Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009633.1 Hibiscus syriacus cultivar Beakdansim tig00117032_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: 2608659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:194347 original size:877 final size:878
Alignment explanation
Indices: 192636--195217 Score: 4400
Period size: 877 Copynumber: 2.9 Consensus size: 878
192626 GAGCAGAGGT
*
192636 AAAAA-AGAGATTAGGATTGAAAAACTGAAGAACCAGTAAGCTTCAACTTCCATAAGGGAAAAAA
1 AAAAAGAGAGATTAGGATTG-AAAACTGAAGAACCAGTAAGCTTCAACTTCCATAAGGGAAGAAA
*
192700 GTTAAGAAGAAGAGAGAGGAAATGAACCTTGGATTGCTTGGCGACCTTTCTTAGTTGCGCATAGA
65 GTTAAGAAGAAGAGAGAGGAAATGAACCTTGGATTGCTTGGCGACCTTTCTTAGATGCGCATAGA
192765 CGACATGACGACCTGCATAGGTTGCCCGGAGTACCTGGCGACCAACTCTATTACTGTAGAAATCA
130 CGACATGACGACCTGCATAGGTTGCCCGGAGTACCTGGCGACCAACTCTATTACTGTAGAAATCA
* *
192830 CGCAATTTCAGCAAATAATTGATCAAATGCAATAAATGAAGAATTTTTTTTCTCAAATCATTATG
195 CGCTATTTCAGCAAATAATTGATCAAATGCAATAAATGAAGAATTTTTTTCCTCAAATCATTATG
*
192895 TGGGCAAAATGGCCGAAATAGGCAAAATTTCTTTAAATAATATAGTGTTTAACTATCAATAACAA
260 TGGGCAAAATGGCCGAAATAGGCAAAATTTCTTTAAATAATATAGTGTTTGACTATCAATAACAA
* * * *
192960 TAAAACACTATTCCCATATACAATGGGGTAAGGGGGAGATAAGGTAGTAGGTTGCCTCCAACGCC
325 TGAAACACTATTCCCATATACAATGGGGTAAGGGGGAGATAGGGTAGTAGGCTGCCCCCAACGCC
* *
193025 AGGTTGAGAGAAGCTTTCGTGGAAGAACTCCGGCAGTCATAAAAATTACAAATAAAAATAAAATG
390 AGGTTGAGAGCAGCTTTCGTGGAAGACCTCCGGCAGTCATAAAAATTACAAATAAAAATAAAATG
* *
193090 CAATGCATGTATAAATAAATATATAGTTGACCCTTTTTTTAATAAGTAGTCTTCTTATGCGCGTC
455 CAATGCATGTATAAATAAATACATAGTTGACCCTTTTTTTAATAAGCAGTCTTCTTATGCGCGTC
* *
193155 TGTAATGAGAAGTAATCCCTGTAAATAAATCCTTGCATAAAAATTTCTGCAATATTGACAGAAAC
520 TGTAATGAGAAGTAATCCC--------AA--C-TGCATAAAAATTTCTGTAATATAGACAGAAAC
193220 GTAAGATCCGACTAAATTTAAAAAGAGGAAACATGAAGAGAATGATACACAGAAGTCAACGATAG
574 GTAAGATCCGACTAAATTTAAAAAGAGGAAACATGAAGAGAATGATACACAGAAGTCAACGATAG
* * *
193285 CAAGCTACGAAAAGGAGTAAAGTAAAATGTGTTAAAACCTAAACTAAGACAACACTATTCCGCTA
639 CAAGCTACGAGAAGGAGTAAAGTCAAATGTGTTAAAACCTAAACTAAGGCAACACTATTCCGCTA
193350 CCCTAGATCTAAGCCTTCATAAATTCCACTGACATAAACGTGAAGAAAGTAGAAGTCAGTGAAAT
704 CCCTAGATCTAAGCCTTCATAAATTCCACTGACATAAACGTGAAGAAAGTAGAAGTCAGTGAAAT
193415 TACTACAAATGCATTAAAAAGAAGACATAGATGTTATGTACCAATCGCAAAGATTATGAAATTAT
769 TACTACAAATGCATTAAAAAGAAGACATAGATGTTATGTACCAATCGCAAAGATTATGAAATTAT
* *
193480 TTTGCTCCATAGCTTCGGCTTGACTAGTGAACGAAACAACAGATA
834 TTTGCACCATAGCTTCGGCTTGACTAGTGAACGAAACAACAAATA
*
193525 AAAAAGAGAGATTAGGATTAGAAAACTGAAGAACCAGTAAGCTTCAACTTCCATACGGGAAGAAA
1 AAAAAGAGAGATTAGGATT-GAAAACTGAAGAACCAGTAAGCTTCAACTTCCATAAGGGAAGAAA
*
193590 GTTAAGAAGAAGAGAGAGGAAATAAACCTTGGATTGCTTGGCGACCTTTCTTAGATGCGCATAGA
65 GTTAAGAAGAAGAGAGAGGAAATGAACCTTGGATTGCTTGGCGACCTTTCTTAGATGCGCATAGA
* *
193655 CGACATGACGACCTACATAGGTTGCCTGGAGTACCTGGCGACCAACTCTATTACTGTAGAAATCA
130 CGACATGACGACCTGCATAGGTTGCCCGGAGTACCTGGCGACCAACTCTATTACTGTAGAAATCA
* *
193720 CGTTATTTCAGCAAATAATTGATCAAATGCAATAAATGAAGAATTATTTTCCCTCAAATCATTAT
195 CGCTATTTCAGCAAATAATTGATCAAATGCAATAAATGAAGAATT-TTTTTCCTCAAATCATTAT
* *
193785 GTGGGCAAAATGGCCGAAATAGGCCAAATTTCTTTAAATAATATAGTGTTTGACTATCAACAACA
259 GTGGGCAAAATGGCCGAAATAGGCAAAATTTCTTTAAATAATATAGTGTTTGACTATCAATAACA
*
193850 ATGAAACACTATTCTCATATACAATGGGGTAAGGGGGAGATAGGGTAGTAGGCTGCCCCCAACGC
324 ATGAAACACTATTCCCATATACAATGGGGTAAGGGGGAGATAGGGTAGTAGGCTGCCCCCAACGC
* * *
193915 CAGGTTGAAAGCAGCTTCCGTGGAAGACCTCCGACAGTCATAAAAATTACAAATAAAAATAAAAT
389 CAGGTTGAGAGCAGCTTTCGTGGAAGACCTCCGGCAGTCATAAAAATTACAAATAAAAATAAAAT
* *
193980 GCAATGTATGTATAAATAAATACATAGTTGACCTTTTTTTTAATAAGCAGTCTTCTTATGCGCGT
454 GCAATGCATGTATAAATAAATACATAGTTGACCCTTTTTTTAATAAGCAGTCTTCTTATGCGCGT
*
194045 CTGTAATGAGAAGTAAT-CC-A-TGCATAAAAATCTCTGTAATATAGACAGAAACGTAAGATCCG
519 CTGTAATGAGAAGTAATCCCAACTGCATAAAAATTTCTGTAATATAGACAGAAACGTAAGATCCG
194107 ACTAAATTTAAAAAGAGGAAACATGAAGAGAATGATACACAGAAGTCAACGATAGCAAGCTACGA
584 ACTAAATTTAAAAAGAGGAAACATGAAGAGAATGATACACAGAAGTCAACGATAGCAAGCTACGA
*
194172 GAAGGAGTAAAGTCAAATGTGTTAAAACCTAAACTAAGGCAACACTATTCTGCTACCCTAGATCT
649 GAAGGAGTAAAGTCAAATGTGTTAAAACCTAAACTAAGGCAACACTATTCCGCTACCCTAGATCT
*
194237 AAGCCTTCATAAATTCCACTGACATAAACGTGAAGAAAATAGAAGTCAGTGAAATTACTACAAAT
714 AAGCCTTCATAAATTCCACTGACATAAACGTGAAGAAAGTAGAAGTCAGTGAAATTACTACAAAT
*
194302 GCATTAAAAAGAAGACATAGATGTTATGTACCAATCGCAAAGATTATGAAATTGTTTTGCACCAT
779 GCATTAAAAAGAAGACATAGATGTTATGTACCAATCGCAAAGATTATGAAATTATTTTGCACCAT
194367 AGCTTCGGCTTGACTAGTGAACGAAACAACAAATA
844 AGCTTCGGCTTGACTAGTGAACGAAACAACAAATA
*
194402 AAAAAGAGAGATTAGGATTGGAAAACTAAAGAACCAGTAAGCTTCAACTTCCATAAGGGAAGAAA
1 AAAAAGAGAGATTAGGATT-GAAAACTGAAGAACCAGTAAGCTTCAACTTCCATAAGGGAAGAAA
*
194467 GTTAAGAAGAAGAGAGAGGAAATGAACCTTGGATTGCTTAGCGACCTTTCTTAGATGCGCATAGA
65 GTTAAGAAGAAGAGAGAGGAAATGAACCTTGGATTGCTTGGCGACCTTTCTTAGATGCGCATAGA
* *
194532 CGACATGACGACCTGCATAGGTCGCCCGGAGTACCTGGCGACCAACTCTATTACTATAGAAATCA
130 CGACATGACGACCTGCATAGGTTGCCCGGAGTACCTGGCGACCAACTCTATTACTGTAGAAATCA
*
194597 CGCTATTTCAGCAAATAATTGATCAAATGCAATAAATGAAGAATTTTTTTGCTCAAATCATTATG
195 CGCTATTTCAGCAAATAATTGATCAAATGCAATAAATGAAGAATTTTTTTCCTCAAATCATTATG
* *
194662 TGGGCAAAAT-GACGAAATAGGTAAAATTTCTTTAAATAATATAGTGTTTGACTATCAATAACAA
260 TGGGCAAAATGGCCGAAATAGGCAAAATTTCTTTAAATAATATAGTGTTTGACTATCAATAACAA
* * * *
194726 TGAAACCCTATTCCCATATACAATGGGGTATGAGGGAGATAGGGTAGTAGGCTGCCCCTAACGCC
325 TGAAACACTATTCCCATATACAATGGGGTAAGGGGGAGATAGGGTAGTAGGCTGCCCCCAACGCC
194791 AGGTTGAGAGCAGCTTTCGTGGAAGACCTCCGGCAGTCATAAAAATTACAAATAAAAATAAAATG
390 AGGTTGAGAGCAGCTTTCGTGGAAGACCTCCGGCAGTCATAAAAATTACAAATAAAAATAAAATG
* *
194856 CAATGCATGTATAAATAAATACATAGTTGACCCTTTTTTTAATAAACATTCTTCTTATGCGCGTC
455 CAATGCATGTATAAATAAATACATAGTTGACCCTTTTTTTAATAAGCAGTCTTCTTATGCGCGTC
194921 TGTAATGAGAAGTAATCCCTGCAAATAAATCCCTGCATAAAAATTTCTGTAATATAGACAGAAAC
520 TGTAATGAGAAGTAAT-CC--C-----AA---CTGCATAAAAATTTCTGTAATATAGACAGAAAC
*
194986 GTAAGAACCGACTAAATTTAAAAAGAGGAAACATGAAGAGAATGATACACAGAAGTCAACGATAG
574 GTAAGATCCGACTAAATTTAAAAAGAGGAAACATGAAGAGAATGATACACAGAAGTCAACGATAG
*
195051 CAAGCTACGAGAAGGAGTAAAGTCAAATGTGTTAAAACCTAAACTAAGGCAACATTATTCCGCTA
639 CAAGCTACGAGAAGGAGTAAAGTCAAATGTGTTAAAACCTAAACTAAGGCAACACTATTCCGCTA
*
195116 CCCTAAATCTAAGCCTTCATAAATTCCACTGACATAAACGTGAAGAAAGTAGAAGTCAGTGAAAT
704 CCCTAGATCTAAGCCTTCATAAATTCCACTGACATAAACGTGAAGAAAGTAGAAGTCAGTGAAAT
*
195181 TACTACAAATGTATTAAAAAGAAGACATAGATGTTAT
769 TACTACAAATGCATTAAAAAGAAGACATAGATGTTAT
195218 AACTTATGAC
Statistics
Matches: 1603, Mismatches: 73, Indels: 34
0.94 0.04 0.02
Matches are distributed among these distances:
875 249 0.16
876 28 0.02
877 557 0.35
879 1 0.00
881 1 0.00
885 1 0.00
889 262 0.16
890 226 0.14
891 278 0.17
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (878 bp):
AAAAAGAGAGATTAGGATTGAAAACTGAAGAACCAGTAAGCTTCAACTTCCATAAGGGAAGAAAG
TTAAGAAGAAGAGAGAGGAAATGAACCTTGGATTGCTTGGCGACCTTTCTTAGATGCGCATAGAC
GACATGACGACCTGCATAGGTTGCCCGGAGTACCTGGCGACCAACTCTATTACTGTAGAAATCAC
GCTATTTCAGCAAATAATTGATCAAATGCAATAAATGAAGAATTTTTTTCCTCAAATCATTATGT
GGGCAAAATGGCCGAAATAGGCAAAATTTCTTTAAATAATATAGTGTTTGACTATCAATAACAAT
GAAACACTATTCCCATATACAATGGGGTAAGGGGGAGATAGGGTAGTAGGCTGCCCCCAACGCCA
GGTTGAGAGCAGCTTTCGTGGAAGACCTCCGGCAGTCATAAAAATTACAAATAAAAATAAAATGC
AATGCATGTATAAATAAATACATAGTTGACCCTTTTTTTAATAAGCAGTCTTCTTATGCGCGTCT
GTAATGAGAAGTAATCCCAACTGCATAAAAATTTCTGTAATATAGACAGAAACGTAAGATCCGAC
TAAATTTAAAAAGAGGAAACATGAAGAGAATGATACACAGAAGTCAACGATAGCAAGCTACGAGA
AGGAGTAAAGTCAAATGTGTTAAAACCTAAACTAAGGCAACACTATTCCGCTACCCTAGATCTAA
GCCTTCATAAATTCCACTGACATAAACGTGAAGAAAGTAGAAGTCAGTGAAATTACTACAAATGC
ATTAAAAAGAAGACATAGATGTTATGTACCAATCGCAAAGATTATGAAATTATTTTGCACCATAG
CTTCGGCTTGACTAGTGAACGAAACAACAAATA
Found at i:202346 original size:20 final size:20
Alignment explanation
Indices: 202321--202370 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
202311 GATTGAATAA
202321 GTATCAATACTGATGTGGAG
1 GTATCAATACTGATGTGGAG
202341 GTATCAATACTGATGTGGAG
1 GTATCAATACTGATGTGGAG
*
202361 GTATCGATAC
1 GTATCAATAC
202371 CAAGAGGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (20 bp):
GTATCAATACTGATGTGGAG
Found at i:202888 original size:15 final size:15
Alignment explanation
Indices: 202851--202921 Score: 79
Period size: 15 Copynumber: 4.7 Consensus size: 15
202841 ATTTTATTTG
* *
202851 TATGTGAATATGTTT
1 TATGTGAAAATGTTC
* *
202866 TATATGAAAATATTC
1 TATGTGAAAATGTTC
*
202881 TATGTGAAAATGTGC
1 TATGTGAAAATGTTC
*
202896 TAAGTGAAAATGTTC
1 TATGTGAAAATGTTC
*
202911 TACGTGAAAAT
1 TATGTGAAAAT
202922 ACCTATGTGA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (15 bp):
TATGTGAAAATGTTC
Found at i:203092 original size:25 final size:25
Alignment explanation
Indices: 203051--203102 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
203041 GAGTCGAGGG
*
203051 TTCTACGAGGTCCTTCGGGACATAT
1 TTCTACGAGGTCCTTCGGGACAAAT
*
203076 TTCTACGCA-GTCTTTCGGGACAAAT
1 TTCTACG-AGGTCCTTCGGGACAAAT
203101 TT
1 TT
203103 GTGTGGCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (25 bp):
TTCTACGAGGTCCTTCGGGACAAAT
Found at i:204459 original size:4 final size:4
Alignment explanation
Indices: 204450--204476 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
204440 TGAATAAGAA
204450 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
204477 AGGATCACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:204727 original size:12 final size:12
Alignment explanation
Indices: 204710--204735 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
204700 TATAAATATC
204710 TTAAAACAAGGT
1 TTAAAACAAGGT
204722 TTAAAACAAGGT
1 TTAAAACAAGGT
204734 TT
1 TT
204736 TAATTAGTAT
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (12 bp):
TTAAAACAAGGT
Found at i:213422 original size:49 final size:49
Alignment explanation
Indices: 213329--213422 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
213319 TTATAAGCAA
* *
213329 TTATACATATATTTATAAATATATAAAAATGAGAAAAATTATGTCAATG
1 TTATACATATATATATAAATATATAAAAATGAGAAAAATGATGTCAATG
* * *
213378 TTATATATATATATATATATA-ATATAAATGAGAAAAATGGATGTC
1 TTATACATATATATATAAATATATAAAAATGAGAAAAAT-GATGTC
213423 GTTATCAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 16 0.41
49 23 0.59
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.37
Consensus pattern (49 bp):
TTATACATATATATATAAATATATAAAAATGAGAAAAATGATGTCAATG
Found at i:214945 original size:19 final size:19
Alignment explanation
Indices: 214921--214970 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
214911 AGAAGTTGTA
214921 TTTTTCCACTTAAATTATT
1 TTTTTCCACTTAAATTATT
*
214940 TTTTTCTACTTAAATTATT
1 TTTTTCCACTTAAATTATT
214959 TTGTTTCACACT
1 TT-TTTC-CACT
214971 GATACTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 20 0.74
20 4 0.15
21 3 0.11
ACGTcount: A:0.24, C:0.16, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTCCACTTAAATTATT
Found at i:215775 original size:15 final size:15
Alignment explanation
Indices: 215755--215783 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
215745 AGGAGACCGT
215755 GGTGGAAGAGGTGGC
1 GGTGGAAGAGGTGGC
215770 GGTGGAAGAGGTGG
1 GGTGGAAGAGGTGG
215784 TGGCCGTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.62, T:0.14
Consensus pattern (15 bp):
GGTGGAAGAGGTGGC
Found at i:215785 original size:18 final size:18
Alignment explanation
Indices: 215764--215798 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
215754 TGGTGGAAGA
*
215764 GGTGGCGGTGGAAGAGGT
1 GGTGGCCGTGGAAGAGGT
*
215782 GGTGGCCGTGGAGGAGG
1 GGTGGCCGTGGAAGAGG
215799 CAGAGATGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.09, G:0.63, T:0.14
Consensus pattern (18 bp):
GGTGGCCGTGGAAGAGGT
Found at i:220056 original size:15 final size:15
Alignment explanation
Indices: 220036--220065 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
220026 AGTATGCATT
220036 TTAAGGCATTCTTAA
1 TTAAGGCATTCTTAA
220051 TTAAGGCATTCTTAA
1 TTAAGGCATTCTTAA
220066 CAAAGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
TTAAGGCATTCTTAA
Found at i:224877 original size:2 final size:2
Alignment explanation
Indices: 224870--224930 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
224860 CCCAAAAATA
224870 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
*
224912 AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
224931 CTAAATTATT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:226955 original size:18 final size:17
Alignment explanation
Indices: 226922--226955 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
226912 GAATAATTAA
226922 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
226939 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
226956 AAACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:234829 original size:18 final size:17
Alignment explanation
Indices: 234796--234829 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
234786 GAATAATTAA
234796 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
234813 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
234830 AAACAGACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:241203 original size:25 final size:25
Alignment explanation
Indices: 241169--241227 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
241159 CTAACATTTA
241169 TTTCATTCCAGTTTAGTGTCGAACG
1 TTTCATTCCAGTTTAGTGTCGAACG
*
241194 TTTCATTCCAGTTTAGTGTCTAACG
1 TTTCATTCCAGTTTAGTGTCGAACG
241219 TTTCATTCC
1 TTTCATTCC
241228 GTTACTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (25 bp):
TTTCATTCCAGTTTAGTGTCGAACG
Found at i:247967 original size:14 final size:15
Alignment explanation
Indices: 247940--247969 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
247930 CGGGTATCCG
247940 GATTTTCAGGTACCC
1 GATTTTCAGGTACCC
247955 GATTTTC-GGTACCC
1 GATTTTCAGGTACCC
247969 G
1 G
247970 GAACTTTCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (15 bp):
GATTTTCAGGTACCC
Found at i:249641 original size:37 final size:37
Alignment explanation
Indices: 249592--249675 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 37
249582 TCGGGCCGGG
249592 TATATACATTTAAATTAAATATATAAATATTATATATA
1 TATATA-ATTTAAATTAAATATATAAATATTATATATA
* *
249630 TATATAATTTAAATTAAATTTATTAATATTATATATA
1 TATATAATTTAAATTAAATATATAAATATTATATATA
249667 TATAATAAT
1 TAT-ATAAT
249676 AATTATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 32 0.74
38 11 0.26
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (37 bp):
TATATAATTTAAATTAAATATATAAATATTATATATA
Found at i:253133 original size:9 final size:9
Alignment explanation
Indices: 253121--253155 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
253111 AATAAATATG
253121 AAATTAAAT
1 AAATTAAAT
253130 AAATTAAAT
1 AAATTAAAT
253139 AAATTAAAT
1 AAATTAAAT
253148 AAATTAAA
1 AAATTAAA
253156 CAACACCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAATTAAAT
Found at i:253322 original size:34 final size:35
Alignment explanation
Indices: 253265--253366 Score: 127
Period size: 34 Copynumber: 2.9 Consensus size: 35
253255 ACAGCTATAA
*
253265 TATATATATATATATTATGTATAAACTATATAGTT
1 TATATATATATATATTATATATAAACTATATAGTT
*
253300 TATATTTATAT-TATTATATATAAACTATATAGTT
1 TATATATATATATATTATATATAAACTATATAGTT
* *
253334 T-TAATATAAATATAGTTAGTATATAAATTATAT
1 TAT-ATATATATATA-TTA-TATATAAACTATAT
253367 GAATTATTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
33 1 0.02
34 29 0.50
35 12 0.21
36 3 0.05
37 13 0.22
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (35 bp):
TATATATATATATATTATATATAAACTATATAGTT
Found at i:253440 original size:42 final size:48
Alignment explanation
Indices: 253393--253489 Score: 116
Period size: 49 Copynumber: 2.1 Consensus size: 48
253383 CAACTTATAT
253393 TTATATTATGTA-TAAT-T-A-T-AAA-TTATATATACTATGTATAAA
1 TTATATTATGTATTAATATAACTAAAATTTATATATACTATGTATAAA
* * *
253435 TTATATTGTTTATTAATATAAACTAAAATTTATATATAGTATGTATAAA
1 TTATATTATGTATTAATAT-AACTAAAATTTATATATACTATGTATAAA
253484 TTATAT
1 TTATAT
253490 AGTTTATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
42 10 0.22
43 4 0.09
44 1 0.02
46 1 0.02
47 1 0.02
48 3 0.07
49 25 0.56
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (48 bp):
TTATATTATGTATTAATATAACTAAAATTTATATATACTATGTATAAA
Found at i:253556 original size:7 final size:7
Alignment explanation
Indices: 253546--253583 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
253536 ATAGTTTATA
253546 AAACCCT
1 AAACCCT
253553 AAACCCT
1 AAACCCT
*
253560 AAA-CAT
1 AAACCCT
253566 AAACCCT
1 AAACCCT
*
253573 AAATCCT
1 AAACCCT
253580 AAAC
1 AAAC
253584 TTTATAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:253571 original size:20 final size:20
Alignment explanation
Indices: 253546--253583 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
253536 ATAGTTTATA
253546 AAACCCTAAACCCTAAACAT
1 AAACCCTAAACCCTAAACAT
*
253566 AAACCCTAAATCCTAAAC
1 AAACCCTAAACCCTAAAC
253584 TTTATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (20 bp):
AAACCCTAAACCCTAAACAT
Found at i:253753 original size:16 final size:16
Alignment explanation
Indices: 253695--253755 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 16
253685 TAAACAATAA
*
253695 TATATGTAACCTATAG
1 TATATGTAACTTATAG
253711 TATATGTATACATGTAAATTA-
1 TATATGTA-AC-T-T--A-TAG
253732 TATATGTAACTTATAG
1 TATATGTAACTTATAG
253748 TATATGTA
1 TATATGTA
253756 TGTACAAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
15 2 0.05
16 17 0.46
17 2 0.05
18 1 0.03
19 2 0.05
20 2 0.05
21 9 0.24
22 2 0.05
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (16 bp):
TATATGTAACTTATAG
Found at i:253776 original size:20 final size:21
Alignment explanation
Indices: 253747--253800 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
253737 GTAACTTATA
* *
253747 GTATATGTATGTACAAACTAT
1 GTATATGTATATAAAAACTAT
253768 GTATA-GTATATAAAAACTAT
1 GTATATGTATATAAAAACTAT
* *
253788 ATATATATATATA
1 GTATATGTATATA
253801 TATATATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (21 bp):
GTATATGTATATAAAAACTAT
Found at i:253790 original size:2 final size:2
Alignment explanation
Indices: 253785--253839 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
253775 ATATAAAAAC
253785 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
253826 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
253840 ACCTATTATA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:254032 original size:2 final size:2
Alignment explanation
Indices: 253962--254022 Score: 99
Period size: 2 Copynumber: 31.0 Consensus size: 2
253952 TATGTAAAAC
253962 TA TA TA T- TA TA TA TA -A CTA 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
254003 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
254023 ACCTATATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.04
2 53 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:254043 original size:13 final size:15
Alignment explanation
Indices: 253964--254044 Score: 69
Period size: 16 Copynumber: 5.4 Consensus size: 15
253954 TGTAAAACTA
253964 TATATTATATATAA-C
1 TATA-TATATATAACC
**
253979 TATATATATATATATA
1 TATATATATATA-ACC
**
253995 TATATATATATATATA
1 TATATATATATA-ACC
254011 TATATATATATAACC
1 TATATATATATAACC
*
254026 TATATATGTA-AACC
1 TATATATATATAACC
254040 -ATATA
1 TATATA
254045 AAGTAAATTA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
13 5 0.08
14 12 0.20
15 15 0.25
16 28 0.47
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.44
Consensus pattern (15 bp):
TATATATATATAACC
Found at i:254143 original size:193 final size:184
Alignment explanation
Indices: 253785--254209 Score: 676
Period size: 193 Copynumber: 2.2 Consensus size: 184
253775 ATATAAAAAC
253785 TATATATATA-TATATATATATATATATATATTATATATATATATATATATATATAACCTATTAT
1 TATATATA-ACTATATATATATATATATATA-TATATATATATATATATATATATAACCTATTAT
253849 AAACCATATAAAGTAATATTTATAAACCATGCATAAACAATATTAATCTGTAACCTATAGTATAC
64 AAACCATATAAAGTAATATTTATAAACCATGCATAAACAATATTAATCTGTAACCTATAGTATAC
253914 GTATACATGTAAACTATATATGTAACTTATAGTACATGTATGTA-AAACTATATAT
129 GTATACATGTAAACTATATATGTAACTTATAGTACATGTATGTATAAACTATATAT
253969 TATATATAACTATATATATATATATATATATATATATATATATATATATATATAACCTATATATG
1 TATATATAACTATATATATATATATATATATATATATATATATATATATATATAACCTAT-TA--
254034 TAAACCATATAAAGTAAATTATTTATAAACACCATGCATAAACAATAGTTAATCTATGTAACCTA
63 TAAACCATATAAAGT-AA-TATTTAT-AA-ACCATGCATAAACAATA-TTAATC--TGTAACCTA
*
254099 TAGTATATGTATACATGTAAACTATATATGTAACTTATAGTACATGTATGTATAAACTATATAT
121 TAGTATACGTATACATGTAAACTATATATGTAACTTATAGTACATGTATGTATAAACTATATAT
**
254163 TATATATAAACTATATATATATATA-ACCTATAGTATATATATATATA
1 TATATAT-AACTATATATATATATATATATATA-TATATATATATATA
254210 CAATCTATTT
Statistics
Matches: 224, Mismatches: 3, Indels: 17
0.92 0.01 0.07
Matches are distributed among these distances:
183 31 0.14
184 30 0.13
186 15 0.07
187 2 0.01
188 7 0.03
189 2 0.01
190 17 0.08
191 6 0.03
193 60 0.27
194 23 0.10
195 31 0.14
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (184 bp):
TATATATAACTATATATATATATATATATATATATATATATATATATATATATAACCTATTATAA
ACCATATAAAGTAATATTTATAAACCATGCATAAACAATATTAATCTGTAACCTATAGTATACGT
ATACATGTAAACTATATATGTAACTTATAGTACATGTATGTATAAACTATATAT
Found at i:254162 original size:35 final size:36
Alignment explanation
Indices: 254088--254162 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
254078 ATAGTTAATC
* *
254088 TATGTAACCTATAGTATATGTATACATGTAAACTATA
1 TATGTAACCTATAGTACATGTATA-ATATAAACTATA
* *
254125 TATGTAACTTATAGTACATGTAT-GTATAAACTATA
1 TATGTAACCTATAGTACATGTATAATATAAACTATA
254160 TAT
1 TAT
254163 TATATATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 13 0.38
37 21 0.62
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (36 bp):
TATGTAACCTATAGTACATGTATAATATAAACTATA
Found at i:254172 original size:18 final size:18
Alignment explanation
Indices: 254149--254207 Score: 84
Period size: 18 Copynumber: 3.2 Consensus size: 18
254139 TACATGTATG
254149 TATAAACTATATATTATA
1 TATAAACTATATATTATA
254167 TATAAACTATATA-TATA
1 TATAAACTATATATTATA
*
254184 TATAACCTATAGTATATATA
1 TATAAACTATA-TAT-TATA
254204 TATA
1 TATA
254208 TACAATCTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
17 14 0.38
18 15 0.41
20 8 0.22
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (18 bp):
TATAAACTATATATTATA
Found at i:254753 original size:31 final size:30
Alignment explanation
Indices: 254697--254767 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 30
254687 ACTATACTAT
254697 ATAATTTATAACATATAGTTTATATTAATA
1 ATAATTTATAACATATAGTTTATATTAATA
* *
254727 TTAATTTGATATAC-TATATTTTATATTAATA
1 ATAATTT-ATA-ACATATAGTTTATATTAATA
254758 ATAA-TTATAA
1 ATAATTTATAA
254768 ATTATAAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 1 0.03
29 3 0.08
30 8 0.22
31 22 0.61
32 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (30 bp):
ATAATTTATAACATATAGTTTATATTAATA
Found at i:254833 original size:12 final size:13
Alignment explanation
Indices: 254780--254853 Score: 53
Period size: 13 Copynumber: 5.5 Consensus size: 13
254770 TATAAACTAG
254780 ATTATATTAATATA
1 ATTATATTAA-ATA
* *
254794 AGTTA-ATATAATTT
1 A-TTATAT-TAAATA
254808 ATTATATTAAATA
1 ATTATATTAAATA
*
254821 ATTATA-TATATA
1 ATTATATTAAATA
*
254833 ATTATTTTAACATTA
1 ATTATATTAA-A-TA
254848 ATTATA
1 ATTATA
254854 AATAGTTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
12 10 0.22
13 15 0.33
14 8 0.17
15 13 0.28
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (13 bp):
ATTATATTAAATA
Found at i:254836 original size:25 final size:28
Alignment explanation
Indices: 254780--254853 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 28
254770 TATAAACTAG
* *
254780 ATTATATTAATATAAGTTA-ATATAATTT
1 ATTATATTAACATAA-TTATATATAATTA
254808 ATTATATTAA-ATAATTATATAT-A-TA
1 ATTATATTAACATAATTATATATAATTA
*
254833 ATTATTTTAACATTAATTATA
1 ATTATATTAACA-TAATTATA
254854 AATAGTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 10 0.24
26 5 0.12
27 16 0.39
28 10 0.24
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
ATTATATTAACATAATTATATATAATTA
Found at i:254837 original size:28 final size:28
Alignment explanation
Indices: 254780--254838 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
254770 TATAAACTAG
*
254780 ATTATATTAATATAAGTTAATATAATTT
1 ATTATATTAATATAAGTTAATATAAATT
254808 ATTATATTAA-ATAA-TTATATATATAATT
1 ATTATATTAATATAAGTTA-ATATA-AATT
254836 ATT
1 ATT
254839 TTAACATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 3 0.11
27 9 0.32
28 16 0.57
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
ATTATATTAATATAAGTTAATATAAATT
Found at i:258703 original size:22 final size:22
Alignment explanation
Indices: 258644--258692 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
258634 ATTCCCCTAA
*
258644 GGGGAATCAGTTTCCCTTCAAAG
1 GGGGAATCAGTTCCCCTTC-AAG
258667 GGGGAATCAGTTCCCCTTCAAG
1 GGGGAATCAGTTCCCCTTCAAG
258689 GGGG
1 GGGG
258693 TATCGATTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (22 bp):
GGGGAATCAGTTCCCCTTCAAG
Found at i:262210 original size:22 final size:21
Alignment explanation
Indices: 262168--262207 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
262158 AAGACTATTT
262168 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
262189 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
262208 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:266881 original size:13 final size:13
Alignment explanation
Indices: 266862--266899 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
266852 TAATTTAATG
266862 ATTATAAATAA-A
1 ATTATAAATAAGA
266874 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
266889 ATTATAAATAA
1 ATTATAAATAA
266900 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:266899 original size:18 final size:17
Alignment explanation
Indices: 266878--266969 Score: 76
Period size: 18 Copynumber: 5.0 Consensus size: 17
266868 AATAAAATTT
*
266878 ATAATATAAGAATTATAA
1 ATAATATAAAAATTA-AA
266896 ATAATATAAAGAATTGAAA
1 ATAATATAAA-AATT-AAA
* *
266915 TTAATATAAAAATCAAA
1 ATAATATAAAAATTAAA
*
266932 TTTATAATATACAAATTATAA
1 ---ATAATATAAAAATTA-AA
*
266953 TTAATATAAAAATTAAA
1 ATAATATAAAAATTAAA
266970 TTTCAAAAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
17 5 0.08
18 25 0.42
19 15 0.25
20 13 0.22
21 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (17 bp):
ATAATATAAAAATTAAA
Found at i:266941 original size:20 final size:19
Alignment explanation
Indices: 266867--266972 Score: 71
Period size: 18 Copynumber: 5.6 Consensus size: 19
266857 TAATGATTAT
*
266867 AAATAAAATTTATAATATAA
1 AAATTAAATTT-TAATATAA
* *
266887 GAATTATAA--ATAATATAA
1 AAATTA-AATTTTAATATAA
266905 AGAATTGAAA--TTAATATAA
1 A-AATT-AAATTTTAATATAA
* *
266924 AAATCAAATTTATAATATAC
1 AAATTAAATTT-TAATATAA
266944 AAATTATAA--TTAATATAA
1 AAATTA-AATTTTAATATAA
266962 AAATTAAATTT
1 AAATTAAATTT
266973 CAAAAAGTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
17 5 0.07
18 24 0.35
19 18 0.26
20 17 0.25
21 4 0.06
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (19 bp):
AAATTAAATTTTAATATAA
Found at i:266958 original size:38 final size:39
Alignment explanation
Indices: 266896--266972 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 39
266886 AGAATTATAA
266896 ATAATATAAAGAATTGAAATTAATATAAAAATCAAATTT
1 ATAATATAAAGAATTGAAATTAATATAAAAATCAAATTT
* *
266935 ATAATATACA-AATT-ATAATTAATATAAAAATTAAATTT
1 ATAATATAAAGAATTGA-AATTAATATAAAAATCAAATTT
266973 CAAAAAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
37 1 0.03
38 25 0.71
39 9 0.26
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (39 bp):
ATAATATAAAGAATTGAAATTAATATAAAAATCAAATTT
Found at i:269937 original size:29 final size:28
Alignment explanation
Indices: 269871--269937 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 28
269861 TAAAATTATG
269871 TAAAAATATATTTTAAAAATCTTCGAATT
1 TAAAAATATATTTTAAAAATCTTC-AATT
* *
269900 GAAATATATATTTTATAAAAT-TT-AATTTT
1 TAAAAATATATTTTA-AAAATCTTCAA--TT
269929 TAAAAATAT
1 TAAAAATAT
269938 TCAAAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
27 2 0.06
29 24 0.77
30 5 0.16
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (28 bp):
TAAAAATATATTTTAAAAATCTTCAATT
Found at i:272723 original size:29 final size:30
Alignment explanation
Indices: 272682--272761 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
272672 GAGGAGCAGG
272682 AGGAGTGCATGGCGACCTAC-AAGGTCGCC
1 AGGAGTGCATGGCGACCTACGAAGGTCGCC
** *
272711 AGGAGTGCATGGCGACCGCCGTAGGTCGCC
1 AGGAGTGCATGGCGACCTACGAAGGTCGCC
*
272741 CGGAAG-GCATGGCGACCTACG
1 AGG-AGTGCATGGCGACCTACG
272762 GCCAACACTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 18 0.42
30 23 0.53
31 2 0.05
ACGTcount: A:0.21, C:0.29, G:0.38, T:0.12
Consensus pattern (30 bp):
AGGAGTGCATGGCGACCTACGAAGGTCGCC
Found at i:278293 original size:82 final size:83
Alignment explanation
Indices: 278155--278312 Score: 239
Period size: 82 Copynumber: 1.9 Consensus size: 83
278145 TCAAATCTTA
* * * *
278155 TAAGATTGTTTTTTTAATTTGGATTCATATTTAGGATGGAAATTTTTTACTTGAGATAATAATAT
1 TAAGATTGTTTTTTTAATTCGGATTCAGATTTAGGATGGAAATTTTTAACTCGAGATAATAATAT
278220 AATTATTCTTTATATATT
66 AATTATTCTTTATATATT
* *
278238 TAAGATTTTTTTTTTAATTCGGATT-AGGTTTAGGAT-GAAACTTTTTAACTCGAGATAATAATA
1 TAAGATTGTTTTTTTAATTCGGATTCAGATTTAGGATGGAAA-TTTTTAACTCGAGATAATAATA
278301 TAATTATTCTTT
65 TAATTATTCTTT
278313 TGTATATTCA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 4 0.06
82 41 0.60
83 23 0.34
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (83 bp):
TAAGATTGTTTTTTTAATTCGGATTCAGATTTAGGATGGAAATTTTTAACTCGAGATAATAATAT
AATTATTCTTTATATATT
Found at i:279632 original size:41 final size:41
Alignment explanation
Indices: 279575--279669 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
279565 CCCTTTTTTT
*
279575 ACTATCGCAACGAATTTGGAAA-ATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAACATCGCAACGAAAACT-TAG
* *
279616 ACTATCGCAACGAATTTGGAAACTATCGCAATGAAAACTTGG
1 ACTATCGCAACGAATTTGGAAAC-ATCGCAACGAAAACTTAG
279658 ACTATCGCAACG
1 ACTATCGCAACG
279670 CGAAATGAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
41 22 0.45
42 14 0.29
43 13 0.27
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAACATCGCAACGAAAACTTAG
Found at i:279721 original size:21 final size:21
Alignment explanation
Indices: 279658--279721 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
279648 GAAAACTTGG
279658 ACTATCGCAACGCGAAATGA-A
1 ACTATCGCAACGCGAAAT-ACA
* ** *
279679 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATACA
*
279699 ACTATCGTAACGCGAAATACA
1 ACTATCGCAACGCGAAATACA
279720 AC
1 AC
279722 GCGAATTTGC
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATACA
Found at i:284154 original size:29 final size:29
Alignment explanation
Indices: 284029--284145 Score: 216
Period size: 29 Copynumber: 4.0 Consensus size: 29
284019 TGATTGATAA
*
284029 TTCAGCTCATCAAAGGGAGACTGAAACCT
1 TTCAGCTCATCAAAAGGAGACTGAAACCT
284058 TTCAGCTCATCAAAAGGAGACTGAAACCT
1 TTCAGCTCATCAAAAGGAGACTGAAACCT
284087 TTCAGCTCATCAAAAGGAGACTGAAACCT
1 TTCAGCTCATCAAAAGGAGACTGAAACCT
*
284116 TTCAGCTCATCAAAAGGAGATTGAAACCT
1 TTCAGCTCATCAAAAGGAGACTGAAACCT
284145 T
1 T
284146 AGGATTCATT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 86 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (29 bp):
TTCAGCTCATCAAAAGGAGACTGAAACCT
Found at i:286973 original size:2 final size:2
Alignment explanation
Indices: 286966--286998 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
286956 ATCAAGGGTT
286966 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
286999 ACCCTTGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:300333 original size:19 final size:20
Alignment explanation
Indices: 300311--300348 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
300301 TTATAATTAA
300311 TATAAATATTT-AATATTTT
1 TATAAATATTTAAATATTTT
300330 TATAAATATTTAAATATTT
1 TATAAATATTTAAATATTT
300349 AACTAGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATAAATATTTAAATATTTT
Found at i:300343 original size:27 final size:28
Alignment explanation
Indices: 300296--300350 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
300286 ATAATTATAT
*
300296 TATTTTTATAATTAATATAAATATTTAA
1 TATTTTTATAAATAATATAAATATTTAA
*
300324 TATTTTTATAAAT-ATTTAAATATTTAA
1 TATTTTTATAAATAATATAAATATTTAA
300351 CTAGCATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TATTTTTATAAATAATATAAATATTTAA
Found at i:302312 original size:19 final size:18
Alignment explanation
Indices: 302284--302368 Score: 57
Period size: 18 Copynumber: 4.6 Consensus size: 18
302274 CTTTGATTCA
302284 TTTA-TTATTTATTATTTT
1 TTTATTTATTTATT-TTTT
302302 TTTATTTATTTCATTTTTT
1 TTTATTTATTT-ATTTTTT
* * **
302321 CTCT-TTGATTTATTTTCC
1 -TTTATTTATTTATTTTTT
*
302339 TTTATTTTTTTATTTTATCT
1 TTTATTTATTTATTTT-T-T
*
302359 TTGATTTATT
1 TTTATTTATT
302369 ATTATTATTT
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
17 2 0.04
18 19 0.38
19 16 0.32
20 13 0.26
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTATTTATTTATTTTTT
Found at i:302319 original size:18 final size:18
Alignment explanation
Indices: 302284--302454 Score: 72
Period size: 19 Copynumber: 9.4 Consensus size: 18
302274 CTTTGATTCA
*
302284 TTTA-TTATTTATTATTTT
1 TTTATTTATTTATT-TTAT
302302 TTTATTTATTTCATTTT-T
1 TTTATTTATTT-ATTTTAT
* * **
302320 TCTCTTTGATTTATTTTCC
1 TTTATTT-ATTTATTTTAT
*
302339 TTTATTTTTTTATTTTAT
1 TTTATTTATTTATTTTAT
302357 CTTTGATTTA-TTATTATTAT
1 -TTT-ATTTATTTATT-TTAT
* *
302377 TTTACATTT-TTTCAATTGA-
1 TTT--ATTTATTT-ATTTTAT
*
302396 TTTATTTGATATATTTTTAT
1 TTTATTT-ATTTA-TTTTAT
** *
302416 TTTA-TT-TTCCTTTGA-
1 TTTATTTATTTATTTTAT
302431 TTTATTT-TTTATTTTAT
1 TTTATTTATTTATTTTAT
302448 TTTATTT
1 TTTATTT
302455 TTCTCCTTTT
Statistics
Matches: 115, Mismatches: 22, Indels: 33
0.68 0.13 0.19
Matches are distributed among these distances:
15 4 0.03
16 12 0.10
17 12 0.10
18 24 0.21
19 38 0.33
20 23 0.20
21 2 0.02
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTATTTATTTATTTTAT
Found at i:302336 original size:16 final size:16
Alignment explanation
Indices: 302317--302368 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
302307 TTATTTCATT
302317 TTTTCTCTTTGATTTA
1 TTTTCTCTTTGATTTA
* **
302333 TTTTCCTTTATTTTTTTA
1 TTTT-CTCT-TTGATTTA
*
302351 TTTTATCTTTGATTTA
1 TTTTCTCTTTGATTTA
302367 TT
1 TT
302369 ATTATTATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
16 12 0.44
17 5 0.19
18 10 0.37
ACGTcount: A:0.13, C:0.10, G:0.04, T:0.73
Consensus pattern (16 bp):
TTTTCTCTTTGATTTA
Found at i:302377 original size:33 final size:34
Alignment explanation
Indices: 302295--302481 Score: 131
Period size: 34 Copynumber: 5.4 Consensus size: 34
302285 TTATTATTTA
* *
302295 TTATT-TTTTTATTTATTTCATTTTTTCTCTTTGAT
1 TTATTATTATTATTTATTT--TATTTTCTCTTTGAT
* *
302330 TTATT-TTCCTTTATTT-TTTTATTTTATCTTTGAT
1 TTATTATT--ATTATTTATTTTATTTTCTCTTTGAT
** **
302364 TTATTATTATTATTTTACATT-TTTTC-AATTGAT
1 TTATTATTATTA-TTTATTTTATTTTCTCTTTGAT
302397 TTATTTGATATATT-TTTATTTTATTTTC-CTTTGAT
1 TTA-TT-AT-TATTATTTATTTTATTTTCTCTTTGAT
302432 TTATT-TT-TTATTTTATTTTATTTTTCTCCTTTTGAT
1 TTATTATTATTA-TTTATTTTA-TTTTCT-C-TTTGAT
302468 TTATTATTATTATT
1 TTATTATTATTATT
302482 ATTATTAGTT
Statistics
Matches: 123, Mismatches: 12, Indels: 32
0.74 0.07 0.19
Matches are distributed among these distances:
30 2 0.02
31 1 0.01
32 10 0.08
33 16 0.13
34 35 0.28
35 27 0.22
36 18 0.15
37 11 0.09
38 3 0.02
ACGTcount: A:0.19, C:0.07, G:0.03, T:0.71
Consensus pattern (34 bp):
TTATTATTATTATTTATTTTATTTTCTCTTTGAT
Found at i:302456 original size:11 final size:11
Alignment explanation
Indices: 302407--302456 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
302397 TTATTTGATA
302407 TATTTTTATTT
1 TATTTTTATTT
**
302418 TATTTTCCTTT
1 TATTTTTATTT
*
302429 GATTTATT-TTT
1 TATTT-TTATTT
302440 TA-TTTTATTT
1 TATTTTTATTT
302450 TATTTTT
1 TATTTTT
302457 CTCCTTTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 2 0.06
10 7 0.23
11 21 0.68
12 1 0.03
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:306723 original size:95 final size:95
Alignment explanation
Indices: 306557--306809 Score: 330
Period size: 95 Copynumber: 2.6 Consensus size: 95
306547 ATTATATATC
*
306557 TACAATAAAGCTTGATATGTCCCTCTAAAGCAATTGGTTAAACTCCCCGGCTTTATGGATAAGAT
1 TACAATAAAGCTTGATATGTCCCTCTAGAGCAATTGGTTAAACTCCCCGGCTTTATGGATAAGAT
*
306622 TCAGCTAGCCTGATAAAAGTGATTACAATA
66 TCAGCTAGCCTGACAAAAGTGATTACAATA
*
306652 TACAATAAAGCTTGAGT-TGTCCCTCTAGAGCAATTGGTTAAACTCCCCGGCTTTATGGATAATA
1 TACAATAAAGCTTGA-TATGTCCCTCTAGAGCAATTGGTTAAACTCCCCGGCTTTATGGATAAGA
* * *
306716 TTTAGCTAGCCTGACAAAGGTGATTATAATA
65 TTCAGCTAGCCTGACAAAAGTGATTACAATA
** * * * **
306747 T-CTATATAATGATATTAATATGTCCCTCTAGAGAAATTGGTTAAACACCATGGCTTTATGGAT
1 TAC-A-ATAA--AGCTTGATATGTCCCTCTAGAGCAATTGGTTAAACTCCCCGGCTTTATGGAT
306810 TCAGCAAGCC
Statistics
Matches: 139, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
94 1 0.01
95 89 0.64
96 5 0.04
97 1 0.01
98 43 0.31
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (95 bp):
TACAATAAAGCTTGATATGTCCCTCTAGAGCAATTGGTTAAACTCCCCGGCTTTATGGATAAGAT
TCAGCTAGCCTGACAAAAGTGATTACAATA
Found at i:308473 original size:36 final size:36
Alignment explanation
Indices: 308422--308502 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
308412 AATTTACTCA
*
308422 AAACAAAGTTTTTGTCTCTCTTAAGACAGTTTCCCTTG
1 AAACAAA--TTTTGTCTCTCTTGAGACAGTTTCCCTTG
308460 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
308496 AAACAAA
1 AAACAAA
308503 ATCTTTGAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
36 35 0.83
38 7 0.17
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:308615 original size:21 final size:21
Alignment explanation
Indices: 308590--308654 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
308580 TGAGACAGGT
308590 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
308611 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
308628 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
308647 TCTCTTGA
1 TCTCTTGA
308655 GACAGTTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 7 0.21
16 1 0.03
17 3 0.09
18 4 0.12
19 3 0.09
20 1 0.03
21 15 0.44
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.42
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:308642 original size:72 final size:72
Alignment explanation
Indices: 308521--308844 Score: 238
Period size: 72 Copynumber: 4.6 Consensus size: 72
308511 ATATGTTTTC
* * *
308521 CTTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCTTTTAGAACTAATTTTGTCTATCTTGAGAC
1 CTTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCCTTGAGAACAAATTTTGTCTATCTTGAGAC
*
308586 AGGTTCT
66 AGGTTCA
* * * *
308593 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA-AACAAATTTTGTCTCTCTTGAGA
1 CTTGAAACAAATTTCGTCTCCCTTAAGACAGTTT-CCTTGAGAACAAATTTTGTCTATCTTGAGA
*
308657 CAGTTTCA
65 CAGGTTCA
* * ** **
308665 CTTGAAACAAA----ATCT---TTAA-ATATGTTTTCCTTGA-AACAAATTTCATCTCCCTTGAG
1 CTTGAAACAAATTTCGTCTCCCTTAAGACA-G-TTTCCTTGAGAACAAATTTTGTCTATCTTGAG
* *
308721 ACAGTTTCT
64 ACAGGTTCA
* * * * * * * *
308730 TTTGGAACTAATTTTTGTCTCTCTTGAGACAGTTTCTCTTGA-AACAAATTTTGTTTCTCTTGAG
1 CTTGAAAC-AAATTTCGTCTCCCTTAAGACAGTTTC-CTTGAGAACAAATTTTGTCTATCTTGAG
* *
308794 ACAGTTTCC
64 ACAGGTTCA
* * *
308803 CTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGA
1 CTTGAAACAAA-TTTCGTCTCCCTTAAGACAGTTTC-CTTGA
308845 AATACCAATC
Statistics
Matches: 208, Mismatches: 30, Indels: 27
0.78 0.11 0.10
Matches are distributed among these distances:
64 2 0.01
65 43 0.21
66 5 0.02
68 3 0.01
70 3 0.01
72 75 0.36
73 75 0.36
74 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (72 bp):
CTTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCCTTGAGAACAAATTTTGTCTATCTTGAGAC
AGGTTCA
Found at i:308725 original size:173 final size:174
Alignment explanation
Indices: 308422--308906 Score: 749
Period size: 173 Copynumber: 2.8 Consensus size: 174
308412 AATTTACTCA
*
308422 AAACAAAGTTTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 AAACAAA--TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
308487 TTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTAAGACAG
64 TTTCACTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAG
308552 TTTCTTTTAGAACTAA-TTTTGTCTATCTTGAGACAGGTTCTCTTG
129 TTTCTTTTAGAACTAATTTTTGTCTATCTTGAGACAGGTTCTCTTG
308597 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
* *
308662 TCACTTGAAACAAAATCTTTAAATATGTTTTCCTTGAAACAAATTTCATCTCCCTTGAGACAGTT
66 TCACTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTT
* * *
308727 TCTTTTGGAACTAATTTTTGTCTCTCTTGAGACAGTTTCTCTTG
131 TCTTTTAGAACTAATTTTTGTCTATCTTGAGACAGGTTCTCTTG
*
308771 AAACAAATTTTGTTTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGT
* * * ** * * *
308836 TTCTCTTGAAATACCAATCTTTGAATAT-ACTTCTCTTGAAACAAAATTTTGCCTCCCTGGAGAC
65 TTCACTTGAAACA-AAATCTTTGAATATGTTTTC-CTTGAAAC-AAATTTCGTCTCCCTTGAGAC
308900 AGTTTCT
127 AGTTTCT
308907 CTTGAAACAC
Statistics
Matches: 286, Mismatches: 19, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
173 131 0.46
174 69 0.24
175 42 0.15
176 20 0.07
177 24 0.08
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (174 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
TCACTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTT
TCTTTTAGAACTAATTTTTGTCTATCTTGAGACAGGTTCTCTTG
Found at i:308743 original size:101 final size:102
Alignment explanation
Indices: 308593--308777 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 102
308583 GACAGGTTCT
** *
308593 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGA
1 CTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTTGTCTCTCTTGAGA
308657 CAGTTTCACTTGAAACAAAATCTTTAAATATGTTTTC
66 CAGTTTCACTTGAAACAAAATCTTTAAATATGTTTTC
** * *
308694 CTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAATTTTTGTCTCTCTTGAGA
1 CTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTTGTCTCTCTTGAGA
*
308759 CAGTTTCTCTTGAAACAAA
66 CAGTTTCACTTGAAACAAA
308778 TTTTGTTTCT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 40 0.53
102 35 0.47
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.39
Consensus pattern (102 bp):
CTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTTGTCTCTCTTGAGA
CAGTTTCACTTGAAACAAAATCTTTAAATATGTTTTC
Found at i:308756 original size:37 final size:36
Alignment explanation
Indices: 308690--308846 Score: 217
Period size: 37 Copynumber: 4.3 Consensus size: 36
308680 TTAAATATGT
** *
308690 TTTC-CTTGAAACAAATTTCATCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
308725 TTTCTTTTGGAACTAATTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
308762 TTTCTCTTGAAACAAATTTTGTTTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
308798 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
308835 TTTCTCTTGAAA
1 TTTCTCTTGAAA
308847 TACCAATCTT
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
35 4 0.04
36 42 0.40
37 60 0.57
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:308813 original size:36 final size:36
Alignment explanation
Indices: 308517--308675 Score: 214
Period size: 36 Copynumber: 4.4 Consensus size: 36
308507 TTGAATATGT
* * *
308517 TTTC-CTTGAAACAAATTTCGTCTCCCTTAAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
308552 TTTCT-TTTAGAACTAATTTTGTCTATCTTGAGACAG
1 TTTCTCTTGA-AACAAATTTTGTCTCTCTTGAGACAG
*
308588 GTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
308624 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
308660 TTTCACTTGAAACAAA
1 TTTCTCTTGAAACAAA
308676 ATCTTTAAAT
Statistics
Matches: 108, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
35 7 0.06
36 98 0.91
37 3 0.03
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:308819 original size:73 final size:73
Alignment explanation
Indices: 308690--308846 Score: 226
Period size: 73 Copynumber: 2.2 Consensus size: 73
308680 TTAAATATGT
** * * *
308690 TTTC-CTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAACTAATTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
308754 TGAGACAG
66 TGAGACAG
** * *
308762 TTTCTCTTGAAACAAATTTTGTTTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
308827 TGAGACAG
66 TGAGACAG
308835 TTTCTCTTGAAA
1 TTTCTCTTGAAA
308847 TACCAATCTT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 4 0.05
73 71 0.95
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
TGAGACAG
Found at i:308983 original size:35 final size:35
Alignment explanation
Indices: 308901--309074 Score: 198
Period size: 35 Copynumber: 5.4 Consensus size: 35
308891 CCTGGAGACA
308901 GTTTCTCTTGAAACAC--AAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATC
* *
308934 ATTTCTCTTG------AAAAAAAACCTTTGAAAAC
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATC
308963 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATC
*
308998 GTTTCTCTTGAAACAC-AGAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATC
*
309032 GTTTTTCTTG----A-AAAAAAAACCTTTGAAAAT-
1 GTTTCTCTTGAAACACAAAAAAAACCTTTG-AAATC
309062 GTTTCTCTTGAAA
1 GTTTCTCTTGAAA
309075 TGCAAAGACC
Statistics
Matches: 120, Mismatches: 8, Indels: 26
0.78 0.05 0.17
Matches are distributed among these distances:
29 25 0.21
30 22 0.18
31 4 0.03
33 9 0.08
34 26 0.22
35 34 0.28
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATC
Found at i:309003 original size:64 final size:65
Alignment explanation
Indices: 308901--309074 Score: 213
Period size: 64 Copynumber: 2.7 Consensus size: 65
308891 CCTGGAGACA
*
308901 GTTTCTCTTGAAACAC--AAAAAACCTTTGAAATCATTTCTCTTGAAA-AAAAACCTTTGAAAAC
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATCGTTTCTCTTGAAAGAAAAACCTTTGAAAAC
308963 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATCGTTTCTCTTGAAACACAGAAAAACCTTTGA
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATCGTTTCTCTTG--A-A-AGAAAAACCTTTGA
*
309028 AATC
62 AAAC
*
309032 GTTTTTCTTG----A-AAAAAAAACCTTTGAAAAT-GTTTCTCTTGAAA
1 GTTTCTCTTGAAACACAAAAAAAACCTTTG-AAATCGTTTCTCTTGAAA
309075 TGCAAAGACC
Statistics
Matches: 101, Mismatches: 3, Indels: 18
0.83 0.02 0.15
Matches are distributed among these distances:
60 1 0.01
61 1 0.01
62 17 0.17
64 50 0.50
65 5 0.05
66 1 0.01
67 1 0.01
68 1 0.01
69 24 0.24
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (65 bp):
GTTTCTCTTGAAACACAAAAAAAACCTTTGAAATCGTTTCTCTTGAAAGAAAAACCTTTGAAAAC
Found at i:309227 original size:80 final size:83
Alignment explanation
Indices: 309077--309280 Score: 193
Period size: 84 Copynumber: 2.5 Consensus size: 83
309067 TCTTGAAATG
* * * * * * * *
309077 CAAAGACCTTCGAGTTCGACTATACTCAACTTCGAGGGCACATCATTTGCAGCATGACTCAATGC
1 CAAAGACCGTAGAGTTCGATTACACTCAGC-TCAAAGGCACAACATTTGCAGCATGACTCAATGC
* *
309142 TAGAAGGG-T-TCT-CTTC
65 GAGAAGGGCTATCTCCATC
* *
309158 CAAAGACCGTAGAGTTCGATTCCACTCAGCTCAAAGGCACAACATTTGCAGCAT-AGCTTAA-GT
1 CAAAGACCGTAGAGTTCGATTACACTCAGCTCAAAGGCACAACATTTGCAGCATGA-CTCAATG-
309221 CGAGAAGGGCTATCTGCCATC
64 CGAGAAGGGCTATCT-CCATC
* * * *
309242 CAAAGACCTTCGAGTTCGATTACATTCAGCTCAGAGGCA
1 CAAAGACCGTAGAGTTCGATTACACTCAGCTCAAAGGCA
309281 AATAAAACTT
Statistics
Matches: 100, Mismatches: 17, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
79 2 0.02
80 33 0.33
81 25 0.25
82 3 0.03
84 37 0.37
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (83 bp):
CAAAGACCGTAGAGTTCGATTACACTCAGCTCAAAGGCACAACATTTGCAGCATGACTCAATGCG
AGAAGGGCTATCTCCATC
Found at i:310755 original size:11 final size:12
Alignment explanation
Indices: 310731--310917 Score: 53
Period size: 13 Copynumber: 14.3 Consensus size: 12
310721 CCTTTGATTC
310731 ATTTATTATTTATT
1 ATTTATT-TTT-TT
310745 ATTT-TTTTATTT
1 ATTTATTTT-TTT
310757 ATTTCATTTTTTTCT
1 ATTT-A-TTTTTT-T
*
310772 CTTTGATTTATTTT
1 ATTT-ATTT-TTTT
*
310786 CCTTTATTTTTTT
1 -ATTTATTTTTTT
* *
310799 ATTTTATCTTTTG
1 A-TTTATTTTTTT
310812 ATTTATTATTATTTT
1 ATTTA-T-TT-TTTT
* *
310827 TTTTACATTTTTTCA
1 ATTT--ATTTTTT-T
*
310842 ATTTATTTATTTG
1 ATTTATTT-TTTT
* *
310855 ATATATTTTTAT
1 ATTTATTTTTTT
*
310867 -TTTA-TTTTAT
1 ATTTATTTTTTT
310877 -TTTATTTTCCTTT
1 ATTTATTTT--TTT
310890 GATTTA-TTTTTT
1 -ATTTATTTTTTT
310902 ATTT-TTTATTTT
1 ATTTATTT-TTTT
310914 ATTT
1 ATTT
310918 TTTCTCCTTT
Statistics
Matches: 135, Mismatches: 16, Indels: 46
0.69 0.08 0.23
Matches are distributed among these distances:
10 10 0.07
11 12 0.09
12 25 0.19
13 31 0.23
14 24 0.18
15 31 0.23
16 1 0.01
17 1 0.01
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (12 bp):
ATTTATTTTTTT
Found at i:310755 original size:18 final size:19
Alignment explanation
Indices: 310732--310917 Score: 75
Period size: 19 Copynumber: 9.6 Consensus size: 19
310722 CTTTGATTCA
310732 TTTA-TTATTT-ATTATTTT
1 TTTATTTATTTCATT-TTTT
310750 TTTATTTATTTCATTTTTT
1 TTTATTTATTTCATTTTTT
* * **
310769 TCTCTTTGATTT-ATTTTCC
1 TTTATTT-ATTTCATTTTTT
*
310788 TTTATTT-TTTTATTTTATCT
1 TTTATTTATTTCATTTT-T-T
*
310808 TTTGATTTATTATTATTTTTT
1 TTT-ATTTATT-TCATTTTTT
* * *
310829 TTACATTT-TTTCA-ATTTA
1 TT-TATTTATTTCATTTTTT
*
310847 TTTATTTGATAT-ATTTTTAT
1 TTTATTT-ATTTCATTTTT-T
* *
310867 TTTATTTTATTTTATTTTCCT
1 TTTA-TTTATTTCATTTT-TT
*
310888 TTGATTTATTT--TTTATTT
1 TTTATTTATTTCATTT-TTT
310906 TTTATTTTATTT
1 TTTA-TTTATTT
310918 TTTCTCCTTT
Statistics
Matches: 128, Mismatches: 21, Indels: 37
0.69 0.11 0.20
Matches are distributed among these distances:
17 7 0.05
18 22 0.17
19 40 0.31
20 26 0.20
21 23 0.18
22 3 0.02
23 7 0.05
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTATTTATTTCATTTTTT
Found at i:310805 original size:5 final size:5
Alignment explanation
Indices: 310739--310918 Score: 62
Period size: 5 Copynumber: 36.6 Consensus size: 5
310729 TCATTTATTA
* * * * **
310739 TTTAT TATTTT TTTA- TTTAT TTCAT TTT-T TTCTCT TTGA- TTTAT TTTCC
1 TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TT-TAT TTTAT TTTAT TTTAT
*
310788 TTTA- TTT-T TTTAT TTTAT CTTT-T GATTTAT TATTAT TTT-T TTTACA
1 TTTAT TTTAT TTTAT TTTAT -TTTAT --TTTAT T-TTAT TTTAT TTTA-T
* * * *
310834 TTT-T TTCAA TTTA- TTTAT TTGA- TATATT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT
* *
310882 TTTCCT TTGA- TTTAT TTT-T TATT-T TTTAT TTTAT TTT
1 TTT-AT TTTAT TTTAT TTTAT T-TTAT TTTAT TTTAT TTT
310919 TTCTCCTTTT
Statistics
Matches: 130, Mismatches: 24, Indels: 42
0.66 0.12 0.21
Matches are distributed among these distances:
4 35 0.27
5 67 0.52
6 27 0.21
7 1 0.01
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:310830 original size:34 final size:34
Alignment explanation
Indices: 310738--310876 Score: 93
Period size: 35 Copynumber: 3.8 Consensus size: 34
310728 TTCATTTATT
* *
310738 ATTTATTATTTTTTTATTTATTTCATTTTTTTCTCTTTG
1 ATTTATTATTATTTT-TTT-TTT-A-TTTTATCT-TTTG
*
310777 ATTTATT-TTCCTTTATTTTTTTATTTTATCTTTTG
1 ATTTATTATT-ATTT-TTTTTTTATTTTATCTTTTG
** * *
310812 ATTTATTATTATTTTTTTTACATTTTTTCAATTT-
1 ATTTATTATTATTTTTTTTTTATTTTATC-TTTTG
*
310846 ATTTATTTGATATATTTTTATTTTATTTTAT
1 ATTTA-TT-AT-TATTTTTTTTTTATTTTAT
310877 TTTATTTTCC
Statistics
Matches: 82, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
34 17 0.21
35 19 0.23
36 11 0.13
37 16 0.20
38 5 0.06
39 13 0.16
40 1 0.01
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (34 bp):
ATTTATTATTATTTTTTTTTTATTTTATCTTTTG
Found at i:310847 original size:24 final size:24
Alignment explanation
Indices: 310820--310880 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
310810 TGATTTATTA
310820 TTATTTTTTTTACAT-TTTTTCAAT
1 TTATTTTTTTTACATATTTTT-AAT
* * * *
310844 TTATTTATTTGATATATTTTTATT
1 TTATTTTTTTTACATATTTTTAAT
310868 TTATTTTATTTTA
1 TTATTTT-TTTTA
310881 TTTTCCTTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (24 bp):
TTATTTTTTTTACATATTTTTAAT
Found at i:310881 original size:34 final size:33
Alignment explanation
Indices: 310833--310917 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
310823 TTTTTTTTAC
*
310833 ATTTTTTCAATTTATTT-ATTTGATATATTTTTAT
1 ATTTTTT-ATTTTATTTCATTTGATATATTTTT-T
* * *
310867 TTTATTTTATTTTATTTTCCTTTGATTTATTTTTT
1 ATT-TTTTATTTTA-TTTCATTTGATATATTTTTT
310902 ATTTTTTATTTTATTT
1 ATTTTTTATTTTATTT
310918 TTTCTCCTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
33 3 0.07
34 17 0.40
35 10 0.23
36 13 0.30
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (33 bp):
ATTTTTTATTTTATTTCATTTGATATATTTTTT
Found at i:310918 original size:11 final size:11
Alignment explanation
Indices: 310858--310919 Score: 65
Period size: 11 Copynumber: 5.6 Consensus size: 11
310848 TTATTTGATA
310858 TATTTTTATTT
1 TATTTTTATTT
310869 TA-TTTTATTT
1 TATTTTTATTT
**
310879 TATTTTCCTTT
1 TATTTTTATTT
*
310890 GATTTATT-TTT
1 TATTT-TTATTT
310901 TATTTTTTATTT
1 TA-TTTTTATTT
310913 TATTTTT
1 TATTTTT
310920 TCTCCTTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 10 0.24
11 23 0.55
12 9 0.21
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.79
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:310931 original size:118 final size:111
Alignment explanation
Indices: 310731--310942 Score: 268
Period size: 114 Copynumber: 1.8 Consensus size: 111
310721 CCTTTGATTC
*
310731 ATTTATTATTTATTATTTTTTTATTTATTTCATTTTTTTCTCTTTGATTTATTTTCCTTTATTTT
1 ATTTATTATTTATTATTTTTATATTTATTTCATTTTTTTCTCTTTGATTTATTTTCCTTTATTTT
310796 TTTATTTTATCTTTTGATTTATTATTATTTTTTTTACATTTTTTCA
66 TTTATTTTATCTTTTGATTTATTATTATTTTTTTTACATTTTTTCA
* *
310842 ATTTATTTATTTGATATATTTTTAT-TTTATTTTATTTTATTT-TCCTTTGATTTATTTT-TTAT
1 ATTTA-TTATTT-AT-TATTTTTATATTTATTTCATTTT-TTTCT-CTTTGATTTATTTTCCT-T
* *
310904 TTTTTATTTTATTTTTTCTCCTTTTGATTTATTATTATT
60 TATTT-TTTTA--TTTTAT-CTTTTGATTTATTATTATT
310943 ATTATTAGTT
Statistics
Matches: 86, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
111 5 0.06
112 6 0.07
113 16 0.19
114 30 0.35
115 5 0.06
117 5 0.06
118 19 0.22
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.73
Consensus pattern (111 bp):
ATTTATTATTTATTATTTTTATATTTATTTCATTTTTTTCTCTTTGATTTATTTTCCTTTATTTT
TTTATTTTATCTTTTGATTTATTATTATTTTTTTTACATTTTTTCA
Found at i:311594 original size:29 final size:29
Alignment explanation
Indices: 311552--311609 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
311542 AGTCGGTCAA
*
311552 GTAGGTCGCCATGCAGTTGGGGTGACCTT
1 GTAGGTCGCCATGCAGTTGGGGCGACCTT
311581 GTAGGTCGCCATGCAGTTGGGGCGACCTT
1 GTAGGTCGCCATGCAGTTGGGGCGACCTT
311610 ATTTTGATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.22, G:0.38, T:0.26
Consensus pattern (29 bp):
GTAGGTCGCCATGCAGTTGGGGCGACCTT
Found at i:312227 original size:7 final size:7
Alignment explanation
Indices: 312211--312261 Score: 66
Period size: 7 Copynumber: 7.3 Consensus size: 7
312201 TTGTTATTAA
312211 AAACCCT
1 AAACCCT
*
312218 AAATCCT
1 AAACCCT
312225 AAACCCT
1 AAACCCT
*
312232 AAACTCT
1 AAACCCT
**
312239 AAACTTT
1 AAACCCT
312246 AAACCCT
1 AAACCCT
312253 AAACCCT
1 AAACCCT
312260 AA
1 AA
312262 CAATTCTCCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:312731 original size:274 final size:283
Alignment explanation
Indices: 312366--312892 Score: 721
Period size: 295 Copynumber: 1.9 Consensus size: 283
312356 ATAAAACTAT
* ** *
312366 TTTAGGATTTAGGGTTTGCAAAATCAATATACAACAAATAATATAAGTAACTATTGATTTTGTAA
1 TTTAGGATTTAAGGTTTAAAAAATCAATATACAACAAATAATATAAGTAACTATTGATTTTATAA
* *
312431 ACCCTAAACCCTAAAATATTTTGGTTA-T-T-A-CT-AA-A-A-C-CCTAAACTTTAAAGCCTAA
66 ACCCTAAACCCTAAAATATGTTGGTTATTATAACCTAAACATATCACCTAAACTTTAAACCCTAA
* * *
312487 ACCCTAACAATTCTCCCTCCAATCAATTTCTTCTTAGAAAAACAAATGTGTAACCACCGTCATGG
131 ACCCTAACAATTCTCCATCCAATCAATTTCTTCTTAGAAAAACAAATCTGTAACCACCATCATGG
**
312552 TAGATATCACCATCCTCTACCACTTTCCTTGCCCTCAACATACCATGAATTTATAAAGGTTTTCA
196 TAGATATCACCATCCTCTACCACTTTCAGTGCCCTCAACATACCATGAATTTATAAAGGTTTTCA
312617 GTAATAACCAAAATATTTTAGGG
261 GTAATAACCAAAATATTTTAGGG
* *
312640 TTTAGGGTTTAAGGTTTAAAAAATCAATATACAACAAATAATATAAGTAACTATTGATTTTATGA
1 TTTAGGATTTAAGGTTTAAAAAATCAATATACAACAAATAATATAAGTAACTATTGATTTTATAA
*
312705 ACCTTAAACCCTAAAATATGTTGGTTATTACTAAAAACCCTAAACCTTATATCATAAACCTAAAC
66 ACCCTAAACCCTAAAATATGTTGGTTATTA-T---AA-CCTAAA-C--ATATC----ACCTAAAC
*
312770 TTTAAACCCTAAACCCTAACAATTCTCCATCCAATCAATTTCTTCTTATAAAAACAAATCTGTAA
119 TTTAAACCCTAAACCCTAACAATTCTCCATCCAATCAATTTCTTCTTAGAAAAACAAATCTGTAA
* * *
312835 CCACCATCATGGTAGATATCACCATCCTCTGCCCCTTTCAGTGTCCTCAACATACCAT
184 CCACCATCATGGTAGATATCACCATCCTCTACCACTTTCAGTGCCCTCAACATACCAT
312893 AATGGTGGTT
Statistics
Matches: 214, Mismatches: 18, Indels: 21
0.85 0.07 0.08
Matches are distributed among these distances:
274 84 0.39
275 1 0.00
277 1 0.00
281 1 0.00
283 2 0.01
284 2 0.01
288 1 0.00
289 1 0.00
290 1 0.00
295 120 0.56
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.32
Consensus pattern (283 bp):
TTTAGGATTTAAGGTTTAAAAAATCAATATACAACAAATAATATAAGTAACTATTGATTTTATAA
ACCCTAAACCCTAAAATATGTTGGTTATTATAACCTAAACATATCACCTAAACTTTAAACCCTAA
ACCCTAACAATTCTCCATCCAATCAATTTCTTCTTAGAAAAACAAATCTGTAACCACCATCATGG
TAGATATCACCATCCTCTACCACTTTCAGTGCCCTCAACATACCATGAATTTATAAAGGTTTTCA
GTAATAACCAAAATATTTTAGGG
Found at i:312963 original size:7 final size:7
Alignment explanation
Indices: 312947--312976 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
312937 GGGAGAATTG
312947 TTAGGGT
1 TTAGGGT
*
312954 TTAAGGT
1 TTAGGGT
312961 TTAGGGT
1 TTAGGGT
312968 TTAGGGT
1 TTAGGGT
312975 TT
1 TT
312977 TTAGCAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:314829 original size:20 final size:22
Alignment explanation
Indices: 314804--314847 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
314794 TAAAAAAAAA
314804 TACCTAAAACATT-AT-TTTTT
1 TACCTAAAACATTAATATTTTT
314824 TACCTAAAACATTAATATTTTT
1 TACCTAAAACATTAATATTTTT
314846 TA
1 TA
314848 ATATTTCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.59
21 2 0.09
22 7 0.32
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.48
Consensus pattern (22 bp):
TACCTAAAACATTAATATTTTT
Found at i:314981 original size:21 final size:21
Alignment explanation
Indices: 314948--314987 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
314938 TAAAACGCCC
*
314948 AATAATAACATTTTCGGTAAA
1 AATAATAACATTTTAGGTAAA
* *
314969 AATACTAATATTTTAGGTA
1 AATAATAACATTTTAGGTA
314988 TTATTTACTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (21 bp):
AATAATAACATTTTAGGTAAA
Found at i:321342 original size:2 final size:2
Alignment explanation
Indices: 321335--321372 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
321325 CAATTTTGTA
321335 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
321373 TATGAATTTA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:322608 original size:50 final size:52
Alignment explanation
Indices: 322506--322640 Score: 220
Period size: 50 Copynumber: 2.6 Consensus size: 52
322496 TGAGTGGTAT
*
322506 TTGATACAAATTACAATGCACTACTCAAAAAAATTAATAAGTTAAAATTTAA
1 TTGATACAAATTACAGTGCACTACTCAAAAAAATTAATAAGTTAAAATTTAA
* *
322558 TTGATACAAATTACAGTGCACTTCT-AAAAAAA-TATTAAGTTAAAATTTAA
1 TTGATACAAATTACAGTGCACTACTCAAAAAAATTAATAAGTTAAAATTTAA
*
322608 TTGATACAAATTTCAGTGCACTACTCAAAAAAA
1 TTGATACAAATTACAGTGCACTACTCAAAAAAA
322641 ATAGTGCAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
50 40 0.52
51 14 0.18
52 23 0.30
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (52 bp):
TTGATACAAATTACAGTGCACTACTCAAAAAAATTAATAAGTTAAAATTTAA
Found at i:322657 original size:2 final size:2
Alignment explanation
Indices: 322652--322723 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
322642 TAGTGCAATC
322652 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
322694 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
322724 TATTTATTTG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:322914 original size:6 final size:6
Alignment explanation
Indices: 322905--323075 Score: 306
Period size: 6 Copynumber: 28.5 Consensus size: 6
322895 ATTGTATTGT
322905 ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC
1 ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC
322953 ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC
1 ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC
323001 ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC
1 ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC ATTGGC
* * * *
323049 ATTCGC ATTCGC ATTCGC ATTCGC ATT
1 ATTGGC ATTGGC ATTGGC ATTGGC ATT
323076 CCCATTCGCA
Statistics
Matches: 164, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 164 1.00
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.34
Consensus pattern (6 bp):
ATTGGC
Found at i:323076 original size:6 final size:6
Alignment explanation
Indices: 322909--323185 Score: 284
Period size: 6 Copynumber: 46.2 Consensus size: 6
322899 TATTGTATTG
* * * * * * * *
322909 GCATTG GCATTG GCATTG GCATTG GCATTG GCATTG GCATTG GCATTG
1 GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC
* * * * * * * *
322957 GCATTG GCATTG GCATTG GCATTG GCATTG GCATTG GCATTG GCATTG
1 GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC
* * * * * * *
323005 GCATTG GCATTG GCATTG GCATTG GCATTG GCATTG GCATTG GCATTC
1 GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC
* * *
323053 GCATTC GCATTC GCATTC GCATTC CCATTC GCATTC CCATTC CCATTC
1 GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC
* * * *
323101 CCATTC CCATTC GCATTC GCATTC GCATTC GCAATC GCAATC GCATTC
1 GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC
323149 GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC G
1 GCATTC GCATTC GCATTC GCATTC GCATTC GCATTC G
323186 TATTAGTATT
Statistics
Matches: 264, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 264 1.00
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.32
Consensus pattern (6 bp):
GCATTC
Found at i:331256 original size:17 final size:18
Alignment explanation
Indices: 331221--331266 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
331211 TTTATTAAAT
*
331221 AATTTAT-ATTTATATTA
1 AATTTATAATATATATTA
331238 AATTTATAATATATA-TA
1 AATTTATAATATATATTA
331255 AATATTA-AATAT
1 AAT-TTATAATAT
331267 TAAAACTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTTATAATATATATTA
Found at i:335467 original size:30 final size:29
Alignment explanation
Indices: 335433--335738 Score: 163
Period size: 30 Copynumber: 10.2 Consensus size: 29
335423 TTATTTAATT
335433 TATTTTATTCTTATCTTAACTAAAAATATA
1 TATTTTATTCTTATCTTAACTAAAAA-ATA
* *
335463 TATTTTAATCTTATCTTAACTTATAAAATA
1 TATTTTATTCTTATCTTAAC-TAAAAAATA
* * *
335493 TATTTTATTCCTACCTTAACTTAAAAATA
1 TATTTTATTCTTATCTTAACTAAAAAATA
*** *
335522 TATTTTATT-TTATCTTAACTTGTTACATA
1 TATTTTATTCTTATCTTAAC-TAAAAAATA
* * **
335551 T-TTATATTCTTAAT-TTAAATTATTAAATA
1 TATTTTATTCTT-ATCTT-AACTAAAAAATA
* * * * **
335580 TATTATATTATTACCTTAAATTATTAAATA
1 TATTTTATTCTTATCTT-AACTAAAAAATA
**
335610 T-TATTTATTCTTATCTTAACTTGAAAATGCA
1 TAT-TTTATTCTTATCTTAACTAAAAAAT--A
* * *
335641 TTTTTTATTTTTATTTTAA-TATATATATTAATA
1 TATTTTATTCTTATCTTAACTA-A-A-A--AATA
* * * * *
335674 TGTTTTATTCTTATTTTAATTTAGAAATA
1 TATTTTATTCTTATCTTAACTAAAAAATA
* *
335703 TATTTTATTTTTATCTTAACTATAAAAAAA
1 TATTTTATTCTTATCTTAACTA-AAAAATA
335733 TATTTT
1 TATTTT
335739 TTTATTTTAA
Statistics
Matches: 217, Mismatches: 41, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
28 14 0.06
29 64 0.29
30 91 0.42
31 22 0.10
32 2 0.01
33 20 0.09
34 1 0.00
35 3 0.01
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.54
Consensus pattern (29 bp):
TATTTTATTCTTATCTTAACTAAAAAATA
Found at i:335581 original size:117 final size:121
Alignment explanation
Indices: 335460--335738 Score: 277
Period size: 117 Copynumber: 2.3 Consensus size: 121
335450 AACTAAAAAT
* *
335460 ATATATTTTAATCTTATCTTAACTTATAAAATATATTTTATTCCTACCTTAACTTAAAAAT-ATA
1 ATATATTTTATTATTATCTTAACTTATAAAATATATTTTATTCCTACCTTAACTTAAAAATCATA
* * *
335524 TTTTA-TTTTATCTTAACT-TGT-TA-CATAT-TTATATTCTTAATTTAAATTATTAA
66 TTTTATTTTTATCTTAA-TATATATATAATATGTTATATTCTTAATTTAAATTA-GAA
* * * * * * *
335577 ATATATTATATTATTACCTTAAATTATTAAATAT-TATTTATTCTTATCTTAACTTGAAAATGCA
1 ATATATTTTATTATTATCTTAACTTATAAAATATAT-TTTATTCCTACCTTAACTTAAAAAT-CA
* * * * *
335641 TTTTTTATTTTTATTTTAATATATATATTAATATGTTTTATTCTTATTTTAATTTAGAA
64 TATTTTATTTTTATCTTAATATATATA-TAATATGTTATATTCTTAATTTAAATTAGAA
* *
335700 ATATATTTTATTTTTATCTTAAC-TATAAAAAAATATTTT
1 ATATATTTTATTATTATCTTAACTTAT-AAAATATATTTT
335739 TTTATTTTAA
Statistics
Matches: 128, Mismatches: 23, Indels: 16
0.77 0.14 0.10
Matches are distributed among these distances:
116 1 0.01
117 50 0.39
119 8 0.06
120 12 0.09
121 2 0.02
122 3 0.02
123 33 0.26
124 19 0.15
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.54
Consensus pattern (121 bp):
ATATATTTTATTATTATCTTAACTTATAAAATATATTTTATTCCTACCTTAACTTAAAAATCATA
TTTTATTTTTATCTTAATATATATATAATATGTTATATTCTTAATTTAAATTAGAA
Found at i:335681 original size:33 final size:31
Alignment explanation
Indices: 335643--335759 Score: 103
Period size: 33 Copynumber: 3.7 Consensus size: 31
335633 AAAATGCATT
* *
335643 TTTTATTTTTATTTTAATATATATATTAATATG
1 TTTTATTTTTATTTTAATATATAGA--AATATA
*
335676 TTTTATTCTTATTTTAAT-T-TAGAAATATA
1 TTTTATTTTTATTTTAATATATAGAAATATA
* * * *
335705 TTTTATTTTTATCTTAACTATAAAAAAATATTT
1 TTTTATTTTTATTTTAA-TATATAGAAATA-TA
* *
335738 TTTTATTTTAATTTTAAAATAT
1 TTTTATTTTTATTTTAATATAT
335760 TATAAAAATA
Statistics
Matches: 68, Mismatches: 12, Indels: 9
0.76 0.13 0.10
Matches are distributed among these distances:
29 20 0.29
30 1 0.01
31 4 0.06
32 10 0.15
33 33 0.49
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.60
Consensus pattern (31 bp):
TTTTATTTTTATTTTAATATATAGAAATATA
Found at i:336150 original size:11 final size:11
Alignment explanation
Indices: 336128--336157 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
336118 ATAAATATAT
336128 TAAATT-AAAA
1 TAAATTAAAAA
336138 TAAATTAAAAA
1 TAAATTAAAAA
336149 TAAATTAAA
1 TAAATTAAA
336158 TCCTCCAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAATTAAAAA
Found at i:336789 original size:21 final size:21
Alignment explanation
Indices: 336738--336790 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
336728 ATTATGACTA
336738 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
336759 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
*
336780 TCGTAATGCGA
1 TCGCAATGCGA
336791 ATTTGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:336843 original size:19 final size:19
Alignment explanation
Indices: 336819--336855 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
336809 CGCGCAATGC
336819 GAATTTGGAAAATCGCAAT
1 GAATTTGGAAAATCGCAAT
336838 GAATTTGGAAAATCGCAA
1 GAATTTGGAAAATCGCAA
336856 CGCGGTACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (19 bp):
GAATTTGGAAAATCGCAAT
Found at i:336874 original size:20 final size:20
Alignment explanation
Indices: 336850--336942 Score: 114
Period size: 20 Copynumber: 4.7 Consensus size: 20
336840 ATTTGGAAAA
* *
336850 TCGCAACGCGGTACTGACTA
1 TCGCAACGCGATACTGACTT
336870 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* * *
336890 TCGCAACTCGATACTTAATT
1 TCGCAACGCGATACTGACTT
* *
336910 TCGCAACTCAATACTGACTT
1 TCGCAACGCGATACTGACTT
*
336930 TCGCAACGAGATA
1 TCGCAACGCGATA
336943 ATACATAATC
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:337167 original size:22 final size:22
Alignment explanation
Indices: 337129--337172 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
337119 CACTCTCTCA
*
337129 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
* *
337151 CCCATCTCCGGCAAAATTCGTC
1 CCCATCTCCGACAAAATCCGTC
337173 TATCTCCATC
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:0.23, C:0.43, G:0.14, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:337414 original size:14 final size:14
Alignment explanation
Indices: 337395--337421 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
337385 ACGCGAAATG
337395 AAAATCGCAACGAC
1 AAAATCGCAACGAC
337409 AAAATCGCAACGA
1 AAAATCGCAACGA
337422 GATTTTATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.26, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:337493 original size:20 final size:20
Alignment explanation
Indices: 337435--337484 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
337425 TTTATTCTCT
* **
337435 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
337455 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
*
337475 TGTTGCGATT
1 CGTTGCGATT
337485 TTTATTTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:338834 original size:18 final size:18
Alignment explanation
Indices: 338813--338860 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
338803 TCCACTTCGG
*
338813 GAGCCATCATCTCACCCA
1 GAGCCATCACCTCACCCA
*
338831 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
338849 GAGCCATCACCT
1 GAGCCATCACCT
338861 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:339429 original size:20 final size:19
Alignment explanation
Indices: 339406--339461 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
339396 CGCAACATGA
339406 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGC-G
* * *
339426 AAATGGCTAGCGCAATGCG
1 AAATGACTATCGCAACGCG
**
339445 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
339462 ACAAAATCGC
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (19 bp):
AAATGACTATCGCAACGCG
Found at i:339458 original size:19 final size:19
Alignment explanation
Indices: 339436--339497 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
339426 AAATGGCTAG
339436 CGCAATGCGAAATGAAAAT
1 CGCAATGCGAAATGAAAAT
*
339455 CGCAA--CG--A-CAAAAT
1 CGCAATGCGAAATGAAAAT
*
339469 CGCAACGCGAAATGAAAAT
1 CGCAATGCGAAATGAAAAT
339488 CGCAATGCGA
1 CGCAATGCGA
339498 TTTGTGTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (19 bp):
CGCAATGCGAAATGAAAAT
Found at i:339569 original size:20 final size:20
Alignment explanation
Indices: 339523--339609 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
339513 GCGATTTTGT
**
339523 CGTTGCGATTTTCATTTC-G
1 CGTTGCGATAGTCATTTCTG
* *
339542 CATTGCGATAGCCATTTCTG
1 CGTTGCGATAGTCATTTCTG
*
339562 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCTG
339582 CGTTGCGATAGTCATTT-TCG
1 CGTTGCGATAGTCATTTCT-G
339602 CGTTGCGA
1 CGTTGCGA
339610 AAGTAAGTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.24
20 44 0.76
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCTG
Found at i:339620 original size:20 final size:19
Alignment explanation
Indices: 339536--339635 Score: 83
Period size: 20 Copynumber: 5.1 Consensus size: 19
339526 TGCGATTTTC
* * **
339536 ATTTCGCATTGCGATAGCC
1 ATTTCGCGTTGCGAAAGTA
* *
339555 ATTTCTGCGTTGCGATAGTC
1 ATTTC-GCGTTGCGAAAGTA
*
339575 ATTTCCGCGTTGCGATAGTCA
1 ATTT-CGCGTTGCGAAAGT-A
*
339596 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
339615 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
339635 A
1 A
339636 ACTATTCTTC
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.09
20 60 0.86
21 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:339627 original size:40 final size:40
Alignment explanation
Indices: 339536--339629 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
339526 TGCGATTTTC
* * *
339536 ATTT-CGCATTGCGATAGCCATTTCTGCGTTGCGATAGTC
1 ATTTCCGCGTTGCGATAGCCATTTCTGCGTTGCGAAAGTA
*
339575 ATTTCCGCGTTGCGATAGTCATTT-TCGCGTTGCGAAAGTA
1 ATTTCCGCGTTGCGATAGCCATTTCT-GCGTTGCGAAAGTA
*
339615 AGTTT-CGTGTTGCGA
1 A-TTTCCGCGTTGCGA
339630 AAGTAAACTA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
39 5 0.11
40 39 0.83
41 3 0.06
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (40 bp):
ATTTCCGCGTTGCGATAGCCATTTCTGCGTTGCGAAAGTA
Found at i:340009 original size:21 final size:21
Alignment explanation
Indices: 339972--340036 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
339962 GCCCGACTCA
*
339972 CCTATCATTCCTCAAGAGTCC
1 CCTATCATCCCTCAAGAGTCC
** *
339993 CCT-TCAATCGTTCAAGAGGCC
1 CCTATC-ATCCCTCAAGAGTCC
340014 CCTATCATCCCTCAAGAGTCC
1 CCTATCATCCCTCAAGAGTCC
340035 CC
1 CC
340037 CCCACCGTTC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
20 2 0.06
21 31 0.89
22 2 0.06
ACGTcount: A:0.23, C:0.40, G:0.12, T:0.25
Consensus pattern (21 bp):
CCTATCATCCCTCAAGAGTCC
Found at i:340063 original size:41 final size:42
Alignment explanation
Indices: 339973--340063 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 42
339963 CCCGACTCAC
* * * *
339973 CTATCATTCCTCAAGAGTCCCCTTCAATCGTTCAAGAGGCCC
1 CTATCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
*
340015 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTATCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
*
340056 CTGTCATC
1 CTATCATC
340064 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 22 0.51
42 21 0.49
ACGTcount: A:0.23, C:0.40, G:0.14, T:0.23
Consensus pattern (42 bp):
CTATCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:341683 original size:34 final size:35
Alignment explanation
Indices: 341620--341687 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
341610 CAGACTATCG
*
341620 CAACACGAAACCGACAAATCGCAATGAGAAAATCA
1 CAACACGAAACCGACAAATCGCAACGAGAAAATCA
* *
341655 CAACACGAAACTGAC-TATCGCAACGAGAAAATC
1 CAACACGAAACCGACAAATCGCAACGAGAAAATC
341688 GCAATGCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.49, C:0.26, G:0.15, T:0.10
Consensus pattern (35 bp):
CAACACGAAACCGACAAATCGCAACGAGAAAATCA
Found at i:341727 original size:20 final size:20
Alignment explanation
Indices: 341704--341747 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
341694 CGATTTTTCA
341704 TTTCAAATTGCGATAGCCAT
1 TTTCAAATTGCGATAGCCAT
***
341724 TTTCGCGTTGCGATAGCCAT
1 TTTCAAATTGCGATAGCCAT
341744 TTTC
1 TTTC
341748 GCGTTGCGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
TTTCAAATTGCGATAGCCAT
Found at i:341748 original size:20 final size:20
Alignment explanation
Indices: 341711--341757 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
341701 TCATTTCAAA
341711 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
341731 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
341751 TTGCGAT
1 TTGCGAT
341758 TTCCCCGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:342020 original size:20 final size:21
Alignment explanation
Indices: 341976--342024 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
341966 ATAGTCAGTA
*
341976 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
341997 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
342017 TCGCATTG
1 TCGCATTG
342025 TGAATTAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:342223 original size:12 final size:12
Alignment explanation
Indices: 342204--342237 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
342194 CTCTCCGGCG
342204 ACATCCGTTCCT
1 ACATCCGTTCCT
*
342216 ATATCCGTTCCT
1 ACATCCGTTCCT
342228 ACATCC-TTCC
1 ACATCCGTTCC
342238 CCATTCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:343026 original size:12 final size:12
Alignment explanation
Indices: 343009--343033 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
342999 ATATAATCCT
343009 GAAGAAGAAAAA
1 GAAGAAGAAAAA
343021 GAAGAAGAAAAA
1 GAAGAAGAAAAA
343033 G
1 G
343034 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:345317 original size:19 final size:19
Alignment explanation
Indices: 345295--345392 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
345285 GGAAATTACT
345295 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
345314 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
345328 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
345347 ATTGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
345361 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
345380 ATCGCAATGCGAA
1 ATCGCAATGCGAA
345393 TTTAGTTTCG
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 18 0.30
15 4 0.07
16 2 0.03
17 2 0.03
18 4 0.07
19 31 0.51
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:345392 original size:33 final size:33
Alignment explanation
Indices: 345296--345395 Score: 148
Period size: 33 Copynumber: 3.0 Consensus size: 33
345286 GAAATTACTA
* *
345296 TCGCAATGCGAAATGAAAATCGCAACGAGAGA-A
1 TCGCAATGCGAAATGAAAATCGCAACGCGA-ATT
*
345329 TCGCAATGCGAAATGAAAATTGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
345362 TCGCAATGCGAAATGAAAATCGCAATGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
345395 T
1 T
345396 AGTTTCGCGT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 1 0.02
33 60 0.98
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:345443 original size:19 final size:19
Alignment explanation
Indices: 345419--345510 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
345409 AATTTTGTCA
345419 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
345438 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
345452 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
345471 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
*
345485 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
345504 TTGCGAT
1 TTGCGAT
345511 AGTACTTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 20 0.34
16 6 0.10
17 6 0.10
19 26 0.45
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:345455 original size:14 final size:14
Alignment explanation
Indices: 345436--345492 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
345426 TTTCATTTCG
345436 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
345450 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
345469 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
345483 CGTTGCGATT
1 CGTTGCGATT
345493 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:345456 original size:33 final size:33
Alignment explanation
Indices: 345419--345510 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
345409 AATTTTGTCA
345419 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
345452 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
345485 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
345511 AGTACTTTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:345636 original size:14 final size:14
Alignment explanation
Indices: 345617--345653 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
345607 CATCAATTAA
345617 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
345631 ACAAATCACCTTTT
1 ACAAATCAACTTTT
345645 ACAAATCAA
1 ACAAATCAA
345654 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:347479 original size:90 final size:90
Alignment explanation
Indices: 347303--347486 Score: 282
Period size: 90 Copynumber: 2.0 Consensus size: 90
347293 ATTTCAAACT
*
347303 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
347368 AGAATTGGCAGCAACCAAATAAATTTAC
63 AGAATTGGCAGCAACCAAATAAATTTAC
347396 TTCAACCAAAAGA-AAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
347459 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCAAATAAATTTAC
347486 T
1 T
347487 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
90 41 0.48
92 5 0.06
93 13 0.15
94 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCAAATAAATTTAC
Found at i:348422 original size:174 final size:173
Alignment explanation
Indices: 348132--348478 Score: 660
Period size: 174 Copynumber: 2.0 Consensus size: 173
348122 ATTGTCGCAG
348132 ATGGTATTAGTCTTCCCAATCCAACAGACGTTTCCTCTTCCAGGAATACCTGGGAATATCATTTG
1 ATGGTATTAGTCTTCCCAATCCAACAGACGTTTCCTCTTCCAGGAATACCTGGGAATATCATTTG
348197 AAGTTTTTATTGCATATGTCTTCATGGCGGGAAAGGCCTCGAATATCCAAATCTACAAACAATAT
66 AAGTTTTTATTGCA-ATGTCTTCATGGCGGGAAAGGCCTCGAATATCCAAATCTACAAACAATAT
348262 AACAAACATTAGTAATTATTAAATAATTAATTATAATTTTGAAT
130 AACAAACATTAGTAATTATTAAATAATTAATTATAATTTTGAAT
348306 ATGGTATTAAGTCTTCCCAATCCAACAGACGTTTCCTCTTCCAGGAAATACCTGGGAATATCATT
1 ATGGTATT-AGTCTTCCCAATCCAACAGACGTTTCCTCTTCCAGG-AATACCTGGGAATATCATT
348371 TGAAGTTTTTATTGC-ATGTCTTCATGGCGGGAAAGGCCTCGAATATCCAAATCTACAAACAATA
64 TGAAGTTTTTATTGCAATGTCTTCATGGCGGGAAAGGCCTCGAATATCCAAATCTACAAACAATA
348435 TAACAAACATTAGTAATTATTAAATAATTAATTATAATTTTGAA
129 TAACAAACATTAGTAATTATTAAATAATTAATTATAATTTTGAA
348479 AACATTATAT
Statistics
Matches: 171, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
174 101 0.59
175 36 0.21
176 34 0.20
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (173 bp):
ATGGTATTAGTCTTCCCAATCCAACAGACGTTTCCTCTTCCAGGAATACCTGGGAATATCATTTG
AAGTTTTTATTGCAATGTCTTCATGGCGGGAAAGGCCTCGAATATCCAAATCTACAAACAATATA
ACAAACATTAGTAATTATTAAATAATTAATTATAATTTTGAAT
Found at i:349224 original size:20 final size:19
Alignment explanation
Indices: 349193--349253 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
349183 TCTTTTGGTT
349193 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
349212 GATAATGAGAATCGCAATGCA
1 GA-AATGAAAATCGCAACG-A
**
349233 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
349252 GA
1 GA
349254 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.14
20 27 0.77
21 3 0.09
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:349275 original size:33 final size:33
Alignment explanation
Indices: 349218--349314 Score: 135
Period size: 33 Copynumber: 2.9 Consensus size: 33
349208 ACGAGATAAT
349218 GAGAATCGCAA-TGCAGAAATGACTATCGCAACGA
1 GAGAATCGCAACT-C-GAAATGACTATCGCAACGA
*
349252 GAGAATCGCAACTCGAAATGACTATTGCAACGA
1 GAGAATCGCAACTCGAAATGACTATCGCAACGA
*
349285 GAGAATCGCAACGCGAAATGA-TAATCGCAA
1 GAGAATCGCAACTCGAAATGACT-ATCGCAA
349315 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
32 1 0.02
33 44 0.76
34 12 0.21
35 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (33 bp):
GAGAATCGCAACTCGAAATGACTATCGCAACGA
Done.