Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 88 of 203
Found at i:28007288 original size:26 final size:23
Alignment explanation
Indices: 28007238--28007296 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 23
28007228 ACAAAAATAT
28007238 TAAAAAAACTTAAAATAATATTACA
1 TAAAAAAA--TAAAATAATATTACA
*
28007263 TAATAAAATAAAATAATGTATATACA
1 TAAAAAAATAAAATAA--TAT-TACA
28007289 TAAAAAAA
1 TAAAAAAA
28007297 ATAGGTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 8 0.28
25 10 0.34
26 11 0.38
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (23 bp):
TAAAAAAATAAAATAATATTACA
Found at i:28007291 original size:23 final size:23
Alignment explanation
Indices: 28007248--28007299 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
28007238 TAAAAAAACT
*
28007248 TAAAATAATATTACATAATAAAA
1 TAAAATAATAGTACATAATAAAA
*
28007271 TAAAATAAT-GTATATACATAAAA
1 TAAAATAATAGTACATA-ATAAAA
28007294 -AAAATA
1 TAAAATA
28007300 GGTAGATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (23 bp):
TAAAATAATAGTACATAATAAAA
Found at i:28007355 original size:24 final size:24
Alignment explanation
Indices: 28007323--28007376 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
28007313 ATAAACTAGT
*
28007323 ATAATAACAAT-ATCAATAATATTA
1 ATAATAACAATGATC-ATAATAATA
28007347 ATAATAACAATGATCATAATAATA
1 ATAATAACAATGATCATAATAATA
*
28007371 GTAATA
1 ATAATA
28007377 GTAAATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.31
Consensus pattern (24 bp):
ATAATAACAATGATCATAATAATA
Found at i:28008481 original size:50 final size:50
Alignment explanation
Indices: 28008400--28009002 Score: 341
Period size: 50 Copynumber: 12.2 Consensus size: 50
28008390 TGTGTCTGTA
* ** * *
28008400 GGGAACTAAGATTTGCTTTTGTAGCTTTAATCGGTTCGACTGCACCGCCA
1 GGGAAGTAAGATTCACTTTTGTAGCTTTAATCGGTTCCACTGCACCGCCG
* * * *
28008450 TGGAAGTAAGATTCACTTTTGTAGCTTTAATCAGTTCCACTGCACCACCA
1 GGGAAGTAAGATTCACTTTTGTAGCTTTAATCGGTTCCACTGCACCGCCG
* * ** * * **
28008500 TGGAAGTAAGATTC-TTTGTTGTAGCTTTAATCTATTCCAGTGCAACATCG
1 GGGAAGTAAGATTCACTT-TTGTAGCTTTAATCGGTTCCACTGCACCGCCG
* * * ** * * **
28008550 GGGAAGTAGGATTCACTGTTGTAGCGTTAATATGTTTCATTGCAATGCCG
1 GGGAAGTAAGATTCACTTTTGTAGCTTTAATCGGTTCCACTGCACCGCCG
*
28008600 GGGAAGTAAGATTCA-TTGTTGTAGCTTTAATCTGTTCCACTGCACCGCCG
1 GGGAAGTAAGATTCACTT-TTGTAGCTTTAATCGGTTCCACTGCACCGCCG
* * * * * *
28008650 GGGAAATAATATTC-GTTGTTGTAGCTTTAATCTGTTTCACTGC-CATGCCG
1 GGGAAGTAAGATTCACTT-TTGTAGCTTTAATCGGTTCCACTGCAC-CGCCG
* * *** * * ***
28008700 GGGAAGTAAGATTCGCTATTGTAGCTTTAATATATTTCATTGCAATTCCG
1 GGGAAGTAAGATTCACTTTTGTAGCTTTAATCGGTTCCACTGCACCGCCG
* * ** * * ***
28008750 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATTTGTTTCACCGCAAAACCG
1 GGGAAGTAAGATTCACTTTTGTAGCTTTAATCGGTTCCACTGCACCGCCG
* * * * *
28008800 GGGAAGTAAGATTC-GTTGTT-TAG--TT--T--GTTCCATTGCACTGTCA
1 GGGAAGTAAGATTCACTT-TTGTAGCTTTAATCGGTTCCACTGCACCGCCG
** * * * * *
28008843 ACGAAGTAAGATTCGCTGTTGTAGCTTTAATCTGTTTCACTGC-CACGCTG
1 GGGAAGTAAGATTCACTTTTGTAGCTTTAATCGGTTCCACTGCAC-CGCCG
* * * ** **
28008893 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTGTTCCACTGCAATGCTA
1 GGGAAGTAAGATTCACTTTTGTAGCTTTAATCGGTTCCACTGCACCGCCG
* * * * * * ***
28008943 GGGAGGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCACTGTAATACCG
1 GGGAAGTAAGATTCACTTTTGTAGCTTTAATCGGTTCCACTGCACCGCCG
28008993 GGGAAGTAAG
1 GGGAAGTAAG
28009003 GTTTGTGGCT
Statistics
Matches: 446, Mismatches: 89, Indels: 36
0.78 0.16 0.06
Matches are distributed among these distances:
43 23 0.05
44 4 0.01
45 1 0.00
46 2 0.00
47 2 0.00
48 1 0.00
49 9 0.02
50 402 0.90
51 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (50 bp):
GGGAAGTAAGATTCACTTTTGTAGCTTTAATCGGTTCCACTGCACCGCCG
Found at i:28008563 original size:100 final size:100
Alignment explanation
Indices: 28008451--28009002 Score: 452
Period size: 100 Copynumber: 5.6 Consensus size: 100
28008441 GCACCGCCAT
* * ** *
28008451 GGAAGTAAGATTCACTTTTGTAGCTTTAATCAGTTCCACTGCACCACCATGGAAGTAAGATTCTT
1 GGAAGTAAGATTCACTGTTGTAGCTTTAATCAGTTTCACTGCACCACCGGGGAAGTAAGATTCAT
*
28008516 TGTTGTAGCTTTAATCTATTCCAGTGCAACATCGG
66 TGTTGTAGCTTTAATCTATTCCACTGCAACATCGG
* * * ***
28008551 GGAAGTAGGATTCACTGTTGTAGCGTTAAT-ATGTTTCATTGCAATGCCGGGGAAGTAAGATTCA
1 GGAAGTAAGATTCACTGTTGTAGCTTTAATCA-GTTTCACTGCACCACCGGGGAAGTAAGATTCA
* * **
28008615 TTGTTGTAGCTTTAATCTGTTCCACTGCACCGCCGG
65 TTGTTGTAGCTTTAATCTATTCCACTGCAACATCGG
* * ** *
28008651 GGAAATAATATTCGTTGTTGTAGCTTTAATCTGTTTCACTG--CCATGCCGGGGAAGTAAGATTC
1 GGAAGTAAGATTCACTGTTGTAGCTTTAATCAGTTTCACTGCACCA--CCGGGGAAGTAAGATTC
** * * * * *
28008714 GCTATTGTAGCTTTAATATATTTCATTGCAA-TTCCGG
64 ATTGTTGTAGCTTTAATCTATTCCACTGCAACAT-CGG
* ** * ** *
28008751 GGAAGTAAGATTCGCTGTTGTAGCTTTAATTTGTTTCACCGCAAAACCGGGGAAGTAAGATTCGT
1 GGAAGTAAGATTCACTGTTGTAGCTTTAATCAGTTTCACTGCACCACCGGGGAAGTAAGATTCAT
** * *
28008816 TGTT-TAG-TTTGTTCCATTGCACTGTC-A-A-C--
66 TGTTGTAGCTTTAATCTATTCCACTG-CAACATCGG
* *
28008845 -GAAGTAAGATTCGCTGTTGTAGCTTTAATCTGTTTCACTG--CCACGCTGGGGAAGTAAGATTC
1 GGAAGTAAGATTCACTGTTGTAGCTTTAATCAGTTTCACTGCACCAC-C-GGGGAAGTAAGATTC
** * *
28008907 GCTGTTGTAGCTTTAATCTGTTCCACTGC-A-ATGCTAG
64 ATTGTTGTAGCTTTAATCTATTCCACTGCAACAT-C-GG
* * * * **
28008944 GGAGGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCACTGTAATACCGGGGAAGTAAG
1 GGAAGTAAGATTCACTGTTGTAGCTTTAATCAGTTTCACTGCACCACCGGGGAAGTAAG
28009003 GTTTGTGGCT
Statistics
Matches: 364, Mismatches: 68, Indels: 40
0.77 0.14 0.08
Matches are distributed among these distances:
91 2 0.01
92 1 0.00
93 58 0.16
94 6 0.02
95 12 0.03
96 2 0.01
98 12 0.03
99 5 0.01
100 262 0.72
101 1 0.00
102 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (100 bp):
GGAAGTAAGATTCACTGTTGTAGCTTTAATCAGTTTCACTGCACCACCGGGGAAGTAAGATTCAT
TGTTGTAGCTTTAATCTATTCCACTGCAACATCGG
Found at i:28008671 original size:150 final size:149
Alignment explanation
Indices: 28008451--28008936 Score: 574
Period size: 150 Copynumber: 3.3 Consensus size: 149
28008441 GCACCGCCAT
* * ** *
28008451 GGAAGTAAGATTCACTTTTGTAGCTTTAATCAGTTCCACTGCACCACCATGGAAGTAAGATTCTT
1 GGAAGTAAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCACCGGGGAAGTAAGATTCGT
* * * *
28008516 TGTTGTAGCTTTAATCTATTCCAGTGCAACATCGGGGAAGTAGGATTCACTGTTGTAGCGTTAAT
66 TGTTGTAGCTTTAATCTATTCCACTGC-ACATCGGGGAAGTAAGATTCGCTGTTGTAGCTTTAAT
28008581 ATGTTTCATTGCAATGCCGG
130 ATGTTTCATTGCAATGCCGG
* * * *
28008601 GGAAGTAAGATTCATTGTTGTAGCTTTAATCTGTTCCACTGCACCGCCGGGGAAATAATATTCGT
1 GGAAGTAAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCACCGGGGAAGTAAGATTCGT
* * *
28008666 TGTTGTAGCTTTAATCTGTTTCACTGC-CATGCCGGGGAAGTAAGATTCGCTATTGTAGCTTTAA
66 TGTTGTAGCTTTAATCTATTCCACTGCACAT--CGGGGAAGTAAGATTCGCTGTTGTAGCTTTAA
* *
28008730 TATATTTCATTGCAATTCCGG
129 TATGTTTCATTGCAATGCCGG
* * * * **
28008751 GGAAGTAAGATTCGCTGTTGTAGCTTTAATTTGTTTCACCGCAAAACCGGGGAAGTAAGATTCGT
1 GGAAGTAAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCACCGGGGAAGTAAGATTCGT
** * *
28008816 TGTT-TAG-TTTGTTCCATTGCACTGTCA-A-C---GAAGTAAGATTCGCTGTTGTAGCTTTAAT
66 TGTTGTAGCTTTAATCTATTCCACTG-CACATCGGGGAAGTAAGATTCGCTGTTGTAGCTTTAAT
* * * * *
28008874 CTGTTTCACTGCCACGCTGG
130 ATGTTTCATTGCAATGCCGG
*
28008894 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTGTTCCACTGCA
1 GGAAGTAAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCA
28008937 ATGCTAGGGA
Statistics
Matches: 288, Mismatches: 44, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
143 81 0.28
146 1 0.00
148 15 0.05
149 5 0.02
150 186 0.65
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (149 bp):
GGAAGTAAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCACCGGGGAAGTAAGATTCGT
TGTTGTAGCTTTAATCTATTCCACTGCACATCGGGGAAGTAAGATTCGCTGTTGTAGCTTTAATA
TGTTTCATTGCAATGCCGG
Found at i:28010371 original size:13 final size:12
Alignment explanation
Indices: 28010339--28010378 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
28010329 GGCCTCTCCA
*
28010339 TTTTTTTCTTTT
1 TTTTTTTATTTT
*
28010351 TTTCTTTATTTT
1 TTTTTTTATTTT
28010363 TTCTTTTTATTTT
1 TT-TTTTTATTTT
28010376 TTT
1 TTT
28010379 AGACTCAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.05, C:0.07, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTTTATTTT
Found at i:28019117 original size:20 final size:19
Alignment explanation
Indices: 28019072--28019121 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
28019062 TGGATTGTTA
28019072 TTTTATTTTATTTTATTTGGT
1 TTTTA-TTTATTTTATTT-GT
28019093 TTTTATTTATTATTATTT-T
1 TTTTATTTATT-TTATTTGT
28019112 TGTTTATTTA
1 T-TTTATTTA
28019122 ATCTGCATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.07
20 14 0.52
21 11 0.41
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (19 bp):
TTTTATTTATTTTATTTGT
Found at i:28019611 original size:38 final size:38
Alignment explanation
Indices: 28019551--28019707 Score: 199
Period size: 38 Copynumber: 4.2 Consensus size: 38
28019541 AGTCCCGTTA
28019551 AACACCGGCACGAA-GCCTGCTAGGCACATAGCCCGAT
1 AACACCGGCACGAAGGCCTGCTAGGCACATAGCCCGAT
* * * * *
28019588 AACACCAGCATGAAGGCTTGCTAGGCACATATCCCAAT
1 AACACCGGCACGAAGGCCTGCTAGGCACATAGCCCGAT
* * * *
28019626 AAAATCGGCACGAAGGCTTGCTAGGCACATAGCCTGAT
1 AACACCGGCACGAAGGCCTGCTAGGCACATAGCCCGAT
* * *
28019664 AACACCGGCACAAAGGCCTACTAGGCATATAGCCCGAT
1 AACACCGGCACGAAGGCCTGCTAGGCACATAGCCCGAT
28019702 AACACC
1 AACACC
28019708 TTATAGACAA
Statistics
Matches: 100, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
37 12 0.12
38 88 0.88
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.15
Consensus pattern (38 bp):
AACACCGGCACGAAGGCCTGCTAGGCACATAGCCCGAT
Found at i:28025596 original size:15 final size:15
Alignment explanation
Indices: 28025576--28025619 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
28025566 ATGCCTCACA
28025576 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
28025591 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
28025606 CACCGTGTTATCAA
1 CACCGTGTTATCAA
28025620 GAAACAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:28026719 original size:13 final size:13
Alignment explanation
Indices: 28026701--28026727 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28026691 AAACAACCAT
28026701 AAATAATCAATTA
1 AAATAATCAATTA
28026714 AAATAATCAATTA
1 AAATAATCAATTA
28026727 A
1 A
28026728 GCTACTAATT
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:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAATCAATTA
Found at i:28032510 original size:17 final size:17
Alignment explanation
Indices: 28032480--28032513 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28032470 TAAGAGGAAT
* *
28032480 AAAAATAAATAAATAAC
1 AAAAAGAAAAAAATAAC
28032497 AAAAAGAAAAAAATAAC
1 AAAAAGAAAAAAATAAC
28032514 GATAAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAAAGAAAAAAATAAC
Found at i:28033766 original size:19 final size:19
Alignment explanation
Indices: 28033738--28033783 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
28033728 GTATGGGTTT
* *
28033738 ATACAATTCGTGTGCCAAG
1 ATACACTTCGTATGCCAAG
*
28033757 ATACACTTCGTATGCCAAT
1 ATACACTTCGTATGCCAAG
28033776 ATACACTT
1 ATACACTT
28033784 TATGTGCCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (19 bp):
ATACACTTCGTATGCCAAG
Found at i:28033791 original size:19 final size:19
Alignment explanation
Indices: 28033738--28033792 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 19
28033728 GTATGGGTTT
* *
28033738 ATACAATTCGTGTGCCAAG
1 ATACACTTCATGTGCCAAG
* * *
28033757 ATACACTTCGTATGCCAAT
1 ATACACTTCATGTGCCAAG
*
28033776 ATACACTTTATGTGCCA
1 ATACACTTCATGTGCCA
28033793 GTTTATTTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (19 bp):
ATACACTTCATGTGCCAAG
Found at i:28034043 original size:36 final size:36
Alignment explanation
Indices: 28033996--28034068 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
28033986 AAACGGTTGG
28033996 ATCTCTCCAACCCTTTATACAAAACAATCTCAACTT
1 ATCTCTCCAACCCTTTATACAAAACAATCTCAACTT
28034032 ATCTCTCCAACCCTTTATACAAAACAATCTCAACTT
1 ATCTCTCCAACCCTTTATACAAAACAATCTCAACTT
28034068 A
1 A
28034069 GGCTTTTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (36 bp):
ATCTCTCCAACCCTTTATACAAAACAATCTCAACTT
Found at i:28040220 original size:42 final size:41
Alignment explanation
Indices: 28040103--28040220 Score: 103
Period size: 43 Copynumber: 2.8 Consensus size: 41
28040093 AAAAAGCTCG
* *
28040103 TACGATGCCAATGTCCCAGACGTGGTCTTACATGAAATCAAA
1 TACGATGCCAATGTCCCAGACATGGTCTTACA-CAAATCAAA
** * * * * * *
28040145 TAAC-AGTGTTACTATCCTAAACAAGGTCTTACACATAATCATA
1 T-ACGA-TGCCAATGTCCCAGACATGGTCTTACACA-AATCAAA
28040188 TACGATGCCAATGTCCCAGACATGGTCTTACAC
1 TACGATGCCAATGTCCCAGACATGGTCTTACAC
28040221 GTAAATCACA
Statistics
Matches: 55, Mismatches: 17, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
42 26 0.47
43 29 0.53
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (41 bp):
TACGATGCCAATGTCCCAGACATGGTCTTACACAAATCAAA
Found at i:28040402 original size:23 final size:22
Alignment explanation
Indices: 28040375--28040427 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
28040365 TATATACATT
28040375 AAAATTTA-ATTCGAAATTTATAA
1 AAAATTTACATTC-AAATTTA-AA
*
28040398 AAAATATACATTCAAATTTAAA
1 AAAATTTACATTCAAATTTAAA
*
28040420 AACATTTA
1 AAAATTTA
28040428 TTTACTTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 8 0.31
23 14 0.54
24 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATTTACATTCAAATTTAAA
Found at i:28047673 original size:21 final size:21
Alignment explanation
Indices: 28047615--28047675 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
28047605 TCTTAAAAAG
*
28047615 TTATTTTTATACAATAATAATATT
1 TTATTTTT-TAAAAT-AT-ATATT
* *
28047639 TTA-ATTTTAGAATATATATT
1 TTATTTTTTAAAATATATATT
28047659 TTATTTTTTAAAATATA
1 TTATTTTTTAAAATATA
28047676 ATTCTATCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 8 0.25
21 13 0.41
22 5 0.16
23 3 0.09
24 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTATTTTTTAAAATATATATT
Found at i:28047688 original size:21 final size:21
Alignment explanation
Indices: 28047630--28047689 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
28047620 TTTATACAAT
* *
28047630 AATA-ATATTTTA-ATTTTAG
1 AATATATATTCTATATTTTAA
* *
28047649 AATATATATTTTATTTTTTAA
1 AATATATATTCTATATTTTAA
28047670 AATATA-ATTCTATCATTTTA
1 AATATATATTCTAT-ATTTTA
28047690 TTGATTTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.12
20 14 0.41
21 16 0.47
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (21 bp):
AATATATATTCTATATTTTAA
Found at i:28047821 original size:45 final size:45
Alignment explanation
Indices: 28047761--28047846 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 45
28047751 CACTGTCTAA
* *
28047761 TTAACTAAATTACATATTATATACTATAAATTATTTATACTAAAT
1 TTAACTAAATCACATAGTATATACTATAAATTATTTATACTAAAT
* * * * *
28047806 TTAAGTAAATCACATAGTATTTATTGTTAATTATTTATACT
1 TTAACTAAATCACATAGTATATACTATAAATTATTTATACT
28047847 CGGTGGAAGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (45 bp):
TTAACTAAATCACATAGTATATACTATAAATTATTTATACTAAAT
Found at i:28053031 original size:13 final size:13
Alignment explanation
Indices: 28053015--28053039 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28053005 ATGGGTCATA
28053015 TGCCCGTGTGTGT
1 TGCCCGTGTGTGT
28053028 TGCCCGTGTGTG
1 TGCCCGTGTGTG
28053040 ACACAAGCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.40, T:0.36
Consensus pattern (13 bp):
TGCCCGTGTGTGT
Found at i:28075430 original size:21 final size:21
Alignment explanation
Indices: 28075370--28075444 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
28075360 GTTACACGAG
* *
28075370 CTACTCACAAGGCCGTGTAACT
1 CTAC-CACACGGCCGTGTGACT
* *
28075392 CTATCACACAGG-CGTGTGTCT
1 CTACCACAC-GGCCGTGTGACT
*
28075413 CTACCACACGGCCGTGTGCCT
1 CTACCACACGGCCGTGTGACT
**
28075434 CTTTCACACGG
1 CTACCACACGG
28075445 GTATGTCACT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.05
21 36 0.84
22 5 0.12
ACGTcount: A:0.20, C:0.35, G:0.21, T:0.24
Consensus pattern (21 bp):
CTACCACACGGCCGTGTGACT
Found at i:28076337 original size:24 final size:24
Alignment explanation
Indices: 28076309--28076356 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
28076299 GTACAGAGTG
*
28076309 TATAGGGACTTAAATCATATTTTA
1 TATAGGGACTTAAAGCATATTTTA
*
28076333 TATAGGGACTTAGAGCATATTTTA
1 TATAGGGACTTAAAGCATATTTTA
28076357 ACTTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (24 bp):
TATAGGGACTTAAAGCATATTTTA
Found at i:28077782 original size:21 final size:21
Alignment explanation
Indices: 28077753--28077800 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
28077743 CTGGTTTAAT
* *
28077753 TAAATAAATTATTAAAAATAA
1 TAAAAAAATTAATAAAAATAA
* *
28077774 TAAAAAAATTAATAAAAGTAT
1 TAAAAAAATTAATAAAAATAA
28077795 TAAAAA
1 TAAAAA
28077801 TAGGGAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAAAAAATTAATAAAAATAA
Found at i:28080630 original size:48 final size:48
Alignment explanation
Indices: 28080556--28080648 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 48
28080546 TGCTATGCAA
* * *
28080556 TGCTAAACTTGGTTTTCCACTTTCTACACTTTTATC-CATATTTATCTT
1 TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCAC-TATTTATCTT
28080604 TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCACTATTTAT
1 TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCACTATTTAT
28080649 TCCCTCTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 40 0.98
49 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.46
Consensus pattern (48 bp):
TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCACTATTTATCTT
Found at i:28080982 original size:54 final size:54
Alignment explanation
Indices: 28080895--28081026 Score: 140
Period size: 54 Copynumber: 2.4 Consensus size: 54
28080885 AAATTGGGAT
* * * * * * *
28080895 ACACGGTCATGTCCCAGCCCGTGTCCTTGCCCGTGTAACTCACTGACTTGAGAC
1 ACACGGTCGTGTCTCAGCCCATGTCCTTACCCGTGCAACTCACTAACTAGAGAC
* * *
28080949 ATACGGTCGTGTCTCAGCCCATGT-CTCTACCCGTGCAACTCACTAACTAGGGTC
1 ACACGGTCGTGTCTCAGCCCATGTCCT-TACCCGTGCAACTCACTAACTAGAGAC
* *
28081003 ACATGGTCGTGTCTCAGGCCATGT
1 ACACGGTCGTGTCTCAGCCCATGT
28081027 GTCAGCCCGT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
53 2 0.03
54 62 0.97
ACGTcount: A:0.19, C:0.33, G:0.23, T:0.26
Consensus pattern (54 bp):
ACACGGTCGTGTCTCAGCCCATGTCCTTACCCGTGCAACTCACTAACTAGAGAC
Found at i:28081987 original size:18 final size:19
Alignment explanation
Indices: 28081945--28081992 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
28081935 GATTCATATC
* *
28081945 TCATTTCATCATTTCATATT
1 TCATTTC-TCATCTCATAGT
28081965 TCATTTCTCATCTCAT-GT
1 TCATTTCTCATCTCATAGT
28081983 TCATTTCTCA
1 TCATTTCTCA
28081993 ACTTTTCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
19 8 0.31
20 7 0.27
ACGTcount: A:0.21, C:0.25, G:0.02, T:0.52
Consensus pattern (19 bp):
TCATTTCTCATCTCATAGT
Found at i:28082845 original size:40 final size:40
Alignment explanation
Indices: 28082790--28082881 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
28082780 TTAAATTTTA
* *
28082790 ACAATTTAGTCCATATTGCTCAAAATTAACAATTAATTCC
1 ACAATTTAGTCCATATTACTCAAAATCAACAATTAATTCC
28082830 ACAATTTAGTCCATATTACTCAAAATCAACAATTAATTCC
1 ACAATTTAGTCCATATTACTCAAAATCAACAATTAATTCC
28082870 ACAATTTAGTCC
1 ACAATTTAGTCC
28082882 TTTTCTACTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (40 bp):
ACAATTTAGTCCATATTACTCAAAATCAACAATTAATTCC
Found at i:28083241 original size:26 final size:26
Alignment explanation
Indices: 28083185--28083241 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
28083175 TGTTATTACG
**
28083185 ACATATATAATATATATAATAAGTTA
1 ACATATATAATATATATAATAACATA
*
28083211 ACATATATAA-ATATATTATAGACATA
1 ACATATATAATATATATAATA-ACATA
*
28083237 TCATA
1 ACATA
28083242 AATGTTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.37
Consensus pattern (26 bp):
ACATATATAATATATATAATAACATA
Found at i:28083631 original size:17 final size:17
Alignment explanation
Indices: 28083609--28083641 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28083599 TTTAAATAAA
*
28083609 TAAATATTTTTCTCAAT
1 TAAATAATTTTCTCAAT
28083626 TAAATAATTTTCTCAA
1 TAAATAATTTTCTCAA
28083642 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATAATTTTCTCAAT
Found at i:28093708 original size:45 final size:45
Alignment explanation
Indices: 28093595--28093708 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 45
28093585 TAAAACTATA
* *
28093595 GTTGAAAAACGCTATGGCATCATAATAAAAATGAGTAAGACCATG
1 GTTGAAAGACGCTATGGCATCATGATAAAAATGAGTAAGACCATG
* * ** * *
28093640 GCTGAAAGATGCTATGGTGTCATGATATAAATGAGTAAGACCCTG
1 GTTGAAAGACGCTATGGCATCATGATAAAAATGAGTAAGACCATG
*
28093685 GTTGAAAGACAGC-ATGACATCATG
1 GTTGAAAGAC-GCTATGGCATCATG
28093709 GAAAGAAGAC
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
45 53 0.96
46 2 0.04
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (45 bp):
GTTGAAAGACGCTATGGCATCATGATAAAAATGAGTAAGACCATG
Found at i:28099848 original size:19 final size:19
Alignment explanation
Indices: 28099824--28099959 Score: 146
Period size: 19 Copynumber: 6.8 Consensus size: 19
28099814 AATTTTTGAG
28099824 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
28099843 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
**
28099862 GATATATGCTCTCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
28099883 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
28099902 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
28099921 GATATGCAATCTTAGAATATAT
1 GATATGCAATCTTAG---ATAT
*
28099943 GATTTTGCAATCTTAGA
1 GA-TATGCAATCTTAGA
28099960 GATCTAATTT
Statistics
Matches: 98, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
19 64 0.65
20 1 0.01
21 15 0.15
22 6 0.06
23 12 0.12
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:28099869 original size:40 final size:40
Alignment explanation
Indices: 28099825--28099931 Score: 155
Period size: 40 Copynumber: 2.7 Consensus size: 40
28099815 ATTTTTGAGG
28099825 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
** * **
28099865 ATATGCTCTCTTAGATATGATATACAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
28099905 ATAT--AATCTTAGATATGATATGCAATC
1 ATATGCAATCTTAGATATGATATGCAATC
28099932 TTAGAATATA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
38 20 0.34
40 39 0.66
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
Found at i:28102131 original size:16 final size:18
Alignment explanation
Indices: 28102107--28102147 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28102097 AACAGCATAA
*
28102107 AAATTAAAT-AAATT-GG
1 AAATAAAATAAAATTGGG
28102123 AAATAAAATAAAATTGGG
1 AAATAAAATAAAATTGGG
28102141 AAATAAA
1 AAATAAA
28102148 TTTGTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (18 bp):
AAATAAAATAAAATTGGG
Found at i:28106999 original size:28 final size:28
Alignment explanation
Indices: 28106936--28107115 Score: 294
Period size: 28 Copynumber: 6.5 Consensus size: 28
28106926 ATATTAAGTC
* * *
28106936 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAGTCAAACT
*
28106963 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
28106991 CGCACACTTAGTGCTACATAGTC-AACT
1 CGCACACTTAGTGCTACATAGTCAAACT
28107018 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
28107046 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAACT
*
28107074 CGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAGTCAAACT
28107101 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28107116 GCACAATTTA
Statistics
Matches: 147, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
27 66 0.45
28 81 0.55
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAGTCAAACT
Found at i:28107020 original size:55 final size:55
Alignment explanation
Indices: 28106936--28107115 Score: 299
Period size: 55 Copynumber: 3.3 Consensus size: 55
28106926 ATATTAAGTC
* * * *
28106936 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
28106991 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
*
28107046 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTCAAACT
28107101 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28107116 GCACAATTTA
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
55 92 0.77
56 27 0.23
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
Found at i:28107056 original size:83 final size:82
Alignment explanation
Indices: 28106936--28107115 Score: 306
Period size: 83 Copynumber: 2.2 Consensus size: 82
28106926 ATATTAAGTC
* *
28106936 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
28107001 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
* *
28107018 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
*
28107083 AGTGCTACATAGTCAATT
65 AGTGCTACATAGTCAACT
28107101 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28107116 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 20 0.22
83 72 0.78
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (82 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAACT
Found at i:28115894 original size:17 final size:18
Alignment explanation
Indices: 28115872--28115907 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
28115862 AAAAATTAAA
28115872 TAAATTG-GAAATAAATT
1 TAAATTGCGAAATAAATT
28115889 TAAATTGCGAAATAAATT
1 TAAATTGCGAAATAAATT
28115907 T
1 T
28115908 GTATTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (18 bp):
TAAATTGCGAAATAAATT
Found at i:28117759 original size:40 final size:38
Alignment explanation
Indices: 28117697--28117787 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 38
28117687 ATCGTCAGAT
28117697 CAACCGAACACACCAGAAAGAAGCTCACAAGAGCTAATC
1 CAACCGAA-ACACCAGAAAGAAGCTCACAAGAGCTAATC
* *
28117736 CAACCGAAACACGCTAGACAGAAGCTCATAAGAGCTAATC
1 CAACCGAAACAC-C-AGAAAGAAGCTCACAAGAGCTAATC
* *
28117776 TAATCGAAACAC
1 CAACCGAAACAC
28117788 ACCAGATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
38 4 0.09
39 9 0.20
40 33 0.72
ACGTcount: A:0.45, C:0.29, G:0.15, T:0.11
Consensus pattern (38 bp):
CAACCGAAACACCAGAAAGAAGCTCACAAGAGCTAATC
Found at i:28121665 original size:22 final size:22
Alignment explanation
Indices: 28121623--28121689 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 22
28121613 AATCGAAATG
28121623 AATA-AAAATTTTA-AAACATA
1 AATATAAAATTTTATAAACATA
*
28121643 AA-ATAAAATTTTATAAATTATA
1 AATATAAAATTTTATAAA-CATA
28121665 AATTATAATACATTTTATAAACATA
1 AA-TATAA-A-ATTTTATAAACATA
28121690 TACATATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 1 0.03
20 11 0.29
21 3 0.08
22 5 0.13
24 4 0.11
25 4 0.11
26 10 0.26
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AATATAAAATTTTATAAACATA
Found at i:28123255 original size:4 final size:4
Alignment explanation
Indices: 28123246--28123272 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
28123236 TGAATTTGGT
28123246 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
28123273 GGGTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:28126418 original size:76 final size:77
Alignment explanation
Indices: 28126326--28126530 Score: 267
Period size: 76 Copynumber: 2.7 Consensus size: 77
28126316 TTTTTCTTGG
* * *
28126326 TTTAGGAATTACTTAATTCCTTAAA-ACTCTTTAAGGTTTTAAGTAACCTTTAATAAATTAAGTA
1 TTTAAGAATTACTTAATTTCTTAAACACTATTTAAGGTTTTAAGTAACCTTTAATAAATTAAGTA
28126390 -TTTTTCCCATGA
66 TTTTTTCCC-TGA
* *
28126402 TTTAAGAATTACTTAATTTCTTAAACAC-ATTTAAGGTTTTAAGTAACCCTTCATAAATTAAGTA
1 TTTAAGAATTACTTAATTTCTTAAACACTATTTAAGGTTTTAAGTAACCTTTAATAAATTAAGTA
*
28126466 TTTTTTTCCTGA
66 TTTTTTCCCTGA
* * *
28126478 TTT-AGAAATTACTTAATTTCTTAAAGA-TATTTTAAGGTTTAAAGCAACCTTTA
1 TTTAAG-AATTACTTAATTTCTTAAACACTA-TTTAAGGTTTTAAGTAACCTTTA
28126531 TGTAATTTTC
Statistics
Matches: 113, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
75 2 0.02
76 83 0.73
77 28 0.25
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (77 bp):
TTTAAGAATTACTTAATTTCTTAAACACTATTTAAGGTTTTAAGTAACCTTTAATAAATTAAGTA
TTTTTTCCCTGA
Found at i:28127082 original size:77 final size:75
Alignment explanation
Indices: 28126933--28127209 Score: 222
Period size: 77 Copynumber: 3.6 Consensus size: 75
28126923 AGGTGATGTT
* * * * * *
28126933 ATTAAGTAACTTTCTCATGGTTTAGGAATTATTTAATTACTTAAAAATCAGTTAATGTTTTAGGT
1 ATTAAGTAACTTTC-CATGATTTAGAAATTACTTAATTTCTTAAAAATCAGATAA-GTTTTAAGT
*
28126998 -GGTGTTAAAGAA
64 AAG-GTTAAAGAA
** * *
28127010 ATTAAGTAGTTTTCTCATGATTTAAAAATTACTTAATTTCTTAAACATCAGATAAGATTTTAAGT
1 ATTAAGTAACTTTC-CATGATTTAGAAATTACTTAATTTCTTAAAAATCAGATAAG-TTTTAAGT
28127075 AAGGTTAAAG-A
64 AAGGTTAAAGAA
* * * * * *
28127086 GTTAAGTAACTATCCAAT-ATTGTATGAGATT-CTTAATTTCTTAAAGACCA-ATTACGGTTTTA
1 ATTAAGTAACTTTCC-ATGATT-TA-GAAATTACTTAATTTCTTAAAAATCAGA-TA-AGTTTTA
**
28127148 AGTAACATTAAAGAA
61 AGTAAGGTTAAAGAA
* * *
28127163 TTTAAGTAATTTTCCATTGATTTAGGAATTACTTAATTTCTTAAAAA
1 ATTAAGTAACTTTCCA-TGATTTAGAAATTACTTAATTTCTTAAAAA
28127210 AAATTGTAAC
Statistics
Matches: 161, Mismatches: 28, Indels: 22
0.76 0.13 0.10
Matches are distributed among these distances:
75 5 0.03
76 56 0.35
77 96 0.60
78 4 0.02
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (75 bp):
ATTAAGTAACTTTCCATGATTTAGAAATTACTTAATTTCTTAAAAATCAGATAAGTTTTAAGTAA
GGTTAAAGAA
Found at i:28127147 original size:76 final size:77
Alignment explanation
Indices: 28127026--28127207 Score: 192
Period size: 76 Copynumber: 2.4 Consensus size: 77
28127016 TAGTTTTCTC
** * **
28127026 ATGATTTAAAAATTACTTAATTTCTTAAACATCAGATAAGATTTTAAGTAAGGTTAAAG-AGTTA
1 ATGATTTAGGAATTACTTAATTTCTTAAACACCAGATAAGATTTTAAGTAACATTAAAGAAGTTA
28127090 AGTAACTATCCA
66 AGTAACTATCCA
* * * * *
28127102 AT-ATTGTATGAGATT-CTTAATTTCTTAAAGACCA-ATTACGGTTTTAAGTAACATTAAAGAAT
1 ATGATT-TAGGA-ATTACTTAATTTCTTAAACACCAGA-TAAGATTTTAAGTAACATTAAAGAAG
* *
28127164 TTAAGTAATTTTCCA
63 TTAAGTAACTATCCA
*
28127179 TTGATTTAGGAATTACTTAATTTCTTAAA
1 ATGATTTAGGAATTACTTAATTTCTTAAA
28127208 AAAAATTGTA
Statistics
Matches: 87, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
75 4 0.05
76 44 0.51
77 36 0.41
78 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (77 bp):
ATGATTTAGGAATTACTTAATTTCTTAAACACCAGATAAGATTTTAAGTAACATTAAAGAAGTTA
AGTAACTATCCA
Found at i:28129286 original size:22 final size:24
Alignment explanation
Indices: 28129259--28129303 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
28129249 TGGTGTCATA
28129259 TTTT-TACAATATTAGAGATAATT
1 TTTTATACAATATTAGAGATAATT
*
28129282 TTTTATACAATATTAGGGATAA
1 TTTTATACAATATTAGAGATAA
28129304 GAGATATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.44
Consensus pattern (24 bp):
TTTTATACAATATTAGAGATAATT
Found at i:28135448 original size:21 final size:21
Alignment explanation
Indices: 28135424--28135466 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28135414 ATAATAAGTA
28135424 TATTAATATAAAAT-TATAAAC
1 TATTAA-ATAAAATATATAAAC
*
28135445 TATTAAATATAATATATAAAC
1 TATTAAATAAAATATATAAAC
28135466 T
1 T
28135467 TATACATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTAAATAAAATATATAAAC
Found at i:28135789 original size:21 final size:21
Alignment explanation
Indices: 28135747--28135794 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28135737 TTTAAAATCC
28135747 AAATTTCAAAAATATAATATA
1 AAATTTCAAAAATATAATATA
*
28135768 AAATTATCATAAATATAA-ATA
1 AAATT-TCAAAAATATAATATA
*
28135789 ATATTT
1 AAATTT
28135795 ATCGTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 12 0.50
22 11 0.46
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATTTCAAAAATATAATATA
Found at i:28135804 original size:21 final size:22
Alignment explanation
Indices: 28135747--28135789 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28135737 TTTAAAATCC
*
28135747 AAATT-TCAAAAATATAATATA
1 AAATTATCATAAATATAATATA
28135768 AAATTATCATAAATATAA-ATA
1 AAATTATCATAAATATAATATA
28135789 A
1 A
28135790 TATTTATCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATTATCATAAATATAATATA
Found at i:28138920 original size:126 final size:126
Alignment explanation
Indices: 28138568--28139173 Score: 1065
Period size: 126 Copynumber: 4.8 Consensus size: 126
28138558 ATTATTTCGA
28138568 GTTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTG
1 GTTGACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTG
* * * *
28138632 TGAAATCACGCCCTCGTGGATGCGATTTTGCTACAGTATGTCATGTAAGAAATAATTTTTTT
65 TGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAACAAATAATTTTTTT
* * * *
28138694 -TCTGATGTTTCTGAGCAAATAGTATAAAATCGTTTCTACGAGAATGCTATTTGAG-AGAAATTG
1 GT-TGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTG
28138757 TGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAACAAATAATTTTTTT
65 TGAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAACAAATAATTTTTTT
*
28138819 GTTGACGTTTCTGAGAAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 GTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
*
28138884 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTT
66 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAACAAATAATTTTTTT
* *
28138945 GTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTATACCAGGATGCTATTTAAGAAGAAATTGT
1 GTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
28139010 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAACAAATAATTTTTTT
66 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAACAAATAATTTTTTT
28139071 GTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 GTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
28139136 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
66 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
28139174 CAAGTTTGGG
Statistics
Matches: 456, Mismatches: 20, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
125 115 0.25
126 340 0.75
127 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (126 bp):
GTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAACAAATAATTTTTTT
Found at i:28142747 original size:10 final size:10
Alignment explanation
Indices: 28142728--28142784 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
28142718 GCCATTGATG
*
28142728 AAAATATAAA
1 AAAATTTAAA
28142738 AAAATTTAAA
1 AAAATTTAAA
**
28142748 ATTATTTAAA
1 AAAATTTAAA
*
28142758 AAAATATAAA
1 AAAATTTAAA
*
28142768 AAATTATTTTAA
1 AAA--ATTTAAA
28142780 AAAAT
1 AAAAT
28142785 AAATTTGAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 29 0.78
12 8 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:28142865 original size:22 final size:22
Alignment explanation
Indices: 28142840--28143036 Score: 160
Period size: 22 Copynumber: 8.3 Consensus size: 22
28142830 AAATATGGGT
28142840 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
28142862 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
** * ***
28142884 TTGAGAGGAAATTAAAATTAAATATGGGT
1 TTGAGA-G-AATT----TTGGA-AGGAAA
28142913 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
28142935 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
** * ***
28142957 TTGAGAGGAAATTAAAATTAAATATGGGT
1 TTGAGA-G-AATT----TTGGA-AGGAAA
28142986 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
28143008 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
28143030 TTGAGAG
1 TTGAGAG
28143037 GAAAAATTAG
Statistics
Matches: 137, Mismatches: 24, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
22 89 0.65
23 8 0.06
24 8 0.06
27 8 0.06
28 8 0.06
29 16 0.12
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:28142866 original size:73 final size:73
Alignment explanation
Indices: 28142789--28143040 Score: 504
Period size: 73 Copynumber: 3.5 Consensus size: 73
28142779 AAAAATAAAT
28142789 TTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTAAAATTAAATATGGGTTTGAGAGAATTTTG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTAAAATTAAATATGGGTTTGAGAGAATTTTG
28142854 GAAGGAAA
66 GAAGGAAA
28142862 TTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTAAAATTAAATATGGGTTTGAGAGAATTTTG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTAAAATTAAATATGGGTTTGAGAGAATTTTG
28142927 GAAGGAAA
66 GAAGGAAA
28142935 TTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTAAAATTAAATATGGGTTTGAGAGAATTTTG
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTAAAATTAAATATGGGTTTGAGAGAATTTTG
28143000 GAAGGAAA
66 GAAGGAAA
28143008 TTGAGAGAATTTTGGAAGGAAATTGAGAGGAAA
1 TTGAGAGAATTTTGGAAGGAAATTGAGAGGAAA
28143041 AATTAGATAG
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 179 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.28
Consensus pattern (73 bp):
TTGAGAGAATTTTGGAAGGAAATTGAGAGGAAATTAAAATTAAATATGGGTTTGAGAGAATTTTG
GAAGGAAA
Found at i:28151179 original size:29 final size:29
Alignment explanation
Indices: 28151113--28151180 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
28151103 GAGAAGTAAT
* * *
28151113 TTTATATTAATTAATTACGAAAAAATATG
1 TTTACATTAATTAATTACGAAAAAAAAAG
* *
28151142 TTTATATTAATTATATTATGAAAAAAAAAG
1 TTTACATTAATTA-ATTACGAAAAAAAAAG
28151172 -TTACATTAA
1 TTTACATTAA
28151181 GGACGTAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (29 bp):
TTTACATTAATTAATTACGAAAAAAAAAG
Found at i:28151653 original size:19 final size:21
Alignment explanation
Indices: 28151611--28151654 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
28151601 AATTAATTTT
*
28151611 TATAGTATTTTAATTTTAGGA
1 TATAGTATTTTAATTTTAGAA
*
28151632 TATA-TATTTTATTTTTA-AA
1 TATAGTATTTTAATTTTAGAA
28151651 TATA
1 TATA
28151655 ATTATATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 12 0.57
21 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TATAGTATTTTAATTTTAGAA
Found at i:28151796 original size:24 final size:23
Alignment explanation
Indices: 28151751--28151821 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
28151741 AATTACATAG
28151751 TATTTATTATAAATTATTTATAC
1 TATTTATTATAAATTATTTATAC
* * *
28151774 TATTTTTTATGAAATTATATATAT
1 TATTTATTAT-AAATTATTTATAC
*
28151798 TATTTATTATTAATTATTTATAC
1 TATTTATTATAAATTATTTATAC
28151821 T
1 T
28151822 TGATTAAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 20 0.50
24 20 0.50
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (23 bp):
TATTTATTATAAATTATTTATAC
Found at i:28155613 original size:41 final size:40
Alignment explanation
Indices: 28155561--28155647 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
28155551 AAACAGGCTT
*
28155561 TTAGCGGCGCTTGGACAAAAAACACCACTAAAAATCAAGCA
1 TTAGCGACGCTTGGAC-AAAAACACCACTAAAAATCAAGCA
** * * * *
28155602 TTAGCGACGCTTTTACAAAAACGCCGCTAAAGATCGAGCA
1 TTAGCGACGCTTGGACAAAAACACCACTAAAAATCAAGCA
28155642 TTAGCG
1 TTAGCG
28155648 GCGCATTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 26 0.67
41 13 0.33
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (40 bp):
TTAGCGACGCTTGGACAAAAACACCACTAAAAATCAAGCA
Found at i:28155662 original size:40 final size:40
Alignment explanation
Indices: 28155578--28155684 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
28155568 CGCTTGGACA
* *
28155578 AAAAACACCACTAAAAATCAAGCATTAGCGACGCTTTTAC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGACGCTTTTAC
* * * *
28155618 AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCATTTT-T
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGACGC-TTTTAC
* *
28155658 AAAAACGCAGCTAAGAAT-AAGCATTAG
1 AAAAACGCCGCTAAAAATCAAGCATTAG
28155685 TGGCATTTTC
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
39 8 0.14
40 44 0.79
41 4 0.07
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGACGCTTTTAC
Found at i:28155854 original size:41 final size:41
Alignment explanation
Indices: 28155743--28155931 Score: 212
Period size: 40 Copynumber: 4.8 Consensus size: 41
28155733 TTTTGGGGTA
* *
28155743 TTTAGCGGCG-TTTTTCAGAAGCGCCGCTAATACTCGGGCC
1 TTTAGCGGCGTTTTTTCAAAAGCGCCGCTAATGCTCGGGCC
* * **
28155783 TTTAGCGGC-ATTTTTCAGAAGCGCCGCTAATGCTCAAGCC
1 TTTAGCGGCGTTTTTTCAAAAGCGCCGCTAATGCTCGGGCC
* *
28155823 TTTAGCGGCGTTTTTTTAAAAGCGCCTCTAATGCTCGGGCC
1 TTTAGCGGCGTTTTTTCAAAAGCGCCGCTAATGCTCGGGCC
* *
28155864 TTTAGCGGCGTTTTTTCAAAA--G-CGCTAATGGT--GGAC
1 TTTAGCGGCGTTTTTTCAAAAGCGCCGCTAATGCTCGGGCC
** *
28155900 TTTAGCGGCGTTTTTGAAAAAGTGCCGCTAAT
1 TTTAGCGGCGTTTTTTCAAAAGCGCCGCTAAT
28155932 AATAAAATCT
Statistics
Matches: 129, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
36 22 0.17
38 9 0.07
39 8 0.06
40 45 0.35
41 45 0.35
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTTCAAAAGCGCCGCTAATGCTCGGGCC
Found at i:28155921 original size:36 final size:38
Alignment explanation
Indices: 28155743--28155921 Score: 123
Period size: 41 Copynumber: 4.6 Consensus size: 38
28155733 TTTTGGGGTA
* * * *
28155743 TTTAGCGGCG-TTTTTCAGAAGCGCCGCTAATACTCGGGCC
1 TTTAGCGGCGTTTTTTAAAAAGCG-C-CTAATGCTC-GGAC
* * * * *
28155783 TTTAGCGGC-ATTTTTCAGAAGCGCCGCTAATGCTCAAGCC
1 TTTAGCGGCGTTTTTTAAAAAGCG-C-CTAATGCTC-GGAC
* *
28155823 TTTAGCGGCGTTTTTTTAAAAGCGCCTCTAATGCTCGGGCC
1 TTTAGCGGCGTTTTTTAAAAAGCG-C-CTAATGCTC-GGAC
* *
28155864 TTTAGCGGCGTTTTTTCAAAAGCG-CTAATGGT-GGAC
1 TTTAGCGGCGTTTTTTAAAAAGCGCCTAATGCTCGGAC
*
28155900 TTTAGCGGCGTTTTTGAAAAAG
1 TTTAGCGGCGTTTTTTAAAAAG
28155922 TGCCGCTAAT
Statistics
Matches: 123, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
36 23 0.19
38 7 0.06
40 45 0.37
41 48 0.39
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (38 bp):
TTTAGCGGCGTTTTTTAAAAAGCGCCTAATGCTCGGAC
Found at i:28159918 original size:5 final size:5
Alignment explanation
Indices: 28159908--28159976 Score: 52
Period size: 5 Copynumber: 13.2 Consensus size: 5
28159898 TTATAATGTT
* * *
28159908 TTTTA TTTTA TTTTA -TGTA TTTACA TTTCTT TTTTA TTTTA TTTTA TAATGTT-
1 TTTTA TTTTA TTTTA TTTTA TTT-TA TTT-TA TTTTA TTTTA TTTTA T--T-TTA
28159961 TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA T
28159977 GTATTTACAT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
4 5 0.10
5 35 0.69
6 7 0.14
7 2 0.04
8 2 0.04
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:28159944 original size:31 final size:31
Alignment explanation
Indices: 28159906--28159995 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 31
28159896 GCTTATAATG
*
28159906 TTTTTTATTTTATTTTATGTATTTACATTTC
1 TTTTTTATTTTATTTTATGTATTTACATTTA
*
28159937 TTTTTTATTTTA--TT-T-TA--TA-A--TG
1 TTTTTTATTTTATTTTATGTATTTACATTTA
28159959 TTTTTTATTTTATTTTATGTATTTACATTTA
1 TTTTTTATTTTATTTTATGTATTTACATTTA
28159990 TTTTTT
1 TTTTTT
28159996 GACTTGTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
22 13 0.27
24 3 0.06
25 3 0.06
26 2 0.04
27 2 0.04
28 3 0.06
29 3 0.06
31 19 0.40
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.73
Consensus pattern (31 bp):
TTTTTTATTTTATTTTATGTATTTACATTTA
Found at i:28160696 original size:12 final size:12
Alignment explanation
Indices: 28160679--28160706 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28160669 GCTAGCCATG
28160679 ATGTTACTATTA
1 ATGTTACTATTA
28160691 ATGTTACTATTA
1 ATGTTACTATTA
28160703 ATGT
1 ATGT
28160707 CCTTAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (12 bp):
ATGTTACTATTA
Found at i:28162015 original size:43 final size:42
Alignment explanation
Indices: 28161952--28162303 Score: 339
Period size: 43 Copynumber: 8.3 Consensus size: 42
28161942 TTATGACCTT
*
28161952 TAGCGGCGTTTATGAGAAAAGCGCCGCTAAAGGTCATGTTCTA
1 TAGCGGCGTTTGTGA-AAAAGCGCCGCTAAAGGTCATGTTCTA
** * * * *
28161995 TAGCGGTATTTGTAGAAAAAGTGCCGCTAAAGGTTAGGTTCTT
1 TAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCATGTTCTA
* * * *
28162038 TAGTGGCGTTTGTGAGAAAAGCGTCACTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGTGA-AAAAGCGCCGCTAAAGGTCATGTTCTA
* * *
28162081 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATCTT
1 TAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCATGTTCTA
* * * ** * * *
28162124 TAGTGGCGTTTTTGGGAGGAGTGCCACTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCATGTTCTA
* * *
28162167 TAGCAGCGTTTGTGATAAAAGCG-C-CTAAAGGTCATGATCTT
1 TAGCGGCGTTTGTGA-AAAAGCGCCGCTAAAGGTCATGTTCTA
* * *
28162208 TAGCGGCGTTTTTGAGAAAGCGCCGCTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCATGTTCTA
* * *
28162250 TAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGATCATGGTCTA
1 TAGCGGCGTTTG-TGAAAAAGCGCCGCTAAAGGTCATGTTCTA
*
28162293 TAGTGGCGTTT
1 TAGCGGCGTTT
28162304 ATTTATAAAA
Statistics
Matches: 244, Mismatches: 58, Indels: 14
0.77 0.18 0.04
Matches are distributed among these distances:
40 6 0.02
41 28 0.11
42 29 0.12
43 177 0.73
44 4 0.02
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (42 bp):
TAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCATGTTCTA
Found at i:28162099 original size:86 final size:86
Alignment explanation
Indices: 28161949--28162303 Score: 425
Period size: 86 Copynumber: 4.2 Consensus size: 86
28161939 TTTTTATGAC
* * * * ** *
28161949 CTTTAGCGGCGTTTATGAGAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGTATTTGTAGAAAA
1 CTTTAGTGGCGTTTTTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGGCGTTTGTGGAAAA
* * *
28162014 AGTGCCGCTAAAGGTTAGGTT
66 AGCGCCGCTAAAGGTCAGGAT
* *
28162035 CTTTAGTGGCGTTTGTGAGAAAAGCGTCACTAAAGGTCTTGTTCTATAGCGGCGTTTGTGGAAAA
1 CTTTAGTGGCGTTTTTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGGCGTTTGTGGAAAA
* *
28162100 AGCGCCGCTAAAAGTCATGAT
66 AGCGCCGCTAAAGGTCAGGAT
* ** * *
28162121 CTTTAGTGGCGTTTTTGGGAGGAGTGCCACTAAAGGTCTTGTTCTATAGCAGCGTTTGT-GATAA
1 CTTTAGTGGCGTTTTTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGGCGTTTGTGGA-AA
*
28162185 AAGCG-C-CTAAAGGTCATGAT
65 AAGCGCCGCTAAAGGTCAGGAT
* *
28162205 CTTTAGCGGCGTTTTTGAG-AAAGCGCCGCTAAAGGTCTTGTTCTATAGCGGCGTTTGTTGG-AA
1 CTTTAGTGGCGTTTTTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGGCGTTTG-TGGAAA
*
28162268 AAGCGCCGCTAAAGATCATGG-T
65 AAGCGCCGCTAAAGGTCA-GGAT
*
28162290 CTATAGTGGCGTTT
1 CTTTAGTGGCGTTT
28162304 ATTTATAAAA
Statistics
Matches: 231, Mismatches: 32, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
83 40 0.17
84 32 0.14
85 26 0.11
86 133 0.58
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (86 bp):
CTTTAGTGGCGTTTTTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGGCGTTTGTGGAAAA
AGCGCCGCTAAAGGTCAGGAT
Found at i:28162261 original size:169 final size:172
Alignment explanation
Indices: 28161978--28162303 Score: 457
Period size: 169 Copynumber: 1.9 Consensus size: 172
28161968 AAAAGCGCCG
* * * * * *
28161978 CTAAAGGTCATGTTCTATAGCGGTATTTGTAGAAAAAGTGCCGCTAAAGGTTAGGTTCTTTAGTG
1 CTAAAGGTCATGTTCTATAGCAGCATTTGTAGAAAAAGCGCCGCTAAAGGTCAGGATCTTTAGCG
*
28162043 GCGTTTGTGAGAAAAGCGTCACTAAAGGTCTTGTTCTATAGCGGCGTTTG-TGGAAAAAGCGCCG
66 GCGTTTGTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGGCGTTTGTTGG-AAAAGCGCCG
*
28162107 CTAAA-AGTCATGATCTTTAGTGGCGTTTTTGGGAGGAGTGCCA
130 CTAAAGA-TCATGATCTATAGTGGCGTTTTTGGGAGGAGTGCCA
* * *
28162150 CTAAAGGTCTTGTTCTATAGCAGCGTTTGT-GATAAAAGCG-C-CTAAAGGTCATGATCTTTAGC
1 CTAAAGGTCATGTTCTATAGCAGCATTTGTAGA-AAAAGCGCCGCTAAAGGTCAGGATCTTTAGC
* *
28162212 GGCGTTTTTGAG-AAAGCGCCGCTAAAGGTCTTGTTCTATAGCGGCGTTTGTTGGAAAAGCGCCG
65 GGCGTTTGTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGGCGTTTGTTGGAAAAGCGCCG
*
28162276 CTAAAGATCATGGTCTATAGTGGCGTTT
130 CTAAAGATCATGATCTATAGTGGCGTTT
28162304 ATTTATAAAA
Statistics
Matches: 137, Mismatches: 14, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
169 70 0.51
170 32 0.23
171 3 0.02
172 32 0.23
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (172 bp):
CTAAAGGTCATGTTCTATAGCAGCATTTGTAGAAAAAGCGCCGCTAAAGGTCAGGATCTTTAGCG
GCGTTTGTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGGCGTTTGTTGGAAAAGCGCCGC
TAAAGATCATGATCTATAGTGGCGTTTTTGGGAGGAGTGCCA
Found at i:28171823 original size:7 final size:8
Alignment explanation
Indices: 28171798--28171832 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
28171788 CATTATGGAG
28171798 AAAGTAAAA
1 AAAG-AAAA
28171807 AAAGGAAAA
1 AAA-GAAAA
28171816 AAAGAAAA
1 AAAGAAAA
28171824 AAAGAAAA
1 AAAGAAAA
28171832 A
1 A
28171833 TGAGTAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 14 0.56
9 10 0.40
10 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (8 bp):
AAAGAAAA
Found at i:28171825 original size:17 final size:17
Alignment explanation
Indices: 28171798--28171832 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28171788 CATTATGGAG
28171798 AAAGTAAAAAAAGGAAAA
1 AAAGTAAAAAAA-GAAAA
28171816 AAAG-AAAAAAAGAAAA
1 AAAGTAAAAAAAGAAAA
28171832 A
1 A
28171833 TGAGTAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 7 0.41
18 4 0.24
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAGTAAAAAAAGAAAA
Found at i:28172695 original size:17 final size:18
Alignment explanation
Indices: 28172673--28172707 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28172663 TTAGAATTAC
*
28172673 GGGCCC-CATGCTCGTGT
1 GGGCCCACAAGCTCGTGT
28172690 GGGCCCACAAGCTCGTGT
1 GGGCCCACAAGCTCGTGT
28172708 AGCCTACACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.11, C:0.34, G:0.34, T:0.20
Consensus pattern (18 bp):
GGGCCCACAAGCTCGTGT
Found at i:28175768 original size:27 final size:26
Alignment explanation
Indices: 28175684--28175770 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 26
28175674 GGTTTCTGAT
*
28175684 TGGCGGCACCAAAGGT-TCTATACTGAC
1 TGGCGGCACCAATGGTGTC-ATA-TGAC
** * *
28175711 TGGCGGCACTGATGGTGCCA-ATGAGGT
1 TGGCGGCACCAATGGTGTCATATGA--C
28175738 TGGCGGCACCAATGGTGTCATATTGAC
1 TGGCGGCACCAATGGTGTCATA-TGAC
28175765 TGGCGG
1 TGGCGG
28175771 GACTATTCGT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
25 3 0.07
26 1 0.02
27 37 0.80
28 2 0.04
29 3 0.07
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.23
Consensus pattern (26 bp):
TGGCGGCACCAATGGTGTCATATGAC
Found at i:28179178 original size:21 final size:21
Alignment explanation
Indices: 28179152--28179252 Score: 64
Period size: 21 Copynumber: 4.7 Consensus size: 21
28179142 TATTCCCTCT
*
28179152 TCTTCTTCTTTCTTTTTTTTC
1 TCTTCTTCTTTCTTTTCTTTC
* *
28179173 TCTTCTCCATTCCTTTTCTTTC
1 TCTTCTTC-TTTCTTTTCTTTC
* *
28179195 -CTTCTTTTTTCTTCTTCTTCTTG
1 TCTTCTTCTTTCTT-TTC-T-TTC
* * *
28179218 TCCTCTCCTTTCCTTTGCTTTC
1 TCTTCTTCTTT-CTTTTCTTTC
28179240 T-TTCTTC-TTCTTT
1 TCTTCTTCTTTCTTT
28179253 CCCTCTCCTT
Statistics
Matches: 60, Mismatches: 14, Indels: 14
0.68 0.16 0.16
Matches are distributed among these distances:
19 4 0.07
20 7 0.12
21 19 0.32
22 15 0.25
23 3 0.05
24 9 0.15
25 3 0.05
ACGTcount: A:0.01, C:0.31, G:0.02, T:0.66
Consensus pattern (21 bp):
TCTTCTTCTTTCTTTTCTTTC
Found at i:28179200 original size:45 final size:45
Alignment explanation
Indices: 28179150--28179253 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
28179140 TTTATTCCCT
* * * *
28179150 CTTCTTCTTCTTTCTTTTTTTTCTCTTCTCCATTCCTTTTCTTTC
1 CTTCTTCTTCTTTCTTCTTCTTCTCCTCTCCATTCCTTTGCTTTC
* * *
28179195 CTTCTT-TTTTCTTCTTCTTCTTGTCCTCTCCTTTCCTTTGCTTTC
1 CTTCTTCTTCT-TTCTTCTTCTTCTCCTCTCCATTCCTTTGCTTTC
*
28179240 TTTCTTCTTCTTTC
1 CTTCTTCTTCTTTC
28179254 CCTCTCCTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
44 3 0.06
45 42 0.88
46 3 0.06
ACGTcount: A:0.01, C:0.32, G:0.02, T:0.65
Consensus pattern (45 bp):
CTTCTTCTTCTTTCTTCTTCTTCTCCTCTCCATTCCTTTGCTTTC
Found at i:28182261 original size:29 final size:29
Alignment explanation
Indices: 28182218--28182297 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
28182208 TTCAGTGTTG
* *
28182218 CGGATATACTGCCAGAACTCCAATATTTA
1 CGGATAAATTGCCAGAACTCCAATATTTA
* * *
28182247 CGGATTAATCT-CCAGAACTCCCATATTTG
1 CGGATAAAT-TGCCAGAACTCCAATATTTA
*
28182276 TGGATAAATTGCCAGAACTCCA
1 CGGATAAATTGCCAGAACTCCA
28182298 CATAACTCCT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.02
29 39 0.95
30 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (29 bp):
CGGATAAATTGCCAGAACTCCAATATTTA
Found at i:28190506 original size:17 final size:16
Alignment explanation
Indices: 28190473--28190503 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28190463 GAGAGATATG
28190473 ATAGTTTAATATTTTA
1 ATAGTTTAATATTTTA
28190489 ATAGTTTAATATTTT
1 ATAGTTTAATATTTT
28190504 TAAAAAAAAA
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:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
ATAGTTTAATATTTTA
Found at i:28191586 original size:200 final size:200
Alignment explanation
Indices: 28191243--28191642 Score: 800
Period size: 200 Copynumber: 2.0 Consensus size: 200
28191233 TTGATATTAT
28191243 ATATTTTATTATAATCTATACTATAACAGTTGTCATAACGTTGCCTACATAAGAGTATGGGGGCC
1 ATATTTTATTATAATCTATACTATAACAGTTGTCATAACGTTGCCTACATAAGAGTATGGGGGCC
28191308 TAGTAAGCAAAGTTAGACATGGAGGGCCTAAATTAATGTAGAGTGGCCATTAACCAATTAGGGCT
66 TAGTAAGCAAAGTTAGACATGGAGGGCCTAAATTAATGTAGAGTGGCCATTAACCAATTAGGGCT
28191373 AAGTTGATTAGCCACCTATCGTCTAAAAGTTTAGAATTAATACTACGAAAAAAATTCTAACAGTC
131 AAGTTGATTAGCCACCTATCGTCTAAAAGTTTAGAATTAATACTACGAAAAAAATTCTAACAGTC
28191438 TAGAC
196 TAGAC
28191443 ATATTTTATTATAATCTATACTATAACAGTTGTCATAACGTTGCCTACATAAGAGTATGGGGGCC
1 ATATTTTATTATAATCTATACTATAACAGTTGTCATAACGTTGCCTACATAAGAGTATGGGGGCC
28191508 TAGTAAGCAAAGTTAGACATGGAGGGCCTAAATTAATGTAGAGTGGCCATTAACCAATTAGGGCT
66 TAGTAAGCAAAGTTAGACATGGAGGGCCTAAATTAATGTAGAGTGGCCATTAACCAATTAGGGCT
28191573 AAGTTGATTAGCCACCTATCGTCTAAAAGTTTAGAATTAATACTACGAAAAAAATTCTAACAGTC
131 AAGTTGATTAGCCACCTATCGTCTAAAAGTTTAGAATTAATACTACGAAAAAAATTCTAACAGTC
28191638 TAGAC
196 TAGAC
28191643 TCGATCTCAT
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.29
Consensus pattern (200 bp):
ATATTTTATTATAATCTATACTATAACAGTTGTCATAACGTTGCCTACATAAGAGTATGGGGGCC
TAGTAAGCAAAGTTAGACATGGAGGGCCTAAATTAATGTAGAGTGGCCATTAACCAATTAGGGCT
AAGTTGATTAGCCACCTATCGTCTAAAAGTTTAGAATTAATACTACGAAAAAAATTCTAACAGTC
TAGAC
Found at i:28194846 original size:17 final size:18
Alignment explanation
Indices: 28194824--28194857 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28194814 TTTGGGCTGA
*
28194824 GTGGG-CCACACAGGCAT
1 GTGGGCCCAAACAGGCAT
28194841 GTGGGCCCAAACAGGCA
1 GTGGGCCCAAACAGGCA
28194858 GACCACATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.26, C:0.29, G:0.35, T:0.09
Consensus pattern (18 bp):
GTGGGCCCAAACAGGCAT
Found at i:28195374 original size:40 final size:40
Alignment explanation
Indices: 28195330--28195423 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 40
28195320 CTGATACTAT
* * * * *
28195330 GATGGGCTAAGGTCGTACTGTAGATTTGATATTGTACTGA
1 GATGGGCTAAGGCCCTACTGCAGATTTGATACTATACTGA
* * * *
28195370 GATGGGTTAAGGCCCTACTGCATATTTGGTGCTATACTGA
1 GATGGGCTAAGGCCCTACTGCAGATTTGATACTATACTGA
28195410 GATGGGCTAAGGCC
1 GATGGGCTAAGGCC
28195424 TAAACACTGA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (40 bp):
GATGGGCTAAGGCCCTACTGCAGATTTGATACTATACTGA
Found at i:28196317 original size:27 final size:27
Alignment explanation
Indices: 28196279--28196345 Score: 93
Period size: 26 Copynumber: 2.5 Consensus size: 27
28196269 AGATCAAAAT
*
28196279 TTTATTTTAAAAAATTTAAACTTT-TCC
1 TTTATTTTAAAAAATCTAAACTTTCT-C
28196306 TTTATTTT-AAAAATCTAAACTTTCTC
1 TTTATTTTAAAAAATCTAAACTTTCTC
*
28196332 TTTTTTTTAAAAAA
1 TTTATTTTAAAAAA
28196346 AAAAAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
26 22 0.61
27 14 0.39
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTATTTTAAAAAATCTAAACTTTCTC
Found at i:28197650 original size:19 final size:20
Alignment explanation
Indices: 28197622--28197665 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
28197612 TATTATAATC
*
28197622 TATATTATAGTAATA-GTTA
1 TATATAATAGTAATACGTTA
*
28197641 TATATAATAGTAGTACGTTA
1 TATATAATAGTAATACGTTA
28197661 TATAT
1 TATAT
28197666 TACTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.45
Consensus pattern (20 bp):
TATATAATAGTAATACGTTA
Found at i:28201040 original size:18 final size:19
Alignment explanation
Indices: 28200999--28201042 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
28200989 ACTTCAACTT
*
28200999 TTTACTTATCTCTCTTACAA
1 TTTA-TTATCCCTCTTACAA
28201019 TTTATTATCCCTCTTA-AA
1 TTTATTATCCCTCTTACAA
28201037 TTTATT
1 TTTATT
28201043 TTGAAGTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 11 0.48
20 4 0.17
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTATTATCCCTCTTACAA
Found at i:28203793 original size:21 final size:24
Alignment explanation
Indices: 28203764--28203812 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
28203754 TATACATTTA
*
28203764 ATTTCTATA-CTTTTTAA-AAATT
1 ATTTCTATACCTTTCTAACAAATT
28203786 ATTT-TATACCTTTCTAATCAAATT
1 ATTTCTATACCTTTCTAA-CAAATT
28203810 ATT
1 ATT
28203813 CTTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 11 0.48
24 8 0.35
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTCTATACCTTTCTAACAAATT
Found at i:28216799 original size:8 final size:7
Alignment explanation
Indices: 28216767--28216797 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28216757 TCAACAGAAG
*
28216767 TTTACTT
1 TTTAATT
28216774 TTTAATT
1 TTTAATT
28216781 TTTAATT
1 TTTAATT
28216788 TTTAATT
1 TTTAATT
28216795 TTT
1 TTT
28216798 TATACAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTAATT
Found at i:28217594 original size:14 final size:14
Alignment explanation
Indices: 28217569--28217601 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28217559 TATAAATGGC
28217569 TAAAAATGATTTTTT
1 TAAAAATGA-TTTTT
28217584 TAAAAAT-ATTTTT
1 TAAAAATGATTTTT
28217597 TAAAA
1 TAAAA
28217602 TTTCTAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 1 0.06
15 7 0.39
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TAAAAATGATTTTT
Found at i:28220521 original size:29 final size:31
Alignment explanation
Indices: 28220488--28220563 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 31
28220478 TTTACCTCAG
28220488 GTTACATTTTAGTCACTTAT-AT-TTGGAAT
1 GTTACATTTTAGTCACTTATGATATTGGAAT
* * * *
28220517 GTTACGTTTTAGTCACTTATGTTATTGTATT
1 GTTACATTTTAGTCACTTATGATATTGGAAT
*
28220548 GTAACATTTTAGTCAC
1 GTTACATTTTAGTCAC
28220564 CGAGCCATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 19 0.49
30 1 0.03
31 19 0.49
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (31 bp):
GTTACATTTTAGTCACTTATGATATTGGAAT
Found at i:28220561 original size:31 final size:29
Alignment explanation
Indices: 28220491--28220563 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
28220481 ACCTCAGGTT
*
28220491 ACATTTTAGTCACTTATATTTGGAATGTT
1 ACATTTTAGTCACTTATATTTGGAATGTA
* * * *
28220520 ACGTTTTAGTCACTTATGTTATTGTATTGTA
1 ACATTTTAGTCACTTAT-AT-TTGGAATGTA
28220551 ACATTTTAGTCAC
1 ACATTTTAGTCAC
28220564 CGAGCCATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 16 0.44
30 1 0.03
31 19 0.53
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (29 bp):
ACATTTTAGTCACTTATATTTGGAATGTA
Found at i:28222046 original size:59 final size:57
Alignment explanation
Indices: 28221967--28222076 Score: 132
Period size: 59 Copynumber: 1.9 Consensus size: 57
28221957 CCTTTTTTTT
* * * * *
28221967 AAAAATATTTTTTAATTTTTAGAGTTCGGACTAAATTGATAGATTTTGTAAATGTTAAC
1 AAAAATATTTTTTAATTTTTAAAATTAGAACTAAAATGA-A-ATTTTGTAAATGTTAAC
*
28222026 AAAAA-ATTTATTTATTTTTTAAAATTAGAACTAAAATGAAATTTTGTAAAT
1 AAAAATATTT-TTTAATTTTTAAAATTAGAACTAAAATGAAATTTTGTAAAT
28222077 ATTGAAGGCT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
57 11 0.25
58 5 0.11
59 28 0.64
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.44
Consensus pattern (57 bp):
AAAAATATTTTTTAATTTTTAAAATTAGAACTAAAATGAAATTTTGTAAATGTTAAC
Found at i:28231971 original size:8 final size:8
Alignment explanation
Indices: 28231955--28231985 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
28231945 AACCATGCCA
28231955 AATTTAAC
1 AATTTAAC
*
28231963 AACTTAAC
1 AATTTAAC
28231971 AATTTAAC
1 AATTTAAC
28231979 AATTTAA
1 AATTTAA
28231986 TCTTTAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (8 bp):
AATTTAAC
Found at i:28233246 original size:9 final size:9
Alignment explanation
Indices: 28233232--28233263 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
28233222 AAAAAACATA
*
28233232 TAATTCGGG
1 TAATTCGGT
28233241 TAATTCGGT
1 TAATTCGGT
28233250 TAATTCGGT
1 TAATTCGGT
28233259 TAATT
1 TAATT
28233264 TTTAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:28235005 original size:26 final size:26
Alignment explanation
Indices: 28234976--28235142 Score: 208
Period size: 26 Copynumber: 6.3 Consensus size: 26
28234966 TAAGGAAAAA
*
28234976 CCTTTGTGGCGTAGTATGAAAGAAAG
1 CCTTTGTGGCGTAATATGAAAGAAAG
*
28235002 CCTTTGTGGCGTAGTATGAAAGAAAG
1 CCTTTGTGGCGTAATATGAAAGAAAG
*
28235028 CCTTTATGGCGTAATATGAAAGAAAG
1 CCTTTGTGGCGTAATATGAAAGAAAG
*
28235054 CCTTTGTGGCATAATATGAAAGAAAG
1 CCTTTGTGGCGTAATATGAAAGAAAG
* * * * *
28235080 CCTTTGTAGTGCAATATAAAAGAATAA
1 CCTTTGTGGCGTAATATGAAAGAA-AG
* * *
28235107 CTTTTGTGGCGTAAAATGAATTGAAAG
1 CCTTTGTGGCGTAATATGAA-AGAAAG
28235134 CCTTTGTGG
1 CCTTTGTGG
28235143 AAAACCATGA
Statistics
Matches: 120, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
26 93 0.77
27 24 0.20
28 3 0.03
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (26 bp):
CCTTTGTGGCGTAATATGAAAGAAAG
Found at i:28235186 original size:27 final size:27
Alignment explanation
Indices: 28235128--28235186 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
28235118 TAAAATGAAT
* *
28235128 TGAAAGCCTTTGTGGAAAACCATGAAA
1 TGAAAGCCTCTGTGGAAAACCACGAAA
* * * *
28235155 AGAAAGCCTCTGTGGTAAATCACGAGA
1 TGAAAGCCTCTGTGGAAAACCACGAAA
28235182 TGAAA
1 TGAAA
28235187 ACTTTTGTAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (27 bp):
TGAAAGCCTCTGTGGAAAACCACGAAA
Found at i:28242209 original size:14 final size:14
Alignment explanation
Indices: 28242184--28242216 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28242174 TATAAATGGC
28242184 TAAAAATGATTTTTT
1 TAAAAATGA-TTTTT
28242199 TAAAAAT-ATTTTT
1 TAAAAATGATTTTT
28242212 TAAAA
1 TAAAA
28242217 TTTCTAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 1 0.06
15 7 0.39
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TAAAAATGATTTTT
Found at i:28245136 original size:29 final size:31
Alignment explanation
Indices: 28245103--28245178 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 31
28245093 TTTACCTCAG
28245103 GTTACATTTTAGTCACTTAT-AT-TTGGAAT
1 GTTACATTTTAGTCACTTATGATATTGGAAT
* * * *
28245132 GTTACGTTTTAGTCACTTATGTTATTGTATT
1 GTTACATTTTAGTCACTTATGATATTGGAAT
*
28245163 GTAACATTTTAGTCAC
1 GTTACATTTTAGTCAC
28245179 CGAGCCATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 19 0.49
30 1 0.03
31 19 0.49
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (31 bp):
GTTACATTTTAGTCACTTATGATATTGGAAT
Found at i:28245176 original size:31 final size:29
Alignment explanation
Indices: 28245106--28245178 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
28245096 ACCTCAGGTT
*
28245106 ACATTTTAGTCACTTATATTTGGAATGTT
1 ACATTTTAGTCACTTATATTTGGAATGTA
* * * *
28245135 ACGTTTTAGTCACTTATGTTATTGTATTGTA
1 ACATTTTAGTCACTTAT-AT-TTGGAATGTA
28245166 ACATTTTAGTCAC
1 ACATTTTAGTCAC
28245179 CGAGCCATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 16 0.44
30 1 0.03
31 19 0.53
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (29 bp):
ACATTTTAGTCACTTATATTTGGAATGTA
Found at i:28249626 original size:43 final size:42
Alignment explanation
Indices: 28249563--28249916 Score: 348
Period size: 43 Copynumber: 8.3 Consensus size: 42
28249553 TTATGACCTT
*
28249563 TAGCGGCGTTTATGAGAAAAGCGCCGCTAAAGGTCATGTTCTA
1 TAGCGGCGTTTGTGA-AAAAGCGCCGCTAAAGGTCATGTTCTA
* * * *
28249606 TAGCGGCATTTGTAGAAAAAGCGCCGCTAAAGGTTAGGTTCTT
1 TAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCATGTTCTA
* * * *
28249649 TAGTGGCGTTTGTGAGAAAAGCGTCACTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGTGA-AAAAGCGCCGCTAAAGGTCATGTTCTA
* * * *
28249692 TAGCGACGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATCTT
1 TAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCATGTTCTA
* * * ** * * *
28249735 TAGTGGCGTTTTTGGGAGGAGTGCCACTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCATGTTCTA
* * *
28249778 TAGCAGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATCTT
1 TAGCGGCGTTTGTGA-AAAAGCGCCGCTAAAGGTCATGTTCTA
* * * *
28249821 TAGCCGCGTTTTTGAGAAAGCGCCGCTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCATGTTCTA
* * * *
28249863 TAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGATTATGGTCTA
1 TAGCGGCGTTTG-TGAAAAAGCGCCGCTAAAGGTCATGTTCTA
*
28249906 TAGTGGCGTTT
1 TAGCGGCGTTT
28249917 ATTTATAAAA
Statistics
Matches: 247, Mismatches: 59, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
42 36 0.15
43 207 0.84
44 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (42 bp):
TAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCATGTTCTA
Found at i:28249710 original size:86 final size:86
Alignment explanation
Indices: 28249560--28249916 Score: 418
Period size: 86 Copynumber: 4.2 Consensus size: 86
28249550 TTTTTATGAC
* * * * * * *
28249560 CTTTAGCGGCGTTTATGAGAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCATTTGTAGAAAA
1 CTTTAGTGGCGTTTTTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGACGTTTGTGGAAAA
* *
28249625 AGCGCCGCTAAAGGTTAGGTT
66 AGCGCCGCTAAAGGTCAGGAT
* *
28249646 CTTTAGTGGCGTTTGTGAGAAAAGCGTCACTAAAGGTCTTGTTCTATAGCGACGTTTGTGGAAAA
1 CTTTAGTGGCGTTTTTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGACGTTTGTGGAAAA
* *
28249711 AGCGCCGCTAAAAGTCATGAT
66 AGCGCCGCTAAAGGTCAGGAT
* ** *
28249732 CTTTAGTGGCGTTTTTGGGAGGAGTGCCACTAAAGGTCTTGTTCTATAGC-AGCGTTTGT-GATA
1 CTTTAGTGGCGTTTTTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGA-CGTTTGTGGA-A
*
28249795 AAAGCGCCGCTAAAGGTCATGAT
64 AAAGCGCCGCTAAAGGTCAGGAT
** * *
28249818 CTTTAGCCGCGTTTTTGAG-AAAGCGCCGCTAAAGGTCTTGTTCTATAGCGGCGTTTGTTGG-AA
1 CTTTAGTGGCGTTTTTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGACGTTTG-TGGAAA
* *
28249881 AAGCGCCGCTAAAGATTATGG-T
65 AAGCGCCGCTAAAGGTCA-GGAT
*
28249903 CTATAGTGGCGTTT
1 CTTTAGTGGCGTTT
28249917 ATTTATAAAA
Statistics
Matches: 232, Mismatches: 33, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
85 65 0.28
86 166 0.72
87 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (86 bp):
CTTTAGTGGCGTTTTTGAGAAAAGCGCCACTAAAGGTCTTGTTCTATAGCGACGTTTGTGGAAAA
AGCGCCGCTAAAGGTCAGGAT
Found at i:28259415 original size:7 final size:8
Alignment explanation
Indices: 28259390--28259424 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
28259380 GATTATGGAG
28259390 AAAGTAAAA
1 AAAG-AAAA
28259399 AAAGGAAAA
1 AAA-GAAAA
28259408 AAAGAAAA
1 AAAGAAAA
28259416 AAAGAAAA
1 AAAGAAAA
28259424 A
1 A
28259425 TGAGTAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 14 0.56
9 10 0.40
10 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (8 bp):
AAAGAAAA
Found at i:28259417 original size:17 final size:17
Alignment explanation
Indices: 28259390--28259424 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28259380 GATTATGGAG
28259390 AAAGTAAAAAAAGGAAAA
1 AAAGTAAAAAAA-GAAAA
28259408 AAAG-AAAAAAAGAAAA
1 AAAGTAAAAAAAGAAAA
28259424 A
1 A
28259425 TGAGTAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 7 0.41
18 4 0.24
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAGTAAAAAAAGAAAA
Found at i:28259823 original size:13 final size:14
Alignment explanation
Indices: 28259805--28259836 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28259795 ACACAAATAG
28259805 CAGAATTA-ATATA
1 CAGAATTAGATATA
28259818 CAGAA-TAGATATA
1 CAGAATTAGATATA
28259831 CAGAAT
1 CAGAAT
28259837 CCTACTGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.12
13 15 0.88
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (14 bp):
CAGAATTAGATATA
Found at i:28263167 original size:8 final size:9
Alignment explanation
Indices: 28263152--28263181 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
28263142 TAAATTATTA
28263152 TAAAAAAAT
1 TAAAAAAAT
28263161 TAAAAAAAT
1 TAAAAAAAT
28263170 TAAAAAATAT
1 TAAAAAA-AT
28263180 TA
1 TA
28263182 TATATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:28263343 original size:27 final size:27
Alignment explanation
Indices: 28263270--28263361 Score: 89
Period size: 27 Copynumber: 3.4 Consensus size: 27
28263260 TGGAGGGTTT
* *
28263270 CTGATTGGCGGCACCAAAGGTTCCATA
1 CTGATTGGCGGCACCAATGGTGCCATA
**
28263297 CTGATTGGCGGCACTGATGGTGCCA-A
1 CTGATTGGCGGCACCAATGGTGCCATA
*
28263323 -TGAGGTTGGCGGCACCAATGGTGTCATA
1 CTGA--TTGGCGGCACCAATGGTGCCATA
* *
28263351 TTGACTGGCGG
1 CTGATTGGCGG
28263362 GACTACTCGT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
25 3 0.06
26 1 0.02
27 45 0.85
28 1 0.02
29 3 0.06
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.24
Consensus pattern (27 bp):
CTGATTGGCGGCACCAATGGTGCCATA
Found at i:28263614 original size:3 final size:3
Alignment explanation
Indices: 28263606--28263658 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
28263596 TTTTAGTTAG
* *
28263606 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28263654 TAT TA
1 TAT TA
28263659 AGATGTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:28266331 original size:160 final size:150
Alignment explanation
Indices: 28265950--28266404 Score: 416
Period size: 161 Copynumber: 2.9 Consensus size: 150
28265940 GCAAGTTGAA
28265950 AAAAAAGTTAGTAAAAAACTCTTACTTCAGCCATTTGTTCGTATTTTTTCTCCGCATTTTATTAC
1 AAAAAAGTTAGTAAAAAACTCTTACTTCAGCCATTTGTTCGTATTTTTT-TCCGCATTTTATTAC
* * *
28266015 TTTAAAAAATATCTTAATTTCTAATTTTATAATTTTACATTATTTCAGTGCGTAATGTTTGAAAT
65 TTTAAAAAATATCTTAATTTCTAATTTTATAATTTTACATTATTCCAATGCATAATGTTTGAAAT
*
28266080 TTATTAATTTAGTGTGTTTTT
130 TTATTAATTTAGTCTGTTTTT
* * * * *
28266101 AAATTAATTTGGTGTAAGAAAAAAACTCTTA-TCCCTGCCATTTGCTT-GTATTATTTTCC-CGA
1 AAA--AA---AGT-T-AGTAAAAAACTCTTACT-TCAGCCATTTG-TTCGTATTTTTTTCCGC-A
* * * *
28266163 TTTTTATTACTTTCAATAAAAATATTTTATTTTCGT-ATTTTATTATTTTATATTATTCCAATGC
56 -TTTTATTACTTT--A-AAAAATATCTTAATTTC-TAATTTTATAATTTTACATTATTCCAATGC
** *
28266227 ATTTTGTTTGAAATATTTGTATTAA-TTATTTCTGAATTTTT
116 ATAATGTTTG-AA-A-TT-TATTAATTTA-GTCTG--TTTTT
* * * *
28266268 AAAAAAGTTAGTAATAAACTCTTACTTCGGCCATTTGTTCATATTTTTTATCCGCATTTTATTAT
1 AAAAAAGTTAGTAAAAAACTCTTACTTCAGCCATTTGTTCGTATTTTTT-TCCGCATTTTATTAC
** * * * * *
28266333 TTTAAAAAATATCGAAATTTTTAATTTTATCATTTTACATTATTTCAGTGCATTATGTTTGAAAT
65 TTTAAAAAATATCTTAATTTCTAATTTTATAATTTTACATTATTCCAATGCATAATGTTTGAAAT
28266398 TTATTAA
130 TTATTAA
28266405 ATATACAATT
Statistics
Matches: 243, Mismatches: 34, Indels: 52
0.74 0.10 0.16
Matches are distributed among these distances:
151 3 0.01
153 8 0.03
154 2 0.01
155 1 0.00
156 6 0.02
157 51 0.21
158 44 0.18
159 4 0.02
160 41 0.17
161 52 0.21
162 6 0.02
163 1 0.00
164 5 0.02
165 11 0.05
167 8 0.03
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (150 bp):
AAAAAAGTTAGTAAAAAACTCTTACTTCAGCCATTTGTTCGTATTTTTTTCCGCATTTTATTACT
TTAAAAAATATCTTAATTTCTAATTTTATAATTTTACATTATTCCAATGCATAATGTTTGAAATT
TATTAATTTAGTCTGTTTTT
Found at i:28266368 original size:157 final size:152
Alignment explanation
Indices: 28265950--28266404 Score: 417
Period size: 157 Copynumber: 2.9 Consensus size: 152
28265940 GCAAGTTGAA
*
28265950 AAAAAAGTTAGTAAAAAACTCTTACTTCAGCCATTTGTTCGTATTTTTTCTCCGCATTTTATTAC
1 AAAAAAGTTAGTAAAAAACTCTTACTTCAGCCATTTGTTCGTATTTTTT-TCCGCATTTTATTAT
* * *
28266015 TTTAAAAAATATCTTAATTTCTAATTTTATAATTTTACATTATTTCAGTGCGTAATGTTTG-AA-
65 TTTAAAAAATATCTTAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAAT
*
28266078 ATTTATTAATTTAGTGTGTTTTT
130 ATTTATTAATTTAGTCTGTTTTT
* * * * *
28266101 AAATTAATTTGGTGTAAGAAAAAAACTCTTA-TCCCTGCCATTTGCTT-GTATTATTTTCC-CGA
1 AAA--AA---AGT-T-AGTAAAAAACTCTTACT-TCAGCCATTTG-TTCGTATTTTTTTCCGC-A
* * * * * *
28266163 TTTTTATTACTTTCAATAAAAATAT-TTTATTTTCGT-ATTTTATTATTTTATATTATTCCAATG
56 -TTTTATTA-TTT-TA-AAAAATATCTTAATTTT--TAATTTTATAATTTTACATTATTTCAGTG
* *
28266226 CATTTTGTTTGAAATATTTGTATTAA-TTATTTCTGAATTTTT
115 CATTATGTTTGAAATA-TT-TATTAATTTA-GTCTG--TTTTT
* * *
28266268 AAAAAAGTTAGTAATAAACTCTTACTTCGGCCATTTGTTCATATTTTTTATCCGCATTTTATTAT
1 AAAAAAGTTAGTAAAAAACTCTTACTTCAGCCATTTGTTCGTATTTTTT-TCCGCATTTTATTAT
** *
28266333 TTTAAAAAATATCGAAATTTTTAATTTTATCATTTTACATTATTTCAGTGCATTATGTTTG-AA-
65 TTTAAAAAATATCTTAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAAT
28266396 ATTTATTAA
130 ATTTATTAA
28266405 ATATACAATT
Statistics
Matches: 241, Mismatches: 34, Indels: 56
0.73 0.10 0.17
Matches are distributed among these distances:
151 3 0.01
153 8 0.03
154 2 0.01
155 1 0.00
156 6 0.02
157 47 0.20
158 45 0.19
159 9 0.04
160 44 0.18
161 45 0.19
162 6 0.02
163 1 0.00
164 5 0.02
165 11 0.05
167 8 0.03
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (152 bp):
AAAAAAGTTAGTAAAAAACTCTTACTTCAGCCATTTGTTCGTATTTTTTTCCGCATTTTATTATT
TTAAAAAATATCTTAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTTGAAATA
TTTATTAATTTAGTCTGTTTTT
Found at i:28266842 original size:35 final size:35
Alignment explanation
Indices: 28266803--28266875 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
28266793 CATTCCTTTT
*
28266803 CTTTCCTTCTTTTTTC-TTCTTCTTCTTGT-CCTCTC
1 CTTTCCTT-TTCTTTCTTTCTTCTTCTT-TCCCTCTC
28266838 CTTTCCTTTTCTTTCTTTCTTCTTCTTTCCCTCTC
1 CTTTCCTTTTCTTTCTTTCTTCTTCTTTCCCTCTC
28266873 CTT
1 CTT
28266876 CTCTCCCCCC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
34 7 0.20
35 28 0.80
ACGTcount: A:0.00, C:0.36, G:0.01, T:0.63
Consensus pattern (35 bp):
CTTTCCTTTTCTTTCTTTCTTCTTCTTTCCCTCTC
Found at i:28267125 original size:2 final size:2
Alignment explanation
Indices: 28267112--28267144 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28267102 ATCCCATTTG
*
28267112 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
28267145 GTTTTCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:28269824 original size:29 final size:29
Alignment explanation
Indices: 28269781--28269860 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
28269771 TTCAGTGTTG
* *
28269781 CGGATATACTGCCAGAACTCCAATATTTA
1 CGGATAAATTGCCAGAACTCCAATATTTA
* * *
28269810 CGGATTAATCT-CCAGAACTCCCATATTTG
1 CGGATAAAT-TGCCAGAACTCCAATATTTA
*
28269839 TGGATAAATTGCCAGAACTCCA
1 CGGATAAATTGCCAGAACTCCA
28269861 CATAACTCCT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.02
29 39 0.95
30 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (29 bp):
CGGATAAATTGCCAGAACTCCAATATTTA
Found at i:28279052 original size:18 final size:18
Alignment explanation
Indices: 28279031--28279069 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28279021 GATTGAGAGT
* *
28279031 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
28279049 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
28279067 GAA
1 GAA
28279070 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:28283642 original size:17 final size:16
Alignment explanation
Indices: 28283616--28283647 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
28283606 CATAGTTTCG
28283616 AAAAAAAAAATTGCAA
1 AAAAAAAAAATTGCAA
28283632 AAAAAAGAAAATTGCA
1 AAAAAA-AAAATTGCA
28283648 TACGGTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.12
Consensus pattern (16 bp):
AAAAAAAAAATTGCAA
Found at i:28285924 original size:24 final size:25
Alignment explanation
Indices: 28285897--28285950 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
28285887 ATGAGTGATA
*
28285897 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
28285921 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
28285945 AAAAAA
1 AAAAAA
28285951 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:28292813 original size:30 final size:30
Alignment explanation
Indices: 28292779--28292876 Score: 85
Period size: 30 Copynumber: 3.3 Consensus size: 30
28292769 AGCTCACTCC
28292779 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * * * *
28292809 TAGCTCA-ACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
* *
28292839 CAGCTCGACT-TT-AGCTCACGAGCTAAAGCT
1 TAGCTC-A-TATTCAGCTCACGAGCTAAACCT
28292869 TAGCTCAT
1 TAGCTCAT
28292877 TTTAGTTTAA
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
28 1 0.02
29 2 0.04
30 45 0.88
31 3 0.06
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.29
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:28296243 original size:56 final size:55
Alignment explanation
Indices: 28296127--28296244 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
28296117 TGCATGCTTT
* * * *
28296127 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
28296181 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
28296237 CATTAAAT
1 CATTAAAT
28296245 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:28296893 original size:20 final size:20
Alignment explanation
Indices: 28296868--28296922 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
28296858 ACGAGTTAAA
* *
28296868 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
28296888 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
28296908 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
28296923 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:28299012 original size:22 final size:22
Alignment explanation
Indices: 28298984--28299027 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
28298974 TTTTGAACCA
28298984 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
28299006 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
28299028 AAATACCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:28299942 original size:15 final size:16
Alignment explanation
Indices: 28299903--28299943 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
28299893 AACAACACTC
28299903 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
28299919 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
28299933 CTTTCTTTTTC
1 CTTTCTTTTTC
28299944 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:28300138 original size:17 final size:15
Alignment explanation
Indices: 28300101--28300139 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
28300091 TATCTCCCAC
28300101 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
28300117 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
28300134 TCATTT
1 TCATTT
28300140 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:28301017 original size:23 final size:23
Alignment explanation
Indices: 28300987--28301038 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
28300977 TCAATCACTC
* *
28300987 TTTTTTTTTTCAATTTCGATTTT
1 TTTTTTTTTTCAATTCCGAATTT
*
28301010 TTTTTTTTTTTAATTCCGAATTT
1 TTTTTTTTTTCAATTCCGAATTT
28301033 TTTTTT
1 TTTTTT
28301039 CTTCTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.75
Consensus pattern (23 bp):
TTTTTTTTTTCAATTCCGAATTT
Found at i:28301113 original size:11 final size:11
Alignment explanation
Indices: 28301097--28301148 Score: 61
Period size: 12 Copynumber: 4.6 Consensus size: 11
28301087 AATACAAACT
28301097 TTTTTTTTGAA
1 TTTTTTTTGAA
28301108 TTTTTTTTCGAA
1 TTTTTTTT-GAA
*
28301120 TTTTTTTTCAA
1 TTTTTTTTGAA
*
28301131 GTTTTTTTT-TA
1 -TTTTTTTTGAA
28301142 TTTTTTT
1 TTTTTTT
28301149 ACAATACCGT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
10 7 0.19
11 11 0.30
12 19 0.51
ACGTcount: A:0.13, C:0.04, G:0.06, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:28301529 original size:30 final size:30
Alignment explanation
Indices: 28301494--28301658 Score: 98
Period size: 30 Copynumber: 5.1 Consensus size: 30
28301484 AGCTCGAATT
*
28301494 AGCTCACA-TGAGCTTAATTTATCTCGTTTG
1 AGCTCA-ATTGAGCTTAATTTAGCTCGTTTG
* *
28301524 AGCTCAATTTAGCTTACTTTAGCTCGTTTG
1 AGCTCAATTGAGCTTAATTTAGCTCGTTTG
** * * * *
28301554 AGCCTCAACAAGCTCAATCTTAGTTTTTCCCAGCTCGATTT
1 AG-CT---CAA--TTGAGCTTA--ATTT---AGCTCGTTTG
**
28301595 AGCTCACATGAGCTTAATTTAGCTCGTTTG
1 AGCTCAATTGAGCTTAATTTAGCTCGTTTG
* *
28301625 AGCTCAATTTAGCTTACTTTAGCTCGTTTG
1 AGCTCAATTGAGCTTAATTTAGCTCGTTTG
28301655 AGCT
1 AGCT
28301659 TGGCTTAAGT
Statistics
Matches: 102, Mismatches: 21, Indels: 24
0.69 0.14 0.16
Matches are distributed among these distances:
29 1 0.01
30 65 0.64
31 2 0.02
33 3 0.03
34 3 0.03
35 5 0.05
36 6 0.06
37 2 0.02
38 3 0.03
40 2 0.02
41 10 0.10
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (30 bp):
AGCTCAATTGAGCTTAATTTAGCTCGTTTG
Found at i:28301608 original size:20 final size:20
Alignment explanation
Indices: 28301585--28301638 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
28301575 AGTTTTTCCC
*
28301585 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
28301605 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
28301625 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
28301639 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:28301621 original size:101 final size:101
Alignment explanation
Indices: 28301456--28301657 Score: 386
Period size: 101 Copynumber: 2.0 Consensus size: 101
28301446 TCAATATCAG
*
28301456 CTCAACAAGCTCAATCTTAGTTTTTCCCAGCTCGAATTAGCTCACATGAGCTTAATTTATCTCGT
1 CTCAACAAGCTCAATCTTAGTTTTTCCCAGCTCGAATTAGCTCACATGAGCTTAATTTAGCTCGT
28301521 TTGAGCTCAATTTAGCTTACTTTAGCTCGTTTGAGC
66 TTGAGCTCAATTTAGCTTACTTTAGCTCGTTTGAGC
*
28301557 CTCAACAAGCTCAATCTTAGTTTTTCCCAGCTCGATTTAGCTCACATGAGCTTAATTTAGCTCGT
1 CTCAACAAGCTCAATCTTAGTTTTTCCCAGCTCGAATTAGCTCACATGAGCTTAATTTAGCTCGT
28301622 TTGAGCTCAATTTAGCTTACTTTAGCTCGTTTGAGC
66 TTGAGCTCAATTTAGCTTACTTTAGCTCGTTTGAGC
28301658 TTGGCTTAAG
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (101 bp):
CTCAACAAGCTCAATCTTAGTTTTTCCCAGCTCGAATTAGCTCACATGAGCTTAATTTAGCTCGT
TTGAGCTCAATTTAGCTTACTTTAGCTCGTTTGAGC
Found at i:28301648 original size:20 final size:20
Alignment explanation
Indices: 28301585--28301649 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
28301575 AGTTTTTCCC
* * * *
28301585 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
28301605 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
28301624 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
28301645 AGCTC
1 AGCTC
28301650 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Done.