Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008480.1 Hibiscus syriacus cultivar Beakdansim tig00111311_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: 2515485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 13
Found at i:2057555 original size:113 final size:113
Alignment explanation
Indices: 2057303--2058425 Score: 2018
Period size: 113 Copynumber: 10.0 Consensus size: 113
2057293 AGAATTATAC
* * * *
2057303 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
2057368 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
*
2057415 AAAAGGTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
2057480 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
2057528 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
2057593 TATGAACTTTCTCTGGAAAAGCTAATCTC-TCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATC-CATCAAATGATGGATTCAGGT
*
2057641 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
2057706 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
*
2057754 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
2057819 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
2057867 AAAAGGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
2057931 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
2057979 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
2058044 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
2058092 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
2058157 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
2058205 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
2058270 TATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
2058318 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** *
2058383 TATGAACTTTCTCTGGAAAAGCTAATCTTTCAAATGATAGATT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATT
2058426 TGAATCTTTG
Statistics
Matches: 981, Mismatches: 26, Indels: 7
0.97 0.03 0.01
Matches are distributed among these distances:
112 180 0.18
113 800 0.82
114 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
Found at i:2057886 original size:451 final size:452
Alignment explanation
Indices: 2057303--2058403 Score: 2026
Period size: 451 Copynumber: 2.4 Consensus size: 452
2057293 AGAATTATAC
* * * *
2057303 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
2057368 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
*
2057432 CTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
2057497 AAAGATGATCCCTCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
196 AAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
*
2057562 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAATCTCTCAAA
261 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAATCCCTCAAA
*
2057627 TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGA
326 TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
2057692 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
391 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
*
2057754 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
2057819 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAAC-AATT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
2057883 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
2057948 AAAGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
196 AAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
*
2058013 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCCTCAAA
261 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAATCCCTCAAA
2058078 TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
326 TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
2058143 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
391 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
2058205 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
2058270 TATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
2058335 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
2058400 AAAG
196 AAAG
2058404 CTAATCTTTC
Statistics
Matches: 629, Mismatches: 19, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
451 509 0.81
452 120 0.19
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (452 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAATCCCTCAAA
TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
Found at i:2059471 original size:83 final size:82
Alignment explanation
Indices: 2059272--2059975 Score: 1169
Period size: 83 Copynumber: 8.5 Consensus size: 82
2059262 ACCAAACCAT
*
2059272 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTTAAACTCAATGATTGTT
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTT
2059337 CTGTCCAACCAGATCAG
66 CTGTCCAACCAGATCAG
* * *
2059354 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGCTTGAT
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTG-T
*
2059419 TCTGTCCAATCAGATCAG
65 TCTGTCCAACCAGATCAG
*
2059437 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTTGAT
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTG-T
*
2059502 TCTGTCCAATCAGATCAG
65 TCTGTCCAACCAGATCAG
*
2059520 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTTGAT
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTG-T
*
2059585 TCTGTCCAATCAGATCAG
65 TCTGTCCAACCAGATCAG
2059603 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTT
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTT
2059668 CTGTCCAACCAGATCAG
66 CTGTCCAACCAGATCAG
**
2059685 ATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAACTCAATGATTGTT
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTT
2059750 CTGTCCAACCAGATCAG
66 CTGTCCAACCAGATCAG
2059767 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTT
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTT
2059832 CTGTCCAACCAGATCAG
66 CTGTCCAACCAGATCAG
* ** *
2059849 ATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCCCAATTCAATGATTGG
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAACTCAATGATT-G
* *
2059913 TTCTG-CTAAACCAGGTCAG
64 TTCTGTC-CAACCAGATCAG
**
2059932 ATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCAT
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
2059976 TTGTTCTATT
Statistics
Matches: 595, Mismatches: 22, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
81 2 0.00
82 293 0.49
83 299 0.50
84 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (82 bp):
ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTT
CTGTCCAACCAGATCAG
Found at i:2061040 original size:27 final size:27
Alignment explanation
Indices: 2061010--2061077 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 27
2061000 CTTGACCCCC
2061010 TTTCTTTTTCTTCTCTTTT-TTT-TTCAT
1 TTTCTTTTTCTTCTCTTTTCTTTCTT--T
2061037 TTTCTATTTTCTT-TCTTTTCTTTCTTT
1 TTTCT-TTTTCTTCTCTTTTCTTTCTTT
2061064 TTTCTTTTTTCTTC
1 TTTC-TTTTTCTTC
2061078 AAGCATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
27 23 0.64
28 11 0.31
29 2 0.06
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTCTTTTTCTTCTCTTTTCTTTCTTT
Found at i:2061046 original size:16 final size:15
Alignment explanation
Indices: 2061009--2061071 Score: 72
Period size: 16 Copynumber: 4.0 Consensus size: 15
2060999 CCTTGACCCC
* *
2061009 CTTTCTTTTTCTTCT
1 CTTTTTTTTTCTTTT
2061024 CTTTTTTTTTCATTTT
1 CTTTTTTTTTC-TTTT
*
2061040 CTATTTTCTTTCTTTT
1 CT-TTTTTTTTCTTTT
2061056 CTTTCTTTTTTCTTTT
1 CTTT-TTTTTTCTTTT
2061072 TTCTTCAAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
15 12 0.29
16 21 0.51
17 8 0.20
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (15 bp):
CTTTTTTTTTCTTTT
Found at i:2071748 original size:26 final size:26
Alignment explanation
Indices: 2071682--2071748 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
2071672 AGAATACTTG
*
2071682 TAAATAAAAAATGAAATAATATATATA
1 TAAATAAAAAA-AAAATAATATATATA
** * *
2071709 TAAATACTATAAAAATAATATGTATA
1 TAAATAAAAAAAAAATAATATATATA
*
2071735 TATATAAAAAAAAA
1 TAAATAAAAAAAAA
2071749 TTATAAATTA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
26 23 0.74
27 8 0.26
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (26 bp):
TAAATAAAAAAAAAATAATATATATA
Found at i:2072480 original size:20 final size:20
Alignment explanation
Indices: 2072457--2072495 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2072447 AAATATAAAC
*
2072457 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
**
2072477 AAATACCACTAAAACAATA
1 AAATAAAACTAAAACAATA
2072496 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:2073871 original size:3 final size:3
Alignment explanation
Indices: 2073863--2073934 Score: 117
Period size: 3 Copynumber: 23.7 Consensus size: 3
2073853 AATATATATT
*
2073863 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2073911 TAA TAA TATT TAA TAA TAA TAA TA
1 TAA TAA TA-A TAA TAA TAA TAA TA
2073935 TGGATAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 62 0.97
4 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2078074 original size:3 final size:3
Alignment explanation
Indices: 2078059--2078103 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
2078049 TTTATTTATG
* * *
2078059 ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA CTTA ATG ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT
2078104 TAATTTCGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 33 0.94
4 2 0.06
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:2081904 original size:19 final size:19
Alignment explanation
Indices: 2081880--2081941 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
2081870 AAAACTGAAA
2081880 TCGGTTTTTTCGGTTCGGT
1 TCGGTTTTTTCGGTTCGGT
*
2081899 TCGGTTTTTT---TAACGGT
1 TCGGTTTTTTCGGT-TCGGT
*
2081916 TCGAG-TTTTTCGGTTCGAT
1 TCG-GTTTTTTCGGTTCGGT
2081935 TCGGTTT
1 TCGGTTT
2081942 ATCGGGTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
16 1 0.03
17 12 0.35
18 2 0.06
19 18 0.53
20 1 0.03
ACGTcount: A:0.06, C:0.15, G:0.27, T:0.52
Consensus pattern (19 bp):
TCGGTTTTTTCGGTTCGGT
Found at i:2098584 original size:21 final size:23
Alignment explanation
Indices: 2098551--2098598 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
2098541 GTGATTCTGC
2098551 CTTTGTGATACAT-TTTTCTTTGT
1 CTTTGTGATACATATTTT-TTTGT
2098574 CTTTGT-A-ACATATTTTTTTGT
1 CTTTGTGATACATATTTTTTTGT
2098595 CTTT
1 CTTT
2098599 TTTTTATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 13 0.54
22 5 0.21
23 6 0.25
ACGTcount: A:0.15, C:0.12, G:0.10, T:0.62
Consensus pattern (23 bp):
CTTTGTGATACATATTTTTTTGT
Found at i:2100468 original size:2 final size:2
Alignment explanation
Indices: 2100461--2100494 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2100451 GAACAACTGC
2100461 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
2100495 GTAACACCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2104018 original size:33 final size:33
Alignment explanation
Indices: 2103951--2104018 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
2103941 TTTACAGCTC
* *
2103951 CCTAGTTTTTCATGGGATAAACTAGAACATTTT
1 CCTAGTTTTTCACGGGATAAACTAGAACACTTT
* *
2103984 CCTAGTTTTTACACGGGCTAAGCTAGAAC-CTTT
1 CCTAGTTTTT-CACGGGATAAACTAGAACACTTT
2104017 CC
1 CC
2104019 CCTTTACAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (33 bp):
CCTAGTTTTTCACGGGATAAACTAGAACACTTT
Found at i:2104259 original size:20 final size:22
Alignment explanation
Indices: 2104234--2104273 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2104224 AGTCGTATAT
2104234 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
2104254 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
2104274 TCTGCAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:2104543 original size:20 final size:20
Alignment explanation
Indices: 2104518--2104564 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2104508 CAATGTATGG
2104518 ATACACTGCAGAGTGCATGA
1 ATACACTGCAGAGTGCATGA
* * *
2104538 ATACACTGCAGGGTGTATGG
1 ATACACTGCAGAGTGCATGA
2104558 ATACACT
1 ATACACT
2104565 TTGACACCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (20 bp):
ATACACTGCAGAGTGCATGA
Found at i:2104814 original size:21 final size:21
Alignment explanation
Indices: 2104785--2104824 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2104775 TGTTTAATGA
2104785 AAAAAGATA-CTAATTGTTAAT
1 AAAAAGATATC-AATTGTTAAT
*
2104806 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
2104825 CAAAATGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAT
Found at i:2110266 original size:16 final size:16
Alignment explanation
Indices: 2110245--2110277 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2110235 GTTCGGTATT
2110245 AAAATCAGAA-AATCAA
1 AAAATCA-AATAATCAA
2110261 AAAATCAAATAATCAA
1 AAAATCAAATAATCAA
2110277 A
1 A
2110278 CTGAACCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.70, C:0.12, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAATCAAATAATCAA
Found at i:2112944 original size:18 final size:18
Alignment explanation
Indices: 2112918--2112981 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
2112908 AATTCTAAAT
2112918 ATTTACAGTTATTAGATG
1 ATTTACAGTTATTAGATG
*
2112936 ATTTTCAGTTATTAGAT-
1 ATTTACAGTTATTAGATG
* *
2112953 ATTTACAGATATCAGATG
1 ATTTACAGTTATTAGATG
*
2112971 ATTTTCAGTTA
1 ATTTACAGTTA
2112982 ACAAATATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 14 0.36
18 25 0.64
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (18 bp):
ATTTACAGTTATTAGATG
Found at i:2112956 original size:35 final size:35
Alignment explanation
Indices: 2112914--2113008 Score: 136
Period size: 35 Copynumber: 2.7 Consensus size: 35
2112904 GATGAATTCT
* * **
2112914 AAATATTTACAGTTATTAGATGATTTTCAGTTATT
1 AAATATTTACAGATATCAGATGATTTTCAGTTAAC
*
2112949 AGATATTTACAGATATCAGATGATTTTCAGTTAAC
1 AAATATTTACAGATATCAGATGATTTTCAGTTAAC
*
2112984 AAATATTTATAGATATCAGATGATT
1 AAATATTTACAGATATCAGATGATT
2113009 ACAATGATCA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (35 bp):
AAATATTTACAGATATCAGATGATTTTCAGTTAAC
Found at i:2112969 original size:17 final size:17
Alignment explanation
Indices: 2112916--2113004 Score: 79
Period size: 18 Copynumber: 5.1 Consensus size: 17
2112906 TGAATTCTAA
*
2112916 ATATTTACAGTTATTAG
1 ATATTTACAGTTATCAG
* *
2112933 ATGATTTTCAGTTATTAG
1 AT-ATTTACAGTTATCAG
*
2112951 ATATTTACAGATATCAG
1 ATATTTACAGTTATCAG
* * *
2112968 ATGATTTTCAGTTAACAA
1 AT-ATTTACAGTTATCAG
* *
2112986 ATATTTATAGATATCAG
1 ATATTTACAGTTATCAG
2113003 AT
1 AT
2113005 GATTACAATG
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
17 28 0.49
18 29 0.51
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (17 bp):
ATATTTACAGTTATCAG
Found at i:2113223 original size:46 final size:46
Alignment explanation
Indices: 2113121--2113225 Score: 165
Period size: 46 Copynumber: 2.3 Consensus size: 46
2113111 GAGTGCTTAT
*
2113121 TAGTTTCAGTTATCAGGTTATGATTGCACTGAAGTGAATCATATCG
1 TAGTTTCAGTTATCAGGTTATGATTGCACTGAAGTGAATCATATAG
* * *
2113167 CAATTTCAGTTATCAGGTTATGATTGCACTGAAGTGCATCATATAG
1 TAGTTTCAGTTATCAGGTTATGATTGCACTGAAGTGAATCATATAG
*
2113213 TAGTTCCAGTTAT
1 TAGTTTCAGTTAT
2113226 GATTCGACAC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (46 bp):
TAGTTTCAGTTATCAGGTTATGATTGCACTGAAGTGAATCATATAG
Found at i:2115603 original size:18 final size:18
Alignment explanation
Indices: 2115580--2115615 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2115570 GTAATCGACC
2115580 CCCAAACCCATTTTTATT
1 CCCAAACCCATTTTTATT
2115598 CCCAAACCCATTTTTATT
1 CCCAAACCCATTTTTATT
2115616 ATTTCTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.39
Consensus pattern (18 bp):
CCCAAACCCATTTTTATT
Found at i:2117896 original size:17 final size:17
Alignment explanation
Indices: 2117874--2117918 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
2117864 TTGAAAAATT
2117874 AGGGTTTATGATTTTGA
1 AGGGTTTATGATTTTGA
2117891 AGGGTTTATGATTTTGA
1 AGGGTTTATGATTTTGA
*
2117908 AGGATTTATGA
1 AGGGTTTATGA
2117919 AAGATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (17 bp):
AGGGTTTATGATTTTGA
Found at i:2128809 original size:29 final size:29
Alignment explanation
Indices: 2128769--2128857 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
2128759 TAAATTTAAA
2128769 AAATATATTTTATTTTTTCTTAACTTATT
1 AAATATATTTTATTTTTTCTTAACTTATT
* *
2128798 AAATATATTTTATTTTTATTTTAA--TATA
1 AAATATATTTTATTTTT-TCTTAACTTATT
*
2128826 AAACTATATTTTATTATTATCTTAACTT-TT
1 AAA-TATATTTTATT-TTTTCTTAACTTATT
2128856 AA
1 AA
2128858 CTGAAGAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
28 6 0.12
29 33 0.66
30 10 0.20
31 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (29 bp):
AAATATATTTTATTTTTTCTTAACTTATT
Found at i:2131049 original size:21 final size:21
Alignment explanation
Indices: 2131023--2131074 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
2131013 GGACTTGGGG
*
2131023 GGACTACCTACATTCCCACGT
1 GGACTACCCACATTCCCACGT
2131044 GGACTACCCACATTCCCACGT
1 GGACTACCCACATTCCCACGT
2131065 GGACTACCCA
1 GGACTACCCA
2131075 TTTAACTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.40, G:0.15, T:0.19
Consensus pattern (21 bp):
GGACTACCCACATTCCCACGT
Found at i:2140261 original size:28 final size:27
Alignment explanation
Indices: 2140221--2140281 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
2140211 GATTTTGAAA
2140221 AAAATTAAAAGTTTAGATACTAAAACAC
1 AAAATTAAAAGTTTAGATA-TAAAACAC
* * * *
2140249 AAAATTGATAGTTTAGGTATTAAACAC
1 AAAATTAAAAGTTTAGATATAAAACAC
*
2140276 ATAATT
1 AAAATT
2140282 TACCCTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (27 bp):
AAAATTAAAAGTTTAGATATAAAACAC
Found at i:2146683 original size:16 final size:16
Alignment explanation
Indices: 2146662--2146694 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2146652 CCTGATACCA
2146662 TGTAGAAAACAGACTG
1 TGTAGAAAACAGACTG
2146678 TGTAGAAAACAGACTG
1 TGTAGAAAACAGACTG
2146694 T
1 T
2146695 AGAAAATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.21
Consensus pattern (16 bp):
TGTAGAAAACAGACTG
Found at i:2146697 original size:14 final size:15
Alignment explanation
Indices: 2146662--2146705 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
2146652 CCTGATACCA
2146662 TGTAGAAAACAGACTG
1 TGTAGAAAACAGAC-G
2146678 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
*
2146692 TGTAGAAAATAGAC
1 TGTAGAAAACAGAC
2146706 AAGTCTGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.48
16 14 0.52
ACGTcount: A:0.48, C:0.11, G:0.23, T:0.18
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:2154452 original size:16 final size:16
Alignment explanation
Indices: 2154431--2154464 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2154421 TTATAAAAAA
2154431 TGATGCCCCTACATGC
1 TGATGCCCCTACATGC
*
2154447 TGATGCTCCTACATGC
1 TGATGCCCCTACATGC
2154463 TG
1 TG
2154465 CCCTGAGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.32, G:0.21, T:0.29
Consensus pattern (16 bp):
TGATGCCCCTACATGC
Found at i:2171434 original size:18 final size:18
Alignment explanation
Indices: 2171411--2171451 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
2171401 ATGCTTGTCA
2171411 AGCAGTTATAGAAGACGG
1 AGCAGTTATAGAAGACGG
2171429 AGCAGTTATAGAAGACGG
1 AGCAGTTATAGAAGACGG
2171447 AGCAG
1 AGCAG
2171452 CATTCTACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.34, T:0.15
Consensus pattern (18 bp):
AGCAGTTATAGAAGACGG
Found at i:2172185 original size:37 final size:37
Alignment explanation
Indices: 2172138--2172208 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
2172128 TCAGGTCGGG
2172138 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTTGTT
1 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTTGTT
*
2172175 TTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTT
1 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTT
2172209 CGGGTTTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.13, C:0.08, G:0.34, T:0.45
Consensus pattern (37 bp):
TTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTTGTT
Found at i:2172295 original size:248 final size:241
Alignment explanation
Indices: 2171920--2172501 Score: 754
Period size: 248 Copynumber: 2.4 Consensus size: 241
2171910 ACTTTATTTT
* * * *
2171920 GGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATA--T---TCGGG-TCGGGTTTAGGGTTAAAAA
1 GGTCGAGTCGGGTCGGATTTTTTTAAGTGTGATATTTGGGTCGGGTTCGGGTTTAGGG-TGAAAA
* * ** *
2171979 AACGGGACTGACCTGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAA
65 AACCGGACCGACCCAAAAATATATATAATTTAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAA
* * *
2172044 ATAAAAATAATTTTTTATTATTTCGGGTC-GAGTTGGATTTCTAGTTCATATATTCGGGTCGGGT
130 ATAAAAATAATTTTTTATTATTTCGGGTCGGAGTCGGATTTCTAATTCATATA-T----TCAGGT
2172108 CGGATGAAACTTTATTTTGTTCAGGTC-G-GGTTTTTTAAGTGTGATATTCG
190 CGGATGAAACTTTATTTTGTTCAGGTCGGAGGTTTTTTAAGTGTGATATTCG
* *
2172158 GGTCGAGTCGGGT-TGTTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTG
1 GGTCGAGTCGGGTCGGATTTTTTTAAGTGTGATATT----T-GGGTCGGGTTCGGGTTTAGGGTG
* * *
2172222 AAAAAACCCGGACCGACCCAAAAATATATATTATTTGGGTCGGGTCGGATTAAGTCATTGTTTTT
61 AAAAAA-CCGGACCGACCCAAAAATATATATAATTTAGGTCGGGTCGGATTAAGTCACTGTTTTT
* * *
2172287 ATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGGTCGGATTTTTAATTCATATATTCAGGT
125 ATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGAGTCGGATTTCTAATTCATATATTCAGGT
*
2172352 CGGATGAAACTTTATTTTGTTCGGGTCGGGTCAGGTTTTTTAAGTGTGATATTCG
190 CGGATGAAACTTTATTTTGTTCAGGTC-GG--AGGTTTTTTAAGTGTGATATTCG
2172407 GGTCGAGTCGGGTCGGATTTTTTTAAGTGTGATATTTGGGTCGGGTTCGGGTTTAGGGTGAAAAA
1 GGTCGAGTCGGGTCGGATTTTTTTAAGTGTGATATTTGGGTCGGGTTCGGGTTTAGGGTGAAAAA
2172472 ACCGGACCGACCCGAAAAA-ATATATAATTT
66 ACCGGACCGACCC-AAAAATATATATAATTT
2172502 TACCTTATAT
Statistics
Matches: 301, Mismatches: 23, Indels: 34
0.84 0.06 0.09
Matches are distributed among these distances:
237 18 0.06
238 11 0.04
243 1 0.00
244 53 0.18
245 34 0.11
246 2 0.01
247 12 0.04
248 96 0.32
249 54 0.18
250 20 0.07
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (241 bp):
GGTCGAGTCGGGTCGGATTTTTTTAAGTGTGATATTTGGGTCGGGTTCGGGTTTAGGGTGAAAAA
ACCGGACCGACCCAAAAATATATATAATTTAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAA
TAAAAATAATTTTTTATTATTTCGGGTCGGAGTCGGATTTCTAATTCATATATTCAGGTCGGATG
AAACTTTATTTTGTTCAGGTCGGAGGTTTTTTAAGTGTGATATTCG
Found at i:2172418 original size:37 final size:37
Alignment explanation
Indices: 2172376--2172458 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 37
2172366 TTTTGTTCGG
2172376 GTCGGGTCAGG-TTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTC-GGATTTTTTAAGTGTGATATTCGGGTCGA
* *
2172413 GTCGGGTCGGATTTTTTTAAGTGTGATATTTGGGTCGG
1 GTCGGGTCGGA-TTTTTTAAGTGTGATATTCGGGTCGA
2172451 GTTCGGGT
1 G-TCGGGT
2172459 TTAGGGTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
36 2 0.05
37 8 0.20
38 25 0.61
39 6 0.15
ACGTcount: A:0.13, C:0.10, G:0.37, T:0.40
Consensus pattern (37 bp):
GTCGGGTCGGATTTTTTAAGTGTGATATTCGGGTCGA
Found at i:2173259 original size:12 final size:12
Alignment explanation
Indices: 2173242--2173268 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2173232 TTAGTTGCGA
2173242 AAATTAAAATTT
1 AAATTAAAATTT
2173254 AAATTAAAATTT
1 AAATTAAAATTT
2173266 AAA
1 AAA
2173269 CATTCAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATTAAAATTT
Found at i:2175746 original size:84 final size:84
Alignment explanation
Indices: 2175612--2175799 Score: 250
Period size: 84 Copynumber: 2.2 Consensus size: 84
2175602 CTAAATGAAA
* * *
2175612 TCGAACTCGTTAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATG
1 TCGAACTCG-AAGGTCTTTGGTTAGCAAATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATG
2175677 TGCCTCGGAGCTGAGAGTAG
65 TGCCTCGGAGCTGAGAGTAG
* * * **
2175697 TCGAACTCGAAGGTCTTTGGTTAGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTAGCAAATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGT
* * *
2175762 GCCTTGGAGTTGAGCGTAG
66 GCCTCGGAGCTGAGAGTAG
* *
2175781 TCGAACTCAAAGGTTTTTG
1 TCGAACTCGAAGGTCTTTG
2175800 TGTTTCAAGA
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 81 0.90
85 9 0.10
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTGGTTAGCAAATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGT
GCCTCGGAGCTGAGAGTAG
Found at i:2175871 original size:21 final size:21
Alignment explanation
Indices: 2175845--2175909 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
2175835 GGAAACTGTC
2175845 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
** *
2175866 TC-A-AGAG---AAA-CCGTC
1 TCAAGAGAGACAAAATTTGTT
2175881 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
2175902 TCAAGAGA
1 TCAAGAGA
2175910 AATTGTCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 4 0.12
16 4 0.12
17 4 0.12
19 4 0.12
20 4 0.12
21 12 0.38
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:2175876 original size:36 final size:36
Alignment explanation
Indices: 2175828--2175932 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
2175818 TTGGTTGGTA
*
2175828 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
2175864 TTTCAAGAGAAACCGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
2175900 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
2175933 CTTTAGTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:2176503 original size:106 final size:106
Alignment explanation
Indices: 2176325--2177148 Score: 1382
Period size: 106 Copynumber: 7.8 Consensus size: 106
2176315 TTCGTCGTAG
* * * *
2176325 AGTTGAAATTGGTTCTGGAACTG-GAAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AGTTGAAATTGGCTCTGAAATTGAG-AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
* * *
2176389 GTTGAACTTGCATTGTCTTGAGTCCAATATCCTTCGCTGTGA
65 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * *
2176431 AGTTTAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
1 AGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
2176496 TTAAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
*
2176537 AGTTGAAATTGGCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AGTTGAAATTGGCTC-TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
2176602 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
65 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * *
2176644 AGTTGAGATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
1 AGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
2176709 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * *
2176750 AGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTAAAG
1 AGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
2176815 TTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * * *
2176856 AGTTGAAATTGGCTCAGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAG
1 AGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
2176921 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
* * *
2176962 AGTTGAAATTGGCTCAGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
1 AGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
2177027 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
66 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
2177068 AGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
1 AGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
2177132 TTGAACTTGCGTTGTCT
66 TTGAACTTGCGTTGTCT
2177149 TGAGCGACCC
Statistics
Matches: 684, Mismatches: 32, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
105 52 0.08
106 527 0.77
107 105 0.15
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
AGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
Found at i:2179175 original size:3 final size:3
Alignment explanation
Indices: 2179169--2179197 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2179159 TGTAAAAAAA
2179169 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2179198 CCAAATGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2179178 original size:27 final size:27
Alignment explanation
Indices: 2179129--2179180 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2179119 TGAGACATGT
*
2179129 GAATGTAAAAAAAAGGAAAAATAATGC
1 GAATGTAAAAAAAAAGAAAAATAATGC
* *
2179156 GAATGTAAAAAAAAATAATAATAAT
1 GAATGTAAAAAAAAAGAAAAATAAT
2179181 AATAATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.65, C:0.02, G:0.13, T:0.19
Consensus pattern (27 bp):
GAATGTAAAAAAAAAGAAAAATAATGC
Found at i:2180823 original size:12 final size:12
Alignment explanation
Indices: 2180806--2180832 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2180796 TTAGTTGCGA
2180806 AAATTAAAATTT
1 AAATTAAAATTT
2180818 AAATTAAAATTT
1 AAATTAAAATTT
2180830 AAA
1 AAA
2180833 CATTCAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATTAAAATTT
Found at i:2193027 original size:2 final size:2
Alignment explanation
Indices: 2193020--2193056 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2193010 ATTTGATCCG
2193020 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 A
2193057 GATAATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2193640 original size:21 final size:21
Alignment explanation
Indices: 2193607--2193651 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2193597 GATTTTGAAA
*
2193607 AAAATTGAAAGTTTAAGTAAT
1 AAAACTGAAAGTTTAAGTAAT
* * *
2193628 AAAACTGATAGTTTAGGTGAT
1 AAAACTGAAAGTTTAAGTAAT
2193649 AAA
1 AAA
2193652 CACATACTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (21 bp):
AAAACTGAAAGTTTAAGTAAT
Found at i:2210082 original size:6 final size:7
Alignment explanation
Indices: 2210067--2210092 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2210057 AAATTAACAT
2210067 AAAATAA
1 AAAATAA
2210074 AAAATAA
1 AAAATAA
2210081 AAAATAA
1 AAAATAA
2210088 AAAAT
1 AAAAT
2210093 TATACTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:2213269 original size:21 final size:21
Alignment explanation
Indices: 2213245--2213305 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
2213235 GGCAACCAAC
2213245 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
**
2213266 TTTGGTAAATG--TTTC----
1 TTTGAAAAATGTTTTTCAAAG
2213281 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
2213302 TTTG
1 TTTG
2213306 GTAGATGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 9 0.30
17 4 0.13
19 4 0.13
21 13 0.43
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (21 bp):
TTTGAAAAATGTTTTTCAAAG
Found at i:2213288 original size:36 final size:36
Alignment explanation
Indices: 2213244--2213323 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
2213234 TGGCAACCAA
2213244 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
2213280 CTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
2213316 -GTTGAAAA
1 CTTTGAAAA
2213324 TAGGAATGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:2213749 original size:16 final size:17
Alignment explanation
Indices: 2213728--2213761 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2213718 ACTATTCACA
2213728 TGAATAGT-AAATTTTG
1 TGAATAGTGAAATTTTG
2213744 TGAATAGTGAAATTTTG
1 TGAATAGTGAAATTTTG
2213761 T
1 T
2213762 CGACGATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
TGAATAGTGAAATTTTG
Found at i:2216715 original size:64 final size:64
Alignment explanation
Indices: 2216646--2216833 Score: 186
Period size: 64 Copynumber: 2.9 Consensus size: 64
2216636 GCATGCACCG
* * *** *
2216646 ATGCATCGATGCACCATTGAATAAATT-GAACATCGAATGCATTTCATGCATCGATGCACTCTCT
1 ATGCATCGATGCACCATTG-ATATATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGCA
* * *
2216710 ATGCATCGATGCA-C-TTGGGTTTTATTAAAACATCGAATGCATTTCAAGCATCGATGCACAAGC
1 ATGCATCGATGCACCATT--GATATATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGC
2216773 A
64 A
* * * * *
2216774 ATGCACCGATGCACTCA-TGCTATTTTCAAACATCGAATGCATTTTATGCATCGATGCACA
1 ATGCATCGATGCAC-CATTGATATATTAAAACATCGAATGCATTTCATGCATCGATGCACA
2216834 CTTGGTGCAC
Statistics
Matches: 102, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
62 2 0.02
63 5 0.05
64 93 0.91
66 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACCATTGATATATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGCA
Found at i:2216843 original size:64 final size:63
Alignment explanation
Indices: 2216674--2216848 Score: 194
Period size: 64 Copynumber: 2.7 Consensus size: 63
2216664 GAATAAATTG
* * * *
2216674 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTTGGCTATTATTAA
* *
2216738 AACATCGAATGCATTTCAAGCATCGATGCACAAGC-AATGCACCGATGCACTCAT-GCTATT-TT
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT--TGGCTATTATT
*
2216800 CA
62 AA
* *
2216802 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATG
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATG
2216849 TACTAAGTGT
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 86 0.91
65 4 0.04
66 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTTGGCTATTATTAA
Found at i:2216986 original size:16 final size:16
Alignment explanation
Indices: 2216965--2216997 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2216955 TTTCACACAA
2216965 TAACGGCTCTATTGAC
1 TAACGGCTCTATTGAC
2216981 TAACGGCTCTATTGAC
1 TAACGGCTCTATTGAC
2216997 T
1 T
2216998 CCACTAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (16 bp):
TAACGGCTCTATTGAC
Found at i:2224295 original size:21 final size:21
Alignment explanation
Indices: 2224253--2224296 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2224243 ACTCCGGGAG
* *
2224253 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
2224274 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
2224295 CT
1 CT
2224297 CCTCCTCCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:2225011 original size:19 final size:20
Alignment explanation
Indices: 2224987--2225026 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2224977 GAGAAGTGTA
*
2224987 AAATGTTTTA-AAGGGGGAG
1 AAATGTTATAGAAGGGGGAG
2225006 AAATGTTATAGTAAGGGGGAG
1 AAATGTTATAG-AAGGGGGAG
2225027 TAATTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (20 bp):
AAATGTTATAGAAGGGGGAG
Found at i:2225457 original size:64 final size:64
Alignment explanation
Indices: 2225381--2225503 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 64
2225371 GCATTAATCC
*
2225381 ATGCATCAATGCATCATT-GAATAAATT-GAACATCGAATGCATTTCATGAATCGATGCACTCTC
1 ATGCATCAATGCA-C-TTGGAATAAATTAAAACATCGAATGCATTTCATGAATCGATGCACTCTC
2225444 T
64 T
* ** ** *
2225445 ATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCAC
1 ATGCATCAATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGAATCGATGCAC
2225504 AAGCAATGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 2 0.04
63 6 0.12
64 42 0.84
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (64 bp):
ATGCATCAATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGAATCGATGCACTCTCT
Found at i:2225578 original size:64 final size:63
Alignment explanation
Indices: 2225409--2225588 Score: 202
Period size: 64 Copynumber: 2.8 Consensus size: 63
2225399 GAATAAATTG
* * * * * *
2225409 AACATCGAATGCATTTCATGAATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTAGGCTATTATTAA
* * *
2225473 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATACACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT-AGGCTATTATTA
2225536 A
63 A
* *
2225537 AACATCGAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACTA
2225589 AGTGTTCCAA
Statistics
Matches: 98, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 89 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTAGGCTATTATTAA
Found at i:2234060 original size:3 final size:3
Alignment explanation
Indices: 2234045--2234104 Score: 52
Period size: 3 Copynumber: 19.7 Consensus size: 3
2234035 TTTATTTAAA
* *
2234045 TAT TAT T-T ATAT TAT TAT TAT AAA TAT TAT TAT T-T ATAT TATT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT
*
2234091 TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TA
2234105 CAAACAGGCC
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 2 0.04
3 39 0.85
4 5 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2234062 original size:12 final size:12
Alignment explanation
Indices: 2234036--2234087 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
2234026 TCTTCATTTT
*
2234036 TTATTTA-AATA
1 TTATTTATATTA
2234047 TTATTTATATTA
1 TTATTTATATTA
2234059 TTATTATAAATATTA
1 TTATT-T--ATATTA
2234074 TTATTTATATTA
1 TTATTTATATTA
2234086 TT
1 TT
2234088 TATTATTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
11 7 0.19
12 16 0.44
13 1 0.03
14 1 0.03
15 11 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTATATTA
Found at i:2234093 original size:12 final size:11
Alignment explanation
Indices: 2234045--2234104 Score: 63
Period size: 12 Copynumber: 5.5 Consensus size: 11
2234035 TTTATTTAAA
2234045 TATTATTTATAT
1 TATTA-TTATAT
*
2234057 TATTATTATAAA
1 TATTATTAT-AT
2234069 TATTATTAT-T
1 TATTATTATAT
2234079 TA-TATTAT-T
1 TATTATTATAT
2234088 TATTATTAATAT
1 TATTATT-ATAT
2234100 TATTA
1 TATTA
2234105 CAAACAGGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 9 0.21
10 6 0.14
11 6 0.14
12 21 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTATTATAT
Found at i:2246844 original size:14 final size:15
Alignment explanation
Indices: 2246819--2246848 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2246809 AAATGAGGGA
2246819 AAAAGAAAGAAAAAG
1 AAAAGAAAGAAAAAG
2246834 AAAAG-AAGAAAAAG
1 AAAAGAAAGAAAAAG
2246848 A
1 A
2246849 GAGGGTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAAG
Found at i:2247243 original size:19 final size:16
Alignment explanation
Indices: 2247201--2247249 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
2247191 TATTTTCTTT
2247201 AAATTCAATTTATTTG
1 AAATTCAATTTATTTG
*
2247217 AGATTCAATTTATTTCCG
1 AAATTCAATTTATTT--G
2247235 AAAATTCAATTTATT
1 -AAATTCAATTTATT
2247250 CTTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 14 0.50
18 1 0.04
19 13 0.46
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (16 bp):
AAATTCAATTTATTTG
Found at i:2248563 original size:114 final size:112
Alignment explanation
Indices: 2248362--2248703 Score: 522
Period size: 114 Copynumber: 3.0 Consensus size: 112
2248352 AAGTGCCATG
* *
2248362 TGCTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATATGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
2248427 TGATTTGATATGAACCCCAAAATCAATCATTGGATTTTAAAGATGAATT
66 TGATTTG-TATGAA-CCCAAAATCAATCATTGGATTTGAAAGATGAATT
*
2248476 TGCTCATAGTAGAAATAAGAATACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
2248541 TGATTTAGTATGAACCCTAAAATCAATCATTGGATTTGAAAGATGAATT
66 TGATTT-GTATGAACCC-AAAATCAATCATTGGATTTGAAAGATGAATT
* *
2248590 TGCTCATAGTAGAAAGAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * *
2248655 TGGTTCGGTAAGAACCACAAAACCAATCATTGAAATTGAAAGATGAATT
66 TGATT-TGTATGAACC-CAAAATCAATCATTGGATTTGAAAGATGAATT
2248704 GCATGATCGT
Statistics
Matches: 211, Mismatches: 13, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
113 3 0.01
114 206 0.98
115 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (112 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTTGTATGAACCCAAAATCAATCATTGGATTTGAAAGATGAATT
Found at i:2249592 original size:113 final size:113
Alignment explanation
Indices: 2249404--2249674 Score: 409
Period size: 113 Copynumber: 2.4 Consensus size: 113
2249394 CATCATTCGG
* * ** *
2249404 TGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAGTT
1 TGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
2249469 CATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
66 CATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
* * *
2249517 TGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 TGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * **
2249581 TCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCGTTTGA
65 TCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
*
2249630 TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATC
1 TGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATC
2249675 ATCTGAAGAA
Statistics
Matches: 142, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
112 1 0.01
113 141 0.99
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (113 bp):
TGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCACTTGA
Found at i:2249809 original size:113 final size:109
Alignment explanation
Indices: 2249684--2249983 Score: 331
Period size: 104 Copynumber: 2.7 Consensus size: 109
2249674 CATCTGAAGA
* *
2249684 AGAAGAAATTGTTCAAATTTTTGCTTAAATTCATCACTCGGTGAATCAACATTTCCAGTTCGAGT
1 AGAAGAAATTGTTCAACTTTTTGCTTAAATTCATCA-T--GTG-ATCAACATTACCAGTTCGAGT
*
2249749 TCATAATAAGAAGAACTCTTCTGAAGAAAGAAGAAGAAGTTCATAATG
62 TCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
* * * * * * *
2249797 AGAAGAACTTGTTTAACTTTTGGCTTGAA-T--TCA--TGATCAATATTACCAGTTCAAGTTTAT
1 AGAAGAAATTGTTCAACTTTTTGCTTAAATTCATCATGTGATCAACATTACCAGTTCGAGTTCAT
*
2249857 AATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
66 AATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
* * * * * *
2249901 AGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGT
1 AGAAGAAATTGTTCAACTTTTTGCTTAAATTCATCA--TG-T-GATCAACATTACCAGTTCGAGT
*
2249966 TCATAATGAGAAGAACTC
62 TCATAATAAGAAGAACTC
2249984 GTCATCTGGA
Statistics
Matches: 154, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
104 86 0.56
105 3 0.02
107 3 0.02
110 3 0.02
112 2 0.01
113 57 0.37
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (109 bp):
AGAAGAAATTGTTCAACTTTTTGCTTAAATTCATCATGTGATCAACATTACCAGTTCGAGTTCAT
AATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG
Found at i:2249981 original size:312 final size:317
Alignment explanation
Indices: 2249389--2250139 Score: 937
Period size: 312 Copynumber: 2.3 Consensus size: 317
2249379 GCAAAGATTA
* * * *
2249389 AAATCCATCATTCGGTGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAT
1 AAATCCATCACTCGGTGAATCAACATTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
* * *
2249454 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCACTTGATG
66 AAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT-ATCAC-TGATC
* * *
2249519 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
129 AATCA-C-TTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* *
2249584 TAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCGTTTGATGGATCAACATTGCCAGGT
192 TAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGT
2249649 AGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGAAGAAATTGTTCAAATTTTTGCTT
257 AGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGAAGAAATTGTTCAAATTTTTGCTT
* *
2249710 AAATTCATCACTCGGTGAATCAACATTTCCAGTTCGAGTTCATAATAAGAAGAACTCTTCTGAAG
1 AAATCCATCACTCGGTGAATCAACATTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
* *
2249775 AAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA-CTTTTGGCTTGAA-T-TCA-TGATCA
66 AAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTCGAATTATCACTGATCA
*** *
2249836 AT-A-TTACCAGTTCAAGTTTATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
130 ATCACTTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
2249899 TGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
195 TGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGA
* * * * *
2249964 GTTCATAATGAGAAGAACTCGTCATCTG--G-AGAAGAATTTATTCAACTTTTTGCAT
260 GTTCATAATGAGAAGAACTCATCATCTGAAGAAGAAGAAATTGTTCAAATTTTTGCTT
* * ** * * ****
2250019 AATTCTATCACAAAAGGAGATAGATCAGCATCAACCTTTCTAGAAAAAGTTCATAATAAGAAGAA
1 AAATCCATCAC---TCG-G-T-G---A--ATCAACATTTCCAGTTCGAGTTCATAATAAGAAGAA
* * *
2250084 CTCATCTGAAG-AAGAAAGAAGAAGTTCATAATGAGAATAGCTTATTCAACCTTTTG
55 CTCATCTGAAGAAAG-AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
2250140 GATGACTCTA
Statistics
Matches: 375, Mismatches: 41, Indels: 29
0.84 0.09 0.07
Matches are distributed among these distances:
309 30 0.08
310 1 0.00
312 145 0.39
313 1 0.00
314 1 0.00
315 2 0.01
316 6 0.02
318 4 0.01
319 3 0.01
320 77 0.21
321 105 0.28
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (317 bp):
AAATCCATCACTCGGTGAATCAACATTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTGAAG
AAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTATCACTGATCAA
TCACTTACCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
GAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGAG
TTCATAATGAGAAGAACTCATCATCTGAAGAAGAAGAAATTGTTCAAATTTTTGCTT
Found at i:2250139 original size:124 final size:121
Alignment explanation
Indices: 2250001--2250227 Score: 276
Period size: 124 Copynumber: 1.9 Consensus size: 121
2249991 GGAGAAGAAT
* * * * *
2250001 TTATTCAACTTTTTGCATAATTCTATCACAAAAGGAGATAGATCAGCATCAACCTTTCTAG-AAA
1 TTATTCAACCTTTTGCATAACTCTATCACAAAAGGAAATAGATCAACATCAACC---CCAGCAAA
2250065 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAATAGC
63 AAGTTCATAATAAGAAGAACTCATCTGAAGAA-AAAGAAGAAGTTCATAATGAGAATAGC
* * * * * **
2250125 TTATTCAACCTTTTGGATGACTCTATCACAGAAGGAAATAGGTCAACATCATCCCCAGCGGAAAG
1 TTATTCAACCTTTTGCATAACTCTATCACAAAAGGAAATAGATCAACATCAACCCCAGCAAAAAG
* * *
2250190 TTCGTAATGAGAAGAACTCATCTGAAGAAAGAGAAGAA
66 TTCATAATAAGAAGAACTCATCTGAAGAAAAAGAAGAA
2250228 TTTATTAAAC
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
121 11 0.13
122 31 0.36
124 45 0.52
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (121 bp):
TTATTCAACCTTTTGCATAACTCTATCACAAAAGGAAATAGATCAACATCAACCCCAGCAAAAAG
TTCATAATAAGAAGAACTCATCTGAAGAAAAAGAAGAAGTTCATAATGAGAATAGC
Found at i:2250391 original size:9 final size:9
Alignment explanation
Indices: 2250377--2250429 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
2250367 TTTTATTTAA
2250377 ATATTATTT
1 ATATTATTT
2250386 ATATTA-TT
1 ATATTATTT
**
2250394 AT-TATAAAT
1 ATAT-TATTT
2250403 ATTATTATTT
1 A-TATTATTT
2250413 ATATTATTT
1 ATATTATTT
2250422 ATATTATT
1 ATATTATT
2250430 ATTACAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
7 1 0.03
8 6 0.16
9 24 0.65
10 5 0.14
11 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
ATATTATTT
Found at i:2250395 original size:12 final size:12
Alignment explanation
Indices: 2250369--2250432 Score: 64
Period size: 12 Copynumber: 5.4 Consensus size: 12
2250359 CTTCATTTTT
*
2250369 TTATTTA-AATA
1 TTATTTATATTA
2250380 TTATTTATATTA
1 TTATTTATATTA
2250392 TTATTATAAATATTA
1 TTATT-T--ATATTA
2250407 TTA-TT-TA-TA
1 TTATTTATATTA
2250416 TTATTTATATTA
1 TTATTTATATTA
2250428 TTATT
1 TTATT
2250433 ACAAACATGC
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
9 5 0.11
10 4 0.09
11 9 0.20
12 15 0.33
13 2 0.04
14 1 0.02
15 9 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTATATTA
Found at i:2250433 original size:15 final size:15
Alignment explanation
Indices: 2250378--2250420 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
2250368 TTTATTTAAA
2250378 TATTATTTATATTAT
1 TATTATTTATATTAT
*
2250393 TATTA--TA-AATAT
1 TATTATTTATATTAT
2250405 TATTATTTATATTAT
1 TATTATTTATATTAT
2250420 T
1 T
2250421 TATATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
12 9 0.39
13 2 0.09
14 2 0.09
15 10 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATTTATATTAT
Found at i:2256705 original size:207 final size:211
Alignment explanation
Indices: 2256139--2256851 Score: 974
Period size: 207 Copynumber: 3.3 Consensus size: 211
2256129 ATTTAAGAAT
* *
2256139 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAACACATTGATGAGGG
1 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAAAAACACA-T-ATAAGGG
* *
2256204 ATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAGGTACTAAATTATACCC
64 ATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCC
* **
2256269 ATTTAAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAATAAGTAATAAGTATGAATCAAT
129 ATTT-AAAAAGTTATGGGCCAATTTAAAAAT---A--AA--AATAAGTAATAAGTATGGGTCAAT
*
2256334 TTCATATGCAAATAAAATTTGGAGAAC
186 TTCA-ATGCAAATAAAATTTGGAGGAC
* * *
2256361 TAAATTGAACAAATATGAAATTAGAAATACAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAA-AA-ACACA-T-ATAAG
* * *
2256426 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTAATAAACTATAC
62 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* *
2256491 CCATTTAAAAATTTATGGGCCAATTTAAAAATAAAAATAAGTAATGAGTATGGGTCAATTTC-A-
127 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAAAAATAAGTAATAAGTATGGGTCAATTTCAAT
2256554 G-AAATAAAATTTGGAGGAC
192 GCAAATAAAATTTGGAGGAC
* *
2256573 TAAAATGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAAAAAACACA-A-AAGGGA
1 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATT-AAAAAACACATATAAGGGA
* * * *
2256636 TCAAATCGAAATAATTTTAAATTTTAAGGTTGAAATTAATACAAAAATGTACTAAATTATACTCA
65 TCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCA
*
2256701 TTTAAAAAGTTATGGGCCAA-TTAACAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATG
130 TTTAAAAAGTTATGGGCCAATTTAA-AAATAAAAATAAGTAATAAGTATGGGTCAATTTCA-ATG
*
2256765 CAAATAAAATGTGGAGGAC
193 CAAATAAAATTTGGAGGAC
* *
2256784 TAAATTGAACAAATATGAAATTATAAATAAAATTTTAAATAAATTAAACAACACA-A-AAGGGAT
1 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAAAAACACATATAAGGGAT
2256847 CAAAT
66 CAAAT
2256852 GTGAAAAAAA
Statistics
Matches: 450, Mismatches: 33, Indels: 28
0.88 0.06 0.05
Matches are distributed among these distances:
206 4 0.01
207 114 0.25
208 1 0.00
209 1 0.00
210 23 0.05
211 64 0.14
212 61 0.14
213 4 0.01
214 1 0.00
216 24 0.05
218 2 0.00
220 1 0.00
222 46 0.10
223 25 0.06
224 79 0.18
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.28
Consensus pattern (211 bp):
TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAAAAACACATATAAGGGAT
CAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCAT
TTAAAAAGTTATGGGCCAATTTAAAAATAAAAATAAGTAATAAGTATGGGTCAATTTCAATGCAA
ATAAAATTTGGAGGAC
Found at i:2257024 original size:6 final size:6
Alignment explanation
Indices: 2257002--2258890 Score: 3302
Period size: 6 Copynumber: 323.7 Consensus size: 6
2256992 AATTTAAGGA
2257002 TTATGGT TTATTGT TTATGT TTATGT TTATGT TTATGT TTATGT TTA-GT
1 TTAT-GT TTA-TGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257051 TTATGT TTATGT TTATGT TTATG- TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257098 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257146 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257194 TTATGT TTATGTT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATG-T TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257243 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257291 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257339 TTATG- TTATG- TTATGT TTATGT TTATGT TTATG- TT-TGT TTATG-
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257382 TTATGT TTATGT TTATG- TT-TG- TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257427 TT-TGT TTATGT TTATG- TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257473 TTATGT TTATGT TTATG- TTATGT TTATGT TT-TG- TTATGT TTATG-
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257517 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257565 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATG-
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257612 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257660 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257708 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATG-
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257755 TTATG- TT-TGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257801 TTATGT TTATG- TTATGT TTATG- TT-TGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
*
2257846 TTATGT TTATGT TTATTT GTTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT -TTATGT TTATGT TTATGT TTATGT TTATGT
2257895 TT-TGT TTATGT TTATGT TTATG- TT-TG- TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257939 TTATGT TTATGT TTATG- TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2257986 TTATGT TTATGT TTATGT TTATGT TTATGT TTATG- TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258033 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATG-
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258080 TTATGT TTATGT TTATG- TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258127 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258175 TTATGT TTATGT TTATGT TTATG- TTATGTTT TTATGT TTATG- TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATG--T TTATGT TTATGT TTATGT
2258223 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258271 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258319 TTATG- TT-TGT TTATGT TTATG- TTATG- TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258363 TTATG- TT-TGT TTATGT TTATG- TTATGT TTATG- TT-TGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258406 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258454 TTATGT TTATG- TTATGT TTATGT TTATGT TTATG- TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258500 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258548 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258596 TTATGT TTATGT TTATGT TTATGT TT-TG- TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258642 TTATGT TTATG- TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258689 TTATGT TTATGT TTATGT TTATG- TT-TG- TTATGT TTATGT TTATG-
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258733 TTATGT TTATGT TTATGT TTATG- TTATGT TTATG- TT-TGT TTATG-
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258777 TT-TGT TTATGT TTATGT TTATG- TTATGT TTATGT TTATG- TT-TGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258821 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT
2258869 TTATGT TTATGT TTATGT TTAT
1 TTATGT TTATGT TTATGT TTAT
2258891 ATACTATATA
Statistics
Matches: 1822, Mismatches: 2, Indels: 117
0.94 0.00 0.06
Matches are distributed among these distances:
4 34 0.02
5 196 0.11
6 1567 0.86
7 19 0.01
8 6 0.00
ACGTcount: A:0.16, C:0.00, G:0.17, T:0.67
Consensus pattern (6 bp):
TTATGT
Found at i:2258921 original size:18 final size:17
Alignment explanation
Indices: 2258900--2258983 Score: 66
Period size: 18 Copynumber: 4.8 Consensus size: 17
2258890 TATACTATAT
2258900 ATATGAACTATAGTTTAC
1 ATATGAACTATA-TTTAC
2258918 ATATGAACTATATATATAC
1 ATATGAACTATAT-T-TAC
* *
2258937 -TA--AAGTTGATATTTAT
1 ATATGAA-CT-ATATTTAC
*
2258953 ATATGAACTATAGTTTAT
1 ATATGAACTATA-TTTAC
2258971 ATATGAACTATAT
1 ATATGAACTATAT
2258984 ATATAAACTA
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
16 4 0.07
17 9 0.16
18 37 0.67
19 5 0.09
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (17 bp):
ATATGAACTATATTTAC
Found at i:2258986 original size:13 final size:13
Alignment explanation
Indices: 2258968--2258997 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2258958 AACTATAGTT
*
2258968 TATATATGAACTA
1 TATATATAAACTA
2258981 TATATATAAACTA
1 TATATATAAACTA
2258994 TATA
1 TATA
2258998 GTTTACATAT
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:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:2258993 original size:31 final size:31
Alignment explanation
Indices: 2258950--2259036 Score: 111
Period size: 33 Copynumber: 2.7 Consensus size: 31
2258940 AGTTGATATT
*
2258950 TATATATGAACTATAGTTTATATATGAACTA
1 TATATATAAACTATAGTTTATATATGAACTA
* *
2258981 TATATATAAACTATATAGTTTACATATGACCTA
1 TATATATAAAC--TATAGTTTATATATGAACTA
* *
2259014 TATATATATACTATAGTTGATAT
1 TATATATAAACTATAGTTTATAT
2259037 TTATATACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.42
33 28 0.58
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (31 bp):
TATATATAAACTATAGTTTATATATGAACTA
Found at i:2259007 original size:86 final size:85
Alignment explanation
Indices: 2258893--2259081 Score: 269
Period size: 86 Copynumber: 2.2 Consensus size: 85
2258883 ATGTTTATAT
*
2258893 ACTATATATATGAAC--TATAGTTTACATATGAAC-TATATATATACTAAAGTTGATATTTATAT
1 ACTATATATATAAACTATATAGTTTACATATGAACATATATATATACTAAAGTTGATATTTATAT
*
2258955 A-TGAACTATAGTTTATATATGA
66 ACT--A-TATAGTTTACATATGA
* *
2258977 ACTATATATATAAACTATATAGTTTACATATGACCTATATATATATACTATAGTTGATATTTATA
1 ACTATATATATAAACTATATAGTTTACATATGAAC-ATATATATATACTAAAGTTGATATTTATA
2259042 TACTATATAGTTTACATATGA
65 TACTATATAGTTTACATATGA
*
2259063 ACTATATATATATACTATA
1 ACTATATATATAAACTATA
2259082 GTTTATATTT
Statistics
Matches: 95, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
84 14 0.15
86 50 0.53
87 1 0.01
88 29 0.31
89 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (85 bp):
ACTATATATATAAACTATATAGTTTACATATGAACATATATATATACTAAAGTTGATATTTATAT
ACTATATAGTTTACATATGA
Found at i:2259053 original size:53 final size:53
Alignment explanation
Indices: 2258980--2259102 Score: 210
Period size: 53 Copynumber: 2.3 Consensus size: 53
2258970 TATATGAACT
* * *
2258980 ATATATATAAACTATATAGTTTACATATGACCTATATATATATACTATAGTTG
1 ATATTTATATACTATATAGTTTACATATGAACTATATATATATACTATAGTTG
*
2259033 ATATTTATATACTATATAGTTTACATATGAACTATATATATATACTATAGTTT
1 ATATTTATATACTATATAGTTTACATATGAACTATATATATATACTATAGTTG
2259086 ATATTTATATACTATAT
1 ATATTTATATACTATAT
2259103 GTAGACACCC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 66 1.00
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (53 bp):
ATATTTATATACTATATAGTTTACATATGAACTATATATATATACTATAGTTG
Found at i:2260503 original size:34 final size:34
Alignment explanation
Indices: 2260460--2260556 Score: 137
Period size: 34 Copynumber: 2.9 Consensus size: 34
2260450 TATGTTTGAT
2260460 ATATATATATATATATACTGGTTTATTGTTGTTG
1 ATATATATATATATATACTGGTTTATTGTTGTTG
* *
2260494 ATATATATATATATATATTGGTTTATTGCTGTTG
1 ATATATATATATATATACTGGTTTATTGTTGTTG
* *
2260528 ATGTA-A-AT-GATATACTGGTTTATTGTTGT
1 ATATATATATATATATACTGGTTTATTGTTGT
2260557 AATGTAAACT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 18 0.32
32 2 0.04
33 1 0.02
34 36 0.63
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (34 bp):
ATATATATATATATATACTGGTTTATTGTTGTTG
Found at i:2260799 original size:2 final size:2
Alignment explanation
Indices: 2260792--2260827 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2260782 ATTGTTGTTG
* *
2260792 AT AT AT AT AA AT AT AT AT AA 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
2260828 TGGTTTATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2260807 original size:10 final size:10
Alignment explanation
Indices: 2260792--2260827 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
2260782 ATTGTTGTTG
2260792 ATATATATAA
1 ATATATATAA
2260802 ATATATATAA
1 ATATATATAA
*
2260812 ATATATATAT
1 ATATATATAA
2260822 ATATAT
1 ATATAT
2260828 TGGTTTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATATATAA
Found at i:2260837 original size:316 final size:299
Alignment explanation
Indices: 2260279--2260892 Score: 1050
Period size: 300 Copynumber: 2.0 Consensus size: 299
2260269 TCATGGATAG
2260279 TTTTTCATACGAGTTGAATTACTCAAGTATTTCCCATTCTTTTTTGTTTCATTTTTCATTTTATT
1 TTTTTCATACGAGTTGAATTACTCAAGTATTTCCCATTCTTTTTTGTTTCATTTTTCATTTTATT
2260344 TTAATATTCAAATTAATTTATTATTTATTTGTTTTGTAGGTCAAAACCAGCAGATCAGAATGACA
66 TTAATATTCAAATTAATTTATTATTTATTTGTTTTGTAGGTCAAAACCAGCAGATCAGAATGACA
2260409 ATCATTCTTAAAGAGGTAAACTGTTCATTCATTTCTTTGTATATGTTTGATATATATATATATAT
131 ATCATTCTTAAAGAGGTAAACTGTTCATTCATTTCTTTGTATATGTTTGA-ATATATATATATAT
2260474 ATACTGGTTTATTGTTGTTGATATATATATATATATATTGGTTTATTGCTGTTGATGTAAATGAT
195 ATACTGGTTTATTGTTGTTGATATATATATATATATATTGGTTTATTGCTGTTGATGTAAATGAT
2260539 ATACTGGTTTATTGTTGTAATGTAAACTAATCATGTTTCA
260 ATACTGGTTTATTGTTGTAATGTAAACTAATCATGTTTCA
2260579 TTTTTCATACGAGTTGAATTACTCAAGTATTTCCCATTCTTTTTTGTTTCATTTTTCATTTTATT
1 TTTTTCATACGAGTTGAATTACTCAAGTATTTCCCATTCTTTTTTGTTTCATTTTTCATTTTATT
2260644 TTAATATTCAAATTAATTTATTATTTATTTGTTTTGTAGGTCAAAACCAGCAGATCAGAATGACA
66 TTAATATTCAAATTAATTTATTATTTATTTGTTTTGTAGGTCAAAACCAGCAGATCAGAATGACA
2260709 ATCATTCTTAAAGAGGTAAACTGTTCATTCATTTCTTTGTATATGTTTG-ATATATATATATATA
131 ATCATTCTTAAAGAGGTAAACTGTTCATTCATTTCTTTGTATATGTTTGAATATATATATATATA
2260773 TACTGGTTTATTGTTGTTGATATATATAAATATATATAAATATATATATATATATTGGTTTATTG
196 TACTGGTTTATTGTTGTTG----------------AT--ATATATATATATATATTGGTTTATTG
2260838 CTGTTGATGTAAATGATATACTGGTTTATTGTTGTAATGTAAACTAATCATGTTT
243 CTGTTGATGTAAATGATATACTGGTTTATTGTTGTAATGTAAACTAATCATGTTT
2260893 TTTTTGTAAG
Statistics
Matches: 296, Mismatches: 0, Indels: 20
0.94 0.00 0.06
Matches are distributed among these distances:
298 34 0.11
300 179 0.60
314 2 0.01
316 81 0.27
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.48
Consensus pattern (299 bp):
TTTTTCATACGAGTTGAATTACTCAAGTATTTCCCATTCTTTTTTGTTTCATTTTTCATTTTATT
TTAATATTCAAATTAATTTATTATTTATTTGTTTTGTAGGTCAAAACCAGCAGATCAGAATGACA
ATCATTCTTAAAGAGGTAAACTGTTCATTCATTTCTTTGTATATGTTTGAATATATATATATATA
TACTGGTTTATTGTTGTTGATATATATATATATATATTGGTTTATTGCTGTTGATGTAAATGATA
TACTGGTTTATTGTTGTAATGTAAACTAATCATGTTTCA
Found at i:2260880 original size:30 final size:31
Alignment explanation
Indices: 2260822--2260880 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2260812 ATATATATAT
* *
2260822 ATATATTGGTTTATTGCTGTTGATGTAAATG
1 ATATACTGGTTTATTGCTGTTAATGTAAATG
*
2260853 ATATACTGGTTTATTGTTG-TAATGTAAA
1 ATATACTGGTTTATTGCTGTTAATGTAAA
2260881 CTAATCATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.47
Consensus pattern (31 bp):
ATATACTGGTTTATTGCTGTTAATGTAAATG
Found at i:2262322 original size:65 final size:66
Alignment explanation
Indices: 2262254--2262383 Score: 149
Period size: 68 Copynumber: 1.9 Consensus size: 66
2262244 CAAAAAAATA
*
2262254 ATCATATTAATTTGA-TTATCATAATAATTTATGATAAAATTTTAAA-AA-ATAATCATATTAAT
1 ATCATA-TAATTT-ATTTATCAT-A-AATTTATGAT-AAATTTAAAATAACATAATCATATTAAT
2262316 TTAATC
61 TTAATC
* * *
2262322 ATCATAATAATTTATTTATCATAAGTTTATTATAAATTTAAAATAACATAATTATATTAATT
1 ATCAT-ATAATTTATTTATCATAAATTTATGATAAATTTAAAATAACATAATCATATTAATT
2262384 GTAACTTCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
65 9 0.17
66 10 0.19
67 16 0.30
68 18 0.33
69 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (66 bp):
ATCATATAATTTATTTATCATAAATTTATGATAAATTTAAAATAACATAATCATATTAATTTAAT
C
Found at i:2262342 original size:17 final size:17
Alignment explanation
Indices: 2262305--2262345 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2262295 TTAAAAAATA
*
2262305 ATCATATTAATTTAATC
1 ATCATAATAATTTAATC
* *
2262322 ATCATAATAATTTATTT
1 ATCATAATAATTTAATC
2262339 ATCATAA
1 ATCATAA
2262346 GTTTATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (17 bp):
ATCATAATAATTTAATC
Found at i:2264068 original size:11 final size:11
Alignment explanation
Indices: 2264041--2264087 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
2264031 ATGAGATATT
2264041 TTAAATATTTTA
1 TTAAATA-TTTA
*
2264053 GTAAATATTTA
1 TTAAATATTTA
2264064 TTAAATATTTA
1 TTAAATATTTA
2264075 --AAATATTCTA
1 TTAAATATT-TA
2264085 TTA
1 TTA
2264088 TTTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 7 0.23
10 2 0.07
11 14 0.47
12 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (11 bp):
TTAAATATTTA
Found at i:2264094 original size:21 final size:20
Alignment explanation
Indices: 2264041--2264087 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 20
2264031 ATGAGATATT
2264041 TTAAATATTTTAGTAAATATTTA
1 TTAAATA-TTTA--AAATATTTA
2264064 TTAAATATTTAAAATATTCTA
1 TTAAATATTTAAAATATT-TA
2264085 TTA
1 TTA
2264088 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
21 5 0.22
22 4 0.17
23 7 0.30
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTAAATATTTAAAATATTTA
Found at i:2264346 original size:20 final size:20
Alignment explanation
Indices: 2264321--2264358 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2264311 TTTGGTTCAC
2264321 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
2264341 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
2264359 GGAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:2264368 original size:16 final size:18
Alignment explanation
Indices: 2264321--2264371 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
2264311 TTTGGTTCAC
2264321 GGAATGTAAGATTACCAGTG
1 GGAA-GTAAGATTACCAG-G
2264341 GGAATGTAAGATTACCA-G
1 GGAA-GTAAGATTACCAGG
2264359 GGAA-TAAGATTAC
1 GGAAGTAAGATTAC
2264372 TGGGAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.29
18 5 0.16
20 17 0.55
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (18 bp):
GGAAGTAAGATTACCAGG
Found at i:2265557 original size:24 final size:24
Alignment explanation
Indices: 2265530--2265582 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2265520 TATATGTTTC
2265530 ATTTCTCCAT-CATATATTTTATTT
1 ATTT-TCCATGCATATATTTTATTT
* * *
2265554 ATTTTTCTTGTATATATTTTATTT
1 ATTTTCCATGCATATATTTTATTT
2265578 ATTTT
1 ATTTT
2265583 TCTTGTCAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (24 bp):
ATTTTCCATGCATATATTTTATTT
Found at i:2265583 original size:24 final size:24
Alignment explanation
Indices: 2265541--2265588 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2265531 TTTCTCCATC
2265541 ATATATTTTATTTATTTTTCTTGT
1 ATATATTTTATTTATTTTTCTTGT
2265565 ATATATTTTATTTATTTTTCTTGT
1 ATATATTTTATTTATTTTTCTTGT
2265589 CAACAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (24 bp):
ATATATTTTATTTATTTTTCTTGT
Found at i:2273495 original size:16 final size:16
Alignment explanation
Indices: 2273474--2273506 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2273464 CAACAATCTC
2273474 CCCCTTTTTGATATAA
1 CCCCTTTTTGATATAA
2273490 CCCCTTTTTGATATAA
1 CCCCTTTTTGATATAA
2273506 C
1 C
2273507 AAAACATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.06, T:0.42
Consensus pattern (16 bp):
CCCCTTTTTGATATAA
Found at i:2281395 original size:815 final size:820
Alignment explanation
Indices: 2279790--2281417 Score: 2971
Period size: 815 Copynumber: 2.0 Consensus size: 820
2279780 TGATTACTGA
* *
2279790 GGAAATTGATACTTCCACAGTTGAATTTTTTCCTATAGACTCAGATCAGTCTCCACAAACAGAAG
1 GGAAATTGATACTTACACAGTTGAATTTTTGCCTATAGACTCAGATCAGTCTCCACAAACAGAAG
*
2279855 AAGAAACCCTAGAAATCTCTATGAATGTTATTACTGGCTCTATTGGTCATACTACATTGATAATC
66 AAGAAACCCTAGAAATCTCTATGAATGCTATTACTGGCTCTATTGGTCATACTACATTGATAATC
2279920 TAGGGCTATATACAAGGAAAATCATTAAATATCCTAATTGATAGTGGCAATACACACAGTTTCTT
131 TAGGGCTATATACAAGGAAAATCATTAAATATCCTAATTGATAGTGGCAATA-ACACAGTTTCTT
2279985 GGCTCCTAAATGGGCTGATGCTGACATTCAGATTACTACCCCTTATCATTTGGCCATCACTGTGG
195 GGCTCCTAAATGGGCTGATGCTGACATTCAGATTACTACCCCTTATCATTTGGCCATCACTGTGG
2280050 CTAATGGTCAGCAACTATTCAGTACTGCTAGATGCAACCAAGTACAGTGGCAAATGCAGGGACAT
260 CTAATGGTCAGCAACTATTCAGTACTGCTAGATGCAACCAAGTACAGTGGCAAATGCAGGGACAT
*
2280115 ACATTTTTGTATGATTTTAGATTACTTAAATTGGGTGTGAGTGACATGGTTTTATGATTGGATTG
325 ACATTTTTGCATGATTTTAGATTACTTAAATTGGGTGTGAGTGACATGGTTTTATGATTGGATTG
2280180 GATGAAGTTATTTAGTCCAATATTAATGGACTTCAACAATATGACTTTAAGTTTTGATCATGAAG
390 GATGAAGTTATTTAGTCCAATATTAATGGACTTCAACAATATGACTTT-AGTTTTGATCATGAAG
2280245 GAAAGCATATTTATATTCAAGGACAGCAGCCCTCAACTGAATTGCAACAAATTTCAGGGGTAACA
454 GAAAGCATATTTATATTCAAGGACAGCAGCCCTCAACTGAATTGCAACAAATTTCAGGGGTAACA
* *
2280310 TTATTAAAAATGAGTGCAGGGGATTCTGATATTATGAGATATATTGTCCTATTGACTATGGCAGG
519 TTATTAAAAA-GAGTGCAGGGGATTATGATATTATGAGACATATTGTCCTATTGACTATGGCAGG
* *
2280375 AAGTTCTTCTTCTATTTCTATGGAACTTCAACATGTATTGGAGAAATACAGCTCAATCTTTGCTG
583 AAGTTCTTCTTCTATTCCTATGGAACTCCAACATGTATTGGAGAAATACAGCTCAATCTTTGCTG
2280440 AACCTAAAGGGCTACCTCCTCAGAGGTCTCATGATCATGCCATTCCACTTAAACCTAATGCTACA
648 AACCTAAAGGGCTACCTCCTCAGAGGTCTCATGATCATGCCATTCCACTTAAACCTAATGCTACA
*
2280505 CCAGTTAATCTGAGGCCTTATAGATTTCCTCATAATCAGAAGGCTAATGTTGAGAAACAGATAAC
713 CCAGTTAATCTGAGGCCTTATAGATTTCCTCACAATCAGAAGGCTAATGTTGAGAAACAGATAAC
2280570 TACAATGCTTTCTTCTTCTGTCATTTAACCTAGTAATCTCTGT
778 TACAATGCTTTCTTCTTCTGTCATTTAACCTAGTAATCTCTGT
* *
2280613 GGAAATTGATACTTACACAGTTGAATTTTTGCCTATAGACTCATATCAGTCTCCACAAATAGAAG
1 GGAAATTGATACTTACACAGTTGAATTTTTGCCTATAGACTCAGATCAGTCTCCACAAACAGAAG
*
2280678 AATAAACCCTAGAAATCTCTATGAATGCTATTACTGGCTCTATTGGTCATACTACATTGATAATC
66 AAGAAACCCTAGAAATCTCTATGAATGCTATTACTGGCTCTATTGGTCATACTACATTGATAATC
* * *
2280743 TAGGGCTCTATACAAGGAAAATCATTAAATATCCTAATTGATAGT-GTAGT-ACACAGTTTCTTG
131 TAGGGCTATATACAAGGAAAATCATTAAATATCCTAATTGATAGTGGCAATAACACAGTTTCTTG
2280806 GCTCCTAAATGGGCTGATGCTGACATTCAGATTACTACCCCTTATCATTTGGCCATCACTGTGGC
196 GCTCCTAAATGGGCTGATGCTGACATTCAGATTACTACCCCTTATCATTTGGCCATCACTGTGGC
2280871 TAATGGTCAGCAACTATTCAGTACTGCTAGATGCAACCAAGTACAGTGGCAAATGCAGGGACATA
261 TAATGGTCAGCAACTATTCAGTACTGCTAGATGCAACCAAGTACAGTGGCAAATGCAGGGACATA
*
2280936 CATTTTTGCATGATTTTAGATTACTTAAATTGGGTGTGAGTGATATGGTTTTATGATTGGATTGG
326 CATTTTTGCATGATTTTAGATTACTTAAATTGGGTGTGAGTGACATGGTTTTATGATTGGATTGG
*
2281001 ATGAAGTTATTTAGTCCAATATTAATGGACTTCAATAATATGAC-TT-GTTTTGATCATGAAGGA
391 ATGAAGTTATTTAGTCCAATATTAATGGACTTCAACAATATGACTTTAGTTTTGATCATGAAGGA
* *
2281064 AAGCATATTTATATTCAAGGACAGCAGCCCTTAACTGAATTGCAACAAATTTTAGGGGCT-ACAT
456 AAGCATATTTATATTCAAGGACAGCAGCCCTCAACTGAATTGCAACAAATTTCAGGGG-TAACAT
2281128 TATTAAAAA-AGTGCAGGGGATTATGATATTATGAGACATATTGTCCTATTGACTATGGCAGGAA
520 TATTAAAAAGAGTGCAGGGGATTATGATATTATGAGACATATTGTCCTATTGACTATGGCAGGAA
*
2281192 GTTCTTCTTCTATTCCTATGGAACTCCAACATGTATTGGAGAAATACAGCTCAGTCTTTGCTGAA
585 GTTCTTCTTCTATTCCTATGGAACTCCAACATGTATTGGAGAAATACAGCTCAATCTTTGCTGAA
* *
2281257 CCTAAAGGGCTACCTCCTCAGAGGTCTCATGATCATGTCATTCCACTTAAACCTAATGGTACACC
650 CCTAAAGGGCTACCTCCTCAGAGGTCTCATGATCATGCCATTCCACTTAAACCTAATGCTACACC
*
2281322 AGTTAATCTGAGGCCTTATAGATTTCCTCACAATCAGAAGGCTGATGTTGAGAAACAGATAACTA
715 AGTTAATCTGAGGCCTTATAGATTTCCTCACAATCAGAAGGCTAATGTTGAGAAACAGATAACTA
2281387 CAATGCTTTCTTCTTCTGTCATTTAACCTAG
780 CAATGCTTTCTTCTTCTGTCATTTAACCTAG
2281418 AAGAATCCCA
Statistics
Matches: 781, Mismatches: 23, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
815 272 0.35
817 86 0.11
818 1 0.00
819 2 0.00
820 249 0.32
822 3 0.00
823 168 0.22
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (820 bp):
GGAAATTGATACTTACACAGTTGAATTTTTGCCTATAGACTCAGATCAGTCTCCACAAACAGAAG
AAGAAACCCTAGAAATCTCTATGAATGCTATTACTGGCTCTATTGGTCATACTACATTGATAATC
TAGGGCTATATACAAGGAAAATCATTAAATATCCTAATTGATAGTGGCAATAACACAGTTTCTTG
GCTCCTAAATGGGCTGATGCTGACATTCAGATTACTACCCCTTATCATTTGGCCATCACTGTGGC
TAATGGTCAGCAACTATTCAGTACTGCTAGATGCAACCAAGTACAGTGGCAAATGCAGGGACATA
CATTTTTGCATGATTTTAGATTACTTAAATTGGGTGTGAGTGACATGGTTTTATGATTGGATTGG
ATGAAGTTATTTAGTCCAATATTAATGGACTTCAACAATATGACTTTAGTTTTGATCATGAAGGA
AAGCATATTTATATTCAAGGACAGCAGCCCTCAACTGAATTGCAACAAATTTCAGGGGTAACATT
ATTAAAAAGAGTGCAGGGGATTATGATATTATGAGACATATTGTCCTATTGACTATGGCAGGAAG
TTCTTCTTCTATTCCTATGGAACTCCAACATGTATTGGAGAAATACAGCTCAATCTTTGCTGAAC
CTAAAGGGCTACCTCCTCAGAGGTCTCATGATCATGCCATTCCACTTAAACCTAATGCTACACCA
GTTAATCTGAGGCCTTATAGATTTCCTCACAATCAGAAGGCTAATGTTGAGAAACAGATAACTAC
AATGCTTTCTTCTTCTGTCATTTAACCTAGTAATCTCTGT
Found at i:2286636 original size:40 final size:40
Alignment explanation
Indices: 2286581--2286721 Score: 176
Period size: 41 Copynumber: 3.5 Consensus size: 40
2286571 ACTTGAGGCT
* * * *
2286581 TTTGTGTACAAACACCACTAAGGTACGAGTCTATAGCGCG
1 TTTGTATAAAAACACCACTAAAGTACGAATCTATAGCGCG
2286621 TTTGTATAAAAACACCACTAAAGTACGAATCTATAGCGGCG
1 TTTGTATAAAAACACCACTAAAGTACGAATCTATAGC-GCG
* * * * *
2286662 TTTGTATAAAAACGCCACTAAAGTATGAATTTTTAG-ACG
1 TTTGTATAAAAACACCACTAAAGTACGAATCTATAGCGCG
*
2286701 TTTGTATAAAAACGCCACTAA
1 TTTGTATAAAAACACCACTAA
2286722 GGTATGAGTA
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 23 0.25
40 33 0.36
41 35 0.38
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (40 bp):
TTTGTATAAAAACACCACTAAAGTACGAATCTATAGCGCG
Found at i:2286714 original size:39 final size:40
Alignment explanation
Indices: 2286581--2286728 Score: 156
Period size: 40 Copynumber: 3.7 Consensus size: 40
2286571 ACTTGAGGCT
* * * * * *
2286581 TTTGTGTACAAACACCACTAAGGTACGAGTCTATAGCG-CG
1 TTTGTATAAAAACGCCACTAAAGTATGAATCTATA-CGACG
* * *
2286621 TTTGTATAAAAACACCACTAAAGTACGAATCTATAGCGGCG
1 TTTGTATAAAAACGCCACTAAAGTATGAATCTATA-CGACG
* *
2286662 TTTGTATAAAAACGCCACTAAAGTATGAATTTTTA-GACG
1 TTTGTATAAAAACGCCACTAAAGTATGAATCTATACGACG
*
2286701 TTTGTATAAAAACGCCACTAAGGTATGA
1 TTTGTATAAAAACGCCACTAAAGTATGA
2286729 GTATTAAACG
Statistics
Matches: 97, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 30 0.31
40 34 0.35
41 33 0.34
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (40 bp):
TTTGTATAAAAACGCCACTAAAGTATGAATCTATACGACG
Found at i:2287418 original size:43 final size:43
Alignment explanation
Indices: 2287332--2287594 Score: 198
Period size: 43 Copynumber: 6.0 Consensus size: 43
2287322 TGATATTAAG
* * *
2287332 TTTTTCAATCTCACTTTGTACCTTTATAATTGA-ACTCATTATT
1 TTTTTCAATCTCACTTTTTACCTTTATAATTGAGTC-CCTTATT
* *
2287375 TTTTTCAATATCACTTTTTACCTTTATAATTGAGTCCCCTATT
1 TTTTTCAATCTCACTTTTTACCTTTATAATTGAGTCCCTTATT
* * * * * * *
2287418 TTATTCAATCCCATTTTTTA-CTTGTAGAATTTAGGGCCCCTATT
1 TTTTTCAATCTCACTTTTTACCTT-TATAATTGA-GTCCCTTATT
* *
2287462 TTTTGT-AATCTCACTTTTTACCTTTAAAATTGAGGT-TCTTAATT
1 TTTT-TCAATCTCACTTTTTACCTTTATAATTGA-GTCCCTT-ATT
* * * *
2287506 TTTTTTAATTCTCACTTTTTACCTTTATAATCGA-TGCCGTTAAT
1 TTTTTCAA-TCTCACTTTTTACCTTTATAATTGAGT-CCCTTATT
* * *
2287550 TTTTTCAATCAT-ACATTTTACTTTTATAATTTAAG-CCCTTATT
1 TTTTTCAATC-TCACTTTTTACCTTTATAA-TTGAGTCCCTTATT
2287593 TT
1 TT
2287595 AATCATTTTA
Statistics
Matches: 175, Mismatches: 32, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
42 3 0.02
43 88 0.50
44 55 0.31
45 29 0.17
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.51
Consensus pattern (43 bp):
TTTTTCAATCTCACTTTTTACCTTTATAATTGAGTCCCTTATT
Found at i:2287480 original size:44 final size:41
Alignment explanation
Indices: 2287371--2287532 Score: 126
Period size: 44 Copynumber: 3.7 Consensus size: 41
2287361 TTGAACTCAT
* * *
2287371 TATTTTTTTCAATATCACTTTTTACCTTTATAATTGAGTCCCC
1 TATTTTTTT-AATCTCACTTTTTA-CTTTAGAATTGAGGCCCC
* * * *
2287414 TATTTTATTCAATCCCATTTTTTACTTGTAGAATTTAGGGCCCC
1 TATTTT-TTTAATCTCACTTTTTACTT-TAGAATTGA-GGCCCC
* ** *
2287458 TATTTTTTGTAATCTCACTTTTTACCTTTAAAATTGAGGTTCT
1 TATTTTTT-TAATCTCACTTTTTA-CTTTAGAATTGAGGCCCC
2287501 TAATTTTTTTTAATTCTCACTTTTTACCTTTA
1 T-A-TTTTTTTAA-TCTCACTTTTTA-CTTTA
2287533 TAATCGATGC
Statistics
Matches: 96, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
42 3 0.03
43 30 0.31
44 36 0.38
45 27 0.28
ACGTcount: A:0.23, C:0.18, G:0.07, T:0.52
Consensus pattern (41 bp):
TATTTTTTTAATCTCACTTTTTACTTTAGAATTGAGGCCCC
Found at i:2287549 original size:45 final size:44
Alignment explanation
Indices: 2287459--2287554 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 44
2287449 TAGGGCCCCT
* *
2287459 ATTTTTTGTAATCTCACTTTTTACCTTTAAAATTGAGGTTCTTA
1 ATTTTTTGTAATCTCACTTTTTACCTTTAAAATCGAGGTCCTTA
* * *
2287503 ATTTTTTTTAATTCTCACTTTTTACCTTTATAATCGATG-CCGTTA
1 ATTTTTTGTAA-TCTCACTTTTTACCTTTAAAATCGAGGTCC-TTA
2287548 ATTTTTT
1 ATTTTTT
2287555 CAATCATACA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 11 0.24
45 34 0.76
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (44 bp):
ATTTTTTGTAATCTCACTTTTTACCTTTAAAATCGAGGTCCTTA
Found at i:2287581 original size:132 final size:130
Alignment explanation
Indices: 2287338--2287582 Score: 289
Period size: 132 Copynumber: 1.9 Consensus size: 130
2287328 TAAGTTTTTC
*
2287338 AATCTCACTTTGTACCTTTATAATTGAACTCATTATTTTTTTCAATATCACTTTTTACCTTTATA
1 AATCTCACTTTGTACCTTTAAAATTGAACTCATTATTTTTTTCAATATCACTTTTTACCTTTATA
* * **
2287403 ATTGAGTCCCCTATTTTATTCAATCCCATTTTTTACTTGTAGAATTTAGGGCCCCTATTTTTTGT
66 ATCGAGTCCCCTATTTTATTCAATCACACATTTTACTTGTAGAATTTAGGGCCCCTATTTTTTGT
* ** * *
2287468 AATCTCACTTTTTACCTTTAAAATTGAGGTTC-TTAATTTTTTTTAATTCTCACTTTTTACCTTT
1 AATCTCACTTTGTACCTTTAAAATTGA-ACTCATT-ATTTTTTTCAA-TATCACTTTTTACCTTT
** * * *
2287532 ATAATCGA-TGCCGTTAATTTT-TTCAATCATACATTTTACTTTTATAATTTA
63 ATAATCGAGT-CCCCT-ATTTTATTCAATCACACATTTTACTTGTAGAATTTA
2287583 AGCCCTTATT
Statistics
Matches: 95, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
130 27 0.28
131 13 0.14
132 50 0.53
133 5 0.05
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.51
Consensus pattern (130 bp):
AATCTCACTTTGTACCTTTAAAATTGAACTCATTATTTTTTTCAATATCACTTTTTACCTTTATA
ATCGAGTCCCCTATTTTATTCAATCACACATTTTACTTGTAGAATTTAGGGCCCCTATTTTTTGT
Found at i:2288148 original size:21 final size:20
Alignment explanation
Indices: 2288107--2288198 Score: 98
Period size: 20 Copynumber: 4.6 Consensus size: 20
2288097 GATTCTTACT
* *
2288107 ATCGCATTGCGATTTCCTAA
1 ATCGCAATGCGATTTCGTAA
*
2288127 TTCGCAATGCGATTTTCGT-A
1 ATCGCAATGCGA-TTTCGTAA
* *
2288147 ATCGCAATGCGAATTTGGAAA
1 ATCGCAATGCG-ATTTCGTAA
*
2288168 ATCGCAATGCGA-TACGTAA
1 ATCGCAATGCGATTTCGTAA
2288187 ATCGCAATGCGA
1 ATCGCAATGCGA
2288199 ATCTGACTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
19 16 0.27
20 26 0.43
21 18 0.30
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCGATTTCGTAA
Found at i:2288211 original size:39 final size:40
Alignment explanation
Indices: 2288128--2288223 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 40
2288118 ATTTCCTAAT
* *
2288128 TCGCAATGCGATTTTCGTAATCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGA-TTACGTAATCGCAATGCGAATCTGGAAAA
**
2288169 TCGCAATGCGA-TACGTAAATCGCAATGCGAATCT-GACTA
1 TCGCAATGCGATTACGT-AATCGCAATGCGAATCTGGAAAA
2288208 TCGCAATGCGACTTAC
1 TCGCAATGCGA-TTAC
2288224 ATAGCGCCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
39 18 0.38
40 16 0.33
41 14 0.29
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (40 bp):
TCGCAATGCGATTACGTAATCGCAATGCGAATCTGGAAAA
Found at i:2288811 original size:20 final size:20
Alignment explanation
Indices: 2288786--2288834 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2288776 CAACGAGTGA
2288786 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
2288806 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
2288826 ATCGCAACG
1 ATCGCAACG
2288835 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2288917 original size:20 final size:20
Alignment explanation
Indices: 2288847--2288933 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 20
2288837 AGAATCGCAA
*
2288847 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGTGT
** **
2288866 TGCGATAGTCAAATTCGTGT
1 TGCGATTTTCATTTTCGTGT
* ** *
2288886 TGTGATAGTCATTTTTGTGT
1 TGCGATTTTCATTTTCGTGT
2288906 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
*
2288926 TGTGATTT
1 TGCGATTT
2288934 AAAGTTTCAG
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
19 9 0.17
20 45 0.83
ACGTcount: A:0.15, C:0.13, G:0.23, T:0.49
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGTGT
Found at i:2290826 original size:20 final size:20
Alignment explanation
Indices: 2290801--2290904 Score: 139
Period size: 20 Copynumber: 5.5 Consensus size: 20
2290791 AGAATAGTTT
2290801 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2290821 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
2290837 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
2290855 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
2290875 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
2290895 ACTATCGCAA
1 ACTATCGCAA
2290905 CGAAAGAATC
Statistics
Matches: 74, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
14 7 0.09
16 4 0.05
17 4 0.05
18 4 0.05
20 55 0.74
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:2290847 original size:34 final size:34
Alignment explanation
Indices: 2290804--2290925 Score: 163
Period size: 34 Copynumber: 3.4 Consensus size: 34
2290794 ATAGTTTACT
*
2290804 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
2290838 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
**
2290876 CTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
2290912 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
2290926 TGAAAATCGC
Statistics
Matches: 78, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
34 40 0.51
36 4 0.05
37 5 0.06
38 4 0.05
40 25 0.32
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.18
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:2290922 original size:74 final size:73
Alignment explanation
Indices: 2290801--2290942 Score: 221
Period size: 74 Copynumber: 1.9 Consensus size: 73
2290791 AGAATAGTTT
* **
2290801 ACTATCGCAATGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCGAAAATGACTATCGCAAT
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG-AAATGAAAATCGCAAT
2290866 GCGAAAATG
65 GCGAAAATG
** *
2290875 ACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCATTG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATG
2290940 CGA
66 CGA
2290943 TTCTCTCGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 17 0.27
74 45 0.73
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.19
Consensus pattern (73 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATG
CGAAAATG
Found at i:2290976 original size:20 final size:20
Alignment explanation
Indices: 2290951--2290997 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2290941 GATTCTCTCG
2290951 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
2290971 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
2290991 TTGCGAT
1 TTGCGAT
2290998 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:2291028 original size:33 final size:34
Alignment explanation
Indices: 2290971--2291064 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
2290961 CAAATTCGCA
* * *
2290971 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
** *
2291005 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
2291038 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCGTTGCGAT
2291065 AGTCATTTGC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 27 0.54
34 23 0.46
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
Found at i:2291590 original size:18 final size:19
Alignment explanation
Indices: 2291551--2291592 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
2291541 CTCACCTGTC
2291551 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
2291572 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
2291590 ATC
1 ATC
2291593 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:2291646 original size:42 final size:42
Alignment explanation
Indices: 2291576--2291667 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
2291566 TCCCCTATCG
* * *
2291576 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCA
1 TTCAAGAGGCCACTATCATCCCTAAAGAGGT-CCCTCCCAACA
* **
2291618 TTCAAGAGGCCACTGTCATCGTTAAAGAGGTCCCTCCCAACA
1 TTCAAGAGGCCACTATCATCCCTAAAGAGGTCCCTCCCAACA
*
2291660 TTCTAGAG
1 TTCAAGAG
2291668 CCTGATTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTAAAGAGGTCCCTCCCAACA
Found at i:2293027 original size:14 final size:14
Alignment explanation
Indices: 2293008--2293043 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2292998 ATTGTTTAAT
2293008 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2293022 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2293036 TGATTTGT
1 TGATTTGT
2293044 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2293189 original size:33 final size:33
Alignment explanation
Indices: 2293144--2293238 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
2293134 CAAAAAGACT
* ** *
2293144 ATCGCAACGCGAAATGACTATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2293177 ATCGCAATGCGAAATGAAAATCGCAATGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2293210 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
2293239 CGAAACTAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 38 0.70
34 16 0.30
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2293234 original size:20 final size:19
Alignment explanation
Indices: 2293176--2293243 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
2293166 GTAACGAGAG
2293176 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2293195 AATCGCAAT--G-AGTG--
1 AATCGCAATGCGAAATGAA
2293209 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
2293229 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
2293244 CTAATTTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 9 0.22
16 4 0.10
17 1 0.03
18 3 0.08
19 12 0.30
20 11 0.28
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2293298 original size:34 final size:34
Alignment explanation
Indices: 2293255--2293348 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
2293245 TAATTTCGCG
2293255 TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
* **
2293289 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTTG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
** * *
2293322 TTGCGATAGTCATTTCCGCTTTGCGAT
1 TTGCGATTTTCATTTTCGCATTGCGAT
2293349 AGTCAATTCC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 28 0.54
34 24 0.46
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
Found at i:2293347 original size:20 final size:20
Alignment explanation
Indices: 2293322--2293389 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
2293312 GATTCTCTTG
2293322 TTGCGATAGTCATTTCCGCT
1 TTGCGATAGTCATTTCCGCT
* *
2293342 TTGCGATAGTCAATTCCGCA
1 TTGCGATAGTCATTTCCGCT
2293362 TTGCGATAGTCATTTCCG-T
1 TTGCGATAGTCATTTCCGCT
2293381 GTTGCGATA
1 -TTGCGATA
2293390 TAGTCATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCT
Found at i:2293673 original size:140 final size:140
Alignment explanation
Indices: 2293418--2293685 Score: 500
Period size: 140 Copynumber: 1.9 Consensus size: 140
2293408 GATTTCCGCA
*
2293418 TTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTGAACATATCATAGCAATGTTCAAAC
1 TTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTGAACAGATCATAGCAATGTTCAAAC
2293483 TCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATACACATAATAGT
66 TCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATACACATAATAGT
2293548 CAAATTCACG
131 CAAATTCACG
* *
2293558 TTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGCAATGTTCAAAC
1 TTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTGAACAGATCATAGCAATGTTCAAAC
*
2293623 TCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACATATAAAATACACATAATA
66 TCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATACACATAATA
2293686 CAACGTTTGC
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.28
Consensus pattern (140 bp):
TTGCGATAGTCAAATGAATGTCTAATAAGTGATAACAACTGAACAGATCATAGCAATGTTCAAAC
TCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATACACATAATAGT
CAAATTCACG
Found at i:2293766 original size:18 final size:18
Alignment explanation
Indices: 2293743--2293777 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2293733 AAGCCGGTTG
*
2293743 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2293761 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
2293778 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2296038 original size:24 final size:24
Alignment explanation
Indices: 2296004--2296057 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2295994 CTGAAAAATC
2296004 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2296028 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2296052 ATCAAA
1 ATCAAA
2296058 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2296071 original size:24 final size:24
Alignment explanation
Indices: 2296004--2296071 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2295994 CTGAAAAATC
* * *
2296004 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2296028 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2296052 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2296072 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2296942 original size:20 final size:20
Alignment explanation
Indices: 2296919--2297026 Score: 108
Period size: 20 Copynumber: 5.3 Consensus size: 20
2296909 CAGAATCTCG
2296919 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
2296939 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** * *
2296959 TTGCGATTTTCCAAATCCGCG
1 TTGCGA-TTTACGTATTCGCA
* ** *
2296980 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
2297001 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
2297021 TTGCGA
1 TTGCGA
2297027 ATTAGGAAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
20 41 0.55
21 34 0.45
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:2296985 original size:21 final size:21
Alignment explanation
Indices: 2296959--2297009 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
2296949 CGTAATCGCA
2296959 TTGCGATTTTCCAAATCCGCG
1 TTGCGATTTTCCAAATCCGCG
*
2296980 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATCCGCG
2297001 TTGCGATTT
1 TTGCGATTT
2297010 ACGTATTCGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.39
Consensus pattern (21 bp):
TTGCGATTTTCCAAATCCGCG
Found at i:2300163 original size:20 final size:19
Alignment explanation
Indices: 2300140--2300196 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
2300130 TTAATATTAA
2300140 ATATATATTAATAATTTACT
1 ATATATATTAA-AATTTACT
* *
2300160 ATATATTATTAAATTTTATT
1 ATATA-TATTAAAATTTACT
2300180 ATATATATTAAATATTT
1 ATATATATTAAA-ATTT
2300197 TAATAGTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 7 0.22
20 19 0.59
21 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATATATTAAAATTTACT
Found at i:2300182 original size:18 final size:18
Alignment explanation
Indices: 2300161--2300213 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2300151 TAATTTACTA
2300161 TATATTATTAAAT-TTTAT
1 TATATTATTAAATATTT-T
2300179 TATATATATTAAATATTTT
1 TATAT-TATTAAATATTTT
* *
2300198 AATAGTATTAAATATT
1 TATATTATTAAATATT
2300214 AAACAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 16 0.52
19 12 0.39
20 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TATATTATTAAATATTTT
Found at i:2300273 original size:22 final size:22
Alignment explanation
Indices: 2300235--2300276 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2300225 TTTTTATACA
*
2300235 AATATTAAATATTTTAATAAAT
1 AATATTAAATATATTAATAAAT
2300257 AATA-TAAATTATATTAATAA
1 AATATTAAA-TATATTAATAA
2300277 TTTATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATTAAATATATTAATAAAT
Done.