Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000482.1 Hibiscus syriacus cultivar Beakdansim tig00000916_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: 2886609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 16
Found at i:9220 original size:59 final size:59
Alignment explanation
Indices: 9123--9234 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
9113 AATACTTCGC
* * *
9123 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAAAAAAAAAAAAAACGT
1 TTAGGATGAAAACCCGAGAGGGCGCCCTAAATTAAAAAAAAAAAAAAAAAAAAAAACGT
* * *
9182 TTAGGGTGAAAACCCG-GAAGGGCGCCCTAAATTAAAAAAAAGAAAAAGAAAAA
1 TTAGGATGAAAACCCGAG-AGGGCGCCCTAAATTAAAAAAAAAAAAAAAAAAAA
9235 GAAGAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 1 0.02
59 45 0.98
ACGTcount: A:0.54, C:0.12, G:0.21, T:0.12
Consensus pattern (59 bp):
TTAGGATGAAAACCCGAGAGGGCGCCCTAAATTAAAAAAAAAAAAAAAAAAAAAAACGT
Found at i:10157 original size:105 final size:104
Alignment explanation
Indices: 9975--10745 Score: 1215
Period size: 105 Copynumber: 7.4 Consensus size: 104
9965 AGGTTTTACC
9975 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
10040 ACGAAGGGACCGCTGGCTGTCAACAAATATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAT-T
*
10080 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
10145 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATA
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATT
10185 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
10250 ACGAAGGGACCGCTGGTTGTCAATAAGCAACTTCTCAATCT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAT-T
* *
10291 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
10356 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAACTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAA-TT
*
10396 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGGAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
10461 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAA-TT
* *
10501 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
10566 ACGAAGGGACCGCTGGTTGTCAACAAACA-TT-TC-ATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
* * ** * * * *
10602 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTATACTCGAGACAGCACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** * * *
10667 ACGAAGGGATGGCTGGTTGTCAACAAATAATTTCCCGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAA-CATTTCTCAATT
*
10707 CCAGAGCCAATTTCAACTTCACAACGGAGGATATTGGAC
1 -CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
10746 CCGGAACAAT
Statistics
Matches: 619, Mismatches: 38, Indels: 17
0.92 0.06 0.03
Matches are distributed among these distances:
101 82 0.13
102 2 0.00
103 4 0.01
104 3 0.00
105 396 0.64
106 132 0.21
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (104 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:10557 original size:316 final size:310
Alignment explanation
Indices: 9975--10745 Score: 1236
Period size: 316 Copynumber: 2.5 Consensus size: 310
9965 AGGTTTTACC
9975 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
10040 ACGAAGGGACCGCTGGCTGTCAACAAATATTTCTCAATGTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAAT-TCAGAGCCAATTTCAACTTCACAACG
*
10105 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
130 AAGGATATTGGACTCCAGACAACGGAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
10170 AACATTTCTCAAATACAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
195 AACATTTCTCAAATACAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* *
10235 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAGCAACTTCTCAATCT
260 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-A-TT-TC-AT-T
* *
10291 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
10356 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAACTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAA-TTCAGAGCCAATTTCAACTTCACAACG
10421 AAGGATATTGGACTCCAGACAACGGAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
130 AAGGATATTGGACTCCAGACAACGGAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
* * * *
10486 AACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGT
195 AACATTTCTCAAATACAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
10551 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCATT
260 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCATT
* * ** * * * *
10602 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTATACTCGAGACAGCACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** * *
10667 ACGAAGGGATGGCTGGTTGTCAACAAATAATTTCCCGATTCCAGAGCCAATTTCAACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAA-AATTTCTCAATT-CAGAGCCAATTTCAACTTCACAAC
*
10732 GGAGGATATTGGAC
129 GAAGGATATTGGAC
10746 CCGGAACAAT
Statistics
Matches: 425, Mismatches: 27, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
311 83 0.20
312 46 0.11
313 2 0.00
314 2 0.00
315 1 0.00
316 290 0.68
317 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (310 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAAAATTTCTCAATTCAGAGCCAATTTCAACTTCACAACGA
AGGATATTGGACTCCAGACAACGGAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
ACATTTCTCAAATACAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCATT
Found at i:17232 original size:2 final size:2
Alignment explanation
Indices: 17225--17273 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
17215 TTACTTTCTT
17225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17267 TA TA TA T
1 TA TA TA T
17274 GTGATGAGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18553 original size:21 final size:22
Alignment explanation
Indices: 18514--18554 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18504 TTTTATTTTA
*
18514 TTTATTTAAATTGAGAATTAGG
1 TTTATTTAAATTGACAATTAGG
*
18536 TTTATTT-ACTTGACAATTA
1 TTTATTTAAATTGACAATTA
18555 CGACGCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (22 bp):
TTTATTTAAATTGACAATTAGG
Found at i:32724 original size:19 final size:18
Alignment explanation
Indices: 32700--32741 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
32690 GAAGTTCTAT
32700 TTTTCTTTCATCT-TTTTAC
1 TTTTCTTTCAT-TATTTT-C
32719 TTTTCTTTCATTATTTTC
1 TTTTCTTTCATTATTTTC
32737 TTTTC
1 TTTTC
32742 ACAATGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTCTTTCATTATTTTC
Found at i:33359 original size:17 final size:17
Alignment explanation
Indices: 33319--33359 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
33309 TATCTCTTTC
33319 AATTATTTATTTTTATTG
1 AATT-TTTATTTTTATTG
**
33337 CTTTTTTATTTTTATTG
1 AATTTTTATTTTTATTG
33354 AATTTT
1 AATTTT
33360 AGTTTATTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (17 bp):
AATTTTTATTTTTATTG
Found at i:39439 original size:82 final size:81
Alignment explanation
Indices: 39173--39443 Score: 292
Period size: 82 Copynumber: 3.3 Consensus size: 81
39163 TATACAAAAT
* * * * * * *
39173 GCCGCTACAGAGTAATACTTTAGCGGTGTTTGTATAAAAATGCAGTAATAGGGTTCATCTACAGT
1 GCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAATGC-GTAATATGGTTCATCTATAGT
* * *
39238 GACATTTTTTCAACAAAT
65 GGC-GTTTTTCAACAAAC
* * *
39256 GCCGCAACATAGTAGTACTTTAGCGGCGTTTTTATACAAATGCCGTAATAT-GTTCATCCATAAT
1 GCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAATG-CGTAATATGGTTCATCTATAGT
*
39320 GGCGTTTCTCAACAAAC
65 GGCGTTTTTCAACAAAC
** ** * *
39337 GTTGTGACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGTCGCAATATGGTTCATCTATAGT
1 GCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAATG-CGTAATATGGTTCATCTATAGT
39402 GGCGTTTTTCAACAAAC
65 GGCGTTTTTCAACAAAC
* * *
39419 ACCGCAATAGAGTATTACTTTAGCG
1 GCCGCAACAGAGTAGTACTTTAGCG
39444 ACTTTTTTCA
Statistics
Matches: 154, Mismatches: 32, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
81 54 0.35
82 57 0.37
83 42 0.27
84 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (81 bp):
GCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAATGCGTAATATGGTTCATCTATAGTG
GCGTTTTTCAACAAAC
Found at i:39451 original size:82 final size:82
Alignment explanation
Indices: 39173--39547 Score: 291
Period size: 81 Copynumber: 4.6 Consensus size: 82
39163 TATACAAAAT
* * * * * * * * * *
39173 GCCGCTACAGAGTAATACTTTAGCGGTGTTTGTATAAAAATGCAGTAATAGGGTTCATCTACAGT
1 GCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCGCAATATGGTTCATCTATAGT
* * *
39238 GACATTTTTTCAACAAAT
66 GGC-GTTTTTCAACAAAC
* * * * *
39256 GCCGCAACATAGTAGTACTTTAGCGGCGTTTTTATACAAATGCCGTAATAT-GTTCATCCATAAT
1 GCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCGCAATATGGTTCATCTATAGT
*
39320 GGCGTTTCTCAACAAAC
66 GGCGTTTTTCAACAAAC
** ** *
39337 GTTGTGACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGTCGCAATATGGTTCATCTATAGT
1 GCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCGCAATATGGTTCATCTATAGT
39402 GGCGTTTTTCAACAAAC
66 GGCGTTTTTCAACAAAC
* * * * ** *
39419 ACCGCAATAGAGTATTACTTTAGCGAC-TTTTT-T-CACAACGCAACAA-AGTAGTTC-T-T-TA
1 GCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACA-AACGCCGCAATA-TGGTTCATCTATA
** *
39477 GCAGCGTTTTTTCAATAAAC
64 GTGGCG-TTTTTCAACAAAC
* * * *
39497 GCCGCAACAAAGTAGTTA-TTTAACGGCCTTTTTTTTACAAACGCCGCAATA
1 GCCGCAACAGAGTAG-TACTTTAGCGG-CGTTTTTATACAAACGCCGCAATA
39548 GTTTTGTATG
Statistics
Matches: 233, Mismatches: 49, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
77 6 0.03
78 30 0.13
79 7 0.03
80 18 0.08
81 68 0.29
82 61 0.26
83 43 0.18
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (82 bp):
GCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCGCAATATGGTTCATCTATAGT
GGCGTTTTTCAACAAAC
Found at i:39678 original size:42 final size:42
Alignment explanation
Indices: 39614--39693 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
39604 CCTTCAGCCC
39614 GATCCCACCTTTTATTTTCCCTAACCTTTTCTGCTTCCCGCG
1 GATCCCACCTTTTATTTTCCCTAACCTTTTCTGCTTCCCGCG
*
39656 GATCTCACCTTTTATTTTCCCTAACCTTTTCTGCTTCC
1 GATCCCACCTTTTATTTTCCCTAACCTTTTCTGCTTCC
39694 TGTATTATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.12, C:0.36, G:0.07, T:0.44
Consensus pattern (42 bp):
GATCCCACCTTTTATTTTCCCTAACCTTTTCTGCTTCCCGCG
Found at i:42961 original size:42 final size:42
Alignment explanation
Indices: 42909--43056 Score: 170
Period size: 42 Copynumber: 3.5 Consensus size: 42
42899 GGCGTTTGAA
* * * *
42909 TCTAAAAACGCCGTTATAGATATAACTTTTTGCAACGTTTGT
1 TCTAAAAACGCCGCTATAGATCTGACATTTTGCAACGTTTGT
**
42951 TCTAAAAACGCCGCTATAGATCTGACATTTTGTGACGTTTGT
1 TCTAAAAACGCCGCTATAGATCTGACATTTTGCAACGTTTGT
* * * * * * *
42993 TCCAAAAACGCCACTATAGTTCTGACCTTTTACAACATTTAT
1 TCTAAAAACGCCGCTATAGATCTGACATTTTGCAACGTTTGT
*
43035 TTTAAAAACGCCGCTATAGATC
1 TCTAAAAACGCCGCTATAGATC
43057 AGACGGACAA
Statistics
Matches: 87, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (42 bp):
TCTAAAAACGCCGCTATAGATCTGACATTTTGCAACGTTTGT
Found at i:51402 original size:25 final size:24
Alignment explanation
Indices: 51358--51421 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
51348 AAATGGGTTA
* * *
51358 TAAGATTTAGGGTTTCATTGTGATT
1 TAAGATTTA-GGATTGATTGAGATT
*
51383 TAAGGTTTAAGGATTGATTGAGATT
1 TAAGATTT-AGGATTGATTGAGATT
*
51408 TGAGATTTAGGATT
1 TAAGATTTAGGATT
51422 TAGTTGAGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 6 0.19
25 25 0.78
26 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.44
Consensus pattern (24 bp):
TAAGATTTAGGATTGATTGAGATT
Found at i:52056 original size:21 final size:21
Alignment explanation
Indices: 52024--52071 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
52014 TAATTTTCAA
*
52024 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
*
52045 ATATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
52066 ACATTG
1 ACATTG
52072 CAATATTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:70336 original size:21 final size:20
Alignment explanation
Indices: 70312--70350 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
70302 AATCAAAGTC
*
70312 TTTGTTGAAGCCATGAAATCG
1 TTTGTAGAAGCCAT-AAATCG
*
70333 TTTGTAGAGGCCATAAAT
1 TTTGTAGAAGCCATAAAT
70351 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (20 bp):
TTTGTAGAAGCCATAAATCG
Found at i:77744 original size:2 final size:2
Alignment explanation
Indices: 77733--77769 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
77723 TATTATACAC
77733 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
77770 AACCCATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:79420 original size:17 final size:17
Alignment explanation
Indices: 79374--79420 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
79364 TGATAAAGTC
79374 TTTTGAGATATATCAAA
1 TTTTGAGATATATCAAA
* *
79391 TTTTGGCATATATATTAAA
1 TTTT-G-AGATATATCAAA
79410 TTTTGAGATAT
1 TTTTGAGATAT
79421 TTGGGATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 9 0.36
18 2 0.08
19 14 0.56
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (17 bp):
TTTTGAGATATATCAAA
Found at i:96651 original size:19 final size:18
Alignment explanation
Indices: 96629--96668 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
96619 AATAAAACTT
96629 AAAATAAAAAAGAAAATGA
1 AAAATAAAAAAGAAAA-GA
**
96648 AAAATTGAAAAGAAAAGA
1 AAAATAAAAAAGAAAAGA
96666 AAA
1 AAA
96669 GAAAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAATAAAAAAGAAAAGA
Found at i:98691 original size:90 final size:88
Alignment explanation
Indices: 98569--98746 Score: 284
Period size: 89 Copynumber: 2.0 Consensus size: 88
98559 TAATCCTGAA
* *
98569 TATTTAATTTCAATAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCCTAATATGATT
1 TATTAAATTCCAATAATTAAATATAGATTTAATTAATTTAAAATAATAAAA-CCCTAATATGATT
* *
98634 AGGGTAACTTGGATATAAGAGGAT
65 AGGGTAACTTAGATATAAAAGGAT
*
98658 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAA-TAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
*
98723 AGGGTAACTTAGCTATAAAAGGAT
65 AGGGTAACTTAGATATAAAAGGAT
98747 GTGTTAGGTC
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 45 0.55
90 37 0.45
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (88 bp):
TATTAAATTCCAATAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATTA
GGGTAACTTAGATATAAAAGGAT
Found at i:112789 original size:6 final size:6
Alignment explanation
Indices: 112775--112815 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
112765 ATTTAAAATA
*
112775 AAAATG AAAACG AAAACG AAAACG AAAACG AAAACG AAAAC
1 AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAAC
112816 TTGAAAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.68, C:0.15, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAACG
Found at i:112831 original size:18 final size:19
Alignment explanation
Indices: 112774--112831 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
112764 AATTTAAAAT
*
112774 AAAAATGAAAACGAAAACG
1 AAAACTGAAAACGAAAACG
112793 AAAAC-GAAAACGAAAACG
1 AAAACTGAAAACGAAAACG
112811 AAAACTTGAAAA-GAAAA-G
1 AAAAC-TGAAAACGAAAACG
112829 AAA
1 AAA
112832 TAACTTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 22 0.61
19 9 0.25
20 5 0.14
ACGTcount: A:0.69, C:0.10, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAACTGAAAACGAAAACG
Found at i:119548 original size:10 final size:10
Alignment explanation
Indices: 119535--119617 Score: 67
Period size: 10 Copynumber: 7.7 Consensus size: 10
119525 CTATTCACGA
119535 TACTGTTTAT
1 TACTGTTTAT
119545 TACTGTTTAT
1 TACTGTTTAT
119555 AGTACTGTTTAT
1 --TACTGTTTAT
* *
119567 TACTGTTAACGG
1 TACTGTTTA--T
*
119579 TACTGTTCAT
1 TACTGTTTAT
119589 TACTGTTTAT
1 TACTGTTTAT
*
119599 AGTATTGTTTAT
1 --TACTGTTTAT
*
119611 TATTGTT
1 TACTGTT
119618 CACGGTAATG
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
10 34 0.56
12 27 0.44
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.54
Consensus pattern (10 bp):
TACTGTTTAT
Found at i:119560 original size:22 final size:22
Alignment explanation
Indices: 119535--119617 Score: 112
Period size: 22 Copynumber: 3.8 Consensus size: 22
119525 CTATTCACGA
119535 TACTGTTTATTACTGTTTATAG
1 TACTGTTTATTACTGTTTATAG
* **
119557 TACTGTTTATTACTGTTAACGG
1 TACTGTTTATTACTGTTTATAG
*
119579 TACTGTTCATTACTGTTTATAG
1 TACTGTTTATTACTGTTTATAG
* *
119601 TATTGTTTATTATTGTT
1 TACTGTTTATTACTGTT
119618 CACGGTAATG
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.54
Consensus pattern (22 bp):
TACTGTTTATTACTGTTTATAG
Found at i:119584 original size:44 final size:44
Alignment explanation
Indices: 119535--119632 Score: 151
Period size: 44 Copynumber: 2.2 Consensus size: 44
119525 CTATTCACGA
*
119535 TACTGTTTATTACTGTTTATAGTACTGTTTATTACTGTTAACGG
1 TACTGTTCATTACTGTTTATAGTACTGTTTATTACTGTTAACGG
* * *
119579 TACTGTTCATTACTGTTTATAGTATTGTTTATTATTGTTCACGG
1 TACTGTTCATTACTGTTTATAGTACTGTTTATTACTGTTAACGG
*
119623 TAATGTTCAT
1 TACTGTTCAT
119633 ACCGTATAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.51
Consensus pattern (44 bp):
TACTGTTCATTACTGTTTATAGTACTGTTTATTACTGTTAACGG
Found at i:119629 original size:22 final size:22
Alignment explanation
Indices: 119523--119629 Score: 97
Period size: 22 Copynumber: 4.9 Consensus size: 22
119513 TAGCATTCGA
* *
119523 TACTATTCACGATACTGTTTAT
1 TACTGTTCACGGTACTGTTTAT
* **
119545 TACTGTTTATAGTACTGTTTAT
1 TACTGTTCACGGTACTGTTTAT
* *
119567 TACTGTTAACGGTACTGTTCAT
1 TACTGTTCACGGTACTGTTTAT
* ** *
119589 TACTGTTTATAGTATTGTTTAT
1 TACTGTTCACGGTACTGTTTAT
* *
119611 TATTGTTCACGGTAATGTT
1 TACTGTTCACGGTACTGTT
119630 CATACCGTAT
Statistics
Matches: 66, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (22 bp):
TACTGTTCACGGTACTGTTTAT
Found at i:120522 original size:23 final size:23
Alignment explanation
Indices: 120489--120532 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
120479 GAGTCGAGGG
120489 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGCGGTCCTTCGGGACAAT
*
120512 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
120533 TATATGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGGGACAAT
Found at i:120673 original size:23 final size:22
Alignment explanation
Indices: 120646--120714 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
120636 AATCTTATAT
120646 GGCACTATGGTGCATTTCTACGC
1 GGCACT-TGGTGCATTTCTACGC
* *
120669 GGCACTTTGGTGCAAATTCTACGT
1 GGCAC-TTGGTGC-ATTTCTACGC
*
120693 GGCACTTCGGTGCATTTATACG
1 GGCACTT-GGTGCATTTCTACG
120715 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (22 bp):
GGCACTTGGTGCATTTCTACGC
Found at i:120696 original size:24 final size:24
Alignment explanation
Indices: 120645--120706 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
120635 CAATCTTATA
* *
120645 TGGCACTATGGTGC-ATTTCTACG
1 TGGCACTTTGGTGCAAATTCTACG
*
120668 CGGCACTTTGGTGCAAATTCTACG
1 TGGCACTTTGGTGCAAATTCTACG
*
120692 TGGCACTTCGGTGCA
1 TGGCACTTTGGTGCA
120707 TTTATACGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 12 0.36
24 21 0.64
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (24 bp):
TGGCACTTTGGTGCAAATTCTACG
Found at i:122968 original size:17 final size:18
Alignment explanation
Indices: 122939--122975 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
122929 ATAATTTATG
122939 TAAAATCAAATTAATATT
1 TAAAATCAAATTAATATT
*
122957 TAAAAT-AAATTATTATT
1 TAAAATCAAATTAATATT
122974 TA
1 TA
122976 TTATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAATCAAATTAATATT
Found at i:124432 original size:3 final size:3
Alignment explanation
Indices: 124424--124484 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
124414 AATTATTTTT
* * *
124424 TAA TAA TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
124470 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
124485 ATAAATAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:124938 original size:113 final size:113
Alignment explanation
Indices: 124755--125174 Score: 705
Period size: 113 Copynumber: 3.7 Consensus size: 113
124745 AGAATCATGC
124755 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCAT
* * *
124820 TATGAACTCGACCTGGTACTGATGTTCCACCGAGTGATGAATTTAAGCA
65 TATGAACTCGAACTGGTACTGCTGTTCCATCGAGTGATGAATTTAAGCA
124869 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
* * * * * *
124934 ATGAACTCGACCTGGTAATGCTGATCCATTGAATGATGAATTCAAGCA
66 ATGAACTCGAACTGGTACTGCTGTTCCATCGAGTGATGAATTTAAGCA
* *
124982 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTATTCTCTTT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
* *
125047 ATGAACTCTAACTGGCACTGCTGTTCCATCGAGTGATGAATTTAAGCA
66 ATGAACTCGAACTGGTACTGCTGTTCCATCGAGTGATGAATTTAAGCA
*
125095 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
125160 ATGAACTCGAACTGG
66 ATGAACTCGAACTGG
125175 AAATGTTGAT
Statistics
Matches: 285, Mismatches: 21, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
113 280 0.98
114 5 0.02
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
ATGAACTCGAACTGGTACTGCTGTTCCATCGAGTGATGAATTTAAGCA
Found at i:125155 original size:226 final size:227
Alignment explanation
Indices: 124755--125197 Score: 780
Period size: 226 Copynumber: 2.0 Consensus size: 227
124745 AGAATCATGC
*
124755 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCAT
1 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTATTCTCAT
* *
124820 TATGAACTCGACCTGGTACTGATGTTCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGTT
66 TATGAACTCGAACTGGCACTGATGTTCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGTT
* *
124885 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTGGT
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGAACTGGA
124950 AATGCTGATCCATTGAATGATGAATTCAAGCA
196 AATGCTGATCCATTGAATGATGAATTCAAGCA
*
124982 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTATTCTCTT
1 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTATTCTCAT
* * *
125046 TATGAACTCTAACTGGCACTGCTGTTCCATCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGTT
66 TATGAACTCGAACTGGCACTGATGTTCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGTT
*
125111 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGAACTGGA
*
125176 AATGTTGATCCATTGAATGATG
196 AATGCTGATCCATTGAATGATG
125198 GATTTTAATC
Statistics
Matches: 205, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
226 200 0.98
227 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (227 bp):
AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTATTCTCAT
TATGAACTCGAACTGGCACTGATGTTCCACCGAGTGATGAATTTAAGCAAAAAGTTGAACAAGTT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGAACTGGA
AATGCTGATCCATTGAATGATGAATTCAAGCA
Found at i:126087 original size:114 final size:114
Alignment explanation
Indices: 125887--126111 Score: 396
Period size: 114 Copynumber: 2.0 Consensus size: 114
125877 ACGATCATGC
* * *
125887 AATTCATCTTGCAATTCTAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAA
1 AATTCATCTTGCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
*
125952 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
66 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCA
* *
126001 AATTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
1 AATTCATCTTGCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
126066 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGA
66 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGA
126112 TAACGTGGCA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 105 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (114 bp):
AATTCATCTTGCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCA
Found at i:126482 original size:20 final size:22
Alignment explanation
Indices: 126457--126496 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
126447 TTGAATTTTC
126457 GAAAATAAA-TT-GAATTTAGA
1 GAAAATAAACTTAGAATTTAGA
126477 GAAAATAAACTTAGAATTTA
1 GAAAATAAACTTAGAATTTA
126497 TTAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (22 bp):
GAAAATAAACTTAGAATTTAGA
Found at i:126842 original size:9 final size:9
Alignment explanation
Indices: 126828--126888 Score: 61
Period size: 9 Copynumber: 6.8 Consensus size: 9
126818 TGACCCTCCT
126828 TTTTTTTTC
1 TTTTTTTTC
126837 TTTTTTTTC
1 TTTTTTTTC
126846 TTTTTTTTTC
1 -TTTTTTTTC
*
126856 ATTTTTTTC
1 TTTTTTTTC
* **
126865 ATTTTCAT-
1 TTTTTTTTC
126873 TTTTTTTTC
1 TTTTTTTTC
*
126882 ATTTTTT
1 TTTTTTT
126889 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
8 5 0.12
9 29 0.67
10 9 0.21
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:126843 original size:11 final size:10
Alignment explanation
Indices: 126826--126863 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
126816 CTTGACCCTC
126826 CTTTTTTTTT
1 CTTTTTTTTT
126836 C-TTTTTTTT
1 CTTTTTTTTT
126845 CTTTTTTTTT
1 CTTTTTTTTT
126855 CATTTTTTT
1 C-TTTTTTT
126864 CATTTTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.35
10 10 0.38
11 7 0.27
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:126848 original size:19 final size:19
Alignment explanation
Indices: 126826--126869 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
126816 CTTGACCCTC
*
126826 CTTTTTTTTTCTTTTTTTT
1 CTTTTTTTTTCATTTTTTT
126845 CTTTTTTTTTCATTTTTTT
1 CTTTTTTTTTCATTTTTTT
126864 CATTTT
1 C-TTTT
126870 CATTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (19 bp):
CTTTTTTTTTCATTTTTTT
Found at i:126880 original size:11 final size:11
Alignment explanation
Indices: 126827--126893 Score: 68
Period size: 11 Copynumber: 6.0 Consensus size: 11
126817 TTGACCCTCC
126827 TTTTTTTTTC-
1 TTTTTTTTTCA
126837 -TTTTTTTTC-
1 TTTTTTTTTCA
126846 TTTTTTTTTCA
1 TTTTTTTTTCA
126857 TTTTTTTCATTTTCA
1 --TTTTT--TTTTCA
126872 TTTTTTTTTCA
1 TTTTTTTTTCA
*
126883 TTTTTTCTTCA
1 TTTTTTTTTCA
126894 AGCATAATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
9 9 0.18
10 9 0.18
11 16 0.32
13 10 0.20
15 6 0.12
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:137559 original size:17 final size:17
Alignment explanation
Indices: 137539--137576 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
137529 AATGAAATAT
137539 AAAT-ATAAATATTATAA
1 AAATAATAAATA-TATAA
*
137556 AAATAATAAGTATATAA
1 AAATAATAAATATATAA
137573 AAAT
1 AAAT
137577 TTGAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
AAATAATAAATATATAA
Found at i:138345 original size:17 final size:17
Alignment explanation
Indices: 138323--138357 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
138313 ATGTAAAATC
138323 AAATTAATATTTAATAT
1 AAATTAATATTTAATAT
* *
138340 AAATTATTATTTATTAT
1 AAATTAATATTTAATAT
138357 A
1 A
138358 TATATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATTAATATTTAATAT
Found at i:139810 original size:3 final size:3
Alignment explanation
Indices: 139802--139860 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
139792 AATTATTTTT
* * *
139802 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TTA TTA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
139849 TAA TAA TAA TAA
1 TAA TAA TAA TAA
139861 ATAAATAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:161434 original size:21 final size:21
Alignment explanation
Indices: 161408--161448 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
161398 GAAAAGAACG
*
161408 TCACCATCTTCGTCTTCTTCT
1 TCACCATCGTCGTCTTCTTCT
161429 TCACCATCGTCGTCTTCTTC
1 TCACCATCGTCGTCTTCTTC
161449 ATCTTCGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.39, G:0.07, T:0.44
Consensus pattern (21 bp):
TCACCATCGTCGTCTTCTTCT
Found at i:161444 original size:18 final size:18
Alignment explanation
Indices: 161417--161460 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
161407 GTCACCATCT
*
161417 TCGTCTTCTTCTTCACCA
1 TCGTCGTCTTCTTCACCA
* *
161435 TCGTCGTCTTCTTCATCT
1 TCGTCGTCTTCTTCACCA
161453 TCGTCGTC
1 TCGTCGTC
161461 GGCTTGGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.07, C:0.36, G:0.11, T:0.45
Consensus pattern (18 bp):
TCGTCGTCTTCTTCACCA
Found at i:161996 original size:10 final size:11
Alignment explanation
Indices: 161969--162022 Score: 53
Period size: 10 Copynumber: 5.2 Consensus size: 11
161959 ATAAGATAAC
161969 TATTAAA-T-T
1 TATTAAATTAT
161978 TATTAAATTAT
1 TATTAAATTAT
161989 TA-TAAATTTAT
1 TATTAAA-TTAT
* *
162000 CATTAAGTT-T
1 TATTAAATTAT
162010 TATTAAATTAT
1 TATTAAATTAT
162021 TA
1 TA
162023 AAAATAGTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 7 0.19
10 13 0.36
11 13 0.36
12 3 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
TATTAAATTAT
Found at i:162005 original size:31 final size:30
Alignment explanation
Indices: 161970--162078 Score: 89
Period size: 31 Copynumber: 3.6 Consensus size: 30
161960 TAAGATAACT
161970 ATTAAATTTATTAAATTATTATAAATTTATC
1 ATTAAATTTATTAAATTATTATAAA-TTATC
* *
162001 ATTAAGTTTTATTAAATTATTA-AAAATAGTC
1 ATTAA-ATTTATTAAATTATTATAAATTA-TC
* * *
162032 ATT--ATTTTTTAAAATTATTGTAAAATAATC
1 ATTAAATTTATT-AAATTATTAT-AAATTATC
* *
162062 ATTAAATTCATCAAATT
1 ATTAAATTTATTAAATT
162079 TTGTGATCGA
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
28 5 0.08
29 8 0.13
30 7 0.11
31 22 0.36
32 19 0.31
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (30 bp):
ATTAAATTTATTAAATTATTATAAATTATC
Found at i:162064 original size:30 final size:30
Alignment explanation
Indices: 161976--162065 Score: 94
Period size: 32 Copynumber: 2.9 Consensus size: 30
161966 AACTATTAAA
* *
161976 TTTATTAAATTATTATAAATTTATCATTAAGT
1 TTTATTAAATTATT-TAAAATAATCATT-AGT
* *
162008 TTTATTAAATTATTAAAAATAGTCATTA-T
1 TTTATTAAATTATTTAAAATAATCATTAGT
162037 TTT-TTAAAATTATTGTAAAATAATCATTA
1 TTTATT-AAATTATT-TAAAATAATCATTA
162066 AATTCATCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
28 2 0.04
29 12 0.24
30 13 0.26
31 9 0.18
32 14 0.28
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (30 bp):
TTTATTAAATTATTTAAAATAATCATTAGT
Found at i:169107 original size:36 final size:36
Alignment explanation
Indices: 169043--169148 Score: 169
Period size: 36 Copynumber: 3.0 Consensus size: 36
169033 AAAGATGAAC
* *
169043 ACTTGAATCGAAAGTG-TGATGCCTCCTTCCGTTCG
1 ACTTGAATCGAAAGTGCAGATGCTTCCTTCCGTTCG
*
169078 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGAAAGTGCAGATGCTTCCTTCCGTTCG
*
169114 ACTTGAATCGAAAGTGCAGATGCTTCCTTTCGTTC
1 ACTTGAATCGAAAGTGCAGATGCTTCCTTCCGTTC
169149 TTCTTATTCA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 16 0.24
36 50 0.76
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (36 bp):
ACTTGAATCGAAAGTGCAGATGCTTCCTTCCGTTCG
Found at i:180055 original size:3 final size:3
Alignment explanation
Indices: 180047--180072 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
180037 TCCCATTCGA
180047 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
180073 ATTAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:184895 original size:22 final size:22
Alignment explanation
Indices: 184867--184926 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
184857 TCGAAGGTTT
184867 CATAGGTCCTTCGGGACATATA
1 CATAGGTCCTTCGGGACATATA
* *
184889 CATAGGTCATTCGGGACATATT
1 CATAGGTCCTTCGGGACATATA
184911 CATAGGTCCTTCGGGA
1 CATAGGTCCTTCGGGA
184927 TAAATTTCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (22 bp):
CATAGGTCCTTCGGGACATATA
Found at i:189108 original size:13 final size:12
Alignment explanation
Indices: 189076--189110 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
189066 AATTCCGTTA
*
189076 TATTTTTATTTT
1 TATTTTTTTTTT
*
189088 TATTTTTTCTTT
1 TATTTTTTTTTT
189100 TATTTTTTTTT
1 TATTTTTTTTT
189111 CTGATTAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (12 bp):
TATTTTTTTTTT
Found at i:189995 original size:17 final size:19
Alignment explanation
Indices: 189973--190010 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
189963 AAAAAAAAAC
189973 AAAAAG-CAG-CTGTTCGA
1 AAAAAGACAGACTGTTCGA
*
189990 AAAAAGAGAGACTGTTCGA
1 AAAAAGACAGACTGTTCGA
190009 AA
1 AA
190011 GAAAAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.47, C:0.13, G:0.24, T:0.16
Consensus pattern (19 bp):
AAAAAGACAGACTGTTCGA
Found at i:191737 original size:14 final size:14
Alignment explanation
Indices: 191712--191747 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
191702 ATATTCTTAT
*
191712 TTTTACTTTAATTAC
1 TTTTA-TTTAATCAC
191727 TTTTATTTAATCAC
1 TTTTATTTAATCAC
191741 TTTTATT
1 TTTTATT
191748 ATCTTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTATTTAATCAC
Found at i:197529 original size:76 final size:76
Alignment explanation
Indices: 197403--197555 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
197393 TATTATGTTT
197403 GATGTCAGAAAATAGGTTTGTAATTGCCCTACAAATTTTAAGATTATATTCGATTTAGTCATTCA
1 GATGTCAGAAAATAGGTTTGTAATTGCCCTACAAATTTTAAGATTATATTCGATTTAGTCATTCA
197468 AATATTAATCA
66 AATATTAATCA
197479 GATGTCAGAAAATAGGTTTGTAATTGCCCTACAAATTTTAAGATTATATTCGATTTAGTCATTCA
1 GATGTCAGAAAATAGGTTTGTAATTGCCCTACAAATTTTAAGATTATATTCGATTTAGTCATTCA
197544 AATATTAATCA
66 AATATTAATCA
197555 G
1 G
197556 TCATTCGAAC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.38
Consensus pattern (76 bp):
GATGTCAGAAAATAGGTTTGTAATTGCCCTACAAATTTTAAGATTATATTCGATTTAGTCATTCA
AATATTAATCA
Found at i:197595 original size:21 final size:21
Alignment explanation
Indices: 197537--197598 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
197527 TTCGATTTAG
* *
197537 TCATTC-AA-ATATTAATCAG
1 TCATTCGAACATATTAATTAT
197556 TCATTCGAACATATTAATTAT
1 TCATTCGAACATATTAATTAT
* *
197577 TCTTTCGAATATATTAATTAT
1 TCATTCGAACATATTAATTAT
197598 T
1 T
197599 ATTTAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.16
20 2 0.05
21 29 0.78
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (21 bp):
TCATTCGAACATATTAATTAT
Found at i:197846 original size:18 final size:18
Alignment explanation
Indices: 197823--197859 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
197813 TACATTTTAA
*
197823 AAACATTTAACAAACATT
1 AAACATTTAAAAAACATT
197841 AAACATTTAAAAAACATT
1 AAACATTTAAAAAACATT
197859 A
1 A
197860 CATAATCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (18 bp):
AAACATTTAAAAAACATT
Found at i:197920 original size:18 final size:18
Alignment explanation
Indices: 197897--197933 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
197887 TGAATTTTAA
*
197897 AAACATTTAACAAACATT
1 AAACATTTAAAAAACATT
197915 AAACATTTAAAAAACATT
1 AAACATTTAAAAAACATT
197933 A
1 A
197934 CAAAATTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (18 bp):
AAACATTTAAAAAACATT
Found at i:198384 original size:21 final size:21
Alignment explanation
Indices: 198358--198422 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
198348 TAAAACCTTA
**
198358 CGGGCTAGGAATGTAACTTTG
1 CGGGCTAGGAATGTAACCCTG
* * *
198379 CGGGCTGGGTATGTACCCCTG
1 CGGGCTAGGAATGTAACCCTG
* *
198400 TGGGCTAGGAATATAACCCTG
1 CGGGCTAGGAATGTAACCCTG
198421 CG
1 CG
198423 ATGGTGGCAT
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.22, G:0.34, T:0.25
Consensus pattern (21 bp):
CGGGCTAGGAATGTAACCCTG
Found at i:198446 original size:42 final size:42
Alignment explanation
Indices: 198400--198479 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
198390 TGTACCCCTG
198400 TGGGCTAGGAATATAACCCTGC-GATGGTGGCATATGAATTGT
1 TGGGCTAGGAATATAACCCTGCGGA-GGTGGCATATGAATTGT
* * *
198442 TGGGCTAGGCATATACCCCTGCGGAGGTGGCATCTGAA
1 TGGGCTAGGAATATAACCCTGCGGAGGTGGCATATGAA
198480 CTGGTAGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.25
Consensus pattern (42 bp):
TGGGCTAGGAATATAACCCTGCGGAGGTGGCATATGAATTGT
Found at i:205677 original size:20 final size:21
Alignment explanation
Indices: 205652--205703 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
205642 TTTTCCCAAT
*
205652 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
205672 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
205693 TCGCAATGCGA
1 TCGCAATGCGA
205704 TACTGACTAT
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:205717 original size:20 final size:20
Alignment explanation
Indices: 205692--205826 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
205682 AATTGGGAAA
205692 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
205712 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
205732 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
205753 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
205773 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
205793 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
205813 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
205827 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:205736 original size:61 final size:61
Alignment explanation
Indices: 205689--205820 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
205679 GCGAATTGGG
* * * * *
205689 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
205750 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
205811 ATAATCGCAA
1 AAAATCGCAA
205821 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:206024 original size:22 final size:22
Alignment explanation
Indices: 205996--206037 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
205986 CTCTCTCACA
205996 CATCTCCGACGAAATCCGTCCC
1 CATCTCCGACGAAATCCGTCCC
206018 CATCTCCGACGAAATCCGTC
1 CATCTCCGACGAAATCCGTC
206038 TATCTCCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.43, G:0.14, T:0.19
Consensus pattern (22 bp):
CATCTCCGACGAAATCCGTCCC
Found at i:206339 original size:20 final size:20
Alignment explanation
Indices: 206302--206358 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
206292 GATTCTCTCG
**
206302 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
**
206322 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCA
**
206342 TTGCGATTTTCATTTTC
1 TTGCGATAGTCATTTTC
206359 AGAAACTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:207696 original size:18 final size:18
Alignment explanation
Indices: 207675--207719 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
207665 TCCACTTCGG
*
207675 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
207693 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
207711 GAGCCATCA
1 GAGCCATCA
207720 TCTGATTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:208255 original size:19 final size:20
Alignment explanation
Indices: 208212--208267 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
208202 CGTAACACGA
208212 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
208232 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
208251 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
208268 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:208275 original size:14 final size:14
Alignment explanation
Indices: 208256--208314 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
208246 ATGCGAAATG
208256 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
208270 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
208289 AAAATCGCAACGAC
1 AAAATCGCAACGAC
208303 AAAATCGCAACG
1 AAAATCGCAACG
208315 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:208282 original size:33 final size:33
Alignment explanation
Indices: 208240--208331 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
208230 GGAAATGGCT
208240 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
208273 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
208306 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
208332 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:208294 original size:19 final size:19
Alignment explanation
Indices: 208240--208336 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
208230 GGAAATGGCT
208240 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
208259 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
208273 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
208292 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
208306 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
208325 ATCGCAATGCGA
1 ATCGCAATGCGA
208337 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:208367 original size:14 final size:14
Alignment explanation
Indices: 208348--208434 Score: 75
Period size: 14 Copynumber: 5.6 Consensus size: 14
208338 TTGTGTTTCG
208348 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
208362 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
208378 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
208394 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
208411 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
208427 CGTTGCGA
1 CGTTGCGA
208435 ATTTCATTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
14 23 0.38
15 3 0.05
16 12 0.20
17 4 0.07
18 12 0.20
19 6 0.10
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:208412 original size:33 final size:32
Alignment explanation
Indices: 208343--208454 Score: 197
Period size: 33 Copynumber: 3.4 Consensus size: 32
208333 GCGATTTGTG
*
208343 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
208375 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGA-TTTCA
208408 TTTCGCATTGCGATTTTGTCGTTGCGAATTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCG-ATTTCA
208441 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
208455 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
32 26 0.34
33 50 0.65
34 1 0.01
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.46
Consensus pattern (32 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTCA
Found at i:208420 original size:19 final size:18
Alignment explanation
Indices: 208364--208454 Score: 90
Period size: 18 Copynumber: 5.4 Consensus size: 18
208354 GATTTTGTCG
208364 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
*
208382 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
208396 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
*
208415 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
208429 TTGCGAATTTCATTTCGCA
1 TTGCG-ATTTCATTTCGCA
208448 TTGCGAT
1 TTGCGAT
208455 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 11 0.19
15 7 0.12
16 8 0.14
17 8 0.14
18 14 0.24
19 11 0.19
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:208473 original size:20 final size:19
Alignment explanation
Indices: 208439--208490 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
208429 TTGCGAATTT
*
208439 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
208458 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
208478 CATTTTCGCGTTG
1 CA-TTTCGCGTTG
208491 TGATTTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 5 0.17
20 21 0.72
21 3 0.10
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.37
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:210390 original size:14 final size:14
Alignment explanation
Indices: 210356--210394 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
210346 TTGATTGTTT
210356 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
210370 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
210384 TGTTGATTTGT
1 AATTGATTTGT
210395 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:210540 original size:14 final size:16
Alignment explanation
Indices: 210521--210593 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 16
210511 GAAACTGACT
210521 ATCGCAACG-A-GAAA
1 ATCGCAACGAATGAAA
210535 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG-AATGAAA
210554 ATCGCAATACGAAATGAAA
1 ATCGC-A-ACG-AATGAAA
210573 ATCGCAACG-A-GAAA
1 ATCGCAACGAATGAAA
210587 ATCGCAA
1 ATCGCAA
210594 TGCGATTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 2 0.04
17 3 0.06
18 2 0.04
19 24 0.46
20 1 0.02
21 1 0.02
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.12
Consensus pattern (16 bp):
ATCGCAACGAATGAAA
Found at i:210555 original size:19 final size:19
Alignment explanation
Indices: 210531--210598 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
210521 ATCGCAACGA
210531 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
210550 GAAAATCGCAATACGAAAT
1 GAAAATCGCAATGCGAAAT
210569 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
210583 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
210599 TTTTTCATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 29 0.64
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:210878 original size:20 final size:20
Alignment explanation
Indices: 210862--210919 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
210852 ATTGCGATTT
*
210862 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCTCGTTGCGATAG
210882 TCAGAATCTCGTTGCGATAG
1 TCAGAATCTCGTTGCGATAG
* * *
210902 TCAGTATCGCATTGCGAT
1 TCAGAATCTCGTTGCGAT
210920 TTTCCAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (20 bp):
TCAGAATCTCGTTGCGATAG
Found at i:210955 original size:20 final size:21
Alignment explanation
Indices: 210908--210959 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
210898 ATAGTCAGTA
*
210908 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
210929 TCACATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
210949 TCGCATTGCGA
1 TCGCATTGCGA
210960 ATTAGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:211989 original size:12 final size:12
Alignment explanation
Indices: 211972--211996 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
211962 ATATAATCCT
211972 GAAGAAGAAAAA
1 GAAGAAGAAAAA
211984 GAAGAAGAAAAA
1 GAAGAAGAAAAA
211996 G
1 G
211997 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:214329 original size:33 final size:33
Alignment explanation
Indices: 214288--214395 Score: 155
Period size: 33 Copynumber: 3.3 Consensus size: 33
214278 GGAAATTACT
*
214288 ATCGCAACGAGAGAATCGCAATACGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* * *
214321 ATCACAACGCGA-ATTTCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGA-ATCGCAATGCGAAATGAAA
*
214354 ATCGCAACGAGGGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
214387 ATCGCAACG
1 ATCGCAACG
214396 CGAATTTAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
32 1 0.02
33 63 0.97
34 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:214360 original size:19 final size:19
Alignment explanation
Indices: 214336--214399 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
214326 AACGCGAATT
214336 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
**
214355 TCGCAA--CG--A-GGGAA
1 TCGCAATGCGAAATGAAAA
214369 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
214388 TCGCAACGCGAA
1 TCGCAATGCGAA
214400 TTTAATTTCG
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 20 0.57
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:214437 original size:19 final size:18
Alignment explanation
Indices: 214399--214470 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 18
214389 CGCAACGCGA
*
214399 ATTTAATTTCGCGTTGCG
1 ATTTCATTTCGCGTTGCG
214417 ATTTTCATTTCGCGTTGCG
1 A-TTTCATTTCGCGTTGCG
*
214436 A-TTC---TCTCGTTGCG
1 ATTTCATTTCGCGTTGCG
*
214450 ATCTTCATTTCGCATTGCG
1 AT-TTCATTTCGCGTTGCG
214469 AT
1 AT
214471 AATACTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
14 10 0.23
16 3 0.07
17 3 0.07
18 1 0.02
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.44
Consensus pattern (18 bp):
ATTTCATTTCGCGTTGCG
Found at i:214592 original size:14 final size:14
Alignment explanation
Indices: 214573--214609 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
214563 CATCAATTAA
214573 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
214587 ACAAATCACCTTTT
1 ACAAATCAACTTTT
214601 ACAAATCAA
1 ACAAATCAA
214610 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:216045 original size:42 final size:42
Alignment explanation
Indices: 215960--216048 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
215950 GTGAATCGGG
* *
215960 CTCTTGAATGGTGGGAGAGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGAGACCTCTTCAACGATGACAGGGGC
* * *
216002 CTCTTGAACGGTGGGAGGGGA-CTC-TCAAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GAGACCTCTTCAACG-ATGACAGGGGC
216044 CTCTT
1 CTCTT
216049 CAATGATAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 5 0.12
42 32 0.80
43 3 0.08
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGAGACCTCTTCAACGATGACAGGGGC
Found at i:216474 original size:91 final size:91
Alignment explanation
Indices: 216300--216484 Score: 293
Period size: 91 Copynumber: 2.0 Consensus size: 91
216290 ATTTCAAACT
* *
216300 TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT-AAG-ATAAACAGTTTAGC
216365 AGAATTGGCAGCAACCGAATAAATTTAC
64 AGAATTGGCAGCAACCGAATAAATTTAC
216393 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AG-TAAACAGTTTAGC
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAGATAAACAGTTTAGC
*
216456 AGTATTGGCAGCAACCGAATAAATTTAC
64 AGAATTGGCAGCAACCGAATAAATTTAC
216484 T
1 T
216485 AAGCAATATA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 40 0.46
93 20 0.23
95 27 0.31
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (91 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAGATAAACAGTTTAGCAG
AATTGGCAGCAACCGAATAAATTTAC
Found at i:218215 original size:40 final size:37
Alignment explanation
Indices: 218171--218316 Score: 121
Period size: 33 Copynumber: 4.1 Consensus size: 37
218161 TCTTTTGGTT
*
218171 GAAATGAAAATCACAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACG-GA-AATGAGAATCGCAACGC
**
218210 GGAAATGACTATCGCAAC-G--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGGAAATGAGAATCGCAACGC
*
218244 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACG-GAAATGAGAATCGCAACGC
* * *
218280 G--A-GAGAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACG-GAAATGAGAATCGCAACGC
218315 GA
1 GA
218317 TTTTGGTTTC
Statistics
Matches: 91, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
33 44 0.48
34 15 0.16
35 4 0.04
36 2 0.02
37 1 0.01
38 11 0.12
40 14 0.15
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (37 bp):
GAAATGAAAATCGCAACGGAAATGAGAATCGCAACGC
Found at i:218257 original size:19 final size:19
Alignment explanation
Indices: 218171--218316 Score: 132
Period size: 19 Copynumber: 8.1 Consensus size: 19
218161 TCTTTTGGTT
* *
218171 GAAATGAAAATCACAACGA
1 GAAATGAAAATCGCAACGC
*
218190 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
218210 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
218228 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
218244 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
218263 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
218280 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
218296 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
218315 GA
1 GA
218317 TTTTGGTTTC
Statistics
Matches: 104, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.18
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 45 0.43
20 26 0.25
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:218329 original size:52 final size:52
Alignment explanation
Indices: 218179--218316 Score: 204
Period size: 52 Copynumber: 2.6 Consensus size: 52
218169 TTGAAATGAA
* * * **
218179 AATCACAACGAGATAATGAGAATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGC-GAAATGAAAATCGCAACGAGAG
218233 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
218285 AATCGCAACGCGAAATGAAAATCGCAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGA
218317 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
52 51 0.65
53 16 0.21
54 11 0.14
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:218872 original size:21 final size:21
Alignment explanation
Indices: 218793--218866 Score: 139
Period size: 21 Copynumber: 3.5 Consensus size: 21
218783 TTATGAGTTG
218793 GGAAAATCGCAACGCGAAATT
1 GGAAAATCGCAACGCGAAATT
218814 GGAAAATCGCAACGCGAAATT
1 GGAAAATCGCAACGCGAAATT
218835 GGAAAATCGCAACGCGAAATT
1 GGAAAATCGCAACGCGAAATT
*
218856 AGAAAATCGCA
1 GGAAAATCGCA
218867 TTGCGATAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.14
Consensus pattern (21 bp):
GGAAAATCGCAACGCGAAATT
Found at i:219218 original size:30 final size:31
Alignment explanation
Indices: 219150--219225 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
219140 TTTATAAATA
* * *
219150 TATATTTTTATCACTTATATTATCAATTTAT
1 TATATTTTAATCAATTATATTATCAATTAAT
* * *
219181 TAAATTTTAATTAATTATATTATCGA-TAAT
1 TATATTTTAATCAATTATATTATCAATTAAT
219211 TATATTTTAATCAAT
1 TATATTTTAATCAAT
219226 GAGTTATTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
30 16 0.43
31 21 0.57
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (31 bp):
TATATTTTAATCAATTATATTATCAATTAAT
Found at i:219258 original size:76 final size:76
Alignment explanation
Indices: 219174--219332 Score: 230
Period size: 76 Copynumber: 2.1 Consensus size: 76
219164 TTATATTATC
* *
219174 AATT-TATTAAATTTTAATTAATTATATTATCGATAATTATATTTTAATCAATGAGTTATTAATT
1 AATTATATTAAATTTTAATCAATTATATTATCGATAATTATATTTTAATCAATGAATTATTAATT
*
219238 TCTATTTATTT
66 ACTATTTATTT
* ** * * *
219249 AATTATATTAAATTTTGATCAATTATATTATCGATTGTTATATTTTAATCATTTAATTGTTAATT
1 AATTATATTAAATTTTAATCAATTATATTATCGATAATTATATTTTAATCAATGAATTATTAATT
219314 ACTATTTATTT
66 ACTATTTATTT
219325 AATTATAT
1 AATTATAT
219333 GATATATCAG
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
75 4 0.05
76 70 0.95
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (76 bp):
AATTATATTAAATTTTAATCAATTATATTATCGATAATTATATTTTAATCAATGAATTATTAATT
ACTATTTATTT
Found at i:224037 original size:13 final size:13
Alignment explanation
Indices: 224016--224084 Score: 68
Period size: 14 Copynumber: 5.2 Consensus size: 13
224006 ACGAGTGGAC
*
224016 ATAAATATTTTAT
1 ATAAATATTATAT
*
224029 ATAAGTATTATAT
1 ATAAATATTATAT
*
224042 ATATATA-TATAT
1 ATAAATATTATAT
*
224054 ATATATATATATAT
1 ATAAATAT-TATAT
*
224068 ATATATATATATAT
1 ATAAATAT-TATAT
224082 ATA
1 ATA
224085 TGAAAATTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
12 12 0.24
13 16 0.32
14 22 0.44
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (13 bp):
ATAAATATTATAT
Found at i:224042 original size:2 final size:2
Alignment explanation
Indices: 224037--224085 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
224027 ATATAAGTAT
224037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
224079 TA TA TA T
1 TA TA TA T
224086 GAAAATTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:224684 original size:2 final size:2
Alignment explanation
Indices: 224667--224722 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
224657 AAAAATACAT
*
224667 TA TA T- TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
224708 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
224723 TACATTATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:225044 original size:37 final size:36
Alignment explanation
Indices: 224990--225310 Score: 376
Period size: 39 Copynumber: 8.5 Consensus size: 36
224980 TTGCAAACGG
224990 TTTTTGAAAATACATATATAATATATAGTTTTTAAAAACA
1 TTTTTGAAAAT---TATATAATATATAGTTTTT-AAAACA
*
225030 -TTTTGAAAATATATATAATATGTAGTTTTTAAAACA
1 TTTTTGAAAAT-TATATAATATATAGTTTTTAAAACA
* ** *
225066 CTTTTGAAAACCATATAATATATAGCTTTTAAAACA
1 TTTTTGAAAATTATATAATATATAGTTTTTAAAACA
* *
225102 CTTTTGAAAACTATATAATATATAGTTTTTAAAATCA
1 TTTTTGAAAATTATATAATATATAGTTTTTAAAA-CA
225139 -TTTTGAAAACTTATATAATATATAGTTTTTTGAAAACA
1 TTTTTGAAAA-TTATATAATATATAG-TTTTT-AAAACA
225177 TTTTTGAAAACTTATATAATATATAGTTTTTTGAAAACA
1 TTTTTGAAAA-TTATATAATATATAG-TTTTT-AAAACA
*
225216 TTTTTGAAACCTTATATAATATATAGTTTTTTGAAAACA
1 TTTTTGAAA-ATTATATAATATATAG-TTTTT-AAAACA
* *
225255 TTTTTGAAAATTTATAGAAAATATATAATTTTTAAAACA
1 TTTTTGAAAA-TTAT--ATAATATATAGTTTTTAAAACA
225294 TTTTTGAAAATTATATA
1 TTTTTGAAAATTATATA
225311 GTTTTTTAAA
Statistics
Matches: 258, Mismatches: 13, Indels: 24
0.87 0.04 0.08
Matches are distributed among these distances:
36 71 0.28
37 44 0.17
38 11 0.04
39 118 0.46
40 5 0.02
41 9 0.03
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (36 bp):
TTTTTGAAAATTATATAATATATAGTTTTTAAAACA
Found at i:225296 original size:29 final size:29
Alignment explanation
Indices: 225254--225322 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
225244 TTTTGAAAAC
*
225254 ATTTTTGAAAATTTATAGAAAA-TATATA-
1 ATTTTTAAAAATTT-TAGAAAATTATATAG
*
225282 ATTTTTAAAACATTTTTGAAAATTATATAG
1 ATTTTTAAAA-ATTTTAGAAAATTATATAG
*
225312 TTTTTTAAAAA
1 ATTTTTAAAAA
225323 ATAGTTTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 15 0.43
29 11 0.31
30 9 0.26
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (29 bp):
ATTTTTAAAAATTTTAGAAAATTATATAG
Found at i:226523 original size:4 final size:4
Alignment explanation
Indices: 226514--226559 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
226504 TTGGCCCTTT
* *
226514 TTTA TTTA TTTA TTTA TTTT TTTA CATT- TTTA TTTA TTT- TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTT
226560 CTAATTTTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 5 0.14
4 28 0.80
5 2 0.06
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:226534 original size:20 final size:18
Alignment explanation
Indices: 226511--226559 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
226501 AACTTGGCCC
226511 TTTTTTATTTATTTATTTA
1 TTTTTTATTT-TTTATTTA
*
226530 TTTTTTTACATTTTTATTTA
1 -TTTTTTA-TTTTTTATTTA
226550 TTTTTTATTT
1 TTTTTTATTT
226560 CTAATTTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.08
19 7 0.27
20 15 0.58
21 2 0.08
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTATTTTTTATTTA
Found at i:226595 original size:2 final size:2
Alignment explanation
Indices: 226588--226648 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
226578 TTCTATCATT
226588 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
226630 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
226649 TTATTATTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:232142 original size:84 final size:84
Alignment explanation
Indices: 232001--233209 Score: 1070
Period size: 84 Copynumber: 14.5 Consensus size: 84
231991 GAGACTATTG
** *
232001 GCAGCATAACTCAAGGCTAGAAGGGTTATCAACCAACAATAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
232066 GCTCCAAGACACATCATTT
66 GCTCCAAGACACATCATTT
* *
232085 GCAGCATAACTCAAGGTTAGAAGGGTTATCTGCCAACAAAAGGCCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
232150 GCTCCAAGACACATCATTT
66 GCTCCAAGACACATCATTT
* * * * * * * * * * *
232169 ACAACATAGCTTAAGTCGAAAAGGGATATCTGCCAACCAAAGGCCTTCGAGTTCGACTACGTTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
**
232234 GCTCCAAGGTACATCATTT
66 GCTCCAAGACACATCATTT
* ** * * * *
232253 GCAGCATAACTCAAGGCTAGAATGGTTATCT-ATAAAAAATATACCTTCGACTTCGACTACGTTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAA-AGACCTTCGAGTTCGACTACGCTC
** * * *
232317 ATATCAAAGGCATATCATTT
65 AGCTCCAAGACACATCATTT
* * * * * * * *
232337 GCAACATAGCTTAAGTCAAGAAGGGCTATCTGCCATCAAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
*
232402 GCTGCAAGACACATCATTT
66 GCTCCAAGACACATCATTT
* * * ** * * *
232421 GTAACATAGCTCAAGGAAAGAAGGGATATTTGCCAACAAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
* * *
232486 GCTCCAAGGCATATCATAT
66 GCTCCAAGACACATCATTT
* * *
232505 GCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
* *
232570 GCTCAAAGGCACATCATTT
66 GCTCCAAGACACATCATTT
* * * * * * * * * * * *
232589 GTAGCATAACTTAAGTCGATAAGGGCTATATGCCAA-TAAAGATCTTTGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
*
232653 GCT-CAACGACATATCATTT
66 GCTCCAA-GACACATCATTT
** * * * * * *
232672 GTGGTATAACTCAAGGCTAGAAGGGCTATCTG-C--C-AAAGACCTTCGGGTTCGATTACACTTA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
* *
232733 GCTTCGAGGGA-ACATCATTT
66 GC-TCCA-AGACACATCATTT
* * *
232753 GTAGCATAACTAAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGTTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
* *
232817 GCTCAAAGGCACATCATTT
66 GCTCCAAGACACATCATTT
* * * * * * * * * * * *
232836 GCAACATAACTTAA-GTTGATAAGGGCTATCTGCTAACCAAAGACGTTCGGGTTCGATTACACTT
1 GCAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTC
* * *
232900 AGCTTCGAGGGCACATCATTT
65 AGC-TCCAAGACACATCATTT
* * * * * * * *
232921 GTAGTATAACTCAAGACTAGAAGAGTTATCTGCTAAC-AAAGACCTTTGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
232985 GCT-CAATGACACATCATTT
66 GCTCCAA-GACACATCATTT
* * * *
233004 G-AGGTATAACTCAAGGCTAGAAGGGCTATCTG-C--C-AAAGACCGTT-GAGTTCGATTACACT
1 GCA-GCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACC-TTCGAGTTCGACTACGCT
* * * *
233063 CAGCTTCGAGGGCATATCATTT
64 CAGC-TCCAAGACACATCATTT
* * *
233085 GCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAATC-AAACACCTTCAAGTTCGACTACGCTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAAGACCTTCGAGTTCGACTACGCTC
*
233149 AGCTCCAAGACACATTATTT
65 AGCTCCAAGACACATCATTT
* * * * * *
233169 ACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAATAAAA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAA
233210 TTGTCGAGTT
Statistics
Matches: 917, Mismatches: 181, Indels: 54
0.80 0.16 0.05
Matches are distributed among these distances:
80 52 0.06
81 77 0.08
82 15 0.02
83 145 0.16
84 559 0.61
85 68 0.07
86 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (84 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
GCTCCAAGACACATCATTT
Found at i:233752 original size:2 final size:2
Alignment explanation
Indices: 233740--233787 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
233730 TATTTTATTT
*
233740 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
233782 TA TA TA
1 TA TA TA
233788 GTTTGCAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:233829 original size:39 final size:37
Alignment explanation
Indices: 233774--234122 Score: 395
Period size: 39 Copynumber: 9.2 Consensus size: 37
233764 TATATATATA
* * *
233774 TATATATATATATAG-TTTGCAAACGGTTTTTGAAAATACG
1 TATATA-ATATATAGTTTTGAAAAC-ATTTTTG-AAA-ACT
* *
233814 TATATAATATATAGTTTTTAAAACACTTTTGAAAAC-
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAACT
* * *
233850 CATATAATATATAGTTTTTAAAACATTTTAGAAAA-T
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAACT
*
233886 ATATATAATATATAGTTTTTAAAATCA-TTTTGAAAACT
1 -TATATAATATATAGTTTTGAAAA-CATTTTTGAAAACT
233924 TATATAATATATAGTTTTTTGAAAACATTTTTGAAAACT
1 TATATAATATATAG--TTTTGAAAACATTTTTGAAAACT
233963 TATATAATATATAGTTTTTTGAAAACATTTTTGAAAACT
1 TATATAATATATAG--TTTTGAAAACATTTTTGAAAACT
234002 TATATAATATATAGTTTTTTGAAAACATTTTT-AAAAGCT
1 TATATAATATATAG--TTTTGAAAACATTTTTGAAAA-CT
* *
234041 TATATAATATATAGTTTTTGAAAGCATTTTTGAAAATTT
1 TATATAATATATAG-TTTTGAAAACATTTTTGAAAA-CT
* *
234080 ATATATAATATATAATTTTTAAAACATTTTTGAAAA-T
1 -TATATAATATATAGTTTTGAAAACATTTTTGAAAACT
234117 TATATA
1 TATATA
234123 GTTTTTAAAA
Statistics
Matches: 282, Mismatches: 16, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
36 38 0.13
37 47 0.17
38 28 0.10
39 143 0.51
40 26 0.09
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (37 bp):
TATATAATATATAGTTTTGAAAACATTTTTGAAAACT
Found at i:234108 original size:29 final size:29
Alignment explanation
Indices: 234066--234162 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 29
234056 TTTTGAAAGC
* *
234066 ATTTTTGAAA-ATTTATATATAA-TATATA
1 ATTTTTAAAACATTT-TATAAAATTATATA
234094 ATTTTTAAAACATTTT-TGAAAATTATATA
1 ATTTTTAAAACATTTTAT-AAAATTATATA
*
234123 GTTTTTAAAAACATTTT-TAAAAATTATATA
1 ATTTTT-AAAACATTTTAT-AAAATTATATA
*
234153 GTTTTTAAAA
1 ATTTTTAAAA
234163 AAATATTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
27 1 0.02
28 13 0.21
29 19 0.31
30 28 0.46
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.48
Consensus pattern (29 bp):
ATTTTTAAAACATTTTATAAAATTATATA
Found at i:234136 original size:30 final size:30
Alignment explanation
Indices: 234088--234184 Score: 133
Period size: 30 Copynumber: 3.2 Consensus size: 30
234078 TTATATATAA
*
234088 TATATAATTTTT-AAAACATTTTTGAAAAT
1 TATATAGTTTTTAAAAACATTTTTGAAAAT
*
234117 TATATAGTTTTTAAAAACATTTTTAAAAAT
1 TATATAGTTTTTAAAAACATTTTTGAAAAT
*
234147 TATATAGTTTTTAAAAAAATATTTTTGAAAATT
1 TATATAGTTTTT--AAAAACATTTTTGAAAA-T
234180 TATAT
1 TATAT
234185 TATATAGTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
29 11 0.18
30 28 0.47
32 15 0.25
33 6 0.10
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.48
Consensus pattern (30 bp):
TATATAGTTTTTAAAAACATTTTTGAAAAT
Found at i:234221 original size:3 final size:3
Alignment explanation
Indices: 234213--234269 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
234203 CTTTTTATAT
234213 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
234262 TTT TTA TT
1 TTA TTA TT
234270 TTTTTGTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:235461 original size:18 final size:19
Alignment explanation
Indices: 235421--235461 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
235411 TCATTTATTT
*
235421 ATTTATTTTTTACGTTCTT
1 ATTTATTTTTTACGTTCTA
*
235440 ATTTATTTTTTA-TTTCTA
1 ATTTATTTTTTACGTTCTA
235458 ATTT
1 ATTT
235462 TGTATATTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (19 bp):
ATTTATTTTTTACGTTCTA
Found at i:235673 original size:4 final size:4
Alignment explanation
Indices: 235666--235704 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
235656 CTTTCTTTTG
* *
235666 ATTT ATTT A-GT ATTT ATGT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
235705 TCTCTAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 2 0.07
4 28 0.93
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:235674 original size:25 final size:25
Alignment explanation
Indices: 235621--235674 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
235611 TATTTTTATT
* *
235621 TTTATTTTTCCCTTTTTTTATTCTT
1 TTTATTCTTCCCTTTTTTTATTCTA
235646 TTTATTCTT-CCTTTCTTTTGATT-TA
1 TTTATTCTTCCCTTT-TTTT-ATTCTA
235671 TTTA
1 TTTA
235675 GTATTTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 5 0.20
25 17 0.68
26 3 0.12
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.72
Consensus pattern (25 bp):
TTTATTCTTCCCTTTTTTTATTCTA
Found at i:239682 original size:9 final size:9
Alignment explanation
Indices: 239669--239699 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
239659 TCCAAAGGCT
*
239669 CTTTATTTT
1 CTTTATTTA
239678 CTTTATTTA
1 CTTTATTTA
239687 CTTTATTTA
1 CTTTATTTA
239696 CTTT
1 CTTT
239700 TGCAATAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (9 bp):
CTTTATTTA
Found at i:241146 original size:21 final size:21
Alignment explanation
Indices: 241120--241187 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
241110 ATTCTGACTA
241120 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
241141 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
241162 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
241183 TCGCA
1 TCGCA
241188 ATGTGAATAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:241208 original size:20 final size:20
Alignment explanation
Indices: 241183--241295 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
241173 TTTTCCTAAT
*
241183 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
241203 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
**
241223 TCGCAATGCGAATATATAAA
1 TCGCAATGCGAATACGTAAA
* *
241243 TCGCAACGCGAAT-C-TGACTA
1 TCGCAATGCGAATACGT-A-AA
**
241263 TCGCAATGCGAATATATAAA
1 TCGCAATGCGAATACGTAAA
*
241283 TCGCAACGCGAAT
1 TCGCAATGCGAAT
241296 CTGACTATCG
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 75 0.95
21 1 0.01
22 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:241229 original size:40 final size:40
Alignment explanation
Indices: 241183--241313 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
241173 TTTTCCTAAT
* ** *
241183 TCGCAATGTGAATACGTAAATCGCAATGCGAATAC-GTA-AA
1 TCGCAATGCGAATATATAAATCGCAACGCGAAT-CTG-ACAA
*
241223 TCGCAATGCGAATATATAAATCGCAACGCGAATCTGACTA
1 TCGCAATGCGAATATATAAATCGCAACGCGAATCTGACAA
*
241263 TCGCAATGCGAATATATAAATCGCAACGCGAATCTGACTA
1 TCGCAATGCGAATATATAAATCGCAACGCGAATCTGACAA
241303 TCGCAATGCGA
1 TCGCAATGCGA
241314 TTTATATAGC
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
39 2 0.02
40 82 0.98
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATATATAAATCGCAACGCGAATCTGACAA
Found at i:241305 original size:20 final size:20
Alignment explanation
Indices: 241242--241313 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
241232 GAATATATAA
241242 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGAATCTGACT
* *
241262 ATCGCAATGCGAATAT-A-T
1 ATCGCAACGCGAATCTGACT
241280 AAATCGCAACGCGAATCTGACT
1 --ATCGCAACGCGAATCTGACT
*
241302 ATCGCAATGCGA
1 ATCGCAACGCGA
241314 TTTATATAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 39 0.91
21 1 0.02
22 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATCTGACT
Found at i:241518 original size:22 final size:22
Alignment explanation
Indices: 241493--241558 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
241483 GGCGACATCC
241493 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
241515 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
*
241537 GTCTCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
241559 TTCACGGTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:241931 original size:33 final size:34
Alignment explanation
Indices: 241883--241955 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
241873 ACTATCGCAA
** *
241883 TGCGATTCTGTCGTTGCGATTTTC-ATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
241916 TGCGATTCT-TGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAGTCAAATTCGCGT
241950 TGCGAT
1 TGCGAT
241956 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.40
Consensus pattern (34 bp):
TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
Found at i:241966 original size:20 final size:20
Alignment explanation
Indices: 241926--241995 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
241916 TGCGATTCTT
**
241926 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCATTTTC
241946 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCATTTTC
* * * **
241966 GTGTTGTGCTTTTCATTTTC
1 GCGTTGCGATAGTCATTTTC
*
241986 GTGTTGCGAT
1 GCGTTGCGAT
241996 TTAAAGTTTC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43
Consensus pattern (20 bp):
GCGTTGCGATAGTCATTTTC
Found at i:243912 original size:20 final size:20
Alignment explanation
Indices: 243887--244065 Score: 152
Period size: 20 Copynumber: 9.6 Consensus size: 20
243877 AGAATAGTTT
243887 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
243907 ACTATCGCAACGTGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
243927 ACTATTGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
243943 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
243960 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
* *
243976 A--ATCGTAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
243994 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
244014 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
**
244034 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
244054 ACTATCGCAATG
1 ACTATCGCAATG
244066 AAAGAATCGC
Statistics
Matches: 131, Mismatches: 14, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
14 12 0.09
16 10 0.08
17 8 0.06
18 4 0.03
19 7 0.05
20 90 0.69
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:244001 original size:34 final size:34
Alignment explanation
Indices: 243910--244003 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 34
243900 GAAAATGACT
* * * * *
243910 ATCGCAACGTGAAAATGACTATTGCAACGAGAGA
1 ATCGCAACGCGAAAATGACTATCGCAACAACAAA
* **
243944 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAAATGACTATCGCAACAACAAA
*
243977 ATCGTAACGCGAAAATGACTATCGCAA
1 ATCGCAACGCGAAAATGACTATCGCAA
244004 TGCGAAAATG
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
33 25 0.53
34 22 0.47
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.16
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGACTATCGCAACAACAAA
Found at i:244075 original size:34 final size:37
Alignment explanation
Indices: 243987--244084 Score: 121
Period size: 40 Copynumber: 2.6 Consensus size: 37
243977 ATCGTAACGC
243987 GAAAATGACTATCGCAATGCGAAAATGACTATCGCAAT
1 GAAAATGAC-ATCGCAATGCGAAAATGACTATCGCAAT
**
244025 GCAAAAATGACTATCGCAATGCGAATTTGACTATCGCAAT
1 G--AAAATGAC-ATCGCAATGCGAAAATGACTATCGCAAT
244065 G-AAA-GA-ATCGCAATGCGAAA
1 GAAAATGACATCGCAATGCGAAA
244085 TGAAAATCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
34 13 0.24
36 2 0.04
37 3 0.05
38 1 0.02
40 36 0.65
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (37 bp):
GAAAATGACATCGCAATGCGAAAATGACTATCGCAAT
Found at i:244086 original size:21 final size:19
Alignment explanation
Indices: 243943--244101 Score: 86
Period size: 20 Copynumber: 8.7 Consensus size: 19
243933 GCAACGAGAG
243943 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
243962 AATCGCAA--C--AA-CAA
1 AATCGCAATGCGAAATGAA
* * *
243976 AATCGTAACGCGAAAATGAC
1 AATCGCAATGCG-AAATGAA
* *
243996 TATCGCAATGCGAAAATGAC
1 AATCGCAATGCG-AAATGAA
* * *
244016 TATCGCAATGCAAAAATGAC
1 AATCGCAATGC-GAAATGAA
* * *
244036 TATCGCAATGCGAATTTGAC
1 AATCGCAATGCGAA-ATGAA
*
244056 TATCGCAAT--GAAA-G--
1 AATCGCAATGCGAAATGAA
244070 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
244089 AATCGCATTGCGA
1 AATCGCAATGCGA
244102 TTCTTTCGTT
Statistics
Matches: 114, Mismatches: 13, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
14 17 0.15
15 2 0.02
16 6 0.05
17 2 0.02
18 3 0.03
19 24 0.21
20 60 0.53
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:244232 original size:20 final size:20
Alignment explanation
Indices: 244110--244225 Score: 169
Period size: 20 Copynumber: 5.8 Consensus size: 20
244100 GATTCTTTCG
* ** *
244110 TTGCAATAGTCAAATTCGTA
1 TTGCGATAGTCATTTTCGCA
**
244130 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
244150 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
244170 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
244190 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
244210 TTGCGATAGTCATTTT
1 TTGCGATAGTCATTTT
244226 TGCGTTGTGA
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 91 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:244811 original size:21 final size:20
Alignment explanation
Indices: 244720--244824 Score: 70
Period size: 21 Copynumber: 5.1 Consensus size: 20
244710 GACTCACCTG
244720 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-C
* *
244740 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGG-CCCTC
** *
244762 TCATCCCTCAAGAGTCTCCTC
1 TCATCGTTCAAGAGGC-CCTC
* * *
244783 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
*
244804 TCATCGTTGAAGAGG-CCTC
1 TCATCGTTCAAGAGGCCCTC
244823 TC
1 TC
244825 CCAACATTCT
Statistics
Matches: 63, Mismatches: 17, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
19 4 0.06
20 4 0.06
21 51 0.81
22 1 0.02
23 3 0.05
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Done.