Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 103 of 189
Found at i:28746556 original size:17 final size:18
Alignment explanation
Indices: 28746520--28746559 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
28746510 AAAATCTATA
**
28746520 AAAAATATTTAAAATTTT
1 AAAAATATTTAAAAAATT
28746538 AAAAA-ATTTAAAAAATT
1 AAAAATATTTAAAAAATT
28746555 AAAAA
1 AAAAA
28746560 GTTGTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATATTTAAAAAATT
Found at i:28747690 original size:7 final size:7
Alignment explanation
Indices: 28747661--28747726 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
28747651 CAAAAATGAC
28747661 ATAAAAA
1 ATAAAAA
28747668 TATAAATAA
1 -ATAAA-AA
*
28747677 ATTAAAA
1 ATAAAAA
28747684 ATAAAAA
1 ATAAAAA
28747691 ACTAAAAA
1 A-TAAAAA
**
28747699 ATAAGTA
1 ATAAAAA
*
28747706 TTAAAAA
1 ATAAAAA
*
28747713 TTAAAAAA
1 AT-AAAAA
28747721 ATAAAA
1 ATAAAA
28747727 TATATCAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
7 23 0.49
8 22 0.47
9 2 0.04
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (7 bp):
ATAAAAA
Found at i:28747698 original size:15 final size:15
Alignment explanation
Indices: 28747661--28747726 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
28747651 CAAAAATGAC
28747661 ATAAAAATATAAATAA
1 ATAAAAA-ATAAATAA
*
28747677 ATTAAAAATAAA-AA
1 ATAAAAAATAAATAA
*
28747691 ACTAAAAAATAAGT-A
1 A-TAAAAAATAAATAA
* * *
28747706 TTAAAAATTAAAAAA
1 ATAAAAAATAAATAA
28747721 ATAAAA
1 ATAAAA
28747727 TATATCAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
14 12 0.31
15 21 0.54
16 6 0.15
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (15 bp):
ATAAAAAATAAATAA
Found at i:28747700 original size:22 final size:20
Alignment explanation
Indices: 28747661--28747726 Score: 51
Period size: 22 Copynumber: 3.0 Consensus size: 20
28747651 CAAAAATGAC
28747661 ATAAAAATATAAATAAATTAAAA
1 ATAAAAA-ATAAA-AAA-TAAAA
*
28747684 ATAAAAAACTAAAAAATAAGTA
1 ATAAAAAA-TAAAAAATAA-AA
* *
28747706 TTAAAAATTAAAAAAATAAAA
1 ATAAAAAAT-AAAAAATAAAA
28747727 TATATCAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
21 5 0.14
22 20 0.56
23 11 0.31
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
ATAAAAAATAAAAAATAAAA
Found at i:28748040 original size:19 final size:20
Alignment explanation
Indices: 28748016--28748054 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
28748006 AAAAGAATTC
28748016 TTTAAAAAATCTAAA-ATAT
1 TTTAAAAAATCTAAATATAT
*
28748035 TTTAAAAACTCTAAATATAT
1 TTTAAAAAATCTAAATATAT
28748055 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAAAAAATCTAAATATAT
Found at i:28748236 original size:44 final size:44
Alignment explanation
Indices: 28748182--28748265 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
28748172 TCATAAATGT
* *
28748182 TAGTTTGTGTTTTAAACTGGTCTACGTTATTTTCTTAAAGCCAC
1 TAGTTTGTGTTTTAAACTGATCTACGTTATTTTCATAAAGCCAC
* *
28748226 TAGTTTGTGTTTTAAATTGATCTACTTTATTTTCATAAAG
1 TAGTTTGTGTTTTAAACTGATCTACGTTATTTTCATAAAG
28748266 TTGCAACCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (44 bp):
TAGTTTGTGTTTTAAACTGATCTACGTTATTTTCATAAAGCCAC
Found at i:28750923 original size:18 final size:16
Alignment explanation
Indices: 28750881--28750923 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
28750871 TGTTGTTCGT
28750881 TTTCAAAATATTATTCA
1 TTTC-AAATATTATTCA
28750898 TTTACAAATCATTATTCAA
1 TTT-CAAAT-ATTATTC-A
28750917 TTTCAAA
1 TTTCAAA
28750924 ATGTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAAATATTATTCA
Found at i:28750925 original size:19 final size:17
Alignment explanation
Indices: 28750881--28750925 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
28750871 TGTTGTTCGT
28750881 TTTCAAAATATTATTCA
1 TTTCAAAATATTATTCA
28750898 TTT-ACAAATCATTATTCAA
1 TTTCA-AAAT-ATTATTC-A
28750917 TTTCAAAAT
1 TTTCAAAAT
28750926 GTTTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.04
17 7 0.29
18 7 0.29
19 8 0.33
20 1 0.04
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTCAAAATATTATTCA
Found at i:28753336 original size:17 final size:18
Alignment explanation
Indices: 28753304--28753338 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28753294 TCATGATGTT
*
28753304 CGCCCGTGTGGGCCCACA
1 CGCCCATGTGGGCCCACA
28753322 CGCCCATGT-GGCCCACA
1 CGCCCATGTGGGCCCACA
28753339 TGACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.46, G:0.29, T:0.11
Consensus pattern (18 bp):
CGCCCATGTGGGCCCACA
Found at i:28756068 original size:161 final size:161
Alignment explanation
Indices: 28755796--28756118 Score: 567
Period size: 161 Copynumber: 2.0 Consensus size: 161
28755786 TAATCAATTT
* *
28755796 CATGAACATAAACATACTTTCGTTGAACATTACCTTTTTATTTCTTTTCATGGATTCTTGATATA
1 CATGAACATAAACATACTTTCATTGAACATTACCTTTTTATTTCTTTTCATGGATTCATGATATA
* *
28755861 AGTCCTTTGAATACTTACCTATCCCTTCCTTTTCATACCTGTTGAATCAAATGAAATAACATCGA
66 AGTCCTTTGAATACTTACCAATCCCTTCCTTTTCATACCCGTTGAATCAAATGAAATAACATCGA
*
28755926 ATAATGAAAATAATATTTTCCGTACAACTTA
131 ATAATGAAAATAATATTTTCAGTACAACTTA
*
28755957 CATGAACATAAACATACTTTCATTGAACATTACCTTTTTA-TTCTTTTTCATGGATTCATGATGT
1 CATGAACATAAACATACTTTCATTGAACATTACCTTTTTATTTC-TTTTCATGGATTCATGATAT
*
28756021 AAGTCCTTTGAATACTTACCAATCCCTTCCTTTTCATACCCGTTGAATCAAATGAAATAACATTG
65 AAGTCCTTTGAATACTTACCAATCCCTTCCTTTTCATACCCGTTGAATCAAATGAAATAACATCG
28756086 AATAATGAAAATAATATTTTCAGTACAACTTA
130 AATAATGAAAATAATATTTTCAGTACAACTTA
28756118 C
1 C
28756119 CTGATACAAT
Statistics
Matches: 154, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
160 3 0.02
161 151 0.98
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (161 bp):
CATGAACATAAACATACTTTCATTGAACATTACCTTTTTATTTCTTTTCATGGATTCATGATATA
AGTCCTTTGAATACTTACCAATCCCTTCCTTTTCATACCCGTTGAATCAAATGAAATAACATCGA
ATAATGAAAATAATATTTTCAGTACAACTTA
Found at i:28756380 original size:38 final size:38
Alignment explanation
Indices: 28756144--28756508 Score: 381
Period size: 41 Copynumber: 9.3 Consensus size: 38
28756134 GACACGAAGA
* * * * *
28756144 CTGCTTGGCTCAAAGCCTGATATAATACATCAGCATAAAGC
1 CTGCTAGGCACAAAGCCTGA-AT-AT-CACCGGCACAAAGC
* * *
28756185 CTGCTAGGCACAAAGCCTAATATAATACACTGGCACGAAGC
1 CTGCTAGGCACAAAGCCTGA-AT-AT-CACCGGCACAAAGC
* ** *
28756226 TTGCTAGGCACAAAGCCTGACATAATACACCAACACGAAGC
1 CTGCTAGGCACAAAGCCTGA-AT-AT-CACCGGCACAAAGC
* *
28756267 CTGCTAGGCACAAAGCCTGATATAATACACCGACACTAAGC
1 CTGCTAGGCACAAAGCCTGA-AT-AT-CACCGGCACAAAGC
28756308 CTGCTAGGCACAAAGCCTGATATATCACCGGCACAAAGC
1 CTGCTAGGCACAAAGCCTGA-ATATCACCGGCACAAAGC
* *
28756347 CTGCTAGGCACAAAGCCCGAATATCACCGGCACAATGC
1 CTGCTAGGCACAAAGCCTGAATATCACCGGCACAAAGC
* *
28756385 CTGCTAGGCACGAAGCCTAAATATCACCGGCACAAAGC
1 CTGCTAGGCACAAAGCCTGAATATCACCGGCACAAAGC
** *
28756423 CTGCTAGGCACGGAGCCTGAATATCACCGGTACAAAGC
1 CTGCTAGGCACAAAGCCTGAATATCACCGGCACAAAGC
* * *
28756461 CTGCTAGGCACGAAG-CTCGAATATCATCGGCATAAAGC
1 CTGCTAGGCACAAAGCCT-GAATATCACCGGCACAAAGC
28756499 CTGCTAGGCA
1 CTGCTAGGCA
28756509 TGGAGCCCAA
Statistics
Matches: 290, Mismatches: 33, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
37 2 0.01
38 127 0.44
39 31 0.11
40 2 0.01
41 128 0.44
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.17
Consensus pattern (38 bp):
CTGCTAGGCACAAAGCCTGAATATCACCGGCACAAAGC
Found at i:28756522 original size:38 final size:38
Alignment explanation
Indices: 28756180--28756526 Score: 334
Period size: 38 Copynumber: 8.9 Consensus size: 38
28756170 ACATCAGCAT
* ** *
28756180 AAAGCCTGCTAGGCACAAAGCCTAATATAATACACTGGCAC
1 AAAGCCTGCTAGGCACGAAGCCCGA-AT-AT-CACCGGCAC
* * * * **
28756221 GAAGCTTGCTAGGCACAAAGCCTGACATAATACACCAACAC
1 AAAGCCTGCTAGGCACGAAGCCCGA-AT-AT-CACCGGCAC
* * * *
28756262 GAAGCCTGCTAGGCACAAAGCCTGATATAATACACCGACAC
1 AAAGCCTGCTAGGCACGAAGCCCGA-AT-AT-CACCGGCAC
* * *
28756303 TAAGCCTGCTAGGCACAAAGCCTGATATATCACCGGCAC
1 AAAGCCTGCTAGGCACGAAGCCCGA-ATATCACCGGCAC
*
28756342 AAAGCCTGCTAGGCACAAAGCCCGAATATCACCGGCAC
1 AAAGCCTGCTAGGCACGAAGCCCGAATATCACCGGCAC
* **
28756380 AATGCCTGCTAGGCACGAAGCCTAAATATCACCGGCAC
1 AAAGCCTGCTAGGCACGAAGCCCGAATATCACCGGCAC
* * *
28756418 AAAGCCTGCTAGGCACGGAGCCTGAATATCACCGGTAC
1 AAAGCCTGCTAGGCACGAAGCCCGAATATCACCGGCAC
* * *
28756456 AAAGCCTGCTAGGCACGAAGCTCGAATATCATCGGCAT
1 AAAGCCTGCTAGGCACGAAGCCCGAATATCACCGGCAC
* * *
28756494 AAAGCCTGCTAGGCATGGAGCCCAAATATCACC
1 AAAGCCTGCTAGGCACGAAGCCCGAATATCACC
28756527 ACGTTTCTAT
Statistics
Matches: 273, Mismatches: 33, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
38 141 0.52
39 31 0.11
40 2 0.01
41 99 0.36
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.16
Consensus pattern (38 bp):
AAAGCCTGCTAGGCACGAAGCCCGAATATCACCGGCAC
Found at i:28758795 original size:96 final size:96
Alignment explanation
Indices: 28758628--28758836 Score: 292
Period size: 96 Copynumber: 2.2 Consensus size: 96
28758618 TTAAACCACA
** * *
28758628 TTGTGGATGAACCACTAATTGTTGTAGATGAACTACTAACGATAAGATTATTGGTGGGTGAACCA
1 TTGTGGATGAACCACTAATCATTGTAGATGAACTACTAACGATAAAAATATTGGTGGGTGAACCA
*
28758693 AACATCGGAGAAGATGAAAACTACTAGTACG
66 AACATCGGAGAAGATCAAAACTACTAGTACG
* *
28758724 TTGTGGATGAACCATTGATCATTGTAGATGAACTACTAACGATAAAAATATTGGTGGGTGAACCA
1 TTGTGGATGAACCACTAATCATTGTAGATGAACTACTAACGATAAAAATATTGGTGGGTGAACCA
** * ** * *
28758789 TCCATCGGTGAAGATCAAAGTTGCTAGTATG
66 AACATCGGAGAAGATCAAAACTACTAGTACG
28758820 TTGTGGATGAACCACTA
1 TTGTGGATGAACCACTA
28758837 GTCGTACAGA
Statistics
Matches: 97, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (96 bp):
TTGTGGATGAACCACTAATCATTGTAGATGAACTACTAACGATAAAAATATTGGTGGGTGAACCA
AACATCGGAGAAGATCAAAACTACTAGTACG
Found at i:28767198 original size:27 final size:27
Alignment explanation
Indices: 28767159--28767226 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
28767149 ATAACATAAA
* * *
28767159 GCAT-ACAATCATTTTATAATATAGGG
1 GCATAACAGTCATTTTACAACATAGGG
* *
28767185 GCATAACAGTCATTTTACCACATGGGG
1 GCATAACAGTCATTTTACAACATAGGG
28767212 GCATAACAGTCATTT
1 GCATAACAGTCATTT
28767227 CATACCAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 4 0.11
27 32 0.89
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (27 bp):
GCATAACAGTCATTTTACAACATAGGG
Found at i:28769155 original size:34 final size:34
Alignment explanation
Indices: 28769108--28769181 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
28769098 TAAAATCATT
28769108 CATG-TTGTGACAAGTCAATACAGTAGCAATAAA
1 CATGCTTGTGACAAGTCAATACAGTAGCAATAAA
* *
28769141 CATGCTTGTGACAAGTCGATACAGTAGCAATTAA
1 CATGCTTGTGACAAGTCAATACAGTAGCAATAAA
28769175 CATGCTT
1 CATGCTT
28769182 ATAATAGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 4 0.11
34 34 0.89
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (34 bp):
CATGCTTGTGACAAGTCAATACAGTAGCAATAAA
Found at i:28779633 original size:20 final size:20
Alignment explanation
Indices: 28779610--28779647 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28779600 TAATAGTTTA
*
28779610 TTTAAGTTAATAAAACTAAG
1 TTTAAGATAATAAAACTAAG
*
28779630 TTTAAGATAATTAAACTA
1 TTTAAGATAATAAAACTA
28779648 GATTAATTAT
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:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (20 bp):
TTTAAGATAATAAAACTAAG
Found at i:28781728 original size:117 final size:117
Alignment explanation
Indices: 28781522--28781739 Score: 373
Period size: 117 Copynumber: 1.9 Consensus size: 117
28781512 CCCTGATTGC
* *
28781522 ACTTACGTGCCTCTATCGTACTTCGGTACCCCTGATCGCACTTACGTGCCCCTATCGTACTTCGG
1 ACTTACGTGCCCCTATCGTACTTCGATACCCCTGATCGCACTTACGTGCCCCTATCGTACTTCGG
*
28781587 TACCCTTGATCGCACTTATGTGCCCCTGTTGTACTTTGGCACCCCTAATCGG
66 TACCCCTGATCGCACTTATGTGCCCCTGTTGTACTTTGGCACCCCTAATCGG
* * * *
28781639 ACTTACGTGCCCCTGTTGTACTTCGATACCCCTGATCGCACTTACGTGCCTCTATTGTACTTCGG
1 ACTTACGTGCCCCTATCGTACTTCGATACCCCTGATCGCACTTACGTGCCCCTATCGTACTTCGG
28781704 TACCCCTGATCGCACTTATGTGCCCCTGTTGTACTT
66 TACCCCTGATCGCACTTATGTGCCCCTGTTGTACTT
28781740 CGACACTATT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 94 1.00
ACGTcount: A:0.15, C:0.33, G:0.18, T:0.33
Consensus pattern (117 bp):
ACTTACGTGCCCCTATCGTACTTCGATACCCCTGATCGCACTTACGTGCCCCTATCGTACTTCGG
TACCCCTGATCGCACTTATGTGCCCCTGTTGTACTTTGGCACCCCTAATCGG
Found at i:28781759 original size:39 final size:39
Alignment explanation
Indices: 28781512--28781741 Score: 316
Period size: 39 Copynumber: 5.9 Consensus size: 39
28781502 ATAATGATAT
* * * *
28781512 CCCTGATTGCACTTACGTGCCTCTATCGTACTTCGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* *
28781551 CCCTGATCGCACTTACGTGCCCCTATCGTACTTCGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* * * *
28781590 CCTTGATCGCACTTATGTGCCCCTGTTGTACTTTGGCAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* * *
28781629 CCCTAATCGGACTTACGTGCCCCTGTTGTACTTCGATAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
* *
28781668 CCCTGATCGCACTTACGTGCCTCTATTGTACTTCGGTAC
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
*
28781707 CCCTGATCGCACTTATGTGCCCCTGTTGTACTTCG
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCG
28781742 ACACTATTGA
Statistics
Matches: 168, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 168 1.00
ACGTcount: A:0.15, C:0.34, G:0.19, T:0.33
Consensus pattern (39 bp):
CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTAC
Found at i:28791486 original size:38 final size:39
Alignment explanation
Indices: 28791264--28791491 Score: 235
Period size: 39 Copynumber: 5.9 Consensus size: 39
28791254 ATAATTATAT
* * *** *
28791264 CCCTGATCGGACTTACGTGCCCCTGGCATACTTTGGTAC
1 CCCTGATCGCACTTACGTGCCCTTGTTGTACTTCGGTAC
** * *
28791303 CTGTGATCGCACTTACGTGCCCTTGTCGTACTTCGGAAC
1 CCCTGATCGCACTTACGTGCCCTTGTTGTACTTCGGTAC
* * * * * * * *
28791342 CCATTATCGAAATTACTTGCCCTTCTAGTACTTTGGTAC
1 CCCTGATCGCACTTACGTGCCCTTGTTGTACTTCGGTAC
* *
28791381 TCCTGATCGCACTTACGTGCCCTTGTTGTACTTCAGTAC
1 CCCTGATCGCACTTACGTGCCCTTGTTGTACTTCGGTAC
28791420 CCCTGATCG-ACTTACGTGCCCTTGTTGTACTTCGGTAC
1 CCCTGATCGCACTTACGTGCCCTTGTTGTACTTCGGTAC
* * *
28791458 CCCTGATCGCACTTACG-CCCCCTATTGTACTTCG
1 CCCTGATCGCACTTACGTGCCCTTGTTGTACTTCG
28791492 ATACTTTTGA
Statistics
Matches: 155, Mismatches: 33, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
38 51 0.33
39 104 0.67
ACGTcount: A:0.16, C:0.32, G:0.19, T:0.33
Consensus pattern (39 bp):
CCCTGATCGCACTTACGTGCCCTTGTTGTACTTCGGTAC
Found at i:28798079 original size:27 final size:27
Alignment explanation
Indices: 28798039--28798164 Score: 121
Period size: 27 Copynumber: 4.7 Consensus size: 27
28798029 TGCGATTCGG
* *
28798039 AAAATTACCAAAATACCCTTGAAGTGT
1 AAAATTACCGAAATACCCTTGAAGGGT
** *
28798066 AAAATTATTGAAATATCCC--AAAGGGT
1 AAAATTACCGAAATA-CCCTTGAAGGGT
* ** *
28798092 AAAATTACCAAAATAAACTCGAAGGGT
1 AAAATTACCGAAATACCCTTGAAGGGT
* *
28798119 AAAATTATCGAAATACCCTTGAAAGGT
1 AAAATTACCGAAATACCCTTGAAGGGT
*
28798146 AAAATTACTGAAATACCCT
1 AAAATTACCGAAATACCCT
28798165 CAAAGGTTAA
Statistics
Matches: 77, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
25 1 0.01
26 17 0.22
27 56 0.73
28 3 0.04
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.25
Consensus pattern (27 bp):
AAAATTACCGAAATACCCTTGAAGGGT
Found at i:28798175 original size:27 final size:27
Alignment explanation
Indices: 28798039--28798191 Score: 114
Period size: 27 Copynumber: 5.7 Consensus size: 27
28798029 TGCGATTCGG
** ** *
28798039 AAAATTACCAAAATACCCTTGAAGTGT
1 AAAATTACTGAAATACCCTCAAAGGGT
* *
28798066 AAAATTATTGAAATATCC-CAAAGGGT
1 AAAATTACTGAAATACCCTCAAAGGGT
** ** *
28798092 AAAATTACCAAAATAAACTCGAAGGGT
1 AAAATTACTGAAATACCCTCAAAGGGT
*
28798119 AAAATTA-TCGAAATACCCTTGAAA-GGT
1 AAAATTACT-GAAATACCC-TCAAAGGGT
*
28798146 AAAATTACTGAAATACCCTCAAAGGTT
1 AAAATTACTGAAATACCCTCAAAGGGT
* **
28798173 AAAATGACTGTTATACCCT
1 AAAATTACTGAAATACCCT
28798192 AGGAGATAAA
Statistics
Matches: 97, Mismatches: 24, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
26 22 0.23
27 71 0.73
28 4 0.04
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTCAAAGGGT
Found at i:28798400 original size:26 final size:26
Alignment explanation
Indices: 28798371--28798469 Score: 94
Period size: 26 Copynumber: 3.8 Consensus size: 26
28798361 TTTGCCACAA
* *
28798371 ATACTGTTACTGGTAGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
* *
28798397 ATACTGATACTGGCAGCTCTGTTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
* * * *
28798423 TTACT-ATTATTGGCAGCTTTGTTGTG
1 ATACTGA-TACTGGCAGCTTTGCTGCG
*
28798449 TTACTGATACTGG-AGCTTTGC
1 ATACTGATACTGGCAGCTTTGC
28798470 AACGATATTG
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
25 8 0.13
26 52 0.85
27 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.39
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCG
Found at i:28798646 original size:30 final size:30
Alignment explanation
Indices: 28798580--28798724 Score: 143
Period size: 30 Copynumber: 4.9 Consensus size: 30
28798570 CTACATTTGT
*
28798580 ACTGATTACTGTTTTGGGCTAAGG--C-CAC
1 ACTG-TTACTGTATTGGGCTAAGGCCCACAC
28798608 ACTGTTACTGTATTGGGCTAAGGCCCACAC
1 ACTGTTACTGTATTGGGCTAAGGCCCACAC
* ** *
28798638 ACTATTACTGTATTGGGCTAAGAACCATAC
1 ACTGTTACTGTATTGGGCTAAGGCCCACAC
* * * *
28798668 TCTGTTATTCTATTGGGCTATGGCCCACAC
1 ACTGTTACTGTATTGGGCTAAGGCCCACAC
* * * *
28798698 ATTGCTACTGTATAGGGCTTAGGCCCA
1 ACTGTTACTGTATTGGGCTAAGGCCCA
28798725 AACTGATTCT
Statistics
Matches: 93, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
27 18 0.19
28 4 0.04
29 1 0.01
30 70 0.75
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.31
Consensus pattern (30 bp):
ACTGTTACTGTATTGGGCTAAGGCCCACAC
Found at i:28805266 original size:27 final size:27
Alignment explanation
Indices: 28805228--28805338 Score: 134
Period size: 27 Copynumber: 4.1 Consensus size: 27
28805218 ATTCATGGGC
* * *
28805228 AAATTACTAAAATTCCCCCAAAAGGTA
1 AAATTACCAAAATACCCCCAAAGGGTA
***
28805255 AAATTACCAAAATACCCTTGAAGGGTA
1 AAATTACCAAAATACCCCCAAAGGGTA
28805282 AAATTACCAAAATA-CCCCAAAGGGTA
1 AAATTACCAAAATACCCCCAAAGGGTA
***
28805308 AAATTATTGAAATACCCCCAAAGGGTA
1 AAATTACCAAAATACCCCCAAAGGGTA
28805335 AAAT
1 AAAT
28805339 ATTTATATGA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
26 20 0.28
27 51 0.72
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.21
Consensus pattern (27 bp):
AAATTACCAAAATACCCCCAAAGGGTA
Found at i:28805321 original size:53 final size:54
Alignment explanation
Indices: 28805228--28805338 Score: 134
Period size: 53 Copynumber: 2.1 Consensus size: 54
28805218 ATTCATGGGC
* * ***
28805228 AAATTACTAAAATTCCCCCAAAAGGTAAAATTACCAAAATACCCTTGAAGGGTA
1 AAATTACCAAAATTACCCCAAAAGGTAAAATTACCAAAATACCCCCAAAGGGTA
* ***
28805282 AAATTACCAAAA-TACCCCAAAGGGTAAAATTATTGAAATACCCCCAAAGGGTA
1 AAATTACCAAAATTACCCCAAAAGGTAAAATTACCAAAATACCCCCAAAGGGTA
28805335 AAAT
1 AAAT
28805339 ATTTATATGA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
53 37 0.77
54 11 0.23
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.21
Consensus pattern (54 bp):
AAATTACCAAAATTACCCCAAAAGGTAAAATTACCAAAATACCCCCAAAGGGTA
Found at i:28805490 original size:26 final size:26
Alignment explanation
Indices: 28805461--28805587 Score: 115
Period size: 26 Copynumber: 5.1 Consensus size: 26
28805451 TTTGTCACAA
*
28805461 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
* *
28805487 ATACTGATACTGGCAGCTCTGCTACG
1 ATACTGATACTGGCAGCTTTGCTGCG
* * * *
28805513 TTACT-ACTACTGGTAGCTTAGTTGCG
1 ATACTGA-TACTGGCAGCTTTGCTGCG
*
28805539 ----T--TACTGGTAGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
*
28805559 TTACTGATACTGGCAGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
28805585 ATA
1 ATA
28805588 TTGGTGTGTT
Statistics
Matches: 81, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
20 17 0.21
22 1 0.01
24 1 0.01
25 1 0.01
26 61 0.75
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCG
Found at i:28805545 original size:20 final size:20
Alignment explanation
Indices: 28805520--28805564 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
28805510 ACGTTACTAC
*
28805520 TACTGGTAGCTTAGTTGCGT
1 TACTGGTAGCTTAGCTGCGT
*
28805540 TACTGGTAGCTTTGCTGCGT
1 TACTGGTAGCTTAGCTGCGT
28805560 TACTG
1 TACTG
28805565 ATACTGGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.13, C:0.18, G:0.29, T:0.40
Consensus pattern (20 bp):
TACTGGTAGCTTAGCTGCGT
Found at i:28805734 original size:27 final size:27
Alignment explanation
Indices: 28805691--28805797 Score: 106
Period size: 30 Copynumber: 3.7 Consensus size: 27
28805681 CTGCATTTGT
*
28805691 ACTGATTACTATTTTGGGCTAAGGCCAC
1 ACTG-TTACTATATTGGGCTAAGGCCAC
28805719 ACTGTTACTATATTGGGCTAAGGCCAAC
1 ACTGTTACTATATTGGGCTAAGGCC-AC
* * *
28805747 AAATTGTTTCTGTATTGGGCTAAGGCCCAC
1 --ACTGTTACTATATTGGGCTAAGG-CCAC
*
28805777 ACTCTGTTACTGTATTGGGCT
1 A--CTGTTACTATATTGGGCT
28805798 TTGACCCACA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
27 20 0.30
28 7 0.10
30 38 0.57
31 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (27 bp):
ACTGTTACTATATTGGGCTAAGGCCAC
Found at i:28805765 original size:30 final size:28
Alignment explanation
Indices: 28805704--28805797 Score: 109
Period size: 30 Copynumber: 3.2 Consensus size: 28
28805694 GATTACTATT
* *
28805704 TTGGGCTAAGGCCAC-ACTGTTACTATA
1 TTGGGCTAAGGCCACAATTGTTACTGTA
*
28805731 TTGGGCTAAGGCCAACAAATTGTTTCTGTA
1 TTGGGCTAAGGCC-AC-AATTGTTACTGTA
*
28805761 TTGGGCTAAGGCCCACACTCTGTTACTGTA
1 TTGGGCTAAGG-CCACAAT-TGTTACTGTA
28805791 TTGGGCT
1 TTGGGCT
28805798 TTGACCCACA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.23
28 2 0.04
29 2 0.04
30 38 0.67
31 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.32
Consensus pattern (28 bp):
TTGGGCTAAGGCCACAATTGTTACTGTA
Found at i:28805806 original size:30 final size:30
Alignment explanation
Indices: 28805716--28805827 Score: 116
Period size: 30 Copynumber: 3.7 Consensus size: 30
28805706 GGGCTAAGGC
* * *
28805716 CACACTGTTACTATATTGGGCTAAGGCCAA
1 CACACTGTTACTGTATTGGGCTAAGACCCA
* * * *
28805746 CAAATTGTTTCTGTATTGGGCTAAGGCCCA
1 CACACTGTTACTGTATTGGGCTAAGACCCA
* **
28805776 CACTCTGTTACTGTATTGGGCTTTGACCCA
1 CACACTGTTACTGTATTGGGCTAAGACCCA
* *
28805806 CACACTGCTACTGTATAGGGCT
1 CACACTGTTACTGTATTGGGCT
28805828 CAGGCCCAGA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.31
Consensus pattern (30 bp):
CACACTGTTACTGTATTGGGCTAAGACCCA
Found at i:28805820 original size:60 final size:58
Alignment explanation
Indices: 28805704--28805835 Score: 140
Period size: 60 Copynumber: 2.3 Consensus size: 58
28805694 GATTACTATT
* * * *
28805704 TTGGGCTAAGG-CCACACTGTTACTATATTGGGCTAAGGCCAACAAATTGTTTCTGTA
1 TTGGGCTAAGGCCCACACTGTTACTATATTGGGCTAAGACCAACAAACTGCTACTGTA
* ** * *
28805761 TTGGGCTAAGGCCCACACTCTGTTACTGTATTGGGCTTTGACCCACACACTGCTACTGTA
1 TTGGGCTAAGGCCCACA--CTGTTACTATATTGGGCTAAGACCAACAAACTGCTACTGTA
* *
28805821 TAGGGCTCAGGCCCA
1 TTGGGCTAAGGCCCA
28805836 GATTGATTCT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
57 11 0.18
58 5 0.08
60 45 0.74
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (58 bp):
TTGGGCTAAGGCCCACACTGTTACTATATTGGGCTAAGACCAACAAACTGCTACTGTA
Found at i:28806669 original size:18 final size:19
Alignment explanation
Indices: 28806634--28806670 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
28806624 CATGACATTG
28806634 AATGAAATGTATGTATACA
1 AATGAAATGTATGTATACA
28806653 AATG-AATGT-TGTGATACA
1 AATGAAATGTATGT-ATACA
28806671 TACGCTGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 10 0.59
19 4 0.24
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (19 bp):
AATGAAATGTATGTATACA
Found at i:28811230 original size:16 final size:16
Alignment explanation
Indices: 28811209--28811239 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28811199 GAAAGATTCG
28811209 ATCTGGGTTATTATTA
1 ATCTGGGTTATTATTA
28811225 ATCTGGGTTATTATT
1 ATCTGGGTTATTATT
28811240 GAAAAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (16 bp):
ATCTGGGTTATTATTA
Found at i:28813493 original size:40 final size:40
Alignment explanation
Indices: 28813410--28813714 Score: 278
Period size: 40 Copynumber: 7.7 Consensus size: 40
28813400 TGTGCTTCGA
* * * *
28813410 TACCCTTGATTGCACATTCGTGCCC-TGCTTGTACATTGG
1 TACCCTTGAATGCACATACGTGCCCTTGTTTGTACTTTGG
*
28813449 TACCCTTGAATGCACATACGTGCCCTTGTTTGTACTTTAG
1 TACCCTTGAATGCACATACGTGCCCTTGTTTGTACTTTGG
* * ** * *
28813489 TACCCCT-AATTTCACATACACGCCCCTGTTTGTACTTCGG
1 TACCCTTGAA-TGCACATACGTGCCCTTGTTTGTACTTTGG
* * * *
28813529 TACCCTTGATTGCACATCCGTGCCTTTGTTTGTACTTCGG
1 TACCCTTGAATGCACATACGTGCCCTTGTTTGTACTTTGG
* * * *
28813569 TACTCGTGAATGCACATACGTGCCTTTGTTTGTACTTCGG
1 TACCCTTGAATGCACATACGTGCCCTTGTTTGTACTTTGG
* * *
28813609 TACCCCTAAATGCACATACGT-ACCTCTGTTTGTA-TTTCGG
1 TACCCTTGAATGCACATACGTGCCCT-TGTTTGTACTTT-GG
* * * *
28813649 TACCCCTAAATGCACATACATGACCC-TGTTTGCACTTTGG
1 TACCCTTGAATGCACATACGTG-CCCTTGTTTGTACTTTGG
* * *
28813689 TACCCTTGAAAGCACTTACATGCCCT
1 TACCCTTGAATGCACATACGTGCCCT
28813715 GCTTATACTC
Statistics
Matches: 220, Mismatches: 37, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
39 32 0.15
40 182 0.83
41 4 0.02
42 2 0.01
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.35
Consensus pattern (40 bp):
TACCCTTGAATGCACATACGTGCCCTTGTTTGTACTTTGG
Found at i:28813616 original size:120 final size:119
Alignment explanation
Indices: 28813399--28813714 Score: 337
Period size: 120 Copynumber: 2.6 Consensus size: 119
28813389 GTGCCGCTAC
* * * *
28813399 TTGTGCTTCGATACCCTTGATTGCACATTCGTGCCCTGCTTGTACATTGGTACCCTTGAATGCAC
1 TTGTACTTCGGTACCCTTGATTGCACATCCGTGCCCTGCTTGTACATTGGTACCCGTGAATGCAC
* * * *
28813464 ATACGTGCCCTTGTTTGTACTTTAGTACCCCTAATTTCACATACACGCCCCTGT
66 ATACGTGCCCTTGTTTGTACTTCAGTACCCCTAAATGCACATACACACCCCTGT
* * *
28813518 TTGTACTTCGGTACCCTTGATTGCACATCCGTGCCTTTGTTTGTAC-TTCGGTACTCGTGAATGC
1 TTGTACTTCGGTACCCTTGATTGCACATCCGTGCC-CTGCTTGTACATT-GGTACCCGTGAATGC
* * ** *
28813582 ACATACGTGCCTTTGTTTGTACTTCGGTACCCCTAAATGCACATACGTACCTCTGT
64 ACATACGTGCCCTTGTTTGTACTTCAGTACCCCTAAATGCACATACACACCCCTGT
* * * * * * * * * * *
28813638 TTGTATTTCGGTACCCCTAAATGCACATACATGACCCTGTTTGCACTTTGGTACCCTTGAAAGCA
1 TTGTACTTCGGTACCCTTGATTGCACATCCGTG-CCCTGCTTGTACATTGGTACCCGTGAATGCA
* *
28813703 CTTACATGCCCT
65 CATACGTGCCCT
28813715 GCTTATACTC
Statistics
Matches: 163, Mismatches: 30, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
119 34 0.21
120 125 0.77
121 4 0.02
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.35
Consensus pattern (119 bp):
TTGTACTTCGGTACCCTTGATTGCACATCCGTGCCCTGCTTGTACATTGGTACCCGTGAATGCAC
ATACGTGCCCTTGTTTGTACTTCAGTACCCCTAAATGCACATACACACCCCTGT
Found at i:28817185 original size:23 final size:23
Alignment explanation
Indices: 28817153--28817224 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
28817143 GATAAGATCG
* *
28817153 ATTCTGTGATGTCTTTGTAGCGT
1 ATTCTATGATGCCTTTGTAGCGT
* * * *
28817176 ATTCTTTGATGCCCTTATGGCGT
1 ATTCTATGATGCCTTTGTAGCGT
* *
28817199 ATTCCATGATGCCTTTGTAGCAT
1 ATTCTATGATGCCTTTGTAGCGT
28817222 ATT
1 ATT
28817225 TTGTAATGAC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (23 bp):
ATTCTATGATGCCTTTGTAGCGT
Found at i:28819886 original size:25 final size:25
Alignment explanation
Indices: 28819858--28819907 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
28819848 AGTTGTAGAC
* *
28819858 CGGTATGCTCTCAGGAGCTATAAAT
1 CGGTATGCTCTCACGAGATATAAAT
28819883 CGGTATGCTCTCACGAGATATAAAT
1 CGGTATGCTCTCACGAGATATAAAT
28819908 TGGCATGATT
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:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (25 bp):
CGGTATGCTCTCACGAGATATAAAT
Found at i:28826906 original size:25 final size:25
Alignment explanation
Indices: 28826872--28826928 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
28826862 TCATGTACAA
28826872 GTATGCTTA-TACGAGTTGTGA-ATCG
1 GTATGCTTATTAC-AGTTGT-ATATCG
*
28826897 GTATGCTTATTTCAGTTGTATATCG
1 GTATGCTTATTACAGTTGTATATCG
28826922 GTATGCT
1 GTATGCT
28826929 CTCATGAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 1 0.03
25 26 0.90
26 2 0.07
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42
Consensus pattern (25 bp):
GTATGCTTATTACAGTTGTATATCG
Found at i:28827796 original size:13 final size:13
Alignment explanation
Indices: 28827778--28827809 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
28827768 ACATTTATCC
28827778 AAATTTCTTAATA
1 AAATTTCTTAATA
28827791 AAATTTCTTAATA
1 AAATTTCTTAATA
28827804 AAATTT
1 AAATTT
28827810 TTCTCTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTTCTTAATA
Found at i:28833548 original size:27 final size:27
Alignment explanation
Indices: 28833506--28833684 Score: 168
Period size: 27 Copynumber: 6.6 Consensus size: 27
28833496 CCCGTGTAGG
*
28833506 GTAAAATTATCGAAATACCCTCAGTTT
1 GTAAAATTATCGAAATACCCTCAATTT
* *
28833533 GTAAAATTACCAAAATACTCCT-AATTT
1 GTAAAATTATCGAAATAC-CCTCAATTT
*
28833560 GTAAAATTATCGAAATACCCCCAATTT
1 GTAAAATTATCGAAATACCCTCAATTT
* *
28833587 TTAAAATCATCGAAATA-CCTCCAATTT
1 GTAAAATTATCGAAATACCCT-CAATTT
* * * * *
28833614 TTTAAATTATCGAAATACCTTTAGTTT
1 GTAAAATTATCGAAATACCCTCAATTT
* *
28833641 GCAAAATTA-CTGAAATACCCTCAGTTT
1 GTAAAATTATC-GAAATACCCTCAATTT
*
28833668 GCAAAATTA-CTGAAATA
1 GTAAAATTATC-GAAATA
28833685 TTGAAATACC
Statistics
Matches: 128, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
26 5 0.04
27 118 0.92
28 5 0.04
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (27 bp):
GTAAAATTATCGAAATACCCTCAATTT
Found at i:28833727 original size:27 final size:27
Alignment explanation
Indices: 28833687--28833775 Score: 133
Period size: 27 Copynumber: 3.3 Consensus size: 27
28833677 CTGAAATATT
28833687 GAAATACCTCTGTAGGGTAGGATTACC
1 GAAATACCTCTGTAGGGTAGGATTACC
* * * *
28833714 AAAATACCTTTGTAGGGTAAGATCACC
1 GAAATACCTCTGTAGGGTAGGATTACC
*
28833741 GAAATACCTCTGTAGGGTAGAATTACC
1 GAAATACCTCTGTAGGGTAGGATTACC
28833768 GAAATACC
1 GAAATACC
28833776 CCCAAAGGGT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (27 bp):
GAAATACCTCTGTAGGGTAGGATTACC
Found at i:28834130 original size:22 final size:22
Alignment explanation
Indices: 28834095--28834154 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
28834085 TTAATCTGAT
*
28834095 TATGGCTTTATGCCAACCTAAA
1 TATGGCTTTGTGCCAACCTAAA
* * * * *
28834117 TATGGCTCTGTGCCATCGTGAT
1 TATGGCTTTGTGCCAACCTAAA
28834139 TATGGCTTTGTGCCAA
1 TATGGCTTTGTGCCAA
28834155 TCATTTTTAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (22 bp):
TATGGCTTTGTGCCAACCTAAA
Found at i:28836186 original size:16 final size:18
Alignment explanation
Indices: 28836158--28836204 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
28836148 GTGAAGAAGA
28836158 AAGGAGTTTCAAAAA-TT
1 AAGGAGTTTCAAAAACTT
28836175 AAGGAG-TTCAAAAACTT
1 AAGGAGTTTCAAAAACTT
* *
28836192 AAGAAATTTCAAA
1 AAGGAGTTTCAAA
28836205 TAATAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 8 0.31
17 12 0.46
18 6 0.23
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.26
Consensus pattern (18 bp):
AAGGAGTTTCAAAAACTT
Found at i:28842104 original size:20 final size:20
Alignment explanation
Indices: 28842060--28842110 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
28842050 TTTTAAATAG
28842060 TTTAAC-TGATTGAAAAAGT
1 TTTAACTTGATTGAAAAAGT
* *
28842079 TCTAACTTGATTGAAATCA-T
1 TTTAACTTGATTGAAA-AAGT
28842099 TTTAACTTGATT
1 TTTAACTTGATT
28842111 AAAGGTTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.19
20 21 0.78
21 1 0.04
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (20 bp):
TTTAACTTGATTGAAAAAGT
Found at i:28844592 original size:23 final size:23
Alignment explanation
Indices: 28844548--28844686 Score: 145
Period size: 23 Copynumber: 6.0 Consensus size: 23
28844538 CTTAATATAT
* *
28844548 TTTTAAATTTATCAT-CAATATTA
1 TTTT-AATTTATCATGTATTATTA
* *
28844571 TTTTAATTTATAATATATTATTA
1 TTTTAATTTATCATGTATTATTA
*
28844594 TTTTAAGTTTATCATGTATTTTTA
1 TTTTAA-TTTATCATGTATTATTA
* *
28844618 TTTAAAGTTATCATGTATTATTA
1 TTTTAATTTATCATGTATTATTA
* * *
28844641 TTTTGAACTTATCATCTATGATTA
1 TTTT-AATTTATCATGTATTATTA
*
28844665 TTTAAATTTATCATGTATTATT
1 TTTTAATTTATCATGTATTATT
28844687 TTATGCATTC
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
22 9 0.09
23 49 0.51
24 38 0.40
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (23 bp):
TTTTAATTTATCATGTATTATTA
Found at i:28844596 original size:47 final size:46
Alignment explanation
Indices: 28844548--28844686 Score: 161
Period size: 47 Copynumber: 3.0 Consensus size: 46
28844538 CTTAATATAT
* * *
28844548 TTTTAAATTTATCATCAATATTATTTTAATTTATAATATATTATTA
1 TTTTAAATTTATCATCAATATTATTTAAATTTATCATGTATTATTA
* * * * *
28844594 TTTTAAGTTTATCATGTATTTTTATTTAAAGTTATCATGTATTATTA
1 TTTTAAATTTATCAT-CAATATTATTTAAATTTATCATGTATTATTA
* * *
28844641 TTTTGAACTTATCATCTATGATTATTTAAATTTATCATGTATTATT
1 TTTTAAATTTATCATCAAT-ATTATTTAAATTTATCATGTATTATT
28844687 TTATGCATTC
Statistics
Matches: 75, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
46 15 0.20
47 60 0.80
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (46 bp):
TTTTAAATTTATCATCAATATTATTTAAATTTATCATGTATTATTA
Found at i:28844961 original size:12 final size:12
Alignment explanation
Indices: 28844944--28844973 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28844934 ACTTTTTACC
28844944 TATATTATTATA
1 TATATTATTATA
*
28844956 TATATTATTATC
1 TATATTATTATA
28844968 TATATT
1 TATATT
28844974 GAGTTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATTATTATA
Found at i:28845185 original size:27 final size:28
Alignment explanation
Indices: 28845129--28845187 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
28845119 ATTTTTAATC
* *
28845129 TATTTCAAACTTTCTTATATATATTATT
1 TATTTCAAAATTTCTTATATATATCATT
*
28845157 TATTTTAAAATTT-TTATATATA-CAGTT
1 TATTTCAAAATTTCTTATATATATCA-TT
28845184 TATT
1 TATT
28845188 GATTATACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 15 0.56
28 11 0.41
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.58
Consensus pattern (28 bp):
TATTTCAAAATTTCTTATATATATCATT
Found at i:28852251 original size:51 final size:51
Alignment explanation
Indices: 28852160--28852408 Score: 304
Period size: 51 Copynumber: 4.9 Consensus size: 51
28852150 ATTCATTATG
* * * *
28852160 GCGAATCTTTTTTTCCCTAGCATTGCAGTGGAACAAATTAAAGCTGAAAGTA
1 GCGAATC-TTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAAGCA
* * * **
28852212 GCAAATTTTATTTCCCTGGCGTTATAGTGGAACAGATTAAAGCT-AAAGGCA
1 GCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAA-GCA
* *
28852263 GCGAATCTTATTTCCCTGGCATTGCAATGGAACAGATTAAAGCTGAAGGCA
1 GCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAAGCA
* * * *
28852314 GCGAATCTTTTTTCCCTAGTC-TTGCGGTGGAACAGATTAAAGCTGAAGGCA
1 GCGAATCTTATTTCCCT-GGCATTGCAGTGGAACAGATTAAAGCTGAAAGCA
* *
28852365 GCGAATCTTATTTCCCTGGAATTGCAGTGGAACAGGTTAAAGCT
1 GCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCT
28852409 ACAAATTATG
Statistics
Matches: 168, Mismatches: 25, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
50 4 0.02
51 155 0.92
52 9 0.05
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (51 bp):
GCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAAGCA
Found at i:28852651 original size:193 final size:191
Alignment explanation
Indices: 28852312--28852871 Score: 707
Period size: 193 Copynumber: 2.9 Consensus size: 191
28852302 AAGCTGAAGG
* *
28852312 CAGCGAATCTTTTTTCCCTAGTCTTGCGGTGGAACAGATTAAAGCTGAAGGCAGCGAATCTTATT
1 CAGCGAATCTTTTTTCCCTAG-CTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATATTATT
* *
28852377 TCCCTGGAATTGCAGTGGAACAGGTTAAAGCTACAAATTATGGCGGATTTTATCTTCCTGAAGTT
65 TCCCTGGCATTGCAGTGGAACAGATTAAAGCTACAAATTATGGC-GATTTTATCTTCCTGAAGTT
* * * * *
28852442 GCAGTAGAGCAGATTGAAGCCACCAGCCTTATCTTCTTGAAGTTACAGCAGAGCAGATTGAAA
129 GCAATGGAGTAGATTGAAGCCACCAGCCTTATCTCCATGAAGTTACAGCAGAGCAGATTGAAA
* * * * * *
28852505 TAGCGAATCTTTTTTCCCTAGCGTTGTAATGGAACAGATTAAAGTTGAAGGTAGCGACTATTATT
1 CAGCGAATCTTTTTTCCCTAGC-TTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATATTATT
* * * * **
28852570 TCCCTGGCGTTACAATGGAACAGATTAAAGCTACAAATTATGGCAGATCTTATCTTCCCAAAGTT
65 TCCCTGGCATTGCAGTGGAACAGATTAAAGCTACAAATTATGGC-GATTTTATCTTCCTGAAGTT
* * **
28852635 GCAATGGAGTAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA
129 GCAATGGAGTAGATTGAAGCCACCAGCCTTATCTCCATGAAGTTACAGCAGAGCAGATTGAAA
* * * *
28852698 CAACGAATCTTTTTTCCCTGGCATTGCAGTGGAATAG----AAGCT-AAGGGCAGCGAATTTTAT
1 CAGCGAATCTTTTTTCCCTAGC-TTGCAGTGGAACAGATTAAAGCTGAA-GGCAGCGAATATTAT
* * *
28852758 TTCCCTGGCATTGCAGTGGAACAAATTAAAGTTACAAGTTATGGCGAATTTTATCTTCCTGAAGT
64 TTCCCTGGCATTGCAGTGGAACAGATTAAAGCTACAAATTATGGCG-ATTTTATCTTCCTGAAGT
* * *
28852823 TGTAATGGAGTGGATTGAAGCCACCAGCTTTATCTCCATGAAGTTACAG
128 TGCAATGGAGTAGATTGAAGCCACCAGCCTTATCTCCATGAAGTTACAG
28852872 TGGATTGAAT
Statistics
Matches: 314, Mismatches: 50, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
188 3 0.01
189 114 0.36
192 1 0.00
193 196 0.62
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (191 bp):
CAGCGAATCTTTTTTCCCTAGCTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATATTATTT
CCCTGGCATTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGATTTTATCTTCCTGAAGTTGC
AATGGAGTAGATTGAAGCCACCAGCCTTATCTCCATGAAGTTACAGCAGAGCAGATTGAAA
Found at i:28854333 original size:23 final size:22
Alignment explanation
Indices: 28854298--28854389 Score: 71
Period size: 23 Copynumber: 4.0 Consensus size: 22
28854288 TGTTTAAGCT
*
28854298 TAATA-TATTTTTAAATTTATCG
1 TAATATTA-TTTTAAATTTATCA
*
28854320 TCAATATTATTTTAATATATAAT-A
1 T-AATATTATTTTAA-AT-TTATCA
* *
28854344 TATTATTATTTTAAGTTTATCA
1 TAATATTATTTTAAATTTATCA
* *
28854366 TTAAAATTATTTTAAGTTTATCA
1 -TAATATTATTTTAAATTTATCA
28854389 T
1 T
28854390 GTATTTTTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
21 3 0.05
22 4 0.07
23 42 0.74
24 5 0.09
25 3 0.05
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (22 bp):
TAATATTATTTTAAATTTATCA
Found at i:28854375 original size:46 final size:47
Alignment explanation
Indices: 28854306--28854412 Score: 119
Period size: 46 Copynumber: 2.3 Consensus size: 47
28854296 CTTAATATAT
* * *
28854306 TTTTAAATTTATCGTCAATATTATTTTAA-TATATAATATATTATTA
1 TTTTAAGTTTATCATCAAAATTATTTTAAGTATATAATATATTATTA
* * * * *
28854352 TTTTAAGTTTATCATTAAAATTATTTTAAGTTTATCATGTATTTTTA
1 TTTTAAGTTTATCATCAAAATTATTTTAAGTATATAATATATTATTA
*
28854399 TTTAAAG-TTATCAT
1 TTTTAAGTTTATCAT
28854413 GTATTATTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
46 32 0.63
47 19 0.37
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (47 bp):
TTTTAAGTTTATCATCAAAATTATTTTAAGTATATAATATATTATTA
Found at i:28854402 original size:23 final size:24
Alignment explanation
Indices: 28854324--28854425 Score: 120
Period size: 23 Copynumber: 4.4 Consensus size: 24
28854314 TTATCGTCAA
* * *
28854324 TATTATTTTAA-TATATAATATAT
1 TATTATTTTAAGTTTATCATGTAT
*
28854347 TATTATTTTAAGTTTATCAT-TAA
1 TATTATTTTAAGTTTATCATGTAT
*
28854370 AATTATTTTAAGTTTATCATGTAT
1 TATTATTTTAAGTTTATCATGTAT
* *
28854394 TTTTATTTAAAG-TTATCATGTAT
1 TATTATTTTAAGTTTATCATGTAT
28854417 TATTATTTT
1 TATTATTTT
28854426 GACCTTATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
23 50 0.75
24 17 0.25
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (24 bp):
TATTATTTTAAGTTTATCATGTAT
Found at i:28854422 original size:47 final size:46
Alignment explanation
Indices: 28854303--28854425 Score: 126
Period size: 47 Copynumber: 2.7 Consensus size: 46
28854293 AAGCTTAATA
* *
28854303 TATT-TTTAAA-TTTATCGTCAATATTATTTTAATATATAATATAT
1 TATTATTTAAAGTTTATCATTAATATTATTTTAATATATAATATAT
* * * * *
28854347 TATTATTTTAAGTTTATCATTAAAATTATTTTAAGTTTATCATGTAT
1 TATTATTTAAAGTTTATCATTAATATTATTTTAA-TATATAATATAT
* *
28854394 TTTTATTTAAAG-TTATCATGTATTATTATTTT
1 TATTATTTAAAGTTTATCAT-TAATATTATTTT
28854426 GACCTTATTT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
44 4 0.06
45 5 0.08
46 26 0.41
47 29 0.45
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (46 bp):
TATTATTTAAAGTTTATCATTAATATTATTTTAATATATAATATAT
Found at i:28854731 original size:12 final size:12
Alignment explanation
Indices: 28854714--28854743 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28854704 ACTTTTTACC
28854714 TATATTATTATA
1 TATATTATTATA
*
28854726 TATATTATTATC
1 TATATTATTATA
28854738 TATATT
1 TATATT
28854744 GAGTTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATTATTATA
Found at i:28854944 original size:27 final size:28
Alignment explanation
Indices: 28854899--28854957 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
28854889 ATTTTTAATC
* **
28854899 TATTTCAAACTTTCTTATATATATTATT
1 TATTTCAAAATTTCTTATATATACAATT
*
28854927 TATTTTAAAATTT-TTATATATACAATT
1 TATTTCAAAATTTCTTATATATACAATT
28854954 TATT
1 TATT
28854958 GATTATACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTTCAAAATTTCTTATATATACAATT
Found at i:28860873 original size:19 final size:17
Alignment explanation
Indices: 28860828--28860876 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 17
28860818 GTGTCGTTCG
28860828 TTTCTAAAATATTATTCA
1 TTTC-AAAATATTATTCA
28860846 TTT-ACAAATCATTATTCAA
1 TTTCA-AAAT-ATTATTC-A
28860865 TTTCAAAATATT
1 TTTCAAAATATT
28860877 TTCTTATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.04
17 4 0.15
18 13 0.48
19 8 0.30
20 1 0.04
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTCAAAATATTATTCA
Found at i:28867612 original size:18 final size:18
Alignment explanation
Indices: 28867584--28867628 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
28867574 TTTTTTTTTC
*
28867584 CAAAACATTATTC-ATTT
1 CAAAACGTTATTCAATTT
*
28867601 ACAAATCGTTATTCAATTT
1 -CAAAACGTTATTCAATTT
28867620 CAAAACGTT
1 CAAAACGTT
28867629 TTCTGATTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (18 bp):
CAAAACGTTATTCAATTT
Found at i:28871174 original size:20 final size:22
Alignment explanation
Indices: 28871149--28871190 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28871139 ATGTTGAAAA
28871149 GTTGAA-AAA-CTTGAAGCAAT
1 GTTGAAGAAATCTTGAAGCAAT
*
28871169 GTTGAAGAAATCTTGATGCAAT
1 GTTGAAGAAATCTTGAAGCAAT
28871191 AGTGTTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 3 0.16
22 10 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (22 bp):
GTTGAAGAAATCTTGAAGCAAT
Found at i:28871398 original size:20 final size:20
Alignment explanation
Indices: 28871354--28871424 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
28871344 AAAACTTGAC
28871354 AGGTATCAAT-ATTTT-TAA
1 AGGTATCAATAATTTTATAA
*
28871372 GCGGGTATCAATAATTTTATAA
1 --AGGTATCAATAATTTTATAA
*
28871394 AGGTATCAACAATTTTA-AA
1 AGGTATCAATAATTTTATAA
*
28871413 ATAGTATCAATA
1 A-GGTATCAATA
28871425 CCAAATCACA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.07
20 32 0.74
21 5 0.12
22 3 0.07
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (20 bp):
AGGTATCAATAATTTTATAA
Found at i:28875331 original size:49 final size:49
Alignment explanation
Indices: 28875266--28875360 Score: 147
Period size: 49 Copynumber: 1.9 Consensus size: 49
28875256 ATTAGGTATA
* * *
28875266 TTTAGCTTGGGATAGTCGTGTC-AAAATTTATGCCTAAAAGTAGAATATG
1 TTTAACTTAGGATAGTCGTG-CGAAAATTGATGCCTAAAAGTAGAATATG
28875315 TTTAACTTAGGATAGTCGTGCGAAAATTGATGCCTAAAAGTAGAAT
1 TTTAACTTAGGATAGTCGTGCGAAAATTGATGCCTAAAAGTAGAAT
28875361 GACCTAAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
48 1 0.02
49 41 0.98
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (49 bp):
TTTAACTTAGGATAGTCGTGCGAAAATTGATGCCTAAAAGTAGAATATG
Found at i:28876863 original size:21 final size:21
Alignment explanation
Indices: 28876837--28876876 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28876827 CATCATCAAC
* *
28876837 AGAAGCTCGAAAGTGCTGAAA
1 AGAAGCTCAAAAGAGCTGAAA
28876858 AGAAGCTCAAAAGAGCTGA
1 AGAAGCTCAAAAGAGCTGA
28876877 TCCACCCGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.15, G:0.28, T:0.12
Consensus pattern (21 bp):
AGAAGCTCAAAAGAGCTGAAA
Found at i:28879200 original size:12 final size:12
Alignment explanation
Indices: 28879183--28879208 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28879173 GACCTTAAGA
28879183 AACTAAAATACC
1 AACTAAAATACC
28879195 AACTAAAATACC
1 AACTAAAATACC
28879207 AA
1 AA
28879209 TTCAAAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (12 bp):
AACTAAAATACC
Found at i:28896302 original size:21 final size:20
Alignment explanation
Indices: 28896276--28896314 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
28896266 TAAAGGTTCC
*
28896276 ATGAGTATTGATACTTTTTAA
1 ATGAGTATCGATA-TTTTTAA
28896297 ATGAGTATCGATATTTTT
1 ATGAGTATCGATATTTTT
28896315 CAAAAAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (20 bp):
ATGAGTATCGATATTTTTAA
Found at i:28897423 original size:20 final size:20
Alignment explanation
Indices: 28897398--28897437 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28897388 AACTTTAAAT
28897398 CAACACATTTACCTTCCTCA
1 CAACACATTTACCTTCCTCA
28897418 CAACACATTTACCTTCCTCA
1 CAACACATTTACCTTCCTCA
28897438 TCTTTGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.40, G:0.00, T:0.30
Consensus pattern (20 bp):
CAACACATTTACCTTCCTCA
Found at i:28903786 original size:24 final size:22
Alignment explanation
Indices: 28903750--28903800 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 22
28903740 TTTTAAATAT
*
28903750 ATTTTTTAGTTTTTAGTTTTTAA
1 ATTTTTTAATTTTTA-TTTTTAA
28903773 AGTTTTTTAATTTTTATTTTTAA
1 A-TTTTTTAATTTTTATTTTTAA
28903796 ATTTT
1 ATTTT
28903801 ATGAATTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 4 0.15
23 9 0.35
24 13 0.50
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (22 bp):
ATTTTTTAATTTTTATTTTTAA
Found at i:28903807 original size:23 final size:24
Alignment explanation
Indices: 28903759--28903807 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
28903749 TATTTTTTAG
*
28903759 TTTTTAGTTTTTAAAGTTTTTTAA
1 TTTTTAGTTTTTAAAGTTTTTGAA
28903783 TTTTTA-TTTTTAAA-TTTTATGAA
1 TTTTTAGTTTTTAAAGTTTT-TGAA
28903806 TT
1 TT
28903808 AAGATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 13 0.57
24 6 0.26
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (24 bp):
TTTTTAGTTTTTAAAGTTTTTGAA
Found at i:28907265 original size:16 final size:16
Alignment explanation
Indices: 28907244--28907279 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28907234 TGGTTAGCTA
*
28907244 TAATGGAATAGATGCG
1 TAATGGAATAGAGGCG
28907260 TAATGGAATAGAGGCG
1 TAATGGAATAGAGGCG
28907276 TAAT
1 TAAT
28907280 AGGTAATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.31, T:0.25
Consensus pattern (16 bp):
TAATGGAATAGAGGCG
Found at i:28907343 original size:44 final size:46
Alignment explanation
Indices: 28907261--28907353 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
28907251 ATAGATGCGT
* *
28907261 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTATGTTTGGTTGAATGG
28907307 AATGAAATAGAGGCGTAAT-GGT-ATTCTTATGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTATGTTTGGTTGAATGG
28907351 AAT
1 AAT
28907354 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 24 0.53
45 3 0.07
46 18 0.40
ACGTcount: A:0.30, C:0.04, G:0.29, T:0.37
Consensus pattern (46 bp):
AATGAAATAGAGGCGTAATAGGTAATTCTTATGTTTGGTTGAATGG
Found at i:28907349 original size:39 final size:44
Alignment explanation
Indices: 28907261--28907366 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 44
28907251 ATAGATGCGT
*
28907261 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTATGTTTGGTT--ATGG
*
28907307 AATGAAATAGAGGCGTAAT-GGT-ATTCTTATGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTATGTTTGGTTATGG
*
28907346 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
28907367 CATAAGGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 18 0.33
40 2 0.04
43 1 0.02
44 13 0.24
45 3 0.05
46 18 0.33
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTATGTTTGGTTATGG
Found at i:28907565 original size:18 final size:17
Alignment explanation
Indices: 28907513--28907565 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
28907503 TTATTATTAA
28907513 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
28907531 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
28907548 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
28907566 CATAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 9 0.27
18 24 0.73
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28908896 original size:13 final size:13
Alignment explanation
Indices: 28908878--28908903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28908868 TAGCTTAATC
28908878 TGTGTTGCACATA
1 TGTGTTGCACATA
28908891 TGTGTTGCACATA
1 TGTGTTGCACATA
28908904 ATAAATGATT
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:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
TGTGTTGCACATA
Found at i:28917093 original size:3 final size:3
Alignment explanation
Indices: 28917087--28917121 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28917077 GAAGAAGAAT
28917087 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
28917122 GTAGTAAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28923528 original size:14 final size:13
Alignment explanation
Indices: 28923501--28923533 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
28923491 CGCTGTTCCC
28923501 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
28923514 TTTTCTTTTTATCT
1 TTTTCTTTTT-TCT
28923528 TTTTCT
1 TTTTCT
28923534 GAGTGCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:28926848 original size:21 final size:19
Alignment explanation
Indices: 28926832--28926895 Score: 85
Period size: 21 Copynumber: 3.3 Consensus size: 19
28926822 CTATTTCTTG
28926832 ATTTTTAAATTTAATTTTTTT
1 ATTTTTAAATTTAA--TTTTT
28926853 ATTTTTAAATTTAATTTTT
1 ATTTTTAAATTTAATTTTT
*
28926872 ATTTTTTAAAATTAA-TTTT
1 A-TTTTTAAATTTAATTTTT
28926891 ATTTT
1 ATTTT
28926896 ACAACCATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
18 4 0.10
19 11 0.27
20 12 0.29
21 14 0.34
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTTAAATTTAATTTTT
Found at i:28928136 original size:16 final size:16
Alignment explanation
Indices: 28928115--28928170 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
28928105 CGTTTAGTTC
*
28928115 GCTGTAATTGAATAGA
1 GCTGTAATGGAATAGA
28928131 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* * *
28928147 GGTATAATGGAATAAA
1 GCTGTAATGGAATAGA
*
28928163 ACTGTAAT
1 GCTGTAAT
28928171 AGTAATTCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:28928444 original size:17 final size:18
Alignment explanation
Indices: 28928402--28928438 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
28928392 ATATTATTAA
*
28928402 ATATAATTTAATAAAAAAT
1 ATATAATTTAAT-AAAATT
28928421 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAATT
28928439 CTTAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAATTTAATAAAATT
Found at i:28928528 original size:10 final size:10
Alignment explanation
Indices: 28928513--28928537 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28928503 AGGAATACAA
28928513 TTAAAACATT
1 TTAAAACATT
28928523 TTAAAACATT
1 TTAAAACATT
28928533 TTAAA
1 TTAAA
28928538 GATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (10 bp):
TTAAAACATT
Found at i:28933415 original size:140 final size:138
Alignment explanation
Indices: 28933205--28933747 Score: 650
Period size: 140 Copynumber: 4.0 Consensus size: 138
28933195 CTAAGACAAT
* ** * *
28933205 ACTTTTGGGCCGACACTTTTCTTAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCTACTC
1 ACTTTTGGGCCGACAC-TTTCCTAAGTGTTGGGATAGACTTGCTGACATACGCTTTGGCCAACTC
* * * *
28933270 TTTGTATAAGGGTTGGGATATGCATGTCTAAGACAACGCTTAAATAAGAGTTGCCTTTGCCCAAC
65 TTTGTATAAGGGTTGGGATATGCATGCCTAAG-CAATGCTTAAATAAGAGTAG-CTTTGTCCAAC
28933335 ACTATGCCGAC
128 ACTATGCCGAC
* * *
28933346 ACTTTTGGGCCAACACTTTCCTAAGTGTCGGGATAGACTTGCTGACATACGCTTTGGCCAACTCA
1 ACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCTGACATACGCTTTGGCCAACTCT
*
28933411 TTGTATAAGGGTTGGGATATGCATGCCTAAGGCAATGTTTAAATAAGAGTCAGCTTTGTCCAACA
66 TTGTATAAGGGTTGGGATATGCATGCCTAA-GCAATGCTTAAATAAGAGT-AGCTTTGTCCAACA
28933476 CTATGCCGAC
129 CTATGCCGAC
* * *
28933486 ACTTATGGGCCGACACTTTCCTAACTGTTGGGATAGACTTG-TCGAAATACGCTTTGGCCAACTC
1 ACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCT-GACATACGCTTTGGCCAACTC
* *
28933550 TTTGTATAAGGGTTGGGATATGCATGCCTAATGCAATGCTTAAATAAAAGTCGACTTTGTCCAAC
65 TTTGTATAAGGGTTGGGATATGCATGCCTAA-GCAATGCTTAAATAAGAGTAG-CTTTGTCCAAC
28933615 AC--T------
128 ACTATGCCGAC
* *
28933618 A----T--GCCGACACTTTCCTAAGTTTTGGGATAGACTTGAC-GACATACGCTTTGGTCAACTC
1 ACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTG-CTGACATACGCTTTGGCCAACTC
* * * * *
28933676 TTTGTATAAGGGTTGAGATATGCATGTCTATGGCAATACTTAAATAAGAGTTGGCTTTGTCCAAC
65 TTTGTATAAGGGTTGGGATATGCATGCCTA-AGCAATGCTTAAATAAGAG-TAGCTTTGTCCAAC
28933741 ACTATGC
128 ACTATGC
28933748 TTAAGGAAAC
Statistics
Matches: 357, Mismatches: 33, Indels: 35
0.84 0.08 0.08
Matches are distributed among these distances:
126 107 0.30
127 2 0.01
128 2 0.01
132 1 0.00
138 1 0.00
139 2 0.01
140 225 0.63
141 17 0.05
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (138 bp):
ACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCTGACATACGCTTTGGCCAACTCT
TTGTATAAGGGTTGGGATATGCATGCCTAAGCAATGCTTAAATAAGAGTAGCTTTGTCCAACACT
ATGCCGAC
Found at i:28933719 original size:126 final size:126
Alignment explanation
Indices: 28933494--28933747 Score: 393
Period size: 126 Copynumber: 2.0 Consensus size: 126
28933484 ACACTTATGG
*
28933494 GCCGACACTTTCCTAACTGTTGGGATAGACTTGTCGAAATACGCTTTGGCCAACTCTTTGTATAA
1 GCCGACACTTTCCTAACTGTTGGGATAGACTTGACGAAATACGCTTTGGCCAACTCTTTGTATAA
* *
28933559 GGGTTGGGATATGCATGCCTAATGCAATGCTTAAATAAAAGTCGACTTTGTCCAACACTAT
66 GGGTTGAGATATGCATGCCTAATGCAATACTTAAATAAAAGTCGACTTTGTCCAACACTAT
* * * *
28933620 GCCGACACTTTCCTAAGTTTTGGGATAGACTTGACGACATACGCTTTGGTCAACTCTTTGTATAA
1 GCCGACACTTTCCTAACTGTTGGGATAGACTTGACGAAATACGCTTTGGCCAACTCTTTGTATAA
* * * *
28933685 GGGTTGAGATATGCATGTCT-ATGGCAATACTTAAATAAGAGTTGGCTTTGTCCAACACTAT
66 GGGTTGAGATATGCATGCCTAAT-GCAATACTTAAATAAAAGTCGACTTTGTCCAACACTAT
28933746 GC
1 GC
28933748 TTAAGGAAAC
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
125 2 0.02
126 114 0.98
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (126 bp):
GCCGACACTTTCCTAACTGTTGGGATAGACTTGACGAAATACGCTTTGGCCAACTCTTTGTATAA
GGGTTGAGATATGCATGCCTAATGCAATACTTAAATAAAAGTCGACTTTGTCCAACACTAT
Found at i:28935889 original size:13 final size:13
Alignment explanation
Indices: 28935863--28935899 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
28935853 TCAATTTATA
28935863 TTAATTAA-ATCT
1 TTAATTAATATCT
28935875 TTAATTAATATCT
1 TTAATTAATATCT
28935888 TTAATTAATATC
1 TTAATTAATATC
28935900 ATTTCAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAATTAATATCT
Found at i:28936266 original size:74 final size:73
Alignment explanation
Indices: 28936002--28936494 Score: 437
Period size: 74 Copynumber: 6.8 Consensus size: 73
28935992 ATGGGACCTG
* * * * *
28936002 AGACAAGATCTATCCTAAC-TTTTTAAGTTTGCCTTAGA-TAGGTCTACCCCAACC-TTTTT-AG
1 AGACAAGATCTATCCCAACATTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTAAA
28936063 GGTTTCCTT
66 GGTTT-CTT
* * * *
28936072 AGA-AAGGTCTA-CTCTAACCTTTTTAGGGTTGCCTTAGAC--GTGTCTATCCCAA-CTTTTTT-
1 AGACAAGATCTATC-CCAACATTTTTAAGGTTGCCTTAGACAAG-GTCTATCCCAACCTTTTTTA
*
28936131 AAGGTTGCCTT
64 AAGGTT-TCTT
** * * *
28936142 AGA-TGGGTCTATCCCAATCATTTTTAAAGGTTGCCTTAGAC-GGGTTTATCCCAACCTTTTTTA
1 AGACAAGATCTATCCCAA-CATTTTT-AAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTA
28936205 AAGGTTGT-TGT
64 AAGGTT-TCT-T
* * *
28936216 AG-CTAAGATTTATCCCAACATTTTTAAGGTTACCTTAGACAAGGTCTATCCCAACTTTTTTTAT
1 AGAC-AAGATCTATCCCAACATTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTA-
*
28936280 AA-GTTGCCTT
64 AAGGTT-TCTT
* * * *
28936290 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGAC-GGGTCTATCCTAACCTTTTTTTAA
1 AGACAAGATCTATCCCAACATTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACC-TTTTTTAA
28936354 AGGTTTCCTT
65 AGGTTT-CTT
* * * *
28936364 AAATAAGGTCTATCCCAATC-TTTTTAAGGTTGCCTTTA-ACAAGGTCTATCCCAACTTTTTTTA
1 AGACAAGATCTATCCCAA-CATTTTTAAGGTTGCC-TTAGACAAGGTCTATCCCAACCTTTTTTA
*
28936427 AAAGTTTCCTT
64 AAGGTTT-CTT
* * *
28936438 AGACAAGATTTATCCCAACCTTTTTAAGGTTGCCTTAGACAATGTCTATCCCAACCT
1 AGACAAGATCTATCCCAACATTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCT
28936495 GTATAAGCCC
Statistics
Matches: 354, Mismatches: 42, Indels: 50
0.79 0.09 0.11
Matches are distributed among these distances:
68 1 0.00
69 14 0.04
70 55 0.16
71 7 0.02
72 24 0.07
73 41 0.12
74 182 0.51
75 30 0.08
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (73 bp):
AGACAAGATCTATCCCAACATTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTTAAA
GGTTTCTT
Found at i:28936315 original size:148 final size:146
Alignment explanation
Indices: 28936002--28936494 Score: 519
Period size: 148 Copynumber: 3.4 Consensus size: 146
28935992 ATGGGACCTG
* * * ** * *
28936002 AGACAAGATCTATCCTAA-CTTTTTAAGTTTGCCTTAGATAGGTCTACCCCAACC--TTTTT-AG
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTTAAA
* * * * *
28936063 GGTTTCCTTAGA-AAGGTCTA-CTCTAACCTTTTTAGGGTTGCCTTAGAC--GTGTCTATCCCAA
66 GGTTT-CTTAAATAAGATCTATC-CCAATCTTTTTAAGGTTGCCTTAGACAAG-GTCTATCCCAA
*
28936124 C-TTTTTTAAGGTTGCCTT
128 CTTTTTTTAAAGTTGCCTT
** * *
28936142 AGA-TGGGTCTATCCCAATCATTTTTAAAGGTTGCCTTAGACGGGTTTATCCCAACC-TTTTTTA
1 AGACAAGGTCTATCCCAA-CCTTTTT-AAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTTA
** * *
28936205 AAGGTTGT-TGTAGCTAAGATTTATCCCAA-CATTTTTAAGGTTACCTTAGACAAGGTCTATCCC
64 AAGGTT-TCT-TAAATAAGATCTATCCCAATC-TTTTTAAGGTTGCCTTAGACAAGGTCTATCCC
28936268 AACTTTTTTTATAAGTTGCCTT
126 AACTTTTTTTA-AAGTTGCCTT
*
28936290 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCTAACCTTTTTTTAAA
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTTAAA
*
28936355 GGTTTCCTTAAATAAGGTCTATCCCAATCTTTTTAAGGTTGCCTTTA-ACAAGGTCTATCCCAAC
66 GGTTT-CTTAAATAAGATCTATCCCAATCTTTTTAAGGTTGCC-TTAGACAAGGTCTATCCCAAC
*
28936419 TTTTTTTAAAAGTTTCCTT
129 TTTTTTT-AAAGTTGCCTT
* * **
28936438 AGACAAGATTTATCCCAACCTTTTTAAGGTTGCCTTAGACAATGTCTATCCCAACCT
1 AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGAC-GGGTCTATCCCAACCT
28936495 GTATAAGCCC
Statistics
Matches: 297, Mismatches: 34, Indels: 35
0.81 0.09 0.10
Matches are distributed among these distances:
139 10 0.03
140 3 0.01
141 5 0.02
142 25 0.08
143 6 0.02
144 9 0.03
145 28 0.09
146 13 0.04
147 37 0.12
148 130 0.44
149 31 0.10
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (146 bp):
AGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGGGTCTATCCCAACCTTTTTTTAAA
GGTTTCTTAAATAAGATCTATCCCAATCTTTTTAAGGTTGCCTTAGACAAGGTCTATCCCAACTT
TTTTTAAAGTTGCCTT
Found at i:28942066 original size:26 final size:26
Alignment explanation
Indices: 28942037--28942092 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
28942027 TTTTCAATTG
28942037 ATGAATGAGGTTGCTTCTTAAAGTTT
1 ATGAATGAGGTTGCTTCTTAAAGTTT
*
28942063 ATGAATGAGGTTGCTTCTTAAATTTT
1 ATGAATGAGGTTGCTTCTTAAAGTTT
28942089 ATGA
1 ATGA
28942093 TGAAATATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (26 bp):
ATGAATGAGGTTGCTTCTTAAAGTTT
Found at i:28945176 original size:35 final size:37
Alignment explanation
Indices: 28945106--28945187 Score: 114
Period size: 36 Copynumber: 2.2 Consensus size: 37
28945096 TAAACAAACT
*
28945106 TTTTTAAAGCTTGCCTTAGACAAGGTCTATCCCAACC
1 TTTTTAAAGCTTGCCTTAGACAAGCTCTATCCCAACC
* *
28945143 TTTTT-AAGGTTGCCTTAGACGA-CTCTATCCCAACC
1 TTTTTAAAGCTTGCCTTAGACAAGCTCTATCCCAACC
28945178 TTTTTTAAAG
1 -TTTTTAAAG
28945188 GTCAGCCTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
35 12 0.30
36 20 0.50
37 8 0.20
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (37 bp):
TTTTTAAAGCTTGCCTTAGACAAGCTCTATCCCAACC
Found at i:28958011 original size:12 final size:12
Alignment explanation
Indices: 28957915--28958011 Score: 52
Period size: 12 Copynumber: 7.8 Consensus size: 12
28957905 ATTCAATAAA
*
28957915 AAAATCAAAATC
1 AAAATAAAAATC
*
28957927 AAAATAAAAAAC
1 AAAATAAAAATC
* **
28957939 AAAA-AGAGAAGA
1 AAAATA-AAAATC
*
28957951 AAAATCAAAATC
1 AAAATAAAAATC
* * *
28957963 AAAGTCAAAAGC
1 AAAATAAAAATC
*
28957975 AAAAAAGAAAAAATC
1 --AAAA-TAAAAATC
*
28957990 AAAATAAAAATG
1 AAAATAAAAATC
28958002 AAAATAAAAA
1 AAAATAAAAA
28958012 GGAGAAAAAG
Statistics
Matches: 63, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
11 1 0.02
12 50 0.79
13 4 0.06
14 3 0.05
15 5 0.08
ACGTcount: A:0.74, C:0.08, G:0.07, T:0.10
Consensus pattern (12 bp):
AAAATAAAAATC
Found at i:28960059 original size:22 final size:22
Alignment explanation
Indices: 28960031--28960073 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28960021 CACTGCGCCG
28960031 ACCGCCGATCTCCGGT-GCCAGC
1 ACCGCCG-TCTCCGGTGGCCAGC
*
28960053 ACCGCCGTCTGCGGTGGCCAG
1 ACCGCCGTCTCCGGTGGCCAG
28960074 AAAAGGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.12, C:0.42, G:0.33, T:0.14
Consensus pattern (22 bp):
ACCGCCGTCTCCGGTGGCCAGC
Found at i:28961223 original size:44 final size:44
Alignment explanation
Indices: 28961174--28961287 Score: 133
Period size: 44 Copynumber: 2.6 Consensus size: 44
28961164 CTAATCCACT
* * *
28961174 CCACTACAACTTTAGGGAGATAGGA-TTTGTTCATTCAGTCTGCC
1 CCACTACAACTTTAGGGAGATAAGACTTTCTT-ACTCAGTCTGCC
* *
28961218 CCACTACAA-TTTCAGGGGGATAAGACTTTCTTACTCAGTCTGCT
1 CCACTACAACTTT-AGGGAGATAAGACTTTCTTACTCAGTCTGCC
* *
28961262 CCACTGCAACTTCAGGGAGATAAGAC
1 CCACTACAACTTTAGGGAGATAAGAC
28961288 CAGATGCGAT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
43 3 0.05
44 49 0.83
45 7 0.12
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (44 bp):
CCACTACAACTTTAGGGAGATAAGACTTTCTTACTCAGTCTGCC
Found at i:28961470 original size:44 final size:44
Alignment explanation
Indices: 28961407--28961659 Score: 151
Period size: 44 Copynumber: 5.8 Consensus size: 44
28961397 CAACTTCAGA
* *
28961407 GAGATAAGATTCTCAATCTTCAACCTATTCCCCTGCTGACCAGG
1 GAGATAAGATTCTCAATCTTCAACCTATTCCACTGCTGACAAGG
*
28961451 GAGATAGGATTCAT-AATCTTCAACCTATTCCACTGCTGACAAGG
1 GAGATAAGATTC-TCAATCTTCAACCTATTCCACTGCTGACAAGG
** **** * * ** * *
28961495 GAGATAAGGCTAGGGA-CTTCGATCTGCTCCACTACTG-CTTAGG
1 GAGATAAGATTCTCAATCTTCAACCTATTCCACTGCTGAC-AAGG
* * * * * * *
28961538 GAGACAAGATATGT-AATTTTCAACCTACTCTACTACTG-CTCAGG
1 GAGATAAGAT-TCTCAATCTTCAACCTATTCCACTGCTGAC-AAGG
* * * *
28961582 GAGACATGATTCACAATCTTTAACCTATTCCACTGCTGACCAA-G
1 GAGATAAGATTCTCAATCTTCAACCTATTCCACTGCTGA-CAAGG
* *
28961626 GAGAT-AGAATTCACAATCTTCAGCCTATTCCACT
1 GAGATAAG-ATTCTCAATCTTCAACCTATTCCACT
28961660 ACTACCTAGG
Statistics
Matches: 160, Mismatches: 40, Indels: 18
0.73 0.18 0.08
Matches are distributed among these distances:
42 1 0.01
43 29 0.18
44 127 0.79
45 2 0.01
46 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (44 bp):
GAGATAAGATTCTCAATCTTCAACCTATTCCACTGCTGACAAGG
Found at i:28961844 original size:88 final size:88
Alignment explanation
Indices: 28961667--28962526 Score: 1218
Period size: 88 Copynumber: 9.8 Consensus size: 88
28961657 ACTACTACCT
* * * * *
28961667 AGGGAGGTAGGGCTGG-GTCATCGATTTCCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
1 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
*
28961731 TTAAACCTGCTCCGCTGCAACCC
66 TTTAACCTGCTCCGCTGCAACCC
* * * * * *
28961754 AGGGAGGCAAGGTTGGTGTCTTTGATCTGCTTCGCTATCAGTACAGGAAGGCAAGATCTGTTATT
1 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
* *
28961819 TCTAACCTGCTCCACTGCAACCC
66 TTTAACCTGCTCCGCTGCAACCC
*** * * * * *
28961842 AGGGAGGCCTTGCTAGTGTCTTTGATCTGCTTCGCTGTCGGTGCAGGAAGGAAATATTTGCTATT
1 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
28961907 TTTAACCTGCTCCGCTGCAACCC
66 TTTAACCTGCTCCGCTGCAACCC
* *
28961930 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCGGTGTAGGAAGGCAAGATCTGCTATT
1 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
*
28961995 TTAAACCTGCTCCGCTGCAACCC
66 TTTAACCTGCTCCGCTGCAACCC
* * ** * * * * *
28962018 AGGGAGGCAAGGTTAGCATCTTTGATCTGCTTCGCTGTCAGTGTAGGAAGACAATATCTGCTATT
1 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
* * *
28962083 TGTAACCTACTCCGCTACAACCC
66 TTTAACCTGCTCCGCTGCAACCC
* *
28962106 AGGGAGGCAAGACTGGTGTCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATT
1 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
28962171 TTTAACCTGCTCCGCTGCAACCC
66 TTTAACCTGCTCCGCTGCAACCC
* **
28962194 AAGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTATTATT
1 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
* * *
28962259 TTTAACCTACTTCACTGCAACCC
66 TTTAACCTGCTCCGCTGCAACCC
* *
28962282 AGGGAGGCAAGGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTATT
1 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
* *
28962347 TTTAACTTGCTCCGCTGGAACCC
66 TTTAACCTGCTCCGCTGCAACCC
*
28962370 AGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
1 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
*
28962435 TTTAAACTGCTCCGCTGCAACCC
66 TTTAACCTGCTCCGCTGCAACCC
* * * *
28962458 AGGGAGGAAAGGCTGGTGTCTTCGATCTGTTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTATC
1 AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
28962523 TTTA
66 TTTA
28962527 CTGATCTGCT
Statistics
Matches: 681, Mismatches: 91, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
87 13 0.02
88 668 0.98
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (88 bp):
AGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATT
TTTAACCTGCTCCGCTGCAACCC
Found at i:28964141 original size:17 final size:17
Alignment explanation
Indices: 28964116--28964153 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
28964106 CCCAGTAGAG
*
28964116 TTTTTTTTTGCGCCATC
1 TTTTCTTTTGCGCCATC
*
28964133 TTTTCTTTTGTGCCATC
1 TTTTCTTTTGCGCCATC
28964150 TTTT
1 TTTT
28964154 TTTGGGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.05, C:0.21, G:0.11, T:0.63
Consensus pattern (17 bp):
TTTTCTTTTGCGCCATC
Found at i:28970818 original size:20 final size:19
Alignment explanation
Indices: 28970793--28970844 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
28970783 ATTCGTATGT
28970793 ATATAAATGATAAAAAATAA
1 ATATAAATG-TAAAAAATAA
*
28970813 ATATAACA-GTAGAAAATAA
1 ATATAA-ATGTAAAAAATAA
*
28970832 ATAAAAATTGTAA
1 ATATAAA-TGTAA
28970845 GTAACAACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.04
19 14 0.54
20 10 0.38
21 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (19 bp):
ATATAAATGTAAAAAATAA
Found at i:28971866 original size:13 final size:13
Alignment explanation
Indices: 28971850--28971876 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28971840 AAAAAGAATG
28971850 GAAAAATGAAAAT
1 GAAAAATGAAAAT
28971863 GAAAAATGAAAAT
1 GAAAAATGAAAAT
28971876 G
1 G
28971877 GAGAGGCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (13 bp):
GAAAAATGAAAAT
Found at i:28973412 original size:128 final size:128
Alignment explanation
Indices: 28973240--28974161 Score: 1382
Period size: 128 Copynumber: 7.2 Consensus size: 128
28973230 AAGATACTAG
* * * *
28973240 CCTATCTCCCTAGTCAGCAGTGGAAT-GTGTTATAAATTACAGATCTTGTTTCCTTAAGCAGTAG
1 CCTATCTCCCTGGTCAGCAGTGGAATAG-GTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAG
* * *
28973304 CGGAGCAGATCGAAGACGGCGAATCTTATTTTCAAGAGTAAGGAAGGAGATTTAAGCCATAAGT
65 CGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
*
28973368 CCTATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* *
28973433 GGAGCCGATCGAAGAC-GCGAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGCCACAAGT
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* * * * *
28973495 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTATAGATCTTGCCTCCCTATGGAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* * *
28973560 GGAGCAGATTGAAGACGGTGAATCTTATCTTCAGGAGTAAGGAAGCAGATTTAAGCCACAAGT
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* * * * *
28973623 CCTATCTCCCTAGTCAGTAGTGGAATAGGTTGGAAATTACAAATCTTGTCTCCCTAGGCAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* *
28973688 GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAACAGATTTAAGCCACAAGT
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* * * *
28973751 CCTATCTCCCTGGTCAGTAGTGGAATAGGTCAAAAATTACAGTTCTTGTCTCCCTAAGCAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* *
28973816 GGAGCAGATCAAAGATGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* * * * ** *
28973879 CCTATCTCCCTGGTCAGTAGTGGAATGGGTTGGAAATTGCAGATCTTGTCTCTTTAGGCAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
*
28973944 GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGGCACAAGT
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* * * * *
28974007 CC-ATCTCCTTTGTCAGTAGTGGAATAAGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* *
28974071 GGAGCAGATCGAAGATGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* *
28974134 TCTATCTCCCTGGTCAGCAATGGAATAG
1 CCTATCTCCCTGGTCAGCAGTGGAATAG
28974162 ATTGAAGATT
Statistics
Matches: 717, Mismatches: 74, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
127 229 0.32
128 487 0.68
129 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (128 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
Found at i:28973691 original size:255 final size:256
Alignment explanation
Indices: 28973240--28974161 Score: 1400
Period size: 255 Copynumber: 3.6 Consensus size: 256
28973230 AAGATACTAG
* * * * *
28973240 CCTATCTCCCTAGTCAGCAGTGGAAT-GTGTTATAAATTACAGATCTTGTTTCCTTAAGCAGTAG
1 CCTATCTCCCTGGTCAGCAGTGGAATAG-GTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAG
* * *
28973304 CGGAGCAGATCGAAGACGGCGAATCTTATTTTCAAGAGTAAGGAAGGAGATTTAAGCCATAAGTC
65 CGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTC
** *
28973369 CTATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCG
130 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAGGCAGTAGCG
* *
28973434 GAGCCGATCGAAGAC-GCGAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGCCACAAGT
195 GAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
** * * * *
28973495 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTATAGATCTTGCCTCCCTATGGAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* * *
28973560 GGAGCAGATTGAAGACGGTGAATCTTATCTTCAGGAGTAAGGAAGCAGATTTAAGCCACAAGTCC
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCC
* * *
28973625 TATCTCCCTAGTCAGTAGTGGAATAGGTTGGAAATTACAAATCTTGTCTCCCTAGGCAGTAGCGG
131 TATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAGGCAGTAGCGG
* *
28973690 AGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAACAGATTTAAGCCACAAGT
196 AGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* * *
28973751 CCTATCTCCCTGGTCAGTAGTGGAATAGGTCAAAAATTACAGTTCTTGTCTCCCTAAGCAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* *
28973816 GGAGCAGATCAAAGATGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCC
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCC
* * * **
28973881 TATCTCCCTGGTCAGTAGTGGAATGGGTTGGAAATTGCAGATCTTGTCTCTTTAGGCAGTAGCGG
131 TATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAGGCAGTAGCGG
*
28973946 AGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGGCACAAGT
196 AGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* * * *
28974007 CC-ATCTCCTTTGTCAGTAGTGGAATAAGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* * *
28974071 GGAGCAGATCGAAGATGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTTC
66 GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCC
*
28974136 TATCTCCCTGGTCAGCAATGGAATAG
131 TATCTCCCTGGTCAGCAGTGGAATAG
28974162 ATTGAAGATT
Statistics
Matches: 606, Mismatches: 59, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
255 327 0.54
256 279 0.46
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (256 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
GGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCC
TATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAGGCAGTAGCGG
AGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
Found at i:28974024 original size:383 final size:383
Alignment explanation
Indices: 28973240--28974161 Score: 1452
Period size: 383 Copynumber: 2.4 Consensus size: 383
28973230 AAGATACTAG
* ** * * * *
28973240 CCTATCTCCCTAGTCAGCAGTGGAATGTGTTATAAATTACAGATCTTGTTTCCTTAAGCAGTAGC
1 CCTATCTCCCTAGTCAGTAGTGGAATAAGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* * * *
28973305 GGAGCAGATCGAAGACGGCGAATCTTATTTTCAAGAGTAAGGAAGGAGATTTAAGCCATAAGTCC
66 GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCC
*
28973370 TATCTCCCTGGTCAGCAGTGGAATAGGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGG
131 TATCTCCCTGGTCAGCAGTGGAATAGGTCAAAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGG
* * *
28973435 AGCCGATCGAAGACGCGAATCTTATCTTCAAGAGTAAGGAAGTAGATTTAAGCCACAAGTCCTAT
196 AGCAGATCAAAGACGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTAT
*
28973500 CTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTATAGATCTTGCCTCCCTATGGAGTAGCGGAGC
261 CTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGCCTCCCTATGGAGTAGCGGAGC
* * *
28973565 AGATTGAAGACGGTGAATCTTATCTTCAGGAGTAAGGAAGCAGATTTAAGCCACAAGT
326 AGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* ** * *
28973623 CCTATCTCCCTAGTCAGTAGTGGAATAGGTTGGAAATTACAAATCTTGTCTCCCTAGGCAGTAGC
1 CCTATCTCCCTAGTCAGTAGTGGAATAAGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
*
28973688 GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAACAGATTTAAGCCACAAGTCC
66 GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCC
* *
28973753 TATCTCCCTGGTCAGTAGTGGAATAGGTCAAAAATTACAGTTCTTGTCTCCCTAAGCAGTAGCGG
131 TATCTCCCTGGTCAGCAGTGGAATAGGTCAAAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGG
*
28973818 AGCAGATCAAAGATGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTA
196 AGCAGATCAAAGA-CGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTA
* * * * **
28973883 TCTCCCTGGTCAGTAGTGGAATGGGTTGGAAATTGCAGATCTTGTCTCTTTA-GGCAGTAGCGGA
260 TCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGCCTCCCTATGG-AGTAGCGGA
*
28973947 GCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGGCACAAGT
324 GCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
* *
28974007 CC-ATCTCCTTTGTCAGTAGTGGAATAAGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
1 CCTATCTCCCTAGTCAGTAGTGGAATAAGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
* *
28974071 GGAGCAGATCGAAGATGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTTC
66 GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCC
*
28974136 TATCTCCCTGGTCAGCAATGGAATAG
131 TATCTCCCTGGTCAGCAGTGGAATAG
28974162 ATTGAAGATT
Statistics
Matches: 493, Mismatches: 44, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
383 332 0.67
384 161 0.33
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (383 bp):
CCTATCTCCCTAGTCAGTAGTGGAATAAGTCAGAAATTACAGATCTTGTCTCCCTAAGCAGTAGC
GGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCC
TATCTCCCTGGTCAGCAGTGGAATAGGTCAAAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGG
AGCAGATCAAAGACGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTAT
CTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGCCTCCCTATGGAGTAGCGGAGC
AGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGT
Found at i:28974400 original size:44 final size:45
Alignment explanation
Indices: 28974349--28974508 Score: 148
Period size: 44 Copynumber: 3.6 Consensus size: 45
28974339 TCGCATCAGG
*
28974349 TCTTATCTCCCTGAGGTTGCAGTGGAGCAAA-CTGAAGAAG-CAGA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAAATC-GAAGAAGACAAA
* ** * * *
28974393 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATGACAAA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAAATCGAAGAAGACAAA
* * ** *
28974437 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGA-TAA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAAATCGAAGAAGACAAA
* * *
28974481 TCCTATCTCCCTGAAGTTGTAGTGGAGC
1 TCTTATCTCCCTGAGGTTGCAGTGGAGC
28974509 GGATTAGAGT
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
43 19 0.20
44 55 0.58
45 21 0.22
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (45 bp):
TCTTATCTCCCTGAGGTTGCAGTGGAGCAAATCGAAGAAGACAAA
Found at i:28974528 original size:88 final size:88
Alignment explanation
Indices: 28974349--28974543 Score: 207
Period size: 88 Copynumber: 2.2 Consensus size: 88
28974339 TCGCATCAGG
* *
28974349 TCTTATCTCCCTGAGGTTGCAGTGGAGCAAACTGAAGAAGCAGATCTTATCTCCCTAAGCAGTAG
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAAACTGAAGAAGCAAATCCTATCTCCCTAAGCAGTAG
* *
28974414 TGGAGCAGATCGAAGATGACAAA
66 TGGAGCAGATAGAAGATAACAAA
* * ** **
28974437 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCG-ATAATCCTATCTCCCTGAAGTTGT
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAAACTGAAGAAGCA-AATCCTATCTCCCT-AAGCAGT
* * *
28974501 AGTGGAGCGGATTAG-AG-TAATAGA
64 AGTGGAGCAGA-TAGAAGATAACAAA
* *
28974525 TCTTATCTCTCTGAAGTTG
1 TCTTATCTCCCTGAGGTTG
28974544 TAGTAGAGAG
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
87 1 0.01
88 69 0.78
89 17 0.19
90 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (88 bp):
TCTTATCTCCCTGAGGTTGCAGTGGAGCAAACTGAAGAAGCAAATCCTATCTCCCTAAGCAGTAG
TGGAGCAGATAGAAGATAACAAA
Found at i:28974532 original size:44 final size:44
Alignment explanation
Indices: 28974349--28974556 Score: 131
Period size: 44 Copynumber: 4.7 Consensus size: 44
28974339 TCGCATCAGG
* * ** * *
28974349 TCTTATCTCCCTGAGGTTGCAGTGGAGCAAACTGAAG--AAGCAGA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTGAAGCCAA-TA-A
** * * **
28974393 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATGACA-AA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTGAAG-CCA-ATAA
* * * *
28974437 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTGAAGCCAATAA
* *
28974481 TCCTATCTCCCTGAAGTTGTAGTGGAGCGGATT-AGAG-TAATAGA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTGA-AGCCAATA-A
* * *
28974525 TCTTATCTCTCTGAAGTTGTAGTAGAGAGGAT
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCGGAT
28974557 CGCATCAGGT
Statistics
Matches: 131, Mismatches: 25, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
43 22 0.17
44 87 0.66
45 20 0.15
46 1 0.01
47 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTGAAGCCAATAA
Found at i:28976204 original size:22 final size:22
Alignment explanation
Indices: 28976179--28976232 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
28976169 ATATAGATCC
28976179 TTTTATTTTATTATATAATATT
1 TTTTATTTTATTATATAATATT
* *
28976201 TTTTATGTTT-TTATGTATTATT
1 TTTTAT-TTTATTATATAATATT
**
28976223 ACTTATTTTA
1 TTTTATTTTA
28976233 CAAATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 20 0.77
23 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTATTTTATTATATAATATT
Found at i:28977556 original size:23 final size:22
Alignment explanation
Indices: 28977529--28977572 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
28977519 ACTTCCATAA
*
28977529 TGTAATTATTTTTATTTTTTATT
1 TGTAATTATTTTT-TTATTTATT
28977552 TGTAATTATTTTTTTATTTAT
1 TGTAATTATTTTTTTATTTAT
28977573 ATATATGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (22 bp):
TGTAATTATTTTTTTATTTATT
Found at i:28979583 original size:37 final size:38
Alignment explanation
Indices: 28979525--28979602 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
28979515 TTACGAAGTC
* * *
28979525 TTACCCGGACATAATCTCCACACGAAGTTATCGGGT-T
1 TTACCCGGACAAAATCCCCACACGAAGTCATCGGGTCT
*
28979562 TTACCCGGACAAAATCCCCACACGTAGTCATCGGGTCT
1 TTACCCGGACAAAATCCCCACACGAAGTCATCGGGTCT
28979600 TTA
1 TTA
28979603 GAGCTCGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 32 0.89
38 4 0.11
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (38 bp):
TTACCCGGACAAAATCCCCACACGAAGTCATCGGGTCT
Found at i:28979844 original size:49 final size:47
Alignment explanation
Indices: 28979719--28979935 Score: 344
Period size: 47 Copynumber: 4.6 Consensus size: 47
28979709 CCCTTCGGGA
* * * * * *
28979719 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28979766 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28979813 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28979862 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28979909 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28979936 ACCAACCCTT
Statistics
Matches: 158, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
47 111 0.70
49 47 0.30
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28979881 original size:96 final size:96
Alignment explanation
Indices: 28979719--28979935 Score: 343
Period size: 96 Copynumber: 2.3 Consensus size: 96
28979709 CCCTTCGGGA
* * * * *
28979719 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATAC
28979782 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
28979813 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATAC
28979878 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
28979909 CTTATCAC--ATATATACACTTTCACATT
1 CTTATCACATATATATACACTTTCACATT
28979936 ACCAACCCTT
Statistics
Matches: 114, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
94 29 0.25
95 1 0.01
96 84 0.74
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28991110 original size:23 final size:23
Alignment explanation
Indices: 28991079--28991177 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
28991069 GGTGTTATTG
*
28991079 ATCACTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28991102 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28991125 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
28991148 AACAGTGGTAGCTTCGGGTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28991171 ATCAGTG
1 ATCAGTG
28991178 TGGCACTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28997491 original size:23 final size:23
Alignment explanation
Indices: 28997460--28997558 Score: 137
Period size: 23 Copynumber: 4.3 Consensus size: 23
28997450 GGTGTTATTG
*
28997460 ATCACTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28997483 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
28997506 TTCAG-GTGTAGCTTCGGCTACAT
1 ATCAGTG-GTAGCTTCGGCTACAT
* * *
28997529 AACAGTGGTAGCTTTGGCTAGAT
1 ATCAGTGGTAGCTTCGGCTACAT
28997552 ATCAGTG
1 ATCAGTG
28997559 TGGCACTTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
22 1 0.01
23 65 0.97
24 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:29003301 original size:44 final size:43
Alignment explanation
Indices: 29003249--29004061 Score: 373
Period size: 44 Copynumber: 18.7 Consensus size: 43
29003239 GATCGCATCT
*
29003249 AGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAACA
* * * **
29003293 AGTCTTATC-CTTCTGAAGTTGCAAT-CAGGCAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AACA
* * * *
29003338 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCAAATA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-AAACA
* * * * *
29003383 A-TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAC-A
* ** * * * * * * *
29003425 GGATCTTATCTCTTTGAAATTGTAG-AGAGCAGA-T-CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAACA
* *
29003466 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAACA
* **
29003510 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGAATGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AACA
* * * ** *
29003555 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTGATA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-AAACA
* * * * *
29003600 A-TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AACCTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAC--A
* * * * * * *
29003643 GGTCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAACA
*
29003683 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAACA
* * **
29003727 AGTCTTATC-CTCCTAAATTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AACA
* * * * **
29003772 AATATTATCTCCCTGAAGTTGTAGTGGAGCAGATTAA-AGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAC-A
* * * * *
29003815 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA-AACCTT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAC-A
* * ** * * * *
29003859 GGATCTTATCTCTCTGAAGTTGCAG-AAAGCAGA-T-CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAACA
*
29003900 AGTCTTATCTCCCTGAAGTGGCAGTGGAGCAGACTAAGTAAACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAACA
* *
29003944 AGTCTTATC-CTCTTGAAGTTGTAGT-GAGGCAGACTGAAGATGGAA-A
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA---AACA
* * * **
29003990 A-TCTTATCTCCCTGAGGTTGCAGTGTAGCAGATTAA-AGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAC-A
* * *
29004032 TAATCCTATCTCCCTGAAGTTGCAGAGGAG
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAG
29004062 TAGATTGAAG
Statistics
Matches: 589, Mismatches: 124, Indels: 112
0.71 0.15 0.14
Matches are distributed among these distances:
40 60 0.10
41 25 0.04
42 15 0.03
43 40 0.07
44 303 0.51
45 131 0.22
46 13 0.02
47 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (43 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAACA
Found at i:29003732 original size:84 final size:85
Alignment explanation
Indices: 29003223--29004061 Score: 301
Period size: 89 Copynumber: 9.7 Consensus size: 85
29003213 TTATCTCTTC
* *
29003223 GAAGTTGCAG-AGAGCAGA-TCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAA
1 GAAGTTGCAGTAGAGCAGATTAGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
*
29003286 GTAAACAAGTCTTATC-CTTCT
66 G-AAACAAGTCTTATCTC-CCT
* * * * *
29003307 GAAGTTGCAATCAG-GCAGACTGAAG-ATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAG
1 GAAGTTGCAGT-AGAGCAGA-T-TAGCAT--CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
* * *
29003370 ATTAAAGCAAATAA-TCCTATCTCCCT
61 ACT-AAG-AAACAAGTCTTATCTCCCT
* * ** * * ** * * *
29003396 GAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTTTGAAATTGTAG-AGAGCAGA-T
1 GAAGTTGCAGTAGAGCAGATTAGCATC-TAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT
* * * *
29003459 -CGCATCTAGTCTTATCTCCCT
64 AAGAAACAAGTCTTATCTCCCT
* * * * * *
29003480 GAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGA
1 GAAGTTGCAGTAGAGCAGA-TTAG-CATCTAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA
* ** *
29003543 ATGAAGATGGCAAATCTTATCTCCCT
62 CT-AAGA-AACAAGTCTTATCTCCCT
* * * * * * *
29003569 GAAGTTGTAGTGGAGCAGATTAAAGC-TGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT
1 GAAGTTGCAGTAGAGCAGATT--AGCAT-CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
* ** *
29003633 TAA-AACCTTGGGTCTTATCTCTCT
63 TAAGAAAC--AAGTCTTATCTCCCT
*
29003657 GAAGTTGCAG-AGAGCAGA-TCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
1 GAAGTTGCAGTAGAGCAGATTAGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
*
29003720 GTAAGCAAGTCTTATC-CTCCT
66 G-AAACAAGTCTTATCTC-CCT
* * * * * * *
29003741 AAATTTGCAGT-GAGGCAGACTGAAG-ATGGCAAATATTATCTCCCTGAAGTTGTAGTGGAGCAG
1 GAAGTTGCAGTAGA-GCAGA-T-TAGCAT--CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
* ** * *
29003804 ATTAA-AGCCGATAATCCTATCTCCCT
61 ACTAAGAAAC-A-AGTCTTATCTCCCT
* ** * * * **
29003830 GAAGTTGCAGTGGAGCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAG-AAAGCAGA-T
1 GAAGTTGCAGTAGAGCAGATTAGCATC-TAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT
* * * *
29003893 -CGCATCTAGTCTTATCTCCCT
64 AAGAAACAAGTCTTATCTCCCT
* * * * * * * *
29003914 GAAGTGGCAGTGGAGCAGACTAAGTAAACAAGTCTTATC-CTCTTGAAGTTGTAGT-GAGGCAGA
1 GAAGTTGCAGTAGAGCAGA-TTAG-CATCTAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA
29003977 CTGAAGATGGAA-AA-TCTTATCTCCCT
62 CT-AAGA---AACAAGTCTTATCTCCCT
* *** * * *
29004003 GAGGTTGCAGT-GTAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGAGGAG
1 GAAGTTGCAGTAG-AGCAGATT--AGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAG
29004062 TAGATTGAAG
Statistics
Matches: 551, Mismatches: 139, Indels: 125
0.68 0.17 0.15
Matches are distributed among these distances:
83 5 0.01
84 160 0.29
85 27 0.05
86 20 0.04
87 28 0.05
88 72 0.13
89 215 0.39
90 23 0.04
91 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (85 bp):
GAAGTTGCAGTAGAGCAGATTAGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
GAAACAAGTCTTATCTCCCT
Found at i:29004094 original size:217 final size:217
Alignment explanation
Indices: 29003121--29004061 Score: 1542
Period size: 217 Copynumber: 4.3 Consensus size: 217
29003111 GGTGGCCAAT
* * * * **
29003121 AATCTTATCTTCCTAAAGTTGTAGTGGAGCATATTAAAGCTGATAATCCTATCTCTTTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
29003186 CAGTGGAGCGGATTAAAACCTTGGATCTTATCTCT-TCGAAGTTGCAGAGAGCAGATCGCATCTA
66 CAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCT-GAAGTTGCAGAGAGCAGATCGCATCTA
* *
29003250 GTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAACAAGTCTTATCCTTCTGAAGTTGC
130 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGC
* *
29003315 AATCAGGCAGACTGAAGATGGCA
195 AGTGAGGCAGACTGAAGATGGCA
* * **
29003338 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCAAATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
* * *
29003403 CAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTTTGAAATTGTAGAGAGCAGATCGCATCTAG
66 CAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
* *
29003468 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCA
131 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGCA
*
29003533 GTGAGGCAGAATGAAGATGGCA
196 GTGAGGCAGACTGAAGATGGCA
*
29003555 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTGATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
*
29003620 CAGTGGAGCGGATTAAAACCTTGGGTCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
66 CAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
* * *
29003685 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTAAATTTGCA
131 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGCA
29003750 GTGAGGCAGACTGAAGATGGCA
196 GTGAGGCAGACTGAAGATGGCA
*
29003772 AATATTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
* *
29003837 CAGTGGAGCAGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAAAGCAGATCGCATCTAG
66 CAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
* * *
29003902 TCTTATCTCCCTGAAGTGGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTCTTGAAGTTGTA
131 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGCA
*
29003967 GTGAGGCAGACTGAAGATGGAA
196 GTGAGGCAGACTGAAGATGGCA
* * *
29003989 AATCTTATCTCCCTGAGGTTGCAGTGTAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
*
29004054 CAGAGGAG
66 CAGTGGAG
29004062 TAGATTGAAG
Statistics
Matches: 676, Mismatches: 47, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
217 675 1.00
218 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (217 bp):
AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
CAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATCCTCCTGAAGTTGCA
GTGAGGCAGACTGAAGATGGCA
Found at i:29005474 original size:21 final size:20
Alignment explanation
Indices: 29005448--29005499 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
29005438 ATTATTTATA
* *
29005448 TATATATATATGTGTTGTTTT
1 TATATACATATGTATT-TTTT
*
29005469 TATATACATATTTATTTTTT
1 TATATACATATGTATTTTTT
*
29005489 TATATTCATAT
1 TATATACATAT
29005500 ATATACACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.62
Consensus pattern (20 bp):
TATATACATATGTATTTTTT
Found at i:29011164 original size:15 final size:15
Alignment explanation
Indices: 29011153--29011208 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
29011143 AAATAAAGTG
29011153 ATAAATAATAAAATA
1 ATAAATAATAAAATA
*
29011168 ATAAATAATACAATAAA
1 ATAAATAATA-AA-ATA
29011185 ATAAAATAATAAAATTA
1 AT-AAATAATAAAA-TA
29011202 A-AAATAA
1 ATAAATAA
29011209 AAATAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
15 16 0.46
16 3 0.09
17 8 0.23
18 8 0.23
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (15 bp):
ATAAATAATAAAATA
Found at i:29011207 original size:25 final size:26
Alignment explanation
Indices: 29011159--29011215 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 26
29011149 AGTGATAAAT
29011159 AATAAAATAATAAATAATACAAT-AA
1 AATAAAATAATAAATAATACAATAAA
29011184 AATAAAATAATAAAATTAA-A-AATAAA
1 AATAAAATAAT-AAA-TAATACAATAAA
29011210 AATAAA
1 AATAAA
29011216 GAAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 14 0.48
26 12 0.41
27 3 0.10
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (26 bp):
AATAAAATAATAAATAATACAATAAA
Found at i:29022509 original size:16 final size:16
Alignment explanation
Indices: 29022458--29022502 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 16
29022448 AGGTGAAAAG
29022458 TAAAAGTTTTGGGGAAAAA
1 TAAAAGTTTTGGGG---AA
29022477 TAAAAAGTTTTGGGGAA
1 T-AAAAGTTTTGGGGAA
29022494 TAAAAGTTT
1 TAAAAGTTT
29022503 GAGGGAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.32
17 3 0.12
19 1 0.04
20 13 0.52
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.31
Consensus pattern (16 bp):
TAAAAGTTTTGGGGAA
Found at i:29029083 original size:15 final size:15
Alignment explanation
Indices: 29029065--29029094 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29029055 ATTAATTTTG
29029065 ATTAAGTAAAATTAA
1 ATTAAGTAAAATTAA
*
29029080 ATTAATTAAAATTAA
1 ATTAAGTAAAATTAA
29029095 TATGATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
ATTAAGTAAAATTAA
Found at i:29029604 original size:68 final size:68
Alignment explanation
Indices: 29029526--29029659 Score: 173
Period size: 68 Copynumber: 2.0 Consensus size: 68
29029516 TTTTAATAAT
* * ** *
29029526 TTAATATTAAATTTAATTTAA-ATCTTATCTTAAT-AGTATTTTATTAATTTAATATTAAAGTGA
1 TTAATATTAAA-TTAATCTAATAT-TTATCTTAATAAATATTAGATGAATTTAATATTAAAGTGA
29029589 TTATC
64 TTATC
* *
29029594 TTAATGTTAAATTAATCTAATATTTATCTTGATAAATATTAGATGAATTTAATATTAAAGTGATT
1 TTAATATTAAATTAATCTAATATTTATCTTAATAAATATTAGATGAATTTAATATTAAAGTGATT
29029659 A
66 A
29029660 AGTTTAATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
67 17 0.30
68 40 0.70
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.49
Consensus pattern (68 bp):
TTAATATTAAATTAATCTAATATTTATCTTAATAAATATTAGATGAATTTAATATTAAAGTGATT
ATC
Found at i:29029855 original size:38 final size:38
Alignment explanation
Indices: 29029812--29029888 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
29029802 TTCTGATTTA
29029812 CAACTTGACCCAAAAGTTTAGAGAAGTTGTGAAATTAT
1 CAACTTGACCCAAAAGTTTAGAGAAGTTGTGAAATTAT
29029850 CAACTTGACCCAAAAGTTTAGAGAAGTTGTGAAATTAT
1 CAACTTGACCCAAAAGTTTAGAGAAGTTGTGAAATTAT
29029888 C
1 C
29029889 CCACTGGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (38 bp):
CAACTTGACCCAAAAGTTTAGAGAAGTTGTGAAATTAT
Found at i:29035048 original size:20 final size:18
Alignment explanation
Indices: 29035001--29035049 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
29034991 CAAGATAAAC
29035001 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
29035018 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
29035038 ATTAAATTAATA
1 ATTAAATTAATA
29035050 AAATATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:29039406 original size:17 final size:17
Alignment explanation
Indices: 29039377--29039409 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29039367 AGATTTTGAA
29039377 TTTTTGAATTAGATTTC
1 TTTTTGAATTAGATTTC
29039394 TTTTT-AATCTAGATTT
1 TTTTTGAAT-TAGATTT
29039410 GAGTTAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.61
Consensus pattern (17 bp):
TTTTTGAATTAGATTTC
Found at i:29044050 original size:20 final size:21
Alignment explanation
Indices: 29044025--29044064 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29044015 TAAAATAAGT
29044025 AAAAAAT-TAATTTTAAATTC
1 AAAAAATATAATTTTAAATTC
*
29044045 AAAAAATATATTTTTAAATT
1 AAAAAATATAATTTTAAATT
29044065 TAGAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAAATATAATTTTAAATTC
Found at i:29045464 original size:29 final size:30
Alignment explanation
Indices: 29045426--29045483 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
29045416 GTTCCATATC
29045426 TTTTACTTTATACAGTAAAGAGATAATTTT
1 TTTTACTTTATACAGTAAAGAGATAATTTT
* *
29045456 TTTTA-TTTATATATTAAAGAGATAATTT
1 TTTTACTTTATACAGTAAAGAGATAATTT
29045484 CTGAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (30 bp):
TTTTACTTTATACAGTAAAGAGATAATTTT
Done.