Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009042.1 Hibiscus syriacus cultivar Beakdansim tig00112452_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: 514287
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:360827 original size:20 final size:20
Alignment explanation
Indices: 360766--360834 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
360756 GATTATGTAT
*
360766 TATCGCGTTGTGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
360786 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
360806 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
360826 TATCTCGTT
1 TATCGCGTT
360835 ACGATTTTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:360900 original size:41 final size:41
Alignment explanation
Indices: 360847--360942 Score: 115
Period size: 41 Copynumber: 2.3 Consensus size: 41
360837 GATTTTGTAT
* *
360847 ATCGCATTGCGATAGTCA-GTA-TCGCATTGTGATTTTCCCAA
1 ATCGCGTTGCGAT--TCACGTATTCGCATTGCGATTTTCCCAA
* *
360888 ATCGCGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAA
1 ATCGCGTTGCGATTCACGTATTCGCATTGCGATTTTCCCAA
*
360929 TTCGCGTTGCGATT
1 ATCGCGTTGCGATT
360943 TTCCCAAATC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.04
40 2 0.04
41 44 0.92
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (41 bp):
ATCGCGTTGCGATTCACGTATTCGCATTGCGATTTTCCCAA
Found at i:360901 original size:21 final size:21
Alignment explanation
Indices: 360867--360964 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
360857 GATAGTCAGT
* *
360867 ATCGCATTGTGATTTTCCCAA
1 ATCGCGTTGCGATTTTCCCAA
* **
360888 ATCGCGTTGCGA-TTTACTTA
1 ATCGCGTTGCGATTTTCCCAA
* *
360908 TTCGCATTGCGATTTTCCCAA
1 ATCGCGTTGCGATTTTCCCAA
*
360929 TTCGCGTTGCGATTTTCCCAA
1 ATCGCGTTGCGATTTTCCCAA
360950 ATCGCGTTGCGATTT
1 ATCGCGTTGCGATTT
360965 ACTTATTCGC
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.23
21 49 0.77
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTCCCAA
Found at i:361605 original size:5 final size:5
Alignment explanation
Indices: 361595--361625 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
361585 GGAATTCTGC
*
361595 CCTTT CCTTT CCTTT CTTTT CCTTT CCTTT C
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT C
361626 GATCGCTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
CCTTT
Found at i:369369 original size:20 final size:21
Alignment explanation
Indices: 369344--369395 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
369334 TTTTCCCAAT
*
369344 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
369364 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
369385 TCGCAATGCGA
1 TCGCAATGCGA
369396 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:369409 original size:20 final size:20
Alignment explanation
Indices: 369384--369491 Score: 101
Period size: 20 Copynumber: 5.3 Consensus size: 20
369374 AATTGGGAAA
369384 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
369404 ATCGCAATACGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
369424 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
369445 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
369465 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
*
369485 TTCGCAA
1 ATCGCAA
369492 CGTGATTTAC
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.03
20 56 0.77
21 13 0.18
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:369492 original size:20 final size:20
Alignment explanation
Indices: 369446--369498 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
369436 TAATACAAAA
*
369446 TCGCAACGAGATACTGACTT
1 TCGCAACGAGATTCTGACTT
*
369466 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
*
369486 TCGCAACGTGATT
1 TCGCAACGAGATT
369499 TACATAGCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGAGATTCTGACTT
Found at i:370093 original size:19 final size:19
Alignment explanation
Indices: 370046--370087 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
370036 ACGAGAGAAT
*
370046 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
370065 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
370084 CGCA
1 CGCA
370088 TTGCGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:370118 original size:19 final size:19
Alignment explanation
Indices: 370083--370295 Score: 181
Period size: 19 Copynumber: 11.1 Consensus size: 19
370073 GAAACAAAAA
*
370083 TCGCATTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
370101 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
370120 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
370139 TCGCGTTGCGATTTTTA-T
1 TCGCGTTGCGATTTTCATT
370157 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
370177 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
370193 T-G-GTCGCGATAGTCA-T
1 TCGCGTTGCGATTTTCATT
370209 TCGCGTTGCGATCTTCGTTGCGATT
1 TCGCGTTGCGA--TT--TT-C-ATT
* **
370234 CTCTCGTTGCGATAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
370254 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
370274 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
370294 TC
1 TC
370296 AACCAAAAGA
Statistics
Matches: 161, Mismatches: 17, Indels: 33
0.76 0.08 0.16
Matches are distributed among these distances:
14 10 0.06
15 1 0.01
16 2 0.01
17 1 0.01
18 21 0.13
19 68 0.42
20 40 0.25
21 2 0.01
22 2 0.01
23 1 0.01
24 2 0.01
25 1 0.01
26 10 0.06
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:370240 original size:14 final size:13
Alignment explanation
Indices: 370212--370246 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
370202 TAGTCATTCG
370212 CGTTGCGA-TCTT
1 CGTTGCGATTCTT
370224 CGTTGCGATTCTCT
1 CGTTGCGATTCT-T
370238 CGTTGCGAT
1 CGTTGCGAT
370247 AGTCATTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.38
13 3 0.14
14 10 0.48
ACGTcount: A:0.09, C:0.26, G:0.26, T:0.40
Consensus pattern (13 bp):
CGTTGCGATTCTT
Found at i:370246 original size:44 final size:46
Alignment explanation
Indices: 370180--370266 Score: 133
Period size: 44 Copynumber: 1.9 Consensus size: 46
370170 TTTCATTTCG
* *
370180 CGTTGCGATTGTCTGGTCGCGATAGTCA-TT-CGCGTTGCGATCTT
1 CGTTGCGATTCTCTCGTCGCGATAGTCATTTCCGCGTTGCGATCTT
*
370224 CGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTCTCTCGTCGCGATAGTCATTTCCGCGTTGCGAT
370267 TCTCATTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 25 0.66
45 2 0.05
46 11 0.29
ACGTcount: A:0.11, C:0.24, G:0.28, T:0.37
Consensus pattern (46 bp):
CGTTGCGATTCTCTCGTCGCGATAGTCATTTCCGCGTTGCGATCTT
Found at i:370272 original size:20 final size:20
Alignment explanation
Indices: 370238--370295 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
370228 GCGATTCTCT
**
370238 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
370258 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
370278 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
370296 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:372723 original size:10 final size:10
Alignment explanation
Indices: 372700--372732 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
372690 GAGGGGTAAG
372700 TCTTATATTTT
1 TCTTATA-TTT
372711 TCTTATATTT
1 TCTTATATTT
372721 TCTTATATTT
1 TCTTATATTT
372731 TC
1 TC
372733 ATTGATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTATATTT
Found at i:373943 original size:19 final size:19
Alignment explanation
Indices: 373869--373934 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
373859 AAAAAGTACT
*
373869 ATCGCAATGCGAAATG-AA
1 ATCGCAACGCGAAATGAAA
*
373887 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
373901 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
373920 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
373935 TAAATTCGCG
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
13 1 0.03
14 9 0.22
16 4 0.10
18 8 0.20
19 18 0.45
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:373961 original size:19 final size:19
Alignment explanation
Indices: 373939--374003 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
373929 CGAAATTAAA
373939 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
373958 TTCGCCTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
373973 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
373991 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
374004 AGTAATTTCC
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
14 8 0.24
16 3 0.09
17 3 0.09
19 20 0.59
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:376499 original size:24 final size:24
Alignment explanation
Indices: 376465--376518 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
376455 CTGAAACATC
* *
376465 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
376489 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
376513 ATCAAA
1 ATCAAA
376519 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:377595 original size:20 final size:20
Alignment explanation
Indices: 377570--377647 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
377560 ATTCATTTGA
*
377570 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
377590 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
377610 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
377630 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
377648 CGCAATGCGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:377658 original size:34 final size:36
Alignment explanation
Indices: 377572--377659 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 36
377562 TCATTTGACT
*
377572 ATCGCAATGCGAAAATGGCTATCGCAACGCGAAAATGG
1 ATCGCAATGCGAAAATGGCTATCGCAACGAGAAAA--G
*
377610 CTATCGCAACGCGAAAATGGCTATCGCAACGAG-AAA-
1 --ATCGCAATGCGAAAATGGCTATCGCAACGAGAAAAG
377646 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
377660 TGAAAATCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 13 0.29
39 3 0.07
40 29 0.64
ACGTcount: A:0.39, C:0.23, G:0.24, T:0.15
Consensus pattern (36 bp):
ATCGCAATGCGAAAATGGCTATCGCAACGAGAAAAG
Found at i:377707 original size:19 final size:19
Alignment explanation
Indices: 377666--377733 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
377656 GAAATGAAAA
377666 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
377682 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
377699 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
377718 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
377734 TCGTTGCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 28 0.62
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:377869 original size:14 final size:14
Alignment explanation
Indices: 377850--377886 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
377840 CATCAATTAA
377850 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
377864 ACAAATCATCTTTT
1 ACAAATCAACATTT
377878 ACAAATCAA
1 ACAAATCAA
377887 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:379773 original size:20 final size:20
Alignment explanation
Indices: 379750--379803 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
379740 GAAACTTAAA
379750 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
379770 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
379790 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
379804 TGAAAATTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:379865 original size:19 final size:19
Alignment explanation
Indices: 379843--379924 Score: 104
Period size: 18 Copynumber: 4.6 Consensus size: 19
379833 GAAACACAAA
379843 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
379862 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
379880 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
379896 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
379913 TCGCATTGCGAT
1 TCGCATTGCGAT
379925 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 20 0.37
19 17 0.31
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:379943 original size:20 final size:19
Alignment explanation
Indices: 379909--379963 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
379899 TTGCGATTTT
*
379909 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
379928 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
379948 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
379964 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:379952 original size:39 final size:34
Alignment explanation
Indices: 379843--379944 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 34
379833 GAAACACAAA
379843 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTCATT
1 TCGCATTGCGA---TCATTTCGCGTTGCGATTTCATT
379880 TCGCATTGCGAT--TTT-GTCGTTGCGATTTTCATT
1 TCGCATTGCGATCATTTCG-CGTTGCGA-TTTCATT
379913 TCGCATTGCGATAGCCATTTCCGCGTTGCGAT
1 TCGCATTGCGAT---CATTT-CGCGTTGCGAT
379945 AGTCATTTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 17
0.77 0.00 0.23
Matches are distributed among these distances:
31 1 0.02
32 11 0.20
33 19 0.34
34 1 0.02
37 11 0.20
38 4 0.07
39 8 0.14
40 1 0.02
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.42
Consensus pattern (34 bp):
TCGCATTGCGATCATTTCGCGTTGCGATTTCATT
Found at i:380479 original size:18 final size:18
Alignment explanation
Indices: 380453--380497 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
380443 GTCGATCAGA
380453 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
*
380471 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
380489 TGATGGCTC
1 TGATGGCTC
380498 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGTGAGG
Found at i:382138 original size:22 final size:22
Alignment explanation
Indices: 382111--382154 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
382101 GATGGAGATA
382111 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
382133 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
382155 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:382428 original size:20 final size:19
Alignment explanation
Indices: 382322--382436 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 19
382312 CGCTTTGAAA
*
382322 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* * *
382343 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGT-AGT
* *
382363 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
382383 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
382404 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGT
382424 ATCGCATTGCGAT
1 ATCGCATTGCGAT
382437 TTTCCCAAAT
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
19 5 0.07
20 46 0.61
21 23 0.30
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:382449 original size:41 final size:41
Alignment explanation
Indices: 382404--382517 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 41
382394 ATTTTGTATT
*
382404 ATCGCATTGCGATAGTCA-GTA-TCGCATTGCGATTTTCCCAA
1 ATCGCGTTGCGAT--TCACGTATTCGCATTGCGATTTTCCCAA
* *
382445 ATCGCGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAA
1 ATCGCGTTGCGATTCACGTATTCGCATTGCGATTTTCCCAA
* * *
382486 TTCGCGTTGCGATTTACTTATTCGCATTGCGA
1 ATCGCGTTGCGATTCACGTATTCGCATTGCGA
382518 ATTGAGAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 63 0.94
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (41 bp):
ATCGCGTTGCGATTCACGTATTCGCATTGCGATTTTCCCAA
Found at i:382454 original size:21 final size:21
Alignment explanation
Indices: 382424--382500 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
382414 GATAGTCAGT
382424 ATCGCATTGCGATTTTCCCAA
1 ATCGCATTGCGATTTTCCCAA
* * **
382445 ATCGCGTTGCGA-TTTACTTA
1 ATCGCATTGCGATTTTCCCAA
*
382465 TTCGCATTGCGATTTTCCCAA
1 ATCGCATTGCGATTTTCCCAA
* *
382486 TTCGCGTTGCGATTT
1 ATCGCATTGCGATTT
382501 ACTTATTCGC
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (21 bp):
ATCGCATTGCGATTTTCCCAA
Found at i:382474 original size:20 final size:20
Alignment explanation
Indices: 382446--382517 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
382436 TTTTCCCAAA
*
382446 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
382466 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
382487 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
382507 TCGCATTGCGA
1 TCGCATTGCGA
382518 ATTGAGAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:382621 original size:20 final size:20
Alignment explanation
Indices: 382596--382641 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
382586 CAACGCGAAT
*
382596 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
382616 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
382635 TTGCGAT
1 TTGCGAT
382642 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:389769 original size:2 final size:2
Alignment explanation
Indices: 389762--389793 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
389752 TACAATCCAT
389762 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
389794 CAGCTAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:393141 original size:3 final size:3
Alignment explanation
Indices: 393133--393179 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
393123 TTAATGATAT
*
393133 TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
393180 GAAAGAACTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:395289 original size:22 final size:22
Alignment explanation
Indices: 395264--395309 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
395254 AATGTGTAAT
395264 CTACCATGAGCATTTGTGCAAG
1 CTACCATGAGCATTTGTGCAAG
395286 CTACCATGAGCATTTGTGCAAG
1 CTACCATGAGCATTTGTGCAAG
395308 CT
1 CT
395310 TTACTACTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (22 bp):
CTACCATGAGCATTTGTGCAAG
Found at i:403656 original size:53 final size:51
Alignment explanation
Indices: 403586--403687 Score: 118
Period size: 53 Copynumber: 2.0 Consensus size: 51
403576 AGGTAAAAAG
* * * *
403586 TTTAATGAATAAGTTTTGA-AACTGTTTTATGAAAGAATTTTGAGAAATGTTTA
1 TTTAATGAATAAATTTTGAGAAATGTTTGATG-AAG-ATTTT-AAAAATGTTTA
403639 TTTAATGAA-AGAATTTTGAGAAATGTTTGATGAAGATTTTAAAAATGTT
1 TTTAATGAATA-AATTTTGAGAAATGTTTGATGAAGATTTTAAAAATGTT
403688 GTCCATTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
51 8 0.19
52 6 0.14
53 19 0.44
54 10 0.23
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.42
Consensus pattern (51 bp):
TTTAATGAATAAATTTTGAGAAATGTTTGATGAAGATTTTAAAAATGTTTA
Found at i:406412 original size:10 final size:10
Alignment explanation
Indices: 406397--406425 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
406387 TACAATTGCA
406397 AATGCAATAC
1 AATGCAATAC
406407 AATGCAATAC
1 AATGCAATAC
406417 AATGCAATA
1 AATGCAATA
406426 AAGGTATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (10 bp):
AATGCAATAC
Found at i:407346 original size:13 final size:13
Alignment explanation
Indices: 407328--407366 Score: 69
Period size: 14 Copynumber: 2.9 Consensus size: 13
407318 GGTTTCAGAC
407328 CTAGAAAAAGGTA
1 CTAGAAAAAGGTA
407341 CTAGAAAAAAGGTA
1 CTAG-AAAAAGGTA
407355 CTAGAAAAAGGT
1 CTAGAAAAAGGT
407367 TCACATATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (13 bp):
CTAGAAAAAGGTA
Found at i:408435 original size:45 final size:45
Alignment explanation
Indices: 408252--408434 Score: 233
Period size: 45 Copynumber: 4.1 Consensus size: 45
408242 AATGGATGAA
** * * *
408252 CACAAATGAAAATGTGTAACTGTGCATTATTGACATAAAAGGTGC
1 CACAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGC
* * *
408297 CACAAATGAAAATGCATGACTGTGCATTATCAGCATAAAAGGTGC
1 CACAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGC
* *
408342 CACAAATGAAAATGCATAACGGTGCATTTTTTGGCATAAAA-GTGC
1 CACAAATGAAAATGCATAACGGTGCA-TTATCGGCATAAAAGGTGC
* * *
408387 CACTAATGAAAATGCATAACGGTGCATTAACGGTATAAAAGGTGC
1 CACAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGC
408432 CAC
1 CAC
408435 TCATGGTATT
Statistics
Matches: 120, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
44 10 0.08
45 99 0.82
46 11 0.09
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (45 bp):
CACAAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGC
Found at i:417572 original size:25 final size:25
Alignment explanation
Indices: 417540--417589 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
417530 TGTTCGAAGC
417540 GTAAAATATTTTCAAACAATTCATT
1 GTAAAATATTTTCAAACAATTCATT
*
417565 GTAAAATATTTTCAAACTATTCATT
1 GTAAAATATTTTCAAACAATTCATT
417590 TTTAGTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (25 bp):
GTAAAATATTTTCAAACAATTCATT
Found at i:424488 original size:21 final size:20
Alignment explanation
Indices: 424402--424559 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
424392 AAATGACCAA
**
424402 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
424421 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
424441 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
424461 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
424482 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
424503 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
424523 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
424544 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
424560 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:424588 original size:20 final size:20
Alignment explanation
Indices: 424526--424795 Score: 269
Period size: 20 Copynumber: 13.5 Consensus size: 20
424516 CGATTTTCCA
* ** *
424526 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
424546 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
424566 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
424586 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
424606 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
424626 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
424646 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
424666 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
424686 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
424706 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
424726 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
424746 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
424766 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
424786 AAATCACAAC
1 AAATCGCAAC
424796 ACTGAAATTT
Statistics
Matches: 210, Mismatches: 32, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 206 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:426158 original size:120 final size:121
Alignment explanation
Indices: 425969--426210 Score: 477
Period size: 120 Copynumber: 2.0 Consensus size: 121
425959 AAAACTGTAT
425969 GTGGCGAATGATTGCAAAGAGAATAAAAGATTGTGGAAATGTTTCAAGTTAGGACTTTTATTGAT
1 GTGGCGAATGATTGCAAAGAGAATAAAAGATTGTGGAAATGTTTCAAGTTAGGACTTTTATTGAT
426034 AAACATACATGTTCAAGAACCCAAGTTTTTCCTCACCATAGACAGGCAAACAAAAA
66 AAACATACATGTTCAAGAACCCAAGTTTTTCCTCACCATAGACAGGCAAACAAAAA
426090 GTGGCGAATGATTGCAAAGAGAATAAAAGATTGT-GAAATGTTTCAAGTTAGGACTTTTATTGAT
1 GTGGCGAATGATTGCAAAGAGAATAAAAGATTGTGGAAATGTTTCAAGTTAGGACTTTTATTGAT
426154 AAACATACATGTTCAAGAACCCAAGTTTTTCCTCACCATAGACAGGCAAACAAAAA
66 AAACATACATGTTCAAGAACCCAAGTTTTTCCTCACCATAGACAGGCAAACAAAAA
426210 G
1 G
426211 GTGTTGGGTG
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
120 87 0.72
121 34 0.28
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (121 bp):
GTGGCGAATGATTGCAAAGAGAATAAAAGATTGTGGAAATGTTTCAAGTTAGGACTTTTATTGAT
AAACATACATGTTCAAGAACCCAAGTTTTTCCTCACCATAGACAGGCAAACAAAAA
Found at i:428074 original size:19 final size:19
Alignment explanation
Indices: 428052--428221 Score: 172
Period size: 19 Copynumber: 9.7 Consensus size: 19
428042 CGCAACGAAG
*
428052 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
428071 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
428085 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
428105 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
428124 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
428143 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
428157 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
428176 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
428190 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
428209 AATCGCATTGCGA
1 AATCGCAATGCGA
428222 TTCTCCCGCG
Statistics
Matches: 127, Mismatches: 8, Indels: 32
0.76 0.05 0.19
Matches are distributed among these distances:
14 32 0.25
15 2 0.02
16 5 0.04
17 5 0.04
18 2 0.02
19 65 0.51
20 16 0.13
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:428161 original size:72 final size:66
Alignment explanation
Indices: 428039--428215 Score: 223
Period size: 72 Copynumber: 2.6 Consensus size: 66
428029 ACGGAATTAC
* * *
428039 AATCGCAACGA-AGAATCACAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGC-GAAATG
428103 AA
65 AA
*
428105 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCG
1 AATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAATCGCAAC-ATGAAAATCGCAATGCG
428169 AAATGAA
60 AAATGAA
* *
428176 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
428216 TTGCGATTCT
Statistics
Matches: 98, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
66 35 0.36
67 1 0.01
68 2 0.02
69 2 0.02
70 1 0.01
71 16 0.16
72 40 0.41
73 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (66 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGAAATGA
A
Found at i:428162 original size:14 final size:14
Alignment explanation
Indices: 428143--428197 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
428133 GCGAAATGAA
428143 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
428157 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
428176 AATCGCAACGAGAG
1 AATCGCAACGAGAG
428190 AATCGCAA
1 AATCGCAA
428198 TGCGAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:428166 original size:33 final size:33
Alignment explanation
Indices: 428039--428215 Score: 232
Period size: 33 Copynumber: 5.2 Consensus size: 33
428029 ACGGAATTAC
*
428039 AATCGCAACGA-AGAATCACAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
428071 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
*
428105 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
428143 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
428176 AATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
428209 AATCGCA
1 AATCGCA
428216 TTGCGATTCT
Statistics
Matches: 131, Mismatches: 6, Indels: 15
0.86 0.04 0.10
Matches are distributed among these distances:
31 1 0.01
32 8 0.06
33 71 0.54
34 16 0.12
36 3 0.02
38 16 0.12
39 16 0.12
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:428261 original size:14 final size:14
Alignment explanation
Indices: 428242--428278 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
428232 CATCAATTAC
428242 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
428256 ACAAATCATCTTTT
1 ACAAATCAACTTTT
428270 ACAAATCAA
1 ACAAATCAA
428279 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:430211 original size:19 final size:19
Alignment explanation
Indices: 430171--430235 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
430161 TAGTTTACTT
*
430171 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
430191 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
*
430210 TCGCAACGCGAAA-TGAAA
1 TCGCAACGCGAAACTAAAA
430228 TCGCAACG
1 TCGCAACG
430236 ACAGAATCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.27
19 17 0.41
20 13 0.32
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:430245 original size:14 final size:14
Alignment explanation
Indices: 430226--430282 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
430216 CGCGAAATGA
*
430226 AATCGCAACGACAG
1 AATCGCAACGAAAG
430240 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
430257 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
430273 AATCGCAACG
1 AATCGCAACG
430283 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:430267 original size:33 final size:32
Alignment explanation
Indices: 430208--430298 Score: 155
Period size: 33 Copynumber: 2.8 Consensus size: 32
430198 GCGAAACCAA
*
430208 AATCGCAACGCGAAATGAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAATCGCAACGAAAG
*
430240 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATG-AAATCGCAACGAAAG
430273 AATCGCAACGCGAAATGAAATCGCAA
1 AATCGCAACGCGAAATGAAATCGCAA
430299 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 25 0.45
33 30 0.55
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (32 bp):
AATCGCAACGCGAAATGAAATCGCAACGAAAG
Found at i:430295 original size:51 final size:51
Alignment explanation
Indices: 430188--430303 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 51
430178 ACGAAACTTA
* *
430188 AAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAATCGCAACGACAG
1 AAATCGCAATGCGAAACCAAAATCGCAAC-CGAAATGAAATCGCAACGAAAG
**
430240 -AATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-AATCGCAACGCGAAATG
1 AAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAATCGCAA--CGAAA-G
430290 AAATCGCAATGCGA
1 AAATCGCAATGCGA
430304 TTTTGGTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
47 8 0.14
48 1 0.02
49 9 0.16
50 1 0.02
51 37 0.66
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (51 bp):
AAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAATCGCAACGAAAG
Found at i:430321 original size:19 final size:19
Alignment explanation
Indices: 430299--430427 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
430289 GAAATCGCAA
430299 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
430318 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
430332 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
430351 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
430365 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
430384 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
430403 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
430423 TGCGA
1 TGCGA
430428 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:430341 original size:33 final size:33
Alignment explanation
Indices: 430299--430390 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
430289 GAAATCGCAA
430299 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
430332 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
430365 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
430391 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:430609 original size:92 final size:93
Alignment explanation
Indices: 430474--430922 Score: 812
Period size: 92 Copynumber: 4.9 Consensus size: 93
430464 ATGGATTGCA
430474 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
430538 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
430566 TTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
430630 TAGCAGAA-TGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
430657 TTACTTTCAACC-AAAGAC-AAA-AAACAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
430718 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
430746 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAG-ATACACAG-T
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
430808 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
430836 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
430901 TAGCAGAA-TGGCAGCAACCGAA
66 TAGCAGAATTGGCAGCAACCGAA
430923 TAAAGCAACC
Statistics
Matches: 347, Mismatches: 2, Indels: 16
0.95 0.01 0.04
Matches are distributed among these distances:
88 42 0.12
89 36 0.10
90 68 0.20
91 71 0.20
92 114 0.33
93 16 0.05
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:430855 original size:180 final size:184
Alignment explanation
Indices: 430474--430922 Score: 808
Period size: 180 Copynumber: 2.5 Consensus size: 184
430464 ATGGATTGCA
430474 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
430538 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTA
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTA
430603 TTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATGGCAGCAACCGAACAAAT
131 TTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATGGCAGCAACCGAACAAAT
*
430657 TTACTTTCAACC-AAAGAC-AAA-AAACAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
430718 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACT
430782 ATTTCACAGTGTTAAAG-ATACACAG-TTAGCAGAATTGGCAGCAACCGAACAAAT
130 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAA-TGGCAGCAACCGAACAAAT
430836 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
430901 TAGCAGAA-TGGCAGCAACCGAA
66 TAGCAGAATTGGCAGCAACCGAA
430923 TAAAGCAACC
Statistics
Matches: 257, Mismatches: 2, Indels: 15
0.94 0.01 0.05
Matches are distributed among these distances:
178 9 0.04
179 39 0.15
180 103 0.40
181 25 0.10
182 22 0.09
183 52 0.20
184 7 0.03
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (184 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTA
TTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATGGCAGCAACCGAACAAAT
Found at i:430931 original size:13 final size:13
Alignment explanation
Indices: 430913--430939 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
430903 GCAGAATGGC
430913 AGCAACCGAATAA
1 AGCAACCGAATAA
430926 AGCAACCGAATAA
1 AGCAACCGAATAA
430939 A
1 A
430940 TTACTAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.15, T:0.07
Consensus pattern (13 bp):
AGCAACCGAATAA
Found at i:432660 original size:33 final size:33
Alignment explanation
Indices: 432620--432733 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
432610 TCTTTTGGTT
432620 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
432653 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
432686 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
432719 G-AATGAAAATCGCAA
1 GAAATGAAAATCGCAA
432734 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
32 14 0.18
33 65 0.82
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:432666 original size:19 final size:18
Alignment explanation
Indices: 432622--432738 Score: 87
Period size: 14 Copynumber: 7.1 Consensus size: 18
432612 TTTTGGTTGA
432622 AATGAAAATCGCAA--CG
1 AATGAAAATCGCAACGCG
*
432638 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
432654 AAATGAAAATCGCAA--C-
1 -AATGAAAATCGCAACGCG
* *
432670 TA-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
432687 AAATGAAAATCGCAA--CG
1 -AATGAAAATCGCAACGCG
*
432704 -A-GAGAATCGCAACGCG
1 AATGAAAATCGCAACGCG
*
432720 AATGAAAATCGCAATGCG
1 AATGAAAATCGCAACGCG
432738 A
1 A
432739 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 26
0.69 0.08 0.23
Matches are distributed among these distances:
14 30 0.38
15 3 0.04
16 5 0.06
17 4 0.05
18 16 0.21
19 20 0.26
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (18 bp):
AATGAAAATCGCAACGCG
Found at i:432782 original size:33 final size:33
Alignment explanation
Indices: 432734--432814 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
432724 AAAATCGCAA
**
432734 TGCGATTTTGGTTTCGCGTTGCGATTCTCTAGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
*
432767 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
432800 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
432815 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
Found at i:432802 original size:14 final size:14
Alignment explanation
Indices: 432750--432806 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
432740 TTTGGTTTCG
432750 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
432764 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
432783 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
432797 CGTTGCGATT
1 CGTTGCGATT
432807 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:432847 original size:41 final size:41
Alignment explanation
Indices: 432790--432867 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
432780 TCGCGTTGCG
*
432790 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
432831 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
432868 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:432852 original size:20 final size:21
Alignment explanation
Indices: 432791--432866 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
432781 CGCGTTGCGA
432791 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
432812 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
432832 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
432853 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
432867 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:432986 original size:32 final size:32
Alignment explanation
Indices: 432947--433015 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
432937 ACTAACTTGA
* *
432947 AAATCGCAACGAGAGAATAGCAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCAAAATG
* *
432979 AAATCGCAACGACAGAATCGTAACGCAAAATG
1 AAATCGCAACGACAGAATAGCAACGCAAAATG
433011 AAATC
1 AAATC
433016 TAAGTGAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (32 bp):
AAATCGCAACGACAGAATAGCAACGCAAAATG
Found at i:433238 original size:22 final size:22
Alignment explanation
Indices: 433186--433240 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
433176 TGGTTGTGAG
**
433186 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
433208 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
433230 GGATTTCTTCG
1 GGATTTCTTCG
433241 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:433447 original size:20 final size:20
Alignment explanation
Indices: 433382--433534 Score: 150
Period size: 20 Copynumber: 7.7 Consensus size: 20
433372 CTTTAAATAT
433382 CGCGTTGCGA-TTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
433401 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
433423 -TCGTTGCAATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
433442 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
433462 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
433482 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
433502 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
433522 CGCGTTGCGATTT
1 CGCGTTGCGATTT
433535 TGGAAAATCG
Statistics
Matches: 110, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
19 12 0.11
20 83 0.75
21 13 0.12
22 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:433508 original size:40 final size:40
Alignment explanation
Indices: 433381--433534 Score: 168
Period size: 40 Copynumber: 3.9 Consensus size: 40
433371 GCTTTAAATA
*
433381 TCGCGTTGCGA-TTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * * *
433421 TATCGTTGCAATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
433461 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
433501 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
433535 TGGAAAATCG
Statistics
Matches: 93, Mismatches: 18, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
40 73 0.78
41 20 0.22
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:433551 original size:21 final size:21
Alignment explanation
Indices: 433521--433603 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
433511 ATTTTCATAT
*
433521 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
433542 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
433563 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
433584 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
433604 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:433594 original size:42 final size:43
Alignment explanation
Indices: 433501--433599 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
433491 ATTTATGTGT
* *
433501 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
433542 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
433584 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
433600 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:436617 original size:39 final size:38
Alignment explanation
Indices: 436540--436627 Score: 131
Period size: 39 Copynumber: 2.3 Consensus size: 38
436530 TACAGCTGTT
*
436540 GCTGCTGCTGTTGTGCTTAGGACATGGCTGCGGCTGTG
1 GCTGCTGCTGTTGTGCTTAGGACATGGCTGCGGATGTG
* * *
436578 GCTGCTGCTGTTGTGGCTTAGGAGATGGTTGTGGATGTG
1 GCTGCTGCTGTTGT-GCTTAGGACATGGCTGCGGATGTG
436617 GCTGCTGCTGT
1 GCTGCTGCTGT
436628 GGTTGTTGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 14 0.31
39 31 0.69
ACGTcount: A:0.08, C:0.17, G:0.41, T:0.34
Consensus pattern (38 bp):
GCTGCTGCTGTTGTGCTTAGGACATGGCTGCGGATGTG
Found at i:442004 original size:21 final size:21
Alignment explanation
Indices: 441962--442000 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
441952 TTAATTGGTA
*
441962 TGATTGAAAAAATTAAAAGAT
1 TGATGGAAAAAATTAAAAGAT
441983 TGATGGAAAAAA-TAAAAG
1 TGATGGAAAAAATTAAAAG
442001 GATTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (21 bp):
TGATGGAAAAAATTAAAAGAT
Found at i:442270 original size:15 final size:15
Alignment explanation
Indices: 442250--442283 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
442240 TAGTATTATT
442250 AATTT-AATTTATAAA
1 AATTTAAATTT-TAAA
442265 AATTTAAATTTTAAA
1 AATTTAAATTTTAAA
442280 AATT
1 AATT
442284 CAATGTATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTAAATTTTAAA
Found at i:442382 original size:20 final size:20
Alignment explanation
Indices: 442357--442394 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
442347 CATTTCTTTA
* *
442357 ATAAATTTTAATTTTTAAAG
1 ATAAATTATAAATTTTAAAG
442377 ATAAATTATAAATTTTAA
1 ATAAATTATAAATTTTAA
442395 TTGTTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
ATAAATTATAAATTTTAAAG
Found at i:443224 original size:15 final size:15
Alignment explanation
Indices: 443204--443235 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
443194 TCTTCTCTGT
443204 TTGTTGTTGTTATTG
1 TTGTTGTTGTTATTG
443219 TTGTTGTTGTTATTG
1 TTGTTGTTGTTATTG
443234 TT
1 TT
443236 TGTTTCTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.25, T:0.69
Consensus pattern (15 bp):
TTGTTGTTGTTATTG
Found at i:451509 original size:10 final size:10
Alignment explanation
Indices: 451496--451525 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
451486 TATGTAAAAT
451496 TTAATATTAA
1 TTAATATTAA
451506 TTAATATTAA
1 TTAATATTAA
*
451516 TTAAAATTAA
1 TTAATATTAA
451526 AATAATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TTAATATTAA
Found at i:453215 original size:33 final size:33
Alignment explanation
Indices: 453149--453215 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
453139 AAAGATAAAT
* * *
453149 TTATCATTTGAATCTTAAATATTTTTCTTATGA
1 TTATAATTTGAATATTAAATATTTTTCTAATGA
453182 TTATAATTTGAATATTAAATTATTTTT-TAATGA
1 TTATAATTTGAATATTAAA-TATTTTTCTAATGA
453215 T
1 T
453216 AATATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (33 bp):
TTATAATTTGAATATTAAATATTTTTCTAATGA
Found at i:459559 original size:16 final size:16
Alignment explanation
Indices: 459535--459566 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
459525 TATCGCCGAC
*
459535 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
459551 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
459567 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:461852 original size:20 final size:20
Alignment explanation
Indices: 461829--461884 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
461819 AAATAACCAA
461829 AAATTTCGCAACGCGATCTC
1 AAATTTCGCAACGCGATCTC
* * *
461849 AAATTTCGCAACCCAGTTTTC
1 AAATTTCGCAACGC-GATCTC
461870 -AATTTCGCAACGCGA
1 AAATTTCGCAACGCGA
461885 ATATGTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 1 0.03
20 25 0.83
21 4 0.13
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (20 bp):
AAATTTCGCAACGCGATCTC
Found at i:461923 original size:21 final size:21
Alignment explanation
Indices: 461894--461960 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
461884 AATATGTAAA
*
461894 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATATTCCAAAT
*
461915 TCGCGTTGCGATATTCCAAAT
1 TCGCATTGCGATATTCCAAAT
** *
461936 TCGCAACGCGATAGT-CAAAT
1 TCGCATTGCGATATTCCAAAT
461956 TCGCA
1 TCGCA
461961 ACGCGAAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 10 0.25
21 30 0.75
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATATTCCAAAT
Found at i:461956 original size:20 final size:20
Alignment explanation
Indices: 461931--461975 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
461921 TGCGATATTC
*
461931 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
461951 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
461971 CAAAT
1 CAAAT
461976 GTTTTTACGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:466487 original size:12 final size:12
Alignment explanation
Indices: 466466--466499 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
466456 GGTTGTGGGT
*
466466 TTTGAGATTGTG
1 TTTGATATTGTG
466478 TTTGATATTGTG
1 TTTGATATTGTG
*
466490 TTTGGTATTG
1 TTTGATATTG
466500 GAAATGCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:467273 original size:20 final size:20
Alignment explanation
Indices: 467237--467407 Score: 136
Period size: 20 Copynumber: 8.6 Consensus size: 20
467227 ACTAAAACCT
*
467237 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
467256 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
**
467275 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGC
**
467295 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGC
*
467315 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAATTT-GAAATTCGC
** *
467336 AATGCG-ATTT-ACATATTCAC
1 GTTGCGAATTTGA-A-ATTCGC
* * *
467356 GTTGCGAAATTGGAAACT-GG
1 GTTGCG-AATTTGAAATTCGC
* *
467376 GTTGCGAAATTGGAATTCGC
1 GTTGCGAATTTGAAATTCGC
467396 GTTGCGAATTTG
1 GTTGCGAATTTG
467408 TTGGTCATTT
Statistics
Matches: 119, Mismatches: 24, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
18 1 0.01
19 34 0.29
20 67 0.56
21 12 0.10
22 4 0.03
23 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:467297 original size:39 final size:40
Alignment explanation
Indices: 467251--467326 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 40
467241 CGAAATTAAA
467251 TTCGCGTTGCGAATTTGAAATTC-AGTTGCGAATTTGACT
1 TTCGCGTTGCGAATTTGAAATTCGAGTTGCGAATTTGACT
** *
467290 TTCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTG
1 TTCGCGTTGCGAATTTGAAATTCGAGTTGCGAATTTG
467327 GAAAATCGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 21 0.64
40 12 0.36
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.39
Consensus pattern (40 bp):
TTCGCGTTGCGAATTTGAAATTCGAGTTGCGAATTTGACT
Found at i:467929 original size:35 final size:35
Alignment explanation
Indices: 467881--468085 Score: 214
Period size: 36 Copynumber: 5.5 Consensus size: 35
467871 TATATATAAT
*
467881 TTTTAAAATATTTTGAAAATAAATATAATATATTG
1 TTTTAAAACATTTTGAAAATAAATATAATATATTG
* * *
467916 TTTTAAAACATTTTTAAAAATATATATATTATATTG
1 TTTTAAAACA-TTTTGAAAATAAATATAATATATTG
**
467952 TTTTTAAAACATTTTGAAAATAAATATAATATATAA
1 -TTTTAAAACATTTTGAAAATAAATATAATATATTG
* *
467988 TTTTAAAACATTTTTAATATATATATATATATATATTATATATT
1 TTTTAAAACA-TTTTGA-A-A-ATA-A-ATATA-A-TATAT-TG
*
468032 TTTTAAAACA-TTTGAAAATAAATATAATATATAG
1 TTTTAAAACATTTTGAAAATAAATATAATATATTG
468066 TTTTTAAAACATTTTGAAAA
1 -TTTTAAAACATTTTGAAAA
468086 CATATATATT
Statistics
Matches: 142, Mismatches: 15, Indels: 25
0.78 0.08 0.14
Matches are distributed among these distances:
35 34 0.24
36 56 0.39
37 16 0.11
38 2 0.01
39 6 0.04
40 2 0.01
41 6 0.04
42 5 0.04
43 5 0.04
44 10 0.07
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (35 bp):
TTTTAAAACATTTTGAAAATAAATATAATATATTG
Found at i:468035 original size:79 final size:79
Alignment explanation
Indices: 467935--468094 Score: 252
Period size: 79 Copynumber: 2.0 Consensus size: 79
467925 ATTTTTAAAA
467935 ATATATATATTATATTGTTTTTAAAACATTTTGAAAATAAATATAATATATA-ATTTTAAAACAT
1 ATATATATATTATATTGTTTTTAAAACA-TTTGAAAATAAATATAATATATAGATTTTAAAACAT
* * *
467999 TTTTAATATATATAT
65 TTTGAAAACATATAT
*
468014 ATATATATATTATATAT-TTTTTAAAACATTTGAAAATAAATATAATATATAGTTTTTAAAACAT
1 ATATATATATTATAT-TGTTTTTAAAACATTTGAAAATAAATATAATATATAGATTTTAAAACAT
468078 TTTGAAAACATATAT
65 TTTGAAAACATATAT
468093 AT
1 AT
468095 TGGTAGAGCA
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
78 23 0.31
79 51 0.68
80 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (79 bp):
ATATATATATTATATTGTTTTTAAAACATTTGAAAATAAATATAATATATAGATTTTAAAACATT
TTGAAAACATATAT
Found at i:468057 original size:43 final size:42
Alignment explanation
Indices: 467899--468064 Score: 117
Period size: 43 Copynumber: 4.2 Consensus size: 42
467889 TATTTTGAAA
** *
467899 ATAA-ATATAATATATTGTTTTAAAACATTTT--TAA-AAAT
1 ATAATATATAATATATAATTTTAAAACATTTTGAAAATAAAT
* **
467937 AT-ATATATTATAT-TGTTTTTAAAACATTTTG-----AAA-
1 ATAATATATAATATATAATTTTAAAACATTTTGAAAATAAAT
* * *
467971 ATAA-ATATAATATATAATTTTAAAACATTTTTAATATATAT
1 ATAATATATAATATATAATTTTAAAACATTTTGAAAATAAAT
* *
468012 ATATATATATATTATATATTTTTTAAAACA-TTTGAAAATAAAT
1 ATA-ATATATAATATATA-ATTTTAAAACATTTTGAAAATAAAT
468055 ATAATATATA
1 ATAATATATA
468065 GTTTTTAAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 22
0.74 0.09 0.16
Matches are distributed among these distances:
34 10 0.10
35 19 0.19
37 16 0.16
38 10 0.10
40 2 0.02
41 3 0.03
42 8 0.08
43 24 0.24
44 10 0.10
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (42 bp):
ATAATATATAATATATAATTTTAAAACATTTTGAAAATAAAT
Found at i:469720 original size:25 final size:26
Alignment explanation
Indices: 469680--469730 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
469670 ATTTTTATTT
**
469680 ATTATTATTATTATTATGT-TTTTTA
1 ATTATTATTAGAATTATGTATTTTTA
*
469705 ATTATTATTAGAATTATTTATTTTTA
1 ATTATTATTAGAATTATGTATTTTTA
469731 CTTCATATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (26 bp):
ATTATTATTAGAATTATGTATTTTTA
Found at i:469785 original size:18 final size:18
Alignment explanation
Indices: 469764--469801 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
469754 ACTTTTTAAA
469764 TAATTGTTT-TTATTTATT
1 TAATT-TTTCTTATTTATT
469782 TAATTTTTCTTATTTATT
1 TAATTTTTCTTATTTATT
469800 TA
1 TA
469802 TTTATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TAATTTTTCTTATTTATT
Found at i:469821 original size:11 final size:11
Alignment explanation
Indices: 469805--469830 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
469795 TTATTTATTT
469805 ATTTAATTTTA
1 ATTTAATTTTA
469816 ATTTAATTTTA
1 ATTTAATTTTA
469827 ATTT
1 ATTT
469831 CTTTGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTAATTTTA
Found at i:469830 original size:26 final size:25
Alignment explanation
Indices: 469770--469851 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
469760 TAAATAATTG
*
469770 TTTTTATTTATTTAATTTTTCTTAT
1 TTTTTATTTATTTAATTTTTCTTAA
469795 TTATTTATTTATTTAATTTTAAT-TTAA
1 TT-TTTATTTATTTAATTTT--TCTTAA
* * * * *
469822 TTTTAATTTCTTTGATTTTTTTTAT
1 TTTTTATTTATTTAATTTTTCTTAA
469847 TTTTT
1 TTTTT
469852 CCATTGATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
24 1 0.02
25 9 0.19
26 31 0.66
27 5 0.11
28 1 0.02
ACGTcount: A:0.22, C:0.02, G:0.01, T:0.74
Consensus pattern (25 bp):
TTTTTATTTATTTAATTTTTCTTAA
Found at i:469895 original size:20 final size:20
Alignment explanation
Indices: 469860--469909 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
469850 TTCCATTGAT
*
469860 TTATTTTCTTTATATTAC-TA
1 TTATTTTATTTATATT-CTTA
* *
469880 TTATTTTATTTTTATTCTTT
1 TTATTTTATTTATATTCTTA
469900 TTATTTTATT
1 TTATTTTATT
469910 GTTTTTGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTTTATTTATATTCTTA
Found at i:469907 original size:14 final size:15
Alignment explanation
Indices: 469883--469937 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
469873 ATTACTATTA
469883 TTTTATTTTTATTCT
1 TTTTATTTTTATTCT
*
469898 TTTTA-TTTTATTGT
1 TTTTATTTTTATTCT
*
469912 TTTTGTCTTTTCATT-T
1 TTTTAT-TTTT-ATTCT
*
469928 ATTTATTTTT
1 TTTTATTTTT
469938 TTACTTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 12 0.36
15 9 0.27
16 9 0.27
17 3 0.09
ACGTcount: A:0.13, C:0.05, G:0.04, T:0.78
Consensus pattern (15 bp):
TTTTATTTTTATTCT
Found at i:469936 original size:22 final size:22
Alignment explanation
Indices: 469883--469937 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
469873 ATTACTATTA
* *
469883 TTTTATTTTTATTCTTTTTATT
1 TTTTATTTTTAGTCTTTTCATT
*
469905 TTATTGTTTTT-GTCTTTTCATT
1 TT-TTATTTTTAGTCTTTTCATT
469927 TATTTATTTTT
1 T-TTTATTTTT
469938 TTACTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.13, C:0.05, G:0.04, T:0.78
Consensus pattern (22 bp):
TTTTATTTTTAGTCTTTTCATT
Found at i:471765 original size:2 final size:2
Alignment explanation
Indices: 471758--471793 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
471748 GTGCACATAA
471758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
471794 AAAGTGATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:472054 original size:20 final size:20
Alignment explanation
Indices: 471952--472055 Score: 90
Period size: 20 Copynumber: 5.2 Consensus size: 20
471942 GAATATATCA
471952 GGTTGAAATTTGAC-AAATCC
1 GGTTGAAATTTGACAAAAT-C
* ** *
471972 AGTTTTAATTTGACAAAATA
1 GGTTGAAATTTGACAAAATC
471992 GG-T-AACGATTTTGACAAAATC
1 GGTTGAA--A-TTTGACAAAATC
*
472013 GATTGGAAA-TTGACAAAATC
1 GGTT-GAAATTTGACAAAATC
472033 GGTTGAAATTTGACAAAATC
1 GGTTGAAATTTGACAAAATC
472053 GGT
1 GGT
472056 AAAGAGCTAC
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.01
19 5 0.07
20 41 0.61
21 16 0.24
22 2 0.03
24 2 0.03
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (20 bp):
GGTTGAAATTTGACAAAATC
Found at i:473175 original size:3 final size:3
Alignment explanation
Indices: 473167--473203 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
473157 TCTATAGTTC
473167 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
473204 TCTCTTCACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:482999 original size:18 final size:17
Alignment explanation
Indices: 482958--483009 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
482948 AGATGTAAGC
*
482958 TAAATTTTGTATTTGAA
1 TAAATTTTGTATGTGAA
482975 TAGAATTTTGTATGTGAA
1 TA-AATTTTGTATGTGAA
*
482993 TGAAATTATGTATGTGA
1 T-AAATTTTGTATGTGA
483010 TGAGCAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 2 0.06
18 28 0.90
19 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (17 bp):
TAAATTTTGTATGTGAA
Found at i:484752 original size:20 final size:21
Alignment explanation
Indices: 484703--484744 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
484693 AGGCATAAAC
484703 ATAATGTATCGATACTTATTAT
1 ATAA-GTATCGATACTTATTAT
484725 ATAAGTATCGATACTT-TTAT
1 ATAAGTATCGATACTTATTAT
484745 TCCAGTATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (21 bp):
ATAAGTATCGATACTTATTAT
Found at i:484930 original size:21 final size:20
Alignment explanation
Indices: 484906--484944 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
484896 CGTAAACATA
484906 AAGTATCGATACTTATTATAT
1 AAGTATCGATACTT-TTATAT
*
484927 AAGTATCGATGCTTTTAT
1 AAGTATCGATACTTTTAT
484945 TCCAATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (20 bp):
AAGTATCGATACTTTTATAT
Found at i:485271 original size:199 final size:199
Alignment explanation
Indices: 484627--485715 Score: 1393
Period size: 199 Copynumber: 5.5 Consensus size: 199
484617 TTTTGAAATG
* * *
484627 TATTACTTTAAAGTAATATGTAAATTTACAATGTAAACGGTAAAAATCTATCGATTTAATGATAA
1 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAA
* * * * * * *
484692 TAGGCATAAACAT-AATGTATCGATACTTATTATATAAGTATCGATACTTTTATTCCAGTATGCA
66 TAGGCGTAAACATCAA-GTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCT
* **
484756 TCTCAAGCAATTTG-AACGCACAAAGTATCGATACACCTGTATAAAGTATCGATAC-AAAGAATT
130 TCTCAA-CAATTTGCAA-GCACAAAGTATCGATACACATGTATAAAGTATCGATACGCGA-AATT
* *
484819 TTGAAACT
192 TCGAAACC
*
484827 TATTTCTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACTC-GTTTAATGATA
1 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTAC-CGGTTTAATGATA
* * * * * *
484891 ATAGGCGTAAACATAAAGTATCGATACTTATTATATAAGTATCGATGCTTTTATTCCAATATG-T
65 ATAGGCGTAAACATCAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCT
* * * ** *
484955 ATCTCAAACAATTTGCATGCAAAAAAGAATCGATACACATGTATAAAGTATCGATACTTGTAATT
130 -TCTC-AACAATTTGCAAGC-ACAAAGTATCGATACACATGTATAAAGTATCGATACGCGAAATT
*
485020 TCAAAACC
192 TCGAAACC
* * * *
485028 TATTACTATAAAGTAATACGTAAATTTACAATGTATACGGTAAAAATCTACCGGTTTAATTATAA
1 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAA
* * * *
485093 TAGACGTAAACATCATGTATTGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGTTT
66 TAGGCGTAAACATCAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTT
* * * *
485158 ATCAACAATTTCCAAGAACAAAGTATCGATACACATGTATACAA-TATCGATACGCGAAATTTCA
131 CTCAACAATTTGCAAGCACAAAGTATCGATACACATGTATA-AAGTATCGATACGCGAAATTTCG
485222 AAACC
195 AAACC
* * ** *
485227 GATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGCCTACTGGTTTAATGATAA
1 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAA
* **
485292 TAGGTGTAAACATCAAGTATCGATACACTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTT
66 TAGGCGTAAACATCAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTT
* * *
485357 CTCAATAATTTGCAAGCACAAAGTATCGATACACATGTATAAAGTATCGATATG-TAGAATTTCG
131 CTCAACAATTTGCAAGCACAAAGTATCGATACACATGTATAAAGTATCGATACGCGA-AATTTCG
485421 AAACC
195 AAACC
* * * * * *
485426 GATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAATTCTATCAGTTTAATGAAAA
1 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAA
* * *
485491 TAGGCGTAAACATCAAGTATCAATACGTTTTGTATAGGTATCGATACTTTTAGTCCAATATGATT
66 TAGGCGTAAACATCAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTT
* * *
485556 CTCAACAATTTGCATGCACAGAGTATCGATACACATGTATAAAGTATCGATACGCGGAATTTCGA
131 CTCAACAATTTGCAAGCACAAAGTATCGATACACATGTATAAAGTATCGATACGCGAAATTTCGA
485621 AACC
196 AACC
* * * * *
485625 TATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACAGGTATATTGATAA
1 TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAA
* *
485690 TAGGCATAAATA-CAAGTATCGATACT
66 TAGGCGTAAACATCAAGTATCGATACT
485716 GTCTATATAG
Statistics
Matches: 783, Mismatches: 93, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
198 15 0.02
199 463 0.59
200 142 0.18
201 162 0.21
202 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (199 bp):
TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAA
TAGGCGTAAACATCAAGTATCGATACTTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTT
CTCAACAATTTGCAAGCACAAAGTATCGATACACATGTATAAAGTATCGATACGCGAAATTTCGA
AACC
Found at i:485784 original size:20 final size:20
Alignment explanation
Indices: 485752--485828 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
485742 ATAGTTAACG
*
485752 AATTTGACTAAACCGATTAA
1 AATTTGACAAAACCGATTAA
* * * *
485772 AAATTGACAAAACTGGTTGA
1 AATTTGACAAAACCGATTAA
**
485792 AATTTGACAAAACCGATTTT
1 AATTTGACAAAACCGATTAA
*
485812 AATTTGAGAAAACCGAT
1 AATTTGACAAAACCGAT
485829 AAAGAGATAC
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (20 bp):
AATTTGACAAAACCGATTAA
Found at i:488809 original size:180 final size:181
Alignment explanation
Indices: 488342--488885 Score: 643
Period size: 180 Copynumber: 3.0 Consensus size: 181
488332 AAGTATCGAT
* *
488342 ATACTTAGAATTTC-GAAACCTATTATTTTAAAGTAATATGTAAATTTACAATGTAAACGGTAAA
1 ATACTTAGAATTTCTGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
** * * * * *
488406 AATCTATTGGTTTAATGATAATAGGT-GTAAATATAATGTATCAATACTTTTTTTTATAGGTATC
66 AATCTACCGGTTTAATGATAATA-GTCGTAAATATAAAGTATCGATACATTTATATATAGGTATC
* * * * *
488470 GGTACTTTTATTCCAGTGTGTTTCTCAAACAATTTGCACGCAAAAAAAGTATTG
130 GATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACGC--AAAATGTATCG
* ** * * * *
488524 ATATTTTTAA-TTCTGAAACCTATTACTATAAAGTAATAGTTAAATTAACAATGTAAAGGGTAAA
1 ATACTTAGAATTTCTGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
* * * * * * * ** *
488588 AGTTTACCAGTATAATGATCATAGGCGTATATACCAAGTATCGATAC-TTTATATATAGGTATCA
66 AATCTACCGGTTTAATGATAATAGTCGTAAATATAAAGTATCGATACATTTATATATAGGTATCG
* *
488652 ATACTTTTAGTT-CAGTATGCATCTCAAACAATTTGCACGCAAAATGCATCG
131 ATACTTTTA-TTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATGTATCG
* *
488703 ATACTCAGAATTTCTGAAACCGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
1 ATACTTAGAATTTCTGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
* * * *
488768 AATCTACCGGTTTAATGGTAATAGTCATAAACATAAAGTATCGATACATTTA-ATATAGGTTTCG
66 AATCTACCGGTTTAATGATAATAGTCGTAAATATAAAGTATCGATACATTTATATATAGGTATCG
*
488832 ATACTTTT-TTCCAATATGCTTCTCAAACAATTTGCACGCAAAATGTATCG
131 ATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATGTATCG
488882 ATAC
1 ATAC
488886 ACATATATAA
Statistics
Matches: 298, Mismatches: 58, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
178 2 0.01
179 54 0.18
180 102 0.34
181 55 0.18
182 85 0.29
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (181 bp):
ATACTTAGAATTTCTGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAA
AATCTACCGGTTTAATGATAATAGTCGTAAATATAAAGTATCGATACATTTATATATAGGTATCG
ATACTTTTATTCCAGTATGCTTCTCAAACAATTTGCACGCAAAATGTATCG
Found at i:489205 original size:126 final size:125
Alignment explanation
Indices: 488902--489219 Score: 365
Period size: 128 Copynumber: 2.5 Consensus size: 125
488892 ATAAATTTTT
* * * * * *
488902 TATATTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTTAATTTACAATGAAAATGATAAA
1 TATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACATGGTAAA
* *
488967 AGTCAATCAGTATAATGATAATAGGCGTAAATATCAAGTATCGATAAACATGTATAAAGTA
66 AGTCAACCAGTATAATGAAAATAGGCGTAAATATCAAGTATCGAT-AACATGTATAAAGTA
* ** *
489028 TCGATACGTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGGTA
1 T--ATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACATGGTA
** * * *
489093 AACTTTTCTACCGGTATAATGAAAATAGTCGT-AATATACAAGTATCGAT-AC-TGTCATATAAG
64 AA--AGTCAACCAGTATAATGAAAATAGGCGTAAATAT-CAAGTATCGATAACATGT-ATA-AAG
489155 TA
124 TA
* *
489157 T-TTCTTATAATTTCGAAACCTATTACTATAAAGTAATAGGTAAATTAACAATGTACATGGTAA
1 TATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACATGGTAA
489220 TATGTTGATA
Statistics
Matches: 162, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
126 57 0.35
127 3 0.02
128 59 0.36
129 11 0.07
130 32 0.20
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (125 bp):
TATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACATGGTAAA
AGTCAACCAGTATAATGAAAATAGGCGTAAATATCAAGTATCGATAACATGTATAAAGTA
Found at i:489609 original size:225 final size:226
Alignment explanation
Indices: 489217--489822 Score: 952
Period size: 225 Copynumber: 2.7 Consensus size: 226
489207 ATGTACATGG
* *
489217 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAATCTATTTTGTTATCGTCGTATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTA
* * * * * **
489282 AGACCCCATCAGCTTTAAACAAGCGCTGCCTATTAAATTAAATAATCTTTACTTGTTATGTTATT
66 AGGCCCCATCAACTTTAAACAAGCGCTACCTATTACATTAAATAAACGCTACTTGTTATGTTATT
* *
489347 ATGGTTGATAATGTGTCCAATAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAG
131 ATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAG
489412 CTTAAAATTTGGTAACATTTTAGGCGCTACC
196 CTTAAAATTTGGTAACATTTTAGGCGCTACC
*
489443 TAATATGTTGATAATACTGATAACAAATC-AGTAATTAACCTATTTTGTTATCGTCGGATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTA
* * *
489507 AGGCCCCATCAACTTTAAACAGGCACTACCTATTGCATTAAATAAACGCTACTTGTTATGTTATT
66 AGGCCCCATCAACTTTAAACAAGCGCTACCTATTACATTAAATAAACGCTACTTGTTATGTTATT
489572 ATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAG
131 ATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAG
489637 CTTAAAATTTGGTAACATTTTAGGCGCTACC
196 CTTAAAATTTGGTAACATTTTAGGCGCTACC
* *
489668 TAATATGTTGATAATATTGATAACAAATCAAGTAACTAACCTATTTTGTTATTGTCGGATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTA
* * * *
489733 AGGCCCCA-CAACTTTAAA-AATGCGCTACCTATTACGTTACATAAGCGCTA-TCT-ATATGTTA
66 AGGCCCCATCAACTTTAAACAA-GCGCTACCTATTACATTAAATAAACGCTACT-TGTTATGTTA
* *
489794 TTATGGTTAATAATATTTCCAGTAATTAA
129 TTATGGTTGATAATGTTTCCAGTAATTAA
489823 TCGATTATGT
Statistics
Matches: 350, Mismatches: 27, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
224 36 0.10
225 245 0.70
226 69 0.20
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (226 bp):
TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTA
AGGCCCCATCAACTTTAAACAAGCGCTACCTATTACATTAAATAAACGCTACTTGTTATGTTATT
ATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAG
CTTAAAATTTGGTAACATTTTAGGCGCTACC
Found at i:491672 original size:14 final size:14
Alignment explanation
Indices: 491632--491673 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
491622 CCCTAATAAC
491632 AAATATTGAAAAAA
1 AAATATTGAAAAAA
* *
491646 AAATGTT-ATAAAA
1 AAATATTGAAAAAA
*
491659 AAATATTGACAAAA
1 AAATATTGAAAAAA
491673 A
1 A
491674 GTTGGACACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (14 bp):
AAATATTGAAAAAA
Found at i:493017 original size:22 final size:21
Alignment explanation
Indices: 492992--493033 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
492982 AAAAAAGTAC
492992 AAAATAAATGTAAAAAT-TTACT
1 AAAA-AAA-GTAAAAATATTACT
*
493014 AAAAAAAGTTAAAATATTAC
1 AAAAAAAGTAAAAATATTAC
493034 CTTCTAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (21 bp):
AAAAAAAGTAAAAATATTACT
Found at i:497549 original size:37 final size:37
Alignment explanation
Indices: 497499--497570 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
497489 CCTTTAATTA
497499 GTACTAAATTTTCTTTTGGGGACATAGTCTCTCTCTC
1 GTACTAAATTTTCTTTTGGGGACATAGTCTCTCTCTC
497536 GTACTAAATTTTCTTTTGGGGACATAGTCTCTCTC
1 GTACTAAATTTTCTTTTGGGGACATAGTCTCTCTC
497571 GTCTATCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (37 bp):
GTACTAAATTTTCTTTTGGGGACATAGTCTCTCTCTC
Found at i:504232 original size:31 final size:31
Alignment explanation
Indices: 504197--504257 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
504187 TTGAATAAAC
*
504197 AAAAAATAATTTTTAACTTTATCTTAACTTT
1 AAAAAATAATTTTTAAATTTATCTTAACTTT
*
504228 AAAAAATATTTTTTAAATTTATCTTAACTT
1 AAAAAATAATTTTTAAATTTATCTTAACTT
504258 AATTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (31 bp):
AAAAAATAATTTTTAAATTTATCTTAACTTT
Found at i:504325 original size:42 final size:43
Alignment explanation
Indices: 504228--504348 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 43
504218 TCTTAACTTT
* * **** *
504228 AAAAAATATTTTTTAAATTTATCTTAAC-TTAATTTTTTTTTA
1 AAAAAATATTTTTTGACTTTATCTTAACTTTAAAAAATATTTA
*
504270 AAAATATATTTTTTGACTTTATCTTAACTTTAAAAAATATTTA
1 AAAAAATATTTTTTGACTTTATCTTAACTTTAAAAAATATTTA
*
504313 AAAAAATATTTTTT-ACTTTATCTTATCTTTAAAAAA
1 AAAAAATATTTTTTGACTTTATCTTAACTTTAAAAAA
504349 ACATTTTTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 46 0.68
43 22 0.32
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (43 bp):
AAAAAATATTTTTTGACTTTATCTTAACTTTAAAAAATATTTA
Found at i:504344 original size:31 final size:31
Alignment explanation
Indices: 504309--504468 Score: 164
Period size: 31 Copynumber: 5.2 Consensus size: 31
504299 TTAAAAAATA
* *
504309 TTTAAAAAAATATTTTTTACTTTATCTTATC
1 TTTAAAAAAATATTTTTAACTTTATCTTAAC
*
504340 TTTAAAAAAACATTTTTAACTTTATCTTAAC
1 TTTAAAAAAATATTTTTAACTTTATCTTAAC
** * * * ***
504371 TTT--AAATTTTTTTTTTATTTTATCACGAC
1 TTTAAAAAAATATTTTTAACTTTATCTTAAC
504400 TTT-AAAAAATATTTTTGAACTTTATCTTAAC
1 TTTAAAAAAATATTTTT-AACTTTATCTTAAC
* *
504431 TTTAAAAAATATATTTTAAATTTTATCTTAAC
1 TTTAAAAAA-ATATTTTTAACTTTATCTTAAC
504463 TTTAAA
1 TTTAAA
504469 CATTATATAC
Statistics
Matches: 103, Mismatches: 22, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
29 20 0.19
30 9 0.09
31 43 0.42
32 24 0.23
33 7 0.07
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (31 bp):
TTTAAAAAAATATTTTTAACTTTATCTTAAC
Found at i:504349 original size:43 final size:43
Alignment explanation
Indices: 504266--504354 Score: 135
Period size: 43 Copynumber: 2.1 Consensus size: 43
504256 TTAATTTTTT
* *
504266 TTTAAAAATATATTTTTTGACTTTATCTTAACTTTAAAAAATA
1 TTTAAAAAAATATTTTTTGACTTTATCTTAACTTTAAAAAACA
*
504309 TTTAAAAAAATATTTTTT-ACTTTATCTTATCTTTAAAAAAACA
1 TTTAAAAAAATATTTTTTGACTTTATCTTAACTTT-AAAAAACA
504352 TTT
1 TTT
504355 TTAACTTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
42 15 0.36
43 27 0.64
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (43 bp):
TTTAAAAAAATATTTTTTGACTTTATCTTAACTTTAAAAAACA
Found at i:504356 original size:73 final size:71
Alignment explanation
Indices: 504197--504376 Score: 202
Period size: 73 Copynumber: 2.5 Consensus size: 71
504187 TTGAATAAAC
***
504197 AAAAAATAATTTTTAACTTTATCTTAACTTTAAAAAATATTTTTTAAATTTATCTTAACTTAATT
1 AAAAAA-AATTTTTAACTTTATCTTAACTTTAAAAAATATTTAAAAAATTTATCTTAACTTAATT
* *
504262 TTTTTTT
65 TATCTTT
* * * *
504269 AAAAATATATTTTTTGACTTTATCTTAACTTTAAAAAATATTTAAAAAAATATT-T-TTTACTTT
1 AAAAA-A-AATTTTTAACTTTATCTTAACTTTAAAAAATATTT-AAAAAAT-TTATCTTAACTTA
504332 ATCTTATCTTT
62 AT-TTATCTTT
504343 AAAAAAACATTTTTAACTTTATCTTAACTTTAAA
1 AAAAAAA-ATTTTTAACTTTATCTTAACTTTAAA
504377 TTTTTTTTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
72 6 0.07
73 68 0.74
74 16 0.17
75 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.51
Consensus pattern (71 bp):
AAAAAAAATTTTTAACTTTATCTTAACTTTAAAAAATATTTAAAAAATTTATCTTAACTTAATTT
ATCTTT
Found at i:511297 original size:22 final size:22
Alignment explanation
Indices: 511261--511330 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
511251 ATATTCCAGA
* * *
511261 AGTGCTAAGACACTTTAGTATG
1 AGTGCAAAGGCACTTTAGTATC
* * **
511283 AGTGCAAATGTACTTCCGTATC
1 AGTGCAAAGGCACTTTAGTATC
* *
511305 AGTGCTAAGGCACTTTAGTACC
1 AGTGCAAAGGCACTTTAGTATC
511327 AGTG
1 AGTG
511331 TTTGTCACTT
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (22 bp):
AGTGCAAAGGCACTTTAGTATC
Done.