Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006530.1 Hibiscus syriacus cultivar Beakdansim tig00015919_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: 612433
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 4 of 4
Found at i:523983 original size:55 final size:55
Alignment explanation
Indices: 523915--524137 Score: 270
Period size: 55 Copynumber: 4.1 Consensus size: 55
523905 CAGATCAATT
* * * *
523915 TTTGGAAGACGGGTCTGCTCAACTTTTCTTCAGGGGAGATCAGACTTGAGAAATC
1 TTTGGAAGACGGGTCTGCTCCACTCTTCTTCAGGGGAGATAAGACTCGAGAAATC
* * * *
523970 TTTGGAAGACGGGTCTGCTCCACTCTTCTTTAAGGGATATAAGACTCGGGAAATC
1 TTTGGAAGACGGGTCTGCTCCACTCTTCTTCAGGGGAGATAAGACTCGAGAAATC
* * * * * *
524025 GTTGGAAGACGGGTTTACTCCATTATTCTTCAGGGGAGATAAGACTC-AGGAAATA
1 TTTGGAAGACGGGTCTGCTCCACTCTTCTTCAGGGGAGATAAGACTCGA-GAAATC
* * *
524080 TTTGGAAGACGAGTCTGCTCCACTCTTCTTTA-GGGAGATAAGACCCGAGAAATC
1 TTTGGAAGACGGGTCTGCTCCACTCTTCTTCAGGGGAGATAAGACTCGAGAAATC
524134 TTTG
1 TTTG
524138 ATTCACTTTG
Statistics
Matches: 139, Mismatches: 27, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
54 22 0.16
55 117 0.84
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (55 bp):
TTTGGAAGACGGGTCTGCTCCACTCTTCTTCAGGGGAGATAAGACTCGAGAAATC
Found at i:524109 original size:110 final size:109
Alignment explanation
Indices: 523916--524133 Score: 305
Period size: 110 Copynumber: 2.0 Consensus size: 109
523906 AGATCAATTT
* * * *
523916 TTGGAAGACGGGTCTGCTCAACTTTTCTTCAGGGGAGATCAGACTTGAGAAATCTTTGGAAGACG
1 TTGGAAGACGGGTCTACTCAACTTTTCTTCAGGGGAGATAAGACTAGAGAAATATTTGGAAGACG
* * * *
523981 GGTCTGCTCCACTCTTCTTTAAGGGATATAAGACTCGGGAAATCG
66 AGTCTGCTCCACTCTTCTTT-AGGGAGATAAGACCCGAGAAATCG
* *
524026 TTGGAAGACGGGTTTACTCCA-TTATTCTTCAGGGGAGATAAGACTCAG-GAAATATTTGGAAGA
1 TTGGAAGACGGGTCTACTCAACTT-TTCTTCAGGGGAGATAAGACT-AGAGAAATATTTGGAAGA
524089 CGAGTCTGCTCCACTCTTCTTTAGGGAGATAAGACCCGAGAAATC
64 CGAGTCTGCTCCACTCTTCTTTAGGGAGATAAGACCCGAGAAATC
524134 TTTGATTCAC
Statistics
Matches: 96, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
109 22 0.23
110 73 0.76
111 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (109 bp):
TTGGAAGACGGGTCTACTCAACTTTTCTTCAGGGGAGATAAGACTAGAGAAATATTTGGAAGACG
AGTCTGCTCCACTCTTCTTTAGGGAGATAAGACCCGAGAAATCG
Found at i:524370 original size:67 final size:67
Alignment explanation
Indices: 524214--524737 Score: 698
Period size: 67 Copynumber: 7.9 Consensus size: 67
524204 ATCAAATCAG
*
524214 AAAGATTGACTCCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTT---GAGGGAGTCAGGAAT-
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
524275 AA
66 AA
* * * *
524277 AAAGATTGACTTCTCTTCACGAGGAAGTCAACGATTGACTCCTCTTTGTGAGGGAGTCAAGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
524342 AA
66 AA
*
524344 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTTAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
*
524409 AC
66 AA
* * * * * *
524411 AAAGATTGACTTCTCTTTACGATGATGTCAAGGATTAACTCCTCTTCGCAAGGGAGTCAAGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
524476 ACA
66 A-A
* * **
524479 AAA-ATTGACTTCTCTTTATGAGGAAGTCAAGGATTGACTCCTCTTCTTGAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
*
524543 AC
66 AA
* * * * * *
524545 AAAGGTTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCCTCTTCGTGATGAAGTCGGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
*
524610 AG
66 AA
* * * ** *
524612 AAAGATTGACTTCTCTTCATGAGGAAGTCAAGGGTTTACTCCTCTTAACGAGGGAGTCATGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
*
524677 AC
66 AA
* *
524679 AAAGATTGACTTCTCTTCACGAGGAATTCAAGGATTGACTCCTCTTCACGAGGGAGTCA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCA
524738 AGGATTGACT
Statistics
Matches: 406, Mismatches: 49, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
63 44 0.11
66 17 0.04
67 342 0.84
68 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (67 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATA
AA
Found at i:524724 original size:96 final size:96
Alignment explanation
Indices: 524615--525235 Score: 320
Period size: 96 Copynumber: 6.3 Consensus size: 96
524605 GAATAAGAAA
* * * * ** *
524615 GATTGACTTCTCTTCATGAGGAAGTCAAGGGTTTACTCCTCTTAACGAGGGAGTCATGAATAACA
1 GATTGACTCCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTAACGAAAGAGTCAGGAATAACA
*
524680 AAGATTGACTTCTCTTCACGAGGAATTCAAG
66 AAGATTGACTTCTCTTCACGAGGAAGTCAAG
* *
524711 GATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATAACA
1 GATTGACTCCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTAACGAAAGAGTCAGGAATAACA
524776 AAGATTGACTTCTCTTCACGAGGAAGTCAAG
66 AAGATTGACTTCTCTTCACGAGGAAGTCAAG
* ** * * * *** *** *
524807 GATTGAATCCTCTTTGCGAGGGAGTCAAGAATAAAAAAGA-TTGACTTAATTTAA-CG--AGGAA
1 GATTGACTCCTCTTCACGAGGAAGTCAAGGAT-----TGACTCCTCTTAACGAAAGAGTCAGGAA
* * * ** * *
524868 GT--CAAGGATTGAATCCTCTTTGCGAGGGAGTCAGGAATAAAAAA
61 -TAACAAAGATTGACTTCTCTTCACGA-GGA---A-G--T--CAAG
** * ** **
524912 GATTGACTTATCTTCACGATGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
1 GATTGACTCCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTAACGAAAGAGTCAGGAATAACA
524977 AAGATTGACTTCTCTTCACGAGGAAGTCAAG
66 AAGATTGACTTCTCTTCACGAGGAAGTCAAG
* * * * ** *
525008 GATTAACTCCTCTTCGGGAGGGAGTCAAGAATAACAAAGATTGACTTTTCTTTACG--AG-G--A
1 GATTGACTCCTCTTC---A-CGAG-GAAG--T--CAAGGATTGACTCCTCTTAACGAAAGAGTCA
* * * *
525068 --AGT--CAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
57 GGAATAACAAAGATTGACTTCTCTTCACGA-GGA---A-G--T--CAAG
** ** **
525113 GATTGACTTATCCTT-ACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAC
1 GATTGACTCCT-CTTCACGAGGAAGTCAAGGATTGACTCCTCTTAACGAAAGAGTCAGGAATAAC
*
525177 AAAGATTGACTTCTCTTCACGAGGAAATCAAG
65 AAAGATTGACTTCTCTTCACGAGGAAGTCAAG
*
525209 GATTGACTCCTCTTCACGAGGGAGTCA
1 GATTGACTCCTCTTCACGAGGAAGTCA
525236 GGAATAACAT
Statistics
Matches: 383, Mismatches: 92, Indels: 100
0.67 0.16 0.17
Matches are distributed among these distances:
95 3 0.01
96 207 0.54
97 11 0.03
98 7 0.02
99 3 0.01
100 18 0.05
101 17 0.04
102 3 0.01
103 7 0.02
104 11 0.03
105 93 0.24
106 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (96 bp):
GATTGACTCCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTAACGAAAGAGTCAGGAATAACA
AAGATTGACTTCTCTTCACGAGGAAGTCAAG
Found at i:524746 original size:163 final size:163
Alignment explanation
Indices: 524546--524900 Score: 473
Period size: 163 Copynumber: 2.2 Consensus size: 163
524536 AGGAATAACA
* * * ** * *
524546 AAGG-TTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCCTCTTCGTG-ATGAAGTCGGGAAT
1 AAGGATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAG-AGTCAGGAAT
* * * * * *
524609 AAGAAAGATTGACTTCTCTTCATGAGGAAGTCAAGGGTTTACTCCTCTTAACGAGGGAGTCATGA
65 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTAACGAGGGAGTCAAGA
* * * *
524674 ATAACAAAGATTGACTT-CTCTTCACGAGGAATTC
130 ATAAAAAAGATTGACTTAAT-TTAACGAGGAAGTC
524708 AAGGATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATA
1 AAGGATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATA
**
524773 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTTGCGAGGGAGTCAAGAA
66 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTAACGAGGGAGTCAAGAA
524838 TAAAAAAGATTGACTTAATTTAACGAGGAAGTC
131 TAAAAAAGATTGACTTAATTTAACGAGGAAGTC
* **
524871 AAGGATTGAATCCTCTTTGCGAGGGAGTCA
1 AAGGATTGACTCCTCTTCACGAGGGAGTCA
524901 GGAATAAAAA
Statistics
Matches: 168, Mismatches: 22, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
162 4 0.02
163 161 0.96
164 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (163 bp):
AAGGATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATA
ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTAACGAGGGAGTCAAGAA
TAAAAAAGATTGACTTAATTTAACGAGGAAGTC
Found at i:524777 original size:230 final size:230
Alignment explanation
Indices: 524482--524967 Score: 668
Period size: 230 Copynumber: 2.1 Consensus size: 230
524472 AATAACAAAA
* * * * ** **
524482 ATTGACTTCTCTTTATGAGGAAGTCAAGGATTGACTCCTCTTCTTGAGGGAGTCAGGAATAACAA
1 ATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATAACAA
* * * * * ** *
524547 AGGTTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCCTCTTCGTGATGAAGTCGGGAATAAG
66 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTCGCGAGGAAGTCAAGAATAAA
* * * * * * *
524612 AAAGATTGACTT-CTCTTCATGAGGAAGTCAAGGGTTTACTCCTCTTAACGAGGGAGTCATGAAT
131 AAAGATTGACTTAAT-TTAACGAGGAAGTCAAGGATTGAATCCTCTTAACGAGGGAGTCAGGAAT
* * *
524676 AACAAAGATTGACTTCTCTTCACGAGGAATTCAAGG
195 AAAAAAGATTGACTTATCTTCACGAGGAAGTCAAGG
524712 ATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATAACAA
1 ATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATAACAA
* *
524777 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTTGCGAGGGAGTCAAGAATAAA
66 AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTCGCGAGGAAGTCAAGAATAAA
**
524842 AAAGATTGACTTAATTTAACGAGGAAGTCAAGGATTGAATCCTCTTTGCGAGGGAGTCAGGAATA
131 AAAGATTGACTTAATTTAACGAGGAAGTCAAGGATTGAATCCTCTTAACGAGGGAGTCAGGAATA
*
524907 AAAAAGATTGACTTATCTTCACGATGAAGTCAAGG
196 AAAAAGATTGACTTATCTTCACGAGGAAGTCAAGG
*
524942 ATTGACTCCTCTTCGCGAGGGAGTCA
1 ATTGACTCCTCTTCACGAGGGAGTCA
524968 GGAATAACAA
Statistics
Matches: 223, Mismatches: 32, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
230 222 1.00
231 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (230 bp):
ATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATAACAA
AGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTCGCGAGGAAGTCAAGAATAAA
AAAGATTGACTTAATTTAACGAGGAAGTCAAGGATTGAATCCTCTTAACGAGGGAGTCAGGAATA
AAAAAGATTGACTTATCTTCACGAGGAAGTCAAGG
Found at i:524782 original size:67 final size:67
Alignment explanation
Indices: 524711--525275 Score: 846
Period size: 67 Copynumber: 8.4 Consensus size: 67
524701 GGAATTCAAG
* * * **
524711 GATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATAACA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
524776 AA
66 AA
* * * *
524778 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTTGCGAGGGAGTCAAGAATAAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
524843 AA
66 AA
* * * * *
524845 GATTGACTTAAT-TTAACGAGGAAGTCAAGGATTGAATCCTCTTTGCGAGGGAGTCAGGAATAAA
1 GATTGACTT-CTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAC
524909 AAA
65 AAA
* *
524912 GATTGACTTATCTTCACGATGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
524977 AA
66 AA
* * *
524979 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTCGGGAGGGAGTCAAGAATAACA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
525044 AA
66 AA
* * *
525046 GATTGACTTTTCTTTACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAACA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
525111 AA
66 AA
*
525113 GATTGACTTATCCTT-ACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAC
1 GATTGACTTCT-CTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAC
525177 AAA
65 AAA
* *
525180 GATTGACTTCTCTTCACGAGGAAATCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAACA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
*
525245 TA
66 AA
* *
525247 GATTGACTTCTATTCACAAGGAAGTCAAG
1 GATTGACTTCTCTTCACGAGGAAGTCAAG
525276 TTGAAGTTTA
Statistics
Matches: 457, Mismatches: 37, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
66 5 0.01
67 448 0.98
68 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (67 bp):
GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
AA
Found at i:524784 original size:201 final size:195
Alignment explanation
Indices: 524212--524804 Score: 555
Period size: 201 Copynumber: 3.0 Consensus size: 195
524202 ATATCAAATC
* * *
524212 AGAAAGATTGACTCCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTT-GAGGGAGTCAGGAATA
1 AGAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTCGAGGGAGTCAAGAATA
* **
524276 A-AAAGATTGACTTCTCTTCACGAGGAAGTCAACGATTGACTCCTCTTTGTGAGGGAGTCAAGAA
66 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCATGAGGGAGTCAAG--
* *
524340 TAAAAAAGATTGACTTCTCTTCACGAGG--A-AGT--CAAGGATTGACTCCTCTTCGCGAGGGAG
129 -------GATTGACTACTCTTCACGAGGTCAGAGTAACAAGGATTGACTCCTCTTCGCGAGGAAG
*
524400 TTAGGAATA
187 TCAGGAATA
* * * *
524409 ACAAAGATTGACTTCTCTTTACGATGATGTCAAGGATTAACTCCTCTTCGCAAGGGAGTCAAGAA
1 AGAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTCG--AGGGAGTCAAGAA
* * * *
524474 TAACAAAAATTGACTTCTCTTTATGAGGAAGTCAAGGATTGACTCCTCTTCTTGAGGGAGTC-AG
64 TAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCATGAGGGAGTCAAG
* * * *
524538 GAATAACAAAGGTTGACTTCTCTTCATGAGG--A-AGT--CAAGGATTGACTCCTCTTCGTGATG
129 G--------A--TTGACTACTCTTCACGAGGTCAGAGTAACAAGGATTGACTCCTCTTCGCGAGG
*
524598 AAGTCGGGAATA
184 AAGTCAGGAATA
* * * *
524610 AGAAAGATTGACTTCTCTTCATGAGGAAGTCAAGGGTTTACTCCTCTTAACGAGGGAGTCATGAA
1 AGAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTT--CGAGGGAGTCAAGAA
* *
524675 TAACAAAGATTGACTTCTCTTCACGAGGAATTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAG
64 TAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCATGAGGGAGTCAAG
* * * * *
524740 GATTGACTCCTCTTCACGAAAGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCA
129 GATTGACTACTCTTCACG--AG-GTCA-GAGTAACAAGGATTGACTCCTCTTCGCGAGGAAGTCA
524805 AGGATTGAAT
Statistics
Matches: 328, Mismatches: 42, Indels: 48
0.78 0.10 0.11
Matches are distributed among these distances:
191 1 0.00
192 14 0.04
194 3 0.01
195 1 0.00
197 43 0.13
198 1 0.00
199 3 0.01
200 17 0.05
201 240 0.73
202 3 0.01
203 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (195 bp):
AGAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTAACTCCTCTTCGAGGGAGTCAAGAATA
ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCATGAGGGAGTCAAGGA
TTGACTACTCTTCACGAGGTCAGAGTAACAAGGATTGACTCCTCTTCGCGAGGAAGTCAGGAATA
Found at i:533452 original size:30 final size:31
Alignment explanation
Indices: 533418--533483 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 31
533408 TTCGATATAA
533418 CAAATTAAGTTAAATGGATTTTAAGATTTT-
1 CAAATTAAGTTAAATGGATTTTAAGATTTTC
533448 CAAATTAAGTTAAATGGATTTTAAGATTTTC
1 CAAATTAAGTTAAATGGATTTTAAGATTTTC
533479 CAAAT
1 CAAAT
533484 GATTTTCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (31 bp):
CAAATTAAGTTAAATGGATTTTAAGATTTTC
Found at i:539574 original size:18 final size:19
Alignment explanation
Indices: 539540--539576 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
539530 TTTTGGTGCA
539540 GAGGGAATCGATCCCCCCT
1 GAGGGAATCGATCCCCCCT
*
539559 GAGGGAA-CGATTCCCCCT
1 GAGGGAATCGATCCCCCCT
539577 TTGAAGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (19 bp):
GAGGGAATCGATCCCCCCT
Found at i:542050 original size:30 final size:31
Alignment explanation
Indices: 542016--542081 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
542006 TTCGATATAA
*
542016 CAAATTAAGTTAAATGGATTTTAAGATTTT-
1 CAAATTAAGTTAAATGGATTTTAAAATTTTC
542046 CAAATTAAGTTAAATGGATTTTAAAATTTTC
1 CAAATTAAGTTAAATGGATTTTAAAATTTTC
542077 CAAAT
1 CAAAT
542082 GATTTTCTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 29 0.85
31 5 0.15
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (31 bp):
CAAATTAAGTTAAATGGATTTTAAAATTTTC
Found at i:543563 original size:3 final size:3
Alignment explanation
Indices: 543557--543583 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
543547 AATTATTATT
543557 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
543584 GGATAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:544726 original size:2 final size:2
Alignment explanation
Indices: 544719--544766 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
544709 CCACTTTTAA
544719 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
544761 AT AT AT
1 AT AT AT
544767 TTGTTATGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:545094 original size:27 final size:27
Alignment explanation
Indices: 545056--545144 Score: 178
Period size: 27 Copynumber: 3.3 Consensus size: 27
545046 CTTAACGTAT
545056 AAGAAAGTTACTTTCGATAATTTTAAA
1 AAGAAAGTTACTTTCGATAATTTTAAA
545083 AAGAAAGTTACTTTCGATAATTTTAAA
1 AAGAAAGTTACTTTCGATAATTTTAAA
545110 AAGAAAGTTACTTTCGATAATTTTAAA
1 AAGAAAGTTACTTTCGATAATTTTAAA
545137 AAGAAAGT
1 AAGAAAGT
545145 ATATCTCATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (27 bp):
AAGAAAGTTACTTTCGATAATTTTAAA
Found at i:546497 original size:76 final size:76
Alignment explanation
Indices: 546371--546552 Score: 276
Period size: 76 Copynumber: 2.4 Consensus size: 76
546361 AAATTTGAAG
* *
546371 CTTAACATTGACTTACATCAGTG-AATGAATACGTAATTCCAGCACTAAACTTATCACATAATTC
1 CTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTA
*
546435 CCGCAGTGAAA
66 CCGCAGGGAAA
* * * *
546446 TTTAACATTGATTTACACCAGTGAAATGAATATGTAATTCTAGCACTAAACTTATCACATAATTA
1 CTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTA
*
546511 CTGCAGGGAAA
66 CCGCAGGGAAA
*
546522 CTTAATATTGACTTACACCAGTGAAATGAAT
1 CTTAACATTGACTTACACCAGTGAAATGAAT
546553 GTGCAACGAT
Statistics
Matches: 95, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 20 0.21
76 75 0.79
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (76 bp):
CTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTA
CCGCAGGGAAA
Found at i:547061 original size:2 final size:2
Alignment explanation
Indices: 547054--547085 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
547044 CTATGAAATA
547054 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
547086 TTTAAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:547819 original size:3 final size:3
Alignment explanation
Indices: 547813--547854 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
547803 ATGTTTTTAC
547813 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
547855 TGCTTTTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:551983 original size:17 final size:17
Alignment explanation
Indices: 551961--552006 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
551951 TCTTTAGTTC
551961 TCAAATTTTAGGCGGGG
1 TCAAATTTTAGGCGGGG
551978 TCAAATTTTAGGCGGGG
1 TCAAATTTTAGGCGGGG
551995 TCAAATTTTAGG
1 TCAAATTTTAGG
552007 GGTTTCACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.33
Consensus pattern (17 bp):
TCAAATTTTAGGCGGGG
Found at i:559399 original size:39 final size:39
Alignment explanation
Indices: 559338--559412 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
559328 AGATGAAACC
559338 TTTAGCTAGACCAATAAAGG-AAATTACAATAAAGTTGAA
1 TTTAGCTAGACCAATAAAGGAAAATTA-AATAAAGTTGAA
*
559377 TTTAGCTAG-CCAA-ACAATGGAAAATTAAATCAAGTT
1 TTTAGCTAGACCAATA-AA-GGAAAATTAAATAAAGTT
559413 TATCAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
37 1 0.03
38 6 0.19
39 19 0.59
40 6 0.19
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.27
Consensus pattern (39 bp):
TTTAGCTAGACCAATAAAGGAAAATTAAATAAAGTTGAA
Found at i:561249 original size:134 final size:133
Alignment explanation
Indices: 561080--561921 Score: 809
Period size: 134 Copynumber: 6.3 Consensus size: 133
561070 GCAAATCGAA
* * * * * * * *
561080 CTCGATTCAATATTCCCTAAAAAATAGTGGAATGAATCAATATTCCTAAATCTGATTTTCCCACT
1 CTCGATTCAATCTTCCCT-GAGAATAGTGGAATGAATCAACATTCCCAGATATGATTTTCCCTCT
* * * *
561145 AGAAGAAGAAGACCAAATCCCTCTCTTTCAATATTTGATCTTCCCTGAGTAATAGTGGAACAAGT
65 AGAAGAAGAAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGT
561210 CTGC
130 CTGC
* * **
561214 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACATCCCCAGATATGATTTTCCCTAA
1 CTCGATTCAATCTTCCCTGAG-AATAGTGGAATGAATCAACATTCCCAGATATGATTTTCCCTCT
* * * ** *
561279 AGAAGAAG-CGAAACAAATCCCTCTCTTTTAAGATTTGATATTCTTTGAGTAATAGTGGAAAAAG
65 AGAAGAAGAAG-AACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAG
*
561343 TCTGT
129 TCTGC
* * * * * * *
561348 CTCAATTCAATCTTCCCTAAAGAACAGTGGATTGAATCAACATCCCCAAATTTGATTTTCCCT-T
1 CTCGATTCAATCTTCCCT-GAGAATAGTGGAATGAATCAACATTCCCAGATATGATTTTCCCTCT
* * * *
561412 AAGAAGAAGATGAACAGATCACTCTCTTTCAATATTTGAAATTCCCTGAGTAATAGTGGAACAAG
65 -AGAAGAAGAAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAG
561477 TCTGC
129 TCTGC
* * * ** * * *
561482 CTCGATTCAATCTTCGCTGAAGAACAGTGGAATTAATCAATGTCCCCAGATATAATTTTCCCTCA
1 CTCGATTCAATCTTCCCTG-AGAATAGTGGAATGAATCAACATTCCCAGATATGATTTTCCCTCT
* * * * *
561547 AGAAGAACCG-A-AACAGGTCCCTCTCTTTTAAGATTTGATATTCCCTAAGGAA-ATGTGGAATA
65 AGAAGAA--GAAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATA-GTGGAACA
561609 AGTCTGC
127 AGTCTGC
* * * * *
561616 CTCGATTCAATCTTCCCTGAAGAATAGTGTAATGAATCAACATTTCCAGATCTGATGTTCCCTCA
1 CTCGATTCAATCTTCCCTG-AGAATAGTGGAATGAATCAACATTCCCAGATATGATTTTCCCTCT
* * * * * * *
561681 AAAAGCAGCAGAACAGATCCCT-TTTTTC-AGATTTGATTTTCCATGAGGAATAGTGGAACAAGT
65 AGAAGAAGAAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGT
*
561744 CTGT
130 CTGC
* * * * * *
561748 CTCGATTCAATCTCCCCTGAAGAATAGTGGAATGAATAAACATTTCCATATATGGTTTTCCTTC-
1 CTCGATTCAATCTTCCCTG-AGAATAGTGGAATGAATCAACATTCCCAGATATGATTTTCCCTCT
* ** * * * * * *
561812 AGGAAGCAGTGGAATAGATCCCTCTCTTTCAAGACTTGATCTTCCCTGAGTAACAGTAGAAAAAG
65 A-GAAGAAGAAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAG
*
561877 TATGC
129 TCTGC
* *
561882 CTCGATTCAATCTTCCATAAAGAATAGTGGAATGAATCAA
1 CTCGATTCAATCTTCCCT-GAGAATAGTGGAATGAATCAA
561922 TATTGCTCGA
Statistics
Matches: 587, Mismatches: 104, Indels: 34
0.81 0.14 0.05
Matches are distributed among these distances:
131 1 0.00
132 106 0.18
133 14 0.02
134 462 0.79
135 3 0.01
136 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (133 bp):
CTCGATTCAATCTTCCCTGAGAATAGTGGAATGAATCAACATTCCCAGATATGATTTTCCCTCTA
GAAGAAGAAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTC
TGC
Found at i:561561 original size:268 final size:266
Alignment explanation
Indices: 561080--561921 Score: 1017
Period size: 268 Copynumber: 3.2 Consensus size: 266
561070 GCAAATCGAA
* * * * *
561080 CTCGATTCAATATTCCCTAAAAAATAGTGGAATGAATCAATATTCCTAAATCTGATTTTCCCACT
1 CTCGATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACATTCCCAAATCTGATTTTCCC-TT
* * *
561145 -AGAAGAAGAAGACCAAATCCCTCTCTTTCAATATTTGATCTTCCCTGAGTAATAGTGGAACAAG
65 AAGAAGAAG-AGAACAGATCCCTCTCTTTCAATATTTGATATTCCCTGAGTAATAGTGGAACAAG
561209 TCTGCCTCGATTCAATCTTCCCTG-AGTAACAGTGGAATGAATCAACATCCCCAGATATGATTTT
129 TCTGCCTCGATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACATCCCCAGATATGATTTT
* * **
561273 CCCTAAAGAAGAAGCGAAACAAATCCCTCTCTTTTAAGATTTGATATTCTTTGAGTAATAGTGGA
193 CCCTCAAGAAGAAGCGAAACAGATCCCTCTCTTTTAAGATTTGATATTCCCTGAGTAA-AGTGGA
*
561338 AAAAGTCTGT
257 AAAAGTCTGC
* * * * *
561348 CTCAATTCAATCTTCCCTAAAGAACAGTGGATTGAATCAACATCCCCAAATTTGATTTTCCCTTA
1 CTCGATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACATTCCCAAATCTGATTTTCCCTTA
* *
561413 AGAAGAAGATGAACAGATCACTCTCTTTCAATATTTGAAATTCCCTGAGTAATAGTGGAACAAGT
66 AGAAGAAGA-GAACAGATCCCTCTCTTTCAATATTTGATATTCCCTGAGTAATAGTGGAACAAGT
* * ** *
561478 CTGCCTCGATTCAATCTTCGCTGAAGAACAGTGGAATTAATCAATGTCCCCAGATATAATTTTCC
130 CTGCCTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATATGATTTTCC
* * * * *
561543 CTCAAGAAGAACCGAAACAGGTCCCTCTCTTTTAAGATTTGATATTCCCTAAGGAAATGTGGAAT
195 CTCAAGAAGAAGCGAAACAGATCCCTCTCTTTTAAGATTTGATATTCCCTGAGTAAA-GTGGAAA
561608 AAGTCTGC
259 AAGTCTGC
* * * * * *
561616 CTCGATTCAATCTTCCCTGAAGAATAGTGTAATGAATCAACATTTCCAGATCTGATGTTCCCTCA
1 CTCGATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACATTCCCAAATCTGATTTTCCCTTA
* * * * * * *
561681 AAAAGCAGCAGAACAGATCCCT-TTTTTC-AGATTTGATTTTCCATGAGGAATAGTGGAACAAGT
66 AGAAGAAG-AGAACAGATCCCTCTCTTTCAATATTTGATATTCCCTGAGTAATAGTGGAACAAGT
* * * * ** * *
561744 CTGTCTCGATTCAATCTCCCCTGAAGAATAGTGGAATGAATAAACATTTCCATATATGGTTTTCC
130 CTGCCTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATATGATTTTCC
* * * * * * * * * *
561809 TTCAGGAAGCAGTGGAATAGATCCCTCTCTTTCAAGACTTGATCTTCCCTGAGTAACAGTAGAAA
195 CTCAAGAAGAAGCGAAACAGATCCCTCTCTTTTAAGATTTGATATTCCCTGAGTAA-AGTGGAAA
*
561874 AAGTATGC
259 AAGTCTGC
*
561882 CTCGATTCAATCTTCCATAAAGAATAGTGGAATGAATCAA
1 CTCGATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAA
561922 TATTGCTCGA
Statistics
Matches: 486, Mismatches: 82, Indels: 14
0.84 0.14 0.02
Matches are distributed among these distances:
266 174 0.36
267 9 0.02
268 300 0.62
269 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (266 bp):
CTCGATTCAATCTTCCCTAAAGAATAGTGGAATGAATCAACATTCCCAAATCTGATTTTCCCTTA
AGAAGAAGAGAACAGATCCCTCTCTTTCAATATTTGATATTCCCTGAGTAATAGTGGAACAAGTC
TGCCTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATCCCCAGATATGATTTTCCC
TCAAGAAGAAGCGAAACAGATCCCTCTCTTTTAAGATTTGATATTCCCTGAGTAAAGTGGAAAAA
GTCTGC
Found at i:563854 original size:3 final size:3
Alignment explanation
Indices: 563848--563891 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
563838 AATTATTATT
** * *
563848 TAA TAA TAA TAA TAA TAA GGA TAA AAA TTA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
563892 TTGACAAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:563900 original size:27 final size:27
Alignment explanation
Indices: 563850--563902 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
563840 TTATTATTTA
*
563850 ATAATAATAATAATAAGGATAAAAATT
1 ATAATAATAATAATAAGGACAAAAATT
**
563877 ATAATAATAATAATATTGACAAAAAT
1 ATAATAATAATAATAAGGACAAAAAT
563903 CATTTTCTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (27 bp):
ATAATAATAATAATAAGGACAAAAATT
Found at i:564366 original size:83 final size:82
Alignment explanation
Indices: 564028--564700 Score: 772
Period size: 82 Copynumber: 8.2 Consensus size: 82
564018 TCCACTACAA
* * * ** * **** *
564028 TTTCTGGGTAGATCAGACTTGATCTGTTCCTCTCCTTCGGGTAGTCAAATC--TGAAAGAAAACG
1 TTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACG
* *
564091 AGACTGCTTCACTCTTC
66 AGTCTGCTCCACTCTTC
* * * * * * * * * *
564108 CTTCAGGGCATAGT-AGACTTTATTTATTCCTCTTTTTCAGGTAGACATATCAATTTTGGAAGAT
1 TTTCAGGGGAGA-TCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGAC
*
564172 GGGTCTGCTCCACTCTTC
65 GAGTCTGCTCCACTCTTC
* * * *
564190 TTTTAGGGGAGATCAGACTTGACT-TGTTCCTC-TTTTCGGGTAGTTAGATCAATTTTAGAAGAT
1 TTTCAGGGGAGATCAGACTTGA-TATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGAC
* *
564253 GGGTCTGCTCCACTTTTC
65 GAGTCTGCTCCACTCTTC
* * * *
564271 TTTCAAGAGAGATCAGACTTGATATGTTTCTCTTTTTTGGGTAGTCAGATCAATTTTTGGAAGAC
1 TTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAA-TTTTGGAAGAC
*
564336 GAGTCTACTCCACTCTTC
65 GAGTCTGCTCCACTCTTC
* *
564354 TTTCAGGGGAGATCAGATTTGATTTGTTCCTCTTTTTCGGGTAGTCAGATCAA-TTTGGAAGAC-
1 TTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACG
564417 ATGTCTGCTCCACTCTTC
66 A-GTCTGCTCCACTCTTC
564435 TTTCA-GGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTTGGAAGAC
1 TTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAA-TTTTGGAAGAC
*
564499 AAGTCTGCTCCACTCTTC
65 GAGTCTGCTCCACTCTTC
* * * * * *
564517 TTTCAAGGTAGATCAAACTTTATATGTTCCTCTTTTTCGGGTAGTCAAATCAATTTTGGAAGA-T
1 TTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACG
564581 ATGTCTGCTCCACTCTTC
66 A-GTCTGCTCCACTCTTC
* * *
564599 TTTTAGGGGAGATCAGATTTGATTTGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTTGGAAGAC
1 TTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAA-TTTTGGAAGAC
* *
564664 GGGTCTGCTCCACTTTTC
65 GAGTCTGCTCCACTCTTC
564682 TTT-AGGGGAGATCAGACTT
1 TTTCAGGGGAGATCAGACTT
564701 AAGAAATCTT
Statistics
Matches: 507, Mismatches: 70, Indels: 30
0.84 0.12 0.05
Matches are distributed among these distances:
80 84 0.17
81 102 0.20
82 177 0.35
83 144 0.28
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (82 bp):
TTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACG
AGTCTGCTCCACTCTTC
Found at i:564469 original size:163 final size:164
Alignment explanation
Indices: 564094--564697 Score: 806
Period size: 163 Copynumber: 3.7 Consensus size: 164
564084 GAAAACGAGA
* * * * * * * * *
564094 CTGCTTCACTCTTCCTTCAGGGCATAGT-AGACTTTATTTATTCCTCTTTTTCAGGTAGACATAT
1 CTGCTCCACTCTTCTTTCAGGG-AGA-TCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGAT
* * * * *
564158 CAA-TTTTGGAAGATGGGTCTGCTCCACTCTTCTTTTAGGGGAGATCAGACTTGACTTGTTCCTC
64 CAATTTTTGGAAGACGAGTCTGCTCCACTCTTCTTTCAGGGGAGATCAGATTTGATTTGTTCCTC
* * **
564222 -TTTTCGGGTAGTTAGATCAATTTTAGAAGATGGGT
129 TTTTTCGGGTAGTCAGATCAATTTTGGAAGATATGT
* * * *
564257 CTGCTCCACTTTTCTTTCAAGAGAGATCAGACTTGATATGTTTCTCTTTTTTGGGTAGTCAGATC
1 CTGCTCCACTCTTCTTTC-AGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATC
*
564322 AATTTTTGGAAGACGAGTCTACTCCACTCTTCTTTCAGGGGAGATCAGATTTGATTTGTTCCTCT
65 AATTTTTGGAAGACGAGTCTGCTCCACTCTTCTTTCAGGGGAGATCAGATTTGATTTGTTCCTCT
*
564387 TTTTCGGGTAGTCAGATCAA-TTTGGAAGACATGT
130 TTTTCGGGTAGTCAGATCAATTTTGGAAGATATGT
564421 CTGCTCCACTCTTCTTTCAGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCA
1 CTGCTCCACTCTTCTTTCAGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCA
* * * * *
564486 ATTTTTGGAAGACAAGTCTGCTCCACTCTTCTTTCAAGGTAGATCAAACTTT-ATATGTTCCTCT
66 ATTTTTGGAAGACGAGTCTGCTCCACTCTTCTTTCAGGGGAGATCAGA-TTTGATTTGTTCCTCT
*
564550 TTTTCGGGTAGTCAAATCAATTTTGGAAGATATGT
130 TTTTCGGGTAGTCAGATCAATTTTGGAAGATATGT
* * *
564585 CTGCTCCACTCTTCTTTTAGGGGAGATCAGATTTGATTTGTTCCTCTTTTTCGGGTAGTCAGATC
1 CTGCTCCACTCTTCTTTCA-GGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATC
* *
564650 AATTTTTGGAAGACGGGTCTGCTCCACTTTTCTTT-AGGGGAGATCAGA
65 AATTTTTGGAAGACGAGTCTGCTCCACTCTTCTTTCAGGGGAGATCAGA
564698 CTTAAGAAAT
Statistics
Matches: 389, Mismatches: 45, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
162 1 0.00
163 165 0.42
164 129 0.33
165 94 0.24
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (164 bp):
CTGCTCCACTCTTCTTTCAGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCA
ATTTTTGGAAGACGAGTCTGCTCCACTCTTCTTTCAGGGGAGATCAGATTTGATTTGTTCCTCTT
TTTCGGGTAGTCAGATCAATTTTGGAAGATATGT
Found at i:564719 original size:55 final size:55
Alignment explanation
Indices: 564653--564875 Score: 234
Period size: 55 Copynumber: 4.1 Consensus size: 55
564643 TCAGATCAAT
* * *
564653 TTTTGGAAGACGGGTCTGCTCCACTTTTCTTTAGGGGAGATCAGACTTAAGAAATC
1 TTTT-GAAGACGGGTCTGCTCCACTCTTCTTTAGGGGAGATAAGACTCAAGAAATC
* * * * **
564709 TTTTGAAGACGGGTGTTCTCCACTCTTCTTTAAGGGCGATAAGACTCGGGAAATC
1 TTTTGAAGACGGGTCTGCTCCACTCTTCTTTAGGGGAGATAAGACTCAAGAAATC
* * * * * * *
564764 -TTTGAAAGAAGGGTCTACTCCATTATTCTTCAGGGGAGATAAGACTCAGGAAATA
1 TTTTG-AAGACGGGTCTGCTCCACTCTTCTTTAGGGGAGATAAGACTCAAGAAATC
* * * *
564819 TTTGGAAGACGAGTCTGCTCCACTCTTCTTTA-GGGAGATAAGGCTCGAGAAATC
1 TTTTGAAGACGGGTCTGCTCCACTCTTCTTTAGGGGAGATAAGACTCAAGAAATC
564873 TTT
1 TTT
564876 GATTCACTTT
Statistics
Matches: 135, Mismatches: 30, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
54 25 0.19
55 103 0.76
56 7 0.05
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (55 bp):
TTTTGAAGACGGGTCTGCTCCACTCTTCTTTAGGGGAGATAAGACTCAAGAAATC
Found at i:564809 original size:110 final size:109
Alignment explanation
Indices: 564654--564877 Score: 288
Period size: 110 Copynumber: 2.0 Consensus size: 109
564644 CAGATCAATT
* * * * * * * *
564654 TTTGGAAGACGGGTCTGCTCCACTTTTCTTTAGGGGAGATCAGACTTAAGAAATCTTTTGAAGAC
1 TTTGAAAGAAGGGTCTACTCCACTTTTCTTCAGGGGAGATAAGACTCAAGAAATATTTGGAAGAC
* * * * *
564719 GGGTGTTCTCCACTCTTCTTTAAGGGCGATAAGACTCGGGAAATC
66 GAGTCTGCTCCACTCTTCTTT-AGGGAGATAAGACTCGAGAAATC
*
564764 TTTGAAAGAAGGGTCTACTCCA-TTATTCTTCAGGGGAGATAAGACTCAGGAAATATTTGGAAGA
1 TTTGAAAGAAGGGTCTACTCCACTT-TTCTTCAGGGGAGATAAGACTCAAGAAATATTTGGAAGA
*
564828 CGAGTCTGCTCCACTCTTCTTTAGGGAGATAAGGCTCGAGAAATC
65 CGAGTCTGCTCCACTCTTCTTTAGGGAGATAAGACTCGAGAAATC
564873 TTTGA
1 TTTGA
564878 TTCACTTTGC
Statistics
Matches: 98, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
109 27 0.28
110 71 0.72
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (109 bp):
TTTGAAAGAAGGGTCTACTCCACTTTTCTTCAGGGGAGATAAGACTCAAGAAATATTTGGAAGAC
GAGTCTGCTCCACTCTTCTTTAGGGAGATAAGACTCGAGAAATC
Found at i:565109 original size:67 final size:67
Alignment explanation
Indices: 564951--565478 Score: 692
Period size: 67 Copynumber: 7.9 Consensus size: 67
564941 ATATCAAATC
* *
564951 AAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTT--C-AGGGAGACAAGAA
1 AAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAA
565013 T-
66 TA
* ***
565014 AAAAAGATTGACTTCTCTTCACGAGGAAGTCAACGATTGACTCCTCTTTGTGAGGGAGTCAAGAA
1 AAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAA
565079 TA
66 TA
** *
565081 AAAAAGATTGACTTCTCTTCATTAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAA
1 AAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAA
565146 TA
66 TA
* *
565148 AAAAAGATTGACTTCTCTTCACGATGG-TGTCAAGGATTGACTCCT-TTC-CGCAAGGGAGTCAG
1 AAAAAGATTGACTTCTCTTCACGA-GGAAGTCAAGGATTGACTCCTCTTCACG--AGGGAGTCAA
565210 GAATA
63 GAATA
* * * **
565215 ACAAAGATTGACTTCTCTTTATGAGGAAGTCAAGGATTGACTCCTCTTCTTGAGGGAGTCAAGAA
1 AAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAA
565280 TA
66 TA
* * ** * * ***
565282 ACAAAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGTGATGAAGTTGGGAA
1 AAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAA
565347 TA
66 TA
* * * * *
565349 AAAAATATTGACTTCTCTTCATGAGGAAGTCAAGGGTTGACTCCTCTTAACGAGGGAGTCATGAA
1 AAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAA
565414 TA
66 TA
* *
565416 ACAAAGATTGACTTCTCTTCACGAGGAATTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAG
1 AAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAG
565479 GATTGACTCC
Statistics
Matches: 406, Mismatches: 49, Indels: 16
0.86 0.10 0.03
Matches are distributed among these distances:
63 46 0.11
65 2 0.00
66 18 0.04
67 334 0.82
68 5 0.01
69 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (67 bp):
AAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAGAA
TA
Found at i:565112 original size:38 final size:38
Alignment explanation
Indices: 565065--565171 Score: 97
Period size: 38 Copynumber: 3.1 Consensus size: 38
565055 TCCTCTTTGT
* *
565065 GAGGGAGTCAAGAATAAAAAAGATTGACTTCTCTTCAT
1 GAGGAAGTCAAGAATAAAAAAGATTGACTTCTCTTCAC
* *
565103 TAGGAAGTCAAG---------GATTGACTCCTCTTCAC
1 GAGGAAGTCAAGAATAAAAAAGATTGACTTCTCTTCAC
* *
565132 GAGGGAGTCAGGAATAAAAAAGATTGACTTCTCTTCAC
1 GAGGAAGTCAAGAATAAAAAAGATTGACTTCTCTTCAC
565170 GA
1 GA
565172 TGGTGTCAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 18
0.67 0.10 0.23
Matches are distributed among these distances:
29 24 0.46
38 28 0.54
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (38 bp):
GAGGAAGTCAAGAATAAAAAAGATTGACTTCTCTTCAC
Found at i:565455 original size:96 final size:96
Alignment explanation
Indices: 565355--565559 Score: 320
Period size: 96 Copynumber: 2.1 Consensus size: 96
565345 AATAAAAAAT
* * * ** *
565355 ATTGACTTCTCTTCATGAGGAAGTCAAGGGTTGACTCCTCTTAACGAGGGAGTCATGAATAACAA
1 ATTGACTCCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTAACGAAAGAGTCAGGAATAACAA
*
565420 AGATTGACTTCTCTTCACGAGGAATTCAAGG
66 AGATTGACTTCTCTTCACGAGGAAGTCAAGG
* *
565451 ATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATAACAA
1 ATTGACTCCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTAACGAAAGAGTCAGGAATAACAA
565516 AGATTGACTTCTCTTCACGAGGAAGTCAAGG
66 AGATTGACTTCTCTTCACGAGGAAGTCAAGG
*
565547 ATTGAATCCTCTT
1 ATTGACTCCTCTT
565560 TGCGAGGGAG
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 99 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (96 bp):
ATTGACTCCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTAACGAAAGAGTCAGGAATAACAA
AGATTGACTTCTCTTCACGAGGAAGTCAAGG
Found at i:565478 original size:163 final size:163
Alignment explanation
Indices: 565285--565636 Score: 453
Period size: 163 Copynumber: 2.2 Consensus size: 163
565275 AAGAATAACA
* * ** * **
565285 AAGG-TTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGTG-ATGAAGTTGGGAAT
1 AAGGATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAG-AGTCAGGAAT
* * * *
565348 AAAAAATATTGACTTCTCTTCATGAGGAAGTCAAGGGTTGACTCCTCTTAACGAGGGAGTC-ATG
65 AAAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTAACGAGGGAGTCGA-G
* * *
565412 AATAACAAAGATTGACTT-CTCTTCACGAGGAA-TT
129 AATAAAAAAGATTGACTTAAT-TTAACGAGGAAGTT
565446 CAAGGATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAAT
1 -AAGGATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAAT
* **
565511 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTTGCGAGGGAGTCGAGA
65 AAAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTAACGAGGGAGTCGAGA
565576 ATAAAAAAGATTGACTTAATTTAACGAGGAAGTT
130 ATAAAAAAGATTGACTTAATTTAACGAGGAAGTT
* **
565610 AAGGATTGAATCCTCTTTGCGAGGGAG
1 AAGGATTGACTCCTCTTCACGAGGGAG
565637 ACAGGAATAA
Statistics
Matches: 165, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
162 4 0.02
163 155 0.94
164 6 0.04
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (163 bp):
AAGGATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATA
AAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTAACGAGGGAGTCGAGAA
TAAAAAAGATTGACTTAATTTAACGAGGAAGTT
Found at i:565513 original size:230 final size:230
Alignment explanation
Indices: 565220--565705 Score: 677
Period size: 230 Copynumber: 2.1 Consensus size: 230
565210 GAATAACAAA
* * * ** **
565220 GATTGACTTCTCTTTATGAGGAAGTCAAGGATTGACTCCTCTTCTTGAGGGAGTCAAGAATAACA
1 GATTGACTCCTCTTCATGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAAGAATAACA
* * * * * *
565285 AAGGTTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGTGATGAAGTTGGGAATAA
66 AAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTCGCGAGGAAGTCGAGAATAA
* * * * * * * *
565350 AAAATATTGACTT-CTCTTCATGAGGAAGTCAAGGGTTGACTCCTCTTAACGAGGGAGTCATGAA
131 AAAAGATTGACTTAAT-TTAACGAGGAAGTCAAGGATTGAATCCTCTTAACGAGGGAGACAGGAA
*
565414 TAACAAAGATTGACTTCTCTTCACGAGGAATTCAAG
195 TAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAG
* *
565450 GATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATAACA
1 GATTGACTCCTCTTCATGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAAGAATAACA
* *
565515 AAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTTGCGAGGGAGTCGAGAATAA
66 AAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTCGCGAGGAAGTCGAGAATAA
* **
565580 AAAAGATTGACTTAATTTAACGAGGAAGTTAAGGATTGAATCCTCTTTGCGAGGGAGACAGGAAT
131 AAAAGATTGACTTAATTTAACGAGGAAGTCAAGGATTGAATCCTCTTAACGAGGGAGACAGGAAT
*
565645 AACAAAGATTGACTTCTCTTCACGATGAAGTCAAG
196 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAG
*
565680 GATTGACTCCTCTTCGTGAGGGAGTC
1 GATTGACTCCTCTTCATGAGGGAGTC
565706 GGGAATAACA
Statistics
Matches: 223, Mismatches: 32, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
230 222 1.00
231 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (230 bp):
GATTGACTCCTCTTCATGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAAGAATAACA
AAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTCGCGAGGAAGTCGAGAATAA
AAAAGATTGACTTAATTTAACGAGGAAGTCAAGGATTGAATCCTCTTAACGAGGGAGACAGGAAT
AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAG
Found at i:565521 original size:67 final size:67
Alignment explanation
Indices: 565450--566014 Score: 803
Period size: 67 Copynumber: 8.4 Consensus size: 67
565440 GGAATTCAAG
* * * **
565450 GATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACGAAAGAGTCAGGAATAACA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
565515 AA
66 AA
* * *
565517 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTTGCGAGGGAGTC-GAGAATAAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAG-GAATAAC
565581 AAA
65 AAA
* * * * * *
565584 GATTGACTTAAT-TTAACGAGGAAGTTAAGGATTGAATCCTCTTTGCGAGGGAGACAGGAATAAC
1 GATTGACTT-CTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAC
565648 AAA
65 AAA
* * *
565651 GATTGACTTCTCTTCACGATGAAGTCAAGGATTGACTCCTCTTCGTGAGGGAGTCGGGAATAACA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
565716 AA
66 AA
* * * * *
565718 GATTTACTTCTTTTCACGAGGAAGTCAAGGATTAACTCCTCTTCGGGAGGGAGTCAGTAATAACA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
565783 AA
66 AA
* * *
565785 GATTGACTTTTCTTTACGAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAGTCAGGAATAACA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
565850 AA
66 AA
*
565852 GATTGACTTATCCTT-ACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAC
1 GATTGACTTCT-CTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAAC
565916 AAA
65 AAA
* * *
565919 GATTGACTTCTCTTCACGAGTAAATCAAGGATTGACTCCTCTTTGCGAGGGAGTCAGGAATAACA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
*
565984 GA
66 AA
*
565986 GATTGACTTCTCTTCACAAGGAAGTCAAG
1 GATTGACTTCTCTTCACGAGGAAGTCAAG
566015 TTGAAGTTTA
Statistics
Matches: 445, Mismatches: 47, Indels: 12
0.88 0.09 0.02
Matches are distributed among these distances:
66 5 0.01
67 435 0.98
68 5 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (67 bp):
GATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACA
AA
Found at i:565523 original size:201 final size:195
Alignment explanation
Indices: 564951--565543 Score: 584
Period size: 201 Copynumber: 3.0 Consensus size: 195
564941 ATATCAAATC
* *
564951 AAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTC-AGGGAGACAAGAATA
1 AAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGAGGGAGTCAAGAATA
* **
565015 A-AAAGATTGACTTCTCTTCACGAGGAAGTCAACGATTGACTCCTCTTTGTGAGGGAGTCAAGAA
66 ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCATGAGGGAGTCAAG--
* *
565079 TAAAAAAGATTGACTTCTCTT--C---ATTAGGAAGTCAAGGATTGACTCCTCTTCACGAGGGAG
129 ------AGATTGACTTCTCTTCACGAGAGTAGGAA-TCAAGGATTGACTCCTCTTCACGAGGAAG
565139 TCAGGAATA
187 TCAGGAATA
* *
565148 AAAAAGATTGACTTCTCTTCACGATGG-TGTCAAGGATTGACTCCT-TTCCGCAAGGGAGTCAGG
1 AAAAAGATTGACTTCTCTTCACGA-GGAAGTCAAGGATTGACTCCTCTT-CG--AGGGAGTCAAG
* * *
565211 AATAACAAAGATTGACTTCTCTTTATGAGGAAGTCAAGGATTGACTCCTCTTCTTGAGGGAGTCA
62 AATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCATGAGGGAGTCA
* * ** *
565276 AGAATAACAAAGGTTGACTTCTCTTCACGAG-G-A--AGTCAAGGATTGACTCCTCTTCGTGATG
127 AG--------AGATTGACTTCTCTTCACGAGAGTAGGAATCAAGGATTGACTCCTCTTCACGAGG
**
565337 AAGTTGGGAATA
184 AAGTCAGGAATA
* * * *
565349 AAAAATATTGACTTCTCTTCATGAGGAAGTCAAGGGTTGACTCCTCTTAACGAGGGAGTCATGAA
1 AAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTT--CGAGGGAGTCAAGAA
* *
565414 TAACAAAGATTGACTTCTCTTCACGAGGAATTCAAGGATTGACTCCTCTTCACGAGGGAGTCAAG
64 TAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCATGAGGGAGTCAAG
* * *
565479 -GATTGACTCCTCTTCACGAAAGAGTCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTC
129 AGATTGACTTCTCTTCACG--AGAGT-AGGAAT--CAAGGATTGACTCCTCTTCACGAGGAAGTC
565543 A
189 A
565544 AGGATTGAAT
Statistics
Matches: 333, Mismatches: 40, Indels: 42
0.80 0.10 0.10
Matches are distributed among these distances:
192 16 0.05
194 2 0.01
195 1 0.00
196 2 0.01
197 42 0.13
198 2 0.01
199 2 0.01
200 16 0.05
201 243 0.73
202 3 0.01
203 3 0.01
204 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (195 bp):
AAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGAGGGAGTCAAGAATA
ACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCATGAGGGAGTCAAGAG
ATTGACTTCTCTTCACGAGAGTAGGAATCAAGGATTGACTCCTCTTCACGAGGAAGTCAGGAATA
Found at i:565569 original size:297 final size:297
Alignment explanation
Indices: 565153--565773 Score: 836
Period size: 297 Copynumber: 2.1 Consensus size: 297
565143 GAATAAAAAA
* * * *
565153 GATTGACTTCTCTTCACGATGGTGTCAAGGATTGACTCCTTTCCGCAAGGGAGTCAGGAATAACA
1 GATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTTTCCGCAAGAGAGTCAGGAATAACA
* * * *
565218 AAGATTGACTTCTCTTTATGAGGAAGTCAAGGATTGACTCCTCTTCTTGAGGGAGTCAAGAATAA
66 AAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTCTCGAGGGAGTCAAGAATAA
* * * * * * * ***
565283 CAAAGGTTGACTT-CTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCGTGATGAAGTTGGGAA
131 AAAAGATTGACTTAAT-TTAACGAGGAAGTCAAGGATTGAATCCTCTTCGCGAGGAAGACAGGAA
* * * *
565347 TAAAAAATATTGACTTCTCTTCATGAGGAAGTCAAGGGTTGACTCCTCTTAACGAGGGAGTCATG
195 TAAAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTAACGAGGGAGTCAGG
*
565412 AATAACAAAGATTGACTTCTCTTCACGAGGAATTCAAG
260 AATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAG
565450 GATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTCTTCACG-AA-AGAGTCAGGAATAA
1 GATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCT-TTC-CGCAAGAGAGTCAGGAATAA
*
565513 CAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTT-TGCGAGGGAGTCGAGAA
64 CAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTCT-CGAGGGAGTCAAGAA
* * *
565577 TAAAAAAGATTGACTTAATTTAACGAGGAAGTTAAGGATTGAATCCTCTTTGCGAGGGAGACAGG
128 TAAAAAAGATTGACTTAATTTAACGAGGAAGTCAAGGATTGAATCCTCTTCGCGAGGAAGACAGG
* * *** *
565642 AATAACAAAGATTGACTTCTCTTCACGATGAAGTCAAGGATTGACTCCTCTTCGTGAGGGAGTCG
193 AATAAAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTAACGAGGGAGTCA
* *
565707 GGAATAACAAAGATTTACTTCTTTTCACGAGGAAGTCAAG
258 GGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAG
* **
565747 GATTAACTCCTCTTCGGGAGGGAGTCA
1 GATTGACTCCTCTTCACGAGGGAGTCA
565774 GTAATAACAA
Statistics
Matches: 282, Mismatches: 38, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
296 1 0.00
297 273 0.97
298 6 0.02
299 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (297 bp):
GATTGACTCCTCTTCACGAGGGAGTCAAGGATTGACTCCTTTCCGCAAGAGAGTCAGGAATAACA
AAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGAATCCTCTTCTCGAGGGAGTCAAGAATAA
AAAAGATTGACTTAATTTAACGAGGAAGTCAAGGATTGAATCCTCTTCGCGAGGAAGACAGGAAT
AAAAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTAACGAGGGAGTCAGGA
ATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAG
Found at i:565827 original size:29 final size:29
Alignment explanation
Indices: 565785--565894 Score: 76
Period size: 29 Copynumber: 3.5 Consensus size: 29
565775 TAATAACAAA
**
565785 GATTGACTTTTCTTTACGAGGAAGTCAAG
1 GATTGACTCCTCTTTACGAGGAAGTCAAG
* *
565814 GATTGACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
1 GATTGACTCCTCTTTACGA-GGA---A-G--T--CAAG
** *
565852 GATTGACTTATCCTTACGAGGAAGTCAAG
1 GATTGACTCCTCTTTACGAGGAAGTCAAG
565881 GATTGACTCCTCTT
1 GATTGACTCCTCTT
565895 CGCGAGGGAG
Statistics
Matches: 60, Mismatches: 12, Indels: 18
0.67 0.13 0.20
Matches are distributed among these distances:
29 30 0.50
30 3 0.05
31 1 0.02
33 2 0.03
34 2 0.03
36 1 0.02
37 3 0.05
38 18 0.30
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (29 bp):
GATTGACTCCTCTTTACGAGGAAGTCAAG
Found at i:565856 original size:38 final size:38
Alignment explanation
Indices: 565814--566012 Score: 148
Period size: 38 Copynumber: 5.7 Consensus size: 38
565804 GGAAGTCAAG
565814 GATTGACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
1 GATTGACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
** *
565852 GATTGACTTATCCTT-ACGA-GGA---A-G--T--CAAG
1 GATTGACTCCT-CTTCACGAGGGAGTCAGGAATAACAAA
*
565881 GATTGACTCCTCTTCGCGAGGGAGTCAGGAATAACAAA
1 GATTGACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
* *
565919 GATTGACTTCTCTTCAC----GAGT-A--AAT--CAAG
1 GATTGACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
** *
565948 GATTGACTCCTCTTTGCGAGGGAGTCAGGAATAACAGA
1 GATTGACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
* * *
565986 GATTGACTTCTCTTCACAAGGAAGTCA
1 GATTGACTCCTCTTCACGAGGGAGTCA
566013 AGTTGAAGTT
Statistics
Matches: 121, Mismatches: 20, Indels: 40
0.67 0.11 0.22
Matches are distributed among these distances:
28 3 0.02
29 32 0.26
30 3 0.02
31 4 0.03
33 7 0.06
34 7 0.06
36 4 0.03
37 3 0.02
38 55 0.45
39 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (38 bp):
GATTGACTCCTCTTCACGAGGGAGTCAGGAATAACAAA
Found at i:577559 original size:76 final size:76
Alignment explanation
Indices: 577418--577562 Score: 211
Period size: 76 Copynumber: 1.9 Consensus size: 76
577408 AGTTTTGACA
** * * *
577418 TAAAATGAATACATAATTCCGGCACTAAACTTATCACCTAATTCTAGCAATGAAATTTAACATTG
1 TAAAATGAATACATAATTCCAACACTAAACTTATCACATAATTCCAGCAATGAAACTTAACATTG
577483 ACTTACACCAG
66 ACTTACACCAG
* *
577494 TAAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAGC-ATCGAAACTTAATATT
1 TAAAATGAATACATAATTCCAACACTAAACTTATCACATAATTCCAGCAAT-GAAACTTAACATT
577558 GACTT
65 GACTT
577563 GTATCTGTGA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
75 2 0.03
76 59 0.97
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (76 bp):
TAAAATGAATACATAATTCCAACACTAAACTTATCACATAATTCCAGCAATGAAACTTAACATTG
ACTTACACCAG
Found at i:577727 original size:76 final size:76
Alignment explanation
Indices: 577601--577782 Score: 285
Period size: 76 Copynumber: 2.4 Consensus size: 76
577591 AAATTTGAAG
*
577601 CTTAACATTGACTTACATCAGTG-AATGAATACGTAATTCCAGCACTAAACTTATCACATAATTC
1 CTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTC
*
577665 CCGCAGTGAAA
66 CCGCAGGGAAA
* * * *
577676 TTTAACATTGATTTACACCAGTGAAATGAATATGTAATTCTAGCACTAAACTTATCACATAATTC
1 CTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTC
*
577741 CTGCAGGGAAA
66 CCGCAGGGAAA
*
577752 CTTAATATTGACTTACACCAGTGAAATGAAT
1 CTTAACATTGACTTACACCAGTGAAATGAAT
577783 GTGCAACGGT
Statistics
Matches: 96, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 20 0.21
76 76 0.79
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (76 bp):
CTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTC
CCGCAGGGAAA
Found at i:579043 original size:3 final size:3
Alignment explanation
Indices: 579037--579139 Score: 197
Period size: 3 Copynumber: 34.0 Consensus size: 3
579027 ATGTTTCTAC
579037 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
579085 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
579131 ATT ATT ATT
1 ATT ATT ATT
579140 TTCTTTTGTA
Statistics
Matches: 99, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 96 0.97
4 3 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:579405 original size:14 final size:14
Alignment explanation
Indices: 579386--579430 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 14
579376 GACATGAAGA
579386 TGGAATCGCTTGGC
1 TGGAATCGCTTGGC
579400 TGGAATCGCTTGGCGGC
1 TGGAATCGCTT---GGC
579417 TGGAATCGCTTGGC
1 TGGAATCGCTTGGC
579431 GGCAGTGCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 14 0.50
17 14 0.50
ACGTcount: A:0.13, C:0.22, G:0.38, T:0.27
Consensus pattern (14 bp):
TGGAATCGCTTGGC
Found at i:579419 original size:17 final size:17
Alignment explanation
Indices: 579386--579433 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
579376 GACATGAAGA
579386 TGGAATCGCTT---GGC
1 TGGAATCGCTTGGCGGC
579400 TGGAATCGCTTGGCGGC
1 TGGAATCGCTTGGCGGC
579417 TGGAATCGCTTGGCGGC
1 TGGAATCGCTTGGCGGC
579434 AGTGCTGTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.35
17 20 0.65
ACGTcount: A:0.12, C:0.23, G:0.40, T:0.25
Consensus pattern (17 bp):
TGGAATCGCTTGGCGGC
Found at i:582189 original size:26 final size:26
Alignment explanation
Indices: 582146--582199 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
582136 GTTTTAAGAA
* * *
582146 AAAAAAATTAAATATTTTCAAATCTT
1 AAAAAAATCAAATATTTTAAAACCTT
582172 AAAAAAATCAAA-ACTTTTAAAACCTT
1 AAAAAAATCAAATA-TTTTAAAACCTT
582198 AA
1 AA
582200 TTTTACTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAAAAATCAAATATTTTAAAACCTT
Found at i:585218 original size:31 final size:31
Alignment explanation
Indices: 585167--585245 Score: 106
Period size: 34 Copynumber: 2.5 Consensus size: 31
585157 CTATTTAATT
585167 TTAATTTATT-ATTATTATTATTATTATTATTA
1 TTAATTTATTAATTATTATTATTATTA-T-TTA
**
585199 TTTTGTTTATTAATTATTATTATTATTATTTA
1 -TTAATTTATTAATTATTATTATTATTATTTA
585231 TTAATTTATTAATTA
1 TTAATTTATTAATTA
585246 CATTTTGTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 13 0.32
32 3 0.07
33 9 0.22
34 16 0.39
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (31 bp):
TTAATTTATTAATTATTATTATTATTATTTA
Found at i:585245 original size:4 final size:3
Alignment explanation
Indices: 585172--585233 Score: 81
Period size: 3 Copynumber: 20.0 Consensus size: 3
585162 TAATTTTAAT
*
585172 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTGT TTA TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TT-A TTA TTA
585218 TTA TTA TTA TTTA TTA
1 TTA TTA TTA -TTA TTA
585234 ATTTATTAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
2 2 0.04
3 44 0.81
4 8 0.15
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:585245 original size:12 final size:11
Alignment explanation
Indices: 585167--585241 Score: 61
Period size: 9 Copynumber: 7.0 Consensus size: 11
585157 CTATTTAATT
585167 TTAATTTATTA
1 TTAATTTATTA
585178 TT-A-TTATTA
1 TTAATTTATTA
585187 TT-A-TTATTA
1 TTAATTTATTA
* *
585196 TTATTTTGTTTA
1 TTAATTT-ATTA
585208 TTAA-TTATTA
1 TTAATTTATTA
*
585218 TTATTATTATTTA
1 TTAAT-TTA-TTA
585231 TTAATTTATTA
1 TTAATTTATTA
585242 ATTACATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
9 17 0.33
10 7 0.13
11 9 0.17
12 12 0.23
13 7 0.13
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (11 bp):
TTAATTTATTA
Found at i:587579 original size:19 final size:21
Alignment explanation
Indices: 587540--587590 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
587530 TTTCCCTAAC
587540 ATTAATTA-A-TTCAAATCAA
1 ATTAATTATATTTCAAATCAA
587559 ATTAATTATATTTC-AAT-AA
1 ATTAATTATATTTCAAATCAA
* *
587578 ATGAATCATATTT
1 ATTAATTATATTT
587591 TAACTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 21 0.75
20 4 0.14
21 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTAATTATATTTCAAATCAA
Found at i:589303 original size:74 final size:74
Alignment explanation
Indices: 589180--589323 Score: 270
Period size: 74 Copynumber: 1.9 Consensus size: 74
589170 TAGTTATCAA
589180 GGAGCGACACACTGACCTCAGCACCGCCGGGGCATTAACGGAGTCAGATTACAAAGCATTGAGGG
1 GGAGCGACACACTGACCTCAGCACCGCCGGGGCATTAACGGAGTCAGATTACAAAGCATTGAGGG
589245 GCATCGGTT
66 GCATCGGTT
* *
589254 GGAGCGACACACTGACCTCAGCACCGCTGGGGCATTAACGGAGTTAGATTACAAAGCATTGAGGG
1 GGAGCGACACACTGACCTCAGCACCGCCGGGGCATTAACGGAGTCAGATTACAAAGCATTGAGGG
589319 GCATC
66 GCATC
589324 AGTTCCAAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.28, C:0.25, G:0.31, T:0.17
Consensus pattern (74 bp):
GGAGCGACACACTGACCTCAGCACCGCCGGGGCATTAACGGAGTCAGATTACAAAGCATTGAGGG
GCATCGGTT
Found at i:589722 original size:15 final size:14
Alignment explanation
Indices: 589689--589725 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
589679 GGATCAATAT
589689 TTTTGCATC-TGCA
1 TTTTGCATCTTGCA
589702 -TTTGCATCTTTGCA
1 TTTTGCATC-TTGCA
589716 TTTTGCATCT
1 TTTTGCATCT
589726 GTATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.38
14 5 0.24
15 8 0.38
ACGTcount: A:0.14, C:0.22, G:0.14, T:0.51
Consensus pattern (14 bp):
TTTTGCATCTTGCA
Found at i:590587 original size:66 final size:66
Alignment explanation
Indices: 590481--590615 Score: 270
Period size: 66 Copynumber: 2.0 Consensus size: 66
590471 CGTCAAACCA
590481 ACATTTTCTACTAATAAGACCTACAGACATTGAGTACAAGATGTTCACTTGAACATGAACCTTCT
1 ACATTTTCTACTAATAAGACCTACAGACATTGAGTACAAGATGTTCACTTGAACATGAACCTTCT
590546 T
66 T
590547 ACATTTTCTACTAATAAGACCTACAGACATTGAGTACAAGATGTTCACTTGAACATGAACCTTCT
1 ACATTTTCTACTAATAAGACCTACAGACATTGAGTACAAGATGTTCACTTGAACATGAACCTTCT
590612 T
66 T
590613 ACA
1 ACA
590616 AGAGGACACA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (66 bp):
ACATTTTCTACTAATAAGACCTACAGACATTGAGTACAAGATGTTCACTTGAACATGAACCTTCT
T
Found at i:591080 original size:24 final size:27
Alignment explanation
Indices: 591053--591115 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 27
591043 AAATCAAAGC
*
591053 AAAGAGAC-AAGAAAAA-TAAAG-AGA
1 AAAGAAACAAAGAAAAAGTAAAGAAGA
591077 AAAGAAACAAAGAAAAAGTAAAGAAGA
1 AAAGAAACAAAGAAAAAGTAAAGAAGA
591104 AAAGAAA-AAAGA
1 AAAGAAACAAAGA
591116 GCAAAGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
24 7 0.20
25 8 0.23
26 10 0.29
27 10 0.29
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (27 bp):
AAAGAAACAAAGAAAAAGTAAAGAAGA
Found at i:591088 original size:32 final size:31
Alignment explanation
Indices: 591052--591144 Score: 90
Period size: 27 Copynumber: 3.1 Consensus size: 31
591042 CAAATCAAAG
591052 CAAAGAGACAAGAAAAATAAAGAGAAAAGAAA
1 CAAAGAG-CAAGAAAAATAAAGAGAAAAGAAA
*
591084 C-AA-AG--A-AAAAGTAAAGAAGAAAAGAAA
1 CAAAGAGCAAGAAAAATAAAG-AGAAAAGAAA
*
591111 -AAAGAGCAAAGAAAAACAAAGAGAAAAGTAAA
1 CAAAGAGC-AAGAAAAATAAAGAGAAAAG-AAA
591143 CA
1 CA
591145 GAAAAAAAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
26 9 0.18
27 13 0.27
28 2 0.04
30 2 0.04
31 10 0.20
32 12 0.24
33 1 0.02
ACGTcount: A:0.72, C:0.06, G:0.18, T:0.03
Consensus pattern (31 bp):
CAAAGAGCAAGAAAAATAAAGAGAAAAGAAA
Found at i:591114 original size:26 final size:25
Alignment explanation
Indices: 591053--591182 Score: 90
Period size: 22 Copynumber: 4.9 Consensus size: 25
591043 AAATCAAAGC
*
591053 AAAGAGAC-AAGAAAAATAAAGAGA
1 AAAGAAACAAAGAAAAATAAAGAGA
591077 AAAGAAACAAAGAAAAAGTAAAGAAGA
1 AAAGAAACAAAGAAAAA-TAAAG-AGA
*
591104 AAAGAAAAAAGAGCAAAGAAAAACAAAGAGA
1 AAAG----AA-A-CAAAGAAAAATAAAGAGA
591135 AAAGTAAAC--AG-AAAA-AAAGAGA
1 AAAG-AAACAAAGAAAAATAAAGAGA
*
591157 CAAAAAAACAAAGAAAAGAGTAAAGA
1 -AAAGAAACAAAGAAAA-A-TAAAGA
591183 AAATGCAAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 28
0.73 0.03 0.24
Matches are distributed among these distances:
22 11 0.13
23 7 0.08
24 11 0.13
25 11 0.13
26 7 0.08
27 8 0.09
28 7 0.08
31 9 0.10
32 5 0.06
33 10 0.12
ACGTcount: A:0.73, C:0.05, G:0.18, T:0.03
Consensus pattern (25 bp):
AAAGAAACAAAGAAAAATAAAGAGA
Found at i:591121 original size:14 final size:13
Alignment explanation
Indices: 591070--591126 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
591060 CAAGAAAAAT
591070 AAAGAGAAAAGAAA
1 AAAGA-AAAAGAAA
591084 CAAAGAAAAAGTAAA
1 -AAAGAAAAAG-AAA
*
591099 GAAG-AAAAGAAA
1 AAAGAAAAAGAAA
*
591111 AAAGAGCAAAGAAA
1 AAAGA-AAAAGAAA
591125 AA
1 AA
591127 CAAAGAGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
12 6 0.17
13 5 0.14
14 17 0.47
15 8 0.22
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:591164 original size:38 final size:39
Alignment explanation
Indices: 591061--591183 Score: 135
Period size: 38 Copynumber: 3.1 Consensus size: 39
591051 GCAAAGAGAC
*
591061 AAGAAAAATAAAGAGA-AAAGAAACAAAGAAAAAGTAAAG
1 AAGAAAAA-AAAGAGACAAAAAAACAAAGAAAAAGTAAAG
*
591100 AAGAAAAGAAAAAAGAGCAAAGAAAAACAAAGAGAAAAGTAAA-
1 AAGAAAA-AAAAGAGA-C-AA-AAAAACAAAGA-AAAAGTAAAG
*
591143 CAG-AAAAAAAGAGACAAAAAAACAAAGAAAAGAGTAAAG
1 AAGAAAAAAAAGAGACAAAAAAACAAAGAAAA-AGTAAAG
591182 AA
1 AA
591184 AATGCAAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
37 3 0.04
38 17 0.24
39 16 0.23
40 2 0.03
41 7 0.10
42 5 0.07
43 12 0.17
44 9 0.13
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (39 bp):
AAGAAAAAAAAGAGACAAAAAAACAAAGAAAAAGTAAAG
Found at i:592090 original size:24 final size:24
Alignment explanation
Indices: 592062--592120 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
592052 AGGAGCAATA
592062 TTTTCAAAACTTTTGATTAAACAT
1 TTTTCAAAACTTTTGATTAAACAT
592086 TTTTCAAAACTTTTGATTAAACAT
1 TTTTCAAAACTTTTGATTAAACAT
592110 TTTTCAAAACT
1 TTTTCAAAACT
592121 CTTTTAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (24 bp):
TTTTCAAAACTTTTGATTAAACAT
Found at i:592975 original size:35 final size:35
Alignment explanation
Indices: 592929--593122 Score: 169
Period size: 35 Copynumber: 5.5 Consensus size: 35
592919 TTGAGATCGT
*
592929 TTTCTCAAAAACAAACTTTGTTTCCCTTGAGACAA
1 TTTCTCAAAAACAAACTTTGTCTCCCTTGAGACAA
*
592964 TTTCTCAAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCAAAAACAAACTTTGTCTCCCTTGAGACAA
* ** *
592999 TTTCTC-AAAACAAATTTTGTCTCGGTTGAGACAG
1 TTTCTCAAAAACAAACTTTGTCTCCCTTGAGACAA
** * *
593033 TTT-TCTTGAAACAAAATTTTGTCTCGCTTGAGAC-A
1 TTTCTC-AAAAAC-AAACTTTGTCTCCCTTGAGACAA
* * * * * *
593068 GTTCTTGAAAAAAAAATTTTGTCTCACTTAAGACAA
1 TTTC-TCAAAAACAAACTTTGTCTCCCTTGAGACAA
* *
593104 TTTATGATAAAACAAACTT
1 TTTCTCA-AAAACAAACTT
593123 CATCTCGCTT
Statistics
Matches: 133, Mismatches: 19, Indels: 13
0.81 0.12 0.08
Matches are distributed among these distances:
33 2 0.02
34 28 0.21
35 67 0.50
36 35 0.26
37 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (35 bp):
TTTCTCAAAAACAAACTTTGTCTCCCTTGAGACAA
Found at i:593290 original size:104 final size:105
Alignment explanation
Indices: 593112--593308 Score: 256
Period size: 104 Copynumber: 1.9 Consensus size: 105
593102 AATTTATGAT
* * * * *
593112 AAAACAAACTTCATCTCGCTTTAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCTTCACA
1 AAAACAAACTTCATCTCGCTTGAGACATTTTCCCTATGAGATACAAATTTCAAACTTGCTTCACA
* *
593177 TGAAACAAAATTAATCTCACTTGAGATTGTTGTTTCTTTC
66 TAAAACAAAATTAATATCACTTGAGATTGTTGTTTCTTTC
* * *
593217 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTCAT-A-ATACAAATTTCAAACTTG-TTGTA
1 AAAACAAACTTCATCTCGCTTGAGACATTTTCCCT-ATGAGATACAAATTTCAAACTTGCTT-CA
*
593279 CTTAAAACAAAATTAATATCACTTGAGATT
64 CATAAAACAAAATTAATATCACTTGAGATT
593309 TTTAAAACTG
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
103 2 0.03
104 44 0.56
105 32 0.41
106 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (105 bp):
AAAACAAACTTCATCTCGCTTGAGACATTTTCCCTATGAGATACAAATTTCAAACTTGCTTCACA
TAAAACAAAATTAATATCACTTGAGATTGTTGTTTCTTTC
Found at i:593481 original size:28 final size:27
Alignment explanation
Indices: 593443--593542 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 27
593433 TCTTGAGACA
* *
593443 GTTTCTCTTGAAACAAATCTTTGAGTCT
1 GTTTCTTTTGAAAAAAATCTTTGAGT-T
*
593471 GTTCCTTTTGAATAAAAATCTTTGAGTT
1 GTTTCTTTTGAA-AAAAATCTTTGAGTT
*
593499 GTTTCTTGTGAGAAAACAATCTTTGAGTTTT
1 GTTTCTTTTGA-AAAA-AATCTTTGAG--TT
*
593530 GTTTATTTTGAAA
1 GTTTCTTTTGAAA
593543 CAAAGTTTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
28 23 0.38
29 24 0.40
30 2 0.03
31 11 0.18
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (27 bp):
GTTTCTTTTGAAAAAAATCTTTGAGTT
Found at i:593591 original size:122 final size:124
Alignment explanation
Indices: 593424--593649 Score: 282
Period size: 122 Copynumber: 1.8 Consensus size: 124
593414 TTAAAACGAT
* * * * *
593424 TTTTGACTCTCTTGAGACAGTTTCTCTTGAAACAAATCTTTGAGTC-TGTTCCTTTTG-AATAAA
1 TTTTGACTCGCTTGAGACAGTTTCTCGTGAAACAAATCTTCGAGTCAT-TT-CTTTCGAAACAAA
*
593487 AATCTTTGAGTTGTTTCTTGTGAGAA-AACAATCTTTGAGTTTTGTTTATTTTGAAACAAAG
64 AATCTTTCAGTTGTTTCTTGTGA-AATAACAATCTTTGAGTTTTGTTTATTTTGAAACAAAG
* * *
593548 TTTTGTCTCGCTTGAGATAGTTTTTCGTG-AA-AAATCTTCGAGTCATTTCTTTCGAAACAAAAA
1 TTTTGACTCGCTTGAGACAGTTTCTCGTGAAACAAATCTTCGAGTCATTTCTTTCGAAACAAAAA
* * *
593611 TCTTTCAGTTGTTTCTTTTGAAATACCTATCTTTGAGTT
66 TCTTTCAGTTGTTTCTTGTGAAATAACAATCTTTGAGTT
593650 AGTTTCTCTT
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
121 7 0.08
122 53 0.61
123 3 0.03
124 24 0.28
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.44
Consensus pattern (124 bp):
TTTTGACTCGCTTGAGACAGTTTCTCGTGAAACAAATCTTCGAGTCATTTCTTTCGAAACAAAAA
TCTTTCAGTTGTTTCTTGTGAAATAACAATCTTTGAGTTTTGTTTATTTTGAAACAAAG
Found at i:593662 original size:30 final size:29
Alignment explanation
Indices: 593610--593695 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 29
593600 CGAAACAAAA
* * * *
593610 ATCTTTCAGTTGTTTCTTTTGAAATACCT
1 ATCTTTGAGTTGTTTCTCTTGAAACACCC
593639 ATCTTTGAGTTAGTTTCTCTTGAAACACCC
1 ATCTTTGAGTT-GTTTCTCTTGAAACACCC
* * * *
593669 ACCTTTGAGATCGTTTCTATTAAAACA
1 ATCTTTGAG-TTGTTTCTCTTGAAACA
593696 AATTTTGTCT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 10 0.21
30 36 0.77
31 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.43
Consensus pattern (29 bp):
ATCTTTGAGTTGTTTCTCTTGAAACACCC
Found at i:593762 original size:31 final size:30
Alignment explanation
Indices: 593727--593791 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
593717 GTTTCTATAA
* *
593727 AAATACAAA-ATCTTTGAGTTTGTTTCTCTTG
1 AAATA-AAACATCTTTGAG-TCGTTTCCCTTG
593758 AAATAAAACCATCTTTGAGTCGTTTCCCTTG
1 AAATAAAA-CATCTTTGAGTCGTTTCCCTTG
593789 AAA
1 AAA
593792 CGAATTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 3 0.10
31 18 0.60
32 9 0.30
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.38
Consensus pattern (30 bp):
AAATAAAACATCTTTGAGTCGTTTCCCTTG
Found at i:593825 original size:97 final size:96
Alignment explanation
Indices: 593639--593850 Score: 225
Period size: 97 Copynumber: 2.2 Consensus size: 96
593629 TGAAATACCT
* * * *
593639 ATCTTTGAGTTAGTTTCTCTTGAAACACCCACCTTTGAGATCGTTTCTATTAAAACAAATTTTGT
1 ATCTTTGAGTTTGTTTCTCTTGAAAAAACCACCTTTGAGATCGTTTCCATTAAAACAAATTTTG-
593704 CTCTCTTGAGGAAGTTTCTATAAAA-ATACAAA
65 CTCTCTTGAGGAAGTTTCTATAAAACA-ACAAA
* * * *
593736 ATCTTTGAGTTTGTTTCTCTTGAAATAAAACCATCTTTGAG-TCGTTTCCCTTGAAACGAATTTT
1 ATCTTTGAGTTTGTTTCTCTTG-AA-AAAACCACCTTTGAGATCGTTTCCATTAAAACAAATTTT
* * * **
593800 G-TCTCTTGA-GACATTTTCTCTTAAAACAATATC
64 GCTCTCTTGAGGA-AGTTTCT-ATAAAACAACAAA
593833 ATCTTTGAGTTTGTTTCT
1 ATCTTTGAGTTTGTTTCT
593851 TTAGAAACAA
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
95 2 0.02
96 14 0.14
97 46 0.47
98 23 0.24
99 12 0.12
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (96 bp):
ATCTTTGAGTTTGTTTCTCTTGAAAAAACCACCTTTGAGATCGTTTCCATTAAAACAAATTTTGC
TCTCTTGAGGAAGTTTCTATAAAACAACAAA
Found at i:593850 original size:32 final size:32
Alignment explanation
Indices: 593736--593860 Score: 85
Period size: 32 Copynumber: 3.9 Consensus size: 32
593726 AAAATACAAA
* * * *
593736 ATCTTTGAGTTTGTTTCTCTTGAAATAAAACC
1 ATCTTTGAGTTTGTTTCTCTTAAAACAATATC
* * * * *
593768 ATCTTTGAG-TCGTTTCCCTTGAAACGAATTTT
1 ATCTTTGAGTTTGTTTCTCTTAAAAC-AATATC
* **
593800 GTCTCTTGAGACAT-TTTCTCTTAAAACAATATC
1 ATCT-TTGAG-TTTGTTTCTCTTAAAACAATATC
593833 ATCTTTGAGTTTGTTTCT-TTAGAAACAA
1 ATCTTTGAGTTTGTTTCTCTTA-AAACAA
593861 GGTCTTTCGA
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
31 17 0.24
32 30 0.43
33 12 0.17
34 11 0.16
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (32 bp):
ATCTTTGAGTTTGTTTCTCTTAAAACAATATC
Found at i:594099 original size:28 final size:29
Alignment explanation
Indices: 594068--594123 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
594058 TCTTAACAAA
*
594068 ATCATCTTTGAGTCTGTTTC-TTTGAAAC
1 ATCATCTTTGAGTCGGTTTCTTTTGAAAC
594096 ATCATCTTTGAGTCGGTTTCTTTTGAAA
1 ATCATCTTTGAGTCGGTTTCTTTTGAAA
594124 TCATTATCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.46
Consensus pattern (29 bp):
ATCATCTTTGAGTCGGTTTCTTTTGAAAC
Found at i:594281 original size:43 final size:44
Alignment explanation
Indices: 594221--594425 Score: 192
Period size: 43 Copynumber: 4.7 Consensus size: 44
594211 GTCACCCCTG
*
594221 ACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA-ACCATAGATA
1 ACCAG-CCGTCCTCATCACGTAGGAACCGTGTCATACCATAGATA
* * * *
594264 ACCAGCCGTCCTCATCACGTAGGAACCGCGTTATCATTCCTAAAGATG
1 ACCAGCCGTCCTCATCACGTAGGAA-C-CG-TGTCATACC-ATAGATA
* * * * *
594312 GCCAGCTGTCCTCATCACGTAGGAACTGTGTCATCCCCT-G---
1 ACCAGCCGTCCTCATCACGTAGGAACCGTGTCATACCATAGATA
* *
594352 ACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA-ATCATAGATA
1 ACCAG-CCGTCCTCATCACGTAGGAACCGTGTCATACCATAGATA
594395 ACCAGCCGTCCTCATCACGTAGGAACCGTGT
1 ACCAGCCGTCCTCATCACGTAGGAACCGTGT
594426 TATCATTCCT
Statistics
Matches: 130, Mismatches: 20, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
39 2 0.02
40 28 0.22
41 1 0.01
42 4 0.03
43 49 0.38
44 1 0.01
45 9 0.07
46 5 0.04
47 3 0.02
48 28 0.22
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (44 bp):
ACCAGCCGTCCTCATCACGTAGGAACCGTGTCATACCATAGATA
Found at i:594375 original size:40 final size:40
Alignment explanation
Indices: 594143--594384 Score: 177
Period size: 40 Copynumber: 5.8 Consensus size: 40
594133 CTAAAGATAG
* * * * *
594143 CCAGAACTCTTCATCACGTATGAGCCATGTCATCTCCTGA
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCCCTGA
* **
594183 CCAGATCTCCTCATCGTGTAGGAGCCGTGTCA-CCCCTGA
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCCCTGA
* *
594222 CCAGACCTCCTCATCACGTAGGAGCCGTGTCA-ACCATAGATAA
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCCCT-G---A
* * * *
594265 CCAG-CCGTCCTCATCACGTAGGAACCGCGTTATCATTCCTAAAGA
1 CCAGACC-TCCTCATCACGTAGGAGCCGTGTCATC--CCCT---GA
* * *
594310 TGGCCAG-CTGTCCTCATCACGTAGGAACTGTGTCATCCCCTGA
1 ---CCAGAC-CTCCTCATCACGTAGGAGCCGTGTCATCCCCTGA
594353 CCAGACCTCCTCATCACGTAGGAGCCGTGTCA
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTCA
594385 ATCATAGATA
Statistics
Matches: 161, Mismatches: 26, Indels: 30
0.74 0.12 0.14
Matches are distributed among these distances:
39 38 0.24
40 54 0.34
41 1 0.01
42 2 0.01
43 29 0.18
45 1 0.01
46 5 0.03
48 31 0.19
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.23
Consensus pattern (40 bp):
CCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCCCTGA
Found at i:594428 original size:131 final size:131
Alignment explanation
Indices: 594190--594506 Score: 478
Period size: 131 Copynumber: 2.4 Consensus size: 131
594180 TGACCAGATC
** *
594190 TCCTCATCGTGTAGGAGCCGTGTCA-CCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAGGAGCAGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCA
594254 ACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGCGTTATCATTCCTAAAGATGGCCA-GC
66 ACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGCGTTATCATTCCTAAAGATGG-CATGC
*
594318 TG
130 CG
* *
594320 TCCTCATCACGTAGGAACTGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAGGAGCAGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCA
* *
594385 ATCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCATTCCTAAAGATGGCATGCC
66 ACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGCGTTATCATTCCTAAAGATGGCATGCC
594450 G
131 G
* * * **
594451 TCCTCATCACCTATGAGCAGTGTCAT-CCTTCGACCAGATTTCCTCATCACGTAGGA
1 TCCTCATCACGTAGGAGCAGTGTCATCCCCT-GACCAGACCTCCTCATCACGTAGGA
594507 ACCGCGTTAA
Statistics
Matches: 170, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
130 26 0.15
131 144 0.85
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (131 bp):
TCCTCATCACGTAGGAGCAGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCA
ACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGCGTTATCATTCCTAAAGATGGCATGCC
G
Found at i:594734 original size:3 final size:3
Alignment explanation
Indices: 594726--594791 Score: 98
Period size: 3 Copynumber: 22.0 Consensus size: 3
594716 TAATTTTAAT
* *
594726 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTT TTT TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
594773 TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA -TTA TTA
594792 ATATATTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:594798 original size:12 final size:12
Alignment explanation
Indices: 594712--594803 Score: 61
Period size: 12 Copynumber: 7.8 Consensus size: 12
594702 GAGTCTTTTC
594712 TATTTAATT-TTA
1 TATTT-ATTATTA
594724 -ATTTATTATTA
1 TATTTATTATTA
594735 T-TATTATTATTA
1 TAT-TTATTATTA
*
594747 T-TATTATT-TTT
1 TAT-TTATTATTA
*
594758 TTTTTATTATTA
1 TATTTATTATTA
594770 T-TATTATTATTA
1 TAT-TTATTATTA
*
594782 TTATTTATTAATA
1 -TATTTATTATTA
*
594795 TATTAATTA
1 TATTTATTA
594804 CATTTTGTAG
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
10 3 0.04
11 17 0.25
12 38 0.56
13 9 0.13
14 1 0.01
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTATTATTA
Found at i:597140 original size:19 final size:21
Alignment explanation
Indices: 597101--597151 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
597091 TTTCCCTAAC
597101 ATTAATTA-A-TTCAAATCAA
1 ATTAATTATATTTCAAATCAA
597120 ATTAATTATATTTC-AAT-AA
1 ATTAATTATATTTCAAATCAA
* *
597139 ATGAATCATATTT
1 ATTAATTATATTT
597152 TAACTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 21 0.75
20 4 0.14
21 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTAATTATATTTCAAATCAA
Found at i:597538 original size:2 final size:2
Alignment explanation
Indices: 597531--597564 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
597521 GACTCATAGA
597531 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
597565 TGAGCACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:600526 original size:12 final size:12
Alignment explanation
Indices: 600498--600535 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
600488 TCTTTATTCC
600498 TTCTCATTTTT-T
1 TTCT-ATTTTTCT
*
600510 CTCTATTTTTCT
1 TTCTATTTTTCT
600522 TTCTATTTTTCT
1 TTCTATTTTTCT
600534 TT
1 TT
600536 TTTCTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (12 bp):
TTCTATTTTTCT
Found at i:600538 original size:20 final size:19
Alignment explanation
Indices: 600505--600557 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
600495 TCCTTCTCAT
600505 TTTTTCTCTATTTTTCT-TTC
1 TTTTTCT-T-TTTTTCTCTTC
600525 TATTTT-TCTTTTTTCTCTTC
1 T-TTTTCT-TTTTTTCTCTTC
600545 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
600558 TAAATGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 17 0.57
20 9 0.30
21 4 0.13
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCTTTTTTTCTCTTC
Found at i:600558 original size:20 final size:19
Alignment explanation
Indices: 600505--600558 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
600495 TCCTTCTCAT
*
600505 TTTTTCTCTATTTTTCTTTC
1 TTTTTCT-TTTTTTTCTTTC
*
600525 TATTTT-TCTTTTTTCTCTTC
1 T-TTTTCTTTTTTTTCT-TTC
600545 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
600559 AAATGAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 11 0.39
20 13 0.46
21 4 0.14
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTTTTTCTTTC
Found at i:601148 original size:237 final size:236
Alignment explanation
Indices: 600754--601468 Score: 968
Period size: 237 Copynumber: 3.0 Consensus size: 236
600744 TGGAAATAGT
* * * * * *
600754 TTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACAC
1 TTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCGAAAATTTCATTTTCAGAAAAGAT
** * * * * *
600819 TAAATGAGAAACTTTCG-AAATTGCTTTCTCATTTTTTGAAAATCATGTGAAAACAT-TTGCCTG
66 TAAATGAGAAACTTT-GAAAATCACTTTCCCA-TTTTTCAAATTCATGTGAAAACATCCTACCTG
** * * * * *
600882 AAGGTATTATAGATGGCCCGAAGGACTTATCATCTTGCTTGAAAGACTAACAAATGACCTGAAGG
129 AAGGTATTACGGATGG-CCGAAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGG
* *
600947 ATTTAATGATAATGTTCGAAAGACTTACTGATGGCCCGAAGGAC
193 ATTTAATCATCATGTTCGAAAGACTTACTGATGGCCCGAAGGAC
* *
600991 TTACTGAGTAAGAAACTTCGGAAATCGTTTTCTTACTTTTCGAAAATTTCATTTTCAGAAAAGAT
1 TTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCGAAAATTTCATTTTCAGAAAAGAT
*
601056 TAAATGAGAAACTTTGAAAATCACTTTCCCATTTTTCAAATTCATGTGAAAACGTCCTACCTGAA
66 TAAATGAGAAACTTTGAAAATCACTTTCCCATTTTTCAAATTCATGTGAAAACATCCTACCTGAA
* * * **
601121 GGTCTTACGGATGGCCTGAAAGACTTATCATCTTGCTCGAAAAACTTACAGATGACCCAAATAAT
131 GGTATTACGGATGGCC-GAAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGAT
601186 TTAATCATCATGCTT-GAAAGACTTACTGATGGCCCGAAGGAC
195 TTAATCATCATG-TTCGAAAGACTTACTGATGGCCCGAAGGAC
* *
601228 TTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTTGAAAATTTCATTTTCAGAAAAGAT
1 TTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCGAAAATTTCATTTTCAGAAAAGAT
* * * *
601293 TACATGAGAAACTTTGAAAATCACTTTCCCATTTTTCAAATCCATGTGAAAATATCCTACCCGAA
66 TAAATGAGAAACTTTGAAAATCACTTTCCCATTTTTCAAATTCATGTGAAAACATCCTACCTGAA
* *
601358 GGTATTACGGATGGTCCGTATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGAT
131 GGTATTACGGATGG-CCGAAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGAT
* * * * *
601423 TTAATTATCATGCTCAAAAGACTTATTGATGGCTCGAAGGAC
195 TTAATCATCATGTTCGAAAGACTTACTGATGGCCCGAAGGAC
601465 TTAC
1 TTAC
601469 CAATTTTGGA
Statistics
Matches: 421, Mismatches: 51, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
236 25 0.06
237 392 0.93
238 4 0.01
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (236 bp):
TTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCGAAAATTTCATTTTCAGAAAAGAT
TAAATGAGAAACTTTGAAAATCACTTTCCCATTTTTCAAATTCATGTGAAAACATCCTACCTGAA
GGTATTACGGATGGCCGAAAGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATT
TAATCATCATGTTCGAAAGACTTACTGATGGCCCGAAGGAC
Found at i:601656 original size:259 final size:257
Alignment explanation
Indices: 601235--601971 Score: 924
Period size: 259 Copynumber: 2.9 Consensus size: 257
601225 GACTTACTAA
** * * *
601235 GTAAGAAACTTTGGAAATCATTTTCTTACTTTTTGAAAATTTCATTTTCA-GAAAAGATTACATG
1 GTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAATTTCATTTT-ATGAAAACACTAAATG
* * * * * *
601299 AGAAACTTTGAAAATCACTTTCCCATTTTT-CAAATCCATGTGAAAATATCCTACCCGAAGGTAT
65 AGAAAATTTGAAAATCGCTTTCTCATTTTTGAAAAT-CATGTGAAAACATCCTACCCGAAGGTCT
** * *
601363 TACGGATGGTCCGTATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
129 TATAGATGGCCCGAATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
* * * *
601428 TATCATGCTCAAAAGACTTATTGATG-GCTCGAAGGACTTACCAATTTTGGAAATAGTTTACTGG
194 CATCATGCTCAAAAGACTTACTGATGACCT-GAAGGACTTACCAATTTTGGAAATAGTTTAATGG
* * * * * *
601492 GTATGAAAATTTTGGAAATCATTTTCCTACTTTTCAAAAAATTCACTTTATGAAAATACTAAATG
1 GTAAG-AAACTTTGGAAATCATTTTCTTACTTTTCAAAAATTTCATTTTATGAAAACACTAAATG
* * * *
601557 AGAAATTTTAAAAATCGCTTTCTCAGTTTTTGAAAATCACGTGAAAACATCCTACTCGAAGGTCT
65 AGAAAATTTGAAAATCGCTTTCTCA-TTTTTGAAAATCATGTGAAAACATCCTACCCGAAGGTCT
* * * * *
601622 TATAGATGGCCCGAATGACTTATCATATTGCTCGAAAGCCTGACAGATGACCTGAAGGATTTAGT
129 TATAGATGGCCCGAATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
* *
601687 CATCATGCTCAAAAGACTTACTGATGACCTGAATGACTTACCGATTTTGGAAATAGTTTAATGG
194 CATCATGCTCAAAAGACTTACTGATGACCTGAAGGACTTACCAATTTTGGAAATAGTTTAATGG
** * *
601751 GTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACACTAAATAA
1 GTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAATTTCATTTTATGAAAACACTAAATGA
* * *
601816 GAAAATTTGGAAATCGCTTTCTCATTTTTTTGAAAATCATGTGAAAACATACTGCCCGAAGGTCT
66 GAAAATTTGAAAATCGCTTTCTCA--TTTTTGAAAATCATGTGAAAACATCCTACCCGAAGGTCT
* * * * *
601881 TGTAGATGGCCCAAAGGACTTATTATCTTGCTTGAAAGACTTACAGATGACCCGAAGGATTTAAT
129 TATAGATGGCCCGAATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
* *
601946 CATCATTCTCGAAATG-CTTACTGATG
194 CATCATGCTC-AAAAGACTTACTGATG
601972 CCAAAATGAC
Statistics
Matches: 409, Mismatches: 64, Indels: 12
0.84 0.13 0.02
Matches are distributed among these distances:
257 5 0.01
258 141 0.34
259 253 0.62
260 10 0.02
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (257 bp):
GTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAATTTCATTTTATGAAAACACTAAATGA
GAAAATTTGAAAATCGCTTTCTCATTTTTGAAAATCATGTGAAAACATCCTACCCGAAGGTCTTA
TAGATGGCCCGAATGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAATCA
TCATGCTCAAAAGACTTACTGATGACCTGAAGGACTTACCAATTTTGGAAATAGTTTAATGG
Found at i:603010 original size:3 final size:3
Alignment explanation
Indices: 603002--603038 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
602992 ATATAAATTT
603002 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
603039 CCTAGACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:603476 original size:42 final size:41
Alignment explanation
Indices: 603371--603484 Score: 113
Period size: 42 Copynumber: 2.8 Consensus size: 41
603361 ATATCCTGCC
* *
603371 CGAAAGTCTTA-TGGATGGCCCGAAGGACTTATAATCTTACT
1 CGAAAGACTTACT-GATGGCCCGAAGGACTTATAATCATACT
* * * * * * *
603412 CGAAACACTGACAGATGACCCGAAGGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGGCCCGAAGGACTT-ATAATCATACT
*
603454 CGAAAGACTTACTGATGGCCCGAATGACTTA
1 CGAAAGACTTACTGATGGCCCGAAGGACTTA
603485 CTTATTTTGG
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
41 24 0.43
42 32 0.57
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (41 bp):
CGAAAGACTTACTGATGGCCCGAAGGACTTATAATCATACT
Found at i:603755 original size:256 final size:256
Alignment explanation
Indices: 603164--603862 Score: 968
Period size: 256 Copynumber: 2.7 Consensus size: 256
603154 AAGTGAGACC
* * * *
603164 GACAGATTACCCAAAGGATTTAATCATCATGCTCGAAATACTTACTAATGGCCCAAATGACTTAC
1 GACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTAC
* ** *
603229 TAATTTTGGAAATAATTTACTGGGTAAAAAACTTTTAAAATTGCTTTCTTACTTTTCAAAAATTT
66 TAATTTTGGAAATAATTTACTGCGTAAAAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
* * *
603294 CATTTTCTAAAAACATTAAATGAGAAACTTTGGAAATGACTTTCTCATTTTCGAAAATCATGTGG
131 CATTTTCTAAAAACATTAAATGAAAAACTTTGGAAATCACTTTCTCATTTTC-AAAATCATGTGA
* * * * *
603359 AAATATCCTGCCCGAAAGTCTTATGGATGGCCCGAAGGACTTATAATCTTACTCGAAACACT
195 AAATATCCTACACGAAAGTCTTACGGATGGCCCGAAGAACTTATAATCTCACTCGAAACACT
*
603421 GACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTAC
1 GACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTAC
* * * * * *
603486 TTATTTTGGAAATAATTTATTGCATAATAAACGTTGGAAATCGCTTTCTCACTTTTCAAAAATTT
66 TAATTTTGGAAATAATTTACTGCGTAAAAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
* * *
603551 CATTTTCTAAAAACATTAAATCAAAAACTTTGGAAATCACTTTCTCATTTTCATATTCATGTGAA
131 CATTTTCTAAAAACATTAAATGAAAAACTTTGGAAATCACTTTCTCATTTTCAAAATCATGTGAA
* * * * *
603616 AATATCCTACACGAAGGTCTTACGGATGGCCCGAAGAACTTATCATCTCGCTCTAAAGACT
196 AATATCCTACACGAAAGTCTTACGGATGGCCCGAAGAACTTATAATCTCACTCGAAACACT
* * *
603677 TACAGTTGACCCTAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTAC
1 GACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTAC
* * * * * *
603742 CAATTTGGGAAATAGTTTACT-CGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAATTT
66 TAATTTTGGAAATAATTTACTGC-GTAAAAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATT
* * * * *
603806 TAATTTTTTGAAAACAATAAATGAAAAACTTTGGAAATCGCTTTCTCATTTTCAAAA
130 TCATTTTCTAAAAACATTAAATGAAAAACTTTGGAAATCACTTTCTCATTTTCAAAA
603863 AATCTTAATG
Statistics
Matches: 388, Mismatches: 53, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
255 1 0.00
256 223 0.57
257 164 0.42
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (256 bp):
GACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTAC
TAATTTTGGAAATAATTTACTGCGTAAAAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
CATTTTCTAAAAACATTAAATGAAAAACTTTGGAAATCACTTTCTCATTTTCAAAATCATGTGAA
AATATCCTACACGAAAGTCTTACGGATGGCCCGAAGAACTTATAATCTCACTCGAAACACT
Done.