Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001381.1 Hibiscus syriacus cultivar Beakdansim tig00002695_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: 64160
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:5113 original size:35 final size:34
Alignment explanation
Indices: 5049--5206 Score: 183
Period size: 36 Copynumber: 4.4 Consensus size: 34
5039 AAAAATCGTT
*
5049 TTTTG-AAATATATATATAATATGGTTTTTTAAAACA
1 TTTTGAAAATATATA-AT-ATATAG-TTTTTAAAACA
*
5085 TTTTGAAAATATATAATATATCGGTTTTTAAAACA
1 TTTTGAAAATATATAATATAT-AGTTTTTAAAACA
* *
5120 TTTTGAAAACTTATATAATATATAATTTTTAAAATA
1 TTTTGAAAA--TATATAATATATAGTTTTTAAAACA
*
5156 TTTTGAATATATATATAATATATAGTTTTTAAAATA
1 TTTTGAA-A-ATATATAATATATAGTTTTTAAAACA
*
5192 TTTTTAAAATATATA
1 TTTTGAAAATATATA
5207 TAATTGAAAA
Statistics
Matches: 111, Mismatches: 5, Indels: 14
0.85 0.04 0.11
Matches are distributed among these distances:
34 7 0.06
35 25 0.23
36 56 0.50
37 22 0.20
38 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (34 bp):
TTTTGAAAATATATAATATATAGTTTTTAAAACA
Found at i:5195 original size:11 final size:11
Alignment explanation
Indices: 5144--5203 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
5134 ATAATATATA
5144 ATTTTTAAAAT
1 ATTTTTAAAAT
* *
5155 ATTTTGAATAT
1 ATTTTTAAAAT
* *
5166 ATATATAATATAT
1 ATTTTTAA-A-AT
5179 AGTTTTTAAAAT
1 A-TTTTTAAAAT
5191 ATTTTTAAAAT
1 ATTTTTAAAAT
5202 AT
1 AT
5204 ATATAATTGA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 26 0.68
12 3 0.08
13 4 0.11
14 5 0.13
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
ATTTTTAAAAT
Found at i:5927 original size:20 final size:20
Alignment explanation
Indices: 5884--5947 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
5874 AATTCGCGTT
*
5884 GCGAATATGTAAATCGCAAT
1 GCGAATATGTAAATCGCAAC
*
5904 GCGAATATGTAAATCGTAAC
1 GCGAATATGTAAATCGCAAC
* *
5924 GCGATTATG-ACTATCGCAAC
1 GCGAATATGTA-AATCGCAAC
5944 GCGA
1 GCGA
5948 TTCTGACTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 1 0.03
20 37 0.97
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (20 bp):
GCGAATATGTAAATCGCAAC
Found at i:5942 original size:40 final size:40
Alignment explanation
Indices: 5896--5983 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
5886 GAATATGTAA
* *
5896 ATCGCAATGCGAATATGTA-AATCGTAACGCGATTATGACT
1 ATCGCAACGCGAATATG-ACAATCGCAACGCGATTATGACT
* * * *
5936 ATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGAATATGACAATCGCAACGCGATTATGACT
*
5976 GTCGCAAC
1 ATCGCAAC
5984 ACTGAATTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.03
40 39 0.98
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACAATCGCAACGCGATTATGACT
Found at i:5948 original size:20 final size:20
Alignment explanation
Indices: 5916--5983 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
5906 GAATATGTAA
* *
5916 ATCGTAACGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
5936 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
5956 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
5976 GTCGCAAC
1 ATCGCAAC
5984 ACTGAATTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:6834 original size:24 final size:24
Alignment explanation
Indices: 6802--6848 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
6792 GTATTCGAAA
6802 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
6826 TTTGATCTTGGTCAATACTCGGA
1 TTTGATCTTGGTCAATACCCGGA
6849 TTTTTATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:7038 original size:3 final size:3
Alignment explanation
Indices: 7030--7068 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
7020 ATATAACCCT
* *
7030 GAA GAA GAA AAA GAA GAA GAA GAA AAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
7069 ATCCCCGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:7050 original size:15 final size:15
Alignment explanation
Indices: 7030--7069 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
7020 ATATAACCCT
7030 GAAGAAGAAAAAGAA
1 GAAGAAGAAAAAGAA
7045 GAAGAAGAAAAAGAA
1 GAAGAAGAAAAAGAA
7060 GAAGAAGAAA
1 GAAGAAGAAA
7070 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAAAAGAA
Found at i:7089 original size:14 final size:14
Alignment explanation
Indices: 7060--7096 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
7050 AGAAAAAGAA
7060 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
7075 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
7089 GAAGAAAA
1 GAAGAAAA
7097 TGCCACGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:9420 original size:13 final size:13
Alignment explanation
Indices: 9402--9430 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
9392 TATTAGTAAC
9402 TTGAGTTTGAACA
1 TTGAGTTTGAACA
9415 TTGAGTTTGAACA
1 TTGAGTTTGAACA
9428 TTG
1 TTG
9431 CTATGATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (13 bp):
TTGAGTTTGAACA
Found at i:9558 original size:54 final size:54
Alignment explanation
Indices: 9469--9776 Score: 189
Period size: 54 Copynumber: 5.6 Consensus size: 54
9459 TTACACATTC
* * * ** *
9469 ATTTGAATATCGCAACGCGAATTTGATTATCGCAACTAAAAAATCGCAATTCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCAA
* * * *
9523 ATTTGACTATCGCAACACGAATATGACTATTGCAACGCAAAAATCGCAACGCAA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCAA
* * ** ***
9577 ATTTGTCTATCGTAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAA--CGAA----AAAATCGCAACGCAA
* * * *
9637 ATTTGACTATCGCAACGAGAA----A--ATCACAACGAAAATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAA----A--ATCGCAACGCAA
* * * * * **
9691 ATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCAA
* *
9745 ATTAGACTATCGCAACGCGAA-TTGACTTTCGC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGC
9777 GTTGCGATTT
Statistics
Matches: 193, Mismatches: 43, Indels: 37
0.71 0.16 0.14
Matches are distributed among these distances:
48 1 0.01
52 4 0.02
53 10 0.05
54 133 0.69
56 5 0.03
58 1 0.01
60 39 0.20
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (54 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCAA
Found at i:9609 original size:40 final size:40
Alignment explanation
Indices: 9469--9727 Score: 153
Period size: 40 Copynumber: 6.9 Consensus size: 40
9459 TTACACATTC
* * *
9469 ATTTGAATATCGCAACGCGAATTTGATTATCGCAAC-TAA
1 ATTTGATTATCGCAACGCGAATTTGACTATCGCAACGCAA
* ** * *
9508 A----A-AATCGCAATTCGAATTTGACTATCGCAACACGA
1 ATTTGATTATCGCAACGCGAATTTGACTATCGCAACGCAA
* * * *
9543 ATATGACTATTGCAACGC-AA----A-AATCGCAACGCAA
1 ATTTGATTATCGCAACGCGAATTTGACTATCGCAACGCAA
* *
9577 ATTTG-TCTATCGTAACGCGAATTTGACTATCGCAACGCGA
1 ATTTGAT-TATCGCAACGCGAATTTGACTATCGCAACGCAA
* *
9617 ATTTGATTATCGCAACGGGTATTTGACTATCGCAACG-AGA
1 ATTTGATTATCGCAACGCGAATTTGACTATCGCAACGCA-A
* ** * *
9657 A----A--ATCACAACGAAAATTTGACTATCACAACGCGA
1 ATTTGATTATCGCAACGCGAATTTGACTATCGCAACGCAA
* *
9691 ATTTGATTATCGCAACGGGTATTTGACTATCGCAACG
1 ATTTGATTATCGCAACGCGAATTTGACTATCGCAACG
9728 AGAAAATCGC
Statistics
Matches: 164, Mismatches: 34, Indels: 43
0.68 0.14 0.18
Matches are distributed among these distances:
34 74 0.45
35 6 0.04
36 1 0.01
38 1 0.01
39 5 0.03
40 76 0.46
41 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (40 bp):
ATTTGATTATCGCAACGCGAATTTGACTATCGCAACGCAA
Found at i:9653 original size:20 final size:20
Alignment explanation
Indices: 9520--9776 Score: 174
Period size: 20 Copynumber: 13.8 Consensus size: 20
9510 AATCGCAATT
*
9520 CGAATTTGACTATCGCAACA
1 CGAATTTGACTATCGCAACG
* *
9540 CGAATATGACTATTGCAACG
1 CGAATTTGACTATCGCAACG
*
9560 C-AA----A-AATCGCAACG
1 CGAATTTGACTATCGCAACG
* * *
9574 CAAATTTGTCTATCGTAACG
1 CGAATTTGACTATCGCAACG
9594 CGAATTTGACTATCGCAACG
1 CGAATTTGACTATCGCAACG
*
9614 CGAATTTGATTATCGCAACG
1 CGAATTTGACTATCGCAACG
* *
9634 GGTATTTGACTATCGCAACG
1 CGAATTTGACTATCGCAACG
* *
9654 AGAA----A--ATCACAACG
1 CGAATTTGACTATCGCAACG
** *
9668 AAAATTTGACTATCACAACG
1 CGAATTTGACTATCGCAACG
*
9688 CGAATTTGATTATCGCAACG
1 CGAATTTGACTATCGCAACG
* *
9708 GGTATTTGACTATCGCAACG
1 CGAATTTGACTATCGCAACG
* *
9728 AGAA----A--ATCGCAAAG
1 CGAATTTGACTATCGCAACG
* *
9742 CGTATTAGACTATCGCAACG
1 CGAATTTGACTATCGCAACG
*
9762 CGAA-TTGACTTTCGC
1 CGAATTTGACTATCGC
9777 GTTGCGATTT
Statistics
Matches: 184, Mismatches: 35, Indels: 37
0.72 0.14 0.14
Matches are distributed among these distances:
14 30 0.16
15 3 0.02
16 2 0.01
18 2 0.01
19 11 0.06
20 136 0.74
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (20 bp):
CGAATTTGACTATCGCAACG
Found at i:9674 original size:74 final size:74
Alignment explanation
Indices: 9596--9767 Score: 281
Period size: 74 Copynumber: 2.3 Consensus size: 74
9586 TCGTAACGCG
9596 AATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAAT
1 AATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAAT
*
9661 CACAACGAA
66 CACAAAGAA
*
9670 AATTTGACTATCACAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAAT
1 AATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAAT
* **
9735 CGCAAAGCG
66 CACAAAGAA
* *
9744 TATTAGACTATCGCAACGCGAATT
1 AATTTGACTATCGCAACGCGAATT
9768 GACTTTCGCG
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 90 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (74 bp):
AATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAAT
CACAAAGAA
Found at i:9727 original size:94 final size:94
Alignment explanation
Indices: 9511--9727 Score: 274
Period size: 94 Copynumber: 2.3 Consensus size: 94
9501 CAACTAAAAA
** * * * *
9511 ATCGCAATTCGAATTTGACTATCGCAACACGAATATGACTATTGCAACGCAAAAATCGCAACGCA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGCAAAAATCACAACGAA
* **
9576 AATTTGTCTATCGTAACGCGAATTTGACT
66 AATTTGACTATCACAACGCGAATTTGACT
* * * *
9605 ATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACG-AGAAAATCACAACGA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGCA-AAAATCACAACGA
*
9669 AAATTTGACTATCACAACGCGAATTTGATT
65 AAATTTGACTATCACAACGCGAATTTGACT
* *
9699 ATCGCAACGGGTATTTGACTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
9728 AGAAAATCGC
Statistics
Matches: 105, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
93 1 0.01
94 104 0.99
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGCAAAAATCACAACGAA
AATTTGACTATCACAACGCGAATTTGACT
Found at i:9747 original size:34 final size:34
Alignment explanation
Indices: 9625--9761 Score: 139
Period size: 34 Copynumber: 3.9 Consensus size: 34
9615 GAATTTGATT
9625 ATCGCAACGGGTATTTGACTATCGCAACGAGAAA
1 ATCGCAACGGGTATTTGACTATCGCAACGAGAAA
* *** * *
9659 ATCACAACGAAAATTTGACTATCACAACGCGAATTTGA
1 ATCGCAACGGGTATTTGACTATCGCAACGAGAA----A
9697 TTATCGCAACGGGTATTTGACTATCGCAACGAGAAA
1 --ATCGCAACGGGTATTTGACTATCGCAACGAGAAA
* * *
9733 ATCGCAAAGCGTATTAGACTATCGCAACG
1 ATCGCAACGGGTATTTGACTATCGCAACG
9762 CGAATTGACT
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
34 53 0.65
36 1 0.01
38 1 0.01
40 27 0.33
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (34 bp):
ATCGCAACGGGTATTTGACTATCGCAACGAGAAA
Found at i:9795 original size:20 final size:20
Alignment explanation
Indices: 9770--9823 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
9760 CGCGAATTGA
*
9770 CTTTCGCGTTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
9790 CTTTCGCATTGCGATTTTGAG
1 CTTTCGCATTGCGATTTTG-G
*
9811 -TTTAGCATTGCGA
1 CTTTCGCATTGCGA
9824 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.13, C:0.19, G:0.26, T:0.43
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:9982 original size:14 final size:14
Alignment explanation
Indices: 9944--9982 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
9934 ATAATATTAA
*
9944 ACAAATCAACTTTT
1 ACAAATCAATTTTT
*
9958 ACAAATAAATTTTT
1 ACAAATCAATTTTT
*
9972 ATAAATCAATT
1 ACAAATCAATT
9983 AAACAAGCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:11471 original size:42 final size:42
Alignment explanation
Indices: 11392--11483 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
11382 CCTCTTCAAC
* * *
11392 GATGACAGTGGCCTCTTGAACGGTTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATAGGAGGGGACTCTTGAGG
* * **
11434 GATGATAGGGGCCTCTTGAACGATAGG-GGAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGATAGGAGG-GGACTCTTGAGG
11476 GATGACAG
1 GATGACAG
11484 ATGAGTCGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 2 0.05
42 39 0.95
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATAGGAGGGGACTCTTGAGG
Found at i:11999 original size:18 final size:18
Alignment explanation
Indices: 11969--12035 Score: 80
Period size: 20 Copynumber: 3.5 Consensus size: 18
11959 AAAACTTAAA
*
11969 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
*
11987 ATCACAACGCGAAAATGACT
1 ATCGCAACGCG--AATGACT
12007 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
12027 ATCGCAACG
1 ATCGCAACG
12036 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 11 0.26
20 31 0.74
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:12005 original size:20 final size:20
Alignment explanation
Indices: 11980--12035 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
11970 TCGCAACACG
*
11980 AATGACTATCACAACGCGAA
1 AATGACTATCGCAACGCGAA
12000 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
12020 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
12036 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:12107 original size:20 final size:20
Alignment explanation
Indices: 12078--12165 Score: 131
Period size: 20 Copynumber: 4.4 Consensus size: 20
12068 GCGATTCTTT
* **
12078 CGTTGAGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
12098 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
12118 CGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCATTTTCG
12138 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
12158 TGTTGCGA
1 CGTTGCGA
12166 AAGTAAACTA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:12336 original size:18 final size:18
Alignment explanation
Indices: 12313--12362 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
12303 TTTACTAAGC
12313 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
*
12331 AATCTAAGTAAAATGGTT
1 AATCTAAGTGAAATGGTT
12349 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
12363 TACGAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:14138 original size:20 final size:20
Alignment explanation
Indices: 14095--14168 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
14085 GAAACTTAAA
* **
14095 ATCGCAACACGAAAATAAAA
1 ATCGCAACACGAAAATGACT
*
14115 ATCGCAACACAAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
14135 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
*
14155 ATCGCAACGCGAAA
1 ATCGCAACACGAAA
14169 CTAAAATCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:14596 original size:22 final size:22
Alignment explanation
Indices: 14561--14617 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
14551 GATGGAGATA
* *
14561 GACGGATTTTGCCGGAGATTGG
1 GACGGATTTCGCCGGAGATGGG
*
14583 GACTGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
14605 GACGGATGTCGCC
1 GACGGATTTCGCC
14618 TTAGAGAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.19, G:0.40, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:14813 original size:20 final size:20
Alignment explanation
Indices: 14784--14899 Score: 151
Period size: 20 Copynumber: 5.8 Consensus size: 20
14774 CGCTTTGAAA
* *
14784 ATCGCATTGCGATAGTTAGC
1 ATCGCGTTGCGATAGTCAGC
*
14804 ATCGCGTTGCGATAGTCATC
1 ATCGCGTTGCGATAGTCAGC
*
14824 ATCGCGTTGCGATAGTCATC
1 ATCGCGTTGCGATAGTCAGC
* *
14844 ATTGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGC
* *
14864 ATCTCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGC
*
14884 ATCGCATTGCGATAGT
1 ATCGCGTTGCGATAGT
14900 TATAATCGCA
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGC
Found at i:14839 original size:40 final size:40
Alignment explanation
Indices: 14783--14913 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 40
14773 GCGCTTTGAA
*
14783 AATCGCATTGCGATAGTTAGCATCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAGCATCGCGTTGCGATAGTCAT
* * * * *
14823 CATCGCGTTGCGATAGTCATCATTGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAGCATCGCGTTGCGATAGTCAT
* * * * *
14863 AATCTCGTTGCGATAGTCAGAATCGCATTGCGATAGTTAT
1 AATCGCATTGCGATAGTCAGCATCGCGTTGCGATAGTCAT
14903 AATCGCATTGC
1 AATCGCATTGC
14914 AATTTACATA
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCAGCATCGCGTTGCGATAGTCAT
Found at i:14906 original size:20 final size:20
Alignment explanation
Indices: 14783--14940 Score: 147
Period size: 20 Copynumber: 7.9 Consensus size: 20
14773 GCGCTTTGAA
* *
14783 AATCGCATTGCGATAGTTAG
1 AATCGCATTGCGATAGTCAT
* *
14803 CATCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAT
* *
14823 CATCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAT
* * * *
14843 CATTGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAT
* * *
14863 AATCTCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAT
*
14883 AATCGCATTGCGATAGTTAT
1 AATCGCATTGCGATAGTCAT
* *
14903 AATCGCATTGCAAT-TTACAT
1 AATCGCATTGCGATAGT-CAT
*
14923 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
14941 GAAAAATCGC
Statistics
Matches: 117, Mismatches: 19, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
19 1 0.01
20 115 0.98
21 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAT
Found at i:14957 original size:22 final size:22
Alignment explanation
Indices: 14932--14983 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
14922 TATTCGCATT
14932 GCGATAGTCGAAAAATCGCAAC
1 GCGATAGTCGAAAAATCGCAAC
* * * *
14954 GCGA-ATTTGGAAAATCGCAAT
1 GCGATAGTCGAAAAATCGCAAC
14975 GCGATAGTC
1 GCGATAGTC
14984 AGAATCGCGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (22 bp):
GCGATAGTCGAAAAATCGCAAC
Found at i:15743 original size:3 final size:3
Alignment explanation
Indices: 15735--15822 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
15725 ATATCAAATA
15735 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15783 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
15823 TAGGGACTGG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:23896 original size:20 final size:21
Alignment explanation
Indices: 23868--23906 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
23858 AGTAAAATGA
23868 AAATATATAA-AATAAATAACT
1 AAATATATAATAA-AAATAACT
23889 AAAT-TATAATAAAAATAA
1 AAATATATAATAAAAATAA
23907 AACTAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATATATAATAAAAATAACT
Found at i:24733 original size:21 final size:19
Alignment explanation
Indices: 24708--24744 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24698 AGTTGTTGTT
24708 GTTTTTTTTTCTTTCTCTG
1 GTTTTTTTTTCTTTCTCTG
*
24727 TTTTTTTTTTCTTTCTCT
1 GTTTTTTTTTCTTTCTCT
24745 CCGGTTCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (19 bp):
GTTTTTTTTTCTTTCTCTG
Found at i:25247 original size:3 final size:3
Alignment explanation
Indices: 25239--25366 Score: 202
Period size: 3 Copynumber: 42.7 Consensus size: 3
25229 TTAATATATT
* * *
25239 TAA TAA TAA TAG TAA TAA TGA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
25287 TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
25335 TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
25367 TGGATAAAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 113 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:26027 original size:113 final size:113
Alignment explanation
Indices: 25683--26350 Score: 966
Period size: 113 Copynumber: 5.9 Consensus size: 113
25673 GAATTATGCG
* * **
25683 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** * * * ** *
25747 TATGAAC-TTCTCCAGAAATGTTGATCCATCAATTGATGAATTCTTGC
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
* *
25794 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
* * * * * *
25859 CATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAGC
63 CATTATGAACT-TTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
* *
25910 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
25975 TATGAACTTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTTAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
26023 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
26088 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
*
26136 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
26201 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
*
26249 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
26314 TATGAAC-TTCTCTGGAAAAGCTAACCCATCAAATGAT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGAT
26351 AGATTTGAAT
Statistics
Matches: 511, Mismatches: 39, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
111 4 0.01
112 69 0.14
113 334 0.65
115 20 0.04
116 82 0.16
117 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
Found at i:27187 original size:84 final size:84
Alignment explanation
Indices: 27041--27409 Score: 702
Period size: 84 Copynumber: 4.4 Consensus size: 84
27031 ATTTCTACTA
*
27041 TGAGTAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
1 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
27106 CACTTCCAGAAGATGCTAT
66 CACTTCCAGAAGATGCTAT
*
27125 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAA
1 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
*
27190 CACTTCCAGAAGATTCTAT
66 CACTTCCAGAAGATGCTAT
27209 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
1 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
27274 CACTTCCAGAAGATGCTAT
66 CACTTCCAGAAGATGCTAT
*
27293 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAA
1 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
27358 CACTTCCAGAAGATGCTAT
66 CACTTCCAGAAGATGCTAT
27377 TGAGCAAATTCATCTTCCAAATTCAATGATTGG
1 TGAGCAAATTCATCTTCCAAATTCAATGATTGG
27410 ACTAAGATAT
Statistics
Matches: 279, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 279 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (84 bp):
TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTAT
Found at i:28182 original size:19 final size:20
Alignment explanation
Indices: 28160--28201 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
28150 AATAGAAAAG
*
28160 AATAAATTGAATTTCCAA-A
1 AATAAATTGAATCTCCAATA
28179 AATAAATTGAATCTCCAATA
1 AATAAATTGAATCTCCAATA
28199 AAT
1 AAT
28202 TGAACTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (20 bp):
AATAAATTGAATCTCCAATA
Found at i:28559 original size:14 final size:14
Alignment explanation
Indices: 28535--28611 Score: 77
Period size: 14 Copynumber: 5.2 Consensus size: 14
28525 CCTTGACCCC
28535 CTTTCTTTTTCTTCT
1 CTTT-TTTTTCTTCT
28550 CTTTTTTTTCATTTTCT
1 CTTTTTTTTC---TTCT
*
28567 ATTTTTTTTCTTCT
1 CTTTTTTTTCTTCT
28581 C-TTTTTTTCTTCTT
1 CTTTTTTTTCTTC-T
28595 CTTTTTTCTT-TTCT
1 CTTTTTT-TTCTTCT
28609 CTT
1 CTT
28612 CAAGCATAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
13 11 0.20
14 16 0.30
15 12 0.22
16 2 0.04
17 13 0.24
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (14 bp):
CTTTTTTTTCTTCT
Found at i:28575 original size:31 final size:30
Alignment explanation
Indices: 28535--28611 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
28525 CCTTGACCCC
*
28535 CTTTCTTTTTCTTCTCTTTTTTTTCATT-TT
1 CTTTTTTTTTCTTCTCTTTTTTTTC-TTCTT
28565 CTATTTTTTTTCTTCTC-TTTTTTTCTTCTT
1 CT-TTTTTTTTCTTCTCTTTTTTTTCTTCTT
*
28595 CTTTTTTCTT-TTCTCTT
1 CTTTTTTTTTCTTCTCTT
28612 CAAGCATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 5 0.12
29 10 0.24
30 14 0.33
31 13 0.31
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (30 bp):
CTTTTTTTTTCTTCTCTTTTTTTTCTTCTT
Found at i:28587 original size:16 final size:16
Alignment explanation
Indices: 28540--28608 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
28530 ACCCCCTTTC
28540 TTTTTCTTCTC--TTT
1 TTTTTCTTCTCTTTTT
* *
28554 TTTTTCATTTTCTATTT
1 TTTTTC-TTCTCTTTTT
28571 TTTTTCTTCTCTTTTT
1 TTTTTCTTCTCTTTTT
*
28587 TTCTTCTTCT-TTTTT
1 TTTTTCTTCTCTTTTT
*
28602 CTTTTCT
1 TTTTTCT
28609 CTTCAAGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
14 6 0.13
15 14 0.30
16 17 0.37
17 9 0.20
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTCTCTTTTT
Found at i:39218 original size:13 final size:15
Alignment explanation
Indices: 39196--39232 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
39186 TTTGACAGAA
39196 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
39208 AAATAAAATACTTGC
1 AAATAAAATACTTGC
39223 AAATAAAATA
1 AAATAAAATA
39233 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:39271 original size:18 final size:17
Alignment explanation
Indices: 39223--39273 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
39213 AAATACTTGC
*
39223 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
39241 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
39259 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
39274 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:39937 original size:20 final size:21
Alignment explanation
Indices: 39914--39954 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
39904 TATTATATGT
**
39914 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
39934 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
39955 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:40025 original size:20 final size:21
Alignment explanation
Indices: 39997--40035 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
39987 AGTAAAATGA
39997 AAATATATAA-AATAAATAACT
1 AAATATATAATAA-AAATAACT
40018 AAAT-TATAATAAAAATAA
1 AAATATATAATAAAAATAA
40036 AACTAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATATATAATAAAAATAACT
Found at i:40867 original size:18 final size:18
Alignment explanation
Indices: 40844--40878 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40834 TTGTTGTTGT
40844 TTTTTTTTTCTTTCTCTG
1 TTTTTTTTTCTTTCTCTG
40862 TTTTTTTTTCTTTCTCT
1 TTTTTTTTTCTTTCTCT
40879 CCGGTTCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTTTTTTCTTTCTCTG
Found at i:41381 original size:3 final size:3
Alignment explanation
Indices: 41373--41506 Score: 214
Period size: 3 Copynumber: 44.7 Consensus size: 3
41363 TTAATATATT
* * *
41373 TAA TAA TAA TAG TAA TAA TGA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
41421 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
41469 TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
41507 TGGATAAAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 119 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:42782 original size:50 final size:50
Alignment explanation
Indices: 42705--42805 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
42695 TACCATTAAA
* *
42705 GAAAAACATTGCTGATTTGAGAGGATTTTTAGCTGATTTTCACGTGGGTT
1 GAAAAACATGGCTGATTTGAGACGATTTTTAGCTGATTTTCACGTGGGTT
42755 GAAAAACATGGCTGATTTGAGACGATTTTTAGCTGATTTTCACGTGGGTT
1 GAAAAACATGGCTGATTTGAGACGATTTTTAGCTGATTTTCACGTGGGTT
42805 G
1 G
42806 GGGGAAACTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.26, C:0.11, G:0.27, T:0.37
Consensus pattern (50 bp):
GAAAAACATGGCTGATTTGAGACGATTTTTAGCTGATTTTCACGTGGGTT
Found at i:46183 original size:13 final size:13
Alignment explanation
Indices: 46165--46211 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
46155 TTTCTAAACA
*
46165 TTTCATATTTTAT
1 TTTCATATTTCAT
*
46178 TTTCATATTTCAC
1 TTTCATATTTCAT
*
46191 TTTCGTA-TTCAT
1 TTTCATATTTCAT
46203 TTTCATATT
1 TTTCATATT
46212 CTTTTCTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.21, C:0.15, G:0.02, T:0.62
Consensus pattern (13 bp):
TTTCATATTTCAT
Found at i:46206 original size:12 final size:12
Alignment explanation
Indices: 46165--46217 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
46155 TTTCTAAACA
*
46165 TTTCATATTTTAT
1 TTTCATA-TTCAT
*
46178 TTTCATATTTCAC
1 TTTCATA-TTCAT
*
46191 TTTCGTATTCAT
1 TTTCATATTCAT
46203 TTTCATATTC-T
1 TTTCATATTCAT
46214 TTTC
1 TTTC
46218 TTTCAGATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
11 5 0.14
12 13 0.37
13 17 0.49
ACGTcount: A:0.19, C:0.17, G:0.02, T:0.62
Consensus pattern (12 bp):
TTTCATATTCAT
Found at i:47468 original size:19 final size:20
Alignment explanation
Indices: 47436--47476 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
47426 TTTAACAAAC
*
47436 TTTTTAAAAGAAGAAAAATA
1 TTTTTAAAACAAGAAAAATA
47456 TTTTT-AAACAAGAAAAATA
1 TTTTTAAAACAAGAAAAATA
47475 TT
1 TT
47477 ATCTAACAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (20 bp):
TTTTTAAAACAAGAAAAATA
Found at i:47484 original size:19 final size:19
Alignment explanation
Indices: 47446--47487 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
47436 TTTTTAAAAG
*
47446 AAGAAAAATATTTTTAAAC
1 AAGAAAAATATTTCTAAAC
47465 AAGAAAAATATTATCT-AAC
1 AAGAAAAATATT-TCTAAAC
47484 AAGA
1 AAGA
47488 TAATTTCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (19 bp):
AAGAAAAATATTTCTAAAC
Found at i:48099 original size:110 final size:110
Alignment explanation
Indices: 47817--48130 Score: 276
Period size: 110 Copynumber: 2.8 Consensus size: 110
47807 GGATAAACCT
* * * *** * *
47817 ATCAACATTTCCAAG-GGAAGGGTTCCTAATGAGAAGAACGT-GTTTGATGAGGGAGAAGAAGTT
1 ATCAACATTTCC-AGTGGAAGGATTCATAATGACAAGAAC-TCGTCCAATGAGAGAGAACAAGTT
* * * * *
47880 CCTAATGAGAAGAGCTTATTCGACCTTGGCTCATCCATCATAGAAAGGGTTGG
64 CCCAATGAGAAGAACTTGTTCGA-C-TCG-T--T-CATCAGAGAAAGGGTTGG
* ***
47933 ATCAACATTTCCAGTGGAAGGATTCATAATGACAAGAACTTGTTTGATGAGAGAGAACCAA-TTC
1 ATCAACATTTCCAGTGGAAGGATTCATAATGACAAGAACTCGTCCAATGAGAGAGAA-CAAGTTC
* *
47997 CTAATGAGAAGAGCTTGTTCGACTCGTTCATCAGAG-AAGGAGTTGG
65 CCAATGAGAAGAACTTGTTCGACTCGTTCATCAGAGAAAGG-GTTGG
** * * * * *
48043 ATCAGTATTTCCAGTGGAAGGGTTCATAATGAGAAGAACTCGTCCAATTAGGGAGAAGAAGTTCC
1 ATCAACATTTCCAGTGGAAGGATTCATAATGACAAGAACTCGTCCAATGAGAGAGAACAAGTTCC
48108 CAATGAGAAGAACTTGTTCGACT
66 CAATGAGAAGAACTTGTTCGACT
48131 TTGGATCTTT
Statistics
Matches: 172, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
109 6 0.03
110 84 0.49
111 1 0.01
113 1 0.01
114 2 0.01
115 4 0.02
116 72 0.42
117 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (110 bp):
ATCAACATTTCCAGTGGAAGGATTCATAATGACAAGAACTCGTCCAATGAGAGAGAACAAGTTCC
CAATGAGAAGAACTTGTTCGACTCGTTCATCAGAGAAAGGGTTGG
Found at i:48404 original size:43 final size:43
Alignment explanation
Indices: 48300--48405 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 43
48290 ACTTTTGTTT
* * * *
48300 GATTCCATCATAGAATGAGGTGGATCAATTTTCCCTTTTTGCTA
1 GATTCCATCATAGAAGGAGGTGGATCAAATTTACC-TTTTACTA
* *
48344 GATTCCATCATATAAGGAGTTGGATCAACATTTACC-TTTACTA
1 GATTCCATCATAGAAGGAGGTGGATCAA-ATTTACCTTTTACTA
*
48387 GATTCTATCATAGAAGGAG
1 GATTCCATCATAGAAGGAG
48406 CTAAATCAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 23 0.43
44 25 0.47
45 5 0.09
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (43 bp):
GATTCCATCATAGAAGGAGGTGGATCAAATTTACCTTTTACTA
Found at i:50207 original size:85 final size:86
Alignment explanation
Indices: 50105--50354 Score: 278
Period size: 85 Copynumber: 2.9 Consensus size: 86
50095 TCCTTTTTTA
* * * * *
50105 TTTTATTTTATTTTATTTTCATTCTTTCATTTTTTTTCTTTATATTTACTCACTTTAATTTTTTG
1 TTTTATTTTATTTTATTTTCATTCTTTAATTTTTGTTATTTACATTTACACACTTTAATTTTTTG
*
50170 TTAATTACATTTTTGCCCC-T
66 TTATTTACATTTTTGCCCCTT
* * * * *
50190 TTTTACTTTATTTTATTTTCATTATTTAATTTTAGTTATTTACATTTACACATTTTATTTATTTT
1 TTTTATTTTATTTTATTTTCATTCTTTAATTTTTGTTATTTACATTTACACACTTTAATT-TTTT
*
50255 GTTATTTATA-TTTT-CCCCTT
65 GTTATTTACATTTTTGCCCCTT
** * *
50275 TTTTATTTTATTTTATTTTTGTTCTTTTAGTTTTGTTATTTACATTTA-AGCACTTT-ATTTTTC
1 TTTTATTTTATTTTATTTTCATTCTTTAATTTTTGTTATTTACATTTACA-CACTTTAATTTTT-
50338 T-TCTATTTACATTTTTG
64 TGT-TATTTACATTTTTG
50355 TCTTTTAAAT
Statistics
Matches: 136, Mismatches: 22, Indels: 13
0.80 0.13 0.08
Matches are distributed among these distances:
83 4 0.03
84 15 0.11
85 105 0.77
86 12 0.09
ACGTcount: A:0.19, C:0.11, G:0.04, T:0.66
Consensus pattern (86 bp):
TTTTATTTTATTTTATTTTCATTCTTTAATTTTTGTTATTTACATTTACACACTTTAATTTTTTG
TTATTTACATTTTTGCCCCTT
Found at i:53078 original size:23 final size:24
Alignment explanation
Indices: 53028--53081 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
53018 TTGATTATTT
**
53028 TGGATA-TTTTGGTTATGCTTATGT
1 TGGATATTTTTGGTTA-GCTTATAA
53052 TGGATATTTTTGGTTA-CTTATAA
1 TGGATATTTTTGGTTAGCTTATAA
53075 TGGATAT
1 TGGATAT
53082 ATATTGGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 12 0.44
24 6 0.22
25 9 0.33
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.52
Consensus pattern (24 bp):
TGGATATTTTTGGTTAGCTTATAA
Found at i:58382 original size:3 final size:3
Alignment explanation
Indices: 58354--58409 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
58344 GAAAAGAAAA
*
58354 AAT AA- AAT AAAT ATT AAT ATAT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT -AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
*
58399 AAT AAA AAT AA
1 AAT AAT AAT AA
58410 AAACAAAACG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 35 0.78
4 6 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:58399 original size:17 final size:17
Alignment explanation
Indices: 58354--58409 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 17
58344 GAAAAGAAAA
*
58354 AATAAAATAAATATTAAT
1 AATAAAAT-AATAATAAT
58372 ATATAATAATAATAATAAT
1 A-ATAA-AATAATAATAAT
*
58391 AATAAAATAATAAAAAT
1 AATAAAATAATAATAAT
58408 AA
1 AA
58410 AAACAAAACG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 13 0.38
18 5 0.15
19 13 0.38
20 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAAAATAATAATAAT
Found at i:58417 original size:20 final size:20
Alignment explanation
Indices: 58376--58417 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
58366 ATTAATATAT
* * *
58376 AATAATAATAATAATAATAA
1 AATAATAAAAATAAAAACAA
58396 AATAATAAAAATAAAAACAA
1 AATAATAAAAATAAAAACAA
58416 AA
1 AA
58418 CGGATGTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (20 bp):
AATAATAAAAATAAAAACAA
Found at i:59367 original size:40 final size:41
Alignment explanation
Indices: 59323--59539 Score: 117
Period size: 40 Copynumber: 5.3 Consensus size: 41
59313 ACTCCTCTTA
59323 CTGAAGGACGTTGAATC-TGGTGATGATCTCACTCTTTTCT
1 CTGAAGGACGTTGAATCATGGTGATGATCTCACTCTTTTCT
* * * * * * *
59363 CTGAAAGACGCTGAGTCGTGG-GACGATCTTACTCTTTCCT
1 CTGAAGGACGTTGAATCATGGTGATGATCTCACTCTTTTCT
* * * *
59403 CTTAAGGATGTT-AAGTCATAATTGGTAGGTGATC-CACTCCTTTT-G
1 CTGAAGGACGTTGAA-TC---A-TGGT-GATGATCTCACT-CTTTTCT
* * *
59448 CTGAAGGATGTTAAATC-TGGTGATGATTTCACTC-TTTCTT
1 CTGAAGGACGTTGAATCATGGTGATGATCTCACTCTTTTC-T
* * * * * * *
59488 CTAAAAGACATTGAGTCACGG-GATGATCTCACTCATTCCT
1 CTGAAGGACGTTGAATCATGGTGATGATCTCACTCTTTTCT
59528 CTGAAGGACGTT
1 CTGAAGGACGTT
59540 AAGTCCTAAT
Statistics
Matches: 129, Mismatches: 33, Indels: 30
0.67 0.17 0.16
Matches are distributed among these distances:
38 3 0.02
39 7 0.05
40 81 0.63
41 8 0.06
44 3 0.02
45 16 0.12
46 11 0.09
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (41 bp):
CTGAAGGACGTTGAATCATGGTGATGATCTCACTCTTTTCT
Found at i:59443 original size:125 final size:125
Alignment explanation
Indices: 59041--59549 Score: 470
Period size: 125 Copynumber: 4.0 Consensus size: 125
59031 CGCTAGGTTG
* ** * * * * *
59041 TAATTGGTAGGTAATGTATTCCTCTTGCTTAAGTACGATGAATTTGGTGATGATCTCACTATTTT
1 TAATTGGTAGGTGATCCACTCCTCTTGCTGAAGGACGTTGAATCTGGTGATGATCTCACTATTTT
** * * * *
59106 CTCTAAAAGACGTTAAGTCATGGGAAAATCTTACTCCTTCCTCTTATGGACT-CTAAGTCG
66 CTCTAAAAGACGTTAAGTCATGGGACGATCTTACTCCTTCCTCTGAAGGA-TGTTAAGTCA
* * * * * *
59166 TAATTGGTAGGT-AACTTACTCCTTTTGTTGAAGGATGTTGAATCTGGTGACGA--TCACTATTT
1 TAATTGGTAGGTGATC-CACTCCTCTTGCTGAAGGACGTTGAATCTGGTGATGATCTCACTATTT
* * * * *
59228 CCTCTAAAAGACGTTAAGTTATGGAACGATCTTACTCCTTCATCTGAATGACGCTAAGTTGTAAG
65 TCTCTAAAAGACGTTAAGTCATGGGACGATCTTACTCCTTCCTCTGAA-G--G--ATG-T-TAAG
59293 TCA
123 TCA
* * *
59296 TAATTGGTAGGTGACCCACTCCTCTTACTGAAGGACGTTGAATCTGGTGATGATCTCACTCTTTT
1 TAATTGGTAGGTGATCCACTCCTCTTGCTGAAGGACGTTGAATCTGGTGATGATCTCACTATTTT
* * * * * *
59361 CTCTGAAAGACGCTGAGTCGTGGGACGATCTTACTCTTTCCTCTTAAGGATGTTAAGTCA
66 CTCTAAAAGACGTTAAGTCATGGGACGATCTTACTCCTTCCTCTGAAGGATGTTAAGTCA
* * * * *
59421 TAATTGGTAGGTGATCCACTCCTTTTGCTGAAGGATGTTAAATCTGGTGATGATTTCACT-CTTT
1 TAATTGGTAGGTGATCCACTCCTCTTGCTGAAGGACGTTGAATCTGGTGATGATCTCACTATTTT
* * * * * * * *
59485 CTTCTAAAAGACATTGAGTCACGGGATGATCTCACTCATTCCTCTGAAGGACGTTAAGTCC
66 C-TCTAAAAGACGTTAAGTCATGGGACGATCTTACTCCTTCCTCTGAAGGATGTTAAGTCA
59546 TAAT
1 TAAT
59550 CTAGGGTCAA
Statistics
Matches: 312, Mismatches: 59, Indels: 26
0.79 0.15 0.07
Matches are distributed among these distances:
123 49 0.16
124 6 0.02
125 153 0.49
126 2 0.01
127 2 0.01
128 1 0.00
129 1 0.00
130 49 0.16
131 3 0.01
132 46 0.15
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (125 bp):
TAATTGGTAGGTGATCCACTCCTCTTGCTGAAGGACGTTGAATCTGGTGATGATCTCACTATTTT
CTCTAAAAGACGTTAAGTCATGGGACGATCTTACTCCTTCCTCTGAAGGATGTTAAGTCA
Found at i:60571 original size:18 final size:17
Alignment explanation
Indices: 60548--60598 Score: 70
Period size: 15 Copynumber: 3.1 Consensus size: 17
60538 AAAATGTTTG
60548 ATGAAAGAATTTTGAAAA
1 ATGAAAGAATTTT-AAAA
*
60566 ATGAAAGAATTTT--TA
1 ATGAAAGAATTTTAAAA
60581 ATGAAAGAATTTTAAAA
1 ATGAAAGAATTTTAAAA
60598 A
1 A
60599 ATGTTGATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 14 0.48
17 2 0.07
18 13 0.45
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (17 bp):
ATGAAAGAATTTTAAAA
Done.