Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006281.1 Hibiscus syriacus cultivar Beakdansim tig00014992_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: 114179
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1820 original size:19 final size:19
Alignment explanation
Indices: 1796--1834 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1786 AAGACTATTT
1796 TCATTTT-TAATTTTGAAAA
1 TCATTTTGT-ATTTTGAAAA
1815 TCATTTTGTATTTTGAAAA
1 TCATTTTGTATTTTGAAAA
1834 T
1 T
1835 AAAGTCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (19 bp):
TCATTTTGTATTTTGAAAA
Found at i:4229 original size:19 final size:19
Alignment explanation
Indices: 4205--4253 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
4195 AATGTAGGGT
4205 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
4224 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
4243 TAATTTTGTAT
1 TAATTTTGTAT
4254 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:5257 original size:201 final size:200
Alignment explanation
Indices: 4698--5260 Score: 835
Period size: 201 Copynumber: 2.8 Consensus size: 200
4688 AACATATGTA
* * *
4698 TCGATACATTTACAAAA-AGTATAGATCCCAAAACCATCGAAACTCATAATTATAATGTAATAGG
1 TCGATACATTTATAAAACA-TATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATAGG
* ** * *
4762 TGATTTTTCAATGTAACTAGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACATAATGTAT
65 TAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGATAGAATAGGTCTACATAATGTAT
* * *
4827 CGACACTTTTGAAATTTGTGTCGATACGTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACGCA
130 CAACACTTTT-AAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCA
4892 TAAAGTG
194 TAAAGTG
* *
4899 TCGATACATTTATAAAACGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAACATATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATAGGT
* * *
4964 AATTTTTCAATGTAACCGATATAAATATACCAGTTTTATG-TGAGAATATGTCTACATAATGTAT
66 AATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAT-AGAATAGGTCTACATAATGTAT
* *
5028 CAATACTTTTTAAGTTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCA
130 CAACAC-TTTTAAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCA
5093 TAAAGTG
194 TAAAGTG
*
5100 TCGATACATTTATAAAACATATCGATCCCAAAAACATCAAAACTCATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAACATATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATAGGT
* * * *
5165 AATTTTTCAATGTAACCGGTATAAATATACCGGTTTTAAGATACAATAGGTTTATATAATGTATC
66 AATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGATAGAATAGGTCTACATAATGTATC
*
5230 AACACATTTTAAATTTATG-CTGATACTTTTT
131 AACAC-TTTTAAATTTGTGTC-GATACTTTTT
5261 AAAATTTTGT
Statistics
Matches: 325, Mismatches: 32, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
200 1 0.00
201 319 0.98
202 5 0.02
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (200 bp):
TCGATACATTTATAAAACATATCGATCCCAAAAACATCGAAACTCATAATTATAATGTAATAGGT
AATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGATAGAATAGGTCTACATAATGTATC
AACACTTTTAAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAACTAGGTGCACGCATA
AAGTG
Found at i:5605 original size:15 final size:15
Alignment explanation
Indices: 5585--5613 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5575 GTCTTTCTCA
5585 AAGCTCTTCTCAACC
1 AAGCTCTTCTCAACC
5600 AAGCTCTTCTCAAC
1 AAGCTCTTCTCAAC
5614 GACAACCTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.38, G:0.07, T:0.28
Consensus pattern (15 bp):
AAGCTCTTCTCAACC
Found at i:5957 original size:2 final size:2
Alignment explanation
Indices: 5950--5985 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5940 ATGGGGAATG
5950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5986 CTCCGGATAC
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):
AT
Found at i:6812 original size:12 final size:12
Alignment explanation
Indices: 6792--6825 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6782 CAAGCGGTCA
* *
6792 ATGAAGATGACG
1 ATGATGATGAAG
6804 ATGATGATGAAG
1 ATGATGATGAAG
6816 ATGATGATGA
1 ATGATGATGA
6826 TGATCCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.03, G:0.32, T:0.24
Consensus pattern (12 bp):
ATGATGATGAAG
Found at i:8226 original size:18 final size:18
Alignment explanation
Indices: 8200--8238 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
8190 ATTTCTATGT
8200 AATTGGAGTTTAAATTTC
1 AATTGGAGTTTAAATTTC
* *
8218 AATTTGAGTTTGAATTTC
1 AATTGGAGTTTAAATTTC
8236 AAT
1 AAT
8239 ATAAATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (18 bp):
AATTGGAGTTTAAATTTC
Found at i:10217 original size:198 final size:198
Alignment explanation
Indices: 9482--10664 Score: 1343
Period size: 198 Copynumber: 6.0 Consensus size: 198
9472 TTCAGTAATC
* * * * *
9482 TCCAAAATGAATGCCCAACCGAGGTGCACGAATAAAGTGTCGATACATTTATTAAA-AGTATTGA
1 TCCAGAATGAATGCCTAAACGA-GTGCACGAATAAAGTGTCGATACATTTA-TAAATTGTATCGA
* *
9546 TCCCAAAAACATCGAATAA--GATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGA-A-
64 TCCCAAAAACATC-AA-AACCGATAATTATAATGTAATAGGT-AACTTCCAATGTAACC-GATAG
* * * * * ** *
9607 ATATATACCAGTTAATTAGAAAATAGGTCTACAAAATATATCGATACTT-TTTAAATTGTGTCGA
125 AAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAATTTGTGTCGA
9671 TACTTTTTG
190 TACTTTTTG
* * *
9680 TCCAGAATGAATGACC-AACCGAGATGCACGAATAAAGTGTTGATACATTTATAACA-AGTATCG
1 TCCAGAATGAATG-CCTAAACGAG-TGCACGAATAAAGTGTCGATACATTTATAA-ATTGTATCG
* *
9743 ATCCCAAAAACATCCAATAA--GATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAG
63 ATCCCAAAAACAT-CAA-AACCGATAATTATAATGTAATAGGT-AACTTCCAATGTAACCGATAG
* * * ** *
9806 AAATATACCGGTTAATTAGAAAATAGGTTTACATAATGTATCAACACTTTTTAAAATTGTGTCGA
125 AAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAATTTGTGTCGA
*
9871 TACGTTTTG
190 TACTTTTTG
* ** * *
9880 ACCAGAATGAATGTCC--AACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAACGTTTAGA
1 TCCAGAATGAATG-CCTAAACGA-GTGCACGAATAAAGTGTCGATACATTTATAAATTGTATCGA
* * * * *
9943 TCCC----A-A--AAAACTGATAAATATAATGTAATATGTAAATTTCCAATGTAACCGGTAGAAA
64 TCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGT-AACTTCCAATGTAACCGATAGAAA
* * * *
10001 TATACCGGTTAATTAGAGAATAGGTCTACATCATGTATCGACACTTGTGGAATTTGTGTTGATAT
128 TATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAATTTGTGTCGATAC
10066 TTTTTG
193 TTTTTG
* *
10072 TCCAGAATGAATGCCTAAAAGAGTGCACGCATAAAGTGTCGATACATTTA-AAATTGTATCGATC
1 TCCAGAATGAATGCCTAAACGAGTGCACGAATAAAGTGTCGATACATTTATAAATTGTATCGATC
*
10136 CCAAAAACATTAAAACCGATAATTATAATGTAATAGGTAACTTCACAATGTAACCGATAGAAATA
66 CCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAACTTC-CAATGTAACCGATAGAAATA
* * * * * *
10201 TACCGATTAATTAGAGAATATGCCTACATCATGTATTGACACTTGTGGAATTTGTGTCGATACTT
130 TACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAATTTGTGTCGATACTT
10266 TTTG
195 TTTG
* * * *
10270 TCCAAAATGAATGCCTAAAGGAGTGCACGCATAAAGTGTCGATACATTTA-AAATTATATCGATC
1 TCCAGAATGAATGCCTAAACGAGTGCACGAATAAAGTGTCGATACATTTATAAATTGTATCGATC
* * * * * *
10334 CCAAAAATATCGAAACCGATAATTATAATGTAATAGGTAACTATACAATGTACCCGGTAGAATTA
66 CCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAACT-TCCAATGTAACCGATAGAAATA
* *
10399 TACCGGTTAATTAGAAAATAGGTTTACATCATGTATCGACACTTGTGGAATTTGTGTCGATA-TG
130 TACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAATTTGTGTCGATACT-
10463 TTTTG
194 TTTTG
* * * * **
10468 TCCATAATGAATGCCTAAAAGAGTGCATGCATAAAGTGTTAATACATTTA-AAATTGTATCGATC
1 TCCAGAATGAATGCCTAAACGAGTGCACGAATAAAGTGTCGATACATTTATAAATTGTATCGATC
*
10532 CCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAACTTTCCAATGTAACC-ACTAGAAAT
66 CCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAAC-TTCCAATGTAACCGA-TAGAAAT
* * * ** *
10596 ATACCGGTTAATTAGAAAATAGATCTACATAATGTATCAACACTTTTTAAAGTTGTGTCGATACT
129 ATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAATTTGTGTCGATACT
10661 TTTT
194 TTTT
10665 TAAATTACGC
Statistics
Matches: 870, Mismatches: 89, Indels: 52
0.86 0.09 0.05
Matches are distributed among these distances:
190 2 0.00
191 16 0.02
192 142 0.16
193 4 0.00
194 1 0.00
195 2 0.00
196 1 0.00
197 11 0.01
198 564 0.65
199 90 0.10
200 37 0.04
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (198 bp):
TCCAGAATGAATGCCTAAACGAGTGCACGAATAAAGTGTCGATACATTTATAAATTGTATCGATC
CCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAACTTCCAATGTAACCGATAGAAATAT
ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTGTGGAATTTGTGTCGATACTTT
TTG
Found at i:10502 original size:396 final size:391
Alignment explanation
Indices: 9482--10664 Score: 1502
Period size: 396 Copynumber: 3.0 Consensus size: 391
9472 TTCAGTAATC
* *
9482 TCCAAAATGAATGCCCAACCGAGGTGCACGAATAAAGTGTCGATACATTTATTAAAAGTATTGAT
1 TCCAAAATGAATG-CCAAACGAGGTGCACGAATAAAGTGTCGATACATTTA-TAAAA-TATAGAT
9547 CCCAAAAACATCGAATA-AGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGG-A-AAT
63 CCCAAAAA-ATCGAA-ACAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAT
* ** * * ** *
9609 ATATACCAGTTAATTAGAAAATAGGTCTACAAAATATATCGATACTT-TTTAAATTGTGTCGATA
126 -TATACCGGTTAATTAGAAAATAGGTCTACATCATGTATCGACACTTGTGGAATTTGTGTCGATA
** *
9673 CTTTTTGTCCAGAATGAATGACC-AACCGAGATGCACGAATAAAGTGTTGATACATTTATAACA-
190 -TTTTTGTCCAGAATGAATG-CCTAAAAGAG-TGCACGCATAAAGTGTTGATACATTTA-AA-AT
* *
9736 AGTATCGATCCCAAAAACATCCAATAA--GATAATTATAATGTAATAGGTCAATTTCCAATGTAA
250 TGTATCGATCCCAAAAACAT-CAA-AACCGATAATTATAATGTAATAGGT-AACTTCCAATGTAA
* *
9799 CCGGTAGAAATATACCGGTTAATTAGAAAATAGGTTTACATAATGTATCAACACTTTTTAAAATT
312 CCGATAGAAATATACCGGTTAATTAGAAAATA-GTCTACATAATGTATCAACACTTTTTAAAATT
*
9864 GTGTCGATACGTTTTG
376 GTGTCGATACTTTTTG
* * *
9880 ACCAGAATGAATGTCC-AACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAACGTTTAGAT
1 TCCAAAATGAATG-CCAAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAA--TATAGAT
* * * * *
9944 CCC---AAA---AAACTGATAAATATAATGTAATATGTAAATTTCCAATGTAACCGGTAGAAATA
63 CCCAAAAAATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAATTA
* *
10003 TACCGGTTAATTAGAGAATAGGTCTACATCATGTATCGACACTTGTGGAATTTGTGTTGATATTT
128 TACCGGTTAATTAGAAAATAGGTCTACATCATGTATCGACACTTGTGGAATTTGTGTCGATA-TT
*
10068 TTTGTCCAGAATGAATGCCTAAAAGAGTGCACGCATAAAGTGTCGATACATTTAAAATTGTATCG
192 TTTGTCCAGAATGAATGCCTAAAAGAGTGCACGCATAAAGTGTTGATACATTTAAAATTGTATCG
*
10133 ATCCCAAAAACATTAAAACCGATAATTATAATGTAATAGGTAACTTCACAATGTAACCGATAGAA
257 ATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAACTTC-CAATGTAACCGATAGAA
* * * * ** * ** *
10198 ATATACCGATTAATTAGAGAATATGCCTACATCATGTATTGACACTTGTGGAATTTGTGTCGATA
321 ATATACCGGTTAATTAGAAAATA-GTCTACATAATGTATCAACACTTTTTAAAATTGTGTCGATA
10263 CTTTTTG
385 CTTTTTG
* * *
10270 TCCAAAATGAATGCCTAAAGGA-GTGCACGCATAAAGTGTCGATACATTTA-AAATTATATCGAT
1 TCCAAAATGAATGCC-AAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAA--ATATAGAT
* * * *
10333 CCCAAAAATATCGAAACCGATAATTATAATGTAATAGGTAACTATACAATGTACCCGGTAGAATT
63 CCCAAAAA-ATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAATT
*
10398 ATACCGGTTAATTAGAAAATAGGTTTACATCATGTATCGACACTTGTGGAATTTGTGTCGATATG
127 ATACCGGTTAATTAGAAAATAGGTCTACATCATGTATCGACACTTGTGGAATTTGTGTCGATAT-
* * *
10463 TTTTGTCCATAATGAATGCCTAAAAGAGTGCATGCATAAAGTGTTAATACATTTAAAATTGTATC
191 TTTTGTCCAGAATGAATGCCTAAAAGAGTGCACGCATAAAGTGTTGATACATTTAAAATTGTATC
*
10528 GATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAACTTTCCAATGTAACC-ACTAG
256 GATCCCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAAC-TTCCAATGTAACCGA-TAG
*
10592 AAATATACCGGTTAATTAGAAAATAGATCTACATAATGTATCAACACTTTTTAAAGTTGTGTCGA
319 AAATATACCGGTTAATTAGAAAATAG-TCTACATAATGTATCAACACTTTTTAAAATTGTGTCGA
10657 TACTTTTT
383 TACTTTTT
10665 TAAATTACGC
Statistics
Matches: 684, Mismatches: 76, Indels: 52
0.84 0.09 0.06
Matches are distributed among these distances:
388 2 0.00
389 22 0.03
390 194 0.28
391 73 0.11
392 41 0.06
393 2 0.00
394 2 0.00
395 3 0.00
396 287 0.42
397 45 0.07
398 13 0.02
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (391 bp):
TCCAAAATGAATGCCAAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAATATAGATCCC
AAAAAATCGAAACAGATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAATTATAC
CGGTTAATTAGAAAATAGGTCTACATCATGTATCGACACTTGTGGAATTTGTGTCGATATTTTTG
TCCAGAATGAATGCCTAAAAGAGTGCACGCATAAAGTGTTGATACATTTAAAATTGTATCGATCC
CAAAAACATCAAAACCGATAATTATAATGTAATAGGTAACTTCCAATGTAACCGATAGAAATATA
CCGGTTAATTAGAAAATAGTCTACATAATGTATCAACACTTTTTAAAATTGTGTCGATACTTTTT
G
Found at i:12263 original size:19 final size:18
Alignment explanation
Indices: 12220--12267 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
12210 AATGTAGGGG
* *
12220 AAATTTTATATATGATTC
1 AAATTTTGTATACGATTC
*
12238 AAATTTTGTATACGATTT
1 AAATTTTGTATACGATTC
12256 ATAATTTTGTAT
1 A-AATTTTGTAT
12268 GTGAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.52
Consensus pattern (18 bp):
AAATTTTGTATACGATTC
Found at i:15487 original size:198 final size:200
Alignment explanation
Indices: 15002--15520 Score: 611
Period size: 200 Copynumber: 2.6 Consensus size: 200
14992 AGATGTATCG
* * ** *
15002 ATACATTTTCTAAAAGTATCGACCCCAAAAACATCGAAACCAAAAATTATAATGTAATAGGTAAA
1 ATACA-TTTATAAAAGTATCGATCCCAAAAACATCGAAACTGATAATTATAATGTAATAGGTAAA
* * * * * * *
15067 TTAACAAT-ATAACCGGTATAAATATACC-AGTTAATTACAAAACAGGTAAACATAATGTATCGA
65 TTTACAATGTTAA-CGGTATAAATATACCGATTTTATTAGAAAATAGGTCAACATAATGTATCGA
* * *
15130 CACTTGTGGAATTTGTGTCGATACTTATTATCCAGAATAAATGCCCAAACGAGGTGCACGCATAA
129 CACTTGTGAAATATGTGTCAATACTTATTATCCAGAATAAATGCCCAAACGAGGTGCACGCATAA
*
15195 AGTGTCG
194 AGTGTCA
* *
15202 ATACATTTATTAAAAGTATCAATCCCAAAAACATCGAAACTGATAATTATGATGTAATAGGTAAA
1 ATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACTGATAATTATAATGTAATAGGTAAA
* ** * *
15267 TTTACAGTG-TAACAAATATAAATATACCGATTTTATGAGATAATAGGTCAACATAATGTATCGA
65 TTTACAATGTTAAC-GGTATAAATATACCGATTTTATTAGAAAATAGGTCAACATAATGTATCGA
* * * * * * * *
15331 CACTTTTTAAATATGTTTCAATA-TTTTTTTCCAGAATGAATGTCC-AATGAGGTGCACGCATAA
129 CACTTGTGAAATATGTGTCAATACTTATTATCCAGAATAAATGCCCAAACGAGGTGCACGCATAA
15394 AGTGTCA
194 AGTGTCA
* *
15401 ATACATTTA-AAATTGTATCGATCCCAAAAACATCGAAACTGATAGTTATAATGTAATAGGTAAA
1 ATACATTTATAAA-AGTATCGATCCCAAAAACATCGAAACTGATAATTATAATGTAATAGGTAAA
* * *
15465 TTTACAATGTTATCGGTATAAATAAACCG-TTTTAGTTAGAAAATAGGTCAATATAA
65 TTTACAATGTTAACGGTATAAATATACCGATTTTA-TTAGAAAATAGGTCAACATAA
15521 ACGCTACCTA
Statistics
Matches: 270, Mismatches: 42, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
197 8 0.03
198 85 0.31
199 39 0.14
200 93 0.34
201 45 0.17
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (200 bp):
ATACATTTATAAAAGTATCGATCCCAAAAACATCGAAACTGATAATTATAATGTAATAGGTAAAT
TTACAATGTTAACGGTATAAATATACCGATTTTATTAGAAAATAGGTCAACATAATGTATCGACA
CTTGTGAAATATGTGTCAATACTTATTATCCAGAATAAATGCCCAAACGAGGTGCACGCATAAAG
TGTCA
Found at i:15616 original size:23 final size:23
Alignment explanation
Indices: 15590--15652 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
15580 CGTTAAATGT
* *
15590 CTATTTTATTATATAATCGCTAC
1 CTATTATATTATATAAACGCTAC
15613 CTATTATATTATATAAACGCTAC
1 CTATTATATTATATAAACGCTAC
* * *
15636 TTAATATGTTAT-TAAAC
1 CTATTATATTATATAAAC
15653 TTGATGATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 5 0.14
23 30 0.86
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (23 bp):
CTATTATATTATATAAACGCTAC
Found at i:16094 original size:14 final size:14
Alignment explanation
Indices: 16075--16102 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16065 ATCTACTGCC
16075 GGTTACAGTAGAGA
1 GGTTACAGTAGAGA
16089 GGTTACAGTAGAGA
1 GGTTACAGTAGAGA
16103 TCTGAGCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.36, T:0.21
Consensus pattern (14 bp):
GGTTACAGTAGAGA
Found at i:17390 original size:15 final size:15
Alignment explanation
Indices: 17372--17410 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
17362 ACCCGTCCCG
17372 CATCCGCCCGCCCCA
1 CATCCGCCCGCCCCA
17387 CATCCGCCCGCCCCA
1 CATCCGCCCGCCCCA
17402 CATCCGCCC
1 CATCCGCCC
17411 ACCCAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.13, C:0.67, G:0.13, T:0.08
Consensus pattern (15 bp):
CATCCGCCCGCCCCA
Found at i:31229 original size:15 final size:17
Alignment explanation
Indices: 31192--31231 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
31182 GCCTCCAGCA
31192 AAAAGAACAAAACAACGC
1 AAAAGAACAAAACAAC-C
31210 AAAAGAACAAAAC-A-C
1 AAAAGAACAAAACAACC
31225 AAAAGAA
1 AAAAGAA
31232 AACCAACACC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
17 1 0.05
18 13 0.59
ACGTcount: A:0.72, C:0.17, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAGAACAAAACAACC
Found at i:32711 original size:16 final size:16
Alignment explanation
Indices: 32669--32737 Score: 60
Period size: 13 Copynumber: 4.7 Consensus size: 16
32659 GTTTAGAACT
* *
32669 GAATTACTGTAGCCGG
1 GAATTACTGTAACCGA
32685 GAA-TA--GTAACCGA
1 GAATTACTGTAACCGA
*
32698 GAATTACTGTAACCGG
1 GAATTACTGTAACCGA
*
32714 GAA-TA--ATAACCGA
1 GAATTACTGTAACCGA
32727 GAATTACTGTA
1 GAATTACTGTA
32738 GCCAGGAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
13 18 0.44
14 4 0.10
15 4 0.10
16 15 0.37
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (16 bp):
GAATTACTGTAACCGA
Found at i:32713 original size:29 final size:29
Alignment explanation
Indices: 32669--32752 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 29
32659 GTTTAGAACT
32669 GAATTACTGTAGCCGGGAATAGTAACCGA
1 GAATTACTGTAGCCGGGAATAGTAACCGA
* *
32698 GAATTACTGTAACCGGGAATAATAACCGA
1 GAATTACTGTAGCCGGGAATAGTAACCGA
*
32727 GAATTACTGTAGCCAGGAATAGTAAC
1 GAATTACTGTAGCCGGGAATAGTAAC
32753 TGTCGACGGT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (29 bp):
GAATTACTGTAGCCGGGAATAGTAACCGA
Found at i:38289 original size:20 final size:20
Alignment explanation
Indices: 38264--38326 Score: 126
Period size: 20 Copynumber: 3.1 Consensus size: 20
38254 GTTAGCTAAG
38264 GTTGTTAGTCAGGTAGTTTA
1 GTTGTTAGTCAGGTAGTTTA
38284 GTTGTTAGTCAGGTAGTTTA
1 GTTGTTAGTCAGGTAGTTTA
38304 GTTGTTAGTCAGGTAGTTTA
1 GTTGTTAGTCAGGTAGTTTA
38324 GTT
1 GTT
38327 CCTAACATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.19, C:0.05, G:0.30, T:0.46
Consensus pattern (20 bp):
GTTGTTAGTCAGGTAGTTTA
Found at i:49528 original size:38 final size:38
Alignment explanation
Indices: 49486--49560 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
49476 CAAATATTAC
49486 AAAAATAAAAATT-AAATTACTAA-ATATATATATATATT
1 AAAAAT-AAAATTAAAATT-CTAATATATATATATATATT
** *
49524 AAAAATACTATTAAAATTTTAATATATATATATATAT
1 AAAAATAAAATTAAAATTCTAATATATATATATATAT
49561 ATATCATAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 7 0.22
38 25 0.78
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (38 bp):
AAAAATAAAATTAAAATTCTAATATATATATATATATT
Found at i:49908 original size:16 final size:16
Alignment explanation
Indices: 49889--49923 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
49879 TTGAGTCGAA
*
49889 CTCGAGTATTACTGAG
1 CTCGAGTATTACTAAG
49905 CTCGAGTATTACTAAG
1 CTCGAGTATTACTAAG
49921 CTC
1 CTC
49924 TATTCAGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (16 bp):
CTCGAGTATTACTAAG
Found at i:50509 original size:11 final size:11
Alignment explanation
Indices: 50495--50522 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
50485 ATTTTGAGTA
50495 TATTTTATATT
1 TATTTTATATT
50506 TATTTTATATT
1 TATTTTATATT
50517 TATTTT
1 TATTTT
50523 TTGAGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TATTTTATATT
Found at i:50559 original size:35 final size:35
Alignment explanation
Indices: 50486--50559 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 35
50476 TTAATTTTTA
* ** *
50486 TTTTGAGTATATTTTATATTTATTTTATATTTATT
1 TTTTGAGTATATTTTATATTTAATTTATAAATAAT
50521 TTTTGAGTAT-TTTTATATTTTAAATTTA-AAATAAT
1 TTTTGAGTATATTTTATA-TTT-AATTTATAAATAAT
50556 TTTT
1 TTTT
50560 ATTTTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
34 7 0.21
35 21 0.64
36 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (35 bp):
TTTTGAGTATATTTTATATTTAATTTATAAATAAT
Found at i:50957 original size:19 final size:20
Alignment explanation
Indices: 50933--50983 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
50923 AATGACCAAT
50933 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
50952 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
50972 AAAATCGCAACG
1 AAAATCGCAACG
50984 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:50977 original size:20 final size:20
Alignment explanation
Indices: 50933--51147 Score: 98
Period size: 20 Copynumber: 10.6 Consensus size: 20
50923 AATGACCAAT
*
50933 AAAATCGCAACGCGA-T-ATC
1 AAAATCGCAACGCGATTGA-G
*
50952 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
** ***
50972 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTGAG
**
50992 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TGAG
**
51012 AAAATCGCAACGCGAGCTT-CC
1 AAAATCGCAACGCGA--TTGAG
**
51033 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA-TT-G-AG
* *
51056 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTGAG
* * *
51076 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTGAG
* * *
51096 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTGAG
* * *
51116 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
*
51136 AGAATCGCAACG
1 AAAATCGCAACG
51148 TTGAAAATCG
Statistics
Matches: 161, Mismatches: 24, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
19 15 0.09
20 115 0.71
21 16 0.10
22 2 0.01
23 12 0.07
24 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTGAG
Found at i:51109 original size:40 final size:40
Alignment explanation
Indices: 51058--51145 Score: 158
Period size: 40 Copynumber: 2.2 Consensus size: 40
51048 TTTAGAAGAA
* *
51058 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGACTGAGAG
51098 AATCGCAATGCGATTGATAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGACTGAGAG
51138 AATCGCAA
1 AATCGCAA
51146 CGTTGAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (40 bp):
AATCGCAATGCGATTGATAGAATCGCAATGCGACTGAGAG
Found at i:51226 original size:6 final size:6
Alignment explanation
Indices: 51215--51293 Score: 158
Period size: 6 Copynumber: 13.2 Consensus size: 6
51205 GACACGTATT
51215 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
51263 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
51294 GACGGCGGCG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.34, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:51982 original size:5 final size:5
Alignment explanation
Indices: 51974--52076 Score: 161
Period size: 5 Copynumber: 19.6 Consensus size: 5
51964 CCGTCTCGTC
51974 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG
52024 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG-GG TCG-GG
52074 TCG
1 TCG
52077 TACGTGTCTT
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 68 0.70
6 29 0.30
ACGTcount: A:0.00, C:0.19, G:0.56, T:0.24
Consensus pattern (5 bp):
TCGGG
Found at i:52177 original size:20 final size:20
Alignment explanation
Indices: 52152--52195 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
52142 TTTTTAACTA
*
52152 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
52172 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
52192 TTCT
1 TTCT
52196 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:52205 original size:20 final size:20
Alignment explanation
Indices: 52182--52488 Score: 127
Period size: 20 Copynumber: 15.6 Consensus size: 20
52172 TTCTTTTTAA
52182 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
52202 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
52222 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
52242 CATTGCGATTTTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
52262 CATTGCGA--TTC----T--
1 CGTTGCGATTTTCTAAATCG
* * * *
52274 C--TCCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
52292 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
52315 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
52335 CATTGCGATTATATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
52355 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
52375 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* *
52398 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
52416 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
*
52438 CGTTGCGATTTTCTAAACCG
1 CGTTGCGATTTTCTAAATCG
* *
52458 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
*
52477 CGTTGCGCTTTT
1 CGTTGCGATTTT
52489 ATTGGTCATT
Statistics
Matches: 223, Mismatches: 44, Indels: 41
0.72 0.14 0.13
Matches are distributed among these distances:
10 4 0.02
12 3 0.01
14 1 0.00
16 1 0.00
18 6 0.03
19 15 0.07
20 156 0.70
21 3 0.01
22 6 0.03
23 28 0.13
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:52228 original size:40 final size:40
Alignment explanation
Indices: 52184--52407 Score: 216
Period size: 40 Copynumber: 5.7 Consensus size: 40
52174 CTTTTTAACG
52184 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * * *
52224 TTGCGATTCTATAAATCGCATTGCGATTTTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* *
52264 TTGCGA--TTC----T--C--TCCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
*
52294 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
52337 TTGCGATTATATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
52377 TTGCGATTTTCTTCTAAATCGCGTTGCGATT
1 TTGCGA--TT-TTCTAAATCGCGTTGCGATT
52408 TTCTTTTGAC
Statistics
Matches: 148, Mismatches: 20, Indels: 29
0.75 0.10 0.15
Matches are distributed among these distances:
30 23 0.16
32 1 0.01
34 1 0.01
35 3 0.02
38 1 0.01
39 1 0.01
40 74 0.50
41 3 0.02
42 2 0.01
43 39 0.26
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:52336 original size:73 final size:70
Alignment explanation
Indices: 52207--52344 Score: 195
Period size: 73 Copynumber: 1.9 Consensus size: 70
52197 AATCGCGTTG
* * *
52207 CGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTTTCTCAGTCGCATTGCGATT
1 CGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGACTCTCTCAATCGCATTGCGATT
52272 CTCTC
66 CTCTC
* * *
52277 CGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCG
1 CGATTCTCTCAATCGCATTGCGA--TTC-TATAAATCGCATTGCGACTCTCTCAATCGCATTGCG
52342 ATT
63 ATT
52345 ATATAAATCG
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
70 22 0.37
72 3 0.05
73 34 0.58
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.37
Consensus pattern (70 bp):
CGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGACTCTCTCAATCGCATTGCGATT
CTCTC
Found at i:54288 original size:32 final size:32
Alignment explanation
Indices: 54246--54307 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
54236 GACAAATCGA
* *
54246 AACAGTTCATAGTTTAGAGGAAACGAATGGGT
1 AACAGATCATAGTTTACAGGAAACGAATGGGT
54278 AACAGATCATAGTTTACAGGAAACGAATGG
1 AACAGATCATAGTTTACAGGAAACGAATGG
54308 CTTACCAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23
Consensus pattern (32 bp):
AACAGATCATAGTTTACAGGAAACGAATGGGT
Found at i:56788 original size:20 final size:20
Alignment explanation
Indices: 56765--56816 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
56755 AACGCGATCC
56765 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
56785 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
56805 CCAAAATCGCAA
1 CCAGAATCGCAA
56817 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:56833 original size:21 final size:20
Alignment explanation
Indices: 56806--56904 Score: 63
Period size: 21 Copynumber: 4.8 Consensus size: 20
56796 AATCAGTTTC
56806 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * * *
56827 GAAAATCACGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
56848 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
56868 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
56889 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
56905 ACACATAAAT
Statistics
Matches: 57, Mismatches: 19, Indels: 5
0.70 0.23 0.06
Matches are distributed among these distances:
20 16 0.28
21 41 0.72
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:56933 original size:20 final size:20
Alignment explanation
Indices: 56871--57064 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
56861 CGATTTTCCA
* ** *
56871 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
56891 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
56911 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
56931 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
56951 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
56971 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
56991 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
57011 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
57031 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
57052 AAATCGCAACGCG
1 AAATCGCAACGCG
57065 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:56955 original size:60 final size:60
Alignment explanation
Indices: 56871--57064 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
56861 CGATTTTCCA
* ** * *
56871 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
56931 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
56991 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
57052 AAATCGCAACGCG
1 AAATCGCAACGCG
57065 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:57484 original size:33 final size:33
Alignment explanation
Indices: 57445--57515 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
57435 TTCACTTAGA
57445 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
57478 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
57511 TTTCA
1 TTTCA
57516 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:57637 original size:20 final size:20
Alignment explanation
Indices: 57595--57650 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
57585 TGCAGAAGAG
*
57595 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
*
57616 TCGCAACGAGAGAATGACAA
1 TCGCAACGAGAGAATGAAAA
57636 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
57651 CGCAACGCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 22 0.67
21 11 0.33
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:57653 original size:14 final size:14
Alignment explanation
Indices: 57634--57690 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
57624 AGAGAATGAC
57634 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
57648 AATCGCAACGCGAAATGG
1 AATCGCAA--CGAGA--G
57666 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
57681 AATCGCAACG
1 AATCGCAACG
57691 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 1 0.03
16 4 0.11
17 4 0.11
18 1 0.03
19 8 0.22
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:57676 original size:33 final size:33
Alignment explanation
Indices: 57614--57695 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
57604 GATAAATGAA
*
57614 AATCGCAACGAGAGAATGACAATCGCAACGAGAG
1 AATCGCAACGCGA-AATGACAATCGCAACGAGAG
57648 AATCGCAACGCGAAATGGA-AATCGCAACGAGAG
1 AATCGCAACGCGAAAT-GACAATCGCAACGAGAG
57681 AATCGCAACGCGAAA
1 AATCGCAACGCGAAA
57696 CCAAAAATCG
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 32 0.70
34 14 0.30
ACGTcount: A:0.44, C:0.22, G:0.26, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACAATCGCAACGAGAG
Found at i:57858 original size:25 final size:24
Alignment explanation
Indices: 57804--57858 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
57794 TTATGTTTAT
* *
57804 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
57828 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
57854 TGTTT
1 TGTTT
57859 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:59740 original size:93 final size:93
Alignment explanation
Indices: 59433--59811 Score: 728
Period size: 93 Copynumber: 4.1 Consensus size: 93
59423 TAGATTGCTT
59433 AGTAAATTTGTTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTG-TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
59498 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
59527 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACA-TGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
59589 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
59617 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
59682 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
59710 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
59775 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
59803 AGTAAATTT
1 AGTAAATTT
59812 ATCCATTCAA
Statistics
Matches: 282, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
90 62 0.22
91 28 0.10
92 28 0.10
93 154 0.55
94 10 0.04
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:59894 original size:19 final size:19
Alignment explanation
Indices: 59854--59982 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
59844 TAGTTTACTT
* *
59854 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
59874 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
59893 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
59912 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
59926 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
59945 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
59959 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
59978 TCGCA
1 TCGCA
59983 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:59933 original size:33 final size:32
Alignment explanation
Indices: 59890--59982 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
59880 CGCGAAACCA
**
59890 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
59922 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
59955 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
59983 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:59980 original size:52 final size:52
Alignment explanation
Indices: 59854--59982 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
59844 TAGTTTACTT
**
59854 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
59906 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
59959 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
59983 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:60000 original size:19 final size:19
Alignment explanation
Indices: 59978--60111 Score: 126
Period size: 19 Copynumber: 7.6 Consensus size: 19
59968 GAAACCAAAA
*
59978 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
59997 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
60013 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
60030 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
60046 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
60063 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
60082 TCGCGTTGCGATTTTAAGT
1 TCGCGTTGCGATTTTCATT
*
60101 TCGTGTTGCGA
1 TCGCGTTGCGA
60112 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 57 0.61
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:60019 original size:14 final size:14
Alignment explanation
Indices: 60000--60056 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
59990 TTTCATTTCG
60000 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
60014 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
60031 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
60047 CGTTGCGATT
1 CGTTGCGATT
60057 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:60025 original size:33 final size:33
Alignment explanation
Indices: 59983--60075 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
59973 CAAAATCGCA
*
59983 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
60016 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
60049 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
60076 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:61952 original size:34 final size:36
Alignment explanation
Indices: 61913--61981 Score: 106
Period size: 38 Copynumber: 1.9 Consensus size: 36
61903 AATTGATTGT
61913 TTTTTGATTGTTT-A-ATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATATTTGTAAAAGTTGATTCAA
61947 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATT
1 TTTTTGATTGTTTAA-T-ATTTGTAAAAGTTGATT
61982 TGTGTAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
34 13 0.42
35 1 0.03
38 17 0.55
ACGTcount: A:0.28, C:0.01, G:0.16, T:0.55
Consensus pattern (36 bp):
TTTTTGATTGTTTAATATTTGTAAAAGTTGATTCAA
Found at i:62107 original size:19 final size:19
Alignment explanation
Indices: 62091--62192 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
62081 AAAAATGACT
62091 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
62110 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
62129 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
62143 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
62162 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
62182 ATCGCAATGCG
1 ATCGCAATGCG
62193 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:62245 original size:19 final size:19
Alignment explanation
Indices: 62221--62473 Score: 287
Period size: 19 Copynumber: 14.4 Consensus size: 19
62211 GATTATCTCG
*
62221 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
62240 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
62259 TTGCGA--TT-ATTTCG--
1 TTGCGATTTTCATTTCGCA
62273 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
62292 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
62311 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
62330 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
62349 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
62364 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
62382 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
62400 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
62414 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
62433 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
62447 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
62466 TTGCGATT
1 TTGCGATT
62474 GTATTTCCGT
Statistics
Matches: 202, Mismatches: 12, Indels: 40
0.80 0.05 0.16
Matches are distributed among these distances:
14 26 0.13
15 2 0.01
16 24 0.12
17 24 0.12
18 20 0.10
19 106 0.52
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:62277 original size:52 final size:52
Alignment explanation
Indices: 62199--62356 Score: 244
Period size: 52 Copynumber: 2.9 Consensus size: 52
62189 TGCGTTTATA
* *
62199 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGTATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
62251 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
62303 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATT
62357 ATGTCGGTTC
Statistics
Matches: 98, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
52 64 0.65
54 2 0.02
55 6 0.06
57 26 0.27
ACGTcount: A:0.16, C:0.18, G:0.17, T:0.48
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:62421 original size:51 final size:52
Alignment explanation
Indices: 62221--62445 Score: 239
Period size: 52 Copynumber: 4.2 Consensus size: 52
62211 GATTATCTCG
* *
62221 TTGCGATTTTCATTTCGTATTGCGATTTTCATTTCGCATTGCGA--TT-ATTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
62273 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
62330 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
62382 TTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
62433 TTGCGATTTTCAT
1 TTGCGATTTTCAT
62446 GTTGGGATTT
Statistics
Matches: 157, Mismatches: 8, Indels: 16
0.87 0.04 0.09
Matches are distributed among these distances:
50 3 0.02
51 44 0.28
52 70 0.45
53 2 0.01
54 5 0.03
55 9 0.06
57 24 0.15
ACGTcount: A:0.16, C:0.19, G:0.17, T:0.48
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:62429 original size:33 final size:33
Alignment explanation
Indices: 62240--62473 Score: 190
Period size: 33 Copynumber: 6.8 Consensus size: 33
62230 TCATTTCGTA
*
62240 TTGCGATTTTCATTTCGCATTGCGATTATTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
*
62273 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TT-ATCTCG
* *
62309 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-ATCTCG
** * * *
62347 CATTGCGATTATGTCGGTTCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTATCTCG
*
62382 TTGCGA-TTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
*
62414 TTGCGATTTTCATTTCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTTCGCATTGCGATTATC-TCG
* *
62447 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
62474 GTATTTCCGT
Statistics
Matches: 172, Mismatches: 16, Indels: 26
0.80 0.07 0.12
Matches are distributed among these distances:
30 9 0.05
31 5 0.03
32 10 0.06
33 79 0.46
34 1 0.01
35 4 0.02
36 6 0.03
37 2 0.01
38 44 0.26
39 3 0.02
40 9 0.05
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTATCTCG
Found at i:64899 original size:12 final size:12
Alignment explanation
Indices: 64882--64906 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64872 TCTTCGGGGA
64882 CTTTTTCTTCTT
1 CTTTTTCTTCTT
64894 CTTTTTCTTCTT
1 CTTTTTCTTCTT
64906 C
1 C
64907 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:65114 original size:24 final size:24
Alignment explanation
Indices: 65080--65126 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
65070 CTGAAACATC
65080 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
65104 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
65127 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:65822 original size:20 final size:20
Alignment explanation
Indices: 65794--66157 Score: 404
Period size: 20 Copynumber: 18.4 Consensus size: 20
65784 AAATTTCAGT
* * * *
65794 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
65814 GTTGCGATTTAC-GATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
65833 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
* *
65853 GTTGCAATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
65873 G-TGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
65892 GTTGCGATTTAC-GATTA-TC
1 GTTGCGATTTACGGA-TACGC
65911 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
65931 GTTGCGATTT--GGATACGC
1 GTTGCGATTTACGGATACGC
*
65949 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
65969 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
65989 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
66009 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
66029 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
66049 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
66069 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
66089 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
66109 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
66129 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
66149 GTTGCGATT
1 GTTGCGATT
66158 ATGGAAAATC
Statistics
Matches: 299, Mismatches: 32, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
18 19 0.06
19 48 0.16
20 230 0.77
21 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:70047 original size:21 final size:21
Alignment explanation
Indices: 70023--70072 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
70013 TTGCGATATA
* * *
70023 GATCCAAGGTTTTCATTTGAT
1 GATCCAAGGTATTCAGTCGAT
70044 GATCCAAGGTATTCAGTCGAT
1 GATCCAAGGTATTCAGTCGAT
*
70065 GAGCCAAG
1 GATCCAAG
70073 AGCTTCCTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (21 bp):
GATCCAAGGTATTCAGTCGAT
Found at i:71532 original size:29 final size:29
Alignment explanation
Indices: 71479--71551 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
71469 AACCCAACCA
* * **
71479 TAGGTCGCCATGTACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACGCCCAGCGACCAAC
*
71508 TAGGTCGCCATGCACGCCC-GACGACCAAG
1 TAGGTCGCCATGCACGCCCAG-CGACCAAC
*
71537 GAGGTCGCCATGCAC
1 TAGGTCGCCATGCAC
71552 TCGGGGCGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 1 0.03
29 36 0.97
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAGCGACCAAC
Found at i:71815 original size:29 final size:29
Alignment explanation
Indices: 71782--71867 Score: 109
Period size: 29 Copynumber: 3.0 Consensus size: 29
71772 AGCAGGGGAT
* * **
71782 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* *
71811 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
71840 GTCGCTGGGAGTGCATGGCGACCTACGA
1 GTCGCCGGGAGTGCATGGCGACCTACGA
71868 CCACTGTTGA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.14, C:0.29, G:0.40, T:0.17
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:73115 original size:21 final size:21
Alignment explanation
Indices: 73066--73122 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
73056 TAAAATAAAT
* *
73066 AAAT-AAATAATATATTAAAGT
1 AAATAAAATAATA-ATAAAAGG
73087 AAATAAAATAATAATAAAAGG
1 AAATAAAATAATAATAAAAGG
73108 AAATAAAATGAATAA
1 AAATAAAAT-AATAA
73123 AAAGTAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 19 0.59
22 13 0.41
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (21 bp):
AAATAAAATAATAATAAAAGG
Found at i:74715 original size:31 final size:29
Alignment explanation
Indices: 74677--74744 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 29
74667 AAAATTATAT
* *
74677 ATTATATATTTTTGAAAAAAATGTTTTCAAA
1 ATTATATAGTTTTCAAAAAAAT-TTTT-AAA
*
74708 ATTATATAGTTTTCAAAAATATTTTTAAA
1 ATTATATAGTTTTCAAAAAAATTTTTAAA
*
74737 ACTATATA
1 ATTATATA
74745 CTATATAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 10 0.30
30 4 0.12
31 19 0.58
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (29 bp):
ATTATATAGTTTTCAAAAAAATTTTTAAA
Found at i:74743 original size:67 final size:63
Alignment explanation
Indices: 74646--74780 Score: 164
Period size: 65 Copynumber: 2.1 Consensus size: 63
74636 TCTATATAAC
* * * * *
74646 ATATATTTTTAAAAGTATTTTAAAATTATATATTATAT-ATTTTTGAAAAAAATGTTTTCAAAAT
1 ATATATTTTCAAAAATATTTTAAAACTATATACTATATAATTTTT---AAAAATGATTTCAAAAT
74710 T
63 T
*
74711 ATATAGTTTTCAAAAATATTTTTAAAACTATATACTATATAATTTTTCAAAATGATTTCAAAATT
1 ATATA-TTTTCAAAAATA-TTTTAAAACTATATACTATATAATTTTTAAAAATGATTTCAAAATT
74776 ATATA
1 ATATA
74781 ATATATATGT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
65 26 0.43
66 10 0.16
67 19 0.31
68 6 0.10
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (63 bp):
ATATATTTTCAAAAATATTTTAAAACTATATACTATATAATTTTTAAAAATGATTTCAAAATT
Found at i:74759 original size:37 final size:37
Alignment explanation
Indices: 74710--75046 Score: 263
Period size: 36 Copynumber: 9.2 Consensus size: 37
74700 TTTTCAAAAT
* *
74710 TATATAGTTTTCAAAAATATTTTTAAAACTATATACTA
1 TATATA-TTTTCAAAAATATTTTAAAAACTATATAATA
* *
74748 TATA-ATTTTTC-AAAATGA-TTTCAAAATTATATAATA
1 TATATA-TTTTCAAAAAT-ATTTTAAAAACTATATAATA
* * * *
74784 TATATGTTTTC-AAAATGTTTT-----TTTTA-AACTA
1 TATATATTTTCAAAAATATTTTAAAAACTATATAA-TA
*
74815 TATATATTTTC-AAAATGTTTTAAAAACTATAT-A-A
1 TATATATTTTCAAAAATATTTTAAAAACTATATAATA
* *
74849 TATATATTTTCAAAAATGTTTTAAAAACTATATATTA
1 TATATATTTTCAAAAATATTTTAAAAACTATATAATA
* *
74886 TATATTTTTTCAAAAATATTTTAAAAACTATATATTA
1 TATATATTTTCAAAAATATTTTAAAAACTATATAATA
* * *
74923 TATTTATTTTC-AAAATGTTTTAAAAACTATACAATA
1 TATATATTTTCAAAAATATTTTAAAAACTATATAATA
* * *
74959 TATAAATGTTTTCAAACATATTTTCAAAACTATATATTATA
1 TAT--ATATTTTCAAAAATATTTTAAAAACTATATA--ATA
* * *
75000 TATATGTTTTTTAAAAAATATTTT-CAAACTATATTTAATA
1 TATA--TATTTTCAAAAATATTTTAAAAACTATA--TAATA
75040 TATATAT
1 TATATAT
75047 ATATATGATA
Statistics
Matches: 248, Mismatches: 29, Indels: 44
0.77 0.09 0.14
Matches are distributed among these distances:
30 2 0.01
31 26 0.10
34 12 0.05
35 21 0.08
36 66 0.27
37 52 0.21
38 12 0.05
39 19 0.08
40 15 0.06
41 21 0.08
42 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (37 bp):
TATATATTTTCAAAAATATTTTAAAAACTATATAATA
Found at i:74829 original size:67 final size:66
Alignment explanation
Indices: 74744--74870 Score: 186
Period size: 67 Copynumber: 1.9 Consensus size: 66
74734 AAAACTATAT
* *
74744 ACTATATAATTTTTCAAAATGATTTCAAAATTATATAATATATATGTTTTC-AAAATGTTTTTTT
1 ACTATATAATTTTTCAAAATGATTTAAAAACTATATAATATATA--TTTTCAAAAATGTTTTTTT
74808 TAA
64 TAA
*
74811 ACTATAT-ATATTTTCAAAATGTTTTAAAAACTATATAATATATATTTTCAAAAATGTTTT
1 ACTATATAAT-TTTTCAAAATGATTTAAAAACTATATAATATATATTTTCAAAAATGTTTT
74871 AAAAACTATA
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
65 5 0.09
66 12 0.22
67 38 0.69
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (66 bp):
ACTATATAATTTTTCAAAATGATTTAAAAACTATATAATATATATTTTCAAAAATGTTTTTTTTA
A
Found at i:74841 original size:103 final size:101
Alignment explanation
Indices: 74631--75033 Score: 327
Period size: 103 Copynumber: 3.8 Consensus size: 101
74621 AATATTTTCC
* * * *
74631 AAAAATCTATATAACATATATTTTT-AAAA-GTATTTTAAAATTATATATTATATAT-TTTTGAA
1 AAAAA-CTATATAATATATATTTTTCAAAATG-ATTTCAAAATTATATAATATATATGTTTT--C
* * *
74693 AAAAATGTTTTCAAAA-T-TATATAGTTTTCAAAAATATTTT
62 AAAAATATTTTAAAAACTATATATA-TTTTC-AAAATGTTTT
* *
74733 TAAAACTATATACTATATAATTTTTCAAAATGATTTCAAAATTATATAATATATATGTTTTCAAA
1 AAAAACTATATAATATAT-ATTTTTCAAAATGATTTCAAAATTATATAATATATATGTTTTCAAA
* * **
74798 ATGTTTTTTTTAAACTATATATATTTTCAAAATGTTTT
65 A-ATATTTTAAAAACTATATATATTTTCAAAATGTTTT
* * * * *
74836 AAAAACTATATAATATATA-TTTTCAAAAATGTTTTAAAAACTATATATTATATATTTTTTCAAA
1 AAAAACTATATAATATATATTTTTC-AAAATGATTTCAAAATTATATAATATATATGTTTTCAAA
74900 AATATTTTAAAAACTATATATTATATTTATTTTCAAAATGTTTT
65 AATATTTTAAAAAC----TA-TATA--TATTTTCAAAATGTTTT
* *
74944 AAAAACTATACAATATATAAATGTTTTCAAACAT-ATTTTCAAAACTATATATTATATATATGTT
1 AAAAACTATATAATATAT--AT-TTTTCAAA-ATGA-TTTCAAAA-T-TATATAATATATATG--
* *
75008 TTTTAAAAAATATTTT-CAAACTATAT
57 TTTTCAAAAATATTTTAAAAACTATAT
75034 TTAATATATA
Statistics
Matches: 245, Mismatches: 31, Indels: 42
0.77 0.10 0.13
Matches are distributed among these distances:
101 25 0.10
102 50 0.20
103 59 0.24
104 11 0.04
105 8 0.03
106 4 0.02
108 34 0.14
110 4 0.02
111 5 0.02
112 14 0.06
114 12 0.05
115 4 0.02
116 15 0.06
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (101 bp):
AAAAACTATATAATATATATTTTTCAAAATGATTTCAAAATTATATAATATATATGTTTTCAAAA
ATATTTTAAAAACTATATATATTTTCAAAATGTTTT
Found at i:80756 original size:32 final size:32
Alignment explanation
Indices: 80718--80784 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
80708 ATCCCTCTTG
*
80718 CTTATGGCTTAGTTGTGAATTTCATCCCTCAA
1 CTTATGGCTAAGTTGTGAATTTCATCCCTCAA
*
80750 CTTATGGCTAAGTTGTGAATTTCATCCCTCGA
1 CTTATGGCTAAGTTGTGAATTTCATCCCTCAA
80782 CTT
1 CTT
80785 CCCAAATGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.40
Consensus pattern (32 bp):
CTTATGGCTAAGTTGTGAATTTCATCCCTCAA
Found at i:85883 original size:17 final size:17
Alignment explanation
Indices: 85857--85899 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
85847 GCAGCAAATT
*
85857 ATCATTCCGGCATCAGA
1 ATCATCCCGGCATCAGA
85874 ATCATCCCGGCATCAGA
1 ATCATCCCGGCATCAGA
85891 ATCATCCCG
1 ATCATCCCG
85900 AAAACCCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.28, C:0.35, G:0.16, T:0.21
Consensus pattern (17 bp):
ATCATCCCGGCATCAGA
Found at i:93946 original size:26 final size:26
Alignment explanation
Indices: 93910--93960 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
93900 GAAGTGCTAG
*
93910 TACACATAAGGTTGTGCCCACCATAA
1 TACACATAAGGTCGTGCCCACCATAA
93936 TACACATAAGGTCGTGCCCACCATA
1 TACACATAAGGTCGTGCCCACCATA
93961 TGCACTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (26 bp):
TACACATAAGGTCGTGCCCACCATAA
Found at i:94903 original size:81 final size:81
Alignment explanation
Indices: 94793--95013 Score: 318
Period size: 81 Copynumber: 2.7 Consensus size: 81
94783 CCCAAAGGCA
* * * * *
94793 TTTAATCTTTCATCTAAGTTGCATGATTGACA-CTTGTCTGCCAAATGCACAGCTAGTCCATTTA
1 TTTAATCATTCATCTAACTGGCATAATTGACACCTT-TCTGCCAAATGCACAGCTAGGCCATTTA
*
94857 TCTTTTACTCAACGATC
65 TCATTTACTCAACGATC
* *
94874 TTTAATCATTCATATAACTGGCATAATTGACACCTTTCTGCCAAATGCACATCTAGGCCATTTAT
1 TTTAATCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTAT
*
94939 CATTTACTCAACGGTC
66 CATTTACTCAACGATC
* * *
94955 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCC
1 TTTAATCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCC
95014 TCAAAGGCAC
Statistics
Matches: 125, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
81 122 0.98
82 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.35
Consensus pattern (81 bp):
TTTAATCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTAT
CATTTACTCAACGATC
Found at i:98506 original size:21 final size:23
Alignment explanation
Indices: 98458--98508 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
98448 ATTCCCCTGT
*
98458 GGGGGAAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
98481 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
98502 GGGGGGA
1 GGGGGGA
98509 TCAATTCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.40
22 3 0.12
23 12 0.48
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.18
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:102428 original size:22 final size:22
Alignment explanation
Indices: 102398--102450 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
102388 AAATTGAAAT
*
102398 TTTCTTTTTCAATACTTTCAAA
1 TTTCATTTTCAATACTTTCAAA
102420 TTTCATTTTCAATACTTTCAAA
1 TTTCATTTTCAATACTTTCAAA
102442 TTTCATTTT
1 TTTCATTTT
102451 TGAGAGTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTCATTTTCAATACTTTCAAA
Found at i:104400 original size:68 final size:68
Alignment explanation
Indices: 104286--104618 Score: 470
Period size: 68 Copynumber: 4.9 Consensus size: 68
104276 GTTTTCAACA
* * * *
104286 CACTTAGCCTTTCATTTAACTGGCATAATTGAAATCTTTCTGTCAAATGCACAATTAGGCCTCAA
1 CACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAA
104351 AGG
66 AGG
* * * *
104354 CACTTAGACTTTCATCTAACTGGCATAATTGGCATCTTTCTATCAAATGCACAGTTAGGCCTCAA
1 CACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAA
*
104419 ATG
66 AGG
*
104422 CACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTC-AATGCATAGTTAGGCCTCAA
1 CACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAA
104486 AGG
66 AGG
* * * * *
104489 CACTTAACCTTTCATCTAACTGGCATAATTAACACCTTTCTGTCAAATACATAGTTAGGCCTAAA
1 CACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAA
**
104554 AAA
66 AGG
* * * *
104557 CACTTAGCCTTTTATCTAACTGGCATAATTCACACATTTCTATCAAATGCACAGTTAGGCCT
1 CACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
104619 ATTAATCTTT
Statistics
Matches: 238, Mismatches: 26, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
67 63 0.26
68 175 0.74
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (68 bp):
CACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAA
AGG
Found at i:104529 original size:135 final size:136
Alignment explanation
Indices: 104285--104618 Score: 483
Period size: 135 Copynumber: 2.5 Consensus size: 136
104275 TGTTTTCAAC
* * * *
104285 ACACTTAGCCTTTCATTTAACTGGCATAATTGAAATCTTTCTGTCAAATGCACAATTAGGCCTCA
1 ACACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCA
** * *
104350 AAGGCACTTAGACTTTCATCTAACTGGCATAATTGGCATCTTTCTATCAAATGCACAGTTAGGCC
66 AAGGCACTTAGACTTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATACACAGTTAGGCC
* *
104415 TCAAAT
131 TAAAAA
* *
104421 GCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTC-AATGCATAGTTAGGCCTCA
1 ACACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCA
* *
104485 AAGGCACTTA-ACCTTTCATCTAACTGGCATAATTAACACCTTTCTGTCAAATACATAGTTAGGC
66 AAGGCACTTAGA-CTTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATACACAGTTAGGC
104549 CTAAAAA
130 CTAAAAA
* * * *
104556 ACACTTAGCCTTTTATCTAACTGGCATAATTCACACATTTCTATCAAATGCACAGTTAGGCCT
1 ACACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
104619 ATTAATCTTT
Statistics
Matches: 176, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
134 1 0.01
135 118 0.67
136 57 0.32
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (136 bp):
ACACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCA
AAGGCACTTAGACTTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATACACAGTTAGGCC
TAAAAA
Found at i:104950 original size:55 final size:55
Alignment explanation
Indices: 104829--105048 Score: 318
Period size: 55 Copynumber: 4.0 Consensus size: 55
104819 ACATATATTT
* * *
104829 CCCATACGAAAATTAATACACTTAGTATGGATTTCTTAG-TTTGCACACATAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
*
104883 CCCATAAGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
104938 CCCATACGGAAATTCATACACTTAGTATTG-ATTTCTTAGTTTTGCACACATAGTG
1 CCCATACGGAAATTCATACACTTAGTA-TGAATTTCTTAGTTTTGCACACATAGTG
* * * * *
104993 CCTATACCGAAATTCATACACTCAATATGAATTTCTTAAGTTTTTGCACACTTAGT
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTT-AG-TTTTGCACACATAGT
105049 TCCATTTGGT
Statistics
Matches: 151, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
54 37 0.25
55 96 0.64
56 4 0.03
57 14 0.09
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (55 bp):
CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
Found at i:106726 original size:16 final size:16
Alignment explanation
Indices: 106691--106739 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
106681 AGCATTTAAG
106691 TTCAAACATCCAAAACAAA
1 TTCAAACATCC---ACAAA
106710 TTCAAACATCCACAAA
1 TTCAAACATCCACAAA
* *
106726 TTTAAACATTCACA
1 TTCAAACATCCACA
106740 TAAATCCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 17 0.61
19 11 0.39
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (16 bp):
TTCAAACATCCACAAA
Found at i:108755 original size:23 final size:23
Alignment explanation
Indices: 108694--108756 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
108684 ACCCTCATGT
* *
108694 GGGGGTATCGATACCCATTCAAA
1 GGGGGTATCGATACCTATGCAAA
*
108717 GAGGGTATCGATACCTATGCAAA
1 GGGGGTATCGATACCTATGCAAA
108740 GGGGGTATCGATACCTA
1 GGGGGTATCGATACCTA
108757 GCGCTTAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (23 bp):
GGGGGTATCGATACCTATGCAAA
Found at i:112574 original size:22 final size:21
Alignment explanation
Indices: 112532--112571 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
112522 AAGACTATTT
112532 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
112553 TCATTTTTTTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
112572 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Done.