Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, 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: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 14 of 18
Found at i:5666706 original size:21 final size:21
Alignment explanation
Indices: 5666664--5666707 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5666654 CAAATAAAAA
*
5666664 AATCATTAATTACAAATGTAT
1 AATCATTAATTACAAATATAT
*
5666685 AATCATTAATTACAAGTATAT
1 AATCATTAATTACAAATATAT
5666706 AA
1 AA
5666708 ATTTAGATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (21 bp):
AATCATTAATTACAAATATAT
Found at i:5667355 original size:252 final size:249
Alignment explanation
Indices: 5666779--5667658 Score: 993
Period size: 252 Copynumber: 3.5 Consensus size: 249
5666769 AATTACAAGT
* * * * * *
5666779 ATATAAATGTAGATGA-TATGTTTTCACTAAAATTATGTTTATATTGTTTAAATTGATTTATTA-
1 ATATAAATGTAAATGATTA-ATTTTCACTAAAAGTATGTTTATTTTATTTAAATTGACTTATTAC
* * *
5666842 AGATAACTCTTACACATTTACATCAATATTTTAACTATATTTATTTCAACTTTATGAATTTTTAT
65 AG-TAACTCTTACACA-TTACGTCAATATTTTAACAATATTTATTTCAACTTTATGATTTTTTAT
* ** * * * *
5666907 GTTTATTCTTATAATTTTTTGTCAATATTTTTAAATGGCTAATCTTCATTATAAGTTTTTTCATT
128 GTTTATTCTTATAAATTTAAGTCAAAATTTTTAAATGGCTAATTTTCATTACAAG-----T-GTT
* * *
5666972 TTTATTTTTATTTTTATACATTTATAAATTAACATGTGGAAATGGTTAAATTGTTTTT-CTTGAG
187 TTTATTTTTA-TTTTATACATTTATAAATTAAAATTTGAAAATGG-TAAATT-TTTTTGCTTGAG
5667036 A
249 A
* * *
5667037 ATATAAATGTAAATGATTAATTTTCACTAAAAGTATGTTTACTTTATTTATATTGAATTATTACA
1 ATATAAATGTAAATGATTAATTTTCACTAAAAGTATGTTTATTTTATTTAAATTGACTTATTACA
*
5667102 GTAACTCTTACACATGTACGTCAATATTTTAACAATGTTTATTTCAACTTTATGATTTTTTTATG
66 GTAACTCTTACACAT-TACGTCAATATTTTAACAATATTTATTTCAACTTTATGA-TTTTTTATG
* * * * **
5667167 TTTATTGTTATAAATTTACGTCAACATTTTCAAAAAGCTAATTTTCATTACAAGTGTTTTTATTT
129 TTTATTCTTATAAATTTAAGTCAAAATTTTTAAATGGCTAATTTTCATTACAAGTGTTTTTATTT
5667232 TTATTTTATACATTTATAAATTAAAATTTGAAAATGGCTAAATTTTTTTGCTTGAGA
194 TTATTTTATACATTTATAAATTAAAATTTGAAAATGG-TAAATTTTTTTGCTTGAGA
* ** * * *
5667289 ATATAAATATAAATGATTAATTTTTGCTAAAAGTATATTTATTTTGA-CTAAATTGACTTGTTAC
1 ATATAAATGTAAATGATTAATTTTCACTAAAAGTATGTTTATTTT-ATTTAAATTGACTTATTAC
* * *
5667353 AGTAACTCTTACATATTGACGTCAATATTTTAACAATATTTATGTCAAATTTATG-TTTTTTATG
65 AGTAACTCTTACACATT-ACGTCAATATTTTAACAATATTTATTTCAACTTTATGATTTTTTATG
* * * *
5667417 CTCATTCTTATAACTTTATAG-CAAAATTTTTAAATGGCTAATTTTCATGACAAGTGTTTTTATT
129 TTTATTCTTATAAATTTA-AGTCAAAATTTTTAAATGGCTAATTTTCATTACAAGTGTTTTTATT
* * *
5667481 TTTATTCTTATACATTTATATATT-AAATTTTATAAATGGTAAAATTTTTTTAGCTCGA-A
193 TTTATT-TTATACATTTATAAATTAAAATTTGA-AAATGGT-AAATTTTTTT-GCTTGAGA
* * * * **
5667540 ATTATAAATGCAAATAATTAATTTTCACTAAAAGTATGTTTATATTATTTAAATTGTCTTGCTAC
1 A-TATAAATGTAAATGATTAATTTTCACTAAAAGTATGTTTATTTTATTTAAATTGACTTATTAC
* * * *
5667605 AGTAACTCTTATACACTTAGGCCAATATTTTAACAATATTTATTGCAACTTTAT
65 AGTAACTCTTACACA-TTACGTCAATATTTTAACAATATTTATTTCAACTTTAT
5667659 TAGTCTGCAC
Statistics
Matches: 537, Mismatches: 70, Indels: 36
0.84 0.11 0.06
Matches are distributed among these distances:
250 75 0.14
251 42 0.08
252 246 0.46
253 15 0.03
254 1 0.00
257 1 0.00
258 101 0.19
259 56 0.10
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (249 bp):
ATATAAATGTAAATGATTAATTTTCACTAAAAGTATGTTTATTTTATTTAAATTGACTTATTACA
GTAACTCTTACACATTACGTCAATATTTTAACAATATTTATTTCAACTTTATGATTTTTTATGTT
TATTCTTATAAATTTAAGTCAAAATTTTTAAATGGCTAATTTTCATTACAAGTGTTTTTATTTTT
ATTTTATACATTTATAAATTAAAATTTGAAAATGGTAAATTTTTTTGCTTGAGA
Found at i:5669034 original size:28 final size:28
Alignment explanation
Indices: 5669002--5669084 Score: 139
Period size: 28 Copynumber: 3.0 Consensus size: 28
5668992 GATATTAATG
5669002 AAGAACACAAATATCCATAATAATATTC
1 AAGAACACAAATATCCATAATAATATTC
* *
5669030 AAGAACACAAATTTTCATAATAATATTC
1 AAGAACACAAATATCCATAATAATATTC
*
5669058 AAGAACACAAACATCCATAATAATATT
1 AAGAACACAAATATCCATAATAATATT
5669085 GTTGTCCTAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.53, C:0.17, G:0.04, T:0.27
Consensus pattern (28 bp):
AAGAACACAAATATCCATAATAATATTC
Found at i:5674473 original size:27 final size:27
Alignment explanation
Indices: 5674435--5674486 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
5674425 CTAGTGCATG
* *
5674435 TGTTGCAAAAAATATTATTACATGTTA
1 TGTTGAAAAAAAAATTATTACATGTTA
5674462 TGTTGAAAAAAAAATTATTACATGT
1 TGTTGAAAAAAAAATTATTACATGT
5674487 CAAATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (27 bp):
TGTTGAAAAAAAAATTATTACATGTTA
Found at i:5675349 original size:34 final size:33
Alignment explanation
Indices: 5675311--5675417 Score: 106
Period size: 34 Copynumber: 3.2 Consensus size: 33
5675301 GTAGATGTCG
*
5675311 CACGCTAAGGTCAAAGTTTCAATACTAGATATTA
1 CACGCTAAGGTCAAAGTTT-AATACCAGATATTA
* * * *
5675345 CACGCCAAGGTCAAAGCTTTAGTACCAAATGTTA
1 CACGCTAAGGTCAAAG-TTTAATACCAGATATTA
* * * *
5675379 TAAGCTTAGGTCAAAGTGTTAACACCAGATATTA
1 CACGCTAAGGTCAAAGT-TTAATACCAGATATTA
5675413 CACGC
1 CACGC
5675418 CAAATCTTCC
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
33 1 0.02
34 52 0.93
35 3 0.05
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (33 bp):
CACGCTAAGGTCAAAGTTTAATACCAGATATTA
Found at i:5682737 original size:203 final size:203
Alignment explanation
Indices: 5682380--5682753 Score: 563
Period size: 203 Copynumber: 1.8 Consensus size: 203
5682370 AGAGAATTAA
* * *
5682380 GAGAAAATCAAGATAAAATATTTTATAACGTTATAAATATCCTAAAAGAATCAAAGACTATATCA
1 GAGAAAATCAAGATAAAATATTTTATAACGTTATAAATATCCTAAAAGAATCAAAAACCAAATCA
* * *
5682445 AGATAAAATTATTTTTCTAATGTTACAAAATATTATAACGGCAAAATGTGAATCAAAGACTAATT
66 AGATAAAATTATTTTTCTAACGTTACAAAATATTATAACGGCAAAATATGAATCAAAAACTAATT
* * *
5682510 CTTTCTTTACATTAAAACGACTAAGTCAAGGTAAGGTAAAATAATTATGAAGAGATACGGTTGAA
131 CTTTCTTCACATGAAAAAGACTAAGTCAAGGTAAGGTAAAATAATTATGAAGAGATACGGTTGAA
5682575 AGAATCGT
196 AGAATCGT
* * * *
5682583 GAGAAAATCAATATAAAATATTTTGTAACGTTATAAATATCTTAAAAGAATTAAAAACCAAATCA
1 GAGAAAATCAAGATAAAATATTTTATAACGTTATAAATATCCTAAAAGAATCAAAAACCAAATCA
* * *
5682648 AGATAAAA-TATTTTGTCTAACGTTACAACATATATATAACGGTAGAATATGAATCAAAAACTAA
66 AGATAAAATTATTTT-TCTAACGTTACAAAATAT-TATAACGGCAAAATATGAATCAAAAACTAA
*
5682712 TTCTTTCTTCACA-GAAAAAGACTAAGTCTAGGTAAGGTAAAA
129 TTCTTTCTTCACATGAAAAAGACTAAGTCAAGGTAAGGTAAAA
5682754 AATAAAATTG
Statistics
Matches: 152, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
202 6 0.04
203 108 0.71
204 38 0.25
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (203 bp):
GAGAAAATCAAGATAAAATATTTTATAACGTTATAAATATCCTAAAAGAATCAAAAACCAAATCA
AGATAAAATTATTTTTCTAACGTTACAAAATATTATAACGGCAAAATATGAATCAAAAACTAATT
CTTTCTTCACATGAAAAAGACTAAGTCAAGGTAAGGTAAAATAATTATGAAGAGATACGGTTGAA
AGAATCGT
Found at i:5684680 original size:356 final size:350
Alignment explanation
Indices: 5683925--5684813 Score: 1165
Period size: 356 Copynumber: 2.5 Consensus size: 350
5683915 GGGATGGTAA
* * * *
5683925 GTATTAATTGTAAAGGTTCTATCTTAGCTTTGAAAAGCTAGTGTTGTTGAGTGGTTATACCTTAC
1 GTATTGATTGTAAAGGTTCTATCTTAACCTTGAAAAGATAGTGTTGTTGAGTGGTTATACCTTAC
* * *
5683990 CAAGTGAAAAGGTAGAGGGGTTAAATCTAAG-TCTTTGAAAATATTGATTGTGAGGGTTATGCTT
66 CAAGTGAAAAGGTAGAGGGGTTAAGTCTAAGCT-TTTGAAAAAACTGATTGTGA-GGTTATGCTT
* * * * *
5684054 TGTCCTAAAAAAACA-TTTTGAGATAATGGATTCTAAACTCCTTAGTGATCCAAGGCCAACTAAA
129 TATCCTAGAAAAGCATTTTTGAGATAATAGATTCTAAACTCCTTAGTGATCTAAGGCCAACTAAA
* * * * * *
5684118 GATTTGTTCAAAATCACTCTTAAAATCAAAATGTTCTTTCATTGAGCTACTTGAGCCTTAAGCTT
194 GATTTCTCCAAAATCACTCTCAAAATCAAAATGCTCTTTCATTAAGCTACTTAAGCCTTAAGCTT
* * * **
5684183 TCTTATTCTTTCAAGACCCTTTATGCTCTTCTTGTATTCATTGTATTATTCAACCTTCTAAAGTT
259 CCTTATTCTTTCAAGACCATTTATGCTCTTCTTGTATTCATTGCATTATTCAACCTTCTAAAGCA
5684248 TGTTAAGCCTTTGTTTTCATCCCCATT
324 TGTTAAGCCTTTGTTTTCATCCCCATT
* * * *
5684275 GTATTGATTGTAAAGGTTTTATCGTAACCTTGAAAAGATATTGTTGTTGAGTAGTTATACCTTAC
1 GTATTGATTGTAAAGGTTCTATCTTAACCTTGAAAAGATAGTGTTGTTGAGTGGTTATACCTTAC
** * *
5684340 CAAGTGAAAAAATAGAGGGGTTAAGTCTAGGCTTTTGAAAAAACTGATTATGAGAGTTATGCTTT
66 CAAGTGAAAAGGTAGAGGGGTTAAGTCTAAGCTTTTGAAAAAACTGATTGTGAG-GTTATGCTTT
* * * * *
5684405 ATCCTAGAGAAGCATTTTTAAGATAATAGATTATAAACTCCTTAGTGATCTAAGGCCAACTCATG
130 ATCCTAGAAAAGCATTTTTGAGATAATAGATTCTAAACTCCTTAGTGATCTAAGGCCAACTAAAG
* * * *
5684470 TTTTCTCCAAGATCACTCTCAAAATGAAAGTGCTCTTTCATTAAGCTACTTAAGCCTTAAGCTTC
195 ATTTCTCCAAAATCACTCTCAAAATCAAAATGCTCTTTCATTAAGCTACTTAAGCCTTAAGCTTC
* * *
5684535 CTTATTCTTTCAAGAGCCTTAATGTTTTGTTTTTCTTGTATTCATTGCATTATTCAACCTTCTAA
260 CTTATTCTTTCAAGA-CC---AT-TTATGCTCTTCTTGTATTCATTGCATTATTCAACCTTCTAA
* * *
5684600 AGGCAT-TTACG-CTTTCTTTTTCATCCTCATT
320 A-GCATGTTAAGCCTTT-GTTTTCATCCCCATT
* * *
5684631 GTATTGATTGTAAAGGTTCTATCTTAACCTTGAAAAAATAGTGTTGTTGAGTGGTTATATCTTAT
1 GTATTGATTGTAAAGGTTCTATCTTAACCTTGAAAAGATAGTGTTGTTGAGTGGTTATACCTTAC
* * *
5684696 TAAGTGAAAAGGTAGAGGGGTTAAGTCTAAGCCTTTGAAAAGACTGATTGTGAGGATTATGCTTT
66 CAAGTGAAAAGGTAGAGGGGTTAAGTCTAAGCTTTTGAAAAAACTGATTGTGAGG-TTATGCTTT
* *
5684761 TTCCTAGAAAAGTATTTTTGAGATAATAGATTCTAAACTCCTTAGTGATCTAA
130 ATCCTAGAAAAGCATTTTTGAGATAATAGATTCTAAACTCCTTAGTGATCTAA
5684814 AGGGGAAAGC
Statistics
Matches: 463, Mismatches: 65, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
349 1 0.00
350 121 0.26
351 114 0.25
352 2 0.00
355 6 0.01
356 217 0.47
357 2 0.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (350 bp):
GTATTGATTGTAAAGGTTCTATCTTAACCTTGAAAAGATAGTGTTGTTGAGTGGTTATACCTTAC
CAAGTGAAAAGGTAGAGGGGTTAAGTCTAAGCTTTTGAAAAAACTGATTGTGAGGTTATGCTTTA
TCCTAGAAAAGCATTTTTGAGATAATAGATTCTAAACTCCTTAGTGATCTAAGGCCAACTAAAGA
TTTCTCCAAAATCACTCTCAAAATCAAAATGCTCTTTCATTAAGCTACTTAAGCCTTAAGCTTCC
TTATTCTTTCAAGACCATTTATGCTCTTCTTGTATTCATTGCATTATTCAACCTTCTAAAGCATG
TTAAGCCTTTGTTTTCATCCCCATT
Found at i:5689167 original size:72 final size:73
Alignment explanation
Indices: 5689091--5689265 Score: 203
Period size: 72 Copynumber: 2.4 Consensus size: 73
5689081 TGAGTCACTG
* *
5689091 CAATTATTATTTCCTGAAGGTGGTTTTCTTC-TCCTTTTCCTTTGAAT-GACAACATCTTGTACT
1 CAATTATTATTCCCTGAAGGTGGTTTTCTTCTTCCTTTT-CTTTGAATAGACAACACCTTGTACT
*
5689154 GATTCAGTA
65 GATTCAATA
* * * * * * *
5689163 CAATTATTACTCCCTGATGGTGGTTTTC-TCTTTCTTTTCTTTGGATAGGCCACACCTTGTGCTG
1 CAATTATTATTCCCTGAAGGTGGTTTTCTTCTTCCTTTTCTTTGAATAGACAACACCTTGTACTG
*
5689227 GTTCAATA
66 ATTCAATA
* *
5689235 CAATTATTATTCCCTGAATGTGGGTTTCTTC
1 CAATTATTATTCCCTGAAGGTGGTTTTCTTC
5689266 GTTTCTTCCT
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
71 9 0.11
72 74 0.87
73 2 0.02
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (73 bp):
CAATTATTATTCCCTGAAGGTGGTTTTCTTCTTCCTTTTCTTTGAATAGACAACACCTTGTACTG
ATTCAATA
Found at i:5694053 original size:1 final size:1
Alignment explanation
Indices: 5694049--5694082 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
5694039 ATGAGAGGGA
5694049 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
5694083 CGGTAAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:5699031 original size:3 final size:3
Alignment explanation
Indices: 5699023--5699077 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
5699013 GACGGAGAGC
* * * * *
5699023 TCT TCT TCT TCT TCT TCT TCT TCA TCT ACC TCC TCT TCT TCT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
5699071 TTT TCT T
1 TCT TCT T
5699078 TTCCGGTGTC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:5704986 original size:62 final size:62
Alignment explanation
Indices: 5704909--5705027 Score: 145
Period size: 62 Copynumber: 1.9 Consensus size: 62
5704899 ACTTACTAAA
* *
5704909 GATGAGAAAAGGGGAAGAA-AAAAGGGTGGAGATCGGAA-AGTATGGAGAGTGGAGACGGGACG
1 GATGAGAAAAGGGGAA-AACAAAAGGGTGGAG-TCGAAAGAGTATGGAGAATGGAGACGGGACG
* * *
5704971 GATGAGAGAAA-GGGAAAACAAGAGGGTGGAGTCTAAAGAGTCTGGAGAATGGAGACG
1 GATGAGA-AAAGGGGAAAACAAAAGGGTGGAGTCGAAAGAGTATGGAGAATGGAGACG
5705028 AGATAGCAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
61 6 0.12
62 40 0.82
63 3 0.06
ACGTcount: A:0.40, C:0.06, G:0.43, T:0.11
Consensus pattern (62 bp):
GATGAGAAAAGGGGAAAACAAAAGGGTGGAGTCGAAAGAGTATGGAGAATGGAGACGGGACG
Found at i:5723795 original size:6 final size:6
Alignment explanation
Indices: 5723780--5723814 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
5723770 CAATATATAT
5723780 AATT-A AATTAA AATTAA AATTAA AATTAA AATTAA
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA
5723815 TAATAATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATTAA
Found at i:5735817 original size:135 final size:134
Alignment explanation
Indices: 5735566--5735819 Score: 332
Period size: 135 Copynumber: 1.9 Consensus size: 134
5735556 GAGATTTCAG
* ** * *
5735566 ATATTTAAGATTTGAATTATTGAGATATTTGAGGATTTTGTTGAGAATTCAGATTATTTCTTGAG
1 ATATTTAAGATTTGAATTATTGAGACATTTGACAATTTCGTTCAGAATTCAGATTATTTCTTGAG
*
5735631 TATTGAGTTTTAGAATACTTGTTCTACATCAAAATGTCTTACACATGTGAATAAGATATTGTGAT
66 TATTGAGTTTTAGAATACTTGTTCTACATCAAAATG-CTTACACATATGAATAAGATATTGTGAT
5735696 ATCAA
130 ATCAA
* *
5735701 ATATTTAAGATTTGAATTCTTGAGACATTTGACAATTTCGTTCAGAATTCTGATTATTTCTTAAG
1 ATATTTAAGATTTGAATTATTGAGACATTTGACAATTTCGTTCAGAATTCAGATTATTTCTT--G
* * * * * *
5735766 GGTTTTGAGTTTTAGCATAGTTGTTCTACATCAGAATG-TTGCA-ATTATGAATAA
64 AGTATTGAGTTTTAGAATACTTGTTCTACATCAAAATGCTTACACA-TATGAATAA
5735820 ACTTTGAAAG
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
134 1 0.01
135 67 0.66
137 34 0.33
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.43
Consensus pattern (134 bp):
ATATTTAAGATTTGAATTATTGAGACATTTGACAATTTCGTTCAGAATTCAGATTATTTCTTGAG
TATTGAGTTTTAGAATACTTGTTCTACATCAAAATGCTTACACATATGAATAAGATATTGTGATA
TCAA
Found at i:5740659 original size:16 final size:17
Alignment explanation
Indices: 5740638--5740671 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5740628 GCATGACCTT
5740638 CAGGGGTG-TGGATTAG
1 CAGGGGTGTTGGATTAG
5740654 CAGGGGTGTTGGATTAG
1 CAGGGGTGTTGGATTAG
5740671 C
1 C
5740672 TTGGATGTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.18, C:0.09, G:0.47, T:0.26
Consensus pattern (17 bp):
CAGGGGTGTTGGATTAG
Found at i:5747770 original size:17 final size:16
Alignment explanation
Indices: 5747728--5747770 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5747718 CTTAAGTTTG
*
5747728 TTTTATTTTTCTTTTC
1 TTTTATTTTTCCTTTC
*
5747744 TTCTTTTTTTTCCTTTC
1 TT-TTATTTTTCCTTTC
5747761 TTTTCATTTT
1 TTTT-ATTTT
5747771 CACCTTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATTTTTCCTTTC
Found at i:5758052 original size:2 final size:2
Alignment explanation
Indices: 5758045--5758090 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
5758035 ATAGAAAATC
* *
5758045 AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT AT GGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
5758087 AT AT
1 AT AT
5758091 GGTTAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.95
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5758089 original size:15 final size:15
Alignment explanation
Indices: 5758045--5758090 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
5758035 ATAGAAAATC
5758045 ATATAT-ATATATAT
1 ATATATAATATATAT
*
5758059 ATATATAATATTTAT
1 ATATATAATATATAT
**
5758074 ATATATGGTATATAT
1 ATATATAATATATAT
5758089 AT
1 AT
5758091 GGTTAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (15 bp):
ATATATAATATATAT
Found at i:5758374 original size:30 final size:29
Alignment explanation
Indices: 5758338--5758412 Score: 91
Period size: 27 Copynumber: 2.6 Consensus size: 29
5758328 GATACGCATG
*
5758338 CATAGTAGTGCCATATCATTCTCATGATGA
1 CATAGTA-TGCCATATCATTATCATGATGA
5758368 CATAGTAT--CATATCATTATCATGATGA
1 CATAGTATGCCATATCATTATCATGATGA
* *
5758395 CATGGTAATGCCACATCA
1 CATAGT-ATGCCATATCA
5758413 ATGTGTCATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 23 0.59
28 2 0.05
29 1 0.03
30 13 0.33
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (29 bp):
CATAGTATGCCATATCATTATCATGATGA
Found at i:5769626 original size:2 final size:2
Alignment explanation
Indices: 5769619--5769653 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5769609 GCTAACATGG
5769619 AT AT 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 AT AT A
5769654 GTCTGCTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5774091 original size:50 final size:50
Alignment explanation
Indices: 5773998--5774094 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
5773988 TGATTCATAT
* **
5773998 AATGATCATTTTGAGAGAAGCCAAAATAAGTAATGATTTTCTCTTTTCAA
1 AATGATCATTTCGAGAGAAGCCAAAATAAGTAATGATGATCTCTTTTCAA
* *
5774048 AATGATCATTTCGAGAGAAGCCAAAATAATTAATGGTGATCTCTTTT
1 AATGATCATTTCGAGAGAAGCCAAAATAAGTAATGATGATCTCTTTT
5774095 TAATAATAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.35
Consensus pattern (50 bp):
AATGATCATTTCGAGAGAAGCCAAAATAAGTAATGATGATCTCTTTTCAA
Found at i:5781486 original size:29 final size:29
Alignment explanation
Indices: 5781454--5781516 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
5781444 TAAATAAAAG
* *
5781454 TAATTTTATTAT-ATTTAATTAAATTTTTA
1 TAATTTTATTATAAATTAAATAAA-TTTTA
*
5781483 TAATTTTATTTTAAATTAAATAAATTTTA
1 TAATTTTATTATAAATTAAATAAATTTTA
5781512 TAATT
1 TAATT
5781517 AATAATTGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TAATTTTATTATAAATTAAATAAATTTTA
Found at i:5793757 original size:27 final size:27
Alignment explanation
Indices: 5793726--5793778 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
5793716 TATTTTGAAA
*
5793726 CTCGAAAATAGTAAATTATTTAACAAG
1 CTCGAAAATACTAAATTATTTAACAAG
*
5793753 CTCGAAAATACTGAATTATTTAACAA
1 CTCGAAAATACTAAATTATTTAACAA
5793779 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.30
Consensus pattern (27 bp):
CTCGAAAATACTAAATTATTTAACAAG
Found at i:5794269 original size:27 final size:26
Alignment explanation
Indices: 5794196--5794288 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 26
5794186 TGACATGGCG
5794196 TGTAACAACTAAAATTTTCAACA-AGATA
1 TGTAACAACT-AAATTTT-AACATAG-TA
* *
5794224 TATAATAACTAAATCTTTAACATAGTA
1 TGTAACAACTAAAT-TTTAACATAGTA
* * *
5794251 TGTAACAATTATAATTTTAATATACTA
1 TGTAACAACTA-AATTTTAACATAGTA
* *
5794278 TGCAATAACTA
1 TGTAACAACTA
5794289 TATCTTCAAC
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
27 36 0.69
28 16 0.31
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (26 bp):
TGTAACAACTAAATTTTAACATAGTA
Found at i:5794290 original size:27 final size:28
Alignment explanation
Indices: 5794227--5794300 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 28
5794217 CAAGATATAT
* *
5794227 AATAACTA-AATCTTTAACATAGTATGT
1 AATAACTATAATCTTTAACATACTATGC
* * *
5794254 AACAATTATAAT-TTTAATATACTATGC
1 AATAACTATAATCTTTAACATACTATGC
*
5794281 AATAACTAT-ATCTTCAACAT
1 AATAACTATAATCTTTAACAT
5794301 GCACTTGAGC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
26 2 0.06
27 31 0.86
28 3 0.08
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.38
Consensus pattern (28 bp):
AATAACTATAATCTTTAACATACTATGC
Found at i:5797385 original size:23 final size:23
Alignment explanation
Indices: 5797359--5797407 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
5797349 AAATTATGAA
*
5797359 GAATAGAATATGGCTCATATTAG
1 GAATAGAACATGGCTCATATTAG
5797382 GAATAGAACATGGCTCATATTAG
1 GAATAGAACATGGCTCATATTAG
5797405 GAA
1 GAA
5797408 GCTTTTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (23 bp):
GAATAGAACATGGCTCATATTAG
Found at i:5844667 original size:80 final size:80
Alignment explanation
Indices: 5844482--5844664 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 80
5844472 NNNNNNNNNN
* *
5844482 TGGTCATTCAATTTATCTCTAAATAAATCTAAATTATTTAGAGATAATATTTATCTTTTGACCAA
1 TGGTCATTCAATTTATCTCTAAATAAATCCAAATAATTTAGAGATAATATTTATCTTTTGACCAA
* *
5844547 TCAAATATTAGCTAT
66 TAAAATATTAACTAT
* * *
5844562 TAGTCATCCAATTTATCTCTAAATAAATCCAAATAATTT-GAAGATAATCTTCATAT-TTTTGAC
1 TGGTCATTCAATTTATCTCTAAATAAATCCAAATAATTTAG-AGATAATATT--TATCTTTTGAC
* *
5844625 CAATTAAAAT-TTAATTGT
63 CAA-TAAAATATTAACTAT
* *
5844643 TGGTCATTTAAATTATCTCTAA
1 TGGTCATTCAATTTATCTCTAA
5844665 TAATTATATT
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
79 1 0.01
80 44 0.51
81 33 0.38
82 8 0.09
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (80 bp):
TGGTCATTCAATTTATCTCTAAATAAATCCAAATAATTTAGAGATAATATTTATCTTTTGACCAA
TAAAATATTAACTAT
Found at i:5844999 original size:18 final size:18
Alignment explanation
Indices: 5844976--5845018 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5844966 GATTCATTCG
5844976 GAAGCATTCGAAGATAGA
1 GAAGCATTCGAAGATAGA
* *
5844994 GAAGCATTCGACGATTGA
1 GAAGCATTCGAAGATAGA
5845012 G-AGCATT
1 GAAGCATT
5845019 TCAGAGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.21
Consensus pattern (18 bp):
GAAGCATTCGAAGATAGA
Found at i:5845086 original size:23 final size:23
Alignment explanation
Indices: 5845060--5845288 Score: 224
Period size: 23 Copynumber: 9.9 Consensus size: 23
5845050 GGTGAAGATC
*
5845060 AAGCAACGGCGAAGTTTGTGATA
1 AAGCAACGGCGAAGTTCGTGATA
5845083 AAGCAACGGCGAAGTTCGTGATA
1 AAGCAACGGCGAAGTTCGTGATA
* * *
5845106 AAGCAACGACGAAATTCGTGATC
1 AAGCAACGGCGAAGTTCGTGATA
* * *
5845129 AAGCAACAGCGAAGTTCATGATC
1 AAGCAACGGCGAAGTTCGTGATA
* *
5845152 AAGTAACGGCGAAGTTTGTGATA
1 AAGCAACGGCGAAGTTCGTGATA
* *
5845175 AATCAACAGCGAAGTTCGTGATA
1 AAGCAACGGCGAAGTTCGTGATA
* ** * * *
5845198 AATCAACGATGAATTTTGTGATC
1 AAGCAACGGCGAAGTTCGTGATA
* *
5845221 AAGCAACAGCGAAGTTCGTGATG
1 AAGCAACGGCGAAGTTCGTGATA
* * *
5845244 AAGCGACGGTGAAGTTCGTGATC
1 AAGCAACGGCGAAGTTCGTGATA
* * *
5845267 AAGACAAAGTCCAAGTTCGTGA
1 AAG-CAACGGCGAAGTTCGTGA
5845289 CTCTTGAAAN
Statistics
Matches: 166, Mismatches: 39, Indels: 1
0.81 0.19 0.00
Matches are distributed among these distances:
23 153 0.92
24 13 0.08
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (23 bp):
AAGCAACGGCGAAGTTCGTGATA
Found at i:5845127 original size:46 final size:46
Alignment explanation
Indices: 5845060--5845288 Score: 262
Period size: 46 Copynumber: 5.0 Consensus size: 46
5845050 GGTGAAGATC
* *
5845060 AAGCAACGGCGAAGTTTGTGATAAAGCAACGGCGAAGTTCGTGATA
1 AAGCAACGGCGAAGTTTGTGATCAAGCAACAGCGAAGTTCGTGATA
* * * * *
5845106 AAGCAACGACGAAATTCGTGATCAAGCAACAGCGAAGTTCATGATC
1 AAGCAACGGCGAAGTTTGTGATCAAGCAACAGCGAAGTTCGTGATA
* * *
5845152 AAGTAACGGCGAAGTTTGTGATAAATCAACAGCGAAGTTCGTGATA
1 AAGCAACGGCGAAGTTTGTGATCAAGCAACAGCGAAGTTCGTGATA
* ** * *
5845198 AATCAACGATGAATTTTGTGATCAAGCAACAGCGAAGTTCGTGATG
1 AAGCAACGGCGAAGTTTGTGATCAAGCAACAGCGAAGTTCGTGATA
* * * *
5845244 AAGCGACGGTGAAGTTCGTGATCAAGACAA-AGTCCAAGTTCGTGA
1 AAGCAACGGCGAAGTTTGTGATCAAG-CAACAG-CGAAGTTCGTGA
5845289 CTCTTGAAAN
Statistics
Matches: 152, Mismatches: 29, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
46 138 0.91
47 14 0.09
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (46 bp):
AAGCAACGGCGAAGTTTGTGATCAAGCAACAGCGAAGTTCGTGATA
Found at i:5845219 original size:92 final size:92
Alignment explanation
Indices: 5845056--5845288 Score: 315
Period size: 92 Copynumber: 2.5 Consensus size: 92
5845046 CTGGGGTGAA
*
5845056 GATCAAGCAACGGCGAAGTTTGTGATAAAGCAACGGCGAAGTTCGTGATAAAGCAACGACGAAAT
1 GATCAAGCAACGGCGAAGTTTGTGATAAAGCAACAGCGAAGTTCGTGATAAAGCAACGACGAAAT
5845121 TCGTGATCAAGCAACAGCGAAGTTCAT
66 TCGTGATCAAGCAACAGCGAAGTTCAT
* * * * *
5845148 GATCAAGTAACGGCGAAGTTTGTGATAAATCAACAGCGAAGTTCGTGATAAATCAACGATGAATT
1 GATCAAGCAACGGCGAAGTTTGTGATAAAGCAACAGCGAAGTTCGTGATAAAGCAACGACGAAAT
* *
5845213 TTGTGATCAAGCAACAGCGAAGTTCGT
66 TCGTGATCAAGCAACAGCGAAGTTCAT
* * * * * *
5845240 GATGAAGCGACGGTGAAGTTCGTGATCAAGACAA-AGTCCAAGTTCGTGA
1 GATCAAGCAACGGCGAAGTTTGTGATAAAG-CAACAG-CGAAGTTCGTGA
5845289 CTCTTGAAAN
Statistics
Matches: 123, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
92 109 0.89
93 14 0.11
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (92 bp):
GATCAAGCAACGGCGAAGTTTGTGATAAAGCAACAGCGAAGTTCGTGATAAAGCAACGACGAAAT
TCGTGATCAAGCAACAGCGAAGTTCAT
Found at i:5850162 original size:90 final size:90
Alignment explanation
Indices: 5850061--5850244 Score: 255
Period size: 90 Copynumber: 2.0 Consensus size: 90
5850051 TCACAATTCG
* *
5850061 TATTCTCATAATAATGATA-TGAATTAATGTTTTAAATATATAGTACATAAAATATTTTAAAA-A
1 TATTCTCATAATAATGATACT-AACTAATGTTTTAAATATATAATACATAAAATATTTTAAAATA
* * *
5850124 TTTTGAGGATTAAATATTTTCCTTATC
65 TTTTGAAG-TCAAATATATTCCTTATC
* * * *
5850151 TATTCTCATAATGATGGTACTAACTAATGTTTTAAATATATAATATATAAAATATTTTAAAATTT
1 TATTCTCATAATAATGATACTAACTAATGTTTTAAATATATAATACATAAAATATTTTAAAATAT
5850216 TTTGAAGTCAAATATATTCCTTATC
66 TTTGAAGTCAAATATATTCCTTATC
5850241 TATT
1 TATT
5850245 ATGATATGAA
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
90 75 0.90
91 8 0.10
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (90 bp):
TATTCTCATAATAATGATACTAACTAATGTTTTAAATATATAATACATAAAATATTTTAAAATAT
TTTGAAGTCAAATATATTCCTTATC
Found at i:5873808 original size:20 final size:21
Alignment explanation
Indices: 5873767--5873808 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5873757 TTCAAACATC
*
5873767 AAAAATCATCTTCAAGTGTCA
1 AAAAATCATCTTCAAGTCTCA
5873788 AAAAATCAT-TCTCAAG-CTCA
1 AAAAATCATCT-TCAAGTCTCA
5873808 A
1 A
5873809 CTTTTGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.26
Consensus pattern (21 bp):
AAAAATCATCTTCAAGTCTCA
Found at i:5878144 original size:48 final size:48
Alignment explanation
Indices: 5878088--5878184 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
5878078 ATTGACTAAT
5878088 TAAATTATCTTACGCCCTTGAAAATTGTCTGGAAATTGTCTTACGCCC
1 TAAATTATCTTACGCCCTTGAAAATTGTCTGGAAATTGTCTTACGCCC
5878136 TAAATTATCTTACGCCCTTGAAAATTGTCTGGAAATTGTCTTACGCCC
1 TAAATTATCTTACGCCCTTGAAAATTGTCTGGAAATTGTCTTACGCCC
5878184 T
1 T
5878185 TCAAGGGCGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (48 bp):
TAAATTATCTTACGCCCTTGAAAATTGTCTGGAAATTGTCTTACGCCC
Found at i:5878146 original size:17 final size:17
Alignment explanation
Indices: 5878120--5878153 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5878110 AATTGTCTGG
*
5878120 AAATTGTCTTACGCCCT
1 AAATTATCTTACGCCCT
5878137 AAATTATCTTACGCCCT
1 AAATTATCTTACGCCCT
5878154 TGAAAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.35
Consensus pattern (17 bp):
AAATTATCTTACGCCCT
Found at i:5878955 original size:34 final size:34
Alignment explanation
Indices: 5878917--5879037 Score: 143
Period size: 35 Copynumber: 3.5 Consensus size: 34
5878907 TAATGGGTTC
* * *
5878917 AAGCACAACTCTCACAATGCCTTTTTACAGGAGG
1 AAGCACAACCCTCACAATGCCTTTTCACAGGAGA
* *
5878951 AAGCACAACCCTCAACAATGCCTTTTCATAGGAGC
1 AAGCACAACCCTC-ACAATGCCTTTTCACAGGAGA
* * * *
5878986 AAGCACAATCCTTACAAAAGCCTTTTCACAGGACA
1 AAGCACAACCCTCAC-AATGCCTTTTCACAGGAGA
5879021 AAGCACAACCCTCACAA
1 AAGCACAACCCTCACAA
5879038 CTAGCTTTTT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
34 16 0.22
35 57 0.78
ACGTcount: A:0.37, C:0.31, G:0.13, T:0.19
Consensus pattern (34 bp):
AAGCACAACCCTCACAATGCCTTTTCACAGGAGA
Found at i:5880595 original size:14 final size:14
Alignment explanation
Indices: 5880576--5880603 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5880566 AGGTAAAGGG
5880576 AAACTCTTATTTAT
1 AAACTCTTATTTAT
5880590 AAACTCTTATTTAT
1 AAACTCTTATTTAT
5880604 TTTAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (14 bp):
AAACTCTTATTTAT
Found at i:5881318 original size:22 final size:22
Alignment explanation
Indices: 5881290--5881351 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
5881280 TAGATATATG
5881290 GTATTGGATTATACAATGAGAA
1 GTATTGGATTATACAATGAGAA
*
5881312 GTATTGG--TATA-TAT-ATG--
1 GTATTGGATTATACAATGA-GAA
5881329 GTATTGGATTATACAATGAGAA
1 GTATTGGATTATACAATGAGAA
5881351 G
1 G
5881352 CAATCTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
17 7 0.23
18 1 0.03
19 7 0.23
20 7 0.23
21 1 0.03
22 8 0.26
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.35
Consensus pattern (22 bp):
GTATTGGATTATACAATGAGAA
Found at i:5881330 original size:39 final size:39
Alignment explanation
Indices: 5881276--5881351 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
5881266 TGGTGTAATC
5881276 TTGGTAGATATATGGTATTGGATTATACAATGAGAAGTA
1 TTGGTAGATATATGGTATTGGATTATACAATGAGAAGTA
*
5881315 TTGGTATATATATGGTATTGGATTATACAATGAGAAG
1 TTGGTAGATATATGGTATTGGATTATACAATGAGAAG
5881352 CAATCTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (39 bp):
TTGGTAGATATATGGTATTGGATTATACAATGAGAAGTA
Found at i:5894600 original size:211 final size:211
Alignment explanation
Indices: 5894215--5894617 Score: 589
Period size: 211 Copynumber: 1.9 Consensus size: 211
5894205 TATTATTTAA
* * *
5894215 ATTTAATTCCTATTATATCCTTATTCTTTCTATCATAACATAATTGCAACATGATTCACAAAAAA
1 ATTTAATTCCTATTATATCATTATTCTTGCTATCATAACATAACTGCAACATGATTCACAAAAAA
* * *
5894280 TATTAAAAAATTTGGGTCTAGACAACCCTTATATCACCATTACTTTTATTTCATTTCTATTCTAT
66 TATTAAAAAATTTAGGTCTAGACAACCCTTATATCACCATTACTTTTATTTAATTCCTATTCTAT
* ** *
5894345 CCTTATTCATTTTATTACGATATTCTGGAGGAACAAAGATTAGTTATTAAATCTTTGTCACTGCA
131 CCTTATTCATTTTATTACAATATTCTGGACCAACAAAGATTAGTTATTAAATCTTTATCACTGCA
5894410 AAAAAAAAAAAATTAT
196 AAAAAAAAAAAATTAT
* *
5894426 ATTTAATTCCTATTATATCATTATTCTTGCTATCATAACATAACTGCAACATGATTTACAAAAAG
1 ATTTAATTCCTATTATATCATTATTCTTGCTATCATAACATAACTGCAACATGATTCACAAAAAA
** *
5894491 TATTAAAAGAAATTTAGGTCTAGATGACCCTTATATCACTATTACTTTTA-TTAATTCCTA-TCA
66 TATT-AAA-AAATTTAGGTCTAGACAACCCTTATATCACCATTACTTTTATTTAATTCCTATTC-
* *
5894554 TATCTTTATTC-TTTCTATTACAATATTCTGGACCTACAAA-ATTAGTTATTAAATCTTTATCAC
128 TATCCTTATTCATTT-TATTACAATATTCTGGACCAACAAAGATTAGTTATTAAATCTTTATCAC
5894617 T
192 T
5894618 CACAAAACTT
Statistics
Matches: 171, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
211 92 0.54
212 42 0.25
213 37 0.22
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (211 bp):
ATTTAATTCCTATTATATCATTATTCTTGCTATCATAACATAACTGCAACATGATTCACAAAAAA
TATTAAAAAATTTAGGTCTAGACAACCCTTATATCACCATTACTTTTATTTAATTCCTATTCTAT
CCTTATTCATTTTATTACAATATTCTGGACCAACAAAGATTAGTTATTAAATCTTTATCACTGCA
AAAAAAAAAAAATTAT
Found at i:5896956 original size:15 final size:15
Alignment explanation
Indices: 5896932--5896990 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
5896922 TTTACAATGC
* *
5896932 AATGTGATTGCAGGT
1 AATGTAATTGCAAGT
5896947 AATGTAATTGCAAGT
1 AATGTAATTGCAAGT
* * * *
5896962 AATATGATTACAAGC
1 AATGTAATTGCAAGT
5896977 AATGTAATTGCAAG
1 AATGTAATTGCAAG
5896991 AAAAATAACA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (15 bp):
AATGTAATTGCAAGT
Found at i:5897268 original size:33 final size:33
Alignment explanation
Indices: 5897206--5897270 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
5897196 TTAATGTCAT
* *
5897206 ATATTTTATTTTTATTTTTTTAATATATATTAC
1 ATATTTTATTTTAATTTTTTTAACATATATTAC
* *
5897239 ATATTTTATTTTAATTTTTTTTACCTATATTA
1 ATATTTTATTTTAATTTTTTTAACATATATTA
5897271 TATAAAGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (33 bp):
ATATTTTATTTTAATTTTTTTAACATATATTAC
Found at i:5897457 original size:15 final size:15
Alignment explanation
Indices: 5897437--5897467 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5897427 TGTAATGTAA
*
5897437 TTTAATTGGGCACAT
1 TTTAATTAGGCACAT
5897452 TTTAATTAGGCACAT
1 TTTAATTAGGCACAT
5897467 T
1 T
5897468 GCAGGGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (15 bp):
TTTAATTAGGCACAT
Found at i:5908616 original size:25 final size:25
Alignment explanation
Indices: 5908588--5908646 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
5908578 TAATGGGGCT
5908588 TTTCTTCTCTTCTTTTTCCCTTACA
1 TTTCTTCTCTTCTTTTTCCCTTACA
5908613 TTTCTTCTCTTCTTTTTCCCTTACA
1 TTTCTTCTCTTCTTTTTCCCTTACA
5908638 TTTCTTCTC
1 TTTCTTCTC
5908647 ATTCAAGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTCTTCTCTTCTTTTTCCCTTACA
Found at i:5909627 original size:32 final size:32
Alignment explanation
Indices: 5909591--5909686 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 32
5909581 TCAAACCTGG
5909591 ATGACTCAAATCTAAAATGATCTAAATCCAAA
1 ATGACTCAAATCTAAAATGATCTAAATCCAAA
* * *
5909623 ATGACTCAAATCTGAAAT-AACTGAA-CCTAAA
1 ATGACTCAAATCTAAAATGATCTAAATCC-AAA
* *
5909654 AGGA-TCCAAATCTAAAATGATCCAAACTCCAAA
1 ATGACT-CAAATCTAAAATGATCTAAA-TCCAAA
5909687 CGACCCAAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
30 3 0.06
31 22 0.43
32 21 0.41
33 3 0.06
34 2 0.04
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.22
Consensus pattern (32 bp):
ATGACTCAAATCTAAAATGATCTAAATCCAAA
Found at i:5909676 original size:16 final size:16
Alignment explanation
Indices: 5909597--5909679 Score: 71
Period size: 16 Copynumber: 5.2 Consensus size: 16
5909587 CTGGATGACT
5909597 CAAATCTAAAATGATC
1 CAAATCTAAAATGATC
* *
5909613 TAAATCCAAAATGA-C
1 CAAATCTAAAATGATC
* *
5909628 TCAAATCTGAAAT-AAC
1 -CAAATCTAAAATGATC
** * *
5909644 TGAACCTAAAAGGATC
1 CAAATCTAAAATGATC
5909660 CAAATCTAAAATGATC
1 CAAATCTAAAATGATC
5909676 CAAA
1 CAAA
5909680 CTCCAAACGA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
15 9 0.18
16 40 0.82
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.22
Consensus pattern (16 bp):
CAAATCTAAAATGATC
Found at i:5912176 original size:14 final size:14
Alignment explanation
Indices: 5912157--5912185 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5912147 CCAAAATTAT
5912157 AACTTATAAAAAAA
1 AACTTATAAAAAAA
5912171 AACTTATAAAAAAA
1 AACTTATAAAAAAA
5912185 A
1 A
5912186 TTTACCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AACTTATAAAAAAA
Found at i:5913981 original size:83 final size:84
Alignment explanation
Indices: 5913829--5913989 Score: 204
Period size: 83 Copynumber: 1.9 Consensus size: 84
5913819 TAATCTTGCC
* * *
5913829 ATTTGTTAATGAAAGTCATTCAATGCAATTAAAATTCTTATTTACAAATTGGATAAATCTCGTTG
1 ATTTGTTAATGAAAGTCATTCAATGCAATTAAAATTCTTATTTACAAATTAGATAAATCTCATTA
5913894 ATATTTATAATAAAATAAT
66 ATATTTATAATAAAATAAT
* * * *
5913913 ATTT-TTAATGAAAGTCATT-ATTTGC-TTTAGAATTTTTATTTAACAAATTAGATAAATC-CTA
1 ATTTGTTAATGAAAGTCATTCA-ATGCAATTAAAATTCTTATTT-ACAAATTAGATAAATCTC-A
5913974 TTAATATTTATAATAA
63 TTAATATTTATAATAA
5913990 TATATTTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
82 15 0.22
83 48 0.72
84 4 0.06
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.43
Consensus pattern (84 bp):
ATTTGTTAATGAAAGTCATTCAATGCAATTAAAATTCTTATTTACAAATTAGATAAATCTCATTA
ATATTTATAATAAAATAAT
Found at i:5919720 original size:13 final size:13
Alignment explanation
Indices: 5919678--5919723 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
5919668 CAAACAACTT
5919678 ATTTATAAAAAAA
1 ATTTATAAAAAAA
*
5919691 ACTTATAAAAAGTAA
1 ATTTATAAAAA--AA
*
5919706 ATTTATTAAAAAA
1 ATTTATAAAAAAA
5919719 ATTTA
1 ATTTA
5919724 ACTTAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 17 0.61
15 11 0.39
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (13 bp):
ATTTATAAAAAAA
Found at i:5928020 original size:17 final size:18
Alignment explanation
Indices: 5927998--5928032 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5927988 ATTGAAATCG
5927998 ATTAAAAATATT-ATTTA
1 ATTAAAAATATTAATTTA
*
5928015 ATTAAAATTATTAATTTA
1 ATTAAAAATATTAATTTA
5928033 TCGAACGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAAAAATATTAATTTA
Found at i:5931916 original size:16 final size:16
Alignment explanation
Indices: 5931897--5931934 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5931887 GGTCAATTTG
*
5931897 GGTTCAGGTCTTTTCA
1 GGTTCAGGTCATTTCA
*
5931913 GGTTTAGGTCATTTCA
1 GGTTCAGGTCATTTCA
5931929 GGTTCA
1 GGTTCA
5931935 AGGTGGGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (16 bp):
GGTTCAGGTCATTTCA
Found at i:5935679 original size:29 final size:29
Alignment explanation
Indices: 5935645--5935711 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
5935635 CAACCAACCC
* * *
5935645 AAAATCGATAGAATCATTGATAATTTGGT
1 AAAATCGATAGAATCATTGAAAACTTGAT
* **
5935674 CAAATCGATCTAATCATTGAAAACTTGAT
1 AAAATCGATAGAATCATTGAAAACTTGAT
5935703 AAAATCGAT
1 AAAATCGAT
5935712 TTCACTGAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (29 bp):
AAAATCGATAGAATCATTGAAAACTTGAT
Found at i:5939543 original size:68 final size:68
Alignment explanation
Indices: 5939434--5939570 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
5939424 TTGCAATTCT
5939434 AGGTTTTAACCTACAAAGTAATGCAGACTTATCAAAGGTAACATCTTGACTCACCATAAACTTGG
1 AGGTTTTAACCTACAAAGTAATGCAGACTTATCAAAGGTAACATCTTGACTCACCATAAACTTGG
5939499 GAG
66 GAG
5939502 AGGTTTTAACCTACAAAGTAATGCAGACTTATCAAAGGTAACATCTTGACTCACCATAAACTTGG
1 AGGTTTTAACCTACAAAGTAATGCAGACTTATCAAAGGTAACATCTTGACTCACCATAAACTTGG
5939567 GAG
66 GAG
5939570 A
1 A
5939571 CTTCAGATCA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (68 bp):
AGGTTTTAACCTACAAAGTAATGCAGACTTATCAAAGGTAACATCTTGACTCACCATAAACTTGG
GAG
Found at i:5953198 original size:13 final size:14
Alignment explanation
Indices: 5953182--5953256 Score: 104
Period size: 13 Copynumber: 5.6 Consensus size: 14
5953172 TCTTTCTCTA
5953182 ATTTATTT-TTATT
1 ATTTATTTATTATT
5953195 ATTTATTTATT-TT
1 ATTTATTTATTATT
5953208 ATTTA-TTATTATT
1 ATTTATTTATTATT
5953221 ATTTTATTTATTATT
1 A-TTTATTTATTATT
5953236 A-TTATTTATTATT
1 ATTTATTTATTATT
*
5953249 ATATATTT
1 ATTTATTT
5953257 CAATGCGTGA
Statistics
Matches: 56, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
12 5 0.09
13 31 0.55
14 11 0.20
15 9 0.16
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTATTTATTATT
Found at i:5953198 original size:26 final size:26
Alignment explanation
Indices: 5953167--5953256 Score: 83
Period size: 26 Copynumber: 3.4 Consensus size: 26
5953157 TTCCCTATCC
* * *
5953167 TTATTTCTTTCTCTAATTTATTTTTA
1 TTATTTATTTATCTAATTTATTATTA
* *
5953193 TTATTTATTTATTTTATTTATTATTA
1 TTATTTATTTATCTAATTTATTATTA
*
5953219 TTATTTTATTTAT-TATTATTATTTATTA
1 TTA-TTTATTTATCTAAT-TTA-TTATTA
*
5953247 TTATATATTT
1 TTATTTATTT
5953257 CAATGCGTGA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
26 26 0.49
27 18 0.34
28 9 0.17
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (26 bp):
TTATTTATTTATCTAATTTATTATTA
Found at i:5953216 original size:3 final size:3
Alignment explanation
Indices: 5953184--5953255 Score: 67
Period size: 3 Copynumber: 22.7 Consensus size: 3
5953174 TTTCTCTAAT
*
5953184 TTA TTT TTA TTA TTTA TTTA TT- TTA TTTA TTA TTA TTA TT- TTA TTTA
1 TTA TTA TTA TTA -TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA
5953231 TTA TTA TTA TTTA TTA TTA TATA TT
1 TTA TTA TTA -TTA TTA TTA T-TA TT
5953256 TCAATGCGTG
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
2 4 0.07
3 37 0.62
4 19 0.32
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:5953231 original size:31 final size:31
Alignment explanation
Indices: 5953184--5953256 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 31
5953174 TTTCTCTAAT
*
5953184 TTATTTTTATTATTTATTTATT-TTATTTATTA
1 TTATTATT-TTATTTA-TTATTATTATTTATTA
5953216 TTATTATTTTATTTATTATTATTATTTATTA
1 TTATTATTTTATTTATTATTATTATTTATTA
5953247 TTATATATTT
1 TTAT-TATTT
5953257 CAATGCGTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
30 5 0.13
31 21 0.55
32 12 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (31 bp):
TTATTATTTTATTTATTATTATTATTTATTA
Found at i:5954044 original size:13 final size:13
Alignment explanation
Indices: 5954026--5954056 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
5954016 TTATTTAGAA
5954026 TAATTACTTGAAT
1 TAATTACTTGAAT
5954039 TAATTACTTGAAT
1 TAATTACTTGAAT
5954052 TAATT
1 TAATT
5954057 GTTATTGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (13 bp):
TAATTACTTGAAT
Found at i:5954733 original size:19 final size:19
Alignment explanation
Indices: 5954709--5954775 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
5954699 TTGAGTTTAA
5954709 TGTCAAACATTTCAAATTG
1 TGTCAAACATTTCAAATTG
* * ** *
5954728 TGTCAATCATATTTTGAGTTTAA
1 TGTCAA--ACA-TTTCAAATT-G
5954751 TGTCAAACATTTCAAATTG
1 TGTCAAACATTTCAAATTG
5954770 TGTCAA
1 TGTCAA
5954776 TCATATTTTT
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
19 12 0.35
20 6 0.18
21 4 0.12
22 6 0.18
23 6 0.18
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (19 bp):
TGTCAAACATTTCAAATTG
Found at i:5954748 original size:42 final size:42
Alignment explanation
Indices: 5954699--5954784 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
5954689 GCATGGTATC
5954699 TTGAGTTTAATGTCAAACATTTCAAATTGTGTCAATCATATT
1 TTGAGTTTAATGTCAAACATTTCAAATTGTGTCAATCATATT
5954741 TTGAGTTTAATGTCAAACATTTCAAATTGTGTCAATCATATT
1 TTGAGTTTAATGTCAAACATTTCAAATTGTGTCAATCATATT
5954783 TT
1 TT
5954785 TCATCCCTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (42 bp):
TTGAGTTTAATGTCAAACATTTCAAATTGTGTCAATCATATT
Found at i:5955407 original size:21 final size:21
Alignment explanation
Indices: 5955381--5955429 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
5955371 AGATTTAATT
5955381 CAAACTTGTGTCTAATGGCTC
1 CAAACTTGTGTCTAATGGCTC
*
5955402 CAAACTTGTGTCTGATGGCTC
1 CAAACTTGTGTCTAATGGCTC
5955423 CAAACTT
1 CAAACTT
5955430 CACTTTAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (21 bp):
CAAACTTGTGTCTAATGGCTC
Found at i:5958087 original size:21 final size:22
Alignment explanation
Indices: 5958062--5958105 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
5958052 AAATGATTAA
5958062 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
5958083 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
5958105 T
1 T
5958106 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:5988389 original size:26 final size:26
Alignment explanation
Indices: 5988360--5988414 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
5988350 ATTTAAAATC
* *
5988360 AATAATTATAAAAAT-AATTATAATAA
1 AATAATAAT-AAAATCAAATATAATAA
*
5988386 AATAATAATAACATCAAATATAATAA
1 AATAATAATAAAATCAAATATAATAA
5988412 AAT
1 AAT
5988415 TTAACATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
AATAATAATAAAATCAAATATAATAA
Found at i:5988405 original size:21 final size:21
Alignment explanation
Indices: 5988381--5988436 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 21
5988371 AAATAATTAT
5988381 AATAAAATAATAA-TAACATCA
1 AATAAAATAATAATTAACAT-A
*
5988402 AATATAATAA-AATTTAACATA
1 AATAAAATAATAA-TTAACATA
*
5988423 AATAATATACATAA
1 AATAAAATA-ATAA
5988437 AATTCATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.07
21 17 0.61
22 7 0.25
23 2 0.07
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAAAATAATAATTAACATA
Found at i:5988582 original size:42 final size:41
Alignment explanation
Indices: 5988536--5988622 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 41
5988526 AACTGTGTCT
** *
5988536 GACACAAAATTATTGTGTGTTAATTATGTTTGACATGATTAA
1 GACACAAAATTATTGTGTGTTAACCATG-TCGACATGATTAA
* * * *
5988578 GACACGAAATTTTTGTGTTTTAACCATGTCGACATGTTTAA
1 GACACAAAATTATTGTGTGTTAACCATGTCGACATGATTAA
5988619 GACA
1 GACA
5988623 TGAAACATGA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 15 0.39
42 23 0.61
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (41 bp):
GACACAAAATTATTGTGTGTTAACCATGTCGACATGATTAA
Found at i:5991984 original size:31 final size:31
Alignment explanation
Indices: 5991949--5992011 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5991939 ATTCCCTTCA
5991949 AAAATTTTCAAAATCATGCCAATCTATCAAT
1 AAAATTTTCAAAATCATGCCAATCTATCAAT
5991980 AAAATTTTCAAAATCATGCCAATCTATCAAT
1 AAAATTTTCAAAATCATGCCAATCTATCAAT
5992011 A
1 A
5992012 GATATAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAATTTTCAAAATCATGCCAATCTATCAAT
Found at i:5992189 original size:20 final size:20
Alignment explanation
Indices: 5992159--5992204 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
5992149 AATAGTTGCC
*
5992159 ATCTATCGATAGATGTTCATT
1 ATCT-TCGATAGATGGTCATT
5992180 ATCTTCGATAGATGGTCATT
1 ATCTTCGATAGATGGTCATT
5992200 ATCTT
1 ATCTT
5992205 TAAGGTCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
ATCTTCGATAGATGGTCATT
Found at i:5993100 original size:22 final size:21
Alignment explanation
Indices: 5993054--5993100 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
5993044 AAGGAATGGT
*
5993054 AAAAATGTAGAATTTTGTCCT
1 AAAAATGTAGAATTTTGTCCG
5993075 AAAAATGTAGAATTTTGTCCAG
1 AAAAATGTAGAATTTTGTCC-G
5993097 AAAA
1 AAAA
5993101 TAGAGTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.32
Consensus pattern (21 bp):
AAAAATGTAGAATTTTGTCCG
Found at i:5993101 original size:21 final size:21
Alignment explanation
Indices: 5993053--5993094 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5993043 TAAGGAATGG
5993053 TAAAAATGTAGAATTTTGTCC
1 TAAAAATGTAGAATTTTGTCC
5993074 TAAAAATGTAGAATTTTGTCC
1 TAAAAATGTAGAATTTTGTCC
5993095 AGAAAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
TAAAAATGTAGAATTTTGTCC
Found at i:5993807 original size:2 final size:2
Alignment explanation
Indices: 5993800--5993824 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5993790 GCACTTGTTA
5993800 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 A
5993825 ATTCTTGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5997419 original size:80 final size:79
Alignment explanation
Indices: 5997228--5997461 Score: 308
Period size: 80 Copynumber: 2.9 Consensus size: 79
5997218 CCATTTGCAG
** * * *
5997228 GATTATG-AATGTATGTTATGAGATGTATGTGTTGAGAATATCGTGTACACTATAGGCTAAGCAT
1 GATTATGAAATGTATGCCATGAGATGTATGTGTTGAGAATATCATGTACACTATGGGCTAAACAT
5997292 AGAATGATTTATAA
66 AGAATGATTTATAA
* * *
5997306 GATTGTGATATGTATGCCATGAGATGTATGTGTTGAGAATATCATGTACATTATGGGCTAAACAT
1 GATTATGAAATGTATGCCATGAGATGTATGTGTTGAGAATATCATGTACACTATGGGCTAAACAT
5997371 GAGAATGATTTATAA
66 -AGAATGATTTATAA
* * * * * * *
5997386 GATTATGAAATGTATGCCATAAGATATATGTGTTGAGAATTTCATATAAACTATGGGTTAAATAT
1 GATTATGAAATGTATGCCATGAGATGTATGTGTTGAGAATATCATGTACACTATGGGCTAAACAT
5997451 AAGAATGATTT
66 -AGAATGATTT
5997462 TATGATAATG
Statistics
Matches: 135, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
78 6 0.04
79 50 0.37
80 79 0.59
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (79 bp):
GATTATGAAATGTATGCCATGAGATGTATGTGTTGAGAATATCATGTACACTATGGGCTAAACAT
AGAATGATTTATAA
Found at i:5998295 original size:2 final size:2
Alignment explanation
Indices: 5998288--5998318 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5998278 ATTCCATTAC
5998288 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
5998319 AAAGCAGAAT
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:5998636 original size:40 final size:38
Alignment explanation
Indices: 5998596--5998696 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 38
5998586 TCATAATTAA
*
5998596 AATAAAAATGTTAAAATAAAATATATAATAT-AAGAA-T
1 AATAAAAA-GTTAAAATAAAATATATAATATAAAAAATT
5998633 --T-AAAAGTTAAAATAAAATATATAATATAAAAAATT
1 AATAAAAAGTTAAAATAAAATATATAATATAAAAAATT
* *
5998668 ATATTAAAAAATAAAAATAAAATATATAA
1 A-A-TAAAAAGTTAAAATAAAATATATAA
5998697 GGTTATAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
33 22 0.41
34 8 0.15
35 2 0.04
39 1 0.02
40 21 0.39
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (38 bp):
AATAAAAAGTTAAAATAAAATATATAATATAAAAAATT
Found at i:5998642 original size:33 final size:33
Alignment explanation
Indices: 5998588--5998663 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 33
5998578 TTGTGATGTC
5998588 ATAAT-TAAAATAAAAATGTTAAAATAAAATAT
1 ATAATATAAAATAAAAATGTTAAAATAAAATAT
*
5998620 ATAATATAAGAATTAAAA-GTTAAAATAAAATAT
1 ATAATATAA-AATAAAAATGTTAAAATAAAATAT
5998653 ATAATATAAAA
1 ATAATATAAAA
5998664 AATTATATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
32 7 0.17
33 27 0.66
34 7 0.17
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (33 bp):
ATAATATAAAATAAAAATGTTAAAATAAAATAT
Found at i:5998692 original size:33 final size:33
Alignment explanation
Indices: 5998641--5998761 Score: 179
Period size: 34 Copynumber: 3.6 Consensus size: 33
5998631 ATTAAAAGTT
* * ** *
5998641 AAAATAAAATATATAATATAAAAAATTATATTAA
1 AAAATAAAA-ATAAAATATATAAGGTTATAATAA
5998675 AAAATAAAAATAAAATATATAAGGTTATAATAA
1 AAAATAAAAATAAAATATATAAGGTTATAATAA
5998708 AAAATAAAAAATAAAATATATAAGGTTATAATAA
1 AAAAT-AAAAATAAAATATATAAGGTTATAATAA
5998742 AAAATAAAAATAAAATATAT
1 AAAATAAAAATAAAATATAT
5998762 GACATTAAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
33 39 0.48
34 42 0.52
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (33 bp):
AAAATAAAAATAAAATATATAAGGTTATAATAA
Found at i:5998708 original size:20 final size:20
Alignment explanation
Indices: 5998683--5998743 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
5998673 AAAAAATAAA
5998683 AATAAAATATATAAGGTTAT
1 AATAAAATATATAAGGTTAT
*
5998703 AATAAAA-A-ATAA----AA
1 AATAAAATATATAAGGTTAT
5998717 AATAAAATATATAAGGTTAT
1 AATAAAATATATAAGGTTAT
5998737 AATAAAA
1 AATAAAA
5998744 AATAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 8 0.24
15 1 0.03
16 4 0.12
18 4 0.12
19 1 0.03
20 15 0.45
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (20 bp):
AATAAAATATATAAGGTTAT
Found at i:6000628 original size:215 final size:213
Alignment explanation
Indices: 6000138--6000760 Score: 863
Period size: 215 Copynumber: 2.9 Consensus size: 213
6000128 AAAAAAGTGC
**
6000138 TTAAATGATTAATCTTTTTTATTAAAATTAAAAAAAATTATCATTAGTTAAAAATTATTAAAAAT
1 TTAAATGA--AATCTTTTTTATT-AAATTAAAAAAAATTATCATTAGTTGGAAATTATTAAAAAT
* ** * * * *
6000203 GTATTTTGTTCATTAAAAATAGATAAAATAATTGAGAATTATTAACATTAAGGGAATTGAGAAGT
63 ATATTACGTTCATTGAAAATAGA-AAAATAATTGAGAATTATTAGCATTATGGGAATTGAAAAGT
* * * * *
6000268 GA-CCAAAAATAGAGATTTATTAGGTAAATAATTAAAAAAGTGAGAGAATACGTAATTTTATT-A
127 GATCAAAAAATAAAGATTTATTAGGCAAATAATTAAGAAAGTGAGAGAATATGTAATTTTATTAA
6000331 AAAGCCTAAAGTACTTAAATAT
192 AAAGCCTAAAGTACTTAAATAT
* *
6000353 TTAAATGAAATCTTTTTTATTAGAATTAAGAAAAATTATCGTTAGTTGGAAATTATTAAAAATAT
1 TTAAATGAAATCTTTTTTATTA-AATTAAAAAAAATTATCATTAGTTGGAAATTATTAAAAATAT
* *
6000418 ATTACGTTCATTGAAAATAGAAAAATAATTGAGAATTATTAGTATTATGGAAATTGAAAAGTGAT
65 ATTACGTTCATTGAAAATAGAAAAATAATTGAGAATTATTAGCATTATGGGAATTGAAAAGTGAT
* *
6000483 CAAAAATATAAAGATTTATTAGGGAAATAATTGAGAAAGTGAGAGAATATGTAATTTTATTAAAA
130 CAAAAA-ATAAAGATTTATTAGGCAAATAATTAAGAAAGTGAGAGAATATGTAATTTTATTAAAA
* * *
6000548 AGCTTAAAGTGCTTTAATAT
194 AGCCTAAAGTACTTAAATAT
* * *
6000568 TTAAATGAAATCTTTTTTATTGAAATTAAAAAAAATTAACATTAGTTGGAAATCATTAAAAACAT
1 TTAAATGAAATCTTTTTTATT-AAATTAAAAAAAATTATCATTAGTTGGAAATTATTAAAAATAT
* * *
6000633 ATTACGTTCATTGAAAATAGGAAAAACAATTGAGAATTATTAGCATTATGGGAATTGATAAGAGA
65 ATTACGTTCATTGAAAATA-GAAAAATAATTGAGAATTATTAGCATTATGGGAATTGAAAAGTGA
* ** *
6000698 TAAAAAAATAAAGATTTATTAGGCAAATAATCCAGAAAGTAAGAGAATATGTAATTTTATTAA
129 TCAAAAAATAAAGATTTATTAGGCAAATAATTAAGAAAGTGAGAGAATATGTAATTTTATTAA
6000761 TTATTTTGAC
Statistics
Matches: 365, Mismatches: 37, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
212 39 0.11
213 73 0.20
214 49 0.13
215 157 0.43
216 47 0.13
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (213 bp):
TTAAATGAAATCTTTTTTATTAAATTAAAAAAAATTATCATTAGTTGGAAATTATTAAAAATATA
TTACGTTCATTGAAAATAGAAAAATAATTGAGAATTATTAGCATTATGGGAATTGAAAAGTGATC
AAAAAATAAAGATTTATTAGGCAAATAATTAAGAAAGTGAGAGAATATGTAATTTTATTAAAAAG
CCTAAAGTACTTAAATAT
Found at i:6005046 original size:25 final size:25
Alignment explanation
Indices: 6005009--6005068 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
6004999 CTCGATGGTT
* *
6005009 TTCATTTG-CACTTATATTGACAAC
1 TTCATGTGTCACTTATATTAACAAC
*
6005033 TTCATGTGTCACTTGTATTAACAAC
1 TTCATGTGTCACTTATATTAACAAC
*
6005058 TTCAAGTGTCA
1 TTCATGTGTCA
6005069 AGTAAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (25 bp):
TTCATGTGTCACTTATATTAACAAC
Found at i:6007226 original size:28 final size:29
Alignment explanation
Indices: 6007195--6007262 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 29
6007185 CTTAAAAAAA
*
6007195 TTAAATGAATTGAATTGATTTAAT-AATT
1 TTAAATGAATTGAATTGATTAAATCAATT
* * * * *
6007223 TTAACTGACTTTAGTTGGTTAAATCAATT
1 TTAAATGAATTGAATTGATTAAATCAATT
6007252 TTAAATGAATT
1 TTAAATGAATT
6007263 TTTTAAATTT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (29 bp):
TTAAATGAATTGAATTGATTAAATCAATT
Found at i:6007555 original size:15 final size:15
Alignment explanation
Indices: 6007524--6007574 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
6007514 TTATCTAATG
*
6007524 TATA-ACTATAAACAA
1 TATATACTATATA-AA
*
6007539 TATATACTGTATAAA
1 TATATACTATATAAA
*
6007554 TATTTACTATATAAA
1 TATATACTATATAAA
*
6007569 TTTATA
1 TATATA
6007575 TAGTATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 23 0.79
16 6 0.21
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (15 bp):
TATATACTATATAAA
Found at i:6007686 original size:19 final size:21
Alignment explanation
Indices: 6007650--6007690 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
6007640 GTATTGTGTA
6007650 TTAATATATTACTATATATAG
1 TTAATATATTACTATATATAG
6007671 TTAATAT-TTACT-TATATAG
1 TTAATATATTACTATATATAG
6007690 T
1 T
6007691 ATATAAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 5 0.25
21 7 0.35
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (21 bp):
TTAATATATTACTATATATAG
Found at i:6028306 original size:43 final size:43
Alignment explanation
Indices: 6028236--6028321 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
6028226 AGTTGTAATT
* * *
6028236 ATTAATTTTAGAAATATTTTGGGAAGAATTTTTTTTTATTTTC
1 ATTAATTTTAGAAATATTTTGGAAAGAATATTTCTTTATTTTC
6028279 ATTAATTTTAGAAATATGTTT-GAAAGAATATTTCTTTATTTTC
1 ATTAATTTTAGAAATAT-TTTGGAAAGAATATTTCTTTATTTTC
6028322 TTTTCACTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
43 36 0.92
44 3 0.08
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.53
Consensus pattern (43 bp):
ATTAATTTTAGAAATATTTTGGAAAGAATATTTCTTTATTTTC
Found at i:6030091 original size:43 final size:43
Alignment explanation
Indices: 6030030--6030117 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
6030020 ATTGTAATTA
6030030 TTAATTCCAAGAATATCTTAGAGAGAATATTTCTCTATTTTTT
1 TTAATTCCAAGAATATCTTAGAGAGAATATTTCTCTATTTTTT
* *
6030073 TTAATTCTAAGAATATCTTAGGGAGAATATTTCTCTATTTTTT
1 TTAATTCCAAGAATATCTTAGAGAGAATATTTCTCTATTTTTT
6030116 TT
1 TT
6030118 TTACTTTGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (43 bp):
TTAATTCCAAGAATATCTTAGAGAGAATATTTCTCTATTTTTT
Found at i:6030445 original size:42 final size:42
Alignment explanation
Indices: 6030385--6030468 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
6030375 TCCTCTTTGG
* *
6030385 GCATCCCTAAAAAGACACAGCACCTTCAATAAGAAGAGTAAT
1 GCATCCCTAAAAAGACACACCACCTTCAATAAGAAAAGTAAT
* *
6030427 GCATCCCT-AAAAGTACACACCACCTTCGATAGGAAAAGTAAT
1 GCATCCCTAAAAAG-ACACACCACCTTCAATAAGAAAAGTAAT
6030469 ATTTCCGAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 5 0.14
42 32 0.86
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.18
Consensus pattern (42 bp):
GCATCCCTAAAAAGACACACCACCTTCAATAAGAAAAGTAAT
Found at i:6041459 original size:45 final size:45
Alignment explanation
Indices: 6041404--6041542 Score: 179
Period size: 45 Copynumber: 3.1 Consensus size: 45
6041394 ATTTTTTTTA
*
6041404 ACATGACGTGTAACAACCTAACCATAACGTGTCACATATTTTTGT
1 ACATGACGTGTAACAACCTAACCATGACGTGTCACATATTTTTGT
* * * **
6041449 ACATGACGTGTAACAACCTGACCATGGCGTGCCACACGTTTTTGT
1 ACATGACGTGTAACAACCTAACCATGACGTGTCACATATTTTTGT
* * * * *
6041494 ACATAACGTGTAGCAATCTAACCATGACGTGTAACATATTTCTGT
1 ACATGACGTGTAACAACCTAACCATGACGTGTCACATATTTTTGT
6041539 ACAT
1 ACAT
6041543 ATTGTATAAT
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (45 bp):
ACATGACGTGTAACAACCTAACCATGACGTGTCACATATTTTTGT
Found at i:6055370 original size:30 final size:30
Alignment explanation
Indices: 6055334--6055434 Score: 112
Period size: 30 Copynumber: 3.7 Consensus size: 30
6055324 CCCGACTTGA
*
6055334 TCCCCCGGCCCCCTTCCCACTCCTACCGAT
1 TCCCCCGACCCCCTTCCCACTCCTACCGAT
*
6055364 TCCCCCGACCCCCTT----C-CC-A-CGAG
1 TCCCCCGACCCCCTTCCCACTCCTACCGAT
*
6055387 T-CCCCGGCCCCC-TCCCACTCCTACCGAT
1 TCCCCCGACCCCCTTCCCACTCCTACCGAT
6055415 TCCCCCGACCCCCTTCCCAC
1 TCCCCCGACCCCCTTCCCAC
6055435 GAGTCTCGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
21 1 0.02
22 10 0.18
23 4 0.07
24 1 0.02
25 3 0.05
26 3 0.05
27 1 0.02
28 4 0.07
29 10 0.18
30 20 0.35
ACGTcount: A:0.11, C:0.62, G:0.10, T:0.17
Consensus pattern (30 bp):
TCCCCCGACCCCCTTCCCACTCCTACCGAT
Found at i:6055419 original size:51 final size:52
Alignment explanation
Indices: 6055336--6055439 Score: 201
Period size: 51 Copynumber: 2.0 Consensus size: 52
6055326 CGACTTGATC
6055336 CCCCGGCCCCCTTCCCACTCCTACCGATTCCCCCGACCCCCTTCCCACGAGT
1 CCCCGGCCCCCTTCCCACTCCTACCGATTCCCCCGACCCCCTTCCCACGAGT
6055388 CCCCGGCCCCC-TCCCACTCCTACCGATTCCCCCGACCCCCTTCCCACGAGT
1 CCCCGGCCCCCTTCCCACTCCTACCGATTCCCCCGACCCCCTTCCCACGAGT
6055439 C
1 C
6055440 TCGAATCCCG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 41 0.79
52 11 0.21
ACGTcount: A:0.12, C:0.61, G:0.12, T:0.16
Consensus pattern (52 bp):
CCCCGGCCCCCTTCCCACTCCTACCGATTCCCCCGACCCCCTTCCCACGAGT
Found at i:6055471 original size:38 final size:38
Alignment explanation
Indices: 6055410--6055506 Score: 110
Period size: 38 Copynumber: 2.5 Consensus size: 38
6055400 CCCACTCCTA
*
6055410 CCGATT-CCCCC-GACCCCCTTCCCACGAGTCTCGAA-TC
1 CCGATTCCCCCCTG-CCCCCCTCCCACGAGTC-CGAATTC
*
6055447 CCGATTCCCCCCTGCCCCCCTCCCACGAGTCCTAATTC
1 CCGATTCCCCCCTGCCCCCCTCCCACGAGTCCGAATTC
*
6055485 CTGATTCCCCCTCGTGCCCCCC
1 CCGATTCCCCC-C-TGCCCCCC
6055507 CACCCCCCCC
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
37 9 0.17
38 33 0.63
39 2 0.04
40 8 0.15
ACGTcount: A:0.12, C:0.55, G:0.12, T:0.21
Consensus pattern (38 bp):
CCGATTCCCCCCTGCCCCCCTCCCACGAGTCCGAATTC
Found at i:6064705 original size:19 final size:20
Alignment explanation
Indices: 6064679--6064721 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
6064669 AAGTTTTAAA
*
6064679 ATTTTTTATTTATTATATAT
1 ATTTTTAATTTATTATATAT
6064699 ATTTTTAAATTTATTATATAT
1 ATTTTT-AATTTATTATATAT
6064720 AT
1 AT
6064722 GTATATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTTAATTTATTATATAT
Found at i:6064726 original size:29 final size:28
Alignment explanation
Indices: 6064672--6064734 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
6064662 TCCTTAAAAG
* *
6064672 TTTTAAAATTTTTTATTTATTATATATA
1 TTTTAAAATTTATTATATATTATATATA
* *
6064700 TTTTTAAATTTATTATATATATGTATATA
1 TTTTAAAATTTATTATATAT-TATATATA
6064729 TTTTAA
1 TTTTAA
6064735 TGAACTCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTAAAATTTATTATATATTATATATA
Found at i:6064731 original size:21 final size:21
Alignment explanation
Indices: 6064685--6064731 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
6064675 TAAAATTTTT
* *
6064685 TATTTATTATATATATTTTTA
1 TATTTATTATATATATGTATA
*
6064706 AATTTATTATATATATGTATA
1 TATTTATTATATATATGTATA
6064727 TATTT
1 TATTT
6064732 TAATGAACTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TATTTATTATATATATGTATA
Found at i:6080534 original size:29 final size:29
Alignment explanation
Indices: 6080498--6080554 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
6080488 GGATATTCAA
*
6080498 TATATCTTGCTTAACTACTGTGGATATTG
1 TATATCTTACTTAACTACTGTGGATATTG
* * *
6080527 TATATCTTATTTAGCTATTGTGGATATT
1 TATATCTTACTTAACTACTGTGGATATT
6080555 ATAAATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.49
Consensus pattern (29 bp):
TATATCTTACTTAACTACTGTGGATATTG
Found at i:6101212 original size:29 final size:29
Alignment explanation
Indices: 6101170--6101226 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
6101160 AGATGAGAAG
6101170 GAAACATTAACTAAAAGCCAAATGTTTGT
1 GAAACATTAACTAAAAGCCAAATGTTTGT
**
6101199 GAAACATTAACTAAATTCCAAATGTTTG
1 GAAACATTAACTAAAAGCCAAATGTTTG
6101227 CTTGATGGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (29 bp):
GAAACATTAACTAAAAGCCAAATGTTTGT
Found at i:6107727 original size:22 final size:21
Alignment explanation
Indices: 6107702--6107746 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
6107692 TTCTCGGGCT
6107702 TTGCGTTTTCTC-TCTTCTCTTC
1 TTGCGTTTTC-CGTCTT-TCTTC
*
6107724 TTGCTTTTTCCGTCTTTCTTC
1 TTGCGTTTTCCGTCTTTCTTC
6107745 TT
1 TT
6107747 CTTATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.00, C:0.29, G:0.09, T:0.62
Consensus pattern (21 bp):
TTGCGTTTTCCGTCTTTCTTC
Found at i:6111109 original size:3 final size:3
Alignment explanation
Indices: 6111101--6111132 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6111091 GTAGAGGATA
6111101 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6111133 CTTAAAGCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6117907 original size:11 final size:11
Alignment explanation
Indices: 6117891--6117915 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6117881 TTTCCTTTAA
6117891 ATATTTCTCTT
1 ATATTTCTCTT
6117902 ATATTTCTCTT
1 ATATTTCTCTT
6117913 ATA
1 ATA
6117916 GTTGCTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTTCTCTT
Found at i:6118618 original size:28 final size:28
Alignment explanation
Indices: 6118587--6118645 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
6118577 AAGTGGATAG
*
6118587 ATACTTGTAACCTACCAAAAGTAGATGA
1 ATACTTGTAACCCACCAAAAGTAGATGA
* *
6118615 ATACTTTTAACCCACCAAAATTAGATGA
1 ATACTTGTAACCCACCAAAAGTAGATGA
6118643 ATA
1 ATA
6118646 ATAAAAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (28 bp):
ATACTTGTAACCCACCAAAAGTAGATGA
Found at i:6118862 original size:78 final size:78
Alignment explanation
Indices: 6118733--6118889 Score: 224
Period size: 78 Copynumber: 2.0 Consensus size: 78
6118723 GTCACATAGT
*
6118733 ACGTCTTAAATTTTAGCAAGCATCACCGAAAACTACAATATCTCGTGATGATTTTAATCATGACA
1 ACGTCTTAAATTTTAGCAAGCATCACCGAAAACTACAACATCTCGTGATGATTTTAATCATGACA
6118798 AAGTTGATATAAC
66 AAGTTGATATAAC
* * * * * * * * *
6118811 ACGTCTTGAATTTTATCAAGCATCATCGAAAACTATAACATCTTGTGATGATTTTCATTATGGCC
1 ACGTCTTAAATTTTAGCAAGCATCACCGAAAACTACAACATCTCGTGATGATTTTAATCATGACA
6118876 AAGTTGATATAAC
66 AAGTTGATATAAC
6118889 A
1 A
6118890 TATTAAGATA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (78 bp):
ACGTCTTAAATTTTAGCAAGCATCACCGAAAACTACAACATCTCGTGATGATTTTAATCATGACA
AAGTTGATATAAC
Found at i:6126666 original size:56 final size:56
Alignment explanation
Indices: 6126580--6126744 Score: 269
Period size: 56 Copynumber: 2.9 Consensus size: 56
6126570 CAACGGCAGA
** *
6126580 TACCACGCTGCCTCTGTCAAGTCATTTGGGAAAGCAA-AATATATGGTAAAGACAGG
1 TACCACGCAACCTTTGTCAAGTCATTTGGGAAAGCAAGAATATATGGTAAAGACA-G
6126636 TACCACGCAACCTTTGTCAAGTCATTTGGGAAAGCAAGAATATATGGTAAAGACAG
1 TACCACGCAACCTTTGTCAAGTCATTTGGGAAAGCAAGAATATATGGTAAAGACAG
* *
6126692 TACCACGCAACCCTTGTTAAGTCATTTGGGAAAGCAAGAATATATGGTAAAGA
1 TACCACGCAACCTTTGTCAAGTCATTTGGGAAAGCAAGAATATATGGTAAAGA
6126745 TAGCTAAAAT
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
56 86 0.83
57 17 0.17
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (56 bp):
TACCACGCAACCTTTGTCAAGTCATTTGGGAAAGCAAGAATATATGGTAAAGACAG
Found at i:6132883 original size:1 final size:1
Alignment explanation
Indices: 6132877--6132902 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
6132867 GAAAATGGAA
6132877 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
6132903 TTGGGTTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:6143642 original size:23 final size:23
Alignment explanation
Indices: 6143612--6143667 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
6143602 CCCTGAACTT
6143612 AACAATATGTTATGTTTGGTTTG
1 AACAATATGTTATGTTTGGTTTG
6143635 AACAATATGTTATGTTTGGTTTG
1 AACAATATGTTATGTTTGGTTTG
**
6143658 TCCAATATGT
1 AACAATATGT
6143668 GGTCACTCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.46
Consensus pattern (23 bp):
AACAATATGTTATGTTTGGTTTG
Found at i:6158069 original size:23 final size:23
Alignment explanation
Indices: 6158043--6158098 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
6158033 GGGTGACAAT
* *
6158043 ATGTGACATGACTTGAAGGGAAA
1 ATGTGACATGACATGAAGAGAAA
* **
6158066 ATGTGATATGACATGGTGAGAAA
1 ATGTGACATGACATGAAGAGAAA
6158089 ATGTGACATG
1 ATGTGACATG
6158099 TTAGTGTCAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.07, G:0.30, T:0.25
Consensus pattern (23 bp):
ATGTGACATGACATGAAGAGAAA
Found at i:6158239 original size:47 final size:47
Alignment explanation
Indices: 6158149--6158341 Score: 210
Period size: 47 Copynumber: 4.1 Consensus size: 47
6158139 CACGCCTATC
* * * * * *
6158149 ACACGGCAGGATTCAGAATTTGTGACATGCCATGGAGGAAATCTGTG
1 ACACGCCAGGGTTAAGAGTTTGTGACACGCCATGGAGGGAATCTGTG
* *
6158196 ACATAG-AAGGGTTAAGAGTTTGTGACACGCCATGGAGGGAATCTGTG
1 ACA-CGCCAGGGTTAAGAGTTTGTGACACGCCATGGAGGGAATCTGTG
* * *
6158243 ACACGCCAGGGTTCAA-AATTTATGACACGCCATGGAGGGAATCTATG
1 ACACGCCAGGGTT-AAGAGTTTGTGACACGCCATGGAGGGAATCTGTG
* * * * *
6158290 ACACGCCAGGGTTTAGAGTTTGTGGCACACCATAGAGGGAATCTGTA
1 ACACGCCAGGGTTAAGAGTTTGTGACACGCCATGGAGGGAATCTGTG
6158337 ACACG
1 ACACG
6158342 ACATGGTTGG
Statistics
Matches: 122, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
46 2 0.02
47 117 0.96
48 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (47 bp):
ACACGCCAGGGTTAAGAGTTTGTGACACGCCATGGAGGGAATCTGTG
Found at i:6158245 original size:23 final size:23
Alignment explanation
Indices: 6158218--6158297 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
6158208 TAAGAGTTTG
*
6158218 TGACACGCCATGGAGGGAATCTG
1 TGACACGCCATGGAGGGAATCTA
* **** *
6158241 TGACACGCCAGGGTTCAAAATTTA
1 TGACACGCCATGG-AGGGAATCTA
6158265 TGACACGCCATGGAGGGAATCTA
1 TGACACGCCATGGAGGGAATCTA
6158288 TGACACGCCA
1 TGACACGCCA
6158298 GGGTTTAGAG
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
23 27 0.63
24 16 0.37
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.19
Consensus pattern (23 bp):
TGACACGCCATGGAGGGAATCTA
Found at i:6158310 original size:94 final size:94
Alignment explanation
Indices: 6158149--6158341 Score: 244
Period size: 94 Copynumber: 2.1 Consensus size: 94
6158139 CACGCCTATC
* * * * *
6158149 ACACGGCAGGATTCAGAATTTGTGACATGCCATGGAGGAAATCTGTGACATAGAAGGGTTAAGAG
1 ACACGCCAGGATTCAAAATTTATGACACGCCATGGAGGAAATCTATGACATAGAAGGGTTAAGAG
* * *
6158214 TTTGTGACACGCCATGGAGGGAATCTGTG
66 TTTGTGACACACCATAGAGGGAATCTGTA
* * * * *
6158243 ACACGCCAGGGTTCAAAATTTATGACACGCCATGGAGGGAATCTATGACA-CGCCAGGGTTTAGA
1 ACACGCCAGGATTCAAAATTTATGACACGCCATGGAGGAAATCTATGACATAG-AAGGGTTAAGA
*
6158307 GTTTGTGGCACACCATAGAGGGAATCTGTA
65 GTTTGTGACACACCATAGAGGGAATCTGTA
6158337 ACACG
1 ACACG
6158342 ACATGGTTGG
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
93 1 0.01
94 83 0.99
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (94 bp):
ACACGCCAGGATTCAAAATTTATGACACGCCATGGAGGAAATCTATGACATAGAAGGGTTAAGAG
TTTGTGACACACCATAGAGGGAATCTGTA
Found at i:6159000 original size:31 final size:31
Alignment explanation
Indices: 6158965--6159168 Score: 309
Period size: 31 Copynumber: 6.6 Consensus size: 31
6158955 GTGTCAGTGT
* *
6158965 TGGCGTGTAACAATATTTTACTTGATATGTA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
6158996 TGGCGTGTAACAATATTTTACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* *
6159027 AGGCGTGTAACAACATTTGACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* *
6159058 TGGCGTGTAACAAAATTTAACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
* *
6159089 TGGCATGTAACAACATTTGACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
6159120 TGGCGTATAACAACATTTTACTTGATATGCA
1 TGGCGTGTAACAACATTTTACTTGATATGCA
*
6159151 TGGTGTGTAACAACATTT
1 TGGCGTGTAACAACATTT
6159169 ATTTCTTTCT
Statistics
Matches: 158, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 158 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (31 bp):
TGGCGTGTAACAACATTTTACTTGATATGCA
Found at i:6163050 original size:93 final size:93
Alignment explanation
Indices: 6162953--6163136 Score: 233
Period size: 93 Copynumber: 2.0 Consensus size: 93
6162943 ATATTCAACG
* * **
6162953 TGTCACGCCATGAATATACCACCACTAAACATGTCACCCTATAAATCTGCTAGTACTCAACGTGT
1 TGTCACGCCATAAATATACCACCACTAAACATGTCACCCCATAAATCTGCTAGTACTCAACGTCC
*
6163018 CACGCCCTAAATCTGGTACCATTCAGCA
66 CACACCCTAAATCTGGTACCATTCAGCA
* * * * ** * * * *
6163046 TGTCACGTCATAAATCTGCTAGTACTTAGCATGTCACCCCATAAATCTTCTAGTACTCAATGTCC
1 TGTCACGCCATAAATATACCACCACTAAACATGTCACCCCATAAATCTGCTAGTACTCAACGTCC
6163111 CACACCCTAAATCTGGTACCATTCAG
66 CACACCCTAAATCTGGTACCATTCAG
6163137 TGTGTAACGT
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.27
Consensus pattern (93 bp):
TGTCACGCCATAAATATACCACCACTAAACATGTCACCCCATAAATCTGCTAGTACTCAACGTCC
CACACCCTAAATCTGGTACCATTCAGCA
Found at i:6163092 original size:62 final size:61
Alignment explanation
Indices: 6162883--6163093 Score: 201
Period size: 62 Copynumber: 3.4 Consensus size: 61
6162873 ATCTACTTTC
* * * *
6162883 ACTTAGCATGTCACGCCCTAAATTTGGTACCACTCAGCATGTCACATCATATATCTGCTAAT
1 ACTTAACATGTCACGCCCTAAATCTGGTACCACTCAGCATGTCAC-TCATAAATCTGCTAGT
* * * * *** * * *
6162945 A-TTCAACGTGTCACGCCATGAATATACCACCACTAAACATGTCACCCTATAAATCTGCTAGT
1 ACTT-AACATGTCACGCCCTAAATCTGGTACCACTCAGCATGTCACTC-ATAAATCTGCTAGT
* * *
6163007 ACTCAACGTGTCACGCCCTAAATCTGGTACCATTCAGCATGTCACGTCATAAATCTGCTAGT
1 ACTTAACATGTCACGCCCTAAATCTGGTACCACTCAGCATGTCAC-TCATAAATCTGCTAGT
*
6163069 ACTTAGCATGTCAC-CCCATAAATCT
1 ACTTAACATGTCACGCCC-TAAATCT
6163094 TCTAGTACTC
Statistics
Matches: 117, Mismatches: 27, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
61 6 0.05
62 109 0.93
63 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (61 bp):
ACTTAACATGTCACGCCCTAAATCTGGTACCACTCAGCATGTCACTCATAAATCTGCTAGT
Found at i:6163147 original size:93 final size:93
Alignment explanation
Indices: 6162982--6163164 Score: 276
Period size: 93 Copynumber: 2.0 Consensus size: 93
6162972 CACCACTAAA
* ** *
6162982 CATGTCACCCTATAAATCTGCTAGTACTCAACGTGTCACGCCCTAAATCTGGTACCATTCAGCAT
1 CATGTCACCCCATAAATCTGCTAGTACTCAACGTCCCACACCCTAAATCTGGTACCATTCAGCAT
*
6163047 GTCACGTCATAAATCTGCTAGTACTTAG
66 GTAACGTCATAAATCTGCTAGTACTTAG
* * **
6163075 CATGTCACCCCATAAATCTTCTAGTACTCAATGTCCCACACCCTAAATCTGGTACCATTCAGTGT
1 CATGTCACCCCATAAATCTGCTAGTACTCAACGTCCCACACCCTAAATCTGGTACCATTCAGCAT
*
6163140 GTAACGTCATATATCTGCTAGTACT
66 GTAACGTCATAAATCTGCTAGTACT
6163165 CAGGGTGTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 80 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (93 bp):
CATGTCACCCCATAAATCTGCTAGTACTCAACGTCCCACACCCTAAATCTGGTACCATTCAGCAT
GTAACGTCATAAATCTGCTAGTACTTAG
Found at i:6163174 original size:93 final size:93
Alignment explanation
Indices: 6162982--6163186 Score: 275
Period size: 93 Copynumber: 2.2 Consensus size: 93
6162972 CACCACTAAA
* ** *
6162982 CATGTCACCCTATAAATCTGCTAGTACTCAACGTGTCACGCCCTAAATCTGGTACCATTCAGCAT
1 CATGTCACCCCATAAATCTGCTAGTACTCAACGTCCCACACCCTAAATCTGGTACCATTCAGCAT
* *
6163047 GTCACGTCATAAATCTGCTAGTACTTAG
66 GTAACGTCATAAATCTGCTAGTACTCAG
* * **
6163075 CATGTCACCCCATAAATCTTCTAGTACTCAATGTCCCACACCCTAAATCTGGTACCATTCAGTGT
1 CATGTCACCCCATAAATCTGCTAGTACTCAACGTCCCACACCCTAAATCTGGTACCATTCAGCAT
*
6163140 GTAACGTCATATATCTGCTAGTACTCAG
66 GTAACGTCATAAATCTGCTAGTACTCAG
** * *
6163168 GGTGTCACACCATCAATCT
1 CATGTCACCCCATAAATCT
6163187 ACCACCACTC
Statistics
Matches: 97, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 97 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (93 bp):
CATGTCACCCCATAAATCTGCTAGTACTCAACGTCCCACACCCTAAATCTGGTACCATTCAGCAT
GTAACGTCATAAATCTGCTAGTACTCAG
Found at i:6163215 original size:93 final size:92
Alignment explanation
Indices: 6163007--6163217 Score: 224
Period size: 93 Copynumber: 2.3 Consensus size: 92
6162997 ATCTGCTAGT
* *
6163007 ACTCAACGTGTCACGCCCTAAATCTGGTACCATTCAGCATGTCACGTCATAAATCTGCTAGTACT
1 ACTCAAAGTGTCACG-CCTAAATCTGGTACCATTCAGCATGTAACGTCATAAATCTGCTAGTACT
* * * * **
6163072 TAGCATGTCACCCCATAAATCTTCTAGT
65 CAGCATGTCACACCATAAATCTACCACC
* ** * ** *
6163100 ACTCAATGTCCCACACCCTAAATCTGGTACCATTCAGTGTGTAACGTCATATATCTGCTAGTACT
1 ACTCAAAGTGTCAC-GCCTAAATCTGGTACCATTCAGCATGTAACGTCATAAATCTGCTAGTACT
** *
6163165 CAGGGTGTCACACCATCAATCTACCACC
65 CAGCATGTCACACCATAAATCTACCACC
*
6163193 ACTCAAAGTGTCATCGCATAAATCT
1 ACTCAAAGTGTCA-CGCCTAAATCT
6163218 ACTAGTACTC
Statistics
Matches: 94, Mismatches: 22, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
93 93 0.99
94 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (92 bp):
ACTCAAAGTGTCACGCCTAAATCTGGTACCATTCAGCATGTAACGTCATAAATCTGCTAGTACTC
AGCATGTCACACCATAAATCTACCACC
Found at i:6163249 original size:93 final size:93
Alignment explanation
Indices: 6163152--6163347 Score: 218
Period size: 93 Copynumber: 2.1 Consensus size: 93
6163142 AACGTCATAT
* * *
6163152 ATCTGCTAGTACTCAGGGTGTCACACCATCAATCTACCACCACTCAA-AGTGTCATCGC-ATAAA
1 ATCTGCTAGTACTCAAGGTGTAACACCATAAATCTACCACCACTCAACA-TGTCATC-CTATAAA
*
6163215 TCTACTAGTACTCACCGTGTCATGCCCTAA
64 TCTACTAGTACTCACCGTGTCACGCCCTAA
** * ** * *
6163245 ATCTGGC-ACCACTCAATGTGTAATGCCATAAATCTACCACCACTCAACATGTGATCCTGTAAAT
1 ATCT-GCTAGTACTCAAGGTGTAACACCATAAATCTACCACCACTCAACATGTCATCCTATAAAT
* *
6163309 CTGCTAGTACTCAGCGTGTCACGCCCTAA
65 CTACTAGTACTCACCGTGTCACGCCCTAA
*
6163338 ATCTGATAGT
1 ATCTGCTAGT
6163348 TTGACATCTA
Statistics
Matches: 83, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
92 2 0.02
93 78 0.94
94 3 0.04
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.27
Consensus pattern (93 bp):
ATCTGCTAGTACTCAAGGTGTAACACCATAAATCTACCACCACTCAACATGTCATCCTATAAATC
TACTAGTACTCACCGTGTCACGCCCTAA
Found at i:6163339 original size:31 final size:31
Alignment explanation
Indices: 6162930--6163347 Score: 169
Period size: 31 Copynumber: 13.5 Consensus size: 31
6162920 CATGTCACAT
* * *
6162930 CATATATCTGCTAATATTCAACGTGTCACGC
1 CATAAATCTGCTAGTACTCAACGTGTCACGC
* * * * ** * *
6162961 CATGAATATACCACCACTAAACATGTCAC-C
1 CATAAATCTGCTAGTACTCAACGTGTCACGC
6162991 CTATAAATCTGCTAGTACTCAACGTGTCACGC
1 C-ATAAATCTGCTAGTACTCAACGTGTCACGC
* * ** * * * *
6163023 CCTAAATCTGGTACCATTCAGCATGTCACGT
1 CATAAATCTGCTAGTACTCAACGTGTCACGC
* * * *
6163054 CATAAATCTGCTAGTACTTAGCATGTCACCC
1 CATAAATCTGCTAGTACTCAACGTGTCACGC
* * ** *
6163085 CATAAATCTTCTAGTACTCAATGTCCCACAC
1 CATAAATCTGCTAGTACTCAACGTGTCACGC
* * ** * ** * *
6163116 CCTAAATCTGGTACCATTCAGTGTGTAACGT
1 CATAAATCTGCTAGTACTCAACGTGTCACGC
* ** *
6163147 CATATATCTGCTAGTACTCAGGGTGTCACAC
1 CATAAATCTGCTAGTACTCAACGTGTCACGC
* * * ** *
6163178 CATCAATCTACCACCACTCAAAGTGTCATCG-
1 CATAAATCTGCTAGTACTCAACGTGTCA-CGC
* * *
6163209 CATAAATCTACTAGTACTCACCGTGTCATGC
1 CATAAATCTGCTAGTACTCAACGTGTCACGC
* ** * * *
6163240 CCTAAATCTGGC-ACCACTCAATGTGTAATGC
1 CATAAATCT-GCTAGTACTCAACGTGTCACGC
* * ** * *
6163271 CATAAATCTACCACCACTCAACATGTGATC-C
1 CATAAATCTGCTAGTACTCAACGTGTCA-CGC
** *
6163302 TGTAAATCTGCTAGTACTCAGCGTGTCACGC
1 CATAAATCTGCTAGTACTCAACGTGTCACGC
* *
6163333 CCTAAATCTGATAGT
1 CATAAATCTGCTAGT
6163348 TTGACATCTA
Statistics
Matches: 274, Mismatches: 105, Indels: 16
0.69 0.27 0.04
Matches are distributed among these distances:
30 5 0.02
31 265 0.97
32 4 0.01
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.28
Consensus pattern (31 bp):
CATAAATCTGCTAGTACTCAACGTGTCACGC
Found at i:6173785 original size:2 final size:2
Alignment explanation
Indices: 6173778--6173802 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6173768 TGTTCAAGCA
6173778 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
6173803 ACCTTGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6179549 original size:28 final size:28
Alignment explanation
Indices: 6179506--6179573 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
6179496 TTAATTACAT
* * * *
6179506 TTTCTTAAAAAAAAAAATCAGTGACTTA
1 TTTCTTCAAAATAAAAATCACTAACTTA
6179534 TTTCTTCAAAATAAAAATCACTAACTTA
1 TTTCTTCAAAATAAAAATCACTAACTTA
*
6179562 TTTCATCAAAAT
1 TTTCTTCAAAAT
6179574 TTAAGATGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (28 bp):
TTTCTTCAAAATAAAAATCACTAACTTA
Found at i:6188493 original size:21 final size:21
Alignment explanation
Indices: 6188467--6188534 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
6188457 TTCACAATCC
*
6188467 AAATAT-ATAAATTATAATTAA
1 AAATATAATAAATAATAA-TAA
6188488 AAATATAATAAATAATAATAA
1 AAATATAATAAATAATAATAA
* ** *
6188509 TAATATTTTTAATAATAATAA
1 AAATATAATAAATAATAATAA
*
6188530 TAATA
1 AAATA
6188535 AAATGATGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
21 31 0.76
22 10 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATATAATAAATAATAATAA
Found at i:6188504 original size:3 final size:3
Alignment explanation
Indices: 6188492--6188535 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
6188482 AATTAAAAAT
* * *
6188492 ATA ATAA ATA ATA ATA ATA ATA TTT TTA ATA ATA ATA ATA ATA A
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6188536 AATGATGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:6188576 original size:2 final size:2
Alignment explanation
Indices: 6188569--6188624 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
6188559 ATTACATTTC
6188569 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
6188611 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
6188625 GACAGAGCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6189207 original size:11 final size:11
Alignment explanation
Indices: 6189188--6189225 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
6189178 TTATATAAAC
* *
6189188 TTTTAATTTGA
1 TTTTTATTTTA
6189199 TTTTTATTTTA
1 TTTTTATTTTA
6189210 TTTTTATTTTA
1 TTTTTATTTTA
6189221 TTTTT
1 TTTTT
6189226 TTCCTCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:6203029 original size:16 final size:17
Alignment explanation
Indices: 6202998--6203033 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
6202988 TTGGTAATCG
6202998 GAAAATAATTTGTTGTA
1 GAAAATAATTTGTTGTA
*
6203015 GAAAA-AATTTTTTGTA
1 GAAAATAATTTGTTGTA
6203031 GAA
1 GAA
6203034 TATTTTATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (17 bp):
GAAAATAATTTGTTGTA
Found at i:6204254 original size:17 final size:15
Alignment explanation
Indices: 6204232--6204277 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 15
6204222 TTTGAAAAGA
6204232 TTTTAAAAAAATATTTT
1 TTTTAAAAAAA-A-TTT
6204249 TTTTAAAGAATAAATTT
1 TTTTAAA-AA-AAATTT
6204266 TTTTAAAAAAAA
1 TTTTAAAAAAAA
6204278 GAGCTTCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.11
16 2 0.07
17 17 0.63
18 3 0.11
19 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
TTTTAAAAAAAATTT
Done.