Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 45 of 91
Found at i:9457647 original size:33 final size:33
Alignment explanation
Indices: 9457596--9457683 Score: 158
Period size: 33 Copynumber: 2.7 Consensus size: 33
9457586 GGAAATGACT
*
9457596 ATCGCAACACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
9457629 ATCGTAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
9457662 ATCGCAACGCGAAATGAAAATC
1 ATCGCAACGCGAAATGAAAATC
9457684 ACAATACGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:9457656 original size:19 final size:19
Alignment explanation
Indices: 9457547--9457683 Score: 114
Period size: 19 Copynumber: 7.6 Consensus size: 19
9457537 TCTTTTGGTT
*
9457547 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
9457566 GAGAATGAAAATTGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
9457586 GGAAATGACTATCGCAACAC
1 -GAAATGAAAATCGCAACGC
9457606 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
9457623 G--A-GAGAATCGTAACGC
1 GAAATGAAAATCGCAACGC
9457639 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
9457656 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
9457672 GAAATGAAAATC
1 GAAATGAAAATC
9457684 ACAATACGAT
Statistics
Matches: 92, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 31 0.34
20 28 0.30
21 2 0.02
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:9457666 original size:14 final size:14
Alignment explanation
Indices: 9457614--9457670 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
9457604 ACGAAATGAA
9457614 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
9457628 AATCGTAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
9457647 AATCGCAACGAGAG
1 AATCGCAACGAGAG
9457661 AATCGCAACG
1 AATCGCAACG
9457671 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:9457736 original size:33 final size:33
Alignment explanation
Indices: 9457699--9457780 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
9457689 ACGATTTTGG
*
9457699 TTTCGCGTTGCGATTATCTTGTTGCAATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCAATTTTCA
* *
9457732 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCAATTTTCA
9457765 TTTCCGCGTTGCGATT
1 TTT-CGCGTTGCGATT
9457781 TTCATTCTCG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 33 0.73
34 12 0.27
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCTCGTTGCAATTTTCA
Found at i:9458356 original size:20 final size:20
Alignment explanation
Indices: 9458333--9458570 Score: 160
Period size: 20 Copynumber: 11.7 Consensus size: 20
9458323 CGATAGTCAG
9458333 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
9458353 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
* *
9458373 AATTCGCATTGCGATTTTCCT
1 -ATTCGCATTGCGATTTACGT
*
9458394 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
*
9458415 AATCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
9458435 ATTCGCATTGCGAATTATGAA
1 ATTCGCATTGCGATTTACG-T
* * *
9458456 AATCGCAATGCGA-ATACGT
1 ATTCGCATTGCGATTTACGT
* * * * *
9458475 AAATCGCAATGCGAATTAAGAAA
1 -ATTCGCATTGCGATTTACG--T
*
9458498 ATT-GCATTGCGATAGT-CAGT
1 ATTCGCATTGCGAT-TTAC-GT
* **
9458518 A-TCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* *
9458538 ATTTGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACGT
9458558 ATTCGCATTGCGA
1 ATTCGCATTGCGA
9458571 ATTGAGAAAA
Statistics
Matches: 174, Mismatches: 32, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.01
20 96 0.55
21 73 0.42
22 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:9458379 original size:21 final size:21
Alignment explanation
Indices: 9458333--9458447 Score: 164
Period size: 20 Copynumber: 5.6 Consensus size: 21
9458323 CGATAGTCAG
*
9458333 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTACCTA
*
9458353 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACCTA
*
9458374 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACCTA
*
9458395 ATTCGCATTGCGATTTACTTA
1 ATTCGCATTGCGATTTACCTA
*
9458416 A-TCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTACCTA
9458435 ATTCGCATTGCGA
1 ATTCGCATTGCGA
9458448 ATTATGAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
19 1 0.01
20 46 0.52
21 41 0.47
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (21 bp):
ATTCGCATTGCGATTTACCTA
Found at i:9458385 original size:41 final size:41
Alignment explanation
Indices: 9458315--9458570 Score: 202
Period size: 41 Copynumber: 6.3 Consensus size: 41
9458305 GCTATGTAAA
** *
9458315 TCGCATTGCGATAGT-CAGATTCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACGTAT
* * *
9458355 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACGT-AT
* **
9458397 TCGCATTGCGATTTACTTAA-TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACGTAT
* * * * * *
9458437 TCGCATTGCGAATTAT-GAAAATCGCAATGCGA-ATACGTAAA
1 TCGCATTGCG-ATTTTCCAAATTCGCATTGCGATTTACGT-AT
* **** *
9458478 TCGCAATGCGAATTAAGAAAATT-GCATTGCGATAGT-CAGTA-
1 TCGCATTGCG-ATTTTCCAAATTCGCATTGCGAT-TTAC-GTAT
* *
9458519 TCGCATTGCGATTTTCCAAATTTGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACGTAT
9458560 TCGCATTGCGA
1 TCGCATTGCGA
9458571 ATTGAGAAAA
Statistics
Matches: 174, Mismatches: 30, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
40 43 0.25
41 102 0.59
42 26 0.15
43 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACGTAT
Found at i:9458467 original size:21 final size:21
Alignment explanation
Indices: 9458437--9458509 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
9458427 ATTTACGTAT
* *
9458437 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
9458458 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTAAGAAAA
9458478 TCGCAATGCGAATTAAGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
9458499 TTGCATTGCGA
1 TCGCAATGCGA
9458510 TAGTCAGTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 18 0.41
21 26 0.59
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:9460203 original size:2 final size:2
Alignment explanation
Indices: 9460196--9460223 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9460186 GTCCACATTT
9460196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9460224 GTTTACAAAT
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):
TA
Found at i:9460387 original size:2 final size:2
Alignment explanation
Indices: 9460382--9460438 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
9460372 ATTTTAAAAA
9460382 AT AT AT -T 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
9460423 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
9460439 TATTTCTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9468095 original size:5 final size:5
Alignment explanation
Indices: 9468087--9468328 Score: 55
Period size: 5 Copynumber: 48.0 Consensus size: 5
9468077 AAAGATACAG
*
9468087 AAAAT -AAA- AAAAT AAAGT AAAGAT AAAA- AATGAAT AAAAT AAAGAT
1 AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AA--AAT AAAAT AAA-AT
* * *
9468133 AAAA- AATGAAT AAAAT -AAAT AAAAT -AAAT ATAAT GAAAT GATAAT
1 AAAAT AA--AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT
* * * *
9468178 AATAAT -ATAT ACATT ATAAAT -AAA- AAAAT AAGAAG AAAAT AAAA-
1 AA-AAT AAAAT AAAAT A-AAAT AAAAT AAAAT AA-AAT AAAAT AAAAT
* * * * * *
9468222 ATAAAT -AAAT -ACAT AAAA- CAAAT ATAAAG GAGAT AAAAT -AAAT AAGAT
1 A-AAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT
* * * * *
9468270 GAAGAT AAAGAAT AAAAAT AAAAAG AAAAT AAAAG AAAAT -AAAC AAAAC
1 -AAAAT -AA-AAT -AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
9468319 AAAAT AAAAT
1 AAAAT AAAAT
9468329 GTATAAATGT
Statistics
Matches: 174, Mismatches: 35, Indels: 56
0.66 0.13 0.21
Matches are distributed among these distances:
4 44 0.25
5 78 0.45
6 43 0.25
7 9 0.05
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:9468123 original size:11 final size:11
Alignment explanation
Indices: 9468109--9468147 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
9468099 TAAAGTAAAG
9468109 ATAAAAAATGA
1 ATAAAAAATGA
*
9468120 ATAAAATAAAG-
1 ATAAAA-AATGA
9468131 ATAAAAAATGA
1 ATAAAAAATGA
9468142 ATAAAA
1 ATAAAA
9468148 TAAATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (11 bp):
ATAAAAAATGA
Found at i:9468129 original size:22 final size:22
Alignment explanation
Indices: 9468097--9468151 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
9468087 AAAATAAAAA
*
9468097 AATAAAGTAAAGATAAAAAATG
1 AATAAAATAAAGATAAAAAATG
9468119 AATAAAATAAAGATAAAAAATG
1 AATAAAATAAAGATAAAAAATG
9468141 AATAAAATAAA
1 AATAAAATAAA
9468152 TAAAATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (22 bp):
AATAAAATAAAGATAAAAAATG
Found at i:9468153 original size:9 final size:9
Alignment explanation
Indices: 9468019--9468328 Score: 107
Period size: 9 Copynumber: 33.0 Consensus size: 9
9468009 AGATAGGGAA
9468019 AAATGAAAAT
1 AAAT-AAAAT
*
9468029 AAATAAAAC
1 AAATAAAAT
* *
9468038 AAAGAAAGT
1 AAATAAAAT
* *
9468047 AAAAAAAAC
1 AAATAAAAT
*
9468056 AAATGAAAT
1 AAATAAAAT
*
9468065 AAAGAAAAT
1 AAATAAAAT
9468074 AAA-AAAGAT
1 AAATAAA-AT
* *
9468083 ACAGAAAAT
1 AAATAAAAT
9468092 AAA-AAAAT
1 AAATAAAAT
9468100 AAAGTAAAGAT
1 AAA-TAAA-AT
9468111 -AA-AAAAT
1 AAATAAAAT
*
9468118 GAATAAAAT
1 AAATAAAAT
9468127 AAAGATAAAAAAT
1 -AA-AT--AAAAT
*
9468140 GAATAAAAT
1 AAATAAAAT
9468149 AAATAAAAT
1 AAATAAAAT
*
9468158 AAATATAAT
1 AAATAAAAT
*
9468167 GAAATGATAAT
1 -AAAT-AAAAT
*
9468178 -AATAATAT
1 AAATAAAAT
* * **
9468186 ATACATTAT
1 AAATAAAAT
9468195 AAATAAAA-
1 AAATAAAAT
*
9468203 AAATAAGAAGA
1 AAATAA-AA-T
9468214 AAATAAAAAT
1 AAAT-AAAAT
9468224 AAAT-AAAT
1 AAATAAAAT
* *
9468232 ACATAAAAC
1 AAATAAAAT
*
9468241 AAATATAAAGG
1 AAATA-AAA-T
*
9468252 AGATAAAAT
1 AAATAAAAT
*
9468261 AAATAAGAT
1 AAATAAAAT
9468270 GAAGATAAAGAAT
1 -AA-AT-AA-AAT
9468283 AAA-AATAA-
1 AAATAA-AAT
*
9468291 AAAGAAAAT
1 AAATAAAAT
*
9468300 AAAAGAAAAT
1 -AAATAAAAT
* *
9468310 AAACAAAACA
1 AAATAAAA-T
9468320 AAATAAAAT
1 AAATAAAAT
9468329 GTATAAATGT
Statistics
Matches: 229, Mismatches: 42, Indels: 59
0.69 0.13 0.18
Matches are distributed among these distances:
7 2 0.01
8 37 0.16
9 107 0.47
10 45 0.20
11 24 0.10
12 7 0.03
13 7 0.03
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:9468154 original size:31 final size:31
Alignment explanation
Indices: 9468024--9468176 Score: 81
Period size: 31 Copynumber: 5.0 Consensus size: 31
9468014 GGGAAAAATG
* * * *
9468024 AAAATAAATAAAACAAAGAAAGTAAA-AAAA
1 AAAATAAATAAAATAAATAAAATAAAGATAA
9468054 ACAAATGAAATAAAGA-AAAT-AAA-AAAGAT-A
1 A-AAAT-AAATAAA-ATAAATAAAATAAAGATAA
* * *
9468084 CAGA-AAATAAAA-AAATAAAGTAAAGATAA
1 AAAATAAATAAAATAAATAAAATAAAGATAA
* * *
9468113 AAAATGAATAAAATAAAGATAAAA-AATGA-AT
1 AAAATAAATAAAAT-AA-ATAAAATAAAGATAA
*
9468144 AAAATAAATAAAATAAATATAATGAAATGATAA
1 AAAATAAATAAAATAAATAAAAT-AAA-GATAA
9468177 TAATAATATA
Statistics
Matches: 92, Mismatches: 16, Indels: 27
0.68 0.12 0.20
Matches are distributed among these distances:
26 5 0.05
27 9 0.10
28 6 0.07
29 10 0.11
30 14 0.15
31 23 0.25
32 18 0.20
33 7 0.08
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.16
Consensus pattern (31 bp):
AAAATAAATAAAATAAATAAAATAAAGATAA
Found at i:9468161 original size:22 final size:22
Alignment explanation
Indices: 9468087--9468266 Score: 74
Period size: 22 Copynumber: 8.1 Consensus size: 22
9468077 AAAGATACAG
** * *
9468087 AAAATAAAAAAATAAAGTAAAG
1 AAAATAAATGAATAAAATAAAT
*
9468109 ATAAA-AAATGAATAAAATAAAG
1 A-AAATAAATGAATAAAATAAAT
9468131 ATAAA-AAATGAATAAAATAAAT
1 A-AAATAAATGAATAAAATAAAT
* *
9468153 AAAATAAATATAATGAAATGATAAT
1 AAAATAAAT-GAATAAAAT-A-AAT
*
9468178 AATAATATAT-ACATTATAAATAAA-
1 AA-AATAAATGA-A-TA-AAATAAAT
* *
9468202 AAAAT-AA-GAAGAAAATAAAA
1 AAAATAAATGAATAAAATAAAT
*
9468222 ATAAATAAAT-ACATAAAACAAAT
1 A-AAATAAATGA-ATAAAATAAAT
*
9468245 ---ATAAAGGAGATAAAATAAAT
1 AAAATAAATGA-ATAAAATAAAT
9468265 AA
1 AA
9468267 GATGAAGATA
Statistics
Matches: 124, Mismatches: 16, Indels: 36
0.70 0.09 0.20
Matches are distributed among these distances:
19 12 0.10
20 13 0.10
21 8 0.06
22 46 0.37
23 21 0.17
24 4 0.03
25 8 0.06
26 8 0.06
27 4 0.03
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.21
Consensus pattern (22 bp):
AAAATAAATGAATAAAATAAAT
Found at i:9468225 original size:29 final size:28
Alignment explanation
Indices: 9468193--9468312 Score: 82
Period size: 29 Copynumber: 4.0 Consensus size: 28
9468183 TATATACATT
9468193 ATAAATAAAAAAATAAGAAGAAAATAAAA
1 ATAAATAAAAAAATAA-AAGAAAATAAAA
* * *
9468222 ATAAATAAATACATAAAACAAATATAAAGGA
1 ATAAATAAAAAAATAAAAGAAA-ATAAA--A
*
9468253 GATAAAATAAATAAGATGAAGATA-AAGAATAAAA
1 -AT-AAATAAA-AAAAT-AA-A-AGAA-AATAAAA
*
9468287 ATAAA-AAGAAAATAAAAGAAAATAAA
1 ATAAATAAAAAAATAAAAGAAAATAAA
9468313 CAAAACAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
27 7 0.10
28 8 0.11
29 21 0.29
30 4 0.05
31 3 0.04
32 5 0.07
33 9 0.12
34 4 0.05
35 2 0.03
36 8 0.11
37 2 0.03
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (28 bp):
ATAAATAAAAAAATAAAAGAAAATAAAA
Found at i:9468366 original size:3 final size:3
Alignment explanation
Indices: 9468358--9468392 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
9468348 AGTAGAATAG
* *
9468358 AAT AAT AAT AAT AAT AAT AAT AAA AAT ATT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9468393 AAGAGTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:9468413 original size:16 final size:18
Alignment explanation
Indices: 9468388--9468433 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 18
9468378 TAAAAATATT
9468388 AATAAAAGAGTAA-TAAA
1 AATAAAAGAGTAAGTAAA
* *
9468405 AA-GAAAGAGAAAGTAAA
1 AATAAAAGAGTAAGTAAA
9468422 AATAAAAGAGTA
1 AATAAAAGAGTA
9468434 TAAGAATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (18 bp):
AATAAAAGAGTAAGTAAA
Found at i:9468477 original size:21 final size:18
Alignment explanation
Indices: 9468438--9468512 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 18
9468428 AGAGTATAAG
9468438 AATAATAATAAATAAATA
1 AATAATAATAAATAAATA
*
9468456 AATAAT-AT--ATATATA
1 AATAATAATAAATAAATA
* **
9468471 TAT-ATAA-AACCAAATA
1 AATAATAATAAATAAATA
*
9468487 GATAATAATAAATAAATA
1 AATAATAATAAATAAATA
9468505 AATAATAA
1 AATAATAA
9468513 CAATAACAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
14 2 0.05
15 9 0.21
16 6 0.14
17 6 0.14
18 20 0.47
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (18 bp):
AATAATAATAAATAAATA
Found at i:9470354 original size:124 final size:124
Alignment explanation
Indices: 9470119--9470701 Score: 722
Period size: 124 Copynumber: 4.7 Consensus size: 124
9470109 AAAATGAAAC
* * * * *
9470119 TGGAAAGCTCATTCGCTGTGAAGTTGAGCTTTGAATTAGATATCCTTCGTCGTGAAGTTGAAATC
1 TGGATAGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
* * * * * * * *
9470184 CAATCTTAAGTTGTATGCTACTTGTGGGCACGATATCCTTCATCGTGAAGTTGAAATAG
66 CAATCTAAAGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCG
* * *
9470243 TGGATAGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATACTTTGTCGTGATGTTGAAATC
1 TGGATAGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
* * *
9470308 CAATATAAAGATGAATGTTGCTGGTGGGCACGATATCATTTGTCGTGAAGTTGAAATCG
66 CAATCTAAAGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCG
* * * * *
9470367 TAGATTA-CCCCTTCGTTGTGAAGTTGAGACTTGAATTGAATATCCTTCATCGTGAAGTTGAAAT
1 TGGA-TAGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAAT
** * * * * * *
9470431 CCAATCTTGAGTTGTATGCTGCTTGTGGGCACGACATCCTTCGTCTTGAAGTTGAAATCG
65 CCAATCTAAAGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCG
* * *
9470491 TGGAT-GGCCACTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTAAAAT
1 TGGATAGCCCA-TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAAT
* *
9470555 CCAATCTAAAGATGAATGTTACTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATTG
65 CCAATCTAAAGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCG
* * * * *
9470615 TGGAT-GTCCCTTTCGTTTTAAAGTTGAGCCTCGAATTGAATATCCTTCGTCGTGAAGTTGAAAT
1 TGGATAG-CCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAAT
* *
9470679 CCAATCTAAGGATGGATGTTGCT
65 CCAATCTAAAGATGAATGTTGCT
9470702 TCGAGTCCAA
Statistics
Matches: 390, Mismatches: 65, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
123 3 0.01
124 383 0.98
125 4 0.01
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (124 bp):
TGGATAGCCCATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
CAATCTAAAGATGAATGTTGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCG
Found at i:9470573 original size:248 final size:247
Alignment explanation
Indices: 9470130--9470685 Score: 821
Period size: 248 Copynumber: 2.2 Consensus size: 247
9470120 GGAAAGCTCA
*
9470130 TTCGCTGTGAAGTTGAGCTTTGAATT-AGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTAAG
1 TTCGTTGTGAAGTTGAGC-TTGAATTGA-ATATCCTTCGTCGTGAAGTTGAAATCCAATCTTAAG
*
9470194 TTGTATGCTACTTGTGGGCACGATATCCTTCATCGTGAAGTTGAAATAGTGGATAGCCCATTCGT
64 TTGTATGCTACTTGTGGGCACGACATCCTTCATCGTGAAGTTGAAATAGTGGATAGCCCATTCGT
** * *
9470259 TGTGAAGTTGAGCCTTGAATTGGATATACTTTGTCGTGATGTTGAAATCCAATATAAAGATGAAT
129 TGTGAAGTTGAGCCTTGAATTGGATATACTTCATCGTGAAGTTAAAATCCAATATAAAGATGAAT
* *
9470324 GTTGCTGGTGGGCACGATATCATTTGTCGTGAAGTTGAAATCGTAGAT-TACCCC
194 GTTACTGGTGGGCACGATATCATTCGTCGTGAAGTTGAAATCGTAGATGT-CCCC
* *
9470378 TTCGTTGTGAAGTTGAGACTTGAATTGAATATCCTTCATCGTGAAGTTGAAATCCAATCTTGAGT
1 TTCGTTGTGAAGTTGAG-CTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTTAAGT
* * * * *
9470443 TGTATGCTGCTTGTGGGCACGACATCCTTCGTCTTGAAGTTGAAATCGTGGAT-GGCCACTTCGT
65 TGTATGCTACTTGTGGGCACGACATCCTTCATCGTGAAGTTGAAATAGTGGATAGCCCA-TTCGT
* *
9470507 TGTGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTAAAATCCAATCTAAAGATGAAT
129 TGTGAAGTTGAGCCTTGAATTGGATATACTTCATCGTGAAGTTAAAATCCAATATAAAGATGAAT
* * * *
9470572 GTTACTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATTGTGGATGTCCCT
194 GTTACTGGTGGGCACGATATCATTCGTCGTGAAGTTGAAATCGTAGATGTCCCC
* * *
9470626 TTCGTTTTAAAGTTGAGCCTCGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCT
1 TTCGTTGTGAAGTTGAG-CTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCT
9470686 AAGGATGGAT
Statistics
Matches: 278, Mismatches: 26, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
247 4 0.01
248 271 0.97
249 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (247 bp):
TTCGTTGTGAAGTTGAGCTTGAATTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTTAAGTT
GTATGCTACTTGTGGGCACGACATCCTTCATCGTGAAGTTGAAATAGTGGATAGCCCATTCGTTG
TGAAGTTGAGCCTTGAATTGGATATACTTCATCGTGAAGTTAAAATCCAATATAAAGATGAATGT
TACTGGTGGGCACGATATCATTCGTCGTGAAGTTGAAATCGTAGATGTCCCC
Found at i:9471597 original size:17 final size:17
Alignment explanation
Indices: 9471577--9471614 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
9471567 CCTAAATATT
9471577 TTTTCTCTTT-TTTGTTC
1 TTTTCT-TTTCTTTGTTC
*
9471594 TTTTCTTTTCTTTTTTC
1 TTTTCTTTTCTTTGTTC
9471611 TTTT
1 TTTT
9471615 TATTCTTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTCTTTGTTC
Found at i:9481809 original size:4 final size:4
Alignment explanation
Indices: 9481800--9481953 Score: 75
Period size: 4 Copynumber: 36.8 Consensus size: 4
9481790 GAAAAAATGA
* * * *
9481800 AAAT AAAT AAAAC AAAG AAAGT AAA- AAA- ATAT AAAT GAAAT AAAGA
1 AAAT AAAT -AAAT AAAT AAA-T AAAT AAAT AAAT AAAT -AAAT AAA-T
* * * *
9481846 AAAT AAAA AAGAT ACAAA AAAT AAAA AAAT AAAGT AAAGAT AAAA AAAT
1 AAAT AAAT AA-AT A-AAT AAAT AAAT AAAT AAA-T -AA-AT AAAT AAAT
* *
9481895 GAAT AAAAT AAAT AAAAT AAAT -AAT -AAT -AAT AATAT ATAT AAAT AAAT
1 AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT
9481943 AAAT AAAT AAA
1 AAAT AAAT AAA
9481954 AATAAGAAGA
Statistics
Matches: 117, Mismatches: 19, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
3 14 0.12
4 68 0.58
5 30 0.26
6 4 0.03
7 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:9481901 original size:18 final size:17
Alignment explanation
Indices: 9481799--9482081 Score: 154
Period size: 18 Copynumber: 16.1 Consensus size: 17
9481789 GGAAAAAATG
*
9481799 AAAATAAATAAAACAAA
1 AAAATAAATAAAATAAA
*
9481816 GAAAGTAAA-AAAATATAA
1 -AAAATAAATAAAATA-AA
*
9481834 ATGAAATAAAGAAAATAAA
1 A--AAATAAATAAAATAAA
9481853 AAAGATACAA-AAAATAAA
1 AAA-ATA-AATAAAATAAA
9481871 AAAATAAAGTAAAGATAAA
1 AAAATAAA-TAAA-ATAAA
*
9481890 AAAATGAATAAAATAAA
1 AAAATAAATAAAATAAA
*
9481907 TAAAATAAATAATAATAAT
1 -AAAATAAATAA-AATAAA
* *
9481926 AATATATAT-AAATAAA
1 AAAATAAATAAAATAAA
* *
9481942 TAAATAAATAAAAATAAG
1 AAAATAAAT-AAAATAAA
*
9481960 AAGA-AAATAAAAATAAA
1 AAAATAAAT-AAAATAAA
*
9481977 AAAATACAT--AA-AAA
1 AAAATAAATAAAATAAA
* ** *
9481991 AATATAAAGGAGATAAA
1 AAAATAAATAAAATAAA
* *
9482008 AAATTAAGATGAAGATACAGA
1 AAAATAA-AT-AAAATA-A-A
*
9482029 ATAA-AAATAAAAATAAA
1 AAAATAAAT-AAAATAAA
9482046 AAGAA-AAGA-AAAATAAA
1 AA-AATAA-ATAAAATAAA
*
9482063 TAAATAAATAAAATAAA
1 AAAATAAATAAAATAAA
9482080 AA
1 AA
9482082 GTAAAAATGT
Statistics
Matches: 207, Mismatches: 33, Indels: 51
0.71 0.11 0.18
Matches are distributed among these distances:
14 9 0.04
15 2 0.01
16 17 0.08
17 62 0.30
18 64 0.31
19 41 0.20
20 9 0.04
21 3 0.01
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (17 bp):
AAAATAAATAAAATAAA
Found at i:9481916 original size:9 final size:9
Alignment explanation
Indices: 9481794--9481994 Score: 136
Period size: 9 Copynumber: 22.6 Consensus size: 9
9481784 AGATAGGAAA
9481794 AAATGAAAAT
1 AAAT-AAAAT
*
9481804 AAATAAAAC
1 AAATAAAAT
* *
9481813 AAAGAAAGT
1 AAATAAAAT
*
9481822 AAAAAAATAT
1 AAATAAA-AT
*
9481832 AAATGAAAT
1 AAATAAAAT
*
9481841 AAAGAAAAT
1 AAATAAAAT
9481850 AAA-AAAGAT
1 AAATAAA-AT
9481859 ACAA-AAAAT
1 A-AATAAAAT
9481868 AAA-AAAAT
1 AAATAAAAT
9481876 AAAGTAAAGAT
1 AAA-TAAA-AT
9481887 AAA-AAAAT
1 AAATAAAAT
*
9481895 GAATAAAAT
1 AAATAAAAT
9481904 AAATAAAAT
1 AAATAAAAT
9481913 AAATAATAAT
1 AAATAA-AAT
*
9481923 -AATAATAT
1 AAATAAAAT
*
9481931 ATAT-AAAT
1 AAATAAAAT
9481939 AAAT-AAAT
1 AAATAAAAT
9481947 AAATAAAA-
1 AAATAAAAT
* *
9481955 ATAAGAAGA-
1 A-AATAAAAT
9481964 AAATAAAAAT
1 AAAT-AAAAT
9481974 AAA-AAAAT
1 AAATAAAAT
*
9481982 ACATAAAA-
1 AAATAAAAT
9481990 AAATA
1 AAATA
9481995 TAAAGGAGAT
Statistics
Matches: 155, Mismatches: 22, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
8 47 0.30
9 79 0.51
10 24 0.15
11 5 0.03
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.18
Consensus pattern (9 bp):
AAATAAAAT
Found at i:9482045 original size:12 final size:12
Alignment explanation
Indices: 9481862--9482089 Score: 71
Period size: 12 Copynumber: 18.5 Consensus size: 12
9481852 AAAAGATACA
9481862 AAAAATAAAAA-
1 AAAAATAAAAAT
*
9481873 AATAAAGTAAAGAT
1 AA-AAA-TAAAAAT
*
9481887 AAAAA-AATGAAT
1 AAAAATAA-AAAT
*
9481899 AAAATAAATAAAAT
1 AAAA-ATA-AAAAT
*
9481913 AAATAATAATAAT
1 AAA-AATAAAAAT
* *
9481926 AATATATATAAAT
1 AA-AAATAAAAAT
*
9481939 AAATAA-ATAAAT
1 AAA-AATAAAAAT
*
9481951 AAAAATAAGAA-
1 AAAAATAAAAAT
*
9481962 GAAAATAAAAAT
1 AAAAATAAAAAT
*
9481974 AAAAA-AATACAT
1 AAAAATAA-AAAT
*
9481986 -AAAA-AAATAT
1 AAAAATAAAAAT
9481996 AAAGGAGATAAAAAAT
1 AAA--A-AT-AAAAAT
* * * *
9482012 TAAGATGAAGAT
1 AAAAATAAAAAT
*
9482024 ACAGAATAAAAAT
1 A-AAAATAAAAAT
9482037 AAAAATAAAAA-
1 AAAAATAAAAAT
* *
9482048 GAAAAGAAAAAT
1 AAAAATAAAAAT
*
9482060 AAATAA-ATAAAT
1 AAA-AATAAAAAT
9482072 -AAAATAAAAAGT
1 AAAAATAAAAA-T
9482084 AAAAAT
1 AAAAAT
9482090 GTGTAAAAAT
Statistics
Matches: 159, Mismatches: 33, Indels: 48
0.66 0.14 0.20
Matches are distributed among these distances:
10 5 0.03
11 40 0.25
12 50 0.31
13 42 0.26
14 13 0.08
15 2 0.01
16 7 0.04
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.19
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:9482061 original size:23 final size:23
Alignment explanation
Indices: 9482031--9482089 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
9482021 GATACAGAAT
9482031 AAAAATAAAAATAAAAAGAAAAG
1 AAAAATAAAAATAAAAAGAAAAG
* * *
9482054 AAAAATAAATAA-ATAAATAAAAT
1 AAAAATAAA-AATAAAAAGAAAAG
9482077 AAAAAGTAAAAAT
1 AAAAA-TAAAAAT
9482090 GTGTAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (23 bp):
AAAAATAAAAATAAAAAGAAAAG
Found at i:9482221 original size:21 final size:21
Alignment explanation
Indices: 9482174--9482224 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
9482164 AAGAAAGAGA
*
9482174 AAGTAAA-AATAAAAGAGTAT
1 AAGTAAATAATAAAAGAATAT
9482194 AAG--AATAATAAAA-AATAAT
1 AAGTAAATAATAAAAGAAT-AT
9482213 AAGTAAATAATA
1 AAGTAAATAATA
9482225 CATACATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 3 0.12
21 7 0.27
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.22
Consensus pattern (21 bp):
AAGTAAATAATAAAAGAATAT
Found at i:9482237 original size:2 final size:2
Alignment explanation
Indices: 9482230--9482256 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9482220 TAATACATAC
9482230 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9482257 ACCAAATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9487150 original size:18 final size:17
Alignment explanation
Indices: 9487127--9487163 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
9487117 TTATGATGTG
*
9487127 AAAATATTATTATTATAA
1 AAAATATAATTATT-TAA
9487145 AAAATATAATTATTTAA
1 AAAATATAATTATTTAA
9487162 AA
1 AA
9487164 GAATTATTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATATAATTATTTAA
Found at i:9487254 original size:17 final size:17
Alignment explanation
Indices: 9487232--9487264 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9487222 TGAGATCACA
9487232 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
9487249 ATATTATATTTTATAT
1 ATATTATATTTTATAT
9487265 AAATAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:9489167 original size:21 final size:21
Alignment explanation
Indices: 9489112--9489168 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
9489102 AATAAGTGTA
* *
9489112 CCGAAGTACCACATATATGTT
1 CCGAAGAACCACATATATGTC
**
9489133 CC-ACAGAATTACATATATGTC
1 CCGA-AGAACCACATATATGTC
*
9489154 CCGAAGGACCACATA
1 CCGAAGAACCACATA
9489169 GAACCCTCGA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (21 bp):
CCGAAGAACCACATATATGTC
Found at i:9495428 original size:15 final size:15
Alignment explanation
Indices: 9495376--9495420 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
9495366 AAAACCATGT
9495376 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
9495391 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
*
9495406 TAGATAAAAATGTAA
1 TAGATAAAAAGGTAA
9495421 GAAATAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.18, T:0.22
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:9495545 original size:21 final size:21
Alignment explanation
Indices: 9495519--9495570 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
9495509 AAATAAATAT
*
9495519 AAAAAATAAAGAAA-AAGAAGA
1 AAAAAATAAAGAAATAA-AACA
*
9495540 AAAAAATATAGAAATAAAACA
1 AAAAAATAAAGAAATAAAACA
*
9495561 AATAAATAAA
1 AAAAAATAAA
9495571 ATAATAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.12
Consensus pattern (21 bp):
AAAAAATAAAGAAATAAAACA
Found at i:9495579 original size:24 final size:24
Alignment explanation
Indices: 9495508--9495620 Score: 72
Period size: 25 Copynumber: 4.5 Consensus size: 24
9495498 AATAGTAAGT
* *
9495508 AAAATAAATATAAA-AAATAAAGAAA
1 AAAATAAATA-AAATATAT-AATAAA
* *
9495533 AAGAAGAAA-AAAATATAGAAATAAA
1 AA-AATAAATAAAATATA-TAATAAA
9495558 ACAAATAAATAAAATA-ATAATAAA
1 A-AAATAAATAAAATATATAATAAA
*
9495582 AAAGTAAA-AATAATATATATATAAA
1 AAAATAAATAA-AATATATA-ATAAA
*
9495607 ATAAAAAAATAAAA
1 A-AAATAAATAAAA
9495621 AAAGTAAATA
Statistics
Matches: 69, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
22 2 0.03
23 10 0.14
24 13 0.19
25 23 0.33
26 19 0.28
27 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (24 bp):
AAAATAAATAAAATATATAATAAA
Found at i:9495593 original size:38 final size:39
Alignment explanation
Indices: 9495504--9495638 Score: 93
Period size: 39 Copynumber: 3.4 Consensus size: 39
9495494 ATAAAATAGT
* * *
9495504 AAGT-AAAATAAATATA-AAAAATAAAGAAAAAGAAGAAAAA
1 AAGTAAAAAT-AATATACAAATA-AAATAAAAA-AATAAAAA
*
9495544 AA-TATAGAAATAA-A-ACAAAT-AAATAAAATAATAATAAAA
1 AAGTA-A-AAATAATATACAAATAAAATAAAAAAAT-A-AAAA
* *
9495583 AAGTAAAAATAATATATATATAAAATAAAAAAATAAAAA
1 AAGTAAAAATAATATACAAATAAAATAAAAAAATAAAAA
*
9495622 AAGTAAATATATATATA
1 AAGTAAAAATA-ATATA
9495639 TATATAATTA
Statistics
Matches: 76, Mismatches: 8, Indels: 22
0.72 0.08 0.21
Matches are distributed among these distances:
37 2 0.03
38 14 0.18
39 24 0.32
40 18 0.24
41 14 0.18
42 4 0.05
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (39 bp):
AAGTAAAAATAATATACAAATAAAATAAAAAAATAAAAA
Found at i:9495597 original size:49 final size:50
Alignment explanation
Indices: 9495509--9495628 Score: 136
Period size: 49 Copynumber: 2.4 Consensus size: 50
9495499 ATAGTAAGTA
9495509 AAATAAATATAAAAAATAAAGAAAAAGAAGAAAAAAATATAGAAATAAAAC
1 AAATAAATA-AAAAAATAAAGAAAAAGAAGAAAAAAATATAGAAATAAAAC
* * * * * *
9495560 AAATAAATAAAATAATAATA-AAAAAGTA-AAAATAATATATATATAAAAT
1 AAATAAATAAAAAAATAA-AGAAAAAGAAGAAAAAAATATAGAAATAAAAC
*
9495609 AAAAAAATAAAAAAAGTAAA
1 AAATAAATAAAAAAA-TAAA
9495629 TATATATATA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
49 31 0.53
50 18 0.31
51 10 0.17
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (50 bp):
AAATAAATAAAAAAATAAAGAAAAAGAAGAAAAAAATATAGAAATAAAAC
Found at i:9495612 original size:30 final size:31
Alignment explanation
Indices: 9495551--9495634 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 31
9495541 AAAAATATAG
*
9495551 AAATAAAACAAA-TAAATAAAATAATAATAAAA
1 AAATAAAA-AAAGTAAAT-ATATAATAATAAAA
* *
9495583 AAGTAAAAATAA-TATATATATAA-AATAAAA
1 AAATAAAAA-AAGTAAATATATAATAATAAAA
9495613 AAATAAAAAAAGTAAATATATA
1 AAATAAAAAAAGTAAATATATA
9495635 TATATATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 2 0.04
30 24 0.53
31 6 0.13
32 13 0.29
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.23
Consensus pattern (31 bp):
AAATAAAAAAAGTAAATATATAATAATAAAA
Found at i:9495623 original size:9 final size:9
Alignment explanation
Indices: 9495507--9495628 Score: 50
Period size: 9 Copynumber: 12.4 Consensus size: 9
9495497 AAATAGTAAG
*
9495507 TAAAATAAA
1 TAAAAAAAA
*
9495516 TATAAAAAA
1 TAAAAAAAA
9495525 TAAAGAAAAA
1 TAAA-AAAAA
*
9495535 GAAGAAAAAA
1 TAA-AAAAAA
* *
9495545 -ATATAGAAA
1 TA-AAAAAAA
*
9495554 TAAAACAAA
1 TAAAAAAAA
9495563 TAAATAAAATAA
1 T-AA-AAAA-AA
9495575 TAATAAAAAA
1 TAA-AAAAAA
9495585 GTAAAAATAATA
1 -TAAAAA-AA-A
*
9495597 TATATATAAAA
1 TA-A-AAAAAA
9495608 T-AAAAAAA
1 TAAAAAAAA
*
9495616 TAAAAAAAG
1 TAAAAAAAA
9495625 TAAA
1 TAAA
9495629 TATATATATA
Statistics
Matches: 88, Mismatches: 12, Indels: 26
0.70 0.10 0.21
Matches are distributed among these distances:
8 6 0.07
9 32 0.36
10 21 0.24
11 20 0.23
12 7 0.08
13 2 0.02
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:9495755 original size:23 final size:21
Alignment explanation
Indices: 9495691--9495766 Score: 61
Period size: 23 Copynumber: 3.6 Consensus size: 21
9495681 ATATATAATC
9495691 TAAAA-AAATAAAAATATATAC-
1 TAAAATAAA-AAAAATAT-TACA
*
9495712 TAAAATAAAAAAGAA-AATACA
1 TAAAATAAAAAA-AATATTACA
9495733 TAAAATGTAAAAAAAATATTACA
1 TAAAA--TAAAAAAAATATTACA
*
9495756 TGAAA-AAAAAA
1 TAAAATAAAAAA
9495767 GAAAAGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
20 9 0.20
21 14 0.30
22 7 0.15
23 16 0.35
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (21 bp):
TAAAATAAAAAAAATATTACA
Found at i:9496101 original size:35 final size:36
Alignment explanation
Indices: 9496031--9496130 Score: 130
Period size: 35 Copynumber: 2.8 Consensus size: 36
9496021 GTGTTTGTAG
* * *
9496031 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGCAAAATTCT
*
9496068 ATCCTATTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
9496103 ATCCTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAG-GAGTTTGAATCCTAG
9496131 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 27 0.48
36 11 0.20
37 18 0.32
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:9496896 original size:106 final size:108
Alignment explanation
Indices: 9496596--9497219 Score: 654
Period size: 109 Copynumber: 5.9 Consensus size: 108
9496586 GTTCCGAGTC
* * * * **
9496596 CAATATCCTCCG-CTGTGAAGTTGAAATTGGTTCTAAAACTGGGAAATTGTTTGTTGACAGTCAG
1 CAATATCCTCCGTC-GTGGAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
* * * *
9496660 CCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-C-
65 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * * * * * *
9496702 TAATATCCTTCG-CTGTGAAGATGAAATTGACTCTG-AA---CGAAA-T-CTTGTTGACAATCAG
1 CAATATCCTCCGTC-GTGGAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG
* *
9496760 CCGTCCCTTCATTATGAAGTTGAACTTGTGTTGTCTCGAGT-C-
65 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * *
9496802 CAATATCCTTCG-C-TGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACAACCA
1 CAATATCCTCCGTCGTG-G-AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCA
9496865 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCA
64 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * ** * *
9496911 CGATATCCTCCGTCGTGGAGTTGAAA-TCGCGAATGAAATT-GAAAAGTTGTTCGTTGACAACCA
1 CAATATCCTCCGTCGTGGAGTTGAAATTGGC-TCTGAAATTGGGAAA-TTGTTTGTTGACAACCA
* *
9496974 GCCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTCGGGTAGCA
64 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * *
9497020 CGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGACAACCAAC
1 CAATATCCTCCGTCGTGGAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGC
*
9497085 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCA
66 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * *
9497129 CGATATCCTCCGTCGTGGAGTTGAAA-TCGATTTCGAAATTGGGAAATTG-TTGTTGGCAACCAG
1 CAATATCCTCCGTCGTGGAGTTGAAATTGGCTCT-GAAATTGGGAAATTGTTTGTTGACAACCAG
9497192 CCGTCCCTTCGTTGTGAAGTTGAACTTG
65 CCGTCCCTTCGTTGTGAAGTTGAACTTG
9497220 ACTCTAGCTA
Statistics
Matches: 449, Mismatches: 51, Indels: 34
0.84 0.10 0.06
Matches are distributed among these distances:
98 2 0.00
100 76 0.17
101 3 0.01
102 4 0.01
104 3 0.01
105 3 0.01
106 81 0.18
108 52 0.12
109 215 0.48
110 8 0.02
111 2 0.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (108 bp):
CAATATCCTCCGTCGTGGAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGC
CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
Found at i:9497890 original size:67 final size:67
Alignment explanation
Indices: 9497791--9497956 Score: 237
Period size: 67 Copynumber: 2.5 Consensus size: 67
9497781 TTCATGAGAA
* *
9497791 ACAAAATTTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAT
1 ACAAAA-TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAA
9497854 GGGAG
63 GGGAG
* *
9497859 ACAAAATTTGTTTCGAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAACTGTCTCAAGGG
1 ACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGG
9497924 AG
66 AG
**
9497926 ACAAAATTTGTTTCAAGGGAAATTATCTCAA
1 ACAAAATTTGTTTCAAGGGAAACAATCTCAA
9497957 GAGAGACGAA
Statistics
Matches: 89, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
65 1 0.01
66 4 0.04
67 78 0.88
68 6 0.07
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (67 bp):
ACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGG
AG
Found at i:9497955 original size:36 final size:36
Alignment explanation
Indices: 9497831--9498307 Score: 264
Period size: 36 Copynumber: 13.9 Consensus size: 36
9497821 AAAGATTTTG
* * *
9497831 TGTTTCAAGAGAAACTGTCTCATGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* ** **
9497867 TGTTTCGAGGGAAACAATCTCAA-AG-G----TTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
9497897 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
9497934 TGTTTCAAGGGAAATTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * *
9497970 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
*
9497998 ATGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAA-TT
*
9498036 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
9498072 CATTTCAAGGGAAA-TGTTTCCA-A-TG-----TTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
9498100 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* *
9498138 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
9498174 CATTTCAA-GGAAAATGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* * *
9498202 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
*
9498240 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
9498276 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
9498308 TGGTGAGCAC
Statistics
Matches: 324, Mismatches: 74, Indels: 86
0.67 0.15 0.18
Matches are distributed among these distances:
28 8 0.02
29 31 0.10
30 18 0.06
31 19 0.06
32 4 0.01
33 4 0.01
34 4 0.01
35 15 0.05
36 122 0.38
37 90 0.28
38 9 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:9498050 original size:37 final size:37
Alignment explanation
Indices: 9497999--9498307 Score: 232
Period size: 37 Copynumber: 8.9 Consensus size: 37
9497989 TCAATGTTTA
*
9497999 TGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAATTT
*
9498036 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
9498072 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
9498100 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
9498138 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * * *
9498174 CATTTCAA-GGAAAATGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
9498202 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
9498240 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
9498276 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
9498308 TGGTGAGCAC
Statistics
Matches: 208, Mismatches: 38, Indels: 52
0.70 0.13 0.17
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 20 0.10
30 12 0.06
32 1 0.00
33 1 0.00
34 1 0.00
35 11 0.05
36 59 0.28
37 86 0.41
38 11 0.05
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:9498071 original size:102 final size:102
Alignment explanation
Indices: 9497898--9498289 Score: 669
Period size: 102 Copynumber: 3.9 Consensus size: 102
9497888 AAAGGTTTTG
* *
9497898 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
9497962 ACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
9497999 TGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
9498064 ACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
9498101 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
9498166 ACAAAACTCATTTCAAGGAAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
9498203 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* **
9498268 ACAAAGTTTGTTTCAAGGGAAA
66 ACAAAATTCATTTCAAGGGAAA
9498290 CTGTCTCAAG
Statistics
Matches: 275, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
101 33 0.12
102 242 0.88
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:9499193 original size:22 final size:22
Alignment explanation
Indices: 9499168--9499218 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
9499158 TTGTGTTTGG
9499168 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
9499190 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
9499212 TCAAAGG
1 TCAAAGG
9499219 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:9499852 original size:20 final size:21
Alignment explanation
Indices: 9499826--9499887 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
9499816 CTTTTTGTTC
*
9499826 CCTTTTTTATTTTTGTTCTTT
1 CCTTTTTTATTCTTGTTCTTT
* *
9499847 -CTTTTTTGTTCTTGTTTTTT
1 CCTTTTTTATTCTTGTTCTTT
*
9499867 CCTTTTTTGCTTCTT-TTCTTT
1 CCTTTTTT-ATTCTTGTTCTTT
9499888 TTTCTTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 12 0.35
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (21 bp):
CCTTTTTTATTCTTGTTCTTT
Found at i:9499898 original size:22 final size:22
Alignment explanation
Indices: 9499844--9499896 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
9499834 ATTTTTGTTC
9499844 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
9499865 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
9499888 TTTCTTTTT
1 TTTCTTTTT
9499897 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:9502913 original size:15 final size:15
Alignment explanation
Indices: 9502895--9502924 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9502885 AAAACCATGT
9502895 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
9502910 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
9502925 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:9502931 original size:15 final size:15
Alignment explanation
Indices: 9502898--9502932 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9502888 ACCATGTTAG
* *
9502898 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
9502913 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
9502928 ATAAA
1 ATAAA
9502933 TAAATAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:9503049 original size:21 final size:21
Alignment explanation
Indices: 9503023--9503074 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
9503013 AAATAAATAT
*
9503023 AAAAAATAAAGAAA-AAGAAGA
1 AAAAAATAAAGAAATAA-AACA
*
9503044 AAAAAATATAGAAATAAAACA
1 AAAAAATAAAGAAATAAAACA
*
9503065 AATAAATAAA
1 AAAAAATAAA
9503075 ATAATAATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.12
Consensus pattern (21 bp):
AAAAAATAAAGAAATAAAACA
Found at i:9503100 original size:23 final size:22
Alignment explanation
Indices: 9503064--9503122 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
9503054 GAAATAAAAC
9503064 AAATAAATAAAATAATA-ATAGA
1 AAATAAA-AAAATAATATATAGA
*
9503086 AAAGTAAAAATAAT-ATATATATA
1 AAA-TAAAAA-AATAATATATAGA
9503109 AAATAAAAAAATAA
1 AAATAAAAAAATAA
9503123 AAAAGTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
21 3 0.09
22 15 0.47
23 14 0.44
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (22 bp):
AAATAAAAAAATAATATATAGA
Found at i:9503110 original size:49 final size:50
Alignment explanation
Indices: 9503013--9503131 Score: 134
Period size: 49 Copynumber: 2.4 Consensus size: 50
9503003 ATAGTAAGTA
9503013 AAATAAATATAAAAAATAAAGAAAAAGAAGAAAAAAATATAGAAATAAAAC
1 AAATAAATA-AAAAAATAAAGAAAAAGAAGAAAAAAATATAGAAATAAAAC
* * * * * *
9503064 AAATAAATAAAATAATAATAG-AAAAGTA-AAAATAATATATATATAAAAT
1 AAATAAATAAAAAAATAA-AGAAAAAGAAGAAAAAAATATAGAAATAAAAC
* *
9503113 AAAAAAATAAAAAAGTAAA
1 AAATAAATAAAAAAATAAA
9503132 TATATATATA
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
48 1 0.02
49 32 0.55
50 14 0.24
51 11 0.19
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (50 bp):
AAATAAATAAAAAAATAAAGAAAAAGAAGAAAAAAATATAGAAATAAAAC
Found at i:9503167 original size:41 final size:38
Alignment explanation
Indices: 9503064--9503185 Score: 108
Period size: 41 Copynumber: 3.1 Consensus size: 38
9503054 GAAATAAAAC
*
9503064 AAATAAATAAAATAATAATAGAAAAGTAAAAATAATATATAT
1 AAAT-AATAAAAT-ATAATA-AAAAGTAAATAT-ATATATAT
9503106 ATAA-AATAAAA-A-AATAAAAAAGTAAATATATATATAT
1 A-AATAATAAAATATAAT-AAAAAGTAAATATATATATAT
*
9503143 AAATTAATAAAACTGATAATAAAAA-TAATATATTTATATAT
1 AAA-TAATAAAA-T-ATAATAAAAAGTAA-ATATATATATAT
9503184 AA
1 AA
9503186 TCTAAAAAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 19
0.77 0.02 0.21
Matches are distributed among these distances:
36 2 0.03
37 9 0.13
38 21 0.30
39 2 0.03
40 3 0.04
41 26 0.38
42 4 0.06
43 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (38 bp):
AAATAATAAAATATAATAAAAAGTAAATATATATATAT
Found at i:9503173 original size:39 final size:34
Alignment explanation
Indices: 9503090--9503197 Score: 103
Period size: 39 Copynumber: 3.0 Consensus size: 34
9503080 AATAGAAAAG
9503090 TAAAAATAATATATATATA-AAATAAAAAAATAA
1 TAAAAATAATATATATATATAAATAAAAAAATAA
*
9503123 -AAAAGTAAATATATATATATAAATTAATAAAACTGATAA
1 TAAAAAT-AATATATATATATAAA-TAA-AAAA---ATAA
* *
9503162 TAAAAATAATATATTTATATATAATCTAAAAAATAA
1 TAAAAATAATATATATATATA-AAT-AAAAAAATAA
9503198 AATATACTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
32 5 0.08
33 12 0.20
34 3 0.05
35 3 0.05
36 8 0.13
39 22 0.36
40 8 0.13
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (34 bp):
TAAAAATAATATATATATATAAATAAAAAAATAA
Found at i:9503202 original size:21 final size:21
Alignment explanation
Indices: 9503178--9503244 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 21
9503168 TAATATATTT
** *
9503178 ATATATAATCTAAAAAATAAA
1 ATATATAAAATAAAAAAGAAA
9503199 ATATACTAAAATAAAAAAGAAA
1 ATATA-TAAAATAAAAAAGAAA
* **
9503221 ATACATAAAATGTAAAA-AAA
1 ATATATAAAATAAAAAAGAAA
9503241 ATAT
1 ATAT
9503245 TACATGAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 6 0.16
21 15 0.39
22 17 0.45
ACGTcount: A:0.69, C:0.04, G:0.03, T:0.24
Consensus pattern (21 bp):
ATATATAAAATAAAAAAGAAA
Found at i:9503248 original size:23 final size:20
Alignment explanation
Indices: 9503191--9503259 Score: 61
Period size: 23 Copynumber: 3.2 Consensus size: 20
9503181 TATAATCTAA
9503191 AAAATAAAATATAC-TAAAAT
1 AAAA-AAAATATACATAAAAT
*
9503211 AAAAAAGAAAATACATAAAATGT
1 AAAAAA-AATATACATAAAA--T
9503234 AAAAAAAATATTACATGAAAA-
1 AAAAAAAATA-TACAT-AAAAT
9503255 AAAAA
1 AAAAA
9503260 GAAAAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
19 2 0.05
20 10 0.24
21 10 0.24
22 3 0.07
23 12 0.29
24 4 0.10
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (20 bp):
AAAAAAAATATACATAAAAT
Found at i:9503594 original size:35 final size:36
Alignment explanation
Indices: 9503524--9503623 Score: 130
Period size: 35 Copynumber: 2.8 Consensus size: 36
9503514 GTGCTTGTAG
* * *
9503524 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGCAAAATTCT
*
9503561 ATCCTATTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
9503596 ATCCTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAG-GAGTTTGAATCCTAG
9503624 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 27 0.48
36 11 0.20
37 18 0.32
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:9510163 original size:36 final size:35
Alignment explanation
Indices: 9510080--9510208 Score: 179
Period size: 35 Copynumber: 3.7 Consensus size: 35
9510070 CCTTAGATTC
*
9510080 GTAAGGAATTACCAATTCGATCGGTTTGAACCTAT
1 GTAAGGAATTACCAGTTCGATCGGTTTGAACCTAT
* * *
9510115 ATAAGGAATTACCAGTTTGATCGAG-TTGAACCTGT
1 GTAAGGAATTACCAGTTCGATCG-GTTTGAACCTAT
9510150 CGTAAGGAATTACCAGTTCGATCGGTTTGAACCTAT
1 -GTAAGGAATTACCAGTTCGATCGGTTTGAACCTAT
* *
9510186 TTAAGGAATTACCAGTTTGATCG
1 GTAAGGAATTACCAGTTCGATCG
9510209 AGCTGAACCT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
35 51 0.62
36 31 0.38
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (35 bp):
GTAAGGAATTACCAGTTCGATCGGTTTGAACCTAT
Found at i:9510194 original size:71 final size:71
Alignment explanation
Indices: 9510078--9510219 Score: 257
Period size: 71 Copynumber: 2.0 Consensus size: 71
9510068 CACCTTAGAT
*
9510078 TCGTAAGGAATTACCAATTCGATCGGTTTGAACCTATATAAGGAATTACCAGTTTGATCGAGTTG
1 TCGTAAGGAATTACCAATTCGATCGGTTTGAACCTATATAAGGAATTACCAGTTTGATCGAGCTG
9510143 AACCTG
66 AACCTG
* *
9510149 TCGTAAGGAATTACCAGTTCGATCGGTTTGAACCTATTTAAGGAATTACCAGTTTGATCGAGCTG
1 TCGTAAGGAATTACCAATTCGATCGGTTTGAACCTATATAAGGAATTACCAGTTTGATCGAGCTG
9510214 AACCTG
66 AACCTG
9510220 GAGAGACTTC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (71 bp):
TCGTAAGGAATTACCAATTCGATCGGTTTGAACCTATATAAGGAATTACCAGTTTGATCGAGCTG
AACCTG
Found at i:9511820 original size:14 final size:14
Alignment explanation
Indices: 9511781--9511821 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
9511771 TAACTTTTCG
*
9511781 GTCAAAGTCAACGA
1 GTCAAAGTCAATGA
* *
9511795 GTCAAAGCCAATGT
1 GTCAAAGTCAATGA
9511809 GTCAAAGTCAATG
1 GTCAAAGTCAATG
9511822 GGTTAACTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (14 bp):
GTCAAAGTCAATGA
Found at i:9523374 original size:6 final size:6
Alignment explanation
Indices: 9523363--9523387 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9523353 AGAAAATGTA
9523363 AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT A
9523388 CCATTAAAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:9525794 original size:35 final size:35
Alignment explanation
Indices: 9525748--9525891 Score: 150
Period size: 35 Copynumber: 4.1 Consensus size: 35
9525738 TCTTAGATCC
*
9525748 ATAAGGAATTACAAGTTCGATCCGTCTGAACCTAT
1 ATAAGGAATTACAAGTTTGATCCGTCTGAACCTAT
* *
9525783 ATAAGGAATTACCAA-TTTGAT-CGAGCTGAACCTGTT
1 ATAAGGAATTA-CAAGTTTGATCCG-TCTGAACCT-AT
* **
9525819 ATAAGGAATTACCAGTTTGATTGGTCTGAACCTAT
1 ATAAGGAATTACAAGTTTGATCCGTCTGAACCTAT
* * *
9525854 TTAAGGAATTACCAGTTTGATCGAGT-TGAACCTAT
1 ATAAGGAATTACAAGTTTGATC-CGTCTGAACCTAT
9525889 ATA
1 ATA
9525892 GAGTTCATAC
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
34 2 0.02
35 58 0.63
36 31 0.34
37 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (35 bp):
ATAAGGAATTACAAGTTTGATCCGTCTGAACCTAT
Found at i:9525864 original size:71 final size:71
Alignment explanation
Indices: 9525748--9525886 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 71
9525738 TCTTAGATCC
9525748 ATAAGGAATTACAAGTTCGATCCGTCTGAACCTATATAAGGAATTACCAATTTGATCGAGCTGAA
1 ATAAGGAATTACAAGTTCGATCCGTCTGAACCTATATAAGGAATTACCAATTTGATCGAGCTGAA
9525813 CCTGTT
66 CCTGTT
* * ** * * *
9525819 ATAAGGAATTACCAGTTTGATTGGTCTGAACCTATTTAAGGAATTACCAGTTTGATCGAGTTGAA
1 ATAAGGAATTACAAGTTCGATCCGTCTGAACCTATATAAGGAATTACCAATTTGATCGAGCTGAA
9525884 CCT
66 CCT
9525887 ATATAGAGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (71 bp):
ATAAGGAATTACAAGTTCGATCCGTCTGAACCTATATAAGGAATTACCAATTTGATCGAGCTGAA
CCTGTT
Found at i:9531381 original size:20 final size:19
Alignment explanation
Indices: 9531352--9531403 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
9531342 TGATTCAATC
* *
9531352 AGTATTGATACTGAAGGGGG
1 AGTATCGATACTGAA-GGGA
*
9531372 AGTATCGATACCGAAGGGA
1 AGTATCGATACTGAAGGGA
9531391 AGGTATCGATACT
1 A-GTATCGATACT
9531404 ATTTTGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.23
Consensus pattern (19 bp):
AGTATCGATACTGAAGGGA
Found at i:9532025 original size:59 final size:59
Alignment explanation
Indices: 9531928--9532162 Score: 382
Period size: 59 Copynumber: 4.0 Consensus size: 59
9531918 ATTATCAAAT
* *
9531928 GGCACTAAGTGTGGTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTATGTGTGCT-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
9531988 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
9532047 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAGGTGTATGAATTTTCGTATTG
1 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * *
9532106 GGCACTTTGTGTGC-AAACATGTTAAGAAATTTATACTAAGTGTATGAATTTTCGTAT
1 GGCACTATGTGTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
9532163 GGGAAATATA
Statistics
Matches: 167, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
58 3 0.02
59 151 0.90
60 13 0.08
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (59 bp):
GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
Found at i:9538935 original size:59 final size:59
Alignment explanation
Indices: 9538834--9539006 Score: 224
Period size: 59 Copynumber: 2.9 Consensus size: 59
9538824 TACCAAATGA
* *
9538834 CACTAAGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGG
1 CACTATGTGTGCT-AAAATGTTTAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGG
* * * * *
9538894 CACTATGTGTGCTAAAATGTTTATAAATTTATACTATGTGTATGAATTTCTGTATTGGG
1 CACTATGTGTGCTAAAATGTTTAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGG
* * *
9538953 CACTTTGTGTGCGAACAT-TTTAAGAAATTCATACTAAGTGTATGAATTT-CGTAT
1 CACTATGTGTGCTAAAATGTTT-AGAAATTCATACTAAGTGTATGAATTTCCGTAT
9539007 GGGAAATATA
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
58 7 0.07
59 79 0.81
60 12 0.12
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (59 bp):
CACTATGTGTGCTAAAATGTTTAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGG
Found at i:9539029 original size:59 final size:60
Alignment explanation
Indices: 9538846--9539029 Score: 175
Period size: 59 Copynumber: 3.1 Consensus size: 60
9538836 CTAAGTGTGC
* * *
9538846 TAAAAATG-TTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTA-TGTGTGC
1 TAAACATGTTTAAGAAATTCATACTAAGTGTATGAATTT-CGTATTGGGCACTATTGTGT-A
* * * *
9538906 TAAA-ATGTTT-ATAAATTTATACTATGTGTATGAATTTCTGTATTGGGCACT-TTGTGTG
1 TAAACATGTTTAAGAAATTCATACTAAGTGTATGAATTTC-GTATTGGGCACTATTGTGTA
** * * *
9538964 CGAACAT-TTTAAGAAATTCATACTAAGTGTATGAATTTCGTA-TGGGAAATATATCTGTA
1 TAAACATGTTTAAGAAATTCATACTAAGTGTATGAATTTCGTATTGGGCACTAT-TGTGTA
9539023 TAAACAT
1 TAAACAT
9539030 AAAATTTCAT
Statistics
Matches: 101, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
57 6 0.06
58 10 0.10
59 79 0.78
60 6 0.06
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (60 bp):
TAAACATGTTTAAGAAATTCATACTAAGTGTATGAATTTCGTATTGGGCACTATTGTGTA
Found at i:9540744 original size:13 final size:13
Alignment explanation
Indices: 9540726--9540750 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9540716 TTAACTTTTT
9540726 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
9540739 GGTCAAAGTCAA
1 GGTCAAAGTCAA
9540751 AAGGTTGACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:9541791 original size:60 final size:61
Alignment explanation
Indices: 9541723--9541841 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 61
9541713 ATATGTCTCT
* * * * * *
9541723 AAATTATAACTCTCGTTTTAAATTAAT-CTTTAAATTTTTGAATATTTTAATTTTATCCTC
1 AAATTATAACTCTCATTCTAAATTAATCCTTAAAATTTTTAAACATTTTAATTTCATCCTC
*
9541783 AAATTATAACTTTCATTCTAAATTAATCCTTAAAATTTTTAAACATTTTAATTTCATCC
1 AAATTATAACTCTCATTCTAAATTAATCCTTAAAATTTTTAAACATTTTAATTTCATCC
9541842 CTAAATTGAC
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 24 0.47
61 27 0.53
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (61 bp):
AAATTATAACTCTCATTCTAAATTAATCCTTAAAATTTTTAAACATTTTAATTTCATCCTC
Found at i:9543029 original size:64 final size:64
Alignment explanation
Indices: 9542954--9543140 Score: 182
Period size: 64 Copynumber: 2.9 Consensus size: 64
9542944 GCATCAACCC
*
9542954 ATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCATTTCATGCATCGATGCACTCTC
1 ATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTC
9543017 T
64 T
** ** *** *
9543018 ATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGCA
1 ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
* * * ** * *
9543082 ATGCACCGATGCACTCAGG-CTATTTTCAAACATCGAATGCATTTTATGCATCGATGCAC
1 ATGCATCGATGCACT-TGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCAC
9543141 ACTTGGTGCA
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
62 2 0.02
63 6 0.06
64 94 0.90
65 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
Found at i:9543151 original size:64 final size:63
Alignment explanation
Indices: 9542982--9543161 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 63
9542972 GAATAAATTG
* * * * *
9542982 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTAGGCTATTATTAA
* *
9543046 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT-AGGCTATTATTA
9543109 A
63 A
* *
9543110 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACTA
9543162 AGTGATATAG
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 92 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTAGGCTATTATTAA
Found at i:9553152 original size:64 final size:64
Alignment explanation
Indices: 9553076--9553262 Score: 164
Period size: 64 Copynumber: 2.9 Consensus size: 64
9553066 GCATCAATCC
*
9553076 ATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGAATTTCATGCATCGATGCACTCTC
1 ATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGAATTTCATGCATCGATGCACTCTC
9553139 T
64 T
** ** * *** *
9553140 ATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGCA
1 ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGAATTTCATGCATCGATGCACTCTCT
* * * ** * * *
9553204 ATGCACCGATGCACTCAGG-CTATTTTCAAACATCGAATGCATTTTATGCATCGATGCAC
1 ATGCATCGATGCACT-TGGAATAAATTAAAACATCGAATGAATTTCATGCATCGATGCAC
9553263 ACTTGGTGCA
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
62 2 0.02
63 6 0.06
64 93 0.90
65 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGAATTTCATGCATCGATGCACTCTCT
Found at i:9553273 original size:64 final size:63
Alignment explanation
Indices: 9553104--9553283 Score: 211
Period size: 64 Copynumber: 2.8 Consensus size: 63
9553094 GAATAAATTG
* * * * * *
9553104 AACATCGAATGAATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTAGGCTATTATTAA
* *
9553168 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT-AGGCTATTATTA
9553231 A
63 A
* *
9553232 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACTA
9553284 AGTGTTCCAA
Statistics
Matches: 100, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 91 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTAGGCTATTATTAA
Found at i:9554305 original size:20 final size:20
Alignment explanation
Indices: 9554280--9554344 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
9554270 TAAAAAGAAA
9554280 TTTAAAAAAATTATAATTTT
1 TTTAAAAAAATTATAATTTT
* * *
9554300 TTTAAAAATATAAGAATTTT
1 TTTAAAAAAATTATAATTTT
9554320 TTTAAAGTTTAAAATTATAATTTT
1 TTTAAA----AAAATTATAATTTT
9554344 T
1 T
9554345 AAAATCTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 23 0.66
24 12 0.34
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTAAAAAAATTATAATTTT
Found at i:9558624 original size:32 final size:32
Alignment explanation
Indices: 9558557--9558682 Score: 137
Period size: 32 Copynumber: 4.0 Consensus size: 32
9558547 CCTAAGGTGA
* * * * * *
9558557 CCTTGGGTAGG-TCTGAGGCCCCAAAGAATTT
1 CCTTGAGTAGGCTCTAAGGCCCCAAGGTACTC
*
9558588 CCTTGGGTAGGCTCTAAGGCCCCAAGGTACTC
1 CCTTGAGTAGGCTCTAAGGCCCCAAGGTACTC
* *
9558620 CCTTGAGTAGGCTCTTAGGCCCTAAGGTACTC
1 CCTTGAGTAGGCTCTAAGGCCCCAAGGTACTC
** *
9558652 CCTTGAGTAGGCTCTCTGGCCCCAAGATACT
1 CCTTGAGTAGGCTCTAAGGCCCCAAGGTACT
9558683 TCTTTAGGTT
Statistics
Matches: 82, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
31 11 0.13
32 71 0.87
ACGTcount: A:0.20, C:0.29, G:0.26, T:0.25
Consensus pattern (32 bp):
CCTTGAGTAGGCTCTAAGGCCCCAAGGTACTC
Found at i:9562224 original size:31 final size:29
Alignment explanation
Indices: 9562156--9562231 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 29
9562146 TCTTATTTAA
* *
9562156 GTACCTAAAGTATTTTTTGGTCAAAATAT
1 GTACCTAAAGTATTTTTTAGTCAAAATAG
* *
9562185 ATATCTAAAGATATATTTTTAGTCAAAATAG
1 GTACCTAAAG-TAT-TTTTTAGTCAAAATAG
9562216 GTACCTAAAGTATTTT
1 GTACCTAAAGTATTTT
9562232 ATTCCAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 11 0.28
30 6 0.15
31 22 0.56
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (29 bp):
GTACCTAAAGTATTTTTTAGTCAAAATAG
Found at i:9565288 original size:22 final size:22
Alignment explanation
Indices: 9565262--9565318 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
9565252 TTTGACTTTT
* *
9565262 TGGTCAAAGTCAAATTCAACGC
1 TGGTCAAAGTCAAAGTCAACGA
*
9565284 TGGTCAAAAG-CAAAGTCAACTA
1 TGGTC-AAAGTCAAAGTCAACGA
*
9565306 TAGTCAAAGTCAA
1 TGGTCAAAGTCAA
9565319 CAATCAAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (22 bp):
TGGTCAAAGTCAAAGTCAACGA
Found at i:9565315 original size:16 final size:16
Alignment explanation
Indices: 9565294--9565347 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
9565284 TGGTCAAAAG
9565294 CAAAGTCAACTATAGT
1 CAAAGTCAACTATAGT
9565310 CAAAGTCAAC-A-A-T
1 CAAAGTCAACTATAGT
*
9565323 C-AAGTCAACTGTCAGT
1 CAAAGTCAACTAT-AGT
9565339 CAAAGTCAA
1 CAAAGTCAA
9565348 TGAGTTGACT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
12 8 0.25
13 2 0.06
14 1 0.03
15 2 0.06
16 12 0.38
17 7 0.22
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.20
Consensus pattern (16 bp):
CAAAGTCAACTATAGT
Found at i:9565317 original size:28 final size:29
Alignment explanation
Indices: 9565286--9565347 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
9565276 TTCAACGCTG
9565286 GTCAA-AAGCAAAGTCAACTAT-AGTCAAA
1 GTCAACAAGC-AAGTCAACTATCAGTCAAA
* *
9565314 GTCAACAATCAAGTCAACTGTCAGTCAAA
1 GTCAACAAGCAAGTCAACTATCAGTCAAA
9565343 GTCAA
1 GTCAA
9565348 TGAGTTGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (29 bp):
GTCAACAAGCAAGTCAACTATCAGTCAAA
Found at i:9568025 original size:2 final size:2
Alignment explanation
Indices: 9568018--9568063 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
9568008 AAAAATGATA
9568018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9568060 AT AT
1 AT AT
9568064 TAAATTAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9571877 original size:21 final size:22
Alignment explanation
Indices: 9571853--9571894 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
9571843 TAAATTTTAA
9571853 TTTATTT-TAATTTAGCCACTG
1 TTTATTTCTAATTTAGCCACTG
*
9571874 TTTATTTCTGATTTAGCCACT
1 TTTATTTCTAATTTAGCCACT
9571895 AACTTGCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (22 bp):
TTTATTTCTAATTTAGCCACTG
Found at i:9573343 original size:34 final size:34
Alignment explanation
Indices: 9573305--9573376 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
9573295 CCTTTACAAC
* * *
9573305 TCCCTAGTTTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
* * *
9573339 TCCCTAGCTTTTAGACGGGCTAAGCTAGAACATT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
9573373 TCCC
1 TCCC
9573377 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACATT
Found at i:9573862 original size:20 final size:19
Alignment explanation
Indices: 9573797--9573872 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 19
9573787 GTGTTTGAGA
*
9573797 GCATGGATGCACTGCATAGT
1 GCATGGATGCACTGCA-GGT
*
9573817 GCATCGATGCACTAGTGGCAGGT
1 GCATGGATGCAC---T-GCAGGT
9573840 GCATGGATGCACTGCAGGGT
1 GCATGGATGCACTGCA-GGT
9573860 GCATGGATGCACT
1 GCATGGATGCACT
9573873 TTGACACCCT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
19 3 0.06
20 28 0.58
23 14 0.29
24 3 0.06
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.22
Consensus pattern (19 bp):
GCATGGATGCACTGCAGGT
Found at i:9577620 original size:2 final size:2
Alignment explanation
Indices: 9577613--9577637 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9577603 AATATGTATG
9577613 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9577638 CCCTTGTTGT
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:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9577907 original size:6 final size:6
Alignment explanation
Indices: 9577896--9577966 Score: 51
Period size: 6 Copynumber: 11.8 Consensus size: 6
9577886 AAACACACAC
* * *
9577896 AAAAAG AAAAAG --AAAG AAAGATAG -AAAAT AAAGAG AAAAAG AAAAAC
1 AAAAAG AAAAAG AAAAAG AAA-A-AG AAAAAG AAAAAG AAAAAG AAAAAG
9577943 AGAAAA- AAAAAG AAAAAG AGAAAA
1 A-AAAAG AAAAAG AAAAAG A-AAAA
9577967 ACACAGAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
4 4 0.08
5 5 0.10
6 30 0.58
7 11 0.21
8 2 0.04
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:9577958 original size:8 final size:8
Alignment explanation
Indices: 9577896--9577994 Score: 63
Period size: 8 Copynumber: 11.2 Consensus size: 8
9577886 AAACACACAC
9577896 AAAAAGAAA
1 AAAAAG-AA
9577905 AAGAAAGAA
1 AA-AAAGAA
* *
9577914 AGATAGAA
1 AAAAAGAA
*
9577922 AATAAAGAG
1 AA-AAAGAA
9577931 AAAAAGAA
1 AAAAAGAA
*
9577939 AAACAGAAAA
1 AAA-A-AGAA
9577949 AAAAAGAA
1 AAAAAGAA
*
9577957 AAAGAGAA
1 AAAAAGAA
9577965 AAACACAGAA
1 AAA-A-AGAA
*
9577975 AAAAACATA
1 AAAAAGA-A
9577984 AAAATAGAA
1 AAAA-AGAA
9577993 AA
1 AA
9577995 CAAAAGAGAG
Statistics
Matches: 70, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
8 29 0.41
9 22 0.31
10 19 0.27
ACGTcount: A:0.78, C:0.04, G:0.14, T:0.04
Consensus pattern (8 bp):
AAAAAGAA
Found at i:9577964 original size:18 final size:18
Alignment explanation
Indices: 9577931--9578031 Score: 71
Period size: 18 Copynumber: 5.4 Consensus size: 18
9577921 AAATAAAGAG
*
9577931 AAAAAGAAAAACAGAAAA
1 AAAAAGAAAAAGAGAAAA
9577949 AAAAAGAAAAAGAGAAAA
1 AAAAAGAAAAAGAGAAAA
* * * *
9577967 ACACAGAAAAAAACATAAA
1 AAAAAGAAAAAGAGA-AAA
*
9577986 AATAGAAAACAAAAGAGAGAAA
1 AA-A-AAGA-AAAAGAGA-AAA
*
9578008 AAAAAG--AGAGAGAAAGA
1 AAAAAGAAAAAGAGAAA-A
9578025 AAAAAGA
1 AAAAAGA
9578032 TATAAAACCG
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
16 2 0.03
17 13 0.20
18 28 0.44
19 4 0.06
20 3 0.05
21 3 0.05
22 11 0.17
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAAGAGAAAA
Found at i:9577978 original size:43 final size:42
Alignment explanation
Indices: 9577896--9578031 Score: 116
Period size: 43 Copynumber: 3.2 Consensus size: 42
9577886 AAACACACAC
* * *
9577896 AAAAAGAAAAAGAAAGAAAGATAGAAAATAAAGAGAAAAAGA
1 AAAAAGAAAAAAAAAGAAAAAGAGAAAATAAAGAGAAAAAGA
* *
9577938 AAAACAGAAAAAAAAAGAAAAAGAGAAAA-ACACAGAAAAA-A
1 AAAA-AGAAAAAAAAAGAAAAAGAGAAAATAAAGAGAAAAAGA
* * * *
9577979 ACATAAA-AATAGAAAACAAAAGAGAGAAAAAAAAGAGAGAGAAAGA
1 A-A-AAAGAAAAAAAAAGAAAA-AGAGAAAATAAAGAGA-A-AAAGA
9578025 AAAAAGA
1 AAAAAGA
9578032 TATAAAACCG
Statistics
Matches: 75, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
41 13 0.17
42 23 0.31
43 28 0.37
44 4 0.05
45 5 0.07
46 2 0.03
ACGTcount: A:0.76, C:0.04, G:0.17, T:0.03
Consensus pattern (42 bp):
AAAAAGAAAAAAAAAGAAAAAGAGAAAATAAAGAGAAAAAGA
Found at i:9577995 original size:53 final size:53
Alignment explanation
Indices: 9577896--9577996 Score: 125
Period size: 53 Copynumber: 1.9 Consensus size: 53
9577886 AAACACACAC
* * *
9577896 AAAAAGAAAAAGAAAGAAAGATAGAAAATAAAGAGAAAAAGAAAAACAGAAAA
1 AAAAAGAAAAAGAAAGAAACACAGAAAATAAACAGAAAAAGAAAAACAGAAAA
* *
9577949 AAAAAGAAAAAGAGAA-AAACACAGAAAA-AAACATAAAAATAGAAAACA
1 AAAAAGAAAAAGA-AAGAAACACAGAAAATAAACAGAAAAAGA-AAAACA
9577997 AAAGAGAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
52 10 0.24
53 29 0.71
54 2 0.05
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.04
Consensus pattern (53 bp):
AAAAAGAAAAAGAAAGAAACACAGAAAATAAACAGAAAAAGAAAAACAGAAAA
Found at i:9578009 original size:15 final size:15
Alignment explanation
Indices: 9577949--9578031 Score: 54
Period size: 15 Copynumber: 5.8 Consensus size: 15
9577939 AAACAGAAAA
*
9577949 AAAAAGAAAA-AGAG
1 AAAAACAAAAGAGAG
*
9577963 AAAAAC-ACAGA-A-
1 AAAAACAAAAGAGAG
* *
9577975 AAAAACATAAAAATAG
1 AAAAACA-AAAGAGAG
9577991 -AAAACAAAAGAGAG
1 AAAAACAAAAGAGAG
9578005 AAAAA-AAAGAGAGAG
1 AAAAACAAA-AGAGAG
9578020 AAAGAA-AAAAGA
1 AAA-AACAAAAGA
9578032 TATAAAACCG
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
12 6 0.11
13 3 0.05
14 18 0.33
15 23 0.42
16 5 0.09
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAAACAAAAGAGAG
Found at i:9578012 original size:13 final size:14
Alignment explanation
Indices: 9577989--9578018 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
9577979 ACATAAAAAT
9577989 AGAAAACAAAAGAG
1 AGAAAACAAAAGAG
9578003 AGAAAA-AAAAGAG
1 AGAAAACAAAAGAG
9578016 AGA
1 AGA
9578019 GAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.73, C:0.03, G:0.23, T:0.00
Consensus pattern (14 bp):
AGAAAACAAAAGAG
Found at i:9578019 original size:17 final size:17
Alignment explanation
Indices: 9577989--9578031 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
9577979 ACATAAAAAT
*
9577989 AGAAAACAAAAGAGAG-A
1 AGAAAA-AAGAGAGAGAA
9578006 A-AAAAAAGAGAGAGAA
1 AGAAAAAAGAGAGAGAA
9578022 AGAAAAAAGA
1 AGAAAAAAGA
9578032 TATAAAACCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 8 0.35
16 6 0.26
17 9 0.39
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.00
Consensus pattern (17 bp):
AGAAAAAAGAGAGAGAA
Found at i:9579061 original size:3 final size:3
Alignment explanation
Indices: 9579053--9579084 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
9579043 GGATACTATC
9579053 ATT ATT ATT ATT ATT A-T ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
9579085 ATAATATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9579777 original size:20 final size:20
Alignment explanation
Indices: 9579748--9579787 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9579738 ACTCTATTAG
*
9579748 CACCACTAATATTTGCTGGC
1 CACCAATAATATTTGCTGGC
9579768 CACCAATAATATTTGCTGGC
1 CACCAATAATATTTGCTGGC
9579788 ACCCATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (20 bp):
CACCAATAATATTTGCTGGC
Found at i:9586571 original size:3 final size:3
Alignment explanation
Indices: 9586563--9586593 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
9586553 CTTTAGTATT
9586563 GAA GAA GAA GAA GAA GAA GAA GAA GATA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA
9586594 AGCCTTGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:9587723 original size:9 final size:9
Alignment explanation
Indices: 9587702--9587747 Score: 78
Period size: 9 Copynumber: 5.3 Consensus size: 9
9587692 CTTAAAGATA
9587702 AAAAAAATG
1 AAAAAAATG
9587711 --AAAAATG
1 AAAAAAATG
9587718 AAAAAAATG
1 AAAAAAATG
9587727 AAAAAAATG
1 AAAAAAATG
9587736 AAAAAAATG
1 AAAAAAATG
9587745 AAA
1 AAA
9587748 TAGAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.20
9 28 0.80
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAAAAATG
Found at i:9587723 original size:16 final size:16
Alignment explanation
Indices: 9587702--9587772 Score: 83
Period size: 16 Copynumber: 4.4 Consensus size: 16
9587692 CTTAAAGATA
9587702 AAAAAAATGAAAAATG
1 AAAAAAATGAAAAATG
9587718 AAAAAAATGAAAAAAATG
1 AAAAAAATG--AAAAATG
*
9587736 AAAAAAATGAAATA-G
1 AAAAAAATGAAAAATG
*
9587751 AAAAATA-GAAAAATAG
1 AAAAAAATGAAAAAT-G
9587767 AAAAAA
1 AAAAAA
9587773 TAAAAAAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
14 5 0.11
15 7 0.15
16 19 0.40
18 16 0.34
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAAAAATGAAAAATG
Found at i:9587780 original size:8 final size:8
Alignment explanation
Indices: 9587702--9587803 Score: 61
Period size: 9 Copynumber: 12.5 Consensus size: 8
9587692 CTTAAAGATA
9587702 AAAAAAAT
1 AAAAAAAT
*
9587710 -GAAAAAT
1 AAAAAAAT
9587717 GAAAAAAAT
1 -AAAAAAAT
9587726 GAAAAAAAT
1 -AAAAAAAT
9587735 GAAAAAAAT
1 -AAAAAAAT
*
9587744 ---GAAAT
1 AAAAAAAT
*
9587749 AGAAAAAT
1 AAAAAAAT
*
9587757 AGAAAAAT
1 AAAAAAAT
9587765 AGAAAAAAT
1 A-AAAAAAT
9587774 AAAAAAA-
1 AAAAAAAT
*
9587781 AGAAGAAAAA
1 A-AA-AAAAT
9587791 AAATAAAAT
1 AAA-AAAAT
9587800 AAAA
1 AAAA
9587804 GGGGGGTTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
5 4 0.05
7 7 0.09
8 22 0.28
9 44 0.56
10 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:9587790 original size:9 final size:8
Alignment explanation
Indices: 9587702--9587803 Score: 61
Period size: 8 Copynumber: 12.5 Consensus size: 8
9587692 CTTAAAGATA
9587702 AAAAAAATG
1 AAAAAAA-G
*
9587711 -AAAAATG
1 AAAAAAAG
9587718 AAAAAAATG
1 AAAAAAA-G
9587727 AAAAAAATG
1 AAAAAAA-G
9587736 AAAAAAATG
1 AAAAAAA-G
*
9587745 --AAATAG
1 AAAAAAAG
*
9587751 AAAAATAG
1 AAAAAAAG
*
9587759 AAAAATAG
1 AAAAAAAG
9587767 AAAAAATA-
1 AAAAAA-AG
9587775 AAAAAAAG
1 AAAAAAAG
9587783 AAGAAAAA-
1 AA-AAAAAG
*
9587791 AAATAAAAT
1 AAA-AAAAG
9587800 AAAA
1 AAAA
9587804 GGGGGGTTCA
Statistics
Matches: 80, Mismatches: 4, Indels: 19
0.78 0.04 0.18
Matches are distributed among these distances:
6 1 0.01
7 7 0.09
8 44 0.55
9 28 0.35
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.11
Consensus pattern (8 bp):
AAAAAAAG
Found at i:9589165 original size:55 final size:55
Alignment explanation
Indices: 9589081--9589304 Score: 382
Period size: 55 Copynumber: 4.1 Consensus size: 55
9589071 TGAAGAAAAA
9589081 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
9589136 GAAGATTATTCGAGTCATATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
9589191 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
9589246 GAAGATTGTTCGAGTCTTATA--CTCTGAAGAAA-AGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
9589298 GGAGATT
1 GAAGATT
9589305 ATTGTTCGAG
Statistics
Matches: 160, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
52 25 0.16
53 10 0.06
55 125 0.78
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:9589368 original size:51 final size:52
Alignment explanation
Indices: 9589300--9589797 Score: 724
Period size: 51 Copynumber: 9.7 Consensus size: 52
9589290 CGATCGTTGG
9589300 AGATTATTGTTCGAGTTCTAGT-CCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
9589351 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
9589403 AGATTATTGTTCGAGTT-TAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
9589454 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * * *
9589506 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
9589558 AGATTATTGTT-GAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
9589609 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGG-
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
9589660 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAA-TGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * * **
9589711 AGATTATCGTTCGAGTTCTACTCCCTGAAG-AAATAGAGAGC-GAACCCGTAAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTG-G-GCAG-ACCCGTAGGA
**
9589764 AGAAGATTGTTCGAGTTCTA-TACCCTGAAGAAAA
1 AGATTATTGTTCGAGTTCTAGT-CCCTGAAGAAAA
9589798 AGAGAGCGAA
Statistics
Matches: 407, Mismatches: 30, Indels: 17
0.90 0.07 0.04
Matches are distributed among these distances:
50 16 0.04
51 183 0.45
52 172 0.42
53 33 0.08
54 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
Found at i:9589429 original size:103 final size:104
Alignment explanation
Indices: 9589300--9589797 Score: 760
Period size: 103 Copynumber: 4.8 Consensus size: 104
9589290 CGATCGTTGG
9589300 AGATTATTGTTCGAGTTCTAGT-CCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
*
9589364 AGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
66 AGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
9589403 AGATTATTGTTCGAGTT-TAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
* * *
9589467 AGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
66 AGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* * * *
9589506 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGAAGATTATTGTT-G
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
9589570 AGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
66 AGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
*
9589609 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGG-AGATTATTGTTCG
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
9589673 AGTTCTAGTCCCTGAAGAAAA-TGGGCAGTCTCGTAGGA
66 AGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* * * ** **
9589711 AGATTATCGTTCGAGTTCTACTCCCTGAAG-AAATAGAGAGC-GAACCCGTAAAAAGAAGATTGT
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTG-G-GCAG-ACCCGTAGGAAGATTATTGT
9589774 TCGAGTTCTA-TACCCTGAAGAAAA
63 TCGAGTTCTAGT-CCCTGAAGAAAA
9589798 AGAGAGCGAA
Statistics
Matches: 365, Mismatches: 22, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
101 5 0.01
102 62 0.17
103 226 0.62
104 72 0.20
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (104 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
AGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
Found at i:9589586 original size:27 final size:27
Alignment explanation
Indices: 9589556--9589639 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 27
9589546 AGTCTCGTAG
9589556 GAAGATTATTGTTGAGTTCTAGTCCCT
1 GAAGATTATTGTTGAGTTCTAGTCCCT
** * * **
9589583 GAAGAAAATTG-GGCAG-TCTCGT--AG
1 GAAGATTATTGTTG-AGTTCTAGTCCCT
9589607 GAAGATTATTGTTCGAGTTCTAGTCCCT
1 GAAGATTATTGTT-GAGTTCTAGTCCCT
9589635 GAAGA
1 GAAGA
9589640 AAATTGGACA
Statistics
Matches: 39, Mismatches: 12, Indels: 11
0.63 0.19 0.18
Matches are distributed among these distances:
24 9 0.23
25 2 0.05
26 12 0.31
27 11 0.28
28 5 0.13
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.32
Consensus pattern (27 bp):
GAAGATTATTGTTGAGTTCTAGTCCCT
Found at i:9589773 original size:155 final size:156
Alignment explanation
Indices: 9589300--9589797 Score: 787
Period size: 155 Copynumber: 3.2 Consensus size: 156
9589290 CGATCGTTGG
9589300 AGATTATTGTTCGAGTTCTAGT-CCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
9589364 AGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGAAGATTATTGTTCGAGTT-TAGTCCCT
66 AGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGAAGATTATTGTTCGAGTTCTAGTCCCT
9589428 GAAGAAAATTGGGCAGACCCGTAGGA
131 GAAGAAAATTGGGCAGACCCGTAGGA
* *
9589454 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTTTTCG
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
9589519 AGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGAAGATTATTGTT-GAGTTCTAGTCCCT
66 AGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGAAGATTATTGTTCGAGTTCTAGTCCCT
* *
9589583 GAAGAAAATTGGGCAGTCTCGTAGGA
131 GAAGAAAATTGGGCAGACCCGTAGGA
*
9589609 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGG-AGATTATTGTTCG
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
* * *
9589673 AGTTCTAGTCCCTGAAGAAAA-TGGGCAGTCTCGTAGGAAGATTATCGTTCGAGTTCTACTCCCT
66 AGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGAAGATTATTGTTCGAGTTCTAGTCCCT
* **
9589737 GAAG-AAATAGAGAGC-GAACCCGTAAAA
131 GAAGAAAATTG-G-GCAG-ACCCGTAGGA
**
9589764 AGAAGATTGTTCGAGTTCTA-TACCCTGAAGAAAA
1 AGATTATTGTTCGAGTTCTAGT-CCCTGAAGAAAA
9589798 AGAGAGCGAA
Statistics
Matches: 320, Mismatches: 17, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
153 31 0.10
154 80 0.25
155 209 0.65
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (156 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
AGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGAAGATTATTGTTCGAGTTCTAGTCCCT
GAAGAAAATTGGGCAGACCCGTAGGA
Found at i:9590712 original size:20 final size:20
Alignment explanation
Indices: 9590689--9590743 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
9590679 GCACTAACTC
9590689 TATTATACT-GCCACCACTAA
1 TATT-TACTGGCCACCACTAA
*
9590709 TATTTGCTGGCCACCACTAA
1 TATTTACTGGCCACCACTAA
*
9590729 TATTTGCTGGCCACC
1 TATTTACTGGCCACC
9590744 CATGTTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (20 bp):
TATTTACTGGCCACCACTAA
Found at i:9591349 original size:146 final size:146
Alignment explanation
Indices: 9591079--9591353 Score: 345
Period size: 146 Copynumber: 1.9 Consensus size: 146
9591069 TCTCGCCGGA
* *
9591079 GATCGGGATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGTCCATCACGAACAACATA
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGTCCAACACGAACAACATA
* ** * ** *
9591144 TTGAAAATTCAAGACGATCGGACGGTGGACGGTGACGGATCGGAGAAAACATATCCGGACGGTTT
66 TTGAAAAATCAAGACGATCGGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTTT
9591209 TTAGCCTCTTGCTGGT
131 TTAGCCTCTTGCTGGT
* * * * * * *
9591225 GATCGGAATCTTCGATCAATATTCCGAATGGTGAAAAGTTGTGTGATG-CCAACACGAACAACCT
1 GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCG-GAAGTCCAACACGAACAACAT
* * * * *
9591289 ATTGAAAAATCAGGACGATCGGACGGTGGATGACGGCAGATCAAAGAAAATACATTCGGACGGTT
65 ATTGAAAAATCAAGACGATCGGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTT
9591354 ATCTTTGTAT
Statistics
Matches: 107, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
146 104 0.97
147 3 0.03
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (146 bp):
GATCGGAATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGTCCAACACGAACAACATA
TTGAAAAATCAAGACGATCGGACGGTGGACGACGACAGATCAAAGAAAACACATCCGGACGGTTT
TTAGCCTCTTGCTGGT
Found at i:9593919 original size:55 final size:55
Alignment explanation
Indices: 9593819--9594101 Score: 351
Period size: 55 Copynumber: 5.2 Consensus size: 55
9593809 AAGATTTTTA
* * *
9593819 AAACTAAGCTCGAGGCACCAACGTGATATGTAGGGGTTTCTTGATGACAATGAAG
1 AAACCAAGCTCGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAATGAAG
* *
9593874 AAACCAAG-TATGAGGGACCAAAGTGATATGTAGGGGTTCCTTGATGACAATGAAG
1 AAACCAAGCT-CGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAATGAAG
* * * *
9593929 AAACCAAGCTCGAGGGACCAACGTGATATATAGGGATTCTTTGATGACAACGAAG
1 AAACCAAGCTCGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAATGAAG
* ** *
9593984 AAACTAAGCTCGAGGGACTGACGTGATATGTAGGGGTTCTTTGATGACAACT-AAG
1 AAACCAAGCTCGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAA-TGAAG
* * *
9594039 TAA-C-AGCTCGAGGGACCAACGTGATATGTAGGGGAATCCTTGATGACACT-AAG
1 AAACCAAGCTCGAGGGACCAACGTGATATGTAGGGG-TTCCTTGATGACAATGAAG
*
9594092 AAACTAAGCT
1 AAACCAAGCT
9594102 TGATTTTCAA
Statistics
Matches: 196, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
53 34 0.17
54 12 0.06
55 149 0.76
56 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.22
Consensus pattern (55 bp):
AAACCAAGCTCGAGGGACCAACGTGATATGTAGGGGTTCCTTGATGACAATGAAG
Found at i:9595319 original size:8 final size:9
Alignment explanation
Indices: 9595293--9595322 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
9595283 TATTCGAACA
9595293 TTTATTTTCT
1 TTTATTTT-T
9595303 TTTATTTTT
1 TTTATTTTT
9595312 TTTATTTTT
1 TTTATTTTT
9595321 TT
1 TT
9595323 CTTTCGTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTATTTTT
Found at i:9598379 original size:14 final size:15
Alignment explanation
Indices: 9598355--9598394 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
9598345 TCCAATCCAA
9598355 ATAAC-AATATTTC-
1 ATAACAAATATTTCG
9598368 ATAACAAATATTTCG
1 ATAACAAATATTTCG
*
9598383 A-AACATATATTT
1 ATAACAAATATTT
9598395 TGATTCTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 5 0.21
14 18 0.75
15 1 0.04
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (15 bp):
ATAACAAATATTTCG
Found at i:9599050 original size:46 final size:46
Alignment explanation
Indices: 9598996--9599084 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
9598986 TTAAACCCTG
*
9598996 ATCCCAATAATCAATTTCTGATAATTAACATAATTAAATAGACAAA
1 ATCCCAATAACCAATTTCTGATAATTAACATAATTAAATAGACAAA
*
9599042 ATCCCAATAACCAGTTTCTGATAATTAACATAATTAAATAGAC
1 ATCCCAATAACCAATTTCTGATAATTAACATAATTAAATAGAC
9599085 GCTTAACTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (46 bp):
ATCCCAATAACCAATTTCTGATAATTAACATAATTAAATAGACAAA
Found at i:9600242 original size:21 final size:23
Alignment explanation
Indices: 9600195--9600252 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 23
9600185 GTAAATAAAG
* * * *
9600195 AAAAATATTAAGAATTTTATTCC
1 AAAAATATTTATATTTTTACTCC
*
9600218 AAAAA-A-TTATATTTTTACTCG
1 AAAAATATTTATATTTTTACTCC
9600239 AAAAATATTTATAT
1 AAAAATATTTATAT
9600253 GCATGCAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 15 0.54
22 2 0.07
23 11 0.39
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (23 bp):
AAAAATATTTATATTTTTACTCC
Found at i:9605821 original size:59 final size:59
Alignment explanation
Indices: 9605755--9606222 Score: 760
Period size: 59 Copynumber: 7.9 Consensus size: 59
9605745 TTCCATACGT
* * * *
9605755 AAATTCATACACTTAGAATAAATTTCTTATCATTTTAGCACAC-AAGGTGTCCC-ATATGG
1 AAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAA-GTG-CCCTATATGG
* *
9605814 AAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACGGAGTGCCCTATATGG
1 AAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATGG
* *
9605873 AAATTCATACAGTTAGTATGAATTCCTTATCATGTTATCACACGAAGTGCCCTATATGG
1 AAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATGG
9605932 AAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATGG
1 AAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATGG
*
9605991 AAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATGTGG
1 AAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATGG
* * *
9606050 AAATTCATGCACTTAGTATGAATTACTTATCATGTTAGCACACTAAGTGCCCTATATGG
1 AAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATGG
* * *
9606109 AAATTCATACACTTATTATGAATTCTTTATCATGTTAGCACACTAAGTGCCCTATATGG
1 AAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATGG
*
9606168 AAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACTAAGTGCCCTAT
1 AAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTAT
9606223 TTATAATCAC
Statistics
Matches: 386, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
58 3 0.01
59 382 0.99
60 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACGAAGTGCCCTATATGG
Found at i:9606689 original size:20 final size:22
Alignment explanation
Indices: 9606635--9606689 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
9606625 TACCCTTACC
*
9606635 ATGGCATCGATACTACTATATT
1 ATGGTATCGATACTACTATATT
* * *
9606657 ATGGTACCTATACTCCT-T-TT
1 ATGGTATCGATACTACTATATT
9606677 ATGGTATCGATAC
1 ATGGTATCGATAC
9606690 CAAAATTAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 13 0.48
21 1 0.04
22 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (22 bp):
ATGGTATCGATACTACTATATT
Found at i:9606754 original size:20 final size:20
Alignment explanation
Indices: 9606729--9606769 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
9606719 GATACCATGG
*
9606729 TACCTCGTTGGTACCGATAC
1 TACCTCATTGGTACCGATAC
*
9606749 TACCTCATTGGTACTGATAC
1 TACCTCATTGGTACCGATAC
9606769 T
1 T
9606770 GATTGAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (20 bp):
TACCTCATTGGTACCGATAC
Found at i:9608313 original size:19 final size:20
Alignment explanation
Indices: 9608284--9608321 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
9608274 TTGAAAAATA
9608284 GCTTGGTGCATCGATGCATG
1 GCTTGGTGCATCGATGCATG
9608304 GCTT-GTGCATCGATGCAT
1 GCTTGGTGCATCGATGCAT
9608322 CAAATGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.32
Consensus pattern (20 bp):
GCTTGGTGCATCGATGCATG
Found at i:9608375 original size:19 final size:19
Alignment explanation
Indices: 9608351--9608389 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
9608341 CAAAGTATTC
9608351 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
9608370 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
9608389 A
1 A
9608390 ATACATTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:9608386 original size:65 final size:65
Alignment explanation
Indices: 9608244--9608452 Score: 191
Period size: 65 Copynumber: 3.2 Consensus size: 65
9608234 TGCACCAAGT
** *
9608244 GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCTT--G-GTGCATCGATGCATGGC
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATA--TTCAGAGTGCATCGATGCATGGA
**
9608306 TT
64 GA
* *
9608308 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAGTATTCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATATTCAGAGTGCATCGATGCATGGAGA
* * * *
9608373 GTGCATCGGTGCATGGAATACATTCGATG--TTC-AATTAATTCATCGA-TGCATCGATGCATGG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGG
9608434 ACTGA
63 A--GA
*
9608439 -TGCATCGGTGCATG
1 GTGCATCGATGCATG
9608453 CCTTTGAATA
Statistics
Matches: 125, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
62 5 0.04
63 8 0.06
64 53 0.42
65 57 0.46
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATATTCAGAGTGCATCGATGCATGGAGA
Done.