Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001523.1 Hibiscus syriacus cultivar Beakdansim tig00002982_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: 1321709
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:229721 original size:21 final size:21
Alignment explanation
Indices: 229695--229734 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
229685 TTTGAAGTAT
229695 AAAAATGGGTTGATTAAATAA
1 AAAAATGGGTTGATTAAATAA
229716 AAAAATGGGTTGATTAAAT
1 AAAAATGGGTTGATTAAAT
229735 GTAATTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (21 bp):
AAAAATGGGTTGATTAAATAA
Found at i:231352 original size:16 final size:17
Alignment explanation
Indices: 231331--231363 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
231321 ACACACTAAA
231331 TCGGTT-TCGATTTTTT
1 TCGGTTATCGATTTTTT
*
231347 TCGGTTATCGGTTTTTT
1 TCGGTTATCGATTTTTT
231364 GGATCGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.06, C:0.12, G:0.21, T:0.61
Consensus pattern (17 bp):
TCGGTTATCGATTTTTT
Found at i:231563 original size:42 final size:42
Alignment explanation
Indices: 231517--231837 Score: 345
Period size: 41 Copynumber: 7.8 Consensus size: 42
231507 TATGAAAATT
231517 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* *
231559 GCGGCGTTTGGTATTAAAACACCACAAAAGTAC-ATGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGA-GTCTATA
* *
231601 GCGGCGTTTATGTA--AAAACGCCACTAAAGTACGAATCTATA
1 GCGGCGTTT-GGTATTAAAACGCCACTAAAGTACGAGTCTATA
* * * *
231642 GCAGCGTTTGGTATTAAAACACCACAAAAGTACGTGTCTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* *
231684 GCGGCGTTTGTGTA--AAAATGCCACTAAAGTATGAGTCTATA
1 GCGGCGTTTG-GTATTAAAACGCCACTAAAGTACGAGTCTATA
* * * * *
231725 GCGGCGTCT-GTATAAAAACGCCACTAAAATACTAGTTTATA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* * * * *
231766 GCGGCGTTT-GTATAAAAACGCCACTACATTACGATTCTTTA
1 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
* *
231807 GCGGCGTTT-TTA-TACAAACACCACTAAAGTA
1 GCGGCGTTTGGTATTA-AAACGCCACTAAAGTA
231838 TAGTATTTTG
Statistics
Matches: 234, Mismatches: 36, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.01
40 4 0.02
41 141 0.60
42 80 0.34
43 6 0.03
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (42 bp):
GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
Found at i:231630 original size:83 final size:81
Alignment explanation
Indices: 231517--231868 Score: 399
Period size: 83 Copynumber: 4.3 Consensus size: 81
231507 TATGAAAATT
231517 GCGGCGTTTG-GTATTAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACAC
1 GCGGCGTTTGTGTA--AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-GTATTAAAACAC
231581 CACAAAAGTACATGTCTATA
63 CACAAAAGTAC-TGTCTATA
* * *
231601 GCGGCGTTTATGTAAAAACGCCACTAAAGTACGAATCTATAGCAGCGTTTGGTATTAAAACACCA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-GTATTAAAACACCA
231666 CAAAAGTACGTGTCTATA
65 CAAAAGTAC-TGTCTATA
* * * * *
231684 GCGGCGTTTGTGTAAAAATGCCACTAAAGTATGAGTCTATAGCGGCGTCTGTATAAAAACGCCAC
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTAAAACACCAC
*
231749 TAAAA-TACTAGTTTATA
66 -AAAAGTACT-GTCTATA
* * * * * *
231766 GCGGCGTTTGTATAAAAACGCCACTACATTACGATTCTTTAGCGGCGTTTTTA-TACAAACACCA
1 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTA-AAACACCA
* * * *
231830 CTAAAGTA-TAGTATTTT
65 CAAAAGTACT-GTCTATA
231847 GCGGCGTTTGT-TCAAAAACGCC
1 GCGGCGTTTGTGT-AAAAACGCC
231869 GCTATATGTA
Statistics
Matches: 234, Mismatches: 28, Indels: 15
0.84 0.10 0.05
Matches are distributed among these distances:
80 1 0.00
81 31 0.13
82 76 0.32
83 114 0.49
84 9 0.04
85 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (81 bp):
GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTAAAACACCAC
AAAAGTACTGTCTATA
Found at i:234499 original size:20 final size:21
Alignment explanation
Indices: 234474--234566 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
234464 TTTTCCCAAT
*
234474 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
234494 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
234515 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
234535 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
234556 TCGCAATGCGA
1 TCGCAATGCGA
234567 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:234519 original size:41 final size:41
Alignment explanation
Indices: 234474--234566 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
234464 TTTTCCCAAT
234474 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
234515 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
234556 TCGCAATGCGA
1 TCGCAATGCGA
234567 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:234579 original size:41 final size:41
Alignment explanation
Indices: 234493--234627 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
234483 GAATAAGTAA
* *
234493 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
234534 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
234575 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
234616 TTCGCAACGCGA
1 ATCGCAACGCGA
234628 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:234580 original size:20 final size:20
Alignment explanation
Indices: 234555--234669 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
234545 AATTGGGAAA
*
234555 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
234575 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
234596 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
234616 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
234636 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
234656 TTCGCAACGCGATA
1 ATCGCAACGCGATA
234670 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:234628 original size:41 final size:41
Alignment explanation
Indices: 234552--234689 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
234542 GCGAATTGGG
* * *
234552 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
234593 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
234635 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
234674 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
234690 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.39
41 44 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:235189 original size:20 final size:20
Alignment explanation
Indices: 235164--235201 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
235154 CGATTCTCTC
235164 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
235184 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
235202 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:235392 original size:25 final size:24
Alignment explanation
Indices: 235338--235392 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
235328 TGTTTATTAT
* *
235338 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
235362 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
235388 TGTTT
1 TGTTT
235393 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:236460 original size:18 final size:18
Alignment explanation
Indices: 236439--236483 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
236429 TCCACTTCGG
*
236439 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
236457 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
236475 GAGCCATCA
1 GAGCCATCA
236484 TCTGATCAAC
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:237019 original size:19 final size:20
Alignment explanation
Indices: 236976--237020 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
236966 CGCAACACGA
236976 AAATGACTATCACAACGCGG
1 AAATGACTATCACAACGCGG
* * *
236996 AAATGGCTATCGCAATGC-G
1 AAATGACTATCACAACGCGG
237015 AAATGA
1 AAATGA
237021 AAATCGCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAATGACTATCACAACGCGG
Found at i:237039 original size:14 final size:14
Alignment explanation
Indices: 237020--237083 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 14
237010 ATGCGAAATG
237020 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
237034 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
237050 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
237066 AAAATCGCAACG-C
1 AAAATCGCAACGAC
237079 AAAAT
1 AAAAT
237084 GAAAATCGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 6 0.14
14 21 0.48
16 8 0.18
18 9 0.20
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:237062 original size:32 final size:33
Alignment explanation
Indices: 237004--237094 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
236994 GGAAATGGCT
237004 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
237037 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
237069 ATCGCAACGCAAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
237095 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:237130 original size:14 final size:14
Alignment explanation
Indices: 237111--237168 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
237101 TTGTGTTTCG
237111 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
237125 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
237141 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
237157 CGTTGCGATTTT
1 CGTTGCGATTTT
237169 CATTTCGCAT
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:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:237149 original size:32 final size:33
Alignment explanation
Indices: 237106--237180 Score: 134
Period size: 32 Copynumber: 2.3 Consensus size: 33
237096 GCGATTTGTG
*
237106 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
237138 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
237171 TTTCGCATTG
1 TTTCGCATTG
237181 TGATAGCCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 26 0.63
33 15 0.37
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:237211 original size:20 final size:19
Alignment explanation
Indices: 237157--237224 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
237147 GCGATTTTGT
**
237157 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
237176 CATTGTGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
237196 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
237216 CGTTGCGAT
1 CGTTGCGAT
237225 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 12 0.31
20 24 0.62
21 3 0.08
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:239125 original size:14 final size:14
Alignment explanation
Indices: 239093--239127 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
239083 GATTGTTTAA
239093 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
239107 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
239121 TTGATTT
1 TTGATTT
239128 ATTTAATTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:239268 original size:19 final size:19
Alignment explanation
Indices: 239246--239313 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
239236 ATCGCAAAGA
239246 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
239265 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
239284 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
239298 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
239314 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:239357 original size:20 final size:20
Alignment explanation
Indices: 239332--239409 Score: 156
Period size: 20 Copynumber: 3.9 Consensus size: 20
239322 TCGCATTGCG
239332 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
239352 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
239372 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
239392 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
239410 TCAAATGAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:240492 original size:24 final size:24
Alignment explanation
Indices: 240465--240518 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
240455 GTATTCGAAA
* *
240465 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
240489 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
240513 TTTGAT
1 TTTGAT
240519 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:240710 original size:12 final size:12
Alignment explanation
Indices: 240693--240717 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
240683 ATATAATCCT
240693 GAAGAAGAAAAA
1 GAAGAAGAAAAA
240705 GAAGAAGAAAAA
1 GAAGAAGAAAAA
240717 G
1 G
240718 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:243042 original size:19 final size:19
Alignment explanation
Indices: 242986--243050 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
242976 AGAAATTACT
*
242986 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
243005 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
243019 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
243038 ATCGCAACGCGAA
1 ATCGCAATGCGAA
243051 TTTAATTTCG
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 21 0.60
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:243068 original size:19 final size:19
Alignment explanation
Indices: 243046--243087 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
243036 AAATCGCAAC
*
243046 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCATT
* *
243065 GCGATTTTCATTTCGCATT
1 GCGAATTTAATTTCGCATT
243084 GCGA
1 GCGA
243088 TAGTACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCATT
Found at i:243214 original size:14 final size:14
Alignment explanation
Indices: 243195--243231 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
243185 CATCAATTAA
243195 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
243209 ACAAATCACCTTTT
1 ACAAATCAACTTTT
243223 ACAAATCAA
1 ACAAATCAA
243232 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:244655 original size:21 final size:21
Alignment explanation
Indices: 244589--244655 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
244579 GTGAATCGGG
*
244589 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGAC
* * **
244610 CTCTTCAACGATGACAGTGG-C
1 CTCTTGAACGGTGGGAG-GGAC
*
244631 CTCTTGAACGGTGGGAGGGAA
1 CTCTTGAACGGTGGGAGGGAC
244652 CTCT
1 CTCT
244656 CGAGGAATGA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
20 2 0.06
21 30 0.88
22 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGAC
Found at i:244674 original size:42 final size:42
Alignment explanation
Indices: 244589--244682 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
244579 GTGAATCGGG
* * *
244589 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGAACTCTTCAACGATGACAGGGGC
* * *
244631 CTCTTGAACGGTGGGAGGGAACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGAACTCTTCAACG-ATGACAGGGGC
*
244673 CTCTTCAACG
1 CTCTTGAACG
244683 ATAGGAGTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 4 0.09
42 40 0.91
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGAACTCTTCAACGATGACAGGGGC
Found at i:244697 original size:42 final size:42
Alignment explanation
Indices: 244628--244707 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
244618 CGATGACAGT
* * *
244628 GGCCTCTTGAACGGTGGGAGGGAACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGAACTCTCGAGGAATGATAGG
* *
244670 GGCCTCTTCAACGATAGGAGTGG-ACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAG-GGAACTCTCGAGGAATGA
244708 CAGGCAAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 30 0.94
43 2 0.06
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGAACTCTCGAGGAATGATAGG
Found at i:246736 original size:20 final size:19
Alignment explanation
Indices: 246705--246865 Score: 74
Period size: 20 Copynumber: 8.8 Consensus size: 19
246695 TCTTTTGGTT
246705 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
246724 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
246745 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
246764 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** ** *
246778 GAAATGACTATCGTGACCA
1 GAAATGAAAATCGCAACGA
* *
246797 GACAATCATAA-CG---CG-
1 GA-AATGAAAATCGCAACGA
*
246812 -AAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
246831 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
246850 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
246866 TGCGATTTTT
Statistics
Matches: 107, Mismatches: 20, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
13 6 0.06
14 13 0.12
16 3 0.03
17 2 0.02
18 2 0.02
19 31 0.29
20 48 0.45
21 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:246787 original size:33 final size:33
Alignment explanation
Indices: 246730--246828 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 33
246720 ACGAGATAAT
*
246730 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
**
246764 GAGAATCGCAACGCGAAATGACTATCGTGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* ** **
246797 GACAATCATAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
246829 GCGAAATAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 41 0.75
34 14 0.25
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:246839 original size:19 final size:19
Alignment explanation
Indices: 246806--246870 Score: 103
Period size: 19 Copynumber: 3.4 Consensus size: 19
246796 AGACAATCAT
246806 AACGCGAAATGAAAATCGC
1 AACGCGAAATGAAAATCGC
*
246825 AACCGCGAAATAAAAATCGC
1 AA-CGCGAAATGAAAATCGC
246845 AACGCGAAATGAAAATCGC
1 AACGCGAAATGAAAATCGC
*
246864 AATGCGA
1 AACGCGA
246871 TTTTTGTTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
19 24 0.57
20 18 0.43
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AACGCGAAATGAAAATCGC
Found at i:247513 original size:20 final size:20
Alignment explanation
Indices: 247464--247577 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
247454 CGCTATGTAA
* * *
247464 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
247484 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
247504 ATCTCATTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
247525 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*
247545 ATCGCATTACGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
247565 ATCGCATTGCGAT
1 ATCGCATTGCGAT
247578 TTTCCCAATT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.77
21 13 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:247562 original size:61 final size:61
Alignment explanation
Indices: 247464--247580 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
247454 CGCTATGTAA
* * * *
247464 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCATTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTCAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
247525 ATCGCATTGCGATAGTCAGTATCGCATTACGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTCAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTT
247581 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:247596 original size:61 final size:61
Alignment explanation
Indices: 247464--247598 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
247454 CGCTATGTAA
* * * * ** *
247464 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCATTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
247525 ATCGCATTGCGATAGTCAGTATCGCATTACGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
247587 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
247599 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTCAGAATCGCATTACGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:248848 original size:11 final size:11
Alignment explanation
Indices: 248832--248860 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
248822 TGGGATATGA
248832 AAGAAAAGAAG
1 AAGAAAAGAAG
248843 AAGAAAAGAAG
1 AAGAAAAGAAG
248854 AAGAAAA
1 AAGAAAA
248861 AAAGGAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAGAAAAGAAG
Found at i:256416 original size:260 final size:260
Alignment explanation
Indices: 255955--256447 Score: 702
Period size: 260 Copynumber: 1.9 Consensus size: 260
255945 TTCAGTATAG
*
255955 CTCAAGGCGAGAAGGGTTATCTATCAACAAAAACCTTTGAGTTCGATTCTATTCAACTCAAAGGC
1 CTCAAGGCGAGAAGGGTTATCTATCAACAAAAACCTTTGAGTTCGATTCCATTCAACTCAAAGGC
* * * ** * *
256020 ATAATAATTTTACAGCATAGCTCAAGGTGAGAAGGGCTCTCTGTCAATGAAGATCATCGAGTTCG
66 ATAATAAATTTACAGCATAGCTCAAGGTGAGAAGGGCTATCTATCAACAAAAATCATCGAGTTCA
* * * * * *
256085 ATTCCATTCAGCTCGATGACATATCAAACACATAGTAGCAGTGATGAACTACTTTCTAGTTGAAG
131 ATTACATTCAACTCGATCACATATCAAACACATAGTAGCAGCGAGGAACTACTTTCCAGTTGAAG
* *
256150 TTTAAACTAAGGTCTTTAAGTCAAGAAGAAGATATGGGGTAATCTCTCAATCTAGTATAGCATAA
196 TTTAAACTAAGGTATTTAAGTCAAGAAGAAGACATGGGGTAATCTCTCAATCTAGTATAGCATAA
* * * *
256215 CTCAAGGTGATGAA-GGTTATCTATCAACAAAAACCTTTGAGTTCGATTCCATTTAGCTGAAAGG
1 CTCAAGGCGA-GAAGGGTTATCTATCAACAAAAACCTTTGAGTTCGATTCCATTCAACTCAAAGG
* * *
256279 CAT-ATCAAATTTATAGCATAGCTCAAGGTGAGAAGGGCTATCTATCAACAAAAATCTTTGAGTT
65 CATAAT-AAATTTACAGCATAGCTCAAGGTGAGAAGGGCTATCTATCAACAAAAATCATCGAGTT
* * * *
256343 CAATTACATTCAACTCGATCACATATCAACCGCATTGTAGCAGCGAGGAACTACTTTCCGGTTGA
129 CAATTACATTCAACTCGATCACATATCAAACACATAGTAGCAGCGAGGAACTACTTTCCAGTTGA
*
256408 AGTTTAAACTGAGGTATTTAAGTCAAGAAGAAGACATGGG
194 AGTTTAAACTAAGGTATTTAAGTCAAGAAGAAGACATGGG
256448 TTAGCTGTGT
Statistics
Matches: 203, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
259 2 0.01
260 198 0.98
261 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (260 bp):
CTCAAGGCGAGAAGGGTTATCTATCAACAAAAACCTTTGAGTTCGATTCCATTCAACTCAAAGGC
ATAATAAATTTACAGCATAGCTCAAGGTGAGAAGGGCTATCTATCAACAAAAATCATCGAGTTCA
ATTACATTCAACTCGATCACATATCAAACACATAGTAGCAGCGAGGAACTACTTTCCAGTTGAAG
TTTAAACTAAGGTATTTAAGTCAAGAAGAAGACATGGGGTAATCTCTCAATCTAGTATAGCATAA
Found at i:263158 original size:22 final size:22
Alignment explanation
Indices: 263114--263166 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
263104 TTTGCATTAG
* *
263114 TTTTATTATTTTTTTATAATAA
1 TTTTACTATTTTGTTATAATAA
*
263136 TATTTACTATTTTGTTAT-CTAA
1 T-TTTACTATTTTGTTATAATAA
263158 TTTGTACTA
1 TTT-TACTA
263167 AATTATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 2 0.08
22 10 0.38
23 14 0.54
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTACTATTTTGTTATAATAA
Found at i:266342 original size:115 final size:116
Alignment explanation
Indices: 266175--266395 Score: 315
Period size: 115 Copynumber: 1.9 Consensus size: 116
266165 GGAACAGATA
* * ** **
266175 AGCACACATAGTGTTGTCACATTGGAAATCGCAATATGTGCACAAAGTGCAATAACATCAGAATA
1 AGCACACATAGTGCTATCACATCAGAAATCGCAATATGCACACAAAGTGCAATAACATCAGAATA
*
266240 TATATACTAG-TGTACAC-TCTGGTACACCACAGTATATCAGATTCAGAAATG
66 TATATACT-GTTGTACACTTC-GGTACACCACAATATATCAGATTCAGAAATG
*
266291 AGCACACATAGTGCTATCACATCAGAAA-CAG-AATATGCACACAAAGTGCAATAACATCGGAAT
1 AGCACACATAGTGCTATCACATCAGAAATC-GCAATATGCACACAAAGTGCAATAACATCAGAAT
266354 ATATATACTGTTGTACACTTCGGTACACCACAATATATCAGA
65 ATATATACTGTTGTACACTTCGGTACACCACAATATATCAGA
266396 ATCGGAACAT
Statistics
Matches: 94, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
114 1 0.01
115 66 0.70
116 27 0.29
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (116 bp):
AGCACACATAGTGCTATCACATCAGAAATCGCAATATGCACACAAAGTGCAATAACATCAGAATA
TATATACTGTTGTACACTTCGGTACACCACAATATATCAGATTCAGAAATG
Found at i:273315 original size:2 final size:2
Alignment explanation
Indices: 273308--273351 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
273298 TTTTCTATGG
273308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
273350 AT
1 AT
273352 TAGGAAGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:273871 original size:14 final size:15
Alignment explanation
Indices: 273852--273885 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
273842 CTCATAACTA
273852 GAAAATTAAAT-ACT
1 GAAAATTAAATGACT
273866 GAAAATTAAATGACT
1 GAAAATTAAATGACT
273881 -AAAAT
1 GAAAAT
273886 GCAAATGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (15 bp):
GAAAATTAAATGACT
Found at i:275141 original size:3 final size:3
Alignment explanation
Indices: 275135--275181 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
275125 AGGACCTGTA
275135 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
275182 ATAAAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:277500 original size:110 final size:110
Alignment explanation
Indices: 277307--277507 Score: 278
Period size: 110 Copynumber: 1.8 Consensus size: 110
277297 ATAGTGGGGT
* * * * * * *
277307 TGGGCATCCATCTAATAGTATGGACCCCTGACGCTTGGTTTGGTGTTGGAGGAGCTTTTTGATGA
1 TGGGCATCCATCTAATAGTATGGACCCCTGAAGCTTGGTTTAGTGATAGAGGAGCTTCTTAAAGA
*
277372 TTCTGACTAGAAGAACTACCCTGACTTAAGATGTTACAATTTGAC
66 TTCTGACTAAAAGAACTACCCTGACTTAAGATGTTACAATTTGAC
* * * *
277417 TGGGCATTCATCTAATAGTGTTGACCCCTGAAGCTTTGTTTAGTGATAGAGGAGCTTCTTAACAG
1 TGGGCATCCATCTAATAGTATGGACCCCTGAAGCTTGGTTTAGTGATAGAGGAGCTTCTTAA-AG
277482 -TTCTGACTAAAAGAACTACCCTGACT
65 ATTCTGACTAAAAGAACTACCCTGACT
277508 AAAGGGTACA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
110 77 0.99
111 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (110 bp):
TGGGCATCCATCTAATAGTATGGACCCCTGAAGCTTGGTTTAGTGATAGAGGAGCTTCTTAAAGA
TTCTGACTAAAAGAACTACCCTGACTTAAGATGTTACAATTTGAC
Found at i:277698 original size:27 final size:27
Alignment explanation
Indices: 277668--277797 Score: 153
Period size: 27 Copynumber: 5.0 Consensus size: 27
277658 AGAATAGTAC
* *
277668 TGCAACAAAAAATATCTCAATACCAAG
1 TGCAACAAAAAATGTCTCAATACCAAA
* *
277695 TGCAA-ACAAATATGTCTCAGTACCAAA
1 TGCAACA-AAAAATGTCTCAATACCAAA
*
277722 TGCAAC--AAACTGTCTCAATACCAAA
1 TGCAACAAAAAATGTCTCAATACCAAA
* *
277747 TGCAACAAAATATTTCTCAATACCAAA
1 TGCAACAAAAAATGTCTCAATACCAAA
277774 TGCAAC--AAAATGTCTCAATACCAA
1 TGCAACAAAAAATGTCTCAATACCAA
277798 GTTTAATATA
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
25 38 0.44
26 1 0.01
27 48 0.55
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.22
Consensus pattern (27 bp):
TGCAACAAAAAATGTCTCAATACCAAA
Found at i:277742 original size:52 final size:52
Alignment explanation
Indices: 277676--277799 Score: 187
Period size: 52 Copynumber: 2.4 Consensus size: 52
277666 ACTGCAACAA
* *
277676 AAAATATCTCAATACCAAGTGCAA-ACAAATATGTCTCAGTACCAAATGCAAC
1 AAAATGTCTCAATACCAAGTGCAACA-AAATATGTCTCAATACCAAATGCAAC
* * *
277728 AAACTGTCTCAATACCAAATGCAACAAAATATTTCTCAATACCAAATGCAAC
1 AAAATGTCTCAATACCAAGTGCAACAAAATATGTCTCAATACCAAATGCAAC
277780 AAAATGTCTCAATACCAAGT
1 AAAATGTCTCAATACCAAGT
277800 TTAATATAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
52 63 0.98
53 1 0.02
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (52 bp):
AAAATGTCTCAATACCAAGTGCAACAAAATATGTCTCAATACCAAATGCAAC
Found at i:280580 original size:51 final size:51
Alignment explanation
Indices: 280498--280622 Score: 153
Period size: 51 Copynumber: 2.5 Consensus size: 51
280488 CTTAGTCTGA
* * * *
280498 CTCAGACTCAACCCCAACCTCAAATGATTCAATAGTTTTATTAACATTAAC
1 CTCAGACTCAACCCTAACCTCAAATGATTCAACAGTTTCATCAACATTAAC
* * *
280549 CTCAAACTCAACCCTTACCTCAGATTG-TTCAACAGTTTCATCAACATTAAC
1 CTCAGACTCAACCCTAACCTCA-AATGATTCAACAGTTTCATCAACATTAAC
* *
280600 CTTAGACTCACCCCTAACCTCAA
1 CTCAGACTCAACCCTAACCTCAA
280623 TTTCTTCCAA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
50 1 0.02
51 58 0.94
52 3 0.05
ACGTcount: A:0.34, C:0.32, G:0.06, T:0.28
Consensus pattern (51 bp):
CTCAGACTCAACCCTAACCTCAAATGATTCAACAGTTTCATCAACATTAAC
Found at i:281128 original size:25 final size:25
Alignment explanation
Indices: 281099--281157 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
281089 TGAAGAACCA
* * *
281099 CAAGCAATACTGTATAAGTGCAAAC
1 CAAGCAATACTATATAAATGAAAAC
*
281124 CAAGCAACACTATATAAATGAAAAC
1 CAAGCAATACTATATAAATGAAAAC
281149 CAAGCAATA
1 CAAGCAATA
281158 ATAAATTCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.17
Consensus pattern (25 bp):
CAAGCAATACTATATAAATGAAAAC
Found at i:284378 original size:17 final size:16
Alignment explanation
Indices: 284358--284397 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
284348 TTTGAAAGAG
*
284358 TTAAAATTTAAACTCAT
1 TTAAAA-TTAAACACAT
284375 TTAATAATTAAACACAT
1 TTAA-AATTAAACACAT
284392 TTAAAA
1 TTAAAA
284398 AGCTAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 17 0.81
18 2 0.10
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAATTAAACACAT
Found at i:286409 original size:9 final size:9
Alignment explanation
Indices: 286395--286419 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
286385 TAGTATTGGC
286395 ATAATAAAA
1 ATAATAAAA
286404 ATAATAAAA
1 ATAATAAAA
286413 ATAATAA
1 ATAATAA
286420 TAATCACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAAAA
Found at i:289301 original size:19 final size:20
Alignment explanation
Indices: 289277--289317 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
289267 ACTAAAGAAC
*
289277 TTAAAA-TCTAAAGTTTCAT
1 TTAAAATTCTAAAGTTTAAT
*
289296 TTAAAATTCTAAGGTTTAAT
1 TTAAAATTCTAAAGTTTAAT
289316 TT
1 TT
289318 TAATATTAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (20 bp):
TTAAAATTCTAAAGTTTAAT
Found at i:291080 original size:22 final size:23
Alignment explanation
Indices: 291046--291088 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
291036 ATATAATAAA
291046 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
291069 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
291089 TATTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:291514 original size:23 final size:24
Alignment explanation
Indices: 291472--291516 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
291462 ATTATTATAT
291472 TATATTATTAAAAATATTAATAAA
1 TATATTATTAAAAATATTAATAAA
* *
291496 TATATT-TTAAATATGTTAATA
1 TATATTATTAAAAATATTAATA
291517 GTTAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TATATTATTAAAAATATTAATAAA
Found at i:310381 original size:13 final size:13
Alignment explanation
Indices: 310363--310388 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
310353 AAAAGTGATT
310363 TAAAGAAAATAAA
1 TAAAGAAAATAAA
310376 TAAAGAAAATAAA
1 TAAAGAAAATAAA
310389 ATTTGAAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
TAAAGAAAATAAA
Found at i:310990 original size:25 final size:24
Alignment explanation
Indices: 310962--311015 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
310952 TAGCATGTTT
*
310962 AAAAATAAAACTTCAAATAAAA-ATG
1 AAAAAGAAAACTTCAAA-AAAAGA-G
* *
310987 AAAACGAAAACTTGAAAAAAAGAG
1 AAAAAGAAAACTTCAAAAAAAGAG
311011 AAAAA
1 AAAAA
311016 ATAACTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.70, C:0.07, G:0.09, T:0.13
Consensus pattern (24 bp):
AAAAAGAAAACTTCAAAAAAAGAG
Found at i:311967 original size:5 final size:5
Alignment explanation
Indices: 311957--312284 Score: 589
Period size: 5 Copynumber: 66.6 Consensus size: 5
311947 TAAAACCAAT
311957 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
312007 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
312057 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA-T-
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
312105 TATTA TATTA TATTA TATTA TA-TA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
312154 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
312204 TATTA TATTA TATTA TA-TA TATTA TATTA TATTA TATTA TA-TA TATTATA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA-T-TA
312254 TATTA TATTA T-TTA TA-TA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TAT
312285 ATACAGAGTG
Statistics
Matches: 314, Mismatches: 0, Indels: 18
0.95 0.00 0.05
Matches are distributed among these distances:
3 2 0.01
4 22 0.07
5 285 0.91
6 1 0.00
7 4 0.01
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:315092 original size:57 final size:57
Alignment explanation
Indices: 315029--315149 Score: 183
Period size: 57 Copynumber: 2.1 Consensus size: 57
315019 AAAATAATTA
* *
315029 CCAAAATAGCA-CATTTTCGAATTAAATTCCTAAAATAGCA-CCTTTTCGAATTAATCC
1 CCAAAATAGCACCA-TTTCGAATT-AATTCCCAAAATAGCACCCATTTCGAATTAATCC
*
315086 CCAAAATAGCACCATTTCGAATTAATTCCCAAAATAGCACCCATTTCGAATTAATTC
1 CCAAAATAGCACCATTTCGAATTAATTCCCAAAATAGCACCCATTTCGAATTAATCC
315143 CCAAAAT
1 CCAAAAT
315150 GTCACCCGGT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
56 15 0.25
57 42 0.71
58 2 0.03
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.29
Consensus pattern (57 bp):
CCAAAATAGCACCATTTCGAATTAATTCCCAAAATAGCACCCATTTCGAATTAATCC
Found at i:315156 original size:29 final size:28
Alignment explanation
Indices: 315023--315149 Score: 184
Period size: 29 Copynumber: 4.5 Consensus size: 28
315013 CTTTTTAAAA
*
315023 TAATTACCAAAATAGCA-CATTTTCGAAT
1 TAATTCCCAAAATAGCACCA-TTTCGAAT
* *
315051 TAAATTCCTAAAATAGCACCTTTTCGAAT
1 T-AATTCCCAAAATAGCACCATTTCGAAT
*
315080 TAATCCCCAAAATAGCACCATTTCGAAT
1 TAATTCCCAAAATAGCACCATTTCGAAT
315108 TAATTCCCAAAATAGCACCCATTTCGAAT
1 TAATTCCCAAAATAGCA-CCATTTCGAAT
315137 TAATTCCCAAAAT
1 TAATTCCCAAAAT
315150 GTCACCCGGT
Statistics
Matches: 89, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
28 41 0.46
29 47 0.53
30 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.30
Consensus pattern (28 bp):
TAATTCCCAAAATAGCACCATTTCGAAT
Found at i:322316 original size:29 final size:29
Alignment explanation
Indices: 322229--322356 Score: 150
Period size: 29 Copynumber: 4.4 Consensus size: 29
322219 CCATTTTACA
* ** * *
322229 AAAATAACACCCTTTTTAAAATAATTACC
1 AAAATATCACCCTTTTCGAATTAATTCCC
322258 AAAATATCA-CCTTTTCGAATTAAATTCCC
1 AAAATATCACCCTTTTCGAATT-AATTCCC
* *
322287 AAAATAGCACCCTTTTCGAATTAATCCCC
1 AAAATATCACCCTTTTCGAATTAATTCCC
* *
322316 AAAATATCACCCATTTCGAATTAATTCCT
1 AAAATATCACCCTTTTCGAATTAATTCCC
*
322345 AAAATGTCACCC
1 AAAATATCACCC
322357 GATCAACGGT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
28 9 0.11
29 64 0.75
30 12 0.14
ACGTcount: A:0.40, C:0.26, G:0.04, T:0.30
Consensus pattern (29 bp):
AAAATATCACCCTTTTCGAATTAATTCCC
Found at i:328219 original size:31 final size:31
Alignment explanation
Indices: 328177--328280 Score: 122
Period size: 31 Copynumber: 3.4 Consensus size: 31
328167 TTATTTCTCC
*
328177 AACAAGCAGTAATACGTAATCGTATTATAA-T
1 AACAAACAGTAATACGTAATCGTATTA-AAGT
*
328208 AA-AAAGTAGTAATACGTAATCGTATTAAAGT
1 AACAAA-CAGTAATACGTAATCGTATTAAAGT
* * *
328239 AACAAACAGTAACACATAATCGTATTACAGT
1 AACAAACAGTAATACGTAATCGTATTAAAGT
*
328270 AACAAGCAGTA
1 AACAAACAGTA
328281 GTATGATGCA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
30 4 0.06
31 56 0.89
32 3 0.05
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.25
Consensus pattern (31 bp):
AACAAACAGTAATACGTAATCGTATTAAAGT
Found at i:331726 original size:2 final size:2
Alignment explanation
Indices: 331719--331757 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
331709 CATGCGTACA
331719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
331758 GAATATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:331765 original size:12 final size:13
Alignment explanation
Indices: 331721--331764 Score: 63
Period size: 14 Copynumber: 3.4 Consensus size: 13
331711 TGCGTACAAT
331721 ATATATATATATA
1 ATATATATATATA
331734 TATATATATATATA
1 -ATATATATATATA
*
331748 ATATA-ATATAGA
1 ATATATATATATA
331760 ATATA
1 ATATA
331765 AATACATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 5 0.17
14 13 0.45
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
ATATATATATATA
Found at i:333616 original size:135 final size:133
Alignment explanation
Indices: 333407--333863 Score: 648
Period size: 135 Copynumber: 3.4 Consensus size: 133
333397 CAGGGTAGAC
* * *
333407 CAGATTTGGAAACGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGACAGACTTGTT
1 CAGATCTGGAAATGTTAATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGACAGACTTGTT
*
333472 CCATTGTTCCTCAAGGAATATCAAATATGGAAAAAAGAGAGATATGTTCCACTGCTTCTTCAGAG
66 CCATTGTTCCTCAAGGAA-ATCAAATATGGAAAAAAGAG-GATATGTTCCGCTGCTTCTTCAGAG
333537 AAAAAT
129 -AAAAT
333543 -AGATCTGGAAATGTTAATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGACAGACTTGTT
1 CAGATCTGGAAATGTTAATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGACAGACTTGTT
* *
333607 CCACTGTTCCTCAAGGAAATCAAATATGGAAAAAAGATGGATATGTTCCGCTGCTTCTTCAG-GG
66 CCATTGTTCCTCAAGGAAATCAAATATGGAAAAAAGA-GGATATGTTCCGCTGCTTCTTCAGAGA
333671 AAAT
130 AAAT
* * *
333675 CAGATCTGGAAATGTTAATTCATTCCACTGTTCTTCAGGGAAGTTTGAATCGAGACAGACTTATT
1 CAGATCTGGAAATGTTAATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGACAGACTTGTT
* * * * * * * *
333740 CCATTATTCCTCAGGGAAGATTAAATCTGGAAAAAAGAGGGATCTATTCTGCTACTTCTTCAGAG
66 CCATTGTTCCTCAAGGAA-ATCAAATATGGAAAAAAGA-GGATATGTTCCGCTGCTTCTTCAGAG
*
333805 AATAT
129 AAAAT
* ** *
333810 CAGATCTGGAAATGTTGATTCATTTGACTGTTCTTCAGGGAAGATTGAATCGAG
1 CAGATCTGGAAATGTTAATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAG
333864 TTCGATTTGC
Statistics
Matches: 292, Mismatches: 25, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
132 4 0.01
133 77 0.26
134 78 0.27
135 133 0.46
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (133 bp):
CAGATCTGGAAATGTTAATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGACAGACTTGTT
CCATTGTTCCTCAAGGAAATCAAATATGGAAAAAAGAGGATATGTTCCGCTGCTTCTTCAGAGAA
AAT
Found at i:334438 original size:21 final size:21
Alignment explanation
Indices: 334413--334458 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
334403 ATGGATGGGC
334413 CGAAGGACTTATCATCTTGCT
1 CGAAGGACTTATCATCTTGCT
334434 CGAAGGACTTATCATCTTGCT
1 CGAAGGACTTATCATCTTGCT
334455 CGAA
1 CGAA
334459 AGACCTATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (21 bp):
CGAAGGACTTATCATCTTGCT
Found at i:339885 original size:89 final size:91
Alignment explanation
Indices: 339721--339916 Score: 242
Period size: 89 Copynumber: 2.2 Consensus size: 91
339711 TTATCCAGGT
* * * *
339721 GGTAAGACCTTACGGA-CTAAAGGATATCCTTGGGTAGGCCCATAGCCCCCCAGGCATATCCTTA
1 GGTAAG-CCCTACGGACCTAAAGGATACCCTTGGGTAGGCCCATAGCCCCCAAGGAATATCCTTA
*
339785 GGTTGGTTCCC-TTTGCTGTGTGCTTAG
65 GGTTGGTTCCCTTTTGCTAT-TGCTTAG
* *
339812 GGTAA-CCCTACGGACCT-AAGGATACCCTTGGGTAGGCCCATAAG-CCCCAAGGAATATCTTTT
1 GGTAAGCCCTACGGACCTAAAGGATACCCTTGGGTAGGCCCAT-AGCCCCCAAGGAATATCCTTA
339874 GGTT-GTCTCCCTTTTGCTATTGCTTAG
65 GGTTGGT-TCCCTTTTGCTATTGCTTAG
*
339901 GGTAAGCCCTATGGAC
1 GGTAAGCCCTACGGAC
339917 GCAGTTATGG
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
88 2 0.02
89 65 0.71
90 20 0.22
91 5 0.05
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.29
Consensus pattern (91 bp):
GGTAAGCCCTACGGACCTAAAGGATACCCTTGGGTAGGCCCATAGCCCCCAAGGAATATCCTTAG
GTTGGTTCCCTTTTGCTATTGCTTAG
Found at i:368751 original size:82 final size:82
Alignment explanation
Indices: 368604--369226 Score: 846
Period size: 82 Copynumber: 7.8 Consensus size: 82
368594 CACCGTTAGA
** * * * * *
368604 CATCTAACTTTCATTAATGGAACCTTTCTACCAAAAATACAAAGCTAGGCATTTAGTCTTTTATC
1 CATCTAACTGGCATTATTGGCACCTTTCTGCC--AAATGCACAGCTAGGCATTTAGTCTTTTATC
*
368669 CCAAAGGAATTTAACCTTT
64 CCAAAGGCATTTAACCTTT
*
368688 CATCTAACTGGCATTATTGGCA-TTGTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCC
1 CATCTAACTGGCATTATTGGCACCT-TTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCC
368752 CAAAGG------------
65 CAAAGGCATTTAACCTTT
* * * *
368758 CATCTAACTGGCATTATTGGTACCTTCCTGCCAAATGCACAACTAGACATTTAGTCTTTTATCCC
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCC
*
368823 AAAGGTATTTAACCTTT
66 AAAGGCATTTAACCTTT
* * *
368840 CATCTAACTGACATTATTGGCACCTTTCTGCCAAATGCACAACTAGGCATTTAGACTTTTATCCC
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCC
*
368905 AAAGGCATTTAGCCTTT
66 AAAGGCATTTAACCTTT
* * *
368922 CATCTAACTGGCATTATTGGCACTTTTCTTCCAAATACACAGCTAGGCATTTAGTCTTTTATCCC
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCC
368987 AAAGGCATTTAACCTTT
66 AAAGGCATTTAACCTTT
* *
369004 CA---AACTGGCATTATTGGGACCTTTCTGCCAAATGCATAGCTAGGCATTTAGTCTTTTATCCC
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCC
369066 AAAGGCATTTAACCTTT
66 AAAGGCATTTAACCTTT
* * *
369083 AATCTAACTAGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTATTATCCC
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCC
369148 AAAGGCATTTAACCTTT
66 AAAGGCATTTAACCTTT
* * *
369165 CATCTAACTGGCATTATTGGTACATTTCTGCCAAATGCACAGCTAGGCATTTAGTATTTTAT
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTAT
369227 TTTAAAACAG
Statistics
Matches: 479, Mismatches: 43, Indels: 36
0.86 0.08 0.06
Matches are distributed among these distances:
70 63 0.13
71 1 0.00
79 73 0.15
82 317 0.66
83 1 0.00
84 24 0.05
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (82 bp):
CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCC
AAAGGCATTTAACCTTT
Found at i:368825 original size:33 final size:33
Alignment explanation
Indices: 368718--368825 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 33
368708 CATTGTTCTG
*
368718 CCAAATGCACAGCTAGGCATTTAGTCTTTTATC
1 CCAAATGCACAACTAGGCATTTAGTCTTTTATC
* * * ** *
368751 CCAAAGGCATCTAACT-GGCATTATTGGTACCTTCCTG
1 CCAAATGCA-C-AACTAGGCA-T-TTAGT-CTTTTATC
*
368788 CCAAATGCACAACTAGACATTTAGTCTTTTATC
1 CCAAATGCACAACTAGGCATTTAGTCTTTTATC
368821 CCAAA
1 CCAAA
368826 GGTATTTAAC
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
33 17 0.31
34 9 0.16
35 9 0.16
36 8 0.15
37 12 0.22
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (33 bp):
CCAAATGCACAACTAGGCATTTAGTCTTTTATC
Found at i:369072 original size:161 final size:162
Alignment explanation
Indices: 368758--369226 Score: 715
Period size: 161 Copynumber: 2.9 Consensus size: 162
368748 ATCCCAAAGG
* * * *
368758 CATCTAACTGGCATTATTGGTACCTTCCTGCCAAATGCACAACTAGACATTTAGTCTTTTATCCC
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCC
* * *
368823 AAAGGTATTTAACCTTTCATCTAACTGACATTATTGGCACCTTTCTGCCAAATGCACAACTAGGC
66 AAAGGCATTTAACCTTTCA--TAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGC
* *
368888 ATTTAGACTTTTATCCCAAAGGCATTTAGCCTTT
129 ATTTAGTCTTTTATCCCAAAGGCATTTAACCTTT
* * *
368922 CATCTAACTGGCATTATTGGCACTTTTCTTCCAAATACACAGCTAGGCATTTAGTCTTTTATCCC
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCC
* *
368987 AAAGGCATTTAACCTTTCA-AACTGGCATTATTGGGACCTTTCTGCCAAATGCATAGCTAGGCAT
66 AAAGGCATTTAACCTTTCATAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCAT
369051 TTAGTCTTTTATCCCAAAGGCATTTAACCTTT
131 TTAGTCTTTTATCCCAAAGGCATTTAACCTTT
* * *
369083 AATCTAACTAGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTATTATCCC
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCC
* *
369148 AAAGGCATTTAACCTTTCATCTAACTGGCATTATTGGTACATTTCTGCCAAATGCACAGCTAGGC
66 AAAGGCATTTAACCTTTCA--TAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGC
*
369213 ATTTAGTATTTTAT
129 ATTTAGTCTTTTAT
369227 TTTAAAACAG
Statistics
Matches: 278, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
161 149 0.54
164 129 0.46
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (162 bp):
CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCC
AAAGGCATTTAACCTTTCATAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCAT
TTAGTCTTTTATCCCAAAGGCATTTAACCTTT
Found at i:369114 original size:243 final size:234
Alignment explanation
Indices: 368648--369226 Score: 892
Period size: 243 Copynumber: 2.4 Consensus size: 234
368638 AAATACAAAG
*
368648 CTAGGCATTTAGTCTTTTATCCCAAAGGAATTTAACCTTTCATCTAACTGGCATTATTGGCA-TT
1 CTAGGCATTTAGTCTTTTATCCCAAAGGCATTTAACCTTTCATCTAACTGGCATTATTGGCACTT
368712 GTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCCAAAGGCATCTAACTGGCATTATTG
66 -TTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCCAAAGGCATCTAACTGGCATTATTG
* * *
368777 GTACCTTCCTGCCAAATGCACAACTAGACATTTAGTCTTTTATCCCAAAGGTATTTAACCTTTCA
130 GGACCTTCCTGCCAAATGCACAACTAGACATTTAGTCTTTTATCCCAAAGGCATTTAACCTTTAA
368842 TCTAACTGACATTATTGGCACCTTTCTGCCAAATGCACAA
195 TCTAACTGACATTATTGGCACCTTTCTGCCAAATGCACAA
* *
368882 CTAGGCATTTAGACTTTTATCCCAAAGGCATTTAGCCTTTCATCTAACTGGCATTATTGGCACTT
1 CTAGGCATTTAGTCTTTTATCCCAAAGGCATTTAACCTTTCATCTAACTGGCATTATTGGCACTT
* *
368947 TTCTTCCAAATACACAGCTAGGCATTTAGTCTTTTATCCCAAAGGCATTTAACCTTTCAAACTGG
66 TTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCCAAAGGCA--T---C--T--AACTGG
* * * *
369012 CATTATTGGGACCTTTCTGCCAAATGCATAGCTAGGCATTTAGTCTTTTATCCCAAAGGCATTTA
122 CATTATTGGGACCTTCCTGCCAAATGCACAACTAGACATTTAGTCTTTTATCCCAAAGGCATTTA
*
369077 ACCTTTAATCTAACT-AGCATTATTGGCACCTTTCTGCCAAATGCACAG
187 ACCTTTAATCTAACTGA-CATTATTGGCACCTTTCTGCCAAATGCACAA
* * *
369125 CTAGGCATTTAGTCTATTATCCCAAAGGCATTTAACCTTTCATCTAACTGGCATTATTGGTACAT
1 CTAGGCATTTAGTCTTTTATCCCAAAGGCATTTAACCTTTCATCTAACTGGCATTATTGGCACTT
*
369190 TTCTGCCAAATGCACAGCTAGGCATTTAGTATTTTAT
66 TTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTAT
369227 TTTAAAACAG
Statistics
Matches: 313, Mismatches: 21, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
234 104 0.33
235 2 0.01
236 1 0.00
239 1 0.00
241 1 0.00
242 1 0.00
243 203 0.65
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (234 bp):
CTAGGCATTTAGTCTTTTATCCCAAAGGCATTTAACCTTTCATCTAACTGGCATTATTGGCACTT
TTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTTATCCCAAAGGCATCTAACTGGCATTATTGG
GACCTTCCTGCCAAATGCACAACTAGACATTTAGTCTTTTATCCCAAAGGCATTTAACCTTTAAT
CTAACTGACATTATTGGCACCTTTCTGCCAAATGCACAA
Found at i:369374 original size:54 final size:54
Alignment explanation
Indices: 369315--369440 Score: 139
Period size: 54 Copynumber: 2.4 Consensus size: 54
369305 AGATGTAGTA
* **
369315 CCAATACGGTAATTCA-CAACTTATTATGAATTACGTGGGTTTGCACAAACAGTG
1 CCAATACGGTAATTCATAAACTTATTATGAATTACGTAAG-TTGCACAAACAGTG
* * * * *
369369 CCAATACAGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
1 CCAATACGGTAATTCATAAACTTATTATGAATTACGTAAGTTGCACAAACAGTG
* *
369423 CCAACATGGTAATT-ATAA
1 CCAATACGGTAATTCATAA
369441 TACATACATT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
53 4 0.07
54 37 0.63
55 18 0.31
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.30
Consensus pattern (54 bp):
CCAATACGGTAATTCATAAACTTATTATGAATTACGTAAGTTGCACAAACAGTG
Found at i:376908 original size:11 final size:11
Alignment explanation
Indices: 376892--376917 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
376882 AGTTCCAATA
376892 AAAAAAATTTT
1 AAAAAAATTTT
376903 AAAAAAATTTT
1 AAAAAAATTTT
376914 AAAA
1 AAAA
376918 GCATTGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAAAATTTT
Found at i:384271 original size:99 final size:99
Alignment explanation
Indices: 384091--384291 Score: 298
Period size: 99 Copynumber: 2.0 Consensus size: 99
384081 ATCGATAACT
* * *
384091 ATATTTACAACTTAACCTATTAAAATAAAATAGGCTCTACCTATTACGTTAAATACCTATCGATT
1 ATATTTACAACTTAACCCATTAAAATAAAATAGGCTATACATATTACGTTAAATACCTATCGATT
* *
384156 TGTTTAATGGTATAATATTAATGTAAACGGTAAA
66 TGTTTAAAGGTATAATAATAATGTAAACGGTAAA
* *
384190 ATATTTACAACTTAGCCCGTTAAAATAAAATAGG-TGATACATATTACGTTAAACTACCTATCGA
1 ATATTTACAACTTAACCCATTAAAATAAAATAGGCT-ATACATATTACGTTAAA-TACCTATCGA
*
384254 TTTGTTTAAAGGT-TAATAATAATGTAAATGGTAAA
64 TTTGTTTAAAGGTATAATAATAATGTAAACGGTAAA
384289 ATA
1 ATA
384292 AAATAGGCGC
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
98 1 0.01
99 69 0.75
100 22 0.24
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.35
Consensus pattern (99 bp):
ATATTTACAACTTAACCCATTAAAATAAAATAGGCTATACATATTACGTTAAATACCTATCGATT
TGTTTAAAGGTATAATAATAATGTAAACGGTAAA
Found at i:384333 original size:75 final size:74
Alignment explanation
Indices: 384210--384355 Score: 220
Period size: 75 Copynumber: 2.0 Consensus size: 74
384200 CTTAGCCCGT
* *
384210 TAAAATAAAATAGGTGATACATATTACGTTAAACTACCTATCGATTTGTTTAAAGGTTAATAATA
1 TAAAATAAAATAGGCGATACATATTACGTTAAACTACCTACCGATTTGTTTAAAGG-TAATAATA
384275 ATGTAAATGG
65 ATGTAAATGG
* * * * *
384285 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTCCCTACCGATTTGTTTAAAGGTAATATTAT
1 TAAAATAAAATAGGCGATACATATTACGTTAAACTACCTACCGATTTGTTTAAAGGTAATAATAA
384350 TGTAAA
66 TGTAAA
384356 CGATCATATA
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
74 13 0.20
75 51 0.80
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (74 bp):
TAAAATAAAATAGGCGATACATATTACGTTAAACTACCTACCGATTTGTTTAAAGGTAATAATAA
TGTAAATGG
Found at i:384387 original size:173 final size:173
Alignment explanation
Indices: 384111--384437 Score: 496
Period size: 173 Copynumber: 1.9 Consensus size: 173
384101 CTTAACCTAT
* * *
384111 TAAAATAAAATAGGCTCTACCTATTACGTTAAATACCTATCGATTTGTTTAATGGTATAATATTA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAATACCTACCGATTTGTTTAAAGG-ATAATATTA
* * *
384176 ATGTAAACGGTAAAATATTTACAACTTAGCCCGTTAAAATAAAATAGGTGA-TACATATTACGTT
65 ATGTAAACGATAAAATATTTACAACTTAACCCGTTAAAATAAAATAGG-AACTACATATTACGTT
384240 AAACTACCTATCGATTTGTTTAAAGGTTAATAATAATGTAAATGG
129 AAACTACCTATCGATTTGTTTAAAGGTTAATAATAATGTAAATGG
*
384285 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTCCCTACCGATTTGTTTAAAGG-TAATATTA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAA-TACCTACCGATTTGTTTAAAGGATAATATTA
* * * * *
384349 TTGTAAACGATCATATATTTACAACTTAACCGGTTAAAATAAAATAGGAACTACCTATTACGTTA
65 ATGTAAACGATAAAATATTTACAACTTAACCCGTTAAAATAAAATAGGAACTACATATTACGTTA
*
384414 AACTACCTATTGATTTGTTTAAAG
130 AACTACCTATCGATTTGTTTAAAG
384438 ATATATTTTT
Statistics
Matches: 138, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
172 1 0.01
173 86 0.62
174 32 0.23
175 19 0.14
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (173 bp):
TAAAATAAAATAGGCGCTACCTATTACGTTAAATACCTACCGATTTGTTTAAAGGATAATATTAA
TGTAAACGATAAAATATTTACAACTTAACCCGTTAAAATAAAATAGGAACTACATATTACGTTAA
ACTACCTATCGATTTGTTTAAAGGTTAATAATAATGTAAATGG
Found at i:387008 original size:95 final size:95
Alignment explanation
Indices: 386897--387097 Score: 307
Period size: 95 Copynumber: 2.1 Consensus size: 95
386887 TCGATACCAT
* *
386897 GGTATCGATACAAGGCCACAAT-GAATCTAAAATTGGTATCGATACCGGAAGGGGGTATCGGTAC
1 GGTATCGATACAAGGCCAC-ATCGAATCTAAAATTGGTATCGATACCGAAAGGAGGTATCGGTAC
386961 CATAGTATGGTAGTATCAATACCATGGTA-A
65 CATAGTATGGTAGTATCAATACCATGGTAGA
* * * *
386991 CGGTATCGATACCAGGCCACATCGAATCTAAAATTGGTATTGATACCGAAATGAGGTATTGGTAC
1 -GGTATCGATACAAGGCCACATCGAATCTAAAATTGGTATCGATACCGAAAGGAGGTATCGGTAC
*
387056 CATAGTATGGTAGTATCGATACCATGGTAGA
65 CATAGTATGGTAGTATCAATACCATGGTAGA
387087 GGTATCGATAC
1 GGTATCGATAC
387098 GGAAGAGCCA
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
94 2 0.02
95 94 0.97
96 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (95 bp):
GGTATCGATACAAGGCCACATCGAATCTAAAATTGGTATCGATACCGAAAGGAGGTATCGGTACC
ATAGTATGGTAGTATCAATACCATGGTAGA
Found at i:387700 original size:58 final size:58
Alignment explanation
Indices: 387435--387763 Score: 426
Period size: 59 Copynumber: 5.7 Consensus size: 58
387425 TAAGTGTGCA
* *
387435 AAAATGTTAAGAAATTCACACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTAC
* *
387493 AAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGACACTTCGTGTAC
1 -AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTAC
* *
387552 AAAAATGTTAAGAAATTCATATTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
1 -AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTAC
* * * * *
387611 AAAAT-TAAAAAAATTCATACTAAGTGTATCAATTTCCGTACTGGGCACTTTGTGTAC
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTAC
* * * * * * * *
387668 AAACTGTTGAGAGATTCATACTAAGTTTATCAATTTTCGTACTGGGCACTTTGTGTAC
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTAC
** * *
387726 AAACCGTTGAGAGATTCATACTAAGTGTATGAATTTCC
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCC
387764 ATATGGGAAA
Statistics
Matches: 243, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
57 49 0.20
58 85 0.35
59 109 0.45
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (58 bp):
AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTAC
Found at i:387743 original size:116 final size:115
Alignment explanation
Indices: 387428--387763 Score: 422
Period size: 116 Copynumber: 2.9 Consensus size: 115
387418 ATGGCATTAA
* *
387428 GTGTGCAAAAATGTTAAGAAATTCACACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
1 GTGTACAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* *
387493 AAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGACACTTC
66 --AAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTACTGGACACTTC
*
387546 GTGTACAAAAATGTTAAGAAATTCATATTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
1 GTGTACAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* * * * *
387611 AAAATTAAAAAAATTCATACTAAGTGTATCAATTTCCGTACTGGGCACTTT
66 AAAGTT-AAGAAATTCATACTAAGTGTATGAATTTCCGTACTGGACACTTC
* * * * * * * * *
387662 GTGTAC-AAACTGTTGAGAGATTCATACTAAGTTTATCAATTTTCGTACTGGGCACTTTGTGTAC
1 GTGTACAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
* *
387726 AAACCGTTGAGAGATTCATACTAAGTGTATGAATTTCC
66 AAA--GTTAAGAAATTCATACTAAGTGTATGAATTTCC
387764 ATATGGGAAA
Statistics
Matches: 190, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
115 53 0.28
116 73 0.38
117 2 0.01
118 62 0.33
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (115 bp):
GTGTACAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
AAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTACTGGACACTTC
Found at i:391529 original size:46 final size:46
Alignment explanation
Indices: 391457--391981 Score: 816
Period size: 46 Copynumber: 11.4 Consensus size: 46
391447 AAATTAAGTA
* * * *
391457 ATAAGTGAAAATGTATAATGGTGCATTATCGGCATGAAAGGATTCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
391503 ATAAATGAAAATTCATAATGGTGCATTATCGGCATAAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
391549 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
391595 ATAAAAGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
391641 ATAAATGAAAATGAATAATGGTGCATTATCGGCATAAAAAGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
391687 ATAAATGAAAATGCATAACGGTGCATTATCGTCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
391733 ATAAATGAAATTACATAACGGTGCATTATCGGCATGAAAGGATACC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
391779 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATACC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
391825 ATAAATGAAAATGCATAACAGTGCATTATCGGCATAAAAGGATACA
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
391871 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATACC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
391917 ATAAATGAAAATGCATAACGGTGCACTATCGGCATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
391963 ATAAATGAAAATACATAAC
1 ATAAATGAAAATGCATAAC
391982 TGTATATTAA
Statistics
Matches: 442, Mismatches: 37, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 442 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:397805 original size:46 final size:46
Alignment explanation
Indices: 397748--398130 Score: 559
Period size: 46 Copynumber: 8.3 Consensus size: 46
397738 TGAAGGAATC
* * *
397748 AATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGTCGTA
1 AATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATA
* ** *
397794 AATAAAAATGCATAACATTGCATTATCGGCATGAAATGATGCCATA
1 AATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATA
*
397840 AATGAAAATGCATAACGATGCATTATCGGCATGAAAGGATGCCATA
1 AATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATA
* * **
397886 AATGAAAATGAATAACGATGCATTATCAACATGAAAGGATGCCATA
1 AATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATA
* * *
397932 AATGAATATGCATAACGGTGCATTATTGGCATGAAATGATGCCATA
1 AATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATA
* *
397978 AATGAAAATGCATAACGGTACATTATCGACATGAAAGGATGCCATA
1 AATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATA
*
398024 AATCAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATA
1 AATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATA
* * * *
398070 AATGAAAATGCATAACGGTGCATAATCGACATGAAAGGATTCCACA
1 AATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATA
*
398116 AATGAAAATACATAA
1 AATGAAAATGCATAA
398131 ATGTATATTA
Statistics
Matches: 302, Mismatches: 35, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 302 1.00
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (46 bp):
AATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATA
Found at i:397897 original size:23 final size:23
Alignment explanation
Indices: 397870--397937 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
397860 CATTATCGGC
397870 ATGAAAGGATGCCATAAATGAAA
1 ATGAAAGGATGCCATAAATGAAA
* * * *
397893 ATGAATAACGATG-CAT-TATCAAC
1 ATG-A-AAGGATGCCATAAATGAAA
397916 ATGAAAGGATGCCATAAATGAA
1 ATGAAAGGATGCCATAAATGAA
397938 TATGCATAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
21 6 0.18
22 4 0.12
23 14 0.41
24 4 0.12
25 6 0.18
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.21
Consensus pattern (23 bp):
ATGAAAGGATGCCATAAATGAAA
Found at i:397927 original size:21 final size:21
Alignment explanation
Indices: 397856--397927 Score: 54
Period size: 23 Copynumber: 3.2 Consensus size: 21
397846 AATGCATAAC
**
397856 GATGCATTATCGGCATGAAAG
1 GATGCATTATCAACATGAAAG
* * * *
397877 GATGCCATAAATGAAAATGAATAAC
1 GATG-CAT-TATCAACATG-A-AAG
397902 GATGCATTATCAACATGAAAG
1 GATGCATTATCAACATGAAAG
397923 GATGC
1 GATGC
397928 CATAAATGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
21 11 0.30
22 4 0.11
23 12 0.32
24 4 0.11
25 6 0.16
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (21 bp):
GATGCATTATCAACATGAAAG
Found at i:403212 original size:13 final size:13
Alignment explanation
Indices: 403178--403220 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
403168 TTTGACTTTT
*
403178 CGGTCAAAATCAA
1 CGGTCAAAGTCAA
*
403191 CGTGTCAAAGCCAA
1 CG-GTCAAAGTCAA
403205 CGGTCAAAGTCAA
1 CGGTCAAAGTCAA
403218 CGG
1 CGG
403221 GTTGACTCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.37, C:0.26, G:0.23, T:0.14
Consensus pattern (13 bp):
CGGTCAAAGTCAA
Found at i:408757 original size:33 final size:33
Alignment explanation
Indices: 408715--408779 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
408705 TATGAATTTA
*
408715 AATTTTAAATAATATTAAT-TATTATAAAAAAAC
1 AATTTTAAATAATATAAATAT-TTATAAAAAAAC
**
408748 AATTTTAAATTCTATAAATATTTATAAAAAAA
1 AATTTTAAATAATATAAATATTTATAAAAAAA
408780 GTATTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (33 bp):
AATTTTAAATAATATAAATATTTATAAAAAAAC
Found at i:412120 original size:15 final size:15
Alignment explanation
Indices: 412102--412134 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
412092 AAATTATAAA
412102 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
412117 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
412132 TAT
1 TAT
412135 ATTTGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:423275 original size:2 final size:2
Alignment explanation
Indices: 423268--423294 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
423258 ACAGCCAAAT
423268 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 T
423295 TCATATCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:428306 original size:17 final size:17
Alignment explanation
Indices: 428259--428330 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
428249 TTGAAAGAGT
*
428259 TAGTTTAATAAATGTAA-
1 TAGTTTAATTAATG-AAC
* * *
428276 TAATTTGATGAATGAAC
1 TAGTTTAATTAATGAAC
428293 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
428310 TAACTTT-ATTAAATGAAC
1 T-AGTTTAATT-AATGAAC
428328 TAG
1 TAG
428331 ATGCATGAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
16 2 0.05
17 30 0.68
18 12 0.27
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:428324 original size:18 final size:18
Alignment explanation
Indices: 428286--428329 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
428276 TAATTTGATG
*
428286 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
428303 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
428320 AAATGAACTA
1 -AATGAACTA
428330 GATGCATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:433461 original size:11 final size:11
Alignment explanation
Indices: 433447--433472 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
433437 CTTTTTCTTA
433447 TTTTTTTAATT
1 TTTTTTTAATT
433458 TTTTTTTAATT
1 TTTTTTTAATT
433469 TTTT
1 TTTT
433473 ACTAACCTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTAATT
Found at i:434791 original size:17 final size:18
Alignment explanation
Indices: 434769--434840 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 18
434759 AATTAAGAGT
434769 TAGTTTAATAAATGGAA-
1 TAGTTTAATAAATGGAAC
* *
434786 TAGTTTGATGAAT-GAAC
1 TAGTTTAATAAATGGAAC
*
434803 TAGTTTAATTAAT-GAAC
1 TAGTTTAATAAATGGAAC
* *
434820 TAACTTTATTAAAT-GAAC
1 T-AGTTTAATAAATGGAAC
434838 TAG
1 TAG
434841 ATGCATGAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
16 3 0.07
17 28 0.62
18 14 0.31
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (18 bp):
TAGTTTAATAAATGGAAC
Found at i:434834 original size:18 final size:18
Alignment explanation
Indices: 434796--434839 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
434786 TAGTTTGATG
*
434796 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
434813 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
434830 AAATGAACTA
1 -AATGAACTA
434840 GATGCATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:441014 original size:22 final size:22
Alignment explanation
Indices: 440977--441022 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
440967 AAATAATAGT
*
440977 AATAATAAGTATTAAAATAAAAA
1 AATAATAAGTAAT-AAATAAAAA
441000 AATAAT-AGTAATAAATAAAAA
1 AATAATAAGTAATAAATAAAAA
441021 AA
1 AA
441023 CAGAAATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 5 0.23
23 6 0.27
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (22 bp):
AATAATAAGTAATAAATAAAAA
Found at i:441021 original size:23 final size:23
Alignment explanation
Indices: 440977--441022 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
440967 AAATAATAGT
* *
440977 AATAATAAGTATTAAAATAAAAA
1 AATAATAAGTAATAAAAAAAAAA
*
441000 AATAAT-AGTAATAAATAAAAAA
1 AATAATAAGTAATAAAAAAAAAA
441022 A
1 A
441023 CAGAAATACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (23 bp):
AATAATAAGTAATAAAAAAAAAA
Found at i:441098 original size:22 final size:23
Alignment explanation
Indices: 441063--441106 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
441053 AAATCAAAGT
*
441063 AAAATAAAGTATAAAT-GAAATAA
1 AAAATAAAGAAT-AATGGAAATAA
441086 AAAATAAA-AATAATGGAAATA
1 AAAATAAAGAATAATGGAAATA
441107 TAAGTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 3 0.16
22 8 0.42
23 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAATAAAGAATAATGGAAATAA
Found at i:442296 original size:24 final size:23
Alignment explanation
Indices: 442245--442296 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
442235 AAATCTCAGA
*
442245 TAAT-ATTTTCTAGTTACTAAAT
1 TAATCATTTTCTAGTTACTAAAC
442267 TGAATCATTTTCTAGTTACTAAAGC
1 T-AATCATTTTCTAGTTACTAAA-C
442292 TAATC
1 TAATC
442297 GATTCATCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 1 0.04
23 3 0.12
24 21 0.81
25 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (23 bp):
TAATCATTTTCTAGTTACTAAAC
Found at i:447250 original size:30 final size:31
Alignment explanation
Indices: 447205--447268 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
447195 AAGCAGGGGT
* * *
447205 TGTAGTGGTTACTGGTGTAGAAAG-AGGTGG
1 TGTAGAGGTTACTGGTGTACAAAGAAAGTGG
*
447235 TGTAGAGGTTGCTGGTGTACAAAGAAAGTGG
1 TGTAGAGGTTACTGGTGTACAAAGAAAGTGG
447266 TGT
1 TGT
447269 TGATGTAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.25, C:0.05, G:0.41, T:0.30
Consensus pattern (31 bp):
TGTAGAGGTTACTGGTGTACAAAGAAAGTGG
Found at i:451169 original size:22 final size:22
Alignment explanation
Indices: 451112--451170 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
451102 ACGCGATTCT
451112 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
451134 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
451155 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
451171 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:451242 original size:20 final size:20
Alignment explanation
Indices: 451155--451288 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
451145 GCGATTTTCC
*
451155 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
451175 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGATTAT
* * *
451195 GACTATCGCAACGTGAATAT
1 GACTATCGCAATGCGATTAT
*
451215 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
* *
451235 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
* *
451255 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
*
451275 GACTGTCGCAATGC
1 GACTATCGCAATGC
451289 TGAATTTCAA
Statistics
Matches: 95, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
19 2 0.02
20 91 0.96
21 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:451263 original size:40 final size:40
Alignment explanation
Indices: 451155--451285 Score: 165
Period size: 40 Copynumber: 3.3 Consensus size: 40
451145 GCGATTTTCC
* *
451155 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATGCGATTAT
*
451195 GACTATCGCAACGTGAATATGTAAATCGCAATGCGATTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATGCGATTAT
* * * * *
451235 GACTATCGCAACGCGATTCTG-ACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGAATATGTA-AATCGCAATGCGATTAT
*
451275 GACTGTCGCAA
1 GACTATCGCAA
451286 TGCTGAATTT
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 1 0.01
40 79 0.99
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (40 bp):
GACTATCGCAACGCGAATATGTAAATCGCAATGCGATTAT
Found at i:452151 original size:24 final size:24
Alignment explanation
Indices: 452100--452153 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
452090 GTATTTGAAA
*
452100 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
452124 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
452148 TTTGAT
1 TTTGAT
452154 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:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:452372 original size:14 final size:14
Alignment explanation
Indices: 452343--452379 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
452333 AGAAAAATAA
452343 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
452358 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
452372 GAAGAAAA
1 GAAGAAAA
452380 TACCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:454434 original size:12 final size:12
Alignment explanation
Indices: 454412--454455 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
454402 CAAGCAAAAG
454412 GCAATCAAAAATC
1 GCAATC-AAAATC
454425 GCAATCAAAATC
1 GCAATCAAAATC
**
454437 AAAATCAAAATC
1 GCAATCAAAATC
*
454449 CCAATCA
1 GCAATCA
454456 CAACCGGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 21 0.78
13 6 0.22
ACGTcount: A:0.55, C:0.25, G:0.05, T:0.16
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:454658 original size:20 final size:20
Alignment explanation
Indices: 454633--454987 Score: 282
Period size: 20 Copynumber: 18.7 Consensus size: 20
454623 CACATTCATT
*
454633 TGACTATCGCAACTCGAATA
1 TGACTATCGCAACGCGAATA
*
454653 TGACTATCGCAACGCAAATA
1 TGACTATCGCAACGCGAATA
* *
454673 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
454693 TGAATATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* * *
454710 T-A--ATCGCAATGCAAAAA
1 TGACTATCGCAACGCGAATA
*
454727 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
*
454747 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* * *
454764 T-A--ATCGGAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
454781 TGACTATCGAAACGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
454801 TGACTACCGCAATGCGAATA
1 TGACTATCGCAACGCGAATA
*
454821 TGACTATCGCAACACGAATA
1 TGACTATCGCAACGCGAATA
454841 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
454861 TTACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
454881 TAACTATCACAACGCGAATT
1 TGACTATCGCAACGCGAATA
* *
454901 TGACTATCACAA--CG-AGA
1 TGACTATCGCAACGCGAATA
454918 T-A--ATCGCAACGCGAA-A
1 TGACTATCGCAACGCGAATA
* *
454934 TGACTATTGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* *
454954 TGATTATCGCAACAG-GAATT
1 TGACTATCGCAAC-GCGAATA
*
454974 TGACTATCGTAACG
1 TGACTATCGCAACG
454988 AGAAAATCGC
Statistics
Matches: 271, Mismatches: 44, Indels: 41
0.76 0.12 0.12
Matches are distributed among these distances:
14 21 0.08
15 1 0.00
16 7 0.03
17 10 0.04
18 4 0.01
19 15 0.06
20 212 0.78
21 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:454805 original size:54 final size:54
Alignment explanation
Indices: 454658--454874 Score: 220
Period size: 54 Copynumber: 3.9 Consensus size: 54
454648 GAATATGACT
* * * *
454658 ATCGCAACGCAAATATGACTATCGCAACGTGAATTTGAATATCGCAACGGGATA
1 ATCGCAATGCAAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
454712 ATCGCAATGCAAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
1 ATCGCAATGCAAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
* * * ** * **
454766 ATCGGAATGCGAAAATGACTATCGAAACGCGAAAATGACTACCGCAATGCGAATATGA
1 ATCGCAATGCAAAAATGACTATCGCAACGCGAATTTGACTATCGCAA--CG-GGAT-A
** * *
454824 CTATCGCAACACGAATATGACTATCGCAACGCGAATATT-ACTATCGCAACG
1 --ATCGCAATGCAAAAATGACTATCGCAACGCGAAT-TTGACTATCGCAACG
454875 CGAATTTAAC
Statistics
Matches: 136, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
54 91 0.67
56 2 0.01
57 2 0.01
58 3 0.02
60 37 0.27
61 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (54 bp):
ATCGCAATGCAAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
Found at i:455162 original size:36 final size:34
Alignment explanation
Indices: 455122--455201 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 34
455112 TCAACTTTTA
455122 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
455158 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
455188 ATCAATTAAACAAA
1 ATCAATTAAACAAA
455202 TCAACTCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 28 0.70
32 2 0.05
34 3 0.08
36 7 0.17
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:455171 original size:30 final size:30
Alignment explanation
Indices: 455137--455202 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
455127 TTAAACAAGC
455137 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
455167 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
455197 ACAAAT
1 ACAAAT
455203 CAACTCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:457125 original size:18 final size:19
Alignment explanation
Indices: 457102--457147 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
457092 GAAACTTAAA
457102 ATCGCAACACG-AATGACT
1 ATCGCAACACGAAATGACT
*
457120 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG-AAATGACT
457140 ATCGCAAC
1 ATCGCAAC
457148 GCTAATTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.40
20 15 0.60
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:457265 original size:20 final size:20
Alignment explanation
Indices: 457211--457278 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
457201 GCGATTCTCT
**
457211 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
457231 CGCTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
457251 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTTCG
457271 CGTTGCGA
1 CGTTGCGA
457279 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:457449 original size:18 final size:18
Alignment explanation
Indices: 457426--457475 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
457416 TTTACTAAGC
457426 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
457444 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
457462 AATCTATGTGAAAT
1 AATCTAAGTGAAAT
457476 TACAAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:459225 original size:20 final size:20
Alignment explanation
Indices: 459202--459297 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
459192 TCTGAAACTT
459202 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
459222 AAAATCGTAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** **
459242 ACTATCGCAACACGAATTTG
1 AAAATCGCAACACGAAAATG
**
459262 ACTATCGCAA-AGCG-AAATG
1 AAAATCGCAACA-CGAAAATG
*
459281 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
459298 CTAAAATCAC
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 14 0.23
20 48 0.77
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:459939 original size:20 final size:20
Alignment explanation
Indices: 459914--459966 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
459904 GCGCTTTGAA
459914 AATCGCATTGCGACAGTCAG
1 AATCGCATTGCGACAGTCAG
* * *
459934 AATCGCATTGTGATAGTCAT
1 AATCGCATTGCGACAGTCAG
459954 AATCGCATTGCGA
1 AATCGCATTGCGA
459967 TTTACATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (20 bp):
AATCGCATTGCGACAGTCAG
Found at i:459974 original size:20 final size:20
Alignment explanation
Indices: 459951--460027 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
459941 TTGTGATAGT
*
459951 CATAATCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
** *
459971 CATATTCGTGTTGCGATAGT-
1 CATATTCGCATTGCGAT-TTA
* * *
459991 CGTACTCGCATTGTGATTTA
1 CATATTCGCATTGCGATTTA
460011 CATATTCGCATTGCGAT
1 CATATTCGCATTGCGAT
460028 AGTCAGAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
CATATTCGCATTGCGATTTA
Found at i:459989 original size:40 final size:40
Alignment explanation
Indices: 459936--460032 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
459926 ACAGTCAGAA
*
459936 TCGCATTGTGATAGTCATAATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
** * * *
459976 TCGTGTTGCGATAGTCGTACTCGCATTGTGATTTACATAT
1 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
460016 TCGCATTGCGATAGTCA
1 TCGCATTGCGATAGTCA
460033 GAAAACCGCA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
Found at i:461125 original size:21 final size:21
Alignment explanation
Indices: 461092--461132 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
461082 ATCCTCAATA
* *
461092 ACTAAGAAGTCTGCCACATCG
1 ACTAAAAAATCTGCCACATCG
*
461113 ACTAAAAAATCTGTCACATC
1 ACTAAAAAATCTGCCACATC
461133 AACTTTTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (21 bp):
ACTAAAAAATCTGCCACATCG
Found at i:462348 original size:18 final size:19
Alignment explanation
Indices: 462327--462365 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
462317 AAATTCATAT
*
462327 AACAATT-TAATAATAGTC
1 AACAATTCTAACAATAGTC
*
462345 AACAATTCTTACAATAGTC
1 AACAATTCTAACAATAGTC
462364 AA
1 AA
462366 TAAACCTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (19 bp):
AACAATTCTAACAATAGTC
Found at i:464006 original size:20 final size:20
Alignment explanation
Indices: 463981--464033 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
463971 GAACCTGTCT
*
463981 GAGTCAACTCAGACTGAACC
1 GAGTCAACTCAAACTGAACC
* * *
464001 GAGTCAACCCAAACTGATCT
1 GAGTCAACTCAAACTGAACC
464021 GAGTCAACTCAAA
1 GAGTCAACTCAAA
464034 TCATTCTGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (20 bp):
GAGTCAACTCAAACTGAACC
Found at i:464063 original size:18 final size:19
Alignment explanation
Indices: 464040--464077 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
464030 CAAATCATTC
*
464040 TGACCCGTTAAC-TTGACT
1 TGACCCATTAACTTTGACT
*
464058 TGACCCATTGACTTTGACT
1 TGACCCATTAACTTTGACT
464077 T
1 T
464078 TTACCAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (19 bp):
TGACCCATTAACTTTGACT
Found at i:468151 original size:20 final size:20
Alignment explanation
Indices: 468076--468146 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
468066 AGTCTGAATC
*
468076 ACCCAAACCGAACCGAGTCA
1 ACCCGAACCGAACCGAGTCA
468096 ACCCGAACCGAACCGAGTCA
1 ACCCGAACCGAACCGAGTCA
* *
468116 ACCCGAACCGATCTGAGTCA
1 ACCCGAACCGAACCGAGTCA
468136 ACCCGAACCGA
1 ACCCGAACCGA
468147 TCTGACTCGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.39, G:0.18, T:0.07
Consensus pattern (20 bp):
ACCCGAACCGAACCGAGTCA
Found at i:470864 original size:6 final size:6
Alignment explanation
Indices: 470845--470898 Score: 65
Period size: 6 Copynumber: 8.8 Consensus size: 6
470835 AAAAAATAGA
* *
470845 AAAAAT AGAAAAT AAAAAT AAAAAG AAAAAT AAAAAT AAATAA- ATAAAT
1 AAAAAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA-AAT AAAAAT
470894 AAAAA
1 AAAAA
470899 AGGGAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 2 0.05
6 31 0.76
7 8 0.20
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:470939 original size:9 final size:8
Alignment explanation
Indices: 470834--470933 Score: 78
Period size: 8 Copynumber: 12.0 Consensus size: 8
470824 AAAAGAGTAT
470834 GAAAAAATA
1 GAAAAAA-A
470843 GAAAAAATA
1 GAAAAAA-A
470852 GAAAATAAA
1 GAAAA-AAA
470861 -AATAAAAA
1 GAA-AAAAA
470869 GAAAAATAA
1 GAAAAA-AA
*
470878 -AAATAAA
1 GAAAAAAA
* *
470885 TAAATAAA
1 GAAAAAAA
* *
470893 TAAAAAAG
1 GAAAAAAA
*
470901 GGAAAAAA
1 GAAAAAAA
470909 GAAAAAAA
1 GAAAAAAA
470917 GAAAAAAA
1 GAAAAAAA
470925 GAGAAAAAA
1 GA-AAAAAA
470934 ATGAAAGAGA
Statistics
Matches: 78, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
7 2 0.03
8 47 0.60
9 27 0.35
10 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (8 bp):
GAAAAAAA
Found at i:473043 original size:64 final size:63
Alignment explanation
Indices: 472946--473157 Score: 230
Period size: 64 Copynumber: 3.3 Consensus size: 63
472936 CACATTCATA
* * * *
472946 AGTGCATCGATGCATTCC-TTTCAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCATAACT
1 AGTGCATCGATGCA-TCCTTTTAAAAGAA-AACATCGAATGCATTTAATGCATCGATGCATAAGT
* * * * *
473010 AATGCATCGATGCATCCTTTTAAAATAATAACATCGAATGCAATCAATGCATCGATGCATAAGG
1 AGTGCATCGATGCATCCTTTTAAAAGAA-AACATCGAATGCATTTAATGCATCGATGCATAAGT
* * * * *
473074 AGTGCATCGATGCAT-CTCATTAATAAGGAAACATCGAATGCATTTTATGCACCGATGCACAAGT
1 AGTGCATCGATGCATCCT-TTTAA-AAGAAAACATCGAATGCATTTAATGCATCGATGCATAAGT
473138 AGTGCATCGATGCATACCTT
1 AGTGCATCGATGCAT-CCTT
473158 CATTGAAAGA
Statistics
Matches: 122, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
63 5 0.04
64 112 0.92
65 3 0.02
66 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (63 bp):
AGTGCATCGATGCATCCTTTTAAAAGAAAACATCGAATGCATTTAATGCATCGATGCATAAGT
Found at i:473858 original size:30 final size:30
Alignment explanation
Indices: 473822--473885 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
473812 AAGGAACATA
* *
473822 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
473852 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
473882 TGGA
1 TGGA
473886 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Done.