Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002998.1 Hibiscus syriacus cultivar Beakdansim tig00006199_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: 76720
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5942 original size:3 final size:3
Alignment explanation
Indices: 5934--5974 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
5924 ATTTGTAAAT
* **
5934 TAA TAA TAA TAG TAA TAA TAA TAA TAA CGA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5975 TATATTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5952 original size:15 final size:18
Alignment explanation
Indices: 5934--5974 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5924 ATTTGTAAAT
5934 TAATAATAAT-A-G-TAA
1 TAATAATAATAACGATAA
5949 TAATAATAATAACGATAA
1 TAATAATAATAACGATAA
5967 TAATAATA
1 TAATAATA
5975 TATATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.43
16 1 0.04
17 1 0.04
18 11 0.48
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (18 bp):
TAATAATAATAACGATAA
Found at i:6341 original size:43 final size:43
Alignment explanation
Indices: 6294--6470 Score: 132
Period size: 43 Copynumber: 4.1 Consensus size: 43
6284 ATGAGGACGG
* * *
6294 CTGGTTATCTAGGGGTGACACGGCTCTTACGCGATGAGGAGAT
1 CTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGAT
*
6337 CTGG---TCT-GGGGAATGACAC-GCTCATACGTGATGAAGAGTT
1 CTGGTTATCTAGGGG--TGACACGGCTCATACGTGATGAAGAGAT
** * * * * * *
6377 CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-G
1 CTGGTTATCT--AGG-GGTGACACGGCTCATACGTGATGAAGA-GAT
* *
6423 CTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGAT
1 CTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGAT
6466 CTGGT
1 CTGGT
6471 CTGGGGATGA
Statistics
Matches: 103, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
39 4 0.04
40 24 0.23
41 6 0.06
42 1 0.01
43 34 0.33
44 2 0.02
45 5 0.05
46 25 0.24
47 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.26
Consensus pattern (43 bp):
CTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGAT
Found at i:6459 original size:129 final size:130
Alignment explanation
Indices: 6167--6484 Score: 437
Period size: 134 Copynumber: 2.4 Consensus size: 130
6157 GGTCTGGTCG
* * * * *
6167 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAAATATGGTC-GAGGGATGACACTTCTCATACG
1 TCTAGGGGTGACACGGCTCATACGTGATGAGGAGATCTGGTCTG-GGGATGACAC-GCTCATACG
*
6231 TGATGAAGAGTTCTTGGCCATCTTTAGGAAAGGTGATAACTCGGTTCCTACGCATGAGGACGGCT
64 TGATGAAGAGTTCTTGGCCATC-TT--GAAAGGTGATAACACGGTTCCTACGCATGAGGACGGCT
6296 GGTTA
126 GGTTA
* *
6301 TCTAGGGGTGACACGGCTCTTACGCGATGAGGAGATCTGGTCTGGGGAATGACACGCTCATACGT
1 TCTAGGGGTGACACGGCTCATACGTGATGAGGAGATCTGGTCTGGGG-ATGACACGCTCATACGT
*
6366 GATGAAGAGTTC-TGGCCATC-T-AAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGT
65 GATGAAGAGTTCTTGGCCATCTTGAAAGGTGATAACACGGTTCCTACG-CATGAGGACGGCTGGT
6428 TA
129 TA
* * *
6430 TCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACG
1 TCTAGGGGTGACACGGCTCATACGTGATGAGGAGATCTGGTCTGGGGATGACACG
6485 GTTCCTACAT
Statistics
Matches: 168, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
128 31 0.18
129 59 0.35
131 1 0.01
133 8 0.05
134 61 0.36
135 8 0.05
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (130 bp):
TCTAGGGGTGACACGGCTCATACGTGATGAGGAGATCTGGTCTGGGGATGACACGCTCATACGTG
ATGAAGAGTTCTTGGCCATCTTGAAAGGTGATAACACGGTTCCTACGCATGAGGACGGCTGGTTA
Found at i:6498 original size:129 final size:130
Alignment explanation
Indices: 6167--6499 Score: 424
Period size: 129 Copynumber: 2.5 Consensus size: 130
6157 GGTCTGGTCG
* * * *
6167 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAAATATGGTC-GAGGGATGACAC-TTCTCATAC
1 TCTAGGGGTGACACGGCTCATACGTGATGAGGAGATCTGGTCTG-GGGATGACACGTTC-C-TAC
*
6230 GTGATGAAGAGTTCTTGGCCATCTTTAGGAAAGGTGATAACTCGGTTCCTACGCATGAGGACGGC
63 GTGATGAAGAGTTCTTGGCCATC-TT--GAAAGGTGATAACACGGTTCCTACGCATGAGGACGGC
6295 TGGTTA
125 TGGTTA
* * * *
6301 TCTAGGGGTGACACGGCTCTTACGCGATGAGGAGATCTGGTCTGGGGAATGACACGCTCATACGT
1 TCTAGGGGTGACACGGCTCATACGTGATGAGGAGATCTGGTCTGGGG-ATGACACGTTCCTACGT
*
6366 GATGAAGAGTTC-TGGCCATC-T-AAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGT
65 GATGAAGAGTTCTTGGCCATCTTGAAAGGTGATAACACGGTTCCTACG-CATGAGGACGGCTGGT
6428 TA
129 TA
* * * *
6430 TCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACAT
1 TCTAGGGGTGACACGGCTCATACGTGATGAGGAGATCTGGTCTGGGGATGACAC-GTTCCTACGT
6495 GATGA
65 GATGA
6500 GGACGGCTGG
Statistics
Matches: 177, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
128 30 0.17
129 71 0.40
131 1 0.01
133 8 0.05
134 57 0.32
135 8 0.05
136 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26
Consensus pattern (130 bp):
TCTAGGGGTGACACGGCTCATACGTGATGAGGAGATCTGGTCTGGGGATGACACGTTCCTACGTG
ATGAAGAGTTCTTGGCCATCTTGAAAGGTGATAACACGGTTCCTACGCATGAGGACGGCTGGTTA
Found at i:6504 original size:83 final size:84
Alignment explanation
Indices: 6350--6509 Score: 225
Period size: 83 Copynumber: 1.9 Consensus size: 84
6340 GTCTGGGGAA
* * *
6350 TGACACGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
1 TGACACGCTCATACGTGATGAAGAGATCTGG-C-TCT--AGGGGATAACACGGTTCCTACATGAT
6415 GAGGACGGCTGGTTATCTATGGT
62 GAGGACGGCTGGTTATCTATGGT
*
6438 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCT-GGGGATGACACGGTTCCTACATGATGAG
1 TGACAC-GCTCATACGTGATGAAGAGATCTGGCTCTAGGGGATAACACGGTTCCTACATGATGAG
6501 GACGGCTGG
65 GACGGCTGG
6510 CCATCTTTAG
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
83 34 0.51
86 3 0.04
88 6 0.09
89 24 0.36
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.25
Consensus pattern (84 bp):
TGACACGCTCATACGTGATGAAGAGATCTGGCTCTAGGGGATAACACGGTTCCTACATGATGAGG
ACGGCTGGTTATCTATGGT
Found at i:6568 original size:28 final size:28
Alignment explanation
Indices: 6548--6609 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
6538 AAACCAAATT
6548 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
6576 AAAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
6604 AAAGAT
1 AAAGAT
6610 GATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:7500 original size:30 final size:28
Alignment explanation
Indices: 7450--7505 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
7440 ACAACATTTG
* *
7450 TTTTTTAAAGAAATAGACTCAAAGATGA
1 TTTTTTAAAGAAACAAACTCAAAGATGA
7478 TTTTGTTAAGAGAAACAAACTCAAAGAT
1 TTTT-TTAA-AGAAACAAACTCAAAGAT
7506 TTTCAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.30
Consensus pattern (28 bp):
TTTTTTAAAGAAACAAACTCAAAGATGA
Found at i:7606 original size:61 final size:58
Alignment explanation
Indices: 7506--7807 Score: 174
Period size: 67 Copynumber: 4.7 Consensus size: 58
7496 ACTCAAAGAT
* * * * *
7506 TTTCAAAATGAACATATTCAAAGATTTACTTCAAGAGAAACTGTCTCAGAGATACAAAATTCA
1 TTTCCAAA-GAACA-ATTCAAAGATTT-TTTCAAAAGAAACTATCT-A-AGAGACAAAATTCA
* * **
7569 TTT-TAAGAGAACAATTCAAAGATTTTTTCCAAAAGAAATTATCTAAGAGACAAAATTTG
1 TTTCCAA-AGAACAATTCAAAGATTTTTT-CAAAAGAAACTATCTAAGAGACAAAATTCA
* * **
7628 TTTCCAAAGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTG
1 TTTCCAAAG-AAC-AATTCAAAGA-TTTTTTCAAAAGAAACTATC-T-A-AGAGACAAAA-TTCA
* *
7693 TTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTT
1 TTTCCAAAG-AAC-AATTCAAAGA--TTT-TTTCAAAAGAAACTATC-T-A-AGAGACAAAA-TT
**
7758 TG
57 CA
* *
7760 TTTCCAAAGAAACCAACTCAAAGATTTTTGTTTCAAAAGAAACAATCT
1 TTTCCAAAG-AA-CAATTCAAAGA--TTT-TTTCAAAAGAAACTATCT
7808 CAAAGATTTT
Statistics
Matches: 214, Mismatches: 12, Indels: 23
0.86 0.05 0.09
Matches are distributed among these distances:
59 16 0.07
60 8 0.04
61 47 0.22
62 14 0.07
63 5 0.02
64 10 0.05
65 28 0.13
66 5 0.02
67 80 0.37
68 1 0.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (58 bp):
TTTCCAAAGAACAATTCAAAGATTTTTTCAAAAGAAACTATCTAAGAGACAAAATTCA
Found at i:7702 original size:37 final size:37
Alignment explanation
Indices: 7646--7771 Score: 124
Period size: 37 Copynumber: 3.6 Consensus size: 37
7636 GAAACAAACT
7646 CAAAGATTTT-TTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAA-ATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
* ** * *
7683 CAAAATTTTGTTTCCAAAGAAACAAAC-TCA-A-AG-
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
*
7716 ---ATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
*
7750 CAAAATTTTGTTTCCAAAGAAA
1 CAAAATTTTGTTTCAAAAGAAA
7772 CCAACTCAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
30 19 0.28
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 7 0.10
37 34 0.50
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
Found at i:7716 original size:65 final size:67
Alignment explanation
Indices: 7584--7801 Score: 362
Period size: 67 Copynumber: 3.4 Consensus size: 67
7574 AGAGAACAAT
*
7584 TCAAAGA-TTTT-TTCCAAAAGAAATTATC-T-A-AGAGACAAAA-TTTGTTTCCAAAGAAACAA
1 TCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
7643 AC
66 AC
7645 TCAAAGA-TTTT-TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
7708 AC
66 AC
*
7710 TCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACCA
1 TCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
7775 AC
66 AC
7777 TCAAAGATTTTTGTTTCAAAAGAAA
1 TCAAAGATTTTTGTTTCAAAAGAAA
7802 CAATCTCAAA
Statistics
Matches: 149, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
61 27 0.18
62 1 0.01
63 1 0.01
64 10 0.07
65 28 0.19
66 4 0.03
67 78 0.52
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (67 bp):
TCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
AC
Found at i:7722 original size:30 final size:30
Alignment explanation
Indices: 7688--7818 Score: 118
Period size: 30 Copynumber: 4.1 Consensus size: 30
7678 AGAGACAAAA
*
7688 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
** * * *
7718 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG----AT
* *
7755 TTTTGTTTCCAAAGAAACCAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
*
7785 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
7815 TTTT
1 TTTT
7819 TTTTTTACAA
Statistics
Matches: 79, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
30 50 0.63
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 2 0.03
37 19 0.24
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.34
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:7963 original size:29 final size:29
Alignment explanation
Indices: 7909--8090 Score: 169
Period size: 29 Copynumber: 6.4 Consensus size: 29
7899 AAAACTTTGT
* * * *
7909 TTCAAAATAAATAGACTCAAAGATTTTTGT
1 TTCAAAAGAAACAAACTCAAAGATTTTT-A
* *
7939 TTCAAACGAAAC-AACTCAAAAATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
7967 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
7996 TTCAAAAGGAACAAACTCAAAGA-TTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
8023 TTCAAGAGGAACAAACTCAAAGA-TTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* * *
8050 TT-AAGAGGAACAAACTCAAAGATTTTTT
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
8078 TCCTCAAAAGAAA
1 T--TCAAAAGAAA
8091 TTGTCTTTAA
Statistics
Matches: 132, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
26 20 0.15
27 32 0.24
28 15 0.11
29 49 0.37
30 10 0.08
31 6 0.05
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (29 bp):
TTCAAAAGAAACAAACTCAAAGATTTTTA
Found at i:7994 original size:58 final size:56
Alignment explanation
Indices: 7923--8077 Score: 174
Period size: 53 Copynumber: 2.8 Consensus size: 56
7913 AAATAAATAG
* *
7923 ACTCAAAGATTTTTGTTTCAAACGAAAC-AACTCAAAAATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-ATTCAAAAGAAACAAACTCAAAAA-TTTT-TTCAAAAGGAACAA
* * * *
7981 ACTCCAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGAAACAAACTCAAAAATTTTTTCAAAAGGAACAA
* * *
8037 ACTCAAAGA-TTTT-TT-AAGAGGAACAAACTCAAAGATTTTTT
1 ACTCAAAGATTTTTATTCAAAAGAAACAAACTCAAAAATTTTTT
8078 TCCTCAAAAG
Statistics
Matches: 88, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
53 25 0.28
54 2 0.02
55 4 0.05
56 21 0.24
57 14 0.16
58 22 0.25
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.30
Consensus pattern (56 bp):
ACTCAAAGATTTTTATTCAAAAGAAACAAACTCAAAAATTTTTTCAAAAGGAACAA
Found at i:8034 original size:27 final size:27
Alignment explanation
Indices: 7923--8077 Score: 179
Period size: 29 Copynumber: 5.6 Consensus size: 27
7913 AAATAAATAG
* *
7923 ACTCAAAGATTTTTGTTTCAAACGAAAC-A
1 ACTCAAAGA--TTT-TTTCAAAAGGAACAA
*
7952 ACTCAAAAATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTT-TTCAAAAGGAACAA
*
7981 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTT-TTCAAAAGGAACAA
*
8010 ACTCAAAGATTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
*
8037 ACTCAAAGATTTTTT-AAGAGGAACAA
1 ACTCAAAGATTTTTTCAAAAGGAACAA
8063 ACTCAAAGATTTTTT
1 ACTCAAAGATTTTTT
8078 TCCTCAAAAG
Statistics
Matches: 117, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
26 26 0.22
27 29 0.25
28 18 0.15
29 44 0.38
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.30
Consensus pattern (27 bp):
ACTCAAAGATTTTTTCAAAAGGAACAA
Found at i:8460 original size:37 final size:36
Alignment explanation
Indices: 8363--8448 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
8353 TTAAGATATA
* **
8363 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* * *
8399 GTCTCAAGCGAGACAAAGTTTGTTTTTTGAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
8435 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
8449 TCAACTTTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 31 0.74
37 11 0.26
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:8508 original size:103 final size:105
Alignment explanation
Indices: 8399--8632 Score: 287
Period size: 105 Copynumber: 2.2 Consensus size: 105
8389 TAGAGAAATT
* *** *
8399 GTCTCAAGCGAGACAAAGTTTGTTTTTTGAG-AA-AACGATCTCAA-GTGAGATCAACTTTGTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATCAACTTTGTTT
* *
8461 A-ATGTGAAACAAATTCTAAATTTGGATCTCAAAGGGAAAAG
65 ATA-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* * *
8502 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATCAACTTTGTTTA
* * *
8567 TAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
66 TAGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
8607 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
8633 AAAATCCTCA
Statistics
Matches: 112, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
103 27 0.24
104 4 0.04
105 80 0.71
106 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (105 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATCAACTTTGTTTA
TAGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:9104 original size:4 final size:4
Alignment explanation
Indices: 9095--9138 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
9085 TTTATGTATC
9095 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
9139 GTATACTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:10341 original size:12 final size:11
Alignment explanation
Indices: 10313--10350 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
10303 CCTCTTTTTG
*
10313 TTCTTTGCTTT
1 TTCTTTGATTT
10324 TTCTTTGATTT
1 TTCTTTGATTT
10335 TTGCTTTGATTT
1 TT-CTTTGATTT
10347 TTCT
1 TTCT
10351 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:10354 original size:13 final size:12
Alignment explanation
Indices: 10308--10355 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
10298 TTTGTCCTCT
10308 TTTTGTTCTTTG-
1 TTTT-TTCTTTGA
*
10320 CTTTTTCTTTGA
1 TTTTTTCTTTGA
*
10332 TTTTTGCTTTGA
1 TTTTTTCTTTGA
10344 TTTTTCTCTTTG
1 TTTTT-TCTTTG
10356 CTCTTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 7 0.23
12 18 0.60
13 5 0.17
ACGTcount: A:0.04, C:0.12, G:0.12, T:0.71
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:11050 original size:46 final size:45
Alignment explanation
Indices: 10958--11051 Score: 152
Period size: 46 Copynumber: 2.1 Consensus size: 45
10948 ATAAATACAG
* *
10958 TGTTTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
11003 TGTTTCAAGGTGGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGTGG-AAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
11049 TGT
1 TGT
11052 CAAAAATTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 13 0.29
46 32 0.71
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:16230 original size:3 final size:3
Alignment explanation
Indices: 16222--16264 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
16212 ATTTGTAAAT
* **
16222 TAA TAA TAA TAA TAG TAA TAA TAA T-A TAA CGA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
16265 TATATTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18144 original size:141 final size:141
Alignment explanation
Indices: 17887--18167 Score: 411
Period size: 141 Copynumber: 2.0 Consensus size: 141
17877 TTATAATTTG
* * ** *
17887 ATAAGCTTAGTTTAAAGATCACAAGATATATGGAGTTCAGTTTGAATATCTAAATTGAAATGTTC
1 ATAAGCTTAGTCTAAAGAGCACAAGATATATGGAGTTCAGACTGAAGATCTAAATTGAAATGTTC
* *
17952 ATTAAGAAAACAAGCGGGGATAGCTCAGTTGGGAGAGCATCAGACTTAAGATTTGAAGGTCACAT
66 ATTAAGAAAACAAGCGGGAATAGCTCAGTTGGGAGAGCATCAGACTTAAGATCTGAAGGTCACAT
*
18017 GTTTGATCCAC
131 GTTCGATCCAC
* * *
18028 ATAAGCTTAGTCTGAAGAGCACAAGATCTATGGAGTTCAGACTGAAGGTCTAAATTGAAATGTTC
1 ATAAGCTTAGTCTAAAGAGCACAAGATATATGGAGTTCAGACTGAAGATCTAAATTGAAATGTTC
* * * *
18093 ATTAAGAAAACTAGCGGGAATAGCTTAGTTGGGAGAGCGTCAGA-TTGAAGATCTGAAGGTCACG
66 ATTAAGAAAACAAGCGGGAATAGCTCAGTTGGGAGAGCATCAGACTT-AAGATCTGAAGGTCACA
18157 TGTTCGATCCA
130 TGTTCGATCCA
18168 TGTTCACCGC
Statistics
Matches: 124, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
140 2 0.02
141 122 0.98
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (141 bp):
ATAAGCTTAGTCTAAAGAGCACAAGATATATGGAGTTCAGACTGAAGATCTAAATTGAAATGTTC
ATTAAGAAAACAAGCGGGAATAGCTCAGTTGGGAGAGCATCAGACTTAAGATCTGAAGGTCACAT
GTTCGATCCAC
Found at i:19184 original size:13 final size:13
Alignment explanation
Indices: 19166--19204 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
19156 CTGCATTTAA
19166 TTAAAATTGAATT
1 TTAAAATTGAATT
19179 TTAAAATTGAATT
1 TTAAAATTGAATT
19192 TTAAAATTGAATT
1 TTAAAATTGAATT
19205 GGAGTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TTAAAATTGAATT
Found at i:19923 original size:226 final size:226
Alignment explanation
Indices: 19522--20162 Score: 824
Period size: 226 Copynumber: 2.8 Consensus size: 226
19512 GCATCTAATT
*
19522 TTATTATGATTT-AAGTCATTAGTTATTTTAAATATAATTACTATATTGTCGATAAGCTTAATGT
1 TTATTATGATTTGAA-TCATTAGTTATTTTAAATATAATTACTATATTGTCGATAAGCTTAGT-T
* * * * *
19586 GAAA-AGCACAAGATCTATGGAGTTTAGACTAAAGGTTTAAATTGAAATGTTCATTAAGAAAACT
64 CAAAGAGCACAAGATCTATGGAGTTCAGACTGAAGGTCTAAATTGAAATGTTCATTAAGAAAACA
* * * * * * *
19650 AGTGGGGATAACTCAATTTGGAAAGCATCAGACTGAAG-ATCTGAAGGTTACGTGTTCGAA-CCA
129 AGCGGGAATAACTCAATTGGGAGAGCGTCAGATTGAAGAAT-TGAAGGTCACGTGTTC-AATCCA
* *
19713 CGTTC-ACAACATCTAGTTTTAATTGAATTGGAGTA
192 CGTTCGAC-ACATCTAATTTTAATTGAATTGCAGTA
* *
19748 TTATTATGGTTTGAATCATTAGTTATTTTAAATATTATTACTATATTGTCGATAAGCTTAGTTCA
1 TTATTATGATTTGAATCATTAGTTATTTTAAATATAATTACTATATTGTCGATAAGCTTAGTTCA
* *
19813 AAGAGCACAAGATCTATGGAGTTCAGACTGAAGGTCAAAATTAAAATGTTCATTAAGAAAACAAG
66 AAGAGCACAAGATCTATGGAGTTCAGACTGAAGGTCTAAATTGAAATGTTCATTAAGAAAACAAG
*
19878 CGGGAATAACTCAATTGGGAGAGCGTCAGATTGAAGAATTGAAGGTCACGTGTTCAATTCACGTT
131 CGGGAATAACTCAATTGGGAGAGCGTCAGATTGAAGAATTGAAGGTCACGTGTTCAATCCACGTT
* * *
19943 CGTCGCATCTAATTTTAATTGAATTGCATTA
196 CGACACATCTAATTTTAATTGAATTGCAGTA
* * * *
19974 TTATTATAATTTGATTCATTAGTTATTTTAAATGTAATAAAAAAATTACTATATTATTGATAAGC
1 TTATTATGATTTGAATCATTAGTTATTTTAAA--T-AT-----AATTACTATATTGTCGATAAGC
** * *
20039 TTAGTTTGAAGAGCATAAGATCTATGGAGTTCAGACTGAAGATCTAAATTGAAATGTTCATTAAG
58 TTAGTTCAAAGAGCACAAGATCTATGGAGTTCAGACTGAAGGTCTAAATTGAAATGTTCATTAAG
* * *
20104 AAAACAAGCGGGAATAACTTAATTGGGAGAGTGTCAGATTGAAGATTTGAAGGTCACGT
123 AAAACAAGCGGGAATAACTCAATTGGGAGAGCGTCAGATTGAAGAATTGAAGGTCACGT
20163 TCATAGCACA
Statistics
Matches: 364, Mismatches: 38, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
225 6 0.02
226 216 0.59
227 5 0.01
228 1 0.00
229 2 0.01
234 134 0.37
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.34
Consensus pattern (226 bp):
TTATTATGATTTGAATCATTAGTTATTTTAAATATAATTACTATATTGTCGATAAGCTTAGTTCA
AAGAGCACAAGATCTATGGAGTTCAGACTGAAGGTCTAAATTGAAATGTTCATTAAGAAAACAAG
CGGGAATAACTCAATTGGGAGAGCGTCAGATTGAAGAATTGAAGGTCACGTGTTCAATCCACGTT
CGACACATCTAATTTTAATTGAATTGCAGTA
Found at i:23590 original size:3 final size:3
Alignment explanation
Indices: 23582--23640 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
23572 AGTGATTCAT
23582 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
23630 TTC TTC TTC TT
1 TTC TTC TTC TT
23641 TCCTTTTGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:28584 original size:141 final size:141
Alignment explanation
Indices: 28327--28607 Score: 388
Period size: 141 Copynumber: 2.0 Consensus size: 141
28317 TTATAATTTG
* * *
28327 ATAAGCTTAGTTTAAAGATCAAAAGATATATGGAGTTCAATCTGAATATCTAAATTGAAATGTCT
1 ATAAGCTTAGTCTAAAGAGCAAAAGATATATGGAGTTCAATCTGAAGATCTAAATTGAAATGTCT
* *
28392 ATTAAGAAAACAAGCGGGGATAGCTATGTTGGGAGAGCATCAGACTTAAGATTTGAAGGTCACAT
66 ATTAAGAAAACAAGCGGGGATAGCTATGTTGGGAGAGCATCAGACTGAAGATCTGAAGGTCACAT
*
28457 GTTTGATCCAC
131 GTTCGATCCAC
* * * *
28468 ATAAGCTTAGTCTGAAGAGCACAAGATCTATGGAGTTCAGA-CTGAAGGTCTAAATTGAAATGT-
1 ATAAGCTTAGTCTAAAGAGCAAAAGATATATGGAGTTCA-ATCTGAAGATCTAAATTGAAATGTC
* * *
28531 TCATTAAGAAAACTAGCGGGGATAGTTCA-GTTGGGAGAGCGTCAGACTGAAGATCTGAAGGTCA
65 T-ATTAAGAAAACAAGCGGGGATAGCT-ATGTTGGGAGAGCATCAGACTGAAGATCTGAAGGTCA
*
28595 TATGTTCGATCCA
128 CATGTTCGATCCA
28608 TGCTCACCTC
Statistics
Matches: 123, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
140 1 0.01
141 120 0.98
142 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (141 bp):
ATAAGCTTAGTCTAAAGAGCAAAAGATATATGGAGTTCAATCTGAAGATCTAAATTGAAATGTCT
ATTAAGAAAACAAGCGGGGATAGCTATGTTGGGAGAGCATCAGACTGAAGATCTGAAGGTCACAT
GTTCGATCCAC
Found at i:29187 original size:231 final size:224
Alignment explanation
Indices: 28641--29259 Score: 782
Period size: 231 Copynumber: 2.7 Consensus size: 224
28631 ATGATTTAAG
* * *
28641 TCATTAGTTATTTTAAATATAATTAGTATATTGTCGATAAGCTTAGTGTGAAAAGCACAAGATCT
1 TCATTAGTTATTTTAAATATAATTACTATATTGTCGATAAGCTTAGTTTGAAGAGCACAAGATCT
* * * *
28706 ATGGAGTTCAGACT-AA-AGGCTAAATTGAAATGTTCATTAAGAAAACTAGCGGGGATAGCTCAA
66 ATGGAGTTCAGACTGAATA-TCTAAATTGAAATGTTCATTAAGAAAACAAGCGGGAATAACTCAA
* * * * * *
28769 TTGGGAGAGCATCAGACTAAAGATCTGAAGGTTACGTGTTCGAACCACATTCACAACATCTAGTT
130 TTGGGAGAGCGTCAGATTGAAGATTTGAAGGTCACGTGTTCGAACCACATTCACAACATCTAATT
*
28834 TTAATTGAATTGGAGTATTATTATGGTTTGAA
195 TTAATTGAATTGCAGTATTATTA--GTTTGAA
* *
28866 TCATTAGTTATTTTAAATATAATTACTATACTGTCGATAAGCTTAGTTCGAAGAGCACAAGATCT
1 TCATTAGTTATTTTAAATATAATTACTATATTGTCGATAAGCTTAGTTTGAAGAGCACAAGATCT
* *
28931 ATGGAGTTCAGACTG-ATGGTCTAAATTAAAATGTTCATTAAGAAAACAAGCGGGAATAACTCAA
66 ATGGAGTTCAGACTGAAT-ATCTAAATTGAAATGTTCATTAAGAAAACAAGCGGGAATAACTCAA
* * * * * *
28995 CTGGTAGAGCGTCAGATTGAAGATTTGAAGGTCACGTGTTC-AATTCACGTTCGTC-GCATCTAA
130 TTGGGAGAGCGTCAGATTGAAGATTTGAAGGTCACGTGTTCGAA-CCACATTC-ACAACATCTAA
* **
29058 TTTTAATTGAATTGCATTATTATTA-TTTGGT
193 TTTTAATTGAATTGCAGTATTATTAGTTTGAA
* *
29089 TCATTAGTTATTTTAAATGTAATAAAAAAATTACTATATTATTGATAAGCTTAGTTTGAAGAGCA
1 TCATTAGTTATTTTAAA--T-AT-----AATTACTATATTGTCGATAAGCTTAGTTTGAAGAGCA
*
29154 TAAGATCTATGGAGTTCAGACTGAATATCTAAATTGAAATGTTCATTAAGAAAACAAGCGGGAAT
58 CAAGATCTATGGAGTTCAGACTGAATATCTAAATTGAAATGTTCATTAAGAAAACAAGCGGGAAT
* *
29219 AACTCAATTGGGAGAGTGTTAGATTGAAGATTTGAAGGTCA
123 AACTCAATTGGGAGAGCGTCAGATTGAAGATTTGAAGGTCA
29260 TGTTCATCGC
Statistics
Matches: 342, Mismatches: 38, Indels: 22
0.85 0.09 0.05
Matches are distributed among these distances:
223 21 0.06
225 78 0.23
226 111 0.32
227 1 0.00
231 129 0.38
232 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (224 bp):
TCATTAGTTATTTTAAATATAATTACTATATTGTCGATAAGCTTAGTTTGAAGAGCACAAGATCT
ATGGAGTTCAGACTGAATATCTAAATTGAAATGTTCATTAAGAAAACAAGCGGGAATAACTCAAT
TGGGAGAGCGTCAGATTGAAGATTTGAAGGTCACGTGTTCGAACCACATTCACAACATCTAATTT
TAATTGAATTGCAGTATTATTAGTTTGAA
Found at i:29621 original size:14 final size:15
Alignment explanation
Indices: 29590--29623 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29580 TATTGCTTTT
29590 TTTTATTTTAATTAA
1 TTTTATTTTAATTAA
*
29605 TTTTGTTTTAA-TAA
1 TTTTATTTTAATTAA
29619 TTTTA
1 TTTTA
29624 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTATTTTAATTAA
Found at i:32857 original size:20 final size:20
Alignment explanation
Indices: 32763--33131 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
32753 GATTTTCCAT
* ** *
32763 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
32783 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
32803 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
32823 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
32843 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
32863 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
32883 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
32903 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
32923 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
32943 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
32963 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
32983 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
33003 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
33023 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
33043 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
33063 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
33083 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
33103 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
33123 AATCACAAC
1 AATCGCAAC
33132 ACTTAAATTT
Statistics
Matches: 303, Mismatches: 36, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.01
20 295 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:33853 original size:24 final size:24
Alignment explanation
Indices: 33814--33860 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
33804 AAATTTGGTC
33814 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
33838 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
33861 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:35971 original size:19 final size:19
Alignment explanation
Indices: 35949--36222 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
35939 CGGAAAATAC
*
35949 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
35968 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
35982 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
36002 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
36016 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36035 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
36054 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
36068 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
36087 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36106 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36125 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36144 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36163 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
36177 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36196 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
36215 AATCGCAA
1 AATCGCAA
36223 CGAGATAATC
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 38 0.17
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 146 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:36100 original size:71 final size:74
Alignment explanation
Indices: 35949--36244 Score: 314
Period size: 71 Copynumber: 4.2 Consensus size: 74
35939 CGGAAAATAC
* *
35949 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-AAATCGCA
*
36009 A--CG--A-GAG
63 ATGCGAAATGAA
*
36016 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G-AATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
*
36078 CGAAATTAA
66 CGAAATGAA
36087 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
36152 TGCGAAATGAA
64 TGCGAAATGAA
36163 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
*
36223 --CG--A-GAT
64 TGCGAAATGAA
36229 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
36245 TATAAACGCA
Statistics
Matches: 203, Mismatches: 8, Indels: 34
0.83 0.03 0.14
Matches are distributed among these distances:
66 18 0.09
67 26 0.13
68 8 0.04
69 6 0.03
70 2 0.01
71 93 0.46
72 13 0.06
73 5 0.02
74 6 0.03
76 26 0.13
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (74 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
CGAAATGAA
Found at i:36148 original size:109 final size:104
Alignment explanation
Indices: 35977--36244 Score: 446
Period size: 109 Copynumber: 2.5 Consensus size: 104
35967 AAATCCCAAC
*
35977 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
36042 ATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
65 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
36082 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAAT
36147 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
61 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
36191 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAAT
36245 TATAAACGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 11
0.91 0.03 0.07
Matches are distributed among these distances:
104 34 0.22
105 16 0.10
106 2 0.01
107 2 0.01
108 1 0.01
109 98 0.64
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:36210 original size:161 final size:157
Alignment explanation
Indices: 35949--36260 Score: 502
Period size: 161 Copynumber: 2.0 Consensus size: 157
35939 CGGAAAATAC
*
35949 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
36014 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
36079 GAAATTA-AAATCGCAATGCGAAATGAA
131 GAAATTATAAA-CGCAATGCGAAATGAA
* *
36106 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
* *
36170 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
61 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGC
*
36235 AATGCGAAATTATAAACGCATTGCGA
126 AATGCGAAATTATAAACGCAATGCGA
36261 TTTTCATTTC
Statistics
Matches: 143, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
157 25 0.17
159 1 0.01
161 98 0.69
162 19 0.13
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (157 bp):
AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATTATAAACGCAATGCGAAATGAA
Found at i:36260 original size:52 final size:52
Alignment explanation
Indices: 35977--36244 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
35967 AAATCCCAAC
35977 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
36030 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
36082 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
36139 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
36191 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
36243 AT
1 AT
36245 TATAAACGCA
Statistics
Matches: 201, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
52 133 0.66
53 17 0.08
54 2 0.01
55 2 0.01
56 1 0.00
57 46 0.23
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:36360 original size:19 final size:19
Alignment explanation
Indices: 36251--36352 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
36241 AAATTATAAA
36251 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
36270 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
36290 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
36306 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
36323 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
36342 CGCATTGCGAT
1 CGCATTGCGAT
36353 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:36477 original size:14 final size:14
Alignment explanation
Indices: 36458--36494 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
36448 CATCAATTAC
36458 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
36472 ACAAATCATCTTTT
1 ACAAATCAACTTTT
36486 ACAAATCAA
1 ACAAATCAA
36495 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:38405 original size:20 final size:19
Alignment explanation
Indices: 38380--38444 Score: 80
Period size: 18 Copynumber: 3.4 Consensus size: 19
38370 TAGTTTACTT
*
38380 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
38400 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
38418 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
38437 TCGCAACG
1 TCGCAACG
38445 ACAGAATCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
18 16 0.40
19 11 0.28
20 13 0.32
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:38439 original size:19 final size:19
Alignment explanation
Indices: 38380--38512 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
38370 TAGTTTACTT
* *
38380 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
38400 TCGCAACGCGAAA-CCAAA
1 TCGCAACGCGAAATGAAAA
38418 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
38437 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
38451 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
38470 TCGCAA--CG-AA-G--AA
1 TCGCAACGCGAAATGAAAA
38483 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
38502 TCGCAATGCGA
1 TCGCAACGCGA
38513 TTTTGGTTTC
Statistics
Matches: 93, Mismatches: 8, Indels: 25
0.74 0.06 0.20
Matches are distributed among these distances:
13 8 0.09
14 8 0.09
15 3 0.03
16 9 0.10
17 8 0.09
18 16 0.17
19 29 0.31
20 12 0.13
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:38488 original size:32 final size:33
Alignment explanation
Indices: 38416--38507 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
38406 CGCGAAACCA
38416 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
38449 AATCGCAATGCGAAATGAAAATCGCAACGA-AG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
38481 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
38508 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 28 0.49
33 29 0.51
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:38530 original size:19 final size:19
Alignment explanation
Indices: 38508--38636 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
38498 AAAATCGCAA
38508 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
38527 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
38541 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
38560 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
38574 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
38593 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
38612 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
38632 TGCGA
1 TGCGA
38637 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:38550 original size:33 final size:33
Alignment explanation
Indices: 38508--38599 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
38498 AAAATCGCAA
38508 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
38541 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
38574 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
38600 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:38856 original size:89 final size:93
Alignment explanation
Indices: 38680--39142 Score: 831
Period size: 93 Copynumber: 5.1 Consensus size: 93
38670 TTGAATGGAT
38680 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAG-ATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
38744 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
38772 AAATTTAC-TTCAACCAAAAGACAAAACAAAGAC-AA-A-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
38833 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
38861 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
38926 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
38954 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
39018 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
39046 -AATTTACTTTCAACCAAAAGACAAAAC-AAGAC-AATACTATTTCACAGTGTT-AAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
39107 AGTTTAGCAGAATTGGCAGCAACCGAA-
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
39134 TAATTTACT
1 AAATTTACT
39143 AAGCAATCTA
Statistics
Matches: 362, Mismatches: 2, Indels: 17
0.95 0.01 0.04
Matches are distributed among these distances:
88 18 0.05
89 91 0.25
90 46 0.13
91 54 0.15
92 61 0.17
93 92 0.25
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:40860 original size:14 final size:14
Alignment explanation
Indices: 40841--40930 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
40831 TTGAAATGAA
40841 AATCGCAACGAGAG
1 AATCGCAACGAGAG
40855 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
40872 ACAATCGCAATGAGAG
1 --AATCGCAACGAGAG
*
40888 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
40907 AATCGCAACGAGAG
1 AATCGCAACGAGAG
40921 AATCGCAACG
1 AATCGCAACG
40931 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 1 0.02
16 7 0.11
17 7 0.11
18 1 0.02
19 18 0.29
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:40878 original size:33 final size:33
Alignment explanation
Indices: 40833--40947 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
40823 TCTTTTGGTT
40833 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
40866 GAGATGACAATCGCAATGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
40899 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
40932 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
40948 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:40879 original size:19 final size:18
Alignment explanation
Indices: 40840--40952 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
40830 GTTGAAATGA
40840 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
40855 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
*
40872 ACAATCGCAA--TGAGA-G
1 A-AATCGCAACGCGAGATG
*
40888 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
40905 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
40921 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
40938 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
40953 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 26
0.71 0.06 0.24
Matches are distributed among these distances:
14 24 0.31
16 14 0.18
17 11 0.14
19 28 0.36
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:40983 original size:14 final size:14
Alignment explanation
Indices: 40964--41017 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
40954 TTTGGTTTCG
40964 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
40978 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
40996 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
41010 CGTTGCGA
1 CGTTGCGA
41018 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 18 0.53
15 3 0.09
17 3 0.09
18 10 0.29
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:41001 original size:18 final size:17
Alignment explanation
Indices: 40959--41005 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
40949 GCGATTTTGG
40959 TTTCGCGTTGCGA-TTC
1 TTTCGCGTTGCGATTTC
*
40975 --TCTCGTTGCGATTTC
1 TTTCGCGTTGCGATTTC
40990 ATTTCGCGTTGCGATT
1 -TTTCGCGTTGCGATT
41006 CTCTCGTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
18 12 0.48
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (17 bp):
TTTCGCGTTGCGATTTC
Found at i:41180 original size:33 final size:33
Alignment explanation
Indices: 41138--41208 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
41128 AATACTAACT
*
41138 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
41171 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
41204 TGAAA
1 TGAAA
41209 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:41439 original size:22 final size:22
Alignment explanation
Indices: 41387--41441 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
41377 TGGTTGTGAG
**
41387 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
41409 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
41431 GGATTTCTTCG
1 GGATTTCTTCG
41442 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:41611 original size:20 final size:20
Alignment explanation
Indices: 41586--41778 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
41576 CTTTAAATAT
41586 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
41606 CGCGTTGTGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
41628 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
41647 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
41667 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
41687 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
41707 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
41727 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
41747 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
41767 CGCGTTGCGATT
1 CGCGTTGCGATT
41779 ATGGAAAATC
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.88
21 14 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:41773 original size:60 final size:60
Alignment explanation
Indices: 41586--41778 Score: 242
Period size: 60 Copynumber: 3.2 Consensus size: 60
41576 CTTTAAATAT
* **
41586 CGCGTTGCGATTTACGGATACGCGTTGTGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
41647 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
41707 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
41767 CGCGTTGCGATT
1 CGCGTTGCGATT
41779 ATGGAAAATC
Statistics
Matches: 110, Mismatches: 22, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
60 83 0.75
61 27 0.25
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:41859 original size:20 final size:20
Alignment explanation
Indices: 41834--41885 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
41824 AAGAATCGCG
*
41834 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
41854 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
41874 TTGCGATTCTGG
1 TTGCGATTCTGG
41886 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:46581 original size:14 final size:14
Alignment explanation
Indices: 46562--46651 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
46552 TTGAAATGAA
46562 AATCGCAACGAGAG
1 AATCGCAACGAGAG
46576 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
46593 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
46609 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
46628 AATCGCAACGAGAG
1 AATCGCAACGAGAG
46642 AATCGCAACG
1 AATCGCAACG
46652 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:46599 original size:33 final size:33
Alignment explanation
Indices: 46554--46668 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
46544 TCTTTTGGTT
46554 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
46587 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
46620 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
46653 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
46669 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:46600 original size:19 final size:18
Alignment explanation
Indices: 46561--46673 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
46551 GTTGAAATGA
46561 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
46576 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
46593 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
46609 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
46626 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
46642 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
46659 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
46674 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:46704 original size:14 final size:14
Alignment explanation
Indices: 46685--46739 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
46675 TTTGGTTTCG
46685 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
46699 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
46718 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
46732 CGTTGCGA
1 CGTTGCGA
46740 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:46717 original size:33 final size:33
Alignment explanation
Indices: 46669--46739 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
46659 AAAATCGCAA
**
46669 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
46702 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
46735 TGCGA
1 TGCGA
46740 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:46747 original size:33 final size:33
Alignment explanation
Indices: 46680--46761 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
46670 GCGATTTTGG
***
46680 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
46713 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
46746 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
46762 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:46766 original size:20 final size:20
Alignment explanation
Indices: 46692--46780 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
46682 TCGCGTTGCG
46692 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
46712 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
46725 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
46745 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
46765 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
46781 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:46902 original size:33 final size:33
Alignment explanation
Indices: 46860--46930 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
46850 AATACTAACT
*
46860 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
46893 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
46926 TGAAA
1 TGAAA
46931 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:47162 original size:22 final size:22
Alignment explanation
Indices: 47110--47164 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
47100 TGGTTGTGAG
**
47110 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
47132 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
47154 GGATTTCTTCG
1 GGATTTCTTCG
47165 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:47335 original size:20 final size:20
Alignment explanation
Indices: 47310--47502 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
47300 CTTTAAATAT
47310 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
47330 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
47352 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
47371 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
47391 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
47411 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
47431 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
47451 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
47471 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
47491 CGCGTTGCGATT
1 CGCGTTGCGATT
47503 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:47497 original size:60 final size:60
Alignment explanation
Indices: 47310--47502 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
47300 CTTTAAATAT
**
47310 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
47371 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
47431 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
47491 CGCGTTGCGATT
1 CGCGTTGCGATT
47503 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:47583 original size:20 final size:20
Alignment explanation
Indices: 47558--47609 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
47548 AAGAATCGCG
*
47558 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
47578 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
47598 TTGCGATTCTGG
1 TTGCGATTCTGG
47610 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:56200 original size:19 final size:19
Alignment explanation
Indices: 56178--56215 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
56168 TATGTTAATG
56178 TTGCTTCTTTATTAGATCT
1 TTGCTTCTTTATTAGATCT
56197 TTGCTTCTTTATTAGATCT
1 TTGCTTCTTTATTAGATCT
56216 ATGCATCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.58
Consensus pattern (19 bp):
TTGCTTCTTTATTAGATCT
Found at i:60825 original size:26 final size:26
Alignment explanation
Indices: 60782--60831 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
60772 GATGAGTTAA
*
60782 AATTTTTTTATTTATTGAAATTGACG
1 AATTTTTTTATTAATTGAAATTGACG
*
60808 AATTTTTTTA-TAACTTGAACTTGA
1 AATTTTTTTATTAA-TTGAAATTGA
60832 GTTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (26 bp):
AATTTTTTTATTAATTGAAATTGACG
Found at i:63159 original size:30 final size:30
Alignment explanation
Indices: 63125--63195 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
63115 AAGTTATTTG
63125 TATAGGTGAGTTAGTGGGGGCAGATATATA
1 TATAGGTGAGTTAGTGGGGGCAGATATATA
63155 TATAGGTGAGTTAGTGGGGGCAGATATATA
1 TATAGGTGAGTTAGTGGGGGCAGATATATA
63185 TATAGGTGAGT
1 TATAGGTGAGT
63196 GGATGAGGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.03, G:0.37, T:0.31
Consensus pattern (30 bp):
TATAGGTGAGTTAGTGGGGGCAGATATATA
Found at i:72281 original size:17 final size:17
Alignment explanation
Indices: 72240--72281 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
72230 TGATAAAAAA
*
72240 TATTTAAAATATTATTT
1 TATTTAAAACATTATTT
*
72257 TATCTAAAACATTATTGT
1 TATTTAAAACATTATT-T
72275 T-TTTAAA
1 TATTTAAA
72282 TATTTTTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (17 bp):
TATTTAAAACATTATTT
Found at i:72547 original size:34 final size:34
Alignment explanation
Indices: 72479--72609 Score: 164
Period size: 32 Copynumber: 3.9 Consensus size: 34
72469 TTCGTCATAC
*
72479 TAGGATTCAAACTCCTAAAAATATG--AGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
*
72511 TAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
*
72545 TAGGATTCAAACT-CTTAAAATAGGATA-ACATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
72579 GCTAGGATTCAAACTCCT-AAAATAGGATAGA
1 --TAGGATTCAAACTCCTAAAAATAGGATAGA
72610 GTTCTACTAA
Statistics
Matches: 89, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
32 26 0.29
33 13 0.15
34 23 0.26
36 24 0.27
37 3 0.03
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:72592 original size:36 final size:33
Alignment explanation
Indices: 72479--72609 Score: 142
Period size: 36 Copynumber: 3.9 Consensus size: 33
72469 TTCGTCATAC
* *
72479 TAGGATTCAAACTCCTAAAA-A-TATGAGAATTT
1 TAGGATTCAAACTCTTAAAATAGGAT-AGAATTT
* *
72511 TAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TAGGATTCAAACT-CTTAAAATAGGATAGAATTT
72545 TAGGATTCAAACTCTTAAAATAGGATA-ACATTTT
1 TAGGATTCAAACTCTTAAAATAGGATAGA-A-TTT
*
72579 GCTAGGATTCAAACTCCTAAAATAGGATAGA
1 --TAGGATTCAAACTCTTAAAATAGGATAGA
72610 GTTCTACTAA
Statistics
Matches: 85, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
32 14 0.16
33 18 0.21
34 24 0.28
35 2 0.02
36 26 0.31
37 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.31
Consensus pattern (33 bp):
TAGGATTCAAACTCTTAAAATAGGATAGAATTT
Found at i:73345 original size:20 final size:21
Alignment explanation
Indices: 73320--73400 Score: 69
Period size: 23 Copynumber: 3.8 Consensus size: 21
73310 TTTTCTATGC
73320 TTTATTTATTT-ATTTATTAT
1 TTTATTTATTTAATTTATTAT
* *
73340 TTTATTTATTTTATTTTATTTCT
1 TTTATTTA-TTTAATTTA-TTAT
73363 TTTATTT-TGGTTGAATTTATTAT
1 TTTATTTAT--TT-AATTTATTAT
*
73386 TTT-TTTATTTCATTT
1 TTTATTTATTTAATTT
73401 TTTTTATATC
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
20 12 0.24
21 6 0.12
22 7 0.14
23 19 0.39
24 5 0.10
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTATTTATTTAATTTATTAT
Found at i:73346 original size:5 final size:5
Alignment explanation
Indices: 73336--73407 Score: 51
Period size: 5 Copynumber: 14.8 Consensus size: 5
73326 TATTTATTTA
* ** * *
73336 TTATT TTA-T TTATT TTATT TTA-T TTCTT TTATT TTGGT TGAAT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
* *
73384 ATTTTT TTATT TCATT TT-TT TTAT
1 -TTATT TTATT TTATT TTATT TTAT
73408 ATCTAACATG
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
4 11 0.22
5 35 0.70
6 4 0.08
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:76379 original size:18 final size:18
Alignment explanation
Indices: 76350--76452 Score: 61
Period size: 18 Copynumber: 5.6 Consensus size: 18
76340 AGATCCAATC
*
76350 AAGAAGAAAAAAGAAAAG
1 AAGAAAAAAAAAGAAAAG
*
76368 AAGCAAAAAAAAA-CAAAG
1 AAG-AAAAAAAAAGAAAAG
*
76386 AAAAAAGAAAAAAGAACAA-
1 AAGAAA-AAAAAAGAA-AAG
* *
76405 AAGGAAAAAAATGAAAA-
1 AAGAAAAAAAAAGAAAAG
*
76422 AATAAAATAAAAA-AGAAAG
1 AAGAAAA-AAAAAGA-AAAG
*
76441 AGGAACAAAAAA
1 AAGAA-AAAAAA
76453 CACATGCAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
17 11 0.17
18 30 0.46
19 20 0.31
20 4 0.06
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.03
Consensus pattern (18 bp):
AAGAAAAAAAAAGAAAAG
Found at i:76412 original size:14 final size:14
Alignment explanation
Indices: 76353--76428 Score: 73
Period size: 15 Copynumber: 5.0 Consensus size: 14
76343 TCCAATCAAG
76353 AAGAAAAAAGAAAA
1 AAGAAAAAAGAAAA
76367 GAAGCAAAAAA-AAACA
1 -AAG-AAAAAAGAAA-A
76383 AAGAAAAAAGAAAA
1 AAGAAAAAAGAAAA
76397 AAGAACAAAAGGAAAAA
1 AAGAA-AAAA-G-AAAA
*
76414 AATGAAAAAATAAAA
1 AA-GAAAAAAGAAAA
76429 TAAAAAAGAA
Statistics
Matches: 53, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
14 12 0.23
15 20 0.38
16 8 0.15
17 10 0.19
18 3 0.06
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.03
Consensus pattern (14 bp):
AAGAAAAAAGAAAA
Found at i:76421 original size:8 final size:7
Alignment explanation
Indices: 76353--76428 Score: 73
Period size: 7 Copynumber: 10.0 Consensus size: 7
76343 TCCAATCAAG
76353 AAGAAAA
1 AAGAAAA
76360 AAGAAAA
1 AAGAAAA
76367 GAAGCAAAA
1 -AAG-AAAA
76376 AA-AAACA
1 AAGAAA-A
76383 AAGAAAA
1 AAGAAAA
76390 AAGAAAA
1 AAGAAAA
76397 AAGAACAA
1 AAGAA-AA
76405 AAGGAAAAA
1 AA-G-AAAA
76414 AATGAAAA
1 AA-GAAAA
*
76422 AATAAAA
1 AAGAAAA
76429 TAAAAAAGAA
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
6 3 0.05
7 27 0.45
8 18 0.30
9 10 0.17
10 2 0.03
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.03
Consensus pattern (7 bp):
AAGAAAA
Done.