAAAA
1 AAAAAAAAAAAA
1519 GGGGTCAAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 21 0.57
29 16 0.43
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAAAAAAAAAAAGAAGAAAAA
Found at i:2690 original size:52 final size:52
Alignment explanation
Indices: 2460--2921 Score: 774
Period size: 52 Copynumber: 9.0 Consensus size: 52
2450 TATGTGCTCA
2460 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
2511 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
*
2562 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG-A-
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
2612 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
* *
2664 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
* * *
2716 ATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
* * *
2768 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAAAAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
*
2820 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG-A-
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
* *
2870 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
2922 CAATCATTGA
Statistics
Matches: 392, Mismatches: 14, Indels: 9
0.94 0.03 0.02
Matches are distributed among these distances:
50 94 0.24
51 100 0.26
52 198 0.51
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
Found at i:3027 original size:50 final size:50
Alignment explanation
Indices: 2952--3092 Score: 282
Period size: 50 Copynumber: 2.8 Consensus size: 50
2942 TGAATTTGCC
2952 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
3002 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
3052 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
3093 GTTTGGTAAG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:3988 original size:118 final size:117
Alignment explanation
Indices: 3745--4390 Score: 1040
Period size: 118 Copynumber: 5.6 Consensus size: 117
3735 CATCATTTGG
*
3745 TGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
1 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAAG
*
3810 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATCGCCAGA
65 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAGA
3863 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAAGA
1 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGA
*
3926 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATCGCCAGA
66 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAGA
3978 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAAGA
1 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGA
* **
4041 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGA
66 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAGA
*
4093 TGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
1 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAAG
*
4158 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAAA
65 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAGA
4211 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
1 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAAG
* ****
4276 AAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGA
65 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAGA
* ** *
4329 TGGAACATCATCCCCAGCAG-AA-AGTTCATAATGAGAAGAA-C-TCATCTGAAGAA-AAAGAAG
1 TGGATCATCATTTCCAG-AGAAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAG
4389 AA
65 AA
4391 TTTATTCAAT
Statistics
Matches: 503, Mismatches: 21, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
113 8 0.02
114 12 0.02
115 225 0.45
116 1 0.00
117 19 0.04
118 236 0.47
119 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (117 bp):
TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAGA
Found at i:4157 original size:233 final size:232
Alignment explanation
Indices: 3745--4390 Score: 1077
Period size: 233 Copynumber: 2.8 Consensus size: 232
3735 CATCATTTGG
*
3745 TGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
1 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAAG
* * **
3810 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATCGCCAGATGGATCATCATT
65 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATT
3875 TCCAGAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
130 TCCAGAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* *
3940 AGAACTTGTTCAACCTTTTGTTTGAATTCATCGCCAGA
195 AGAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAAA
3978 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAAGA
1 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGA
*
4041 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAACATTT
66 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTT
4106 CCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
131 CCAGAGAAAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
4171 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAAA
193 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAAA
4211 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
1 TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGGAAGAAG
* * * *
4276 AAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGAACATCATC
65 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATT
* *
4341 CCCAGCAG-AA-AGTTCATAATGAGAAGAACTCATCTGAAGAA-AAAGAAGAA
130 TCCAG-AGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
4391 TTTATTCAAT
Statistics
Matches: 391, Mismatches: 15, Indels: 16
0.93 0.04 0.04
Matches are distributed among these distances:
230 109 0.28
231 9 0.02
232 13 0.03
233 153 0.39
235 19 0.05
236 86 0.22
237 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (232 bp):
TGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTT
CCAGAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTTTTGCTTGAATTCATCGCCAAA
Found at i:4538 original size:3 final size:3
Alignment explanation
Indices: 4530--4603 Score: 103
Period size: 3 Copynumber: 24.0 Consensus size: 3
4520 TATCCATATC
* *
4530 ATT ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
*
4576 ATT ATT ATT ATT AAT ATT ATAT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT
4604 TAATAAATAA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
3 58 0.92
4 5 0.08
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5965 original size:20 final size:21
Alignment explanation
Indices: 5919--5965 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
5909 CCACTTTTAA
5919 ATATATTGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
5940 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
5959 ATATATT
1 ATATATT
5966 TAAATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:7409 original size:33 final size:32
Alignment explanation
Indices: 7342--7416 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
7332 AAAAGTTTAA
** *
7342 TAATATATAAATCATTAATTTTTTAATTATTT
1 TAATATATAAATCATTAATTTTTTAAAAAATT
*
7374 TAATATATAAA-CTTTTAATTTTTTTAAAAAATT
1 TAATATATAAATC-ATTAA-TTTTTTAAAAAATT
7407 TAATAT-TAAA
1 TAATATATAAA
7417 ATTTGAATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 1 0.03
32 19 0.51
33 17 0.46
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (32 bp):
TAATATATAAATCATTAATTTTTTAAAAAATT
Found at i:8155 original size:21 final size:20
Alignment explanation
Indices: 8127--8165 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
8117 AATTTACTGC
*
8127 TTAACTCGACTCGTTGCTTG
1 TTAACTCGACTCATTGCTTG
8147 TTAAGCTCGACTCATTGCT
1 TTAA-CTCGACTCATTGCT
8166 CATTAAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (20 bp):
TTAACTCGACTCATTGCTTG
Found at i:8171 original size:21 final size:21
Alignment explanation
Indices: 8127--8172 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
8117 AATTTACTGC
* **
8127 TTAA-CTCGACTCGTTGCTTG
1 TTAAGCTCGACTCATTGCTCA
8147 TTAAGCTCGACTCATTGCTCA
1 TTAAGCTCGACTCATTGCTCA
8168 TTAAG
1 TTAAG
8173 ATTTCTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (21 bp):
TTAAGCTCGACTCATTGCTCA
Found at i:8322 original size:20 final size:20
Alignment explanation
Indices: 8299--8361 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
8289 ATTATTTTTG
8299 TATATTTTAAATTAAAATAA
1 TATATTTTAAATTAAAATAA
*
8319 TATATGTTAAATTAAAATAA
1 TATATTTTAAATTAAAATAA
* *
8339 TATATGTTTAAGTTTAAATAA
1 TATAT-TTTAAATTAAAATAA
8360 TA
1 TA
8362 AAAGAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
TATATTTTAAATTAAAATAA
Found at i:8849 original size:20 final size:20
Alignment explanation
Indices: 8826--8865 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
8816 TCATTATTTG
8826 TTGTATCATGGGACATAAAT
1 TTGTATCATGGGACATAAAT
*
8846 TTGTATCATGGGAGATAAAT
1 TTGTATCATGGGACATAAAT
8866 GAAAAACGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (20 bp):
TTGTATCATGGGACATAAAT
Found at i:14918 original size:19 final size:19
Alignment explanation
Indices: 14896--14946 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
14886 AGGTTTTTGT
14896 ATTAATTTTTAGT-TTTTAA
1 ATTAATTTTTA-TATTTTAA
*
14915 ATTAATATTTATATTTTAA
1 ATTAATTTTTATATTTTAA
*
14934 AAT-ATTTTTATAT
1 ATTAATTTTTATAT
14947 CAATCCTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTAATTTTTATATTTTAA
Found at i:17272 original size:29 final size:29
Alignment explanation
Indices: 17239--17295 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
17229 AACATAAATG
*
17239 AATAGTCGAGTGACCATTT-TATAACTTTT
1 AATAGTCGAGGGACCATTTGTAT-ACTTTT
17268 AATAGTCGAGGGACCATTTGTATACTTT
1 AATAGTCGAGGGACCATTTGTATACTTT
17296 ACCCAATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (29 bp):
AATAGTCGAGGGACCATTTGTATACTTTT
Found at i:32927 original size:33 final size:33
Alignment explanation
Indices: 32890--32958 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
32880 CAACATTAAC
*
32890 ACATTAAACTTGTAGCAGGGAACATCATATACA
1 ACATTAAACTTGTAGCAAGGAACATCATATACA
32923 ACATTAAACTTGTAGCAAGGAACATCATATACA
1 ACATTAAACTTGTAGCAAGGAACATCATATACA
32956 ACA
1 ACA
32959 ACAACAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (33 bp):
ACATTAAACTTGTAGCAAGGAACATCATATACA
Found at i:35599 original size:27 final size:28
Alignment explanation
Indices: 35546--35606 Score: 97
Period size: 27 Copynumber: 2.1 Consensus size: 28
35536 TACACTAATC
35546 ATCACTGTGTGTACAACAACAACAACAATT
1 ATCACTGTGTGT--AACAACAACAACAATT
35576 ATCACTGTGTGT-ACAACAACAACAATT
1 ATCACTGTGTGTAACAACAACAACAATT
35603 ATCA
1 ATCA
35607 ATTACTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 19 0.61
30 12 0.39
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.25
Consensus pattern (28 bp):
ATCACTGTGTGTAACAACAACAACAATT
Found at i:39145 original size:27 final size:27
Alignment explanation
Indices: 39104--39178 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
39094 GTGATCCTAC
39104 ACTTACCACGACAACATCATTAACTCT
1 ACTTACCACGACAACATCATTAACTCT
* * *
39131 ACTTACCATGGCAACGTCATTAACTCT
1 ACTTACCACGACAACATCATTAACTCT
* *
39158 ACTTGCCACGACAACGTCATT
1 ACTTACCACGACAACATCATT
39179 CACTTAATAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.27
Consensus pattern (27 bp):
ACTTACCACGACAACATCATTAACTCT
Found at i:45995 original size:29 final size:29
Alignment explanation
Indices: 45946--46001 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
45936 TGAAATCTGG
*
45946 TCCAACCCTGAAGACATCGAGAGATCTAA
1 TCCAACCCTGAAGACACCGAGAGATCTAA
* *
45975 TCCAACCCTGAAGACGCCGAGATATCT
1 TCCAACCCTGAAGACACCGAGAGATCT
46002 CACACACTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.18
Consensus pattern (29 bp):
TCCAACCCTGAAGACACCGAGAGATCTAA
Found at i:49251 original size:18 final size:20
Alignment explanation
Indices: 49202--49252 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
49192 TTTAATATAC
*
49202 TTATTTT-TTAAAAAATTGA
1 TTATTTTATTAAATAATTGA
49221 TTA-TTTATCTAAATAA-T-A
1 TTATTTTAT-TAAATAATTGA
49239 TTATTTTATTAAAT
1 TTATTTTATTAAAT
49253 TTTTTAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 12 0.43
19 10 0.36
20 6 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TTATTTTATTAAATAATTGA
Found at i:54480 original size:32 final size:32
Alignment explanation
Indices: 54419--54488 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
54409 GATCTGTTTG
* * * *
54419 ATTTAAGTCCCTCAATTGGTAATTTTCGTTCA
1 ATTTTAGTCCCTCAACTGGGAATTCTCGTTCA
*
54451 ATTTTAGTCCCTCAGCTGGGAATTCTCGTTCA
1 ATTTTAGTCCCTCAACTGGGAATTCTCGTTCA
54483 ATTTTA
1 ATTTTA
54489 ATCCTTCGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (32 bp):
ATTTTAGTCCCTCAACTGGGAATTCTCGTTCA
Found at i:55174 original size:45 final size:45
Alignment explanation
Indices: 55087--55220 Score: 162
Period size: 45 Copynumber: 3.0 Consensus size: 45
55077 CAAACTCGAG
* * * *
55087 ACTTTAAAGAATAGCAACA-ATTTTTTACTACTGAGGTGATTTAA
1 ACTTTAAAGAATAACAACATTTTTTTTACTACCGAGATGATTTAA
* * * *
55131 ACTTCAAAGAATAACAACATTTTTTTTACTACCGAAATAATTTAG
1 ACTTTAAAGAATAACAACATTTTTTTTACTACCGAGATGATTTAA
* *
55176 ACTTTAAAGAATAACAATAATTTTTTTTATTACCGAGATGATTTA
1 ACTTTAAAGAATAACAA-CATTTTTTTTACTACCGAGATGATTTA
55221 GTTCGTGCTG
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
44 17 0.23
45 35 0.47
46 23 0.31
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (45 bp):
ACTTTAAAGAATAACAACATTTTTTTTACTACCGAGATGATTTAA
Found at i:59919 original size:196 final size:193
Alignment explanation
Indices: 59588--59977 Score: 712
Period size: 196 Copynumber: 2.0 Consensus size: 193
59578 GATCTACTCT
59588 TACCGAAACTCAAACATGAAATCCTCAGTCTTTCTCACAACCAAACAAACAGCAATCTAAGGAAG
1 TACCGAAACTCAAACATGAAATCCTCAGTCTTTCTCACAACCAAACAAACAGCAATCTAAGGAAG
59653 AAAAACAGTTTTCACTTATTGCTTCCTTACCTCGTGAAGCGTGCCACAAATCAAAACTTCATGAA
66 AAAAACAGTTTTCACTTATTGCTTCCTTACCTCGTGAAGCGTGCCACAAATCAAAACTTCATGAA
59718 GCCGAGAAGAAAGAAAAATTAGAGAGATTA-GAAGGAAATCGAAAGGATCTGAGAAGGAAGAAG
131 GCCGAGAAG-AAGAAAAATTAGAGAGATTAGGAAGGAAATCGAAAGGATCTGAGAAGGAAGAAG
59781 TACCGAAACTCAAACATGAAATCCTCAGTCTTTCTCAGCAACCAAACAAACAGCAATCTAAGGAA
1 TACCGAAACTCAAACATGAAATCCTCAGTCTTTCTCA-CAACCAAACAAACAGCAATCTAAGGAA
59846 GAAAAAAACAG-TTTCACTTATTTGCTTCCTTACCTCGTGAAGCGTGCCACAAATCAAAACTTCA
65 G--AAAAACAGTTTTCACTTA-TTGCTTCCTTACCTCGTGAAGCGTGCCACAAATCAAAACTTCA
59910 TGAAGCCGAGAAGAAGAAAAATTAGAGAGATTAGTGAAGGAAATCGAAAGGATCTGAGAAGGAAG
127 TGAAGCCGAGAAGAAGAAAAATTAGAGAGATTAG-GAAGGAAATCGAAAGGATCTGAGAAGGAAG
59975 AAG
191 AAG
59978 ATAGTGAAGA
Statistics
Matches: 191, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
193 37 0.19
194 28 0.15
195 29 0.15
196 64 0.34
197 33 0.17
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.20
Consensus pattern (193 bp):
TACCGAAACTCAAACATGAAATCCTCAGTCTTTCTCACAACCAAACAAACAGCAATCTAAGGAAG
AAAAACAGTTTTCACTTATTGCTTCCTTACCTCGTGAAGCGTGCCACAAATCAAAACTTCATGAA
GCCGAGAAGAAGAAAAATTAGAGAGATTAGGAAGGAAATCGAAAGGATCTGAGAAGGAAGAAG
Found at i:63703 original size:22 final size:22
Alignment explanation
Indices: 63678--63755 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
63668 GGGTATATTA
*
63678 GTCCTTCGGGATGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
63700 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
63722 GTTCTTCGGGACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
63744 GTCTTTTGGGAC
1 GTCCTTCGGGAC
63756 ATAATAGTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.13, C:0.22, G:0.32, T:0.33
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:69059 original size:39 final size:39
Alignment explanation
Indices: 69005--69084 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
68995 TCTTTTAATA
69005 ATTTATATAATATTTAACAAAAGTAACTAAAATCATTAC
1 ATTTATATAATATTTAACAAAAGTAACTAAAATCATTAC
69044 ATTTATATAATATTTAACAAAAGTAACTAAAATCATTAC
1 ATTTATATAATATTTAACAAAAGTAACTAAAATCATTAC
69083 AT
1 AT
69085 GTAGATCAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (39 bp):
ATTTATATAATATTTAACAAAAGTAACTAAAATCATTAC
Found at i:69628 original size:23 final size:23
Alignment explanation
Indices: 69602--69647 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
69592 CTGAATGATT
*
69602 CAGTGTTGAATGATTCAACAAAA
1 CAGTGCTGAATGATTCAACAAAA
69625 CAGTGCTGAATGATTCAACAAAA
1 CAGTGCTGAATGATTCAACAAAA
69648 TAGTACATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (23 bp):
CAGTGCTGAATGATTCAACAAAA
Found at i:69660 original size:23 final size:23
Alignment explanation
Indices: 69608--69653 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
69598 GATTCAGTGT
*
69608 TGAATGATTCAACAAAACAGTGC
1 TGAATGATTCAACAAAACAGTAC
*
69631 TGAATGATTCAACAAAATAGTAC
1 TGAATGATTCAACAAAACAGTAC
69654 ATTATGAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (23 bp):
TGAATGATTCAACAAAACAGTAC
Found at i:71108 original size:32 final size:31
Alignment explanation
Indices: 71058--71117 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
71048 AACTAATATT
*
71058 AATAAATATATTATTCGATATCATTTTTAAAA
1 AATAAATATATTAGTCGATATC-TTTTTAAAA
*
71090 AATAAATAGT-TTAGTCGATTTCTTTTTA
1 AATAAATA-TATTAGTCGATATCTTTTTA
71118 CTTTTTCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 6 0.24
32 18 0.72
33 1 0.04
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (31 bp):
AATAAATATATTAGTCGATATCTTTTTAAAA
Found at i:72146 original size:19 final size:19
Alignment explanation
Indices: 72115--72153 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
72105 ATTTTGGTTG
72115 ATTTAAATTAAATAT-ATT
1 ATTTAAATTAAATATGATT
72133 ATTTAAATTTAAATATGATT
1 ATTTAAA-TTAAATATGATT
72153 A
1 A
72154 CCTAATGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 8 0.42
20 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
ATTTAAATTAAATATGATT
Found at i:72430 original size:18 final size:18
Alignment explanation
Indices: 72396--72429 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
72386 AAATTTGATT
*
72396 AAAAAATAAACTTAAAAC
1 AAAAAATAAAATTAAAAC
72414 AAAAAA-AAAATTAAAA
1 AAAAAATAAAATTAAAA
72430 ATATGAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAAATAAAATTAAAAC
Found at i:84661 original size:31 final size:31
Alignment explanation
Indices: 84623--84778 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
84613 CCCGAAGGAC
* * *
84623 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
84654 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
84685 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
84716 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
84747 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
84778 C
1 C
84779 CCTCGACCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:84982 original size:23 final size:22
Alignment explanation
Indices: 84954--84998 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
84944 CATATCTTGT
*
84954 TTTCACATATATATTTCATATCA
1 TTTCACATACA-ATTTCATATCA
*
84977 TTTCACATACACTTTCATATCA
1 TTTCACATACAATTTCATATCA
84999 CATGCCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTCACATACAATTTCATATCA
Found at i:85625 original size:21 final size:21
Alignment explanation
Indices: 85595--85639 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
85585 ATTCTGCCGT
* *
85595 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
85616 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
85637 TTG
1 TTG
85640 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:88864 original size:21 final size:21
Alignment explanation
Indices: 88835--88887 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
88825 ATTCTGACTA
88835 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
88856 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
88877 TCGCAATGCGA
1 TCGCATTGCGA
88888 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:88902 original size:20 final size:20
Alignment explanation
Indices: 88877--88970 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
88867 TTTTCCTAAT
88877 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
88897 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
88918 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
88938 TCGCAATGCGAATACGTATA
1 TCGCAATGCGAATACGTAAA
88958 TCGCAATGCGAAT
1 TCGCAATGCGAAT
88971 CTGACTATCG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:88950 original size:61 final size:60
Alignment explanation
Indices: 88877--88990 Score: 174
Period size: 61 Copynumber: 1.9 Consensus size: 60
88867 TTTTCCTAAT
*
88877 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCT-GAAAATCGCAATGCGATTACGTAAA
* * **
88938 TCGCAATGCGAATACGTATATCGCAATGCGAATCTGACTATCGCAATGCGATT
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAATCGCAATGCGATT
88991 TACATAGCGT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 16 0.33
61 32 0.67
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAATCGCAATGCGATTACGTAAA
Found at i:88979 original size:20 final size:20
Alignment explanation
Indices: 88877--88988 Score: 111
Period size: 20 Copynumber: 5.5 Consensus size: 20
88867 TTTTCCTAAT
*
88877 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTATA
* ** * *
88897 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTATA
* *
88918 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTATA
88938 TCGCAATGCGAATACGTATA
1 TCGCAATGCGAATACGTATA
88958 TCGCAATGCGAAT-C-TGACTA
1 TCGCAATGCGAATACGT-A-TA
88978 TCGCAATGCGA
1 TCGCAATGCGA
88989 TTTACATAGC
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
18 1 0.01
19 2 0.03
20 60 0.77
21 15 0.19
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTATA
Found at i:89183 original size:22 final size:22
Alignment explanation
Indices: 89158--89219 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 22
89148 GGCGACATCC
89158 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
89180 GTCCCCA----CGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
89198 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
89220 TTCACGGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 16 0.50
22 16 0.50
ACGTcount: A:0.26, C:0.39, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:89592 original size:33 final size:33
Alignment explanation
Indices: 89544--89657 Score: 95
Period size: 40 Copynumber: 3.2 Consensus size: 33
89534 ACTATCGCAA
89544 TGCGATTC-TGTCGTTGCGATTTTCATTTCGCGT
1 TGCGATTCTTG-CGTTGCGATTTTCATTTCGCGT
** *
89577 TGCGATTCTTGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTTGCGTTGCGATTTTC-ATTTCGCGT
* *
89611 TGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGTGT
1 TGCGAT--TC---TT-GCGTTGCGATTTTCA-TTTCGCGT
89651 TGCGATT
1 TGCGATT
89658 TAAAGTTTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
33 19 0.30
34 16 0.25
36 2 0.03
38 1 0.02
39 3 0.05
40 23 0.36
ACGTcount: A:0.13, C:0.18, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTCTTGCGTTGCGATTTTCATTTCGCGT
Found at i:89612 original size:20 final size:20
Alignment explanation
Indices: 89587--89636 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
89577 TGCGATTCTT
89587 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
89607 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
89627 GTGTTGCGAT
1 GCGTTGCGAT
89637 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:89613 original size:34 final size:33
Alignment explanation
Indices: 89544--89616 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
89534 ACTATCGCAA
** *
89544 TGCGATTCTGTCGTTGCGATTTTCATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTCAATTCGCGT
89577 TGCGATTCT-TGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAGTC-AATTCGCGT
89611 TGCGAT
1 TGCGAT
89617 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.40
Consensus pattern (33 bp):
TGCGATTCTGTCGTTGCGATAGTCAATTCGCGT
Found at i:89642 original size:20 final size:20
Alignment explanation
Indices: 89604--89658 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
89594 GATAGTCAAA
* **
89604 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
89624 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
89644 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
89659 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:89666 original size:20 final size:20
Alignment explanation
Indices: 89623--89666 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
89613 CGATAGTCAT
** *
89623 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
89643 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
89663 TTTC
1 TTTC
89667 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:91554 original size:20 final size:20
Alignment explanation
Indices: 91529--91632 Score: 105
Period size: 20 Copynumber: 5.5 Consensus size: 20
91519 AGAATAGTTT
91529 ACTATCGCAATACGAAAATG
1 ACTATCGCAATACGAAAATG
*
91549 ACTATCGC-A-ACG-AGA-G
1 ACTATCGCAATACGAAAATG
91565 A--ATCGCAA-AGCGAAAATG
1 ACTATCGCAATA-CGAAAATG
*
91583 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATACGAAAATG
* **
91603 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATACGAAAATG
91623 ACTATCGCAA
1 ACTATCGCAA
91633 CGAAAGAATC
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
14 5 0.07
15 2 0.03
16 4 0.06
17 4 0.06
18 5 0.07
19 1 0.01
20 51 0.71
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATACGAAAATG
Found at i:91579 original size:34 final size:34
Alignment explanation
Indices: 91532--91653 Score: 129
Period size: 34 Copynumber: 3.4 Consensus size: 34
91522 ATAGTTTACT
*
91532 ATCGCAATA-CGAAAATGACTATCGCAACGAGAGA
1 ATCGCAA-AGCGAAAATGACTATCGCAACGAAAGA
91566 ATCGCAAAGCGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAAAGCGAAAATGACTATCGCAA--CG-AAA-GA
* **
91604 CTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 --ATCGCAAAGCGAAAATGACTATCGCAACGAAAGA
*
91640 ATCGCAATGCGAAA
1 ATCGCAAAGCGAAA
91654 TGAAAATCAC
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
33 1 0.01
34 38 0.50
36 4 0.05
37 5 0.07
38 4 0.05
40 24 0.32
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (34 bp):
ATCGCAAAGCGAAAATGACTATCGCAACGAAAGA
Found at i:91704 original size:20 final size:20
Alignment explanation
Indices: 91679--91765 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
91669 GATTCTCTCG
91679 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
91699 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
91719 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
91739 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
91759 TTGCGAT
1 TTGCGAT
91766 TTTGTTGTTG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:91796 original size:33 final size:34
Alignment explanation
Indices: 91730--91835 Score: 115
Period size: 34 Copynumber: 3.1 Consensus size: 34
91720 TGCGATAGTC
* * *
91730 ATTTTCGCATTGCGATAGTCATTTTCGCGTTGCG
1 ATTTTCTCGTTGCGATAGTCATTTTCGCATTGCG
* * ** *
91764 ATTTTGTTGTTGCGATTTTCA-TTTCGTATTGCG
1 ATTTTCTCGTTGCGATAGTCATTTTCGCATTGCG
* *
91797 ATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCG
1 ATTTTCTCGTTGCGATAGTCATTTTCGCATTGCG
91831 ATTTT
1 ATTTT
91836 AAGTTTCAGA
Statistics
Matches: 55, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
33 26 0.47
34 29 0.53
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (34 bp):
ATTTTCTCGTTGCGATAGTCATTTTCGCATTGCG
Found at i:92407 original size:21 final size:21
Alignment explanation
Indices: 92316--92414 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
92306 GACTCACCTG
*
92316 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
92338 T-ATCGTTCAAGATGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
92358 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
92379 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
*
92400 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
92415 TCTCTCCCAA
Statistics
Matches: 58, Mismatches: 18, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
20 3 0.05
21 54 0.93
22 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:92413 original size:42 final size:42
Alignment explanation
Indices: 92313--92423 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
92303 CCCGACTCAC
* * * *
92313 CTGTCATCGTTCAAGAGGCCTCCCCTATCGTTCAAGATGCCC
1 CTGTCATCGTTCAAGAGGCCTCCCCCACCGTTCAAGAGGCCA
* ** *
92355 CTATCATCCCTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGCCTCC-CCCACCGTTCAAGAGGCCA
* * *
92397 CTGTCATCGTTGAAGAGGTCTCTCCCA
1 CTGTCATCGTTCAAGAGGCCTCCCCCA
92424 ACATTTTAGA
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
41 2 0.04
42 49 0.94
43 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGGCCTCCCCCACCGTTCAAGAGGCCA
Found at i:93800 original size:14 final size:14
Alignment explanation
Indices: 93781--93816 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
93771 ATTGTTTAAT
93781 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
93795 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
93809 TGATTTGT
1 TGATTTGT
93817 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:93957 original size:14 final size:14
Alignment explanation
Indices: 93938--93972 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
93928 GGAAATGACT
93938 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
93952 ATCGCAACGAGTGA
1 ATCGCAACGAGAGA
93966 ATCGCAA
1 ATCGCAA
93973 TGCGAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:94068 original size:20 final size:20
Alignment explanation
Indices: 94043--94131 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
94033 GCGATTCACT
94043 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
94063 CGTTGCGATAGTCAATTCTG
1 CGTTGCGATAGTCATTTCCG
*
94083 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
94103 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
94123 CGTTGCGAT
1 CGTTGCGAT
94132 TTCTGCGTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:94100 original size:40 final size:40
Alignment explanation
Indices: 94045--94131 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
94035 GATTCACTCG
94045 TTGCGATAGTCATTTCCGCGTTGCGATAGTCA-ATTCTGCA
1 TTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTC-GCA
* *
94085 TTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTCGCG
1 TTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCGCA
94125 TTGCGAT
1 TTGCGAT
94132 TTCTGCGTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (40 bp):
TTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCGCA
Found at i:96598 original size:24 final size:24
Alignment explanation
Indices: 96564--96617 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
96554 CTGAAAAATC
96564 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
96588 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
96612 ATCAAA
1 ATCAAA
96618 TTTCAAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:97491 original size:20 final size:20
Alignment explanation
Indices: 97468--97546 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
97458 TTGCGATAGT
* *
97468 CAGAATCTCGTTGCGATTTA
1 CAGAATCGCATTGCGATTTA
*
97488 CAGATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTTA
*
97508 C-GTATTCGCATTGCGATTTA
1 CAG-AATCGCATTGCGATTTA
*
97528 C-GTAATTGCATTGCGATTT
1 CAG-AATCGCATTGCGATTT
97547 TCCAAATTCG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
19 1 0.02
20 52 0.98
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
CAGAATCGCATTGCGATTTA
Found at i:97554 original size:20 final size:20
Alignment explanation
Indices: 97478--97569 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 20
97468 CAGAATCTCG
*
97478 TTGCGATTTA-CAGATTCGCA
1 TTGCGATTTACCAAATT-GCA
**
97498 TTGCGATTTA-CGTATTCGCA
1 TTGCGATTTACCAAATT-GCA
**
97518 TTGCGATTTACGTAATTGCA
1 TTGCGATTTACCAAATTGCA
* **
97538 TTGCGATTTTCCAAATTCGTG
1 TTGCGATTTACCAAATT-GCA
97559 TTGCGATTTAC
1 TTGCGATTTAC
97570 GTATTCGCAT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACCAAATTGCA
Found at i:97607 original size:21 final size:21
Alignment explanation
Indices: 97583--97626 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
97573 TTCGCATTGT
97583 GAATTAGGAAAATCGCAACGC
1 GAATTAGGAAAATCGCAACGC
* * *
97604 GAATTTGGGAAATCGCAATGC
1 GAATTAGGAAAATCGCAACGC
97625 GA
1 GA
97627 TAGTCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (21 bp):
GAATTAGGAAAATCGCAACGC
Found at i:98949 original size:30 final size:31
Alignment explanation
Indices: 98915--98974 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 31
98905 AAGTAATATT
98915 AGATA-TTTTTATAGGTATTAGATACTGTAG
1 AGATATTTTTTATAGGTATTAGATACTGTAG
98945 AGATATTTTTTTATAGGTATTAGATACTGT
1 AGATA-TTTTTTATAGGTATTAGATACTGT
98975 TGTCAAACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 5 0.18
32 23 0.82
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (31 bp):
AGATATTTTTTATAGGTATTAGATACTGTAG
Found at i:99623 original size:13 final size:14
Alignment explanation
Indices: 99600--99630 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
99590 ATATCTAATC
99600 TTAATTAATAAATA
1 TTAATTAATAAATA
99614 TTAA-TAATAAATA
1 TTAATTAATAAATA
99627 TTAA
1 TTAA
99631 CCTACTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAATTAATAAATA
Found at i:110895 original size:49 final size:49
Alignment explanation
Indices: 110823--110916 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 49
110813 TTCATTCTTT
110823 TGAAGGATACACAGATTTACTTTATTTTTTGATTAAACATAGATTAGGA
1 TGAAGGATACACAGATTTACTTTATTTTTTGATTAAACATAGATTAGGA
*
110872 TGAAGGATACACAGATTTGCTTTATTTTTTGATTAAACATAGATT
1 TGAAGGATACACAGATTTACTTTATTTTTTGATTAAACATAGATT
110917 TACTTTAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (49 bp):
TGAAGGATACACAGATTTACTTTATTTTTTGATTAAACATAGATTAGGA
Found at i:119446 original size:20 final size:20
Alignment explanation
Indices: 119381--119630 Score: 229
Period size: 20 Copynumber: 12.5 Consensus size: 20
119371 CGATTTTCCA
* ** *
119381 AAATCGCAACGCGAATATGA
1 AAATCGCAACGTGAATCCGT
* *
119401 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGTGAATC-CGT
*
119421 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
119441 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
119461 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
119481 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
119501 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
119521 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
119541 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
119561 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
119581 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
119601 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
119621 AAATCACAAC
1 AAATCGCAAC
119631 ACTGAAATTT
Statistics
Matches: 195, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
20 194 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:120352 original size:24 final size:24
Alignment explanation
Indices: 120313--120359 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
120303 AAATTTGGTC
120313 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
120337 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
120360 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:120550 original size:12 final size:12
Alignment explanation
Indices: 120533--120557 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
120523 ATATAATCCT
120533 GAAGAAGAAAAA
1 GAAGAAGAAAAA
120545 GAAGAAGAAAAA
1 GAAGAAGAAAAA
120557 G
1 G
120558 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:122934 original size:19 final size:19
Alignment explanation
Indices: 122892--122989 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
122882 GATTCTCTCG
*
122892 TTGCGATTTTCATTTCCACA
1 TTGCGATTTTCATTT-CGCA
122912 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
122931 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
122945 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
122964 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
122983 TTGCGAT
1 TTGCGAT
122990 AGTCAATTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 35 0.50
20 15 0.21
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:122940 original size:53 final size:52
Alignment explanation
Indices: 122873--122989 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 52
122863 GAAATGAAAA
122873 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCACATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CACATTGCGATTTTCATT
*
122926 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACATTGCGATTTTCATT
122978 TCGCATTGCGAT
1 TCGCATTGCGAT
122990 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCACATTGCGATTTTCATT
Found at i:123072 original size:19 final size:19
Alignment explanation
Indices: 123048--123214 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
123038 CCATTACATT
123048 TCGCAATGCGGAAATG-AAA
1 TCGCAATGC-GAAATGAAAA
*
123067 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
123081 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
123100 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
123119 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
123133 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
123152 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
123171 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
123185 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
123204 TCGCATTGCGA
1 TCGCAATGCGA
123215 TTCTCCCATT
Statistics
Matches: 124, Mismatches: 8, Indels: 32
0.76 0.05 0.20
Matches are distributed among these distances:
13 1 0.01
14 29 0.23
15 2 0.02
16 7 0.06
17 5 0.04
18 3 0.02
19 77 0.62
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:123085 original size:33 final size:32
Alignment explanation
Indices: 123048--123208 Score: 137
Period size: 33 Copynumber: 4.7 Consensus size: 32
123038 CCATTACATT
123048 TCGCAATGCGGAAATGAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAATCGCAACGAGAGAA
*
123081 TCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATG-AAATCGCAA--CG--A-GAGAA
* * * * *
123119 TCGCAACGAGAGAATCGCAATGCGAAATGA-A-AA
1 TCGCAATGCGA-AAT-GAAAT-CGCAACGAGAGAA
123152 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATG-AAATCGCAACGAGAGAA
*
123185 TCGCAATGCGAAATTAAAATCGCA
1 TCGCAATGCGAAA-TGAAATCGCA
123209 TTGCGATTCT
Statistics
Matches: 103, Mismatches: 12, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
31 7 0.07
32 13 0.13
33 52 0.50
34 2 0.02
35 2 0.02
36 1 0.01
37 1 0.01
38 14 0.14
39 6 0.06
40 5 0.05
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (32 bp):
TCGCAATGCGAAATGAAATCGCAACGAGAGAA
Found at i:123126 original size:52 final size:52
Alignment explanation
Indices: 123048--123214 Score: 300
Period size: 52 Copynumber: 3.2 Consensus size: 52
123038 CCATTACATT
123048 TCGCAATGCGGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
123100 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
123152 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
123204 TCGCATTGCGA
1 TCGCAATGCGA
123215 TTCTCCCATT
Statistics
Matches: 112, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
51 6 0.05
52 106 0.95
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:123263 original size:19 final size:19
Alignment explanation
Indices: 123221--123320 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
123211 GCGATTCTCC
123221 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
123241 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
123260 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
123276 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
123293 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
123312 CATTGCGAT
1 CATTGCGAT
123321 AGTCAATTTG
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:123317 original size:52 final size:53
Alignment explanation
Indices: 123204--123320 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
123194 GAAATTAAAA
123204 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
123257 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
123309 TCGCATTGCGAT
1 TCGCATTGCGAT
123321 AGTCAATTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:123445 original size:14 final size:14
Alignment explanation
Indices: 123426--123462 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
123416 CATCAATTAC
123426 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
123440 ACAAATCATCTTTT
1 ACAAATCAACTTTT
123454 ACAAATCAA
1 ACAAATCAA
123463 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:125413 original size:20 final size:19
Alignment explanation
Indices: 125388--125452 Score: 80
Period size: 18 Copynumber: 3.4 Consensus size: 19
125378 TAGTTTACTT
*
125388 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
125408 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
125426 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
125445 TCGCAACG
1 TCGCAACG
125453 ACAGAATCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
18 16 0.40
19 11 0.28
20 13 0.32
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:125447 original size:19 final size:19
Alignment explanation
Indices: 125388--125521 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
125378 TAGTTTACTT
* *
125388 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
125408 TCGCAACGCGAAA-CCAAA
1 TCGCAACGCGAAATGAAAA
125426 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
125445 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
125459 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
125478 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
125492 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
125511 TCGCAATGCGA
1 TCGCAACGCGA
125522 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
18 16 0.17
19 29 0.31
20 12 0.13
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:125462 original size:14 final size:14
Alignment explanation
Indices: 125443--125499 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
125433 GCGAAATGAA
*
125443 AATCGCAACGACAG
1 AATCGCAACGAAAG
125457 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
125474 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
125490 AATCGCAACG
1 AATCGCAACG
125500 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:125470 original size:33 final size:33
Alignment explanation
Indices: 125388--125516 Score: 168
Period size: 33 Copynumber: 3.8 Consensus size: 33
125378 TAGTTTACTT
* * *
125388 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAA
1 TCGCAACGCGAAA-TGAAAATCGCAA--CGAAA--GAA
*
125426 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
*
125459 TCGCAATGCGAAATGAAAATCGCAACGAAAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
125492 TCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAATGAAAATCGCAA
125517 TGCGATTTTG
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 57 0.68
35 4 0.05
37 11 0.13
38 12 0.14
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (33 bp):
TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
Found at i:125533 original size:19 final size:19
Alignment explanation
Indices: 125517--125645 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
125507 AAAATCGCAA
125517 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
125536 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
125550 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
125569 TGCGATTTT-G--T--CAT
1 TGCGATTTTGGTTTCGCGT
**
125583 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
125602 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
125621 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
125641 TGCGA
1 TGCGA
125646 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:0.16, G:0.28, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:125608 original size:33 final size:33
Alignment explanation
Indices: 125517--125611 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
125507 AAAATCGCAA
* *
125517 TGCGATTTTGGTTTCGCGTTGCGATCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCAT
125550 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCAT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCAT
**
125583 TGCGATTTTCATTTCGCGTTGCGATTTTG
1 TGCGATTTTGGTTTCGCGTTGCGATTTTG
125612 GTTTCGCGTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.08, C:0.17, G:0.27, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTCAT
Found at i:125848 original size:93 final size:93
Alignment explanation
Indices: 125689--126069 Score: 735
Period size: 93 Copynumber: 4.1 Consensus size: 93
125679 TTGAATGGAT
125689 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
125754 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
125782 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
125847 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
125875 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
125940 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
125968 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
* *
126033 AGTTTAGCATAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
126061 AAATTTACT
1 AAATTTACT
126070 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 284 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:127810 original size:33 final size:33
Alignment explanation
Indices: 127765--127878 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
127755 TCTTTTGGTT
127765 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
127798 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
127831 GAAATGAAAATCGCAACGACAGAATCGTAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
127864 GAAATG-AAATCGCAA
1 GAAATGAAAATCGCAA
127879 TGCGATTTTG
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 9 0.12
33 66 0.88
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:127811 original size:19 final size:18
Alignment explanation
Indices: 127772--127883 Score: 77
Period size: 14 Copynumber: 6.8 Consensus size: 18
127762 GTTGAAATGA
127772 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
127787 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
127804 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
127820 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
127837 AAAATCGCAA--CGACA-G
1 -AAATCGCAACGCGAGATG
* *
127853 -AATCGTAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
127870 AAATCGCAATGCGA
1 AAATCGCAACGCGA
127884 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
14 23 0.30
16 15 0.19
17 12 0.16
18 11 0.14
19 16 0.21
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:127914 original size:14 final size:14
Alignment explanation
Indices: 127895--127951 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
127885 TTTGGTTTCG
127895 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
127909 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
127928 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
127942 CGTTGCGATT
1 CGTTGCGATT
127952 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:127927 original size:33 final size:33
Alignment explanation
Indices: 127879--127959 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
127869 GAAATCGCAA
**
127879 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
127912 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
127945 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
127960 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:127984 original size:23 final size:21
Alignment explanation
Indices: 127936--127991 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
127926 CGCGTTGCGA
127936 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
127957 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
127978 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
127992 CTCTTCTGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.11, C:0.23, G:0.16, T:0.50
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:128118 original size:33 final size:33
Alignment explanation
Indices: 128071--128141 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
128061 AATACTAACT
* *
128071 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
128104 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
128137 TGAAA
1 TGAAA
128142 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:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:128375 original size:22 final size:22
Alignment explanation
Indices: 128323--128377 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
128313 TGGTTGTGAG
**
128323 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
128345 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
128367 GGATTTCTTCG
1 GGATTTCTTCG
128378 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:128548 original size:20 final size:20
Alignment explanation
Indices: 128523--128716 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
128513 CTTTAAATAT
128523 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
128543 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
128565 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
128584 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
128604 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
128624 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
128644 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
128664 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
128684 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
128704 CGCGTTGCGATTT
1 CGCGTTGCGATTT
128717 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:128710 original size:60 final size:60
Alignment explanation
Indices: 128523--128716 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
128513 CTTTAAATAT
**
128523 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
128584 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
128644 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
128704 CGCGTTGCGATTT
1 CGCGTTGCGATTT
128717 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:128733 original size:21 final size:21
Alignment explanation
Indices: 128703--128785 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
128693 ATTTTCATAT
*
128703 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
128724 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
128745 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
128766 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
128786 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:128776 original size:42 final size:43
Alignment explanation
Indices: 128683--128781 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
128673 ATTTATGTGT
* *
128683 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
128724 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
128766 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
128782 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:129987 original size:14 final size:15
Alignment explanation
Indices: 129957--129989 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
129947 AATAGAATAA
129957 ATAAATAAATATTAT
1 ATAAATAAATATTAT
*
129972 ATAAATATAT-TTAT
1 ATAAATAAATATTAT
129986 ATAA
1 ATAA
129990 CTTAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATAAATATTAT
Found at i:130077 original size:15 final size:14
Alignment explanation
Indices: 130047--130106 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
130037 TATCAAACGT
130047 AATAATAAAA-TAA
1 AATAATAAAATTAA
130060 AATAATAATAATTAA
1 AATAATAA-AATTAA
130075 AATGAA-AGAAATTAA
1 AAT-AATA-AAATTAA
*
130090 AAGTAATAATATTAA
1 AA-TAATAAAATTAA
130105 AA
1 AA
130107 ACTAATGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.20
14 2 0.05
15 25 0.62
16 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AATAATAAAATTAA
Found at i:131467 original size:3 final size:3
Alignment explanation
Indices: 131454--131522 Score: 59
Period size: 3 Copynumber: 23.0 Consensus size: 3
131444 TATATATATT
* * * * *
131454 TAA TAAA TAA TAA TAA TAA -CA TTA TTA TAA TAA TAA TAA TAT TTA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
131499 TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
131523 ACGAAAAATT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 1 0.02
3 49 0.92
4 3 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:131503 original size:15 final size:15
Alignment explanation
Indices: 131481--131522 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
131471 AACATTATTA
131481 TAATAATAATAATATT
1 TAATAATAATAAT-TT
131497 T-ATAATAATAATTT
1 TAATAATAATAATTT
131511 TAATAATAATAA
1 TAATAATAATAA
131523 ACGAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.12
15 21 0.84
16 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATAATAATAATTT
Found at i:131953 original size:76 final size:76
Alignment explanation
Indices: 131669--131926 Score: 480
Period size: 76 Copynumber: 3.4 Consensus size: 76
131659 GAGGTCTTAA
* *
131669 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
131734 AGGCTTTTTGG
66 AGGCTTTTTGG
*
131745 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
131810 AGGCTTTTTGG
66 AGGCTTTTTGG
131821 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
131886 AGGCTTTTTGG
66 AGGCTTTTTGG
*
131897 AAACATCATACACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
131927 TAGGAAATAG
Statistics
Matches: 178, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 178 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:135004 original size:114 final size:114
Alignment explanation
Indices: 134804--135143 Score: 599
Period size: 114 Copynumber: 3.0 Consensus size: 114
134794 ACAATCATGC
* * * *
134804 AATTCATCTTTCAATTCTAATGATTGGTTCTGGGGTTCCTACCAAACCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
* *
134869 GAACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTGCTATGAGCA
66 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
* *
134918 AATTCATTTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
134983 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
66 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
*
135032 AATTAATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
135097 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
66 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
135144 AACGTGGCAC
Statistics
Matches: 215, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 215 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (114 bp):
AATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
Found at i:137286 original size:7 final size:7
Alignment explanation
Indices: 137269--137319 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
137259 ATTTCTCCTT
137269 TTTTTTC
1 TTTTTTC
137276 -TTTTTC
1 TTTTTTC
137282 TTTTTTC
1 TTTTTTC
*
137289 TTTTTGC
1 TTTTTTC
*
137296 TTTTCT-
1 TTTTTTC
137302 TTTTTTC
1 TTTTTTC
137309 TTTCTTTC
1 TTT-TTTC
137317 TTT
1 TTT
137320 ATTTTTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 11 0.30
7 19 0.51
8 7 0.19
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:137287 original size:13 final size:13
Alignment explanation
Indices: 137269--137345 Score: 72
Period size: 13 Copynumber: 6.0 Consensus size: 13
137259 ATTTCTCCTT
137269 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
137282 TTTTTTCTTTTTGC
1 TTTTTTCTTTTT-C
137296 TTTTCTT-TTTTTC
1 TTTT-TTCTTTTTC
*
137309 TTTCTTTC--TTTA
1 TTT-TTTCTTTTTC
*
137321 TTTTTTCTTTTTG
1 TTTTTTCTTTTTC
*
137334 TTGTTT-TTTTTC
1 TTTTTTCTTTTTC
137346 AAGTATAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
11 4 0.07
12 11 0.20
13 26 0.48
14 11 0.20
15 2 0.04
ACGTcount: A:0.01, C:0.13, G:0.04, T:0.82
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:137298 original size:20 final size:19
Alignment explanation
Indices: 137270--137345 Score: 75
Period size: 19 Copynumber: 4.0 Consensus size: 19
137260 TTTCTCCTTT
*
137270 TTTTTCTTTTTCTTTTTTC
1 TTTTTGTTTTTCTTTTTTC
*
137289 TTTTTGCTTTTCTTTTTTTC
1 TTTTTGTTTTTC-TTTTTTC
* *
137309 TTTCTT-TCTTTATTTTTTC
1 TTT-TTGTTTTTCTTTTTTC
*
137328 TTTTTGTTGTT-TTTTTTC
1 TTTTTGTTTTTCTTTTTTC
137346 AAGTATAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
18 9 0.19
19 23 0.49
20 13 0.28
21 2 0.04
ACGTcount: A:0.01, C:0.13, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTTTGTTTTTCTTTTTTC
Found at i:137307 original size:27 final size:26
Alignment explanation
Indices: 137267--137342 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 26
137257 CAATTTCTCC
137267 TTTTTT-TTCTTTTTCTTTTTTCTTT-
1 TTTTTTCTT-TTTTTCTTTTTTCTTTA
137292 TTGCTTTTCTTTTTTTCTTTCTTTCTTTA
1 TT--TTTTCTTTTTTTCTTT-TTTCTTTA
*
137321 TTTTTTCTTTTTGTTGTTTTTT
1 TTTTTTCTTTTT-TTCTTTTTT
137343 TTCAAGTATA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
25 2 0.05
27 26 0.59
28 14 0.32
29 2 0.05
ACGTcount: A:0.01, C:0.12, G:0.04, T:0.83
Consensus pattern (26 bp):
TTTTTTCTTTTTTTCTTTTTTCTTTA
Found at i:142341 original size:22 final size:24
Alignment explanation
Indices: 142298--142341 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
142288 AAAAGTATAA
142298 AAATAATAAGTAATAAAAAATTTG
1 AAATAATAAGTAATAAAAAATTTG
*
142322 AAATAA-AAG-AATTAAAAATT
1 AAATAATAAGTAATAAAAAATT
142342 AAATATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 3 0.16
24 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (24 bp):
AAATAATAAGTAATAAAAAATTTG
Found at i:143188 original size:14 final size:15
Alignment explanation
Indices: 143158--143190 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
143148 AATAGAATAA
143158 ATAAATAAATATTAT
1 ATAAATAAATATTAT
*
143173 ATAAATATAT-TTAT
1 ATAAATAAATATTAT
143187 ATAA
1 ATAA
143191 CTTAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATAAATATTAT
Found at i:143281 original size:15 final size:14
Alignment explanation
Indices: 143251--143310 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
143241 TATCAAACGT
143251 AATAATAAAA-TAA
1 AATAATAAAATTAA
143264 AATAATAATAATTAA
1 AATAATAA-AATTAA
143279 AATGAA-AGAAATTAA
1 AAT-AATA-AAATTAA
*
143294 AAGTAATAATATTAA
1 AA-TAATAAAATTAA
143309 AA
1 AA
143311 ACTAATGAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 8 0.20
14 2 0.05
15 25 0.62
16 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AATAATAAAATTAA
Found at i:144659 original size:3 final size:3
Alignment explanation
Indices: 144651--144727 Score: 104
Period size: 3 Copynumber: 26.0 Consensus size: 3
144641 TATATATATT
144651 TAA TAA TAAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* **
144695 TTA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
144728 ACGAAAAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
2 4 0.06
3 59 0.89
4 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:144664 original size:23 final size:22
Alignment explanation
Indices: 144638--144727 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 22
144628 ATGTAATTTG
144638 TAATATATATATTTAATAATAAA
1 TAATATATATATTTAATAAT-AA
*
144661 TAATA-ATA-ATATAATAATAA
1 TAATATATATATTTAATAATAA
144681 TAATA-ATAATAATATT-ATAATAA
1 TAATATAT-AT-AT-TTAATAATAA
144704 TAATA-ATA-ATTTTAATAATAA
1 TAATATATATA-TTTAATAATAA
144725 TAA
1 TAA
144728 ACGAAAAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
20 12 0.20
21 21 0.36
22 4 0.07
23 21 0.36
24 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATATATATATTTAATAATAA
Found at i:144688 original size:26 final size:26
Alignment explanation
Indices: 144651--144723 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 26
144641 TATATATATT
144651 TAATAATAAATAATAATAATATAATAA
1 TAATAAT-AATAATAATAATATAATAA
*
144678 TAATAATAATAATAATATTATAATAA
1 TAATAATAATAATAATAATATAATAA
**
144704 TAATAATAATTTTAATAATA
1 TAATAATAATAATAATAATA
144724 ATAAACGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 35 0.83
27 7 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATAATAATAATAATAATATAATAA
Found at i:162071 original size:54 final size:54
Alignment explanation
Indices: 162010--162127 Score: 218
Period size: 54 Copynumber: 2.2 Consensus size: 54
162000 AAATTTAATC
162010 TTTGTCCCTAATTTGATATGATTTAGTTTATTAATTTTAGGGAAAATGACAACT
1 TTTGTCCCTAATTTGATATGATTTAGTTTATTAATTTTAGGGAAAATGACAACT
*
162064 TTTGTCCCTAATTTGATATGATTTGGTTTATTAATTTTAGGGAAAATGACAACT
1 TTTGTCCCTAATTTGATATGATTTAGTTTATTAATTTTAGGGAAAATGACAACT
*
162118 TTTATCCCTA
1 TTTGTCCCTA
162128 TAATAAACTC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (54 bp):
TTTGTCCCTAATTTGATATGATTTAGTTTATTAATTTTAGGGAAAATGACAACT
Found at i:166763 original size:12 final size:12
Alignment explanation
Indices: 166746--166772 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
166736 TATTAAAAAT
166746 TTTCCAGAGGAG
1 TTTCCAGAGGAG
166758 TTTCCAGAGGAG
1 TTTCCAGAGGAG
166770 TTT
1 TTT
166773 ATAATGGCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (12 bp):
TTTCCAGAGGAG
Found at i:179368 original size:59 final size:59
Alignment explanation
Indices: 179276--179574 Score: 454
Period size: 59 Copynumber: 5.1 Consensus size: 59
179266 TCTCTCTAAA
* *
179276 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCATAAAGGTGCCAATAATACAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * *
179335 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCATAAAGGTACCAATAATGTAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
*
179394 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATACAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* ** * *
179453 GTGAAAGGTTAAATGTATAACTGTGCATTTGGCAGAAATGTGACAATAATGCAAGTTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
* * * * *
179512 ATGAAAGGTTAAATGTCTAACTGTGCATTTGGCAGAAATGTTCCACTAATGCAAATTAG
1 ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
179571 ATGA
1 ATGA
179575 GAAACAGTGT
Statistics
Matches: 221, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 221 1.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (59 bp):
ATGAAAGGTTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATAATGCAAGTTAG
Found at i:182275 original size:19 final size:18
Alignment explanation
Indices: 182244--182285 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
182234 TTAACAACAA
*
182244 AAAATACATAAAAAATTT
1 AAAATACATAAAAAAATT
*
182262 AAAATATATAAAAAAAATT
1 AAAATACAT-AAAAAAATT
182281 AAAAT
1 AAAAT
182286 TTTAGATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATACATAAAAAAATT
Found at i:182867 original size:64 final size:65
Alignment explanation
Indices: 182761--182885 Score: 173
Period size: 64 Copynumber: 1.9 Consensus size: 65
182751 GAATGCATTT
* ** *
182761 CATGTATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGC
1 CATGCATCGATGCACTCAGACTTTTATGAAAACATCGAATGCATTTGATGCACCGATGCACCAGC
* *
182826 CATGCATCGATGCACTCAGACTATTT-TG-AAACATTGAATGCATTTTATGCACCGATGCAC
1 CATGCATCGATGCACTCAGACT-TTTATGAAAACATCGAATGCATTTGATGCACCGATGCAC
182886 TAAGGGTCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 29 0.55
65 21 0.40
66 3 0.06
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (65 bp):
CATGCATCGATGCACTCAGACTTTTATGAAAACATCGAATGCATTTGATGCACCGATGCACCAGC
Found at i:195292 original size:17 final size:17
Alignment explanation
Indices: 195267--195301 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
195257 AAAGGGGGAG
195267 AAAAATGTTATAGTGTT
1 AAAAATGTTATAGTGTT
*
195284 AAAAGTGTTATAGTGTT
1 AAAAATGTTATAGTGTT
195301 A
1 A
195302 TAGTGGGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (17 bp):
AAAAATGTTATAGTGTT
Found at i:195298 original size:8 final size:8
Alignment explanation
Indices: 195272--195306 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
195262 GGGAGAAAAA
195272 TGTTATAG
1 TGTTATAG
*
195280 TGTTAAAAG
1 TGTT-ATAG
195289 TGTTATAG
1 TGTTATAG
195297 TGTTATAG
1 TGTTATAG
195305 TG
1 TG
195307 GGGGGAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (8 bp):
TGTTATAG
Found at i:195769 original size:65 final size:63
Alignment explanation
Indices: 195700--195857 Score: 203
Period size: 65 Copynumber: 2.5 Consensus size: 63
195690 ATAAATTGAG
* *
195700 CATCGAATGTATTTCATGCATCGATGCACATACCATGCATTAATGCACTCAGAG-T-TTTATGAA
1 CATCGAATGCATTTCATGCATCGATGCACA-ACCATGCATCAATGCACTCAG-GCTATTT-TG-A
195763 AA
62 AA
* * *
195765 CATCGAATACATTTGATGCATCGATGCACCAACCATGCATCGATGCACTCAGGCTATTTTGAAA
1 CATCGAATGCATTTCATGCATCGATGCA-CAACCATGCATCAATGCACTCAGGCTATTTTGAAA
*
195829 CATCGAATGCATTTTATGCATCGATGCAC
1 CATCGAATGCATTTCATGCATCGATGCAC
195858 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
63 1 0.01
64 30 0.36
65 47 0.57
66 5 0.06
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (63 bp):
CATCGAATGCATTTCATGCATCGATGCACAACCATGCATCAATGCACTCAGGCTATTTTGAAA
Found at i:196171 original size:21 final size:21
Alignment explanation
Indices: 196142--196185 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
196132 ATTCTGACTA
196142 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
196163 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
196184 TC
1 TC
196186 ACAATGCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:196274 original size:20 final size:20
Alignment explanation
Indices: 196187--196277 Score: 110
Period size: 20 Copynumber: 4.5 Consensus size: 20
196177 TCCTAATTCA
*
196187 CAATGCAAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
* * ** *
196207 CAACGCAAATTTGGAAAATCG
1 CAATGCGAA-TACGTAAATCG
*
196228 CAATGCGATTACGTAAATCG
1 CAATGCGAATACGTAAATCG
196248 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
196268 CAATGCGAAT
1 CAATGCGAAT
196278 CTGACTATCG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:196498 original size:22 final size:22
Alignment explanation
Indices: 196473--196534 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 22
196463 GGCGACATCC
196473 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
196495 GTCCCCA----CGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* **
196513 GTCTCCATCTCCGGTGAAATCA
1 GTCCCCATCTCCGACGAAATCA
196535 TTCACGGCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
18 16 0.52
22 15 0.48
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:196921 original size:21 final size:20
Alignment explanation
Indices: 196863--196930 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 20
196853 GCGATTCTGT
**
196863 CGTTGCGATTTTC-ATTTCG
1 CGTTGCGATAGTCAATTTCG
*
196882 CG-TGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
*
196901 CGTTTGCGATAGTCATTTTCG
1 CG-TTGCGATAGTCAATTTCG
*
196922 TGTTGCGAT
1 CGTTGCGAT
196931 TTAAAGTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 8 0.20
19 9 0.22
20 7 0.17
21 16 0.40
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:198805 original size:20 final size:20
Alignment explanation
Indices: 198776--198874 Score: 111
Period size: 20 Copynumber: 5.2 Consensus size: 20
198766 AGAATAGTTT
*
198776 ACTATTGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
198796 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
198816 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAACGCGAAAATG
*
198832 A--ATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
* *
198850 ACTATCGCAATGCGAAAATA
1 ACTATCGCAACGCGAAAATG
198870 ACTAT
1 ACTAT
198875 TCTGGATAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
14 7 0.10
16 4 0.06
17 4 0.06
18 4 0.06
20 50 0.72
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Done.