Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007465.1 Hibiscus syriacus cultivar Beakdansim tig00020481_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: 65127
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:4050 original size:8 final size:9
Alignment explanation
Indices: 4017--4049 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
4007 GATAAACCAT
4017 TTTATTATA
1 TTTATTATA
4026 TTATATTATA
1 TT-TATTATA
4036 TTTATT-TA
1 TTTATTATA
4044 TTTATT
1 TTTATT
4050 TTTCTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 6 0.26
10 9 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTATTATA
Found at i:4722 original size:20 final size:20
Alignment explanation
Indices: 4680--4719 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
4670 AAGATATTTC
4680 AAAAAAAAAAGAGGAAAAAAT
1 AAAAAAAAAAGAGG-AAAAAT
4701 AAAAAAAATAAGAGGAAAA
1 AAAAAAAA-AAGAGGAAAA
4720 TAAGCGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAAGAGGAAAAAT
Found at i:4907 original size:22 final size:22
Alignment explanation
Indices: 4881--4923 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4871 GGTTAATTGT
4881 TTTTTATTTG-TTAATCTTGTCA
1 TTTTTATTTGATT-ATCTTGTCA
*
4903 TTTTTGTTTGATTATCTTGTC
1 TTTTTATTTGATTATCTTGTC
4924 TAACTCCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.09, G:0.12, T:0.65
Consensus pattern (22 bp):
TTTTTATTTGATTATCTTGTCA
Found at i:5370 original size:20 final size:20
Alignment explanation
Indices: 5325--5361 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5315 GTTATTTTTG
5325 TTATTATTTTATTTAAAAAT
1 TTATTATTTTATTTAAAAAT
*
5345 TAATTATTTTA-TTAAAA
1 TTATTATTTTATTTAAAA
5362 CTCTTATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTATTTTATTTAAAAAT
Found at i:7366 original size:15 final size:15
Alignment explanation
Indices: 7338--7381 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
7328 TGAATATGAG
7338 ATATGAGAATATGTTTT
1 ATATGA-AA-ATGTTTT
7355 ATATGAAAATGTTTT
1 ATATGAAAATGTTTT
*
7370 ATGTGAAAATGT
1 ATATGAAAATGT
7382 GCTAAGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 18 0.69
16 2 0.08
17 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (15 bp):
ATATGAAAATGTTTT
Found at i:7390 original size:15 final size:15
Alignment explanation
Indices: 7358--7409 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
7348 ATGTTTTATA
* *
7358 TGAAAATGTTTTATG
1 TGAAAATGTTCTAAG
*
7373 TGAAAATGTGCTAAG
1 TGAAAATGTTCTAAG
*
7388 TGAAAATGTTCTACG
1 TGAAAATGTTCTAAG
7403 TGAAAAT
1 TGAAAAT
7410 ACCCTATCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (15 bp):
TGAAAATGTTCTAAG
Found at i:7567 original size:24 final size:24
Alignment explanation
Indices: 7540--7585 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
7530 GATTCGAGGG
7540 TTCTAAGCGGTCCTTCGGGACAAA
1 TTCTAAGCGGTCCTTCGGGACAAA
*
7564 TTCTACGCGGTCCTTCGGGACA
1 TTCTAAGCGGTCCTTCGGGACA
7586 TATCTATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (24 bp):
TTCTAAGCGGTCCTTCGGGACAAA
Found at i:7615 original size:24 final size:24
Alignment explanation
Indices: 7588--7641 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
7578 TCGGGACATA
7588 TCTATGTGGCACTTCAGTGCAAAT
1 TCTATGTGGCACTTCAGTGCAAAT
* *
7612 TCTACGTGGCACTTCGGTGCAAAT
1 TCTATGTGGCACTTCAGTGCAAAT
*
7636 TATATG
1 TCTATG
7642 AGCAGTTGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (24 bp):
TCTATGTGGCACTTCAGTGCAAAT
Found at i:16630 original size:4 final size:4
Alignment explanation
Indices: 16607--16698 Score: 66
Period size: 4 Copynumber: 22.0 Consensus size: 4
16597 CATGTTAGAT
*
16607 ATAA A-AA ATAA AGAAA ATAA ATAA ATAA ATTTAA CCA-AA ATAAA ATAAA
1 ATAA ATAA ATAA A-TAA ATAA ATAA ATAA A--TAA --ATAA AT-AA AT-AA
*
16656 ATAA A-ATA ATAA ATAA ATAA ATAA ATAA ATAA AT-G ATAA ATAA
1 ATAA ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
16699 GAATGATAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
3 7 0.10
4 47 0.64
5 15 0.21
6 3 0.04
8 1 0.01
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:16695 original size:45 final size:45
Alignment explanation
Indices: 16621--16738 Score: 104
Period size: 45 Copynumber: 2.6 Consensus size: 45
16611 AAAATAAAGA
*
16621 AAATAAATAAATAAATTTAACCAAAATAAAATAA-AAT-AAAATAAT
1 AAATAAATAAATAAA-TTAAACAAAAT-AAATAAGAATGAAAATAAT
* *
16666 AAATAAATAAATAAA-TAAATAAATGATAAATAAGAATGATAATAAT
1 AAATAAATAAATAAATTAAACAAA--ATAAATAAGAATGAAAATAAT
*
16712 -AATAAA-AAATGATATTAAA-AATAATAA
1 AAATAAATAAAT-AAATTAAACAA-AATAA
16739 GTAATAGGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
43 6 0.10
44 14 0.23
45 30 0.48
46 12 0.19
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.25
Consensus pattern (45 bp):
AAATAAATAAATAAATTAAACAAAATAAATAAGAATGAAAATAAT
Found at i:16697 original size:49 final size:51
Alignment explanation
Indices: 16607--16721 Score: 121
Period size: 49 Copynumber: 2.3 Consensus size: 51
16597 CATGTTAGAT
* *
16607 ATAAAA-AATAAAGAAAATAAATAAATAAATTTAACCAAAATAA-AAT-AAA
1 ATAAAATAATAAA-TAAATAAATAAATAAATTAAACCAAAATAAGAATGAAA
** *
16656 ATAAAATAATAAATAAATAAATAAATAAA-TAAATGATAAATAAGAATGATA
1 ATAAAATAATAAATAAATAAATAAATAAATTAAACCA-AAATAAGAATGAAA
*
16707 ATAATAATAAAAAAT
1 ATAA-AATAATAAAT
16722 GATATTAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
48 4 0.07
49 27 0.49
50 9 0.16
51 6 0.11
52 9 0.16
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.23
Consensus pattern (51 bp):
ATAAAATAATAAATAAATAAATAAATAAATTAAACCAAAATAAGAATGAAA
Found at i:16811 original size:17 final size:18
Alignment explanation
Indices: 16780--16845 Score: 77
Period size: 17 Copynumber: 3.8 Consensus size: 18
16770 ATAAGAATGA
*
16780 AATATATATATAATACCAT
1 AATATATA-ATAATAACAT
16799 AATA-ATAATAATAACAT
1 AATATATAATAATAACAT
*
16816 AATATATAAT-ATAACGT
1 AATATATAATAATAACAT
16833 AAT-TA-AATAATAA
1 AATATATAATAATAA
16846 AAAATAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
15 3 0.07
16 6 0.14
17 22 0.51
18 8 0.19
19 4 0.09
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (18 bp):
AATATATAATAATAACAT
Found at i:17976 original size:16 final size:16
Alignment explanation
Indices: 17940--17973 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17930 ACATGAAATG
17940 AAATAAAAAAATTAAT
1 AAATAAAAAAATTAAT
*
17956 AAATAATAAAA-TAAT
1 AAATAAAAAAATTAAT
17971 AAA
1 AAA
17974 ATATGTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAAAAAAATTAAT
Found at i:18795 original size:105 final size:105
Alignment explanation
Indices: 18479--19256 Score: 1277
Period size: 105 Copynumber: 7.4 Consensus size: 105
18469 GTATTGTTCC
* * * * * * *
18479 GAGTCCAATATCCTCCGCTGTGAAGTTGAAACTGGTTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
* * * *
18544 CTAACGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCCG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * **
18585 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTTGAAATTGAGAAGTTGTCGGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAA-ATGTTTGTTGACA
** *** *
18650 GTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTT
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
18692 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
18757 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
18797 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
18862 CAGCGGTCCCTTTGTCGTGAAGTTGAACATGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
18902 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
18967 CAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
19007 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
19072 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
19112 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
19177 CAGCGGTCCCTTCGTCGTGAAGTGGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
19217 GAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
19257 GGTAAAACCT
Statistics
Matches: 630, Mismatches: 40, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
105 495 0.79
106 45 0.07
107 90 0.14
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:30555 original size:19 final size:20
Alignment explanation
Indices: 30510--30580 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 20
30500 AATAAAATAA
30510 AATAATAAATAAATAAAT-A-
1 AATAATAAAT-AATAAATGAT
* *
30529 AATGATAAATAA-GAATGAT
1 AATAATAAATAATAAATGAT
30548 AATAAT-AATAATAAATGAT
1 AATAATAAATAATAAATGAT
*
30567 ATTAA-AAATAATAA
1 AATAATAAATAATAA
30581 GTAATAGGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 3 0.07
18 8 0.19
19 32 0.74
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (20 bp):
AATAATAAATAATAAATGAT
Found at i:31798 original size:15 final size:16
Alignment explanation
Indices: 31773--31810 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
31763 TGGAAACATG
31773 AAATGAAATAA-AAAAT
1 AAAT-AAATAATAAAAT
31789 AAATAAATAATAAAAT
1 AAATAAATAATAAAAT
31805 -AATAAA
1 AAATAAA
31811 ATATGTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AAATAAATAATAAAAT
Found at i:32676 original size:23 final size:22
Alignment explanation
Indices: 32650--32721 Score: 67
Period size: 23 Copynumber: 3.3 Consensus size: 22
32640 TTCCTTTTTA
32650 TTTTTATAATTGAAATTTGTAAT
1 TTTTTATAATTGAAATTT-TAAT
* ** *
32673 TTTTTAT-ATTCATTTTTTTA-
1 TTTTTATAATTGAAATTTTAAT
*
32693 CTTTTATAATTGAAATCTTTAAT
1 TTTTTATAATTGAAAT-TTTAAT
32716 TTTTTA
1 TTTTTA
32722 ATTTTATTTT
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
20 6 0.17
21 7 0.19
22 11 0.31
23 12 0.33
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTTATAATTGAAATTTTAAT
Found at i:32731 original size:43 final size:41
Alignment explanation
Indices: 32586--32744 Score: 153
Period size: 43 Copynumber: 3.8 Consensus size: 41
32576 TTATAATTAG
* * *
32586 ATTTTTAAATTTTATTTTTTAATCTTTATAATT-AAATTCTA
1 ATTTTTTAATTTTATTTTTTACT-TTTATAATTGAAATTTTA
* ** *
32627 ATTTTATTCAATGTTCCTTTTTATTTTTATAATTGAAATTTGTA
1 ATTTT-TT-AATTTTATTTTTTACTTTTATAATTGAAATTT-TA
*
32671 ATTTTTT-ATATTCATTTTTTTACTTTTATAATTGAAATCTTTA
1 ATTTTTTAAT-TTTA-TTTTTTACTTTTATAATTGAAAT-TTTA
*
32714 ATTTTTTAATTTTATTTTTAAC-TTTATAATT
1 ATTTTTTAATTTTATTTTTTACTTTTATAATT
32745 AATAACCTGA
Statistics
Matches: 97, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
41 16 0.16
42 18 0.19
43 52 0.54
44 11 0.11
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.62
Consensus pattern (41 bp):
ATTTTTTAATTTTATTTTTTACTTTTATAATTGAAATTTTA
Found at i:32840 original size:42 final size:43
Alignment explanation
Indices: 32780--33019 Score: 134
Period size: 42 Copynumber: 5.3 Consensus size: 43
32770 CACTTTCTAC
*
32780 CTTTTTTACTTTTATAATTGAGACCTCTAA-TTTTTTAATCACA
1 CTTTTTAAC-TTTATAATTGAGACCTCTAAGTTTTTTAATCACA
* *
32823 CTTTTTAACTTTATAATTAAGTCC-CTTAAGTTTTTTAATCTCAATTTCCA
1 CTTTTTAACTTTATAATTGAGACCTC-TAAGTTTTTTAA--TC-A----CA
* * * **
32873 CCGTTTCTATCTTTACAATTGAGA-CTCCTAAGTTTTTTCAATCTTA
1 -C-TTTTTAACTTTATAATTGAGACCT-CTAAGTTTTTT-AATCACA
* * *
32919 ATTTTTATCTTTATAATTGAGACCCCTAA-TTTTTTAATC-CTA
1 CTTTTTAACTTTATAATTGAGACCTCTAAGTTTTTTAATCAC-A
* *
32961 C-TTTTAACATTTATAATTGAGGCC-CTTAAGTTTTTTCAATCTCA
1 CTTTTTAAC-TTTATAATTGAGACCTC-TAAGTTTTTT-AATCACA
* * *
33005 ATTTCTACCTTTATA
1 CTTTTTAACTTTATA
33020 GTTAAGGGCC
Statistics
Matches: 154, Mismatches: 21, Indels: 43
0.71 0.10 0.20
Matches are distributed among these distances:
41 8 0.05
42 38 0.25
43 28 0.18
44 34 0.22
45 9 0.06
46 2 0.01
50 2 0.01
51 4 0.03
52 26 0.17
53 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (43 bp):
CTTTTTAACTTTATAATTGAGACCTCTAAGTTTTTTAATCACA
Found at i:32857 original size:95 final size:91
Alignment explanation
Indices: 32686--32957 Score: 269
Period size: 95 Copynumber: 2.9 Consensus size: 91
32676 TTATATTCAT
* * * *
32686 TTTTTTACTTTTATAATTGAAATCTTTAATTTTTTAATTTTATTTTTAACTTTATAATTAA-TAA
1 TTTTTTACTTTTATAATTGAGA-CTCTAATTTTTTAATCTTATTTTTAACTTTATAATTAAGT-C
* * *
32750 CCTGAAATTTTTTTTAATCTCACTTTCTACC
64 CCT-TAA--TTTTTTAATCTCAATTTCCACC
**
32781 TTTTTTACTTTTATAATTGAGACCTCTAATTTTTTAATCACACTTTTTAACTTTATAATTAAGTC
1 TTTTTTACTTTTATAATTGAGA-CTCTAATTTTTTAATCTTA-TTTTTAACTTTATAATTAAGTC
32846 CCTTAAGTTTTTTAATCTCAATTTCCACC
64 CCTTAA-TTTTTTAATCTCAATTTCCACC
* * * * *
32875 GTTTCTA-TCTTTACAATTGAGACTCCTAAGTTTTTTCAATCTTAATTTTTATCTTTATAATTGA
1 TTTTTTACT-TTTATAATTGAGACT-CTAA-TTTTTT-AATCTT-ATTTTTAACTTTATAATTAA
* *
32939 GACCCCTAATTTTTTAATC
61 GTCCCTTAATTTTTTAATC
32958 CTACTTTTAA
Statistics
Matches: 150, Mismatches: 20, Indels: 14
0.82 0.11 0.08
Matches are distributed among these distances:
93 3 0.02
94 41 0.27
95 54 0.36
96 50 0.33
97 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.52
Consensus pattern (91 bp):
TTTTTTACTTTTATAATTGAGACTCTAATTTTTTAATCTTATTTTTAACTTTATAATTAAGTCCC
TTAATTTTTTAATCTCAATTTCCACC
Found at i:32910 original size:96 final size:93
Alignment explanation
Indices: 32727--32957 Score: 225
Period size: 96 Copynumber: 2.4 Consensus size: 93
32717 TTTTAATTTT
* * * * * *
32727 ATTTTTAACTTTATAATTAA-TAACCTGAAATTTTTTTTAATCTCACTTTCTACCTTTTTTACTT
1 ATTTTTAACTTTATAATTAAGT-CCCT-TAA--TTTTTTAATCTCAATTTCCACCGTTTCTACTT
* *
32791 TTATAATTGAGACCTCTAATTTTTTAATCACA
62 TTACAATTGAGACCTCTAATTTTTCAATCACA
*
32823 CTTTTTAACTTTATAATTAAGTCCCTTAAGTTTTTTAATCTCAATTTCCACCGTTTCTA-TCTTT
1 ATTTTTAACTTTATAATTAAGTCCCTTAA-TTTTTTAATCTCAATTTCCACCGTTTCTACT-TTT
**
32887 ACAATTGAGA-CTCCTAAGTTTTTTCAATCTTA
64 ACAATTGAGACCT-CTAA--TTTTTCAATCACA
* * * *
32919 ATTTTTATCTTTATAATTGAGACCCCTAATTTTTTAATC
1 ATTTTTAACTTTATAATTAAGTCCCTTAATTTTTTAATC
32958 CTACTTTTAA
Statistics
Matches: 113, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
93 3 0.03
94 41 0.36
95 12 0.11
96 56 0.50
97 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (93 bp):
ATTTTTAACTTTATAATTAAGTCCCTTAATTTTTTAATCTCAATTTCCACCGTTTCTACTTTTAC
AATTGAGACCTCTAATTTTTCAATCACA
Found at i:32930 original size:44 final size:43
Alignment explanation
Indices: 32880--33067 Score: 179
Period size: 44 Copynumber: 4.4 Consensus size: 43
32870 CCACCGTTTC
*
32880 TATCTTTACAATTGAGACTCCTAAGTTTTTTCAATCTTAATTTT
1 TATCTTTATAATTGAGAC-CCTAAGTTTTTTCAATCTTAATTTT
* *
32924 TATCTTTATAATTGAGACCCCTAA-TTTTTT-AATCCT-ACTTT
1 TATCTTTATAATTGAGA-CCCTAAGTTTTTTCAATCTTAATTTT
* * * *
32965 TAACATTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCAATTTC
1 TATC-TTTATAATTGAGACCC-TAAGTTTTTTCAATCTTAATTTT
* * * * *
33010 TACCTTTATAGTTAAGGGCCCTAAG-TTTTTCAATCTTAA-TTA
1 TATCTTTATAATTGA-GACCCTAAGTTTTTTCAATCTTAATTTT
*
33052 AATCTTTATAATTGAG
1 TATCTTTATAATTGAG
33068 GTCCTTATCC
Statistics
Matches: 119, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
41 11 0.09
42 33 0.28
43 25 0.21
44 38 0.32
45 12 0.10
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (43 bp):
TATCTTTATAATTGAGACCCTAAGTTTTTTCAATCTTAATTTT
Found at i:33039 original size:86 final size:86
Alignment explanation
Indices: 32881--33074 Score: 214
Period size: 86 Copynumber: 2.3 Consensus size: 86
32871 CACCGTTTCT
* * * * * *
32881 ATCTTTACAATTGAGACTCC-TAAGTTTTTTCAATCTTAATTTTTATCTTTATAATTGAGACCCC
1 ATCTTTATAATTGAGGC-CCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTAAGACCCC
* * *
32945 TAA-TTTTTTAATCCTACTTTTA
65 TAAGTTTTTCAATCCTA-ATTAA
* **
32967 A-CATTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAGTTAAGGGCCC
1 ATC-TTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTAAGACCCC
*
33031 TAAGTTTTTCAATCTTAATTAA
65 TAAGTTTTTCAATCCTAATTAA
*
33053 ATCTTTATAATTGAGGTCCTTA
1 ATCTTTATAATTGAGGCCCTTA
33075 TCCCTTTCTT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
85 3 0.03
86 75 0.83
87 12 0.13
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (86 bp):
ATCTTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTAAGACCCCT
AAGTTTTTCAATCCTAATTAA
Found at i:42861 original size:21 final size:18
Alignment explanation
Indices: 42826--42882 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
42816 ATGTTTAATG
* *
42826 AAAAAGAGACTAATTGTT
1 AAAAAGATACCAATTGTT
*
42844 AACAAAAGGATATCAATTGTT
1 -A-AAAA-GATACCAATTGTT
42865 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
42883 GGAAAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 12 0.38
19 5 0.16
20 5 0.16
21 10 0.31
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:42873 original size:18 final size:21
Alignment explanation
Indices: 42837--42882 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 21
42827 AAAAGAGACT
*
42837 AATTGTTAACAAAAGGATATC
1 AATTGTTAACAAAAGGATACC
42858 AATTGTT-A-AAAA-GATACC
1 AATTGTTAACAAAAGGATACC
42876 AATTGTT
1 AATTGTT
42883 GGAAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
19 4 0.17
20 1 0.04
21 7 0.29
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (21 bp):
AATTGTTAACAAAAGGATACC
Found at i:50833 original size:96 final size:97
Alignment explanation
Indices: 50726--50939 Score: 276
Period size: 96 Copynumber: 2.2 Consensus size: 97
50716 ATTTTCAATA
* **
50726 CTTTTTTTACTTTTATAATTGATGCCCCTAATTTTTTAAATCTA-TTTTTTAA-CTTTATAATTA
1 CTTTTTCTACTTTTATAATTGATGCCCCTAATTTTTT-AATC-ACACTTTTAAGCTTTATAATTA
* * *
50789 AGATCCTTAAG-TTTTTTCTATCTCACTTTCTAC
64 AGACCCTTAAGTTTTTTTCAATCTCACTTTCCAC
* *
50822 CTTTTTCTACTTTTATAATTGATGCCTCTAATTTTTTAATCACACTTTTAAGCTTTATAATTGAG
1 CTTTTTCTACTTTTATAATTGATGCCCCTAATTTTTTAATCACACTTTTAAGCTTTATAATTAAG
*
50887 CCCCTTAAGTTTTTTTCAATCTCACTTTCCAC
66 ACCCTTAAGTTTTTTTCAATCTCACTTTCCAC
*
50919 C-TTTTCTA-TCTTTACAATTGA
1 CTTTTTCTACT-TTTATAATTGA
50940 GGCTCTTAAG
Statistics
Matches: 104, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
94 1 0.01
95 11 0.11
96 71 0.68
97 21 0.20
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.51
Consensus pattern (97 bp):
CTTTTTCTACTTTTATAATTGATGCCCCTAATTTTTTAATCACACTTTTAAGCTTTATAATTAAG
ACCCTTAAGTTTTTTTCAATCTCACTTTCCAC
Found at i:50974 original size:53 final size:54
Alignment explanation
Indices: 50874--50975 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 54
50864 CACTTTTAAG
* * *
50874 CTTTATAATTGAGCCCCTTAAGTTTTTTTCAATCTCACTTTCCACCTTTTCTAT
1 CTTTACAATTGAGCCCCTTAAGTATTTTTCAATCTCAATTTCCACCTTTTCTAT
* * *
50928 CTTTACAATTGAGGCTCTTAAGTATTTTT-AATCTCAATTTCTACCTTT
1 CTTTACAATTGAGCCCCTTAAGTATTTTTCAATCTCAATTTCCACCTTT
50976 ATAATCGAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 17 0.40
54 25 0.60
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.48
Consensus pattern (54 bp):
CTTTACAATTGAGCCCCTTAAGTATTTTTCAATCTCAATTTCCACCTTTTCTAT
Found at i:50986 original size:44 final size:44
Alignment explanation
Indices: 50921--51111 Score: 151
Period size: 44 Copynumber: 4.4 Consensus size: 44
50911 CTTTCCACCT
* * * * *
50921 TTTCTATCTTTACAATTGAGGCTCTTAAGTATTTTT-AATCTCAA
1 TTTCTACCTTTATAATCGAGGCCCTTAAAT-TTTTTAAATCTCAA
* * *
50965 TTTCTACCTTTATAATCGAGGCCCCT-AATTTTTT-AATCCCAGT
1 TTTCTACCTTTATAATCGAGGCCCTTAAATTTTTTAAATCTCA-A
* ** * *
51008 TTTTTAATTTTATAATTGAGGCCATTAAATTTTTTAAATCTCAA
1 TTTCTACCTTTATAATCGAGGCCCTTAAATTTTTTAAATCTCAA
* *
51052 TTT-TAACATTTATAACTGCGA--CCCTTAAATTTTTTCAATCTCAA
1 TTTCT-ACCTTTATAA-T-CGAGGCCCTTAAATTTTTTAAATCTCAA
*
51096 TTTCTACTTTTATAAT
1 TTTCTACCTTTATAAT
51112 TAAGGGCCCT
Statistics
Matches: 118, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
42 11 0.09
43 24 0.20
44 73 0.62
45 8 0.07
46 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (44 bp):
TTTCTACCTTTATAATCGAGGCCCTTAAATTTTTTAAATCTCAA
Found at i:50997 original size:97 final size:97
Alignment explanation
Indices: 50726--50998 Score: 249
Period size: 96 Copynumber: 2.8 Consensus size: 97
50716 ATTTTCAATA
* * * * ** **
50726 CTTTTTTTACTTTTATAATTGATGCCCCTAATTTTTTAAATCTA-TTTTTTAA-CTTTATAATTA
1 CTTTTTCTACTTTTACAATTGAGGCCTCTAATTTTTT-AATC-ACAATTTTAACCTTTATAATCG
** * *
50789 AGATCCTTAAG-TTTTTTCTATCTCACTTTCTAC
64 AGCCCCTTAAGTTTTTTTCAATCTCACTTTCCAC
* * * * *
50822 CTTTTTCTACTTTTATAATTGATGCCTCTAATTTTTTAATCACACTTTTAAGCTTTATAATTGAG
1 CTTTTTCTACTTTTACAATTGAGGCCTCTAATTTTTTAATCACAATTTTAACCTTTATAATCGAG
50887 CCCCTTAAGTTTTTTTCAATCTCACTTTCCAC
66 CCCCTTAAGTTTTTTTCAATCTCACTTTCCAC
*
50919 C-TTTTCTA-TCTTTACAATTGAGG-CTCTTAAGTATTTTTAATCTCAATTTCT-ACCTTTATAA
1 CTTTTTCTACT-TTTACAATTGAGGCCTC-TAA-T-TTTTTAATCACAATTT-TAACCTTTATAA
50980 TCGAGGCCCC-TAA-TTTTTT
61 TCGA-GCCCCTTAAGTTTTTT
50999 AATCCCAGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
94 1 0.01
95 14 0.09
96 75 0.49
97 28 0.18
98 29 0.19
99 6 0.04
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.50
Consensus pattern (97 bp):
CTTTTTCTACTTTTACAATTGAGGCCTCTAATTTTTTAATCACAATTTTAACCTTTATAATCGAG
CCCCTTAAGTTTTTTTCAATCTCACTTTCCAC
Found at i:51129 original size:44 final size:43
Alignment explanation
Indices: 50952--51135 Score: 151
Period size: 44 Copynumber: 4.2 Consensus size: 43
50942 CTCTTAAGTA
* * *
50952 TTTTTAATCTCAATTTCTACCTTTATAATCGAGGCCCCT-AAT
1 TTTTTAATCTCAATTTCTACTTTTATAATTGAGGGCCCTAAAT
* * * * *
50994 TTTTTAATCCCAGTTTTTTAATTTTATAATTGA-GGCCATTAAAT
1 TTTTTAATCTCA-ATTTCTACTTTTATAATTGAGGGCC-CTAAAT
* * * *
51038 TTTTTAAATCTCAATTT-TAACATTTATAACTG-CGACCCTTAAAT
1 TTTTT-AATCTCAATTTCT-ACTTTTATAATTGAGGGCCC-TAAAT
* *
51082 TTTTTCAATCTCAATTTCTACTTTTATAATTAAGGGCCCTAAGT
1 TTTTT-AATCTCAATTTCTACTTTTATAATTGAGGGCCCTAAAT
*
51126 TTTTCAATCT
1 TTTTTAATCT
51136 TAACTATATC
Statistics
Matches: 110, Mismatches: 23, Indels: 17
0.73 0.15 0.11
Matches are distributed among these distances:
42 14 0.13
43 22 0.20
44 63 0.57
45 11 0.10
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (43 bp):
TTTTTAATCTCAATTTCTACTTTTATAATTGAGGGCCCTAAAT
Found at i:54216 original size:20 final size:20
Alignment explanation
Indices: 54173--54221 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
54163 AATATCAAAC
* *
54173 AAAATATTATATGGTAAAAT
1 AAAATATTATATGATAAAAA
54193 AAAATATTGA-ATGATAAAAA
1 AAAATATT-ATATGATAAAAA
*
54213 AAAAAATTA
1 AAAATATTA
54222 GAAGATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
AAAATATTATATGATAAAAA
Found at i:54328 original size:28 final size:27
Alignment explanation
Indices: 54296--54351 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
54286 GTCACAAGAG
* *
54296 AAATAAATAAAAATTAGGGAAAATATTA
1 AAATAAACAAAAATTA-AGAAAATATTA
*
54324 AAATAAACAATAATTAAGAAAATATTA
1 AAATAAACAAAAATTAAGAAAATATTA
54351 A
1 A
54352 TGTCTAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (27 bp):
AAATAAACAAAAATTAAGAAAATATTA
Found at i:55743 original size:83 final size:83
Alignment explanation
Indices: 55604--55807 Score: 266
Period size: 83 Copynumber: 2.5 Consensus size: 83
55594 AACTTCTTGT
** * *
55604 TGACAGATAGCCCTTCTCGCCTTGAGCTATACTATAAATTTGATATGTCCGTGAGCTGAATGTAA
1 TGACAGATAGCCCTTCTTACCTTGAGCTATGCTATAAATTTGACATGTCCGTGAGCTGAATGTAA
55669 TCGAACTCAAAGATTTAC
66 TCGAACTCAAAGATTTAC
* * * * *
55687 TGACAGATAGCTCTTCTTACCTTAAGCTATGCTGTAAATTTGCCATGTCCTTGAGCTGAATGTAA
1 TGACAGATAGCCCTTCTTACCTTGAGCTATGCTATAAATTTGACATGTCCGTGAGCTGAATGTAA
* * **
55752 TCGAACTCGAAGGTTTTT
66 TCGAACTCAAAGATTTAC
* *
55770 TG-CAGATAACCCTTCTTACCTTGAGCTATGCTACAAAT
1 TGACAGATAGCCCTTCTTACCTTGAGCTATGCTATAAAT
55808 GATGTGCCTT
Statistics
Matches: 103, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
82 31 0.30
83 72 0.70
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (83 bp):
TGACAGATAGCCCTTCTTACCTTGAGCTATGCTATAAATTTGACATGTCCGTGAGCTGAATGTAA
TCGAACTCAAAGATTTAC
Found at i:56216 original size:243 final size:241
Alignment explanation
Indices: 55655--56416 Score: 985
Period size: 243 Copynumber: 3.1 Consensus size: 241
55645 GATATGTCCG
* * * * * *
55655 TGAGCTGAATGTAATCGAACTCAAAGAT-TTACTGACAGATAGCTCTTCTTACCTTAAGCTATGC
1 TGAGCTGAGTGTAATCGAACTCAAAGGTCTT--TGGCAGATAGCCCTTCTTGCCTTGAGCTATGC
* * *
55719 TGTAAATTTGCCATG-TCC-TTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCAGATAACCC
64 TGCAAA--TG--ATGTTCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGATAACCC
* * *
55782 TTCTTACCTTGAGCTATGCTACAAATGATGTGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTC
125 TTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA-GT-
* * * *
55847 TTTTGTTGGCAAATAACCCTTATTGCCTTTAGCTATGTTGCAAATGATGTGCCTT
188 TTTTGTT-GCAGATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTT
* * * *
55902 TGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTA
1 TGAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTG
* *
55967 CAAATGATGTTCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGGTAGCCCTTCTTG
66 CAAATGATGTTCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGATAACCCTTCTTG
56032 CCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAACGTTTTTGTT
131 CCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA-GTTTTTGTT
* * *
56097 GATAGATAACCCTTCTAACCTTGAGCTATGTTGTAAATGATGTGCCTT
195 G-CAGATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTT
* *
56145 TGAGCTGAGTGTAATCAAACTTAAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTG
1 TGAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTG
* * * * * *
56210 CAAATGATGTACCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGAAAATAACCTTTCTCG
66 CAAATGATGTTCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGATAACCCTTCTTG
* * * * * *
56275 CCTTGAGCTATGCTGCAAATGATGTGACTTTGAGCTGAATGGAATCGAACTCGAAGATCTT-TAG
131 CCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGTTTTTGTTG
* * * *
56339 CAGATAACCCTTCTAGCCTTGAGTTAT-TATGCAAATCATGTGCATC
196 CAGATAACCCTTCTAGCCTTGAGCTATGT-TGCAAATGATGTGCCTT
*
56385 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTT
1 TGAGCTGAGTGTAATCGAACTCAAAGGTCTTT
56417 ATCAAACTCG
Statistics
Matches: 454, Mismatches: 56, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
239 1 0.00
240 66 0.15
241 2 0.00
242 8 0.02
243 217 0.48
244 103 0.23
246 31 0.07
247 24 0.05
248 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (241 bp):
TGAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTG
CAAATGATGTTCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGATAACCCTTCTTG
CCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGTTTTTGTTG
CAGATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTT
Found at i:56296 original size:323 final size:322
Alignment explanation
Indices: 55614--56412 Score: 978
Period size: 323 Copynumber: 2.5 Consensus size: 322
55604 TGACAGATAG
* * * * ** *
55614 CCCTTCTCGCCTTGAGCTATACTATAAATTTGATATGTCCGTGAGCTGAATGTAATCGAACTCAA
1 CCCTTCTCGCCTTGAGCTATGCTACAAA--TGATGTGACTTTGAGCTGAATGTAATCGAACTCGA
* * * * *
55679 AGAT-TTACTGACAGATAGCTCTTCTTACCTTAAGCTATGCTGTAAATTTGCCATGT-CC-TTGA
64 AGATCTT-TTG-CAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA--TG--ATGTGCCTTTGA
* *
55741 GCTGAATGTAATCGAACTCGAAGGTTTTTTGCAGATAACCCTTCTTACCTTGAGCTATGCTACAA
123 GCTGAGTGTAATCGAACTCGAAGGTTTTTTGCAGATAACCCTTCTAACCTTGAGCTATGCTACAA
* * *
55806 ATGATGTGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTATT
188 ATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTC--TTGTTGGCAAATAACCCTTATT
* * *
55871 GCCTTTAGCTATGTTGCAAATGATGTGCCTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGG
251 GCCTTGAGCTATGCTGCAAATGATGTACCTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGG
* ** *
55936 CAGGTAG
316 AAAATAA
* ** *
55943 CCCTTCTTGCCTTGAGCTATGCTACAAATGATGTTCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTCGCCTTGAGCTATGCTACAAATGATGTGACTTTGAGCTGAATGTAATCGAACTCGAAG
* *
56008 GTCTTTTGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
66 ATCTTTTGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* * * **
56073 TAATCGAACTCGAACGTTTTTGTTGATAGATAACCCTTCTAACCTTGAGCTATGTTGTAAATGAT
131 TAATCGAACTCGAA-GGTTTT-TTG-CAGATAACCCTTCTAACCTTGAGCTATGCTACAAATGAT
* * * *
56138 GTGCCTTTGAGCTGAGTGTAATCAAACTTAAAGGTC-T-TTGGCAGATAGCCCTTCTTGCCTTGA
193 GTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTCTTGTTGGCAAATAACCCTTATTGCCTTGA
*
56201 GCTATGCTGCAAATGATGTACCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGAAAATAA
258 GCTATGCTGCAAATGATGTACCTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGAAAATAA
* * *
56266 CCTTTCTCGCCTTGAGCTATGCTGCAAATGATGTGACTTTGAGCTGAATGGAATCGAACTCGAAG
1 CCCTTCTCGCCTTGAGCTATGCTACAAATGATGTGACTTTGAGCTGAATGTAATCGAACTCGAAG
* * * * ** * * *
56331 ATCTTTAGCAGATAACCCTTCTAGCCTTGAGTTATTATGCAAATCATGTGCATCTGAGCTGAGTG
66 ATCTTTTGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
56396 TAATCGAACTCGAAGGT
131 TAATCGAACTCGAAGGT
56413 CTTTATCAAA
Statistics
Matches: 406, Mismatches: 58, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
322 6 0.01
323 208 0.51
324 28 0.07
325 5 0.01
326 33 0.08
327 99 0.24
328 2 0.00
329 25 0.06
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (322 bp):
CCCTTCTCGCCTTGAGCTATGCTACAAATGATGTGACTTTGAGCTGAATGTAATCGAACTCGAAG
ATCTTTTGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
TAATCGAACTCGAAGGTTTTTTGCAGATAACCCTTCTAACCTTGAGCTATGCTACAAATGATGTG
CCTTTGAGCTGAGTGTAATCAAACTCAAAGGTCTTGTTGGCAAATAACCCTTATTGCCTTGAGCT
ATGCTGCAAATGATGTACCTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGAAAATAA
Found at i:56417 original size:80 final size:80
Alignment explanation
Indices: 55655--56416 Score: 891
Period size: 80 Copynumber: 9.4 Consensus size: 80
55645 GATATGTCCG
* * * * * * * *
55655 TGAGCTGAATGTAATCGAACTCAAAGAT-TTACTGACAGATAGCTCTTCTTACCTTAAGCTATGC
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTT--TGGCAGATAACCCTTCTTGCCTTGAGCTATGC
*
55719 TGTAAATTTGCCATGT-CC-T
64 TGCAAA--TG--ATGTGCCTT
* * * * *
55738 TGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCAGATAACCCTTCTTACCTTGAGCTATGCTA
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
55803 CAAATGATGTGCCTT
66 CAAATGATGTGCCTT
* * * *
55818 TGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTATTGCCTTTAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTAT
*
55883 GTTGCAAATGATGTGCCTT
62 GCTGCAAATGATGTGCCTT
* * * *
55902 TGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTA
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
*
55967 CAAATGATGTTCCTT
66 CAAATGATGTGCCTT
* * *
55982 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
56047 CAAATGATGTGCCTT
66 CAAATGATGTGCCTT
* * * **
56062 TGAGCTGAGTGTAATCGAACTCGAACGTTTTTGTTGATAGATAACCCTTCTAACCTTGAGCTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTTGCCTTGAGCTATG
* *
56127 TTGTAAATGATGTGCCTT
63 CTGCAAATGATGTGCCTT
* ** *
56145 TGAGCTGAGTGTAATCAAACTTAAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
*
56210 CAAATGATGTACCTT
66 CAAATGATGTGCCTT
* * * *
56225 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGAAAATAACCTTTCTCGCCTTGAGCTATGCTG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
*
56290 CAAATGATGTGACTT
66 CAAATGATGTGCCTT
* * * * * * **
56305 TGAGCTGAATGGAATCGAACTCGAAGATCTTTAGCAGATAACCCTTCTAGCCTTGAGTTATTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
* * *
56370 CAAATCATGTGCATC
66 CAAATGATGTGCCTT
56385 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTT
56417 ATCAAACTCG
Statistics
Matches: 586, Mismatches: 83, Indels: 23
0.85 0.12 0.03
Matches are distributed among these distances:
78 4 0.01
79 2 0.00
80 380 0.65
81 2 0.00
82 32 0.05
83 94 0.16
84 72 0.12
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (80 bp):
TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
CAAATGATGTGCCTT
Found at i:57747 original size:98 final size:98
Alignment explanation
Indices: 57619--57822 Score: 390
Period size: 98 Copynumber: 2.1 Consensus size: 98
57609 GCCATTGTCT
*
57619 GGCTAGCTGAATCATATCCATAAAGCTAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAA
1 GGCTAGCTAAATCATATCCATAAAGCTAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAA
57684 CTTTATTGTATATATATTATAATCACCTTTACA
66 CTTTATTGTATATATATTATAATCACCTTTACA
*
57717 GGCTAGCTAAATCATATCCATAAAGCTAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAG
1 GGCTAGCTAAATCATATCCATAAAGCTAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAA
57782 CTTTATTGTATATATATTATAATCACCTTTACA
66 CTTTATTGTATATATATTATAATCACCTTTACA
57815 GGCTAGCT
1 GGCTAGCT
57823 GAAGGATTCA
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 104 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (98 bp):
GGCTAGCTAAATCATATCCATAAAGCTAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAA
CTTTATTGTATATATATTATAATCACCTTTACA
Found at i:62568 original size:2 final size:2
Alignment explanation
Indices: 62561--62614 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
62551 ATTTGATTAT
* *
62561 TA TA TA TA TC TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62603 TA TA TA TA TA TA
1 TA TA TA TA TA TA
62615 CGAAATACAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:63587 original size:62 final size:63
Alignment explanation
Indices: 63449--63671 Score: 224
Period size: 64 Copynumber: 3.5 Consensus size: 63
63439 TTGTTTAAAG
** **
63449 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAA-AAA-ACATCGAATGCAATT
*
63512 T
63 A
* *
63513 GCGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAAC-TCG-ATGCAATTA
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAA-AAAACATCGAATGCAATTA
* * * *
63575 GTGCATCGATGCATAAGGTA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTA
1 GTGCATCGATGCATAA-GTAGTGCATCGATGCATCCCATTAATAA-AAAACATCGAATGCAATTA
* *
63639 -TGCACCGATGCAATCAGTAGTGCATCGATGCAT
1 GTGCATCGATGC-ATAAGTAGTGCATCGATGCAT
63672 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 17, Indels: 14
0.81 0.10 0.08
Matches are distributed among these distances:
62 49 0.36
63 22 0.16
64 59 0.44
65 5 0.04
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (63 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAAAAACATCGAATGCAATTA
Found at i:64528 original size:102 final size:103
Alignment explanation
Indices: 64405--64631 Score: 438
Period size: 102 Copynumber: 2.2 Consensus size: 103
64395 GTCGAGGGTC
64405 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
64470 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGT-A
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
64507 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
64572 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
*
64610 TATGTGGTCCTTCGGGACATAT
1 TATGTGGTCCTTCGGGATATAT
64632 TATATGGCAC
Statistics
Matches: 123, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
102 101 0.82
103 22 0.18
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
Found at i:64670 original size:23 final size:23
Alignment explanation
Indices: 64637--64699 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
64627 CATATTATAT
64637 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
64660 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
64683 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
64700 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Done.