Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014975.1 Kokia drynarioides strain JFW-HI SEQ_130019, 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: 356896
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:3224 original size:12 final size:12
Alignment explanation
Indices: 3207--3233 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3197 AGATGGAGTG
3207 ATTGAATTATTC
1 ATTGAATTATTC
3219 ATTGAATTATTC
1 ATTGAATTATTC
3231 ATT
1 ATT
3234 CCCCATTCAT
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:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (12 bp):
ATTGAATTATTC
Found at i:4672 original size:93 final size:93
Alignment explanation
Indices: 4560--5273 Score: 1128
Period size: 93 Copynumber: 7.7 Consensus size: 93
4550 TTAAAATTAT
*
4560 TTATTATAATATTTCAATTTATATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATT
1 TTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATT
4625 CAAATTTTAAATTTATTTAAATAAAAAA
66 CAAATTTTAAATTTATTTAAATAAAAAA
* *
4653 TTATTATAATATTTCAATTTTTATCAAATAATGTGTTAATTTGACAATACATTATTTACTAAATT
1 TTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATT
* ***
4718 CAAATTTTAAATTTATTAAAAT-AATTT
66 CAAATTTTAAATTTATTTAAATAAAAAA
* * *
4745 TTTTTATAATATTT-AATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTTATCAAATT
1 TTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATT
4809 CAAATTTTAAATTTATTTAAATAAAAAAA
66 CAAATTTTAAATTTATTTAAAT-AAAAAA
*
4838 TTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATT
1 TTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATT
4903 CAAATTTTAAATTTATTTAAATAAAAAA
66 CAAATTTTAAATTTATTTAAATAAAAAA
* * * * * *
4931 ATATTATAATATTTTAATTTTTATTAAATAATGTGTTGATTTAACATTACATTATTTACCAATTT
1 TTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATT
*
4996 TAAATTTTAAATTTATTTAAATAAAAAA
66 CAAATTTTAAATTTATTTAAATAAAAAA
* *
5024 -TAATATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTAAATT
1 TTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATT
* *
5088 CAAATTTTAAATTTATTTAAATATAATA
66 CAAATTTTAAATTTATTTAAATAAAAAA
* * * *
5116 TTATTATAATATTTCAATTTTTATCAAATAATATGTTGATTTGATAATGCATTATTTATCAAATT
1 TTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATT
*
5181 CAAATTTTAAATTTATTTAGATAAAAAAGA
66 CAAATTTTAAATTTATTTAAAT-AAAAA-A
*
5211 TTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTATCAAA
1 TTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAA
5274 ATACCGTTAA
Statistics
Matches: 565, Mismatches: 50, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
91 67 0.12
92 97 0.17
93 268 0.47
94 72 0.13
95 61 0.11
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (93 bp):
TTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATT
CAAATTTTAAATTTATTTAAATAAAAAA
Found at i:4865 original size:185 final size:185
Alignment explanation
Indices: 4554--5268 Score: 1148
Period size: 185 Copynumber: 3.8 Consensus size: 185
4544 ATTAATTTAA
*
4554 AATTATTTATTATAATATTTCAATTTATATCAAATAATGTGTTGATTTGACAATACATTATTTAC
1 AATTA-TTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTAC
4619 CAAATTCAAATTTTAAATTTATTTAAATAAAAAATTATTATAATATTTCAATTTTTATCAAATAA
65 CAAATTCAAATTTTAAATTTATTTAAATAAAAAATTATTATAATATTTCAATTTTTATCAAATAA
*
4684 TGTGTTAATTTGACAATACATTATTTACTAAATTCAAATTTTAAATTTATTAAAAT
130 TGTGTTGATTTGACAATACATTATTTACTAAATTCAAATTTTAAATTTATTAAAAT
* * * *
4740 AATTTTTTTTATAATATTT-AATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTTATC
1 AATTATTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACC
4804 AAATTCAAATTTTAAATTTATTTAAATAAAAAAATTATTATAATATTTCAATTTTTATCAAATAA
66 AAATTCAAATTTTAAATTTATTTAAAT-AAAAAATTATTATAATATTTCAATTTTTATCAAATAA
*
4869 TGTGTTGATTTGACAATACATTATTTACTAAATTCAAATTTTAAATTTATTTAAAT
130 TGTGTTGATTTGACAATACATTATTTACTAAATTCAAATTTTAAATTTATTAAAAT
** * * * * *
4925 AAAAAAATATTATAATATTTTAATTTTTATTAAATAATGTGTTGATTTAACATTACATTATTTAC
1 -AATTATTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTAC
* * *
4990 CAATTTTAAATTTTAAATTTATTTAAATAAAAAA-TAATATAATATTTCAATTTTTATCAAATAA
65 CAAATTCAAATTTTAAATTTATTTAAATAAAAAATTATTATAATATTTCAATTTTTATCAAATAA
5054 TGTGTTGATTTGACAATACATTATTTACTAAATTCAAATTTTAAATTTATTTAAATAT
130 TGTGTTGATTTGACAATACATTATTTACTAAATTCAAATTTTAAATTTA-TTAAA-AT
* * * *
5112 AA-TATTATTATAATATTTCAATTTTTATCAAATAATATGTTGATTTGATAATGCATTATTTATC
1 AATTATTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACC
*
5176 AAATTCAAATTTTAAATTTATTTAGATAAAAAAGATTATTATAATATTTCAATTTTTATCAAATA
66 AAATTCAAATTTTAAATTTATTTAAAT-AAAAA-ATTATTATAATATTTCAATTTTTATCAAATA
5241 ATGTGTTGATTTGACAATACATTATTTA
129 ATGTGTTGATTTGACAATACATTATTTA
5269 TCAAAATACC
Statistics
Matches: 486, Mismatches: 35, Indels: 14
0.91 0.07 0.03
Matches are distributed among these distances:
184 69 0.14
185 258 0.53
186 35 0.07
187 68 0.14
188 56 0.12
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (185 bp):
AATTATTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACC
AAATTCAAATTTTAAATTTATTTAAATAAAAAATTATTATAATATTTCAATTTTTATCAAATAAT
GTGTTGATTTGACAATACATTATTTACTAAATTCAAATTTTAAATTTATTAAAAT
Found at i:5121 original size:278 final size:277
Alignment explanation
Indices: 4537--5273 Score: 1131
Period size: 278 Copynumber: 2.6 Consensus size: 277
4527 AAAAAATCAC
* * *
4537 TTTTAAAATTAATTTAAA-ATTAT-TTATTATAATATTTCAATTTATATCAAATAATGTGTTGAT
1 TTTT-AAATTTATTTAAATATAATATTATTATAATATTTCAATTTTTATCAAATAATGTGTTGAT
* *
4600 TTGACAATACATTATTTACCAAATTCAAATTTTAAATTTATTTAAATAAAAAATTATTATAATAT
65 TTGACAATACATTATTTACTAAATTCAAATTTTAAATTTATTTAAATAAAAAAATATTATAATAT
* *
4665 TTCAATTTTTATCAAATAATGTGTTAATTTGACAATACATTATTTACTAAATTCAAATTTTAAAT
130 TTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATTCAAATTTTAAAT
**** ** *
4730 TTATTAAAATAATTTTTTTTATAATATTTAATTTTTATCAAATAATGTGTTGATTTGACAATATA
195 TTATTAAAATAAAAAATAATATAATATTTAATTTTTATCAAATAATGTGTTGATTTGACAATACA
4795 TTATTTATCAAATTCAAA
260 TTATTTATCAAATTCAAA
* *
4813 TTTTAAATTTATTTAAATAAAAAAATTATTATAATATTTCAATTTTTATCAAATAATGTGTTGAT
1 TTTTAAATTTATTTAAAT-ATAATATTATTATAATATTTCAATTTTTATCAAATAATGTGTTGAT
4878 TTGACAATACATTATTTACTAAATTCAAATTTTAAATTTATTTAAATAAAAAAATATTATAATAT
65 TTGACAATACATTATTTACTAAATTCAAATTTTAAATTTATTTAAATAAAAAAATATTATAATAT
* * * * * *
4943 TTTAATTTTTATTAAATAATGTGTTGATTTAACATTACATTATTTACCAATTTTAAATTTTAAAT
130 TTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATTCAAATTTTAAAT
*
5008 TTATTTAAATAAAAAATAATATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATAC
195 TTATTAAAATAAAAAATAATATAATATTT-AATTTTTATCAAATAATGTGTTGATTTGACAATAC
5073 ATTATTTA-CTAAATTCAAA
259 ATTATTTATC-AAATTCAAA
*
5092 TTTTAAATTTATTTAAATATAATATTATTATAATATTTCAATTTTTATCAAATAATATGTTGATT
1 TTTTAAATTTATTTAAATATAATATTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATT
* * *
5157 TGATAATGCATTATTTA-TCAAATTCAAATTTTAAATTTATTTAGATAAAAAAGATTATTATAAT
66 TGACAATACATTATTTACT-AAATTCAAATTTTAAATTTATTTAAATAAAAAA-A-TATTATAAT
*
5221 ATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTATCAAA
128 ATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAA
5274 ATACCGTTAA
Statistics
Matches: 418, Mismatches: 35, Indels: 12
0.90 0.08 0.03
Matches are distributed among these distances:
275 12 0.03
276 4 0.01
277 3 0.01
278 273 0.65
279 70 0.17
280 56 0.13
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (277 bp):
TTTTAAATTTATTTAAATATAATATTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATT
TGACAATACATTATTTACTAAATTCAAATTTTAAATTTATTTAAATAAAAAAATATTATAATATT
TCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACCAAATTCAAATTTTAAATT
TATTAAAATAAAAAATAATATAATATTTAATTTTTATCAAATAATGTGTTGATTTGACAATACAT
TATTTATCAAATTCAAA
Found at i:6525 original size:20 final size:19
Alignment explanation
Indices: 6500--6590 Score: 63
Period size: 20 Copynumber: 5.1 Consensus size: 19
6490 GATGTAAGAT
6500 ATATTTTCGAATTTTTTAAA
1 ATATTTTCGAATTTTTT-AA
*
6520 ATATTTT----TTTTTT-C
1 ATATTTTCGAATTTTTTAA
**
6534 A-ATTTTCGAATTGTTTTTT
1 ATATTTTCGAATT-TTTTAA
*
6553 ATATTTTCGAATTTTTTTAG
1 ATATTTTCGAA-TTTTTTAA
6573 AT-TTTT-GAATTTTTTAA
1 ATATTTTCGAATTTTTTAA
6590 A
1 A
6591 ATTATTTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
13 5 0.09
14 1 0.02
16 6 0.10
17 10 0.17
18 7 0.12
19 5 0.09
20 22 0.38
21 2 0.03
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63
Consensus pattern (19 bp):
ATATTTTCGAATTTTTTAA
Found at i:6550 original size:18 final size:18
Alignment explanation
Indices: 6526--6587 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
6516 TAAAATATTT
6526 TTTTTTTCA-ATTTTCGAA
1 TTTTTTT-AGATTTTCGAA
*
6544 TTGTTTTTTATATTTTCGAA
1 -T-TTTTTTAGATTTTCGAA
*
6564 TTTTTTTAGATTTTTGAA
1 TTTTTTTAGATTTTCGAA
6582 TTTTTT
1 TTTTTT
6588 AAAATTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 21 0.54
19 3 0.08
20 15 0.38
ACGTcount: A:0.19, C:0.05, G:0.08, T:0.68
Consensus pattern (18 bp):
TTTTTTTAGATTTTCGAA
Found at i:7733 original size:30 final size:30
Alignment explanation
Indices: 7699--7760 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
7689 TTTTGATTTT
* ** *
7699 TTTCGTTTATTTTTTATGTTTAATTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
7729 TTTCGTTTATATTTTAAATTTAATTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
7759 TT
1 TT
7761 ATTTTTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.05, G:0.06, T:0.65
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTCTAA
Found at i:7737 original size:23 final size:23
Alignment explanation
Indices: 7711--7755 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
7701 TCGTTTATTT
*
7711 TTTAT-GTTTAATTTGTAATTTCG
1 TTTATAGTTTAAATT-TAATTTCG
*
7734 TTTATATTTTAAATTTAATTTC
1 TTTATAGTTTAAATTTAATTTC
7756 TAATTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (23 bp):
TTTATAGTTTAAATTTAATTTCG
Found at i:8758 original size:109 final size:109
Alignment explanation
Indices: 8625--9005 Score: 335
Period size: 109 Copynumber: 3.5 Consensus size: 109
8615 AAAAAAATTA
* * ** *
8625 TTTTTTATCAGATAAAAAAAGTGGTGTCGACCAAGCATTGGTTAACACTAGAAAAAAAATTTATC
1 TTTTTTATCAGACAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACAC-AAAAAAAAAATTTATC
* *
8690 TAATAAAAAAGGT-GTGTCGACCAATGTATGG-CTAACACCAAAAT
65 TAATAAAAAAGGTGGTGTCAACCAATGCATGGTC-AACACCAAAAT
* * * *
8734 TTTTTTATCAGACAAAAAAGGTGGTGTCGATCAATACA-TGACCAACACAAAAAAAAAATTTATT
1 TTTTTTATCAGACAAAAAAGGTGGTGTCGACCAA-GCATTGGCCAACACAAAAAAAAAATTTATC
* * *
8798 TGATAAAAAAGGTGGTGTCAATCAATGCATGGTCAACACCAAATT
65 TAATAAAAAAGGTGGTGTCAACCAATGCATGGTCAACACCAAAAT
* * * * * ****
8843 TTTTTTATCAGAGAAAAAAGGTGGTGTCGGCCAAGCATTGGCTAATAC-CAAAATTTTTTTATCT
1 TTTTTTATCAGACAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACAAAAAAAAAATTTATCT
* * ** * ** **
8907 GATAAGAAATGCCGATGTCGGCCAATGCATGACCAACACC-AAAT
66 AATAA-AAAAGGTGGTGTCAACCAATGCATGGTCAACACCAAAAT
* * * *
8951 TTTTTTATCTGATTAAAAAA-GTGGTGTCGACCAATGCA-TGACCAACACCAAAAAA
1 TTTTTTATCAGA-CAAAAAAGGTGGTGTCGACCAA-GCATTGGCCAACACAAAAAAA
9006 TATCATTTTT
Statistics
Matches: 219, Mismatches: 45, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
108 77 0.35
109 139 0.63
110 3 0.01
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (109 bp):
TTTTTTATCAGACAAAAAAGGTGGTGTCGACCAAGCATTGGCCAACACAAAAAAAAAATTTATCT
AATAAAAAAGGTGGTGTCAACCAATGCATGGTCAACACCAAAAT
Found at i:8835 original size:55 final size:55
Alignment explanation
Indices: 8581--8836 Score: 187
Period size: 55 Copynumber: 4.6 Consensus size: 55
8571 GAAAGGAGGG
* * ** * *
8581 AAAGTTGGTGTCGGCCAATGCATGACCAACACCAAAAAAAATTATTTTTTATCAGATAAA
1 AAAGGTGGTGTCGACCAATGCATGGTCAACA-CAAAAAAAA--A--ATTTATCTGATAAA
* * * *
8641 AAAAGTGGTGTCGACCAA-GCATTGGTTAACACTAGAAAAAAAATTTATCTAATAAA
1 AAAGGTGGTGTCGACCAATGCA-TGGTCAACAC-AAAAAAAAAATTTATCTGATAAA
* * **** * *
8697 AAAGGT-GTGTCGACCAATGTATGG-CTAACAC-CAAAATTTTTTTATCAGACAAA
1 AAAGGTGGTGTCGACCAATGCATGGTC-AACACAAAAAAAAAATTTATCTGATAAA
* * ** *
8750 AAAGGTGGTGTCGATCAATACATGACCAACACAAAAAAAAAATTTATTTGATAAA
1 AAAGGTGGTGTCGACCAATGCATGGTCAACACAAAAAAAAAATTTATCTGATAAA
* *
8805 AAAGGTGGTGTCAATCAATGCATGGTCAACAC
1 AAAGGTGGTGTCGACCAATGCATGGTCAACAC
8837 CAAATTTTTT
Statistics
Matches: 152, Mismatches: 37, Indels: 19
0.73 0.18 0.09
Matches are distributed among these distances:
53 20 0.13
54 19 0.12
55 62 0.41
56 18 0.12
58 1 0.01
59 4 0.03
60 28 0.18
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (55 bp):
AAAGGTGGTGTCGACCAATGCATGGTCAACACAAAAAAAAAATTTATCTGATAAA
Found at i:8861 original size:55 final size:54
Alignment explanation
Indices: 8581--9003 Score: 316
Period size: 54 Copynumber: 7.7 Consensus size: 54
8571 GAAAGGAGGG
* * *
8581 AAAGTTGGTGTCGGCCAATGCATGACCAACACCAAAAAAAATTATTTTTTATCAGATAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACC----AAAA-T-TTTTTTATCTGATAAA
* *** * **** *
8641 AAAAGTGGTGTCGACCAA-GCATTGGTTAACACTAGAAAAAAAATTTATCTAATAAA
1 AAAGGTGGTGTCGACCAATGCA-TGACCAACAC--CAAAATTTTTTTATCTGATAAA
* * * * *
8697 AAAGGT-GTGTCGACCAATGTATGGCTAACACCAAAATTTTTTTATCAGACAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAATTTTTTTATCTGATAAA
* * * **** *
8750 AAAGGTGGTGTCGATCAATACATGACCAACACAAAAAAAAAATTTATTTGATAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACAC-CAAAATTTTTTTATCTGATAAA
* * ** * * *
8805 AAAGGTGGTGTCAATCAATGCATGGTCAACACCAAATTTTTTTTATCAGAGAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAATTTTTTTATCTGATAAA
* * * *
8859 AAAGGTGGTGTCGGCCAA-GCATTGGCTAATACCAAAATTTTTTTATCTGATAAGA
1 AAAGGTGGTGTCGACCAATGCA-TGACCAACACCAAAATTTTTTTATCTGATAA-A
* ** * *
8914 AATGCCGATGTCGGCCAATGCATGACCAACACC-AAATTTTTTTATCTGATTAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAATTTTTTTATCTGA-TAAA
8968 AAA-GTGGTGTCGACCAATGCATGACCAACACCAAAA
1 AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAA
9004 AATATCATTT
Statistics
Matches: 281, Mismatches: 71, Indels: 28
0.74 0.19 0.07
Matches are distributed among these distances:
53 48 0.17
54 95 0.34
55 88 0.31
56 21 0.07
58 4 0.01
59 3 0.01
60 22 0.08
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (54 bp):
AAAGGTGGTGTCGACCAATGCATGACCAACACCAAAATTTTTTTATCTGATAAA
Found at i:9328 original size:42 final size:44
Alignment explanation
Indices: 9273--9355 Score: 102
Period size: 42 Copynumber: 1.9 Consensus size: 44
9263 ATATTTTTTT
9273 AAAAATACAAATTTTAG-AATTTTTATAAATATTTTG-AATTTAAA
1 AAAAATACAAATTTTAGAAATTTTT-T-AATATTTTGTAATTTAAA
* *
9317 AAAAAT-C-AATTTTTGAAATTTTTTAGTATTTTGTAATTT
1 AAAAATACAAATTTTAGAAATTTTTTAATATTTTGTAATTT
9356 TTGTTAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
41 8 0.23
42 13 0.37
43 8 0.23
44 6 0.17
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.48
Consensus pattern (44 bp):
AAAAATACAAATTTTAGAAATTTTTTAATATTTTGTAATTTAAA
Found at i:10496 original size:21 final size:21
Alignment explanation
Indices: 10454--10496 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
10444 CCAACTCAAC
*
10454 TAATGTCTCAGCTGCTGCTTT
1 TAATGTCTCAGCTGCAGCTTT
* * *
10475 TAATGTTTCAGCTTCAGGTTT
1 TAATGTCTCAGCTGCAGCTTT
10496 T
1 T
10497 CTGCTCTTGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.47
Consensus pattern (21 bp):
TAATGTCTCAGCTGCAGCTTT
Found at i:15377 original size:20 final size:20
Alignment explanation
Indices: 15354--15393 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
15344 AGTAAAAGGT
15354 TTATCAAAAAAATATAAAAA
1 TTATCAAAAAAATATAAAAA
** *
15374 TTATTGAAAATATATAAAAA
1 TTATCAAAAAAATATAAAAA
15394 AATTTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (20 bp):
TTATCAAAAAAATATAAAAA
Found at i:15412 original size:21 final size:21
Alignment explanation
Indices: 15380--15450 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
15370 AAAATTATTG
*
15380 AAAA-TATATAAAAAAATTTA
1 AAAATTATTTAAAAAAATTTA
*
15400 AAAATTATTTAAAAAAAGTTACA
1 AAAATTATTTAAAAAAA-TT-TA
**
15423 AAAACTTA-TTAAAAGCA-TTA
1 AAAA-TTATTTAAAAAAATTTA
15443 AAAATTAT
1 AAAATTAT
15451 AAAAATTAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 3 0.07
20 9 0.22
21 12 0.29
22 2 0.05
23 12 0.29
24 3 0.07
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (21 bp):
AAAATTATTTAAAAAAATTTA
Found at i:43771 original size:27 final size:27
Alignment explanation
Indices: 43707--43773 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
43697 CCCCCAACAC
*
43707 AATAATTTTTAATATTTTTAAAAAAATA
1 AATAATTTTTAA-AATTTTAAAAAAATA
* *
43735 ACT-ATATTTAAAATTTTAAAAATAA-A
1 AATAATTTTTAAAATTTTAAAAA-AATA
43761 AATAATTTTTAAA
1 AATAATTTTTAAA
43774 TGTTAACAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
26 13 0.41
27 17 0.53
28 2 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (27 bp):
AATAATTTTTAAAATTTTAAAAAAATA
Found at i:44460 original size:26 final size:25
Alignment explanation
Indices: 44418--44468 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
44408 TTAAAGAGTT
*
44418 AAATTAATTTTTAATTATTTCTAAAA
1 AAATTAATTTTTAATTAATT-TAAAA
44444 AAATTAAATTTTT-ATTAATTTAAAA
1 AAATT-AATTTTTAATTAATTTAAAA
44469 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 11 0.48
27 7 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
AAATTAATTTTTAATTAATTTAAAA
Found at i:44482 original size:16 final size:16
Alignment explanation
Indices: 44441--44485 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
44431 ATTATTTCTA
*
44441 AAAAAATTAAATTTTT
1 AAAAAATTAAAATTTT
** *
44457 ATTAATTTAAAATTTT
1 AAAAAATTAAAATTTT
44473 AAAAAATTAAAAT
1 AAAAAATTAAAAT
44486 GACAAAATTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAAAATTAAAATTTT
Found at i:44810 original size:5 final size:5
Alignment explanation
Indices: 44802--44834 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
44792 TCCAAGCCCC
*
44802 ATACC ATACG ATACG ATACG ATACG ATACG ATA
1 ATACG ATACG ATACG ATACG ATACG ATACG ATA
44835 GGAGAGAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.21
Consensus pattern (5 bp):
ATACG
Found at i:52846 original size:55 final size:54
Alignment explanation
Indices: 52721--52836 Score: 198
Period size: 55 Copynumber: 2.1 Consensus size: 54
52711 AAACATTAAC
*
52721 TTTAAAAAACTAAAAAGAATGAGAATAAAAAATGAAAAACAAAAAACAGAAAATT
1 TTTAAAAAACTAAAAAAAATGAGAATAAAAAATGAAAAACAAAAAACAG-AAATT
*
52776 TTTAAAAAACTAAAAAAAATGTGAATAAAAAATGAAAAACAAAAAACAG-AATT
1 TTTAAAAAACTAAAAAAAATGAGAATAAAAAATGAAAAACAAAAAACAGAAATT
52829 TTTAAAAA
1 TTTAAAAA
52837 TTTTAAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
53 12 0.20
55 47 0.80
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.19
Consensus pattern (54 bp):
TTTAAAAAACTAAAAAAAATGAGAATAAAAAATGAAAAACAAAAAACAGAAATT
Found at i:53089 original size:105 final size:105
Alignment explanation
Indices: 52907--53120 Score: 385
Period size: 105 Copynumber: 2.0 Consensus size: 105
52897 ATTAGATTGA
* * * *
52907 GAATTAATTGAGGTATTGGTTCGGTGAGAGGTAAATATTGTTTCACCTGTAAATCAACATAAATT
1 GAATTAATCGAGGTATTGGTTCGGTGAGAGGTAAATAATGTTTCACCCGTAAACCAACATAAATT
52972 GGTTGAATCAATTTCGAATTAATCTAACCAATTGATTTTC
66 GGTTGAATCAATTTCGAATTAATCTAACCAATTGATTTTC
53012 GAATTAATCGAGGTATTGGTTCGGTGAGAGGTAAATAATGTTTCACCCGTAAACCAACATAAATT
1 GAATTAATCGAGGTATTGGTTCGGTGAGAGGTAAATAATGTTTCACCCGTAAACCAACATAAATT
53077 GGTTGAATCAATTTCGAATTAATCTAACCAATTGATTTTC
66 GGTTGAATCAATTTCGAATTAATCTAACCAATTGATTTTC
53117 -AATT
1 GAATT
53121 CCGACTAGTT
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
104 4 0.04
105 101 0.96
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (105 bp):
GAATTAATCGAGGTATTGGTTCGGTGAGAGGTAAATAATGTTTCACCCGTAAACCAACATAAATT
GGTTGAATCAATTTCGAATTAATCTAACCAATTGATTTTC
Found at i:54693 original size:12 final size:12
Alignment explanation
Indices: 54676--54700 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54666 CATAATATTT
54676 TAAAATTTAATA
1 TAAAATTTAATA
54688 TAAAATTTAATA
1 TAAAATTTAATA
54700 T
1 T
54701 TAATTACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAATTTAATA
Found at i:56016 original size:6 final size:6
Alignment explanation
Indices: 56001--56044 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
55991 ATATCCGGTA
*
56001 CCAT-G CCATCG CCATCG CCATCG CCATCG CCATCA CCATCG CCA
1 CCATCG CCATCG CCATCG CCATCG CCATCG CCATCG CCATCG CCA
56045 AGCCTTTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.20, C:0.50, G:0.14, T:0.16
Consensus pattern (6 bp):
CCATCG
Found at i:60754 original size:19 final size:21
Alignment explanation
Indices: 60730--60770 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
60720 GTTTTAAATG
*
60730 TTTAC-ATATTT-TATAATTT
1 TTTACAATATTTATAAAATTT
60749 TTTACAATATTTATAAAATTT
1 TTTACAATATTTATAAAATTT
60770 T
1 T
60771 ATAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 6 0.32
21 8 0.42
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTACAATATTTATAAAATTT
Found at i:60771 original size:19 final size:19
Alignment explanation
Indices: 60725--60771 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
60715 TATAAGTTTT
60725 AAATGTTTACATATTTTATA
1 AAAT-TTTACATATTTTATA
**
60745 ATTTTTTACA-ATATTTATA
1 AAATTTTACATAT-TTTATA
60764 AAATTTTA
1 AAATTTTA
60772 TAATTTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 2 0.09
19 18 0.82
20 2 0.09
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (19 bp):
AAATTTTACATATTTTATA
Found at i:65447 original size:29 final size:29
Alignment explanation
Indices: 65414--65469 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
65404 ATTCACTATA
* *
65414 TTGTATTTAAACAAGCCCTTAACCTATTT
1 TTGTAGTTAAACAAACCCTTAACCTATTT
*
65443 TTGTAGTTAAATAAACCCTTAACCTAT
1 TTGTAGTTAAACAAACCCTTAACCTAT
65470 GATTTTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (29 bp):
TTGTAGTTAAACAAACCCTTAACCTATTT
Found at i:75104 original size:6 final size:6
Alignment explanation
Indices: 75093--75117 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
75083 AGGATTTGCA
75093 CCTTTC CCTTTC CCTTTC CCTTTC C
1 CCTTTC CCTTTC CCTTTC CCTTTC C
75118 TCCAAATCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CCTTTC
Found at i:76104 original size:19 final size:19
Alignment explanation
Indices: 76080--76118 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
76070 CATCAAGCAC
76080 TAGTGCTATAATCCGAACA
1 TAGTGCTATAATCCGAACA
76099 TAGTGCTATAATCCGAACA
1 TAGTGCTATAATCCGAACA
76118 T
1 T
76119 CTGCAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (19 bp):
TAGTGCTATAATCCGAACA
Found at i:82787 original size:20 final size:20
Alignment explanation
Indices: 82762--82801 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
82752 TATATAGACT
82762 AATTTTAAAATAATTTTTAG
1 AATTTTAAAATAATTTTTAG
* * *
82782 AATTTTTAATTATTTTTTAG
1 AATTTTAAAATAATTTTTAG
82802 CTTAAATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
AATTTTAAAATAATTTTTAG
Found at i:85822 original size:12 final size:12
Alignment explanation
Indices: 85805--85830 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
85795 AATTTGTTTG
85805 TTGTTTTAATAT
1 TTGTTTTAATAT
85817 TTGTTTTAATAT
1 TTGTTTTAATAT
85829 TT
1 TT
85831 TTAAGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:86493 original size:22 final size:23
Alignment explanation
Indices: 86463--86519 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
86453 TGATATGTTC
* * *
86463 AAATTTATTTTTATT-TTAATTT
1 AAATATATTTTAATTATCAATTT
86485 AAATATATTTTAATTATCAATTT
1 AAATATATTTTAATTATCAATTT
* *
86508 AATTATACTTTA
1 AAATATATTTTA
86520 TAATAATTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
AAATATATTTTAATTATCAATTT
Found at i:86817 original size:19 final size:20
Alignment explanation
Indices: 86793--86845 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
86783 TTTTTTTATT
*
86793 TTTTAATATTAAAAAA-AAA
1 TTTTAAAATTAAAAAATAAA
86812 TTTTAAAATTAAAAAATAAA
1 TTTTAAAATTAAAAAATAAA
86832 -TTT--AATTAAAAAAT
1 TTTTAAAATTAAAAAAT
86846 TCAGTATGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 11 0.34
19 18 0.56
20 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTTAAAATTAAAAAATAAA
Found at i:89986 original size:6 final size:6
Alignment explanation
Indices: 89915--89982 Score: 84
Period size: 6 Copynumber: 11.3 Consensus size: 6
89905 CTAAGCCTAG
* * *
89915 GCCCGA GCACGA GCACGA -TCCGAA GCCCGA GCCCGA GCCCGA GCCCGA
1 GCCCGA GCCCGA GCCCGA GCCCG-A GCCCGA GCCCGA GCCCGA GCCCGA
*
89963 GCCCGA GCCCGA GCTCGA GC
1 GCCCGA GCCCGA GCCCGA GC
89983 TCGATCCTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
5 2 0.04
6 50 0.91
7 3 0.05
ACGTcount: A:0.21, C:0.44, G:0.32, T:0.03
Consensus pattern (6 bp):
GCCCGA
Found at i:90086 original size:27 final size:27
Alignment explanation
Indices: 90056--90115 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
90046 TTCCAGGGTA
* *
90056 GTCAGGCGAT-AAGTATCATACAAGTTG
1 GTCAGGAGATGAA-TATAATACAAGTTG
* *
90083 GTCAGGAGATGCATATAATACGAGTTG
1 GTCAGGAGATGAATATAATACAAGTTG
90110 GTCAGG
1 GTCAGG
90116 GCACGAGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (27 bp):
GTCAGGAGATGAATATAATACAAGTTG
Found at i:90556 original size:28 final size:26
Alignment explanation
Indices: 90525--90587 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
90515 TTTGGTTTGT
* *
90525 GGTTTAGGCTATATGGTTTAGAATTTAA
1 GGTTTAGGCT-TAGGGTTTAG-AGTTAA
* *
90553 GGTTTTGAGCTTAGGGTTTTGAGTTAA
1 GGTTTAG-GCTTAGGGTTTAGAGTTAA
90580 GGTTTAGG
1 GGTTTAGG
90588 GTTACCCAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.03
27 11 0.38
28 14 0.48
29 3 0.10
ACGTcount: A:0.22, C:0.03, G:0.32, T:0.43
Consensus pattern (26 bp):
GGTTTAGGCTTAGGGTTTAGAGTTAA
Found at i:90570 original size:14 final size:13
Alignment explanation
Indices: 90549--90584 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
90539 GGTTTAGAAT
90549 TTAAGGTTTTGAG
1 TTAAGGTTTTGAG
*
90562 CTTAGGGTTTTGAG
1 -TTAAGGTTTTGAG
90576 TTAAGGTTT
1 TTAAGGTTT
90585 AGGGTTACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.19, C:0.03, G:0.31, T:0.47
Consensus pattern (13 bp):
TTAAGGTTTTGAG
Found at i:90732 original size:16 final size:17
Alignment explanation
Indices: 90711--90742 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
90701 AAATCCAAAA
90711 CCTTAAAAA-CCTAAAT
1 CCTTAAAAACCCTAAAT
90727 CCTTAAAAACCCTAAA
1 CCTTAAAAACCCTAAA
90743 CTCAAAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (17 bp):
CCTTAAAAACCCTAAAT
Found at i:90774 original size:24 final size:25
Alignment explanation
Indices: 90707--90774 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 25
90697 CCCTAAATCC
* * *
90707 AAAACCTTAAAAACCTAAATCCTTA
1 AAAACCCTAAAACCCTAAACCCTTA
* *
90732 AAAACCCT-AAACTCAAAACCCTTA
1 AAAACCCTAAAACCCTAAACCCTTA
*
90756 AAAA-TCTAAAACCCTAAAC
1 AAAACCCTAAAACCCTAAAC
90775 TTGTAACTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
23 2 0.06
24 25 0.74
25 7 0.21
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (25 bp):
AAAACCCTAAAACCCTAAACCCTTA
Found at i:90816 original size:22 final size:22
Alignment explanation
Indices: 90758--90817 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
90748 AACCCTTAAA
* *
90758 AATCTAAAACCCTAAA-CTTGT
1 AATCTTAAACCCTAAATCTTAT
* *
90779 AA-CTTTAAATCTTAAATCTTAT
1 AATC-TTAAACCCTAAATCTTAT
90801 AATCTTAAACCCTAAAT
1 AATCTTAAACCCTAAAT
90818 TCTAAACTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.03
21 11 0.37
22 17 0.57
23 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (22 bp):
AATCTTAAACCCTAAATCTTAT
Found at i:90904 original size:26 final size:26
Alignment explanation
Indices: 90875--90934 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
90865 CATCAACGTA
* *
90875 ATTAATTAAATACAAATATAAACATC
1 ATTAATTAAATACAAACATAAAAATC
* * *
90901 ATTAATTTAATATAAACATAAAAATT
1 ATTAATTAAATACAAACATAAAAATC
90927 ATTAATTA
1 ATTAATTA
90935 CGTAATATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (26 bp):
ATTAATTAAATACAAACATAAAAATC
Found at i:94083 original size:31 final size:30
Alignment explanation
Indices: 94048--94113 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
94038 GAATGAAATT
94048 TTTAACATAAAAAAATTAATTTATTTTTTAA
1 TTTAACATAAAAAAATTAATTTATTTTTT-A
* * * *
94079 TTTAACGTATAGAGATTAATTTATTTTTTA
1 TTTAACATAAAAAAATTAATTTATTTTTTA
94109 TTTAA
1 TTTAA
94114 TAAAGAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (30 bp):
TTTAACATAAAAAAATTAATTTATTTTTTA
Found at i:94540 original size:19 final size:19
Alignment explanation
Indices: 94518--94570 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
94508 AAAAAATTAA
94518 ATTTTATATTAATATTTAT
1 ATTTTATATTAATATTTAT
* *
94537 A-TTTATAGTAAATAATTAT
1 ATTTTATA-TTAATATTTAT
*
94556 -TATTATATTAATATT
1 ATTTTATATTAATATT
94571 AAATTAAACC
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTTATATTAATATTTAT
Found at i:96450 original size:30 final size:32
Alignment explanation
Indices: 96406--96470 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 32
96396 TTTTAATAGT
96406 AAAATTACACTTTAAT-TTCTTAAAAATGATAA
1 AAAATTACACTTTAATCTT-TTAAAAATGATAA
*
96438 AAAATTA-A-TTTAATCTTTTAAAAATTATAA
1 AAAATTACACTTTAATCTTTTAAAAATGATAA
96468 AAA
1 AAA
96471 TATAAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 21 0.68
31 3 0.10
32 7 0.23
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (32 bp):
AAAATTACACTTTAATCTTTTAAAAATGATAA
Found at i:96892 original size:9 final size:9
Alignment explanation
Indices: 96878--96907 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
96868 TCGGTCATTG
96878 AATTTTAAA
1 AATTTTAAA
96887 AATTTTAAA
1 AATTTTAAA
96896 AATTTTAAA
1 AATTTTAAA
96905 AAT
1 AAT
96908 AATTATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AATTTTAAA
Found at i:96943 original size:22 final size:22
Alignment explanation
Indices: 96899--96944 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
96889 TTTTAAAAAT
*
96899 TTTAAAAATAATTATTTAATTA
1 TTTAAAAATAATTAGTTAATTA
*
96921 TTTAAAAAT-ATTCGTTAAGTTA
1 TTTAAAAATAATTAGTTAA-TTA
96943 TT
1 TT
96945 AGATTGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
TTTAAAAATAATTAGTTAATTA
Found at i:98486 original size:18 final size:15
Alignment explanation
Indices: 98445--98484 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
98435 TTTTCACTTT
*
98445 TTTTTTCTTCTCTTC
1 TTTTTTCCTCTCTTC
98460 TTTTTTCCTCTCTTC
1 TTTTTTCCTCTCTTC
98475 TTTTTTCCTC
1 TTTTTTCCTC
98485 CTTTGAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTTCCTCTCTTC
Found at i:100620 original size:4 final size:4
Alignment explanation
Indices: 100611--100678 Score: 64
Period size: 4 Copynumber: 16.5 Consensus size: 4
100601 AAATAAACGG
* * *
100611 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * *
100661 GGAA GAAG GAGA GAAA GA
1 GAAA GAAA GAAA GAAA GA
100679 TAATGTGTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
4 44 0.85
5 8 0.15
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:100630 original size:13 final size:13
Alignment explanation
Indices: 100612--100661 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
100602 AATAAACGGG
100612 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
100625 AAAGAAAGAAAG-
1 AAAGAAAGAAAGA
* *
100637 AAAGGAAGAAGGA
1 AAAGAAAGAAAGA
* *
100650 GAGGAAAGAAAG
1 AAAGAAAGAAAG
100662 GAAGAAGGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:100646 original size:29 final size:28
Alignment explanation
Indices: 100613--100678 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
100603 ATAAACGGGA
100613 AAGAAAGAAAGAAAAGAAAGAAAGAAAGG
1 AAGAAAGAAAGAAAAGAAAGAAAG-AAGG
* * * *
100642 AAGAAGGAGAGGAAAGAAAGGAAGAAGG
1 AAGAAAGAAAGAAAAGAAAGAAAGAAGG
100670 AGAGAAAGA
1 A-AGAAAGA
100679 TAATGTGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (28 bp):
AAGAAAGAAAGAAAAGAAAGAAAGAAGG
Found at i:100656 original size:21 final size:21
Alignment explanation
Indices: 100610--100678 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
100600 CAAATAAACG
* *
100610 GGAAAGAAAGAAAGAA-AAGAA
1 GGAAAGAAAGGAAGAAGGAG-A
*
100631 AGAAAGAAAGGAAGAAGGAGA
1 GGAAAGAAAGGAAGAAGGAGA
100652 GGAAAGAAAGGAAGAAGGAGA
1 GGAAAGAAAGGAAGAAGGAGA
100673 -GAAAGA
1 GGAAAGA
100679 TAATGTGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 6 0.14
21 35 0.81
22 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (21 bp):
GGAAAGAAAGGAAGAAGGAGA
Found at i:100752 original size:20 final size:20
Alignment explanation
Indices: 100729--100772 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
100719 TTTAAAATCG
* *
100729 TATTTTATTTATTAA-AATTT
1 TATTTAATTT-TTAACAAATT
100749 TATTTAATTTTTAACAAATT
1 TATTTAATTTTTAACAAATT
100769 TATT
1 TATT
100773 GAAGATGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTAATTTTTAACAAATT
Found at i:103328 original size:4 final size:4
Alignment explanation
Indices: 103319--103362 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
103309 AATAAATCTT
103319 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
103363 AATGATATCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:105412 original size:41 final size:41
Alignment explanation
Indices: 105367--105592 Score: 235
Period size: 41 Copynumber: 5.5 Consensus size: 41
105357 TGAGAAAACA
* *
105367 TCGCTAATGCTCTGATCTTTAGTGGCGCTTCCCCATAAGCG
1 TCGCTAATGCTCTGACCTTTAGTGGCGCTTCCCCACAAGCG
* * ** * *
105408 TCGCTAATGCTTTGACTTTTACCGACGCTTCCCTACAAGCG
1 TCGCTAATGCTCTGACCTTTAGTGGCGCTTCCCCACAAGCG
* * *
105449 TCGTTAATGCTCTGATCTTTA-TCGGCGCTTCCTCACAAGCG
1 TCGCTAATGCTCTGACCTTTAGT-GGCGCTTCCCCACAAGCG
* ** *
105490 TCGCTAATGCTC-GACCTTTAGTGGTGCTTTTCCATAAGCG
1 TCGCTAATGCTCTGACCTTTAGTGGCGCTTCCCCACAAGCG
* * *
105530 CTTGCTAATGCTCTGACCTTTAGCGGCGCTTTCCCACAAGCG
1 -TCGCTAATGCTCTGACCTTTAGTGGCGCTTCCCCACAAGCG
105572 -CAGCTAATGCTC-GACCTTTAG
1 TC-GCTAATGCTCTGACCTTTAG
105593 CAGCGCTTAC
Statistics
Matches: 151, Mismatches: 29, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
40 29 0.19
41 98 0.65
42 24 0.16
ACGTcount: A:0.18, C:0.30, G:0.20, T:0.32
Consensus pattern (41 bp):
TCGCTAATGCTCTGACCTTTAGTGGCGCTTCCCCACAAGCG
Found at i:105580 original size:123 final size:122
Alignment explanation
Indices: 105367--105600 Score: 294
Period size: 123 Copynumber: 1.9 Consensus size: 122
105357 TGAGAAAACA
* * *
105367 TCGCTAATGCTCTGATCTTTAGTGGCGCTTCCCCATAAGCGTCGCTAATGCTTTGACTTTTACCG
1 TCGCTAATGCTCTGACCTTTAGTGGCGCTTCCCCATAAGCGTCGCTAATGCTCTGACCTTTACCG
* * * *
105432 ACGCTTCCCTACAAGCGTCGTTAATGCTCTGATCTTTATCGGCGCTTCCTCACAAGCG
66 ACGCTTCCCTACAAGCGTCGCTAATGCTC-GACCTTTAGCAGCGCTTCCTCACAAGCG
* ** * *
105490 TCGCTAATGCTC-GACCTTTAGTGGTGCTTTTCCATAAGCGCTTGCTAATGCTCTGACCTTTAGC
1 TCGCTAATGCTCTGACCTTTAGTGGCGCTTCCCCATAAGCG-TCGCTAATGCTCTGACCTTTACC
*
105554 GGCGCTTTCCC-ACAAGCG-CAGCTAATGCTCGACCTTTAGCAGCGCTT
65 GACGC-TTCCCTACAAGCGTC-GCTAATGCTCGACCTTTAGCAGCGCTT
105601 ACTAATGCTC
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
122 39 0.41
123 51 0.54
124 5 0.05
ACGTcount: A:0.18, C:0.30, G:0.21, T:0.32
Consensus pattern (122 bp):
TCGCTAATGCTCTGACCTTTAGTGGCGCTTCCCCATAAGCGTCGCTAATGCTCTGACCTTTACCG
ACGCTTCCCTACAAGCGTCGCTAATGCTCGACCTTTAGCAGCGCTTCCTCACAAGCG
Found at i:105606 original size:27 final size:27
Alignment explanation
Indices: 105575--105627 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
105565 ACAAGCGCAG
105575 CTAATGCTCGACCTTTAGCAGCGCTTA
1 CTAATGCTCGACCTTTAGCAGCGCTTA
105602 CTAATGCTCGACCTTTAGCAGCGCTT
1 CTAATGCTCGACCTTTAGCAGCGCTT
105628 TTCCATAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (27 bp):
CTAATGCTCGACCTTTAGCAGCGCTTA
Found at i:119355 original size:61 final size:61
Alignment explanation
Indices: 119280--119401 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
119270 AAAATGAAAA
* *
119280 CTATATGCCAAAATTCCTATGTTACCCCCTACACTTTAGAAAACACATTGTCCTCAATGTG
1 CTATATGCCAAAATTCCTATGTTACCCCCCACACTTTAAAAAACACATTGTCCTCAATGTG
119341 CTATATGCCAAAATTCCTATGTTACCCCCCACACTTTAAAAAACACATTGTCCTCAATGTG
1 CTATATGCCAAAATTCCTATGTTACCCCCCACACTTTAAAAAACACATTGTCCTCAATGTG
119402 TAGCCCTATA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.30
Consensus pattern (61 bp):
CTATATGCCAAAATTCCTATGTTACCCCCCACACTTTAAAAAACACATTGTCCTCAATGTG
Found at i:121271 original size:41 final size:41
Alignment explanation
Indices: 121222--121358 Score: 220
Period size: 41 Copynumber: 3.3 Consensus size: 41
121212 AAGACTTTTG
121222 TCTCGAGATGAGAATGAGACTATGAATAAGGAAGACTCATT
1 TCTCGAGATGAGAATGAGACTATGAATAAGGAAGACTCATT
* * * *
121263 TCTTGAGATGAGAATGAGATTATGAATAAGAAAGACTTATT
1 TCTCGAGATGAGAATGAGACTATGAATAAGGAAGACTCATT
*
121304 TCTCGAGATGAGAATGAGACTATGAATAAGGAAGACTCATG
1 TCTCGAGATGAGAATGAGACTATGAATAAGGAAGACTCATT
*
121345 TCTCAAGATGAGAA
1 TCTCGAGATGAGAA
121359 AGAGCATATG
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (41 bp):
TCTCGAGATGAGAATGAGACTATGAATAAGGAAGACTCATT
Found at i:128250 original size:41 final size:41
Alignment explanation
Indices: 128198--128369 Score: 218
Period size: 41 Copynumber: 4.2 Consensus size: 41
128188 TGTATAAATA
*
128198 GAAGACTCATGTCTCGAGATAAGAATGAGACTATGAATAAG
1 GAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAAG
*
128239 GAAGACTCATGTCTCAAGATGAGAATGAGACTATGAATAAG
1 GAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAAG
* * * * * * *
128280 GAAGTCTCATGTCTTGAAATGAGAATGAGATTTTGATTAAA
1 GAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAAG
* * **
128321 GAAGACTCATATCTCGAGATGAGAATGAGAATATGGTTAAAG
1 GAAGACTCATGTCTCGAGATGAGAATGAGACTATGAAT-AAG
128363 GAAGACT
1 GAAGACT
128370 TATGATGCGA
Statistics
Matches: 112, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 103 0.92
42 9 0.08
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.25
Consensus pattern (41 bp):
GAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAAG
Found at i:132164 original size:36 final size:36
Alignment explanation
Indices: 132109--132236 Score: 193
Period size: 36 Copynumber: 3.6 Consensus size: 36
132099 ATGGCACTCG
** *
132109 GTGCCTAGCAAATATACTGCAATGAATTTGCACCCA
1 GTGCCTAGCGGATAAACTGCAATGAATTTGCACCCA
132145 GTGCCTAGCGGATAAACTGCAATGAATTTGCACCCA
1 GTGCCTAGCGGATAAACTGCAATGAATTTGCACCCA
* * *
132181 GTGCCTAGTGGATAAACTGCAATGAATTTGCGCCTA
1 GTGCCTAGCGGATAAACTGCAATGAATTTGCACCCA
*
132217 GTGCCTAGCTGATAAACTGC
1 GTGCCTAGCGGATAAACTGC
132237 TAGTCAGATT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 84 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (36 bp):
GTGCCTAGCGGATAAACTGCAATGAATTTGCACCCA
Found at i:132591 original size:133 final size:133
Alignment explanation
Indices: 132348--132591 Score: 425
Period size: 133 Copynumber: 1.8 Consensus size: 133
132338 TTAATAAAAT
* * *
132348 TTGCGCCCAGCACTAGTCGAATAAATTGACGAATATGTGCCCAACACTAGTTAGTTAAATTGACG
1 TTGCACCCAGCACTAGTCGAATAAATCGACGAATATGTGCCCAACACTAGTCAGTTAAATTGACG
132413 AACAATAACTGAGCCCAGCTCTAATTGGTTTAACCAACGGTATTGCGTCCAATGTTTAACCAACG
66 AACAATAACTGAGCCCAGCTCTAATTGGTTTAACCAACGGTATTGCGTCCAATGTTTAACCAACG
132478 GTA
131 GTA
* * * *
132481 TTGCACCCAGCTCTAGTCGTATAAATCGACGAATGTGTGCCCAGCACTAGTCAGTTAAATTGACG
1 TTGCACCCAGCACTAGTCGAATAAATCGACGAATATGTGCCCAACACTAGTCAGTTAAATTGACG
132546 AACAATAACTGAGCCCAGCTCTAATTGGTTTAACCAACGGTATTGC
66 AACAATAACTGAGCCCAGCTCTAATTGGTTTAACCAACGGTATTGC
132592 ACCCAACTCT
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 104 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (133 bp):
TTGCACCCAGCACTAGTCGAATAAATCGACGAATATGTGCCCAACACTAGTCAGTTAAATTGACG
AACAATAACTGAGCCCAGCTCTAATTGGTTTAACCAACGGTATTGCGTCCAATGTTTAACCAACG
GTA
Found at i:137642 original size:27 final size:27
Alignment explanation
Indices: 137605--137665 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
137595 AGTACGAGAG
*
137605 AAAATAATAGATTTGTTTGCAAGCATA
1 AAAATAATAGAGTTGTTTGCAAGCATA
137632 AAAATAATAGAGTTGTTTGCAAGCATA
1 AAAATAATAGAGTTGTTTGCAAGCATA
137659 AAAATAA
1 AAAATAA
137666 AAAGATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.30
Consensus pattern (27 bp):
AAAATAATAGAGTTGTTTGCAAGCATA
Found at i:144509 original size:17 final size:17
Alignment explanation
Indices: 144487--144524 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
144477 AAGACGAAAG
144487 ATCCTGGCAGCTTCACA
1 ATCCTGGCAGCTTCACA
144504 ATCCTGGCAGCTTCACA
1 ATCCTGGCAGCTTCACA
144521 ATCC
1 ATCC
144525 CATGCTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.24
Consensus pattern (17 bp):
ATCCTGGCAGCTTCACA
Found at i:156318 original size:20 final size:20
Alignment explanation
Indices: 156290--156330 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
156280 TTATGAACAA
156290 CATCACTT-ACTAAATTCATT
1 CATCACTTAACTAAA-TCATT
*
156310 CATCTCTTAACTAAATCATT
1 CATCACTTAACTAAATCATT
156330 C
1 C
156331 TAATAAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (20 bp):
CATCACTTAACTAAATCATT
Found at i:168514 original size:25 final size:25
Alignment explanation
Indices: 168459--168844 Score: 353
Period size: 25 Copynumber: 15.3 Consensus size: 25
168449 ACAGAGTTTA
* *
168459 GCTCTTATGAGCCTAGATAGAATATC
1 GCTCTTACGAGCC-AGACAGAATATC
* * ** *
168485 ACTCTTACAAGCCAGTTAGAACATC
1 GCTCTTACGAGCCAGACAGAATATC
* ** *
168510 GCTCTTACAAGCCAGTTAGAACATC
1 GCTCTTACGAGCCAGACAGAATATC
168535 GCTCTTACGAGCCAGACAGAATATC
1 GCTCTTACGAGCCAGACAGAATATC
* * *
168560 GCTCTTACGATCCAGAAAAAATATC
1 GCTCTTACGAGCCAGACAGAATATC
* * ** *
168585 ACTCTTATGAGCCA-ATCAGAACGTT
1 GCTCTTACGAGCCAGA-CAGAATATC
*
168610 GCTCTTACGAGCCAGACAAAATATC
1 GCTCTTACGAGCCAGACAGAATATC
*
168635 GCTCTTACGAGCCAGATAGAATATC
1 GCTCTTACGAGCCAGACAGAATATC
* ** *
168660 GCTCTTACGAGCTAGTTAGAACATC
1 GCTCTTACGAGCCAGACAGAATATC
* * * *
168685 GCCCTTACGAGCTAGTCAGAACATC
1 GCTCTTACGAGCCAGACAGAATATC
* *
168710 GCTCTATTTCGAGCCAGACAGAATATT
1 GCTC--TTACGAGCCAGACAGAATATC
* * *
168737 GCTCTTATGAGCCAAACAGAATATT
1 GCTCTTACGAGCCAGACAGAATATC
* *
168762 GCTCTTACAAGCCA-ATCAGAACATC
1 GCTCTTACGAGCCAGA-CAGAATATC
* *
168787 ACTCTTACGAGCCAGATAGAATATC
1 GCTCTTACGAGCCAGACAGAATATC
* *
168812 GCTCTTACGAGCCAAACATAATATC
1 GCTCTTACGAGCCAGACAGAATATC
168837 GCTCTTAC
1 GCTCTTAC
168845 AAACCAGAGT
Statistics
Matches: 299, Mismatches: 55, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
24 2 0.01
25 265 0.89
26 12 0.04
27 20 0.07
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (25 bp):
GCTCTTACGAGCCAGACAGAATATC
Found at i:168846 original size:75 final size:75
Alignment explanation
Indices: 168459--168844 Score: 396
Period size: 75 Copynumber: 5.1 Consensus size: 75
168449 ACAGAGTTTA
* * * * * * *
168459 GCTCTTATGAGCCTAGATAGAATATCACTCTTACAAGCCAGTTAGAACATCGCTCTTACAAGCCA
1 GCTCTTACGAGCC-AGACAGAATATCGCTCTTACGAGCCAGATAGAATATCGCTCTTACGAGCCA
* *
168524 GTTAGAACATC
65 ATCAGAACATC
* * * * *
168535 GCTCTTACGAGCCAGACAGAATATCGCTCTTACGATCCAGAAAAAATATCACTCTTATGAGCCAA
1 GCTCTTACGAGCCAGACAGAATATCGCTCTTACGAGCCAGATAGAATATCGCTCTTACGAGCCAA
* *
168600 TCAGAACGTT
66 TCAGAACATC
* * *
168610 GCTCTTACGAGCCAGACAAAATATCGCTCTTACGAGCCAGATAGAATATCGCTCTTACGAGCTAG
1 GCTCTTACGAGCCAGACAGAATATCGCTCTTACGAGCCAGATAGAATATCGCTCTTACGAGCCAA
*
168675 TTAGAACATC
66 TCAGAACATC
* * * * * * * *
168685 GCCCTTACGAGCTAGTCAGAACATCGCTCTATTTCGAGCCAGACAGAATATTGCTCTTATGAGCC
1 GCTCTTACGAGCCAGACAGAATATCGCTC--TTACGAGCCAGATAGAATATCGCTCTTACGAGCC
* * *
168750 AAACAGAATATT
64 AATCAGAACATC
* * *
168762 GCTCTTACAAGCCA-ATCAGAACATCACTCTTACGAGCCAGATAGAATATCGCTCTTACGAGCCA
1 GCTCTTACGAGCCAGA-CAGAATATCGCTCTTACGAGCCAGATAGAATATCGCTCTTACGAGCCA
* * *
168826 AACATAATATC
65 ATCAGAACATC
168837 GCTCTTAC
1 GCTCTTAC
168845 AAACCAGAGT
Statistics
Matches: 254, Mismatches: 53, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
75 183 0.72
76 12 0.05
77 59 0.23
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (75 bp):
GCTCTTACGAGCCAGACAGAATATCGCTCTTACGAGCCAGATAGAATATCGCTCTTACGAGCCAA
TCAGAACATC
Found at i:182401 original size:13 final size:14
Alignment explanation
Indices: 182383--182412 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
182373 GTCAACGCAA
182383 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
182396 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
182410 TCA
1 TCA
182413 ATGTACTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:184259 original size:19 final size:19
Alignment explanation
Indices: 184237--184281 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
184227 TTTTATTAGG
184237 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
184256 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
184275 ATTTAAT
1 ATTTAAT
184282 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:185081 original size:15 final size:16
Alignment explanation
Indices: 185063--185092 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
185053 CACTCCTATT
185063 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
185078 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
185093 TTTTTATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:185100 original size:16 final size:16
Alignment explanation
Indices: 185059--185100 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
185049 TCGACACTCC
185059 TATTTTCTA-TTTCTTT
1 TATTTT-TATTTTCTTT
* *
185075 TAATTCTATTTTCTTT
1 TATTTTTATTTTCTTT
185091 TATTTTTATT
1 TATTTTTATT
185101 GTTTCCCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTATTTTCTTT
Found at i:186562 original size:21 final size:21
Alignment explanation
Indices: 186538--186581 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
186528 GAATTTCAGC
* *
186538 AGCAATCTATAGATTTTCAAA
1 AGCAAACTATAAATTTTCAAA
*
186559 AGCAAACTGTAAATTTTCAAA
1 AGCAAACTATAAATTTTCAAA
186580 AG
1 AG
186582 AAAATTGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (21 bp):
AGCAAACTATAAATTTTCAAA
Found at i:188668 original size:106 final size:107
Alignment explanation
Indices: 188500--188693 Score: 275
Period size: 106 Copynumber: 1.8 Consensus size: 107
188490 TGTGTTAAAC
* * * *
188500 TGAGTAACCGGGGTGGAGTGCTTGGTTGTCATTTCATTTCGCATCAAAAGGGCTACCACATTC-T
1 TGAGTAACCGGGATGGAGTGCTTGGGTGTCATTTCATTTCGCATCAAAAGGGCCAACACATTCTT
188564 AAACAAAGAAAAAAA-AAAGAAAAAATTGAGAGCATGTTAGGT
66 AAACAAA-AAAAAAAGAAAGAAAAAATTGAGAGCATGTTAGGT
* * **
188606 TGAGTAACCGGGATGGAGTGCTTGGGTGTCATTTCATTTCGCGTCAAAAGGTCCAATGCATTCTT
1 TGAGTAACCGGGATGGAGTGCTTGGGTGTCATTTCATTTCGCATCAAAAGGGCCAACACATTCTT
* *
188671 AAAGAAAAAAAAAAGAGAGAAAA
66 AAACAAAAAAAAAAGAAAGAAAA
188694 TCGACAAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
106 62 0.82
107 14 0.18
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (107 bp):
TGAGTAACCGGGATGGAGTGCTTGGGTGTCATTTCATTTCGCATCAAAAGGGCCAACACATTCTT
AAACAAAAAAAAAAGAAAGAAAAAATTGAGAGCATGTTAGGT
Found at i:189278 original size:19 final size:19
Alignment explanation
Indices: 189256--189300 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
189246 TTTTATTAGG
189256 ATTTAATATTTAATATAT-T
1 ATTTAATATTTAA-ATATGT
* *
189275 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
189294 ATTTAAT
1 ATTTAAT
189301 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:189285 original size:26 final size:25
Alignment explanation
Indices: 189239--189291 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
189229 TTTATTTTAA
189239 AATATATTTTTATTAGGATTTAATATTT
1 AATATATTTTTATT--GATTTAA-ATTT
189267 AATATATTATTTATT-ATTTAAATTT
1 AATATATT-TTTATTGATTTAAATTT
189292 GTATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.17
26 6 0.25
28 8 0.33
29 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
AATATATTTTTATTGATTTAAATTT
Found at i:194076 original size:7 final size:7
Alignment explanation
Indices: 194064--194089 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
194054 TCATCCCATT
194064 TTCTTTC
1 TTCTTTC
194071 TTCTTTC
1 TTCTTTC
194078 TTCTTTC
1 TTCTTTC
194085 TTCTT
1 TTCTT
194090 CACACGACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTTC
Found at i:201161 original size:41 final size:41
Alignment explanation
Indices: 201114--201245 Score: 147
Period size: 41 Copynumber: 3.2 Consensus size: 41
201104 TTGTATAAAT
* * *
201114 GGAAGACTTATGTCTCGAGATAAGAATGAGATTATGAATAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATTAA
* * * *
201155 GGAAGACTCGTGTCTCAAAATGAGAATGAGATTTTGATTAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATTAA
* * * * *
201196 GAAAGACTCATGTCTTGAGTTGAGAATGAGAATATGGTTAAA
1 GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT-AA
201238 GGAAGACT
1 GGAAGACT
201246 TATGACTCAA
Statistics
Matches: 73, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
41 64 0.88
42 9 0.12
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.27
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATTAA
Found at i:207704 original size:13 final size:14
Alignment explanation
Indices: 207686--207715 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
207676 GTCAACACAA
207686 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
207699 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
207713 TCA
1 TCA
207716 ATGTATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:210145 original size:25 final size:26
Alignment explanation
Indices: 210106--210157 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
210096 TGATTTAATT
* *
210106 AGTAGAGGGTGAGAG-AGGTGACACC
1 AGTAGAGAGTAAGAGAAGGTGACACC
210131 AGTAGAGAGTAAGAGAAAGGTGACACC
1 AGTAGAGAGTAAGAG-AAGGTGACACC
210158 TATATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 13 0.57
27 10 0.43
ACGTcount: A:0.38, C:0.12, G:0.38, T:0.12
Consensus pattern (26 bp):
AGTAGAGAGTAAGAGAAGGTGACACC
Found at i:211312 original size:18 final size:19
Alignment explanation
Indices: 211274--211318 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
211264 GAGAGAGACC
* *
211274 AAAAGCATTGTGAGGG-TT
1 AAAAGCATTGAGAGGGATA
*
211292 AAAAGCATTGAGAGTGATA
1 AAAAGCATTGAGAGGGATA
211311 AAAAGCAT
1 AAAAGCAT
211319 GGATTGGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.44, C:0.07, G:0.27, T:0.22
Consensus pattern (19 bp):
AAAAGCATTGAGAGGGATA
Found at i:219506 original size:44 final size:44
Alignment explanation
Indices: 219451--219538 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
219441 GTGATAATGG
219451 TAGGTTTTAGAAGGGTGAATGGATGAATATACAATGGATAAATA
1 TAGGTTTTAGAAGGGTGAATGGATGAATATACAATGGATAAATA
*
219495 TAGGTTTTAGAAGGGTGGATGGATGAATATACAATGGATAAATA
1 TAGGTTTTAGAAGGGTGAATGGATGAATATACAATGGATAAATA
219539 ATGATAGGCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.40, C:0.02, G:0.28, T:0.30
Consensus pattern (44 bp):
TAGGTTTTAGAAGGGTGAATGGATGAATATACAATGGATAAATA
Found at i:220726 original size:45 final size:45
Alignment explanation
Indices: 220670--220759 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
220660 GCTCGCCCTT
* *
220670 CATCCATGCTCACAA-TGCGAGTGTTCGCAACGTGAGTGCTCACAA
1 CATCAATGCTCACAACTGC-AGTGTTCGCAACATGAGTGCTCACAA
* * *
220715 CATCAATGCTCACAACTTCAGTGTTCGCAGCATGAGTTCTCACAA
1 CATCAATGCTCACAACTGCAGTGTTCGCAACATGAGTGCTCACAA
220760 TACTAGTGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 37 0.95
46 2 0.05
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (45 bp):
CATCAATGCTCACAACTGCAGTGTTCGCAACATGAGTGCTCACAA
Found at i:221686 original size:123 final size:122
Alignment explanation
Indices: 221418--221757 Score: 456
Period size: 122 Copynumber: 2.8 Consensus size: 122
221408 TTTTGCTATC
* * * * *
221418 TTTCCTTTTATTTAATATATCATATTAAAATGAAATTATTCCTTTGTAAAAATATATGGAAGGTT
1 TTTCCTTTTATTTAATATCTCATATTAAAATGAAAGTATTCTTTTGGAGAAATATATGGAAGGTT
* * *
221483 TATTAAAACCA-T-TATCATTTCCAAAAGGATATTAGCTTTAATGTTTTAATATTCAA
66 TATTAAAA-CATTATATCCTTTCCAAAAGGATAATAACTTTAATGTTTTAATATTCAA
* *
221539 TTTCCTTTTATTTAATATCTCATATTAAAACGGAAA-TATTCTTTTGGAGAAAGATATGGAAGGT
1 TTTCCTTTTATTTAATATCTCATATTAAAA-TGAAAGTATTCTTTTGGAGAAATATATGGAAGGT
* *
221603 TTATTAAAACATTATATCCTTTCCAAAATGATAATAACTTTTATGTTTTTAATATTCAA
65 TTATTAAAACATTATATCCTTTCCAAAAGGATAATAACTTTAATG-TTTTAATATTCAA
* * * *
221662 TTTCCTTTTATTTAACATCTCATATTAAAATGAAAGTATT-TATTTAGAGATATATATGGAAAG-
1 TTTCCTTTTATTTAATATCTCATATTAAAATGAAAGTATTCT-TTTGGAGAAATATATGGAAGGT
*
221725 TTATCAAAACATTATATCCTTTCCAAAAGGATA
65 TTATTAAAACATTATATCCTTTCCAAAAGGATA
221758 GTAATATCCA
Statistics
Matches: 194, Mismatches: 19, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
120 2 0.01
121 63 0.32
122 66 0.34
123 63 0.32
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (122 bp):
TTTCCTTTTATTTAATATCTCATATTAAAATGAAAGTATTCTTTTGGAGAAATATATGGAAGGTT
TATTAAAACATTATATCCTTTCCAAAAGGATAATAACTTTAATGTTTTAATATTCAA
Found at i:222649 original size:7 final size:7
Alignment explanation
Indices: 222637--222661 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
222627 GATAGTGGTG
222637 TGGATGA
1 TGGATGA
222644 TGGATGA
1 TGGATGA
222651 TGGATGA
1 TGGATGA
222658 TGGA
1 TGGA
222662 ATTGGGGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.44, T:0.28
Consensus pattern (7 bp):
TGGATGA
Found at i:225244 original size:27 final size:27
Alignment explanation
Indices: 225202--225274 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
225192 AGGAGTAATA
* *
225202 TGATTCTGGCTCGAAAGAGCATTATTC
1 TGATTCTGGCTTGAAAGAGCATCATTC
* * *
225229 TGATTCTGACTTGAAAGAGCGTCATTT
1 TGATTCTGGCTTGAAAGAGCATCATTC
225256 TGATTCTGGCTTGAAAGAG
1 TGATTCTGGCTTGAAAGAG
225275 TACGAGCCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (27 bp):
TGATTCTGGCTTGAAAGAGCATCATTC
Found at i:228030 original size:7 final size:7
Alignment explanation
Indices: 228018--228069 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
228008 ACAACATATA
228018 TTTCTTT
1 TTTCTTT
228025 TTTCTTCT
1 TTTCTT-T
*
228033 TTTCTCT
1 TTTCTTT
*
228040 TTTC-CT
1 TTTCTTT
228046 TTTCTTT
1 TTTCTTT
228053 CTTTCTTT
1 -TTTCTTT
228061 TTT-TTT
1 TTTCTTT
228067 TTT
1 TTT
228070 ATAAATGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 12 0.30
7 15 0.38
8 13 0.32
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTCTTT
Found at i:228042 original size:15 final size:15
Alignment explanation
Indices: 228018--228069 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
228008 ACAACATATA
228018 TTTCTTTTTTCTTCT
1 TTTCTTTTTTCTTCT
*
228033 TTTCTCTTTTC--CT
1 TTTCTTTTTTCTTCT
228046 TTTCTTTCTTTCTT-T
1 TTTCTTT-TTTCTTCT
228061 TTT-TTTTTT
1 TTTCTTTTTT
228070 ATAAATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 11 0.34
14 7 0.22
15 14 0.44
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTCTTTTTTCTTCT
Found at i:239674 original size:79 final size:80
Alignment explanation
Indices: 239568--239781 Score: 270
Period size: 79 Copynumber: 2.7 Consensus size: 80
239558 GATTTAACCG
* *
239568 ACTAGAGTTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTAGGTGCTAGGATTTGATGGATA-
1 ACTAGAGTTGGGCTCACATTTGCGGTTTATCTGCTAGGCACTAGGTGCCAGGATTTGATGGATAT
* *
239632 TTATTGGTTAATCTA
66 TTATTAGTTAATCCA
* * * * * *
239647 ACTAGAGTTGGACTCATATTTGGGGTTTAGCTGCTAGGCACTGGGTGCCAGTATTTGATGGATAT
1 ACTAGAGTTGGGCTCACATTTGCGGTTTATCTGCTAGGCACTAGGTGCCAGGATTTGATGGATAT
*
239712 TTGTTAGTTAATCCA
66 TTATTAGTTAATCCA
* * * *
239727 ACTAGAGCTGGGCTCACATTTGCGATTTATTTGCTAGGCACT-GGATGCCATGATT
1 ACTAGAGTTGGGCTCACATTTGCGGTTTATCTGCTAGGCACTAGG-TGCCAGGATT
239782 GTCGGTTTAT
Statistics
Matches: 113, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
79 58 0.51
80 55 0.49
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (80 bp):
ACTAGAGTTGGGCTCACATTTGCGGTTTATCTGCTAGGCACTAGGTGCCAGGATTTGATGGATAT
TTATTAGTTAATCCA
Found at i:239766 original size:80 final size:79
Alignment explanation
Indices: 239568--239781 Score: 275
Period size: 80 Copynumber: 2.7 Consensus size: 79
239558 GATTTAACCG
* * *
239568 ACTAGAGTTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTAGGTGCTAGGATTTGATGGATAT
1 ACTAGAGTTGGGCTCACATTTGCGGTTTATCTGCTAGGCACTGGGTGCCAGGATTTGATGGATAT
* *
239633 TATTGGTTAATCTA
66 TATTAGTTAATCCA
* * * * *
239647 ACTAGAGTTGGACTCATATTTGGGGTTTAGCTGCTAGGCACTGGGTGCCAGTATTTGATGGATAT
1 ACTAGAGTTGGGCTCACATTTGCGGTTTATCTGCTAGGCACTGGGTGCCAGGATTTGATGGATA-
*
239712 TTGTTAGTTAATCCA
65 TTATTAGTTAATCCA
* * * * *
239727 ACTAGAGCTGGGCTCACATTTGCGATTTATTTGCTAGGCACTGGATGCCATGATT
1 ACTAGAGTTGGGCTCACATTTGCGGTTTATCTGCTAGGCACTGGGTGCCAGGATT
239782 GTCGGTTTAT
Statistics
Matches: 113, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
79 56 0.50
80 57 0.50
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (79 bp):
ACTAGAGTTGGGCTCACATTTGCGGTTTATCTGCTAGGCACTGGGTGCCAGGATTTGATGGATAT
TATTAGTTAATCCA
Found at i:243089 original size:122 final size:122
Alignment explanation
Indices: 242801--243169 Score: 456
Period size: 123 Copynumber: 3.0 Consensus size: 122
242791 TTCTGCTATC
* *
242801 TTTCATTTTATTTAATATCTCATATTAAAACAGAATTATTCCTTTATAGAAATATATGGAAGGTT
1 TTTCA-TTTATTTAATATCTCATATTAAAACAGAATTATTCCTTTAAAGAAATATATGGAAAGTT
** *
242866 TATTAAAACCATTATATCCTTTCCAAAACAATATTAACTTCCATGTTTTAATATTCAAT
65 TATTAAAA-CATTATATCCTTTCCAAAAGGATATTAACTTACATGTTTTAATATTCAAT
* * *
242925 TTTCTTTTATTTAATATCTCATATTAAAACAGAAATATTCCTTTAAAGAAATATATGGAATGTTT
1 TTTCATTTATTTAATATCTCATATTAAAACAGAATTATTCCTTTAAAGAAATATATGGAAAGTTT
* * **
242990 ATTAAAACATTTTATCCTTTCCGAAAGGATATTAACTTATTTGTTTTGAATATTCAA-
66 ATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTACATGTTTT-AATATTCAAT
** * * *
243047 TTTCATTTATTTAATATCTCATATTAAAATGGAATTACTCCTTTAGATAAATACATATATATGAA
1 TTTCATTTATTTAATATCTCATATTAAAACAGAATTATTCC-TT---TAAAGA-A-ATATATGGA
* *
243112 AAG-TTATTAAAACATTATATCCTTCCCAAAAGGATATTAA-TATTCATGTTTTAATATT
60 AAGTTTATTAAAACATTATATCCTTTCCAAAAGGATATTAACT-TACATGTTTTAATATT
243170 TAACGAAGTC
Statistics
Matches: 212, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
122 69 0.33
123 75 0.35
124 4 0.02
126 12 0.06
127 42 0.20
128 10 0.05
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (122 bp):
TTTCATTTATTTAATATCTCATATTAAAACAGAATTATTCCTTTAAAGAAATATATGGAAAGTTT
ATTAAAACATTATATCCTTTCCAAAAGGATATTAACTTACATGTTTTAATATTCAAT
Found at i:254072 original size:6 final size:6
Alignment explanation
Indices: 254061--254086 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
254051 GAGCATAAAT
254061 GAAAAG GAAAAG GAAAAG GAAAAG GA
1 GAAAAG GAAAAG GAAAAG GAAAAG GA
254087 TATATGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:256946 original size:33 final size:33
Alignment explanation
Indices: 256908--256979 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
256898 ATCTAATTAT
* *
256908 TTTTTTATCCTTCTTTT-TCACGTTTCTTCTTCG
1 TTTTTTAT-CTTCTTTTCTCACGTTTCTTCTCCA
*
256941 TTTTTTATTTTCTTTTCTCACGTTTCTTCTCCA
1 TTTTTTATCTTCTTTTCTCACGTTTCTTCTCCA
256974 TTTTTT
1 TTTTTT
256980 TTCCAAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 7 0.20
33 28 0.80
ACGTcount: A:0.07, C:0.22, G:0.04, T:0.67
Consensus pattern (33 bp):
TTTTTTATCTTCTTTTCTCACGTTTCTTCTCCA
Found at i:261212 original size:18 final size:18
Alignment explanation
Indices: 261186--261255 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
261176 AAAATCCGGG
*
261186 AAATGATGTTAACATTTG
1 AAATGATGTTAACATTTC
* *
261204 AATTGATGTTAACACTTC
1 AAATGATGTTAACATTTC
**
261222 AAATGATGTTCGCATTTC
1 AAATGATGTTAACATTTC
261240 AAATGATGTTAACATT
1 AAATGATGTTAACATT
261256 GATGGAAATA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (18 bp):
AAATGATGTTAACATTTC
Found at i:261764 original size:72 final size:70
Alignment explanation
Indices: 261674--261855 Score: 242
Period size: 70 Copynumber: 2.6 Consensus size: 70
261664 CAATGTTAAA
* *
261674 CTAGTTTTATCAATAGTTGTTTATGTTTTGTTTTTGGATATTGAATTTATGTTTTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTTGTTTTTGGATATTG-A-GTATGTTCTACTTATTTAT
*
261739 GTGTAAT
64 GTGCAAT
* * *
261746 TTAGTTTTATCAATAGTTGTTTATG-TTTGATTTTTAGATATTGAGTGTGTTCTACTTATTTATG
1 CTAGTTTTATCAATAGTTGTTTATGTTTTG-TTTTTGGATATTGAGTATGTTCTACTTATTTATG
261810 TGCAAT
65 TGCAAT
* * *
261816 CTAATTTTATCAATAGTTGTTTATATTTT-ATTTTGGATAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTTGTTTTTGGATAT
261856 AAAATTTGTT
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
69 9 0.09
70 44 0.45
71 8 0.08
72 36 0.37
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.57
Consensus pattern (70 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTTGTTTTTGGATATTGAGTATGTTCTACTTATTTATGT
GCAAT
Found at i:264299 original size:17 final size:17
Alignment explanation
Indices: 264268--264308 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
264258 CTAAAGTACC
*
264268 ATGACAAATGGAAATACA
1 ATGAC-AATGCAAATACA
*
264286 ATGACAATGCAAATGCA
1 ATGACAATGCAAATACA
264303 ATGACA
1 ATGACA
264309 GTTAAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (17 bp):
ATGACAATGCAAATACA
Found at i:275856 original size:26 final size:26
Alignment explanation
Indices: 275759--275862 Score: 79
Period size: 26 Copynumber: 4.1 Consensus size: 26
275749 ATTCTGGGCG
*
275759 CAATTCT--ACATGCTCATACAGCGA
1 CAATTCTGGACATGCTCATGCAGCGA
* * * * *
275783 CAACTCTGAACATGTTCATGCAACCA
1 CAATTCTGGACATGCTCATGCAGCGA
* * * *
275809 TAATTCTGGACAAGTTTC-TGCAGTGA
1 CAATTCTGGACATG-CTCATGCAGCGA
*
275835 CAATTCTGGACATGCTCATGCAACGA
1 CAATTCTGGACATGCTCATGCAGCGA
275861 CA
1 CA
275863 TTAGTAGTAA
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
24 6 0.10
25 2 0.03
26 48 0.81
27 3 0.05
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
CAATTCTGGACATGCTCATGCAGCGA
Found at i:277483 original size:20 final size:22
Alignment explanation
Indices: 277460--277509 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
277450 AAATATCATA
277460 ATATTAATTAATTTA-AATA-C
1 ATATTAATTAATTTATAATATC
* *
277480 ATATTTATTATTTTATAATATC
1 ATATTAATTAATTTATAATATC
277502 ATACTTAA
1 ATA-TTAA
277510 AATAAACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 13 0.54
21 4 0.17
22 4 0.17
23 3 0.12
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTAATTAATTTATAATATC
Found at i:281963 original size:42 final size:42
Alignment explanation
Indices: 281855--281952 Score: 196
Period size: 42 Copynumber: 2.3 Consensus size: 42
281845 ATAAATTATC
281855 ATATTTTTCATATTATTGTTAAATTAAATTTTATAAAATCTA
1 ATATTTTTCATATTATTGTTAAATTAAATTTTATAAAATCTA
281897 ATATTTTTCATATTATTGTTAAATTAAATTTTATAAAATCTA
1 ATATTTTTCATATTATTGTTAAATTAAATTTTATAAAATCTA
281939 ATATTTTTCATATT
1 ATATTTTTCATATT
281953 TTATAAAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (42 bp):
ATATTTTTCATATTATTGTTAAATTAAATTTTATAAAATCTA
Found at i:284148 original size:15 final size:15
Alignment explanation
Indices: 284128--284158 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
284118 AATCTAAAGT
284128 ATTAATCTAAACTAA
1 ATTAATCTAAACTAA
*
284143 ATTAATCTAAATTAA
1 ATTAATCTAAACTAA
284158 A
1 A
284159 GCCAAAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAATCTAAACTAA
Found at i:284170 original size:27 final size:27
Alignment explanation
Indices: 284136--284199 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
284126 GTATTAATCT
*
284136 AAACTAAATTAATCTAAATTAAAGCCA
1 AAACTAAATTAATCTAAATTAAAGCAA
* *
284163 AAACTAAATTAATCTAAGTTTAAGCAA
1 AAACTAAATTAATCTAAATTAAAGCAA
284190 AAACTAAATT
1 AAACTAAATT
284200 CCAATGCACG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (27 bp):
AAACTAAATTAATCTAAATTAAAGCAA
Found at i:284898 original size:12 final size:12
Alignment explanation
Indices: 284883--284908 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
284873 AATTAAAGAA
284883 ATAATAGCATTC
1 ATAATAGCATTC
284895 ATAATAGCATTC
1 ATAATAGCATTC
284907 AT
1 AT
284909 CATGATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:287633 original size:2 final size:2
Alignment explanation
Indices: 287628--287652 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
287618 CGCGCGCGCG
287628 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
287653 TCTTTCTCTC
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:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:291139 original size:2 final size:2
Alignment explanation
Indices: 291134--291163 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
291124 ACACACACTT
291134 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
291164 CTTTAGTCTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:295068 original size:39 final size:39
Alignment explanation
Indices: 294887--295285 Score: 352
Period size: 39 Copynumber: 10.0 Consensus size: 39
294877 TCATCAGGAA
* *
294887 GATGGCTTCAATCTGCCCAATGATCGGGGTAAGAGATTGG
1 GATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATT-G
* * * *
294927 ATGATGGCTTCAATCTGCCCTATGATCTGGGTAAAAGATTG
1 --GATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * *
294968 GATGATGACTGTAATCTG-CCCATAATTGGGGTAAGAGATTGG
1 GATG--G-CTGCAATCTGCCCCATGATCGGGGTAAGAGATT-G
* *
295010 TTGATGGCTGCAATCTGCCCCATGATTGGGGTAAAAGATTG
1 --GATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTG
* *
295051 GATGGCTGCAATTTGCCCCATGATCGGGATAAGAGATTG
1 GATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTG
** * * * *
295090 GATGATTTTCAATCTGCCCTATAATCGGGGTAAGAGATTA
1 GATG-GCTGCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * *
295130 GATGGCTGCGATTTGCCTCATGATCGGGGTAAGAGATTG
1 GATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * * *
295169 GATGGTTTTCAATCCGCCTCATGATCGGGGTAAGAGATTG
1 GATGG-CTGCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * * *
295209 AATGGCTACGATCTGCCCCATGATCGGGATAAGAGATTG
1 GATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTG
** * * **
295248 CCTGTCTTCAATCTGCCCTC-TGATTAGGGTAAGAGATT
1 GATGGCTGCAATCTGCCC-CATGATCGGGGTAAGAGATT
295286 TAGATGCTTC
Statistics
Matches: 293, Mismatches: 54, Indels: 23
0.79 0.15 0.06
Matches are distributed among these distances:
39 130 0.44
40 65 0.22
41 29 0.10
42 65 0.22
44 4 0.01
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (39 bp):
GATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTG
Found at i:295122 original size:79 final size:79
Alignment explanation
Indices: 294887--295285 Score: 408
Period size: 79 Copynumber: 5.0 Consensus size: 79
294877 TCATCAGGAA
* *
294887 GATGGCTTCAATCTGCCCAATGATCGGGGTAAGAGATTGGATGATGGCTTCAATCTGCCCTATGA
1 GATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGAT--CTTCAATCTGCCCTATGA
*
294952 TCTGGGTAAAAGATTG
64 TCGGGGTAAAAGATTG
* * * * * *
294968 GATGATGACTGTAATCTG-CCCATAATTGGGGTAAGAGATTGGTTGATGGCTGCAATCTGCCCCA
1 GATG--G-CTGCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGAT--CTTCAATCTGCCCTA
*
295032 TGATTGGGGTAAAAGATTG
61 TGATCGGGGTAAAAGATTG
* * * *
295051 GATGGCTGCAATTTGCCCCATGATCGGGATAAGAGATTGGATGATTTTCAATCTGCCCTATAATC
1 GATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATCTTCAATCTGCCCTATGATC
* *
295116 GGGGTAAGAGATTA
66 GGGGTAAAAGATTG
* * * * * *
295130 GATGGCTGCGATTTGCCTCATGATCGGGGTAAGAGATTGGATGGTTTTCAATCCG-CCTCATGAT
1 GATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATCTTCAATCTGCCCT-ATGAT
*
295194 CGGGGTAAGAGATTG
65 CGGGGTAAAAGATTG
* * * * ** * *
295209 AATGGCTACGATCTGCCCCATGATCGGGATAAGAGATTGCCTG-TCTTCAATCTGCCCTCTGATT
1 GATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATCTTCAATCTGCCCTATGATC
* *
295273 AGGGTAAGAGATT
66 GGGGTAAAAGATT
295286 TAGATGCTTC
Statistics
Matches: 270, Mismatches: 42, Indels: 15
0.83 0.13 0.05
Matches are distributed among these distances:
78 28 0.10
79 134 0.50
80 8 0.03
81 30 0.11
83 62 0.23
84 8 0.03
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (79 bp):
GATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATCTTCAATCTGCCCTATGATC
GGGGTAAAAGATTG
Found at i:295223 original size:118 final size:115
Alignment explanation
Indices: 294886--295285 Score: 349
Period size: 118 Copynumber: 3.3 Consensus size: 115
294876 CTCATCAGGA
* *
294886 AGATGGCTTCAATCTGCCCAATGATCGGGGTAAGAGATTGGATGATGGCTTCAATCTGCCCTATG
1 AGATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATT-G--GATGGCTTCAATCTGCCC-ATG
* * *
294951 ATCTGGGTAAAAGATTGGAT-GATGACTGTAATCTGCCCATAATTGGGGTAAGAGATTGGT
62 ATCGGGGTAAGAGATTGGATGGAT-AC-G--ATCTGCCCATAATCGGGGTAAGAGA-T--T
* * * * *
295011 TGATGGCTGCAATCTGCCCCATGATTGGGGTAAAAGATTGGATGGCTGCAATTTGCCCCATGATC
1 AGATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTCAATCTG-CCCATGATC
* * *
295076 GGGATAAGAGATTGGAT-GATTTTCAATCTGCCCTATAATCGGGGTAAGAGATT
65 GGGGTAAGAGATTGGATGGA--TACGATCTGCCC-ATAATCGGGGTAAGAGATT
* * * * *
295129 AGATGGCTGCGATTTGCCTCATGATCGGGGTAAGAGATTGGATGGTTTTCAATCCGCCTCATGAT
1 AGATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGG-CTTCAATCTGCC-CATGAT
* * * *
295194 CGGGGTAAGAGATTGAATGGCTACGATCTGCCCCATGATCGGGATAAGAGATT
64 CGGGGTAAGAGATTGGATGGATACGATCTG-CCCATAATCGGGGTAAGAGATT
* * * **
295247 -GCCTGTCTTCAATCTGCCCTC-TGATTAGGGTAAGAGATT
1 AG-ATGGCTGCAATCTGCCC-CATGATCGGGGTAAGAGATT
295286 TAGATGCTTC
Statistics
Matches: 227, Mismatches: 38, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
117 1 0.00
118 93 0.41
119 32 0.14
120 10 0.04
121 16 0.07
122 35 0.15
123 4 0.02
124 2 0.01
125 34 0.15
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (115 bp):
AGATGGCTGCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTCAATCTGCCCATGATCG
GGGTAAGAGATTGGATGGATACGATCTGCCCATAATCGGGGTAAGAGATT
Found at i:308296 original size:2 final size:2
Alignment explanation
Indices: 308291--308318 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
308281 TTTTTTTTAC
308291 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
308319 TCGGTTTCAT
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:315478 original size:20 final size:21
Alignment explanation
Indices: 315453--315492 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
315443 GCAGGTTTTT
315453 TTTC-TTCATTCTTC-TCTTCC
1 TTTCTTTC-TTCTTCTTCTTCC
315473 TTTCTTTCTTCTTCTTCTTC
1 TTTCTTTCTTCTTCTTCTTC
315493 TGCTTGACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTCTTTCTTCTTCTTCTTCC
Found at i:328743 original size:17 final size:17
Alignment explanation
Indices: 328721--328767 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
328711 TACAATGTAG
*
328721 ATGCAGTGATAATAAAA
1 ATGCAGTGACAATAAAA
*
328738 ATGCAGTGACAATAGAA
1 ATGCAGTGACAATAAAA
*
328755 ATGCAGGGACAAT
1 ATGCAGTGACAAT
328768 TATACTACAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (17 bp):
ATGCAGTGACAATAAAA
Found at i:332389 original size:37 final size:37
Alignment explanation
Indices: 332332--332655 Score: 270
Period size: 37 Copynumber: 8.8 Consensus size: 37
332322 CTCGGGCTAC
* * *
332332 GTGCCTAGTAGGCTTCATGCCGGTGAATTCTGACTAT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAGACTTT
* ** * *
332369 GTGTCTAGTAGGCTTAATGCCGGTGTATTCAGCCTTT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAGACTTT
* *** * *
332406 GTACCTAGTAGGCTTCGTGCCAAAGAATTCAAACTGT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAGACTTT
* * * ** *
332443 GTGTCTAATAGGCTTCGTGACGGTGTCTTCAGGCTTT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAGACTTT
* * * * * *
332480 GTGCCTAATAGGCATGGTGCCGGTGAATCCAAACTAT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAGACTTT
* * * * *
332517 GTGTCTAGTAGGCTTTGTGTCGGTGTATTCAGGCTTT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAGACTTT
* * ** *
332554 GTACCTAGTAGGTTTCGTGCCAATGAATTCAGACTGT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAGACTTT
* * * *
332591 GTGTCTAGTAGGCTTCATGCCGGTGTATTCAGGCTTT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAGACTTT
* *
332628 GTGCCTAGTAGGCTTGGTGTCGGTGAAT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAAT
332656 CAAGAAGGAA
Statistics
Matches: 214, Mismatches: 73, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
37 214 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (37 bp):
GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAGACTTT
Found at i:332603 original size:148 final size:148
Alignment explanation
Indices: 332349--332656 Score: 463
Period size: 148 Copynumber: 2.1 Consensus size: 148
332339 GTAGGCTTCA
* **
332349 TGCCGGTGAATTCTGACTATGTGTCTAGTAGGCTTAATGCCGGTGTATTCAGCCTTTGTACCTAG
1 TGCCGGTGAATCCAAACTATGTGTCTAGTAGGCTTAATGCCGGTGTATTCAGCCTTTGTACCTAG
* *
332414 TAGGCTTCGTGCCAAAGAATTCAAACTGTGTGTCTAATAGGCTTCGTGACGGTGTCTTCAGGCTT
66 TAGGCTTCGTGCCAAAGAATTCAAACTGTGTGTCTAATAGGCTTCATGACGGTGTATTCAGGCTT
332479 TGTGCCTAATAGGCATGG
131 TGTGCCTAATAGGCATGG
** * *
332497 TGCCGGTGAATCCAAACTATGTGTCTAGTAGGCTTTGTGTCGGTGTATTCAGGCTTTGTACCTAG
1 TGCCGGTGAATCCAAACTATGTGTCTAGTAGGCTTAATGCCGGTGTATTCAGCCTTTGTACCTAG
* * * * *
332562 TAGGTTTCGTGCCAATGAATTCAGACTGTGTGTCTAGTAGGCTTCATGCCGGTGTATTCAGGCTT
66 TAGGCTTCGTGCCAAAGAATTCAAACTGTGTGTCTAATAGGCTTCATGACGGTGTATTCAGGCTT
* *
332627 TGTGCCTAGTAGGCTTGG
131 TGTGCCTAATAGGCATGG
*
332645 TGTCGGTGAATC
1 TGCCGGTGAATC
332657 AAGAAGGAAC
Statistics
Matches: 143, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
148 143 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (148 bp):
TGCCGGTGAATCCAAACTATGTGTCTAGTAGGCTTAATGCCGGTGTATTCAGCCTTTGTACCTAG
TAGGCTTCGTGCCAAAGAATTCAAACTGTGTGTCTAATAGGCTTCATGACGGTGTATTCAGGCTT
TGTGCCTAATAGGCATGG
Found at i:332655 original size:74 final size:74
Alignment explanation
Indices: 332332--332655 Score: 387
Period size: 74 Copynumber: 4.4 Consensus size: 74
332322 CTCGGGCTAC
* ** *
332332 GTGCCTAGTAGGCTTCATGCCGGTGAATTCTGACTATGTGTCTAGTAGGCTTAATGCCGGTGTAT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAAACTATGTGTCTAGTAGGCTTCATGCCGGTGTAT
*
332397 TCAGCCTTT
66 TCAGGCTTT
* *** * * * * *
332406 GTACCTAGTAGGCTTCGTGCCAAAGAATTCAAACTGTGTGTCTAATAGGCTTCGTGACGGTGTCT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAAACTATGTGTCTAGTAGGCTTCATGCCGGTGTAT
332471 TCAGGCTTT
66 TCAGGCTTT
* * * * ** *
332480 GTGCCTAATAGGCATGGTGCCGGTGAATCCAAACTATGTGTCTAGTAGGCTTTGTGTCGGTGTAT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAAACTATGTGTCTAGTAGGCTTCATGCCGGTGTAT
332545 TCAGGCTTT
66 TCAGGCTTT
* * ** * *
332554 GTACCTAGTAGGTTTCGTGCCAATGAATTCAGACTGTGTGTCTAGTAGGCTTCATGCCGGTGTAT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAAACTATGTGTCTAGTAGGCTTCATGCCGGTGTAT
332619 TCAGGCTTT
66 TCAGGCTTT
* *
332628 GTGCCTAGTAGGCTTGGTGTCGGTGAAT
1 GTGCCTAGTAGGCTTCGTGCCGGTGAAT
332656 CAAGAAGGAA
Statistics
Matches: 204, Mismatches: 46, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
74 204 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (74 bp):
GTGCCTAGTAGGCTTCGTGCCGGTGAATTCAAACTATGTGTCTAGTAGGCTTCATGCCGGTGTAT
TCAGGCTTT
Found at i:335672 original size:47 final size:47
Alignment explanation
Indices: 335603--335698 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
335593 GTCCAAGTGA
335603 TAGCCACTTCGATAGATTTTATTCTTTATTTTCTTATTATTTAATTT
1 TAGCCACTTCGATAGATTTTATTCTTTATTTTCTTATTATTTAATTT
335650 TAGCCACTTCGATAGATTTTATTCTTTATTTTCTTATTATTTAATTT
1 TAGCCACTTCGATAGATTTTATTCTTTATTTTCTTATTATTTAATTT
335697 TA
1 TA
335699 TCATGTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.57
Consensus pattern (47 bp):
TAGCCACTTCGATAGATTTTATTCTTTATTTTCTTATTATTTAATTT
Found at i:340729 original size:20 final size:20
Alignment explanation
Indices: 340704--340747 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
340694 ATCTCTTGAG
*
340704 CTATAACAAA-AAAAGTTGTT
1 CTATAA-AAACAAAAGTTATT
340724 CTATAAAAACAAAAGTTATT
1 CTATAAAAACAAAAGTTATT
340744 CTAT
1 CTAT
340748 CAGATCGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (20 bp):
CTATAAAAACAAAAGTTATT
Found at i:342981 original size:20 final size:20
Alignment explanation
Indices: 342956--343002 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
342946 GGCCAACCCG
*
342956 TGTGGCTCCACACACGGTCA
1 TGTGGCTCCACACACGGCCA
*
342976 TGTGGCTCCACACCCGGCCA
1 TGTGGCTCCACACACGGCCA
342996 TGTGGCT
1 TGTGGCT
343003 ACCCTACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.36, G:0.28, T:0.21
Consensus pattern (20 bp):
TGTGGCTCCACACACGGCCA
Found at i:343701 original size:21 final size:21
Alignment explanation
Indices: 343677--343716 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
343667 AATAATAGTT
*
343677 TTTC-ATCTCACTTTTTTTTTC
1 TTTCTATCT-ACTATTTTTTTC
343698 TTTCTATCTACTATTTTTT
1 TTTCTATCTACTATTTTTT
343717 AAATTTCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTCTATCTACTATTTTTTTC
Found at i:352507 original size:18 final size:17
Alignment explanation
Indices: 352482--352558 Score: 66
Period size: 18 Copynumber: 4.2 Consensus size: 17
352472 TAAGAAAATA
352482 TTATTAATATTTTTATT
1 TTATTAATATTTTTATT
*
352499 TTGATTAATATAATTATTATC
1 TT-ATTAATAT--TT-TTATT
* *
352520 TTATTAATGTTATTAGTT
1 TTATTAATATTTTTA-TT
352538 TTATTAA-ATTTTTATGT
1 TTATTAATATTTTTAT-T
352555 TTAT
1 TTAT
352559 ATAACTAGAC
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
16 1 0.02
17 15 0.31
18 17 0.35
20 9 0.19
21 6 0.12
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.62
Consensus pattern (17 bp):
TTATTAATATTTTTATT
Found at i:354751 original size:76 final size:77
Alignment explanation
Indices: 354623--354893 Score: 292
Period size: 76 Copynumber: 3.6 Consensus size: 77
354613 CCAAAAAAAA
* *
354623 ATTCTATTGTATTTTACATCAAT-A-ACATACTTATTTACAATCTACAAAAAAAATTAAAAAAAT
1 ATTCTATTGTATTTTACATCAATAATATATACTTATTTACAATCTA-AGAAAAAATTAAAAAAAT
*
354686 TTGTTTGTTTTGC
65 TTGTTTGTATTGC
* * *
354699 ATTCTATTATATTTTATATCAATAATATATACTTATTTACAATCTATGAAAAAATT--AAAAATT
1 ATTCTATTGTATTTTACATCAATAATATATACTTATTTACAATCTAAGAAAAAATTAAAAAAATT
354762 TGTTTGTATTGC
66 TGTTTGTATTGC
*
354774 ATTCTATTGTATGTCTT-C-TCAATAAT-T-TACTTATTTACAATC-AACGGAAAAAAATGAAAA
1 ATTCTATTGTAT-T-TTACATCAATAATATATACTTATTTACAATCTAA--G-AAAAAATTAAAA
* *
354834 AAA-TTGTTTATATTGT
61 AAATTTGTTTGTATTGC
* * * *
354850 ATTCTACTGTACTTTACATAAAAAATTATATACTTATTTACAAT
1 ATTCTATTGTATTTTACATCAATAA-TATATACTTATTTACAAT
354894 TTACCAAAAA
Statistics
Matches: 165, Mismatches: 16, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
72 1 0.01
73 15 0.09
74 4 0.02
75 46 0.28
76 48 0.29
77 17 0.10
78 20 0.12
79 14 0.08
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (77 bp):
ATTCTATTGTATTTTACATCAATAATATATACTTATTTACAATCTAAGAAAAAATTAAAAAAATT
TGTTTGTATTGC
Found at i:354903 original size:151 final size:151
Alignment explanation
Indices: 354623--354903 Score: 352
Period size: 151 Copynumber: 1.9 Consensus size: 151
354613 CCAAAAAAAA
* *
354623 ATTCTATTGTATTTTACATCAATAACATACTTATTTACAATCTACAAAAAAAATTAAAAAAATTT
1 ATTCTATTGTATTTTACATCAATAACATACTTATTTACAATCAACAAAAAAAATGAAAAAAATTT
* * * * * * * *
354688 GTTTGTTTTGCATTCTATTATATTTTATATCAATAATATATACTTATTTACAATCTATGAAAAAA
66 GTTTATATTGCATTCTACTATACTTTACATAAAAAATATATACTTATTTACAATCTATCAAAAAA
354753 TTAAAAATTTGTTTGTATTGC
131 TTAAAAATTTGTTTGTATTGC
** *
354774 ATTCTATTGTATGTCTT-C-TCAATAATTTACTTATTTACAATCAACGGAAAAAAATGAAAAAAA
1 ATTCTATTGTAT-T-TTACATCAATAACATACTTATTTACAATCAAC-AAAAAAAATGAAAAAAA
* * * *
354837 -TTGTTTATATTGTATTCTACTGTACTTTACATAAAAAATTATATACTTATTTACAATTTACCAA
63 TTTGTTTATATTGCATTCTACTATACTTTACATAAAAAA-TATATACTTATTTACAATCTATCAA
354901 AAA
127 AAA
354904 CTGAGAAGCA
Statistics
Matches: 109, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
151 65 0.60
152 42 0.39
153 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (151 bp):
ATTCTATTGTATTTTACATCAATAACATACTTATTTACAATCAACAAAAAAAATGAAAAAAATTT
GTTTATATTGCATTCTACTATACTTTACATAAAAAATATATACTTATTTACAATCTATCAAAAAA
TTAAAAATTTGTTTGTATTGC
Found at i:356866 original size:11 final size:11
Alignment explanation
Indices: 356850--356896 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
356840 GGGGACCAAT
* *
356850 GAAAAATGAAG
1 GAAAAAAGAAA
356861 GAAAAAAGAAA
1 GAAAAAAGAAA
356872 GAAAAAAG--A
1 GAAAAAAGAAA
356881 GAAAGAAAGAAA
1 GAAA-AAAGAAA
356893 GAAA
1 GAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 5 0.16
10 4 0.13
11 17 0.55
12 5 0.16
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Done.