Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009213.1 Hibiscus syriacus cultivar Beakdansim tig00112800_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: 747713
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:776 original size:26 final size:27
Alignment explanation
Indices: 747--809 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
737 TTTTATCCCG
* *
747 TTTTTCATTTATTTCATT-TTATT-TTA
1 TTTTTAATTTATTTC-TTATCATTATTA
773 TTTTTAATTTATTTCTTATCATTATTA
1 TTTTTAATTTATTTCTTATCATTATTA
*
800 TTTTTGATTT
1 TTTTTAATTT
810 CCTTCTCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.06
26 18 0.56
27 12 0.38
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTTAATTTATTTCTTATCATTATTA
Found at i:2672 original size:18 final size:19
Alignment explanation
Indices: 2639--2682 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
2629 ATTTAGACAT
2639 TTTGCA-TTTCTTA-TTTC
1 TTTGCATTTTCTTATTTTC
*
2656 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
2675 TTTGCATT
1 TTTGCATT
2683 CACATTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.25
18 6 0.25
19 12 0.50
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:5996 original size:84 final size:85
Alignment explanation
Indices: 5885--6423 Score: 618
Period size: 84 Copynumber: 6.5 Consensus size: 85
5875 AGCTTTGAGG
*
5885 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
*
5950 GCTCAGCTCCAA-GGCATAT
66 GCTCAGCTCCAACGGCACAT
* * * *
5969 CATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACACAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
6034 GCTCAGCTCCAA-GGCACAT
66 GCTCAGCTCCAACGGCACAT
* * * * *
6053 CATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCTT-AAGTTCGATTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGA-CCTTCGAGTTCGACTA
* * * *
6113 CACTCAGCTTCAAGGGCATA-
65 CGCTCAGCTCCAACGGCACAT
* * * * * ** * * * *
6133 CATTTACAGCATAACTCAAGGCTAGAAGGGTTAGCTGTGATCAAAATACCTTTGAGTTCGACTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
6198 GCTCAGCT-CAACGGCACAT
66 GCTCAGCTCCAACGGCACAT
* ** * * *
6217 CATTTCCAGTGTAGCTTAAGTCGAGAAGGGCTA--TGCCAACAAAAGACCTTCGAGTTCGACTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
*
6280 GCTCAGCTCCAA-GGCATAT
66 GCTCAGCTCCAACGGCACAT
* * * * *
6299 CATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
6364 GCTCAGCT-CAACGGCACAT
66 GCTCAGCTCCAACGGCACAT
* *
6383 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
6424 AGACCCCTGG
Statistics
Matches: 379, Mismatches: 64, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
80 53 0.14
81 10 0.03
82 65 0.17
83 20 0.05
84 231 0.61
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (85 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAACGGCACAT
Found at i:6192 original size:164 final size:164
Alignment explanation
Indices: 5885--6491 Score: 693
Period size: 164 Copynumber: 3.7 Consensus size: 164
5875 AGCTTTGAGG
* * *
5885 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAT
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCTTCGAGTTCGACTAC
* * * * *
5950 GCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACACAA
62 ACTCAGCTCCAAGGCATATCATTTACAGCACAACTCAAGGCTAGAAGGGTTGTCTGCCAACAAAA
*
6015 GACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACAT
127 GACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACAT
* * *
6053 CATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTT-AAGTTCGATTACACT
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCTTCGAGTTCGACTACACT
* * ** * *
6117 CAGCTTCAAGGGCATA-CATTTACAGCATAACTCAAGGCTAGAAGGGTTAG-CTGTGATCAAAAT
65 CAGCTCCAA-GGCATATCATTTACAGCACAACTCAAGGCTAGAAGGGTT-GTCTGCCAACAAAAG
*
6180 ACCTTTGAGTTCGACTATGCTCAGCTCAACGGCACAT
128 ACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACAT
* ** ** * **
6217 CATTTCCAGTGTAGCTTAAGTCGAGAAGGGCTATGCCAACAAAAGACCTTCGAGTTCGACTATGC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT--CTGCCAAAGACCTTCGAGTTCGACTACAC
* * * *
6282 TCAGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGA
64 TCAGCTCCAAGGCATATCATTTACAGCACAACTCAAGGCTAGAAGGGTTGTCTGCCAACAAAAGA
6347 CCTTTGAGTTCGACTACGCTCAGCTCAACGGCACAT
129 CCTTTGAGTTCGACTACGCTCAGCTCAACGGCACAT
* * *
6383 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC-CCTGGGTTCGATTACACT
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTC-GAGTTCGACTACACT
* * ** * * * *
6447 CAACTTCGGGGTCATATCATTTACAACATAGCTCAAGGCAAGAAG
65 CAGCTCCAAGG-CATATCATTTACAGCACAACTCAAGGCTAGAAG
6492 AGCTATTTGT
Statistics
Matches: 365, Mismatches: 63, Indels: 25
0.81 0.14 0.06
Matches are distributed among these distances:
163 4 0.01
164 149 0.41
165 48 0.13
166 129 0.35
167 1 0.00
168 34 0.09
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (164 bp):
CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTC
AGCTCCAAGGCATATCATTTACAGCACAACTCAAGGCTAGAAGGGTTGTCTGCCAACAAAAGACC
TTTGAGTTCGACTACGCTCAGCTCAACGGCACAT
Found at i:6360 original size:166 final size:166
Alignment explanation
Indices: 5885--6416 Score: 725
Period size: 166 Copynumber: 3.2 Consensus size: 166
5875 AGCTTTGAGG
* * *
5885 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAT
1 CATTTGCAGAATAGCTTAAGTCGAGAAGGGCTA--TGCCAACAAAAGACCTTCGAGTTCGACTAT
*
5950 GCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACACAA
64 GCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAA
*
6015 GACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACAT
129 GACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACAT
** * * * **
6053 CATTTGCAGAATAGCTTAAGTCGAGAAGGGCTAT--CTGCCAAAGACCCTT-AAGTTCGATTACA
1 CATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATGCCAACAAAAGA-CCTTCGAGTTCGACTATG
* * * * * ** *
6115 CTCAGCTTCAAGGGCATA-CATTTACAGCATAACTCAAGGCTAGAAGGGTTAG-CTGTGATCAAA
65 CTCAGCTCCAA-GGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTT-GTCTGCCAACAAA
* *
6178 ATACCTTTGAGTTCGACTATGCTCAGCTCAACGGCACAT
128 AGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACAT
* **
6217 CATTTCCAGTGTAGCTTAAGTCGAGAAGGGCTATGCCAACAAAAGACCTTCGAGTTCGACTATGC
1 CATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATGCCAACAAAAGACCTTCGAGTTCGACTATGC
*
6282 TCAGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGA
66 TCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGA
6347 CCTTTGAGTTCGACTACGCTCAGCTCAACGGCACAT
131 CCTTTGAGTTCGACTACGCTCAGCTCAACGGCACAT
*
6383 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
1 CATTTGCAGAATAGCTTAAGTCGAGAAGGGCTAT
6417 CTGCCAAAGA
Statistics
Matches: 309, Mismatches: 46, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
163 3 0.01
164 124 0.40
165 22 0.07
166 130 0.42
168 30 0.10
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (166 bp):
CATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATGCCAACAAAAGACCTTCGAGTTCGACTATGC
TCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGA
CCTTTGAGTTCGACTACGCTCAGCTCAACGGCACAT
Found at i:7183 original size:36 final size:37
Alignment explanation
Indices: 7086--7265 Score: 151
Period size: 36 Copynumber: 4.9 Consensus size: 37
7076 TTGCAAATTG
7086 TTTTTGAAAATACATATATAATATATAG--TTTAAAACA
1 TTTTTGAAAAT--ATATATAATATATAGTTTTTAAAACA
* * * *
7123 TTTTTTGAAAATATGTATATTATATAGTTTTTCAAATA
1 -TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
* *
7161 TTTTTGAAAAT-TATATAATATATAGTTTTGAAAACG
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
* *
7197 TTTTT--AAA-ATATAT-ATATATACTTTTGAAAAC-
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
* * * *
7229 GTTATGAAAACATTTATATAATATATAATTTTTAAAA
1 TTTTTG-AAA-ATATATATAATATATAGTTTTTAAAA
7266 AAAACCATTT
Statistics
Matches: 117, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
32 3 0.03
33 17 0.15
34 8 0.07
35 2 0.02
36 38 0.32
37 16 0.14
38 33 0.28
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:7293 original size:127 final size:126
Alignment explanation
Indices: 7161--7412 Score: 454
Period size: 129 Copynumber: 2.0 Consensus size: 126
7151 TTTTCAAATA
7161 TTTTTGAAAATTATATAATATATAG-TTTTGAAAACGTTTTTAAAATATAT-ATATATACTTTTG
1 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATAATATATACTTTTG
7224 AAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAAAAACCATTTTGAAAATATATT
66 AAAACGTTATGAAAACATTTATATAATATATAATTTTT---AAAAACCATTTTGAAAATATATT
7288 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATAATATATACTTTTG
1 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATAATATATACTTTTG
*
7353 AAAATGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
66 AAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
7413 ATAATATATA
Statistics
Matches: 122, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
126 22 0.18
127 25 0.20
128 25 0.20
129 50 0.41
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (126 bp):
TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATAATATATACTTTTG
AAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATATT
Found at i:7336 original size:26 final size:25
Alignment explanation
Indices: 7272--7338 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
7262 AAAAAAAACC
* *
7272 ATTTTGAAAATATATTTTTTTGAAA
1 ATTTTTAAAATATATGTTTTTGAAA
* *
7297 A-TTATATAATATATAGTTTTTGAAA
1 ATTTTTAAAATATAT-GTTTTTGAAA
7322 ACGTTTTTAAAATATAT
1 A--TTTTTAAAATATAT
7339 AATATATACT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
24 10 0.31
25 11 0.34
28 11 0.34
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (25 bp):
ATTTTTAAAATATATGTTTTTGAAA
Found at i:7414 original size:38 final size:37
Alignment explanation
Indices: 7289--7470 Score: 167
Period size: 38 Copynumber: 5.0 Consensus size: 37
7279 AAATATATTT
* *
7289 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAATTTTTGAAAACA
* * **
7325 TTTT-TAAA-ATATATAATATAT-ACTTTTGAAAATG
1 TTTTGAAAATATATATAATATATAATTTTTGAAAACA
* * *
7359 TTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTG-AAA-ATATATATAATATATAATTTTTGAAAA-CA
* *
7399 TTTTGAAAATATATATAATATATAGTTTTTTAAAACA
1 TTTTGAAAATATATATAATATATAATTTTTGAAAACA
* * * *
7436 TTTTAAAAATTTATATATTATAT-GTTTTTGAAAAC
1 TTTTGAAAATATATATAATATATAATTTTTGAAAAC
7471 GTTTATATAT
Statistics
Matches: 120, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
34 13 0.11
35 15 0.12
36 17 0.14
37 23 0.19
38 36 0.30
39 12 0.10
40 4 0.03
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAATTTTTGAAAACA
Found at i:7526 original size:18 final size:17
Alignment explanation
Indices: 7494--7545 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
7484 ATATTATTAC
7494 TATTTATTT-TTATTTT
1 TATTTATTTATTATTTT
7510 TAATTTA-TTACTTATTTT
1 T-ATTTATTTA-TTATTTT
7528 TATTTATTTATTATTTT
1 TATTTATTTATTATTTT
7545 T
1 T
7546 TTTCTTTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.09
17 18 0.56
18 11 0.34
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (17 bp):
TATTTATTTATTATTTT
Found at i:7526 original size:28 final size:28
Alignment explanation
Indices: 7482--7536 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
7472 TTTATATATA
7482 TAATATTATTACTATTTATT-TTTATTTT
1 TAATATTATTACTATTT-TTATTTATTTT
7510 TAAT-TTATTACTTATTTTTATTTATTT
1 TAATATTATTAC-TATTTTTATTTATTT
7537 ATTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (28 bp):
TAATATTATTACTATTTTTATTTATTTT
Found at i:7541 original size:11 final size:11
Alignment explanation
Indices: 7502--7543 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
7492 ACTATTTATT
7502 TTTATT-TTTAA
1 TTTATTATTT-A
*
7513 TTTATTACTTA
1 TTTATTATTTA
7524 TTT-TTATTTA
1 TTTATTATTTA
7534 TTTATTATTT
1 TTTATTATTT
7544 TTTTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
11 16 0.59
12 2 0.07
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:7541 original size:24 final size:23
Alignment explanation
Indices: 7487--7542 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
7477 ATATATAATA
* *
7487 TTATTACTATTTATTTTTATTTT
1 TTATTATTACTTATTTTTATTTT
*
7510 TAATTTATTACTTATTTTTATTTAT
1 TTA-TTATTACTTATTTTTATTT-T
7535 TTATTATT
1 TTATTATT
7543 TTTTTTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.07
24 22 0.81
25 3 0.11
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (23 bp):
TTATTATTACTTATTTTTATTTT
Found at i:8768 original size:5 final size:5
Alignment explanation
Indices: 8750--8788 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
8740 TTATCCCGTT
* *
8750 TTTTCA TTTTA TTTCA TTTTA TTTTA TTTTA ATTTA TTT
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
8789 CTATCATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:8775 original size:15 final size:15
Alignment explanation
Indices: 8750--8810 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
8740 TTATCCCGTT
8750 TTTTCATTTTATTTCA
1 TTTT-ATTTTATTTCA
*
8766 TTTTATTTTATTTTA
1 TTTTATTTTATTTCA
*
8781 ATTTATTTCTA--TCA
1 TTTTATTT-TATTTCA
8795 TTATTATTTTGATTTC
1 TT-TTATTTT-ATTTC
8811 CTTCTCTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 4 0.11
15 24 0.67
16 6 0.17
17 2 0.06
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTTATTTTATTTCA
Found at i:8976 original size:15 final size:16
Alignment explanation
Indices: 8956--8985 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8946 AATTATCATT
8956 TTTTTTTG-ATATTTC
1 TTTTTTTGAATATTTC
8971 TTTTTTTGAATATTT
1 TTTTTTTGAATATTT
8986 TTAGTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTTTTTGAATATTTC
Found at i:11648 original size:19 final size:18
Alignment explanation
Indices: 11624--11659 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11614 TCTCTTGTTT
11624 GGAACAAAAATTTCTTAAG
1 GGAACAAAAATTT-TTAAG
*
11643 GGAACAAACATTTTTAA
1 GGAACAAAAATTTTTAA
11660 AATTTTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (18 bp):
GGAACAAAAATTTTTAAG
Found at i:19932 original size:24 final size:23
Alignment explanation
Indices: 19875--19932 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
19865 GAAAATATTA
19875 AAAATAATAATA-ACAAAAAATG
1 AAAATAATAATACACAAAAAATG
*
19897 AAAATTA-AATACATCCAAAAAA-G
1 AAAATAATAATACA--CAAAAAATG
19920 AAAATAATAATAC
1 AAAATAATAATAC
19933 TTATAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 4 0.13
22 7 0.23
23 7 0.23
24 12 0.40
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.19
Consensus pattern (23 bp):
AAAATAATAATACACAAAAAATG
Found at i:20005 original size:10 final size:8
Alignment explanation
Indices: 19979--20028 Score: 57
Period size: 8 Copynumber: 6.0 Consensus size: 8
19969 ATAATATTGT
19979 AAATAAAA
1 AAATAAAA
19987 AAATAAAA
1 AAATAAAA
19995 AGAAGTAAAA
1 A-AA-TAAAA
*
20005 AAA-AATA
1 AAATAAAA
20012 AAATAAAA
1 AAATAAAA
20020 ATAATAAAA
1 A-AATAAAA
20029 TAACTAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
7 6 0.17
8 13 0.36
9 11 0.31
10 6 0.17
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.14
Consensus pattern (8 bp):
AAATAAAA
Found at i:20019 original size:11 final size:10
Alignment explanation
Indices: 19983--20028 Score: 56
Period size: 10 Copynumber: 4.4 Consensus size: 10
19973 TATTGTAAAT
19983 AAAAAAATAA
1 AAAAAAATAA
* *
19993 AAAGAAGTAA
1 AAAAAAATAA
20003 AAAAAAATAA
1 AAAAAAATAA
20013 AATAAAAATAA
1 AA-AAAAATAA
20024 TAAAA
1 -AAAA
20029 TAACTAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 18 0.60
11 10 0.33
12 2 0.07
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.13
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:20019 original size:14 final size:14
Alignment explanation
Indices: 20002--20031 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19992 AAAAGAAGTA
20002 AAAAAAAATAAAAT
1 AAAAAAAATAAAAT
*
20016 AAAAATAATAAAAT
1 AAAAAAAATAAAAT
20030 AA
1 AA
20032 CTAAATAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAAAATAAAAT
Found at i:20178 original size:4 final size:4
Alignment explanation
Indices: 20165--20204 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
20155 TATATATAGG
*
20165 TAAA TGAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
20205 AGGGACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:21412 original size:37 final size:38
Alignment explanation
Indices: 21366--21622 Score: 121
Period size: 37 Copynumber: 6.5 Consensus size: 38
21356 AATATTTTCA
21366 AAAAC-ATATAATATATAAATTTTC-AAAATGTTTTTT
1 AAAACTATATAATATATAAATTTTCAAAAATGTTTTTT
* * * * *
21402 TAAACTATATAATATACGAATGTTTTC-AACATG-TTTTC
1 AAAACTATATAATATA-TAA-ATTTTCAAAAATGTTTTTT
** * * * * *
21440 AAAAAAAAATATTATATAAGTTTTCAAAAACG-TTTTA
1 AAAACTATATAATATATAAATTTTCAAAAATGTTTTTT
*
21477 AAAACTATATAATATATAAATGTTTTCAAAACTATAATATATATGTTTT
1 AAAACTATATAATATATAAA--TTTTC---A--A-AA-ATGT-T-TTTT
* * *
21526 CAAAAACTATATATATATATAAGTTTTC-AAAATGATTTTA
1 --AAAACTATATA-ATATATAAATTTTCAAAAATGTTTTTT
* * * *
21566 AAAATTATATATTATATATATTTTCTAAAATGTTTTTTT
1 AAAACTATATAATATATAAATTTTCAAAAATG-TTTTTT
* *
21605 TAAACTATATATTATATA
1 AAAACTATATAATATATA
21623 GTTTTAAAAA
Statistics
Matches: 166, Mismatches: 34, Indels: 39
0.69 0.14 0.16
Matches are distributed among these distances:
36 10 0.06
37 46 0.28
38 33 0.20
39 35 0.21
40 3 0.02
41 1 0.01
42 3 0.02
43 2 0.01
44 2 0.01
45 2 0.01
46 1 0.01
48 1 0.01
49 3 0.02
50 5 0.03
51 11 0.07
52 8 0.05
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (38 bp):
AAAACTATATAATATATAAATTTTCAAAAATGTTTTTT
Found at i:21464 original size:75 final size:75
Alignment explanation
Indices: 21360--21505 Score: 195
Period size: 75 Copynumber: 1.9 Consensus size: 75
21350 TACATAAATA
* * * ** *
21360 TTTTCAAAAACATATAATATATAAATTTTC-AAAATGTTTTTTTAAACTATATAATATACGAATG
1 TTTTCAAAAAAAAATAATATATAAATTTTCAAAAACG-TTTTAAAAACTATATAATATACAAATG
21424 TTTTCAACATG
65 TTTTCAACATG
* * *
21435 TTTTCAAAAAAAAATATTATATAAGTTTTCAAAAACGTTTTAAAAACTATATAATATATAAATGT
1 TTTTCAAAAAAAAATAATATATAAATTTTCAAAAACGTTTTAAAAACTATATAATATACAAATGT
21500 TTTCAA
66 TTTCAA
21506 AACTATAATA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 56 0.92
76 5 0.08
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (75 bp):
TTTTCAAAAAAAAATAATATATAAATTTTCAAAAACGTTTTAAAAACTATATAATATACAAATGT
TTTCAACATG
Found at i:21507 original size:27 final size:27
Alignment explanation
Indices: 21471--21557 Score: 105
Period size: 25 Copynumber: 3.4 Consensus size: 27
21461 TTTCAAAAAC
*
21471 GTTTTAAAAACTATATAATATATAAAT
1 GTTTTCAAAACTATATAATATATAAAT
21498 GTTTTCAAAAC--TATAATATAT--AT
1 GTTTTCAAAACTATATAATATATAAAT
21521 GTTTTCAAAAACTATAT-ATATATATAA-
1 GTTTTC-AAAACTATATAATATATA-AAT
21548 GTTTTCAAAA
1 GTTTTCAAAA
21558 TGATTTTAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
23 8 0.15
24 5 0.09
25 16 0.30
26 7 0.13
27 16 0.30
28 1 0.02
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (27 bp):
GTTTTCAAAACTATATAATATATAAAT
Found at i:21539 original size:21 final size:21
Alignment explanation
Indices: 21488--21543 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 21
21478 AAACTATATA
*
21488 ATATATAAATGTTTTCAAAAC
1 ATATATATATGTTTTCAAAAC
21509 TATAATATATATGTTTTCAAAAAC
1 -AT-ATATATATGTTTTC-AAAAC
21533 TATATATATAT
1 -ATATATATAT
21544 ATAAGTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 2 0.06
23 21 0.68
24 8 0.26
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (21 bp):
ATATATATATGTTTTCAAAAC
Found at i:21569 original size:125 final size:127
Alignment explanation
Indices: 21403--21674 Score: 285
Period size: 126 Copynumber: 2.1 Consensus size: 127
21393 ATGTTTTTTT
* *
21403 AAACTATATA-ATATACGAATGTTTTCAACATGTTTTCAAAAA-AAAATATTATATA-AGTTTTC
1 AAACTATATATATATA-TAATGTTTTCAAAATGTTTTCAAAAATAAAATATTATATATA-TTTTC
* *
21465 AAAAACG-TTTTAAAAACTATATAATATATAAATGTTTTCAAAACTATA-A-TATATATGT-TTT
64 AAAAACGTTTTTAAAAACTATAT-AT-TATAAA-GTTTTAAAAACTATATATTATATACGTATTT
21526 CAA
126 C-A
* * *
21529 AAACTATATATATATATAA-GTTTTCAAAATGATTTT-AAAAATTATATATTATATATATTTTCT
1 AAACTATATATATATATAATGTTTTCAAAATG-TTTTCAAAAATAAAATATTATATATATTTTCA
* ** *
21592 AAAATGTTTTTTTTAAACTATATATTATATAGTTTTAAAAACTATATATTATATACGTAGTTTCA
65 AAAACG-TTTTTAAAAACTATATATTATAAAGTTTTAAAAACTATATATTATATACGTA-TTTCA
*
21657 AAA-TATGTATATATATAA
1 AAACTATATATATATATAA
21675 ATATGTAGGT
Statistics
Matches: 124, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
125 30 0.24
126 43 0.35
127 30 0.24
128 17 0.14
129 4 0.03
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (127 bp):
AAACTATATATATATATAATGTTTTCAAAATGTTTTCAAAAATAAAATATTATATATATTTTCAA
AAACGTTTTTAAAAACTATATATTATAAAGTTTTAAAAACTATATATTATATACGTATTTCA
Found at i:21614 original size:39 final size:39
Alignment explanation
Indices: 21522--21622 Score: 118
Period size: 39 Copynumber: 2.6 Consensus size: 39
21512 AATATATATG
21522 TTTTCAAAAACTATATA-TATATATAAGTTTTCAAAATGA
1 TTTT-AAAAACTATATATTATATATAAGTTTTCAAAATGA
* *
21561 TTTTAAAAATTATATATTATATAT-A-TTTTCTAAAATGTT
1 TTTTAAAAACTATATATTATATATAAGTTTTC-AAAATG-A
**
21600 TTTTTTAAACTATATATTATATA
1 TTTTAAAAACTATATATTATATA
21623 GTTTTAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
37 5 0.09
38 18 0.33
39 31 0.57
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.50
Consensus pattern (39 bp):
TTTTAAAAACTATATATTATATATAAGTTTTCAAAATGA
Found at i:21630 original size:22 final size:23
Alignment explanation
Indices: 21601--21646 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
21591 TAAAATGTTT
*
21601 TTTTTAAACTATATATTATATAG
1 TTTTAAAACTATATATTATATAG
21624 TTTTAAAAACTATATATTATATA
1 TTTT-AAAACTATATATTATATA
21647 CGTAGTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTTAAAACTATATATTATATAG
Found at i:22606 original size:84 final size:84
Alignment explanation
Indices: 22291--23169 Score: 887
Period size: 84 Copynumber: 10.6 Consensus size: 84
22281 GTTTGCCTCT
* * * * *
22291 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTAT
* *
22355 GCTGCAAATGATGTGCCCTCG
65 GCTGCAAATGATATG-CCTTG
* * * * *
22376 AAGCTGAGCGTAATCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
*
22441 CTGCAAATGATATGTCCTCG
66 CTGCAAATGATATG-CCTTG
* * * * * * * * *
22461 AAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTATCGATTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
*
22522 CTGTAAATGATATGCCTTG
66 CTGCAAATGATATGCCTTG
* *
22541 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
*
22606 CTGCAAATGATGTGCCGTT-
66 CTGCAAATGATATGCC-TTG
* * ** * *
22625 GAGCTGAGCGTACTCGAACTCGAAGGTCTTTGGGTGATAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* *
22690 CTGTAAATGATGTGCCTTG
66 CTGCAAATGATATGCCTTG
* * * *
22709 GAACTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGACAACCTTTCTAGACTTAAGTTGTG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
22774 CTGCAAATGATATGCCTTG
66 CTGCAAATGATATGCCTTG
* * * *
22793 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGATTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* * *
22857 CTGTAAACGATATGCCCTCG
66 CTGCAAATGATATG-CCTTG
* * * * * * * *
22877 AAGCTGAACGTAGTCGAACTCGAGGGTC--T--TTGGCAGATAGCCTTTCTCGACTTAAGCTATT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
*
22938 CTGCAAATGATGTGCCTTG
66 CTGCAAATGATATGCCTTG
* * ** * * *
22957 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-GCTAACAGATAACACTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* *
23021 CTGTAAATGTTATGCCCTTG
66 CTGCAAATGATATG-CCTTG
* * * * * * * *
23041 AAGCTTAGTGTAATCGAACT-TAAGGGTC--T--TTGGCAGATAGCTCTTCTAGACTTAAGCTAT
1 GAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTAT
* *
23101 ACTGCAAATGATGTGCCTTG
65 GCTGCAAATGATATGCCTTG
* *
23121 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGG-TGGCAGGTAGCCCTTCT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
23170 GGCCTTGAGC
Statistics
Matches: 652, Mismatches: 124, Indels: 39
0.80 0.15 0.05
Matches are distributed among these distances:
80 80 0.12
81 108 0.17
82 19 0.03
83 73 0.11
84 276 0.42
85 96 0.15
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (84 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
CTGCAAATGATATGCCTTG
Found at i:22746 original size:168 final size:168
Alignment explanation
Indices: 22291--23178 Score: 1070
Period size: 164 Copynumber: 5.4 Consensus size: 168
22281 GTTTGCCTCT
* *
22291 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * * *
22356 CTGCAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCAAAGGTCTTTGGTTGGCAGACAAC
65 CTGTAAATGATATGCCTTCGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAAC
* * *
22421 CCTTCTAGACTTAAGTTGTGCTGCAAATGATATGTCCTCG
130 CCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG
* * * * * * * ** * *
22461 AAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G-G-CAGATAGCCCTTATCGATTTAAGCTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
*
22523 TGTAAATGATATGCCTT-GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACC
66 TGTAAATGATATGCCTTCGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACC
*
22587 CTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCGTT-
131 CTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTG
* *
22625 GAGCTGAGCGTACTCGAACTCGAAGGTCTTTGGGTGATAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * *
22690 CTGTAAATGATGTGCCTTGGAA-CTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGACAAC
65 CTGTAAATGATATGCCTTCGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAAC
* * *
22754 CTTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTG
130 CCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTG
*
22793 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGATTTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
* * * * * *
22858 TGTAAACGATATGCCCTCGAAGCTGAACGTAGTCGAACTCGAGGGTC--T--TTGGCAGATAGCC
66 TGTAAATGATATGCCTTCGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACC
* * * *
22919 TTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTG
131 CTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTG
* * * *
22957 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACACTTCTAGCCTTGAGTTATGC
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
* * * * * * *
23022 TGTAAATGTTATGCCCTT-GAAGCTTAGTGTAATCGAACTTAAGGGTC--T--TTGGCAGATAGC
66 TGTAAATGATATG-CCTTCGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAAC
* * *
23082 TCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTTG
130 CCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTG
* * * *
23121 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGGTGGCAGGTAGCCCTTCTGGCCTTGAG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
23179 CTAAGCTGCA
Statistics
Matches: 628, Mismatches: 81, Indels: 25
0.86 0.11 0.03
Matches are distributed among these distances:
163 23 0.04
164 242 0.39
165 78 0.12
166 38 0.06
167 53 0.08
168 163 0.26
169 5 0.01
170 26 0.04
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (168 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
TGTAAATGATATGCCTTCGAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACC
CTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTG
Found at i:26644 original size:19 final size:19
Alignment explanation
Indices: 26620--26667 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
26610 AGTTAATGTG
* *
26620 AATGCAAAGAAAATAACCA
1 AATGCAAAAAAAATAACAA
26639 AATGCAAAAAAAATAACAA
1 AATGCAAAAAAAATAACAA
26658 AATGCAAAAA
1 AATGCAAAAA
26668 GTCTAAATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.69, C:0.12, G:0.08, T:0.10
Consensus pattern (19 bp):
AATGCAAAAAAAATAACAA
Found at i:28493 original size:24 final size:23
Alignment explanation
Indices: 28436--28493 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
28426 GAAAATATTA
28436 AAAATAATAATA-ACAAAAAATG
1 AAAATAATAATACACAAAAAATG
*
28458 AAAATTA-AATACATCCAAAAAA-G
1 AAAATAATAATACA--CAAAAAATG
28481 AAAATAATAATAC
1 AAAATAATAATAC
28494 TAATAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 4 0.13
22 7 0.23
23 7 0.23
24 12 0.40
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.19
Consensus pattern (23 bp):
AAAATAATAATACACAAAAAATG
Found at i:28734 original size:4 final size:4
Alignment explanation
Indices: 28721--28760 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
28711 TATATATAGG
* * *
28721 TAAA TGAA TAAA TAAT TAAA TAAA TAAT TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
28761 AGGGACCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (4 bp):
TAAA
Found at i:28744 original size:12 final size:12
Alignment explanation
Indices: 28727--28759 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
28717 TAGGTAAATG
28727 AATAAATAATTA
1 AATAAATAATTA
28739 AATAAATAATTA
1 AATAAATAATTA
28751 AATAAATAA
1 AATAAATAA
28760 AAGGGACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AATAAATAATTA
Found at i:29948 original size:37 final size:36
Alignment explanation
Indices: 29906--30155 Score: 229
Period size: 37 Copynumber: 6.8 Consensus size: 36
29896 TTTCAAAAAC
**
29906 ATAATATATAAATTTTCAAAATGTTTTTTTAAACTAT
1 ATAATATATAAATTTTCAAAATG-TTTTAAAAACTAT
* * * *
29943 ATAATATACAAATGTTTTCAACATGTTTTCAAAAA-AAA
1 ATAATATATAAA--TTTTCAAAATGTTTT-AAAAACTAT
* * *
29981 ATATTATATAAGTTTTCAAAAACGTTTTAAAAACTAT
1 ATAATATATAAATTTTC-AAAATGTTTTAAAAACTAT
*
30018 ATAATATATAAATGTTTTCAAAATGTTTTCAAAAC--T
1 ATAATATATAAA--TTTTCAAAATGTTTTAAAAACTAT
**
30054 ATAATATATATGTTTTCAAAAATGTTTTCAAAAACTAT
1 ATAATATATAAATTTTC-AAAATGTTTT-AAAAACTAT
* *
30092 AT-ATATATAAGTTTTCAAAATGATTTTAAAAATTAT
1 ATAATATATAAATTTTCAAAATG-TTTTAAAAACTAT
* *
30128 ATATTATATATATTTTCTAAAATGTTTT
1 ATAATATATAAATTTTC-AAAATGTTTT
30156 TTTTAAACTA
Statistics
Matches: 174, Mismatches: 25, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
34 5 0.03
35 10 0.06
36 42 0.24
37 62 0.36
38 37 0.21
39 18 0.10
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (36 bp):
ATAATATATAAATTTTCAAAATGTTTTAAAAACTAT
Found at i:29990 original size:75 final size:75
Alignment explanation
Indices: 29900--30174 Score: 269
Period size: 75 Copynumber: 3.7 Consensus size: 75
29890 AAATATTTTC
* * **
29900 AAAAACATAATATATAAATTTTC-AAAATGTTTTTTTAAACTATATAATATACAAATGTTTTCAA
1 AAAAAAATATTATATAAATTTTCAAAAATGTTTTTAAAAACTATATAATATA-AAATGTTTTCAA
*
29964 CATGTTTTCAA
65 AATGTTTTCAA
* *
29975 AAAAAAATATTATATAAGTTTTCAAAAACG-TTTTAAAAACTATATAATATATAAATGTTTTCAA
1 AAAAAAATATTATATAAATTTTCAAAAATGTTTTTAAAAACTATATAATATA-AAATGTTTTCAA
30039 AATGTTTTCAA
65 AATGTTTTCAA
* * * * *
30050 AACTATAATA-TATAT--GTTTTCAAAAATGTTTTCAAAAACTATAT-ATATATAA-GTTTTCAA
1 AA-AAAAATATTATATAAATTTTCAAAAATGTTTTTAAAAACTATATAATATAAAATGTTTTCAA
30110 AATGATTTT-AA
65 AATG-TTTTCAA
* * * * ** *
30121 AAATTATATATTATATATATTTTCTAAAATGTTTTTTTTAAACTATATATTATA
1 AAA-AAAATATTATATAAATTTTCAAAAATG-TTTTTAAAAACTATATAATATA
30175 TAGTTTTAAA
Statistics
Matches: 167, Mismatches: 23, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
71 19 0.11
72 11 0.07
73 17 0.10
74 25 0.15
75 81 0.49
76 14 0.08
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (75 bp):
AAAAAAATATTATATAAATTTTCAAAAATGTTTTTAAAAACTATATAATATAAAATGTTTTCAAA
ATGTTTTCAA
Found at i:30043 original size:11 final size:11
Alignment explanation
Indices: 30027--30051 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30017 TATAATATAT
30027 AAATGTTTTCA
1 AAATGTTTTCA
30038 AAATGTTTTCA
1 AAATGTTTTCA
30049 AAA
1 AAA
30052 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:30080 original size:12 final size:12
Alignment explanation
Indices: 30063--30087 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30053 TATAATATAT
30063 ATGTTTTCAAAA
1 ATGTTTTCAAAA
30075 ATGTTTTCAAAA
1 ATGTTTTCAAAA
30087 A
1 A
30088 CTATATATAT
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:30168 original size:37 final size:35
Alignment explanation
Indices: 29890--30185 Score: 142
Period size: 38 Copynumber: 8.1 Consensus size: 35
29880 ATATATACAT
* * *
29890 AAATATTTTCAAAAAC-ATAATATATAAATTTTC-A
1 AAATGTTTTTAAAAACTAT-ATATATATATTTTCTA
** *
29924 AAATGTTTTTTTAAACTATATAATATACAAATGTTT-TCA
1 AAATGTTTTTAAAAACTATAT-ATAT--ATAT-TTTCT-A
* * * * *
29963 ACATGTTTTCAAAAA-AAAATATTATATAAGTTTTCAA
1 AAATGTTTTTAAAAACTATATA-TATAT-A-TTTTCTA
*
30000 AAACG-TTTTAAAAACTATATAATATATAAATGTTT-TCA
1 AAATGTTTTTAAAAACTATAT-ATATAT--AT-TTTCT-A
* * *
30038 AAATG-TTTTCAAAACTATAATATATATGTTTTCAA
1 AAATGTTTTTAAAAACTAT-ATATATATATTTTCTA
*
30073 AAATGTTTTCAAAAACTATATATATATAAGTTTTC-A
1 AAATGTTTTTAAAAACTATATATATAT-A-TTTTCTA
* *
30109 AAATGATTTTAAAAATTATATATTATATATATTTTCTA
1 AAATGTTTTTAAAAA--CTATA-TATATATATTTTCTA
** *
30147 AAATGTTTTTTTTAAACTATATATTATATAGTTT-TA
1 AAATG-TTTTTAAAAACTATATA-TATATATTTTCTA
30183 AAA
1 AAA
30186 ACTATATATT
Statistics
Matches: 202, Mismatches: 33, Indels: 52
0.70 0.11 0.18
Matches are distributed among these distances:
34 14 0.07
35 23 0.11
36 42 0.21
37 45 0.22
38 50 0.25
39 28 0.14
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (35 bp):
AAATGTTTTTAAAAACTATATATATATATTTTCTA
Found at i:30184 original size:22 final size:23
Alignment explanation
Indices: 30155--30200 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
30145 TAAAATGTTT
*
30155 TTTTTAAACTATATATTATATAG
1 TTTTAAAACTATATATTATATAG
30178 TTTTAAAAACTATATATTATATA
1 TTTT-AAAACTATATATTATATA
30201 CGTAGTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTTAAAACTATATATTATATAG
Found at i:41275 original size:2 final size:2
Alignment explanation
Indices: 41268--41302 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
41258 ATAAAAATGG
41268 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41303 CCCATACTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42032 original size:25 final size:24
Alignment explanation
Indices: 41998--42045 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
41988 GGTTCGATCT
*
41998 TAATTCTTAACGTTTGTGCTTTGAA
1 TAATTCTTAACGTTTATG-TTTGAA
*
42023 TAATTCTTAATGTTTATGTTTGA
1 TAATTCTTAACGTTTATGTTTGA
42046 TGTGTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (24 bp):
TAATTCTTAACGTTTATGTTTGAA
Found at i:42707 original size:2 final size:2
Alignment explanation
Indices: 42702--42733 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42692 AGAAGAGAGA
42702 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
42734 GGTGATGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44873 original size:20 final size:21
Alignment explanation
Indices: 44848--44886 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
44838 GACTTATACC
44848 AATGTTGATC-AATGACGAAA
1 AATGTTGATCAAATGACGAAA
*
44868 AATGTTGTTCAAATGACGA
1 AATGTTGATCAAATGACGA
44887 CATTATGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (21 bp):
AATGTTGATCAAATGACGAAA
Found at i:45279 original size:31 final size:31
Alignment explanation
Indices: 45146--45284 Score: 129
Period size: 31 Copynumber: 4.3 Consensus size: 31
45136 TTGGATAGTA
* *
45146 CTCGACTCGTGCTCGTTAAAAAATTTTGTTG
1 CTCGACTCATGCTCGTTAAGAAATTTTGTTG
* * * *
45177 CTCGACTCGTGCTTGTTAAGAAAATTTGTTA
1 CTCGACTCATGCTCGTTAAGAAATTTTGTTG
*
45208 CTCGACTCATTGCTCGTTAAGCTTGTTAAA-ATT-TTG
1 CTCGACTCA-TGCTCGTTAA----G--AAATTTTGTTG
*
45244 CTCGACTCATGCTCATTAAGAAATTTTGTTG
1 CTCGACTCATGCTCGTTAAGAAATTTTGTTG
45275 CTCGACTCAT
1 CTCGACTCAT
45285 TAAGGTCATT
Statistics
Matches: 89, Mismatches: 10, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
29 3 0.03
30 2 0.02
31 49 0.55
32 9 0.10
35 9 0.10
36 12 0.13
37 2 0.02
38 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (31 bp):
CTCGACTCATGCTCGTTAAGAAATTTTGTTG
Found at i:49913 original size:20 final size:21
Alignment explanation
Indices: 49884--49924 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
49874 TATTTATATC
49884 AAATACATTT-TAAAATTATA
1 AAATACATTTATAAAATTATA
* *
49904 AAATATATTTATAATATTATA
1 AAATACATTTATAAAATTATA
49925 TTTTAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATACATTTATAAAATTATA
Found at i:58526 original size:31 final size:32
Alignment explanation
Indices: 58490--58550 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
58480 GTTTAATTTT
*
58490 TTTTAATTTAATTTA-T-TAACTTTCAAATTAC
1 TTTTAATTTAA-TCACTCTAACTTTCAAATTAC
58521 TTTTAATTTAATCACTCTAACTTTCAAATT
1 TTTTAATTTAATCACTCTAACTTTCAAATT
58551 TTTCTTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 2 0.07
31 12 0.44
32 13 0.48
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.52
Consensus pattern (32 bp):
TTTTAATTTAATCACTCTAACTTTCAAATTAC
Found at i:87756 original size:2 final size:2
Alignment explanation
Indices: 87749--87775 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
87739 ACAACAAACG
87749 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
87776 ACAAAAGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90548 original size:20 final size:21
Alignment explanation
Indices: 90523--90573 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
90513 AAAAAAAAAA
90523 TATAAAAT-TCATTATATTAT
1 TATAAAATATCATTATATTAT
* *
90543 TATAAAATACTTATTATATTTT
1 TATAAAATA-TCATTATATTAT
90565 TATAAAATA
1 TATAAAATA
90574 ATAATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 8 0.30
22 19 0.70
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
TATAAAATATCATTATATTAT
Found at i:96905 original size:2 final size:2
Alignment explanation
Indices: 96898--96923 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
96888 GAATGAAGCT
96898 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
96924 AAGCAAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107070 original size:16 final size:16
Alignment explanation
Indices: 107049--107093 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
107039 AGGTCTCCAA
107049 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
107065 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
107081 CGTGTATGTTCGT
1 CGTTTATGTTCGT
107094 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.07, C:0.13, G:0.27, T:0.53
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:107182 original size:16 final size:16
Alignment explanation
Indices: 107161--107193 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
107151 AAAAAAATTT
107161 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
107177 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
107193 T
1 T
107194 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:109368 original size:16 final size:16
Alignment explanation
Indices: 109347--109377 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
109337 AGGTCTCCAA
*
109347 CGTTTATGTTCGTGTT
1 CGTTTATGTTAGTGTT
109363 CGTTTATGTTAGTGT
1 CGTTTATGTTAGTGT
109378 ATGTTCGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.26, T:0.55
Consensus pattern (16 bp):
CGTTTATGTTAGTGTT
Found at i:109995 original size:10 final size:10
Alignment explanation
Indices: 109980--110041 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
109970 CATTTAAATA
109980 ATAAACGAAC
1 ATAAACGAAC
109990 ATAAAC-AA-
1 ATAAACGAAC
**
109998 ACGAACGAAC
1 ATAAACGAAC
110008 ATAAACGAAC
1 ATAAACGAAC
*
110018 ATAATAAATGAAC
1 ---ATAAACGAAC
110031 ATAAACGAAC
1 ATAAACGAAC
110041 A
1 A
110042 CAATAAATGA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
8 4 0.10
9 4 0.10
10 24 0.59
13 9 0.22
ACGTcount: A:0.61, C:0.18, G:0.10, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:110001 original size:14 final size:14
Alignment explanation
Indices: 109982--110036 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
109972 TTTAAATAAT
109982 AAACGAACATAAAC
1 AAACGAACATAAAC
* *
109996 AAACGAACGA-ACAT
1 AAACGAAC-ATAAAC
*
110010 AAACGAACAT-AAT
1 AAACGAACATAAAC
*
110023 AAATGAACATAAAC
1 AAACGAACATAAAC
110037 GAACACAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
13 12 0.36
14 20 0.61
15 1 0.03
ACGTcount: A:0.62, C:0.18, G:0.09, T:0.11
Consensus pattern (14 bp):
AAACGAACATAAAC
Found at i:110030 original size:13 final size:13
Alignment explanation
Indices: 109977--110054 Score: 65
Period size: 13 Copynumber: 6.1 Consensus size: 13
109967 GTTCATTTAA
109977 ATAATAAACGAAC
1 ATAATAAACGAAC
*
109990 ATAAACAAACGAAC
1 AT-AATAAACGAAC
110004 GA-ACATAAACGAAC
1 -ATA-ATAAACGAAC
*
110018 ATAATAAATGAAC
1 ATAATAAACGAAC
110031 ---ATAAACGAAC
1 ATAATAAACGAAC
* *
110041 ACAATAAATGAAC
1 ATAATAAACGAAC
110054 A
1 A
110055 ACACAAACAC
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 9 0.17
13 23 0.43
14 20 0.38
15 1 0.02
ACGTcount: A:0.62, C:0.17, G:0.09, T:0.13
Consensus pattern (13 bp):
ATAATAAACGAAC
Found at i:110030 original size:23 final size:23
Alignment explanation
Indices: 110004--110054 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
109994 ACAAACGAAC
*
110004 GAACATAAACGAACATAATAAAT
1 GAACATAAACGAACACAATAAAT
110027 GAACATAAACGAACACAATAAAT
1 GAACATAAACGAACACAATAAAT
110050 GAACA
1 GAACA
110055 ACACAAACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.61, C:0.16, G:0.10, T:0.14
Consensus pattern (23 bp):
GAACATAAACGAACACAATAAAT
Found at i:128437 original size:11 final size:11
Alignment explanation
Indices: 128418--128460 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
128408 TGTCGGATTG
*
128418 ATTTTTATAAA
1 ATTTATATAAA
128429 ATTTATATAAA
1 ATTTATATAAA
*
128440 ATTAATA-AAA
1 ATTTATATAAA
128450 ATTTATATAAA
1 ATTTATATAAA
128461 GATTCGACGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTTATATAAA
Found at i:129216 original size:60 final size:59
Alignment explanation
Indices: 129138--129300 Score: 188
Period size: 60 Copynumber: 2.7 Consensus size: 59
129128 GCTATAATCA
* * *
129138 ATTT-TAAATTGATCCTTAAACTTTTGAATATTTTAATTTTAT-TTTAAAATTATGACTCTC
1 ATTTCTAAATTG-TCCTTAAACTTTTGAATATTTTAATTTCATCTCT-AAACTATGAC-CTC
* *
129198 A-TTCTAAATTAGTCCTTAAACTTTTGAACATTCTAATTTCATCTCTAAACTATGACCTC
1 ATTTCTAAATT-GTCCTTAAACTTTTGAATATTTTAATTTCATCTCTAAACTATGACCTC
* * *
129257 ATTTCTAATTTTGTCCCTAAACTTTTGAATATTTCAATTTCATC
1 ATTTCTAA-ATTGTCCTTAAACTTTTGAATATTTTAATTTCATC
129301 CCCAAATTAA
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
59 6 0.07
60 77 0.88
61 5 0.06
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.47
Consensus pattern (59 bp):
ATTTCTAAATTGTCCTTAAACTTTTGAATATTTTAATTTCATCTCTAAACTATGACCTC
Found at i:129246 original size:29 final size:29
Alignment explanation
Indices: 129197--129302 Score: 74
Period size: 29 Copynumber: 3.6 Consensus size: 29
129187 TTATGACTCT
* *
129197 CATTCTAAATT-AGTCCTTAAACTTTTGAA
1 CATTCTAATTTCA-TCCCTAAACTTTTGAA
* * *
129226 CATTCTAATTTCATCTCTAAAC-TATGACCT
1 CATTCTAATTTCATCCCTAAACTTTTGA--A
**
129256 CATTTCTAATTTTGTCCCTAAACTTTTGAA
1 CA-TTCTAATTTCATCCCTAAACTTTTGAA
*
129286 TATT-TCAATTTCATCCC
1 CATTCT-AATTTCATCCC
129303 CAAATTAATC
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
28 5 0.09
29 28 0.48
30 4 0.07
31 17 0.29
32 4 0.07
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.43
Consensus pattern (29 bp):
CATTCTAATTTCATCCCTAAACTTTTGAA
Found at i:141469 original size:17 final size:17
Alignment explanation
Indices: 141447--141480 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
141437 CAACTGATCC
141447 GTGTTTTGAAGATAGTA
1 GTGTTTTGAAGATAGTA
141464 GTGTTTTGAAGATAGTA
1 GTGTTTTGAAGATAGTA
141481 TAGAACCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (17 bp):
GTGTTTTGAAGATAGTA
Found at i:156511 original size:4 final size:4
Alignment explanation
Indices: 156502--156591 Score: 61
Period size: 4 Copynumber: 24.5 Consensus size: 4
156492 AAATAATTAT
* * * *
156502 TATA TATA TATA TATA TATA -ATA T-TA -ATA AATT TA-A TTTA AAT-
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * *
156545 TA-A TATA TATA TATA TA-A TATA TATA TATT TA-A TTTA AATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
156590 TA
1 TA
156592 CCCGGCCCGA
Statistics
Matches: 65, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
3 15 0.23
4 50 0.77
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:156513 original size:6 final size:6
Alignment explanation
Indices: 156502--156591 Score: 61
Period size: 6 Copynumber: 16.3 Consensus size: 6
156492 AAATAATTAT
* * * *
156502 TATATA TATATA TATATA TA-ATA T-TA-A TAAATT TA-ATT TAAAT-
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * *
156545 TA-ATA TATATA TATATA -ATATA TATATA TTTA-A TTTAAA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
156590 TA
1 TA
156592 CCCGGCCCGA
Statistics
Matches: 71, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
4 4 0.06
5 25 0.35
6 42 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATA
Found at i:156539 original size:40 final size:38
Alignment explanation
Indices: 156505--156591 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 38
156495 TAATTATTAT
156505 ATATATATATATATATAATAT-TAATAAATTTAATTTAA
1 ATATATATATATATATAATATAT-ATAAATTTAATTTAA
*
156543 ATTAATATATATATATATAATATATATATATTTAATTTAA
1 A-T-ATATATATATATATAATATATATAAATTTAATTTAA
156583 ATATATATA
1 ATATATATA
156592 CCCGGCCCGA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
38 8 0.18
39 2 0.04
40 34 0.76
41 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
ATATATATATATATATAATATATATAAATTTAATTTAA
Found at i:159100 original size:20 final size:20
Alignment explanation
Indices: 159075--159122 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
159065 AACATACTAT
159075 TATTTTTATA-ATG-CAACTGA
1 TATTTTTATATATGACAA-T-A
*
159095 TATTTTAATATATGACAATA
1 TATTTTTATATATGACAATA
159115 TATTTTTA
1 TATTTTTA
159123 ATTTTGTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 17 0.71
21 4 0.17
22 3 0.12
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (20 bp):
TATTTTTATATATGACAATA
Found at i:159335 original size:32 final size:32
Alignment explanation
Indices: 159299--159363 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
159289 AGTACAAGTT
* *
159299 TGTCGCCATCCCTTCCATGCGATACAAAAGGG
1 TGTCGCCATCCCTTCCATACGACACAAAAGGG
*
159331 TGTCGCCATCCCTTCCATACGACACCAAAGGG
1 TGTCGCCATCCCTTCCATACGACACAAAAGGG
159363 T
1 T
159364 ATCACCAAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.22
Consensus pattern (32 bp):
TGTCGCCATCCCTTCCATACGACACAAAAGGG
Found at i:159397 original size:23 final size:23
Alignment explanation
Indices: 159367--159421 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
159357 AAAGGGTATC
159367 ACCAAGCTTTCCAGTCGGCTTGG
1 ACCAAGCTTTCCAGTCGGCTTGG
159390 ACCAAGCTTTCCAGTCGGCTTGG
1 ACCAAGCTTTCCAGTCGGCTTGG
159413 ACCAAGCTT
1 ACCAAGCTT
159422 CTTGATCGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.25
Consensus pattern (23 bp):
ACCAAGCTTTCCAGTCGGCTTGG
Found at i:162820 original size:38 final size:38
Alignment explanation
Indices: 162769--162864 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
162759 CTCATATAAA
* *
162769 TGTCCCGAAGGACCAATCATCCCGAAGGATATCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATATAATCTG
* * *
162807 TGTCCCGAAGGACCTGTCATCCTGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATATAATCTG
*
162845 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
162865 ATGTCTTATA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATATAATCTG
Found at i:163070 original size:46 final size:46
Alignment explanation
Indices: 163017--163117 Score: 175
Period size: 46 Copynumber: 2.2 Consensus size: 46
163007 GTAACCATGT
*
163017 ATTTCATATCATATCACATGTATCACGTATTACATATTCATATGCC
1 ATTTCATATCATATCACATGTATCACGTATTACATATTCATATACC
* *
163063 ATTTCATATCATATCACATGTATCACGTATTGCATATTCATATATC
1 ATTTCATATCATATCACATGTATCACGTATTACATATTCATATACC
163109 ATTTCATAT
1 ATTTCATAT
163118 AGTCACATAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.42
Consensus pattern (46 bp):
ATTTCATATCATATCACATGTATCACGTATTACATATTCATATACC
Found at i:169580 original size:21 final size:21
Alignment explanation
Indices: 169554--169620 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
169544 ACCAATCATT
169554 CCGAAGGATGTCATCTGTGTC
1 CCGAAGGATGTCATCTGTGTC
*
169575 CCGAAGGA---C--CTGTCATC
1 CCGAAGGATGTCATCTGT-GTC
*
169592 CCGAAGGATGTAATCTGTGTC
1 CCGAAGGATGTCATCTGTGTC
*
169613 CCGTAGGA
1 CCGAAGGA
169621 CCTATCATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
16 4 0.11
17 10 0.28
18 1 0.03
21 17 0.47
22 4 0.11
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.24
Consensus pattern (21 bp):
CCGAAGGATGTCATCTGTGTC
Found at i:169584 original size:38 final size:38
Alignment explanation
Indices: 169533--169628 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
169523 CTTATATAAA
* * *
169533 TGTCCCGAAGGACCAATCATTCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
169571 TGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
169609 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
169629 ATGTCTTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:169834 original size:46 final size:46
Alignment explanation
Indices: 169777--169881 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
169767 ATGTGTAACC
169777 ATGT-ATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
* **
169822 ATGTCATTTCATATCGTATCACATGTATCACGTATTGTATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
169868 ATATCATTTCATAT
1 ATGTCATTTCATAT
169882 AGTCACATAG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
45 4 0.07
46 51 0.93
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
Found at i:172593 original size:31 final size:30
Alignment explanation
Indices: 172535--172608 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 30
172525 CTTTTTTATT
* * *
172535 TAAGTACCT-GAGATATTTTTTGGTCAAAA
1 TAAGTACCTAAAGTTATTTTTTGATCAAAA
172564 TAAGTACCTAAAGTTATCTTTTTGATCAAAA
1 TAAGTACCTAAAGTTAT-TTTTTGATCAAAA
*
172595 TAGGTACCTAAAGT
1 TAAGTACCTAAAGT
172609 ATTCAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 9 0.23
30 5 0.13
31 25 0.64
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (30 bp):
TAAGTACCTAAAGTTATTTTTTGATCAAAA
Found at i:172875 original size:8 final size:8
Alignment explanation
Indices: 172862--172904 Score: 77
Period size: 8 Copynumber: 5.4 Consensus size: 8
172852 ATAGACACAC
172862 ATGCATGT
1 ATGCATGT
172870 ATGCATGT
1 ATGCATGT
172878 ATGCATGT
1 ATGCATGT
172886 ATGCATGT
1 ATGCATGT
*
172894 ATGTATGT
1 ATGCATGT
172902 ATG
1 ATG
172905 AATTCTAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (8 bp):
ATGCATGT
Found at i:172899 original size:4 final size:4
Alignment explanation
Indices: 172866--172904 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
172856 ACACACATGC
* * *
172866 ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
172905 AATTCTAGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (4 bp):
ATGT
Found at i:182917 original size:22 final size:22
Alignment explanation
Indices: 182883--182934 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
182873 TGTCGTCAAA
182883 ATTAAAT-ATGATTAGTGGTCG
1 ATTAAATCATGATTAGTGGTCG
**
182904 AGTTAAATCA-GATTTTTGGTCG
1 A-TTAAATCATGATTAGTGGTCG
182926 ATCTAAATC
1 AT-TAAATC
182935 CGACTAGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 2 0.08
22 23 0.88
23 1 0.04
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
ATTAAATCATGATTAGTGGTCG
Found at i:183574 original size:34 final size:33
Alignment explanation
Indices: 183520--183583 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
183510 GAGACAGTTG
** *
183520 AAAAATATAGAGGGTCATTATAACAATTATACCT
1 AAAAATATAGAGAATAATTAT-ACAATTATACCT
*
183554 AAAAATATAGAGAATAATTATACTATTATA
1 AAAAATATAGAGAATAATTATACAATTATA
183584 TCGGATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 8 0.31
34 18 0.69
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (33 bp):
AAAAATATAGAGAATAATTATACAATTATACCT
Found at i:187018 original size:2 final size:2
Alignment explanation
Indices: 187011--187047 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
187001 ATATTTAAAT
187011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
187048 TATTTAAGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:187082 original size:31 final size:31
Alignment explanation
Indices: 187042--187113 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
187032 ATATATATAT
*
187042 ATATATTATTTAAGTCTTTAAATTGGTACTC
1 ATATATTATTTAAGTATTTAAATTGGTACTC
* * *
187073 ATATTTTATTTAAGTATTTAAATTGGTAATT
1 ATATATTATTTAAGTATTTAAATTGGTACTC
187104 ATATA-TATTT
1 ATATATTATTT
187114 TTATTGATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 5 0.14
31 31 0.86
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (31 bp):
ATATATTATTTAAGTATTTAAATTGGTACTC
Found at i:187268 original size:2 final size:2
Alignment explanation
Indices: 187263--187295 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
187253 AGTGTAGACA
187263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
187296 GTACCCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:189047 original size:14 final size:15
Alignment explanation
Indices: 189028--189061 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
189018 TGAAATGATA
189028 TATATTTTA-TACAT
1 TATATTTTATTACAT
*
189042 TATATTTTATTGCAT
1 TATATTTTATTACAT
189057 TATAT
1 TATAT
189062 AGTACACAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (15 bp):
TATATTTTATTACAT
Found at i:201820 original size:30 final size:31
Alignment explanation
Indices: 201743--201827 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
201733 TAACTCTTAC
201743 ATTTTAAATAAAATATTAATTTAATCCTCAA
1 ATTTTAAATAAAATATTAATTTAATCCTCAA
* * *
201774 ATTTTAGATTAAATATTAATTTAATCCTTAA
1 ATTTTAAATAAAATATTAATTTAATCCTCAA
201805 A-TTTAAATAAAATATTAATTTAA
1 ATTTTAAATAAAATATTAATTTAA
201828 CATAAATCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 20 0.41
31 29 0.59
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (31 bp):
ATTTTAAATAAAATATTAATTTAATCCTCAA
Found at i:208671 original size:41 final size:41
Alignment explanation
Indices: 208614--208696 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
208604 AGAAATCGAA
208614 TGGAACCTAGTTGATCTCACGTCCTACACGAGGTGATTAAC
1 TGGAACCTAGTTGATCTCACGTCCTACACGAGGTGATTAAC
208655 TGGAACCTAGTTGATCTCACGTCCTACACGAGGTGATTAAC
1 TGGAACCTAGTTGATCTCACGTCCTACACGAGGTGATTAAC
208696 T
1 T
208697 AACATTCTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.28
Consensus pattern (41 bp):
TGGAACCTAGTTGATCTCACGTCCTACACGAGGTGATTAAC
Found at i:209602 original size:2 final size:2
Alignment explanation
Indices: 209595--209646 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
209585 TACGTTGCAA
209595 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
209637 AT AT AT AT AT
1 AT AT AT AT AT
209647 TCATAACATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:212223 original size:2 final size:2
Alignment explanation
Indices: 212218--212242 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
212208 TGTGTGTGTG
212218 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
212243 TCACTGTCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:212975 original size:2 final size:2
Alignment explanation
Indices: 212970--213002 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
212960 TGTGTGTGTG
212970 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
213003 TAGATTCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:213824 original size:2 final size:2
Alignment explanation
Indices: 213817--213850 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
213807 TTTAACCATA
213817 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
213851 TCCCCCACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:216981 original size:2 final size:2
Alignment explanation
Indices: 216974--217041 Score: 120
Period size: 2 Copynumber: 34.0 Consensus size: 2
216964 ATAGGCCTTT
216974 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
217016 TA TA TA TA TA TA -A TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA
217042 AAATGAGATA
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 61 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:217677 original size:185 final size:182
Alignment explanation
Indices: 217369--217755 Score: 605
Period size: 185 Copynumber: 2.1 Consensus size: 182
217359 TTTTCTAATT
* * * * *
217369 TATATAA-AAATTAAATGTTTTTTAATTCAAAAAAATTATAATTAATTTAAATAATATAGAATTA
1 TATATAATATATTTAATATTTTTTAATTAAAAAAAATTACAATTAATTTAAATAATATAGAATTA
** *
217433 TAAAATAAAAATTTCAGATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGG
66 TAAAATAAAAATTTCAGATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAG
* *
217498 ATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTGAGCCCATATATTA
131 ATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGGCTGAGCCCATATATTA
*
217550 TATATAATATATTTAATATTTTTTAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTAAAAAAA-A--TTACAATTAATTTAAATAATATAGAA
* * *
217615 TTATAAAATACAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
63 TTATAAAATAAAAATTTCAGATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
*
217680 TAGATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGGCTGAGCCCATATGTTA
128 TAGATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGGCTGAGCCCATATATTA
217735 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
217756 AAAATTTAAT
Statistics
Matches: 187, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
181 7 0.04
182 23 0.12
183 1 0.01
185 156 0.83
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (182 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAAATTACAATTAATTTAAATAATATAGAATTA
TAAAATAAAAATTTCAGATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAG
ATCTTAAATTATTAATTGGGTTTTAAATAGTTTGGGCTGAGCCCATATATTA
Found at i:219940 original size:121 final size:122
Alignment explanation
Indices: 219796--220095 Score: 320
Period size: 121 Copynumber: 2.5 Consensus size: 122
219786 ATTTTTTGAA
* * * * * *
219796 AAAAAATATGAAAGTTTAGGTACTAAAACGGATAAAAACTAATATTTTAGGTACTAAACGCTTTA
1 AAAAAA-ATGAAAGTTTAAGTACTAAAACGGATCAAAACTAATAATTTAAGTACTAAACACGTTA
* * *
219861 AGTTTTTAATGGTG-GATACTAAAATAAAATAAAAACTAAATGTT-AGATATGATTTTG
65 AATTTTTAATGGTGTGATACTAAAATAAAATAAAAACTAAACGTTAAG-TAAGATTTTG
** * * * ** *
219918 AAAAAAATGAAAGTTTAAGTACTAAAATAGACCGAAACTGATAGCTTAAGTATTAAACACGTTAA
1 AAAAAAATGAAAGTTTAAGTACTAAAACGGATCAAAACTAATAATTTAAGTACTAAACACGTTAA
* *
219983 ATTTTTAATGGTGTGGTACTAAAATAAAATGAAAACTAAACGTTAAGTAAGATTTTG
66 ATTTTTAATGGTGTGATACTAAAATAAAATAAAAACTAAACGTTAAGTAAGATTTTG
*** * * *
220040 -AAATTTTGAAAGTTTATGCACTAAAACGGATCAAAATTAATAATTTATA-TACTAAA
1 AAAAAAATGAAAGTTTAAGTACTAAAACGGATCAAAACTAATAATTTA-AGTACTAAA
220096 TCCATAATTT
Statistics
Matches: 143, Mismatches: 32, Indels: 7
0.79 0.18 0.04
Matches are distributed among these distances:
121 98 0.69
122 43 0.30
123 2 0.01
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.32
Consensus pattern (122 bp):
AAAAAAATGAAAGTTTAAGTACTAAAACGGATCAAAACTAATAATTTAAGTACTAAACACGTTAA
ATTTTTAATGGTGTGATACTAAAATAAAATAAAAACTAAACGTTAAGTAAGATTTTG
Found at i:220238 original size:11 final size:11
Alignment explanation
Indices: 220195--220255 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
220185 AAAATAATTT
*
220195 TTAAATAATTA
1 TTAAATTATTA
* * *
220206 TAAAATGATCA
1 TTAAATTATTA
220217 TTAAATT-TTA
1 TTAAATTATTA
220227 TTAAATTATTA
1 TTAAATTATTA
*
220238 -TACAGTTATTA
1 TTA-AATTATTA
220249 TTAAATT
1 TTAAATT
220256 TATCAAATAG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
10 11 0.28
11 26 0.67
12 2 0.05
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (11 bp):
TTAAATTATTA
Found at i:220238 original size:32 final size:31
Alignment explanation
Indices: 220190--220308 Score: 95
Period size: 31 Copynumber: 3.8 Consensus size: 31
220180 ATTAAAAAAT
*
220190 AATTT-TTAAATAATTATAAAATGATCATTA
1 AATTTATTAAATTATTATAAAATGATCATTA
* * * *
220220 AATTTTATTAAATTATTATACAGTTATTATTA
1 AA-TTTATTAAATTATTATAAAATGATCATTA
*
220252 AATTTATCAAA-TAGTTATAAAAT-ACTTC-TTA
1 AATTTATTAAATTA-TTATAAAATGA--TCATTA
220283 AATTTATTAAATT-TTAGATAAAATGA
1 AATTTATTAAATTATT--ATAAAATGA
220309 CAAAATTAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 15
0.74 0.11 0.16
Matches are distributed among these distances:
30 7 0.10
31 31 0.44
32 31 0.44
33 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (31 bp):
AATTTATTAAATTATTATAAAATGATCATTA
Found at i:220267 original size:23 final size:22
Alignment explanation
Indices: 220224--220269 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
220214 TCATTAAATT
* *
220224 TTATTAAATTATTATACAGTTA
1 TTATTAAATTATCAAACAGTTA
*
220246 TTATTAAATTTATCAAATAGTTA
1 TTATTAAA-TTATCAAACAGTTA
220269 T
1 T
220270 AAAATACTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (22 bp):
TTATTAAATTATCAAACAGTTA
Found at i:220609 original size:18 final size:18
Alignment explanation
Indices: 220586--220630 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
220576 ACATTATCAG
220586 TAATCTTATCCCCACCGA
1 TAATCTTATCCCCACCGA
* * * *
220604 TAATCTCATTCCCACTGG
1 TAATCTTATCCCCACCGA
220622 TAATCTTAT
1 TAATCTTAT
220631 ATTCCGTGAA
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:0.27, C:0.31, G:0.07, T:0.36
Consensus pattern (18 bp):
TAATCTTATCCCCACCGA
Found at i:223096 original size:51 final size:51
Alignment explanation
Indices: 222980--223120 Score: 133
Period size: 51 Copynumber: 2.8 Consensus size: 51
222970 GAATACGAGT
* * * **
222980 TCAGCACCAGTGAATAAG-AATCCGCAGTTGATTAGACAACCGGTTCAGGCA
1 TCAGCAACAGTGAAT-AGCAATCCGCAGTTGACTAGACAACCAGTTCAAACA
* * *
223031 TCTGCAACAATGAATAGCAATCCGCAGTTGGCTAGACAACCAGTTCAAACA
1 TCAGCAACAGTGAATAGCAATCCGCAGTTGACTAGACAACCAGTTCAAACA
* * * * *
223082 TCAGCATCGGTGAATAACAATCAAG-AGTTGATTAGACAA
1 TCAGCAACAGTGAATAGCAATC-CGCAGTTGACTAGACAA
223121 GCATTAGCTC
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
50 2 0.03
51 69 0.96
52 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (51 bp):
TCAGCAACAGTGAATAGCAATCCGCAGTTGACTAGACAACCAGTTCAAACA
Found at i:223231 original size:162 final size:162
Alignment explanation
Indices: 222956--223731 Score: 370
Period size: 171 Copynumber: 4.6 Consensus size: 162
222946 ACAACGGATT
* * * * ** *
222956 CAAGCATCAGCTCCGAATACGAGTTCAGCACCAGTGAATAAGAATCCGCAGTTGATTAGACAACC
1 CAAGCATCAGCTCCGAATACAAATTCAGCACCAGTAAATAACAATAAGCAGTTGACTAGACAACC
* * * * * *
223021 GGTTCAGGCATCTGCAACAATGAATAGCAATCCGCAGTTGGCTAGACAACCAGTTCAAACATCAG
66 GATTCAAGCATCAGCAACAATGAATAACAATCCGCAGTTAGCTAGACAACCAATTCAAACATCAG
223086 CATCGGTGAATAACAATCAAGAGTTGATTAGA
131 CATCGGTGAATAACAATCAAGAGTTGATTAGA
* * * * *
223118 CAAGCATTAGCTCTGTATACAAATTCAGCACCAGTAAATAACAATAATCAGTTGACTAGACAACT
1 CAAGCATCAGCTCCGAATACAAATTCAGCACCAGTAAATAACAATAAGCAGTTGACTAGACAACC
* * *
223183 GATTCAAGCATCAGC-ACTATTGAATAACAATCCAG-AGTTAGCTAGACAACTAATTCAAGCATC
66 GATTCAAGCATCAGCAAC-AATGAATAACAATCC-GCAGTTAGCTAGACAACCAATTCAAACATC
* * *
223246 AGC-TCCGT--AT-ACAAGTTC-AGCACCGGTGAATA-A
129 AGCATCGGTGAATAACAA--TCAAG-A--GTTGATTAGA
* * * * * * * * *
223279 CAATCAGCAGTTGACACGACAACCGGTTCAAGCA-TCAGCACAAGTGAATAACGATCCA-CAAAT
1 CAAGCATCAGCT--C-CG--AA----TACAA--ATTCAGCACCAGTAAATAACAAT-AAGC-AGT
* ** * * *
223342 T-ACTAGACAACCGATTCAAGCATCAGCACCGGTGAAAAACAATCAGCAGTT-GACT--A-AATC
53 TGACTAGACAACCGATTCAAGCATCAGCAACAATGAATAACAATCCGCAGTTAG-CTAGACAACC
* * * * **
223402 GATTCAAACATCAGCACCAGTGAATAACAATCCAGAGTTGGCTAGA
117 AATTCAAACATCAGCATCGGTGAATAACAATCAAGAGTTGATTAGA
* * * * *
223448 CAACTGATTCAAACATCAGCTCC-ATATACAAGTTCAACACC-GATGAATAAAAATCAGCAGTTG
1 CAA--G-------CATCAGCTCCGA-ATACAAATTCAGCACCAG-TAAATAACAATAAGCAGTTG
* * * *
223511 AC-ACGACAACCGATTCAAGCATCAGCACCAGTGAATAACAATCCACA--AACGACTAGACAACC
55 ACTA-GACAACCGATTCAAGCATCAGCAACAATGAATAACAATCCGCAGTTA-G-CTAGACAACC
* * * *
223573 GATTCAAGCATCAGCACCGGTGAATAACAATC-AGCAGTTGACTAGACAACCTA
117 AATTCAAACATCAGCATCGGTGAATAACAATCAAG-AGTTGATTAG-------A
* * * * * * *
223626 TTCAAGCATTAGCTCCGTATACCAACTCAGCACCAGTGAATAACAATCAGCAGCTGACTAGACAA
1 --CAAGCATCAGCTCCGAATACAAATTCAGCACCAGTAAATAACAATAAGCAGTTGACTAGACAA
* * * * *
223691 CCGATTCAAACATCAGCACCAGTGAATAATAATCAGCAGTT
64 CCGATTCAAGCATCAGCAACAATGAATAACAATCCGCAGTT
223732 GACTAGATAC
Statistics
Matches: 467, Mismatches: 83, Indels: 117
0.70 0.12 0.18
Matches are distributed among these distances:
158 4 0.01
159 4 0.01
160 3 0.01
161 15 0.03
162 111 0.24
163 2 0.00
164 1 0.00
166 1 0.00
167 7 0.01
168 81 0.17
169 12 0.03
170 12 0.03
171 187 0.40
172 13 0.03
173 1 0.00
175 1 0.00
176 1 0.00
178 8 0.02
180 3 0.01
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (162 bp):
CAAGCATCAGCTCCGAATACAAATTCAGCACCAGTAAATAACAATAAGCAGTTGACTAGACAACC
GATTCAAGCATCAGCAACAATGAATAACAATCCGCAGTTAGCTAGACAACCAATTCAAACATCAG
CATCGGTGAATAACAATCAAGAGTTGATTAGA
Found at i:223336 original size:120 final size:120
Alignment explanation
Indices: 223118--223368 Score: 326
Period size: 120 Copynumber: 2.1 Consensus size: 120
223108 GTTGATTAGA
* * * *
223118 CAAGCATTAGCTCTGTATACAAATTCAGCACCAGTAAATAACAATAATCAGTTGACTAGACAACT
1 CAAGCATCAGCTCCGTATACAAATTCAGCACCAGTAAATAACAATAAGCAGTTGACTAGACAACC
* * * * *
223183 GATTCAAGCATCAGCACTATTGAATAACAATCCA-GAGTTAGCTAGACAACTAATT
66 GATTCAAGCATCAGCACAAGTGAATAACAATCCACAAATTA-CTAGACAACCAATT
* * * *
223238 CAAGCATCAGCTCCGTATACAAGTTCAGCACCGGTGAATAACAATCAGCAGTTGAC-ACGACAAC
1 CAAGCATCAGCTCCGTATACAAATTCAGCACCAGTAAATAACAATAAGCAGTTGACTA-GACAAC
* * *
223302 CGGTTCAAGCATCAGCACAAGTGAATAACGATCCACAAATTACTAGACAACCGATT
65 CGATTCAAGCATCAGCACAAGTGAATAACAATCCACAAATTACTAGACAACCAATT
223358 CAAGCATCAGC
1 CAAGCATCAGC
223369 ACCGGTGAAA
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
119 1 0.01
120 108 0.96
121 4 0.04
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (120 bp):
CAAGCATCAGCTCCGTATACAAATTCAGCACCAGTAAATAACAATAAGCAGTTGACTAGACAACC
GATTCAAGCATCAGCACAAGTGAATAACAATCCACAAATTACTAGACAACCAATT
Found at i:223377 original size:51 final size:51
Alignment explanation
Indices: 223262--223467 Score: 219
Period size: 51 Copynumber: 4.1 Consensus size: 51
223252 GTATACAAGT
* * *
223262 TCAGCACCGGTGAATAACAATCAGCAGTTGAC-ACGACAACCGGTTCAAGCA
1 TCAGCACCAGTGAATAACAATCAGCAGTTGACTA-GACAACCGATTCAAACA
* * * *
223313 TCAGCACAAGTGAATAACGATCCA-CAAATT-ACTAGACAACCGATTCAAGCA
1 TCAGCACCAGTGAATAACAAT-CAGC-AGTTGACTAGACAACCGATTCAAACA
* * *
223364 TCAGCACCGGTGAAAAACAATCAGCAGTTGACT--A-AATCGATTCAAACA
1 TCAGCACCAGTGAATAACAATCAGCAGTTGACTAGACAACCGATTCAAACA
* *
223412 TCAGCACCAGTGAATAACAATCCAG-AGTTGGCTAGACAACTGATTCAAACA
1 TCAGCACCAGTGAATAACAAT-CAGCAGTTGACTAGACAACCGATTCAAACA
223463 TCAGC
1 TCAGC
223468 TCCATATACA
Statistics
Matches: 129, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
48 38 0.29
49 4 0.03
50 6 0.05
51 75 0.58
52 6 0.05
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.18
Consensus pattern (51 bp):
TCAGCACCAGTGAATAACAATCAGCAGTTGACTAGACAACCGATTCAAACA
Found at i:223447 original size:99 final size:101
Alignment explanation
Indices: 223262--223467 Score: 265
Period size: 99 Copynumber: 2.0 Consensus size: 101
223252 GTATACAAGT
* * *
223262 TCAGCACCGGTGAATAACAATCAGCAGTTGACACGACAACCGGTTCAAGCATCAGCACAAGTGAA
1 TCAGCACCGGTGAAAAACAATCAGCAGTTGA-ACGACAACCGATTCAAACATCAGCACAAGTGAA
* *
223327 TAACGATCCACAAATTACTAGACAACCGATTCAAGCA
65 TAACAATCCACAAATTACTAGACAACCGATTCAAACA
* * *
223364 TCAGCACCGGTGAAAAACAATCAGCAGTTG-ACTA-AATCGATTCAAACATCAGCACCAGTGAAT
1 TCAGCACCGGTGAAAAACAATCAGCAGTTGAACGACAACCGATTCAAACATCAGCACAAGTGAAT
* * * *
223427 AACAATCCA-GAGTTGGCTAGACAACTGATTCAAACA
66 AACAATCCACAAATT-ACTAGACAACCGATTCAAACA
223463 TCAGC
1 TCAGC
223468 TCCATATACA
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
98 3 0.03
99 56 0.62
100 3 0.03
102 29 0.32
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.18
Consensus pattern (101 bp):
TCAGCACCGGTGAAAAACAATCAGCAGTTGAACGACAACCGATTCAAACATCAGCACAAGTGAAT
AACAATCCACAAATTACTAGACAACCGATTCAAACA
Found at i:223568 original size:219 final size:222
Alignment explanation
Indices: 223142--223630 Score: 745
Period size: 219 Copynumber: 2.2 Consensus size: 222
223132 GTATACAAAT
* * * * * *
223142 TCAGCACCAGT-AAATAACAATAATCAGTTGACTAGACAACTGATTCAAGCATCAGCACTATTGA
1 TCAGCACCGGTGAAA-AACAATCAGCAGTTGACTAGACAACTGATTCAAACATCAGCACCAGTGA
* * *
223206 ATAACAATCCAGAGTTAGCTAGACAACTAATTCAAGCATCAGCTCCGTATACAAGTTCAGCACCG
65 ATAACAATCCAGAGTTAGCTAGACAACTAATTCAAACATCAGCTCCATATACAAGTTCAACACCG
* * * *
223271 GTGAATAACAATCAGCAGTTGACACGACAACCGGTTCAAGCATCAGCACAAGTGAATAACGATCC
130 ATGAATAAAAATCAGCAGTTGACACGACAACCGATTCAAGCATCAGCACAAGTGAATAACAATCC
**
223336 ACAAATTACTAGACAACCGATTCAAGCA
195 ACAAACGACTAGACAACCGATTCAAGCA
*
223364 TCAGCACCGGTGAAAAACAATCAGCAGTTGACTA-A-ATC-GATTCAAACATCAGCACCAGTGAA
1 TCAGCACCGGTGAAAAACAATCAGCAGTTGACTAGACAACTGATTCAAACATCAGCACCAGTGAA
* *
223426 TAACAATCCAGAGTTGGCTAGACAACTGATTCAAACATCAGCTCCATATACAAGTTCAACACCGA
66 TAACAATCCAGAGTTAGCTAGACAACTAATTCAAACATCAGCTCCATATACAAGTTCAACACCGA
*
223491 TGAATAAAAATCAGCAGTTGACACGACAACCGATTCAAGCATCAGCACCAGTGAATAACAATCCA
131 TGAATAAAAATCAGCAGTTGACACGACAACCGATTCAAGCATCAGCACAAGTGAATAACAATCCA
223556 CAAACGACTAGACAACCGATTCAAGCA
196 CAAACGACTAGACAACCGATTCAAGCA
*
223583 TCAGCACCGGTGAATAACAATCAGCAGTTGACTAGACAACCT-ATTCAA
1 TCAGCACCGGTGAAAAACAATCAGCAGTTGACTAGACAA-CTGATTCAA
223631 GCATTAGCTC
Statistics
Matches: 241, Mismatches: 21, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
219 199 0.83
220 3 0.01
221 2 0.01
222 34 0.14
223 3 0.01
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (222 bp):
TCAGCACCGGTGAAAAACAATCAGCAGTTGACTAGACAACTGATTCAAACATCAGCACCAGTGAA
TAACAATCCAGAGTTAGCTAGACAACTAATTCAAACATCAGCTCCATATACAAGTTCAACACCGA
TGAATAAAAATCAGCAGTTGACACGACAACCGATTCAAGCATCAGCACAAGTGAATAACAATCCA
CAAACGACTAGACAACCGATTCAAGCA
Found at i:223570 original size:51 final size:51
Alignment explanation
Indices: 223515--223634 Score: 179
Period size: 51 Copynumber: 2.4 Consensus size: 51
223505 CAGTTGACAC
223515 GACAACCGATTCAAGCATCAGCACCAGTGAATAACAATCCA-CAAACGACTA
1 GACAACCGATTCAAGCATCAGCACCAGTGAATAACAAT-CAGCAAACGACTA
* ***
223566 GACAACCGATTCAAGCATCAGCACCGGTGAATAACAATCAGCAGTTGACTA
1 GACAACCGATTCAAGCATCAGCACCAGTGAATAACAATCAGCAAACGACTA
*
223617 GACAACCTATTCAAGCAT
1 GACAACCGATTCAAGCAT
223635 TAGCTCCGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 2 0.03
51 61 0.97
ACGTcount: A:0.40, C:0.28, G:0.16, T:0.17
Consensus pattern (51 bp):
GACAACCGATTCAAGCATCAGCACCAGTGAATAACAATCAGCAAACGACTA
Found at i:223578 original size:120 final size:117
Alignment explanation
Indices: 223368--223587 Score: 298
Period size: 120 Copynumber: 1.9 Consensus size: 117
223358 CAAGCATCAG
* * *
223368 CACCGGTGAAAAACAATCAGCAGTTGACTAAATCGATTCAAACATCAGCACCAGTGAATAACAAT
1 CACCGATGAAAAACAATCAGCAGTTGACGAAACCGATTCAAACATCAGCACCAGTGAATAACAAT
* *** * *
223433 CCAGAGTTGGCTAGACAACTGATTCAAACATCAGCTCCATATACAAGTTCAA
66 CCACAAACGACTAGACAACCGATTCAAACATCAGCTCCATATACAAGTTCAA
*
223485 CACCGATGAATAAA-AATCAGCAGTTGACACGACAACCGATTCAAGCATCAGCACCAGTGAATAA
1 CACCGATGAA-AAACAATCAGCAGTTG--ACGA-AACCGATTCAAACATCAGCACCAGTGAATAA
*
223549 CAATCCACAAACGACTAGACAACCGATTCAAGCATCAGC
62 CAATCCACAAACGACTAGACAACCGATTCAAACATCAGC
223588 ACCGGTGAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
117 21 0.24
118 3 0.03
119 3 0.03
120 61 0.69
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.18
Consensus pattern (117 bp):
CACCGATGAAAAACAATCAGCAGTTGACGAAACCGATTCAAACATCAGCACCAGTGAATAACAAT
CCACAAACGACTAGACAACCGATTCAAACATCAGCTCCATATACAAGTTCAA
Found at i:223621 original size:171 final size:169
Alignment explanation
Indices: 223343--223728 Score: 482
Period size: 171 Copynumber: 2.3 Consensus size: 169
223333 TCCACAAATT
* * *** *
223343 ACTAGACAACCGATTCAAGCATCAGCACCGGTGAAAAACAAT-CAGCAGTTGACTAAATCGATTC
1 ACTAGACAACCGATTCAAGCATCAGCACCAGTGAATAACAATCCAGCAAACGACTAAACCGATTC
*
223407 AAACATCAGCACCAGTGAATAACAATCCAGAGTTGGCTAGACAA-CTGATTCAAACATCAGCTCC
66 AAACATCAGCACCAGTGAATAACAATCCAGAGTTGACTAGACAACCT-ATTCAAACATCAGCTCC
* *
223471 ATATA-CAAGTTCAACACC-GATGAATAAAAATCAGCAGTTG
130 ATATACCAA-CTCAACACCAG-TGAATAAAAATCAGCAGCTG
223511 AC-ACGACAACCGATTCAAGCATCAGCACCAGTGAATAACAATCCA-CAAACGACTAGACAACCG
1 ACTA-GACAACCGATTCAAGCATCAGCACCAGTGAATAACAATCCAGCAAACGACT--A-AACCG
* * * *
223574 ATTCAAGCATCAGCACCGGTGAATAACAAT-CAGCAGTTGACTAGACAACCTATTCAAGCATTAG
62 ATTCAAACATCAGCACCAGTGAATAACAATCCAG-AGTTGACTAGACAACCTATTCAAACATCAG
* * *
223638 CTCCGTATACCAACTCAGCACCAGTGAATAACAATCAGCAGCTG
126 CTCCATATACCAACTCAACACCAGTGAATAAAAATCAGCAGCTG
* *
223682 ACTAGACAACCGATTCAAACATCAGCACCAGTGAATAATAAT-CAGCA
1 ACTAGACAACCGATTCAAGCATCAGCACCAGTGAATAACAATCCAGCA
223729 GTTGACTAGA
Statistics
Matches: 189, Mismatches: 18, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
167 1 0.01
168 44 0.23
169 2 0.01
170 6 0.03
171 129 0.68
172 7 0.04
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (169 bp):
ACTAGACAACCGATTCAAGCATCAGCACCAGTGAATAACAATCCAGCAAACGACTAAACCGATTC
AAACATCAGCACCAGTGAATAACAATCCAGAGTTGACTAGACAACCTATTCAAACATCAGCTCCA
TATACCAACTCAACACCAGTGAATAAAAATCAGCAGCTG
Found at i:227748 original size:2 final size:2
Alignment explanation
Indices: 227741--227766 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
227731 CTTTATGGCA
227741 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
227767 TCTCTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:231096 original size:21 final size:21
Alignment explanation
Indices: 231072--231146 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
231062 ATCCCATTTG
231072 AAATAATATATTTATTAAAAA
1 AAATAATATATTTATTAAAAA
* * * *
231093 AAATATTATTTTTATTCAATA
1 AAATAATATATTTATTAAAAA
*
231114 AAGTAGA-A-ATTTAATTAAAAGA
1 AAATA-ATATATTT-ATTAAAA-A
231136 AAATAATATAT
1 AAATAATATAT
231147 AGATGAATAT
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
20 3 0.08
21 28 0.72
22 6 0.15
23 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (21 bp):
AAATAATATATTTATTAAAAA
Found at i:237429 original size:18 final size:16
Alignment explanation
Indices: 237397--237427 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
237387 AATATTGAAA
237397 CTTGAACTCAAAAAAG
1 CTTGAACTCAAAAAAG
237413 CTTGAACTCAAAAAA
1 CTTGAACTCAAAAAA
237428 AAATTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
CTTGAACTCAAAAAAG
Found at i:237499 original size:14 final size:14
Alignment explanation
Indices: 237480--237507 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
237470 AAGTGAAAAA
237480 ATAGTTATATAATT
1 ATAGTTATATAATT
237494 ATAGTTATATAATT
1 ATAGTTATATAATT
237508 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:239839 original size:26 final size:27
Alignment explanation
Indices: 239788--239848 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
239778 ACTTATCTTG
* *
239788 ATATATTTATTAAAATATATT-TTTTA
1 ATATTTTTATTAAAATATATTATTTAA
* *
239814 TTATTTTTATATAAAATA-CTTATTTAA
1 ATATTTTTAT-TAAAATATATTATTTAA
239841 ATATTTTT
1 ATATTTTT
239849 TTAGTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
ATATTTTTATTAAAATATATTATTTAA
Found at i:239866 original size:22 final size:21
Alignment explanation
Indices: 239839--239879 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
239829 ATACTTATTT
*
239839 AAATATTTTTTTAGTTTTTTTA
1 AAATA-TTTTTTAGATTTTTTA
239861 AAATATTTTTTAGATTTTT
1 AAATATTTTTTAGATTTTT
239880 ACCCATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
AAATATTTTTTAGATTTTTTA
Found at i:241924 original size:2 final size:2
Alignment explanation
Indices: 241917--241956 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
241907 ATCCATTTGA
241917 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
241957 TAGTTGGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:245801 original size:25 final size:25
Alignment explanation
Indices: 245773--245820 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
245763 ACTATTAGAT
*
245773 TTGGTCCATTTTAATACTTAAACTA
1 TTGGTCCATTTTAATACCTAAACTA
*
245798 TTGGTTCATTTTAATACCTAAAC
1 TTGGTCCATTTTAATACCTAAAC
245821 CATATGTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (25 bp):
TTGGTCCATTTTAATACCTAAACTA
Found at i:254156 original size:43 final size:42
Alignment explanation
Indices: 254096--254179 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 42
254086 ATCTTATAAG
*
254096 AAATTAACTCAATTTTTAAGATAGAAACTTGCATTCGATCTA
1 AAATTAACTCAATTTTTAAGATAAAAACTTGCATTCGATCTA
*
254138 AAATTCAACTCGATTTTTAAGATAAAAACTTGCATTCGATCT
1 AAATT-AACTCAATTTTTAAGATAAAAACTTGCATTCGATCT
254180 GATTCGAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 5 0.13
43 34 0.87
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (42 bp):
AAATTAACTCAATTTTTAAGATAAAAACTTGCATTCGATCTA
Found at i:259951 original size:17 final size:17
Alignment explanation
Indices: 259929--259961 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
259919 CCAGAATGTC
*
259929 CAGGGGTATCGATTCCT
1 CAGGGGAATCGATTCCT
259946 CAGGGGAATCGATTCC
1 CAGGGGAATCGATTCC
259962 CCCTAAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.24
Consensus pattern (17 bp):
CAGGGGAATCGATTCCT
Found at i:260570 original size:15 final size:15
Alignment explanation
Indices: 260546--260593 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
260536 GAGGGTTCTG
260546 AGTCCTTCGGGACGT
1 AGTCCTTCGGGACGT
*
260561 AGTTCTTCGGGACGT
1 AGTCCTTCGGGACGT
260576 AGTCCTTCGGGACGT
1 AGTCCTTCGGGACGT
260591 AGT
1 AGT
260594 GGTCCTACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.29
Consensus pattern (15 bp):
AGTCCTTCGGGACGT
Found at i:269116 original size:30 final size:30
Alignment explanation
Indices: 269082--269166 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 30
269072 TTAAACGGCA
*
269082 AGGTACTAAAATGAAATAAAACT-AAAGGTT
1 AGGTACTAAAATGAAAAAAAACTGAAA-GTT
** *
269112 AGGTA-TAATTTTGAAAAAAAATTGAAAGTT
1 AGGTACTAA-AATGAAAAAAAACTGAAAGTT
* **
269142 AGGTACTAAAACGAACCAAAACTGA
1 AGGTACTAAAATGAAAAAAAACTGA
269167 TATTTTAATA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
29 3 0.07
30 33 0.79
31 6 0.14
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (30 bp):
AGGTACTAAAATGAAAAAAAACTGAAAGTT
Found at i:281219 original size:2 final size:2
Alignment explanation
Indices: 281212--281239 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
281202 AACATGACAA
281212 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
281240 TGTTTCATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:283088 original size:57 final size:56
Alignment explanation
Indices: 283009--283127 Score: 157
Period size: 57 Copynumber: 2.1 Consensus size: 56
282999 GAATAAAAAT
* ** * * **
283009 TAAAATCACTCAAATATTTTTAAATAACATTTAAAGTAAAATTTAATTTAATTTAA
1 TAAAATAACTCAAATACATTTAAATAACATTTAAAATAAAATTGAATCCAATTTAA
*
283065 TACAAATAACTCAAATACATTTAAATAATATTTAAAATAAAATTGAATCCAATTTAA
1 TA-AAATAACTCAAATACATTTAAATAACATTTAAAATAAAATTGAATCCAATTTAA
283122 TAAAAT
1 TAAAAT
283128 TTATAAAACA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
56 6 0.11
57 48 0.89
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (56 bp):
TAAAATAACTCAAATACATTTAAATAACATTTAAAATAAAATTGAATCCAATTTAA
Found at i:284717 original size:2 final size:2
Alignment explanation
Indices: 284710--284760 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
284700 ATCGGGTCGG
* * * *
284710 TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
284750 TA TA TA TA TA T
1 TA TA TA TA TA T
284761 TTAAATTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:286044 original size:21 final size:22
Alignment explanation
Indices: 286000--286072 Score: 130
Period size: 22 Copynumber: 3.4 Consensus size: 22
285990 TTAACCGAAC
286000 AAACGAACAAACACAAACAACT
1 AAACGAACAAACACAAACAACT
*
286022 AAACAAACAAACACAAA-AACT
1 AAACGAACAAACACAAACAACT
286043 AAACGAACAAACACAAACAACT
1 AAACGAACAAACACAAACAACT
286065 AAACGAAC
1 AAACGAAC
286073 GAAATTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.42
22 28 0.58
ACGTcount: A:0.66, C:0.26, G:0.04, T:0.04
Consensus pattern (22 bp):
AAACGAACAAACACAAACAACT
Done.