Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 179 of 325
Found at i:55148815 original size:71 final size:71
Alignment explanation
Indices: 55148726--55148889 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
55148716 GAGATGTATC
55148726 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
55148791 AGGACA
66 AGGACA
55148797 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
55148862 AGGACA
66 AGGACA
55148868 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
55148890 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:55151221 original size:8 final size:8
Alignment explanation
Indices: 55151208--55151232 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
55151198 CTCTAGCATA
55151208 TATATATG
1 TATATATG
55151216 TATATATG
1 TATATATG
55151224 TATATATG
1 TATATATG
55151232 T
1 T
55151233 TTGCACACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (8 bp):
TATATATG
Found at i:55155106 original size:17 final size:16
Alignment explanation
Indices: 55155076--55155109 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
55155066 ATCAGTTCCA
55155076 TAATTTACTCACTATT
1 TAATTTACTCACTATT
*
55155092 TAATTCTACTTACTATT
1 TAATT-TACTCACTATT
55155109 T
1 T
55155110 TTAGTGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTTACTCACTATT
Found at i:55155927 original size:27 final size:28
Alignment explanation
Indices: 55155897--55155966 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
55155887 ATAATAAGTC
*
55155897 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
55155924 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
55155952 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55155967 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:55158229 original size:634 final size:629
Alignment explanation
Indices: 55157002--55158250 Score: 1419
Period size: 634 Copynumber: 2.0 Consensus size: 629
55156992 GGCTAACATG
* ** *
55157002 CACATCAAGTTAGCAACCAAAACAAGCATGAATCTCATGACACAACCTCAAACATACCTTAATCT
1 CACATCAAGTTAGCAACCAAAACAAGCATGAAACTCACAACACAACCCCAAACATACCTTAATCT
* * * * * *
55157067 TGATGCAAGTATAGCCAAATCTCCTTCTAGTTCTCTTCTAAACCAAGCATGAAGCAAAAATCCTC
66 TGATGCAAATATAACCAAATCACCTTCTAGATCTCTTCTAAACAAAGAATGAAGCAAAAA--CTC
* *
55157132 CCTTTTTCCTTAGTATTTTCGGCCAAAGAAGAGAAAAATGGATGAACAAAATTTTTCTTTTCTCT
129 CCTTTTCCCTTAGTATTTTCGGCCAAAGAAGAGAAAAATGGATGAACAAAATTTTTCTTTTCTCC
** * *
55157197 TCCACAATGCACGGCAAGGGGGGGGGGGTTTCACTCACACACACACATTTTTTTTTTCTTTCTTT
194 TCCACAATGCACGGCAAGGGGGGGGGGAATGCACTCACACACACACATTTTTTTTTTCATTCTTT
*
55157262 ATTACCCATACTCATTTGTTTATTGTTTCTCCCTAGTGCACCAACAAAACATGTTTCATGACATG
259 ATTACCCATACTCATTTGTTTATTGTTTCTCCCTAATGCACCAACAAAACATGTTTCATGACATG
* * ***
55157327 TTTAGCCCATGATTCCTTGTCATGGCCGGCCACTTCATGTTAGGGGGGGGAAATTTGACATGCAA
324 TTTAACCCATGATTCCTTGTCATGGCCGGCCACTTCATGTAAAAAGGGGGAAATTTGACATGCAA
* * *
55157392 ATCCCTTATTTTTGCATGCATTATCAACTAGTCATCCCACATTTCCCCATCATACTTTCAATGTT
389 ATCCATTATTTTTGCATGCATTATCAACTAGTCATCACACATTTCCCCATCATACTTTCAAAGTT
* * **
55157457 TACTACTAGGCCCTTTCTAGTGAAATTCACATTTATAACTCTAAATCGAAACATCAAAAATGTCA
454 TACTACTAAGCCCTTTCTAGTGAAATTCACATATATAACTAAAAATCGAAACATCAAAAATGTCA
* * * * * * *
55157522 CACATGAATTAACACATATTATAGGCATCAAAATAAATTATAAATTATTTTTATGCCTCAGTTTT
519 CACATCAATTAACACATATAATAAGCATCAAAATAAACTATAAATTATTCTTATGACTCAGTTTC
55157587 GTGGTCCCGAAACCACATC-CCGACTAGGGTAAATTTTGGGATGTCA
584 GTGGTCCCGAAACCAC-TCTCCGACTAGGGTAAATTTTGGGATGTCA
* * *
55157633 CACATCAAGTTAGCAACCAAAACATGCATGAAACTCCCAACACAACCCCATACATACCTTAATCT
1 CACATCAAGTTAGCAACCAAAACAAGCATGAAACTCACAACACAACCCCAAACATACCTTAATCT
*
55157698 TGATGCAAATTTAACCAAATCACCTTCTAGATCTCTTCTAAACAAAGGAAATGAAGCAAAAA-TC
66 TGATGCAAATATAACCAAATCACCTTCTAGATCTCTTCTAAACAAA-G-AATGAAGCAAAAACTC
* ** *
55157762 CCTTCTTCCTCTTAGTATTTTCGGCCAAA-AAGATGAGAAA-GGATGAACAAGTTTTTTTGTTTT
129 CCTT-TTCC-CTTAGTATTTTCGGCCAAAGAAGA-GAAAAATGGATGAACAA-AATTTTTCTTTT
***** * *
55157825 CTCCTCTTGGTTGCACGGCAATGGGGGGGGGGAATGCTACTCTCTCACACACATTTTTTTTTTCA
190 CTCCTCCACAATGCACGGCAA-GGGGGGGGGGAATGC-ACTCACACACACACATTTTTTTTTTCA
* *
55157890 TTCTTT-TCTCACCCATGCTTATTTGTTTA-TGATTTTCTCCCTAATGC-CCAACAAAACATGTT
253 TTCTTTAT-T-ACCCATACTCATTTGTTTATTG--TTTCTCCCTAATGCACCAACAAAACATGTT
* *
55157952 TCATGACATGTTTAACCCAT-ATTTCTTTGTCATGGCCGGCCA-TTACTTGTAAAAAGGGGG-AA
314 TCATGACATGTTTAACCCATGA-TTCCTTGTCATGGCCGGCCACTT-CATGTAAAAAGGGGGAAA
* * * * *
55158014 TTTGACATGCAAGTCCATTA-TTTTGCATGCATGCT-TTAATTAGTCATCACATATTTCCCTATC
377 TTTGACATGCAAATCCATTATTTTTGCATGCAT--TATCAACTAGTCATCACACATTTCCCCATC
* * *
55158077 GTACTTTCAAAGTTTACTACTAAGTCCTTTCTTA-T-AAATTAGCACCTA-ATTAA-TAAAAATC
440 ATACTTTCAAAGTTTACTACTAAGCCCTTTC-TAGTGAAATT--CACATATA-TAACTAAAAATC
* * * * * * *
55158138 GAGACA-CGAAATAT-TTACGCATACCAATT-CCACAT-TCAATAAGTA-CGGAATATAACACT-
501 GAAACATC-AAAAATGTCACACAT--CAATTAACACATAT-AATAAGCATC--AAAATAA-ACTA
* *
55158197 T-AATTATTCTTGTGACTCGGTTTCGTGGTCCCGAAACCACTCTCCGACTAGGGT
559 TAAATTATTCTTATGACTCAGTTTCGTGGTCCCGAAACCACTCTCCGACTAGGGT
55158251 CACATTCGGG
Statistics
Matches: 518, Mismatches: 72, Indels: 53
0.81 0.11 0.08
Matches are distributed among these distances:
630 6 0.01
631 115 0.22
632 49 0.09
633 53 0.10
634 179 0.35
635 101 0.19
636 15 0.03
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33
Consensus pattern (629 bp):
CACATCAAGTTAGCAACCAAAACAAGCATGAAACTCACAACACAACCCCAAACATACCTTAATCT
TGATGCAAATATAACCAAATCACCTTCTAGATCTCTTCTAAACAAAGAATGAAGCAAAAACTCCC
TTTTCCCTTAGTATTTTCGGCCAAAGAAGAGAAAAATGGATGAACAAAATTTTTCTTTTCTCCTC
CACAATGCACGGCAAGGGGGGGGGGAATGCACTCACACACACACATTTTTTTTTTCATTCTTTAT
TACCCATACTCATTTGTTTATTGTTTCTCCCTAATGCACCAACAAAACATGTTTCATGACATGTT
TAACCCATGATTCCTTGTCATGGCCGGCCACTTCATGTAAAAAGGGGGAAATTTGACATGCAAAT
CCATTATTTTTGCATGCATTATCAACTAGTCATCACACATTTCCCCATCATACTTTCAAAGTTTA
CTACTAAGCCCTTTCTAGTGAAATTCACATATATAACTAAAAATCGAAACATCAAAAATGTCACA
CATCAATTAACACATATAATAAGCATCAAAATAAACTATAAATTATTCTTATGACTCAGTTTCGT
GGTCCCGAAACCACTCTCCGACTAGGGTAAATTTTGGGATGTCA
Found at i:55158288 original size:6 final size:6
Alignment explanation
Indices: 55158268--55158379 Score: 90
Period size: 6 Copynumber: 18.5 Consensus size: 6
55158258 GGGGTGTCAC
* *
55158268 AATCAG TAA-CAG AATCAG AATCAG AATTAG -GTGACAG AATCAG AATCAG
1 AATCAG -AATCAG AATCAG AATCAG AATCAG AAT--CAG AATCAG AATCAG
* * *
55158317 AATCAG TAA-CAG AATCAG AATTAG AATCA- ATATTAG TAA-CAT AATCAG
1 AATCAG -AATCAG AATCAG AATCAG AATCAG A-ATCAG -AATCAG AATCAG
55158365 AATCAG AATCAG AAT
1 AATCAG AATCAG AAT
55158380 TACGTGACAG
Statistics
Matches: 85, Mismatches: 10, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
5 8 0.09
6 68 0.80
7 7 0.08
8 2 0.02
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.21
Consensus pattern (6 bp):
AATCAG
Found at i:55158333 original size:24 final size:24
Alignment explanation
Indices: 55158268--55158379 Score: 120
Period size: 24 Copynumber: 4.6 Consensus size: 24
55158258 GGGGTGTCAC
55158268 AATCAGTAACAGAATCAGAATCAG
1 AATCAGTAACAGAATCAGAATCAG
* *
55158292 AATTAGGTGACAGAATCAGAATCAG
1 AATCA-GTAACAGAATCAGAATCAG
*
55158317 AATCAGTAACAGAATCAGAATTAG
1 AATCAGTAACAGAATCAGAATCAG
* ** *
55158341 AATCAATATTAGTAA-CATAATCAG
1 AATCAGTAACAG-AATCAGAATCAG
55158365 AATCAG-AATCAGAAT
1 AATCAGTAA-CAGAAT
55158380 TACGTGACAG
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
23 3 0.04
24 44 0.62
25 24 0.34
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.21
Consensus pattern (24 bp):
AATCAGTAACAGAATCAGAATCAG
Found at i:55158343 original size:30 final size:30
Alignment explanation
Indices: 55158302--55158404 Score: 136
Period size: 30 Copynumber: 3.4 Consensus size: 30
55158292 AATTAGGTGA
*
55158302 CAGAATCAGAATCAGAATCAGTAACAGAAT
1 CAGAATCAGAATCAGAATTAGTAACAGAAT
* *
55158332 CAGAATTAGAATCA-ATATTAGTAACATAAT
1 CAGAATCAGAATCAGA-ATTAGTAACAGAAT
*
55158362 CAGAATCAGAATCAGAATTACGTGACAGAAT
1 CAGAATCAGAATCAGAATTA-GTAACAGAAT
*
55158393 CAAAATCAGAAT
1 CAGAATCAGAAT
55158405 GTGAATGCAA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
29 1 0.02
30 42 0.67
31 20 0.32
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (30 bp):
CAGAATCAGAATCAGAATTAGTAACAGAAT
Found at i:55158570 original size:27 final size:26
Alignment explanation
Indices: 55158526--55158595 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
55158516 ATGGCTGCCA
* * *
55158526 AACAGATATCGTGACAGAGTCACCAG
1 AACAGATATTGTGGCAGAGCCACCAG
55158552 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
55158579 AATCAGATAATGTGGCA
1 AA-CAGATATTGTGGCA
55158596 AACCCACCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.05
27 36 0.95
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:55158602 original size:27 final size:27
Alignment explanation
Indices: 55158546--55158603 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
55158536 GTGACAGAGT
* * *
55158546 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
55158573 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
55158600 CACC
1 CACC
55158604 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:55158808 original size:22 final size:22
Alignment explanation
Indices: 55158760--55158811 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
55158750 GTAAATACGT
*
55158760 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
55158782 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
55158804 TTGGCACA
1 TTGGCACA
55158812 GAGCTATTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:55158987 original size:27 final size:26
Alignment explanation
Indices: 55158909--55158987 Score: 95
Period size: 27 Copynumber: 3.0 Consensus size: 26
55158899 ATTGGTCAAT
* * *
55158909 AGATATTGTGACAGAGTCACCAAATAC
1 AGATATTGTGGCAGAGCCACCAGA-AC
55158936 AGATATTGTGGCAGAGCCACCAGAAC
1 AGATATTGTGGCAGAGCCACCAGAAC
* *
55158962 AGATATTTGTGGCATAGCCACTAGAA
1 AGATA-TTGTGGCAGAGCCACCAGAA
55158988 TGCTTCCTCC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 7 0.15
27 39 0.85
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.22
Consensus pattern (26 bp):
AGATATTGTGGCAGAGCCACCAGAAC
Found at i:55159217 original size:27 final size:27
Alignment explanation
Indices: 55159187--55159374 Score: 205
Period size: 27 Copynumber: 7.0 Consensus size: 27
55159177 GGGGCAAAAT
* * *
55159187 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
55159214 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
55159241 GATATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * *
55159268 GATAATTCTACCTTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
55159295 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
55159322 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * *
55159349 AGAAATTCTATCCTACAGGGGTATTT
1 GGTAATTCTACCCTACAAGGGTATTT
55159375 TAGTAATTTC
Statistics
Matches: 138, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 138 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:55159331 original size:81 final size:81
Alignment explanation
Indices: 55159205--55159382 Score: 227
Period size: 81 Copynumber: 2.2 Consensus size: 81
55159195 TACCCCACAA
* * * *
55159205 GGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGATATTTCTACCCTACAAGGGTATTTC-G
1 GGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAAGGGTATTTCAG
55159269 ATAATTCTA-CCTTACAG
66 A-AATTCTATCC-TACAG
* * * *
55159286 GGGTATTTTGGTAATTCTATCCTATAAGGGTATTTC-AGTAATTCTACCCTATAGGGGTATTTCA
1 GGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCGA-TAATTCTACCCTACAAGGGTATTTCA
55159350 GAAATTCTATCCTACAG
65 GAAATTCTATCCTACAG
*
55159367 GGGTATTTTAGTAATT
1 GGGTATTTTGGTAATT
55159383 TCACAATCAA
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
80 1 0.01
81 80 0.94
82 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (81 bp):
GGGTATTTTGGTAATTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAAGGGTATTTCAG
AAATTCTATCCTACAG
Found at i:55159417 original size:27 final size:27
Alignment explanation
Indices: 55159387--55159632 Score: 266
Period size: 27 Copynumber: 9.2 Consensus size: 27
55159377 GTAATTTCAC
*
55159387 AATCAAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
55159414 AATCGAGGGTAGAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
55159441 AA-CTGA-GGTAAACCAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
** * **
55159467 AATTAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
55159494 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
55159521 AATCGAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * *
55159548 AATTGAGGGCAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
**
55159575 AATCGAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
55159602 AA-CTGAGGGTAAAACGGTAATT-TGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
55159628 AATCG
1 AATCG
55159633 GGAGTACTTT
Statistics
Matches: 179, Mismatches: 35, Indels: 11
0.80 0.16 0.05
Matches are distributed among these distances:
26 27 0.15
27 152 0.85
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:55161660 original size:6 final size:6
Alignment explanation
Indices: 55161649--55161810 Score: 156
Period size: 6 Copynumber: 26.8 Consensus size: 6
55161639 AACCAAAATG
* *
55161649 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATT AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* * *
55161697 AGTAA-C AGAATC AGAATT AGAATC AGAATT AGGTGAT- AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC
* *
55161746 AAAATC AGTAA-C AGAATC AGAATC AGAATC AGTATC AGTAA-C AGAATC
1 AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC
55161794 AGAATC AGAATC AGAAT
1 AGAATC AGAATC AGAAT
55161811 TACGTGACAG
Statistics
Matches: 130, Mismatches: 13, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
5 11 0.08
6 108 0.83
7 8 0.06
8 3 0.02
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21
Consensus pattern (6 bp):
AGAATC
Found at i:55161752 original size:85 final size:85
Alignment explanation
Indices: 55161649--55161831 Score: 294
Period size: 85 Copynumber: 2.2 Consensus size: 85
55161639 AACCAAAATG
* * *
55161649 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATTAGAATCAATATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAAAATCAGTAACAGAATCAGAATCAGAATCAATATCAGTAACAGAATCAGAAT
* * *
55161714 TAGAATCAGAATTAGGTGAT
66 CAGAATCAGAATTACGTGAC
*
55161734 AGAATCAGAATCAAAATCAGTAACAGAATCAGAATCAGAATCAGTATCAGTAACAGAATCAGAAT
1 AGAATCAGAATCAAAATCAGTAACAGAATCAGAATCAGAATCAATATCAGTAACAGAATCAGAAT
55161799 CAGAATCAGAATTACGTGAC
66 CAGAATCAGAATTACGTGAC
*
55161819 AGAATCAAAATCA
1 AGAATCAGAATCA
55161832 GAATGTGAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 90 1.00
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (85 bp):
AGAATCAGAATCAAAATCAGTAACAGAATCAGAATCAGAATCAATATCAGTAACAGAATCAGAAT
CAGAATCAGAATTACGTGAC
Found at i:55161989 original size:27 final size:26
Alignment explanation
Indices: 55161953--55162018 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
55161943 AGCATGGCTG
*
55161953 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
55161979 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
55162006 CCAGAATCAGATA
1 CCAGAA-CAGATA
55162019 ATGTGGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:55162023 original size:27 final size:27
Alignment explanation
Indices: 55161953--55162026 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
55161943 AGCATGGCTG
* *
55161953 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
*
55161979 CCAG-ATACAGATATTGTGGCAGAGCCA
1 CCAGAAT-CAGATAATGTGGCAGAGCCA
55162006 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
55162027 AACCCACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.10
27 32 0.80
28 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:55162033 original size:27 final size:27
Alignment explanation
Indices: 55161977--55162034 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
55161967 GTGACAGAGT
* * *
55161977 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
55162004 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
55162031 CACC
1 CACC
55162035 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:55165654 original size:27 final size:26
Alignment explanation
Indices: 55165576--55165654 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 26
55165566 ATCGGTCAAT
* * *
55165576 AGATATTGTGACAGAGTCACCAAATAC
1 AGATATTGTGGCAGAGCCACCAGA-AC
*
55165603 AGATATTGTGGTAGAGCCACCAGAAC
1 AGATATTGTGGCAGAGCCACCAGAAC
* *
55165629 AGATATTTGTGGCATAGCCACTAGAA
1 AGATA-TTGTGGCAGAGCCACCAGAA
55165655 TGCTTCCTCC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 7 0.16
27 37 0.84
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
AGATATTGTGGCAGAGCCACCAGAAC
Found at i:55165884 original size:27 final size:27
Alignment explanation
Indices: 55165856--55166042 Score: 203
Period size: 27 Copynumber: 6.9 Consensus size: 27
55165846 GGCAAAATGG
* * * *
55165856 TAATTTTACCCCATAAGGGTATCTCGG
1 TAATTCTACCCTATAAGGGTATTTCGA
*
55165883 TAATTCTACCCTATAGGGGTATTTCGA
1 TAATTCTACCCTATAAGGGTATTTCGA
* *
55165910 TATTTCTACCCTACAAGGGTATTTCGA
1 TAATTCTACCCTATAAGGGTATTTCGA
* * * *
55165937 TAATTCTACCCTACAGGGGTATTTTGG
1 TAATTCTACCCTATAAGGGTATTTCGA
* * *
55165964 TAATTTTATCCTATAAGGGTATTTCAA
1 TAATTCTACCCTATAAGGGTATTTCGA
* *
55165991 TAATTCTACCCTATAGGGGTATTTCAA
1 TAATTCTACCCTATAAGGGTATTTCGA
* * *
55166018 AAATTCTACCCTACAGGGGTATTTC
1 TAATTCTACCCTATAAGGGTATTTC
55166043 AGTAATTTCA
Statistics
Matches: 136, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 136 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (27 bp):
TAATTCTACCCTATAAGGGTATTTCGA
Found at i:55165998 original size:81 final size:81
Alignment explanation
Indices: 55165872--55166050 Score: 250
Period size: 81 Copynumber: 2.2 Consensus size: 81
55165862 TACCCCATAA
* * * * * *
55165872 GGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCGATATTTCTACCCTACAAGGGTATTTCGA
1 GGGTATTTCGGTAATTTTACCCTATAAGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCAA
*
55165937 TAATTCTACCCTACAG
66 AAATTCTACCCTACAG
* * * *
55165953 GGGTATTTTGGTAATTTTATCCTATAAGGGTATTTCAATAATTCTACCCTATAGGGGTATTTCAA
1 GGGTATTTCGGTAATTTTACCCTATAAGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCAA
55166018 AAATTCTACCCTACAG
66 AAATTCTACCCTACAG
*
55166034 GGGTATTTCAGTAATTT
1 GGGTATTTCGGTAATTT
55166051 CACAATCAAG
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (81 bp):
GGGTATTTCGGTAATTTTACCCTATAAGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCAA
AAATTCTACCCTACAG
Found at i:55166038 original size:54 final size:54
Alignment explanation
Indices: 55165856--55166049 Score: 226
Period size: 54 Copynumber: 3.6 Consensus size: 54
55165846 GGCAAAATGG
* * * * **
55165856 TAATTTTACCCCATAAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCGA
1 TAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTATAGGGGTATTTCGA
* * * * *
55165910 TATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTTGG
1 TAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTATAGGGGTATTTCGA
* * * *
55165964 TAATTTTATCCTATAAGGGTATTTCAATAATTCTACCCTATAGGGGTATTTCAA
1 TAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTATAGGGGTATTTCGA
* * *
55166018 AAATTCTACCCTACAGGGGTATTTCAGTAATT
1 TAATTCTACCCTACAAGGGTATTTCAATAATT
55166050 TCACAATCAA
Statistics
Matches: 116, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 116 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (54 bp):
TAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTATAGGGGTATTTCGA
Found at i:55166084 original size:27 final size:27
Alignment explanation
Indices: 55166054--55166302 Score: 288
Period size: 27 Copynumber: 9.3 Consensus size: 27
55166044 GTAATTTCAC
*
55166054 AATCAAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
* * *
55166081 AATCGAGGGTAGAACAATAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
* *
55166108 AA-CTGTGGG-CAAACAGTAATTCTGTA
1 AATC-GAGGGTAAAACAGTAATTCTGTA
* ** * *
55166134 AATCAAGGGTAAAATGGTAATTTTATA
1 AATCGAGGGTAAAACAGTAATTCTGTA
*
55166161 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
55166188 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
* * * * *
55166215 AATTGAAGGTAAAACGGTAATTTTGAA
1 AATCGAGGGTAAAACAGTAATTCTGTA
*
55166242 AATCGAGGGTAAAATAGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
*
55166269 AA-CTGAGGGTAAAACGGTAATTCTGTA
1 AATC-GAGGGTAAAACAGTAATTCTGTA
55166296 AATCGAG
1 AATCGAG
55166303 AGTACTTTGG
Statistics
Matches: 183, Mismatches: 34, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
26 20 0.11
27 162 0.89
28 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTGTA
Found at i:55166329 original size:81 final size:80
Alignment explanation
Indices: 55166080--55166331 Score: 294
Period size: 81 Copynumber: 3.1 Consensus size: 80
55166070 GTAATTCTGT
* * * * * * *
55166080 AAATCGAGGGTAGAACAATAATTTTGTAAACTGTGGG-CAAACAGTAATTCTGTAAATCAAGGGT
1 AAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAACAGTAATTCTGTAAATCGAGAGT
55166144 AAAATGGTAATTTTA
66 AAAATGGTAATTTTA
* *
55166159 TAAATCGAGGGTAAAACGGTAATTCTGTAAA-TCGAGGGTAAAACAGTAATTCTGTAAATTGA-A
1 -AAATCGAGGGTAAAACAGTAATTCTGTAAACT-GAGGGTAAAACAGTAATTCTGTAAATCGAGA
*
55166222 GGTAAAACGGTAATTTTGA
64 -GTAAAATGGTAATTTT-A
* *
55166241 AAATCGAGGGTAAAATAGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTGTAAATCGAGAGT
1 AAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAACAGTAATTCTGTAAATCGAGAGT
***
55166306 ACTTTGGTAATTTTA
66 AAAATGGTAATTTTA
*
55166321 CAAGTCGAGGG
1 -AAATCGAGGG
55166332 CATTTCAGTA
Statistics
Matches: 146, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
79 1 0.01
80 31 0.21
81 111 0.76
82 3 0.02
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (80 bp):
AAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAACAGTAATTCTGTAAATCGAGAGT
AAAATGGTAATTTTA
Found at i:55167724 original size:25 final size:25
Alignment explanation
Indices: 55167696--55167745 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
55167686 TAAAGGGGGG
*
55167696 TAAGGCATTTCACATGAATTTTTAA
1 TAAGCCATTTCACATGAATTTTTAA
*
55167721 TAAGCCATTTCCCATGAATTTTTAA
1 TAAGCCATTTCACATGAATTTTTAA
55167746 AGTATGTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (25 bp):
TAAGCCATTTCACATGAATTTTTAA
Found at i:55169060 original size:7 final size:7
Alignment explanation
Indices: 55169040--55169108 Score: 57
Period size: 7 Copynumber: 9.3 Consensus size: 7
55169030 TTAGCATGTC
*
55169040 TAGGGTA
1 TAGGGTT
55169047 TAGGGTT
1 TAGGGTT
55169054 TAGGGTTT
1 TAGGG-TT
55169062 TAGGGTTT
1 TAGGG-TT
55169070 TAGGGTTT
1 TAGGG-TT
*
55169078 TAAGGTTT
1 T-AGGGTT
* *
55169086 TAAGTTT
1 TAGGGTT
55169093 TAGGGTT
1 TAGGGTT
*
55169100 TAGGTTT
1 TAGGGTT
55169107 TA
1 TA
55169109 ATGTTGCCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
7 29 0.54
8 22 0.41
9 3 0.06
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (7 bp):
TAGGGTT
Found at i:55169065 original size:8 final size:8
Alignment explanation
Indices: 55169047--55169108 Score: 78
Period size: 8 Copynumber: 8.2 Consensus size: 8
55169037 GTCTAGGGTA
55169047 TAGGG-TT
1 TAGGGTTT
55169054 TAGGGTTT
1 TAGGGTTT
55169062 TAGGGTTT
1 TAGGGTTT
55169070 TAGGGTTT
1 TAGGGTTT
*
55169078 TAAGGTTT
1 TAGGGTTT
*
55169086 TA-AGTTT
1 TAGGGTTT
55169093 TAGGG-TT
1 TAGGGTTT
55169100 TA-GGTTT
1 TAGGGTTT
55169107 TA
1 TA
55169109 ATGTTGCCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
6 2 0.04
7 19 0.39
8 28 0.57
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (8 bp):
TAGGGTTT
Found at i:55171404 original size:40 final size:40
Alignment explanation
Indices: 55171349--55171555 Score: 249
Period size: 40 Copynumber: 5.2 Consensus size: 40
55171339 TGAATGATAC
* *
55171349 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
55171389 CCGGGCTAAGTCCCGAAGGCA-TTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
55171428 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * ** *
55171468 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * * *
55171508 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
55171548 CC-GGCTAA
1 CCGGGCTAA
55171556 ATTCCGAAGA
Statistics
Matches: 144, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 44 0.31
40 98 0.68
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:55171483 original size:79 final size:79
Alignment explanation
Indices: 55171349--55171555 Score: 240
Period size: 79 Copynumber: 2.6 Consensus size: 79
55171339 TGAATGATAC
* * *
55171349 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGTCCCGAAGGCA-TT
1 CCGGGCTAAGACCCGAAGGCA-TTGTGCTAGTTG-TTATATCCGGGCTAAGACCCGAAGGCATTT
* ** *
55171412 ATGCTAGTGATTATAT
64 ATGCAAGTGACCAAAT
* *
55171428 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATT-GTGCTAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTA
*
55171493 TGCAAGTTACCAAAT
65 TGCAAGTGACCAAAT
* * *
55171508 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGC-ATTGTGCTAGTTGTTATATCCGGGCTAA
55171556 ATTCCGAAGA
Statistics
Matches: 110, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
78 2 0.02
79 57 0.52
80 48 0.44
81 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCATTGTGCTAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTAT
GCAAGTGACCAAAT
Found at i:55179443 original size:40 final size:40
Alignment explanation
Indices: 55179388--55179600 Score: 234
Period size: 40 Copynumber: 5.4 Consensus size: 40
55179378 AATGATACCC
*
55179388 GGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATATCCG
*
55179428 GGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATATCCG
* * *
55179468 GGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTATATCCG
* * * ** *
55179508 GGCTAAG-ACCGAAGGCATTTGTGCAAGTTACCAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATATCCG
* * * * *
55179547 GGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATATCCG
* *
55179586 GGCTAAATTCCGAAG
1 GGCTAAGTCCCGAAG
55179601 AAGCTCGGTT
Statistics
Matches: 145, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 40 0.28
40 102 0.70
41 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTATATCCG
Found at i:55179558 original size:79 final size:79
Alignment explanation
Indices: 55179388--55179600 Score: 234
Period size: 79 Copynumber: 2.7 Consensus size: 79
55179378 AATGATACCC
* * *
55179388 GGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGTCCCGAAGGCATTTATG
1 GGCTAAGACCCGAAGGCA-TTGTGCTAGTTG-TTATATCCGGGCTAAGTACCGAAGGCATTTATG
* ** *
55179452 CTAGTGATTATATCCG
64 CAAGTGACCAAATCCG
* *
55179468 GGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATATCCGGGCTAAG-ACCGAAGGCATTTGTGC
1 GGCTAAGACCCGAAGGCATT-GTGCTAGTTGTTATATCCGGGCTAAGTACCGAAGGCATTTATGC
*
55179532 AAGTTACCAAATCCG
65 AAGTGACCAAATCCG
* * * * *
55179547 GGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAAATTCCGAAG
1 GGCTAAGACCCGAAGGC-ATTGTGCTAGTTGTTATATCCGGGCTAAGTACCGAAG
55179601 AAGCTCGGTT
Statistics
Matches: 113, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
78 6 0.05
79 64 0.57
80 41 0.36
81 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (79 bp):
GGCTAAGACCCGAAGGCATTGTGCTAGTTGTTATATCCGGGCTAAGTACCGAAGGCATTTATGCA
AGTGACCAAATCCG
Found at i:55181051 original size:25 final size:25
Alignment explanation
Indices: 55181023--55181072 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
55181013 TAAAGTGGGG
*
55181023 TAAGGCATTTCACATGAATTTTTAA
1 TAAGCCATTTCACATGAATTTTTAA
*
55181048 TAAGCCATTTCCCATGAATTTTTAA
1 TAAGCCATTTCACATGAATTTTTAA
55181073 AGTATGTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (25 bp):
TAAGCCATTTCACATGAATTTTTAA
Found at i:55187766 original size:29 final size:29
Alignment explanation
Indices: 55187711--55187767 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
55187701 CTTTTGAAAA
* * **
55187711 TATTTACAAAAAGAGCATCTAGTTTTTAT
1 TATTTACAAAAAGAGCAACCAAATTTTAT
*
55187740 TATTTACGAAAAGAGCAACCAAATTTTA
1 TATTTACAAAAAGAGCAACCAAATTTTA
55187768 AAAATACTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (29 bp):
TATTTACAAAAAGAGCAACCAAATTTTAT
Found at i:55191935 original size:40 final size:40
Alignment explanation
Indices: 55191876--55192083 Score: 236
Period size: 40 Copynumber: 5.2 Consensus size: 40
55191866 CAATTGAATG
* * *
55191876 ATATCCGGGCTAAGTCCCGAAGACATTTGTGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
55191916 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
55191956 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
55191996 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
55192036 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
55192076 ATATCCGG
1 ATATCCGG
55192084 TTGTAATCCG
Statistics
Matches: 145, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 145 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:55192014 original size:80 final size:80
Alignment explanation
Indices: 55191878--55192083 Score: 261
Period size: 80 Copynumber: 2.6 Consensus size: 80
55191868 ATTGAATGAT
* * * * * *
55191878 ATCCGGGCTAAGTCCCGAAGACATTTGTGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
*
55191943 TGTGCTAGT-GACTAC
66 TGTGCAAGTCG-CTAC
* * * *
55191958 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
* *
55192023 TGTGCAAGTCGTTAT
66 TGTGCAAGTCGCTAC
* *
55192038 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
55192084 TTGTAATCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
80 108 0.99
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCAAGTCGCTAC
Found at i:55200064 original size:40 final size:40
Alignment explanation
Indices: 55200005--55200211 Score: 236
Period size: 40 Copynumber: 5.2 Consensus size: 40
55199995 CAATTGAATG
* * *
55200005 ATATCCGGGCTAAGTCCCGAAGACATTTGTGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
55200045 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
55200085 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* **
55200125 A-ATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
55200164 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
55200204 ATATCCGG
1 ATATCCGG
55200212 TTGTAATCCG
Statistics
Matches: 145, Mismatches: 21, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
39 36 0.25
40 109 0.75
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:55200154 original size:79 final size:80
Alignment explanation
Indices: 55200007--55200211 Score: 261
Period size: 79 Copynumber: 2.6 Consensus size: 80
55199997 ATTGAATGAT
* * * * * *
55200007 ATCCGGGCTAAGTCCCGAAGACATTTGTGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
*
55200072 TGTGCTAGT-GACTAC
66 TGTGCAAGTCG-CTAC
* * *
55200087 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTA-ATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
* *
55200151 TGTGCAAGTCGTTAT
66 TGTGCAAGTCGCTAC
* *
55200166 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
55200212 TTGTAATCCG
Statistics
Matches: 109, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
79 69 0.63
80 40 0.37
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT
TGTGCAAGTCGCTAC
Found at i:55203522 original size:39 final size:39
Alignment explanation
Indices: 55203478--55203703 Score: 280
Period size: 39 Copynumber: 5.8 Consensus size: 39
55203468 TATCCAAACA
55203478 TAGAGTCCGCAGGCTATGTGCTGGAATTATATCCGGACT
1 TAGAGTCCGCAGGCTATGTGCTGGAATTATATCCGGACT
55203517 TAGAGTCCGCAGGCTATGTGCTGGAATTATATCCGGACT
1 TAGAGTCCGCAGGCTATGTGCTGGAATTATATCCGGACT
*
55203556 AAGAGTCCGCAGGCTATGTGCTGGAATTATATCCGGACT
1 TAGAGTCCGCAGGCTATGTGCTGGAATTATATCCGGACT
* * *
55203595 TA-AGGTCTGCAGGCTATGTACTGGAATTATAACCGGACT
1 TAGA-GTCCGCAGGCTATGTGCTGGAATTATATCCGGACT
* * * *
55203634 TA-AGGTCCGTAGGCTACGTGCTGGAAATATGTCCAGG-C-
1 TAGA-GTCCGCAGGCTATGTGCTGGAATTATATCC-GGACT
* * * *
55203672 TAAAGTCCCGCAGGCTTTGAGCTGGTATTATA
1 TAGAGT-CCGCAGGCTATGTGCTGGAATTATA
55203704 CTGGGTTTAA
Statistics
Matches: 164, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
38 5 0.03
39 157 0.96
40 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (39 bp):
TAGAGTCCGCAGGCTATGTGCTGGAATTATATCCGGACT
Found at i:55211847 original size:79 final size:78
Alignment explanation
Indices: 55211757--55211910 Score: 229
Period size: 79 Copynumber: 2.0 Consensus size: 78
55211747 CAGTGATGTT
* *
55211757 TATCCGGACTT-AGAGTCCGCAGGCTATGTGTTAGAATTATATCCGGACTTAAGAGTCTGCAGGC
1 TATCCGGACTTAAG-GTCCGCAGGCTATGTGCTAGAATTATAACCGGACTTAAG-GTCTGCAGGC
*
55211821 TATGTACTGGAATTA
64 TACGTACTGGAATTA
* *
55211836 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTGGAGTTATAACCGGACTTAAGGTCTGCAGGCTA
1 TATCCGGACTTAAGGTCCGCAGGCTATGTGCTAGAATTATAACCGGACTTAAGGTCTGCAGGCTA
*
55211901 CGTGCTGGAA
66 CGTACTGGAA
55211911 ATATGTTTGG
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
78 20 0.29
79 46 0.68
80 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (78 bp):
TATCCGGACTTAAGGTCCGCAGGCTATGTGCTAGAATTATAACCGGACTTAAGGTCTGCAGGCTA
CGTACTGGAATTA
Found at i:55211870 original size:39 final size:40
Alignment explanation
Indices: 55211757--55211910 Score: 215
Period size: 39 Copynumber: 3.9 Consensus size: 40
55211747 CAGTGATGTT
* *
55211757 TATCCGGACTT-AGAGTCCGCAGGCTATGTGTTAGAATTA
1 TATCCGGACTTAAGAGTCCGCAGGCTATGTGCTGGAATTA
* *
55211796 TATCCGGACTTAAGAGTCTGCAGGCTATGTACTGGAATTA
1 TATCCGGACTTAAGAGTCCGCAGGCTATGTGCTGGAATTA
*
55211836 TATCCGGACTTAAG-GTCCGCAGGCTATGTGCTGGAGTTA
1 TATCCGGACTTAAGAGTCCGCAGGCTATGTGCTGGAATTA
* * *
55211875 TAACCGGACTTAAG-GTCTGCAGGCTACGTGCTGGAA
1 TATCCGGACTTAAGAGTCCGCAGGCTATGTGCTGGAA
55211911 ATATGTTTGG
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 65 0.63
40 38 0.37
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (40 bp):
TATCCGGACTTAAGAGTCCGCAGGCTATGTGCTGGAATTA
Found at i:55218658 original size:20 final size:18
Alignment explanation
Indices: 55218633--55218678 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
55218623 ACCATGTTCA
55218633 TATTTTTTACATGACTTAAT
1 TATTTTTTA-AT-ACTTAAT
* *
55218653 TATTTTATAATATTTAAT
1 TATTTTTTAATACTTAAT
55218671 TATTTTTT
1 TATTTTTT
55218679 GACAAGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 13 0.57
19 2 0.09
20 8 0.35
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
TATTTTTTAATACTTAAT
Found at i:55226658 original size:50 final size:50
Alignment explanation
Indices: 55226581--55226866 Score: 286
Period size: 50 Copynumber: 5.7 Consensus size: 50
55226571 AAGCTCTCTA
* * * * *
55226581 GTACACATAGTAGCTTGCACTTGGTACTACACATGCGACCTAACAATCTG
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCAG
* *
55226631 GTACACATAGTAGCTTGCACTTAGTACTACACACGTGACCTAACCATCAG
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCAG
* * * * * *
55226681 ATACACATAGTAGCCTGCACTTAGTACTACACACATGATCGAAGCTATCAA
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CAATCAG
*** ** *
55226732 GTATGTATAGTAGCCTGCACTTAGTACTACACTTGTGACCTAACAATCTG
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCAG
* * * * *
55226782 GCACACATAGTAGCCTGCACTTAGTACTACACACGTAACCCAA-AACCATT
1 GTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCA-G
* * *
55226832 TTAAACACATAGTAACCTGCACATAGTACTACACA
1 GT--ACACATAGTAGCCTGCACTTAGTACTACACA
55226867 TGTGTTCTCA
Statistics
Matches: 193, Mismatches: 39, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
49 3 0.02
50 122 0.63
51 39 0.20
52 29 0.15
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.25
Consensus pattern (50 bp):
GTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCAG
Found at i:55226816 original size:151 final size:153
Alignment explanation
Indices: 55226587--55226866 Score: 420
Period size: 151 Copynumber: 1.8 Consensus size: 153
55226577 TCTAGTACAC
* * * *
55226587 ATAGTAGCTTGCACTTGGTACTACACATGCGACCTAACAATCTGGTACACATAGTAGCTTGCACT
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGCACACATAGTAGCCTGCACT
* * * * *
55226652 TAGTACTACACACGTGA-CC-TAACCATCAGATACACATAGTAGCCTGCACTTAGTACTACACAC
66 TAGTACTACACACGTAACCCAAAACCATCAGAAACACATAGTAACCTGCACATAGTACTACACAC
55226715 ATGATCGAAGCTATCAAGTATGT
131 ATGATCGAAGCTATCAAGTATGT
* *
55226738 ATAGTAGCCTGCACTTAGTACTACACTTGTGACCTAACAATCTGGCACACATAGTAGCCTGCACT
1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGCACACATAGTAGCCTGCACT
***
55226803 TAGTACTACACACGTAACCCAAAACCATTTTAAACACATAGTAACCTGCACATAGTACTACACA
66 TAGTACTACACACGTAACCCAAAACCATCAGAAACACATAGTAACCTGCACATAGTACTACACA
55226867 TGTGTTCTCA
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
151 75 0.66
152 2 0.02
153 36 0.32
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (153 bp):
ATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGCACACATAGTAGCCTGCACT
TAGTACTACACACGTAACCCAAAACCATCAGAAACACATAGTAACCTGCACATAGTACTACACAC
ATGATCGAAGCTATCAAGTATGT
Found at i:55234092 original size:30 final size:30
Alignment explanation
Indices: 55234047--55234106 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
55234037 ATTTAATACG
* *
55234047 AACTTTGGCAAAATTATATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
55234077 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
55234107 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:55238552 original size:65 final size:65
Alignment explanation
Indices: 55238448--55238578 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
55238438 CCCCTAGGGT
*
55238448 TAAGGTTGACCTGAATACATGTTTGACTGTTACTATTTACTGCATGCCATGTTAGTATTATCTGA
1 TAAGGTTGACCTGAATACATGTTTGACTGTTACTATTTACTACATGCCATGTTAGTATTATCTGA
* *
55238513 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTACATGCCATGTTATTATTATCTGA
1 TAAGGTTGACCTGAATACATGTTTGACTGTTACTATTTACTACATGCCATGTTAGTATTATCTGA
55238578 T
1 T
55238579 GCATGGGACT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (65 bp):
TAAGGTTGACCTGAATACATGTTTGACTGTTACTATTTACTACATGCCATGTTAGTATTATCTGA
Found at i:55240940 original size:11 final size:12
Alignment explanation
Indices: 55240905--55240941 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
55240895 CCGGCACTGA
55240905 TTCAACTTTCTT
1 TTCAACTTTCTT
55240917 TTCAACTTTCTT
1 TTCAACTTTCTT
55240929 TTCAAC-TTCTT
1 TTCAACTTTCTT
55240940 TT
1 TT
55240942 GTATTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.28
12 18 0.72
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TTCAACTTTCTT
Found at i:55242142 original size:24 final size:23
Alignment explanation
Indices: 55242107--55242151 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
55242097 ATGTTCCCCT
55242107 GCTTTAATTCAAGAAACTCTTTGC
1 GCTTTAATTCAAGAAA-TCTTTGC
*
55242131 GCTTCTAA-TCAATAAATCTTT
1 GCTT-TAATTCAAGAAATCTTT
55242152 CACGGATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 11 0.58
25 3 0.16
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (23 bp):
GCTTTAATTCAAGAAATCTTTGC
Found at i:55247081 original size:40 final size:40
Alignment explanation
Indices: 55247036--55247202 Score: 194
Period size: 40 Copynumber: 4.2 Consensus size: 40
55247026 CGGAATATAA
55247036 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
55247076 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
55247116 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
55247156 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
55247195 CCGGATAT
1 CCGGATAT
55247203 CATTCAATTT
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
39 14 0.13
40 95 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:55248049 original size:17 final size:19
Alignment explanation
Indices: 55248026--55248071 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
55248016 AAGAAGCATG
55248026 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
55248044 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
55248062 AATCATGCTC
1 AATCATGCTC
55248072 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:55255061 original size:40 final size:40
Alignment explanation
Indices: 55255016--55255182 Score: 194
Period size: 40 Copynumber: 4.2 Consensus size: 40
55255006 CGGAATATAA
55255016 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
55255056 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
55255096 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
55255136 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
55255175 CCGGATAT
1 CCGGATAT
55255183 CATTCAATTT
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
39 14 0.13
40 95 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:55256028 original size:17 final size:19
Alignment explanation
Indices: 55256005--55256050 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
55255995 AAGAAGCATG
55256005 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
55256023 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
55256041 AATCATGCTC
1 AATCATGCTC
55256051 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:55259895 original size:45 final size:45
Alignment explanation
Indices: 55259844--55259933 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
55259834 ACTTAATTGG
55259844 TTAATTATTGTTATTACATGCCAAGCATACCATATACAGTCCTAA
1 TTAATTATTGTTATTACATGCCAAGCATACCATATACAGTCCTAA
*
55259889 TTAATTATTGTTCTTACATGCCAAGCATACCATATACAGTCCTAA
1 TTAATTATTGTTATTACATGCCAAGCATACCATATACAGTCCTAA
55259934 AAATAAGTAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (45 bp):
TTAATTATTGTTATTACATGCCAAGCATACCATATACAGTCCTAA
Found at i:55264867 original size:20 final size:20
Alignment explanation
Indices: 55264844--55264922 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
55264834 TACTTTCGTA
*
55264844 CTCCTAATAGCACTACGGTG
1 CTCCTGATAGCACTACGGTG
* * *
55264864 CTCCTGATAGTACTTTC-GTA
1 CTCCTGATAGCAC-TACGGTG
* * *
55264884 CTCCTGTTAGTAGTACGGTG
1 CTCCTGATAGCACTACGGTG
*
55264904 CTCTTGATAGCACTACGGT
1 CTCCTGATAGCACTACGGT
55264923 ACCCCTAATT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
19 2 0.04
20 41 0.91
21 2 0.04
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (20 bp):
CTCCTGATAGCACTACGGTG
Found at i:55264887 original size:40 final size:40
Alignment explanation
Indices: 55264724--55264906 Score: 197
Period size: 40 Copynumber: 4.6 Consensus size: 40
55264714 CGAATAAGTG
* * *
55264724 CTCCTCATAGCACTACGGTGCTCCTGGCAGTACTTCCGTA
1 CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCGTA
* * * *
55264764 CTCTTGATAGCACTACGATGCTCCTAAC-GATACTTTTGTA
1 CTCCTGATAGCACTACGGTGCTCCTGACAG-TACTTTCGTA
* ** * *
55264804 CTCTTGATAGCACTATAGTGCTACTAACAGTACTTTCGTA
1 CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCGTA
* *
55264844 CTCCTAATAGCACTACGGTGCTCCTGATAGTACTTTCGTA
1 CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCGTA
* * *
55264884 CTCCTGTTAGTAGTACGGTGCTC
1 CTCCTGATAGCACTACGGTGCTC
55264907 TTGATAGCAC
Statistics
Matches: 118, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 116 0.98
41 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (40 bp):
CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCGTA
Found at i:55265950 original size:27 final size:27
Alignment explanation
Indices: 55265920--55266017 Score: 83
Period size: 27 Copynumber: 3.6 Consensus size: 27
55265910 GTAAATCTAC
*
55265920 AAACCAAGGGTGTTTC-AGTAATTTTGT
1 AAACCAAGGGTATTTCTA-TAATTTTGT
*
55265947 AAACCAATGGTATTTCTATAATTTT-T
1 AAACCAAGGGTATTTCTATAATTTTGT
* * *
55265973 AGAAAGTCAAGGGTATTTTTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCTATAATTTTGT
* *
55266003 AAATCAGGGGTATTT
1 AAACCAAGGGTATTT
55266018 TGGTAATTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
26 1 0.02
27 32 0.54
28 7 0.12
29 18 0.31
30 1 0.02
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (27 bp):
AAACCAAGGGTATTTCTATAATTTTGT
Found at i:55266023 original size:27 final size:26
Alignment explanation
Indices: 55265983--55266166 Score: 179
Period size: 27 Copynumber: 6.8 Consensus size: 26
55265973 AGAAAGTCAA
* **
55265983 GGGTATTTTTGTAATTTTGTAAATCAG
1 GGGTATTTTGGTAATTTTACAAA-CAG
**
55266010 GGGTATTTTGGTAATTTTACAAATTG
1 GGGTATTTTGGTAATTTTACAAACAG
*
55266036 AGGGTATTTCGGTAATTTTACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAA-CAG
* *
55266064 TGGTATTTCGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAAC-AG
*
55266091 GGGCATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAAC-AG
* **
55266118 GGGTATTTTGGTAATTCTATCCTACAG
1 GGGTATTTTGGTAATTTTA-CAAACAG
* **
55266145 GGATATTTCAGTAATTTTACAA
1 GGGTATTTTGGTAATTTTACAA
55266167 TCGAGGGTAA
Statistics
Matches: 131, Mismatches: 22, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
26 3 0.02
27 124 0.95
28 4 0.03
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTACAAACAG
Found at i:55266152 original size:81 final size:81
Alignment explanation
Indices: 55266008--55266166 Score: 207
Period size: 81 Copynumber: 2.0 Consensus size: 81
55265998 TTTGTAAATC
* * *
55266008 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAGTGGTATTTC
1 AGGGGCATTTTGGTAATTTTACAAATAGAGGGTATTTCGGTAATTCTACAAACCAGTGGTATTTC
*
55266073 GGTAATTTTACAAACT
66 AGTAATTTTACAAACT
* **
55266089 AGGGGCATTTTGGTAATTTTACAAACTAG-GGGTATTTTGGTAATTCTATCCTA-CAG-GGATAT
1 AGGGGCATTTTGGTAATTTTACAAA-TAGAGGGTATTTCGGTAATTCTA-CAAACCAGTGG-TAT
55266151 TTCAGTAATTTTACAA
63 TTCAGTAATTTTACAA
55266167 TCGAGGGTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
80 2 0.03
81 62 0.91
82 4 0.06
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.39
Consensus pattern (81 bp):
AGGGGCATTTTGGTAATTTTACAAATAGAGGGTATTTCGGTAATTCTACAAACCAGTGGTATTTC
AGTAATTTTACAAACT
Found at i:55266199 original size:27 final size:27
Alignment explanation
Indices: 55266165--55266361 Score: 218
Period size: 27 Copynumber: 7.3 Consensus size: 27
55266155 GTAATTTTAC
*
55266165 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
*
55266192 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTTTGTA
* *
55266219 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * *
55266246 AATCGAGGGTAAAATGGTAA-TCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
55266272 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * * * *
55266299 AATCGAGGATGAAACGATAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * * **
55266326 GATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAACGGTAATTTTGTA
55266353 AATCGAGGG
1 AATCGAGGG
55266362 CATTTCAGTA
Statistics
Matches: 146, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
26 26 0.18
27 119 0.82
28 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:55266239 original size:80 final size:78
Alignment explanation
Indices: 55266155--55266361 Score: 227
Period size: 80 Copynumber: 2.6 Consensus size: 78
55266145 GGATATTTCA
* * *
55266155 GTAATTTTACAATCGAGGGTAAAACGATAATTTTGTAAA-CTGAGGGTAAAATGGTAATTTTGTA
1 GTAATTTTA-AATCGAGGGTAAAACGATAA-TCTATAAATC-GAGGGTAAAACGGTAATTTTGTA
*
55266219 AATCGAGGGTAAAACG
63 AATCGAGGATAAAACG
* *
55266235 GTAATTCTATAAATCGAGGGTAAAATGGTAATCTATAAATCGAGGGTAAAACGGTAATTTTGTAA
1 GTAATT-T-TAAATCGAGGGTAAAACGATAATCTATAAATCGAGGGTAAAACGGTAATTTTGTAA
*
55266300 ATCGAGGATGAAACG
64 ATCGAGGATAAAACG
* * * * *
55266315 ATAATTCTATAGATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
1 GTAATT-T-TAAATCGAGGGTAAAACGATAA-TCTATAAATCGAGGG
55266362 CATTTCAGTA
Statistics
Matches: 113, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
80 77 0.68
81 34 0.30
82 2 0.02
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.29
Consensus pattern (78 bp):
GTAATTTTAAATCGAGGGTAAAACGATAATCTATAAATCGAGGGTAAAACGGTAATTTTGTAAAT
CGAGGATAAAACG
Found at i:55266373 original size:107 final size:108
Alignment explanation
Indices: 55266149--55266374 Score: 271
Period size: 107 Copynumber: 2.1 Consensus size: 108
55266139 CTACAGGGAT
* * * *
55266149 ATTTCAGTAATTTTACAATCGAGGGTAAAACGATAATTTTGTAAACTGAGGGTAAAATGGTAATT
1 ATTTCAGTAATTATACAATCGAGGGTAAAACGATAATTTTGTAAACTGAGGATAAAACGATAATT
* * *
55266214 TTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTA
66 CTATAAATCGAGGGTAAAACGGTAATTCTACAAATCGAGGGTA
** * * *
55266257 AAAT-GGTAATCTATA-AATCGAGGGTAAAACGGTAATTTTGTAAA-TCGAGGATGAAACGATAA
1 ATTTCAGTAAT-TATACAATCGAGGGTAAAACGATAATTTTGTAAACT-GAGGATAAAACGATAA
* * *
55266319 TTCTATAGATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG-C
64 TTCTATAAATCGAGGGTAAAACGGTAATTCTACAAATCGAGGGTA
55266363 ATTTCAGTAATT
1 ATTTCAGTAATT
55266375 TGGTAAACTA
Statistics
Matches: 97, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
106 4 0.04
107 88 0.91
108 5 0.05
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.30
Consensus pattern (108 bp):
ATTTCAGTAATTATACAATCGAGGGTAAAACGATAATTTTGTAAACTGAGGATAAAACGATAATT
CTATAAATCGAGGGTAAAACGGTAATTCTACAAATCGAGGGTA
Found at i:55269380 original size:46 final size:46
Alignment explanation
Indices: 55269327--55269554 Score: 230
Period size: 46 Copynumber: 4.8 Consensus size: 46
55269317 TGTAACCCGC
* * *
55269327 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
55269373 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGC-A--T
* ***
55269419 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
55269466 CCATAAGTGAACTCGGACTCGGACTCAACTCAACAAGTTTGGACATTCGCAT
1 CCATAAGTG-A-----ACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
55269518 CCATAAGTGAAATCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
55269555 TGCCCAAATA
Statistics
Matches: 150, Mismatches: 17, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
43 1 0.01
44 3 0.02
46 65 0.43
47 32 0.21
49 4 0.03
50 1 0.01
51 1 0.01
52 43 0.29
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:55269490 original size:52 final size:51
Alignment explanation
Indices: 55269425--55269554 Score: 189
Period size: 52 Copynumber: 2.6 Consensus size: 51
55269415 AGTTACATCT
55269425 CTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAA
1 CTCG-ACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAA
* *
55269477 CTCGGACTCGGACTCAACTCAACAAGTTTGGACATTCGCATCCATAAGTGAA
1 CTC-GACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAA
55269529 ----A-TCGGACTCAACTCAACGAGTTCGGA
1 CTCGACTCGGACTCAACTCAACGAGTTCGGA
55269555 TGCCCAAATA
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
46 23 0.32
47 1 0.01
52 48 0.66
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (51 bp):
CTCGACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAA
Found at i:55281640 original size:16 final size:16
Alignment explanation
Indices: 55281593--55281641 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
55281583 CGATAAATCC
*
55281593 CGAAATGCTGAAAAGC
1 CGAAATGCTGAAAAGT
* *
55281609 CGAAACGCAGAAAAGT
1 CGAAATGCTGAAAAGT
*
55281625 TGAAATGCTGAAAAGT
1 CGAAATGCTGAAAAGT
55281641 C
1 C
55281642 AAAAGTTTGG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.45, C:0.16, G:0.24, T:0.14
Consensus pattern (16 bp):
CGAAATGCTGAAAAGT
Found at i:55283819 original size:24 final size:24
Alignment explanation
Indices: 55283776--55283827 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
55283766 CACAAACGCA
55283776 GCTCTTCATGAGCATCCTGATATAG
1 GCTCTTCATGAGCATCCTGATAT-G
* *
55283801 GCTCTT-ATGGGCTTCCTGATATG
1 GCTCTTCATGAGCATCCTGATATG
55283824 GCTC
1 GCTC
55283828 GCTTGAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.20
24 14 0.56
25 6 0.24
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (24 bp):
GCTCTTCATGAGCATCCTGATATG
Found at i:55283972 original size:25 final size:25
Alignment explanation
Indices: 55283943--55283990 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
55283933 TTTAGCCCGA
*
55283943 ATGAGCTTCCTGATACATGGCTCAC
1 ATGAGCATCCTGATACATGGCTCAC
*
55283968 ATGAGCATCCTGATATATGGCTC
1 ATGAGCATCCTGATACATGGCTC
55283991 GAGAGTGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (25 bp):
ATGAGCATCCTGATACATGGCTCAC
Found at i:55304332 original size:50 final size:49
Alignment explanation
Indices: 55304200--55304383 Score: 199
Period size: 50 Copynumber: 3.7 Consensus size: 49
55304190 ATCTATTGTC
* * * * * *
55304200 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTG
1 AGGTCACATGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGAT--GTG
* * * **
55304251 TGATCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTATTAGATGGTG
1 AGGTCACATGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGAT-GTG
*
55304301 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGT-
1 AGGTCACATGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGA-TGTG
* *
55304350 TGGTCGCATGTGTAGTACTAAGTGCAAGCTACTA
1 AGGTCACATGTGTAGTACTAAGTGCAAGCTACTA
55304384 TGCGTACTAG
Statistics
Matches: 111, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 31 0.28
50 43 0.39
51 37 0.33
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (49 bp):
AGGTCACATGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGATGTG
Found at i:55307646 original size:2 final size:2
Alignment explanation
Indices: 55307639--55307669 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55307629 GAGACTAGTC
55307639 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
55307670 CATGTCATGA
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:55311565 original size:112 final size:112
Alignment explanation
Indices: 55311429--55311691 Score: 368
Period size: 112 Copynumber: 2.3 Consensus size: 112
55311419 GTGATTATGT
* * *
55311429 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGAGTAAGACCA
1 GTAAGACCACGTTTAATACATTGGCATCGATATGTGATTCCGATATATGGGTGCGAGTAAGACCA
* * * * *
55311494 CGTTTAATACGTTGGCATCGGTATGTGATTTCGATATATGTGTACGA
66 CATTTAATACGTTGGCATCGATATGTGACTCCGACATATGTGTACGA
*
55311541 GTAAGACCACGTTTAATACATTGGCATCGATATGTGACTCCGATATATGGGTGCGAGTAAGACCA
1 GTAAGACCACGTTTAATACATTGGCATCGATATGTGATTCCGATATATGGGTGCGAGTAAGACCA
* *
55311606 CATTTAATACGTTGGCATCGATATGTGACTCCGACATGTGTGTGCGA
66 CATTTAATACGTTGGCATCGATATGTGACTCCGACATATGTGTACGA
** *
55311653 GTAAGACC-C-TATCTAGGACAGTGGCATCGATATGTGATT
1 GTAAGACCACGT-T-TAATACATTGGCATCGATATGTGATT
55311692 ACATGTAAGA
Statistics
Matches: 134, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
110 1 0.01
111 2 0.01
112 131 0.98
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (112 bp):
GTAAGACCACGTTTAATACATTGGCATCGATATGTGATTCCGATATATGGGTGCGAGTAAGACCA
CATTTAATACGTTGGCATCGATATGTGACTCCGACATATGTGTACGA
Found at i:55311689 original size:56 final size:56
Alignment explanation
Indices: 55311429--55311660 Score: 365
Period size: 56 Copynumber: 4.1 Consensus size: 56
55311419 GTGATTATGT
* *
55311429 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCTGATATATGTGTGCGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGACTCCGATATATGTGTGCGA
* * * *
55311485 GTAAGACCACGTTTAATACGTTGGCATCGGTATGTGATTTCGATATATGTGTACGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGACTCCGATATATGTGTGCGA
* *
55311541 GTAAGACCACGTTTAATACATTGGCATCGATATGTGACTCCGATATATGGGTGCGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGACTCCGATATATGTGTGCGA
* * *
55311597 GTAAGACCACATTTAATACGTTGGCATCGATATGTGACTCCGACATGTGTGTGCGA
1 GTAAGACCACGTTTAATACGTTGGCATCGATATGTGACTCCGATATATGTGTGCGA
55311653 GTAAGACC
1 GTAAGACC
55311661 CTATCTAGGA
Statistics
Matches: 161, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 161 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (56 bp):
GTAAGACCACGTTTAATACGTTGGCATCGATATGTGACTCCGATATATGTGTGCGA
Found at i:55311908 original size:2 final size:2
Alignment explanation
Indices: 55311901--55311928 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55311891 ATAAAAACAA
55311901 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
55311929 GAACTTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55320031 original size:46 final size:44
Alignment explanation
Indices: 55319981--55320067 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 44
55319971 CATTTTCTCA
* *
55319981 CTCTTTTGTTCTTTTTCACCCTTTTTTTTCTCA-TTTTCTTTTCACT
1 CTCTTTTATTCTTTTT---CCTCTTTTTTCTCACTTTTCTTTTCACT
*
55320027 CTCTTTTATTGTTTTTCCTCTTTTTTCTCACTTTTCTTTTC
1 CTCTTTTATTCTTTTTCCTCTTTTTTCTCACTTTTCTTTTC
55320068 TTTTACATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 13 0.35
44 10 0.27
46 14 0.38
ACGTcount: A:0.06, C:0.25, G:0.02, T:0.67
Consensus pattern (44 bp):
CTCTTTTATTCTTTTTCCTCTTTTTTCTCACTTTTCTTTTCACT
Found at i:55321940 original size:13 final size:13
Alignment explanation
Indices: 55321922--55321947 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55321912 TTGTTATACG
55321922 AACTTACTAAGCA
1 AACTTACTAAGCA
55321935 AACTTACTAAGCA
1 AACTTACTAAGCA
55321948 TTTGAAATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
AACTTACTAAGCA
Found at i:55324236 original size:29 final size:28
Alignment explanation
Indices: 55324203--55324303 Score: 105
Period size: 28 Copynumber: 3.5 Consensus size: 28
55324193 ATAGTGAATC
*
55324203 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
*
55324232 CGCACACTTGGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
55324260 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
55324290 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55324304 CATACCCTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 4 0.06
28 22 0.35
29 17 0.27
30 19 0.31
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:55324352 original size:29 final size:29
Alignment explanation
Indices: 55324291--55324421 Score: 165
Period size: 29 Copynumber: 4.5 Consensus size: 29
55324281 TTTTAAACCC
*** *
55324291 GCACACTTAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** * *
55324319 CGCACACCCAGTGTCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
55324349 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
*
55324378 GCACACTTAGTGCCATATATTTTCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
55324407 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
55324422 ATCTCGTCAC
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
29 87 0.99
30 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:55332356 original size:28 final size:28
Alignment explanation
Indices: 55332291--55332391 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
55332281 ATAGTGAATC
*
55332291 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
55332320 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
55332348 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
55332378 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55332392 CATACCCTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:55332440 original size:29 final size:29
Alignment explanation
Indices: 55332379--55332509 Score: 174
Period size: 29 Copynumber: 4.5 Consensus size: 29
55332369 TTTTAAACCC
*** *
55332379 GCACACTTAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
55332407 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
55332437 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
*
55332466 GCACACTTAGTGCCATATATTTTCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
55332495 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
55332510 ATCTCGTCAC
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
29 89 0.99
30 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:55335298 original size:35 final size:35
Alignment explanation
Indices: 55335252--55335321 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
55335242 CGGACAACAC
* *
55335252 TTCACCATTTGAAGTAACATTTAGTTTACTCATTT
1 TTCACCATTTGAAGTAACACTTAGTTTACTAATTT
55335287 TTCACCATTTGAAGTAACACTTAGTTTACTAATTT
1 TTCACCATTTGAAGTAACACTTAGTTTACTAATTT
55335322 AAGTTCAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (35 bp):
TTCACCATTTGAAGTAACACTTAGTTTACTAATTT
Found at i:55337889 original size:28 final size:28
Alignment explanation
Indices: 55337843--55337911 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
55337833 TTTAAAACCC
*
55337843 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
55337870 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
55337898 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
55337912 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:55339535 original size:20 final size:20
Alignment explanation
Indices: 55339512--55339549 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55339502 CACATCCAAA
*
55339512 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
55339532 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
55339550 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:55348627 original size:47 final size:47
Alignment explanation
Indices: 55348576--55348699 Score: 167
Period size: 47 Copynumber: 2.6 Consensus size: 47
55348566 TTCTAGTTGG
*
55348576 CCTTTGTGGCATATTTGGTTTGTTGCCTTTGTTTCATACCCTAGTAT
1 CCTTTGTGGCATATTCGGTTTGTTGCCTTTGTTTCATACCCTAGTAT
* * *
55348623 CCTTTGTGGCATATCCGGTTTGTTGCCTTTGTTTCATACTCTGGTAT
1 CCTTTGTGGCATATTCGGTTTGTTGCCTTTGTTTCATACCCTAGTAT
* * * * *
55348670 CTTTTATGGCATATTCAGTATGTTTCCTTT
1 CCTTTGTGGCATATTCGGTTTGTTGCCTTT
55348700 ATGGCATACT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.49
Consensus pattern (47 bp):
CCTTTGTGGCATATTCGGTTTGTTGCCTTTGTTTCATACCCTAGTAT
Found at i:55348651 original size:25 final size:25
Alignment explanation
Indices: 55348575--55348654 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
55348565 ATTCTAGTTG
**
55348575 GCCTTTGTGGCATATTTGGTTTGTT
1 GCCTTTGTGGCATATCCGGTTTGTT
** * *
55348600 GCCTTTGTTTCATA-CC--CTAGTAT
1 GCCTTTGTGGCATATCCGGTTTGT-T
55348623 -CCTTTGTGGCATATCCGGTTTGTT
1 GCCTTTGTGGCATATCCGGTTTGTT
55348647 GCCTTTGT
1 GCCTTTGT
55348655 TTCATACTCT
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
22 14 0.35
23 3 0.08
24 1 0.03
25 22 0.55
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (25 bp):
GCCTTTGTGGCATATCCGGTTTGTT
Found at i:55348726 original size:22 final size:21
Alignment explanation
Indices: 55348696--55348747 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
55348686 AGTATGTTTC
* *
55348696 CTTTATGGCATACTTTGATAG
1 CTTTGTGGCATACTCTGATAG
*
55348717 TCTTTGTGGCGTACTCTGATAG
1 -CTTTGTGGCATACTCTGATAG
55348739 CTTTTGTGG
1 C-TTTGTGG
55348748 TATATTCAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.44
Consensus pattern (21 bp):
CTTTGTGGCATACTCTGATAG
Found at i:55353215 original size:40 final size:40
Alignment explanation
Indices: 55353170--55353339 Score: 198
Period size: 40 Copynumber: 4.2 Consensus size: 40
55353160 CGGAATACAA
*
55353170 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* * * *
55353210 CCGGATATAACGAGTTGCACAAATGCCTTCGGGTGTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* * * *
55353250 CTGGATTTAACAACTTGCACGAATGCCTTCAGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* ** * *
55353290 CCGGATGTAGTCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTTGCACGAA-TGCCTTCGGGTCTTAGC
55353330 CCGGATATAA
1 CCGGATATAA
55353340 TTATTAGCAT
Statistics
Matches: 107, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
39 2 0.02
40 105 0.98
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
Found at i:55353348 original size:40 final size:40
Alignment explanation
Indices: 55353170--55353371 Score: 192
Period size: 40 Copynumber: 5.0 Consensus size: 40
55353160 CGGAATACAA
* * *
55353170 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAGC
* * *
55353210 CCGGATATAACGAGTTGCACAAATGCCTTCGGGTGTTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAGC
* * * *
55353250 CTGGATTTAACAACTTGCACGAATGCCTTCAGGTCTTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
55353290 CCGGATGTAGTC-ACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATA-ACAACTTGCACAAATGCCTTCGGGTCTTAGC
** * * *
55353330 CCGGATATAATTA-TTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACAACTT-GCACAAATGCCTTCGGGTCTTAGC
55353370 CC
1 CC
55353372 AGATGTCATT
Statistics
Matches: 130, Mismatches: 29, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
39 1 0.01
40 128 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (40 bp):
CCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAGC
Found at i:55357306 original size:57 final size:56
Alignment explanation
Indices: 55357198--55357339 Score: 153
Period size: 57 Copynumber: 2.5 Consensus size: 56
55357188 ATTTATAAAA
** * * * *
55357198 TAGGATTACCAGTCCAGGCTAAATCCCATCTTTAGCATTCGCTCTTAAGAGCTTAT
1 TAGGATTACCAGTCCAGGCTAAATCCCATCGATAACATTAGCTCTTAAGAGCCTAC
* *
55357254 TCAGGATTACCAGTCCAGGCTAAATCCCTTCGATAACGTTAGCTCATT-AGAGCCTAC
1 T-AGGATTACCAGTCCAGGCTAAATCCCATCGATAACATTAGCTC-TTAAGAGCCTAC
* *
55357311 TATGGATTACCCGTCCGGGCTAAA-CCCAT
1 TA-GGATTACCAGTCCAGGCTAAATCCCAT
55357340 TTCATGACAT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
56 6 0.08
57 64 0.89
58 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (56 bp):
TAGGATTACCAGTCCAGGCTAAATCCCATCGATAACATTAGCTCTTAAGAGCCTAC
Found at i:55360976 original size:46 final size:45
Alignment explanation
Indices: 55360899--55361061 Score: 143
Period size: 46 Copynumber: 3.6 Consensus size: 45
55360889 AGTTTTGCCA
*
55360899 AGGTTCTGAGCT-TCTGCATA-GTTTGCTAACTCAAGAATATAGGAAT
1 AGGTTCTGAGCTCT-TGCATATG-TTGCAAACTCAAGAAT-TAGGAAT
55360945 AGGTTCTGAGCTCTTGCATATGTTGCAAACTCAAGAATTCAGGAAT
1 AGGTTCTGAGCTCTTGCATATGTTGCAAACTCAAGAATT-AGGAAT
* * * * * ** * * *
55360991 AGATT-TCAAGCTCTTACATCTATTGCGGACCCGAGAATTTAGGTAT
1 AGGTTCT-GAGCTCTTGCATATGTTGCAAACTCAAGAA-TTAGGAAT
*
55361037 AGGTTCTGAGCTCTTCCATATGTTG
1 AGGTTCTGAGCTCTTGCATATGTTG
55361062 AATACTTGAG
Statistics
Matches: 95, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
45 2 0.02
46 88 0.93
47 5 0.05
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (45 bp):
AGGTTCTGAGCTCTTGCATATGTTGCAAACTCAAGAATTAGGAAT
Found at i:55364471 original size:25 final size:25
Alignment explanation
Indices: 55364436--55364545 Score: 120
Period size: 25 Copynumber: 4.5 Consensus size: 25
55364426 TACATGTATT
* *
55364436 CTCATATGAGCTATGAATCGGTATG
1 CTCATACGAGCTATGAATCGGTAAG
* *
55364461 CTC-TCACGAGCTATAAATCGATAAG
1 CTCAT-ACGAGCTATGAATCGGTAAG
* *
55364486 CTCATATGAGCTAAGAATCGGTAAG
1 CTCATACGAGCTATGAATCGGTAAG
55364511 CTC-TCACGAGCTA--AATCGGTAAG
1 CTCAT-ACGAGCTATGAATCGGTAAG
55364534 CTCATACGAGCT
1 CTCATACGAGCT
55364546 GAGAATCAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
23 20 0.28
24 3 0.04
25 48 0.67
26 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (25 bp):
CTCATACGAGCTATGAATCGGTAAG
Found at i:55364514 original size:50 final size:49
Alignment explanation
Indices: 55364436--55364576 Score: 185
Period size: 48 Copynumber: 2.9 Consensus size: 49
55364426 TACATGTATT
* *
55364436 CTCATATGAGCTATGAATCGGTATGCTCTCACGAGCTATAAATCGATAAG
1 CTCATATGAGCTAAGAATCGGTAAGCTCTCACGAGCT-TAAATCGATAAG
*
55364486 CTCATATGAGCTAAGAATCGGTAAGCTCTCACGAGC-TAAATCGGTAAG
1 CTCATATGAGCTAAGAATCGGTAAGCTCTCACGAGCTTAAATCGATAAG
* * ** * *
55364534 CTCATACGAGCTGAGAATCAATAAGCTCTCACAAGCTGAAATC
1 CTCATATGAGCTAAGAATCGGTAAGCTCTCACGAGCTTAAATC
55364577 AGTAATCCCT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
48 42 0.52
49 5 0.06
50 34 0.42
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (49 bp):
CTCATATGAGCTAAGAATCGGTAAGCTCTCACGAGCTTAAATCGATAAG
Found at i:55364558 original size:25 final size:24
Alignment explanation
Indices: 55364451--55364576 Score: 105
Period size: 25 Copynumber: 5.2 Consensus size: 24
55364441 ATGAGCTATG
* * *
55364451 AATCGGTATGCTCTCACGAGCTATA
1 AATCGATAAGCTCTCACGAGCT-GA
* *
55364476 AATCGATAAGCTCAT-ATGAGCTAA
1 AATCGATAAGCTC-TCACGAGCTGA
*
55364500 GAATCGGTAAGCTCTCACGAGCT-A
1 -AATCGATAAGCTCTCACGAGCTGA
*
55364524 AATCGGTAAGCTCAT-ACGAGCTGA
1 AATCGATAAGCTC-TCACGAGCTGA
* *
55364548 GAATCAATAAGCTCTCACAAGCTGA
1 -AATCGATAAGCTCTCACGAGCTGA
55364573 AATC
1 AATC
55364577 AGTAATCCCT
Statistics
Matches: 85, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
23 20 0.24
24 10 0.12
25 54 0.64
26 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (24 bp):
AATCGATAAGCTCTCACGAGCTGA
Found at i:55368147 original size:23 final size:23
Alignment explanation
Indices: 55368098--55368155 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
55368088 TTCTAAAGTC
**
55368098 TAATAAAAAATAAAAAATAATTT
1 TAATAAAAAATAAAAAATAATAA
*
55368121 TAATAAAAATTAAAAACATAA-AA
1 TAATAAAAAATAAAAA-ATAATAA
55368144 TAATAAATAAAT
1 TAATAAA-AAAT
55368156 GTTTTTAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
TAATAAAAAATAAAAAATAATAA
Found at i:55376511 original size:45 final size:45
Alignment explanation
Indices: 55376412--55376631 Score: 331
Period size: 45 Copynumber: 5.0 Consensus size: 45
55376402 CCAAATTCAT
* * *
55376412 TCACCGGCATT-TCA-CCTGCTAGGCTCGAA-GCCCG-ATATTATT
1 TCACCGGCATTAT-AGCCTGCTAGGCTCAAAGGCCCGAATAGTATA
* *
55376454 TCACCTGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATA
*
55376499 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCTCGAATAGTATA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATA
55376544 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATA
* *
55376589 TCACCAGCACTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
55376632 CTGTACGATA
Statistics
Matches: 164, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
42 11 0.07
43 15 0.09
44 5 0.03
45 133 0.81
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATA
Found at i:55377159 original size:2 final size:2
Alignment explanation
Indices: 55377152--55377185 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55377142 TCATATTTTC
55377152 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
55377186 CTTTACCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55377503 original size:25 final size:25
Alignment explanation
Indices: 55377491--55377645 Score: 213
Period size: 25 Copynumber: 6.2 Consensus size: 25
55377481 TAATAAGGGA
*
55377491 AAATTTAACCAGAAATATTAAGAGC
1 AAATTTAACCAGAAATATTAAGAAC
* *
55377516 AAATTTAACCGGAATTATTAAGAAC
1 AAATTTAACCAGAAATATTAAGAAC
55377541 AAATTTAACC-GAAATTATTAAGAAC
1 AAATTTAACCAGAAA-TATTAAGAAC
* *
55377566 AAATTTAACCGGAATTATTAAGAAC
1 AAATTTAACCAGAAATATTAAGAAC
* *
55377591 AAATTTAACCAGAATTATTAAGAGC
1 AAATTTAACCAGAAATATTAAGAAC
* *
55377616 AAATTTAACCGGAATTATTAAGAAC
1 AAATTTAACCAGAAATATTAAGAAC
55377641 AAATT
1 AAATT
55377646 AACAAGCTTA
Statistics
Matches: 119, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
24 3 0.03
25 113 0.95
26 3 0.03
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.28
Consensus pattern (25 bp):
AAATTTAACCAGAAATATTAAGAAC
Found at i:55377569 original size:50 final size:50
Alignment explanation
Indices: 55377491--55377645 Score: 269
Period size: 50 Copynumber: 3.1 Consensus size: 50
55377481 TAATAAGGGA
55377491 AAATTTAACCAGAAA-TATTAAGAGCAAATTTAACCGGAATTATTAAGAAC
1 AAATTTAACC-GAAATTATTAAGAGCAAATTTAACCGGAATTATTAAGAAC
*
55377541 AAATTTAACCGAAATTATTAAGAACAAATTTAACCGGAATTATTAAGAAC
1 AAATTTAACCGAAATTATTAAGAGCAAATTTAACCGGAATTATTAAGAAC
55377591 AAATTTAACC-AGAATTATTAAGAGCAAATTTAACCGGAATTATTAAGAAC
1 AAATTTAACCGA-AATTATTAAGAGCAAATTTAACCGGAATTATTAAGAAC
55377641 AAATT
1 AAATT
55377646 AACAAGCTTA
Statistics
Matches: 101, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
49 5 0.05
50 96 0.95
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.28
Consensus pattern (50 bp):
AAATTTAACCGAAATTATTAAGAGCAAATTTAACCGGAATTATTAAGAAC
Found at i:55377570 original size:75 final size:75
Alignment explanation
Indices: 55377491--55377645 Score: 256
Period size: 75 Copynumber: 2.1 Consensus size: 75
55377481 TAATAAGGGA
* *
55377491 AAATTTAACCAGAAATATTAAGAGCAAATTTAACCGGAATTATTAAGAACAAATTTAACCGAAAT
1 AAATTTAACCAGAAATATTAAGAACAAATTTAACCAGAATTATTAAGAACAAATTTAACCGAAAT
55377556 TATTAAGAAC
66 TATTAAGAAC
* * * *
55377566 AAATTTAACCGGAATTATTAAGAACAAATTTAACCAGAATTATTAAGAGCAAATTTAACCGGAAT
1 AAATTTAACCAGAAATATTAAGAACAAATTTAACCAGAATTATTAAGAACAAATTTAACCGAAAT
55377631 TATTAAGAAC
66 TATTAAGAAC
55377641 AAATT
1 AAATT
55377646 AACAAGCTTA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.28
Consensus pattern (75 bp):
AAATTTAACCAGAAATATTAAGAACAAATTTAACCAGAATTATTAAGAACAAATTTAACCGAAAT
TATTAAGAAC
Found at i:55378830 original size:27 final size:27
Alignment explanation
Indices: 55378800--55378939 Score: 124
Period size: 27 Copynumber: 5.2 Consensus size: 27
55378790 ATTACCGTTT
* * *
55378800 TACCCTCAATTTACAGAATTACCAAAA
1 TACCCTCAGTTTATAAAATTACCAAAA
** *
55378827 TACCCTTGGTTTATAAAATCACCAAAA
1 TACCCTCAGTTTATAAAATTACCAAAA
* *
55378854 TACCC-CTAGTTTGTAAAATTACTAAAA
1 TACCCTC-AGTTTATAAAATTACCAAAA
**
55378881 TACCCTTTGTTTATAAAATTACCAAAA
1 TACCCTCAGTTTATAAAATTACCAAAA
* *
55378908 TACCCAT-GGTTTGA-AAAATTACTAAAA
1 TACCC-TCAGTTT-ATAAAATTACCAAAA
55378935 TACCC
1 TACCC
55378940 CTGTAGGGTA
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
27 90 0.98
28 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.31
Consensus pattern (27 bp):
TACCCTCAGTTTATAAAATTACCAAAA
Found at i:55378858 original size:54 final size:54
Alignment explanation
Indices: 55378802--55378939 Score: 152
Period size: 54 Copynumber: 2.5 Consensus size: 54
55378792 TACCGTTTTA
*
55378802 CCCTCAATTTACAGAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATAC
1 CCCT-AATTTACAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATAC
* ** * * *
55378857 CCCTAGTTTGTAAAATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATAC
1 CCCTAATTTACAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATAC
* ** *
55378911 CCATGGTTTGA-AAAATTACTAAAATACCC
1 CCCTAATTT-ACAAAATTACCAAAATACCC
55378940 CTGTAGGGTA
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
54 68 0.94
55 4 0.06
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (54 bp):
CCCTAATTTACAAAATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATAC
Found at i:55378952 original size:27 final size:27
Alignment explanation
Indices: 55378922--55378983 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
55378912 CATGGTTTGA
55378922 AAAATTACTAAAATACCCCTGTAGGGT
1 AAAATTACTAAAATACCCCTGTAGGGT
* * *
55378949 AAAATTACTGAAATACCCTTGTGGGGT
1 AAAATTACTAAAATACCCCTGTAGGGT
55378976 AAAATTAC
1 AAAATTAC
55378984 CATTTTGCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (27 bp):
AAAATTACTAAAATACCCCTGTAGGGT
Found at i:55378952 original size:54 final size:54
Alignment explanation
Indices: 55378816--55378966 Score: 153
Period size: 54 Copynumber: 2.8 Consensus size: 54
55378806 CAATTTACAG
* ** * * *
55378816 AATTACCAAAATACCCT-TGGTTTATAAAATCACCAAAATACCCCTAGTTTGTAA
1 AATTACTAAAATACCCTCT-GTGGATAAAATTACCAAAATACCCATAGTTTGAAA
* ** *
55378870 AATTACTAAAATACCCTTTGTTTATAAAATTACCAAAATACCCATGGTTTGAAA
1 AATTACTAAAATACCCTCTGTGGATAAAATTACCAAAATACCCATAGTTTGAAA
* **
55378924 AATTACTAAAATACCC-CTGTAGGGTAAAATTACTGAAATACCC
1 AATTACTAAAATACCCTCTGT-GGATAAAATTACCAAAATACCC
55378967 TTGTGGGGTA
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 3 0.04
54 80 0.95
55 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.30
Consensus pattern (54 bp):
AATTACTAAAATACCCTCTGTGGATAAAATTACCAAAATACCCATAGTTTGAAA
Found at i:55378968 original size:81 final size:81
Alignment explanation
Indices: 55378816--55378968 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
55378806 CAATTTACAG
* **
55378816 AATTACCAAAATACCCTTGGTTTATAAAATCACCAAAATACCCCTAGTTTGTAAAATTACTAAAA
1 AATTACCAAAATACCCATGGTTTATAAAATCACCAAAATACCCCTAGTGGGTAAAATTACTAAAA
55378881 TACCCTTTGTTTATAA
66 TACCCTTTGTTTATAA
* * *
55378897 AATTACCAAAATACCCATGGTTTGA-AAAATTACTAAAATACCCCT-GTAGGGTAAAATTACTGA
1 AATTACCAAAATACCCATGGTTT-ATAAAATCACCAAAATACCCCTAGT-GGGTAAAATTACTAA
55378960 AATACCCTT
64 AATACCCTT
55378969 GTGGGGTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
80 2 0.03
81 61 0.95
82 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (81 bp):
AATTACCAAAATACCCATGGTTTATAAAATCACCAAAATACCCCTAGTGGGTAAAATTACTAAAA
TACCCTTTGTTTATAA
Found at i:55379667 original size:27 final size:28
Alignment explanation
Indices: 55379603--55379671 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
55379593 GCGTAGAGCA
*
55379603 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGAAAAATTAC
55379631 CGAAATTACCCCTAAAGAGAAAAATTAC
1 CGAAATTACCCCTAAAGAGAAAAATTAC
*
55379659 CGATA-TACCCCTA
1 CGAAATTACCCCTA
55379672 GGGTTTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 8 0.21
28 31 0.79
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGAAAAATTAC
Found at i:55380310 original size:11 final size:10
Alignment explanation
Indices: 55380289--55380315 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
55380279 ATTTGGGTTA
55380289 TTTTATTTTT
1 TTTTATTTTT
55380299 TTTTATTTTT
1 TTTTATTTTT
55380309 TTTTATT
1 TTTTATT
55380316 ATGCTTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:55385173 original size:52 final size:52
Alignment explanation
Indices: 55385095--55385193 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
55385085 AACCTTCTAC
*
55385095 ACTAGAGTTGAAACCCTTGCCGCTGCATTTAAAATATTCTTACTTGGTTCCT
1 ACTAGAGTTGAAACCCTTGCCGCTGCATTTAAAATATGCTTACTTGGTTCCT
* *
55385147 ACTAGAGTTGAAATCCTTGCTGCTGCATTTAAAATATGCTTACTTGG
1 ACTAGAGTTGAAACCCTTGCCGCTGCATTTAAAATATGCTTACTTGG
55385194 AAGACAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (52 bp):
ACTAGAGTTGAAACCCTTGCCGCTGCATTTAAAATATGCTTACTTGGTTCCT
Found at i:55387225 original size:40 final size:39
Alignment explanation
Indices: 55387180--55387387 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 39
55387170 CGGAATACAA
*
55387180 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
55387220 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
55387260 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * ** * *
55387300 CCAGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
55387340 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
55387380 CCGGATAT
1 CCGGATAT
55387388 CATTCAATTG
Statistics
Matches: 140, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
39 1 0.01
40 139 0.99
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:55398045 original size:39 final size:39
Alignment explanation
Indices: 55397991--55398170 Score: 281
Period size: 39 Copynumber: 4.6 Consensus size: 39
55397981 AATGTTCGAG
*
55397991 GATATCC-GGCTAAGCCCGAAGGCAATTGTGCAAATTGT
1 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTAT
* *
55398029 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTAT
1 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTAT
* *
55398068 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTAT
1 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTAT
*
55398107 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGT
1 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTAT
*
55398146 GATATCCGGGTTAAGTCCCGAAGGC
1 GATATCCGGGCTAAG-CCCGAAGGC
55398171 CTTTGTGCGG
Statistics
Matches: 133, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
38 7 0.05
39 117 0.88
40 9 0.07
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (39 bp):
GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTAT
Found at i:55398132 original size:117 final size:118
Alignment explanation
Indices: 55397991--55398210 Score: 345
Period size: 117 Copynumber: 1.9 Consensus size: 118
55397981 AATGTTCGAG
55397991 GATATCCGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAG-CCCGAAGGCAA
1 GATATCCGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGCAA
** *
55398055 TTGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTAT
66 TTGTGCGAGTTACCATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTAT
* *
55398107 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGCC
1 GATATCC-GGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGCA
* * *
55398172 TTTGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGGC
65 ATTGTGCGAGTTACCATAACCGGGCTAAGTCCCGAAGGC
55398211 GTTTGAACGA
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
116 7 0.08
117 45 0.48
118 32 0.34
119 9 0.10
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (118 bp):
GATATCCGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGCAA
TTGTGCGAGTTACCATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTAT
Found at i:55406155 original size:39 final size:39
Alignment explanation
Indices: 55406101--55406281 Score: 290
Period size: 39 Copynumber: 4.6 Consensus size: 39
55406091 AATGTTCGAG
*
55406101 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGT
1 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTAT
* *
55406140 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTAT
1 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTAT
* *
55406179 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTAT
1 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTAT
*
55406218 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGT
1 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTAT
*
55406257 GATATCCGGGTTAAGTCCCGAAGGC
1 GATATCCGGGCTAAG-CCCGAAGGC
55406282 CTTTGTGCGG
Statistics
Matches: 134, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 125 0.93
40 9 0.07
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.23
Consensus pattern (39 bp):
GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTAT
Found at i:55406244 original size:117 final size:119
Alignment explanation
Indices: 55406101--55406321 Score: 356
Period size: 117 Copynumber: 1.9 Consensus size: 119
55406091 AATGTTCGAG
55406101 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAG-CCCGAAGGCA
1 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGCA
** *
55406165 ATTGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTAT
66 ATTGTGCGAGTTACCATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTAT
* *
55406218 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGCC
1 GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGCA
* * *
55406283 TTTGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGGC
66 ATTGTGCGAGTTACCATAACCGGGCTAAGTCCCGAAGGC
55406322 GTTTGAACGA
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
117 53 0.56
118 32 0.34
119 9 0.10
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (119 bp):
GATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGCA
ATTGTGCGAGTTACCATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTAT
Found at i:55410690 original size:47 final size:48
Alignment explanation
Indices: 55410556--55410690 Score: 168
Period size: 48 Copynumber: 2.8 Consensus size: 48
55410546 ATAATCTCAC
* * *
55410556 CCATAATGAACTCAGAACGCAACTCAACGAGCTCAGGTG-TTCGCATCT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCAGATGCTTCGCA-CT
* *
55410604 CCATAATGAACTCGGAACACAACTCAACGAGTTCGGATGCTT-GCA-T
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCAGATGCTTCGCACT
* *
55410650 CCATAGGTGAACTCGGAACGCAACTCAACGAGTTTAGATGC
1 CCATA-ATGAACTCGGAACGCAACTCAACGAGTTCAGATGC
55410691 CTCATAATTC
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 6 0.08
47 31 0.41
48 37 0.49
49 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (48 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCAGATGCTTCGCACT
Found at i:55413402 original size:40 final size:40
Alignment explanation
Indices: 55413344--55413501 Score: 133
Period size: 40 Copynumber: 4.0 Consensus size: 40
55413334 TGAATATGCC
* *
55413344 TTCAAGAGTACTAGAGTACTAA-CAAGGGCACGTATGTGCT
1 TTCAAGGGTACTAAAGTAC-AACCAAGGGCACGTATGTGCT
* * *
55413384 TTCAAGGGTACTAAAGTACAAGCAGGGGCACGTATGTGCA
1 TTCAAGGGTACTAAAGTACAACCAAGGGCACGTATGTGCT
* ** * * *
55413424 TTCAGGGGTACCGAAGTACAACCAGGGGCATGTATATG-T
1 TTCAAGGGTACTAAAGTACAACCAAGGGCACGTATGTGCT
* * * *
55413463 ATTC-AGGGGATCTAAAGTACAAACAAGGGAACATATGTG
1 -TTCAAGGGTA-CTAAAGTACAACCAAGGGCACGTATGTG
55413502 AATTTAGGGG
Statistics
Matches: 94, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
39 6 0.06
40 88 0.94
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (40 bp):
TTCAAGGGTACTAAAGTACAACCAAGGGCACGTATGTGCT
Found at i:55413563 original size:40 final size:40
Alignment explanation
Indices: 55413507--55414049 Score: 521
Period size: 40 Copynumber: 13.6 Consensus size: 40
55413497 ATGTGAATTT
* *
55413507 AGGGGCACGT-TGGTGCATTTAGGGGTACCGAAGTACAAAC
1 AGGGGCACGTGT-GTGCATTCAGGGGTACCAAAGTACAAAC
* *
55413547 AGGGGCACATGTGTGCATTCAGGGGTACTAAAGTACAAAC
1 AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
* * * * * *
55413587 AAGTGCACGTCTGTGCATTCAGCGATACCAAAGTACAAAT
1 AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
** * * **
55413627 AGGGGCACGCATGTGCATTTAGTGGTACTGAAGTACAAAC
1 AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
* * *
55413667 AGGGGCATGTGTGTGCATTTAGGGGTACCAAAGTACAAAT
1 AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
* * * * * *
55413707 AGGGGTATGTGTGTGTATTCAGGGGTATCGAAGTACAAAT
1 AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
* * * * * *
55413747 AAGGGCATGTGTGTTCATTCAGGGGTACCGAAGTGCAAAT
1 AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
* * * *
55413787 AGGGGTACGTGTGTGCATTTAGGGGTACCGAAGTATAAAC
1 AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
* *
55413827 AGGAGCACGTGTGTGCATTCAGGGGTACCAAAGTACAACC
1 AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
* * * *
55413867 AGGGGCACGTGTATGCATTTAGGGGTATCAAAGTACAAAT
1 AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
* *
55413907 AGGGGCACGTGTATGCATTTAGGGGTACCAAAGTACAAAC
1 AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
* ** * * *
55413947 AGGTGCGTGTATGTGCATTCAGGGGTATCTAAGTACAAAC
1 AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
* ** * * ** * *
55413987 AGGGGCATGCATGTCCATTCAAGGGTACTGAAGTAGAAAT
1 AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
* * *
55414027 AAGGGCATGTATGTGCATTCAGG
1 AGGGGCACGTGTGTGCATTCAGG
55414050 CAATAATTAT
Statistics
Matches: 418, Mismatches: 84, Indels: 2
0.83 0.17 0.00
Matches are distributed among these distances:
40 417 1.00
41 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.23
Consensus pattern (40 bp):
AGGGGCACGTGTGTGCATTCAGGGGTACCAAAGTACAAAC
Found at i:55413567 original size:100 final size:100
Alignment explanation
Indices: 55413407--55413589 Score: 271
Period size: 100 Copynumber: 1.8 Consensus size: 100
55413397 AAGTACAAGC
* ** *
55413407 AGGGGCACGTATGTGCATTCAGGGGTACCGAAGTACAACCAGGGGCATGTATATGTATTCAGGGG
1 AGGGGCACGTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACATATATGCATTCAGGGG
55413472 -ATCTAAAGTACAAACAAGGGAACATATGTGAATTT
66 TA-CTAAAGTACAAACAAGGGAACATATGTGAATTT
* * *
55413507 AGGGGCACGT-TGGTGCATTTAGGGGTACCGAAGTACAAACAGGGGCACATGTGTGCATTCAGGG
1 AGGGGCACGTAT-GTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACATATATGCATTCAGGG
55413571 GTACTAAAGTACAAACAAG
65 GTACTAAAGTACAAACAAG
55413590 TGCACGTCTG
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
99 1 0.01
100 72 0.97
101 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.21
Consensus pattern (100 bp):
AGGGGCACGTATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACATATATGCATTCAGGGG
TACTAAAGTACAAACAAGGGAACATATGTGAATTT
Found at i:55413890 original size:20 final size:20
Alignment explanation
Indices: 55413867--55413931 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
55413857 AAGTACAACC
55413867 AGGGGCACGTGTATGCATTT
1 AGGGGCACGTGTATGCATTT
* ** **
55413887 AGGGGTATCAAAGTA--CAAAT
1 AGGGGCA-C-GTGTATGCATTT
55413907 AGGGGCACGTGTATGCATTT
1 AGGGGCACGTGTATGCATTT
55413927 AGGGG
1 AGGGG
55413932 TACCAAAGTA
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
18 3 0.10
19 1 0.03
20 23 0.74
21 1 0.03
22 3 0.10
ACGTcount: A:0.28, C:0.12, G:0.35, T:0.25
Consensus pattern (20 bp):
AGGGGCACGTGTATGCATTT
Found at i:55414591 original size:47 final size:45
Alignment explanation
Indices: 55414510--55414765 Score: 214
Period size: 46 Copynumber: 5.5 Consensus size: 45
55414500 GCCAATGCTG
* *
55414510 TGTCCCAGACATGGTCTTACACTAGCTCAT-ATCTCATGTCGATGCCA
1 TGTCCCAGACAT-GTCTTACACTGGCT-ATCATCTCATGCCGATG-CA
* * *
55414557 TGTCCCAGACATGGTCTTACAGTGGCTATCATCTCGTAGCCAATGCA
1 TGTCCCAGACAT-GTCTTACACTGGCTATCATCTCAT-GCCGATGCA
* * *
55414604 TATCCCAGACATGTCTTACACTGGCT-TACATCTCGAGGTCGATGCA
1 TGTCCCAGACATGTCTTACACTGGCTAT-CATCTC-ATGCCGATGCA
* * * * *
55414650 TGTCCCAGACATGTCTTGCACTAGC-ACCCGTCTCGGTGCCGATGCCA
1 TGTCCCAGACATGTCTTACACTGGCTA-TCATCTC-ATGCCGATG-CA
* * * *
55414697 TGTCCTAGACATGGTCTTACACTGGCTCTCATAAT-ATGGCTGATGCA
1 TGTCCCAGACAT-GTCTTACACTGGCTATCAT-CTCAT-GCCGATGCA
55414744 TGTCCCAGACATGTCTTACACT
1 TGTCCCAGACATGTCTTACACT
55414766 AGCCCACAAT
Statistics
Matches: 169, Mismatches: 29, Indels: 23
0.76 0.13 0.10
Matches are distributed among these distances:
45 1 0.01
46 72 0.43
47 71 0.42
48 24 0.14
49 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (45 bp):
TGTCCCAGACATGTCTTACACTGGCTATCATCTCATGCCGATGCA
Found at i:55414636 original size:46 final size:47
Alignment explanation
Indices: 55414510--55414765 Score: 199
Period size: 47 Copynumber: 5.5 Consensus size: 47
55414500 GCCAATGCTG
* * * *
55414510 TGTCCCAGACATGGTCTTACACTAGCTCATATCTCAT-GTCGATGCCA
1 TGTCCCAGACATGGTCTTACACTGGCTTACATCTCGTAGTCGATG-CA
* * *
55414557 TGTCCCAGACATGGTCTTACAGTGGC-TATCATCTCGTAGCCAATGCA
1 TGTCCCAGACATGGTCTTACACTGGCTTA-CATCTCGTAGTCGATGCA
*
55414604 TATCCCAGACAT-GTCTTACACTGGCTTACATCTCG-AGGTCGATGCA
1 TGTCCCAGACATGGTCTTACACTGGCTTACATCTCGTA-GTCGATGCA
* * *** * *
55414650 TGTCCCAGACAT-GTCTTGCACTAGCACCCGTCTCGGT-GCCGATGCCA
1 TGTCCCAGACATGGTCTTACACTGGCTTACATCTC-GTAGTCGATG-CA
* ** *
55414697 TGTCCTAGACATGGTCTTACACTGGC-T-C-TCATAATATGGCTGATGCA
1 TGTCCCAGACATGGTCTTACACTGGCTTACATC-TCGTA-GTC-GATGCA
55414744 TGTCCCAGACAT-GTCTTACACT
1 TGTCCCAGACATGGTCTTACACT
55414766 AGCCCACAAT
Statistics
Matches: 170, Mismatches: 27, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
45 4 0.02
46 72 0.42
47 74 0.44
48 20 0.12
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (47 bp):
TGTCCCAGACATGGTCTTACACTGGCTTACATCTCGTAGTCGATGCA
Found at i:55418708 original size:20 final size:20
Alignment explanation
Indices: 55418683--55418723 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
55418673 AAGTTTGGTT
55418683 TAATGTAATGGCACTAAGTG
1 TAATGTAATGGCACTAAGTG
55418703 TAATGTAATGGCACTAAGTG
1 TAATGTAATGGCACTAAGTG
55418723 T
1 T
55418724 GCGATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (20 bp):
TAATGTAATGGCACTAAGTG
Found at i:55423698 original size:18 final size:19
Alignment explanation
Indices: 55423663--55423703 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
55423653 TTGGGCCTAG
55423663 ATGGGTCGTGTGGACCCA-
1 ATGGGTCGTGTGGACCCAC
*
55423681 ATGGGCTCGTG-GGCCCCAC
1 ATGGG-TCGTGTGGACCCAC
55423700 ATGG
1 ATGG
55423704 ATTAAATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.15, C:0.27, G:0.39, T:0.20
Consensus pattern (19 bp):
ATGGGTCGTGTGGACCCAC
Found at i:55423990 original size:27 final size:27
Alignment explanation
Indices: 55423914--55423966 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
55423904 GACCCCGATT
*
55423914 TGTAAAATCACCGA-AATACCCTTGTAG
1 TGTAAAATGACC-ATAATACCCTTGTAG
55423941 TGTAAAATGACCATAATACCCTTGTA
1 TGTAAAATGACCATAATACCCTTGTA
55423967 TGGTAGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (27 bp):
TGTAAAATGACCATAATACCCTTGTAG
Done.