Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008124.1 Hibiscus syriacus cultivar Beakdansim tig00110678_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: 3296903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 19
Found at i:2760544 original size:13 final size:13
Alignment explanation
Indices: 2760516--2760563 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
2760506 TTTTCTTCAA
2760516 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
2760528 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
2760540 ATTTTCTCTTTGTT
1 -TTTTCTCTTTGTT
*
2760554 TTTCCTCTTT
1 TTTTCTCTTT
2760564 TTTCTCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
12 7 0.22
13 23 0.72
14 2 0.06
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:2760552 original size:26 final size:25
Alignment explanation
Indices: 2760515--2760565 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
2760505 TTTTTCTTCA
*
2760515 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTCCTCTTTTT
2760540 ATTTTCTCTTTGTTTTTCCTCTTTTT
1 ATTTTC-CTTTGTTTTTCCTCTTTTT
2760566 TCTCTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTCCTCTTTTT
Found at i:2763630 original size:35 final size:34
Alignment explanation
Indices: 2763577--2763669 Score: 97
Period size: 33 Copynumber: 2.8 Consensus size: 34
2763567 GTTAGATTGT
*
2763577 AAAAATAAA-ATAAAAATAAAAAATGAATAAT-AA
1 AAAAATAAATATAATAATAAAAAAT-AATAATGAA
*
2763610 AAAAATTTAATATAATAATAATAAAAT-A-AATGAA
1 AAAAA-TAAATATAATAATAA-AAAATAATAATGAA
*
2763644 AAAAATAAATA-AATAAGAAAAAATAA
1 AAAAATAAATATAATAATAAAAAATAA
2763670 ATAAAAGTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
31 5 0.10
32 8 0.16
33 13 0.25
34 11 0.22
35 9 0.18
36 5 0.10
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (34 bp):
AAAAATAAATATAATAATAAAAAATAATAATGAA
Found at i:2763669 original size:14 final size:14
Alignment explanation
Indices: 2763576--2763675 Score: 58
Period size: 17 Copynumber: 6.4 Consensus size: 14
2763566 AGTTAGATTG
2763576 TAAAAATAAAATAAA
1 TAAAAA-AAAATAAA
*
2763591 -AATAAAAAATGAATAA
1 TAAAAAAAAAT--A-AA
2763607 TAAAAAAATTTAATATAA
1 TAAAAAAA---AATA-AA
*
2763625 TAATAATAAAATAAA
1 TAA-AAAAAAATAAA
2763640 TGAAAAAAATAAATAAA
1 T--AAAAAA-AAATAAA
*
2763657 TAAGAAAAAATAAA
1 TAAAAAAAAATAAA
2763671 TAAAA
1 TAAAA
2763676 GTGAGTAGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 23
0.70 0.06 0.24
Matches are distributed among these distances:
13 5 0.07
14 15 0.22
15 9 0.13
16 9 0.13
17 16 0.24
18 7 0.10
19 4 0.06
20 3 0.04
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (14 bp):
TAAAAAAAAATAAA
Found at i:2763671 original size:18 final size:17
Alignment explanation
Indices: 2763577--2763674 Score: 78
Period size: 18 Copynumber: 5.8 Consensus size: 17
2763567 GTTAGATTGT
2763577 AAAAATAAAATAAA-AATA
1 AAAAAT-AAATAAATAA-A
*
2763595 AAAAATGAAT-AATAAA
1 AAAAATAAATAAATAAA
* * *
2763611 AAAATTTAAT--ATAAT
1 AAAAATAAATAAATAAA
* *
2763626 AATAATAAAATAAATGAA
1 AAAAAT-AAATAAATAAA
2763644 AAAAATAAATAAATAAGA
1 AAAAATAAATAAATAA-A
2763662 AAAAATAAATAAA
1 AAAAATAAATAAA
2763675 AGTGAGTAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
15 8 0.12
16 14 0.22
17 14 0.22
18 28 0.44
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAATAAATAAATAAA
Found at i:2765596 original size:20 final size:19
Alignment explanation
Indices: 2765573--2765625 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
2765563 AATATTTTTT
*
2765573 AATTCAATAAAATAATTTAC
1 AATT-AATAAAATAATATAC
* *
2765593 AATTAATTTAAATAATATAT
1 AATTAA-TAAAATAATATAC
2765613 AATT-ATAAAATAA
1 AATTAATAAAATAA
2765626 AAATTTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.25
19 3 0.11
20 18 0.64
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAATAAAATAATATAC
Found at i:2765687 original size:182 final size:183
Alignment explanation
Indices: 2765367--2765751 Score: 654
Period size: 182 Copynumber: 2.1 Consensus size: 183
2765357 TTTTCTAATT
* * *
2765367 TATATAA-AAATTAAATA-TTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
2765430 TTATAAAATAAAAATTTTAGATAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
66 TTATAAAATAAAAATTTTAGATAAATTTTT-ATTAATTAATATTGATTTAGGTTTAAAAGTTATT
* *
2765495 GGATCTTAAATTGTTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
130 GGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
2765549 TATATAATATATTTAATATTTTTTAATTCAATAAAATAA-TTTACAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTTTAATTCAA-AAAA-AAGTTTACAATTAATTTAAATAATATAT
*
2765613 AATTATAAAATAAAAATTTTATATAAA-TTTT-TTAATTAATATTGATTTAGGTTTAAAAGTTAT
64 AATTATAAAATAAAAATTTTAGATAAATTTTTATTAATTAATATTGATTTAGGTTTAAAAGTTAT
2765676 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
129 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
2765731 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
2765752 AAAATTTAAT
Statistics
Matches: 193, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
182 113 0.59
183 8 0.04
184 16 0.08
185 54 0.28
186 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAATTTTAGATAAATTTTTATTAATTAATATTGATTTAGGTTTAAAAGTTATTG
GATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:2767437 original size:15 final size:15
Alignment explanation
Indices: 2767411--2767459 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
2767401 TTTCGTTTGA
*
2767411 AATTTATGTTATTTT
1 AATTTATATTATTTT
* *
2767426 AATTTCTATTATTAT
1 AATTTATATTATTTT
* *
2767441 ATTTTATGTTATTTT
1 AATTTATATTATTTT
2767456 AATT
1 AATT
2767460 ATGTGACTAA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (15 bp):
AATTTATATTATTTT
Found at i:2768126 original size:199 final size:199
Alignment explanation
Indices: 2767736--2768234 Score: 519
Period size: 199 Copynumber: 2.5 Consensus size: 199
2767726 TACTAGCCTC
* * * * *
2767736 AATTGAAACATAAG-TACTAATACCACGCCTTTAATCTTATAAATTACGAAAAAATTTAGATTAA
1 AATTGAAAGATAAGTTAC-AATACTACGCCTCTAATCTTATAAATTACG-AAAATTTTAAATTAA
* * *
2767800 CTTCTCGAAAATA-CTCATTGAATATGCATATCAAACCATTTTAGCTTCTGTTTAACGCACAAAA
64 CTACCCGAAAA-ACCTC-TTGAATATGCCTATCAAACCATTTTAGCTTCTGTTTAACGCACAAAA
* * * * ** * * **
2767864 TTAAGTTTTGAAACCATTTTCAACGTGATTTTTAACCTGCTTATAATGTCTCTTATGTGTCGATA
127 TCAAGCTTTGAAACCATTTTCAACGCGATTTTGAACCCACTTACAATATCTAGTATGTGTCGATA
2767929 TT-A-CTT
192 TTGACCTT
*
2767935 ACAGTTGAAAGATAAGTTACAATACTACGCCTGTAATCTTATAAATTACGAAAATTTTCAAATTA
1 A-A-TTGAAAGATAAGTTACAATACTACGCCTCTAATCTTATAAATTACGAAAATTTT-AAATTA
* * * * *
2768000 ACTACCCGAAAACCCTCTCGAATATGCCTATCAAACCATTTTAGCTT-TTTCTTCATGCACAAAA
63 ACTACCCGAAAAACCTCTTGAATATGCCTATCAAACCATTTTAGCTTCTGT-TTAACGCACAAAA
*
2768064 -CCAGCTTTGAAA-CATTTTTCAACGCGATTTTGAACCCACTTACAATATCTAGTATGTGTCGAT
127 TCAAGCTTTGAAACCA-TTTTCAACGCGATTTTGAACCCACTTACAATATCTAGTATGTGTCGAT
2768127 ATTGACCTT
191 ATTGACCTT
* * * * * * * *
2768136 AACTAAAAGATAAATTCCAATACTACACCTCTAATCTCATAAGTTACGAAATTTTTTAAATTAAC
1 AATTGAAAGATAAGTTACAATACTACGCCTCTAATCTTATAAATTACGAAA-ATTTTAAATTAAC
* * *
2768201 TAGCCTAAAATACCTCTTGAACATGCCTAT-AAAC
65 TACCCGAAAA-ACCTCTTGAATATGCCTATCAAAC
2768235 ACTTGCAATG
Statistics
Matches: 251, Mismatches: 38, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
198 2 0.01
199 116 0.46
200 69 0.27
201 61 0.24
202 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (199 bp):
AATTGAAAGATAAGTTACAATACTACGCCTCTAATCTTATAAATTACGAAAATTTTAAATTAACT
ACCCGAAAAACCTCTTGAATATGCCTATCAAACCATTTTAGCTTCTGTTTAACGCACAAAATCAA
GCTTTGAAACCATTTTCAACGCGATTTTGAACCCACTTACAATATCTAGTATGTGTCGATATTGA
CCTT
Found at i:2770438 original size:21 final size:21
Alignment explanation
Indices: 2770413--2770452 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2770403 TTAGTAAAAA
*
2770413 TTTATTTAAAATATTATTAAT
1 TTTATTAAAAATATTATTAAT
2770434 TTTATTAAAAATATTATTA
1 TTTATTAAAAATATTATTA
2770453 TTGAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATTAAAAATATTATTAAT
Found at i:2770581 original size:21 final size:21
Alignment explanation
Indices: 2770556--2770599 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2770546 AGAAATATTA
* *
2770556 AAAAATATTAATGTTTTAGAT
1 AAAAATAATAATGTTTTAAAT
*
2770577 AAAAATAATAATTTTTTAAAT
1 AAAAATAATAATGTTTTAAAT
2770598 AA
1 AA
2770600 TTTTTCATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
AAAAATAATAATGTTTTAAAT
Found at i:2784682 original size:24 final size:25
Alignment explanation
Indices: 2784640--2784688 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
2784630 TTTCAAATAT
*
2784640 ATATAATATATATTTTTTTTGAAAAC
1 ATATAATATATA-TGTTTTTGAAAAC
*
2784666 ATATAATATATA-GTTTTTTAAAA
1 ATATAATATATATGTTTTTGAAAA
2784689 TGGTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
26 12 0.57
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (25 bp):
ATATAATATATATGTTTTTGAAAAC
Found at i:2784733 original size:24 final size:25
Alignment explanation
Indices: 2784696--2784742 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2784686 AAATGGTTTT
2784696 TTTTGAAAACATATATA-ATATAGC
1 TTTTGAAAACATATATATATATAGC
* *
2784720 TTTTGAATATATATATATATATA
1 TTTTGAAAACATATATATATATA
2784743 TATATAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTTGAAAACATATATATATATAGC
Found at i:2784812 original size:20 final size:21
Alignment explanation
Indices: 2784779--2784827 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
2784769 AAACGTATAA
2784779 ATATATATAATTTTTGAAAAC
1 ATATATATAATTTTTGAAAAC
* *
2784800 ATAT-TATAGTTTTTGAAAAT
1 ATATATATAATTTTTGAAAAC
2784820 ATA-ATATA
1 ATATATATA
2784828 CATTATATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (21 bp):
ATATATATAATTTTTGAAAAC
Found at i:2784885 original size:19 final size:18
Alignment explanation
Indices: 2784861--2784924 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
2784851 ATAGTGTACG
2784861 TATTATTTATTATATTATA
1 TATTATTTATTAT-TTATA
**
2784880 TATTATACATTATTT-TA
1 TATTATTTATTATTTATA
2784897 TATTTATTATATTACTTTAT-
1 TA-TTATT-TATTA-TTTATA
2784917 TATTATTT
1 TATTATTT
2784925 TATTTGTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
17 4 0.11
18 7 0.19
19 20 0.54
20 5 0.14
21 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTATTTATTATTTATA
Found at i:2785584 original size:7 final size:7
Alignment explanation
Indices: 2785572--2785596 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2785562 ATTTCTTTTA
2785572 ATTTAAT
1 ATTTAAT
2785579 ATTTAAT
1 ATTTAAT
2785586 ATTTAAT
1 ATTTAAT
2785593 ATTT
1 ATTT
2785597 TTATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTAAT
Found at i:2785594 original size:31 final size:31
Alignment explanation
Indices: 2785556--2785622 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
2785546 TTAATCCTTC
2785556 TTTAATATTTCT-TTTAATTTAATATTTAATA
1 TTTAATATTTCTATTTAATTTAAT-TTTAATA
* * * *
2785587 TTTAATATTTTTATTTTATTTTATTTTATTA
1 TTTAATATTTCTATTTAATTTAATTTTAATA
2785618 TTTAA
1 TTTAA
2785623 CATTAATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (31 bp):
TTTAATATTTCTATTTAATTTAATTTTAATA
Found at i:2788297 original size:30 final size:30
Alignment explanation
Indices: 2788231--2788306 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
2788221 TATGAGCTAT
* *
2788231 GTGACAAAGGTATGGAAAATGATATGTATAT
1 GTGATAAAGGTAT-GAAAATGATATGTATAG
* *
2788262 ATGATAAAGGTATGAAAATGATATGTCTAG
1 GTGATAAAGGTATGAAAATGATATGTATAG
*
2788292 GTGATATAAGCTATG
1 GTGATA-AAGGTATG
2788307 TGAATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 20 0.53
31 18 0.47
ACGTcount: A:0.41, C:0.04, G:0.25, T:0.30
Consensus pattern (30 bp):
GTGATAAAGGTATGAAAATGATATGTATAG
Found at i:2788565 original size:23 final size:23
Alignment explanation
Indices: 2788531--2788607 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
2788521 ATATATTATA
*
2788531 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
2788554 TGGCACTTCGGTGCAGTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
2788577 CGGTC-CTTCGG-GACAAATTCTATG
1 TGG-CACTTCGGTG-C-AATTCTACG
2788601 TGGCACT
1 TGGCACT
2788608 ATGGTGTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
22 1 0.02
23 31 0.70
24 12 0.27
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:2789031 original size:22 final size:22
Alignment explanation
Indices: 2788986--2789035 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
2788976 TGTTCCTGAC
* *
2788986 ACTGTTCATTACTGTTCACAGT
1 ACTGTTCATTACGGTTAACAGT
*
2789008 ACTGTTCATTACGGTTAACGGT
1 ACTGTTCATTACGGTTAACAGT
2789030 ACTGTT
1 ACTGTT
2789036 TATACCGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (22 bp):
ACTGTTCATTACGGTTAACAGT
Found at i:2796894 original size:2 final size:2
Alignment explanation
Indices: 2796887--2796925 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2796877 CTACTCAAAA
2796887 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2796926 AACAGAAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2810643 original size:9 final size:9
Alignment explanation
Indices: 2810613--2810664 Score: 56
Period size: 8 Copynumber: 6.1 Consensus size: 9
2810603 ATCTGCAAAA
2810613 AAATTAAAT
1 AAATTAAAT
*
2810622 -AAGTAAA-
1 AAATTAAAT
*
2810629 ATATTAAAT
1 AAATTAAAT
2810638 AAATTAAAT
1 AAATTAAAT
*
2810647 -ACTTAAAT
1 AAATTAAAT
2810655 AAATTAAAT
1 AAATTAAAT
2810664 A
1 A
2810665 CAAAATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 18 0.53
9 16 0.47
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:2810645 original size:17 final size:17
Alignment explanation
Indices: 2810610--2810662 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
2810600 TATATCTGCA
* *
2810610 AAAAAATTAAAT-AAGT
1 AAAATATTAAATAAATT
2810626 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
2810643 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
2810660 AAA
1 AAA
2810663 TACAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 16 0.50
17 14 0.44
18 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:2810663 original size:17 final size:17
Alignment explanation
Indices: 2810616--2810665 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
2810606 TGCAAAAAAA
* *
2810616 TTAAATAAGTAAAATA-
1 TTAAATAAATTAAATAC
2810632 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
2810649 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
2810666 AAAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:2812053 original size:21 final size:21
Alignment explanation
Indices: 2812029--2812090 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
2812019 AAATGAACAG
*
2812029 TGCTACAGTGCATCGATGTAT
1 TGCTACAGTGCATCGATGCAT
2812050 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAT
*
2812071 TGCTACAGTACATCGATGCA
1 TGCTACAGTGCATCGATGCA
2812091 CCAAATATCG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (21 bp):
TGCTACAGTGCATCGATGCAT
Found at i:2817952 original size:26 final size:27
Alignment explanation
Indices: 2817899--2817954 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
2817889 TGAAAAATAA
*
2817899 ATAAATAAATATTAAAATAATTTATAT
1 ATAAAAAAATATTAAAATAATTTATAT
2817926 ATAAAAAAATA-TAAAAT-ATTTATTAT
1 ATAAAAAAATATTAAAATAATTTA-TAT
2817952 ATA
1 ATA
2817955 TATATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 5 0.19
26 12 0.44
27 10 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
ATAAAAAAATATTAAAATAATTTATAT
Found at i:2819363 original size:3 final size:3
Alignment explanation
Indices: 2819357--2819405 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
2819347 TAATATTTAT
*
2819357 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TGA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
2819401 TAA TA
1 TAA TA
2819406 TTTAAATGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.85
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2819670 original size:17 final size:17
Alignment explanation
Indices: 2819648--2819698 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2819638 TTGAATAAGA
2819648 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
* *
2819665 TCTTCTTCA-GATG-AGT
1 TCTTC-TCATTATGAACT
2819681 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
2819698 T
1 T
2819699 TCTCTGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 3 0.11
16 10 0.37
17 11 0.41
18 3 0.11
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.47
Consensus pattern (17 bp):
TCTTCTCATTATGAACT
Found at i:2819694 original size:16 final size:16
Alignment explanation
Indices: 2819648--2819694 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2819638 TTGAATAAGA
2819648 TCTTCTCATTATGAACT
1 TCTTCTCATTATG-ACT
* *
2819665 TCTTCTTCA-GATGAGT
1 TCTTC-TCATTATGACT
2819681 TCTTCTCATTATGA
1 TCTTCTCATTATGA
2819695 ACTTTCTCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.12
16 11 0.44
17 8 0.32
18 3 0.12
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (16 bp):
TCTTCTCATTATGACT
Found at i:2819759 original size:117 final size:118
Alignment explanation
Indices: 2819552--2819827 Score: 348
Period size: 117 Copynumber: 2.4 Consensus size: 118
2819542 ATTCTTTTTT
* * *
2819552 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCGCTGG---GGATGATGTTGACCTATTTCCT
1 TTCTTCAGATGAGTTCTTCTCATTATGAAC-TTTCTCTGGAAAGGATGATGCTAACCTATTTCCT
* * *
2819614 TCTGTGATAGAGTCATTCAAAAGGTTGAATAAGATCTTCTCATTATGAA-CTTC
65 TCTGTGATAAAATCATTCAAAAGGTTGAACAAGATCTTCTCATTATGAATCTTC
** * *
2819667 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTTTGATGCTAATCTATTTGCTT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTATTTCCTT
* * * *
2819732 CTGTGATAAAATTATGT-AAAAGGTTGAACAAGCTTTTCTCATTGTGAACTTCTTC
66 CTGTGATAAAATCAT-TCAAAAGGTTGAACAAGATCTTCTCATTATGAA--TCTTC
2819787 TTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAA
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
2819828 AGCTGATCCA
Statistics
Matches: 140, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
114 8 0.06
115 30 0.21
117 56 0.40
118 1 0.01
119 11 0.08
120 34 0.24
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (118 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTATTTCCTT
CTGTGATAAAATCATTCAAAAGGTTGAACAAGATCTTCTCATTATGAATCTTC
Found at i:2820077 original size:228 final size:223
Alignment explanation
Indices: 2819749--2820265 Score: 757
Period size: 228 Copynumber: 2.3 Consensus size: 223
2819739 AAAATTATGT
* *
2819749 AAAAGGTTGAACAAGCTT-TTCTCATTGTGAA-CTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
1 AAAAGGTTGAACAA-ATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
*
2819812 TGAAC-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCT
65 TGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCT
*
2819876 TCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CT-
130 TCTCATTATGAATTTCTTCTTCCTTCTTCAGATGA--A-TTCTTCTCATTACGAACT-TACTCTG
2819939 GACAA-TGTT-AACCATCAAATGATGAATTTAAAC
191 GA-AAGT-TTGAACCATCAAATGATGAATTTAAAC
2819972 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA--TCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
*
2820037 TACGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATT
63 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATT
*
2820102 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGGA
128 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTACTCTGGA
* * ** *
2820167 AAGTTTGATCCATCAAGTGATGGTTTTGAAC
193 AAGTTTGAACCATCAAATGATGAATTTAAAC
* *
2820198 AAAAAGTTGAACAAATTCTTCTCATTATGAAT-TTCTTC-T-TTCAGATGAGTTATTCTCATTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
2820260 GAACTT
66 GAACTT
2820266 CTTCTTCTTC
Statistics
Matches: 270, Mismatches: 14, Indels: 23
0.88 0.05 0.07
Matches are distributed among these distances:
220 27 0.10
221 1 0.00
222 3 0.01
223 31 0.11
224 3 0.01
225 23 0.09
226 59 0.22
227 30 0.11
228 93 0.34
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (223 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTT
CTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTACTCTGGAAAG
TTTGAACCATCAAATGATGAATTTAAAC
Found at i:2820121 original size:113 final size:113
Alignment explanation
Indices: 2819749--2820237 Score: 665
Period size: 113 Copynumber: 4.4 Consensus size: 113
2819739 AAAATTATGT
* *
2819749 AAAAGGTTGAACAAGCTT-TTCTCATTGTGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 AAAAGGTTGAACAA-ATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
2819809 TTATGAAC-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC
65 TTACGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAAC
2819857 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
* * * * * * *
2819922 CATTATGAACTCTAC-CT-GACAATG-TTAACCATCAAATGATGAATTTAAAC
63 CATTACGAACT-TTCTCTGGA-AAAGCTGATCCATCAAATGATGGATTTGAAC
*
2819972 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
2820037 TACGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
66 TACGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAAC
*
2820085 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
2820150 TACGAACTTCCTCTGG-AAAGTTTGATCCATCAAGTGATGGTTTTGAAC
66 TACGAACTTTCTCTGGAAAAG-CTGATCCATCAAATGATGGATTTGAAC
*
2820198 AAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT
2820238 TCAGATGAGT
Statistics
Matches: 339, Mismatches: 27, Indels: 25
0.87 0.07 0.06
Matches are distributed among these distances:
107 2 0.01
108 26 0.08
111 8 0.02
112 40 0.12
113 163 0.48
115 93 0.27
116 5 0.01
117 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TACGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAAC
Found at i:2820258 original size:34 final size:36
Alignment explanation
Indices: 2820216--2820304 Score: 137
Period size: 36 Copynumber: 2.5 Consensus size: 36
2820206 GAACAAATTC
2820216 TTCTCATTATGAATTTCTTC-T-TTCAGATGAGTTA
1 TTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTA
* *
2820250 TTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTC
1 TTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTA
2820286 TTCTCATTATGAACTTTCT
1 TTCTCATTATGAA-TTTCT
2820305 CTGGAAAAGC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
34 19 0.39
35 1 0.02
36 25 0.51
37 4 0.08
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.49
Consensus pattern (36 bp):
TTCTCATTATGAATTTCTTCTTCTTCAGATGAGTTA
Found at i:2820300 original size:143 final size:149
Alignment explanation
Indices: 2820103--2820414 Score: 449
Period size: 143 Copynumber: 2.1 Consensus size: 149
2820093 GAACAAATTC
2820103 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGG-A
1 TTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGGAA
* * *
2820167 AAGTTTGATCCATCAAGTGATGGTTTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAA-T-
63 AAG-CTGACCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTC
2820230 TTCTT-C-T-TTCAGATGAGTTA
127 TTCTTCCTTCTTCAGATGAGTTA
* * *
2820250 TTCTCATTATGAACTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAG
1 TTCTCATTATGAACTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGGAAAAG
* *
2820314 CTGACCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTC
66 CTGACCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAAC-TCTTC
*
2820379 TTCCTTCTTCAGATGAGTTC
130 TTCCTTCTTCAGATGAGTTA
2820399 TTCTCATTATGAACTT
1 TTCTCATTATGAACTT
2820415 TCTCTGGAAA
Statistics
Matches: 149, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
143 90 0.60
144 10 0.07
145 1 0.01
146 5 0.03
147 14 0.09
148 1 0.01
149 28 0.19
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (149 bp):
TTCTCATTATGAACTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGGAAAAG
CTGACCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTCTTCT
TCCTTCTTCAGATGAGTTA
Found at i:2821386 original size:115 final size:115
Alignment explanation
Indices: 2821138--2821370 Score: 369
Period size: 115 Copynumber: 2.0 Consensus size: 115
2821128 GATCATGCAG
* * * * * * * *
2821138 TTCATCTTTTAATTCCAATGATTAG-TTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
2821202 AACACTTCCAGAAGATGCTATTGGGTCTTTTTATTTCTACTATGAGCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
2821252 TTCATCTTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
2821317 AATACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
2821367 TTCA
1 TTCA
2821371 CTTGCTCCAA
Statistics
Matches: 108, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
114 21 0.19
115 87 0.81
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (115 bp):
TTCATCTTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
Found at i:2822739 original size:10 final size:10
Alignment explanation
Indices: 2822724--2822772 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
2822714 CTTGACACCC
2822724 TCTTTTTTTT
1 TCTTTTTTTT
2822734 TC--TTTTTT
1 TCTTTTTTTT
2822742 TCTTTCTTCTTCT
1 TCTTT-TT-TT-T
2822755 TCTTTTTTTT
1 TCTTTTTTTT
2822765 TCTTTTTT
1 TCTTTTTT
2822773 CTTTTTCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
8 8 0.24
10 12 0.35
11 4 0.12
12 4 0.12
13 6 0.18
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:2822741 original size:7 final size:7
Alignment explanation
Indices: 2822729--2822778 Score: 55
Period size: 7 Copynumber: 6.7 Consensus size: 7
2822719 CACCCTCTTT
2822729 TTTTTTC
1 TTTTTTC
2822736 TTTTTTTC
1 -TTTTTTC
*
2822744 TTTCTTC
1 TTTTTTC
*
2822751 TTCTTCTTT
1 TT-TT-TTC
2822760 TTTTTTC
1 TTTTTTC
2822767 TTTTTTC
1 TTTTTTC
2822774 TTTTT
1 TTTTT
2822779 CTTCAAGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 22 0.61
8 10 0.28
9 4 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:2822762 original size:31 final size:29
Alignment explanation
Indices: 2822724--2822782 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 29
2822714 CTTGACACCC
2822724 TCTTTTTTTTTCTTTTTTTCTTTCTTCTTCT
1 TCTTTTTTTTTC-TTTTTTCTTT-TTCTTCT
2822755 TCTTTTTTTTTCTTTTTTCTTTTTCTTC
1 TCTTTTTTTTTCTTTTTTCTTTTTCTTC
2822783 AAGCATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 6 0.21
30 10 0.36
31 12 0.43
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (29 bp):
TCTTTTTTTTTCTTTTTTCTTTTTCTTCT
Found at i:2822766 original size:23 final size:23
Alignment explanation
Indices: 2822736--2822781 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2822726 TTTTTTTTTC
2822736 TTTTTTTCTTTCTTCTTCTTCTT
1 TTTTTTTCTTTCTTCTTCTTCTT
* *
2822759 TTTTTTTCTTTTTTCTTTTTCTT
1 TTTTTTTCTTTCTTCTTCTTCTT
2822782 CAAGCATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTTTTCTTTCTTCTTCTTCTT
Found at i:2835429 original size:3 final size:3
Alignment explanation
Indices: 2835423--2835471 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
2835413 TAATATTTAT
2835423 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
2835467 TAA TA
1 TAA TA
2835472 TTTAAATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2837326 original size:21 final size:21
Alignment explanation
Indices: 2837300--2837342 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2837290 TTCAATAGAT
*
2837300 ATAGATTGTGAATCGTCTTCC
1 ATAGATTGTGAATCGCCTTCC
*
2837321 ATAGATTGTGACTCGCCTTCC
1 ATAGATTGTGAATCGCCTTCC
2837342 A
1 A
2837343 AATCCACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (21 bp):
ATAGATTGTGAATCGCCTTCC
Found at i:2839250 original size:21 final size:21
Alignment explanation
Indices: 2839225--2839294 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
2839215 AGAACCTATC
2839225 ATCCCGAAGGATGTCATCTGT
1 ATCCCGAAGGATGTCATCTGT
2839246 ATCCCGAAGGA---C--CTGT
1 ATCCCGAAGGATGTCATCTGT
*
2839262 CATCCCGAAGGATGTAATCTGT
1 -ATCCCGAAGGATGTCATCTGT
* *
2839284 GTCCCGTAGGA
1 ATCCCGAAGGA
2839295 CCTATCATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
16 4 0.10
17 11 0.28
18 1 0.03
21 20 0.50
22 4 0.10
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (21 bp):
ATCCCGAAGGATGTCATCTGT
Found at i:2839265 original size:38 final size:38
Alignment explanation
Indices: 2839209--2839302 Score: 143
Period size: 38 Copynumber: 2.5 Consensus size: 38
2839199 CGTATAAATG
* *
2839209 TCCCGAAGAACCTATCATCCCGAAGGATGTCATCTGTA
1 TCCCGAAGGACCTATCATCCCGAAGGATGTAATCTGTA
* *
2839247 TCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGACCTATCATCCCGAAGGATGTAATCTGTA
*
2839285 TCCCGTAGGACCTATCAT
1 TCCCGAAGGACCTATCAT
2839303 ATGTCTTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (38 bp):
TCCCGAAGGACCTATCATCCCGAAGGATGTAATCTGTA
Found at i:2839268 original size:17 final size:17
Alignment explanation
Indices: 2839209--2839273 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
2839199 CGTATAAATG
* *
2839209 TCCCGAAGAACCTATCA
1 TCCCGAAGGACCTGTCA
2839226 TCCCGAAGGATGTCATCTGT-A
1 TCCCGAAGGA---C--CTGTCA
2839247 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTGTCA
2839264 TCCCGAAGGA
1 TCCCGAAGGA
2839274 TGTAATCTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
16 4 0.10
17 20 0.50
18 1 0.03
20 1 0.03
21 11 0.28
22 3 0.08
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.20
Consensus pattern (17 bp):
TCCCGAAGGACCTGTCA
Found at i:2839508 original size:46 final size:46
Alignment explanation
Indices: 2839451--2839555 Score: 185
Period size: 46 Copynumber: 2.3 Consensus size: 46
2839441 ATGTGTAACC
2839451 ATGT-ATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
2839496 ATGTCATTTCATATCATATCACATGTATCACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
*
2839542 ATATCATTTCATAT
1 ATGTCATTTCATAT
2839556 AGTCACATAG
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 4 0.07
46 53 0.93
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
Found at i:2840014 original size:37 final size:37
Alignment explanation
Indices: 2839964--2840037 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
2839954 TCATTTAGGG
*
2839964 GGGGAATCGATACCCCCCCCA-TGGGGAATCTGTTCCC
1 GGGGAATCGATA-CCCCCCCAGGGGGGAATCTGTTCCC
*
2840001 GGGGAATCGATACCCCCCCAGGGGGGAATTTGTTCCC
1 GGGGAATCGATACCCCCCCAGGGGGGAATCTGTTCCC
2840038 CCCTGCACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 8 0.24
37 26 0.76
ACGTcount: A:0.19, C:0.32, G:0.30, T:0.19
Consensus pattern (37 bp):
GGGGAATCGATACCCCCCCAGGGGGGAATCTGTTCCC
Found at i:2842067 original size:10 final size:10
Alignment explanation
Indices: 2842052--2842076 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2842042 ATGCTCGACA
2842052 GTGGTTCACG
1 GTGGTTCACG
2842062 GTGGTTCACG
1 GTGGTTCACG
2842072 GTGGT
1 GTGGT
2842077 CGATGGTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.16, G:0.44, T:0.32
Consensus pattern (10 bp):
GTGGTTCACG
Found at i:2857437 original size:16 final size:16
Alignment explanation
Indices: 2857416--2857476 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
2857406 GACAAAATTT
2857416 TTTACTATTCACGAAA
1 TTTACTATTCACGAAA
2857432 TTTACTATTCACGAAA
1 TTTACTATTCACGAAA
*
2857448 TTTACTATTCATGAAA
1 TTTACTATTCACGAAA
2857464 TTTACTATTCACG
1 TTTACTATTCACG
2857477 TTAATAGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (16 bp):
TTTACTATTCACGAAA
Found at i:2860228 original size:20 final size:20
Alignment explanation
Indices: 2860207--2860293 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
2860197 AAATCACAAT
*
2860207 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
2860227 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
* *
2860248 GAGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* * *
2860268 ACGATTCTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
2860288 GCGATA
1 GCGATA
2860294 ATACATAATC
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
19 2 0.04
20 35 0.67
21 13 0.25
22 2 0.04
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:2860826 original size:20 final size:20
Alignment explanation
Indices: 2860787--2860845 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
2860777 GCGATTCTCT
* **
2860787 CGTTGCTATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
2860807 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
2860827 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
2860846 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2861036 original size:25 final size:24
Alignment explanation
Indices: 2860982--2861036 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
2860972 TGTTTATTAT
* *
2860982 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
2861006 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
2861032 TGTTT
1 TGTTT
2861037 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:2862183 original size:18 final size:18
Alignment explanation
Indices: 2862162--2862206 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2862152 TCCACTTCGG
*
2862162 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2862180 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2862198 GAGCCATCA
1 GAGCCATCA
2862207 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2862742 original size:19 final size:20
Alignment explanation
Indices: 2862699--2862754 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
2862689 AGCAACACGA
2862699 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
2862719 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
2862738 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
2862755 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:2862762 original size:14 final size:14
Alignment explanation
Indices: 2862743--2862800 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2862733 ATGCGAAATG
2862743 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2862757 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
2862773 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2862789 AAAATCGCAACG
1 AAAATCGCAACG
2862801 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2862785 original size:32 final size:33
Alignment explanation
Indices: 2862727--2862817 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
2862717 GGAAATGGCT
2862727 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2862760 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2862792 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2862818 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2862811 original size:19 final size:19
Alignment explanation
Indices: 2862727--2862822 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
2862717 GGAAATGGCT
2862727 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2862746 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
2862760 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
2862778 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
2862792 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2862811 ATCGCAATGCGA
1 ATCGCAATGCGA
2862823 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
14 20 0.33
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.18
19 21 0.34
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2862853 original size:14 final size:14
Alignment explanation
Indices: 2862834--2862924 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
2862824 TTGTGTTTCG
2862834 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2862848 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2862864 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
2862880 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
2862897 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
2862913 CGTTGCGATTTT
1 CGTTGCGATTTT
2862925 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 27 0.42
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.09
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2862898 original size:33 final size:33
Alignment explanation
Indices: 2862829--2862940 Score: 208
Period size: 33 Copynumber: 3.4 Consensus size: 33
2862819 GCGATTTGTG
*
2862829 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
2862861 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
2862894 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
2862927 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
2862941 AGCCATTTTC
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 26 0.33
33 52 0.67
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2862952 original size:20 final size:20
Alignment explanation
Indices: 2862927--2862980 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2862917 GCGATTTTCA
*
2862927 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
2862947 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
2862967 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
2862981 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:2862960 original size:39 final size:36
Alignment explanation
Indices: 2862840--2862980 Score: 154
Period size: 33 Copynumber: 4.0 Consensus size: 36
2862830 TTCGCGTTGC
2862840 GATTTTGTCGTTGCGA-TTTCATTTCGCATTGC---
1 GATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
2862872 GATTTTGTCGTTGCGATTTTCATTTCGCATTGC---
1 GATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
2862905 GATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
1 GATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
** *
2862941 AGCCATTTTCG-CGTTGCGATAGTCATTTTCGCGTTGCGAT
1 -G--ATTTT-GTCGTTGCGATTTTCA-TTTCGCATTGCGAT
2862981 TTTAAGTTTC
Statistics
Matches: 97, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
32 16 0.16
33 49 0.51
37 1 0.01
39 17 0.18
40 14 0.14
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (36 bp):
GATTTTGTCGTTGCGATTTTCATTTCGCATTGCGAT
Found at i:2862990 original size:20 final size:20
Alignment explanation
Indices: 2862927--2863005 Score: 59
Period size: 20 Copynumber: 4.0 Consensus size: 20
2862917 GCGATTTTCA
* ** *
2862927 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGTAAG
* *
2862947 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTAAG
**
2862967 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATAGTAAG
* * *
2862987 TTTCGTGCTGCGAAAGTAA
1 TTTCGCGTTGCGATAGTAA
2863006 ACTATTCTTC
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTAAG
Found at i:2866067 original size:19 final size:19
Alignment explanation
Indices: 2866045--2866103 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
2866035 GGAAATTACT
*
2866045 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2866064 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2866078 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2866097 ATCGCAA
1 ATCGCAA
2866104 CGCTAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.50
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2866145 original size:33 final size:33
Alignment explanation
Indices: 2866050--2866145 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 33
2866040 TTACTATCGT
* *
2866050 AATGCGAAATGAAAATCGCAACGAGAGA-ATCGC
1 AATGCGAAATGAAAATCGCAACGCGA-ATTTCGC
* *
2866083 AATGCGAAATGAAAATCGCAACGCTAATTTTGC
1 AATGCGAAATGAAAATCGCAACGCGAATTTCGC
2866116 AATGCGAAATGAAAATCGCAACGCGAATTT
1 AATGCGAAATGAAAATCGCAACGCGAATTT
2866146 AATTTCGCGT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 1 0.02
33 56 0.98
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.19
Consensus pattern (33 bp):
AATGCGAAATGAAAATCGCAACGCGAATTTCGC
Found at i:2866160 original size:19 final size:19
Alignment explanation
Indices: 2866147--2866199 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
2866137 CGCGAATTTA
2866147 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
2866166 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
2866185 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
2866200 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:2866327 original size:14 final size:14
Alignment explanation
Indices: 2866308--2866344 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2866298 CATCAATTAA
2866308 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2866322 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2866336 ACAAATCAA
1 ACAAATCAA
2866345 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2867759 original size:42 final size:41
Alignment explanation
Indices: 2867700--2867905 Score: 164
Period size: 42 Copynumber: 4.9 Consensus size: 41
2867690 GTGAATCGGG
* *
2867700 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
2867742 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
2867784 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
2867826 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
2867868 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
2867906 GCGAGTCGGG
Statistics
Matches: 127, Mismatches: 29, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
41 9 0.07
42 107 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:2867841 original size:84 final size:84
Alignment explanation
Indices: 2867730--2867905 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
2867720 CCTCTTCAAC
2867730 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
2867795 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
2867814 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
2867879 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
2867898 GATGACAG
1 GATGACAG
2867906 GCGAGTCGGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:2867850 original size:21 final size:21
Alignment explanation
Indices: 2867700--2867850 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
2867690 GTGAATCGGG
*
2867700 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2867720 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2867742 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** *
2867763 CTCTCG-A-GGAATGATAGGGGC
1 CTCTTGAACGG--TGGGAGGGGA
* * * *
2867784 CTCTTCAACGATAGGAGTGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** * *
2867805 CTCTTG-AGGGATGACAGTGGC
1 CTCTTGAACGG-TGGGAGGGGA
2867826 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2867847 CTCT
1 CTCT
2867851 CGAGGAATGA
Statistics
Matches: 86, Mismatches: 37, Indels: 14
0.63 0.27 0.10
Matches are distributed among these distances:
19 2 0.02
20 3 0.03
21 74 0.86
22 6 0.07
23 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2868299 original size:91 final size:91
Alignment explanation
Indices: 2868127--2868308 Score: 287
Period size: 91 Copynumber: 2.0 Consensus size: 91
2868117 TCAAACTTTC
*
2868127 AACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATGCACAGTTTAGCAGA
1 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAA--CACAGTTTAGCAGA
2868192 ATTGGCAGCAACCGAATAAATTTACTTG
64 ATTGGCAGCAACCGAATAAATTTACTTG
* *
2868220 AACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAA-ACAGTTTAGCAGT
1 AACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAAGAACACAGTTTAGCAGA
2868283 ATTGGCAGCAACCGAATAAATTTACT
64 ATTGGCAGCAACCGAATAAATTTACT
2868309 AAGCAATCTA
Statistics
Matches: 84, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
91 38 0.45
93 15 0.18
94 4 0.05
95 27 0.32
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (91 bp):
AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAACACAGTTTAGCAGAAT
TGGCAGCAACCGAATAAATTTACTTG
Found at i:2870026 original size:20 final size:19
Alignment explanation
Indices: 2869995--2870116 Score: 75
Period size: 20 Copynumber: 6.8 Consensus size: 19
2869985 TCTTTTGGTT
2869995 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
2870014 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
2870035 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
2870054 G--A-G--AATCGCAATGC
1 GAAATGAAAATCGCAACGA
**
2870068 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
2870087 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
2870101 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
2870117 TGCAATTTTG
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
14 19 0.24
16 4 0.05
17 4 0.05
19 20 0.26
20 29 0.37
21 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:2870063 original size:14 final size:14
Alignment explanation
Indices: 2870044--2870099 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
2870034 GGAAATGACT
2870044 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2870058 ATCGCAATGCGAAATGA
1 ATCGCAA--CGAGA-GA
2870075 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
2870091 ATCGCAACG
1 ATCGCAACG
2870100 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:2870077 original size:33 final size:33
Alignment explanation
Indices: 2870020--2870116 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
2870010 ACGAGATAAT
2870020 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
2870054 GAGAATCGCAATGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
2870087 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
2870117 TGCAATTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:2870082 original size:19 final size:16
Alignment explanation
Indices: 2870022--2870108 Score: 56
Period size: 14 Copynumber: 5.2 Consensus size: 16
2870012 GAGATAATGA
2870022 GAATCGCAACGCGGAAAT
1 GAATCGCAA-GC-GAAAT
*
2870040 GACTATCGCAA-CGAGA-
1 GA--ATCGCAAGCGAAAT
2870056 GAATCGCAATGCGAAAT
1 GAATCGCAA-GCGAAAT
*
2870073 GACTATCGCAA-CGAGA-
1 GA--ATCGCAAGCGAAAT
2870089 GAATCGCAACGCGAAAT
1 GAATCGCAA-GCGAAAT
2870106 GAA
1 GAA
2870109 AATCGCAATG
Statistics
Matches: 55, Mismatches: 4, Indels: 21
0.69 0.05 0.26
Matches are distributed among these distances:
14 14 0.25
16 12 0.22
17 12 0.22
18 3 0.05
19 7 0.13
20 7 0.13
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.13
Consensus pattern (16 bp):
GAATCGCAAGCGAAAT
Found at i:2870721 original size:20 final size:20
Alignment explanation
Indices: 2870696--2870748 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2870686 TGGCTATGTA
2870696 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
2870716 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
2870736 TATCTCGTTGCGA
1 AATCGCGTTGCGA
2870749 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:2870786 original size:20 final size:20
Alignment explanation
Indices: 2870761--2870810 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2870751 TTGTATTATT
2870761 GCATTGCGATAGTAAGTATC
1 GCATTGCGATAGTAAGTATC
*
2870781 GCATTGCGATAGTCAGTATC
1 GCATTGCGATAGTAAGTATC
2870801 GCATTGCGAT
1 GCATTGCGAT
2870811 TTTCCCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (20 bp):
GCATTGCGATAGTAAGTATC
Found at i:2870829 original size:61 final size:61
Alignment explanation
Indices: 2870698--2870831 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
2870688 GCTATGTAAA
* * * * * **
2870698 TCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTAT
1 TCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCA-TAT
* * *
2870760 T-GCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCA-AT
1 TCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCATAT
2870820 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2870832 TTACTTATTC
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
60 3 0.05
61 54 0.92
62 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (61 bp):
TCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCATAT
Found at i:2876935 original size:15 final size:17
Alignment explanation
Indices: 2876917--2876949 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2876907 CACAATCTGC
2876917 ACATAC-AAAACA-AAA
1 ACATACTAAAACACAAA
2876932 ACATACTAAAACACAAA
1 ACATACTAAAACACAAA
2876949 A
1 A
2876950 TGGATAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.70, C:0.21, G:0.00, T:0.09
Consensus pattern (17 bp):
ACATACTAAAACACAAA
Found at i:2882753 original size:181 final size:182
Alignment explanation
Indices: 2882449--2882811 Score: 719
Period size: 181 Copynumber: 2.0 Consensus size: 182
2882439 TGCACAAACA
2882449 AGATAGTTCACTTATGCAAGCACAGATGAACAGTAAAGCATGATTAATGAAGTCAGATGGGAAAG
1 AGATAGTTCACTTATGCAAGCACAGATGAACAGTAAAGCATGATTAATGAAGTCAGATGGGAAAG
2882514 ATACCTGACCCAGATTGAGATGAAATAGCATAGGATAGAAACTTTATAAAAAATAATAACAAATT
66 ATACCTGACCCAGATTGAGATGAAATAGCATAGGATAGAAACTTTATAAAAAATAATAACAAATT
2882579 ATGCCAACATC-AAGGCAGAAAACTACCTCAAAGTAATGTGCATGGATGAGT
131 ATGCCAACATCAAAGGCAGAAAACTACCTCAAAGTAATGTGCATGGATGAGT
2882630 AGATAGTTCACTTATGCAAGCACAGATGAACAGTAAAGCATGATTAATGAAGTCAGATGGGAAAG
1 AGATAGTTCACTTATGCAAGCACAGATGAACAGTAAAGCATGATTAATGAAGTCAGATGGGAAAG
2882695 ATACCTGACCCAGATTGAGATGAAATAGCATAGGATAGAAACTTTATAAAAAATAATAACAAATT
66 ATACCTGACCCAGATTGAGATGAAATAGCATAGGATAGAAACTTTATAAAAAATAATAACAAATT
2882760 ATGCCAACATCAAAGGCAGAAAACTACCTCAAAGTAATGTGCATGGATGAGT
131 ATGCCAACATCAAAGGCAGAAAACTACCTCAAAGTAATGTGCATGGATGAGT
2882812 TTTGTCAGTA
Statistics
Matches: 181, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
181 141 0.78
182 40 0.22
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (182 bp):
AGATAGTTCACTTATGCAAGCACAGATGAACAGTAAAGCATGATTAATGAAGTCAGATGGGAAAG
ATACCTGACCCAGATTGAGATGAAATAGCATAGGATAGAAACTTTATAAAAAATAATAACAAATT
ATGCCAACATCAAAGGCAGAAAACTACCTCAAAGTAATGTGCATGGATGAGT
Found at i:2886232 original size:2 final size:2
Alignment explanation
Indices: 2886225--2886264 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2886215 GCAATCCCCT
2886225 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2886265 CCACCTATCA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2886608 original size:12 final size:12
Alignment explanation
Indices: 2886578--2886607 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
2886568 TAATGTGCCC
2886578 AATTTTTATTTT
1 AATTTTTATTTT
2886590 AATTTTTA-TTT
1 AATTTTTATTTT
2886601 AATTTTT
1 AATTTTT
2886608 TGAATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
AATTTTTATTTT
Found at i:2886943 original size:153 final size:154
Alignment explanation
Indices: 2886758--2887065 Score: 609
Period size: 153 Copynumber: 2.0 Consensus size: 154
2886748 TTTTCAAAAA
2886758 ATTAATGATTATATTATTTAACTTTTTTAATATATTGTTTTTAATTATTTTAAAACTATATTTTA
1 ATTAATGATTATATTATTTAACTTTTTTAATATATTGTTTTTAATTATTTTAAAACTATATTTTA
2886823 ATATTAATCAATATATATATATTTAATAAATTCCCCC-AAAATTTTGGCTAAAGAAACGACAACA
66 ATATTAATCAATATATATATATTTAATAAATTCCCCCAAAAATTTTGGCTAAAGAAACGACAACA
2886887 TAAAAGTCGTGTTTTGTATTTCCG
131 TAAAAGTCGTGTTTTGTATTTCCG
2886911 ATTAATGATTATATTATTTAACTTTTTTAATATATTGTTTTTAATTATTTTAAAACTATATTTTA
1 ATTAATGATTATATTATTTAACTTTTTTAATATATTGTTTTTAATTATTTTAAAACTATATTTTA
2886976 ATATTAATCAATATATATATATTTAATAAATTCCCCCAAAAATTTTGGCTAAAGAAACGACAACA
66 ATATTAATCAATATATATATATTTAATAAATTCCCCCAAAAATTTTGGCTAAAGAAACGACAACA
2887041 TAAAAGTCGTGTTTTGTATTTCCG
131 TAAAAGTCGTGTTTTGTATTTCCG
2887065 A
1 A
2887066 ATAAATTTTA
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
153 102 0.66
154 52 0.34
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (154 bp):
ATTAATGATTATATTATTTAACTTTTTTAATATATTGTTTTTAATTATTTTAAAACTATATTTTA
ATATTAATCAATATATATATATTTAATAAATTCCCCCAAAAATTTTGGCTAAAGAAACGACAACA
TAAAAGTCGTGTTTTGTATTTCCG
Found at i:2888146 original size:2 final size:2
Alignment explanation
Indices: 2888139--2888164 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2888129 TAAACATTTC
2888139 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
2888165 TCACATGATT
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:2889922 original size:39 final size:39
Alignment explanation
Indices: 2889868--2890316 Score: 638
Period size: 39 Copynumber: 11.6 Consensus size: 39
2889858 TGGAATAAGC
* * * *
2889868 TCTTCAGACTATGAACTTCTTCTTTCTCTTCAGATGGGT
1 TCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGT
* * *
2889907 TCTTCAGATTATGAACT-C--CTTCCTCTTCATATGAGT
1 TCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGT
* *
2889943 TCTTCGGGCTATGAACTCCTTCTTCCTCTTCAGACGAGT
1 TCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGT
*
2889982 TCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACGAGT
1 TCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGT
* * * *
2890021 TCTTCAGACTATGAAC-CCAATATTCCTCTTCATATGAGT
1 TCTTCAGACTATGAACTCC-TTCTTCCTCTTCAGACGAGT
* *
2890060 TCTTCAGATTATGAACTCATTCTTCCTCTTCAGACGAGT
1 TCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGT
*
2890099 TCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACGAGT
1 TCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGT
* * *
2890138 TCTTCAGACTATGAAC-CCATTATTCCTCTTCATATGAGT
1 TCTTCAGACTATGAACTCC-TTCTTCCTCTTCAGACGAGT
*
2890177 TCTTCAGATTATGAACTCCTTCTTCCTCTTCAGACGAGT
1 TCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGT
* *
2890216 TCTTTAGATTATGAACTCCTTCTTCCTCTTCAGACGAGT
1 TCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGT
2890255 TCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGT
1 TCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGT
2890294 TCTTCAGACTATGAACTCCTTCT
1 TCTTCAGACTATGAACTCCTTCT
2890317 GGAAATATTT
Statistics
Matches: 368, Mismatches: 35, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
36 29 0.08
37 1 0.00
38 5 0.01
39 330 0.90
40 3 0.01
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.39
Consensus pattern (39 bp):
TCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAGT
Found at i:2890443 original size:73 final size:73
Alignment explanation
Indices: 2890324--2890655 Score: 504
Period size: 73 Copynumber: 4.5 Consensus size: 73
2890314 TCTGGAAATA
* * *
2890324 TTTTAAGAAAAATAATCTCAAGTGAGATAAATTGTTATTT-AGAGTGAAACTTTCTCCAGCGAGA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCA-AGTGAAACTTTCTCCAGCGAAA
2890388 AACAGTTTG
65 AACAGTTTG
*
2890397 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCTAGCGAAAA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAAAA
* **
2890462 AAAAATTG
66 ACAGTTTG
* * *
2890470 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGAAAATTTCTCCAGCGAAAA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAAAA
* *
2890535 ATAGTTTA
66 ACAGTTTG
* * *
2890543 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCAAGTGAAACTTTCTCCAGTGAGAA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAAAA
2890608 ACAGTTTG
66 ACAGTTTG
*
2890616 TTTTAAGAAAAATAATCTCAAGTGAGATAAATTGCTATTT
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
2890656 GAAAACATCC
Statistics
Matches: 233, Mismatches: 25, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
73 232 1.00
74 1 0.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (73 bp):
TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAAAA
ACAGTTTG
Found at i:2891788 original size:54 final size:54
Alignment explanation
Indices: 2891729--2891872 Score: 234
Period size: 54 Copynumber: 2.7 Consensus size: 54
2891719 CAATGTTTCA
*
2891729 TAAAACATTTGACAACATATTCATCATTTCTTGTGGTTTCTGCACAGATGTTCG
1 TAAAACATTTGACAACACATTCATCATTTCTTGTGGTTTCTGCACAGATGTTCG
* * * *
2891783 TAAAACATTTGACTACACATTCATTATTTCCTGTGGTTTCTGCCCAGATGTTCG
1 TAAAACATTTGACAACACATTCATCATTTCTTGTGGTTTCTGCACAGATGTTCG
*
2891837 TAAAACATTTGACAACACATTCATCTTTTCTTGTGG
1 TAAAACATTTGACAACACATTCATCATTTCTTGTGG
2891873 CTTTTGCTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (54 bp):
TAAAACATTTGACAACACATTCATCATTTCTTGTGGTTTCTGCACAGATGTTCG
Found at i:2892304 original size:42 final size:42
Alignment explanation
Indices: 2892224--2892324 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
2892214 GCTGATTTGA
* * * *
2892224 GCCTTCAAAATGCCCCATATGGGTCATTTTTGTCTGAAATTG
1 GCCTTCAAAATGCCCCACATGGATCATTTTAGTCTGAAATAG
**
2892266 GCCTTCAAAATGCTTCACATGGATCATTTCTAGT-TGAAATAG
1 GCCTTCAAAATGCCCCACATGGATCATTT-TAGTCTGAAATAG
* **
2892308 GCTTTCAGTATGCCCCA
1 GCCTTCAAAATGCCCCA
2892325 GTATATTATT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
42 44 0.94
43 3 0.06
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (42 bp):
GCCTTCAAAATGCCCCACATGGATCATTTTAGTCTGAAATAG
Found at i:2893843 original size:7 final size:8
Alignment explanation
Indices: 2893824--2893889 Score: 50
Period size: 8 Copynumber: 8.8 Consensus size: 8
2893814 AAATTCATCT
2893824 TTTTTTCC
1 TTTTTTCC
2893832 TTTTTTCC
1 TTTTTTCC
2893840 TTTTTT--
1 TTTTTTCC
* * *
2893846 TCTCTTCT
1 TTTTTTCC
2893854 TTTTTTCC
1 TTTTTTCC
2893862 TTTTTT--
1 TTTTTTCC
* * *
2893868 TCTCTTCT
1 TTTTTTCC
2893876 TTTTTTCC
1 TTTTTTCC
2893884 TTTTTT
1 TTTTTT
2893890 ATGATGAATG
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
6 8 0.18
8 36 0.82
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCC
Found at i:2893857 original size:13 final size:13
Alignment explanation
Indices: 2893839--2893882 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
2893829 TCCTTTTTTC
2893839 CTTTTTTTCTCTT
1 CTTTTTTTCTCTT
2893852 C-TTTTTT-TC--
1 CTTTTTTTCTCTT
2893861 CTTTTTTTCTCTT
1 CTTTTTTTCTCTT
2893874 CTTTTTTTC
1 CTTTTTTTC
2893883 CTTTTTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
9 1 0.04
10 6 0.22
11 4 0.15
12 6 0.22
13 10 0.37
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
CTTTTTTTCTCTT
Found at i:2893858 original size:12 final size:12
Alignment explanation
Indices: 2893841--2893880 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2893831 CTTTTTTCCT
2893841 TTTTTTCTCTTC
1 TTTTTTCTCTTC
*
2893853 TTTTTT-TCCT-
1 TTTTTTCTCTTC
2893863 TTTTTTCTCTTC
1 TTTTTTCTCTTC
2893875 TTTTTT
1 TTTTTT
2893881 TCCTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 6 0.25
11 6 0.25
12 12 0.50
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTCTCTTC
Found at i:2893860 original size:22 final size:22
Alignment explanation
Indices: 2893832--2893889 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
2893822 CTTTTTTTCC
2893832 TTTTTTCCTTTTTTTCTCTTCT
1 TTTTTTCCTTTTTTTCTCTTCT
2893854 TTTTTTCCTTTTTTTCTCTTCT
1 TTTTTTCCTTTTTTTCTCTTCT
2893876 TTTTTTCCTTTTTT
1 TTTTTTCCTTTTTT
2893890 ATGATGAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTTCCTTTTTTTCTCTTCT
Found at i:2896595 original size:9 final size:8
Alignment explanation
Indices: 2896564--2896592 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2896554 TGCATAAAAC
2896564 TAAAAA-T
1 TAAAAATT
2896571 TAAAAATT
1 TAAAAATT
2896579 TAAAAATT
1 TAAAAATT
2896587 TAAAAA
1 TAAAAA
2896593 ATTAGAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
TAAAAATT
Found at i:2897564 original size:2 final size:2
Alignment explanation
Indices: 2897557--2897581 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2897547 ACTAAAGTAA
2897557 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2897582 AGTAATAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2904919 original size:446 final size:447
Alignment explanation
Indices: 2904059--2904952 Score: 1310
Period size: 446 Copynumber: 2.0 Consensus size: 447
2904049 GGTATGATAC
*
2904059 TAAATGACTATTATGAACTAAGAAAGAAAGGCAATATCGATACTCTTGAACCGAGTATTGATACT
1 TAAATGACTATTATGAACTAAGAAAGAAAGGCAATATCGATACTCTTGAACCGAGTATCGATACT
* * *
2904124 TCTATACTAAGGTACCGATAATGTCTTGAGTATCGATACAAAATTAAGTTTTGATGTTTTGAAAA
66 TCTATAATAAGGTACCGATAATGTCTTGAGTATCGATACAAAATTAAGCTTCGATGTTTTGAAAA
* * *
2904189 ATACCTCAGATCGATAGCTCTACTGGGAGTATCGATACTCTACACTAATATCGATACTCTCATGA
131 ATACCTCAGATCGATACCTCTACTGGGAGTATCGATACTCTACACCAATATCAATACTCTCATGA
* * * * * *
2904254 GTACTGATACCAAATATGGCTACTGATATTTTCTAAGTGGTCTTAGTATCGATACTCTTCTTAAA
196 GTACCGATACCAAATATGACTACTGATATTTTCTAAGTGGTCTCAGTATCAATACCCTTATTAAA
* * * *
2904319 GGTATCAAGACTTAACCTTCAGTATCGATACCTTATGAAGGAGTAGCGATACTTTTATACTAAAC
261 GGTATCAAGACTCAACCATCAATATCGATACCTTATAAAGGAGTAGCGATACTTTTATACTAAAC
* * *
2904384 TTCATTGTTTTGAACCACCTGACAAATAATATCGATATTGTTCTTCCACTAACGATATTTGTACC
326 TTCATTATTTTGAACCACCTCACAAATAATATCGATATTGTTCTTCCAATAACGATATTTGTACC
* *
2904449 CAGAAATACATTATTTTAGGCACGAAAAAGACTAACTCCCCTCCCCAAAGACCTTAT
391 CAGAAATACACTATTTTAGGCACGAAAAAGACTAACTCCCCTCCCCAAAGACCCTAT
* * * * *
2904506 TAAATGGCTATTGTGAACTAAGAAAGAAAGGCATTATTGATCCTCTTGAACCGAGTATCGATACT
1 TAAATGACTATTATGAACTAAGAAAGAAAGGCAATATCGATACTCTTGAACCGAGTATCGATACT
* * *
2904571 TCTATAATAAGGTA-CTATACTGTCTTGAGTATCGATACCAAATTAAGCTTCGATGTTTTGAAAA
66 TCTATAATAAGGTACCGATAATGTCTTGAGTATCGATACAAAATTAAGCTTCGATGTTTTGAAAA
*
2904635 ATACCTCAGTATCGATACCTCTACT-GGAGTATCGATACTCTACCCCAATATCAATACTCTCATG
131 ATACCTCAG-ATCGATACCTCTACTGGGAGTATCGATACTCTACACCAATATCAATACTCTCATG
2904699 AGTACCGATACCAAATATGACTACTGATATTTTCTAAGTGGTCTCAGTATCAATACCCTTATTAA
195 AGTACCGATACCAAATATGACTACTGATATTTTCTAAGTGGTCTCAGTATCAATACCCTTATTAA
* *
2904764 AGGTAT-AGAGACTCAACCATCAATATCGATATCC-TATAAAGGAGTATCGATATTTTTATACTA
260 AGGTATCA-AGACTCAACCATCAATATCGATA-CCTTATAAAGGAGTAGCGATACTTTTATACTA
* * * ** *
2904827 AGCTTTATTATTTTGAACCACCTCACAAATAATATCGGTATTGTTCTTTTAATATCGATATTTGT
323 AACTTCATTATTTTGAACCACCTCACAAATAATATCGATATTGTTCTTCCAATAACGATATTTGT
* * * * * ***
2904892 GCCCATAAATACACTATTTTGGGCACGAAAAGGACTAATTTTTCTCCCCAAAGACCCTAT
388 ACCCAGAAATACACTATTTTAGGCACGAAAAAGACTAACTCCCCTCCCCAAAGACCCTAT
2904952 T
1 T
2904953 GAGGTTCCCA
Statistics
Matches: 397, Mismatches: 47, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
445 1 0.00
446 308 0.78
447 88 0.22
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (447 bp):
TAAATGACTATTATGAACTAAGAAAGAAAGGCAATATCGATACTCTTGAACCGAGTATCGATACT
TCTATAATAAGGTACCGATAATGTCTTGAGTATCGATACAAAATTAAGCTTCGATGTTTTGAAAA
ATACCTCAGATCGATACCTCTACTGGGAGTATCGATACTCTACACCAATATCAATACTCTCATGA
GTACCGATACCAAATATGACTACTGATATTTTCTAAGTGGTCTCAGTATCAATACCCTTATTAAA
GGTATCAAGACTCAACCATCAATATCGATACCTTATAAAGGAGTAGCGATACTTTTATACTAAAC
TTCATTATTTTGAACCACCTCACAAATAATATCGATATTGTTCTTCCAATAACGATATTTGTACC
CAGAAATACACTATTTTAGGCACGAAAAAGACTAACTCCCCTCCCCAAAGACCCTAT
Found at i:2907086 original size:25 final size:26
Alignment explanation
Indices: 2907039--2907087 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
2907029 TATTTTACCA
2907039 GTGTAAGTATATATTAAGTTTCACCG
1 GTGTAAGTATATATTAAGTTTCACCG
*
2907065 GTGTAAGTATA-GTTAAGTTTCAC
1 GTGTAAGTATATATTAAGTTTCAC
2907088 TGATAGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (26 bp):
GTGTAAGTATATATTAAGTTTCACCG
Found at i:2907173 original size:26 final size:26
Alignment explanation
Indices: 2907132--2907186 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
2907122 TACGGGTTCA
* * *
2907132 TTTTACTTGTGTAAGTATATGTTAAG
1 TTTTACTAGTGCAAGTACATGTTAAG
*
2907158 TTTTACTAGTGCAAGTACATTTTAAG
1 TTTTACTAGTGCAAGTACATGTTAAG
2907184 TTT
1 TTT
2907187 CATTGATTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.49
Consensus pattern (26 bp):
TTTTACTAGTGCAAGTACATGTTAAG
Found at i:2907246 original size:102 final size:102
Alignment explanation
Indices: 2907018--2907375 Score: 380
Period size: 102 Copynumber: 3.5 Consensus size: 102
2907008 TCAATGATAG
* * * * ** *
2907018 AATTACGGGTTTATTTTACCAGTGTAAGTATATATTAAGTTTCACCGGTGTAAGTATA-GTTAAG
1 AATTACGTGTTTATTTTACCGGTGTAAGTATATGTTAAGTTTTACTAGTGTAAGTATATATTAAG
* * *
2907082 TTTCACTGATAGAATTATGTGTTAAGTTCAGTGCTAA
66 TTTCATTGATAGAATTATGTGTTAAGTTCAGTGTTGA
* * ** * * *
2907119 AATTACGGGTTCATTTTACTTGTGTAAGTATATGTTAAGTTTTACTAGTGCAAGTACATTTTAAG
1 AATTACGTGTTTATTTTACCGGTGTAAGTATATGTTAAGTTTTACTAGTGTAAGTATATATTAAG
* * *
2907184 TTTCATTGATTGAATTATTTGCTAAGTTCAGTGTTGA
66 TTTCATTGATAGAATTATGTGTTAAGTTCAGTGTTGA
* * * * *
2907221 AATTACATGTTTATTTCACCGGTGTAAGTATATGTTAAGTTTTATCT-GTATAAATATGTATTAA
1 AATTACGTGTTTATTTTACCGGTGTAAGTATATGTTAAGTTTTA-CTAGTGTAAGTATATATTAA
* ** * *
2907285 GTTTCATTGATGGGGTTATGTATTAAGTTCAGTGTTGG
65 GTTTCATTGATAGAATTATGTGTTAAGTTCAGTGTTGA
* * *
2907323 AATTACGTGTTAATTTTACAGGTGTAAGTACATGTTAAAGTTTT-CTAGTGTAA
1 AATTACGTGTTTATTTTACCGGTGTAAGTATATGTT-AAGTTTTACTAGTGTAA
2907376 AAGGCGTTGT
Statistics
Matches: 212, Mismatches: 41, Indels: 7
0.82 0.16 0.03
Matches are distributed among these distances:
101 51 0.24
102 152 0.72
103 9 0.04
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (102 bp):
AATTACGTGTTTATTTTACCGGTGTAAGTATATGTTAAGTTTTACTAGTGTAAGTATATATTAAG
TTTCATTGATAGAATTATGTGTTAAGTTCAGTGTTGA
Found at i:2907585 original size:40 final size:40
Alignment explanation
Indices: 2907540--2907749 Score: 158
Period size: 40 Copynumber: 5.2 Consensus size: 40
2907530 ACGAAAGCGA
*
2907540 TGATGTATTGCAC-GGACTACACACTCAACTACAAGAACGG
1 TGATGTATTGCACGGGA-TACACACTCAACTACAAGAAAGG
* ** * *
2907580 TGATGTGTTGTC-CATGATACACACCTCAA-TACGAGAATGG
1 TGATGTATTG-CACGGGATACACA-CTCAACTACAAGAAAGG
* * *
2907620 TGATGTATTGCACGGGAAACACA-TCCTACTACAAGAAAAG
1 TGATGTATTGCACGGGATACACACT-CAACTACAAGAAAGG
* * * ** ** *
2907660 TGATGTATTGTACGGGATACACACTTAAATATGAGAGTGA
1 TGATGTATTGCACGGGATACACACTCAACTACAAGAAAGG
** * * *
2907700 CAATGTATTACACGAGATACACACTCAACTACAATAAAGG
1 TGATGTATTGCACGGGATACACACTCAACTACAAGAAAGG
2907740 TGATGTATTG
1 TGATGTATTG
2907750 TATGGGAAAC
Statistics
Matches: 124, Mismatches: 39, Indels: 14
0.70 0.22 0.08
Matches are distributed among these distances:
38 1 0.01
39 3 0.02
40 111 0.90
41 9 0.07
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (40 bp):
TGATGTATTGCACGGGATACACACTCAACTACAAGAAAGG
Found at i:2907679 original size:80 final size:80
Alignment explanation
Indices: 2907517--2907770 Score: 248
Period size: 80 Copynumber: 3.2 Consensus size: 80
2907507 ACTCGCACAA
* *
2907517 GATACACA--TAAATACGA-AAGCGATGATGTATTGCAC-GGACTACACACTCAACTACAAGAAC
1 GATACACACCTAAATACGAGAA-TGATGATGTATTGCACGGGA-TACACACTCAACTACAAGAAA
* * **
2907578 GGTGATGTGTTGTCCAT
64 GGTGATGTATTGTACGG
* * * * *
2907595 GATACACACCTCAATACGAGAATGGTGATGTATTGCACGGGAAACACA-TCCTACTACAAGAAAA
1 GATACACACCTAAATACGAGAATGATGATGTATTGCACGGGATACACACT-CAACTACAAGAAAG
2907659 GTGATGTATTGTACGG
65 GTGATGTATTGTACGG
* * * ** * * *
2907675 GATACACACTTAAATATGAGAGTGACAATGTATTACACGAGATACACACTCAACTACAATAAAGG
1 GATACACACCTAAATACGAGAATGATGATGTATTGCACGGGATACACACTCAACTACAAGAAAGG
*
2907740 TGATGTATTGTATGG
66 TGATGTATTGTACGG
* *
2907755 GAAACACATCTAAATA
1 GATACACACCTAAATA
2907771 TAAGAGTGGC
Statistics
Matches: 142, Mismatches: 28, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
78 8 0.06
79 1 0.01
80 127 0.89
81 6 0.04
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (80 bp):
GATACACACCTAAATACGAGAATGATGATGTATTGCACGGGATACACACTCAACTACAAGAAAGG
TGATGTATTGTACGG
Found at i:2907801 original size:39 final size:40
Alignment explanation
Indices: 2907758--2907854 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 40
2907748 TGTATGGGAA
2907758 ACACATCTAAATATAAGAGTGGCGA-GAATTACAC-ATGAT
1 ACACATCTAAATATAAGAGTGGCGATGAATTACACGA-GAT
* * * *
2907797 ACACATCCAATTACAAGAGTGGCGATGCATTACACGAGAT
1 ACACATCTAAATATAAGAGTGGCGATGAATTACACGAGAT
*
2907837 ACACA-CTTAACTATAAGA
1 ACACATC-TAAATATAAGA
2907855 ATACTTACTT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
39 23 0.48
40 24 0.50
41 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (40 bp):
ACACATCTAAATATAAGAGTGGCGATGAATTACACGAGAT
Found at i:2907840 original size:40 final size:39
Alignment explanation
Indices: 2907758--2907841 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 39
2907748 TGTATGGGAA
* *
2907758 ACACATCTAAATATAAGAGTGGCGAGAATTACACATGAT
1 ACACATCCAAATACAAGAGTGGCGAGAATTACACATGAT
* *
2907797 ACACATCCAATTACAAGAGTGGCGATGCATTACACGA-GAT
1 ACACATCCAAATACAAGAGTGGCGA-GAATTACAC-ATGAT
2907837 ACACA
1 ACACA
2907842 CTTAACTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
39 22 0.56
40 16 0.41
41 1 0.03
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (39 bp):
ACACATCCAAATACAAGAGTGGCGAGAATTACACATGAT
Found at i:2908692 original size:60 final size:60
Alignment explanation
Indices: 2908598--2908737 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 60
2908588 ATTTTAGGGT
** * * *
2908598 AAAG-TATACAAATGATCATTTGACTATATAGTGTTGCTTTATTAAGTCCTCTGACTATTA
1 AAAGTTATA-AAATGATCACCTGACTATAGAGTGTTGCTTTATTAAGTCCCCCGACTATTA
* * * *
2908658 AAAGTTATAAAATGGTCACCTGACTATAGGGTGTTGCTTTGTTGAGTCCCCCGACTATTA
1 AAAGTTATAAAATGATCACCTGACTATAGAGTGTTGCTTTATTAAGTCCCCCGACTATTA
*
2908718 AAAGTTATATAATGATCACC
1 AAAGTTATAAAATGATCACC
2908738 AACCTATTCA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 64 0.94
61 4 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (60 bp):
AAAGTTATAAAATGATCACCTGACTATAGAGTGTTGCTTTATTAAGTCCCCCGACTATTA
Found at i:2909306 original size:16 final size:15
Alignment explanation
Indices: 2909281--2909311 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2909271 AAAGCAATTC
2909281 TCTTATCTTCTTCTT
1 TCTTATCTTCTTCTT
2909296 TCTTCATCTTCTTCTT
1 TCTT-ATCTTCTTCTT
2909312 CTCCTAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (15 bp):
TCTTATCTTCTTCTT
Found at i:2910417 original size:22 final size:21
Alignment explanation
Indices: 2910360--2910423 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
2910350 AGTCGAGGGT
* *
2910360 TTCATAGGTCTTTCGAGACAA
1 TTCATAGGTCATTCGGGACAA
*
2910381 CTCATAGGTCATTCGGGACATA
1 TTCATAGGTCATTCGGGACA-A
* *
2910403 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCATTCGGGACAA
2910424 ATTTCATATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 18 0.50
22 18 0.50
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (21 bp):
TTCATAGGTCATTCGGGACAA
Found at i:2911010 original size:21 final size:22
Alignment explanation
Indices: 2910976--2911021 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
2910966 GTAGCAATAA
2910976 TGTAGCAGGGGAATCGATACCC
1 TGTAGCAGGGGAATCGATACCC
* *
2910998 TGTAGCA-GGGAATCGGTTCCC
1 TGTAGCAGGGGAATCGATACCC
2911019 TGT
1 TGT
2911022 TTGCAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.24
Consensus pattern (22 bp):
TGTAGCAGGGGAATCGATACCC
Found at i:2911080 original size:12 final size:12
Alignment explanation
Indices: 2911063--2911127 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
2911053 TATCAGGTGT
2911063 TGTTCATGATAC
1 TGTTCATGATAC
2911075 TGTTCATGATAC
1 TGTTCATGATAC
* * * *
2911087 TATTCACGGTAT
1 TGTTCATGATAC
2911099 TGTTCAT--TAC
1 TGTTCATGATAC
* * *
2911109 TTTTCACGGTAC
1 TGTTCATGATAC
2911121 TGTTCAT
1 TGTTCAT
2911128 ACCGTATTTT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
10 7 0.17
12 33 0.82
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (12 bp):
TGTTCATGATAC
Found at i:2911114 original size:22 final size:23
Alignment explanation
Indices: 2911072--2911128 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
2911062 TTGTTCATGA
2911072 TACTGTTCATGATACTATTCACGG
1 TACTGTTCAT-ATACTATTCACGG
* *
2911096 TATTGTTCAT-TACTTTTCACGG
1 TACTGTTCATATACTATTCACGG
2911118 TACTGTTCATA
1 TACTGTTCATA
2911129 CCGTATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 20 0.69
24 9 0.31
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (23 bp):
TACTGTTCATATACTATTCACGG
Found at i:2911671 original size:4 final size:4
Alignment explanation
Indices: 2911662--2912018 Score: 511
Period size: 4 Copynumber: 89.8 Consensus size: 4
2911652 TTTTCATTAA
2911662 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2911710 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2911758 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
2911806 GTA- -TAT ATAT GTAT GTAT GTAT GTAT ATAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2911852 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * * * * * *
2911900 GGAT GCAT GTAT GCAT GCAT GCAT GTAT GCAT GCAT GCAT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * * * * *
2911948 GTAT GCAT GCAT GCAT GTAT GCAT GTAT GCAT GCAT GCAT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
2911996 GTAT GCAT GTAT GCAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTA
2912019 CAAATAAACT
Statistics
Matches: 327, Mismatches: 24, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
2 2 0.01
4 325 0.99
ACGTcount: A:0.26, C:0.05, G:0.25, T:0.45
Consensus pattern (4 bp):
GTAT
Found at i:2912684 original size:28 final size:28
Alignment explanation
Indices: 2912614--2912678 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
2912604 GGCTTGGAAT
2912614 AAACATAGATTATTGTTTAATTTGAGGC
1 AAACATAGATTATTGTTTAATTTGAGGC
*
2912642 AAACATAGATTATTGTTTAATTTGAGGG
1 AAACATAGATTATTGTTTAATTTGAGGC
2912670 AAACATAGA
1 AAACATAGA
2912679 CAATTGCAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (28 bp):
AAACATAGATTATTGTTTAATTTGAGGC
Found at i:2916361 original size:21 final size:21
Alignment explanation
Indices: 2916337--2916381 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
2916327 GTTATGGTTT
*
2916337 AGATATAGTGTTAAAATAAGA
1 AGATATAGTGTGAAAATAAGA
2916358 AGATATAGTGTGAAAATAAGA
1 AGATATAGTGTGAAAATAAGA
2916379 AGA
1 AGA
2916382 AAAAAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
AGATATAGTGTGAAAATAAGA
Found at i:2918699 original size:28 final size:28
Alignment explanation
Indices: 2918665--2918719 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
2918655 ACTATCTAAA
2918665 CAAAATATTAATTGAAGTAGCTAAACAG
1 CAAAATATTAATTGAAGTAGCTAAACAG
2918693 CAAAATATTAATTGAAGTAGCTAAACA
1 CAAAATATTAATTGAAGTAGCTAAACA
2918720 ATCTTATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (28 bp):
CAAAATATTAATTGAAGTAGCTAAACAG
Found at i:2919665 original size:3 final size:3
Alignment explanation
Indices: 2919657--2919719 Score: 53
Period size: 3 Copynumber: 21.3 Consensus size: 3
2919647 ACGAATAAAT
* *
2919657 ATA ATA ATA ATA ATTA ATA ATA ATA ATA ATT A-A AT- TTA ATAA ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
2919702 ATTA A-A AT- ATA ATA ATA A
1 A-TA ATA ATA ATA ATA ATA A
2919720 ATAAATATAG
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
2 6 0.12
3 34 0.69
4 9 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:2919676 original size:13 final size:13
Alignment explanation
Indices: 2919658--2919767 Score: 65
Period size: 14 Copynumber: 8.6 Consensus size: 13
2919648 CGAATAAATA
2919658 TAATAATAATAAT
1 TAATAATAATAAT
2919671 TAATAATAATAA-
1 TAATAATAATAAT
*
2919683 TAAT--TAA-ATT
1 TAATAATAATAAT
2919693 TAAT-A-AATAAT
1 TAATAATAATAAT
*
2919704 TAAAATATAATAAT
1 TAATA-ATAATAAT
*
2919718 AAATAAATATAGTAAT
1 TAAT-AATA-A-TAAT
*
2919734 TAA-AATATATATT
1 TAATAATA-ATAAT
*
2919747 TTATAAATAATAAT
1 TAAT-AATAATAAT
2919761 T-ATAATA
1 TAATAATA
2919768 TATTTTGAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
9 1 0.01
10 9 0.12
11 5 0.06
12 8 0.10
13 20 0.26
14 22 0.29
15 6 0.08
16 6 0.08
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:2919676 original size:16 final size:16
Alignment explanation
Indices: 2919657--2919767 Score: 80
Period size: 16 Copynumber: 7.4 Consensus size: 16
2919647 ACGAATAAAT
2919657 ATAATAATAATAATTA
1 ATAATAATAATAATTA
2919673 ATAATAATAATAATTA
1 ATAATAATAATAATTA
*
2919689 A-ATTTAATAAATAATTA
1 ATA-ATAAT-AATAATTA
*
2919706 A-AAT-ATAATAATAA
1 ATAATAATAATAATTA
*
2919720 ATAA-ATATAGTAATTA
1 ATAATA-ATAATAATTA
* *
2919736 A-AAT-AT-ATATTTT
1 ATAATAATAATAATTA
2919749 AT-A-AATAATAATT-
1 ATAATAATAATAATTA
2919762 ATAATA
1 ATAATA
2919768 TATTTTGAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
13 10 0.13
14 16 0.21
15 8 0.11
16 31 0.41
17 10 0.13
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (16 bp):
ATAATAATAATAATTA
Found at i:2919703 original size:17 final size:16
Alignment explanation
Indices: 2919660--2919733 Score: 87
Period size: 16 Copynumber: 4.5 Consensus size: 16
2919650 AATAAATATA
2919660 ATAATAATAATT-AAT
1 ATAATAATAATTAAAT
2919675 AATAATAATAATTAAAT
1 -ATAATAATAATTAAAT
*
2919692 TTAATAAATAATTAAAAT
1 ATAAT-AATAATT-AAAT
*
2919710 ATAATAATAAATAAAT
1 ATAATAATAATTAAAT
*
2919726 ATAGTAAT
1 ATAATAAT
2919734 TAAAATATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
16 27 0.53
17 16 0.31
18 8 0.16
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (16 bp):
ATAATAATAATTAAAT
Found at i:2932548 original size:168 final size:168
Alignment explanation
Indices: 2932235--2932570 Score: 640
Period size: 168 Copynumber: 2.0 Consensus size: 168
2932225 TATCAAAGGG
2932235 TAGATGTCTCCTTGACAATCCTATACCACTTCAAAACCCACATCCTTGAAGAAATCAGATTGGAA
1 TAGATGTCTCCTTGACAATCCTATACCACTTCAAAACCCACATCCTTGAAGAAATCAGATTGGAA
2932300 ATTGGATGAGGTACTGGTTTATGGGCTTTTAAACCCGGTAAACAAACTCCGAGAGCTAGTTCCTC
66 ATTGGATGAGGTACTGGTTTATGGGCTTTTAAACCCGGTAAACAAACTCCGAGAGCTAGTTCCTC
2932365 ATGAGTTGCTCCTAGCT-C-CTCGTGCTCCTCCTGCTC
131 ATGAGTTGCTCCTAGCTCCTCTCGTGCTCCTCCTGCTC
2932401 TAGATGTCTCCCTTGACAATCCTATACCACTTCAAAACCCACATCCTTGAAGAAATCAGATTGGA
1 TAGATGTCT-CCTTGACAATCCTATACCACTTCAAAACCCACATCCTTGAAGAAATCAGATTGGA
2932466 AATTGGATGAGGTAACTGGTTTATGGGCTTTTAAACCCGGTAAACAAACTCCGAGAGCTAGTTCC
65 AATTGGATGAGGT-ACTGGTTTATGGGCTTTTAAACCCGGTAAACAAACTCCGAGAGCTAGTTCC
2932531 TCATGAGTTGCTCCTAGCTCCTCTCGTGCTCCTCCTGCTC
129 TCATGAGTTGCTCCTAGCTCCTCTCGTGCTCCTCCTGCTC
2932571 CGGCTTCTGA
Statistics
Matches: 166, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
166 9 0.05
167 68 0.41
168 70 0.42
169 1 0.01
170 18 0.11
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (168 bp):
TAGATGTCTCCTTGACAATCCTATACCACTTCAAAACCCACATCCTTGAAGAAATCAGATTGGAA
ATTGGATGAGGTACTGGTTTATGGGCTTTTAAACCCGGTAAACAAACTCCGAGAGCTAGTTCCTC
ATGAGTTGCTCCTAGCTCCTCTCGTGCTCCTCCTGCTC
Found at i:2935721 original size:14 final size:14
Alignment explanation
Indices: 2935704--2935749 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
2935694 ATTCCAAAAT
2935704 ATATTATAATTATA
1 ATATTATAATTATA
2935718 ATATTATTAATTAT-
1 ATATTA-TAATTATA
*
2935732 TTATTAT-ATTATA
1 ATATTATAATTATA
2935745 CATAT
1 -ATAT
2935750 AAATTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 5 0.19
13 1 0.04
14 14 0.52
15 7 0.26
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
ATATTATAATTATA
Found at i:2935763 original size:30 final size:33
Alignment explanation
Indices: 2935703--2935763 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
2935693 AATTCCAAAA
2935703 TATATTATAATTATAATATTATTAATTATTTAT
1 TATATTATAATTATAATATTATTAATTATTTAT
2935736 TATATTATACA-TATAA-ATT-TT-ATTATTT
1 TATATTATA-ATTATAATATTATTAATTATTT
2935764 CAAAATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 7 0.26
31 2 0.07
32 3 0.11
33 14 0.52
34 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (33 bp):
TATATTATAATTATAATATTATTAATTATTTAT
Found at i:2935785 original size:12 final size:12
Alignment explanation
Indices: 2935770--2935807 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
2935760 ATTTCAAAAT
2935770 TTATAAAATATA
1 TTATAAAATATA
2935782 TTAT-AAATATTA
1 TTATAAAATA-TA
2935794 TTTATAAAATATA
1 -TTATAAAATATA
2935807 T
1 T
2935808 ATTTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 5 0.22
12 7 0.30
13 6 0.26
14 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTATAAAATATA
Found at i:2936197 original size:38 final size:38
Alignment explanation
Indices: 2936152--2936229 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
2936142 TATAAAATTA
2936152 CCTCAAGATAAATCATAACATTAATTATTAATATATTG
1 CCTCAAGATAAATCATAACATTAATTATTAATATATTG
2936190 CCTCAAGATAAATCATAACATTAATTATTAATATATTG
1 CCTCAAGATAAATCATAACATTAATTATTAATATATTG
2936228 CC
1 CC
2936230 ACTTTTTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (38 bp):
CCTCAAGATAAATCATAACATTAATTATTAATATATTG
Found at i:2941527 original size:21 final size:20
Alignment explanation
Indices: 2941500--2941598 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
2941490 AATCAGTTTC
2941500 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2941521 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2941542 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
*
2941562 CCAAAATCGCAACGCGAATATT
1 -CAAAATCGCAACGCG-ATTTT
2941584 -AAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2941599 ACACATAAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
19 1 0.02
20 15 0.24
21 42 0.68
22 4 0.06
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.22
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Done.