Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004868.1 Hibiscus syriacus cultivar Beakdansim tig00010976_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: 66756
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:826 original size:20 final size:21
Alignment explanation
Indices: 782--839 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
772 TGCATGGTAG
782 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T-AAGAA
806 TGCATCGATGCACTG-AAGAA
1 TGCATCGATGCACTGTAAGAA
* *
826 TGCACCGATCCACT
1 TGCATCGATGCACT
840 TCAATGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
23 2 0.06
24 13 0.41
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (21 bp):
TGCATCGATGCACTGTAAGAA
Found at i:1675 original size:21 final size:21
Alignment explanation
Indices: 1635--1714 Score: 137
Period size: 20 Copynumber: 3.9 Consensus size: 21
1625 GAGTCGAGGG
1635 TCTATGTGGTCCTT-GGGACA
1 TCTATGTGGTCCTTCGGGACA
1655 TCTATGTGGTCCTTCGGGACA
1 TCTATGTGGTCCTTCGGGACA
*
1676 TCTATGTGGTCTTTC-GGACA
1 TCTATGTGGTCCTTCGGGACA
1696 TCTATGTGGTCCTTCGGGA
1 TCTATGTGGTCCTTCGGGA
1715 AAATTCTACG
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
20 33 0.59
21 23 0.41
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (21 bp):
TCTATGTGGTCCTTCGGGACA
Found at i:1695 original size:41 final size:41
Alignment explanation
Indices: 1635--1714 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
1625 GAGTCGAGGG
*
1635 TCTATGTGGTCCTTGGGACATCTATGTGGTCCTTCGGGACA
1 TCTATGTGGTCCTTCGGACATCTATGTGGTCCTTCGGGACA
*
1676 TCTATGTGGTCTTTCGGACATCTATGTGGTCCTTCGGGA
1 TCTATGTGGTCCTTCGGACATCTATGTGGTCCTTCGGGA
1715 AAATTCTACG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (41 bp):
TCTATGTGGTCCTTCGGACATCTATGTGGTCCTTCGGGACA
Found at i:4040 original size:33 final size:33
Alignment explanation
Indices: 3998--4064 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
3988 TTGTTATGAG
3998 ATTTCATTAGCAAATATCTAGAGTACACAAATT
1 ATTTCATTAGCAAATATCTAGAGTACACAAATT
4031 ATTTCATTAGCAAATATCTAGAGTACACAAATT
1 ATTTCATTAGCAAATATCTAGAGTACACAAATT
4064 A
1 A
4065 AATATATCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (33 bp):
ATTTCATTAGCAAATATCTAGAGTACACAAATT
Found at i:7816 original size:23 final size:24
Alignment explanation
Indices: 7774--7822 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
7764 GCGAGGCATA
*
7774 ATCAATGATATAAAAATAAAACAT
1 ATCAATAATATAAAAATAAAACAT
*
7798 ATCAATAATAT-AAAATAAATCAT
1 ATCAATAATATAAAAATAAAACAT
7821 AT
1 AT
7823 AAAAAAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (24 bp):
ATCAATAATATAAAAATAAAACAT
Found at i:7831 original size:24 final size:23
Alignment explanation
Indices: 7781--7846 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 23
7771 ATAATCAATG
* * *
7781 ATATAAAAATAAAACATATCAATA
1 ATAT-AAAATAAATCATATAAAAA
7805 ATATAAAATAAATCATATAAAAAA
1 ATATAAAATAAATCATAT-AAAAA
* * *
7829 ATACAAAACATATCATAT
1 ATATAAAATAAATCATAT
7847 GATATTATAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 13 0.37
24 22 0.63
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (23 bp):
ATATAAAATAAATCATATAAAAA
Found at i:9757 original size:2 final size:2
Alignment explanation
Indices: 9744--9803 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
9734 AGGAAAACAA
*
9744 AT AT AA 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
9786 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
9804 CAAAGTATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10334 original size:18 final size:17
Alignment explanation
Indices: 10313--10355 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
10303 ATATATACAT
10313 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
10331 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
10348 ATAA-AATA
1 ATAATAATA
10356 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:10761 original size:37 final size:37
Alignment explanation
Indices: 10711--10815 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
10701 GTGCTTGTGG
* * * *
10711 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
10748 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
*
10785 ATCCCATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
10816 GACGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:11660 original size:105 final size:105
Alignment explanation
Indices: 11358--11988 Score: 882
Period size: 105 Copynumber: 6.0 Consensus size: 105
11348 GCATTGTTCC
* * **
11358 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGATA-TTGTTTGTTGAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGA-AGTTG-TTGTTGAC
* * * * *
11421 AA-CTAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTC
63 AAGC-AGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
* * *
11464 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* * *
11524 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTATG
66 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
11564 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
11629 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
11669 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
11734 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
* * *
11774 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
11839 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
* * *
11879 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * * ** * *
11944 CCAACCGTACCTTCGTTATGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
11985 GAGT
1 GAGT
11989 GTCACGATAT
Statistics
Matches: 481, Mismatches: 35, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
100 80 0.17
101 3 0.01
102 5 0.01
104 5 0.01
105 306 0.64
106 82 0.17
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:12235 original size:36 final size:36
Alignment explanation
Indices: 12188--12263 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
12178 TGTTTGGAGA
* * *
12188 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
12224 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
12260 GAAA
1 GAAA
12264 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:12439 original size:102 final size:101
Alignment explanation
Indices: 12173--12533 Score: 468
Period size: 101 Copynumber: 3.7 Consensus size: 101
12163 TGTTTTCAAA
** *
12173 GTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGGAAACTATCTC
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
*
12235 AAGCGAG-ATAAAATTCATTTCAAGGGAAATGTTTTCAAT
66 AAG-GAGAAAAAAATTCATTTCAAGGGAAATG-TTT--AT
*
12274 GTTTATGTTTCAAGAGAAACTGTCTCAAGGAAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
* *
12339 AAGAGAGAAAAAAAAATCATTTTAAGGGAAATGTTTAT
66 AAG-GAG-AAAAAAATTCATTTCAAGGGAAATGTTTAT
12377 GTTTATGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
*
12441 -AGGAGAGAAAAAATTAATTTCAAGGG-AA-----AT
66 AAGGAGA-AAAAAATTCATTTCAAGGGAAATGTTTAT
12471 G----T-TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
12531 AAG
66 AAG
12534 CAAGATAAAA
Statistics
Matches: 240, Mismatches: 12, Indels: 26
0.86 0.04 0.09
Matches are distributed among these distances:
89 21 0.09
90 37 0.15
91 2 0.01
94 3 0.01
99 3 0.01
100 19 0.08
101 38 0.16
102 35 0.15
103 33 0.14
104 25 0.10
105 3 0.01
106 21 0.09
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.29
Consensus pattern (101 bp):
GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC
AAGGAGAAAAAAATTCATTTCAAGGGAAATGTTTAT
Found at i:12653 original size:36 final size:36
Alignment explanation
Indices: 12613--12795 Score: 133
Period size: 36 Copynumber: 5.1 Consensus size: 36
12603 CTCAAGCGAG
*
12613 ATAAATCTTGTTTTAAGAAAAATAATCTTGAGTGAA
1 ATAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAA
** * ** *
12649 ATAAATCTT-TTTCGAGAAAAACAGTCTCAAGTGAG
1 ATAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAA
* *
12684 ACAAAGT-ATGTTTTAAGAAAAACAATCTTGAGTGAA
1 ATAAA-TCTTGTTTTAAGAAAAACAATCTTGAGTGAA
* * * ** *
12720 ATAAATATT-TTTTCGAGAAAAACAGTCTCAAGTGAG
1 ATAAATCTTGTTTT-AAGAAAAACAATCTTGAGTGAA
* * *
12756 ACAAAGT-ATGTTTTAAGAAAAACAAAT-TTGAGTGAG
1 ATAAA-TCTTGTTTTAAGAAAAAC-AATCTTGAGTGAA
12792 ATAA
1 ATAA
12796 TCATCTGCAT
Statistics
Matches: 111, Mismatches: 29, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
35 29 0.26
36 75 0.68
37 7 0.06
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (36 bp):
ATAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAA
Found at i:12765 original size:72 final size:72
Alignment explanation
Indices: 12564--12795 Score: 301
Period size: 72 Copynumber: 3.2 Consensus size: 72
12554 AAAAACAGCT
* * * * *
12564 TTGAGTGAAATAAA-ATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGATAAA-TCTTGTTTT
1 TTGAGTGAAATAAATAT---TT-TTTCGAG-AAAAACAGTCTCAAGTGAGACAAAGT-ATGTTTT
*
12627 AAGAAAAATAATC
60 AAGAAAAACAATC
*
12640 TTGAGTGAAATAAAT-CTTTTTCGAGAAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAGAAA
1 TTGAGTGAAATAAATATTTTTTCGAGAAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAGAAA
12704 AACAATC
66 AACAATC
12711 TTGAGTGAAATAAATATTTTTTCGAGAAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAGAAA
1 TTGAGTGAAATAAATATTTTTTCGAGAAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAGAAA
12776 AACAAAT-
66 AAC-AATC
*
12783 TTGAGTGAGATAA
1 TTGAGTGAAATAA
12796 TCATCTGCAT
Statistics
Matches: 143, Mismatches: 9, Indels: 12
0.87 0.05 0.07
Matches are distributed among these distances:
71 53 0.37
72 71 0.50
73 5 0.03
76 14 0.10
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.29
Consensus pattern (72 bp):
TTGAGTGAAATAAATATTTTTTCGAGAAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAGAAA
AACAATC
Found at i:14233 original size:183 final size:183
Alignment explanation
Indices: 13919--14272 Score: 602
Period size: 183 Copynumber: 1.9 Consensus size: 183
13909 ATCAGGTTTA
*
13919 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTAATAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTAACAAAAGCAGTGGAGCAAACACCGAATT
** *
13984 GCCAAGTGTCCGAGCAATGTCATGATTTGAATGTAATATATTCATAAAGCCAGAGCTTTTGAGTT
66 GCCAAGTGTCCGAGCAATGTCATGATTTGAACATAATATATTCATAAAGCCAGAGCTTTCGAGTT
14049 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* * *
14102 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAATCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTAACAAAAGCAGTGGAGCAAACACCGAATT
* * *
14167 GCCAAGTGTCCGAGCAGTGTCAT-AGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAATGTCATGA-TTTGAACATAATATATTCATAAAGCCAGAGCTTTCGAGT
14231 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
14273 CGGATTTAAT
Statistics
Matches: 160, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
182 1 0.01
183 159 0.99
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTAACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATGATTTGAACATAATATATTCATAAAGCCAGAGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:18882 original size:18 final size:17
Alignment explanation
Indices: 18861--18903 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
18851 ATACACACAT
18861 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
18879 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
18896 ATAA-AATA
1 ATAATAATA
18904 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:19310 original size:37 final size:37
Alignment explanation
Indices: 19260--19364 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
19250 GTGCTTGTGG
* * * *
19260 ATCCTATCTTTAGGATTTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * * * *
19297 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
19334 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
19365 GACGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:19415 original size:20 final size:20
Alignment explanation
Indices: 19390--19441 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
19380 TGACACTTCA
* *
19390 GTATCGGTACTAACCTTTAG
1 GTATCGATACTAACCTATAG
19410 GTATCGATACTAACCTATAG
1 GTATCGATACTAACCTATAG
*
19430 GTATCAATACTA
1 GTATCGATACTA
19442 TTGACTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (20 bp):
GTATCGATACTAACCTATAG
Found at i:19597 original size:15 final size:15
Alignment explanation
Indices: 19577--19607 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
19567 AAAATATATA
19577 AGTATCGATACCCCT
1 AGTATCGATACCCCT
19592 AGTATCGATACCCCT
1 AGTATCGATACCCCT
19607 A
1 A
19608 TTGGGGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (15 bp):
AGTATCGATACCCCT
Found at i:24292 original size:116 final size:116
Alignment explanation
Indices: 24082--24311 Score: 379
Period size: 116 Copynumber: 2.0 Consensus size: 116
24072 TATCTCTATC
* * *
24082 ACACACAATCAATTATAGTATCCCATGAAATCGAACTATTTTTCGAATATATGACTCAACATACT
1 ACACACAATCAATTATAGTATCCCATGAAATCAAACTATCTATCGAATATATGACTCAACATACT
* *
24147 TATCCATAGAATTATTGGTTTGAACGGGAATGAAGTGTGTTAACTTAGTTA
66 TATCCATAGAATTATTAGTTCGAACGGGAATGAAGTGTGTTAACTTAGTTA
* * *
24198 ACACACAATCGATTCTAGTATCCCATGAATTCAAACTATCTATCGAATATATGACTCAACATACT
1 ACACACAATCAATTATAGTATCCCATGAAATCAAACTATCTATCGAATATATGACTCAACATACT
*
24263 TATCCATAGAATTATTAGTTCGAATGGGAATGAAGTGTGTTAACTTAGT
66 TATCCATAGAATTATTAGTTCGAACGGGAATGAAGTGTGTTAACTTAGT
24312 CAATTTATCA
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
116 105 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (116 bp):
ACACACAATCAATTATAGTATCCCATGAAATCAAACTATCTATCGAATATATGACTCAACATACT
TATCCATAGAATTATTAGTTCGAACGGGAATGAAGTGTGTTAACTTAGTTA
Found at i:25483 original size:16 final size:16
Alignment explanation
Indices: 25462--25511 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 16
25452 TGCACTGTTA
*
25462 TACATGAGCTATGTGT
1 TACATGACCTATGTGT
25478 TACATGTCATCCTATGTGT
1 TACATG--A-CCTATGTGT
*
25497 TACATGATCTATGTG
1 TACATGACCTATGTG
25512 GATATATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 13 0.45
17 1 0.03
18 1 0.03
19 14 0.48
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (16 bp):
TACATGACCTATGTGT
Found at i:25711 original size:23 final size:23
Alignment explanation
Indices: 25661--25705 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
25651 AGAGTCGAGG
*
25661 ATCTACGAGGTCCTTTGGGATAA
1 ATCTACGAGGTCCTTTGGGACAA
* *
25684 ATCTACGTGTTCCTTTGGGACA
1 ATCTACGAGGTCCTTTGGGACA
25706 TTTCTATGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (23 bp):
ATCTACGAGGTCCTTTGGGACAA
Found at i:25761 original size:23 final size:23
Alignment explanation
Indices: 25685--25766 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 23
25675 TTGGGATAAA
* * *
25685 TCTACGTGTTCCTTTGGGACATT
1 TCTATGTGGTCCTTCGGGACATT
* * *
25708 TCTATGCGATCCTTCGGGACAAT
1 TCTATGTGGTCCTTCGGGACATT
* * *
25731 ACTGTGTGGTCCTTCGGAACATT
1 TCTATGTGGTCCTTCGGGACATT
25754 TCTATGTGG-CCTT
1 TCTATGTGGTCCTT
25767 TCAGTGCAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
22 4 0.09
23 42 0.91
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGACATT
Found at i:25983 original size:32 final size:32
Alignment explanation
Indices: 25920--25983 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
25910 GTGCATAGTA
* * *
25920 TTACATGTTCTTGTTTGGTTAAATGCGTGATG
1 TTACATGTTATTGTTTGGTTAAATACATGATG
* *
25952 TTACATGTTATTGTTTTGTTAAATATATGATG
1 TTACATGTTATTGTTTGGTTAAATACATGATG
25984 CATTCTGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.50
Consensus pattern (32 bp):
TTACATGTTATTGTTTGGTTAAATACATGATG
Found at i:32596 original size:43 final size:43
Alignment explanation
Indices: 32532--32904 Score: 424
Period size: 43 Copynumber: 8.7 Consensus size: 43
32522 CCGTATGCTT
* * *
32532 CTTTGCTATGTGCAAGGGTAAGACCTTACCATTTCCTAGGCTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* * * * *
32575 CTCTGCTATGTGCAAGGGTAAGTCTTTACCGTTTCCCAGGTTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* * * *
32618 CTTTTCTATGTGCAAGGATAAGACTTTACCATTTCCCAAGCTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* *
32661 CTTTACTATGTGCAAGGATAAGACCTTACCGTTTACCAGGCTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* * *
32704 CTTTGCTATTTGCAAGGATAAGACCTTATCGTTTCTCAGGCTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* * **
32747 TTTTGCTATGTACAAGGATAAGACCTTACCGTTTCCCATACTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* * * **
32790 TTTTGTTATGTGTAAGGATAAGACCTTACTATTTCCCAGGCTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
* * * ** *
32833 TTTTGCTATGTGCAAGGGTAAGACCTTATCGTTTTTGCAAGCTC
1 CTTTGCTATGTGCAAGGATAAGACCTTACCG-TTTCCCAGGCTC
*
32877 TTTTGCTATGTGCAAAGG-TAAGACCTTA
1 CTTTGCTATGTGC-AAGGATAAGACCTTA
32905 TTGTTTTTGT
Statistics
Matches: 282, Mismatches: 46, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
43 246 0.87
44 32 0.11
45 4 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (43 bp):
CTTTGCTATGTGCAAGGATAAGACCTTACCGTTTCCCAGGCTC
Found at i:32767 original size:129 final size:128
Alignment explanation
Indices: 32532--32904 Score: 473
Period size: 129 Copynumber: 2.9 Consensus size: 128
32522 CCGTATGCTT
* *
32532 CTTTGCTATGTGCAAGGGTAAGACCTTACCATTTCCTAGGCTCCTCTGCTATGTGCAAGGGTAAG
1 CTTTGCTATGTGCAAGGATAAGACCTTACCATTTCC-AGGCTCCTTTGCTATGTGCAAGGGTAAG
* * * * * *
32597 TCTTTACCGTTTCCCAGGTTCCTTTT-CTATGTGCAAGGATAAGACTTTACCATTTCCCA-AGCT
65 ACCTTATCGTTTCTCAGGCT-CTTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCCATA-CT
32660 C
128 C
* * * *
32661 CTTTACTATGTGCAAGGATAAGACCTTACCGTTTACCAGGCTCCTTTGCTATTTGCAAGGATAAG
1 CTTTGCTATGTGCAAGGATAAGACCTTACCATTT-CCAGGCTCCTTTGCTATGTGCAAGGGTAAG
* *
32726 ACCTTATCGTTTCTCAGGCTCTTTTGCTATGTACAAGGATAAGACCTTACCGTTTCCCATACTC
65 ACCTTATCGTTTCTCAGGCTCTTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCCATACTC
* * * * *
32790 TTTTGTTATGTGTAAGGATAAGACCTTACTATTTCCCAGGCTCTTTTGCTATGTGCAAGGGTAAG
1 CTTTGCTATGTGCAAGGATAAGACCTTACCATTT-CCAGGCTCCTTTGCTATGTGCAAGGGTAAG
* *
32855 ACCTTATCGTTTTTGCAAGCTCTTTTGCTATGTGCAAAGG-TAAGACCTTA
65 ACCTTATCGTTTCT-CAGGCTCTTTTGCTATGTGC-AAGGATAAGACCTTA
32905 TTGTTTTTGT
Statistics
Matches: 212, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
128 5 0.02
129 172 0.81
130 31 0.15
131 4 0.02
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (128 bp):
CTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCAGGCTCCTTTGCTATGTGCAAGGGTAAGA
CCTTATCGTTTCTCAGGCTCTTTTGCTATGTGCAAGGATAAGACCTTACCATTTCCCATACTC
Found at i:32926 original size:44 final size:44
Alignment explanation
Indices: 32654--32942 Score: 177
Period size: 43 Copynumber: 6.6 Consensus size: 44
32644 TACCATTTCC
* * * **
32654 CAAGCTCCTTTACTATGTGC-AAGGATAAGACCTTACCG-TTTAC
1 CAAGCTCATTTGCTATGTGCAAAGG-TAAGACCTTATCGTTTTTG
* * * *
32697 CAGGCTCCTTTGCTATTTGC-AAGGATAAGACCTTATCGTTTCT-
1 CAAGCTCATTTGCTATGTGCAAAGG-TAAGACCTTATCGTTTTTG
* * * * **
32740 CAGGCTCTTTTGCTATGTAC-AAGGATAAGACCTTACCG-TTTCC
1 CAAGCTCATTTGCTATGTGCAAAGG-TAAGACCTTATCGTTTTTG
* * * **
32783 CATA-CTCTTTTGTTATGTG-TAAGGATAAGACCTTA-C-TATTTCC
1 CA-AGCTCATTTGCTATGTGCAAAGG-TAAGACCTTATCGT-TTTTG
* * *
32826 CAGGCTCTTTTGCTATGTGCAAGGGTAAGACCTTATCGTTTTTG
1 CAAGCTCATTTGCTATGTGCAAAGGTAAGACCTTATCGTTTTTG
* *
32870 CAAGCTCTTTTGCTATGTGCAAAGGTAAGACCTTATTGTTTTTG
1 CAAGCTCATTTGCTATGTGCAAAGGTAAGACCTTATCGTTTTTG
* * *
32914 -TAGTCTCATTTGCTTTGTTCACAAGGTAA
1 CAAG-CTCATTTGCTATGTGCA-AAGGTAA
32943 ATATGTTTTA
Statistics
Matches: 206, Mismatches: 28, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
42 3 0.01
43 131 0.64
44 64 0.31
45 8 0.04
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (44 bp):
CAAGCTCATTTGCTATGTGCAAAGGTAAGACCTTATCGTTTTTG
Found at i:36801 original size:16 final size:16
Alignment explanation
Indices: 36766--36804 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
36756 AAGATATAAG
36766 CTATGTG-ACAATGAT
1 CTATGTGAACAATGAT
36781 CTATGTGAACACATG-T
1 CTATGTGAACA-ATGAT
36797 CTATGTGA
1 CTATGTGA
36805 TAACCTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.32
16 12 0.55
17 3 0.14
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (16 bp):
CTATGTGAACAATGAT
Found at i:37012 original size:25 final size:25
Alignment explanation
Indices: 36983--37040 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
36973 CATTCGGGAC
* * *
36983 ATTTCTATGTGGCATTTCGGTGCAA
1 ATTTCTACGCGGCACTTCGGTGCAA
37008 ATTTCTACGCGGCACTTCGGTGC-A
1 ATTTCTACGCGGCACTTCGGTGCAA
*
37032 ATTTATACG
1 ATTTCTACG
37041 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 9 0.31
25 20 0.69
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (25 bp):
ATTTCTACGCGGCACTTCGGTGCAA
Found at i:39038 original size:18 final size:18
Alignment explanation
Indices: 39017--39058 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
39007 TAATTCATCA
39017 TACATTCACAATTGATC-G
1 TACATTCACAATTG-TCTG
* *
39035 TACATTGACCATTGTCTG
1 TACATTCACAATTGTCTG
39053 TACATT
1 TACATT
39059 GTATTTCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (18 bp):
TACATTCACAATTGTCTG
Found at i:39940 original size:27 final size:27
Alignment explanation
Indices: 39902--39953 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
39892 AAAGGAATAG
39902 GCAGTTTACCTCTTTCAGAATGTTCAA
1 GCAGTTTACCTCTTTCAGAATGTTCAA
39929 GCAGTTTACCTCTTTCAGAATGTTC
1 GCAGTTTACCTCTTTCAGAATGTTC
39954 TTCATTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (27 bp):
GCAGTTTACCTCTTTCAGAATGTTCAA
Found at i:40185 original size:18 final size:18
Alignment explanation
Indices: 40138--40188 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
40128 CATATTTAGA
*
40138 TTTGGGTTTGGATTCGAG
1 TTTGGGTTTGGGTTCGAG
*
40156 TTCGGGTTTGGGTTCGAG
1 TTTGGGTTTGGGTTCGAG
40174 TTTGGGTTTGGGTTC
1 TTTGGGTTTGGGTTC
40189 AGGTTCAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.06, C:0.08, G:0.41, T:0.45
Consensus pattern (18 bp):
TTTGGGTTTGGGTTCGAG
Found at i:40193 original size:12 final size:12
Alignment explanation
Indices: 40155--40223 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 12
40145 TTGGATTCGA
**
40155 GTTCGGGTTTGG
1 GTTCGGGTTCAG
* **
40167 GTTCGAGTTTGG
1 GTTCGGGTTCAG
*
40179 GTTTGGGTTCAG
1 GTTCGGGTTCAG
*
40191 GTTCAGGTTCAG
1 GTTCGGGTTCAG
* *
40203 GATCGGGTTCAT
1 GTTCGGGTTCAG
40215 GTTCGGGTT
1 GTTCGGGTT
40224 TGGTTTCAGG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.09, C:0.12, G:0.41, T:0.39
Consensus pattern (12 bp):
GTTCGGGTTCAG
Found at i:40199 original size:18 final size:17
Alignment explanation
Indices: 40142--40241 Score: 65
Period size: 18 Copynumber: 5.6 Consensus size: 17
40132 TTTAGATTTG
* *
40142 GGTTTGGATTCGAGTTCG
1 GGTTTGGGTTCG-GTTCA
**
40160 GGTTTGGGTTCGAGTTTG
1 GGTTTGGGTTCG-GTTCA
40178 GGTTTGGGTTCAGGTTCA
1 GGTTTGGGTTC-GGTTCA
** *
40196 GGTTCAGGATCGGGTTCA
1 GGTTTGGGTTC-GGTTCA
* * *
40214 TGTTCGGGTTTGGTTTCA
1 GGTTTGGGTTCGG-TTCA
40232 GGTTTGGGTT
1 GGTTTGGGTT
40242 TAGATTCATA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
17 2 0.03
18 63 0.95
19 1 0.02
ACGTcount: A:0.09, C:0.10, G:0.40, T:0.41
Consensus pattern (17 bp):
GGTTTGGGTTCGGTTCA
Found at i:40757 original size:93 final size:93
Alignment explanation
Indices: 40624--40818 Score: 268
Period size: 93 Copynumber: 2.1 Consensus size: 93
40614 GGATGCACAC
* *
40624 GGATGAACAAGGGTTGAATTTTGGGAATTTGATTGAAAAAAACACGAAATGGTTTGGGTTTCAGT
1 GGATGAACAAGGGTTGAATTTTGGGAATTAGATTGAAAAAAACACGAAATGGCTTGGGTTTCAGT
*
40689 GTTTGTGAAGATC-AATTGAGTGTTTTTG
66 GTTTGTGAAGATCAAATT-AGGGTTTTTG
* * ** * **
40717 GGATGAACAAGTGTTGAGTTTTTGGGTGTTAGGTTG-AAAAAACACGAAATGGCTTGGGTTTTGG
1 GGATGAACAAGGGTTGA-ATTTTGGGAATTAGATTGAAAAAAACACGAAATGGCTTGGGTTTCAG
40781 TGTTTGTGAAGATCAAATTAGGGTTTTTG
65 TGTTTGTGAAGATCAAATTAGGGTTTTTG
40810 GGATGAACA
1 GGATGAACA
40819 CAGATGAATT
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
93 73 0.81
94 17 0.19
ACGTcount: A:0.29, C:0.06, G:0.31, T:0.35
Consensus pattern (93 bp):
GGATGAACAAGGGTTGAATTTTGGGAATTAGATTGAAAAAAACACGAAATGGCTTGGGTTTCAGT
GTTTGTGAAGATCAAATTAGGGTTTTTG
Found at i:40849 original size:22 final size:21
Alignment explanation
Indices: 40819--40859 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
40809 GGGATGAACA
40819 CAGATGAATTTCTAGAGAGAAGT
1 CAGATGAATTT-T-GAGAGAAGT
40842 CAGA-GAATTTTGAGAGAA
1 CAGATGAATTTTGAGAGAA
40860 TCGAAGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 6 0.33
23 4 0.22
ACGTcount: A:0.41, C:0.07, G:0.27, T:0.24
Consensus pattern (21 bp):
CAGATGAATTTTGAGAGAAGT
Found at i:41090 original size:61 final size:61
Alignment explanation
Indices: 41015--41151 Score: 211
Period size: 61 Copynumber: 2.2 Consensus size: 61
41005 TCTTAGTTTT
* * *
41015 AAATTTGTTTAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAATCTTCATATTTA
1 AAATTTATTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAACTTCATATTTA
* *
41076 AAATTTATTCAATTTAGTCCAAATTTAATGTTGCAATTTATTAATTTAAACTTCATATTTA
1 AAATTTATTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAACTTCATATTTA
* *
41137 AATTTTTTTCAATTT
1 AAATTTATTCAATTT
41152 GATCCTTATA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.50
Consensus pattern (61 bp):
AAATTTATTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAACTTCATATTTA
Found at i:41253 original size:18 final size:18
Alignment explanation
Indices: 41230--41370 Score: 79
Period size: 18 Copynumber: 8.3 Consensus size: 18
41220 ACTAATAAAC
41230 TATATAATATATAATTTA
1 TATATAATATATAATTTA
*** *
41248 TATATACGGTATAGTTTA
1 TATATAATATATAATTTA
41266 TATAT-ATA-ATGAA--T-
1 TATATAATATAT-AATTTA
*
41280 TATATAATATATAGTTTA
1 TATATAATATATAATTTA
*
41298 TATAT-ATATAT-ATATA
1 TATATAATATATAATTTA
* *
41314 TATATACTA-ATGAA---C
1 TATATAATATAT-AATTTA
*
41329 TATATAATATATAGTTTA
1 TATATAATATATAATTTA
** *
41347 TATATACCATATACTTTA
1 TATATAATATATAATTTA
41365 TATATA
1 TATATA
41371 TAATTTTTAT
Statistics
Matches: 91, Mismatches: 19, Indels: 26
0.67 0.14 0.19
Matches are distributed among these distances:
14 5 0.05
15 14 0.15
16 16 0.18
17 10 0.11
18 46 0.51
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATAATATATAATTTA
Found at i:41383 original size:2 final size:2
Alignment explanation
Indices: 41264--41372 Score: 61
Period size: 2 Copynumber: 54.0 Consensus size: 2
41254 CGGTATAGTT
*
41264 TA TA TA TA TA -A TGA -A T- TA TA TA -A TA TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
*
41304 TA TA TA TA TA TA TA TA CTA -A TGA -A CTA TA TA -A TA TA TA GTT
1 TA TA TA TA TA TA TA TA -TA TA T-A TA -TA TA TA TA TA TA TA -TA
* *
41345 TA TA TA TA CCA TA TA CTT TA TA TA TA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA
41373 ATTTTTATAT
Statistics
Matches: 84, Mismatches: 8, Indels: 30
0.69 0.07 0.25
Matches are distributed among these distances:
1 7 0.08
2 68 0.81
3 9 0.11
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:41383 original size:13 final size:13
Alignment explanation
Indices: 41236--41319 Score: 51
Period size: 16 Copynumber: 5.5 Consensus size: 13
41226 AAACTATATA
41236 ATATATAATTTAT
1 ATATATAATTTAT
41249 ATATACGGTATAGTTTAT
1 ATATA---TA-A-TTTAT
41267 ATATATAATGAATTAT
1 ATATATAAT---TTAT
41283 ATAATATATAGTTTAT
1 AT-ATATA-A-TTTAT
*
41299 ATATATATATATAT
1 ATATATA-ATTTAT
41313 ATATATA
1 ATATATA
41320 CTAATGAACT
Statistics
Matches: 59, Mismatches: 1, Indels: 21
0.73 0.01 0.26
Matches are distributed among these distances:
13 6 0.10
14 12 0.20
15 9 0.15
16 14 0.24
17 6 0.10
18 11 0.19
19 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (13 bp):
ATATATAATTTAT
Found at i:41441 original size:9 final size:9
Alignment explanation
Indices: 41412--41442 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
41402 AAACTATATA
41412 TATATAGTT
1 TATATAGTT
*
41421 TACATAGTT
1 TATATAGTT
41430 TATATAGTT
1 TATATAGTT
41439 TATA
1 TATA
41443 CATATAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (9 bp):
TATATAGTT
Found at i:41564 original size:18 final size:18
Alignment explanation
Indices: 41552--41586 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41542 ATATAGTTTA
41552 TACATAATATATATATAG
1 TACATAATATATATATAG
*
41570 TTCATAATATATATATA
1 TACATAATATATATATA
41587 TATATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
TACATAATATATATATAG
Found at i:41569 original size:22 final size:22
Alignment explanation
Indices: 41541--41590 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
41531 ATCTATAAAC
*
41541 TATATAGTTTATACATA-ATATA
1 TATATAGTTCATA-ATATATATA
41563 TATATAGTTCATAATATATATA
1 TATATAGTTCATAATATATATA
41585 TATATA
1 TATATA
41591 TATTAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (22 bp):
TATATAGTTCATAATATATATA
Found at i:43895 original size:20 final size:22
Alignment explanation
Indices: 43855--43896 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43845 AATTAATTAA
*
43855 TTTAAAAATAATTATGATTTTT
1 TTTAAAAATAATGATGATTTTT
43877 TTTAAAAA-AATGA-GATTTTT
1 TTTAAAAATAATGATGATTTTT
43897 ATAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTAAAAATAATGATGATTTTT
Found at i:43996 original size:15 final size:16
Alignment explanation
Indices: 43978--44012 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
43968 ATCGTCATTT
43978 AAAAT-AATTTTAAGA
1 AAAATCAATTTTAAGA
*
43993 AAAATCATTTTTAAGA
1 AAAATCAATTTTAAGA
44009 AAAA
1 AAAA
44013 AATGTTTGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAATCAATTTTAAGA
Found at i:46072 original size:20 final size:20
Alignment explanation
Indices: 46023--46072 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
46013 AGAAAAACGT
*
46023 CAACGATCAAAGTCAACGGC
1 CAACGATCAAAGTCAACAGC
* * *
46043 CAATGTTCAAAGTCAACAGT
1 CAACGATCAAAGTCAACAGC
*
46063 TAACGATCAA
1 CAACGATCAA
46073 CAAGTCGGGT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (20 bp):
CAACGATCAAAGTCAACAGC
Found at i:49636 original size:14 final size:14
Alignment explanation
Indices: 49617--49652 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
49607 CATTACTATG
49617 AAATCATCCTCCTT
1 AAATCATCCTCCTT
*
49631 ACATCATCCTCCTT
1 AAATCATCCTCCTT
49645 AAATCATC
1 AAATCATC
49653 AAATTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATCATCCTCCTT
Found at i:51301 original size:20 final size:20
Alignment explanation
Indices: 51278--51322 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
51268 TCAGTATCTG
* *
51278 TACTAACCTATGGGTATCGA
1 TACTAACCTATGGATATCAA
*
51298 TACTAGCCTATGGATATCAA
1 TACTAACCTATGGATATCAA
51318 TACTA
1 TACTA
51323 CTGACTATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (20 bp):
TACTAACCTATGGATATCAA
Found at i:51381 original size:20 final size:21
Alignment explanation
Indices: 51356--51404 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
51346 AAAGGGCTAG
51356 TATTGATAC-TCTAGT-TTGAA
1 TATTGATACTTCTAGTCTTG-A
*
51376 TATTGATACTTCTAGTCTTGG
1 TATTGATACTTCTAGTCTTGA
51397 TATTGATA
1 TATTGATA
51405 TTGTCTTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.35
21 14 0.54
22 3 0.12
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (21 bp):
TATTGATACTTCTAGTCTTGA
Found at i:51489 original size:20 final size:20
Alignment explanation
Indices: 51464--51501 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
51454 CTTAATAACA
51464 ATACTCTACCCCCAGTATTT
1 ATACTCTACCCCCAGTATTT
51484 ATACTCTACCCCCAGTAT
1 ATACTCTACCCCCAGTAT
51502 CGACACACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.37, G:0.05, T:0.32
Consensus pattern (20 bp):
ATACTCTACCCCCAGTATTT
Found at i:55252 original size:11 final size:10
Alignment explanation
Indices: 55222--55251 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
55212 GTAATAAATT
55222 ATTATTTTTA
1 ATTATTTTTA
55232 ACTTATTTTTA
1 A-TTATTTTTA
55243 ATTATTTTT
1 ATTATTTTT
55252 TTAAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTATTTTTA
Found at i:56637 original size:77 final size:78
Alignment explanation
Indices: 56463--56654 Score: 242
Period size: 77 Copynumber: 2.5 Consensus size: 78
56453 ATGATGCCTT
* * * **
56463 AGCTGATATGTATATGGGCACATTATCGGCATAAAAAAATAATGCATATGGGTGCATTAATGGCA
1 AGCTGAAATGCATATGGGTACATTATCAACAT-AAAAAATAATGCATATGGGTGCATTAATGGCA
* **
56528 TGAAAGTATGCCTT
65 TGAAAGGATGCCAA
* *
56542 AGCTGATATGTATATGGGTACATTATCAACATAAAAAATAATGCATAT-GGTGCATTAATGGCAT
1 AGCTGAAATGCATATGGGTACATTATCAACATAAAAAATAATGCATATGGGTGCATTAATGGCAT
56606 GAAAGGATGCCAA
66 GAAAGGATGCCAA
* * * *
56619 AGTTGAAATGCATGTGGGTGCATTATCAATATAAAA
1 AGCTGAAATGCATATGGGTACATTATCAACATAAAA
56655 GAGGAAATCA
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
77 56 0.55
78 16 0.16
79 29 0.29
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (78 bp):
AGCTGAAATGCATATGGGTACATTATCAACATAAAAAATAATGCATATGGGTGCATTAATGGCAT
GAAAGGATGCCAA
Found at i:56749 original size:60 final size:60
Alignment explanation
Indices: 56656--56804 Score: 253
Period size: 60 Copynumber: 2.5 Consensus size: 60
56646 AATATAAAAG
*
56656 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTTTGCTAAAATGATA
1 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
* * * *
56716 AGGAAATAATACTGAGTGTTTGAATTTCTAGATAAGGGCACTTTGTGTGCTAAAATGATA
1 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
56776 AGGAAATCATACTAAGTGTATGAATTTCC
1 AGGAAATCATACTAAGTGTATGAATTTCC
56805 GTATAGGAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 80 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (60 bp):
AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
Found at i:59163 original size:2 final size:2
Alignment explanation
Indices: 59156--59213 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
59146 GTCATAAATA
59156 AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
59197 AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
59214 CTTTTATGGT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59972 original size:12 final size:12
Alignment explanation
Indices: 59955--60005 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
59945 TTCAAAAAGG
59955 TTTTATATTTAA
1 TTTTATATTTAA
59967 TTTTATA-TTATA
1 TTTTATATTTA-A
*
59979 TTTGAT-TTTAA
1 TTTTATATTTAA
59990 TTTTA-ATATTAA
1 TTTTATAT-TTAA
60002 TTTT
1 TTTT
60006 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:60009 original size:14 final size:14
Alignment explanation
Indices: 59990--60102 Score: 68
Period size: 14 Copynumber: 8.8 Consensus size: 14
59980 TTGATTTTAA
59990 TTTTAATATTAATT
1 TTTTAATATTAATT
60004 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
60014 ATTAAATATTAATT
1 TTTTAATATTAATT
* *
60028 TATTAATATT-ATA
1 TTTTAATATTAATT
*
60041 TTATAGATATTAA--
1 TTTTA-ATATTAATT
*
60054 CTTTAATATTAATT
1 TTTTAATATTAATT
60068 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
60078 ATTAAATATTAATT
1 TTTTAATATTAATT
60092 TTTTAATATTA
1 TTTTAATATTA
60103 TATTATAGAT
Statistics
Matches: 72, Mismatches: 15, Indels: 24
0.65 0.14 0.22
Matches are distributed among these distances:
10 8 0.11
11 2 0.03
12 19 0.26
13 10 0.14
14 32 0.44
15 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:60064 original size:64 final size:64
Alignment explanation
Indices: 59971--60115 Score: 249
Period size: 64 Copynumber: 2.3 Consensus size: 64
59961 ATTTAATTTT
* *
59971 ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTATTA
1 ATATTATATTATAGATATTAACTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTATTA
*
60033 ATATTATATTATAGATATTAACTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTA
1 ATATTATATTATAGATATTAACTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTATTA
60097 ATATTATATTATAGATATT
1 ATATTATATTATAGATATT
60116 TAATTTTATA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
62 10 0.13
63 1 0.01
64 67 0.86
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (64 bp):
ATATTATATTATAGATATTAACTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTATTA
Found at i:60142 original size:19 final size:17
Alignment explanation
Indices: 60117--60166 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
60107 ATAGATATTT
60117 AATTTTATATCA-TATAA
1 AATTTTATAT-ATTATAA
60134 ATTATTTTATATATTATAA
1 A--ATTTTATATATTATAA
60153 AATTTTATAT-TTAT
1 AATTTTATATATTAT
60167 TTTAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.13
17 10 0.33
18 1 0.03
19 15 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTTATATATTATAA
Found at i:60677 original size:31 final size:31
Alignment explanation
Indices: 60640--60699 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
60630 TAGTTGTATG
* *
60640 AATTATTTAAATTTCAATATTGTAAAACTAA
1 AATTATTTAAATCTCAATATTGCAAAACTAA
*
60671 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAATATTGCAAAACT
60700 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATTGCAAAACTAA
Found at i:62455 original size:60 final size:60
Alignment explanation
Indices: 62371--62518 Score: 233
Period size: 60 Copynumber: 2.5 Consensus size: 60
62361 AATATAAAAG
* *
62371 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTTTGCTAAAATGATA
1 AGGAAATAATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
* * *
62431 AGGAAATAATATTGAGTGTTTGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
1 AGGAAATAATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
* *
62491 AGGAAATCATACTAAGTGTATAAATTTC
1 AGGAAATAATACTAAGTGTATGAATTTC
62519 GTATAAGAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 78 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (60 bp):
AGGAAATAATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
Found at i:63819 original size:21 final size:21
Alignment explanation
Indices: 63794--63868 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
63784 ATAATTACTA
*
63794 TCGCAGTGCGATTTT-CCAATT
1 TCGCATTGCGATTTTCCCAA-T
63815 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
63836 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
63857 TCGCAATGCGAT
1 TCGCATTGCGAT
63869 ACTGACTATC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 47 0.92
22 4 0.08
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:63882 original size:20 final size:20
Alignment explanation
Indices: 63856--63962 Score: 92
Period size: 20 Copynumber: 5.3 Consensus size: 20
63846 ATTTTCCCAA
63856 TTCGCAATGCGATACTGACT
1 TTCGCAATGCGATACTGACT
* * * *
63876 ATCGCAACGCGATAAT-ACAA
1 TTCGCAATGCGATACTGAC-T
* *
63896 ATCGCAATGCGATACTTACT
1 TTCGCAATGCGATACTGACT
* * *
63916 TTCGCAACGTGATACTTACT
1 TTCGCAATGCGATACTGACT
*
63936 TTCGCAACT-AGATACTGACT
1 TTCGCAA-TGCGATACTGACT
63956 TTCGCAA
1 TTCGCAA
63963 CGAGATAATA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.03
20 67 0.94
21 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (20 bp):
TTCGCAATGCGATACTGACT
Found at i:63906 original size:40 final size:40
Alignment explanation
Indices: 63857--63989 Score: 144
Period size: 40 Copynumber: 3.3 Consensus size: 40
63847 TTTTCCCAAT
* *
63857 TCGCAATGCGATACTGACTATCGCAACGCGATAATACAAA
1 TCGCAATGCGATACTGACTTTCGCAACGAGATAATACAAA
* * * **
63897 TCGCAATGCGATACTTACTTTCGCAACGTGATACTTAC-TT
1 TCGCAATGCGATACTGACTTTCGCAACGAGATA-ATACAAA
* *
63937 TCGCAACT-AGATACTGACTTTCGCAACGAGATAATATATAA
1 TCGCAA-TGCGATACTGACTTTCGCAACGAGATAATACA-AA
63978 TCGCAATGCGAT
1 TCGCAATGCGAT
63990 TTTCAAAGCG
Statistics
Matches: 74, Mismatches: 14, Indels: 9
0.76 0.14 0.09
Matches are distributed among these distances:
39 2 0.03
40 59 0.80
41 13 0.18
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (40 bp):
TCGCAATGCGATACTGACTTTCGCAACGAGATAATACAAA
Found at i:63963 original size:20 final size:20
Alignment explanation
Indices: 63906--63969 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
63896 ATCGCAATGC
63906 GATACTTACTTTCGCAACGT-
1 GATACTTACTTTCGCAAC-TA
63926 GATACTTACTTTCGCAACTA
1 GATACTTACTTTCGCAACTA
* *
63946 GATACTGACTTTCGCAACGA
1 GATACTTACTTTCGCAACTA
63966 GATA
1 GATA
63970 ATATATAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 1 0.02
20 40 0.98
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (20 bp):
GATACTTACTTTCGCAACTA
Found at i:64195 original size:21 final size:22
Alignment explanation
Indices: 64155--64197 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
64145 CACTCTCTCA
64155 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
64177 CCCATCTTCGGCG-AATCCGTC
1 CCCATCTCCGACGAAATCCGTC
64198 TATCTCCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.19, C:0.44, G:0.16, T:0.21
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:64426 original size:18 final size:19
Alignment explanation
Indices: 64403--64447 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
64393 TTATTCTCTT
64403 GTTGCG-TAGTCAATTCGC
1 GTTGCGATAGTCAATTCGC
* * *
64421 GTTGCGATTGTCATTTCGT
1 GTTGCGATAGTCAATTCGC
64440 GTTGCGAT
1 GTTGCGAT
64448 TTTCATTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.13, C:0.18, G:0.29, T:0.40
Consensus pattern (19 bp):
GTTGCGATAGTCAATTCGC
Found at i:64438 original size:19 final size:19
Alignment explanation
Indices: 64411--64455 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
64401 TTGTTGCGTA
*
64411 GTCAATTCGCGTTGCGATT
1 GTCATTTCGCGTTGCGATT
*
64430 GTCATTTCGTGTTGCGATT
1 GTCATTTCGCGTTGCGATT
*
64449 TTCATTT
1 GTCATTT
64456 TCAGAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (19 bp):
GTCATTTCGCGTTGCGATT
Found at i:64643 original size:25 final size:24
Alignment explanation
Indices: 64589--64643 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
64579 TGTTTATTAT
* *
64589 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
64613 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
64639 TGTTT
1 TGTTT
64644 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:65801 original size:18 final size:18
Alignment explanation
Indices: 65755--65803 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
65745 TCCACTTCGG
*
65755 GAGCCATCACCTCACCCA
1 GAGCTATCACCTCACCCA
65773 GAGCTATCACCTCACCCA
1 GAGCTATCACCTCACCCA
65791 GA-CTATACACCTC
1 GAGCTAT-CACCTC
65804 CACAACGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 4 0.14
18 25 0.86
ACGTcount: A:0.29, C:0.45, G:0.10, T:0.16
Consensus pattern (18 bp):
GAGCTATCACCTCACCCA
Found at i:66249 original size:17 final size:17
Alignment explanation
Indices: 66215--66259 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
66205 ACTGCTAAAC
66215 TGTTTTT-GTTAGTATT
1 TGTTTTTGGTTAGTATT
* *
66231 TGTTTTTGGTTTGTTTT
1 TGTTTTTGGTTAGTATT
66248 TGTCTTTTGGTT
1 TGT-TTTTGGTT
66260 GAAGTAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 7 0.28
17 10 0.40
18 8 0.32
ACGTcount: A:0.04, C:0.02, G:0.22, T:0.71
Consensus pattern (17 bp):
TGTTTTTGGTTAGTATT
Found at i:66363 original size:19 final size:20
Alignment explanation
Indices: 66320--66375 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
66310 TCGCACACGA
66320 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
66340 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
66359 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
66376 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:66383 original size:14 final size:14
Alignment explanation
Indices: 66364--66416 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
66354 ATGCGAAATG
66364 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
66378 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
66397 AAAATCGCAACGAC
1 AAAATCGCAACGAC
66411 AAAATC
1 AAAATC
66417 AACGCGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 16 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.31
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:66390 original size:33 final size:33
Alignment explanation
Indices: 66348--66437 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
66338 GGAAATGGCT
66348 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
66381 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
66414 AT--CAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
66438 TGCGAAATGA
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 21 0.38
33 35 0.62
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:66402 original size:19 final size:19
Alignment explanation
Indices: 66348--66461 Score: 117
Period size: 19 Copynumber: 6.6 Consensus size: 19
66338 GGAAATGGCT
66348 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
66367 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
66381 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
66400 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
66414 AT--CAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
66431 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
66450 ATCGCAATGCGA
1 ATCGCAATGCGA
66462 TTGTGTTTCG
Statistics
Matches: 78, Mismatches: 5, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
12 3 0.04
14 17 0.22
15 2 0.03
16 3 0.04
17 9 0.12
18 1 0.01
19 43 0.55
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:66510 original size:19 final size:19
Alignment explanation
Indices: 66488--66545 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
66478 GATTTTGTTG
66488 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
66507 TGCGATTTTC---TCG--T
1 TGCGATTTTCATTTCGCAT
66521 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
66540 TGCGAT
1 TGCGAT
66546 AGCCATTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 11 0.32
16 3 0.09
17 3 0.09
19 17 0.50
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCAT
Found at i:66530 original size:33 final size:32
Alignment explanation
Indices: 66467--66545 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 32
66457 TGCGATTGTG
* * *
66467 TTTCGCGTTGCGATTTTGTTGTGCGATTTTCA
1 TTTCGCATTGCGATTTTCTCGTGCGATTTTCA
66499 TTTCGCATTGCGATTTTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCTCG-TGCGATTTTCA
66532 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
66546 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 18 0.42
33 25 0.58
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (32 bp):
TTTCGCATTGCGATTTTCTCGTGCGATTTTCA
Found at i:66552 original size:19 final size:19
Alignment explanation
Indices: 66530--66582 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
66520 TTGCGATTTT
*
66530 CATTTCGCATTGCGATAGC
1 CATTTCCCATTGCGATAGC
* *
66549 CATTTCCCTTTGCGATAGT
1 CATTTCCCATTGCGATAGC
* *
66568 CATTTTCCGTTGCGA
1 CATTTCCCATTGCGA
66583 AAGTATGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (19 bp):
CATTTCCCATTGCGATAGC
Found at i:66593 original size:19 final size:19
Alignment explanation
Indices: 66558--66607 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
66548 CCATTTCCCT
*
66558 TTGCGATAGTCATTTTC-CG
1 TTGCGAAAGT-ATTTTCGCG
*
66577 TTGCGAAAGTATGTTTCGTG
1 TTGCGAAAGTAT-TTTCGCG
66597 TTGCGAAAGTA
1 TTGCGAAAGTA
66608 AACTATTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 13 0.48
20 12 0.44
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (19 bp):
TTGCGAAAGTATTTTCGCG
Done.