Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008227.1 Hibiscus syriacus cultivar Beakdansim tig00110863_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: 654371
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 3
Found at i:51 original size:14 final size:14
Alignment explanation
Indices: 32--85 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
22 CGAAATGGCT
32 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
46 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
65 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
79 ATCGCAA
1 ATCGCAA
86 TGCGATTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:58 original size:33 final size:33
Alignment explanation
Indices: 13--90 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
3 AAAACAGATT
* ***
13 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
46 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
79 ATCGCAATGCGA
1 ATCGCAATGCGA
91 TTTCATTTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:133 original size:20 final size:20
Alignment explanation
Indices: 108--145 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
98 TCGCATTGCG
*
108 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
128 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
146 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1227 original size:24 final size:24
Alignment explanation
Indices: 1200--1253 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1190 GTATTCGAAA
* *
1200 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1224 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1248 TTTGAT
1 TTTGAT
1254 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:3764 original size:19 final size:19
Alignment explanation
Indices: 3742--3872 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
3732 GGAAATTACT
3742 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3761 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3775 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
3794 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
3808 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
3827 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
3841 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3860 ATCGCAACGCGAA
1 ATCGCAATGCGAA
3873 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3784 original size:33 final size:33
Alignment explanation
Indices: 3742--3868 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
3732 GGAAATTACT
3742 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
3775 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
3807 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3841 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3869 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3849 original size:66 final size:66
Alignment explanation
Indices: 3743--3875 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
3733 GAAATTACTA
*
3743 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
3808 T
66 T
*
3809 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
3874 T
66 T
3875 T
1 T
3876 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:3890 original size:19 final size:20
Alignment explanation
Indices: 3868--3910 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3858 AAATCGCAAC
3868 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
3887 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
3907 GCGA
1 GCGA
3911 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:3895 original size:14 final size:14
Alignment explanation
Indices: 3896--3929 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3886 TGCGATTTTC
3896 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
3910 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
3924 ATTTTC
1 ATTTTC
3930 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:4070 original size:14 final size:14
Alignment explanation
Indices: 4051--4087 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4041 CATCAATTAA
4051 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4065 ACAAATCACCTTTT
1 ACAAATCAACTTTT
4079 ACAAATCAA
1 ACAAATCAA
4088 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5520 original size:42 final size:42
Alignment explanation
Indices: 5444--5562 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
5434 GTGAATCGGG
* ** *
5444 CTCTTGAATGGTGGGA-GGGACCTCTTC-AACAATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGAATGACAGGGGC
*
5486 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGGGGC
* * * * * *
5528 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGA
5563 TAGGCGAGTC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.03
42 58 0.91
43 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGGGGC
Found at i:5563 original size:42 final size:42
Alignment explanation
Indices: 5474--5566 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
5464 CCTCTTCAAC
* * * * *
5474 AATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGG
1 AATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
* *
5516 AATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGG
1 AATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
*
5558 GATGATAGG
1 AATGATAGG
5567 CGAGTCGGGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.25, C:0.16, G:0.38, T:0.22
Consensus pattern (42 bp):
AATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
Found at i:7613 original size:20 final size:19
Alignment explanation
Indices: 7568--7628 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
7558 TCTTTTGGTT
7568 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
7587 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
7608 GAAATGACTATTGCAACGA
1 GAAATGAAAATCGCAACGA
7627 GA
1 GA
7629 GAATCGTAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 4 0.12
20 28 0.82
21 2 0.06
ACGTcount: A:0.44, C:0.16, G:0.25, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:7650 original size:33 final size:33
Alignment explanation
Indices: 7593--7680 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
7583 ACGAGATAAT
** *
7593 GAGAATCGCAACGCGGAAATGACTATTGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCACAACCA
* *
7627 GAGAATCGTAACGCGAAATGACTATCACGACCA
1 GAGAATCGCAACGCGAAATGACTATCACAACCA
*
7660 GACAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
7681 AAATCGCAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 34 0.72
34 13 0.28
ACGTcount: A:0.40, C:0.23, G:0.24, T:0.14
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCACAACCA
Found at i:7696 original size:20 final size:18
Alignment explanation
Indices: 7663--7733 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 18
7653 ACGACCAGAC
7663 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAAT-AA
7682 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAAT-AA
7702 AATCGCAACGCGAAATAA
1 AATCGCAACGCGAAATAA
*
7720 AATTCGCAATGCGA
1 AA-TCGCAACGCGA
7734 TTTTTGTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.08
19 26 0.54
20 18 0.38
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (18 bp):
AATCGCAACGCGAAATAA
Found at i:7744 original size:19 final size:19
Alignment explanation
Indices: 7722--7764 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
7712 CGAAATAAAA
*
7722 TTCGCAATGCGATTTTTGT
1 TTCGCAATGCGATTTTTAT
** *
7741 TTCGCGTTGCGTTTTTTAT
1 TTCGCAATGCGATTTTTAT
7760 TTCGC
1 TTCGC
7765 GTTGCGATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (19 bp):
TTCGCAATGCGATTTTTAT
Found at i:7765 original size:19 final size:19
Alignment explanation
Indices: 7729--7795 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
7719 AAATTCGCAA
*
7729 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
7748 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
7767 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
7787 TGCGATTTT
1 TGCGATTTT
7796 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:8401 original size:20 final size:20
Alignment explanation
Indices: 8316--8429 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
8306 CGCTATGTAA
* * *
8316 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
8336 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
8356 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
8377 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
8397 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
8417 ATCGCATTGCGAT
1 ATCGCATTGCGAT
8430 TTTCCCAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 65 0.79
21 12 0.15
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:8414 original size:61 final size:61
Alignment explanation
Indices: 8316--8432 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
8306 CGCTATGTAA
* * * *
8316 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
8377 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
8433 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:8448 original size:61 final size:61
Alignment explanation
Indices: 8316--8450 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
8306 CGCTATGTAA
* * * * ** *
8316 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
8377 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
8439 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
8451 TTACTTATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:8903 original size:40 final size:43
Alignment explanation
Indices: 8836--8929 Score: 122
Period size: 40 Copynumber: 2.3 Consensus size: 43
8826 ACCTTAATTT
* *
8836 TTTTTTCAATCTCACTTTTTACCTTTAAAATTAAGATCCCT-A
1 TTTTTTCAATCTCACCTTTTACCTTTAAAATTAAGACCCCTAA
* *
8878 TTTTTT-AAT-TCACCTTTTACTTTTAAAATTGAGACCCCTAA
1 TTTTTTCAATCTCACCTTTTACCTTTAAAATTAAGACCCCTAA
*
8919 TTTTTTTAATC
1 TTTTTTCAATC
8930 ATATTTTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
40 26 0.58
41 10 0.22
42 9 0.20
ACGTcount: A:0.28, C:0.19, G:0.03, T:0.50
Consensus pattern (43 bp):
TTTTTTCAATCTCACCTTTTACCTTTAAAATTAAGACCCCTAA
Found at i:20777 original size:30 final size:31
Alignment explanation
Indices: 20741--20817 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
20731 AGAGAGGATG
* * *
20741 AAGCTTAGCAAAGCTTA-TGATTA-TGATTAA
1 AAGCTTAGCAAAGCTTAGAGATAATTGAGT-A
*
20771 AAGCTTAGAAAAG-TTAGAGATAATTGAGTA
1 AAGCTTAGCAAAGCTTAGAGATAATTGAGTA
20801 AAGCTTAGCAAAGCTTA
1 AAGCTTAGCAAAGCTTA
20818 AAATAACGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 3 0.08
30 29 0.74
31 7 0.18
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (31 bp):
AAGCTTAGCAAAGCTTAGAGATAATTGAGTA
Found at i:21965 original size:30 final size:29
Alignment explanation
Indices: 21929--22005 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
21919 AGAGAGGGTG
*
21929 AAGCTTAGCAAAGCTTAG-GAATATGATTGA
1 AAGCTTAGCAAAGCTTAGAGAAT-TGAGT-A
* *
21959 AAGCTTAGAAAAGCTAGAGAGAATTGAGTA
1 AAGCTTAGCAAAGCT-TAGAGAATTGAGTA
21989 AAGCTTAGCAAAGCTTA
1 AAGCTTAGCAAAGCTTA
22006 AAATAACGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 29 0.73
31 6 0.15
32 4 0.10
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.23
Consensus pattern (29 bp):
AAGCTTAGCAAAGCTTAGAGAATTGAGTA
Found at i:22572 original size:19 final size:19
Alignment explanation
Indices: 22548--22589 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
22538 TATATTTATG
* * *
22548 TTAAAATGGACGATTGAGA
1 TTAAAATAGACAACTGAGA
22567 TTAAAATAGACAACTGAGA
1 TTAAAATAGACAACTGAGA
22586 TTAA
1 TTAA
22590 CAGTAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (19 bp):
TTAAAATAGACAACTGAGA
Found at i:23263 original size:12 final size:12
Alignment explanation
Indices: 23246--23270 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23236 TCAGAGGGAG
23246 TGAACCATTAAA
1 TGAACCATTAAA
23258 TGAACCATTAAA
1 TGAACCATTAAA
23270 T
1 T
23271 TAAAGATGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (12 bp):
TGAACCATTAAA
Found at i:26148 original size:30 final size:30
Alignment explanation
Indices: 26087--26186 Score: 128
Period size: 30 Copynumber: 3.3 Consensus size: 30
26077 CTAAGGAACA
* * ***
26087 TATGGATAGTTTACCTAGGTTCTTCGGGACC
1 TATGGATAG-TTACCGAGGATCTTTATGACC
26118 TATGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
*
26148 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
*
26178 TCTGGATAG
1 TATGGATAG
26187 GTCCTTCGGA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 54 0.86
31 9 0.14
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (30 bp):
TATGGATAGTTACCGAGGATCTTTATGACC
Found at i:27098 original size:29 final size:29
Alignment explanation
Indices: 27052--27135 Score: 150
Period size: 29 Copynumber: 2.9 Consensus size: 29
27042 ATGGTTGCTG
*
27052 GGCGTGCATGGTGACCTACCATGTCGCCT
1 GGCGTGCATGGCGACCTACCATGTCGCCT
*
27081 GGCGTGCATGGCGGCCTACCATGTCGCCT
1 GGCGTGCATGGCGACCTACCATGTCGCCT
27110 GGCGTGCATGGCGACCTACCATGTCG
1 GGCGTGCATGGCGACCTACCATGTCG
27136 TTGGGATGCC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.13, C:0.32, G:0.33, T:0.21
Consensus pattern (29 bp):
GGCGTGCATGGCGACCTACCATGTCGCCT
Found at i:40271 original size:21 final size:21
Alignment explanation
Indices: 40247--40307 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
40237 GGCAACCAAC
40247 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
**
40268 TTTGGTAAATG--TTTC----
1 TTTGAAAAATGTTTTTCAAAG
40283 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
40304 TTTG
1 TTTG
40308 GTAAAGTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 9 0.30
17 4 0.13
19 4 0.13
21 13 0.43
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (21 bp):
TTTGAAAAATGTTTTTCAAAG
Found at i:40293 original size:36 final size:35
Alignment explanation
Indices: 40246--40316 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 35
40236 TGGCAACCAA
40246 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
40282 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
40317 GGTAGATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 4 0.11
36 31 0.89
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
Found at i:49648 original size:12 final size:12
Alignment explanation
Indices: 49631--49655 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49621 AGGAACATGT
49631 AGTTCCAATTTG
1 AGTTCCAATTTG
49643 AGTTCCAATTTG
1 AGTTCCAATTTG
49655 A
1 A
49656 TCAAAATTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGTTCCAATTTG
Found at i:63914 original size:29 final size:28
Alignment explanation
Indices: 63868--63923 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
63858 CGTTCTACAA
63868 AGGTTATTTCTACATTTAATTT-TTTTCC
1 AGGTTATTTCTACATTT-ATTTATTTTCC
**
63896 AGGTTATATTCTATTTTTATTTATTTTC
1 AGGTTAT-TTCTACATTTATTTATTTTC
63924 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (28 bp):
AGGTTATTTCTACATTTATTTATTTTCC
Found at i:63917 original size:28 final size:29
Alignment explanation
Indices: 63868--63923 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
63858 CGTTCTACAA
63868 AGGTTATTTCTACATTTAATTT-TTTTCC
1 AGGTTATTTCTACATTTAATTTATTTTCC
* *
63896 AGGTTATATTCTA-TTTTTATTTATTTTC
1 AGGTTAT-TTCTACATTTAATTTATTTTC
63924 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (29 bp):
AGGTTATTTCTACATTTAATTTATTTTCC
Found at i:70786 original size:14 final size:15
Alignment explanation
Indices: 70769--70797 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
70759 TATATGATAT
70769 GCATA-AACATAAGA
1 GCATATAACATAAGA
70783 GCATATAACATAAGA
1 GCATATAACATAAGA
70798 TATGTGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.17
Consensus pattern (15 bp):
GCATATAACATAAGA
Found at i:71060 original size:15 final size:15
Alignment explanation
Indices: 71042--71074 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
71032 CGAGGGTTCT
71042 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
71057 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
71072 GTA
1 GTA
71075 ATGGTCCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.24, G:0.33, T:0.27
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:71109 original size:22 final size:19
Alignment explanation
Indices: 71059--71111 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
71049 TTCGGGACGT
*
71059 AGTCCTTCGGGACGTAATG
1 AGTCCTTCGGGACATAATG
*
71078 -GTCCTACGGGACATATATAG
1 AGTCCTTCGGGACATA-AT-G
71098 CAGTCCTTCGGGAC
1 -AGTCCTTCGGGAC
71112 GAATACTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.48
19 2 0.07
20 1 0.04
22 11 0.41
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (19 bp):
AGTCCTTCGGGACATAATG
Found at i:72239 original size:15 final size:15
Alignment explanation
Indices: 72219--72247 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
72209 GGATCAATAC
72219 ATTTTGCATACATTT
1 ATTTTGCATACATTT
72234 ATTTTGCATACATT
1 ATTTTGCATACATT
72248 CATTATTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (15 bp):
ATTTTGCATACATTT
Found at i:72259 original size:22 final size:22
Alignment explanation
Indices: 72234--72280 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
72224 GCATACATTT
72234 ATTTTGCATACATTCATTATTC
1 ATTTTGCATACATTCATTATTC
*
72256 ATTTTGCATACATTCATTGTTC
1 ATTTTGCATACATTCATTATTC
72278 ATT
1 ATT
72281 GCATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (22 bp):
ATTTTGCATACATTCATTATTC
Found at i:79514 original size:20 final size:20
Alignment explanation
Indices: 79491--79528 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
79481 TATTATGCTT
79491 AAAGAAGAATAA-AAAAAGAA
1 AAAGAAGAA-AATAAAAAGAA
*
79511 AAAGTAGAAAATAAAAAG
1 AAAGAAGAAAATAAAAAG
79529 GAGGGTCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (20 bp):
AAAGAAGAAAATAAAAAGAA
Found at i:79897 original size:18 final size:18
Alignment explanation
Indices: 79874--79910 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
79864 TCCAAGTTTA
79874 TCTTTTCGAAACTCAATT
1 TCTTTTCGAAACTCAATT
* *
79892 TCTTTTTGAAATTCAATT
1 TCTTTTCGAAACTCAATT
79910 T
1 T
79911 ATTCTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.51
Consensus pattern (18 bp):
TCTTTTCGAAACTCAATT
Found at i:80486 original size:17 final size:17
Alignment explanation
Indices: 80464--80505 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
80454 ACTGAAGAAG
80464 AAGAAGAAGTTCATAAT
1 AAGAAGAAGTTCATAAT
80481 AAGAAGAAGTTCATAAT
1 AAGAAGAAGTTCATAAT
80498 AAGAAGAA
1 AAGAAGAA
80506 CTTATCTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19
Consensus pattern (17 bp):
AAGAAGAAGTTCATAAT
Found at i:80515 original size:56 final size:56
Alignment explanation
Indices: 80428--80544 Score: 173
Period size: 56 Copynumber: 2.1 Consensus size: 56
80418 ACATTTCAAG
* *
80428 GAAG-AGTTTATAATGAGAAGAACTCAACTGAAGAAGAAGAAGAAGTTCATAATAA
1 GAAGAAGTTCATAATAAGAAGAACTCAACTGAAGAAGAAGAAGAAGTTCATAATAA
* * * *
80483 GAAGAAGTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGA
1 GAAGAAGTTCATAATAAGAAGAACTCAACTGAAGAAGAAGAAGAAGTTCATAATAA
80539 GAAGAA
1 GAAGAA
80545 TTTGTTCAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
55 4 0.07
56 51 0.93
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (56 bp):
GAAGAAGTTCATAATAAGAAGAACTCAACTGAAGAAGAAGAAGAAGTTCATAATAA
Found at i:80733 original size:122 final size:123
Alignment explanation
Indices: 80483--80765 Score: 478
Period size: 122 Copynumber: 2.3 Consensus size: 123
80473 TTCATAATAA
* * *
80483 GAAGAAGTTCATAATAAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTT
1 GAAG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATAT
* *
80548 GTTCAACCTTTCGCTTGATTCTATCATAAAAGGAGATAGATCAGCATCAACATTGCCAG
65 GTTCAACCTTTCGCTTGATTCTATCACAAAAGGAGATAGATCAACATCAACATTGCCAG
80607 GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA-ATG
1 GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATATG
* * *
80671 TTCAACCTTTCGCTTGATTCTATCACAGAAGGAGATATATCAACATCAACATTTCCAG
66 TTCAACCTTTCGCTTGATTCTATCACAAAAGGAGATAGATCAACATCAACATTGCCAG
80729 GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGA
1 GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGA
80766 TTAACATTTT
Statistics
Matches: 151, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
122 92 0.61
123 55 0.36
124 4 0.03
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (123 bp):
GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATATG
TTCAACCTTTCGCTTGATTCTATCACAAAAGGAGATAGATCAACATCAACATTGCCAG
Found at i:81105 original size:16 final size:16
Alignment explanation
Indices: 81056--81097 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
81046 GTTCATAATG
81056 AGAAGAACTCATCTGA
1 AGAAGAACTCATCTGA
81072 AGAAGAA-TCCATCTGA
1 AGAAGAACT-CATCTGA
81088 AGAAGAACTC
1 AGAAGAACTC
81098 GTCCGAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (16 bp):
AGAAGAACTCATCTGA
Found at i:81919 original size:2 final size:2
Alignment explanation
Indices: 81914--81942 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
81904 TTTTACATGA
81914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
81943 ATTCATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83424 original size:22 final size:22
Alignment explanation
Indices: 83399--83446 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
83389 CTAATATTAT
83399 AGATGAAACAATTAAATTGAAA
1 AGATGAAACAATTAAATTGAAA
* *
83421 AGATGAAACAATTGAGTTGAAA
1 AGATGAAACAATTAAATTGAAA
83443 AGAT
1 AGAT
83447 CGTTCTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.04, G:0.19, T:0.23
Consensus pattern (22 bp):
AGATGAAACAATTAAATTGAAA
Found at i:85933 original size:2 final size:2
Alignment explanation
Indices: 85926--85981 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
85916 AGTTTCACAA
85926 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
85968 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
85982 CAAAGTGAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89327 original size:31 final size:31
Alignment explanation
Indices: 89291--89349 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
89281 AACTTAAAAG
* *
89291 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
89322 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
89350 CTATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:89464 original size:22 final size:22
Alignment explanation
Indices: 89415--89463 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
89405 AAAAATTATT
**
89415 TAAAATAAATCAATCGATATTT
1 TAAAATAAATCAATCGATATAA
*
89437 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCGATA-TAA
89460 TAAA
1 TAAA
89464 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCGATATAA
Found at i:89471 original size:32 final size:32
Alignment explanation
Indices: 89435--89873 Score: 196
Period size: 32 Copynumber: 14.5 Consensus size: 32
89425 CAATCGATAT
89435 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
89467 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
89489 TTTAAAATAAATCAATCCATACTAA-AAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
89520 TTTAAAATAAATCAA--T-T-C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
89542 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
**
89574 TTTAAAATAAATCAATCCATATTTTAAAATAAATTAA
1 TTTAAAATAAATCAAT-C-TATACT--AATAAATT-A
** * * *
89611 TCCACACTAATAAAT-TAT-T-TA-AAATAAATCAA
1 TTTA-A--AATAAATCAATCTATACTAATAAAT-TA
* * * * * *
89643 TTCATACTAATAAA-CTATTTAAAATAAATCAATTCATA
1 TT--TA-AAATAAATCAATCTATACT-AAT-AAAT--TA
89681 TTTTAAAATAAATCAAT-TCATACTAATAAATTA
1 -TTTAAAATAAATCAATCT-ATACTAATAAATTA
* *
89714 TTTAAAATTAATCAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCTATACTAA-TAAATTA
89744 --T--AATAAATCAATC--TA-T-AT------
1 TTTAAAATAAATCAATCTATACTAATAAATTA
89762 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
89794 TTTAAAATAAATCAATCAATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
89826 TTTAAAATAAATCAAT-TCATACT-TTAAAATTA
1 TTTAAAATAAATCAATCT-ATACTAAT-AAATTA
89858 TTTAAAATAAATCAAT
1 TTTAAAATAAATCAAT
89874 TCATACTTTA
Statistics
Matches: 316, Mismatches: 30, Indels: 122
0.68 0.06 0.26
Matches are distributed among these distances:
20 1 0.00
22 45 0.14
23 3 0.01
24 6 0.02
25 3 0.01
26 17 0.05
27 1 0.00
28 6 0.02
29 1 0.00
30 3 0.01
31 19 0.06
32 147 0.47
33 5 0.02
34 6 0.02
35 4 0.01
36 22 0.07
37 14 0.04
38 2 0.01
39 4 0.01
40 7 0.02
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACTAATAAATTA
Found at i:89489 original size:54 final size:54
Alignment explanation
Indices: 89365--89896 Score: 535
Period size: 54 Copynumber: 9.6 Consensus size: 54
89355 CAACTACAAT
89365 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA-AAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
89418 AATAAATCAATCGATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
89472 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA-AAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
89525 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
89579 AATAAATCAATCCATATTTTAAAATAAATTAATCCACACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* ** * ** * ** **
89633 AATAAATCAATTCATACTAATAAACTATTTAAAATAAAT-C-AATTCA-TATTTTAA
1 AATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATACTAATAAATTA-TTTAA
* ** * * * *
89687 AATAAATCAATTCATACTAATAAATTATTTAAAATTAATCAAT-CT-ATACAACTA--CAA
1 AATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCCATACTAATA-AATTATTTAA
* *
89744 TAATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 -AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
89799 AATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATTCATACT-TTAAAATTATTTAA
1 AATAAATCAATC----C--AT--A-T-TTTAAAATAAATCAATCCATACTAAT-AAATTATTTAA
* *
89863 AATAAATCAATTCATACTTTAAAATAAATCAATC
1 AATAAATCAATCCATATTTTAAAATAAATCAATC
89897 AAAACGACCG
Statistics
Matches: 407, Mismatches: 43, Indels: 57
0.80 0.08 0.11
Matches are distributed among these distances:
52 10 0.02
53 101 0.25
54 192 0.47
55 12 0.03
56 5 0.01
57 7 0.02
58 26 0.06
59 3 0.01
60 5 0.01
62 1 0.00
63 2 0.00
64 43 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:89493 original size:22 final size:22
Alignment explanation
Indices: 89467--89509 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
89457 TAATAAATTA
89467 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
89489 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
89510 CTAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:89546 original size:22 final size:22
Alignment explanation
Indices: 89520--89562 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
89510 CTAAAAATTA
*
89520 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
89542 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
89563 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:89571 original size:22 final size:22
Alignment explanation
Indices: 89522--89570 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
89512 AAAAATTATT
* **
89522 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
89544 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
89567 TAAA
1 TAAA
89571 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:89638 original size:86 final size:86
Alignment explanation
Indices: 89542--89855 Score: 444
Period size: 86 Copynumber: 3.7 Consensus size: 86
89532 CAATTCATAT
89542 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
* *
89607 TTAATCCACACTAATAAATTA
66 TCAATCCATACTAATAAATTA
* * *
89628 TTTAAAATAAATCAATTCATACTAATAAACTATTTAAAATAAATCAATTCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
*
89693 TCAATTCATACTAATAAATTA
66 TCAATCCATACTAATAAATTA
* * * *
89714 TTTAAAATTAATCAATCTATAC-AACTACA--A--T--AATAAATCAATCTATATTTTAAAATAA
1 TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAA
*
89772 ATCAATCTATACTAATAAATTA
65 ATCAATCCATACTAATAAATTA
* * *
89794 TTTAAAATAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATTCATACTTTAAAAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAAT
89856 TATTTAAAAT
Statistics
Matches: 200, Mismatches: 20, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
80 68 0.34
81 2 0.01
82 2 0.01
84 2 0.01
85 2 0.01
86 124 0.62
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (86 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATCCATACTAATAAATTA
Found at i:89686 original size:22 final size:22
Alignment explanation
Indices: 89660--89702 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
89650 TAATAAACTA
89660 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATTCATAT
89682 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATTCATA
89703 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATTCATAT
Found at i:89711 original size:22 final size:22
Alignment explanation
Indices: 89662--89710 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
89652 ATAAACTATT
**
89662 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATTCATATAA
89684 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATTCATA-TAA
89707 TAAA
1 TAAA
89711 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATTCATATAA
Found at i:89791 original size:22 final size:22
Alignment explanation
Indices: 89716--89790 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
89706 ATAAATTATT
* *
89716 TAAAATTAATCAATCTATACAA
1 TAAAATAAATCAATCTATATAA
**
89738 CTACAATAATAAATCAATCTATATTT
1 -T--AA-AATAAATCAATCTATATAA
89764 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATA-TAA
89787 TAAA
1 TAAA
89791 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCTATATAA
Found at i:93086 original size:12 final size:13
Alignment explanation
Indices: 93048--93085 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
93038 TTTACTTTTT
*
93048 TATTTAAAAAAAA
1 TATTTTAAAAAAA
93061 TATTTTAAAAAAA
1 TATTTTAAAAAAA
93074 TATTTTAAAAAA
1 TATTTTAAAAAA
93086 TCCCCCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TATTTTAAAAAAA
Found at i:104415 original size:93 final size:92
Alignment explanation
Indices: 104304--104472 Score: 275
Period size: 93 Copynumber: 1.8 Consensus size: 92
104294 CTGTTAATTC
* * *
104304 TTTAACAATAGGTAACTAAAGTAAAATCAAAACTATCATCATGCATAGTTTAAAAAAAACAGTTG
1 TTTAAAAATAGGTAACTAAAGTAAAATCAAAACTAACATCATGCACAGTTT-AAAAAAACAGTTG
104369 AATGATCAAAACGATTTTGTTAATTTTT
65 AATGATCAAAACGATTTTGTTAATTTTT
* *
104397 TTTAAAAATAGGTGACTAAAGTAAAATCAAAACTAACATTATGCACAGTTTAAAAAAACAGTTGA
1 TTTAAAAATAGGTAACTAAAGTAAAATCAAAACTAACATCATGCACAGTTTAAAAAAACAGTTGA
*
104462 GTGATCAAAAC
66 ATGATCAAAAC
104473 AAAATCGGCT
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 24 0.34
93 46 0.66
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (92 bp):
TTTAAAAATAGGTAACTAAAGTAAAATCAAAACTAACATCATGCACAGTTTAAAAAAACAGTTGA
ATGATCAAAACGATTTTGTTAATTTTT
Found at i:113317 original size:2 final size:2
Alignment explanation
Indices: 113310--113349 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
113300 ATCGCTAATC
113310 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
113350 TCCTTGTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115754 original size:175 final size:175
Alignment explanation
Indices: 115463--115813 Score: 684
Period size: 175 Copynumber: 2.0 Consensus size: 175
115453 GTGTTACAAA
115463 ACACTCACTACTCACAAGAAAGCTCTCTAGTATTGGGAAAAAGAAAATAATTTGGGATGATTTTG
1 ACACTCACTACTCACAAGAAAGCTCTCTAGTATTGGGAAAAAGAAAATAATTTGGGATGATTTTG
115528 AAGCTAAATGAGCTAGGGTATTTATAGTTGAAGCTTAGGGACTAATCTTATAAATACCCTAAAGT
66 AAGCTAAATGAGCTAGGGTATTTATAGTTGAAGCTTAGGGACTAATCTTATAAATACCCTAAAGT
115593 TCAATGACTCAATTTTATAATTATCCCTTGCCCAAATTAAAACAC
131 TCAATGACTCAATTTTATAATTATCCCTTGCCCAAATTAAAACAC
* *
115638 ACACTCACTACTCATAAGAAAGCTCTCTAGTATTGGGAGAAAGAAAATAATTTGGGATGATTTTG
1 ACACTCACTACTCACAAGAAAGCTCTCTAGTATTGGGAAAAAGAAAATAATTTGGGATGATTTTG
115703 AAGCTAAATGAGCTAGGGTATTTATAGTTGAAGCTTAGGGACTAATCTTATAAATACCCTAAAGT
66 AAGCTAAATGAGCTAGGGTATTTATAGTTGAAGCTTAGGGACTAATCTTATAAATACCCTAAAGT
115768 TCAATGACTCAATTTTATAATTATCCCTTGCCCAAATTAAAACAC
131 TCAATGACTCAATTTTATAATTATCCCTTGCCCAAATTAAAACAC
115813 A
1 A
115814 TGGGCTGCCT
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 174 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (175 bp):
ACACTCACTACTCACAAGAAAGCTCTCTAGTATTGGGAAAAAGAAAATAATTTGGGATGATTTTG
AAGCTAAATGAGCTAGGGTATTTATAGTTGAAGCTTAGGGACTAATCTTATAAATACCCTAAAGT
TCAATGACTCAATTTTATAATTATCCCTTGCCCAAATTAAAACAC
Found at i:132280 original size:20 final size:20
Alignment explanation
Indices: 132237--132283 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
132227 TTTTAAAGCC
* **
132237 CATTTAGAATCATGTAGATG
1 CATTTAGAAGCATGTAGAAA
*
132257 CATTTAGAAGCATTTAGAAA
1 CATTTAGAAGCATGTAGAAA
132277 CATTTAG
1 CATTTAG
132284 TTGCATGTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (20 bp):
CATTTAGAAGCATGTAGAAA
Found at i:137442 original size:20 final size:20
Alignment explanation
Indices: 137417--137459 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
137407 TTTTAAAGCC
*
137417 CATTTAGAATCATGTAGATG
1 CATTTAGAAGCATGTAGATG
* *
137437 CATTTAGAAGCATTTAGTTG
1 CATTTAGAAGCATGTAGATG
137457 CAT
1 CAT
137460 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (20 bp):
CATTTAGAAGCATGTAGATG
Found at i:154952 original size:2 final size:2
Alignment explanation
Indices: 154947--154979 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
154937 CACGCGCGCG
*
154947 CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
154980 TGAAGATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.48, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:166144 original size:42 final size:42
Alignment explanation
Indices: 166081--166183 Score: 179
Period size: 42 Copynumber: 2.5 Consensus size: 42
166071 AAATCAATTC
* * *
166081 CGTAATTTGTTTTCCGAAAAACGTTTTTCCGTGTTTGTTTCA
1 CGTAATTCGTTTTCCGGAAAACGTTTTCCCGTGTTTGTTTCA
166123 CGTAATTCGTTTTCCGGAAAACGTTTTCCCGTGTTTGTTTCA
1 CGTAATTCGTTTTCCGGAAAACGTTTTCCCGTGTTTGTTTCA
166165 CGTAATTCGTTTTCCGGAA
1 CGTAATTCGTTTTCCGGAA
166184 TGTAATTCAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.44
Consensus pattern (42 bp):
CGTAATTCGTTTTCCGGAAAACGTTTTCCCGTGTTTGTTTCA
Found at i:166431 original size:29 final size:29
Alignment explanation
Indices: 166381--166547 Score: 92
Period size: 29 Copynumber: 6.0 Consensus size: 29
166371 AAATATTTAA
166381 AATATAT-TTATTAATACT-TATAATAATAT
1 AATATATATT-TTAATA-TATATAATAATAT
166410 AATATATATTTTAATATATATAA-AATAAT
1 AATATATATTTTAATATATATAATAAT-AT
* *
166439 CAAT-TATATTATAATA-ATATAA-GATAT
1 -AATATATATTTTAATATATATAATAATAT
* *
166466 --TATAT-TTTTATTTTA-ATAAT-ATAT
1 AATATATATTTTAATATATATAATAATAT
* * * *
166490 AATAAATTTTTTTATATATTTAATAATGAAT
1 AATATATATTTTAATATATATAATAAT--AT
*
166521 AATAT-TA-TTT-ATATATTTCAATAATAT
1 AATATATATTTTAATATATAT-AATAATAT
166548 TTTAGTAAAG
Statistics
Matches: 111, Mismatches: 12, Indels: 32
0.72 0.08 0.21
Matches are distributed among these distances:
24 14 0.13
25 4 0.04
26 4 0.04
27 11 0.10
28 24 0.22
29 42 0.38
30 6 0.05
31 6 0.05
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (29 bp):
AATATATATTTTAATATATATAATAATAT
Found at i:166773 original size:20 final size:20
Alignment explanation
Indices: 166715--166764 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
166705 TTTCCAGATG
166715 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
166735 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
166755 TTTTCCAGAA
1 TTTTCCAGAA
166765 TTCAAATTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:166783 original size:15 final size:15
Alignment explanation
Indices: 166747--166828 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
166737 TTACAGAAAT
**
166747 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
166762 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
166776 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
166791 GTAATTCAAATTACA
1 GTAATTCAAATTCCA
166806 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
166821 GTAATTCA
1 GTAATTCA
166829 TTTTCTGGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:166799 original size:30 final size:30
Alignment explanation
Indices: 166747--166828 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
166737 TTACAGAAAT
*
166747 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTACA
166776 GTAATTCATTTTCCAGTAATTCAAATTACA
1 GTAATTCATTTTCCAGTAATTCAAATTACA
**
166806 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
166829 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTACA
Found at i:166907 original size:2 final size:2
Alignment explanation
Indices: 166900--166930 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
166890 CAAAAGCCTC
166900 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
166931 GGTTGTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:167059 original size:18 final size:19
Alignment explanation
Indices: 167021--167064 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
167011 TTAATTACGA
167021 TTATA-ATTATATCAATGT
1 TTATATATTATATCAATGT
*
167039 TTATATATTATATTAAT-T
1 TTATATATTATATCAATGT
*
167057 TTAAATAT
1 TTATATAT
167065 AGTCATTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TTATATATTATATCAATGT
Found at i:168477 original size:16 final size:16
Alignment explanation
Indices: 168456--168504 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
168446 ACTTAAATTT
168456 TAAAAATATATTATTA
1 TAAAAATATATTATTA
*
168472 TAAAAATATTCATGTATTT
1 TAAAAATA-T-AT-TATTA
*
168491 TAAATATATATTAT
1 TAAAAATATATTAT
168505 AAAATAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
18 3 0.11
19 11 0.39
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (16 bp):
TAAAAATATATTATTA
Found at i:176880 original size:64 final size:64
Alignment explanation
Indices: 176736--176888 Score: 170
Period size: 64 Copynumber: 2.4 Consensus size: 64
176726 AAGGTGTATT
* * * * *
176736 GATGCACAGGTAGTGCATCGATGCA-CTCTTTTAAATAAAACCATCGAATGCAATTAGTGCATC
1 GATGCACAAGTAGTGCATCGATGCATCCCATTAAAATAAAACCATCGAATGCAATTAGTGCACC
* * *
176799 GATGCATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAA-CATCGAATGCATTTTA-TGCA
1 GATGCACAA-GTAGTGCATCGATGCATCCCATTAA-AATAAAACCATCGAATGCA-ATTAGTGCA
176861 CC
63 CC
*
176863 GATGCACAAGTAGTGCATCAATGCAT
1 GATGCACAAGTAGTGCATCGATGCAT
176889 ACCTTCATTA
Statistics
Matches: 74, Mismatches: 11, Indels: 9
0.79 0.12 0.10
Matches are distributed among these distances:
63 21 0.28
64 43 0.58
65 10 0.14
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (64 bp):
GATGCACAAGTAGTGCATCGATGCATCCCATTAAAATAAAACCATCGAATGCAATTAGTGCACC
Found at i:177433 original size:15 final size:15
Alignment explanation
Indices: 177415--177448 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
177405 GAGGGTATAA
*
177415 TAGTCCTTTGGGACG
1 TAGTCCTTCGGGACG
*
177430 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
177445 TAGT
1 TAGT
177449 GGTTCTACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.32, T:0.35
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:183710 original size:63 final size:64
Alignment explanation
Indices: 183643--183799 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 64
183633 TTAAAGGTGT
* * * *
183643 ATCGATGCACAGGTAGTGCATCGGTGCA-CTCTTTTA-AATAAAAACATCGAATGCAATTAATGC
1 ATCGATGCACAGGTAGTGCATCGATGCATCCCATTAATAAT-AAAACATCGAATGCAATTAATGC
* * * * *
183706 ATCGATGCATAAGGCA-TGCATCGATACATCCCATTAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTAATGC
* *
183770 ACCGATGCACAAGTAAGTGCATCGATGCAT
1 ATCGATGCACAGGT-AGTGCATCGATGCAT
183800 ACCTTCATTA
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
63 21 0.28
64 39 0.52
65 15 0.20
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTAATGC
Found at i:185708 original size:22 final size:22
Alignment explanation
Indices: 185677--185743 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
185667 AATATTAGAT
*
185677 TATAAGTAAAATATTA-AAAGAA
1 TATAAGTAAAATAATATAAA-AA
*
185699 TATAATTAAAATAATATAAAAA
1 TATAAGTAAAATAATATAAAAA
*
185721 TAT-AGTAAAA-AATAATGAAAA
1 TATAAGTAAAATAAT-ATAAAAA
185742 TA
1 TA
185744 ATTATATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
20 3 0.08
21 14 0.36
22 19 0.49
23 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (22 bp):
TATAAGTAAAATAATATAAAAA
Found at i:187189 original size:105 final size:105
Alignment explanation
Indices: 186981--187511 Score: 812
Period size: 105 Copynumber: 5.0 Consensus size: 105
186971 GCATTGTTCC
* * ** * *
186981 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTT-GTTGTTGACA
* * * *
187045 ACCAGCCGTCCCTTCGTTGTGGAGTTGAACTTGCGTTGTCTG
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
187087 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
187152 CAGAGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
187192 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
187257 TAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
187297 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
187362 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
187402 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
187467 CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
187508 GAGT
1 GAGT
187512 GTCACGATAT
Statistics
Matches: 396, Mismatches: 27, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
105 300 0.76
106 95 0.24
107 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:187757 original size:35 final size:35
Alignment explanation
Indices: 187711--187784 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
187701 TGTTTGGAGA
* *
187711 GAAACTGTCTCAAGGGAGACAAAATTC-GTTCAAGG
1 GAAACTATCTCAAGCGAGA-AAAATTCAGTTCAAGG
* *
187746 GAAACTATCTCAAGCGAGATAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGAAAAATTCAGTTCAAGG
187781 GAAA
1 GAAA
187785 TGTTTTCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 6 0.18
35 28 0.82
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (35 bp):
GAAACTATCTCAAGCGAGAAAAATTCAGTTCAAGG
Found at i:187907 original size:105 final size:104
Alignment explanation
Indices: 187686--188002 Score: 439
Period size: 105 Copynumber: 3.1 Consensus size: 104
187676 TTCATTAAAT
* ** * * *
187686 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAA---ATTCG-TTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTTTTGTTTCGAGGG
* *
187747 AAACTATCTCAAGCGAG-ATAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
*
187785 TGTTTTCAATATTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTTTTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTTTTGTTTCGAGGG
*
187850 AAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAATTCATTTCAAGGGAAA
* * *
187890 TGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTCTT-TTTCGAGA
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTTTTTTGTTTCGAGG
* *
187954 GAAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAA
65 GAAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
187994 TGTTTTCAA
1 TGTTTTCAA
188003 GAGAAACTGT
Statistics
Matches: 194, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
99 44 0.23
102 3 0.02
103 23 0.12
104 29 0.15
105 86 0.44
106 9 0.05
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTTTTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:188211 original size:72 final size:74
Alignment explanation
Indices: 188073--188251 Score: 199
Period size: 72 Copynumber: 2.4 Consensus size: 74
188063 TAAAATCTTC
** * * **
188073 TTAA-AAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CATTCTTTCGAGTAAAAACAATCTCAAGCGAGA
*
188137 CAAA-TCTTGTT
64 CAAAGT-ATGTT
*
188148 TTAAGAAAAACAATCTTGAGTGAAATAAAT-ATTCTTTCGAG-AAAAACAATCTCAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAATCATTCTTTCGAGTAAAAACAATCTCAAGCGAGACA
188211 AAGTATGTT
66 AAGTATGTT
*
188220 TTAAGAAAAACAAAT-TTGAGTGAGAT-AATCAT
1 TTAAGAAAAAC-AATCTTGAGTGAAATAAATCAT
188252 CTGCATTAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
71 3 0.03
72 47 0.52
73 14 0.15
75 8 0.09
76 19 0.21
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATCATTCTTTCGAGTAAAAACAATCTCAAGCGAGACA
AAGTATGTT
Found at i:188242 original size:36 final size:35
Alignment explanation
Indices: 188133--188244 Score: 111
Period size: 36 Copynumber: 3.1 Consensus size: 35
188123 GGTCTCAAGC
*
188133 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
1 GAGACAAAT-ATGTTTTAAGAAAAACAATCTTGAGT
* * * **
188169 GAAATAAATAT-TCTTTCGAGAAAAACAATCTCAAGT
1 GAGACAAATATGT-TTT-AAGAAAAACAATCTTGAGT
188205 GAGACAAAGTATGTTTTAAGAAAAACAAAT-TTGAGT
1 GAGACAAA-TATGTTTTAAGAAAAAC-AATCTTGAGT
188241 GAGA
1 GAGA
188245 TAATCATCTG
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
34 1 0.02
35 4 0.07
36 45 0.75
37 9 0.15
38 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.28
Consensus pattern (35 bp):
GAGACAAATATGTTTTAAGAAAAACAATCTTGAGT
Found at i:189693 original size:183 final size:183
Alignment explanation
Indices: 189381--189917 Score: 914
Period size: 183 Copynumber: 2.9 Consensus size: 183
189371 ATCAGGTTTA
* *
189381 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTAGAGCAAACACCGAATT
* *
189446 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGT
* *
189510 TTCCTCTATAACCAATTTCCTTAGTAGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* * * *
189564 ACTTAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGAAGTTGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTAGAGCAAACACCGAATT
*
189629 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
189694 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
189747 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTAGAGCAAACACTGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTAGAGCAAACACCGAATT
* * * *
189812 ACCAAGTGTCTGAACAGTGTCATAGTTTGAATATAATCTATTCATAAAGCTAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
189877 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
189918 CGGATTTAAT
Statistics
Matches: 333, Mismatches: 20, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
183 332 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTAGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAATATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:194028 original size:21 final size:22
Alignment explanation
Indices: 193987--194058 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
193977 TAAAGAAAAC
*
193987 AAATAAGATACAATGAAATAATA
1 AAATAAGATAAAAT-AAATAATA
194010 AAATAA-ATAAAATAAATAAGTA
1 AAATAAGATAAAATAAATAA-TA
* * *
194032 AGATAAGA-AAAAAAAATAGTA
1 AAATAAGATAAAATAAATAATA
194053 AAATAA
1 AAATAA
194059 TAATTATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
21 13 0.31
22 22 0.52
23 7 0.17
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.19
Consensus pattern (22 bp):
AAATAAGATAAAATAAATAATA
Found at i:194112 original size:2 final size:2
Alignment explanation
Indices: 194105--194129 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
194095 TATTAAAGAA
194105 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 A
194130 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:194631 original size:37 final size:37
Alignment explanation
Indices: 194581--194684 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
194571 GTGCTTGTGG
* * * *
194581 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAACTCT
* * *
194618 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAACTCT
194655 ATCCTATTTTTAGGAGTTTGAATCTTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCTTAGTA
194685 TGACGAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.44
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAACTCT
Found at i:196780 original size:32 final size:32
Alignment explanation
Indices: 196717--196819 Score: 153
Period size: 27 Copynumber: 3.3 Consensus size: 32
196707 TTCATCCTAA
196717 ACCCGACCCGAATATCACACTT-AAAAA----
1 ACCCGACCCGAATATCACACTTAAAAAACCCG
196744 ACCCGACCCGAATATCACACTTAAAAAACCCG
1 ACCCGACCCGAATATCACACTTAAAAAACCCG
*
196776 ACCCGACCCAAATATCACACTTAAAAAAACCCG
1 ACCCGACCCGAATATCACACTT-AAAAAACCCG
196809 ACCCGACCCGA
1 ACCCGACCCGA
196820 TCAAAATATG
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
27 22 0.32
28 5 0.07
32 21 0.31
33 20 0.29
ACGTcount: A:0.42, C:0.38, G:0.09, T:0.12
Consensus pattern (32 bp):
ACCCGACCCGAATATCACACTTAAAAAACCCG
Found at i:205427 original size:23 final size:23
Alignment explanation
Indices: 205397--205442 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
205387 TTTATTAATC
205397 TTATTGATTATGTTCTGCGAAAA
1 TTATTGATTATGTTCTGCGAAAA
205420 TTATTGATTATGTTCTGCGAAAA
1 TTATTGATTATGTTCTGCGAAAA
205443 GGTTTAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (23 bp):
TTATTGATTATGTTCTGCGAAAA
Found at i:211605 original size:17 final size:19
Alignment explanation
Indices: 211569--211606 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
211559 AGTTATCTAA
211569 TAATTATTGTGATTTTATTT
1 TAATTATTGTGA-TTTATTT
211589 TAATTATT-TGA-TTATTT
1 TAATTATTGTGATTTATTT
211606 T
1 T
211607 TTAAAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
19 3 0.17
20 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (19 bp):
TAATTATTGTGATTTATTT
Found at i:211608 original size:19 final size:20
Alignment explanation
Indices: 211569--211610 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
211559 AGTTATCTAA
211569 TAATTATTGTGATTTTATTT
1 TAATTATTGTGATTTTATTT
211589 TAATTATT-TGATTATT-TTT
1 TAATTATTGTGATT-TTATTT
211608 TAA
1 TAA
211611 AATCATGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (20 bp):
TAATTATTGTGATTTTATTT
Found at i:213420 original size:29 final size:29
Alignment explanation
Indices: 213368--213428 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
213358 ATATCACCAT
* *
213368 ATTTTTCTAATATTTTCGATGTAACA-TC
1 ATTTTTCTAATATTTTCAAAGTAACACTC
*
213396 ATTTTTTTAATATTTTCCAAAGTAACACTC
1 ATTTTTCTAATATTTT-CAAAGTAACACTC
213426 ATT
1 ATT
213429 CGGCTAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 15 0.54
29 8 0.29
30 5 0.18
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (29 bp):
ATTTTTCTAATATTTTCAAAGTAACACTC
Found at i:214019 original size:25 final size:25
Alignment explanation
Indices: 213991--214067 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
213981 ATCGAACCTT
* * *
213991 ACCCTAAACCACTTTATCATAGACA
1 ACCCTAAACCACTTTACCATAAAAA
* * *
214016 ACCCTTAACCGCTCTTACCTTAAAAA
1 ACCCTAAACCACT-TTACCATAAAAA
214042 ACCCTAAACCACTTTAACCTATAAAA
1 ACCCTAAACCACTTT-ACC-ATAAAA
214068 TCTTTCATCA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
25 13 0.32
26 22 0.55
27 5 0.12
ACGTcount: A:0.40, C:0.32, G:0.03, T:0.25
Consensus pattern (25 bp):
ACCCTAAACCACTTTACCATAAAAA
Found at i:231468 original size:3 final size:3
Alignment explanation
Indices: 231453--231498 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
231443 TTATATTTAT
* *
231453 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
231499 CATTGCAGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 36 0.95
4 2 0.05
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:233182 original size:137 final size:136
Alignment explanation
Indices: 233032--233280 Score: 308
Period size: 137 Copynumber: 1.8 Consensus size: 136
233022 ATCATAATTT
* * * *
233032 TTATTTATATATTTATTAAATAT-TAAGAAATG-G-TAGTCTTAAAACAACTGGATGTCCATTTT
1 TTATTTATATATTT-TTAAATATCAAAGAAAAGAGCT-GTCTTAAAACAACTAGAAGTCC-TTTT
*
233094 CTGATA-TTCTTAAATAAATAAATATCATATTTTTATAAATTATATATATTTATTATTATTAGAA
63 CTGATATTTC-TAAATAAATAAATATCATATTTATATAAATTA-ATATATTTATTATTATTAGAA
233158 AAATGTTTTAA
126 AAATGTTTTAA
* * ** *
233169 TTATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTG
1 TTATTTATATATTTTTAAATATCAAAGAAAAGAGCTGTCTTAAAACAACTAGAAGTCCTTTTCTG
* * *
233234 ATATTTCTAAATAAGTAAATATCTTATTTATATATATTAATATATTT
66 ATATTTCTAAATAAATAAATATCATATTTATATAAATTAATATATTT
233281 TCTTAAAATT
Statistics
Matches: 95, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
136 15 0.16
137 58 0.61
138 21 0.22
139 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.46
Consensus pattern (136 bp):
TTATTTATATATTTTTAAATATCAAAGAAAAGAGCTGTCTTAAAACAACTAGAAGTCCTTTTCTG
ATATTTCTAAATAAATAAATATCATATTTATATAAATTAATATATTTATTATTATTAGAAAAATG
TTTTAA
Found at i:234383 original size:46 final size:49
Alignment explanation
Indices: 234307--234398 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 49
234297 ATTTTCCTTT
* *
234307 ATTTTTCCTAAATAAACACATGCGAACTAGAAATCATGCA-GTTAGGTTA
1 ATTTTTCCTAAACAAACACATGCGAACTAGAAAGCATG-AGGTTAGGTTA
*
234356 ATTTTTCC-AAACAAA-GCATG-GAACTAGAAAGCATGAGGTTAGG
1 ATTTTTCCTAAACAAACACATGCGAACTAGAAAGCATGAGGTTAGG
234399 ATACATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
45 1 0.03
46 20 0.51
47 4 0.10
48 6 0.15
49 8 0.21
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (49 bp):
ATTTTTCCTAAACAAACACATGCGAACTAGAAAGCATGAGGTTAGGTTA
Found at i:235770 original size:8 final size:7
Alignment explanation
Indices: 235746--235787 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
235736 TTTTCATACA
235746 TGCA-TT
1 TGCATTT
235752 TGCATTT
1 TGCATTT
235759 TGCATCTT
1 TGCAT-TT
235767 TGCATTT
1 TGCATTT
* *
235774 TTCATTG
1 TGCATTT
235781 TGCATTT
1 TGCATTT
235788 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:235770 original size:15 final size:14
Alignment explanation
Indices: 235746--235787 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
235736 TTTTCATACA
235746 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
235759 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
235774 TTCATTGTGCATTT
1 TGCATTTTGCATTT
235788 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:235864 original size:15 final size:15
Alignment explanation
Indices: 235846--235875 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
235836 ACATTCAATA
235846 TTTACATTTGCATTT
1 TTTACATTTGCATTT
*
235861 TTTACATTTGTATTT
1 TTTACATTTGCATTT
235876 ACATTTCATT
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:0.20, C:0.10, G:0.07, T:0.63
Consensus pattern (15 bp):
TTTACATTTGCATTT
Found at i:236359 original size:235 final size:228
Alignment explanation
Indices: 235900--236362 Score: 854
Period size: 235 Copynumber: 2.0 Consensus size: 228
235890 ATAATACATT
235900 TGGTTTTAACTATTTACATACATTTAAACATGAAAACATGAGAGTATTCGTGGAGGATTCCATGA
1 TGGTTTTAACTATTTACATACATTTAAACATGAAAACATGAGAGTATTCGTGGAGGATTCCATGA
*
235965 CAAATTTCTGAAATCAAAGTGGAGCTAACTTGGTCTTCCTAAACAAGGATAAGAACCATGAATGA
66 CAAATTTCTAAAATCAAAGTGGAGCTAACTTGGTCTTCCTAAACAAGGATAAGAACCATGAATGA
236030 GATTTTAGCAAGGGTTGGAATTGAGAAACTACAAGAGCAACTTATCAAGACTCAACAAGAGATGA
131 GATTTTAGCAAGGGTTGGAATTGAGAAACTACAAGAGCAACTTATCAAGACTCAACAAGAGATGA
236095 TTGATCAATTAAAAAAATCCCATAATGATTCAA
196 TTGATCAATTAAAAAAATCCCATAATGATTCAA
236128 TGGTTTTAAACTATTTTACATACATTTAAACATGAAAACATGAGAGTAATTCGTGGAGGATTCCA
1 TGGTTTT-AACTA-TTTACATACATTTAAACATGAAAACATGAGAGT-ATTCGTGGAGGATTCCA
236193 TGACAGAATTTCTAAAATCAAAGTGGAGCTAACTTGGTCTTCCTAAACAAGGATAAGAACCATGA
63 TGACA-AATTTCTAAAATCAAAGTGGAGCTAACTTGGTCTTCCTAAACAAGGATAAGAACCATGA
236258 ATGAGATTTTAGCAAGGGTTGGTGGAATTGAGAAACTACAAGAGCAACTTATCAAGACTCAACAA
127 ATGAGATTTTAGCAAGGG-T--TGGAATTGAGAAACTACAAGAGCAACTTATCAAGACTCAACAA
236323 GAGATGATTGATCAATTAAAAAAATCCCATAATGATTCAA
189 GAGATGATTGATCAATTAAAAAAATCCCATAATGATTCAA
236363 AAGAGCAAAT
Statistics
Matches: 227, Mismatches: 1, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
228 7 0.03
229 5 0.02
230 33 0.15
231 22 0.10
232 76 0.33
233 1 0.00
235 83 0.37
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (228 bp):
TGGTTTTAACTATTTACATACATTTAAACATGAAAACATGAGAGTATTCGTGGAGGATTCCATGA
CAAATTTCTAAAATCAAAGTGGAGCTAACTTGGTCTTCCTAAACAAGGATAAGAACCATGAATGA
GATTTTAGCAAGGGTTGGAATTGAGAAACTACAAGAGCAACTTATCAAGACTCAACAAGAGATGA
TTGATCAATTAAAAAAATCCCATAATGATTCAA
Found at i:236903 original size:70 final size:68
Alignment explanation
Indices: 236790--236929 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 68
236780 CAAAGCCTTA
236790 TGCCCATTGCTATGATCAAAATAGCTTCTGTAATTTTCACTTGGGGGTATCTGGAAATTCAACAG
1 TGCCCATTGCTATGATCAAAATAGCTTCTGTAATTTTCACTT-GGGGTATCTGG-AATTCAACAG
236855 GGAAT
64 GGAAT
236860 TGCCCATTGCTATGATCAAAATAGCTTCTGTAATTTTCACTTGGGGTATCTGGAATTCAACAGGG
1 TGCCCATTGCTATGATCAAAATAGCTTCTGTAATTTTCACTTGGGGTATCTGGAATTCAACAGGG
236925 AAT
66 AAT
236928 TG
1 TG
236930 TTGGTCACTG
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
68 17 0.24
69 11 0.16
70 42 0.60
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (68 bp):
TGCCCATTGCTATGATCAAAATAGCTTCTGTAATTTTCACTTGGGGTATCTGGAATTCAACAGGG
AAT
Found at i:242774 original size:22 final size:22
Alignment explanation
Indices: 242746--242805 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
242736 TACATCTACA
*
242746 CTCTTTTCAAAGATGATAGTTT
1 CTCTTTTCAAAGATGATAGATT
*
242768 CTCTTTTTAAAGATGATAGATT
1 CTCTTTTCAAAGATGATAGATT
*
242790 CTCTTTTCAAATATGA
1 CTCTTTTCAAAGATGA
242806 AAGCTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (22 bp):
CTCTTTTCAAAGATGATAGATT
Found at i:243581 original size:76 final size:76
Alignment explanation
Indices: 243482--243789 Score: 528
Period size: 76 Copynumber: 4.1 Consensus size: 76
243472 CTATTTCCCA
** *
243482 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
243547 AGCCTCAGGGT
66 AGCCTCAGGGT
*
243558 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
243623 AGCCTTAGGGT
66 AGCCTCAGGGT
*
243634 CATCTGTAATTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
243699 AGCCTTAGGGT
66 AGCCTCAGGGT
243710 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
243775 AGTCTTC-GGGT
66 AG-CCTCAGGGT
243786 CATC
1 CATC
243790 CATAAGACCT
Statistics
Matches: 221, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
76 219 0.99
77 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTCAGGGT
Found at i:244023 original size:112 final size:112
Alignment explanation
Indices: 243824--244137 Score: 495
Period size: 112 Copynumber: 2.8 Consensus size: 112
243814 TTTTTCTTAA
* * *
243824 AACATTTTCAGGTAGAGTTCATAATGAGAAGAACTCATCTAAAG-AGGAAGAAAAAGTTCATAAT
1 AACATTTTCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
*
243888 GAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCATTCGATGGATT
65 GAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATT
*
243936 AGCATTTTCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 AACATTTTCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
**
244001 AGAAGAACTTGTTCAAGTTTTTGCTCGAATTCATCATTCGATGGATT
66 AGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATT
* * * *
244048 AACATTTCCAAAAGAGTTCATAATGAGAAGAACCCATCTGAAGAAAGAAGAAGAAGTTCATAATG
1 AACATTTTCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* *
244113 AGAAAAACTTATTCAACCTTTTGCT
66 AGAAGAACTTGTTCAACCTTTTGCT
244138 TGACTCCATT
Statistics
Matches: 185, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
111 31 0.17
112 154 0.83
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (112 bp):
AACATTTTCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATT
Found at i:245446 original size:64 final size:64
Alignment explanation
Indices: 245375--245581 Score: 220
Period size: 64 Copynumber: 3.2 Consensus size: 64
245365 ATGCACAGGA
**
245375 AGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCATGCATCAATGCATAAG
1 AGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTCATGCATCAATGCATAAG
*
245438 T
64 G
* * ** *
245439 AGTGCATCGATGTATCCCATTAATAATGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCAATGCATAAGG
** * * * * * * * *
245503 AGTGCATCGATGCATCCCAGCAATAATACAACATCGAATACATTTTATGCACCGATGCATCAGT
1 AGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCAATGCATAAGG
245567 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
245582 ACCTTCATTA
Statistics
Matches: 121, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
64 115 0.95
65 6 0.05
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (64 bp):
AGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCAATGCATAAGG
Found at i:246133 original size:31 final size:31
Alignment explanation
Indices: 246089--246248 Score: 284
Period size: 31 Copynumber: 5.2 Consensus size: 31
246079 AAAGTCGAGG
246089 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
246120 GTTTATATTTGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
246151 GTTTACATATGTTTAAAGGAACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
246182 GTTTATATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
246213 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
246244 GTTTA
1 GTTTA
246249 TATTGTGACC
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 121 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:252233 original size:42 final size:41
Alignment explanation
Indices: 252167--252273 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 41
252157 TTCACAATTT
* * * *
252167 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * *
252208 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* *
252250 ATAAGTCCTTCGGGCCATCCGTAA
1 ATAAATCCTTCGGGCCATCAGTAA
252274 AACCTTCGGG
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
41 20 0.37
42 34 0.63
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:252430 original size:214 final size:214
Alignment explanation
Indices: 252061--252447 Score: 684
Period size: 214 Copynumber: 1.8 Consensus size: 214
252051 CATTCATAAG
* *
252061 ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAATGATGTTTTAAGAAGATGGAAT
1 ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTAAGAAGATGAAAT
*
252126 TTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAA
66 TTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAA
* *
252191 GTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGT
131 GTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATCTGTAAGCCTTTAGAGCAAGATGATAAGT
252256 CCTTCGGGCCATCCGTAAA
196 CCTTCGGGCCATCCGTAAA
* *
252275 ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATGAAAAACGATGTTTTGAGAAGATGAAAT
1 ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTAAGAAGATGAAAT
* *
252340 TTTTGAAAACAAATAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGTCCATCAGTAA
66 TTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAA
*
252405 GTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAG
131 GTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATCTGTAAG
252448 TCTTCACCGA
Statistics
Matches: 163, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
214 163 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (214 bp):
ACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATAAAAAACGATGTTTTAAGAAGATGAAAT
TTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAA
GTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATCTGTAAGCCTTTAGAGCAAGATGATAAGT
CCTTCGGGCCATCCGTAAA
Found at i:252493 original size:13 final size:13
Alignment explanation
Indices: 252475--252499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
252465 TGAAGCAAAC
252475 CCATCAGTAAGTG
1 CCATCAGTAAGTG
252488 CCATCAGTAAGT
1 CCATCAGTAAGT
252500 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:252546 original size:42 final size:42
Alignment explanation
Indices: 252487--252570 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
252477 ATCAGTAAGT
252487 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
*
252529 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
252571 ATAATTTGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
Found at i:252679 original size:42 final size:41
Alignment explanation
Indices: 252616--252707 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 41
252606 AAATTCATCA
*
252616 GTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTT
1 GTAAGTCTTTCGAGCATGATGAT-AAATCCTTCGGGCCATTT
* *
252658 GTAAGTCTTTCGAGTGA-GATGATAAGTCCTTCGGGCCATTT
1 GTAAGTCTTTCGAG-CATGATGATAAATCCTTCGGGCCATTT
*
252699 -TAAGCCTTT
1 GTAAGTCTTT
252708 TCGGAATAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
40 8 0.18
41 16 0.36
42 20 0.44
43 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (41 bp):
GTAAGTCTTTCGAGCATGATGATAAATCCTTCGGGCCATTT
Found at i:253154 original size:53 final size:53
Alignment explanation
Indices: 253074--253281 Score: 339
Period size: 53 Copynumber: 3.9 Consensus size: 53
253064 AGAATCACAC
* *
253074 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTATTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* *
253127 CAGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACCCGTAAG
1 CAGAAGATTATTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
*
253180 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
1 CAGAAGATTATTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
*
253233 CAGAAGATTATTCAAATTCTACTCCCTGAA-CAAGAGGGAGC-AGACCCGT
1 CAGAAGATTATTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGA-ACCCGT
253282 CATTCGAAGA
Statistics
Matches: 145, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
51 1 0.01
52 17 0.12
53 127 0.88
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (53 bp):
CAGAAGATTATTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
Found at i:255381 original size:19 final size:19
Alignment explanation
Indices: 255357--255407 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
255347 ATGCAATTCA
255357 TGCATCGATGCATAAGTAG
1 TGCATCGATGCATAAGTAG
255376 TGCATCGATGCATAAGTAG
1 TGCATCGATGCATAAGTAG
255395 TGCATCGATGCAT
1 TGCATCGATGCAT
255408 CCCATTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (19 bp):
TGCATCGATGCATAAGTAG
Found at i:255397 original size:83 final size:83
Alignment explanation
Indices: 255296--255467 Score: 233
Period size: 83 Copynumber: 2.1 Consensus size: 83
255286 TTGAAGGTGT
**
255296 ATCGATGCAAAGGAAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCATG
1 ATCGATGCAAAGGAAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTCATG
*
255359 CATCGATGCATAAGTAGTGC
64 CATCGATGCATAAGGAGTGC
* * **
255379 ATCGATGCATAA-GTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCA-AAGGAAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
255443 ATCGATGCATAAGGAGTGC
65 ATCGATGCATAAGGAGTGC
255462 ATCGAT
1 ATCGAT
255468 ACATCCCAGC
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
83 71 0.90
84 8 0.10
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (83 bp):
ATCGATGCAAAGGAAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCA
TCGATGCATAAGGAGTGC
Found at i:255443 original size:64 final size:64
Alignment explanation
Indices: 255375--255535 Score: 216
Period size: 64 Copynumber: 2.5 Consensus size: 64
255365 TGCATAAGTA
** *
255375 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGA-AACATCGAATGCAATTG
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAAT-ACAACATCGAATACAATTG
* * * *
255439 GTGCATCGATGCATAAGGAGTGCATCGATACATCCCAGCAATAATACAACATCGAATACATTTT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACAACATCGAATACAATTG
* * *
255503 ATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCAT
255536 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 1 0.01
64 83 0.99
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (64 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACAACATCGAATACAATTG
Found at i:256100 original size:16 final size:16
Alignment explanation
Indices: 256079--256163 Score: 52
Period size: 16 Copynumber: 5.4 Consensus size: 16
256069 ATGAACATTT
256079 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
* ***
256095 ACATATG--AACAATTT
1 ACATATGTTTA-AAGGC
256110 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
* ***
256126 ACATATG--AACAATTT
1 ACATATGTTTA-AAGGC
256141 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
256157 ACATATG
1 ACATATG
256164 AACAGTTTAT
Statistics
Matches: 47, Mismatches: 16, Indels: 12
0.63 0.21 0.16
Matches are distributed among these distances:
14 2 0.04
15 18 0.38
16 25 0.53
17 2 0.04
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (16 bp):
ACATATGTTTAAAGGC
Found at i:256113 original size:31 final size:31
Alignment explanation
Indices: 256046--256234 Score: 335
Period size: 31 Copynumber: 6.1 Consensus size: 31
256036 GAGTCGAGGG
*
256046 TTTACATATGTTTAAAGGAACATATGAAC-A
1 TTTACATATGTTTAAAGGCACATATGAACAA
256076 TTTACATATGTTTAAAGGCACATATGAACAA
1 TTTACATATGTTTAAAGGCACATATGAACAA
256107 TTTACATATGTTTAAAGGCACATATGAACAA
1 TTTACATATGTTTAAAGGCACATATGAACAA
*
256138 TTTACATATGTTTAAAGGCACATATGAACAG
1 TTTACATATGTTTAAAGGCACATATGAACAA
*
256169 TTTATATATGTTTAAAGGCACATATGAACAA
1 TTTACATATGTTTAAAGGCACATATGAACAA
*
256200 TTTACATATGTTTAAAGGCACATATGAACAG
1 TTTACATATGTTTAAAGGCACATATGAACAA
256231 TTTA
1 TTTA
256235 TATTGTGACC
Statistics
Matches: 152, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
30 28 0.18
31 124 0.82
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.34
Consensus pattern (31 bp):
TTTACATATGTTTAAAGGCACATATGAACAA
Found at i:257163 original size:3 final size:3
Alignment explanation
Indices: 257157--257215 Score: 75
Period size: 3 Copynumber: 19.0 Consensus size: 3
257147 TTGATTTTTT
*
257157 TTA TTA TTA TTA -TA TTTA TTTA TTA TTA TTA TTA TTA TTA TTAA ATA
1 TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TT-A TTA
257204 TTA TTA TTA TTA
1 TTA TTA TTA TTA
257216 CATTGCAGGC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 2 0.04
3 41 0.80
4 8 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:257185 original size:22 final size:22
Alignment explanation
Indices: 257150--257213 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
257140 TTTCCATTTG
257150 ATTT-TTT-TTATTATTATTAT
1 ATTTATTTATTATTATTATTAT
257170 ATTTATTTATTATTATTATTAT
1 ATTTATTTATTATTATTATTAT
* *
257192 -TATTATTAAATATTATTATTAT
1 AT-TTATTTATTATTATTATTAT
257214 TACATTGCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.10
21 4 0.10
22 31 0.79
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTATTTATTATTATTATTAT
Found at i:257194 original size:19 final size:19
Alignment explanation
Indices: 257156--257214 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
257146 TTTGATTTTT
257156 TTTATTATTATTA-TATTTA
1 TTTATTATTATTATTA-TTA
257175 TTTATTATTATTATTATTA
1 TTTATTATTATTATTATTA
*
257194 -TTATTAAATATTATTATTA
1 TTTATT-ATTATTATTATTA
257213 TT
1 TT
257215 ACATTGCAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 5 0.14
19 28 0.78
20 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATTATTATTATTATTA
Found at i:257214 original size:22 final size:23
Alignment explanation
Indices: 257158--257215 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 23
257148 TGATTTTTTT
* *
257158 TATTATTATTA-TATTTATTTAT
1 TATTATTATTATTATTTATTAAA
257180 TATTATTATTATTA-TTATTAAA
1 TATTATTATTATTATTTATTAAA
257202 TATTATTATTATTA
1 TATTATTATTATTA
257216 CATTGCAGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 31 0.94
23 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTATTATTATTATTTATTAAA
Found at i:261542 original size:17 final size:16
Alignment explanation
Indices: 261516--261549 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
261506 CTAAAATCAT
261516 ATTTTGCTTAGTTTAA
1 ATTTTGCTTAGTTTAA
261532 ATTTCTGCTTAGTTTAA
1 ATTT-TGCTTAGTTTAA
261549 A
1 A
261550 GGGTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (16 bp):
ATTTTGCTTAGTTTAA
Done.