Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009595.1 Hibiscus syriacus cultivar Beakdansim tig00116974_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: 1046665
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:603004 original size:18 final size:18
Alignment explanation
Indices: 602983--603019 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
602973 GTAATTGGAG
602983 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
603001 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
603019 T
1 T
603020 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:603026 original size:24 final size:24
Alignment explanation
Indices: 602975--603027 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
602965 TTTCATATGT
* * *
602975 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
602999 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
603023 AATTT
1 AATTT
603028 CGACTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:603639 original size:19 final size:20
Alignment explanation
Indices: 603614--603670 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
603604 GCAACGCTTA
603614 TTTCGCGTTGTGAATTTGAC
1 TTTCGCGTTGTGAATTTGAC
*
603634 -TTCGCGTTGTGAATTTAAC
1 TTTCGCGTTGTGAATTTGAC
*
603653 TTTCGCATTGTGAATTTG
1 TTTCGCGTTGTGAATTTG
603671 TACCTTCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.46
Consensus pattern (20 bp):
TTTCGCGTTGTGAATTTGAC
Found at i:603860 original size:61 final size:64
Alignment explanation
Indices: 603729--603869 Score: 168
Period size: 66 Copynumber: 2.2 Consensus size: 64
603719 TTTTAGAAAC
*
603729 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAA-CAAAAAAATAATTATTATTTAC-AATCAAATT
603794 A
64 A
*
603795 AACAAATCAACTTTTACAAATCAATTAATCAA-AAAATAAAT-ATTATT-TCTT-C-ATC-AATT
1 AACAAATCAACTTTTACAAATCAATTAAACAACAAAA-AAATAATTATTAT-TTACAATCAAATT
*
603854 GT
64 -A
603856 AACAAATCAACTTT
1 AACAAATCAACTTT
603870 CAATGTAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
60 4 0.06
61 17 0.25
63 2 0.03
64 11 0.16
65 4 0.06
66 31 0.45
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.32
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAACAAAAAAATAATTATTATTTACAATCAAATTA
Found at i:605296 original size:42 final size:42
Alignment explanation
Indices: 605250--605332 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
605240 GATGACAAGA
* * * *
605250 GCCTCTTGAACGGTGGGAGGGGCTTCTTCG-ATGATGATAGGG
1 GCCTCTTGAACGATAGGAGGCGCCTCTT-GAATGATGATAGGG
605292 GCCTCTTGAACGATAGGAGGCGCCTCTTGAATGATGATAGG
1 GCCTCTTGAACGATAGGAGGCGCCTCTTGAATGATGATAGG
605333 TGCATCGGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.20, C:0.18, G:0.36, T:0.25
Consensus pattern (42 bp):
GCCTCTTGAACGATAGGAGGCGCCTCTTGAATGATGATAGGG
Found at i:605504 original size:4 final size:4
Alignment explanation
Indices: 605472--605517 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
605462 GGGCCGCTGA
* * * *
605472 AAAT AAAT TAAT ATAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
605518 TGCCGAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:607546 original size:19 final size:20
Alignment explanation
Indices: 607522--607564 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
607512 AGATCGCAAC
*
607522 GCGATTTT-AGTTTCGTGTT
1 GCGATTTTCAGTTTCGCGTT
*
607541 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
607561 GCGA
1 GCGA
607565 ATTTGGTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:607862 original size:22 final size:22
Alignment explanation
Indices: 607834--607884 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
607824 GATGGAGATA
607834 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATGGG
*
607856 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAAATGGG
607878 GACGGAT
1 GACGGAT
607885 GTCGCCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATGGG
Found at i:608039 original size:20 final size:20
Alignment explanation
Indices: 608014--608084 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
608004 GTAAAAACAT
608014 TTGACTTTCGCGTTGCGAAA
1 TTGACTTTCGCGTTGCGAAA
*
608034 TTGAC-TTCTGTGTTGCG--A
1 TTGACTTTC-GCGTTGCGAAA
* * *
608052 TTTACAAATTCGCGTTGCGAAT
1 TTGAC--TTTCGCGTTGCGAAA
608074 TTGACTTTCGC
1 TTGACTTTCGC
608085 AACGCGAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
18 5 0.13
19 3 0.08
20 24 0.62
21 3 0.08
22 4 0.10
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGAAA
Found at i:608136 original size:20 final size:21
Alignment explanation
Indices: 608081--608137 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
608071 AATTTGACTT
**
608081 TCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGAATTTAAAAAA
608102 TCGCAACGCGAATTTAAAAAA
1 TCGCAACGCGAATTTAAAAAA
*
608123 TCGCAATGCG-ATTTA
1 TCGCAACGCGAATTTA
608138 CATACATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (21 bp):
TCGCAACGCGAATTTAAAAAA
Found at i:616840 original size:38 final size:34
Alignment explanation
Indices: 616814--616881 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
616804 TATAAGGTGA
*
616814 ATGAATGGTACATCTTGGTTTGTATATTATTTAC
1 ATGAATGGTACATCTTGGTTTGTATATTATTGAC
*
616848 ATGAATGGTACATCTTGGTTTGTATATTTTTGAC
1 ATGAATGGTACATCTTGGTTTGTATATTATTGAC
616882 GTTTACTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.47
Consensus pattern (34 bp):
ATGAATGGTACATCTTGGTTTGTATATTATTGAC
Found at i:622349 original size:2 final size:2
Alignment explanation
Indices: 622342--622368 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
622332 TGAGGGAGTT
622342 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
622369 GGAGGATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:626949 original size:44 final size:45
Alignment explanation
Indices: 626879--626980 Score: 145
Period size: 44 Copynumber: 2.2 Consensus size: 45
626869 ATTTATTTTC
626879 GTTTTTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAG
1 GTTTTTTTT-GAATAAATGCATGCGAACTAGATATCATGCGGTTAG
*
626925 GTTTATTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAG
1 GTTT-TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAG
626969 GATTTCTTTTTG
1 G-TTT-TTTTTG
626981 TGGATAACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
44 28 0.54
45 11 0.21
46 8 0.15
47 5 0.10
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (45 bp):
GTTTTTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAG
Found at i:629477 original size:21 final size:23
Alignment explanation
Indices: 629442--629487 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
629432 TTTGCATCGC
629442 ATTTTATTCATTCA-TAATCATAT
1 ATTTTATTCATTCATTAATCA-AT
629465 ATTTTA-T-ATTCATTAATCAAT
1 ATTTTATTCATTCATTAATCAAT
629486 AT
1 AT
629488 CAGCGATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.41
22 7 0.32
23 6 0.27
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTTATTCATTCATTAATCAAT
Found at i:636657 original size:16 final size:15
Alignment explanation
Indices: 636638--636748 Score: 55
Period size: 16 Copynumber: 6.7 Consensus size: 15
636628 AAGAAGAAAT
636638 AAAAGAGAAAAGAAGA
1 AAAAGAGAAAA-AAGA
636654 AAAA-ATGAGAAAAAGA
1 AAAAGA-GA-AAAAAGA
636670 AAAATGATGGAAAAAACG-
1 AAAA-GA--GAAAAAA-GA
*
636688 AAAAGAAAAAATAAGAGA
1 AAAAG-AGAAA-AA-AGA
*
636706 AAAAGAGAAAAATGGAA
1 AAAAGAGAAAAA-AG-A
**
636723 AAAAGAGAAAAGTGAA
1 AAAAGAGAAAAAAG-A
636739 AAAAGAGAAA
1 AAAAGAGAAA
636749 TAAAAGGAGG
Statistics
Matches: 77, Mismatches: 7, Indels: 22
0.73 0.07 0.21
Matches are distributed among these distances:
15 1 0.01
16 33 0.43
17 23 0.30
18 17 0.22
19 3 0.04
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.05
Consensus pattern (15 bp):
AAAAGAGAAAAAAGA
Found at i:636673 original size:25 final size:25
Alignment explanation
Indices: 636638--636744 Score: 71
Period size: 25 Copynumber: 4.2 Consensus size: 25
636628 AAGAAGAAAT
636638 AAAAGAGAAAAGAAGA-AAAAATGAGA
1 AAAAGA-AAAAGAAGAGAAAAATGA-A
* *
636664 AAAAGAAAAATGATG-GAAAAAACGAA
1 AAAAGAAAAA-GAAGAG-AAAAATGAA
* *
636690 AAGA-AAAAATAAGAGAAAAA-GAGA
1 AAAAGAAAAAGAAGAGAAAAATGA-A
* *
636714 AAAATGGAAAA-AAGAGAAAAGTGAA
1 AAAA-GAAAAAGAAGAGAAAAATGAA
636739 AAAAGA
1 AAAAGA
636745 GAAATAAAAG
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
23 2 0.03
24 12 0.19
25 24 0.38
26 19 0.30
27 7 0.11
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.06
Consensus pattern (25 bp):
AAAAGAAAAAGAAGAGAAAAATGAA
Found at i:636708 original size:10 final size:9
Alignment explanation
Indices: 636688--636748 Score: 58
Period size: 9 Copynumber: 7.1 Consensus size: 9
636678 GGAAAAAACG
*
636688 AAAAGAAAA
1 AAAAGAGAA
636697 AATAAGAG-A
1 AA-AAGAGAA
636706 AAAAGAGAA
1 AAAAGAGAA
*
636715 AAATG-GAA
1 AAAAGAGAA
636723 AAAAGAG--
1 AAAAGAGAA
*
636730 AAAAGTGAA
1 AAAAGAGAA
636739 AAAAGAGAA
1 AAAAGAGAA
636748 A
1 A
636749 TAAAAGGAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
7 6 0.14
8 12 0.29
9 20 0.48
10 4 0.10
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (9 bp):
AAAAGAGAA
Found at i:636725 original size:17 final size:16
Alignment explanation
Indices: 636638--636748 Score: 77
Period size: 17 Copynumber: 6.6 Consensus size: 16
636628 AAGAAGAAAT
*
636638 AAAAGAGAAAAGAAGAA
1 AAAAGAGAAAA-ATGAA
636655 AAAATGAGAAAAA-GAA
1 AAAA-GAGAAAAATGAA
* *
636671 AAATGATGGAAAAA--ACG
1 AAAAGA--GAAAAATGA-A
636688 AAAAGA-AAAAATAAGAGA
1 AAAAGAGAAAAAT--GA-A
636706 AAAAGAGAAAAATGGAA
1 AAAAGAGAAAAAT-GAA
*
636723 AAAAGAGAAAAGTGAA
1 AAAAGAGAAAAATGAA
636739 AAAAGAGAAA
1 AAAAGAGAAA
636749 TAAAAGGAGG
Statistics
Matches: 78, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
14 5 0.06
15 2 0.03
16 20 0.26
17 29 0.37
18 16 0.21
19 6 0.08
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.05
Consensus pattern (16 bp):
AAAAGAGAAAAATGAA
Found at i:636733 original size:50 final size:49
Alignment explanation
Indices: 636638--636733 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 49
636628 AAGAAGAAAT
* *
636638 AAAAGAGAAAAGAAGAAAAAATGAGAAAAAGAAAAATGATGGAAAAAACG
1 AAAAGAAAAAAGAAGAAAAAATGAGAAAAAGAAAAAAGA-GGAAAAAACG
*
636688 AAAAGAAAAAATAAGAGAAAAA-GAGAAAAATGGAAAAAAGA-GAAAA
1 AAAAGAAAAAAGAAGA-AAAAATGAGAAAAA--GAAAAAAGAGGAAAA
636734 GTGAAAAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
50 27 0.68
51 5 0.12
52 8 0.20
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (49 bp):
AAAAGAAAAAAGAAGAAAAAATGAGAAAAAGAAAAAAGAGGAAAAAACG
Found at i:637943 original size:51 final size:51
Alignment explanation
Indices: 637882--638449 Score: 735
Period size: 51 Copynumber: 10.9 Consensus size: 51
637872 AAATTTGTTT
*
637882 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
637933 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
637984 GTTGAAGATTGAGTCCTATA--CTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
638033 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
638084 GTTGAGGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
638135 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* *
638186 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* * ** *
638237 GTTAAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCTGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* * * * ** *
638288 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTC
* * * * ** *
638344 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTT
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTC
* * * *
638400 ATTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 GTTGAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
638450 CATTTTGAAG
Statistics
Matches: 483, Mismatches: 23, Indels: 17
0.92 0.04 0.03
Matches are distributed among these distances:
49 48 0.10
51 299 0.62
52 1 0.00
53 2 0.00
54 2 0.00
55 34 0.07
56 97 0.20
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
Found at i:640091 original size:15 final size:15
Alignment explanation
Indices: 640071--640099 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
640061 AGTTATTAAT
640071 TATATTGTTTTATTA
1 TATATTGTTTTATTA
640086 TATATTGTTTTATT
1 TATATTGTTTTATT
640100 TTAATGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
TATATTGTTTTATTA
Found at i:644072 original size:16 final size:17
Alignment explanation
Indices: 644042--644083 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
644032 CGAAATAACC
644042 TAAAT-TATTAAATATG
1 TAAATATATTAAATATG
*
644058 -AAATATATTATATATG
1 TAAATATATTAAATATG
644074 TTAAATATAT
1 -TAAATATAT
644084 ATTTTAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 10 0.45
18 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
TAAATATATTAAATATG
Found at i:654113 original size:22 final size:22
Alignment explanation
Indices: 654069--654113 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
654059 ATGTTTCATA
**
654069 TTCTGTTTAGTTGGGAGACATG
1 TTCTGTTTAGTTCAGAGACATG
* *
654091 TTCTGTTTAGTTCATAGATATG
1 TTCTGTTTAGTTCAGAGACATG
654113 T
1 T
654114 CACATTAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.09, G:0.24, T:0.47
Consensus pattern (22 bp):
TTCTGTTTAGTTCAGAGACATG
Found at i:657872 original size:53 final size:53
Alignment explanation
Indices: 657792--657894 Score: 206
Period size: 53 Copynumber: 1.9 Consensus size: 53
657782 TAGTTCACCA
657792 TTCTTTTATGCTAATTATTTATTTGATTAGTTTCTTGATCTGCAGGGATCCCG
1 TTCTTTTATGCTAATTATTTATTTGATTAGTTTCTTGATCTGCAGGGATCCCG
657845 TTCTTTTATGCTAATTATTTATTTGATTAGTTTCTTGATCTGCAGGGATC
1 TTCTTTTATGCTAATTATTTATTTGATTAGTTTCTTGATCTGCAGGGATC
657895 TAGTAGCGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (53 bp):
TTCTTTTATGCTAATTATTTATTTGATTAGTTTCTTGATCTGCAGGGATCCCG
Found at i:658503 original size:23 final size:24
Alignment explanation
Indices: 658460--658505 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
658450 AATAATTAAT
*
658460 TATAATTTAATCTTACTTTTTGTA
1 TATAATTTAATCATACTTTTTGTA
658484 TATAA-TTAATCAT-CTATTTTGT
1 TATAATTTAATCATACT-TTTTGT
658506 GTAACTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 13 0.65
24 5 0.25
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (24 bp):
TATAATTTAATCATACTTTTTGTA
Found at i:658503 original size:24 final size:25
Alignment explanation
Indices: 658460--658508 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
658450 AATAATTAAT
658460 TATAATTTAATCTTACTTTT-TGTA
1 TATAATTTAATCTTACTTTTGTGTA
658484 TATAA-TTAATCATCTA-TTTTGTGTA
1 TATAATTTAATC-T-TACTTTTGTGTA
658509 ACTTTAAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
23 6 0.27
24 10 0.45
25 6 0.27
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.55
Consensus pattern (25 bp):
TATAATTTAATCTTACTTTTGTGTA
Found at i:659130 original size:2 final size:2
Alignment explanation
Indices: 659125--659161 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
659115 ATATATATAT
*
659125 AG AG AG AG AG AG AG AG AG AT AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
659162 ATCACCATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (2 bp):
AG
Found at i:660284 original size:120 final size:121
Alignment explanation
Indices: 660070--660302 Score: 378
Period size: 120 Copynumber: 1.9 Consensus size: 121
660060 TTCAACAGCT
* * *
660070 TTAATTTATTTTAATGCAACACCATGGGAGAACTGTTTCAGTTGAAAATGTCTGAATCCGCCGAC
1 TTAATTTATTTTAATGCAACACCATGGGAGAACTGTTTCAGTTGAAAATATCTGAATCCACCAAC
660135 AGCAGCCATGATATTAGTTTACAAAAAAGAAAAGTCCAACAAATGGATACAGCTTC
66 AGCAGCCATGATATTAGTTTACAAAAAAGAAAAGTCCAACAAATGGATACAGCTTC
* **
660191 TTAATTTATTTTAATGCAATACCATGGGAGAACTGTTTCAG-TGAAAATATCTGAATCCATTAAC
1 TTAATTTATTTTAATGCAACACCATGGGAGAACTGTTTCAGTTGAAAATATCTGAATCCACCAAC
* * *
660255 AGCAGCCATGATATTGGTTTACTAAAAAGAAAAGTCCAACAATTGGAT
66 AGCAGCCATGATATTAGTTTACAAAAAAGAAAAGTCCAACAAATGGAT
660303 GAATTTCCAT
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
120 63 0.61
121 40 0.39
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (121 bp):
TTAATTTATTTTAATGCAACACCATGGGAGAACTGTTTCAGTTGAAAATATCTGAATCCACCAAC
AGCAGCCATGATATTAGTTTACAAAAAAGAAAAGTCCAACAAATGGATACAGCTTC
Found at i:660376 original size:3 final size:3
Alignment explanation
Indices: 660368--660393 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
660358 CCTAAACAAA
660368 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
660394 AATGTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:666452 original size:19 final size:22
Alignment explanation
Indices: 666406--666452 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 22
666396 AAAATATCAT
666406 AATTATAACATTTATTTAATAA
1 AATTATAACATTTATTTAATAA
*
666428 AA-TATATCA-TT-TTTAA-AA
1 AATTATAACATTTATTTAATAA
666446 AATTATA
1 AATTATA
666453 CAACTCGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 9 0.39
20 2 0.09
21 6 0.26
22 2 0.09
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTATAACATTTATTTAATAA
Found at i:668440 original size:17 final size:18
Alignment explanation
Indices: 668420--668454 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
668410 AACGGAATGT
668420 AAGATTATCA-GGAATAA
1 AAGATTATCAGGGAATAA
668437 AAGATTATCAGGGAATAA
1 AAGATTATCAGGGAATAA
668455 GATTACTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (18 bp):
AAGATTATCAGGGAATAA
Found at i:668458 original size:16 final size:15
Alignment explanation
Indices: 668419--668459 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 15
668409 TAACGGAATG
668419 TAAGATTATCAGGAA
1 TAAGATTATCAGGAA
668434 TAAAAGATTATCAGGGAA
1 T--AAGATTATCA-GGAA
668452 TAAGATTA
1 TAAGATTA
668460 CTAGAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 7 0.30
17 10 0.43
18 5 0.22
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.27
Consensus pattern (15 bp):
TAAGATTATCAGGAA
Found at i:669311 original size:39 final size:39
Alignment explanation
Indices: 669251--669341 Score: 155
Period size: 39 Copynumber: 2.3 Consensus size: 39
669241 ATGACTAGAC
* * *
669251 GCTGCGTCAGCTTATTGTAAGATACGTTATCCACGTATA
1 GCTGAGTCAGCTTATTATAAGATACGTCATCCACGTATA
669290 GCTGAGTCAGCTTATTATAAGATACGTCATCCACGTATA
1 GCTGAGTCAGCTTATTATAAGATACGTCATCCACGTATA
669329 GCTGAGTCAGCTT
1 GCTGAGTCAGCTT
669342 CCTACTCCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (39 bp):
GCTGAGTCAGCTTATTATAAGATACGTCATCCACGTATA
Found at i:673677 original size:23 final size:23
Alignment explanation
Indices: 673647--673705 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
673637 CTCATATAAA
673647 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
673670 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
673693 TTCACCGTAGTGC
1 TGCACCGAAGTGC
673706 TATATAAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:675683 original size:22 final size:22
Alignment explanation
Indices: 675642--675708 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
675632 CTCGTATAAA
*
675642 TGCACCAAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
675665 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
675687 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
675709 GATGTCCATA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
22 31 0.74
23 11 0.26
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:677427 original size:21 final size:21
Alignment explanation
Indices: 677403--677447 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
677393 TCTTGTTCGT
* *
677403 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
677424 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
677445 TTG
1 TTG
677448 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:680623 original size:22 final size:22
Alignment explanation
Indices: 680582--680648 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
680572 CTCGTATAAA
680582 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
680605 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
680627 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
680649 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:682373 original size:21 final size:21
Alignment explanation
Indices: 682349--682393 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
682339 TCTTGTTCGT
* *
682349 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
682370 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
682391 TTG
1 TTG
682394 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:686507 original size:16 final size:16
Alignment explanation
Indices: 686486--686517 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
686476 ATGCACCGAA
686486 GTGCCACATAGAATTG
1 GTGCCACATAGAATTG
*
686502 GTGCCACGTAGAATTG
1 GTGCCACATAGAATTG
686518 CACCGTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (16 bp):
GTGCCACATAGAATTG
Found at i:688704 original size:31 final size:31
Alignment explanation
Indices: 688666--688735 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
688656 GACTTAAATA
*
688666 GACTAATTCCACAACATAAATATAGTACAGG
1 GACTAATTCCACAACATAAATATAGTAAAGG
688697 GACTAATTCCACAACATAAATATAGTAAAGG
1 GACTAATTCCACAACATAAATATAGTAAAGG
688728 GACTAATT
1 GACTAATT
688736 ATAGAAATCG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (31 bp):
GACTAATTCCACAACATAAATATAGTAAAGG
Found at i:703313 original size:23 final size:22
Alignment explanation
Indices: 703282--703324 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 22
703272 AATTTTGAGA
703282 ATTTATTAATTTTTTAAAAAAAAT
1 ATTTATTAA--TTTTAAAAAAAAT
703306 ATTT-TTAATTTTAAAAAAA
1 ATTTATTAATTTTAAAAAAA
703325 CCAAACAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
23 4 0.21
24 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTATTAATTTTAAAAAAAAT
Found at i:705298 original size:36 final size:36
Alignment explanation
Indices: 705257--705328 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
705247 TAATTTAAAC
705257 CATCTATTTTCTCTCATCCAACGATCTTAAATTTGT
1 CATCTATTTTCTCTCATCCAACGATCTTAAATTTGT
705293 CATCTATTTTCTCTCATCCAACGATCTTAAATTTGT
1 CATCTATTTTCTCTCATCCAACGATCTTAAATTTGT
705329 GTAAAACTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (36 bp):
CATCTATTTTCTCTCATCCAACGATCTTAAATTTGT
Found at i:708288 original size:50 final size:51
Alignment explanation
Indices: 708226--708335 Score: 204
Period size: 50 Copynumber: 2.2 Consensus size: 51
708216 ACATATAATG
708226 ATAATAATAGTAGCAAAAGAGAAAAACATATTTATATACGTTAATAGT-AA
1 ATAATAATAGTAGCAAAAGAGAAAAACATATTTATATACGTTAATAGTAAA
*
708276 ATAATAATAGTAGCAAAAGAGAAAAATATATTTATATACGTTAATAGTAAA
1 ATAATAATAGTAGCAAAAGAGAAAAACATATTTATATACGTTAATAGTAAA
708327 ATAATAATA
1 ATAATAATA
708336 AATATAATAG
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
50 47 0.81
51 11 0.19
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29
Consensus pattern (51 bp):
ATAATAATAGTAGCAAAAGAGAAAAACATATTTATATACGTTAATAGTAAA
Found at i:708359 original size:2 final size:2
Alignment explanation
Indices: 708347--708419 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
708337 ATATAATAGT
*
708347 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
708389 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
708420 GATAACTTTA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:708972 original size:36 final size:37
Alignment explanation
Indices: 708900--709000 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 37
708890 GTGCTTGTGG
* * * *
708900 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
708937 ATCCTATTTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
708973 ATCCTATTTTT-GAGAGTTTGAATCCTAG
1 ATCCTATTTTTAG-GAGTTTGAATCCTAG
709001 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.02
36 30 0.53
37 26 0.46
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:709773 original size:106 final size:107
Alignment explanation
Indices: 709468--710091 Score: 547
Period size: 109 Copynumber: 5.9 Consensus size: 107
709458 GTTCCGAGTC
* *** * **
709468 CAATATCCTCCG-CTGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGACAGTCAG
1 CAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCT-GAAATTGGAAAATGTTTGTTGACAACCAG
* * * *
709532 CCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-C-
64 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * * * **
709574 TAATATCCTTCG-CTGTGAAGTTGAAATTGACTCTG-AA--CG-AAAT-CTTGTTGACAATTAGC
1 CAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCTGAAATTGGAAAATGTTTGTTGACAACCAGC
* *
709633 CGTCACTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGT-C-
65 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * * *
709674 CAATATCCTTCATTGTGAAATTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACAACCAGC
1 CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAA-TTGGAAAATGTTTGTTGACAACCAGC
* *
709739 TGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCA
65 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * ** * **
709783 CGATATCCTCCATCGTGGAGTTGAAA-TCGCGGATGAAACT-GAAAAGTTGTTCATTGACAACCA
1 CAATATCCTCCGTCGTGAAGTTGAAATTGGC-TCTGAAATTGGAAAA--TGTTTGTTGACAACCA
* * *
709846 GCCGTCCCTTCGTTGTGAAGTTGGACTTGTGTTTTCTCGGGTAGCA
63 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * * ** * *
709892 CGATATCCTCCGTCGTGGAGTTGAAATCGGTTCTGGAATTGGGAAGTTGTTCGTTGACAACCAAC
1 CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATT-GGAAAATGTTTGTTGACAACCAGC
*
709957 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCA
65 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCA
* * * * * *
710001 CGATATCCTCCGTCGTGGAGTTGAAATCGGCTCCGAAATTGGGAAAT-TATTGTTGGCAACCAGC
1 CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATGT-TTGTTGACAACCAGC
710065 CGTCCCTTCGTTGTGAAGTTGAACTTG
65 CGTCCCTTCGTTGTGAAGTTGAACTTG
710092 ACTCTAGCTA
Statistics
Matches: 432, Mismatches: 69, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
100 77 0.18
101 5 0.01
102 1 0.00
104 1 0.00
105 5 0.01
106 81 0.19
107 5 0.01
108 48 0.11
109 205 0.47
110 1 0.00
111 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (107 bp):
CAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATGTTTGTTGACAACCAGCC
GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
Found at i:710811 original size:36 final size:36
Alignment explanation
Indices: 710699--711175 Score: 264
Period size: 36 Copynumber: 13.9 Consensus size: 36
710689 AAAGATTTTG
* *
710699 TGTTTCAAGAGAAACTGTCTCATGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* ** **
710735 TGTTTCGAGGGAAACAATCTCAA-AG-G----TTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
710765 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * * *
710802 TGTTTCAAGAGAAATTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * *
710838 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
*
710866 ATGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAA-TT
*
710904 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
710940 CATTTCAAGGGAAA-TGTTTCCA-A-TG-----TTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
710968 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* *
711006 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
711042 CATTTCAA-GGAAAATGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* * *
711070 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
*
711108 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
711144 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
711176 TGGTGAGCAC
Statistics
Matches: 325, Mismatches: 73, Indels: 86
0.67 0.15 0.18
Matches are distributed among these distances:
28 8 0.02
29 31 0.10
30 18 0.06
31 19 0.06
32 4 0.01
33 4 0.01
34 4 0.01
35 16 0.05
36 122 0.38
37 90 0.28
38 9 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:710822 original size:67 final size:67
Alignment explanation
Indices: 710687--710824 Score: 213
Period size: 67 Copynumber: 2.1 Consensus size: 67
710677 GGAGATAAAT
* * *
710687 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCATGAGAGACAAAATTTGTTTCGAGGGAAACAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAA
710752 TC
66 TC
* * **
710754 TCAAAGGTTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAATTA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAA
710819 TC
66 TC
710821 TCAA
1 TCAA
710825 GAGAGACGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAA
TC
Found at i:710918 original size:37 final size:37
Alignment explanation
Indices: 710867--711175 Score: 232
Period size: 37 Copynumber: 8.9 Consensus size: 37
710857 TCAATGTTTA
*
710867 TGTTTC-AGGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGG-GAAACTGTCTCAAGAGAGACAAAATTT
*
710904 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
710940 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
710968 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
711006 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * * *
711042 CATTTCAA-GGAAAATGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
711070 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
711108 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
711144 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
711176 TGGTGAGCAC
Statistics
Matches: 208, Mismatches: 38, Indels: 52
0.70 0.13 0.17
Matches are distributed among these distances:
27 3 0.01
28 3 0.01
29 20 0.10
30 12 0.06
32 1 0.00
33 1 0.00
34 1 0.00
35 11 0.05
36 59 0.28
37 86 0.41
38 11 0.05
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:710944 original size:102 final size:102
Alignment explanation
Indices: 710699--711157 Score: 668
Period size: 102 Copynumber: 4.5 Consensus size: 102
710689 AAAGATTTTG
* * * ** * *** * *
710699 TGTTTCAAGAGAAACTGTCTCATGAGAGACAAAATTTGTTTCGAGGGAAACAATCTCAAAGGTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTC-AATG-TT
* *
710764 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TT
64 TATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
* * *
710802 TGTTTCAAGAGAAATTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
710867 TGTTTCAGGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
*
710904 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
710969 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
* *
711006 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGAAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
711071 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
* * **
711108 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
711158 CTGTCTCAAG
Statistics
Matches: 326, Mismatches: 29, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
101 36 0.11
102 244 0.75
103 46 0.14
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
Found at i:712704 original size:24 final size:24
Alignment explanation
Indices: 712677--712726 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
712667 CCCTTTTTTA
712677 TTTTTG-TTCTTGTT-TTTTTTCCT
1 TTTTTGCTTCTT-TTCTTTTTTCCT
712700 TTTTTGCTTCTTTTCTTTTTTCCT
1 TTTTTGCTTCTTTTCTTTTTTCCT
712724 TTT
1 TTT
712727 GCCCTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (24 bp):
TTTTTGCTTCTTTTCTTTTTTCCT
Found at i:716012 original size:2 final size:2
Alignment explanation
Indices: 716002--716066 Score: 107
Period size: 2 Copynumber: 33.5 Consensus size: 2
715992 AAACATTATG
716002 AT AT A- 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
*
716043 AT AT AT AT AT AT AT A- AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
716067 ATAAAAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:716104 original size:21 final size:20
Alignment explanation
Indices: 716055--716105 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
716045 ATATATATAT
716055 ATAATAAATATAATAAAAAAA
1 ATAAT-AATATAATAAAAAAA
* *
716076 ATAATAATTTAATAAAGTAAA
1 ATAATAATATAATAAA-AAAA
716097 ATAATAATA
1 ATAATAATA
716106 ATGTAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
ATAATAATATAATAAAAAAA
Found at i:716106 original size:16 final size:16
Alignment explanation
Indices: 716085--716122 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
716075 AATAATAATT
716085 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
716101 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
716117 T-ATAAA
1 TAATAAA
716123 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:716300 original size:49 final size:51
Alignment explanation
Indices: 716244--716352 Score: 186
Period size: 50 Copynumber: 2.2 Consensus size: 51
716234 ACATATAATG
*
716244 ATAATAATAGTAGTAAAAGAG-AAAACATATTTATATACGTTAATAGT-AA
1 ATAATAATAGTAGCAAAAGAGAAAAACATATTTATATACGTTAATAGTAAA
*
716293 ATAATAATAGTAGCAAAAGAGAAAAATATATTTATATACGTTAATAGTAAA
1 ATAATAATAGTAGCAAAAGAGAAAAACATATTTATATACGTTAATAGTAAA
716344 ATAATAATA
1 ATAATAATA
716353 AATATAATAG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
49 20 0.36
50 25 0.45
51 11 0.20
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (51 bp):
ATAATAATAGTAGCAAAAGAGAAAAACATATTTATATACGTTAATAGTAAA
Found at i:716371 original size:2 final size:2
Alignment explanation
Indices: 716364--716434 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
716354 ATATAATAGT
716364 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
716406 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
716435 GATAACTTTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:716988 original size:36 final size:37
Alignment explanation
Indices: 716916--717016 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 37
716906 GTGCTTGTGG
* * * *
716916 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
716953 ATCCTATTTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
716989 ATCCTATTTTT-GAGAGTTTGAATCCTAG
1 ATCCTATTTTTAG-GAGTTTGAATCCTAG
717017 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.02
36 30 0.53
37 26 0.46
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:720384 original size:12 final size:12
Alignment explanation
Indices: 720367--720413 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
720357 AAAAATACAG
*
720367 CAACAGCATCAA
1 CAACAGCAGCAA
*
720379 CAACAGCAGCAG
1 CAACAGCAGCAA
*
720391 CAGCAGCAGCAA
1 CAACAGCAGCAA
*
720403 CAGCAGCAGCA
1 CAACAGCAGCA
720414 GCAGGAGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.43, C:0.34, G:0.21, T:0.02
Consensus pattern (12 bp):
CAACAGCAGCAA
Found at i:720388 original size:3 final size:3
Alignment explanation
Indices: 720382--720422 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
720372 GCATCAACAA
* *
720382 CAG CAG CAG CAG CAG CAG CAA CAG CAG CAG CAG CAG GAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
720423 ACATTACAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.37, C:0.32, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:720417 original size:21 final size:21
Alignment explanation
Indices: 720364--720425 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
720354 AACAAAAATA
* * *
720364 CAGCAACAGCATCAACAACAG
1 CAGCAGCAGCAGCAGCAACAG
720385 CAGCAGCAGCAGCAGCAACAG
1 CAGCAGCAGCAGCAGCAACAG
*
720406 CAGCAGCAGCAGGAGCAACA
1 CAGCAGCAGCAGCAGCAACA
720426 TTACAGACTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.42, C:0.32, G:0.24, T:0.02
Consensus pattern (21 bp):
CAGCAGCAGCAGCAGCAACAG
Found at i:723354 original size:13 final size:13
Alignment explanation
Indices: 723329--723362 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
723319 GAATCTAGTA
723329 TAAAACATTTTAAT
1 TAAAAC-TTTTAAT
723343 TAAAACTTTTAAT
1 TAAAACTTTTAAT
723356 TAAAACT
1 TAAAACT
723363 AATATAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAAACTTTTAAT
Found at i:732742 original size:19 final size:19
Alignment explanation
Indices: 732699--732749 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
732689 ATTAATTGAA
732699 CATCGAATGCA-T-TCCACG
1 CATCG-ATGCACTCTCCACG
* *
732717 CACCGATGCACTCTCCATG
1 CATCGATGCACTCTCCACG
732736 CATCGATGCACTCT
1 CATCGATGCACTCT
732750 GAATTTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 5 0.18
18 5 0.18
19 18 0.64
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.24
Consensus pattern (19 bp):
CATCGATGCACTCTCCACG
Found at i:732766 original size:65 final size:63
Alignment explanation
Indices: 732648--732856 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 63
732638 TATTCAAAGG
** *
732648 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAATTAATT-GAACATCGAATGCAT
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATTTTTTCAAACATCGAATGCAT
*
732711 TC
62 TT
*
732713 CACGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATTTTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATTTTTTC-AAACATCGAATGCATTT
* * *** * ** *
732778 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTCTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAAT-TTTTTCAAACATCGAATGCATTT
*
732842 CATGCATCGATGCAC
1 CATGCACCGATGCAC
732857 ACTTGGTGCA
Statistics
Matches: 123, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
63 8 0.07
64 51 0.41
65 62 0.50
66 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATTTTTTCAAACATCGAATGCATTT
Found at i:736769 original size:31 final size:31
Alignment explanation
Indices: 736699--736822 Score: 117
Period size: 31 Copynumber: 4.0 Consensus size: 31
736689 GTCGAGGGTT
* * *
736699 TACCCATGTTCTACGGAACATATGGACA-TAA
1 TACCTATGTTCTTCGGGACATATGGACAGT-A
*
736730 TTACCTATG-TCTTTCGGGACATATGGATAGTA
1 -TACCTATGTTC-TTCGGGACATATGGACAGTA
** * *
736762 TACCTATGTTCTAAGGAATATATGGACAGTA
1 TACCTATGTTCTTCGGGACATATGGACAGTA
* *
736793 TACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTTCGGGACATATGGACAGT
736823 TGCCAAGGAT
Statistics
Matches: 74, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
31 49 0.66
32 24 0.32
33 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTTCGGGACATATGGACAGTA
Found at i:736817 original size:62 final size:63
Alignment explanation
Indices: 736699--736818 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 63
736689 GTCGAGGGTT
* *
736699 TACCCATGTTCTACGGAACATATGGACATAATTACCTATGTCTTTCGGGACATATGGATAGTA
1 TACCCATGTTCTAAGGAACATATGGACATAATTACCTAGGTCTTTCGGGACATATGGATAGTA
* * *
736762 TACCTATGTTCTAAGGAATATATGGACAGT-A-TACCTAGGT-TCTTCGGGACCTATGGA
1 TACCCATGTTCTAAGGAACATATGGACA-TAATTACCTAGGTCT-TTCGGGACATATGGA
736819 CAGTTGCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
61 1 0.02
62 22 0.44
63 26 0.52
64 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (63 bp):
TACCCATGTTCTAAGGAACATATGGACATAATTACCTAGGTCTTTCGGGACATATGGATAGTA
Found at i:741625 original size:3 final size:3
Alignment explanation
Indices: 741619--741663 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
741609 TTAGTATTAT
*
741619 TAA TAA TAA T-A TAT TAA T-A TAA TAA TAA TAA TAA TCAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
741662 TA
1 TA
741664 TATACTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
2 6 0.17
3 27 0.75
4 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:741643 original size:19 final size:21
Alignment explanation
Indices: 741619--741663 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
741609 TTAGTATTAT
*
741619 TAATAATAATATATTAATATAA
1 TAATAATAATA-ATCAATATAA
741641 TAATAATAATAATCAATATAA
1 TAATAATAATAATCAATATAA
741662 TA
1 TA
741664 TATACTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATAATAATAATCAATATAA
Found at i:741960 original size:51 final size:53
Alignment explanation
Indices: 741847--742089 Score: 161
Period size: 55 Copynumber: 4.5 Consensus size: 53
741837 CCAGCGGGTT
** * * ** * *
741847 CGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAGAAATCTTTTGA-AAACGGGTT
1 CGCTCCCTATTTATTCAGAGAGTATAGAACT-TA-AAATC-TTCAACAAACGTGTC
* * * *
741902 CGCTCCCTCTTTTTTCAGGGAGTATAGAAC-T-AGATCTTCAACAAACGTGTC
1 CGCTCCCTATTTATTCAGAGAGTATAGAACTTAAAATCTTCAACAAACGTGTC
* * *
741953 CGCTCCCTATTCATTCAGAGAGTATAGGACTTGAACAAATCTTCAACAAATGTGTC
1 CGCTCCCTATTTATTCAGAGAGTATAGAACTT--A-AAATCTTCAACAAACGTGTC
* * * * **
742009 TGCTCCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATTTTCAACATTCGTGTC
1 CGCTCCCTATTTATTCAGAGAGTATAGA-ACT-TAA-AATCTTCAACAAACGTGTC
* * *
742064 TGCTCTCTATTTCTTCAGAGAGTATA
1 CGCTCCCTATTTATTCAGAGAGTATA
742090 AGACTCGAAC
Statistics
Matches: 153, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
50 3 0.02
51 36 0.24
52 1 0.01
54 1 0.01
55 68 0.44
56 44 0.29
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (53 bp):
CGCTCCCTATTTATTCAGAGAGTATAGAACTTAAAATCTTCAACAAACGTGTC
Found at i:742014 original size:56 final size:56
Alignment explanation
Indices: 741935--742101 Score: 232
Period size: 55 Copynumber: 3.0 Consensus size: 56
741925 ATAGAACTAG
* * * *
741935 ATCTTCAACAAACGTGTCCGCTCCCTA-TTCATTCAGAGAGTATAGGACTTGAACAA
1 ATCTTCAACAAATGTGTCTGCTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAA
741991 ATCTTCAACAAATGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC-A
1 ATCTTCAACAAATGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* * *
742046 ATTTTCAAC-ATTCGTGTCTGCTCTCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 ATCTTCAACAAAT-GTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
742102 TTTTCAATAA
Statistics
Matches: 101, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
54 2 0.02
55 49 0.49
56 47 0.47
57 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (56 bp):
ATCTTCAACAAATGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
Found at i:742164 original size:111 final size:109
Alignment explanation
Indices: 741898--742269 Score: 265
Period size: 107 Copynumber: 3.4 Consensus size: 109
741888 TTTGAAAACG
* *
741898 GGTTCGCTCCCTCTTTTTTCAGGGAGTATAGAAC-T--AGA-TCTTCAACAAACGTGTCCGCTCC
1 GGTTCGCTCCCTCTTCTTT-AGGGAGTATAGAACTTGAACATTCTTCAACAAACGTGTCCGCTCC
* *
741959 CTATTCATTCAGAGAGTATAGGACTTGAACAAATCTTCAACAAAT
65 CTATTCATTCAGAGAGTATAAGACTCGAACAAATCTTCAACAAAT
* * * * ** *
742004 -GTGTCTGCTCCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATT-TTCAACATTCGTGTCTG
1 GGT-TC-GCTCCCT-CTTCTTTAGGGAGTATAGA-ACTTGAAC-ATTCTTCAACAAACGTGTCCG
* * * *
742066 CTCTCTATTTC-TTCAGAGAGTATAAGACTCGAAC-AATTTTCAATAATCT
61 CTCCCTA-TTCATTCAGAGAGTATAAGACTCGAACAAATCTTCAACAA-AT
* *
742115 GGTTCGCTCCCTCTCTCTTTAGGGAGTATAGAACTTGAACATCTCTT---CAAACGGGTTCGCTC
1 GGTTCGCTCCCTCT-TCTTTAGGGAGTATAGAACTTGAACAT-TCTTCAACAAACGTGTCCGCTC
* * * * ** *
742177 CCTCTTTCTTTCAG-GAGTATGAA-ACTCG--GATATCTTCTTCAAAC
64 CCT-ATTCATTCAGAGAGTAT-AAGACTCGAACAAATCTTCAACAAAT
* *
742221 GGTTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACA-TCTTCAA
1 GG-TTCGCTCCCTC-TTCTTTAGGGAGTATAGAACTTGAACATTCTTCAA
742270 ACGGGTTCGC
Statistics
Matches: 205, Mismatches: 36, Indels: 48
0.71 0.12 0.17
Matches are distributed among these distances:
105 6 0.03
106 5 0.02
107 60 0.29
108 31 0.15
109 10 0.05
110 39 0.19
111 48 0.23
112 6 0.03
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (109 bp):
GGTTCGCTCCCTCTTCTTTAGGGAGTATAGAACTTGAACATTCTTCAACAAACGTGTCCGCTCCC
TATTCATTCAGAGAGTATAAGACTCGAACAAATCTTCAACAAAT
Found at i:742288 original size:51 final size:51
Alignment explanation
Indices: 742115--742656 Score: 617
Period size: 51 Copynumber: 10.4 Consensus size: 51
742105 TCAATAATCT
* * *
742115 GGTTCGCTCCCTCTCTCTTTAGGGAGTATAGAACTTGAACATCTCTTCAAACG
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACA--TCTTCAAACG
* *
742168 GGTTCGCTCCCTCTTTCTTTCA-GGAGTAT-GAAACTCGGATATCTTCTTCAAACG
1 GGTTCGCTCCCTCTTTCTCT-AGGGAGTATAG-AACTC-GA-A-CATCTTCAAACG
*
742222 GTTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACG
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACG
* * **
742273 GGTTCGCTCCCTCTTTCTCTAGGGAGTATATAACTCGTACATCTTCTTCTTACG
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCG-A-A-CATCTTCAAACG
* * * *
742327 GGTTCGTTCCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTTAAACG
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACG
* *
742378 GGTTCGCTCCCTCTTTCT-TCAGGGAGAATAGAACTCGAATATCTTATTCAAACG
1 GGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACATC---TTCAAACG
*
742432 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAACG
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACG
* * * *
742483 GGTTCACTCCCTCTTTCT-TCAGGGAGAATAGAACTCGAATATCTTCTTCAAACA
1 GGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCG-A-A-CATCTTCAAACG
* *
742537 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAACA
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACG
* * * *
742588 GGTTTGCTCCCTCTTTCTTTAGGGAGTATAGAACTCAAAAATCTTCAAACG
1 GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACG
* *
742639 TG-TCTGCTCCCTATTTCT
1 GGTTC-GCTCCCTCTTTCT
742657 TCAGAGAATA
Statistics
Matches: 422, Mismatches: 46, Indels: 44
0.82 0.09 0.09
Matches are distributed among these distances:
50 3 0.01
51 199 0.47
52 6 0.01
53 37 0.09
54 172 0.41
55 4 0.01
56 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (51 bp):
GGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACG
Found at i:742308 original size:105 final size:105
Alignment explanation
Indices: 741841--742633 Score: 766
Period size: 105 Copynumber: 7.5 Consensus size: 105
741831 ATTCGACCAG
* * * *
741841 CGGGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAGAAATCTT-TTGAAAACGGGTTCGC
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGA-ATATCTTCTT-CAAACGGGTTCGC
* * * * * **
741905 TCCCTCTTT-TTTCAGGGAGTATAGAACTAGATCTTCAACAAA
64 TCCCTCTTTCTCT-AGGGAGTATGGAACTCGAACATCTTCAAA
* * * * * * * ** * *
741947 CGTGTCCGCTCCCT-ATTCATTCAGAGAGTATAGGACTTGAACAAATCTTCAACAAATGTG-TCT
1 CGGGTTCGCTCCCTCTTTC-TTCAGGGAGTATAGAACTCG-A-ATATCTTCTTCAAACGGGTTC-
* * * *
742010 GCTCCCTATTTCT-TCAGAGAGTAT-AAGACTCGAACAATTTTCAACA
62 GCTCCCTCTTTCTCT-AGGGAGTATGGA-ACTCGAAC-ATCTTCAA-A
* * * * * * *
742056 TTCGTG-TCTGCTCTCTATTTCTTCAGAGAGTATA-AGACTCGAACA-ATT-TTCAATAATCTGG
1 --CGGGTTC-GCTCCCTCTTTCTTCAGGGAGTATAGA-ACTCGAATATCTTCTTC-A-AA-CGGG
* * * *
742117 TTCGCTCCCTCTCTCTTTAGGGAGTATAGAACTTGAACATCTCTTCAAA
59 TTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACA--TCTTCAAA
* *
742166 CGGGTTCGCTCCCTCTTTCTTTCA-GGAGTAT-GAAACTCGGATATCTTCTTCAAACGGTTTCGC
1 CGGGTTCGCTCCCTCTTTC-TTCAGGGAGTATAG-AACTCGAATATCTTCTTCAAACGGGTTCGC
*
742229 TCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAA
64 TCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAA
* * * ** *
742271 CGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATATAACTCGTACATCTTCTTCTTACGGGTTCGTT
1 CGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAATATCTTCTTCAAACGGGTTCGCT
* *
742335 CCCTCTTTATCTAGGGAGTATGGAACTCGAACATCTTTAAA
65 CCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAA
* *
742376 CGGGTTCGCTCCCTCTTTCTTCAGGGAGAATAGAACTCGAATATCTTATTCAAACGGGTTCGCTC
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAATATCTTCTTCAAACGGGTTCGCTC
742441 CCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAA
66 CCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAA
* * *
742481 CGGGTTCACTCCCTCTTTCTTCAGGGAGAATAGAACTCGAATATCTTCTTCAAACAGGTTCGCTC
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAATATCTTCTTCAAACGGGTTCGCTC
742546 CCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAA
66 CCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAA
* * * * *
742586 CAGGTTTGCTCCCTCTTTCTTTAGGGAGTATAGAACTCAAAAATCTTC
1 CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAATATCTTC
742634 AAACGTGTCT
Statistics
Matches: 574, Mismatches: 82, Indels: 63
0.80 0.11 0.09
Matches are distributed among these distances:
103 2 0.00
104 1 0.00
105 334 0.58
106 34 0.06
107 78 0.14
108 36 0.06
109 16 0.03
110 33 0.06
111 37 0.06
112 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (105 bp):
CGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAATATCTTCTTCAAACGGGTTCGCTC
CCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTCAAA
Found at i:756800 original size:151 final size:155
Alignment explanation
Indices: 756579--756884 Score: 584
Period size: 151 Copynumber: 2.0 Consensus size: 155
756569 TGGAAAACAA
756579 TATGCATTTGTCTTGGTAGATGACTATTCTAGATATATTTGGGTTTCTATTCTTAAGTACTAAAT
1 TATGCATTTGTCTTGGTAGATGACTATTCTAGATATATTTGGGTTTCTATTCTTAAGTACTAAAT
756644 GAAGCATTAGAAAATTTCATCACATTTTCAAAAGTAATCCAAAACG-AAAGGGTTACTCTATCAC
66 GAAGCATTAGAAAATTTCATCACATTTTCAAAAGTAATCCAAAACGAAAAGGGTTACTCTATCAC
756708 TAGTGTTAGAAGTGATCATGGCACT
131 TAGTGTTAGAAGTGATCATGGCACT
756733 TATGCA-TTGTCTTGGTAGATGACTATTCTAGATATA-TTGGG-TTCTATTCTTAAGTACTAAAT
1 TATGCATTTGTCTTGGTAGATGACTATTCTAGATATATTTGGGTTTCTATTCTTAAGTACTAAAT
756795 GAAGCATTAGAAAATTTCATCACATTTTCAAAAGTAATCCAAAACGAAAAGGGTTACTCTATCAC
66 GAAGCATTAGAAAATTTCATCACATTTTCAAAAGTAATCCAAAACGAAAAGGGTTACTCTATCAC
756860 TAGTGTTAGAAGTGATCATGGCACT
131 TAGTGTTAGAAGTGATCATGGCACT
756885 GAATTTGAAA
Statistics
Matches: 151, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
151 67 0.44
152 48 0.32
153 30 0.20
154 6 0.04
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (155 bp):
TATGCATTTGTCTTGGTAGATGACTATTCTAGATATATTTGGGTTTCTATTCTTAAGTACTAAAT
GAAGCATTAGAAAATTTCATCACATTTTCAAAAGTAATCCAAAACGAAAAGGGTTACTCTATCAC
TAGTGTTAGAAGTGATCATGGCACT
Found at i:760212 original size:19 final size:20
Alignment explanation
Indices: 760164--760224 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 20
760154 TACCCCCTTA
*
760164 AAGGGGAACCGATTCCCACTTT
1 AAGGGGAACCGATTCCC-C-CT
760186 GAAGGGGAACCGATTCCCCCT
1 -AAGGGGAACCGATTCCCCCT
* *
760207 -AGGGGAATCGATACCCCC
1 AAGGGGAACCGATTCCCCC
760225 CTGGGGTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 16 0.46
21 1 0.03
22 1 0.03
23 17 0.49
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.16
Consensus pattern (20 bp):
AAGGGGAACCGATTCCCCCT
Found at i:760226 original size:20 final size:19
Alignment explanation
Indices: 760188--760230 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
760178 CCCACTTTGA
*
760188 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATCCCCCCT
*
760207 AGGGGAATCGATACCCCCCT
1 AGGGGAACCGAT-CCCCCCT
760227 -GGGG
1 AGGGG
760231 TTCTGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.21, C:0.33, G:0.33, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATCCCCCCT
Found at i:766000 original size:19 final size:20
Alignment explanation
Indices: 765976--766015 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
765966 AATTTAATCG
*
765976 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
765995 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
766015 A
1 A
766016 TTCACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:766300 original size:30 final size:30
Alignment explanation
Indices: 766230--766316 Score: 111
Period size: 31 Copynumber: 2.9 Consensus size: 30
766220 GCCAAGAGTC
* * *
766230 GAGGGTTACCTATGTCTTTCGAGATATATG
1 GAGGTTTACCTATGTCTTTCGGGACATATG
* *
766260 GATAGTTTACCTATGTCCTTCGGGACATATG
1 GA-GGTTTACCTATGTCTTTCGGGACATATG
*
766291 GAGGTTTACCTATGTTTTTCGGGACA
1 GAGGTTTACCTATGTCTTTCGGGACA
766317 AATTTTAAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 23 0.48
31 25 0.52
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (30 bp):
GAGGTTTACCTATGTCTTTCGGGACATATG
Found at i:769482 original size:57 final size:56
Alignment explanation
Indices: 769407--769750 Score: 478
Period size: 57 Copynumber: 6.1 Consensus size: 56
769397 CATATAGTTC
* * *
769407 CCATACGGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGCACACAAAGTG
1 CCATACGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACGAAGTG
* *
769463 CTCATACGAAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGCACATGAAGTG
1 C-CATACGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACGAAGTG
* * *
769520 CCCATAGGGAAATTCGTACACTT-GTTATGAATTTCTTAACTTTTTGCACACGAAGTG
1 -CCATACGAAAATTCATACACTTAG-TATGAATTTCTTAACTTTTTGCACACGAAGTG
769577 CCTATAC-AGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACGAAGTG
1 CC-ATACGA-AAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACGAAGTG
* * *
769634 CCCATACGGAAATTCATACAATTAGTATGAATTTTTTAACTTTTTGCACACGAAGTGG
1 -CCATACGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACGAAGT-G
* * *
769692 CCATATGAAAATTCATACACTTAGTATGAATTTCTTAAC-TTTTGCACACCAAGTA
1 CCATACGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACGAAGTG
769747 CCAT
1 CCAT
769751 TTGATAATCA
Statistics
Matches: 259, Mismatches: 20, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
55 4 0.02
56 18 0.07
57 232 0.90
58 5 0.02
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (56 bp):
CCATACGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACGAAGTG
Found at i:770138 original size:19 final size:20
Alignment explanation
Indices: 770070--770140 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 20
770060 GATTCTTTAG
* *
770070 TATCGATACTCTTACCATGA
1 TATCGATACTCATACTATGA
*
770090 TATCGATACTACCATACTATGG
1 TATCGATACT--CATACTATGA
*
770112 TA-CTGATACTC-TATTATGA
1 TATC-GATACTCATACTATGA
770131 TATCGATACT
1 TATCGATACT
770141 ATTTTTGCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 14 0.33
20 12 0.29
21 1 0.02
22 15 0.36
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (20 bp):
TATCGATACTCATACTATGA
Found at i:775854 original size:31 final size:31
Alignment explanation
Indices: 775816--775876 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
775806 GGTAACTATT
775816 TGAATAAGCT-GTTGAACTCTATCATTTTATA
1 TGAATAAG-TAGTTGAACTCTATCATTTTATA
* *
775847 TGAATAAGTATTTGAACTTTATCATTTTAT
1 TGAATAAGTAGTTGAACTCTATCATTTTAT
775877 TTAAATAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (31 bp):
TGAATAAGTAGTTGAACTCTATCATTTTATA
Found at i:779463 original size:18 final size:18
Alignment explanation
Indices: 779442--779478 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
779432 ATCCGCTTGT
779442 ACGATAAAAAACTCATTA
1 ACGATAAAAAACTCATTA
*
779460 ACGATATAAAACTCATTA
1 ACGATAAAAAACTCATTA
779478 A
1 A
779479 TTTTTTAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.16, G:0.05, T:0.24
Consensus pattern (18 bp):
ACGATAAAAAACTCATTA
Found at i:785418 original size:44 final size:44
Alignment explanation
Indices: 785330--785424 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 44
785320 GTTTCCCTTT
* * * * **
785330 ATTAAAATTTGATTGGATCTTGAACTTTTAGCGGGTATGGTATG
1 ATTAAAATTTGATTAGATCTTGAAATTTTAACGCGTATAATATG
*
785374 ATTAAAATTTGATTAGATCTTGAAATTTTAATGCGTATAATATG
1 ATTAAAATTTGATTAGATCTTGAAATTTTAACGCGTATAATATG
785418 ATTAAAA
1 ATTAAAA
785425 ATTGTAAGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (44 bp):
ATTAAAATTTGATTAGATCTTGAAATTTTAACGCGTATAATATG
Found at i:798786 original size:17 final size:17
Alignment explanation
Indices: 798757--798791 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
798747 AACTAAAGCT
798757 ATTTCTTTTAATAGGAA
1 ATTTCTTTTAATAGGAA
798774 ATTT-TTTTGAATAGGAA
1 ATTTCTTTT-AATAGGAA
798791 A
1 A
798792 CTAAAGCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (17 bp):
ATTTCTTTTAATAGGAA
Found at i:808825 original size:18 final size:18
Alignment explanation
Indices: 808787--808825 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
808777 CATGGGTAAT
*
808787 AGACTCGTTTTGGATATC
1 AGACTCGTTTTGGATAGC
808805 AGACTCGTTTTGTG-TAGC
1 AGACTCGTTTTG-GATAGC
808823 AGA
1 AGA
808826 GTTACATGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (18 bp):
AGACTCGTTTTGGATAGC
Found at i:810092 original size:15 final size:16
Alignment explanation
Indices: 810062--810092 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
810052 GTGGGAATAA
810062 AAGATTACTAGGGAAT
1 AAGATTACTAGGGAAT
810078 AAGATTACT-GGGAAT
1 AAGATTACTAGGGAAT
810093 GTTGTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
AAGATTACTAGGGAAT
Found at i:810298 original size:37 final size:37
Alignment explanation
Indices: 810225--810299 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
810215 GTTGGAAAAT
* *
810225 ATTTATATATTTTCTTTAAAAATTTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTTAAAAATCATAAA
*
810262 ATTTATATATTTTTTTTTACAAAA-TTAAAAAT-ATAAA
1 ATTTATATA-TTTTCTTTA-AAAATTTAAAAATCATAAA
810299 A
1 A
810300 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 15 0.45
38 14 0.42
39 4 0.12
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAATTTAAAAATCATAAA
Found at i:818274 original size:23 final size:23
Alignment explanation
Indices: 818244--818291 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
818234 ATCAATACAA
* *
818244 AATTTTTATATATAGGTTATCAT
1 AATTTTTATATATAGCTTAGCAT
*
818267 AATTTTTATATGTAGCTTAGCAT
1 AATTTTTATATATAGCTTAGCAT
818290 AA
1 AA
818292 ATAAAATCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (23 bp):
AATTTTTATATATAGCTTAGCAT
Found at i:826317 original size:2 final size:2
Alignment explanation
Indices: 826310--826365 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
826300 AGTTCTAGGG
826310 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
826352 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
826366 TGAGATTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:828417 original size:12 final size:12
Alignment explanation
Indices: 828400--828424 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
828390 TTTATCAACA
828400 ACCTGTAGTCAG
1 ACCTGTAGTCAG
828412 ACCTGTAGTCAG
1 ACCTGTAGTCAG
828424 A
1 A
828425 AAATACATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (12 bp):
ACCTGTAGTCAG
Found at i:834052 original size:26 final size:29
Alignment explanation
Indices: 833995--834052 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
833985 TTACCTTCAA
* *
833995 ATAGTCTTATACTTCCTTAATCAAATATT
1 ATAGTCTTATAATTCCTTAATCAAATAAT
834024 ATAGTCTTATAATT-C-T-ATCAAATAAT
1 ATAGTCTTATAATTCCTTAATCAAATAAT
834050 ATA
1 ATA
834053 ATGTAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 12 0.44
27 1 0.04
28 1 0.04
29 13 0.48
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (29 bp):
ATAGTCTTATAATTCCTTAATCAAATAAT
Found at i:836075 original size:8 final size:9
Alignment explanation
Indices: 836058--836113 Score: 54
Period size: 8 Copynumber: 6.9 Consensus size: 9
836048 ATAATAAAAA
836058 ATAT-TAAT
1 ATATATAAT
836066 ATA-ATAAT
1 ATATATAAT
836074 AT-TAATAA-
1 ATAT-ATAAT
836082 ATATAT-AT
1 ATATATAAT
836090 ATATAT-AT
1 ATATATAAT
836098 ATATAT-AT
1 ATATATAAT
836106 ATATATAA
1 ATATATAA
836114 CAATGTAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
7 1 0.02
8 35 0.83
9 6 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATATATAAT
Found at i:836076 original size:14 final size:13
Alignment explanation
Indices: 836049--836089 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
836039 GAGAAAAGAA
*
836049 TAATAAAAAATAT
1 TAATAAATAATAT
836062 TAATATAATAATAT
1 TAATA-AATAATAT
836076 TAATAAATATATAT
1 TAATAAATA-ATAT
836090 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATAAATAATAT
Found at i:836089 original size:2 final size:2
Alignment explanation
Indices: 836082--836112 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
836072 ATATTAATAA
836082 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 A
836113 ACAATGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:836727 original size:110 final size:110
Alignment explanation
Indices: 836534--837412 Score: 1370
Period size: 110 Copynumber: 8.0 Consensus size: 110
836524 AGAATCAAAT
836534 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA
1 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA
* **
836599 AAAGTTGTTTGTTGACAGTTAGTCGCCCCTTCGCTAAGAAGTTGA
66 AAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
* *
836644 GCTTGTGTTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGA
1 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA
* * * *
836709 AAAGTTATTTATTGACAGTCAGTCGCCCATTCACTGTGAAGTTGA
66 AAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
* ** * * *
836754 GCTTGTGTTGTCTCGAGTCCAATATCCTTTACTGTGAAGTTTAAATTGACTCTAAATGAAACTAA
1 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA
*
836819 AAAGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
66 AAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
* *
836864 GCTTGTGTTCTCTCGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTG-
1 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA
*
836928 --AGTTGTTTGTTGACAGTCAGTCGCCCTTTCGCTGTGAAGTTGA
66 AAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
* * *
836971 GCTTGTGTTGTCTCGAGTCTAATATCATTCGCTGTGAAATTAAAATTGACTCTGAATGAAACTGA
1 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA
* * * *
837036 AAAGTTATTTGTTGACAGTCAGCCGCCCATTCGTTGTGAAGTTGA
66 AAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
*
837081 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTTA
1 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA
* *
837146 AAAGTTGTTTGTTTACAGTCAG-CTGCCCCTTCGTTGTGAAGTTGA
66 AAAGTTGTTTGTTGACAGTCAGTC-GCCCCTTCGCTGTGAAGTTGA
*
837191 GCTTGTGTTGTCTCGAGTCCAATATCATTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGA
1 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA
* **
837256 AAAGTTGTTTGTTGACAGTCAGTCGCCCCATCGCTGTGCTGTTGA
66 AAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
* * * * *
837301 GCTTGTGTTGTCTCGAGTCCAATATCTTTCGTTATGAAGTTGAAATTGACTCTAAAAGAAACTGA
1 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA
*
837366 AAAGTTGTTTGTTGACTGTCAGTCGCCCCTTCGCTGTGAAGTTGA
66 AAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
837411 GC
1 GC
837413 AACCACCATC
Statistics
Matches: 706, Mismatches: 58, Indels: 10
0.91 0.07 0.01
Matches are distributed among these distances:
107 100 0.14
109 1 0.00
110 604 0.86
111 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (110 bp):
GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA
AAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
Found at i:837348 original size:437 final size:438
Alignment explanation
Indices: 836534--837412 Score: 1386
Period size: 437 Copynumber: 2.0 Consensus size: 438
836524 AGAATCAAAT
* *
836534 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGA
1 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAATTAAAATTGACTCTGAATGAAACTGA
* * * *
836599 AAAGTTGTTTGTTGACAGTTAGTCGCCCCTTCGCTAAGAAGTTGAGCTTGTGTTGTCTCGAGTCC
66 AAAGTTATTTGTTGACAGTCAGCCGCCCATTCGCTAAGAAGTTGAGCTTGTGTTGTCTCGAGTCC
*
836664 AATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTATTGACAGTC
131 AATATCATTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTATTGACAGTC
* *
836729 AGTCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTTACTGTGAAGT
196 AGTCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTGACTGTGAAGT
* *
836794 TTAAATTGACTCTAAATGAAACTAAAAAGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAA
261 TGAAATTGACTCTAAATGAAACTAAAAAGTTATTTGTTGACAGTCAGTCGCCCCATCGCTGTGAA
* * *
836859 GTTGAGCTTGTGTTCTCTCGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAA
326 GTTGAGCTTGTGTTCTCTCGAGTCCAATATCATTCGTTATGAAGTTGAAATTGACTCTAAAAGAA
*
836924 ACTG-AGTTGTTTGTTGACAGTCAGTCGCCCTTTCGCTGTGAAGTTGA
391 ACTGAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
*
836971 GCTTGTGTTGTCTCGAGTCTAATATCATTCGCTGTGAAATTAAAATTGACTCTGAATGAAACTGA
1 GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAATTAAAATTGACTCTGAATGAAACTGA
* **
837036 AAAGTTATTTGTTGACAGTCAGCCGCCCATTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCC
66 AAAGTTATTTGTTGACAGTCAGCCGCCCATTCGCTAAGAAGTTGAGCTTGTGTTGTCTCGAGTCC
* * * * *
837101 AATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTTAAAAGTTGTTTGTTTACAGTC
131 AATATCATTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTATTGACAGTC
* **
837166 AG-CTGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTCGA-TGTGAA
196 AGTC-GCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATT-GACTGTGAA
* * *
837229 GTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCCCCATCGCTGTG
259 GTTGAAATTGACTCTAAATGAAACTAAAAAGTTATTTGTTGACAGTCAGTCGCCCCATCGCTGTG
** * *
837294 CTGTTGAGCTTGTGTTGTCTCGAGTCCAATATCTTTCGTTATGAAGTTGAAATTGACTCTAAAAG
324 AAGTTGAGCTTGTGTTCTCTCGAGTCCAATATCATTCGTTATGAAGTTGAAATTGACTCTAAAAG
*
837359 AAACTGAAAAGTTGTTTGTTGACTGTCAGTCGCCCCTTCGCTGTGAAGTTGA
389 AAACTG--AAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
837411 GC
1 GC
837413 AACCACCATC
Statistics
Matches: 402, Mismatches: 35, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
436 1 0.00
437 357 0.89
438 1 0.00
440 43 0.11
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (438 bp):
GCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAATTAAAATTGACTCTGAATGAAACTGA
AAAGTTATTTGTTGACAGTCAGCCGCCCATTCGCTAAGAAGTTGAGCTTGTGTTGTCTCGAGTCC
AATATCATTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTATTGACAGTC
AGTCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTGACTGTGAAGT
TGAAATTGACTCTAAATGAAACTAAAAAGTTATTTGTTGACAGTCAGTCGCCCCATCGCTGTGAA
GTTGAGCTTGTGTTCTCTCGAGTCCAATATCATTCGTTATGAAGTTGAAATTGACTCTAAAAGAA
ACTGAAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGA
Found at i:841111 original size:21 final size:21
Alignment explanation
Indices: 841069--841111 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
841059 TTTTCGGGCT
* * *
841069 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
841090 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
841111 A
1 A
841112 CGAATATGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:841218 original size:66 final size:67
Alignment explanation
Indices: 841091--841240 Score: 266
Period size: 66 Copynumber: 2.3 Consensus size: 67
841081 ACCCATTCAA
*
841091 GGGGAACCGATACCCCCTCAACGAATATGGATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
841156 GG
66 GG
*
841158 GGGGAACCGATACCCCCTCAACGAATAT-GAATTCCAGAATGCTAGTGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
841222 GG
66 GG
*
841224 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
841241 ATGAGAAAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
66 52 0.65
67 28 0.35
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GG
Found at i:841229 original size:20 final size:20
Alignment explanation
Indices: 841204--841241 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
841194 GAATGCTAGT
*
841204 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
841224 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
841242 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:841261 original size:13 final size:14
Alignment explanation
Indices: 841243--841271 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
841233 ATTCCCCCAT
841243 GAGAAAAAAA-AAA
1 GAGAAAAAAAGAAA
841256 GAGAAAAAAAGAAA
1 GAGAAAAAAAGAAA
841270 GA
1 GA
841272 AAGACTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
GAGAAAAAAAGAAA
Found at i:841761 original size:23 final size:23
Alignment explanation
Indices: 841695--841753 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
841685 ATCATTATAT
*
841695 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
841717 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
841740 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
841754 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:844986 original size:136 final size:136
Alignment explanation
Indices: 844742--845014 Score: 546
Period size: 136 Copynumber: 2.0 Consensus size: 136
844732 GAGTAACGAA
844742 TGCACCTGCTGCTTTCATGGATCTTATGAACAGGATTTTTCAGCCCTACTTGGACCAGTTTGTTG
1 TGCACCTGCTGCTTTCATGGATCTTATGAACAGGATTTTTCAGCCCTACTTGGACCAGTTTGTTG
844807 TTGTCTTTATTGATGACATACTGGTGTACTCGAAATCCCATGAAGAGCATAGCACACATCTGAGG
66 TTGTCTTTATTGATGACATACTGGTGTACTCGAAATCCCATGAAGAGCATAGCACACATCTGAGG
844872 ATCGTC
131 ATCGTC
844878 TGCACCTGCTGCTTTCATGGATCTTATGAACAGGATTTTTCAGCCCTACTTGGACCAGTTTGTTG
1 TGCACCTGCTGCTTTCATGGATCTTATGAACAGGATTTTTCAGCCCTACTTGGACCAGTTTGTTG
844943 TTGTCTTTATTGATGACATACTGGTGTACTCGAAATCCCATGAAGAGCATAGCACACATCTGAGG
66 TTGTCTTTATTGATGACATACTGGTGTACTCGAAATCCCATGAAGAGCATAGCACACATCTGAGG
845008 ATCGTC
131 ATCGTC
845014 T
1 T
845015 TGCAAATTTT
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 137 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.33
Consensus pattern (136 bp):
TGCACCTGCTGCTTTCATGGATCTTATGAACAGGATTTTTCAGCCCTACTTGGACCAGTTTGTTG
TTGTCTTTATTGATGACATACTGGTGTACTCGAAATCCCATGAAGAGCATAGCACACATCTGAGG
ATCGTC
Found at i:848010 original size:21 final size:21
Alignment explanation
Indices: 847968--848010 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
847958 TTTTCGGGCT
* * *
847968 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
847989 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
848010 A
1 A
848011 CGAATATGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:848047 original size:64 final size:63
Alignment explanation
Indices: 847965--848136 Score: 195
Period size: 63 Copynumber: 2.7 Consensus size: 63
847955 GGATTTTCGG
* * * *
847965 GCTAGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCCTCAACGAATATGGATTTCAGAA
1 GCTAGGGGAATCGATACCC--CCAGAGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAA
*
848029 -CTAGAGGGAATCGATACCCCCAGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAA
1 GCTAG-GGGAATCGATACCCCCAGAGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAA
* * *
848092 TGCTAGTGGGGAATCGATACCCCCAGGGGGGGAATCGATTCCCCC
1 -GCTA--GGGGAATCGATACCCCCA-GAGGGGAACCGATACCCCC
848137 ATGAGAAAAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
62 2 0.02
63 41 0.44
64 13 0.14
65 3 0.03
66 17 0.18
67 18 0.19
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (63 bp):
GCTAGGGGAATCGATACCCCCAGAGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAA
Found at i:848059 original size:63 final size:66
Alignment explanation
Indices: 847990--848136 Score: 219
Period size: 63 Copynumber: 2.3 Consensus size: 66
847980 ACCCATTCAA
* *
847990 GGGGAACCGATACCCCCTCAACGAATATGGATTTCAGAA-CTAG-AGGGAATCGATACCCCCA-G
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAAGCTAGTAGGGAATCGATACCCCCAGG
848052 G
66 G
*
848053 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGTGGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAA-GCTAGTAGGGAATCGATACCCCCAG
848118 GG
65 GG
* *
848120 GGGGAATCGATTCCCCC
1 GGGGAACCGATACCCCC
848137 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
63 37 0.49
65 4 0.05
66 17 0.23
67 17 0.23
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAAGCTAGTAGGGAATCGATACCCCCAGG
G
Found at i:848818 original size:23 final size:23
Alignment explanation
Indices: 848751--848810 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
848741 ATCATTATAT
*
848751 GGCACTACGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
848774 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
848797 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
848811 TTTATACGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:850723 original size:25 final size:25
Alignment explanation
Indices: 850673--850720 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
850663 AAAAATAATA
850673 AAATAAAAATATAATAATAATAAAT
1 AAATAAAAATATAATAATAATAAAT
850698 AAATAAATAA-ATAAT-ATAATAAA
1 AAATAAA-AATATAATAATAATAAA
850721 ATATTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
25 12 0.55
26 2 0.09
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
AAATAAAAATATAATAATAATAAAT
Found at i:864225 original size:7 final size:7
Alignment explanation
Indices: 864213--864244 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
864203 GTTAAGGAAC
864213 AAATAAA
1 AAATAAA
864220 AAATAAA
1 AAATAAA
864227 AAATAAA
1 AAATAAA
864234 AAATAAA
1 AAATAAA
864241 AAAT
1 AAAT
864245 GATTAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:865028 original size:12 final size:12
Alignment explanation
Indices: 865007--865043 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
864997 AAATGTTAAA
*
865007 AAATTTAAAATC
1 AAATTCAAAATC
865019 AAATTCAAAATC
1 AAATTCAAAATC
*
865031 AAAATCAAAATC
1 AAATTCAAAATC
865043 A
1 A
865044 TTAATCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATTCAAAATC
Found at i:865032 original size:6 final size:6
Alignment explanation
Indices: 865013--865043 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
865003 TAAAAAATTT
*
865013 AAAATC AAATTC AAAATC AAAATC AAAATC A
1 AAAATC AAAATC AAAATC AAAATC AAAATC A
865044 TTAATCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATC
Found at i:866408 original size:24 final size:24
Alignment explanation
Indices: 866361--866408 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
866351 AAAAAAATAT
* *
866361 AATTATAATTATAATTCTATTAAA
1 AATTATAATTAAAATTCTAATAAA
*
866385 AATTATAATTAAAATTTTAATAAA
1 AATTATAATTAAAATTCTAATAAA
866409 TGGTTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AATTATAATTAAAATTCTAATAAA
Found at i:867132 original size:2 final size:2
Alignment explanation
Indices: 867120--867158 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
867110 GAGTGCAATT
* *
867120 TC TC TC CC TC TC TC TC TC TC TC TC CC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
867159 GAGAGCGATG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:867496 original size:60 final size:59
Alignment explanation
Indices: 867426--867550 Score: 133
Period size: 60 Copynumber: 2.1 Consensus size: 59
867416 GTAAAGTACA
* * * *
867426 AAAATGTCCCCCAACTATAATATATTATTTTGTTGAGCCCCTTTACTATTAAAAATTAC
1 AAAATGTCCCCCAACTATAAGACATTACTTTGTTGAGCCCCTTGACTATTAAAAATTAC
** * * * * * *
867485 AAAATGATCCCCTGACTATAGGGCATTGCTTTGTTGAGTCCCTTGACTATTAAAAGTTAT
1 AAAATG-TCCCCCAACTATAAGACATTACTTTGTTGAGCCCCTTGACTATTAAAAATTAC
867545 AAAATG
1 AAAATG
867551 GTCACCCGAC
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
59 6 0.11
60 47 0.89
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (59 bp):
AAAATGTCCCCCAACTATAAGACATTACTTTGTTGAGCCCCTTGACTATTAAAAATTAC
Found at i:868470 original size:15 final size:15
Alignment explanation
Indices: 868450--868482 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
868440 AAATACATTT
*
868450 TACTCTATATAATTA
1 TACTCTATAAAATTA
868465 TACTCTATAAAATTA
1 TACTCTATAAAATTA
868480 TAC
1 TAC
868483 GTATAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (15 bp):
TACTCTATAAAATTA
Found at i:869629 original size:10 final size:9
Alignment explanation
Indices: 869614--869760 Score: 70
Period size: 10 Copynumber: 15.6 Consensus size: 9
869604 TGGAGTGGAG
869614 ATAAAAGTAA
1 ATAAAA-TAA
869624 ATAAAATAAAA
1 ATAAAAT--AA
869635 ATAAAGATAA
1 ATAAA-ATAA
*
869645 AGAAAATAAA
1 ATAAAAT-AA
869655 ATAAAATAA
1 ATAAAATAA
* *
869664 AAAATAAAAA
1 ATAA-AATAA
869674 ATAAAGATAA
1 ATAAA-ATAA
* *
869684 AGACAATAA
1 ATAAAATAA
*
869693 AT-AAATGA
1 ATAAAATAA
869701 AT-AAATAAA
1 ATAAAAT-AA
*
869710 ATGAAGATAA
1 AT-AAAATAA
*
869720 AGAAAA-AA
1 ATAAAATAA
869728 ATTAAAA-AA
1 A-TAAAATAA
*
869737 ATAAAGAGAA
1 ATAAA-ATAA
869747 GA-AAAATAA
1 -ATAAAATAA
869756 ATAAA
1 ATAAA
869761 CAAGACAAGG
Statistics
Matches: 106, Mismatches: 17, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
8 18 0.17
9 34 0.32
10 41 0.39
11 11 0.10
12 2 0.02
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.16
Consensus pattern (9 bp):
ATAAAATAA
Found at i:869662 original size:36 final size:36
Alignment explanation
Indices: 869614--869741 Score: 133
Period size: 36 Copynumber: 3.6 Consensus size: 36
869604 TGGAGTGGAG
869614 ATAAAAGTAAAT-AAAATAAAAATAAAGATAAAGAAA
1 ATAAAA-TAAATAAAAATAAAAATAAAGATAAAGAAA
*
869650 ATAAAATAAAATAAAAAATAAAAAATAAAGATAAAGACA
1 ATAAAAT-AAAT-AAAAAT-AAAAATAAAGATAAAGAAA
*
869689 AT-AAATAAATGAATAAAT-AAAATGAAGATAAAG-AA
1 ATAAAATAAAT-AA-AAATAAAAATAAAGATAAAGAAA
*
869724 A-AAAATTAA-AAAAATAAA
1 ATAAAATAAATAAAAATAAA
869742 GAGAAGAAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
32 4 0.05
33 4 0.05
35 9 0.11
36 24 0.30
37 6 0.08
38 13 0.16
39 20 0.25
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (36 bp):
ATAAAATAAATAAAAATAAAAATAAAGATAAAGAAA
Found at i:869683 original size:39 final size:39
Alignment explanation
Indices: 869626--869734 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 39
869616 AAAAGTAAAT
869626 AAAATAAAAATAAAGATAAAGAAAATAAAATAAAAT-AA
1 AAAATAAAAATAAAGATAAAGAAAATAAAATAAAATGAA
*
869664 AAAATAAAAAATAAAGATAAAGACAAT-AAAT-AAATGAA
1 AAAAT-AAAAATAAAGATAAAGAAAATAAAATAAAATGAA
* * *
869702 TAAAT-AAAATGAAGATAAAGAAAA-AAATTAAAA
1 AAAATAAAAATAAAGATAAAGAAAATAAAATAAAA
869735 AAATAAAGAG
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
36 20 0.32
37 7 0.11
38 15 0.24
39 20 0.32
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (39 bp):
AAAATAAAAATAAAGATAAAGAAAATAAAATAAAATGAA
Found at i:869686 original size:6 final size:5
Alignment explanation
Indices: 869622--869684 Score: 60
Period size: 5 Copynumber: 12.4 Consensus size: 5
869612 AGATAAAAGT
*
869622 AAATA AAATAA AAATA AAGAT- AAAGA AAATA AAATA AAATA AAA-A ATAA-A
1 AAATA AAAT-A AAATA AA-ATA AAATA AAATA AAATA AAATA AAATA A-AATA
869672 AAATA AAGATA AA
1 AAATA AA-ATA AA
869685 GACAATAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
4 5 0.10
5 33 0.66
6 12 0.24
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (5 bp):
AAATA
Found at i:869760 original size:27 final size:28
Alignment explanation
Indices: 869614--869760 Score: 95
Period size: 31 Copynumber: 5.0 Consensus size: 28
869604 TGGAGTGGAG
* *
869614 ATAAAAGTAAATAAAATAAAAATAAAGATAA
1 ATAAAA-TAAAGAAAAGAAAAAT-AA-ATAA
* * *
869645 AGAAAATAAAATAAAATAAAAAATAAA-AA
1 ATAAAAT-AAAGAAAA-GAAAAATAAATAA
*
869674 ATAAAGATAAAGACAATA-AATAAATGAATAA
1 ATAAA-ATAAAGA-AA-AGAA-AAATAAATAA
* *
869705 ATAAAATGAAGATAAAGAAAAA-AATTAA
1 ATAAAATAAAGA-AAAGAAAAATAAATAA
*
869733 A-AAAATAAAGAGAAGAAAAATAAATAA
1 ATAAAATAAAGAAAAGAAAAATAAATAA
869760 A
1 A
869761 CAAGACAAGG
Statistics
Matches: 95, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
26 8 0.08
27 15 0.16
28 5 0.05
29 16 0.17
30 22 0.23
31 23 0.24
32 6 0.06
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.16
Consensus pattern (28 bp):
ATAAAATAAAGAAAAGAAAAATAAATAA
Found at i:870056 original size:24 final size:24
Alignment explanation
Indices: 870017--870066 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
870007 TATATATATA
870017 AATAAGTAGGAAAAAAA-AGAAAAT
1 AATAAGTAGGAAAAAAATA-AAAAT
870041 AATAA-TAGGAATAAAAATAAAAAT
1 AATAAGTAGGAA-AAAAATAAAAAT
870065 AA
1 AA
870067 ATAAATAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 6 0.25
24 17 0.71
25 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (24 bp):
AATAAGTAGGAAAAAAATAAAAAT
Found at i:870130 original size:40 final size:42
Alignment explanation
Indices: 870054--870145 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 42
870044 AATAGGAATA
* * *
870054 AAAATAAAAATAAATAAATAAGATATATATAGTAAAA-GA-T
1 AAAATAAAAATAAATAAACAAGATATATAAAATAAAAGGATT
870094 AAAATAAAAATAGAATAAACAA-ATA-ATGAAAATAAAAGGATT
1 AAAATAAAAATA-AATAAACAAGATATAT-AAAATAAAAGGATT
870136 AAAATAAAAA
1 AAAATAAAAA
870146 AATAAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
39 2 0.04
40 22 0.49
41 10 0.22
42 11 0.24
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.21
Consensus pattern (42 bp):
AAAATAAAAATAAATAAACAAGATATATAAAATAAAAGGATT
Done.