Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_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: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 21
Found at i:2337550 original size:2 final size:2
Alignment explanation
Indices: 2337543--2337589 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2337533 ATTTTATAAA
2337543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2337585 AT AT A
1 AT AT A
2337590 ATTTATGAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2337799 original size:33 final size:38
Alignment explanation
Indices: 2337760--2337838 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 38
2337750 ACAAAATACA
2337760 ACATTCCCA-G-TAATCCT-ATTC-C-CTGGTAATCTT
1 ACATTCCCACGATAATCCTAATTCTCACTGGTAATCTT
*
2337793 ACATTCCCACTGATAATCTTACATTCTCACTGGTAATCTT
1 ACATTCCCAC-GATAATCCTA-ATTCTCACTGGTAATCTT
2337833 ACATTC
1 ACATTC
2337839 TCACTGGTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
33 9 0.24
35 1 0.03
36 6 0.16
38 4 0.11
39 1 0.03
40 17 0.45
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.37
Consensus pattern (38 bp):
ACATTCCCACGATAATCCTAATTCTCACTGGTAATCTT
Found at i:2337811 original size:20 final size:20
Alignment explanation
Indices: 2337782--2337857 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
2337772 ATCCTATTCC
*
2337782 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCTCA
*
2337802 CTGATAATCTTACATTCTCA
1 CTGGTAATCTTACATTCTCA
2337822 CTGGTAATCTTACATTCTCA
1 CTGGTAATCTTACATTCTCA
2337842 CTGGTAATCTTACATT
1 CTGGTAATCTTACATT
2337858 TCGTGAACCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCTCA
Found at i:2350338 original size:20 final size:20
Alignment explanation
Indices: 2350313--2350350 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2350303 TTTTGGTGCA
*
2350313 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
2350333 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
2350351 CCACAGGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:2359206 original size:17 final size:17
Alignment explanation
Indices: 2359184--2359221 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2359174 AACAATGTCT
2359184 ATTCATCAGACGAG-TTC
1 ATTCATC-GACGAGTTTC
*
2359201 ATTCATCGACGTGTTTC
1 ATTCATCGACGAGTTTC
2359218 ATTC
1 ATTC
2359222 GTGTGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (17 bp):
ATTCATCGACGAGTTTC
Found at i:2364238 original size:5 final size:5
Alignment explanation
Indices: 2364228--2364269 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
2364218 TTAGTCTTGT
2364228 TTGGC TTGGC TTGGC TTGGC TTGGC TTGGC TTGGC TTGGC TT
1 TTGGC TTGGC TTGGC TTGGC TTGGC TTGGC TTGGC TTGGC TT
2364270 CGATGGATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.43
Consensus pattern (5 bp):
TTGGC
Found at i:2367116 original size:19 final size:19
Alignment explanation
Indices: 2367092--2367131 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2367082 TTCCAGTAAA
2367092 CACCCTAGTAAGATTTTAT
1 CACCCTAGTAAGATTTTAT
2367111 CACCCTAGTAAGATTTTAT
1 CACCCTAGTAAGATTTTAT
2367130 CA
1 CA
2367132 TGTTGCTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.35
Consensus pattern (19 bp):
CACCCTAGTAAGATTTTAT
Found at i:2371088 original size:29 final size:29
Alignment explanation
Indices: 2371055--2371136 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
2371045 CTCACCTAAC
2371055 TAAATTGATGTAA-CAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
2371084 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
2371113 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
2371137 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.16
29 42 0.84
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:2374524 original size:15 final size:15
Alignment explanation
Indices: 2374504--2374548 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
2374494 CTTTCTCATA
2374504 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
2374519 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
2374534 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
2374549 CCAGCCTCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.13, C:0.00, G:0.31, T:0.56
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:2375882 original size:29 final size:29
Alignment explanation
Indices: 2375839--2375921 Score: 148
Period size: 29 Copynumber: 2.8 Consensus size: 29
2375829 CTCACCTAAC
2375839 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
2375869 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
2375898 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
2375922 ATTTAGTTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 47 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:2376543 original size:23 final size:23
Alignment explanation
Indices: 2376517--2376565 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2376507 GAATTTGCAG
2376517 AGGGAGCATTTGATGCCTTGGCA
1 AGGGAGCATTTGATGCCTTGGCA
2376540 AGGGAGCATTTGATGCCTTGGCA
1 AGGGAGCATTTGATGCCTTGGCA
2376563 AGG
1 AGG
2376566 CGTCAAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.37, T:0.24
Consensus pattern (23 bp):
AGGGAGCATTTGATGCCTTGGCA
Found at i:2389987 original size:2 final size:2
Alignment explanation
Indices: 2389980--2390010 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2389970 TGTCCTTACA
2389980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2390011 ATTAGGATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2392367 original size:2 final size:2
Alignment explanation
Indices: 2392360--2392408 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
2392350 GACATTCAGT
2392360 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2392402 TA CTA TA
1 TA -TA TA
2392409 ATTTAATTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2393805 original size:18 final size:18
Alignment explanation
Indices: 2393779--2393834 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
2393769 GAGCGCTATT
* *
2393779 GCGGCGATTGCAGGTGTC
1 GCGGTGATTGCGGGTGTC
2393797 GCGGTGATTGCGGGTGTC
1 GCGGTGATTGCGGGTGTC
*
2393815 ACGGTGATTGCGGGTGTC
1 GCGGTGATTGCGGGTGTC
2393833 GC
1 GC
2393835 AGTCAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.09, C:0.20, G:0.46, T:0.25
Consensus pattern (18 bp):
GCGGTGATTGCGGGTGTC
Found at i:2400945 original size:2 final size:2
Alignment explanation
Indices: 2400938--2400975 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2400928 CAAAGAAATT
2400938 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2400976 ATACATCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2406702 original size:166 final size:166
Alignment explanation
Indices: 2406414--2406742 Score: 606
Period size: 166 Copynumber: 2.0 Consensus size: 166
2406404 ACTAAACATG
*
2406414 TTTTTAATGGACGTTACAACCAATGCACTTTGCACCTATATTGACCGGGAAAAAATTAGGCACCT
1 TTTTTAATGGACGTTACAACCAATGCACTTTGCACCTATATTGACCGGAAAAAAATTAGGCACCT
2406479 AAATGAGAAAAAATGTATAATTTAGGCAATTTTTTATATTAAGCCATTATAAAAATAGATGTTTC
66 AAATGAGAAAAAATGTATAATTTAGGCAATTTTTTATATTAAGCCATTATAAAAATAGATGTTTC
2406544 CTTAAGAAGTTAAATATCAATTAAATTGTTCATGTT
131 CTTAAGAAGTTAAATATCAATTAAATTGTTCATGTT
*
2406580 TTTTTAATGGACGTTACAACCAATGCACTTTGCACCTATATTGATCGGAAAAAAATTAGGCACCT
1 TTTTTAATGGACGTTACAACCAATGCACTTTGCACCTATATTGACCGGAAAAAAATTAGGCACCT
*
2406645 AAATGAGAAAAAAATGTATAGTTTAGGCAATTTTTTATATTAAGCCATTAT-AAAATAGATGTTT
66 AAATGAG-AAAAAATGTATAATTTAGGCAATTTTTTATATTAAGCCATTATAAAAATAGATGTTT
*
2406709 CCTTAAGAAGTTAGATATCAATTAAATTGTTCAT
130 CCTTAAGAAGTTAAATATCAATTAAATTGTTCAT
2406743 ATTTGTTTCT
Statistics
Matches: 158, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
166 116 0.73
167 42 0.27
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (166 bp):
TTTTTAATGGACGTTACAACCAATGCACTTTGCACCTATATTGACCGGAAAAAAATTAGGCACCT
AAATGAGAAAAAATGTATAATTTAGGCAATTTTTTATATTAAGCCATTATAAAAATAGATGTTTC
CTTAAGAAGTTAAATATCAATTAAATTGTTCATGTT
Found at i:2407747 original size:20 final size:21
Alignment explanation
Indices: 2407700--2407747 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
2407690 TAAGTCGTTG
* * *
2407700 ACTTAATGAGACATATAAAGT
1 ACTTAATAAAACATATAAAAT
*
2407721 ACGTAATAAAACAT-TAAAAT
1 ACTTAATAAAACATATAAAAT
2407741 ACTTAAT
1 ACTTAAT
2407748 CATATTCAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.29
Consensus pattern (21 bp):
ACTTAATAAAACATATAAAAT
Found at i:2407818 original size:2 final size:2
Alignment explanation
Indices: 2407811--2407838 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2407801 TAACAAAAAC
2407811 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2407839 GTCATCGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2407855 original size:12 final size:12
Alignment explanation
Indices: 2407840--2407865 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2407830 TATATATATG
2407840 TCATCGTCATCA
1 TCATCGTCATCA
2407852 TCATCGTCATCA
1 TCATCGTCATCA
2407864 TC
1 TC
2407866 GTCATCACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.35, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCGTCATCA
Found at i:2407861 original size:9 final size:9
Alignment explanation
Indices: 2407839--2407872 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2407829 ATATATATAT
*
2407839 GTCATCGTC
1 GTCATCATC
*
2407848 ATCATCATC
1 GTCATCATC
2407857 GTCATCATC
1 GTCATCATC
2407866 GTCATCA
1 GTCATCA
2407873 CTGTTCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (9 bp):
GTCATCATC
Found at i:2414225 original size:16 final size:16
Alignment explanation
Indices: 2414184--2414242 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
2414174 CAATTAGTAA
*
2414184 TTAGCGGTTAGAAAGG
1 TTAGCGGTTAGAAAAG
**
2414200 TTAGTTGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
*
2414216 TTAGCGGTTATAAAAG
1 TTAGCGGTTAGAAAAG
2414232 TTAGCGGTTAG
1 TTAGCGGTTAG
2414243 CAGAGTCTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:2414579 original size:4 final size:4
Alignment explanation
Indices: 2414566--2414599 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2414556 CGAATAATAG
2414566 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2414600 CAATGGTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2416265 original size:40 final size:42
Alignment explanation
Indices: 2416166--2416274 Score: 116
Period size: 43 Copynumber: 2.6 Consensus size: 42
2416156 GGTATAATGG
* *
2416166 AGATAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTA
1 AGATGACACGGTTCCTACGTGATGAGGAAGTCTGGTTAGCTA
*** * *
2416208 AGGATGACACAACTCCTACGTGATGAGG-AGATCTGG-TCGGT-
1 A-GATGACACGGTTCCTACGTGATGAGGAAG-TCTGGTTAGCTA
2416249 AGATGACACGGTTCCTACGTGATGAG
1 AGATGACACGGTTCCTACGTGATGAG
2416275 CACGGCTGGC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
40 22 0.40
41 1 0.02
42 5 0.09
43 27 0.49
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (42 bp):
AGATGACACGGTTCCTACGTGATGAGGAAGTCTGGTTAGCTA
Found at i:2416280 original size:137 final size:137
Alignment explanation
Indices: 2416033--2417249 Score: 1593
Period size: 137 Copynumber: 9.0 Consensus size: 137
2416023 ATTTAAAGAC
* * * *
2416033 AACACGATTCCTACGTGATGAGGAAATCTGGTTATCTAAGGGTGACG-ATGCTCTTACGTGATGA
1 AACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGACGCA-ACTCCTACGTGATGA
* ** * * *
2416097 GGATATCTGGTCGGTGGATGACACAATTCCTACGTGATGAGGACGGCTAGCCATCTTTAGGTATA
65 GGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGACTGGCCATCTTTAGGGATA
2416162 ATGGAGAT
130 ATGGAGAT
* *
2416170 AACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACACAACTCCTACGTGATGAG
1 AACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGACGCAACTCCTACGTGATGAG
* * *
2416235 GAGATCTGGTCGGTAGATGACACGGTTCCTACGTGATGAGCACGGCTGGCCATCTTTAGGGATAA
66 GAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGACTGGCCATCTTTAGGGATAA
*
2416300 TGAAGAT
131 TGGAGAT
* * * *
2416307 AACACGGTTCTTACGTGATGAGGAAGTATGGTTATCTAAGGATGACGTAGA-TCCTACGTGAT--
1 AACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGACGCA-ACTCCTACGTGATGA
* * * *
2416369 -GAGATATGGTCAGTGGATGACACGATTCTTACGTGATGAGGACGACTGGCCATCTTTAGGGATA
65 GGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGACTGGCCATCTTTAGGGATA
*
2416433 ATAGAGAT
130 ATGGAGAT
* * * *
2416441 AACACGATTCCTACGCGATAAGGAAGTCTGGTTATCTAAGGGTGACGCGACTCCTACGTGAT---
1 AACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGACGCAACTCCTACGTGATGAG
* *
2416503 GAGATCTGGTCGGTGGATGACACGGTTCCTACGTGAT-AGGGACGTCTGGACATCTTTAGGGATA
66 GAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGA-GGACGACTGGCCATCTTTAGGGAT-
2416567 AATGGAGAT
129 AATGGAGAT
* * * * * ** *
2416576 AACACGGTTCTTTCATGATGAGAAAGTCTGGTTATCTAAGGGTGACACTGCTCCTACGCGATGAG
1 AACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGACGCAACTCCTACGTGATGAG
* * * *
2416641 GAGATATGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGGCTAGCCATCTTTAGGTATAA
66 GAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGACTGGCCATCTTTAGGGATAA
2416706 TGGAGAT
131 TGGAGAT
*
2416713 AACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACGCAACTCCTACGTGATGAG
1 AACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGACGCAACTCCTACGTGATGAG
* *
2416778 GAGATCTGGTCGGTGGATGACACGGTTCTTACGTGATGAGGACGACTGACCATCTTTAGGGATAA
66 GAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGACTGGCCATCTTTAGGGATAA
*
2416843 TGAAGAT
131 TGGAGAT
* *
2416850 AACACGGTTCTTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACGCAGA-TCCTACGTGAT--
1 AACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGACGCA-ACTCCTACGTGATGA
* * *
2416912 -GAGATCTGGTCAGTGGATGACACGGTTCTTACGTGATGAGGACGACTGACCATCTTTAGGGATA
65 GGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGACTGGCCATCTTTAGGGATA
2416976 ATGGAGAT
130 ATGGAGAT
** * * * *
2416984 AACACATTTTCTACGCGATAAGGAAGTCTGGTTATCTAAGGGTGACGCGACTCCTACGTGAT---
1 AACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGACGCAACTCCTACGTGATGAG
* * *
2417046 GAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATAAGGACGTCTGGTCATCTTTAGGGATAA
66 GAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGACTGGCCATCTTTAGGGAT-A
2417111 ATGGAGAT
130 ATGGAGAT
* * * * **** *
2417119 AACACGGTTCCTTCGCGATGAGAAAGTCTGATTATCTAAGGGTGACATTGCTCCTACGCGATGAG
1 AACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGACGCAACTCCTACGTGATGAG
* * * * *
2417184 GAGATCTGGTAGATGGATGACACGGTTCCTACGTGATGAAGACGTCTGACCATCTTTAGGGATAA
66 GAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGACTGGCCATCTTTAGGGATAA
2417249 T
131 T
2417250 TTGTTTCAAG
Statistics
Matches: 956, Mismatches: 109, Indels: 30
0.87 0.10 0.03
Matches are distributed among these distances:
133 3 0.00
134 349 0.37
135 118 0.12
137 369 0.39
138 116 0.12
139 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (137 bp):
AACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGGTGACGCAACTCCTACGTGATGAG
GAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGACTGGCCATCTTTAGGGATAA
TGGAGAT
Found at i:2417075 original size:543 final size:542
Alignment explanation
Indices: 2416033--2417249 Score: 2062
Period size: 543 Copynumber: 2.2 Consensus size: 542
2416023 ATTTAAAGAC
* * * * *
2416033 AACACGATTCCTACGTGATGAGGAAA-TCTGGTTATCTAAGGGTGACGATGCTCTTACGTGATGA
1 AACACGGTTCCTTCATGATGA-GAAAGTCTGGTTATCTAAGGGTGAC-ATGCTCCTACGCGATGA
* **
2416097 GGATATCTGGTCGGTGGATGACACAATTCCTACGTGATGAGGACGGCTAGCCATCTTTAGGTATA
64 GGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGGCTAGCCATCTTTAGGTATA
2416162 ATGGAGATAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACACAACTCCTAC
129 ATGGAGATAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACACAACTCCTAC
* *
2416227 GTGATGAGGAGATCTGGTCGGTAGATGACACGGTTCCTACGTGATGAGCACGGCTGGCCATCTTT
194 GTGATGAGGAGATCTGGTCGGTAGATGACACGGTTCCTACGTGATGAGCACGACTGACCATCTTT
*
2416292 AGGGATAATGAAGATAACACGGTTCTTACGTGATGAGGAAGTATGGTTATCTAAGGATGACGTAG
259 AGGGATAATGAAGATAACACGGTTCTTACGTGATGAGGAAGTATGGTTATCTAAGGATGACGCAG
*
2416357 ATCCTACGTGATGAGATATGGTCAGTGGATGACACGATTCTTACGTGATGAGGACGACTGGCCAT
324 ATCCTACGTGATGAGATATGGTCAGTGGATGACACGATTCTTACGTGATGAGGACGACTGACCAT
2416422 CTTTAGGGATAATAGAGATAACACGATTCCTACGCGATAAGGAAGTCTGGTTATCTAAGGGTGAC
389 CTTTAGGGATAATAGAGATAACACGATTCCTACGCGATAAGGAAGTCTGGTTATCTAAGGGTGAC
*
2416487 GCGACTCCTACGTGATGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATAGGGACGTCTGG
454 GCGACTCCTACGTGATGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATAAGGACGTCTGG
2416552 ACATCTTTAGGGATAAATGGAGAT
519 ACATCTTTAGGGATAAATGGAGAT
*
2416576 AACACGGTTCTTTCATGATGAGAAAGTCTGGTTATCTAAGGGTGACACTGCTCCTACGCGATGAG
1 AACACGGTTCCTTCATGATGAGAAAGTCTGGTTATCTAAGGGTGACA-TGCTCCTACGCGATGAG
*
2416641 GAGATATGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGGCTAGCCATCTTTAGGTATAA
65 GAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGGCTAGCCATCTTTAGGTATAA
*
2416706 TGGAGATAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACGCAACTCCTACG
130 TGGAGATAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACACAACTCCTACG
* * *
2416771 TGATGAGGAGATCTGGTCGGTGGATGACACGGTTCTTACGTGATGAGGACGACTGACCATCTTTA
195 TGATGAGGAGATCTGGTCGGTAGATGACACGGTTCCTACGTGATGAGCACGACTGACCATCTTTA
*
2416836 GGGATAATGAAGATAACACGGTTCTTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACGCAGA
260 GGGATAATGAAGATAACACGGTTCTTACGTGATGAGGAAGTATGGTTATCTAAGGATGACGCAGA
* *
2416901 TCCTACGTGATGAGATCTGGTCAGTGGATGACACGGTTCTTACGTGATGAGGACGACTGACCATC
325 TCCTACGTGATGAGATATGGTCAGTGGATGACACGATTCTTACGTGATGAGGACGACTGACCATC
* *
2416966 TTTAGGGATAATGGAGATAACAC-ATTTTCTACGCGATAAGGAAGTCTGGTTATCTAAGGGTGAC
390 TTTAGGGATAATAGAGATAACACGA-TTCCTACGCGATAAGGAAGTCTGGTTATCTAAGGGTGAC
2417030 GCGACTCCTACGTGATGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATAAGGACGTCTGG
454 GCGACTCCTACGTGATGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATAAGGACGTCTGG
*
2417095 TCATCTTTAGGGATAAATGGAGAT
519 ACATCTTTAGGGATAAATGGAGAT
** *
2417119 AACACGGTTCCTTCGCGATGAGAAAGTCTGATTATCTAAGGGTGACATTGCTCCTACGCGATGAG
1 AACACGGTTCCTTCATGATGAGAAAGTCTGGTTATCTAAGGGTGACA-TGCTCCTACGCGATGAG
* * * * *
2417184 GAGATCTGGTAGATGGATGACACGGTTCCTACGTGATGAAGACGTCT-GACCATCTTTAGGGATA
65 GAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGGCTAG-CCATCTTTAGGTATA
2417248 AT
129 AT
2417250 TTGTTTCAAG
Statistics
Matches: 634, Mismatches: 36, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
542 7 0.01
543 627 0.99
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (542 bp):
AACACGGTTCCTTCATGATGAGAAAGTCTGGTTATCTAAGGGTGACATGCTCCTACGCGATGAGG
AGATCTGGTCGGTGGATGACACGGTTCCTACGTGATGAGGACGGCTAGCCATCTTTAGGTATAAT
GGAGATAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATCTAAGGATGACACAACTCCTACGT
GATGAGGAGATCTGGTCGGTAGATGACACGGTTCCTACGTGATGAGCACGACTGACCATCTTTAG
GGATAATGAAGATAACACGGTTCTTACGTGATGAGGAAGTATGGTTATCTAAGGATGACGCAGAT
CCTACGTGATGAGATATGGTCAGTGGATGACACGATTCTTACGTGATGAGGACGACTGACCATCT
TTAGGGATAATAGAGATAACACGATTCCTACGCGATAAGGAAGTCTGGTTATCTAAGGGTGACGC
GACTCCTACGTGATGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATAAGGACGTCTGGAC
ATCTTTAGGGATAAATGGAGAT
Found at i:2417347 original size:17 final size:19
Alignment explanation
Indices: 2417325--2417363 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2417315 TTATGTTTCA
2417325 AGAG-AAAC-TGTCTCAAG
1 AGAGAAAACTTGTCTCAAG
*
2417342 AGAGAAAACTTGTTTCAAG
1 AGAGAAAACTTGTCTCAAG
2417361 AGA
1 AGA
2417364 AACAATCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 11 0.58
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (19 bp):
AGAGAAAACTTGTCTCAAG
Found at i:2417364 original size:17 final size:16
Alignment explanation
Indices: 2417318--2417365 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
2417308 AATGTTTTTA
2417318 TGTTTCAAGAG-AAAC
1 TGTTTCAAGAGAAAAC
*
2417333 TGTCTCAAGAGAGAAAAC
1 TGTTTC-A-AGAGAAAAC
2417351 TTGTTTCAAGAGAAA
1 -TGTTTCAAGAGAAA
2417366 CAATCTCTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 5 0.19
16 1 0.04
17 11 0.41
18 5 0.19
19 5 0.19
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (16 bp):
TGTTTCAAGAGAAAAC
Found at i:2427804 original size:20 final size:21
Alignment explanation
Indices: 2427757--2427809 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
2427747 TTGAAGGATG
*
2427757 GTATCGATACTGGTTGAAGTGG
1 GTATCGATACTGGTTG-AGTGA
2427779 GTATCGATACTGAGTTG-G-GA
1 GTATCGATACTG-GTTGAGTGA
2427799 GTATCGATACT
1 GTATCGATACT
2427810 AAGGGTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 12 0.41
21 1 0.03
22 12 0.41
23 4 0.14
ACGTcount: A:0.25, C:0.11, G:0.32, T:0.32
Consensus pattern (21 bp):
GTATCGATACTGGTTGAGTGA
Found at i:2428726 original size:22 final size:22
Alignment explanation
Indices: 2428698--2428741 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2428688 AGTCGAGGGT
*
2428698 TCTATGTGGTCCTTCGGGACAA
1 TCTATGTGGTCATTCGGGACAA
2428720 TCTATGTGGTCATTCGGGACAA
1 TCTATGTGGTCATTCGGGACAA
2428742 ACCTACGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (22 bp):
TCTATGTGGTCATTCGGGACAA
Found at i:2428765 original size:23 final size:23
Alignment explanation
Indices: 2428739--2428788 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
2428729 TCATTCGGGA
2428739 CAAACCTACGTGGCACTTCAATG
1 CAAACCTACGTGGCACTTCAATG
* * *
2428762 CAAATCTATGTGGCACTTCAGTG
1 CAAACCTACGTGGCACTTCAATG
2428785 CAAA
1 CAAA
2428789 ACTTATGTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (23 bp):
CAAACCTACGTGGCACTTCAATG
Found at i:2428826 original size:21 final size:24
Alignment explanation
Indices: 2428748--2428833 Score: 83
Period size: 23 Copynumber: 3.8 Consensus size: 24
2428738 ACAAACCTAC
* *
2428748 GTGGCACTTCAATGCAAATC-TAT
1 GTGGCACTTCAGTGCAAAACTTAT
2428771 GTGGCACTTCAGTGCAAAACTTAT
1 GTGGCACTTCAGTGCAAAACTTAT
* *
2428795 GTGGTC-TTTCAG-G-ATAA-TTAT
1 GTGG-CACTTCAGTGCAAAACTTAT
*
2428816 GTGGCACTTCAATGCAAA
1 GTGGCACTTCAGTGCAAA
2428834 TTACGAGCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 12 0.24
22 4 0.08
23 21 0.41
24 12 0.24
25 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (24 bp):
GTGGCACTTCAGTGCAAAACTTAT
Found at i:2434567 original size:22 final size:22
Alignment explanation
Indices: 2434539--2434582 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2434529 AGTCGAGAGT
2434539 TCTATGTAGTCCTTCGGGACAA
1 TCTATGTAGTCCTTCGGGACAA
* * *
2434561 TCTATGTGGTTCTTTGGGACAA
1 TCTATGTAGTCCTTCGGGACAA
2434583 ACCTATGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (22 bp):
TCTATGTAGTCCTTCGGGACAA
Found at i:2434591 original size:23 final size:22
Alignment explanation
Indices: 2434540--2434591 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2434530 GTCGAGAGTT
* *
2434540 CTATGTAGTCCTTCGGGACAAT
1 CTATGTGGTCCTTCGGGACAAC
* *
2434562 CTATGTGGTTCTTTGGGACAAAC
1 CTATGTGGTCCTTCGGGAC-AAC
2434585 CTATGTG
1 CTATGTG
2434592 ACATTTCGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (22 bp):
CTATGTGGTCCTTCGGGACAAC
Found at i:2434606 original size:23 final size:23
Alignment explanation
Indices: 2434580--2434638 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
2434570 TTCTTTGGGA
* *
2434580 CAAACCTATGTGACATTTCGGTG
1 CAAACCTATGTGACACTTCGATG
* *
2434603 CAAATCTATGTGGCACTTCGATG
1 CAAACCTATGTGACACTTCGATG
*
2434626 CAAAACTTATGTG
1 C-AAACCTATGTG
2434639 GTCTTTCGGG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (23 bp):
CAAACCTATGTGACACTTCGATG
Found at i:2436412 original size:15 final size:14
Alignment explanation
Indices: 2436382--2436430 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2436372 TGATTGAAAA
**
2436382 AAAATTAATTAATT
1 AAAATTAATTTTTT
2436396 AAAATTAATATTTTT
1 AAAATTAAT-TTTTT
*
2436411 AATAATTTATTTTTT
1 AA-AATTAATTTTTT
2436426 AAAAT
1 AAAAT
2436431 ATATTTGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 12 0.40
15 12 0.40
16 6 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AAAATTAATTTTTT
Found at i:2439873 original size:24 final size:24
Alignment explanation
Indices: 2439841--2439893 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
2439831 TGATAAAACC
*
2439841 GACGATCCTGACTGAGAAGTGTCT
1 GACGATCCTGACTGAGAAGTGTCA
2439865 GACGATCCTGACTGAGAAGTGTCA
1 GACGATCCTGACTGAGAAGTGTCA
2439889 GACGA
1 GACGA
2439894 AAACCCAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (24 bp):
GACGATCCTGACTGAGAAGTGTCA
Found at i:2445368 original size:20 final size:19
Alignment explanation
Indices: 2445345--2445390 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
2445335 CGATATACCA
2445345 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
2445365 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
2445385 GGTAAA
1 GGTAAA
2445391 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2445535 original size:20 final size:19
Alignment explanation
Indices: 2445512--2445558 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2445502 CGATATAACA
*
2445512 GGTAAAAATATGATAAAGCC
1 GGTAAAAA-ATGATAAAACC
*
2445532 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
2445552 GGTAAAA
1 GGTAAAA
2445559 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2447841 original size:21 final size:21
Alignment explanation
Indices: 2447794--2447858 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2447784 AAGACAATCA
* *
2447794 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
2447816 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
2447836 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
2447857 AG
1 AG
2447859 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:2447939 original size:33 final size:33
Alignment explanation
Indices: 2447892--2447957 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2447882 AAATAGATGG
* *
2447892 AGTGGTGAATGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
2447925 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2447958 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.48, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2449777 original size:19 final size:19
Alignment explanation
Indices: 2449753--2449801 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2449743 AATGTAGGGT
2449753 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2449772 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
2449791 TATTTTTGTAT
1 TAATTTTGTAT
2449802 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2450413 original size:199 final size:199
Alignment explanation
Indices: 2450163--2451076 Score: 1704
Period size: 199 Copynumber: 4.6 Consensus size: 199
2450153 ATAAAAAAGT
*
2450163 ATCGATCCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
1 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
*
2450228 TATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCA
66 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCA
*
2450293 GAATAAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
131 GAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
2450358 AATC
196 AATC
2450362 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
1 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
*
2450427 TATGAGAAAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCA
66 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCA
2450492 GAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
131 GAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
2450557 AATC
196 AATC
***
2450561 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTTATTT
1 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
* *
2450626 TATGAGAGAATATGTCTAAATAATGTGTCGAAAATAATATAGTTTGTGTCGATATTT-TTTTCCA
66 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCA
2450690 GAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
131 GAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
2450755 AATC
196 AATC
***
2450759 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTTATTT
1 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
2450824 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCA
66 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCA
2450889 GAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
131 GAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
2450954 AATC
196 AATC
2450958 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
1 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
*
2451023 TATGAGAGAATATGTCTAAAAAATGTGTCGACACTAATATAGTTTGTGTCGATA
66 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
2451077 CTAATTTAAA
Statistics
Matches: 698, Mismatches: 16, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
198 196 0.28
199 502 0.72
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (199 bp):
ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCA
GAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
AATC
Found at i:2450817 original size:397 final size:398
Alignment explanation
Indices: 2450163--2451076 Score: 1704
Period size: 397 Copynumber: 2.3 Consensus size: 398
2450153 ATAAAAAAGT
*
2450163 ATCGATCCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
1 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
*
2450228 TATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCA
66 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCA
2450293 GAATAAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
131 GAATAAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
2450358 AATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCG
196 AATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCG
*
2450423 GTTTTATGAGAAAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTT
261 ATTTTATGAGAAAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTT
2450488 TCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATC
326 TCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATC
2450553 CCAAAATC
391 CCAAAATC
***
2450561 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTTATTT
1 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
* *
2450626 TATGAGAGAATATGTCTAAATAATGTGTCGAAAATAATATAGTTTGTGTCGATATTT-TTTTCCA
66 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCA
*
2450690 GAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
131 GAATAAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
**
2450755 AATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTT
196 AATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCG
*
2450820 ATTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTT
261 ATTTTATGAGAAAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTT
2450885 TCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATC
326 TCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATC
2450950 CCAAAATC
391 CCAAAATC
2450958 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
1 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
*
2451023 TATGAGAGAATATGTCTAAAAAATGTGTCGACACTAATATAGTTTGTGTCGATA
66 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
2451077 CTAATTTAAA
Statistics
Matches: 498, Mismatches: 18, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
397 383 0.77
398 115 0.23
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (398 bp):
ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCA
GAATAAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
AATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCG
ATTTTATGAGAAAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTT
TCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATC
CCAAAATC
Found at i:2452557 original size:12 final size:12
Alignment explanation
Indices: 2452540--2452592 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
2452530 GGTCGCAGAA
*
2452540 GATGAAGCTGAC
1 GATGAAGATGAC
2452552 GATGAAGATGAC
1 GATGAAGATGAC
*
2452564 GATGATGATGAC
1 GATGAAGATGAC
* *
2452576 GATGATGATGAT
1 GATGAAGATGAC
2452588 GATGA
1 GATGA
2452593 TGAAGATGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.36, C:0.08, G:0.34, T:0.23
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:2452572 original size:3 final size:3
Alignment explanation
Indices: 2452552--2452605 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
2452542 TGAAGCTGAC
* * * *
2452552 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
2452600 GAT GAT
1 GAT GAT
2452606 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:2452573 original size:18 final size:18
Alignment explanation
Indices: 2452537--2452605 Score: 72
Period size: 18 Copynumber: 4.0 Consensus size: 18
2452527 AGCGGTCGCA
* *
2452537 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
2452555 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
*
2452573 GACGAT---GATGATGAT
1 GAAGATGAAGATGATGAT
*
2452588 GATGATGAAGATGATGAT
1 GAAGATGAAGATGATGAT
2452606 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 14 0.33
18 29 0.67
ACGTcount: A:0.38, C:0.06, G:0.33, T:0.23
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:2452593 original size:12 final size:12
Alignment explanation
Indices: 2452548--2452605 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
2452538 AAGATGAAGC
*
2452548 TGACGATGAAGA
1 TGACGATGATGA
2452560 TGACGATGATGA
1 TGACGATGATGA
2452572 TGACGATGATGA
1 TGACGATGATGA
*
2452584 TGATGATGATGA
1 TGACGATGATGA
* *
2452596 AGATGATGAT
1 TGACGATGAT
2452606 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.26
Consensus pattern (12 bp):
TGACGATGATGA
Found at i:2454337 original size:183 final size:183
Alignment explanation
Indices: 2454029--2455286 Score: 2336
Period size: 183 Copynumber: 6.9 Consensus size: 183
2454019 CTTTCAACAT
** * * *
2454029 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
2454094 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
2454159 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
2454212 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
2454277 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
2454342 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
* *
2454395 ATTATAATATAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCACGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
2454460 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
2454525 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
2454578 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
2454643 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
2454708 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
*
2454761 TTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
2454826 GGTCTACAACCTATCTCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
2454891 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
*
2454944 TTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
2455009 GGTCTACAACCTATCTCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
2455074 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
*
2455127 TTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
2455192 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
2455257 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACGATTTAAAAAAGTGTCG
2455287 GTAATTTTAA
Statistics
Matches: 1055, Mismatches: 20, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 1055 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
Found at i:2457788 original size:25 final size:25
Alignment explanation
Indices: 2457754--2457818 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
2457744 TTATCATTAA
2457754 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
2457779 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
2457804 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
2457819 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:2458140 original size:23 final size:23
Alignment explanation
Indices: 2458109--2458172 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2458099 ATAGGTAAAC
*
2458109 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
2458132 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
2458155 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2458173 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2458179 original size:23 final size:23
Alignment explanation
Indices: 2458109--2458181 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
2458099 ATAGGTAAAC
* **
2458109 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
2458132 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
2458155 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
2458178 ATAT
1 ATAT
2458182 TGTAAAATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:2458221 original size:21 final size:20
Alignment explanation
Indices: 2458184--2458223 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2458174 GGTTATATTG
* *
2458184 TAAAATGTCTATCCTTTTTA
1 TAAAATGTCCATACTTTTTA
2458204 TAAAAGTGTCCATACTTTTT
1 TAAAA-TGTCCATACTTTTT
2458224 TCTTCTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (20 bp):
TAAAATGTCCATACTTTTTA
Found at i:2459612 original size:35 final size:35
Alignment explanation
Indices: 2459566--2459638 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
2459556 GCATGGTGAA
*
2459566 TTCATGATCAACATGGGTTCCGACAGTAAAGTAAT
1 TTCATGATCAACATGGGTTCCGACAGCAAAGTAAT
*
2459601 TTCATGATCAACATGGGTTCTGACAGCAAAGTAAT
1 TTCATGATCAACATGGGTTCCGACAGCAAAGTAAT
2459636 TTC
1 TTC
2459639 CCAAAAACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (35 bp):
TTCATGATCAACATGGGTTCCGACAGCAAAGTAAT
Found at i:2465173 original size:24 final size:24
Alignment explanation
Indices: 2465141--2465190 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2465131 AATTTATTTT
*
2465141 TAAAAATAA-ATATCATTTATAATA
1 TAAAAATAATATAT-ATTAATAATA
*
2465165 TAAATATAATATATATTAATAATA
1 TAAAAATAATATATATTAATAATA
2465189 TA
1 TA
2465191 TTTTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAAAATAATATATATTAATAATA
Found at i:2465620 original size:22 final size:22
Alignment explanation
Indices: 2465592--2465633 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2465582 TTTAGAGGGG
*
2465592 TTTTTTTTGGAAATTTAAGATT
1 TTTTTTTTGAAAATTTAAGATT
2465614 TTTTTTTTGAAAATTTAAGA
1 TTTTTTTTGAAAATTTAAGA
2465634 ATTTCAGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (22 bp):
TTTTTTTTGAAAATTTAAGATT
Found at i:2465709 original size:20 final size:20
Alignment explanation
Indices: 2465684--2465730 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2465674 TATATTAATA
2465684 TATAATACATCAATATTATT
1 TATAATACATCAATATTATT
* * *
2465704 TATAATATATTAGTATTATT
1 TATAATACATCAATATTATT
2465724 TATAATA
1 TATAATA
2465731 TATTTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (20 bp):
TATAATACATCAATATTATT
Found at i:2465736 original size:11 final size:11
Alignment explanation
Indices: 2465695--2465743 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
2465685 ATAATACATC
2465695 AATATTATTTAT
1 AATA-TATTTAT
2465707 AATATA-TTAGT
1 AATATATTTA-T
2465718 -AT-TATTTAT
1 AATATATTTAT
2465727 AATATATTTAT
1 AATATATTTAT
*
2465738 ATTATA
1 AATATA
2465744 AATAATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
9 3 0.09
10 10 0.31
11 15 0.47
12 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
AATATATTTAT
Found at i:2465740 original size:20 final size:19
Alignment explanation
Indices: 2465696--2465742 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
2465686 TAATACATCA
2465696 ATATTATTTATAATATATT
1 ATATTATTTATAATATATT
2465715 AGTATTATTTATAATATATTT
1 A-TATTATTTATAATATA-TT
2465736 ATATTAT
1 ATATTAT
2465743 AAATAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.04
20 22 0.85
21 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATATTATTTATAATATATT
Found at i:2465748 original size:20 final size:20
Alignment explanation
Indices: 2465705--2465749 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2465695 AATATTATTT
**
2465705 ATAATATATTAGTATTATTT
1 ATAATATATTAGTATTATAA
2465725 ATAATATATTTA-TATTATAA
1 ATAATATA-TTAGTATTATAA
2465745 ATAAT
1 ATAAT
2465750 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATAATATATTAGTATTATAA
Found at i:2467416 original size:302 final size:300
Alignment explanation
Indices: 2466809--2468003 Score: 1360
Period size: 312 Copynumber: 3.9 Consensus size: 300
2466799 CACGGTTTAA
** * * * * *
2466809 ATTAATAATAAGAAATTGTTTAAGTGTAAACCTGCAGAGTTTTGTTATATATACATTGTGTTTGG
1 ATTAATAATAATCAATTGTTTAGGTGCAAACCTTCAGAGTTTTGTAATATATACA-T-TATTTGG
* * *
2466874 CCATGATAGAGTTATAGACTACTTAGAATGCAAACACTGCCAATG------AA-TCCTAAGTGCT
64 CC---AT-GA--T-T-GACTATTTAGAATGCAAACACTGCTAATGAATCCTAATTCCTAATTGCT
* * *
2466932 ACTGCTTATGCTGCCAATGGATCCTATTTGTAGAGAAATTGGCTGATGGGAATAGTATTTCTGTA
121 ACTGCTTATGCTGCCAATGGATCCTATTTATAGAGAGATTGGCTGATGGGAATAGTATCTCTGTA
* * * *
2466997 AGATGTCTTTTTGTTTGGGTTAAAATATTAGCATTTTTATGGTCAATG-AAGCCTTGTCACTTGT
186 AGATGTTTTTTTGTTAGGGTTAACATATTAACATTTTTATGGTCAATGAAAGCC---T--C--GT
* * * * *
2467061 CAGTGTTTGTCCTG-TTTTTGAGAGTTCTTTATATAGAAAGTTCATTTGCTGGTTAC
244 AAGTGTTTGTTCTGTTTTTTGAGAGTTCTTTATATTGAAAGTTCGTTAGCTGGTTAC
* * * *
2467117 ATTAGTAATAATCAATTGTTTAGGTGCAAACCTTCAGAGTTTTGTAGTATATACATTTTTTGCCC
1 ATTAATAATAATCAATTGTTTAGGTGCAAACCTTCAGAGTTTTGTAATATATACATTATTTGGCC
**
2467182 ATGATTGACTATTTAGAATGCAAACACTGCTAATGAATCCTAAATTCCTAATTGCTACTTTTTAT
66 ATGATTGACTATTTAGAATGCAAACACTGCTAATGAATCCT-AATTCCTAATTGCTACTGCTTAT
* * *
2467247 GCTGCCAATGGATCCTATGTTATAGAGAGATTCGCTGATGGGAATAGTATCTATATAAGATGTTT
130 GCTGCCAATGGATCCTAT-TTATAGAGAGATTGGCTGATGGGAATAGTATCTCTGTAAGATGTTT
* * *
2467312 TTCTTGTTAGGGTTAACATATTAACATTTGTATGGTCAATGAAAGCCTTGTCAGTGTTTGTTCTG
194 TT-TTGTTAGGGTTAACATATTAACATTTTTATGGTCAATGAAAGCCTCGTAAGTGTTTGTTCTG
2467377 -TTTTTGAGAGTTCTTTATATTGAAAGTTCGTTAGCTGGTTAC
258 TTTTTTGAGAGTTCTTTATATTGAAAGTTCGTTAGCTGGTTAC
* ** *
2467419 ATTAATAATAATCAATTGTCTAGAAGCAAACCTTCAGAGTTTTGTAATATATACATTGTTTGGCC
1 ATTAATAATAATCAATTGTTTAGGTGCAAACCTTCAGAGTTTTGTAATATATACATTATTTGGCC
* * *
2467484 ATGATTGACTATTGAGAATGCAAACACTGCTAATGAAT-C-----CC-GATTGCTACCGCTTATG
66 ATGATTGACTATTTAGAATGCAAACACTGCTAATGAATCCTAATTCCTAATTGCTACTGCTTATG
* *
2467542 CTGCCAATGGATCCTTTTTATAGAGAGATTGGCTGATGGGATTAGTATCTCTGTAAGATGTTTTT
131 CTGCCAATGGATCCTATTTATAGAGAGATTGGCTGATGGGAATAGTATCTCTGTAAGATGTTTTT
*
2467607 TTGTTAGGG-TAACCGTATTAACATTTTTATGGTCAATGAAAGCCTCGTAAGTGTTTGTTCTGTT
196 TTGTTAGGGTTAA-CATATTAACATTTTTATGGTCAATGAAAGCCTCGTAAGTGTTTGTTCTGTT
*
2467671 TTTTTAGAGTTCTTTATATTGAAAGTTCGTTAGCTTAAAAATTGGGATGACATGGGTTAC
260 TTTTGAGAGTTCTTTATATTGAAAGTTC----G--------TT---A-G-C-T-GGTTAC
* *
2467731 ATTAATAATAATCAATTGTTTAGGTGCAAACCTACAGAGTTTTGTAATACATACATTATTTGGCC
1 ATTAATAATAATCAATTGTTTAGGTGCAAACCTTCAGAGTTTTGTAATATATACATTATTTGGCC
* *
2467796 ATGATTGACTATTTAGAATGCAAACACTGCTAATGAATCCTAATTGCT-A----T-C-GTTTATG
66 ATGATTGACTATTTAGAATGCAAACACTGCTAATGAATCCTAATTCCTAATTGCTACTGCTTATG
* * *
2467854 CTGCCAATGGATCCTATTTATAGAGAGATTGGCTGATGGGATTAGTATTTCTGTATGATGTTTTT
131 CTGCCAATGGATCCTATTTATAGAGAGATTGGCTGATGGGAATAGTATCTCTGTAAGATG-TTTT
*
2467919 TTTGTTAGGGTTAACATATTAACATTTTTATGGTCAATGAGAGCCTCGTAAGTGTTTGTTCTGTT
195 TTTGTTAGGGTTAACATATTAACATTTTTATGGTCAATGAAAGCCTCGTAAGTGTTTGTTCTGTT
*
2467984 TTTTGAGAGTTCTGTATATT
260 TTTTGAGAGTTCTTTATATT
2468004 TATTTAAGTC
Statistics
Matches: 777, Mismatches: 69, Indels: 77
0.84 0.07 0.08
Matches are distributed among these distances:
291 3 0.00
292 54 0.07
293 72 0.09
294 29 0.04
295 2 0.00
297 1 0.00
298 27 0.03
299 1 0.00
300 1 0.00
301 1 0.00
302 151 0.19
303 2 0.00
305 4 0.01
306 43 0.06
307 42 0.05
308 82 0.11
309 6 0.01
310 1 0.00
311 1 0.00
312 165 0.21
313 83 0.11
314 4 0.01
318 2 0.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.40
Consensus pattern (300 bp):
ATTAATAATAATCAATTGTTTAGGTGCAAACCTTCAGAGTTTTGTAATATATACATTATTTGGCC
ATGATTGACTATTTAGAATGCAAACACTGCTAATGAATCCTAATTCCTAATTGCTACTGCTTATG
CTGCCAATGGATCCTATTTATAGAGAGATTGGCTGATGGGAATAGTATCTCTGTAAGATGTTTTT
TTGTTAGGGTTAACATATTAACATTTTTATGGTCAATGAAAGCCTCGTAAGTGTTTGTTCTGTTT
TTTGAGAGTTCTTTATATTGAAAGTTCGTTAGCTGGTTAC
Found at i:2478518 original size:29 final size:31
Alignment explanation
Indices: 2478462--2478533 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 31
2478452 AAATTATCAC
2478462 ATTTTGATCACTTATATTACTGATTTATTAT
1 ATTTTGATCACTTATATTACTGATTTATTAT
*
2478493 -TTTTGATCACTTATGTTA-TCGA-TTATTAT
1 ATTTTGATCACTTATATTACT-GATTTATTAT
2478522 ATTTTGATCACT
1 ATTTTGATCACT
2478534 AAGTCATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
29 8 0.21
30 30 0.79
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.54
Consensus pattern (31 bp):
ATTTTGATCACTTATATTACTGATTTATTAT
Found at i:2478552 original size:32 final size:29
Alignment explanation
Indices: 2478463--2478544 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 29
2478453 AATTATCACA
*
2478463 TTTTGATCACTTATATTA-CTGATTTATTAT
1 TTTTGATCACTAATATTATC-GA-TTATTAT
* *
2478493 TTTTGATCACTTATGTTATCGATTATTAT
1 TTTTGATCACTAATATTATCGATTATTAT
2478522 ATTTTGATCACTAAGTCATTATC
1 -TTTTGATCACTAA-T-ATTATC
2478545 TCTTATTAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
29 7 0.16
30 31 0.69
31 2 0.04
32 5 0.11
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (29 bp):
TTTTGATCACTAATATTATCGATTATTAT
Found at i:2484551 original size:23 final size:23
Alignment explanation
Indices: 2484503--2484551 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
2484493 ATATATATAA
*
2484503 TAAGTAAAATAATATTGATAATT
1 TAAGTAAAATAATATTGAAAATT
* *
2484526 TAAGTAATATATTATT-AAAATAT
1 TAAGTAAAATAATATTGAAAAT-T
2484549 TAA
1 TAA
2484552 TCATAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (23 bp):
TAAGTAAAATAATATTGAAAATT
Found at i:2488360 original size:2 final size:2
Alignment explanation
Indices: 2488353--2488382 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2488343 GAGAGGATAA
2488353 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2488383 GCAAATGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2488701 original size:16 final size:16
Alignment explanation
Indices: 2488680--2488726 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
2488670 AACTTGAATT
*
2488680 AAAATAATTTGAGTTG
1 AAAATAATTTGAGTTA
*
2488696 AAAATAATTTGAATTA
1 AAAATAATTTGAGTTA
*
2488712 AAAATAATTCGAGTT
1 AAAATAATTTGAGTT
2488727 TAATTTACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (16 bp):
AAAATAATTTGAGTTA
Found at i:2497905 original size:21 final size:21
Alignment explanation
Indices: 2497880--2497965 Score: 154
Period size: 21 Copynumber: 4.1 Consensus size: 21
2497870 AATATAAATT
* *
2497880 GTGTATCGATGCACCGCTACA
1 GTGTACCGATGCACTGCTACA
2497901 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
2497922 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
2497943 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
2497964 GT
1 GT
2497966 AACTTCAGCT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTACA
Found at i:2498627 original size:32 final size:32
Alignment explanation
Indices: 2498571--2498892 Score: 405
Period size: 32 Copynumber: 10.4 Consensus size: 32
2498561 ATTCCTAAGA
2498571 ACATAGGTAA-C-TGTCCATATGTCCCGAAAG
1 ACATAGGTAATCATGTCCATATGTCCCGAAAG
*
2498601 ACATAGGTAATCATGTACATATGTCCCGAAAG
1 ACATAGGTAATCATGTCCATATGTCCCGAAAG
* *
2498633 ACATAGTTAATCCTG-CCTATATGTCCCGAAAG
1 ACATAGGTAATCATGTCC-ATATGTCCCGAAAG
* *
2498665 ACATATGTAATCATGTCCATATATCCCGAAAG
1 ACATAGGTAATCATGTCCATATGTCCCGAAAG
2498697 ACATAGGTAATCATGTCCATATGTCCCGAAAG
1 ACATAGGTAATCATGTCCATATGTCCCGAAAG
* * *
2498729 ACATAGGTAATCCTGTCTATATGTCCTGAAAG
1 ACATAGGTAATCATGTCCATATGTCCCGAAAG
* * *
2498761 ACATAGTTAATCTTGTACATATGTCCCGAAAG
1 ACATAGGTAATCATGTCCATATGTCCCGAAAG
* *
2498793 ACATAGGCAATCCTGTCCATA--T---G---G
1 ACATAGGTAATCATGTCCATATGTCCCGAAAG
* * **
2498817 ACATAGGCAATCCTGTCCATATGTCCTAAAAG
1 ACATAGGTAATCATGTCCATATGTCCCGAAAG
2498849 ACATAGGTAATCATGTCCATATGTCCCGAAAG
1 ACATAGGTAATCATGTCCATATGTCCCGAAAG
2498881 ACATAGGTAATC
1 ACATAGGTAATC
2498893 CTCGACTCTT
Statistics
Matches: 253, Mismatches: 27, Indels: 22
0.84 0.09 0.07
Matches are distributed among these distances:
24 22 0.09
26 1 0.00
27 1 0.00
30 11 0.04
31 2 0.01
32 214 0.85
33 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (32 bp):
ACATAGGTAATCATGTCCATATGTCCCGAAAG
Found at i:2498819 original size:24 final size:24
Alignment explanation
Indices: 2498792--2498839 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2498782 TGTCCCGAAA
2498792 GACATAGGCAATCCTGTCCATATG
1 GACATAGGCAATCCTGTCCATATG
2498816 GACATAGGCAATCCTGTCCATATG
1 GACATAGGCAATCCTGTCCATATG
2498840 TCCTAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (24 bp):
GACATAGGCAATCCTGTCCATATG
Found at i:2498838 original size:56 final size:56
Alignment explanation
Indices: 2498760--2498871 Score: 152
Period size: 56 Copynumber: 2.0 Consensus size: 56
2498750 TGTCCTGAAA
** * * *
2498760 GACATAGTTAATCTTGTACATATGTCCCGAAAGACATAGGCAATCCTGTCCATATG
1 GACATAGGCAATCCTGTACATATGTCCCAAAAGACATAGGCAATCATGTCCATATG
* * *
2498816 GACATAGGCAATCCTGTCCATATGTCCTAAAAGACATAGGTAATCATGTCCATATG
1 GACATAGGCAATCCTGTACATATGTCCCAAAAGACATAGGCAATCATGTCCATATG
2498872 TCCCGAAAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (56 bp):
GACATAGGCAATCCTGTACATATGTCCCAAAAGACATAGGCAATCATGTCCATATG
Found at i:2498870 original size:88 final size:88
Alignment explanation
Indices: 2498728--2498894 Score: 271
Period size: 88 Copynumber: 1.9 Consensus size: 88
2498718 TGTCCCGAAA
* * * * *
2498728 GACATAGGTAATCCTGTCTATATGTCCTGAAAGACATAGTTAATCTTGTACATATGTCCCGAAAG
1 GACATAGGCAATCCTGTCCATATGTCCTAAAAGACATAGGTAATCATGTACATATGTCCCGAAAG
2498793 ACATAGGCAATCCTGTCCATATG
66 ACATAGGCAATCCTGTCCATATG
*
2498816 GACATAGGCAATCCTGTCCATATGTCCTAAAAGACATAGGTAATCATGTCCATATGTCCCGAAAG
1 GACATAGGCAATCCTGTCCATATGTCCTAAAAGACATAGGTAATCATGTACATATGTCCCGAAAG
*
2498881 ACATAGGTAATCCT
66 ACATAGGCAATCCT
2498895 CGACTCTTAG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 72 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (88 bp):
GACATAGGCAATCCTGTCCATATGTCCTAAAAGACATAGGTAATCATGTACATATGTCCCGAAAG
ACATAGGCAATCCTGTCCATATG
Found at i:2502699 original size:21 final size:21
Alignment explanation
Indices: 2502675--2502715 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2502665 CTATAAACAG
*
2502675 TGCTACATTGTACCGATGCAT
1 TGCTACAGTGTACCGATGCAT
2502696 TGCTACAGTGTACCGATGCA
1 TGCTACAGTGTACCGATGCA
2502716 CATAAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (21 bp):
TGCTACAGTGTACCGATGCAT
Found at i:2503439 original size:32 final size:32
Alignment explanation
Indices: 2503368--2503620 Score: 386
Period size: 32 Copynumber: 8.0 Consensus size: 32
2503358 GAAGGACCTA
* * *
2503368 TCCATATGTTCC-TAAGAACATAGGTAA--CTA
1 TCCATATGTCCCGAAAG-ACATAGGTAATCCTG
2503398 TCCATATGTCCCGAAAGACATAGGTAATCCTG
1 TCCATATGTCCCGAAAGACATAGGTAATCCTG
*
2503430 TCCATATGTCCCGAAAGACATAGTTAATCCTG
1 TCCATATGTCCCGAAAGACATAGGTAATCCTG
* *
2503462 TCCATATGTCCCGAAATACATAGTTAATCCTG
1 TCCATATGTCCCGAAAGACATAGGTAATCCTG
*
2503494 TCCATATGTCCCGAAAGACATAGTTAATCCTG
1 TCCATATGTCCCGAAAGACATAGGTAATCCTG
*
2503526 TCCATATGTCCCGAAAGACATAGGTAATCCTA
1 TCCATATGTCCCGAAAGACATAGGTAATCCTG
* *
2503558 TCCATATGTCCCGAAAGACATATGTAATCTTG
1 TCCATATGTCCCGAAAGACATAGGTAATCCTG
2503590 TCCATATGTCCCGAAAGACATAGGTAATCCT
1 TCCATATGTCCCGAAAGACATAGGTAATCCT
2503621 CGACTCTTAG
Statistics
Matches: 207, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
30 21 0.10
31 3 0.01
32 183 0.88
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.28
Consensus pattern (32 bp):
TCCATATGTCCCGAAAGACATAGGTAATCCTG
Found at i:2504606 original size:19 final size:21
Alignment explanation
Indices: 2504570--2504611 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
2504560 AAACCTTTCA
2504570 GGGGGAATCGGTACCCCT-TG
1 GGGGGAATCGGTACCCCTCTG
* *
2504590 GGGGGTATCTGTA-CCCTCTG
1 GGGGGAATCGGTACCCCTCTG
2504610 GG
1 GG
2504612 CAATCTGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCTCTG
Found at i:2504825 original size:19 final size:20
Alignment explanation
Indices: 2504801--2504840 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2504791 AATTTAATCG
*
2504801 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
2504820 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
2504840 A
1 A
2504841 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:2505261 original size:9 final size:9
Alignment explanation
Indices: 2505247--2505292 Score: 53
Period size: 8 Copynumber: 5.4 Consensus size: 9
2505237 AATAAACATT
2505247 CAAACAATC
1 CAAACAATC
*
2505256 CAAAC-ATT
1 CAAACAATC
*
2505264 CAGACAATC
1 CAAACAATC
2505273 CAAAC-ATC
1 CAAACAATC
2505281 CAAACAA-C
1 CAAACAATC
2505289 CAAA
1 CAAA
2505293 TCCAAAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
8 19 0.61
9 12 0.39
ACGTcount: A:0.54, C:0.33, G:0.02, T:0.11
Consensus pattern (9 bp):
CAAACAATC
Found at i:2505262 original size:17 final size:17
Alignment explanation
Indices: 2505240--2505292 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 17
2505230 AAACCAAAAT
2505240 AAACATTCAAACAATCC
1 AAACATTCAAACAATCC
*
2505257 AAACATTCAGACAATCC
1 AAACATTCAAACAATCC
*
2505274 AAACATCCAAACAA-CC
1 AAACATTCAAACAATCC
2505290 AAA
1 AAA
2505293 TCCAAAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 5 0.15
17 28 0.85
ACGTcount: A:0.55, C:0.30, G:0.02, T:0.13
Consensus pattern (17 bp):
AAACATTCAAACAATCC
Found at i:2505283 original size:8 final size:8
Alignment explanation
Indices: 2505240--2505292 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
2505230 AAACCAAAAT
*
2505240 AAACATTC
1 AAACATCC
2505248 AAACAATCC
1 AAAC-ATCC
*
2505257 AAACATTC
1 AAACATCC
*
2505265 AGACAATCC
1 AAAC-ATCC
2505274 AAACATCC
1 AAACATCC
*
2505282 AAACAACC
1 AAACATCC
2505290 AAA
1 AAA
2505293 TCCAAAACAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
8 24 0.65
9 13 0.35
ACGTcount: A:0.55, C:0.30, G:0.02, T:0.13
Consensus pattern (8 bp):
AAACATCC
Found at i:2506755 original size:21 final size:21
Alignment explanation
Indices: 2506710--2506757 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
2506700 ATATGTAGTT
2506710 TTCAAAAACAACATAATTAAA
1 TTCAAAAACAACATAATTAAA
*
2506731 -TCAAAAACAACA-ATTTAAAA
1 TTCAAAAACAACATAATT-AAA
2506751 TTCAAAA
1 TTCAAAA
2506758 CATTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 3 0.12
20 15 0.62
21 6 0.25
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (21 bp):
TTCAAAAACAACATAATTAAA
Found at i:2507228 original size:21 final size:22
Alignment explanation
Indices: 2507202--2507243 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2507192 TACCCATTCA
*
2507202 AAGGGGAATCGGTTCC-CCTGT
1 AAGGGGAATCGATTCCTCCTGT
*
2507223 AAGGGGTATCGATTCCTCCTG
1 AAGGGGAATCGATTCCTCCTG
2507244 CACTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.26
Consensus pattern (22 bp):
AAGGGGAATCGATTCCTCCTGT
Found at i:2512715 original size:20 final size:20
Alignment explanation
Indices: 2512682--2512723 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2512672 AAACCTTTCA
2512682 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
* * *
2512702 GGGGGTATCTGTACCCTCTG
1 GGGGGAATCGGTACCCCCTG
2512722 GG
1 GG
2512724 CAATCTGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.26, G:0.40, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:2512937 original size:19 final size:20
Alignment explanation
Indices: 2512913--2512952 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2512903 AATTTAATCG
*
2512913 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
2512932 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
2512952 A
1 A
2512953 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:2518276 original size:101 final size:101
Alignment explanation
Indices: 2518154--2518350 Score: 290
Period size: 101 Copynumber: 2.0 Consensus size: 101
2518144 CTAGATTATA
* * * * * * *
2518154 ATATTATATGTATTCAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCT-TCGGCT
1 ATATTATATATATACAATAAAGCTTGAACTGTCCCTCTAGAACAATTGGTTAAA-GATCCCGACT
2518218 TTATGGAT-AGAATTCAGCTAGCCTGATAAAGGTGATT
65 TTATGGATAAG-ATTCAGCTAGCCTGATAAAGGTGATT
*
2518255 ATATTATATATATACAATAAAGCTTGAACTGTCCCTCTAGAACAATTGGTTAAATATCCCGACTT
1 ATATTATATATATACAATAAAGCTTGAACTGTCCCTCTAGAACAATTGGTTAAAGATCCCGACTT
2518320 TATGGATAAGATTCAGCTAGCCTGATAAAGG
66 TATGGATAAGATTCAGCTAGCCTGATAAAGG
2518351 AAAATTACAA
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
100 1 0.01
101 83 0.97
102 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (101 bp):
ATATTATATATATACAATAAAGCTTGAACTGTCCCTCTAGAACAATTGGTTAAAGATCCCGACTT
TATGGATAAGATTCAGCTAGCCTGATAAAGGTGATT
Found at i:2520680 original size:36 final size:36
Alignment explanation
Indices: 2520624--2520738 Score: 158
Period size: 36 Copynumber: 3.2 Consensus size: 36
2520614 CTCGACCTTC
*
2520624 GAAGCCAGTCAATCTTAAGCCTTCACGGAAGAGTAGT
1 GAAGCAAGTC-ATCTTAAGCCTTCACGGAAGAGTAGT
2520661 GAAGCAAGTCATCTTAAGCCTTCACGGAAGAGTAGT
1 GAAGCAAGTCATCTTAAGCCTTCACGGAAGAGTAGT
* * * * * *
2520697 TAAGCAAATCATCTTAAGCCTTTATGGAAGAATAAT
1 GAAGCAAGTCATCTTAAGCCTTCACGGAAGAGTAGT
2520733 GAAGCA
1 GAAGCA
2520739 TAATCATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
36 61 0.87
37 9 0.13
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (36 bp):
GAAGCAAGTCATCTTAAGCCTTCACGGAAGAGTAGT
Found at i:2521064 original size:165 final size:163
Alignment explanation
Indices: 2520745--2521341 Score: 685
Period size: 165 Copynumber: 3.6 Consensus size: 163
2520735 AGCATAATCA
* * * * *
2520745 TTTTATGAAGATTGTTCGAG-TCTTATACTCCTTGAGAGAATAGGGAGC-AGACACGTTTGCTGA
1 TTTTA-GAAGATTGTTCGAGTTC-TATACTCCCTGAAAGAATAGGGAGCGA-ACCCGTTTTCAGA
* * * *
2520808 AGATTGTTCGAGTCTTATACTCCCTGAAAGAATAGGGAG-CAGACACGTTGGTT-GAAGATCGTT
63 AGATTGTTCGAGTCTTATACTCCCTAAAAGAATAGGGAGTGA-ACCCGTT--TTAGAAGATTGTT
* * *
2520871 CGAG-TCTTATACTCCCTAAAAGAATAGGGATC-AGACACGT
125 CGAGTTC-TATACTCCCT-GAAGAATAGGGAGCGA-ACCCGT
* *
2520911 TTTCAGAAGATTGTTCGTGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGA
1 TTTTAGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGA
* * *
2520976 TTGTTTGAGT-TCTATACTCCCTAAAAGAATAGGGAGTGAACCCGTTTTCAAAAGATTGTTTGAG
66 TTGTTCGAGTCT-TATACTCCCTAAAAGAATAGGGAGTGAACCCGTTTT-AGAAGATTGTTCGAG
* *
2521040 TTCTATATTCCCTGAAGCAATAGGGAGCGAACCCAT
129 TTCTATACTCCCTGAAG-AATAGGGAGCGAACCCGT
* *
2521076 TTTTAGAAGATTGTTCAAGTTCTATACTCCCTG-AAGCAATAGGGAGCGAACCCGTTTTTAGAAG
1 TTTTAGAAGATTGTTCGAGTTCTATACTCCCTGAAAG-AATAGGGAGCGAACCCGTTTTCAGAAG
*
2521140 ATTGTTCGAGTTCTT-TACTCCC-AGAAGCAATAGGGAGTGAACCCGTTTTTAGAAGATTGTTCG
65 ATTGTTCGAG-TCTTATACTCCCTAAAAG-AATAGGGAGTGAACCCG-TTTTAGAAGATTGTTCG
*
2521203 AGTTCTATACTGCCTGAAGTAATAGGGAGCGAACCCGT
127 AGTTCTATACTCCCTGAAG-AATAGGGAGCGAACCCGT
* * * *
2521241 TTTTAGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTATGTC-GAAT
1 TTTTAGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGT-TTTCAGAAG
* * *
2521305 ATTTTTCAAGTCTTATACTCTCTAAAAGAATAGGGAG
65 ATTGTTCGAGTCTTATACTCCCTAAAAGAATAGGGAG
2521342 CAGACATGTT
Statistics
Matches: 372, Mismatches: 41, Indels: 37
0.83 0.09 0.08
Matches are distributed among these distances:
163 2 0.01
164 15 0.04
165 328 0.88
166 26 0.07
167 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (163 bp):
TTTTAGAAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCAGAAGA
TTGTTCGAGTCTTATACTCCCTAAAAGAATAGGGAGTGAACCCGTTTTAGAAGATTGTTCGAGTT
CTATACTCCCTGAAGAATAGGGAGCGAACCCGT
Found at i:2521364 original size:55 final size:55
Alignment explanation
Indices: 2520751--2521342 Score: 609
Period size: 55 Copynumber: 10.8 Consensus size: 55
2520741 ATCATTTTAT
* * * * * *
2520751 GAAGATTGTTCGAG-TCTTATACTCCTTGAGAGAATAGGGAGC-AGACACGTTTGCT
1 GAAGATTGTTCGAGTTC-TATACTCCCTAAAAGAATAGGGAGCGA-ACCCGTTTTCA
* *
2520806 GAAGATTGTTCGAG-TCTTATACTCCCTGAAAGAATAGGGAGC-AGACACGTTGGTT--
1 GAAGATTGTTCGAGTTC-TATACTCCCTAAAAGAATAGGGAGCGA-ACCCGTT--TTCA
* * *
2520861 GAAGATCGTTCGAG-TCTTATACTCCCTAAAAGAATAGGGATC-AGACACGTTTTCA
1 GAAGATTGTTCGAGTTC-TATACTCCCTAAAAGAATAGGGAGCGA-ACCCGTTTTCA
* *
2520916 GAAGATTGTTCGTGTTCTATACTCCCTGAAAGAATAGGGAGCGAACCCGTTTTCA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAAGAATAGGGAGCGAACCCGTTTTCA
* *
2520971 GAAGATTGTTTGAGTTCTATACTCCCTAAAAGAATAGGGAGTGAACCCGTTTTCA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAAGAATAGGGAGCGAACCCGTTTTCA
* * * * * *
2521026 AAAGATTGTTTGAGTTCTATATTCCCT-GAAGCAATAGGGAGCGAACCCATTTTTA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAAG-AATAGGGAGCGAACCCGTTTTCA
* * *
2521081 GAAGATTGTTCAAGTTCTATACTCCCT-GAAGCAATAGGGAGCGAACCCGTTTTTA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAAG-AATAGGGAGCGAACCCGTTTTCA
* * * *
2521136 GAAGATTGTTCGAGTTCTTTACTCCC-AGAAGCAATAGGGAGTGAACCCGTTTTTA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAAG-AATAGGGAGCGAACCCGTTTTCA
* * *
2521191 GAAGATTGTTCGAGTTCTATACTGCCT-GAAGTAATAGGGAGCGAACCCGTTTTTA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAAG-AATAGGGAGCGAACCCGTTTTCA
* * * *
2521246 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTATGTC-
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAAGAATAGGGAGCGAACCCGT-TTTCA
* * * *
2521301 GAATATTTTTCAAG-TCTTATACTCTCTAAAAGAATAGGGAGC
1 GAAGATTGTTCGAGTTC-TATACTCCCTAAAAGAATAGGGAGC
2521343 AGACATGTTT
Statistics
Matches: 481, Mismatches: 44, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
53 2 0.00
54 5 0.01
55 465 0.97
56 8 0.02
57 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (55 bp):
GAAGATTGTTCGAGTTCTATACTCCCTAAAAGAATAGGGAGCGAACCCGTTTTCA
Found at i:2532443 original size:42 final size:44
Alignment explanation
Indices: 2532369--2532462 Score: 156
Period size: 42 Copynumber: 2.2 Consensus size: 44
2532359 GTTAGGTTAT
* *
2532369 TCCACTAGTATTGAGTGTTAAATCCACTAGTATTAAGTGTTAAA
1 TCCACTAGCATTAAGTGTTAAATCCACTAGTATTAAGTGTTAAA
2532413 TCCACTAGCATTAAGTG-T-AATCCACTAGTATTAAGTGTTAAA
1 TCCACTAGCATTAAGTGTTAAATCCACTAGTATTAAGTGTTAAA
2532455 TCCACTAG
1 TCCACTAG
2532463 TATTGAATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 32 0.67
43 1 0.02
44 15 0.31
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (44 bp):
TCCACTAGCATTAAGTGTTAAATCCACTAGTATTAAGTGTTAAA
Found at i:2532475 original size:22 final size:22
Alignment explanation
Indices: 2532369--2532466 Score: 164
Period size: 22 Copynumber: 4.5 Consensus size: 22
2532359 GTTAGGTTAT
*
2532369 TCCACTAGTATTGAGTGTTAAA
1 TCCACTAGTATTAAGTGTTAAA
2532391 TCCACTAGTATTAAGTGTTAAA
1 TCCACTAGTATTAAGTGTTAAA
*
2532413 TCCACTAGCATTAAGTG-T-AA
1 TCCACTAGTATTAAGTGTTAAA
2532433 TCCACTAGTATTAAGTGTTAAA
1 TCCACTAGTATTAAGTGTTAAA
2532455 TCCACTAGTATT
1 TCCACTAGTATT
2532467 GAATATTAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 18 0.25
21 2 0.03
22 51 0.72
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (22 bp):
TCCACTAGTATTAAGTGTTAAA
Found at i:2536942 original size:31 final size:31
Alignment explanation
Indices: 2536907--2536967 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
2536897 TCAAAACCAA
*
2536907 GAAGTTCCTAGTGAGAATGACATATTGAATG
1 GAAGTTCATAGTGAGAATGACATATTGAATG
2536938 GAAGTTCATAGTGAGAATGACATATTGAAT
1 GAAGTTCATAGTGAGAATGACATATTGAAT
2536968 TCACCGAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.30
Consensus pattern (31 bp):
GAAGTTCATAGTGAGAATGACATATTGAATG
Found at i:2537664 original size:22 final size:22
Alignment explanation
Indices: 2537556--2537655 Score: 173
Period size: 22 Copynumber: 4.5 Consensus size: 22
2537546 GTTAGGTTAT
*
2537556 TCCACTAGTATTGAGTGTTAAA
1 TCCACTAGTATTAAGTGTTAAA
2537578 TCCACTAGTATTAAGTGTTAAA
1 TCCACTAGTATTAAGTGTTAAA
* *
2537600 TCCACTAGCATTAAGTGATAAA
1 TCCACTAGTATTAAGTGTTAAA
2537622 TCCACTAGTATTAAGTGTTAAA
1 TCCACTAGTATTAAGTGTTAAA
2537644 TCCACTAGTATT
1 TCCACTAGTATT
2537656 GAATATTAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 73 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (22 bp):
TCCACTAGTATTAAGTGTTAAA
Found at i:2544422 original size:5 final size:5
Alignment explanation
Indices: 2544409--2544443 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
2544399 CAAATTCTCT
*
2544409 AGATA AGATG AGATA AGATA AGATA AGATA AGATA
1 AGATA AGATA AGATA AGATA AGATA AGATA AGATA
2544444 TGATTCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (5 bp):
AGATA
Found at i:2544600 original size:61 final size:61
Alignment explanation
Indices: 2544526--2544649 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
2544516 GGTTCCTCAC
2544526 CTCATTTGTATTTATTATATTCTTTCAGAGTAATACAACTATGCATTTACTCTATTTCTCT
1 CTCATTTGTATTTATTATATTCTTTCAGAGTAATACAACTATGCATTTACTCTATTTCTCT
2544587 CTCATTTGTATTTATTATATTCTTTCAGAGTAATACAACTATGCATTTACTCTATTTCTCT
1 CTCATTTGTATTTATTATATTCTTTCAGAGTAATACAACTATGCATTTACTCTATTTCTCT
2544648 CT
1 CT
2544650 TGTCGCTTGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (61 bp):
CTCATTTGTATTTATTATATTCTTTCAGAGTAATACAACTATGCATTTACTCTATTTCTCT
Found at i:2550033 original size:29 final size:29
Alignment explanation
Indices: 2549988--2550045 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2549978 GTGTTGGTCG
* *
2549988 TAGGTCGTCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
2550017 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
2550046 AAGAGATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:2550098 original size:10 final size:11
Alignment explanation
Indices: 2550085--2550139 Score: 53
Period size: 10 Copynumber: 5.0 Consensus size: 11
2550075 ACACGCTGGG
2550085 CATCCGAG-GC
1 CATCCGAGAGC
2550095 CATCCGACCGAGAC
1 CATCCGA--GAG-C
*
2550109 CATTCGAGAG-
1 CATCCGAGAGC
2550119 CATCCGAG-GC
1 CATCCGAGAGC
2550129 CATCCGAGAGC
1 CATCCGAGAGC
2550140 ATTCGAGGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
9 1 0.03
10 22 0.59
11 2 0.05
12 4 0.11
13 1 0.03
14 7 0.19
ACGTcount: A:0.25, C:0.36, G:0.27, T:0.11
Consensus pattern (11 bp):
CATCCGAGAGC
Found at i:2550131 original size:20 final size:20
Alignment explanation
Indices: 2550102--2550155 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
2550092 GGCCATCCGA
* *
2550102 CCGAGACCATTCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
2550122 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
* *
2550142 TCGAGGTCATCCGA
1 CCGAGGCCATCCGA
2550156 CCGAGGCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.31, G:0.28, T:0.15
Consensus pattern (20 bp):
CCGAGGCCATCCGAGAGCAT
Found at i:2550143 original size:30 final size:31
Alignment explanation
Indices: 2550083--2550155 Score: 96
Period size: 34 Copynumber: 2.3 Consensus size: 31
2550073 CAACACGCTG
2550083 GGCATCCGAGGCCATCCGACCGAGACCATTCGA
1 GGCATCCGAGGCCATCCGA-CGAGA-CATTCGA
2550116 GAGCATCCGAGGCCATCCGA-GAG-CATTCGA
1 G-GCATCCGAGGCCATCCGACGAGACATTCGA
2550146 GGTCATCCGA
1 GG-CATCCGA
2550156 CCGAGGCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
29 1 0.03
30 15 0.39
32 3 0.08
33 1 0.03
34 18 0.47
ACGTcount: A:0.25, C:0.33, G:0.29, T:0.14
Consensus pattern (31 bp):
GGCATCCGAGGCCATCCGACGAGACATTCGA
Found at i:2550267 original size:29 final size:28
Alignment explanation
Indices: 2550234--2550317 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 28
2550224 GAGCGAGGGT
2550234 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAG-GCATGGCGACCTACA
*
2550263 AGGTCGCCCGGAGGGTATGGCGACCTACA
1 AGGTCGCCCGGA-GGCATGGCGACCTACA
2550292 AGGTCGCCCGGAGGCATGGCGACCTA
1 AGGTCGCCCGGAGGCATGGCGACCTA
2550318 TGTGTTGGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
28 13 0.25
29 38 0.73
30 1 0.02
ACGTcount: A:0.20, C:0.30, G:0.37, T:0.13
Consensus pattern (28 bp):
AGGTCGCCCGGAGGCATGGCGACCTACA
Found at i:2550421 original size:29 final size:29
Alignment explanation
Indices: 2550376--2550461 Score: 154
Period size: 29 Copynumber: 3.0 Consensus size: 29
2550366 GAGCAAGGGT
2550376 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
* *
2550405 AGGTCGCCCGGAATGCATGGCAACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
2550434 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
2550462 GACCAACACT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.22, C:0.31, G:0.33, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:2554435 original size:60 final size:60
Alignment explanation
Indices: 2554310--2554436 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 60
2554300 TTGGAACATG
* * * *
2554310 TCATTTTATAATTTTTAATAGTCATGGGACTCAATAAAATAGTGACCTATAATTGAGGAA
1 TCATTTTATAATTTTTAATAGTCATGGGACTAAACAAAATAGCGACCTATAATAGAGGAA
* * * *
2554370 CCATTTTAT-ATATTTTAATAGTTA-GGTGACTAAACAAAATAGCGTCCTATAGTCAGAGG-A
1 TCATTTTATAAT-TTTTAATAGTCATGG-GACTAAACAAAATAGCGACCTATAAT-AGAGGAA
2554430 TCATTTT
1 TCATTTT
2554437 GTACTTTACC
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
59 4 0.07
60 47 0.85
61 4 0.07
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (60 bp):
TCATTTTATAATTTTTAATAGTCATGGGACTAAACAAAATAGCGACCTATAATAGAGGAA
Found at i:2576853 original size:2 final size:2
Alignment explanation
Indices: 2576840--2576895 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
2576830 TAACCCATAC
*
2576840 AT AT AC AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2576881 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
2576896 GATGGGCATG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2592835 original size:36 final size:37
Alignment explanation
Indices: 2592752--2593068 Score: 186
Period size: 37 Copynumber: 8.4 Consensus size: 37
2592742 TTGAAAATAC
* *
2592752 ATATATAG--TTTAAAACATTTTTGAAAATATGTATA
1 ATATATAGTTTTTAAAACATTTTTAAAAATATATATA
* *
2592787 TTATATAGTTTTTAAAATATTTTTAAAAAT-TATATA
1 ATATATAGTTTTTAAAACATTTTTAAAAATATATATA
*
2592823 ATATATAGTTTTTGAAAACGTTTTT-AAAATATATATA
1 ATATATAGTTTTT-AAAACATTTTTAAAAATATATATA
* * * * * *
2592860 ATATATACTTTTGAAAACGTTATGAAAACATTTATATA
1 ATATATAGTTTTTAAAACATTTTTAAAA-ATATATATA
* *
2592898 ATATATAATTTTTAAAAACCATTTTGAAAATATATTTTGAAAATTATATA
1 ATATATAGTTTTT-AAAA-CATTTT-TAAA-A-A---T----A-TATATA
*
2592948 ATATATAGTTTTTGAAAAC-GTTTT--AAA-ATATATA
1 ATATATAGTTTTT-AAAACATTTTTAAAAATATATATA
* * * * * *
2592982 ATATATA-CTTTTGAAACGTTATGAAAACATTTATATA
1 ATATATAGTTTTTAAAACATTTTTAAAA-ATATATATA
* * * *
2593019 ATATATAATTTTAAAAACCA-TTTTGAAAATACATATA
1 ATATATAGTTTTTAAAA-CATTTTTAAAAATATATATA
2593056 ATATATAGTTTTT
1 ATATATAGTTTTT
2593069 TTTTTAAAAA
Statistics
Matches: 217, Mismatches: 40, Indels: 48
0.71 0.13 0.16
Matches are distributed among these distances:
32 4 0.02
33 6 0.03
34 13 0.06
35 10 0.05
36 32 0.15
37 78 0.36
38 30 0.14
39 5 0.02
40 4 0.02
41 3 0.01
42 2 0.01
43 1 0.00
44 1 0.00
45 2 0.01
48 3 0.01
49 1 0.00
50 22 0.10
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
ATATATAGTTTTTAAAACATTTTTAAAAATATATATA
Found at i:2592978 original size:25 final size:25
Alignment explanation
Indices: 2592882--2592980 Score: 73
Period size: 25 Copynumber: 3.9 Consensus size: 25
2592872 GAAAACGTTA
2592882 TGAAAACATTTATATAATATATAATTTT
1 TGAAAACATTTATA-AA-ATAT-ATTTT
*
2592910 TAAAAACCATTT-TGAAAATATA-TTT
1 TGAAAA-CATTTAT-AAAATATATTTT
*
2592935 TG-AAA-ATTATATAATATATAGTTTT
1 TGAAAACATT-TATAAAATATA-TTTT
*
2592960 TGAAAACGTTT-TAAAATATAT
1 TGAAAACATTTATAAAATATAT
2592981 AATATATACT
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
22 3 0.05
23 8 0.14
24 5 0.09
25 17 0.29
26 5 0.09
27 6 0.10
28 8 0.14
29 6 0.10
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (25 bp):
TGAAAACATTTATAAAATATATTTT
Found at i:2593086 original size:120 final size:119
Alignment explanation
Indices: 2592812--2593052 Score: 394
Period size: 121 Copynumber: 2.0 Consensus size: 119
2592802 AATATTTTTA
*
2592812 AAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTTTGAAAA
1 AAAATTATATAATATATAGTTTTTAAAAACG-TTTT-AAA-ATATATAATATATACTTTTG-AAA
*
2592877 CGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATATTTTG
62 CGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATACA--TTG
*
2592937 AAAATTATATAATATATAGTTTTTGAAAACGTTTTAAAATATATAATATATACTTTTGAAACGTT
1 AAAATTATATAATATATAGTTTTTAAAAACGTTTTAAAATATATAATATATACTTTTGAAACGTT
2593002 ATGAAAACATTTATATAATATATAA-TTTTAAAAACCATTTTGAAAATACAT
66 ATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATACAT
2593053 ATAATATATA
Statistics
Matches: 115, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
118 1 0.01
120 24 0.21
121 32 0.28
122 20 0.17
123 3 0.03
124 4 0.03
125 31 0.27
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (119 bp):
AAAATTATATAATATATAGTTTTTAAAAACGTTTTAAAATATATAATATATACTTTTGAAACGTT
ATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATACATTG
Found at i:2593120 original size:25 final size:26
Alignment explanation
Indices: 2593088--2593137 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
2593078 AAAAAAAACA
2593088 TTTTAAAA-TTTATATAT-TATATGT
1 TTTTAAAAGTTTATATATATATATGT
2593112 TTTTGAAAATGTTTATATATATATAT
1 TTTT-AAAA-GTTTATATATATATAT
2593138 TATTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.18
25 4 0.18
27 9 0.41
28 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (26 bp):
TTTTAAAAGTTTATATATATATATGT
Found at i:2593156 original size:16 final size:17
Alignment explanation
Indices: 2593137--2593169 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2593127 TATATATATA
2593137 TTATTATT-ATTTATTT
1 TTATTATTAATTTATTT
*
2593153 TTATTTTTAATTTATTT
1 TTATTATTAATTTATTT
2593170 ATTTCTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTATTAATTTATTT
Found at i:2596182 original size:18 final size:18
Alignment explanation
Indices: 2596159--2596201 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
2596149 TTAGACATTT
2596159 TGCATTTCTTATTTTCTG
1 TGCATTTCTTATTTTCTG
* *
2596177 TGCATTTTGTTATTTTCTT
1 TGCA-TTTCTTATTTTCTG
2596196 TGCATT
1 TGCATT
2596202 CACATTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.12, C:0.14, G:0.12, T:0.63
Consensus pattern (18 bp):
TGCATTTCTTATTTTCTG
Found at i:2599705 original size:85 final size:84
Alignment explanation
Indices: 2599569--2600385 Score: 994
Period size: 85 Copynumber: 9.8 Consensus size: 84
2599559 CCAAGACCTT
* *
2599569 CGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
1 CGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
2599634 TCTGTGACCAAAAGACCCC
66 TCTGTGACCAAAAGACCCC
* * *
2599653 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
1 CGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
2599718 ATCTGTGACCAAAAGACCCC
65 ATCTGTGACCAAAAGACCCC
* * *
2599738 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
1 CGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
**
2599803 ATCTGTGACC--AAGACCTT
65 ATCTGTGACCAAAAGACCCC
* * * * * * * *
2599821 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTA
1 CGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
2599886 TC--TG-CCAAAAGACCCC
66 TCTGTGACCAAAAGACCCC
* * * * * * * *
2599902 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTA
1 CGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
2599967 TC--TG-CC-AAAGACCCC
66 TCTGTGACCAAAAGACCCC
* * *
2599982 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
1 CGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
*
2600047 ATCTATGACCAAAAGACCCC
65 ATCTGTGACCAAAAGACCCC
* * *
2600067 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
1 CGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
**
2600132 ATCTGTGACCAAAAGACCTT
65 ATCTGTGACCAAAAGACCCC
* * * * * * * *
2600152 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGCGCTA
1 CGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
2600217 TC--TG-CC-AAAGACCCC
66 TCTGTGACCAAAAGACCCC
* * *
2600232 CGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
1 CGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
**
2600297 ATCTGTGACCAAAAGACCTT
65 ATCTGTGACCAAAAGACCCC
* * * * * * * *
2600317 CGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA
1 CGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
2600382 TCTG
66 TCTG
2600386 CTAAAGACCT
Statistics
Matches: 649, Mismatches: 71, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
79 2 0.00
80 54 0.08
81 155 0.24
82 40 0.06
83 28 0.04
84 101 0.16
85 269 0.41
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (84 bp):
CGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
TCTGTGACCAAAAGACCCC
Found at i:2600074 original size:165 final size:166
Alignment explanation
Indices: 2599520--2600408 Score: 1102
Period size: 165 Copynumber: 5.4 Consensus size: 166
2599510 TAAACAAACT
* * * * * * ** * *
2599520 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTA-CCTGCCACCAAGACCTTCGAGTTCGACTACGC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTTGCCA-AAAGACCCCCGAGTTCGATTACAC
* * *
2599584 TCAGC-TCCAAGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAG
65 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC-GTGACCAAAAG
** * * * *
2599648 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
129 ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATC
* * * * * *
2599687 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT-TG-CCAAAAGACCCCCGAGTTCGATTACA
2599752 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC--AA
64 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC-GTGACCAAAA
2599815 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
128 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * *
2599854 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATC-TGCCAAAAGACCCCCGAGTTCGACTACGCT
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTTGCCAAAAGACCCCCGAGTTCGATTACACT
* * * * * * * * *
2599918 CAGC-TCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATC-TG-CC-AAAGAC
66 CAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCGTGACCAAAAGAC
** * * * *
2599979 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
131 CTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATC
* * * * * *
2600016 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT-TG-CCAAAAGACCCCCGAGTTCGATTACA
2600081 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAA
64 CTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC-GTGACCAAAA
2600146 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
128 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
2600185 ATTTGCAGCATAGCTTAAGTCGAGAAGCGCTATC-TGCC-AAAGACCCCCGAGTTCGATTACACT
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTTGCCAAAAGACCCCCGAGTTCGATTACACT
2600248 CAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGA
66 CAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC-GTGACCAAAAGA
*
2600313 CCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATC
130 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* **
2600350 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC-TG-CTAAAGACCTTCGAGTTCGATTA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTTGCCAAAAGACCCCCGAGTTCGATTA
2600409 TATTCAACTT
Statistics
Matches: 628, Mismatches: 79, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
160 2 0.00
161 26 0.04
162 38 0.06
163 38 0.06
164 33 0.05
165 212 0.34
166 40 0.06
167 67 0.11
168 27 0.04
169 66 0.11
170 79 0.13
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (166 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTTGCCAAAAGACCCCCGAGTTCGATTACACT
CAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCGTGACCAAAAGAC
CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:2600228 original size:250 final size:246
Alignment explanation
Indices: 2599561--2600405 Score: 1210
Period size: 250 Copynumber: 3.4 Consensus size: 246
2599551 ACCTGCCACC
* *
2599561 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAGGCTAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCGAG
* * * * *
2599626 AAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
66 AAGGGCTATC--TG-CCAAAAGACCCCCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTT
* * * * * *
2599691 ACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCCCGAGTTCGATTACACTCA
127 GCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCCCGAGTTCGATTACACTCA
2599756 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC--
188 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
* * * * *
2599813 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCGAG
2599878 AAGGGCTATCTGCCAAAAGACCCCCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
66 AAGGGCTATCTGCCAAAAGACCCCCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
*
2599943 AATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAG
131 CATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAG
*
2600008 GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATGACCAA
196 GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
** * * * * *
2600059 AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCGA
* **
2600124 GAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
65 GAAGGGCTATC--TG-CCAAAAGACCCCCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
*
2600189 GCAGCATAGCTTAAGTCGAGAAGCGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTT
127 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTT
2600254 CGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
192 CGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
* * * * *
2600309 AAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCGAG
* **
2600374 AAGGGCTATCTG-CTAAAGACCTTCGAGTTCGA
66 AAGGGCTATCTGCCAAAAGACCCCCGAGTTCGA
2600406 TTATATTCAA
Statistics
Matches: 535, Mismatches: 52, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
244 83 0.16
245 21 0.04
246 26 0.05
247 40 0.07
248 38 0.07
249 71 0.13
250 189 0.35
252 67 0.13
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (246 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCGAG
AAGGGCTATCTGCCAAAAGACCCCCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
CATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAG
GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAA
Found at i:2600499 original size:84 final size:84
Alignment explanation
Indices: 2600372--2600575 Score: 360
Period size: 84 Copynumber: 2.5 Consensus size: 84
2600362 GCTTAAGTCG
* *
2600372 AGAAGGGCTATCTG-CTAA-AGACCT-TCGAGTTCGATTATATTCAACTTAGAGGCAAATCAAGC
1 AGAAGGGCTATCTGTC-AACAAAACTGTCGAGTTCGATTATATTCAACTTAGAGGCAAATCAAGC
2600434 TTACAGAATAGCTCAATGCA
65 TTACAGAATAGCTCAATGCA
2600454 AGAAGGGCTATCTGTCAACAAAACTGTCGAGTTCGATTATATTCAACTTAGAGGCAAATCAAGCT
1 AGAAGGGCTATCTGTCAACAAAACTGTCGAGTTCGATTATATTCAACTTAGAGGCAAATCAAGCT
2600519 TACAGAATAGCTCAATGCA
66 TACAGAATAGCTCAATGCA
2600538 AGAAGGGCTATCTGTCAACAAAACTGTCGAGTTCGATT
1 AGAAGGGCTATCTGTCAACAAAACTGTCGAGTTCGATT
2600576 CTAATCAGAA
Statistics
Matches: 117, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
82 16 0.14
83 5 0.04
84 96 0.82
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (84 bp):
AGAAGGGCTATCTGTCAACAAAACTGTCGAGTTCGATTATATTCAACTTAGAGGCAAATCAAGCT
TACAGAATAGCTCAATGCA
Found at i:2601183 original size:36 final size:37
Alignment explanation
Indices: 2601100--2601280 Score: 174
Period size: 37 Copynumber: 4.9 Consensus size: 37
2601090 TTGAAAATAC
* *
2601100 ATATATAG--TTTAAAACATTTTTGAAAATATGTATA
1 ATATATAGTTTTTAAAACATTTTTAAAAATATATATA
* *
2601135 TTATATAGTTTTTAAAATATTTTTAAAAAT-TATATA
1 ATATATAGTTTTTAAAACATTTTTAAAAATATATATA
*
2601171 ATATATAGTTTTTGAAAACGTTTTT-AAAATATATATA
1 ATATATAGTTTTT-AAAACATTTTTAAAAATATATATA
* * * * * *
2601208 ATATATACTTTTGAAAACGTTATGAAAACATTTATATA
1 ATATATAGTTTTTAAAACATTTTTAAAA-ATATATATA
* *
2601246 ATATATAATTTTTAAAAACCA-TTTTGAAAATATAT
1 ATATATAGTTTTT-AAAA-CATTTTTAAAAATATAT
2601281 TTTTGAAAAT
Statistics
Matches: 119, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
35 7 0.06
36 31 0.26
37 47 0.39
38 24 0.20
39 9 0.08
40 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATATAGTTTTTAAAACATTTTTAAAAATATATATA
Found at i:2601262 original size:27 final size:27
Alignment explanation
Indices: 2601232--2601330 Score: 82
Period size: 27 Copynumber: 3.7 Consensus size: 27
2601222 AAACGTTATG
2601232 AAAACATTTATATAATATATAATTTTTA
1 AAAACATTT-TATAATATATAATTTTTA
2601260 AAAACCATTTTGA-AA-ATAT-ATTTTT-
1 AAAA-CATTTT-ATAATATATAATTTTTA
* * * *
2601285 GAAA-ATTATATAATATATAGTTTTTG
1 AAAACATTTTATAATATATAATTTTTA
* *
2601311 AAAACGTTTTAAAATATATA
1 AAAACATTTTATAATATATA
2601331 TAATATATAC
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
22 1 0.02
23 6 0.11
24 4 0.07
25 8 0.14
26 9 0.16
27 16 0.28
28 7 0.12
29 6 0.11
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (27 bp):
AAAACATTTTATAATATATAATTTTTA
Found at i:2601286 original size:14 final size:15
Alignment explanation
Indices: 2601267--2601295 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2601257 TTAAAAACCA
2601267 TTTTGAAAA-TATAT
1 TTTTGAAAATTATAT
2601281 TTTTGAAAATTATAT
1 TTTTGAAAATTATAT
2601296 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (15 bp):
TTTTGAAAATTATAT
Found at i:2601313 original size:25 final size:24
Alignment explanation
Indices: 2601239--2601314 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 24
2601229 ATGAAAACAT
*
2601239 TTATATAATATATAATTTTTAAAAA
1 TTATATAATATAT-ATTTTTGAAAA
** * *
2601264 CCATTTTGAAAATATATTTTTGAAAA
1 TTA-TAT-AATATATATTTTTGAAAA
2601290 TTATATAATATATAGTTTTTGAAAA
1 TTATATAATATATA-TTTTTGAAAA
2601315 CGTTTTAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
24 7 0.18
25 13 0.33
26 13 0.33
27 6 0.15
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (24 bp):
TTATATAATATATATTTTTGAAAA
Found at i:2601335 original size:36 final size:37
Alignment explanation
Indices: 2601281--2601421 Score: 171
Period size: 38 Copynumber: 3.8 Consensus size: 37
2601271 GAAAATATAT
2601281 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
*
2601317 TTTT-AAAATATATATAATATATA-CTTTTGAAAACG
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
* * * * *
2601352 TTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAA-CG
*
2601392 TTTTGAAAATACATATAATATATAGTTTTT
1 TTTTGAAAATATATATAATATATAGTTTTT
2601422 TTTTTTTAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
35 19 0.21
36 17 0.19
37 3 0.03
38 34 0.38
39 11 0.12
40 5 0.06
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACG
Found at i:2601359 original size:125 final size:126
Alignment explanation
Indices: 2601151--2601402 Score: 488
Period size: 125 Copynumber: 2.0 Consensus size: 126
2601141 AGTTTTTAAA
2601151 ATATTTTTAAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATAC
1 ATATTTTTAAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATAC
2601216 TTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAAT
66 TTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAAT
*
2601277 ATATTTTTGAAAATTATATAATATATAGTTTTTGAAAACG-TTTTAAAATATATATAATATATAC
1 ATATTTTTAAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATAC
2601341 TTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAAT
66 TTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAAT
2601402 A
1 A
2601403 CATATAATAT
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
125 86 0.69
126 39 0.31
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (126 bp):
ATATTTTTAAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATAC
TTTTGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAAT
Found at i:2601509 original size:16 final size:17
Alignment explanation
Indices: 2601490--2601522 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2601480 TATATATATA
2601490 TTATTATT-ATTTATTT
1 TTATTATTAATTTATTT
*
2601506 TTATTTTTAATTTATTT
1 TTATTATTAATTTATTT
2601523 ATTTCTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTATTAATTTATTT
Found at i:2608499 original size:66 final size:65
Alignment explanation
Indices: 2608392--2608555 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 65
2608382 TTTGTTGAAG
* * *
2608392 GTGCATCGATGCACATGGAGTGTATCGATGCA-CTCATTTAAAATAAATGAACATCGAAT-GTCA
1 GTGCATCGATGCATAAGGAGTGCATCGATGCACCTCA-TTAAAATAAA--AACATCGAATAG-CA
2608455 -TTA
62 TTTA
* *
2608458 GTGCATCGATGCATAAGGAGTGCATCGATGCACCTGC-TTAAAATACAAACATCGAATAGGATTT
1 GTGCATCGATGCATAAGGAGTGCATCGATGCACCT-CATTAAAATAAAAACATCGAATAGCATTT
2608522 A
65 A
* *
2608523 -TGCACCGATGCAT-GGGTAGTGCATCGATGCACC
1 GTGCATCGATGCATAAGG-AGTGCATCGATGCACC
2608556 CGTCAAGGGA
Statistics
Matches: 86, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
63 2 0.02
64 39 0.45
65 4 0.05
66 38 0.44
67 2 0.02
68 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (65 bp):
GTGCATCGATGCATAAGGAGTGCATCGATGCACCTCATTAAAATAAAAACATCGAATAGCATTTA
Found at i:2609690 original size:21 final size:21
Alignment explanation
Indices: 2609664--2609708 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2609654 GATTTCTGGG
* *
2609664 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2609685 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2609706 CAA
1 CAA
2609709 ACGACAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2610312 original size:18 final size:18
Alignment explanation
Indices: 2610289--2610323 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2610279 CTAGGAGATT
2610289 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
2610307 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
2610324 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:2610409 original size:21 final size:22
Alignment explanation
Indices: 2610380--2610423 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2610370 GTTGTATGAT
2610380 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
2610401 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
2610423 A
1 A
2610424 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Done.