Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008124.1 Hibiscus syriacus cultivar Beakdansim tig00110678_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: 3296903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 19
Found at i:1597329 original size:20 final size:19
Alignment explanation
Indices: 1597301--1597355 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1597291 CAATCATCTT
*
1597301 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
1597321 AATGACTATCGCAAAGCGA
1 AATGACTATCGCAACGCGA
**
1597340 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
1597356 AGGGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:1597343 original size:19 final size:20
Alignment explanation
Indices: 1597301--1597344 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1597291 CAATCATCTT
* *
1597301 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAAAGCGGA
1597321 AATGACTATCGCAAAGC-GA
1 AATGACTATCGCAAAGCGGA
1597340 AATGA
1 AATGA
1597345 AAATCGCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAAAGCGGA
Found at i:1597350 original size:19 final size:19
Alignment explanation
Indices: 1597308--1597391 Score: 70
Period size: 19 Copynumber: 4.6 Consensus size: 19
1597298 CTTAATGTCT
* **
1597308 ATCGCAACGCGGAAATGACT
1 ATCGCAAAGC-GAAATGAAA
1597328 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
**
1597347 ATCGC-AA-CG--A-GGGA
1 ATCGCAAAGCGAAATGAAA
1597361 ATCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
1597380 ATCGCAATGCGA
1 ATCGCAAAGCGA
1597392 TTTTAGTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
14 7 0.14
15 3 0.06
16 2 0.04
17 2 0.04
18 3 0.06
19 25 0.49
20 9 0.18
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:1597435 original size:33 final size:33
Alignment explanation
Indices: 1597387--1597469 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
1597377 AAAATCGCAA
* *
1597387 TGCGATTTT-AGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTCA-TTTCGCGTTGCGATTCTCTCGT
*
1597420 TGCGATTTTCATTTCGAGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1597453 TGCGATTTTCATTTCGC
1 TGCGATTTTCATTTCGC
1597470 ATTGTGATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 44 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1597442 original size:19 final size:18
Alignment explanation
Indices: 1597418--1597468 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 18
1597408 CGATTTTGTC
1597418 GTTGCGATTTTCATTTCG
1 GTTGCGATTTTCATTTCG
*
1597436 AGTTGCGA--TTC-TCTC-
1 -GTTGCGATTTTCATTTCG
1597451 GTTGCGATTTTCATTTCG
1 GTTGCGATTTTCATTTCG
1597469 CATTGTGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
14 7 0.27
16 6 0.23
17 6 0.23
19 7 0.27
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.47
Consensus pattern (18 bp):
GTTGCGATTTTCATTTCG
Found at i:1597605 original size:14 final size:14
Alignment explanation
Indices: 1597584--1597620 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1597574 CATCAATTAA
1597584 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
1597598 ATAAATCATCTTTT
1 ACAAATCAACTTTT
1597612 ACAAATCAA
1 ACAAATCAA
1597621 TTAAACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1599045 original size:42 final size:42
Alignment explanation
Indices: 1598996--1599079 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1598986 CGATGACAGT
* * *
1598996 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1599038 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
1599080 TGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1599549 original size:33 final size:33
Alignment explanation
Indices: 1599507--1599593 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
1599497 CTATCGCAAT
** * *
1599507 GCGAAATGAAAATCTTAACGAGAGAATCACAAC
1 GCGAAATGAAAATCGCAACGACAAAATCACAAC
*
1599540 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
1 GCGAAATGAAAATCGCAACGACAAAATCACAAC
**
1599573 GCGAAACCAAAAATCGCAACG
1 GCGAAA-TGAAAATCGCAACG
1599594 CGATTATAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 34 0.74
34 12 0.26
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.10
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGACAAAATCACAAC
Found at i:1599640 original size:33 final size:36
Alignment explanation
Indices: 1599603--1599691 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 36
1599593 GCGATTATAG
1599603 TTTCGCGTTGCGATTTT-G-T-CATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCGTTCCATTGCGATTTTCA
*
1599636 TTTCGCGTTGCGATTTTCGTTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCG-TTC-CATTGCGATTTTCA
*
1599674 TTCTCTCGTTGCGATTTT
1 TT-TCGCGTTGCGATTTT
1599692 TATTTCAACC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
33 17 0.35
34 1 0.02
36 1 0.02
38 15 0.31
39 14 0.29
ACGTcount: A:0.09, C:0.20, G:0.21, T:0.49
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCGTTCCATTGCGATTTTCA
Found at i:1599685 original size:20 final size:19
Alignment explanation
Indices: 1599624--1599697 Score: 112
Period size: 19 Copynumber: 3.8 Consensus size: 19
1599614 GATTTTGTCA
1599624 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
1599643 TTGCGATTTTCGTTTCGCG
1 TTGCGATTTTCATTTCGCG
*
1599662 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TCGCG
*
1599682 TTGCGATTTTTATTTC
1 TTGCGATTTTCATTTC
1599698 AACCAAAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 33 0.66
20 17 0.34
ACGTcount: A:0.09, C:0.20, G:0.19, T:0.51
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:1599932 original size:93 final size:93
Alignment explanation
Indices: 1599786--1600061 Score: 392
Period size: 90 Copynumber: 3.1 Consensus size: 93
1599776 ATGGATTGCA
* *
1599786 TTACTTCAACCAAAAGACAAAAC-AAGACAAATACTAACTTCAGAGTATTAAAGAATACACAG-T
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
1599849 TAGCAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGCAAACGAACAAAT
1599877 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1599942 TTAGCAGAATTGGCAGC-AAC---CGAAT
65 TTAGCAGAATTGGCAGCAAACGAACAAAT
* *
1599967 ATACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
1600028 TTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAAACGAACAAAT
1600057 TTACT
1 TTACT
1600062 AAGCAATCTA
Statistics
Matches: 167, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
86 25 0.15
87 2 0.01
89 19 0.11
90 41 0.25
91 4 0.02
92 19 0.11
93 40 0.24
94 17 0.10
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAAACGAACAAAT
Found at i:1600013 original size:90 final size:89
Alignment explanation
Indices: 1599787--1600053 Score: 384
Period size: 93 Copynumber: 3.0 Consensus size: 89
1599777 TGGATTGCAT
* *
1599787 TACTTCAACCAAAAGACAAAAC-AAGACAAATACTAACTTCAGAGTATTAAAGAATACACAG-TT
1 TACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTT
* *
1599850 AGCAGAATTGGCAGCAAACGAACAAATT
66 AGCAGAATTGGCAGC-AAC---CGAATA
1599878 TACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
1 TAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
1599943 TAGCAGAATTGGCAGCAACCGAATA
65 TAGCAGAATTGGCAGCAACCGAATA
*
1599968 TACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTT
1 TACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
1600029 TAGCAGTATTGGCAGCAACCGAATA
65 TAGCAGAATTGGCAGCAACCGAATA
1600054 AATTTACTAA
Statistics
Matches: 166, Mismatches: 6, Indels: 13
0.90 0.03 0.07
Matches are distributed among these distances:
86 34 0.20
89 19 0.11
90 34 0.20
91 3 0.02
92 19 0.11
93 40 0.24
94 17 0.10
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.20
Consensus pattern (89 bp):
TACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTT
AGCAGAATTGGCAGCAACCGAATA
Found at i:1601765 original size:20 final size:20
Alignment explanation
Indices: 1601740--1601799 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1601730 TGGTTGAAAT
1601740 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGAGAGAATG
* *
1601760 AAAATCGCAACGCGGAAAATG
1 AAAATCGCAACG-AGAGAATG
** *
1601781 ACTATCACAACGAGAGAAT
1 AAAATCGCAACGAGAGAAT
1601800 CGCAACACTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGAGAGAATG
Found at i:1601801 original size:35 final size:33
Alignment explanation
Indices: 1601775--1601837 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1601765 CGCAACGCGG
**
1601775 AAAATGACTATCACAACGAGAGAATCGCAACAC
1 AAAATGAAAATCACAACGAGAGAATCGCAACAC
* *
1601808 TAAATGAAAATCGCAACGAGAGAATCGCAA
1 AAAATGAAAATCACAACGAGAGAATCGCAA
1601838 TGCGATTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (33 bp):
AAAATGAAAATCACAACGAGAGAATCGCAACAC
Found at i:1601860 original size:19 final size:20
Alignment explanation
Indices: 1601838--1601889 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1601828 AGAATCGCAA
1601838 TGCGATTTTCATTT-CGCGT
1 TGCGATTTTCATTTCCGCGT
**
1601857 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTTCCGCGT
1601877 TGCGATTTTCATT
1 TGCGATTTTCATT
1601890 CTCGAAACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (20 bp):
TGCGATTTTCATTTCCGCGT
Found at i:1602457 original size:20 final size:20
Alignment explanation
Indices: 1602434--1602527 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
1602424 CGATAGTCAG
1602434 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
1602454 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
1602474 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
1602495 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1602515 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1602528 ATTATGAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 46 0.72
21 18 0.28
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1602483 original size:41 final size:40
Alignment explanation
Indices: 1602434--1602527 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
1602424 CGATAGTCAG
* *
1602434 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
1602474 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
1602515 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1602528 ATTATGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:1602540 original size:41 final size:41
Alignment explanation
Indices: 1602434--1602542 Score: 123
Period size: 41 Copynumber: 2.7 Consensus size: 41
1602424 CGATAGTCAG
* * *
1602434 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTATGTAATCGCATTGCGATTTACCTA
* *
1602475 ATTCGCATTGCGATTTACT-TAATCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTA-TGTAATCGCATTGCGATTTACCTA
* *
1602515 ATTCGCATTGCGAATTATGAAAATCGCA
1 ATTCGCATTGCGATTTATG-TAATCGCA
1602543 ACGCGAATAC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
39 1 0.02
40 16 0.28
41 40 0.70
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (41 bp):
ATTCGCATTGCGATTTATGTAATCGCATTGCGATTTACCTA
Found at i:1602560 original size:20 final size:19
Alignment explanation
Indices: 1602535--1602611 Score: 64
Period size: 22 Copynumber: 3.7 Consensus size: 19
1602525 CGAATTATGA
*
1602535 AAATCGCAACGCGAATACGT
1 AAATCGCAACGCGAATA-GG
*
1602555 AAATCGCAATGCGAATTTAGG
1 AAATCGCAACGCGAA--TAGG
*
1602576 AGAATCGCAACGCGAATTTGGG
1 A-AATCGCAACGCGAA--TAGG
*
1602598 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1602612 TAGTCAGAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.29
21 14 0.29
22 21 0.43
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (19 bp):
AAATCGCAACGCGAATAGG
Found at i:1602560 original size:61 final size:61
Alignment explanation
Indices: 1602436--1602573 Score: 145
Period size: 61 Copynumber: 2.2 Consensus size: 61
1602426 ATAGTCAGAT
* * * ** * *
1602436 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAA
* *
1602497 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTAT-GAAAATCGCAACGCGA-ATACGTAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCG-ATTATCCAAAATCGCAACGCGATATAC-TAAA
*
1602558 TCGCAATGCGAATTTA
1 TCGCATTGCG-ATTTA
1602574 GGAGAATCGC
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
60 3 0.05
61 51 0.81
62 9 0.14
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (61 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAA
Found at i:1602583 original size:22 final size:22
Alignment explanation
Indices: 1602556--1602631 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
1602546 CGAATACGTA
1602556 AATCGCAATGCGAATTTAGGAG
1 AATCGCAATGCGAATTTAGGAG
* *
1602578 AATCGCAACGCGAATTTGGGA-
1 AATCGCAATGCGAATTTAGGAG
*
1602599 AATCGCAATGCG-A--TAGTCAG
1 AATCGCAATGCGAATTTAG-GAG
1602619 AATCGCAATGCGA
1 AATCGCAATGCGA
1602632 TAATCAGAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 13 0.28
21 11 0.24
22 19 0.41
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (22 bp):
AATCGCAATGCGAATTTAGGAG
Found at i:1602590 original size:42 final size:42
Alignment explanation
Indices: 1602517--1602611 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
1602507 ATTTACGTAT
* * *
1602517 TCGCATTGCGAATTATGAAAATCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTAGGAAAATCGCAACGCGAATTACGGAAA
* **
1602558 TCGCAATGCGAATTTAGGAGAATCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAA-TTAGGAAAATCGCAACGCGAATTACGGAAA
1602601 TCGCAATGCGA
1 TCGCAATGCGA
1602612 TAGTCAGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 11 0.24
42 19 0.41
43 16 0.35
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (42 bp):
TCGCAATGCGAATTAGGAAAATCGCAACGCGAATTACGGAAA
Found at i:1602651 original size:20 final size:20
Alignment explanation
Indices: 1602599--1602644 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1602589 GAATTTGGGA
*
1602599 AATCGCAATGCGATAGTCAG
1 AATCGCAATGCGATAATCAG
1602619 AATCGCAATGCGATAATCAG
1 AATCGCAATGCGATAATCAG
1602639 AATCGC
1 AATCGC
1602645 GTTGCGAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (20 bp):
AATCGCAATGCGATAATCAG
Found at i:1607919 original size:23 final size:23
Alignment explanation
Indices: 1607889--1607940 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1607879 ACCTCTTGCT
1607889 TTTAACCACCTAACCAAATATAG
1 TTTAACCACCTAACCAAATATAG
*
1607912 TTTAACCACCTAACCATATATAG
1 TTTAACCACCTAACCAAATATAG
1607935 TTTAAC
1 TTTAAC
1607941 ATTCACCCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.40, C:0.25, G:0.04, T:0.31
Consensus pattern (23 bp):
TTTAACCACCTAACCAAATATAG
Found at i:1611873 original size:26 final size:26
Alignment explanation
Indices: 1611837--1611888 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1611827 CATACAATTA
*
1611837 AGATATCATTTTATTTGGTCTCTTCT
1 AGATATCATTTTATTCGGTCTCTTCT
1611863 AGATATCATTTTATTCGGTCTCTTCT
1 AGATATCATTTTATTCGGTCTCTTCT
1611889 GGAAGATGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (26 bp):
AGATATCATTTTATTCGGTCTCTTCT
Found at i:1612787 original size:7 final size:7
Alignment explanation
Indices: 1612777--1612806 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1612767 AAAATATATG
1612777 ATATAAT
1 ATATAAT
1612784 ATATATAT
1 ATATA-AT
1612792 ATATAAT
1 ATATAAT
1612799 ATATAAT
1 ATATAAT
1612806 A
1 A
1612807 ACGAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATAAT
Found at i:1612797 original size:15 final size:16
Alignment explanation
Indices: 1612770--1612803 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1612760 TAAACAAAAA
1612770 ATATATGATATAATAT
1 ATATATGATATAATAT
1612786 ATATAT-ATATAATAT
1 ATATATGATATAATAT
1612801 ATA
1 ATA
1612804 ATAACGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
ATATATGATATAATAT
Found at i:1612828 original size:21 final size:22
Alignment explanation
Indices: 1612802--1612843 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1612792 ATATAATATA
*
1612802 TAATAACG-AAAAAAAATAATT
1 TAATAAAGTAAAAAAAATAATT
*
1612823 TAATAAAGTAAAAATAATAAT
1 TAATAAAGTAAAAAAAATAAT
1612844 GTACTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (22 bp):
TAATAAAGTAAAAAAAATAATT
Found at i:1613558 original size:37 final size:37
Alignment explanation
Indices: 1613508--1613599 Score: 107
Period size: 36 Copynumber: 2.5 Consensus size: 37
1613498 GTGCTTGTGG
*
1613508 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAAACATAGCAAAATTCT
* * * **
1613545 ATCCTATTTTTAGGAG-TTGAATCCTAGCGGAATTCT
1 ATCCTATTTTTAGGAGTTTAAAACATAGCAAAATTCT
1613581 ATCCTATTTTT-GAGAGTTT
1 ATCCTATTTTTAG-GAGTTT
1613600 GAATCCTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 1 0.02
36 29 0.62
37 17 0.36
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAAACATAGCAAAATTCT
Found at i:1613586 original size:36 final size:37
Alignment explanation
Indices: 1613539--1613608 Score: 117
Period size: 36 Copynumber: 1.9 Consensus size: 37
1613529 AACATAGCAA
1613539 AATTCTATCCTATTTTT-AGGAG-TTGAATCCTAGCGG
1 AATTCTATCCTATTTTTGA-GAGTTTGAATCCTAGCGG
1613575 AATTCTATCCTATTTTTGAGAGTTTGAATCCTAG
1 AATTCTATCCTATTTTTGAGAGTTTGAATCCTAG
1613609 TAGGACGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
36 20 0.62
37 12 0.38
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (37 bp):
AATTCTATCCTATTTTTGAGAGTTTGAATCCTAGCGG
Found at i:1614313 original size:109 final size:109
Alignment explanation
Indices: 1614199--1614564 Score: 483
Period size: 109 Copynumber: 3.4 Consensus size: 109
1614189 AAAAATATTT
* *
1614199 GTTGACAACCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GACACGATATC
1 GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAG-CACGATATC
*
1614263 CTCCGTCGTGGAGTTGAAATCGCGGATGAAACTGAAAAGTTGTTC
65 CTCCGTCGTGGAGTTGAAATCGCGGATGAAATTGAAAAGTTGTTC
* * *
1614308 ATTGACAACCAGTCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCC
1 GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCC
** * ** *
1614373 TCCGTCGTGGAGTTGAAATCG-GTTCTGGAATTGGGAAGTTTTTC
66 TCCGTCGTGGAGTTGAAATCGCG-GATGAAATTGAAAAGTTGTTC
* * *
1614417 GTTGACAACCAGCCGTCTCTTCTTTGTGAAGTTGAACTTATGTTGTCTCGGGTAGCACGATATCC
1 GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCC
*
1614482 TCCGTCGTGGAGTTGAAAT--CGGTTCCGAAATTGGAAAA-TTGTT-
66 TCCGTCGTGGAGTTGAAATCGCGGAT--GAAATT-GAAAAGTTGTTC
* *
1614525 GTTGGCAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTG
1 GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
1614565 ACTCTAGCTA
Statistics
Matches: 222, Mismatches: 29, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
107 1 0.00
108 37 0.17
109 180 0.81
110 4 0.02
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (109 bp):
GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCC
TCCGTCGTGGAGTTGAAATCGCGGATGAAATTGAAAAGTTGTTC
Found at i:1614424 original size:218 final size:213
Alignment explanation
Indices: 1614121--1614564 Score: 547
Period size: 218 Copynumber: 2.1 Consensus size: 213
1614111 AACCGGGAAA
* *
1614121 AAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAAT
1 AAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTCCGCTGTGAAGTTGAAATCGGCTCTGAAAT
* *
1614186 TTGAAAAATATTTGTTGACAACCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAG
66 TTGAAAAATATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTATGTTGTCTCGAG
1614251 T-GACACGATATCCTCCGTCGTGGAGTTGAAATCGCGGAT-GAAACT-GAAAAGTTGTTCATTGA
131 TAG-CACGATATCCTCCGTCGTGGAGTTGAAAT--CGGATCGAAACTGGAAAA-TTGTT-ATTGA
**
1614313 CAACCAGTCGTCCCTTCGTTATG
191 CAACCAACCGTCCCTTCGTTATG
* * * *
1614336 AAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCG-TCGTGGAGTTGAAATCGGTTCTG
1 AAGTTGAACTTGTGTTGTCTCGAGT--C-CAATATCCTCCGCT-GTGAAGTTGAAATCGGCTCTG
* ** * * * *
1614400 GAA-TTGGGAAGTTTTTCGTTGACAACCAGCCGTCTCTTCTTTGTGAAGTTGAACTTATGTTGTC
62 AAATTTGAAAAATATTT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTATGTTGTC
* * * *
1614464 TCGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATCGGTTCCGAAATTGGAAAATTGTTGTTG
126 TCGAGTAGCACGATATCCTCCGTCGTGGAGTTGAAATCGGAT-CGAAACTGGAAAATTGTTATTG
* *
1614529 GCAACCAACCGTCCCTTCGTTGTG
190 ACAACCAACCGTCCCTTCGTTATG
1614553 AAGTTGAACTTG
1 AAGTTGAACTTG
1614565 ACTCTAGCTA
Statistics
Matches: 197, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
215 24 0.12
216 4 0.02
217 46 0.23
218 117 0.59
219 6 0.03
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (213 bp):
AAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTCCGCTGTGAAGTTGAAATCGGCTCTGAAAT
TTGAAAAATATTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTATGTTGTCTCGAG
TAGCACGATATCCTCCGTCGTGGAGTTGAAATCGGATCGAAACTGGAAAATTGTTATTGACAACC
AACCGTCCCTTCGTTATG
Found at i:1615144 original size:104 final size:102
Alignment explanation
Indices: 1614960--1615209 Score: 247
Period size: 104 Copynumber: 2.4 Consensus size: 102
1614950 ATTTTGTTTT
* * * * * * *
1614960 AAGA-AAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGA
1 AAGAGAAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGAGAAACTGTCTCACAGAGAGACGA
1615024 AATTAGTTCCAAGGAAAACATATTCAAAGATGATGCTTC
65 AATTAGTTCCAAGG-AAACATATTCAAAGATGATGCTTC
* *
1615063 AAGAGAAAACTGTCTCAAGGGAGACAAAATTTTTTTTCAAGAGAAACTGTCTCA-AGAGAGACGA
1 AAGAGAAAACTGTCTCAAGAGAGACAAAA-TTTATTTCAAGAGAAACTGTCTCACAGAGAGACGA
* ** * * * * *
1615127 AATTCA-TTTCAAGGGAAATGTTTTCAATGTTTATGTTTC
65 AATT-AGTTCCAA-GGAAACATATTCAAAGATGATGCTTC
* * *
1615166 AAGAG-AAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAA
1 AAGAGAAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAA
1615210 TGTTTTCAAT
Statistics
Matches: 121, Mismatches: 22, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
101 14 0.12
102 20 0.17
103 42 0.35
104 43 0.36
105 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (102 bp):
AAGAGAAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCACAGAGAGACGAA
ATTAGTTCCAAGGAAACATATTCAAAGATGATGCTTC
Found at i:1615201 original size:65 final size:65
Alignment explanation
Indices: 1615097--1615275 Score: 286
Period size: 65 Copynumber: 2.7 Consensus size: 65
1615087 CAAAATTTTT
* *
1615097 TTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATA
*
1615162 TTTCAAGAGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATA
* * * *
1615227 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCGAGGGAAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TTTATTTCAAGGGAAA
1615276 CTATCTCAAG
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 91 0.87
66 14 0.13
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (65 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATA
Found at i:1615266 original size:102 final size:102
Alignment explanation
Indices: 1615160--1615616 Score: 738
Period size: 102 Copynumber: 4.5 Consensus size: 102
1615150 TCAATGTTTA
* * *
1615160 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
1615225 TATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
1615262 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
1615327 TGTTTCAAGAGAAACTGTATCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
1615364 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
1615429 TGTTTCAAGAGAAACTGTCTCAATGGAGACAGAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
1615466 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGTGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
1615531 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAAATT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAG-ACAAAATTT
* * **
1615569 TGTTTCAAGGGAAAC--TGTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
1615617 CTGTCTCAAG
Statistics
Matches: 330, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
101 27 0.08
102 282 0.85
103 21 0.06
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:1615285 original size:37 final size:37
Alignment explanation
Indices: 1615227--1615634 Score: 168
Period size: 37 Copynumber: 11.8 Consensus size: 37
1615217 AATGTTTATA
* * *
1615227 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTTG
* **
1615264 TTTCGAGGGAAACTATCTCAAGAGAGACAAAA-TTCA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTTG
* * *
1615300 TTTCAAGGGAAA-TGTTTTC-A-A-TG------TTTATG
1 TTTCAAGGGAAACT-ATCTCAAGAGAGACAAAATTT-TG
* * * *
1615329 TTTCAAGAGAAACTGTATCAAGGGAGACAAAATTTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTTG
**
1615366 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTCA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTTG
* * **
1615402 TTTCAAGGGAAA-TGTTTC--------CAATGTTTATG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTT-TG
* * *
1615431 TTTCAAGAGAAACTGTCTCAATG-GAGACAGAATTTTG
1 TTTCAAGGGAAACTATCTCAA-GAGAGACAAAATTTTG
* **
1615468 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CTCA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTTG
* * * *
1615504 TTTCAAGTGAAA-TGTTTTC-A-A-TG------TTTATG
1 TTTCAAGGGAAACT-ATCTCAAGAGAGACAAAATTT-TG
* * * * *
1615533 TTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAAATTTG
1 TTTCAAGGGAAACTATCTCAAGAGAG-ACAAAATTTTG
* *
1615571 TTTCAAGGGAAAC--TGTCAAGAGAGAC-AAAGTTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTTG
*
1615605 TTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAA
1615635 TGGTGATATC
Statistics
Matches: 270, Mismatches: 59, Indels: 84
0.65 0.14 0.20
Matches are distributed among these distances:
27 3 0.01
28 5 0.02
29 39 0.14
30 9 0.03
32 2 0.01
33 2 0.01
34 22 0.08
35 9 0.03
36 67 0.25
37 88 0.33
38 22 0.08
39 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (37 bp):
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTTG
Found at i:1615610 original size:34 final size:35
Alignment explanation
Indices: 1615531--1615634 Score: 129
Period size: 34 Copynumber: 2.9 Consensus size: 35
1615521 TCAATGTTTA
* * *
1615531 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAAATT
1 TGTTTCAAGGGAAACTG-CTCAA--GAGAGACAAAATT
*
1615569 TGTTTCAAGGGAAACTG-TCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGCTCAAGAGAGACAAAATT
1615603 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTG-CTCAAGAGAGACAA
1615635 TGGTGATATC
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
34 27 0.45
36 17 0.28
38 16 0.27
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.23
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTGCTCAAGAGAGACAAAATT
Found at i:1616425 original size:22 final size:22
Alignment explanation
Indices: 1616400--1616449 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
1616390 TTGTGTTGGT
1616400 CAAAGGTTTGGCATTTGATGCG
1 CAAAGGTTTGGCATTTGATGCG
* *
1616422 CAAAGGTTTGGTATTTGATGCT
1 CAAAGGTTTGGCATTTGATGCG
1616444 CAAAGG
1 CAAAGG
1616450 ATTGATGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.32
Consensus pattern (22 bp):
CAAAGGTTTGGCATTTGATGCG
Found at i:1617051 original size:20 final size:20
Alignment explanation
Indices: 1617026--1617085 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
1617016 TTTTTGTCCC
*
1617026 CTTTTTTATTTTTGTTCTTT
1 CTTTTTTATTCTTGTTCTTT
* *
1617046 CTTTTTTGTTCTTGTTTTTT
1 CTTTTTTATTCTTGTTCTTT
**
1617066 CCTTTTTGCTTCTT-TTCTTT
1 -CTTTTTTATTCTTGTTCTTT
1617086 TTTCTTTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 22 0.67
21 11 0.33
ACGTcount: A:0.02, C:0.15, G:0.07, T:0.77
Consensus pattern (20 bp):
CTTTTTTATTCTTGTTCTTT
Found at i:1618950 original size:146 final size:145
Alignment explanation
Indices: 1618756--1619063 Score: 541
Period size: 148 Copynumber: 2.1 Consensus size: 145
1618746 CATAATTGCA
*
1618756 CCGAAGTGCCGCGTAGAATTCACCTAGTGCCATATATAATGTTCCATAAGGACCACATATTATTC
1 CCGAAG-GACGCGTAGAATTCACCTAGTGCCATATATAATGTTCCATAAGGACCACATATTATTC
1618821 CTTAAGAATCA-TACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAA
65 CTTAAGAATCAGTACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAA
1618885 AGAATATACATATGTC
130 AGAATATACATATGTC
1618901 CCGAAGGACGCGTAGAATTGCACCGTAGTGCCATATAATAATG-TCCATAAGGACCACATATTAT
1 CCGAAGGACGCGTAGAATT-CACC-TAGTGCCATAT-ATAATGTTCCATAAGGACCACATATTAT
1618965 TCCTTAAGAATCATGTACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
63 TCCTTAAGAATCA-GTACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
1619030 CAAAGAATATACATATGTC
127 CAAAGAATATACATATGTC
1619049 CCGAAGGAC-CGTAGA
1 CCGAAGGACGCGTAGA
1619064 CCCTCGACTC
Statistics
Matches: 157, Mismatches: 1, Indels: 8
0.95 0.01 0.05
Matches are distributed among these distances:
144 12 0.08
145 10 0.06
146 45 0.29
147 12 0.08
148 78 0.50
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (145 bp):
CCGAAGGACGCGTAGAATTCACCTAGTGCCATATATAATGTTCCATAAGGACCACATATTATTCC
TTAAGAATCAGTACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAA
GAATATACATATGTC
Found at i:1620495 original size:21 final size:21
Alignment explanation
Indices: 1620456--1620495 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1620446 TGAGGCAATC
*
1620456 ATTAGATACCTACATCTTATA
1 ATTAGATACCTACAACTTATA
1620477 ATTAGATA-CTAGCAACTTA
1 ATTAGATACCTA-CAACTTA
1620496 AACGAACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (21 bp):
ATTAGATACCTACAACTTATA
Found at i:1623895 original size:23 final size:23
Alignment explanation
Indices: 1623869--1623913 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1623859 CACCACAGCT
*
1623869 CGTATAATTGCACCGA-AGTGCCG
1 CGTAGAATTGCACC-ATAGTGCCG
1623892 CGTAGAATTGCACCATAGTGCC
1 CGTAGAATTGCACCATAGTGCC
1623914 ATATAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCATAGTGCCG
Found at i:1624073 original size:149 final size:149
Alignment explanation
Indices: 1623881--1624195 Score: 587
Period size: 149 Copynumber: 2.1 Consensus size: 149
1623871 TATAATTGCA
1623881 CCGAAGTG-CCGCGTAGAATTGCACCATAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCATAGTGCCATATAATAATGTCCATAAGGACCACATATTA
*
1623945 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACAAATGTT
1624010 CCAAAGAATATACATATATC
130 CCAAAGAATATACATATATC
*
1624030 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCATAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1624095 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACAAATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACAAATGTTC
*
1624160 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
1624179 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1624196 CCCTCGACTC
Statistics
Matches: 162, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 161 0.99
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCATAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACAAATGTTC
CAAAGAATATACATATATC
Found at i:1625643 original size:21 final size:21
Alignment explanation
Indices: 1625604--1625643 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1625594 TGAGGCAATC
*
1625604 ATTAGATACCTACACCTTATA
1 ATTAGATACCTACAACTTATA
1625625 ATTAGATA-CTAGCAACTTA
1 ATTAGATACCTA-CAACTTA
1625644 AACGAACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (21 bp):
ATTAGATACCTACAACTTATA
Found at i:1625771 original size:21 final size:21
Alignment explanation
Indices: 1625747--1625791 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1625737 TTTTGTTCGT
* *
1625747 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1625768 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1625789 TTG
1 TTG
1625792 CCTAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1628545 original size:15 final size:17
Alignment explanation
Indices: 1628507--1628547 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1628497 ATAAGAGTAA
1628507 ATGAAATAAAGAAAATAG
1 ATGAAA-AAAGAAAATAG
*
1628525 AAGAAAAAA-AAAAT-G
1 ATGAAAAAAGAAAATAG
1628540 ATGAAAAA
1 ATGAAAAA
1628548 CTAAAAGAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 8 0.38
16 5 0.24
17 3 0.14
18 5 0.24
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (17 bp):
ATGAAAAAAGAAAATAG
Found at i:1628847 original size:15 final size:16
Alignment explanation
Indices: 1628827--1628863 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1628817 AAAAATAATT
1628827 TAATAAAGTAA-ATAA
1 TAATAAAGTAATATAA
*
1628842 TAATAATGTAATATAA
1 TAATAAAGTAATATAA
1628858 T-ATAAA
1 TAATAAA
1628864 TACATGAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAATATAA
Found at i:1629061 original size:2 final size:2
Alignment explanation
Indices: 1629049--1629080 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1629039 ATATAATAGT
*
1629049 TA TA AA 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
1629081 ACTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1630729 original size:20 final size:21
Alignment explanation
Indices: 1630700--1630772 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 21
1630690 CGTTGGAGCC
1630700 AAAGTATCGAAACT-TTAAGG
1 AAAGTATCGAAACTCTTAAGG
*
1630720 AAAGTTTCGAAACTCTTAA-G
1 AAAGTATCGAAACTCTTAAGG
* * * *
1630740 ATAGTTTCAAAACTCTT--GA
1 AAAGTATCGAAACTCTTAAGG
1630759 AAAGTATCGAAACT
1 AAAGTATCGAAACT
1630773 TTTTGGGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 11 0.25
20 29 0.66
21 4 0.09
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (21 bp):
AAAGTATCGAAACTCTTAAGG
Found at i:1631400 original size:26 final size:23
Alignment explanation
Indices: 1631371--1631426 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 23
1631361 TTTAAAAAAG
*
1631371 TTTAAATAAGAATAAAATATATATCT
1 TTTAAATAA-AATAAAA-AAATAT-T
*
1631397 TTTAATTAAAATAAAAAAATATT
1 TTTAAATAAAATAAAAAAATATT
1631420 TTTAAAT
1 TTTAAAT
1631427 TAAGTTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 7 0.26
24 5 0.19
25 7 0.26
26 8 0.30
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TTTAAATAAAATAAAAAAATATT
Found at i:1631427 original size:24 final size:24
Alignment explanation
Indices: 1631371--1631487 Score: 87
Period size: 24 Copynumber: 4.6 Consensus size: 24
1631361 TTTAAAAAAG
1631371 TTTAAA-TAAGAATAAAATATATATCT
1 TTTAAATTAA-AATAAAA-ATATAT-T
*
1631397 TTT-AATTAAAATAAAAAAATATT
1 TTTAAATTAAAATAAAAATATATT
1631420 TTTAAATTAAGTTAATAATAAATTATATT
1 TTTAAATTAA---AATAA-AAA-TATATT
* * *
1631449 TAATAAGTTAATATAAAAATAT-TT
1 T-TTAAATTAAAATAAAAATATATT
1631473 TTTAAAGTTAAAATA
1 TTTAAA-TTAAAATA
1631488 TTATGAATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 20
0.73 0.08 0.20
Matches are distributed among these distances:
23 7 0.09
24 21 0.28
25 12 0.16
26 9 0.12
27 9 0.12
28 3 0.04
29 6 0.08
30 7 0.09
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (24 bp):
TTTAAATTAAAATAAAAATATATT
Found at i:1631443 original size:16 final size:17
Alignment explanation
Indices: 1631422--1631454 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1631412 AAAATATTTT
1631422 TAAATTA-AGTTAATAA
1 TAAATTATAGTTAATAA
*
1631438 TAAATTATATTTAATAA
1 TAAATTATAGTTAATAA
1631455 GTTAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATTATAGTTAATAA
Found at i:1636325 original size:51 final size:51
Alignment explanation
Indices: 1636223--1636327 Score: 165
Period size: 51 Copynumber: 2.1 Consensus size: 51
1636213 ATAATATTTA
* *
1636223 TATTTTATTAAAATGTCTACTATAATACATGAACTATCATCCTTATGTTAT
1 TATTGTATTAAAATGTCTACTATAATACATGAACTATCATCCTTATATTAT
* * *
1636274 TATTGTATTAAAATGTCTACTATAATACATGAACTATTATTCTTCTATTAT
1 TATTGTATTAAAATGTCTACTATAATACATGAACTATCATCCTTATATTAT
1636325 TAT
1 TAT
1636328 AATACTTGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (51 bp):
TATTGTATTAAAATGTCTACTATAATACATGAACTATCATCCTTATATTAT
Found at i:1641239 original size:26 final size:26
Alignment explanation
Indices: 1641203--1641256 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1641193 ACCGAAGTGC
*
1641203 TAATACACATAAGGTCATGCTCACCA
1 TAATACACATAAGGTCATGCCCACCA
* *
1641229 TAATACTCATAAGGTCGTGCCCACCA
1 TAATACACATAAGGTCATGCCCACCA
1641255 TA
1 TA
1641257 TGCATTAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (26 bp):
TAATACACATAAGGTCATGCCCACCA
Found at i:1641729 original size:6 final size:6
Alignment explanation
Indices: 1641718--1641752 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1641708 TTTCTAGTTT
*
1641718 GATTTC GATTTC GATTTT GATTTC GATTTC GATTT
1 GATTTC GATTTC GATTTC GATTTC GATTTC GATTT
1641753 ATGTATATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.54
Consensus pattern (6 bp):
GATTTC
Found at i:1641736 original size:18 final size:18
Alignment explanation
Indices: 1641715--1641752 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1641705 CTTTTTCTAG
1641715 TTTGATTTCGATTTCGAT
1 TTTGATTTCGATTTCGAT
1641733 TTTGATTTCGATTTCGAT
1 TTTGATTTCGATTTCGAT
1641751 TT
1 TT
1641753 ATGTATATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.58
Consensus pattern (18 bp):
TTTGATTTCGATTTCGAT
Found at i:1642307 original size:22 final size:23
Alignment explanation
Indices: 1642282--1642333 Score: 97
Period size: 22 Copynumber: 2.3 Consensus size: 23
1642272 TAATACGTAC
1642282 AACATAATATTCTCATAA-TTCT
1 AACATAATATTCTCATAATTTCT
1642304 AACATAATATTCTCATAATTTCT
1 AACATAATATTCTCATAATTTCT
1642327 AACATAA
1 AACATAA
1642334 AATATCAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.38
Consensus pattern (23 bp):
AACATAATATTCTCATAATTTCT
Found at i:1645427 original size:3 final size:3
Alignment explanation
Indices: 1645419--1645452 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1645409 CTGGTTTTCC
*
1645419 AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1645453 CTAAACATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1649679 original size:12 final size:12
Alignment explanation
Indices: 1649662--1649712 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
1649652 TTCAAAGAGG
1649662 TTTTATATTTAA
1 TTTTATATTTAA
*
1649674 TTTTATATTAAA
1 TTTTATATTTAA
*
1649686 TTTGAT-TTTAA
1 TTTTATATTTAA
1649697 TTTTA-ATATTAA
1 TTTTATAT-TTAA
1649709 TTTT
1 TTTT
1649713 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:1649728 original size:24 final size:27
Alignment explanation
Indices: 1649695--1649821 Score: 86
Period size: 26 Copynumber: 4.7 Consensus size: 27
1649685 ATTTGATTTT
*
1649695 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
1649720 AATTA-AATATTAA-TTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
*
1649745 TATTATAGATATTAA--TTTTAATATTA
1 AATTATA-ATATTAATTTTTTAATATTA
* * * *
1649771 ATTTTTTAAATAAATTAAATATTTAATATTA
1 A-ATTAT-AAT--ATTAATTTTTTAATATTA
*
1649802 GATTATAGATATTTAATTTT
1 AATTATA-ATA-TTAATTTT
1649822 ATATCATATA
Statistics
Matches: 79, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
23 7 0.09
24 9 0.11
25 10 0.13
26 12 0.15
27 12 0.15
28 2 0.03
29 12 0.15
30 5 0.06
31 10 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:1649766 original size:57 final size:57
Alignment explanation
Indices: 1649698--1649822 Score: 139
Period size: 57 Copynumber: 2.2 Consensus size: 57
1649688 TGATTTTAAT
* * * *
1649698 TTTAATATTAAT-TT-TTTAAATAAATTAAATATTAATTTTTAATATTATATTATAGATA
1 TTTAATTTTAATATTATTT-AATAAA-TAAAT-TAAATATTTAATATTAGATTATAGATA
**
1649756 -TTAATTTTAATATTAATTTTTTAAATAAATTAAATATTTAATATTAGATTATAGATA
1 TTTAATTTTAATATT-ATTTAATAAATAAATTAAATATTTAATATTAGATTATAGATA
1649813 TTTAATTTTA
1 TTTAATTTTA
1649823 TATCATATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
57 34 0.60
58 16 0.28
59 4 0.07
60 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (57 bp):
TTTAATTTTAATATTATTTAATAAATAAATTAAATATTTAATATTAGATTATAGATA
Found at i:1649769 original size:63 final size:59
Alignment explanation
Indices: 1649670--1649793 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 59
1649660 GGTTTTATAT
*
1649670 TTAATTTTATATTAAATTTGATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATA
1 TTAATTTTATATTAAATTTGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATA
*
1649729 TTAATTTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATA
1 TTAA-TTTT-ATATTAAATT-T-GATATTAATTTTAATATTAATTTTTTAAATAAATTAAATA
1649792 TT
1 TT
1649794 TAATATTAGA
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
59 4 0.07
60 4 0.07
61 9 0.15
62 1 0.02
63 41 0.69
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (59 bp):
TTAATTTTATATTAAATTTGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATA
Found at i:1649770 original size:12 final size:12
Alignment explanation
Indices: 1649670--1649775 Score: 92
Period size: 12 Copynumber: 8.7 Consensus size: 12
1649660 GGTTTTATAT
1649670 TTAATTTT-ATA
1 TTAATTTTAATA
* * *
1649681 TTAAATTTGATT
1 TTAATTTTAATA
1649693 TTAATTTTAATA
1 TTAATTTTAATA
1649705 TTAATTTTTTAA-A
1 TTAA--TTTTAATA
* *
1649718 -TAAATTAAATA
1 TTAATTTTAATA
1649729 TTAATTTTTAATA
1 TTAA-TTTTAATA
*
1649742 TTATATTATAGATA
1 TTA-ATTTTA-ATA
1649756 TTAATTTTAATA
1 TTAATTTTAATA
1649768 TTAATTTT
1 TTAATTTT
1649776 TTAAATAAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
10 4 0.05
11 8 0.11
12 32 0.42
13 19 0.25
14 13 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:1649877 original size:20 final size:19
Alignment explanation
Indices: 1649817--1649878 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1649807 TAGATATTTA
*
1649817 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
1649836 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
1649854 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
1649874 ATTTT
1 ATTTT
1649879 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:1650379 original size:31 final size:31
Alignment explanation
Indices: 1650342--1650401 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1650332 TAGTTGTATG
* * *
1650342 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAATATTGCAAAACTAA
1650373 AATTATTTAAATCTCAATATTGCAAAACT
1 AATTATTTAAATCTCAATATTGCAAAACT
1650402 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATTGCAAAACTAA
Found at i:1651164 original size:15 final size:15
Alignment explanation
Indices: 1651144--1651173 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1651134 GGTATAGCGC
1651144 GGTGCAGAGCCGCGT
1 GGTGCAGAGCCGCGT
1651159 GGTGCAGAGCCGCGT
1 GGTGCAGAGCCGCGT
1651174 CTTACCACAA
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:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GGTGCAGAGCCGCGT
Found at i:1651399 original size:9 final size:9
Alignment explanation
Indices: 1651387--1651438 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
1651377 TAATATTTTG
1651387 TATTTAATT
1 TATTTAATT
*
1651396 TATTTAA-G
1 TATTTAATT
1651404 TATTTAATT
1 TATTTAATT
1651413 TATTTAA--
1 TATTTAATT
*
1651420 TATTTTATT
1 TATTTAATT
*
1651429 TAATTAATT
1 TATTTAATT
1651438 T
1 T
1651439 TTTTGCATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:1651408 original size:17 final size:17
Alignment explanation
Indices: 1651386--1651435 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
1651376 TTAATATTTT
1651386 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1651403 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
1651420 -TATTTTATTTAATTAA
1 GTATTTAATTTATTTAA
1651436 TTTTTTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1657526 original size:20 final size:20
Alignment explanation
Indices: 1657501--1657546 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1657491 CGAAGGTTTT
1657501 GGTGATGTTTGAAGAGGTCC
1 GGTGATGTTTGAAGAGGTCC
1657521 GGTGATGTTTGAAGAGGTCC
1 GGTGATGTTTGAAGAGGTCC
1657541 GGTGAT
1 GGTGAT
1657547 CGTAGCTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.09, G:0.41, T:0.30
Consensus pattern (20 bp):
GGTGATGTTTGAAGAGGTCC
Found at i:1658078 original size:17 final size:16
Alignment explanation
Indices: 1658056--1658118 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
1658046 GGGTTTTGTA
1658056 ATATTAATAAATAATAT
1 ATATTAAT-AATAATAT
1658073 ATATTAATAATAATA-
1 ATATTAATAATAATAT
*
1658088 ATAATT-ATTATAAT-T
1 AT-ATTAATAATAATAT
*
1658103 ATAATAAATAATAATA
1 AT-ATTAATAATAATA
1658119 AAAATGGGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 14 0.36
16 17 0.44
17 8 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTAATAATAATAT
Found at i:1658083 original size:3 final size:3
Alignment explanation
Indices: 1658054--1658119 Score: 60
Period size: 3 Copynumber: 21.0 Consensus size: 3
1658044 TTGGGTTTTG
* * * *
1658054 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TTA TTA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1658101 TTA TAA TAAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA
1658120 AAATGGGTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
3 43 0.83
4 9 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:1658490 original size:123 final size:122
Alignment explanation
Indices: 1658257--1658900 Score: 674
Period size: 123 Copynumber: 5.3 Consensus size: 122
1658247 GTTGAATAAA
* * ** * *
1658257 TTCTTC-TCTTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTGCTGG---GGATGATGTGGA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTCT-CTGGAAAAGTTGATGT-GA
* * * * * * *
1658318 CCTATTTCCTTCTGTGATAGAGTCATTCAAAATGTTAAATAAGCTCTTCTCATTATGAAC
64 TCTATCTCCTTCTGTGATAGAGTGA-GCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
* * * * *
1658378 TTCTTCTTTCTCCTTCAGATGAGTTCTTCTCATTATGAACACT-TCTGGAAAGGTTTATGCTAAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTCTCTGGAAAAGTTGATG-TGAT
* * * * * *
1658442 CTATCTGCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAAC
65 CTATCTCCTTCTGTGATAGAGTGA-GCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
* * ** *
1658501 TTATTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGGTGTCGAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTCTCTGGAAAAGTTGATGT-GAT
* *
1658565 CTATCTCCTTCTGTGATAGCGTCGAGCAAAAGATTAAACAAGTTCTTCTCATTATGAAC
65 CTATCTCCTTCTGTGATAGAGT-GAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
*
1658624 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACT-TCTGGCAAA--TG-T-TGATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTCTCTGGAAAAGTTGATGTGATC
* ** * * * *
1658684 CA--T-C--AAGAGAT-GAATTCGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
66 TATCTCCTTCTGTGATAG-AGT-GAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
** *
1658737 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCCGAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTCTCTGGAAAAGTTGATG-TGAT
* *
1658802 CTATCTCCTTCTGTGATAGCGTCGAGCAAAAGGTTAAACAAATTCTTCTCATTATGAAC
65 CTATCTCCTTCTGTGATAGAGT-GAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
1658861 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1658901 TCGATCTAGC
Statistics
Matches: 437, Mismatches: 64, Indels: 41
0.81 0.12 0.08
Matches are distributed among these distances:
112 1 0.00
113 80 0.18
114 8 0.02
115 1 0.00
116 3 0.01
117 1 0.00
118 5 0.01
119 6 0.01
120 5 0.01
121 10 0.02
122 60 0.14
123 146 0.33
124 110 0.25
125 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (122 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTCTCTGGAAAAGTTGATGTGATC
TATCTCCTTCTGTGATAGAGTGAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
Found at i:1658722 original size:113 final size:117
Alignment explanation
Indices: 1658345--1658900 Score: 493
Period size: 124 Copynumber: 4.6 Consensus size: 117
1658335 TAGAGTCATT
* * * * *
1658345 CAAAATGTTAAATAAGCTCTTCTCATTATGAACTTCTTCTTTCTCCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * * * *
1658410 TTATGAACACT-TCTGGAAAGGTTTATGCTAATCTATCTGCTTCTGTGATAGAAT-TATG
66 TTATGAACACTCTCTGGAAAAGTTGATGC----CGA--T-CTACAGAGATAGAGTCGA-G
* * * * * *
1658468 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTATTCTTCC-TCTTCAGATAAGTTCTTCTCA
1 CAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * * * * *
1658532 TTATGAACTTTCTCTGGAAAAGTTGGTGTCGATCTATCTCCTTCTGTGATAGCGTCGAG
66 TTATGAACACTCTCTGGAAAAGTTGATGCCGATCTA-------CAGAGATAGAGTCGAG
1658591 C-AAAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAAG-TTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1658655 ATTATGAACACT-TCTGGCAAATGTTGAT-CC-ATC-A-AGAGAT-GAATTCGAG
65 ATTATGAACACTCTCTGG-AAAAGTTGATGCCGATCTACAGAGATAG-AGTCGAG
*
1658704 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * * *
1658769 TTATGAACTTTCTCTGGAAAAGTTGATGCCGATCTATCTCCTTCTGTGATAGCGTCGAG
66 TTATGAACACTCTCTGGAAAAGTTGATGCCGATCTA-------CAGAGATAGAGTCGAG
* *
1658828 CAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1658893 TTATGAAC
66 TTATGAAC
1658901 TCGATCTAGC
Statistics
Matches: 361, Mismatches: 45, Indels: 53
0.79 0.10 0.12
Matches are distributed among these distances:
112 1 0.00
113 85 0.24
114 12 0.03
115 3 0.01
116 3 0.01
117 1 0.00
119 2 0.01
121 1 0.00
122 35 0.10
123 100 0.28
124 117 0.32
125 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (117 bp):
CAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACACTCTCTGGAAAAGTTGATGCCGATCTACAGAGATAGAGTCGAG
Found at i:1658826 original size:237 final size:241
Alignment explanation
Indices: 1658257--1658900 Score: 839
Period size: 237 Copynumber: 2.7 Consensus size: 241
1658247 GTTGAATAAA
* * * * *
1658257 TTCTTC-TCTTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTGCTGG---GGATGATGTGGA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGTTGATGTCGA
* * * * * *
1658318 CCTATTTCCTTCTGTGATAGAGTC-ATTCAAAATGTTAAATAAGCTCTTCTCATTATGAACTTCT
65 TCTATCTCCTTCTGTGATAGCGTCGA-GCAAAA-GTTAAACAAGTTCTTCTCATTATGAACTTCT
* * * *
1658382 TCTTTCTCCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAAGGTTTATGCTAATCTATC
128 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAA-GTGTATG--AATCCA-C
** * * *
1658447 TGCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAAC
189 TGC-TAAGAGATAGAATTATGCAAAAAGTTGAACAAGCTCTTCTCATTATGAAC
* * *
1658501 TTATTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGGTGTCGAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTCGAT
1658565 CTATCTCCTTCTGTGATAGCGTCGAGCAAAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTC
66 CTATCTCCTTCTGTGATAGCGTCGAGCAAAAG-TTAAACAAGTTCTTCTCATTATGAACTTCTTC
1658630 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGCAAA-TGT-TG-ATCCA-T-C-A
130 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGG-AAAGTGTATGAATCCACTGCTA
*
1658689 AGAGAT-GAATTCGA-GCAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
194 AGAGATAGAATT--ATGCAAAAAGTTGAACAAGCTCTTCTCATTATGAAC
*
1658737 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCCGAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTCGAT
*
1658802 CTATCTCCTTCTGTGATAGCGTCGAGCAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTC
66 CTATCTCCTTCTGTGATAGCGTCGAGCAAAA-GTTAAACAAGTTCTTCTCATTATGAACTTCTTC
1658867 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
130 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1658901 TCGATCTAGC
Statistics
Matches: 360, Mismatches: 29, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
235 5 0.01
236 44 0.12
237 148 0.41
238 2 0.01
239 1 0.00
241 4 0.01
243 4 0.01
244 39 0.11
245 5 0.01
246 104 0.29
247 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (241 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTCGAT
CTATCTCCTTCTGTGATAGCGTCGAGCAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTTCT
TCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAAGTGTATGAATCCACTGCTAAG
AGATAGAATTATGCAAAAAGTTGAACAAGCTCTTCTCATTATGAAC
Found at i:1659393 original size:95 final size:95
Alignment explanation
Indices: 1659230--1659429 Score: 382
Period size: 95 Copynumber: 2.1 Consensus size: 95
1659220 TGCAACATGT
1659230 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
1 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
*
1659295 GTTCTTTTAATACAGAGAAATCTTGATTTC
66 GTTCTTTTAATACAGAGAAATCTTGAATTC
1659325 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
1 TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
*
1659390 GTTCTTTTAATACCGAGAAATCTTGAATTC
66 GTTCTTTTAATACAGAGAAATCTTGAATTC
1659420 TGATTCTGAT
1 TGATTCTGAT
1659430 GAGAAATAAA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 103 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (95 bp):
TGATTCTGATAACAACTCATCTGATTATGAAGTGACCTTTCAAGATGATTTCACAGATATCGATA
GTTCTTTTAATACAGAGAAATCTTGAATTC
Found at i:1659981 original size:83 final size:83
Alignment explanation
Indices: 1659842--1660145 Score: 556
Period size: 83 Copynumber: 3.7 Consensus size: 83
1659832 CCGTGGTTCA
1659842 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1659907 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
*
1659925 TACCAAACCAGATCAGACAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1659990 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
*
1660008 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCA
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
* * *
1660073 AAATT-AATGACTGGTTA
66 AAATTCAATGATTGATTT
1660090 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1660146 GGCATTTGTT
Statistics
Matches: 215, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
82 65 0.30
83 150 0.70
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (83 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
AAATTCAATGATTGATTT
Found at i:1660069 original size:166 final size:169
Alignment explanation
Indices: 1659747--1660145 Score: 610
Period size: 166 Copynumber: 2.3 Consensus size: 169
1659737 GTTCTGGGTT
* * * *
1659747 TTATATCAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCT
1 TTATACCAAACCAGATCAGACAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCT
*
1659812 TCCAAATTCAATAACTGGTTCCGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTC
66 TCCAAATTC-A-AACTGATT-CGT-GTT-ATACCAAACCAGATCAGATAACTCAAAGAACACTTC
* *
1659877 CAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAATGATTGA
126 CAGAAGATGCTATGAGCACATTCCTCTTCAAAATT-AATGACTGA
*
1659922 TTTTACCAAACCAGATCAGACAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCT
1 TTATACCAAACCAGATCAGACAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCT
1659987 TCCAAATTC-AA-TGATT-GAT-TT-TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
66 TCCAAATTCAAACTGATTCG-TGTTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
*
1660047 AGATGCTATGAGCACATTCCTCTTCAAAATTAATGACTGG
130 AGATGCTATGAGCACATTCCTCTTCAAAATTAATGACTGA
*
1660087 TTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1 TTATACCAAACCAGATCAGACAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1660146 GGCATTTGTT
Statistics
Matches: 212, Mismatches: 11, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
165 64 0.30
166 69 0.33
168 2 0.01
169 1 0.00
170 1 0.00
171 4 0.02
172 2 0.01
175 69 0.33
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (169 bp):
TTATACCAAACCAGATCAGACAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCT
TCCAAATTCAAACTGATTCGTGTTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
GATGCTATGAGCACATTCCTCTTCAAAATTAATGACTGA
Found at i:1661190 original size:16 final size:17
Alignment explanation
Indices: 1661137--1661191 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 17
1661127 TTCATAGAAG
*
1661137 AATAAATTGAATTTTCGAA
1 AATAAATTGAATCTT--AA
1661156 AATAAATTGAATCTT-A
1 AATAAATTGAATCTTAA
1661172 AATAAATTGAA-CTTAA
1 AATAAATTGAATCTTAA
1661188 AATA
1 AATA
1661192 GATAGAATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 3 0.09
16 17 0.50
19 14 0.41
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (17 bp):
AATAAATTGAATCTTAA
Found at i:1661535 original size:13 final size:13
Alignment explanation
Indices: 1661515--1661558 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
1661505 ACCCCCCCCT
1661515 TTTTTTTTTCTT-
1 TTTTTTTTTCTTC
1661527 TTTTCTTTTTCTTC
1 TTTT-TTTTTCTTC
1661541 TTTTTTTTTCTTC
1 TTTTTTTTTCTTC
1661554 TTTTT
1 TTTTT
1661559 CTTCTCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.13
13 22 0.73
14 4 0.13
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTCTTC
Found at i:1661544 original size:22 final size:22
Alignment explanation
Indices: 1661518--1661563 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1661508 CCCCCCTTTT
*
1661518 TTTTTTCTTTTTTCTTTTTCTTC
1 TTTTTT-TTTCTTCTTTTTCTTC
1661541 TTTTTTTTTCTTCTTTTTCTTC
1 TTTTTTTTTCTTCTTTTTCTTC
1661563 T
1 T
1661564 CTTCAAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTTTTTCTTCTTTTTCTTC
Found at i:1668902 original size:15 final size:15
Alignment explanation
Indices: 1668879--1668910 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1668869 TGAAATGAAT
1668879 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1668894 AATGCATGTATGCAA
1 AATGAATGTATGCAA
1668909 AA
1 AA
1668911 AGGTATTGAT
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:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1674345 original size:15 final size:13
Alignment explanation
Indices: 1674302--1674344 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1674292 TTGGGTTTTT
1674302 TAATAT-TAATAAA
1 TAATATATAAT-AA
1674315 TAATATATAATAA
1 TAATATATAATAA
*
1674328 TAAT-TATTATAA
1 TAATATATAATAA
1674340 TAATA
1 TAATA
1674345 AAAATGGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 11 0.41
13 12 0.44
14 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TAATATATAATAA
Found at i:1675171 original size:17 final size:18
Alignment explanation
Indices: 1675149--1675188 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1675139 CTATTAAAGG
* *
1675149 CTATTTGTACTCTTT-CT
1 CTATTTGTAATATTTCCT
1675166 CTATTTGTAATATTTCCT
1 CTATTTGTAATATTTCCT
1675184 CTATT
1 CTATT
1675189 AGTGAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.17, C:0.20, G:0.05, T:0.57
Consensus pattern (18 bp):
CTATTTGTAATATTTCCT
Found at i:1682128 original size:36 final size:34
Alignment explanation
Indices: 1682065--1682132 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 34
1682055 ACGGCTGAGC
*
1682065 AATTCAAATTCAAGAAATTAGATTTATCTTTTAG
1 AATTCAAATTCAAAAAATTAGATTTATCTTTTAG
1682099 AATT-AAATTCAAAAAAATTTAGGATTTATCTTTT
1 AATTCAAATTC-AAAAAA-TTA-GATTTATCTTTT
1682133 GTAATTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 6 0.20
34 9 0.30
35 3 0.10
36 12 0.40
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (34 bp):
AATTCAAATTCAAAAAATTAGATTTATCTTTTAG
Found at i:1686539 original size:21 final size:21
Alignment explanation
Indices: 1686513--1686566 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1686503 GAAAAAAAAA
1686513 TAGCCTTTGGTTTGAATATAT
1 TAGCCTTTGGTTTGAATATAT
1686534 TAGCCTTTGGTTTGAATATAT
1 TAGCCTTTGGTTTGAATATAT
*
1686555 TATCCTTTGGTT
1 TAGCCTTTGGTT
1686567 ATTTCGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (21 bp):
TAGCCTTTGGTTTGAATATAT
Found at i:1686996 original size:23 final size:24
Alignment explanation
Indices: 1686970--1687024 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
1686960 TCTCTGTTTT
*
1686970 ATTGTGATTTGTT-GAGCAGTTGG
1 ATTGTGAATTGTTGGAGCAGTTGG
1686993 ATTGTGAATTGTTGGAGCAGTTGG
1 ATTGTGAATTGTTGGAGCAGTTGG
1687017 ATTGTGAA
1 ATTGTGAA
1687025 ATGAGTTAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.22, C:0.04, G:0.35, T:0.40
Consensus pattern (24 bp):
ATTGTGAATTGTTGGAGCAGTTGG
Found at i:1693294 original size:53 final size:53
Alignment explanation
Indices: 1693233--1693338 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 53
1693223 AATATTAATA
* * *
1693233 TTACAATATTAATA-AAAGACTATATCAAAATACGGTTATAACTTACAAACTAT
1 TTACAATATCAATAGAAA-ACTATATCAAAAGACGGTTATAACTCACAAACTAT
* *
1693286 TTACAATATCAATAGAAAACTATATCAAGAGATGGTTATAACTCACAAACTAT
1 TTACAATATCAATAGAAAACTATATCAAAAGACGGTTATAACTCACAAACTAT
1693339 CTTATCTTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 44 0.94
54 3 0.06
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (53 bp):
TTACAATATCAATAGAAAACTATATCAAAAGACGGTTATAACTCACAAACTAT
Found at i:1696609 original size:6 final size:6
Alignment explanation
Indices: 1696595--1696645 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
1696585 TTCTGTGAAC
*
1696595 TTTAGA TTTATA TTTA-A -TTATA TTTATA TTTATA TTTA-A -TTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1696639 TTT-TA TT
1 TTTATA TT
1696646 GGTTTTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
4 6 0.15
5 8 0.20
6 26 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (6 bp):
TTTATA
Found at i:1696617 original size:10 final size:10
Alignment explanation
Indices: 1696602--1696641 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
1696592 AACTTTAGAT
1696602 TTATATTTAA
1 TTATATTTAA
1696612 TTATATTTATA
1 TTATATTTA-A
1696623 TTTATATTTAA
1 -TTATATTTAA
1696634 TTATATTT
1 TTATATTT
1696642 TATTGGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 17 0.61
11 2 0.07
12 9 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTATATTTAA
Found at i:1696621 original size:16 final size:16
Alignment explanation
Indices: 1696600--1696645 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1696590 TGAACTTTAG
1696600 ATTTATATTTA-ATTAT
1 ATTTATATTTATATT-T
1696616 ATTTATATTTATATTT
1 ATTTATATTTATATTT
*
1696632 AATTATATTT-TATT
1 ATTTATATTTATATT
1696646 GGTTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 4 0.14
16 21 0.75
17 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATATTTATATTT
Found at i:1696625 original size:22 final size:22
Alignment explanation
Indices: 1696595--1696645 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1696585 TTCTGTGAAC
*
1696595 TTTAGATTTATATTTAATTATA
1 TTTATATTTATATTTAATTATA
1696617 TTTATATTTATATTTAATTATA
1 TTTATATTTATATTTAATTATA
1696639 TTT-TATT
1 TTTATATT
1696646 GGTTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTATATTTATATTTAATTATA
Found at i:1699756 original size:20 final size:20
Alignment explanation
Indices: 1699720--1699757 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1699710 ATCATATTCT
**
1699720 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1699740 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1699758 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1700171 original size:2 final size:2
Alignment explanation
Indices: 1700164--1700206 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1700154 CCCTGTTTAT
1700164 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
1700206 T
1 T
1700207 TATTTTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1700221 original size:18 final size:18
Alignment explanation
Indices: 1700202--1700235 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1700192 TATATATATA
1700202 TATATT-ATTTT-TATTT
1 TATATTAATTTTGTATTT
1700218 TATATTAATTTTGTATTT
1 TATATTAATTTTGTATTT
1700236 ATAATTCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TATATTAATTTTGTATTT
Found at i:1700475 original size:2 final size:2
Alignment explanation
Indices: 1700468--1700513 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1700458 AGAATTTTTC
1700468 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
1700510 TA TA
1 TA TA
1700514 AATAATATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1701546 original size:33 final size:34
Alignment explanation
Indices: 1701509--1701578 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
1701499 AATACATAAC
1701509 TTTACAAGAACACACGCCCTAATTATACT-ATTT
1 TTTACAAGAACACACGCCCTAATTATACTAATTT
* * *
1701542 TTTACAAGGACCCGCGCCCTAATTATACTAATTT
1 TTTACAAGAACACACGCCCTAATTATACTAATTT
1701576 TTT
1 TTT
1701579 TAATTGTCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 26 0.79
34 7 0.21
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (34 bp):
TTTACAAGAACACACGCCCTAATTATACTAATTT
Found at i:1719925 original size:27 final size:28
Alignment explanation
Indices: 1719862--1719928 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
1719852 CCTAAATCCG
1719862 AACCCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGAATATCACACTTAAAAA
*
1719890 AACCCGACCCGAATATCATACTT-AAAA
1 AACCCGACCCGAATATCACACTTAAAAA
*
1719917 AACCTGACCCGA
1 AACCCGACCCGA
1719929 CCCAACCCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 15 0.41
28 22 0.59
ACGTcount: A:0.43, C:0.33, G:0.09, T:0.15
Consensus pattern (28 bp):
AACCCGACCCGAATATCACACTTAAAAA
Found at i:1719937 original size:37 final size:37
Alignment explanation
Indices: 1719891--1720000 Score: 175
Period size: 37 Copynumber: 2.9 Consensus size: 37
1719881 ACTTAAAAAA
*
1719891 ACCCGACCCGAATATCATACTTAAAAAACCTGACCCG
1 ACCCAACCCGAATATCATACTTAAAAAACCTGACCCG
* *
1719928 ACCCAACCCGAATATCATACTTAAAAAACCCGAACCG
1 ACCCAACCCGAATATCATACTTAAAAAACCTGACCCG
*
1719965 ACCCAACCCGAATATCAAACTTAAAAAAACCTGACC
1 ACCCAACCCGAATATCATACTT-AAAAAACCTGACC
1720001 TGAAGCCGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
37 55 0.83
38 11 0.17
ACGTcount: A:0.43, C:0.35, G:0.08, T:0.15
Consensus pattern (37 bp):
ACCCAACCCGAATATCATACTTAAAAAACCTGACCCG
Found at i:1720043 original size:30 final size:30
Alignment explanation
Indices: 1719987--1720073 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
1719977 TATCAAACTT
* **
1719987 AAAAAAACCTGACCTGAAGCCGAATTTTTAA
1 AAAAAAACC-GACCCGACCCCGAATTTTTAA
* * **
1720018 AAAAAAATCCTACCCGATCCC-AATTTTTTT
1 AAAAAAA-CCGACCCGACCCCGAATTTTTAA
1720048 AAAAAAACCGACCCGACCCCGAATTT
1 AAAAAAACCGACCCGACCCCGAATTT
1720074 ATTTATTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
29 11 0.24
30 19 0.41
31 14 0.30
32 2 0.04
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.23
Consensus pattern (30 bp):
AAAAAAACCGACCCGACCCCGAATTTTTAA
Found at i:1720061 original size:29 final size:29
Alignment explanation
Indices: 1719985--1720093 Score: 83
Period size: 30 Copynumber: 3.5 Consensus size: 29
1719975 AATATCAAAC
* * *
1719985 TTAAAAAAACCTGACCTGAAGCCGAATTTTT
1 TTAAAAAAACC-GACCCG-ACCCCAATTTTT
** * *
1720016 AAAAAAAAATCCTACCCGATCCCAATTTTT
1 TTAAAAAAA-CCGACCCGACCCCAATTTTT
1720046 TTAAAAAAACCGACCCGACCCCGAATTTATTT
1 TTAAAAAAACCGACCCGACCCC-AA-TT-TTT
*
1720078 ATTAAAAAATCCGACC
1 -TTAAAAAAACCGACC
1720094 TGAATACTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
29 11 0.18
30 19 0.31
31 13 0.21
32 5 0.08
33 14 0.23
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (29 bp):
TTAAAAAAACCGACCCGACCCCAATTTTT
Found at i:1721665 original size:21 final size:21
Alignment explanation
Indices: 1721640--1721704 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
1721630 ATCTGTTCCC
1721640 GGGGAATCGATACCCCCACAG
1 GGGGAATCGATACCCCCACAG
*
1721661 GGGGAATCTG-T---TCC-C--
1 GGGGAATC-GATACCCCCACAG
1721676 GGGGAATCGATACCCCCACAG
1 GGGGAATCGATACCCCCACAG
1721697 GGGGAATC
1 GGGGAATC
1721705 TGTTCCCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
14 1 0.03
15 9 0.26
17 1 0.03
18 4 0.12
19 1 0.03
21 17 0.50
22 1 0.03
ACGTcount: A:0.25, C:0.29, G:0.32, T:0.14
Consensus pattern (21 bp):
GGGGAATCGATACCCCCACAG
Found at i:1721669 original size:36 final size:36
Alignment explanation
Indices: 1721605--1721711 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
1721595 TTTCATTTAG
1721605 GGGGAATCGATACCCCC-CAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCACAGGGGGAATCTGTTCCC
1721640 GGGGAATCGATACCCCCACAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCACAGGGGGAATCTGTTCCC
1721676 GGGGAATCGATACCCCCACAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCACAGGGGGAATCTGTTCCC
1721712 CCTGCACATA
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
35 17 0.24
36 54 0.76
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.17
Consensus pattern (36 bp):
GGGGAATCGATACCCCCACAGGGGGAATCTGTTCCC
Found at i:1721712 original size:21 final size:21
Alignment explanation
Indices: 1721652--1721713 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
1721642 GGAATCGATA
1721652 CCCCCACAGGGGGAATCTGTT
1 CCCCCACAGGGGGAATCTGTT
*
1721673 ---CC-C--GGGGAATC-GATA
1 CCCCCACAGGGGGAATCTG-TT
1721688 CCCCCACAGGGGGAATCTGTT
1 CCCCCACAGGGGGAATCTGTT
1721709 CCCCC
1 CCCCC
1721714 TGCACATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 16
0.63 0.04 0.33
Matches are distributed among these distances:
14 1 0.03
15 9 0.29
17 1 0.03
18 4 0.13
19 1 0.03
21 14 0.45
22 1 0.03
ACGTcount: A:0.19, C:0.37, G:0.27, T:0.16
Consensus pattern (21 bp):
CCCCCACAGGGGGAATCTGTT
Found at i:1725057 original size:2 final size:2
Alignment explanation
Indices: 1724994--1725042 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1724984 ATCAAATTAT
1724994 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
1725036 TA TA TA T
1 TA TA TA T
1725043 TTTCCAATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1726638 original size:20 final size:20
Alignment explanation
Indices: 1726613--1726653 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1726603 ACTCTATACA
1726613 CAACAAAATACATACTTTGT
1 CAACAAAATACATACTTTGT
1726633 CAACAAAATACATACTTTGT
1 CAACAAAATACATACTTTGT
1726653 C
1 C
1726654 GATTACTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (20 bp):
CAACAAAATACATACTTTGT
Found at i:1732147 original size:18 final size:18
Alignment explanation
Indices: 1732124--1732166 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1732114 AGCTGGAACC
1732124 GCCGCAGACTTATGCGGA
1 GCCGCAGACTTATGCGGA
1732142 GCCGCAGACTTATGCGGA
1 GCCGCAGACTTATGCGGA
1732160 GCCGCAG
1 GCCGCAG
1732167 CCGTTGGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.30, G:0.35, T:0.14
Consensus pattern (18 bp):
GCCGCAGACTTATGCGGA
Found at i:1733072 original size:2 final size:2
Alignment explanation
Indices: 1733065--1733090 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1733055 TAATGTTAGA
1733065 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
1733091 TTAAAATTTG
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:1737304 original size:22 final size:22
Alignment explanation
Indices: 1737274--1737376 Score: 134
Period size: 22 Copynumber: 4.4 Consensus size: 22
1737264 AATAAAAATT
*
1737274 TATGAATACAATTAATTTTTCA
1 TATGTATACAATTAATTTTTCA
1737296 TATGTATACAATTAATTTTTCA
1 TATGTATACAATTAATTTTTCA
1737318 TATGTATACAATTAATTTTTCATTTTTCA
1 TATGTATACAATT-A------ATTTTTCA
1737347 TATGTATACAATTAATTTTTCA
1 TATGTATACAATTAATTTTTCA
1737369 TATGTATA
1 TATGTATA
1737377 TTATATTCCA
Statistics
Matches: 73, Mismatches: 1, Indels: 14
0.83 0.01 0.16
Matches are distributed among these distances:
22 50 0.68
23 1 0.01
28 1 0.01
29 21 0.29
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (22 bp):
TATGTATACAATTAATTTTTCA
Found at i:1737344 original size:29 final size:29
Alignment explanation
Indices: 1737310--1737369 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1737300 TATACAATTA
1737310 ATTTTTCATATGTATACAATTAATTTTTC
1 ATTTTTCATATGTATACAATTAATTTTTC
1737339 ATTTTTCATATGTATACAATTAATTTTTC
1 ATTTTTCATATGTATACAATTAATTTTTC
1737368 AT
1 AT
1737370 ATGTATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTTTCATATGTATACAATTAATTTTTC
Found at i:1752356 original size:2 final size:2
Alignment explanation
Indices: 1752349--1752425 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
1752339 ACTTTTGACA
1752349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1752391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1752426 ATCTGTTACT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1755082 original size:10 final size:10
Alignment explanation
Indices: 1755067--1755098 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1755057 TATTATTATT
1755067 TCGGGTCGGA
1 TCGGGTCGGA
*
1755077 TCGGGTCGGG
1 TCGGGTCGGA
1755087 TCGGGTCGGA
1 TCGGGTCGGA
1755097 TC
1 TC
1755099 AAATTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.06, C:0.22, G:0.50, T:0.22
Consensus pattern (10 bp):
TCGGGTCGGA
Found at i:1757308 original size:18 final size:17
Alignment explanation
Indices: 1757273--1757323 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
1757263 AAATGAAATT
1757273 AAATGAATAA-AATGAAAA
1 AAAT-AATAATAAT-AAAA
1757291 GAAATAATAATAATAAAA
1 -AAATAATAATAATAAAA
*
1757309 ATACTAATAATAATA
1 A-AATAATAATAATA
1757324 TAGACTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.03
18 21 0.72
19 7 0.24
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.24
Consensus pattern (17 bp):
AAATAATAATAATAAAA
Found at i:1757310 original size:15 final size:15
Alignment explanation
Indices: 1757292--1757321 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1757282 AAATGAAAAG
1757292 AAATAATAATAATAA
1 AAATAATAATAATAA
*
1757307 AAATACTAATAATAA
1 AAATAATAATAATAA
1757322 TATAGACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAATAATAATAA
Found at i:1757441 original size:32 final size:32
Alignment explanation
Indices: 1757405--1757472 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
1757395 ACTATATACC
1757405 ATAT-AGTTTTCAAAAATGA-TTTTAAAAATATT
1 ATATAAGTTTTCAAAAAT-ATTTTTAAAAATA-T
* *
1757437 ATATAAGTTTTCCAAAATATTTTTAAAACTAT
1 ATATAAGTTTTCAAAAATATTTTTAAAAATAT
1757469 ATAT
1 ATAT
1757473 TATATAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (32 bp):
ATATAAGTTTTCAAAAATATTTTTAAAAATAT
Found at i:1757490 original size:37 final size:37
Alignment explanation
Indices: 1757432--1757633 Score: 118
Period size: 35 Copynumber: 5.5 Consensus size: 37
1757422 GATTTTAAAA
* *
1757432 ATATTATATAAGTTTTCCAAAATATTTTTAAAACTAT
1 ATATTATATAAATTTTTCAAAATATTTTTAAAACTAT
* *
1757469 ATATTATATAAATTTTTCAAAAATGTTTTTTTTAAACTAT
1 ATATTATATAAATTTTTC-AAAA--TATTTTTAAAACTAT
* * *
1757509 ACA-T-TAT--A-TTTTCAAAATGA-TTTCAAAAATAT
1 ATATTATATAAATTTTTCAAAAT-ATTTTTAAAACTAT
* *
1757541 ATGTTATAT-AA-TTTTCAAAAT-GTTTTAAAACTTAT
1 ATATTATATAAATTTTTCAAAATATTTTTAAAAC-TAT
* * * **
1757576 ATATTGTATATAAGTTTTCAAAA-ACATTTTAAAAAAACT
1 ATATTATATA-AATTTTTCAAAATA-TTTTTAAAACTA-T
*
1757615 ATATTATATATATATTTTC
1 ATATTATATAAAT-TTTTC
1757634 GGAAACCGTT
Statistics
Matches: 128, Mismatches: 21, Indels: 30
0.72 0.12 0.17
Matches are distributed among these distances:
32 11 0.09
33 1 0.01
34 14 0.11
35 26 0.20
36 1 0.01
37 18 0.14
38 18 0.14
39 24 0.19
40 15 0.12
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (37 bp):
ATATTATATAAATTTTTCAAAATATTTTTAAAACTAT
Found at i:1757560 original size:107 final size:108
Alignment explanation
Indices: 1757406--1757599 Score: 265
Period size: 107 Copynumber: 1.8 Consensus size: 108
1757396 CTATATACCA
* *
1757406 TATAGTTTTCAAAAATGATTTTAAAAATATTATATAAGTTTTCCAAAATATTTTTAAAAC-TATA
1 TATAGTTTTCAAAAATGATTTAAAAAATATTATATAAGTTTTCCAAAAT-GTTTTAAAACTTATA
*
1757470 TATTATATA-AATTTTTCAAAAATGTTTTTTTTAAACTATACAT
65 TATTATATATAAGTTTTCAAAAATGTTTTTTTTAAACTATACAT
1757513 TATA-TTTTC-AAAATGATTTCAAAAATATATGTTATATAA-TTTT-CAAAATGTTTTAAAACTT
1 TATAGTTTTCAAAAATGATTT-AAAAA-ATA--TTATATAAGTTTTCCAAAATGTTTTAAAACTT
*
1757574 ATATATTGTATATAAGTTTTCAAAAA
62 ATATATTATATATAAGTTTTCAAAAA
1757600 CATTTTAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
105 10 0.13
106 18 0.23
107 25 0.32
108 16 0.21
109 8 0.10
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (108 bp):
TATAGTTTTCAAAAATGATTTAAAAAATATTATATAAGTTTTCCAAAATGTTTTAAAACTTATAT
ATTATATATAAGTTTTCAAAAATGTTTTTTTTAAACTATACAT
Found at i:1758511 original size:80 final size:80
Alignment explanation
Indices: 1758307--1758584 Score: 394
Period size: 80 Copynumber: 3.4 Consensus size: 80
1758297 GTTTGCCTCT
* * * * *
1758307 GAGCTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGACAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-T---TTGGCAGATAGCCCTTCTCGACTTAAGCTATG
* *
1758372 TTGCAAATGATGTGCCCTCG
62 CTGCAAATGATGTG-CCTTG
* * *
1758392 AAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
*
1758457 AAATGATATGCCTTG
66 AAATGATGTGCCTTG
* *
1758472 GAGCTGAGCGGAGTCAAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
1758537 AAATGATGTGCCTTG
66 AAATGATGTGCCTTG
1758552 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
1758585 TCGGCACGAT
Statistics
Matches: 178, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
80 109 0.61
81 41 0.23
84 1 0.01
85 27 0.15
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (80 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
AAATGATGTGCCTTG
Found at i:1758760 original size:94 final size:94
Alignment explanation
Indices: 1758598--1759469 Score: 1473
Period size: 94 Copynumber: 9.3 Consensus size: 94
1758588 GCACGATTCT
**
1758598 CTTCG-TCGTGAAGTTGAAACCGTGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
1 CTTCGTTC-TGAAGTTGAAATTG-GGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
*
1758662 GTTGAACTTACGTTGTCTGGAGTCCAATATC
64 GTTGAACTTGCGTTGTCTGGAGTCCAATATC
*
1758693 CTTCGTTCTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTTGTCGTGAAGT
1 CTTCGTTCTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1758758 TGAACTTGCGTTGTCTGGAGTCCAATATC
66 TGAACTTGCGTTGTCTGGAGTCCAATATC
* * *
1758787 CTTCGTTGTGAAGTTGAAATTAGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1 CTTCGTTCTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1758852 TGAACTTGCGTTGTCTGGAGTCCAATATC
66 TGAACTTGCGTTGTCTGGAGTCCAATATC
*
1758881 CTTCGTTGC-GAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTCCGTCGTGAAG
1 CTTCGTT-CTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
1758945 TTGAACTTGCGTTGTCTGGAGTCCAATATC
65 TTGAACTTGCGTTGTCTGGAGTCCAATATC
* *
1758975 CTTCATTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1 CTTCGTTCTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1759040 TGAACTTGCGTTGTCTGGAGTCCAATATC
66 TGAACTTGCGTTGTCTGGAGTCCAATATC
* *
1759069 CTTCGTTGC-GAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCATCAAG
1 CTTCGTT-CTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
1759133 TTGAACTTGCGTTGTCTGGAGTCCAATATC
65 TTGAACTTGCGTTGTCTGGAGTCCAATATC
* * *
1759163 CTTCGTTGC-GAAGTTGAAATTAGGAAATTGTTTATTAACAACCAGCGGTCCCTTCGCCGTGAAG
1 CTTCGTT-CTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
1759227 TTGAACTTGCGTTGTCTGGAGTCCAATATC
65 TTGAACTTGCGTTGTCTGGAGTCCAATATC
* * * *
1759257 CTTCGTTGTGAATTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTAAATT
1 CTTCGTTCTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1759322 TGAACTTGCGTTGTCTGGAGTCCAATATC
66 TGAACTTGCGTTGTCTGGAGTCCAATATC
*
1759351 CTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1 CTTCGTTCTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
1759416 TGAACTTGCGTTGTCTGGAGTCCAATATC
66 TGAACTTGCGTTGTCTGGAGTCCAATATC
* *
1759445 CTTTGTTGTGAAGTTGAAATTGGGA
1 CTTCGTTCTGAAGTTGAAATTGGGA
1759470 GTGTGGGTAC
Statistics
Matches: 737, Mismatches: 35, Indels: 11
0.94 0.04 0.01
Matches are distributed among these distances:
94 718 0.97
95 17 0.02
96 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (94 bp):
CTTCGTTCTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTGGAGTCCAATATC
Found at i:1758898 original size:43 final size:43
Alignment explanation
Indices: 1758837--1759180 Score: 116
Period size: 43 Copynumber: 7.4 Consensus size: 43
1758827 ACCAGCGGTC
* *
1758837 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTTGCGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * ** ***
1758880 CCTTCGTTGCGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTTGCGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
* * *
1758930 CCCTCCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTTGCGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * * ** ***
1758974 CCTTCATTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTTGCGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
* *
1759024 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTTGCGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * ** ***
1759068 CCTTCGTTGCGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTTGCGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT
1759118 CCCTTCGTCAT-C-AAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGT--TGCGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1759162 CCTTCGTTGCGAAGTTGAA
1 CCTTCGTTGCGAAGTTGAA
1759181 ATTAGGAAAT
Statistics
Matches: 207, Mismatches: 66, Indels: 56
0.63 0.20 0.17
Matches are distributed among these distances:
41 1 0.00
42 1 0.00
43 77 0.37
44 3 0.01
45 9 0.04
46 21 0.10
48 21 0.10
49 9 0.04
50 3 0.01
51 60 0.29
52 1 0.00
53 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (43 bp):
CCTTCGTTGCGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:1759274 original size:43 final size:43
Alignment explanation
Indices: 1759221--1759462 Score: 124
Period size: 43 Copynumber: 5.3 Consensus size: 43
1759211 TCCCTTCGCC
1759221 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
* * * * * ** *** *
1759264 GTGAATTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTC
1 GTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT-CCTTCGTT
* *
1759315 GTAAATTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
* * * * ** *** *
1759358 GTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTC
1 GTGAAGTTGAACTTGCG---TTG--TCTGGA-GTCCA-ATAT-CCTTCGTT
*
1759409 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTTGTT
1 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1759452 GTGAAGTTGAA
1 GTGAAGTTGAA
1759463 ATTGGGAGTG
Statistics
Matches: 138, Mismatches: 45, Indels: 32
0.64 0.21 0.15
Matches are distributed among these distances:
43 51 0.37
44 2 0.01
45 6 0.04
46 14 0.10
48 14 0.10
49 6 0.04
50 2 0.01
51 43 0.31
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (43 bp):
GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
Done.