Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008702.1 Hibiscus syriacus cultivar Beakdansim tig00111741_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: 3201804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:466278 original size:3 final size:3
Alignment explanation
Indices: 466270--466307 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
466260 AACAAGTTGC
466270 ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT A
466308 GTGGACGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:467846 original size:10 final size:10
Alignment explanation
Indices: 467833--467862 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
467823 CAAACGGATG
467833 TAAACGAACA
1 TAAACGAACA
*
467843 TAAACGAACG
1 TAAACGAACA
467853 TAAACGAACA
1 TAAACGAACA
467863 CATATTGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.10
Consensus pattern (10 bp):
TAAACGAACA
Found at i:468098 original size:24 final size:24
Alignment explanation
Indices: 468053--468108 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
468043 GATTGAGCTA
* *
468053 AACATAAATGAGCGCACATAAACG
1 AACATAAATGAACGAACATAAACG
* *
468077 AATATAAATGAACGAACGTAAACG
1 AACATAAATGAACGAACATAAACG
468101 AACATAAA
1 AACATAAA
468109 CAAACATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.14
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:475733 original size:13 final size:13
Alignment explanation
Indices: 475715--475750 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
475705 TGCAAATTTT
*
475715 CAAATCCGCCCTA
1 CAAATCCACCCTA
475728 CAAATCCACCCTA
1 CAAATCCACCCTA
475741 CAAATCCACC
1 CAAATCCACC
475751 TACCAAAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.47, G:0.03, T:0.14
Consensus pattern (13 bp):
CAAATCCACCCTA
Found at i:482650 original size:3 final size:3
Alignment explanation
Indices: 482639--482699 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
482629 TTTTTTTCCG
** *
482639 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
482684 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
482700 CATATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:482705 original size:28 final size:28
Alignment explanation
Indices: 482645--482710 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
482635 TCCGTTATTT
* *
482645 TATTATTATTATTATTATTATCGTTATCT
1 TATTATT-TTATTATTATTATCATTATCA
*
482674 TATTATTTTATTATTATTTATTATTA-CA
1 TATTATTTTATTATTA-TTATCATTATCA
*
482702 TATTTTTTT
1 TATTATTTT
482711 GCAGGCCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTTTATTATTATTATCATTATCA
Found at i:489929 original size:11 final size:11
Alignment explanation
Indices: 489901--489938 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
489891 AAGAGCAAAG
489901 AGAAAAATCAA
1 AGAAAAATCAA
489912 AGCAAAAATCAA
1 AG-AAAAATCAA
*
489924 AGAAAAAGCAA
1 AGAAAAATCAA
489935 AGAA
1 AGAA
489939 CAAAAAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:491164 original size:25 final size:24
Alignment explanation
Indices: 491124--491178 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 24
491114 ATTGAGAAAC
491124 ATACATCAACTCATACATACATAT
1 ATACATCAACTCATACATACATAT
491148 ATACATCAAACTCATACATACATAT
1 ATACATC-AACTCATACATACATAT
491173 ATACAT
1 ATACAT
491179 ACATCAACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 7 0.23
25 23 0.77
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (24 bp):
ATACATCAACTCATACATACATAT
Found at i:491793 original size:105 final size:103
Alignment explanation
Indices: 491601--491844 Score: 284
Period size: 105 Copynumber: 2.4 Consensus size: 103
491591 GACAACTTTC
* * *
491601 TCTTT-AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTGGAGATACAAATTTTGAATTTGA
1 TCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTGGAGATACAAATTTCGAATTTGA
*
491665 TTCACTAAAAACAAAATTAATCTCACCTT-AGATTGTTATT
66 TTCACTAAAAACAAAATTAATCTCA-CTTGAGATCG-T-TT
* * * *
491705 TCTTTCAAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGT
1 TCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTGGAGATACAAATTTCGAATTTGA
* * *
491770 TTCAC-ATTAAACAAAGTTGATCTCACTTGAGATCGTTT
66 TTCACTA-AAAACAAAATTAATCTCACTTGAGATCGTTT
*
491808 TC--TCAAAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 TCTTTC-AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
491845 TCTAAAAACA
Statistics
Matches: 122, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
101 2 0.02
102 26 0.21
103 7 0.06
104 10 0.08
105 77 0.63
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38
Consensus pattern (103 bp):
TCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTGGAGATACAAATTTCGAATTTGA
TTCACTAAAAACAAAATTAATCTCACTTGAGATCGTTT
Found at i:491835 original size:36 final size:34
Alignment explanation
Indices: 491790--491908 Score: 114
Period size: 36 Copynumber: 3.4 Consensus size: 34
491780 ACAAAGTTGA
*
491790 TCTCACTTGAGATCGTTTTCTCAAAAACAAACTTTG
1 TCTCACTTGAGA-C-TTTTCTCAAAAACAAATTTTG
* *
491826 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGAC-TTTTCTC-AAAAACAAATTTTG
* * * *
491862 TCTCATTTGAGACTATATCT-TAAAGCAAATTTTG
1 TCTCACTTGAGACT-TTTCTCAAAAACAAATTTTG
*
491896 TCTCGCTTGAGAC
1 TCTCACTTGAGAC
491909 ATCATTTTCT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 23 0.33
35 7 0.10
36 39 0.57
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (34 bp):
TCTCACTTGAGACTTTTCTCAAAAACAAATTTTG
Found at i:491896 original size:34 final size:36
Alignment explanation
Indices: 491808--491909 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
491798 GAGATCGTTT
* *
491808 TCTC-AAAAACAAACTTTGTCTCGCTTGAGACAATT
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
** *
491843 TCTCTAAAAACAAATTTTGTCTCATTTGAGACTATA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
*
491879 TCT-T-AAAGCAAATTTTGTCTCGCTTGAGACA
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
491910 TCATTTTCTC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 23 0.40
35 5 0.09
36 29 0.51
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATA
Found at i:492065 original size:26 final size:25
Alignment explanation
Indices: 492015--492065 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
492005 CAATTTTGTG
* *
492015 AAAAAATCTTTGAGTTGTTTCTTTT
1 AAAAAATCTTTGAGTTATTTATTTT
492040 AAAAAATCTTTGAGTCTATTTATTTT
1 AAAAAATCTTTGAGT-TATTTATTTT
492066 GAAACAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (25 bp):
AAAAAATCTTTGAGTTATTTATTTT
Found at i:492143 original size:52 final size:53
Alignment explanation
Indices: 492065--492167 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
492055 CTATTTATTT
492065 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAGCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAGTC
* *
492117 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAG
492168 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 36 0.75
53 12 0.25
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAAGCTTTGAGTC
Found at i:492205 original size:26 final size:26
Alignment explanation
Indices: 492155--492209 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
492145 AATTTTGTGA
* *
492155 AAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAATCTTTGAGATTATTTATTTTG
492181 AAAAATCTTTGAG-TCTATTTATTTTG
1 AAAAATCTTTGAGAT-TATTTATTTTG
492207 AAA
1 AAA
492210 CAAAGTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (26 bp):
AAAAATCTTTGAGATTATTTATTTTG
Found at i:492226 original size:140 final size:140
Alignment explanation
Indices: 491988--492382 Score: 623
Period size: 140 Copynumber: 2.8 Consensus size: 140
491978 TTAAAACGAT
*
491988 TTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAG-TTGTTTCTTTTAAAAAATCTTTG
1 TTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTG
*
492052 AGTCTATTTATTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAGCTTTGAGTC
66 AGTCTATTTATTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAGCCTTGAGTC
492117 TGAAACAAAG
131 TGAAACAAAG
492127 TTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTG
1 TTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTG
* *
492192 AGTCTATTTATTTTGAAACAAAGTTTTGTTTCTCTTGAGACAATTTCGTGAAAAATCCTTGAGTC
66 AGTCTATTTATTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAGCCTTGAGTC
492257 TGAAACAAAG
131 TGAAACAAAG
*
492267 TTTTGTCTTTCTTGAGACAATTTTGTGAAAAAAAAAATCTTTGAGA-TGTTTCTTTTGAAAAAAT
1 TTTTGTCTCTCTTGAGACAATTTTGTG----AAAAAATCTTTGAGATTGTTTCTTTTG-AAAAAT
* * * * * * *
492331 CTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTC
61 CTTTGAGTCTATTTATTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTC
492383 TTTTGAAAAA
Statistics
Matches: 237, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
139 41 0.17
140 120 0.51
143 11 0.05
144 65 0.27
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (140 bp):
TTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAGATTGTTTCTTTTGAAAAATCTTTG
AGTCTATTTATTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAGCCTTGAGTC
TGAAACAAAG
Found at i:492334 original size:26 final size:27
Alignment explanation
Indices: 492298--492353 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
492288 TTTGTGAAAA
*
492298 AAAAAATCTTTGAG-ATGTTTCTTTTG
1 AAAAAATCTTTGAGTATGTTTCTTTGG
*
492324 AAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAAAAATCTTTGAGTATGTTTCTTTGG
492351 AAA
1 AAA
492354 CAAAATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (27 bp):
AAAAAATCTTTGAGTATGTTTCTTTGG
Found at i:492388 original size:64 final size:64
Alignment explanation
Indices: 492315--492609 Score: 509
Period size: 64 Copynumber: 4.5 Consensus size: 64
492305 CTTTGAGATG
492315 TTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
492379 TTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
492443 TTTCTTTTGAAACAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
1 TTTCTTTTG----AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
492508 TAA
62 TAA
492511 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTG--A-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
492576 AA
63 AA
* *
492578 TTTCTTTTGAAAAAATCTTTGAATCTGTTTCT
1 TTTCTTTTGAAAAAATCTTTGAGTTTGTTTCT
492610 CTTAAAATGA
Statistics
Matches: 223, Mismatches: 3, Indels: 10
0.94 0.01 0.04
Matches are distributed among these distances:
64 93 0.42
65 1 0.00
66 2 0.01
67 63 0.28
68 64 0.29
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (64 bp):
TTTCTTTTGAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:492497 original size:68 final size:68
Alignment explanation
Indices: 492324--492589 Score: 497
Period size: 68 Copynumber: 4.0 Consensus size: 68
492314 GTTTCTTTTG
492324 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTG-
1 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
492388 ---
66 AAC
492388 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
1 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
492453 AAC
66 AAC
492456 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
1 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
492521 AAC
66 AAC
492524 -AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
1 AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
492588 AA
66 AA
492590 AAATCTTTGA
Statistics
Matches: 198, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
64 64 0.32
67 66 0.33
68 68 0.34
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (68 bp):
AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
AAC
Found at i:493142 original size:15 final size:15
Alignment explanation
Indices: 493121--493156 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
493111 GTTACAATTA
493121 AAAACATTTTCTCTT
1 AAAACATTTTCTCTT
*
493136 GAAACATTTTCTCTT
1 AAAACATTTTCTCTT
493151 AAAACA
1 AAAACA
493157 AGATCATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (15 bp):
AAAACATTTTCTCTT
Found at i:493734 original size:43 final size:42
Alignment explanation
Indices: 493632--494003 Score: 247
Period size: 43 Copynumber: 8.7 Consensus size: 42
493622 CTAAAGATGG
* * * ** *
493632 CCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGATCA
1 CCAGCC-TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
* *
493675 -GAG-CTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGCCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
* * * **
493715 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGCC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-ATAGATAA
* * * * * *
493761 CCAGAACTCTTCATCACGTATGAGCCGTGTC-ATC--AGCTGA
1 CCAG-CCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
*
493801 CCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAG-CCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
* * * * **
493844 CCAGCCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGG
1 CCAGCC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-ATAGATAA
* * * * **
493890 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGAT--
1 CCAG-CCTCCTCATCACGTAGGAGCCGTGTCA-ACCATAGATAA
*
493932 -CAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAG-CCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
*
493974 CCAGCCGTCCTCATCACGTAGGAACCGTGT
1 CCAGCC-TCCTCATCACGTAGGAGCCGTGT
494004 TATCACCTTA
Statistics
Matches: 256, Mismatches: 54, Indels: 38
0.74 0.16 0.11
Matches are distributed among these distances:
40 67 0.26
41 33 0.13
42 5 0.02
43 79 0.31
44 4 0.02
45 8 0.03
46 58 0.23
47 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (42 bp):
CCAGCCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAA
Found at i:493856 original size:129 final size:127
Alignment explanation
Indices: 493673--494092 Score: 651
Period size: 130 Copynumber: 3.2 Consensus size: 127
493663 ATCCCCAGAT
* *
493673 CAGAGCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGA
1 CAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGA
493738 ACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCAGCTGAC
66 ACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATC--CTGAC
493802 CAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGA
1 CAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGA
* * *
493867 ACTGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAGAT
66 ACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCA-T--CCTGAC
493932 CAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGA
1 CAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGA
* * **
493997 ACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTCATCATGTATGAGTAGTGTCATCCTTCGAC
66 ACCGTGTTATCACCTTTAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTGTCATCC-T-GAC
* * * *
494062 CAGATGTCTTCATCACGTAGGAACCATGTCA
1 CAGATCTCCTCATCACGTAGGAGCCGTGTCA
494093 CCCTTAGACG
Statistics
Matches: 269, Mismatches: 16, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
128 2 0.01
129 117 0.43
130 122 0.45
131 27 0.10
132 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (127 bp):
CAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGA
ACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCTGAC
Found at i:493997 original size:130 final size:129
Alignment explanation
Indices: 493642--494092 Score: 688
Period size: 129 Copynumber: 3.5 Consensus size: 129
493632 CCAGCCGTCC
* * * * * *
493642 TCATCATGTAGGAACCGTGTCATCCCCAGATCAGAGCTCTTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
493707 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
** *
493771 TCATCACGTATGAGCCGTGTCATCAGCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
*
493836 ATAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
493900 TCATCACGTATGAGCCGTGTCATTCCCCAGATCAGATCTCCTCATCACGTAGGAGCCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAAC
*
493965 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTC
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTC
494030 T
129 T
* ** * * * * *
494031 TCATCATGTATGAGTAGTGTCATCCTTC-GACCAGATGTCTTCATCACGTAGGAACCATGTCA
1 TCATCACGTATGAGCCGTGTCATCC-CCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
494093 CCCTTAGACG
Statistics
Matches: 294, Mismatches: 25, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
129 141 0.48
130 125 0.43
131 28 0.10
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:494317 original size:3 final size:3
Alignment explanation
Indices: 494306--494366 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
494296 TTTTTTTCCG
** *
494306 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
494351 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
494367 CATATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:494372 original size:28 final size:28
Alignment explanation
Indices: 494312--494377 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
494302 TCCGTTATTT
* *
494312 TATTATTATTATTATTATTATCGTTATCT
1 TATTATT-TTATTATTATTATCATTATCA
*
494341 TATTATTTTATTATTATTTATTATTA-CA
1 TATTATTTTATTATTA-TTATCATTATCA
*
494369 TATTTTTTT
1 TATTATTTT
494378 TGCAGGCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTTTATTATTATTATCATTATCA
Found at i:499097 original size:2 final size:2
Alignment explanation
Indices: 499090--499115 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
499080 TGAAGAAGCC
499090 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
499116 GTACTTCCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:502754 original size:20 final size:19
Alignment explanation
Indices: 502729--502787 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 19
502719 GGCTGCTGGA
502729 AACCGGTTTGACCGGTTTT
1 AACCGGTTTGACCGGTTTT
502748 CAACCGGTTCTGACCGGTTTT
1 -AACCGGTT-TGACCGGTTTT
*
502769 AACCGGTTCGAACCGGTTT
1 AACCGGTTTG-ACCGGTTT
502788 GACCGGTCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 1 0.03
20 24 0.67
21 11 0.31
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.32
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTTT
Found at i:502765 original size:10 final size:10
Alignment explanation
Indices: 502730--502819 Score: 66
Period size: 10 Copynumber: 9.3 Consensus size: 10
502720 GCTGCTGGAA
502730 ACCGGTT-TG
1 ACCGGTTCTG
* *
502739 ACCGGTTTTCA
1 ACCGGTTCT-G
502750 ACCGGTTCTG
1 ACCGGTTCTG
* *
502760 ACCGGTTTTA
1 ACCGGTTCTG
502770 ACCGGTTC-G
1 ACCGGTTCTG
502779 AACCGGTT-TG
1 -ACCGGTTCTG
502789 ACCGG-TCTG
1 ACCGGTTCTG
*
502798 AATCGGTT-TG
1 -ACCGGTTCTG
502808 ACCGG-TCTG
1 ACCGGTTCTG
502817 ACC
1 ACC
502820 CGACCCGACC
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
8 2 0.03
9 23 0.36
10 30 0.47
11 9 0.14
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.30
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:502794 original size:19 final size:20
Alignment explanation
Indices: 502750--502817 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
502740 CCGGTTTTCA
*
502750 ACCGGTTCTG-ACCGGTTTTA
1 ACCGGTTCTGAACCGG-TTTG
502770 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
*
502789 ACCGG-TCTGAATCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
502808 ACCGG-TCTGA
1 ACCGGTTCTGA
502818 CCCGACCCGA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
18 2 0.05
19 29 0.66
20 13 0.30
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.29
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:502826 original size:5 final size:5
Alignment explanation
Indices: 502816--502863 Score: 51
Period size: 5 Copynumber: 8.8 Consensus size: 5
502806 TGACCGGTCT
*
502816 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTC GACCC GACC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACC
502864 ATTGACCGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 28 0.76
7 9 0.24
ACGTcount: A:0.19, C:0.52, G:0.23, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:502838 original size:12 final size:12
Alignment explanation
Indices: 502821--502884 Score: 60
Period size: 12 Copynumber: 5.3 Consensus size: 12
502811 GGTCTGACCC
502821 GACCCGACCGTT
1 GACCCGACCGTT
*
502833 GACCCGACC--C
1 GACCCGACCGTT
*
502843 GACCCGACCGTC
1 GACCCGACCGTT
*
502855 GACCCGACCATT
1 GACCCGACCGTT
*
502867 GACCGTTGACCGTT
1 GACC--CGACCGTT
502881 GACC
1 GACC
502885 GTTGACTTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
10 9 0.21
12 24 0.56
14 10 0.23
ACGTcount: A:0.19, C:0.44, G:0.23, T:0.14
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:502842 original size:22 final size:22
Alignment explanation
Indices: 502816--502863 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
502806 TGACCGGTCT
*
502816 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTCGACCC
502838 GACCCGACCCGACCGTCGACCC
1 GACCCGACCCGACCGTCGACCC
502860 GACC
1 GACC
502864 ATTGACCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.52, G:0.23, T:0.06
Consensus pattern (22 bp):
GACCCGACCCGACCGTCGACCC
Found at i:502857 original size:17 final size:15
Alignment explanation
Indices: 502816--502863 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
502806 TGACCGGTCT
*
502816 GACCCGACCCGACCGTT
1 GACCCGACCCGACC--C
502833 GACCCGACCCGACCC
1 GACCCGACCCGACCC
502848 GACCGTCGACCCGACC
1 GACC--CGACCCGACC
502864 ATTGACCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 4 0.14
17 24 0.86
ACGTcount: A:0.19, C:0.52, G:0.23, T:0.06
Consensus pattern (15 bp):
GACCCGACCCGACCC
Found at i:502870 original size:7 final size:7
Alignment explanation
Indices: 502860--502890 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
502850 CCGTCGACCC
*
502860 GACCATT
1 GACCGTT
502867 GACCGTT
1 GACCGTT
502874 GACCGTT
1 GACCGTT
502881 GACCGTT
1 GACCGTT
502888 GAC
1 GAC
502891 TTTCTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:503825 original size:63 final size:63
Alignment explanation
Indices: 503757--503880 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
503747 CTAATGTGAC
* ** * *
503757 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
503820 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
503881 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:510081 original size:9 final size:9
Alignment explanation
Indices: 510067--510186 Score: 96
Period size: 10 Copynumber: 12.3 Consensus size: 9
510057 GCTGCTGGAA
510067 ACCGGTTTG
1 ACCGGTTTG
*
510076 ACCGGTTTTTA
1 ACCGG--TTTG
510087 ACCGGTTTTG
1 ACCGG-TTTG
*
510097 ACCGGTTTTCA
1 ACCGG-TTT-G
510108 ACCGGTTCTG
1 ACCGGTT-TG
510118 ACCGGTTTG
1 ACCGGTTTG
*
510127 ACCGGTTTTA
1 ACCGG-TTTG
*
510137 ACCGGTTCG
1 ACCGGTTTG
510146 AACCGGTTTG
1 -ACCGGTTTG
*
510156 ACCGGTCTG
1 ACCGGTTTG
*
510165 AATCGGTTTG
1 -ACCGGTTTG
*
510175 ACCGGTCTG
1 ACCGGTTTG
510184 ACC
1 ACC
510187 CGACCCGACC
Statistics
Matches: 91, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
9 32 0.35
10 45 0.49
11 14 0.15
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.33
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:510098 original size:21 final size:21
Alignment explanation
Indices: 510066--510161 Score: 103
Period size: 21 Copynumber: 4.8 Consensus size: 21
510056 GGCTGCTGGA
510066 AACCGG-TTTGACCGGTTTTT
1 AACCGGTTTTGACCGGTTTTT
*
510086 AACCGGTTTTGACCGGTTTTC
1 AACCGGTTTTGACCGGTTTTT
*
510107 AACCGGTTCTGACCGG--TTT
1 AACCGGTTTTGACCGGTTTTT
* * **
510126 GACCGGTTTTAACCGG-TTCG
1 AACCGGTTTTGACCGGTTTTT
510146 AACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
510162 CTGAATCGGT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
19 23 0.37
20 12 0.19
21 28 0.44
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (21 bp):
AACCGGTTTTGACCGGTTTTT
Found at i:510132 original size:19 final size:19
Alignment explanation
Indices: 510067--510186 Score: 95
Period size: 19 Copynumber: 6.2 Consensus size: 19
510057 GCTGCTGGAA
* *
510067 ACCGGTTTGACCGGTTTTTA
1 ACCGGTTTGACCGG-TTCTG
* *
510087 ACCGGTTTTGACCGGTTTTCA
1 ACCGG-TTTGACCGGTTCT-G
510108 ACCGGTTCTGACCGGTT-TG
1 ACCGGTT-TGACCGGTTCTG
*
510127 ACCGGTTTTAACCGGTTC-G
1 ACCGG-TTTGACCGGTTCTG
510146 AACCGGTTTGACCGG-TCTG
1 -ACCGGTTTGACCGGTTCTG
*
510165 AATCGGTTTGACCGG-TCTG
1 -ACCGGTTTGACCGGTTCTG
510184 ACC
1 ACC
510187 CGACCCGACC
Statistics
Matches: 88, Mismatches: 5, Indels: 16
0.81 0.05 0.15
Matches are distributed among these distances:
18 4 0.05
19 41 0.47
20 19 0.22
21 24 0.27
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.33
Consensus pattern (19 bp):
ACCGGTTTGACCGGTTCTG
Found at i:510150 original size:29 final size:31
Alignment explanation
Indices: 510076--510161 Score: 124
Period size: 29 Copynumber: 2.8 Consensus size: 31
510066 AACCGGTTTG
* *
510076 ACCGGTTTTTAACCGGTTTTGACCGGTTTTCA
1 ACCGGTTCTGAACCGG-TTTGACCGGTTTTCA
510108 ACCGGTTCTG-ACCGGTTTGACCGGTTTT-A
1 ACCGGTTCTGAACCGGTTTGACCGGTTTTCA
510137 ACCGGTTC-GAACCGGTTTGACCGGT
1 ACCGGTTCTGAACCGGTTTGACCGGT
510162 CTGAATCGGT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
28 1 0.02
29 24 0.47
30 13 0.25
31 5 0.10
32 8 0.16
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (31 bp):
ACCGGTTCTGAACCGGTTTGACCGGTTTTCA
Found at i:510193 original size:5 final size:5
Alignment explanation
Indices: 510183--510247 Score: 58
Period size: 5 Copynumber: 11.8 Consensus size: 5
510173 TGACCGGTCT
* *
510183 GACCC GACCC GACCGTT GACCC GACCC GACCGTT GACCC GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACC--C GACCC GACCC GACCC
510232 GACCGTC GACCC GACC
1 GACC--C GACCC GACC
510248 GTTGACCGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
5 37 0.74
7 13 0.26
ACGTcount: A:0.18, C:0.51, G:0.23, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:510204 original size:17 final size:17
Alignment explanation
Indices: 510182--510254 Score: 105
Period size: 17 Copynumber: 4.3 Consensus size: 17
510172 TTGACCGGTC
510182 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
510199 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
510216 TGACCCGACCCGACC--
1 TGACCCGACCCGACCGT
*
510231 CGACCGTCGACCCGACCGT
1 TGACC--CGACCCGACCGT
510250 TGACC
1 TGACC
510255 GTTGACCGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
15 4 0.08
17 42 0.84
19 4 0.08
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:510209 original size:22 final size:22
Alignment explanation
Indices: 510200--510247 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
510190 CCCGACCGTT
*
510200 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTCGACCC
510222 GACCCGACCCGACCGTCGACCC
1 GACCCGACCCGACCGTCGACCC
510244 GACC
1 GACC
510248 GTTGACCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.52, G:0.23, T:0.06
Consensus pattern (22 bp):
GACCCGACCCGACCGTCGACCC
Found at i:510254 original size:7 final size:7
Alignment explanation
Indices: 510244--510288 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
510234 CCGTCGACCC
510244 GACCGTT
1 GACCGTT
510251 GACCGTT
1 GACCGTT
510258 GACCGTT
1 GACCGTT
510265 GACCGTT
1 GACCGTT
510272 GACCGTT
1 GACCGTT
510279 GACCGTT
1 GACCGTT
510286 GAC
1 GAC
510289 TTTCTTTGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:512113 original size:15 final size:15
Alignment explanation
Indices: 512093--512121 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
512083 TTAATATTAT
512093 ATAAAATAAACCTAC
1 ATAAAATAAACCTAC
512108 ATAAAATAAACCTA
1 ATAAAATAAACCTA
512122 AAATAATGTA
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:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (15 bp):
ATAAAATAAACCTAC
Found at i:515004 original size:23 final size:22
Alignment explanation
Indices: 514956--515010 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
514946 ATTTTATAAA
*
514956 TTATATATATCTTAAAATTTAAT
1 TTATATCTATCTTAAAATTT-AT
514979 TTATATCTATCTTGAACAATTT-T
1 TTATATCTATCTT-AA-AATTTAT
515002 TTAATATCT
1 TT-ATATCT
515011 GAGTATTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 15 0.54
24 8 0.29
25 5 0.18
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATATCTATCTTAAAATTTAT
Found at i:529070 original size:16 final size:18
Alignment explanation
Indices: 529039--529071 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
529029 GGGAGGCGGT
529039 GGAGCATGAGAAGAGCTA
1 GGAGCATGAGAAGAGCTA
529057 GGAGCA-GA-AAGAGCT
1 GGAGCATGAGAAGAGCT
529072 CGTGAAGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.39, C:0.12, G:0.39, T:0.09
Consensus pattern (18 bp):
GGAGCATGAGAAGAGCTA
Found at i:532066 original size:28 final size:28
Alignment explanation
Indices: 532026--532245 Score: 354
Period size: 28 Copynumber: 7.8 Consensus size: 28
532016 TAACACTTTT
532026 TTTTTTCGAAATAATTACCAAAATATCA
1 TTTTTTCGAAATAATTACCAAAATATCA
532054 TTTTTTCGAAATAATTACCAAAATATCA
1 TTTTTTCGAAATAATTACCAAAATATCA
532082 CTTTTTT-GAAATAATTACCAAAATATCA
1 -TTTTTTCGAAATAATTACCAAAATATCA
*
532110 CTTTTTCGAAATAATTACCAAAATATCA
1 TTTTTTCGAAATAATTACCAAAATATCA
532138 TTTTTTCGAAATAATTACCAAAATATCA
1 TTTTTTCGAAATAATTACCAAAATATCA
532166 TTTTTTCGAAATAATTACCAAAATATCA
1 TTTTTTCGAAATAATTACCAAAATATCA
* *
532194 TTTTTTCAAAATAATTACCAAAATAATACT
1 TTTTTTCGAAATAATTACCAAAAT-AT-CA
* *
532224 TTTTTTCAAAATATTTA-CAAAA
1 TTTTTTCGAAATAATTACCAAAA
532246 CTAACACCTT
Statistics
Matches: 183, Mismatches: 5, Indels: 7
0.94 0.03 0.04
Matches are distributed among these distances:
27 5 0.03
28 148 0.81
29 13 0.07
30 17 0.09
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.40
Consensus pattern (28 bp):
TTTTTTCGAAATAATTACCAAAATATCA
Found at i:532265 original size:29 final size:29
Alignment explanation
Indices: 532233--532303 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
532223 TTTTTTTCAA
532233 AATATTTACAAAACTAACACCTTCTTAAC
1 AATATTTACAAAACTAACACCTTCTTAAC
* ** *
532262 AATATTTACGAAACTAACATTTTTTTAAC
1 AATATTTACAAAACTAACACCTTCTTAAC
532291 AATATTTACAAAA
1 AATATTTACAAAA
532304 TACCACCATA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.35
Consensus pattern (29 bp):
AATATTTACAAAACTAACACCTTCTTAAC
Found at i:533359 original size:44 final size:44
Alignment explanation
Indices: 533270--533366 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 44
533260 GACAGTGTGC
* *
533270 ATCGATGCACATTCAAGAAATGCATCGGTGCATCTTTATGATGT
1 ATCGATGCACATTCAAGAAATGCATCGATGCATATTTATGATGT
* **
533314 ATCGATGTACATTCAAAGGGATGCATCGATGCACTATTTA-G-TGT
1 ATCGATGCACATTC-AAGAAATGCATCGATGCA-TATTTATGATGT
*
533358 ATCAATGCA
1 ATCGATGCA
533367 TTATGCACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
44 23 0.52
45 16 0.36
46 5 0.11
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (44 bp):
ATCGATGCACATTCAAGAAATGCATCGATGCATATTTATGATGT
Found at i:537307 original size:2 final size:2
Alignment explanation
Indices: 537300--537351 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
537290 ACACGCCGAA
537300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
537342 AT AT AT AT AT
1 AT AT AT AT AT
537352 GACTTTTATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:538496 original size:91 final size:91
Alignment explanation
Indices: 538335--538694 Score: 492
Period size: 91 Copynumber: 4.0 Consensus size: 91
538325 ATCGAGTGAT
* *
538335 AGGTTGAACAAGCTCTTCTCATTATGAACTT-TTC-TCCCTTGTTGGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATAAACTTCTTCTTCCC-TGTCGGATGAGTTCTTCTCATTAT
** *
538398 GAACTCTCTGCTGGAAATATTGA-GTCA
65 GAACTCTCCACTGGAAATGTTGATG-CA
* * * * * * *
538425 AGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCCCGTCGGATGAATTCTTATCATTAGG
1 AGGTTGAACAAGCTCTTCTCATTATAAACTTCTTCTTCCCTGTCGGATGAGTTCTTCTCATTATG
*
538490 AACTCTCCACTAGAAATGTTGATGCA
66 AACTCTCCACTGGAAATGTTGATGCA
* * * *
538516 AGGTTGAACAAGCTCTTCTCTTTATAAACTTCTTCTTCCTTGTCGAATGAGCTCTTCTCATTATG
1 AGGTTGAACAAGCTCTTCTCATTATAAACTTCTTCTTCCCTGTCGGATGAGTTCTTCTCATTATG
538581 AACTCTCCACTGGAAATGTTGATGCA
66 AACTCTCCACTGGAAATGTTGATGCA
* *
538607 AGGTTGAACAAGCTCTTCTCATTATAAACTTATTCTTCCTTGTCGGATGAGTTCTTCTCATTATG
1 AGGTTGAACAAGCTCTTCTCATTATAAACTTCTTCTTCCCTGTCGGATGAGTTCTTCTCATTATG
* *
538672 AACTCTTCATTGGAAATGTTGAT
66 AACTCTCCACTGGAAATGTTGAT
538695 TGGTTTATCT
Statistics
Matches: 238, Mismatches: 29, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
90 29 0.12
91 204 0.86
92 5 0.02
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (91 bp):
AGGTTGAACAAGCTCTTCTCATTATAAACTTCTTCTTCCCTGTCGGATGAGTTCTTCTCATTATG
AACTCTCCACTGGAAATGTTGATGCA
Found at i:539061 original size:30 final size:30
Alignment explanation
Indices: 539027--539135 Score: 182
Period size: 30 Copynumber: 3.6 Consensus size: 30
539017 AGACAAAATT
* **
539027 TGTTTCAAGGGAAACAATCTCAAAGGTTGG
1 TGTTTCAAGAGAAACTGTCTCAAAGGTTGG
539057 TGTTTCAAGAGAAACTGTCTCAAAGGTTGG
1 TGTTTCAAGAGAAACTGTCTCAAAGGTTGG
539087 TGTTTCAAGAGAAACTGTCTCAAAGGTTGG
1 TGTTTCAAGAGAAACTGTCTCAAAGGTTGG
*
539117 CGTTTCAAGAGAAACTGTC
1 TGTTTCAAGAGAAACTGTC
539136 ATAAGAGAGA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (30 bp):
TGTTTCAAGAGAAACTGTCTCAAAGGTTGG
Found at i:539208 original size:66 final size:65
Alignment explanation
Indices: 538990--539374 Score: 351
Period size: 66 Copynumber: 5.9 Consensus size: 65
538980 AAAAAATTCT
* *
538990 TGTTTCAAGGGAAAACTGTTTCAAGCA-AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGT
1 TGTTTCAAGAG-AAACTGTCTCAAG-AGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAA-GT
539054 TGG
63 TGG
* **
539057 TGTTTCAAGAGAAACTGTCTCAA-AG-G------TTGGTGTTTCAAGAGAAACTGTCTCAAAGGT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT--TGTTTCAAGGGAAACAATCTCAAA-GT
539114 TGG
63 TGG
* ** *
539117 CGTTTCAAGAGAAACTGTCAT-AAGAGAGACAAAACATGTTTCAAGGGAAACAATCTCAAATGTG
1 TGTTTCAAGAGAAACTGTC-TCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAA-GTT
539181 GG
64 GG
* * ** * ** *
539183 TGTTTCAAGGGAAATTGTCTCAAGAGAGACGGAATTCGTTTCAAGGGAAATGATCTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAG-TTG
*
539248 T
65 G
* * * * *
539249 TGTTTCAAGAGAAATTGTCTTAAGGGAGACAAAATTTGTTGCAAGAGAAACATAT-TCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACA-ATCTCAAAG--T
*
539313 TTG
63 TGG
* *
539316 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGGGAAACTATCTCAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAA
539375 GAGAGACAAA
Statistics
Matches: 257, Mismatches: 44, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
58 2 0.01
60 47 0.18
61 3 0.01
62 1 0.00
64 2 0.01
65 2 0.01
66 135 0.53
67 65 0.25
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTTGG
Found at i:539299 original size:132 final size:131
Alignment explanation
Indices: 539017--539374 Score: 401
Period size: 132 Copynumber: 2.7 Consensus size: 131
539007 GTTTCAAGCA
539017 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAA-A
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAA-GTTGGTGTTTCAAGAGAAACTGTCTCAAGA
** * *
539081 G-GTTGG---TGTTTCAAGAGAAACTG-TCTCAAAGGTTGGCGTTTCAAGAGAAACTGTCATAAG
65 GAGACGGAATTGTTTCAAGGGAAACTGATCTCAAAGATTGGCGTTTCAAGAGAAACTGTCATAAG
539141 AG
130 AG
** * * *
539143 AGACAAAACATGTTTCAAGGGAAACAATCTCAAATGTGGGTGTTTCAAGGGAAATTGTCTCAAGA
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAA-GTTGGTGTTTCAAGAGAAACTGTCTCAAGA
*** * *
539208 GAGACGGAATTCGTTTCAAGGGAAA-TGATCTCAAAGATTTTTGTTTCAAGAGAAATTGTCTTAA
65 GAGACGGAATT-GTTTCAAGGGAAACTGATCTCAAAGATTGGCGTTTCAAGAGAAACTGTCATAA
*
539272 GGG
129 GAG
* * *
539275 AGACAAAATTTGTTGCAAGAGAAACATAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAA
1 AGACAAAATTTGTTTCAAGGGAAACA-ATCTCAAAG--TTGGTGTTTCAAGAGAAACTGTCTCAA
* **
539339 GCGAGACAAAATTTGTTTCAAGGGAAACT-ATCTCAA
63 GAGAGACGGAA-TTGTTTCAAGGGAAACTGATCTCAA
539375 GAGAGACAAA
Statistics
Matches: 193, Mismatches: 27, Indels: 17
0.81 0.11 0.07
Matches are distributed among these distances:
126 57 0.30
127 2 0.01
128 3 0.02
131 4 0.02
132 71 0.37
133 53 0.27
134 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.28
Consensus pattern (131 bp):
AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGTTGGTGTTTCAAGAGAAACTGTCTCAAGAG
AGACGGAATTGTTTCAAGGGAAACTGATCTCAAAGATTGGCGTTTCAAGAGAAACTGTCATAAGA
G
Found at i:539366 original size:36 final size:35
Alignment explanation
Indices: 539316--539422 Score: 171
Period size: 36 Copynumber: 3.0 Consensus size: 35
539306 AAAGATTTTG
*
539316 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATT
*
539352 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATT
539388 TGTTTCAAGGGAAACTGTCTCAA-GAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATT
539422 T
1 T
539423 TATTTCAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
34 12 0.18
36 55 0.82
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATT
Found at i:539694 original size:42 final size:41
Alignment explanation
Indices: 539611--539724 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 41
539601 ACACAGGGGT
* * * *
539611 CTTATGGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATTGATGGCCCGAAGGACGTATCATCATGCTCGAAAGA
*
539652 CTTATAT-ATGGCCCGATGGACGTATGCATCATGCTCGAAAGA
1 CTTAT-TGATGGCCCGAAGGACGTAT-CATCATGCTCGAAAGA
*
539694 CTTATTGATGGCCCGAAGGACTTACTCATCA
1 CTTATTGATGGCCCGAAGGACGTA-TCATCA
539725 AGAAACCCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
41 21 0.34
42 40 0.65
43 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (41 bp):
CTTATTGATGGCCCGAAGGACGTATCATCATGCTCGAAAGA
Found at i:539813 original size:43 final size:43
Alignment explanation
Indices: 539760--539887 Score: 193
Period size: 43 Copynumber: 3.0 Consensus size: 43
539750 TTCTTAGTTG
* * *
539760 TCATAAAGGAACCCCTATATATCACGTTGGTCCCTCAAGTTTC
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
* *
539803 TCATCAAGGAACCCTTACACATCACGTTGGTCCCTCAAGCTTC
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
* *
539846 TCATCAAGGAACTCCTACATATCACGTTGGTCCTTCAAGCTT
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTT
539888 AGTTTCTTAT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (43 bp):
TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTC
Found at i:541882 original size:22 final size:21
Alignment explanation
Indices: 541842--541898 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
541832 TGGATTTGTT
541842 TCTTTATTCTTTCATTCTTTT
1 TCTTTATTCTTTCATTCTTTT
*
541863 TCTTTCTCTCTTTC-TCTCTTTT
1 TCTTTAT-TCTTTCAT-TCTTTT
541885 TCTTTTATTTCTTT
1 TC-TTTA-TTCTTT
541899 TTTCTCTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 7 0.23
22 14 0.47
23 8 0.27
24 1 0.03
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (21 bp):
TCTTTATTCTTTCATTCTTTT
Found at i:541895 original size:27 final size:25
Alignment explanation
Indices: 541873--541990 Score: 130
Period size: 27 Copynumber: 4.5 Consensus size: 25
541863 TCTTTCTCTC
*
541873 TTTCTCTCTTTTTCTTTTATTTCTTT
1 TTTCTCTTTTTTTCTTTTATTTC-TT
541899 TTTCTCTATTTTTTCTTTTATTTCTT
1 TTTCTCT-TTTTTTCTTTTATTTCTT
*
541925 TTATTTCTTTTATTTCTTTTATTTCTT
1 TT-TCTCTTTT-TTTCTTTTATTTCTT
*
541952 TTATTTCTTTTATTTCTTTT-TTTCTT
1 TT-TCTCTTTT-TTTCTTTTATTTCTT
*
541978 TTATTTCTTTTTT
1 TT-TCTCTTTTTT
541991 ATATATCATT
Statistics
Matches: 87, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
25 2 0.02
26 31 0.36
27 54 0.62
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTCTCTTTTTTTCTTTTATTTCTT
Found at i:541897 original size:9 final size:9
Alignment explanation
Indices: 541883--541988 Score: 173
Period size: 9 Copynumber: 11.9 Consensus size: 9
541873 TTTCTCTCTT
541883 TTTCTTTTA
1 TTTCTTTTA
541892 TTTCTTTT-
1 TTTCTTTTA
541900 TTCTCTATTT-
1 TT-TCT-TTTA
541910 TTTCTTTTA
1 TTTCTTTTA
541919 TTTCTTTTA
1 TTTCTTTTA
541928 TTTCTTTTA
1 TTTCTTTTA
541937 TTTCTTTTA
1 TTTCTTTTA
541946 TTTCTTTTA
1 TTTCTTTTA
541955 TTTCTTTTA
1 TTTCTTTTA
541964 TTTCTTTT-
1 TTTCTTTTA
541972 TTTCTTTTA
1 TTTCTTTTA
541981 TTTCTTTT
1 TTTCTTTT
541989 TTATATATCA
Statistics
Matches: 93, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
8 13 0.14
9 75 0.81
10 5 0.05
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTTA
Found at i:544154 original size:2 final size:2
Alignment explanation
Indices: 544147--544171 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
544137 TGATTAGTCA
544147 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
544172 ATTTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:548296 original size:16 final size:17
Alignment explanation
Indices: 548253--548286 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
548243 CGGATTTGGA
548253 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
548270 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
548287 TTTTAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (17 bp):
ATTAGAGTTTTCAAAGT
Found at i:549352 original size:32 final size:30
Alignment explanation
Indices: 549308--549377 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 30
549298 ATTTGCATTG
**
549308 AAAAAATAGCTACAATGATAAGCAAATGACA
1 AAAAAATAGCTACAACAATAAGCAAATGA-A
* *
549339 AAAAAAGTTGCTACAACAATAAGCCAATGAA
1 AAAAAA-TAGCTACAACAATAAGCAAATGAA
549370 AAAAAATA
1 AAAAAATA
549378 TGATTATTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 1 0.03
31 13 0.39
32 19 0.58
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.16
Consensus pattern (30 bp):
AAAAAATAGCTACAACAATAAGCAAATGAA
Found at i:549393 original size:2 final size:2
Alignment explanation
Indices: 549388--549424 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
549378 TGATTATTAG
549388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
549425 AATTATACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:553267 original size:21 final size:21
Alignment explanation
Indices: 553235--553290 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
553225 AGGCCTGCCC
*
553235 ATATTATTTTATTTTTAATATA
1 ATATT-TTTTATTTTTAATAAA
553257 ATATTTTTTA-TTTTAATAAA
1 ATATTTTTTATTTTTAATAAA
553277 AGTA-TTTTTATTTT
1 A-TATTTTTTATTTT
553291 GTTATACGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 16 0.52
21 10 0.32
22 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATATTTTTTATTTTTAATAAA
Found at i:553392 original size:59 final size:59
Alignment explanation
Indices: 553311--553427 Score: 189
Period size: 59 Copynumber: 2.0 Consensus size: 59
553301 ATCATGTAGT
* *
553311 CGCTGATACTCAAATCTGGAATCTTTACGGATAACAACCATCCCTTTAATCATTGAGGC
1 CGCTAATACTCAAATCCGGAATCTTTACGGATAACAACCATCCCTTTAATCATTGAGGC
* **
553370 CGCTAATACTCAAATCCGGAATCTTTATGGATAACAATGATCCCTTTAATCATTGAGG
1 CGCTAATACTCAAATCCGGAATCTTTACGGATAACAACCATCCCTTTAATCATTGAGG
553428 TCATTTATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (59 bp):
CGCTAATACTCAAATCCGGAATCTTTACGGATAACAACCATCCCTTTAATCATTGAGGC
Found at i:555021 original size:3 final size:3
Alignment explanation
Indices: 555013--555042 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
555003 CCTGGTTAAT
555013 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
555043 ACTGGCTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:555862 original size:2 final size:2
Alignment explanation
Indices: 555855--555884 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
555845 ACATGTTGAT
555855 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
555885 AAATGTATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:559355 original size:29 final size:29
Alignment explanation
Indices: 559313--559390 Score: 129
Period size: 29 Copynumber: 2.7 Consensus size: 29
559303 TAAATTGATG
*
559313 TCATTGCTTACATCATTTAAGTAAAGATT
1 TCATTGCTTACATCATTTAAGTAAAGATA
*
559342 TCATTGCTTACATCATTTAAGTAATGATA
1 TCATTGCTTACATCATTTAAGTAAAGATA
559371 TCATTGCTTACATCAATTTA
1 TCATTGCTTACATC-ATTTA
559391 GTTAGGTGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 41 0.89
30 5 0.11
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (29 bp):
TCATTGCTTACATCATTTAAGTAAAGATA
Found at i:564119 original size:29 final size:29
Alignment explanation
Indices: 564077--564158 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
564067 AAACTAAATT
564077 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
564106 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
564135 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
564159 GTTAGGTGAG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 46 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:566526 original size:121 final size:122
Alignment explanation
Indices: 566311--566536 Score: 400
Period size: 121 Copynumber: 1.9 Consensus size: 122
566301 TTTATTATGT
* *
566311 TACATTTGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCGGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
566376 TGCTAAATCCAACTCACGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
66 TGCTAAATCCAACTCACGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
*
566433 TACATATGGAGATTATGGTACCAAACTACTAATGG-CATACAATGAACGTAGCCCTCCAGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
* *
566497 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGA
66 TGCTAAATCCAACTCACGACTTTCACATAGTTCAATCTGA
566537 TTGTGGCTGG
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
121 66 0.67
122 33 0.33
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (122 bp):
TACATATGGAGATTATGGTACCAAACTACCAATGGCCATACAATGAACGTAGCCCTCCAGCATTC
TGCTAAATCCAACTCACGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
Found at i:568630 original size:12 final size:12
Alignment explanation
Indices: 568613--568639 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
568603 TTATTGAAAA
568613 ATATATACTAAT
1 ATATATACTAAT
568625 ATATATACTAAT
1 ATATATACTAAT
568637 ATA
1 ATA
568640 ATTTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATACTAAT
Found at i:570883 original size:18 final size:20
Alignment explanation
Indices: 570850--570887 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
570840 AATATAATAA
570850 ATGATTATAGATATATTATT
1 ATGATTATAGATATATTATT
570870 ATGATTA-A-ATATATTATT
1 ATGATTATAGATATATTATT
570888 TTAATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 1 0.06
20 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (20 bp):
ATGATTATAGATATATTATT
Found at i:570894 original size:18 final size:18
Alignment explanation
Indices: 570860--570894 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
570850 ATGATTATAG
*
570860 ATATATTATTATGATTAA
1 ATATATTATTATAATTAA
*
570878 ATATATTATTTTAATTA
1 ATATATTATTATAATTA
570895 TTTTAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATATATTATTATAATTAA
Found at i:576910 original size:14 final size:14
Alignment explanation
Indices: 576876--576918 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
576866 CCGAAATACA
576876 GAAATCAGATATCAG
1 GAAATCA-ATATCAG
576891 GAAATCAATATTCAG
1 GAAATCAATA-TCAG
576906 G-AATCAAGTATCA
1 GAAATCAA-TATCA
576919 TGTATCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (14 bp):
GAAATCAATATCAG
Found at i:577692 original size:29 final size:29
Alignment explanation
Indices: 577656--577775 Score: 163
Period size: 29 Copynumber: 4.1 Consensus size: 29
577646 TATTTTACAG
*
577656 AAATAGCACCATTTTCAAAATAATTACTA
1 AAATAGCACCATTTTCAAATTAATTACTA
* *
577685 AAATAGCACCAATTTCGAATTAATTACTA
1 AAATAGCACCATTTTCAAATTAATTACTA
*
577714 AAATAGCACCCATTTT-GAATTAATTACTA
1 AAATAGCA-CCATTTTCAAATTAATTACTA
*
577743 GAATAGCACC-TATTTCAAATTAATTACTA
1 AAATAGCACCAT-TTTCAAATTAATTACTA
577772 AAAT
1 AAAT
577776 GTCATCCGGT
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
27 1 0.01
28 5 0.06
29 69 0.85
30 6 0.07
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.33
Consensus pattern (29 bp):
AAATAGCACCATTTTCAAATTAATTACTA
Found at i:577821 original size:18 final size:17
Alignment explanation
Indices: 577798--577858 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
577788 ACGATCAACG
577798 GGTCGGGTCGGGTTAAC
1 GGTCGGGTCGGGTTAAC
*
577815 AGGTCGGGTC-GGATAAC
1 -GGTCGGGTCGGGTTAAC
* *
577832 GGTTCGAGTCGGGTCAAC
1 GG-TCGGGTCGGGTTAAC
577850 GGGTCGGGT
1 -GGTCGGGT
577859 AAAAACCGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 2 0.06
17 12 0.34
18 19 0.54
19 2 0.06
ACGTcount: A:0.15, C:0.18, G:0.46, T:0.21
Consensus pattern (17 bp):
GGTCGGGTCGGGTTAAC
Found at i:577889 original size:21 final size:21
Alignment explanation
Indices: 577859--577914 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
577849 CGGGTCGGGT
*
577859 AAAAACCGGTCAAACATTGAA
1 AAAAATCGGTCAAACATTGAA
577880 AAAAATCGGTCAAACATTGAA
1 AAAAATCGGTCAAACATTGAA
*
577901 AAAAATTGGTCAAA
1 AAAAATCGGTCAAA
577915 TCGGTCAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.18
Consensus pattern (21 bp):
AAAAATCGGTCAAACATTGAA
Found at i:577940 original size:28 final size:29
Alignment explanation
Indices: 577882--577949 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
577872 ACATTGAAAA
**
577882 AAATCGGTCAAACATTGAAAAAAATTGGTC
1 AAATCGGTCAAACATT-AAAAAAACCGGTC
577912 AAATCGGTCAAACATT-AAAAAACCGGTC
1 AAATCGGTCAAACATTAAAAAAACCGGTC
*
577940 AAACCGGTCA
1 AAATCGGTCA
577950 TTTTGAGCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 19 0.54
30 16 0.46
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.19
Consensus pattern (29 bp):
AAATCGGTCAAACATTAAAAAAACCGGTC
Found at i:581527 original size:94 final size:94
Alignment explanation
Indices: 581366--581545 Score: 351
Period size: 94 Copynumber: 1.9 Consensus size: 94
581356 CTGGGGCTCC
581366 CCACGGTGATACACTGGGTCGGATAAATCCCCGGTCCAATAAATCCTAAAGTTGGATTTTCAGTT
1 CCACGGTGATACACTGGGTCGGATAAATCCCCGGTCCAATAAATCCTAAAGTTGGATTTTCAGTT
581431 CCTTAAGTTCCTTTGGGGCCAACTCCTCA
66 CCTTAAGTTCCTTTGGGGCCAACTCCTCA
*
581460 CCACGGTGATACACTGGGTCGGATAAATCCCCTGTCCAATAAATCCTAAAGTTGGATTTTCAGTT
1 CCACGGTGATACACTGGGTCGGATAAATCCCCGGTCCAATAAATCCTAAAGTTGGATTTTCAGTT
581525 CCTTAAGTTCCTTTGGGGCCA
66 CCTTAAGTTCCTTTGGGGCCA
581546 TACGATAAGG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 85 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (94 bp):
CCACGGTGATACACTGGGTCGGATAAATCCCCGGTCCAATAAATCCTAAAGTTGGATTTTCAGTT
CCTTAAGTTCCTTTGGGGCCAACTCCTCA
Found at i:587664 original size:30 final size:30
Alignment explanation
Indices: 587630--587701 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
587620 CCCGAAGGAC
*
587630 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
587660 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
587690 CTGTCCATAGGT
1 CTATCCAGAGGT
587702 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:587729 original size:31 final size:31
Alignment explanation
Indices: 587691--587812 Score: 129
Period size: 31 Copynumber: 3.9 Consensus size: 31
587681 CCTCGGCAAC
* *
587691 TGTCCATAGGTTCCGAAGAACCTAGGTAAAT
1 TGTCCATATGTTCCGAAGAACATAGGTAAAT
** * *
587722 TGTCCATATGTTCCTTAGAACATAGGTATAC
1 TGTCCATATGTTCCGAAGAACATAGGTAAAT
** *
587753 TGTCCATATGTCTCAAAAG-ACATAGGTAATT
1 TGTCCATATGT-TCCGAAGAACATAGGTAAAT
*
587784 ATGTCCATATGTTCCGTAGAACATAGGTA
1 -TGTCCATATGTTCCGAAGAACATAGGTA
587813 TACCCTCGAC
Statistics
Matches: 73, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
31 49 0.67
32 24 0.33
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (31 bp):
TGTCCATATGTTCCGAAGAACATAGGTAAAT
Found at i:590750 original size:14 final size:14
Alignment explanation
Indices: 590717--590758 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
590707 CGAAATATAA
590717 AAATCAGATATCAGG
1 AAATCA-ATATCAGG
590732 AAATCAATATTCAGG
1 AAATCAATA-TCAGG
590747 -AATCAAGTATCA
1 AAATCAA-TATCA
590759 TGTATCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (14 bp):
AAATCAATATCAGG
Found at i:591577 original size:28 final size:29
Alignment explanation
Indices: 591517--591610 Score: 147
Period size: 28 Copynumber: 3.3 Consensus size: 29
591507 CTTTTTAAAA
591517 TAATTACTAAAATAGCACCAATTTTGAAT
1 TAATTACTAAAATAGCACCAATTTTGAAT
*
591546 TAATTACTAAAATAGCATC-ATTTTGAAT
1 TAATTACTAAAATAGCACCAATTTTGAAT
* *
591574 TAATTACT-AAATAGCACCTATTTAGAAT
1 TAATTACTAAAATAGCACCAATTTTGAAT
591602 TAATTACTA
1 TAATTACTA
591611 TAATGTCACC
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
27 9 0.15
28 33 0.55
29 18 0.30
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (29 bp):
TAATTACTAAAATAGCACCAATTTTGAAT
Found at i:591652 original size:18 final size:18
Alignment explanation
Indices: 591629--591680 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
591619 CCCGGTCAAC
591629 GGTCAACGGGTCAGGTCG
1 GGTCAACGGGTCAGGTCG
* *
591647 GGTCAACAGGTCTGGTCG
1 GGTCAACGGGTCAGGTCG
* *
591665 GAT-AATGGGTCAGGTC
1 GGTCAACGGGTCAGGTC
591681 AACGGGTCGG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.21
Consensus pattern (18 bp):
GGTCAACGGGTCAGGTCG
Found at i:592650 original size:65 final size:63
Alignment explanation
Indices: 592528--592671 Score: 164
Period size: 65 Copynumber: 2.2 Consensus size: 63
592518 CGATGCATAG
* ** * *
592528 AATGCATTCGATGTTTTGAAAAAGTCTGAGTGCATCGATGCATGATCTATGCGTCGATACATCA
1 AATGCATTCGATGTTTTCAAAAACCCTGAATGCATCGATGCATGATCTAT-CATCGATACATCA
* * **
592592 AATGCATTTGATGTTTTCATAAAACCCTGAATGCATCGATGCATGGTATGTAT-ATCGATGTATC
1 AATGCATTCGATGTTTTCA-AAAACCCTGAATGCATCGATGCAT-G-ATCTATCATCGATACATC
592656 A
63 A
592657 AATGCATTCGATGTT
1 AATGCATTCGATGTT
592672 CAATTAATTC
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
64 17 0.25
65 44 0.66
66 1 0.01
67 5 0.07
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (63 bp):
AATGCATTCGATGTTTTCAAAAACCCTGAATGCATCGATGCATGATCTATCATCGATACATCA
Found at i:592712 original size:20 final size:21
Alignment explanation
Indices: 592687--592727 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
592677 AATTCATTAG
592687 TGCATCGATGCATGG-TTTGA
1 TGCATCGATGCATGGCTTTGA
*
592707 TGCATCGGTGCATGGCTTTGA
1 TGCATCGATGCATGGCTTTGA
592728 ATAATTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.17, C:0.17, G:0.32, T:0.34
Consensus pattern (21 bp):
TGCATCGATGCATGGCTTTGA
Found at i:593288 original size:13 final size:13
Alignment explanation
Indices: 593270--593294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
593260 AGCCATTAGT
593270 TTCATAAACAATA
1 TTCATAAACAATA
593283 TTCATAAACAAT
1 TTCATAAACAAT
593295 GTAATGGATA
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
TTCATAAACAATA
Found at i:599395 original size:22 final size:21
Alignment explanation
Indices: 599353--599392 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
599343 GAGTTTATTT
*
599353 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
599374 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
599393 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:601472 original size:20 final size:21
Alignment explanation
Indices: 601447--601487 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
601437 AATTCATTAG
601447 TGCATC-GATGCATGG-TTTGA
1 TGCATCAGA-GCATGGCTTTGA
601467 TGCATCAGAGCATGGCTTTGA
1 TGCATCAGAGCATGGCTTTGA
601488 ATAATTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (21 bp):
TGCATCAGAGCATGGCTTTGA
Found at i:609439 original size:17 final size:17
Alignment explanation
Indices: 609417--609450 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
609407 AGGATTTGGA
609417 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
609434 ATTAGAGTTTTCAAAGT
1 ATTAGAGTTTTCAAAGT
609451 TTTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (17 bp):
ATTAGAGTTTTCAAAGT
Found at i:614397 original size:21 final size:21
Alignment explanation
Indices: 614365--614420 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
614355 AGGCCTGCCC
*
614365 ATATTATTTTATTTTTAATATA
1 ATATT-TTTTATTTTTAATAAA
614387 ATATTTTTTA-TTTTAATAAA
1 ATATTTTTTATTTTTAATAAA
614407 AGTA-TTTTTATTTT
1 A-TATTTTTTATTTT
614421 GTTATACGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 16 0.52
21 10 0.32
22 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATATTTTTTATTTTTAATAAA
Found at i:614533 original size:59 final size:59
Alignment explanation
Indices: 614441--614557 Score: 198
Period size: 59 Copynumber: 2.0 Consensus size: 59
614431 ATCATGTAGT
*
614441 CGCTGATACTCAAATCTGGAATCTTTACGGATAACAACCATCCCTTTAATCATTGAGGC
1 CGCTGATACTCAAATCCGGAATCTTTACGGATAACAACCATCCCTTTAATCATTGAGGC
* **
614500 CGCTGATACTCAAATCCGGAATCTTTATGGATAACAATGATCCCTTTAATCATTGAGG
1 CGCTGATACTCAAATCCGGAATCTTTACGGATAACAACCATCCCTTTAATCATTGAGG
614558 TCATTTATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (59 bp):
CGCTGATACTCAAATCCGGAATCTTTACGGATAACAACCATCCCTTTAATCATTGAGGC
Found at i:616142 original size:3 final size:3
Alignment explanation
Indices: 616134--616172 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
616124 CCTGGTTAAT
616134 TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
616173 CTGGCTGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:622656 original size:121 final size:122
Alignment explanation
Indices: 622441--622666 Score: 391
Period size: 121 Copynumber: 1.9 Consensus size: 122
622431 TTTATTATGG
* *
622441 TACATTTGGAGATTATGGTACCAAACTACCAATGACCATACAATGAACGTAGCCCTCCGGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGACCATACAATGAACGTAGCCCTCCAGCATTC
622506 TGCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
66 TGCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
* * *
622563 TACATATGGAGATTATGGTACCAAACTACTAATG-GCATACAATGAACGTATCCCTCCAGCATTC
1 TACATATGGAGATTATGGTACCAAACTACCAATGACCATACAATGAACGTAGCCCTCCAGCATTC
*
622627 TGCTAAATCCAACTCGCTACTTTCACATAGTTCAATCTGA
66 TGCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGA
622667 TTGTGGCTGG
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
121 66 0.67
122 32 0.33
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (122 bp):
TACATATGGAGATTATGGTACCAAACTACCAATGACCATACAATGAACGTAGCCCTCCAGCATTC
TGCTAAATCCAACTCGCGACTTTCACATAGTTCAATCTGAGACTTCCAAGTTGGCCA
Found at i:631348 original size:12 final size:12
Alignment explanation
Indices: 631331--631366 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
631321 CATCTCATCA
631331 ACTTTTTTATTT
1 ACTTTTTTATTT
631343 ACTTTTTTATTT
1 ACTTTTTTATTT
631355 ACTTTTTTATTT
1 ACTTTTTTATTT
631367 GTATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (12 bp):
ACTTTTTTATTT
Found at i:633437 original size:28 final size:29
Alignment explanation
Indices: 633382--633437 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
633372 TATAAAAGTG
* *
633382 AAAGACTTAAAATTGAAATAAATTAAAAA
1 AAAGACTTAAAATCGAAATAAATCAAAAA
633411 AAAGA-TT-AAATCGAAATAAATACAAAA
1 AAAGACTTAAAATCGAAATAAAT-CAAAA
633438 TGTGAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.54
28 6 0.25
29 5 0.21
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.21
Consensus pattern (29 bp):
AAAGACTTAAAATCGAAATAAATCAAAAA
Found at i:633523 original size:17 final size:16
Alignment explanation
Indices: 633492--633526 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
633482 AAATTGAAAA
633492 AATATAATATATATAT
1 AATATAATATATATAT
*
633508 AATATAAGTTTATATAT
1 AATATAA-TATATATAT
633525 AA
1 AA
633527 ACTATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AATATAATATATATAT
Found at i:633536 original size:17 final size:18
Alignment explanation
Indices: 633516--633551 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
633506 ATAATATAAG
633516 TTTATA-TATAAACTATA
1 TTTATATTATAAACTATA
633533 TTTATATTATAAACTATA
1 TTTATATTATAAACTATA
633551 T
1 T
633552 AATTATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATATTATAAACTATA
Found at i:633538 original size:15 final size:15
Alignment explanation
Indices: 633520--633624 Score: 56
Period size: 15 Copynumber: 6.9 Consensus size: 15
633510 TATAAGTTTA
633520 TATATAAACTATATTT
1 TATATAAACTATA-TT
633536 ATATTATAAACTATATAAT
1 -TA-TATAAACTATAT--T
*
633555 TAT-TATAAGT-TATT
1 TATATA-AACTATATT
* *
633569 TATATAAATTATGTT
1 TATATAAACTATATT
* *
633584 TATATCAA-T-TATA
1 TATATAAACTATATT
* *
633597 TATGTAAACTATATA
1 TATATAAACTATATT
*
633612 TGTATAAACTATA
1 TATATAAACTATA
633625 AAAGTATGTA
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
13 8 0.11
14 9 0.13
15 27 0.39
16 5 0.07
17 7 0.10
18 13 0.19
19 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (15 bp):
TATATAAACTATATT
Found at i:633558 original size:18 final size:17
Alignment explanation
Indices: 633517--633562 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
633507 TAATATAAGT
*
633517 TTATATATAAACTATATT
1 TTAT-TATAAACTATATA
633535 TATATTATAAACTATATAA
1 T-TATTATAAACTATAT-A
633554 TTATTATAA
1 TTATTATAA
633563 GTTATTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATTATAAACTATATA
Found at i:633671 original size:2 final size:2
Alignment explanation
Indices: 633659--633707 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
633649 ATTTATATTA
633659 AT AT A- 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
633700 AT AT AT AT
1 AT AT AT AT
633708 TATTCAAAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:633789 original size:19 final size:19
Alignment explanation
Indices: 633765--633873 Score: 67
Period size: 19 Copynumber: 5.3 Consensus size: 19
633755 TTTTATTTGG
633765 GAATTTAGAAGGAAATTGA
1 GAATTTAGAAGGAAATTGA
633784 GAATTTTTTAGAATATAGGAAAATTGA
1 GAA---TTTAG---A-AGG-AAATTGA
*
633811 GAATTTAGAGGGAAATTGA
1 GAATTTAGAAGGAAATTGA
* *
633830 GAAATTTAG-AGGGAATAGA
1 G-AATTTAGAAGGAAATTGA
* * *
633849 AAATTTTGGAGAGAAATTGA
1 GAATTTAGAAG-GAAATTGA
633869 GAATT
1 GAATT
633874 GAGATTTTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
18 6 0.09
19 20 0.29
20 19 0.27
21 1 0.01
22 5 0.07
24 5 0.07
25 1 0.01
26 3 0.04
27 10 0.14
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (19 bp):
GAATTTAGAAGGAAATTGA
Found at i:633824 original size:20 final size:21
Alignment explanation
Indices: 633801--633844 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
633791 TTAGAATATA
633801 GGAAAATTGAG-AATTTAGAG
1 GGAAAATTGAGAAATTTAGAG
633821 GG-AAATTGAGAAATTTAGAG
1 GGAAAATTGAGAAATTTAGAG
633841 GGAA
1 GGAA
633845 TAGAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.36
20 13 0.59
21 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (21 bp):
GGAAAATTGAGAAATTTAGAG
Found at i:634067 original size:2 final size:2
Alignment explanation
Indices: 634060--634208 Score: 74
Period size: 2 Copynumber: 80.0 Consensus size: 2
634050 TTTAATTTTC
* * *
634060 TA TA TA TA TA TA TA TA TG TA TA TA AA T- TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
634101 CTA TA TA -A GA TA TA TA GTT TA TA AA T- TA TA -A TT TA TA T- TA
1 -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
634141 -A TA TA TA -A TA TA TA TG TA TG TA TA -A CTA -A TA TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
634178 -A TC TA TA GA T- TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
634209 GAAACACAAT
Statistics
Matches: 109, Mismatches: 21, Indels: 34
0.66 0.13 0.21
Matches are distributed among these distances:
1 14 0.13
2 92 0.84
3 3 0.03
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:634130 original size:25 final size:23
Alignment explanation
Indices: 634061--634130 Score: 77
Period size: 25 Copynumber: 2.9 Consensus size: 23
634051 TTAATTTTCT
*
634061 ATATATATATATATATGTATATAA
1 ATATATATATATAAAT-TATATAA
*
634085 ATTATATATATATAAACTATATAA
1 A-TATATATATATAAATTATATAA
*
634109 GATATATAGTTTATAAATTATA
1 -ATATATA-TATATAAATTATA
634131 ATTTATATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
24 14 0.36
25 25 0.64
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (23 bp):
ATATATATATATAAATTATATAA
Found at i:634600 original size:15 final size:15
Alignment explanation
Indices: 634575--634617 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
634565 ATAAACCATG
634575 TATAGTATATATAAAC
1 TATA-TATATATAAAC
*
634591 TATATATATATAACC
1 TATATATATATAAAC
634606 TATATATATATA
1 TATATATATATA
634618 CTATATAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:634624 original size:15 final size:14
Alignment explanation
Indices: 634580--634624 Score: 67
Period size: 13 Copynumber: 3.3 Consensus size: 14
634570 CCATGTATAG
634580 TATATATA-AACTA
1 TATATATATAACTA
634593 TATATATATAACCTA
1 TATATATATAA-CTA
634608 TATATATAT-ACTA
1 TATATATATAACTA
634621 TATA
1 TATA
634625 AAGTAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 15 0.50
14 3 0.10
15 12 0.40
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (14 bp):
TATATATATAACTA
Found at i:635993 original size:16 final size:16
Alignment explanation
Indices: 635974--636015 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
635964 TGTCAGGTTA
*
635974 AAAATAGGTCAGATTG
1 AAAACAGGTCAGATTG
*
635990 AAAACAGGTCAGGTTG
1 AAAACAGGTCAGATTG
636006 AAAACAGGTC
1 AAAACAGGTC
636016 GGGTAATACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.12, G:0.26, T:0.19
Consensus pattern (16 bp):
AAAACAGGTCAGATTG
Found at i:645271 original size:19 final size:18
Alignment explanation
Indices: 645229--645271 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
645219 TCCCTCAAAG
645229 GTATCATTTTTTGGGTTTT
1 GTATC-TTTTTTGGGTTTT
*
645248 -CATCTTTTTTGTGGTTTT
1 GTATCTTTTTTG-GGTTTT
645266 GTATCT
1 GTATCT
645272 GGTTCGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.09, C:0.09, G:0.19, T:0.63
Consensus pattern (18 bp):
GTATCTTTTTTGGGTTTT
Found at i:645386 original size:30 final size:30
Alignment explanation
Indices: 645350--645411 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
645340 GTCTTTTCGT
645350 TTTTTCTTGCTCTCCAAAATTCATCCCTTC
1 TTTTTCTTGCTCTCCAAAATTCATCCCTTC
645380 TTTTTCTTGCTCTCCAAAATTCATCCCTTC
1 TTTTTCTTGCTCTCCAAAATTCATCCCTTC
645410 TT
1 TT
645412 CGAATCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.16, C:0.32, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTTTCTTGCTCTCCAAAATTCATCCCTTC
Found at i:646837 original size:19 final size:19
Alignment explanation
Indices: 646816--646877 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
646806 AAATATAATA
646816 TATATATATATATATATAA-
1 TATATATATATATATA-AAC
*
646835 TATA-AGTTTATATATAAAC
1 TATATA-TATATATATAAAC
*
646854 TATATTTATAT-TATAAAC
1 TATATATATATATATAAAC
646872 TATATA
1 TATATA
646878 ATTATTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 15 0.42
19 21 0.58
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (19 bp):
TATATATATATATATAAAC
Found at i:646870 original size:18 final size:17
Alignment explanation
Indices: 646818--646876 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 17
646808 ATATAATATA
*
646818 TATATATATATATATAA-
1 TATATTTATATATA-AAC
646835 TATAAGTTTATATATAAAC
1 TAT-A-TTTATATATAAAC
646854 TATATTTATATTATAAAC
1 TATATTTATA-TATAAAC
646872 TATAT
1 TATAT
646877 AATTATTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 9 0.24
18 16 0.43
19 12 0.32
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (17 bp):
TATATTTATATATAAAC
Found at i:646883 original size:18 final size:17
Alignment explanation
Indices: 646842--646887 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
646832 TAATATAAGT
*
646842 TTATATATAAACTATATT
1 TTAT-TATAAACTATATA
646860 TATATTATAAACTATATAA
1 T-TATTATAAACTATAT-A
646879 TTATTATAA
1 TTATTATAA
646888 GTTATTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATTATAAACTATATA
Found at i:646992 original size:2 final size:2
Alignment explanation
Indices: 646985--647012 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
646975 ATTTATATTA
646985 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
647013 TATTCAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:647372 original size:2 final size:2
Alignment explanation
Indices: 647365--647600 Score: 201
Period size: 2 Copynumber: 122.0 Consensus size: 2
647355 TTTAATTTTC
647365 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
647407 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
* * * * *
647449 TA TA T- TA TA TG TA TG TA TG TA TG TA TA TA AA CTA 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
* * * * *
647491 TA AA CTA TA TA -A GA TA TA TA GTT TA TA AA T- TA TA -A TT TA T-
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * *
647531 TT TA -A TA TA TA -A TA TA TA TG TA TG TA TA -A CTA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
647569 GTA -A TC TA TA GA T- TA TA TA TA TA TA TA T- TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
647601 GAAACACAAT
Statistics
Matches: 188, Mismatches: 28, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
1 13 0.07
2 170 0.90
3 5 0.03
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:647979 original size:20 final size:20
Alignment explanation
Indices: 647947--648011 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 20
647937 ATTTTATATA
*
647947 ATAT-GTATGTATAAACCAT
1 ATATAGTATATATAAACCAT
*
647966 GTATAGTATATATAAA-C-T
1 ATATAGTATATATAAACCAT
647984 ATATA-TATATAT-AACC-T
1 ATATAGTATATATAAACCAT
648001 ATATA-TATATA
1 ATATAGTATATA
648012 CTATATAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 2 0.05
17 20 0.49
18 5 0.12
19 4 0.10
20 10 0.24
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (20 bp):
ATATAGTATATATAAACCAT
Found at i:647994 original size:17 final size:17
Alignment explanation
Indices: 647967--648011 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
647957 ATAAACCATG
647967 TATAGTATATATAAACTA
1 TATA-TATATATAAACTA
*
647985 TATATATATATAACCTA
1 TATATATATATAAACTA
648002 TATATATATA
1 TATATATATA
648012 CTATATAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (17 bp):
TATATATATATAAACTA
Found at i:649377 original size:16 final size:15
Alignment explanation
Indices: 649355--649441 Score: 93
Period size: 16 Copynumber: 5.5 Consensus size: 15
649345 CGGATCATTT
649355 ACAGGTCAGGTTAAA
1 ACAGGTCAGGTTAAA
*
649370 ATCAGGTCAGTTTAAAA
1 A-CAGGTCAGGTT-AAA
* *
649387 ACAGGTTAGTTTAAAA
1 ACAGGTCAGGTT-AAA
*
649403 ACAGGTCAGATTGAAA
1 ACAGGTCAGGTT-AAA
649419 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTT-AAA
649435 ACAGGTC
1 ACAGGTC
649442 GGGTAATACC
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
15 1 0.02
16 59 0.92
17 4 0.06
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (15 bp):
ACAGGTCAGGTTAAA
Found at i:649391 original size:32 final size:31
Alignment explanation
Indices: 649355--649441 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 31
649345 CGGATCATTT
*
649355 ACAGGTCAGGTTAAAATCAGGTCAGTTTAAAA
1 ACAGGTCAGGTTAAAA-CAGGTCAGATTAAAA
* * *
649387 ACAGGTTAGTTTAAAAACAGGTCAGATTGAAA
1 ACAGGTCAGGTT-AAAACAGGTCAGATTAAAA
649419 ACAGGTCAGGTTGAAAACAGGTC
1 ACAGGTCAGGTT-AAAACAGGTC
649442 GGGTAATACC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 43 0.91
33 4 0.09
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (31 bp):
ACAGGTCAGGTTAAAACAGGTCAGATTAAAA
Found at i:650446 original size:3 final size:3
Alignment explanation
Indices: 650392--650427 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
650382 TTCACTATCA
650392 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
650428 ACAATTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.