Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006268.1 Hibiscus syriacus cultivar Beakdansim tig00014947_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: 105218
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:66 original size:20 final size:19
Alignment explanation
Indices: 43--275 Score: 167
Period size: 20 Copynumber: 12.1 Consensus size: 19
33 AATTTGTAAA
43 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
**
63 TCGCAATGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
** *
83 TCTAAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
**
103 TCGCAACGTGATA-TC-AAT
1 TCGCAACACGA-AGTCAAAT
121 TCGCAACAC-AAGTCAAAT
1 TCGCAACACGAAGTCAAAT
* *
139 TCACAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
159 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
179 TCGCAACACAAAAGTC-AAT
1 TCGCAACAC-GAAGTCAAAT
*
198 TCGCAACACAAAGTCAAAT
1 TCGCAACACGAAGTCAAAT
*
217 TCGCAACGCGAATTTGT-AAA-
1 TCGCAACACGAA---GTCAAAT
*
237 TCTCAACACAGAAGTC-AAT
1 TCGCAACAC-GAAGTCAAAT
*
256 TCGC-ACGCGAAAGTCAAAT
1 TCGCAACACG-AAGTCAAAT
275 T
1 T
276 TTTTGCGCGA
Statistics
Matches: 177, Mismatches: 21, Indels: 31
0.77 0.09 0.14
Matches are distributed among these distances:
16 1 0.01
17 4 0.02
18 38 0.21
19 37 0.21
20 88 0.50
21 7 0.04
22 2 0.01
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:123 original size:18 final size:20
Alignment explanation
Indices: 55--227 Score: 205
Period size: 20 Copynumber: 8.9 Consensus size: 20
45 GCAACACAGA
*
55 AGTCAAATTCGCAATGCGAT
1 AGTCAAATTCGCAACGCGAT
**
75 AGTCAAATTCTAAACGCGAT
1 AGTCAAATTCGCAACGCGAT
*
95 AGTCAAATTCGCAACGTGAT
1 AGTCAAATTCGCAACGCGAT
*
115 A-TC-AATTCGCAACAC-A-
1 AGTCAAATTCGCAACGCGAT
*
131 AGTCAAATTCACAACGCGAT
1 AGTCAAATTCGCAACGCGAT
151 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* * *
171 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCGAT
* *
191 AGTC-AATTCGCAACAC-AA
1 AGTCAAATTCGCAACGCGAT
209 AGTCAAATTCGCAACGCGA
1 AGTCAAATTCGCAACGCGA
228 ATTTGTAAAT
Statistics
Matches: 132, Mismatches: 15, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
16 1 0.01
17 3 0.02
18 26 0.20
19 26 0.20
20 76 0.58
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:150 original size:76 final size:78
Alignment explanation
Indices: 43--227 Score: 275
Period size: 76 Copynumber: 2.4 Consensus size: 78
33 AATTTGTAAA
* *
43 TCGCAACACAGAAGTCAAATTCGCAATGCGATAGTCAAATTCTAAACGCGATAGTCAAATTCGCA
1 TCGCAACACA-AAGTCAAATTCGCAACGCGATAGTCAAATTCGAAACGCGATAGTCAAATTCGCA
*** *
108 ACGTGATA-TCAAT
65 ACACAAAAGTCAAT
* *
121 TCGCAACAC-AAGTCAAATTCACAACGCGATAGTCAAATTCGCAACGCGATAGTCAAATTCGCAA
1 TCGCAACACAAAGTCAAATTCGCAACGCGATAGTCAAATTCGAAACGCGATAGTCAAATTCGCAA
185 CACAAAAGTCAAT
66 CACAAAAGTCAAT
198 TCGCAACACAAAGTCAAATTCGCAACGCGA
1 TCGCAACACAAAGTCAAATTCGCAACGCGA
228 ATTTGTAAAT
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
76 54 0.56
77 14 0.15
78 28 0.29
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (78 bp):
TCGCAACACAAAGTCAAATTCGCAACGCGATAGTCAAATTCGAAACGCGATAGTCAAATTCGCAA
CACAAAAGTCAAT
Found at i:213 original size:58 final size:58
Alignment explanation
Indices: 55--275 Score: 222
Period size: 58 Copynumber: 3.8 Consensus size: 58
45 GCAACACAGA
** * ** * *
55 AGTCAAATTCGCAATGCGATAGTCAAATTCTAAACGCGATAGTCAAATTCGCAACGTGAT
1 AGTCAAATTCGCAACAC-AAAGTC-AATTCGCAACGCGAAAGTCAAATTCGCAACGCGAT
* *
115 A-TC-AATTCGCAACAC-AAGTCAAATTCACAACGCGATAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACACAAAGTC-AATTCGCAACGCGAAAGTCAAATTCGCAACGCGAT
*
171 AGTCAAATTCGCAACACAAAAGTCAATTCGCAACAC-AAAGTCAAATTCGCAACGCGAATT
1 AGTCAAATTCGCAACAC-AAAGTCAATTCGCAACGCGAAAGTCAAATTCGCAACGCG-A-T
* *
231 TGT-AAA-TCTCAACACAGAAGTCAATTCGC-ACGCGAAAGTCAAATT
1 AGTCAAATTCGCAACACA-AAGTCAATTCGCAACGCGAAAGTCAAATT
276 TTTTGCGCGA
Statistics
Matches: 141, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
56 38 0.27
57 6 0.04
58 72 0.51
59 16 0.11
60 9 0.06
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (58 bp):
AGTCAAATTCGCAACACAAAGTCAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAT
Found at i:2944 original size:21 final size:21
Alignment explanation
Indices: 2903--3000 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
2893 GATGCACCTA
* * *
2903 TCATCATTCAAGAGACGCCTC
1 TCATCGTTCAAGAGGCCCCTC
2924 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
2945 TCATC-ATCGAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * *
2966 CCACCGTTCAAGAGG-CCCTA
1 TCATCGTTCAAGAGGCCCCTC
2986 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
3001 TCCTGCCCCC
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
20 20 0.33
21 38 0.62
22 3 0.05
ACGTcount: A:0.26, C:0.35, G:0.18, T:0.21
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:2950 original size:42 final size:42
Alignment explanation
Indices: 2899--3019 Score: 119
Period size: 42 Copynumber: 3.0 Consensus size: 42
2889 GCCCGATGCA
* * *
2899 CCTATCATCATTCAAGAGA-CGCCTCCTATCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAGAGCCCCTCCCACCGTTCAAGAGG-C
*
2941 CCTCTCATCA-TCGAAGA-AGCCCCTCCCACCGTTCAAGAGGC
1 CCTATCATCATTC-AAGAGAGCCCCTCCCACCGTTCAAGAGGC
* *
2982 CCTATCATCGTTCAAGAG-G-TCCTGCCC-CCGTTCAAGAG
1 CCTATCATCATTCAAGAGAGCCCCT-CCCACCGTTCAAGAG
3020 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
40 14 0.21
41 20 0.30
42 33 0.49
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.21
Consensus pattern (42 bp):
CCTATCATCATTCAAGAGAGCCCCTCCCACCGTTCAAGAGGC
Found at i:4434 original size:64 final size:65
Alignment explanation
Indices: 4358--4500 Score: 218
Period size: 65 Copynumber: 2.2 Consensus size: 65
4348 TTTTACATTG
*
4358 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGATTTATTTTTTT-ATTGATTAATTGATTTGT
1 AAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATTATTTTTTTGATTG-TTAATTGATTTGT
4421 A
65 A
* * * *
4422 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTATTGATTTGTA
1 AAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATTATTTTTTTGATTGTTAATTGATTTGTA
4487 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
4501 GTTTCTAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
64 17 0.24
65 52 0.72
66 3 0.04
ACGTcount: A:0.30, C:0.01, G:0.17, T:0.52
Consensus pattern (65 bp):
AAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATTATTTTTTTGATTGTTAATTGATTTGTA
Found at i:4594 original size:20 final size:20
Alignment explanation
Indices: 4557--4594 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4547 GTTGAAGGTA
*
4557 CAAATTCGCAACGTGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
4577 CAAATTCGCGACGCGAAA
1 CAAATTCGCAACGCGAAA
4595 TAAGTATTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:4678 original size:20 final size:20
Alignment explanation
Indices: 4655--4693 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4645 GATTTTCGGT
*
4655 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTATCGCG
4675 TTGCGAATTTGACTATCGC
1 TTGCGAATTTGACTATCGC
4694 AACGCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCG
Found at i:4959 original size:39 final size:39
Alignment explanation
Indices: 4905--4993 Score: 142
Period size: 39 Copynumber: 2.3 Consensus size: 39
4895 ACTCAAGTTG
* *
4905 TAGATTTTGATTTCCTTTTGCTTGGCACCGTATGAGATT
1 TAGATTTTGATTTCCTTTTGCTTGGAACCATATGAGATT
*
4944 TAGATTTTGATTTCCTTTTGCTTGGAACCATATGAGCTT
1 TAGATTTTGATTTCCTTTTGCTTGGAACCATATGAGATT
*
4983 TGGATTTTGAT
1 TAGATTTTGAT
4994 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.19, C:0.13, G:0.20, T:0.47
Consensus pattern (39 bp):
TAGATTTTGATTTCCTTTTGCTTGGAACCATATGAGATT
Found at i:5325 original size:18 final size:18
Alignment explanation
Indices: 5302--5338 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5292 CAAAATTTAT
5302 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
5320 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
5338 A
1 A
5339 CTCCAATTAC
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:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:5788 original size:20 final size:20
Alignment explanation
Indices: 5763--5804 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5753 TGTACAAGAT
* *
5763 GAAAGTTAAATTCGCAATGC
1 GAAAGTCAAATTCGCAACGC
5783 GAAAGTCAAATTCGCAACGC
1 GAAAGTCAAATTCGCAACGC
5803 GA
1 GA
5805 TTTTCGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
GAAAGTCAAATTCGCAACGC
Found at i:5836 original size:20 final size:20
Alignment explanation
Indices: 5813--5855 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
5803 GATTTTCGGT
5813 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
*
5833 TTGCGAATTTGACTTTTGCG
1 TTGCGAATTTGACTTTCGCG
5853 TTG
1 TTG
5856 ATCGCAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:6164 original size:18 final size:18
Alignment explanation
Indices: 6141--6176 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6131 AAGCCGGTTG
*
6141 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
6159 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
6177 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:8465 original size:24 final size:24
Alignment explanation
Indices: 8438--8497 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
8428 CCATCACATC
*
8438 ATCAAAATTCGAGTATTCCCCAAG
1 ATCAAAATTCGAGTATTCACCAAG
* * * *
8462 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTCACCAAG
*
8486 ATCAAATTTCGA
1 ATCAAAATTCGA
8498 ATACTGACTA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTCACCAAG
Found at i:9221 original size:14 final size:15
Alignment explanation
Indices: 9185--9222 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
9175 GAAATCATTG
9185 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
9200 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
9215 AAAAATTA
1 AAAAATTA
9223 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:9409 original size:19 final size:19
Alignment explanation
Indices: 9385--9489 Score: 104
Period size: 19 Copynumber: 5.4 Consensus size: 19
9375 ACCTAATGCA
9385 AATTTGAAATTCAGTTGCG
1 AATTTGAAATTCAGTTGCG
*
9404 AATTTGAAATTCAGTTGCT
1 AATTTGAAATTCAGTTGCG
*
9423 AATTTGAAATTCCGCGTTGCG
1 AATTTGAAATT-C-AGTTGCG
** **
9444 AATTTGACTTTGTGTTGCG
1 AATTTGAAATTCAGTTGCG
*
9463 AATTTGACTATTGC-GTTGCG
1 AATTTGA-AATT-CAGTTGCG
9483 AATTTGA
1 AATTTGA
9490 CTATCGCGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
19 42 0.58
20 16 0.22
21 14 0.19
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (19 bp):
AATTTGAAATTCAGTTGCG
Found at i:9449 original size:40 final size:39
Alignment explanation
Indices: 9385--9489 Score: 115
Period size: 40 Copynumber: 2.7 Consensus size: 39
9375 ACCTAATGCA
* *
9385 AATTTGAAATTC-AGTTGCGAATTTGAAATTCAGTTGCT
1 AATTTGAAATTCGCGTTGCGAATTTGAAATTCAGTTGCG
** **
9423 AATTTGAAATTCCGCGTTGCGAATTTGACTTTGTGTTGCG
1 AATTTGAAATT-CGCGTTGCGAATTTGAAATTCAGTTGCG
*
9463 AATTTGACTATT-GCGTTGCGAATTTGA
1 AATTTGA-AATTCGCGTTGCGAATTTGA
9490 CTATCGCGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
38 11 0.19
39 16 0.28
40 27 0.47
41 3 0.05
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (39 bp):
AATTTGAAATTCGCGTTGCGAATTTGAAATTCAGTTGCG
Found at i:9463 original size:59 final size:60
Alignment explanation
Indices: 9398--9568 Score: 169
Period size: 60 Copynumber: 2.9 Consensus size: 60
9388 TTGAAATTCA
* *
9398 GTTGCGAATTTGA-AATT-CAGTTGCTAATTTGAA-ATTCCGCGTTGCGAATTTGACTT-TGT
1 GTTGCGAATTTGACAATTGC-GTTGCGAATTTGAATA-T-CGCGTTGCGAATTTGACTTCCGT
* *
9457 GTTGCGAATTTGACTATTGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCCGT
1 GTTGCGAATTTGACAATTGCGTTGCGAATTTGAATATCGCGTTGCGAATTTGACTTCCGT
* *
9517 GTTGCG-ATTT-ACAAATTCGCGTTGCG-ATTT-ACAGATTCGCGTTGTGAATTTG
1 GTTGCGAATTTGAC-AATT-GCGTTGCGAATTTGA-ATA-TCGCGTTGCGAATTTG
9569 GAAAATCGCA
Statistics
Matches: 96, Mismatches: 8, Indels: 15
0.81 0.07 0.13
Matches are distributed among these distances:
58 3 0.03
59 44 0.46
60 47 0.49
61 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (60 bp):
GTTGCGAATTTGACAATTGCGTTGCGAATTTGAATATCGCGTTGCGAATTTGACTTCCGT
Found at i:9482 original size:20 final size:20
Alignment explanation
Indices: 9398--9511 Score: 128
Period size: 20 Copynumber: 5.8 Consensus size: 20
9388 TTGAAATTCA
*
9398 GTTGCGAATTTGA-AATT-C
1 GTTGCGAATTTGACTATTGC
* *
9416 AGTTGCTAATTTGA-AATTCCGC
1 -GTTGCGAATTTGACTATT--GC
*
9438 GTTGCGAATTTGACT-TTGT
1 GTTGCGAATTTGACTATTGC
9457 GTTGCGAATTTGACTATTGC
1 GTTGCGAATTTGACTATTGC
*
9477 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATTGC
9497 GTTGCGAATTTGACT
1 GTTGCGAATTTGACT
9512 TCCGTGTTGC
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
19 32 0.38
20 37 0.44
21 14 0.17
22 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGACTATTGC
Found at i:9490 original size:39 final size:40
Alignment explanation
Indices: 9436--9511 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
9426 TTGAAATTCC
* *
9436 GCGTTGCGAATTTGACT-TTGTGTTGCGAATTTGACTATT
1 GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATT
9475 GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT
1 GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT
9512 TCCGTGTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 17 0.50
40 17 0.50
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.39
Consensus pattern (40 bp):
GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATT
Found at i:9540 original size:20 final size:20
Alignment explanation
Indices: 9517--9560 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
9507 TGACTTCCGT
9517 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
9537 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
9557 GTTG
1 GTTG
9561 TGAATTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:14851 original size:3 final size:3
Alignment explanation
Indices: 14843--14925 Score: 51
Period size: 3 Copynumber: 27.7 Consensus size: 3
14833 TATTGGGGGG
* * ** * * *
14843 CAT CAT CAT CACT C-T GAT CAT CAC CAT CAT CAT CCC CAC CAC CAC
1 CAT CAT CAT CA-T CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
* * * *
14888 CAC CAC CAT CAC CAT CAC CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
14926 ACCTTATCTA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
2 1 0.02
3 63 0.95
4 2 0.03
ACGTcount: A:0.31, C:0.46, G:0.01, T:0.22
Consensus pattern (3 bp):
CAT
Found at i:14870 original size:6 final size:6
Alignment explanation
Indices: 14861--14922 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
14851 TCACTCTGAT
* * *
14861 CATCAC CATCAT CATC-C C--CAC CACCAC CACCAC CATCAC CATCAC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC
* *
14906 CATCAT CATCAT CATCA
1 CATCAC CATCAC CATCA
14923 TCAACCTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 1 0.02
6 45 0.92
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
CATCAC
Found at i:14874 original size:12 final size:12
Alignment explanation
Indices: 14843--14925 Score: 69
Period size: 12 Copynumber: 6.7 Consensus size: 12
14833 TATTGGGGGG
14843 CATCATCATCAC
1 CATCATCATCAC
*
14855 TC-TGATCATCAC
1 -CATCATCATCAC
14867 CATCATCATCCCCAC
1 CATCATCAT---CAC
* * *
14882 CACCACCACCAC
1 CATCATCATCAC
*
14894 CATCACCATCAC
1 CATCATCATCAC
*
14906 CATCATCATCAT
1 CATCATCATCAC
14918 CATCATCA
1 CATCATCA
14926 ACCTTATCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
11 1 0.02
12 46 0.81
13 1 0.02
15 9 0.16
ACGTcount: A:0.31, C:0.46, G:0.01, T:0.22
Consensus pattern (12 bp):
CATCATCATCAC
Found at i:15989 original size:52 final size:52
Alignment explanation
Indices: 15899--16019 Score: 138
Period size: 52 Copynumber: 2.3 Consensus size: 52
15889 GGAGTGATTT
* *
15899 TAGGTTAAAGTGGTATA-AGGTTCGTTAAGGTGAAAGTGG-CAAAGGATTTTG
1 TAGGTTAAAGTGGTTTAGAGGTTCGTTAAGGTGAAAGTGGTC-AAGGATTATG
* ** * *
15950 TAGGTTAAAGTGGTTTAGAGTTTTTTTAAGGTGAGAGTGGTCAAGGGTTATG
1 TAGGTTAAAGTGGTTTAGAGGTTCGTTAAGGTGAAAGTGGTCAAGGATTATG
* *
16002 TATGTTAAAATGGTTTAG
1 TAGGTTAAAGTGGTTTAG
16020 GGTAAGGTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
51 16 0.27
52 42 0.71
53 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.32, T:0.36
Consensus pattern (52 bp):
TAGGTTAAAGTGGTTTAGAGGTTCGTTAAGGTGAAAGTGGTCAAGGATTATG
Found at i:17379 original size:26 final size:25
Alignment explanation
Indices: 17336--17384 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
17326 TTATCATCAA
17336 AAAATTAAAATAACATAAACTAAAAC
1 AAAATTAAAATAACATAAA-TAAAAC
* **
17362 AAAATTTAAATATTATAAATAAA
1 AAAATTAAAATAACATAAATAAA
17385 TAAACTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (25 bp):
AAAATTAAAATAACATAAATAAAAC
Found at i:17851 original size:4 final size:4
Alignment explanation
Indices: 17842--17988 Score: 122
Period size: 4 Copynumber: 36.8 Consensus size: 4
17832 ATATCCCTTC
** * **
17842 AAAT AAAT AAAT AAAT AAAT TCA- AAAT AACT AAAT AAAT AAAT TCA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
17888 AAAT AATT AAAT AAAT AAATTT GAAAT AAAT AAAT GAAT AAAT AAAT GAAT
1 AAAT AAAT AAAT AAAT AAA--T -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
** * *
17939 AAAT AAAT TCA- AAAT AAAT AAAT CAAA- AAAT ATAT AAAT AAAT ATAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT
17986 AAA
1 AAA
17989 AATTAAAACA
Statistics
Matches: 111, Mismatches: 24, Indels: 16
0.74 0.16 0.11
Matches are distributed among these distances:
3 6 0.05
4 97 0.87
5 4 0.04
6 1 0.01
7 3 0.03
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:17875 original size:23 final size:23
Alignment explanation
Indices: 17842--18009 Score: 146
Period size: 23 Copynumber: 7.7 Consensus size: 23
17832 ATATCCCTTC
17842 AAATAAATAAATAAATAAATTCA
1 AAATAAATAAATAAATAAATTCA
*
17865 AAATAACTAAATAAATAAATTCA
1 AAATAAATAAATAAATAAATTCA
*
17888 AAATAATTAAATAAATAAATT--
1 AAATAAATAAATAAATAAATTCA
*
17909 ---TGAAATAAATAAATGAA-T--
1 AAAT-AAATAAATAAATAAATTCA
*
17927 AAATAAATGAATAAATAAATTCA
1 AAATAAATAAATAAATAAATTCA
17950 AAATAAATAAATCAAA-AAATAT-A
1 AAATAAATAAAT-AAATAAAT-TCA
*
17973 TAAATAAATATAT-AA-AAATT-A
1 -AAATAAATAAATAAATAAATTCA
* *
17994 AAACAAATCAATAAAT
1 AAATAAATAAATAAAT
18010 GAAAATTACT
Statistics
Matches: 122, Mismatches: 11, Indels: 25
0.77 0.07 0.16
Matches are distributed among these distances:
18 2 0.02
19 13 0.11
20 22 0.18
21 6 0.05
22 6 0.05
23 58 0.48
24 15 0.12
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATAAATAAATAAATAAATTCA
Found at i:17942 original size:39 final size:38
Alignment explanation
Indices: 17846--17982 Score: 132
Period size: 39 Copynumber: 3.4 Consensus size: 38
17836 CCCTTCAAAT
* *
17846 AAATAAATAAATAAATTCAAAATAACTAAATAAATAAATTC-A
1 AAATAAATAAATAAA-T--AAAT-TCAAAATAAATAAA-TCAA
* ** *
17888 AAATAATTAAATAAATAAATTTGAAATAAATAAATGAA
1 AAATAAATAAATAAATAAATTCAAAATAAATAAATCAA
*
17926 TAAATAAATGAATAAATAAATTCAAAATAAATAAATCAAA
1 -AAATAAATAAATAAATAAATTCAAAATAAATAAATC-AA
*
17966 AAATATATAAATAAATA
1 AAATAAATAAATAAATA
17983 TATAAAAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
37 1 0.01
38 12 0.15
39 50 0.62
40 2 0.03
41 1 0.01
42 14 0.17
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (38 bp):
AAATAAATAAATAAATAAATTCAAAATAAATAAATCAA
Found at i:18737 original size:86 final size:86
Alignment explanation
Indices: 18592--18759 Score: 239
Period size: 86 Copynumber: 2.0 Consensus size: 86
18582 AACTCTCAGC
* * * * *
18592 CATCTGATAATGAACGCTCAATCACATGTTGCAATCGTTGGTGCTCGAACCCGTAACCATTAAGA
1 CATCTGACAATGAACGCTCAAGCACATGGTACAATCGTTGGTGCTCGAACCCGTAACCATTAAAA
*
18657 ATAACGACAATTTTTTTCAAT
66 ATAACAACAATTTTTTTCAAT
* *
18678 CATCTGACAATGAACGCTTAAGCACCTGGTACAATCGCTT-GTGCTCGAACCCGTAACCATTAAA
1 CATCTGACAATGAACGCTCAAGCACATGGTACAATCG-TTGGTGCTCGAACCCGTAACCATTAAA
*
18742 AATAACAATAATTTTTTT
65 AATAACAACAATTTTTTT
18760 AACCATTTAG
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 70 0.97
87 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (86 bp):
CATCTGACAATGAACGCTCAAGCACATGGTACAATCGTTGGTGCTCGAACCCGTAACCATTAAAA
ATAACAACAATTTTTTTCAAT
Found at i:27446 original size:24 final size:24
Alignment explanation
Indices: 27419--27464 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
27409 CATGACATTG
27419 TACATAGATGTTTTATACATCACA
1 TACATAGATGTTTTATACATCACA
27443 TACATAGATGTTTTATACATCA
1 TACATAGATGTTTTATACATCA
27465 TCAGGAAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (24 bp):
TACATAGATGTTTTATACATCACA
Found at i:28426 original size:23 final size:24
Alignment explanation
Indices: 28384--28431 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
28374 TGCATGACAT
28384 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
28408 TGTACATAGAT-TTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
28431 T
1 T
28432 CAGGAAGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:34620 original size:251 final size:251
Alignment explanation
Indices: 34177--34651 Score: 869
Period size: 251 Copynumber: 1.9 Consensus size: 251
34167 ATATAAGTTT
* * *
34177 TAAACTTTGAAAAGTGTAGGGACCAAAATTGTAATTTTTAAAAGTTATATATATTTTAGTCTGTA
1 TAAACTTTGAAAAGTATAGGGACCAAAATTATAATTTTTAAAAGTTATATATATTTTAGCCTGTA
* * *
34242 AATGAACAGTTTGGATTAAAACAAAGATTTTAGTGGGAATCATATTTTTGGTACGGGAATTGTGT
66 AATGAACAATTTGGATTAAAACAAAGATTTTAGTGAGAATCATATTTTTGGTACGAGAATTGTGT
34307 TAAAAGCTATAAAGCAGTAAAGTTCGGTATTGAAATCGAATATTCGGATCGAATTGGAATTTTAC
131 TAAAAGCTATAAAGCAGTAAAGTTCGGTATTGAAATCGAATATTCGGATCGAATTGGAATTTTAC
34372 AAAAATTTGAAGGATGTTATAAAATGGTTACCAAATATTATTTAGTGGCTCAAGTG
196 AAAAATTTGAAGGATGTTATAAAATGGTTACCAAATATTATTTAGTGGCTCAAGTG
34428 TAAACTTTGAAAAGTATAGGGACCAAAATTATAATTTTTAAAAGTTATATATATTTTAGCCTGTA
1 TAAACTTTGAAAAGTATAGGGACCAAAATTATAATTTTTAAAAGTTATATATATTTTAGCCTGTA
*
34493 AATGAACAATTTGGATTAAAACAGAGATTTTAGTGAGAATCATATTTTTGGTACGAGAATTGTGT
66 AATGAACAATTTGGATTAAAACAAAGATTTTAGTGAGAATCATATTTTTGGTACGAGAATTGTGT
*
34558 TAAAAGCTATAAAGCAGTAAAGTTCGGTATTGAAATCGAATATTCGGATCGAATTGGAATTTTAT
131 TAAAAGCTATAAAGCAGTAAAGTTCGGTATTGAAATCGAATATTCGGATCGAATTGGAATTTTAC
*
34623 GAAAATTTGAAGGATGTTATAAAATGGTT
196 AAAAATTTGAAGGATGTTATAAAATGGTT
34652 GGAAGTATTA
Statistics
Matches: 215, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
251 215 1.00
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.35
Consensus pattern (251 bp):
TAAACTTTGAAAAGTATAGGGACCAAAATTATAATTTTTAAAAGTTATATATATTTTAGCCTGTA
AATGAACAATTTGGATTAAAACAAAGATTTTAGTGAGAATCATATTTTTGGTACGAGAATTGTGT
TAAAAGCTATAAAGCAGTAAAGTTCGGTATTGAAATCGAATATTCGGATCGAATTGGAATTTTAC
AAAAATTTGAAGGATGTTATAAAATGGTTACCAAATATTATTTAGTGGCTCAAGTG
Found at i:37378 original size:45 final size:45
Alignment explanation
Indices: 37325--37413 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
37315 CTTTTAAATT
* *
37325 GGGAAATGTTTTAAGTAAATCATGTGACGTCTATAACCTGTATTA
1 GGGAAATGTTTTAAGTAAATCATGTGACATCTATAACATGTATTA
37370 GGGAAATGTTTTAAGTAAATCATGTGACATCTATAACATGTATT
1 GGGAAATGTTTTAAGTAAATCATGTGACATCTATAACATGTATT
37414 GATATAAGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (45 bp):
GGGAAATGTTTTAAGTAAATCATGTGACATCTATAACATGTATTA
Found at i:46480 original size:18 final size:18
Alignment explanation
Indices: 46457--46501 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
46447 CTATGTTTTA
46457 CATTATTTTCATTTTGGT
1 CATTATTTTCATTTTGGT
** *
46475 CATTATTTGGATTTTGTT
1 CATTATTTTCATTTTGGT
*
46493 TATTATTTT
1 CATTATTTT
46502 ATTATAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (18 bp):
CATTATTTTCATTTTGGT
Found at i:49425 original size:16 final size:16
Alignment explanation
Indices: 49375--49427 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
49365 AATTTAACAC
**
49375 TTCATATTTTAAAAAA
1 TTCATATTTTAAATTA
*
49391 ATCATCATTTTAATCATTA
1 TTCAT-ATTTTAA--ATTA
49410 TTCATATTTTAAATTA
1 TTCATATTTTAAATTA
49426 TT
1 TT
49428 TGTTTTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 10 0.33
17 7 0.23
18 7 0.23
19 6 0.20
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (16 bp):
TTCATATTTTAAATTA
Found at i:59183 original size:74 final size:75
Alignment explanation
Indices: 59062--59209 Score: 174
Period size: 74 Copynumber: 2.0 Consensus size: 75
59052 AAATTTAAGG
* * ** * *
59062 CTTCACATCAGTATTATGTTATTTTAATAACGATCATTTTATTATAAATCAA-TAGCGTTAGTGA
1 CTTCACATCAATATTATGTTATTCTAATAACGATCAACTTATTATAAATCAATTAGCATTAGTAA
59126 TCAAATTGTA
66 TCAAATTGTA
* * * *
59136 CTTCACATCAATATCT-TGTTATTCTAATAATGATTAACTTGTTATAAATTAATTAGCATTAGTA
1 CTTCACATCAATAT-TATGTTATTCTAATAACGATCAACTTATTATAAATCAATTAGCATTAGTA
*
59200 ATCGAATTGT
65 ATCAAATTGT
59210 TAATCTTGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
74 42 0.69
75 19 0.31
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (75 bp):
CTTCACATCAATATTATGTTATTCTAATAACGATCAACTTATTATAAATCAATTAGCATTAGTAA
TCAAATTGTA
Found at i:59445 original size:21 final size:20
Alignment explanation
Indices: 59418--59516 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
59408 AATCAGTTTC
59418 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
59439 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
59460 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
59480 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
59501 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
59517 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:59545 original size:20 final size:20
Alignment explanation
Indices: 59484--59712 Score: 239
Period size: 20 Copynumber: 11.4 Consensus size: 20
59474 GATTTTCCAG
* ** *
59484 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
59504 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
59524 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
59544 AACCGCAATGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
59564 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
59584 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
59604 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
59624 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
59644 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
59664 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
59684 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
59704 AATCACAAC
1 AATCGCAAC
59713 ACTGAAATTT
Statistics
Matches: 177, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 173 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:60642 original size:12 final size:12
Alignment explanation
Indices: 60625--60649 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60615 ATATAATCCT
60625 GAAGAAGAAAAA
1 GAAGAAGAAAAA
60637 GAAGAAGAAAAA
1 GAAGAAGAAAAA
60649 G
1 G
60650 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:63008 original size:53 final size:53
Alignment explanation
Indices: 62945--63173 Score: 241
Period size: 53 Copynumber: 4.2 Consensus size: 53
62935 ACAACGAGAG
*
62945 AATCGCAATGCGA-AAT-GAAAAT-CCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAGAATCG-AAATGCGCAA-ATGAAAATCGCAATGC-GAAATGAA
*
62998 AATCGCAATGCGAAATGAAAATCGCAATGCG-AAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCG--A-G--AATCGAAATGCGCAAATGAAAATCGCAATGCGAAATGAA
* * * * *
63055 AATCGCAACGAGAGAATCGCAATGTGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAGAATCGAAATGCGCAAATGAAAATCGCAATGCGAAATGAA
* * * * *
63108 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAATGCGAGAATCGAAATGCGCAAATGAAAATCGCAATGCGAAATGAA
*
63161 AATCGCATTGCGA
1 AATCGCAATGCGA
63174 TTCTCTCGTT
Statistics
Matches: 157, Mismatches: 10, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
52 11 0.07
53 99 0.63
54 1 0.01
55 2 0.01
57 18 0.11
58 16 0.10
59 8 0.05
60 2 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (53 bp):
AATCGCAATGCGAGAATCGAAATGCGCAAATGAAAATCGCAATGCGAAATGAA
Found at i:63014 original size:19 final size:19
Alignment explanation
Indices: 62945--63173 Score: 272
Period size: 19 Copynumber: 12.7 Consensus size: 19
62935 ACAACGAGAG
62945 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
62964 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
62978 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
62998 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
63017 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
63036 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
63055 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
63069 AATCGCAATGTGGAAATGAA
1 AATCGCAATG-CGAAATGAA
63089 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
63108 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
63122 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
63142 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
63161 AATCGCATTGCGA
1 AATCGCAATGCGA
63174 TTCTCTCGTT
Statistics
Matches: 181, Mismatches: 11, Indels: 36
0.79 0.05 0.16
Matches are distributed among these distances:
14 32 0.18
15 2 0.01
16 2 0.01
17 7 0.04
19 98 0.54
20 40 0.22
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:63030 original size:72 final size:73
Alignment explanation
Indices: 62945--63173 Score: 294
Period size: 72 Copynumber: 3.2 Consensus size: 73
62935 ACAACGAGAG
*
62945 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
63009 GAAATGAA
66 GAAATGAA
*
63017 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--C-G--A-GAGAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAAAATCGCAATGCGGAAATGAAAATCGCA
*
63076 ATGTGGAAATGAA
62 ATG-CGAAATGAA
* * *
63089 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAACGC
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
63153 GAAATGAA
66 GAAATGAA
*
63161 AATCGCATTGCGA
1 AATCGCAATGCGA
63174 TTCTCTCGTT
Statistics
Matches: 136, Mismatches: 9, Indels: 24
0.80 0.05 0.14
Matches are distributed among these distances:
67 10 0.07
68 1 0.01
69 1 0.01
70 2 0.01
71 12 0.09
72 83 0.61
73 11 0.08
74 2 0.01
75 1 0.01
77 13 0.10
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (73 bp):
AATCGCAATGCGAAATGAAAATCGCAACAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
GAAATGAA
Found at i:63100 original size:91 final size:87
Alignment explanation
Indices: 62931--63151 Score: 320
Period size: 91 Copynumber: 2.5 Consensus size: 87
62921 CGGAAATTAC
* * *
62931 AATCACAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAAT
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAATGCGGAAAT
62995 GAAAATCGCAATGCGAAATGAA
66 GAAAATCGCAATGCGAAATGAA
* *
63017 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGTG
1 AATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAATGCG
63081 GAAATGAAAATCGCAATGCGAAATGAA
61 GAAATGAAAATCGCAATGCGAAATGAA
*
63108 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAACG
1 AATCGCAACGAGAAAATCGCAATGC-GAAATGAAAATCGCAACG
63152 CGAAATGAAA
Statistics
Matches: 122, Mismatches: 6, Indels: 13
0.87 0.04 0.09
Matches are distributed among these distances:
86 20 0.16
87 19 0.16
88 2 0.02
89 2 0.02
90 1 0.01
91 77 0.63
92 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (87 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAATGCGGAAAT
GAAAATCGCAATGCGAAATGAA
Found at i:63206 original size:19 final size:20
Alignment explanation
Indices: 63182--63227 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
63172 GATTCTCTCG
63182 TTGCGATTTTCATTT-CGCA
1 TTGCGATTTTCATTTCCGCA
63201 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCCGCA
63221 TTGCGAT
1 TTGCGAT
63228 AGTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCGCA
Found at i:63233 original size:20 final size:19
Alignment explanation
Indices: 63191--63235 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
63181 GTTGCGATTT
**
63191 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
63210 TCATTTCCGCATTGCGATAG
1 TCATTT-CGCATTGCGATAG
63230 TCATTT
1 TCATTT
63236 TTGCCTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:63353 original size:14 final size:14
Alignment explanation
Indices: 63334--63370 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
63324 CATCAATTAA
63334 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
63348 ACAAATCATCTTTT
1 ACAAATCAACTTTT
63362 ACAAATCAA
1 ACAAATCAA
63371 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:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:65336 original size:19 final size:19
Alignment explanation
Indices: 65294--65485 Score: 179
Period size: 19 Copynumber: 10.6 Consensus size: 19
65284 TAGTTTACTT
* *
65294 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
65314 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
65333 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
65352 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
65371 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
65390 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
65409 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
65423 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
65442 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
65456 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
65475 TCGCAATGCGA
1 TCGCAACGCGA
65486 TTTTGGTTTC
Statistics
Matches: 147, Mismatches: 15, Indels: 21
0.80 0.08 0.11
Matches are distributed among these distances:
14 18 0.12
15 1 0.01
16 7 0.05
17 7 0.05
18 1 0.01
19 101 0.69
20 12 0.08
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:65359 original size:38 final size:35
Alignment explanation
Indices: 65310--65480 Score: 197
Period size: 33 Copynumber: 4.8 Consensus size: 35
65300 CACGAAACTT
*
65310 AAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAG--A-C
** *
65348 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAA--CGAGA-C
65386 AAAATCGCAACGCGAAATGAAAATCGCAAC--GAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAGAC
* *
65419 AGAATCGCAATGCGAAATGAAAATCGCAACGAG--
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAGAC
*
65452 AGAATCGCAACGCGAAATGAAAATCGCAA
1 AAAATCGCAACGCGAAATGAAAATCGCAA
65481 TGCGATTTTG
Statistics
Matches: 119, Mismatches: 10, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
33 57 0.48
34 1 0.01
35 1 0.01
36 1 0.01
38 56 0.47
40 3 0.03
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.09
Consensus pattern (35 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAGAC
Found at i:65426 original size:14 final size:14
Alignment explanation
Indices: 65407--65463 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
65397 GCGAAATGAA
*
65407 AATCGCAACGACAG
1 AATCGCAACGAAAG
65421 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
65438 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
65454 AATCGCAACG
1 AATCGCAACG
65464 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:65516 original size:14 final size:14
Alignment explanation
Indices: 65497--65555 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
65487 TTTGGTTTCG
65497 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
65511 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
65528 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
65544 CGTTGCGATTTT
1 CGTTGCGATTTT
65556 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:65523 original size:33 final size:33
Alignment explanation
Indices: 65481--65575 Score: 163
Period size: 33 Copynumber: 2.9 Consensus size: 33
65471 AAAATCGCAA
65481 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
*
65514 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
**
65547 TGCGATTTTCATTTCGCGTTGCGATTTTG
1 TGCGATTTTGGTTTCGCGTTGCGATTTTG
65576 GTTTCGCGTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.07, C:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
Found at i:65535 original size:19 final size:19
Alignment explanation
Indices: 65481--65609 Score: 134
Period size: 19 Copynumber: 7.3 Consensus size: 19
65471 AAAATCGCAA
65481 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
65500 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
65514 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
65533 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
65547 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
65566 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
65585 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
65605 TGCGA
1 TGCGA
65610 AATTAAACTA
Statistics
Matches: 92, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 23 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 49 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:65615 original size:20 final size:20
Alignment explanation
Indices: 65558--65615 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
65548 GCGATTTTCA
* **
65558 TTTCGCGTTGCG-ATTTTGG
1 TTTCGCGTTGCGAAATTAAG
**
65577 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGAAATTAAG
*
65597 TTTCGTGTTGCGAAATTAA
1 TTTCGCGTTGCGAAATTAA
65616 ACTATTTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.38
20 20 0.62
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCGAAATTAAG
Found at i:67565 original size:20 final size:20
Alignment explanation
Indices: 67535--67631 Score: 109
Period size: 20 Copynumber: 5.2 Consensus size: 20
67525 TTTTGGTTGA
67535 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
**
67555 AATGACTATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
67575 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
67594 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
67609 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
67629 AAT
1 AAT
67632 CGCAACGCGA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
14 9 0.14
16 4 0.06
17 2 0.03
19 15 0.23
20 21 0.33
21 13 0.20
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:67586 original size:21 final size:21
Alignment explanation
Indices: 67533--67597 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
67523 TCTTTTGGTT
67533 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
**
67554 G-AATGACTATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
67574 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
67595 GAA
1 GAA
67598 TCGCAACGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 18 0.46
21 21 0.54
ACGTcount: A:0.49, C:0.15, G:0.25, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:67601 original size:14 final size:14
Alignment explanation
Indices: 67582--67638 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
67572 GAGAAATGAA
67582 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
67596 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
67615 AATCGCAACGAGAG
1 AATCGCAACGAGAG
67629 AATCGCAACG
1 AATCGCAACG
67639 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:67615 original size:33 final size:33
Alignment explanation
Indices: 67533--67655 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
67523 TCTTTTGGTT
*
67533 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGAGA
1 GAAATGAAAATCGCAAC--GAG-A-GA--ATCGCAAC--GC
67574 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
67607 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
67640 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
67656 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 8 0.10
37 2 0.02
38 1 0.01
39 3 0.04
41 17 0.21
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:67691 original size:14 final size:14
Alignment explanation
Indices: 67672--67728 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
67662 TTTGGTTTCG
67672 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
67686 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
67705 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
67719 CGTTGCGATT
1 CGTTGCGATT
67729 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:67704 original size:33 final size:33
Alignment explanation
Indices: 67656--67736 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
67646 AAAATCGCAA
**
67656 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
67689 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
67722 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
67737 TCTCGTTGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:67739 original size:21 final size:21
Alignment explanation
Indices: 67713--67789 Score: 104
Period size: 21 Copynumber: 3.7 Consensus size: 21
67703 CGCGTTGCGA
67713 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
67734 TTCTCTCGTTGC-ATATAGTCAT
1 TTCTCTCGTTGCGAT-T-TTCAT
*
67756 TT-TCGCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
67776 TTCTCTCGTTGCGA
1 TTCTCTCGTTGCGA
67790 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
20 8 0.17
21 32 0.67
22 8 0.17
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:67911 original size:33 final size:33
Alignment explanation
Indices: 67869--67939 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
67859 AATACTAACT
67869 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
*
67902 TGAAAATCGCAACGAGAGAATCGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
67935 TGAAA
1 TGAAA
67940 TCTAAGTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.48, C:0.18, G:0.24, T:0.10
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:67915 original size:19 final size:19
Alignment explanation
Indices: 67891--67939 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 19
67881 CGAGAGAATA
67891 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
67910 GCAA--CG--A-GAGAATC
1 GCAACGCGAAATGAAAATC
67924 GCAACGCGAAATGAAA
1 GCAACGCGAAATGAAA
67940 TCTAAGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 10
0.66 0.06 0.29
Matches are distributed among these distances:
14 10 0.43
15 1 0.04
16 2 0.09
17 2 0.09
18 1 0.04
19 7 0.30
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.08
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:67925 original size:14 final size:14
Alignment explanation
Indices: 67873--67929 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
67863 CTAACTTGAA
67873 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
67887 AATAGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
67906 AATCGCAACGAGAG
1 AATCGCAACGAGAG
67920 AATCGCAACG
1 AATCGCAACG
67930 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.21, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:68333 original size:20 final size:20
Alignment explanation
Indices: 68308--68500 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
68298 CTTTAAAAAT
68308 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
68328 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
68348 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
68369 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
68389 CGCATTGCGATTTACGTATA
1 CGCGTTGCGATTTACGGATA
68409 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
68429 CACGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
68449 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
68469 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
68489 CGCGTTGCGATT
1 CGCGTTGCGATT
68501 CTGGAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 132 0.88
21 18 0.12
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:68495 original size:60 final size:60
Alignment explanation
Indices: 68308--68500 Score: 271
Period size: 60 Copynumber: 3.2 Consensus size: 60
68298 CTTTAAAAAT
68308 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCG-CGTTGCGATTTACGGATA
* *
68369 CGCGTTGCGATTTACGGATACGCATTGCGATTTACGTATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATA
* * * * * ** *
68429 CACGTTGCGGTTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATA
68489 CGCGTTGCGATT
1 CGCGTTGCGATT
68501 CTGGAAAATC
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
60 87 0.74
61 30 0.26
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATA
Found at i:70371 original size:15 final size:15
Alignment explanation
Indices: 70353--70390 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
70343 AAGGAAAATA
70353 ATTAAAATATCAGT-G
1 ATTAAAATAT-AGTAG
*
70368 ATTAAAATATAGTAT
1 ATTAAAATATAGTAG
70383 ATTAAAAT
1 ATTAAAAT
70391 TAAAAGCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.37
Consensus pattern (15 bp):
ATTAAAATATAGTAG
Found at i:71228 original size:45 final size:45
Alignment explanation
Indices: 71164--71261 Score: 151
Period size: 45 Copynumber: 2.2 Consensus size: 45
71154 TGGAACGGGG
*
71164 ACGTGGAGGGACTGCTGGCAGTGCTGGAAGCTACTGGAAATTGCA
1 ACGTGGAGGGACTGCTGGCAATGCTGGAAGCTACTGGAAATTGCA
* * * *
71209 ACGTGGAGGGGCTGTTGGCAATGCTGGAAGCTACTGGAATTTGTA
1 ACGTGGAGGGACTGCTGGCAATGCTGGAAGCTACTGGAAATTGCA
71254 ACGTGGAG
1 ACGTGGAG
71262 CTGCTGGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.22
Consensus pattern (45 bp):
ACGTGGAGGGACTGCTGGCAATGCTGGAAGCTACTGGAAATTGCA
Found at i:71583 original size:39 final size:39
Alignment explanation
Indices: 71507--71800 Score: 384
Period size: 39 Copynumber: 7.7 Consensus size: 39
71497 AGGTTGAATA
*
71507 AGTTCTTCAGACTATGAA---CTTCTTCCTCTTCAAATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
* * *
71543 AGTTCTTCAGATTATGAACTCCTTCTTTCTCTTCATATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
* * * *
71582 AGTTCTTCAAACTATGAACTTCTTCTTCCTCTTTAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
71621 AGTTCTTCAGACTATGAACT-C--CTTCCTCTTCAGATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
*
71657 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
* * *
71696 AGTCCTTCATACTATGAACTCCTTCTTTCTCTTCAGATG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
* * * **
71735 AGTTCTTCAGATTGTGAACTTCTTCTTCCTCTTCAGGCG
1 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
*
71774 AGTTCTTCAGATTATGAACTCCTTCTT
1 AGTTCTTCAGACTATGAACTCCTTCTT
71801 GAAATGTTTT
Statistics
Matches: 224, Mismatches: 28, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
36 50 0.22
37 1 0.00
38 1 0.00
39 172 0.77
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.40
Consensus pattern (39 bp):
AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGATG
Found at i:71637 original size:78 final size:78
Alignment explanation
Indices: 71507--71800 Score: 429
Period size: 78 Copynumber: 3.8 Consensus size: 78
71497 AGGTTGAATA
* * *
71507 AGTTCTTCAGACTATGAA---CTTCTTCCTCTTCAAATGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
*
71569 TTCTCTTCATATG
66 TTCTCTTCAGATG
* *
71582 AGTTCTTCAAACTATGAACTTCTTCTTCCTCTTTAGACGAGTTCTTCAGACTATGAACTCCTTC-
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
71646 --CTCTTCAGATG
66 TTCTCTTCAGATG
* * *
71657 AGTTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGTCCTTCATACTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
71722 TTCTCTTCAGATG
66 TTCTCTTCAGATG
* * * *
71735 AGTTCTTCAGATTGTGAACTTCTTCTTCCTCTTCAGGCGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
71800 T
66 T
71801 GAAATGTTTT
Statistics
Matches: 195, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
75 86 0.44
78 109 0.56
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.40
Consensus pattern (78 bp):
AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGACTATGAACTCCTTCT
TTCTCTTCAGATG
Found at i:71639 original size:114 final size:114
Alignment explanation
Indices: 71507--71800 Score: 417
Period size: 114 Copynumber: 2.6 Consensus size: 114
71497 AGGTTGAATA
* *
71507 AGTTCTTCAGACTATGAACTTCTTCCTCTTCAAATGAGTTCTTCAGATTATGAACTCCTTCTTTC
1 AGTTCTTCAGACTATGAACTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCTTCC
* * * * *
71572 TCTTCATATGAGTTCTTCAAACTATGAACTTCTTCTTCCTCTTTAGACG
66 TCTTCAGACGAGTCCTTCAAACTATGAACTCCTTCTTCCTCTTCAGACG
* *
71621 AGTTCTTCAGACTATGAACTCCTTCCTCTTCAGATGAGTTCTTCAGACTATGAACTCCTTCTTCC
1 AGTTCTTCAGACTATGAACTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCTTCC
* * *
71686 TCTTCAGACGAGTCCTTCATACTATGAACTCCTTCTTTCTCTTCAGATG
66 TCTTCAGACGAGTCCTTCAAACTATGAACTCCTTCTTCCTCTTCAGACG
* * **
71735 AGTTCTTCAGATTGTGAACTTCTTCTTCCTCTTCAGGCGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAA---CTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCT
71800 T
63 T
71801 GAAATGTTTT
Statistics
Matches: 159, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
114 118 0.74
117 41 0.26
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.40
Consensus pattern (114 bp):
AGTTCTTCAGACTATGAACTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTCTTCC
TCTTCAGACGAGTCCTTCAAACTATGAACTCCTTCTTCCTCTTCAGACG
Found at i:71925 original size:72 final size:72
Alignment explanation
Indices: 71805--72064 Score: 387
Period size: 73 Copynumber: 3.6 Consensus size: 72
71795 CTTCTTGAAA
* * *
71805 TGTTTTAAGAAAAATAATCTCAATTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGGA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGGA
*
71870 AACATTT
66 AACAATT
* ** * * *
71877 TATTTTAAGAAAAACAATCTCAAGTGAGATAAATTATTATTTCGAGTGAAATTTTCTCAAGCAAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGC-GG
71942 AAA-AAGTT
65 AAACAA-TT
71950 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCG-G
72015 AAACAATT
65 AAACAATT
*
72023 TGTTTTAAGAAAAATAATCTCAAGTGAGATAAATTGCTATTT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
72065 GAAAACATCC
Statistics
Matches: 167, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
72 55 0.33
73 110 0.66
74 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (72 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGGA
AACAATT
Found at i:71973 original size:36 final size:35
Alignment explanation
Indices: 71931--72057 Score: 112
Period size: 36 Copynumber: 3.5 Consensus size: 35
71921 AGTGAAATTT
*
71931 TCTCAAGCAAGAAAAAGTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGAAAAA-TTTGTTTTAAGAAAAACAA
* * ** **
71967 TCTCAAGTGAGATAAA-TTGCTATTTCAAGTGAAACTT
1 TCTCAAGCGAGAAAAATTTG-T-TTT-AAGAAAAACAA
*
72004 TCTCAAGCGAGAAACAATTTGTTTTAAGAAAAATAA
1 TCTCAAGCGAGAAA-AATTTGTTTTAAGAAAAACAA
* *
72040 TCTCAAGTGAGATAAATT
1 TCTCAAGCGAGAAAAATT
72058 GCTATTTGAA
Statistics
Matches: 70, Mismatches: 16, Indels: 11
0.72 0.16 0.11
Matches are distributed among these distances:
34 3 0.04
35 5 0.07
36 34 0.49
37 22 0.31
38 3 0.04
39 3 0.04
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (35 bp):
TCTCAAGCGAGAAAAATTTGTTTTAAGAAAAACAA
Found at i:73252 original size:54 final size:54
Alignment explanation
Indices: 73167--73270 Score: 181
Period size: 54 Copynumber: 1.9 Consensus size: 54
73157 TTATTGGTTT
* *
73167 GTAAAATATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGATGTTC
1 GTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGATGTTC
*
73221 GTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCTCAGAT
1 GTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
73271 TTCTCAATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGATGTTC
Found at i:77205 original size:18 final size:18
Alignment explanation
Indices: 77178--77212 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
77168 ATGAAGAAAA
77178 AAATAAAAAAATGCAAAT
1 AAATAAAAAAATGCAAAT
*
77196 AAATATAAAAATGCAAA
1 AAATAAAAAAATGCAAA
77213 CACAAACATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (18 bp):
AAATAAAAAAATGCAAAT
Found at i:80712 original size:45 final size:45
Alignment explanation
Indices: 80659--80753 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
80649 AACGGGGACA
80659 TGGAGGGACTGCTGGCAGTGCTGGAAGCTACTAGAATTTGCAACG
1 TGGAGGGACTGCTGGCAGTGCTGGAAGCTACTAGAATTTGCAACG
* *
80704 TGGAGGGACTGCTGGCAGTGCTGGAAGCTACTGGAATTTGTAACG
1 TGGAGGGACTGCTGGCAGTGCTGGAAGCTACTAGAATTTGCAACG
80749 TGGAG
1 TGGAG
80754 CTGCTGGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.23
Consensus pattern (45 bp):
TGGAGGGACTGCTGGCAGTGCTGGAAGCTACTAGAATTTGCAACG
Found at i:85997 original size:23 final size:23
Alignment explanation
Indices: 85971--86039 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
85961 CACCACAGCT
*
85971 CGTATAATTACACCGAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
* *
85994 CGTATAATTGCACCGGAGTGCCG
1 CGTATAATTGCACCGAAGTGCCA
* *
86017 CGTAGAATTGCACCGTAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
86040 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTATAATTGCACCGAAGTGCCA
Found at i:87085 original size:2 final size:2
Alignment explanation
Indices: 87080--87129 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
87070 TCATATATTC
87080 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
87122 AT AT AT AT
1 AT AT AT AT
87130 GTCAATGATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91151 original size:23 final size:23
Alignment explanation
Indices: 91125--91185 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
91115 TCACCACACT
91125 CGTATAATTGCACCAAAGTGCCA
1 CGTATAATTGCACCAAAGTGCCA
* *
91148 CGTATAATTGCACCGAAGTGCCG
1 CGTATAATTGCACCAAAGTGCCA
*
91171 CGTAGAATTGCACCA
1 CGTATAATTGCACCA
91186 GTGCCATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CGTATAATTGCACCAAAGTGCCA
Found at i:92241 original size:2 final size:2
Alignment explanation
Indices: 92234--92263 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
92224 TCTTATATTC
92234 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
92264 GTCAATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92462 original size:18 final size:18
Alignment explanation
Indices: 92420--92462 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
92410 TTAGTCATGC
* *
92420 ATACATATAATTAATGTA
1 ATACATATAATCAATATA
92438 ATACATATAATCACATATA
1 ATACATATAATCA-ATATA
92457 AT-CATA
1 ATACATA
92463 ACAAACACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (18 bp):
ATACATATAATCAATATA
Found at i:96750 original size:21 final size:21
Alignment explanation
Indices: 96724--96764 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
96714 TTTGATTATA
*
96724 TTATTAT-TATACAAGTTCAAC
1 TTATTATAGATACAA-TTCAAC
96745 TTATTATAGATACAATTCAA
1 TTATTATAGATACAATTCAA
96765 ATATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (21 bp):
TTATTATAGATACAATTCAAC
Found at i:98361 original size:20 final size:20
Alignment explanation
Indices: 98309--98361 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
98299 GATTCAAGTG
* * *
98309 GTATCGATAGCAAGAGGGGA
1 GTATCGATACCATGAGGAGA
*
98329 GTATCGATACCATGAGGATA
1 GTATCGATACCATGAGGAGA
98349 GTATCGATACCAT
1 GTATCGATACCAT
98362 TGAGCACTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (20 bp):
GTATCGATACCATGAGGAGA
Found at i:98863 original size:55 final size:57
Alignment explanation
Indices: 98773--98886 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 57
98763 ATTACCAAAT
* *
98773 GGCACTGAGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTGAGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTAAGAATTTCCATATG
98830 GGCACT-ATGTGTGC-AAAA-CTAAGAAATTCATACTAAGTGTAAGAATTTCCATATG
1 GGCACTGA-GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTAAGAATTTCCATATG
98885 GG
1 GG
98887 AAATATATGT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
55 37 0.69
56 5 0.09
57 12 0.22
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (57 bp):
GGCACTGAGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTAAGAATTTCCATATG
Found at i:98908 original size:55 final size:55
Alignment explanation
Indices: 98788--98916 Score: 170
Period size: 55 Copynumber: 2.3 Consensus size: 55
98778 TGAGTGTGCA
* * * * * *
98788 AAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGC
1 AAAA-CTAAGAAATTCATACTAAGTGTAAGAATTTCCATATGGGAAATATATGTAC
98844 AAAACTAAGAAATTCATACTAAGTGTAAGAATTTCCATATGGGAAATATATGTAC
1 AAAACTAAGAAATTCATACTAAGTGTAAGAATTTCCATATGGGAAATATATGTAC
*
98899 AAATA-TAAGAAGTTCATA
1 AAA-ACTAAGAAATTCATA
98917 ATAATTAGGT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 60 0.92
56 5 0.08
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (55 bp):
AAAACTAAGAAATTCATACTAAGTGTAAGAATTTCCATATGGGAAATATATGTAC
Found at i:99210 original size:68 final size:68
Alignment explanation
Indices: 99097--99293 Score: 324
Period size: 68 Copynumber: 2.9 Consensus size: 68
99087 AAGATTAAAT
* *
99097 GCCTAACTGTGCATTTGACAA-AAAAGATGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 GCCTAACTGTGCATTTGA-AAGAAATG-TGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCT
99161 TTGAG
64 TTGAG
99166 GCCTAACTGTGCATTTGAAAGAAATGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGAAAGAAATGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCTTT
99231 GAG
66 GAG
* * *
99234 GCCTAACTGTGCATTTGACAGAAATGTGTCAACCATGCTAGTTAGATGAAAGACTAAGTG
1 GCCTAACTGTGCATTTGAAAGAAATGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTG
99294 TGATGTAGGG
Statistics
Matches: 122, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
68 100 0.82
69 22 0.18
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (68 bp):
GCCTAACTGTGCATTTGAAAGAAATGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCTTT
GAG
Found at i:104310 original size:14 final size:14
Alignment explanation
Indices: 104291--104337 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
104281 AGTGCTTCAA
104291 CTTTTCTTTCTT-TT
1 CTTTTCTTT-TTCTT
104305 CTTTTCTTTTTCTT
1 CTTTTCTTTTTCTT
104319 CTTTT-TGTTTTCTT
1 CTTTTCT-TTTTCTT
104333 CTTTT
1 CTTTT
104338 GAGTGCTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.10
14 28 0.90
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTTCTT
Done.