Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009350.1 Hibiscus syriacus cultivar Beakdansim tig00113145_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: 2139524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1859704 original size:22 final size:21
Alignment explanation
Indices: 1859673--1859713 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1859663 CCAATCAGTT
*
1859673 TTGGTATATTGGATTGGTTTA
1 TTGGTATATTAGATTGGTTTA
1859694 TTGGTGATATTAGATTGGTT
1 TTGGT-ATATTAGATTGGTT
1859714 CTTAGGTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (21 bp):
TTGGTATATTAGATTGGTTTA
Found at i:1859721 original size:22 final size:22
Alignment explanation
Indices: 1859678--1859721 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1859668 CAGTTTTGGT
* *
1859678 ATATTGGATTGGTTTATTGGTG
1 ATATTAGATTGGTTTATAGGTG
1859700 ATATTAGATTGGTTCT-TAGGTG
1 ATATTAGATTGGTT-TATAGGTG
1859722 TAATTGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.48
Consensus pattern (22 bp):
ATATTAGATTGGTTTATAGGTG
Found at i:1862394 original size:13 final size:13
Alignment explanation
Indices: 1862352--1862386 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1862342 CTATGACGCA
* *
1862352 CATTTATGAAAAG
1 CATTTATGACACG
1862365 CATTTATGACACG
1 CATTTATGACACG
1862378 CATTTATGA
1 CATTTATGA
1862387 TGCGCATTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (13 bp):
CATTTATGACACG
Found at i:1862571 original size:2 final size:2
Alignment explanation
Indices: 1862564--1862604 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1862554 TGTCGTAAAT
1862564 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1862605 TGTAGATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1864094 original size:27 final size:27
Alignment explanation
Indices: 1864056--1864110 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1864046 TAGCATGAAT
1864056 TGTTTTCCCCTCGTCCAACTTCTTGGA
1 TGTTTTCCCCTCGTCCAACTTCTTGGA
1864083 TGTTTTCCCCTCGTCCAACTTCTTGGA
1 TGTTTTCCCCTCGTCCAACTTCTTGGA
1864110 T
1 T
1864111 TTCTTACTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.11, C:0.33, G:0.15, T:0.42
Consensus pattern (27 bp):
TGTTTTCCCCTCGTCCAACTTCTTGGA
Found at i:1866254 original size:28 final size:28
Alignment explanation
Indices: 1866191--1866255 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
1866181 ATATGTAACC
**
1866191 TTTGTATTAATAATCTATTATTTTGATA
1 TTTGTATTTTTAATCTATTATTTTGATA
*
1866219 TTTTTATTTTTAATC-ATTATTTT-ATA
1 TTTGTATTTTTAATCTATTATTTTGATA
1866245 TATATGTATTT
1 T-T-TGTATTT
1866256 AAGTTATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 4 0.13
27 9 0.29
28 18 0.58
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (28 bp):
TTTGTATTTTTAATCTATTATTTTGATA
Found at i:1868825 original size:23 final size:25
Alignment explanation
Indices: 1868799--1868852 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
1868789 AAATCCAGCA
*
1868799 AAGAAAAAT-AAAGCACTC-AAATG
1 AAGAAAAATGAAAGCACTCAAAAAG
*
1868822 AAG-AAATTGAAAGCACTCAAAAAG
1 AAGAAAAATGAAAGCACTCAAAAAG
1868846 AAGAAAA
1 AAGAAAA
1868853 GCAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 4 0.15
23 12 0.46
24 7 0.27
25 3 0.12
ACGTcount: A:0.63, C:0.11, G:0.15, T:0.11
Consensus pattern (25 bp):
AAGAAAAATGAAAGCACTCAAAAAG
Found at i:1870640 original size:43 final size:43
Alignment explanation
Indices: 1870592--1870881 Score: 381
Period size: 43 Copynumber: 6.8 Consensus size: 43
1870582 AACAAAAAAT
* *
1870592 GCCGCAAAAGGTCGAGATATATAGCGACATTTTTGGAACAAAC
1 GCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTGGAACAAAC
* *
1870635 GCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATCAAAC
1 GCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTGGAACAAAC
* * *
1870678 GCCGCAAAAGGTCGAGATTTATAGCAGCATTTTTGGAAAAAAC
1 GCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTGGAACAAAC
* *
1870721 GTCGCAAAAGGTCGAGATCTATAGCGGC-GTTTTGGAACAAAC
1 GCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTGGAACAAAC
* * *
1870763 GCCGCTAAAA-GTCGAGATTTATAGCGGCGTTTTTGGAACAAAT
1 GCCGC-AAAAGGTCGAGATCTATAGCGGCATTTTTGGAACAAAC
* * * * *
1870806 GCCACAAAAGTTC-ATATCTATAGTGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTGGAACAAAC
1870848 GCCGCAAAAGGTCGAGAAT-TATAGCGGCATTTTT
1 GCCGCAAAAGGTCGAG-ATCTATAGCGGCATTTTT
1870882 CTATACAAAC
Statistics
Matches: 213, Mismatches: 29, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
42 73 0.34
43 138 0.65
44 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (43 bp):
GCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTGGAACAAAC
Found at i:1870814 original size:85 final size:86
Alignment explanation
Indices: 1870592--1870881 Score: 433
Period size: 85 Copynumber: 3.4 Consensus size: 86
1870582 AACAAAAAAT
* *
1870592 GCCGCAAAAGGTCGAGATATATAGCGACATTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTAT
1 GCCGCAAAAGGTCGAGATTTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTAT
*
1870657 AGCGGCGTTTTTGGATCAAAC
66 AGCGGCGTTTTTGGAACAAAC
* * *
1870678 GCCGCAAAAGGTCGAGATTTATAGCAGCATTTTTGGAAAAAACGTCGCAAAAGGTCGAGATCTAT
1 GCCGCAAAAGGTCGAGATTTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTAT
1870743 AGCGGCG-TTTTGGAACAAAC
66 AGCGGCGTTTTTGGAACAAAC
* * * * *
1870763 GCCGCTAAAA-GTCGAGATTTATAGCGGCGTTTTTGGAACAAATGCCACAAAAGTTC-ATATCTA
1 GCCGC-AAAAGGTCGAGATTTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTA
*
1870826 TAGTGGCGTTTTTGGAACAAAC
65 TAGCGGCGTTTTTGGAACAAAC
*
1870848 GCCGCAAAAGGTCGAGAATTATAGCGGCATTTTT
1 GCCGCAAAAGGTCGAGATTTATAGCGGCATTTTT
1870882 CTATACAAAC
Statistics
Matches: 184, Mismatches: 17, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
84 17 0.09
85 96 0.52
86 71 0.39
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (86 bp):
GCCGCAAAAGGTCGAGATTTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTAT
AGCGGCGTTTTTGGAACAAAC
Found at i:1871040 original size:21 final size:21
Alignment explanation
Indices: 1871016--1871076 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
1871006 TAATTAAGAC
1871016 ACAAACTTGAAATCCATAACA
1 ACAAACTTGAAATCCATAACA
1871037 ACAAACTTGAAATCCATAACA
1 ACAAACTTGAAATCCATAACA
*
1871058 AGAAACTTGAAATCCATAA
1 ACAAACTTGAAATCCATAA
1871077 TAATAAATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.20
Consensus pattern (21 bp):
ACAAACTTGAAATCCATAACA
Found at i:1874994 original size:41 final size:39
Alignment explanation
Indices: 1874926--1875213 Score: 135
Period size: 41 Copynumber: 7.0 Consensus size: 39
1874916 TAAACGCTAA
* *
1874926 TAAAGTACT-AGGTTTTAGCGGCATTTTTCTAAAATCGTCAC
1 TAAAGTA-TGAGGTTTTAGCGGCGTTTTT-TAAAAT-GCCAC
*
1874967 TAAAGTATGA-GTATTTAACGGCGTTTTTGAATAAAATGCCAC
1 TAAAGTATGAGGT-TTTAGCGGCGTTTTT---TAAAATGCCAC
* * *
1875009 TAAAGTATTAGGTTTTAGCGGCGTTTATTTAAAAACGCAAC
1 TAAAGTATGAGGTTTTAGCGGCGTTT-TTT-AAAATGCCAC
* ** *
1875050 GATATA-TAT-ACCCTATT-GCGGCGTTTGTTTAAAAATGCCAC
1 --TAAAGTATGA-GGTTTTAGCGGCGTTT-TTT-AAAATGCCAC
* * *
1875091 TAAAGAATGA--TTCTATGGCGGCGTTTGTTTACAAACGCCAC
1 TAAAGTATGAGGTT-T-TAGCGGCGTTT-TTTA-AAATGCCAC
* * *
1875132 TAAAGTA-CAAGTTTTAGCGGCGTTTTTGCATAAAATGCCTC
1 TAAAGTATGAGGTTTTAGCGGCGTTTTT---TAAAATGCCAC
* *
1875173 TAAAGTACT-AGGTTTTAGCTGCGTTTATCTAAAAATGCCAC
1 TAAAGTA-TGAGGTTTTAGCGGCGTTT-T-TTAAAATGCCAC
1875214 AATATATGTA
Statistics
Matches: 194, Mismatches: 28, Indels: 50
0.71 0.10 0.18
Matches are distributed among these distances:
38 1 0.01
39 6 0.03
40 19 0.10
41 103 0.53
42 50 0.26
43 14 0.07
44 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (39 bp):
TAAAGTATGAGGTTTTAGCGGCGTTTTTTAAAATGCCAC
Found at i:1875113 original size:82 final size:81
Alignment explanation
Indices: 1875026--1875288 Score: 234
Period size: 82 Copynumber: 3.2 Consensus size: 81
1875016 TTAGGTTTTA
* *
1875026 GCGGCGTTTATTTAAAAACGCAACGATATATATACCCTATTGCGGCGTTTGTTTAAAAATGCCAC
1 GCGGCGTTTATTTAAAAACGCCAC-ATATATATACCCTATTGCGGCGTTTGTTCAAAAATGCCAC
1875091 TAAAGAATGATTCTATG
65 TAAAGAATGATTCTATG
* * ** *
1875108 GCGGCGTTTGTTTACAAACGCCAC-TA-A-AGTACAAGTTTTAGCGGCGTTT-TTGCATAAAATG
1 GCGGCGTTTATTTAAAAACGCCACATATATA-TAC-CCTATT-GCGGCGTTTGTT-CA-AAAATG
* * * *
1875169 CCTCTAAAGTACTAGGTT-T-TA
61 CCACTAAAG-AAT-GATTCTATG
* * * * *
1875190 GCTGCGTTTATCTAAAAATGCCACAATATATGTACCCTATTGCGGCGTTTGTTCAAAAACGCCAC
1 GCGGCGTTTATTTAAAAACGCCAC-ATATATATACCCTATTGCGGCGTTTGTTCAAAAATGCCAC
*
1875255 TAAAGAACGATTCTATG
65 TAAAGAATGATTCTATG
*
1875272 GCGGCGTTT-TTAAAAAA
1 GCGGCGTTTATTTAAAAA
1875289 AACGCCGCTA
Statistics
Matches: 138, Mismatches: 29, Indels: 29
0.70 0.15 0.15
Matches are distributed among these distances:
78 1 0.01
79 4 0.03
80 10 0.07
81 18 0.13
82 77 0.56
83 14 0.10
84 10 0.07
85 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (81 bp):
GCGGCGTTTATTTAAAAACGCCACATATATATACCCTATTGCGGCGTTTGTTCAAAAATGCCACT
AAAGAATGATTCTATG
Found at i:1875256 original size:164 final size:165
Alignment explanation
Indices: 1874964--1875363 Score: 504
Period size: 164 Copynumber: 2.4 Consensus size: 165
1874954 CTAAAATCGT
** *
1874964 CACTAAAGTATGAGTATTTAACGGCGTTTTTGAATAAAATGCCACTAAAGTATTAGGTTTTAGCG
1 CACTAAAGTACAAGTATTTAACGGCGTTTTTGAATAAAATGCCACTAAAGTACTAGGTTTTAGCG
* * * *
1875029 GCGTTTATTTAAAAACGCAACGATATATATACCCTATTGCGGCGTTTGTTTAAAAATGCCACTAA
66 GCGTTTATCTAAAAACGCAACAATATATATACCCTATTGCGGCGTTTGTTCAAAAACGCCACTAA
*
1875094 AGAATGATTCTATGGCGGCGTTTGTTTACAAACGC
131 AGAACGATTCTATGGCGGCGTTTGTTTACAAACGC
* * * *
1875129 CACTAAAGTACAAGT-TTTAGCGGCGTTTTTGCATAAAATGCCTCTAAAGTACTAGGTTTTAGCT
1 CACTAAAGTACAAGTATTTAACGGCGTTTTTGAATAAAATGCCACTAAAGTACTAGGTTTTAGCG
* * *
1875193 GCGTTTATCTAAAAATGCCACAATATATGTACCCTATTGCGGCGTTTGTTCAAAAACGCCACTAA
66 GCGTTTATCTAAAAACGCAACAATATATATACCCTATTGCGGCGTTTGTTCAAAAACGCCACTAA
* *
1875258 AGAACGATTCTATGGCGGCGTTT-TTAAAAAAAACGC
131 AGAACGATTCTATGGCGGCGTTTGTT--TACAAACGC
* * * * * * * *
1875294 CGCTAAAGTACTTA-TCTTTAGCGGCGCTTGTCGAAT-AAACGCCACTAAAGTACGA-GTTTTAG
1 CACTAAAGTAC-AAGTATTTAACGGCG-TTTTTGAATAAAATGCCACTAAAGTACTAGGTTTTAG
1875356 CGGCGTTT
64 CGGCGTTT
1875364 GTTGAAAAAC
Statistics
Matches: 204, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
163 2 0.01
164 124 0.61
165 45 0.22
166 27 0.13
167 6 0.03
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (165 bp):
CACTAAAGTACAAGTATTTAACGGCGTTTTTGAATAAAATGCCACTAAAGTACTAGGTTTTAGCG
GCGTTTATCTAAAAACGCAACAATATATATACCCTATTGCGGCGTTTGTTCAAAAACGCCACTAA
AGAACGATTCTATGGCGGCGTTTGTTTACAAACGC
Found at i:1875276 original size:41 final size:41
Alignment explanation
Indices: 1875062--1875376 Score: 170
Period size: 41 Copynumber: 7.7 Consensus size: 41
1875052 TATATATACC
* * * * *
1875062 CTATTGCGGCGTTTGTTTAAAAATGCCACTAAAGAATGATT
1 CTATAGCGGCGTTTGTTCAAAAACGCCACTAAAGTACGATT
* * * *
1875103 CTATGGCGGCGTTTGTTTACAAACGCCACTAAAGTACAAGTT
1 CTATAGCGGCGTTTGTTCAAAAACGCCACTAAAGTACGA-TT
* * *
1875145 -T-TAGCGGCGTTT-TTGCATAAAATGCCTCTAAAGTACTAGGTT
1 CTATAGCGGCGTTTGTT-CA-AAAACGCCACTAAAGTAC--GATT
* * * * **
1875187 -T-TAGCTGCGTTT-ATCTAAAAATGCCAC-AATA-TATGTACC
1 CTATAGCGGCGTTTGTTC-AAAAACGCCACTAA-AGTACG-ATT
* *
1875226 CTATTGCGGCGTTTGTTCAAAAACGCCACTAAAGAACGATT
1 CTATAGCGGCGTTTGTTCAAAAACGCCACTAAAGTACGATT
* * * *
1875267 CTATGGCGGCGTTT-TTAAAAAAAACGCCGCTAAAGTAC-TTAT
1 CTATAGCGGCGTTTGTT--CAAAAACGCCACTAAAGTACGAT-T
* *
1875309 CTTTAGCGGCGCTTG-TCGAATAAACGCCACTAAAGTACGAGTT
1 CTATAGCGGCGTTTGTTC-AA-AAACGCCACTAAAGTACGA-TT
*
1875352 -T-TAGCGGCGTTTGTTGAAAAACGCC
1 CTATAGCGGCGTTTGTTCAAAAACGCC
1875377 GTTAATGTTA
Statistics
Matches: 211, Mismatches: 41, Indels: 45
0.71 0.14 0.15
Matches are distributed among these distances:
38 1 0.00
39 2 0.01
40 25 0.12
41 110 0.52
42 71 0.34
43 1 0.00
44 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (41 bp):
CTATAGCGGCGTTTGTTCAAAAACGCCACTAAAGTACGATT
Found at i:1875318 original size:42 final size:41
Alignment explanation
Indices: 1875123--1875372 Score: 118
Period size: 42 Copynumber: 6.0 Consensus size: 41
1875113 GTTTGTTTAC
* ** *
1875123 AAACGCCACTAAAGTACAAGTTTTAGCGGCGTTTTTGCATA
1 AAACGCCACTAAAGTACGAGTTTTAGCGGCGTTTTTAAAAA
* * * * * **
1875164 AAATGCCTCTAAAGTACTAGGTTTTAGCTGCGTTTAT-CTAA
1 AAACGCCACTAAAGTACGA-GTTTTAGCGGCGTTTTTAAAAA
* * ** * *
1875205 AAATGCCACAATATATGTAC-CCTATT-GCGGCGTTTGTT--CAA
1 AAACGCCAC--TA-AAGTACGAGTTTTAGCGGCGTTT-TTAAAAA
* *
1875246 AAACGCCACTAAAGAACGA-TTCTATGGCGGCGTTTTTAAAAA
1 AAACGCCACTAAAGTACGAGTT-T-TAGCGGCGTTTTTAAAAA
* * * * ** *
1875288 AAACGCCGCTAAAGTACTTA-TCTTTAGCGGCGCTTGTCGAAT
1 AAACGCCACTAAAGTAC-GAGT-TTTAGCGGCGTTTTTAAAAA
*
1875330 AAACGCCACTAAAGTACGAGTTTTAGCGGCGTTTGTTGAAAA
1 AAACGCCACTAAAGTACGAGTTTTAGCGGCGTTT-TTAAAAA
1875372 A
1 A
1875373 CGCCGTTAAT
Statistics
Matches: 157, Mismatches: 37, Indels: 29
0.70 0.17 0.13
Matches are distributed among these distances:
38 5 0.03
39 3 0.02
40 3 0.02
41 66 0.42
42 69 0.44
43 5 0.03
44 6 0.04
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTTTTAGCGGCGTTTTTAAAAA
Found at i:1884868 original size:3 final size:3
Alignment explanation
Indices: 1884860--1885023 Score: 97
Period size: 3 Copynumber: 54.0 Consensus size: 3
1884850 TTTTTGTCTG
*
1884860 TTA TTA TTAA TTA TATA TTA TTA TTA TTA -TA TTA TTA TATA TAA TTA
1 TTA TTA TT-A TTA T-TA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* * * * * * *
1884907 TTA -TA TGA -TA TTA TCA -CA TTA TTA TTA TTA TTA TTG TTG TTG TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
1884952 TTGT TTG TTG TTG TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA
1 TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
1884998 TTTA TTA -TA TATA ATA TATA TTA TTA
1 -TTA TTA TTA T-TA TTA T-TA TTA TTA
1885024 AATTATATTT
Statistics
Matches: 135, Mismatches: 12, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
2 11 0.08
3 103 0.76
4 20 0.15
5 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1885022 original size:35 final size:34
Alignment explanation
Indices: 1884965--1885031 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
1884955 TTTGTTGTTG
* *
1884965 TTATTATTATTATTATTATTATTATATTATATAT
1 TTATTATTATAATTATTATTATTAAATTATATAT
1884999 TTATTATATATAA-TATATATTATTAAATTATAT
1 TTATTAT-TATAATTAT-TATTATTAAATTATAT
1885032 TTGCATTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 10 0.34
35 19 0.66
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TTATTATTATAATTATTATTATTAAATTATATAT
Found at i:1885841 original size:16 final size:17
Alignment explanation
Indices: 1885820--1885852 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1885810 GGTAAATTAG
1885820 GATTT-GATTTAGGGTA
1 GATTTGGATTTAGGGTA
*
1885836 GATTTGGCTTTAGGGTA
1 GATTTGGATTTAGGGTA
1885853 AATTAGGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.21, C:0.03, G:0.33, T:0.42
Consensus pattern (17 bp):
GATTTGGATTTAGGGTA
Found at i:1885849 original size:17 final size:17
Alignment explanation
Indices: 1885827--1885863 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1885817 TAGGATTTGA
* *
1885827 TTTAGGGTAGATTTGGC
1 TTTAGGGTAAATTAGGC
1885844 TTTAGGGTAAATTAGGC
1 TTTAGGGTAAATTAGGC
1885861 TTT
1 TTT
1885864 TATTTAGGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.05, G:0.30, T:0.43
Consensus pattern (17 bp):
TTTAGGGTAAATTAGGC
Found at i:1893038 original size:4 final size:4
Alignment explanation
Indices: 1893002--1893174 Score: 274
Period size: 4 Copynumber: 43.2 Consensus size: 4
1892992 GGATAAAATG
* * * *
1893002 GTAT GTAT GCAT ATAT GTAT ATAT GTTT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
1893050 GTAT ATAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1893098 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
1893146 GTAT GTAT GTAT GTAT ATAT GCAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1893175 CATACATACA
Statistics
Matches: 153, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 153 1.00
ACGTcount: A:0.27, C:0.02, G:0.23, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:1893175 original size:8 final size:8
Alignment explanation
Indices: 1893032--1893383 Score: 184
Period size: 8 Copynumber: 43.5 Consensus size: 8
1893022 ATATGTTTGT
*
1893032 ATGTATGT
1 ATGTATGC
*
1893040 ATGTATGT
1 ATGTATGC
**
1893048 ATGTATAT
1 ATGTATGC
1893056 ATGTATGC
1 ATGTATGC
*
1893064 ATGTATGT
1 ATGTATGC
*
1893072 ATGTATGT
1 ATGTATGC
*
1893080 ATGTATGT
1 ATGTATGC
*
1893088 ATGTATGT
1 ATGTATGC
*
1893096 ATGTATGT
1 ATGTATGC
*
1893104 ATGTATGT
1 ATGTATGC
*
1893112 ATGTATGT
1 ATGTATGC
*
1893120 ATGTATGT
1 ATGTATGC
*
1893128 ATGTATGT
1 ATGTATGC
*
1893136 ATGTATGT
1 ATGTATGC
*
1893144 ATGTATGT
1 ATGTATGC
*
1893152 ATGTATGT
1 ATGTATGC
*
1893160 ATATATGC
1 ATGTATGC
1893168 ATGTATGC
1 ATGTATGC
** *
1893176 ATACATAC
1 ATGTATGC
* *
1893184 ATATATAC
1 ATGTATGC
1893192 ATGCATACATGC
1 ATG--T--ATGC
**
1893204 ATACATGC
1 ATGTATGC
**
1893212 ATACATGC
1 ATGTATGC
**
1893220 ATACATGC
1 ATGTATGC
1893228 AT-TCATGC
1 ATGT-ATGC
**
1893236 ATACATGC
1 ATGTATGC
* *
1893244 ATGCATCC
1 ATGTATGC
**
1893252 ATACATGC
1 ATGTATGC
*
1893260 ATGCATGC
1 ATGTATGC
** *
1893268 ATACATAC
1 ATGTATGC
*
1893276 ATGCATGC
1 ATGTATGC
** *
1893284 ATACATCC
1 ATGTATGC
* *
1893292 ATGCATGT
1 ATGTATGC
1893300 ATGTATGC
1 ATGTATGC
*
1893308 ATGTATGG
1 ATGTATGC
*
1893316 ATGCATGC
1 ATGTATGC
1893324 ATGTATGC
1 ATGTATGC
*
1893332 ATGAATGC
1 ATGTATGC
1893340 ATGTATGC
1 ATGTATGC
**
1893348 ATGTATAT
1 ATGTATGC
*
1893356 ATGTATGT
1 ATGTATGC
*
1893364 ATGTATGT
1 ATGTATGC
*
1893372 ATGTATGT
1 ATGTATGC
1893380 ATGT
1 ATGT
1893384 GTGTGTATAT
Statistics
Matches: 296, Mismatches: 42, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
8 290 0.98
10 1 0.00
12 5 0.02
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (8 bp):
ATGTATGC
Found at i:1893191 original size:12 final size:12
Alignment explanation
Indices: 1893175--1893289 Score: 86
Period size: 12 Copynumber: 9.6 Consensus size: 12
1893165 TGCATGTATG
1893175 CATACATACATA
1 CATACATACATA
* *
1893187 TATACATGCATA
1 CATACATACATA
* *
1893199 CATGCATACATG
1 CATACATACATA
*
1893211 CATACATGCATA
1 CATACATACATA
* * *
1893223 CATGCATTCATG
1 CATACATACATA
* *
1893235 CATACATGCATG
1 CATACATACATA
* *
1893247 CATCCATACATG
1 CATACATACATA
* *
1893259 CATGCATGCATA
1 CATACATACATA
* *
1893271 CATACATGCATG
1 CATACATACATA
1893283 CATACAT
1 CATACAT
1893290 CCATGCATGT
Statistics
Matches: 82, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 82 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (12 bp):
CATACATACATA
Found at i:1893364 original size:4 final size:4
Alignment explanation
Indices: 1893296--1893383 Score: 95
Period size: 4 Copynumber: 22.0 Consensus size: 4
1893286 ACATCCATGC
* * * * * * *
1893296 ATGT ATGT ATGC ATGT ATGG ATGC ATGC ATGT ATGC ATGA ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
1893344 ATGC ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1893384 GTGTGTATAT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 71 1.00
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (4 bp):
ATGT
Found at i:1894907 original size:26 final size:26
Alignment explanation
Indices: 1894836--1894910 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
1894826 TGGCTGCAAC
* *
1894836 AAAGATAAGAAAAGGAAGATG-ATTAAT
1 AAAGATAAG-AAATGAA-ATGAAATAAT
*
1894863 AAAG-GAAG-AAT-AAATGAAATAAT
1 AAAGATAAGAAATGAAATGAAATAAT
1894886 AAAGATAAGAAATGAAATGAAATAA
1 AAAGATAAGAAATGAAATGAAATAA
1894911 AGAAGGGATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 3 0.08
23 11 0.28
24 5 0.12
25 3 0.08
26 14 0.35
27 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (26 bp):
AAAGATAAGAAATGAAATGAAATAAT
Found at i:1894979 original size:17 final size:18
Alignment explanation
Indices: 1894948--1894981 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1894938 ATTGGTCTTG
*
1894948 ATGGATGATGTTGATGAA
1 ATGGATGATGGTGATGAA
1894966 ATGGA-GATGGTGATGA
1 ATGGATGATGGTGATGA
1894982 TGTTGTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (18 bp):
ATGGATGATGGTGATGAA
Found at i:1898877 original size:9 final size:9
Alignment explanation
Indices: 1898863--1898919 Score: 53
Period size: 10 Copynumber: 6.0 Consensus size: 9
1898853 TCTTTTTGAA
1898863 TTTCTTTTT
1 TTTCTTTTT
1898872 TTTCTTTTT
1 TTTCTTTTT
1898881 TTT-TGATTTT
1 TTTCT--TTTT
*
1898891 TTCTCCTTTT
1 TT-TCTTTTT
*
1898901 TGTCTTTTCT
1 TTTCTTTT-T
1898911 TTTCTTTTT
1 TTTCTTTTT
1898920 GCACTCCAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
8 1 0.03
9 18 0.46
10 19 0.49
11 1 0.03
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.81
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:1898892 original size:18 final size:17
Alignment explanation
Indices: 1898869--1898920 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
1898859 TGAATTTCTT
1898869 TTTTTTCTTTTTTTTTG
1 TTTTTTCTTTTTTTTTG
**
1898886 ATTTTTTC-TCCTTTTTG
1 -TTTTTTCTTTTTTTTTG
*
1898903 TCTTTTCTTTTCTTTTTG
1 TTTTTTCTTTT-TTTTTG
1898921 CACTCCAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 6 0.22
17 8 0.30
18 13 0.48
ACGTcount: A:0.02, C:0.13, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTTTCTTTTTTTTTG
Found at i:1903825 original size:17 final size:18
Alignment explanation
Indices: 1903794--1903827 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1903784 ATTGGTCTTG
*
1903794 ATGGATGATGTTGATGAA
1 ATGGATGATGGTGATGAA
1903812 ATGGA-GATGGTGATGA
1 ATGGATGATGGTGATGA
1903828 TGTTGTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (18 bp):
ATGGATGATGGTGATGAA
Found at i:1910203 original size:29 final size:31
Alignment explanation
Indices: 1910170--1910227 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
1910160 TTGGTTAATG
*
1910170 ACCAAAATACAAA-TTTTG-AAAGTTTAGTA
1 ACCAAAATACAAACTTTGGAAAAGTTTAGTA
* *
1910199 ACCAAAGTATAAACTTTGGAAAAGTTTAG
1 ACCAAAATACAAACTTTGGAAAAGTTTAG
1910228 GGACGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.46
30 4 0.17
31 9 0.38
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (31 bp):
ACCAAAATACAAACTTTGGAAAAGTTTAGTA
Found at i:1915031 original size:13 final size:14
Alignment explanation
Indices: 1914992--1915034 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1914982 GTCTGAGTCA
*
1914992 ACCTGTTGACTTTG
1 ACCTATTGACTTTG
1915006 ACCTATTGACTTTG
1 ACCTATTGACTTTG
*
1915020 ACC-ATTGTCTTTG
1 ACCTATTGACTTTG
1915033 AC
1 AC
1915035 AAAAATAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (14 bp):
ACCTATTGACTTTG
Found at i:1917636 original size:23 final size:24
Alignment explanation
Indices: 1917590--1917645 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
1917580 TTCACGAGGT
* **
1917590 TCTTCGGGACATTTCTACGTAGTC
1 TCTTTGGGACATTTCTACACAGTC
1917614 -CTTTGGGACATTTCTACACAGTC
1 TCTTTGGGACATTTCTACACAGTC
*
1917637 TTTTTGGGA
1 TCTTTGGGA
1917646 AATCTATGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (24 bp):
TCTTTGGGACATTTCTACACAGTC
Found at i:1932602 original size:22 final size:22
Alignment explanation
Indices: 1932526--1932608 Score: 62
Period size: 24 Copynumber: 3.7 Consensus size: 22
1932516 AGAACCCGTG
*
1932526 GGGGGTATCGATT-CCC-TCAA
1 GGGGGAATCGATTCCCCTTCAA
* * * *
1932546 GGAGGGAATTGGTTCTCATTCAAA
1 GG-GGGAATCGATTCCCCTTC-AA
*
1932570 TGGGGGAATCGGTTCCCCTTCAA
1 -GGGGGAATCGATTCCCCTTCAA
*
1932593 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
1932609 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.04
21 8 0.17
22 15 0.31
23 4 0.08
24 17 0.35
25 2 0.04
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:1937093 original size:59 final size:59
Alignment explanation
Indices: 1936994--1937130 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 59
1936984 CAGCAGGCTG
** * * *
1936994 CATATTCGGGAATACACTAAAGGATACCTAATGTATATGGTGGGCATGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAATACAGATGGTGGACACGACCTTATGTGT
* ** * *
1937053 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAATACAGATGGTGGACACGACCTTATGTGT
*
1937112 GATATTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
1937131 CGGTGCTTAT
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
58 1 0.02
59 61 0.98
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAATACAGATGGTGGACACGACCTTATGTGT
Found at i:1937325 original size:47 final size:45
Alignment explanation
Indices: 1937231--1937356 Score: 191
Period size: 47 Copynumber: 2.8 Consensus size: 45
1937221 GTAAGCATAC
* *
1937231 AAATAAGCTTACGAGCTTTTGGAAT-AATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
* *
1937275 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATGGGTA
1937322 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1937357 GGATTTTATA
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
44 23 0.31
45 11 0.15
46 1 0.01
47 40 0.53
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
Found at i:1942929 original size:73 final size:73
Alignment explanation
Indices: 1942831--1942994 Score: 192
Period size: 73 Copynumber: 2.2 Consensus size: 73
1942821 CATAAAATGT
* * * *
1942831 TAACATTATAGGTTATAATTCATAAAACAATTGTAAGTTG-ACATTACAAGTT-AAATGGAAAA-
1 TAACATTATAGGTTATAATTAATAAAACAAGTGTAA--TGAACATTAAAAGTTGAAAT-AAAAAT
1942893 TAGGTTGTATA
63 TAGGTTGTATA
1942904 TAACATTATAGGTT-TAAGTTAATAAAACAAGTGTAATGAAACATTAAAAGTTGAAATAAAAATG
1 TAACATTATAGGTTATAA-TTAATAAAACAAGTGTAATG-AACATTAAAAGTTGAAATAAAAA--
1942968 TTAGGTTGTATA
62 TTAGGTTGTATA
*
1942980 TAACATAATAGGTTA
1 TAACATTATAGGTTA
1942995 AACTAAAATT
Statistics
Matches: 78, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
71 2 0.03
72 3 0.04
73 45 0.58
74 4 0.05
76 24 0.31
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (73 bp):
TAACATTATAGGTTATAATTAATAAAACAAGTGTAATGAACATTAAAAGTTGAAATAAAAATTAG
GTTGTATA
Found at i:1976061 original size:21 final size:21
Alignment explanation
Indices: 1976021--1976107 Score: 131
Period size: 21 Copynumber: 4.2 Consensus size: 21
1976011 GAAGAAGTGG
* *
1976021 AAGTACATGAATTA-CTTGGT
1 AAGTAGATGAAGTACCTTGGT
1976041 AAGTAGATGAAGTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
1976062 AAGTAGATGAAGTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
* *
1976083 AAATAGGTGAAGTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
1976104 AAGT
1 AAGT
1976108 GTCTCAGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
20 12 0.20
21 49 0.80
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.30
Consensus pattern (21 bp):
AAGTAGATGAAGTACCTTGGT
Found at i:1988177 original size:21 final size:21
Alignment explanation
Indices: 1988151--1988196 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1988141 AAACAAAAGT
1988151 AGTACCGATACTCCCTTTAGG
1 AGTACCGATACTCCCTTTAGG
1988172 AGTACCGATACTCCCTTTAGG
1 AGTACCGATACTCCCTTTAGG
1988193 AGTA
1 AGTA
1988197 TCGGTACCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (21 bp):
AGTACCGATACTCCCTTTAGG
Found at i:1990281 original size:5 final size:5
Alignment explanation
Indices: 1990271--1990295 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1990261 TTATAAAGTT
1990271 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
1990296 AAGTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:1990323 original size:24 final size:24
Alignment explanation
Indices: 1990281--1990331 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
1990271 TTTTCTTTTC
* * *
1990281 TTTTCTTTTCTTTTCAAGTTTTTAT
1 TTTTATTTTATTTTCAAG-TGTTAT
1990306 TTTTATTTTATTTT-AAGTGTTAT
1 TTTTATTTTATTTTCAAGTGTTAT
1990329 TTT
1 TTT
1990332 CAAACATGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 8 0.35
24 3 0.13
25 12 0.52
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.73
Consensus pattern (24 bp):
TTTTATTTTATTTTCAAGTGTTAT
Found at i:1993024 original size:18 final size:19
Alignment explanation
Indices: 1992992--1993029 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1992982 GAATGTTTTT
*
1992992 GGAATGACATGATTGTTTA
1 GGAATGACATAATTGTTTA
1993011 GGAAT-ACATAATTGTTTA
1 GGAATGACATAATTGTTTA
1993029 G
1 G
1993030 ATTAAGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (19 bp):
GGAATGACATAATTGTTTA
Found at i:1994676 original size:13 final size:13
Alignment explanation
Indices: 1994637--1994688 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
1994627 GTCATAAATC
*
1994637 TATGATGCGCATT
1 TATGACGCGCATT
* *
1994650 TATGACACACATT
1 TATGACGCGCATT
*
1994663 TATGACGCGTATT
1 TATGACGCGCATT
*
1994676 TATGACGCTCATT
1 TATGACGCGCATT
1994689 GCGTGTCATT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:1994767 original size:2 final size:2
Alignment explanation
Indices: 1994760--1994792 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1994750 TTTCGTAAAT
1994760 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1994793 TGTAGATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1998939 original size:12 final size:11
Alignment explanation
Indices: 1998909--1998942 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1998899 TTCTTTTCAA
1998909 AATTTTATTTT
1 AATTTTATTTT
*
1998920 TATTTTATTTT
1 AATTTTATTTT
1998931 AAGTTTTATTTT
1 AA-TTTTATTTT
1998943 CAAACTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (11 bp):
AATTTTATTTT
Found at i:2006374 original size:33 final size:31
Alignment explanation
Indices: 2006312--2006381 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 31
2006302 ATCTATAATT
2006312 TTAAAAATAAAAATATTAAGATTATTATTTTCA
1 TTAAAAATAAAAATATTAAGATTATTA-TTT-A
*
2006345 TTAAAAATAAAATTATTATCA-ATTA-TATTTA
1 TTAAAAATAAAAATATTA--AGATTATTATTTA
2006376 TTAAAA
1 TTAAAA
2006382 TATGAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
31 7 0.21
32 3 0.09
33 19 0.56
34 4 0.12
35 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
TTAAAAATAAAAATATTAAGATTATTATTTA
Found at i:2006507 original size:21 final size:21
Alignment explanation
Indices: 2006483--2006529 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2006473 TTTTTATGAA
* *
2006483 ATTAATAAATAATTTTATTTT
1 ATTAATAAATAATTATATATT
* *
2006504 ATTAATAATTTATTATATATT
1 ATTAATAAATAATTATATATT
2006525 ATTAA
1 ATTAA
2006530 AATAAAAGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTAATAAATAATTATATATT
Found at i:2008897 original size:20 final size:19
Alignment explanation
Indices: 2008872--2008916 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
2008862 TTACATGCAT
2008872 TTACATAC-ATGAGCTATGTG
1 TTACATACTA-GA-CTATGTG
*
2008892 TTACATGCTAGACTATGTG
1 TTACATACTAGACTATGTG
2008911 TTACAT
1 TTACAT
2008917 GATCTATGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 13 0.57
20 9 0.39
21 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (19 bp):
TTACATACTAGACTATGTG
Found at i:2008898 original size:16 final size:16
Alignment explanation
Indices: 2008877--2008926 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 16
2008867 TGCATTTACA
2008877 TACATGAGCTATGTGT
1 TACATGAGCTATGTGT
2008893 TACATGCTAGACTATGTGT
1 TACATG--AG-CTATGTGT
*
2008912 TACATGATCTATGTG
1 TACATGAGCTATGTG
2008927 GATATATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 13 0.43
17 1 0.03
18 2 0.07
19 14 0.47
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (16 bp):
TACATGAGCTATGTGT
Found at i:2009750 original size:23 final size:23
Alignment explanation
Indices: 2009718--2009778 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
2009708 CTCATATAAA
*
2009718 TGCACTGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
2009741 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
2009764 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
2009779 TATAAGATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:2016635 original size:21 final size:21
Alignment explanation
Indices: 2016605--2016750 Score: 123
Period size: 21 Copynumber: 6.8 Consensus size: 21
2016595 AAGGTTCTAC
2016605 GTGGTCCTTTGGGACATATAT
1 GTGGTCCTTTGGGACATATAT
* *
2016626 GTGATCCTTTGGAACATATAT
1 GTGGTCCTTTGGGACATATAT
* *
2016647 GAGGTCCTTCTTGGACATATAT
1 GTGGTCCTT-TGGGACATATAT
*
2016669 TTGGTCCTTT-GGACCATATAT
1 GTGGTCCTTTGGGA-CATATAT
** ** * *
2016690 GTGGTTATACGGGATAATTCTAT
1 GTGGTCCTTTGGGA-CA-TATAT
* *
2016713 GTGATCCTATGGGACATATAT
1 GTGGTCCTTTGGGACATATAT
*
2016734 GTGGTCCTTCGGGACAT
1 GTGGTCCTTTGGGACAT
2016751 TTTATATGGT
Statistics
Matches: 96, Mismatches: 25, Indels: 8
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.03
21 57 0.59
22 22 0.23
23 14 0.15
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.37
Consensus pattern (21 bp):
GTGGTCCTTTGGGACATATAT
Found at i:2016667 original size:43 final size:42
Alignment explanation
Indices: 2016607--2016750 Score: 126
Period size: 43 Copynumber: 3.4 Consensus size: 42
2016597 GGTTCTACGT
2016607 GGTCCTTTGGGACATATATGTGATCCTTTGGAACATATATGA
1 GGTCCTTTGGGACATATATGTGATCCTTTGGAACATATATGA
* * * * *
2016649 GGTCCTTCTTGGACATATATTTGGTCCTTTGGACCATATATGT
1 GGTCCTT-TGGGACATATATGTGATCCTTTGGAACATATATGA
** ** * * * * *
2016692 GGTTATACGGGATAATTCTATGTGATCCTATGGGACATATATGT
1 GGTCCTTTGGGA-CA-TATATGTGATCCTTTGGAACATATATGA
*
2016736 GGTCCTTCGGGACAT
1 GGTCCTTTGGGACAT
2016751 TTTATATGGT
Statistics
Matches: 78, Mismatches: 21, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
42 11 0.14
43 36 0.46
44 31 0.40
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (42 bp):
GGTCCTTTGGGACATATATGTGATCCTTTGGAACATATATGA
Found at i:2021604 original size:18 final size:19
Alignment explanation
Indices: 2021568--2021605 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2021558 TCTTCATGAG
2021568 GTATCGATACCGAAAGGGTA
1 GTATCGATACC-AAAGGGTA
2021588 GTATCGATACC-AAGGGTA
1 GTATCGATACCAAAGGGTA
2021606 CCGATACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (19 bp):
GTATCGATACCAAAGGGTA
Found at i:2022324 original size:21 final size:21
Alignment explanation
Indices: 2022291--2022441 Score: 95
Period size: 21 Copynumber: 7.0 Consensus size: 21
2022281 AGTTGAGGGT
*
2022291 TATACGTGGTCCTTCGGGACA
1 TATATGTGGTCCTTCGGGACA
* * * *
2022312 TATATGTGATCCTTTGGAATA
1 TATATGTGGTCCTTCGGGACA
** *
2022333 TATATAAGGTCCTTCTTGGACA
1 TATATGTGGTCCTTC-GGGACA
* * * * *
2022355 TATATTTAGTCCTTTGGAATA
1 TATATGTGGTCCTTCGGGACA
* *
2022376 TATATGTGGTCATACGGGACAA
1 TATATGTGGTCCTTCGGGAC-A
* * *
2022398 TTCTATGTGGTCATACGGGACA
1 -TATATGTGGTCCTTCGGGACA
* *
2022420 TATATGTGGTCTTTCAGGACA
1 TATATGTGGTCCTTCGGGACA
2022441 T
1 T
2022442 TTTATATGGT
Statistics
Matches: 96, Mismatches: 31, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
21 61 0.64
22 16 0.17
23 19 0.20
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TATATGTGGTCCTTCGGGACA
Found at i:2022358 original size:43 final size:42
Alignment explanation
Indices: 2022298--2022380 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 42
2022288 GGTTATACGT
2022298 GGTCCTTCGGGACATATATGTGA-TCCTTTGGAATATATATAA
1 GGTCCTTCGGGACATATAT-TGAGTCCTTTGGAATATATATAA
* *
2022340 GGTCCTTCTTGGACATATATTTAGTCCTTTGGAATATATAT
1 GGTCCTTC-GGGACATATATTGAGTCCTTTGGAATATATAT
2022381 GTGGTCATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 10 0.27
43 27 0.73
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (42 bp):
GGTCCTTCGGGACATATATTGAGTCCTTTGGAATATATATAA
Found at i:2026329 original size:50 final size:50
Alignment explanation
Indices: 2026232--2026330 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
2026222 GCACATTAAG
* * ** *
2026232 ACTTTGGTGCCATGATGAACCAACACATCATCATTCAGTCAATGGAGATA
1 ACTTTGGTGCCAAGATGAACCAACACATCACCATTCAACCAAAGGAGATA
*
2026282 ACTTTGGTGCCAAGATGAA-CAAGCATATCACCATTCAACCAAAGGAGAT
1 ACTTTGGTGCCAAGATGAACCAA-CACATCACCATTCAACCAAAGGAGAT
2026331 GTATCTTCAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 3 0.07
50 39 0.93
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (50 bp):
ACTTTGGTGCCAAGATGAACCAACACATCACCATTCAACCAAAGGAGATA
Found at i:2031204 original size:47 final size:45
Alignment explanation
Indices: 2031134--2031259 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
2031124 TATAAAATCT
*
2031134 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTCCCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTCCCAAAATA
* ** *
2031179 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCTTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTCCCAAAATA
* * *
2031226 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
2031260 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTCCCAAAATA
Found at i:2038356 original size:44 final size:46
Alignment explanation
Indices: 2038236--2038361 Score: 143
Period size: 47 Copynumber: 2.8 Consensus size: 46
2038226 TATAAAATCT
* *
2038236 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTAGCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
2038281 CTTAGCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTAGCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
2038328 CTT-GCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTAG-CATTTAATTCCATAAGCTCGTAAGCTTATTT
2038362 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
44 23 0.32
45 9 0.13
46 3 0.04
47 36 0.51
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (46 bp):
CTTAGCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:2045189 original size:16 final size:16
Alignment explanation
Indices: 2045168--2045214 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 16
2045158 TGCATTGACA
2045168 TACATGAGCTATGTGT
1 TACATGAGCTATGTGT
2045184 TACATGCTAGCCTATGTGT
1 TACATG--AG-CTATGTGT
*
2045203 TACATGATCTAT
1 TACATGAGCTAT
2045215 ATGGATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 10 0.37
17 1 0.04
18 2 0.07
19 14 0.52
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (16 bp):
TACATGAGCTATGTGT
Found at i:2045459 original size:46 final size:46
Alignment explanation
Indices: 2045370--2045509 Score: 217
Period size: 46 Copynumber: 3.0 Consensus size: 46
2045360 GAGTCAAGGG
* * * *
2045370 TTCTACGCGGTCCTTCGGGACAATTCTACGTGGTCCTTTGGGACAT
1 TTCTACGCGGTCCTTCAGGACAATACTATGTGGTCCTTCGGGACAT
* * *
2045416 TTCTATGCGGTCCTTCAGGAAAATACTATGTGGCCCTTCGGGACAT
1 TTCTACGCGGTCCTTCAGGACAATACTATGTGGTCCTTCGGGACAT
2045462 TTCTACGCGGTCCTTCAGGACAATACTATGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCAGGACAATACTATGTGGTCCTTCGGGACAT
2045508 TT
1 TT
2045510 TTATGTGGCA
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 84 1.00
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCAGGACAATACTATGTGGTCCTTCGGGACAT
Found at i:2045514 original size:23 final size:23
Alignment explanation
Indices: 2045378--2045517 Score: 145
Period size: 23 Copynumber: 6.1 Consensus size: 23
2045368 GGTTCTACGC
*
2045378 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGGGACAATTCTATGT
* * *
2045401 GGTCCTTTGGGACATTTCTATGC
1 GGTCCTTCGGGACAATTCTATGT
* * *
2045424 GGTCCTTCAGGAAAATACTATGT
1 GGTCCTTCGGGACAATTCTATGT
* * * *
2045447 GGCCCTTCGGGACATTTCTACGC
1 GGTCCTTCGGGACAATTCTATGT
* *
2045470 GGTCCTTCAGGACAATACTATGT
1 GGTCCTTCGGGACAATTCTATGT
* *
2045493 GGTCCTTCGGGACATTTTTATGT
1 GGTCCTTCGGGACAATTCTATGT
2045516 GG
1 GG
2045518 CACTTTGGTG
Statistics
Matches: 90, Mismatches: 27, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 90 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.33
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTATGT
Found at i:2045557 original size:24 final size:25
Alignment explanation
Indices: 2045506--2045563 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
2045496 CCTTCGGGAC
* *
2045506 ATTTTTATGTGGCACTTTGGTGTAA
1 ATTTTTACGCGGCACTTTGGTGTAA
2045531 ATTTTTACGCGGCA-TTTCGGTGT-A
1 ATTTTTACGCGGCACTTT-GGTGTAA
*
2045555 ATTTATACG
1 ATTTTTACG
2045564 AGTTGTGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.45
Consensus pattern (25 bp):
ATTTTTACGCGGCACTTTGGTGTAA
Found at i:2055822 original size:18 final size:18
Alignment explanation
Indices: 2055799--2055840 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
2055789 AGTTTTAAAA
*
2055799 AAATAAAAGAT-ATGAATT
1 AAATAAAAAATAAT-AATT
2055817 AAATAAAAAATAATAATT
1 AAATAAAAAATAATAATT
2055835 AAATAA
1 AAATAA
2055841 GTAATCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
AAATAAAAAATAATAATT
Found at i:2056252 original size:12 final size:12
Alignment explanation
Indices: 2056231--2056265 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2056221 AGAAGTGTGC
2056231 GAAAAATAGAGA
1 GAAAAATAGAGA
*
2056243 GAAAACTAGAGA
1 GAAAAATAGAGA
2056255 GAAAAAT-GAGA
1 GAAAAATAGAGA
2056266 TTTTATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.63, C:0.03, G:0.26, T:0.09
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:2057301 original size:42 final size:42
Alignment explanation
Indices: 2057169--2057395 Score: 119
Period size: 42 Copynumber: 5.3 Consensus size: 42
2057159 TTTAGATTAC
* * * *
2057169 TCCCCTTCATGGGAAAGCCAAGTGGTATATTCTTCAGGTGGT
1 TCCCCTTCACGGGAAAGTCAGGTGGTATATTCTTTAGGTGGT
* * *
2057211 TCCCCTTCGCGGGTCTGAA-CCAGGTGAG-ATGA-TCTTT-GGATGAG-
1 TCCCCTTCACGGG---AAAGTCAGGTG-GTAT-ATTCTTTAGG-TG-GT
*
2057255 TCCCCTTCACGGGAAAGTCATGTGGTATATTCTTTAGGTGGT
1 TCCCCTTCACGGGAAAGTCAGGTGGTATATTCTTTAGGTGGT
** * * * **
2057297 TCCCCTTCGTGGGTCTAAAAT-AGGTGAG-AT-TATCTTTTGATGAC
1 TCCCCTTCACGGG---AAAGTCAGGTG-GTATAT-TCTTTAGGTGGT
* * *
2057341 CCCCCTTCACGGGAAAGTCATGTGGTATATTCTTTAGGTAGT
1 TCCCCTTCACGGGAAAGTCAGGTGGTATATTCTTTAGGTGGT
*
2057383 TCCCCTTCGCGGG
1 TCCCCTTCACGGG
2057396 TCTGAACCAG
Statistics
Matches: 136, Mismatches: 29, Indels: 40
0.66 0.14 0.20
Matches are distributed among these distances:
41 10 0.07
42 60 0.44
43 6 0.04
44 50 0.37
45 10 0.07
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.32
Consensus pattern (42 bp):
TCCCCTTCACGGGAAAGTCAGGTGGTATATTCTTTAGGTGGT
Found at i:2057302 original size:86 final size:86
Alignment explanation
Indices: 2057157--2057533 Score: 526
Period size: 86 Copynumber: 4.4 Consensus size: 86
2057147 TAGTCATAAT
* * * * *
2057157 TCTTTAGATTACTCCCCTTCATGGGAAAGCCAAGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
2057222 GGTCTGAACCAGGTGAGATGA
66 GGTCTGAACCAGGTGAGATGA
* * *
2057243 TCTTTGGATGAGTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTTAGGTGGTTCCCCTTCGTG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
* ** *
2057308 GGTCTAAAATAGGTGAGATTA
66 GGTCTGAACCAGGTGAGATGA
* * * *
2057329 TCTTTTGATGACCCCCCTTCACGGGAAAGTCATGTGGTATATTCTTTAGGTAGTTCCCCTTCGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
2057394 GGTCTGAACCAGGTGAGATGA
66 GGTCTGAACCAGGTGAGATGA
* * * *
2057415 TCTTTGAATGACTCCCCTTCATGAGAAATTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
* *
2057480 GGTCTGAACTAGGT--GATTA
66 GGTCTGAACCAGGTGAGATGA
*
2057499 TCTTGGGATGACTCCCCTTCAC-GGAAAGTCATGTG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTG
2057534 AGATGTTCTT
Statistics
Matches: 255, Mismatches: 36, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
83 11 0.04
84 23 0.09
86 221 0.87
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (86 bp):
TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
GGTCTGAACCAGGTGAGATGA
Found at i:2061993 original size:46 final size:46
Alignment explanation
Indices: 2061943--2062349 Score: 485
Period size: 46 Copynumber: 8.8 Consensus size: 46
2061933 TAATATAATA
* * * *
2061943 CATCCGTTCATACATTTTAGTTAGGGCATCATTTCATGCCTTAGTG
1 CATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAGTG
* *
2061989 CATCCGTTCATGCACTTTAGTTATGGAATCCTTTCATGCCTTAATG
1 CATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAGTG
* * *
2062035 CATCCATTCATGCACTTTATTTACGGCATCCTTTCATGCCTTAGTG
1 CATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAGTG
* *
2062081 CATCCGTTCATGCACTTTAGTTATGGAATCCTTTCATGCCTTAATG
1 CATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAGTG
* * * * *
2062127 CATCCATTCATGCATTTTATTTATGGTAAT-CTTTCATTCCTTAGTG
1 CATCCGTTCATGCACTTTAGTTATGG-CATCCTTTCATGCCTTAGTG
* * * * *
2062173 AATCCGCTCATGTACTTTATTTATGACATCCTTAT-ATGCCTTAGTG
1 CATCCGTTCATGCACTTTAGTTATGGCATCCTT-TCATGCCTTAGTG
* * * * * *
2062219 CATTCATTCATTCACTTTAGTTATGACATCCTTTCATTCCTTAATG
1 CATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAGTG
* * *
2062265 CATACGTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAGTG
1 CATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAGTG
* **
2062311 CATCCGTTCATGTACTTTAGTTATGGCATTTTTTCATGC
1 CATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGC
2062350 TTTGGTGATA
Statistics
Matches: 305, Mismatches: 52, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
45 3 0.01
46 298 0.98
47 4 0.01
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (46 bp):
CATCCGTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAGTG
Found at i:2061998 original size:20 final size:20
Alignment explanation
Indices: 2061963--2062139 Score: 93
Period size: 20 Copynumber: 8.0 Consensus size: 20
2061953 TACATTTTAG
* *
2061963 TTAGGGCATCATTTCATGCC
1 TTAGTGCATCCTTTCATGCC
*
2061983 TTAGTGCATCCGTTCATGCAC
1 TTAGTGCATCCTTTCATGC-C
*
2062004 TTTAGTTATGGAATCCTTTCATGCC
1 -TTAG---T-GCATCCTTTCATGCC
* *
2062029 TTAATGCATCCATTCATGCAC
1 TTAGTGCATCCTTTCATGC-C
*
2062050 TTTATTTACGGCATCCTTTCATGCC
1 -TTA-GT---GCATCCTTTCATGCC
*
2062075 TTAGTGCATCCGTTCATGCAC
1 TTAGTGCATCCTTTCATGC-C
*
2062096 TTTAGTTATGGAATCCTTTCATGCC
1 -TTAG---T-GCATCCTTTCATGCC
* *
2062121 TTAATGCATCCATTCATGC
1 TTAGTGCATCCTTTCATGC
2062140 ATTTTATTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 36
0.70 0.10 0.21
Matches are distributed among these distances:
20 53 0.43
21 5 0.04
22 11 0.09
23 2 0.02
24 9 0.07
25 5 0.04
26 37 0.30
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.38
Consensus pattern (20 bp):
TTAGTGCATCCTTTCATGCC
Found at i:2062019 original size:26 final size:26
Alignment explanation
Indices: 2061943--2062349 Score: 122
Period size: 26 Copynumber: 17.5 Consensus size: 26
2061933 TAATATAATA
* * * *
2061943 CATCCGTTCATACATTTTAGTTAGGG
1 CATCCTTTCATGCACTTTAGTTATGG
*
2061969 CATCATTTCATGC-C-TTAG---T-G
1 CATCCTTTCATGCACTTTAGTTATGG
*
2061989 CATCCGTTCATGCACTTTAGTTATGG
1 CATCCTTTCATGCACTTTAGTTATGG
*
2062015 AATCCTTTCATGC-C-TTA---AT-G
1 CATCCTTTCATGCACTTTAGTTATGG
* * *
2062035 CATCCATTCATGCACTTTATTTACGG
1 CATCCTTTCATGCACTTTAGTTATGG
2062061 CATCCTTTCATGC-C-TTAG---T-G
1 CATCCTTTCATGCACTTTAGTTATGG
*
2062081 CATCCGTTCATGCACTTTAGTTATGG
1 CATCCTTTCATGCACTTTAGTTATGG
*
2062107 AATCCTTTCATGC-C-TTA---AT-G
1 CATCCTTTCATGCACTTTAGTTATGG
* * *
2062127 CATCCATTCATGCATTTTATTTATGG
1 CATCCTTTCATGCACTTTAGTTATGG
* *
2062153 TAAT-CTTTCATTC-C-TTAG---T-G
1 -CATCCTTTCATGCACTTTAGTTATGG
* ** * * *
2062173 AATCCGCTCATGTACTTTATTTATGA
1 CATCCTTTCATGCACTTTAGTTATGG
2062199 CATCCTTAT-ATGC-C-TTAG---T-G
1 CATCCTT-TCATGCACTTTAGTTATGG
* * * *
2062219 CATTCATTCATTCACTTTAGTTATGA
1 CATCCTTTCATGCACTTTAGTTATGG
*
2062245 CATCCTTTCATTC-C-TTA---AT-G
1 CATCCTTTCATGCACTTTAGTTATGG
* * * *
2062265 CATACGTTCATGCATTTTATTTATGG
1 CATCCTTTCATGCACTTTAGTTATGG
2062291 CATCCTTTCATGC-C-TTAG---T-G
1 CATCCTTTCATGCACTTTAGTTATGG
* *
2062311 CATCCGTTCATGTACTTTAGTTATGG
1 CATCCTTTCATGCACTTTAGTTATGG
**
2062337 CATTTTTTCATGC
1 CATCCTTTCATGC
2062350 TTTGGTGATA
Statistics
Matches: 270, Mismatches: 59, Indels: 104
0.62 0.14 0.24
Matches are distributed among these distances:
19 4 0.01
20 85 0.31
21 15 0.06
22 28 0.10
24 25 0.09
25 15 0.06
26 95 0.35
27 3 0.01
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (26 bp):
CATCCTTTCATGCACTTTAGTTATGG
Found at i:2069094 original size:46 final size:46
Alignment explanation
Indices: 2069044--2069439 Score: 517
Period size: 46 Copynumber: 8.6 Consensus size: 46
2069034 CATTAATTTC
* * ** * *
2069044 AGTTATGGCAT-CTTTCCATGCATTAATATATCCGTTCATACATTTT
1 AGTTATGGCATCCTTT-CATGCCTTAGTGCATCCGTTCATGCACTTT
* * *
2069090 AGTTAGGGCATCCTTTCATGTCTTAGTGCATCTGTTCATGCACTTT
1 AGTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTT
* * *
2069136 AGTTACGGTATCCTTTCATTCCTTAGTGCATCCGTTCATGCACTTT
1 AGTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTT
* * *
2069182 ATTTATGGCATCATTTCATGCCTTAGTGCATCCGTTCATACACTTT
1 AGTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTT
* * * *
2069228 AGTTATGGCATCCGTTCGTGCCTTAGTGCATTCGTTCATGCATTTT
1 AGTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTT
2069274 A-TTGATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTT
1 AGTT-ATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTT
* *
2069320 AGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTT
1 AGTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTT
* * * *
2069366 ATTTATGGCATCATTTCATGCCTTAGTGCATCCTTTCAAGCACTTT
1 AGTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTT
* *
2069412 AGTTATGGAATCTTTTCATGCCTTAGTG
1 AGTTATGGCATCCTTTCATGCCTTAGTG
2069440 ATAACATAGT
Statistics
Matches: 305, Mismatches: 42, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
45 2 0.01
46 297 0.97
47 6 0.02
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (46 bp):
AGTTATGGCATCCTTTCATGCCTTAGTGCATCCGTTCATGCACTTT
Found at i:2071306 original size:66 final size:66
Alignment explanation
Indices: 2071184--2071474 Score: 332
Period size: 66 Copynumber: 4.4 Consensus size: 66
2071174 ATACCATGGG
* * * * *
2071184 TGGCACCTTTTATGCCGATAATGCGCCATTATGCATTAAACAAAATCGATCAATAATTTTCATTA
1 TGGCACCTTTTATGCCAATAATGCACCATTATGCATTAATCAAAATCAATCGATAATTTTCATTA
*
2071249 G
66 A
* * * ** * * * *
2071250 TAGCACCTTTTATGTCGATAATGCACCGCTATGTATTAGTCATAATCAATTGATAATTTTCATTA
1 TGGCACCTTTTATGCCAATAATGCACCATTATGCATTAATCAAAATCAATCGATAATTTTCATTA
*
2071315 G
66 A
* * * * * *
2071316 TGGTACATTTTATGCCTATAATGCATCGTTATGCATTAATCAAAA-CGATCGATAATTTTCATTT
1 TGGCACCTTTTATGCCAATAATGCACCATTATGCATTAATCAAAATCAATCGATAATTTTCA-TT
2071380 AA
65 AA
* *
2071382 TGGCATCTTTTATGCCAATAATGCACAATTATGCATTAATCAAAATCAATCGATAATTTTCATTA
1 TGGCACCTTTTATGCCAATAATGCACCATTATGCATTAATCAAAATCAATCGATAATTTTCATTA
2071447 A
66 A
* *
2071448 TGTCATCTTTTATGCCAATAATGCACC
1 TGGCACCTTTTATGCCAATAATGCACC
2071475 TATGACTCTC
Statistics
Matches: 188, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
65 14 0.07
66 159 0.85
67 15 0.08
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (66 bp):
TGGCACCTTTTATGCCAATAATGCACCATTATGCATTAATCAAAATCAATCGATAATTTTCATTA
A
Found at i:2080097 original size:20 final size:21
Alignment explanation
Indices: 2080073--2080121 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2080063 TTCTGGAAAC
2080073 ATTTCTTCCTGT-TTT-ATTTT
1 ATTTCTTCC-GTATTTAATTTT
* *
2080093 CTTTCTTTCGTATTTAATTTT
1 ATTTCTTCCGTATTTAATTTT
2080114 ATTTCTTC
1 ATTTCTTC
2080122 ATTCAATGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.09
20 10 0.43
21 11 0.48
ACGTcount: A:0.12, C:0.16, G:0.04, T:0.67
Consensus pattern (21 bp):
ATTTCTTCCGTATTTAATTTT
Found at i:2085479 original size:24 final size:26
Alignment explanation
Indices: 2085426--2085479 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
2085416 TTTTAAAAGG
2085426 ATTTTTGAAAACATATATAATATATA
1 ATTTTTGAAAACATATATAATATATA
*
2085452 ATTTTTGAAAACATA-AT-ATATATT
1 ATTTTTGAAAACATATATAATATATA
2085476 ATTT
1 ATTT
2085480 GTATATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 10 0.37
25 2 0.07
26 15 0.56
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (26 bp):
ATTTTTGAAAACATATATAATATATA
Found at i:2085491 original size:5 final size:5
Alignment explanation
Indices: 2085470--2085583 Score: 81
Period size: 5 Copynumber: 22.0 Consensus size: 5
2085460 AAACATAATA
* * * *
2085470 TATAT TATTT GTATAT TATATTT TATCT TGTAT ATATAT TATAT TATAG
1 TATAT TATAT -TATAT TATA--T TATAT TATAT -TATAT TATAT TATAT
* * *
2085519 TATAT AATAT TATAT TATAT TATGA- TATAG TATA- TATAT TTTA- TATAT
1 TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT TATAT
2085567 TATTTAT TATAT TATAT
1 TA--TAT TATAT TATAT
2085584 ATTGTATTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
4 8 0.09
5 61 0.70
6 9 0.10
7 9 0.10
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:2085507 original size:2 final size:2
Alignment explanation
Indices: 2085500--2085585 Score: 57
Period size: 2 Copynumber: 46.5 Consensus size: 2
2085490 TTTTATCTTG
2085500 TA TA TA TA T- TA TA T- TA TA GTA TA TA -A TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
2085538 T- TA TGA TA TA GTA TA TA TA T- TT TA TA TA T- TA TT TA T- TA TA
1 TA TA T-A TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2085578 T- TA TA TA T
1 TA TA TA TA T
2085586 TGTATTTTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 26
0.70 0.03 0.27
Matches are distributed among these distances:
1 10 0.15
2 52 0.76
3 6 0.09
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (2 bp):
TA
Found at i:2085512 original size:7 final size:7
Alignment explanation
Indices: 2085502--2085586 Score: 54
Period size: 7 Copynumber: 12.1 Consensus size: 7
2085492 TTATCTTGTA
2085502 TATATAT
1 TATATAT
2085509 TATATTAT
1 TATA-TAT
*
2085517 AGTATATAA
1 --TATATAT
2085526 TATTATAT
1 TA-TATAT
2085534 TATATTAT
1 TATA-TAT
* *
2085542 GATATAG
1 TATATAT
2085549 TATATA-
1 TATATAT
2085555 TAT-T-T
1 TATATAT
2085560 TATATAT
1 TATATAT
*
2085567 TATTTA-
1 TATATAT
2085573 T-TATAT
1 TATATAT
2085579 TATATAT
1 TATATAT
2085586 T
1 T
2085587 GTATTTTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
5 7 0.11
6 6 0.10
7 27 0.44
8 15 0.25
9 2 0.03
10 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:2085540 original size:30 final size:29
Alignment explanation
Indices: 2085500--2085584 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 29
2085490 TTTTATCTTG
2085500 TATATATATTATATTATAGTATATAATAT
1 TATATATATTATATTATAGTATATAATAT
2085529 TATATTATATTATGA-TATAGTATAT-ATAT
1 TATA-TATATTAT-ATTATAGTATATAATAT
* *
2085558 TTTATATATTATTTATTATATTATATA
1 TATATATATTA--TATTATAGTATATA
2085585 TTGTATTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
28 7 0.15
29 12 0.25
30 28 0.58
31 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (29 bp):
TATATATATTATATTATAGTATATAATAT
Found at i:2085582 original size:28 final size:28
Alignment explanation
Indices: 2085483--2085600 Score: 96
Period size: 28 Copynumber: 4.1 Consensus size: 28
2085473 ATTATTTGTA
* *
2085483 TATTATATTTTATCTTGTATATA-TATT
1 TATTATATTATATATTGTATATATTATT
* * *
2085510 ATATTATAGTATATAATAT-TATATTATAT
1 -TATTATATTATATATTGTATATATTAT-T
*
2085539 TATGATATAGTATATATATTTTATATATTATT
1 TAT--TATA-T-TATATATTGTATATATTATT
* *
2085571 TATTATATTATATATTGTATTTTTTATT
1 TATTATATTATATATTGTATATATTATT
2085599 TA
1 TA
2085601 ACTTTTTTGT
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
27 4 0.06
28 38 0.53
29 2 0.03
30 8 0.11
32 12 0.17
33 8 0.11
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (28 bp):
TATTATATTATATATTGTATATATTATT
Found at i:2085585 original size:30 final size:30
Alignment explanation
Indices: 2085468--2085585 Score: 100
Period size: 30 Copynumber: 3.9 Consensus size: 30
2085458 GAAAACATAA
* * *
2085468 TATATATTATTT-GTATATTATATTTTATCTT
1 TATATATTATTTATTATAGTATA-TATAT-TT
*
2085499 GTATATA-TATTATATTATAGTATATAATATTA
1 -TATATATTATT-TATTATAGTATAT-ATATTT
*
2085531 TATTATATTA-TGA-TATAGTATATATATTT
1 TA-TATATTATTTATTATAGTATATATATTT
*
2085560 TATATATTATTTATTATATTATATAT
1 TATATATTATTTATTATAGTATATAT
2085586 TGTATTTTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
28 7 0.10
29 9 0.13
30 21 0.30
31 7 0.10
32 14 0.20
33 13 0.18
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (30 bp):
TATATATTATTTATTATAGTATATATATTT
Found at i:2085598 original size:12 final size:12
Alignment explanation
Indices: 2085506--2085598 Score: 55
Period size: 12 Copynumber: 7.3 Consensus size: 12
2085496 CTTGTATATA
*
2085506 TATTATATTATAG
1 TATTATATTAT-T
*
2085519 TA-TATAATATT
1 TATTATATTATT
2085530 ATATTATATTATGAT
1 -TATTATATTAT--T
*
2085545 ATAGTATATATATT
1 -TATTATAT-TATT
2085559 T-TATATATTATT
1 TAT-TATATTATT
*
2085571 TATTATATTATA
1 TATTATATTATT
* *
2085583 TATTGTATTTTT
1 TATTATATTATT
2085595 TATT
1 TATT
2085599 TAACTTTTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
12 35 0.55
13 16 0.25
14 1 0.02
15 9 0.14
16 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (12 bp):
TATTATATTATT
Found at i:2085666 original size:22 final size:22
Alignment explanation
Indices: 2085636--2085678 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2085626 AGGGTTTCAG
* *
2085636 GTCCGATCCAGTCCAATAAAGA
1 GTCCAATCCAGTCCAACAAAGA
2085658 GTCCAATCCAGTCCAACAAAG
1 GTCCAATCCAGTCCAACAAAG
2085679 GGGCCCAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.30, G:0.16, T:0.16
Consensus pattern (22 bp):
GTCCAATCCAGTCCAACAAAGA
Found at i:2086836 original size:29 final size:30
Alignment explanation
Indices: 2086760--2086841 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
2086750 AATTTGAGTT
* *
2086760 TTTTAATTTAATTTAATTAATTTAAATTTTA
1 TTTTATTTTAA-TTAATTTATTTAAATTTTA
*
2086791 TTTTATTTCT--TTCATTTATTT-AATATTTA
1 TTTTATTT-TAATTAATTTATTTAAAT-TTTA
2086820 TTTTATTTTAATT-ATTTATTTA
1 TTTTATTTTAATTAATTTATTTA
2086842 CTTTATTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
28 4 0.09
29 29 0.67
30 2 0.05
31 7 0.16
32 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (30 bp):
TTTTATTTTAATTAATTTATTTAAATTTTA
Found at i:2091696 original size:54 final size:55
Alignment explanation
Indices: 2091627--2091748 Score: 192
Period size: 55 Copynumber: 2.2 Consensus size: 55
2091617 TACATCAGCT
* *
2091627 GTGTATAGATACCCAAATTACATTCGATGTT-GGGGTGTATCGATACATCAAAGA
1 GTGTATCGGTACCCAAATTACATTCGATGTTGGGGGTGTATCGATACATCAAAGA
* * *
2091681 GTGTATCGGTACCCAAATTATATTCGATGTTGGGGGTTTATCGATACATCCAAGA
1 GTGTATCGGTACCCAAATTACATTCGATGTTGGGGGTGTATCGATACATCAAAGA
2091736 GTGTATCGGTACC
1 GTGTATCGGTACC
2091749 TCCCTTTGTA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
54 28 0.45
55 34 0.55
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (55 bp):
GTGTATCGGTACCCAAATTACATTCGATGTTGGGGGTGTATCGATACATCAAAGA
Found at i:2092065 original size:13 final size:13
Alignment explanation
Indices: 2092047--2092080 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2092037 TAAGATTTTC
*
2092047 TTTGAAAATCATT
1 TTTGAAAATCAAT
2092060 TTTG-AAATCAAT
1 TTTGAAAATCAAT
2092072 TTTGAAAAT
1 TTTGAAAAT
2092081 TACTCCCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:2092111 original size:21 final size:22
Alignment explanation
Indices: 2092077--2092119 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
2092067 TCAATTTTGA
2092077 AAATTACTCCCCTTACTTTATT
1 AAATTACTCCCCTTACTTTATT
2092099 AAATTAC-CCCCTTACTTTATT
1 AAATTACTCCCCTTACTTTATT
2092120 CTCCCACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATTACTCCCCTTACTTTATT
Found at i:2100284 original size:53 final size:54
Alignment explanation
Indices: 2100218--2100352 Score: 166
Period size: 55 Copynumber: 2.5 Consensus size: 54
2100208 GGAGCTAGGA
* * * *
2100218 GTGTATCGGTACATC-AGTTGTGTATCGATTCCCAAATTACATTCGATAT-TGGG
1 GTGTATCGATACATCAAG-AGTGTATCGATACCCAAATTACATTCGATATGGGGG
* * *
2100271 GTGTATCAATACATCAAAGAGTGTATCGGTACCCAAATTACATTCGATGTGGGGG
1 GTGTATCGATACATC-AAGAGTGTATCGATACCCAAATTACATTCGATATGGGGG
2100326 GTGTATCGATACATCCAAGAGTGTATC
1 GTGTATCGATACAT-CAAGAGTGTATC
2100353 TGTACCTCCC
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
53 13 0.19
54 27 0.39
55 29 0.41
56 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (54 bp):
GTGTATCGATACATCAAGAGTGTATCGATACCCAAATTACATTCGATATGGGGG
Found at i:2100307 original size:54 final size:55
Alignment explanation
Indices: 2100237--2100358 Score: 174
Period size: 55 Copynumber: 2.2 Consensus size: 55
2100227 TACATCAGTT
* * *
2100237 GTGTATCGATTCCCAAATTACATTCGATAT-TGGGGTGTATCAATACATCAAAGA
1 GTGTATCGGTACCCAAATTACATTCGATATGGGGGGTGTATCAATACATCAAAGA
* * *
2100291 GTGTATCGGTACCCAAATTACATTCGATGTGGGGGGTGTATCGATACATCCAAGA
1 GTGTATCGGTACCCAAATTACATTCGATATGGGGGGTGTATCAATACATCAAAGA
*
2100346 GTGTATCTGTACC
1 GTGTATCGGTACC
2100359 TCCCTTTGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
54 27 0.45
55 33 0.55
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (55 bp):
GTGTATCGGTACCCAAATTACATTCGATATGGGGGGTGTATCAATACATCAAAGA
Found at i:2101694 original size:81 final size:81
Alignment explanation
Indices: 2100735--2101683 Score: 1342
Period size: 82 Copynumber: 11.7 Consensus size: 81
2100725 GCCAGTTAGA
* * * * * * *
2100735 CTTTCATCTAACTTGCATGATTGATACCTTTTTGCCAAATGCACAACTAGGCCGTTAATATTTTA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
*
2100800 CTCAAATGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * *
2100816 ATTTCATCTAACTGGCATTATTGACACCTTTCTGCCAAATGCACGGCTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
2100881 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* **
2100897 CTTTCATCTAACT-GCATAATTGACACCATTCTGGAAAATGCACAGCTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
2100961 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * * * *
2100977 CTTTCGTCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAGATAGACCATTAATATTTTA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
*
2101042 CATCAAATGTATTTAAC
66 C-TCAAAGGTATTTAAC
* *
2101059 CTTTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGTCATTAATCTTTTA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
2101124 CATCAAAGGTATTTAAC
66 C-TCAAAGGTATTTAAC
* * * *
2101141 CTTTCATCTAACTAGCATAATTGACACATATCTGCCAAATGTACAACTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
2101206 CATCAAAGGTATTTAAC
66 C-TCAAAGGTATTTAAC
* * * *
2101223 CTTTCATTTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTAATATTTTA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
2101288 CATCAAAGGTATTTAAC
66 C-TCAAAGGTATTTAAC
* * *
2101305 CTTTCATCTAACTAGCATAATTGACACATATCTGCCAAATGTACAGCTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
2101370 CATCAAAGGTATTTAAC
66 C-TCAAAGGTATTTAAC
* * **
2101387 CTTTCATTTAACTAGCATAATTGACACCTTTCTACCAAATGCATGGCTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
* *
2101452 CTCAAATGTATTTAAT
66 CTCAAAGGTATTTAAC
* * * * * * *
2101468 ATTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATACACAACTAGTCCTTTAGTCTTTTA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
2101533 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * * *
2101549 CTTTCAGCTAACTGGCATAATTGACAGCTTTCTGTCAAATGCTCAGCTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
2101614 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * *
2101630 CTTTCATCTAACTAGCATTATTGACACATTTCTGCCAAATACACAGCTAGGCCA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCA
2101684 CAAATGTTTT
Statistics
Matches: 772, Mismatches: 94, Indels: 4
0.89 0.11 0.00
Matches are distributed among these distances:
80 74 0.10
81 326 0.42
82 372 0.48
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (81 bp):
CTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
CTCAAAGGTATTTAAC
Found at i:2104673 original size:21 final size:21
Alignment explanation
Indices: 2104625--2104684 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2104615 AAATTCAGTT
* *
2104625 AGAGATCGATCCTTTGCCTGAA
1 AGAGATCGATCCTTT-TCAGAA
*
2104647 AG-GATCGATCCTTTTCAGCA
1 AGAGATCGATCCTTTTCAGAA
*
2104667 AGAGATCAATCTCTTTTC
1 AGAGATCGATC-CTTTTC
2104685 TACAAAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.16
21 19 0.59
22 8 0.25
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (21 bp):
AGAGATCGATCCTTTTCAGAA
Found at i:2104910 original size:27 final size:27
Alignment explanation
Indices: 2104872--2104925 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
2104862 CAAAGTCAAA
2104872 TTTTGCATATAAA-TATAACTTAAACAC
1 TTTTGCATATAAAGT-TAACTTAAACAC
*
2104899 TTTTTCATATAAAGTTAACTTAAACAC
1 TTTTGCATATAAAGTTAACTTAAACAC
2104926 AATTTACCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.39
Consensus pattern (27 bp):
TTTTGCATATAAAGTTAACTTAAACAC
Found at i:2107854 original size:18 final size:18
Alignment explanation
Indices: 2107831--2107865 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2107821 GCTTGAGATA
2107831 ACCTAAAGAAAATAAAAT
1 ACCTAAAGAAAATAAAAT
* *
2107849 ACCTAAGGGAAATAAAA
1 ACCTAAAGAAAATAAAA
2107866 ACACCAAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.14
Consensus pattern (18 bp):
ACCTAAAGAAAATAAAAT
Found at i:2112596 original size:21 final size:21
Alignment explanation
Indices: 2112568--2112642 Score: 134
Period size: 21 Copynumber: 3.6 Consensus size: 21
2112558 TCATAAGCGA
2112568 ATGG-ACAACCACTCACCTAG
1 ATGGTACAACCACTCACCTAG
2112588 ATGGTACAACCACTCACCTAG
1 ATGGTACAACCACTCACCTAG
2112609 ATGGTACAACCACTCACCTAG
1 ATGGTACAACCACTCACCTAG
*
2112630 ATGGTGCAACCAC
1 ATGGTACAACCAC
2112643 ATGATTCAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 4 0.08
21 49 0.92
ACGTcount: A:0.33, C:0.33, G:0.16, T:0.17
Consensus pattern (21 bp):
ATGGTACAACCACTCACCTAG
Found at i:2116545 original size:20 final size:20
Alignment explanation
Indices: 2116520--2116558 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2116510 TCCTTCTCTG
2116520 CATCCAAATAAATTCATCAA
1 CATCCAAATAAATTCATCAA
2116540 CATCCAAATAAATTCATCA
1 CATCCAAATAAATTCATCA
2116559 TATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (20 bp):
CATCCAAATAAATTCATCAA
Found at i:2116569 original size:19 final size:20
Alignment explanation
Indices: 2116525--2116569 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2116515 CTCTGCATCC
**
2116525 AAATAAATTCATCAACATCC
1 AAATAAATTCATCAACATAA
*
2116545 AAATAAATTCATC-ATATAA
1 AAATAAATTCATCAACATAA
2116564 AAATAA
1 AAATAA
2116570 CATATTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATAAATTCATCAACATAA
Found at i:2117345 original size:20 final size:20
Alignment explanation
Indices: 2117317--2117376 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
2117307 TGACGATGAA
2117317 GAATGGGGGAAATGAGGAAC
1 GAATGGGGGAAATGAGGAAC
* * * * *
2117337 GAATTGGGG-ATTTAGAAATT
1 GAATGGGGGAAATGAGGAA-C
2117357 GAATGGGGGAAATGAGGAAC
1 GAATGGGGGAAATGAGGAAC
2117377 AAATTAGGGA
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
19 6 0.21
20 16 0.57
21 6 0.21
ACGTcount: A:0.38, C:0.03, G:0.40, T:0.18
Consensus pattern (20 bp):
GAATGGGGGAAATGAGGAAC
Found at i:2117362 original size:40 final size:40
Alignment explanation
Indices: 2117317--2117397 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
2117307 TGACGATGAA
* *
2117317 GAATGGGGGAAATGAGGAACGAATTGGGGATTTAGAAATT
1 GAATGGGGGAAATGAGGAACAAATTAGGGATTTAGAAATT
2117357 GAATGGGGGAAATGAGGAACAAATTAGGGATTTAGAAATT
1 GAATGGGGGAAATGAGGAACAAATTAGGGATTTAGAAATT
2117397 G
1 G
2117398 TTACCTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.40, C:0.02, G:0.36, T:0.22
Consensus pattern (40 bp):
GAATGGGGGAAATGAGGAACAAATTAGGGATTTAGAAATT
Found at i:2125998 original size:24 final size:24
Alignment explanation
Indices: 2125958--2126003 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2125948 TCTATTGAAG
*
2125958 TATCAACCAAGTCTATTATTAAAC
1 TATCAACCAAGTATATTATTAAAC
*
2125982 TATCAACCATA-TATATTGTTAA
1 TATCAACCA-AGTATATTATTAA
2126004 TAGCATGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.37
Consensus pattern (24 bp):
TATCAACCAAGTATATTATTAAAC
Found at i:2126775 original size:20 final size:21
Alignment explanation
Indices: 2126750--2126801 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2126740 TTTTCCCAAT
*
2126750 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2126770 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2126791 TCGCAATGCGA
1 TCGCAATGCGA
2126802 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2126880 original size:20 final size:20
Alignment explanation
Indices: 2126832--2126884 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2126822 TAATACAAAA
* *
2126832 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
2126852 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
2126872 TCGCAACGCGATT
1 TCGCAACGCGATT
2126885 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:2127462 original size:19 final size:19
Alignment explanation
Indices: 2127402--2127482 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
2127392 TTCGAGAGTG
2127402 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
2127422 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
2127438 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
2127455 AAAATCGCAACACGAAACC
1 AAAATCGCAACGCGAAATA
2127474 AAAATCGCA
1 AAAATCGCA
2127483 TTGCGATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
14 7 0.15
16 5 0.10
17 4 0.08
18 1 0.02
19 23 0.48
20 8 0.17
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:2127500 original size:19 final size:19
Alignment explanation
Indices: 2127478--2127662 Score: 147
Period size: 19 Copynumber: 10.1 Consensus size: 19
2127468 GAAACCAAAA
*
2127478 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2127497 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2127516 TTGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
2127535 TCGCAGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
**
2127555 TCGCGTTGCGATAGTC---
1 TCGCGTTGCGATTTTCATT
* **
2127571 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2127588 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2127602 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
2127621 TCCACGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
2127641 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2127661 TC
1 TC
2127663 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 21 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 57 0.42
20 49 0.36
21 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2127555 original size:39 final size:38
Alignment explanation
Indices: 2127478--2127662 Score: 147
Period size: 33 Copynumber: 5.1 Consensus size: 38
2127468 GAAACCAAAA
*
2127478 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
2127516 TTGCGTTGCGATTTTTATTTCGCAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
** * **
2127555 TCGCGTTGCGATAGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
2127588 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
2127621 TCCACGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
2127661 TC
1 TC
2127663 AACCAAAAGA
Statistics
Matches: 120, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
31 3 0.03
33 38 0.32
34 9 0.08
35 1 0.01
36 3 0.03
38 20 0.17
39 28 0.23
40 18 0.15
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:2127639 original size:20 final size:20
Alignment explanation
Indices: 2127605--2127662 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2127595 GCGATTCTCT
**
2127605 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATTCTCATTTCCA
*
2127625 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCA
*
2127645 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
2127663 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCA
Found at i:2129713 original size:42 final size:42
Alignment explanation
Indices: 2129653--2129775 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
2129643 GCCCGACTCG
* * *
2129653 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
2129695 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
2129737 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
2129776 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:2129733 original size:21 final size:21
Alignment explanation
Indices: 2129709--2129775 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2129699 TCATTCCTCG
2129709 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2129730 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2129751 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2129772 AGAG
1 AGAG
2129776 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2131161 original size:14 final size:14
Alignment explanation
Indices: 2131127--2131163 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2131117 GATTGTTTAA
2131127 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
2131141 GTAATTTGTAAAAG
1 TTGATTTGTAAAAG
2131155 TTGATTTGT
1 TTGATTTGT
2131164 TTAATTGATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:2131364 original size:19 final size:19
Alignment explanation
Indices: 2131342--2131492 Score: 62
Period size: 19 Copynumber: 8.7 Consensus size: 19
2131332 CGAAATTAAA
2131342 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2131361 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
2131376 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
2131394 TTCGCATTGTGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
2131408 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2131427 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2131442 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * ** *
2131460 TTTGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
2131479 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2131493 GGACATTAAG
Statistics
Matches: 91, Mismatches: 25, Indels: 31
0.62 0.17 0.21
Matches are distributed among these distances:
14 27 0.30
16 6 0.07
17 6 0.07
19 43 0.47
20 9 0.10
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2131388 original size:33 final size:32
Alignment explanation
Indices: 2131346--2131472 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
2131336 ATTAAATTCG
2131346 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
2131379 CGTTGCGATTTTCATTTCGCATTGTGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
2131412 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
2131445 CGTTGCGATTTTCATTTTGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2131473 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:2131435 original size:66 final size:66
Alignment explanation
Indices: 2131339--2131468 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
2131329 ACGCGAAATT
*
2131339 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
2131404 G
66 G
* *
2131405 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTGCATTG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTG
2131469 CGATAGTAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGT
G
Found at i:2133772 original size:13 final size:13
Alignment explanation
Indices: 2133754--2133778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2133744 CTTCGGGGAC
2133754 TTTTTCTTCTTCT
1 TTTTTCTTCTTCT
2133767 TTTTTCTTCTTC
1 TTTTTCTTCTTC
2133779 AGGATTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCTTCTTCT
Found at i:2133987 original size:24 final size:24
Alignment explanation
Indices: 2133953--2134006 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2133943 CTGAAACATC
*
2133953 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
*
2133977 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
2134001 ATCAAA
1 ATCAAA
2134007 TTTCGAATAT
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:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAT
Found at i:2135083 original size:20 final size:20
Alignment explanation
Indices: 2135058--2135115 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
2135048 ATTCATTTGA
2135058 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
2135078 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
2135098 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
2135116 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:2135182 original size:19 final size:19
Alignment explanation
Indices: 2135152--2135199 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2135142 CGATTTTCTG
2135152 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2135170 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2135189 TTGCGATTTTC
1 TTGCGATTTTC
2135200 TCGTTGCGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2137267 original size:19 final size:19
Alignment explanation
Indices: 2137187--2137304 Score: 86
Period size: 20 Copynumber: 6.4 Consensus size: 19
2137177 TAGTTTACTT
* *
2137187 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2137207 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
2137226 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
* *
2137246 TCGCAATGCGAAATTAAAA
1 TCGCAACGCGAAATGAAAA
*
2137265 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2137279 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
2137297 TCGCAACG
1 TCGCAACG
2137305 ACAAATCGCA
Statistics
Matches: 80, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.15
19 24 0.30
20 29 0.36
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2137280 original size:14 final size:14
Alignment explanation
Indices: 2137261--2137314 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2137251 ATGCGAAATT
2137261 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2137275 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2137291 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2137307 -AAATCGCA
1 AAAATCGCA
2137315 CGCGAAACAC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 8 0.24
14 10 0.29
16 7 0.21
18 9 0.26
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2137290 original size:33 final size:31
Alignment explanation
Indices: 2137245--2137332 Score: 115
Period size: 31 Copynumber: 2.8 Consensus size: 31
2137235 GGAAATGGCT
*
2137245 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
1 ATCGCAACGCGAAA-TAAAATCGCAACGAC-AA
*
2137278 ATCGCAACGCGAAATGAAATCGCAACGACAA
1 ATCGCAACGCGAAATAAAATCGCAACGACAA
*
2137309 ATCGC-ACGCGAAACACAAATCGCA
1 ATCGCAACGCGAAATA-AAATCGCA
2137333 TTGCGATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.16
31 15 0.30
32 14 0.28
33 13 0.26
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.11
Consensus pattern (31 bp):
ATCGCAACGCGAAATAAAATCGCAACGACAA
Found at i:2137303 original size:32 final size:32
Alignment explanation
Indices: 2137245--2137321 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 32
2137235 GGAAATGGCT
*
2137245 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATTAAAATCGCAACGAC-AA
*
2137278 ATCGCAACGCGAAA-TGAAATCGCAACGACAA
1 ATCGCAACGCGAAATTAAAATCGCAACGACAA
2137309 ATCGC-ACGCGAAA
1 ATCGCAACGCGAAA
2137322 CACAAATCGC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
30 8 0.19
31 7 0.17
32 14 0.33
33 13 0.31
ACGTcount: A:0.45, C:0.25, G:0.18, T:0.12
Consensus pattern (32 bp):
ATCGCAACGCGAAATTAAAATCGCAACGACAA
Found at i:2137310 original size:18 final size:18
Alignment explanation
Indices: 2137204--2137304 Score: 84
Period size: 19 Copynumber: 5.6 Consensus size: 18
2137194 ACGAAACTTA
2137204 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
2137222 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAACGC-GAAAT-G
** * *
2137243 CTATCGCAATGCGAAATTA
1 AAATCGCAACGCGAAA-TG
*
2137262 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
2137276 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
2137294 AAATCGCAACG
1 AAATCGCAACG
2137305 ACAAATCGCA
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
14 9 0.13
16 4 0.06
17 4 0.06
18 12 0.18
19 21 0.31
20 16 0.24
21 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.21, T:0.14
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:2137350 original size:19 final size:19
Alignment explanation
Indices: 2137328--2137409 Score: 95
Period size: 18 Copynumber: 4.6 Consensus size: 19
2137318 GAAACACAAA
2137328 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2137347 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
* *
2137365 TCACATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
2137381 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2137398 TCGCATTGCGAT
1 TCGCATTGCGAT
2137410 AGCCATTCCG
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 3 0.06
17 4 0.08
18 19 0.37
19 17 0.33
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2137416 original size:19 final size:19
Alignment explanation
Indices: 2137394--2137436 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2137384 TTGCGATTTT
2137394 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* * *
2137413 CATTCCGCGTTGCGATAGT
1 CATTTCGCATTGCGATAGC
2137432 CATTT
1 CATTT
2137437 TCGTGTTGCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.35
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:2139284 original size:20 final size:20
Alignment explanation
Indices: 2139259--2139312 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
2139249 AATAGTTTCT
2139259 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
2139279 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
2139299 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
2139313 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Done.