Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001634.1 Hibiscus syriacus cultivar Beakdansim tig00003259_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: 59943
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:698 original size:28 final size:29
Alignment explanation
Indices: 662--773 Score: 142
Period size: 28 Copynumber: 4.0 Consensus size: 29
652 AAATTGTCAT
*
662 TTTTTCACAAAAATTC-CATAATGTCACC
1 TTTTTCACAAAAATTCTCAGAATGTCACC
* *
690 TTTTCCACAAAAAATC-CTAGAATGTCACC
1 TTTTTCACAAAAATTCTC-AGAATGTCACC
* *
719 TTTTTCATAAAAA-TCTTAGAATGTCACC
1 TTTTTCACAAAAATTCTCAGAATGTCACC
747 -TTTTCACAAAAATTCTCAGAATGTCAC
1 TTTTTCACAAAAATTCTCAGAATGTCAC
774 TGGGGGGTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 11 0.15
28 41 0.56
29 21 0.29
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (29 bp):
TTTTTCACAAAAATTCTCAGAATGTCACC
Found at i:731 original size:57 final size:56
Alignment explanation
Indices: 662--773 Score: 147
Period size: 57 Copynumber: 2.0 Consensus size: 56
652 AAATTGTCAT
*
662 TTTTTCACAAAAAT-TCCATAATGTCACCTTTTCCACAAAAAATCCT-AGAATGTCACC
1 TTTTTCACAAAAATCT-CAGAATGTCACCTTTT-CAC-AAAAATCCTCAGAATGTCACC
* * *
719 TTTTTCATAAAAATCTTAGAATGTCACCTTTTCACAAAAATTCTCAGAATGTCAC
1 TTTTTCACAAAAATCTCAGAATGTCACCTTTTCACAAAAATCCTCAGAATGTCAC
774 TGGGGGGTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
55 8 0.16
56 13 0.27
57 27 0.55
58 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (56 bp):
TTTTTCACAAAAATCTCAGAATGTCACCTTTTCACAAAAATCCTCAGAATGTCACC
Found at i:841 original size:18 final size:19
Alignment explanation
Indices: 807--850 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
797 TCGGGTCAGA
807 CGGTCAACCAGGTTCGGAC
1 CGGTCAACCAGGTTCGGAC
*
826 CGGTTAACCA-GTTCGGAC
1 CGGTCAACCAGGTTCGGAC
844 CGGTCAA
1 CGGTCAA
851 AACGGTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.18
Consensus pattern (19 bp):
CGGTCAACCAGGTTCGGAC
Found at i:7747 original size:29 final size:29
Alignment explanation
Indices: 7686--7790 Score: 142
Period size: 29 Copynumber: 3.7 Consensus size: 29
7676 TCCACATTCG
*
7686 AAAATTCCCA-AATTGTCA-TTTTTTCACA
1 AAAATTCCCAGAA-TGTCACATTTTTCACA
*
7714 AAAATTCCCAGAATGTCACATTTTCCACA
1 AAAATTCCCAGAATGTCACATTTTTCACA
* *
7743 AAAATTCACAGAATGTCACCTTTTTCACA
1 AAAATTCCCAGAATGTCACATTTTTCACA
*
7772 AATATTCCCAGAATGTCAC
1 AAAATTCCCAGAATGTCAC
7791 TGGTCGGGTC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
28 15 0.22
29 53 0.78
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.31
Consensus pattern (29 bp):
AAAATTCCCAGAATGTCACATTTTTCACA
Found at i:7807 original size:13 final size:13
Alignment explanation
Indices: 7789--7813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7779 CCAGAATGTC
7789 ACTGGTCGGGTCA
1 ACTGGTCGGGTCA
7802 ACTGGTCGGGTC
1 ACTGGTCGGGTC
7814 GGTCAACGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (13 bp):
ACTGGTCGGGTCA
Found at i:7819 original size:17 final size:16
Alignment explanation
Indices: 7792--7831 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
7782 GAATGTCACT
*
7792 GGTCGGGTCAACTGGTC
1 GGTC-GGTCAACGGGTC
7809 GGGTCGGTCAACGGGTC
1 -GGTCGGTCAACGGGTC
7826 GGTCGG
1 GGTCGG
7832 GTTAGACCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 11 0.52
18 4 0.19
ACGTcount: A:0.10, C:0.23, G:0.47, T:0.20
Consensus pattern (16 bp):
GGTCGGTCAACGGGTC
Found at i:7860 original size:19 final size:19
Alignment explanation
Indices: 7836--7902 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
7826 GGTCGGGTTA
7836 GACCGGTCAACCTGGTTTG
1 GACCGGTCAACCTGGTTTG
*
7855 GACCGGTCAACCTGGTTCG
1 GACCGGTCAACCTGGTTTG
* *
7874 GACCTGTCAAGCC-GGTTTA
1 GACCGGTCAA-CCTGGTTTG
7893 GACCGGTCAA
1 GACCGGTCAA
7903 ACCGGTCATA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 40 0.95
20 2 0.05
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.22
Consensus pattern (19 bp):
GACCGGTCAACCTGGTTTG
Found at i:8690 original size:19 final size:18
Alignment explanation
Indices: 8671--8719 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
8661 GTTGTTTTTA
8671 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
8689 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
8708 AAATAAACAAAT
1 AAATAAA-AAAT
8720 TAAAGAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:8985 original size:12 final size:12
Alignment explanation
Indices: 8968--9006 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
8958 ACGTTTTGAA
8968 TTTAGCCTTCGC
1 TTTAGCCTTCGC
8980 TTTAGCCTTCGC
1 TTTAGCCTTCGC
8992 TTTAGCCTTCAGC
1 TTTAGCCTTC-GC
9005 TT
1 TT
9007 GAAAGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.10, C:0.31, G:0.15, T:0.44
Consensus pattern (12 bp):
TTTAGCCTTCGC
Found at i:9258 original size:65 final size:65
Alignment explanation
Indices: 9189--9374 Score: 313
Period size: 64 Copynumber: 2.9 Consensus size: 65
9179 CCAAAACATC
9189 TTAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAAAAATAATACAATATT
1 TTAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAAAAATAATACAATATT
9254 TTAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCT-AAAAAATAATACAATATT
1 TTAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAAAAATAATACAATATT
* * *
9318 CTAAATCCTAATTAAAACAC-TAAAACCTATTTCAACTAAAATACCTAAAAAAGATAA
1 TTAAATCCTAATTAAAACACTTAAAA-CTATCTAAACTAAAATACCTAAAAAA-ATAA
9375 AATATAAAAA
Statistics
Matches: 115, Mismatches: 3, Indels: 5
0.93 0.02 0.04
Matches are distributed among these distances:
63 5 0.04
64 55 0.48
65 51 0.44
66 4 0.03
ACGTcount: A:0.55, C:0.17, G:0.01, T:0.28
Consensus pattern (65 bp):
TTAAATCCTAATTAAAACACTTAAAACTATCTAAACTAAAATACCTAAAAAAATAATACAATATT
Found at i:14683 original size:3 final size:3
Alignment explanation
Indices: 14675--14723 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
14665 ATTAAAACAT
* * *
14675 AAC AAC AAC AAC AAC AAA AAC AAC AAC AAC AAC AAT AAT AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
14723 A
1 A
14724 TCATATAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.69, C:0.27, G:0.00, T:0.04
Consensus pattern (3 bp):
AAC
Found at i:14698 original size:18 final size:18
Alignment explanation
Indices: 14675--14723 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
14665 ATTAAAACAT
14675 AACAACAACAACAACAAA
1 AACAACAACAACAACAAA
*
14693 AACAACAACAACAACAAT
1 AACAACAACAACAACAAA
*
14711 AATAACAACAACA
1 AACAACAACAACA
14724 TCATATAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.69, C:0.27, G:0.00, T:0.04
Consensus pattern (18 bp):
AACAACAACAACAACAAA
Found at i:20384 original size:4 final size:4
Alignment explanation
Indices: 20355--20411 Score: 55
Period size: 4 Copynumber: 14.0 Consensus size: 4
20345 AATTCAATAA
* *
20355 AAAT GAAAT AAAT ATAT AATAA AAAT AAAT AAAT AAAT -AA- AAAT AAATT
1 AAAT -AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T
20404 AAAT AAAT
1 AAAT AAAT
20412 GAAAACAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
3 4 0.09
4 29 0.66
5 11 0.25
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:20406 original size:19 final size:19
Alignment explanation
Indices: 20350--20416 Score: 82
Period size: 18 Copynumber: 3.4 Consensus size: 19
20340 CTGAAAATTC
*
20350 AATAAAAATGAAATAAATATA
1 AATAAAAAT-AAATTAA-ATA
20371 TAATAAAAATAAA-TAAATA
1 -AATAAAAATAAATTAAATA
20390 AATAAAAATAAATTAAATA
1 AATAAAAATAAATTAAATA
20409 AATGAAAA
1 AAT-AAAA
20417 CAAAAATGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
18 12 0.29
19 12 0.29
20 6 0.14
21 3 0.07
22 9 0.21
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (19 bp):
AATAAAAATAAATTAAATA
Found at i:21558 original size:56 final size:56
Alignment explanation
Indices: 21334--22252 Score: 688
Period size: 56 Copynumber: 16.3 Consensus size: 56
21324 ACCCACATCC
* * * * *
21334 CAAATATGGGAGTTTGAATAGCATTGTAATGCTTAACTTATCCAAGTTGTTACATT
1 CAAAGATGGAAGTTTGAATAACGTTGTAATGTTTAACTTATCCAAGTTGTTACATT
* * * *
21390 CAAAGATAGAAGTTTGGATAACGTTGTAATGTCTTAACTTA-CTGAAGTTGTTATATT
1 CAAAGATGGAAGTTTGAATAACGTTGTAATGT-TTAACTTATC-CAAGTTGTTACATT
* * * * *
21447 CCAAA-ATGAAAGTTTGAATAACATTTTAAT-TTCCTAACTTATCTAAGTTATTACATT
1 -CAAAGATGGAAGTTTGAATAACGTTGTAATGTT--TAACTTATCCAAGTTGTTACATT
* * * *
21504 CAAATATGGAAGTTTCAATAATGTTGTAATGTTTAACATATCCAAGTTGTTACATT
1 CAAAGATGGAAGTTTGAATAACGTTGTAATGTTTAACTTATCCAAGTTGTTACATT
* * * * * *
21560 CAAAG-GGGTAG-TTGAGTAGCGATGTAGA-GTTTAACTTATCCATGTTGTTACATT
1 CAAAGATGGAAGTTTGAATAACGTTGTA-ATGTTTAACTTATCCAAGTTGTTACATT
* ** * * * *
21614 GAAAGATAAAAGTTTGAATAACATTGTAATGTTTAACTCATCCAACTTGTTTCATT
1 CAAAGATGGAAGTTTGAATAACGTTGTAATGTTTAACTTATCCAAGTTGTTACATT
* * * *
21670 CAAAGATGAAAGGTTGAATAACGTTGTAATGTTTAATTTATCCATGTTGTTACATT
1 CAAAGATGGAAGTTTGAATAACGTTGTAATGTTTAACTTATCCAAGTTGTTACATT
* * * * *
21726 CAAGGATGAAAGTTTTAATAGCGTTGTAATGTTTAAGTTATCCAAGTTGTTACATT
1 CAAAGATGGAAGTTTGAATAACGTTGTAATGTTTAACTTATCCAAGTTGTTACATT
* * * * * * ** * *
21782 TAAAGATAGAAAATTTGAATAGCATTGTAACGTTTATGTTTTTCCAAGTTGTTACATC
1 CAAAGAT-GGAAGTTTGAATAACGTTGTAATGTTTA-ACTTATCCAAGTTGTTACATT
* * * * * *
21840 CAAAGATGGAAGTTTAAATAATGTTTTAAAGTTTAACTTATCCAAGCTGTTACATA
1 CAAAGATGGAAGTTTGAATAACGTTGTAATGTTTAACTTATCCAAGTTGTTACATT
* * * * * * *
21896 CAAAAACT-AAAGCTTAAATAGCGTTGTAATGTCTTAAATTATCCAAGTCGTTACATT
1 CAAAGA-TGGAAGTTTGAATAACGTTGTAATGT-TTAACTTATCCAAGTTGTTACATT
* ** * * * *
21953 CAAATATGGAAACTTGAATAGCGTTGTAATGTCTTAGCTTGTTCAAGTTGTTACATT
1 CAAAGATGGAAGTTTGAATAACGTTGTAATGT-TTAACTTATCCAAGTTGTTACATT
* * * * * ** * *
22010 TAAAGATGGAAGATTGATTAGCATTGTAGGGTTTAACTTAT-CATGCTTGCTACATT
1 CAAAGATGGAAGTTTGAATAACGTTGTAATGTTTAACTTATCCAAG-TTGTTACATT
* * ** * * * * * * * *
22066 CAAAGACGAAAGCCTGAATAACATTTTACTGTTTGACTTATCCAACTTATGACATA
1 CAAAGATGGAAGTTTGAATAACGTTGTAATGTTTAACTTATCCAAGTTGTTACATT
* * * * * * *
22122 CAAAAATGGAAGTTTCAATAGCATTGT-ATGGTTTAGCTTAT-CATATTTGATACATT
1 CAAAGATGGAAGTTTGAATAACGTTGTAAT-GTTTAACTTATCCA-AGTTGTTACATT
* * * * **
22178 AAAAGATGGAAGTTTGAATAGCATTGTAATGTTTAACTTATCCAAGTTGTGACACA
1 CAAAGATGGAAGTTTGAATAACGTTGTAATGTTTAACTTATCCAAGTTGTTACATT
* *
22234 AAAAAATGGAAGTTTGAAT
1 CAAAGATGGAAGTTTGAAT
22253 TATTGGGACC
Statistics
Matches: 678, Mismatches: 162, Indels: 46
0.77 0.18 0.05
Matches are distributed among these distances:
54 38 0.06
55 15 0.02
56 376 0.55
57 219 0.32
58 30 0.04
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (56 bp):
CAAAGATGGAAGTTTGAATAACGTTGTAATGTTTAACTTATCCAAGTTGTTACATT
Found at i:21918 original size:170 final size:167
Alignment explanation
Indices: 21357--22227 Score: 591
Period size: 170 Copynumber: 5.2 Consensus size: 167
21347 TTGAATAGCA
* ** *
21357 TTGTAATGCTTAACTTATCCAAGTTGTTACATTCAAAGATAGAAGTTTGGATAACGTTGTAATGT
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATA-AAG-TTAAATAGCGTTGTAATGT
* * * * * *
21422 CTTAACTTA-CTGAAGTTGTTATATTCCAAA-AT-GAAAGTTTGAATAACATTTTAAT-TTCCTA
64 -TTAAATTATC-CAAGTTGTTACATT-CAAAGATAGAAAATTTGAATAGCATTGTAATGTT--T-
* * * * * *
21483 ACTT-ATCTAAGTTATTACATTCAAATATGGAAGTTTCAATAATG
123 AGTTCTTCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAATG
* **** * * *
21527 TTGTAATGTTTAACATATCCAAGTTGTTACATTCAAAGGGGTAGTTGAGTAGCGATGTAGA-GTT
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATAAAGTTAAATAGCGTTGTA-ATGTT
* * * * * ** *
21591 TAACTTATCCATGTTGTTACATTGAAAGATA-AAAGTTTGAATAACATTGTAATGTTTAACTCAT
65 TAAATTATCCAAGTTGTTACATTCAAAGATAGAAAATTTGAATAGCATTGTAATGTTTAGTTCTT
* * * * * *
21655 CCAACTTGTTTCATTCAAAGATGAAAGGTTGAATAACG
130 CCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAATG
* * * *
21693 TTGTAATGTTTAATTTATCCATGTTGTTACATTCAAGGATGAAAGTTTTAATAGCGTTGTAATGT
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGAT-AAAG-TTAAATAGCGTTGTAATGT
* * * *
21758 TTAAGTTATCCAAGTTGTTACATTTAAAGATAGAAAATTTGAATAGCATTGTAACGTTTATGTTT
64 TTAAATTATCCAAGTTGTTACATTCAAAGATAGAAAATTTGAATAGCATTGTAATGTTTA-GTTC
*
21823 TTCCAAGTTGTTACATCCAAAGATGGAAGTTTAAATAATG
128 TTCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAATG
* * * * *
21863 TTTTAAAGTTTAACTTATCCAAGCTGTTACATACAAAAACTAAAGCTTAAATAGCGTTGTAATGT
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGA-TAAAG-TTAAATAGCGTTGTAATGT
* * * * *
21928 CTTAAATTATCCAAGTCGTTACATTCAAATAT-GGAAACTTGAATAGCGTTGTAATGTCTTAGCT
64 -TTAAATTATCCAAGTTGTTACATTCAAAGATAGAAAATTTGAATAGCATTGTAATGT-TTAG-T
* * * * * ***
21992 TGTT-CAAGTTGTTACATTTAAAGATGGAAGATTGATTAGCA
126 TCTTCCAAGTTGTTACATTCAAAGATGGAAGTTTAAATAATG
** * * * * * * * * *
22033 TTGTAGGGTTTAACTTAT-CATGCTTGCTACATTCAAAGACGAAAGCCTGAATAACATTTTACTG
1 TTGTAATGTTTAACTTATCCAAG-TTGTTACATTCAAAGA-TAAAG-TTAAATAGCGTTGTAATG
* * * * * * * * * *
22097 TTTGACTTATCCAACTTATGACATACAAAAAT-GGAAGTTTCAATAGCATTGT-ATGGTTTAG--
63 TTTAAATTATCCAAGTTGTTACATTCAAAGATAGAAAATTTGAATAGCATTGTAAT-GTTTAGTT
* * * * * ***
22158 CTTATCATATTTGATACATTAAAAGATGGAAGTTTGAATAGCA
127 CTT-CCA-AGTTGTTACATTCAAAGATGGAAGTTTAAATAATG
22201 TTGTAATGTTTAACTTATCCAAGTTGT
1 TTGTAATGTTTAACTTATCCAAGTTGT
22228 GACACAAAAA
Statistics
Matches: 562, Mismatches: 118, Indels: 44
0.78 0.16 0.06
Matches are distributed among these distances:
165 4 0.01
166 69 0.12
167 47 0.08
168 114 0.20
169 74 0.13
170 219 0.39
171 35 0.06
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (167 bp):
TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATAAAGTTAAATAGCGTTGTAATGTTT
AAATTATCCAAGTTGTTACATTCAAAGATAGAAAATTTGAATAGCATTGTAATGTTTAGTTCTTC
CAAGTTGTTACATTCAAAGATGGAAGTTTAAATAATG
Found at i:23802 original size:31 final size:31
Alignment explanation
Indices: 23764--23842 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
23754 AGGGTCGAGG
23764 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACT
* *
23795 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATAGACT
* *
23826 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
23843 TGAATATATG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATAGACT
Found at i:23852 original size:31 final size:31
Alignment explanation
Indices: 23766--23854 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
23756 GGTCGAGGGT
* * *
23766 TTACCTATGTTCTTCGGGACATATAGACTGT
1 TTACCTATGTTCTTCTGGACATATGGACTGA
23797 TTACCTATGTTCTT-TGGGACATATGGACTGA
1 TTACCTATGTTCTTCT-GGACATATGGACTGA
* * *
23828 TTACCTAGGTTCTTCTGAATATATGGA
1 TTACCTATGTTCTTCTGGACATATGGA
23855 ATGGTTCTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 49 0.98
32 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCTGGACATATGGACTGA
Found at i:29848 original size:2 final size:2
Alignment explanation
Indices: 29841--29886 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
29831 AAAGGAAAGA
29841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29883 AT AT
1 AT AT
29887 GGATAGTTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30808 original size:56 final size:55
Alignment explanation
Indices: 30738--31121 Score: 262
Period size: 56 Copynumber: 6.9 Consensus size: 55
30728 ATGTTGTTAT
*
30738 GTTTAACTTATCCAAGTTGTTACATTCAAAAATGGAAGTTTGAATAGTGTTATATA
1 GTTTAATTTATCCAAGTTGTTACATTCAAAAATGGAAGTTTGAATAGTGTTATA-A
* * * * ** *
30794 GTTCAATTTATCCAAGTTGTCACATT-AATAGATGAAAGTTTGAATAGCATTTTAA
1 GTTTAATTTATCCAAGTTGTTACATTCAA-AAATGGAAGTTTGAATAGTGTTATAA
* * * * *
30849 TGTTTAATTT-TCCCAAGTTGTTATATTCAAAGATGAAAGTTTGAATA-TCATTTTAA
1 -GTTTAATTTAT-CCAAGTTGTTACATTCAAAAATGGAAGTTTGAATAGT-GTTATAA
* * *
30905 TGTTTAATTT-TCCCAAGTTGTTACATTCAAAAATGGAAGTTTAAATAATGTTTTAAA
1 -GTTTAATTTAT-CCAAGTTGTTACATTCAAAAATGGAAGTTTGAATAGTGTTAT-AA
* * * * * * * * * *
30962 GTTTAACTTATCCATGTTATTACATACAAAAGTTGAAGCTTAAATAGCGTTGTAA
1 GTTTAATTTATCCAAGTTGTTACATTCAAAAATGGAAGTTTGAATAGTGTTATAA
* * * * * *
31017 TGTCTTACA-TTATCCAAGTCT-TTATATTCAAATATGGAA-ATTGAGTAGCGTTGTAA
1 -GT-TTA-ATTTATCCAAGT-TGTTACATTCAAAAATGGAAGTTTGAATAGTGTTATAA
* * *
31073 GGTCTT-ATCTTGTCCAAGTTGTTACATTTAAACATGGAAGTTTGAATAG
1 -GT-TTAAT-TTATCCAAGTTGTTACATTCAAAAATGGAAGTTTGAATAG
31122 CATTGTGATA
Statistics
Matches: 269, Mismatches: 43, Indels: 31
0.78 0.13 0.09
Matches are distributed among these distances:
54 1 0.00
55 7 0.03
56 221 0.82
57 38 0.14
58 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (55 bp):
GTTTAATTTATCCAAGTTGTTACATTCAAAAATGGAAGTTTGAATAGTGTTATAA
Found at i:31217 original size:20 final size:20
Alignment explanation
Indices: 31192--31234 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
31182 TCTAAAAGCC
*
31192 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
31212 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
31232 CAT
1 CAT
31235 GTGGTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:41565 original size:56 final size:56
Alignment explanation
Indices: 41349--41708 Score: 300
Period size: 56 Copynumber: 6.4 Consensus size: 56
41339 TCATATTTGC
** ** * * * * *
41349 TACATTCAAAGATGGAAGCCTGAATAACATTCTAATGTTTGACTTATCAAAGTTAT
1 TACATTCAAAGATGGAAGTTTGAATAATGTTGTAATGTTTAATTTATCCAAGTTGT
* * * *** * *** *
41405 GACATACAAAAATGGAAGTTTGAATAGCATTGT-ATGGTTTAACTTATTGTATTTGT
1 TACATTCAAAGATGGAAGTTTGAATAATGTTGTAAT-GTTTAATTTATCCAAGTTGT
* * *
41461 TACATTCAAAGATGGAAGATTGAATAACGTTGTAATGTTTAAATTATCCAAGTTGT
1 TACATTCAAAGATGGAAGTTTGAATAATGTTGTAATGTTTAATTTATCCAAGTTGT
* * *
41517 GACATTTAAAGATGTAAGTTTGAATAATGTTGTAATGTTTAATTTATCCAAGTT-T
1 TACATTCAAAGATGGAAGTTTGAATAATGTTGTAATGTTTAATTTATCCAAGTTGT
* * * * * * *
41572 TCACTTTCAAAAAATGGAAGTTT-AGATAGTGTTCTAATTTTTAACTCATCCAAGTTGT
1 T-ACATTC-AAAGATGGAAGTTTGA-ATAATGTTGTAATGTTTAATTTATCCAAGTTGT
* *
41630 TACATTCAAAGATGGAAGTTTGTAT-ATCGTTATAGA-GTTTAAATTT-TCCAAGTTGT
1 TACATTCAAAGATGGAAGTTTGAATAAT-GTTGTA-ATGTTT-AATTTATCCAAGTTGT
41686 TACATTCAAAGATGGAAGTTTGA
1 TACATTCAAAGATGGAAGTTTGA
41709 GTAGCGTTGG
Statistics
Matches: 245, Mismatches: 49, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
55 4 0.02
56 190 0.78
57 49 0.20
58 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (56 bp):
TACATTCAAAGATGGAAGTTTGAATAATGTTGTAATGTTTAATTTATCCAAGTTGT
Found at i:41821 original size:56 final size:55
Alignment explanation
Indices: 41759--42140 Score: 229
Period size: 56 Copynumber: 7.0 Consensus size: 55
41749 AATTAAAGAG
* * *
41759 TTTAACTTATCCAAGTTGTTAAATTTAAAGATGGAAGTTTAAATAGAATTGTAGAA
1 TTTAACTTATCCAAGTTGTTACATTAAAAGATGGAAGTTTGAATAGAATTGTA-AA
* * * * *
41815 TTTAACTTAGT-CAAATT-TTTCTACTGAAAGATGGAAGTTTAAATAG-A--GT---
1 TTTAACTTA-TCCAAGTTGTTAC-ATTAAAAGATGGAAGTTTGAATAGAATTGTAAA
* ** * * *
41864 TTT-AGTTATCCAAGTTGTTACATGCAAATATGGAAGTTTGAATA-ATGTTGTAATG
1 TTTAACTTATCCAAGTTGTTACATTAAAAGATGGAAGTTTGAATAGA-ATTGTAA-A
* * ** * *
41919 TTTAACTTATTCAATTTGTTACATTCTAAGCTGGAAGTTTGAATA-ACATTGTAATG
1 TTTAACTTATCCAAGTTGTTACATTAAAAGATGGAAGTTTGAATAGA-ATTGTAA-A
* * ** *
41975 TTTAACTTAT-TAGAGTTGTTACATTAAAAAATGGAAG-TTGAAATAGTGTT-TTAA
1 TTTAACTTATCCA-AGTTGTTACATTAAAAGATGGAAGTTTG-AATAGAATTGTAAA
* * * **
42029 TGTCATAATTTATCTAAGTTGTTATATTAAAAGATGGAAGTTTGAATAGCGTTGTAGAA
1 T-T--TAACTTATCCAAGTTGTTACATTAAAAGATGGAAGTTTGAATAGAATTGTA-AA
* * *
42088 TTTAATTTATCCAAGTT-TTACATTCAAAA-ATGAAAGTTTGAATAGCATTGTAA
1 TTTAACTTATCCAAGTTGTTACATT-AAAAGATGGAAGTTTGAATAGAATTGTAA
42141 TGTCTTAACA
Statistics
Matches: 260, Mismatches: 42, Indels: 50
0.74 0.12 0.14
Matches are distributed among these distances:
47 1 0.00
48 27 0.10
49 6 0.02
51 2 0.01
53 2 0.01
54 2 0.01
55 40 0.15
56 132 0.51
57 38 0.15
58 7 0.03
59 3 0.01
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (55 bp):
TTTAACTTATCCAAGTTGTTACATTAAAAGATGGAAGTTTGAATAGAATTGTAAA
Found at i:42109 original size:112 final size:111
Alignment explanation
Indices: 41869--42131 Score: 273
Period size: 112 Copynumber: 2.3 Consensus size: 111
41859 AGAGTTTTAG
* * * *
41869 TTATCCAAGTTGTTACATGCAAATATGGAAGTTTGAATAATGTTGTAATGTTTAACTTATTCAAT
1 TTATCCAAGTTGTTACATTCAAAAATGGAAG-TTGAATAATGTTGTAATGTATAACTTATTCAAG
** * *
41934 TTGTTACATTCTAAGCTGGAAGTTTGAATAACATTGTAATGTTTAAC
65 TTGTTACATTAAAAGATGGAAGTTTGAATAACATTGTAATATTTAAC
* * * * *
41981 TTAT-TAGAGTTGTTACATTAAAAAATGGAAGTTGAAATAGTGTTTTAATGTCATAATTTA-TCT
1 TTATCCA-AGTTGTTACATTCAAAAATGGAAGTTG-AATAATGTTGTAATGT-ATAACTTATTC-
* * * *
42044 AAGTTGTTATATTAAAAGATGGAAGTTTGAATAGCGTTGTAGA-ATTTAAT
62 AAGTTGTTACATTAAAAGATGGAAGTTTGAATAACATTGTA-ATATTTAAC
*
42094 TTATCCAAGTT-TTACATTCAAAAATGAAAGTTTGAATA
1 TTATCCAAGTTGTTACATTCAAAAATGGAAG-TTGAATA
42132 GCATTGTAAT
Statistics
Matches: 124, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
111 4 0.03
112 62 0.50
113 56 0.45
114 2 0.02
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.40
Consensus pattern (111 bp):
TTATCCAAGTTGTTACATTCAAAAATGGAAGTTGAATAATGTTGTAATGTATAACTTATTCAAGT
TGTTACATTAAAAGATGGAAGTTTGAATAACATTGTAATATTTAAC
Found at i:42244 original size:421 final size:421
Alignment explanation
Indices: 41457--42224 Score: 967
Period size: 421 Copynumber: 1.8 Consensus size: 421
41447 CTTATTGTAT
*
41457 TTGTTACATTCAAAGATGGAAGATTGAATAACGTTGTAATGTTTAAATTATCCAAGTTGTGACAT
1 TTGTTACATGCAAAGATGGAAGATTGAATAACGTTGTAATGTTTAAATTATCCAAGTTGTGACAT
* ** * *
41522 TTAAAGATGTAAGTTTGAATAATGTTGTAATGTTTAATTTATCCAAGTTTTCACTTTCAAAAAAT
66 TTAAAGATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCCAAGTTTTCACATTCAAAAAAT
* * ** *
41587 GGAAGTTTAGATAGTGTTCTAATTTTTAACTCATCCAAGTTGTTACATTCAAAGATGGAAGTTTG
131 GGAAGTTGAAATAGTGTTCTAATTCATAACTCATCCAAGTTGTTACATTAAAAGATGGAAGTTTG
* * * * * * *
41652 TATATCGTTATAGAGTTTAAATTTTCCAAGTTGTTACATTCAAAGATGGAAGTTTGAGTAGCGTT
196 AATAGCGTTATAGAATTTAAATTTTCCAAGTTGTTACATTCAAAAATGAAAGTTTGAATAGCATT
* * * * * *
41717 GGAATTTTTGAATAACCAATTAGATGTTTATGAATTAAAGAGTTTAACTTATCCAAGTTGTTAAA
261 GGAATTCTTGAACAACAAATTAGACGTTTACGAACTAAAGAGTTTAACTTATCCAAGTTGTTAAA
* *
41782 TTTAAAGATGGAAGTTTAAATAGAATTGTAGAATTTAACTTAGTCAAATTTTTCTACTGAAAGAT
326 TTAAAAAATGGAAGTTTAAATAGAATTGTAGAATTTAACTTAGTCAAATTTTTCTACTGAAAGAT
41847 GGAAGTTTAAATAGAGTTTTAGTTATCCAAG
391 GGAAGTTTAAATAGAGTTTTAGTTATCCAAG
* * * * * * *
41878 TTGTTACATGCAAATATGGAAGTTTGAATAATGTTGTAATGTTTAACTTATTCAATTTGTTACAT
1 TTGTTACATGCAAAGATGGAAGATTGAATAACGTTGTAATGTTTAAATTATCCAAGTTGTGACAT
* *
41943 TCT-AAGCTGGAAGTTTGAATAACATTGTAATGTTTAACTTAT-TAGAGTTGTT-ACATT-AAAA
66 T-TAAAGATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCCA-AGTT-TTCACATTCAAAA
* * * * *
42004 AATGGAAGTTGAAATAGTGTTTTAATGTCATAATTTATCTAAGTTGTTATATTAAAAGATGGAAG
128 AATGGAAGTTGAAATAGTGTTCTAAT-TCATAACTCATCCAAGTTGTTACATTAAAAGATGGAAG
*
42069 TTTGAATAGCGTTGTAGAATTT-AATTTATCCAAGTT-TTACATTCAAAAATGAAAGTTTGAATA
192 TTTGAATAGCGTTATAGAATTTAAATTT-TCCAAGTTGTTACATTCAAAAATGAAAGTTTGAATA
* * * * *
42132 GCATTGTAATGTCTT-AACAA-AATACTTTGACGTTTACGAACTAAAGAGTTTAGCTTATCGATG
256 GCATTGGAAT-TCTTGAACAACAA-A-TTAGACGTTTACGAACTAAAGAGTTTAACTTATCCAAG
* * *
42195 TTGTTACATTAAAAAATGTAAGTTTTAATA
318 TTGTTAAATTAAAAAATGGAAGTTTAAATA
42225 ATGTTGTAAT
Statistics
Matches: 290, Mismatches: 49, Indels: 16
0.82 0.14 0.05
Matches are distributed among these distances:
419 1 0.00
420 70 0.24
421 216 0.74
422 3 0.01
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (421 bp):
TTGTTACATGCAAAGATGGAAGATTGAATAACGTTGTAATGTTTAAATTATCCAAGTTGTGACAT
TTAAAGATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCCAAGTTTTCACATTCAAAAAAT
GGAAGTTGAAATAGTGTTCTAATTCATAACTCATCCAAGTTGTTACATTAAAAGATGGAAGTTTG
AATAGCGTTATAGAATTTAAATTTTCCAAGTTGTTACATTCAAAAATGAAAGTTTGAATAGCATT
GGAATTCTTGAACAACAAATTAGACGTTTACGAACTAAAGAGTTTAACTTATCCAAGTTGTTAAA
TTAAAAAATGGAAGTTTAAATAGAATTGTAGAATTTAACTTAGTCAAATTTTTCTACTGAAAGAT
GGAAGTTTAAATAGAGTTTTAGTTATCCAAG
Found at i:42253 original size:23 final size:23
Alignment explanation
Indices: 42219--42263 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
42209 AATGTAAGTT
*
42219 TTAATAATGTTGTAATATTTAAC
1 TTAATAATGTTGTAACATTTAAC
*
42242 TTAACTAA-GTTGTTACATTTAA
1 TTAA-TAATGTTGTAACATTTAA
42264 AAATGGAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (23 bp):
TTAATAATGTTGTAACATTTAAC
Found at i:42266 original size:56 final size:56
Alignment explanation
Indices: 42194--42316 Score: 174
Period size: 56 Copynumber: 2.2 Consensus size: 56
42184 GCTTATCGAT
* * *
42194 GTTGTTACATTAAAAAATGTAAGTTTTAATAATGTTGTAATATTTAACTTAACTAA
1 GTTGTTACATTAAAAAATGGAAGTTTAAATAATGTTGTAATATTCAACTTAACTAA
* * * *
42250 GTTGTTACATTTAAAAATGGAAGTTTAAATAGTGTTGTAATGTTCAACTTATCTAA
1 GTTGTTACATTAAAAAATGGAAGTTTAAATAATGTTGTAATATTCAACTTAACTAA
*
42306 TTTGTTACATT
1 GTTGTTACATT
42317 GAATAGAGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.44
Consensus pattern (56 bp):
GTTGTTACATTAAAAAATGGAAGTTTAAATAATGTTGTAATATTCAACTTAACTAA
Found at i:42272 original size:421 final size:421
Alignment explanation
Indices: 41457--42492 Score: 954
Period size: 421 Copynumber: 2.5 Consensus size: 421
41447 CTTATTGTAT
*
41457 TTGTTACATTCAAAGATGGAAGATTGAATAACGTTGTAATGTTTAAATTATCCAAGTTGTGACAT
1 TTGTTACATGCAAAGATGGAAGATTGAATAACGTTGTAATGTTTAAATTATCCAAGTTGTGACAT
* ** * *
41522 TTAAAGATGTAAGTTTGAATAATGTTGTAATGTTTAATTTATCCAAGTTTTCACTTTCAAAAAAT
66 TTAAAGATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCCAAGTTTTCACATTCAAAAAAT
* * ** *
41587 GGAAGTTTAGATAGTGTTCTAATTTTTAACTCATCCAAGTTGTTACATTCAAAGATGGAAGTTTG
131 GGAAGTTGAAATAGTGTTCTAATTCATAACTCATCCAAGTTGTTACATTAAAAGATGGAAGTTTG
* * * * * * *
41652 TATATCGTTATAGAGTTTAAATTTTCCAAGTTGTTACATTCAAAGATGGAAGTTTGAGTAGCGTT
196 AATAGCGTTATAGAATTTAAATTTTCCAAGTTGTTACATTCAAAAATGAAAGTTTGAATAGCATT
* * * * * *
41717 GGAATTTTTGAATAACCAATTAGATGTTTATGAATTAAAGAGTTTAACTTATCCAAGTTGTTAAA
261 GGAATTCTTGAACAACAAATTAGACGTTTACGAACTAAAGAGTTTAACTTATCCAAGTTGTTAAA
* * * * *
41782 TTTAAAGATGGAAGTTTAAATAGAATTGTAGAATTTAACTTAGTCAAATTTTTCTACTGAAAGAT
326 TTAAAAAATGGAAGTTTAAATAGAATTGTAGAATTTAACTTACTCAAATTTTACTACTGAAAAAT
41847 GGAAGTTTAAATAGAGTTTTAGTTATCCAAG
391 GGAAGTTTAAATAGAGTTTTAGTTATCCAAG
* * * * * * *
41878 TTGTTACATGCAAATATGGAAGTTTGAATAATGTTGTAATGTTTAACTTATTCAATTTGTTACAT
1 TTGTTACATGCAAAGATGGAAGATTGAATAACGTTGTAATGTTTAAATTATCCAAGTTGTGACAT
* *
41943 TCT-AAGCTGGAAGTTTGAATAACATTGTAATGTTTAACTTAT-TAGAGTTGTT-ACATT-AAAA
66 T-TAAAGATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCCA-AGTT-TTCACATTCAAAA
* * * * *
42004 AATGGAAGTTGAAATAGTGTTTTAATGTCATAATTTATCTAAGTTGTTATATTAAAAGATGGAAG
128 AATGGAAGTTGAAATAGTGTTCTAAT-TCATAACTCATCCAAGTTGTTACATTAAAAGATGGAAG
*
42069 TTTGAATAGCGTTGTAGAATTT-AATTTATCCAAGTT-TTACATTCAAAAATGAAAGTTTGAATA
192 TTTGAATAGCGTTATAGAATTTAAATTT-TCCAAGTTGTTACATTCAAAAATGAAAGTTTGAATA
* * * * *
42132 GCATTGTAATGTCTT-AACAA-AATACTTTGACGTTTACGAACTAAAGAGTTTAGCTTATCGATG
256 GCATTGGAAT-TCTTGAACAACAA-A-TTAGACGTTTACGAACTAAAGAGTTTAACTTATCCAAG
* * * * *
42195 TTGTTACATTAAAAAATGTAAGTTTTAATA-ATGTTGTA-ATATTTAACTTAACT-AAGTTGTTA
318 TTGTTAAATTAAAAAATGGAAGTTTAAATAGA-ATTGTAGA-ATTTAACTT-ACTCAAATT-TTA
* * * * *
42257 C-ATTTAAAAATGGAAGTTTAAATAGTGTTGTAATGT-T-CAA-
379 CTACTGAAAAATGGAAGTTTAAATAGAGTTTTAGT-TATCCAAG
* * ** ** * * * *
42297 --CTT--AT-CTAATTTGTTACATTGAATAGA-GTTGTAATGTGTT-AATATATCCAATTTATTA
1 TTGTTACATGCAAAGATGGAAGATTGAATA-ACGTTGTAATGT-TTAAAT-TATCCAAGTTGTGA
* * * *
42355 CATTCAAAAAAGGAAGTTTGAATAACATTGTAATGTTTAACTTAACCAAGTTGTT-ACATTC-AA
63 CATTTAAAGATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCCAAGTT-TTCACATTCAAA
* * ** * * * * * *
42418 AGATAGAAGTTTTAATAGTATTGTAGAGGT-A-AAATTATCCAAGTTGTTACATTCAAAAAATGG
127 AAATGGAAGTTGAAATAGTGTTCTA-A-TTCATAACTCATCCAAGTTGTTACATT-AAAAGATGG
*
42481 AAGTTGGAATAG
189 AAGTTTGAATAG
42493 TGTTGTAATG
Statistics
Matches: 506, Mismatches: 87, Indels: 50
0.79 0.14 0.08
Matches are distributed among these distances:
414 45 0.09
415 109 0.22
416 3 0.01
417 2 0.00
419 1 0.00
420 75 0.15
421 262 0.52
422 9 0.02
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (421 bp):
TTGTTACATGCAAAGATGGAAGATTGAATAACGTTGTAATGTTTAAATTATCCAAGTTGTGACAT
TTAAAGATGGAAGTTTGAATAACATTGTAATGTTTAACTTATCCAAGTTTTCACATTCAAAAAAT
GGAAGTTGAAATAGTGTTCTAATTCATAACTCATCCAAGTTGTTACATTAAAAGATGGAAGTTTG
AATAGCGTTATAGAATTTAAATTTTCCAAGTTGTTACATTCAAAAATGAAAGTTTGAATAGCATT
GGAATTCTTGAACAACAAATTAGACGTTTACGAACTAAAGAGTTTAACTTATCCAAGTTGTTAAA
TTAAAAAATGGAAGTTTAAATAGAATTGTAGAATTTAACTTACTCAAATTTTACTACTGAAAAAT
GGAAGTTTAAATAGAGTTTTAGTTATCCAAG
Found at i:42373 original size:98 final size:105
Alignment explanation
Indices: 42248--42528 Score: 279
Period size: 98 Copynumber: 2.7 Consensus size: 105
42238 TAACTTAACT
* * * * * *
42248 AAGTTGTTACATTTAAAAATGGAAGTTTAAATAGTGTTGTAATGTTCAACTTATCTAATTTGTTA
1 AAGTTATTACATTCAAAAAAGGAAGTTTGAATAGTGTTGTAATGTTTAACTTATCTAAGTTGTTA
* *
42313 CATT-GA-ATAG-AGTTGTAAT-G-TGT-TAATA-TATCC
66 CATTAAAGATAGAAGTTGTAATAGTTGTGTAAAATTATCC
* *** * *
42346 AATTTATTACATTCAAAAAAGGAAGTTTGAATAACATTGTAATGTTTAACTTAACCAAGTTGTTA
1 AAGTTATTACATTCAAAAAAGGAAGTTTGAATAGTGTTGTAATGTTTAACTTATCTAAGTTGTTA
*
42411 CATTCAAAGATAGAAGTTTTAATAGTATTGTAGAGGTAAAATTATCC
66 CATT-AAAGATAGAAGTTGTAATAG--TTGT----GTAAAATTATCC
* *
42458 AAGTTGTTACATTCAAAAAATGGAAGTTGGAATAGTGTTGTAATGTCTTAACTTATCTAAGTTGT
1 AAGTTATTACATTCAAAAAA-GGAAGTTTGAATAGTGTTGTAATGT-TTAACTTATCTAAGTTGT
42523 TACATT
64 TACATT
42529 CAATGACGAC
Statistics
Matches: 144, Mismatches: 23, Indels: 16
0.79 0.13 0.09
Matches are distributed among these distances:
98 57 0.40
100 1 0.01
101 4 0.03
102 8 0.06
103 1 0.01
106 3 0.02
111 4 0.03
112 23 0.16
113 21 0.15
114 22 0.15
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (105 bp):
AAGTTATTACATTCAAAAAAGGAAGTTTGAATAGTGTTGTAATGTTTAACTTATCTAAGTTGTTA
CATTAAAGATAGAAGTTGTAATAGTTGTGTAAAATTATCC
Found at i:42427 original size:56 final size:56
Alignment explanation
Indices: 42325--43503 Score: 866
Period size: 56 Copynumber: 20.9 Consensus size: 56
42315 TTGAATAGAG
* * * *
42325 TTGTAATGTGTTAA-TATATCCAATTTATTACATTCAAAAAAGGAAGTTTGAATAACA
1 TTGTAATGT-TTAACT-TATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * * **
42382 TTGTAATGTTTAACTTAACCAAGTTGTTACATTCAAAGATAGAAGTTTTAATAGTA
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * * * * ***
42438 TTGTAGA-GGTAAAATTATCCAAGTTGTTACATTCAAAAAATGGAAGTTGGAATAGTG
1 TTGTA-ATGTTTAACTTATCCAAGTTGTTACATTC-AAAGATGGAAGTTTGAATAACA
* * * *
42495 TTGTAATGTCTTAACTTATCTAAGTTGTTACATTCAATGA-CGACTGTTTGAATAACA
1 TTGTAATGT-TTAACTTATCCAAGTTGTTACATTCAAAGATGGA-AGTTTGAATAACA
* * * * * *
42552 CTGTAATGTATTAACTTATCAAAGTTGTTATATTCAAAAATGGAAGTTTGAATAGCT
1 TTGTAATGT-TTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * * * * * **
42609 TTGTAATGTCTACACATATCCAAGTT-TTGATATGCAAAGATGGTAGCTTGAATAATG
1 TTGTAATGTTTA-ACTTATCCAAGTTGTT-ACATTCAAAGATGGAAGTTTGAATAACA
* * * *** * * *
42666 TTGTAATGTTTAACTATTTTCAAGTTGTTACATTCAAGGATTTTAGTTTGAGTAGCG
1 TTGTAATGTTTAACT-TATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * * * * *
42723 TTATAGA-GCTTAACTTGTCCAATTTGTTACATTGAAAGATGCAAGTTTGAATAACA
1 TTGTA-ATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
** * ** *
42779 TTGTAATGTTTATTTTATCCAAGTTGTTACATTCGAAGATGGAAAATTGAATAAAA
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * * *
42835 TTGTAATGTTTAACTCATCCAAGTTGTTAAACTCAAAGATGGAA-TATTGAATAACGC
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGT-TTGAATAAC-A
* * * ** *
42892 TT-TAATGTTTAACTCATCCAAGTTGTTACACTCAAAGATAGAAGAATGAATAACT
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * ***
42947 TTGTAATGTTTAGCTTATCCAAGTTGTTACATTCAAATATGGAAGTTTGAATAGTG
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
** * * *
43003 TTCCAGA-GTTTAATTTATCCAAGTTATTATATTCAAAGATGGAAGTTT-AACTAACA
1 TTGTA-ATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAA-TAACA
* * * * * * *
43059 TTTTAAAGTTTAACTTATCCAAGTTGTTACATACAAA-ATTGAA-TATAAATTAGCA
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAA-TAACA
** * * ***
43114 TTGTAATGTTTTAAAATATCCAAGTTGTTAAATTCAAATATGGAAGTTTGAATAGTG
1 TTGTAATG-TTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * * * * * *
43171 TTGTAATGTCTTAACTTGTCCAAGTTGTTATACTCAAAGACGAAACTTTGAATAACT
1 TTGTAATGT-TTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * * * * * * *
43228 TTGT-ATGGTATAAATTATCTAATTTGCTGCATCCAAAGAT-GAGAGTATGAATAAC-
1 TTGTAAT-GTTTAACTTATCCAAGTTGTTACATTCAAAGATGGA-AGTTTGAATAACA
* ** * * **
43283 TTGTAATGTTTAACTTATCTAA-TATGCGACATTCAAATATGAAAGTTTGAATAATG
1 TTGTAATGTTTAACTTATCCAAGT-TGTTACATTCAAAGATGGAAGTTTGAATAACA
* ** *
43339 TTGTAATGTTTAACTTATCCAAGTTGTCACATTCAAA-ATGGAAGTTT-ACATTGCG
1 TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGA-ATAACA
* * * * * *
43394 TTATAATGTCTTAACCTATCCAAGTTGTTATATTCAAACATGGAAGTTTGAATATCT
1 TTGTAATGT-TTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
* * * *
43451 TTATAGA-GTGTAACATATCCAAGTTGTTACATTCAAAGAT-TAATGTTTGAATA
1 TTGTA-ATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAA-GTTTGAATA
43504 GAGTTGCAAT
Statistics
Matches: 886, Mismatches: 198, Indels: 77
0.76 0.17 0.07
Matches are distributed among these distances:
54 4 0.00
55 85 0.10
56 505 0.57
57 259 0.29
58 33 0.04
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (56 bp):
TTGTAATGTTTAACTTATCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAACA
Found at i:42672 original size:171 final size:170
Alignment explanation
Indices: 42370--42702 Score: 394
Period size: 171 Copynumber: 2.0 Consensus size: 170
42360 AAAAAAGGAA
* * * *
42370 GTTTGAATAACATTGTAATGTTTAACTTAACCAAGTTGTTACATTCAAAGATAGAAGTTTTAATA
1 GTTTGAATAACACTGTAATGTTTAACTTAACAAAGTTGTTACATTCAAAAATAGAAGTTTGAATA
* * *
42435 GTATTGTAGAGGTAAAATTATCCAAGTTGTTACATTCAAAAAATGGAAGTTGGAATAGTGTTGTA
66 GTATTGTAGAGCTAAAATTATCCAAGTTGTTACATGCAAAAAATGGAAGTTGGAATAATGTTGTA
42500 ATGTCTTAACT-TATCT-AAGTTGTTACATTCAATGACGACT
131 ATGT-TTAACTAT-TCTCAAGTTGTTACATTCAATGACGACT
* * *
42540 GTTTGAATAACACTGTAATGTATTAACTTATCAAAGTTGTTATATTCAAAAATGGAAGTTTGAAT
1 GTTTGAATAACACTGTAATGT-TTAACTTAACAAAGTTGTTACATTCAAAAATAGAAGTTTGAAT
* * * *
42605 AGCT-TTGTA-ATGTCTACACA-TATCCAAGTT-TTGATATGC-AAAGATGGTAGCTT-GAATAA
65 AG-TATTGTAGA-G-CTA-AAATTATCCAAGTTGTT-ACATGCAAAAAATGGAAG-TTGGAATAA
*
42664 TGTTGTAATGTTTAACTATTTTCAAGTTGTTACATTCAA
124 TGTTGTAATGTTTAACTATTCTCAAGTTGTTACATTCAA
42703 GGATTTTAGT
Statistics
Matches: 139, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
170 29 0.21
171 89 0.64
172 19 0.14
173 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (170 bp):
GTTTGAATAACACTGTAATGTTTAACTTAACAAAGTTGTTACATTCAAAAATAGAAGTTTGAATA
GTATTGTAGAGCTAAAATTATCCAAGTTGTTACATGCAAAAAATGGAAGTTGGAATAATGTTGTA
ATGTTTAACTATTCTCAAGTTGTTACATTCAATGACGACT
Found at i:43632 original size:93 final size:94
Alignment explanation
Indices: 43455--43677 Score: 256
Period size: 93 Copynumber: 2.4 Consensus size: 94
43445 ATATCTTTAT
* * * * *
43455 AGAGTGTAACATATCCAAGTTGTTACATTCAAAGAT-TAATGTTTGAATAGAGTTGCAATAACTT
1 AGAGTTTAACTTAGCCAAGTTGTTACATTTAAAGATGGAATGTTTGAATAGAGTTGCAATAACTT
* *
43519 AACAAAATAGATTGATGTTTACGAACTAA
66 AACAAAATACATTGACGTTTACGAACTAA
* * * * **
43548 ATAGTTTAA-TATAGCCAAGTCGTTACATTTAAAGATGGAAT-TTTGAATAGCGTTGTAATTTC-
1 AGAGTTTAACT-TAGCCAAGTTGTTACATTTAAAGATGGAATGTTTGAATAGAGTTGCAATAACT
*
43610 TAGACAAAATACTTTGACGTTTACGAACTAA
65 TA-ACAAAATACATTGACGTTTACGAACTAA
* *
43641 AGAGTTTAACTTATCCAAGTTGTTATATTTAAAGATG
1 AGAGTTTAACTTAGCCAAGTTGTTACATTTAAAGATG
43678 TAAGTTTTAA
Statistics
Matches: 108, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
92 2 0.02
93 102 0.94
94 4 0.04
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (94 bp):
AGAGTTTAACTTAGCCAAGTTGTTACATTTAAAGATGGAATGTTTGAATAGAGTTGCAATAACTT
AACAAAATACATTGACGTTTACGAACTAA
Found at i:43874 original size:98 final size:98
Alignment explanation
Indices: 43701--43879 Score: 225
Period size: 98 Copynumber: 1.8 Consensus size: 98
43691 CTTTGAAATA
* * * * *
43701 GTTAACTTATCCAAGTTGTTACATTAAAAAATGGAAGTTTAAATAGTGTTTTAATGTTCAACTTA
1 GTTAACATATCCAAGTTATTACATTAAAAAATAGAAGATTAAATAGTGTTGTAATGTTCAACTTA
* * *
43766 TCTAATTTGTTACATTGATTAATGTTGTAATGT
66 CCCAAGTTGTTACATTGATTAATGTTGTAATGT
* * * *
43799 GTTAACATATCCAAGTTATTACATTCAAAGATAGAAGATTGAATAGCT-TTGTAATGTTTAACTT
1 GTTAACATATCCAAGTTATTACATTAAAAAATAGAAGATTAAATAG-TGTTGTAATGTTCAACTT
*
43863 CCCCAAGTTGTTACATT
65 ACCCAAGTTGTTACATT
43880 CAAAGATGGA
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
98 66 0.99
99 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (98 bp):
GTTAACATATCCAAGTTATTACATTAAAAAATAGAAGATTAAATAGTGTTGTAATGTTCAACTTA
CCCAAGTTGTTACATTGATTAATGTTGTAATGT
Found at i:43877 original size:56 final size:57
Alignment explanation
Indices: 43790--43901 Score: 163
Period size: 56 Copynumber: 2.0 Consensus size: 57
43780 TTGATTAATG
*
43790 TTGTAATGTGTTAACATATCCAAGTTATTACATTCAAAGATAGAAGATTGAATAGCT
1 TTGTAATGTGTTAACATACCCAAGTTATTACATTCAAAGATAGAAGATTGAATAGCT
* * * * *
43847 TTGTAATGT-TTAACTTCCCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAGC
1 TTGTAATGTGTTAACATACCCAAGTTATTACATTCAAAGATAGAAGATTGAATAGC
43902 ATTTTAGAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
56 40 0.82
57 9 0.18
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (57 bp):
TTGTAATGTGTTAACATACCCAAGTTATTACATTCAAAGATAGAAGATTGAATAGCT
Found at i:43930 original size:154 final size:154
Alignment explanation
Indices: 43646--43935 Score: 345
Period size: 154 Copynumber: 1.9 Consensus size: 154
43636 ACTAAAGAGT
* * * * * * *
43646 TTAACTTATCCAAGTTGTTATATTTAAAGATGTAAGTTTTAATAACTTTGAAATAGTTAACTTAT
1 TTAACATATCCAAGTTATTACATTCAAAGATGTAAGATTGAATAACTTTGAAATAGTTAACTTAC
** * * *
43711 CCAAGTTGTTACATTAAAAAATGGAAGTTTAAATAGTGTTTTAATGTTCAACTTATCTAATTTGT
66 CCAAGTTGTTACATTAAAAAATGGAAGTTTAAATAGCATTTTAATGTTCAACTCATCCAAGTTGT
43776 TACATTGATTAATGTTGTAATGTG
131 TACATTGATTAATGTTGTAATGTG
* *
43800 TTAACATATCCAAGTTATTACATTCAAAGATAG-AAGATTGAATAGCTTTGTAAT-GTTTAACTT
1 TTAACATATCCAAGTTATTACATTCAAAGAT-GTAAGATTGAATAACTTTGAAATAG-TTAACTT
* * * * *
43863 CCCCAAGTTGTTACATTCAAAGATGGAAGTTTGAATAGCATTTTAGA-GTT-AGAGTCATCCAAG
64 ACCCAAGTTGTTACATTAAAAAATGGAAGTTTAAATAGCATTTTA-ATGTTCA-ACTCATCCAAG
43926 TTGTTACATT
127 TTGTTACATT
43936 AAAAAATTGA
Statistics
Matches: 113, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
153 2 0.02
154 109 0.96
155 2 0.02
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (154 bp):
TTAACATATCCAAGTTATTACATTCAAAGATGTAAGATTGAATAACTTTGAAATAGTTAACTTAC
CCAAGTTGTTACATTAAAAAATGGAAGTTTAAATAGCATTTTAATGTTCAACTCATCCAAGTTGT
TACATTGATTAATGTTGTAATGTG
Found at i:44405 original size:13 final size:12
Alignment explanation
Indices: 44390--44432 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
44380 GATTAATATG
44390 GAAATAATAAAT
1 GAAATAATAAAT
*
44402 GGAATAATAAGAT
1 GAAATAATAA-AT
44415 -AAATAATGAAAT
1 GAAATAAT-AAAT
44427 GAAATA
1 GAAATA
44433 GTAGGGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (12 bp):
GAAATAATAAAT
Found at i:49188 original size:22 final size:22
Alignment explanation
Indices: 49163--49236 Score: 139
Period size: 22 Copynumber: 3.4 Consensus size: 22
49153 TCTCACAAGT
49163 TCACTCCAAAGAAATGATAAGA
1 TCACTCCAAAGAAATGATAAGA
49185 TCACTCCAAAGAAATGATAAGA
1 TCACTCCAAAGAAATGATAAGA
49207 TCACTCCAAAGAAATGATAAGA
1 TCACTCCAAAGAAATGATAAGA
*
49229 TTACTCCA
1 TCACTCCA
49237 CTCAATACTC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.20
Consensus pattern (22 bp):
TCACTCCAAAGAAATGATAAGA
Found at i:49684 original size:20 final size:20
Alignment explanation
Indices: 49661--49700 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
49651 CTTTCTGAAA
49661 TTCTTCTATTT-TTTCTTTTT
1 TTCTTCT-TTTCTTTCTTTTT
49681 TTCTTCTTTTCTTTCTTTTT
1 TTCTTCTTTTCTTTCTTTTT
49701 GTACTCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (20 bp):
TTCTTCTTTTCTTTCTTTTT
Found at i:52209 original size:22 final size:23
Alignment explanation
Indices: 52170--52219 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
52160 GAGTTCAAAG
* * *
52170 AAAAAAAGTAGAAGAAGA-ATTC
1 AAAAAAAGAAAAAAAAGAGATTC
*
52192 AAAAAAAGAAAAAAAAGAGTTTC
1 AAAAAAAGAAAAAAAAGAGATTC
52215 AAAAA
1 AAAAA
52220 GAAATCAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.70, C:0.04, G:0.14, T:0.12
Consensus pattern (23 bp):
AAAAAAAGAAAAAAAAGAGATTC
Found at i:57777 original size:56 final size:56
Alignment explanation
Indices: 57672--58254 Score: 143
Period size: 56 Copynumber: 10.7 Consensus size: 56
57662 AGAGCTTAAC
* * * *
57672 TTATTCAAGTTGTTACATTGAAAGATGCATATTTGAATAACATTGTAATGATTATG
1 TTATCCAAGTTGTTACATTCAAAGATGAAGATTTGAATAACATTGTAATGATTATG
* * * * * **
57728 TTATCCAAGTTGTTATATTCAAAGATTGAAGA-TTGAGTAATATTTTAATGTTTAAC
1 TTATCCAAGTTGTTACATTCAAAGA-TGAAGATTTGAATAACATTGTAATGATTATG
** * *
57784 TCGTCCAAGTTGTTAC--TC-AAGATGGAAGA-TTGAAT-AC-TTGTAAT-ATTTTAC
1 TTATCCAAGTTGTTACATTCAAAGAT-GAAGATTTGAATAACATTGTAATGATTAT-G
* ** * * **
57835 TCGA-CCAAGTTGTTACACTGGAAA-ATGGAA-A--TGAATAA-ACTTGTAAAGTTTAAC
1 T-TATCCAAGTTGTTACA-TTCAAAGAT-GAAGATTTGAATAACA-TTGTAATGATTATG
* * ***
57889 TTATCGATGTTGTTACATTCAAAGATGGAAG-TTTGAATAGTGTTGT-A-GATTAAT-
1 TTATCCAAGTTGTTACATTCAAAGAT-GAAGATTTGAATAACATTGTAATGATT-ATG
* * * ** * *
57943 TTATCCAAGTTATTATATTCAAAGATGAA-AGTTTAAATAATGTTTTGAA-GTTTAAT-
1 TTATCCAAGTTGTTACATTCAAAGATGAAGA-TTTGAATAACATTGT-AATGATT-ATG
* ** * * * * *** *
57999 TTATCCAAGATGTTACAAACAAAAATTG-A-ATATAAATTAGGGT-TAAT-ATCT-TA
1 TTATCCAAGTTGTTACATTCAAAGA-TGAAGATTTGAATAACATTGTAATGAT-TATG
* * * * * * **
58052 TTATCCAAGTTGTTACATTAAAATATGAAG-TTTGTATAGCGTTGTAATGTCTTAAC
1 TTATCCAAGTTGTTACATTCAAAGATGAAGATTTGAATAACATTGTAATG-ATTATG
* * ** *
58108 TTGTCCAAGTTGTTACATTCAAAGATGAAG-TTTGAA-AACGTTGTAGGGTTTA-G
1 TTATCCAAGTTGTTACATTCAAAGATGAAGATTTGAATAACATTGTAATGATTATG
* * * * * ** **
58161 TTTATTCTA-TTTTTACATTCAAAGACG-AGAGTCTGAATAACATTGTAATTTTTAAC
1 -TTATCCAAGTTGTTACATTCAAAGATGAAGA-TTTGAATAACATTGTAATGATTATG
* **
58217 TTATCCAAATTGCGACATTCAAAGATGGAAG-TTTGAAT
1 TTATCCAAGTTGTTACATTCAAAGAT-GAAGATTTGAAT
58255 TGTTGTAATG
Statistics
Matches: 388, Mismatches: 98, Indels: 82
0.68 0.17 0.14
Matches are distributed among these distances:
50 2 0.01
51 20 0.05
52 12 0.03
53 70 0.18
54 89 0.23
55 43 0.11
56 143 0.37
57 7 0.02
58 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (56 bp):
TTATCCAAGTTGTTACATTCAAAGATGAAGATTTGAATAACATTGTAATGATTATG
Found at i:57947 original size:54 final size:54
Alignment explanation
Indices: 57884--57986 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 54
57874 CTTGTAAAGT
* * * * * *
57884 TTAACTTATCGATGTTGTTACATTCAAAGATGGAAGTTTGAATAGTGTTGTAGA
1 TTAACTTATCCAAGTTATTACATTCAAAGATGAAAGTTTAAATAATGTTGTAGA
* *
57938 TTAATTTATCCAAGTTATTATATTCAAAGATGAAAGTTTAAATAATGTT
1 TTAACTTATCCAAGTTATTACATTCAAAGATGAAAGTTTAAATAATGTT
57987 TTGAAGTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (54 bp):
TTAACTTATCCAAGTTATTACATTCAAAGATGAAAGTTTAAATAATGTTGTAGA
Done.