Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007956.1 Hibiscus syriacus cultivar Beakdansim tig00110383_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: 3102597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2944372 original size:28 final size:28
Alignment explanation
Indices: 2944332--2944385 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2944322 AAATAAAATA
* *
2944332 AAATTAATTAATAA-AATATATAATAAAG
1 AAATAAATAAATAATAATA-ATAATAAAG
2944360 AAATAAATAAATAATAATAATAATAA
1 AAATAAATAAATAATAATAATAATAA
2944386 TAATAGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (28 bp):
AAATAAATAAATAATAATAATAATAAAG
Found at i:2944375 original size:3 final size:3
Alignment explanation
Indices: 2944317--2944390 Score: 50
Period size: 3 Copynumber: 24.3 Consensus size: 3
2944307 CCTCGAGAAA
*
2944317 AAT AAA AAT AA- AAT AA- AATT AATT AAT AA- AAT ATAT AAT AA- AGA-
1 AAT AAT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT A-AT AAT AAT A-AT
2944361 AAT AAAT AAAT AAT AAT AAT AAT AAT AAT A
1 AAT -AAT -AAT AAT AAT AAT AAT AAT AAT A
2944391 GATTATATAA
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
2 8 0.13
3 37 0.61
4 16 0.26
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2944438 original size:23 final size:23
Alignment explanation
Indices: 2944394--2944438 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2944384 AATAATAGAT
2944394 TATATAAAAATATTTTCAAAAAC
1 TATATAAAAATATTTTCAAAAAC
*
2944417 TATATAATATATATTTTCAAAA
1 TATATAA-AAATATTTTCAAAA
2944439 TTATTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
TATATAAAAATATTTTCAAAAAC
Found at i:2944528 original size:35 final size:35
Alignment explanation
Indices: 2944400--2944802 Score: 456
Period size: 36 Copynumber: 11.1 Consensus size: 35
2944390 AGATTATATA
* *
2944400 AAAATATTTTCAAAAACTATATAATATATA-TTTTC
1 AAAATGTTTTC-AAAACTATATATTATATAGTTTTC
* * *
2944435 AAAAT-TATTTTAAAACTATATATTATATATTTTTTA
1 AAAATGT-TTTCAAAACTATATATTATATA-GTTTTC
* *
2944471 AAAATGTTTTAAAAACTATATATCATATAGTTTTC
1 AAAATGTTTTCAAAACTATATATTATATAGTTTTC
2944506 AAAAATGTTTT-AAAACTATATATTATATATGTTTTC
1 -AAAATGTTTTCAAAACTATATATTATATA-GTTTTC
*
2944542 AAAAATGTTTTCAAAACTATATATTATATAATTTTC
1 -AAAATGTTTTCAAAACTATATATTATATAGTTTTC
* *
2944578 ATAATGATTTCAAAACTATATATTATATAAG-TTTC
1 AAAATGTTTTCAAAACTATATATTATAT-AGTTTTC
* *
2944613 AAAATGTTTTCAAAAAATATATATTATATAATTTTTC
1 AAAATGTTTTC-AAAACTATATATTATAT-AGTTTTC
*
2944650 AAAATGTTTTCAAAAAATATATATTATATAAGTTTTC
1 AAAATGTTTTC-AAAACTATATATTATAT-AGTTTTC
* *
2944687 AAAATGATTTCAAAACTATATATTATATAAGTTTTT
1 AAAATGTTTTCAAAACTATATATTATAT-AGTTTTC
*
2944723 AAAATGTTTTCATAAACTATATTATATATATATATATATTC
1 AAAATGTTTTCA-AAACTATA-TAT-TATATA-GT-T-TTC
2944764 AAAATGTTTTCAAAATCTATATATTATATA-TTTTC
1 AAAATGTTTTCAAAA-CTATATATTATATAGTTTTC
2944799 AAAA
1 AAAA
2944803 ACTATATAAT
Statistics
Matches: 328, Mismatches: 23, Indels: 34
0.85 0.06 0.09
Matches are distributed among these distances:
34 18 0.05
35 75 0.23
36 115 0.35
37 78 0.24
38 4 0.01
39 12 0.04
40 7 0.02
41 19 0.06
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (35 bp):
AAAATGTTTTCAAAACTATATATTATATAGTTTTC
Found at i:2944797 original size:24 final size:26
Alignment explanation
Indices: 2944770--2944829 Score: 88
Period size: 24 Copynumber: 2.4 Consensus size: 26
2944760 ATTCAAAATG
* *
2944770 TTTTCAAAATCTATAT-AT-TATATA
1 TTTTCAAAAACTATATAATATATACA
2944794 TTTTCAAAAACTATATAATATATACA
1 TTTTCAAAAACTATATAATATATACA
2944820 TTTTCAAAAA
1 TTTTCAAAAA
2944830 TCGTTTTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 15 0.47
25 2 0.06
26 15 0.47
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (26 bp):
TTTTCAAAAACTATATAATATATACA
Found at i:2945777 original size:86 final size:86
Alignment explanation
Indices: 2945687--2945859 Score: 258
Period size: 86 Copynumber: 2.0 Consensus size: 86
2945677 AATGCCAAGC
* * * *
2945687 GGTATATTCTTCATGTGGTTCCCCTTCA-CGGGTCTGAACCATGTGAGATGCTCTTTAGATGACT
1 GGTATATTCCTCAGGTGGTTCCCCTT-AGCGGGTCTGAACCAAGTGAGATGATCTTTAGATGACT
*
2945751 CCCCTTCAGGGGAAAGCCATGT
65 CCCCTTCACGGGAAAGCCATGT
* *
2945773 GGTATATTCCTCAGGTGGTTCCCCTTAGCGGGTCTGAACCAAGTGAGATGATCTTTGGGTGACTC
1 GGTATATTCCTCAGGTGGTTCCCCTTAGCGGGTCTGAACCAAGTGAGATGATCTTTAGATGACTC
*
2945838 CCCTTCACGGGAAAGTCATGT
66 CCCTTCACGGGAAAGCCATGT
2945859 G
1 G
2945860 AGATGTTCTT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
85 1 0.01
86 77 0.99
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.30
Consensus pattern (86 bp):
GGTATATTCCTCAGGTGGTTCCCCTTAGCGGGTCTGAACCAAGTGAGATGATCTTTAGATGACTC
CCCTTCACGGGAAAGCCATGT
Found at i:2947154 original size:95 final size:95
Alignment explanation
Indices: 2946991--2947184 Score: 280
Period size: 95 Copynumber: 2.0 Consensus size: 95
2946981 GGACAACTCA
* * * * *
2946991 ATATTATAATTACCTTTATCAACCTAGCTGAATCTTATCCATAAAGCCGGGGTATTTAACCAATT
1 ATATTAGAATCACCTTTATCAACCTAGCTGAATCTTATACATAAAGCCAGGGCATTTAACCAATT
*
2947056 GCTTTAGAGGGACAGCTCAATCTTTATTGT
66 GCTTTAGAGGGACAGCTCAAGCTTTATTGT
** ** *
2947086 ATATTAGAATCACCTTTATCAGGCTAGCTGAATCTTATACATAAATTCAGGGCGTTTAACCAATT
1 ATATTAGAATCACCTTTATCAACCTAGCTGAATCTTATACATAAAGCCAGGGCATTTAACCAATT
*
2947151 GCTTTAGATGGACAGCTCAAGCTTTATTGT
66 GCTTTAGAGGGACAGCTCAAGCTTTATTGT
2947181 ATAT
1 ATAT
2947185 ATATAATATT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 87 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (95 bp):
ATATTAGAATCACCTTTATCAACCTAGCTGAATCTTATACATAAAGCCAGGGCATTTAACCAATT
GCTTTAGAGGGACAGCTCAAGCTTTATTGT
Found at i:2949485 original size:60 final size:60
Alignment explanation
Indices: 2949364--2949528 Score: 160
Period size: 60 Copynumber: 2.8 Consensus size: 60
2949354 TGAAAAGTTC
* * * * *
2949364 TAAAATTTTGGAGACTAATTTAGAATGAATGTCATAATTTGAGGATGAAAATGAAATATT
1 TAAAAGTTTGAAGACTAATTTAGAATGAATATCATAATTTAAGGATGAAAATGAAACATT
* * * *
2949424 TATAAGTTTGAAGACTAATGTAGAATG-ATAATCATATTTTAAGGATG-AAATTAGAACATT
1 TAAAAGTTTGAAGACTAATTTAGAATGAAT-ATCATAATTTAAGGATGAAAATGA-AACATT
*
2949484 TAAAAGTGT-AGAGACTAATTTAGAAT-AAGTGA-CATAATTTAAGGA
1 TAAAAGTTTGA-AGACTAATTTAGAATGAA-T-ATCATAATTTAAGGA
2949529 AGTGTGGTGC
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
59 8 0.09
60 76 0.88
61 2 0.02
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.33
Consensus pattern (60 bp):
TAAAAGTTTGAAGACTAATTTAGAATGAATATCATAATTTAAGGATGAAAATGAAACATT
Found at i:2950078 original size:41 final size:41
Alignment explanation
Indices: 2950021--2950101 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
2950011 CCGAATACGA
2950021 GTTAAGGATGTTACATTACATTTATAACATGTTTCCTATAT
1 GTTAAGGATGTTACATTACATTTATAACATGTTTCCTATAT
*
2950062 GTTAAGGATGTTACATTACATTTATAACATGTTTCTTATA
1 GTTAAGGATGTTACATTACATTTATAACATGTTTCCTATA
2950102 CGAAAACCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.44
Consensus pattern (41 bp):
GTTAAGGATGTTACATTACATTTATAACATGTTTCCTATAT
Found at i:2950999 original size:62 final size:61
Alignment explanation
Indices: 2950877--2951027 Score: 176
Period size: 62 Copynumber: 2.5 Consensus size: 61
2950867 TATAAATGTA
* * * * *
2950877 CATTGGGCAGTTCAAACCTAAAATCATGCATAACCATGTAGTAAAGTATCATATAAAAATG
1 CATTGGGTAGTTCATACCCAAAATCATCCATAACCATGTAGTAAAATATCATATAAAAATG
* * * * *
2950938 CATTGGGTAGTTCGTACCCAAAATTATCCATAAACCATTTCGTAAAATATTATATAAAAATG
1 CATTGGGTAGTTCATACCCAAAATCATCCAT-AACCATGTAGTAAAATATCATATAAAAATG
* * *
2951000 TATTGGATAATTCATACCCAAAATCATC
1 CATTGGGTAGTTCATACCCAAAATCATC
2951028 TGAATACCAT
Statistics
Matches: 74, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
61 25 0.34
62 49 0.66
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (61 bp):
CATTGGGTAGTTCATACCCAAAATCATCCATAACCATGTAGTAAAATATCATATAAAAATG
Found at i:2953176 original size:98 final size:96
Alignment explanation
Indices: 2953007--2953202 Score: 365
Period size: 98 Copynumber: 2.0 Consensus size: 96
2952997 TTCAAATCAA
*
2953007 CATCAATTCATACTCAAGTCAACTTGAAATCATCACCACCTTCGAGACACAAATCATTTTGAGAT
1 CATCAATTCATACTCAAGTCAACTGGAAATCATCACCACCTTCGAGACACAAATCATTTTGAGAT
2953072 TTCGCTACCTAAGACTCTGTCATGTTTCACGTT
66 TTCGCTACCTAAGA--CTGTCATGTTTCACGTT
2953105 CATCAATTCATACTCAAGTCAACTGGAAATCATCACCACCTTCGAGACACAAATCATTTTGAGAT
1 CATCAATTCATACTCAAGTCAACTGGAAATCATCACCACCTTCGAGACACAAATCATTTTGAGAT
2953170 TTCGCTACCTAAGACTGTCATGTTTCACGTT
66 TTCGCTACCTAAGACTGTCATGTTTCACGTT
2953201 CA
1 CA
2953203 AATAGTTCTG
Statistics
Matches: 97, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
96 19 0.20
98 78 0.80
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (96 bp):
CATCAATTCATACTCAAGTCAACTGGAAATCATCACCACCTTCGAGACACAAATCATTTTGAGAT
TTCGCTACCTAAGACTGTCATGTTTCACGTT
Found at i:2953575 original size:81 final size:81
Alignment explanation
Indices: 2953463--2953623 Score: 243
Period size: 81 Copynumber: 2.0 Consensus size: 81
2953453 ATGAAAAACA
* *
2953463 CATCAGATGCATAACGTTGCAGCTTTCAGGTT-AGCTAAGGTTATAGATATTGACCTAAAGTTTA
1 CATCAGATGAATAACGTTGCAGCTTTCAGGTTGA-CCAAGGTTATAGATATTGACCTAAAGTTTA
2953527 TAATAATTTCATATATG
65 TAATAATTTCATATATG
* * * * *
2953544 CATCAGATGAATGACTTTGCAGCTTTTAGGTTGACCAAGGTTATAGGTATTGACCTCAAGTTTAT
1 CATCAGATGAATAACGTTGCAGCTTTCAGGTTGACCAAGGTTATAGATATTGACCTAAAGTTTAT
2953609 AATAATTTCATATAT
66 AATAATTTCATATAT
2953624 ATATATATAT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 71 0.99
82 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (81 bp):
CATCAGATGAATAACGTTGCAGCTTTCAGGTTGACCAAGGTTATAGATATTGACCTAAAGTTTAT
AATAATTTCATATATG
Found at i:2953625 original size:2 final size:2
Alignment explanation
Indices: 2953618--2953648 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2953608 TAATAATTTC
2953618 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
2953649 CATGGATCTA
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:2959789 original size:24 final size:24
Alignment explanation
Indices: 2959757--2959803 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2959747 TACTTAAGTT
2959757 TTTTCTTCCCGTTAAATTTTGAAA
1 TTTTCTTCCCGTTAAATTTTGAAA
2959781 TTTTCTTCCCGTTAAATTTTGAA
1 TTTTCTTCCCGTTAAATTTTGAA
2959804 GAGAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.51
Consensus pattern (24 bp):
TTTTCTTCCCGTTAAATTTTGAAA
Found at i:2959908 original size:29 final size:29
Alignment explanation
Indices: 2959865--2959922 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2959855 AAGAGATTTT
2959865 GTGCATTGATCGTGAGAATTTGAAAAGAC
1 GTGCATTGATCGTGAGAATTTGAAAAGAC
*
2959894 GTGCATTGATTGTGAGAATTTGAAAAGAC
1 GTGCATTGATCGTGAGAATTTGAAAAGAC
2959923 CAAAATTAAA
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:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (29 bp):
GTGCATTGATCGTGAGAATTTGAAAAGAC
Found at i:2961044 original size:10 final size:9
Alignment explanation
Indices: 2961026--2961063 Score: 58
Period size: 10 Copynumber: 4.0 Consensus size: 9
2961016 ATTATATTTG
2961026 ATATATTAT
1 ATATATTAT
2961035 ATAGTATTAT
1 ATA-TATTAT
2961045 ATATATATAT
1 ATATAT-TAT
2961055 ATATATTAT
1 ATATATTAT
2961064 GTGGTTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
ATATATTAT
Found at i:2962155 original size:23 final size:23
Alignment explanation
Indices: 2962091--2962156 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
2962081 TAAGAATTGT
* *
2962091 AATAATATAAATTATTCAGTATTAC
1 AATAATATATATAATT-A-TATTAC
*
2962116 AATAATATATTTAATTATATTAC
1 AATAATATATATAATTATATTAC
2962139 AATAATATATGAT-ATTAT
1 AATAATATAT-ATAATTAT
2962157 TCGTATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 21 0.58
24 2 0.06
25 13 0.36
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (23 bp):
AATAATATATATAATTATATTAC
Found at i:2966442 original size:58 final size:59
Alignment explanation
Indices: 2966241--2966461 Score: 311
Period size: 59 Copynumber: 3.8 Consensus size: 59
2966231 CACCAAATTT
* * * * *
2966241 CTAACCCGAATATGACACATAAGTTCATGCCCACCATATGCACTAGGTGTCCTTTAATG
1 CTAACCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTG
* * ** *
2966300 CTAACCTGAATATGACACATAAGGTTGTAACCACCATATACACTAAGTATCCTTTAGTG
1 CTAACCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTG
*
2966359 CTAACCCGAATATGACACATAAGGTCGTGCCCACCATCTACACTAGGTATCCTTT-GTG
1 CTAACCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTG
*
2966417 CTAA-CCGAAATATGACACATAAGGTCGTGCCCACTATATACACTA
1 CTAACCCG-AATATGACACATAAGGTCGTGCCCACCATATACACTA
2966462 AGTACTGGAC
Statistics
Matches: 143, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
57 3 0.02
58 42 0.29
59 98 0.69
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (59 bp):
CTAACCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTG
Found at i:2968300 original size:229 final size:229
Alignment explanation
Indices: 2967899--2968357 Score: 864
Period size: 229 Copynumber: 2.0 Consensus size: 229
2967889 TTAAGGTGCT
*
2967899 TTTCAATTCTCACATTGGAATTGAGTAATCACTTAAGCTCTCGGATTATGAGAGAATTAGCTAAG
1 TTTCAATTCTCACATTGGAATTGAGTAATCACTTAAGCTCTCGGATTATGAGAAAATTAGCTAAG
2967964 CATGACAAAAGTCATACTTAGCATGTTTAAAAATTAAAAGTAAAATAAAATAAAAATGAAAACTT
66 CATGACAAAAGTCATACTTAGCATGTTTAAAAATTAAAAGTAAAATAAAATAAAAATGAAAACTT
*
2968029 GAAAAGAAAAGAAAGAACTTTATAAAACTAGAAAGAAGAAGAAGGAGAGTAAATTTTGAGTTGTG
131 GAAAAGAAAAGAAAGAACTTTATAAAACTAGAAAGAAGAAGAAGAAGAGTAAATTTTGAGTTGTG
* *
2968094 TGTTTAGGCTTACCCCAGGAGGGTATTTATAGCC
196 TATTTAGGCTTACCCCAAGAGGGTATTTATAGCC
* *
2968128 TTTCAATTCTCACATTGGAATTGATTAATCACTTAAGCTCTCGGCTTATGAGAAAATTAGCTAAG
1 TTTCAATTCTCACATTGGAATTGAGTAATCACTTAAGCTCTCGGATTATGAGAAAATTAGCTAAG
2968193 CATGACAAAAGTCATACTTAGCATGTTTAAAAATTAAAAGTAAAATAAAATAAAAATGAAAACTT
66 CATGACAAAAGTCATACTTAGCATGTTTAAAAATTAAAAGTAAAATAAAATAAAAATGAAAACTT
2968258 GAAAAGAAAAGAAAGAACTTTATAAAACTAGAAAGAAGAAGAAGAAGAGTAAATTTTGAGTTGTG
131 GAAAAGAAAAGAAAGAACTTTATAAAACTAGAAAGAAGAAGAAGAAGAGTAAATTTTGAGTTGTG
2968323 TATTTAGGCTTACCCCAAGAGGGTATTTATAGCC
196 TATTTAGGCTTACCCCAAGAGGGTATTTATAGCC
2968357 T
1 T
2968358 CTAAAACCTT
Statistics
Matches: 224, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
229 224 1.00
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (229 bp):
TTTCAATTCTCACATTGGAATTGAGTAATCACTTAAGCTCTCGGATTATGAGAAAATTAGCTAAG
CATGACAAAAGTCATACTTAGCATGTTTAAAAATTAAAAGTAAAATAAAATAAAAATGAAAACTT
GAAAAGAAAAGAAAGAACTTTATAAAACTAGAAAGAAGAAGAAGAAGAGTAAATTTTGAGTTGTG
TATTTAGGCTTACCCCAAGAGGGTATTTATAGCC
Found at i:2978024 original size:60 final size:60
Alignment explanation
Indices: 2977941--2978113 Score: 201
Period size: 60 Copynumber: 2.9 Consensus size: 60
2977931 GATGAATTTG
** *
2977941 AAATGTTCTAAAAGTTTGTAGACTAATTTAGAATGAATGTCATAATTTGAGGATGAAA-ATA
1 AAAT-TTC-AAAAGTTTAAAGACTAATTTAGAATGAATGTCATAATTTAAGGATGAAATATA
* *
2978002 AAATATTCAAAAGTTTAAAGACTAATTTAGAATG-ATAGTCATAGTTTAAGGATGAAATTGTA
1 AAAT-TTCAAAAGTTTAAAGACTAATTTAGAATGAAT-GTCATAATTTAAGGATGAAA-TATA
* *
2978064 AAATTT-AAAAGTTTAGAGACTAATTTAGAATGAGTGAT-ATAATTTAAGGA
1 AAATTTCAAAAGTTTAAAGACTAATTTAGAATGAATG-TCATAATTTAAGGA
2978114 AGTGTGGTGC
Statistics
Matches: 98, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
59 2 0.02
60 79 0.81
61 11 0.11
62 6 0.06
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (60 bp):
AAATTTCAAAAGTTTAAAGACTAATTTAGAATGAATGTCATAATTTAAGGATGAAATATA
Found at i:2979476 original size:28 final size:28
Alignment explanation
Indices: 2979435--2979500 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
2979425 CGAGTGTGTG
*
2979435 AAATATGCACTCGAAAGTGCCTCGTAGAT
1 AAAT-TGCACTCGAAAGTGCCTCGCAGAT
*
2979464 AAATTGCACTCGAAAGTGTCTCGCAGAT
1 AAATTGCACTCGAAAGTGCCTCGCAGAT
*
2979492 AATTTGCAC
1 AAATTGCAC
2979501 AATAGGTGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 30 0.88
29 4 0.12
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (28 bp):
AAATTGCACTCGAAAGTGCCTCGCAGAT
Found at i:2981638 original size:29 final size:30
Alignment explanation
Indices: 2981564--2981645 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 30
2981554 GATAACATTT
*
2981564 AAAAATTATACTTTGGTCCCTAAACTTTTC
1 AAAAATTATACTTTGGTCACTAAACTTTTC
*
2981594 CAAAATGTATACTTTGGTCACTAAAC-TTTC
1 AAAAAT-TATACTTTGGTCACTAAACTTTTC
* *
2981624 AAAAATTAAATTTTGGTCACTA
1 AAAAATTATACTTTGGTCACTA
2981646 GTCAAAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 14 0.30
30 14 0.30
31 18 0.39
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.38
Consensus pattern (30 bp):
AAAAATTATACTTTGGTCACTAAACTTTTC
Found at i:2982267 original size:4 final size:4
Alignment explanation
Indices: 2982258--2982308 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
2982248 ATAATAAATT
* * *
2982258 ATAC ATAC ATAT ATAC -TAC AAAC ATAC ATAG ATAC ATATC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA-C ATAC ATAC
2982306 ATA
1 ATA
2982309 TATCTATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 3 0.08
4 32 0.82
5 4 0.10
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:2987714 original size:16 final size:16
Alignment explanation
Indices: 2987693--2987742 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2987683 TATATAATCT
2987693 AATTTATAATCTAATA
1 AATTTATAATCTAATA
2987709 AATTTAATAATC-AATA
1 AATTT-ATAATCTAATA
* * *
2987725 AATTAATCATTTAATA
1 AATTTATAATCTAATA
2987741 AA
1 AA
2987743 ATTAATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 4 0.14
16 19 0.66
17 6 0.21
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTATAATCTAATA
Found at i:2988693 original size:49 final size:49
Alignment explanation
Indices: 2988594--2988693 Score: 110
Period size: 49 Copynumber: 2.0 Consensus size: 49
2988584 CTTCGAGACG
* * * * *** *
2988594 CAAATCATTTTGAGATTTCGCTACCTAAAACTCTGTCATGTTTTACGTT
1 CAAATAATTCTGAGATTTCGCCACCTAAAACTATAAAATGTTTCACGTT
* *
2988643 CAAATAATTCTGAGATTTCGCCACCTAAAATTATAAAATGTTTCATGTT
1 CAAATAATTCTGAGATTTCGCCACCTAAAACTATAAAATGTTTCACGTT
2988692 CA
1 CA
2988694 CCCAATTCCC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (49 bp):
CAAATAATTCTGAGATTTCGCCACCTAAAACTATAAAATGTTTCACGTT
Found at i:2989016 original size:81 final size:83
Alignment explanation
Indices: 2988903--2989070 Score: 250
Period size: 81 Copynumber: 2.0 Consensus size: 83
2988893 CATGAAAAAC
* * *
2988903 ACATCAGATGCATGACGTTGTAGCTTTCAGGTTGGCCAAGGTTATAGATATTGACCTAAAGTTTA
1 ACATCAGATGAATGACGTTGCAGCTTTCAGGTTGACCAAGGTTATAGATATTGACCTAAAGTTTA
*
2988968 TAATAATT-TCT-TATAT
66 TAATAATTATATATATAT
* * * *
2988984 ACATCAGATGAATGACTTTGCAGCTTTTAGGTTGACCAAGGTTATAGGTATTGACCTCAAGTTTA
1 ACATCAGATGAATGACGTTGCAGCTTTCAGGTTGACCAAGGTTATAGATATTGACCTAAAGTTTA
2989049 TAATAATTATATATATAT
66 TAATAATTATATATATAT
2989067 ACAT
1 ACAT
2989071 GGCTCTATGG
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 66 0.86
82 2 0.03
83 9 0.12
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (83 bp):
ACATCAGATGAATGACGTTGCAGCTTTCAGGTTGACCAAGGTTATAGATATTGACCTAAAGTTTA
TAATAATTATATATATAT
Found at i:2991696 original size:23 final size:23
Alignment explanation
Indices: 2991619--2991703 Score: 93
Period size: 25 Copynumber: 3.6 Consensus size: 23
2991609 AAAAATATTC
2991619 ATTAGTAA-AATATATTTATTAAT
1 ATTA-TAATAATATATTTATTAAT
* *
2991642 AATTTTAATAATATAAATTATTCAAT
1 -ATTATAATAATAT-ATTTATT-AAT
2991668 ATTATAATAATATATTTAATT-AT
1 ATTATAATAATATATTT-ATTAAT
2991691 ATTATAATAATAT
1 ATTATAATAATAT
2991704 CATTACTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
23 18 0.34
24 11 0.21
25 21 0.40
26 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (23 bp):
ATTATAATAATATATTTATTAAT
Found at i:2992575 original size:2 final size:2
Alignment explanation
Indices: 2992568--2992599 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2992558 AGCGGAATAA
2992568 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
2992600 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2997266 original size:22 final size:22
Alignment explanation
Indices: 2997238--2997281 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2997228 ATGGTATCGA
*
2997238 TACCATAAC-ATGGTATCGATAC
1 TACCAT-ACTATGGTACCGATAC
2997260 TACCATACTATGGTACCGATAC
1 TACCATACTATGGTACCGATAC
2997282 CATGGTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (22 bp):
TACCATACTATGGTACCGATAC
Found at i:2997802 original size:79 final size:79
Alignment explanation
Indices: 2997716--2998007 Score: 406
Period size: 79 Copynumber: 3.7 Consensus size: 79
2997706 TGAGTAATTA
* *
2997716 AATAATGCATATGGGTGTATTATTGGCATGAAAGGATTCCATAAATGAATTGCATATGGGTGCAT
1 AATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAAATGAAATGCATATGGGTGCAT
*
2997781 TATCGACATAAAAG
66 TATCGGCATAAAAG
* ** * **
2997795 AATAATGCATATGGCTGCATTATTGGCATGAAATTATACCATAGCTGAAATGCATATGGGTGCAT
1 AATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAAATGAAATGCATATGGGTGCAT
* *
2997860 AATTGGCATAAAAG
66 TATCGGCATAAAAG
* **
2997874 AATAATGCATATGGGTGCATTATTGGCATAAAAGGATGT-CATAGCTGAAATGCATATGGGTGCA
1 AATAATGCATATGGGTGCATTATTGGCATGAAAGGAT-TCCATAAATGAAATGCATATGGGTGCA
2997938 TTATCGGCATAAAAG
65 TTATCGGCATAAAAG
* ** *
2997953 AATAATGCATATGGGTGCATTATTGGTATGAAAGGATGACATAAATAAAATGCAT
1 AATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAAATGAAATGCAT
2998008 GAAAGTATGC
Statistics
Matches: 187, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
79 187 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (79 bp):
AATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAAATGAAATGCATATGGGTGCAT
TATCGGCATAAAAG
Found at i:2997805 original size:34 final size:34
Alignment explanation
Indices: 2997766--2997907 Score: 140
Period size: 34 Copynumber: 3.9 Consensus size: 34
2997756 ATAAATGAAT
* *
2997766 TGCATATGGGTGCATTATCGACATAAAAGAATAA
1 TGCATATGGGTGCATTATTGGCATAAAAGAATAA
* *
2997800 TGCATATGGCTGCATTATTGGCATGAAATTATACCATAGCTGAAA
1 TGCATATGGGTGCATTATTGGCAT--AA--A-A-GA-A--T--AA
*
2997845 TGCATATGGGTGCATAATTGGCATAAAAGAATAA
1 TGCATATGGGTGCATTATTGGCATAAAAGAATAA
2997879 TGCATATGGGTGCATTATTGGCATAAAAG
1 TGCATATGGGTGCATTATTGGCATAAAAG
2997908 GATGTCATAG
Statistics
Matches: 89, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
34 51 0.57
36 3 0.03
38 2 0.02
39 2 0.02
40 2 0.02
41 2 0.02
43 3 0.03
45 24 0.27
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.29
Consensus pattern (34 bp):
TGCATATGGGTGCATTATTGGCATAAAAGAATAA
Found at i:2997847 original size:45 final size:41
Alignment explanation
Indices: 2997798--2997951 Score: 142
Period size: 45 Copynumber: 3.7 Consensus size: 41
2997788 ATAAAAGAAT
*
2997798 AATGCATATGGCTGCATTATTGGCATGAAATTATACCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCAT-AAA--ATA-CATAGCTGA
* *
2997843 AATGCATATGGGTGCATAATTGGCAT-AAA-AGA-A--T--
1 AATGCATATGGGTGCATTATTGGCATAAAATACATAGCTGA
*
2997877 AATGCATATGGGTGCATTATTGGCATAAAAGGATGTCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCAT-AAA--AT-ACATAGCTGA
*
2997922 AATGCATATGGGTGCATTATCGGCATAAAA
1 AATGCATATGGGTGCATTATTGGCATAAAA
2997952 GAATAATGCA
Statistics
Matches: 91, Mismatches: 7, Indels: 25
0.74 0.06 0.20
Matches are distributed among these distances:
34 25 0.27
36 3 0.03
38 2 0.02
39 1 0.01
40 2 0.02
41 2 0.02
42 1 0.01
43 3 0.03
44 3 0.03
45 49 0.54
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (41 bp):
AATGCATATGGGTGCATTATTGGCATAAAATACATAGCTGA
Found at i:3000518 original size:2 final size:2
Alignment explanation
Indices: 3000513--3000539 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3000503 TATATATATA
3000513 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
3000540 ATAGATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3002352 original size:79 final size:79
Alignment explanation
Indices: 3002262--3002547 Score: 403
Period size: 79 Copynumber: 3.6 Consensus size: 79
3002252 GAACGAATAA
* * *
3002262 ATAAAAGAATAATGCATATGGGTGTATTATTGGCATGAAAGGATGTTATAGCTGAAATGTATGTG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGTATATG
*
3002327 GATGCATTATCGAC
66 GGTGCATTATCGAC
* * * * *
3002341 ATAAAATAATAATGCATATGGCTGCATTATTGGCATGAAAGGATGTCATAGCTTAAATATATTTG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGTATATG
*
3002406 GGTGCATTATCAAC
66 GGTGCATTATCGAC
* * * *
3002420 ATAAAAGAATAATGCATATAGGTGTATTATTGGCATGAGAGGATGTCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGTATATG
*
3002485 GGTGCATTATCGGC
66 GGTGCATTATCGAC
* * *
3002499 ATAAAA-AACAATTCATATGGGTGCATTATTGGCATGAAAGGATGCCATA
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATA
3002548 AATAAAATGT
Statistics
Matches: 181, Mismatches: 26, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
78 37 0.20
79 144 0.80
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.30
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGTATATG
GGTGCATTATCGAC
Found at i:3002579 original size:46 final size:46
Alignment explanation
Indices: 3002520--3002647 Score: 202
Period size: 46 Copynumber: 2.8 Consensus size: 46
3002510 TTCATATGGG
* *
3002520 TGCATTATTGGCATGAAAGGATGCCATAAATAAAATGTATGAAATGA
1 TGCATTA-AGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGA
* * *
3002567 TGCATTAAGGCATGAAAAGATGCGACAAATAAAATGCATGAAATGA
1 TGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGA
3002613 TGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
1 TGCATTAAGGCATGAAAGGATGCCATAAATAAAAT
3002648 AATATTTAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
46 66 0.90
47 7 0.10
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.23
Consensus pattern (46 bp):
TGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGA
Found at i:3002583 original size:20 final size:20
Alignment explanation
Indices: 3002558--3002635 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
3002548 AATAAAATGT
3002558 ATGAAATGATGCATTAAGGC
1 ATGAAATGATGCATTAAGGC
* * *
3002578 ATGAAAAGATGCGACAAATAAAATGC
1 ATGAAATGAT--G-C--AT-TAAGGC
3002604 ATGAAATGATGCATTAAGGC
1 ATGAAATGATGCATTAAGGC
*
3002624 ATGAAAGGATGC
1 ATGAAATGATGC
3002636 CATAAATAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
20 24 0.53
21 2 0.04
22 1 0.02
23 2 0.04
24 1 0.02
25 2 0.04
26 13 0.29
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (20 bp):
ATGAAATGATGCATTAAGGC
Found at i:3004197 original size:23 final size:23
Alignment explanation
Indices: 3004167--3004232 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
3004157 TCAAGGGTTT
*
3004167 TATGTAGTCCTTCGGGACAATCC
1 TATGTAGTCCTTCAGGACAATCC
*
3004190 TATGTAGTCCTTCAGGATAATCC
1 TATGTAGTCCTTCAGGACAATCC
*
3004213 TATAT-GTTCCTTCAGGACAA
1 TATGTAG-TCCTTCAGGACAA
3004233 ATATGTGGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 1 0.03
23 37 0.97
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (23 bp):
TATGTAGTCCTTCAGGACAATCC
Found at i:3009765 original size:42 final size:42
Alignment explanation
Indices: 3009704--3009790 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
3009694 AATCATAATT
*
3009704 TTTTAAAAGGTCGACCCATCTTCTCTTTCTCAAGTTCAGTTC
1 TTTTAAAAGCTCGACCCATCTTCTCTTTCTCAAGTTCAGTTC
*
3009746 TTTTAAAAGCTCGATCCATCTTCTCTTTCTCAAGTTCAGTTC
1 TTTTAAAAGCTCGACCCATCTTCTCTTTCTCAAGTTCAGTTC
3009788 TTT
1 TTT
3009791 CTGAGTTAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.44
Consensus pattern (42 bp):
TTTTAAAAGCTCGACCCATCTTCTCTTTCTCAAGTTCAGTTC
Found at i:3019360 original size:21 final size:22
Alignment explanation
Indices: 3019334--3019382 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
3019324 TCGAGGGTTC
3019334 TATGTGGTC-CTTCGG-GACAA-A
1 TATGTGG-CACTTCGGTGA-AATA
3019355 TATGTGGCACTTCGGTGAAATA
1 TATGTGGCACTTCGGTGAAATA
3019377 TATGTG
1 TATGTG
3019383 AGCAGTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 1 0.04
21 15 0.60
22 9 0.36
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGAAATA
Found at i:3024336 original size:20 final size:20
Alignment explanation
Indices: 3024295--3024344 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3024285 CTGATGAACA
**
3024295 GTATCGATACTGAGGTGGAG
1 GTATCGATACCAAGGTGGAG
3024315 GTATCGATACCAAGG-GGAAG
1 GTATCGATACCAAGGTGG-AG
*
3024335 GTATCAATAC
1 GTATCGATAC
3024345 TATTTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.22
Consensus pattern (20 bp):
GTATCGATACCAAGGTGGAG
Found at i:3024839 original size:15 final size:16
Alignment explanation
Indices: 3024819--3024849 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3024809 TGTACATGAT
3024819 TGTGAATATG-TTATA
1 TGTGAATATGCTTATA
3024834 TGTGAATATGCTTATA
1 TGTGAATATGCTTATA
3024850 CTAAAATGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (16 bp):
TGTGAATATGCTTATA
Found at i:3029485 original size:298 final size:306
Alignment explanation
Indices: 3028941--3029545 Score: 1136
Period size: 298 Copynumber: 2.0 Consensus size: 306
3028931 AACGAGGGCG
3028941 TCCAGTCAAGCCACCCCACCACAGGGAGTTTCCATTTTAGTTTTAGTTTTTTTTTTTTTGTTATT
1 TCCAGTCAAGCCACCCCACCACAGGGAGTTTCCATTTTAGTTTTAGTTTTTTTTTTTTTGTTATT
3029006 TTCGCATCTGCATATAACATCATGTAGTTTTAGTTTTCATGCATTGAGGGTAATGCATCCATCAA
66 TTCGCATCTGCATATAACATCA-GTAGTTTTAGTTTTCATGCATTGAGGGTAATGCATCCATCAA
3029071 GTTTGGGGGAGGTATTATGCCATATTTTGTCATACTTTGTTAAAAAAATAATTGATGATGATTGG
130 GTTTGGGGGAGGTATTATGCCATATTTTGTCATACTTTGTTAAAAAAATAATTGATGATGATTGG
*
3029136 TTGAAAATTTTAGTTGACATGACATAAGCAGGTTAAGACTATTGTTTGGAATGAATTAGGGATGC
195 TTGAAAATTTTAGTTGACATGACATAAGCAGGTTAAGACTATTGGTTGGAATGAATTAGGGATGC
3029201 CCAATGACGAATGCATACATTTATTGCCTAGGTCAT-ATTA-TATTA
260 CCAATGACGAATGCATACATTTATTGCCTAGGTCATAATTATTATTA
3029246 TCCAGTCAAGCCACCCCACCACAGGGAGTTTCCATTTTAGTTTTAG-TTTTTTTTTTTTGTTATT
1 TCCAGTCAAGCCACCCCACCACAGGGAGTTTCCATTTTAGTTTTAGTTTTTTTTTTTTTGTTATT
3029310 TTCGCATCTGCATATAACA-C-GTAGTTTTAGTTTTCATGCA-TGAGGGTAATGCATCCATCAAG
66 TTCGCATCTGCATATAACATCAGTAGTTTTAGTTTTCATGCATTGAGGGTAATGCATCCATCAAG
3029372 -TTGGGGGAGGTATTATGCCATATTTTGTCATACTTTGTTAAAAAAA-AATTGATGATGATTGGT
131 TTTGGGGGAGGTATTATGCCATATTTTGTCATACTTTGTTAAAAAAATAATTGATGATGATTGGT
3029435 TGAAAATTTTAGTTGACATGACATAAGCAGGTTAAGACTATTGGTTGGAATGAATTAGGGATGCC
196 TGAAAATTTTAGTTGACATGACATAAGCAGGTTAAGACTATTGGTTGGAATGAATTAGGGATGCC
3029500 CAATGACGAATGCATACATTTATTGCCTAGGTCATAATTATTATTA
261 CAATGACGAATGCATACATTTATTGCCTAGGTCATAATTATTATTA
3029546 GACTGTCTAA
Statistics
Matches: 297, Mismatches: 1, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
298 116 0.39
299 50 0.17
300 27 0.09
301 20 0.07
303 1 0.00
304 37 0.12
305 46 0.15
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.38
Consensus pattern (306 bp):
TCCAGTCAAGCCACCCCACCACAGGGAGTTTCCATTTTAGTTTTAGTTTTTTTTTTTTTGTTATT
TTCGCATCTGCATATAACATCAGTAGTTTTAGTTTTCATGCATTGAGGGTAATGCATCCATCAAG
TTTGGGGGAGGTATTATGCCATATTTTGTCATACTTTGTTAAAAAAATAATTGATGATGATTGGT
TGAAAATTTTAGTTGACATGACATAAGCAGGTTAAGACTATTGGTTGGAATGAATTAGGGATGCC
CAATGACGAATGCATACATTTATTGCCTAGGTCATAATTATTATTA
Found at i:3031127 original size:15 final size:15
Alignment explanation
Indices: 3031107--3031148 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
3031097 TGATGAATTA
*
3031107 TGTTTTGCTTATGAT
1 TGTTTTGCTCATGAT
3031122 TGTTTTGCTCATGAT
1 TGTTTTGCTCATGAT
*
3031137 TGTTTTTCTCAT
1 TGTTTTGCTCAT
3031149 TGTTTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.60
Consensus pattern (15 bp):
TGTTTTGCTCATGAT
Found at i:3036292 original size:18 final size:18
Alignment explanation
Indices: 3036240--3036279 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3036230 GATAGAAAAT
*
3036240 TTACATTAAAATTTAAAC
1 TTACCTTAAAATTTAAAC
3036258 TTACCTTAAAATTTAAAC
1 TTACCTTAAAATTTAAAC
3036276 TTAC
1 TTAC
3036280 TCTTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (18 bp):
TTACCTTAAAATTTAAAC
Found at i:3036724 original size:9 final size:9
Alignment explanation
Indices: 3036706--3036981 Score: 87
Period size: 9 Copynumber: 27.8 Consensus size: 9
3036696 AAGGTAATGT
3036706 AAATAAATA
1 AAATAAATA
*
3036715 AAATATATAAA
1 AAATA-A-ATA
* *
3036726 AAACAAATG
1 AAATAAATA
3036735 AAATAAATA
1 AAATAAATA
3036744 AAATAAGATA
1 AAATAA-ATA
*
3036754 AAGA-AGAAGAA
1 AA-ATA-AA-TA
3036765 GAAATAAATA
1 -AAATAAATA
3036775 AAATAAAAATTA
1 AAAT--AAA-TA
*
3036787 AAATAAAGA
1 AAATAAATA
3036796 AAATATATATA
1 AAATA-A-ATA
*
3036807 AATATAAA-G
1 AA-ATAAATA
3036816 AAATAAATA
1 AAATAAATA
*
3036825 AAGATAAAGA
1 AA-ATAAATA
3036835 GAAA-AAATAA
1 -AAATAAAT-A
3036845 AAATAAAATA
1 AAAT-AAATA
3036855 AGGGAA-AAAT-
1 A---AATAAATA
3036865 AAATAAGATA
1 AAATAA-ATA
* *
3036875 AAGGTAAAGA
1 AA-ATAAATA
*
3036885 AAATAAAGA
1 AAATAAATA
*
3036894 AAATAAAAA
1 AAATAAATA
3036903 CAAAGTCAAGATA
1 -AAA-T-AA-ATA
*
3036916 AAAAATAAT-
1 AAATA-AATA
3036925 AAATAAATAA
1 AAATAAAT-A
*
3036935 AAATAGAAAAA
1 AAAT--AAATA
*
3036946 AAATAAAAA
1 AAATAAATA
3036955 TAAATAAGATA
1 -AAATAA-ATA
*
3036966 ACATAAATA
1 AAATAAATA
3036975 AAATAAA
1 AAATAAA
3036982 ACAAATGGCA
Statistics
Matches: 204, Mismatches: 25, Indels: 76
0.67 0.08 0.25
Matches are distributed among these distances:
7 2 0.01
8 10 0.05
9 73 0.36
10 53 0.26
11 42 0.21
12 20 0.10
13 4 0.02
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.17
Consensus pattern (9 bp):
AAATAAATA
Found at i:3036837 original size:20 final size:19
Alignment explanation
Indices: 3036785--3036851 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
3036775 AAATAAAAAT
*
3036785 TAAAATAAAGA-AAATATA
1 TAAAATAAAGAGAAATAAA
3036803 TATAAATATAA-AGAAATAAA
1 TA-AAATA-AAGAGAAATAAA
3036823 TAAAGATAAAGAGAAA-AAA
1 TAAA-ATAAAGAGAAATAAA
3036842 TAAAAATAAA
1 T-AAAATAAA
3036852 ATAAGGGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
18 2 0.05
19 19 0.45
20 21 0.50
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.19
Consensus pattern (19 bp):
TAAAATAAAGAGAAATAAA
Found at i:3036844 original size:19 final size:18
Alignment explanation
Indices: 3036770--3036851 Score: 76
Period size: 19 Copynumber: 4.4 Consensus size: 18
3036760 AAGAAGAAAT
* *
3036770 AAATAAA-ATAAAAATTA
1 AAATAAAGAAAAAAATAA
3036787 AAATAAAGAAAATATATATAA
1 AAATAAAGAAAA-A-A-ATAA
* *
3036808 ATATAAAGAAATAAATAA
1 AAATAAAGAAAAAAATAA
*
3036826 AGATAAAGAGAAAAAATAA
1 AAATAAAGA-AAAAAATAA
3036845 AAATAAA
1 AAATAAA
3036852 ATAAGGGAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
17 7 0.13
18 15 0.28
19 16 0.30
20 2 0.04
21 13 0.25
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (18 bp):
AAATAAAGAAAAAAATAA
Found at i:3036870 original size:20 final size:21
Alignment explanation
Indices: 3036735--3036875 Score: 66
Period size: 21 Copynumber: 6.7 Consensus size: 21
3036725 AAAACAAATG
*
3036735 AAATAAATAAAATAAGATAAA
1 AAATAAATAAAATAAGAGAAA
* * *
3036756 GAAGAAGA-AGAAATAA-ATAAA
1 AAATAA-ATA-AAATAAGAGAAA
3036777 ATAA-AAATTAAAATAA-AGAAA
1 A-AATAAA-TAAAATAAGAGAAA
* *
3036798 ATATATATAAATATAA-AG---
1 AAATAAATAAA-ATAAGAGAAA
3036816 AAATAAATAAAGATAAAGAGAAA
1 AAATAAATAAA-AT-AAGAGAAA
*
3036839 AAATAAAAATAAAATAAG-GGAA
1 AAAT--AAATAAAATAAGAGAAA
*
3036861 AAATAAATAAGATAA
1 AAATAAATAAAATAA
3036876 AGGTAAAGAA
Statistics
Matches: 95, Mismatches: 11, Indels: 29
0.70 0.08 0.21
Matches are distributed among these distances:
18 11 0.12
19 2 0.02
20 18 0.19
21 31 0.33
22 17 0.18
23 7 0.07
24 2 0.02
25 7 0.07
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (21 bp):
AAATAAATAAAATAAGAGAAA
Found at i:3036938 original size:41 final size:39
Alignment explanation
Indices: 3036885--3036986 Score: 100
Period size: 41 Copynumber: 2.6 Consensus size: 39
3036875 AAGGTAAAGA
* * * *
3036885 AAATAAAGAAAATAAAAACAAAGTCAAGATAAAAAATAAT
1 AAATAAATAAAATAAAAACAAAATAAAAATAAAAAA-AAT
* *
3036925 AAATAAATAAAAATAGAAAA-AAAATAAAAATAAATAAGAT
1 AAATAAAT-AAAATA-AAAACAAAATAAAAATAAAAAAAAT
3036965 AACATAAATAAAAT-AAAACAAA
1 AA-ATAAATAAAATAAAAACAAA
3036987 TGGCATAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
38 4 0.08
39 3 0.06
40 16 0.31
41 25 0.48
42 4 0.08
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (39 bp):
AAATAAATAAAATAAAAACAAAATAAAAATAAAAAAAAT
Found at i:3036944 original size:24 final size:24
Alignment explanation
Indices: 3036891--3036948 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
3036881 AAGAAAATAA
* *
3036891 AGAAAATAAAAACAAAGTCAAGAT
1 AGAAAATAAAAACAAAGTAAAAAT
* *
3036915 AAAAAATAATAAATAAA-TAAAAAT
1 AGAAAATAA-AAACAAAGTAAAAAT
3036939 AGAAAA-AAAA
1 AGAAAATAAAA
3036949 TAAAAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 2 0.07
23 2 0.07
24 18 0.64
25 6 0.21
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (24 bp):
AGAAAATAAAAACAAAGTAAAAAT
Found at i:3036979 original size:50 final size:50
Alignment explanation
Indices: 3036705--3037003 Score: 152
Period size: 52 Copynumber: 5.8 Consensus size: 50
3036695 AAAGGTAATG
* * ** *
3036705 TAAATAAATA-AAATATATAAAAA-ACAAATGAAATAAATA-AAATAAGA
1 TAAATAAATAGAAATAAATAAAAATAGAAAAAAAATAAAAATAAATAAGA
* * * *
3036752 TAAAGAAGAAGAAGAAATAAAT-AAAATA-AAAATTAAAATAAAGA-AAATATATA
1 TAAA-TA-AA-TAGAAATAAATAAAAATAGAAAA--AAAATAAAAATAAATA-AGA
* *
3036805 TAAATATAA-AGAAATAAATAAAGATAAAGAGAAAAAATAAAAATAAAATAAGGGA
1 TAAATA-AATAGAAATAAATAAA-A-ATAGAAAAAAAATAAAAAT-AAATAA--GA
* * * * * *
3036860 AAAATAAATA-AGATAAAGGTAAAGAAAATAAAGAAAATAAAAACAAAGTCAAGA
1 TAAATAAATAGAAATAAA--TAAA-AATAGAAAAAAAATAAAAATAAA-T-AAGA
*
3036914 TAAA-AAATAATAAATAAATAAAAATAGAAAAAAAATAAAAATAAATAAGA
1 TAAATAAAT-AGAAATAAATAAAAATAGAAAAAAAATAAAAATAAATAAGA
* * *
3036964 TAACATAAATA-AAATAAA-ACAAATGGCATAAAAAATAAAA
1 TAA-ATAAATAGAAATAAATAAAAATAG-AAAAAAAATAAAA
3037004 GCATATATAC
Statistics
Matches: 198, Mismatches: 28, Indels: 49
0.72 0.10 0.18
Matches are distributed among these distances:
47 4 0.02
48 1 0.01
49 8 0.04
50 44 0.22
51 13 0.07
52 49 0.25
53 17 0.09
54 25 0.13
55 29 0.15
56 8 0.04
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.17
Consensus pattern (50 bp):
TAAATAAATAGAAATAAATAAAAATAGAAAAAAAATAAAAATAAATAAGA
Found at i:3036987 original size:14 final size:14
Alignment explanation
Indices: 3036706--3036987 Score: 97
Period size: 14 Copynumber: 19.6 Consensus size: 14
3036696 AAGGTAATGT
3036706 AAATAAATAAAATA
1 AAATAAATAAAATA
*
3036720 TATAA-AAA-ACAAATG
1 -A-AATAAATA-AAATA
3036735 AAATAAATAAAATA
1 AAATAAATAAAATA
* * *
3036749 AGATAAAGAAGA-A
1 AAATAAATAAAATA
* *
3036762 GAAGAAAT-AAATA
1 AAATAAATAAAATA
*
3036775 AAAT-AA-AAATTA
1 AAATAAATAAAATA
*
3036787 AAATAAAGAAAATA
1 AAATAAATAAAATA
* *
3036801 TATATAAATATAAA-G
1 -AAATAAATA-AAATA
3036816 AAATAAATAAAGATA
1 AAATAAATAAA-ATA
*
3036831 AAGA-GAA-AAAATAA
1 AA-ATAAATAAAAT-A
*
3036845 AAATAAAATAAGGGA-A
1 AAAT-AAATAA--AATA
*
3036861 AAATAAATAAGATA
1 AAATAAATAAAATA
* *
3036875 AAGGTAAAGAAAATA
1 AA-ATAAATAAAATA
3036890 AAGA-AAATAAAA-A
1 AA-ATAAATAAAATA
3036903 CAAAGTCAAGATAAAA-A
1 -AAA-T-AA-ATAAAATA
3036920 ATAATAAAT-AAATAA
1 A-AATAAATAAAAT-A
*
3036935 AAATAGAAAAAAAATAA
1 AAAT--AAATAAAAT-A
*
3036952 AAATAAATAAGATA
1 AAATAAATAAAATA
*
3036966 ACATAAATAAAATA
1 AAATAAATAAAATA
*
3036980 AAACAAAT
1 AAATAAAT
3036988 GGCATAAAAA
Statistics
Matches: 201, Mismatches: 34, Indels: 65
0.67 0.11 0.22
Matches are distributed among these distances:
12 12 0.06
13 24 0.12
14 74 0.37
15 51 0.25
16 20 0.10
17 19 0.09
18 1 0.00
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (14 bp):
AAATAAATAAAATA
Found at i:3039990 original size:37 final size:38
Alignment explanation
Indices: 3039877--3039998 Score: 131
Period size: 38 Copynumber: 3.2 Consensus size: 38
3039867 AGGAATTGTA
* * *
3039877 CCTAGAAAGCTTGATCTAGTCTTTCTCAATATTATTTC
1 CCTAGAAACCTTAATCTAGTCTTTCTCAAGATTATTTC
* * **
3039915 CCTAGAAACCTTAAT-TTGATCTTTCTTAAGATCGTTTC
1 CCTAGAAACCTTAATCTAG-TCTTTCTCAAGATTATTTC
* *
3039953 CCTTGAAACTTTAATCTAGT-TTTCTCAAGATTATTTC
1 CCTAGAAACCTTAATCTAGTCTTTCTCAAGATTATTTC
*
3039990 CCTGGAAAC
1 CCTAGAAAC
3039999 ATTATTTAGG
Statistics
Matches: 68, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
37 24 0.35
38 42 0.62
39 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (38 bp):
CCTAGAAACCTTAATCTAGTCTTTCTCAAGATTATTTC
Found at i:3041060 original size:12 final size:12
Alignment explanation
Indices: 3041043--3041072 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
3041033 GGGAATTTAA
3041043 TGCCCCGACTAC
1 TGCCCCGACTAC
3041055 TGCCCCGACTAC
1 TGCCCCGACTAC
3041067 TGCCCC
1 TGCCCC
3041073 TGTTACCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.53, G:0.17, T:0.17
Consensus pattern (12 bp):
TGCCCCGACTAC
Found at i:3042244 original size:76 final size:76
Alignment explanation
Indices: 3042142--3042290 Score: 208
Period size: 76 Copynumber: 2.0 Consensus size: 76
3042132 TGAGCATGTG
*** * * * *
3042142 CCCACCCTGGAATTTGAATTTCTTTATGTTAGTTATTTATTTTATTGAATATGTCCACCATGAAA
1 CCCACCCTGGAATCCAAATTTATTTATGTTAATTATTTATTTTATTGAAGATGCCCACCATGAAA
3042207 TTTTATTTGTT
66 TTTTATTTGTT
* * *
3042218 CCCACCCTGGAATCCAAATTTATTTATGTTAATTGTTTATTTTATTGAAGGTGCCCACCCTGAAA
1 CCCACCCTGGAATCCAAATTTATTTATGTTAATTATTTATTTTATTGAAGATGCCCACCATGAAA
3042283 TTTTATTT
66 TTTTATTT
3042291 TTGCCTACCC
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 63 1.00
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.46
Consensus pattern (76 bp):
CCCACCCTGGAATCCAAATTTATTTATGTTAATTATTTATTTTATTGAAGATGCCCACCATGAAA
TTTTATTTGTT
Found at i:3047030 original size:3 final size:3
Alignment explanation
Indices: 3047022--3047081 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
3047012 TTACAAAAGA
3047022 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3047070 ATT ATT ATT ATT
1 ATT ATT ATT ATT
3047082 TGAAAATATG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3048554 original size:3 final size:3
Alignment explanation
Indices: 3048548--3048594 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
3048538 TAATATTTTT
* *
3048548 TTA TTA TTA TTA TTA TTA TTA TTA TTA AT- TTA TATA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
3048593 TT
1 TT
3048595 TTGTGGGCCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 34 0.89
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3050704 original size:14 final size:14
Alignment explanation
Indices: 3050688--3050845 Score: 83
Period size: 14 Copynumber: 10.9 Consensus size: 14
3050678 TGGTTTATTT
3050688 TTTTATTTTATTTT-
1 TTTTATTTT-TTTTA
*
3050702 TTTTATTTTTATT-
1 TTTTATTTTTTTTA
*
3050715 TTTTATTATTTTTA
1 TTTTATTTTTTTTA
* *
3050729 TTTTATTACTTTTAA
1 TTTTATT-TTTTTTA
* **
3050744 CATTTAACTTTTTTA
1 -TTTTATTTTTTTTA
*
3050759 TTTTATCTTTTTTA
1 TTTTATTTTTTTTA
*
3050773 TCTTT-TTTCCTCTTTGA
1 T-TTTATTT--T-TTTTA
*
3050790 -TTTATTTTTTTTC
1 TTTTATTTTTTTTA
*
3050803 TTTT-TTTCTTTTTT
1 TTTTATTT-TTTTTA
*
3050817 TCTTTATTTATTTTA
1 T-TTTATTTTTTTTA
3050832 TTTTATTTTATTTT
1 TTTTATTTT-TTTT
3050846 TTCTTTGATT
Statistics
Matches: 111, Mismatches: 20, Indels: 25
0.71 0.13 0.16
Matches are distributed among these distances:
13 20 0.18
14 48 0.43
15 28 0.25
16 11 0.10
17 4 0.04
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.77
Consensus pattern (14 bp):
TTTTATTTTTTTTA
Found at i:3050707 original size:9 final size:9
Alignment explanation
Indices: 3050681--3050847 Score: 68
Period size: 10 Copynumber: 17.1 Consensus size: 9
3050671 GGATGCTTGG
3050681 TTTA-TTTT
1 TTTATTTTT
3050689 TTTATTTTAT
1 TTTATTTT-T
*
3050699 TTTTTTTATT
1 TTTATTT-TT
3050709 TTTATTTTT
1 TTTATTTTT
3050718 TATTATTTTTAT
1 T-TTA-TTTT-T
3050730 TTTATTACTTT
1 TTTATT--TTT
** **
3050741 TAACATTTAAC
1 T-TTATTT-TT
*
3050752 TTT-TTTAT
1 TTTATTTTT
*
3050760 TTTATCTTT
1 TTTATTTTT
3050769 TTTATCTTTT
1 TTTAT-TTTT
* **
3050779 TTCCTCTTTGA
1 TT--TATTTTT
3050790 TTTATTTTT
1 TTTATTTTT
*
3050799 TTTCTTTTT
1 TTTATTTTT
*
3050808 TTCTTTTTTT
1 TT-TATTTTT
*
3050818 CTTTATTTAT
1 -TTTATTTTT
3050828 TTTATTTTAT
1 TTTATTTT-T
3050838 TTTATTTTT
1 TTTATTTTT
3050847 T
1 T
3050848 CTTTGATTTA
Statistics
Matches: 119, Mismatches: 23, Indels: 33
0.68 0.13 0.19
Matches are distributed among these distances:
8 8 0.07
9 40 0.34
10 45 0.38
11 17 0.14
12 9 0.08
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.78
Consensus pattern (9 bp):
TTTATTTTT
Found at i:3050717 original size:16 final size:16
Alignment explanation
Indices: 3050685--3050732 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
3050675 GCTTGGTTTA
3050685 TTTTTTTA-TTTTA-T
1 TTTTTTTATTTTTATT
3050699 TTTTTTTATTTTTATT
1 TTTTTTTATTTTTATT
*
3050715 TTTTATTATTTTTATT
1 TTTTTTTATTTTTATT
3050731 TT
1 TT
3050733 ATTACTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 8 0.26
15 5 0.16
16 18 0.58
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTATTTTTATT
Found at i:3050832 original size:38 final size:36
Alignment explanation
Indices: 3050759--3050840 Score: 107
Period size: 34 Copynumber: 2.3 Consensus size: 36
3050749 AACTTTTTTA
*
3050759 TTTTATCTTTTTTATCTTTTTTCCTCTTTGATTTATT
1 TTTTTTCTTTTTT-TCTTTTTTCCTCTTTGATTTATT
3050796 TTTTTTCTTTTTTTCTTTTTT--TCTTT-ATTTATT
1 TTTTTTCTTTTTTTCTTTTTTCCTCTTTGATTTATT
*
3050829 TTATTTTATTTT
1 TT-TTTTCTTTT
3050841 ATTTTTTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
33 9 0.21
34 13 0.31
36 8 0.19
37 12 0.29
ACGTcount: A:0.10, C:0.10, G:0.01, T:0.79
Consensus pattern (36 bp):
TTTTTTCTTTTTTTCTTTTTTCCTCTTTGATTTATT
Found at i:3050846 original size:38 final size:36
Alignment explanation
Indices: 3050754--3050851 Score: 108
Period size: 38 Copynumber: 2.7 Consensus size: 36
3050744 CATTTAACTT
* *
3050754 TTTTATTTTATCTTTTTTATCTTTTTTCCTCTTTGA
1 TTTTATTTTATTTTTTTTTTCTTTTTTCCTCTTTGA
* * * *
3050790 -TTTATTTTTTTTCTTTTTTTCTTTTTTTCTTTATTTA
1 TTTTATTTTATTT-TTTTTTTCTTTTTTCCTCT-TTGA
3050827 TTTTATTTTATTTTATTTTTTCTTT
1 TTTTATTTTATTTT-TTTTTTCTTT
3050852 GATTTATTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
35 10 0.20
36 16 0.31
37 4 0.08
38 21 0.41
ACGTcount: A:0.10, C:0.09, G:0.01, T:0.80
Consensus pattern (36 bp):
TTTTATTTTATTTTTTTTTTCTTTTTTCCTCTTTGA
Found at i:3050857 original size:31 final size:31
Alignment explanation
Indices: 3050783--3050881 Score: 103
Period size: 31 Copynumber: 3.1 Consensus size: 31
3050773 TCTTTTTTCC
* * *
3050783 TCTTTGATTTATTTTTTTTCTTTTTTTCTTTTTT
1 TCTTTGATTTA-TTTTATT-TTATTTT-ATTTTT
3050817 TCTTT-ATTTATTTTATTTTATTTTATTTTT
1 TCTTTGATTTATTTTATTTTATTTTATTTTT
* *
3050847 TCTTTGATTTATTTAATATTTA-TTTATTATT
1 TCTTTGATTTATTTTAT-TTTATTTTATTTTT
3050878 TCTT
1 TCTT
3050882 GTCTAACATT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.17
31 28 0.48
32 10 0.17
33 5 0.09
34 5 0.09
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (31 bp):
TCTTTGATTTATTTTATTTTATTTTATTTTT
Found at i:3050867 original size:38 final size:37
Alignment explanation
Indices: 3050789--3050871 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 37
3050779 TTCCTCTTTG
* * * *
3050789 ATTTATTTTTTTTCTTTTTTTCTTTTTTTCTTTATTT
1 ATTTATTTTTTTTCATTTTTTCTTTATTTATTTATAT
3050826 ATTTTATTTTATTTT-ATTTTTTCTTTGATTTATTTA-AT
1 A-TTTATTTT-TTTTCATTTTTTCTTT-ATTTATTTATAT
3050864 ATTTATTT
1 ATTTATTT
3050872 ATTATTTCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
37 8 0.21
38 20 0.51
39 11 0.28
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (37 bp):
ATTTATTTTTTTTCATTTTTTCTTTATTTATTTATAT
Found at i:3052556 original size:7 final size:7
Alignment explanation
Indices: 3052544--3052569 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3052534 GAATATTTCA
3052544 TGCATTT
1 TGCATTT
3052551 TGCATTT
1 TGCATTT
3052558 TGCATTT
1 TGCATTT
3052565 TGCAT
1 TGCAT
3052570 CTACATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (7 bp):
TGCATTT
Found at i:3053846 original size:19 final size:18
Alignment explanation
Indices: 3053811--3053884 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 18
3053801 CAATCAGAAC
*
3053811 AAAAAGAG-AAAAGAAGA
1 AAAAAGAGAAAAAAAAGA
3053828 AAAAAGAGAAAAACAAAGA
1 AAAAAGAGAAAAA-AAAGA
* *
3053847 AAAAAAAGCAAAGAGAAAATA
1 AAAAAGAG-AAA-A-AAAAGA
3053868 AAAAAGAGAAACAAAAA
1 AAAAAGAGAAA-AAAAA
3053885 CAAAGAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
17 8 0.17
18 4 0.09
19 15 0.32
20 7 0.15
21 12 0.26
22 1 0.02
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.01
Consensus pattern (18 bp):
AAAAAGAGAAAAAAAAGA
Found at i:3053858 original size:14 final size:14
Alignment explanation
Indices: 3053813--3053895 Score: 66
Period size: 14 Copynumber: 5.8 Consensus size: 14
3053803 ATCAGAACAA
3053813 AAAGAGAAAAGAAGA-
1 AAAGAGAAAA-AA-AC
* *
3053828 AAAAAGAGAAAAAC
1 AAAGAGAAAAAAAC
3053842 AAAGA-AAAAAAAGC
1 AAAGAGAAAAAAA-C
3053856 AAAGAGAAAATAAA-
1 AAAGAGAAAA-AAAC
3053870 AAAGAGAAACAAAAAC
1 AAAGAG-AA-AAAAAC
3053886 AAAGA-AAAAA
1 AAAGAGAAAAA
3053896 GTGAAAAAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
13 10 0.18
14 20 0.35
15 17 0.30
16 10 0.18
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.01
Consensus pattern (14 bp):
AAAGAGAAAAAAAC
Found at i:3055041 original size:32 final size:32
Alignment explanation
Indices: 3054959--3055078 Score: 170
Period size: 32 Copynumber: 3.8 Consensus size: 32
3054949 AGGAACAATG
** * *
3054959 GGGGCATCTTTAAAGATTCAACATCAAATGTT
1 GGGGCATCTTTGGAGATTCAACATCGAATATT
*
3054991 GGGGTAT-TTTGGAGATTCAACATCGAATATT
1 GGGGCATCTTTGGAGATTCAACATCGAATATT
* *
3055022 AGGGCATCTTTGGATATTCAACATCGAATATT
1 GGGGCATCTTTGGAGATTCAACATCGAATATT
3055054 GGGGCATCTTTGGAGATTCAACATC
1 GGGGCATCTTTGGAGATTCAACATC
3055079 CTGATGCGAA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
31 25 0.32
32 52 0.68
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (32 bp):
GGGGCATCTTTGGAGATTCAACATCGAATATT
Found at i:3057232 original size:21 final size:20
Alignment explanation
Indices: 3057203--3057241 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3057193 AAAACAATAT
*
3057203 TTTATTATTATTATTATTAA
1 TTTATTATTATAATTATTAA
3057223 TTTATATATTATAATTATT
1 TTTAT-TATTATAATTATT
3057242 TTATGGGCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATTATTATAATTATTAA
Found at i:3057234 original size:18 final size:17
Alignment explanation
Indices: 3057207--3057245 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
3057197 CAATATTTTA
*
3057207 TTATTATTATTATTAAT
1 TTATTATTATAATTAAT
*
3057224 TTATATATTATAATTATT
1 TTAT-TATTATAATTAAT
3057242 TTAT
1 TTAT
3057246 GGGCCCTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTATTATAATTAAT
Found at i:3058208 original size:3 final size:3
Alignment explanation
Indices: 3058202--3058227 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3058192 TGTTTTTTTA
3058202 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
3058228 AAGGCGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3058281 original size:21 final size:19
Alignment explanation
Indices: 3058246--3058291 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
3058236 TGATGCTTCG
3058246 TTTATTTTTTTATTTTCT-T
1 TTTATTTTTTTATTTT-TAT
3058265 TTTATTTCTTATTATTTTTAT
1 TTTATTT-TT-TTATTTTTAT
3058286 TTTATT
1 TTTATT
3058292 ACTTTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.29
20 3 0.12
21 14 0.58
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTATTTTTTTATTTTTAT
Found at i:3058376 original size:18 final size:15
Alignment explanation
Indices: 3058353--3058398 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
3058343 TTTTTATCTT
3058353 TTTTTCCTCTTTGATTTA
1 TTTTTCCT-TTT--TTTA
3058371 TTTTTCCTTTTTTTA
1 TTTTTCCTTTTTTTA
3058386 TTTTTCCTTTTTT
1 TTTTTCCTTTTTT
3058399 CCTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.61
17 3 0.11
18 8 0.29
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTTCCTTTTTTTA
Found at i:3058419 original size:23 final size:23
Alignment explanation
Indices: 3058371--3058419 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
3058361 CTTTGATTTA
* *
3058371 TTTTTCC-TTTTTTTATTTTTCC
1 TTTTTCCTTTTTTTTATTTCTAC
3058393 TTTTTTCCTTTTTTTTATTTCTA-
1 -TTTTTCCTTTTTTTTATTTCTAC
3058416 TTTT
1 TTTT
3058420 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 7 0.30
24 12 0.52
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTCCTTTTTTTTATTTCTAC
Found at i:3058449 original size:39 final size:37
Alignment explanation
Indices: 3058310--3058451 Score: 117
Period size: 39 Copynumber: 3.7 Consensus size: 37
3058300 AATTTAACTT
* * *
3058310 TTTTTATTTTATTTTTTTGATCTATTTAATATTTTTTTA
1 TTTTTATTTT-TTTCTTTGATTTATTTTAT-TTTTTTTA
* **
3058349 TCTTT-TTTTCCTCTTTGATTTATTTT-TCCTTTTTTTA
1 TTTTTATTTTTTTCTTTGATTTATTTTAT--TTTTTTTA
* * **
3058386 TTTTTCCTTTTTTCCTTTTTTTTATTTCTATTTTATTTTA
1 TTTTT-ATTTTTTTCTTTGATTTATTT-TATTTT-TTTTA
3058426 TTTTTATTTTTTTCTTTGATTTATTT
1 TTTTTATTTTTTTCTTTGATTTATTT
3058452 AATACTTATT
Statistics
Matches: 80, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
36 1 0.01
37 24 0.30
38 4 0.05
39 39 0.49
40 11 0.14
41 1 0.01
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (37 bp):
TTTTTATTTTTTTCTTTGATTTATTTTATTTTTTTTA
Found at i:3061946 original size:23 final size:23
Alignment explanation
Indices: 3061918--3061983 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
3061908 TATACTTTGA
3061918 TATTGAATCATTCAGCACTGTTT
1 TATTGAATCATTCAGCACTGTTT
* ** *
3061941 TGTTGAATCATTTTGTACTGTTT
1 TATTGAATCATTCAGCACTGTTT
*
3061964 TATTGAATCAGTCAGCACTG
1 TATTGAATCATTCAGCACTG
3061984 AATCATTCAG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (23 bp):
TATTGAATCATTCAGCACTGTTT
Found at i:3065840 original size:21 final size:21
Alignment explanation
Indices: 3065811--3065863 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3065801 ATTCTGACTA
3065811 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
3065832 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
3065853 TCGCAATGCGA
1 TCGCATTGCGA
3065864 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:3065896 original size:21 final size:20
Alignment explanation
Indices: 3065853--3065944 Score: 116
Period size: 20 Copynumber: 4.5 Consensus size: 20
3065843 TTTTCCTAAT
3065853 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
3065873 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
3065894 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
3065914 TCGCAATGCAAAT-C-TAACTA
1 TCGCAATGCGAATACGTAA--A
3065934 TCGCAATGCGA
1 TCGCAATGCGA
3065945 TTTACATAGC
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.05
19 1 0.02
20 41 0.65
21 18 0.29
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:3066532 original size:19 final size:19
Alignment explanation
Indices: 3066510--3066621 Score: 153
Period size: 19 Copynumber: 6.1 Consensus size: 19
3066500 AAAACCAAAA
*
3066510 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3066529 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3066548 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3066562 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3066581 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3066600 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3066620 TC
1 TC
3066622 AATCAAAAGA
Statistics
Matches: 83, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 49 0.59
20 18 0.22
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3066574 original size:33 final size:34
Alignment explanation
Indices: 3066532--3066621 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 34
3066522 TTTCATTTCG
3066532 CGTTGCGATTTTCATTTCGCGTTGCG-ATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGTATTCTCT
3066565 CGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCG----T-ATTCTCT
3066604 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
3066622 AATCAAAAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
33 26 0.51
39 25 0.49
ACGTcount: A:0.10, C:0.23, G:0.19, T:0.48
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTCGCGTTGCGTATTCTCT
Found at i:3068485 original size:94 final size:93
Alignment explanation
Indices: 3068296--3068671 Score: 598
Period size: 94 Copynumber: 4.1 Consensus size: 93
3068286 TAGATTGCTT
* *
3068296 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3068357 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
3068386 AGTAAATTTATTCGGTTGCTGCCAATTCGGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
3068451 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
3068480 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
3068545 ATTTGTCTTTGTTTTTTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
3068574 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTTTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3068639 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
3068667 AGTAA
1 AGTAA
3068672 TGCAATCCAT
Statistics
Matches: 269, Mismatches: 12, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
90 34 0.13
92 3 0.01
93 27 0.10
94 205 0.76
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:3068788 original size:20 final size:20
Alignment explanation
Indices: 3068763--3068824 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
3068753 TTTTGGTTGA
3068763 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
3068783 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
3068802 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
3068822 AAT
1 AAT
3068825 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.50, C:0.18, G:0.23, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:3068809 original size:39 final size:35
Alignment explanation
Indices: 3068761--3068884 Score: 139
Period size: 33 Copynumber: 3.5 Consensus size: 35
3068751 TCTTTTGGTT
3068761 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAG-A-G--AATCGCAACGC
*
3068800 GAAACGAAAATCGCAAC--GAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAGAATCGCAACGC
*
3068833 GAAATGAAAATCGCAACGACA-A-AATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAGAATCGCAACGC
**
3068866 GAAACCAAAAATCGCAACG
1 GAAA-TGAAAATCGCAACG
3068885 CGAAACTATA
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
33 42 0.55
34 13 0.17
35 2 0.03
36 1 0.01
37 3 0.04
39 16 0.21
ACGTcount: A:0.48, C:0.23, G:0.21, T:0.08
Consensus pattern (35 bp):
GAAATGAAAATCGCAACGAGAGAGAATCGCAACGC
Found at i:3068831 original size:33 final size:33
Alignment explanation
Indices: 3068787--3068884 Score: 151
Period size: 33 Copynumber: 2.9 Consensus size: 33
3068777 CGAGAGAATG
*
3068787 AAAATCGCAACGCGAAACGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
* *
3068820 AGAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
*
3068853 AAAATCGCAACGCGAAACCAAAAATCGCAACG
1 AAAATCGCAACGCGAAA-CGAAAATCGCAACG
3068885 CGAAACTATA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.79
34 12 0.21
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACGAAAATCGCAACGAC
Found at i:3068876 original size:20 final size:20
Alignment explanation
Indices: 3068853--3068890 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3068843 TCGCAACGAC
3068853 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
3068873 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
3068891 TATAATCGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.29, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:3068918 original size:19 final size:19
Alignment explanation
Indices: 3068896--3069043 Score: 108
Period size: 19 Copynumber: 7.9 Consensus size: 19
3068886 GAAACTATAA
3068896 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTAATT
* *
3068915 TCGCATTGCGA---T--TC
1 TCGCGTTGCGATTTTAATT
* *
3068929 TCTCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTAATT
* **
3068948 TTGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTAATT
* *
3068967 TTGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATT
* *
3068986 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTAATT
* *
3069006 TCGCGTTGCGATAGTCAATTT
1 TCGCGTTGCGAT-TTTAA-TT
*
3069027 TCACGTTGCGATTTTAA
1 TCGCGTTGCGATTTTAA
3069044 GTTCCAGAAA
Statistics
Matches: 102, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
14 10 0.10
16 1 0.01
17 1 0.01
19 55 0.54
20 22 0.22
21 13 0.13
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAATT
Found at i:3069001 original size:39 final size:38
Alignment explanation
Indices: 3068896--3069041 Score: 124
Period size: 39 Copynumber: 3.9 Consensus size: 38
3068886 GAAACTATAA
* * *
3068896 TCGCGTTGCGATTTTAATTTCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATTTCTCGTTGCGATTTTCATT
* * *
3068929 TCTCGTTGCGATTTTTATTT-TGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATTTCT-CGTTGCGATTTTCATT
*
3068967 TTGCGTTGCGATTTTCATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT-TCTCGTTGCGATTTTCATT
** *
3069006 TCGCGTTGCGATAGTCAATTTTCACGTTGCGATTTT
1 TCGCGTTGCGATTTTC-A-TTTCTCGTTGCGATTTT
3069042 AAGTTCCAGA
Statistics
Matches: 91, Mismatches: 12, Indels: 13
0.78 0.10 0.11
Matches are distributed among these distances:
33 25 0.27
35 3 0.03
38 16 0.18
39 29 0.32
40 16 0.18
41 2 0.02
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCTCGTTGCGATTTTCATT
Found at i:3069555 original size:21 final size:20
Alignment explanation
Indices: 3069496--3069556 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
3069486 CTCGAGAGTC
3069496 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
3069516 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
3069537 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
3069557 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:3070925 original size:14 final size:14
Alignment explanation
Indices: 3070906--3070941 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3070896 ATTGTTTAAT
3070906 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3070920 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3070934 TGATTTGT
1 TGATTTGT
3070942 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3071070 original size:19 final size:19
Alignment explanation
Indices: 3071048--3071101 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
3071038 AAAAATTACT
* *
3071048 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCAAAATGAAA
*
3071067 ATCGCAACGCAAAATGCAA
1 ATCGCAACGCAAAATGAAA
3071086 ATCGCAACGACAAAAT
1 ATCGCAACG-CAAAAT
3071102 CGCAACGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 25 0.81
20 6 0.19
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCAAAATGAAA
Found at i:3071147 original size:19 final size:18
Alignment explanation
Indices: 3071120--3071269 Score: 101
Period size: 19 Copynumber: 8.7 Consensus size: 18
3071110 GAATCTAAAT
3071120 TTTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
3071137 TTTCGCTTTGCGA--TTC-
1 TTTCGC-TTGCGATTTTCA
**
3071153 CCTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
3071170 TTTCGCATTGCGA--TTC-
1 TTTCGC-TTGCGATTTTCA
*
3071186 TCTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
3071203 TTTCGCATTGCGA--TTC-
1 TTTCGC-TTGCGATTTTCA
*
3071219 TCTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
**
3071236 TTTCGCATTGCGATAGTCA
1 TTTCGC-TTGCGATTTTCA
3071255 TTTCCGCTTTGCGAT
1 TTT-CGC-TTGCGAT
3071270 AGACATTAAG
Statistics
Matches: 104, Mismatches: 11, Indels: 33
0.70 0.07 0.22
Matches are distributed among these distances:
14 18 0.17
16 20 0.19
17 25 0.24
19 31 0.30
20 10 0.10
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (18 bp):
TTTCGCTTGCGATTTTCA
Found at i:3071164 original size:33 final size:33
Alignment explanation
Indices: 3071122--3071249 Score: 238
Period size: 33 Copynumber: 3.9 Consensus size: 33
3071112 ATCTAAATTT
* *
3071122 TCGTTGCGATTTTCATTTCGCTTTGCGATTCCC
1 TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
3071155 TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1 TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
3071188 TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1 TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
3071221 TCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGTTGCGATTTTCATTTCGCATTGCGAT
3071250 AGTCATTTCC
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 93 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
Found at i:3071196 original size:14 final size:14
Alignment explanation
Indices: 3071144--3071231 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
3071134 TCATTTCGCT
*
3071144 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
3071158 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
3071175 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
3071191 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
3071208 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
3071224 TTGCGATT
1 TTGCGATT
3071232 TTCATTTCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 13 0.22
19 12 0.20
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:3071315 original size:20 final size:21
Alignment explanation
Indices: 3071243--3071315 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 21
3071233 TCATTTCGCA
*
3071243 TTGCGATAGTCATTTCCGCT-
1 TTGCGATAGTCATTTCCGATG
* **
3071263 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCGATG
3071283 ATTGCGA-ACGTCATTTCCG-TG
1 -TTGCGATA-GTCATTTCCGATG
3071304 TTGCGATAGTCA
1 TTGCGATAGTCA
3071316 AATGAATGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 4 0.10
20 22 0.54
21 12 0.29
22 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (21 bp):
TTGCGATAGTCATTTCCGATG
Found at i:3073789 original size:24 final size:24
Alignment explanation
Indices: 3073755--3073808 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3073745 CTGAAAAATC
3073755 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3073779 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
3073803 ATCAAA
1 ATCAAA
3073809 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3073822 original size:24 final size:24
Alignment explanation
Indices: 3073755--3073822 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
3073745 CTGAAAAATC
* * *
3073755 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
3073779 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
3073803 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
3073823 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:3074693 original size:20 final size:21
Alignment explanation
Indices: 3074670--3074940 Score: 220
Period size: 20 Copynumber: 13.3 Consensus size: 21
3074660 AGAATATCGT
3074670 TGCGATTTAC-TAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
3074690 TGCGA-TTACGTAAATCG-AA
1 TGCGATTTACGTAAATCGCAA
* * *
3074709 GTGCGAATTAGGAAAATCGCAA
1 -TGCGATTTACGTAAATCGCAA
3074731 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
3074751 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
3074772 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
3074792 TGCGA-TTATGT-ATTCGCAT
1 TGCGATTTACGTAAATCGCAA
*
3074811 TGCGATTTACGT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
* * *
3074831 TGCGATTTTCGTAATTCGCAT
1 TGCGATTTACGTAAATCGCAA
* * * *
3074852 TGCGATTTTCCTAATTCGCAT
1 TGCGATTTACGTAAATCGCAA
* * *
3074873 TGCGATTTACGT-ATTCACAT
1 TGCGATTTACGTAAATCGCAA
* * *
3074893 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
3074914 CGCGAATTT-GGGAAATCGCAA
1 TGCG-ATTTACGTAAATCGCAA
3074935 TGCGAT
1 TGCGAT
3074941 AGTCAGAATC
Statistics
Matches: 213, Mismatches: 29, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
19 17 0.08
20 99 0.46
21 92 0.43
22 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:3074732 original size:41 final size:41
Alignment explanation
Indices: 3074681--3074835 Score: 219
Period size: 41 Copynumber: 3.8 Consensus size: 41
3074671 GCGATTTACT
3074681 AAATCGCAATGCGATTACGTAAATCG-AAGTGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAA-TGCGAATTAGGA
3074722 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
*
3074763 AAATCGCAATGCGATTACGTAAATCGCAATGCG-ATTATG-
1 AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
* * * *
3074802 TATTCGCATTGCGATTTACGT-AATCGCATTGCGA
1 AAATCGCAATGCGA-TTACGTAAATCGCAATGCGA
3074836 TTTTCGTAAT
Statistics
Matches: 106, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
39 22 0.21
40 11 0.10
41 71 0.67
42 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (41 bp):
AAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGA
Found at i:3074857 original size:41 final size:40
Alignment explanation
Indices: 3074670--3074918 Score: 191
Period size: 41 Copynumber: 6.1 Consensus size: 40
3074660 AGAATATCGT
* *
3074670 TGCGATTTAC-TAAATCGCAATGCGATTACGTAAATCG-AA
1 TGCGATTTACGT-ATTCGCATTGCGATTACGTAAATCGCAA
* * * * *
3074709 GTGCGAATTAGGAAAATCGCAATGCGATTACGTAAATCGCAA
1 -TGCGATTTACG-TATTCGCATTGCGATTACGTAAATCGCAA
* * * * *
3074751 TGCGAATTAGGAAAATCGCAATGCGATTACGTAAATCGCAA
1 TGCGATTTACG-TATTCGCATTGCGATTACGTAAATCGCAA
* *
3074792 TGCGA-TTATGTATTCGCATTGCGATTTACGT-AATCGCAT
1 TGCGATTTACGTATTCGCATTGCGA-TTACGTAAATCGCAA
* * * * *
3074831 TGCGATTTTCGTAATTCGCATTGCGATTTTCCTAATTCGCAT
1 TGCGATTTACGT-ATTCGCATTGCGA-TTACGTAAATCGCAA
* * *
3074873 TGCGATTTACGTATTCACATTGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTATTCGCATTGCG-ATTACGTAAATCGCAA
*
3074914 CGCGA
1 TGCGA
3074919 ATTTGGGAAA
Statistics
Matches: 179, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
39 23 0.13
40 22 0.12
41 113 0.63
42 21 0.12
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (40 bp):
TGCGATTTACGTATTCGCATTGCGATTACGTAAATCGCAA
Found at i:3074920 original size:21 final size:21
Alignment explanation
Indices: 3074894--3074939 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3074884 TATTCACATT
3074894 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
3074915 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
3074936 GCGA
1 GCGA
3074940 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:3081413 original size:2 final size:2
Alignment explanation
Indices: 3081406--3081439 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3081396 CCCTTAAACC
* *
3081406 TA TA TA TA TA TA TA TA TA TA TA TA CA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3081440 GTGCTAGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3083418 original size:20 final size:20
Alignment explanation
Indices: 3083393--3083451 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
3083383 ATTCATCCTA
3083393 GTTCAT-CAAGTATCGATATT
1 GTTCATCCAA-TATCGATATT
3083413 GTTCATCCAATATCGATATT
1 GTTCATCCAATATCGATATT
3083433 GTTCATCCAATATCGATAT
1 GTTCATCCAATATCGATAT
3083452 CCTAACCCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 35 0.92
21 3 0.08
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (20 bp):
GTTCATCCAATATCGATATT
Found at i:3084611 original size:20 final size:20
Alignment explanation
Indices: 3084583--3084630 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3084573 ACTCAGTTAT
3084583 GCCAACTCAGACCAAACCGA
1 GCCAACTCAGACCAAACCGA
* *
3084603 GCTAACTCAGACCAAACTGA
1 GCCAACTCAGACCAAACCGA
3084623 GCCAACTC
1 GCCAACTC
3084631 GTTGATTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.38, G:0.15, T:0.10
Consensus pattern (20 bp):
GCCAACTCAGACCAAACCGA
Found at i:3087022 original size:21 final size:21
Alignment explanation
Indices: 3086996--3087048 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
3086986 CTTCCAATGC
3086996 ATCACAATTCATAATTAATAT
1 ATCACAATTCATAATTAATAT
3087017 ATCACAATTCATAATTAATAT
1 ATCACAATTCATAATTAATAT
*
3087038 ATCATAATTCA
1 ATCACAATTCA
3087049 CATGCTTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (21 bp):
ATCACAATTCATAATTAATAT
Found at i:3088690 original size:37 final size:37
Alignment explanation
Indices: 3088596--3088691 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
3088586 AAAGACTCCA
*
3088596 GGAGTGCACGACGTCTTCAGGCTGGGGAGAGACACAT
1 GGAGTGCACGACGTCTTCAGTCTGGGGAGAGACACAT
3088633 GGAGTGCACGACGTCTTCAGTCTGGGGAGAGACACAT
1 GGAGTGCACGACGTCTTCAGTCTGGGGAGAGACACAT
3088670 GGAGTGCACGACGTCTTCAGTC
1 GGAGTGCACGACGTCTTCAGTC
3088692 CATGCAGAAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.23, C:0.23, G:0.35, T:0.19
Consensus pattern (37 bp):
GGAGTGCACGACGTCTTCAGTCTGGGGAGAGACACAT
Found at i:3089275 original size:92 final size:91
Alignment explanation
Indices: 3089171--3089337 Score: 244
Period size: 92 Copynumber: 1.8 Consensus size: 91
3089161 TTTAAATTAT
* * * * * *
3089171 AATTATTAGACTATTTATTTTGATTTTACATATTAAGTTGTATTTGATTAGTTTGGTAAGTTTAG
1 AATTATTAGACTAATTATTTTGATTTTACAGATTAAATCGTATTTGAGTAGTTTGATAAGTTTA-
3089236 GTTTAAATTTTTTTATTGAGTAATATA
65 GTTTAAATTTTTTTATTGAGTAATATA
* *
3089263 AATTATTAGACTAATTATTTTTATTTTACAGATTAAATCGTATTTGAGTGGTTTGATAAGTTTAG
1 AATTATTAGACTAATTATTTTGATTTTACAGATTAAATCGTATTTGAGTAGTTTGATAAGTTTAG
*
3089328 TTTGAATTTT
66 TTTAAATTTT
3089338 ATTGTTTTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
91 10 0.15
92 56 0.85
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (91 bp):
AATTATTAGACTAATTATTTTGATTTTACAGATTAAATCGTATTTGAGTAGTTTGATAAGTTTAG
TTTAAATTTTTTTATTGAGTAATATA
Found at i:3091253 original size:16 final size:16
Alignment explanation
Indices: 3091232--3091270 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3091222 AATTTGGGAA
3091232 ATATTAGATTAAAATT
1 ATATTAGATTAAAATT
*
3091248 ATATTAGATTAAAGTT
1 ATATTAGATTAAAATT
3091264 ACTATTA
1 A-TATTA
3091271 TTATTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (16 bp):
ATATTAGATTAAAATT
Found at i:3091408 original size:48 final size:48
Alignment explanation
Indices: 3091305--3091432 Score: 163
Period size: 48 Copynumber: 2.7 Consensus size: 48
3091295 TTGTTTCTAT
* * *
3091305 CATTTTTACTACAAATACTAATTC-AATATT-ATTTTAACCTTTTTAA
1 CATTTTTACTAGAAATACTAAATCAAATATTGATTCTAACCTTTTTAA
* * *
3091351 CAATGTTACTAGAAATACTAAATCAAATATTGATTCTAA-TTATTTTAA
1 CATTTTTACTAGAAATACTAAATCAAATATTGATTCTAACCT-TTTTAA
*
3091399 CATTTTTACTAGAAATACTAAATCAAATGTTGAT
1 CATTTTTACTAGAAATACTAAATCAAATATTGAT
3091433 CAAACTATAC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 20 0.29
47 7 0.10
48 43 0.61
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.42
Consensus pattern (48 bp):
CATTTTTACTAGAAATACTAAATCAAATATTGATTCTAACCTTTTTAA
Found at i:3091597 original size:16 final size:17
Alignment explanation
Indices: 3091566--3091597 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3091556 ATAACTACTT
3091566 ATGATTAAATTATAATA
1 ATGATTAAATTATAATA
3091583 ATGATTAAA-TATAAT
1 ATGATTAAATTATAAT
3091598 TAAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATGATTAAATTATAATA
Found at i:3092052 original size:28 final size:28
Alignment explanation
Indices: 3092019--3092094 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 28
3092009 AAATAGATAT
3092019 ATTTTATTCAAATAATA-TTTCAAATAAA
1 ATTTTATTCAAATAATACTTT-AAATAAA
** *
3092047 ATTTTATTTGAATAATACTTTAAATAAT
1 ATTTTATTCAAATAATACTTTAAATAAA
* *
3092075 GTCTTATTCAAATAATACTT
1 ATTTTATTCAAATAATACTT
3092095 ACAGATTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 37 0.93
29 3 0.08
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (28 bp):
ATTTTATTCAAATAATACTTTAAATAAA
Found at i:3095729 original size:21 final size:21
Alignment explanation
Indices: 3095699--3095749 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
3095689 ATTTTGGTAA
*
3095699 TTGATTAGCACTGCAAATTAC
1 TTGATCAGCACTGCAAATTAC
3095720 TTGATCAGCACTGCAAATTAC
1 TTGATCAGCACTGCAAATTAC
3095741 TTGATCAGC
1 TTGATCAGC
3095750 TTAGGTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (21 bp):
TTGATCAGCACTGCAAATTAC
Found at i:3099091 original size:173 final size:172
Alignment explanation
Indices: 3098894--3099270 Score: 639
Period size: 173 Copynumber: 2.2 Consensus size: 172
3098884 TTCCCATATG
* *
3098894 GAAATTCATACACTTAGTATGAATCTCTTAACGGTTTACACACAAAGTGCCTAATACGAAAATTC
1 GAAATTCATACACTTAGTATGAATCTCTTAACGGTTTACACACAAAGTACCCAATACGAAAATTC
*
3098959 ATACATTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGAAAATTCATACACTT
66 ATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGAAAATTCATACACTT
*
3099024 AGTATGAGTTTCTTGATA-TTTTACACACGAAATGCCCAATACA
131 AGTATGAATTTCTT-A-ACTTTTACACACGAAATGCCCAATACA
*
3099067 GAAATTCATACACTTAGTATGAATCTCTTAACGGTTTGCACACAAAGTACCCAATACGAAAATTC
1 GAAATTCATACACTTAGTATGAATCTCTTAACGGTTTACACACAAAGTACCCAATACGAAAATTC
*
3099132 ATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCTCAATACGAAAATTCATACACTT
66 ATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGAAAATTCATACACTT
* * *
3099197 AGTATGAATTTCTTAACTTTTGCACTCGAAGTGCCCAATACA
131 AGTATGAATTTCTTAACTTTTACACACGAAATGCCCAATACA
*
3099239 GAAATTCATACACTTAGTATGAATTTCTTAAC
1 GAAATTCATACACTTAGTATGAATCTCTTAAC
3099271 TTTTGCACAC
Statistics
Matches: 193, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
171 1 0.01
172 54 0.28
173 138 0.72
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (172 bp):
GAAATTCATACACTTAGTATGAATCTCTTAACGGTTTACACACAAAGTACCCAATACGAAAATTC
ATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGAAAATTCATACACTT
AGTATGAATTTCTTAACTTTTACACACGAAATGCCCAATACA
Found at i:3099288 original size:57 final size:57
Alignment explanation
Indices: 3098895--3099280 Score: 562
Period size: 57 Copynumber: 6.7 Consensus size: 57
3098885 TCCCATATGG
* * * * *
3098895 AAATTCATACACTTAGTATGAATCTCTTAACGGTTTACACACAAAGTGCCTAATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAAC-TTTTGCACACGAAGTGCCCAATACGA
*
3098953 AAATTCATACATTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGA
* * *
3099010 AAATTCATACACTTAGTATGAGTTTCTTGATA-TTTTACACACGAAATGCCCAATAC-A
1 AAATTCATACACTTAGTATGAATTTCTT-A-ACTTTTGCACACGAAGTGCCCAATACGA
* * * *
3099067 GAAATTCATACACTTAGTATGAATCTCTTAACGGTTTGCACACAAAGTACCCAATACGA
1 -AAATTCATACACTTAGTATGAATTTCTTAAC-TTTTGCACACGAAGTGCCCAATACGA
*
3099126 AAATTCATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCTCAATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGA
*
3099183 AAATTCATACACTTAGTATGAATTTCTTAACTTTTGCACTCGAAGTGCCCAATAC-A
1 AAATTCATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGA
3099239 GAAATTCATACACTTAGTATGAATTTCTTAACTTTTGCACAC
1 -AAATTCATACACTTAGTATGAATTTCTTAACTTTTGCACAC
3099281 TTAGTGCCAT
Statistics
Matches: 296, Mismatches: 25, Indels: 15
0.88 0.07 0.04
Matches are distributed among these distances:
56 2 0.01
57 165 0.56
58 127 0.43
59 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (57 bp):
AAATTCATACACTTAGTATGAATTTCTTAACTTTTGCACACGAAGTGCCCAATACGA
Found at i:3099681 original size:19 final size:22
Alignment explanation
Indices: 3099629--3099682 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 22
3099619 ACCCCCTTCC
3099629 ATGGTATCGATACTACCATACT
1 ATGGTATCGATACTACCATACT
*
3099651 ATGGTA-CTGATA-T-CC-TATT
1 ATGGTATC-GATACTACCATACT
3099670 ATGGTATCGATAC
1 ATGGTATCGATAC
3099683 CATTTTTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 13 0.46
20 3 0.11
21 2 0.07
22 10 0.36
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (22 bp):
ATGGTATCGATACTACCATACT
Found at i:3099731 original size:20 final size:20
Alignment explanation
Indices: 3099706--3099777 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
3099696 TGTTTTGAAA
3099706 TGGTATCGATACCCTCTCTT
1 TGGTATCGATACCCTCTCTT
3099726 TGGTATCGATACCCTCTCTT
1 TGGTATCGATACCCTCTCTT
*
3099746 TGGTATCGATACCC-C-ATT
1 TGGTATCGATACCCTCTCTT
*
3099764 CGGTATCGATACCC
1 TGGTATCGATACCC
3099778 CATTCGGTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
18 15 0.30
19 1 0.02
20 34 0.68
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.35
Consensus pattern (20 bp):
TGGTATCGATACCCTCTCTT
Found at i:3099770 original size:18 final size:20
Alignment explanation
Indices: 3099707--3099793 Score: 110
Period size: 20 Copynumber: 4.5 Consensus size: 20
3099697 GTTTTGAAAT
* *
3099707 GGTATCGATACCCTCTCTTT
1 GGTATCGATACCCTCTATTC
* *
3099727 GGTATCGATACCCTCTCTTT
1 GGTATCGATACCCTCTATTC
3099747 GGTATCGATACCC-C-ATTC
1 GGTATCGATACCCTCTATTC
3099765 GGTATCGATACCC-C-ATTC
1 GGTATCGATACCCTCTATTC
3099783 GGTATCGATAC
1 GGTATCGATAC
3099794 TACGAGCTGA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
18 31 0.48
19 1 0.02
20 33 0.51
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (20 bp):
GGTATCGATACCCTCTATTC
Done.