Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005842.1 Hibiscus syriacus cultivar Beakdansim tig00013706_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: 197362
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 1 of 2
Found at i:2768 original size:29 final size:29
Alignment explanation
Indices: 2734--2830 Score: 106
Period size: 29 Copynumber: 3.4 Consensus size: 29
2724 ATAGAATTAT
** *
2734 AATAAAGGACAAATTGTTTTGGAATTTCC
1 AATAAAGGACAAAACGTTTTGGAATTTAC
* * * *
2763 AATAAAGGATAAAGCGTTTTGAAATTTAT
1 AATAAAGGACAAAACGTTTTGGAATTTAC
*
2792 AATAAAGGACAAAACGTTGT-GAATTTAC
1 AATAAAGGACAAAACGTTTTGGAATTTAC
*
2820 AATTAAGGACA
1 AATAAAGGACA
2831 TTTTTTTTAA
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
28 16 0.29
29 40 0.71
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (29 bp):
AATAAAGGACAAAACGTTTTGGAATTTAC
Found at i:2904 original size:27 final size:26
Alignment explanation
Indices: 2834--2905 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 26
2824 AAGGACATTT
*
2834 TTTTTAAAAATTACAATAAAGTATATA
1 TTTTT-AAAATTACAATAAAGTATAAA
2861 TTCTTT-AAATTACAATAAAGTATAAAA
1 TT-TTTAAAATTACAATAAAGTAT-AAA
2888 CTTTTTAAAATTA-AATAA
1 -TTTTTAAAATTACAATAA
2906 TGACATTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
26 17 0.43
27 12 0.30
28 11 0.28
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (26 bp):
TTTTTAAAATTACAATAAAGTATAAA
Found at i:9644 original size:20 final size:20
Alignment explanation
Indices: 9621--9688 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
9611 AGAAAAGAAA
9621 GAAAAAAAAAAAGAGAAAAT
1 GAAAAAAAAAAAGAGAAAAT
* *
9641 GAAAATGAAAAATGA-AAAAT
1 GAAAA-AAAAAAAGAGAAAAT
* *
9661 GAAAAATGAAAAA-TGAAAAT
1 GAAAAA-AAAAAAGAGAAAAT
9681 GAAAAAAA
1 GAAAAAAA
9689 GAAGAAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
19 1 0.03
20 30 0.79
21 7 0.18
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (20 bp):
GAAAAAAAAAAAGAGAAAAT
Found at i:9645 original size:14 final size:14
Alignment explanation
Indices: 9628--9691 Score: 71
Period size: 14 Copynumber: 4.7 Consensus size: 14
9618 AAAGAAAAAA
9628 AAAAAGAGAAAATG
1 AAAAAGAGAAAATG
*
9642 AAAATGA-AAAATG
1 AAAAAGAGAAAATG
9655 AAAAATGA-AAAATG
1 AAAAA-GAGAAAATG
*
9669 AAAAA-TGAAAATG
1 AAAAAGAGAAAATG
*
9682 AAAAAAAGAA
1 AAAAAGAGAA
9692 GAAAAAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
13 21 0.49
14 22 0.51
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAAAGAGAAAATG
Found at i:9652 original size:7 final size:7
Alignment explanation
Indices: 9636--9686 Score: 88
Period size: 7 Copynumber: 7.6 Consensus size: 7
9626 AAAAAAAGAG
9636 AAAATG-
1 AAAATGA
9642 AAAATGA
1 AAAATGA
9649 AAAATGA
1 AAAATGA
9656 AAAATGA
1 AAAATGA
9663 AAAATGA
1 AAAATGA
9670 AAAATG-
1 AAAATGA
9676 AAAATGA
1 AAAATGA
9683 AAAA
1 AAAA
9687 AAGAAGAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.28
7 31 0.72
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAATGA
Found at i:9666 original size:21 final size:21
Alignment explanation
Indices: 9627--9686 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
9617 GAAAGAAAAA
*
9627 AAAAAAGAGAAAATG-AAAATG
1 AAAAATGA-AAAATGAAAAATG
9648 AAAAATGAAAAATGAAAAATG
1 AAAAATGAAAAATGAAAAATG
9669 AAAAATG-AAAATGAAAAA
1 AAAAATGAAAAATGAAAAA
9687 AAGAAGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (21 bp):
AAAAATGAAAAATGAAAAATG
Found at i:9700 original size:7 final size:7
Alignment explanation
Indices: 9618--9702 Score: 50
Period size: 7 Copynumber: 12.0 Consensus size: 7
9608 GATAGAAAAG
9618 AAAG-AA
1 AAAGAAA
9624 AAA-AAA
1 AAAGAAA
9630 AAAGAGAA
1 AAAGA-AA
*
9638 AATG-AA
1 AAAGAAA
*
9644 AATGAAA
1 AAAGAAA
*
9651 AATGAAA
1 AAAGAAA
*
9658 AATGAAA
1 AAAGAAA
*
9665 AATGAAA
1 AAAGAAA
*
9672 AATGAAA
1 AAAGAAA
*
9679 ATGAAAAAA
1 A--AAGAAA
9688 AGAAGAAA
1 A-AAGAAA
9696 AAAGAAA
1 AAAGAAA
9703 GAAAACCGAT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
6 14 0.20
7 38 0.55
8 12 0.17
9 5 0.07
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.08
Consensus pattern (7 bp):
AAAGAAA
Found at i:11324 original size:65 final size:64
Alignment explanation
Indices: 11250--11374 Score: 189
Period size: 64 Copynumber: 1.9 Consensus size: 64
11240 AACAAAATTG
* * * *
11250 ATAAACTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTC-CATTGAGACAGTTTCTCTTGTAA
1 ATAAACTTTGAGAATGTTTCCCTTGAAA-AAATTTTATCTCTC-TTGAGACAATTTCTCTTGTAA
11314 A
64 A
11315 ATAAACTTTGAGAATGTTTCCCTTGAAAAAATTTTATCTCTCTTGAGACAATTTCTCTTG
1 ATAAACTTTGAGAATGTTTCCCTTGAAAAAATTTTATCTCTCTTGAGACAATTTCTCTTG
11375 GAACAAAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
64 28 0.51
65 27 0.49
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.42
Consensus pattern (64 bp):
ATAAACTTTGAGAATGTTTCCCTTGAAAAAATTTTATCTCTCTTGAGACAATTTCTCTTGTAAA
Found at i:11650 original size:74 final size:74
Alignment explanation
Indices: 11477--11650 Score: 176
Period size: 74 Copynumber: 2.3 Consensus size: 74
11467 CTTCAAATAG
* * * * *
11477 ACTTTGTCTCACTTGAGACATTTTTTACTCAAAACAAGACATTTCGTTTCACTATAGATTATTTT
1 ACTTCGTCTCGCTTGAGACA-GTTTTACCCAAAACAAGACATTTCGTTTCACTATAGATTATGTT
11542 TCTTAAAACA
65 TCTTAAAACA
* * * * *
11552 AGATTCATCTCGCTTGAG-CTAGTTTTACCCAAAACAAGA-ATATT-TTTTTACTCA-AGATTGT
1 A-CTTCGTCTCGCTTGAGAC-AGTTTTACCCAAAACAAGACAT-TTCGTTTCACT-ATAGATTAT
11613 GTTTCTTAAAACCA
62 GTTTCTTAAAA-CA
11627 ACTTCGTCTCGCTTGAGACAGTTT
1 ACTTCGTCTCGCTTGAGACAGTTT
11651 CCCTTGAAAC
Statistics
Matches: 81, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
74 43 0.53
75 25 0.31
76 13 0.16
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (74 bp):
ACTTCGTCTCGCTTGAGACAGTTTTACCCAAAACAAGACATTTCGTTTCACTATAGATTATGTTT
CTTAAAACA
Found at i:11661 original size:36 final size:36
Alignment explanation
Indices: 11621--11693 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
11611 GTGTTTCTTA
* * *
11621 AAACCAACTTCGTCTCGCTTGAGACAGTTTCCCTTG
1 AAACCAACTTCGTCTCCCTTGAGACAGTCTCACTTG
* *
11657 AAACCAATTTTGTCTCCCTTGAGACAGTCTCACTTG
1 AAACCAACTTCGTCTCCCTTGAGACAGTCTCACTTG
11693 A
1 A
11694 GACAGTTTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.32
Consensus pattern (36 bp):
AAACCAACTTCGTCTCCCTTGAGACAGTCTCACTTG
Found at i:11707 original size:15 final size:15
Alignment explanation
Indices: 11668--11708 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
11658 AACCAATTTT
11668 GTCTCCCTTGAGACA
1 GTCTCCCTTGAGACA
*
11683 GTCTCACTTGAGACA
1 GTCTCCCTTGAGACA
*
11698 GTTTCCCTTGA
1 GTCTCCCTTGA
11709 AACAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.32
Consensus pattern (15 bp):
GTCTCCCTTGAGACA
Found at i:11708 original size:51 final size:51
Alignment explanation
Indices: 11632--11733 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
11622 AACCAACTTC
*
11632 GTCTCGCTTGAGACAGTTTCCCTTGAAACCAAT-TTTGTCTCCCTTGAGACA
1 GTCTCACTTGAGACAGTTTCCCTTGAAA-CAATATTTGTCTCCCTTGAGACA
11683 GTCTCACTTGAGACAGTTTCCCTTGAAACAATATTTGTCTCCCTTGAGACA
1 GTCTCACTTGAGACAGTTTCCCTTGAAACAATATTTGTCTCCCTTGAGACA
11734 ATTTCCCTTG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 4 0.08
51 45 0.92
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (51 bp):
GTCTCACTTGAGACAGTTTCCCTTGAAACAATATTTGTCTCCCTTGAGACA
Found at i:11744 original size:51 final size:51
Alignment explanation
Indices: 11633--11749 Score: 173
Period size: 51 Copynumber: 2.3 Consensus size: 51
11623 ACCAACTTCG
* *
11633 TCTCGCTTGAGACAGTTTCCCTTGAAACCAATTTTGTCTCCCTTGAGACAG
1 TCTCACTTGAGACAGTTTCCCTTGAAACCAATTTTGTCTCCCTTGAGACAA
11684 TCTCACTTGAGACAGTTTCCCTTGAAA-CAATATTTGTCTCCCTTGAGACAA
1 TCTCACTTGAGACAGTTTCCCTTGAAACCAAT-TTTGTCTCCCTTGAGACAA
* * *
11735 TTTCCCTTGACACAG
1 TCTCACTTGAGACAG
11750 AAGATTTTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 4 0.07
51 56 0.93
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33
Consensus pattern (51 bp):
TCTCACTTGAGACAGTTTCCCTTGAAACCAATTTTGTCTCCCTTGAGACAA
Found at i:12867 original size:138 final size:138
Alignment explanation
Indices: 12606--13331 Score: 1096
Period size: 138 Copynumber: 5.2 Consensus size: 138
12596 CAAACCAGTT
* *
12606 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCC-A-ATGAGGGAGAAGAAGTTCATA
1 AACATTTCCA--GAAGAGTTCATAATGAGAAGAACTCATCCGACA-AAGGGAGAAGAAGTTCATA
* * * *
12669 ATGAGAAGCACTTGTTCAACCTTAGCTTGATTCATCGCATATAGAGTTGAATTAGCAACACCTCA
63 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCA
12734 CTCGAGGGATC
128 CTCGAGGGATC
*
12745 AACATTTCTAGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATG
* * ***
12810 AGAAGAACTTATTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAACACCTTTTTT
66 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACC-TCACT
12875 CGAGGGATC
130 CGAGGGATC
* * *
12884 AATATTTCCAGAAGAGTTTATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATG
* * *
12949 AGAAGAACTTGTTCAACCTTAGCCCGATTCATCACATATGGAGTTGAATCAGCAACACCTTACTC
66 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
13014 GAGGGATC
131 GAGGGATC
* * *
13022 AATATTTCCATAAGAGTTCATAATGAGAAGAACCCATCCGACAAAGGGAGAAGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATG
* * *
13087 AGAAGAACTTGTTCAAGCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGTAACACCTCACTT
66 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
*
13152 AAGGGATC
131 GAGGGATC
* * * *
13160 AACATTTCCAGAATAGTTCATAATGAGAAGAACTCATCTGAAAAAGGGAGAAAAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATG
* * *
13225 AGAAGAACTTGTTCAAGCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAATACCTCACAC
66 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
*
13290 GAGGGATT
131 GAGGGATC
*
13298 AACATTTCCAGAAGAATTCATAATGAGAAGAACT
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACT
13332 TGTTCAACCT
Statistics
Matches: 536, Mismatches: 48, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
137 28 0.05
138 371 0.69
139 137 0.26
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (138 bp):
AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
GAGGGATC
Found at i:13146 original size:277 final size:276
Alignment explanation
Indices: 12606--13330 Score: 1119
Period size: 277 Copynumber: 2.6 Consensus size: 276
12596 CAAACCAGTT
* * *
12606 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAAT-GAGGGAGAAGAAGTTCATAA
1 AACATTTCCA--GAAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAA
* * * *
12670 TGAGAAGCACTTGTTCAACCTTAGCTTGATTCATCGCATATAGAGTTGAATTAGCAACACCTCAC
64 TGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCAC
* *
12735 TCGAGGGATCAACATTTCTAGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAA
129 TCGAGGGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACCCATCCGACAAAGGGAGAAGAA
12800 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAA
194 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAA
*** *
12865 CACCTTTTTTCGAGGGATC
259 CACCTCACTT-AAGGGATC
* *
12884 AATATTTCCAGAAGAGTTTATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATG
* * *
12949 AGAAGAACTTGTTCAACCTTAGCCCGATTCATCACATATGGAGTTGAATCAGCAACACCTTACTC
66 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
* *
13014 GAGGGATCAATATTTCCATAAGAGTTCATAATGAGAAGAACCCATCCGACAAAGGGAGAAGAAGT
131 GAGGGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACCCATCCGACAAAGGGAGAAGAAGT
* * **
13079 TCATAATGAGAAGAACTTGTTCAAGCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGTAACA
196 TCATAATGAGAAGAACTTATTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAACA
13144 CCTCACTTAAGGGATC
261 CCTCACTTAAGGGATC
* * * *
13160 AACATTTCCAGAATAGTTCATAATGAGAAGAACTCATCTGAAAAAGGGAGAAAAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATG
* * *
13225 AGAAGAACTTGTTCAAGCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAATACCTCACAC
66 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
* *
13290 GAGGGATTAACATTTCCAGAAGAATTCATAATGAGAAGAAC
131 GAGGGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAAC
13331 TTGTTCAACC
Statistics
Matches: 406, Mismatches: 40, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
276 191 0.47
277 206 0.51
278 9 0.02
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (276 bp):
AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
GAGGGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACCCATCCGACAAAGGGAGAAGAAGT
TCATAATGAGAAGAACTTATTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAACAACA
CCTCACTTAAGGGATC
Found at i:13385 original size:98 final size:100
Alignment explanation
Indices: 13208--13429 Score: 351
Period size: 98 Copynumber: 2.2 Consensus size: 100
13198 TGAAAAAGGG
*
13208 AGAA-AAAGTTCATAATGAGAAGAACTTGTTCAAGCTTAGCTCGATTCATCGCATATGGAGTTGA
1 AGAAGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGA
* *
13272 ATCAGCAATACCTCACACGAGGGATTAACATTTCC
66 ATCAGCAACACCTCACACGAGGGATCAACATTTCC
13307 AGAAG-AA-TTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGA
1 AGAAGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGA
* * *
13370 ATCAGCAACATCTCACTCGAGGGATCAACATTTTC
66 ATCAGCAACACCTCACACGAGGGATCAACATTTCC
**
13405 AGTGGAAAGTTCATAATGAGAAGAA
1 AGAAGAAAGTTCATAATGAGAAGAA
13430 GTTCATAATG
Statistics
Matches: 112, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
98 88 0.79
99 8 0.07
100 16 0.14
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (100 bp):
AGAAGAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGA
ATCAGCAACACCTCACACGAGGGATCAACATTTCC
Found at i:13433 original size:17 final size:17
Alignment explanation
Indices: 13411--13446 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
13401 TTTCAGTGGA
13411 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
13428 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
13445 AA
1 AA
13447 CTTGTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (17 bp):
AAGTTCATAATGAGAAG
Found at i:14419 original size:14 final size:15
Alignment explanation
Indices: 14388--14420 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
14378 TAGTAGAGGA
14388 TTTTATCCTATTTTTC
1 TTTTATCCTA-TTTTC
14404 TTTTATCCTA-TTTC
1 TTTTATCCTATTTTC
14418 TTT
1 TTT
14421 CGTTCGAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
16 10 0.59
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATCCTATTTTC
Found at i:17658 original size:153 final size:153
Alignment explanation
Indices: 17370--17698 Score: 532
Period size: 153 Copynumber: 2.2 Consensus size: 153
17360 TGCAGTGTCT
* * * *
17370 TTGCTCCATCGTTAACAGTTGGCTTTGACAACGTTGCAGTCGGTTGCTGAACATGGAGAACATTG
1 TTGCTCCATCATTAACAGTTGGCGTAGACAACGTTGCACTCGGTTGCTGAACATGGAGAACATTG
*
17435 TTATTCGGCTGAGTCGCGACCGAGTTAGGACCTTCAAATATGACATCACTGTTATTACCATCTGC
66 TTATTCGGCTGAGTCGCGACCGAGTTAGGACCTTCAAATATGACATCACTGTTATTACCAGCTGC
17500 CATCAACCAAGCTTCAATGGCCA
131 CATCAACCAAGCTTCAATGGCCA
* *
17523 TTGCTCCATCATTAACAGTTGGCGTAGACAACGTTGCACTTGGTTGCTGAACGTGGAGAACATTG
1 TTGCTCCATCATTAACAGTTGGCGTAGACAACGTTGCACTCGGTTGCTGAACATGGAGAACATTG
*
17588 TTATTCGGCTGAGTCGCGACCGAGTTAGGACCTTCAAATATGACATTACTGTTATTACCAGCTGC
66 TTATTCGGCTGAGTCGCGACCGAGTTAGGACCTTCAAATATGACATCACTGTTATTACCAGCTGC
* * * **
17653 TATCAACGAAGCTTCATTGTTCA
131 CATCAACCAAGCTTCAATGGCCA
*
17676 TTGCTCCATCATTGACAGTTGGC
1 TTGCTCCATCATTAACAGTTGGC
17699 CGAAACGATG
Statistics
Matches: 162, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
153 162 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (153 bp):
TTGCTCCATCATTAACAGTTGGCGTAGACAACGTTGCACTCGGTTGCTGAACATGGAGAACATTG
TTATTCGGCTGAGTCGCGACCGAGTTAGGACCTTCAAATATGACATCACTGTTATTACCAGCTGC
CATCAACCAAGCTTCAATGGCCA
Found at i:17736 original size:153 final size:153
Alignment explanation
Indices: 17370--17736 Score: 468
Period size: 153 Copynumber: 2.4 Consensus size: 153
17360 TGCAGTGTCT
* * ** * * * * **
17370 TTGCTCCATCGTTAACAGTTGGCTTTGACAACGTTGCAGTCGGTTGCTGAACATGGAGAACATTG
1 TTGCTCCATCATTAACAGTTGGCGTAAACAACGTTGCACTTGGATGCTGAACGTCAAGAACATTG
*
17435 TTATTCGGCTGAGTCGCGACCGAGTTAGGACCTTCAAATATGACATCACTGTTATTACCATCTGC
66 TTATTCGGCTGAGTCGCGACCGAGTTAGGACCTTCAAATATGACATCACTGTTATTACCAGCTGC
17500 CATCAACCAAGCTTCAATGGCCA
131 CATCAACCAAGCTTCAATGGCCA
* * **
17523 TTGCTCCATCATTAACAGTTGGCGTAGACAACGTTGCACTTGGTTGCTGAACGTGGAGAACATTG
1 TTGCTCCATCATTAACAGTTGGCGTAAACAACGTTGCACTTGGATGCTGAACGTCAAGAACATTG
*
17588 TTATTCGGCTGAGTCGCGACCGAGTTAGGACCTTCAAATATGACATTACTGTTATTACCAGCTGC
66 TTATTCGGCTGAGTCGCGACCGAGTTAGGACCTTCAAATATGACATCACTGTTATTACCAGCTGC
* * * **
17653 TATCAACGAAGCTTCATTGTTCA
131 CATCAACCAAGCTTCAATGGCCA
* * * * *
17676 TTGCTCCATCATTGACAGTTGGCCG-AAACGATGTTG-AGTTCGGATGCTGAACTTCAAGAAC
1 TTGCTCCATCATTAACAGTTGG-CGTAAACAACGTTGCACTT-GGATGCTGAACGTCAAGAAC
17737 GTTACAATTA
Statistics
Matches: 190, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
152 3 0.02
153 185 0.97
154 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (153 bp):
TTGCTCCATCATTAACAGTTGGCGTAAACAACGTTGCACTTGGATGCTGAACGTCAAGAACATTG
TTATTCGGCTGAGTCGCGACCGAGTTAGGACCTTCAAATATGACATCACTGTTATTACCAGCTGC
CATCAACCAAGCTTCAATGGCCA
Found at i:27566 original size:17 final size:17
Alignment explanation
Indices: 27522--27593 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
27512 ATTCATGAAT
27522 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
* *
27539 GTTAGTCCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
27557 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
27574 TTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
27591 CTA
1 CTA
27594 AATCTTAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
17 31 0.72
18 12 0.28
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:27589 original size:34 final size:35
Alignment explanation
Indices: 27522--27593 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
27512 ATTCATGAAT
27522 CTAGTTCATTGAATAAAGTTAGTCCATTAATTAAA
1 CTAGTTCATTGAATAAAGTTAGTCCATTAATTAAA
* * *
27557 CTAGTTCATT-CATCAAA-TTAGTTCATTTATTAAA
1 CTAGTTCATTGAAT-AAAGTTAGTCCATTAATTAAA
27591 CTA
1 CTA
27594 AATCTTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 20 0.61
35 13 0.39
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (35 bp):
CTAGTTCATTGAATAAAGTTAGTCCATTAATTAAA
Found at i:28436 original size:49 final size:49
Alignment explanation
Indices: 28379--28477 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
28369 TGGTCAGCCA
28379 TCAAAGGATAAGAAGAATGACAAGTCATTTAATTGAATTCAATTGCATT
1 TCAAAGGATAAGAAGAATGACAAGTCATTTAATTGAATTCAATTGCATT
28428 TCAAAGGATAAGAAGAATGACAAGTCATTTAATTGAATTCAATTGCATT
1 TCAAAGGATAAGAAGAATGACAAGTCATTTAATTGAATTCAATTGCATT
28477 T
1 T
28478 AGGTGATTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (49 bp):
TCAAAGGATAAGAAGAATGACAAGTCATTTAATTGAATTCAATTGCATT
Found at i:29550 original size:75 final size:73
Alignment explanation
Indices: 29467--29657 Score: 221
Period size: 75 Copynumber: 2.6 Consensus size: 73
29457 ATATAATTAT
* * *
29467 TAAATTATAATTAATAAATAAAATTAAGAATTATTTCTTTCATTGATAAAAAATAAAAATATATA
1 TAAATTATAATTAATAAATAAAATTAAGAATTATTTCTTCCATTAACAAAAAATAAAAATATAT-
* *
29532 ATAATTTTTG
65 A-AACTATTG
* * *
29542 TAAATTATAGTTAATAAATAGAAA-TAAAAATCATTTCTTCCATTAACAAAAAATAAAAATATAT
1 TAAATTATAATTAATAAATA-AAATTAAGAATTATTTCTTCCATTAACAAAAAATAAAAATATAT
29606 AAACTATTG
65 AAACTATTG
* *
29615 TAAGTTATAGA-TAAT--A-AAAATTAAGAATTATTTATTCCATTAA
1 TAAATTATA-ATTAATAAATAAAATTAAGAATTATTTCTTCCATTAA
29658 AACAATAAGA
Statistics
Matches: 100, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
69 3 0.03
70 20 0.20
71 1 0.01
73 18 0.18
74 1 0.01
75 54 0.54
76 3 0.03
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (73 bp):
TAAATTATAATTAATAAATAAAATTAAGAATTATTTCTTCCATTAACAAAAAATAAAAATATATA
AACTATTG
Found at i:29874 original size:13 final size:14
Alignment explanation
Indices: 29856--29923 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
29846 ATTAATTCAA
*
29856 AAATAATTTA-AAT
1 AAATAAATTATAAT
*
29869 AAATAAATTATATT
1 AAATAAATTATAAT
*
29883 AAATAAATAAATAAT
1 AAATAAAT-TATAAT
29898 AAAT-AATTATGAA-
1 AAATAAATTAT-AAT
29911 AATATAAATTATA
1 AA-ATAAATTATA
29924 TCAATAGATC
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
13 13 0.29
14 18 0.40
15 14 0.31
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (14 bp):
AAATAAATTATAAT
Found at i:31482 original size:3 final size:3
Alignment explanation
Indices: 31474--31503 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31464 AGCACAACAC
31474 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
31504 GGAACATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:33710 original size:153 final size:153
Alignment explanation
Indices: 33432--34011 Score: 907
Period size: 153 Copynumber: 3.8 Consensus size: 153
33422 CATGGATGTT
33432 GACCTTCAAATATGACATTACTGTTATTACCAGCTGCCATCAACGAAGCTTCATTGTTCATTGCT
1 GACCTTCAAATATGACATTACTGTTATTACCAGCTGCCATCAACGAAGCTTCATTGTTCATTGCT
*
33497 CCATCATTAACAGTTGGCCAGAACGATGTTGAGTTCGGTTGCTGAACATCGAGAACATTGTTATT
66 CCATCATTAACAGTTGGCCAGAACGATGTTGAGTTCGATTGCTGAACATCGAGAACATTGTTATT
33562 CGGCTGAGTCGCGACCAAGTTAC
131 CGGCTGAGTCGCGACCAAGTTAC
* * *
33585 GACCTTCAAATATGACATTACTGTTATTACCATCTGCCATCAATC-AAGCTTCAATGGTCATTGC
1 GACCTTCAAATATGACATTACTGTTATTACCAGCTGCCATCAA-CGAAGCTTCATTGTTCATTGC
* *
33649 TCCATCATTAACAGTTGGCCAGAACGATGTTGAGTTCCATTGCTGAACATTGAGAACATTGTTAT
65 TCCATCATTAACAGTTGGCCAGAACGATGTTGAGTTCGATTGCTGAACATCGAGAACATTGTTAT
* *
33714 TCAGCTGAGTCGCGACCAAGTTAT
130 TCGGCTGAGTCGCGACCAAGTTAC
*
33738 GACCTTCAAATATGACATTACTGTCATTACCAGCTGCCATCAACGAAGCTTCATTGTTCATTGCT
1 GACCTTCAAATATGACATTACTGTTATTACCAGCTGCCATCAACGAAGCTTCATTGTTCATTGCT
* * * *
33803 CCATCATTAACAGTTGGCCAAAACGTTGTTGAGTTGGGA-TGCTGAACATGGAGAACATTGTTAT
66 CCATCATTAACAGTTGGCCAGAACGATGTTGAGTT-CGATTGCTGAACATCGAGAACATTGTTAT
* *
33867 TCGGCTGAGTCGTGACCGAGTTAC
130 TCGGCTGAGTCGCGACCAAGTTAC
* * *
33891 TACCTTCAAATATGAAATTACTGTTATTACCAGCTGTCATCAACGAAGCTTCATTGTTCATTGCT
1 GACCTTCAAATATGACATTACTGTTATTACCAGCTGCCATCAACGAAGCTTCATTGTTCATTGCT
* * *
33956 TCATCATTAACAGTTGGCC-GAAACGATGTTGAGTTCGGA-TGCTGAACTTCAAGAAC
66 CCATCATTAACAGTTGGCCAG-AACGATGTTGAGTTC-GATTGCTGAACATCGAGAAC
34012 GTTACCATTA
Statistics
Matches: 390, Mismatches: 32, Indels: 10
0.90 0.07 0.02
Matches are distributed among these distances:
152 1 0.00
153 387 0.99
154 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (153 bp):
GACCTTCAAATATGACATTACTGTTATTACCAGCTGCCATCAACGAAGCTTCATTGTTCATTGCT
CCATCATTAACAGTTGGCCAGAACGATGTTGAGTTCGATTGCTGAACATCGAGAACATTGTTATT
CGGCTGAGTCGCGACCAAGTTAC
Found at i:37171 original size:2 final size:2
Alignment explanation
Indices: 37166--37480 Score: 162
Period size: 2 Copynumber: 159.5 Consensus size: 2
37156 GAAAAAAATA
*
37166 AT AT AT GT AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
37206 AT AT -T AT AT GA- ACT AT AT AT AT AT -T AT GT AT AA ACT AT AA
1 AT AT AT AT AT -AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * **
37246 AT AT A- AT TT AT AT -T A- AT AA ACT AT AT AGT GC AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT A-T
* * * * *
37286 TT AT AT AT AT -T AC AT AT AT AA ACT AT GT AT AT AA ACT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT A-T
* * * * *
37330 TT AT -T A- AT AT AA AC A- AT AT AT AA AT -T AT AT AGT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
37369 AT AA AGT AT AT AT AT -T AT AT AT AT AA ACT AT AT AGT TT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
* *
37411 -T A- AT GT -T AT -T AT AT ACT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
37450 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37481 AACTACATAT
Statistics
Matches: 236, Mismatches: 45, Indels: 64
0.68 0.13 0.19
Matches are distributed among these distances:
1 18 0.08
2 203 0.86
3 15 0.06
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:37316 original size:13 final size:13
Alignment explanation
Indices: 37300--37324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37290 ATATATTACA
37300 TATATAAACTATG
1 TATATAAACTATG
37313 TATATAAACTAT
1 TATATAAACTAT
37325 ATAGTTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (13 bp):
TATATAAACTATG
Found at i:37327 original size:11 final size:11
Alignment explanation
Indices: 37187--37402 Score: 65
Period size: 11 Copynumber: 19.5 Consensus size: 11
37177 TATTAATATA
*
37187 TATATATATA-
1 TATATATAAAC
*
37197 TATATATATA-
1 TATATATAAAC
*
37207 TATTATATGAAC
1 TA-TATATAAAC
* *
37219 TATATATATAT
1 TATATATAAAC
*
37230 TATGTATAAAC
1 TATATATAAAC
**
37241 TATAAATATAATT
1 TAT--ATATAAAC
37254 TATATTAATAAAC
1 TATA-T-ATAAAC
*
37267 TATATAGT--GC
1 TATATA-TAAAC
***
37277 -ATATATAGTT
1 TATATATAAAC
*
37287 TATATATATTAC
1 TATATATA-AAC
37299 -ATATATAAAC
1 TATATATAAAC
37309 TATGTATATAAAC
1 TA--TATATAAAC
** *
37322 TATATAGTTTAT
1 TATATA-TAAAC
37334 TA-ATATAAAC
1 TATATATAAAC
*
37344 AATATATAAA-
1 TATATATAAAC
***
37354 T-TATATAGTG
1 TATATATAAAC
*
37364 TATATATAAAG
1 TATATATAAAC
*
37375 TATATATATTA-
1 TATATATA-AAC
37386 TATATATAAAC
1 TATATATAAAC
37397 TATATA
1 TATATA
37403 GTTTATATTA
Statistics
Matches: 152, Mismatches: 34, Indels: 39
0.68 0.15 0.17
Matches are distributed among these distances:
8 1 0.01
9 11 0.07
10 20 0.13
11 83 0.55
12 10 0.07
13 27 0.18
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.44
Consensus pattern (11 bp):
TATATATAAAC
Found at i:37560 original size:22 final size:21
Alignment explanation
Indices: 37535--37680 Score: 92
Period size: 22 Copynumber: 7.0 Consensus size: 21
37525 ATTGAACTAT
37535 ATATAAACTATATAGTTTATTA
1 ATATAAACTATATAGTTTA-TA
*
37557 ATATAAATTATATAGTTTA-A
1 ATATAAACTATATAGTTTATA
* *
37577 ATATAAAGTATATAAGTATAT-
1 ATATAAACTATAT-AGTTTATA
37598 ATATAAACTATA-A--TTATA
1 ATATAAACTATATAGTTTATA
*
37616 TATATAAAGTATA-A-TTTA-A
1 -ATATAAACTATATAGTTTATA
* * * *
37635 AGACTAAAGTATATAAATATATA
1 ATA-TAAACTATAT-AGTTTATA
* *
37658 ATATAAAATATATGAGTATATA
1 ATATAAACTATAT-AGTTTATA
37680 A
1 A
37681 AGTATATATA
Statistics
Matches: 102, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
17 3 0.03
18 2 0.02
19 23 0.23
20 16 0.16
21 17 0.17
22 38 0.37
23 3 0.03
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (21 bp):
ATATAAACTATATAGTTTATA
Found at i:37609 original size:19 final size:19
Alignment explanation
Indices: 37532--37715 Score: 99
Period size: 19 Copynumber: 9.4 Consensus size: 19
37522 ATTATTGAAC
* *
37532 TATATATAAACTATATAGTT
1 TATATATAAAATATA-AGTA
* *
37552 TATTAATATAAATTATATAGTT
1 TA-T-ATATAAAATATA-AGTA
*
37574 TAAATATAAAGTATATAAGTA
1 TATATATAAA--ATATAAGTA
* *
37595 TATATATAAACTATAATTA
1 TATATATAAAATATAAGTA
* *
37614 TATATATAAAGTATAA-TT
1 TATATATAAAATATAAGTA
* * *
37632 TAAAGACTAAAGTATATAAATA
1 TATATA-TAAA--ATATAAGTA
*
37654 TATAATATAAAATATATG-A
1 TAT-ATATAAAATATAAGTA
* *
37673 -GTATATAAAGTAT-A-TA
1 TATATATAAAATATAAGTA
*
37689 TACATATAAAATATAAGTA
1 TATATATAAAATATAAGTA
37708 TATATATA
1 TATATATA
37716 TATATAACTA
Statistics
Matches: 127, Mismatches: 24, Indels: 27
0.71 0.13 0.15
Matches are distributed among these distances:
16 1 0.01
17 20 0.16
18 7 0.06
19 36 0.28
20 14 0.11
21 18 0.14
22 29 0.23
23 2 0.02
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (19 bp):
TATATATAAAATATAAGTA
Found at i:37680 original size:17 final size:16
Alignment explanation
Indices: 37642--37721 Score: 71
Period size: 17 Copynumber: 5.1 Consensus size: 16
37632 TAAAGACTAA
37642 AGTATAT-AAATATAT
1 AGTATATAAAATATAT
37657 A--ATATAAAATATAT
1 AGTATATAAAATATAT
37671 GAGTATATAAAGTATATAT
1 -AGTATATAAA--ATATAT
*
37690 A-CATATAAAATATA-
1 AGTATATAAAATATAT
*
37704 AGTATATATATATATAT
1 AGTATATA-AAATATAT
37721 A
1 A
37722 ACTATAAAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
13 4 0.08
14 9 0.17
15 12 0.23
16 6 0.11
17 15 0.28
18 1 0.02
19 6 0.11
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (16 bp):
AGTATATAAAATATAT
Found at i:37685 original size:58 final size:60
Alignment explanation
Indices: 37557--37688 Score: 164
Period size: 59 Copynumber: 2.2 Consensus size: 60
37547 TAGTTTATTA
* * * * *
37557 ATATAAATTATATAGTTTAAATATAAAGTATATAAGTATATATATAAACTATAATTATAT
1 ATATAAAGTATATAGTTTAAAGATAAAGTATATAAATATATATATAAAATATAATGATAT
*
37617 ATATAAAGTATA-A-TTTAAAGACTAAAGTATATAAATATATAATATAAAATAT-ATGA-GT
1 ATATAAAGTATATAGTTTAAAGA-TAAAGTATATAAATATAT-ATATAAAATATAATGATAT
37675 ATATAAAGTATATA
1 ATATAAAGTATATA
37689 TACATATAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
58 20 0.32
59 22 0.35
60 21 0.33
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (60 bp):
ATATAAAGTATATAGTTTAAAGATAAAGTATATAAATATATATATAAAATATAATGATAT
Found at i:37710 original size:23 final size:24
Alignment explanation
Indices: 37675--37728 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
37665 ATATATGAGT
37675 ATATAAAGTATATATACATATA-AA
1 ATAT-AAGTATATATACATATATAA
*
37699 ATATAAGTATATATATATATATAA
1 ATATAAGTATATATACATATATAA
*
37723 CTATAA
1 ATATAA
37729 AGTACACACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (24 bp):
ATATAAGTATATATACATATATAA
Found at i:37727 original size:8 final size:8
Alignment explanation
Indices: 37639--37719 Score: 69
Period size: 8 Copynumber: 10.2 Consensus size: 8
37629 ATTTAAAGAC
37639 TAAAGTATA
1 TAAA-TATA
37648 TAAATATA
1 TAAATATA
37656 T-AATATA
1 TAAATATA
37663 -AAATATA
1 TAAATATA
* *
37670 TGAGTATA
1 TAAATATA
37678 TAAAGTATA
1 TAAA-TATA
* *
37687 TATACATA
1 TAAATATA
37695 TAAA-ATA
1 TAAATATA
*
37702 TAAGTATA
1 TAAATATA
*
37710 TATATATA
1 TAAATATA
37718 TA
1 TA
37720 TAACTATAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
7 18 0.31
8 29 0.50
9 11 0.19
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (8 bp):
TAAATATA
Found at i:37752 original size:8 final size:8
Alignment explanation
Indices: 37739--37801 Score: 81
Period size: 8 Copynumber: 7.9 Consensus size: 8
37729 AGTACACACA
37739 CATACATG
1 CATACATG
37747 CATACATG
1 CATACATG
37755 CATACATG
1 CATACATG
*
37763 CATACATA
1 CATACATG
*
37771 CATGCATG
1 CATACATG
*
37779 CATACATA
1 CATACATG
* *
37787 CATGCATA
1 CATACATG
37795 CATACAT
1 CATACAT
37802 TAAAAAGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 48 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (8 bp):
CATACATG
Found at i:37760 original size:16 final size:16
Alignment explanation
Indices: 37738--37801 Score: 92
Period size: 16 Copynumber: 4.0 Consensus size: 16
37728 AAGTACACAC
37738 ACATACATGCATACAT
1 ACATACATGCATACAT
*
37754 GCATACATGCATACAT
1 ACATACATGCATACAT
*
37770 ACATGCATGCATACAT
1 ACATACATGCATACAT
* *
37786 ACATGCATACATACAT
1 ACATACATGCATACAT
37802 TAAAAAGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (16 bp):
ACATACATGCATACAT
Found at i:37770 original size:12 final size:12
Alignment explanation
Indices: 37747--37801 Score: 83
Period size: 12 Copynumber: 4.6 Consensus size: 12
37737 CACATACATG
37747 CATACATGCATA
1 CATACATGCATA
* *
37759 CATGCATACATA
1 CATACATGCATA
*
37771 CATGCATGCATA
1 CATACATGCATA
37783 CATACATGCATA
1 CATACATGCATA
37795 CATACAT
1 CATACAT
37802 TAAAAAGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.25
Consensus pattern (12 bp):
CATACATGCATA
Found at i:37836 original size:8 final size:7
Alignment explanation
Indices: 37823--38039 Score: 91
Period size: 7 Copynumber: 30.0 Consensus size: 7
37813 AGTATAAAGT
37823 ATATATA
1 ATATATA
37830 CATATATA
1 -ATATATA
37838 ATAATATA
1 AT-ATATA
37846 A-AGTATA
1 ATA-TATA
*
37853 AGTATATT
1 A-TATATA
37861 ATATAT-
1 ATATATA
37867 ATATAT-
1 ATATATA
37873 ATATATA
1 ATATATA
37880 TATATTATA
1 -ATA-TATA
37889 AT-TATA
1 ATATATA
*
37895 A-AGATTAA
1 ATATA-T-A
37903 AGTATATAA
1 A-TATAT-A
*
37912 ACATATA
1 ATATATA
37919 ATATAT-
1 ATATATA
37925 ATATAT-
1 ATATATA
37931 ATATATA
1 ATATATA
37938 AGTATATAA
1 A-TATAT-A
37947 AGTATATA
1 A-TATATA
*
37955 TACATATA
1 -ATATATA
37963 A-AGTATA
1 ATA-TATA
*
37970 AGTATGTA
1 A-TATATA
37978 TATATATA
1 -ATATATA
37986 ATATA-A
1 ATATATA
37992 ACTATATA
1 A-TATATA
* *
38000 GTGTATA
1 ATATATA
38007 A-ATA-A
1 ATATATA
38012 AGTATATA
1 A-TATATA
*
38020 TTATAT-
1 ATATATA
38026 ATATA-A
1 ATATATA
38032 ACTATATA
1 A-TATATA
38040 GTTTATATTT
Statistics
Matches: 167, Mismatches: 14, Indels: 56
0.70 0.06 0.24
Matches are distributed among these distances:
5 2 0.01
6 41 0.25
7 52 0.31
8 50 0.30
9 20 0.12
10 2 0.01
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (7 bp):
ATATATA
Found at i:37894 original size:27 final size:27
Alignment explanation
Indices: 37822--38077 Score: 72
Period size: 25 Copynumber: 9.4 Consensus size: 27
37812 TAGTATAAAG
*
37822 TATATATACATA-TATAA-TA-ATATA
1 TATATATATATATTATAATTATATATA
*
37846 AAGTATA-AGTATATTAT-ATATATATATA
1 TA-TATATA-TATATTATAAT-TATATATA
* *
37874 TATAT--ATATATTATAATTATAAAGA
1 TATATATATATATTATAATTATATATA
* * *
37899 TTAAAGTATATAAACATATAA-TATATATA
1 -TATA-TATATATA-TTATAATTATATATA
* *
37928 TATATATATA-AGTAT-A-TAAAGTATA
1 TATATATATATATTATAATTATA-TATA
* * * * *
37953 TATACATATAAAGTATAAGTATGTATA
1 TATATATATATATTATAATTATATATA
* * *
37980 TATATAATATAAACTATATAGTGTATAAATA
1 TATAT-ATATATA-T-TATAAT-TATATATA
* * *
38011 AAGTATATATTATATATATAAACTATATAGTT
1 TA-TATATA-TATAT-TAT-AATTATATA-TA
*
38043 TATATTTATAT-TTAT-ATTAT-TATA
1 TATATATATATATTATAATTATATATA
38067 TACTATATATA
1 TA-TATATATA
38078 AACTATATAT
Statistics
Matches: 174, Mismatches: 33, Indels: 49
0.68 0.13 0.19
Matches are distributed among these distances:
24 9 0.05
25 47 0.27
26 19 0.11
27 21 0.12
28 21 0.12
29 11 0.06
30 12 0.07
31 25 0.14
32 9 0.05
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (27 bp):
TATATATATATATTATAATTATATATA
Found at i:38092 original size:25 final size:25
Alignment explanation
Indices: 38055--38113 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
38045 TATTTATATT
*
38055 TATATTATTATATACTATATATAAAC
1 TATA-TATAATATACTATATATAAAC
* *
38081 TATATATAATATATTATGTATAAAC
1 TATATATAATATACTATATATAAAC
*
38106 AATATATA
1 TATATATA
38114 CCATTTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TATATATAATATACTATATATAAAC
Found at i:38113 original size:2 final size:2
Alignment explanation
Indices: 37822--38094 Score: 128
Period size: 2 Copynumber: 137.5 Consensus size: 2
37812 TAGTATAAAG
* *
37822 TA TA TA TA CA TA TA TA -A TA -A TA TA AA GTA TA -A GTA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* *
37862 TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A T- TA TA AA GA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
37900 TA AA GTA TA TA AA CA TA TA -A TA TA TA TA TA TA TA TA TA -A GTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
37942 TA TA AA GTA TA TA TA CA TA TA AA GTA TA -A GTA TG 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
* * * *
37984 TA -A TA TA AA CTA TA TA GTG TA TA AA TA AA GTA TA TA T- TA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
38025 TA TA TA AA CTA TA TA GTT TA TA TT TA TA TT TA TA T- TA T- TA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
38067 TA CTA TA TA TA AA CTA TA TA TA -A TA TA T
1 TA -TA TA TA TA TA -TA TA TA TA TA TA TA T
38095 TATGTATAAA
Statistics
Matches: 203, Mismatches: 38, Indels: 60
0.67 0.13 0.20
Matches are distributed among these distances:
1 16 0.08
2 172 0.85
3 15 0.07
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.43
Consensus pattern (2 bp):
TA
Found at i:38139 original size:45 final size:46
Alignment explanation
Indices: 38024--38139 Score: 119
Period size: 45 Copynumber: 2.5 Consensus size: 46
38014 TATATATTAT
* ** * *
38024 ATATATAAACTATATAGTTTATATTTATATTTATATTATTATATACT
1 ATATATAAACTATATAGTTTATA-TTATATATATAACAATATATACC
* *
38071 ATATATAAACTATATA-TAATATATTATGTATA-AACAATATATACC
1 ATATATAAACTATATAGT-TTATATTATATATATAACAATATATACC
* *
38116 ATTTATAAACTATAGAGTTTATAT
1 ATATATAAACTATATAGTTTATAT
38140 ATGAACTATT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
45 28 0.49
46 9 0.16
47 20 0.35
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (46 bp):
ATATATAAACTATATAGTTTATATTATATATATAACAATATATACC
Found at i:38182 original size:22 final size:22
Alignment explanation
Indices: 38157--38198 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
38147 ATTGAACTAT
38157 ATATAAACAATATAGTTTATTA
1 ATATAAACAATATAGTTTATTA
**
38179 ATATAAATTATATAGTTTAT
1 ATATAAACAATATAGTTTAT
38199 GTAACCCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
ATATAAACAATATAGTTTATTA
Found at i:40693 original size:14 final size:15
Alignment explanation
Indices: 40670--40707 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
40660 CAAAGTCAAT
*
40670 GGGTTAACTCAGA-C
1 GGGTTGACTCAGACC
40684 GGGTTGACTCAGACC
1 GGGTTGACTCAGACC
*
40699 GAGTTGACT
1 GGGTTGACT
40708 TGGTGACTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (15 bp):
GGGTTGACTCAGACC
Found at i:41471 original size:2 final size:2
Alignment explanation
Indices: 41464--41925 Score: 260
Period size: 2 Copynumber: 241.0 Consensus size: 2
41454 AAAGTAAAAG
* * *
41464 TA TA TA TA TA AA CTA TA AA CTA TA TA TA CA TA TA TA -A TA -A TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * *
41506 TA AA GTA TA -A GTA TA TA TA TA TA TG TA TG 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
* * * *
41549 TA TA TA AA GT- TT TA GTA TA -A AA TA TA TA TA CA TA TA -A TA -A
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
41589 TA TA AA GTA TA -A GTA TA T- TA TA TA CA TA TA AA GTA TA -A T-
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * * *
41628 TA TA AA GA -A TA -A AA CA TA TA -A GCA TA TA -A TA TA AA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * *
41668 -A AA AA TA AA GTA T- TA -A GTA TA -A TA TA TA TA TA CA TA TA -A
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
41707 TA TA TA -A TA TA TA -A TA TA TA -A 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
41746 TA TA -A TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
41784 TA T- TT TA TA -A GTA T- TA TA TA TA AA AA TA TA TA T- 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
*
41823 TGA GTA T- TA TA TA T- TA TA TA TA TA TT TA T- TA TA TA -A TA TA
1 T-A -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
41863 TA TA -A GTA T- TA AA 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
41904 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
41926 AGTATTTTTT
Statistics
Matches: 363, Mismatches: 43, Indels: 108
0.71 0.08 0.21
Matches are distributed among these distances:
1 37 0.10
2 308 0.85
3 17 0.05
4 1 0.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (2 bp):
TA
Found at i:41476 original size:26 final size:26
Alignment explanation
Indices: 41442--41526 Score: 100
Period size: 26 Copynumber: 3.2 Consensus size: 26
41432 TATATATATG
41442 TATATAAACTATAAAGTAAAAGTATA
1 TATATAAACTATAAAGTAAAAGTATA
* * *
41468 TATATAAACTATAAACTATATA-TACA
1 TATATAAACTATAAAGTA-AAAGTATA
* *
41494 TATATAATAATATAAAGTATAAGTATA
1 TATATAA-ACTATAAAGTAAAAGTATA
41521 TATATA
1 TATATA
41527 TATGTATGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
26 28 0.58
27 20 0.42
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (26 bp):
TATATAAACTATAAAGTAAAAGTATA
Found at i:41489 original size:20 final size:19
Alignment explanation
Indices: 41451--41491 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
41441 GTATATAAAC
* *
41451 TATAAAGTAAAAGTATATA
1 TATAAACTAAAACTATATA
41470 TATAAACTATAAACTATATA
1 TATAAACTA-AAACTATATA
41490 TA
1 TA
41492 CATATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (19 bp):
TATAAACTAAAACTATATA
Found at i:41587 original size:85 final size:84
Alignment explanation
Indices: 41319--41786 Score: 290
Period size: 89 Copynumber: 5.5 Consensus size: 84
41309 ATATAGTTTA
* * * *
41319 AATATAAAGTATATAAGTATATATATATAAAGTATATATACATATATAATAATATAAAGTATAAT
1 AATATAAAG--TATAAGTATATATATAT-ATGTATATATATATATATAAT-ATATAAAGTTTAAC
*
41384 TATAAAGAATAAAGATATA-AGTATATAT
62 TAT-AA-AAT--ATATATACA-TATA-AT
* * * * * * *
41412 ACATATAAAGTTTAAGTATGTATATATATGTATATAAACTATAAAGTAAAAGTATATA-TATAAA
1 A-ATATAAAGTATAAGTATATATATATATGTATATATA-TATATA-TAATA-TATAAAGT-TTAA
*
41476 CTATAAACTATATATACATATATAAT
61 CTATAAAATATATATAC--ATATAAT
* * *
41502 AATATAAAGTATAAGTATATATATATATGTATGTATATATATATATATATATAAAGTTTTAGTAT
1 AATATAAAGTATAAGTATATATATATATGTATATATATATATATA-ATATATAAAGTTTAACTAT
41567 AAAATATATATACATATAAT
65 AAAATATATATACATATAAT
* * **
41587 AATATAAAGTATAAGTATAT-TATATA--CATATA-A-A-GTATAAT-TATAAAGAATAAAACAT
1 AATATAAAGTATAAGTATATATATATATGTATATATATATATATAATATATAAAG--TTTAAC-T
* *
41645 ATAAGCATATAATATAAAGTATAA-
63 ATAA-AATAT-ATATACA-TATAAT
* * * *
41669 AAAATAAAGTATTAAGTATA-ATATATATATACATATA-ATATATAATATATAATA-TATAA-TA
1 AATATAAAGTA-TAAGTATATATATATATGTATATATATATATATAATATATAA-AGTTTAACTA
* *
41730 TATATATATATATATATATAAT
64 TA-AAATATATATACATATAAT
* *
41752 ATTAT-AA-TAT-A-TATATATATATATATATATA-ATAT
1 AATATAAAGTATAAGTATATATATATATGTATATATATAT
41787 TTTATAAGTA
Statistics
Matches: 304, Mismatches: 43, Indels: 70
0.73 0.10 0.17
Matches are distributed among these distances:
77 7 0.02
78 7 0.02
79 23 0.08
80 7 0.02
81 7 0.02
82 27 0.09
83 28 0.09
84 14 0.05
85 32 0.11
86 6 0.02
87 30 0.10
88 13 0.04
89 39 0.13
90 3 0.01
91 15 0.05
92 24 0.08
93 14 0.05
94 8 0.03
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (84 bp):
AATATAAAGTATAAGTATATATATATATGTATATATATATATATAATATATAAAGTTTAACTATA
AAATATATATACATATAAT
Found at i:41592 original size:38 final size:34
Alignment explanation
Indices: 41414--41926 Score: 154
Period size: 35 Copynumber: 15.0 Consensus size: 34
41404 GTATATATAC
* **
41414 ATATAAAGTTTAAGTATGTATATATATGTATATAA-
1 ATATAAAGTATAAGTA--TATATATATACATATAAT
* *
41449 ACTATAAAGTAAAAGTATATATATAAAC-TATAA-
1 A-TATAAAGTATAAGTATATATATATACATATAAT
*
41482 ACTAT--A-TATACA-TATATAATAATATAAAGTATAAGT
1 A-TATAAAGTATA-AGTATAT-AT-ATATACA-TATAA-T
* * * *
41518 ATATATA-TATATGTATGTATATATATATAT-AT
1 ATATAAAGTATAAGTATATATATATACATATAAT
* *
41550 ATATAAAGTTTTAGTATAAAATATATATACATATAAT
1 ATATAAAGTATAAGTAT---ATATATATACATATAAT
41587 AATATAAAGTATAAGTATAT-TATATACATATAA-
1 -ATATAAAGTATAAGTATATATATATACATATAAT
* * * *
41620 AGTAT-AATTATAAAGAATAAAACATATAAGCATAT-A-
1 A-TATAAAGTAT-AAGTAT-ATATATAT-A-CATATAAT
* * *
41656 ATATAAAGTATAA-AAAATAAAGTATTA-AGTATAAT
1 ATATAAAGTATAAGTATATATA-TA-TACA-TATAAT
*
41691 ATAT--A-TATACA-TATA-ATATATAATATATAAT
1 ATATAAAGTATA-AGTATATATATAT-ACATATAAT
*
41722 ATAT-AA-TAT-A-TATATATATATATATATAAT
1 ATATAAAGTATAAGTATATATATATACATATAAT
*
41752 AT-TATAA-TATATA-TATATATATATATATATAAT
1 ATATA-AAGTATA-AGTATATATATATACATATAAT
* * * * * *
41785 ATTTTATAAGTATTA-TATATAAAAATATATATTAT
1 A-TATA-AAGTATAAGTATATATATATACATATAAT
* * * *
41820 ATATGAGTATTATATATTATATATATATTTATTATATAAT
1 ATAT-A-AAGTATA-AGTATATATATA--TA-CATATAAT
* *
41860 ATATATAAGTATTAAATATATATATATATATAT-AT
1 ATATA-AAGTA-TAAGTATATATATATACATATAAT
* *
41895 ATATATA-TATATA-TATATATATATATATATAA
1 ATATAAAGTATA-AGTATATATATATACATATAA
41927 GTATTTTTTA
Statistics
Matches: 381, Mismatches: 47, Indels: 102
0.72 0.09 0.19
Matches are distributed among these distances:
29 1 0.00
30 25 0.07
31 28 0.07
32 48 0.13
33 61 0.16
34 40 0.10
35 62 0.16
36 45 0.12
37 26 0.07
38 15 0.04
39 17 0.04
40 13 0.03
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (34 bp):
ATATAAAGTATAAGTATATATATATACATATAAT
Found at i:41625 original size:7 final size:7
Alignment explanation
Indices: 41589--41689 Score: 50
Period size: 7 Copynumber: 14.7 Consensus size: 7
41579 CATATAATAA
41589 TATAAAG
1 TATAAAG
41596 TAT-AAG
1 TATAAAG
*
41602 TATATTA-
1 TATA-AAG
*
41609 TATACA-
1 TATAAAG
41615 TATAAAG
1 TATAAAG
*
41622 TAT-AAT
1 TATAAAG
41628 TATAAAG
1 TATAAAG
* *
41635 AATAAAA
1 TATAAAG
*
41642 CATATAAG
1 TATA-AAG
*
41650 CATATAA-
1 TATA-AAG
41657 TATAAAG
1 TATAAAG
*
41664 TATAAAA
1 TATAAAG
*
41671 AATAAAG
1 TATAAAG
*
41678 TATTAAG
1 TATAAAG
41685 TATAA
1 TATAA
41690 TATATATATA
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
6 19 0.26
7 43 0.60
8 10 0.14
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (7 bp):
TATAAAG
Found at i:46785 original size:20 final size:20
Alignment explanation
Indices: 46760--46806 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
46750 AAAGGTGTTT
*
46760 ACAAAATTTATCTCACAAGA
1 ACAAAATTTAGCTCACAAGA
*
46780 ACAAAATTTAGCTCACAAGT
1 ACAAAATTTAGCTCACAAGA
46800 ACAAAAT
1 ACAAAAT
46807 ATTTATAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.19, G:0.06, T:0.23
Consensus pattern (20 bp):
ACAAAATTTAGCTCACAAGA
Found at i:47910 original size:20 final size:21
Alignment explanation
Indices: 47859--47911 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
47849 ATGGAATAAT
47859 AAAAAATAAAATATAAAGTAA
1 AAAAAATAAAATATAAAGTAA
** *
47880 ACTAAACAAAA-ATAAAG-AA
1 AAAAAATAAAATATAAAGTAA
47899 GAAAAAATAAAAT
1 -AAAAAATAAAAT
47912 GCTCTAGCGA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
19 2 0.08
20 14 0.58
21 8 0.33
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (21 bp):
AAAAAATAAAATATAAAGTAA
Found at i:52604 original size:244 final size:243
Alignment explanation
Indices: 52199--52748 Score: 606
Period size: 244 Copynumber: 2.3 Consensus size: 243
52189 ACCCAAGATT
* * * *
52199 GACTTAACTCGCAATGAAAGAGTCATCCACAATATAGCTTAACTCAATAGCGAGGAGATATTTTC
1 GACTTAACTCGCAATGAAAGAGTCATCCACAACATAGCTTAACTCAACAACAAGGAGATATTTTC
* * * * * **
52264 CAACCAAGGTTTTTAAGTCAACTTTTAATTTCATTACGAAGGATATTGGACTAGAAAAAGACCCA
66 CAACCAAGGTCTTCAAGTCAAATTTCAACTTCACAACGAAGGATATTGGACTAGAAAAAGACCCA
*
52329 AAAATGACTGTGATTTAGCTTAACTCAACAACAAAGAGCTAGCTT-TCAGCCCATATTTCT-AGT
131 AAAATGACTGTGATTTAGCTTAACTCAACAACAAAGAGCTA-CTTCTCAACCCATATTT-TGAGT
*
52392 TAGATTTCAACTTTACGACAAAATATATCAAAATCGAGTCATTTAGGATC
194 TAGATTTCAACTTCACGACAAAATATATCAAAATCGAGTCATTTAGGATC
* * ** * *
52442 GACTTAACTCGCAATGGAGGAGTTTTCCACAACATAGCTTAACTTAACAACAAGGAGCTATTTTC
1 GACTTAACTCGCAATGAAAGAGTCATCCACAACATAGCTTAACTCAACAACAAGGAGATATTTTC
* * * * * *
52507 GAACACAATGTCTTCAATTCAAATTTCAACTTCACAATGAAGGATATTGGATTAGAAGAAGACCC
66 CAAC-CAAGGTCTTCAAGTCAAATTTCAACTTCACAACGAAGGATATTGGACTAGAAAAAGACCC
* *
52572 -AAAATCGACTGTGATTTAGCTTAACTCAACAACGAGGAGCTACTTCTCAACCCATATTTTGAGT
130 AAAAAT-GACTGTGATTTAGCTTAACTCAACAACAAAGAGCTACTTCTCAACCCATATTTTGAGT
* ** *** * * *
52636 TTGATTTCAACTTCACGA-GGAATGATATCATGCTCGAGTCATTCAAGATT
194 TAGATTTCAACTTCACGACAAAAT-ATATCAAAATCGAGTCATTTAGGATC
* * * * * * * * *
52686 GACTTTACTCACAATGGATA-AGTCATCTATAATATAACTTAACTCAACAACGAGGAGCTATTT
1 GACTTAACTCGCAAT-GAAAGAGTCATCCACAACATAGCTTAACTCAACAACAAGGAGATATTT
52749 ATAACTAGAT
Statistics
Matches: 252, Mismatches: 49, Indels: 11
0.81 0.16 0.04
Matches are distributed among these distances:
243 70 0.28
244 181 0.72
245 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (243 bp):
GACTTAACTCGCAATGAAAGAGTCATCCACAACATAGCTTAACTCAACAACAAGGAGATATTTTC
CAACCAAGGTCTTCAAGTCAAATTTCAACTTCACAACGAAGGATATTGGACTAGAAAAAGACCCA
AAAATGACTGTGATTTAGCTTAACTCAACAACAAAGAGCTACTTCTCAACCCATATTTTGAGTTA
GATTTCAACTTCACGACAAAATATATCAAAATCGAGTCATTTAGGATC
Found at i:53320 original size:23 final size:24
Alignment explanation
Indices: 53268--53320 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
53258 ATCATTTTCA
* *
53268 TTTTATCTTTATACTTTTATTACT
1 TTTTATCTATATACTATTATTACT
* *
53292 TATTAT-TATATACTATTATTATT
1 TTTTATCTATATACTATTATTACT
53315 TTTTAT
1 TTTTAT
53321 ATTAGTTACT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTATCTATATACTATTATTACT
Found at i:53469 original size:15 final size:15
Alignment explanation
Indices: 53444--53485 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
53434 TATATGCTAT
*
53444 TTATA-TTATTATAG
1 TTATATTTATTATAC
53458 TTATATTTATTATAC
1 TTATATTTATTATAC
*
53473 TAATATTTATTAT
1 TTATATTTATTAT
53486 TTTGTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
TTATATTTATTATAC
Found at i:64711 original size:16 final size:17
Alignment explanation
Indices: 64685--64719 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
64675 GGATTCCAAG
*
64685 TGAAGAAAAAGTAAAAA
1 TGAAGAAAAAGGAAAAA
64702 TGAA-AAAAAGGAAAAA
1 TGAAGAAAAAGGAAAAA
64718 TG
1 TG
64720 CAAAGAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (17 bp):
TGAAGAAAAAGGAAAAA
Found at i:66619 original size:16 final size:16
Alignment explanation
Indices: 66598--66632 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
66588 TTCACATCTT
66598 TGCATAGCACATTCAA
1 TGCATAGCACATTCAA
66614 TGCATAGCACATTCAA
1 TGCATAGCACATTCAA
66630 TGC
1 TGC
66633 TTATGCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (16 bp):
TGCATAGCACATTCAA
Found at i:70188 original size:54 final size:54
Alignment explanation
Indices: 70123--70749 Score: 631
Period size: 54 Copynumber: 11.7 Consensus size: 54
70113 AAATAGGCAT
* *
70123 TAAGTGTGCAAATCACGGAATTAATCATATGTTGATGAACAACCATTTCGACAC
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
* * * *
70177 TAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAATCGTTTCGACAG
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
* * *
70231 TATGTGTACAAATCACAGAATTCATCATATGTTGATGAATAACCATTTCGACAC
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
* * *
70285 TAAGTGTGCAAATCACGGAATTCATCACATGTTGATGAATAA-C---TGGGCAC
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
** * * *
70335 TAAGTGTGCAAATCACATAATTCATTATATGTTGATGAATAACCGTTTCGGCAC
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
* * *
70389 TAAGTGTGCAAATCACAGAATTCATCATATGTTG-TGAATAA-CAGTTTTGGA-AT
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCA--TTTCGACAC
* *** * *
70442 TAAGTGTGTAAATCATATAATTCATCATATATTGATGGATAACCATTTC-AGCAC
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGA-CAC
* ** *
70496 TAAGTGTGAAAAGT-ACGGAATTCATCATATGTTGATGAATAACTGTTTCGGCAC
1 TAAGTGTGCAAA-TCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
* **
70550 TAAGTGTACAAAGTACAC--AATTCATCATATGTTGATGAATAACTGTTTC-AGCAC
1 TAAGTGTGCAAA-T-CACGGAATTCATCATATGTTGATGAATAACCATTTCGA-CAC
* * * *
70604 GAAGTGCGCAAAGT-ACGAAATTCATCATATGTTGATGAATAATCATTTC-AGCAC
1 TAAGTGTGCAAA-TCACGGAATTCATCATATGTTGATGAATAACCATTTCGA-CAC
* * *
70658 TAAGTGTGCAAAGT-ACGGAATTCATCATAGGTT-ATGTATAATCATTTC-AGCAC
1 TAAGTGTGCAAA-TCACGGAATTCATCATATGTTGATGAATAACCATTTCGA-CAC
* * * * *
70711 TATGTGTGCAAAACACGAAATTCATAATATGTTTATGAA
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAA
70750 AAGATCGTAT
Statistics
Matches: 488, Mismatches: 66, Indels: 38
0.82 0.11 0.06
Matches are distributed among these distances:
50 43 0.09
51 1 0.00
52 4 0.01
53 88 0.18
54 347 0.71
55 3 0.01
56 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (54 bp):
TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
Found at i:77445 original size:7 final size:7
Alignment explanation
Indices: 77435--77475 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
77425 GAAATTTTGG
77435 GTTTTTT
1 GTTTTTT
77442 GTTTTTT
1 GTTTTTT
77449 -TTTCTTT
1 GTTT-TTT
*
77456 TTTTTTT
1 GTTTTTT
77463 GTTTTTT
1 GTTTTTT
77470 GTTTTT
1 GTTTTT
77476 GAAAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 3 0.10
7 25 0.81
8 3 0.10
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (7 bp):
GTTTTTT
Found at i:77451 original size:10 final size:10
Alignment explanation
Indices: 77436--77469 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
77426 AAATTTTGGG
77436 TTTTTTGTTT
1 TTTTTTGTTT
*
77446 TTTTTTCTTTT
1 TTTTTT-GTTT
77457 TTTTTTGTTT
1 TTTTTTGTTT
77467 TTT
1 TTT
77470 GTTTTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.91
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:81365 original size:18 final size:18
Alignment explanation
Indices: 81342--81377 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
81332 TTGCTCGCGA
*
81342 GCTTTTCGAGTTGAGTAT
1 GCTTTTCAAGTTGAGTAT
81360 GCTTTTCAAGTTGAGTAT
1 GCTTTTCAAGTTGAGTAT
81378 CAAATAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.25, T:0.44
Consensus pattern (18 bp):
GCTTTTCAAGTTGAGTAT
Found at i:87024 original size:17 final size:16
Alignment explanation
Indices: 86982--87024 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
86972 TTCAATTGCA
86982 TGTTTAATTTTCAATT
1 TGTTTAATTTTCAATT
* *
86998 TATTTCAATTTATCCATT
1 TGTTT-AATTT-TCAATT
87016 TGTTTAATT
1 TGTTTAATT
87025 CACATAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 9 0.41
ACGTcount: A:0.26, C:0.09, G:0.05, T:0.60
Consensus pattern (16 bp):
TGTTTAATTTTCAATT
Found at i:96029 original size:12 final size:13
Alignment explanation
Indices: 96005--96033 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
95995 AAATGAAAAA
96005 AAATGCAAAATGT
1 AAATGCAAAATGT
96018 AAATGC-AAATGT
1 AAATGCAAAATGT
96030 AAAT
1 AAAT
96034 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:97600 original size:41 final size:47
Alignment explanation
Indices: 97554--97646 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 47
97544 AGAAATATTC
97554 AAATAATTAAATGAAAAAT-T-T-AATA-TATGAAAAT-A-AAGTAA-
1 AAATAATTAAAT-AAAAATATATAAATATTATGAAAATCATAAGTAAT
97595 AAATAA--AAATAAAAATATATAAATATTATGAAAATCATAAGTAAT
1 AAATAATTAAATAAAAATATATAAATATTATGAAAATCATAAGTAAT
97640 AAA-AATT
1 AAATAATT
97647 TGAAAGAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
38 6 0.14
39 5 0.12
40 1 0.02
41 10 0.23
42 9 0.21
43 1 0.02
44 8 0.19
45 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (47 bp):
AAATAATTAAATAAAAATATATAAATATTATGAAAATCATAAGTAAT
Found at i:99948 original size:3 final size:3
Alignment explanation
Indices: 99940--99999 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
99930 AGCTTGTTTG
**
99940 TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* *
99985 TTA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA
100000 AAAAATGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:105321 original size:63 final size:63
Alignment explanation
Indices: 105203--105327 Score: 146
Period size: 65 Copynumber: 2.0 Consensus size: 63
105193 GTTTGCTGTT
* * *
105203 TTAGTGTAAGTTTTTACAATTTAATATATTGCTTCTATAATAGCAGTATTGATATATTATATA
1 TTAGTGTAAGTTTTTACAATTTAATACATTGCTTCAATAATAGCAGTATTGATATAATATATA
* * * **
105266 TTAGTGTAAGAATTTTTACGATTTAATACATTGTTTCAATTATAGTTGT-TT-ATATAATATAT
1 TTAGTGTAAG--TTTTTACAATTTAATACATTGCTTCAATAATAGCAGTATTGATATAATATAT
105328 TGTTTCTATA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
63 20 0.38
64 2 0.04
65 30 0.58
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (63 bp):
TTAGTGTAAGTTTTTACAATTTAATACATTGCTTCAATAATAGCAGTATTGATATAATATATA
Found at i:105332 original size:16 final size:16
Alignment explanation
Indices: 105306--105349 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
105296 TTGTTTCAAT
105306 TATAGTTGTTTATATAA
1 TATA-TTGTTTATATAA
*
105323 TATATTGTTTCTATAA
1 TATATTGTTTATATAA
*
105339 CATATTGTTTA
1 TATATTGTTTA
105350 GTTTAAGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (16 bp):
TATATTGTTTATATAA
Found at i:106055 original size:21 final size:21
Alignment explanation
Indices: 106026--106069 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
106016 TTGTGAATAA
* *
106026 GTTACTAAGGTTGTTGAGGGT
1 GTTAATAAGATTGTTGAGGGT
*
106047 GTTAATAAGATTGTTGATGGT
1 GTTAATAAGATTGTTGAGGGT
106068 GT
1 GT
106070 GATAATTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.02, G:0.34, T:0.41
Consensus pattern (21 bp):
GTTAATAAGATTGTTGAGGGT
Found at i:106704 original size:15 final size:15
Alignment explanation
Indices: 106684--106718 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
106674 TATTGGAGAG
106684 GATGTTGTGGAAGAA
1 GATGTTGTGGAAGAA
106699 GATGTTGTGGAAGAA
1 GATGTTGTGGAAGAA
106714 GATGT
1 GATGT
106719 AGTAAACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.40, T:0.29
Consensus pattern (15 bp):
GATGTTGTGGAAGAA
Found at i:108729 original size:54 final size:54
Alignment explanation
Indices: 108606--109060 Score: 597
Period size: 54 Copynumber: 8.4 Consensus size: 54
108596 TGGTTTTCGT
* * ** * * * **
108606 ACACGTAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTTGGGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTC-TTAAGTTGC
* *
108661 ACACATAGTGCCAATACAAAAATTCATAAACTTATTATGAACTTCTTAAGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
* * * *
108715 ACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTTC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
*
108769 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAACTTCTTAAGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
* * * * * * *
108823 ACACACAGTTCCAGTAGGGAAATTCATAACCTTATTATGAATTTCTTAGGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
*
108877 ACACATAGTGCTAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
* * *
108931 ACACACATTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
* *
108985 ACACATAGTGCCAATACGAAAATTCATAAAATTATTTTGAATTTCTTAAGGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAA-GTTGC
**
109040 AC-CATAACGCCAATACTGAAA
1 ACACATAGTGCCAATAC-GAAA
109061 CTCATTATGA
Statistics
Matches: 349, Mismatches: 49, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
54 302 0.87
55 47 0.13
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (54 bp):
ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
Found at i:108802 original size:108 final size:108
Alignment explanation
Indices: 108612--109041 Score: 671
Period size: 108 Copynumber: 4.0 Consensus size: 108
108602 TCGTACACGT
* * * * * *
108612 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTTGGGTTGCACACATAGTGCCAATA
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACATAGTGCCAATA
*
108677 CAAAAATTCATAAACTTATTATGAACTTCTTAAGTTGCACACAC
65 CGAAAATTCATAAACTTATTATGAACTTCTTAAGTTGCACACAC
*
108721 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTTCACACATAGTGCCAATAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATAC
108786 GAAAATTCATAAACTTATTATGAACTTCTTAAGTTGCACACAC
66 GAAAATTCATAAACTTATTATGAACTTCTTAAGTTGCACACAC
* * * * *
108829 AGTTCCAGTAGGGAAATTCATAACCTTATTATGAATTTCTTAGGTTGCACACATAGTGCTAATAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATAC
*
108894 GAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
66 GAAAATTCATAAACTTATTATGAACTTCTTAAGTTGCACACAC
* *
108937 ATTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATAC
* * *
109002 GAAAATTCATAAAATTATTTTGAATTTCTTAAGGTTGCAC
66 GAAAATTCATAAACTTATTATGAACTTCTTAA-GTTGCAC
109042 CATAACGCCA
Statistics
Matches: 296, Mismatches: 24, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
108 255 0.86
109 41 0.14
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (108 bp):
AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATAC
GAAAATTCATAAACTTATTATGAACTTCTTAAGTTGCACACAC
Found at i:113525 original size:18 final size:19
Alignment explanation
Indices: 113502--113549 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
113492 GATGCAGTTA
* *
113502 GTATCGATAC-TGATGTGG
1 GTATCGATACATGAGGTAG
113520 GTATCGATACTATGAGGTAG
1 GTATCGATAC-ATGAGGTAG
113540 GTATCGATAC
1 GTATCGATAC
113550 CGTGGATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
20 16 0.62
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.31
Consensus pattern (19 bp):
GTATCGATACATGAGGTAG
Found at i:113617 original size:22 final size:22
Alignment explanation
Indices: 113591--113652 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
113581 ACTGCAAGGG
* *
113591 AGTATCGGTACCATATTATAGA
1 AGTATCGATACCATAGTATAGA
113613 AGTATCGATACCATAGTATAGA
1 AGTATCGATACCATAGTATAGA
*
113635 AGTATCGATACCACAGTA
1 AGTATCGATACCATAGTA
113653 GAGGTACCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGA
Found at i:114303 original size:61 final size:60
Alignment explanation
Indices: 114062--114366 Score: 346
Period size: 60 Copynumber: 5.1 Consensus size: 60
114052 ATGCTCTAAA
* * * *
114062 ATGA-AAGTTAAATGCCTGACGGTGCATTTTGGCAGAAATGTGTCACTAATGCAAGTTAG
1 ATGATAAGTTAAATGCCTAAAGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
* * *
114121 ATGATAAGATAAATGGCTAACA-TTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
1 ATGATAAGTTAAATGCCTAA-AGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
* * * * *
114181 ATGATAAGTTAAATGTCTAATGGTGCATTTTGGCAGAAAAGTGTCATTAATGCAAGTTAG
1 ATGATAAGTTAAATGCCTAAAGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
* *
114241 ATGATAAGTTAAATGACTAAAGGTGCATTTTTGACAGAAAGGTGCCACTAATGCAAGTTAG
1 ATGATAAGTTAAATGCCTAAAGGTGCA-TTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
* * * * * * ** *
114302 ATTAAAAATTTAAATGCCT-AATGAGAATTTTTGGCATTAAGGTGCCACTAATGCTAGTTAG
1 A-TGATAAGTTAAATGCCTAAAGGTGCA-TTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
114363 ATGA
1 ATGA
114367 AAAAACAATG
Statistics
Matches: 209, Mismatches: 32, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
59 4 0.02
60 126 0.60
61 66 0.32
62 13 0.06
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (60 bp):
ATGATAAGTTAAATGCCTAAAGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
Found at i:117933 original size:54 final size:54
Alignment explanation
Indices: 117849--118191 Score: 474
Period size: 54 Copynumber: 6.3 Consensus size: 54
117839 ATCACGTGGG
* * *
117849 GTTGCACCCATAGTGCCAATACAGAAATTCATAAACTTATTATGAACTTCTTAA
1 GTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAA
* * *
117903 GTTTCACACACAGTGCCAATACGGAAATTCATAAAATTATTATGAATTTCTT-A
1 GTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAA
* **
117956 GTTTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAGCTTCTTAA
1 G-TTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAA
* * * *
118011 GTTGCACACACAGTTCCAATAGGGAAATTCATAAACTTATTATGAATTTCTTAG
1 GTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAA
*
118065 GTTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAA
1 GTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAA
* * * *
118119 GGTTGTACACATAGTTCCAATACAGAAATTCATAAACTCATTATGAATTT-TGTAA
1 -GTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCT-TAA
118174 GGTTGCACACATAGTGCC
1 -GTTGCACACATAGTGCC
118192 CTTTCGGTAA
Statistics
Matches: 254, Mismatches: 31, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
53 2 0.01
54 187 0.74
55 65 0.26
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (54 bp):
GTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAA
Found at i:118007 original size:108 final size:108
Alignment explanation
Indices: 117812--118191 Score: 523
Period size: 108 Copynumber: 3.5 Consensus size: 108
117802 TATTATGCCG
* * * ** ** *
117812 ATACGGTAATTCACAAACTCATTATGAATCACGTGGGGTTGCACCCATAGTGCCAATAC-AGAAA
1 ATACGGAAATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACATAGTGCCAATACGA-AAA
*
117876 TTCATAAACTTATTATGAACTTCTTAAGTTTCACACACAGTGCCA
64 TTCATAAACTTATTATGAACTTCTTAAGTTTCACACACAGTTCCA
* *
117921 ATACGGAAATTCATAAAATTATTATGAATTTCTTAGTTTGCACACATAGTGCCAATACGAAAATT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATT
* *
117986 CATAAACTTATTATGAGCTTCTTAAGTTGCACACACAGTTCCA
66 CATAAACTTATTATGAACTTCTTAAGTTTCACACACAGTTCCA
*
118029 ATAGGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATT
* *
118094 CATAAACTTATTATGAATTTCTTAAGGTTGT-ACACATAGTTCCA
66 CATAAACTTATTATGAACTTCTTAA-GTT-TCACACACAGTTCCA
* *
118138 ATACAGAAATTCATAAACTCATTATGAATTT-TGTAAGGTTGCACACATAGTGCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCT-T-AGGTTGCACACATAGTGCC
118192 CTTTCGGTAA
Statistics
Matches: 243, Mismatches: 23, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
108 153 0.63
109 71 0.29
110 19 0.08
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (108 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATT
CATAAACTTATTATGAACTTCTTAAGTTTCACACACAGTTCCA
Found at i:120331 original size:18 final size:19
Alignment explanation
Indices: 120308--120344 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
120298 TGACAAGCCT
120308 ATATTGGAAATG-TTGAAA
1 ATATTGGAAATGTTTGAAA
120326 ATATTGGAAATGTTTGAAA
1 ATATTGGAAATGTTTGAAA
120345 TAAGCCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (19 bp):
ATATTGGAAATGTTTGAAA
Found at i:121040 original size:27 final size:27
Alignment explanation
Indices: 121000--121055 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
120990 TTTTGTATTT
* *
121000 TGGTCTTTTGTTTTGTATGCAACAAGC
1 TGGTCTTTTATTTTGTATGAAACAAGC
121027 TGGTCTTTTATTTTGTATGAAACAAGC
1 TGGTCTTTTATTTTGTATGAAACAAGC
121054 TG
1 TG
121056 ATTGATGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (27 bp):
TGGTCTTTTATTTTGTATGAAACAAGC
Found at i:124011 original size:14 final size:14
Alignment explanation
Indices: 123992--124040 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
123982 AAGTCAATGG
123992 GTTGACTCAGAAGA
1 GTTGACTCAGAAGA
124006 GTTGACTCAGACA-A
1 GTTGACTCAGA-AGA
124020 GTTGACTCA-AACGA
1 GTTGACTCAGAA-GA
124034 GTTGACT
1 GTTGACT
124041 TGATTTAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.03
13 1 0.03
14 29 0.91
15 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (14 bp):
GTTGACTCAGAAGA
Found at i:131740 original size:40 final size:40
Alignment explanation
Indices: 131685--131846 Score: 254
Period size: 40 Copynumber: 4.0 Consensus size: 40
131675 TGCAGGTTTA
131685 TAATACACTTCGGTGTATATGGTGGGCACGAACTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGAACTTATGTG
*
131725 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGAACTTATGTG
* * ** *
131765 TAATACACTTTGGTGTATATGGTTGGCAATACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGAACTTATGTG
131805 TAATACACTTCGGTGTATATGGTGGGCAC-AACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGAA-CTTATGTG
131845 TA
1 TA
131847 GCACGACGGT
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.01
40 111 0.99
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGAACTTATGTG
Found at i:131994 original size:44 final size:44
Alignment explanation
Indices: 131923--132016 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 44
131913 TGGTATATGG
*
131923 TTATGGAATAATGGCAAGTGTAATGGTAAAATAAGCTTACGAGC
1 TTATGGAATAATGGCAAGTATAATGGTAAAATAAGCTTACGAGC
* *
131967 TTATGG-ATATATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATA-ATGGCAAGTATAATGGTAAAATAAGCTTACGAGC
132011 TTATGG
1 TTATGG
132017 TATTAAATGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 3 0.07
44 43 0.93
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.32
Consensus pattern (44 bp):
TTATGGAATAATGGCAAGTATAATGGTAAAATAAGCTTACGAGC
Found at i:135506 original size:23 final size:24
Alignment explanation
Indices: 135471--135515 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
135461 TGCAAGCTAT
*
135471 AAATGTACAACT-ATTGTTGAAGG
1 AAATGTACAACTAATGGTTGAAGG
135494 AAATG-ACACACTAATGGTTGAA
1 AAATGTACA-ACTAATGGTTGAA
135516 TAAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 8 0.42
24 8 0.42
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (24 bp):
AAATGTACAACTAATGGTTGAAGG
Found at i:139169 original size:40 final size:40
Alignment explanation
Indices: 139114--139275 Score: 279
Period size: 40 Copynumber: 4.0 Consensus size: 40
139104 TGCAGGTTTA
* * *
139114 TAATACACTTTGGTGTTTATGTTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
139154 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATATG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
139194 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
139234 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
139274 TA
1 TA
139276 GCACGACGGT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 117 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:139401 original size:44 final size:44
Alignment explanation
Indices: 139352--139455 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 44
139342 TGGTATATGG
* *
139352 TTATGGA-ATAATGGCAAGTGTATTGGTAAAATAGGCTTACGAGC
1 TTATGGATA-AATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
* * *
139396 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTATGATC
1 TTATGGATAAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
139440 TTATGGTATTAAATGG
1 TTATGG-A-TAAATGG
139456 TAAAATATTG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 43 0.83
45 2 0.04
46 7 0.13
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.35
Consensus pattern (44 bp):
TTATGGATAAATGGCAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:139959 original size:19 final size:19
Alignment explanation
Indices: 139923--139959 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
139913 AATGATTTTG
*
139923 GGGTACCGATACCCCCACA
1 GGGTACCGATACCACCACA
*
139942 GGGTACCGATTCCACCAC
1 GGGTACCGATACCACCAC
139960 TGTTCACGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.41, G:0.22, T:0.14
Consensus pattern (19 bp):
GGGTACCGATACCACCACA
Found at i:141217 original size:22 final size:22
Alignment explanation
Indices: 141145--141222 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
141135 ATCGAAAGGG
* * *
141145 AGTATCAATACCATAGTGTAGT
1 AGTATCGATACCATAGTATAGA
* *
141167 AGTATCGATACTA-AG-AGA-A
1 AGTATCGATACCATAGTATAGA
141186 AGATATCGATACCATAGTATAGA
1 AG-TATCGATACCATAGTATAGA
141209 AGTATCGATACCAT
1 AGTATCGATACCAT
141223 GATAAGGGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 2 0.04
20 11 0.24
21 4 0.09
22 25 0.56
23 3 0.07
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGA
Found at i:141235 original size:42 final size:42
Alignment explanation
Indices: 141146--141239 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
141136 TCGAAAGGGA
* * * *
141146 GTATCAATACCATAGTGTAGTAGTATCGATACTAAGAGAAAG
1 GTATCGATACCATAGTATAGAAGTATCGATACCAAGAGAAAG
* * * *
141188 ATATCGATACCATAGTATAGAAGTATCGATACCATGATAAGG
1 GTATCGATACCATAGTATAGAAGTATCGATACCAAGAGAAAG
141230 GTATCGATAC
1 GTATCGATAC
141240 TATTGTGTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (42 bp):
GTATCGATACCATAGTATAGAAGTATCGATACCAAGAGAAAG
Found at i:141695 original size:46 final size:46
Alignment explanation
Indices: 141642--141851 Score: 325
Period size: 46 Copynumber: 4.6 Consensus size: 46
141632 TAAAAAAAAT
* * *
141642 CCATAAATGAAATGCATGAAA-TAGTGCATTAAGGTATGAAAAGATG
1 CCATAAATGAAATGCATGAAAGGA-TGCATTAAGGCATGAAAGGATG
141688 CCATAAATG-AATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
141733 CCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
141779 CCATAAATGAAATGCATTAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
141825 CCATATATGAAATGAATGAAAGGATGC
1 CCATAAATGAAATGCATGAAAGGATGC
141852 CATAAATCAA
Statistics
Matches: 151, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 40 0.26
46 111 0.74
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.22
Consensus pattern (46 bp):
CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:141725 original size:20 final size:20
Alignment explanation
Indices: 141700--141825 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
141690 ATAAATGAAT
141700 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
141720 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
141746 GCATGAAAGGATACATTAAG
1 GCATGAAAGGATGCATTAAG
*
141766 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
141792 GCATTAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
141812 GCATGAAAGGATGC
1 GCATGAAAGGATGC
141826 CATATATGAA
Statistics
Matches: 84, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
20 41 0.49
21 6 0.07
22 2 0.02
24 2 0.02
25 6 0.07
26 27 0.32
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:141750 original size:26 final size:25
Alignment explanation
Indices: 141677--141877 Score: 153
Period size: 26 Copynumber: 8.5 Consensus size: 25
141667 GCATTAAGGT
*
141677 ATGAAAAGATGCCATAAATGAATGC
1 ATGAAAGGATGCCATAAATGAATGC
*
141702 ATGAAAGGATG-CAT---T-AAGGC
1 ATGAAAGGATGCCATAAATGAATGC
141722 ATGAAAGGATGCCATAAATGAAATGC
1 ATGAAAGGATGCCATAAATG-AATGC
* *
141748 ATGAAAGGAT-ACAT---T-AAGGC
1 ATGAAAGGATGCCATAAATGAATGC
141768 ATGAAAGGATGCCATAAATGAAATGC
1 ATGAAAGGATGCCATAAATG-AATGC
* * *
141794 ATTAAATGATG-CAT---T-AAGGC
1 ATGAAAGGATGCCATAAATGAATGC
* *
141814 ATGAAAGGATGCCATATATGAAATGA
1 ATGAAAGGATGCCATAAATG-AATGC
* *
141840 ATGAAAGGATGCCATAAATCAAATAC
1 ATGAAAGGATGCCATAAAT-GAATGC
*
141866 ATGATAGGATGC
1 ATGAAAGGATGC
141878 ATTAAGGCAT
Statistics
Matches: 138, Mismatches: 19, Indels: 37
0.71 0.10 0.19
Matches are distributed among these distances:
20 42 0.30
21 10 0.07
22 2 0.01
24 6 0.04
25 16 0.12
26 62 0.45
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (25 bp):
ATGAAAGGATGCCATAAATGAATGC
Found at i:141936 original size:118 final size:117
Alignment explanation
Indices: 141722--141937 Score: 265
Period size: 118 Copynumber: 1.8 Consensus size: 117
141712 GCATTAAGGC
* *
141722 ATGAAAGGATGCCATAAATGAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAAT
1 ATGAAAGGATGCCATAAATCAAATACATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAAT
** * * * *
141787 GAAATGCATTAAATGATGCATTAAGGCATGAAAGGATGCCATATATGAAATGA
66 GAAATGCACCAAATAATACAATAA-GAATGAAAGGATGCCATATATGAAATGA
* * * *
141840 ATGAAAGGATGCCATAAATCAAATACATGATAGGATGCATTAAGGCATGAAAGGATGCGATGAAT
1 ATGAAAGGATGCCATAAATCAAATACATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAAT
*
141905 GAAAT-TACCAAATAATTACTAAATAA-AATGAAA
66 GAAATGCACCAAATAA-TAC--AATAAGAATGAAA
141938 AAAATATACA
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
117 6 0.07
118 72 0.88
120 4 0.05
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (117 bp):
ATGAAAGGATGCCATAAATCAAATACATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAAT
GAAATGCACCAAATAATACAATAAGAATGAAAGGATGCCATATATGAAATGA
Found at i:142920 original size:16 final size:16
Alignment explanation
Indices: 142899--142935 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
142889 AATCTCAAAA
142899 GAGCTGAAGAGATTTG
1 GAGCTGAAGAGATTTG
*
142915 GAGCTGAAGAGCTTTG
1 GAGCTGAAGAGATTTG
142931 GAGCT
1 GAGCT
142936 CCAGAGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.11, G:0.38, T:0.24
Consensus pattern (16 bp):
GAGCTGAAGAGATTTG
Found at i:142941 original size:16 final size:16
Alignment explanation
Indices: 142899--142941 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
142889 AATCTCAAAA
*
142899 GAGCTGAAGAGATTTG
1 GAGCTCAAGAGATTTG
* *
142915 GAGCTGAAGAGCTTTG
1 GAGCTCAAGAGATTTG
*
142931 GAGCTCCAGAG
1 GAGCTCAAGAG
142942 TTCTGGGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.28, C:0.14, G:0.37, T:0.21
Consensus pattern (16 bp):
GAGCTCAAGAGATTTG
Found at i:148520 original size:12 final size:12
Alignment explanation
Indices: 148503--148670 Score: 85
Period size: 12 Copynumber: 14.5 Consensus size: 12
148493 CATGAATGAA
148503 ATGCATGAAAGG
1 ATGCATGAAAGG
*
148515 ATGCAT-TAA-G
1 ATGCATGAAAGG
148525 --GCATGAAAGG
1 ATGCATGAAAGG
* * **
148535 ATTCCATAAATAAA
1 A-TGCATGAA-AGG
148549 ATGCATGAAAGG
1 ATGCATGAAAGG
*
148561 ATGCAT-TAA-G
1 ATGCATGAAAGG
148571 --GCATGAAAGG
1 ATGCATGAAAGG
*
148581 ATGTCAT-AAATGA
1 ATG-CATGAAA-GG
148594 AGTGCATGAAAGG
1 A-TGCATGAAAGG
*
148607 ATGCAT-TAA-G
1 ATGCATGAAAGG
148617 -T-CATGAAAGG
1 ATGCATGAAAGG
*
148627 ATGCAAT-AAATGAA
1 ATGC-ATGAAA-G-G
148641 ATGCATGAAAGG
1 ATGCATGAAAGG
148653 ATGCATGAAAGG
1 ATGCATGAAAGG
148665 ATGCAT
1 ATGCAT
148671 TAAGGCATGA
Statistics
Matches: 116, Mismatches: 18, Indels: 44
0.65 0.10 0.25
Matches are distributed among these distances:
8 11 0.09
9 7 0.06
10 6 0.05
11 7 0.06
12 44 0.38
13 27 0.23
14 14 0.12
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.21
Consensus pattern (12 bp):
ATGCATGAAAGG
Found at i:148556 original size:26 final size:25
Alignment explanation
Indices: 148525--148654 Score: 84
Period size: 26 Copynumber: 5.5 Consensus size: 25
148515 ATGCATTAAG
148525 GCATGAAAGGATTCCATAAATAAAAT
1 GCATGAAAGGATTCCATAAAT-AAAT
* *
148551 GCATGAAAGGA-TGCAT---T-AAG
1 GCATGAAAGGATTCCATAAATAAAT
*
148571 GCATGAAAGGATGT-CATAAATGAAGT
1 GCATGAAAGGAT-TCCATAAAT-AAAT
* *
148597 GCATGAAAGGA-TGCAT---TAAGT
1 GCATGAAAGGATTCCATAAATAAAT
* *
148618 -CATGAAAGGATGCAATAAATGAAAT
1 GCATGAAAGGATTCCATAAAT-AAAT
148643 GCATGAAAGGAT
1 GCATGAAAGGAT
148655 GCATGAAAGG
Statistics
Matches: 82, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
20 23 0.28
21 9 0.11
22 3 0.04
24 3 0.04
25 10 0.12
26 34 0.41
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.22
Consensus pattern (25 bp):
GCATGAAAGGATTCCATAAATAAAT
Found at i:148558 original size:46 final size:46
Alignment explanation
Indices: 148491--148838 Score: 392
Period size: 46 Copynumber: 7.3 Consensus size: 46
148481 CTAAAACAAA
*
148491 TCCATGAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
*
148537 TCCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* *
148583 GT-CATAAATGAAGTGCATGAAAGGATGCATTAAGTCATGAAAGGAT
1 -TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
** *
148629 GCAATAAATGAAATGCATGAAAGGATGCATGAAAGGATGCATTAAGGCATGAAAAGAT
1 ----TCCAT--AA---ATG-AA--ATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* * * *
148687 GCCATAAATGAAATGTATGAAAGGATGCATTAAGGTATGAAAAGAT
1 TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
** *
148733 AGCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGAT
1 TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* * * *
148779 GCCATAAATGAAATGCATTAAAGGGTGCATTAAGGCATGAAAAGAT
1 TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* *
148825 GCCATGAATGAAAT
1 TCCATAAATGAAAT
148839 TAACAAATAA
Statistics
Matches: 262, Mismatches: 27, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
46 211 0.81
47 1 0.00
48 2 0.01
49 4 0.02
50 2 0.01
52 4 0.02
54 2 0.01
55 3 0.01
56 2 0.01
58 31 0.12
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.22
Consensus pattern (46 bp):
TCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
Found at i:148693 original size:104 final size:104
Alignment explanation
Indices: 148549--148762 Score: 351
Period size: 104 Copynumber: 2.1 Consensus size: 104
148539 CATAAATAAA
* * *
148549 ATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAAATGAAGTGCATGAAAGGATGCATT
1 ATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATGAAATGCATGAAAGGATGCATT
*
148614 AA-GTCATGAAAGGAT-GCAATAAATGAAATGCATGAAAGG
66 AAGGT-ATGAAAAGATAGC-ATAAATGAAATGCATGAAAGG
*
148653 ATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATGAAATGTATGAAAGGATGCATT
1 ATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATGAAATGCATGAAAGGATGCATT
148718 AAGGTATGAAAAGATAGCATAAATGAAATGCATGAAAGG
66 AAGGTATGAAAAGATAGCATAAATGAAATGCATGAAAGG
148757 ATGCAT
1 ATGCAT
148763 TAAGGAATGA
Statistics
Matches: 103, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
104 99 0.96
105 4 0.04
ACGTcount: A:0.44, C:0.08, G:0.26, T:0.21
Consensus pattern (104 bp):
ATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATGAAATGCATGAAAGGATGCATT
AAGGTATGAAAAGATAGCATAAATGAAATGCATGAAAGG
Found at i:148713 original size:26 final size:25
Alignment explanation
Indices: 148653--148808 Score: 90
Period size: 20 Copynumber: 6.7 Consensus size: 25
148643 GCATGAAAGG
148653 ATGCATGAAAGGATGCAT---T--A
1 ATGCATGAAAGGATGCATAAATGAA
* *
148673 AGGCATGAAAAGATGCCATAAATGAA
1 ATGCATGAAAGGATG-CATAAATGAA
*
148699 ATGTATGAAAGGATGCAT---T--A
1 ATGCATGAAAGGATGCATAAATGAA
* * *
148719 AGGTATGAAAAGATAGCATAAATGAA
1 ATGCATGAAAGGAT-GCATAAATGAA
148745 ATGCATGAAAGGATGCAT---T--A
1 ATGCATGAAAGGATGCATAAATGAA
* *
148765 AGGAATGAAAGGATGCCATAAATGAA
1 ATGCATGAAAGGATG-CATAAATGAA
* *
148791 ATGCATTAAAGGGTGCAT
1 ATGCATGAAAGGATGCAT
148809 TAAGGCATGA
Statistics
Matches: 102, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
20 40 0.39
21 10 0.10
22 2 0.02
24 3 0.03
25 10 0.10
26 37 0.36
ACGTcount: A:0.45, C:0.08, G:0.25, T:0.22
Consensus pattern (25 bp):
ATGCATGAAAGGATGCATAAATGAA
Found at i:148774 original size:150 final size:150
Alignment explanation
Indices: 148503--148808 Score: 488
Period size: 150 Copynumber: 2.0 Consensus size: 150
148493 CATGAATGAA
* *
148503 ATGCATGAAAGGATGCATTAAGGCATGAAAGGATTCCATAAATAAAATGCATGAAAGGATGCATT
1 ATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATAAAATGCATGAAAGGATGCATT
* * **
148568 AAGGCATGAAAGGATGTCATAAATGAAGTGCATGAAAGGATGCATTAAGTCATGAAAGGATGCAA
66 AAGGCATGAAAAGATGTCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCAA
148633 TAAATGAAATGCATGAAAGG
131 TAAATGAAATGCATGAAAGG
* *
148653 ATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATGAAATGTATGAAAGGATGCATT
1 ATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATAAAATGCATGAAAGGATGCATT
* *
148718 AAGGTATGAAAAGATAG-CATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCC
66 AAGGCATGAAAAGAT-GTCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCA
*
148782 ATAAATGAAATGCATTAAAGG
130 ATAAATGAAATGCATGAAAGG
*
148803 GTGCAT
1 ATGCAT
148809 TAAGGCATGA
Statistics
Matches: 143, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
150 142 0.99
151 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.22
Consensus pattern (150 bp):
ATGCATGAAAGGATGCATTAAGGCATGAAAAGATGCCATAAATAAAATGCATGAAAGGATGCATT
AAGGCATGAAAAGATGTCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCAA
TAAATGAAATGCATGAAAGG
Found at i:151371 original size:19 final size:19
Alignment explanation
Indices: 151347--151385 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
151337 TAGCTCAGGC
151347 TTAGACTAAGAATGAAGAG
1 TTAGACTAAGAATGAAGAG
151366 TTAGACTAAGAATGAAGAG
1 TTAGACTAAGAATGAAGAG
151385 T
1 T
151386 ATAGTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.26, T:0.23
Consensus pattern (19 bp):
TTAGACTAAGAATGAAGAG
Found at i:156608 original size:36 final size:37
Alignment explanation
Indices: 156549--156619 Score: 117
Period size: 36 Copynumber: 1.9 Consensus size: 37
156539 TTATTAAGAG
*
156549 AAGTCTATCTTTGTTATTCTTGACTTTCTCATGAAAA
1 AAGTCAATCTTTGTTATTCTTGACTTTCTCATGAAAA
*
156586 AAGTCAATCTTT-TTATTCTTGACTTTCTCGTGAA
1 AAGTCAATCTTTGTTATTCTTGACTTTCTCATGAA
156620 GAGAAGTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 21 0.66
37 11 0.34
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.46
Consensus pattern (37 bp):
AAGTCAATCTTTGTTATTCTTGACTTTCTCATGAAAA
Found at i:156632 original size:37 final size:38
Alignment explanation
Indices: 156544--156632 Score: 128
Period size: 37 Copynumber: 2.4 Consensus size: 38
156534 CTTCCTTATT
*
156544 AAGAGAAGTCTATCTTTGTTATTCTTGACTTTCTCATG
1 AAGAGAAGTCAATCTTTGTTATTCTTGACTTTCTCATG
* *
156582 AA-AAAAGTCAATCTTT-TTATTCTTGACTTTCTCGTG
1 AAGAGAAGTCAATCTTTGTTATTCTTGACTTTCTCATG
*
156618 AAGAGAAGTGAATCT
1 AAGAGAAGTCAATCT
156633 CTCAATATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 21 0.47
37 22 0.49
38 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (38 bp):
AAGAGAAGTCAATCTTTGTTATTCTTGACTTTCTCATG
Found at i:156731 original size:45 final size:45
Alignment explanation
Indices: 156601--156904 Score: 220
Period size: 45 Copynumber: 6.8 Consensus size: 45
156591 AATCTTTTTA
** * * * * * *
156601 TTCTTGACTTTCTCGTGAAGAGAAGTGAATCTCTCAATATTATCC
1 TTCTTGACTTTCTCACGAAGAGAAGTCAATCTTTTAGTGTTGTCC
* * *
156646 TTCTTGAATTTCTCACGAAGATG-AGACAATATTTTAGTGTTGTCC
1 TTCTTGACTTTCTCACGAAGA-GAAGTCAATCTTTTAGTGTTGTCC
* **
156691 TTCTTGACTTTCTCACGAAGAGAATTCAATCTTTCGGTGTTGT-C
1 TTCTTGACTTTCTCACGAAGAGAAGTCAATCTTTTAGTGTTGTCC
**** * * ** * *
156735 TTCATTGACTTTCTTGTAAAGAGGAGTTAATAGTTTAGTATTGTTCG
1 TTC-TTGACTTTCTCACGAAGAGAAGTCAATCTTTTAGTGTTG-TCC
* * * *
156782 TT-TTGACTATCTCATGAAGAGGAGTCAATCTTTTAGTGTTTTCC
1 TTCTTGACTTTCTCACGAAGAGAAGTCAATCTTTTAGTGTTGTCC
* * * * * *
156826 TTTTTTACATTCTCACGAAGAGAAGTCGATCTTTTGGTGTTGTTC
1 TTCTTGACTTTCTCACGAAGAGAAGTCAATCTTTTAGTGTTGTCC
* * *
156871 TTTTTGACTTTCTCACGGAGAGGAGTCAA-CTTTT
1 TTCTTGACTTTCTCACGAAGAGAAGTCAATCTTTT
156905 CAGTATCATC
Statistics
Matches: 199, Mismatches: 54, Indels: 13
0.75 0.20 0.05
Matches are distributed among these distances:
44 14 0.07
45 181 0.91
46 2 0.01
47 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (45 bp):
TTCTTGACTTTCTCACGAAGAGAAGTCAATCTTTTAGTGTTGTCC
Found at i:156910 original size:135 final size:134
Alignment explanation
Indices: 156656--156899 Score: 301
Period size: 135 Copynumber: 1.8 Consensus size: 134
156646 TTCTTGAATT
* * *
156656 TCTCACGAAGATGAGACAATATTTTAGTGTTGTCCTTCTTGACTTTCTCACGAAGAGAATTCAAT
1 TCTCACGAAGAGGAGACAATATTTTAGTGTTGTCCTTCTTGACATTCTCACGAAGAGAAGTCAAT
*** *
156721 CTTTCGGTGTTGTCTTCATTGACTTTCTTGTAAAGAGGAGTTAATAGTTTAGTATTGTTCGTTTT
66 CTTTCGGTGTTGTCTTCATTGACTTTCTCACAAAGAGGAGTCAATA-TTTAGTATTGTTCGTTTT
156786 GACTA
130 GACTA
* * * * * * *
156791 TCTCATGAAGAGGAGTCAATCTTTTAGTGTTTTCCTTTTTTACATTCTCACGAAGAGAAGTCGAT
1 TCTCACGAAGAGGAGACAATATTTTAGTGTTGTCCTTCTTGACATTCTCACGAAGAGAAGTCAAT
* * **
156856 CTTTTGGTGTTGTTCTT-TTTGACTTTCTCACGGAGAGGAGTCAA
66 CTTTCGGTGTTG-TCTTCATTGACTTTCTCACAAAGAGGAGTCAA
156900 CTTTTCAGTA
Statistics
Matches: 90, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
135 86 0.96
136 4 0.04
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (134 bp):
TCTCACGAAGAGGAGACAATATTTTAGTGTTGTCCTTCTTGACATTCTCACGAAGAGAAGTCAAT
CTTTCGGTGTTGTCTTCATTGACTTTCTCACAAAGAGGAGTCAATATTTAGTATTGTTCGTTTTG
ACTA
Found at i:157691 original size:134 final size:134
Alignment explanation
Indices: 157492--158041 Score: 730
Period size: 134 Copynumber: 4.1 Consensus size: 134
157482 GCATACAGTG
* * * *
157492 TTCTGATTCAATCTTCCCTAAAGAGCAGTGAGGTGGATCAAAATTTTCTCGAGTCTGATCTCCCC
1 TTCTGATTCAATCTTCCCTGAAGAGAAGTGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCCC
* * * *
157557 TAAAGAGTAGTGGAGAATATTCTTCTTCTTTCAGAGTTGGTCTTCCTAAAGAGCAATGAAGCAAA
66 TAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAGATTTGGTATTCCTGAAGAGCAATGAAGCAAA
157622 TCGA
131 TCGA
* * * * *
157626 TTCTGATTCAATATTTCCTGAAGAGAAGTAAAGTCGACCAAAGTTTTCTCGAGTCTGATCTCCCC
1 TTCTGATTCAATCTTCCCTGAAGAGAAGTGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCCC
* * * *
157691 TAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAAATTTGGTATTCCTGAAGAGGAGTGAAGCAAA
66 TAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAGATTTGGTATTCCTGAAGAGCAATGAAGCAAA
157756 TCGA
131 TCGA
* *
157760 TTCTGAATCAATCTTCCCTGAAGA-ATAGTGAAGTGGATCAAAGTTTTCTCGAGTATGATCTCCC
1 TTCTGATTCAATCTTCCCTGAAGAGA-AGTGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCC
* * * *
157824 TTAAATAGTAGTGGA-ATAGATTATTCTTCTTTCAGATTTGGTATTCCTGAAGAGCAATGAAGTA
65 CTAAAGAGTAGTGGAGA-AGATTCTTCTTCTTTCAGATTTGGTATTCCTGAAGAGCAATGAAGCA
*
157888 AATTGA
129 AATCGA
* * * *
157894 TTCTAATTCAATCTTCCATGAAGAGCAA-TGAAGTAGATCAAACTTTTCTCGAGTCTGATCTCCC
1 TTCTGATTCAATCTTCCCTGAAGAG-AAGTGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCC
* * * * *
157958 CTAAAGAGTAGTGGAGCAA-ATTCTTATTCTTTCAGATTTGGTCTTCATGAAGAGCAATGCAGAA
65 CTAAAGAGTAGTGGAG-AAGATTCTTCTTCTTTCAGATTTGGTATTCCTGAAGAGCAATGAAGCA
158022 AATCGA
129 AATCGA
*
158028 TTCCGATTCAATCT
1 TTCTGATTCAATCT
158042 CCTCGGAAGA
Statistics
Matches: 360, Mismatches: 50, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
133 1 0.00
134 355 0.99
135 2 0.01
136 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (134 bp):
TTCTGATTCAATCTTCCCTGAAGAGAAGTGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCCC
TAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAGATTTGGTATTCCTGAAGAGCAATGAAGCAAA
TCGA
Found at i:158257 original size:15 final size:15
Alignment explanation
Indices: 158237--158266 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
158227 TTCCATCTAG
*
158237 ATATTATTAATATTA
1 ATATTAATAATATTA
158252 ATATTAATAATATTA
1 ATATTAATAATATTA
158267 TTTTTATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTAATAATATTA
Found at i:158404 original size:15 final size:16
Alignment explanation
Indices: 158378--158408 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
158368 TAACAGAGCT
158378 AAACCACTAGGGTTTC
1 AAACCACTAGGGTTTC
158394 AAACC-CTAGGGTTTC
1 AAACCACTAGGGTTTC
158409 CATCTACCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (16 bp):
AAACCACTAGGGTTTC
Found at i:167721 original size:14 final size:14
Alignment explanation
Indices: 167702--167767 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
167692 AAGTTAATAG
167702 GTTGACTCGGACGA
1 GTTGACTCGGACGA
* ** *
167716 GTTGACACATATGA
1 GTTGACTCGGACGA
* ** *
167730 GTTAACTTTGACCA
1 GTTGACTCGGACGA
*
167744 GTTGACTTGGACGA
1 GTTGACTCGGACGA
167758 GTTGACTCGG
1 GTTGACTCGG
167768 TTTAGACTGG
Statistics
Matches: 37, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (14 bp):
GTTGACTCGGACGA
Found at i:178391 original size:54 final size:54
Alignment explanation
Indices: 178304--178807 Score: 358
Period size: 54 Copynumber: 9.4 Consensus size: 54
178294 CAATTATGAG
* * * * * *
178304 CTCTACACTTCCATAACCAAGGAACGCTAGAGCTTGCTCGATCTTAAAAATTTT
1 CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACTTGATCTTAAAAATTTT
* * **
178358 CTCTACTCCTCCAAAACAAAGAAACGCTGGAGCTTAC-ACAGTCTT-AAAATTTT
1 CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACTTGA-TCTTAAAAATTTT
* **
178411 GCTCTACACCTCCATAACAAAGAAACAATAGAGCTTA--TGTAGTCTTAAAAATTTT
1 -CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACTTG-A-TCTTAAAAATTTT
* * * *
178466 CTCTACTCCTCAATAAGAAAGGAATGCTAGAGCTTA-TAT-AGTCTT-AAAATTTT
1 CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACT-TGA-TCTTAAAAATTTT
* *
178519 CTCTACTCCTCCATAGA-AAATG-AACGCTAGAGCTTTCTTGTTCTT-AAAATTTT
1 CTCTACTCCTCCATA-ACAAA-GAAACGCTAGAGCTTACTTGATCTTAAAAATTTT
* ** * * * *
178572 GATCTA---CTCCATAGTAAAGGAATC-CTAGAGCTTACTGGGTCTTAAATATTTT
1 -CTCTACTCCTCCATAACAAA-GAAACGCTAGAGCTTACTTGATCTTAAAAATTTT
* * * *
178624 CTCTACTCCTCCATAACAAAGGAATGCTAGAG-TGTGC-TAAGTCTTAAAAAATTTT
1 CTCTACTCCTCCATAACAAAGAAACGCTAGAGCT-TACTTGA-TCTT-AAAAATTTT
** * *
178679 CTCTACTCCTTTATAACAAAGAAACGCTAGAGCATACTTGATCTTTAAAATTTGT
1 CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACTTGATCTTAAAAATTT-T
* * * * * * * * *
178734 -TATACTCATCCATAAGAAAGGAATGCTAGAGCGTGCTTGGTCTTAAAAATTTG
1 CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACTTGATCTTAAAAATTTT
* *
178787 ATGTACTCCTCCATAACAAAG
1 CTCTACTCCTCCATAACAAAG
178808 TGTCACAATG
Statistics
Matches: 356, Mismatches: 69, Indels: 50
0.75 0.15 0.11
Matches are distributed among these distances:
51 31 0.09
52 9 0.03
53 62 0.17
54 200 0.56
55 51 0.14
56 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (54 bp):
CTCTACTCCTCCATAACAAAGAAACGCTAGAGCTTACTTGATCTTAAAAATTTT
Found at i:178628 original size:158 final size:162
Alignment explanation
Indices: 178345--178807 Score: 445
Period size: 158 Copynumber: 2.9 Consensus size: 162
178335 GCTTGCTCGA
* * * **
178345 TCTTAAAAATTTTCTCTACTCCTCCAAAACAAAGAAACGCTGGAGCTTAC-ACAGTC-TTAAAAT
1 TCTTAAAAATTTTCTCTACTCCTCCATAACAAAGAAACGCTAGAGCATACTTGA-TCTTTAAAAT
* * * * *
178408 TT-TGCT-CTACACCTCCATAACAAA-GAAACAATAGAGCTTA-TGTAGTCTTAAAAATTTTCTC
65 TTGTGATACT-CA--TCCATAAGAAAGGAATC-CTAGAGCTTACTG-GGTCTTAAAAATTTTCTC
*
178469 TACTCCTCAATAAGAAAGGAATGCTAGAGCT-T-ATATAG
125 TACTCCTCAATAACAAAGGAATGCTAGAG-TGTGATA-AG
* * *
178507 TCTT-AAAATTTTCTCTACTCCTCCATAGA-AAATG-AACGCTAGAGCTTTCTTGTTC-TTAAAA
1 TCTTAAAAATTTTCTCTACTCCTCCATA-ACAAA-GAAACGCTAGAGCATACTTGATCTTTAAAA
*
178568 TTT-TGAT-CT-ACTCCAT-AGTAAAGGAATCCTAGAGCTTACTGGGTCTTAAATATTTTCTCTA
64 TTTGTGATACTCA-TCCATAAG-AAAGGAATCCTAGAGCTTACTGGGTCTTAAAAATTTTCTCTA
* *
178629 CTCCTCCATAACAAAGGAATGCTAGAGTGTGCTAAG
127 CTCCTCAATAACAAAGGAATGCTAGAGTGTGATAAG
**
178665 TCTTAAAAAATTTTCTCTACTCCTTTATAACAAAGAAACGCTAGAGCATACTTGATCTTTAAAAT
1 TCTT-AAAAATTTTCTCTACTCCTCCATAACAAAGAAACGCTAGAGCATACTTGATCTTTAAAAT
* * * * * ** *
178730 TTGTTATACTCATCCATAAGAAAGGAATGCTAGAGCGTGCTTGGTCTTAAAAATTTGATGTACTC
65 TTGTGATACTCATCCATAAGAAAGGAATCCTAGAGCTTACTGGGTCTTAAAAATTTTCTCTACTC
*
178795 CTCCATAACAAAG
130 CTCAATAACAAAG
178808 TGTCACAATG
Statistics
Matches: 255, Mismatches: 29, Indels: 33
0.80 0.09 0.10
Matches are distributed among these distances:
157 2 0.01
158 68 0.27
159 11 0.04
160 42 0.16
161 63 0.25
162 9 0.04
163 57 0.22
164 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (162 bp):
TCTTAAAAATTTTCTCTACTCCTCCATAACAAAGAAACGCTAGAGCATACTTGATCTTTAAAATT
TGTGATACTCATCCATAAGAAAGGAATCCTAGAGCTTACTGGGTCTTAAAAATTTTCTCTACTCC
TCAATAACAAAGGAATGCTAGAGTGTGATAAG
Found at i:179427 original size:23 final size:24
Alignment explanation
Indices: 179382--179427 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
179372 CCCTTTCGGG
179382 TTTTCACTTTCGTTTCTTCTTCTA
1 TTTTCACTTTCGTTTCTTCTTCTA
* *
179406 TTTTCTCTTT-GTTTCTTTTTCT
1 TTTTCACTTTCGTTTCTTCTTCT
179428 TTTCATTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.04, C:0.22, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTCACTTTCGTTTCTTCTTCTA
Found at i:179432 original size:45 final size:40
Alignment explanation
Indices: 179382--179483 Score: 95
Period size: 39 Copynumber: 2.5 Consensus size: 40
179372 CCCTTTCGGG
*
179382 TTTTCACTTTCGTTTCTTCTTCTATTTTCTCTTTGTTTCTTTTTC
1 TTTTCACTTTC-TTTCTTCTTC---TTTC-CTTTCTTTCTTTTTC
* *
179427 TTTTCA-TTTCATTT-TCCTTCTTTCCTTTCTTTTTTTTTC
1 TTTTCACTTTC-TTTCTTCTTCTTTCCTTTCTTTCTTTTTC
179466 TTTT-ACTTT-TTTCTTCTT
1 TTTTCACTTTCTTTCTTCTT
179484 TTCTTTCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
37 3 0.06
38 5 0.10
39 20 0.40
40 4 0.08
43 5 0.10
44 7 0.14
45 6 0.12
ACGTcount: A:0.05, C:0.22, G:0.02, T:0.72
Consensus pattern (40 bp):
TTTTCACTTTCTTTCTTCTTCTTTCCTTTCTTTCTTTTTC
Found at i:179436 original size:10 final size:9
Alignment explanation
Indices: 179423--179490 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
179413 TTTGTTTCTT
179423 TTTCTTTTC
1 TTTCTTTTC
179432 ATTTCATTTTC
1 -TTTC-TTTTC
* *
179443 CTTCTTTCC
1 TTTCTTTTC
*
179452 TTTCTTTTTT
1 TTTC-TTTTC
179462 TTTCTTTTAC
1 TTTCTTTT-C
179472 -TT-TTTTC
1 TTTCTTTTC
179479 -TTCTTTTC
1 TTTCTTTTC
179487 TTTC
1 TTTC
179491 ACTTTTTCTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
7 3 0.06
8 9 0.19
9 16 0.34
10 14 0.30
11 5 0.11
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:179436 original size:16 final size:15
Alignment explanation
Indices: 179417--179489 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 15
179407 TTTCTCTTTG
*
179417 TTTCTTTTTCTTTTCA
1 TTTCTTTTT-TTTTCT
*
179433 TTTCATTTTCCTTCTTTCC
1 TTTC-TTTT--TT-TTTCT
179452 TTTCTTTTTTTTTCT
1 TTTCTTTTTTTTTCT
*
179467 TTTACTTTTTTCTTCT
1 TTT-CTTTTTTTTTCT
179483 TTTCTTT
1 TTTCTTT
179490 CACTTTTTCT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
15 11 0.22
16 20 0.41
17 4 0.08
18 5 0.10
19 9 0.18
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTCTTTTTTTTTCT
Found at i:179449 original size:20 final size:20
Alignment explanation
Indices: 179424--179503 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
179414 TTGTTTCTTT
*
179424 TTCTTTTCATTTCATTTTCC
1 TTCTTTTCATTTCATTTTTC
* * *
179444 TTC-TTTCCTTTCTTTTTTT
1 TTCTTTTCATTTCATTTTTC
*
179463 TTCTTTT-A---CTTTTTTC
1 TTCTTTTCATTTCATTTTTC
179479 TTCTTTTC-TTTCACTTTTTC
1 TTCTTTTCATTTCA-TTTTTC
179499 TTCTT
1 TTCTT
179504 CATCAGCAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
16 14 0.30
19 16 0.34
20 17 0.36
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (20 bp):
TTCTTTTCATTTCATTTTTC
Found at i:179457 original size:35 final size:36
Alignment explanation
Indices: 179417--179506 Score: 103
Period size: 35 Copynumber: 2.5 Consensus size: 36
179407 TTTCTCTTTG
179417 TTTCTTTTTCTTTTCATTT-CATTTTCCTTCTTTCC
1 TTTCTTTTTCTTTTCATTTACATTTTCCTTCTTTCC
* * * *
179452 TTTCTTTTT-TTTTCTTTTACTTTTTTCTTCTTTTC
1 TTTCTTTTTCTTTTCATTTACATTTTCCTTCTTTCC
179487 TTTCACTTTTTCTTCTTCAT
1 TTT--CTTTTTCTT-TTCAT
179507 CAGCAGGAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
34 8 0.18
35 25 0.56
37 6 0.13
38 2 0.04
39 4 0.09
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (36 bp):
TTTCTTTTTCTTTTCATTTACATTTTCCTTCTTTCC
Found at i:179464 original size:5 final size:5
Alignment explanation
Indices: 179417--179489 Score: 53
Period size: 5 Copynumber: 14.4 Consensus size: 5
179407 TTTCTCTTTG
* * * *
179417 TTTCTT TTTCT TTTCA TTTCAT TTTC- CTTC- TTTCC TTTCT TTTTT TTTCT
1 TTTC-T TTTCT TTTCT TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
179467 TTTACT TTT-T TCTTCT TTTCT TT
1 TTT-CT TTTCT T-TTCT TTTCT TT
179490 CACTTTTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
4 8 0.15
5 32 0.58
6 15 0.27
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTCT
Found at i:179466 original size:55 final size:58
Alignment explanation
Indices: 179388--179503 Score: 136
Period size: 55 Copynumber: 2.1 Consensus size: 58
179378 CGGGTTTTCA
* *
179388 CTTTCGTTTCTTCTTCTATTTTCTCTTT-GTTTCTTT-TTCTTTTCATTTCA-TTTTCCTT
1 CTTTCCTTTCTTCTTCTATTTTCT-TTTACTTT-TTTCTTCTTTTC-TTTCACTTTTCCTT
*
179446 CTTTCCTTTCTT-TT-T-TTTTCTTTTACTTTTTTCTTCTTTTCTTTCACTTTTTCTT
1 CTTTCCTTTCTTCTTCTATTTTCTTTTACTTTTTTCTTCTTTTCTTTCACTTTTCCTT
179501 CTT
1 CTT
179504 CATCAGCAGG
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
54 11 0.21
55 27 0.52
56 1 0.02
57 2 0.04
58 11 0.21
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (58 bp):
CTTTCCTTTCTTCTTCTATTTTCTTTTACTTTTTTCTTCTTTTCTTTCACTTTTCCTT
Done.