Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009626.1 Hibiscus syriacus cultivar Beakdansim tig00117018_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: 478969
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:115802 original size:14 final size:14
Alignment explanation
Indices: 115783--115840 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
115773 ATGCGAAATA
115783 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
115797 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
115813 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
115829 AAAATCGCAACG
1 AAAATCGCAACG
115841 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:115825 original size:32 final size:32
Alignment explanation
Indices: 115767--115857 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
115757 GGAAATGGCT
*
115767 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAAT-GAAATCGCAACGACAAA
115800 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
115832 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATG-AAATCGCAA
115858 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:115934 original size:20 final size:19
Alignment explanation
Indices: 115900--115954 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
115890 TTGCGGTTTT
*
115900 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
115919 CATTTCTGCGTTGCGATAGT
1 CATTTC-GCGTTGCGATAGC
115939 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
115955 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:117824 original size:14 final size:14
Alignment explanation
Indices: 117805--117840 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
117795 ATTGTTTAAT
117805 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
117819 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
117833 TGATTTGT
1 TGATTTGT
117841 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:117979 original size:19 final size:19
Alignment explanation
Indices: 117957--118024 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
117947 ATCGCAACGA
117957 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
117976 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
117995 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
118009 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
118025 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 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 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:118068 original size:20 final size:20
Alignment explanation
Indices: 118043--118080 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
118033 TCGCATTGCG
*
118043 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
118063 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
118081 TCAAATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:119049 original size:24 final size:24
Alignment explanation
Indices: 119022--119075 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
119012 GTATTCGAAA
* *
119022 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
119046 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
119070 TTTGAT
1 TTTGAT
119076 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:121601 original size:33 final size:33
Alignment explanation
Indices: 121559--121685 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
121549 GGAAATTACT
121559 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
121592 ATCGCAATGCGAAATGAAAATTGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
121624 TTTCGCAATGCGAAATAAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
121658 ATCGCAACGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
121686 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:121670 original size:66 final size:66
Alignment explanation
Indices: 121560--121692 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
121550 GAAATTACTA
* * * *
121560 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATTGCAACGCTAAT
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAT
121625 T
66 T
*
121626 TCGCAATGCGAAATAAAAATCGCAACGAGGGAATCGCAACGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAT
121691 T
66 T
121692 T
1 T
121693 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:121700 original size:19 final size:19
Alignment explanation
Indices: 121539--121689 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
121529 CTTAATGTCC
* **
121539 ATCGCAACGCGGAAATTACT
1 ATCGCAACGC-GAAATGAAA
*
121559 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
121578 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
121592 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
121611 ATTGCAACGC----T-AAT
1 ATCGCAACGCGAAATGAAA
* * *
121625 TTCGCAATGCGAAATAAAA
1 ATCGCAACGCGAAATGAAA
**
121644 ATCGCAA--CG--A-GGGA
1 ATCGCAACGCGAAATGAAA
121658 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
121677 ATCGCAACGCGAA
1 ATCGCAACGCGAA
121690 TTTAATTTCG
Statistics
Matches: 97, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
14 27 0.28
15 3 0.03
16 4 0.04
17 4 0.04
18 3 0.03
19 47 0.48
20 9 0.09
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:121707 original size:19 final size:20
Alignment explanation
Indices: 121685--121727 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
121675 AAATCGCAAC
121685 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
121704 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
121724 GCGA
1 GCGA
121728 TTCTCTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:121887 original size:14 final size:14
Alignment explanation
Indices: 121868--121904 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
121858 CATCAATTAA
121868 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
121882 ACAAATCACCTTTT
1 ACAAATCAACTTTT
121896 ACAAATCAA
1 ACAAATCAA
121905 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:123329 original size:21 final size:21
Alignment explanation
Indices: 123263--123329 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
123253 GTGAATCGGG
*
123263 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
123283 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
123305 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
123326 CTCT
1 CTCT
123330 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:123348 original size:42 final size:41
Alignment explanation
Indices: 123263--123385 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
123253 GTGAATCGGG
* * * * *
123263 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
123305 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
123347 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
123386 CGAGTCGAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:124531 original size:21 final size:22
Alignment explanation
Indices: 124489--124531 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
124479 AATAACAAAC
*
124489 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
124511 ATTA-TAATT-TTAAAAACATTA
1 ATTAGTAATTGTTAAAAA-ATTA
124532 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:125467 original size:33 final size:33
Alignment explanation
Indices: 125410--125508 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
125400 ACGAGATAAT
**
125410 GAGAATCGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
125444 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
125477 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
125509 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:125502 original size:19 final size:19
Alignment explanation
Indices: 125480--125550 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
125470 GCGACCAGAC
125480 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
125499 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
125519 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
125538 AATCGCAATGCGA
1 AATCGCAACGCGA
125551 TTTTTGCTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 30 0.62
20 18 0.38
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:125513 original size:20 final size:19
Alignment explanation
Indices: 125385--125550 Score: 118
Period size: 20 Copynumber: 9.1 Consensus size: 19
125375 TCTTTTGGTT
* *
125385 GAAATGAAAACCGCAACGA
1 GAAATGAAAATCGCAACGC
*
125404 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
125424 GGAAATGACTATCGCAA--T
1 -GAAATGAAAATCGCAACGC
*
125442 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
125458 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
125476 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
125491 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
125511 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
125530 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
125549 GA
1 GA
125551 TTTTTGCTTC
Statistics
Matches: 116, Mismatches: 18, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 1 0.01
17 1 0.01
18 3 0.03
19 43 0.37
20 44 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:125580 original size:19 final size:19
Alignment explanation
Indices: 125546--125626 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
125536 AAAATCGCAA
**
125546 TGCGATTTTTGCTTCGCGT
1 TGCGATTTTTATTTCGCGT
125565 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
125584 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
125598 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
125618 TGCGATTTT
1 TGCGATTTT
125627 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:126163 original size:20 final size:20
Alignment explanation
Indices: 126138--126190 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
126128 GCGCTATGTA
126138 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
126158 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
126178 TATCTCGTTGCGA
1 AATCGCGTTGCGA
126191 TTTTGTATTA
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:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:126224 original size:20 final size:20
Alignment explanation
Indices: 126199--126272 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
126189 GATTTTGTAT
126199 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
126219 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
126239 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
126259 TATCGCATTGCGAT
1 TATCGCATTGCGAT
126273 TTTCCCAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:126291 original size:81 final size:81
Alignment explanation
Indices: 126139--126293 Score: 186
Period size: 81 Copynumber: 1.9 Consensus size: 81
126129 CGCTATGTAA
* * * * * ** *
126139 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCG
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
126204 CATTGCGATAGTAAGT
66 CATTGCGATAGTAAGT
* * *
126220 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TC
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATC
*
126284 GCGTTGCGAT
65 GCATTGCGAT
126294 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
81 59 0.97
82 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (81 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCG
CATTGCGATAGTAAGT
Found at i:126383 original size:21 final size:21
Alignment explanation
Indices: 126340--126383 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
126330 GACATTGTAT
**
126340 ACTATCGCAACGCGATTTCCA
1 ACTATCGCAACGCGAAATCCA
*
126361 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATCCA
126382 AC
1 AC
126384 GCGAATTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATCCA
Found at i:126876 original size:2 final size:2
Alignment explanation
Indices: 126869--126894 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
126859 TGTCACATTC
126869 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
126895 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128009 original size:189 final size:190
Alignment explanation
Indices: 127685--128034 Score: 519
Period size: 189 Copynumber: 1.8 Consensus size: 190
127675 ATTTTTTACT
* *
127685 ATTGCAAATTAAAAGATAATTTTTAATTTGAATATCAATAGGATAATTACTCTTTTAATAAGTCA
1 ATTGCAAATTAAAAGATAATTTTTAATTTGAATATCAATAGGATAATTACTCTCTGAATAAGTCA
* * * *
127750 ATTTAAAAGGTATTTGTTATCTTTTTAATTTTGAATATTAAAAGATAATTATATACTTTTGTATA
66 ATTTAAAAGGTATATGTTATCTTTTTAACTTTGAATATTAAAAGATAATTATATACTTTTATACA
* *
127815 TTTCAAATTAAAATAATGCATGTTTAAGTTTGAATAATAAAATGAATTTACCTTTTGACC
131 TTTCAAATTAAAATAATACATATTTAAGTTTGAATAATAAAATGAATTTACCTTTTGACC
* * *
127875 ATTGCAAATT-AAATAT-ATTATTTAATTTGAATATTAATAGGATAATTACTCTCTGAATATGTC
1 ATTGCAAATTAAAAGATAATT-TTTAATTTGAATATCAATAGGATAATTACTCTCTGAATAAGTC
* *
127938 AATTTAAAAATGTATATGTTA-CATTTTTTACTTTGAATATT-AAAGATAATTATATACTTTTAT
65 AATTT-AAAAGGTATATGTTATC-TTTTTAACTTTGAATATTAAAAGATAATTATATACTTTTAT
*
128001 ACATTTCAAATTAAAATAATATATATTTAAGTTT
128 ACATTTCAAATTAAAATAATACATATTTAAGTTT
128035 AAATGGTAAA
Statistics
Matches: 143, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
188 3 0.02
189 101 0.71
190 39 0.27
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.45
Consensus pattern (190 bp):
ATTGCAAATTAAAAGATAATTTTTAATTTGAATATCAATAGGATAATTACTCTCTGAATAAGTCA
ATTTAAAAGGTATATGTTATCTTTTTAACTTTGAATATTAAAAGATAATTATATACTTTTATACA
TTTCAAATTAAAATAATACATATTTAAGTTTGAATAATAAAATGAATTTACCTTTTGACC
Found at i:139073 original size:37 final size:37
Alignment explanation
Indices: 139032--139106 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
139022 AGAACCACAC
* **
139032 GTTATTTGGGTGAGTGAGAACATGTTTAGAAAATAAG
1 GTTATCTGGGTGAGTGAGAACAAATTTAGAAAATAAG
*
139069 GTTATCTGGTTGAGTGAGAACAAATTTAGAAAATAAG
1 GTTATCTGGGTGAGTGAGAACAAATTTAGAAAATAAG
139106 G
1 G
139107 GTCCGCTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.31
Consensus pattern (37 bp):
GTTATCTGGGTGAGTGAGAACAAATTTAGAAAATAAG
Found at i:149367 original size:17 final size:17
Alignment explanation
Indices: 149345--149377 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
149335 TAGAAAAGAC
149345 ATAAAAAAATTTAAAAT
1 ATAAAAAAATTTAAAAT
*
149362 ATAAAATAATTTAAAA
1 ATAAAAAAATTTAAAA
149378 ATTTCAGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAAAAAATTTAAAAT
Found at i:150882 original size:27 final size:24
Alignment explanation
Indices: 150828--150888 Score: 61
Period size: 27 Copynumber: 2.5 Consensus size: 24
150818 ATAATCCAAA
150828 AAAAATA-ATAAAATAAAAAAAAC
1 AAAAATATATAAAATAAAAAAAAC
* *
150851 TAAAATATATAATAATAATAACAAAC
1 AAAAATATATAA-AATAA-AAAAAAC
*
150877 GAAAAAAATATA
1 -AAAAATATATA
150889 TTAAAAGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 6 0.20
24 4 0.13
25 5 0.17
26 6 0.20
27 9 0.30
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.20
Consensus pattern (24 bp):
AAAAATATATAAAATAAAAAAAAC
Found at i:151086 original size:27 final size:27
Alignment explanation
Indices: 151027--151092 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
151017 TGAGAATAAT
151027 GAATAATAA-AAATACATAATTAAATA
1 GAATAATAATAAATACATAATTAAATA
* *
151053 TGGATAATAATAAATACACTATTTAAATA
1 -GAATAATAATAAATACA-TAATTAAATA
151082 -AATAATAATAA
1 GAATAATAATAA
151093 GAAAAAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 18 0.53
28 7 0.21
29 9 0.26
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (27 bp):
GAATAATAATAAATACATAATTAAATA
Found at i:152822 original size:105 final size:106
Alignment explanation
Indices: 152599--153013 Score: 476
Period size: 105 Copynumber: 4.0 Consensus size: 106
152589 AGTATTGTTC
* ** * *
152599 TGAGTCCAATATCC-TCTGCTGTGAAGTTGAGATTGGTTCTGGAACCGGGAAATTGTTTATTGAC
1 TGAGTCCAATATCCTTC-GCTGTGAAGTTGAAATTGGCCCTGGAACTGGGAAATTGTTTGTTGAC
** *
152663 AGTCAGCCGCCCCTTCGCTGCGAAGTT-AAGCTTGTGCTGTCT
65 AACCAGCCGCCCCTTCGCTGTGAAGTTGAA-CTTGTGCTGTCT
* * *
152705 TGGGTCCAATATCCTTCGCTGTGAAGTTGAAACTGGCCCTGGAACTGGTAAATTG-TTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGGAACTGGGAAATTGTTTGTTGACA
* * * *
152769 ACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * *
152810 CGAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGG--CT----C--CGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGGAACTGGGAAATTGTTTGTTGACA
** *
152867 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * *
152908 TGGGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTG-TTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGGAACTGGGAAATTGTTTGTTGACA
* * *
152972 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
153013 T
1 T
153014 AGGTAGCATG
Statistics
Matches: 257, Mismatches: 41, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
97 6 0.02
98 74 0.29
99 1 0.00
100 2 0.01
103 2 0.01
104 1 0.00
105 115 0.45
106 54 0.21
107 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGGAACTGGGAAATTGTTTGTTGACA
ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
Found at i:152900 original size:203 final size:203
Alignment explanation
Indices: 152647--153012 Score: 660
Period size: 203 Copynumber: 1.8 Consensus size: 203
152637 CTGGAACCGG
152647 GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTAAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTAAGCTTGTGCTGTCTTGGGTCC
* * *
152712 AATATCCTTCGCTGTGAAGTTGAAACTGGCCCTGGAACTGGTAAATTGTTGTTGACAACCAACCG
66 AATATCCTCCGCTGTGAAGTTGAAACTGGCCCTGAAACTGGGAAATTGTTGTTGACAACCAACCG
152777 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAGA
131 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAGA
152842 TTGGCTCC
196 TTGGCTCC
* * *
152850 GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTAAGCTTGTGCTGTCTTGGGTCC
* *
152915 AATATCCTCCGCTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTGTTGTTGACAACCAGCCG
66 AATATCCTCCGCTGTGAAGTTGAAACTGGCCCTGAAACTGGGAAATTGTTGTTGACAACCAACCG
152980 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
131 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
153013 TAGGTAGCAT
Statistics
Matches: 155, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
203 155 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (203 bp):
GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTAAGCTTGTGCTGTCTTGGGTCC
AATATCCTCCGCTGTGAAGTTGAAACTGGCCCTGAAACTGGGAAATTGTTGTTGACAACCAACCG
TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAGA
TTGGCTCC
Found at i:152907 original size:98 final size:97
Alignment explanation
Indices: 152754--153012 Score: 284
Period size: 98 Copynumber: 2.6 Consensus size: 97
152744 TGGAACTGGT
* * *
152754 AAATTGTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAA
1 AAATTGTTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAA
* * *
152819 TATCCTTCGTTGTGAAGTTGAGATTGGCTCCG
66 TATCCTCCGCTGTGAAGTTGAAATTGGCTCCG
** * * * *
152851 AAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCA
1 AAATTG-TTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
*
152916 ATATCCTCCGCTGTGAAGTTGAAATTGGCCCTGAAACTGGG
65 ATATCCTCCGCTGTGAAGTTGAAATTGG--CT----C--CG
* * * *
152957 AAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 AAATTGTTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
153013 TAGGTAGCAT
Statistics
Matches: 134, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
97 6 0.04
98 74 0.55
100 2 0.01
104 1 0.01
105 44 0.33
106 7 0.05
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (97 bp):
AAATTGTTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAA
TATCCTCCGCTGTGAAGTTGAAATTGGCTCCG
Found at i:153074 original size:105 final size:103
Alignment explanation
Indices: 152955--153145 Score: 303
Period size: 105 Copynumber: 1.8 Consensus size: 103
152945 CCTGAAACTG
152955 GGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT-AGGTA
1 GGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGA-GTA
* *
153019 GCATGATATCATCCGTCGTGGAAAATCAGCTTTGAAATT
65 GCACGATATCATCCATCGTGGAAAATCAGCTTTGAAATT
*
153058 GGAAAGTTGTTCGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
1 GGAAA-TTGTT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
* *
153123 GGCACGATATCCTCCATCGTGGA
64 AGCACGATATCATCCATCGTGGA
153146 GTTGAAATCG
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
103 5 0.06
104 5 0.06
105 69 0.86
106 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (103 bp):
GGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTAG
CACGATATCATCCATCGTGGAAAATCAGCTTTGAAATT
Found at i:153898 original size:17 final size:19
Alignment explanation
Indices: 153862--153903 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
153852 CTTTTTGTTC
*
153862 TTTTTCTTTTTCTCTTATT
1 TTTTTCTTTTTCTCTGATT
153881 TTTTTCTTTTT-TC-GATT
1 TTTTTCTTTTTCTCTGATT
153898 TTTTTC
1 TTTTTC
153904 AATTTAGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 2 0.09
19 11 0.50
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTCTTTTTCTCTGATT
Found at i:153966 original size:49 final size:51
Alignment explanation
Indices: 153888--153985 Score: 130
Period size: 49 Copynumber: 1.9 Consensus size: 51
153878 ATTTTTTTCT
* *
153888 TTTTTCGATTTTTTTCAATTTAGGGCG-CCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTCGATTTTTTT-AACTTAGGACGCCCCTTT-GGGTTTTCACCCTAAACG
*
153940 TTTTTC-ATTTTTTT-ACTTAGGACGCCCCTTTGGGTTTTCATCCTAA
1 TTTTTCGATTTTTTTAACTTAGGACGCCCCTTTGGGTTTTCACCCTAA
153986 GCGAAGTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
49 22 0.52
50 6 0.14
51 8 0.19
52 6 0.14
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.47
Consensus pattern (51 bp):
TTTTTCGATTTTTTTAACTTAGGACGCCCCTTTGGGTTTTCACCCTAAACG
Found at i:164831 original size:27 final size:27
Alignment explanation
Indices: 164772--164837 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
164762 TGAGAATAAT
164772 GAATAATAA-AAATACATAATTAAATA
1 GAATAATAATAAATACATAATTAAATA
* *
164798 TGGATAATAATAAATACACTATTTAAATA
1 -GAATAATAATAAATACA-TAATTAAATA
164827 -AATAATAATAA
1 GAATAATAATAA
164838 GAAAAAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 18 0.53
28 7 0.21
29 9 0.26
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (27 bp):
GAATAATAATAAATACATAATTAAATA
Found at i:168447 original size:24 final size:25
Alignment explanation
Indices: 168411--168457 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
168401 AAAAATAAGA
168411 ATATTATTATTTTCTAA-TTTTTAT
1 ATATTATTATTTTCTAACTTTTTAT
*
168435 ATATT-TTATTTTTTTAACTTTTT
1 ATATTATTA-TTTTCTAACTTTTT
168458 TTCAATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.15
24 12 0.60
25 5 0.25
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (25 bp):
ATATTATTATTTTCTAACTTTTTAT
Found at i:170933 original size:17 final size:17
Alignment explanation
Indices: 170908--170941 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
170898 ACGTATTTTT
*
170908 ATTTTTTTTTTAATTTA
1 ATTTATTTTTTAATTTA
*
170925 ATTTATTTTTTATTTTA
1 ATTTATTTTTTAATTTA
170942 TTATTTGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTATTTTTTAATTTA
Found at i:184612 original size:23 final size:21
Alignment explanation
Indices: 184561--184621 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 21
184551 TTTGGTGCAA
*
184561 AGGGAATCGA-TCCCCCCTTG
1 AGGGAACCGATTCCCCCCTTG
*
184581 AGGGAACCGATTCCCCCTTTG
1 AGGGAACCGATTCCCCCCTTG
184602 AAGGGGAACCGATTCCCCCC
1 -A-GGGAACCGATTCCCCCC
184622 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.36, G:0.25, T:0.18
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCCTTG
Found at i:187429 original size:18 final size:19
Alignment explanation
Indices: 187406--187442 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
187396 ATTTTACACT
187406 TAGGGA-ACCGATTCCCCA
1 TAGGGAGACCGATTCCCCA
187424 TAGGGAGTACCGATTCCCC
1 TAGGGAG-ACCGATTCCCC
187443 CCACGCTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.19
Consensus pattern (19 bp):
TAGGGAGACCGATTCCCCA
Found at i:192246 original size:24 final size:24
Alignment explanation
Indices: 192219--192280 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
192209 CGTTCGTGAA
*
192219 CGTTCGGTTATGTTCATTTATATG
1 CGTTCAGTTATGTTCATTTATATG
* * *
192243 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCATTTATATG
*
192267 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
192281 TAACCTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.15, C:0.11, G:0.21, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCATTTATATG
Found at i:195975 original size:10 final size:10
Alignment explanation
Indices: 195960--196017 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
195950 GGTCTCCAAT
195960 GTTTATGTTC
1 GTTTATGTTC
195970 GTTTATGTTC
1 GTTTATGTTC
* *
195980 GTGTT-CGTTTAT
1 GT-TTATG-TT-C
*
195992 GTTTGTGTTC
1 GTTTATGTTC
196002 GTTTATGTTC
1 GTTTATGTTC
196012 GTTTAT
1 GTTTAT
196018 TTATTAAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 28 0.72
11 8 0.21
12 3 0.08
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.60
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:195984 original size:16 final size:16
Alignment explanation
Indices: 195965--196013 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
195955 CCAATGTTTA
195965 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
195981 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
195997 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
196013 T
1 T
196014 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.06, C:0.10, G:0.24, T:0.59
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:199040 original size:17 final size:18
Alignment explanation
Indices: 199018--199058 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
199008 ATATTAAAAA
199018 ATATTTGATAAT-ATTTT
1 ATATTTGATAATAATTTT
*
199035 ATATTT-CTAATAATTTT
1 ATATTTGATAATAATTTT
199052 ATATTTG
1 ATATTTG
199059 TTATATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (18 bp):
ATATTTGATAATAATTTT
Found at i:208355 original size:2 final size:2
Alignment explanation
Indices: 208350--208380 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
208340 TCTCTCTCTC
208350 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
208381 TCAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:218960 original size:237 final size:237
Alignment explanation
Indices: 218677--219147 Score: 897
Period size: 237 Copynumber: 2.0 Consensus size: 237
218667 TCTCCAATCA
218677 AATTGTGACACATATAGGCTAATTGAGAATAAAAACGGATAAGTGAGAACTTACATATAGACCAA
1 AATTGTGACACATATAGGCTAATTGAGAATAAAAACGGATAAGTGAGAACTTACATATAGACCAA
218742 TTTATTTATAATTGTTTTAAGATTTTAATATTTTTAAACTAAATTTATTGTTTTTCTATTTTTAA
66 TTTATTTATAATTGTTTTAAGATTTTAATATTTTTAAACTAAATTTATTGTTTTTCTATTTTTAA
218807 TGATAATATATATGAAATCATTTAAAAATAATTTAATATTAAAATCATAATCATTAATAAATAAA
131 TGATAATATATATGAAATCATTTAAAAATAATTTAATATTAAAATCATAATCATTAATAAATAAA
*
218872 ATGAAATAAATAATTTTAATTTTAAAAAAACTATAAATTTAT
196 ATGAAATAAATAATTTTAATTTAAAAAAAACTATAAATTTAT
* *
218914 AATTGTGACACATATAGGCTAATTGAGAATAAAAATGGATAAGTGAGAACTTACATCTAGACCAA
1 AATTGTGACACATATAGGCTAATTGAGAATAAAAACGGATAAGTGAGAACTTACATATAGACCAA
218979 TTTATTTATAATTGTTTTAAGATTTTAATATTTTTAAACTAAATTTATTGTTTTTCTATTTTTAA
66 TTTATTTATAATTGTTTTAAGATTTTAATATTTTTAAACTAAATTTATTGTTTTTCTATTTTTAA
* *
219044 TGATAATATATATGAAATCATTTAAAAATAATTTAATATTCAAATTATAATCATTAATAAATAAA
131 TGATAATATATATGAAATCATTTAAAAATAATTTAATATTAAAATCATAATCATTAATAAATAAA
219109 ATGAAATAAATAATTTTAATTTAAAAAAAACTATAAATT
196 ATGAAATAAATAATTTTAATTTAAAAAAAACTATAAATT
219148 AATTATAAAT
Statistics
Matches: 229, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
237 229 1.00
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.41
Consensus pattern (237 bp):
AATTGTGACACATATAGGCTAATTGAGAATAAAAACGGATAAGTGAGAACTTACATATAGACCAA
TTTATTTATAATTGTTTTAAGATTTTAATATTTTTAAACTAAATTTATTGTTTTTCTATTTTTAA
TGATAATATATATGAAATCATTTAAAAATAATTTAATATTAAAATCATAATCATTAATAAATAAA
ATGAAATAAATAATTTTAATTTAAAAAAAACTATAAATTTAT
Found at i:230679 original size:16 final size:16
Alignment explanation
Indices: 230658--230691 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
230648 TTACTATTCA
*
230658 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
230674 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
230690 CG
1 CG
230692 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:236555 original size:6 final size:6
Alignment explanation
Indices: 236544--236575 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
236534 GCTCATCTGC
236544 ATGCCT ATGCCT ATGCCT ATGCCT ATGCCT AT
1 ATGCCT ATGCCT ATGCCT ATGCCT ATGCCT AT
236576 TGCATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (6 bp):
ATGCCT
Found at i:237535 original size:26 final size:26
Alignment explanation
Indices: 237492--237571 Score: 106
Period size: 26 Copynumber: 3.0 Consensus size: 26
237482 TTAATAATTT
* *
237492 TCAAATAAATTTCTATTCAATTAATGG
1 TCAAAT-AATTTCGATTCGATTAATGG
*
237519 TCAAATAATTTCGATTCGATTAACGG
1 TCAAATAATTTCGATTCGATTAATGG
* *
237545 TCAAATAAATTCGGTTCGATTAATGG
1 TCAAATAATTTCGATTCGATTAATGG
237571 T
1 T
237572 TAAAGAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 41 0.87
27 6 0.13
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (26 bp):
TCAAATAATTTCGATTCGATTAATGG
Found at i:237735 original size:194 final size:187
Alignment explanation
Indices: 237364--237723 Score: 479
Period size: 194 Copynumber: 1.9 Consensus size: 187
237354 AATGATAAAA
*
237364 AAATTCGATTCGATTAATGGTTAAAGAAAAAAATTCGGTTAATTCAATTCGGTAAATAATTTTCA
1 AAATTCGATTCGATTAATGGTTAAAGAAAAAAATGCGGTTAATTCAATTCGGTAAATAATTTTCA
* * * *
237429 AATAAATTTTGGTTAGATTAACAATTAAGGAAAAAATAATTTATTTTATTCGGTTAATAATTTTC
66 AATAAATTTCGGGTAGATTAACAATTAAGAAAAAAATAATTTATTTTATTCGGTTAATAATTTTA
* * *
237494 AAATAAATTTCTATTCAATTAATGGTCAAATAATTTCGATTCGATTAACGGTCAAAT
131 AAATAAAATTCGATTCAATTAACGGTCAAATAATTTCGATTCGATTAACGGTCAAAT
* * *** *
237551 AAATTCGGTTCGATTAATGGTTAAAGAAAAAAA-GCGGTTGATTTGGTTCGGTTAATAATTTTCA
1 AAATTCGATTCGATTAATGGTTAAAGAAAAAAATGCGGTTAATTCAATTCGGTAAATAATTTTCA
* ** *
237615 AATAAATTTCGGGTCGATTAACGGTTAAAGAAAAATAATTTATTTTATTCAGTTAATTCGGTTAA
66 AATAAATTTCGGGTAGATTAACAATT-AAGAAAAA-AA--TAATTTATT---TT-ATTCGGTTAA
237680 TAATTTTAAAATAAAATTCGATTCAATTAACGGTCAAATAATTT
123 TAATTTTAAAATAAAATTCGATTCAATTAACGGTCAAATAATTT
237724 ATGTTCGATT
Statistics
Matches: 147, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
186 46 0.31
187 39 0.27
188 2 0.01
190 8 0.05
193 2 0.01
194 50 0.34
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (187 bp):
AAATTCGATTCGATTAATGGTTAAAGAAAAAAATGCGGTTAATTCAATTCGGTAAATAATTTTCA
AATAAATTTCGGGTAGATTAACAATTAAGAAAAAAATAATTTATTTTATTCGGTTAATAATTTTA
AAATAAAATTCGATTCAATTAACGGTCAAATAATTTCGATTCGATTAACGGTCAAAT
Found at i:237803 original size:94 final size:95
Alignment explanation
Indices: 237671--237852 Score: 298
Period size: 94 Copynumber: 1.9 Consensus size: 95
237661 ATTCAGTTAA
237671 TTCGGTTAATAATTTTAAAATAAAATTCGATTCAATTAACGGTCAAATAATTTAT-GTTCGATTA
1 TTCGGTTAATAATTTTAAAATAAAATTCGATTCAATTAACGGTCAAATAATTT-TGGTTCGATTA
237735 ATGGTTAAAG-AAAAAAATCGGTTTATTTGG
65 ATGGTTAAAGAAAAAAAATCGGTTTATTTGG
* * *
237765 TTCGGTTAATAATTTTCAAATAAATTTC-AGTTCGATTAACGGTCAAATAATTTTGGTTCGATTA
1 TTCGGTTAATAATTTTAAAATAAAATTCGA-TTCAATTAACGGTCAAATAATTTTGGTTCGATTA
237829 ATGGTTAAAGAAAAAAAATCGGTT
65 ATGGTTAAAGAAAAAAAATCGGTT
237853 AATAATTTTC
Statistics
Matches: 82, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
93 2 0.02
94 67 0.82
95 13 0.16
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (95 bp):
TTCGGTTAATAATTTTAAAATAAAATTCGATTCAATTAACGGTCAAATAATTTTGGTTCGATTAA
TGGTTAAAGAAAAAAAATCGGTTTATTTGG
Found at i:237806 original size:168 final size:172
Alignment explanation
Indices: 237528--237961 Score: 538
Period size: 168 Copynumber: 2.5 Consensus size: 172
237518 GTCAAATAAT
* * *
237528 TTCGATTCGATTAACGGTCAAATAAATTCGGTTCGATTAATGGTTAAAGAAAAAAAGCGGTTGAT
1 TTCGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTTAT
* * *
237593 TTGGTTCGGTTAATAATTTTCAAATAAATTTCGGGTCGATTAACGGTTAAAGAAAAATAATT-TA
66 TTGGTTCGGTTAATAATTTTCAAATAAATTTCAGGTCGATTAACGGTCAAAGAAAAATAATTCGA
* * ** *
237657 TT-TTATT-CAG-TTAATTCGGTTAATAATTTTAAAATAAAA
131 TTATGATTAAAGAAAAAATCGGTTAATAATTTTAAAATAAAA
* **
237696 TTCGATTCAATTAACGGTCAAATAATTTATGTTCGATTAATGGTTAAAGAAAAAAATCGGTTTAT
1 TTCGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTTAT
* * *** **
237761 TTGGTTCGGTTAATAATTTTCAAATAAATTTCAGTTCGATTAACGGTCAAATAATTTTGGTTCGA
66 TTGGTTCGGTTAATAATTTTCAAATAAATTTCAGGTCGATTAACGGTCAAAGAAAAATAATTCGA
* * *
237826 TTAATGGTTAAAGAAAAAAAATCGGTTAATAATTTTCAAATAAAT
131 TT-ATGATTAAAG--AAAAAATCGGTTAATAATTTTAAAATAAAA
* *
237871 TTCGGTTCGATTAACGGTCAAAAAATTTCGGTTCGATTAAT-GTTAAAGAAAAAAATTC-GTTTA
1 TTCGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAA-TCGGTTT-
*
237934 ATTTGTTTCGGTTAATAATTTTCAAATA
64 ATTTGGTTCGGTTAATAATTTTCAAATA
237962 TTTTTTGGTT
Statistics
Matches: 227, Mismatches: 30, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
168 112 0.49
169 3 0.01
171 3 0.01
172 2 0.01
174 18 0.08
175 89 0.39
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (172 bp):
TTCGATTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTTAT
TTGGTTCGGTTAATAATTTTCAAATAAATTTCAGGTCGATTAACGGTCAAAGAAAAATAATTCGA
TTATGATTAAAGAAAAAATCGGTTAATAATTTTAAAATAAAA
Found at i:237898 original size:26 final size:26
Alignment explanation
Indices: 237780--237910 Score: 95
Period size: 26 Copynumber: 4.9 Consensus size: 26
237770 TTAATAATTT
*
237780 TCAAATAAATTTCAGTTCGATTAACGG
1 TCAAA-AAATTTCGGTTCGATTAACGG
* * *
237807 TCAAATAATTTTGGTTCGATTAATGG
1 TCAAAAAATTTCGGTTCGATTAACGG
* ** * ***
237833 TTAAAGAAAAAAAATCGGTT--AATAATTT
1 -T---CAAAAAATTTCGGTTCGATTAACGG
237861 TCAAATAAATTTCGGTTCGATTAACGG
1 TCAAA-AAATTTCGGTTCGATTAACGG
237888 TCAAAAAATTTCGGTTCGATTAA
1 TCAAAAAATTTCGGTTCGATTAA
237911 TGTTAAAGAA
Statistics
Matches: 78, Mismatches: 19, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
24 3 0.04
25 9 0.12
26 35 0.45
27 16 0.21
28 5 0.06
30 10 0.13
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (26 bp):
TCAAAAAATTTCGGTTCGATTAACGG
Found at i:237904 original size:81 final size:80
Alignment explanation
Indices: 237766--237935 Score: 286
Period size: 81 Copynumber: 2.1 Consensus size: 80
237756 TTTATTTGGT
* *
237766 TCGGTTAATAATTTTCAAATAAATTTCAGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAAT
1 TCGGTTAATAATTTTCAAATAAATTTCAGTTCGATTAACGGTCAAAAAATTTCGGTTCGATTAAT
237831 GGTTAAAGAAAAAAAA
66 -GTTAAAGAAAAAAAA
*
237847 TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAAAAATTTCGGTTCGATTAAT
1 TCGGTTAATAATTTTCAAATAAATTTCAGTTCGATTAACGGTCAAAAAATTTCGGTTCGATTAAT
*
237912 GTTAAAGAAAAAAAT
66 GTTAAAGAAAAAAAA
*
237927 TCGTTTAAT
1 TCGGTTAAT
237936 TTGTTTCGGT
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 22 0.26
81 62 0.74
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (80 bp):
TCGGTTAATAATTTTCAAATAAATTTCAGTTCGATTAACGGTCAAAAAATTTCGGTTCGATTAAT
GTTAAAGAAAAAAAA
Found at i:237946 original size:175 final size:174
Alignment explanation
Indices: 237672--238029 Score: 540
Period size: 175 Copynumber: 2.1 Consensus size: 174
237662 TTCAGTTAAT
* *
237672 TCGGTTAATAATTTTAAAATAAAATTCGATTCAATTAACGGTCAAATAATTTATGTTCGATTAAT
1 TCGGTTAATAATTTTAAAATAAAATTCGATTCAATTAACGGTCAAAAAATTTAGGTTCGATTAAT
237737 GGTTAAAGAAAAAAATCGGTTTATTTGGTTCGGTTAATAATTTTCAAATAAATTTCAGTTCGATT
66 GGTTAAAGAAAAAAATCGGTTTATTTGGTTCGGTTAATAATTTTCAAATAAATTTCAGTTCGATT
*
237802 AACGGTCAAATAATTTTGGTTCGATTAATGGTTAAAGAAAAAAAA
131 AACGGTCAAATAATTTCGGTTCGATTAAT-GTTAAAGAAAAAAAA
* * * * *
237847 TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAAAAATTTCGGTTCGATTAAT
1 TCGGTTAATAATTTTAAAATAAAATTCGATTCAATTAACGGTCAAAAAATTTAGGTTCGATTAAT
* ** ** *
237912 -GTTAAAGAAAAAAATTC-GTTTAATTTGTTTCGGTTAATAATTTTCAAATATTTTTTGGTTTGA
66 GGTTAAAGAAAAAAA-TCGGTTT-ATTTGGTTCGGTTAATAATTTTCAAATAAATTTCAGTTCGA
237975 TTAACGGTCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAAA
129 TTAACGGTCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAAA
*
238021 TTGGTTAAT
1 TCGGTTAAT
238030 TTGGTTCGGT
Statistics
Matches: 166, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
174 41 0.25
175 125 0.75
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (174 bp):
TCGGTTAATAATTTTAAAATAAAATTCGATTCAATTAACGGTCAAAAAATTTAGGTTCGATTAAT
GGTTAAAGAAAAAAATCGGTTTATTTGGTTCGGTTAATAATTTTCAAATAAATTTCAGTTCGATT
AACGGTCAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAAA
Found at i:238008 original size:94 final size:94
Alignment explanation
Indices: 237847--238074 Score: 359
Period size: 94 Copynumber: 2.4 Consensus size: 94
237837 AGAAAAAAAA
237847 TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAAAAATTTCGGTTCGATTAAT
1 TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAAAAATTTCGGTTCGATTAAT
* *
237912 GTTAAAG-AAAAAAATTCGTTTAATTTGTT
66 GTTAAAGAAAAAAAATT-GGTTAATTTGGT
** * * *
237941 TCGGTTAATAATTTTCAAATATTTTTTGGTTTGATTAACGGTCAAATAATTTCGGTTCGATTAAT
1 TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAAAAATTTCGGTTCGATTAAT
238006 GTTAAAGAAAAAAAATTGGTTAATTTGGT
66 GTTAAAGAAAAAAAATTGGTTAATTTGGT
* *
238035 TCGGTTAATAATTTTTAAATAAATTTCGGTTCAATTAACG
1 TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACG
238075 ATTAAAGAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
94 111 0.93
95 9 0.08
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.41
Consensus pattern (94 bp):
TCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAAAAATTTCGGTTCGATTAAT
GTTAAAGAAAAAAAATTGGTTAATTTGGT
Found at i:238487 original size:30 final size:30
Alignment explanation
Indices: 238451--238507 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
238441 ATAATATGTA
238451 AATATTAAGGACCAAATATATAATTATTCC
1 AATATTAAGGACCAAATATATAATTATTCC
*
238481 AATATTAAGGATCAAATATATAATTAT
1 AATATTAAGGACCAAATATATAATTAT
238508 ATCAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (30 bp):
AATATTAAGGACCAAATATATAATTATTCC
Found at i:239982 original size:18 final size:18
Alignment explanation
Indices: 239959--240003 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
239949 AAGCTCGACA
239959 AACTCCTTGGACATGGCT
1 AACTCCTTGGACATGGCT
* *
239977 AACTCCTCTTGTACTTGGCT
1 AACT-C-CTTGGACATGGCT
239997 AACTCCT
1 AACTCCT
240004 CTTGTACTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.26
19 2 0.09
20 15 0.65
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.33
Consensus pattern (18 bp):
AACTCCTTGGACATGGCT
Found at i:239995 original size:20 final size:20
Alignment explanation
Indices: 239972--240016 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
239962 TCCTTGGACA
239972 TGGCTAACTCCTCTTGTACT
1 TGGCTAACTCCTCTTGTACT
239992 TGGCTAACTCCTCTTGTACT
1 TGGCTAACTCCTCTTGTACT
240012 TGGCT
1 TGGCT
240017 TCTACTTGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.40
Consensus pattern (20 bp):
TGGCTAACTCCTCTTGTACT
Found at i:251457 original size:21 final size:22
Alignment explanation
Indices: 251436--251477 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
251426 CAGATTGCCC
251436 AGAGGGAACCGATTCCCCCCCA
1 AGAGGGAACCGATTCCCCCCCA
* *
251458 AGGGGGTACCGATTCCCCCC
1 AGAGGGAACCGATTCCCCCC
251478 TGAATGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.40, G:0.26, T:0.12
Consensus pattern (22 bp):
AGAGGGAACCGATTCCCCCCCA
Found at i:252449 original size:21 final size:22
Alignment explanation
Indices: 252425--252468 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
252415 AAACATTTTC
252425 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* *
252446 TTAATATAATAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
252468 T
1 T
252469 ATTCAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Found at i:252670 original size:21 final size:23
Alignment explanation
Indices: 252646--252690 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
252636 TGATATTGAA
252646 AATAAATATACA-TTA-TTATTT
1 AATAAATATACATTTATTTATTT
* *
252667 AATACATATATATTTATTTATTT
1 AATAAATATACATTTATTTATTT
252690 A
1 A
252691 TGTGACTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 3 0.15
23 7 0.35
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
AATAAATATACATTTATTTATTT
Found at i:252719 original size:17 final size:17
Alignment explanation
Indices: 252697--252730 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
252687 TTTATGTGAC
252697 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
252714 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
252731 CAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:252755 original size:16 final size:16
Alignment explanation
Indices: 252736--252768 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
252726 AATAACAAAT
252736 TAATA-TTATAAATAAA
1 TAATATTTA-AAATAAA
252752 TAATATTTAAAATAAA
1 TAATATTTAAAATAAA
252768 T
1 T
252769 TTAAAAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATATTTAAAATAAA
Found at i:254046 original size:3 final size:3
Alignment explanation
Indices: 254026--254103 Score: 106
Period size: 3 Copynumber: 26.0 Consensus size: 3
254016 ATTGGGCCTG
*
254026 TAA T-A TAA TAA -AA TTAA TAA TAAA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
*
254071 TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
254104 ATAAAACCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.06
3 58 0.87
4 5 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:264811 original size:20 final size:21
Alignment explanation
Indices: 264786--264833 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
264776 GACCCAATCT
264786 AAAATAATATATTTATT-AAA
1 AAAATAATATATTTATTCAAA
* * *
264806 AAAATATTATTTTTATTCAAT
1 AAAATAATATATTTATTCAAA
264827 AAAATAA
1 AAAATAA
264834 GGAGTTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATAATATATTTATTCAAA
Found at i:269349 original size:35 final size:34
Alignment explanation
Indices: 269264--269350 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
269254 ATTAGGTATT
*
269264 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
269298 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
269336 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
269351 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:269573 original size:3 final size:3
Alignment explanation
Indices: 269565--269599 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
269555 CTCGCTGTCA
*
269565 TCG TCG TCG TCG TCA TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
269600 CTGAGCAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.29, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:271695 original size:17 final size:18
Alignment explanation
Indices: 271652--271692 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
271642 GAATTATATT
271652 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
271669 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
271687 ATTAAA
1 AGTAAA
271693 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:276359 original size:29 final size:29
Alignment explanation
Indices: 276326--276384 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 29
276316 CATGTACAGT
276326 ATATGAAATCTGTGTTCATTA-TGGTTTAA
1 ATATGAAATCTGTGTTCA-TAGTGGTTTAA
276355 ATATGAAATCTGTGTTCATAGTGGTTTAA
1 ATATGAAATCTGTGTTCATAGTGGTTTAA
276384 A
1 A
276385 CTAATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (29 bp):
ATATGAAATCTGTGTTCATAGTGGTTTAA
Found at i:277503 original size:99 final size:99
Alignment explanation
Indices: 277330--277513 Score: 269
Period size: 99 Copynumber: 1.9 Consensus size: 99
277320 CTGCGTCTTA
* * * * *
277330 GTCTAACCCTATTTTATTTTGGGATAAAGCATCTGGTACCTATATTTTTGCAACATCTTGTTTAA
1 GTCTAACCCCATCTTAGTTTGGGATAAAGCATCTGGTACCTATATTTTGGCAACACCTTGTTTAA
*
277395 AAATTTAGTTCTTAATTTTTGGCAACATCTAGTT
66 AAATCTAGTTCTTAATTTTTGGCAACATCTAGTT
* * * **
277429 GTCTAACCCCATCTTAGTTTGGTATAAAGCATCTGGTACCTATATTTTGGCAATACCTTTTTTTG
1 GTCTAACCCCATCTTAGTTTGGGATAAAGCATCTGGTACCTATATTTTGGCAACACCTTGTTTAA
277494 AAATCTAGTTCTTAATTTTT
66 AAATCTAGTTCTTAATTTTT
277514 ATTCACATTA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
99 74 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (99 bp):
GTCTAACCCCATCTTAGTTTGGGATAAAGCATCTGGTACCTATATTTTGGCAACACCTTGTTTAA
AAATCTAGTTCTTAATTTTTGGCAACATCTAGTT
Found at i:287137 original size:21 final size:21
Alignment explanation
Indices: 287111--287150 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
287101 CCCCCTTTGA
*
287111 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
287132 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
287151 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:289836 original size:20 final size:20
Alignment explanation
Indices: 289805--289857 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
289795 CTCAGAGGGA
289805 ACCGATTTCCCCCAAGGGGGT
1 ACCGA-TTCCCCCAAGGGGGT
289826 ACCGATTCCCCCAAGGGGGT
1 ACCGATTCCCCCAAGGGGGT
289846 ACCGATTCCCCC
1 ACCGATTCCCCC
289858 TTAATGGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.19, C:0.40, G:0.25, T:0.17
Consensus pattern (20 bp):
ACCGATTCCCCCAAGGGGGT
Found at i:301077 original size:18 final size:18
Alignment explanation
Indices: 301054--301135 Score: 119
Period size: 18 Copynumber: 4.6 Consensus size: 18
301044 GTCATAAACC
301054 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCCGTT
*
301072 GACCCGACCCGACTCGTT
1 GACCCGACCCGACCCGTT
* *
301090 GACCTGACCCGACTCGTT
1 GACCCGACCCGACCCGTT
* *
301108 GACCCGACCCGACCTGCT
1 GACCCGACCCGACCCGTT
301126 GACCCGACCC
1 GACCCGACCC
301136 ATTGACCGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.17, C:0.48, G:0.22, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:302016 original size:18 final size:18
Alignment explanation
Indices: 301990--302024 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
301980 TCGAAAGGAC
*
301990 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
302008 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
302025 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:304377 original size:22 final size:22
Alignment explanation
Indices: 304352--304406 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
304342 ATTTTTACAG
* * *
304352 TGTGACGCTCTGGTGGCCCTAA
1 TGTGACACTCCGGTGACCCTAA
304374 TGTGACACTCCGGTGACCCTAA
1 TGTGACACTCCGGTGACCCTAA
304396 TGTGACACTCC
1 TGTGACACTCC
304407 AAAGCGGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.31, G:0.25, T:0.25
Consensus pattern (22 bp):
TGTGACACTCCGGTGACCCTAA
Found at i:312047 original size:16 final size:16
Alignment explanation
Indices: 312023--312054 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
312013 TATCGCCGAC
*
312023 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
312039 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
312055 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:319276 original size:16 final size:16
Alignment explanation
Indices: 319255--319296 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
319245 GTACTCAATT
319255 TAACTCGAATAGAAA-A
1 TAACTCGAATA-AAACA
*
319271 TAACTCAAATAAAACA
1 TAACTCGAATAAAACA
*
319287 TAACTTGAAT
1 TAACTCGAAT
319297 CTAAAGCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (16 bp):
TAACTCGAATAAAACA
Found at i:319580 original size:48 final size:48
Alignment explanation
Indices: 319509--319607 Score: 135
Period size: 48 Copynumber: 2.1 Consensus size: 48
319499 TCTAAACTCG
* * ** * *
319509 AAATGACCCGATTGAAATCGAACTTAAACTGAATACAATTCAAACTTA
1 AAATGACCCGATTGAAATAGAACTCAAACCAAATACAATCCAAACTAA
*
319557 AAATGACCCGATTGAACTAGAACTCAAACCAAATACAATCCAAACTAA
1 AAATGACCCGATTGAAATAGAACTCAAACCAAATACAATCCAAACTAA
319605 AAA
1 AAA
319608 AATGACCTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.49, C:0.21, G:0.09, T:0.20
Consensus pattern (48 bp):
AAATGACCCGATTGAAATAGAACTCAAACCAAATACAATCCAAACTAA
Found at i:332930 original size:18 final size:19
Alignment explanation
Indices: 332894--332937 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
332884 ATATTTATTC
*
332894 ATTTT-ATTAATTTTTATA
1 ATTTTAATTAATTTTAATA
332912 ATTTTAATTAA-TTTAATA
1 ATTTTAATTAATTTTAATA
*
332930 AATTTAAT
1 ATTTTAAT
332938 CTCCAATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTTAATTAATTTTAATA
Found at i:334006 original size:32 final size:33
Alignment explanation
Indices: 333960--334022 Score: 119
Period size: 32 Copynumber: 1.9 Consensus size: 33
333950 CAGTGACATA
333960 TCACTATTTAATTGAAGATTAAATTTATTAATG
1 TCACTATTTAATTGAAGATTAAATTTATTAATG
333993 TCACTA-TTAATTGAAGATTAAATTTATTAA
1 TCACTATTTAATTGAAGATTAAATTTATTAA
334023 ATTGAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 24 0.80
33 6 0.20
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.44
Consensus pattern (33 bp):
TCACTATTTAATTGAAGATTAAATTTATTAATG
Found at i:334078 original size:23 final size:23
Alignment explanation
Indices: 334048--334093 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
334038 TGATCAAACT
334048 GACAATGTACATAAATATTGAAA
1 GACAATGTACATAAATATTGAAA
334071 GACAATGTACATAAATATTGAAA
1 GACAATGTACATAAATATTGAAA
334094 ATCAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (23 bp):
GACAATGTACATAAATATTGAAA
Found at i:338263 original size:2 final size:2
Alignment explanation
Indices: 338246--338281 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
338236 AATAATTCAT
338246 TA TA T- TA TA T- 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
338282 AACTAACCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:349715 original size:24 final size:25
Alignment explanation
Indices: 349686--349734 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
349676 AAGATTATAT
*
349686 TAAAATTT-TAGAGGTACGAAATTA
1 TAAAATTTCAAGAGGTACGAAATTA
*
349710 TAAAATTTCAAGAGGTGCGAAATTA
1 TAAAATTTCAAGAGGTACGAAATTA
349735 CATAATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (25 bp):
TAAAATTTCAAGAGGTACGAAATTA
Found at i:354519 original size:2 final size:2
Alignment explanation
Indices: 354512--354541 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
354502 TCACCTAATC
354512 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
354542 TTGAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:354991 original size:14 final size:15
Alignment explanation
Indices: 354972--355006 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
354962 AAACTAAGTT
354972 AAAACTAAT-AATAA
1 AAAACTAATAAATAA
354986 AAAACTAATAAAATAA
1 AAAACTAAT-AAATAA
355002 AAAAC
1 AAAAC
355007 GAACGCGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
16 10 0.53
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAACTAATAAATAA
Found at i:356358 original size:26 final size:27
Alignment explanation
Indices: 356328--356380 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
356318 ATTTTTGTTC
356328 GGTAATATAATTA-TTTTTTTATAAAA
1 GGTAATATAATTATTTTTTTTATAAAA
*
356354 GGTAATATGATTATTTTTTTTATAAAA
1 GGTAATATAATTATTTTTTTTATAAAA
356381 AATGAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (27 bp):
GGTAATATAATTATTTTTTTTATAAAA
Found at i:367526 original size:60 final size:59
Alignment explanation
Indices: 367446--367558 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 59
367436 AAATAGTCTC
* * * *
367446 TGATAATAGGATATTATTTCGTCGAGTATCTCGATTATTAAAAGTTATAAAATGATATAT
1 TGATAATAGGACAATATTTCGTCGAGTATCT-GACTATTAAAAGTTACAAAATGATATAT
* * * *
367506 TGATAATAGGACAATGTTTCGTTGATTTTCTGACTATTAAAAGTTACAAAATG
1 TGATAATAGGACAATATTTCGTCGAGTATCTGACTATTAAAAGTTACAAAATG
367559 GTTACTCGAC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 20 0.44
60 25 0.56
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (59 bp):
TGATAATAGGACAATATTTCGTCGAGTATCTGACTATTAAAAGTTACAAAATGATATAT
Found at i:374480 original size:22 final size:22
Alignment explanation
Indices: 374455--374509 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
374445 TCAGGAGTTA
* *
374455 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
374477 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
374499 CGGGAGTTATA
1 CAGGAGTTATA
374510 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:385374 original size:14 final size:13
Alignment explanation
Indices: 385356--385380 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
385346 AAAAAGGTTA
385356 AAAAAATTTATCC
1 AAAAAATTTATCC
385369 AAAAAATTTATC
1 AAAAAATTTATC
385381 TTAAACAAAG
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:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAATTTATCC
Found at i:385906 original size:17 final size:17
Alignment explanation
Indices: 385866--385913 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
385856 ATTTCCTTTA
385866 ATAATA-ATATTCA-AT
1 ATAATATATATTCACAT
*
385881 ATCATATATATTCACAT
1 ATAATATATATTCACAT
*
385898 TTAATATATATTCACA
1 ATAATATATATTCACA
385914 CTGAATTGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 5 0.18
16 7 0.25
17 16 0.57
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATATATATTCACAT
Found at i:389940 original size:16 final size:17
Alignment explanation
Indices: 389908--389940 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
389898 AATTTCTAAT
389908 TTTTGGTATCCAAATTC
1 TTTTGGTATCCAAATTC
*
389925 TTTTGGT-TCCATATTC
1 TTTTGGTATCCAAATTC
389941 ATTAGTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (17 bp):
TTTTGGTATCCAAATTC
Found at i:392011 original size:45 final size:46
Alignment explanation
Indices: 391961--392047 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
391951 AGTGCATCGG
391961 TGCATTCGATG-TTTCA-AAATAGCCAGAGTGCATCGATGCATCAAA
1 TGCATTCGATGTTTTCATAAA-AGCCAGAGTGCATCGATGCATCAAA
* **
392006 TGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGATGCAT
1 TGCATTCGATGTTTTCATAAAAGCCAGAGTGCATCGATGCAT
392048 GGTATGTGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 11 0.30
46 23 0.62
47 3 0.08
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (46 bp):
TGCATTCGATGTTTTCATAAAAGCCAGAGTGCATCGATGCATCAAA
Found at i:392122 original size:65 final size:64
Alignment explanation
Indices: 391988--392133 Score: 170
Period size: 65 Copynumber: 2.2 Consensus size: 64
391978 AATAGCCAGA
* *
391988 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCATAGTGCAACGATGCATGGTAT
* ** * *
392053 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCAACGATGCATGG-AT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCCATAGTGCAACGATGCATGGTA-
392116 T
64 T
*
392117 GGTGCATCGGTGCATCA
1 -GTGCATCGATGCATCA
392134 CTTTGATAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
63 4 0.06
64 23 0.33
65 42 0.61
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCATAGTGCAACGATGCATGGTAT
Found at i:394933 original size:17 final size:18
Alignment explanation
Indices: 394900--394933 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
394890 AATATATAAT
*
394900 ATTTTATTTTTATATATG
1 ATTTTATTTTAATATATG
394918 ATTTTA-TTTAATATAT
1 ATTTTATTTTAATATAT
394934 ACTTAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
ATTTTATTTTAATATATG
Found at i:400056 original size:2 final size:2
Alignment explanation
Indices: 400051--400079 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
400041 AACGAAACTG
400051 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
400080 CAACTAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:405054 original size:297 final size:291
Alignment explanation
Indices: 404470--405059 Score: 1101
Period size: 297 Copynumber: 2.0 Consensus size: 291
404460 ATGCTCCGTA
404470 TCTTGGCACTCAGATGGATATTTACTTACGCATTTTGACTTTACAAAATTTTTCTTTATATATAG
1 TCTTGGCACTCAGATGGATATTTACTTACGCATTTTGACTTTACAAAATTTTTCTTTATATATAG
404535 AATCAAACTGCGGCTTGGCCTTTGGAGTTATGTTGACGCTTGCTCACTTGATGTAGGAATTATTA
66 AATCAAACTGCGGCTTGGCCTTTGGAGTTATGTTGACGCTTGCTCACTTGATGTAGGAATTATTA
404600 CAGATGCTCAAATCCTGGATGCCCTGTCAAGAAACATGTAGAGAGGGCATCTCATGATGCAAAAT
131 CAGATGCTCAAATCCTGGATGCCCTGTCAAGAAACATGTAGAGAGGGCATCTCATGATGCAAAAT
*
404665 TGGTTATAACTACTTACGAGGGACAACATGATCATGATTTGCCTCCGAATAGGACTGTTACTCGC
196 TGGTTATAACTACTTACGAGGGACAACATGATCATGATTTGCCTCCGAATAGGACTGTTACTCAC
404730 AATATAACAGGGTAAATGTCCATCCAGCAGC
261 AATATAACAGGGTAAATGTCCATCCAGCAGC
404761 TCTTGGCACTCAGATGGATATTTTACTTATCGCATTTTGACTTTACAAAATTTTGCTTCTTTATA
1 TCTTGGCACTCAGATGGATA-TTTACTTA-CGCATTTTGACTTTACAAAA-TTT--TTCTTTATA
404826 TATAGAATCAAACTGCGGCTTGGCCTTTGGAGTTATGTTGACGCTCTGCTCACTTGATGTAGGAA
61 TATAGAATCAAACTGCGGCTTGGCCTTTGGAGTTATGTTGACGCT-TGCTCACTTGATGTAGGAA
404891 TTATTACAGATGCTCAAATCCTGGATGCCCTGTCAAGAAACATGTAGAGAGGGCATCTCATGATG
125 TTATTACAGATGCTCAAATCCTGGATGCCCTGTCAAGAAACATGTAGAGAGGGCATCTCATGATG
404956 CAAAATTGGTTATAACTACTTACGAGGGACAACATGATCATGATTTGCCTCCGAATAGGACTGTT
190 CAAAATTGGTTATAACTACTTACGAGGGACAACATGATCATGATTTGCCTCCGAATAGGACTGTT
405021 ACTCAC-ATATAACAGGAGTAAATGTCCATCCAGCAGC
255 ACTCACAATATAACAGG-GTAAATGTCCATCCAGCAGC
405058 TC
1 TC
405060 ATAATGTCGA
Statistics
Matches: 291, Mismatches: 1, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
291 20 0.07
292 8 0.03
293 20 0.07
294 3 0.01
296 64 0.22
297 176 0.60
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (291 bp):
TCTTGGCACTCAGATGGATATTTACTTACGCATTTTGACTTTACAAAATTTTTCTTTATATATAG
AATCAAACTGCGGCTTGGCCTTTGGAGTTATGTTGACGCTTGCTCACTTGATGTAGGAATTATTA
CAGATGCTCAAATCCTGGATGCCCTGTCAAGAAACATGTAGAGAGGGCATCTCATGATGCAAAAT
TGGTTATAACTACTTACGAGGGACAACATGATCATGATTTGCCTCCGAATAGGACTGTTACTCAC
AATATAACAGGGTAAATGTCCATCCAGCAGC
Found at i:409183 original size:23 final size:23
Alignment explanation
Indices: 409119--409183 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
409109 AATATAACCA
*
409119 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATTAACG
* *
409142 ATACCTATTACATTATATTAGCG
1 CTACCTATTACATTATATTAACG
*
409165 CTACATATTACATTATATT
1 CTACCTATTACATTATATT
409184 TTTACCTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (23 bp):
CTACCTATTACATTATATTAACG
Found at i:409562 original size:431 final size:431
Alignment explanation
Indices: 408761--409815 Score: 1960
Period size: 431 Copynumber: 2.5 Consensus size: 431
408751 TATTACATTA
408761 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
408826 TTATGTTTCAA-TTTTTTTAATAGTGTTTCA--TTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
408888 ATTTGCACAAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATT
131 ATTTGCAC-AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATT
*
408953 TAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTATTAAATTAATA
195 TAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATA
*
409018 TCTTAAAACTCACTCAAAATATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACAC
260 TCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACAC
*
409083 TTTTATAAAAAGTATAGGCACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCT
325 TTTTATAAAAAGTATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCT
* *
409148 ATTACATTATATTAGCGCTACATATTACATTATATTTTTACC
390 ATTACATTATATAAGCGCTACATATTACATCATATTTTTACC
*
409190 TATTATATTGAAAGTGTCCATACATTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
409255 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
409320 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
*
409385 AATAATAATATATATCGTAACGTAAAAAATAAATTATTAGACGCCTATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
*
409450 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGTACACT
261 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
409515 TTTATAAAAA-TGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCT
326 TTTATAAAAAGT-ATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCT
* *
409579 ATTACATTATATAAGCGCTACCTATTACATCATATTTTTACT
390 ATTACATTATATAAGCGCTACATATTACATCATATTTTTACC
409621 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
409686 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
409751 ATTTGCACAAAAAATTATTTGA-T-TTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
409814 AA
196 AA
409816 CAACATTAAC
Statistics
Matches: 611, Mismatches: 11, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
429 117 0.19
430 21 0.03
431 433 0.71
432 40 0.07
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (431 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
TTTATAAAAAGTATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
TTACATTATATAAGCGCTACATATTACATCATATTTTTACC
Found at i:409577 original size:23 final size:23
Alignment explanation
Indices: 409551--409613 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
409541 ATATAACCAC
409551 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
409574 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
409597 TACCTATTACATCATAT
1 TACCTATTACATTATAT
409614 TTTTACTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:410085 original size:39 final size:39
Alignment explanation
Indices: 410031--410114 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
410021 AAGTTGTAGA
*
410031 TTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGAAT
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGAAT
* *
410070 TTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGGAT
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGAAT
410109 TTTGAT
1 TTTGAT
410115 GAGCATCGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.18, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGAAT
Found at i:410428 original size:24 final size:24
Alignment explanation
Indices: 410373--410418 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
410363 CGAAATATAT
410373 ATTGAAATTCAAACTCAAATTAAA
1 ATTGAAATTCAAACTCAAATTAAA
* *
410397 ATTTAAATTCAAACTCCAATTA
1 ATTGAAATTCAAACTCAAATTA
410419 CATATGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTAAA
Found at i:410871 original size:23 final size:23
Alignment explanation
Indices: 410845--410907 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
410835 ATATAACCAC
410845 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
410868 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
410891 TACCTATTACATCATAT
1 TACCTATTACATTATAT
410908 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:412475 original size:181 final size:183
Alignment explanation
Indices: 411987--412476 Score: 862
Period size: 182 Copynumber: 2.7 Consensus size: 183
411977 TTAAAATTAC
* *
411987 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAATTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
412052 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
412117 ATATTATAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTATAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
412170 CGACACTTTTTTAAATCGTATCGACACA-TTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
412234 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
412299 ATATTA-CAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTATAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
412351 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
412415 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATA-TTATACCG
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
412477 ATAGCATTGC
Statistics
Matches: 295, Mismatches: 10, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
181 74 0.25
182 194 0.66
183 27 0.09
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTATAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
Found at i:413974 original size:3 final size:3
Alignment explanation
Indices: 413966--414010 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
413956 ACTTGTTTGG
* * *
413966 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
414011 GTCAGCTTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.27, C:0.33, G:0.02, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:414011 original size:12 final size:12
Alignment explanation
Indices: 413970--414046 Score: 82
Period size: 12 Copynumber: 6.4 Consensus size: 12
413960 GTTTGGATCA
* *
413970 TCATCTTCATCA
1 TCATCGTCATCT
* *
413982 TCATCATCATCA
1 TCATCGTCATCT
413994 TCATCGTCATCT
1 TCATCGTCATCT
*
414006 TCATCGTCAGCT
1 TCATCGTCATCT
*
414018 TCATCGTTATCT
1 TCATCGTCATCT
* *
414030 TTATCGTCAGCT
1 TCATCGTCATCT
414042 TCATC
1 TCATC
414047 TTCTGCGACC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 55 1.00
ACGTcount: A:0.21, C:0.31, G:0.08, T:0.40
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:414049 original size:6 final size:6
Alignment explanation
Indices: 413970--414049 Score: 63
Period size: 6 Copynumber: 13.3 Consensus size: 6
413960 GTTTGGATCA
* * * * * *
413970 TCATCT TCATCA TCATCA TCATCA TCATCG TCATCT TCATCG TCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * *
414018 TCATCGT T-ATCT TTATCG TCAGCT TCATCT TC
1 TCATC-T TCATCT TCATCT TCATCT TCATCT TC
414050 TGCGACCGCT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
5 2 0.03
6 56 0.93
7 2 0.03
ACGTcount: A:0.20, C:0.31, G:0.07, T:0.41
Consensus pattern (6 bp):
TCATCT
Found at i:414362 original size:57 final size:58
Alignment explanation
Indices: 414273--414386 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 58
414263 ATTCCATCAC
414273 GGTCTTAATTGTGACATCCTCTGCAACTGGAGCTTCTTCCATCATTGCGTCTCCACTT
1 GGTCTTAATTGTGACATCCTCTGCAACTGGAGCTTCTTCCATCATTGCGTCTCCACTT
414331 GGTCTTAA-TGTGACATCCTCTGCAACTGGAGCTTCTTCCATCATTGCGTCTCCACT
1 GGTCTTAATTGTGACATCCTCTGCAACTGGAGCTTCTTCCATCATTGCGTCTCCACT
414387 GGTTGCTCTT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 48 0.86
58 8 0.14
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.35
Consensus pattern (58 bp):
GGTCTTAATTGTGACATCCTCTGCAACTGGAGCTTCTTCCATCATTGCGTCTCCACTT
Found at i:416097 original size:196 final size:198
Alignment explanation
Indices: 415549--416500 Score: 1600
Period size: 196 Copynumber: 4.9 Consensus size: 198
415539 TTTAAATTAG
* *
415549 TATCGACACAAACTAAA-AAGTGTCGACATATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA-A
*
415613 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
415677 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGACCA
130 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
415742 AAAA
195 AAAA
*
415746 TATCGACAC-AACTAAA-AAGTGTCGACACATTATTTAGACATA-T-TCTCATAAAACCGGTATA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA-A
*
415807 CTTGTACCGGTTAGATTGAAAAATT--ATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
415869 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAAC-
130 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
415933 AAAA
195 AAAA
415937 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
* *
416002 TTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGAGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
*
416066 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTATGGAACAA
131 GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
416131 AAA
196 AAA
416134 TATCGACACAAA-TAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
* *
416198 CTCGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGAT
66 -TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
416263 CGACACTTTTTATATA--GATAGACACTTTATGGTTGCACCCTTTTTTCCATTCATTCTGGAACA
130 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACA
416326 AAAA
195 AAAA
416330 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
*
416394 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATG-TTTTGGGAT
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGAT
416458 -G--ACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
130 CGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
416501 GGCCATATGT
Statistics
Matches: 724, Mismatches: 17, Indels: 31
0.94 0.02 0.04
Matches are distributed among these distances:
191 13 0.02
192 118 0.16
193 43 0.06
194 77 0.11
195 85 0.12
196 246 0.34
197 69 0.10
198 73 0.10
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (198 bp):
TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAA
AAA
Found at i:416638 original size:18 final size:19
Alignment explanation
Indices: 416617--416660 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
416607 TTATATTCAC
416617 ATACAAAAATAT-AATCGT
1 ATACAAAAATATAAATCGT
* *
416635 ATACAAAATTATAAATCTT
1 ATACAAAAATATAAATCGT
416654 ATACAAA
1 ATACAAA
416661 TTAACCCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACAAAAATATAAATCGT
Found at i:418485 original size:32 final size:33
Alignment explanation
Indices: 418425--418486 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
418415 CATCTTAATA
*
418425 TCACCCCTTAACACCCCAAACTTCTTTCACACT
1 TCACCCCTCAACACCCCAAACTTCTTTCACACT
* *
418458 TCACCCCTCAACACCTC-TACTTCTTTCAC
1 TCACCCCTCAACACCCCAAACTTCTTTCAC
418487 CACTCCATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.42
33 15 0.58
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAAACTTCTTTCACACT
Found at i:418559 original size:20 final size:21
Alignment explanation
Indices: 418522--418564 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
418512 CCCCTTATGC
418522 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
*
418543 CTCTCAAGT-TCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
418563 CT
1 CT
418565 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.16, C:0.33, G:0.12, T:0.40
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:420828 original size:20 final size:19
Alignment explanation
Indices: 420773--420819 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
420763 TCCGGTATCA
420773 TTTTACCAGTTTTATCATT
1 TTTTACCAGTTTTATCATT
* *
420792 TTGATACCGGTTTTATCATAT
1 TT-TTACCAGTTTTATCAT-T
420813 TTTTACC
1 TTTTACC
420820 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCAGTTTTATCATT
Found at i:420981 original size:20 final size:20
Alignment explanation
Indices: 420954--421000 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
420944 TCCGGTAACG
420954 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
420973 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
420994 TTTTACC
1 TTTTACC
421001 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:421738 original size:229 final size:228
Alignment explanation
Indices: 421049--421767 Score: 1289
Period size: 228 Copynumber: 3.2 Consensus size: 228
421039 ACTTTTATAC
421049 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
421114 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
66 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
*
421179 TATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAT
131 TATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
*
421244 ATAATAATAAATATATTTTCCACAGTAAAATAA
196 ATAATAATAAATATATTTTCCACAGTGAAATAA
421277 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
* * *
421342 TTTTAATAGTGTTTCATATTTTCCACATACAATATTAATTTAATAATTTCATTTATACAAAAAAT
66 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
* *
421407 TATTTGATTATTTGATATTTTATAAAATATTATTTAGAGTTTAAATTTAACAATATTAACCAAAG
131 TATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
*
421472 ATAATAATAAATATGTTTTCCACAGTGAAATAA
196 ATAATAATAAATATATTTTCCACAGTGAAATAA
421505 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TT
* * *
421570 TTTTTAATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTTATTTACACATAAAA
65 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
421635 TTATTTGATTTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
130 TTATTTGA-TTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAA
421700 AGATAATAATAAATATATTTT-CACAGTGAAATAA
194 AGATAATAATAAATATATTTTCCACAGTGAAATAA
* *
421734 GTATGGACACTTTTATAAAAAGGATAGATA-TTTT
1 GTATGGACACTTTTATAAAAATGATATATACTTTT
421768 ACAATATAAC
Statistics
Matches: 470, Mismatches: 19, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
228 286 0.61
229 110 0.23
230 74 0.16
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (228 bp):
GTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAAT
TATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAG
ATAATAATAAATATATTTTCCACAGTGAAATAA
Found at i:422499 original size:12 final size:12
Alignment explanation
Indices: 422484--422508 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
422474 ATATTTATGA
422484 TAAAATATTATT
1 TAAAATATTATT
422496 TAAAATATTATT
1 TAAAATATTATT
422508 T
1 T
422509 TTTTATCAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:424595 original size:92 final size:94
Alignment explanation
Indices: 424417--424599 Score: 248
Period size: 92 Copynumber: 2.0 Consensus size: 94
424407 TCTAAGGATG
* * *
424417 ATTAGAGTTAAATTTAAAATTTATTAAAAAAATATTTTTCGTGTTTATAATATTTGTCCTTTACC
1 ATTAGAGTTAAATTTAAAATTTATCAAAAAAATAATTTTCGTGTTTATAATATTTGTCCTTTACA
424482 GAATTGAACATGAATATCAACAATATACA
66 GAATTGAACATGAATATCAACAATATACA
* * * * *
424511 ATTAGGGTTAAATTTAGAATTTGTCAAGAAAAGTTAATTTTCGTG-TT-T-ATATTTGTCTTTTA
1 ATTAGAGTTAAATTTAAAATTTATCAA-AAAA-ATAATTTTCGTGTTTATAATATTTGTCCTTTA
424573 CAG-ATTGAACATGAATATCAACAATAT
64 CAGAATTGAACATGAATATCAACAATAT
424600 CTAGAGTATA
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
92 24 0.30
93 15 0.19
94 24 0.30
95 6 0.08
96 10 0.13
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (94 bp):
ATTAGAGTTAAATTTAAAATTTATCAAAAAAATAATTTTCGTGTTTATAATATTTGTCCTTTACA
GAATTGAACATGAATATCAACAATATACA
Found at i:437710 original size:2 final size:2
Alignment explanation
Indices: 437703--437731 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
437693 TACCTTCTGA
437703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
437732 CAATACCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:449215 original size:2 final size:2
Alignment explanation
Indices: 449158--449197 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
449148 TTTAATCCAC
449158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
449198 TTAAATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:449547 original size:21 final size:21
Alignment explanation
Indices: 449523--449576 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
449513 CATACCCCAA
* *
449523 GTATCGATATTCCTTGAAGAG
1 GTATCGATACTCCTCGAAGAG
449544 GTATCGATACTCCTCGAAGAG
1 GTATCGATACTCCTCGAAGAG
449565 GTATCGATACTC
1 GTATCGATACTC
449577 ACCCTCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (21 bp):
GTATCGATACTCCTCGAAGAG
Done.