Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008942.1 Hibiscus syriacus cultivar Beakdansim tig00112261_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: 2383254
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1839885 original size:18 final size:17
Alignment explanation
Indices: 1839839--1839885 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
1839829 TTATATAATC
1839839 TAATAAAATT-A-TATT
1 TAATAAAATTAATTATT
*
1839854 TAAT-AAATAAATTATT
1 TAATAAAATTAATTATT
1839870 TAATAAAATTACATTA
1 TAATAAAATTA-ATTA
1839886 ATGATTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.15
15 5 0.19
16 8 0.31
17 5 0.19
18 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATAAAATTAATTATT
Found at i:1841781 original size:13 final size:13
Alignment explanation
Indices: 1841751--1841775 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1841741 TGATTATCTT
1841751 TTATTTTATTTTA
1 TTATTTTATTTTA
1841764 TTATTTTATTTT
1 TTATTTTATTTT
1841776 TATATTAAAT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:1843617 original size:42 final size:43
Alignment explanation
Indices: 1843512--1843624 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 43
1843502 TTTGTTAACC
* * *
1843512 AAAAACGCCACAATAGGTATTGATATTTAGCGGCGTTTGTCTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCAGCGTTTGTCTT
* *
1843555 AAAAACGCCGTAATAGGTGTTGATATTTAGTAGCGTTT-T-TT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCAGCGTTTGTCTT
* *
1843596 CACAAACGCCGCAATAAGTGTTGATATTT
1 -AAAAACGCCGCAATAGGTGTTGATATTT
1843625 CACGGCATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 2 0.03
42 26 0.43
43 33 0.54
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCAGCGTTTGTCTT
Found at i:1843636 original size:42 final size:40
Alignment explanation
Indices: 1843512--1843658 Score: 134
Period size: 43 Copynumber: 3.5 Consensus size: 40
1843502 TTTGTTAACC
* *
1843512 AAAAACGCCACAATAGGTATTGATATTTAGCGGCGTTTGTCTT
1 AAAAACGCCGCAATAGGTGTTGATATTTA-CGGCGTTT-T-TT
*
1843555 AAAAACGCCGTAATAGGTGTTGATATTTA-GTAGCGTTTTTT
1 AAAAACGCCGCAATAGGTGTTGATATTTACG--GCGTTTTTT
* * *
1843596 CACAAACGCCGCAATAAGTGTTGATATTTCACGGCATTTTTTT
1 -AAAAACGCCGCAATAGGTGTTGATATTT-ACGGC-GTTTTTT
*
1843639 ATGAAAACGTCGCAATAGGT
1 A--AAAACGCCGCAATAGGT
1843659 CTGGTATTTA
Statistics
Matches: 86, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
41 3 0.03
42 29 0.34
43 39 0.45
44 15 0.17
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (40 bp):
AAAAACGCCGCAATAGGTGTTGATATTTACGGCGTTTTTT
Found at i:1843691 original size:44 final size:44
Alignment explanation
Indices: 1843643--1843827 Score: 210
Period size: 44 Copynumber: 4.2 Consensus size: 44
1843633 TTTTTTATGA
* * * * *
1843643 AAACGTCGCAATAGGTCTGGTATTTAGTGGCATTTTTAGGGTAC
1 AAACGCCGCGATAGGTCTGGTATATAGCGGCATTTTTAGGATAC
* * * * *
1843687 AAACGCCGCTATAGGACTGGTATATAGCGGCGTTCTT-GCTATAC
1 AAACGCCGCGATAGGTCTGGTATATAGCGGCATTTTTAG-GATAC
* *
1843731 AAACGCCGCGATAGGTGTGGTATATAGCGGCATTTTTAGGACAC
1 AAACGCCGCGATAGGTCTGGTATATAGCGGCATTTTTAGGATAC
* * * *
1843775 AAACACCACGATAGCTCTGGTATATAGCGGCATTTGTAGGATAC
1 AAACGCCGCGATAGGTCTGGTATATAGCGGCATTTTTAGGATAC
1843819 AAACGCCGC
1 AAACGCCGC
1843828 TAAAATTTGG
Statistics
Matches: 115, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
43 1 0.01
44 113 0.98
45 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (44 bp):
AAACGCCGCGATAGGTCTGGTATATAGCGGCATTTTTAGGATAC
Found at i:1843861 original size:43 final size:41
Alignment explanation
Indices: 1843814--1843919 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 41
1843804 GCATTTGTAG
**
1843814 GATACAAACGCCGCTAAA-ATTTGGTACATA-GCGGCGTTTTTTT
1 GATACAAACGCCGCTAAATAAAT-G-ACATATGCGGCG--TTTTT
*
1843857 GATACAAATGCCGCTAAATAAATGACATATTGCGGCGTTTTT
1 GATACAAACGCCGCTAAATAAATGACATA-TGCGGCGTTTTT
*
1843899 GTTACAAACGCCGCTAAATAA
1 GATACAAACGCCGCTAAATAA
1843920 CACAAAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
42 29 0.53
43 18 0.33
44 8 0.15
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (41 bp):
GATACAAACGCCGCTAAATAAATGACATATGCGGCGTTTTT
Found at i:1849329 original size:671 final size:671
Alignment explanation
Indices: 1848048--1849389 Score: 2549
Period size: 671 Copynumber: 2.0 Consensus size: 671
1848038 TCCCATAATT
* *
1848048 GTTTCAACTCTGCAATTAGCGGCTGTATGTAAATATTAATATCATTCCCGGGGCCTTTCTCGCCG
1 GTTTCAACTCTGCAATTAGCAGCTGTATGTAAATATTAATATCATTCCCGGGGCCTTTCTCGCAG
*
1848113 GGGATTATCATGGATAAGATGAAAGATGATTGTTTCATGCAAATCCAGGGAGGCAAATTATATGG
66 GGGATTATCATGAATAAGATGAAAGATGATTGTTTCATGCAAATCCAGGGAGGCAAATTATATGG
1848178 AACAAGGACAACAAGCCAAGTACTATACGAAGTACTCATGGTTTTGAATGGATTAAACCCATCAG
131 AACAAGGACAACAAGCCAAGTACTATACGAAGTACTCATGGTTTTGAATGGATTAAACCCATCAG
1848243 TTGCAAGACCGAGCCTGAAATTTCGAGGATCTCTTGCAAAAGTTGGGTACTTGTTGTCAAATGAC
196 TTGCAAGACCGAGCCTGAAATTTCGAGGATCTCTTGCAAAAGTTGGGTACTTGTTGTCAAATGAC
*
1848308 TTCCAAGATAAAGAATCCGCAGGATGCCGTAATAATCCAACATTGGTTCTGCCATCATGATGCCA
261 TTCCAAGATAAAGAATCCGCAGGATGCCGTAATAATCCAACATTAGTTCTGCCATCATGATGCCA
*
1848373 CCTCATAGACTCAACAGTCTTGGAGGACATAAACAATCTTTGTAGCCTAGGTATAAGAGGAAAAT
326 CCTCATAGACTCAACAGTCTTGGAGGACATAAACAATCTTTGTAGACTAGGTATAAGAGGAAAAT
1848438 ATCGTAGAATCTTGACCAGTTTCTTTCTTGATCGTGCTTGAGCTTCATCCTCAGTAACATTTTCT
391 ATCGTAGAATCTTGACCAGTTTCTTTCTTGATCGTGCTTGAGCTTCATCCTCAGTAACATTTTCT
*
1848503 GCCTCCTTAATCATCCATCGAGATTTTCCGCATACATGGCAAGAGTCCTGATTTTTTCGATCACC
456 GCCTCCCTAATCATCCATCGAGATTTTCCGCATACATGGCAAGAGTCCTGATTTTTTCGATCACC
*
1848568 CCAATACAACATACAATCATTCGGACAACTATGAATTTTGTCATATTCAAGACCCAAATCTTTTA
521 CCAATACAACATACAATCATTCGGACAACTATGAATTTTGTCATATCCAAGACCCAAATCTTTTA
*
1848633 TCATTTTATTCATATCTTTGCATGATTGAGGGATTTTTGCAAAAGGAAGCACTTCTCCTAGTAAC
586 TCATTTTATTCATATCTTTGCATGATTGAGGGAATTTTGCAAAAGGAAGCACTTCTCCTAGTAAC
*
1848698 TCCAATAATTGCATAAAGGAG
651 TCCAACAATTGCATAAAGGAG
1848719 GTTTCAACTCTGCAATTAGCAGCTGTATGTAAATATTAATATCATTCCCGGGGCCTTTCTCGCAG
1 GTTTCAACTCTGCAATTAGCAGCTGTATGTAAATATTAATATCATTCCCGGGGCCTTTCTCGCAG
1848784 GGGATTATCATGAATAAGATGAAAGATGATTGTTTCATGCAAATCCAGGGAGGCAAATTATATGG
66 GGGATTATCATGAATAAGATGAAAGATGATTGTTTCATGCAAATCCAGGGAGGCAAATTATATGG
1848849 AACAAGGACAACAAGCCAAGTACTATACGAAGTACTCATGGTTTTGAATGGATTAAACCCATCAG
131 AACAAGGACAACAAGCCAAGTACTATACGAAGTACTCATGGTTTTGAATGGATTAAACCCATCAG
*
1848914 TTGCAAGACTGAGCCTGAAATTTCGAGGATCTCTTGCAAAAGTTGGGTACTTGTTGTCAAATGAC
196 TTGCAAGACCGAGCCTGAAATTTCGAGGATCTCTTGCAAAAGTTGGGTACTTGTTGTCAAATGAC
1848979 TTCCAAGATAAAGAATCCGCAGGATGCCGTAATAATCCAACATTAGTTCTGCCATCATGATGCCA
261 TTCCAAGATAAAGAATCCGCAGGATGCCGTAATAATCCAACATTAGTTCTGCCATCATGATGCCA
*
1849044 CCTCATAGACTCAACAGTCTTGGAGGACATAAACACTCTTTGTAGACTAGGTATAAGAGGAAAAT
326 CCTCATAGACTCAACAGTCTTGGAGGACATAAACAATCTTTGTAGACTAGGTATAAGAGGAAAAT
*
1849109 ATCGTAGAATCTTGACCAGTTTCTTTCTTGATCGTGCTTGAGGTTCATCCTCAGTAACATTTTCT
391 ATCGTAGAATCTTGACCAGTTTCTTTCTTGATCGTGCTTGAGCTTCATCCTCAGTAACATTTTCT
*
1849174 GCCTCCCTAATCATCCATCGAGATTTTTCGCATACATGGCAAGAGTCCTGATTTTTTCGATCACC
456 GCCTCCCTAATCATCCATCGAGATTTTCCGCATACATGGCAAGAGTCCTGATTTTTTCGATCACC
1849239 CCAATACAACATACAATCATTCGGACAACTATGAATTTTGTCATATCCAAGACCCAAATCTTTTA
521 CCAATACAACATACAATCATTCGGACAACTATGAATTTTGTCATATCCAAGACCCAAATCTTTTA
*
1849304 TCATTTTCTTCATATCTTTGCATGATTGAGGGAATTTTGCAAAAGGAAGCACTTCTCCTAGTAAC
586 TCATTTTATTCATATCTTTGCATGATTGAGGGAATTTTGCAAAAGGAAGCACTTCTCCTAGTAAC
*
1849369 TCCAACAATTGCGTAAAGGAG
651 TCCAACAATTGCATAAAGGAG
1849390 TTACCAGCCA
Statistics
Matches: 656, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
671 656 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (671 bp):
GTTTCAACTCTGCAATTAGCAGCTGTATGTAAATATTAATATCATTCCCGGGGCCTTTCTCGCAG
GGGATTATCATGAATAAGATGAAAGATGATTGTTTCATGCAAATCCAGGGAGGCAAATTATATGG
AACAAGGACAACAAGCCAAGTACTATACGAAGTACTCATGGTTTTGAATGGATTAAACCCATCAG
TTGCAAGACCGAGCCTGAAATTTCGAGGATCTCTTGCAAAAGTTGGGTACTTGTTGTCAAATGAC
TTCCAAGATAAAGAATCCGCAGGATGCCGTAATAATCCAACATTAGTTCTGCCATCATGATGCCA
CCTCATAGACTCAACAGTCTTGGAGGACATAAACAATCTTTGTAGACTAGGTATAAGAGGAAAAT
ATCGTAGAATCTTGACCAGTTTCTTTCTTGATCGTGCTTGAGCTTCATCCTCAGTAACATTTTCT
GCCTCCCTAATCATCCATCGAGATTTTCCGCATACATGGCAAGAGTCCTGATTTTTTCGATCACC
CCAATACAACATACAATCATTCGGACAACTATGAATTTTGTCATATCCAAGACCCAAATCTTTTA
TCATTTTATTCATATCTTTGCATGATTGAGGGAATTTTGCAAAAGGAAGCACTTCTCCTAGTAAC
TCCAACAATTGCATAAAGGAG
Found at i:1850526 original size:22 final size:22
Alignment explanation
Indices: 1850501--1850544 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1850491 TGGTTTTTCC
1850501 AGCTTTGGTATATGCTTTCAAA
1 AGCTTTGGTATATGCTTTCAAA
1850523 AGCTTTGGTATATGCTTTCAAA
1 AGCTTTGGTATATGCTTTCAAA
1850545 CTATTTGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (22 bp):
AGCTTTGGTATATGCTTTCAAA
Found at i:1850551 original size:22 final size:22
Alignment explanation
Indices: 1850504--1850554 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1850494 TTTTTCCAGC
*
1850504 TTTGGTATATGCTTTCAAAAGC
1 TTTGGTATATGCTTTCAAAAGA
**
1850526 TTTGGTATATGCTTTCAAACTA
1 TTTGGTATATGCTTTCAAAAGA
1850548 TTTGGTA
1 TTTGGTA
1850555 ATAAATGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (22 bp):
TTTGGTATATGCTTTCAAAAGA
Found at i:1851074 original size:25 final size:25
Alignment explanation
Indices: 1851046--1851101 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
1851036 CACCGTGTGG
1851046 GAGGAGCTGCTATGGCTAGTTGGAA
1 GAGGAGCTGCTATGGCTAGTTGGAA
1851071 GAGGAGCTGCTATGGCTAGTTGGAA
1 GAGGAGCTGCTATGGCTAGTTGGAA
1851096 GAGGAG
1 GAGGAG
1851102 GGTTAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.25, C:0.11, G:0.43, T:0.21
Consensus pattern (25 bp):
GAGGAGCTGCTATGGCTAGTTGGAA
Found at i:1860590 original size:73 final size:73
Alignment explanation
Indices: 1860400--1860643 Score: 199
Period size: 73 Copynumber: 3.3 Consensus size: 73
1860390 AAAAAACAAT
* * * * * **
1860400 TCAAAATTTTAAATATCGATACTTAATA-TATTATTATCGATACTAGTAAATATTGAAAAAGTTG
1 TCAAAAGTTAAAATATCGATACTT-ATACGATCATGATCGATACTTTTAAATATTGAAAAAGTTG
*
1860464 AAGATAAGA
65 AAGAAAAGA
* * *
1860473 TCAAAAGTTAAAATATCGATTCTTATACGGTCATGATCGATACTTTTAAA-AGTTGAAATAGTTG
1 TCAAAAGTTAAAATATCGATACTTATACGATCATGATCGATACTTTTAAATA-TTGAAAAAGTTG
1860537 ATA-AAAAGA
65 A-AGAAAAGA
* ** * * * * *
1860546 TCAAAATTTAAAATATTTATACTTATGCGATGATGATCGATACTTTTTTAGATATTTAACAAGTT
1 TCAAAAGTTAAAATATCGATACTTATACGATCATGATCGATAC--TTTTAAATATTGAAAAAGTT
* *
1860611 GATGAATATGA
64 GAAGAA-AAGA
*
1860622 TCGATAA-TTAAAATATCGATAC
1 TC-AAAAGTTAAAATATCGATAC
1860644 ATATGTTATG
Statistics
Matches: 135, Mismatches: 27, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
72 4 0.03
73 90 0.67
74 1 0.01
75 18 0.13
76 19 0.14
77 3 0.02
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (73 bp):
TCAAAAGTTAAAATATCGATACTTATACGATCATGATCGATACTTTTAAATATTGAAAAAGTTGA
AGAAAAGA
Found at i:1861238 original size:99 final size:101
Alignment explanation
Indices: 1861091--1861675 Score: 624
Period size: 100 Copynumber: 5.9 Consensus size: 101
1861081 ATGAGCAACC
* *
1861091 TTTGTCTTACTTTTTCATAATAT-AAT-AGTTTGCATACTTATACCTTAAACTGTTGACAT-AAA
1 TTTGTCTTACTTTTGCATAATATAAATGAGTTT-CATACTTATAACTTAAACTGTTGACATAAAA
* ** * *
1861153 AAAGACGTTAGTTACTACGTTATTATGAGAAACATGT
65 AAAGACGGTACCTACTACGTTATCATGAAAAACATGT
* * * *
1861190 TTTGTCTTACTTTTGTATAATATAAATGA-TTTTATACTTCTAACTTAAATTGTTGACATAAAAA
1 TTTGTCTTACTTTTGCATAATATAAATGAGTTTCATACTTATAACTTAAACTGTTGACATAAAAA
* ** *
1861254 AAAAGCAATACCTACTACATTATCATGAAAAA-A--T
66 AAGA-CGGTACCTACTACGTTATCATGAAAAACATGT
* * *
1861288 ATTGTCTTACTTTTGCGTAATATAAA-CAGTTTCATACTTATAACTTAAAC-GATTGACATAAAA
1 TTTGTCTTACTTTTGCATAATATAAATGAGTTTCATACTTATAACTTAAACTG-TTGACATAAAA
*
1861351 AAATGCAC--TACCAACTACGTTATCATGAAAAACATGT
65 AAA-G-ACGGTACCTACTACGTTATCATGAAAAACATGT
* * **
1861388 TTTGTCTTACTTTTACATAATATAAA-CAGTTTCATACTTATAACTTAAGTTGTTGACATAAAAA
1 TTTGTCTTACTTTTGCATAATATAAATGAGTTTCATACTTATAACTTAAACTGTTGACATAAAAA
* *
1861452 ATG-TGGTACCTACTACGTTATCATGAAAAACATGT
66 AAGACGGTACCTACTACGTTATCATGAAAAACATGT
* * *
1861487 TTTGTCTTACTTTTGCATAATATAAACG-GTTTTATACTTATAACTTAAACAGTTGACATAAAAA
1 TTTGTCTTACTTTTGCATAATATAAATGAGTTTCATACTTATAACTTAAACTGTTGACATAAAAA
* * * *
1861551 AAGGCGGTACCTGCTACGTTATCATGAGAAACTTGT
66 AAGACGGTACCTACTACGTTATCATGAAAAACATGT
* * * ** * * *
1861587 TTCGTCTTTCTTTTTCATCGTATAAAT-CGTTTCATACTTATAACTTATACGGTTGACATTAAAA
1 TTTGTCTTACTTTTGCATAATATAAATGAGTTTCATACTTATAACTTAAACTGTTGACA-TAAAA
** *
1861651 AAAGGTGTTACCTACTACGTTATCA
65 AAAGACGGTACCTACTACGTTATCA
1861676 CGAGCATAAC
Statistics
Matches: 413, Mismatches: 55, Indels: 34
0.82 0.11 0.07
Matches are distributed among these distances:
97 24 0.06
98 57 0.14
99 133 0.32
100 150 0.36
101 49 0.12
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (101 bp):
TTTGTCTTACTTTTGCATAATATAAATGAGTTTCATACTTATAACTTAAACTGTTGACATAAAAA
AAGACGGTACCTACTACGTTATCATGAAAAACATGT
Found at i:1861863 original size:21 final size:20
Alignment explanation
Indices: 1861806--1861860 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
1861796 TTTAAATTTG
1861806 AAAGTATCAATACTTGTGAA
1 AAAGTATCAATACTTGTGAA
1861826 AAAGTATCAATACTTGTGAA
1 AAAGTATCAATACTTGTGAA
1861846 AAAGTATCAATACTT
1 AAAGTATCAATACTT
1861861 TGTACCCTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (20 bp):
AAAGTATCAATACTTGTGAA
Found at i:1863749 original size:26 final size:26
Alignment explanation
Indices: 1863711--1863775 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
1863701 GTAATAAATC
*
1863711 TATGACGTGCATTTATGACACTCATT
1 TATGACGCGCATTTATGACACTCATT
* **
1863737 TATGACGCACATTTATGATGCTCATT
1 TATGACGCGCATTTATGACACTCATT
1863763 TATGACGCGCATT
1 TATGACGCGCATT
1863776 GCGCGTCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (26 bp):
TATGACGCGCATTTATGACACTCATT
Found at i:1863775 original size:13 final size:13
Alignment explanation
Indices: 1863711--1863775 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
1863701 GTAATAAATC
*
1863711 TATGACGTGCATT
1 TATGACGCGCATT
* *
1863724 TATGACACTCATT
1 TATGACGCGCATT
*
1863737 TATGACGCACATT
1 TATGACGCGCATT
* *
1863750 TATGATGCTCATT
1 TATGACGCGCATT
1863763 TATGACGCGCATT
1 TATGACGCGCATT
1863776 GCGCGTCATT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:1872707 original size:34 final size:32
Alignment explanation
Indices: 1872654--1872723 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1872644 ACCTTACAAC
*
1872654 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1872686 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1872720 TCCC
1 TCCC
1872724 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1873031 original size:21 final size:21
Alignment explanation
Indices: 1873005--1873046 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1872995 CCAGAATGGG
*
1873005 GGGAATCGGTACCCATTCATA
1 GGGAATCGATACCCATTCATA
*
1873026 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCATTCATA
1873047 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCATTCATA
Found at i:1873180 original size:19 final size:19
Alignment explanation
Indices: 1873152--1873218 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1873142 GAGCCTCGGG
*
1873152 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
* *
1873171 TTATTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* *
1873190 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
1873209 TTACTATTCA
1 TTACTGTTCA
1873219 TAAAAACATT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:1873315 original size:29 final size:31
Alignment explanation
Indices: 1873283--1873342 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1873273 AAATTTTGAA
*
1873283 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1873312 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1873343 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1873779 original size:17 final size:17
Alignment explanation
Indices: 1873757--1873828 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
1873747 AATTAAGAGT
1873757 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
1873774 TAGTTTGATGAATAAAC
1 TAGTTTAATAAATGAAC
*
1873791 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * *
1873808 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
1873826 TAG
1 TAG
1873829 ATGCATGAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
17 30 0.68
18 14 0.32
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:1879091 original size:3 final size:3
Alignment explanation
Indices: 1879079--1879119 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1879069 TAAAAATTTG
1879079 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1879120 ATATAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1879517 original size:134 final size:135
Alignment explanation
Indices: 1879273--1879529 Score: 410
Period size: 134 Copynumber: 1.9 Consensus size: 135
1879263 GCTCATACTT
* *
1879273 GATGACACTGCTCATACGTGATTAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTC
1 GATGACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAGGAAGGGTGATAACTCGGTTC
* * *
1879338 CTACTCGATGAGGACGACTAGTTATCTATGGGTGACACAGCTCATACGTGATGAAGAGATCTGGT
66 CTACGCGATGAGGACGACTAGTTATCTAGGGGTGACACAGCTCATACGTGATAAAGAGATCTGGT
1879403 CGGGG
131 CGGGG
*
1879408 GATGACA-TGGCTCATACGTGATGAAGAGTTC-TAGTCATCTTTAGGAAGGGTGATAACTCGGTT
1 GATGACACT-GCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAGGAAGGGTGATAACTCGGTT
* * *
1879471 CCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACACGGTTCATACGTGATAAAGAG
65 CCTACGCGATGAGGACGACTAGTTATCTAGGGGTGACACAGCTCATACGTGATAAAGAG
1879530 TCGGGGAATG
Statistics
Matches: 112, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
134 84 0.75
135 28 0.25
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.27
Consensus pattern (135 bp):
GATGACACTGCTCATACGTGATGAAGAGTTCTTAGCCATCTTTAGGAAGGGTGATAACTCGGTTC
CTACGCGATGAGGACGACTAGTTATCTAGGGGTGACACAGCTCATACGTGATAAAGAGATCTGGT
CGGGG
Found at i:1879624 original size:29 final size:29
Alignment explanation
Indices: 1879581--1879698 Score: 150
Period size: 29 Copynumber: 4.0 Consensus size: 29
1879571 CATCTATAGG
*
1879581 GATAATGATTTCAAAAGAAACTGACTCAAA
1 GATAATG-TTTCAAAAGAAACAGACTCAAA
*
1879611 GATAATGTTTCAAAAGAAACAAACTCAAA
1 GATAATGTTTCAAAAGAAACAGACTCAAA
*
1879640 GATGATGTTTCAAAAGAAACAGACTCAAA
1 GATAATGTTTCAAAAGAAACAGACTCAAA
* *
1879669 GA-AATATTTTTAAAAGAAACA-ATCTCAAA
1 GATAAT-GTTTCAAAAGAAACAGA-CTCAAA
1879698 G
1 G
1879699 GTTGATTTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
28 3 0.04
29 69 0.87
30 7 0.09
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.23
Consensus pattern (29 bp):
GATAATGTTTCAAAAGAAACAGACTCAAA
Found at i:1879653 original size:58 final size:58
Alignment explanation
Indices: 1879589--1879698 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
1879579 GGGATAATGA
*
1879589 TTTCAAAAGAAACTGACTCAAAGATAAT-GTTTCAAAAGAAACAAACTCAAAGATGATG
1 TTTCAAAAGAAACAGACTCAAAGA-AATAGTTTCAAAAGAAACAAACTCAAAGATGATG
* * *
1879647 TTTCAAAAGAAACAGACTCAAAGAAATATTTTTAAAAGAAACAATCTCAAAG
1 TTTCAAAAGAAACAGACTCAAAGAAATAGTTTCAAAAGAAACAAACTCAAAG
1879699 GTTGATTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
57 3 0.06
58 44 0.94
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.23
Consensus pattern (58 bp):
TTTCAAAAGAAACAGACTCAAAGAAATAGTTTCAAAAGAAACAAACTCAAAGATGATG
Found at i:1879882 original size:91 final size:89
Alignment explanation
Indices: 1879782--1880008 Score: 217
Period size: 91 Copynumber: 2.5 Consensus size: 89
1879772 GTTAAGAGAC
* *
1879782 ACAATCTCAAAGATTTTTCAAAAGGAACATACTCAAAGATATTTCGCAGGAAAAACTATCTCAAG
1 ACAAACTCAAAGATTTTTCAAAAGGAACATACTCAAAGATATTTCGCACG--AAACTATCTCAAG
** *
1879847 AGTGACAAAACTTTGTTTCAAAAGAA
64 AGAAACAAAACTTTGGTTCAAAAGAA
* ** * * *
1879873 ACAAACTCAAAGATTTTGATTTCAAAA-GAA-ATGACTCAAATAT-TTTTTCACGAAATTGTCTT
1 ACAAACTCAAAGA--TT--TTTCAAAAGGAACAT-ACTCAAAGATATTTCGCACGAAACTATCTC
*
1879935 AAGAGAAACAAAACTTTGGTTCGAAAGAA
61 AAGAGAAACAAAACTTTGGTTCAAAAGAA
* * * *
1879964 ACAGACTCAAAGAATTTTTCAAAAGAAACAGACTCAAAGAAATTT
1 ACAAACTCAAAG-ATTTTTCAAAAGGAACATACTCAAAGATATTT
1880009 TCAAAAGAAA
Statistics
Matches: 110, Mismatches: 17, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
88 8 0.07
89 10 0.09
90 6 0.05
91 55 0.50
92 1 0.01
93 10 0.09
94 12 0.11
95 8 0.07
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (89 bp):
ACAAACTCAAAGATTTTTCAAAAGGAACATACTCAAAGATATTTCGCACGAAACTATCTCAAGAG
AAACAAAACTTTGGTTCAAAAGAA
Found at i:1879910 original size:29 final size:29
Alignment explanation
Indices: 1879858--1880139 Score: 131
Period size: 29 Copynumber: 9.6 Consensus size: 29
1879848 GTGACAAAAC
1879858 TTTGTTTCAAAAGAAACAAACTCAAAGAT
1 TTTGTTTCAAAAGAAACAAACTCAAAGAT
** *
1879887 TTTGATTTCAAAAGAAA-TGACTCAAATA-
1 TTTG-TTTCAAAAGAAACAAACTCAAAGAT
* *
1879915 TTT-TTTCACGAAATTGTCTTAAGAGAAA--CAAA-AC
1 TTTGTTTCA--AAA--G----AA-ACAAACTCAAAGAT
* * *
1879949 TTTGGTTCGAAAGAAACAGACTCAAAGA-
1 TTTGTTTCAAAAGAAACAAACTCAAAGAT
* *
1879977 ATT-TTTCAAAAGAAACAGACTCAAAGA-
1 TTTGTTTCAAAAGAAACAAACTCAAAGAT
**
1880004 AAT-TTTCAAAAGAAAC-AACTCAAAGATT
1 TTTGTTTCAAAAGAAACAAACTCAAAGA-T
* *
1880032 TTTATTTCAAAAGAAAC-AACTTACAAA-CT
1 TTTGTTTCAAAAGAAACAAAC-T-CAAAGAT
*
1880061 TTTGTTTCAAAAGAAACAAACTCAAATATAGGT
1 TTTGTTTCAAAAGAAACAAACTC--A-A-AGAT
** *
1880094 TTTGTTTCAAGGGAAACAATCTCAAAGAT
1 TTTGTTTCAAAAGAAACAAACTCAAAGAT
* *
1880123 GTTTGTTTTAAGAGAAA
1 -TTTGTTTCAAAAGAAA
1880140 TTGTCTTAAA
Statistics
Matches: 200, Mismatches: 25, Indels: 55
0.71 0.09 0.20
Matches are distributed among these distances:
26 17 0.09
27 39 0.19
28 14 0.07
29 50 0.25
30 33 0.17
31 7 0.04
32 1 0.00
33 25 0.12
34 9 0.05
35 4 0.02
36 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.29
Consensus pattern (29 bp):
TTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:1879988 original size:27 final size:27
Alignment explanation
Indices: 1879958--1880086 Score: 127
Period size: 27 Copynumber: 4.6 Consensus size: 27
1879948 CTTTGGTTCG
1879958 AAAGAAACAGACTCAAAGAATT-TTTCA
1 AAAGAAACA-ACTCAAAGAATTATTTCA
*
1879985 AAAGAAACAGACTCAAAGAAAT-TTTCA
1 AAAGAAACA-ACTCAAAGAATTATTTCA
*
1880012 AAAGAAACAACTCAAAGATTTTTATTTCA
1 AAAGAAACAACTCAAAGA--ATTATTTCA
*** *
1880041 AAAGAAACAACTTACAAACTTTTGTTTCA
1 AAAGAAACAAC-T-CAAAGAATTATTTCA
1880070 AAAGAAACAAACTCAAA
1 AAAGAAAC-AACTCAAA
1880087 TATAGGTTTT
Statistics
Matches: 90, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
26 9 0.10
27 35 0.39
28 5 0.06
29 33 0.37
30 4 0.04
31 4 0.04
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.23
Consensus pattern (27 bp):
AAAGAAACAACTCAAAGAATTATTTCA
Found at i:1880269 original size:49 final size:49
Alignment explanation
Indices: 1880211--1880311 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 49
1880201 AGGAACTATC
*
1880211 TCAAAAGAGACAAAATTTTG-TTTCCAAAGAAACATACTCAAAGATTCTT
1 TCAAAAGAGACAAAATTTTGCTAT-CAAAGAAACATACTCAAAGATTCTT
* *
1880260 TCAAAAGAGACAAAATTTTGCTATCAAATAAACATACTCAAAGATTTTT
1 TCAAAAGAGACAAAATTTTGCTATCAAAGAAACATACTCAAAGATTCTT
1880309 TCA
1 TCA
1880312 TTTTGTTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
49 46 0.96
50 2 0.04
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.30
Consensus pattern (49 bp):
TCAAAAGAGACAAAATTTTGCTATCAAAGAAACATACTCAAAGATTCTT
Found at i:1880512 original size:36 final size:36
Alignment explanation
Indices: 1880472--1880609 Score: 147
Period size: 36 Copynumber: 3.8 Consensus size: 36
1880462 ATAATTTGGA
*
1880472 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * * *
1880508 AAATTGTCTCAAACGAGACAAAAATTGTTTTTAGGG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
*
1880544 AAATTGTCTCAAGCGAGACAA-AGCTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAACA-TTTGTTTTTAGAG
** *
1880579 AAAAAGATCTCAAGTGAGATCAAC-TTTGTTT
1 AAATTG-TCTCAAGCGAGA-CAACATTTGTTT
1880610 AATGTGAAAC
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
35 7 0.08
36 76 0.88
37 3 0.03
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:1880738 original size:107 final size:103
Alignment explanation
Indices: 1880548--1880875 Score: 326
Period size: 107 Copynumber: 3.1 Consensus size: 103
1880538 TTAGGGAAAT
* *
1880548 TGTCTCAAGCGAGAC-AAAGCTTGTTTTTG--AGAAAA-AGATCTCAAGTGAGATCAACTTTGTT
1 TGTCTCAAACGAGACGAAA--TT-TTTTTGAAAGAAAACA-ATCTCAAATGAGATCAACTTTGTT
1880609 TAATGTGAAACAAATTCGAAATTTGTATTCTCAAATGAAAAA
62 TAATGTGAAACAAATTCGAAATTTGTATTCTCAAATGAAAAA
* * * * *
1880651 TGCCTCAAATGAGACGAAATTTATTTTGAAAGAAATAACAATCTCAATTGAGATTAATTTTTGTT
1 TGTCTCAAACGAGACGAAATTT-TTTTGAAAG-AA-AACAATCTCAAATGAGATCAA-CTTTGTT
* * * *
1880716 TCAA-GTGAATCAAATTCAAAATTTGTA-TGTCAAAGGAAAAAAA
62 T-AATGTGAAACAAATTCGAAATTTGTATTCTCAAATG--AAAAA
* * * * ** * * *
1880759 TGTTTCAAACAAGACGGAGTTTTTTTTTAAGAAAGCGATCTCAAATGAGATCGACTTTGTTTAAT
1 TGTCTCAAACGAGACGAAATTTTTTTGAAAGAAAACAATCTCAAATGAGATCAACTTTGTTTAAT
*
1880824 GTGAAACAAATTTGAAATTTGTATTCTCAAATGAAAAA
66 GTGAAACAAATTCGAAATTTGTATTCTCAAATGAAAAA
1880862 TGTCTCAAACGAGA
1 TGTCTCAAACGAGA
1880876 AAGAATTTGA
Statistics
Matches: 181, Mismatches: 31, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
101 1 0.01
102 7 0.04
103 31 0.17
104 32 0.18
105 25 0.14
106 26 0.14
107 36 0.20
108 23 0.13
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (103 bp):
TGTCTCAAACGAGACGAAATTTTTTTGAAAGAAAACAATCTCAAATGAGATCAACTTTGTTTAAT
GTGAAACAAATTCGAAATTTGTATTCTCAAATGAAAAA
Found at i:1881215 original size:16 final size:16
Alignment explanation
Indices: 1881194--1881233 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1881184 CTCATGTAAT
**
1881194 ATGTATGTATGTGTTG
1 ATGTATGTATGCATTG
1881210 ATGTATGTATGCATTG
1 ATGTATGTATGCATTG
1881226 ATGTATGT
1 ATGTATGT
1881234 TTTCTCGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.03, G:0.28, T:0.47
Consensus pattern (16 bp):
ATGTATGTATGCATTG
Found at i:1884833 original size:19 final size:19
Alignment explanation
Indices: 1884796--1884835 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1884786 ATGATGATGC
*
1884796 AATGCAAAGAATGATGAAA
1 AATGCAAACAATGATGAAA
1884815 AATGACAAACAATGA-GAAA
1 AATG-CAAACAATGATGAAA
1884834 AA
1 AA
1884836 ATGAGTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.62, C:0.07, G:0.17, T:0.12
Consensus pattern (19 bp):
AATGCAAACAATGATGAAA
Found at i:1892746 original size:10 final size:9
Alignment explanation
Indices: 1892725--1892754 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1892715 TTATCATCCA
1892725 TCCACCCAC
1 TCCACCCAC
1892734 TCCACCACAC
1 TCCACC-CAC
1892744 TCCACCCAC
1 TCCACCCAC
1892753 TC
1 TC
1892755 TACAATTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.23, C:0.63, G:0.00, T:0.13
Consensus pattern (9 bp):
TCCACCCAC
Found at i:1894661 original size:2 final size:2
Alignment explanation
Indices: 1894649--1894692 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
1894639 AAGTGACTTA
* *
1894649 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT ACT CT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
1894691 AT
1 AT
1894693 TAATTGTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.94
3 1 0.03
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1896772 original size:54 final size:54
Alignment explanation
Indices: 1896699--1896843 Score: 159
Period size: 54 Copynumber: 2.7 Consensus size: 54
1896689 CAAATGATTC
* * * *
1896699 ATGAAGAATGACATTCGATGATTGAAGAAATCTT-AAACAGATTGAAGACAGTCT
1 ATGAAAAAAGACATCCGATGAATGAAGAAAT-TTGAAACAGATTGAAGACAGTCT
* * *
1896753 ATGAAAAAAGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGACCGATCC
1 ATGAAAAAAGACATCCGATGAATGAAGAAATTTGAAACAGATTGAAGACAG-TCT
* * *
1896808 ATGAAGAAAGA-AGTCCAATGAAGGAAGAAATTTGAA
1 ATGAAAAAAGACA-TCCGATGAATGAAGAAATTTGAA
1896844 GCTGAGTGAA
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
53 2 0.03
54 43 0.55
55 33 0.42
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.21
Consensus pattern (54 bp):
ATGAAAAAAGACATCCGATGAATGAAGAAATTTGAAACAGATTGAAGACAGTCT
Found at i:1896835 original size:55 final size:54
Alignment explanation
Indices: 1896722--1896856 Score: 157
Period size: 55 Copynumber: 2.5 Consensus size: 54
1896712 TTCGATGATT
* * * *
1896722 GAAGAAATCTT-AAACAGATTGAAGACAGTCTATGAAAAAAGACATCCGATGAAT
1 GAAGAAAT-TTGAAACTGATTGAAGACAGTCCATGAAAAAAGACATCCAATGAAG
* *
1896776 GAAGAAATTTGAAACTGATTGAAGACCGATCCATGAAGAAAGA-AGTCCAATGAAG
1 GAAGAAATTTGAAACTGATTGAAGACAG-TCCATGAAAAAAGACA-TCCAATGAAG
* *
1896831 GAAGAAATTTGAAGCTGAGTGAAGAC
1 GAAGAAATTTGAAACTGATTGAAGAC
1896857 TTTCTTTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
53 2 0.03
54 24 0.34
55 44 0.63
ACGTcount: A:0.46, C:0.12, G:0.23, T:0.19
Consensus pattern (54 bp):
GAAGAAATTTGAAACTGATTGAAGACAGTCCATGAAAAAAGACATCCAATGAAG
Found at i:1900161 original size:11 final size:11
Alignment explanation
Indices: 1900142--1900208 Score: 64
Period size: 11 Copynumber: 5.9 Consensus size: 11
1900132 AGATCCAATC
*
1900142 AGAACAAAAAG
1 AGAAAAAAAAG
1900153 AGAAAAAAAAG
1 AGAAAAAAAAG
*
1900164 AGAAAAAGAAAT
1 AGAAAAA-AAAG
**
1900176 AGAGCAAAAAG
1 AGAAAAAAAAG
1900187 A-AAAGAAAAAG
1 AGAAA-AAAAAG
1900198 AGAACAAAAAA
1 AGAA-AAAAAA
1900209 AGTAAAGCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
10 1 0.02
11 28 0.62
12 15 0.33
13 1 0.02
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:1900256 original size:14 final size:14
Alignment explanation
Indices: 1900226--1900255 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1900216 CAAGGATAAT
1900226 AAAGAAAAAAAAGA
1 AAAGAAAAAAAAGA
1900240 AAAG-AAAAAAAGA
1 AAAGAAAAAAAAGA
1900253 AAA
1 AAA
1900256 AAGTAAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAGA
Found at i:1902137 original size:2 final size:2
Alignment explanation
Indices: 1902125--1902178 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
1902115 AAGTGACTTA
*
1902125 AT AT AT GT 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
*
1902167 -T AT -T AT TT AT AT
1 AT AT AT AT AT AT AT
1902179 TAATTGTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
AT
Found at i:1907889 original size:287 final size:286
Alignment explanation
Indices: 1907358--1907896 Score: 674
Period size: 287 Copynumber: 1.9 Consensus size: 286
1907348 TTTATAGAAT
*
1907358 TTGAAATGAAGTTTATGATGTGATTTATAGGGTTTGGAGTAAATAACAAAATAGAAATAATTATG
1 TTGAAATGAAGTTTATGATGTGATTTATAGGGTTTGGAGTAAATAACAAAATAGAAATAAGTATG
* * ** * *
1907423 GGGTAATGTCGGATAAAAATATAATTTTATGGGCAAAATTGAACAAATGTGAAATTACAAGCTAA
66 GGGCAATGTCGGATAAAAATATAATTTTATGGACAAAATTGAACAAACATAAAATTACAAGATAA
* * ** * * * * *
1907488 AATTTAAATAAACTAAACAACATGCAAAGATTAGATTGAAACTATTGTAAAATGTAGAGTTGAAA
131 AATTTAAATAAACTAAACAACATGCAAAGATCAAATCAAAACAATTATAAAATATAAACTTGAAA
* *
1907553 TTAATATAAAAATTGACTAAATTGTATCCATTTAAAATATTAATGAACAAAAGTTTATAGGATTT
196 TTAATATAAAAATTGACTAAATTGCATCCATTTAAAATAGTAATGAACAAAAGTTTATAGGATTT
1907618 ACATATTATGATATAATTTATAAGGC
261 ACATATTATGATATAATTTATAAGGC
* *
1907644 TTGAAATGAAGTTTATGATGTGATTTATAGGGTTTGGAGTAAATTACAAAAATATAAATAAGTAT
1 TTGAAATGAAGTTTATGATGTGATTTATAGGGTTTGGAGTAAATAAC-AAAATAGAAATAAGTAT
* * ** * *
1907709 -GGGCAATTTTGGATAAATAATATAATTTTAAT-GATTAAATTGAACAAACATAAAATTATAATA
65 GGGGCAATGTCGGATAAA-AATATAATTTT-ATGGACAAAATTGAACAAACATAAAATTACAAGA
* * **
1907772 TGAAATTTAAATAAATTAAACAACATGCAGTGATCAAATCAAAACAATTATAAAATATGAAACTT
128 TAAAATTTAAATAAACTAAACAACATGCAAAGATCAAATCAAAACAATTATAAAATAT-AAACTT
* * * * *
1907837 -AAATTAATA-ATAAATTGGATTAAATTGCATTCATTT-TAATAGTAGGTGAACAAAAGTTTA
192 GAAATTAATATAAAAATT-GACTAAATTGCATCCATTTAAAATAGTA-ATGAACAAAAGTTTA
1907897 ACATCTTAAT
Statistics
Matches: 212, Mismatches: 35, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
286 72 0.34
287 134 0.63
288 6 0.03
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.33
Consensus pattern (286 bp):
TTGAAATGAAGTTTATGATGTGATTTATAGGGTTTGGAGTAAATAACAAAATAGAAATAAGTATG
GGGCAATGTCGGATAAAAATATAATTTTATGGACAAAATTGAACAAACATAAAATTACAAGATAA
AATTTAAATAAACTAAACAACATGCAAAGATCAAATCAAAACAATTATAAAATATAAACTTGAAA
TTAATATAAAAATTGACTAAATTGCATCCATTTAAAATAGTAATGAACAAAAGTTTATAGGATTT
ACATATTATGATATAATTTATAAGGC
Found at i:1908171 original size:21 final size:21
Alignment explanation
Indices: 1908147--1908190 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1908137 ATATCATACT
*
1908147 TACATATATGCAT-CAATATCA
1 TACATATATACATAC-ATATCA
1908168 TACATATATACATACATATCA
1 TACATATATACATACATATCA
1908189 TA
1 TA
1908191 TATTAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.34
Consensus pattern (21 bp):
TACATATATACATACATATCA
Found at i:1908192 original size:17 final size:17
Alignment explanation
Indices: 1908166--1908225 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
1908156 GCATCAATAT
1908166 CATA-CATATATACATA
1 CATATCATATATACATA
1908182 CATATCATATATTA-ATA
1 CATATCATATA-TACATA
*
1908199 -A-ATTATATATACATA
1 CATATCATATATACATA
*
1908214 CATAACATATAT
1 CATATCATATAT
1908226 TAATAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
14 2 0.06
15 10 0.28
16 6 0.17
17 16 0.44
18 2 0.06
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (17 bp):
CATATCATATATACATA
Found at i:1908212 original size:32 final size:32
Alignment explanation
Indices: 1908171--1908242 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
1908161 AATATCATAC
*
1908171 ATATATACATACATATCATATATTAATAAATT
1 ATATATACATACATAACATATATTAATAAATT
1908203 ATATATACATACATAACATATATTAATAAATT
1 ATATATACATACATAACATATATTAATAAATT
*
1908235 ATACATAC
1 ATATATAC
1908243 GTAAGTACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (32 bp):
ATATATACATACATAACATATATTAATAAATT
Found at i:1909227 original size:13 final size:13
Alignment explanation
Indices: 1909176--1909228 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
1909166 CATTTAATAA
1909176 AATTA-AATTAAT
1 AATTATAATTAAT
*
1909188 GATTATAATTGAA-
1 AATTATAATT-AAT
*
1909201 AATTTTAATCTAAT
1 AATTATAAT-TAAT
1909215 AATTATAATTAAT
1 AATTATAATTAAT
1909228 A
1 A
1909229 TAGAAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
12 4 0.12
13 18 0.55
14 11 0.33
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (13 bp):
AATTATAATTAAT
Found at i:1909247 original size:38 final size:41
Alignment explanation
Indices: 1909203--1909302 Score: 116
Period size: 38 Copynumber: 2.5 Consensus size: 41
1909193 TAATTGAAAA
1909203 TTTTAATCTAATAATTATAATTAAT-ATA-GAAAATAA-TT
1 TTTTAATCTAATAATTATAATTAATAATATGAAAATAAGTT
* * *
1909241 TTTTAATCTAATGATCATAATTAATAAATATTGAAAGTAAGTT
1 TTTTAATCTAATAATTATAATTAAT-AATA-TGAAAATAAGTT
* *
1909284 TATTAATTTAATAATTATA
1 TTTTAATCTAATAATTATA
1909303 TTTAGATTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
38 23 0.46
40 3 0.06
42 7 0.14
43 17 0.34
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (41 bp):
TTTTAATCTAATAATTATAATTAATAATATGAAAATAAGTT
Found at i:1912107 original size:19 final size:19
Alignment explanation
Indices: 1912083--1912154 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
1912073 ACCTTTCTTT
*
1912083 ATTTTCATATTCATAACTC
1 ATTTTCAGATTCATAACTC
* * *
1912102 ATTTTCAAATTCATAATTT
1 ATTTTCAGATTCATAACTC
1912121 ATTTTCAGATT-ATAACTC
1 ATTTTCAGATTCATAACTC
*
1912139 TTTTTTCAGATTCATA
1 -ATTTTCAGATTCATA
1912155 GCACAATGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 5 0.11
19 36 0.82
20 3 0.07
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (19 bp):
ATTTTCAGATTCATAACTC
Found at i:1912123 original size:38 final size:38
Alignment explanation
Indices: 1912080--1912154 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
1912070 TTCACCTTTC
*
1912080 TTTATTTTCATATTCATAACTC-ATTTTCAAATTCATAA
1 TTTATTTTCAGATT-ATAACTCTATTTTCAAATTCATAA
* *
1912118 TTTATTTTCAGATTATAACTCTTTTTTCAGATTCATA
1 TTTATTTTCAGATTATAACTCTATTTTCAAATTCATA
1912155 GCACAATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 7 0.21
38 26 0.79
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.52
Consensus pattern (38 bp):
TTTATTTTCAGATTATAACTCTATTTTCAAATTCATAA
Found at i:1914756 original size:28 final size:30
Alignment explanation
Indices: 1914688--1914758 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 30
1914678 AAAATTATAT
* *
1914688 TTTTGGTCCCTAAATTTTGCAAAGTTTATA
1 TTTTGGTCACTAAATTTTGCAAAGTTTACA
* *
1914718 CTTTGGCCACTAAATTTT-CAAA-TTTACA
1 TTTTGGTCACTAAATTTTGCAAAGTTTACA
1914746 TTTTGGTCACTAA
1 TTTTGGTCACTAA
1914759 CAAAAATTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 16 0.46
29 4 0.11
30 15 0.43
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (30 bp):
TTTTGGTCACTAAATTTTGCAAAGTTTACA
Found at i:1922028 original size:19 final size:20
Alignment explanation
Indices: 1922004--1922063 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 20
1921994 TTTTGGTGCA
*
1922004 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
1922023 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
*
1922044 AAAGGGGAACCGATTCCCCC
1 -GA-GGGAACCGATTCCCCC
1922064 ATAGGGGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.29
20 6 0.17
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:1922071 original size:20 final size:20
Alignment explanation
Indices: 1922025--1922088 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
1922015 TCCCCCTTGA
*
1922025 GGGAACCGATTCCCCCTTTAAAG
1 GGGAACCGATTCCCCC---ATAG
1922048 GGGAACCGATTCCCCCATAG
1 GGGAACCGATTCCCCCATAG
* *
1922068 GGGAATCGATACCCCC-TAG
1 GGGAACCGATTCCCCCATAG
1922087 GG
1 GG
1922089 TTCTGGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 5 0.13
20 17 0.45
23 16 0.42
ACGTcount: A:0.25, C:0.31, G:0.27, T:0.17
Consensus pattern (20 bp):
GGGAACCGATTCCCCCATAG
Found at i:1929188 original size:12 final size:12
Alignment explanation
Indices: 1929171--1929198 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1929161 GCTTAAGCAT
1929171 GTCTGAGTCCGA
1 GTCTGAGTCCGA
1929183 GTCTGAGTCCGA
1 GTCTGAGTCCGA
1929195 GTCT
1 GTCT
1929199 TATGTATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.25, G:0.32, T:0.29
Consensus pattern (12 bp):
GTCTGAGTCCGA
Found at i:1929674 original size:57 final size:55
Alignment explanation
Indices: 1929566--1929675 Score: 130
Period size: 57 Copynumber: 2.0 Consensus size: 55
1929556 ACTTCGTCAT
* * *
1929566 CTTCTTCAACTTCATCCTTTCTATACTTCATCTTGAAGTACATTCTGTACTTCCA
1 CTTCTTCAACTTCATCCTTTCTATACTTCATCTTCAAGTACATCCTCTACTTCCA
* * * * *
1929621 CTTCTTCAATTTCATCCTCTATTTCTACTTCATCTTCTATTACATCCTCTACTTC
1 CTTCTTCAACTTCATCCT-T-TCTATACTTCATCTTCAAGTACATCCTCTACTTC
1929676 TAATTTTTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
55 17 0.38
56 1 0.02
57 27 0.60
ACGTcount: A:0.20, C:0.31, G:0.03, T:0.46
Consensus pattern (55 bp):
CTTCTTCAACTTCATCCTTTCTATACTTCATCTTCAAGTACATCCTCTACTTCCA
Found at i:1945223 original size:27 final size:27
Alignment explanation
Indices: 1945193--1945363 Score: 288
Period size: 27 Copynumber: 6.3 Consensus size: 27
1945183 TCCTACCTCG
*
1945193 CAGTTCACCCTGCTCTGACCGCTCATA
1 CAGTACACCCTGCTCTGACCGCTCATA
*
1945220 CAGTACACCTTGCTCTGACCGCTCATA
1 CAGTACACCCTGCTCTGACCGCTCATA
*
1945247 CAGTACACCCTACTCTGACCGCTCATA
1 CAGTACACCCTGCTCTGACCGCTCATA
*
1945274 CAGTACACCCTGCTCTGATCGCTCATA
1 CAGTACACCCTGCTCTGACCGCTCATA
*
1945301 CAATACACCCTGCTCTGACCGCTCATA
1 CAGTACACCCTGCTCTGACCGCTCATA
*
1945328 TAGTACACCCTGCTCTGACCGCTCATA
1 CAGTACACCCTGCTCTGACCGCTCATA
1945355 CAGTACACC
1 CAGTACACC
1945364 ACTATCACCA
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 133 1.00
ACGTcount: A:0.23, C:0.39, G:0.13, T:0.24
Consensus pattern (27 bp):
CAGTACACCCTGCTCTGACCGCTCATA
Found at i:1948623 original size:20 final size:21
Alignment explanation
Indices: 1948585--1948625 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1948575 ATAAAAATAA
* *
1948585 TTTTTCAAAAATTTCATTTTG
1 TTTTTCAAAAATCTAATTTTG
1948606 TTTTTC-AAAATCTAATTTTG
1 TTTTTCAAAAATCTAATTTTG
1948626 CCTTCACAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTTCAAAAATCTAATTTTG
Found at i:1958934 original size:16 final size:16
Alignment explanation
Indices: 1958915--1958953 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1958905 ATAAATGCAT
1958915 GATGCATGAAATGTTC
1 GATGCATGAAATGTTC
1958931 GATGCATGAAATGTTC
1 GATGCATGAAATGTTC
*
1958947 GAGGCAT
1 GATGCAT
1958954 TGATCCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (16 bp):
GATGCATGAAATGTTC
Found at i:1959750 original size:16 final size:16
Alignment explanation
Indices: 1959729--1959764 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1959719 TGTAAATGAT
1959729 AAAAAAT-AAAGGAAGA
1 AAAAAATGAAAGGAA-A
1959745 AAAAAATGAAAGGAAA
1 AAAAAATGAAAGGAAA
1959761 AAAA
1 AAAA
1959765 GTTAGTGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (16 bp):
AAAAAATGAAAGGAAA
Found at i:1960911 original size:50 final size:51
Alignment explanation
Indices: 1960807--1960914 Score: 118
Period size: 50 Copynumber: 2.2 Consensus size: 51
1960797 ACATTAGATT
* ** *
1960807 AAAAAAT-AAATCAAAGAAGGAAATATTAAATTATATAAAAATGTTAAAAG
1 AAAAAATAAAATCAAAGAAGAAAATATTAAATTATATAAAAATGAAAAAAA
1960857 AAAAAATAAAAT-AAATGAAGAAAATATTAAATT-T-TAGAAAA-GAAAAATAA
1 AAAAAATAAAATCAAA-GAAGAAAATATTAAATTATATA-AAAATGAAAAA-AA
1960907 AAAAAATA
1 AAAAAATA
1960915 TTAAAAAATG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
49 6 0.12
50 24 0.48
51 20 0.40
ACGTcount: A:0.69, C:0.01, G:0.08, T:0.22
Consensus pattern (51 bp):
AAAAAATAAAATCAAAGAAGAAAATATTAAATTATATAAAAATGAAAAAAA
Found at i:1960942 original size:5 final size:5
Alignment explanation
Indices: 1960932--1960979 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
1960922 ATGTTAAAAG
* *
1960932 ATAAA ATAAAA ATGAA ACAAA ATAAA ATAAA ATAAA ATAAA ATTAAA A
1 ATAAA AT-AAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A-TAAA A
1960980 AAGAAGTGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
5 27 0.73
6 10 0.27
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:1961139 original size:16 final size:16
Alignment explanation
Indices: 1961120--1961170 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1961110 TTGAAAAGGT
1961120 ATAATAAAATAAAATA
1 ATAATAAAATAAAATA
1961136 ATAAT-AAATAAAA-A
1 ATAATAAAATAAAATA
*
1961150 GGA-AATATAATAAAATA
1 --ATAATAAAATAAAATA
1961167 ATAA
1 ATAA
1961171 ATAATAGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
14 1 0.03
15 12 0.41
16 15 0.52
17 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (16 bp):
ATAATAAAATAAAATA
Found at i:1961147 original size:20 final size:20
Alignment explanation
Indices: 1961122--1961176 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1961112 GAAAAGGTAT
1961122 AATAAAATAAAATAATAATA
1 AATAAAATAAAATAATAATA
1961142 AATAAAA-AGGAAAT-ATAATA
1 AATAAAATA--AAATAATAATA
*
1961162 AA-ATAAT-AAATAATA
1 AATAAAATAAAATAATA
1961177 GTAGTAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
17 4 0.13
18 3 0.10
19 4 0.13
20 15 0.50
21 4 0.13
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (20 bp):
AATAAAATAAAATAATAATA
Found at i:1961165 original size:31 final size:34
Alignment explanation
Indices: 1961086--1961179 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 34
1961076 CATGGATTAA
* *
1961086 AATAAACATAAAATAGTAATAAAGTTGAAAAGGTAT
1 AATAAA-ATAAAATAATAATAAAG-TAAAAAGGTAT
1961122 AATAAAATAAAATAATAATAAA-TAAAAAGG-A-
1 AATAAAATAAAATAATAATAAAGTAAAAAGGTAT
*
1961153 AATATAATAAAATAATAAATAATAGTA
1 AATAAAATAAAATAAT-AATAA-AGTA
1961180 GTAAAGATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
31 15 0.29
32 6 0.12
33 8 0.15
34 2 0.04
35 15 0.29
36 6 0.12
ACGTcount: A:0.66, C:0.01, G:0.09, T:0.24
Consensus pattern (34 bp):
AATAAAATAAAATAATAATAAAGTAAAAAGGTAT
Found at i:1961237 original size:18 final size:18
Alignment explanation
Indices: 1961216--1961258 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1961206 GTTGTTTTTA
1961216 AAATAAAAGATAAA-AATT
1 AAATAAAAGA-AAATAATT
1961234 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
1961252 AAATAAA
1 AAATAAA
1961259 TAATCTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:1961944 original size:25 final size:24
Alignment explanation
Indices: 1961891--1961946 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1961881 TTATCTTAAT
* * * *
1961891 TAAAACACTTAAAACTATTTAAAC
1 TAAAATACTTAAAACAATATAAAA
1961915 TAAAATACTTAAAACAATGATAAAA
1 TAAAATACTTAAAACAAT-ATAAAA
1961940 TAAAATA
1 TAAAATA
1961947 ATATTTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.27
Consensus pattern (24 bp):
TAAAATACTTAAAACAATATAAAA
Found at i:1961957 original size:12 final size:13
Alignment explanation
Indices: 1961940--1961968 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1961930 AATGATAAAA
1961940 TAAAATAATATT-
1 TAAAATAATATTC
1961952 TAAAATAATATTC
1 TAAAATAATATTC
1961965 TAAA
1 TAAA
1961969 TTCTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAATATTC
Found at i:1963095 original size:39 final size:39
Alignment explanation
Indices: 1963052--1963170 Score: 136
Period size: 39 Copynumber: 3.1 Consensus size: 39
1963042 TTTAAAAAAT
*
1963052 AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTAAA
1 AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTATA
* * *
1963091 AATTTAGAATGTT-GTGGTAGCAA-AATTTAAGAAATTATG
1 AATTTAGAATGTTAAT-GTA-AAATAATTTAAGAAATTATA
* * *
1963130 AATTTAGAATGTTAAAGTGAAATAATTTGA-AAATTATA
1 AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTATA
1963168 AAT
1 AAT
1963171 AAACATTTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
38 13 0.20
39 51 0.77
40 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.14, T:0.36
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTAAAATAATTTAAGAAATTATA
Found at i:1963199 original size:17 final size:18
Alignment explanation
Indices: 1963167--1963201 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1963157 TGAAAATTAT
*
1963167 AAATAAACATTTAATATA
1 AAATAAACATTAAATATA
1963185 AAATAAACA-TAAATATA
1 AAATAAACATTAAATATA
1963202 TATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAACATTAAATATA
Found at i:1963863 original size:2 final size:2
Alignment explanation
Indices: 1963856--1963926 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1963846 TTTAATATCT
1963856 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1963898 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1963927 GTAAAGGTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1965424 original size:22 final size:22
Alignment explanation
Indices: 1965396--1965446 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1965386 ACTTTAATTC
1965396 TAAATTCAAAGAATTTTGTATT
1 TAAATTCAAAGAATTTTGTATT
1965418 TAAATTCAAAGAATTTTGTATT
1 TAAATTCAAAGAATTTTGTATT
1965440 TAAATTC
1 TAAATTC
1965447 GGTGGCGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (22 bp):
TAAATTCAAAGAATTTTGTATT
Found at i:1965628 original size:2 final size:2
Alignment explanation
Indices: 1965617--1965661 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1965607 GCCCAATTTC
1965617 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1965658 TA TA
1 TA TA
1965662 CTATCATGGC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1970691 original size:89 final size:90
Alignment explanation
Indices: 1970540--1970712 Score: 285
Period size: 89 Copynumber: 1.9 Consensus size: 90
1970530 CAAAAAAAAA
** * *
1970540 AACTTTAAAAGTTTTGAATTTCCTCACTGATCTTAATAAATTAGATTTTTTTGGTCACTGAACTT
1 AACTTTAAAAAATTTGAATTTCCTCACTGAACTTAATAAATTAGATTGTTTTGGTCACTGAACTT
1970605 TA-CTCTCTCCTATTTTGTTCACTG
66 TACCTCTCTCCTATTTTGTTCACTG
*
1970629 AACTTTAAAAAATTTGAATTTCCTCACTGAACTTAATACATTAGATTGTTTTGGTCACTGAACTT
1 AACTTTAAAAAATTTGAATTTCCTCACTGAACTTAATAAATTAGATTGTTTTGGTCACTGAACTT
1970694 TACTCTCTCTCCTATTTTG
66 TAC-CTCTCTCCTATTTTG
1970713 GTCATTTAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 62 0.81
91 15 0.19
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.45
Consensus pattern (90 bp):
AACTTTAAAAAATTTGAATTTCCTCACTGAACTTAATAAATTAGATTGTTTTGGTCACTGAACTT
TACCTCTCTCCTATTTTGTTCACTG
Found at i:1971954 original size:19 final size:20
Alignment explanation
Indices: 1971917--1971959 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1971907 CATGATTTTA
1971917 TTATATTATATAAAATTAAT
1 TTATATTATATAAAATTAAT
**
1971937 TTATATT-TATAAGTTTAAT
1 TTATATTATATAAAATTAAT
1971956 TTAT
1 TTAT
1971960 TTTTTATGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTATATTATATAAAATTAAT
Found at i:1972230 original size:27 final size:27
Alignment explanation
Indices: 1972196--1972266 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
1972186 ATTGAAAATC
*
1972196 TAGAGGGAAATTGGGAAATTTTGTGAA
1 TAGAGGGAAATTGGGAAATTTTGAGAA
* *
1972223 TAGGGGGAAATTGAGAAATTTTGAGAA
1 TAGAGGGAAATTGGGAAATTTTGAGAA
* *
1972250 TAGAAGAAAATTGGGAA
1 TAGAGGGAAATTGGGAA
1972267 TTTAGAAGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.25
Consensus pattern (27 bp):
TAGAGGGAAATTGGGAAATTTTGAGAA
Found at i:1972296 original size:15 final size:15
Alignment explanation
Indices: 1972276--1972304 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1972266 ATTTAGAAGG
1972276 AAATTTTGGGAATAT
1 AAATTTTGGGAATAT
1972291 AAATTTTGGGAATA
1 AAATTTTGGGAATA
1972305 GAGGGAAATT
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:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (15 bp):
AAATTTTGGGAATAT
Found at i:1972296 original size:53 final size:53
Alignment explanation
Indices: 1972238--1972340 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 53
1972228 GGAAATTGAG
*
1972238 AAATTTTGAGAATAGAAGAAAATTGGGAATTTAGAAG-GAAATTTTGGGAATAT
1 AAATTTTGAGAATAGAAGAAAATTGGAAATTTAG-AGTGAAATTTTGGGAATAT
* * *
1972291 AAATTTTGGGAATAGAGGGAAATTGGAAATTTAGAGTGAAATTTTGGGAA
1 AAATTTTGAGAATAGAAGAAAATTGGAAATTTAGAGTGAAATTTTGGGAA
1972341 GTTGGGAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 2 0.04
53 43 0.96
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (53 bp):
AAATTTTGAGAATAGAAGAAAATTGGAAATTTAGAGTGAAATTTTGGGAATAT
Found at i:1972411 original size:2 final size:2
Alignment explanation
Indices: 1972404--1972505 Score: 85
Period size: 2 Copynumber: 53.0 Consensus size: 2
1972394 TCATACATGC
*
1972404 AT AT AT AT AT -T TT 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
* *
1972445 AT ACT -T AT ACT AT AT AGT TT AT AC A- AT A- AT AT AT -T AT AT
1 AT A-T AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
1972484 ACT -T AT AT AT AT A- AT -T AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT
1972506 TTTATTTTAT
Statistics
Matches: 84, Mismatches: 4, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
1 8 0.10
2 71 0.85
3 5 0.06
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1972888 original size:199 final size:199
Alignment explanation
Indices: 1972543--1972938 Score: 539
Period size: 199 Copynumber: 2.0 Consensus size: 199
1972533 AACCTAATTT
*
1972543 TCTCTCATTGATGTATTGTTCATCTTATTTCTTTTTCGTCTTTATTGATCAGCATCGACACCAAC
1 TCTCTCATTGATGTATTGTTCATCTTATTTCTTTTCCGTCTTTATTGATCAGCATCGACACCAAC
***
1972608 TTTAATGTTGGTTGCCGACCGTTGGTATTCTTTATTTTCTTTTTATTTTCTATAATGTATCTTTA
66 TTTAATGTTGGTTGCCGACCGCCAGTATTCTTTATTTTCTTTTTATTTTCTATAATGTATCTTTA
* * *
1972673 TTTTCTTTTCTTTTTTTATTTTTAATAAGTCTGCATGTGTTACACGTTTTCATCTGCCTCTATGA
131 TTTTCTTTTCTTTTTTTATTTTCAATAAGTATGCATGAGTTACACGTTTTCATCTGCCTCTATGA
1972738 CACG
196 CACG
* * * *
1972742 TCTCTCATTTG-TGTGTTGTTCATCTCT-TTTCTTTTCCGTCTTTGTTGATCGGCAAT-GGCACC
1 TCTCTCA-TTGATGTATTGTTCATCT-TATTTCTTTTCCGTCTTTATTGATCAGC-ATCGACACC
* * *
1972804 AACTTTAATGGTT-GTTGTCGATCGCCAGTATTCTTTATTTTCTTTTTATTTTCTATATTGTATC
63 AACTTTAAT-GTTGGTTGCCGACCGCCAGTATTCTTTATTTTCTTTTTATTTTCTATAATGTATC
* ** ** * *
1972868 TTTATTTTCTTTTGTTTTTTTATTTTCAATAAGTATGTTTGAGTTGTACGTTTTCATCTGTCTTT
127 TTTATTTTCTTTTCTTTTTTTATTTTCAATAAGTATGCATGAGTTACACGTTTTCATCTGCCTCT
1972933 ATGACA
192 ATGACA
1972939 TATTTTTTTA
Statistics
Matches: 172, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
199 163 0.95
200 9 0.05
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (199 bp):
TCTCTCATTGATGTATTGTTCATCTTATTTCTTTTCCGTCTTTATTGATCAGCATCGACACCAAC
TTTAATGTTGGTTGCCGACCGCCAGTATTCTTTATTTTCTTTTTATTTTCTATAATGTATCTTTA
TTTTCTTTTCTTTTTTTATTTTCAATAAGTATGCATGAGTTACACGTTTTCATCTGCCTCTATGA
CACG
Found at i:1973432 original size:2 final size:2
Alignment explanation
Indices: 1973421--1973532 Score: 81
Period size: 2 Copynumber: 56.5 Consensus size: 2
1973411 ATAAAAACAA
1973421 AT AT -T 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
* * * * * * * *
1973462 A- AA AT TT AT AT AT -T TT AT AGT TT AA AT GCT TT AT AGT GT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT -AT AT AT A-T AT AT
1973503 AT ACT -T AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1973533 CTTATATTGT
Statistics
Matches: 88, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
1 5 0.06
2 79 0.90
3 4 0.05
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1990737 original size:17 final size:15
Alignment explanation
Indices: 1990701--1990741 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
1990691 TCATTTTCTA
1990701 TTCATTA-TTTATTT
1 TTCATTATTTTATTT
1990715 TT-ATTATTTTATTACT
1 TTCATTATTTTATT--T
1990731 TTCATTATTTT
1 TTCATTATTTT
1990742 TAAGCCCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
16 3 0.13
17 8 0.35
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (15 bp):
TTCATTATTTTATTT
Found at i:1993093 original size:24 final size:23
Alignment explanation
Indices: 1993066--1993125 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 23
1993056 AGTATGTATG
1993066 ATAATATATA-A-TTTCAGAAAAT
1 ATAATATATATAGTTTCA-AAAAT
1993088 ACATAATATATATAGTTTTCAAAAAT
1 --ATAATATATATAG-TTTCAAAAAT
1993114 ATAATATATATA
1 ATAATATATATA
1993126 TATAATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
24 22 0.67
25 1 0.03
26 5 0.15
27 5 0.15
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (23 bp):
ATAATATATATAGTTTCAAAAAT
Found at i:1993098 original size:26 final size:27
Alignment explanation
Indices: 1993069--1993133 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
1993059 ATGTATGATA
*
1993069 ATATATAATTTCAGAAAATA-CATA-AT
1 ATATATAATTTCA-AAAATATAATATAT
*
1993095 ATATATAGTTTTCAAAAATATAATATAT
1 ATATATA-ATTTCAAAAATATAATATAT
1993123 ATATATAATTT
1 ATATATAATTT
1993134 TTGTTTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 13 0.39
27 11 0.33
28 9 0.27
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (27 bp):
ATATATAATTTCAAAAATATAATATAT
Found at i:1993124 original size:28 final size:26
Alignment explanation
Indices: 1993066--1993134 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 26
1993056 AGTATGTATG
*
1993066 ATAATATATA-A-TTTCAGAAAATAC
1 ATAATATATATATTTTCAGAAAATAA
1993090 ATAATATATATAGTTTTCA-AAAATATA
1 ATAATATATATA-TTTTCAGAAAATA-A
1993117 ATATATATATATAATTTT
1 ATA-ATATATAT-ATTTT
1993135 TGTTTGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
24 10 0.26
25 1 0.03
26 6 0.16
27 8 0.21
28 12 0.32
29 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (26 bp):
ATAATATATATATTTTCAGAAAATAA
Found at i:1993177 original size:36 final size:36
Alignment explanation
Indices: 1993095--1993191 Score: 121
Period size: 34 Copynumber: 2.8 Consensus size: 36
1993085 AATACATAAT
*
1993095 ATATATAGTTTTCAAAA-ATATAATATATATATATA
1 ATATATAGTTTTGAAAATATATAATATATATATATA
* *
1993130 AT-TTTTG-TTTGAAAATATAT-ATCATATATATATA
1 ATATATAGTTTTGAAAATATATAAT-ATATATATATA
*
1993164 ATATATAGTTTTGAAAATATATTATATA
1 ATATATAGTTTTGAAAATATATAATATA
1993192 GTTTTTGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
33 9 0.17
34 20 0.38
35 5 0.10
36 16 0.31
37 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (36 bp):
ATATATAGTTTTGAAAATATATAATATATATATATA
Found at i:1993189 original size:21 final size:22
Alignment explanation
Indices: 1993159--1993324 Score: 139
Period size: 22 Copynumber: 7.5 Consensus size: 22
1993149 TATCATATAT
*
1993159 ATATAATATATAG-TTTTGAAA
1 ATATATTATATAGTTTTTGAAA
1993180 ATATATTATATAGTTTTTGAAA
1 ATATATTATATAGTTTTTGAAA
*
1993202 ACATATTATATAG-TTTTGAAA
1 ATATATTATATAGTTTTTGAAA
1993223 ACGTATAATATATATAGTTTTTG--A
1 A--TAT-AT-TATATAGTTTTTGAAA
*
1993247 A-A-A-TATATAGTTTTCGAAAA
1 ATATATTATATAGTTTTTG-AAA
* * *
1993267 CATGTAATATATATTTTTTGAAAA
1 -ATATATTATATAGTTTTTG-AAA
* *
1993291 ACATATTATATATTTTTTGAAA
1 ATATATTATATAGTTTTTGAAA
*
1993313 ATATAATATATA
1 ATATATTATATA
1993325 TTAAATAGTT
Statistics
Matches: 120, Mismatches: 12, Indels: 25
0.76 0.08 0.16
Matches are distributed among these distances:
17 12 0.10
19 1 0.01
20 1 0.01
21 23 0.19
22 33 0.28
23 19 0.16
24 19 0.16
25 7 0.06
26 5 0.04
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (22 bp):
ATATATTATATAGTTTTTGAAA
Found at i:1993212 original size:43 final size:43
Alignment explanation
Indices: 1993165--1993324 Score: 168
Period size: 43 Copynumber: 3.6 Consensus size: 43
1993155 ATATATATAA
*
1993165 TATATAGTTTTGAAAATATATTATATAGTTTTTGAAAACATAT
1 TATATAGTTTTGAAAATATAATATATAGTTTTTGAAAACATAT
1993208 TATATAGTTTTGAAAACGTATAATATATATAGTTTTTG--AA-A-A-
1 TATATAGTTTTGAAAA--TAT-A-ATATATAGTTTTTGAAAACATAT
* *
1993250 TATATAGTTTTCGAAAACATGTAATATATATTTTTTGAAAAACATAT
1 TATATAGTTTT-G-AAA-ATATAATATATAGTTTTTG-AAAACATAT
*
1993297 TATATATTTTTTGAAAATATAATATATA
1 TATATA-GTTTTGAAAATATAATATATA
1993325 TTAAATAGTT
Statistics
Matches: 98, Mismatches: 5, Indels: 26
0.76 0.04 0.20
Matches are distributed among these distances:
41 13 0.13
42 12 0.12
43 20 0.20
44 6 0.06
45 18 0.18
46 5 0.05
47 20 0.20
48 4 0.04
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (43 bp):
TATATAGTTTTGAAAATATAATATATAGTTTTTGAAAACATAT
Found at i:1993254 original size:17 final size:17
Alignment explanation
Indices: 1993232--1993266 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1993222 AACGTATAAT
*
1993232 ATATATAGTTTTTGAAA
1 ATATATAGTTTTCGAAA
1993249 ATATATAGTTTTCGAAA
1 ATATATAGTTTTCGAAA
1993266 A
1 A
1993267 CATGTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (17 bp):
ATATATAGTTTTCGAAA
Found at i:1993259 original size:64 final size:63
Alignment explanation
Indices: 1993186--1993317 Score: 162
Period size: 64 Copynumber: 2.1 Consensus size: 63
1993176 GAAAATATAT
* *
1993186 TATATAGTTTTTGAAAACA-TATTATATA-GTTTTG-AAAACGTATAATATATATAGTTTTTGAA
1 TATATAGTTTTCGAAAACAGTAATATATATGTTTTGAAAAAC--AT-AT-TATATAGTTTTTGAA
1993248 AA
62 AA
* *
1993250 TATATAGTTTTCGAAAACATGTAATATATATTTTTTGAAAAACATATTATATATTTTTTGAAAA
1 TATATAGTTTTCGAAAACA-GTAATATATATGTTTTGAAAAACATATTATATAGTTTTTGAAAA
1993314 TATA
1 TATA
1993318 ATATATATTA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
64 38 0.63
65 2 0.03
66 10 0.17
67 5 0.08
68 5 0.08
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (63 bp):
TATATAGTTTTCGAAAACAGTAATATATATGTTTTGAAAAACATATTATATAGTTTTTGAAAA
Found at i:1993336 original size:29 final size:27
Alignment explanation
Indices: 1993293--1993350 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 27
1993283 TTTGAAAAAC
* *
1993293 ATATTATATATTTTTTGAAAATATAATAT
1 ATATTAAATAGTTTTT-AAAAT-TAATAT
*
1993322 ATATTAAATAGTTTTTAAAATTTATAT
1 ATATTAAATAGTTTTTAAAATTAATAT
1993349 AT
1 AT
1993351 GTATATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 7 0.27
28 5 0.19
29 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (27 bp):
ATATTAAATAGTTTTTAAAATTAATAT
Found at i:1993395 original size:4 final size:4
Alignment explanation
Indices: 1993386--1993413 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1993376 TTATTATTAT
1993386 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1993414 ATATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:1993430 original size:12 final size:12
Alignment explanation
Indices: 1993365--1993430 Score: 55
Period size: 12 Copynumber: 5.3 Consensus size: 12
1993355 ATAGTAAACA
*
1993365 TATTATTATTGT
1 TATTATTATTTT
1993377 TATTATTA-TTT
1 TATTATTATTTT
*
1993388 TATTTATT-TATT
1 TA-TTATTATTTT
*
1993400 TATTTATTTATTTAA
1 TA-TTA-TTATTT-T
1993415 TATTATTATTTT
1 TATTATTATTTT
1993427 TATT
1 TATT
1993431 TTCAAGGGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 4 0.09
12 25 0.57
13 8 0.18
14 5 0.11
15 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (12 bp):
TATTATTATTTT
Found at i:1994444 original size:20 final size:18
Alignment explanation
Indices: 1994421--1994476 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 18
1994411 TATGACCATA
1994421 AATTATTAAAATAATAACTC
1 AATTA-TAAAATAATAA-TC
*
1994441 AATTATCAAAATAA-AATG
1 AATTAT-AAAATAATAATC
1994459 AATTA-AAAATAATAATC
1 AATTATAAAATAATAATC
1994476 A
1 A
1994477 TAAAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 7 0.22
17 4 0.12
18 6 0.19
19 3 0.09
20 12 0.38
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (18 bp):
AATTATAAAATAATAATC
Found at i:1996197 original size:15 final size:15
Alignment explanation
Indices: 1996171--1996218 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
1996161 TTCAAACATC
*
1996171 CAAACAAATCCAAAGT
1 CAAAC-AATCCAAAAT
*
1996187 CTAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
1996204 CAAACAATCCAAAAT
1 CAAACAATCCAAAAT
1996219 ATTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:2002053 original size:20 final size:20
Alignment explanation
Indices: 2002011--2002053 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2002001 TTATTTTCAT
* *
2002011 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
2002031 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
2002051 TTT
1 TTT
2002054 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:2003532 original size:23 final size:23
Alignment explanation
Indices: 2003496--2003542 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2003486 TTGGGTCGGG
2003496 TATATATATATATTTAAATTAAA
1 TATATATATATATTTAAATTAAA
* *
2003519 TATATATTTTTATTTAAATTAAA
1 TATATATATATATTTAAATTAAA
2003542 T
1 T
2003543 TTATTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TATATATATATATTTAAATTAAA
Found at i:2003571 original size:34 final size:33
Alignment explanation
Indices: 2003519--2003587 Score: 77
Period size: 34 Copynumber: 2.0 Consensus size: 33
2003509 TTAAATTAAA
* * *
2003519 TATATATTTTTATTTAAATTAA-ATTTATTAATAT
1 TATATATATATATATAAA-TAATATTT-TTAATAT
2003553 TATATATATATATATAAATAATTATTTTTAATAT
1 TATATATATATATATAAATAA-TATTTTTAATAT
2003587 T
1 T
2003588 TATCGGGTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
33 3 0.10
34 23 0.77
35 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
TATATATATATATATAAATAATATTTTTAATAT
Found at i:2003611 original size:12 final size:13
Alignment explanation
Indices: 2003589--2003637 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
2003579 TTTAATATTT
*
2003589 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
*
2003601 ATCAGGGCGGGTA
1 ATCGGGGCGGGTA
*
2003614 ATCGGGGTGGGTA
1 ATCGGGGCGGGTA
2003627 ATCGGGGCGGG
1 ATCGGGGCGGG
2003638 GATTACCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.14, C:0.14, G:0.53, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:2006407 original size:437 final size:436
Alignment explanation
Indices: 2005590--2006517 Score: 1403
Period size: 437 Copynumber: 2.1 Consensus size: 436
2005580 GGTAAATACG
* * * * *
2005590 CCTACAAGAGATGGACAAGGCTTGAGGAAATCGATGAAAAATACATATTTATAGAAATGATTCTG
1 CCTACAAGAGA-AGACAAGGCTTGAGGAAATCGATGAAAAATACATATTTACAGAAATAATCCCG
* *
2005655 AGAACATTCCAGAAAGCCAAACGTCATTAGCAAGACAACGAGTGGCGTGCGAAGACCACGCACCG
65 AGAACATTCCAGAAAGCCAAACGTCATTAGCAAGACAACGAGTGGCGTACGAAGACCACGCACCA
* * **
2005720 AGTGGATTTGGAAAGATCCTTGCTGATCCACAAGGAAATCCCATAAAAATGGAAAATCGAATCAA
130 AGAGAATTTGGAAAGATCCTTGCTGATCCACAAGGAAATCCCATAAAAACAGAAAATCGAATCAA
* ** *
2005785 CCCAAAAAAAGGAGGATCTCCTGTGAAGCAAAGCCAAGAAGAATTAATAAAGATATAACACTGAA
195 CCCAAAAAAAGGAGGATCTCCTATGAAGCAAAGCCAAGAAGAACAAATAAAGATATAACACCGAA
* *
2005850 TCAAAACAGTCAATCGAGTTGAAATCATAAACAAATCCCTTTGTATGCATAATTAAGATGAACCA
260 TCAAAACAATCAATCGAGTTGAAATCAGAAACAAATCCCTTTGTATGCATAATTAAGATGAACCA
* ** *
2005915 AATAAAGAAATTTCATTTTGGTCCAAGGTAAATCGAAAATAAGGGAGACAATCCCTTTGATTTTG
325 AAGAAAGAAATTTCATTTCAGTCCAAGGCAAATCGAAAATAAGGGAGACAATCCCTTTGATTTTG
*
2005980 GGGACAAAAAGAGACAAAGAAACCCTTTCGAGTCCCCTATAAAAACC
390 GGGACAAAAAGAGACAAAGAAACCCCTTCGAGTCCCCTATAAAAACC
* * * *
2006027 CCTACAAGAGACAAACAATGCTTGATGAAATCGATGAAAAATACATATTTACATAAATAATCCCG
1 CCTACAAGAGA-AGACAAGGCTTGAGGAAATCGATGAAAAATACATATTTACAGAAATAATCCCG
* * * *
2006092 AGAACATTTCAGAAAGTCAAACGTCATTAGCAAGACAATGAGTGGTGTACGAAGACCACGCACCA
65 AGAACATTCCAGAAAGCCAAACGTCATTAGCAAGACAACGAGTGGCGTACGAAGACCACGCACCA
* * *
2006157 AGAGAATTTGGAAATAT-CTTCGTTGATCCACAAGGAAATCCCATAAAAACAGAAAATCGAATGA
130 AGAGAATTTGGAAAGATCCTT-GCTGATCCACAAGGAAATCCCATAAAAACAGAAAATCGAATCA
2006221 ACCCCAAAAAAA-GAGGATCTCCTATGAAGCAAA-CCTAAGAAGAACAAATAAAGATATAACACC
194 A-CCCAAAAAAAGGAGGATCTCCTATGAAGCAAAGCC-AAGAAGAACAAATAAAGATATAACACC
* *
2006284 GAATCAAAATAATCAATCGAGTTGAAATCAGATACAAATCCCTTTGTATGCATAATTAAGATGAA
257 GAATCAAAACAATCAATCGAGTTGAAATCAGAAACAAATCCCTTTGTATGCATAATTAAGATGAA
* * *
2006349 CCAAAGAAAGAAATTTCCTTTCAGTCCAAGGCAAATCGGAAATAAGGGAGATAATCCCTTTGATT
322 CCAAAGAAAGAAATTTCATTTCAGTCCAAGGCAAATCGAAAATAAGGGAGACAATCCCTTTGATT
* **
2006414 TTGTGGACAAAAAGAGGGAAAGAAACCCCTTCGAGTCCCCTATAAAAACC
387 TTGGGGACAAAAAGAGACAAAGAAACCCCTTCGAGTCCCCTATAAAAACC
2006464 CCTACAAGAGAAGGACAAGGCTTGAGGAAATCGATGAAAAAATACATATTTACA
1 CCTACAAGAGAA-GACAAGGCTTGAGGAAATCGATG-AAAAATACATATTTACA
2006518 AAAGATAGAG
Statistics
Matches: 441, Mismatches: 45, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
436 6 0.01
437 408 0.93
438 27 0.06
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (436 bp):
CCTACAAGAGAAGACAAGGCTTGAGGAAATCGATGAAAAATACATATTTACAGAAATAATCCCGA
GAACATTCCAGAAAGCCAAACGTCATTAGCAAGACAACGAGTGGCGTACGAAGACCACGCACCAA
GAGAATTTGGAAAGATCCTTGCTGATCCACAAGGAAATCCCATAAAAACAGAAAATCGAATCAAC
CCAAAAAAAGGAGGATCTCCTATGAAGCAAAGCCAAGAAGAACAAATAAAGATATAACACCGAAT
CAAAACAATCAATCGAGTTGAAATCAGAAACAAATCCCTTTGTATGCATAATTAAGATGAACCAA
AGAAAGAAATTTCATTTCAGTCCAAGGCAAATCGAAAATAAGGGAGACAATCCCTTTGATTTTGG
GGACAAAAAGAGACAAAGAAACCCCTTCGAGTCCCCTATAAAAACC
Found at i:2006982 original size:18 final size:18
Alignment explanation
Indices: 2006955--2006991 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2006945 AATCAATTTT
*
2006955 GTCACTTATTGTAAATTG
1 GTCACCTATTGTAAATTG
2006973 GTCACCTATTGTAAATTG
1 GTCACCTATTGTAAATTG
2006991 G
1 G
2006992 CCAGCAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (18 bp):
GTCACCTATTGTAAATTG
Found at i:2007091 original size:18 final size:18
Alignment explanation
Indices: 2007068--2007152 Score: 170
Period size: 18 Copynumber: 4.7 Consensus size: 18
2007058 CTTAATCAGT
2007068 TTTTTTTATTTTTGTAAC
1 TTTTTTTATTTTTGTAAC
2007086 TTTTTTTATTTTTGTAAC
1 TTTTTTTATTTTTGTAAC
2007104 TTTTTTTATTTTTGTAAC
1 TTTTTTTATTTTTGTAAC
2007122 TTTTTTTATTTTTGTAAC
1 TTTTTTTATTTTTGTAAC
2007140 TTTTTTTATTTTT
1 TTTTTTTATTTTT
2007153 ACCCTAACAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTTTTATTTTTGTAAC
Found at i:2007180 original size:54 final size:51
Alignment explanation
Indices: 2007066--2007180 Score: 124
Period size: 54 Copynumber: 2.1 Consensus size: 51
2007056 ACCTTAATCA
* ** *
2007066 GTTTTTTTTATTTTTGTAACTTTTTTTATTTTTGTAACTTTTTTTATTTTT
1 GTTTTTTTTATTTTTGTAACTTTTTTTATTTTTCTAACTTAATTTATCTTT
2007117 GTAACTTTTTTTATTTTTGTAACTTTTTTTATTTTTACCCTAACATTAATTT-TCTTT
1 GT---TTTTTTTATTTTTGTAACTTTTTTTATTTTT---CTAAC-TTAATTTATCTTT
2007174 GTTTTTT
1 GTTTTTT
2007181 AAAGGGCCCG
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
51 2 0.04
54 36 0.68
57 10 0.19
58 5 0.09
ACGTcount: A:0.17, C:0.08, G:0.05, T:0.70
Consensus pattern (51 bp):
GTTTTTTTTATTTTTGTAACTTTTTTTATTTTTCTAACTTAATTTATCTTT
Found at i:2007388 original size:15 final size:16
Alignment explanation
Indices: 2007362--2007391 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2007352 TGACACATCT
2007362 CTGGTAAAACACAAGC
1 CTGGTAAAACACAAGC
2007378 CTGGT-AAACACAAG
1 CTGGTAAAACACAAG
2007392 TAGGTGTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.13
Consensus pattern (16 bp):
CTGGTAAAACACAAGC
Found at i:2014262 original size:37 final size:37
Alignment explanation
Indices: 2014099--2014330 Score: 167
Period size: 38 Copynumber: 6.3 Consensus size: 37
2014089 ATAATGTAGC
* * * *
2014099 TTTTGAAAAAAACA-TTTCGAAAAAATATAATATATAG
1 TTTTG-AAAACACATTTTTGAAAACATATATTATATAG
* * *
2014136 TTTTTAGAAAACA-TTTTTTGAAAGCATATAATATATAG
1 -TTTT-GAAAACACATTTTTGAAAACATATATTATATAG
* ** *
2014174 TTTTTAAAA-ATTGGTTTTTG-AAA-ATATA--ATATGG
1 TTTTGAAAACA--CATTTTTGAAAACATATATTATATAG
* *
2014208 TTTTGAAAATACGTTTTTGAAAACATATATTATATAG
1 TTTTGAAAACACATTTTTGAAAACATATATTATATAG
* *
2014245 TTTTGAAAACACATTTTTAAAAACGTATAATATATATAG
1 TTTTGAAAACACATTTTTGAAAACATAT-AT-TATATAG
* * *
2014284 TTTT-AAAA-ATGATTTTTGAAAACGTATATAATATAG
1 TTTTGAAAACA-CATTTTTGAAAACATATATTATATAG
2014320 TTTTGAAAACA
1 TTTTGAAAACA
2014331 TATATATAGT
Statistics
Matches: 160, Mismatches: 19, Indels: 30
0.77 0.09 0.14
Matches are distributed among these distances:
33 7 0.04
34 16 0.10
35 7 0.04
36 19 0.12
37 42 0.26
38 57 0.36
39 12 0.08
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (37 bp):
TTTTGAAAACACATTTTTGAAAACATATATTATATAG
Found at i:2014327 original size:23 final size:20
Alignment explanation
Indices: 2014297--2014343 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
2014287 TAAAAATGAT
2014297 TTTTGAAAACGTATATAATATAG
1 TTTTGAAAAC--ATAT-ATATAG
2014320 TTTTGAAAACATATATATAG
1 TTTTGAAAACATATATATAG
2014340 TTTT
1 TTTT
2014344 TTAAAACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.42
21 4 0.17
23 10 0.42
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (20 bp):
TTTTGAAAACATATATATAG
Found at i:2014344 original size:21 final size:23
Alignment explanation
Indices: 2014296--2014353 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 23
2014286 TTAAAAATGA
2014296 TTTTTGAAAACGTATATAATATAG
1 TTTTTGAAAACG-ATATAATATAG
2014320 -TTTTGAAAAC-ATAT-ATATAG
1 TTTTTGAAAACGATATAATATAG
*
2014340 TTTTTTAAAACGAT
1 TTTTTGAAAACGAT
2014354 TTTTTGGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 6 0.19
21 13 0.42
22 2 0.06
23 10 0.32
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.43
Consensus pattern (23 bp):
TTTTTGAAAACGATATAATATAG
Found at i:2014383 original size:39 final size:42
Alignment explanation
Indices: 2014332--2014426 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
2014322 TTGAAAACAT
* *
2014332 ATATATAGTTTTT-TAAAACGATT-TTTTGGAAAATAT-ATA
1 ATATATAGTTTTTAAAAAAAGATTATTTTGGAAAATATAATA
* * *
2014371 ATATATAATTTTTAAAAAAATATTATTTTTGAAAATATAATA
1 ATATATAGTTTTTAAAAAAAGATTATTTTGGAAAATATAATA
*
2014413 TTATATAGTTTTTA
1 ATATATAGTTTTTA
2014427 TTATATATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
39 12 0.26
40 7 0.15
41 12 0.26
42 15 0.33
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.48
Consensus pattern (42 bp):
ATATATAGTTTTTAAAAAAAGATTATTTTGGAAAATATAATA
Found at i:2014398 original size:17 final size:20
Alignment explanation
Indices: 2014366--2014416 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2014356 TTTGGAAAAT
2014366 ATATAATATATAATTTTT-AAA
1 ATATAATAT-T-ATTTTTGAAA
2014387 A-A-AATATTATTTTTGAAA
1 ATATAATATTATTTTTGAAA
2014405 ATATAATATTAT
1 ATATAATATTAT
2014417 ATAGTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 6 0.22
18 5 0.19
19 6 0.22
20 9 0.33
21 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATATAATATTATTTTTGAAA
Found at i:2014436 original size:21 final size:19
Alignment explanation
Indices: 2014410--2014472 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 19
2014400 TGAAAATATA
*
2014410 ATATTATATAGTTTTTATTAT
1 ATATTATATA-TTATTATT-T
2014431 ATATTATTTATATTATTATTT
1 ATATTA--TATATTATTATTT
2014452 ATATTAT-TATTTAGTTATTT
1 ATATTATATA-TTA-TTATTT
2014472 A
1 A
2014473 ATTTTATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
18 2 0.05
19 4 0.11
20 7 0.19
21 13 0.35
22 7 0.19
23 4 0.11
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
ATATTATATATTATTATTT
Found at i:2014444 original size:16 final size:15
Alignment explanation
Indices: 2014410--2014463 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 15
2014400 TGAAAATATA
*
2014410 ATATTATATAGTTTT
1 ATATTATATATTTTT
2014425 -TATTATATATTATTT
1 ATATTATATATT-TTT
2014440 ATATTAT-TA--TTT
1 ATATTATATATTTTT
2014452 ATATTAT-TATTT
1 ATATTATATATTT
2014464 AGTTATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
12 12 0.35
14 11 0.32
15 5 0.15
16 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
ATATTATATATTTTT
Found at i:2014447 original size:12 final size:12
Alignment explanation
Indices: 2014427--2014464 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
2014417 ATAGTTTTTA
2014427 TTATA-TATTAT
1 TTATATTATTAT
2014438 TTATATTATTAT
1 TTATATTATTAT
2014450 TTATATTATTAT
1 TTATATTATTAT
2014462 TTA
1 TTA
2014465 GTTATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.19
12 21 0.81
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATATTATTAT
Found at i:2014469 original size:16 final size:16
Alignment explanation
Indices: 2014406--2014469 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 16
2014396 TTTTTGAAAA
*
2014406 TATAATATTATATAGT
1 TATATTATTATATAGT
2014422 T-T-TTATTATATA-T
1 TATATTATTATATAGT
* *
2014435 TATTTATATTAT-TATT
1 TATAT-TATTATATAGT
*
2014451 TATATTATTATTTAGT
1 TATATTATTATATAGT
2014467 TAT
1 TAT
2014470 TTAATTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 2 0.05
14 10 0.25
15 10 0.25
16 18 0.45
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TATATTATTATATAGT
Found at i:2014469 original size:28 final size:30
Alignment explanation
Indices: 2014410--2014469 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
2014400 TGAAAATATA
* *
2014410 ATATTATATAGTTTTTATTATATATTATTT
1 ATATTATATAGTTTATATTATATATTAGTT
2014440 ATATTAT-TA-TTTATATTAT-TATTTAGTT
1 ATATTATATAGTTTATATTATATA-TTAGTT
2014468 AT
1 AT
2014470 TTAATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.07
28 16 0.59
29 2 0.07
30 7 0.26
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (30 bp):
ATATTATATAGTTTATATTATATATTAGTT
Found at i:2015755 original size:5 final size:5
Alignment explanation
Indices: 2015745--2015807 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
2015735 TCCCTCTTAA
* * *
2015745 ATTTT ATTTT ATTTT ATTTT AATTTA ATTTA ATTTAT ATTTTT ATGTT
1 ATTTT ATTTT ATTTT ATTTT -ATTTT ATTTT ATTT-T A-TTTT ATTTT
* *
2015793 GTCTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT
2015808 TTTCTTATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
5 38 0.79
6 7 0.15
7 3 0.06
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (5 bp):
ATTTT
Found at i:2015765 original size:15 final size:15
Alignment explanation
Indices: 2015745--2015807 Score: 54
Period size: 16 Copynumber: 4.0 Consensus size: 15
2015735 TCCCTCTTAA
2015745 ATTTTATTTTATTTT
1 ATTTTATTTTATTTT
* *
2015760 ATTTTAATTTAATTTA
1 ATTTT-ATTTTATTTT
*
2015776 ATTTATATTTTTATGTT
1 ATTT-TA-TTTTATTTT
* *
2015793 GTCTTATTTTATTTT
1 ATTTTATTTTATTTT
2015808 TTTCTTATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
15 13 0.35
16 15 0.41
17 9 0.24
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTTATTTTATTTT
Found at i:2020641 original size:23 final size:23
Alignment explanation
Indices: 2020615--2020662 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2020605 ATAAAGTACA
*
2020615 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
2020638 ATAATGTAATAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGCTTAT
2020661 AT
1 AT
2020663 TGACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2021190 original size:22 final size:23
Alignment explanation
Indices: 2021135--2021196 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
2021125 CAATATAGCA
2021135 CTACCTATTACA-TATATAAACG
1 CTACCTATTACATTATATAAACG
* **
2021157 CTACATATTACATTATATAAGTG
1 CTACCTATTACATTATATAAACG
*
2021180 CTACCTA-TACATCATAT
1 CTACCTATTACATTATAT
2021197 TTTACCTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 20 0.59
23 14 0.41
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (23 bp):
CTACCTATTACATTATATAAACG
Found at i:2021561 original size:25 final size:25
Alignment explanation
Indices: 2021533--2021597 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
2021523 ACTCAAAAGA
*
2021533 TGTATATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
2021558 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
2021583 TGTACATACCTAAAT
1 TGTACATACCTAAAT
2021598 TTAATGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (25 bp):
TGTACATACCTAAATATGTAGTTAT
Found at i:2024686 original size:180 final size:181
Alignment explanation
Indices: 2023993--2024727 Score: 1308
Period size: 180 Copynumber: 4.1 Consensus size: 181
2023983 TTAAAATTAT
*
2023993 CGACACAATATTAAAAAGTGTCGA-ATAGGTTGTAGACCTATTCGCTCAT-AACCCGGTATATTT
1 CGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
2024056 ATACGGTTATATTACAAAA-TATTTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAC
65 ATACGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAC
*
2024120 ACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACTTAAAGTAC
130 ACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTAC
2024172 CGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTA
1 CGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTA
*
2024237 TACCGGTTATATTACAAAATTATCTATTACATTATAATTCTAGGTTCCGATGTGTAAATGGTCG-
66 TA-CGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAAT-GTCGA
*
2024301 CACTTTTTGACAAGGTATCGACACA-TTTTCTTCCAATCTAGACATAAAGTAC
129 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTAC
2024353 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
2024418 A-CCGGTTATATTACAAAATTATCTATTACATTAT-ATTCT-GGTTCCGATGTGTAAATGTCGAC
65 ATACGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAC
2024480 ACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTAC
130 ACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTAC
2024532 CGACACAATATTAAAAGT-TCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTA
1 CGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTA
*
2024596 TACGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCAACA
66 TACGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGACA
2024661 CTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTAC
131 CTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTAC
2024712 CGACACAATATTAAAA
1 CGACACAATATTAAAA
2024728 TACCGACACA
Statistics
Matches: 536, Mismatches: 9, Indels: 21
0.95 0.02 0.04
Matches are distributed among these distances:
177 50 0.09
178 91 0.17
179 85 0.16
180 138 0.26
181 53 0.10
182 115 0.21
183 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (181 bp):
CGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTA
TACGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGACA
CTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTAC
Found at i:2024731 original size:19 final size:19
Alignment explanation
Indices: 2024704--2024746 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
2024694 AATCTGGACA
*
2024704 TAAAGTACCGACACAATAT
1 TAAAATACCGACACAATAT
2024723 TAAAATACCGACACAATAT
1 TAAAATACCGACACAATAT
2024742 TAAAA
1 TAAAA
2024747 AGTGTCGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.53, C:0.19, G:0.07, T:0.21
Consensus pattern (19 bp):
TAAAATACCGACACAATAT
Found at i:2025045 original size:378 final size:382
Alignment explanation
Indices: 2023983--2025105 Score: 1732
Period size: 378 Copynumber: 3.0 Consensus size: 382
2023973 ACCGCGTTAC
* *
2023983 TTAAAATTATCGACACAATATTAAAAAGTGTCGA-ATAGGTTGTAGACCTATTCGCTCAT-AACC
1 TTAAAA-TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAAC
*
2024046 CGGTATATTTATA-CGGTTATATTACAAAA-TATTTATTACATTATAATTCTGGGTTCCGATGTG
65 CGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTG
*
2024109 TAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACTTAAAGTACCG
130 TAAATGTCGACACTTTTTGACAAGGTATCGA-ACATTTTTCTTCCAATCTGGACATAAAGTACCG
2024174 ACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATA
194 ACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATA
* *
2024239 CCGGTTATATTACAAAATTATCTATTACATTATAATTCTAGGTTCCGATGTGTA-AATGGTCG-C
259 CCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTTTATAA---TCGAC
2024302 ACTTTTTGACAAGGTATCGACACA-TTTTCTTCCAA--T---C------TA--G--AC---A
321 ACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
*
2024345 -TAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACC
1 TTAAAATACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACC
2024409 GGTATA-TT-TACCGGTTATATTACAAAATTATCTATTACATTAT-ATTCT-GGTTCCGATGTGT
66 GGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGT
2024470 AAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGA
131 AAATGTCGACACTTTTTGACAAGGTATCGA-ACATTTTTCTTCCAATCTGGACATAAAGTACCGA
2024535 CACAATATTAAAAGT-TCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATA-
195 CACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATAC
* *
2024598 CGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTA-AATGTCAACAC
260 CGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTTTATAA--TCGACAC
2024662 TTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
323 TTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
2024722 TTAAAATACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACC
1 TTAAAATACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACC
2024787 GGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGT
66 GGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGT
* *
2024852 AAA-GTCGACACTTTTTGACAA-GTATTG-ACATTTTTCTTCCAATATGGACATAAAGTACCGAC
131 AAATGTCGACACTTTTTGACAAGGTATCGAACATTTTTCTTCCAATCTGGACATAAAGTACCGAC
*
2024914 ACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCAT-AAACCGATATATTTATAC
196 ACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATAC
*
2024978 CGGTTATATTACAAAATTATCTATTACA-T-TAATT-TGGGTTCCGATGTTTTTTCAATCGACAC
260 CGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG-TTTAT-AATCGACAC
* *
2025040 TTTTTGAAAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATA
323 TTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
2025100 TTAAAA
1 TTAAAA
2025106 AGTGTGAAAA
Statistics
Matches: 709, Mismatches: 17, Indels: 54
0.91 0.02 0.07
Matches are distributed among these distances:
357 3 0.00
358 79 0.11
359 59 0.08
360 120 0.17
361 53 0.07
362 24 0.03
364 1 0.00
370 2 0.00
372 1 0.00
374 2 0.00
377 13 0.02
378 188 0.27
379 25 0.04
380 100 0.14
381 23 0.03
382 16 0.02
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (382 bp):
TTAAAATACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACC
GGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGT
AAATGTCGACACTTTTTGACAAGGTATCGAACATTTTTCTTCCAATCTGGACATAAAGTACCGAC
ACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACC
GGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTTTATAATCGACACTTT
TTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
Found at i:2028296 original size:199 final size:200
Alignment explanation
Indices: 2027736--2028499 Score: 1307
Period size: 199 Copynumber: 3.8 Consensus size: 200
2027726 AACATTAAAC
* * * *
2027736 AGTGTCGATACA-TATTATATACCAATTCTCTCATAAAACCGGTATACTTATACCGGTTAGATTG
1 AGTGTCGACACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
2027800 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
65 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
* *
2027865 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCAACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
*
2027930 TAAAAAA
195 T-ACAAA
2027937 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
2028002 AAAATTACCTATTACTTTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * **
2028067 GATCGACACTTTATTGTTGCACCCTGTTTTCCATTCATTCTATACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
2028132 ACAAA
196 ACAAA
* *
2028137 AGTGTTGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG-
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
2028201 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
2028266 GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
2028331 ACAAA
196 ACAAA
* * *
2028336 AGTGTCGATACATTATTTTGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
2028401 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
2028466 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
2028500 ATTGTAAATT
Statistics
Matches: 536, Mismatches: 25, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
199 188 0.35
200 163 0.30
201 181 0.34
202 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (200 bp):
AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:2028623 original size:18 final size:18
Alignment explanation
Indices: 2028600--2028660 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
2028590 TCTCATTCAT
*
2028600 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
2028618 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
2028637 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
2028656 AATTA
1 AATTA
2028661 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Done.