Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008521.1 Hibiscus syriacus cultivar Beakdansim tig00111388_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: 1601068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:994928 original size:15 final size:15
Alignment explanation
Indices: 994908--994942 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
994898 CGTAGGGACC
994908 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
994923 ACTACGTTCCGAAGG
1 ACTACGTCCCGAAGG
994938 ACTAC
1 ACTAC
994943 AATACCCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:996488 original size:25 final size:24
Alignment explanation
Indices: 996460--996618 Score: 124
Period size: 25 Copynumber: 6.5 Consensus size: 24
996450 ATGGTCAATA
*
996460 GTTATTAATTGTAAATATTAATTAC
1 GTTATTAATTGT-AATATTAATTAT
* ** *
996485 GTTATTAATTATGTTGATTAATTTT
1 GTTATTAATTGTAAT-ATTAATTAT
* * *
996510 GTTATTAATTATATTATTAATGAT
1 GTTATTAATTGTAATATTAATTAT
*
996534 GTTGTTAATTGTGAATATTAATTAT
1 GTTATTAATTGT-AATATTAATTAT
* *
996559 GTTATTAATGGTAAATATTAA--GT
1 GTTATTAATTGT-AATATTAATTAT
* *
996582 GAATATTAATTGGTAATATTAATTAA
1 G-TTATTAATT-GTAATATTAATTAT
*
996608 GTTAGTAATTG
1 GTTATTAATTG
996619 ATATTTGTAA
Statistics
Matches: 106, Mismatches: 22, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
23 2 0.02
24 34 0.32
25 69 0.65
26 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.50
Consensus pattern (24 bp):
GTTATTAATTGTAATATTAATTAT
Found at i:996492 original size:12 final size:12
Alignment explanation
Indices: 996475--996567 Score: 105
Period size: 12 Copynumber: 7.6 Consensus size: 12
996465 TAATTGTAAA
*
996475 TATTAATTACGT
1 TATTAATTATGT
996487 TATTAATTATGT
1 TATTAATTATGT
*
996499 TGATTAATTTTGT
1 T-ATTAATTATGT
*
996512 TATTAATTATAT
1 TATTAATTATGT
*
996524 TATTAATGATGT
1 TATTAATTATGT
* * *
996536 TGTTAATTGTGAA
1 TATTAATTATG-T
996549 TATTAATTATGT
1 TATTAATTATGT
996561 TATTAAT
1 TATTAAT
996568 GGTAAATATT
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
12 46 0.70
13 20 0.30
ACGTcount: A:0.33, C:0.01, G:0.11, T:0.55
Consensus pattern (12 bp):
TATTAATTATGT
Found at i:996518 original size:37 final size:37
Alignment explanation
Indices: 996464--996568 Score: 140
Period size: 37 Copynumber: 2.8 Consensus size: 37
996454 TCAATAGTTA
* * *
996464 TTAATTGTAAATATTAATTACGTTATTAATTATGTTG
1 TTAATTGTGAATATTAATTATGTTATTAATGATGTTG
* * *
996501 ATTAATTTTG-TTATTAATTATATTATTAATGATGTTG
1 -TTAATTGTGAATATTAATTATGTTATTAATGATGTTG
996538 TTAATTGTGAATATTAATTATGTTATTAATG
1 TTAATTGTGAATATTAATTATGTTATTAATG
996569 GTAAATATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
36 8 0.14
37 42 0.74
38 7 0.12
ACGTcount: A:0.34, C:0.01, G:0.11, T:0.53
Consensus pattern (37 bp):
TTAATTGTGAATATTAATTATGTTATTAATGATGTTG
Found at i:996605 original size:13 final size:13
Alignment explanation
Indices: 996561--996605 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
996551 TTAATTATGT
996561 TATTAA-TGGTAAA
1 TATTAATTGGT-AA
*
996574 TATTAAGT-G-AA
1 TATTAATTGGTAA
996585 TATTAATTGGTAA
1 TATTAATTGGTAA
996598 TATTAATT
1 TATTAATT
996606 AAGTTAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 9 0.32
12 1 0.04
13 17 0.61
14 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (13 bp):
TATTAATTGGTAA
Found at i:996699 original size:2 final size:2
Alignment explanation
Indices: 996692--996717 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
996682 ATCAGTATCA
996692 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
996718 TATTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1001008 original size:20 final size:21
Alignment explanation
Indices: 1000958--1001023 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 21
1000948 AAATGACCAA
*
1000958 CAAA-TTCGCAACGCGAACTT-
1 CAAATTTCGCAACGCG-ATTTC
*
1000978 C-AATTTCGCAACTC-AGTTTC
1 CAAATTTCGCAACGCGA-TTTC
1000998 CAAATTT-GCAACGCGATTTC
1 CAAATTTCGCAACGCGATTTC
1001018 CAAATT
1 CAAATT
1001024 CGTAACACTG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
18 1 0.03
19 4 0.11
20 27 0.71
21 6 0.16
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (21 bp):
CAAATTTCGCAACGCGATTTC
Found at i:1001910 original size:12 final size:12
Alignment explanation
Indices: 1001893--1001921 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1001883 CACCACATTT
1001893 ACAATATCAAAC
1 ACAATATCAAAC
1001905 ACAATATCAAAC
1 ACAATATCAAAC
1001917 ACAAT
1 ACAAT
1001922 CTTAAAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.17
Consensus pattern (12 bp):
ACAATATCAAAC
Found at i:1002104 original size:24 final size:24
Alignment explanation
Indices: 1002051--1002106 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1002041 CAGTATTCGA
* *
1002051 AATTTGATCTTGGTCAATACCCGG
1 AATTTGATCTTAGTCAATACCCAG
*
1002075 AATTTGATCTTAGTCAATACTCAG
1 AATTTGATCTTAGTCAATACCCAG
*
1002099 ATTTTGAT
1 AATTTGAT
1002107 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (24 bp):
AATTTGATCTTAGTCAATACCCAG
Found at i:1004398 original size:18 final size:18
Alignment explanation
Indices: 1004364--1004399 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1004354 AAGCAAAAGG
**
1004364 AAATCAAAATCGTAATCA
1 AAATCAAAATCCCAATCA
1004382 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1004400 TAACCGGCTT
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:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1004605 original size:20 final size:20
Alignment explanation
Indices: 1004580--1004627 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1004570 GTTGCGATTG
*
1004580 TTGCGAAAGTCAAATTCGCA
1 TTGCGAAAGTCAAATTCGAA
1004600 TTGCGAAAGTCAAATTCGAA
1 TTGCGAAAGTCAAATTCGAA
*
1004620 ATGCGAAA
1 TTGCGAAA
1004628 TCACAACGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
TTGCGAAAGTCAAATTCGAA
Found at i:1004658 original size:20 final size:20
Alignment explanation
Indices: 1004635--1004672 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1004625 AAATCACAAC
1004635 GCGAATTTGACTTTCGCATT
1 GCGAATTTGACTTTCGCATT
1004655 GCGAATTTGACTTTCGCA
1 GCGAATTTGACTTTCGCA
1004673 ACCATCGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCATT
Found at i:1004728 original size:20 final size:20
Alignment explanation
Indices: 1004685--1004728 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1004675 CATCGCAACG
* *
1004685 CGAATTTGACTTTCGAGTTG
1 CGAATTTAACTTTCGAGTTA
* *
1004705 CGAATTTAATTTTCGCGTTA
1 CGAATTTAACTTTCGAGTTA
1004725 CGAA
1 CGAA
1004729 AGTGTACCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (20 bp):
CGAATTTAACTTTCGAGTTA
Found at i:1004886 original size:64 final size:64
Alignment explanation
Indices: 1004787--1004935 Score: 235
Period size: 64 Copynumber: 2.3 Consensus size: 64
1004777 AATTTAAAAC
1004787 AATAAATCAACTTTTACAAATCAATCAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AATAAATCAACTTTTACAAATCAATCAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
* *** * *
1004851 AATAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AATAAATCAACTTTTACAAATCAATCAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*
1004915 AACAAATCAACTTTTACAAAT
1 AATAAATCAACTTTTACAAAT
1004936 ACATTAATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 78 1.00
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.30
Consensus pattern (64 bp):
AATAAATCAACTTTTACAAATCAATCAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:1006188 original size:21 final size:20
Alignment explanation
Indices: 1006159--1006234 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
1006149 GTGAATCGGG
* *
1006159 CTCTCGAACGGTGGGAAGGAC
1 CTCTTGAACGATGGGAAGG-C
** *
1006180 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGGGA-AGGC
*
1006201 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATGGGA-AGGC
*
1006222 CTCTTGAATGATG
1 CTCTTGAACGATG
1006235 ACAGGTGAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
21 41 0.95
22 2 0.05
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.21
Consensus pattern (20 bp):
CTCTTGAACGATGGGAAGGC
Found at i:1006647 original size:21 final size:21
Alignment explanation
Indices: 1006623--1006672 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1006613 ACCATTGTCT
* *
1006623 TCACGTAAAGTACCGACCTCC
1 TCACGTAAAGCACCGACCTCA
* **
1006644 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCACCGACCTCA
1006665 TCACGTAA
1 TCACGTAA
1006673 CTCCCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:1007888 original size:19 final size:20
Alignment explanation
Indices: 1007840--1007892 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
1007830 ATAGTTTCTG
*
1007840 AAACTTAAAATCGTAACGCGA
1 AAAC-TAAAATCGCAACGCGA
1007861 AAA-TGAAAATCGCAACGC-A
1 AAACT-AAAATCGCAACGCGA
1007880 AAACTAAAATCGC
1 AAACTAAAATCGC
1007893 GTTGTGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 13 0.45
20 13 0.45
21 3 0.10
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (20 bp):
AAACTAAAATCGCAACGCGA
Found at i:1008285 original size:22 final size:22
Alignment explanation
Indices: 1008258--1008315 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
1008248 GATGGAGATA
1008258 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
1008280 GACGGATTTTGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
1008302 GACGGATGTCGTCG
1 GACGGATTTCGTCG
1008316 TAGAGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.14, G:0.45, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:1008475 original size:20 final size:20
Alignment explanation
Indices: 1008450--1008500 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1008440 CGCGCGCGCT
1008450 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
*
1008470 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTATGTG
*
1008490 TTGTGAATTTG
1 TTGCGAATTTG
1008501 GAATCTGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.18, C:0.10, G:0.25, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:1008507 original size:20 final size:21
Alignment explanation
Indices: 1008450--1008540 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 21
1008440 CGCGCGCGCT
* *
1008450 TTGCGAATTT-GACTTATGTG
1 TTGCGAATTTGGACATCTGTG
*
1008470 TTGCGAATTT-GACTTCTGTG
1 TTGCGAATTTGGACATCTGTG
* *
1008490 TTGTGAATTTGGA-ATCTGAG
1 TTGCGAATTTGGACATCTGTG
* ** *
1008510 TTGCGAAATTGGAGTTC-GCG
1 TTGCGAATTTGGACATCTGTG
1008530 TTGCGAATTTG
1 TTGCGAATTTG
1008541 TTGGTCATTT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
20 56 0.93
21 4 0.07
ACGTcount: A:0.20, C:0.11, G:0.29, T:0.41
Consensus pattern (21 bp):
TTGCGAATTTGGACATCTGTG
Found at i:1011550 original size:23 final size:23
Alignment explanation
Indices: 1011522--1011570 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
1011512 TTATAAAATA
1011522 TTTTGTACTT-TAACTATGTATTT
1 TTTTGTA-TTGTAACTATGTATTT
*
1011545 TTTTGTATTGTAACTATGTCTTT
1 TTTTGTATTGTAACTATGTATTT
1011568 TTT
1 TTT
1011571 AACTATGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.18, C:0.08, G:0.10, T:0.63
Consensus pattern (23 bp):
TTTTGTATTGTAACTATGTATTT
Found at i:1011583 original size:13 final size:14
Alignment explanation
Indices: 1011555--1011587 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1011545 TTTTGTATTG
1011555 TAACTATGTCTTTTT
1 TAACTATG-CTTTTT
1011570 TAACTATG-TTTTT
1 TAACTATGCTTTTT
1011583 TAACT
1 TAACT
1011588 TGTATTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
15 8 0.44
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (14 bp):
TAACTATGCTTTTT
Found at i:1017424 original size:24 final size:23
Alignment explanation
Indices: 1017406--1017467 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
1017396 TAAATTATAT
1017406 AAATATCATTTTCTAAAATTTAAA
1 AAAT-TCATTTTCTAAAATTTAAA
1017430 AAATTCATTTTCTAAAATTTAAA
1 AAATTCATTTTCTAAAATTTAAA
1017453 AAATTCATTTTCTAA
1 AAATTCATTTTCTAA
1017468 TAGGTGGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 34 0.89
24 4 0.11
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTCATTTTCTAAAATTTAAA
Found at i:1019118 original size:27 final size:27
Alignment explanation
Indices: 1019075--1019126 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
1019065 AGCTGTATCT
1019075 AAGACATTTCCAAGTCACGATTGATCC
1 AAGACATTTCCAAGTCACGATTGATCC
1019102 AAGACATTT-CAAGGTCACGATTGAT
1 AAGACATTTCCAA-GTCACGATTGAT
1019127 TGAATGCGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 3 0.12
27 21 0.88
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (27 bp):
AAGACATTTCCAAGTCACGATTGATCC
Found at i:1023484 original size:29 final size:30
Alignment explanation
Indices: 1023405--1023490 Score: 81
Period size: 29 Copynumber: 2.9 Consensus size: 30
1023395 CTAATTAAAT
*
1023405 ATTTTAATTTCATCCCTAAAC-TATGACTCTC
1 ATTTTAATTTCATCCCTAAACTTATGA--CAC
* * *
1023436 ATTTTAAATT-AGTCCTTAAACTTTTGA-AC
1 ATTTTAATTTCA-TCCCTAAACTTATGACAC
1023465 ATTTTAATTTCATCCCTAAAC-TATGA
1 ATTTTAATTTCATCCCTAAACTTATGA
1023491 TCCTCATTCT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.09
29 18 0.40
30 2 0.04
31 17 0.38
32 4 0.09
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.43
Consensus pattern (30 bp):
ATTTTAATTTCATCCCTAAACTTATGACAC
Found at i:1023521 original size:60 final size:60
Alignment explanation
Indices: 1023405--1023519 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 60
1023395 CTAATTAAAT
* *
1023405 ATTTTAATTTCATCCCTAAACTATGACTCTCATTTTAAATTAGTCCTTAAACTTTTGAAC
1 ATTTTAATTTCATCCCTAAACTATGACTCTCATTCTAAATTAGTCCTCAAACTTTTGAAC
*
1023465 ATTTTAATTTCATCCCTAAACTATGA-TCCTCATTCTAAATTGGT-CTCAAACTTTT
1 ATTTTAATTTCATCCCTAAACTATGACT-CTCATTCTAAATTAGTCCTCAAACTTTT
1023520 TGCAGATTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
59 11 0.22
60 40 0.78
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.43
Consensus pattern (60 bp):
ATTTTAATTTCATCCCTAAACTATGACTCTCATTCTAAATTAGTCCTCAAACTTTTGAAC
Found at i:1023534 original size:60 final size:60
Alignment explanation
Indices: 1023410--1023540 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 60
1023400 TAAATATTTT
* * **
1023410 AATTTCATCCCTAAACTATGACTCTCATTTTAAATTAGTCCTTAAACTTTTGAACATTTT
1 AATTTCATCCCTAAACTATGACTCTCATTCTAAATTAGTCCTCAAACTTTTGAACATTCC
* * *
1023470 AATTTCATCCCTAAACTATGA-TCCTCATTCTAAATTGGT-CTCAAACTTTTTGCAGATTCC
1 AATTTCATCCCTAAACTATGACT-CTCATTCTAAATTAGTCCTCAAAC-TTTTGAACATTCC
*
1023530 AATTTTATCCC
1 AATTTCATCCC
1023541 AAATTCATCG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 7 0.11
60 54 0.89
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (60 bp):
AATTTCATCCCTAAACTATGACTCTCATTCTAAATTAGTCCTCAAACTTTTGAACATTCC
Found at i:1027373 original size:16 final size:17
Alignment explanation
Indices: 1027352--1027386 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1027342 TACTATTTAC
1027352 GTGAATAGT-AAATTTT
1 GTGAATAGTAAAATTTT
1027368 GTGAATAGTAAAATTTT
1 GTGAATAGTAAAATTTT
1027385 GT
1 GT
1027387 TGGCAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (17 bp):
GTGAATAGTAAAATTTT
Found at i:1030159 original size:52 final size:52
Alignment explanation
Indices: 1030091--1030248 Score: 273
Period size: 52 Copynumber: 3.0 Consensus size: 52
1030081 AAGTGAGAGG
*
1030091 TTGTT-AAAGTGAATTCGGTGGCCAGCCAACGATTGTTGAAGATTCAAACAA
1 TTGTTAAAAGTGAATTCGGTGGCCAGCCAACAATTGTTGAAGATTCAAACAA
1030142 TTGTTAAAAGTGAATTCGGTGGCCAGCCAACAATTGTTGAAGATTCAAACAA
1 TTGTTAAAAGTGAATTCGGTGGCCAGCCAACAATTGTTGAAGATTCAAACAA
* *
1030194 TTGTTAAAAGTCAATTCGGTGGCCAGCCAACAATTGTTGAAGAATCAAAGCAA
1 TTGTTAAAAGTGAATTCGGTGGCCAGCCAACAATTGTTGAAGATTCAAA-CAA
1030247 TT
1 TT
1030249 TTCGGTGGGT
Statistics
Matches: 102, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
51 5 0.05
52 92 0.90
53 5 0.05
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (52 bp):
TTGTTAAAAGTGAATTCGGTGGCCAGCCAACAATTGTTGAAGATTCAAACAA
Found at i:1034790 original size:64 final size:64
Alignment explanation
Indices: 1034722--1034843 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 64
1034712 ATTATTCAAG
* ** * * *
1034722 GTGTATCAATGCACATG-AGGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATTA
1 GTGTATCAATGCACAAGTA-GTACATCAATGCACCCCCTTAAAATAAAAACATCGAATGTCATTA
* * *
1034786 GTGTATCGATGCCCAAGTAGTACATCAATGCACCCCCTTAAAATATAAACATCGAATG
1 GTGTATCAATGCACAAGTAGTACATCAATGCACCCCCTTAAAATAAAAACATCGAATG
1034844 AGATTTATGT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
64 47 0.98
65 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (64 bp):
GTGTATCAATGCACAAGTAGTACATCAATGCACCCCCTTAAAATAAAAACATCGAATGTCATTA
Found at i:1034873 original size:64 final size:63
Alignment explanation
Indices: 1034749--1034884 Score: 150
Period size: 64 Copynumber: 2.1 Consensus size: 63
1034739 AGGTGTATCG
* * * *
1034749 ATGCACTCCTTTAAAATAAAAACATCGAATGTCATTAGTGTATCGATGCCCAAGTAGTACATCA
1 ATGCACCCCCTTAAAATAAAAACATCGAATGACATTAGTGTACCGATG-CCAAGTAGTACATCA
* * *
1034813 ATGCACCCCCTTAAAATATAAACATCGAATGAGATTTA-TGTACCGATG-CATAGATTGTACATC
1 ATGCACCCCCTTAAAATAAAAACATCGAATGACA-TTAGTGTACCGATGCCA-AG-TAGTACATC
*
1034876 G
63 A
1034877 ATGCACCC
1 ATGCACCC
1034885 GTCAAGGGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
62 2 0.03
63 2 0.03
64 54 0.89
65 3 0.05
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (63 bp):
ATGCACCCCCTTAAAATAAAAACATCGAATGACATTAGTGTACCGATGCCAAGTAGTACATCA
Found at i:1035479 original size:18 final size:18
Alignment explanation
Indices: 1035456--1035528 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
1035446 AGGGATTATC
1035456 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
* *
1035474 AGTGGTTCTT-TGGAACAAT
1 AGTGGTCCTTCAGG-AC-AT
*
1035493 CAGTGGTCCTTCAAGACAT
1 -AGTGGTCCTTCAGGACAT
* *
1035512 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCAGGACA
1035529 AATATTCAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
17 2 0.05
18 25 0.58
19 4 0.09
20 11 0.26
21 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:1039505 original size:19 final size:20
Alignment explanation
Indices: 1039464--1039512 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1039454 GCCCCAACAA
*
1039464 TATCGATACCGACCCTTGGG
1 TATCGATACCGACCCTTGAG
1039484 TATCGATACTC-A-CCTTGAG
1 TATCGATAC-CGACCCTTGAG
*
1039503 TATTGATACC
1 TATCGATACC
1039513 AAAAATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 14 0.54
20 10 0.38
21 1 0.04
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (20 bp):
TATCGATACCGACCCTTGAG
Found at i:1045312 original size:40 final size:40
Alignment explanation
Indices: 1045257--1045342 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
1045247 TTGGCCAATC
1045257 GCAATGTGGTGCTTTAATCACTCCGATATTATGACTCCAT
1 GCAATGTGGTGCTTTAATCACTCCGATATTATGACTCCAT
1045297 GCAATGTGGTGCTTTAATCACTCCGATATTATGACTCCAT
1 GCAATGTGGTGCTTTAATCACTCCGATATTATGACTCCAT
*
1045337 TCAATG
1 GCAATG
1045343 CTCTTTTATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (40 bp):
GCAATGTGGTGCTTTAATCACTCCGATATTATGACTCCAT
Found at i:1045653 original size:24 final size:23
Alignment explanation
Indices: 1045621--1045669 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
1045611 ATGATGATAG
*
1045621 ATTTGATCTAATATTCAATACAAT
1 ATTTAATCTAATATT-AATACAAT
*
1045645 ATTTAATCTAATATTAATAGAAT
1 ATTTAATCTAATATTAATACAAT
1045668 AT
1 AT
1045670 AATAGTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (23 bp):
ATTTAATCTAATATTAATACAAT
Found at i:1053745 original size:27 final size:27
Alignment explanation
Indices: 1053692--1053746 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
1053682 ACCTGAACCC
*
1053692 GACCTGGCCCAACACCACATTTAAAAA
1 GACCTGACCCAACACCACATTTAAAAA
*
1053719 GACCTGACCCGAACACCACCTTTAAAAA
1 GACCTGACCC-AACACCACATTTAAAAA
1053747 ACTCGACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.40, C:0.35, G:0.11, T:0.15
Consensus pattern (27 bp):
GACCTGACCCAACACCACATTTAAAAA
Found at i:1084768 original size:18 final size:18
Alignment explanation
Indices: 1084745--1084817 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
1084735 ACTGAATATT
1084745 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1084763 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
1084782 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
1084801 TGTCCCGAATGACCACT
1 TGTCCCGAAGGACCACT
1084818 GATAATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 31 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.27, C:0.32, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1084791 original size:38 final size:38
Alignment explanation
Indices: 1084744--1084820 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
1084734 TACTGAATAT
*
1084744 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
* *
1084782 TTGTTCCGAAGAACCACTATGTCCCGAATGACCACTGA
1 TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
1084820 T
1 T
1084821 AATCCCTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATGTCCCGAAGGACCACTGA
Found at i:1086067 original size:2 final size:2
Alignment explanation
Indices: 1086060--1086085 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1086050 CGTGGAGCTA
1086060 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
1086086 CCCTTCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1091656 original size:18 final size:18
Alignment explanation
Indices: 1091633--1091667 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1091623 ACTGAATATT
1091633 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1091651 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1091668 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1093876 original size:32 final size:32
Alignment explanation
Indices: 1093840--1094009 Score: 186
Period size: 32 Copynumber: 5.4 Consensus size: 32
1093830 GTTCTACAGA
* *
1093840 ACATATGGATAAAATTACCTATGTCTTTCGGG
1 ACATATGGACAGAATTACCTATGTCTTTCGGG
*
1093872 ACATACGGACAGAATTACCTATGTCTTTCGGG
1 ACATATGGACAGAATTACCTATGTCTTTCGGG
*
1093904 ACATATGGACAGAATTACCTATGTTTTTCGGG
1 ACATATGGACAGAATTACCTATGTCTTTCGGG
* * ** *
1093936 ACATATGGACAGTA-TACATATGT-TCTAAGGA
1 ACATATGGACAGAATTACCTATGTCT-TTCGGG
* *
1093967 ACATATGGACAG-TTTACCTAGGT-TCTTCGGG
1 ACATATGGACAGAATTACCTATGTCT-TTCGGG
*
1093998 ACCTATGGACAG
1 ACATATGGACAG
1094010 TTGCTGAGGT
Statistics
Matches: 119, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
30 1 0.01
31 46 0.39
32 72 0.61
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (32 bp):
ACATATGGACAGAATTACCTATGTCTTTCGGG
Found at i:1093971 original size:31 final size:32
Alignment explanation
Indices: 1093904--1094010 Score: 92
Period size: 31 Copynumber: 3.4 Consensus size: 32
1093894 GTCTTTCGGG
* * * ** *
1093904 ACATATGGACAGAATTACCTATGTTTTTCGGG
1 ACATATGGACAGTATTACATATGTTCTAAGGA
1093936 ACATATGGACAGTA-TACATATGTTCTAAGGA
1 ACATATGGACAGTATTACATATGTTCTAAGGA
* * ** *
1093967 ACATATGGACAGT-TTACCTAGGTTCTTCGGG
1 ACATATGGACAGTATTACATATGTTCTAAGGA
*
1093998 ACCTATGGACAGT
1 ACATATGGACAGT
1094011 TGCTGAGGTT
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
31 49 0.79
32 13 0.21
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (32 bp):
ACATATGGACAGTATTACATATGTTCTAAGGA
Found at i:1094011 original size:31 final size:31
Alignment explanation
Indices: 1093820--1094011 Score: 172
Period size: 32 Copynumber: 6.1 Consensus size: 31
1093810 AGAGTCGAGG
* * * *
1093820 GTTTACCTATGTTCTACAGAACATATGGATAA
1 GTTTACCTATGTTCTTCGGGACATATGGA-CA
** *
1093852 AATTACCTATG-TCTTTCGGGACATACGGACA
1 GTTTACCTATGTTC-TTCGGGACATATGGACA
*
1093883 GAATTACCTATG-TCTTTCGGGACATATGGACA
1 G-TTTACCTATGTTC-TTCGGGACATATGGACA
* *
1093915 GAATTACCTATGTTTTTCGGGACATATGGACA
1 G-TTTACCTATGTTCTTCGGGACATATGGACA
* * ** *
1093947 GTATACATATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
* *
1093978 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
1094009 GTT
1 GTT
1094012 GCTGAGGTTC
Statistics
Matches: 133, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
31 53 0.40
32 79 0.59
33 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACA
Found at i:1094808 original size:21 final size:22
Alignment explanation
Indices: 1094783--1094823 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1094773 CTGTAGCAGT
*
1094783 CCTGTAGCA-AGGTATCGGTTC
1 CCTGTAGCAGAGGAATCGGTTC
1094804 CCTGTAGCAGAGGAATCGGT
1 CCTGTAGCAGAGGAATCGGT
1094824 ACCCCTCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.24
Consensus pattern (22 bp):
CCTGTAGCAGAGGAATCGGTTC
Found at i:1095204 original size:27 final size:29
Alignment explanation
Indices: 1095157--1095220 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 29
1095147 AATTTCATAG
*
1095157 AATA-AATATTATTTAATTA-TTAATAAT
1 AATATAATATTATTTAAGTATTTAATAAT
* *
1095184 AA-ATAATATTATTTACGTATTTAATATT
1 AATATAATATTATTTAAGTATTTAATAAT
1095212 AATATAATA
1 AATATAATA
1095221 ATTTATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 15 0.48
28 9 0.29
29 6 0.19
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (29 bp):
AATATAATATTATTTAAGTATTTAATAAT
Found at i:1095424 original size:22 final size:21
Alignment explanation
Indices: 1095393--1095436 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1095383 ATAAATTATT
1095393 TTAATATTTTAAAACAATAATA
1 TTAATATTTTAAAA-AATAATA
* *
1095415 TTAATTTTTTAATAAATAATA
1 TTAATATTTTAAAAAATAATA
1095436 T
1 T
1095437 ATTTTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATATTTTAAAAAATAATA
Found at i:1104442 original size:17 final size:16
Alignment explanation
Indices: 1104416--1104447 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1104406 TTTCGATATG
1104416 ATAAATTTAAATAAAA
1 ATAAATTTAAATAAAA
1104432 ATAATATTTAAATAAA
1 ATAA-ATTTAAATAAA
1104448 TTATCATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAATTTAAATAAAA
Found at i:1115324 original size:51 final size:50
Alignment explanation
Indices: 1115255--1115352 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 50
1115245 GCATAAAATA
* * *
1115255 AAATAATAGTTACTAAAATGCAAGAAAATAAAA-AATAGTAGTTAAATAGG
1 AAATAATAGTGACCAAAATGCAA-AAAATAAAATAACAGTAGTTAAATAGG
* *
1115305 AAATAAATAGTGACCAAAATGTAAAAATTAAAATAACAGTAGTTAAAT
1 AAAT-AATAGTGACCAAAATGCAAAAAATAAAATAACAGTAGTTAAAT
1115353 CAGAAACTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 12 0.29
51 29 0.71
ACGTcount: A:0.58, C:0.05, G:0.12, T:0.24
Consensus pattern (50 bp):
AAATAATAGTGACCAAAATGCAAAAAATAAAATAACAGTAGTTAAATAGG
Found at i:1115555 original size:2 final size:2
Alignment explanation
Indices: 1115548--1115573 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1115538 CTTTCGGCCA
1115548 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
1115574 TCTTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1117492 original size:14 final size:14
Alignment explanation
Indices: 1117473--1117508 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1117463 TTTATTTAGA
1117473 GGGATGAATTGAAT
1 GGGATGAATTGAAT
1117487 GGGATGAATTGAAT
1 GGGATGAATTGAAT
1117501 GGGATGAA
1 GGGATGAA
1117509 ATATCGTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.39, T:0.25
Consensus pattern (14 bp):
GGGATGAATTGAAT
Found at i:1117819 original size:24 final size:22
Alignment explanation
Indices: 1117792--1117846 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
1117782 TGATAATTTT
1117792 TAAATTTTATTTAAATTTAAAAAA
1 TAAATTTTA--TAAATTTAAAAAA
* *
1117816 TAAAATTTATATATTTAAAAAA
1 TAAATTTTATAAATTTAAAAAA
1117838 TATAATTTT
1 TA-AATTTT
1117847 TGAAATATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.52
23 5 0.19
24 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAATTTTATAAATTTAAAAAA
Found at i:1118290 original size:30 final size:30
Alignment explanation
Indices: 1118254--1118311 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
1118244 TTTAAAAAGC
1118254 AAATTTCAAAATTATCAAATTGTGACACGT
1 AAATTTCAAAATTATCAAATTGTGACACGT
*
1118284 AAATTTCAAAATTATCAACTTGTGACAC
1 AAATTTCAAAATTATCAAATTGTGACAC
1118312 ATGTCAACGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (30 bp):
AAATTTCAAAATTATCAAATTGTGACACGT
Found at i:1120587 original size:19 final size:20
Alignment explanation
Indices: 1120557--1120607 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
1120547 TTTTCCAAAT
*
1120557 TTACGGTAGTCCAAATT-CG
1 TTACGATAGTCCAAATTACG
*
1120576 TTGCGATAGTCCAAATTCACG
1 TTACGATAGTCCAAATT-ACG
1120597 TTACGATAGTC
1 TTACGATAGTC
1120608 GAAGTTCGCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 15 0.56
21 12 0.44
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (20 bp):
TTACGATAGTCCAAATTACG
Found at i:1120619 original size:21 final size:21
Alignment explanation
Indices: 1120563--1120624 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1120553 AAATTTACGG
1120563 TAGTCCAAATT--CGTTGCGA
1 TAGTCCAAATTCACGTTGCGA
*
1120582 TAGTCCAAATTCACGTTACGA
1 TAGTCCAAATTCACGTTGCGA
* * *
1120603 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCCAAATTCACGTTGCGA
1120624 T
1 T
1120625 TTTTTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 11 0.31
21 25 0.69
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (21 bp):
TAGTCCAAATTCACGTTGCGA
Found at i:1121087 original size:20 final size:20
Alignment explanation
Indices: 1121025--1121102 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1121015 GATTTTTCAT
*
1121025 TATCGCAACAC-TTTT-CAC
1 TATCGCAACACATTTTAAAC
*
1121043 TATCGCAACAACACGTTTTTCAAC
1 TATCGCAAC-ACA---TTTTAAAC
*
1121067 TCTCGCAACACATTTTAAAC
1 TATCGCAACACATTTTAAAC
1121087 TATCGCAACACATTTT
1 TATCGCAACACATTTT
1121103 TTAAAATCGC
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
18 9 0.18
19 2 0.04
20 22 0.44
23 7 0.14
24 10 0.20
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (20 bp):
TATCGCAACACATTTTAAAC
Found at i:1127237 original size:3 final size:3
Alignment explanation
Indices: 1127200--1127257 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
1127190 GACTTAAAAA
* * *
1127200 TAT TA- TAT TGT TAT TTT TAT TA- TAT AAT TACT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
*
1127244 TAG TAT TAT TAT TA
1 TAT TAT TAT TAT TA
1127258 ATTTATATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1132168 original size:64 final size:64
Alignment explanation
Indices: 1132067--1132488 Score: 621
Period size: 64 Copynumber: 6.6 Consensus size: 64
1132057 TGCAGCTTTT
*
1132067 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* ** *
1132131 AGAGTCAATTTCAATTTCACAGTGAAGGATATTGGACTCAACAAACAACTTTCCAATTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * * * * *
1132195 AGAGTCAATTTCAAATTCATAATGAAGGATATTAGACTCAACAAACAATTTTCCAATTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
1132259 AGAGTCTATTTCAACTTCACAACGAAAGATATTGGACTCAACAAACAACTTTCTAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * * *
1132323 ATAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCAACAAACAACTTTCTAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* *
1132387 AGAGTCAATTTCAACTTCACAACGAATGATATTGGACTCAACAAATAACTTTCCAGCTTT-ATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAG-TTTCATTC
* * *
1132451 AGAGTCAATTTCAACTTCATAACAAATGATATTGGACT
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACT
1132489 TGAAACAATG
Statistics
Matches: 330, Mismatches: 27, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
64 327 0.99
65 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:1132661 original size:121 final size:121
Alignment explanation
Indices: 1132516--1132734 Score: 384
Period size: 121 Copynumber: 1.8 Consensus size: 121
1132506 CACAAGCTTA
1132516 GATTTCAAATTCAAGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
1 GATTTCAAATTCAAGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
1132581 CAATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTG
66 CAATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTG
* * * *
1132637 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATTCG
1 GATTTCAAATTCAAGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
* *
1132702 CGATTTCAACTTCACGACGAATGATATCGTGCC
66 CAATTTCAACTTCACGACGAAGGATATCGTGCC
1132735 TAACGGATCG
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 92 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (121 bp):
GATTTCAAATTCAAGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
CAATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTG
Found at i:1134325 original size:19 final size:20
Alignment explanation
Indices: 1134288--1134325 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1134278 AGTGTTAATG
*
1134288 AATTTTAATATTTTATATTA
1 AATTTTAATATTATATATTA
1134308 AATTTTAA-ATTATATATT
1 AATTTTAATATTATATATT
1134326 CGATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTTTAATATTATATATTA
Found at i:1137522 original size:21 final size:22
Alignment explanation
Indices: 1137481--1137522 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1137471 TTTAATGTCG
* *
1137481 ATATTATTTTTAATCAAAATCT
1 ATATAATTATTAATCAAAATCT
1137503 ATATAATTATTAAT-AAAATC
1 ATATAATTATTAATCAAAATC
1137523 CAAGATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATAATTATTAATCAAAATCT
Found at i:1139907 original size:15 final size:15
Alignment explanation
Indices: 1139884--1139915 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1139874 TAATTTCCCC
*
1139884 TTTTGTAAATACAAA
1 TTTTATAAATACAAA
1139899 TTTTATAAATACAAA
1 TTTTATAAATACAAA
1139914 TT
1 TT
1139916 AACATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (15 bp):
TTTTATAAATACAAA
Found at i:1154436 original size:88 final size:87
Alignment explanation
Indices: 1154283--1154446 Score: 204
Period size: 88 Copynumber: 1.9 Consensus size: 87
1154273 AGTCGAAAAG
* * *
1154283 CGAGTCAATAAACTAATTATTCGTGAACATAAATGAATCATGCACACATTTATTGGAGTTTGTAT
1 CGAGTCAATAAACTAATTATTCGTGAACATAAACGAATCAT-CACACATTTATTCGAGTTCGTAT
1154348 ATTTATTAAATGAAGTAAGTAAA
65 ATTTATTAAATGAAGTAAGTAAA
* * * * * * *
1154371 CGAGTCAATAAATTGACTTGTTCGTGAATATCAACGAATCAT-ATACATTTTATTCGTGTTCGTA
1 CGAGTCAATAAACT-AATTATTCGTGAACATAAACGAATCATCACACA-TTTATTCGAGTTCGTA
1154435 TATTTATTAAAT
64 TATTTATTAAAT
1154447 AATATAAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
87 4 0.06
88 38 0.59
89 22 0.34
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (87 bp):
CGAGTCAATAAACTAATTATTCGTGAACATAAACGAATCATCACACATTTATTCGAGTTCGTATA
TTTATTAAATGAAGTAAGTAAA
Found at i:1160328 original size:3 final size:3
Alignment explanation
Indices: 1160320--1160397 Score: 138
Period size: 3 Copynumber: 26.0 Consensus size: 3
1160310 CAATTTTGAC
1160320 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
1160368 ATT ATT ATT ATT ATT ATC ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1160398 TCATTCCTCT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1162404 original size:15 final size:15
Alignment explanation
Indices: 1162384--1162413 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1162374 AATAGTGGAT
1162384 TTTTGGAGTATATTA
1 TTTTGGAGTATATTA
1162399 TTTTGGAGTATATTA
1 TTTTGGAGTATATTA
1162414 GCCCTCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (15 bp):
TTTTGGAGTATATTA
Found at i:1166422 original size:21 final size:21
Alignment explanation
Indices: 1166358--1166415 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
1166348 TTTCTGGGCT
1166358 AAGGGAATCGATACCCATTCA
1 AAGGGAATCGATACCCATTCA
1166379 AAGGGAATCGATACCCATTCA
1 AAGGGAATCGATACCCATTCA
1166400 AAGGGAATCGATACCC
1 AAGGGAATCGATACCC
1166416 CCTCAAACGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (21 bp):
AAGGGAATCGATACCCATTCA
Found at i:1166473 original size:19 final size:19
Alignment explanation
Indices: 1166449--1166485 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1166439 GAACACTAGA
*
1166449 GGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCAG
*
1166468 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
1166486 TAAAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (19 bp):
GGGGAACCGATACCCCCAG
Found at i:1167147 original size:103 final size:103
Alignment explanation
Indices: 1166963--1167177 Score: 376
Period size: 103 Copynumber: 2.1 Consensus size: 103
1166953 GTAGAGGGTC
* *
1166963 TATGTTGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGATCTGGTGAGACACCTAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGATCTGGTGAGACACATAC
* *
1167028 TTGATCCTTGGTATATGTATATGATTATTAAGGAATGA
66 TTGATCCTTGGCATATGTATATAATTATTAAGGAATGA
*
1167066 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGATCTGGTGAGACACATAC
*
1167131 TTGATCCTTGGCATATGTATATAATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATAATTATTAAGGAATGA
1167169 TATGTGGTC
1 TATGTGGTC
1167178 TTTATGGACA
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGATCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATAATTATTAAGGAATGA
Found at i:1167233 original size:23 final size:23
Alignment explanation
Indices: 1167196--1167264 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
1167186 CATTATTATA
*
1167196 TGGCACTACGATGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1167219 TGGCACTCCGGTGCAATTCTAAG
1 TGGCACTACGGTGCAATTCTACG
*
1167242 TGGCACTTA-GGTGCAATTATACG
1 TGGCAC-TACGGTGCAATTCTACG
1167265 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1173345 original size:21 final size:21
Alignment explanation
Indices: 1173303--1173345 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1173293 TTTCTGGGCT
*
1173303 AGGGGAATCGACACCCATTCA
1 AGGGGAATCGACACCCACTCA
* *
1173324 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGACACCCACTCA
1173345 A
1 A
1173346 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.14
Consensus pattern (21 bp):
AGGGGAATCGACACCCACTCA
Found at i:1174117 original size:103 final size:103
Alignment explanation
Indices: 1173892--1174105 Score: 374
Period size: 103 Copynumber: 2.1 Consensus size: 103
1173882 GTAGAGGGTC
* *
1173892 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACGCCTAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
* * *
1173957 TTGATCCTTGGTATATGTATATGATTCTTAAGGACTGA
66 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
*
1173995 TATTTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1174060 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
1174098 TATGTGGT
1 TATGTGGT
1174106 TCTTATGGAC
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1174183 original size:23 final size:23
Alignment explanation
Indices: 1174125--1174188 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1174115 CATTATTATA
* *
1174125 TGGCACTCCGGTGAAATTCTACG
1 TGGCACTCCGGTGCAATTCTAAG
*
1174148 CGGCACTCCGGTGCAATTCTAAG
1 TGGCACTCCGGTGCAATTCTAAG
**
1174171 TGGCACTTAGGTGCAATT
1 TGGCACTCCGGTGCAATT
1174189 ATGCGAGCTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTCTAAG
Found at i:1175937 original size:19 final size:19
Alignment explanation
Indices: 1175884--1175938 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
1175874 CGATCAGACC
* *
1175884 AGTCAACAGGTCAGGTTAA
1 AGTCAACAGGTCGGGTCAA
* *
1175903 AGTCAACGGGTTGGGTCAA
1 AGTCAACAGGTCGGGTCAA
*
1175922 AGTCAACAAGTCGGGTC
1 AGTCAACAGGTCGGGTC
1175939 GGGTTGACTC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (19 bp):
AGTCAACAGGTCGGGTCAA
Found at i:1182975 original size:31 final size:31
Alignment explanation
Indices: 1182938--1183015 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
1182928 TAAAAAAACA
* * *
1182938 TAAGTTTTAGTCACTTACGTTATTGTTTTAT
1 TAAGTTTTGGTCACTTACATTATCGTTTTAT
*
1182969 TAAGTTTTGGTGTA-TTACATTATCGTTTTAT
1 TAAGTTTTGGT-CACTTACATTATCGTTTTAT
1183000 TAAGTTTTGGTCACTT
1 TAAGTTTTGGTCACTT
1183016 GGACATTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.03
31 38 0.95
32 1 0.03
ACGTcount: A:0.22, C:0.09, G:0.15, T:0.54
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACATTATCGTTTTAT
Found at i:1191788 original size:24 final size:24
Alignment explanation
Indices: 1191749--1191795 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1191739 TTTTTATATA
*
1191749 TAATAATATTACATATTTAATTAT
1 TAATAATATTACATATTAAATTAT
* *
1191773 TAATAATTTTATATATTAAATTA
1 TAATAATATTACATATTAAATTA
1191796 AACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATAATATTACATATTAAATTAT
Found at i:1199217 original size:24 final size:24
Alignment explanation
Indices: 1199172--1199221 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1199162 TGGTGGTTGG
*
1199172 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
1199196 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
1199220 TT
1 TT
1199222 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:1202733 original size:37 final size:37
Alignment explanation
Indices: 1202692--1202788 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
1202682 GGATCTTATC
*
1202692 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATCCTAGTAGAACTCTATCCTATT
* * *
1202729 TTTAGGAGTTTAAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTAAATCCTAGTAGAACTCTATCCTATT
*
1202766 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTAAATCCTAGTAG
1202789 GACGAAAAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCCTAGTAGAACTCTATCCTATT
Found at i:1203843 original size:106 final size:106
Alignment explanation
Indices: 1203518--1204996 Score: 2082
Period size: 106 Copynumber: 14.0 Consensus size: 106
1203508 GCATTGTTCT
* * * * ** *
1203518 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAACTGTCTCTGGAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
1203582 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1203624 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-GA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * * * * * *
1203683 TTAGCCG-CCTCTTCATCATGAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * *
1203725 G-GTTCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1203789 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
1203830 GAGTCCAATATCCTACGTTGTAAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1203895 CCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1203936 GAGTCAAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTGGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1204001 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1204042 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1204107 CCAGC-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1204147 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGCCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1204212 CCAGCGGTCTCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** * *
1204253 GAGTTCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGCTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1204318 CAAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1204359 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGCCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1204424 CCAGAGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1204465 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1204530 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1204571 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1204636 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1204677 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGAAAGTTGTTTATTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1204742 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1204783 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1204848 CCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGT-TG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1204888 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * *
1204952 TCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1204993 GAGT
1 GAGT
1204997 GGCACGATAT
Statistics
Matches: 1231, Mismatches: 129, Indels: 27
0.89 0.09 0.02
Matches are distributed among these distances:
99 2 0.00
100 74 0.06
101 4 0.00
102 4 0.00
104 44 0.04
105 161 0.13
106 939 0.76
107 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1205826 original size:22 final size:22
Alignment explanation
Indices: 1205800--1205869 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
1205790 TTATGTTTGG
1205800 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* *
1205822 TCAAAGGTTTGTCATGTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1205844 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1205866 TCAA
1 TCAA
1205870 CAGTTTGATG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1206532 original size:16 final size:14
Alignment explanation
Indices: 1206491--1206540 Score: 68
Period size: 16 Copynumber: 3.6 Consensus size: 14
1206481 TTCTTTTTGA
1206491 TTTTTGTTCTTTCT
1 TTTTTGTTCTTTCT
1206505 TTTTT-TTC-TTCT
1 TTTTTGTTCTTTCT
1206517 TTTTTGCTTCTTTTCT
1 TTTTTG-TTC-TTTCT
1206533 TTTTTGTT
1 TTTTTGTT
1206541 TTTGCCCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 9 0.28
13 3 0.09
14 8 0.25
15 2 0.06
16 10 0.31
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (14 bp):
TTTTTGTTCTTTCT
Found at i:1211105 original size:37 final size:37
Alignment explanation
Indices: 1211007--1211108 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
1210997 GTGCTTGTGG
* * ** *
1211007 ATCCTATCTTTAGGAGTTTAAATCATAATAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
*
1211044 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
*
1211081 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAG
1211109 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTCT
Found at i:1211416 original size:35 final size:34
Alignment explanation
Indices: 1211374--1211483 Score: 93
Period size: 35 Copynumber: 3.1 Consensus size: 34
1211364 TTCATCTTGG
1211374 TTGGTGGCCAAACTTTGAACATGGGAATTTCATAT
1 TTGGTGGCCAAACTTTGAACATGGGAA-TTCATAT
* *
1211409 TTGGTGG-CTAAC-TTGTACACATTGGAAAATTC-T-T
1 TTGGTGGCCAAACTTTG-A-ACA-TGG-GAATTCATAT
1211443 TGGTAGGTGGCCAAACTTTGAACATGGGAATTCAATAT
1 T--T-GGTGGCCAAACTTTGAACATGGGAATTC-ATAT
1211481 TTG
1 TTG
1211484 ATCCCTAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 24
0.68 0.05 0.28
Matches are distributed among these distances:
33 3 0.05
34 7 0.12
35 17 0.29
36 11 0.19
37 11 0.19
38 7 0.12
39 3 0.05
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (34 bp):
TTGGTGGCCAAACTTTGAACATGGGAATTCATAT
Found at i:1214436 original size:37 final size:37
Alignment explanation
Indices: 1214394--1214524 Score: 137
Period size: 37 Copynumber: 3.6 Consensus size: 37
1214384 TATTATAATG
*
1214394 TAGTTTTTGAAAATATTTTTTGAAAACATATAATATA
1 TAGTTTTTGAAAATAGTTTTTGAAAACATATAATATA
* *
1214431 TAGTTTTTAGAAAA-CGTTTTTGAAAGCATATAATATA
1 TAGTTTTT-GAAAATAGTTTTTGAAAACATATAATATA
* *
1214468 TAGTTTTTAAAAATCGGTTTTT-AAAA-ATAT-ATA-A
1 TAGTTTTTGAAAAT-AGTTTTTGAAAACATATAATATA
*
1214502 TATGGTTTTGAAAATACGTTTTT
1 TA-GTTTTTGAAAATA-GTTTTT
1214525 ACTACATTTC
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
34 3 0.04
35 19 0.24
36 8 0.10
37 39 0.49
38 11 0.14
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (37 bp):
TAGTTTTTGAAAATAGTTTTTGAAAACATATAATATA
Found at i:1214488 original size:38 final size:37
Alignment explanation
Indices: 1214410--1214504 Score: 138
Period size: 37 Copynumber: 2.5 Consensus size: 37
1214400 TTGAAAATAT
1214410 TTTTTGAAAACATATAATATATAGTTTTTAGAAAACG
1 TTTTTGAAAACATATAATATATAGTTTTTAGAAAACG
*
1214447 TTTTTGAAAGCATATAATATATAGTTTTTA-AAAATCGG
1 TTTTTGAAAACATATAATATATAGTTTTTAGAAAA-C-G
* *
1214485 TTTTTAAAAATATATAATAT
1 TTTTTGAAAACATATAATAT
1214505 GGTTTTGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
36 4 0.08
37 30 0.58
38 18 0.35
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (37 bp):
TTTTTGAAAACATATAATATATAGTTTTTAGAAAACG
Found at i:1220202 original size:17 final size:18
Alignment explanation
Indices: 1220165--1220209 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 18
1220155 TTAGCGGTCT
1220165 AAGTAAGCAGTTAACTGGGC
1 AAGTAAGCAGTT-A-TGGGC
1220185 AAGTAAGCAGTT-TGGGC
1 AAGTAAGCAGTTATGGGC
1220202 AAGTAAGC
1 AAGTAAGC
1220210 GTCACCTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.52
20 12 0.48
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (18 bp):
AAGTAAGCAGTTATGGGC
Found at i:1221429 original size:26 final size:26
Alignment explanation
Indices: 1221400--1221456 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
1221390 AATCGAGGAG
*
1221400 TATTTATACGTCCCATAGTCG-AGCAC
1 TATTTATACATCCCATAGTCGAAG-AC
1221426 TATTTATACATCCCATAGTCGAAGAC
1 TATTTATACATCCCATAGTCGAAGAC
1221452 TATTT
1 TATTT
1221457 GTGTACTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (26 bp):
TATTTATACATCCCATAGTCGAAGAC
Found at i:1232027 original size:35 final size:35
Alignment explanation
Indices: 1231988--1232065 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 35
1231978 CACAGTCATA
* *
1231988 AATTACATTCTAAGCCCCAAAATTCAAAATACTTC
1 AATTACATCCTAAACCCCAAAATTCAAAATACTTC
* *
1232023 AATTACATCCTAAACCTCAAATTTCAAAATACTTC
1 AATTACATCCTAAACCCCAAAATTCAAAATACTTC
1232058 AATTACAT
1 AATTACAT
1232066 GTTATCACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (35 bp):
AATTACATCCTAAACCCCAAAATTCAAAATACTTC
Found at i:1233065 original size:36 final size:36
Alignment explanation
Indices: 1233025--1233110 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 36
1233015 GTGGTTAGTC
1233025 ATGTAATTGAAGTATTTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTTTTGGAATTTGAGGTTTAGA
* *
1233061 ATGTAATTGAAATA-TTTTGGAATTTGGGGTTTAGA
1 ATGTAATTGAAGTATTTTTGGAATTTGAGGTTTAGA
* *
1233096 ATGCAATTGATGTAT
1 ATGTAATTGAAGTAT
1233111 GTGTTGCAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 31 0.70
36 13 0.30
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.43
Consensus pattern (36 bp):
ATGTAATTGAAGTATTTTTGGAATTTGAGGTTTAGA
Found at i:1247820 original size:17 final size:18
Alignment explanation
Indices: 1247795--1247836 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1247785 AGGCTCAAAC
* *
1247795 TTGACCTCG-ATTCTAGT
1 TTGAACTCGAATTCAAGT
1247812 TTGAACTCGAATTCAAGT
1 TTGAACTCGAATTCAAGT
*
1247830 ATGAACT
1 TTGAACT
1247837 TTAAGTACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (18 bp):
TTGAACTCGAATTCAAGT
Found at i:1249070 original size:27 final size:27
Alignment explanation
Indices: 1249010--1249070 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
1249000 GGTTTATTTC
*
1249010 AATTTTTTGTTTTTTTTTTAAATATAT
1 AATTTTTAGTTTTTTTTTTAAATATAT
1249037 AA-TTTTAGTTTTTTAATTTTAAATA-A-
1 AATTTTTAGTTTTTT--TTTTAAATATAT
1249063 AATTTTTA
1 AATTTTTA
1249071 AAATTATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 13 0.43
27 8 0.27
28 9 0.30
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (27 bp):
AATTTTTAGTTTTTTTTTTAAATATAT
Found at i:1249405 original size:20 final size:22
Alignment explanation
Indices: 1249383--1249454 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
1249373 CGAAAAAATA
* *
1249383 ATATCTATCTATAT-TATATA-
1 ATATATATATATATATATATAT
1249403 ATATATATATATATATATATAT
1 ATATATATATATATATATATAT
1249425 ATATATATATATATATATATAT
1 ATATATATATATATATATATAT
1249447 ATATATAT
1 ATATATAT
1249455 TTCCTCGGTG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.25
21 6 0.12
22 30 0.62
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATATATATATATATATATAT
Found at i:1249408 original size:2 final size:2
Alignment explanation
Indices: 1249392--1249454 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
1249382 AATATCTATC
1249392 TA TA T- TA TA TA -A 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
1249432 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1249455 TTCCTCGGTG
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1251094 original size:21 final size:21
Alignment explanation
Indices: 1251065--1251117 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1251055 ATTCTGACTA
1251065 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1251086 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1251107 TCGCAATGCGA
1 TCGCATTGCGA
1251118 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1251132 original size:20 final size:20
Alignment explanation
Indices: 1251107--1251274 Score: 196
Period size: 20 Copynumber: 8.3 Consensus size: 20
1251097 TTTTCCTAAT
*
1251107 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
1251127 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
1251147 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
1251167 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCG-ATTACGTAAA
1251188 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* * * *
1251208 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGA-TTACGTAAA
* *
1251229 TCACATTGCGATTTACGT-AA
1 TCGCAATGCGA-TTACGTAAA
*
1251249 TCGCATTGCGATTTA-GTAAA
1 TCGCAATGCGA-TTACGTAAA
1251269 TCGCAA
1 TCGCAA
1251275 CGAGATTCTG
Statistics
Matches: 128, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
19 2 0.02
20 89 0.70
21 37 0.29
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:1251137 original size:41 final size:41
Alignment explanation
Indices: 1251092--1251274 Score: 201
Period size: 41 Copynumber: 4.5 Consensus size: 41
1251082 AAATTCGCGT
* * *
1251092 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTACCTAAATCGCAATGCGATTACGTAAATCGCAA
*
1251133 TGCGA-TTACGTAAATCGCAATGCGATTACGTAAATCGCAA
1 TGCGATTTACCTAAATCGCAATGCGATTACGTAAATCGCAA
* ***
1251173 TGCGAATTAGGAAAATCGCAATGCGATTACGTAAATCGCAA
1 TGCGATTTACCTAAATCGCAATGCGATTACGTAAATCGCAA
* * * * * *
1251214 TGCAATTTTCCTAATTCACATTGCGATTTACGT-AATCGCAT
1 TGCGATTTACCTAAATCGCAATGCGA-TTACGTAAATCGCAA
*
1251255 TGCGATTTA-GTAAATCGCAA
1 TGCGATTTACCTAAATCGCAA
1251275 CGAGATTCTG
Statistics
Matches: 118, Mismatches: 22, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
40 43 0.36
41 69 0.58
42 6 0.05
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (41 bp):
TGCGATTTACCTAAATCGCAATGCGATTACGTAAATCGCAA
Found at i:1251251 original size:61 final size:60
Alignment explanation
Indices: 1251096--1251274 Score: 209
Period size: 61 Copynumber: 2.9 Consensus size: 60
1251086 TCGCGTTGCG
* *
1251096 ATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAATCGCAATGCG
1 ATTTTCCTAATTCGCAATGCGATTACGT-AATCGCAATGCGATTACGTAAATCGCAATGCA
* * * * *
1251157 A-TTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATTACGTAAATCGCAATGCA
1 ATTTTCCTAATTCGCAATGCG-ATTACG-TAATCGCAATGCGATTACGTAAATCGCAATGCA
* * *
1251218 ATTTTCCTAATTCACATTGCGATTTACGTAATCGCATTGCGATTTA-GTAAATCGCAA
1 ATTTTCCTAATTCGCAATGCGA-TTACGTAATCGCAATGCGA-TTACGTAAATCGCAA
1251275 CGAGATTCTG
Statistics
Matches: 98, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
60 16 0.16
61 61 0.62
62 21 0.21
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (60 bp):
ATTTTCCTAATTCGCAATGCGATTACGTAATCGCAATGCGATTACGTAAATCGCAATGCA
Found at i:1252936 original size:31 final size:31
Alignment explanation
Indices: 1252898--1253051 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
1252888 CCCGAAGGAC
* * *
1252898 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1252929 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1252960 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1252991 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1253022 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1253052 CCCTCGACCC
Statistics
Matches: 119, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1254216 original size:13 final size:15
Alignment explanation
Indices: 1254185--1254220 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
1254175 TTCACACGTG
1254185 GAGAAGAGAAAATGA
1 GAGAAGAGAAAATGA
1254200 -AGAAG-GAAAA-GA
1 GAGAAGAGAAAATGA
1254212 GAGAAGAGA
1 GAGAAGAGA
1254221 TTTTTCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.11
13 10 0.53
14 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (15 bp):
GAGAAGAGAAAATGA
Found at i:1254575 original size:24 final size:24
Alignment explanation
Indices: 1254548--1254601 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1254538 GTATTCAAAA
1254548 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1254572 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1254596 TTTGAT
1 TTTGAT
1254602 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1257178 original size:33 final size:33
Alignment explanation
Indices: 1257141--1257234 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
1257131 GGAAATGACT
* *
1257141 ATCGCAATGCGAAATAAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1257174 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1257207 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1257235 CAAATTTAGC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1257197 original size:19 final size:19
Alignment explanation
Indices: 1257121--1257232 Score: 73
Period size: 19 Copynumber: 6.4 Consensus size: 19
1257111 TTTAATGTCT
* **
1257121 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
*
1257141 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
1257160 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
1257174 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1257193 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
1257207 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1257226 ATCGCAA
1 ATCGCAA
1257233 CGCAAATTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
14 19 0.27
15 2 0.03
16 3 0.04
17 3 0.04
18 2 0.03
19 33 0.46
20 9 0.13
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1257342 original size:14 final size:14
Alignment explanation
Indices: 1257323--1257359 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1257313 CATCAATTAA
*
1257323 ACAAATTAACTTTT
1 ACAAATCAACTTTT
*
1257337 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1257351 ACAAATCAA
1 ACAAATCAA
1257360 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1259269 original size:19 final size:19
Alignment explanation
Indices: 1259229--1259355 Score: 102
Period size: 19 Copynumber: 6.8 Consensus size: 19
1259219 TCTGGAACTT
*
1259229 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
1259250 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
1259269 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGCGA-AATG
* *
1259289 AAAATCGCAATGCGAAACG
1 AAAATCGCAACGCGAAATG
1259308 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* * *
1259322 AGAATCGCAATGCGAAATT
1 AAAATCGCAACGCGAAATG
*
1259341 AAAATTGCAACGCGA
1 AAAATCGCAACGCGA
1259356 TTATAGTTTC
Statistics
Matches: 86, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 42 0.49
20 17 0.20
21 11 0.13
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1259298 original size:39 final size:39
Alignment explanation
Indices: 1259229--1259326 Score: 133
Period size: 39 Copynumber: 2.5 Consensus size: 39
1259219 TCTGGAACTT
* * ** *
1259229 AAAATCGCAACGTGAAAAATGACTATCGCAACGCGAAATG
1 AAAATCGCAACGAG-AGAATGAAAATCGCAACGCGAAACG
*
1259269 AAAATCGCAACGAGAGAATGAAAATCGCAATGCGAAACG
1 AAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACG
1259308 AAAATCGCAACGAGAGAAT
1 AAAATCGCAACGAGAGAAT
1259327 CGCAATGCGA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 39 0.75
40 13 0.25
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.12
Consensus pattern (39 bp):
AAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACG
Found at i:1259333 original size:33 final size:36
Alignment explanation
Indices: 1259253--1259352 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 36
1259243 AAAAATGACT
*
1259253 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAAC--GAGAATG-AA
*
1259292 ATCGCAATGCGAAACGAAAATCGCAACGAG-A-G-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAATGAA
* *
1259325 ATCGCAATGCGAAATTAAAATTGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1259353 CGATTATAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
33 26 0.46
35 1 0.02
36 1 0.02
37 3 0.05
39 25 0.45
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAATGAA
Found at i:1259374 original size:19 final size:19
Alignment explanation
Indices: 1259352--1259437 Score: 93
Period size: 20 Copynumber: 4.4 Consensus size: 19
1259342 AAATTGCAAC
*
1259352 GCGATTATAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
1259371 GCGATTTTTGGTTTCGCGTT
1 GCGA-TTTTAGTTTCGCGTT
*
1259391 GCGATTTTCGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
* *
1259410 ACGATTTTCA-TTCTCTCGTT
1 GCGATTTT-AGTT-TCGCGTT
1259430 GCGATTTT
1 GCGATTTT
1259438 CATTTCAACC
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
19 27 0.47
20 30 0.53
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1259386 original size:20 final size:20
Alignment explanation
Indices: 1259361--1259437 Score: 95
Period size: 19 Copynumber: 3.9 Consensus size: 20
1259351 CGCGATTATA
*
1259361 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTC
1259381 GTTTCGCGTTGCGA-TTTTC
1 GTTTCGCGTTGCGATTTTTC
*
1259400 GTTTCGCGTTACGA-TTTTC
1 GTTTCGCGTTGCGATTTTTC
* *
1259419 ATTCTCTCGTTGCGATTTT
1 GTT-TCGCGTTGCGATTTT
1259438 CATTTCAACC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 24 0.48
20 23 0.46
21 3 0.06
ACGTcount: A:0.08, C:0.19, G:0.23, T:0.49
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTC
Found at i:1259430 original size:39 final size:39
Alignment explanation
Indices: 1259352--1259443 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
1259342 AAATTGCAAC
* * * **
1259352 GCGATTATAGTTTCGCGTTGCGATTTTTGGTTTCGCGTT
1 GCGATTTTCGTTTCGCGTTACGATTTTTCATTTCGCGTT
*
1259391 GCGATTTTCGTTTCGCGTTACGA-TTTTCATTCTCTCGTT
1 GCGATTTTCGTTTCGCGTTACGATTTTTCATT-TCGCGTT
*
1259430 GCGATTTTCATTTC
1 GCGATTTTCGTTTC
1259444 AACCAAAAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 6 0.13
39 39 0.87
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.48
Consensus pattern (39 bp):
GCGATTTTCGTTTCGCGTTACGATTTTTCATTTCGCGTT
Found at i:1259438 original size:20 final size:19
Alignment explanation
Indices: 1259362--1259443 Score: 101
Period size: 20 Copynumber: 4.2 Consensus size: 19
1259352 GCGATTATAG
**
1259362 TTTCGCGTTGCGATTTTTGG
1 TTTCGCGTTGCGA-TTTTCA
*
1259382 TTTCGCGTTGCGATTTTCG
1 TTTCGCGTTGCGATTTTCA
*
1259401 TTTCGCGTTACGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
1259420 TTCTCTCGTTGCGATTTTCA
1 TT-TCGCGTTGCGATTTTCA
1259440 TTTC
1 TTTC
1259444 AACCAAAAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
19 26 0.46
20 30 0.54
ACGTcount: A:0.09, C:0.21, G:0.21, T:0.50
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1259645 original size:94 final size:94
Alignment explanation
Indices: 1259534--1259898 Score: 530
Period size: 94 Copynumber: 4.1 Consensus size: 94
1259524 ATGGATTGCA
* *
1259534 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1259598 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1259627 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1259692 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1259721 TTACTTTCAA-C------C---A-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1259775 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
1259804 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAT
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
1259864 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1259894 TTACT
1 TTACT
1259899 AAGCAATCTA
Statistics
Matches: 251, Mismatches: 7, Indels: 30
0.87 0.02 0.10
Matches are distributed among these distances:
82 5 0.02
83 74 0.29
84 1 0.00
87 1 0.00
89 1 0.00
90 40 0.16
92 1 0.00
93 5 0.02
94 123 0.49
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1259790 original size:83 final size:82
Alignment explanation
Indices: 1259651--1259824 Score: 330
Period size: 83 Copynumber: 2.1 Consensus size: 82
1259641 AAGACAAAAC
1259651 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1259716 CAAATTTACTTTCAACCA
66 CAAATTTAC-TTCAACCA
1259734 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
*
1259799 TAAATTTACTTCAACCA
66 CAAATTTACTTCAACCA
1259816 AAAGACAAA
1 AAAGACAAA
1259825 ACAAAAGACA
Statistics
Matches: 90, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 17 0.19
83 73 0.81
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (82 bp):
AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
CAAATTTACTTCAACCA
Found at i:1259853 original size:177 final size:173
Alignment explanation
Indices: 1259557--1259898 Score: 560
Period size: 177 Copynumber: 2.0 Consensus size: 173
1259547 AAGACAAAAC
*
1259557 AAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAACGAA
1 AAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAACGAA
*
1259622 CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAC
66 CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT----AATAA
1259687 ACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCA
127 ACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCA
* *
1259734 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAACGAA
*
1259799 TAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAATAAACA
66 CAAATTTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAATAAACA
* * *
1259863 TTTTAGCAGTATTGGCAGCAACCGAATAAATTTACT
130 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1259899 AAGCAATCTA
Statistics
Matches: 156, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
173 40 0.26
176 19 0.12
177 97 0.62
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (173 bp):
AAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAACGAA
CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAATAAACAG
TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCA
Found at i:1260286 original size:21 final size:21
Alignment explanation
Indices: 1260262--1260336 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
1260252 GTGACGGGAT
1260262 AGGTGATGGCTCTCGTTGTAG
1 AGGTGATGGCTCTCGTTGTAG
* ** *
1260283 AGGTGTATAG-TCGGGTTG-ACC
1 AGGTG-ATGGCTCTCGTTGTA-G
*
1260304 AGGTGATGGCTCT-G-GGT-G
1 AGGTGATGGCTCTCGTTGTAG
1260322 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
1260337 AAGTGGAGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
18 13 0.32
19 2 0.05
20 5 0.12
21 18 0.44
22 3 0.07
ACGTcount: A:0.15, C:0.15, G:0.41, T:0.29
Consensus pattern (21 bp):
AGGTGATGGCTCTCGTTGTAG
Found at i:1261618 original size:20 final size:20
Alignment explanation
Indices: 1261593--1261655 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
1261583 TTTTGGTTGA
1261593 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
* *
1261613 AATGAAAATCACAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
1261632 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
1261653 AAT
1 AAT
1261656 TGCAACGCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1261715 original size:14 final size:14
Alignment explanation
Indices: 1261696--1261752 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1261686 TTTGGTTTCG
1261696 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
1261710 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
*
1261729 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
1261743 CGTTGCGATT
1 CGTTGCGATT
1261753 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:1261728 original size:33 final size:33
Alignment explanation
Indices: 1261680--1261760 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1261670 AAAATCGCAA
**
1261680 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
1261713 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
1261746 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1261761 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:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:1261763 original size:21 final size:20
Alignment explanation
Indices: 1261744--1261815 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
1261734 CGATTCTCTC
1261744 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
1261764 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
1261785 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
1261805 GTTGCGATTTT
1 GTTGCGATTTT
1261816 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:1262399 original size:21 final size:21
Alignment explanation
Indices: 1262375--1262420 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1262365 GATTCGCATT
1262375 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1262396 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1262417 GCGA
1 GCGA
1262421 TAGTTAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1263819 original size:43 final size:43
Alignment explanation
Indices: 1263754--1263835 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
1263744 GAATCTGTAA
*
1263754 GAATTAGAATTCAATTCTATATTCTGTTTGGTTGGCAGAAATG
1 GAATTAGAATTCAATTCTATATTCTGTTTGGTTCGCAGAAATG
1263797 GAATTAGAA-TCTAATT-TCATATTCTGTTTGGTTCGCAGA
1 GAATTAGAATTC-AATTCT-ATATTCTGTTTGGTTCGCAGA
1263836 CATGTCAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (43 bp):
GAATTAGAATTCAATTCTATATTCTGTTTGGTTCGCAGAAATG
Found at i:1271726 original size:3 final size:3
Alignment explanation
Indices: 1271718--1271743 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1271708 TACTTTTGAT
1271718 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1271744 TTACTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1271767 original size:20 final size:20
Alignment explanation
Indices: 1271742--1271779 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1271732 ATTATTATTA
1271742 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
1271762 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
1271780 TTTACTCATT
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:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Done.