Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008339.1 Hibiscus syriacus cultivar Beakdansim tig00111061_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: 1048908
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:348470 original size:93 final size:93
Alignment explanation
Indices: 348311--348784 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
348301 TTGAATGGAT
348311 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
348376 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
348404 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
348469 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
348497 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
348562 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
348590 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
348655 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
348683 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
348748 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
348776 AAATTTACT
1 AAATTTACT
348785 AAGCAATCTA
Statistics
Matches: 378, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 378 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:350510 original size:14 final size:14
Alignment explanation
Indices: 350491--350580 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
350481 TTGAAATGAA
350491 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
350505 AATCGCAACGCGAGATAAC
1 AATCGCAA--CGAG---AG
350524 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
350538 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
350557 AATCGCAACGAGAG
1 AATCGCAACGAGAG
350571 AATCGCAACG
1 AATCGCAACG
350581 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 29 0.47
15 1 0.02
16 6 0.10
17 6 0.10
18 1 0.02
19 19 0.31
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:350528 original size:33 final size:33
Alignment explanation
Indices: 350483--350597 Score: 205
Period size: 33 Copynumber: 3.5 Consensus size: 33
350473 TCTTTTGGTT
350483 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
350516 GAGAT-AACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAA-AATCGCAACGAGAGAATCGCAACGC
350549 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
350582 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
350598 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
32 2 0.03
33 74 0.95
34 2 0.03
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:350562 original size:19 final size:19
Alignment explanation
Indices: 350538--350602 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
350528 GCAACGAGAG
350538 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
350557 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
350571 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
350590 AATCGCAATGCGA
1 AATCGCAACGCGA
350603 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:350633 original size:14 final size:14
Alignment explanation
Indices: 350614--350667 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
350604 TTTGGTTTCG
350614 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
350628 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
350647 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
350661 CGTTGCG
1 CGTTGCG
350668 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.07, C:0.26, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:350646 original size:33 final size:33
Alignment explanation
Indices: 350598--350678 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
350588 AAAATCGCAA
**
350598 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
350631 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
350664 TGCGCTTTTCATTTC
1 TGCGATTTTCATTTC
350679 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.07, C:0.23, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:350714 original size:41 final size:41
Alignment explanation
Indices: 350654--350731 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
350644 TCGCGTTGCG
* *
350654 ATTCTCTCGTTGCGCTTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
350695 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
350732 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:350730 original size:21 final size:21
Alignment explanation
Indices: 350655--350730 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
350645 CGCGTTGCGA
*
350655 TTCTCTCGTTGCGCTTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
350676 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
350696 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
350717 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
350731 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:350846 original size:32 final size:33
Alignment explanation
Indices: 350810--350879 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 33
350800 AATACTAACT
* *
350810 TGAAAATCGGAACGAGAGAATAGCAACGCG-AA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
350842 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
350875 TGAAA
1 TGAAA
350880 TCTAATTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 26 0.79
33 7 0.21
ACGTcount: A:0.47, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:351279 original size:39 final size:40
Alignment explanation
Indices: 351236--351317 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
351226 TACGCGTAGC
*
351236 GATTATAATGGCGCTTTA-A-ATATCGCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGAT-TCGCGTTGCGATTTACG
** * *
351275 GATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
351315 GAT
1 GAT
351318 ACGCGTTGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.39
40 20 0.56
41 2 0.06
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (40 bp):
GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
Found at i:351452 original size:20 final size:20
Alignment explanation
Indices: 351259--351451 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
351249 CTTTAAATAT
351259 CGCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
* * *
351280 -TCGTTGCGATTTACAGATT
1 CGCGTTGCGATTTACGGATA
*
351299 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
351319 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
351339 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
351359 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
351379 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
351399 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
351419 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
351439 CGCGTTGCGATTT
1 CGCGTTGCGATTT
351452 TGGAAAATCG
Statistics
Matches: 149, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
19 1 0.01
20 147 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:351468 original size:21 final size:21
Alignment explanation
Indices: 351438--351520 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
351428 ATTTTCATAT
*
351438 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
351459 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
351480 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
351501 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
351521 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:351511 original size:42 final size:43
Alignment explanation
Indices: 351418--351516 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
351408 ATTTATGTGT
* *
351418 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
351459 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
351501 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
351517 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:357474 original size:15 final size:15
Alignment explanation
Indices: 357456--357486 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
357446 ATTAAAATGC
357456 TAAAATTTTAAATTA
1 TAAAATTTTAAATTA
357471 TAAAATTTTAAATTA
1 TAAAATTTTAAATTA
357486 T
1 T
357487 TTTGAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATTTTAAATTA
Found at i:359477 original size:37 final size:37
Alignment explanation
Indices: 359424--359520 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
359414 CCTTGTCGTC
*
359424 CTATTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTATTAGGATTTAAACTCCTAAAAATATGATAGAATT
* * * *
359461 TTGTTAGGATTTAAACTCTTAAAAATATGATAGAGTT
1 CTATTAGGATTTAAACTCCTAAAAATATGATAGAATT
* *
359498 CTACTATGATTTAAACTCCTAAA
1 CTATTAGGATTTAAACTCCTAAA
359521 GATAGGATCC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36
Consensus pattern (37 bp):
CTATTAGGATTTAAACTCCTAAAAATATGATAGAATT
Found at i:360131 original size:24 final size:23
Alignment explanation
Indices: 360077--360122 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
360067 TTCTTTGCAT
*
360077 TTTTATTATTACTATTATATTTA
1 TTTTATTTTTACTATTATATTTA
360100 TTATTATTTTTACTATTATATTT
1 TT-TTATTTTTACTATTATATTT
360123 TCCTTTATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATTTTTACTATTATATTTA
Found at i:360237 original size:14 final size:15
Alignment explanation
Indices: 360218--360246 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
360208 ATATTACTTG
360218 TATTATTT-TTATAT
1 TATTATTTGTTATAT
360232 TATTATTTGTTATAT
1 TATTATTTGTTATAT
360247 ATATATATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TATTATTTGTTATAT
Found at i:360398 original size:22 final size:20
Alignment explanation
Indices: 360349--360394 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
360339 TAATATATAC
360349 ATATATTTTTCTATTATTTT
1 ATATATTTTTCTATTATTTT
* *
360369 CTATATTTTT-TATTATCATT
1 ATATATTTTTCTATTAT-TTT
360389 ATATAT
1 ATATAT
360395 ATTTATTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (20 bp):
ATATATTTTTCTATTATTTT
Found at i:360450 original size:2 final size:2
Alignment explanation
Indices: 360445--360485 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
360435 ATTTTACTAT
360445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
360486 TCTACACAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:360801 original size:13 final size:13
Alignment explanation
Indices: 360783--360807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
360773 GTTATTATTA
360783 TTTTATTTATTTG
1 TTTTATTTATTTG
360796 TTTTATTTATTT
1 TTTTATTTATTT
360808 TCTTTTTCTT
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:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTTG
Found at i:364493 original size:22 final size:22
Alignment explanation
Indices: 364427--364496 Score: 131
Period size: 22 Copynumber: 3.2 Consensus size: 22
364417 CATCAAATCG
364427 TTGAGCATCAAATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
*
364449 ATGAGCATCAAATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
364471 TTGAGCATCAAATGCCAAACCT
1 TTGAGCATCAAATGCCAAACCT
364493 TTGA
1 TTGA
364497 CCAAACATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (22 bp):
TTGAGCATCAAATGCCAAACCT
Found at i:365497 original size:106 final size:106
Alignment explanation
Indices: 365300--366673 Score: 2000
Period size: 106 Copynumber: 13.0 Consensus size: 106
365290 ATATCGTGTC
* * ** * * * *
365300 ACTCAAGACAACACAAGTTCAACTTCATAACGAAGGGACGGCTGGTTGTCAA-CAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
365364 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
365405 ACTCCAGAGAACGCAAGTTCAACTTCACGACGAAAGGACCGTTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
365470 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
365511 ACTCCAGACAACACAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAATAAACAACATT-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC-TTCC
*
365575 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
365617 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
365682 AATTTCAGAGCCAACTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
365723 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTTAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
365788 AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
365829 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
365894 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGC
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
365935 ACTCAACACAACGCAAGTTCAACTTCACGACGAA-GGAACACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
365999 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
366040 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGA-CGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
366104 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
366145 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
366210 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
366251 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
366316 AATTTCAGAGCCAATTTCAACTTCACAACGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
366357 ACTCAAGAAAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * * *
366422 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGA
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * * *
366463 AC-CGAAGGCAACACAAGCTCAACTTCACGATGAAGAGG-CGGCTGATTGTCAA-AAACAAATT-
1 ACTC-CAGACAACGCAAGTTCAACTTCACGACGAAG-GGACCGCTGGTTGTCAATAAACAACTTC
*
366524 -C-ATTT-AGAGTCC-ATTTCAACTTCACAGCGAAGGATATTGG
64 CCAATTTCAGAG-CCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
366564 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGAACGGCTGGTTGTCAACAAACAA-TTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
366628 TAGTTCTAGAGCCAATTTCAACTTCACGACGAAGGATATTGG
66 AATTTC-AGAGCCAATTTCAACTTCACAACGAAGGATATTGG
366670 ACTC
1 ACTC
366674 AGAACAATGC
Statistics
Matches: 1161, Mismatches: 91, Indels: 33
0.90 0.07 0.03
Matches are distributed among these distances:
100 1 0.00
101 72 0.06
102 13 0.01
103 2 0.00
104 3 0.00
105 258 0.22
106 808 0.70
107 4 0.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:366514 original size:634 final size:630
Alignment explanation
Indices: 365299--366673 Score: 2109
Period size: 634 Copynumber: 2.2 Consensus size: 630
365289 GATATCGTGT
* * *
365299 CACTCAAGACAACACAAGTTCAACTTCATAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTTC
1 CACTCAAGACAACACAAGTTCAACTTCACAACGAAGGAACGGCTGGTTGTCAACAAACAATTCT-
* * *
365363 CAATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAGAACGCAAGTTCAAC
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* * *
365428 TTCACGACGAAAGGACCGTTGGTTGTCAATAAACAATTTCCCAATTTCAGATCCAATTTCAACTT
130 TTCACGACGAAAGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTT
* *
365493 CACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTTACGACGAAGGGACCGCTGGTT
195 CACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
* *
365558 GTCAATAAACAACATTCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
260 GTCAACAAACAACATTCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
* *
365623 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
325 GACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
* *
365688 AGAGCCAACTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGA
390 AGAGCCAACTTCAACTTCACAACGAAGGATATTAGACTCAAGAAAACGCAAGTTCAACTTCACGA
*
365753 CGAAGGGACCGCTGATTGTTAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACG
455 CGAAGGGACCGCTGATTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACG
* * * * *
365818 AAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACA
520 AAAGATATTGAACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACCGCTGATTGTCAA-A
*
365883 AACAACTTCTCAATTTCAGAG-CCAATTTCAACTTCACAACGAAGGATATTG
584 AACAA-AT-TC-ATTT-AGAGTCC-ATTTCAACTTCACAACGAAGGATATTG
* * * *
365934 CACTCAACACAACGCAAGTTCAACTTCACGACGAAGGAAC-ACTGGTTGTCAACAAACAACTTCT
1 CACTCAAGACAACACAAGTTCAACTTCACAACGAAGGAACGGCTGGTTGTCAACAAACAA-TTCT
*
365998 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAAC
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
*
366063 TTCACGACGAAGGGA-CGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTT
130 TTCACGACGAAAGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTT
*
366127 CACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
195 CACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
*
366192 GTCAACAAACAAC-TTCTCAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
260 GTCAACAAACAACATTC-CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
366256 AGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
324 AGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * *
366321 CAGAGCCAATTTCAACTTCACAACGTAGGATATTGGACTCAAGAAAACGCAAGTTCAACTTCACG
389 CAGAGCCAACTTCAACTTCACAACGAAGGATATTAGACTCAAGAAAACGCAAGTTCAACTTCACG
* * *
366386 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCTCAGC
454 ACGAAGGGACCGCTGATTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAAC
* * * * * *
366451 GAAGGATCTTGAAC-CGAAGGCAACACAAGCTCAACTTCACGATGAAGAGG-CGGCTGATTGTCA
519 GAAAGATATTGAACTC-AAGACAACACAAGCTCAACTTCACAACGAAG-GGACCGCTGATTGTCA
*
366514 AAAACAAATTCATTTAGAGTCCATTTCAACTTCACAGCGAAGGATATTG
582 AAAACAAATTCATTTAGAGTCCATTTCAACTTCACAACGAAGGATATTG
* *
366563 GACTCGAGACAACACAAGTTCAACTTCACAACGAAGGAACGGCTGGTTGTCAACAAACAATT-TC
1 CACTCAAGACAACACAAGTTCAACTTCACAACGAAGGAACGGCTGGTTGTCAACAAACAATTCT-
* * *
366627 CTAGTTCTAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTC
65 CAATTTC-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
366674 AGAACAATGC
Statistics
Matches: 675, Mismatches: 56, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
628 1 0.00
629 72 0.11
630 62 0.09
631 2 0.00
632 1 0.00
633 10 0.01
634 407 0.60
635 117 0.17
636 3 0.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (630 bp):
CACTCAAGACAACACAAGTTCAACTTCACAACGAAGGAACGGCTGGTTGTCAACAAACAATTCTC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAAGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
TCAACAAACAACATTCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
ACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCA
GAGCCAACTTCAACTTCACAACGAAGGATATTAGACTCAAGAAAACGCAAGTTCAACTTCACGAC
GAAGGGACCGCTGATTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGA
AAGATATTGAACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACCGCTGATTGTCAAAAA
CAAATTCATTTAGAGTCCATTTCAACTTCACAACGAAGGATATTG
Found at i:367464 original size:37 final size:37
Alignment explanation
Indices: 367402--367507 Score: 131
Period size: 37 Copynumber: 2.9 Consensus size: 37
367392 CCTTTTCGTC
* *
367402 CTACTAGAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * * * *
367439 TTGCTAGGATTTAAACTCTTAAAAATAGAATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
367476 CTACTATGATTTAAACTCCTAAAGATAGGATA
1 CTACTAGGATTTAAACTCCTAAAAATAGGATA
367508 CACAAGCACT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:368092 original size:24 final size:24
Alignment explanation
Indices: 368065--368168 Score: 90
Period size: 24 Copynumber: 4.3 Consensus size: 24
368055 CTTTGCATTT
368065 TTATTATTACTATTATATTTATTA
1 TTATTATTACTATTATATTTATTA
* *
368089 TTATTTTTACTATTATATTTCCTT-
1 TTATTATTACTATTATATTT-ATTA
368113 TTATTA-TACTTATT-TATATTATATA
1 TTATTATTAC-TATTATAT-TTAT-TA
** *
368138 TGTA-TATTTTTTTTATATTTATTA
1 T-TATTATTACTATTATATTTATTA
368162 TTATTAT
1 TTATTAT
368169 ATTTTTACTT
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
23 9 0.14
24 37 0.58
25 12 0.19
26 6 0.09
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (24 bp):
TTATTATTACTATTATATTTATTA
Found at i:368214 original size:12 final size:11
Alignment explanation
Indices: 368184--368228 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
368174 TACTTTCTCT
*
368184 TTCTTTTATTA
1 TTCTTGTATTA
368195 TTCTTGTATTA
1 TTCTTGTATTA
368206 TTACTTGTATTA
1 TT-CTTGTATTA
368218 TT-TT-TATTA
1 TTCTTGTATTA
368227 TT
1 TT
368229 ATTTTGTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 7 0.22
10 2 0.06
11 12 0.38
12 11 0.34
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.69
Consensus pattern (11 bp):
TTCTTGTATTA
Found at i:368231 original size:15 final size:15
Alignment explanation
Indices: 368061--368231 Score: 63
Period size: 15 Copynumber: 11.0 Consensus size: 15
368051 TTTTCTTTGC
*
368061 ATTTTTATTATTACT
1 ATTTTTATTATTATT
*
368076 A-TTATATTTATTATT
1 ATTTTTA-TTATTATT
*
368091 ATTTTTACTATTATAT
1 ATTTTTATTATTAT-T
*
368107 TTCCTTTTATTA-TACTT
1 AT--TTTTATTATTA-TT
*
368124 ATTTATATTATATATGT
1 ATTTTTATTAT-TAT-T
368141 ATATTTT-TT-TTA-T
1 AT-TTTTATTATTATT
368154 ATTTATTATTATTA-T
1 ATTT-TTATTATTATT
*
368169 ATTTTTACTT-TCTCTT
1 ATTTTTA-TTAT-TATT
*
368185 -TCTTTTATTATTCTTGT
1 AT-TTTTATTATT-AT-T
* *
368202 ATTATTACTT-GTATT
1 ATTTTTA-TTATTATT
368217 ATTTTTATTATTATT
1 ATTTTTATTATTATT
368232 TTGTTATATA
Statistics
Matches: 117, Mismatches: 16, Indels: 46
0.65 0.09 0.26
Matches are distributed among these distances:
12 2 0.02
13 5 0.04
14 12 0.10
15 50 0.43
16 17 0.15
17 17 0.15
18 14 0.12
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (15 bp):
ATTTTTATTATTATT
Found at i:368764 original size:24 final size:22
Alignment explanation
Indices: 368733--368807 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
368723 TTATTCGTAC
*
368733 TTTGTTAT-TATTATTTTGTTTA
1 TTTGTTTTATATTATTTT-TTTA
368755 TTTGTTTTAT-TTATTTTCTTT-
1 TTTGTTTTATATTATTTT-TTTA
* *
368776 TTCTTTTTTATATATATTTTATTA
1 TT-TGTTTTATAT-TATTTTTTTA
368800 TTTGTTTT
1 TTTGTTTT
368808 TTTACTTACT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 2 0.05
22 24 0.56
23 9 0.21
24 8 0.19
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (22 bp):
TTTGTTTTATATTATTTTTTTA
Found at i:379471 original size:135 final size:135
Alignment explanation
Indices: 379229--379500 Score: 508
Period size: 135 Copynumber: 2.0 Consensus size: 135
379219 ATATCTAAGT
379229 ACATGCCAACTAGTAATATCAAAATAAACATCTAGAGATGTCATACTGCTACTGATGAGACAACC
1 ACATGCCAACTAGTAATATCAAAATAAACATCTAGAGATGTCATACTGCTACTGATGAGACAACC
*
379294 CTTGACAGATGATATCAGCTGCACTCCTCACTTCGATTCGTACACAAAACCTACGCGTGAAAATC
66 CTTGACAGATGATATCAGCTGCACTCCTCACTCCGATTCGTACACAAAACCTACGCGTGAAAATC
379359 ATCAC
131 ATCAC
*
379364 ACATGCCAACTAGTAATATCAAAATAAACATCTAGAGATGTCATACTGCTACTGATGAGGCAACC
1 ACATGCCAACTAGTAATATCAAAATAAACATCTAGAGATGTCATACTGCTACTGATGAGACAACC
* *
379429 CTTGACAGATGATATCAGTTGCACTCCTCACTCCGATTCGTACACTAAACCTACGCGTGAAAATC
66 CTTGACAGATGATATCAGCTGCACTCCTCACTCCGATTCGTACACAAAACCTACGCGTGAAAATC
379494 ATCAC
131 ATCAC
379499 AC
1 AC
379501 GCTAAGTATT
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
135 133 1.00
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (135 bp):
ACATGCCAACTAGTAATATCAAAATAAACATCTAGAGATGTCATACTGCTACTGATGAGACAACC
CTTGACAGATGATATCAGCTGCACTCCTCACTCCGATTCGTACACAAAACCTACGCGTGAAAATC
ATCAC
Found at i:385903 original size:250 final size:250
Alignment explanation
Indices: 385606--386096 Score: 722
Period size: 250 Copynumber: 2.0 Consensus size: 250
385596 TCATCAAATA
* *
385606 AAGGACCAAAATAAAGAAAGTCAAAAGTAAATCTAATTAAAAAATAAATAAAAATAAAAAAGCTA
1 AAGGACCAAAATAAAGAAAGTCAAAAGTAAAGCTAATTAAAAAATAAAGAAAAATAAAAAAGCTA
* * *
385671 CAATTTAAGGGCTGAAATATAAGTGCTGGAAATTTAATGGATGAAATTAAAAGTGCATAAAATTA
66 CAACTTAAGGGCTGAAATATAAATGCTGGAAATTTAATGGATGAAATTAAAAGTACATAAAATTA
* *
385736 AAGGGGTAGAACCATAAATAAAAAAATGA-CAATCAAATAAA-ATTAAAAGTTAGTTGTTAATAT
131 AAGGGGTAGAAACATAAAT-AAAAAATGACCAATCAAATAAAGA-TAAAAGTTAATTGTTAATAT
*
385799 TTAATAATTTTATATGAATAATAATAATGTGGGTCATA-TCCTAGAACGAGTCATCAC
194 TTAATAATTTTATATGAATAATAATAATATGGGTCATACT-CTAGAACGAGTCATCAC
* * *
385856 AAGGGCCAAAATAAAGAAAGT-AGAAA-TAAAGCTAATTAAGAAAATAAAGATAACTAAAAAAGC
1 AAGGACCAAAATAAAGAAAGTCA-AAAGTAAAGCTAATTAA-AAAATAAAGAAAAATAAAAAAGC
* * * * *
385919 TAGAACTTAAGGGCTGAAATATAAATGTTGGAAATTTGATGGCTGAAATTAAAATTACATAAAAT
64 TACAACTTAAGGGCTGAAATATAAATGCTGGAAATTTAATGGATGAAATTAAAAGTACATAAAAT
*
385984 TAAAGGGGTAGAAACGTAAATAAAAAATGACCAATCAAATAAAGATAAAAGTTAATTGTTAATAT
129 TAAAGGGGTAGAAACATAAATAAAAAATGACCAATCAAATAAAGATAAAAGTTAATTGTTAATAT
* * *
386049 TTAATAATTTTATCTGAATCATAATAATATGGTTCATACTCTAGAACG
194 TTAATAATTTTATATGAATAATAATAATATGGGTCATACTCTAGAACG
386097 GGTTACTACA
Statistics
Matches: 216, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
249 22 0.10
250 192 0.89
251 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (250 bp):
AAGGACCAAAATAAAGAAAGTCAAAAGTAAAGCTAATTAAAAAATAAAGAAAAATAAAAAAGCTA
CAACTTAAGGGCTGAAATATAAATGCTGGAAATTTAATGGATGAAATTAAAAGTACATAAAATTA
AAGGGGTAGAAACATAAATAAAAAATGACCAATCAAATAAAGATAAAAGTTAATTGTTAATATTT
AATAATTTTATATGAATAATAATAATATGGGTCATACTCTAGAACGAGTCATCAC
Found at i:386268 original size:15 final size:15
Alignment explanation
Indices: 386245--386278 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
386235 TTTTAAAAGT
* *
386245 TTAGTAATTAGCAAG
1 TTAGCAATTAACAAG
386260 TTAGCAATTAACAAG
1 TTAGCAATTAACAAG
386275 TTAG
1 TTAG
386279 AGTTTTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (15 bp):
TTAGCAATTAACAAG
Found at i:391914 original size:35 final size:35
Alignment explanation
Indices: 391868--391939 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
391858 AAACAAAGTG
391868 CTTCTAACTACTTCAAACAATCCACCAACTAACTC
1 CTTCTAACTACTTCAAACAATCCACCAACTAACTC
* *
391903 CTTCTAACTACTTCTAACAGTCCACCAACTAACTC
1 CTTCTAACTACTTCAAACAATCCACCAACTAACTC
391938 CT
1 CT
391940 AACACACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.33, C:0.38, G:0.01, T:0.28
Consensus pattern (35 bp):
CTTCTAACTACTTCAAACAATCCACCAACTAACTC
Found at i:393176 original size:26 final size:24
Alignment explanation
Indices: 393114--393176 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
393104 CATTTTAATC
393114 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
393138 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
393161 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
393177 ACTTTTCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:393215 original size:51 final size:51
Alignment explanation
Indices: 393160--393261 Score: 131
Period size: 51 Copynumber: 2.0 Consensus size: 51
393150 TTAATATTTC
*
393160 TAATAATAT-A-ATATTATACTTTTCATATTATAATAA-A-ATAATTAATTATTA
1 TAATAATATAAGATATTATA-TTTT-AT-TT-TAATAATATATAATAAATTATTA
393211 TAATAATATAAGATATTATATTTTATTTTAATAATATATAATAAATTATTA
1 TAATAATATAAGATATTATATTTTATTTTAATAATATATAATAAATTATTA
393262 ATAAAATTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
49 6 0.13
50 3 0.07
51 24 0.52
52 5 0.11
53 8 0.17
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (51 bp):
TAATAATATAAGATATTATATTTTATTTTAATAATATATAATAAATTATTA
Found at i:393228 original size:21 final size:21
Alignment explanation
Indices: 393185--393229 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
393175 ATACTTTTCA
*
393185 TATTATAATAAAATAATTAAT
1 TATTATAATAAAATAAATAAT
*
393206 TATTATAATAATATAAGAT-AT
1 TATTATAATAAAATAA-ATAAT
393227 TAT
1 TAT
393230 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TATTATAATAAAATAAATAAT
Found at i:393340 original size:27 final size:28
Alignment explanation
Indices: 393294--393347 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
393284 ATTTCATAGA
393294 AATAATATTATTAAATTA-TTAATATTG
1 AATAATATTATTAAATTATTTAATATTG
*
393321 AATAATATTATT-TATATATTTAATATT
1 AATAATATTATTAAAT-TATTTAATATT
393348 AATGTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 2 0.08
27 14 0.58
28 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
AATAATATTATTAAATTATTTAATATTG
Found at i:393533 original size:20 final size:20
Alignment explanation
Indices: 393503--393553 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
393493 AATAAAATTA
393503 TAAAAATAATATTTTAATA-T
1 TAAAAA-AATATTTTAATATT
393523 TAAATAAAATATTTTAATATT
1 TAAA-AAAATATTTTAATATT
393544 TAAAAAAATA
1 TAAAAAAATA
393554 ATAATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAAAATATTTTAATATT
Found at i:398586 original size:126 final size:126
Alignment explanation
Indices: 398436--398672 Score: 357
Period size: 126 Copynumber: 1.9 Consensus size: 126
398426 GTGCCTATTT
* * * **
398436 ATGTTCAAGAATTAATTAGTGGTAATGCGCATGGCATGGTTCCCACAAACGTTTAAGAATTAAAC
1 ATGTTCAAGAATTAATTAGAGGTAATACACATGGCATGGTTCCCACAAACGTACAAGAATTAAAC
* * * **
398501 AATGGTGTGCCCACTCATGTTGAAGAATTAAATATTGGTGCACATGACATGGTGCCCACTC
66 AATGGTGCGCACAATCATGTTGAAGAATTAAATATTAATGCACATGACATGGTGCCCACTC
* *
398562 ATGTTCAAGAATTAATTAGAGGTAATATACATGGCATGGTTCCCACAAATGTACAAGAATTAAAC
1 ATGTTCAAGAATTAATTAGAGGTAATACACATGGCATGGTTCCCACAAACGTACAAGAATTAAAC
*
398627 AATGGTGCGCATAATCATGTTGAAGAATTAAATATTAATGCACATG
66 AATGGTGCGCACAATCATGTTGAAGAATTAAATATTAATGCACATG
398673 GAACTTGAGT
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
126 98 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (126 bp):
ATGTTCAAGAATTAATTAGAGGTAATACACATGGCATGGTTCCCACAAACGTACAAGAATTAAAC
AATGGTGCGCACAATCATGTTGAAGAATTAAATATTAATGCACATGACATGGTGCCCACTC
Found at i:406571 original size:36 final size:36
Alignment explanation
Indices: 406522--406684 Score: 256
Period size: 36 Copynumber: 4.6 Consensus size: 36
406512 TTCGTTCAAA
* * *
406522 TTGAATCGAAAGTGTCTATGCTTCCTTCCGTTTGAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCGAC
* *
406558 TCGAATCGAAAGTGCCGATGCTTCCTTCCGTTCGTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCGAC
406594 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCGAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCGAC
*
406630 TTGAATCGAAAGTGCCGATGCTTCCTTCCTTTC-AC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCGAC
*
406665 TTGAATCGAAAGTGCTGATG
1 TTGAATCGAAAGTGCCGATG
406685 TTTTCGTTCT
Statistics
Matches: 118, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 21 0.18
36 97 0.82
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.33
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCGAC
Found at i:408282 original size:27 final size:26
Alignment explanation
Indices: 408227--408288 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
408217 ACATTTCAAT
**
408227 TTAATAT-ATAATGATGTACGATTTT
1 TTAATATAATAATGATGTACGATTAA
* *
408252 TTAATATAATTATCGATGTTCGATTAA
1 TTAATATAATAAT-GATGTACGATTAA
408279 TTAAT-TAATA
1 TTAATATAATA
408289 TAAATTTAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 7 0.23
26 8 0.27
27 15 0.50
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.47
Consensus pattern (26 bp):
TTAATATAATAATGATGTACGATTAA
Found at i:409766 original size:20 final size:22
Alignment explanation
Indices: 409721--409766 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
409711 AGATAATTCA
*
409721 AGATAGGATAAAAGCAATATTC
1 AGATAGGATAAAAGCAATATGC
*
409743 -GATA-GATAAAATC-ATATGC
1 AGATAGGATAAAAGCAATATGC
409762 AGATA
1 AGATA
409767 TGAGTTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.24
20 12 0.57
21 4 0.19
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (22 bp):
AGATAGGATAAAAGCAATATGC
Found at i:413652 original size:19 final size:20
Alignment explanation
Indices: 413610--413656 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
413600 AATATTGAAA
* *
413610 TTAGATTGGAACTTGAATTT
1 TTAGGTTGGAACCTGAATTT
413630 TTAGGTTGGAACCTGAA-TT
1 TTAGGTTGGAACCTGAATTT
413649 TTAGGTTG
1 TTAGGTTG
413657 CAAACCAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.43
Consensus pattern (20 bp):
TTAGGTTGGAACCTGAATTT
Found at i:413670 original size:19 final size:19
Alignment explanation
Indices: 413628--413784 Score: 149
Period size: 19 Copynumber: 8.2 Consensus size: 19
413618 GAACTTGAAT
* *
413628 TTTTAGGTTG-GAACCTGAA
1 TTTTAGGTTGCAAACCAG-A
413647 TTTTAGGTTGCAAACCAGA
1 TTTTAGGTTGCAAACCAGA
* * * *
413666 GTTTAGGTTGTAAGCCATA
1 TTTTAGGTTGCAAACCAGA
* * *
413685 TTTTAAGGTTGGAATCCATA
1 TTTT-AGGTTGCAAACCAGA
413705 TTTTAGGTTGCAAACCAGA
1 TTTTAGGTTGCAAACCAGA
* *
413724 TTTTAGGTTGTAAGCCAGA
1 TTTTAGGTTGCAAACCAGA
*
413743 TTTTAAAGTTG-AAAGCCAGA
1 TTTT-AGGTTGCAAA-CCAGA
413763 TTTTAGGTTGCAAACCAG-
1 TTTTAGGTTGCAAACCAGA
413781 TTTT
1 TTTT
413785 TTAAATTACA
Statistics
Matches: 116, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
18 4 0.03
19 73 0.63
20 39 0.34
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.36
Consensus pattern (19 bp):
TTTTAGGTTGCAAACCAGA
Found at i:413694 original size:58 final size:58
Alignment explanation
Indices: 413626--413780 Score: 208
Period size: 58 Copynumber: 2.7 Consensus size: 58
413616 TGGAACTTGA
* *
413626 ATTTTTAGGTTGGAA-CCTGAATTTTAGGTTGCAAACCAGAGTTTAGGTTGTAAGCCAT
1 ATTTTAAGGTTGGAAGCC-GAATTTTAGGTTGCAAACCAGAGTTTAGGTTGTAAGCCAG
* *
413684 ATTTTAAGGTTGGAATCC-ATATTTTAGGTTGCAAACCAGATTTTAGGTTGTAAGCCAG
1 ATTTTAAGGTTGGAAGCCGA-ATTTTAGGTTGCAAACCAGAGTTTAGGTTGTAAGCCAG
* *
413742 ATTTTAAAGTTGAAAGCC-AGATTTTAGGTTGCAAACCAG
1 ATTTTAAGGTTGGAAGCCGA-ATTTTAGGTTGCAAACCAG
413781 TTTTTTAAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
57 1 0.01
58 85 0.97
59 2 0.02
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (58 bp):
ATTTTAAGGTTGGAAGCCGAATTTTAGGTTGCAAACCAGAGTTTAGGTTGTAAGCCAG
Found at i:413710 original size:39 final size:38
Alignment explanation
Indices: 413628--413772 Score: 141
Period size: 39 Copynumber: 3.8 Consensus size: 38
413618 GAACTTGAAT
* * * *
413628 TTTTAGGTTGGAA-CCTGAATTTTAGGTTGCAAACCAGA
1 TTTTAGGTTGAAAGCCAG-ATTTTAGGTTGGAAGCCAGA
* * * * *
413666 GTTTAGGTTGTAAGCCATATTTTAAGGTTGGAATCCATA
1 TTTTAGGTTGAAAGCCAGATTTT-AGGTTGGAAGCCAGA
*
413705 TTTTAGGTTGCAAA-CCAGATTTTAGGTTGTAAGCCAGA
1 TTTTAGGTTG-AAAGCCAGATTTTAGGTTGGAAGCCAGA
*
413743 TTTTAAAGTTGAAAGCCAGATTTTAGGTTG
1 TTTT-AGGTTGAAAGCCAGATTTTAGGTTG
413773 CAAACCAGTT
Statistics
Matches: 88, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
38 35 0.40
39 51 0.58
40 2 0.02
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (38 bp):
TTTTAGGTTGAAAGCCAGATTTTAGGTTGGAAGCCAGA
Found at i:413862 original size:40 final size:40
Alignment explanation
Indices: 413801--414027 Score: 173
Period size: 40 Copynumber: 5.7 Consensus size: 40
413791 TACAAGCAAT
* *
413801 GTGATGTATCGTA-TGGCTACACACCTAAATATGAAAGTG
1 GTGATGTATCGTACGGGATACACACCTAAATATGAAAGTG
* * *
413840 GTGATGTATTGTATGGGATACACATCC--AAT-T-ACAAGCAAG
1 GTGATGTATCGTACGGGATACACA-CCTAAATATGA-AAG--TG
* *
413880 GTTATGTATCGTACGTG-TACACACCTAAATATGAAAGTG
1 GTGATGTATCGTACGGGATACACACCTAAATATGAAAGTG
* * * * *
413919 GTGATGTATTGTACGGGATACGCACCCAATTACAAGAAA--G
1 GTGATGTATCGTACGGGATACACACCTAA--ATATGAAAGTG
* *
413959 GCGATGTATCGTACGGAATACACACCTAAATATGAAAGTG
1 GTGATGTATCGTACGGGATACACACCTAAATATGAAAGTG
* * ** *
413999 GTGATCTATTGTACTAGATACAAACCTAA
1 GTGATGTATCGTACGGGATACACACCTAA
414028 TTACAAGCAA
Statistics
Matches: 144, Mismatches: 30, Indels: 27
0.72 0.15 0.13
Matches are distributed among these distances:
37 1 0.01
38 12 0.08
39 36 0.25
40 82 0.57
41 6 0.04
42 7 0.05
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (40 bp):
GTGATGTATCGTACGGGATACACACCTAAATATGAAAGTG
Found at i:413919 original size:79 final size:79
Alignment explanation
Indices: 413788--414038 Score: 337
Period size: 79 Copynumber: 3.2 Consensus size: 79
413778 CAGTTTTTTA
* * *
413788 AATTACAAGCAATGTGATGTATCGTATGGCTACACACCTAAATATGAAAGTGGTGATGTATTGTA
1 AATTACAAGCAAGGTGATGTATCGTACGGATACACACCTAAATATGAAAGTGGTGATGTATTGTA
*
413853 TGGGATACACATCC
66 TGGGATACACAACC
*
413867 AATTACAAGCAAGGTTATGTATCGTACGTG-TACACACCTAAATATGAAAGTGGTGATGTATTGT
1 AATTACAAGCAAGGTGATGTATCGTACG-GATACACACCTAAATATGAAAGTGGTGATGTATTGT
* * *
413931 ACGGGATACGCACCC
65 ATGGGATACACAACC
* * *
413946 AATTACAAGAAAGGCGATGTATCGTACGGAATACACACCTAAATATGAAAGTGGTGATCTATTGT
1 AATTACAAGCAAGGTGATGTATCGTACGG-ATACACACCTAAATATGAAAGTGGTGATGTATTGT
*
414011 ACT-AGATACA-AACC
65 A-TGGGATACACAACC
414025 TAATTACAAGCAAG
1 -AATTACAAGCAAG
414039 AATCAAAGGT
Statistics
Matches: 152, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
78 1 0.01
79 99 0.65
80 52 0.34
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (79 bp):
AATTACAAGCAAGGTGATGTATCGTACGGATACACACCTAAATATGAAAGTGGTGATGTATTGTA
TGGGATACACAACC
Found at i:415690 original size:16 final size:16
Alignment explanation
Indices: 415669--415703 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
415659 TTAACGTTAT
415669 TTTAAAATTAAATTAA
1 TTTAAAATTAAATTAA
* *
415685 TTTAAATTTAAATTGA
1 TTTAAAATTAAATTAA
415701 TTT
1 TTT
415704 TTTCTCATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTAAAATTAAATTAA
Found at i:416263 original size:19 final size:20
Alignment explanation
Indices: 416219--416263 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
416209 ATTTGTTCTT
*
416219 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
416239 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
416258 AATAAA
1 AATAAA
416264 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:417597 original size:19 final size:21
Alignment explanation
Indices: 417565--417617 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
417555 TAAATTGAGT
417565 CAAATTTATATATAATCGAGC
1 CAAATTTATATATAATCGAGC
417586 CAAATTTATATATAATCGAGC
1 CAAATTTATATATAATCGAGC
417607 CAAATTTATAT
1 CAAATTTATAT
417618 GTAGACATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (21 bp):
CAAATTTATATATAATCGAGC
Found at i:421241 original size:17 final size:17
Alignment explanation
Indices: 421219--421259 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
421209 TATAATAAAC
421219 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
421236 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
*
421253 ATATGAT
1 TTATGAT
421260 TACTTTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
TTATGATAATTAAATTA
Found at i:421287 original size:51 final size:52
Alignment explanation
Indices: 421229--421326 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 52
421219 TTATGATAAT
*
421229 TAAATTATTATGATAATTAAATTAATATGATTAC-TTTTTGAAATTTTATCA
1 TAAATTATTATGATAATCAAATTAATATGATTACTTTTTTGAAATTTTATCA
421280 TAAATTATTATGATAATCAAATTAATATGATTACTTTTTTGAAATTT
1 TAAATTATTATGATAATCAAATTAATATGATTACTTTTTTGAAATTT
421327 AGTTTTATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 33 0.73
52 12 0.27
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (52 bp):
TAAATTATTATGATAATCAAATTAATATGATTACTTTTTTGAAATTTTATCA
Found at i:422483 original size:26 final size:26
Alignment explanation
Indices: 422454--422507 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
422444 AGAGCAGTAT
422454 AAGTCGGTTAATATAAGAATGAATTA
1 AAGTCGGTTAATATAAGAATGAATTA
422480 AAGTCGGTTAATATAAGAATGAATTA
1 AAGTCGGTTAATATAAGAATGAATTA
422506 AA
1 AA
422508 CATGATCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.48, C:0.04, G:0.19, T:0.30
Consensus pattern (26 bp):
AAGTCGGTTAATATAAGAATGAATTA
Found at i:428142 original size:13 final size:13
Alignment explanation
Indices: 428124--428167 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
428114 ATGATAAATA
*
428124 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
428137 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
428150 AAACAACTACAAT
1 AAAAAACTACAAT
428163 AAAAA
1 AAAAA
428168 GTACTAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:430404 original size:9 final size:9
Alignment explanation
Indices: 430390--430423 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
430380 TAAGTAAAAT
430390 ATTAAATAA
1 ATTAAATAA
430399 ATTAAAT-A
1 ATTAAATAA
*
430407 CTTAAATAA
1 ATTAAATAA
430416 ATTAAATA
1 ATTAAATA
430424 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:430422 original size:17 final size:17
Alignment explanation
Indices: 430386--430424 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
430376 TAATTAAGTA
430386 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
430402 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
430419 AAATAC
1 AAATAC
430425 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:430483 original size:10 final size:10
Alignment explanation
Indices: 430470--430509 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
430460 AGAGATTATA
*
430470 AGAGTATTTG
1 AGAGAATTTG
*
430480 AGAGAAGTTG
1 AGAGAATTTG
*
430490 AGAGAAATTG
1 AGAGAATTTG
430500 AGAGAATTTG
1 AGAGAATTTG
430510 GTGTGATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.28
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:431428 original size:9 final size:9
Alignment explanation
Indices: 431414--431464 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
431404 AATAAATTAA
431414 TATATAGTT
1 TATATAGTT
*
431423 TATATA-TAC
1 TATATAGT-T
431432 TATATAGTT
1 TATATAGTT
*
431441 TATATA-TAC
1 TATATAGT-T
431450 TATATAGTT
1 TATATAGTT
431459 TATATA
1 TATATA
431465 TACTAATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
8 2 0.06
9 30 0.88
10 2 0.06
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (9 bp):
TATATAGTT
Found at i:431435 original size:18 final size:18
Alignment explanation
Indices: 431414--431606 Score: 183
Period size: 18 Copynumber: 11.1 Consensus size: 18
431404 AATAAATTAA
431414 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
431432 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
431450 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
431468 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
431483 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
431501 TAT-T-G--AACTATATAG
1 TATATAGTTTA-TATATAC
431516 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
431534 TA-AT-GAATTATATATAA
1 TATATAG-TTTATATATAC
*
431551 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
431569 CATATAGTCTATATATA-
1 TATATAGTTTATATATAC
*
431586 TCATATAGATTATATATAC
1 T-ATATAGTTTATATATAC
431605 TA
1 TA
431607 ATAAACTATA
Statistics
Matches: 141, Mismatches: 19, Indels: 30
0.74 0.10 0.16
Matches are distributed among these distances:
14 2 0.01
15 17 0.12
16 6 0.04
17 17 0.12
18 95 0.67
19 4 0.03
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:431487 original size:33 final size:33
Alignment explanation
Indices: 431411--431630 Score: 237
Period size: 33 Copynumber: 6.4 Consensus size: 33
431401 ATTAATAAAT
*
431411 TAATATATAGTTTATATATACTATATAGTTTA-TATA
1 TAATATATAGTTTATATATACTA-AT-G--AACTATA
*
431447 TACTATATAGTTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
*
431480 TAATATATAGTTTATATATACTATTGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
* *
431513 TAGTATATAGTTTATATATACTAATGAATTATATA
1 TAATATATAGTTTATATATACTAATGAA--CTATA
* * *
431548 TAATGTATAGTTTATATATACCATAT-AGTCTATA
1 TAATATATAGTTTATATATACTA-ATGA-ACTATA
* *
431582 TATATCATATAGATTATATATACTAATAAACTATA
1 TA-AT-ATATAGTTTATATATACTAATGAACTATA
*
431617 TAATGTATAGTTTA
1 TAATATATAGTTTA
431631 GGGTTTAGGT
Statistics
Matches: 158, Mismatches: 18, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
32 1 0.01
33 69 0.44
34 9 0.06
35 38 0.24
36 41 0.26
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (33 bp):
TAATATATAGTTTATATATACTAATGAACTATA
Found at i:431648 original size:13 final size:14
Alignment explanation
Indices: 431625--431659 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
431615 TATAATGTAT
431625 AGTTTAGGGTTTAG
1 AGTTTAGGGTTTAG
*
431639 -GTTTATGGTTTAG
1 AGTTTAGGGTTTAG
431652 AGTTTAGG
1 AGTTTAGG
431660 ATTTTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (14 bp):
AGTTTAGGGTTTAG
Found at i:431706 original size:9 final size:9
Alignment explanation
Indices: 431692--431733 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
431682 TAAATTATAC
431692 TATATAGTA
1 TATATAGTA
431701 TATATAGTTTA
1 TATATAG--TA
431712 TATATA-TAA
1 TATATAGT-A
431721 TATATAGTA
1 TATATAGTA
431730 TATA
1 TATA
431734 AATATAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 1 0.03
9 19 0.66
10 1 0.03
11 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (9 bp):
TATATAGTA
Found at i:431708 original size:34 final size:36
Alignment explanation
Indices: 431665--431733 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
431655 TTAGGATTTT
*
431665 TATATATAGTTCATATGTA-AAT-TATACTATATAG
1 TATATATAGTTCATATATATAATATATACTATATAG
* *
431699 TATATATAGTTTATATATATAATATATAGTATATA
1 TATATATAGTTCATATATATAATATATACTATATA
431734 AATATAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 17 0.57
35 3 0.10
36 10 0.33
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (36 bp):
TATATATAGTTCATATATATAATATATACTATATAG
Found at i:431717 original size:20 final size:20
Alignment explanation
Indices: 431692--431866 Score: 102
Period size: 20 Copynumber: 8.4 Consensus size: 20
431682 TAAATTATAC
431692 TATATAGTA-TATATAGTTTA
1 TATATA-TACTATATAGTTTA
*
431712 TATATATAATATATAGTATATA
1 TATATATACTATATAGT-T-TA
* * *
431734 AATATAAACTATAGTATGTAGTA
1 TATATATACTATA-TA-GT-TTA
* *
431757 TATAAATATTAACTATAGTTTA
1 TATATATACT-A-TATAGTTTA
* * * *
431779 TATATATAGTGTATACTATA
1 TATATATACTATATAGTTTA
* * *
431799 TAAATAGT-GTATATAGTTCA
1 TATATA-TACTATATAGTTTA
* *
431819 TATGTAAACTATATAGTTTA
1 TATATATACTATATAGTTTA
* *
431839 TATGTAAACTATATAGTTTA
1 TATATATACTATATAGTTTA
431859 TATATATA
1 TATATATA
431867 GTTCATGTGT
Statistics
Matches: 120, Mismatches: 26, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.02
20 74 0.62
21 2 0.02
22 22 0.18
23 12 0.10
24 6 0.05
25 2 0.02
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.44
Consensus pattern (20 bp):
TATATATACTATATAGTTTA
Found at i:431746 original size:27 final size:27
Alignment explanation
Indices: 431716--431786 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
431706 AGTTTATATA
*
431716 TATAATATATAGTATATAAATATAAAC
1 TATAGTATATAGTATATAAATATAAAC
* *
431743 TATAGTATGTAGTATATAAATATTAAC
1 TATAGTATATAGTATATAAATATAAAC
*
431770 TATAGTTTATA-TATATA
1 TATAGTATATAGTATATA
431787 GTGTATACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 6 0.15
27 33 0.85
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (27 bp):
TATAGTATATAGTATATAAATATAAAC
Found at i:431798 original size:18 final size:18
Alignment explanation
Indices: 431777--431811 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
431767 AACTATAGTT
*
431777 TATATATATAGTGTATAC
1 TATATAAATAGTGTATAC
431795 TATATAAATAGTGTATA
1 TATATAAATAGTGTATA
431812 TAGTTCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (18 bp):
TATATAAATAGTGTATAC
Found at i:431885 original size:31 final size:32
Alignment explanation
Indices: 431828--431892 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
431818 ATATGTAAAC
* *
431828 TATATAGTTTATATGTAAACTATATAGTTTATA
1 TATATAGTTCATATGTAAAC-ATATAGTTCATA
*
431861 TATATAGTTCATGTGTAAAC-TATAGTTCATA
1 TATATAGTTCATATGTAAACATATAGTTCATA
431892 T
1 T
431893 GTAAATATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 11 0.38
33 18 0.62
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (32 bp):
TATATAGTTCATATGTAAACATATAGTTCATA
Found at i:431886 original size:18 final size:18
Alignment explanation
Indices: 431810--431939 Score: 90
Period size: 18 Copynumber: 6.9 Consensus size: 18
431800 AAATAGTGTA
431810 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
*
431828 TATATAGTTTATATGTAAAC
1 --TATAGTTCATATGTAAAC
*
431848 TATATAGTT--TA--TATA-
1 --TATAGTTCATATGTAAAC
*
431863 TATAGTTCATGTGTAAAC
1 TATAGTTCATATGTAAAC
431881 TATAGTTCATATGTAAATATCAAC
1 TATAGTTCATATG----TA--AAC
*
431905 TATAGTTTATATGTAAAC
1 TATAGTTCATATGTAAAC
*
431923 TATAGTTCATATATAAA
1 TATAGTTCATATGTAAA
431940 TATCAACCTT
Statistics
Matches: 91, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
13 7 0.08
15 1 0.01
16 3 0.03
17 3 0.03
18 32 0.35
20 28 0.31
22 2 0.02
24 15 0.16
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:431922 original size:42 final size:42
Alignment explanation
Indices: 431863--431946 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
431853 AGTTTATATA
* *
431863 TATAGTTCATGTGTAAACTATAGTTCATATGTAAATATCAAC
1 TATAGTTCATATGTAAACTATAGTTCATATATAAATATCAAC
*
431905 TATAGTTTATATGTAAACTATAGTTCATATATAAATATCAAC
1 TATAGTTCATATGTAAACTATAGTTCATATATAAATATCAAC
431947 CTTAGTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (42 bp):
TATAGTTCATATGTAAACTATAGTTCATATATAAATATCAAC
Found at i:431958 original size:42 final size:42
Alignment explanation
Indices: 431874--431958 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
431864 ATAGTTCATG
* *
431874 TGTAAACTATAGTTCATATGTAAATATCAACTATAGTTTATA
1 TGTAAACTATAGTTCATATATAAATATCAACTATAGTATATA
431916 TGTAAACTATAGTTCATATATAAATATCAACCT-TAGTATATA
1 TGTAAACTATAGTTCATATATAAATATCAA-CTATAGTATATA
431958 T
1 T
431959 ATATTTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 38 0.95
43 2 0.05
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (42 bp):
TGTAAACTATAGTTCATATATAAATATCAACTATAGTATATA
Found at i:432009 original size:18 final size:17
Alignment explanation
Indices: 431964--432009 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
431954 TATATATATT
431964 TATATATATAGTTCATA
1 TATATATATAGTTCATA
* *
431981 TGTAAACTATAGTTCATA
1 TATATA-TATAGTTCATA
431999 TATATAGTATA
1 TATATA-TATA
432010 TAAATATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (17 bp):
TATATATATAGTTCATA
Found at i:432020 original size:33 final size:32
Alignment explanation
Indices: 431983--432049 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
431973 AGTTCATATG
*
431983 TAAACTATAGTTCATATATATAGTATATAAATA
1 TAAACTATAGTTCATATAAATAGTATA-AAATA
*
432016 TAAACTATAGTTTATATAAATAGTATAAAATA
1 TAAACTATAGTTCATATAAATAGTATAAAATA
432048 TA
1 TA
432050 GTATATACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 7 0.22
33 25 0.78
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (32 bp):
TAAACTATAGTTCATATAAATAGTATAAAATA
Found at i:432024 original size:20 final size:20
Alignment explanation
Indices: 432000--432073 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
431990 TAGTTCATAT
432000 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
432020 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
*
432045 ATATAGTATATACATATAAA
1 ATATAGTATATAAATATAAA
*
432065 TTATAGTAT
1 ATATAGTAT
432074 GCAGTTTACA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
20 19 0.42
21 1 0.02
22 6 0.13
23 7 0.16
24 1 0.02
25 11 0.24
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:432155 original size:9 final size:9
Alignment explanation
Indices: 432116--432218 Score: 54
Period size: 9 Copynumber: 11.3 Consensus size: 9
432106 ACCCTAAACC
*
432116 ATATATACT
1 ATATATAAT
432125 ATATAT-AT
1 ATATATAAT
432133 ATATATAA-
1 ATATATAAT
432141 ACTATATAAT
1 A-TATATAAT
*
432151 TTATATTAAT
1 ATATA-TAAT
432161 AAACTATATAAT
1 --A-TATATAAT
* * *
432173 TTGTACAAT
1 ATATATAAT
432182 ATATAT--T
1 ATATATAAT
*
432189 ATTTATAATT
1 ATATATAA-T
*
432199 ATACATAAT
1 ATATATAAT
432208 ATATA-AAT
1 ATATATAAT
432216 ATA
1 ATA
432219 AATTGTATAG
Statistics
Matches: 71, Mismatches: 13, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
7 6 0.08
8 14 0.20
9 32 0.45
10 11 0.15
12 4 0.06
13 4 0.06
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.45
Consensus pattern (9 bp):
ATATATAAT
Found at i:432162 original size:22 final size:24
Alignment explanation
Indices: 432128--432260 Score: 87
Period size: 26 Copynumber: 5.3 Consensus size: 24
432118 ATATACTATA
432128 TATATATATATAAACTATATAATT
1 TATATATATATAAACTATATAATT
432152 TATAT-TA-ATAAACTATATAATT
1 TATATATATATAAACTATATAATT
* * * *
432174 TGTACAATATATATTA-TTTATAATT
1 TATA-TATATATA-AACTATATAATT
*
432199 ATACATAATATATAAA-TATA-AATT
1 -TATAT-ATATATAAACTATATAATT
*
432223 GTATAGTTTATATATAATTCATATATAATT
1 -TATA---TATATATAA-AC-TATATAATT
432253 TATATATA
1 TATATATA
432261 AACTATGTAG
Statistics
Matches: 84, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
22 18 0.21
23 2 0.02
24 14 0.17
25 15 0.18
26 22 0.26
27 1 0.01
29 8 0.10
30 4 0.05
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
TATATATATATAAACTATATAATT
Found at i:432239 original size:20 final size:20
Alignment explanation
Indices: 432214--432424 Score: 99
Period size: 20 Copynumber: 10.1 Consensus size: 20
432204 TAATATATAA
*
432214 ATATAAATTGTATAGTTTAT
1 ATATAAATTATATAGTTTAT
* *
432234 ATATAATTCATATATAATTTAT
1 ATATAAAT--TATATAGTTTAT
* * *
432256 ATATAAACTATGTAGTTTCT
1 ATATAAATTATATAGTTTAT
* *
432276 ATAT-AGTTCA-ATAGTTCAT
1 ATATAAATT-ATATAGTTTAT
*
432295 ATATAAACTATATAGTATTAT
1 ATATAAATTATATAGT-TTAT
*
432316 AGTTTATACATGGTATATATAGTTTAT
1 A---TATA-A--AT-TATATAGTTTAT
* * * *
432343 ACT-T-TA-TACATAATATAT
1 A-TATAAATTATATAGTTTAT
*
432361 ATATAAACTATATAGTTTAT
1 ATATAAATTATATAGTTTAT
* *
432381 ATATATAATACATATACTTTAT
1 ATATA-AAT-TATATAGTTTAT
*
432403 ATATAAACTATATAGTTTAT
1 ATATAAATTATATAGTTTAT
432423 AT
1 AT
432425 TATATATATA
Statistics
Matches: 139, Mismatches: 34, Indels: 36
0.67 0.16 0.17
Matches are distributed among these distances:
17 1 0.01
18 11 0.08
19 14 0.10
20 54 0.39
21 8 0.06
22 31 0.22
24 5 0.04
25 2 0.01
27 5 0.04
28 8 0.06
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (20 bp):
ATATAAATTATATAGTTTAT
Found at i:432256 original size:9 final size:10
Alignment explanation
Indices: 432180--432261 Score: 53
Period size: 11 Copynumber: 7.8 Consensus size: 10
432170 AATTTGTACA
432180 ATATAT-ATT
1 ATATATAATT
*
432189 ATTTATAATT
1 ATATATAATT
*
432199 ATACATAATAT
1 ATATATAAT-T
432210 ATAAATATAAATT
1 AT--ATAT-AATT
*
432223 GTATAGT--TT
1 ATATA-TAATT
432232 ATATATAATT
1 ATATATAATT
432242 CATATATAATTT
1 -ATATATAA-TT
432254 ATATATAA
1 ATATATAA
432262 ACTATGTAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
8 1 0.02
9 11 0.19
10 12 0.21
11 22 0.39
12 3 0.05
13 5 0.09
14 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (10 bp):
ATATATAATT
Found at i:432259 original size:13 final size:11
Alignment explanation
Indices: 432224--432261 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
432214 ATATAAATTG
*
432224 TATAGTTTATA
1 TATAATTTATA
*
432235 TATAATTCATA
1 TATAATTTATA
432246 TATAATTTATA
1 TATAATTTATA
432257 TATAA
1 TATAA
432262 ACTATGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TATAATTTATA
Found at i:432349 original size:27 final size:28
Alignment explanation
Indices: 432303--432363 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
432293 ATATATAAAC
* **
432303 TATATAGTATTATAGTTTATACATGGTA
1 TATATAGTATTATACTTTATACATAATA
432331 TATATAGT-TTATACTTTATACATAATA
1 TATATAGTATTATACTTTATACATAATA
432358 TATATA
1 TATATA
432364 TAAACTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (28 bp):
TATATAGTATTATACTTTATACATAATA
Found at i:432372 original size:22 final size:20
Alignment explanation
Indices: 432356--432414 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 20
432346 TTATACATAA
*
432356 TATATATATAAACTATATAGTT
1 TATATATATAAACTATACA--T
432378 TATATATATAATACATATAC-T
1 TATATATATAA-AC-TATACAT
432399 T-TATATATAAACTATA
1 TATATATATAAACTATA
432415 TAGTTTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 9 0.26
21 2 0.06
22 11 0.32
23 2 0.06
24 4 0.12
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (20 bp):
TATATATATAAACTATACAT
Found at i:432414 original size:42 final size:41
Alignment explanation
Indices: 432331--432430 Score: 136
Period size: 42 Copynumber: 2.5 Consensus size: 41
432321 ATACATGGTA
432331 TATATAGTTTATACT-T-T-ATACATAATATATATATAAAC
1 TATATAGTTTATACTATATAATACATAATATATATATAAAC
*
432369 TATATAGTTTATA-TATATAATACATATACTTTATATATAAAC
1 TATATAGTTTATACTATATAATACATA-A-TATATATATAAAC
*
432411 TATATAGTTTATATTATATA
1 TATATAGTTTATACTATATA
432431 TATATTAGTT
Statistics
Matches: 55, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
37 1 0.02
38 14 0.25
39 1 0.02
40 7 0.13
41 1 0.02
42 25 0.45
43 6 0.11
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (41 bp):
TATATAGTTTATACTATATAATACATAATATATATATAAAC
Found at i:432434 original size:20 final size:20
Alignment explanation
Indices: 432329--432440 Score: 81
Period size: 20 Copynumber: 5.5 Consensus size: 20
432319 TTATACATGG
432329 TATATATAGTTTATACTT-TA
1 TATATATAGTTTATA-TTATA
* *
432349 TACATA-A-TATATA-TATA
1 TATATATAGTTTATATTATA
*
432366 AACTATATAGTTTATATATATAA
1 TA-TATATAGTTTATAT-TAT-A
* *
432389 TACATATACTTTATA-TATA
1 TATATATAGTTTATATTATA
*
432408 AACTATATAGTTTATATTATA
1 TA-TATATAGTTTATATTATA
432429 TATATATTAGTT
1 TATATA-TAGTT
432441 GTTTTAATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
16 1 0.01
17 3 0.04
18 8 0.11
19 4 0.06
20 28 0.40
21 10 0.14
22 14 0.20
23 2 0.03
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (20 bp):
TATATATAGTTTATATTATA
Found at i:432875 original size:223 final size:221
Alignment explanation
Indices: 432460--433071 Score: 897
Period size: 217 Copynumber: 2.8 Consensus size: 221
432450 TTTTTTCTCA
* * *
432460 ACTTATTACTTATTTCTATTTATTAATTGGCCCATAACTTTTAAAATGAGTATAATTTAGTACAT
1 ACTTATTACTTATTTCTATTT-TAAATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACTT
* *
432525 TTTTATATTAATTTCAACCTCAAAATTTAAAATTTATTTCTATTTGATCCCT--T---T-TGTGT
65 TTTTGTATTAATTTCAACCTC-AAATTTAAAA-TTATTTCGATTTGATCCCTCATCAATGTGTGT
* *
432584 TGTTTAATATATTTAAATTTTTATTTATAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTA
128 TGTTTAATTTATTTAAATTTTTATTTATAATTTCATATTTGTTCAATTGAGTCCTCCAAATTTTA
* *
432649 TTTGCACCTGAAATTGACCCATACTTATT
193 TTTGCACATGAAAATGACCCATACTTATT
* *
432678 ACTTATTACTTATTTCTATTTTAAAATTGGCCCATATCTTTTTAAATGTGTATAATTTAGTACTT
1 ACTTATTACTTATTTCTATTTT-AAATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACTT
*
432743 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
65 TTTTGTATTAATTTCAACCTCA-AATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
*
432808 GTTTAATTTATTTAAATTTTTATTTTTAATTTCATATTTGTTCAATTGAGTCCTCCAAATTTTAT
129 GTTTAATTTATTTAAATTTTTATTTATAATTTCATATTTGTTCAATTGAGTCCTCCAAATTTTAT
* *
432873 TTGCATATGAAAATGATCCATACTTATT
194 TTGCACATGAAAATGACCCATACTTATT
* * *
432901 ACCTAATT-C-TA-TT-T-TTTT-AATTGGCTCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 A-CTTATTACTTATTTCTATTTTAAATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACTT
*
432960 TTTTGTATTAATTTCAACCTCAATATTTAAAATTATTTCGATTTGATCTCTCATCAATGTGTGTT
65 TTTTGTATTAATTTCAACCTCAA-ATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
*
433025 GTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATT
129 GTTTAATTTATTTAAATTTTTATTTATAATTTCATATTTGTTCAATT
433072 TAATTCTTAA
Statistics
Matches: 362, Mismatches: 22, Indels: 21
0.89 0.05 0.05
Matches are distributed among these distances:
216 1 0.00
217 165 0.46
218 86 0.24
219 5 0.01
220 1 0.00
221 2 0.01
222 3 0.01
223 94 0.26
224 5 0.01
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (221 bp):
ACTTATTACTTATTTCTATTTTAAATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTACTTT
TTTGTATTAATTTCAACCTCAAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGT
TTAATTTATTTAAATTTTTATTTATAATTTCATATTTGTTCAATTGAGTCCTCCAAATTTTATTT
GCACATGAAAATGACCCATACTTATT
Found at i:437084 original size:65 final size:65
Alignment explanation
Indices: 436988--437148 Score: 177
Period size: 65 Copynumber: 2.5 Consensus size: 65
436978 TCTTAATTTA
* * * *
436988 ATTATTTTA-T-TTATAAATTA-GTTATTTTATTTAATTAGAAA-TCTCAATAGAATTTTTAGTT
1 ATTATTTTATTATTATTAATTATTTTA-TTTATTTAATTAGAAATTCT-AATAGAATTTTTAATA
437049 TG
64 TG
* * *
437051 ATTATTTTATTATTATTAATTATTTTATTTATTTATTTAGAAATTCTAGTAGGATTTTTAATATG
1 ATTATTTTATTATTATTAATTATTTTATTTATTTAATTAGAAATTCTAATAGAATTTTTAATATG
**
437116 ATTATTTTATTTAGGAATTAATTATTTTATTTA
1 ATTATTTTA-TTA-TTATTAATTATTTTATTTA
437149 CTTAGAACTC
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
63 9 0.11
64 1 0.01
65 47 0.57
66 9 0.11
67 17 0.20
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (65 bp):
ATTATTTTATTATTATTAATTATTTTATTTATTTAATTAGAAATTCTAATAGAATTTTTAATATG
Found at i:437931 original size:15 final size:14
Alignment explanation
Indices: 437911--437962 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
437901 TTTATTTACT
437911 TTATTTATTATCTCA
1 TTATTTATTAT-TCA
* *
437926 TTATTTATCATTTA
1 TTATTTATTATTCA
437940 TTATTTTATTACTTTCA
1 TTA-TTTATTA--TTCA
437957 TTATTT
1 TTATTT
437963 TTAAATCCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 5 0.17
15 16 0.53
16 3 0.10
17 6 0.20
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATTATTCA
Found at i:437950 original size:22 final size:21
Alignment explanation
Indices: 437906--437958 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
437896 TCTATTTTAT
437906 TTACTTT-ATTTATTATCTCA
1 TTACTTTCATTTATTATCTCA
* * *
437926 TTATTTATCATTTATTATTTTA
1 TTACTT-TCATTTATTATCTCA
437948 TTACTTTCATT
1 TTACTTTCATT
437959 ATTTTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.19
21 6 0.22
22 16 0.59
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (21 bp):
TTACTTTCATTTATTATCTCA
Found at i:438324 original size:23 final size:23
Alignment explanation
Indices: 438294--438339 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
438284 GTGTTGCTCA
*
438294 TTATCATTATATATCTTAAATTC
1 TTATCATTATATATATTAAATTC
438317 TTATCATTATATATATTAAATTC
1 TTATCATTATATATATTAAATTC
438340 ACATATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATCATTATATATATTAAATTC
Found at i:439053 original size:5 final size:5
Alignment explanation
Indices: 439039--439084 Score: 85
Period size: 5 Copynumber: 9.4 Consensus size: 5
439029 CCGCCACCGC
439039 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
439085 GGTCGGGGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.10
5 37 0.90
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:439095 original size:6 final size:6
Alignment explanation
Indices: 439085--439147 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
439075 TCTCGTCTCG
* * *
439085 GGTCGG GGTCGG GGTCAT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
439133 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
439148 AATACGTGTC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.02, C:0.16, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:439307 original size:20 final size:20
Alignment explanation
Indices: 439282--439435 Score: 173
Period size: 20 Copynumber: 7.6 Consensus size: 20
439272 ACTGTAGACT
*
439282 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
439302 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
** ** *
439322 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAACTGGAA-A
439343 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
** ** *
439363 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAACTGGAA-A
*
439384 ATCGCAACGTGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
439404 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
439424 ATCGCAACGCGA
1 ATCGCAACGCGA
439436 TTTTCAATTA
Statistics
Matches: 108, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
20 79 0.73
21 29 0.27
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAACTGGAAA
Found at i:439345 original size:61 final size:62
Alignment explanation
Indices: 439279--439464 Score: 196
Period size: 61 Copynumber: 3.0 Consensus size: 62
439269 ACAACTGTAG
* ** *
439279 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAACTGGAA-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAACTGCAACAATCGCAACGCGAACTGCA
* ** * * * *
439340 ACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAACTATCGCAACGTGAACTGGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAACTGCAACAATCGCAACGCGAACTGCA
* ** * ** *
439402 A-AATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAATTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAACTGCAACAATCGCAACGCGAACTGCA
439463 AC
1 AC
439465 GCGAATTTGC
Statistics
Matches: 106, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
61 92 0.87
62 14 0.13
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAACTGCAACAATCGCAACGCGAACTGCA
Found at i:439354 original size:41 final size:41
Alignment explanation
Indices: 439302--439415 Score: 219
Period size: 41 Copynumber: 2.8 Consensus size: 41
439292 GAAATGGAAA
439302 ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAACT
439343 ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAACT
*
439384 ATCGCAACGTGAACTGGAAAATCGCAACGCGA
1 ATCGCAACGCGAACTGGAAAATCGCAACGCGA
439416 AATGGAAAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (41 bp):
ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAACT
Found at i:439634 original size:27 final size:28
Alignment explanation
Indices: 439603--439672 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
439593 TATTTTCTCT
439603 TAAAAATATATATTT-TGTTTC-TTAACA
1 TAAAAATATAT-TTTCTGTTTCTTTAACA
* *
439630 TAAAAATATATTTTCTTTTTCTTTTAACT
1 TAAAAATATATTTTCTGTTTC-TTTAACA
439659 TAAAAATATATTTT
1 TAAAAATATATTTT
439673 AATTTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 3 0.08
27 16 0.42
29 19 0.50
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (28 bp):
TAAAAATATATTTTCTGTTTCTTTAACA
Found at i:439657 original size:29 final size:26
Alignment explanation
Indices: 439603--439698 Score: 88
Period size: 29 Copynumber: 3.5 Consensus size: 26
439593 TATTTTCTCT
*
439603 TAAAAATATATATTTTGTTTC-TTAAC
1 TAAAAATATAT-TTTTTTTTCTTTAAC
439629 ATAAAAATATATTTTCTTTTTCTTTTAAC
1 -TAAAAATATATTTT-TTTTTC-TTTAAC
439658 TTAAAAATATATTTTAATTTTT-TATTAAC
1 -TAAAAATATATTTT--TTTTTCT-TTAAC
*
439687 TTAAAATATATT
1 TAAAAATATATT
439699 ATTTATTATT
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
26 3 0.05
27 16 0.27
28 12 0.20
29 24 0.40
30 5 0.08
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (26 bp):
TAAAAATATATTTTTTTTTCTTTAAC
Found at i:439702 original size:25 final size:27
Alignment explanation
Indices: 439653--439715 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 27
439643 TCTTTTTCTT
*
439653 TTAACTTAAAAATATATTTTAATTTTTTA
1 TTAACTT-AAAATATA-TTTAATTTATTA
439682 TTAACTTAAAATATA-TT-ATTTATTA
1 TTAACTTAAAATATATTTAATTTATTA
*
439707 TTACCTTAA
1 TTAACTTAA
439716 TTTAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 15 0.47
26 2 0.06
28 8 0.25
29 7 0.22
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAACTTAAAATATATTTAATTTATTA
Found at i:439799 original size:27 final size:27
Alignment explanation
Indices: 439777--439849 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 27
439767 AAAATATACC
439777 TTTAAAATAAAATTAAAATAATAAAAA
1 TTTAAAATAAAATTAAAATAATAAAAA
* * * **
439804 TTTTAAATTAAATTAAAAT-ATACATT
1 TTTAAAATAAAATTAAAATAATAAAAA
*
439830 TTTAAATTAAAA-TAAAATAA
1 TTTAAAATAAAATTAAAATAA
439850 AATAACATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
25 6 0.16
26 14 0.38
27 17 0.46
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (27 bp):
TTTAAAATAAAATTAAAATAATAAAAA
Found at i:439815 original size:33 final size:31
Alignment explanation
Indices: 439778--439931 Score: 117
Period size: 32 Copynumber: 4.9 Consensus size: 31
439768 AAATATACCT
*
439778 TTAAAATAAAATTAAAATAATAAAAATTTTAAA
1 TTAAAATAAAA-TAAAATAAT-AAATTTTTAAA
*
439811 TT-AAAT----TAAAAT-ATACATTTTTAAA
1 TTAAAATAAAATAAAATAATAAATTTTTAAA
439836 TTAAAATAAAATAAAATAACATATACATTTTTAAA
1 TTAAAATAAAATAAAAT-A-ATA-A-ATTTTTAAA
*
439871 TTAAATTTAAAAAATAAAAT-ATAAATTTTTAAA
1 TTAAA---ATAAAATAAAATAATAAATTTTTAAA
*
439904 TTAAAAATAAGAATAAAAT-ATCAATTTT
1 TT-AAAATAA-AATAAAATAATAAATTTT
439932 ATGTTAAAAT
Statistics
Matches: 100, Mismatches: 6, Indels: 31
0.73 0.04 0.23
Matches are distributed among these distances:
25 11 0.11
26 6 0.06
27 6 0.06
30 6 0.06
31 3 0.03
32 20 0.20
33 16 0.16
34 4 0.04
35 17 0.17
38 11 0.11
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.37
Consensus pattern (31 bp):
TTAAAATAAAATAAAATAATAAATTTTTAAA
Found at i:439836 original size:20 final size:20
Alignment explanation
Indices: 439811--439875 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
439801 AAATTTTAAA
439811 TTAAATTAAAATATACATTT
1 TTAAATTAAAATATACATTT
439831 TTAAATTAAAATA-A-A---
1 TTAAATTAAAATATACATTT
* * *
439846 ATAAAATAACATATACATTT
1 TTAAATTAAAATATACATTT
439866 TTAAATTAAA
1 TTAAATTAAA
439876 TTTAAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
15 10 0.29
16 1 0.03
17 1 0.03
18 1 0.03
19 1 0.03
20 20 0.59
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAATTAAAATATACATTT
Found at i:439838 original size:25 final size:25
Alignment explanation
Indices: 439766--439848 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
439756 AAGATAAAAA
* * *
439766 TAAAATATAC-CTTTAAAATAAAAT
1 TAAAATATACAATTTTAAATTAAAT
*
439790 TAAAATAATAAAAATTTTAAATTAAAT
1 TAAAAT-AT-ACAATTTTAAATTAAAT
* *
439817 TAAAATATACATTTTTAAATTAAAA
1 TAAAATATACAATTTTAAATTAAAT
439842 TAAAATA
1 TAAAATA
439849 AAATAACATA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
24 6 0.12
25 23 0.47
26 3 0.06
27 17 0.35
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (25 bp):
TAAAATATACAATTTTAAATTAAAT
Found at i:439861 original size:35 final size:35
Alignment explanation
Indices: 439807--439923 Score: 148
Period size: 35 Copynumber: 3.3 Consensus size: 35
439797 ATAAAAATTT
* *
439807 TAAATTAAATTAAAATATACATTTTTAAATTAAAA
1 TAAAATAAAATAAAATATACATTTTTAAATTAAAA
*
439842 TAAAATAAAATAACATATACATTTTTAAATT-AAA
1 TAAAATAAAATAAAATATACATTTTTAAATTAAAA
** *
439876 TTTAA-AAAATAAAATATAAATTTTTAAATTAAAAA
1 TAAAATAAAATAAAATATACATTTTTAAATT-AAAA
439911 TAAGAATAAAATA
1 TAA-AATAAAATA
439924 TCAATTTTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
33 23 0.33
34 6 0.09
35 32 0.46
36 2 0.03
37 6 0.09
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.36
Consensus pattern (35 bp):
TAAAATAAAATAAAATATACATTTTTAAATTAAAA
Found at i:439918 original size:27 final size:27
Alignment explanation
Indices: 439871--439922 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 27
439861 CATTTTTAAA
439871 TTAAATTTAAAAAATAAAATATAAATTT
1 TTAAATTTAAAAAATAAAATA-AAATTT
439899 TTAAA-TT-AAAAATAAGAATAAAAT
1 TTAAATTTAAAAAATAA-AATAAAAT
439923 ATCAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 12 0.52
27 6 0.26
28 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
TTAAATTTAAAAAATAAAATAAAATTT
Found at i:440070 original size:29 final size:29
Alignment explanation
Indices: 439842--440182 Score: 224
Period size: 29 Copynumber: 11.4 Consensus size: 29
439832 TAAATTAAAA
* *
439842 TAAAAT-AAAATAACATATACATTTTTAAAT
1 TAAAATAAAAATAA-A-ATATATTTTTAAGT
* *
439872 TAAATTTAAAAAATAAAATATAAATTTTTAAAT
1 TAAA-AT-AAAAATAAAATAT--ATTTTTAAGT
* * *
439905 TAAAAATAAGAATAAAATATCAATTTTATGT
1 T-AAAATAAAAATAAAATAT-ATTTTTAAGT
*** * * *
439936 TAAAATATGGATAAATTATATTTAATAATT
1 TAAAATAAAAATAAAATATATTT-TTAAGT
** * * * **
439966 TAAGTTAAGAATATAATATGTGTAATAAGT
1 TAAAATAAAAATAAAATATAT-TTTTAAGT
* *
439996 TAAAATAAAAATAAGATATATTTTTAGAAGC
1 TAAAATAAAAATAAAATATATTTTT--AAGT
*
440027 TAAGATAAAAATAAAATATATTTTTAAGT
1 TAAAATAAAAATAAAATATATTTTTAAGT
* *
440056 TAAAATAAGATTAAAATATATTTTTAAGT
1 TAAAATAAAAATAAAATATATTTTTAAGT
* * *
440085 TAAAATAAAAATAAAATATAATTTTAGGC
1 TAAAATAAAAATAAAATATATTTTTAAGT
* * *
440114 TAAAATAAAAATAAAATAAATTTAATAATT
1 TAAAATAAAAATAAAATATATTT-TTAAGT
* *
440144 TAAAAT-AAAAT--AATGTGA-CTTTAAGT
1 TAAAATAAAAATAAAATAT-ATTTTTAAGT
440170 TAAAATAAAAATA
1 TAAAATAAAAATA
440183 GATATGTGAA
Statistics
Matches: 242, Mismatches: 55, Indels: 30
0.74 0.17 0.09
Matches are distributed among these distances:
26 10 0.04
27 9 0.04
28 1 0.00
29 84 0.35
30 64 0.26
31 39 0.16
32 13 0.05
33 19 0.08
34 3 0.01
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (29 bp):
TAAAATAAAAATAAAATATATTTTTAAGT
Found at i:440118 original size:58 final size:58
Alignment explanation
Indices: 439880--440182 Score: 200
Period size: 60 Copynumber: 5.1 Consensus size: 58
439870 ATTAAATTTA
* * * *
439880 AAAAATAAAATATAAATTTTTAAATTAAAAATAAGAATAAAATATCAATTTTATGTTAAAAT
1 AAAAATAAAATAT--ATTTTTAAGTT-AAAATAAAAATAAAATAT-AATTTTAAGCTAAAAT
*** * * * ** * * * * *
439942 ATGGATAAATTATATTTAATAATTTAAGTTAAGAATATAATAT-GTGTAATAAGTTAAAAT
1 AAAAATAAAATATATTT-TTAAGTTAAAATAAAAATAAAATATAAT-T-TTAAGCTAAAAT
* * * * *
440002 AAAAATAAGATATATTTTTAGAAGCTAAGATAAAAATAAAATATATTTTTAAGTTAAAAT
1 AAAAATAAAATATATTTTT--AAGTTAAAATAAAAATAAAATATAATTTTAAGCTAAAAT
* * *
440062 AAGATTAAAATATATTTTTAAGTTAAAATAAAAATAAAATATAATTTTAGGCTAAAAT
1 AAAAATAAAATATATTTTTAAGTTAAAATAAAAATAAAATATAATTTTAAGCTAAAAT
* * * * * * *
440120 AAAAATAAAATAAATTTAATAATTTAAAAT-AAAAT--AATGTGACTTTAAGTTAAAAT
1 AAAAATAAAATATATTT-TTAAGTTAAAATAAAAATAAAATATAATTTTAAGCTAAAAT
440176 AAAAATA
1 AAAAATA
440183 GATATGTGAA
Statistics
Matches: 191, Mismatches: 43, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
56 23 0.12
58 54 0.28
59 12 0.06
60 68 0.36
61 24 0.13
62 10 0.05
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (58 bp):
AAAAATAAAATATATTTTTAAGTTAAAATAAAAATAAAATATAATTTTAAGCTAAAAT
Found at i:446373 original size:23 final size:23
Alignment explanation
Indices: 446332--446375 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
446322 TAACATTGTT
* **
446332 ATCATCAACATTATTAATATTAA
1 ATCACCAACATTAACAATATTAA
446355 ATCACCAACATTAACAATATT
1 ATCACCAACATTAACAATATT
446376 TTCATTTTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (23 bp):
ATCACCAACATTAACAATATTAA
Found at i:451359 original size:18 final size:18
Alignment explanation
Indices: 451333--451368 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
451323 TCGAAATGAC
*
451333 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
451351 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
451369 CGGATGACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:452514 original size:24 final size:23
Alignment explanation
Indices: 452487--452590 Score: 73
Period size: 24 Copynumber: 4.3 Consensus size: 23
452477 AATTATTTTA
*
452487 TCTGATTTTCGACTTGAATTCTGT
1 TCTGATTTT-GACCTGAATTCTGT
**
452511 TCTGATACATGACCTGAATTCTGT
1 TCTGAT-TTTGACCTGAATTCTGT
** *
452535 TCTGATTTCTGATATGGATTCTGT
1 TCTGATTT-TGACCTGAATTCTGT
* * **
452559 TCTAATATCTGTTCTGAATTCTGT
1 TCTGAT-TTTGACCTGAATTCTGT
*
452583 TTTGATTT
1 TCTGATTT
452591 CTGATATCTC
Statistics
Matches: 61, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
23 1 0.02
24 58 0.95
25 2 0.03
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.49
Consensus pattern (23 bp):
TCTGATTTTGACCTGAATTCTGT
Found at i:452539 original size:12 final size:12
Alignment explanation
Indices: 452501--452593 Score: 73
Period size: 12 Copynumber: 7.8 Consensus size: 12
452491 ATTTTCGACT
452501 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
452513 TG-ATACATGACC
1 TGAATTC-TGTTC
452525 TGAATTCTGTTC
1 TGAATTCTGTTC
* * *
452537 TGATTTCTGATA
1 TGAATTCTGTTC
*
452549 TGGATTCTGTTC
1 TGAATTCTGTTC
452561 T-AATATCTGTTC
1 TGAAT-TCTGTTC
*
452573 TGAATTCTGTTT
1 TGAATTCTGTTC
*
452585 TGATTTCTG
1 TGAATTCTG
452594 ATATCTCCGT
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
11 5 0.08
12 50 0.82
13 6 0.10
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.48
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:452556 original size:48 final size:48
Alignment explanation
Indices: 452504--452597 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
452494 TTCGACTTGA
*
452504 ATTCTGTTCTGATA-CATGACCTGAATTCTGTTCTGATTTCTGATATGG
1 ATTCTGTTCTAATATC-TGACCTGAATTCTGTTCTGATTTCTGATATGG
** *
452552 ATTCTGTTCTAATATCTGTTCTGAATTCTGTTTTGATTTCTGATAT
1 ATTCTGTTCTAATATCTGACCTGAATTCTGTTCTGATTTCTGATAT
452598 CTCCGTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 40 0.98
49 1 0.02
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (48 bp):
ATTCTGTTCTAATATCTGACCTGAATTCTGTTCTGATTTCTGATATGG
Found at i:452593 original size:24 final size:24
Alignment explanation
Indices: 452501--452595 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
452491 ATTTTCGACT
* *
452501 TGAATTCTGTTCTGA-TACATGACC
1 TGAATTCTGTTCTGATTTC-TGATC
*
452525 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATC
* * * *
452549 TGGATTCTGTTCTAATATCTGTTC
1 TGAATTCTGTTCTGATTTCTGATC
*
452573 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATTTCTGAT
452596 ATCTCCGTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
24 55 0.96
25 2 0.04
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATC
Found at i:452768 original size:2 final size:2
Alignment explanation
Indices: 452761--452785 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
452751 GGGATGGGGG
452761 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 T
452786 GTTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:456122 original size:20 final size:20
Alignment explanation
Indices: 456097--456137 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
456087 TTATATCACA
456097 ATTCATATTCAAAACAAGTC
1 ATTCATATTCAAAACAAGTC
*
456117 ATTCATATTCAAAGCAAGTC
1 ATTCATATTCAAAACAAGTC
456137 A
1 A
456138 AACATATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (20 bp):
ATTCATATTCAAAACAAGTC
Found at i:456143 original size:20 final size:20
Alignment explanation
Indices: 456100--456144 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
456090 TATCACAATT
**
456100 CATATTCAAAACAAGTCATT
1 CATATTCAAAACAAGTCAAA
*
456120 CATATTCAAAGCAAGTCAAA
1 CATATTCAAAACAAGTCAAA
456140 CATAT
1 CATAT
456145 AAGTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (20 bp):
CATATTCAAAACAAGTCAAA
Found at i:460761 original size:51 final size:51
Alignment explanation
Indices: 460685--460786 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
460675 TAAATCTCGC
460685 AACCAAGTTCATTGTATGTGGTGCCAGCTCATTTAGTTGGGGCTCCGCGGT
1 AACCAAGTTCATTGTATGTGGTGCCAGCTCATTTAGTTGGGGCTCCGCGGT
460736 AACCAAGTTCATTGTATGTGGTGCCAGCTCATTTAGTTGGGGCTCCGCGGT
1 AACCAAGTTCATTGTATGTGGTGCCAGCTCATTTAGTTGGGGCTCCGCGGT
460787 TTTGGCATCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (51 bp):
AACCAAGTTCATTGTATGTGGTGCCAGCTCATTTAGTTGGGGCTCCGCGGT
Found at i:461161 original size:2 final size:2
Alignment explanation
Indices: 461154--461208 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
461144 TTATAAGAAT
461154 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
461196 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
461209 TAGTTTCAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:461816 original size:21 final size:21
Alignment explanation
Indices: 461744--461828 Score: 100
Period size: 21 Copynumber: 4.0 Consensus size: 21
461734 TTATATTCCG
*
461744 CAACCATTTTAGA-GGCCACCA
1 CAACCATTTCAGATGG-CACCA
461765 CAACCATTTCAGATGGCACCA
1 CAACCATTTCAGATGGCACCA
* * *
461786 CAACCGTTTCTGATGTCACCA
1 CAACCATTTCAGATGGCACCA
* *
461807 CAACCATTTCATATGCCACCA
1 CAACCATTTCAGATGGCACCA
461828 C
1 C
461829 CGCTGGGTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
21 53 0.96
22 2 0.04
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.22
Consensus pattern (21 bp):
CAACCATTTCAGATGGCACCA
Found at i:462251 original size:25 final size:25
Alignment explanation
Indices: 462223--462301 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
462213 GATAGACTTA
462223 TTTTTATTTATTTTGTTTCTTAATG
1 TTTTTATTTATTTTGTTTCTTAATG
* * *
462248 TTTTTATTTA----ATTAC--AGA-C
1 TTTTTATTTATTTTGTTTCTTA-ATG
462267 TTTTTATTTATTTTGTTTCTTAATG
1 TTTTTATTTATTTTGTTTCTTAATG
462292 TTTTTATTTA
1 TTTTTATTTA
462302 ATTATGAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 16
0.65 0.10 0.26
Matches are distributed among these distances:
19 11 0.28
20 1 0.03
21 3 0.08
23 3 0.08
24 1 0.03
25 21 0.52
ACGTcount: A:0.20, C:0.05, G:0.06, T:0.68
Consensus pattern (25 bp):
TTTTTATTTATTTTGTTTCTTAATG
Found at i:462378 original size:91 final size:88
Alignment explanation
Indices: 462223--462390 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 88
462213 GATAGACTTA
*
462223 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTACAGACTTTTTATTTATTTTGTTTCTT
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTACAGACTTTTTATTGATTTTGTTTCTT
462288 AATGTTTTTATTTAATTATGAAG
66 AATGTTTTTATTTAATTATGAAG
** *
462311 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATGGACTTTTTATTGATTTTTTTT
1 TTTTTATTTATTTTGTTTCTTAATG--TTT-TTATTTAATTACAGACTTTTTATTGATTTTGTTT
462376 CTTAATGTTTTTATT
63 CTTAATGTTTTTATT
462391 ATTTAATTGT
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
88 25 0.34
90 3 0.04
91 45 0.62
ACGTcount: A:0.21, C:0.04, G:0.08, T:0.67
Consensus pattern (88 bp):
TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTACAGACTTTTTATTGATTTTGTTTCTT
AATGTTTTTATTTAATTATGAAG
Found at i:462387 original size:25 final size:24
Alignment explanation
Indices: 462267--462394 Score: 81
Period size: 24 Copynumber: 5.5 Consensus size: 24
462257 AATTACAGAC
*
462267 TTTTTATTTATTTTGTTTCTTAATG
1 TTTTTA-TTATTTTATTTCTTAATG
* * *
462292 --TTT-TTA-TTTAATTATGAA-G
1 TTTTTATTATTTTATTTCTTAATG
*
462311 TTTTTATTTATTTTGTTTCTTAATG
1 TTTTTA-TTATTTTATTTCTTAATG
* * ** *
462336 TTTTTATTA-TTTAATTATGGA-C
1 TTTTTATTATTTTATTTCTTAATG
*
462358 TTTTTATTGATTTTTTTTCTTAATG
1 TTTTTATT-ATTTTATTTCTTAATG
462383 TTTTTATTATTT
1 TTTTTATTATTT
462395 AATTGTTTGA
Statistics
Matches: 74, Mismatches: 20, Indels: 19
0.65 0.18 0.17
Matches are distributed among these distances:
19 1 0.01
20 8 0.11
21 6 0.08
22 8 0.11
23 14 0.19
24 22 0.30
25 15 0.20
ACGTcount: A:0.20, C:0.03, G:0.08, T:0.69
Consensus pattern (24 bp):
TTTTTATTATTTTATTTCTTAATG
Found at i:462398 original size:47 final size:44
Alignment explanation
Indices: 462223--462390 Score: 255
Period size: 44 Copynumber: 3.8 Consensus size: 44
462213 GATAGACTTA
**
462223 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTACAGAC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGAC
* *
462267 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAAG
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGAC
462311 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATGGAC
1 TTTTTATTTATTTTGTTTCTTAATG--TTT-TTATTTAATTATGGAC
* *
462358 TTTTTATTGATTTTTTTTCTTAATGTTTTTATT
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATT
462391 ATTTAATTGT
Statistics
Matches: 113, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
44 70 0.62
45 3 0.03
46 3 0.03
47 37 0.33
ACGTcount: A:0.21, C:0.04, G:0.08, T:0.67
Consensus pattern (44 bp):
TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGAC
Found at i:462488 original size:16 final size:16
Alignment explanation
Indices: 462467--462498 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
462457 ATTTAATTTG
462467 CACTTGAGTAGCACAT
1 CACTTGAGTAGCACAT
462483 CACTTGAGTAGCACAT
1 CACTTGAGTAGCACAT
462499 TAACTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (16 bp):
CACTTGAGTAGCACAT
Done.