Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009625.1 Hibiscus syriacus cultivar Beakdansim tig00117017_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: 6938204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 25
Found at i:2331025 original size:52 final size:53
Alignment explanation
Indices: 2330960--2331061 Score: 170
Period size: 52 Copynumber: 1.9 Consensus size: 53
2330950 TCACAATGCG
**
2330960 GAAATGACTATCGCAACGAGAGAATCGCAATGCG-AAATGAAAATCGCAATGT
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAATGT
*
2331012 GAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAAATCGCAA
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAA
2331062 CGCGAAATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 31 0.67
53 15 0.33
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.16
Consensus pattern (53 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAATGT
Found at i:2331135 original size:33 final size:33
Alignment explanation
Indices: 2331078--2331162 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
2331068 ATTAGTTTCG
*
2331078 CGTTGCGATTTTAATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
2331112 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* **
2331145 CATTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
2331163 CGCGTTACGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 33 0.72
34 13 0.28
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:2331294 original size:14 final size:14
Alignment explanation
Indices: 2331275--2331311 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2331265 CATCAATTAA
2331275 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2331289 ACAAATCATCTTTT
1 ACAAATCAACATTT
2331303 ACAAATCAA
1 ACAAATCAA
2331312 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2332760 original size:42 final size:42
Alignment explanation
Indices: 2332681--2332773 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
2332671 CCTCTTCAAC
* * *
2332681 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
2332723 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
2332765 GATGACAGG
1 GATGACAGG
2332774 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:2333276 original size:20 final size:20
Alignment explanation
Indices: 2333253--2333339 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
2333243 GAAACTTAAA
*
2333253 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
2333273 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
2333293 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
2333313 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
2333333 ATCGCAA
1 ATCGCAA
2333340 CGAGAGAATC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:2333410 original size:19 final size:19
Alignment explanation
Indices: 2333383--2333436 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
2333373 CGCAATTATA
2333383 GTTTTGCGTTGCGATTTTG
1 GTTTTGCGTTGCGATTTTG
*
2333402 GTTTCGCGTTGCGATTTTG
1 GTTTTGCGTTGCGATTTTG
2333421 GTTTTGCGTTGCGATT
1 GTTTTGCGTTGCGATT
2333437 CTCTCGTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.06, C:0.13, G:0.31, T:0.50
Consensus pattern (19 bp):
GTTTTGCGTTGCGATTTTG
Found at i:2333700 original size:94 final size:94
Alignment explanation
Indices: 2333554--2333933 Score: 629
Period size: 94 Copynumber: 4.1 Consensus size: 94
2333544 ATGGATTGCA
* *
2333554 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2333618 TTAGCAGAATTGGCAGCAATCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
2333647 TTACTTTCAACCAAAAAACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2333712 TTAGCAGAATTGGTAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
2333741 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2333806 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
2333835 TTAC-TTCGACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAATAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
2333899 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
2333929 TTACT
1 TTACT
2333934 AAGCAATCTA
Statistics
Matches: 270, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
93 22 0.08
94 248 0.92
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2335708 original size:33 final size:33
Alignment explanation
Indices: 2335658--2335783 Score: 180
Period size: 33 Copynumber: 3.8 Consensus size: 33
2335648 GAGAATGACT
* ** *
2335658 ATCGCAATGCGGAAATGACTATCACAACGAGAGA
1 ATCGCAACGC-GAAATGAAAATCGCAACGAGAGA
2335692 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
2335725 ATCGCAATGTGAAATTAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
2335758 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
2335784 TGCGATTTTG
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 73 0.89
34 9 0.11
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:2335715 original size:19 final size:18
Alignment explanation
Indices: 2335691--2335788 Score: 68
Period size: 19 Copynumber: 5.7 Consensus size: 18
2335681 ACAACGAGAG
2335691 AATCGCAACGCGAAATGAA
1 AATCGCAA-GCGAAATGAA
*
2335710 AATCGCAA-CG--A-GAG
1 AATCGCAAGCGAAATGAA
* *
2335724 AATCGCAATGTGAAATTAA
1 AATCGCAA-GCGAAATGAA
*
2335743 AATCGCAA-CG--A-GAG
1 AATCGCAAGCGAAATGAA
2335757 AATCGCAACGCGAAATGAA
1 AATCGCAA-GCGAAATGAA
2335776 AATCGCAATGCGA
1 AATCGCAA-GCGA
2335789 TTTTGGTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 31 0.52
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (18 bp):
AATCGCAAGCGAAATGAA
Found at i:2335819 original size:14 final size:14
Alignment explanation
Indices: 2335800--2335856 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2335790 TTTGGTTTCG
2335800 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
2335814 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
*
2335833 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
2335847 CGTTGCGATT
1 CGTTGCGATT
2335857 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:2335832 original size:33 final size:33
Alignment explanation
Indices: 2335784--2335864 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
2335774 AAAATCGCAA
**
2335784 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
2335817 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
2335850 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
2335865 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:2335867 original size:21 final size:20
Alignment explanation
Indices: 2335848--2335919 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
2335838 CGATTCTCTC
2335848 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
2335868 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
2335889 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
2335909 GTTGCGATTTT
1 GTTGCGATTTT
2335920 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:2336503 original size:20 final size:20
Alignment explanation
Indices: 2336478--2336732 Score: 264
Period size: 20 Copynumber: 12.6 Consensus size: 20
2336468 CTTTAAAAAT
2336478 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2336498 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
2336518 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
2336539 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
2336559 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
2336579 TGCGTTGCGATTTACGTAT-
1 CGCGTTGCGATTTACGGATA
*
2336598 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* *
2336619 CGCATTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
2336639 TGTCGTTGCAATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
2336660 CGCGTTACGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
2336681 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2336701 CGCGTTACGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
2336722 CTCGTTGCGAT
1 CGCGTTGCGAT
2336733 AGTCAGAATC
Statistics
Matches: 192, Mismatches: 33, Indels: 20
0.78 0.13 0.08
Matches are distributed among these distances:
19 2 0.01
20 121 0.63
21 69 0.36
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2336564 original size:40 final size:41
Alignment explanation
Indices: 2336480--2336732 Score: 366
Period size: 41 Copynumber: 6.2 Consensus size: 41
2336470 TTAAAAATCG
*
2336480 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
2336521 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
2336561 CGTTGCGATTTACAGATATGCGTTGCGA-TTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
2336601 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * *
2336642 CGTTGCAATTTACGGATACGCGTTACGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
2336683 CGTTGCGATTTACGGATACGCGTTACGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
2336724 CGTTGCGAT
1 CGTTGCGAT
2336733 AGTCAGAATC
Statistics
Matches: 195, Mismatches: 16, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
40 72 0.37
41 123 0.63
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:2336764 original size:20 final size:20
Alignment explanation
Indices: 2336741--2336793 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2336731 ATAGTCAGAA
*
2336741 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
2336761 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
2336781 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2336794 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:2336892 original size:20 final size:19
Alignment explanation
Indices: 2336843--2336896 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2336833 ATTCTTCATA
2336843 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
2336862 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
2336883 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
2336897 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:2343499 original size:3 final size:3
Alignment explanation
Indices: 2343488--2343524 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
2343478 ACAAAAATAA
2343488 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2343525 ACAAATGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2348779 original size:13 final size:12
Alignment explanation
Indices: 2348757--2348790 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2348747 AAATAAAGGG
2348757 CAAAGAAAAAAAT
1 CAAAG-AAAAAAT
*
2348770 CAAAGCAAAAAT
1 CAAAGAAAAAAT
2348782 CAAAGAAAA
1 CAAAGAAAA
2348791 GGAACAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.74, C:0.12, G:0.09, T:0.06
Consensus pattern (12 bp):
CAAAGAAAAAAT
Found at i:2350208 original size:66 final size:64
Alignment explanation
Indices: 2350137--2350450 Score: 322
Period size: 66 Copynumber: 4.8 Consensus size: 64
2350127 AACTTTGAAA
* * *
2350137 TTGTTTCTCTTGAAACAAAGTTTTGTTTCTCTTGAAATAGTTTCTTTTGAAGAAAAATCTTTGAG
1 TTGTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGATAGTTTCTCTTGAA-AAAAATCTTTGAG
2350202 T
64 T
* * * * *
2350203 TTGTTTCTCTGGAAACAAAATTTTGTCTCTCTTGAGACATTTTCTTTTGAAAAAAATCTTTGAAT
1 TTGTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAAAAAATCTTTGAGT
* * * *
2350268 TTGTTTCTCTGGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACACCAATATTTGA
1 TTGTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAA-A-AAATCTTTGA
2350333 GT
63 GT
* * * * * * **
2350335 ATATTTCCCTTGAAACAAATTTTATCTTTCTTGAGACAGTTTCTCTTGAAACACCCATCTTTGAG
1 TTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAA-A-AAATCTTTGAG
*
2350400 A
64 T
* * * * *
2350401 TCGTTTCCCTAGAAACAAATTTTGTCTCTCTTGAGATAGCTTCTCCTGAA
1 TTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAA
2350451 GCATCATCTG
Statistics
Matches: 211, Mismatches: 33, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
64 3 0.01
65 57 0.27
66 124 0.59
67 27 0.13
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (64 bp):
TTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAAAAAATCTTTGAGT
Found at i:2350283 original size:131 final size:132
Alignment explanation
Indices: 2350124--2350450 Score: 369
Period size: 131 Copynumber: 2.5 Consensus size: 132
2350114 CTTTATTAAG
* * * *
2350124 ACAAA-CTTTGAAATTGTTTCTCTTGAAACAAAGTTTTGTTTCTCTTGAAATAGTTTCTTTTGAA
1 ACAAATCTTTG-AATTGTTTCTCTAGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAA
* * * * * * *
2350188 GA-A-AAATCTTTGAGTTTGTTTCTCTGGAAACAAAATTTTGTCTCTCTTGAGACATTTTCTTTT
65 -ACACAAATATTTGAGTATATTTCCCTGGAAAC-AAATTTTATCTCTCTTGAGACAGTTTCTCTT
2350251 GAAA-
128 GAAAC
* *
2350255 A-AAATCTTTGAATTTGTTTCTCTGGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAA
1 ACAAATCTTTGAA-TTGTTTCTCTAGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAA
* * *
2350319 ACACCAATATTTGAGTATATTTCCCTTGAAACAAATTTTATCTTTCTTGAGACAGTTTCTCTTGA
65 ACACAAATATTTGAGTATATTTCCCTGGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGA
2350384 AAC
130 AAC
** * * * *
2350387 ACCCATCTTTGAGATCGTTTCCCTAGAAACAAA-TTTTGTCTCTCTTGAGATAGCTTCTCCTGAA
1 ACAAATCTTTGA-ATTGTTTCTCTAGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAA
2350451 GCATCATCTG
Statistics
Matches: 166, Mismatches: 23, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
130 6 0.04
131 84 0.51
132 51 0.31
133 24 0.14
134 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (132 bp):
ACAAATCTTTGAATTGTTTCTCTAGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAA
CACAAATATTTGAGTATATTTCCCTGGAAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAA
AC
Found at i:2350562 original size:40 final size:40
Alignment explanation
Indices: 2350507--2350701 Score: 124
Period size: 40 Copynumber: 4.6 Consensus size: 40
2350497 TGGCCTACCG
* * *
2350507 TCCTCATCGCTTAGGAACCGTGTCATCC-ACCGACCAAACC
1 TCCTCATCACGTAGGAACCGTGTCATCCTAACGACC-AACC
* * * ** *
2350547 TCCTCATTACGTAGGAGCCGTGTCACCCTTAGATAACCAGCC
1 TCCTCATCACGTAGGAACCGTGTCATCC-TA-ACGACCAACC
* * * *
2350589 ATCATCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGCCTACA
1 -TCCTCATCACGTAGGAACCGTG---TCAT-CCTAACGA---CCAACC
* *
2350637 TCCTCATCATGTAGGAACCGTGTCATCC-ACCGACCAAACC
1 TCCTCATCACGTAGGAACCGTGTCATCCTAACGACC-AACC
*
2350677 TCCTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
2350702 CCCCTAGATA
Statistics
Matches: 117, Mismatches: 26, Indels: 24
0.70 0.16 0.14
Matches are distributed among these distances:
39 2 0.02
40 48 0.41
42 7 0.06
43 24 0.21
44 4 0.03
45 2 0.02
46 5 0.04
47 22 0.19
48 3 0.03
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCTAACGACCAACC
Found at i:2350831 original size:132 final size:130
Alignment explanation
Indices: 2350488--2350817 Score: 417
Period size: 130 Copynumber: 2.5 Consensus size: 130
2350478 AAACCATTAT
* * *
2350488 CCCTAAAAATGGCCTACCGTCCTCATCGCTTAGGAACCGTGTCATCCACCGACCAAACCTCCTCA
1 CCCTAAAGATGGCCTA-CATCCTCATCGCATAGGAACCGTGTCATCCACCGACCAAACCTCCTCA
* * ** * *
2350553 TTACGTAGGAGCCGTGTCACCCTTAGATAACCAGCCATCATCATCACGTAGGAACCGTGTTATCA
65 TCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCATCATCATCACACAGGAACCATGTTAACA
*
2350618 T
130 C
***
2350619 CCCTAAAGATGGCCTACATCCTCATCATGTAGGAACCGTGTCATCCACCGACCAAACCTCCTCAT
1 CCCTAAAGATGGCCTACATCCTCATCGCATAGGAACCGTGTCATCCACCGACCAAACCTCCTCAT
* * * *
2350684 CACGTAGGAGCCGTGTCACCCCTAGATAGCCAGCTATCCTCATCGCACAGGAACCATGTTAACAC
66 CACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCATCATCATCACACAGGAACCATGTTAACA-
2350749 C
130 C
** * * ** *
2350750 CCCTAAAGATGGTTTGCCATCCTCATCGCATAGGAACCGCGTCATCCACATACCAAATCTCCTCA
1 CCCTAAAGATGGCCT-ACATCCTCATCGCATAGGAACCGTGTCATCCACCGACCAAACCTCCTCA
2350815 TCA
65 TCA
2350818 TATATGAGTC
Statistics
Matches: 171, Mismatches: 26, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
130 99 0.58
131 28 0.16
132 44 0.26
ACGTcount: A:0.27, C:0.35, G:0.16, T:0.22
Consensus pattern (130 bp):
CCCTAAAGATGGCCTACATCCTCATCGCATAGGAACCGTGTCATCCACCGACCAAACCTCCTCAT
CACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCATCATCATCACACAGGAACCATGTTAACAC
Found at i:2351801 original size:7 final size:7
Alignment explanation
Indices: 2351791--2351819 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2351781 AAAAATAGAA
2351791 AAGAGAG
1 AAGAGAG
2351798 AAGAGAG
1 AAGAGAG
2351805 AAGAGAG
1 AAGAGAG
2351812 AAGAGAG
1 AAGAGAG
2351819 A
1 A
2351820 GGGGAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
AAGAGAG
Found at i:2358198 original size:34 final size:34
Alignment explanation
Indices: 2358134--2358199 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
2358124 CTCACCTGAG
*
2358134 ATCCCAGAGGAGGATAACACATCACCAAAAAAGA
1 ATCCCAGAGGAGGATAACACATCACAAAAAAAGA
* *
2358168 ATCCCAGAGGAGGATAACGCATCAGAAAAAAA
1 ATCCCAGAGGAGGATAACACATCACAAAAAAA
2358200 AAGAGAGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.50, C:0.21, G:0.20, T:0.09
Consensus pattern (34 bp):
ATCCCAGAGGAGGATAACACATCACAAAAAAAGA
Found at i:2365485 original size:21 final size:20
Alignment explanation
Indices: 2365457--2365495 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2365447 CATTGCCGGA
*
2365457 ATTTATGGCTTCGACAAAAG
1 ATTTATGGCTTCAACAAAAG
*
2365477 ATTTCATGGTTTCAACAAA
1 ATTT-ATGGCTTCAACAAA
2365496 GACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
ATTTATGGCTTCAACAAAAG
Found at i:2382645 original size:21 final size:21
Alignment explanation
Indices: 2382607--2382646 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2382597 TAATCTTATT
**
2382607 TGTTTTCATTCACTTGATTGG
1 TGTTTTCATTCAAATGATTGG
*
2382628 TGTTTTGATTCAAATGATT
1 TGTTTTCATTCAAATGATT
2382647 ATTTTGAGCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.53
Consensus pattern (21 bp):
TGTTTTCATTCAAATGATTGG
Found at i:2385130 original size:21 final size:22
Alignment explanation
Indices: 2385104--2385149 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2385094 TATATACATA
*
2385104 TATATACTATTTATTTTTTA-T
1 TATATACTATTGATTTTTTACT
* *
2385125 TATATATTGTTGATTTTTTACT
1 TATATACTATTGATTTTTTACT
2385147 TAT
1 TAT
2385150 GTACATACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (22 bp):
TATATACTATTGATTTTTTACT
Found at i:2385191 original size:32 final size:32
Alignment explanation
Indices: 2385154--2385243 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
2385144 ACTTATGTAC
* *
2385154 ATACTATTAATTTTTATATTCAATATACATAT
1 ATACTACTAATTTTTATATTTAATATACATAT
* *
2385186 ATACTACTATTTTTTACATTTAATATACATAT
1 ATACTACTAATTTTTATATTTAATATACATAT
* *
2385218 ATACTGCTAAATTTTATATTTAATAT
1 ATACTACTAATTTTTATATTTAATAT
2385244 GCTAATTAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (32 bp):
ATACTACTAATTTTTATATTTAATATACATAT
Found at i:2389045 original size:13 final size:13
Alignment explanation
Indices: 2389027--2389060 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2389017 AGCTTAGAGA
*
2389027 AATAATTGAATTT
1 AATAATTAAATTT
2389040 AATAATTAAATTT
1 AATAATTAAATTT
2389053 AATAATTA
1 AATAATTA
2389061 GCAGTCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
AATAATTAAATTT
Found at i:2389847 original size:21 final size:21
Alignment explanation
Indices: 2389821--2389864 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2389811 CTCATACATG
*
2389821 AAATCTTGTCGAGAAGAACTA
1 AAATCTCGTCGAGAAGAACTA
*
2389842 AAATCTCGTTGAGAAGAACTA
1 AAATCTCGTCGAGAAGAACTA
2389863 AA
1 AA
2389865 GTGTTTGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (21 bp):
AAATCTCGTCGAGAAGAACTA
Found at i:2396039 original size:11 final size:13
Alignment explanation
Indices: 2396008--2396036 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2395998 GGCCAAAGAT
2396008 GAAAAGGTATGTA
1 GAAAAGGTATGTA
2396021 GAAAAGGTATGT-
1 GAAAAGGTATGTA
2396033 GAAA
1 GAAA
2396037 GGTGTTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (13 bp):
GAAAAGGTATGTA
Found at i:2401079 original size:23 final size:22
Alignment explanation
Indices: 2401053--2401102 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
2401043 AAATATGCAA
*
2401053 AAAGATAAAAGAAAGCATGCCAC
1 AAAGA-AAAAGAAAACATGCCAC
* *
2401076 AAAGGAAGATGAAAACATGCCAC
1 AAA-GAAAAAGAAAACATGCCAC
2401099 AAAG
1 AAAG
2401103 GTAGATGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 20 0.87
24 2 0.09
ACGTcount: A:0.56, C:0.16, G:0.20, T:0.08
Consensus pattern (22 bp):
AAAGAAAAAGAAAACATGCCAC
Found at i:2401103 original size:23 final size:23
Alignment explanation
Indices: 2401063--2401113 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
2401053 AAAGATAAAA
*
2401063 GAAAGCATGCCACAAAGGAAGAT
1 GAAAACATGCCACAAAGGAAGAT
*
2401086 GAAAACATGCCACAAAGGTAGAT
1 GAAAACATGCCACAAAGGAAGAT
2401109 GAAAA
1 GAAAA
2401114 TACTGACAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.51, C:0.16, G:0.24, T:0.10
Consensus pattern (23 bp):
GAAAACATGCCACAAAGGAAGAT
Found at i:2401984 original size:16 final size:17
Alignment explanation
Indices: 2401951--2401985 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2401941 ATTATTATCT
2401951 AATAATATTATATTATA
1 AATAATATTATATTATA
*
2401968 AATATTATTAT-TTATA
1 AATAATATTATATTATA
2401984 AA
1 AA
2401986 CCCTGAAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATAATATTATATTATA
Found at i:2410936 original size:16 final size:14
Alignment explanation
Indices: 2410897--2410939 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
2410887 ATTGATGAAT
*
2410897 TATTATATAAT-AA
1 TATTATATTATAAA
2410910 TATTATATTATAAA
1 TATTATATTATAAA
2410924 TATTATTAGTTATAAA
1 TATTA-TA-TTATAAA
2410940 GCCTGAAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 10 0.38
14 7 0.27
15 2 0.08
16 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
TATTATATTATAAA
Found at i:2415935 original size:20 final size:20
Alignment explanation
Indices: 2415910--2415947 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2415900 TCCCATTTTT
*
2415910 GCATCTTTGCATTTGCATTA
1 GCATCTTTGCATTAGCATTA
2415930 GCATCTTTGCATTAGCAT
1 GCATCTTTGCATTAGCAT
2415948 CTATACATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (20 bp):
GCATCTTTGCATTAGCATTA
Found at i:2415938 original size:14 final size:14
Alignment explanation
Indices: 2415921--2415949 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2415911 CATCTTTGCA
2415921 TTTGCATTAGCATC
1 TTTGCATTAGCATC
2415935 TTTGCATTAGCATC
1 TTTGCATTAGCATC
2415949 T
1 T
2415950 ATACATCGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (14 bp):
TTTGCATTAGCATC
Found at i:2417292 original size:21 final size:20
Alignment explanation
Indices: 2417265--2417355 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 20
2417255 AATATCTAGC
2417265 AAAAAAAGAAGAAAAAAAGA
1 AAAAAAAGAAGAAAAAAAGA
2417285 AGAAAAAAG-AG-AAAAAAGA
1 A-AAAAAAGAAGAAAAAAAGA
*
2417304 AAAAATAACAA-AGAAAAAAG-
1 AAAAA-AAGAAGA-AAAAAAGA
2417324 AAAAAAAGAGAGAAAAGAAAGA
1 AAAAAAAGA-AGAAAA-AAAGA
*
2417346 AAAGAAAGAA
1 AAAAAAAGAA
2417356 ATAAGAAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 17
0.75 0.04 0.22
Matches are distributed among these distances:
18 4 0.07
19 14 0.24
20 13 0.22
21 20 0.34
22 8 0.14
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAAAAAGAAGAAAAAAAGA
Found at i:2417300 original size:30 final size:30
Alignment explanation
Indices: 2417265--2417356 Score: 111
Period size: 30 Copynumber: 3.1 Consensus size: 30
2417255 AATATCTAGC
2417265 AAAAAAAGAAGAAAA-AAAGAAGAAAAAAG
1 AAAAAAAGAAGAAAAGAAAGAAGAAAAAAG
*
2417294 AGAAAAAAGAA-AAAATAACA-AAGAAAAAAG
1 A-AAAAAAGAAGAAAAGAA-AGAAGAAAAAAG
*
2417324 AAAAAAAGAGAGAAAAGAAAGAA-AAGAAAG
1 AAAAAAAGA-AGAAAAGAAAGAAGAAAAAAG
2417354 AAA
1 AAA
2417357 TAAGAAATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
29 13 0.24
30 33 0.60
31 9 0.16
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (30 bp):
AAAAAAAGAAGAAAAGAAAGAAGAAAAAAG
Found at i:2417307 original size:37 final size:35
Alignment explanation
Indices: 2417266--2417363 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 35
2417256 ATATCTAGCA
2417266 AAAAAAGAAGAAAAAAAGAAGAAAAAAGAGAAAAAAG
1 AAAAAA-AAGAAAAAAA-AAGAAAAAAGAGAAAAAAG
* *
2417303 AAAAAATAACAAAGAAAAAAGAAAAAAAGAGAGAAAAG
1 AAAAAA-AAGAAA-AAAAAAG-AAAAAAGAGAAAAAAG
* *
2417341 AAAGAAAAGAAAGAAATAAGAAA
1 AAAAAAAAGAAA-AAAAAAGAAA
2417364 TAAAATTGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
36 3 0.06
37 26 0.49
38 24 0.45
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.02
Consensus pattern (35 bp):
AAAAAAAAGAAAAAAAAAGAAAAAAGAGAAAAAAG
Found at i:2417321 original size:40 final size:38
Alignment explanation
Indices: 2417277--2417368 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 38
2417267 AAAAAGAAGA
2417277 AAAAAAGAAGAAAAAAGAGAAAAAAGAAAAAATAACAAAG
1 AAAAAAGAA-AAAAAAGAGAAAAAAGAAAAAA-AACAAAG
* * *
2417317 AAAAAAG-AAAAAAAGAGAGAAAAGAAAGAAAAGAAAG
1 AAAAAAGAAAAAAAAGAGAAAAAAGAAAAAAAACAAAG
* *
2417354 AAATAAGAAATAAAA
1 AAAAAAGAAAAAAAA
2417369 TTGATCAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
37 12 0.26
38 26 0.57
39 1 0.02
40 7 0.15
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.03
Consensus pattern (38 bp):
AAAAAAGAAAAAAAAGAGAAAAAAGAAAAAAAACAAAG
Found at i:2417358 original size:48 final size:48
Alignment explanation
Indices: 2417264--2417368 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 48
2417254 AAATATCTAG
2417264 CAAAAAAAGAAGAAAAAAAGAAGAAAAAAGAGAAAAAAGAAAAAATAA
1 CAAAAAAAGAAGAAAAAAAGAAGAAAAAAGAGAAAAAAGAAAAAATAA
*
2417312 CAAAGAAAA-AAGAAAAAAAG-AGAGAAAAGA-AAGAAAAGAAAGAAATAA
1 CAAA-AAAAGAAGAAAAAAAGAAGAAAAAAGAGAA-AAAAGAAA-AAATAA
*
2417360 GAAATAAAA
1 CAAA-AAAA
2417369 TTGATCAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
46 2 0.04
47 17 0.33
48 28 0.55
49 4 0.08
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (48 bp):
CAAAAAAAGAAGAAAAAAAGAAGAAAAAAGAGAAAAAAGAAAAAATAA
Found at i:2418111 original size:53 final size:53
Alignment explanation
Indices: 2418053--2418157 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 53
2418043 GGAATCCTAA
* * *
2418053 GCCTTATATTACCATTAATCTTTACATTTTTCAAATGTGCATAATTTTTGAAT
1 GCCTTATATCAACATTAATCTTTACACTTTTCAAATGTGCATAATTTTTGAAT
* *
2418106 GCCTTATATCAACATTAATTTTTACACTTTTCAAATGTGTATAATTTTTGAA
1 GCCTTATATCAACATTAATCTTTACACTTTTCAAATGTGCATAATTTTTGAA
2418158 GGATTAAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (53 bp):
GCCTTATATCAACATTAATCTTTACACTTTTCAAATGTGCATAATTTTTGAAT
Found at i:2419287 original size:54 final size:53
Alignment explanation
Indices: 2419221--2419322 Score: 150
Period size: 54 Copynumber: 1.9 Consensus size: 53
2419211 GGCTAATGCA
* * * *
2419221 ATTTTTTTAGAAACTAAGTCCGATTTTTGGATGTTTCTTGATTATTTTAAATG
1 ATTTTTTAAGAAACTAAGTCCGATTTTTAGAAGTTTCTTGATGATTTTAAATG
*
2419274 ATTTTTTAAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGATGATTTT
1 ATTTTTT-AAGAAACTAAGTCCGATTTTTAGAAGTTTCTTGATGATTTT
2419323 TAAACGAGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 7 0.16
54 36 0.84
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (53 bp):
ATTTTTTAAGAAACTAAGTCCGATTTTTAGAAGTTTCTTGATGATTTTAAATG
Found at i:2419508 original size:54 final size:53
Alignment explanation
Indices: 2419367--2419569 Score: 246
Period size: 53 Copynumber: 3.8 Consensus size: 53
2419357 TGACATGATT
* ** * *
2419367 AATTTAAAAGAAGCTAAGCTTAATTTTTAGGGGTTTCTTGATGTTTTCAAATT
1 AATTTTAAAGAAATTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
* *
2419420 AATTTGAAAG-AATCTAAGCCTAATTTTTAGGGGTTTCTTAATGTTTTCAAATG
1 AATTTTAAAGAAAT-TAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
* * * ** *
2419473 AATTTTCAAAGAAATTAAGTCTGATTTTCAGGGGTTTCTTGATACTTTCATATG
1 AATTTT-AAAGAAATTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
* *
2419527 AATTTTAAAGAAGTTAAGCCTAATTTTTAGGGGTTTTTTGATG
1 AATTTTAAAGAAATTAAGCCTAATTTTTAGGGGTTTCTTGATG
2419570 ATGACTAAAA
Statistics
Matches: 127, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.64
54 42 0.33
55 3 0.02
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (53 bp):
AATTTTAAAGAAATTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATG
Found at i:2420088 original size:274 final size:273
Alignment explanation
Indices: 2419592--2420134 Score: 761
Period size: 274 Copynumber: 2.0 Consensus size: 273
2419582 CGAAAGTTTT
** **
2419592 TAAGAAACTAAACTTGATTTTCAAGGGTTTCTTAATATGTAAGTCCTTTGGGGTATTTGTAAGTC
1 TAAGAAACTAAACTTGATTTTCAAGGGTTTCTTAATATGTAAGTCCTTTGGGCCATCGGTAAGTC
* * *
2419657 TTTCGAGCATGATATTTAAATCCTTCGGGTTATCTATAAGTCTTTCGAGCAAGATGATAAGTCCT
66 TTTCAAGCATGATATTTAAATCCTTCGGGTCATCTATAAGTATTTCGAGCAAGATGATAAGTCCT
* *
2419722 TCAAGCCATCCATAAGACCTCCGGACAGGATGTTTTCAAATGATATTTTAGAAACTAAGCCTGAT
131 TCAAGCCATCCATAAGACCTCCGGACAAGATGTTTTCAAATGATATTTTAGAAACTAAGCCTAAT
* * * * * * *
2419787 TTTTAGGGTTTCTTGATGATTATCTCCAAATAGTTTTTGAAATGAAGCTAAGCTTAATTTTTAAG
196 TTTCAGGGTTTCTTGACGATAATCTCCAAAGAATTTTT-AAAGGAAGCTAAGCCTAATTTTTAAG
2419852 GGTTCCTTGACAAC
260 GGTTCCTTGACAAC
*
2419866 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTAATGA-GTAAGTCCTTTGGGCCATCGGTAAGT
1 TAAGAAACTAAACTTGATTTTCAAGGGTTTCTTAAT-ATGTAAGTCCTTTGGGCCATCGGTAAGT
* * *
2419930 CTTTCAATCGTGAT-TCTTAAATTCTTCGGGTCATCTATAAGTATTTCGAGCAAGATGATAAGTC
65 CTTTCAAGCATGATAT-TTAAATCCTTCGGGTCATCTATAAGTATTTCGAGCAAGATGATAAGTC
** * * *
2419994 CTTCGGGCCATCCATAAGACCTTCGGGCAAGAT-TTTTCAAATGAGT-TTTTAGAAACTAATCCT
129 CTTCAAGCCATCCATAAGACCTCCGGACAAGATGTTTTCAAATGA-TATTTTAGAAACTAAGCCT
* *
2420057 AATTTTCAGGGGTTTCTTGACGGTAATCTCCAAAGAATTTTTAAAGGAAGTTAAGCCTAATTTTT
193 AATTTTCA-GGGTTTCTTGACGATAATCTCCAAAGAATTTTTAAAGGAAGCTAAGCCTAATTTTT
*
2420122 AGGGGTTCCTTGA
257 AAGGGTTCCTTGA
2420135 TGACAACCAA
Statistics
Matches: 237, Mismatches: 28, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
273 66 0.28
274 170 0.72
275 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (273 bp):
TAAGAAACTAAACTTGATTTTCAAGGGTTTCTTAATATGTAAGTCCTTTGGGCCATCGGTAAGTC
TTTCAAGCATGATATTTAAATCCTTCGGGTCATCTATAAGTATTTCGAGCAAGATGATAAGTCCT
TCAAGCCATCCATAAGACCTCCGGACAAGATGTTTTCAAATGATATTTTAGAAACTAAGCCTAAT
TTTCAGGGTTTCTTGACGATAATCTCCAAAGAATTTTTAAAGGAAGCTAAGCCTAATTTTTAAGG
GTTCCTTGACAAC
Found at i:2421421 original size:105 final size:105
Alignment explanation
Indices: 2421297--2421596 Score: 379
Period size: 105 Copynumber: 2.9 Consensus size: 105
2421287 AAGGGAGAAG
* * *
2421297 AAGTTCATAATGAGAAAAACTGGTTCATTTCAAATCAACAACAGAAGGAGGTGGATCGACATTTT
1 AAGTTCATAATGAGAAAAACTTGTTCATTTCAAATCCACAACAGAAGGAGGTGGATCGACATTTC
* *
2421362 CGGAATAGTTCATAACGAGAAAAACTAAC-CT-TAAAGGAGA
66 CAGAAGAGTTCATAACGAGAAAAACT--CGCTCTAAAGGAGA
* * * *
2421402 AAGTTCATAATGAGAAAAACTTGTTCCTTTCAAATCCACAGCAGAAGGAGATGGATCGAAATTTC
1 AAGTTCATAATGAGAAAAACTTGTTCATTTCAAATCCACAACAGAAGGAGGTGGATCGACATTTC
* * * * *
2421467 CAGAAGATTTCATAATGGGAAGAACTCGCTCTAAATGAGA
66 CAGAAGAGTTCATAACGAGAAAAACTCGCTCTAAAGGAGA
** * *
2421507 AAGTTCATAATGAGATGAACTTGTTCATTTCAAATCCACCACAGAATGAGGTGGATCGACATTTC
1 AAGTTCATAATGAGAAAAACTTGTTCATTTCAAATCCACAACAGAAGGAGGTGGATCGACATTTC
* * *
2421572 CAGAAGAGTACATGATGAGAAAAAC
66 CAGAAGAGTTCATAACGAGAAAAAC
2421597 CCATAACCAG
Statistics
Matches: 166, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
103 1 0.01
104 2 0.01
105 163 0.98
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (105 bp):
AAGTTCATAATGAGAAAAACTTGTTCATTTCAAATCCACAACAGAAGGAGGTGGATCGACATTTC
CAGAAGAGTTCATAACGAGAAAAACTCGCTCTAAAGGAGA
Found at i:2424831 original size:31 final size:30
Alignment explanation
Indices: 2424752--2424818 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
2424742 GGGAATCCAT
* * *
2424752 TTTTTTTGCATGTATGATTAGGACTCTTAA
1 TTTTTTTACATTTATAATTAGGACTCTTAA
2424782 TTTTTTTACATTTATAATTAGGGAC-CTT-A
1 TTTTTTTACATTTATAATTA-GGACTCTTAA
2424811 TTTTTTTA
1 TTTTTTTA
2424819 TAATTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 9 0.27
30 20 0.61
31 4 0.12
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (30 bp):
TTTTTTTACATTTATAATTAGGACTCTTAA
Found at i:2424979 original size:124 final size:117
Alignment explanation
Indices: 2424783--2425019 Score: 280
Period size: 118 Copynumber: 2.0 Consensus size: 117
2424773 GACTCTTAAT
* * * ** * *
2424783 TTTTTTACATTTATAATTAGGGACCTTATTTTTTTATAATTTTATAATTTTTTTAGTTTTTATCC
1 TTTTTTACATTTATAATTAGGGACCTCATATTTTTATAATTTCATAAAATGTTTAGTTTTTACCC
* *
2424848 TCTTTTTCCTTTTATTTTTTCTTATTAATTCATTTTATTTTGAATTAAATTTAACTAA
66 TCTTTTTCC----A-TTTCTCTTATT-ATTCATTTAATTTTGAATTAAATTTAACTAA
*
2424906 TTTTTTATATTTATAATTAGGG-CTCTCA-ATTTTTATAATTTCATAAAATGTTTAGTTTTTTTA
1 TTTTTTACATTTATAATTAGGGAC-CTCATATTTTTATAATTTCATAAAATGTTTAG--TTTTTA
*
2424969 CCCTCTTTTTCCATTTCTCTTATTTTTCATTTAATTTTGAATTAAATTTAA
63 CCCTCTTTTTCCATTTCTCTTATTATTCATTTAATTTTGAATTAAATTTAA
2425020 TCATATTTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
118 25 0.25
119 10 0.10
120 1 0.01
122 23 0.23
123 24 0.24
124 17 0.17
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.59
Consensus pattern (117 bp):
TTTTTTACATTTATAATTAGGGACCTCATATTTTTATAATTTCATAAAATGTTTAGTTTTTACCC
TCTTTTTCCATTTCTCTTATTATTCATTTAATTTTGAATTAAATTTAACTAA
Found at i:2425006 original size:123 final size:123
Alignment explanation
Indices: 2424783--2425006 Score: 258
Period size: 123 Copynumber: 1.8 Consensus size: 123
2424773 GACTCTTAAT
* * * ** * *
2424783 TTTTTTACATTTATAATTAGGGACCTTATTTTTTTATAATTTTATAATTTTTTTAGTTTTTATCC
1 TTTTTTACATTTATAATTAGGGACCTCATATTTTTATAATTTCATAAAATGTTTAGTTTTTACCC
* * * *
2424848 TCTTTTTCCTTTTATTTTTTCTTATTAATTCATTTTATTTTGAATTAAATTTAACTAA
66 TCTTTTTCCATTTATTTATTCTTATCAATTAATTTTATTTTGAATTAAATTTAACTAA
*
2424906 TTTTTTATATTTATAATTAGGG-CTCTCA-ATTTTTATAATTTCATAAAATGTTTAGTTTTTTTA
1 TTTTTTACATTTATAATTAGGGAC-CTCATATTTTTATAATTTCATAAAATGTTTAG--TTTTTA
* *
2424969 CCCTCTTTTTCCATTTCTCTTATT-TT-TCATTTAATTTT
63 CCCTCTTTTTCCATTTAT-TTATTCTTATCAATTAATTTT
2425007 GAATTAAATT
Statistics
Matches: 83, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
122 23 0.28
123 33 0.40
124 23 0.28
125 4 0.05
ACGTcount: A:0.24, C:0.11, G:0.04, T:0.61
Consensus pattern (123 bp):
TTTTTTACATTTATAATTAGGGACCTCATATTTTTATAATTTCATAAAATGTTTAGTTTTTACCC
TCTTTTTCCATTTATTTATTCTTATCAATTAATTTTATTTTGAATTAAATTTAACTAA
Found at i:2427590 original size:30 final size:30
Alignment explanation
Indices: 2427554--2427614 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2427544 TAATATCTTG
2427554 ACGACCCCGTTGGGGATGAATTAGAGAGTC
1 ACGACCCCGTTGGGGATGAATTAGAGAGTC
2427584 ACGACCCCGTTGGGGATGAATTAGAGAGTC
1 ACGACCCCGTTGGGGATGAATTAGAGAGTC
2427614 A
1 A
2427615 GGCCAATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.20
Consensus pattern (30 bp):
ACGACCCCGTTGGGGATGAATTAGAGAGTC
Found at i:2429031 original size:2 final size:2
Alignment explanation
Indices: 2429024--2429048 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2429014 TGGTGTCATA
2429024 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2429049 CATACACACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2429796 original size:13 final size:13
Alignment explanation
Indices: 2429778--2429802 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2429768 AAATTTTTAG
2429778 GATGAAGCATCAT
1 GATGAAGCATCAT
2429791 GATGAAGCATCA
1 GATGAAGCATCA
2429803 GAGTGCTTTA
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:0.16, G:0.24, T:0.20
Consensus pattern (13 bp):
GATGAAGCATCAT
Found at i:2431382 original size:19 final size:19
Alignment explanation
Indices: 2431358--2431399 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
2431348 AAAAAACCGA
2431358 TTGAACACCCATATATTTG
1 TTGAACACCCATATATTTG
2431377 TTGAACACCCATATATTTG
1 TTGAACACCCATATATTTG
2431396 TTGA
1 TTGA
2431400 GTAATGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (19 bp):
TTGAACACCCATATATTTG
Found at i:2436725 original size:40 final size:41
Alignment explanation
Indices: 2436618--2436729 Score: 108
Period size: 40 Copynumber: 2.8 Consensus size: 41
2436608 AGACTATTTC
* *
2436618 CAAGATGAGTAAGTCCTTCAGGTCATC-AGTAAGTCTTTTAAG
1 CAAGATGA-TAAGT-CTTCGGGTCATCTAGTAAGTCTTTCAAG
* *
2436660 -AATGATGATAA-TCTTTTGGGTCATCTA-TAAGTCTTTCGAG
1 CAA-GATGATAAGTC-TTCGGGTCATCTAGTAAGTCTTTCAAG
*
2436700 CAAGATGATAAGTCTTCGGGCCATCT-GTAA
1 CAAGATGATAAGTCTTCGGGTCATCTAGTAA
2436730 AACCTTCAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
39 1 0.02
40 42 0.72
41 10 0.17
42 5 0.09
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (41 bp):
CAAGATGATAAGTCTTCGGGTCATCTAGTAAGTCTTTCAAG
Found at i:2437334 original size:23 final size:22
Alignment explanation
Indices: 2437291--2437340 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
2437281 AATAAAGGGT
*
2437291 AATAATATAAGTAATGAAAATA
1 AATAATATAAGAAATGAAAATA
2437313 AATAATAATAATGAAATG-AAATA
1 AATAAT-ATAA-GAAATGAAAATA
2437336 AATAA
1 AATAA
2437341 AAAGATAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 6 0.24
23 14 0.56
24 5 0.20
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (22 bp):
AATAATATAAGAAATGAAAATA
Found at i:2441585 original size:11 final size:11
Alignment explanation
Indices: 2441571--2441626 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
2441561 TCTTTTTGAA
2441571 TTCTTTTTCTT
1 TTCTTTTTCTT
2441582 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
2441595 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
2441608 TGTCTTTTTC-T
1 T-TCTTTTTCTT
2441619 TTCTTTTT
1 TTCTTTTT
2441627 GTACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:2441595 original size:19 final size:18
Alignment explanation
Indices: 2441571--2441626 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
2441561 TCTTTTTGAA
2441571 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
2441589 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
2441608 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
2441626 T
1 T
2441627 GTACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:2441917 original size:23 final size:22
Alignment explanation
Indices: 2441874--2441923 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
2441864 AATAAAGGGT
*
2441874 AATAATATAAGTAATGAAAATA
1 AATAATATAAGAAATGAAAATA
2441896 AATAATAATAATGAAATG-AAATA
1 AATAAT-ATAA-GAAATGAAAATA
2441919 AATAA
1 AATAA
2441924 AAAGATAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 6 0.24
23 14 0.56
24 5 0.20
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (22 bp):
AATAATATAAGAAATGAAAATA
Found at i:2456728 original size:54 final size:54
Alignment explanation
Indices: 2456670--2456774 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
2456660 AGGAACTAAA
* * *
2456670 TGTGCAACCCATGGTATTCATAATGTGTTTATGAATGACCATTTCGGCACTATG
1 TGTGCAACACATGGAATTCATAATGAGTTTATGAATGACCATTTCGGCACTATG
* * * **
2456724 TGTGCAATATATGGAATTCATAATGAGTTTGTGAATTCCCATTTCGGCACT
1 TGTGCAACACATGGAATTCATAATGAGTTTATGAATGACCATTTCGGCACT
2456775 TCGGTGTAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (54 bp):
TGTGCAACACATGGAATTCATAATGAGTTTATGAATGACCATTTCGGCACTATG
Found at i:2467009 original size:30 final size:31
Alignment explanation
Indices: 2466973--2467048 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 31
2466963 TAAGATGACC
* *
2466973 CTTGGGTAGGCTCTGAGTCCCCGAG-ACTTT
1 CTTGGGTAGGCTCTAAGGCCCCGAGAACTTT
* *
2467003 CTTGGGTAGGCTCCCAAGGCCCTGAGAACTTT
1 CTTGGGTAGGCT-CTAAGGCCCCGAGAACTTT
*
2467035 CTTGAGTAGGCTCT
1 CTTGGGTAGGCTCT
2467049 CAGGTTCTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 12 0.32
31 10 0.26
32 16 0.42
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (31 bp):
CTTGGGTAGGCTCTAAGGCCCCGAGAACTTT
Found at i:2475218 original size:2 final size:2
Alignment explanation
Indices: 2475206--2475249 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
2475196 TATAAATTTA
2475206 AT AT AT A- AT AT AT AT AT AT AT AT A- AT AT AT -T 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
2475245 AT AT A
1 AT AT A
2475250 AAGAGAGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2475223 original size:24 final size:24
Alignment explanation
Indices: 2475196--2475247 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2475186 CATGCTAAAC
*
2475196 TATAAATTTAATATATAATATATA
1 TATAAATATAATATATAATATATA
* *
2475220 TATATATATAATATATTATATATA
1 TATAAATATAATATATAATATATA
2475244 TATA
1 TATA
2475248 TAAAGAGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATAAATATAATATATAATATATA
Found at i:2475233 original size:22 final size:22
Alignment explanation
Indices: 2475208--2475249 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2475198 TAAATTTAAT
2475208 ATATAATATATATATATATATA
1 ATATAATATATATATATATATA
*
2475230 ATATATTATATATATATATA
1 ATATAATATATATATATATA
2475250 AAGAGAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATAATATATATATATATATA
Found at i:2475248 original size:24 final size:24
Alignment explanation
Indices: 2475204--2475249 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2475194 ACTATAAATT
2475204 TAATATATAATATATATATATATA
1 TAATATATAATATATATATATATA
*
2475228 TAATATATTATATATATATATA
1 TAATATATAATATATATATATA
2475250 AAGAGAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATATATAATATATATATATATA
Found at i:2477885 original size:23 final size:22
Alignment explanation
Indices: 2477843--2477886 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2477833 CAGGAGTTAT
2477843 AGGAGTTATCTGATTTAATTTC
1 AGGAGTTATCTGATTTAATTTC
2477865 AGGAGTTATAACT-ATTTAATTT
1 AGGAGTTAT--CTGATTTAATTT
2477887 TTTTGCAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 9 0.45
24 2 0.10
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (22 bp):
AGGAGTTATCTGATTTAATTTC
Found at i:2482555 original size:31 final size:31
Alignment explanation
Indices: 2482517--2482576 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
2482507 AAGAGTTTGG
2482517 GAGTTCCTACTGAGAAGGACATATTGAATGA
1 GAGTTCCTACTGAGAAGGACATATTGAATGA
*
2482548 GAGTTCCTAGTGAGAAGGACATATTGAAT
1 GAGTTCCTACTGAGAAGGACATATTGAAT
2482577 TCACCAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.27
Consensus pattern (31 bp):
GAGTTCCTACTGAGAAGGACATATTGAATGA
Found at i:2483404 original size:23 final size:22
Alignment explanation
Indices: 2483360--2483404 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2483350 TCAGGAGTTA
2483360 CAGGAGTTATCTGATTTAATTT
1 CAGGAGTTATCTGATTTAATTT
2483382 CAGGAGTTATAACTG-TTTAATTT
1 CAGGAGTTAT--CTGATTTAATTT
2483405 TTATGCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 8 0.38
24 3 0.14
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (22 bp):
CAGGAGTTATCTGATTTAATTT
Found at i:2486429 original size:18 final size:18
Alignment explanation
Indices: 2486383--2486417 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2486373 GAACTAGTTT
*
2486383 GACCAGTTGAATTTGACA
1 GACCAGTTGACTTTGACA
*
2486401 GACCTGTTGACTTTGAC
1 GACCAGTTGACTTTGAC
2486418 CCGACCGTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (18 bp):
GACCAGTTGACTTTGACA
Found at i:2490045 original size:50 final size:50
Alignment explanation
Indices: 2489970--2490074 Score: 165
Period size: 50 Copynumber: 2.1 Consensus size: 50
2489960 CTTATTGTAA
* * * *
2489970 CTCTTTAAAATAATATGAATTTAAATCACAAGTTTAGAAGAAACCTTGGG
1 CTCTTTAAAAGAATATGAATTTAAATCAAAAGTTTAAAAGAAACCTCGGG
*
2490020 CTCTTTAAAAGAATATGAATTTAAATCAAAAGTTTAAAAGACACCTCGGG
1 CTCTTTAAAAGAATATGAATTTAAATCAAAAGTTTAAAAGAAACCTCGGG
2490070 CTCTT
1 CTCTT
2490075 CAAGAGCTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (50 bp):
CTCTTTAAAAGAATATGAATTTAAATCAAAAGTTTAAAAGAAACCTCGGG
Found at i:2494506 original size:22 final size:22
Alignment explanation
Indices: 2494457--2494526 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
2494447 GCTTTTTTTG
* * **
2494457 TCAAAGTCAATAATCAAACTAA
1 TCAAAGTCAACAATCAGACCGA
*
2494479 TTAAAGTCAACAATCAGACCGA
1 TCAAAGTCAACAATCAGACCGA
* * *
2494501 TCAAAGTCATCGATCAGACCGG
1 TCAAAGTCAACAATCAGACCGA
2494523 TCAA
1 TCAA
2494527 CTGTCAACGG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.20
Consensus pattern (22 bp):
TCAAAGTCAACAATCAGACCGA
Found at i:2494609 original size:20 final size:20
Alignment explanation
Indices: 2494584--2494638 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
2494574 GGTCAGTTCA
** *
2494584 GGTTGACTCAGTTTGGGTCG
1 GGTTGACTCAGTTCAGATCG
* *
2494604 GGTTGACTCGGTTCAGATCT
1 GGTTGACTCAGTTCAGATCG
2494624 GGTTGACTCAGTTCA
1 GGTTGACTCAGTTCA
2494639 AGTCAAAGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.35
Consensus pattern (20 bp):
GGTTGACTCAGTTCAGATCG
Found at i:2507610 original size:44 final size:44
Alignment explanation
Indices: 2507560--2507789 Score: 255
Period size: 44 Copynumber: 5.2 Consensus size: 44
2507550 GTTTGAGATT
*
2507560 TAGCGGCGTTTTTTGGATACAAACGCCGCTAAAGGTCTGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
* * * *
2507604 TAGCGGCGTTTTCAGGATACAAATGTCGCTAAAGGTATGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
* * * * *
2507648 TAGCGGTGTTTTTAGAATTCAAATGCCGCTAAAGATCTGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
* * ** * *
2507692 TAGTGTCCATTTTAGGATACAAACACCGTTAAAGGTCTGGTATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
* * * * *
2507736 TAGTGACATTTTTAGTATACAAACGCCGCTAAAGGT-TGATATA
1 TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
*
2507779 TAGTGGCGTTT
1 TAGCGGCGTTT
2507790 GTTACAAAAA
Statistics
Matches: 154, Mismatches: 32, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
43 15 0.10
44 139 0.90
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (44 bp):
TAGCGGCGTTTTTAGGATACAAACGCCGCTAAAGGTCTGGTATA
Found at i:2511501 original size:21 final size:21
Alignment explanation
Indices: 2511475--2511517 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2511465 ACCATAAAGT
2511475 CTCCGATCTTTAACACTAACA
1 CTCCGATCTTTAACACTAACA
*
2511496 CTCCGATCTTTAACACTGACA
1 CTCCGATCTTTAACACTAACA
2511517 C
1 C
2511518 AACGAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.35, G:0.07, T:0.28
Consensus pattern (21 bp):
CTCCGATCTTTAACACTAACA
Found at i:2515830 original size:13 final size:13
Alignment explanation
Indices: 2515812--2515841 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2515802 TTACTCGACC
*
2515812 TGACCCGACCCGT
1 TGACCCGACCCAT
2515825 TGACCCGACCCAT
1 TGACCCGACCCAT
2515838 TGAC
1 TGAC
2515842 TCGGCCCGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.17
Consensus pattern (13 bp):
TGACCCGACCCAT
Found at i:2515833 original size:23 final size:24
Alignment explanation
Indices: 2515789--2515834 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2515779 GTTACAACCC
* *
2515789 GACCCGATCCCGTTTACTCGACCT
1 GACCCGATCCCGTTGACCCGACCT
2515813 GACCCGA-CCCGTTGACCCGACC
1 GACCCGATCCCGTTGACCCGACC
2515835 CATTGACTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.17, C:0.46, G:0.20, T:0.17
Consensus pattern (24 bp):
GACCCGATCCCGTTGACCCGACCT
Found at i:2518660 original size:32 final size:31
Alignment explanation
Indices: 2518586--2518707 Score: 88
Period size: 31 Copynumber: 3.9 Consensus size: 31
2518576 CTAATGTGAC
* *
2518586 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
* * * **
2518617 TATTGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
* * *
2518649 TCTTAGGTAGGCTCC-ACAGCCCCAAAATC-T
1 TCTTAGGTAGGC-CCTACGGCCCTAAGATCAT
*
2518679 ATCTTAGGTAGGCTCT-CAGGCCCTAAGAT
1 -TCTTAGGTAGGCCCTAC-GGCCCTAAGAT
2518708 GTTCCCTTAG
Statistics
Matches: 68, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
30 3 0.04
31 43 0.63
32 20 0.29
33 2 0.03
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:2521246 original size:42 final size:41
Alignment explanation
Indices: 2521171--2521279 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 41
2521161 TGTTTATATT
* * * * *
2521171 AAAACGCCACTAAGGGACCAAACTTCTGTGGCGTTTATTACA
1 AAAACGCCTCTAAAGGACAAAACTACTGCGGCGTTTATTA-A
*
2521213 AAAAAGCCTCTAAAGGACAAAACTACTGCGGCGTTTATTAA
1 AAAACGCCTCTAAAGGACAAAACTACTGCGGCGTTTATTAA
*
2521254 AGAAACGCCAT-TAAATGACAAAACTA
1 A-AAACGCC-TCTAAAGGACAAAACTA
2521280 TTACGACATT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
41 2 0.04
42 54 0.95
43 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (41 bp):
AAAACGCCTCTAAAGGACAAAACTACTGCGGCGTTTATTAA
Found at i:2521342 original size:40 final size:41
Alignment explanation
Indices: 2521278--2521363 Score: 129
Period size: 40 Copynumber: 2.1 Consensus size: 41
2521268 ATGACAAAAC
*
2521278 TATTACGACATTTTTTTTATAAACGCCGCTAAAGAACATGAA
1 TATTACGA-ATTTTTTTTACAAACGCCGCTAAAGAACATGAA
* *
2521320 TATTACG-ATTTTTTTTACAAACGCCGCTAAAGTACATGGA
1 TATTACGAATTTTTTTTACAAACGCCGCTAAAGAACATGAA
2521360 TATT
1 TATT
2521364 GCGGCGTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 34 0.83
42 7 0.17
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (41 bp):
TATTACGAATTTTTTTTACAAACGCCGCTAAAGAACATGAA
Found at i:2523278 original size:82 final size:81
Alignment explanation
Indices: 2523189--2523460 Score: 235
Period size: 83 Copynumber: 3.3 Consensus size: 81
2523179 AAATGACACG
* * * * *
2523189 ATAAACAACATATTACGGCGTTTGTGGGACAAACGTCACTAAATTATTACTCTAATACGGTGTTT
1 ATAAACAACATATTGCGGCGTTTGT-AGAAAAACGCCGCTAAATTATTACTCTAATACGGTGTTT
* *
2523254 TTTGCACAAACGCCACT
65 ATTGAACAAACGCCACT
* * * * * *
2523271 ATAAACAACCGTTTTGTGGCGTTTGTTTGATAAACGCCGCTAAATTACTT-CTC-AATA-GCATC
1 ATAAACAA-CATATTGCGGCGTTTG-TAGAAAAACGCCGCTAAATTA-TTACTCTAATACG-GT-
*
2523333 GTTTGTTGAACAAACGCCACT
61 GTTTATTGAACAAACGCCACT
* * * ** *
2523354 ATAAACAAGACTATCGCGGCGTTTGTATAAAAACGCCGCTAAATTACCACTCTATTACGGTGTTT
1 ATAAACAACA-TATTGCGGCGTTTGTAGAAAAACGCCGCTAAATTATTACTCTAATACGGTGTTT
* **
2523419 ATTGAAAAAATACCACT
65 ATTGAACAAACGCCACT
*
2523436 ATAAACAACTCTATTGCGGCGTTTG
1 ATAAACAAC-ATATTGCGGCGTTTG
2523461 AGCTACAAAC
Statistics
Matches: 150, Mismatches: 30, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
81 1 0.01
82 72 0.48
83 73 0.49
84 4 0.03
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (81 bp):
ATAAACAACATATTGCGGCGTTTGTAGAAAAACGCCGCTAAATTATTACTCTAATACGGTGTTTA
TTGAACAAACGCCACT
Found at i:2531622 original size:55 final size:55
Alignment explanation
Indices: 2531511--2531889 Score: 555
Period size: 55 Copynumber: 6.9 Consensus size: 55
2531501 CTATATGAGA
* ** *
2531511 ATTCATCAACCCATGATGAATTCCGTGGGTA-GCACA-AATAGTGCATGTACAGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAA-AGTGCATGTACGGTG
* * *
2531565 ATTCATTAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCTTGTACAGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTG
*
2531620 ATTCATCAACTCATGATGAATTACGTGAATATGCACACAAAGTGCATGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTG
* *
2531675 ATTCATCAACTCATGATGAATTCCATGAATATGCACACAAAGTGCCTGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTG
* * * *
2531730 ATTCATCAACTCATGATGAATTCCATGAATATGCACACAAAGTTCTTGTAGGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTG
* **
2531785 ATTCATCAACTCATGATAAATTTTGTGAATATGCACACAAAGTGCATGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTG
* * *
2531840 ATTCATCAACTCATGATAAATTCCTTGAATATGTACACAAAGTGCATGTA
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTA
2531890 GTACATAGTA
Statistics
Matches: 297, Mismatches: 26, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
54 27 0.09
55 268 0.90
56 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTG
Found at i:2532330 original size:20 final size:20
Alignment explanation
Indices: 2532300--2532380 Score: 92
Period size: 20 Copynumber: 4.0 Consensus size: 20
2532290 AGGTTCGATG
2532300 TTACC-TGGTATCGATACCC
1 TTACCATGGTATCGATACCC
*
2532319 TTACCATGGTATCGATACAC
1 TTACCATGGTATCGATACCC
*
2532339 TTACCATGGTATCAATACTACC
1 TTACCATGGTATCGATAC--CC
* * *
2532361 CTACTATGGTACCGATACCC
1 TTACCATGGTATCGATACCC
2532381 CCTACCATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
19 5 0.10
20 32 0.62
22 15 0.29
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.30
Consensus pattern (20 bp):
TTACCATGGTATCGATACCC
Found at i:2532371 original size:22 final size:22
Alignment explanation
Indices: 2532314--2532388 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 22
2532304 CTGGTATCGA
*
2532314 TACCCTTACCATGGTATCGATAC
1 TACCC-TACCATGGTATCAATAC
*
2532337 -A-CTTACCATGGTATCAATAC
1 TACCCTACCATGGTATCAATAC
* * *
2532357 TACCCTACTATGGTACCGATAC
1 TACCCTACCATGGTATCAATAC
*
2532379 -CCCCTACCAT
1 TACCCTACCAT
2532389 TATCTATACC
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 16 0.38
21 10 0.24
22 16 0.38
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (22 bp):
TACCCTACCATGGTATCAATAC
Found at i:2541817 original size:55 final size:55
Alignment explanation
Indices: 2541708--2541970 Score: 366
Period size: 55 Copynumber: 4.8 Consensus size: 55
2541698 CTATACGAGA
* * *** * * *
2541708 ATTCATCAACCCATGATGAATTCTGT-AGGCTGCACACATAGTGCATGCATGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTG
*
2541762 ATTCATCAATTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTG
* *
2541817 ATTCATCAACTCATGATGAATTCCATGAATATGCACACAAAGTGCCTGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTG
* * * *
2541872 ATTCATCGACTCATTATGAATTCCGAGAATATGCACACAAAGTGCATATACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTG
* *
2541927 ATTCATCAACTCATGATGAATTCCGTGAATATACACATAAAGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTG
2541971 ACTGTAGTAC
Statistics
Matches: 185, Mismatches: 23, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
54 23 0.12
55 162 0.88
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCATGTACGGTG
Found at i:2551632 original size:17 final size:18
Alignment explanation
Indices: 2551605--2551652 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
2551595 ATAAATAAAC
2551605 ATCGAATGCACTG-AGTGT
1 ATCG-ATGCACTGTAGTGT
*
2551623 ATCGATGCACAGGTAGTGT
1 ATCGATGCAC-TGTAGTGT
2551642 ATCGATGCACT
1 ATCGATGCACT
2551653 CCCTTAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 15 0.58
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (18 bp):
ATCGATGCACTGTAGTGT
Found at i:2551694 original size:64 final size:63
Alignment explanation
Indices: 2551557--2551717 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 63
2551547 CTGGGCAAGC
* *
2551557 TGCATCGATGCATAAGTAGTGTACCGATGCA-CACTTAAATAAATAAACATCGAATGCACTGAG
1 TGCATCGATGCATAGGTAGTGTATCGATGCACCACTTAAAT-AATAAACATCGAATGCACTGAG
* * * * *
2551620 TGTATCGATGCACAGGTAGTGTATCGATGCACTCCCTTAAGAT-GTAAACATCGAATGCA-TATA
1 TGCATCGATGCATAGGTAGTGTATCGATGCAC-CACTTAA-ATAATAAACATCGAATGCACT-GA
2551683 G
63 G
*
2551684 TGCATCGATGCGTAGGCT-GTGTATCGATGCACCA
1 TGCATCGATGCATAGG-TAGTGTATCGATGCACCA
2551718 GAGAGAGGAT
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
63 29 0.35
64 44 0.54
65 7 0.09
66 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAGGTAGTGTATCGATGCACCACTTAAATAATAAACATCGAATGCACTGAG
Found at i:2552136 original size:58 final size:59
Alignment explanation
Indices: 2552054--2552402 Score: 211
Period size: 58 Copynumber: 6.0 Consensus size: 59
2552044 ATGACACTTT
* *
2552054 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATGGAGCACTAA
* *** * *
2552113 GTGTGCT-AAATGATAAGGAAATCATATTGAAAATA-AGGATTTCCAGATAGG-GCATTTTA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATA-GATTTCCAGAT-GGAGCA-CTAA
* * * * * **
2552172 -TGTTCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATAAAGCACTAA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATGGAGCACTAA
** *** * *
2552230 G-GATGCT-AAATGATAAGGAAATCATTTTGAAAATATGGATTTCCAGACAGG-GCA-TATTA
1 GTG-TGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGA-TGGAGCACTA--A
* ** * * **
2552289 -TGTGCTAAAATGGTAACAAAATCATACT-AATGGTATAGATTTCGA-ATAGGA-CACTTT
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGT-GTATAGATTTCCAGAT-GGAGCACTAA
* * * * *
2552346 CTGTGCTAAAATGAAAAGGGAAGCATACTAAGTGTAT-GATTTTCCAGATGGAGCACT
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGA-TTTCCAGATGGAGCACT
2552403 GATAGTGCTA
Statistics
Matches: 216, Mismatches: 52, Indels: 44
0.69 0.17 0.14
Matches are distributed among these distances:
57 5 0.02
58 125 0.58
59 86 0.40
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.29
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCAGATGGAGCACTAA
Found at i:2552270 original size:117 final size:117
Alignment explanation
Indices: 2552055--2552331 Score: 378
Period size: 117 Copynumber: 2.4 Consensus size: 117
2552045 TGACACTTTG
* * ** *
2552055 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCAGATAAAGCACTAAGTGTGCT
* *
2552120 AAATGATAAGGAAATCATATTGAAAATAAGGATTTCCAGATAGGGCATTTTA
66 AAATGATAAGGAAATCATATTGAAAATAAGGATTTCCAGACAGGGCATATTA
* * * *
2552172 TGTTCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATAAAGCACTAAG-GATGC
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCAGATAAAGCACTAAGTG-TGC
* *
2552236 TAAATGATAAGGAAATCATTTTGAAAATATGGATTTCCAGACAGGGCATATTA
65 TAAATGATAAGGAAATCATATTGAAAATAAGGATTTCCAGACAGGGCATATTA
** *
2552289 TGTGCTAAAATGGTAACAAAATCATACT-AATGGTATAGATTTC
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGT-GTATAGATTTC
2552332 GAATAGGACA
Statistics
Matches: 138, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
116 3 0.02
117 135 0.98
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.30
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCCAGATAAAGCACTAAGTGTGCT
AAATGATAAGGAAATCATATTGAAAATAAGGATTTCCAGACAGGGCATATTA
Found at i:2552358 original size:117 final size:116
Alignment explanation
Indices: 2552055--2552364 Score: 349
Period size: 117 Copynumber: 2.6 Consensus size: 116
2552045 TGACACTTTG
* * * *
2552055 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCAATA-GGAGCACTTAATGTGCT
* *
2552120 AAATGATAAGGAAATCATATTGAAAATAAGGATTTCCAGATAGGGCATTTTA
65 AAATGATAAGGAAATCATATTGAAAATAAGGATTTCCAGACAGGGCATATTA
* * * * * *
2552172 TGTTCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATA-AAGCAC-TAAGGATG
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTT-CA-ATAGGAGCACTTAATG-TG
* *
2552235 CTAAATGATAAGGAAATCATTTTGAAAATATGGATTTCCAGACAGGGCATATTA
63 CTAAATGATAAGGAAATCATATTGAAAATAAGGATTTCCAGACAGGGCATATTA
** * **
2552289 TGTGCTAAAATGGTAACAAAATCATACT-AATGGTATAGATTTCGAATAGGA-CACTTTCTGTGC
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGT-GTATAGATTTC-AATAGGAGCACTTAATGTGC
*
2552352 TAAAATGAAAAGG
64 T-AAATGATAAGG
2552365 GAAGCATACT
Statistics
Matches: 159, Mismatches: 26, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
116 15 0.09
117 140 0.88
118 1 0.01
119 3 0.02
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (116 bp):
TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATAGATTTCAATAGGAGCACTTAATGTGCTA
AATGATAAGGAAATCATATTGAAAATAAGGATTTCCAGACAGGGCATATTA
Found at i:2552898 original size:21 final size:21
Alignment explanation
Indices: 2552874--2552913 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2552864 ACTGTACGTT
*
2552874 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTACATCGATGC
2552895 ACTGTAGCAGTACATCGAT
1 ACTGTAGCAGTACATCGAT
2552914 AAACTGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTACATCGATGC
Found at i:2552919 original size:21 final size:21
Alignment explanation
Indices: 2552874--2552920 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2552864 ACTGTACGTT
* **
2552874 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTACATCGATAA
2552895 ACTGTAGCAGTACATCGATAA
1 ACTGTAGCAGTACATCGATAA
2552916 ACTGT
1 ACTGT
2552921 TCAATGTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (21 bp):
ACTGTAGCAGTACATCGATAA
Found at i:2552940 original size:21 final size:21
Alignment explanation
Indices: 2552916--2552958 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2552906 ACATCGATAA
*
2552916 ACTGTTCAATGTACACTATTC
1 ACTGTTCAATATACACTATTC
* *
2552937 ACTGTTCACTATTCACTATTC
1 ACTGTTCAATATACACTATTC
2552958 A
1 A
2552959 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.40
Consensus pattern (21 bp):
ACTGTTCAATATACACTATTC
Found at i:2552944 original size:7 final size:7
Alignment explanation
Indices: 2552929--2552958 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2552919 GTTCAATGTA
2552929 CACTATT
1 CACTATT
*
2552936 CACTGTT
1 CACTATT
2552943 CACTATT
1 CACTATT
2552950 CACTATT
1 CACTATT
2552957 CA
1 CA
2552959 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.30, G:0.03, T:0.40
Consensus pattern (7 bp):
CACTATT
Found at i:2561867 original size:41 final size:41
Alignment explanation
Indices: 2561776--2561867 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
2561766 GCCTTGATTA
* * * *
2561776 AATTGAATTAGATTGTGAGTTAATACATGTTACCATGATCT
1 AATTGAATTGGATTGTGAATAAATACATGTTACCATGATCG
* * **
2561817 AATTGAATTGGTTTGTGAATAAATGCATGTTTTCATGATCG
1 AATTGAATTGGATTGTGAATAAATACATGTTACCATGATCG
2561858 AATTGAATTG
1 AATTGAATTG
2561868 AATTATGGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.40
Consensus pattern (41 bp):
AATTGAATTGGATTGTGAATAAATACATGTTACCATGATCG
Found at i:2563048 original size:2 final size:2
Alignment explanation
Indices: 2563043--2563089 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2563033 TTTATTGTAA
2563043 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
2563085 AT AT A
1 AT AT A
2563090 AGATGGGTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2569532 original size:7 final size:6
Alignment explanation
Indices: 2569516--2569545 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
2569506 TCAGTTAATT
2569516 TTTTTA TTTTTA TTTTTA CTTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA -TTTTTA TTTTT
2569546 GTTCAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:2571200 original size:22 final size:21
Alignment explanation
Indices: 2571174--2571216 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2571164 AAAATGTTGA
2571174 AAAAAAATAGCAGTTCGAAAAAG
1 AAAAAAA-A-CAGTTCGAAAAAG
*
2571197 AAAAAAAACTGTTCGAAAAA
1 AAAAAAAACAGTTCGAAAAA
2571217 AAAGACATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.63, C:0.09, G:0.14, T:0.14
Consensus pattern (21 bp):
AAAAAAAACAGTTCGAAAAAG
Found at i:2575681 original size:21 final size:21
Alignment explanation
Indices: 2575646--2575724 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
2575636 AATGAAAACC
*
2575646 AAATCTAATTAAATTGAAATTT
1 AAAT-TAATTGAATTGAAATTT
* *
2575668 AAATTAATGGAATT-AAA-TA
1 AAATTAATTGAATTGAAATTT
*
2575687 AAGATCTAATTGAATTGAATTTTT
1 AA-AT-TAATTGAATTGAA-ATTT
2575711 AAATTAATTGAATT
1 AAATTAATTGAATT
2575725 ATATGGATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
19 3 0.07
20 5 0.11
21 17 0.37
22 16 0.35
23 2 0.04
24 3 0.07
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.41
Consensus pattern (21 bp):
AAATTAATTGAATTGAAATTT
Found at i:2575739 original size:41 final size:41
Alignment explanation
Indices: 2575652--2575744 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 41
2575642 AACCAAATCT
* *
2575652 AATTAAATTGAAATTTAAATTAATGGAATTAAATAAAGATCT
1 AATTGAATTGAAATTTAAATTAATGGAATT-AATAAAGATCA
* * **
2575694 AATTGAATTGAATTTTTAAATTAATTGAATT-ATATGGATCA
1 AATTGAATTGAA-ATTTAAATTAATGGAATTAATAAAGATCA
2575735 AATTGAATTG
1 AATTGAATTG
2575745 CCTAAGTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 17 0.39
42 11 0.25
43 16 0.36
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (41 bp):
AATTGAATTGAAATTTAAATTAATGGAATTAATAAAGATCA
Found at i:2581652 original size:21 final size:21
Alignment explanation
Indices: 2581626--2581689 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
2581616 GAAGTGGAAA
2581626 TAGATG-AGTTACCTTGGTAAG
1 TAGATGAAG-TACCTTGGTAAG
* *
2581647 TAGATGAAGTATCTTGGTAAA
1 TAGATGAAGTACCTTGGTAAG
*
2581668 TAGGTGAAGTACCTTGGTAAG
1 TAGATGAAGTACCTTGGTAAG
2581689 T
1 T
2581690 GTCTTTGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (21 bp):
TAGATGAAGTACCTTGGTAAG
Found at i:2595999 original size:18 final size:18
Alignment explanation
Indices: 2595976--2596015 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2595966 ATCAATCTTC
* *
2595976 TTCACAATCAAAGAAAGT
1 TTCACAACCAAAAAAAGT
2595994 TTCACAACCAAAAAAAGT
1 TTCACAACCAAAAAAAGT
2596012 TTCA
1 TTCA
2596016 ATGATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (18 bp):
TTCACAACCAAAAAAAGT
Found at i:2611433 original size:35 final size:35
Alignment explanation
Indices: 2611382--2611452 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
2611372 GGCGTGGTTG
2611382 GAGCGTAATTTCGAACCGAAAAAATACCAAAAATT
1 GAGCGTAATTTCGAACCGAAAAAATACCAAAAATT
*
2611417 GAGCGTAATTTTGAACCGAAAAAATACCAAAAATT
1 GAGCGTAATTTCGAACCGAAAAAATACCAAAAATT
2611452 G
1 G
2611453 TAAAATATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.21
Consensus pattern (35 bp):
GAGCGTAATTTCGAACCGAAAAAATACCAAAAATT
Found at i:2614572 original size:18 final size:18
Alignment explanation
Indices: 2614546--2614615 Score: 95
Period size: 18 Copynumber: 3.9 Consensus size: 18
2614536 CTCTTCGTAT
* *
2614546 ACCTAGTCCAGCGCACCC
1 ACCTAGTCCAGCTCATCC
* *
2614564 ACTTAGTCCAACTCATCC
1 ACCTAGTCCAGCTCATCC
*
2614582 ACCTAGTCTAGCTCATCC
1 ACCTAGTCCAGCTCATCC
2614600 ACCTAGTCCAGCTCAT
1 ACCTAGTCCAGCTCAT
2614616 AATGACTCCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.24, C:0.41, G:0.11, T:0.23
Consensus pattern (18 bp):
ACCTAGTCCAGCTCATCC
Found at i:2616893 original size:90 final size:89
Alignment explanation
Indices: 2616740--2616914 Score: 278
Period size: 90 Copynumber: 2.0 Consensus size: 89
2616730 CCTAACACAC
* * *
2616740 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
2616805 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
* * *
2616830 CCTTTTATATCCAAGTTATCTTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
2616895 ATTTAATTAATTGAAATTAA
66 ATTTAATTAATTGAAATTAA
2616915 ATATTAGGGA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 7 0.09
90 71 0.91
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAATAAT
Found at i:2623328 original size:90 final size:90
Alignment explanation
Indices: 2623175--2623352 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
2623165 CCTAACACAC
* * *
2623175 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
2623240 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
2623265 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
2623330 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
2623353 TTCGGGATTA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:2637485 original size:55 final size:55
Alignment explanation
Indices: 2637425--2637538 Score: 201
Period size: 55 Copynumber: 2.1 Consensus size: 55
2637415 GAGATCCGAA
2637425 GAATGAAGAAATTTCAACCTGATTGAAGAACGATTCATGAAGAAGGACATCAAAT
1 GAATGAAGAAATTTCAACCTGATTGAAGAACGATTCATGAAGAAGGACATCAAAT
* * *
2637480 GAATGAAGAAATTTGAACTTGATTGAAGAACGATTCATGAAGAAGGACATCCAAT
1 GAATGAAGAAATTTCAACCTGATTGAAGAACGATTCATGAAGAAGGACATCAAAT
2637535 GAAT
1 GAAT
2637539 AGAGTTTGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (55 bp):
GAATGAAGAAATTTCAACCTGATTGAAGAACGATTCATGAAGAAGGACATCAAAT
Found at i:2640113 original size:29 final size:27
Alignment explanation
Indices: 2640047--2640109 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
2640037 AGAGAAAAGG
2640047 AAAAGAA-AAGATGAAAAAAAAAGAAAA
1 AAAAGAAGAA-ATGAAAAAAAAAGAAAA
**
2640074 AAAATTAGAAATGAAAAATAAAA-ATAAA
1 AAAAGAAGAAATGAAAAA-AAAAGA-AAA
2640102 AAAAGAAG
1 AAAAGAAG
2640110 GAAAGAGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.10
Consensus pattern (27 bp):
AAAAGAAGAAATGAAAAAAAAAGAAAA
Found at i:2640290 original size:20 final size:20
Alignment explanation
Indices: 2640265--2640317 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
2640255 TAGCCTTTCA
*
2640265 GTATCGATACCCCTACCCTG
1 GTATCGATACCCCTACCATG
* *
2640285 GTATCGATACTACTCTACTATG
1 GTATCGATAC--CCCTACCATG
2640307 GTATCGATACC
1 GTATCGATACC
2640318 TCCTTCTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 11 0.39
22 17 0.61
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCCTACCATG
Found at i:2640463 original size:94 final size:95
Alignment explanation
Indices: 2640265--2640483 Score: 277
Period size: 94 Copynumber: 2.3 Consensus size: 95
2640255 TAGCCTTTCA
* * * *
2640265 GTATCGATACCC-CTACCCTGGTATCGATACTACTCTACTATGGTATCGATACCTCCTTCTAGTA
1 GTATCGATACCCTC-ACCATGGTATCGATACTACTATACTATGGTACCGATACCTCCCTCTAGTA
*
2640329 TCAATACCAAAATTAGATTCGATGTAGTCTG
65 TCAATACCAAAATTAGATTCGATGTAGTCAG
* *
2640360 GTATCGATACCCTCACTATGGTATCGATAGC-ACTATTCTATGGTACCGATACC-CCCT-TAGGT
1 GTATCGATACCCTCACCATGGTATCGATA-CTACTATACTATGGTACCGATACCTCCCTCTA-GT
* *
2640422 ATCGATACCAAAATTAGATTCGATGT-TTACAG
64 ATCAATACCAAAATTAGATTCGATGTAGT-CAG
*
2640454 GTATCGATACCCTTACCATGGTATCGATAC
1 GTATCGATACCCTCACCATGGTATCGATAC
2640484 CAATATTGCT
Statistics
Matches: 109, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
93 4 0.04
94 59 0.54
95 44 0.40
96 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (95 bp):
GTATCGATACCCTCACCATGGTATCGATACTACTATACTATGGTACCGATACCTCCCTCTAGTAT
CAATACCAAAATTAGATTCGATGTAGTCAG
Found at i:2641940 original size:25 final size:25
Alignment explanation
Indices: 2641912--2641961 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2641902 AAGATTAAGA
*
2641912 TTAAGAGATTTAATAAAATGAGGTT
1 TTAAGAGATTTAATAAAATAAGGTT
* * *
2641937 TTAAGTGATTTGATGAAATAAGGTT
1 TTAAGAGATTTAATAAAATAAGGTT
2641962 GGTTATTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (25 bp):
TTAAGAGATTTAATAAAATAAGGTT
Found at i:2642361 original size:20 final size:20
Alignment explanation
Indices: 2642316--2642369 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2642306 TGATTTAAAG
* *
2642316 AAGTATCGATACTGAGGTGG
1 AAGTATCGATACCGAGGTGA
*
2642336 AGGTATCGATACCGAGAG-GA
1 AAGTATCGATACCGAG-GTGA
2642356 AAGTATCGATACCG
1 AAGTATCGATACCG
2642370 TAATCAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.20
Consensus pattern (20 bp):
AAGTATCGATACCGAGGTGA
Found at i:2642864 original size:54 final size:54
Alignment explanation
Indices: 2642777--2643046 Score: 364
Period size: 54 Copynumber: 5.0 Consensus size: 54
2642767 AATGTATATG
* * *
2642777 TTGT-AATTACCGTATCGACACTATGTGTACAACCCACGTAATTCACAATAAGT
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGT
* *
2642830 TTATGAATTACCGTATCCACACTATGTGTGCAACCCACGTAATTCATAATGAGT
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGT
** * *
2642884 TTGTGAATTATTGTATCGGCACTATGTGTGCAA-CCACATAATTCATAATGAGT
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGT
* * **
2642937 TTGTTAATTACCGTTTCGACACTATCAGTGCAACCCACGTAATTCATAATGAGT
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGT
* * * *
2642991 TTGTGAATTACCGTATCGACACTATGTGTGCAAAACCATGGAATTTATAATGAGT
1 TTGTGAATTACCGTATCGACACTATGTGTGC-AACCCACGTAATTCATAATGAGT
2643046 T
1 T
2643047 GAAATATTAA
Statistics
Matches: 187, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
53 48 0.26
54 119 0.64
55 20 0.11
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (54 bp):
TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGT
Found at i:2642968 original size:107 final size:108
Alignment explanation
Indices: 2642777--2643023 Score: 363
Period size: 107 Copynumber: 2.3 Consensus size: 108
2642767 AATGTATATG
* *
2642777 TTGT-AATTACCGTATCGACACTATGTGTACAACCCACGTAATTCACAATAAGTTTATGAATTAC
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACATAATTCACAATAAGTTTATGAATTAC
**
2642841 CGTATCCACACTATGTGTGCAACCCACGTAATTCATAATGAGT
66 CGTATCCACACTATCAGTGCAACCCACGTAATTCATAATGAGT
** * * * * *
2642884 TTGTGAATTATTGTATCGGCACTATGTGTGCAA-CCACATAATTCATAATGAGTTTGTTAATTAC
1 TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACATAATTCACAATAAGTTTATGAATTAC
* *
2642948 CGTTTCGACACTATCAGTGCAACCCACGTAATTCATAATGAGT
66 CGTATCCACACTATCAGTGCAACCCACGTAATTCATAATGAGT
2642991 TTGTGAATTACCGTATCGACACTATGTGTGCAA
1 TTGTGAATTACCGTATCGACACTATGTGTGCAA
2643024 AACCATGGAA
Statistics
Matches: 123, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
107 99 0.80
108 24 0.20
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (108 bp):
TTGTGAATTACCGTATCGACACTATGTGTGCAACCCACATAATTCACAATAAGTTTATGAATTAC
CGTATCCACACTATCAGTGCAACCCACGTAATTCATAATGAGT
Found at i:2645331 original size:104 final size:104
Alignment explanation
Indices: 2645151--2645358 Score: 416
Period size: 104 Copynumber: 2.0 Consensus size: 104
2645141 GAAATTTCCT
2645151 TGTGACGAATTTAAAATTATTTTAGGCATGGATTGGTTGTCTCCACATCATGGATAGGTTGATTG
1 TGTGACGAATTTAAAATTATTTTAGGCATGGATTGGTTGTCTCCACATCATGGATAGGTTGATTG
2645216 TCACAAGAAACGATTATTTTTTAAGGATGCGAAAGGTTC
66 TCACAAGAAACGATTATTTTTTAAGGATGCGAAAGGTTC
2645255 TGTGACGAATTTAAAATTATTTTAGGCATGGATTGGTTGTCTCCACATCATGGATAGGTTGATTG
1 TGTGACGAATTTAAAATTATTTTAGGCATGGATTGGTTGTCTCCACATCATGGATAGGTTGATTG
2645320 TCACAAGAAACGATTATTTTTTAAGGATGCGAAAGGTTC
66 TCACAAGAAACGATTATTTTTTAAGGATGCGAAAGGTTC
2645359 AGAAGTCATA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.36
Consensus pattern (104 bp):
TGTGACGAATTTAAAATTATTTTAGGCATGGATTGGTTGTCTCCACATCATGGATAGGTTGATTG
TCACAAGAAACGATTATTTTTTAAGGATGCGAAAGGTTC
Found at i:2648601 original size:15 final size:15
Alignment explanation
Indices: 2648581--2648637 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
2648571 AACCGGGTAT
2648581 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
2648596 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
* *
2648613 CGGGAACCTGATTAC
1 CGGGTACCCGATTAC
*
2648628 CAGGTACCCG
1 CGGGTACCCG
2648638 TAACATCCGG
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
15 18 0.58
16 4 0.13
17 9 0.29
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:2648634 original size:32 final size:32
Alignment explanation
Indices: 2648581--2648648 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
2648571 AACCGGGTAT
* *
2648581 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1 CGGGAACCCGATTACCAGGTACCCGCAAAATC
* * *
2648613 CGGGAACCTGATTACCAGGTACCCGTAACATC
1 CGGGAACCCGATTACCAGGTACCCGCAAAATC
2648645 CGGG
1 CGGG
2648649 TCGGGACACG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.16
Consensus pattern (32 bp):
CGGGAACCCGATTACCAGGTACCCGCAAAATC
Found at i:2649226 original size:2 final size:2
Alignment explanation
Indices: 2649221--2649261 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2649211 TGTTTTTTGC
2649221 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2649262 ATTACTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2659803 original size:6 final size:6
Alignment explanation
Indices: 2659792--2659852 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
2659782 TAAATTCTCT
*
2659792 TGTATA TGTATA TGTATA TGTATA TGTATA TGTTTA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
* *
2659840 TATGTA TGTATA T
1 TGTATA TGTATA T
2659853 ATATCCTCTC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTATA
Found at i:2663335 original size:1 final size:1
Alignment explanation
Indices: 2663329--2663408 Score: 52
Period size: 1 Copynumber: 80.0 Consensus size: 1
2663319 TTGCCTGAAG
* * * * * * * * * *
2663329 AAAAAAAAAAGAAAAAAAGAGAAGAAAAAGAAAAAGAAAAAAGAAAAGAAAAAAGAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2663394 AATAAAAGAAAAAAA
1 AAAAAAAAAAAAAAA
2663409 TAAATAAAAT
Statistics
Matches: 55, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (1 bp):
A
Found at i:2663356 original size:19 final size:17
Alignment explanation
Indices: 2663332--2663408 Score: 88
Period size: 18 Copynumber: 4.4 Consensus size: 17
2663322 CCTGAAGAAA
2663332 AAAAAAAGAAAAAAAGAG
1 AAAAAAAGAAAAAAA-AG
2663350 AAGAAAAAGAAAAAGAAA-
1 AA-AAAAAGAAAAA-AAAG
2663368 AAAGAAAAG--AAAAAAG
1 AAA-AAAAGAAAAAAAAG
2663384 AAAAAAAGAAAATAAAAG
1 AAAAAAAGAAAA-AAAAG
2663402 AAAAAAA
1 AAAAAAA
2663409 TAAATAAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.15
16 6 0.12
17 3 0.06
18 21 0.40
19 12 0.23
20 2 0.04
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.01
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAAG
Done.